gnu/packages/bioinformatics.scm

   1 ;;; GNU Guix --- Functional package management for GNU
   2 ;;; Copyright © 2014, 2015, 2016, 2017, 2018, 2019 Ricardo Wurmus <rekado@elephly.net>
   3 ;;; Copyright © 2015, 2016, 2017, 2018 Ben Woodcroft <donttrustben@gmail.com>
   4 ;;; Copyright © 2015, 2016 Pjotr Prins <pjotr.guix@thebird.nl>
   5 ;;; Copyright © 2015 Andreas Enge <andreas@enge.fr>
   6 ;;; Copyright © 2016 Roel Janssen <roel@gnu.org>
   7 ;;; Copyright © 2016, 2017, 2018, 2019 Efraim Flashner <efraim@flashner.co.il>
   8 ;;; Copyright © 2016 Marius Bakke <mbakke@fastmail.com>
   9 ;;; Copyright © 2016, 2018 Raoul Bonnal <ilpuccio.febo@gmail.com>
  10 ;;; Copyright © 2017, 2018 Tobias Geerinckx-Rice <me@tobias.gr>
  11 ;;; Copyright © 2017 Arun Isaac <arunisaac@systemreboot.net>
  12 ;;; Copyright © 2018 Joshua Sierles, Nextjournal <joshua@nextjournal.com>
  13 ;;; Copyright © 2018 Gábor Boskovits <boskovits@gmail.com>
  14 ;;; Copyright © 2018 Mădălin Ionel Patrașcu <madalinionel.patrascu@mdc-berlin.de>
  15 ;;;
  16 ;;; This file is part of GNU Guix.
  17 ;;;
  18 ;;; GNU Guix is free software; you can redistribute it and/or modify it
  19 ;;; under the terms of the GNU General Public License as published by
  20 ;;; the Free Software Foundation; either version 3 of the License, or (at
  21 ;;; your option) any later version.
  22 ;;;
  23 ;;; GNU Guix is distributed in the hope that it will be useful, but
  24 ;;; WITHOUT ANY WARRANTY; without even the implied warranty of
  25 ;;; MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
  26 ;;; GNU General Public License for more details.
  27 ;;;
  28 ;;; You should have received a copy of the GNU General Public License
  29 ;;; along with GNU Guix.  If not, see <http://www.gnu.org/licenses/>.
  30
  31 (define-module (gnu packages bioinformatics)
  32   #:use-module ((guix licenses) #:prefix license:)
  33   #:use-module (guix packages)
  34   #:use-module (guix utils)
  35   #:use-module (guix download)
  36   #:use-module (guix git-download)
  37   #:use-module (guix hg-download)
  38   #:use-module (guix build-system ant)
  39   #:use-module (guix build-system gnu)
  40   #:use-module (guix build-system cmake)
  41   #:use-module (guix build-system haskell)
  42   #:use-module (guix build-system ocaml)
  43   #:use-module (guix build-system perl)
  44   #:use-module (guix build-system python)
  45   #:use-module (guix build-system r)
  46   #:use-module (guix build-system ruby)
  47   #:use-module (guix build-system scons)
  48   #:use-module (guix build-system trivial)
  49   #:use-module (gnu packages)
  50   #:use-module (gnu packages autotools)
  51   #:use-module (gnu packages algebra)
  52   #:use-module (gnu packages base)
  53   #:use-module (gnu packages bash)
  54   #:use-module (gnu packages bison)
  55   #:use-module (gnu packages bioconductor)
  56   #:use-module (gnu packages boost)
  57   #:use-module (gnu packages check)
  58   #:use-module (gnu packages compression)
  59   #:use-module (gnu packages cpio)
  60   #:use-module (gnu packages cran)
  61   #:use-module (gnu packages curl)
  62   #:use-module (gnu packages documentation)
  63   #:use-module (gnu packages databases)
  64   #:use-module (gnu packages datastructures)
  65   #:use-module (gnu packages file)
  66   #:use-module (gnu packages flex)
  67   #:use-module (gnu packages gawk)
  68   #:use-module (gnu packages gcc)
  69   #:use-module (gnu packages gd)
  70   #:use-module (gnu packages gtk)
  71   #:use-module (gnu packages glib)
  72   #:use-module (gnu packages graph)
  73   #:use-module (gnu packages groff)
  74   #:use-module (gnu packages guile)
  75   #:use-module (gnu packages haskell)
  76   #:use-module (gnu packages haskell-check)
  77   #:use-module (gnu packages haskell-web)
  78   #:use-module (gnu packages image)
  79   #:use-module (gnu packages imagemagick)
  80   #:use-module (gnu packages java)
  81   #:use-module (gnu packages jemalloc)
  82   #:use-module (gnu packages dlang)
  83   #:use-module (gnu packages linux)
  84   #:use-module (gnu packages logging)
  85   #:use-module (gnu packages machine-learning)
  86   #:use-module (gnu packages man)
  87   #:use-module (gnu packages maths)
  88   #:use-module (gnu packages mpi)
  89   #:use-module (gnu packages ncurses)
  90   #:use-module (gnu packages ocaml)
  91   #:use-module (gnu packages pcre)
  92   #:use-module (gnu packages parallel)
  93   #:use-module (gnu packages pdf)
  94   #:use-module (gnu packages perl)
  95   #:use-module (gnu packages perl-check)
  96   #:use-module (gnu packages pkg-config)
  97   #:use-module (gnu packages popt)
  98   #:use-module (gnu packages protobuf)
  99   #:use-module (gnu packages python)
 100   #:use-module (gnu packages python-web)
 101   #:use-module (gnu packages readline)
 102   #:use-module (gnu packages ruby)
 103   #:use-module (gnu packages serialization)
 104   #:use-module (gnu packages shells)
 105   #:use-module (gnu packages statistics)
 106   #:use-module (gnu packages swig)
 107   #:use-module (gnu packages tbb)
 108   #:use-module (gnu packages tex)
 109   #:use-module (gnu packages texinfo)
 110   #:use-module (gnu packages textutils)
 111   #:use-module (gnu packages time)
 112   #:use-module (gnu packages tls)
 113   #:use-module (gnu packages vim)
 114   #:use-module (gnu packages web)
 115   #:use-module (gnu packages xml)
 116   #:use-module (gnu packages xorg)
 117   #:use-module (srfi srfi-1)
 118   #:use-module (ice-9 match))
 119
 120 (define-public aragorn
 121   (package
 122     (name "aragorn")
 123     (version "1.2.38")
 124     (source (origin
 125               (method url-fetch)
 126               (uri (string-append
 127                     "http://mbio-serv2.mbioekol.lu.se/ARAGORN/Downloads/aragorn"
 128                     version ".tgz"))
 129               (sha256
 130                (base32
 131                 "09i1rg716smlbnixfm7q1ml2mfpaa2fpn3hwjg625ysmfwwy712b"))))
 132     (build-system gnu-build-system)
 133     (arguments
 134      `(#:tests? #f ; there are no tests
 135        #:phases
 136        (modify-phases %standard-phases
 137          (delete 'configure)
 138          (replace 'build
 139            (lambda _
 140              (invoke "gcc"
 141                      "-O3"
 142                      "-ffast-math"
 143                      "-finline-functions"
 144                      "-o"
 145                      "aragorn"
 146                      (string-append "aragorn" ,version ".c"))
 147              #t))
 148          (replace 'install
 149            (lambda* (#:key outputs #:allow-other-keys)
 150              (let* ((out (assoc-ref outputs "out"))
 151                     (bin (string-append out "/bin"))
 152                     (man (string-append out "/share/man/man1")))
 153                (install-file "aragorn" bin)
 154                (install-file "aragorn.1" man))
 155              #t)))))
 156     (home-page "http://mbio-serv2.mbioekol.lu.se/ARAGORN")
 157     (synopsis "Detect tRNA, mtRNA and tmRNA genes in nucleotide sequences")
 158     (description
 159      "Aragorn identifies transfer RNA, mitochondrial RNA and
 160 transfer-messenger RNA from nucleotide sequences, based on homology to known
 161 tRNA consensus sequences and RNA structure.  It also outputs the secondary
 162 structure of the predicted RNA.")
 163     (license license:gpl2)))
 164
 165 (define-public bamm
 166   (package
 167     (name "bamm")
 168     (version "1.7.3")
 169     (source (origin
 170               (method git-fetch)
 171               ;; BamM is not available on pypi.
 172               (uri (git-reference
 173                     (url "https://github.com/Ecogenomics/BamM.git")
 174                     (commit version)
 175                     (recursive? #t)))
 176               (file-name (git-file-name name version))
 177               (sha256
 178                (base32
 179                 "1p83ahi984ipslxlg4yqy1gdnya9rkn1v71z8djgxkm9d2chw4c5"))
 180               (modules '((guix build utils)))
 181               (snippet
 182                `(begin
 183                   ;; Delete bundled htslib.
 184                   (delete-file-recursively "c/htslib-1.3.1")
 185                   #t))))
 186     (build-system python-build-system)
 187     (arguments
 188      `(#:python ,python-2 ; BamM is Python 2 only.
 189        ;; Do not use bundled libhts.  Do use the bundled libcfu because it has
 190        ;; been modified from its original form.
 191        #:configure-flags
 192        (let ((htslib (assoc-ref %build-inputs "htslib")))
 193          (list "--with-libhts-lib" (string-append htslib "/lib")
 194                "--with-libhts-inc" (string-append htslib "/include/htslib")))
 195        #:phases
 196        (modify-phases %standard-phases
 197          (add-after 'unpack 'autogen
 198            (lambda _
 199              (with-directory-excursion "c"
 200                (let ((sh (which "sh")))
 201                  (for-each make-file-writable (find-files "." ".*"))
 202                  ;; Use autogen so that 'configure' works.
 203                  (substitute* "autogen.sh" (("/bin/sh") sh))
 204                  (setenv "CONFIG_SHELL" sh)
 205                  (invoke "./autogen.sh")))
 206              #t))
 207          (delete 'build)
 208          ;; Run tests after installation so compilation only happens once.
 209          (delete 'check)
 210          (add-after 'install 'wrap-executable
 211            (lambda* (#:key outputs #:allow-other-keys)
 212             (let* ((out  (assoc-ref outputs "out"))
 213                    (path (getenv "PATH")))
 214               (wrap-program (string-append out "/bin/bamm")
 215                 `("PATH" ":" prefix (,path))))
 216             #t))
 217          (add-after 'wrap-executable 'post-install-check
 218            (lambda* (#:key inputs outputs #:allow-other-keys)
 219              (setenv "PATH"
 220                      (string-append (assoc-ref outputs "out")
 221                                     "/bin:"
 222                                     (getenv "PATH")))
 223              (setenv "PYTHONPATH"
 224                      (string-append
 225                       (assoc-ref outputs "out")
 226                       "/lib/python"
 227                       (string-take (string-take-right
 228                                     (assoc-ref inputs "python") 5) 3)
 229                       "/site-packages:"
 230                       (getenv "PYTHONPATH")))
 231              ;; There are 2 errors printed, but they are safe to ignore:
 232              ;; 1) [E::hts_open_format] fail to open file ...
 233              ;; 2) samtools view: failed to open ...
 234              (invoke "nosetests")
 235              #t)))))
 236     (native-inputs
 237      `(("autoconf" ,autoconf)
 238        ("automake" ,automake)
 239        ("libtool" ,libtool)
 240        ("zlib" ,zlib)
 241        ("python-nose" ,python2-nose)
 242        ("python-pysam" ,python2-pysam)))
 243     (inputs
 244      `(("htslib" ,htslib-1.3) ; At least one test fails on htslib-1.4+.
 245        ("samtools" ,samtools)
 246        ("bwa" ,bwa)
 247        ("grep" ,grep)
 248        ("sed" ,sed)
 249        ("coreutils" ,coreutils)))
 250     (propagated-inputs
 251      `(("python-numpy" ,python2-numpy)))
 252     (home-page "http://ecogenomics.github.io/BamM/")
 253     (synopsis "Metagenomics-focused BAM file manipulator")
 254     (description
 255      "BamM is a C library, wrapped in python, to efficiently generate and
 256 parse BAM files, specifically for the analysis of metagenomic data.  For
 257 instance, it implements several methods to assess contig-wise read coverage.")
 258     (license license:lgpl3+)))
 259
 260 (define-public bamtools
 261   (package
 262     (name "bamtools")
 263     (version "2.5.1")
 264     (source (origin
 265               (method git-fetch)
 266               (uri (git-reference
 267                     (url "https://github.com/pezmaster31/bamtools.git")
 268                     (commit (string-append "v" version))))
 269               (file-name (git-file-name name version))
 270               (sha256
 271                (base32
 272                 "0nfb2ypcx9959xnbz6wxh6py3xfizgmg8nrknxl95c507m9hmq8b"))))
 273     (build-system cmake-build-system)
 274     (arguments
 275      `(#:tests? #f ;no "check" target
 276        #:phases
 277        (modify-phases %standard-phases
 278          (add-before
 279           'configure 'set-ldflags
 280           (lambda* (#:key outputs #:allow-other-keys)
 281             (setenv "LDFLAGS"
 282                     (string-append
 283                      "-Wl,-rpath="
 284                      (assoc-ref outputs "out") "/lib/bamtools"))
 285             #t)))))
 286     (inputs `(("zlib" ,zlib)))
 287     (home-page "https://github.com/pezmaster31/bamtools")
 288     (synopsis "C++ API and command-line toolkit for working with BAM data")
 289     (description
 290      "BamTools provides both a C++ API and a command-line toolkit for handling
 291 BAM files.")
 292     (license license:expat)))
 293
 294 (define-public bcftools
 295   (package
 296     (name "bcftools")
 297     (version "1.9")
 298     (source (origin
 299               (method url-fetch)
 300               (uri (string-append "https://github.com/samtools/bcftools/"
 301                                   "releases/download/"
 302                                   version "/bcftools-" version ".tar.bz2"))
 303               (sha256
 304                (base32
 305                 "1j3h638i8kgihzyrlnpj82xg1b23sijibys9hvwari3fy7kd0dkg"))
 306               (modules '((guix build utils)))
 307               (snippet '(begin
 308                           ;; Delete bundled htslib.
 309                           (delete-file-recursively "htslib-1.9")
 310                           #t))))
 311     (build-system gnu-build-system)
 312     (arguments
 313      `(#:configure-flags
 314        (list "--enable-libgsl")
 315        #:test-target "test"
 316        #:phases
 317        (modify-phases %standard-phases
 318          (add-before 'check 'patch-tests
 319            (lambda _
 320              (substitute* "test/test.pl"
 321                (("/bin/bash") (which "bash")))
 322              #t)))))
 323     (native-inputs
 324      `(("htslib" ,htslib)
 325        ("perl" ,perl)))
 326     (inputs
 327      `(("gsl" ,gsl)
 328        ("zlib" ,zlib)))
 329     (home-page "https://samtools.github.io/bcftools/")
 330     (synopsis "Utilities for variant calling and manipulating VCFs and BCFs")
 331     (description
 332      "BCFtools is a set of utilities that manipulate variant calls in the
 333 Variant Call Format (VCF) and its binary counterpart BCF.  All commands work
 334 transparently with both VCFs and BCFs, both uncompressed and BGZF-compressed.")
 335     ;; The sources are dual MIT/GPL, but becomes GPL-only when USE_GPL=1.
 336     (license (list license:gpl3+ license:expat))))
 337
 338 (define-public bedops
 339   (package
 340     (name "bedops")
 341     (version "2.4.35")
 342     (source (origin
 343               (method git-fetch)
 344               (uri (git-reference
 345                     (url "https://github.com/bedops/bedops.git")
 346                     (commit (string-append "v" version))))
 347               (file-name (git-file-name name version))
 348               (sha256
 349                (base32
 350                 "0mmgsgwz5r9w76hzgxkxc9s9lkdhhaf7vr6i02b09vbswvs1fyqx"))))
 351     (build-system gnu-build-system)
 352     (arguments
 353      '(#:tests? #f
 354        #:make-flags (list (string-append "BINDIR=" %output "/bin"))
 355        #:phases
 356        (modify-phases %standard-phases
 357          (add-after 'unpack 'unpack-tarballs
 358            (lambda _
 359              ;; FIXME: Bedops includes tarballs of minimally patched upstream
 360              ;; libraries jansson, zlib, and bzip2.  We cannot just use stock
 361              ;; libraries because at least one of the libraries (zlib) is
 362              ;; patched to add a C++ function definition (deflateInit2cpp).
 363              ;; Until the Bedops developers offer a way to link against system
 364              ;; libraries we have to build the in-tree copies of these three
 365              ;; libraries.
 366
 367              ;; See upstream discussion:
 368              ;; https://github.com/bedops/bedops/issues/124
 369
 370              ;; Unpack the tarballs to benefit from shebang patching.
 371              (with-directory-excursion "third-party"
 372                (invoke "tar" "xvf" "jansson-2.6.tar.bz2")
 373                (invoke "tar" "xvf" "zlib-1.2.7.tar.bz2")
 374                (invoke "tar" "xvf" "bzip2-1.0.6.tar.bz2"))
 375              ;; Disable unpacking of tarballs in Makefile.
 376              (substitute* "system.mk/Makefile.linux"
 377                (("^\tbzcat .*") "\t@echo \"not unpacking\"\n")
 378                (("\\./configure") "CONFIG_SHELL=bash ./configure"))
 379              (substitute* "third-party/zlib-1.2.7/Makefile.in"
 380                (("^SHELL=.*$") "SHELL=bash\n"))
 381              #t))
 382          (delete 'configure))))
 383     (home-page "https://github.com/bedops/bedops")
 384     (synopsis "Tools for high-performance genomic feature operations")
 385     (description
 386      "BEDOPS is a suite of tools to address common questions raised in genomic
 387 studies---mostly with regard to overlap and proximity relationships between
 388 data sets.  It aims to be scalable and flexible, facilitating the efficient
 389 and accurate analysis and management of large-scale genomic data.
 390
 391 BEDOPS provides tools that perform highly efficient and scalable Boolean and
 392 other set operations, statistical calculations, archiving, conversion and
 393 other management of genomic data of arbitrary scale.  Tasks can be easily
 394 split by chromosome for distributing whole-genome analyses across a
 395 computational cluster.")
 396     (license license:gpl2+)))
 397
 398 (define-public bedtools
 399   (package
 400     (name "bedtools")
 401     (version "2.27.1")
 402     (source (origin
 403               (method url-fetch)
 404               (uri (string-append "https://github.com/arq5x/bedtools2/releases/"
 405                                   "download/v" version "/"
 406                                   "bedtools-" version ".tar.gz"))
 407               (sha256
 408                (base32
 409                 "1ndg5yknrxl4djx8ddzgk12rrbiidfpmkkg5z3f95jzryfxarhn8"))))
 410     (build-system gnu-build-system)
 411     (arguments
 412      '(#:test-target "test"
 413        #:make-flags
 414        (list (string-append "prefix=" (assoc-ref %outputs "out")))
 415        #:phases
 416        (modify-phases %standard-phases
 417          (delete 'configure))))
 418     (native-inputs `(("python" ,python-2)))
 419     (inputs
 420      `(("samtools" ,samtools)
 421        ("zlib" ,zlib)))
 422     (home-page "https://github.com/arq5x/bedtools2")
 423     (synopsis "Tools for genome analysis and arithmetic")
 424     (description
 425      "Collectively, the bedtools utilities are a swiss-army knife of tools for
 426 a wide-range of genomics analysis tasks.  The most widely-used tools enable
 427 genome arithmetic: that is, set theory on the genome.  For example, bedtools
 428 allows one to intersect, merge, count, complement, and shuffle genomic
 429 intervals from multiple files in widely-used genomic file formats such as BAM,
 430 BED, GFF/GTF, VCF.")
 431     (license license:gpl2)))
 432
 433 ;; Later releases of bedtools produce files with more columns than
 434 ;; what Ribotaper expects.
 435 (define-public bedtools-2.18
 436   (package (inherit bedtools)
 437     (name "bedtools")
 438     (version "2.18.0")
 439     (source (origin
 440               (method url-fetch)
 441               (uri (string-append "https://github.com/arq5x/bedtools2/"
 442                                   "releases/download/v" version
 443                                   "/bedtools-" version ".tar.gz"))
 444               (sha256
 445                (base32
 446                 "11rvca19ncg03kxd0wzlfx5ws7r3nisd0z8s9j9n182d8ksp2pxz"))))
 447     (arguments
 448      '(#:test-target "test"
 449        #:phases
 450        (modify-phases %standard-phases
 451          (delete 'configure)
 452          (replace 'install
 453            (lambda* (#:key outputs #:allow-other-keys)
 454              (let ((bin (string-append (assoc-ref outputs "out") "/bin/")))
 455                (for-each (lambda (file)
 456                            (install-file file bin))
 457                          (find-files "bin" ".*")))
 458              #t)))))))
 459
 460 ;; Needed for pybedtools.
 461 (define-public bedtools-2.26
 462   (package (inherit bedtools)
 463     (name "bedtools")
 464     (version "2.26.0")
 465     (source (origin
 466               (method url-fetch)
 467               (uri (string-append "https://github.com/arq5x/bedtools2/releases/"
 468                                   "download/v" version "/"
 469                                   "bedtools-" version ".tar.gz"))
 470               (sha256
 471                (base32
 472                 "0jhavwifnf7lmkb11h9y7dynr8d699h0rd2l52j1pfgircr2zwv5"))))))
 473
 474 (define-public ribotaper
 475   (package
 476     (name "ribotaper")
 477     (version "1.3.1")
 478     (source (origin
 479               (method url-fetch)
 480               (uri (string-append "https://ohlerlab.mdc-berlin.de/"
 481                                   "files/RiboTaper/RiboTaper_Version_"
 482                                   version ".tar.gz"))
 483               (sha256
 484                (base32
 485                 "0ykjbps1y3z3085q94npw8i9x5gldc6shy8vlc08v76zljsm07hv"))))
 486     (build-system gnu-build-system)
 487     (arguments
 488      `(#:phases
 489        (modify-phases %standard-phases
 490          (add-after 'install 'wrap-executables
 491            (lambda* (#:key inputs outputs #:allow-other-keys)
 492              (let* ((out (assoc-ref outputs "out")))
 493                (for-each
 494                 (lambda (script)
 495                   (wrap-program (string-append out "/bin/" script)
 496                     `("R_LIBS_SITE" ":" = (,(getenv "R_LIBS_SITE")))))
 497                 '("create_annotations_files.bash"
 498                   "create_metaplots.bash"
 499                   "Ribotaper_ORF_find.sh"
 500                   "Ribotaper.sh")))
 501              #t)))))
 502     (inputs
 503      `(("bedtools" ,bedtools-2.18)
 504        ("samtools" ,samtools-0.1)
 505        ("r-minimal" ,r-minimal)
 506        ("r-foreach" ,r-foreach)
 507        ("r-xnomial" ,r-xnomial)
 508        ("r-domc" ,r-domc)
 509        ("r-multitaper" ,r-multitaper)
 510        ("r-seqinr" ,r-seqinr)))
 511     (home-page "https://ohlerlab.mdc-berlin.de/software/RiboTaper_126/")
 512     (synopsis "Define translated ORFs using ribosome profiling data")
 513     (description
 514      "Ribotaper is a method for defining translated @dfn{open reading
 515 frames} (ORFs) using ribosome profiling (ribo-seq) data.  This package
 516 provides the Ribotaper pipeline.")
 517     (license license:gpl3+)))
 518
 519 (define-public ribodiff
 520   (package
 521     (name "ribodiff")
 522     (version "0.2.2")
 523     (source
 524      (origin
 525        (method git-fetch)
 526        (uri (git-reference
 527              (url "https://github.com/ratschlab/RiboDiff.git")
 528              (commit (string-append "v" version))))
 529        (file-name (git-file-name name version))
 530        (sha256
 531         (base32
 532          "0x75nlp7qnmm64jasbi6l21f2cy99r2cjyl6b4hr8zf2bq22drnz"))))
 533     (build-system python-build-system)
 534     (arguments
 535      `(#:python ,python-2
 536        #:phases
 537        (modify-phases %standard-phases
 538          ;; Generate an installable executable script wrapper.
 539          (add-after 'unpack 'patch-setup.py
 540            (lambda _
 541              (substitute* "setup.py"
 542                (("^(.*)packages=.*" line prefix)
 543                 (string-append line "\n"
 544                                prefix "scripts=['scripts/TE.py'],\n")))
 545              #t)))))
 546     (inputs
 547      `(("python-numpy" ,python2-numpy)
 548        ("python-matplotlib" ,python2-matplotlib)
 549        ("python-scipy" ,python2-scipy)
 550        ("python-statsmodels" ,python2-statsmodels)))
 551     (native-inputs
 552      `(("python-mock" ,python2-mock)
 553        ("python-nose" ,python2-nose)))
 554     (home-page "http://public.bmi.inf.ethz.ch/user/zhongy/RiboDiff/")
 555     (synopsis "Detect translation efficiency changes from ribosome footprints")
 556     (description "RiboDiff is a statistical tool that detects the protein
 557 translational efficiency change from Ribo-Seq (ribosome footprinting) and
 558 RNA-Seq data.  It uses a generalized linear model to detect genes showing
 559 difference in translational profile taking mRNA abundance into account.  It
 560 facilitates us to decipher the translational regulation that behave
 561 independently with transcriptional regulation.")
 562     (license license:gpl3+)))
 563
 564 (define-public bioawk
 565   (package
 566     (name "bioawk")
 567     (version "1.0")
 568     (source (origin
 569               (method git-fetch)
 570               (uri (git-reference
 571                     (url "https://github.com/lh3/bioawk.git")
 572                     (commit (string-append "v" version))))
 573               (file-name (git-file-name name version))
 574               (sha256
 575                (base32
 576                 "1pxc3zdnirxbf9a0az698hd8xdik7qkhypm7v6hn922x8y9qmspm"))))
 577     (build-system gnu-build-system)
 578     (inputs
 579      `(("zlib" ,zlib)))
 580     (native-inputs
 581      `(("bison" ,bison)))
 582     (arguments
 583      `(#:tests? #f ; There are no tests to run.
 584        ;; Bison must generate files, before other targets can build.
 585        #:parallel-build? #f
 586        #:phases
 587        (modify-phases %standard-phases
 588          (delete 'configure) ; There is no configure phase.
 589          (replace 'install
 590            (lambda* (#:key outputs #:allow-other-keys)
 591              (let* ((out (assoc-ref outputs "out"))
 592                     (bin  (string-append out "/bin"))
 593                     (man (string-append out "/share/man/man1")))
 594                (mkdir-p man)
 595                (copy-file "awk.1" (string-append man "/bioawk.1"))
 596                (install-file "bioawk" bin))
 597              #t)))))
 598     (home-page "https://github.com/lh3/bioawk")
 599     (synopsis "AWK with bioinformatics extensions")
 600     (description "Bioawk is an extension to Brian Kernighan's awk, adding the
 601 support of several common biological data formats, including optionally gzip'ed
 602 BED, GFF, SAM, VCF, FASTA/Q and TAB-delimited formats with column names.  It
 603 also adds a few built-in functions and a command line option to use TAB as the
 604 input/output delimiter.  When the new functionality is not used, bioawk is
 605 intended to behave exactly the same as the original BWK awk.")
 606     (license license:x11)))
 607
 608 (define-public python-pybedtools
 609   (package
 610     (name "python-pybedtools")
 611     (version "0.7.10")
 612     (source (origin
 613               (method url-fetch)
 614               (uri (pypi-uri "pybedtools" version))
 615               (sha256
 616                (base32
 617                 "0l2b2wrnj85azfqgr0zwr60f7j58vlla1hcgxvr9rwikpl8j72ji"))))
 618     (build-system python-build-system)
 619     (arguments
 620      `(#:phases
 621        (modify-phases %standard-phases
 622          ;; See https://github.com/daler/pybedtools/issues/261
 623          (add-after 'unpack 'disable-broken-tests
 624            (lambda _
 625              ;; This test (pybedtools.test.test_scripts.test_venn_mpl) needs a
 626              ;; graphical environment.
 627              (substitute* "pybedtools/test/test_scripts.py"
 628                (("def test_venn_mpl")
 629                 "def _do_not_test_venn_mpl"))
 630              ;; Requires internet access.
 631              (substitute* "pybedtools/test/test_helpers.py"
 632                (("def test_chromsizes")
 633                 "def _do_not_test_chromsizes"))
 634              ;; FIXME: these two fail for no good reason.
 635              (substitute* "pybedtools/test/test1.py"
 636                (("def test_issue_157")
 637                 "def _do_not_test_issue_157")
 638                (("def test_to_dataframe")
 639                 "def _do_not_test_to_dataframe"))
 640              #t)))))
 641     (propagated-inputs
 642      ;; Tests don't pass with Bedtools 2.27.1.
 643      ;; See https://github.com/daler/pybedtools/issues/260
 644      `(("bedtools" ,bedtools-2.26)
 645        ("samtools" ,samtools)
 646        ("python-matplotlib" ,python-matplotlib)
 647        ("python-pysam" ,python-pysam)
 648        ("python-pyyaml" ,python-pyyaml)))
 649     (native-inputs
 650      `(("python-numpy" ,python-numpy)
 651        ("python-pandas" ,python-pandas)
 652        ("python-cython" ,python-cython)
 653        ("python-nose" ,python-nose)
 654        ("kentutils" ,kentutils) ; for bedGraphToBigWig
 655        ("python-six" ,python-six)))
 656     (home-page "https://pythonhosted.org/pybedtools/")
 657     (synopsis "Python wrapper for BEDtools programs")
 658     (description
 659      "pybedtools is a Python wrapper for Aaron Quinlan's BEDtools programs,
 660 which are widely used for genomic interval manipulation or \"genome algebra\".
 661 pybedtools extends BEDTools by offering feature-level manipulations from with
 662 Python.")
 663     (license license:gpl2+)))
 664
 665 (define-public python2-pybedtools
 666   (let ((pkg (package-with-python2 python-pybedtools)))
 667     (package (inherit pkg)
 668       (arguments
 669        `(#:modules ((ice-9 ftw)
 670                     (srfi srfi-1)
 671                     (srfi srfi-26)
 672                     (guix build utils)
 673                     (guix build python-build-system))
 674          ;; See https://github.com/daler/pybedtools/issues/192
 675          ,@(substitute-keyword-arguments (package-arguments pkg)
 676              ((#:phases phases)
 677               `(modify-phases ,phases
 678                  (replace 'check
 679                    (lambda _
 680                      (let ((cwd (getcwd)))
 681                        (setenv "PYTHONPATH"
 682                                (string-append cwd "/build/"
 683                                               (find (cut string-prefix? "lib" <>)
 684                                                     (scandir (string-append cwd "/build")))
 685                                               ":" (getenv "PYTHONPATH"))))
 686                      ;; The tests need to be run from elsewhere...
 687                      (mkdir-p "/tmp/test")
 688                      (copy-recursively "pybedtools/test" "/tmp/test")
 689                      (with-directory-excursion "/tmp/test"
 690                        (invoke "nosetests"
 691                                ;; This test fails for unknown reasons
 692                                "--exclude=.*test_getting_example_beds"))
 693                      #t))))))))))
 694
 695 (define-public python-biom-format
 696   (package
 697     (name "python-biom-format")
 698     (version "2.1.7")
 699     (source
 700      (origin
 701        (method git-fetch)
 702        ;; Use GitHub as source because PyPI distribution does not contain
 703        ;; test data: https://github.com/biocore/biom-format/issues/693
 704        (uri (git-reference
 705              (url "https://github.com/biocore/biom-format.git")
 706              (commit version)))
 707        (file-name (git-file-name name version))
 708        (sha256
 709         (base32
 710          "1rna16lyk5aqhnv0dp77wwaplias93f1vw28ad3jmyw6hwkai05v"))))
 711     (build-system python-build-system)
 712     (arguments
 713      `(#:phases
 714        (modify-phases %standard-phases
 715          (add-after 'unpack 'use-cython
 716            (lambda _ (setenv "USE_CYTHON" "1") #t))
 717          (add-after 'unpack 'disable-broken-test
 718            (lambda _
 719              (substitute* "biom/tests/test_cli/test_validate_table.py"
 720                (("^(.+)def test_invalid_hdf5" m indent)
 721                 (string-append indent
 722                                "@npt.dec.skipif(True, msg='Guix')\n"
 723                                m)))
 724              #t))
 725          (add-before 'reset-gzip-timestamps 'make-files-writable
 726            (lambda* (#:key outputs #:allow-other-keys)
 727              (let ((out (assoc-ref outputs "out")))
 728                (for-each (lambda (file) (chmod file #o644))
 729                          (find-files out "\\.gz"))
 730                #t))))))
 731     (propagated-inputs
 732      `(("python-numpy" ,python-numpy)
 733        ("python-scipy" ,python-scipy)
 734        ("python-flake8" ,python-flake8)
 735        ("python-future" ,python-future)
 736        ("python-click" ,python-click)
 737        ("python-h5py" ,python-h5py)
 738        ("python-pandas" ,python-pandas)))
 739     (native-inputs
 740      `(("python-cython" ,python-cython)
 741        ("python-pytest" ,python-pytest)
 742        ("python-pytest-cov" ,python-pytest-cov)
 743        ("python-nose" ,python-nose)))
 744     (home-page "http://www.biom-format.org")
 745     (synopsis "Biological Observation Matrix (BIOM) format utilities")
 746     (description
 747      "The BIOM file format is designed to be a general-use format for
 748 representing counts of observations e.g. operational taxonomic units, KEGG
 749 orthology groups or lipid types, in one or more biological samples
 750 e.g. microbiome samples, genomes, metagenomes.")
 751     (license license:bsd-3)
 752     (properties `((python2-variant . ,(delay python2-biom-format))))))
 753
 754 (define-public python2-biom-format
 755   (let ((base (package-with-python2 (strip-python2-variant python-biom-format))))
 756     (package
 757       (inherit base)
 758       (arguments
 759        (substitute-keyword-arguments (package-arguments base)
 760          ((#:phases phases)
 761           `(modify-phases ,phases
 762              ;; Do not require the unmaintained pyqi library.
 763              (add-after 'unpack 'remove-pyqi
 764                (lambda _
 765                  (substitute* "setup.py"
 766                    (("install_requires.append\\(\"pyqi\"\\)") "pass"))
 767                  #t)))))))))
 768
 769 (define-public bioperl-minimal
 770   (let* ((inputs `(("perl-module-build" ,perl-module-build)
 771                    ("perl-data-stag" ,perl-data-stag)
 772                    ("perl-libwww" ,perl-libwww)
 773                    ("perl-uri" ,perl-uri)))
 774          (transitive-inputs
 775           (map (compose package-name cadr)
 776                (delete-duplicates
 777                 (concatenate
 778                  (map (compose package-transitive-target-inputs cadr) inputs))))))
 779     (package
 780       (name "bioperl-minimal")
 781       (version "1.7.0")
 782       (source
 783        (origin
 784          (method url-fetch)
 785          (uri (string-append "https://github.com/bioperl/bioperl-live/"
 786                              "archive/release-"
 787                              (string-map (lambda (c)
 788                                            (if (char=? c #\.)
 789                                                #\- c)) version)
 790                              ".tar.gz"))
 791          (sha256
 792           (base32
 793            "12phgpxwgkqflkwfb9dcqg7a31dpjlfhar8wcgv0aj5ln4akfz06"))))
 794       (build-system perl-build-system)
 795       (arguments
 796        `(#:phases
 797          (modify-phases %standard-phases
 798            (add-after
 799             'install 'wrap-programs
 800             (lambda* (#:key outputs #:allow-other-keys)
 801               ;; Make sure all executables in "bin" find the required Perl
 802               ;; modules at runtime.  As the PERL5LIB variable contains also
 803               ;; the paths of native inputs, we pick the transitive target
 804               ;; inputs from %build-inputs.
 805               (let* ((out  (assoc-ref outputs "out"))
 806                      (bin  (string-append out "/bin/"))
 807                      (path (string-join
 808                             (cons (string-append out "/lib/perl5/site_perl")
 809                                   (map (lambda (name)
 810                                          (assoc-ref %build-inputs name))
 811                                        ',transitive-inputs))
 812                             ":")))
 813                 (for-each (lambda (file)
 814                             (wrap-program file
 815                               `("PERL5LIB" ":" prefix (,path))))
 816                           (find-files bin "\\.pl$"))
 817                 #t))))))
 818       (inputs inputs)
 819       (native-inputs
 820        `(("perl-test-most" ,perl-test-most)))
 821       (home-page "https://metacpan.org/release/BioPerl")
 822       (synopsis "Bioinformatics toolkit")
 823       (description
 824        "BioPerl is the product of a community effort to produce Perl code which
 825 is useful in biology.  Examples include Sequence objects, Alignment objects
 826 and database searching objects.  These objects not only do what they are
 827 advertised to do in the documentation, but they also interact - Alignment
 828 objects are made from the Sequence objects, Sequence objects have access to
 829 Annotation and SeqFeature objects and databases, Blast objects can be
 830 converted to Alignment objects, and so on.  This means that the objects
 831 provide a coordinated and extensible framework to do computational biology.")
 832       (license license:perl-license))))
 833
 834 (define-public python-biopython
 835   (package
 836     (name "python-biopython")
 837     (version "1.70")
 838     (source (origin
 839               (method url-fetch)
 840               ;; use PyPi rather than biopython.org to ease updating
 841               (uri (pypi-uri "biopython" version))
 842               (sha256
 843                (base32
 844                 "0nz4n9d2y2dg849gn1z0vjlkwcpzzkzy3fij7x94a6ixy2c54z2a"))))
 845     (build-system python-build-system)
 846     (arguments
 847      `(#:phases
 848        (modify-phases %standard-phases
 849          (add-before 'check 'set-home
 850            ;; Some tests require a home directory to be set.
 851            (lambda _ (setenv "HOME" "/tmp") #t)))))
 852     (propagated-inputs
 853      `(("python-numpy" ,python-numpy)))
 854     (home-page "http://biopython.org/")
 855     (synopsis "Tools for biological computation in Python")
 856     (description
 857      "Biopython is a set of tools for biological computation including parsers
 858 for bioinformatics files into Python data structures; interfaces to common
 859 bioinformatics programs; a standard sequence class and tools for performing
 860 common operations on them; code to perform data classification; code for
 861 dealing with alignments; code making it easy to split up parallelizable tasks
 862 into separate processes; and more.")
 863     (license (license:non-copyleft "http://www.biopython.org/DIST/LICENSE"))))
 864
 865 (define-public python2-biopython
 866   (package-with-python2 python-biopython))
 867
 868 (define-public python-fastalite
 869   (package
 870     (name "python-fastalite")
 871     (version "0.3")
 872     (source
 873      (origin
 874        (method url-fetch)
 875        (uri (pypi-uri "fastalite" version))
 876        (sha256
 877         (base32
 878          "1qli6pxp77i9xn2wfciq2zaxhl82bdxb33cpzqzj1z25yd036wqj"))))
 879     (build-system python-build-system)
 880     (arguments
 881      `(#:tests? #f)) ; Test data is not distributed.
 882     (home-page "https://github.com/nhoffman/fastalite")
 883     (synopsis "Simplest possible FASTA parser")
 884     (description "This library implements a FASTA and a FASTQ parser without
 885 relying on a complex dependency tree.")
 886     (license license:expat)))
 887
 888 (define-public python2-fastalite
 889   (package-with-python2 python-fastalite))
 890
 891 (define-public bpp-core
 892   ;; The last release was in 2014 and the recommended way to install from source
 893   ;; is to clone the git repository, so we do this.
 894   ;; http://biopp.univ-montp2.fr/wiki/index.php/Main_Page
 895   (let ((commit "7d8bced0d1a87291ea8dd7046b7fb5ff9c35c582"))
 896     (package
 897       (name "bpp-core")
 898       (version (string-append "2.2.0-1." (string-take commit 7)))
 899       (source (origin
 900                 (method git-fetch)
 901                 (uri (git-reference
 902                       (url "http://biopp.univ-montp2.fr/git/bpp-core")
 903                       (commit commit)))
 904                 (file-name (string-append name "-" version "-checkout"))
 905                 (sha256
 906                  (base32
 907                   "10djsq5vlnkilv436gnmh4irpk49v29pa69r6xiryg32xmvn909j"))))
 908       (build-system cmake-build-system)
 909       (arguments
 910        `(#:parallel-build? #f))
 911       (inputs
 912        `(("gcc" ,gcc-5))) ; Compilation of bpp-phyl fails with GCC 4.9 so we
 913                           ; compile all of the bpp packages with GCC 5.
 914       (home-page "http://biopp.univ-montp2.fr")
 915       (synopsis "C++ libraries for Bioinformatics")
 916       (description
 917        "Bio++ is a set of C++ libraries for Bioinformatics, including sequence
 918 analysis, phylogenetics, molecular evolution and population genetics.  It is
 919 Object Oriented and is designed to be both easy to use and computer efficient.
 920 Bio++ intends to help programmers to write computer expensive programs, by
 921 providing them a set of re-usable tools.")
 922       (license license:cecill-c))))
 923
 924 (define-public bpp-phyl
 925   ;; The last release was in 2014 and the recommended way to install from source
 926   ;; is to clone the git repository, so we do this.
 927   ;; http://biopp.univ-montp2.fr/wiki/index.php/Main_Page
 928   (let ((commit "0c07167b629f68b569bf274d1ad0c4af83276ae2"))
 929     (package
 930       (name "bpp-phyl")
 931       (version (string-append "2.2.0-1." (string-take commit 7)))
 932       (source (origin
 933                 (method git-fetch)
 934                 (uri (git-reference
 935                       (url "http://biopp.univ-montp2.fr/git/bpp-phyl")
 936                       (commit commit)))
 937                 (file-name (string-append name "-" version "-checkout"))
 938                 (sha256
 939                  (base32
 940                   "1ssjgchzwj3iai26kyly7gwkdv8sk59nqhkb1wpap3sf5m6kyllh"))))
 941       (build-system cmake-build-system)
 942       (arguments
 943        `(#:parallel-build? #f
 944          ;; If out-of-source, test data is not copied into the build directory
 945          ;; so the tests fail.
 946          #:out-of-source? #f))
 947       (inputs
 948        `(("bpp-core" ,bpp-core)
 949          ("bpp-seq" ,bpp-seq)
 950          ;; GCC 4.8 fails due to an 'internal compiler error', so we use a more
 951          ;; modern GCC.
 952          ("gcc" ,gcc-5)))
 953       (home-page "http://biopp.univ-montp2.fr")
 954       (synopsis "Bio++ phylogenetic Library")
 955       (description
 956        "Bio++ is a set of C++ libraries for Bioinformatics, including sequence
 957 analysis, phylogenetics, molecular evolution and population genetics.  This
 958 library provides phylogenetics-related modules.")
 959       (license license:cecill-c))))
 960
 961 (define-public bpp-popgen
 962   ;; The last release was in 2014 and the recommended way to install from source
 963   ;; is to clone the git repository, so we do this.
 964   ;; http://biopp.univ-montp2.fr/wiki/index.php/Main_Page
 965   (let ((commit "e472bac9b1a148803895d747cd6d0c5904f85d9f"))
 966     (package
 967       (name "bpp-popgen")
 968       (version (string-append "2.2.0-1." (string-take commit 7)))
 969       (source (origin
 970                 (method git-fetch)
 971                 (uri (git-reference
 972                       (url "http://biopp.univ-montp2.fr/git/bpp-popgen")
 973                       (commit commit)))
 974                 (file-name (string-append name "-" version "-checkout"))
 975                 (sha256
 976                  (base32
 977                   "0yn82dzn1n5629nzja68xfrhi655709rjanyryb36vzkmymy6dw5"))))
 978       (build-system cmake-build-system)
 979       (arguments
 980        `(#:parallel-build? #f
 981          #:tests? #f)) ; There are no tests.
 982       (inputs
 983        `(("bpp-core" ,bpp-core)
 984          ("bpp-seq" ,bpp-seq)
 985          ("gcc" ,gcc-5)))
 986       (home-page "http://biopp.univ-montp2.fr")
 987       (synopsis "Bio++ population genetics library")
 988       (description
 989        "Bio++ is a set of C++ libraries for Bioinformatics, including sequence
 990 analysis, phylogenetics, molecular evolution and population genetics.  This
 991 library provides population genetics-related modules.")
 992       (license license:cecill-c))))
 993
 994 (define-public bpp-seq
 995   ;; The last release was in 2014 and the recommended way to install from source
 996   ;; is to clone the git repository, so we do this.
 997   ;; http://biopp.univ-montp2.fr/wiki/index.php/Main_Page
 998   (let ((commit "6cfa07965ce152e5598a89df2fa80a75973bfa33"))
 999     (package
1000       (name "bpp-seq")
1001       (version (string-append "2.2.0-1." (string-take commit 7)))
1002       (source (origin
1003                 (method git-fetch)
1004                 (uri (git-reference
1005                       (url "http://biopp.univ-montp2.fr/git/bpp-seq")
1006                       (commit commit)))
1007                 (file-name (string-append name "-" version "-checkout"))
1008                 (sha256
1009                  (base32
1010                   "1nys5jq7jqvdg40d91wsmj3q2yzy4276cp7sp44n67p468f27zf2"))))
1011       (build-system cmake-build-system)
1012       (arguments
1013        `(#:parallel-build? #f
1014          ;; If out-of-source, test data is not copied into the build directory
1015          ;; so the tests fail.
1016          #:out-of-source? #f))
1017       (inputs
1018        `(("bpp-core" ,bpp-core)
1019          ("gcc" ,gcc-5))) ; Use GCC 5 as per 'bpp-core'.
1020       (home-page "http://biopp.univ-montp2.fr")
1021       (synopsis "Bio++ sequence library")
1022       (description
1023        "Bio++ is a set of C++ libraries for Bioinformatics, including sequence
1024 analysis, phylogenetics, molecular evolution and population genetics.  This
1025 library provides sequence-related modules.")
1026       (license license:cecill-c))))
1027
1028 (define-public bppsuite
1029   ;; The last release was in 2014 and the recommended way to install from source
1030   ;; is to clone the git repository, so we do this.
1031   ;; http://biopp.univ-montp2.fr/wiki/index.php/Main_Page
1032   (let ((commit "c516147f57aa50961121cd505bed52cd7603698b"))
1033     (package
1034       (name "bppsuite")
1035       (version (string-append "2.2.0-1." (string-take commit 7)))
1036       (source (origin
1037                 (method git-fetch)
1038                 (uri (git-reference
1039                       (url "http://biopp.univ-montp2.fr/git/bppsuite")
1040                       (commit commit)))
1041                 (file-name (string-append name "-" version "-checkout"))
1042                 (sha256
1043                  (base32
1044                   "1y87pxvw0jxjizhq2dr9g2r91md45k1p9ih2sl1yy1y3p934l2kb"))))
1045       (build-system cmake-build-system)
1046       (arguments
1047        `(#:parallel-build? #f
1048          #:tests? #f)) ; There are no tests.
1049       (native-inputs
1050        `(("groff" ,groff)
1051          ("man-db" ,man-db)
1052          ("texinfo" ,texinfo)))
1053       (inputs
1054        `(("bpp-core" ,bpp-core)
1055          ("bpp-seq" ,bpp-seq)
1056          ("bpp-phyl" ,bpp-phyl)
1057          ("bpp-phyl" ,bpp-popgen)
1058          ("gcc" ,gcc-5)))
1059       (home-page "http://biopp.univ-montp2.fr")
1060       (synopsis "Bioinformatics tools written with the Bio++ libraries")
1061       (description
1062        "Bio++ is a set of C++ libraries for Bioinformatics, including sequence
1063 analysis, phylogenetics, molecular evolution and population genetics.  This
1064 package provides command line tools using the Bio++ library.")
1065       (license license:cecill-c))))
1066
1067 (define-public blast+
1068   (package
1069     (name "blast+")
1070     (version "2.6.0")
1071     (source (origin
1072               (method url-fetch)
1073               (uri (string-append
1074                     "ftp://ftp.ncbi.nlm.nih.gov/blast/executables/blast+/"
1075                     version "/ncbi-blast-" version "+-src.tar.gz"))
1076               (sha256
1077                (base32
1078                 "15n937pw5aqmyfjb6l387d18grqbb96l63d5xj4l7yyh0zbf2405"))
1079               (patches (search-patches "blast+-fix-makefile.patch"))
1080               (modules '((guix build utils)))
1081               (snippet
1082                '(begin
1083                   ;; Remove bundled bzip2, zlib and pcre.
1084                   (delete-file-recursively "c++/src/util/compress/bzip2")
1085                   (delete-file-recursively "c++/src/util/compress/zlib")
1086                   (delete-file-recursively "c++/src/util/regexp")
1087                   (substitute* "c++/src/util/compress/Makefile.in"
1088                     (("bzip2 zlib api") "api"))
1089                   ;; Remove useless msbuild directory
1090                   (delete-file-recursively
1091                    "c++/src/build-system/project_tree_builder/msbuild")
1092                   #t))))
1093     (build-system gnu-build-system)
1094     (arguments
1095      `(;; There are two(!) tests for this massive library, and both fail with
1096        ;; "unparsable timing stats".
1097        ;; ERR [127] --  [serial/datatool] datatool.sh     (unparsable timing stats)
1098        ;; ERR [127] --  [serial/datatool] datatool_xml.sh     (unparsable timing stats)
1099        #:tests? #f
1100        #:out-of-source? #t
1101        #:parallel-build? #f ; not supported
1102        #:phases
1103        (modify-phases %standard-phases
1104          (add-before 'configure 'set-HOME
1105           ;; $HOME needs to be set at some point during the configure phase
1106           (lambda _ (setenv "HOME" "/tmp") #t))
1107          (add-after 'unpack 'enter-dir
1108           (lambda _ (chdir "c++") #t))
1109          (add-after 'enter-dir 'fix-build-system
1110           (lambda _
1111             (define (which* cmd)
1112               (cond ((string=? cmd "date")
1113                      ;; make call to "date" deterministic
1114                      "date -d @0")
1115                     ((which cmd)
1116                      => identity)
1117                     (else
1118                      (format (current-error-port)
1119                              "WARNING: Unable to find absolute path for ~s~%"
1120                              cmd)
1121                      #f)))
1122
1123             ;; Rewrite hardcoded paths to various tools
1124             (substitute* (append '("src/build-system/configure.ac"
1125                                    "src/build-system/configure"
1126                                    "src/build-system/helpers/run_with_lock.c"
1127                                    "scripts/common/impl/if_diff.sh"
1128                                    "scripts/common/impl/run_with_lock.sh"
1129                                    "src/build-system/Makefile.configurables.real"
1130                                    "src/build-system/Makefile.in.top"
1131                                    "src/build-system/Makefile.meta.gmake=no"
1132                                    "src/build-system/Makefile.meta.in"
1133                                    "src/build-system/Makefile.meta_l"
1134                                    "src/build-system/Makefile.meta_p"
1135                                    "src/build-system/Makefile.meta_r"
1136                                    "src/build-system/Makefile.mk.in"
1137                                    "src/build-system/Makefile.requirements"
1138                                    "src/build-system/Makefile.rules_with_autodep.in")
1139                                  (find-files "scripts/common/check" "\\.sh$"))
1140               (("(/usr/bin/|/bin/)([a-z][-_.a-z]*)" all dir cmd)
1141                (or (which* cmd) all)))
1142
1143             (substitute* (find-files "src/build-system" "^config.*")
1144               (("LN_S=/bin/\\$LN_S") (string-append "LN_S=" (which "ln")))
1145               (("^PATH=.*") ""))
1146
1147             ;; rewrite "/var/tmp" in check script
1148             (substitute* "scripts/common/check/check_make_unix.sh"
1149               (("/var/tmp") "/tmp"))
1150
1151             ;; do not reset PATH
1152             (substitute* (find-files "scripts/common/impl/" "\\.sh$")
1153               (("^ *PATH=.*") "")
1154               (("action=/bin/") "action=")
1155               (("export PATH") ":"))
1156             #t))
1157          (replace 'configure
1158            (lambda* (#:key inputs outputs #:allow-other-keys)
1159              (let ((out     (assoc-ref outputs "out"))
1160                    (lib     (string-append (assoc-ref outputs "lib") "/lib"))
1161                    (include (string-append (assoc-ref outputs "include")
1162                                            "/include/ncbi-tools++")))
1163                ;; The 'configure' script doesn't recognize things like
1164                ;; '--enable-fast-install'.
1165                (invoke "./configure.orig"
1166                        (string-append "--with-build-root=" (getcwd) "/build")
1167                        (string-append "--prefix=" out)
1168                        (string-append "--libdir=" lib)
1169                        (string-append "--includedir=" include)
1170                        (string-append "--with-bz2="
1171                                       (assoc-ref inputs "bzip2"))
1172                        (string-append "--with-z="
1173                                       (assoc-ref inputs "zlib"))
1174                        (string-append "--with-pcre="
1175                                       (assoc-ref inputs "pcre"))
1176                        ;; Each library is built twice by default, once
1177                        ;; with "-static" in its name, and again
1178                        ;; without.
1179                        "--without-static"
1180                        "--with-dll")
1181                #t))))))
1182     (outputs '("out"       ;  21 MB
1183                "lib"       ; 226 MB
1184                "include")) ;  33 MB
1185     (inputs
1186      `(("bzip2" ,bzip2)
1187        ("zlib" ,zlib)
1188        ("pcre" ,pcre)
1189        ("perl" ,perl)
1190        ("python" ,python-wrapper)))
1191     (native-inputs
1192      `(("cpio" ,cpio)))
1193     (home-page "http://blast.ncbi.nlm.nih.gov")
1194     (synopsis "Basic local alignment search tool")
1195     (description
1196      "BLAST is a popular method of performing a DNA or protein sequence
1197 similarity search, using heuristics to produce results quickly.  It also
1198 calculates an “expect value” that estimates how many matches would have
1199 occurred at a given score by chance, which can aid a user in judging how much
1200 confidence to have in an alignment.")
1201     ;; Most of the sources are in the public domain, with the following
1202     ;; exceptions:
1203     ;;   * Expat:
1204     ;;     * ./c++/include/util/bitset/
1205     ;;     * ./c++/src/html/ncbi_menu*.js
1206     ;;   * Boost license:
1207     ;;     * ./c++/include/util/impl/floating_point_comparison.hpp
1208     ;;   * LGPL 2+:
1209     ;;     * ./c++/include/dbapi/driver/odbc/unix_odbc/
1210     ;;   * ASL 2.0:
1211     ;;     * ./c++/src/corelib/teamcity_*
1212     (license (list license:public-domain
1213                    license:expat
1214                    license:boost1.0
1215                    license:lgpl2.0+
1216                    license:asl2.0))))
1217
1218 (define-public bless
1219   (package
1220     (name "bless")
1221     (version "1p02")
1222     (source (origin
1223               (method url-fetch)
1224               (uri (string-append "mirror://sourceforge/bless-ec/bless.v"
1225                                   version ".tgz"))
1226               (sha256
1227                (base32
1228                 "0rm0gw2s18dqwzzpl3c2x1z05ni2v0xz5dmfk3d33j6g4cgrlrdd"))
1229               (modules '((guix build utils)))
1230               (snippet
1231                `(begin
1232                   ;; Remove bundled boost, pigz, zlib, and .git directory
1233                   ;; FIXME: also remove bundled sources for murmurhash3 and
1234                   ;; kmc once packaged.
1235                   (delete-file-recursively "boost")
1236                   (delete-file-recursively "pigz")
1237                   (delete-file-recursively "google-sparsehash")
1238                   (delete-file-recursively "zlib")
1239                   (delete-file-recursively ".git")
1240                   #t))))
1241     (build-system gnu-build-system)
1242     (arguments
1243      '(#:tests? #f ;no "check" target
1244        #:make-flags
1245        (list (string-append "ZLIB="
1246                             (assoc-ref %build-inputs "zlib:static")
1247                             "/lib/libz.a")
1248              (string-append "LDFLAGS="
1249                             (string-join '("-lboost_filesystem"
1250                                            "-lboost_system"
1251                                            "-lboost_iostreams"
1252                                            "-lz"
1253                                            "-fopenmp"
1254                                            "-std=c++11"))))
1255        #:phases
1256        (modify-phases %standard-phases
1257          (add-after 'unpack 'do-not-build-bundled-pigz
1258           (lambda* (#:key inputs outputs #:allow-other-keys)
1259             (substitute* "Makefile"
1260               (("cd pigz/pigz-2.3.3; make") ""))
1261             #t))
1262          (add-after 'unpack 'patch-paths-to-executables
1263           (lambda* (#:key inputs outputs #:allow-other-keys)
1264             (substitute* "parse_args.cpp"
1265               (("kmc_binary = .*")
1266                (string-append "kmc_binary = \""
1267                               (assoc-ref outputs "out")
1268                               "/bin/kmc\";"))
1269               (("pigz_binary = .*")
1270                (string-append "pigz_binary = \""
1271                               (assoc-ref inputs "pigz")
1272                               "/bin/pigz\";")))
1273             #t))
1274          (replace 'install
1275           (lambda* (#:key outputs #:allow-other-keys)
1276             (let ((bin (string-append (assoc-ref outputs "out") "/bin/")))
1277               (for-each (lambda (file)
1278                           (install-file file bin))
1279                         '("bless" "kmc/bin/kmc"))
1280               #t)))
1281          (delete 'configure))))
1282     (native-inputs
1283      `(("perl" ,perl)))
1284     (inputs
1285      `(("openmpi" ,openmpi)
1286        ("boost" ,boost)
1287        ("sparsehash" ,sparsehash)
1288        ("pigz" ,pigz)
1289        ("zlib:static" ,zlib "static")
1290        ("zlib" ,zlib)))
1291     (supported-systems '("x86_64-linux"))
1292     (home-page "https://sourceforge.net/p/bless-ec/wiki/Home/")
1293     (synopsis "Bloom-filter-based error correction tool for NGS reads")
1294     (description
1295      "@dfn{Bloom-filter-based error correction solution for high-throughput
1296 sequencing reads} (BLESS) uses a single minimum-sized bloom filter is a
1297 correction tool for genomic reads produced by @dfn{Next-generation
1298 sequencing} (NGS).  BLESS produces accurate correction results with much less
1299 memory compared with previous solutions and is also able to tolerate a higher
1300 false-positive rate.  BLESS can extend reads like DNA assemblers to correct
1301 errors at the end of reads.")
1302     (license license:gpl3+)))
1303
1304 (define-public bowtie
1305   (package
1306     (name "bowtie")
1307     (version "2.3.4.3")
1308     (source (origin
1309               (method git-fetch)
1310               (uri (git-reference
1311                     (url "https://github.com/BenLangmead/bowtie2.git")
1312                     (commit (string-append "v" version))))
1313               (file-name (git-file-name name version))
1314               (sha256
1315                (base32
1316                 "1zl3cf327y2p7p03cavymbh7b00djc7lncfaqih33n96iy9q8ibp"))
1317               (modules '((guix build utils)))
1318               (snippet
1319                '(begin
1320                   (substitute* "Makefile"
1321                     ;; replace BUILD_HOST and BUILD_TIME for deterministic build
1322                     (("-DBUILD_HOST=.*") "-DBUILD_HOST=\"\\\"guix\\\"\"")
1323                     (("-DBUILD_TIME=.*") "-DBUILD_TIME=\"\\\"0\\\"\""))
1324                   #t))))
1325     (build-system gnu-build-system)
1326     (arguments
1327      '(#:make-flags
1328        (list "allall"
1329              "WITH_TBB=1"
1330              (string-append "prefix=" (assoc-ref %outputs "out")))
1331        #:phases
1332        (modify-phases %standard-phases
1333          (delete 'configure)
1334          (replace 'check
1335            (lambda _
1336              (invoke "perl"
1337                      "scripts/test/simple_tests.pl"
1338                      "--bowtie2=./bowtie2"
1339                      "--bowtie2-build=./bowtie2-build")
1340              #t)))))
1341     (inputs
1342      `(("tbb" ,tbb)
1343        ("zlib" ,zlib)
1344        ("python" ,python-wrapper)))
1345     (native-inputs
1346      `(("perl" ,perl)
1347        ("perl-clone" ,perl-clone)
1348        ("perl-test-deep" ,perl-test-deep)
1349        ("perl-test-simple" ,perl-test-simple)))
1350     (home-page "http://bowtie-bio.sourceforge.net/bowtie2/index.shtml")
1351     (synopsis "Fast and sensitive nucleotide sequence read aligner")
1352     (description
1353      "Bowtie 2 is a fast and memory-efficient tool for aligning sequencing
1354 reads to long reference sequences.  It is particularly good at aligning reads
1355 of about 50 up to 100s or 1,000s of characters, and particularly good at
1356 aligning to relatively long (e.g. mammalian) genomes.  Bowtie 2 indexes the
1357 genome with an FM Index to keep its memory footprint small: for the human
1358 genome, its memory footprint is typically around 3.2 GB.  Bowtie 2 supports
1359 gapped, local, and paired-end alignment modes.")
1360     (supported-systems '("x86_64-linux"))
1361     (license license:gpl3+)))
1362
1363 (define-public tophat
1364   (package
1365     (name "tophat")
1366     (version "2.1.1")
1367     (source (origin
1368               (method url-fetch)
1369               (uri (string-append
1370                     "http://ccb.jhu.edu/software/tophat/downloads/tophat-"
1371                     version ".tar.gz"))
1372               (sha256
1373                (base32
1374                 "19add02kv2xhd6ihd779dr7x35ggym3jqr0m5c4315i1yfb0p11p"))
1375               (modules '((guix build utils)))
1376               (snippet
1377                '(begin
1378                   ;; Remove bundled SeqAn and samtools
1379                   (delete-file-recursively "src/SeqAn-1.4.2")
1380                   (delete-file-recursively "src/samtools-0.1.18")
1381                   #t))))
1382     (build-system gnu-build-system)
1383     (arguments
1384      '(#:parallel-build? #f ; not supported
1385        #:phases
1386        (modify-phases %standard-phases
1387          (add-after 'unpack 'use-system-samtools
1388            (lambda* (#:key inputs #:allow-other-keys)
1389              (substitute* "src/Makefile.in"
1390                (("(noinst_LIBRARIES = )\\$\\(SAMLIB\\)" _ prefix) prefix)
1391                (("\\$\\(SAMPROG\\): \\$\\(SAMLIB\\)") "")
1392                (("SAMPROG = samtools_0\\.1\\.18") "")
1393                (("\\$\\(samtools_0_1_18_SOURCES\\)") "")
1394                (("am__EXEEXT_1 = samtools_0\\.1\\.18\\$\\(EXEEXT\\)") ""))
1395              (substitute* '("src/common.cpp"
1396                             "src/tophat.py")
1397                (("samtools_0.1.18") (which "samtools")))
1398              (substitute* '("src/common.h"
1399                             "src/bam2fastx.cpp")
1400                (("#include \"bam.h\"") "#include <samtools/bam.h>")
1401                (("#include \"sam.h\"") "#include <samtools/sam.h>"))
1402              (substitute* '("src/bwt_map.h"
1403                             "src/map2gtf.h"
1404                             "src/align_status.h")
1405                (("#include <bam.h>") "#include <samtools/bam.h>")
1406                (("#include <sam.h>") "#include <samtools/sam.h>"))
1407              #t)))))
1408     (inputs
1409      `(("boost" ,boost)
1410        ("bowtie" ,bowtie)
1411        ("samtools" ,samtools-0.1)
1412        ("ncurses" ,ncurses)
1413        ("python" ,python-2)
1414        ("perl" ,perl)
1415        ("zlib" ,zlib)
1416        ("seqan" ,seqan-1)))
1417     (home-page "http://ccb.jhu.edu/software/tophat/index.shtml")
1418     (synopsis "Spliced read mapper for RNA-Seq data")
1419     (description
1420      "TopHat is a fast splice junction mapper for nucleotide sequence
1421 reads produced by the RNA-Seq method.  It aligns RNA-Seq reads to
1422 mammalian-sized genomes using the ultra high-throughput short read
1423 aligner Bowtie, and then analyzes the mapping results to identify
1424 splice junctions between exons.")
1425     ;; TopHat is released under the Boost Software License, Version 1.0
1426     ;; See https://github.com/infphilo/tophat/issues/11#issuecomment-121589893
1427     (license license:boost1.0)))
1428
1429 (define-public bwa
1430   (package
1431     (name "bwa")
1432     (version "0.7.17")
1433     (source (origin
1434               (method url-fetch)
1435               (uri (string-append
1436                     "https://github.com/lh3/bwa/releases/download/v"
1437                     version "/bwa-" version ".tar.bz2"))
1438               (sha256
1439                (base32
1440                 "1zfhv2zg9v1icdlq4p9ssc8k01mca5d1bd87w71py2swfi74s6yy"))))
1441     (build-system gnu-build-system)
1442     (arguments
1443      '(#:tests? #f ;no "check" target
1444        #:phases
1445        (modify-phases %standard-phases
1446          (replace 'install
1447            (lambda* (#:key outputs #:allow-other-keys)
1448              (let ((bin (string-append
1449                          (assoc-ref outputs "out") "/bin"))
1450                    (doc (string-append
1451                          (assoc-ref outputs "out") "/share/doc/bwa"))
1452                    (man (string-append
1453                          (assoc-ref outputs "out") "/share/man/man1")))
1454                (install-file "bwa" bin)
1455                (install-file "README.md" doc)
1456                (install-file "bwa.1" man))
1457              #t))
1458            ;; no "configure" script
1459           (delete 'configure))))
1460     (inputs `(("zlib" ,zlib)))
1461     ;; Non-portable SSE instructions are used so building fails on platforms
1462     ;; other than x86_64.
1463     (supported-systems '("x86_64-linux"))
1464     (home-page "http://bio-bwa.sourceforge.net/")
1465     (synopsis "Burrows-Wheeler sequence aligner")
1466     (description
1467      "BWA is a software package for mapping low-divergent sequences against a
1468 large reference genome, such as the human genome.  It consists of three
1469 algorithms: BWA-backtrack, BWA-SW and BWA-MEM.  The first algorithm is
1470 designed for Illumina sequence reads up to 100bp, while the rest two for
1471 longer sequences ranged from 70bp to 1Mbp.  BWA-MEM and BWA-SW share similar
1472 features such as long-read support and split alignment, but BWA-MEM, which is
1473 the latest, is generally recommended for high-quality queries as it is faster
1474 and more accurate.  BWA-MEM also has better performance than BWA-backtrack for
1475 70-100bp Illumina reads.")
1476     (license license:gpl3+)))
1477
1478 (define-public bwa-pssm
1479   (package (inherit bwa)
1480     (name "bwa-pssm")
1481     (version "0.5.11")
1482     (source (origin
1483               (method git-fetch)
1484               (uri (git-reference
1485                     (url "https://github.com/pkerpedjiev/bwa-pssm.git")
1486                     (commit version)))
1487               (file-name (git-file-name name version))
1488               (sha256
1489                (base32
1490                 "076c4q0cdqz8jgylb067y9zmvxglppnzi3qiscn0xiypgc6lgb5r"))))
1491     (build-system gnu-build-system)
1492     (inputs
1493      `(("gdsl" ,gdsl)
1494        ("zlib" ,zlib)
1495        ("perl" ,perl)))
1496     (home-page "http://bwa-pssm.binf.ku.dk/")
1497     (synopsis "Burrows-Wheeler transform-based probabilistic short read mapper")
1498     (description
1499      "BWA-PSSM is a probabilistic short genomic sequence read aligner based on
1500 the use of @dfn{position specific scoring matrices} (PSSM).  Like many of the
1501 existing aligners it is fast and sensitive.  Unlike most other aligners,
1502 however, it is also adaptible in the sense that one can direct the alignment
1503 based on known biases within the data set.  It is coded as a modification of
1504 the original BWA alignment program and shares the genome index structure as
1505 well as many of the command line options.")
1506     (license license:gpl3+)))
1507
1508 (define-public python-bx-python
1509   (package
1510     (name "python-bx-python")
1511     (version "0.8.2")
1512     (source (origin
1513               (method url-fetch)
1514               (uri (pypi-uri "bx-python" version))
1515               (sha256
1516                (base32
1517                 "11kksg2rbzihpmcid823xvg42xi88m7sz58rzk29abybkxy0rszs"))))
1518     (build-system python-build-system)
1519     ;; Tests fail because test data are not included
1520     (arguments '(#:tests? #f))
1521     (propagated-inputs
1522      `(("python-numpy" ,python-numpy)
1523        ("python-six" ,python-six)))
1524     (inputs
1525      `(("zlib" ,zlib)))
1526     (native-inputs
1527      `(("python-lzo" ,python-lzo)
1528        ("python-nose" ,python-nose)
1529        ("python-cython" ,python-cython)))
1530     (home-page "https://github.com/bxlab/bx-python")
1531     (synopsis "Tools for manipulating biological data")
1532     (description
1533      "bx-python provides tools for manipulating biological data, particularly
1534 multiple sequence alignments.")
1535     (license license:expat)))
1536
1537 (define-public python2-bx-python
1538   (package-with-python2 python-bx-python))
1539
1540 (define-public python-pysam
1541   (package
1542     (name "python-pysam")
1543     (version "0.15.1")
1544     (source (origin
1545               (method git-fetch)
1546               ;; Test data is missing on PyPi.
1547               (uri (git-reference
1548                     (url "https://github.com/pysam-developers/pysam.git")
1549                     (commit (string-append "v" version))))
1550               (file-name (git-file-name name version))
1551               (sha256
1552                (base32
1553                 "1vj367w6xbn9bpmksm162l1aipf7cj97h1q83y7jcpm33ihwpf7x"))
1554               (modules '((guix build utils)))
1555               (snippet '(begin
1556                           ;; Drop bundled htslib. TODO: Also remove samtools
1557                           ;; and bcftools.
1558                           (delete-file-recursively "htslib")
1559                           #t))))
1560     (build-system python-build-system)
1561     (arguments
1562      `(#:modules ((ice-9 ftw)
1563                   (srfi srfi-26)
1564                   (guix build python-build-system)
1565                   (guix build utils))
1566        #:phases
1567        (modify-phases %standard-phases
1568          (add-before 'build 'set-flags
1569            (lambda* (#:key inputs #:allow-other-keys)
1570              (setenv "HTSLIB_MODE" "external")
1571              (setenv "HTSLIB_LIBRARY_DIR"
1572                      (string-append (assoc-ref inputs "htslib") "/lib"))
1573              (setenv "HTSLIB_INCLUDE_DIR"
1574                      (string-append (assoc-ref inputs "htslib") "/include"))
1575              (setenv "LDFLAGS" "-lncurses")
1576              (setenv "CFLAGS" "-D_CURSES_LIB=1")
1577              #t))
1578          (replace 'check
1579            (lambda* (#:key inputs outputs #:allow-other-keys)
1580              ;; This file contains tests that require a connection to the
1581              ;; internet.
1582              (delete-file "tests/tabix_test.py")
1583              ;; FIXME: This test fails
1584              (delete-file "tests/AlignmentFile_test.py")
1585              ;; Add first subdirectory of "build" directory to PYTHONPATH.
1586              (setenv "PYTHONPATH"
1587                      (string-append
1588                       (getenv "PYTHONPATH")
1589                       ":" (getcwd) "/build/"
1590                       (car (scandir "build"
1591                                     (negate (cut string-prefix? "." <>))))))
1592              ;; Step out of source dir so python does not import from CWD.
1593              (with-directory-excursion "tests"
1594                (setenv "HOME" "/tmp")
1595                (invoke "make" "-C" "pysam_data")
1596                (invoke "make" "-C" "cbcf_data")
1597                ;; Running nosetests without explicitly asking for a single
1598                ;; process leads to a crash.  Running with multiple processes
1599                ;; fails because the tests are not designed to run in parallel.
1600
1601                ;; FIXME: tests keep timing out on some systems.
1602                (invoke "nosetests" "-v" "--processes" "1")))))))
1603     (propagated-inputs
1604      `(("htslib" ,htslib))) ; Included from installed header files.
1605     (inputs
1606      `(("ncurses" ,ncurses)
1607        ("curl" ,curl)
1608        ("zlib" ,zlib)))
1609     (native-inputs
1610      `(("python-cython" ,python-cython)
1611        ;; Dependencies below are are for tests only.
1612        ("samtools" ,samtools)
1613        ("bcftools" ,bcftools)
1614        ("python-nose" ,python-nose)))
1615     (home-page "https://github.com/pysam-developers/pysam")
1616     (synopsis "Python bindings to the SAMtools C API")
1617     (description
1618      "Pysam is a Python module for reading and manipulating files in the
1619 SAM/BAM format.  Pysam is a lightweight wrapper of the SAMtools C API.  It
1620 also includes an interface for tabix.")
1621     (license license:expat)))
1622
1623 (define-public python2-pysam
1624   (package-with-python2 python-pysam))
1625
1626 (define-public python-twobitreader
1627   (package
1628     (name "python-twobitreader")
1629     (version "3.1.6")
1630     (source (origin
1631               (method git-fetch)
1632               (uri (git-reference
1633                     (url "https://github.com/benjschiller/twobitreader")
1634                     (commit version)))
1635               (file-name (git-file-name name version))
1636               (sha256
1637                (base32
1638                 "1qbxvv1h58cismbk1anpjrkpghsaiy64a11ir3lhy6qch6xf8n62"))))
1639     (build-system python-build-system)
1640     ;; Tests are not included
1641     (arguments '(#:tests? #f))
1642     (native-inputs
1643      `(("python-sphinx" ,python-sphinx)))
1644     (home-page "https://github.com/benjschiller/twobitreader")
1645     (synopsis "Python library for reading .2bit files")
1646     (description
1647      "twobitreader is a Python library for reading .2bit files as used by the
1648 UCSC genome browser.")
1649     (license license:artistic2.0)))
1650
1651 (define-public python2-twobitreader
1652   (package-with-python2 python-twobitreader))
1653
1654 (define-public python-plastid
1655   (package
1656     (name "python-plastid")
1657     (version "0.4.8")
1658     (source (origin
1659               (method url-fetch)
1660               (uri (pypi-uri "plastid" version))
1661               (sha256
1662                (base32
1663                 "0l24dd3q66if8yj042m4s0g95n6acn7im1imqd3p6h8ns43kxhj8"))))
1664     (build-system python-build-system)
1665     (arguments
1666      ;; Some test files are not included.
1667      `(#:tests? #f))
1668     (propagated-inputs
1669      `(("python-numpy" ,python-numpy)
1670        ("python-scipy" ,python-scipy)
1671        ("python-pandas" ,python-pandas)
1672        ("python-pysam" ,python-pysam)
1673        ("python-matplotlib" ,python-matplotlib)
1674        ("python-biopython" ,python-biopython)
1675        ("python-twobitreader" ,python-twobitreader)
1676        ("python-termcolor" ,python-termcolor)))
1677     (native-inputs
1678      `(("python-cython" ,python-cython)
1679        ("python-nose" ,python-nose)))
1680     (home-page "https://github.com/joshuagryphon/plastid")
1681     (synopsis "Python library for genomic analysis")
1682     (description
1683      "plastid is a Python library for genomic analysis – in particular,
1684 high-throughput sequencing data – with an emphasis on simplicity.")
1685     (license license:bsd-3)))
1686
1687 (define-public python2-plastid
1688   (package-with-python2 python-plastid))
1689
1690 (define-public cd-hit
1691   (package
1692     (name "cd-hit")
1693     (version "4.6.8")
1694     (source (origin
1695               (method url-fetch)
1696               (uri (string-append "https://github.com/weizhongli/cdhit"
1697                                   "/releases/download/V" version
1698                                   "/cd-hit-v" version
1699                                   "-2017-0621-source.tar.gz"))
1700               (sha256
1701                (base32
1702                 "1b4mwm2520ixjbw57sil20f9iixzw4bkdqqwgg1fc3pzm6rz4zmn"))))
1703     (build-system gnu-build-system)
1704     (arguments
1705      `(#:tests? #f ; there are no tests
1706        #:make-flags
1707        ;; Executables are copied directly to the PREFIX.
1708        (list (string-append "PREFIX=" (assoc-ref %outputs "out") "/bin"))
1709        #:phases
1710        (modify-phases %standard-phases
1711          ;; No "configure" script
1712          (delete 'configure)
1713          ;; Remove sources of non-determinism
1714          (add-after 'unpack 'be-timeless
1715            (lambda _
1716              (substitute* "cdhit-utility.c++"
1717                ((" \\(built on \" __DATE__ \"\\)") ""))
1718              (substitute* "cdhit-common.c++"
1719                (("__DATE__") "\"0\"")
1720                (("\", %s, \" __TIME__ \"\\\\n\", date") ""))
1721              #t))
1722          ;; The "install" target does not create the target directory.
1723          (add-before 'install 'create-target-dir
1724            (lambda* (#:key outputs #:allow-other-keys)
1725              (mkdir-p (string-append (assoc-ref outputs "out") "/bin"))
1726              #t)))))
1727     (inputs
1728      `(("perl" ,perl)))
1729     (home-page "http://weizhongli-lab.org/cd-hit/")
1730     (synopsis "Cluster and compare protein or nucleotide sequences")
1731     (description
1732      "CD-HIT is a program for clustering and comparing protein or nucleotide
1733 sequences.  CD-HIT is designed to be fast and handle extremely large
1734 databases.")
1735     ;; The manual says: "It can be copied under the GNU General Public License
1736     ;; version 2 (GPLv2)."
1737     (license license:gpl2)))
1738
1739 (define-public clipper
1740   (package
1741     (name "clipper")
1742     (version "1.2.1")
1743     (source (origin
1744               (method git-fetch)
1745               (uri (git-reference
1746                     (url "https://github.com/YeoLab/clipper.git")
1747                     (commit version)))
1748               (file-name (git-file-name name version))
1749               (sha256
1750                (base32
1751                 "0fja1rj84wp9vpj8rxpj3n8zqzcqq454m904yp9as1w4phccirjb"))
1752               (modules '((guix build utils)))
1753               (snippet
1754                '(begin
1755                   ;; remove unnecessary setup dependency
1756                   (substitute* "setup.py"
1757                     (("setup_requires = .*") ""))
1758                   #t))))
1759     (build-system python-build-system)
1760     (arguments
1761      `(#:python ,python-2 ; only Python 2 is supported
1762        #:phases
1763        (modify-phases %standard-phases
1764          ;; This is fixed in upstream commit
1765          ;; f6c2990198f906bf97730d95695b4bd5a6d01ddb.
1766          (add-after 'unpack 'fix-typo
1767            (lambda _
1768              (substitute* "clipper/src/readsToWiggle.pyx"
1769                (("^sc.*") ""))
1770              #t)))))
1771     (inputs
1772      `(("htseq" ,python2-htseq)
1773        ("python-pybedtools" ,python2-pybedtools)
1774        ("python-cython" ,python2-cython)
1775        ("python-scikit-learn" ,python2-scikit-learn)
1776        ("python-matplotlib" ,python2-matplotlib)
1777        ("python-pandas" ,python2-pandas)
1778        ("python-pysam" ,python2-pysam)
1779        ("python-numpy" ,python2-numpy)
1780        ("python-scipy" ,python2-scipy)))
1781     (native-inputs
1782      `(("python-mock" ,python2-mock)   ; for tests
1783        ("python-nose" ,python2-nose)   ; for tests
1784        ("python-pytz" ,python2-pytz))) ; for tests
1785     (home-page "https://github.com/YeoLab/clipper")
1786     (synopsis "CLIP peak enrichment recognition")
1787     (description
1788      "CLIPper is a tool to define peaks in CLIP-seq datasets.")
1789     (license license:gpl2)))
1790
1791 (define-public codingquarry
1792   (package
1793     (name "codingquarry")
1794     (version "2.0")
1795     (source (origin
1796               (method url-fetch)
1797               (uri (string-append
1798                     "mirror://sourceforge/codingquarry/CodingQuarry_v"
1799                     version ".tar.gz"))
1800               (sha256
1801                (base32
1802                 "0115hkjflsnfzn36xppwf9h9avfxlavr43djqmshkkzbgjzsz60i"))))
1803     (build-system gnu-build-system)
1804     (arguments
1805      '(#:tests? #f ; no "check" target
1806        #:phases
1807        (modify-phases %standard-phases
1808          (delete 'configure)
1809          (replace 'install
1810            (lambda* (#:key outputs #:allow-other-keys)
1811              (let* ((out (assoc-ref outputs "out"))
1812                     (bin (string-append out "/bin"))
1813                     (doc (string-append out "/share/doc/codingquarry")))
1814                (install-file "INSTRUCTIONS.pdf" doc)
1815                (copy-recursively "QuarryFiles"
1816                                  (string-append out "/QuarryFiles"))
1817                (install-file "CodingQuarry" bin)
1818                (install-file "CufflinksGTF_to_CodingQuarryGFF3.py" bin))
1819              #t)))))
1820     (inputs `(("openmpi" ,openmpi)))
1821     (native-search-paths
1822      (list (search-path-specification
1823             (variable "QUARRY_PATH")
1824             (files '("QuarryFiles")))))
1825     (native-inputs `(("python" ,python-2))) ; Only Python 2 is supported
1826     (synopsis "Fungal gene predictor")
1827     (description "CodingQuarry is a highly accurate, self-training GHMM fungal
1828 gene predictor designed to work with assembled, aligned RNA-seq transcripts.")
1829     (home-page "https://sourceforge.net/projects/codingquarry/")
1830     (license license:gpl3+)))
1831
1832 (define-public couger
1833   (package
1834     (name "couger")
1835     (version "1.8.2")
1836     (source (origin
1837               (method url-fetch)
1838               (uri (string-append
1839                     "http://couger.oit.duke.edu/static/assets/COUGER"
1840                     version ".zip"))
1841               (sha256
1842                (base32
1843                 "04p2b14nmhzxw5h72mpzdhalv21bx4w9b87z0wpw0xzxpysyncmq"))))
1844     (build-system gnu-build-system)
1845     (arguments
1846      `(#:tests? #f
1847        #:phases
1848        (modify-phases %standard-phases
1849          (delete 'configure)
1850          (delete 'build)
1851          (replace
1852           'install
1853           (lambda* (#:key outputs #:allow-other-keys)
1854             (let* ((out (assoc-ref outputs "out"))
1855                    (bin (string-append out "/bin")))
1856               (copy-recursively "src" (string-append out "/src"))
1857               (mkdir bin)
1858               ;; Add "src" directory to module lookup path.
1859               (substitute* "couger"
1860                 (("from argparse")
1861                  (string-append "import sys\nsys.path.append(\""
1862                                 out "\")\nfrom argparse")))
1863               (install-file "couger" bin))
1864             #t))
1865          (add-after
1866           'install 'wrap-program
1867           (lambda* (#:key inputs outputs #:allow-other-keys)
1868             ;; Make sure 'couger' runs with the correct PYTHONPATH.
1869             (let* ((out (assoc-ref outputs "out"))
1870                    (path (getenv "PYTHONPATH")))
1871               (wrap-program (string-append out "/bin/couger")
1872                 `("PYTHONPATH" ":" prefix (,path))))
1873             #t)))))
1874     (inputs
1875      `(("python" ,python-2)
1876        ("python2-pillow" ,python2-pillow)
1877        ("python2-numpy" ,python2-numpy)
1878        ("python2-scipy" ,python2-scipy)
1879        ("python2-matplotlib" ,python2-matplotlib)))
1880     (propagated-inputs
1881      `(("r-minimal" ,r-minimal)
1882        ("libsvm" ,libsvm)
1883        ("randomjungle" ,randomjungle)))
1884     (native-inputs
1885      `(("unzip" ,unzip)))
1886     (home-page "http://couger.oit.duke.edu")
1887     (synopsis "Identify co-factors in sets of genomic regions")
1888     (description
1889      "COUGER can be applied to any two sets of genomic regions bound by
1890 paralogous TFs (e.g., regions derived from ChIP-seq experiments) to identify
1891 putative co-factors that provide specificity to each TF.  The framework
1892 determines the genomic targets uniquely-bound by each TF, and identifies a
1893 small set of co-factors that best explain the in vivo binding differences
1894 between the two TFs.
1895
1896 COUGER uses classification algorithms (support vector machines and random
1897 forests) with features that reflect the DNA binding specificities of putative
1898 co-factors.  The features are generated either from high-throughput TF-DNA
1899 binding data (from protein binding microarray experiments), or from large
1900 collections of DNA motifs.")
1901     (license license:gpl3+)))
1902
1903 (define-public clustal-omega
1904   (package
1905     (name "clustal-omega")
1906     (version "1.2.4")
1907     (source (origin
1908               (method url-fetch)
1909               (uri (string-append "http://www.clustal.org/omega/clustal-omega-"
1910                                   version ".tar.gz"))
1911               (sha256
1912                (base32
1913                 "1vm30mzncwdv881vrcwg11vzvrsmwy4wg80j5i0lcfk6dlld50w6"))))
1914     (build-system gnu-build-system)
1915     (inputs
1916      `(("argtable" ,argtable)))
1917     (home-page "http://www.clustal.org/omega/")
1918     (synopsis "Multiple sequence aligner for protein and DNA/RNA")
1919     (description
1920      "Clustal-Omega is a general purpose multiple sequence alignment (MSA)
1921 program for protein and DNA/RNA.  It produces high quality MSAs and is capable
1922 of handling data-sets of hundreds of thousands of sequences in reasonable
1923 time.")
1924     (license license:gpl2+)))
1925
1926 (define-public crossmap
1927   (package
1928     (name "crossmap")
1929     (version "0.2.9")
1930     (source (origin
1931               (method url-fetch)
1932               (uri (pypi-uri "CrossMap" version))
1933               (sha256
1934                (base32
1935                 "1byhclrqnqpvc1rqkfh4jwj6yhn0x9y7jk47i0qcjlhk0pjkw92p"))))
1936     (build-system python-build-system)
1937     (arguments `(#:python ,python-2))
1938     (inputs
1939      `(("python-bx-python" ,python2-bx-python)
1940        ("python-numpy" ,python2-numpy)
1941        ("python-pysam" ,python2-pysam)
1942        ("zlib" ,zlib)))
1943     (native-inputs
1944      `(("python-cython" ,python2-cython)
1945        ("python-nose" ,python2-nose)))
1946     (home-page "http://crossmap.sourceforge.net/")
1947     (synopsis "Convert genome coordinates between assemblies")
1948     (description
1949      "CrossMap is a program for conversion of genome coordinates or annotation
1950 files between different genome assemblies.  It supports most commonly used
1951 file formats including SAM/BAM, Wiggle/BigWig, BED, GFF/GTF, VCF.")
1952     (license license:gpl2+)))
1953
1954 (define-public python-dnaio
1955   (package
1956     (name "python-dnaio")
1957     (version "0.3")
1958     (source
1959      (origin
1960        (method url-fetch)
1961        (uri (pypi-uri "dnaio" version))
1962        (sha256
1963         (base32
1964          "0f16m7hdlm0fz1n7y5asy0v9ghyrq17ni1p9iybq22ddzyd49r27"))))
1965     (build-system python-build-system)
1966     (native-inputs
1967      `(("python-cython" ,python-cython)
1968        ("python-pytest" ,python-pytest)
1969        ("python-xopen" ,python-xopen)))
1970     (home-page "https://github.com/marcelm/dnaio/")
1971     (synopsis "Read FASTA and FASTQ files efficiently")
1972     (description
1973      "dnaio is a Python library for fast parsing of FASTQ and also FASTA
1974 files.  The code was previously part of the cutadapt tool.")
1975     (license license:expat)))
1976
1977 (define-public cutadapt
1978   (package
1979     (name "cutadapt")
1980     (version "1.18")
1981     (source (origin
1982               (method git-fetch)
1983               (uri (git-reference
1984                     (url "https://github.com/marcelm/cutadapt.git")
1985                     (commit (string-append "v" version))))
1986               (file-name (git-file-name name version))
1987               (sha256
1988                (base32
1989                 "08bbfwyc0kvcd95jf2s95xiv9s3cbsxm39ydl0qck3fw3cviwxpg"))))
1990     (build-system python-build-system)
1991     (inputs
1992      `(("python-dnaio" ,python-dnaio)
1993        ("python-xopen" ,python-xopen)))
1994     (native-inputs
1995      `(("python-cython" ,python-cython)
1996        ("python-pytest" ,python-pytest)))
1997     (home-page "https://cutadapt.readthedocs.io/en/stable/")
1998     (synopsis "Remove adapter sequences from nucleotide sequencing reads")
1999     (description
2000      "Cutadapt finds and removes adapter sequences, primers, poly-A tails and
2001 other types of unwanted sequence from high-throughput sequencing reads.")
2002     (license license:expat)))
2003
2004 (define-public libbigwig
2005   (package
2006     (name "libbigwig")
2007     (version "0.4.2")
2008     (source (origin
2009               (method git-fetch)
2010               (uri (git-reference
2011                     (url "https://github.com/dpryan79/libBigWig.git")
2012                     (commit version)))
2013               (file-name (string-append name "-" version "-checkout"))
2014               (sha256
2015                (base32
2016                 "0h2smg24v5srdcqzrmz2g23cmlp4va465mgx8r2z571sfz8pv454"))))
2017     (build-system gnu-build-system)
2018     (arguments
2019      `(#:test-target "test"
2020        #:tests? #f ; tests require access to the web
2021        #:make-flags
2022        (list "CC=gcc"
2023              (string-append "prefix=" (assoc-ref %outputs "out")))
2024        #:phases
2025        (modify-phases %standard-phases
2026          (delete 'configure))))
2027     (inputs
2028      `(("zlib" ,zlib)
2029        ("curl" ,curl)))
2030     (native-inputs
2031      `(("doxygen" ,doxygen)
2032        ;; Need for tests
2033        ("python" ,python-2)))
2034     (home-page "https://github.com/dpryan79/libBigWig")
2035     (synopsis "C library for handling bigWig files")
2036     (description
2037      "This package provides a C library for parsing local and remote BigWig
2038 files.")
2039     (license license:expat)))
2040
2041 (define-public python-pybigwig
2042   (package
2043     (name "python-pybigwig")
2044     (version "0.3.12")
2045     (source (origin
2046               (method url-fetch)
2047               (uri (pypi-uri "pyBigWig" version))
2048               (sha256
2049                (base32
2050                 "00w4kfnm2c5l7wdwr2nj1z5djv8kzgf7h1zhsgv6njff1rwr26g0"))
2051               (modules '((guix build utils)))
2052               (snippet
2053                '(begin
2054                   ;; Delete bundled libBigWig sources
2055                   (delete-file-recursively "libBigWig")
2056                   #t))))
2057     (build-system python-build-system)
2058     (arguments
2059      `(#:phases
2060        (modify-phases %standard-phases
2061          (add-after 'unpack 'link-with-libBigWig
2062            (lambda* (#:key inputs #:allow-other-keys)
2063              (substitute* "setup.py"
2064                (("libs=\\[") "libs=[\"BigWig\", "))
2065              #t)))))
2066     (propagated-inputs
2067      `(("python-numpy" ,python-numpy)))
2068     (inputs
2069      `(("libbigwig" ,libbigwig)
2070        ("zlib" ,zlib)
2071        ("curl" ,curl)))
2072     (home-page "https://github.com/dpryan79/pyBigWig")
2073     (synopsis "Access bigWig files in Python using libBigWig")
2074     (description
2075      "This package provides Python bindings to the libBigWig library for
2076 accessing bigWig files.")
2077     (license license:expat)))
2078
2079 (define-public python2-pybigwig
2080   (package-with-python2 python-pybigwig))
2081
2082 (define-public python-dendropy
2083   (package
2084     (name "python-dendropy")
2085     (version "4.4.0")
2086     (source
2087      (origin
2088        (method git-fetch)
2089        ;; Source from GitHub so that tests are included.
2090        (uri (git-reference
2091              (url "https://github.com/jeetsukumaran/DendroPy.git")
2092              (commit (string-append "v" version))))
2093        (file-name (git-file-name name version))
2094        (sha256
2095         (base32
2096          "097hfyv2kaf4x92i4rjx0paw2cncxap48qivv8zxng4z7nhid0x9"))))
2097     (build-system python-build-system)
2098     (home-page "http://packages.python.org/DendroPy/")
2099     (synopsis "Library for phylogenetics and phylogenetic computing")
2100     (description
2101      "DendroPy is a library for phylogenetics and phylogenetic computing: reading,
2102 writing, simulation, processing and manipulation of phylogenetic
2103 trees (phylogenies) and characters.")
2104     (license license:bsd-3)))
2105
2106 (define-public python2-dendropy
2107   (let ((base (package-with-python2 python-dendropy)))
2108     (package
2109       (inherit base)
2110       (arguments
2111        `(#:phases
2112          (modify-phases %standard-phases
2113            (add-after 'unpack 'remove-failing-test
2114              (lambda _
2115                ;; This test fails when the full test suite is run, as documented
2116                ;; at https://github.com/jeetsukumaran/DendroPy/issues/74
2117                (substitute* "tests/test_dataio_nexml_reader_tree_list.py"
2118                  (("test_collection_comments_and_annotations")
2119                   "do_not_test_collection_comments_and_annotations"))
2120                #t)))
2121          ,@(package-arguments base))))))
2122
2123 (define-public python-py2bit
2124   (package
2125     (name "python-py2bit")
2126     (version "0.3.0")
2127     (source
2128      (origin
2129        (method url-fetch)
2130        (uri (pypi-uri "py2bit" version))
2131        (sha256
2132         (base32
2133          "1vw2nvw1yrl7ikkqsqs1pg239yr5nspvd969r1x9arms1k25a1a5"))))
2134     (build-system python-build-system)
2135     (home-page "https://github.com/dpryan79/py2bit")
2136     (synopsis "Access 2bit files using lib2bit")
2137     (description
2138      "This package provides Python bindings for lib2bit to access 2bit files
2139 with Python.")
2140     (license license:expat)))
2141
2142 (define-public deeptools
2143   (package
2144     (name "deeptools")
2145     (version "3.1.3")
2146     (source (origin
2147               (method git-fetch)
2148               (uri (git-reference
2149                     (url "https://github.com/deeptools/deepTools.git")
2150                     (commit version)))
2151               (file-name (git-file-name name version))
2152               (sha256
2153                (base32
2154                 "1vggnf52g6q2vifdl4cyi7s2fnfqq0ky2zrkj5zv2qfzsc3p3siw"))))
2155     (build-system python-build-system)
2156     (arguments
2157      `(#:phases
2158        (modify-phases %standard-phases
2159          ;; This phase fails, but it's not needed.
2160          (delete 'reset-gzip-timestamps))))
2161     (inputs
2162      `(("python-plotly" ,python-plotly)
2163        ("python-scipy" ,python-scipy)
2164        ("python-numpy" ,python-numpy)
2165        ("python-numpydoc" ,python-numpydoc)
2166        ("python-matplotlib" ,python-matplotlib)
2167        ("python-pysam" ,python-pysam)
2168        ("python-py2bit" ,python-py2bit)
2169        ("python-pybigwig" ,python-pybigwig)))
2170     (native-inputs
2171      `(("python-mock" ,python-mock)   ;for tests
2172        ("python-nose" ,python-nose)   ;for tests
2173        ("python-pytz" ,python-pytz))) ;for tests
2174     (home-page "https://github.com/deeptools/deepTools")
2175     (synopsis "Tools for normalizing and visualizing deep-sequencing data")
2176     (description
2177      "DeepTools addresses the challenge of handling the large amounts of data
2178 that are now routinely generated from DNA sequencing centers.  To do so,
2179 deepTools contains useful modules to process the mapped reads data to create
2180 coverage files in standard bedGraph and bigWig file formats.  By doing so,
2181 deepTools allows the creation of normalized coverage files or the comparison
2182 between two files (for example, treatment and control).  Finally, using such
2183 normalized and standardized files, multiple visualizations can be created to
2184 identify enrichments with functional annotations of the genome.")
2185     (license license:gpl3+)))
2186
2187 (define-public delly
2188   (package
2189     (name "delly")
2190     (version "0.7.9")
2191     (source (origin
2192               (method git-fetch)
2193               (uri (git-reference
2194                     (url "https://github.com/dellytools/delly.git")
2195                     (commit (string-append "v" version))))
2196               (file-name (git-file-name name version))
2197               (sha256
2198                (base32 "034jqsxswy9gqdh2zkgc1js99qkv75ks4xvzgmh0284sraagv61z"))
2199               (modules '((guix build utils)))
2200               (snippet
2201                '(begin
2202                   (delete-file-recursively "src/htslib")
2203                   #t))))
2204     (build-system gnu-build-system)
2205     (arguments
2206      `(#:tests? #f ; There are no tests to run.
2207        #:make-flags
2208        (list "PARALLEL=1"  ; Allow parallel execution at run-time.
2209              (string-append "prefix=" (assoc-ref %outputs "out")))
2210        #:phases
2211        (modify-phases %standard-phases
2212          (delete 'configure) ; There is no configure phase.
2213          (add-after 'install 'install-templates
2214            (lambda* (#:key outputs #:allow-other-keys)
2215              (let ((templates (string-append (assoc-ref outputs "out")
2216                                              "/share/delly/templates")))
2217                (mkdir-p templates)
2218                (copy-recursively "excludeTemplates" templates)
2219                #t))))))
2220     (inputs
2221      `(("boost" ,boost)
2222        ("htslib" ,htslib)
2223        ("zlib" ,zlib)
2224        ("bzip2" ,bzip2)))
2225     (home-page "https://github.com/dellytools/delly")
2226     (synopsis "Integrated structural variant prediction method")
2227     (description "Delly is an integrated structural variant prediction method
2228 that can discover and genotype deletions, tandem duplications, inversions and
2229 translocations at single-nucleotide resolution in short-read massively parallel
2230 sequencing data.  It uses paired-ends and split-reads to sensitively and
2231 accurately delineate genomic rearrangements throughout the genome.")
2232     (license license:gpl3+)))
2233
2234 (define-public diamond
2235   (package
2236     (name "diamond")
2237     (version "0.9.22")
2238     (source (origin
2239               (method git-fetch)
2240               (uri (git-reference
2241                     (url "https://github.com/bbuchfink/diamond.git")
2242                     (commit (string-append "v" version))))
2243               (file-name (git-file-name name version))
2244               (sha256
2245                (base32
2246                 "0bky78v79g3wmdpsd706cscckgw1v09fg8vdd0z8z0d5b97aj9zl"))))
2247     (build-system cmake-build-system)
2248     (arguments
2249      '(#:tests? #f ; no "check" target
2250        #:phases
2251        (modify-phases %standard-phases
2252          (add-after 'unpack 'remove-native-compilation
2253            (lambda _
2254              (substitute* "CMakeLists.txt" (("-march=native") ""))
2255              #t)))))
2256     (inputs
2257      `(("zlib" ,zlib)))
2258     (home-page "https://github.com/bbuchfink/diamond")
2259     (synopsis "Accelerated BLAST compatible local sequence aligner")
2260     (description
2261      "DIAMOND is a BLAST-compatible local aligner for mapping protein and
2262 translated DNA query sequences against a protein reference database (BLASTP
2263 and BLASTX alignment mode).  The speedup over BLAST is up to 20,000 on short
2264 reads at a typical sensitivity of 90-99% relative to BLAST depending on the
2265 data and settings.")
2266     (license license:agpl3+)))
2267
2268 (define-public discrover
2269   (package
2270     (name "discrover")
2271     (version "1.6.0")
2272     (source
2273      (origin
2274        (method git-fetch)
2275        (uri (git-reference
2276              (url "https://github.com/maaskola/discrover.git")
2277              (commit version)))
2278        (file-name (git-file-name name version))
2279        (sha256
2280         (base32
2281          "173fwi2vb6a5kp406hm3jj6j7v4whww796f2qcygp4rpvamh307y"))))
2282     (build-system cmake-build-system)
2283     (arguments
2284      `(#:tests? #f                      ; there are no tests
2285        #:phases
2286        (modify-phases %standard-phases
2287          (add-after 'unpack 'add-missing-includes
2288            (lambda _
2289              (substitute* "src/executioninformation.hpp"
2290                (("#define EXECUTIONINFORMATION_HPP" line)
2291                 (string-append line "\n#include <random>")))
2292              (substitute* "src/plasma/fasta.hpp"
2293                (("#define FASTA_HPP" line)
2294                 (string-append line "\n#include <random>")))
2295              #t)))))
2296     (inputs
2297      `(("boost" ,boost)
2298        ("cairo" ,cairo)))
2299     (native-inputs
2300      `(("texlive" ,texlive)
2301        ;; TODO: Replace texlive with minimal texlive-union.
2302        ;; ("texlive" ,(texlive-union (list texlive-latex-doi
2303        ;;                             texlive-latex-hyperref
2304        ;;                             texlive-latex-oberdiek
2305        ;;                             texlive-generic-ifxetex
2306        ;;                             texlive-latex-url
2307        ;;                             texlive-latex-pgf
2308        ;;                             texlive-latex-examplep
2309        ;;                             texlive-latex-natbib
2310        ;;                             texlive-latex-verbatimbox
2311        ;;                             texlive-latex-ms
2312        ;;                             texlive-latex-xcolor
2313        ;;                             texlive-fonts-amsfonts
2314        ;;                             texlive-latex-amsfonts
2315        ;;                             ;; ...
2316        ;;                             )))
2317        ("imagemagick" ,imagemagick)))
2318     (home-page "http://dorina.mdc-berlin.de/public/rajewsky/discrover/")
2319     (synopsis "Discover discriminative nucleotide sequence motifs")
2320     (description "Discrover is a motif discovery method to find binding sites
2321 of nucleic acid binding proteins.")
2322     (license license:gpl3+)))
2323
2324 (define-public eigensoft
2325   (package
2326     (name "eigensoft")
2327     (version "7.2.1")
2328     (source
2329      (origin
2330        (method git-fetch)
2331        (uri (git-reference
2332              (url "https://github.com/DReichLab/EIG.git")
2333              (commit (string-append "v" version))))
2334        (file-name (git-file-name name version))
2335        (sha256
2336         (base32
2337          "1c141fqvhnzibmnf22sv23vbmzm20kjjyrib44cfh75wyndp2d9k"))
2338        (modules '((guix build utils)))
2339        ;; Remove pre-built binaries.
2340        (snippet '(begin
2341                    (delete-file-recursively "bin")
2342                    (mkdir "bin")
2343                    #t))))
2344     (build-system gnu-build-system)
2345     (arguments
2346      `(#:tests? #f                    ; There are no tests.
2347        #:make-flags '("CC=gcc")
2348        #:phases
2349        (modify-phases %standard-phases
2350          ;; There is no configure phase, but the Makefile is in a
2351          ;; sub-directory.
2352          (replace 'configure
2353            (lambda _ (chdir "src") #t))
2354          ;; The provided install target only copies executables to
2355          ;; the "bin" directory in the build root.
2356          (add-after 'install 'actually-install
2357            (lambda* (#:key outputs #:allow-other-keys)
2358              (let* ((out (assoc-ref outputs "out"))
2359                     (bin  (string-append out "/bin")))
2360                (for-each (lambda (file)
2361                            (install-file file bin))
2362                          (find-files "../bin" ".*"))
2363                #t))))))
2364     (inputs
2365      `(("gsl" ,gsl)
2366        ("lapack" ,lapack)
2367        ("openblas" ,openblas)
2368        ("perl" ,perl)
2369        ("gfortran" ,gfortran "lib")))
2370     (home-page "https://github.com/DReichLab/EIG")
2371     (synopsis "Tools for population genetics")
2372     (description "The EIGENSOFT package provides tools for population
2373 genetics and stratification correction.  EIGENSOFT implements methods commonly
2374 used in population genetics analyses such as PCA, computation of Tracy-Widom
2375 statistics, and finding related individuals in structured populations.  It
2376 comes with a built-in plotting script and supports multiple file formats and
2377 quantitative phenotypes.")
2378     ;; The license of the eigensoft tools is Expat, but since it's
2379     ;; linking with the GNU Scientific Library (GSL) the effective
2380     ;; license is the GPL.
2381     (license license:gpl3+)))
2382
2383 (define-public edirect
2384   (package
2385     (name "edirect")
2386     (version "10.2.20181018")
2387     (source (origin
2388               (method url-fetch)
2389               (uri (string-append "ftp://ftp.ncbi.nlm.nih.gov/entrez/entrezdirect"
2390                                   "/versions/" version
2391                                   "/edirect-" version ".tar.gz"))
2392               (sha256
2393                (base32
2394                 "091f4aigzpbqih6h82nq566gkp3y07i72yqndmqskfgar1vwgci7"))))
2395     (build-system perl-build-system)
2396     (arguments
2397      `(#:phases
2398        (modify-phases %standard-phases
2399          (delete 'configure)
2400          (delete 'build)
2401          (delete 'check)                ; simple check after install
2402          (replace 'install
2403            (lambda* (#:key outputs #:allow-other-keys)
2404              (install-file "edirect.pl"
2405                            (string-append (assoc-ref outputs "out") "/bin"))
2406              #t))
2407          (add-after 'install 'wrap-program
2408            (lambda* (#:key outputs #:allow-other-keys)
2409              ;; Make sure 'edirect.pl' finds all perl inputs at runtime.
2410              (let* ((out (assoc-ref outputs "out"))
2411                     (path (getenv "PERL5LIB")))
2412                (wrap-program (string-append out "/bin/edirect.pl")
2413                  `("PERL5LIB" ":" prefix (,path))))
2414              #t))
2415          (add-after 'wrap-program 'check
2416            (lambda* (#:key outputs #:allow-other-keys)
2417              (invoke (string-append (assoc-ref outputs "out")
2418                                     "/bin/edirect.pl")
2419                      "-filter" "-help")
2420              #t)))))
2421     (inputs
2422      `(("perl-html-parser" ,perl-html-parser)
2423        ("perl-encode-locale" ,perl-encode-locale)
2424        ("perl-file-listing" ,perl-file-listing)
2425        ("perl-html-tagset" ,perl-html-tagset)
2426        ("perl-html-tree" ,perl-html-tree)
2427        ("perl-http-cookies" ,perl-http-cookies)
2428        ("perl-http-date" ,perl-http-date)
2429        ("perl-http-message" ,perl-http-message)
2430        ("perl-http-negotiate" ,perl-http-negotiate)
2431        ("perl-lwp-mediatypes" ,perl-lwp-mediatypes)
2432        ("perl-lwp-protocol-https" ,perl-lwp-protocol-https)
2433        ("perl-net-http" ,perl-net-http)
2434        ("perl-uri" ,perl-uri)
2435        ("perl-www-robotrules" ,perl-www-robotrules)
2436        ("perl-xml-simple" ,perl-xml-simple)
2437        ("perl" ,perl)))
2438     (home-page "http://www.ncbi.nlm.nih.gov/books/NBK179288/")
2439     (synopsis "Tools for accessing the NCBI's set of databases")
2440     (description
2441      "Entrez Direct (EDirect) is a method for accessing the National Center
2442 for Biotechnology Information's (NCBI) set of interconnected
2443 databases (publication, sequence, structure, gene, variation, expression,
2444 etc.) from a terminal.  Functions take search terms from command-line
2445 arguments.  Individual operations are combined to build multi-step queries.
2446 Record retrieval and formatting normally complete the process.
2447
2448 EDirect also provides an argument-driven function that simplifies the
2449 extraction of data from document summaries or other results that are returned
2450 in structured XML format.  This can eliminate the need for writing custom
2451 software to answer ad hoc questions.")
2452     (license license:public-domain)))
2453
2454 (define-public exonerate
2455   (package
2456     (name "exonerate")
2457     (version "2.4.0")
2458     (source
2459      (origin
2460        (method url-fetch)
2461        (uri
2462         (string-append
2463          "http://ftp.ebi.ac.uk/pub/software/vertebrategenomics/exonerate/"
2464          "exonerate-" version ".tar.gz"))
2465        (sha256
2466         (base32
2467          "0hj0m9xygiqsdxvbg79wq579kbrx1mdrabi2bzqz2zn9qwfjcjgq"))))
2468     (build-system gnu-build-system)
2469     (arguments
2470      `(#:parallel-build? #f)) ; Building in parallel fails on some machines.
2471     (native-inputs
2472      `(("pkg-config" ,pkg-config)))
2473     (inputs
2474      `(("glib" ,glib)))
2475     (home-page
2476      "https://www.ebi.ac.uk/about/vertebrate-genomics/software/exonerate")
2477     (synopsis "Generic tool for biological sequence alignment")
2478     (description
2479      "Exonerate is a generic tool for pairwise sequence comparison.  It allows
2480 the alignment of sequences using a many alignment models, either exhaustive
2481 dynamic programming or a variety of heuristics.")
2482     (license license:gpl3)))
2483
2484 (define-public express
2485   (package
2486     (name "express")
2487     (version "1.5.1")
2488     (source (origin
2489               (method url-fetch)
2490               (uri
2491                (string-append
2492                 "http://bio.math.berkeley.edu/eXpress/downloads/express-"
2493                 version "/express-" version "-src.tgz"))
2494               (sha256
2495                (base32
2496                 "03rczxd0gjp2l1jxcmjfmf5j94j77zqyxa6x063zsc585nj40n0c"))))
2497     (build-system cmake-build-system)
2498     (arguments
2499      `(#:tests? #f ;no "check" target
2500        #:phases
2501        (modify-phases %standard-phases
2502          (add-after 'unpack 'use-shared-boost-libs-and-set-bamtools-paths
2503            (lambda* (#:key inputs #:allow-other-keys)
2504              (substitute* "CMakeLists.txt"
2505                (("set\\(Boost_USE_STATIC_LIBS ON\\)")
2506                 "set(Boost_USE_STATIC_LIBS OFF)")
2507                (("\\$\\{CMAKE_CURRENT_SOURCE_DIR\\}/bamtools/include")
2508                 (string-append (assoc-ref inputs "bamtools") "/include/bamtools")))
2509              (substitute* "src/CMakeLists.txt"
2510                (("\\$\\{CMAKE_CURRENT_SOURCE_DIR\\}/\\.\\./bamtools/lib")
2511                 (string-append (assoc-ref inputs "bamtools") "/lib"))
2512                (("libprotobuf.a") "libprotobuf.so"))
2513              #t)))))
2514     (inputs
2515      `(("boost" ,boost)
2516        ("bamtools" ,bamtools)
2517        ("protobuf" ,protobuf)
2518        ("zlib" ,zlib)))
2519     (home-page "http://bio.math.berkeley.edu/eXpress")
2520     (synopsis "Streaming quantification for high-throughput genomic sequencing")
2521     (description
2522      "eXpress is a streaming tool for quantifying the abundances of a set of
2523 target sequences from sampled subsequences.  Example applications include
2524 transcript-level RNA-Seq quantification, allele-specific/haplotype expression
2525 analysis (from RNA-Seq), transcription factor binding quantification in
2526 ChIP-Seq, and analysis of metagenomic data.")
2527     (license license:artistic2.0)))
2528
2529 (define-public express-beta-diversity
2530   (package
2531    (name "express-beta-diversity")
2532    (version "1.0.8")
2533    (source (origin
2534              (method git-fetch)
2535              (uri (git-reference
2536                    (url "https://github.com/dparks1134/ExpressBetaDiversity.git")
2537                    (commit (string-append "v" version))))
2538              (file-name (git-file-name name version))
2539              (sha256
2540               (base32
2541                "0s0yzg5c21349rh7x4w9266jsvnp7j1hp9cf8sk32hz8nvrj745x"))))
2542    (build-system gnu-build-system)
2543    (arguments
2544     `(#:phases
2545       (modify-phases %standard-phases
2546         (delete 'configure)
2547         (add-before 'build 'enter-source (lambda _ (chdir "source") #t))
2548         (replace 'check
2549           (lambda _ (invoke "../bin/ExpressBetaDiversity" "-u") #t))
2550         (replace 'install
2551           (lambda* (#:key outputs #:allow-other-keys)
2552             (let ((bin (string-append (assoc-ref outputs "out") "/bin")))
2553               (install-file "../scripts/convertToEBD.py" bin)
2554               (install-file "../bin/ExpressBetaDiversity" bin)
2555               #t))))))
2556    (inputs
2557     `(("python" ,python-2)))
2558    (home-page "http://kiwi.cs.dal.ca/Software/ExpressBetaDiversity")
2559    (synopsis "Taxon- and phylogenetic-based beta diversity measures")
2560    (description
2561     "Express Beta Diversity (EBD) calculates ecological beta diversity
2562 (dissimilarity) measures between biological communities.  EBD implements a
2563 variety of diversity measures including those that make use of phylogenetic
2564 similarity of community members.")
2565    (license license:gpl3+)))
2566
2567 (define-public fasttree
2568   (package
2569    (name "fasttree")
2570    (version "2.1.10")
2571    (source (origin
2572              (method url-fetch)
2573              (uri (string-append
2574                    "http://www.microbesonline.org/fasttree/FastTree-"
2575                    version ".c"))
2576              (sha256
2577               (base32
2578                "0vcjdvy1j4m702vmak4svbfkrpcw63k7wymfksjp9a982zy8kjsl"))))
2579    (build-system gnu-build-system)
2580    (arguments
2581     `(#:tests? #f ; no "check" target
2582       #:phases
2583       (modify-phases %standard-phases
2584         (delete 'unpack)
2585         (delete 'configure)
2586         (replace 'build
2587           (lambda* (#:key source #:allow-other-keys)
2588             (invoke "gcc"
2589                     "-O3"
2590                     "-finline-functions"
2591                     "-funroll-loops"
2592                     "-Wall"
2593                     "-o"
2594                     "FastTree"
2595                     source
2596                     "-lm")
2597             (invoke "gcc"
2598                     "-DOPENMP"
2599                     "-fopenmp"
2600                     "-O3"
2601                     "-finline-functions"
2602                     "-funroll-loops"
2603                     "-Wall"
2604                     "-o"
2605                     "FastTreeMP"
2606                     source
2607                     "-lm")
2608             #t))
2609         (replace 'install
2610           (lambda* (#:key outputs #:allow-other-keys)
2611             (let ((bin (string-append (assoc-ref outputs "out") "/bin")))
2612               (install-file "FastTree" bin)
2613               (install-file "FastTreeMP" bin)
2614               #t))))))
2615    (home-page "http://www.microbesonline.org/fasttree")
2616    (synopsis "Infers approximately-maximum-likelihood phylogenetic trees")
2617    (description
2618     "FastTree can handle alignments with up to a million of sequences in a
2619 reasonable amount of time and memory.  For large alignments, FastTree is
2620 100-1,000 times faster than PhyML 3.0 or RAxML 7.")
2621    (license license:gpl2+)))
2622
2623 (define-public fastx-toolkit
2624   (package
2625     (name "fastx-toolkit")
2626     (version "0.0.14")
2627     (source (origin
2628               (method url-fetch)
2629               (uri
2630                (string-append
2631                 "https://github.com/agordon/fastx_toolkit/releases/download/"
2632                 version "/fastx_toolkit-" version ".tar.bz2"))
2633               (sha256
2634                (base32
2635                 "01jqzw386873sr0pjp1wr4rn8fsga2vxs1qfmicvx1pjr72007wy"))))
2636     (build-system gnu-build-system)
2637     (inputs
2638      `(("libgtextutils" ,libgtextutils)))
2639     (native-inputs
2640      `(("pkg-config" ,pkg-config)))
2641     (home-page "http://hannonlab.cshl.edu/fastx_toolkit/")
2642     (synopsis "Tools for FASTA/FASTQ file preprocessing")
2643     (description
2644      "The FASTX-Toolkit is a collection of command line tools for Short-Reads
2645 FASTA/FASTQ files preprocessing.
2646
2647 Next-Generation sequencing machines usually produce FASTA or FASTQ files,
2648 containing multiple short-reads sequences.  The main processing of such
2649 FASTA/FASTQ files is mapping the sequences to reference genomes.  However, it
2650 is sometimes more productive to preprocess the files before mapping the
2651 sequences to the genome---manipulating the sequences to produce better mapping
2652 results.  The FASTX-Toolkit tools perform some of these preprocessing tasks.")
2653     (license license:agpl3+)))
2654
2655 (define-public flexbar
2656   (package
2657     (name "flexbar")
2658     (version "3.4.0")
2659     (source (origin
2660               (method git-fetch)
2661               (uri (git-reference
2662                     (url "https://github.com/seqan/flexbar.git")
2663                     (commit (string-append "v" version))))
2664               (file-name (git-file-name name version))
2665               (sha256
2666                (base32
2667                 "1pq9sxvdnldl14libk234m72dqhwgzs3acgl943wchwdqlcsi5r2"))))
2668     (build-system cmake-build-system)
2669     (arguments
2670      `(#:phases
2671        (modify-phases %standard-phases
2672          (replace 'check
2673            (lambda* (#:key outputs #:allow-other-keys)
2674              (setenv "PATH" (string-append (getcwd) ":" (getenv "PATH")))
2675              (with-directory-excursion "../source/test"
2676                (invoke "bash" "flexbar_test.sh"))
2677              #t))
2678          (replace 'install
2679            (lambda* (#:key outputs #:allow-other-keys)
2680              (let* ((out (string-append (assoc-ref outputs "out")))
2681                     (bin (string-append out "/bin/")))
2682                (install-file "flexbar" bin))
2683              #t)))))
2684     (inputs
2685      `(("tbb" ,tbb)
2686        ("zlib" ,zlib)))
2687     (native-inputs
2688      `(("pkg-config" ,pkg-config)
2689        ("seqan" ,seqan)))
2690     (home-page "https://github.com/seqan/flexbar")
2691     (synopsis "Barcode and adapter removal tool for sequencing platforms")
2692     (description
2693      "Flexbar preprocesses high-throughput nucleotide sequencing data
2694 efficiently.  It demultiplexes barcoded runs and removes adapter sequences.
2695 Moreover, trimming and filtering features are provided.  Flexbar increases
2696 read mapping rates and improves genome and transcriptome assemblies.  It
2697 supports next-generation sequencing data in fasta/q and csfasta/q format from
2698 Illumina, Roche 454, and the SOLiD platform.")
2699     (license license:bsd-3)))
2700
2701 (define-public fraggenescan
2702   (package
2703     (name "fraggenescan")
2704     (version "1.30")
2705     (source
2706      (origin
2707        (method url-fetch)
2708        (uri
2709         (string-append "mirror://sourceforge/fraggenescan/"
2710                        "FragGeneScan" version ".tar.gz"))
2711        (sha256
2712         (base32 "158dcnwczgcyhwm4qlx19sanrwgdpzf6bn2y57mbpx55lkgz1mzj"))))
2713     (build-system gnu-build-system)
2714     (arguments
2715      `(#:phases
2716        (modify-phases %standard-phases
2717          (delete 'configure)
2718          (add-before 'build 'patch-paths
2719            (lambda* (#:key outputs #:allow-other-keys)
2720              (let* ((out (string-append (assoc-ref outputs "out")))
2721                     (share (string-append out "/share/fraggenescan/")))
2722                (substitute* "run_FragGeneScan.pl"
2723                  (("system\\(\"rm")
2724                   (string-append "system(\"" (which "rm")))
2725                  (("system\\(\"mv")
2726                   (string-append "system(\"" (which "mv")))
2727                  (("\\\"awk") (string-append "\"" (which "awk")))
2728                  ;; This script and other programs expect the training files
2729                  ;; to be in the non-standard location bin/train/XXX. Change
2730                  ;; this to be share/fraggenescan/train/XXX instead.
2731                  (("^\\$train.file = \\$dir.*")
2732                   (string-append "$train_file = \""
2733                                  share
2734                                  "train/\".$FGS_train_file;")))
2735                (substitute* "run_hmm.c"
2736                  (("^  strcat\\(train_dir, \\\"train/\\\"\\);")
2737                   (string-append "  strcpy(train_dir, \"" share "/train/\");"))))
2738              #t))
2739          (replace 'build
2740            (lambda _
2741              (invoke "make" "clean")
2742              (invoke "make" "fgs")
2743              #t))
2744          (replace 'install
2745            (lambda* (#:key outputs #:allow-other-keys)
2746              (let* ((out (string-append (assoc-ref outputs "out")))
2747                     (bin (string-append out "/bin/"))
2748                     (share (string-append out "/share/fraggenescan/train")))
2749                (install-file "run_FragGeneScan.pl" bin)
2750                (install-file "FragGeneScan" bin)
2751                (copy-recursively "train" share))
2752              #t))
2753          (delete 'check)
2754          (add-after 'install 'post-install-check
2755            ;; In lieu of 'make check', run one of the examples and check the
2756            ;; output files gets created.
2757            (lambda* (#:key outputs #:allow-other-keys)
2758              (let* ((out (string-append (assoc-ref outputs "out")))
2759                     (bin (string-append out "/bin/"))
2760                     (frag (string-append bin "run_FragGeneScan.pl")))
2761                ;; Test complete genome.
2762                (invoke frag
2763                        "-genome=./example/NC_000913.fna"
2764                        "-out=./test2"
2765                        "-complete=1"
2766                        "-train=complete")
2767                (unless (and (file-exists? "test2.faa")
2768                             (file-exists? "test2.ffn")
2769                             (file-exists? "test2.gff")
2770                             (file-exists? "test2.out"))
2771                  (error "Expected files do not exist."))
2772                ;; Test incomplete sequences.
2773                (invoke frag
2774                        "-genome=./example/NC_000913-fgs.ffn"
2775                        "-out=out"
2776                        "-complete=0"
2777                        "-train=454_30")
2778                #t))))))
2779     (inputs
2780      `(("perl" ,perl)
2781        ("python" ,python-2))) ;not compatible with python 3.
2782     (home-page "https://sourceforge.net/projects/fraggenescan/")
2783     (synopsis "Finds potentially fragmented genes in short reads")
2784     (description
2785      "FragGeneScan is a program for predicting bacterial and archaeal genes in
2786 short and error-prone DNA sequencing reads.  It can also be applied to predict
2787 genes in incomplete assemblies or complete genomes.")
2788     ;; GPL3+ according to private correspondense with the authors.
2789     (license license:gpl3+)))
2790
2791 (define-public fxtract
2792   (let ((util-commit "776ca85a18a47492af3794745efcb4a905113115"))
2793     (package
2794       (name "fxtract")
2795       (version "2.3")
2796       (source
2797        (origin
2798          (method git-fetch)
2799          (uri (git-reference
2800                (url "https://github.com/ctSkennerton/fxtract.git")
2801                (commit version)))
2802          (file-name (git-file-name name version))
2803          (sha256
2804           (base32
2805            "0hab3gpwf4w9s87qlbswq6ws1qqybh4dcqk79q1ahyldzai5fgp5"))))
2806       (build-system gnu-build-system)
2807       (arguments
2808        `(#:make-flags (list
2809                        (string-append "PREFIX=" (assoc-ref %outputs "out"))
2810                        "CC=gcc")
2811          #:test-target "fxtract_test"
2812          #:phases
2813          (modify-phases %standard-phases
2814            (delete 'configure)
2815            (add-before 'build 'copy-util
2816              (lambda* (#:key inputs #:allow-other-keys)
2817                (rmdir "util")
2818                (copy-recursively (assoc-ref inputs "ctskennerton-util") "util")
2819                #t))
2820            ;; Do not use make install as this requires additional dependencies.
2821            (replace 'install
2822              (lambda* (#:key outputs #:allow-other-keys)
2823                (let* ((out (assoc-ref outputs "out"))
2824                       (bin (string-append out"/bin")))
2825                  (install-file "fxtract" bin)
2826                  #t))))))
2827       (inputs
2828        `(("pcre" ,pcre)
2829          ("zlib" ,zlib)))
2830       (native-inputs
2831        ;; ctskennerton-util is licensed under GPL2.
2832        `(("ctskennerton-util"
2833           ,(origin
2834              (method git-fetch)
2835              (uri (git-reference
2836                    (url "https://github.com/ctSkennerton/util.git")
2837                    (commit util-commit)))
2838              (file-name (string-append
2839                          "ctstennerton-util-" util-commit "-checkout"))
2840              (sha256
2841               (base32
2842                "0cls1hd4vgj3f36fpzzg4xc77d6f3hpc60cbpfmn2gdr7ykzzad7"))))))
2843       (home-page "https://github.com/ctSkennerton/fxtract")
2844       (synopsis "Extract sequences from FASTA and FASTQ files")
2845       (description
2846        "Fxtract extracts sequences from a protein or nucleotide fastx (FASTA
2847 or FASTQ) file given a subsequence.  It uses a simple substring search for
2848 basic tasks but can change to using POSIX regular expressions, PCRE, hash
2849 lookups or multi-pattern searching as required.  By default fxtract looks in
2850 the sequence of each record but can also be told to look in the header,
2851 comment or quality sections.")
2852       ;; 'util' requires SSE instructions.
2853       (supported-systems '("x86_64-linux"))
2854       (license license:expat))))
2855
2856 (define-public gemma
2857   (package
2858     (name "gemma")
2859     (version "0.98")
2860     (source (origin
2861               (method git-fetch)
2862               (uri (git-reference
2863                     (url "https://github.com/xiangzhou/GEMMA.git")
2864                     (commit (string-append "v" version))))
2865               (file-name (git-file-name name version))
2866               (sha256
2867                (base32
2868                 "1s3ncnbn45r2hh1cvrqky1kbqq6546biypr4f5mkw1kqlrgyh0yg"))))
2869     (inputs
2870      `(("eigen" ,eigen)
2871        ("gfortran" ,gfortran "lib")
2872        ("gsl" ,gsl)
2873        ("lapack" ,lapack)
2874        ("openblas" ,openblas)
2875        ("zlib" ,zlib)))
2876     (build-system gnu-build-system)
2877     (arguments
2878      `(#:make-flags
2879        '(,@(match (%current-system)
2880          ("x86_64-linux"
2881           '("FORCE_DYNAMIC=1"))
2882          ("i686-linux"
2883           '("FORCE_DYNAMIC=1" "FORCE_32BIT=1"))
2884          (_
2885           '("FORCE_DYNAMIC=1" "NO_INTEL_COMPAT=1"))))
2886        #:phases
2887        (modify-phases %standard-phases
2888          (delete 'configure)
2889          (add-after 'unpack 'find-eigen
2890            (lambda* (#:key inputs #:allow-other-keys)
2891              ;; Ensure that Eigen headers can be found
2892              (setenv "CPLUS_INCLUDE_PATH"
2893                      (string-append (getenv "CPLUS_INCLUDE_PATH")
2894                                     ":"
2895                                     (assoc-ref inputs "eigen")
2896                                     "/include/eigen3"))
2897              #t))
2898          (add-before 'build 'bin-mkdir
2899           (lambda _
2900             (mkdir-p "bin")
2901             #t))
2902          (replace 'install
2903            (lambda* (#:key outputs #:allow-other-keys)
2904              (let ((out (assoc-ref outputs "out")))
2905                (install-file "bin/gemma"
2906                              (string-append
2907                               out "/bin")))
2908              #t)))
2909        #:tests? #f)) ; no tests included yet
2910     (home-page "https://github.com/xiangzhou/GEMMA")
2911     (synopsis "Tool for genome-wide efficient mixed model association")
2912     (description
2913      "Genome-wide Efficient Mixed Model Association (GEMMA) provides a
2914 standard linear mixed model resolver with application in genome-wide
2915 association studies (GWAS).")
2916     (license license:gpl3)))
2917
2918 (define-public grit
2919   (package
2920     (name "grit")
2921     (version "2.0.5")
2922     (source (origin
2923               (method git-fetch)
2924               (uri (git-reference
2925                     (url "https://github.com/nboley/grit.git")
2926                     (commit version)))
2927               (file-name (git-file-name name version))
2928               (sha256
2929                (base32
2930                 "1l5v8vfvfbrpmgnrvbrbv40d0arhxcnmxgv2f1mlcqfa3q6bkqm9"))))
2931     (build-system python-build-system)
2932     (arguments
2933      `(#:python ,python-2
2934        #:phases
2935        (modify-phases %standard-phases
2936          (add-after 'unpack 'generate-from-cython-sources
2937            (lambda* (#:key inputs outputs #:allow-other-keys)
2938              ;; Delete these C files to force fresh generation from pyx sources.
2939              (delete-file "grit/sparsify_support_fns.c")
2940              (delete-file "grit/call_peaks_support_fns.c")
2941              (substitute* "setup.py"
2942                (("Cython.Setup") "Cython.Build"))
2943              #t)))))
2944     (inputs
2945      `(("python-scipy" ,python2-scipy)
2946        ("python-numpy" ,python2-numpy)
2947        ("python-pysam" ,python2-pysam)
2948        ("python-networkx" ,python2-networkx)))
2949     (native-inputs
2950      `(("python-cython" ,python2-cython)))
2951     (home-page "http://grit-bio.org")
2952     (synopsis "Tool for integrative analysis of RNA-seq type assays")
2953     (description
2954      "GRIT is designed to use RNA-seq, TES, and TSS data to build and quantify
2955 full length transcript models.  When none of these data sources are available,
2956 GRIT can be run by providing a candidate set of TES or TSS sites.  In
2957 addition, GRIT can merge in reference junctions and gene boundaries.  GRIT can
2958 also be run in quantification mode, where it uses a provided GTF file and just
2959 estimates transcript expression.")
2960     (license license:gpl3+)))
2961
2962 (define-public hisat
2963   (package
2964     (name "hisat")
2965     (version "0.1.4")
2966     (source (origin
2967               (method url-fetch)
2968               (uri (string-append
2969                     "http://ccb.jhu.edu/software/hisat/downloads/hisat-"
2970                     version "-beta-source.zip"))
2971               (sha256
2972                (base32
2973                 "1k381ydranqxp09yf2y7w1d0chz5d59vb6jchi89hbb0prq19lk5"))))
2974     (build-system gnu-build-system)
2975     (arguments
2976      `(#:tests? #f ;no check target
2977        #:make-flags '("allall"
2978                       ;; Disable unsupported `popcnt' instructions on
2979                       ;; architectures other than x86_64
2980                       ,@(if (string-prefix? "x86_64"
2981                                             (or (%current-target-system)
2982                                                 (%current-system)))
2983                             '()
2984                             '("POPCNT_CAPABILITY=0")))
2985        #:phases
2986        (modify-phases %standard-phases
2987          (add-after 'unpack 'patch-sources
2988            (lambda _
2989              ;; XXX Cannot use snippet because zip files are not supported
2990              (substitute* "Makefile"
2991                (("^CC = .*$") "CC = gcc")
2992                (("^CPP = .*$") "CPP = g++")
2993                ;; replace BUILD_HOST and BUILD_TIME for deterministic build
2994                (("-DBUILD_HOST=.*") "-DBUILD_HOST=\"\\\"guix\\\"\"")
2995                (("-DBUILD_TIME=.*") "-DBUILD_TIME=\"\\\"0\\\"\""))
2996              (substitute* '("hisat-build" "hisat-inspect")
2997                (("/usr/bin/env") (which "env")))
2998              #t))
2999          (replace 'install
3000            (lambda* (#:key outputs #:allow-other-keys)
3001              (let ((bin (string-append (assoc-ref outputs "out") "/bin/")))
3002                (for-each (lambda (file)
3003                            (install-file file bin))
3004                          (find-files
3005                           "."
3006                           "hisat(-(build|align|inspect)(-(s|l)(-debug)*)*)*$")))
3007              #t))
3008          (delete 'configure))))
3009     (native-inputs
3010      `(("unzip" ,unzip)))
3011     (inputs
3012      `(("perl" ,perl)
3013        ("python" ,python)
3014        ("zlib" ,zlib)))
3015     ;; Non-portable SSE instructions are used so building fails on platforms
3016     ;; other than x86_64.
3017     (supported-systems '("x86_64-linux"))
3018     (home-page "http://ccb.jhu.edu/software/hisat/index.shtml")
3019     (synopsis "Hierarchical indexing for spliced alignment of transcripts")
3020     (description
3021      "HISAT is a fast and sensitive spliced alignment program for mapping
3022 RNA-seq reads.  In addition to one global FM index that represents a whole
3023 genome, HISAT uses a large set of small FM indexes that collectively cover the
3024 whole genome.  These small indexes (called local indexes) combined with
3025 several alignment strategies enable effective alignment of RNA-seq reads, in
3026 particular, reads spanning multiple exons.")
3027     (license license:gpl3+)))
3028
3029 (define-public hisat2
3030   (package
3031     (name "hisat2")
3032     (version "2.0.5")
3033     (source
3034      (origin
3035        (method url-fetch)
3036        (uri (string-append "ftp://ftp.ccb.jhu.edu/pub/infphilo/hisat2"
3037                            "/downloads/hisat2-" version "-source.zip"))
3038        (sha256
3039         (base32
3040          "0lywnr8kijwsc2aw10dwxic0n0yvip6fl3rjlvc8zzwahamy4x7g"))))
3041     (build-system gnu-build-system)
3042     (arguments
3043      `(#:tests? #f                      ; no check target
3044        #:make-flags (list "CC=gcc" "CXX=g++" "allall")
3045        #:modules ((guix build gnu-build-system)
3046                   (guix build utils)
3047                   (srfi srfi-26))
3048        #:phases
3049        (modify-phases %standard-phases
3050          (add-after 'unpack 'make-deterministic
3051            (lambda _
3052              (substitute* "Makefile"
3053                (("`date`") "0"))
3054              #t))
3055          (delete 'configure)
3056          (replace 'install
3057            (lambda* (#:key outputs #:allow-other-keys)
3058              (let* ((out (assoc-ref outputs "out"))
3059                     (bin (string-append out "/bin/"))
3060                     (doc (string-append out "/share/doc/hisat2/")))
3061                (for-each
3062                 (cut install-file <> bin)
3063                 (find-files "."
3064                             "hisat2(-(build|align|inspect)(-(s|l)(-debug)*)*)*$"))
3065                (mkdir-p doc)
3066                (install-file "doc/manual.inc.html" doc))
3067              #t)))))
3068     (native-inputs
3069      `(("unzip" ,unzip)                 ; needed for archive from ftp
3070        ("perl" ,perl)
3071        ("pandoc" ,ghc-pandoc)))         ; for documentation
3072     (home-page "http://ccb.jhu.edu/software/hisat2/index.shtml")
3073     (synopsis "Graph-based alignment of genomic sequencing reads")
3074     (description "HISAT2 is a fast and sensitive alignment program for mapping
3075 next-generation sequencing reads (both DNA and RNA) to a population of human
3076 genomes (as well as to a single reference genome).  In addition to using one
3077 global @dfn{graph FM} (GFM) index that represents a population of human
3078 genomes, HISAT2 uses a large set of small GFM indexes that collectively cover
3079 the whole genome.  These small indexes, combined with several alignment
3080 strategies, enable rapid and accurate alignment of sequencing reads.  This new
3081 indexing scheme is called a @dfn{Hierarchical Graph FM index} (HGFM).")
3082     ;; HISAT2 contains files from Bowtie2, which is released under
3083     ;; GPLv2 or later.  The HISAT2 source files are released under
3084     ;; GPLv3 or later.
3085     (license license:gpl3+)))
3086
3087 (define-public hmmer
3088   (package
3089     (name "hmmer")
3090     (version "3.2.1")
3091     (source
3092      (origin
3093        (method url-fetch)
3094        (uri (string-append
3095              "http://eddylab.org/software/hmmer/hmmer-" version ".tar.gz"))
3096        (sha256
3097         (base32
3098          "171bivy6xhgjsz5nv53n81pc3frnwz29ylblawk2bv46szwjjqd5"))))
3099     (build-system gnu-build-system)
3100     (native-inputs `(("perl" ,perl)))
3101     (home-page "http://hmmer.org/")
3102     (synopsis "Biosequence analysis using profile hidden Markov models")
3103     (description
3104      "HMMER is used for searching sequence databases for homologs of protein
3105 sequences, and for making protein sequence alignments.  It implements methods
3106 using probabilistic models called profile hidden Markov models (profile
3107 HMMs).")
3108     ;; hmmer uses non-portable SSE intrinsics so building fails on other
3109     ;; platforms.
3110     (supported-systems '("x86_64-linux" "i686-linux"))
3111     (license license:bsd-3)))
3112
3113 (define-public htseq
3114   (package
3115     (name "htseq")
3116     (version "0.9.1")
3117     (source (origin
3118               (method url-fetch)
3119               (uri (pypi-uri "HTSeq" version))
3120               (sha256
3121                (base32
3122                 "11flgb1381xdhk43bzbfm3vhnszkpqg6jk76rpa5xd1zbrvvlnxg"))))
3123     (build-system python-build-system)
3124     (native-inputs
3125      `(("python-cython" ,python-cython)))
3126     ;; Numpy needs to be propagated when htseq is used as a Python library.
3127     (propagated-inputs
3128      `(("python-numpy" ,python-numpy)))
3129     (inputs
3130      `(("python-pysam" ,python-pysam)
3131        ("python-matplotlib" ,python-matplotlib)))
3132     (home-page "http://www-huber.embl.de/users/anders/HTSeq/")
3133     (synopsis "Analysing high-throughput sequencing data with Python")
3134     (description
3135      "HTSeq is a Python package that provides infrastructure to process data
3136 from high-throughput sequencing assays.")
3137     (license license:gpl3+)))
3138
3139 (define-public python2-htseq
3140   (package-with-python2 htseq))
3141
3142 (define-public java-htsjdk
3143   (package
3144     (name "java-htsjdk")
3145     (version "2.3.0") ; last version without build dependency on gradle
3146     (source (origin
3147               (method git-fetch)
3148               (uri (git-reference
3149                     (url "https://github.com/samtools/htsjdk.git")
3150                     (commit version)))
3151               (file-name (git-file-name name version))
3152               (sha256
3153                (base32
3154                 "1b178ixcabanm834ydjl3jiakpyxdmki32hqfv2abrzn3rcwa28i"))
3155               (modules '((guix build utils)))
3156               (snippet
3157                ;; Delete pre-built binaries
3158                '(begin
3159                   (delete-file-recursively "lib")
3160                   (mkdir-p "lib")
3161                   #t))))
3162     (build-system ant-build-system)
3163     (arguments
3164      `(#:tests? #f ; test require Internet access
3165        #:jdk ,icedtea-8
3166        #:make-flags
3167        (list (string-append "-Ddist=" (assoc-ref %outputs "out")
3168                             "/share/java/htsjdk/"))
3169        #:build-target "all"
3170        #:phases
3171        (modify-phases %standard-phases
3172          ;; The build phase also installs the jars
3173          (delete 'install))))
3174     (inputs
3175      `(("java-ngs" ,java-ngs)
3176        ("java-snappy-1" ,java-snappy-1)
3177        ("java-commons-compress" ,java-commons-compress)
3178        ("java-commons-logging-minimal" ,java-commons-logging-minimal)
3179        ("java-commons-jexl-2" ,java-commons-jexl-2)
3180        ("java-xz" ,java-xz)))
3181     (native-inputs
3182      `(("java-testng" ,java-testng)))
3183     (home-page "http://samtools.github.io/htsjdk/")
3184     (synopsis "Java API for high-throughput sequencing data (HTS) formats")
3185     (description
3186      "HTSJDK is an implementation of a unified Java library for accessing
3187 common file formats, such as SAM and VCF, used for high-throughput
3188 sequencing (HTS) data.  There are also an number of useful utilities for
3189 manipulating HTS data.")
3190     (license license:expat)))
3191
3192 (define-public java-htsjdk-latest
3193   (package
3194     (name "java-htsjdk")
3195     (version "2.14.3")
3196     (source (origin
3197               (method git-fetch)
3198               (uri (git-reference
3199                     (url "https://github.com/samtools/htsjdk.git")
3200                     (commit version)))
3201               (file-name (string-append name "-" version "-checkout"))
3202               (sha256
3203                (base32
3204                 "1lmya1fdjy03mz6zmdmd86j9v9vfhqb3952mqq075navx1i6g4bc"))))
3205     (build-system ant-build-system)
3206     (arguments
3207      `(#:tests? #f                      ; test require Scala
3208        #:jdk ,icedtea-8
3209        #:jar-name "htsjdk.jar"
3210        #:phases
3211        (modify-phases %standard-phases
3212          (add-after 'unpack 'remove-useless-build.xml
3213            (lambda _ (delete-file "build.xml") #t))
3214          ;; The tests require the scalatest package.
3215          (add-after 'unpack 'remove-tests
3216            (lambda _ (delete-file-recursively "src/test") #t)))))
3217     (inputs
3218      `(("java-ngs" ,java-ngs)
3219        ("java-snappy-1" ,java-snappy-1)
3220        ("java-commons-compress" ,java-commons-compress)
3221        ("java-commons-logging-minimal" ,java-commons-logging-minimal)
3222        ("java-commons-jexl-2" ,java-commons-jexl-2)
3223        ("java-xz" ,java-xz)))
3224     (native-inputs
3225      `(("java-junit" ,java-junit)))
3226     (home-page "http://samtools.github.io/htsjdk/")
3227     (synopsis "Java API for high-throughput sequencing data (HTS) formats")
3228     (description
3229      "HTSJDK is an implementation of a unified Java library for accessing
3230 common file formats, such as SAM and VCF, used for high-throughput
3231 sequencing (HTS) data.  There are also an number of useful utilities for
3232 manipulating HTS data.")
3233     (license license:expat)))
3234
3235 ;; This is needed for picard 2.10.3
3236 (define-public java-htsjdk-2.10.1
3237   (package (inherit java-htsjdk-latest)
3238     (name "java-htsjdk")
3239     (version "2.10.1")
3240     (source (origin
3241               (method git-fetch)
3242               (uri (git-reference
3243                     (url "https://github.com/samtools/htsjdk.git")
3244                     (commit version)))
3245               (file-name (string-append name "-" version "-checkout"))
3246               (sha256
3247                (base32
3248                 "1kxh7slm2pm3x9p6jxa1wqsq9a31dhiiflhxnxqcisan4k3rwia2"))))
3249     (build-system ant-build-system)
3250     (arguments
3251      `(#:tests? #f                      ; tests require Scala
3252        #:jdk ,icedtea-8
3253        #:jar-name "htsjdk.jar"
3254        #:phases
3255        (modify-phases %standard-phases
3256          (add-after 'unpack 'remove-useless-build.xml
3257            (lambda _ (delete-file "build.xml") #t))
3258          ;; The tests require the scalatest package.
3259          (add-after 'unpack 'remove-tests
3260            (lambda _ (delete-file-recursively "src/test") #t)))))))
3261
3262 ;; This version matches java-htsjdk 2.3.0.  Later versions also require a more
3263 ;; recent version of java-htsjdk, which depends on gradle.
3264 (define-public java-picard
3265   (package
3266     (name "java-picard")
3267     (version "2.3.0")
3268     (source (origin
3269               (method git-fetch)
3270               (uri (git-reference
3271                     (url "https://github.com/broadinstitute/picard.git")
3272                     (commit version)))
3273               (file-name (string-append "java-picard-" version "-checkout"))
3274               (sha256
3275                (base32
3276                 "1ll7mf4r3by92w2nhlmpa591xd1f46xlkwh59mq6fvbb5pdwzvx6"))
3277               (modules '((guix build utils)))
3278               (snippet
3279                '(begin
3280                   ;; Delete pre-built binaries.
3281                   (delete-file-recursively "lib")
3282                   (mkdir-p "lib")
3283                   (substitute* "build.xml"
3284                     ;; Remove build-time dependency on git.
3285                     (("failifexecutionfails=\"true\"")
3286                      "failifexecutionfails=\"false\"")
3287                     ;; Use our htsjdk.
3288                     (("depends=\"compile-htsjdk, ")
3289                      "depends=\"")
3290                     (("depends=\"compile-htsjdk-tests, ")
3291                      "depends=\"")
3292                     ;; Build picard-lib.jar before building picard.jar
3293                     (("name=\"picard-jar\" depends=\"" line)
3294                      (string-append line "picard-lib-jar, ")))
3295                   #t))))
3296     (build-system ant-build-system)
3297     (arguments
3298      `(#:build-target "picard-jar"
3299        #:test-target "test"
3300        ;; Tests require jacoco:coverage.
3301        #:tests? #f
3302        #:make-flags
3303        (list (string-append "-Dhtsjdk_lib_dir="
3304                             (assoc-ref %build-inputs "java-htsjdk")
3305                             "/share/java/htsjdk/")
3306              "-Dhtsjdk-classes=dist/tmp"
3307              (string-append "-Dhtsjdk-version="
3308                             ,(package-version java-htsjdk)))
3309        #:jdk ,icedtea-8
3310        #:phases
3311        (modify-phases %standard-phases
3312          ;; FIXME: this phase fails with "duplicate entry: htsjdk/samtools/AbstractBAMFileIndex$1.class"
3313          (delete 'generate-jar-indices)
3314          (add-after 'unpack 'use-our-htsjdk
3315            (lambda* (#:key inputs #:allow-other-keys)
3316              (substitute* "build.xml"
3317                (("\\$\\{htsjdk\\}/lib")
3318                 (string-append (assoc-ref inputs "java-htsjdk")
3319                                "/share/java/htsjdk/")))
3320              #t))
3321          (add-after 'unpack 'make-test-target-independent
3322            (lambda* (#:key inputs #:allow-other-keys)
3323              (substitute* "build.xml"
3324                (("name=\"test\" depends=\"compile, ")
3325                 "name=\"test\" depends=\""))
3326              #t))
3327          (replace 'install (install-jars "dist")))))
3328     (inputs
3329      `(("java-htsjdk" ,java-htsjdk)
3330        ("java-guava" ,java-guava)))
3331     (native-inputs
3332      `(("java-testng" ,java-testng)))
3333     (home-page "http://broadinstitute.github.io/picard/")
3334     (synopsis "Tools for manipulating high-throughput sequencing data and formats")
3335     (description "Picard is a set of Java command line tools for manipulating
3336 high-throughput sequencing (HTS) data and formats.  Picard is implemented
3337 using the HTSJDK Java library to support accessing file formats that are
3338 commonly used for high-throughput sequencing data such as SAM, BAM, CRAM and
3339 VCF.")
3340     (license license:expat)))
3341
3342 ;; This is needed for dropseq-tools
3343 (define-public java-picard-2.10.3
3344   (package
3345     (name "java-picard")
3346     (version "2.10.3")
3347     (source (origin
3348               (method git-fetch)
3349               (uri (git-reference
3350                     (url "https://github.com/broadinstitute/picard.git")
3351                     (commit version)))
3352               (file-name (string-append "java-picard-" version "-checkout"))
3353               (sha256
3354                (base32
3355                 "1ajlx31l6i1k3y2rhnmgq07sz99g2czqfqgkr9mihmdjp3gwjhvi"))))
3356     (build-system ant-build-system)
3357     (arguments
3358      `(#:jar-name "picard.jar"
3359        ;; Tests require jacoco:coverage.
3360        #:tests? #f
3361        #:jdk ,icedtea-8
3362        #:main-class "picard.cmdline.PicardCommandLine"
3363        #:modules ((guix build ant-build-system)
3364                   (guix build utils)
3365                   (guix build java-utils)
3366                   (sxml simple)
3367                   (sxml transform)
3368                   (sxml xpath))
3369        #:phases
3370        (modify-phases %standard-phases
3371          ;; FIXME: this phase fails with "duplicate entry: htsjdk/samtools/AbstractBAMFileIndex$1.class"
3372          (delete 'generate-jar-indices)
3373          (add-after 'unpack 'remove-useless-build.xml
3374            (lambda _ (delete-file "build.xml") #t))
3375          ;; This is necessary to ensure that htsjdk is found when using
3376          ;; picard.jar as an executable.
3377          (add-before 'build 'edit-classpath-in-manifest
3378            (lambda* (#:key inputs #:allow-other-keys)
3379              (chmod "build.xml" #o664)
3380              (call-with-output-file "build.xml.new"
3381                (lambda (port)
3382                  (sxml->xml
3383                   (pre-post-order
3384                    (with-input-from-file "build.xml"
3385                      (lambda _ (xml->sxml #:trim-whitespace? #t)))
3386                    `((target    . ,(lambda (tag . kids)
3387                                      (let ((name ((sxpath '(name *text*))
3388                                                   (car kids)))
3389                                            ;; FIXME: We're breaking the line
3390                                            ;; early with a dummy path to
3391                                            ;; ensure that the store reference
3392                                            ;; isn't broken apart and can still
3393                                            ;; be found by the reference
3394                                            ;; scanner.
3395                                            (msg (format #f
3396                                                         "\
3397 Class-Path: /~a \
3398  ~a/share/java/htsjdk.jar${line.separator}${line.separator}"
3399                                                         ;; maximum line length is 70
3400                                                         (string-tabulate (const #\b) 57)
3401                                                         (assoc-ref inputs "java-htsjdk"))))
3402                                        (if (member "manifest" name)
3403                                            `(,tag ,@kids
3404                                                   (replaceregexp
3405                                                    (@ (file "${manifest.file}")
3406                                                       (match "\\r\\n\\r\\n")
3407                                                       (replace "${line.separator}")))
3408                                                   (echo
3409                                                    (@ (message ,msg)
3410                                                       (file "${manifest.file}")
3411                                                       (append "true"))))
3412                                            `(,tag ,@kids)))))
3413                      (*default* . ,(lambda (tag . kids) `(,tag ,@kids)))
3414                      (*text*    . ,(lambda (_ txt) txt))))
3415                   port)))
3416              (rename-file "build.xml.new" "build.xml")
3417              #t)))))
3418     (propagated-inputs
3419      `(("java-htsjdk" ,java-htsjdk-2.10.1)))
3420     (native-inputs
3421      `(("java-testng" ,java-testng)
3422        ("java-guava" ,java-guava)))
3423     (home-page "http://broadinstitute.github.io/picard/")
3424     (synopsis "Tools for manipulating high-throughput sequencing data and formats")
3425     (description "Picard is a set of Java command line tools for manipulating
3426 high-throughput sequencing (HTS) data and formats.  Picard is implemented
3427 using the HTSJDK Java library to support accessing file formats that are
3428 commonly used for high-throughput sequencing data such as SAM, BAM, CRAM and
3429 VCF.")
3430     (license license:expat)))
3431
3432 ;; This is the last version of Picard to provide net.sf.samtools
3433 (define-public java-picard-1.113
3434   (package (inherit java-picard)
3435     (name "java-picard")
3436     (version "1.113")
3437     (source (origin
3438               (method git-fetch)
3439               (uri (git-reference
3440                     (url "https://github.com/broadinstitute/picard.git")
3441                     (commit version)))
3442               (file-name (string-append "java-picard-" version "-checkout"))
3443               (sha256
3444                (base32
3445                 "0lkpvin2fz3hhly4l02kk56fqy8lmlgyzr9kmvljk6ry6l1hw973"))
3446               (modules '((guix build utils)))
3447               (snippet
3448                '(begin
3449                   ;; Delete pre-built binaries.
3450                   (delete-file-recursively "lib")
3451                   (mkdir-p "lib")
3452                   #t))))
3453     (build-system ant-build-system)
3454     (arguments
3455      `(#:build-target "picard-jar"
3456        #:test-target "test"
3457        ;; FIXME: the class path at test time is wrong.
3458        ;; [testng] Error: A JNI error has occurred, please check your installation and try again
3459        ;; [testng] Exception in thread "main" java.lang.NoClassDefFoundError: com/beust/jcommander/ParameterException
3460        #:tests? #f
3461        #:jdk ,icedtea-8
3462        ;; This is only used for tests.
3463        #:make-flags
3464        (list "-Dsamjdk.intel_deflater_so_path=lib/jni/libIntelDeflater.so")
3465        #:phases
3466        (modify-phases %standard-phases
3467          ;; FIXME: This phase fails.
3468          (delete 'generate-jar-indices)
3469          ;; Do not use bundled ant bzip2.
3470          (add-after 'unpack 'use-ant-bzip
3471            (lambda* (#:key inputs #:allow-other-keys)
3472              (substitute* "build.xml"
3473                (("\\$\\{lib\\}/apache-ant-1.8.2-bzip2.jar")
3474                 (string-append (assoc-ref inputs "ant")
3475                                "/lib/ant.jar")))
3476              #t))
3477          (add-after 'unpack 'make-test-target-independent
3478            (lambda* (#:key inputs #:allow-other-keys)
3479              (substitute* "build.xml"
3480                (("name=\"test\" depends=\"compile, ")
3481                 "name=\"test\" depends=\"compile-tests, ")
3482                (("name=\"compile\" depends=\"compile-src, compile-tests\"")
3483                 "name=\"compile\" depends=\"compile-src\""))
3484              #t))
3485          (add-after 'unpack 'fix-deflater-path
3486            (lambda* (#:key outputs #:allow-other-keys)
3487              (substitute* "src/java/net/sf/samtools/Defaults.java"
3488                (("getStringProperty\\(\"intel_deflater_so_path\", null\\)")
3489                 (string-append "getStringProperty(\"intel_deflater_so_path\", \""
3490                                (assoc-ref outputs "out")
3491                                "/lib/jni/libIntelDeflater.so"
3492                                "\")")))
3493              #t))
3494          ;; Build the deflater library, because we've previously deleted the
3495          ;; pre-built one.  This can only be built with access to the JDK
3496          ;; sources.
3497          (add-after 'build 'build-jni
3498            (lambda* (#:key inputs #:allow-other-keys)
3499              (mkdir-p "lib/jni")
3500              (mkdir-p "jdk-src")
3501              (invoke "tar" "--strip-components=1" "-C" "jdk-src"
3502                      "-xf" (assoc-ref inputs "jdk-src"))
3503              (invoke "javah" "-jni"
3504                      "-classpath" "classes"
3505                      "-d" "lib/"
3506                      "net.sf.samtools.util.zip.IntelDeflater")
3507              (with-directory-excursion "src/c/inteldeflater"
3508                (invoke "gcc" "-I../../../lib" "-I."
3509                        (string-append "-I" (assoc-ref inputs "jdk")
3510                                       "/include/linux")
3511                        "-I../../../jdk-src/src/share/native/common/"
3512                        "-I../../../jdk-src/src/solaris/native/common/"
3513                        "-c" "-O3" "-fPIC" "IntelDeflater.c")
3514                (invoke "gcc" "-shared"
3515                        "-o" "../../../lib/jni/libIntelDeflater.so"
3516                        "IntelDeflater.o" "-lz" "-lstdc++"))
3517              #t))
3518          ;; We can only build everything else after building the JNI library.
3519          (add-after 'build-jni 'build-rest
3520            (lambda* (#:key make-flags #:allow-other-keys)
3521              (apply invoke `("ant" "all" ,@make-flags))
3522              #t))
3523          (add-before 'build 'set-JAVA6_HOME
3524            (lambda _
3525              (setenv "JAVA6_HOME" (getenv "JAVA_HOME"))
3526              #t))
3527          (replace 'install (install-jars "dist"))
3528          (add-after 'install 'install-jni-lib
3529            (lambda* (#:key outputs #:allow-other-keys)
3530              (let ((jni (string-append (assoc-ref outputs "out")
3531                                        "/lib/jni")))
3532                (mkdir-p jni)
3533                (install-file "lib/jni/libIntelDeflater.so" jni)
3534                #t))))))
3535     (inputs
3536      `(("java-snappy-1" ,java-snappy-1)
3537        ("java-commons-jexl-2" ,java-commons-jexl-2)
3538        ("java-cofoja" ,java-cofoja)
3539        ("ant" ,ant) ; for bzip2 support at runtime
3540        ("zlib" ,zlib)))
3541     (native-inputs
3542      `(("ant-apache-bcel" ,ant-apache-bcel)
3543        ("ant-junit" ,ant-junit)
3544        ("java-testng" ,java-testng)
3545        ("java-commons-bcel" ,java-commons-bcel)
3546        ("java-jcommander" ,java-jcommander)
3547        ("jdk" ,icedtea-8 "jdk")
3548        ("jdk-src" ,(car (assoc-ref (package-native-inputs icedtea-8) "jdk-drop")))))))
3549
3550 (define-public fastqc
3551   (package
3552     (name "fastqc")
3553     (version "0.11.5")
3554     (source
3555      (origin
3556        (method url-fetch)
3557        (uri (string-append "http://www.bioinformatics.babraham.ac.uk/"
3558                            "projects/fastqc/fastqc_v"
3559                            version "_source.zip"))
3560        (sha256
3561         (base32
3562          "18rrlkhcrxvvvlapch4dpj6xc6mpayzys8qfppybi8jrpgx5cc5f"))))
3563     (build-system ant-build-system)
3564     (arguments
3565      `(#:tests? #f                      ; there are no tests
3566        #:build-target "build"
3567        #:phases
3568        (modify-phases %standard-phases
3569          (add-after 'unpack 'fix-dependencies
3570            (lambda* (#:key inputs #:allow-other-keys)
3571              (substitute* "build.xml"
3572                (("jbzip2-0.9.jar")
3573                 (string-append (assoc-ref inputs "java-jbzip2")
3574                                "/share/java/jbzip2.jar"))
3575                (("sam-1.103.jar")
3576                 (string-append (assoc-ref inputs "java-picard-1.113")
3577                                "/share/java/sam-1.112.jar"))
3578                (("cisd-jhdf5.jar")
3579                 (string-append (assoc-ref inputs "java-cisd-jhdf5")
3580                                "/share/java/sis-jhdf5.jar")))
3581              #t))
3582          ;; There is no installation target
3583          (replace 'install
3584            (lambda* (#:key inputs outputs #:allow-other-keys)
3585              (let* ((out   (assoc-ref outputs "out"))
3586                     (bin   (string-append out "/bin"))
3587                     (share (string-append out "/share/fastqc/"))
3588                     (exe   (string-append share "/fastqc")))
3589                (for-each mkdir-p (list bin share))
3590                (copy-recursively "bin" share)
3591                (substitute* exe
3592                  (("my \\$java_bin = 'java';")
3593                   (string-append "my $java_bin = '"
3594                                  (assoc-ref inputs "java")
3595                                  "/bin/java';")))
3596                (chmod exe #o555)
3597                (symlink exe (string-append bin "/fastqc"))
3598                #t))))))
3599     (inputs
3600      `(("java" ,icedtea)
3601        ("perl" ,perl)                   ; needed for the wrapper script
3602        ("java-cisd-jhdf5" ,java-cisd-jhdf5)
3603        ("java-picard-1.113" ,java-picard-1.113)
3604        ("java-jbzip2" ,java-jbzip2)))
3605     (native-inputs
3606      `(("unzip" ,unzip)))
3607     (home-page "http://www.bioinformatics.babraham.ac.uk/projects/fastqc/")
3608     (synopsis "Quality control tool for high throughput sequence data")
3609     (description
3610      "FastQC aims to provide a simple way to do some quality control
3611 checks on raw sequence data coming from high throughput sequencing
3612 pipelines.  It provides a modular set of analyses which you can use to
3613 give a quick impression of whether your data has any problems of which
3614 you should be aware before doing any further analysis.
3615
3616 The main functions of FastQC are:
3617
3618 @itemize
3619 @item Import of data from BAM, SAM or FastQ files (any variant);
3620 @item Providing a quick overview to tell you in which areas there may
3621   be problems;
3622 @item Summary graphs and tables to quickly assess your data;
3623 @item Export of results to an HTML based permanent report;
3624 @item Offline operation to allow automated generation of reports
3625   without running the interactive application.
3626 @end itemize\n")
3627     (license license:gpl3+)))
3628
3629 (define-public fastp
3630   (package
3631     (name "fastp")
3632     (version "0.14.1")
3633     (source
3634      (origin
3635        (method git-fetch)
3636        (uri (git-reference
3637              (url "https://github.com/OpenGene/fastp.git")
3638              (commit (string-append "v" version))))
3639        (file-name (git-file-name name version))
3640        (sha256
3641         (base32
3642          "1r6ms5zbf5rps4rgp4z73nczadl00b5rqylw8f684isfz27dp0xh"))))
3643     (build-system gnu-build-system)
3644     (arguments
3645      `(#:tests? #f ; there are none
3646        #:make-flags
3647        (list (string-append "BINDIR=" (assoc-ref %outputs "out") "/bin"))
3648        #:phases
3649        (modify-phases %standard-phases
3650          (delete 'configure)
3651          (add-before 'install 'create-target-dir
3652            (lambda* (#:key outputs #:allow-other-keys)
3653              (mkdir-p (string-append (assoc-ref outputs "out") "/bin"))
3654              #t)))))
3655     (inputs
3656      `(("zlib" ,zlib)))
3657     (home-page "https://github.com/OpenGene/fastp/")
3658     (synopsis "All-in-one FastQ preprocessor")
3659     (description
3660      "Fastp is a tool designed to provide fast all-in-one preprocessing for
3661 FastQ files.  This tool has multi-threading support to afford high
3662 performance.")
3663     (license license:expat)))
3664
3665 (define-public htslib
3666   (package
3667     (name "htslib")
3668     (version "1.9")
3669     (source (origin
3670               (method url-fetch)
3671               (uri (string-append
3672                     "https://github.com/samtools/htslib/releases/download/"
3673                     version "/htslib-" version ".tar.bz2"))
3674               (sha256
3675                (base32
3676                 "16ljv43sc3fxmv63w7b2ff8m1s7h89xhazwmbm1bicz8axq8fjz0"))))
3677     (build-system gnu-build-system)
3678     (inputs
3679      `(("openssl" ,openssl)
3680        ("curl" ,curl)
3681        ("zlib" ,zlib)))
3682     (native-inputs
3683      `(("perl" ,perl)))
3684     (home-page "http://www.htslib.org")
3685     (synopsis "C library for reading/writing high-throughput sequencing data")
3686     (description
3687      "HTSlib is a C library for reading/writing high-throughput sequencing
3688 data.  It also provides the @command{bgzip}, @command{htsfile}, and
3689 @command{tabix} utilities.")
3690     ;; Files under cram/ are released under the modified BSD license;
3691     ;; the rest is released under the Expat license
3692     (license (list license:expat license:bsd-3))))
3693
3694 ;; This package should be removed once no packages rely upon it.
3695 (define htslib-1.3
3696   (package
3697     (inherit htslib)
3698     (version "1.3.1")
3699     (source (origin
3700               (method url-fetch)
3701               (uri (string-append
3702                     "https://github.com/samtools/htslib/releases/download/"
3703                     version "/htslib-" version ".tar.bz2"))
3704               (sha256
3705                (base32
3706                 "1rja282fwdc25ql6izkhdyh8ppw8x2fs0w0js78zgkmqjlikmma9"))))))
3707
3708 (define-public idr
3709   (package
3710     (name "idr")
3711     (version "2.0.3")
3712     (source (origin
3713               (method git-fetch)
3714               (uri (git-reference
3715                     (url "https://github.com/nboley/idr.git")
3716                     (commit version)))
3717               (file-name (git-file-name name version))
3718               (sha256
3719                (base32
3720                 "04j876h6z444v2q79drxx283d3k5snd72kj895wbalnl42206x9g"))
3721               ;; Delete generated C code.
3722               (snippet
3723                '(begin (delete-file "idr/inv_cdf.c") #t))))
3724     (build-system python-build-system)
3725     ;; There is only one test ("test_inv_cdf.py") and it tests features that
3726     ;; are no longer part of this package.  It also asserts False, which
3727     ;; causes the tests to always fail.
3728     (arguments `(#:tests? #f))
3729     (propagated-inputs
3730      `(("python-scipy" ,python-scipy)
3731        ("python-sympy" ,python-sympy)
3732        ("python-numpy" ,python-numpy)
3733        ("python-matplotlib" ,python-matplotlib)))
3734     (native-inputs
3735      `(("python-cython" ,python-cython)))
3736     (home-page "https://github.com/nboley/idr")
3737     (synopsis "Tool to measure the irreproducible discovery rate (IDR)")
3738     (description
3739      "The IDR (Irreproducible Discovery Rate) framework is a unified approach
3740 to measure the reproducibility of findings identified from replicate
3741 experiments and provide highly stable thresholds based on reproducibility.")
3742     (license license:gpl2+)))
3743
3744 (define-public jellyfish
3745   (package
3746     (name "jellyfish")
3747     (version "2.2.10")
3748     (source (origin
3749               (method url-fetch)
3750               (uri (string-append "https://github.com/gmarcais/Jellyfish/"
3751                                   "releases/download/v" version
3752                                   "/jellyfish-" version ".tar.gz"))
3753               (sha256
3754                (base32
3755                 "1k4pc3fvv6w1km2yph4m5sd78fbxp21d6xyzgmy0gjihzc6mb249"))))
3756     (build-system gnu-build-system)
3757     (outputs '("out"      ;for library
3758                "ruby"     ;for Ruby bindings
3759                "python")) ;for Python bindings
3760     (arguments
3761      `(#:configure-flags
3762        (list (string-append "--enable-ruby-binding="
3763                             (assoc-ref %outputs "ruby"))
3764              (string-append "--enable-python-binding="
3765                             (assoc-ref %outputs "python")))
3766        #:phases
3767        (modify-phases %standard-phases
3768          (add-before 'check 'set-SHELL-variable
3769            (lambda _
3770              ;; generator_manager.hpp either uses /bin/sh or $SHELL
3771              ;; to run tests.
3772              (setenv "SHELL" (which "bash"))
3773              #t)))))
3774     (native-inputs
3775      `(("bc" ,bc)
3776        ("time" ,time)
3777        ("ruby" ,ruby)
3778        ("python" ,python-2)
3779        ("pkg-config" ,pkg-config)))
3780     (inputs
3781      `(("htslib" ,htslib)))
3782     (synopsis "Tool for fast counting of k-mers in DNA")
3783     (description
3784      "Jellyfish is a tool for fast, memory-efficient counting of k-mers in
3785 DNA.  A k-mer is a substring of length k, and counting the occurrences of all
3786 such substrings is a central step in many analyses of DNA sequence.  Jellyfish
3787 is a command-line program that reads FASTA and multi-FASTA files containing
3788 DNA sequences.  It outputs its k-mer counts in a binary format, which can be
3789 translated into a human-readable text format using the @code{jellyfish dump}
3790 command, or queried for specific k-mers with @code{jellyfish query}.")
3791     (home-page "http://www.genome.umd.edu/jellyfish.html")
3792     ;; JELLYFISH seems to be 64-bit only.
3793     (supported-systems '("x86_64-linux" "aarch64-linux" "mips64el-linux"))
3794     ;; The combined work is published under the GPLv3 or later.  Individual
3795     ;; files such as lib/jsoncpp.cpp are released under the Expat license.
3796     (license (list license:gpl3+ license:expat))))
3797
3798 (define-public khmer
3799   (package
3800     (name "khmer")
3801     (version "2.1.2")
3802     (source
3803      (origin
3804        (method git-fetch)
3805        (uri (git-reference
3806              (url "https://github.com/dib-lab/khmer.git")
3807              (commit (string-append "v" version))))
3808        (file-name (git-file-name name version))
3809        (sha256
3810         (base32
3811          "02x38d9jw2r58y8dmnj4hffy9wxv1yc1jwbvdbhby9dxndv94r9m"))
3812        (patches (search-patches "khmer-use-libraries.patch"))
3813        (modules '((guix build utils)))
3814        (snippet
3815         '(begin
3816            ;; Delete bundled libraries.  We do not replace the bundled seqan
3817            ;; as it is a modified subset of the old version 1.4.1.
3818            ;;
3819            ;; We do not replace the bundled MurmurHash as the canonical
3820            ;; repository for this code 'SMHasher' is unsuitable for providing
3821            ;; a library.  See
3822            ;; https://lists.gnu.org/archive/html/guix-devel/2016-06/msg00977.html
3823            (delete-file-recursively "third-party/zlib")
3824            (delete-file-recursively "third-party/bzip2")
3825            #t))))
3826     (build-system python-build-system)
3827     (arguments
3828      `(#:phases
3829        (modify-phases %standard-phases
3830          (add-after 'unpack 'set-cc
3831            (lambda _ (setenv "CC" "gcc") #t))
3832          ;; FIXME: This fails with "permission denied".
3833          (delete 'reset-gzip-timestamps))))
3834     (native-inputs
3835      `(("python-cython" ,python-cython)
3836        ("python-pytest" ,python-pytest)
3837        ("python-pytest-runner" ,python-pytest-runner)))
3838     (inputs
3839      `(("zlib" ,zlib)
3840        ("bzip2" ,bzip2)
3841        ("python-screed" ,python-screed)
3842        ("python-bz2file" ,python-bz2file)))
3843     (home-page "https://khmer.readthedocs.org/")
3844     (synopsis "K-mer counting, filtering and graph traversal library")
3845     (description "The khmer software is a set of command-line tools for
3846 working with DNA shotgun sequencing data from genomes, transcriptomes,
3847 metagenomes and single cells.  Khmer can make de novo assemblies faster, and
3848 sometimes better.  Khmer can also identify and fix problems with shotgun
3849 data.")
3850     ;; When building on i686, armhf and mips64el, we get the following error:
3851     ;; error: ['khmer', 'khmer.tests', 'oxli'] require 64-bit operating system
3852     (supported-systems '("x86_64-linux" "aarch64-linux"))
3853     (license license:bsd-3)))
3854
3855 (define-public kaiju
3856   (package
3857     (name "kaiju")
3858     (version "1.6.3")
3859     (source (origin
3860               (method git-fetch)
3861               (uri (git-reference
3862                     (url "https://github.com/bioinformatics-centre/kaiju")
3863                     (commit (string-append "v" version))))
3864               (file-name (git-file-name name version))
3865               (sha256
3866                (base32
3867                 "119pzi0ddzv9mjg4wwa6han0cwr3k3ssn7kirvsjfcq05mi5ka0x"))))
3868     (build-system gnu-build-system)
3869     (arguments
3870      `(#:tests? #f ; There are no tests.
3871        #:phases
3872        (modify-phases %standard-phases
3873          (delete 'configure)
3874          (add-before 'build 'move-to-src-dir
3875            (lambda _ (chdir "src") #t))
3876          (replace 'install
3877            (lambda* (#:key inputs outputs #:allow-other-keys)
3878              (let ((bin (string-append (assoc-ref outputs "out") "/bin")))
3879                (mkdir-p bin)
3880                (chdir "..")
3881                (copy-recursively "bin" bin))
3882              #t)))))
3883     (inputs
3884      `(("perl" ,perl)
3885        ("zlib" ,zlib)))
3886     (home-page "http://kaiju.binf.ku.dk/")
3887     (synopsis "Fast and sensitive taxonomic classification for metagenomics")
3888     (description "Kaiju is a program for sensitive taxonomic classification
3889 of high-throughput sequencing reads from metagenomic whole genome sequencing
3890 experiments.")
3891     (license license:gpl3+)))
3892
3893 (define-public macs
3894   (package
3895     (name "macs")
3896     (version "2.1.1.20160309")
3897     (source (origin
3898               (method url-fetch)
3899               (uri (pypi-uri "MACS2" version))
3900               (sha256
3901                (base32
3902                 "09ixspd1vcqmz1c81ih70xs4m7qml2iy5vyx1y74zww3iy1vl210"))))
3903     (build-system python-build-system)
3904     (arguments
3905      `(#:python ,python-2 ; only compatible with Python 2.7
3906        #:tests? #f)) ; no test target
3907     (inputs
3908      `(("python-numpy" ,python2-numpy)))
3909     (home-page "https://github.com/taoliu/MACS/")
3910     (synopsis "Model based analysis for ChIP-Seq data")
3911     (description
3912      "MACS is an implementation of a ChIP-Seq analysis algorithm for
3913 identifying transcript factor binding sites named Model-based Analysis of
3914 ChIP-Seq (MACS).  MACS captures the influence of genome complexity to evaluate
3915 the significance of enriched ChIP regions and it improves the spatial
3916 resolution of binding sites through combining the information of both
3917 sequencing tag position and orientation.")
3918     (license license:bsd-3)))
3919
3920 (define-public mafft
3921   (package
3922     (name "mafft")
3923     (version "7.394")
3924     (source (origin
3925               (method url-fetch)
3926               (uri (string-append
3927                     "https://mafft.cbrc.jp/alignment/software/mafft-" version
3928                     "-without-extensions-src.tgz"))
3929               (file-name (string-append name "-" version ".tgz"))
3930               (sha256
3931                (base32
3932                 "0bacjkxfg944p5khhyh5rd4y7wkjc9qk4v2jjj442sqlq0f8ar7b"))))
3933     (build-system gnu-build-system)
3934     (arguments
3935      `(#:tests? #f ; no automated tests, though there are tests in the read me
3936        #:make-flags (let ((out (assoc-ref %outputs "out")))
3937                       (list (string-append "PREFIX=" out)
3938                             (string-append "BINDIR="
3939                                            (string-append out "/bin"))))
3940        #:phases
3941        (modify-phases %standard-phases
3942          (add-after 'unpack 'enter-dir
3943            (lambda _ (chdir "core") #t))
3944          (add-after 'enter-dir 'patch-makefile
3945            (lambda _
3946              ;; on advice from the MAFFT authors, there is no need to
3947              ;; distribute mafft-profile, mafft-distance, or
3948              ;; mafft-homologs.rb as they are too "specialised".
3949              (substitute* "Makefile"
3950                ;; remove mafft-homologs.rb from SCRIPTS
3951                (("^SCRIPTS = mafft mafft-homologs.rb")
3952                 "SCRIPTS = mafft")
3953                ;; remove mafft-homologs from MANPAGES
3954                (("^MANPAGES = mafft.1 mafft-homologs.1")
3955                 "MANPAGES = mafft.1")
3956                ;; remove mafft-distance from PROGS
3957                (("^PROGS = dvtditr dndfast7 dndblast sextet5 mafft-distance")
3958                 "PROGS = dvtditr dndfast7 dndblast sextet5")
3959                ;; remove mafft-profile from PROGS
3960                (("splittbfast disttbfast tbfast mafft-profile 2cl mccaskillwrap")
3961                 "splittbfast disttbfast tbfast f2cl mccaskillwrap")
3962                (("^rm -f mafft-profile mafft-profile.exe") "#")
3963                (("^rm -f mafft-distance mafft-distance.exe") ")#")
3964                ;; do not install MAN pages in libexec folder
3965                (("^\t\\$\\(INSTALL\\) -m 644 \\$\\(MANPAGES\\) \
3966 \\$\\(DESTDIR\\)\\$\\(LIBDIR\\)") "#"))
3967              #t))
3968          (add-after 'enter-dir 'patch-paths
3969            (lambda* (#:key inputs #:allow-other-keys)
3970              (substitute* '("pairash.c"
3971                             "mafft.tmpl")
3972                (("perl") (which "perl"))
3973                (("([\"`| ])awk" _ prefix)
3974                 (string-append prefix (which "awk")))
3975                (("grep") (which "grep")))
3976              #t))
3977          (delete 'configure)
3978          (add-after 'install 'wrap-programs
3979            (lambda* (#:key outputs #:allow-other-keys)
3980              (let* ((out (assoc-ref outputs "out"))
3981                     (bin (string-append out "/bin"))
3982                     (path (string-append
3983                            (assoc-ref %build-inputs "coreutils") "/bin:")))
3984                (for-each (lambda (file)
3985                            (wrap-program file
3986                              `("PATH" ":" prefix (,path))))
3987                          (find-files bin)))
3988              #t)))))
3989     (inputs
3990      `(("perl" ,perl)
3991        ("ruby" ,ruby)
3992        ("gawk" ,gawk)
3993        ("grep" ,grep)
3994        ("coreutils" ,coreutils)))
3995     (home-page "http://mafft.cbrc.jp/alignment/software/")
3996     (synopsis "Multiple sequence alignment program")
3997     (description
3998      "MAFFT offers a range of multiple alignment methods for nucleotide and
3999 protein sequences.  For instance, it offers L-INS-i (accurate; for alignment
4000 of <~200 sequences) and FFT-NS-2 (fast; for alignment of <~30,000
4001 sequences).")
4002     (license (license:non-copyleft
4003               "http://mafft.cbrc.jp/alignment/software/license.txt"
4004               "BSD-3 with different formatting"))))
4005
4006 (define-public mash
4007   (package
4008     (name "mash")
4009     (version "2.1")
4010     (source (origin
4011               (method git-fetch)
4012               (uri (git-reference
4013                     (url "https://github.com/marbl/mash.git")
4014                     (commit (string-append "v" version))))
4015               (file-name (git-file-name name version))
4016               (sha256
4017                (base32
4018                 "049hwcc059p2fd9vwndn63laifvvsi0wmv84i6y1fr79k15dxwy6"))
4019               (modules '((guix build utils)))
4020               (snippet
4021                '(begin
4022                   ;; Delete bundled kseq.
4023                   ;; TODO: Also delete bundled murmurhash and open bloom filter.
4024                   (delete-file "src/mash/kseq.h")
4025                   #t))))
4026     (build-system gnu-build-system)
4027     (arguments
4028      `(#:tests? #f ; No tests.
4029        #:configure-flags
4030        (list
4031         (string-append "--with-capnp=" (assoc-ref %build-inputs "capnproto"))
4032         (string-append "--with-gsl=" (assoc-ref %build-inputs "gsl")))
4033        #:make-flags (list "CC=gcc")
4034        #:phases
4035        (modify-phases %standard-phases
4036          (add-after 'unpack 'fix-includes
4037            (lambda _
4038              (substitute* '("src/mash/Sketch.cpp"
4039                             "src/mash/CommandFind.cpp"
4040                             "src/mash/CommandScreen.cpp")
4041                (("^#include \"kseq\\.h\"")
4042                 "#include \"htslib/kseq.h\""))
4043              #t))
4044          (add-after 'fix-includes 'use-c++14
4045            (lambda _
4046              ;; capnproto 0.7 requires c++14 to build
4047              (substitute* "configure.ac"
4048                (("c\\+\\+11") "c++14"))
4049              (substitute* "Makefile.in"
4050                (("c\\+\\+11") "c++14"))
4051              #t)))))
4052     (native-inputs
4053      `(("autoconf" ,autoconf)
4054        ;; Capnproto and htslib are statically embedded in the final
4055        ;; application. Therefore we also list their licenses, below.
4056        ("capnproto" ,capnproto)
4057        ("htslib" ,htslib)))
4058     (inputs
4059      `(("gsl" ,gsl)
4060        ("zlib" ,zlib)))
4061     (supported-systems '("x86_64-linux"))
4062     (home-page "https://mash.readthedocs.io")
4063     (synopsis "Fast genome and metagenome distance estimation using MinHash")
4064     (description "Mash is a fast sequence distance estimator that uses the
4065 MinHash algorithm and is designed to work with genomes and metagenomes in the
4066 form of assemblies or reads.")
4067     (license (list license:bsd-3          ; Mash
4068                    license:expat          ; HTSlib and capnproto
4069                    license:public-domain  ; MurmurHash 3
4070                    license:cpl1.0))))     ; Open Bloom Filter
4071
4072 (define-public metabat
4073   (package
4074     (name "metabat")
4075     (version "2.12.1")
4076     (source
4077      (origin
4078        (method git-fetch)
4079        (uri (git-reference
4080              (url "https://bitbucket.org/berkeleylab/metabat.git")
4081              (commit (string-append "v" version))))
4082        (file-name (git-file-name name version))
4083        (sha256
4084         (base32
4085          "0hyg2smw1nz69mfvjpk45xyyychmda92c80a0cv7baji84ri4iyn"))
4086        (patches (search-patches "metabat-fix-compilation.patch"))))
4087     (build-system scons-build-system)
4088     (arguments
4089      `(#:scons ,scons-python2
4090        #:scons-flags
4091        (list (string-append "PREFIX=" (assoc-ref %outputs "out"))
4092              (string-append "BOOST_ROOT=" (assoc-ref %build-inputs "boost")))
4093        #:tests? #f ;; Tests are run during the build phase.
4094        #:phases
4095        (modify-phases %standard-phases
4096          (add-after 'unpack 'fix-includes
4097            (lambda _
4098              (substitute* "src/BamUtils.h"
4099                (("^#include \"bam/bam\\.h\"")
4100                 "#include \"samtools/bam.h\"")
4101                (("^#include \"bam/sam\\.h\"")
4102                 "#include \"samtools/sam.h\""))
4103              (substitute* "src/KseqReader.h"
4104                (("^#include \"bam/kseq\\.h\"")
4105                 "#include \"htslib/kseq.h\""))
4106              #t))
4107          (add-after 'unpack 'fix-scons
4108            (lambda* (#:key inputs #:allow-other-keys)
4109              (substitute* "SConstruct"
4110                (("^htslib_dir += 'samtools'")
4111                 (string-append "htslib_dir = '"
4112                                (assoc-ref inputs "htslib")
4113                                "'"))
4114                (("^samtools_dir = 'samtools'")
4115                 (string-append "samtools_dir = '"
4116                                (assoc-ref inputs "samtools")
4117                                "'"))
4118                (("^findStaticOrShared\\('bam', hts_lib")
4119                 (string-append "findStaticOrShared('bam', '"
4120                                (assoc-ref inputs "samtools")
4121                                "/lib'"))
4122                ;; Do not distribute README.
4123                (("^env\\.Install\\(idir_prefix, 'README\\.md'\\)") ""))
4124              #t)))))
4125     (inputs
4126      `(("zlib" ,zlib)
4127        ("perl" ,perl)
4128        ("samtools" ,samtools)
4129        ("htslib" ,htslib)
4130        ("boost" ,boost)))
4131     (home-page "https://bitbucket.org/berkeleylab/metabat")
4132     (synopsis
4133      "Reconstruction of single genomes from complex microbial communities")
4134     (description
4135      "Grouping large genomic fragments assembled from shotgun metagenomic
4136 sequences to deconvolute complex microbial communities, or metagenome binning,
4137 enables the study of individual organisms and their interactions.  MetaBAT is
4138 an automated metagenome binning software, which integrates empirical
4139 probabilistic distances of genome abundance and tetranucleotide frequency.")
4140     ;; The source code contains inline assembly.
4141     (supported-systems '("x86_64-linux" "i686-linux"))
4142     (license (license:non-copyleft "file://license.txt"
4143                                    "See license.txt in the distribution."))))
4144
4145 (define-public minced
4146   (package
4147     (name "minced")
4148     (version "0.3.2")
4149     (source (origin
4150               (method git-fetch)
4151               (uri (git-reference
4152                     (url "https://github.com/ctSkennerton/minced.git")
4153                     (commit version)))
4154               (file-name (git-file-name name version))
4155               (sha256
4156                (base32
4157                 "1f5h9him0gd355cnx7p6pnxpknhckd4g0v62mg8zyhfbx9as25fv"))))
4158     (build-system gnu-build-system)
4159     (arguments
4160      `(#:test-target "test"
4161        #:phases
4162        (modify-phases %standard-phases
4163          (delete 'configure)
4164          (add-before 'check 'fix-test
4165            (lambda _
4166              ;; Fix test for latest version.
4167              (substitute* "t/Aquifex_aeolicus_VF5.expected"
4168                (("minced:0.1.6") "minced:0.2.0"))
4169              #t))
4170          (replace 'install ; No install target.
4171            (lambda* (#:key inputs outputs #:allow-other-keys)
4172              (let* ((out (assoc-ref outputs "out"))
4173                     (bin (string-append out "/bin"))
4174                     (wrapper (string-append bin "/minced")))
4175                ;; Minced comes with a wrapper script that tries to figure out where
4176                ;; it is located before running the JAR. Since these paths are known
4177                ;; to us, we build our own wrapper to avoid coreutils dependency.
4178                (install-file "minced.jar" bin)
4179                (with-output-to-file wrapper
4180                  (lambda _
4181                    (display
4182                     (string-append
4183                      "#!" (assoc-ref inputs "bash") "/bin/sh\n\n"
4184                      (assoc-ref inputs "jre") "/bin/java -jar "
4185                      bin "/minced.jar \"$@\"\n"))))
4186                (chmod wrapper #o555))
4187              #t)))))
4188     (native-inputs
4189      `(("jdk" ,icedtea "jdk")))
4190     (inputs
4191      `(("bash" ,bash)
4192        ("jre" ,icedtea "out")))
4193     (home-page "https://github.com/ctSkennerton/minced")
4194     (synopsis "Mining CRISPRs in Environmental Datasets")
4195     (description
4196      "MinCED is a program to find Clustered Regularly Interspaced Short
4197 Palindromic Repeats (CRISPRs) in DNA sequences.  It can be used for
4198 unassembled metagenomic reads, but is mainly designed for full genomes and
4199 assembled metagenomic sequence.")
4200     (license license:gpl3+)))
4201
4202 (define-public miso
4203   (package
4204     (name "miso")
4205     (version "0.5.4")
4206     (source (origin
4207               (method url-fetch)
4208               (uri (pypi-uri "misopy" version))
4209               (sha256
4210                (base32
4211                 "1z3x0vd8ma7pdrnywj7i3kgwl89sdkwrrn62zl7r5calqaq2hyip"))
4212               (modules '((guix build utils)))
4213               (snippet '(begin
4214                           (substitute* "setup.py"
4215                             ;; Use setuptools, or else the executables are not
4216                             ;; installed.
4217                             (("distutils.core") "setuptools")
4218                             ;; use "gcc" instead of "cc" for compilation
4219                             (("^defines")
4220                              "cc.set_executables(
4221 compiler='gcc',
4222 compiler_so='gcc',
4223 linker_exe='gcc',
4224 linker_so='gcc -shared'); defines"))
4225                           #t))))
4226     (build-system python-build-system)
4227     (arguments
4228      `(#:python ,python-2 ; only Python 2 is supported
4229        #:tests? #f)) ; no "test" target
4230     (inputs
4231      `(("samtools" ,samtools)
4232        ("python-numpy" ,python2-numpy)
4233        ("python-pysam" ,python2-pysam)
4234        ("python-scipy" ,python2-scipy)
4235        ("python-matplotlib" ,python2-matplotlib)))
4236     (native-inputs
4237      `(("python-mock" ,python2-mock)   ;for tests
4238        ("python-pytz" ,python2-pytz))) ;for tests
4239     (home-page "http://genes.mit.edu/burgelab/miso/index.html")
4240     (synopsis "Mixture of Isoforms model for RNA-Seq isoform quantitation")
4241     (description
4242      "MISO (Mixture-of-Isoforms) is a probabilistic framework that quantitates
4243 the expression level of alternatively spliced genes from RNA-Seq data, and
4244 identifies differentially regulated isoforms or exons across samples.  By
4245 modeling the generative process by which reads are produced from isoforms in
4246 RNA-Seq, the MISO model uses Bayesian inference to compute the probability
4247 that a read originated from a particular isoform.")
4248     (license license:gpl2)))
4249
4250 (define-public muscle
4251   (package
4252     (name "muscle")
4253     (version "3.8.1551")
4254     (source (origin
4255               (method url-fetch/tarbomb)
4256               (uri (string-append
4257                     "http://www.drive5.com/muscle/muscle_src_"
4258                     version ".tar.gz"))
4259               (sha256
4260                (base32
4261                 "0bj8kj7sdizy3987zx6w7axihk40fk8rn76mpbqqjcnd64i5a367"))))
4262     (build-system gnu-build-system)
4263     (arguments
4264      `(#:make-flags (list "LDLIBS = -lm")
4265        #:phases
4266        (modify-phases %standard-phases
4267          (delete 'configure)
4268          (replace 'check
4269            ;; There are no tests, so just test if it runs.
4270            (lambda _ (invoke "./muscle" "-version") #t))
4271          (replace 'install
4272            (lambda* (#:key outputs #:allow-other-keys)
4273              (let* ((out (assoc-ref outputs "out"))
4274                     (bin (string-append out "/bin")))
4275                (install-file "muscle" bin)
4276                #t))))))
4277     (home-page "http://www.drive5.com/muscle")
4278     (synopsis "Multiple sequence alignment program")
4279     (description
4280      "MUSCLE aims to be a fast and accurate multiple sequence alignment
4281 program for nucleotide and protein sequences.")
4282     ;; License information found in 'muscle -h' and usage.cpp.
4283     (license license:public-domain)))
4284
4285 (define-public newick-utils
4286   ;; There are no recent releases so we package from git.
4287   (let ((commit "da121155a977197cab9fbb15953ca1b40b11eb87"))
4288     (package
4289       (name "newick-utils")
4290       (version (string-append "1.6-1." (string-take commit 8)))
4291       (source (origin
4292                 (method git-fetch)
4293                 (uri (git-reference
4294                       (url "https://github.com/tjunier/newick_utils.git")
4295                       (commit commit)))
4296                 (file-name (string-append name "-" version "-checkout"))
4297                 (sha256
4298                  (base32
4299                   "1hkw21rq1mwf7xp0rmbb2gqc0i6p11108m69i7mr7xcjl268pxnb"))))
4300     (build-system gnu-build-system)
4301     (inputs
4302      ;; XXX: TODO: Enable Lua and Guile bindings.
4303      ;; https://github.com/tjunier/newick_utils/issues/13
4304      `(("libxml2" ,libxml2)
4305        ("flex" ,flex)
4306        ("bison" ,bison)))
4307     (native-inputs
4308      `(("autoconf" ,autoconf)
4309        ("automake" ,automake)
4310        ("libtool" ,libtool)))
4311     (synopsis "Programs for working with newick format phylogenetic trees")
4312     (description
4313      "Newick-utils is a suite of utilities for processing phylogenetic trees
4314 in Newick format.  Functions include re-rooting, extracting subtrees,
4315 trimming, pruning, condensing, drawing (ASCII graphics or SVG).")
4316     (home-page "https://github.com/tjunier/newick_utils")
4317     (license license:bsd-3))))
4318
4319 (define-public orfm
4320   (package
4321     (name "orfm")
4322     (version "0.7.1")
4323     (source (origin
4324               (method url-fetch)
4325               (uri (string-append
4326                     "https://github.com/wwood/OrfM/releases/download/v"
4327                     version "/orfm-" version ".tar.gz"))
4328               (sha256
4329                (base32
4330                 "16iigyr2gd8x0imzkk1dr3k5xsds9bpmwg31ayvjg0f4pir9rwqr"))))
4331     (build-system gnu-build-system)
4332     (inputs `(("zlib" ,zlib)))
4333     (native-inputs
4334      `(("ruby-bio-commandeer" ,ruby-bio-commandeer)
4335        ("ruby-rspec" ,ruby-rspec)
4336        ("ruby" ,ruby)))
4337     (synopsis "Simple and not slow open reading frame (ORF) caller")
4338     (description
4339      "An ORF caller finds stretches of DNA that, when translated, are not
4340 interrupted by stop codons.  OrfM finds and prints these ORFs.")
4341     (home-page "https://github.com/wwood/OrfM")
4342     (license license:lgpl3+)))
4343
4344 (define-public pplacer
4345   (let ((commit "807f6f3"))
4346     (package
4347       (name "pplacer")
4348       ;; The commit should be updated with each version change.
4349       (version "1.1.alpha19")
4350       (source
4351        (origin
4352          (method git-fetch)
4353          (uri (git-reference
4354                (url "https://github.com/matsen/pplacer.git")
4355                (commit (string-append "v" version))))
4356          (file-name (git-file-name name version))
4357          (sha256
4358           (base32 "11ppbbbx20p2g9wj3ff64dhnarb12q79v7qh4rk0gj6lkbz4n7cn"))))
4359       (build-system ocaml-build-system)
4360       (arguments
4361        `(#:ocaml ,ocaml-4.01
4362          #:findlib ,ocaml4.01-findlib
4363          #:modules ((guix build ocaml-build-system)
4364                     (guix build utils)
4365                     (ice-9 ftw))
4366          #:phases
4367          (modify-phases %standard-phases
4368            (delete 'configure)
4369            (add-after 'unpack 'replace-bundled-cddlib
4370              (lambda* (#:key inputs #:allow-other-keys)
4371                (let* ((cddlib-src (assoc-ref inputs "cddlib-src"))
4372                       (local-dir "cddlib_guix"))
4373                  (mkdir local-dir)
4374                  (with-directory-excursion local-dir
4375                    (invoke "tar" "xvf" cddlib-src))
4376                  (let ((cddlib-src-folder
4377                         (string-append local-dir "/"
4378                                        (list-ref (scandir local-dir) 2)
4379                                        "/lib-src")))
4380                    (for-each make-file-writable (find-files "cdd_src" ".*"))
4381                    (for-each
4382                     (lambda (file)
4383                       (copy-file file
4384                                  (string-append "cdd_src/" (basename file))))
4385                     (find-files cddlib-src-folder ".*[ch]$")))
4386                  #t)))
4387            (add-after 'unpack 'fix-makefile
4388              (lambda _
4389                ;; Remove system calls to 'git'.
4390                (substitute* "Makefile"
4391                  (("^DESCRIPT:=pplacer-.*")
4392                   (string-append
4393                    "DESCRIPT:=pplacer-$(shell uname)-v" ,version "\n")))
4394                (substitute* "myocamlbuild.ml"
4395                  (("git describe --tags --long .*\\\" with")
4396                   (string-append
4397                    "echo -n v" ,version "-" ,commit "\" with")))
4398                #t))
4399            (replace 'install
4400              (lambda* (#:key outputs #:allow-other-keys)
4401                (let* ((out (assoc-ref outputs "out"))
4402                       (bin (string-append out "/bin")))
4403                  (copy-recursively "bin" bin))
4404                #t)))))
4405       (native-inputs
4406        `(("zlib" ,zlib)
4407          ("gsl" ,gsl)
4408          ("ocaml-ounit" ,ocaml4.01-ounit)
4409          ("ocaml-batteries" ,ocaml4.01-batteries)
4410          ("ocaml-camlzip" ,ocaml4.01-camlzip)
4411          ("ocaml-csv" ,ocaml4.01-csv)
4412          ("ocaml-sqlite3" ,ocaml4.01-sqlite3)
4413          ("ocaml-xmlm" ,ocaml4.01-xmlm)
4414          ("ocaml-mcl" ,ocaml4.01-mcl)
4415          ("ocaml-gsl" ,ocaml4.01-gsl)
4416          ("cddlib-src" ,(package-source cddlib))))
4417       (propagated-inputs
4418        `(("pplacer-scripts" ,pplacer-scripts)))
4419       (synopsis "Phylogenetic placement of biological sequences")
4420       (description
4421        "Pplacer places query sequences on a fixed reference phylogenetic tree
4422 to maximize phylogenetic likelihood or posterior probability according to a
4423 reference alignment.  Pplacer is designed to be fast, to give useful
4424 information about uncertainty, and to offer advanced visualization and
4425 downstream analysis.")
4426       (home-page "http://matsen.fhcrc.org/pplacer")
4427       (license license:gpl3))))
4428
4429 ;; This package is installed alongside 'pplacer'.  It is a separate package so
4430 ;; that it can use the python-build-system for the scripts that are
4431 ;; distributed alongside the main OCaml binaries.
4432 (define pplacer-scripts
4433   (package
4434     (inherit pplacer)
4435     (name "pplacer-scripts")
4436     (build-system python-build-system)
4437     (arguments
4438      `(#:python ,python-2
4439        #:phases
4440        (modify-phases %standard-phases
4441          (add-after 'unpack 'enter-scripts-dir
4442            (lambda _ (chdir "scripts") #t))
4443          (replace 'check
4444            (lambda _ (invoke "python" "-m" "unittest" "discover" "-v") #t))
4445          (add-after 'install 'wrap-executables
4446            (lambda* (#:key inputs outputs #:allow-other-keys)
4447              (let* ((out (assoc-ref outputs "out"))
4448                     (bin (string-append out "/bin")))
4449                (let ((path (string-append
4450                             (assoc-ref inputs "hmmer") "/bin:"
4451                             (assoc-ref inputs "infernal") "/bin")))
4452                  (display path)
4453                  (wrap-program (string-append bin "/refpkg_align.py")
4454                    `("PATH" ":" prefix (,path))))
4455                (let ((path (string-append
4456                             (assoc-ref inputs "hmmer") "/bin")))
4457                  (wrap-program (string-append bin "/hrefpkg_query.py")
4458                    `("PATH" ":" prefix (,path)))))
4459              #t)))))
4460     (inputs
4461      `(("infernal" ,infernal)
4462        ("hmmer" ,hmmer)))
4463     (propagated-inputs
4464      `(("python-biopython" ,python2-biopython)
4465        ("taxtastic" ,taxtastic)))
4466     (synopsis "Pplacer Python scripts")))
4467
4468 (define-public python2-pbcore
4469   (package
4470     (name "python2-pbcore")
4471     (version "1.2.10")
4472     (source (origin
4473               (method url-fetch)
4474               (uri (pypi-uri "pbcore" version))
4475               (sha256
4476                (base32
4477                 "1kjmv891d6qbpp4shhhvkl02ff4q5xlpnls2513sm2cjcrs52f1i"))))
4478     (build-system python-build-system)
4479     (arguments `(#:python ,python-2)) ; pbcore requires Python 2.7
4480     (propagated-inputs
4481      `(("python-cython" ,python2-cython)
4482        ("python-numpy" ,python2-numpy)
4483        ("python-pysam" ,python2-pysam)
4484        ("python-h5py" ,python2-h5py)))
4485     (native-inputs
4486      `(("python-nose" ,python2-nose)
4487        ("python-sphinx" ,python2-sphinx)
4488        ("python-pyxb" ,python2-pyxb)))
4489     (home-page "http://pacificbiosciences.github.io/pbcore/")
4490     (synopsis "Library for reading and writing PacBio data files")
4491     (description
4492      "The pbcore package provides Python APIs for interacting with PacBio data
4493 files and writing bioinformatics applications.")
4494     (license license:bsd-3)))
4495
4496 (define-public python2-warpedlmm
4497   (package
4498     (name "python2-warpedlmm")
4499     (version "0.21")
4500     (source
4501      (origin
4502        (method url-fetch)
4503        (uri (string-append
4504              "https://pypi.python.org/packages/source/W/WarpedLMM/WarpedLMM-"
4505              version ".zip"))
4506        (sha256
4507         (base32
4508          "1agfz6zqa8nc6cw47yh0s3y14gkpa9wqazwcj7mwwj3ffnw39p3j"))))
4509     (build-system python-build-system)
4510     (arguments
4511      `(#:python ,python-2))  ; requires Python 2.7
4512     (propagated-inputs
4513      `(("python-scipy" ,python2-scipy)
4514        ("python-numpy" ,python2-numpy)
4515        ("python-matplotlib" ,python2-matplotlib)
4516        ("python-fastlmm" ,python2-fastlmm)
4517        ("python-pandas" ,python2-pandas)
4518        ("python-pysnptools" ,python2-pysnptools)))
4519     (native-inputs
4520      `(("python-mock" ,python2-mock)
4521        ("python-nose" ,python2-nose)
4522        ("unzip" ,unzip)))
4523     (home-page "https://github.com/PMBio/warpedLMM")
4524     (synopsis "Implementation of warped linear mixed models")
4525     (description
4526      "WarpedLMM is a Python implementation of the warped linear mixed model,
4527 which automatically learns an optimal warping function (or transformation) for
4528 the phenotype as it models the data.")
4529     (license license:asl2.0)))
4530
4531 (define-public pbtranscript-tofu
4532   (let ((commit "8f5467fe6a4472bcfb4226c8720993c8507adfe4"))
4533     (package
4534       (name "pbtranscript-tofu")
4535       (version (string-append "2.2.3." (string-take commit 7)))
4536       (source (origin
4537                 (method git-fetch)
4538                 (uri (git-reference
4539                       (url "https://github.com/PacificBiosciences/cDNA_primer.git")
4540                       (commit commit)))
4541                 (file-name (string-append name "-" version "-checkout"))
4542                 (sha256
4543                  (base32
4544                   "1lgnpi35ihay42qx0b6yl3kkgra723i413j33kvs0kvs61h82w0f"))
4545                 (modules '((guix build utils)))
4546                 (snippet
4547                  '(begin
4548                     ;; remove bundled Cython sources
4549                     (delete-file "pbtranscript-tofu/pbtranscript/Cython-0.20.1.tar.gz")
4550                     #t))))
4551       (build-system python-build-system)
4552       (arguments
4553        `(#:python ,python-2
4554          ;; FIXME: Tests fail with "No such file or directory:
4555          ;; pbtools/pbtranscript/modified_bx_intervals/intersection_unique.so"
4556          #:tests? #f
4557          #:phases
4558          (modify-phases %standard-phases
4559            (add-after 'unpack 'enter-directory
4560             (lambda _
4561               (chdir "pbtranscript-tofu/pbtranscript/")
4562               #t))
4563            ;; With setuptools version 18.0 and later this setup.py hack causes
4564            ;; a build error, so we disable it.
4565            (add-after 'enter-directory 'patch-setuppy
4566             (lambda _
4567               (substitute* "setup.py"
4568                 (("if 'setuptools.extension' in sys.modules:")
4569                  "if False:"))
4570               #t)))))
4571       (inputs
4572        `(("python-numpy" ,python2-numpy)
4573          ("python-bx-python" ,python2-bx-python)
4574          ("python-networkx" ,python2-networkx)
4575          ("python-scipy" ,python2-scipy)
4576          ("python-pbcore" ,python2-pbcore)
4577          ("python-h5py" ,python2-h5py)))
4578       (native-inputs
4579        `(("python-cython" ,python2-cython)
4580          ("python-nose" ,python2-nose)))
4581       (home-page "https://github.com/PacificBiosciences/cDNA_primer")
4582       (synopsis "Analyze transcriptome data generated with the Iso-Seq protocol")
4583       (description
4584        "pbtranscript-tofu contains scripts to analyze transcriptome data
4585 generated using the PacBio Iso-Seq protocol.")
4586       (license license:bsd-3))))
4587
4588 (define-public prank
4589   (package
4590     (name "prank")
4591     (version "150803")
4592     (source (origin
4593               (method url-fetch)
4594               (uri (string-append
4595                     "http://wasabiapp.org/download/prank/prank.source."
4596                     version ".tgz"))
4597               (sha256
4598                (base32
4599                 "0am4z94fs3w2n5xpfls9zda61vq7qqz4q2i7b9hlsxz5q4j3kfm4"))))
4600     (build-system gnu-build-system)
4601     (arguments
4602      `(#:phases
4603        (modify-phases %standard-phases
4604          (add-after 'unpack 'enter-src-dir
4605             (lambda _
4606               (chdir "src")
4607               #t))
4608          (add-after 'unpack 'remove-m64-flag
4609            ;; Prank will build with the correct 'bit-ness' without this flag
4610            ;; and this allows building on 32-bit machines.
4611            (lambda _ (substitute* "src/Makefile"
4612                                   (("-m64") ""))
4613              #t))
4614          (delete 'configure)
4615          (replace 'install
4616            (lambda* (#:key outputs #:allow-other-keys)
4617              (let* ((out (assoc-ref outputs "out"))
4618                     (bin (string-append out "/bin"))
4619                     (man (string-append out "/share/man/man1"))
4620                     (path (string-append
4621                            (assoc-ref %build-inputs "mafft") "/bin:"
4622                            (assoc-ref %build-inputs "exonerate") "/bin:"
4623                            (assoc-ref %build-inputs "bppsuite") "/bin")))
4624                (install-file "prank" bin)
4625                (wrap-program (string-append bin "/prank")
4626                  `("PATH" ":" prefix (,path)))
4627                (install-file "prank.1" man))
4628              #t)))))
4629     (inputs
4630      `(("mafft" ,mafft)
4631        ("exonerate" ,exonerate)
4632        ("bppsuite" ,bppsuite)))
4633     (home-page "http://wasabiapp.org/software/prank/")
4634     (synopsis "Probabilistic multiple sequence alignment program")
4635     (description
4636      "PRANK is a probabilistic multiple sequence alignment program for DNA,
4637 codon and amino-acid sequences.  It is based on a novel algorithm that treats
4638 insertions correctly and avoids over-estimation of the number of deletion
4639 events.  In addition, PRANK borrows ideas from maximum likelihood methods used
4640 in phylogenetics and correctly takes into account the evolutionary distances
4641 between sequences.  Lastly, PRANK allows for defining a potential structure
4642 for sequences to be aligned and then, simultaneously with the alignment,
4643 predicts the locations of structural units in the sequences.")
4644     (license license:gpl2+)))
4645
4646 (define-public proteinortho
4647   (package
4648     (name "proteinortho")
4649     (version "5.16b")
4650     (source
4651      (origin
4652       (method url-fetch)
4653       (uri
4654        (string-append
4655         "http://www.bioinf.uni-leipzig.de/Software/proteinortho/proteinortho_v"
4656         version "_src.tar.gz"))
4657       (sha256
4658        (base32
4659         "1wl0dawpssqwfjvr651r4wlww8hhjin8nba6xh71ks7sbypx886j"))))
4660     (build-system gnu-build-system)
4661     (arguments
4662      `(#:test-target "test"
4663        #:phases
4664        (modify-phases %standard-phases
4665          (replace 'configure
4666            ;; There is no configure script, so we modify the Makefile directly.
4667            (lambda* (#:key outputs #:allow-other-keys)
4668              (substitute* "Makefile"
4669                (("INSTALLDIR=.*")
4670                 (string-append
4671                  "INSTALLDIR=" (assoc-ref outputs "out") "/bin\n")))
4672              #t))
4673          (add-before 'install 'make-install-directory
4674            ;; The install directory is not created during 'make install'.
4675            (lambda* (#:key outputs #:allow-other-keys)
4676              (mkdir-p (string-append (assoc-ref outputs "out") "/bin"))
4677              #t))
4678          (add-after 'install 'wrap-programs
4679            (lambda* (#:key inputs outputs #:allow-other-keys)
4680              (let* ((path (getenv "PATH"))
4681                     (out (assoc-ref outputs "out"))
4682                     (binary (string-append out "/bin/proteinortho5.pl")))
4683                (wrap-program binary `("PATH" ":" prefix (,path))))
4684              #t)))))
4685     (inputs
4686      `(("perl" ,perl)
4687        ("python" ,python-2)
4688        ("blast+" ,blast+)))
4689     (home-page "http://www.bioinf.uni-leipzig.de/Software/proteinortho")
4690     (synopsis "Detect orthologous genes across species")
4691     (description
4692      "Proteinortho is a tool to detect orthologous genes across different
4693 species.  For doing so, it compares similarities of given gene sequences and
4694 clusters them to find significant groups.  The algorithm was designed to handle
4695 large-scale data and can be applied to hundreds of species at once.")
4696     (license license:gpl2+)))
4697
4698 (define-public pyicoteo
4699   (package
4700     (name "pyicoteo")
4701     (version "2.0.7")
4702     (source
4703      (origin
4704        (method git-fetch)
4705        (uri (git-reference
4706              (url "https://bitbucket.org/regulatorygenomicsupf/pyicoteo.git")
4707              (commit (string-append "v" version))))
4708        (file-name (git-file-name name version))
4709        (sha256
4710         (base32
4711          "0hz5g8d25lbjy1wpscr490l0lmyvaix893hhax4fxnh1h9w34w8p"))))
4712     (build-system python-build-system)
4713     (arguments
4714      `(#:python ,python-2 ; does not work with Python 3
4715        #:tests? #f))      ; there are no tests
4716     (inputs
4717      `(("python2-matplotlib" ,python2-matplotlib)))
4718     (home-page "https://bitbucket.org/regulatorygenomicsupf/pyicoteo")
4719     (synopsis "Analyze high-throughput genetic sequencing data")
4720     (description
4721      "Pyicoteo is a suite of tools for the analysis of high-throughput genetic
4722 sequencing data.  It works with genomic coordinates.  There are currently six
4723 different command-line tools:
4724
4725 @enumerate
4726 @item pyicoregion: for generating exploratory regions automatically;
4727 @item pyicoenrich: for differential enrichment between two conditions;
4728 @item pyicoclip: for calling CLIP-Seq peaks without a control;
4729 @item pyicos: for genomic coordinates manipulation;
4730 @item pyicoller: for peak calling on punctuated ChIP-Seq;
4731 @item pyicount: to count how many reads from N experiment files overlap in a
4732   region file;
4733 @item pyicotrocol: to combine operations from pyicoteo.
4734 @end enumerate\n")
4735     (license license:gpl3+)))
4736
4737 (define-public prodigal
4738   (package
4739     (name "prodigal")
4740     (version "2.6.3")
4741     (source (origin
4742               (method git-fetch)
4743               (uri (git-reference
4744                     (url "https://github.com/hyattpd/Prodigal.git")
4745                     (commit (string-append "v" version))))
4746               (file-name (git-file-name name version))
4747               (sha256
4748                (base32
4749                 "1fs1hqk83qjbjhrvhw6ni75zakx5ki1ayy3v6wwkn3xvahc9hi5s"))))
4750     (build-system gnu-build-system)
4751     (arguments
4752      `(#:tests? #f ;no check target
4753        #:make-flags (list (string-append "INSTALLDIR="
4754                                          (assoc-ref %outputs "out")
4755                                          "/bin"))
4756        #:phases
4757        (modify-phases %standard-phases
4758          (delete 'configure))))
4759     (home-page "http://prodigal.ornl.gov")
4760     (synopsis "Protein-coding gene prediction for Archaea and Bacteria")
4761     (description
4762      "Prodigal runs smoothly on finished genomes, draft genomes, and
4763 metagenomes, providing gene predictions in GFF3, Genbank, or Sequin table
4764 format.  It runs quickly, in an unsupervised fashion, handles gaps, handles
4765 partial genes, and identifies translation initiation sites.")
4766     (license license:gpl3+)))
4767
4768 (define-public roary
4769   (package
4770     (name "roary")
4771     (version "3.12.0")
4772     (source
4773      (origin
4774        (method url-fetch)
4775        (uri (string-append
4776              "mirror://cpan/authors/id/A/AJ/AJPAGE/Bio-Roary-"
4777              version ".tar.gz"))
4778        (sha256
4779         (base32
4780          "0qxrds9wx7cfhlkihrp6697kx0flhhxymap9fwan0b3rbdhcnmff"))))
4781     (build-system perl-build-system)
4782     (arguments
4783      `(#:phases
4784        (modify-phases %standard-phases
4785          (delete 'configure)
4786          (delete 'build)
4787          (replace 'check
4788            (lambda _
4789              ;; The tests are not run by default, so we run each test file
4790              ;; directly.
4791              (setenv "PATH" (string-append (getcwd) "/bin" ":"
4792                                            (getenv "PATH")))
4793              (setenv "PERL5LIB" (string-append (getcwd) "/lib" ":"
4794                                                (getenv "PERL5LIB")))
4795              (for-each (lambda (file)
4796                          (display file)(display "\n")
4797                          (invoke "perl" file))
4798                        (find-files "t" ".*\\.t$"))
4799              #t))
4800          (replace 'install
4801            ;; There is no 'install' target in the Makefile.
4802            (lambda* (#:key outputs #:allow-other-keys)
4803              (let* ((out (assoc-ref outputs "out"))
4804                     (bin (string-append out "/bin"))
4805                     (perl (string-append out "/lib/perl5/site_perl"))
4806                     (roary-plots "contrib/roary_plots"))
4807                (mkdir-p bin)
4808                (mkdir-p perl)
4809                (copy-recursively "bin" bin)
4810                (copy-recursively "lib" perl)
4811                #t)))
4812          (add-after 'install 'wrap-programs
4813            (lambda* (#:key inputs outputs #:allow-other-keys)
4814              (let* ((out (assoc-ref outputs "out"))
4815                     (perl5lib (getenv "PERL5LIB"))
4816                     (path (getenv "PATH")))
4817                (for-each (lambda (prog)
4818                            (let ((binary (string-append out "/" prog)))
4819                              (wrap-program binary
4820                                `("PERL5LIB" ":" prefix
4821                                  (,(string-append perl5lib ":" out
4822                                                   "/lib/perl5/site_perl"))))
4823                              (wrap-program binary
4824                                `("PATH" ":" prefix
4825                                  (,(string-append path ":" out "/bin"))))))
4826                          (find-files "bin" ".*[^R]$"))
4827                (let ((file
4828                       (string-append out "/bin/roary-create_pan_genome_plots.R"))
4829                      (r-site-lib (getenv "R_LIBS_SITE"))
4830                      (coreutils-path
4831                       (string-append (assoc-ref inputs "coreutils") "/bin")))
4832                  (wrap-program file
4833                    `("R_LIBS_SITE" ":" prefix
4834                      (,(string-append r-site-lib ":" out "/site-library/"))))
4835                  (wrap-program file
4836                    `("PATH" ":" prefix
4837                      (,(string-append coreutils-path ":" out "/bin"))))))
4838              #t)))))
4839     (native-inputs
4840      `(("perl-env-path" ,perl-env-path)
4841        ("perl-test-files" ,perl-test-files)
4842        ("perl-test-most" ,perl-test-most)
4843        ("perl-test-output" ,perl-test-output)))
4844     (inputs
4845      `(("perl-array-utils" ,perl-array-utils)
4846        ("bioperl" ,bioperl-minimal)
4847        ("perl-digest-md5-file" ,perl-digest-md5-file)
4848        ("perl-exception-class" ,perl-exception-class)
4849        ("perl-file-find-rule" ,perl-file-find-rule)
4850        ("perl-file-grep" ,perl-file-grep)
4851        ("perl-file-slurper" ,perl-file-slurper)
4852        ("perl-file-which" ,perl-file-which)
4853        ("perl-graph" ,perl-graph)
4854        ("perl-graph-readwrite" ,perl-graph-readwrite)
4855        ("perl-log-log4perl" ,perl-log-log4perl)
4856        ("perl-moose" ,perl-moose)
4857        ("perl-perlio-utf8_strict" ,perl-perlio-utf8_strict)
4858        ("perl-text-csv" ,perl-text-csv)
4859        ("bedtools" ,bedtools)
4860        ("cd-hit" ,cd-hit)
4861        ("blast+" ,blast+)
4862        ("mcl" ,mcl)
4863        ("parallel" ,parallel)
4864        ("prank" ,prank)
4865        ("mafft" ,mafft)
4866        ("fasttree" ,fasttree)
4867        ("grep" ,grep)
4868        ("sed" ,sed)
4869        ("gawk" ,gawk)
4870        ("r-minimal" ,r-minimal)
4871        ("r-ggplot2" ,r-ggplot2)
4872        ("coreutils" ,coreutils)))
4873     (home-page "http://sanger-pathogens.github.io/Roary")
4874     (synopsis "High speed stand-alone pan genome pipeline")
4875     (description
4876      "Roary is a high speed stand alone pan genome pipeline, which takes
4877 annotated assemblies in GFF3 format (produced by the Prokka program) and
4878 calculates the pan genome.  Using a standard desktop PC, it can analyse
4879 datasets with thousands of samples, without compromising the quality of the
4880 results.  128 samples can be analysed in under 1 hour using 1 GB of RAM and a
4881 single processor.  Roary is not intended for metagenomics or for comparing
4882 extremely diverse sets of genomes.")
4883     (license license:gpl3)))
4884
4885 (define-public raxml
4886   (package
4887     (name "raxml")
4888     (version "8.2.12")
4889     (source
4890      (origin
4891        (method git-fetch)
4892        (uri (git-reference
4893              (url "https://github.com/stamatak/standard-RAxML.git")
4894              (commit (string-append "v" version))))
4895        (file-name (git-file-name name version))
4896        (sha256
4897         (base32
4898          "1jqjzhch0rips0vp04prvb8vmc20c5pdmsqn8knadcf91yy859fh"))))
4899     (build-system gnu-build-system)
4900     (arguments
4901      `(#:tests? #f ; There are no tests.
4902        ;; Use 'standard' Makefile rather than SSE or AVX ones.
4903        #:make-flags (list "-f" "Makefile.HYBRID.gcc")
4904        #:phases
4905        (modify-phases %standard-phases
4906          (delete 'configure)
4907          (replace 'install
4908            (lambda* (#:key outputs #:allow-other-keys)
4909              (let* ((out (assoc-ref outputs "out"))
4910                     (bin (string-append out "/bin"))
4911                     (executable "raxmlHPC-HYBRID"))
4912                (install-file executable bin)
4913                (symlink (string-append bin "/" executable) "raxml"))
4914              #t)))))
4915     (inputs
4916      `(("openmpi" ,openmpi)))
4917     (home-page "http://sco.h-its.org/exelixis/web/software/raxml/index.html")
4918     (synopsis "Randomized Axelerated Maximum Likelihood phylogenetic trees")
4919     (description
4920      "RAxML is a tool for phylogenetic analysis and post-analysis of large
4921 phylogenies.")
4922     ;; The source includes x86 specific code
4923     (supported-systems '("x86_64-linux" "i686-linux"))
4924     (license license:gpl2+)))
4925
4926 (define-public rsem
4927   (package
4928     (name "rsem")
4929     (version "1.3.1")
4930     (source
4931      (origin
4932        (method git-fetch)
4933        (uri (git-reference
4934              (url "https://github.com/deweylab/RSEM.git")
4935              (commit (string-append "v" version))))
4936        (sha256
4937         (base32 "1jlq11d1p8qp64w75yj8cnbbd1a93viq10pzsbwal7vdn8fg13j1"))
4938        (file-name (git-file-name name version))
4939        (modules '((guix build utils)))
4940        (snippet
4941         '(begin
4942            ;; remove bundled copy of boost and samtools
4943            (delete-file-recursively "boost")
4944            (delete-file-recursively "samtools-1.3")
4945            #t))))
4946     (build-system gnu-build-system)
4947     (arguments
4948      `(#:tests? #f ;no "check" target
4949        #:make-flags
4950        (list (string-append "BOOST="
4951                             (assoc-ref %build-inputs "boost")
4952                             "/include/")
4953              (string-append "SAMHEADERS="
4954                             (assoc-ref %build-inputs "htslib")
4955                             "/include/htslib/sam.h")
4956              (string-append "SAMLIBS="
4957                             (assoc-ref %build-inputs "htslib")
4958                             "/lib/libhts.a"))
4959        #:phases
4960        (modify-phases %standard-phases
4961          ;; No "configure" script.
4962          ;; Do not build bundled samtools library.
4963          (replace 'configure
4964            (lambda _
4965              (substitute* "Makefile"
4966                (("^all : \\$\\(PROGRAMS\\).*") "all: $(PROGRAMS)\n")
4967                (("^\\$\\(SAMLIBS\\).*") ""))
4968              #t))
4969          (replace 'install
4970            (lambda* (#:key outputs #:allow-other-keys)
4971              (let* ((out (string-append (assoc-ref outputs "out")))
4972                     (bin (string-append out "/bin/"))
4973                     (perl (string-append out "/lib/perl5/site_perl")))
4974                (mkdir-p bin)
4975                (mkdir-p perl)
4976                (for-each (lambda (file)
4977                            (install-file file bin))
4978                          (find-files "." "rsem-.*"))
4979                (install-file "rsem_perl_utils.pm" perl))
4980              #t))
4981          (add-after 'install 'wrap-program
4982            (lambda* (#:key outputs #:allow-other-keys)
4983              (let ((out (assoc-ref outputs "out")))
4984                (for-each (lambda (prog)
4985                            (wrap-program (string-append out "/bin/" prog)
4986                              `("PERL5LIB" ":" prefix
4987                                (,(string-append out "/lib/perl5/site_perl")))))
4988                          '("rsem-calculate-expression"
4989                            "rsem-control-fdr"
4990                            "rsem-generate-data-matrix"
4991                            "rsem-generate-ngvector"
4992                            "rsem-plot-transcript-wiggles"
4993                            "rsem-prepare-reference"
4994                            "rsem-run-ebseq"
4995                            "rsem-run-prsem-testing-procedure")))
4996              #t)))))
4997     (inputs
4998      `(("boost" ,boost)
4999        ("r-minimal" ,r-minimal)
5000        ("perl" ,perl)
5001        ("htslib" ,htslib-1.3)
5002        ("zlib" ,zlib)))
5003     (home-page "http://deweylab.biostat.wisc.edu/rsem/")
5004     (synopsis "Estimate gene expression levels from RNA-Seq data")
5005     (description
5006      "RSEM is a software package for estimating gene and isoform expression
5007 levels from RNA-Seq data.  The RSEM package provides a user-friendly
5008 interface, supports threads for parallel computation of the EM algorithm,
5009 single-end and paired-end read data, quality scores, variable-length reads and
5010 RSPD estimation.  In addition, it provides posterior mean and 95% credibility
5011 interval estimates for expression levels.  For visualization, it can generate
5012 BAM and Wiggle files in both transcript-coordinate and genomic-coordinate.")
5013     (license license:gpl3+)))
5014
5015 (define-public rseqc
5016   (package
5017     (name "rseqc")
5018     (version "2.6.1")
5019     (source
5020      (origin
5021        (method url-fetch)
5022        (uri
5023         (string-append "mirror://sourceforge/rseqc/"
5024                        "RSeQC-" version ".tar.gz"))
5025        (sha256
5026         (base32 "15ly0254yi032qzkdplg00q144qfdsd986gh62829rl5bkxhj330"))
5027        (modules '((guix build utils)))
5028        (snippet
5029         '(begin
5030            ;; remove bundled copy of pysam
5031            (delete-file-recursively "lib/pysam")
5032            (substitute* "setup.py"
5033              ;; remove dependency on outdated "distribute" module
5034              (("^from distribute_setup import use_setuptools") "")
5035              (("^use_setuptools\\(\\)") "")
5036              ;; do not use bundled copy of pysam
5037              (("^have_pysam = False") "have_pysam = True"))
5038            #t))))
5039     (build-system python-build-system)
5040     (arguments `(#:python ,python-2))
5041     (inputs
5042      `(("python-cython" ,python2-cython)
5043        ("python-pysam" ,python2-pysam)
5044        ("python-numpy" ,python2-numpy)
5045        ("zlib" ,zlib)))
5046     (native-inputs
5047      `(("python-nose" ,python2-nose)))
5048     (home-page "http://rseqc.sourceforge.net/")
5049     (synopsis "RNA-seq quality control package")
5050     (description
5051      "RSeQC provides a number of modules that can comprehensively evaluate
5052 high throughput sequence data, especially RNA-seq data.  Some basic modules
5053 inspect sequence quality, nucleotide composition bias, PCR bias and GC bias,
5054 while RNA-seq specific modules evaluate sequencing saturation, mapped reads
5055 distribution, coverage uniformity, strand specificity, etc.")
5056     (license license:gpl3+)))
5057
5058 (define-public seek
5059   ;; There are no release tarballs.  According to the installation
5060   ;; instructions at http://seek.princeton.edu/installation.jsp, the latest
5061   ;; stable release is identified by this changeset ID.
5062   (let ((changeset "2329130")
5063         (revision "1"))
5064     (package
5065       (name "seek")
5066       (version (string-append "0-" revision "." changeset))
5067       (source (origin
5068                 (method hg-fetch)
5069                 (uri (hg-reference
5070                       (url "https://bitbucket.org/libsleipnir/sleipnir")
5071                       (changeset changeset)))
5072                 (file-name (string-append name "-" version "-checkout"))
5073                 (sha256
5074                  (base32
5075                   "0qrvilwh18dpbhkf92qvxbmay0j75ra3jg2wrhz67gf538zzphsx"))))
5076       (build-system gnu-build-system)
5077       (arguments
5078        `(#:modules ((srfi srfi-1)
5079                     (guix build gnu-build-system)
5080                     (guix build utils))
5081          #:phases
5082          (let ((dirs '("SeekMiner"
5083                        "SeekEvaluator"
5084                        "SeekPrep"
5085                        "Distancer"
5086                        "Data2DB"
5087                        "PCL2Bin")))
5088            (modify-phases %standard-phases
5089              (replace 'bootstrap
5090                (lambda _
5091                  (substitute* "gen_tools_am"
5092                    (("/usr/bin/env.*") (which "perl")))
5093                  (invoke "bash" "gen_auto")
5094                  #t))
5095              (add-after 'build 'build-additional-tools
5096                (lambda* (#:key make-flags #:allow-other-keys)
5097                  (for-each (lambda (dir)
5098                              (with-directory-excursion (string-append "tools/" dir)
5099                                (apply invoke "make" make-flags)))
5100                            dirs)
5101                  #t))
5102              (add-after 'install 'install-additional-tools
5103                (lambda* (#:key make-flags #:allow-other-keys)
5104                  (for-each (lambda (dir)
5105                              (with-directory-excursion (string-append "tools/" dir)
5106                                (apply invoke `("make" ,@make-flags "install"))))
5107                            dirs)
5108                  #t))))))
5109       (inputs
5110        `(("gsl" ,gsl)
5111          ("boost" ,boost)
5112          ("libsvm" ,libsvm)
5113          ("readline" ,readline)
5114          ("gengetopt" ,gengetopt)
5115          ("log4cpp" ,log4cpp)))
5116       (native-inputs
5117        `(("autoconf" ,autoconf)
5118          ("automake" ,automake)
5119          ("perl" ,perl)))
5120       (home-page "http://seek.princeton.edu")
5121       (synopsis "Gene co-expression search engine")
5122       (description
5123        "SEEK is a computational gene co-expression search engine.  SEEK provides
5124 biologists with a way to navigate the massive human expression compendium that
5125 now contains thousands of expression datasets.  SEEK returns a robust ranking
5126 of co-expressed genes in the biological area of interest defined by the user's
5127 query genes.  It also prioritizes thousands of expression datasets according
5128 to the user's query of interest.")
5129       (license license:cc-by3.0))))
5130
5131 (define-public samtools
5132   (package
5133     (name "samtools")
5134     (version "1.9")
5135     (source
5136      (origin
5137        (method url-fetch)
5138        (uri
5139         (string-append "mirror://sourceforge/samtools/samtools/"
5140                        version "/samtools-" version ".tar.bz2"))
5141        (sha256
5142         (base32
5143          "10ilqbmm7ri8z431sn90lvbjwizd0hhkf9rcqw8j823hf26nhgq8"))
5144        (modules '((guix build utils)))
5145        (snippet '(begin
5146                    ;; Delete bundled htslib.
5147                    (delete-file-recursively "htslib-1.9")
5148                    #t))))
5149     (build-system gnu-build-system)
5150     (arguments
5151      `(#:modules ((ice-9 ftw)
5152                   (ice-9 regex)
5153                   (guix build gnu-build-system)
5154                   (guix build utils))
5155        #:configure-flags (list "--with-ncurses")
5156        #:phases
5157        (modify-phases %standard-phases
5158          (add-after 'unpack 'patch-tests
5159            (lambda _
5160              (substitute* "test/test.pl"
5161                ;; The test script calls out to /bin/bash
5162                (("/bin/bash") (which "bash")))
5163              #t))
5164          (add-after 'install 'install-library
5165            (lambda* (#:key outputs #:allow-other-keys)
5166              (let ((lib (string-append (assoc-ref outputs "out") "/lib")))
5167                (install-file "libbam.a" lib)
5168                #t)))
5169          (add-after 'install 'install-headers
5170            (lambda* (#:key outputs #:allow-other-keys)
5171              (let ((include (string-append (assoc-ref outputs "out")
5172                                            "/include/samtools/")))
5173                (for-each (lambda (file)
5174                            (install-file file include))
5175                          (scandir "." (lambda (name) (string-match "\\.h$" name))))
5176                #t))))))
5177     (native-inputs `(("pkg-config" ,pkg-config)))
5178     (inputs
5179      `(("htslib" ,htslib)
5180        ("ncurses" ,ncurses)
5181        ("perl" ,perl)
5182        ("python" ,python)
5183        ("zlib" ,zlib)))
5184     (home-page "http://samtools.sourceforge.net")
5185     (synopsis "Utilities to efficiently manipulate nucleotide sequence alignments")
5186     (description
5187      "Samtools implements various utilities for post-processing nucleotide
5188 sequence alignments in the SAM, BAM, and CRAM formats, including indexing,
5189 variant calling (in conjunction with bcftools), and a simple alignment
5190 viewer.")
5191     (license license:expat)))
5192
5193 (define-public samtools-0.1
5194   ;; This is the most recent version of the 0.1 line of samtools.  The input
5195   ;; and output formats differ greatly from that used and produced by samtools
5196   ;; 1.x and is still used in many bioinformatics pipelines.
5197   (package (inherit samtools)
5198     (version "0.1.19")
5199     (source
5200      (origin
5201        (method url-fetch)
5202        (uri
5203         (string-append "mirror://sourceforge/samtools/samtools/"
5204                        version "/samtools-" version ".tar.bz2"))
5205        (sha256
5206         (base32 "1m33xsfwz0s8qi45lylagfllqg7fphf4dr0780rsvw75av9wk06h"))))
5207     (arguments
5208      `(#:tests? #f ;no "check" target
5209        #:make-flags
5210        (list "LIBCURSES=-lncurses")
5211        ,@(substitute-keyword-arguments (package-arguments samtools)
5212            ((#:phases phases)
5213             `(modify-phases ,phases
5214                (replace 'install
5215                  (lambda* (#:key outputs #:allow-other-keys)
5216                    (let ((bin (string-append
5217                                (assoc-ref outputs "out") "/bin")))
5218                      (mkdir-p bin)
5219                      (install-file "samtools" bin)
5220                      #t)))
5221                (delete 'patch-tests)
5222                (delete 'configure))))))))
5223
5224 (define-public mosaik
5225   (let ((commit "5c25216d3522d6a33e53875cd76a6d65001e4e67"))
5226     (package
5227       (name "mosaik")
5228       (version "2.2.30")
5229       (source (origin
5230                 ;; There are no release tarballs nor tags.
5231                 (method git-fetch)
5232                 (uri (git-reference
5233                       (url "https://github.com/wanpinglee/MOSAIK.git")
5234                       (commit commit)))
5235                 (file-name (string-append name "-" version))
5236                 (sha256
5237                  (base32
5238                   "17gj3s07cm77r41z92awh0bim7w7q7fbn0sf5nkqmcm1vw052qgw"))))
5239       (build-system gnu-build-system)
5240       (arguments
5241        `(#:tests? #f ; no tests
5242          #:make-flags (list "CC=gcc")
5243          #:phases
5244          (modify-phases %standard-phases
5245            (replace 'configure
5246                     (lambda _ (chdir "src") #t))
5247            (replace 'install
5248                     (lambda* (#:key outputs #:allow-other-keys)
5249                       (let ((bin (string-append (assoc-ref outputs "out")
5250                                                 "/bin")))
5251                         (mkdir-p bin)
5252                         (copy-recursively "../bin" bin)
5253                         #t))))))
5254       (inputs
5255        `(("perl" ,perl)
5256          ("zlib:static" ,zlib "static")
5257          ("zlib" ,zlib)))
5258       (supported-systems '("x86_64-linux"))
5259       (home-page "https://github.com/wanpinglee/MOSAIK")
5260       (synopsis "Map nucleotide sequence reads to reference genomes")
5261       (description
5262        "MOSAIK is a program for mapping second and third-generation sequencing
5263 reads to a reference genome.  MOSAIK can align reads generated by all the
5264 major sequencing technologies, including Illumina, Applied Biosystems SOLiD,
5265 Roche 454, Ion Torrent and Pacific BioSciences SMRT.")
5266       ;; MOSAIK is released under the GPLv2+ with the exception of third-party
5267       ;; code released into the public domain:
5268       ;; 1. fastlz by Ariya Hidayat - http://www.fastlz.org/
5269       ;; 2. MD5 implementation - RSA Data Security, RFC 1321
5270       (license (list license:gpl2+ license:public-domain)))))
5271
5272 (define-public ngs-sdk
5273   (package
5274     (name "ngs-sdk")
5275     (version "2.9.3")
5276     (source (origin
5277               (method git-fetch)
5278               (uri (git-reference
5279                     (url "https://github.com/ncbi/ngs.git")
5280                     (commit version)))
5281               (file-name (git-file-name name version))
5282               (sha256
5283                (base32
5284                 "17c0v1nah3g3d2ib5bbi0vhma1ghd6vb9xycavqsh64lhp840rk3"))))
5285     (build-system gnu-build-system)
5286     (arguments
5287      `(#:parallel-build? #f ; not supported
5288        #:tests? #f ; no "check" target
5289        #:phases
5290        (modify-phases %standard-phases
5291          (replace 'configure
5292            (lambda* (#:key outputs #:allow-other-keys)
5293              (let ((out (assoc-ref outputs "out")))
5294                ;; Allow 'konfigure.perl' to find 'package.prl'.
5295                (setenv "PERL5LIB"
5296                        (string-append ".:" (getenv "PERL5LIB")))
5297
5298                ;; The 'configure' script doesn't recognize things like
5299                ;; '--enable-fast-install'.
5300                (invoke "./configure"
5301                        (string-append "--build-prefix=" (getcwd) "/build")
5302                        (string-append "--prefix=" out))
5303                #t)))
5304          (add-after 'unpack 'enter-dir
5305            (lambda _ (chdir "ngs-sdk") #t)))))
5306     (native-inputs `(("perl" ,perl)))
5307     ;; According to the test
5308     ;;   unless ($MARCH =~ /x86_64/i || $MARCH =~ /i?86/i)
5309     ;; in ngs-sdk/setup/konfigure.perl
5310     (supported-systems '("i686-linux" "x86_64-linux"))
5311     (home-page "https://github.com/ncbi/ngs")
5312     (synopsis "API for accessing Next Generation Sequencing data")
5313     (description
5314      "NGS is a domain-specific API for accessing reads, alignments and pileups
5315 produced from Next Generation Sequencing.  The API itself is independent from
5316 any particular back-end implementation, and supports use of multiple back-ends
5317 simultaneously.")
5318     (license license:public-domain)))
5319
5320 (define-public java-ngs
5321   (package (inherit ngs-sdk)
5322     (name "java-ngs")
5323     (arguments
5324      `(,@(substitute-keyword-arguments
5325              `(#:modules ((guix build gnu-build-system)
5326                           (guix build utils)
5327                           (srfi srfi-1)
5328                           (srfi srfi-26))
5329                          ,@(package-arguments ngs-sdk))
5330            ((#:phases phases)
5331             `(modify-phases ,phases
5332                (replace 'enter-dir (lambda _ (chdir "ngs-java") #t)))))))
5333     (inputs
5334      `(("jdk" ,icedtea "jdk")
5335        ("ngs-sdk" ,ngs-sdk)))
5336     (synopsis "Java bindings for NGS SDK")))
5337
5338 (define-public ncbi-vdb
5339   (package
5340     (name "ncbi-vdb")
5341     (version "2.9.3")
5342     (source (origin
5343               (method git-fetch)
5344               (uri (git-reference
5345                     (url "https://github.com/ncbi/ncbi-vdb.git")
5346                     (commit version)))
5347               (file-name (git-file-name name version))
5348               (sha256
5349                (base32
5350                 "1l4ny67nxwv1lagk9wwjbrgm7ln7adci6dnpc7k1yaln6shj0qpm"))))
5351     (build-system gnu-build-system)
5352     (arguments
5353      `(#:parallel-build? #f ; not supported
5354        #:tests? #f ; no "check" target
5355        #:phases
5356        (modify-phases %standard-phases
5357          (add-after 'unpack 'make-files-writable
5358            (lambda _ (for-each make-file-writable (find-files "." ".*")) #t))
5359          (add-before 'configure 'set-perl-search-path
5360            (lambda _
5361              ;; Work around "dotless @INC" build failure.
5362              (setenv "PERL5LIB"
5363                      (string-append (getcwd) "/setup:"
5364                                     (getenv "PERL5LIB")))
5365              #t))
5366          (replace 'configure
5367            (lambda* (#:key inputs outputs #:allow-other-keys)
5368              (let ((out (assoc-ref outputs "out")))
5369                ;; Override include path for libmagic
5370                (substitute* "setup/package.prl"
5371                  (("name => 'magic', Include => '/usr/include'")
5372                   (string-append "name=> 'magic', Include => '"
5373                                  (assoc-ref inputs "libmagic")
5374                                  "/include" "'")))
5375
5376                ;; Install kdf5 library (needed by sra-tools)
5377                (substitute* "build/Makefile.install"
5378                  (("LIBRARIES_TO_INSTALL =")
5379                   "LIBRARIES_TO_INSTALL = kdf5.$(VERSION_LIBX) kdf5.$(VERSION_SHLX)"))
5380
5381                (substitute* "build/Makefile.env"
5382                  (("CFLAGS      =" prefix)
5383                   (string-append prefix "-msse2 ")))
5384
5385                ;; Override search path for ngs-java
5386                (substitute* "setup/package.prl"
5387                  (("/usr/local/ngs/ngs-java")
5388                   (assoc-ref inputs "java-ngs")))
5389
5390                ;; The 'configure' script doesn't recognize things like
5391                ;; '--enable-fast-install'.
5392                (invoke "./configure"
5393                        (string-append "--build-prefix=" (getcwd) "/build")
5394                        (string-append "--prefix=" (assoc-ref outputs "out"))
5395                        (string-append "--debug")
5396                        (string-append "--with-xml2-prefix="
5397                                       (assoc-ref inputs "libxml2"))
5398                        (string-append "--with-ngs-sdk-prefix="
5399                                       (assoc-ref inputs "ngs-sdk"))
5400                        (string-append "--with-hdf5-prefix="
5401                                       (assoc-ref inputs "hdf5")))
5402                #t)))
5403          (add-after 'install 'install-interfaces
5404            (lambda* (#:key outputs #:allow-other-keys)
5405              ;; Install interface libraries.  On i686 the interface libraries
5406              ;; are installed to "linux/gcc/i386", so we need to use the Linux
5407              ;; architecture name ("i386") instead of the target system prefix
5408              ;; ("i686").
5409              (mkdir (string-append (assoc-ref outputs "out") "/ilib"))
5410              (copy-recursively (string-append "build/ncbi-vdb/linux/gcc/"
5411                                               ,(system->linux-architecture
5412                                                 (or (%current-target-system)
5413                                                     (%current-system)))
5414                                               "/rel/ilib")
5415                                (string-append (assoc-ref outputs "out")
5416                                               "/ilib"))
5417              ;; Install interface headers
5418              (copy-recursively "interfaces"
5419                                (string-append (assoc-ref outputs "out")
5420                                               "/include"))
5421              #t))
5422          ;; These files are needed by sra-tools.
5423          (add-after 'install 'install-configuration-files
5424            (lambda* (#:key outputs #:allow-other-keys)
5425              (let ((target (string-append (assoc-ref outputs "out") "/kfg")))
5426                (mkdir target)
5427                (install-file "libs/kfg/default.kfg" target)
5428                (install-file "libs/kfg/certs.kfg" target))
5429              #t)))))
5430     (inputs
5431      `(("libxml2" ,libxml2)
5432        ("ngs-sdk" ,ngs-sdk)
5433        ("java-ngs" ,java-ngs)
5434        ("libmagic" ,file)
5435        ("hdf5" ,hdf5)))
5436     (native-inputs `(("perl" ,perl)))
5437     ;; NCBI-VDB requires SSE capability.
5438     (supported-systems '("i686-linux" "x86_64-linux"))
5439     (home-page "https://github.com/ncbi/ncbi-vdb")
5440     (synopsis "Database engine for genetic information")
5441     (description
5442      "The NCBI-VDB library implements a highly compressed columnar data
5443 warehousing engine that is most often used to store genetic information.
5444 Databases are stored in a portable image within the file system, and can be
5445 accessed/downloaded on demand across HTTP.")
5446     (license license:public-domain)))
5447
5448 (define-public plink
5449   (package
5450     (name "plink")
5451     (version "1.07")
5452     (source
5453      (origin
5454        (method url-fetch)
5455        (uri (string-append
5456              "http://pngu.mgh.harvard.edu/~purcell/plink/dist/plink-"
5457              version "-src.zip"))
5458        (sha256
5459         (base32 "0as8gxm4pjyc8dxmm1sl873rrd7wn5qs0l29nqfnl31x8i467xaa"))
5460        (patches (search-patches "plink-1.07-unclobber-i.patch"
5461                                 "plink-endian-detection.patch"))))
5462     (build-system gnu-build-system)
5463     (arguments
5464      '(#:tests? #f ;no "check" target
5465        #:make-flags (list (string-append "LIB_LAPACK="
5466                                          (assoc-ref %build-inputs "lapack")
5467                                          "/lib/liblapack.so")
5468                           "WITH_LAPACK=1"
5469                           "FORCE_DYNAMIC=1"
5470                           ;; disable phoning home
5471                           "WITH_WEBCHECK=")
5472        #:phases
5473        (modify-phases %standard-phases
5474          ;; no "configure" script
5475          (delete 'configure)
5476          (replace 'install
5477                   (lambda* (#:key outputs #:allow-other-keys)
5478                     (let ((bin (string-append (assoc-ref outputs "out")
5479                                               "/bin/")))
5480                       (install-file "plink" bin)
5481                       #t))))))
5482     (inputs
5483      `(("zlib" ,zlib)
5484        ("lapack" ,lapack)))
5485     (native-inputs
5486      `(("unzip" ,unzip)))
5487     (home-page "http://pngu.mgh.harvard.edu/~purcell/plink/")
5488     (synopsis "Whole genome association analysis toolset")
5489     (description
5490      "PLINK is a whole genome association analysis toolset, designed to
5491 perform a range of basic, large-scale analyses in a computationally efficient
5492 manner.  The focus of PLINK is purely on analysis of genotype/phenotype data,
5493 so there is no support for steps prior to this (e.g. study design and
5494 planning, generating genotype or CNV calls from raw data).  Through
5495 integration with gPLINK and Haploview, there is some support for the
5496 subsequent visualization, annotation and storage of results.")
5497     ;; Code is released under GPLv2, except for fisher.h, which is under
5498     ;; LGPLv2.1+
5499     (license (list license:gpl2 license:lgpl2.1+))))
5500
5501 (define-public plink-ng
5502   (package (inherit plink)
5503     (name "plink-ng")
5504     (version "1.90b4")
5505     (source
5506      (origin
5507        (method git-fetch)
5508        (uri (git-reference
5509              (url "https://github.com/chrchang/plink-ng.git")
5510              (commit (string-append "v" version))))
5511        (file-name (git-file-name name version))
5512        (sha256
5513         (base32 "02npdwgkpfkdnhw819rhj5kw02a5k5m90b14zq9zzya4hyg929c0"))))
5514     (build-system gnu-build-system)
5515     (arguments
5516      '(#:tests? #f ;no "check" target
5517        #:make-flags (list "BLASFLAGS=-llapack -lopenblas"
5518                           "CFLAGS=-Wall -O2 -DDYNAMIC_ZLIB=1"
5519                           "ZLIB=-lz"
5520                           "-f" "Makefile.std")
5521        #:phases
5522        (modify-phases %standard-phases
5523          (add-after 'unpack 'chdir
5524            (lambda _ (chdir "1.9") #t))
5525          (delete 'configure) ; no "configure" script
5526          (replace 'install
5527                   (lambda* (#:key outputs #:allow-other-keys)
5528                     (let ((bin (string-append (assoc-ref outputs "out")
5529                                               "/bin/")))
5530                       (install-file "plink" bin)
5531                       #t))))))
5532     (inputs
5533      `(("zlib" ,zlib)
5534        ("lapack" ,lapack)
5535        ("openblas" ,openblas)))
5536     (home-page "https://www.cog-genomics.org/plink/")
5537     (license license:gpl3+)))
5538
5539 (define-public smithlab-cpp
5540   (let ((revision "1")
5541         (commit "728a097bec88c6f4b8528b685932049e660eff2e"))
5542     (package
5543       (name "smithlab-cpp")
5544       (version (string-append "0." revision "." (string-take commit 7)))
5545       (source (origin
5546                 (method git-fetch)
5547                 (uri (git-reference
5548                       (url "https://github.com/smithlabcode/smithlab_cpp.git")
5549                       (commit commit)))
5550                 (file-name (string-append name "-" version "-checkout"))
5551                 (sha256
5552                  (base32
5553                   "0d476lmj312xk77kr9fzrv7z1bv96yfyx0w7y62ycmnfbx32ll74"))))
5554       (build-system gnu-build-system)
5555       (arguments
5556        `(#:modules ((guix build gnu-build-system)
5557                     (guix build utils)
5558                     (srfi srfi-26))
5559          #:tests? #f ;no "check" target
5560          #:phases
5561          (modify-phases %standard-phases
5562            (add-after 'unpack 'use-samtools-headers
5563             (lambda _
5564               (substitute* '("SAM.cpp"
5565                              "SAM.hpp")
5566                 (("sam.h") "samtools/sam.h"))
5567               #t))
5568            (replace 'install
5569             (lambda* (#:key outputs #:allow-other-keys)
5570               (let* ((out     (assoc-ref outputs "out"))
5571                      (lib     (string-append out "/lib"))
5572                      (include (string-append out "/include/smithlab-cpp")))
5573                 (mkdir-p lib)
5574                 (mkdir-p include)
5575                 (for-each (cut install-file <> lib)
5576                           (find-files "." "\\.o$"))
5577                 (for-each (cut install-file <> include)
5578                           (find-files "." "\\.hpp$")))
5579               #t))
5580            (delete 'configure))))
5581       (inputs
5582        `(("samtools" ,samtools-0.1)
5583          ("zlib" ,zlib)))
5584       (home-page "https://github.com/smithlabcode/smithlab_cpp")
5585       (synopsis "C++ helper library for functions used in Smith lab projects")
5586       (description
5587        "Smithlab CPP is a C++ library that includes functions used in many of
5588 the Smith lab bioinformatics projects, such as a wrapper around Samtools data
5589 structures, classes for genomic regions, mapped sequencing reads, etc.")
5590       (license license:gpl3+))))
5591
5592 (define-public preseq
5593   (package
5594     (name "preseq")
5595     (version "2.0.3")
5596     (source (origin
5597               (method url-fetch)
5598               (uri (string-append "https://github.com/smithlabcode/preseq/"
5599                                   "releases/download/v" version
5600                                   "/preseq_v" version ".tar.bz2"))
5601               (sha256
5602                (base32 "149x9xmk1wy1gff85325yfzqc0qk4sgp1w6gbyj9cnji4x1dszbl"))
5603               (modules '((guix build utils)))
5604               (snippet '(begin
5605                           ;; Remove bundled samtools.
5606                           (delete-file-recursively "samtools")
5607                           #t))))
5608     (build-system gnu-build-system)
5609     (arguments
5610      `(#:tests? #f ;no "check" target
5611        #:phases
5612        (modify-phases %standard-phases
5613          (delete 'configure))
5614        #:make-flags
5615        (list (string-append "PREFIX="
5616                             (assoc-ref %outputs "out"))
5617              (string-append "LIBBAM="
5618                             (assoc-ref %build-inputs "samtools")
5619                             "/lib/libbam.a")
5620              (string-append "SMITHLAB_CPP="
5621                             (assoc-ref %build-inputs "smithlab-cpp")
5622                             "/lib")
5623              "PROGS=preseq"
5624              "INCLUDEDIRS=$(SMITHLAB_CPP)/../include/smithlab-cpp $(SAMTOOLS_DIR)")))
5625     (inputs
5626      `(("gsl" ,gsl)
5627        ("samtools" ,samtools-0.1)
5628        ("smithlab-cpp" ,smithlab-cpp)
5629        ("zlib" ,zlib)))
5630     (home-page "http://smithlabresearch.org/software/preseq/")
5631     (synopsis "Program for analyzing library complexity")
5632     (description
5633      "The preseq package is aimed at predicting and estimating the complexity
5634 of a genomic sequencing library, equivalent to predicting and estimating the
5635 number of redundant reads from a given sequencing depth and how many will be
5636 expected from additional sequencing using an initial sequencing experiment.
5637 The estimates can then be used to examine the utility of further sequencing,
5638 optimize the sequencing depth, or to screen multiple libraries to avoid low
5639 complexity samples.")
5640     (license license:gpl3+)))
5641
5642 (define-public python-screed
5643   (package
5644     (name "python-screed")
5645     (version "1.0")
5646     (source
5647      (origin
5648        (method url-fetch)
5649        (uri (pypi-uri "screed" version))
5650        (sha256
5651         (base32
5652          "148vcb7w2wr6a4w6vs2bsxanbqibxfk490zbcbg4m61s8669zdjx"))))
5653     (build-system python-build-system)
5654     (arguments
5655      '(#:phases
5656        (modify-phases %standard-phases
5657          ;; Tests must be run after installation, as the "screed" command does
5658          ;; not exist right after building.
5659          (delete 'check)
5660          (add-after 'install 'check
5661            (lambda* (#:key inputs outputs #:allow-other-keys)
5662              (let ((out (assoc-ref outputs "out")))
5663                (setenv "PYTHONPATH"
5664                        (string-append out "/lib/python"
5665                                       (string-take (string-take-right
5666                                                     (assoc-ref inputs "python")
5667                                                     5) 3)
5668                                       "/site-packages:"
5669                                       (getenv "PYTHONPATH")))
5670                (setenv "PATH" (string-append out "/bin:" (getenv "PATH"))))
5671              (invoke "python" "setup.py" "test")
5672              #t)))))
5673     (native-inputs
5674      `(("python-pytest" ,python-pytest)
5675        ("python-pytest-cov" ,python-pytest-cov)
5676        ("python-pytest-runner" ,python-pytest-runner)))
5677     (inputs
5678      `(("python-bz2file" ,python-bz2file)))
5679     (home-page "https://github.com/dib-lab/screed/")
5680     (synopsis "Short read sequence database utilities")
5681     (description "Screed parses FASTA and FASTQ files and generates databases.
5682 Values such as sequence name, sequence description, sequence quality and the
5683 sequence itself can be retrieved from these databases.")
5684     (license license:bsd-3)))
5685
5686 (define-public python2-screed
5687   (package-with-python2 python-screed))
5688
5689 (define-public sra-tools
5690   (package
5691     (name "sra-tools")
5692     (version "2.9.3")
5693     (source
5694      (origin
5695        (method git-fetch)
5696        (uri (git-reference
5697              (url "https://github.com/ncbi/sra-tools.git")
5698              (commit version)))
5699        (file-name (git-file-name name version))
5700        (sha256
5701         (base32
5702          "0663gcdxkziwsmlznjxysb00621rllpbz6jwsfifq7z3dj3lwm8b"))))
5703     (build-system gnu-build-system)
5704     (arguments
5705      `(#:parallel-build? #f ; not supported
5706        #:tests? #f ; no "check" target
5707        #:make-flags
5708        (list (string-append "DEFAULT_CRT="
5709                             (assoc-ref %build-inputs "ncbi-vdb")
5710                             "/kfg/certs.kfg")
5711              (string-append "DEFAULT_KFG="
5712                             (assoc-ref %build-inputs "ncbi-vdb")
5713                             "/kfg/default.kfg")
5714              (string-append "VDB_LIBDIR="
5715                             (assoc-ref %build-inputs "ncbi-vdb")
5716                             ,(if (string-prefix? "x86_64"
5717                                                  (or (%current-target-system)
5718                                                      (%current-system)))
5719                                  "/lib64"
5720                                  "/lib32")))
5721        #:phases
5722        (modify-phases %standard-phases
5723          (add-before 'configure 'set-perl-search-path
5724            (lambda _
5725              ;; Work around "dotless @INC" build failure.
5726              (setenv "PERL5LIB"
5727                      (string-append (getcwd) "/setup:"
5728                                     (getenv "PERL5LIB")))
5729              #t))
5730          (replace 'configure
5731            (lambda* (#:key inputs outputs #:allow-other-keys)
5732              ;; The build system expects a directory containing the sources and
5733              ;; raw build output of ncbi-vdb, including files that are not
5734              ;; installed.  Since we are building against an installed version of
5735              ;; ncbi-vdb, the following modifications are needed.
5736              (substitute* "setup/konfigure.perl"
5737                ;; Make the configure script look for the "ilib" directory of
5738                ;; "ncbi-vdb" without first checking for the existence of a
5739                ;; matching library in its "lib" directory.
5740                (("^            my \\$f = File::Spec->catdir\\(\\$libdir, \\$lib\\);")
5741                 "my $f = File::Spec->catdir($ilibdir, $ilib);")
5742                ;; Look for interface libraries in ncbi-vdb's "ilib" directory.
5743                (("my \\$ilibdir = File::Spec->catdir\\(\\$builddir, 'ilib'\\);")
5744                 "my $ilibdir = File::Spec->catdir($dir, 'ilib');"))
5745
5746              ;; Dynamic linking
5747              (substitute* "tools/copycat/Makefile"
5748                (("smagic-static") "lmagic"))
5749
5750              ;; The 'configure' script doesn't recognize things like
5751              ;; '--enable-fast-install'.
5752              (invoke "./configure"
5753                      (string-append "--build-prefix=" (getcwd) "/build")
5754                      (string-append "--prefix=" (assoc-ref outputs "out"))
5755                      (string-append "--debug")
5756                      (string-append "--with-fuse-prefix="
5757                                     (assoc-ref inputs "fuse"))
5758                      (string-append "--with-magic-prefix="
5759                                     (assoc-ref inputs "libmagic"))
5760                      ;; TODO: building with libxml2 fails with linker errors
5761                      ;; (string-append "--with-xml2-prefix="
5762                      ;;                (assoc-ref inputs "libxml2"))
5763                      (string-append "--with-ncbi-vdb-sources="
5764                                     (assoc-ref inputs "ncbi-vdb"))
5765                      (string-append "--with-ncbi-vdb-build="
5766                                     (assoc-ref inputs "ncbi-vdb"))
5767                      (string-append "--with-ngs-sdk-prefix="
5768                                     (assoc-ref inputs "ngs-sdk"))
5769                      (string-append "--with-hdf5-prefix="
5770                                     (assoc-ref inputs "hdf5")))
5771              #t)))))
5772     (native-inputs `(("perl" ,perl)))
5773     (inputs
5774      `(("ngs-sdk" ,ngs-sdk)
5775        ("ncbi-vdb" ,ncbi-vdb)
5776        ("libmagic" ,file)
5777        ("fuse" ,fuse)
5778        ("hdf5" ,hdf5)
5779        ("zlib" ,zlib)))
5780     (home-page "http://www.ncbi.nlm.nih.gov/Traces/sra/sra.cgi?view=software")
5781     (synopsis "Tools and libraries for reading and writing sequencing data")
5782     (description
5783      "The SRA Toolkit from NCBI is a collection of tools and libraries for
5784 reading of sequencing files from the Sequence Read Archive (SRA) database and
5785 writing files into the .sra format.")
5786     (license license:public-domain)))
5787
5788 (define-public seqan
5789   (package
5790     (name "seqan")
5791     (version "2.4.0")
5792     (source (origin
5793               (method url-fetch)
5794               (uri (string-append "https://github.com/seqan/seqan/releases/"
5795                                   "download/seqan-v" version
5796                                   "/seqan-library-" version ".tar.xz"))
5797               (sha256
5798                (base32
5799                 "19a1rlxx03qy1i1iriicly68w64yjxbv24g9gdywnfmq998v35yx"))))
5800     ;; The documentation is 7.8MB and the includes are 3.6MB heavy, so it
5801     ;; makes sense to split the outputs.
5802     (outputs '("out" "doc"))
5803     (build-system trivial-build-system)
5804     (arguments
5805      `(#:modules ((guix build utils))
5806        #:builder
5807        (begin
5808          (use-modules (guix build utils))
5809          (let ((tar (assoc-ref %build-inputs "tar"))
5810                (xz  (assoc-ref %build-inputs "xz"))
5811                (out (assoc-ref %outputs "out"))
5812                (doc (assoc-ref %outputs "doc")))
5813            (setenv "PATH" (string-append tar "/bin:" xz "/bin"))
5814            (invoke "tar" "xvf" (assoc-ref %build-inputs "source"))
5815            (chdir (string-append "seqan-library-" ,version))
5816            (copy-recursively "include" (string-append out "/include"))
5817            (copy-recursively "share"  (string-append doc "/share"))
5818            #t))))
5819     (native-inputs
5820      `(("source" ,source)
5821        ("tar" ,tar)
5822        ("xz" ,xz)))
5823     (home-page "http://www.seqan.de")
5824     (synopsis "Library for nucleotide sequence analysis")
5825     (description
5826      "SeqAn is a C++ library of efficient algorithms and data structures for
5827 the analysis of sequences with the focus on biological data.  It contains
5828 algorithms and data structures for string representation and their
5829 manipulation, online and indexed string search, efficient I/O of
5830 bioinformatics file formats, sequence alignment, and more.")
5831     (license license:bsd-3)))
5832
5833 (define-public seqan-1
5834   (package (inherit seqan)
5835     (name "seqan")
5836     (version "1.4.2")
5837     (source (origin
5838               (method url-fetch)
5839               (uri (string-append "http://packages.seqan.de/seqan-library/"
5840                                   "seqan-library-" version ".tar.bz2"))
5841               (sha256
5842                (base32
5843                 "05s3wrrwn50f81aklfm65i4a749zag1vr8z03k21xm0pdxy47yvp"))))
5844     ;; The documentation is 7.8MB and the includes are 3.6MB heavy, so it
5845     ;; makes sense to split the outputs.
5846     (outputs '("out" "doc"))
5847     (build-system trivial-build-system)
5848     (arguments
5849      `(#:modules ((guix build utils))
5850        #:builder
5851        (begin
5852          (use-modules (guix build utils))
5853          (let ((tar  (assoc-ref %build-inputs "tar"))
5854                (bzip (assoc-ref %build-inputs "bzip2"))
5855                (out  (assoc-ref %outputs "out"))
5856                (doc  (assoc-ref %outputs "doc")))
5857            (setenv "PATH" (string-append tar "/bin:" bzip "/bin"))
5858            (invoke "tar" "xvf" (assoc-ref %build-inputs "source"))
5859            (chdir (string-append "seqan-library-" ,version))
5860            (copy-recursively "include" (string-append out "/include"))
5861            (copy-recursively "share"  (string-append doc "/share"))
5862            #t))))
5863     (native-inputs
5864      `(("source" ,source)
5865        ("tar" ,tar)
5866        ("bzip2" ,bzip2)))))
5867
5868 (define-public seqmagick
5869   (package
5870     (name "seqmagick")
5871     (version "0.7.0")
5872     (source
5873      (origin
5874        (method url-fetch)
5875        (uri (pypi-uri "seqmagick" version))
5876        (sha256
5877         (base32
5878          "12bfyp8nqi0hd36rmj450aygafp01qy3hkbvlwn3bk39pyjjkgg5"))))
5879     (build-system python-build-system)
5880     (inputs
5881      `(("python-biopython" ,python-biopython)))
5882     (native-inputs
5883      `(("python-nose" ,python-nose)))
5884     (home-page "https://github.com/fhcrc/seqmagick")
5885     (synopsis "Tools for converting and modifying sequence files")
5886     (description
5887      "Bioinformaticians often have to convert sequence files between formats
5888 and do little manipulations on them, and it's not worth writing scripts for
5889 that.  Seqmagick is a utility to expose the file format conversion in
5890 BioPython in a convenient way.  Instead of having a big mess of scripts, there
5891 is one that takes arguments.")
5892     (license license:gpl3)))
5893
5894 (define-public seqtk
5895   (package
5896     (name "seqtk")
5897     (version "1.3")
5898     (source (origin
5899               (method git-fetch)
5900               (uri (git-reference
5901                     (url "https://github.com/lh3/seqtk.git")
5902                     (commit (string-append "v" version))))
5903               (file-name (git-file-name name version))
5904               (sha256
5905                (base32
5906                 "1bfzlqa84b5s1qi22blmmw2s8xdyp9h9ydcq22pfjhh5gab3yz6l"))))
5907     (build-system gnu-build-system)
5908     (arguments
5909      `(#:phases
5910        (modify-phases %standard-phases
5911          (delete 'configure)
5912          (replace 'check
5913            ;; There are no tests, so we just run a sanity check.
5914            (lambda _ (invoke "./seqtk" "seq") #t))
5915          (replace 'install
5916            (lambda* (#:key outputs #:allow-other-keys)
5917              (let ((bin (string-append (assoc-ref outputs "out") "/bin/")))
5918                (install-file "seqtk" bin)
5919                #t))))))
5920     (inputs
5921      `(("zlib" ,zlib)))
5922     (home-page "https://github.com/lh3/seqtk")
5923     (synopsis "Toolkit for processing biological sequences in FASTA/Q format")
5924     (description
5925      "Seqtk is a fast and lightweight tool for processing sequences in the
5926 FASTA or FASTQ format.  It parses both FASTA and FASTQ files which can be
5927 optionally compressed by gzip.")
5928       (license license:expat)))
5929
5930 (define-public snap-aligner
5931   (package
5932     (name "snap-aligner")
5933     (version "1.0beta.18")
5934     (source (origin
5935               (method git-fetch)
5936               (uri (git-reference
5937                     (url "https://github.com/amplab/snap.git")
5938                     (commit (string-append "v" version))))
5939               (file-name (git-file-name name version))
5940               (sha256
5941                (base32
5942                 "01w3qq4wm07z73vky0cfwlmrbf50n3w722cxrlzxfi99mnb808d8"))))
5943     (build-system gnu-build-system)
5944     (arguments
5945      '(#:phases
5946        (modify-phases %standard-phases
5947          (delete 'configure)
5948          (replace 'check (lambda _ (invoke "./unit_tests") #t))
5949          (replace 'install
5950            (lambda* (#:key outputs #:allow-other-keys)
5951              (let* ((out (assoc-ref outputs "out"))
5952                     (bin (string-append out "/bin")))
5953                (install-file "snap-aligner" bin)
5954                (install-file "SNAPCommand" bin)
5955                #t))))))
5956     (native-inputs
5957      `(("zlib" ,zlib)))
5958     (home-page "http://snap.cs.berkeley.edu/")
5959     (synopsis "Short read DNA sequence aligner")
5960     (description
5961      "SNAP is a fast and accurate aligner for short DNA reads.  It is
5962 optimized for modern read lengths of 100 bases or higher, and takes advantage
5963 of these reads to align data quickly through a hash-based indexing scheme.")
5964     ;; 32-bit systems are not supported by the unpatched code.
5965     ;; Following the bug reports https://github.com/amplab/snap/issues/68 and
5966     ;; https://bugs.debian.org/cgi-bin/bugreport.cgi?bug=812378 we see that
5967     ;; systems without a lot of memory cannot make good use of this program.
5968     (supported-systems '("x86_64-linux"))
5969     (license license:asl2.0)))
5970
5971 (define-public sortmerna
5972   (package
5973     (name "sortmerna")
5974     (version "2.1b")
5975     (source
5976      (origin
5977        (method git-fetch)
5978        (uri (git-reference
5979              (url "https://github.com/biocore/sortmerna.git")
5980              (commit version)))
5981        (file-name (git-file-name name version))
5982        (sha256
5983         (base32
5984          "0j3mbz4n25738yijmjbr5r4fyvkgm8v5vn3sshyfvmyqf5q9byqf"))))
5985     (build-system gnu-build-system)
5986     (outputs '("out"      ;for binaries
5987                "db"))     ;for sequence databases
5988     (arguments
5989      `(#:phases
5990        (modify-phases %standard-phases
5991          (replace 'install
5992            (lambda* (#:key outputs #:allow-other-keys)
5993              (let* ((out   (assoc-ref outputs "out"))
5994                     (bin   (string-append out "/bin"))
5995                     (db    (assoc-ref outputs "db"))
5996                     (share
5997                      (string-append db "/share/sortmerna/rRNA_databases")))
5998                (install-file "sortmerna" bin)
5999                (install-file "indexdb_rna" bin)
6000                (for-each (lambda (file)
6001                            (install-file file share))
6002                          (find-files "rRNA_databases" ".*fasta"))
6003                #t))))))
6004     (inputs
6005      `(("zlib" ,zlib)))
6006     (home-page "http://bioinfo.lifl.fr/RNA/sortmerna")
6007     (synopsis "Biological sequence analysis tool for NGS reads")
6008     (description
6009      "SortMeRNA is a biological sequence analysis tool for filtering, mapping
6010 and operational taxonomic unit (OTU) picking of next generation
6011 sequencing (NGS) reads.  The core algorithm is based on approximate seeds and
6012 allows for fast and sensitive analyses of nucleotide sequences.  The main
6013 application of SortMeRNA is filtering rRNA from metatranscriptomic data.")
6014     ;; The source includes x86 specific code
6015     (supported-systems '("x86_64-linux" "i686-linux"))
6016     (license license:lgpl3)))
6017
6018 (define-public star
6019   (package
6020     (name "star")
6021     (version "2.6.0c")
6022     (source (origin
6023               (method git-fetch)
6024               (uri (git-reference
6025                     (url "https://github.com/alexdobin/STAR.git")
6026                     (commit version)))
6027               (file-name (string-append name "-" version "-checkout"))
6028               (sha256
6029                (base32
6030                 "04cj6jw8d9q6lk9c78wa4fky6jdlicf1d13plq7182h8vqiz8p59"))
6031               (modules '((guix build utils)))
6032               (snippet
6033                '(begin
6034                   (substitute* "source/Makefile"
6035                     (("/bin/rm") "rm"))
6036                   ;; Remove pre-built binaries and bundled htslib sources.
6037                   (delete-file-recursively "bin/MacOSX_x86_64")
6038                   (delete-file-recursively "bin/Linux_x86_64")
6039                   (delete-file-recursively "bin/Linux_x86_64_static")
6040                   (delete-file-recursively "source/htslib")
6041                   #t))))
6042     (build-system gnu-build-system)
6043     (arguments
6044      '(#:tests? #f ;no check target
6045        #:make-flags '("STAR")
6046        #:phases
6047        (modify-phases %standard-phases
6048          (add-after 'unpack 'enter-source-dir
6049            (lambda _ (chdir "source") #t))
6050          (add-after 'enter-source-dir 'make-reproducible
6051            (lambda _
6052              (substitute* "Makefile"
6053                (("(COMPILATION_TIME_PLACE=\")(.*)(\")" _ pre mid post)
6054                 (string-append pre "Built with Guix" post)))
6055              #t))
6056          (add-after 'enter-source-dir 'do-not-use-bundled-htslib
6057            (lambda _
6058              (substitute* "Makefile"
6059                (("(Depend.list: \\$\\(SOURCES\\) parametersDefault\\.xxd) htslib"
6060                  _ prefix) prefix))
6061              (substitute* '("BAMfunctions.cpp"
6062                             "signalFromBAM.h"
6063                             "bam_cat.h"
6064                             "bam_cat.c"
6065                             "STAR.cpp"
6066                             "bamRemoveDuplicates.cpp")
6067                (("#include \"htslib/([^\"]+\\.h)\"" _ header)
6068                 (string-append "#include <" header ">")))
6069              (substitute* "IncludeDefine.h"
6070                (("\"htslib/(htslib/[^\"]+.h)\"" _ header)
6071                 (string-append "<" header ">")))
6072              #t))
6073          (replace 'install
6074            (lambda* (#:key outputs #:allow-other-keys)
6075              (let ((bin (string-append (assoc-ref outputs "out") "/bin/")))
6076                (install-file "STAR" bin))
6077              #t))
6078          (delete 'configure))))
6079     (native-inputs
6080      `(("xxd" ,xxd)))
6081     (inputs
6082      `(("htslib" ,htslib)
6083        ("zlib" ,zlib)))
6084     (home-page "https://github.com/alexdobin/STAR")
6085     (synopsis "Universal RNA-seq aligner")
6086     (description
6087      "The Spliced Transcripts Alignment to a Reference (STAR) software is
6088 based on a previously undescribed RNA-seq alignment algorithm that uses
6089 sequential maximum mappable seed search in uncompressed suffix arrays followed
6090 by seed clustering and stitching procedure.  In addition to unbiased de novo
6091 detection of canonical junctions, STAR can discover non-canonical splices and
6092 chimeric (fusion) transcripts, and is also capable of mapping full-length RNA
6093 sequences.")
6094     ;; Only 64-bit systems are supported according to the README.
6095     (supported-systems '("x86_64-linux" "mips64el-linux"))
6096     ;; STAR is licensed under GPLv3 or later; htslib is MIT-licensed.
6097     (license license:gpl3+)))
6098
6099 (define-public subread
6100   (package
6101     (name "subread")
6102     (version "1.6.0")
6103     (source (origin
6104               (method url-fetch)
6105               (uri (string-append "mirror://sourceforge/subread/subread-"
6106                                   version "/subread-" version "-source.tar.gz"))
6107               (sha256
6108                (base32
6109                 "0ah0n4jx6ksk2m2j7xk385x2qzmk1y4rfc6a4mfrdqrlq721w99i"))))
6110     (build-system gnu-build-system)
6111     (arguments
6112      `(#:tests? #f ;no "check" target
6113       ;; The CC and CCFLAGS variables are set to contain a lot of x86_64
6114       ;; optimizations by default, so we override these flags such that x86_64
6115       ;; flags are only added when the build target is an x86_64 system.
6116        #:make-flags
6117        (list (let ((system ,(or (%current-target-system)
6118                                 (%current-system)))
6119                    (flags '("-ggdb" "-fomit-frame-pointer"
6120                             "-ffast-math" "-funroll-loops"
6121                             "-fmessage-length=0"
6122                             "-O9" "-Wall" "-DMAKE_FOR_EXON"
6123                             "-DMAKE_STANDALONE"
6124                             "-DSUBREAD_VERSION=\\\"${SUBREAD_VERSION}\\\""))
6125                    (flags64 '("-mmmx" "-msse" "-msse2" "-msse3")))
6126                (if (string-prefix? "x86_64" system)
6127                    (string-append "CCFLAGS=" (string-join (append flags flags64)))
6128                    (string-append "CCFLAGS=" (string-join flags))))
6129              "-f" "Makefile.Linux"
6130              "CC=gcc ${CCFLAGS}")
6131        #:phases
6132        (modify-phases %standard-phases
6133          (add-after 'unpack 'enter-dir
6134            (lambda _ (chdir "src") #t))
6135          (replace 'install
6136            (lambda* (#:key outputs #:allow-other-keys)
6137              (let ((bin (string-append (assoc-ref outputs "out") "/bin/")))
6138                (mkdir-p bin)
6139                (copy-recursively "../bin" bin))
6140              #t))
6141          ;; no "configure" script
6142          (delete 'configure))))
6143     (inputs `(("zlib" ,zlib)))
6144     (home-page "http://bioinf.wehi.edu.au/subread-package/")
6145     (synopsis "Tool kit for processing next-gen sequencing data")
6146     (description
6147      "The subread package contains the following tools: subread aligner, a
6148 general-purpose read aligner; subjunc aligner: detecting exon-exon junctions
6149 and mapping RNA-seq reads; featureCounts: counting mapped reads for genomic
6150 features; exactSNP: a SNP caller that discovers SNPs by testing signals
6151 against local background noises.")
6152     (license license:gpl3+)))
6153
6154 (define-public stringtie
6155   (package
6156     (name "stringtie")
6157     (version "1.2.1")
6158     (source (origin
6159               (method url-fetch)
6160               (uri (string-append "http://ccb.jhu.edu/software/stringtie/dl/"
6161                                   "stringtie-" version ".tar.gz"))
6162               (sha256
6163                (base32
6164                 "1cqllsc1maq4kh92isi8yadgzbmnf042hlnalpk3y59aph1z3bfz"))
6165               (modules '((guix build utils)))
6166               (snippet
6167                '(begin
6168                   (delete-file-recursively "samtools-0.1.18")
6169                   #t))))
6170     (build-system gnu-build-system)
6171     (arguments
6172      `(#:tests? #f ;no test suite
6173        #:phases
6174        (modify-phases %standard-phases
6175          ;; no configure script
6176          (delete 'configure)
6177          (add-before 'build 'use-system-samtools
6178            (lambda _
6179              (substitute* "Makefile"
6180                (("stringtie: \\$\\{BAM\\}/libbam\\.a")
6181                 "stringtie: "))
6182              (substitute* '("gclib/GBam.h"
6183                             "gclib/GBam.cpp")
6184                (("#include \"(bam|sam|kstring).h\"" _ header)
6185                 (string-append "#include <samtools/" header ".h>")))
6186              #t))
6187          (add-after 'unpack 'remove-duplicate-typedef
6188            (lambda _
6189              ;; This typedef conflicts with the typedef in
6190              ;; glibc-2.25/include/bits/types.h
6191              (substitute* "gclib/GThreads.h"
6192                (("typedef long long __intmax_t;") ""))
6193              #t))
6194          (replace 'install
6195           (lambda* (#:key outputs #:allow-other-keys)
6196             (let ((bin (string-append (assoc-ref outputs "out") "/bin/")))
6197               (install-file "stringtie" bin)
6198               #t))))))
6199     (inputs
6200      `(("samtools" ,samtools-0.1)
6201        ("zlib" ,zlib)))
6202     (home-page "http://ccb.jhu.edu/software/stringtie/")
6203     (synopsis "Transcript assembly and quantification for RNA-Seq data")
6204     (description
6205      "StringTie is a fast and efficient assembler of RNA-Seq sequence
6206 alignments into potential transcripts.  It uses a novel network flow algorithm
6207 as well as an optional de novo assembly step to assemble and quantitate
6208 full-length transcripts representing multiple splice variants for each gene
6209 locus.  Its input can include not only the alignments of raw reads used by
6210 other transcript assemblers, but also alignments of longer sequences that have
6211 been assembled from those reads.  To identify differentially expressed genes
6212 between experiments, StringTie's output can be processed either by the
6213 Cuffdiff or Ballgown programs.")
6214     (license license:artistic2.0)))
6215
6216 (define-public taxtastic
6217   (package
6218     (name "taxtastic")
6219     (version "0.8.5")
6220     (source (origin
6221               (method url-fetch)
6222               (uri (pypi-uri "taxtastic" version))
6223               (sha256
6224                (base32
6225                 "03pysw79lsrvz4lwzis88j15067ffqbi4cid5pqhrlxmd6bh8rrk"))))
6226     (build-system python-build-system)
6227     (arguments
6228      `(#:python ,python-2
6229        #:phases
6230        (modify-phases %standard-phases
6231          (replace 'check
6232            (lambda _ (invoke "python" "-m" "unittest" "discover" "-v") #t)))))
6233     (propagated-inputs
6234      `(("python-sqlalchemy" ,python2-sqlalchemy)
6235        ("python-decorator" ,python2-decorator)
6236        ("python-biopython" ,python2-biopython)
6237        ("python-pandas" ,python2-pandas)
6238        ("python-psycopg2" ,python2-psycopg2)
6239        ("python-fastalite" ,python2-fastalite)
6240        ("python-pyyaml" ,python2-pyyaml)
6241        ("python-six" ,python2-six)
6242        ("python-jinja2" ,python2-jinja2)
6243        ("python-dendropy" ,python2-dendropy)))
6244     (home-page "https://github.com/fhcrc/taxtastic")
6245     (synopsis "Tools for taxonomic naming and annotation")
6246     (description
6247      "Taxtastic is software written in python used to build and maintain
6248 reference packages i.e. collections of reference trees, reference alignments,
6249 profiles, and associated taxonomic information.")
6250     (license license:gpl3+)))
6251
6252 (define-public vcftools
6253   (package
6254     (name "vcftools")
6255     (version "0.1.15")
6256     (source (origin
6257               (method url-fetch)
6258               (uri (string-append
6259                     "https://github.com/vcftools/vcftools/releases/download/v"
6260                     version "/vcftools-" version ".tar.gz"))
6261               (sha256
6262                (base32
6263                 "1qw30c45wihgy632rbz4rh3njnwj4msj46l1rsgdhyg6bgypmr1i"))))
6264     (build-system gnu-build-system)
6265     (arguments
6266      `(#:tests? #f ; no "check" target
6267        #:make-flags (list
6268                      "CFLAGS=-O2" ; override "-m64" flag
6269                      (string-append "PREFIX=" (assoc-ref %outputs "out"))
6270                      (string-append "MANDIR=" (assoc-ref %outputs "out")
6271                                     "/share/man/man1"))))
6272     (native-inputs
6273      `(("pkg-config" ,pkg-config)))
6274     (inputs
6275      `(("perl" ,perl)
6276        ("zlib" ,zlib)))
6277     (home-page "https://vcftools.github.io/")
6278     (synopsis "Tools for working with VCF files")
6279     (description
6280      "VCFtools is a program package designed for working with VCF files, such
6281 as those generated by the 1000 Genomes Project.  The aim of VCFtools is to
6282 provide easily accessible methods for working with complex genetic variation
6283 data in the form of VCF files.")
6284     ;; The license is declared as LGPLv3 in the README and
6285     ;; at https://vcftools.github.io/license.html
6286     (license license:lgpl3)))
6287
6288 (define-public infernal
6289   (package
6290     (name "infernal")
6291     (version "1.1.2")
6292     (source (origin
6293               (method url-fetch)
6294               (uri (string-append "http://eddylab.org/software/infernal/"
6295                                   "infernal-" version ".tar.gz"))
6296               (sha256
6297                (base32
6298                 "0sr2hiz3qxfwqpz3whxr6n82p3x27336v3f34iqznp10hks2935c"))))
6299     (build-system gnu-build-system)
6300     (native-inputs
6301      `(("perl" ,perl))) ; for tests
6302     (home-page "http://eddylab.org/infernal/")
6303     (synopsis "Inference of RNA alignments")
6304     (description "Infernal (\"INFERence of RNA ALignment\") is a tool for
6305 searching DNA sequence databases for RNA structure and sequence similarities.
6306 It is an implementation of a special case of profile stochastic context-free
6307 grammars called @dfn{covariance models} (CMs).  A CM is like a sequence
6308 profile, but it scores a combination of sequence consensus and RNA secondary
6309 structure consensus, so in many cases, it is more capable of identifying RNA
6310 homologs that conserve their secondary structure more than their primary
6311 sequence.")
6312     ;; Infernal 1.1.2 requires VMX or SSE capability for parallel instructions.
6313     (supported-systems '("i686-linux" "x86_64-linux"))
6314     (license license:bsd-3)))
6315
6316 (define-public r-centipede
6317   (package
6318     (name "r-centipede")
6319     (version "1.2")
6320     (source (origin
6321               (method url-fetch)
6322               (uri (string-append "http://download.r-forge.r-project.org/"
6323                                   "src/contrib/CENTIPEDE_" version ".tar.gz"))
6324               (sha256
6325                (base32
6326                 "1hsx6qgwr0i67fhy9257zj7s0ppncph2hjgbia5nn6nfmj0ax6l9"))))
6327     (build-system r-build-system)
6328     (home-page "http://centipede.uchicago.edu/")
6329     (synopsis "Predict transcription factor binding sites")
6330     (description
6331      "CENTIPEDE applies a hierarchical Bayesian mixture model to infer regions
6332 of the genome that are bound by particular transcription factors.  It starts
6333 by identifying a set of candidate binding sites, and then aims to classify the
6334 sites according to whether each site is bound or not bound by a transcription
6335 factor.  CENTIPEDE is an unsupervised learning algorithm that discriminates
6336 between two different types of motif instances using as much relevant
6337 information as possible.")
6338     (license (list license:gpl2+ license:gpl3+))))
6339
6340 (define-public r-vegan
6341   (package
6342     (name "r-vegan")
6343     (version "2.5-3")
6344     (source
6345      (origin
6346        (method url-fetch)
6347        (uri (cran-uri "vegan" version))
6348        (sha256
6349         (base32
6350          "023xznh0iy0496icpchadmp7a3rk3nj9s48fvwlvp3dssw58yp3c"))))
6351     (build-system r-build-system)
6352     (native-inputs
6353      `(("gfortran" ,gfortran)))
6354     (propagated-inputs
6355      `(("r-cluster" ,r-cluster)
6356        ("r-knitr" ,r-knitr) ; needed for vignettes
6357        ("r-lattice" ,r-lattice)
6358        ("r-mass" ,r-mass)
6359        ("r-mgcv" ,r-mgcv)
6360        ("r-permute" ,r-permute)))
6361     (home-page "https://cran.r-project.org/web/packages/vegan")
6362     (synopsis "Functions for community ecology")
6363     (description
6364      "The vegan package provides tools for descriptive community ecology.  It
6365 has most basic functions of diversity analysis, community ordination and
6366 dissimilarity analysis.  Most of its multivariate tools can be used for other
6367 data types as well.")
6368     (license license:gpl2+)))
6369
6370 (define-public r-annotate
6371   (package
6372     (name "r-annotate")
6373     (version "1.60.0")
6374     (source
6375      (origin
6376        (method url-fetch)
6377        (uri (bioconductor-uri "annotate" version))
6378        (sha256
6379         (base32
6380          "0p6c96lay23a67dyirgnwzm2yw22m592z780vy6p4nqwla8ha18n"))))
6381     (build-system r-build-system)
6382     (propagated-inputs
6383      `(("r-annotationdbi" ,r-annotationdbi)
6384        ("r-biobase" ,r-biobase)
6385        ("r-biocgenerics" ,r-biocgenerics)
6386        ("r-dbi" ,r-dbi)
6387        ("r-rcurl" ,r-rcurl)
6388        ("r-xml" ,r-xml)
6389        ("r-xtable" ,r-xtable)))
6390     (home-page
6391      "https://bioconductor.org/packages/annotate")
6392     (synopsis "Annotation for microarrays")
6393     (description "This package provides R environments for the annotation of
6394 microarrays.")
6395     (license license:artistic2.0)))
6396
6397 (define-public r-copynumber
6398   (package
6399     (name "r-copynumber")
6400     (version "1.22.0")
6401     (source (origin
6402               (method url-fetch)
6403               (uri (bioconductor-uri "copynumber" version))
6404               (sha256
6405                (base32
6406                 "0ipwj9i5p1bwhg5d80jdjagm02krpj2v0j47qdgw41h8wncdyal3"))))
6407     (build-system r-build-system)
6408     (propagated-inputs
6409      `(("r-s4vectors" ,r-s4vectors)
6410        ("r-iranges" ,r-iranges)
6411        ("r-genomicranges" ,r-genomicranges)
6412        ("r-biocgenerics" ,r-biocgenerics)))
6413     (home-page "https://bioconductor.org/packages/copynumber")
6414     (synopsis "Segmentation of single- and multi-track copy number data")
6415     (description
6416      "This package segments single- and multi-track copy number data by a
6417 penalized least squares regression method.")
6418     (license license:artistic2.0)))
6419
6420 (define-public r-geneplotter
6421   (package
6422     (name "r-geneplotter")
6423     (version "1.60.0")
6424     (source
6425      (origin
6426        (method url-fetch)
6427        (uri (bioconductor-uri "geneplotter" version))
6428        (sha256
6429         (base32
6430          "10khr0pznxf3m0f5gzck9ymljrwcv3vamfmpskd51yjh36lhllqz"))))
6431     (build-system r-build-system)
6432     (propagated-inputs
6433      `(("r-annotate" ,r-annotate)
6434        ("r-annotationdbi" ,r-annotationdbi)
6435        ("r-biobase" ,r-biobase)
6436        ("r-biocgenerics" ,r-biocgenerics)
6437        ("r-lattice" ,r-lattice)
6438        ("r-rcolorbrewer" ,r-rcolorbrewer)))
6439     (home-page "https://bioconductor.org/packages/geneplotter")
6440     (synopsis "Graphics functions for genomic data")
6441     (description
6442      "This package provides functions for plotting genomic data.")
6443     (license license:artistic2.0)))
6444
6445 (define-public r-genefilter
6446   (package
6447     (name "r-genefilter")
6448     (version "1.64.0")
6449     (source
6450      (origin
6451        (method url-fetch)
6452        (uri (bioconductor-uri "genefilter" version))
6453        (sha256
6454         (base32
6455          "0p64s1n1627yafnp25wjr4b22p34lqw574fx2qg4s1m0lffh1z6i"))))
6456     (build-system r-build-system)
6457     (native-inputs
6458      `(("gfortran" ,gfortran)))
6459     (propagated-inputs
6460      `(("r-annotate" ,r-annotate)
6461        ("r-annotationdbi" ,r-annotationdbi)
6462        ("r-biobase" ,r-biobase)
6463        ("r-s4vectors" ,r-s4vectors)
6464        ("r-survival" ,r-survival)))
6465     (home-page "https://bioconductor.org/packages/genefilter")
6466     (synopsis "Filter genes from high-throughput experiments")
6467     (description
6468      "This package provides basic functions for filtering genes from
6469 high-throughput sequencing experiments.")
6470     (license license:artistic2.0)))
6471
6472 (define-public r-deseq2
6473   (package
6474     (name "r-deseq2")
6475     (version "1.22.1")
6476     (source
6477      (origin
6478        (method url-fetch)
6479        (uri (bioconductor-uri "DESeq2" version))
6480        (sha256
6481         (base32
6482          "1b2bmvcsfzvks47d7w46zplcwz0kgcdhx5xmx3x9lp2gvx2p84r5"))))
6483     (properties `((upstream-name . "DESeq2")))
6484     (build-system r-build-system)
6485     (propagated-inputs
6486      `(("r-biobase" ,r-biobase)
6487        ("r-biocgenerics" ,r-biocgenerics)
6488        ("r-biocparallel" ,r-biocparallel)
6489        ("r-genefilter" ,r-genefilter)
6490        ("r-geneplotter" ,r-geneplotter)
6491        ("r-genomicranges" ,r-genomicranges)
6492        ("r-ggplot2" ,r-ggplot2)
6493        ("r-hmisc" ,r-hmisc)
6494        ("r-iranges" ,r-iranges)
6495        ("r-locfit" ,r-locfit)
6496        ("r-rcpp" ,r-rcpp)
6497        ("r-rcpparmadillo" ,r-rcpparmadillo)
6498        ("r-s4vectors" ,r-s4vectors)
6499        ("r-summarizedexperiment" ,r-summarizedexperiment)))
6500     (home-page "https://bioconductor.org/packages/DESeq2")
6501     (synopsis "Differential gene expression analysis")
6502     (description
6503      "This package provides functions to estimate variance-mean dependence in
6504 count data from high-throughput nucleotide sequencing assays and test for
6505 differential expression based on a model using the negative binomial
6506 distribution.")
6507     (license license:lgpl3+)))
6508
6509 (define-public r-dexseq
6510   (package
6511     (name "r-dexseq")
6512     (version "1.28.0")
6513     (source
6514      (origin
6515        (method url-fetch)
6516        (uri (bioconductor-uri "DEXSeq" version))
6517        (sha256
6518         (base32
6519          "0jh1640cnzpk8x3155cqc8dvrs1rciw3d6nv2k70baw96bhrynp8"))))
6520     (properties `((upstream-name . "DEXSeq")))
6521     (build-system r-build-system)
6522     (propagated-inputs
6523      `(("r-annotationdbi" ,r-annotationdbi)
6524        ("r-biobase" ,r-biobase)
6525        ("r-biocgenerics" ,r-biocgenerics)
6526        ("r-biocparallel" ,r-biocparallel)
6527        ("r-biomart" ,r-biomart)
6528        ("r-deseq2" ,r-deseq2)
6529        ("r-genefilter" ,r-genefilter)
6530        ("r-geneplotter" ,r-geneplotter)
6531        ("r-genomicranges" ,r-genomicranges)
6532        ("r-hwriter" ,r-hwriter)
6533        ("r-iranges" ,r-iranges)
6534        ("r-rcolorbrewer" ,r-rcolorbrewer)
6535        ("r-rsamtools" ,r-rsamtools)
6536        ("r-s4vectors" ,r-s4vectors)
6537        ("r-statmod" ,r-statmod)
6538        ("r-stringr" ,r-stringr)
6539        ("r-summarizedexperiment" ,r-summarizedexperiment)))
6540     (home-page "https://bioconductor.org/packages/DEXSeq")
6541     (synopsis "Inference of differential exon usage in RNA-Seq")
6542     (description
6543      "This package is focused on finding differential exon usage using RNA-seq
6544 exon counts between samples with different experimental designs.  It provides
6545 functions that allows the user to make the necessary statistical tests based
6546 on a model that uses the negative binomial distribution to estimate the
6547 variance between biological replicates and generalized linear models for
6548 testing.  The package also provides functions for the visualization and
6549 exploration of the results.")
6550     (license license:gpl3+)))
6551
6552 (define-public r-annotationforge
6553   (package
6554     (name "r-annotationforge")
6555     (version "1.24.0")
6556     (source
6557      (origin
6558        (method url-fetch)
6559        (uri (bioconductor-uri "AnnotationForge" version))
6560        (sha256
6561         (base32
6562          "13yvhf3yskmvhs8szs6rkw93h81h5xqa3h19h91pp6nprhc8s3ll"))))
6563     (properties
6564      `((upstream-name . "AnnotationForge")))
6565     (build-system r-build-system)
6566     (propagated-inputs
6567      `(("r-annotationdbi" ,r-annotationdbi)
6568        ("r-biobase" ,r-biobase)
6569        ("r-biocgenerics" ,r-biocgenerics)
6570        ("r-dbi" ,r-dbi)
6571        ("r-rcurl" ,r-rcurl)
6572        ("r-rsqlite" ,r-rsqlite)
6573        ("r-s4vectors" ,r-s4vectors)
6574        ("r-xml" ,r-xml)))
6575     (home-page "https://bioconductor.org/packages/AnnotationForge")
6576     (synopsis "Code for building annotation database packages")
6577     (description
6578      "This package provides code for generating Annotation packages and their
6579 databases.  Packages produced are intended to be used with AnnotationDbi.")
6580     (license license:artistic2.0)))
6581
6582 (define-public r-rbgl
6583   (package
6584     (name "r-rbgl")
6585     (version "1.58.0")
6586     (source
6587      (origin
6588        (method url-fetch)
6589        (uri (bioconductor-uri "RBGL" version))
6590        (sha256
6591         (base32
6592          "0jy95m38c4qp0a12097hhm2gg63k96k6ydhb11dy379h3ziapcar"))))
6593     (properties `((upstream-name . "RBGL")))
6594     (build-system r-build-system)
6595     (propagated-inputs `(("r-graph" ,r-graph)))
6596     (home-page "https://www.bioconductor.org/packages/RBGL")
6597     (synopsis "Interface to the Boost graph library")
6598     (description
6599      "This package provides a fairly extensive and comprehensive interface to
6600 the graph algorithms contained in the Boost library.")
6601     (license license:artistic2.0)))
6602
6603 (define-public r-gseabase
6604   (package
6605     (name "r-gseabase")
6606     (version "1.44.0")
6607     (source
6608      (origin
6609        (method url-fetch)
6610        (uri (bioconductor-uri "GSEABase" version))
6611        (sha256
6612         (base32
6613          "110al7x0ig8plzrprvhwc7xshi1jzpj2n8llhhg2fh6v6k0k6awr"))))
6614     (properties `((upstream-name . "GSEABase")))
6615     (build-system r-build-system)
6616     (propagated-inputs
6617      `(("r-annotate" ,r-annotate)
6618        ("r-annotationdbi" ,r-annotationdbi)
6619        ("r-biobase" ,r-biobase)
6620        ("r-biocgenerics" ,r-biocgenerics)
6621        ("r-graph" ,r-graph)
6622        ("r-xml" ,r-xml)))
6623     (home-page "https://bioconductor.org/packages/GSEABase")
6624     (synopsis "Gene set enrichment data structures and methods")
6625     (description
6626      "This package provides classes and methods to support @dfn{Gene Set
6627 Enrichment Analysis} (GSEA).")
6628     (license license:artistic2.0)))
6629
6630 (define-public r-category
6631   (package
6632     (name "r-category")
6633     (version "2.48.0")
6634     (source
6635      (origin
6636        (method url-fetch)
6637        (uri (bioconductor-uri "Category" version))
6638        (sha256
6639         (base32
6640          "1jdm83bwdfhpfm1y6hwgvxzj6l83h1bdkqv23799kzywnwm016kv"))))
6641     (properties `((upstream-name . "Category")))
6642     (build-system r-build-system)
6643     (propagated-inputs
6644      `(("r-annotate" ,r-annotate)
6645        ("r-annotationdbi" ,r-annotationdbi)
6646        ("r-biobase" ,r-biobase)
6647        ("r-biocgenerics" ,r-biocgenerics)
6648        ("r-genefilter" ,r-genefilter)
6649        ("r-graph" ,r-graph)
6650        ("r-gseabase" ,r-gseabase)
6651        ("r-matrix" ,r-matrix)
6652        ("r-rbgl" ,r-rbgl)
6653        ("r-dbi" ,r-dbi)))
6654     (home-page "https://bioconductor.org/packages/Category")
6655     (synopsis "Category analysis")
6656     (description
6657      "This package provides a collection of tools for performing category
6658 analysis.")
6659     (license license:artistic2.0)))
6660
6661 (define-public r-gostats
6662   (package
6663     (name "r-gostats")
6664     (version "2.48.0")
6665     (source
6666      (origin
6667        (method url-fetch)
6668        (uri (bioconductor-uri "GOstats" version))
6669        (sha256
6670         (base32
6671          "0wlqqgfynwqnqhckhsfjwg9zkj6hkmzwd5y76dhqz720vy21rcln"))))
6672     (properties `((upstream-name . "GOstats")))
6673     (build-system r-build-system)
6674     (propagated-inputs
6675      `(("r-annotate" ,r-annotate)
6676        ("r-annotationdbi" ,r-annotationdbi)
6677        ("r-annotationforge" ,r-annotationforge)
6678        ("r-biobase" ,r-biobase)
6679        ("r-category" ,r-category)
6680        ("r-go-db" ,r-go-db)
6681        ("r-graph" ,r-graph)
6682        ("r-rgraphviz" ,r-rgraphviz)
6683        ("r-rbgl" ,r-rbgl)))
6684     (home-page "https://bioconductor.org/packages/GOstats")
6685     (synopsis "Tools for manipulating GO and microarrays")
6686     (description
6687      "This package provides a set of tools for interacting with GO and
6688 microarray data.  A variety of basic manipulation tools for graphs, hypothesis
6689 testing and other simple calculations.")
6690     (license license:artistic2.0)))
6691
6692 (define-public r-shortread
6693   (package
6694     (name "r-shortread")
6695     (version "1.40.0")
6696     (source
6697      (origin
6698        (method url-fetch)
6699        (uri (bioconductor-uri "ShortRead" version))
6700        (sha256
6701         (base32
6702          "0iks123i1adkb9i2q4wvfqdmmj9dy867jvngj9757y8gj6xbcpy1"))))
6703     (properties `((upstream-name . "ShortRead")))
6704     (build-system r-build-system)
6705     (inputs
6706      `(("zlib" ,zlib)))
6707     (propagated-inputs
6708      `(("r-biobase" ,r-biobase)
6709        ("r-biocgenerics" ,r-biocgenerics)
6710        ("r-biocparallel" ,r-biocparallel)
6711        ("r-biostrings" ,r-biostrings)
6712        ("r-genomeinfodb" ,r-genomeinfodb)
6713        ("r-genomicalignments" ,r-genomicalignments)
6714        ("r-genomicranges" ,r-genomicranges)
6715        ("r-hwriter" ,r-hwriter)
6716        ("r-iranges" ,r-iranges)
6717        ("r-lattice" ,r-lattice)
6718        ("r-latticeextra" ,r-latticeextra)
6719        ("r-rsamtools" ,r-rsamtools)
6720        ("r-s4vectors" ,r-s4vectors)
6721        ("r-xvector" ,r-xvector)
6722        ("r-zlibbioc" ,r-zlibbioc)))
6723     (home-page "https://bioconductor.org/packages/ShortRead")
6724     (synopsis "FASTQ input and manipulation tools")
6725     (description
6726      "This package implements sampling, iteration, and input of FASTQ files.
6727 It includes functions for filtering and trimming reads, and for generating a
6728 quality assessment report.  Data are represented as
6729 @code{DNAStringSet}-derived objects, and easily manipulated for a diversity of
6730 purposes.  The package also contains legacy support for early single-end,
6731 ungapped alignment formats.")
6732     (license license:artistic2.0)))
6733
6734 (define-public r-systempiper
6735   (package
6736     (name "r-systempiper")
6737     (version "1.16.0")
6738     (source
6739      (origin
6740        (method url-fetch)
6741        (uri (bioconductor-uri "systemPipeR" version))
6742        (sha256
6743         (base32
6744          "0l26q8zjdmzg84g7f25gv9z60sykybahlpg5bg9bmpbg5lzcsx04"))))
6745     (properties `((upstream-name . "systemPipeR")))
6746     (build-system r-build-system)
6747     (propagated-inputs
6748      `(("r-annotate" ,r-annotate)
6749        ("r-batchjobs" ,r-batchjobs)
6750        ("r-biocgenerics" ,r-biocgenerics)
6751        ("r-biostrings" ,r-biostrings)
6752        ("r-deseq2" ,r-deseq2)
6753        ("r-edger" ,r-edger)
6754        ("r-genomicfeatures" ,r-genomicfeatures)
6755        ("r-genomicranges" ,r-genomicranges)
6756        ("r-ggplot2" ,r-ggplot2)
6757        ("r-go-db" ,r-go-db)
6758        ("r-gostats" ,r-gostats)
6759        ("r-limma" ,r-limma)
6760        ("r-pheatmap" ,r-pheatmap)
6761        ("r-rjson" ,r-rjson)
6762        ("r-rsamtools" ,r-rsamtools)
6763        ("r-shortread" ,r-shortread)
6764        ("r-summarizedexperiment" ,r-summarizedexperiment)
6765        ("r-variantannotation" ,r-variantannotation)))
6766     (home-page "https://github.com/tgirke/systemPipeR")
6767     (synopsis "Next generation sequencing workflow and reporting environment")
6768     (description
6769      "This R package provides tools for building and running automated
6770 end-to-end analysis workflows for a wide range of @dfn{next generation
6771 sequence} (NGS) applications such as RNA-Seq, ChIP-Seq, VAR-Seq and Ribo-Seq.
6772 Important features include a uniform workflow interface across different NGS
6773 applications, automated report generation, and support for running both R and
6774 command-line software, such as NGS aligners or peak/variant callers, on local
6775 computers or compute clusters.  Efficient handling of complex sample sets and
6776 experimental designs is facilitated by a consistently implemented sample
6777 annotation infrastructure.")
6778     (license license:artistic2.0)))
6779
6780 (define-public r-grohmm
6781   (package
6782     (name "r-grohmm")
6783     (version "1.16.0")
6784     (source
6785      (origin
6786        (method url-fetch)
6787        (uri (bioconductor-uri "groHMM" version))
6788        (sha256
6789         (base32
6790          "1ph92fv44b90v7mk4b1mjvv0dlrhl8ba01klxbnd0vs4qn9zxplh"))))
6791     (properties `((upstream-name . "groHMM")))
6792     (build-system r-build-system)
6793     (propagated-inputs
6794      `(("r-genomeinfodb" ,r-genomeinfodb)
6795        ("r-genomicalignments" ,r-genomicalignments)
6796        ("r-genomicranges" ,r-genomicranges)
6797        ("r-iranges" ,r-iranges)
6798        ("r-mass" ,r-mass)
6799        ("r-rtracklayer" ,r-rtracklayer)
6800        ("r-s4vectors" ,r-s4vectors)))
6801     (home-page "https://github.com/Kraus-Lab/groHMM")
6802     (synopsis "GRO-seq analysis pipeline")
6803     (description
6804      "This package provides a pipeline for the analysis of GRO-seq data.")
6805     (license license:gpl3+)))
6806
6807 (define-public r-txdb-hsapiens-ucsc-hg19-knowngene
6808   (package
6809     (name "r-txdb-hsapiens-ucsc-hg19-knowngene")
6810     (version "3.2.2")
6811     (source (origin
6812               (method url-fetch)
6813               ;; We cannot use bioconductor-uri here because this tarball is
6814               ;; located under "data/annotation/" instead of "bioc/".
6815               (uri (string-append "https://bioconductor.org/packages/"
6816                                   "release/data/annotation/src/contrib"
6817                                   "/TxDb.Hsapiens.UCSC.hg19.knownGene_"
6818                                   version ".tar.gz"))
6819               (sha256
6820                (base32
6821                 "1sajhcqqwazgz2lqbik7rd935i7kpnh08zxbp2ra10j72yqy4g86"))))
6822     (properties
6823      `((upstream-name . "TxDb.Hsapiens.UCSC.hg19.knownGene")))
6824     (build-system r-build-system)
6825     ;; As this package provides little more than a very large data file it
6826     ;; doesn't make sense to build substitutes.
6827     (arguments `(#:substitutable? #f))
6828     (propagated-inputs
6829      `(("r-genomicfeatures" ,r-genomicfeatures)))
6830     (home-page
6831      "https://bioconductor.org/packages/TxDb.Hsapiens.UCSC.hg19.knownGene/")
6832     (synopsis "Annotation package for human genome in TxDb format")
6833     (description
6834      "This package provides an annotation database of Homo sapiens genome
6835 data.  It is derived from the UCSC hg19 genome and based on the \"knownGene\"
6836 track.  The database is exposed as a @code{TxDb} object.")
6837     (license license:artistic2.0)))
6838
6839 (define-public r-sparql
6840   (package
6841   (name "r-sparql")
6842   (version "1.16")
6843   (source (origin
6844            (method url-fetch)
6845            (uri (cran-uri "SPARQL" version))
6846            (sha256
6847             (base32
6848              "0gak1q06yyhdmcxb2n3v0h9gr1vqd0viqji52wpw211qp6r6dcrc"))))
6849   (properties `((upstream-name . "SPARQL")))
6850   (build-system r-build-system)
6851   (propagated-inputs
6852    `(("r-rcurl" ,r-rcurl)
6853      ("r-xml" ,r-xml)))
6854   (home-page "https://cran.r-project.org/web/packages/SPARQL")
6855   (synopsis "SPARQL client for R")
6856   (description "This package provides an interface to use SPARQL to pose
6857 SELECT or UPDATE queries to an end-point.")
6858   ;; The only license indication is found in the DESCRIPTION file,
6859   ;; which states GPL-3.  So we cannot assume GPLv3+.
6860   (license license:gpl3)))
6861
6862 (define-public vsearch
6863   (package
6864     (name "vsearch")
6865     (version "2.9.1")
6866     (source
6867      (origin
6868        (method git-fetch)
6869        (uri (git-reference
6870              (url "https://github.com/torognes/vsearch.git")
6871              (commit (string-append "v" version))))
6872        (file-name (git-file-name name version))
6873        (sha256
6874         (base32
6875          "0vhrpjfdf75ba04b24xknp41790cvcgwl0vgpy7qbzj5xh2521ss"))
6876        (patches (search-patches "vsearch-unbundle-cityhash.patch"))
6877        (snippet
6878         '(begin
6879            ;; Remove bundled cityhash sources.  The vsearch source is adjusted
6880            ;; for this in the patch.
6881            (delete-file "src/city.h")
6882            (delete-file "src/citycrc.h")
6883            (delete-file "src/city.cc")
6884            #t))))
6885     (build-system gnu-build-system)
6886     (inputs
6887      `(("zlib" ,zlib)
6888        ("bzip2" ,bzip2)
6889        ("cityhash" ,cityhash)))
6890     (native-inputs
6891      `(("autoconf" ,autoconf)
6892        ("automake" ,automake)))
6893     (synopsis "Sequence search tools for metagenomics")
6894     (description
6895      "VSEARCH supports DNA sequence searching, clustering, chimera detection,
6896 dereplication, pairwise alignment, shuffling, subsampling, sorting and
6897 masking.  The tool takes advantage of parallelism in the form of SIMD
6898 vectorization as well as multiple threads to perform accurate alignments at
6899 high speed.  VSEARCH uses an optimal global aligner (full dynamic programming
6900 Needleman-Wunsch).")
6901     (home-page "https://github.com/torognes/vsearch")
6902     ;; vsearch uses non-portable SSE intrinsics so building fails on other
6903     ;; platforms.
6904     (supported-systems '("x86_64-linux"))
6905     ;; Dual licensed; also includes public domain source.
6906     (license (list license:gpl3 license:bsd-2))))
6907
6908 (define-public pardre
6909   (package
6910     (name "pardre")
6911     ;; The source of 1.1.5 changed in place, so we append "-1" to the version.
6912     (version "1.1.5-1")
6913     (source
6914      (origin
6915        (method url-fetch)
6916        (uri (string-append "mirror://sourceforge/pardre/ParDRe-rel"
6917                            "1.1.5" ".tar.gz"))
6918        (sha256
6919         (base32
6920          "17j73nc0viq4f6qj50nrndsrif5d6b71q8fl87m54psiv0ilns2b"))))
6921     (build-system gnu-build-system)
6922     (arguments
6923      `(#:tests? #f ; no tests included
6924        #:phases
6925        (modify-phases %standard-phases
6926          (delete 'configure)
6927          (replace 'install
6928            (lambda* (#:key outputs #:allow-other-keys)
6929              (let ((bin (string-append (assoc-ref outputs "out") "/bin")))
6930                (install-file "ParDRe" bin)
6931                #t))))))
6932     (inputs
6933      `(("openmpi" ,openmpi)
6934        ("zlib" ,zlib)))
6935     (synopsis "Parallel tool to remove duplicate DNA reads")
6936     (description
6937      "ParDRe is a parallel tool to remove duplicate genetic sequence reads.
6938 Duplicate reads can be seen as identical or nearly identical sequences with
6939 some mismatches.  This tool lets users avoid the analysis of unnecessary
6940 reads, reducing the time of subsequent procedures with the
6941 dataset (e.g. assemblies, mappings, etc.).  The tool is implemented with MPI
6942 in order to exploit the parallel capabilities of multicore clusters.  It is
6943 faster than multithreaded counterparts (end of 2015) for the same number of
6944 cores and, thanks to the message-passing technology, it can be executed on
6945 clusters.")
6946     (home-page "https://sourceforge.net/projects/pardre/")
6947     (license license:gpl3+)))
6948
6949 (define-public ruby-bio-kseq
6950   (package
6951     (name "ruby-bio-kseq")
6952     (version "0.0.2")
6953     (source
6954      (origin
6955        (method url-fetch)
6956        (uri (rubygems-uri "bio-kseq" version))
6957        (sha256
6958         (base32
6959          "1xyaha46khb5jc6wzkbf7040jagac49jbimn0vcrzid0j8jdikrz"))))
6960     (build-system ruby-build-system)
6961     (arguments
6962      `(#:test-target "spec"))
6963     (native-inputs
6964      `(("bundler" ,bundler)
6965        ("ruby-rspec" ,ruby-rspec)
6966        ("ruby-rake-compiler" ,ruby-rake-compiler)))
6967     (inputs
6968      `(("zlib" ,zlib)))
6969     (synopsis "Ruby bindings for the kseq.h FASTA/Q parser")
6970     (description
6971      "@code{Bio::Kseq} provides ruby bindings to the @code{kseq.h} FASTA and
6972 FASTQ parsing code.  It provides a fast iterator over sequences and their
6973 quality scores.")
6974     (home-page "https://github.com/gusevfe/bio-kseq")
6975     (license license:expat)))
6976
6977 (define-public bio-locus
6978   (package
6979     (name "bio-locus")
6980     (version "0.0.7")
6981     (source
6982      (origin
6983        (method url-fetch)
6984        (uri (rubygems-uri "bio-locus" version))
6985        (sha256
6986         (base32
6987          "02vmrxyimkj9sahsp4zhfhnmbvz6dbbqz1y01vglf8cbwvkajfl0"))))
6988     (build-system ruby-build-system)
6989     (native-inputs
6990      `(("ruby-rspec" ,ruby-rspec)))
6991     (synopsis "Tool for fast querying of genome locations")
6992     (description
6993      "Bio-locus is a tabix-like tool for fast querying of genome
6994 locations.  Many file formats in bioinformatics contain records that
6995 start with a chromosome name and a position for a SNP, or a start-end
6996 position for indels.  Bio-locus allows users to store this chr+pos or
6997 chr+pos+alt information in a database.")
6998     (home-page "https://github.com/pjotrp/bio-locus")
6999     (license license:expat)))
7000
7001 (define-public bio-blastxmlparser
7002   (package
7003     (name "bio-blastxmlparser")
7004     (version "2.0.4")
7005     (source (origin
7006               (method url-fetch)
7007               (uri (rubygems-uri "bio-blastxmlparser" version))
7008               (sha256
7009                (base32
7010                 "1wf4qygcmdjgcqm6flmvsagfr1gs9lf63mj32qv3z1f481zc5692"))))
7011     (build-system ruby-build-system)
7012     (propagated-inputs
7013      `(("ruby-bio-logger" ,ruby-bio-logger)
7014        ("ruby-nokogiri" ,ruby-nokogiri)))
7015     (inputs
7016      `(("ruby-rspec" ,ruby-rspec)))
7017     (synopsis "Fast big data BLAST XML parser and library")
7018     (description
7019      "Very fast parallel big-data BLAST XML file parser which can be used as
7020 command line utility.  Use blastxmlparser to: Parse BLAST XML; filter output;
7021 generate FASTA, JSON, YAML, RDF, JSON-LD, HTML, CSV, tabular output etc.")
7022     (home-page "https://github.com/pjotrp/blastxmlparser")
7023     (license license:expat)))
7024
7025 (define-public bioruby
7026   (package
7027     (name "bioruby")
7028     (version "1.5.2")
7029     (source
7030      (origin
7031        (method url-fetch)
7032        (uri (rubygems-uri "bio" version))
7033        (sha256
7034         (base32
7035          "1d56amdsjv1mag7m6gv2w0xij8hqx1v5xbdjsix8sp3yp36m7938"))))
7036     (build-system ruby-build-system)
7037     (propagated-inputs
7038      `(("ruby-libxml" ,ruby-libxml)))
7039     (native-inputs
7040      `(("which" ,which)))  ; required for test phase
7041     (arguments
7042      `(#:phases
7043        (modify-phases %standard-phases
7044          (add-before 'build 'patch-test-command
7045           (lambda _
7046             (substitute* '("test/functional/bio/test_command.rb")
7047               (("/bin/sh") (which "sh")))
7048             (substitute* '("test/functional/bio/test_command.rb")
7049               (("/bin/ls") (which "ls")))
7050             (substitute* '("test/functional/bio/test_command.rb")
7051               (("which") (which "which")))
7052             (substitute* '("test/functional/bio/test_command.rb",
7053                            "test/data/command/echoarg2.sh")
7054               (("/bin/echo") (which "echo")))
7055             #t)))))
7056     (synopsis "Ruby library, shell and utilities for bioinformatics")
7057     (description "BioRuby comes with a comprehensive set of Ruby development
7058 tools and libraries for bioinformatics and molecular biology.  BioRuby has
7059 components for sequence analysis, pathway analysis, protein modelling and
7060 phylogenetic analysis; it supports many widely used data formats and provides
7061 easy access to databases, external programs and public web services, including
7062 BLAST, KEGG, GenBank, MEDLINE and GO.")
7063     (home-page "http://bioruby.org/")
7064     ;; Code is released under Ruby license, except for setup
7065     ;; (LGPLv2.1+) and scripts in samples (which have GPL2 and GPL2+)
7066     (license (list license:ruby license:lgpl2.1+ license:gpl2+ ))))
7067
7068 (define-public r-acsnminer
7069   (package
7070     (name "r-acsnminer")
7071     (version "0.16.8.25")
7072     (source (origin
7073               (method url-fetch)
7074               (uri (cran-uri "ACSNMineR" version))
7075               (sha256
7076                (base32
7077                 "0gh604s8qall6zfjlwcg2ilxjvz08dplf9k5g47idhv43scm748l"))))
7078     (properties `((upstream-name . "ACSNMineR")))
7079     (build-system r-build-system)
7080     (propagated-inputs
7081       `(("r-ggplot2" ,r-ggplot2)
7082         ("r-gridextra" ,r-gridextra)))
7083     (home-page "https://cran.r-project.org/web/packages/ACSNMineR")
7084     (synopsis "Gene enrichment analysis")
7085     (description
7086      "This package provides tools to compute and represent gene set enrichment
7087 or depletion from your data based on pre-saved maps from the @dfn{Atlas of
7088 Cancer Signalling Networks} (ACSN) or user imported maps.  The gene set
7089 enrichment can be run with hypergeometric test or Fisher exact test, and can
7090 use multiple corrections.  Visualization of data can be done either by
7091 barplots or heatmaps.")
7092     (license license:gpl2+)))
7093
7094 (define-public r-biocgenerics
7095   (package
7096     (name "r-biocgenerics")
7097     (version "0.28.0")
7098     (source (origin
7099               (method url-fetch)
7100               (uri (bioconductor-uri "BiocGenerics" version))
7101               (sha256
7102                (base32
7103                 "0cvpsrhg7sn7lpqgxvqrsagv6j7xj5rafq5xdjfd8zc4gxrs5rb8"))))
7104     (properties
7105      `((upstream-name . "BiocGenerics")))
7106     (build-system r-build-system)
7107     (home-page "https://bioconductor.org/packages/BiocGenerics")
7108     (synopsis "S4 generic functions for Bioconductor")
7109     (description
7110      "This package provides S4 generic functions needed by many Bioconductor
7111 packages.")
7112     (license license:artistic2.0)))
7113
7114 (define-public r-biocinstaller
7115   (package
7116     (name "r-biocinstaller")
7117     (version "1.32.1")
7118     (source (origin
7119               (method url-fetch)
7120               (uri (bioconductor-uri "BiocInstaller" version))
7121               (sha256
7122                (base32
7123                 "1s1f9qhyf3mc73ir25x2zlgi9hf45a37lg4z8fbva4i21hqisgsl"))))
7124     (properties
7125      `((upstream-name . "BiocInstaller")))
7126     (build-system r-build-system)
7127     (home-page "https://bioconductor.org/packages/BiocInstaller")
7128     (synopsis "Install Bioconductor packages")
7129     (description "This package is used to install and update R packages from
7130 Bioconductor, CRAN, and Github.")
7131     (license license:artistic2.0)))
7132
7133 (define-public r-biocviews
7134   (package
7135     (name "r-biocviews")
7136     (version "1.50.5")
7137     (source (origin
7138               (method url-fetch)
7139               (uri (bioconductor-uri "biocViews" version))
7140               (sha256
7141                (base32
7142                 "0rc1n89n04ylvy9gvsgvizcs77bh70jg1nkjjsjs7rqbr3zzdysz"))))
7143     (properties
7144      `((upstream-name . "biocViews")))
7145     (build-system r-build-system)
7146     (propagated-inputs
7147      `(("r-biobase" ,r-biobase)
7148        ("r-graph" ,r-graph)
7149        ("r-rbgl" ,r-rbgl)
7150        ("r-rcurl" ,r-rcurl)
7151        ("r-xml" ,r-xml)
7152        ("r-runit" ,r-runit)))
7153     (home-page "https://bioconductor.org/packages/biocViews")
7154     (synopsis "Bioconductor package categorization helper")
7155     (description "The purpose of biocViews is to create HTML pages that
7156 categorize packages in a Bioconductor package repository according to keywords,
7157 also known as views, in a controlled vocabulary.")
7158     (license license:artistic2.0)))
7159
7160 (define-public r-bookdown
7161   (package
7162     (name "r-bookdown")
7163     (version "0.7")
7164     (source (origin
7165               (method url-fetch)
7166               (uri (cran-uri "bookdown" version))
7167               (sha256
7168                (base32
7169                 "1b3fw1f41zph5yw3kynb47aijq53vhaa6mnnvxly72zamyzdf95q"))))
7170     (build-system r-build-system)
7171     (propagated-inputs
7172      `(("r-htmltools" ,r-htmltools)
7173        ("r-knitr" ,r-knitr)
7174        ("r-rmarkdown" ,r-rmarkdown)
7175        ("r-tinytex" ,r-tinytex)
7176        ("r-yaml" ,r-yaml)
7177        ("r-xfun" ,r-xfun)))
7178     (home-page "https://github.com/rstudio/bookdown")
7179     (synopsis "Authoring books and technical documents with R markdown")
7180     (description "This package provides output formats and utilities for
7181 authoring books and technical documents with R Markdown.")
7182     (license license:gpl3)))
7183
7184 (define-public r-biocstyle
7185   (package
7186     (name "r-biocstyle")
7187     (version "2.10.0")
7188     (source (origin
7189               (method url-fetch)
7190               (uri (bioconductor-uri "BiocStyle" version))
7191               (sha256
7192                (base32
7193                 "01lm8xljilj666fcl3wnw82dxkcxnlr294lddr553rm8xr5nwg31"))))
7194     (properties
7195      `((upstream-name . "BiocStyle")))
7196     (build-system r-build-system)
7197     (propagated-inputs
7198      `(("r-biocmanager" ,r-biocmanager)
7199        ("r-bookdown" ,r-bookdown)
7200        ("r-knitr" ,r-knitr)
7201        ("r-rmarkdown" ,r-rmarkdown)
7202        ("r-yaml" ,r-yaml)))
7203     (home-page "https://bioconductor.org/packages/BiocStyle")
7204     (synopsis "Bioconductor formatting styles")
7205     (description "This package provides standard formatting styles for
7206 Bioconductor PDF and HTML documents.  Package vignettes illustrate use and
7207 functionality.")
7208     (license license:artistic2.0)))
7209
7210 (define-public r-bioccheck
7211   (package
7212     (name "r-bioccheck")
7213     (version "1.18.0")
7214     (source (origin
7215               (method url-fetch)
7216               (uri (bioconductor-uri "BiocCheck" version))
7217               (sha256
7218                (base32
7219                 "0zamvs5jar38293ff27imvwy0ra25y64ls9z8w3q1y4jcp8p8pg7"))))
7220     (properties
7221      `((upstream-name . "BiocCheck")))
7222     (build-system r-build-system)
7223     (arguments
7224      '(#:phases
7225        (modify-phases %standard-phases
7226          ;; This package can be used by calling BiocCheck(<package>) from
7227          ;; within R, or by running R CMD BiocCheck <package>.  This phase
7228          ;; makes sure the latter works.  For this to work, the BiocCheck
7229          ;; script must be somewhere on the PATH (not the R bin directory).
7230          (add-after 'install 'install-bioccheck-subcommand
7231            (lambda* (#:key outputs #:allow-other-keys)
7232              (let* ((out (assoc-ref outputs "out"))
7233                     (dest-dir (string-append out "/bin"))
7234                     (script-dir
7235                      (string-append out "/site-library/BiocCheck/script/")))
7236                (mkdir-p dest-dir)
7237                (symlink (string-append script-dir "/checkBadDeps.R")
7238                         (string-append dest-dir "/checkBadDeps.R"))
7239                (symlink (string-append script-dir "/BiocCheck")
7240                         (string-append dest-dir "/BiocCheck")))
7241              #t)))))
7242     (propagated-inputs
7243      `(("r-codetools" ,r-codetools)
7244        ("r-graph" ,r-graph)
7245        ("r-httr" ,r-httr)
7246        ("r-knitr" ,r-knitr)
7247        ("r-optparse" ,r-optparse)
7248        ("r-biocmanager" ,r-biocmanager)
7249        ("r-biocviews" ,r-biocviews)
7250        ("r-stringdist" ,r-stringdist)))
7251     (home-page "https://bioconductor.org/packages/BiocCheck")
7252     (synopsis "Executes Bioconductor-specific package checks")
7253     (description "This package contains tools to perform additional quality
7254 checks on R packages that are to be submitted to the Bioconductor repository.")
7255     (license license:artistic2.0)))
7256
7257 (define-public r-optparse
7258   (package
7259     (name "r-optparse")
7260     (version "1.6.0")
7261     (source
7262      (origin
7263        (method url-fetch)
7264        (uri (cran-uri "optparse" version))
7265        (sha256
7266         (base32
7267          "1d7v5gl45x4amsfmzn5zyyffyqlc7a82h01szlnda22viyxids0h"))))
7268     (build-system r-build-system)
7269     (propagated-inputs
7270      `(("r-getopt" ,r-getopt)))
7271     (home-page
7272      "https://github.com/trevorld/optparse")
7273     (synopsis "Command line option parser")
7274     (description
7275      "This package provides a command line parser inspired by Python's
7276 @code{optparse} library to be used with Rscript to write shebang scripts
7277 that accept short and long options.")
7278     (license license:gpl2+)))
7279
7280 (define-public r-dnacopy
7281   (package
7282     (name "r-dnacopy")
7283     (version "1.56.0")
7284     (source (origin
7285               (method url-fetch)
7286               (uri (bioconductor-uri "DNAcopy" version))
7287               (sha256
7288                (base32
7289                 "04cqdqxhva66xwh1s2vffi56b9fcrqd4slcrvqasj5lp2rkjli82"))))
7290     (properties
7291      `((upstream-name . "DNAcopy")))
7292     (build-system r-build-system)
7293     (inputs
7294      `(("gfortran" ,gfortran)))
7295     (home-page "https://bioconductor.org/packages/DNAcopy")
7296     (synopsis "Implementation of a circular binary segmentation algorithm")
7297     (description "This package implements the circular binary segmentation (CBS)
7298 algorithm to segment DNA copy number data and identify genomic regions with
7299 abnormal copy number.")
7300     (license license:gpl2+)))
7301
7302 (define-public r-s4vectors
7303   (package
7304     (name "r-s4vectors")
7305     (version "0.20.1")
7306     (source (origin
7307               (method url-fetch)
7308               (uri (bioconductor-uri "S4Vectors" version))
7309               (sha256
7310                (base32
7311                 "18whrw67nxn82xshckl2pjy7d14sa3c27h3n9naqyqwz88lr6dzg"))))
7312     (properties
7313      `((upstream-name . "S4Vectors")))
7314     (build-system r-build-system)
7315     (propagated-inputs
7316      `(("r-biocgenerics" ,r-biocgenerics)))
7317     (home-page "https://bioconductor.org/packages/S4Vectors")
7318     (synopsis "S4 implementation of vectors and lists")
7319     (description
7320      "The S4Vectors package defines the @code{Vector} and @code{List} virtual
7321 classes and a set of generic functions that extend the semantic of ordinary
7322 vectors and lists in R.  Package developers can easily implement vector-like
7323 or list-like objects as concrete subclasses of @code{Vector} or @code{List}.
7324 In addition, a few low-level concrete subclasses of general interest (e.g.
7325 @code{DataFrame}, @code{Rle}, and @code{Hits}) are implemented in the
7326 S4Vectors package itself.")
7327     (license license:artistic2.0)))
7328
7329 (define-public r-seqinr
7330   (package
7331     (name "r-seqinr")
7332     (version "3.4-5")
7333     (source
7334       (origin
7335         (method url-fetch)
7336         (uri (cran-uri "seqinr" version))
7337         (sha256
7338           (base32
7339             "17zv0n5cji17izwmwg0jcbxbjl3w5rls91w15svcnlpxjms38ahn"))))
7340     (build-system r-build-system)
7341     (propagated-inputs
7342      `(("r-ade4" ,r-ade4)
7343        ("r-segmented" ,r-segmented)))
7344     (inputs
7345      `(("zlib" ,zlib)))
7346     (home-page "http://seqinr.r-forge.r-project.org/")
7347     (synopsis "Biological sequences retrieval and analysis")
7348     (description
7349      "This package provides tools for exploratory data analysis and data
7350 visualization of biological sequence (DNA and protein) data.  It also includes
7351 utilities for sequence data management under the ACNUC system.")
7352     (license license:gpl2+)))
7353
7354 (define-public r-iranges
7355   (package
7356     (name "r-iranges")
7357     (version "2.16.0")
7358     (source (origin
7359               (method url-fetch)
7360               (uri (bioconductor-uri "IRanges" version))
7361               (sha256
7362                (base32
7363                 "0ljppsk611xi72gc8mbdx1311b63b1ijd401jz5xmxk5frla1nc1"))))
7364     (properties
7365      `((upstream-name . "IRanges")))
7366     (build-system r-build-system)
7367     (propagated-inputs
7368      `(("r-biocgenerics" ,r-biocgenerics)
7369        ("r-s4vectors" ,r-s4vectors)))
7370     (home-page "https://bioconductor.org/packages/IRanges")
7371     (synopsis "Infrastructure for manipulating intervals on sequences")
7372     (description
7373      "This package provides efficient low-level and highly reusable S4 classes
7374 for storing ranges of integers, RLE vectors (Run-Length Encoding), and, more
7375 generally, data that can be organized sequentially (formally defined as
7376 @code{Vector} objects), as well as views on these @code{Vector} objects.
7377 Efficient list-like classes are also provided for storing big collections of
7378 instances of the basic classes.  All classes in the package use consistent
7379 naming and share the same rich and consistent \"Vector API\" as much as
7380 possible.")
7381     (license license:artistic2.0)))
7382
7383 (define-public r-genomeinfodbdata
7384   (package
7385     (name "r-genomeinfodbdata")
7386     (version "1.2.0")
7387     (source (origin
7388               (method url-fetch)
7389               ;; We cannot use bioconductor-uri here because this tarball is
7390               ;; located under "data/annotation/" instead of "bioc/".
7391               (uri (string-append "https://bioconductor.org/packages/release/"
7392                                   "data/annotation/src/contrib/GenomeInfoDbData_"
7393                                   version ".tar.gz"))
7394               (sha256
7395                (base32
7396                 "0di6nlqpsyqf693k2na65ayqldih563x3zfrczpqc5q2hl5kg35c"))))
7397     (properties
7398      `((upstream-name . "GenomeInfoDbData")))
7399     (build-system r-build-system)
7400     (home-page "https://bioconductor.org/packages/GenomeInfoDbData")
7401     (synopsis "Species and taxonomy ID look up tables for GenomeInfoDb")
7402     (description "This package contains data for mapping between NCBI taxonomy
7403 ID and species.  It is used by functions in the GenomeInfoDb package.")
7404     (license license:artistic2.0)))
7405
7406 (define-public r-genomeinfodb
7407   (package
7408     (name "r-genomeinfodb")
7409     (version "1.18.1")
7410     (source (origin
7411               (method url-fetch)
7412               (uri (bioconductor-uri "GenomeInfoDb" version))
7413               (sha256
7414                (base32
7415                 "049pyzr8iszv3g7wdqf3pz7vg7bzd450c20ln6fgw4g5xnkkr10s"))))
7416     (properties
7417      `((upstream-name . "GenomeInfoDb")))
7418     (build-system r-build-system)
7419     (propagated-inputs
7420      `(("r-biocgenerics" ,r-biocgenerics)
7421        ("r-genomeinfodbdata" ,r-genomeinfodbdata)
7422        ("r-iranges" ,r-iranges)
7423        ("r-rcurl" ,r-rcurl)
7424        ("r-s4vectors" ,r-s4vectors)))
7425     (home-page "https://bioconductor.org/packages/GenomeInfoDb")
7426     (synopsis "Utilities for manipulating chromosome identifiers")
7427     (description
7428      "This package contains data and functions that define and allow
7429 translation between different chromosome sequence naming conventions (e.g.,
7430 \"chr1\" versus \"1\"), including a function that attempts to place sequence
7431 names in their natural, rather than lexicographic, order.")
7432     (license license:artistic2.0)))
7433
7434 (define-public r-edger
7435   (package
7436     (name "r-edger")
7437     (version "3.24.0")
7438     (source (origin
7439               (method url-fetch)
7440               (uri (bioconductor-uri "edgeR" version))
7441               (sha256
7442                (base32
7443                 "0ihihgzrgb4q3xc8xkzp1v76ndgihrj4gas00fa25vggfs1v6hvg"))))
7444     (properties `((upstream-name . "edgeR")))
7445     (build-system r-build-system)
7446     (propagated-inputs
7447      `(("r-limma" ,r-limma)
7448        ("r-locfit" ,r-locfit)
7449        ("r-rcpp" ,r-rcpp)
7450        ("r-statmod" ,r-statmod))) ;for estimateDisp
7451     (home-page "http://bioinf.wehi.edu.au/edgeR")
7452     (synopsis "EdgeR does empirical analysis of digital gene expression data")
7453     (description "This package can do differential expression analysis of
7454 RNA-seq expression profiles with biological replication.  It implements a range
7455 of statistical methodology based on the negative binomial distributions,
7456 including empirical Bayes estimation, exact tests, generalized linear models
7457 and quasi-likelihood tests.  It be applied to differential signal analysis of
7458 other types of genomic data that produce counts, including ChIP-seq, SAGE and
7459 CAGE.")
7460     (license license:gpl2+)))
7461
7462 (define-public r-variantannotation
7463   (package
7464     (name "r-variantannotation")
7465     (version "1.28.1")
7466     (source (origin
7467               (method url-fetch)
7468               (uri (bioconductor-uri "VariantAnnotation" version))
7469               (sha256
7470                (base32
7471                 "0gvah258mkaafhbna81zwknx8qr3lidbcx5qvwk39q3yswr9mi49"))))
7472     (properties
7473      `((upstream-name . "VariantAnnotation")))
7474     (inputs
7475      `(("zlib" ,zlib)))
7476     (propagated-inputs
7477      `(("r-annotationdbi" ,r-annotationdbi)
7478        ("r-biobase" ,r-biobase)
7479        ("r-biocgenerics" ,r-biocgenerics)
7480        ("r-biostrings" ,r-biostrings)
7481        ("r-bsgenome" ,r-bsgenome)
7482        ("r-dbi" ,r-dbi)
7483        ("r-genomeinfodb" ,r-genomeinfodb)
7484        ("r-genomicfeatures" ,r-genomicfeatures)
7485        ("r-genomicranges" ,r-genomicranges)
7486        ("r-iranges" ,r-iranges)
7487        ("r-summarizedexperiment" ,r-summarizedexperiment)
7488        ("r-rsamtools" ,r-rsamtools)
7489        ("r-rtracklayer" ,r-rtracklayer)
7490        ("r-s4vectors" ,r-s4vectors)
7491        ("r-xvector" ,r-xvector)
7492        ("r-zlibbioc" ,r-zlibbioc)))
7493     (build-system r-build-system)
7494     (home-page "https://bioconductor.org/packages/VariantAnnotation")
7495     (synopsis "Package for annotation of genetic variants")
7496     (description "This R package can annotate variants, compute amino acid
7497 coding changes and predict coding outcomes.")
7498     (license license:artistic2.0)))
7499
7500 (define-public r-limma
7501   (package
7502     (name "r-limma")
7503     (version "3.38.2")
7504     (source (origin
7505               (method url-fetch)
7506               (uri (bioconductor-uri "limma" version))
7507               (sha256
7508                (base32
7509                 "1wkh362rmn24q7bkinb6nx62a31wl3r3myg5l326gx65wpwdnx97"))))
7510     (build-system r-build-system)
7511     (home-page "http://bioinf.wehi.edu.au/limma")
7512     (synopsis "Package for linear models for microarray and RNA-seq data")
7513     (description "This package can be used for the analysis of gene expression
7514 studies, especially the use of linear models for analysing designed experiments
7515 and the assessment of differential expression.  The analysis methods apply to
7516 different technologies, including microarrays, RNA-seq, and quantitative PCR.")
7517     (license license:gpl2+)))
7518
7519 (define-public r-xvector
7520   (package
7521     (name "r-xvector")
7522     (version "0.22.0")
7523     (source (origin
7524               (method url-fetch)
7525               (uri (bioconductor-uri "XVector" version))
7526               (sha256
7527                (base32
7528                 "01fph1ydd6g0rl5mcw54spx22glq2kqv7wyw8bqw0plmabzcwwdm"))))
7529     (properties
7530      `((upstream-name . "XVector")))
7531     (build-system r-build-system)
7532     (arguments
7533      `(#:phases
7534        (modify-phases %standard-phases
7535          (add-after 'unpack 'use-system-zlib
7536            (lambda _
7537              (substitute* "DESCRIPTION"
7538                (("zlibbioc, ") ""))
7539              (substitute* "NAMESPACE"
7540                (("import\\(zlibbioc\\)") ""))
7541              #t)))))
7542     (inputs
7543      `(("zlib" ,zlib)))
7544     (propagated-inputs
7545      `(("r-biocgenerics" ,r-biocgenerics)
7546        ("r-iranges" ,r-iranges)
7547        ("r-s4vectors" ,r-s4vectors)))
7548     (home-page "https://bioconductor.org/packages/XVector")
7549     (synopsis "Representation and manpulation of external sequences")
7550     (description
7551      "This package provides memory efficient S4 classes for storing sequences
7552 \"externally\" (behind an R external pointer, or on disk).")
7553     (license license:artistic2.0)))
7554
7555 (define-public r-genomicranges
7556   (package
7557     (name "r-genomicranges")
7558     (version "1.34.0")
7559     (source (origin
7560               (method url-fetch)
7561               (uri (bioconductor-uri "GenomicRanges" version))
7562               (sha256
7563                (base32
7564                 "0bgh14d15dpf2iy36qinw45r6n45rqkf0ghazrdl3jfva6vbrb29"))))
7565     (properties
7566      `((upstream-name . "GenomicRanges")))
7567     (build-system r-build-system)
7568     (propagated-inputs
7569      `(("r-biocgenerics" ,r-biocgenerics)
7570        ("r-genomeinfodb" ,r-genomeinfodb)
7571        ("r-iranges" ,r-iranges)
7572        ("r-s4vectors" ,r-s4vectors)
7573        ("r-xvector" ,r-xvector)))
7574     (home-page "https://bioconductor.org/packages/GenomicRanges")
7575     (synopsis "Representation and manipulation of genomic intervals")
7576     (description
7577      "This package provides tools to efficiently represent and manipulate
7578 genomic annotations and alignments is playing a central role when it comes to
7579 analyzing high-throughput sequencing data (a.k.a. NGS data).  The
7580 GenomicRanges package defines general purpose containers for storing and
7581 manipulating genomic intervals and variables defined along a genome.")
7582     (license license:artistic2.0)))
7583
7584 (define-public r-biobase
7585   (package
7586     (name "r-biobase")
7587     (version "2.42.0")
7588     (source (origin
7589               (method url-fetch)
7590               (uri (bioconductor-uri "Biobase" version))
7591               (sha256
7592                (base32
7593                 "10nr6nrkj5vlq8hsgbhbhv669z0dbpz4m3vz9k32rx1czbrrqwin"))))
7594     (properties
7595      `((upstream-name . "Biobase")))
7596     (build-system r-build-system)
7597     (propagated-inputs
7598      `(("r-biocgenerics" ,r-biocgenerics)))
7599     (home-page "https://bioconductor.org/packages/Biobase")
7600     (synopsis "Base functions for Bioconductor")
7601     (description
7602      "This package provides functions that are needed by many other packages
7603 on Bioconductor or which replace R functions.")
7604     (license license:artistic2.0)))
7605
7606 (define-public r-annotationdbi
7607   (package
7608     (name "r-annotationdbi")
7609     (version "1.44.0")
7610     (source (origin
7611               (method url-fetch)
7612               (uri (bioconductor-uri "AnnotationDbi" version))
7613               (sha256
7614                (base32
7615                 "1954vimkx5yb9irppq8vssq0f3yjkg36w38b9r0rqmijx1ps7x5d"))))
7616     (properties
7617      `((upstream-name . "AnnotationDbi")))
7618     (build-system r-build-system)
7619     (propagated-inputs
7620      `(("r-biobase" ,r-biobase)
7621        ("r-biocgenerics" ,r-biocgenerics)
7622        ("r-dbi" ,r-dbi)
7623        ("r-iranges" ,r-iranges)
7624        ("r-rsqlite" ,r-rsqlite)
7625        ("r-s4vectors" ,r-s4vectors)))
7626     (home-page "https://bioconductor.org/packages/AnnotationDbi")
7627     (synopsis "Annotation database interface")
7628     (description
7629      "This package provides user interface and database connection code for
7630 annotation data packages using SQLite data storage.")
7631     (license license:artistic2.0)))
7632
7633 (define-public r-biomart
7634   (package
7635     (name "r-biomart")
7636     (version "2.38.0")
7637     (source (origin
7638               (method url-fetch)
7639               (uri (bioconductor-uri "biomaRt" version))
7640               (sha256
7641                (base32
7642                 "1lshkknp7dmr3p6dd2zbv86cc71h53ggh9ji83jcjym8sgbbspl2"))))
7643     (properties
7644      `((upstream-name . "biomaRt")))
7645     (build-system r-build-system)
7646     (propagated-inputs
7647      `(("r-annotationdbi" ,r-annotationdbi)
7648        ("r-httr" ,r-httr)
7649        ("r-progress" ,r-progress)
7650        ("r-rcurl" ,r-rcurl)
7651        ("r-stringr" ,r-stringr)
7652        ("r-xml" ,r-xml)))
7653     (home-page "https://bioconductor.org/packages/biomaRt")
7654     (synopsis "Interface to BioMart databases")
7655     (description
7656      "biomaRt provides an interface to a growing collection of databases
7657 implementing the @url{BioMart software suite, http://www.biomart.org}.  The
7658 package enables retrieval of large amounts of data in a uniform way without
7659 the need to know the underlying database schemas or write complex SQL queries.
7660 Examples of BioMart databases are Ensembl, COSMIC, Uniprot, HGNC, Gramene,
7661 Wormbase and dbSNP mapped to Ensembl.  These major databases give biomaRt
7662 users direct access to a diverse set of data and enable a wide range of
7663 powerful online queries from gene annotation to database mining.")
7664     (license license:artistic2.0)))
7665
7666 (define-public r-biocparallel
7667   (package
7668     (name "r-biocparallel")
7669     (version "1.16.0")
7670     (source (origin
7671               (method url-fetch)
7672               (uri (bioconductor-uri "BiocParallel" version))
7673               (sha256
7674                (base32
7675                 "0g16cy0vjapqkb188z63r1b6y96m9g8vx0a3v2qavzxc177k0cja"))))
7676     (properties
7677      `((upstream-name . "BiocParallel")))
7678     (build-system r-build-system)
7679     (propagated-inputs
7680      `(("r-futile-logger" ,r-futile-logger)
7681        ("r-snow" ,r-snow)
7682        ("r-bh" ,r-bh)))
7683     (home-page "https://bioconductor.org/packages/BiocParallel")
7684     (synopsis "Bioconductor facilities for parallel evaluation")
7685     (description
7686      "This package provides modified versions and novel implementation of
7687 functions for parallel evaluation, tailored to use with Bioconductor
7688 objects.")
7689     (license (list license:gpl2+ license:gpl3+))))
7690
7691 (define-public r-biostrings
7692   (package
7693     (name "r-biostrings")
7694     (version "2.50.1")
7695     (source (origin
7696               (method url-fetch)
7697               (uri (bioconductor-uri "Biostrings" version))
7698               (sha256
7699                (base32
7700                 "1qyv1ps7vy6gy78pm2rcikg0bgf1mv7falahjp3pkwqq1272hrl8"))))
7701     (properties
7702      `((upstream-name . "Biostrings")))
7703     (build-system r-build-system)
7704     (propagated-inputs
7705      `(("r-biocgenerics" ,r-biocgenerics)
7706        ("r-iranges" ,r-iranges)
7707        ("r-s4vectors" ,r-s4vectors)
7708        ("r-xvector" ,r-xvector)))
7709     (home-page "https://bioconductor.org/packages/Biostrings")
7710     (synopsis "String objects and algorithms for biological sequences")
7711     (description
7712      "This package provides memory efficient string containers, string
7713 matching algorithms, and other utilities, for fast manipulation of large
7714 biological sequences or sets of sequences.")
7715     (license license:artistic2.0)))
7716
7717 (define-public r-rsamtools
7718   (package
7719     (name "r-rsamtools")
7720     (version "1.34.0")
7721     (source (origin
7722               (method url-fetch)
7723               (uri (bioconductor-uri "Rsamtools" version))
7724               (sha256
7725                (base32
7726                 "01v4bjhj2i126pwyk0v9lvmfp2ih495xsq903k3xa2z24bjxphbi"))))
7727     (properties
7728      `((upstream-name . "Rsamtools")))
7729     (build-system r-build-system)
7730     (arguments
7731      `(#:phases
7732        (modify-phases %standard-phases
7733          (add-after 'unpack 'use-system-zlib
7734            (lambda _
7735              (substitute* "DESCRIPTION"
7736                (("zlibbioc, ") ""))
7737              (substitute* "NAMESPACE"
7738                (("import\\(zlibbioc\\)") ""))
7739              #t)))))
7740     (inputs
7741      `(("zlib" ,zlib)))
7742     (propagated-inputs
7743      `(("r-biocgenerics" ,r-biocgenerics)
7744        ("r-biocparallel" ,r-biocparallel)
7745        ("r-biostrings" ,r-biostrings)
7746        ("r-bitops" ,r-bitops)
7747        ("r-genomeinfodb" ,r-genomeinfodb)
7748        ("r-genomicranges" ,r-genomicranges)
7749        ("r-iranges" ,r-iranges)
7750        ("r-s4vectors" ,r-s4vectors)
7751        ("r-xvector" ,r-xvector)))
7752     (home-page "https://bioconductor.org/packages/release/bioc/html/Rsamtools.html")
7753     (synopsis "Interface to samtools, bcftools, and tabix")
7754     (description
7755      "This package provides an interface to the 'samtools', 'bcftools', and
7756 'tabix' utilities for manipulating SAM (Sequence Alignment / Map), FASTA,
7757 binary variant call (BCF) and compressed indexed tab-delimited (tabix)
7758 files.")
7759     (license license:expat)))
7760
7761 (define-public r-delayedarray
7762   (package
7763     (name "r-delayedarray")
7764     (version "0.8.0")
7765     (source (origin
7766               (method url-fetch)
7767               (uri (bioconductor-uri "DelayedArray" version))
7768               (sha256
7769                (base32
7770                 "0cl5anqkjwvqx19snjhz0zj8cp8ibckiifl28h821h50g62nvb2f"))))
7771     (properties
7772      `((upstream-name . "DelayedArray")))
7773     (build-system r-build-system)
7774     (propagated-inputs
7775      `(("r-biocgenerics" ,r-biocgenerics)
7776        ("r-biocparallel" ,r-biocparallel)
7777        ("r-s4vectors" ,r-s4vectors)
7778        ("r-iranges" ,r-iranges)
7779        ("r-matrixstats" ,r-matrixstats)))
7780     (home-page "https://bioconductor.org/packages/DelayedArray")
7781     (synopsis "Delayed operations on array-like objects")
7782     (description
7783      "Wrapping an array-like object (typically an on-disk object) in a
7784 @code{DelayedArray} object allows one to perform common array operations on it
7785 without loading the object in memory.  In order to reduce memory usage and
7786 optimize performance, operations on the object are either delayed or executed
7787 using a block processing mechanism.  Note that this also works on in-memory
7788 array-like objects like @code{DataFrame} objects (typically with Rle columns),
7789 @code{Matrix} objects, and ordinary arrays and data frames.")
7790     (license license:artistic2.0)))
7791
7792 (define-public r-summarizedexperiment
7793   (package
7794     (name "r-summarizedexperiment")
7795     (version "1.12.0")
7796     (source (origin
7797               (method url-fetch)
7798               (uri (bioconductor-uri "SummarizedExperiment" version))
7799               (sha256
7800                (base32
7801                 "07805572xhpj5mfwq6kw1ha21wgalqvhh4ydvafyl1bnf3r20vps"))))
7802     (properties
7803      `((upstream-name . "SummarizedExperiment")))
7804     (build-system r-build-system)
7805     (propagated-inputs
7806      `(("r-biobase" ,r-biobase)
7807        ("r-biocgenerics" ,r-biocgenerics)
7808        ("r-delayedarray" ,r-delayedarray)
7809        ("r-genomeinfodb" ,r-genomeinfodb)
7810        ("r-genomicranges" ,r-genomicranges)
7811        ("r-iranges" ,r-iranges)
7812        ("r-matrix" ,r-matrix)
7813        ("r-s4vectors" ,r-s4vectors)))
7814     (home-page "https://bioconductor.org/packages/SummarizedExperiment")
7815     (synopsis "Container for representing genomic ranges by sample")
7816     (description
7817      "The SummarizedExperiment container contains one or more assays, each
7818 represented by a matrix-like object of numeric or other mode.  The rows
7819 typically represent genomic ranges of interest and the columns represent
7820 samples.")
7821     (license license:artistic2.0)))
7822
7823 (define-public r-genomicalignments
7824   (package
7825     (name "r-genomicalignments")
7826     (version "1.18.0")
7827     (source (origin
7828               (method url-fetch)
7829               (uri (bioconductor-uri "GenomicAlignments" version))
7830               (sha256
7831                (base32
7832                 "0a3zhwripfw2508fvgx3wzqa8nq8vnslg97a911znpwvxh53jl24"))))
7833     (properties
7834      `((upstream-name . "GenomicAlignments")))
7835     (build-system r-build-system)
7836     (propagated-inputs
7837      `(("r-biocgenerics" ,r-biocgenerics)
7838        ("r-biocparallel" ,r-biocparallel)
7839        ("r-biostrings" ,r-biostrings)
7840        ("r-genomeinfodb" ,r-genomeinfodb)
7841        ("r-genomicranges" ,r-genomicranges)
7842        ("r-iranges" ,r-iranges)
7843        ("r-rsamtools" ,r-rsamtools)
7844        ("r-s4vectors" ,r-s4vectors)
7845        ("r-summarizedexperiment" ,r-summarizedexperiment)))
7846     (home-page "https://bioconductor.org/packages/GenomicAlignments")
7847     (synopsis "Representation and manipulation of short genomic alignments")
7848     (description
7849      "This package provides efficient containers for storing and manipulating
7850 short genomic alignments (typically obtained by aligning short reads to a
7851 reference genome).  This includes read counting, computing the coverage,
7852 junction detection, and working with the nucleotide content of the
7853 alignments.")
7854     (license license:artistic2.0)))
7855
7856 (define-public r-rtracklayer
7857   (package
7858     (name "r-rtracklayer")
7859     (version "1.42.0")
7860     (source (origin
7861               (method url-fetch)
7862               (uri (bioconductor-uri "rtracklayer" version))
7863               (sha256
7864                (base32
7865                 "0a4mhd926w9slkfil5xgngjsfdj024a4w57w2bm3d4r0pj8y5da7"))))
7866     (build-system r-build-system)
7867     (arguments
7868      `(#:phases
7869        (modify-phases %standard-phases
7870          (add-after 'unpack 'use-system-zlib
7871            (lambda _
7872              (substitute* "DESCRIPTION"
7873                ((" zlibbioc,") ""))
7874              (substitute* "NAMESPACE"
7875                (("import\\(zlibbioc\\)") ""))
7876              #t)))))
7877     (native-inputs
7878      `(("pkg-config" ,pkg-config)))
7879     (inputs
7880      `(("zlib" ,zlib)))
7881     (propagated-inputs
7882      `(("r-biocgenerics" ,r-biocgenerics)
7883        ("r-biostrings" ,r-biostrings)
7884        ("r-genomeinfodb" ,r-genomeinfodb)
7885        ("r-genomicalignments" ,r-genomicalignments)
7886        ("r-genomicranges" ,r-genomicranges)
7887        ("r-iranges" ,r-iranges)
7888        ("r-rcurl" ,r-rcurl)
7889        ("r-rsamtools" ,r-rsamtools)
7890        ("r-s4vectors" ,r-s4vectors)
7891        ("r-xml" ,r-xml)
7892        ("r-xvector" ,r-xvector)))
7893     (home-page "https://bioconductor.org/packages/rtracklayer")
7894     (synopsis "R interface to genome browsers and their annotation tracks")
7895     (description
7896      "rtracklayer is an extensible framework for interacting with multiple
7897 genome browsers (currently UCSC built-in) and manipulating annotation tracks
7898 in various formats (currently GFF, BED, bedGraph, BED15, WIG, BigWig and 2bit
7899 built-in).  The user may export/import tracks to/from the supported browsers,
7900 as well as query and modify the browser state, such as the current viewport.")
7901     (license license:artistic2.0)))
7902
7903 (define-public r-genomicfeatures
7904   (package
7905     (name "r-genomicfeatures")
7906     (version "1.34.1")
7907     (source (origin
7908               (method url-fetch)
7909               (uri (bioconductor-uri "GenomicFeatures" version))
7910               (sha256
7911                (base32
7912                 "0slq6hv5bmc3bgrl824jzmr6db3fvaj6b7ihwmdn76pgqqbq2fq6"))))
7913     (properties
7914      `((upstream-name . "GenomicFeatures")))
7915     (build-system r-build-system)
7916     (propagated-inputs
7917      `(("r-annotationdbi" ,r-annotationdbi)
7918        ("r-biobase" ,r-biobase)
7919        ("r-biocgenerics" ,r-biocgenerics)
7920        ("r-biomart" ,r-biomart)
7921        ("r-biostrings" ,r-biostrings)
7922        ("r-dbi" ,r-dbi)
7923        ("r-genomeinfodb" ,r-genomeinfodb)
7924        ("r-genomicranges" ,r-genomicranges)
7925        ("r-iranges" ,r-iranges)
7926        ("r-rcurl" ,r-rcurl)
7927        ("r-rsqlite" ,r-rsqlite)
7928        ("r-rtracklayer" ,r-rtracklayer)
7929        ("r-s4vectors" ,r-s4vectors)
7930        ("r-xvector" ,r-xvector)))
7931     (home-page "https://bioconductor.org/packages/GenomicFeatures")
7932     (synopsis "Tools for working with transcript centric annotations")
7933     (description
7934      "This package provides a set of tools and methods for making and
7935 manipulating transcript centric annotations.  With these tools the user can
7936 easily download the genomic locations of the transcripts, exons and cds of a
7937 given organism, from either the UCSC Genome Browser or a BioMart
7938 database (more sources will be supported in the future).  This information is
7939 then stored in a local database that keeps track of the relationship between
7940 transcripts, exons, cds and genes.  Flexible methods are provided for
7941 extracting the desired features in a convenient format.")
7942     (license license:artistic2.0)))
7943
7944 (define-public r-go-db
7945   (package
7946     (name "r-go-db")
7947     (version "3.7.0")
7948     (source (origin
7949               (method url-fetch)
7950               (uri (string-append "https://www.bioconductor.org/packages/"
7951                                   "release/data/annotation/src/contrib/GO.db_"
7952                                   version ".tar.gz"))
7953               (sha256
7954                (base32
7955                 "0i3wcf5h3n0dawzc1hy0kv74f06j80c47n4p3g3fmrcxlhi3jpa5"))))
7956     (properties
7957      `((upstream-name . "GO.db")))
7958     (build-system r-build-system)
7959     (propagated-inputs
7960      `(("r-annotationdbi" ,r-annotationdbi)))
7961     (home-page "https://bioconductor.org/packages/GO.db")
7962     (synopsis "Annotation maps describing the entire Gene Ontology")
7963     (description
7964      "The purpose of this GO.db annotation package is to provide detailed
7965 information about the latest version of the Gene Ontologies.")
7966     (license license:artistic2.0)))
7967
7968 (define-public r-topgo
7969   (package
7970     (name "r-topgo")
7971     (version "2.34.0")
7972     (source (origin
7973               (method url-fetch)
7974               (uri (bioconductor-uri "topGO" version))
7975               (sha256
7976                (base32
7977                 "1j1jcd16j564kr6qz28140fzmnh9xasi84v1c1fi98sqv30zq9bh"))))
7978     (properties
7979      `((upstream-name . "topGO")))
7980     (build-system r-build-system)
7981     (propagated-inputs
7982      `(("r-annotationdbi" ,r-annotationdbi)
7983        ("r-dbi" ,r-dbi)
7984        ("r-biobase" ,r-biobase)
7985        ("r-biocgenerics" ,r-biocgenerics)
7986        ("r-go-db" ,r-go-db)
7987        ("r-graph" ,r-graph)
7988        ("r-lattice" ,r-lattice)
7989        ("r-matrixstats" ,r-matrixstats)
7990        ("r-sparsem" ,r-sparsem)))
7991     (home-page "https://bioconductor.org/packages/topGO")
7992     (synopsis "Enrichment analysis for gene ontology")
7993     (description
7994      "The topGO package provides tools for testing @dfn{gene ontology} (GO)
7995 terms while accounting for the topology of the GO graph.  Different test
7996 statistics and different methods for eliminating local similarities and
7997 dependencies between GO terms can be implemented and applied.")
7998     ;; Any version of the LGPL applies.
7999     (license license:lgpl2.1+)))
8000
8001 (define-public r-bsgenome
8002   (package
8003     (name "r-bsgenome")
8004     (version "1.50.0")
8005     (source (origin
8006               (method url-fetch)
8007               (uri (bioconductor-uri "BSgenome" version))
8008               (sha256
8009                (base32
8010                 "07z4zxx0khrc86qqvc7vxww8df9fh6pyks9ajxkc9gdqr5nn79j7"))))
8011     (properties
8012      `((upstream-name . "BSgenome")))
8013     (build-system r-build-system)
8014     (propagated-inputs
8015      `(("r-biocgenerics" ,r-biocgenerics)
8016        ("r-biostrings" ,r-biostrings)
8017        ("r-genomeinfodb" ,r-genomeinfodb)
8018        ("r-genomicranges" ,r-genomicranges)
8019        ("r-iranges" ,r-iranges)
8020        ("r-rsamtools" ,r-rsamtools)
8021        ("r-rtracklayer" ,r-rtracklayer)
8022        ("r-s4vectors" ,r-s4vectors)
8023        ("r-xvector" ,r-xvector)))
8024     (home-page "https://bioconductor.org/packages/BSgenome")
8025     (synopsis "Infrastructure for Biostrings-based genome data packages")
8026     (description
8027      "This package provides infrastructure shared by all Biostrings-based
8028 genome data packages and support for efficient SNP representation.")
8029     (license license:artistic2.0)))
8030
8031 (define-public r-bsgenome-hsapiens-1000genomes-hs37d5
8032   (package
8033     (name "r-bsgenome-hsapiens-1000genomes-hs37d5")
8034     (version "0.99.1")
8035     (source (origin
8036               (method url-fetch)
8037               ;; We cannot use bioconductor-uri here because this tarball is
8038               ;; located under "data/annotation/" instead of "bioc/".
8039               (uri (string-append "https://www.bioconductor.org/packages/"
8040                                   "release/data/annotation/src/contrib/"
8041                                   "BSgenome.Hsapiens.1000genomes.hs37d5_"
8042                                   version ".tar.gz"))
8043               (sha256
8044                (base32
8045                 "1cg0g5fqmsvwyw2p9hp2yy4ilk21jkbbrnpgqvb5c36ihjwvc7sr"))))
8046     (properties
8047      `((upstream-name . "BSgenome.Hsapiens.1000genomes.hs37d5")))
8048     (build-system r-build-system)
8049     ;; As this package provides little more than a very large data file it
8050     ;; doesn't make sense to build substitutes.
8051     (arguments `(#:substitutable? #f))
8052     (propagated-inputs
8053      `(("r-bsgenome" ,r-bsgenome)))
8054     (home-page
8055      "https://www.bioconductor.org/packages/BSgenome.Hsapiens.1000genomes.hs37d5/")
8056     (synopsis "Full genome sequences for Homo sapiens")
8057     (description
8058      "This package provides full genome sequences for Homo sapiens from
8059 1000genomes phase2 reference genome sequence (hs37d5), based on NCBI GRCh37.")
8060     (license license:artistic2.0)))
8061
8062 (define-public r-impute
8063   (package
8064     (name "r-impute")
8065     (version "1.56.0")
8066     (source (origin
8067               (method url-fetch)
8068               (uri (bioconductor-uri "impute" version))
8069               (sha256
8070                (base32
8071                 "08z0pj1dz5iq967nwj67qyka7ir7m5an2ggv7bsrlz3apzfsla33"))))
8072     (inputs
8073      `(("gfortran" ,gfortran)))
8074     (build-system r-build-system)
8075     (home-page "https://bioconductor.org/packages/impute")
8076     (synopsis "Imputation for microarray data")
8077     (description
8078      "This package provides a function to impute missing gene expression
8079 microarray data, using nearest neighbor averaging.")
8080     (license license:gpl2+)))
8081
8082 (define-public r-seqpattern
8083   (package
8084     (name "r-seqpattern")
8085     (version "1.14.0")
8086     (source (origin
8087               (method url-fetch)
8088               (uri (bioconductor-uri "seqPattern" version))
8089               (sha256
8090                (base32
8091                 "0di83qi83mrlw7i12khsq55d03hlazcywaa9m9pki1sfhafpq733"))))
8092     (properties
8093      `((upstream-name . "seqPattern")))
8094     (build-system r-build-system)
8095     (propagated-inputs
8096      `(("r-biostrings" ,r-biostrings)
8097        ("r-genomicranges" ,r-genomicranges)
8098        ("r-iranges" ,r-iranges)
8099        ("r-kernsmooth" ,r-kernsmooth)
8100        ("r-plotrix" ,r-plotrix)))
8101     (home-page "https://bioconductor.org/packages/seqPattern")
8102     (synopsis "Visualising oligonucleotide patterns and motif occurrences")
8103     (description
8104      "This package provides tools to visualize oligonucleotide patterns and
8105 sequence motif occurrences across a large set of sequences centred at a common
8106 reference point and sorted by a user defined feature.")
8107     (license license:gpl3+)))
8108
8109 (define-public r-genomation
8110   (package
8111     (name "r-genomation")
8112     (version "1.14.0")
8113     (source (origin
8114               (method url-fetch)
8115               (uri (bioconductor-uri "genomation" version))
8116               (sha256
8117                (base32
8118                 "0g0v4alfpqlinqinjnyzl3mrjnpbdx9ri34mcaiqbvbvg8ic8wvg"))))
8119     (build-system r-build-system)
8120     (propagated-inputs
8121      `(("r-biostrings" ,r-biostrings)
8122        ("r-bsgenome" ,r-bsgenome)
8123        ("r-data-table" ,r-data-table)
8124        ("r-genomeinfodb" ,r-genomeinfodb)
8125        ("r-genomicalignments" ,r-genomicalignments)
8126        ("r-genomicranges" ,r-genomicranges)
8127        ("r-ggplot2" ,r-ggplot2)
8128        ("r-gridbase" ,r-gridbase)
8129        ("r-impute" ,r-impute)
8130        ("r-iranges" ,r-iranges)
8131        ("r-matrixstats" ,r-matrixstats)
8132        ("r-plotrix" ,r-plotrix)
8133        ("r-plyr" ,r-plyr)
8134        ("r-rcpp" ,r-rcpp)
8135        ("r-readr" ,r-readr)
8136        ("r-reshape2" ,r-reshape2)
8137        ("r-rsamtools" ,r-rsamtools)
8138        ("r-rtracklayer" ,r-rtracklayer)
8139        ("r-runit" ,r-runit)
8140        ("r-s4vectors" ,r-s4vectors)
8141        ("r-seqpattern" ,r-seqpattern)))
8142     (home-page "http://bioinformatics.mdc-berlin.de/genomation/")
8143     (synopsis "Summary, annotation and visualization of genomic data")
8144     (description
8145      "This package provides a package for summary and annotation of genomic
8146 intervals.  Users can visualize and quantify genomic intervals over
8147 pre-defined functional regions, such as promoters, exons, introns, etc.  The
8148 genomic intervals represent regions with a defined chromosome position, which
8149 may be associated with a score, such as aligned reads from HT-seq experiments,
8150 TF binding sites, methylation scores, etc.  The package can use any tabular
8151 genomic feature data as long as it has minimal information on the locations of
8152 genomic intervals.  In addition, it can use BAM or BigWig files as input.")
8153     (license license:artistic2.0)))
8154
8155 (define-public r-genomationdata
8156   (package
8157     (name "r-genomationdata")
8158     (version "1.14.0")
8159     (source (origin
8160               (method url-fetch)
8161               ;; We cannot use bioconductor-uri here because this tarball is
8162               ;; located under "data/annotation/" instead of "bioc/".
8163               (uri (string-append "https://bioconductor.org/packages/"
8164                                   "release/data/experiment/src/contrib/"
8165                                   "genomationData_" version ".tar.gz"))
8166               (sha256
8167                (base32
8168                 "10xyb8akjrhmak2i0mnv1agny2ipy364q9nlibyplpzc7vdb6bw7"))))
8169     (build-system r-build-system)
8170     ;; As this package provides little more than large data files, it doesn't
8171     ;; make sense to build substitutes.
8172     (arguments `(#:substitutable? #f))
8173     (native-inputs
8174      `(("r-knitr" ,r-knitr)))
8175     (home-page "http://bioinformatics.mdc-berlin.de/genomation/")
8176     (synopsis "Experimental data for use with the genomation package")
8177     (description
8178      "This package contains experimental genetic data for use with the
8179 genomation package.  Included are Chip Seq, Methylation and Cage data,
8180 downloaded from Encode.")
8181     (license license:gpl3+)))
8182
8183 (define-public r-org-hs-eg-db
8184   (package
8185     (name "r-org-hs-eg-db")
8186     (version "3.7.0")
8187     (source (origin
8188               (method url-fetch)
8189               ;; We cannot use bioconductor-uri here because this tarball is
8190               ;; located under "data/annotation/" instead of "bioc/".
8191               (uri (string-append "https://www.bioconductor.org/packages/"
8192                                   "release/data/annotation/src/contrib/"
8193                                   "org.Hs.eg.db_" version ".tar.gz"))
8194               (sha256
8195                (base32
8196                 "1qxz9l80yg3qdqszs6dsscp7lrpfi1bgd0pxh9j7q34vprzwhdim"))))
8197     (properties
8198      `((upstream-name . "org.Hs.eg.db")))
8199     (build-system r-build-system)
8200     (propagated-inputs
8201      `(("r-annotationdbi" ,r-annotationdbi)))
8202     (home-page "https://www.bioconductor.org/packages/org.Hs.eg.db/")
8203     (synopsis "Genome wide annotation for Human")
8204     (description
8205      "This package contains genome-wide annotations for Human, primarily based
8206 on mapping using Entrez Gene identifiers.")
8207     (license license:artistic2.0)))
8208
8209 (define-public r-org-ce-eg-db
8210   (package
8211     (name "r-org-ce-eg-db")
8212     (version "3.7.0")
8213     (source (origin
8214               (method url-fetch)
8215               ;; We cannot use bioconductor-uri here because this tarball is
8216               ;; located under "data/annotation/" instead of "bioc/".
8217               (uri (string-append "https://www.bioconductor.org/packages/"
8218                                   "release/data/annotation/src/contrib/"
8219                                   "org.Ce.eg.db_" version ".tar.gz"))
8220               (sha256
8221                (base32
8222                 "1w5br1ss4ha8wv4v2saj7cmbjc2jw0dyj2f2y269l078z31wcnaz"))))
8223     (properties
8224      `((upstream-name . "org.Ce.eg.db")))
8225     (build-system r-build-system)
8226     (propagated-inputs
8227      `(("r-annotationdbi" ,r-annotationdbi)))
8228     (home-page "https://www.bioconductor.org/packages/org.Ce.eg.db/")
8229     (synopsis "Genome wide annotation for Worm")
8230     (description
8231      "This package provides mappings from Entrez gene identifiers to various
8232 annotations for the genome of the model worm Caenorhabditis elegans.")
8233     (license license:artistic2.0)))
8234
8235 (define-public r-org-dm-eg-db
8236   (package
8237     (name "r-org-dm-eg-db")
8238     (version "3.7.0")
8239     (source (origin
8240               (method url-fetch)
8241               ;; We cannot use bioconductor-uri here because this tarball is
8242               ;; located under "data/annotation/" instead of "bioc/".
8243               (uri (string-append "https://www.bioconductor.org/packages/"
8244                                   "release/data/annotation/src/contrib/"
8245                                   "org.Dm.eg.db_" version ".tar.gz"))
8246               (sha256
8247                (base32
8248                 "1pqjrzlyg72bjpy8zsxvaglc7jsv176bnyi87xdajmkvsgxpm7b3"))))
8249     (properties
8250      `((upstream-name . "org.Dm.eg.db")))
8251     (build-system r-build-system)
8252     (propagated-inputs
8253      `(("r-annotationdbi" ,r-annotationdbi)))
8254     (home-page "https://www.bioconductor.org/packages/org.Dm.eg.db/")
8255     (synopsis "Genome wide annotation for Fly")
8256     (description
8257      "This package provides mappings from Entrez gene identifiers to various
8258 annotations for the genome of the model fruit fly Drosophila melanogaster.")
8259     (license license:artistic2.0)))
8260
8261 (define-public r-org-mm-eg-db
8262   (package
8263     (name "r-org-mm-eg-db")
8264     (version "3.7.0")
8265     (source (origin
8266               (method url-fetch)
8267               ;; We cannot use bioconductor-uri here because this tarball is
8268               ;; located under "data/annotation/" instead of "bioc/".
8269               (uri (string-append "https://www.bioconductor.org/packages/"
8270                                   "release/data/annotation/src/contrib/"
8271                                   "org.Mm.eg.db_" version ".tar.gz"))
8272               (sha256
8273                (base32
8274                 "1i3nvrd3wjigf1rmgxq1p5xxc3p8v02h5gwi62s30rkrsyjjfjxx"))))
8275     (properties
8276      `((upstream-name . "org.Mm.eg.db")))
8277     (build-system r-build-system)
8278     (propagated-inputs
8279      `(("r-annotationdbi" ,r-annotationdbi)))
8280     (home-page "https://www.bioconductor.org/packages/org.Mm.eg.db/")
8281     (synopsis "Genome wide annotation for Mouse")
8282     (description
8283      "This package provides mappings from Entrez gene identifiers to various
8284 annotations for the genome of the model mouse Mus musculus.")
8285     (license license:artistic2.0)))
8286
8287 (define-public r-seqlogo
8288   (package
8289     (name "r-seqlogo")
8290     (version "1.48.0")
8291     (source
8292      (origin
8293        (method url-fetch)
8294        (uri (bioconductor-uri "seqLogo" version))
8295        (sha256
8296         (base32
8297          "022vr9ydwcivs7rw7kwj73gfk5gc7ckwa1q66vhd4kw9ylh70v68"))))
8298     (properties `((upstream-name . "seqLogo")))
8299     (build-system r-build-system)
8300     (home-page "https://bioconductor.org/packages/seqLogo")
8301     (synopsis "Sequence logos for DNA sequence alignments")
8302     (description
8303      "seqLogo takes the position weight matrix of a DNA sequence motif and
8304 plots the corresponding sequence logo as introduced by Schneider and
8305 Stephens (1990).")
8306     (license license:lgpl2.0+)))
8307
8308 (define-public r-bsgenome-hsapiens-ucsc-hg19
8309   (package
8310     (name "r-bsgenome-hsapiens-ucsc-hg19")
8311     (version "1.4.0")
8312     (source (origin
8313               (method url-fetch)
8314               ;; We cannot use bioconductor-uri here because this tarball is
8315               ;; located under "data/annotation/" instead of "bioc/".
8316               (uri (string-append "https://www.bioconductor.org/packages/"
8317                                   "release/data/annotation/src/contrib/"
8318                                   "BSgenome.Hsapiens.UCSC.hg19_"
8319                                   version ".tar.gz"))
8320               (sha256
8321                (base32
8322                 "1y0nqpk8cw5a34sd9hmin3z4v7iqm6hf6l22cl81vlbxqbjibxc8"))))
8323     (properties
8324      `((upstream-name . "BSgenome.Hsapiens.UCSC.hg19")))
8325     (build-system r-build-system)
8326     ;; As this package provides little more than a very large data file it
8327     ;; doesn't make sense to build substitutes.
8328     (arguments `(#:substitutable? #f))
8329     (propagated-inputs
8330      `(("r-bsgenome" ,r-bsgenome)))
8331     (home-page
8332      "https://www.bioconductor.org/packages/BSgenome.Hsapiens.UCSC.hg19/")
8333     (synopsis "Full genome sequences for Homo sapiens")
8334     (description
8335      "This package provides full genome sequences for Homo sapiens as provided
8336 by UCSC (hg19, February 2009) and stored in Biostrings objects.")
8337     (license license:artistic2.0)))
8338
8339 (define-public r-bsgenome-mmusculus-ucsc-mm9
8340   (package
8341     (name "r-bsgenome-mmusculus-ucsc-mm9")
8342     (version "1.4.0")
8343     (source (origin
8344               (method url-fetch)
8345               ;; We cannot use bioconductor-uri here because this tarball is
8346               ;; located under "data/annotation/" instead of "bioc/".
8347               (uri (string-append "https://www.bioconductor.org/packages/"
8348                                   "release/data/annotation/src/contrib/"
8349                                   "BSgenome.Mmusculus.UCSC.mm9_"
8350                                   version ".tar.gz"))
8351               (sha256
8352                (base32
8353                 "1birqw30g2azimxpnjfzmkphan7x131yy8b9h85lfz5fjdg7841i"))))
8354     (properties
8355      `((upstream-name . "BSgenome.Mmusculus.UCSC.mm9")))
8356     (build-system r-build-system)
8357     ;; As this package provides little more than a very large data file it
8358     ;; doesn't make sense to build substitutes.
8359     (arguments `(#:substitutable? #f))
8360     (propagated-inputs
8361      `(("r-bsgenome" ,r-bsgenome)))
8362     (home-page
8363      "https://www.bioconductor.org/packages/BSgenome.Mmusculus.UCSC.mm9/")
8364     (synopsis "Full genome sequences for Mouse")
8365     (description
8366      "This package provides full genome sequences for Mus musculus (Mouse) as
8367 provided by UCSC (mm9, July 2007) and stored in Biostrings objects.")
8368     (license license:artistic2.0)))
8369
8370 (define-public r-bsgenome-mmusculus-ucsc-mm10
8371   (package
8372     (name "r-bsgenome-mmusculus-ucsc-mm10")
8373     (version "1.4.0")
8374     (source (origin
8375               (method url-fetch)
8376               ;; We cannot use bioconductor-uri here because this tarball is
8377               ;; located under "data/annotation/" instead of "bioc/".
8378               (uri (string-append "https://www.bioconductor.org/packages/"
8379                                   "release/data/annotation/src/contrib/"
8380                                   "BSgenome.Mmusculus.UCSC.mm10_"
8381                                   version ".tar.gz"))
8382               (sha256
8383                (base32
8384                 "12s0nm2na9brjad4rn9l7d3db2aj8qa1xvz0y1k7gk08wayb6bkf"))))
8385     (properties
8386      `((upstream-name . "BSgenome.Mmusculus.UCSC.mm10")))
8387     (build-system r-build-system)
8388     ;; As this package provides little more than a very large data file it
8389     ;; doesn't make sense to build substitutes.
8390     (arguments `(#:substitutable? #f))
8391     (propagated-inputs
8392      `(("r-bsgenome" ,r-bsgenome)))
8393     (home-page
8394      "https://www.bioconductor.org/packages/BSgenome.Mmusculus.UCSC.mm10/")
8395     (synopsis "Full genome sequences for Mouse")
8396     (description
8397      "This package provides full genome sequences for Mus
8398 musculus (Mouse) as provided by UCSC (mm10, December 2011) and stored
8399 in Biostrings objects.")
8400     (license license:artistic2.0)))
8401
8402 (define-public r-txdb-mmusculus-ucsc-mm10-knowngene
8403   (package
8404     (name "r-txdb-mmusculus-ucsc-mm10-knowngene")
8405     (version "3.4.4")
8406     (source (origin
8407               (method url-fetch)
8408               ;; We cannot use bioconductor-uri here because this tarball is
8409               ;; located under "data/annotation/" instead of "bioc/".
8410               (uri (string-append "https://www.bioconductor.org/packages/"
8411                                   "release/data/annotation/src/contrib/"
8412                                   "TxDb.Mmusculus.UCSC.mm10.knownGene_"
8413                                   version ".tar.gz"))
8414               (sha256
8415                (base32
8416                 "01lgxc1fx5nhlpbwjd5zqghkkbmh6axd98ikx4b0spv0jdg6gf39"))))
8417     (properties
8418      `((upstream-name . "TxDb.Mmusculus.UCSC.mm10.knownGene")))
8419     (build-system r-build-system)
8420     ;; As this package provides little more than a very large data file it
8421     ;; doesn't make sense to build substitutes.
8422     (arguments `(#:substitutable? #f))
8423     (propagated-inputs
8424      `(("r-bsgenome" ,r-bsgenome)
8425        ("r-genomicfeatures" ,r-genomicfeatures)
8426        ("r-annotationdbi" ,r-annotationdbi)))
8427     (home-page
8428      "https://bioconductor.org/packages/TxDb.Mmusculus.UCSC.mm10.knownGene/")
8429     (synopsis "Annotation package for TxDb knownGene object(s) for Mouse")
8430     (description
8431      "This package loads a TxDb object, which is an R interface to
8432 prefabricated databases contained in this package.  This package provides
8433 the TxDb object of Mouse data as provided by UCSC (mm10, December 2011)
8434 based on the knownGene track.")
8435     (license license:artistic2.0)))
8436
8437 (define-public r-bsgenome-celegans-ucsc-ce6
8438   (package
8439     (name "r-bsgenome-celegans-ucsc-ce6")
8440     (version "1.4.0")
8441     (source (origin
8442               (method url-fetch)
8443               ;; We cannot use bioconductor-uri here because this tarball is
8444               ;; located under "data/annotation/" instead of "bioc/".
8445               (uri (string-append "https://www.bioconductor.org/packages/"
8446                                   "release/data/annotation/src/contrib/"
8447                                   "BSgenome.Celegans.UCSC.ce6_"
8448                                   version ".tar.gz"))
8449               (sha256
8450                (base32
8451                 "0mqzb353xv2c3m3vkb315dkmnxkgczp7ndnknyhpgjlybyf715v9"))))
8452     (properties
8453      `((upstream-name . "BSgenome.Celegans.UCSC.ce6")))
8454     (build-system r-build-system)
8455     ;; As this package provides little more than a very large data file it
8456     ;; doesn't make sense to build substitutes.
8457     (arguments `(#:substitutable? #f))
8458     (propagated-inputs
8459      `(("r-bsgenome" ,r-bsgenome)))
8460     (home-page
8461      "https://www.bioconductor.org/packages/BSgenome.Celegans.UCSC.ce6/")
8462     (synopsis "Full genome sequences for Worm")
8463     (description
8464      "This package provides full genome sequences for Caenorhabditis
8465 elegans (Worm) as provided by UCSC (ce6, May 2008) and stored in Biostrings
8466 objects.")
8467     (license license:artistic2.0)))
8468
8469 (define-public r-bsgenome-celegans-ucsc-ce10
8470   (package
8471     (name "r-bsgenome-celegans-ucsc-ce10")
8472     (version "1.4.0")
8473     (source (origin
8474               (method url-fetch)
8475               ;; We cannot use bioconductor-uri here because this tarball is
8476               ;; located under "data/annotation/" instead of "bioc/".
8477               (uri (string-append "https://www.bioconductor.org/packages/"
8478                                   "release/data/annotation/src/contrib/"
8479                                   "BSgenome.Celegans.UCSC.ce10_"
8480                                   version ".tar.gz"))
8481               (sha256
8482                (base32
8483                 "1zaym97jk4npxk14ifvwz2rvhm4zx9xgs33r9vvx9rlynp0gydrk"))))
8484     (properties
8485      `((upstream-name . "BSgenome.Celegans.UCSC.ce10")))
8486     (build-system r-build-system)
8487     ;; As this package provides little more than a very large data file it
8488     ;; doesn't make sense to build substitutes.
8489     (arguments `(#:substitutable? #f))
8490     (propagated-inputs
8491      `(("r-bsgenome" ,r-bsgenome)))
8492     (home-page
8493      "https://www.bioconductor.org/packages/BSgenome.Celegans.UCSC.ce10/")
8494     (synopsis "Full genome sequences for Worm")
8495     (description
8496      "This package provides full genome sequences for Caenorhabditis
8497 elegans (Worm) as provided by UCSC (ce10, Oct 2010) and stored in Biostrings
8498 objects.")
8499     (license license:artistic2.0)))
8500
8501 (define-public r-bsgenome-dmelanogaster-ucsc-dm3
8502   (package
8503     (name "r-bsgenome-dmelanogaster-ucsc-dm3")
8504     (version "1.4.0")
8505     (source (origin
8506               (method url-fetch)
8507               ;; We cannot use bioconductor-uri here because this tarball is
8508               ;; located under "data/annotation/" instead of "bioc/".
8509               (uri (string-append "https://www.bioconductor.org/packages/"
8510                                   "release/data/annotation/src/contrib/"
8511                                   "BSgenome.Dmelanogaster.UCSC.dm3_"
8512                                   version ".tar.gz"))
8513               (sha256
8514                (base32
8515                 "19bm3lkhhkag3gnwp419211fh0cnr0x6fa0r1lr0ycwrikxdxsv8"))))
8516     (properties
8517      `((upstream-name . "BSgenome.Dmelanogaster.UCSC.dm3")))
8518     (build-system r-build-system)
8519     ;; As this package provides little more than a very large data file it
8520     ;; doesn't make sense to build substitutes.
8521     (arguments `(#:substitutable? #f))
8522     (propagated-inputs
8523      `(("r-bsgenome" ,r-bsgenome)))
8524     (home-page
8525      "https://www.bioconductor.org/packages/BSgenome.Dmelanogaster.UCSC.dm3/")
8526     (synopsis "Full genome sequences for Fly")
8527     (description
8528      "This package provides full genome sequences for Drosophila
8529 melanogaster (Fly) as provided by UCSC (dm3, April 2006) and stored in
8530 Biostrings objects.")
8531     (license license:artistic2.0)))
8532
8533 (define-public r-motifrg
8534   (package
8535     (name "r-motifrg")
8536     (version "1.26.0")
8537     (source
8538      (origin
8539        (method url-fetch)
8540        (uri (bioconductor-uri "motifRG" version))
8541        (sha256
8542         (base32
8543          "1wxww6i0jgyapqclcwy0zzf9kqjvrvylr89z7yhg1izi7jnw2fka"))))
8544     (properties `((upstream-name . "motifRG")))
8545     (build-system r-build-system)
8546     (propagated-inputs
8547      `(("r-biostrings" ,r-biostrings)
8548        ("r-bsgenome" ,r-bsgenome)
8549        ("r-bsgenome-hsapiens-ucsc-hg19" ,r-bsgenome-hsapiens-ucsc-hg19)
8550        ("r-iranges" ,r-iranges)
8551        ("r-seqlogo" ,r-seqlogo)
8552        ("r-xvector" ,r-xvector)))
8553     (home-page "https://bioconductor.org/packages/motifRG")
8554     (synopsis "Discover motifs in high throughput sequencing data")
8555     (description
8556      "This package provides tools for discriminative motif discovery in high
8557 throughput genetic sequencing data sets using regression methods.")
8558     (license license:artistic2.0)))
8559
8560 (define-public r-qtl
8561  (package
8562   (name "r-qtl")
8563   (version "1.42-8")
8564   (source
8565    (origin
8566     (method url-fetch)
8567     (uri (string-append "mirror://cran/src/contrib/qtl_"
8568                         version ".tar.gz"))
8569     (sha256
8570      (base32
8571       "1l528dwvfpdlr05imrrm4rq32axp6hld9nqm6mm43kn5n7z2f5k6"))))
8572   (build-system r-build-system)
8573   (home-page "http://rqtl.org/")
8574   (synopsis "R package for analyzing QTL experiments in genetics")
8575   (description "R/qtl is an extension library for the R statistics
8576 system.  It is used to analyze experimental crosses for identifying
8577 genes contributing to variation in quantitative traits (so-called
8578 quantitative trait loci, QTLs).
8579
8580 Using a hidden Markov model, R/qtl allows to estimate genetic maps, to
8581 identify genotyping errors, and to perform single-QTL and two-QTL,
8582 two-dimensional genome scans.")
8583   (license license:gpl3)))
8584
8585 (define-public r-zlibbioc
8586   (package
8587     (name "r-zlibbioc")
8588     (version "1.28.0")
8589     (source (origin
8590               (method url-fetch)
8591               (uri (bioconductor-uri "zlibbioc" version))
8592               (sha256
8593                (base32
8594                 "0bjvzy24kab7ank02cc1qk2ikcz4dllgf66wpsdl0d3zp4gn3l2h"))))
8595     (properties
8596      `((upstream-name . "zlibbioc")))
8597     (build-system r-build-system)
8598     (home-page "https://bioconductor.org/packages/zlibbioc")
8599     (synopsis "Provider for zlib-1.2.5 to R packages")
8600     (description "This package uses the source code of zlib-1.2.5 to create
8601 libraries for systems that do not have these available via other means.")
8602     (license license:artistic2.0)))
8603
8604 (define-public r-r4rna
8605   (package
8606     (name "r-r4rna")
8607     (version "0.1.4")
8608     (source
8609      (origin
8610        (method url-fetch)
8611        (uri (string-append "http://www.e-rna.org/r-chie/files/R4RNA_"
8612                            version ".tar.gz"))
8613        (sha256
8614         (base32
8615          "1p0i78wh76jfgmn9jphbwwaz6yy6pipzfg08xs54cxavxg2j81p5"))))
8616     (build-system r-build-system)
8617     (propagated-inputs
8618      `(("r-optparse" ,r-optparse)
8619        ("r-rcolorbrewer" ,r-rcolorbrewer)))
8620     (home-page "http://www.e-rna.org/r-chie/index.cgi")
8621     (synopsis "Analysis framework for RNA secondary structure")
8622     (description
8623      "The R4RNA package aims to be a general framework for the analysis of RNA
8624 secondary structure and comparative analysis in R.")
8625     (license license:gpl3+)))
8626
8627 (define-public r-rhtslib
8628   (package
8629     (name "r-rhtslib")
8630     (version "1.14.0")
8631     (source
8632      (origin
8633        (method url-fetch)
8634        (uri (bioconductor-uri "Rhtslib" version))
8635        (sha256
8636         (base32
8637          "1h4q54f8za3aaxgy186zf2165sar5c3cgxkk44lq5hzx5pxkl5wn"))))
8638     (properties `((upstream-name . "Rhtslib")))
8639     (build-system r-build-system)
8640     (propagated-inputs
8641      `(("r-zlibbioc" ,r-zlibbioc)))
8642     (inputs
8643      `(("zlib" ,zlib)))
8644     (native-inputs
8645      `(("pkg-config" ,pkg-config)))
8646     (home-page "https://github.com/nhayden/Rhtslib")
8647     (synopsis "High-throughput sequencing library as an R package")
8648     (description
8649      "This package provides the HTSlib C library for high-throughput
8650 nucleotide sequence analysis.  The package is primarily useful to developers
8651 of other R packages who wish to make use of HTSlib.")
8652     (license license:lgpl2.0+)))
8653
8654 (define-public r-bamsignals
8655   (package
8656     (name "r-bamsignals")
8657     (version "1.14.0")
8658     (source
8659      (origin
8660        (method url-fetch)
8661        (uri (bioconductor-uri "bamsignals" version))
8662        (sha256
8663         (base32
8664          "19irfx1y1izf903vq59wxsdbf88g143zy9l89gxqawh7jfxds8w8"))))
8665     (build-system r-build-system)
8666     (propagated-inputs
8667      `(("r-biocgenerics" ,r-biocgenerics)
8668        ("r-genomicranges" ,r-genomicranges)
8669        ("r-iranges" ,r-iranges)
8670        ("r-rcpp" ,r-rcpp)
8671        ("r-rhtslib" ,r-rhtslib)
8672        ("r-zlibbioc" ,r-zlibbioc)))
8673     (inputs
8674      `(("zlib" ,zlib)))
8675     (home-page "https://bioconductor.org/packages/bamsignals")
8676     (synopsis "Extract read count signals from bam files")
8677     (description
8678      "This package allows to efficiently obtain count vectors from indexed bam
8679 files.  It counts the number of nucleotide sequence reads in given genomic
8680 ranges and it computes reads profiles and coverage profiles.  It also handles
8681 paired-end data.")
8682     (license license:gpl2+)))
8683
8684 (define-public r-rcas
8685   (package
8686     (name "r-rcas")
8687     (version "1.8.0")
8688     (source (origin
8689               (method url-fetch)
8690               (uri (bioconductor-uri "RCAS" version))
8691               (sha256
8692                (base32
8693                 "0ss5hcg2m7gjji6dd23zxa5bd5a7knwcnada4qs5q2l4clgk39ad"))))
8694     (build-system r-build-system)
8695     (propagated-inputs
8696      `(("r-annotationdbi" ,r-annotationdbi)
8697        ("r-biocgenerics" ,r-biocgenerics)
8698        ("r-biomart" ,r-biomart)
8699        ("r-biostrings" ,r-biostrings)
8700        ("r-bsgenome-hsapiens-ucsc-hg19" ,r-bsgenome-hsapiens-ucsc-hg19)
8701        ("r-cowplot" ,r-cowplot)
8702        ("r-data-table" ,r-data-table)
8703        ("r-dbi" ,r-dbi)
8704        ("r-dt" ,r-dt)
8705        ("r-genomation" ,r-genomation)
8706        ("r-genomeinfodb" ,r-genomeinfodb)
8707        ("r-genomicfeatures" ,r-genomicfeatures)
8708        ("r-genomicranges" ,r-genomicranges)
8709        ("r-ggplot2" ,r-ggplot2)
8710        ("r-ggseqlogo" ,r-ggseqlogo)
8711        ("r-knitr" ,r-knitr)
8712        ("r-motifrg" ,r-motifrg)
8713        ("r-org-hs-eg-db" ,r-org-hs-eg-db)
8714        ("r-pbapply" ,r-pbapply)
8715        ("r-pheatmap" ,r-pheatmap)
8716        ("r-plotly" ,r-plotly)
8717        ("r-plotrix" ,r-plotrix)
8718        ("r-proxy" ,r-proxy)
8719        ("r-rsqlite" ,r-rsqlite)
8720        ("r-rtracklayer" ,r-rtracklayer)
8721        ("r-rmarkdown" ,r-rmarkdown)
8722        ("r-s4vectors" ,r-s4vectors)
8723        ("r-topgo" ,r-topgo)))
8724     (synopsis "RNA-centric annotation system")
8725     (description
8726      "RCAS aims to be a standalone RNA-centric annotation system that provides
8727 intuitive reports and publication-ready graphics.  This package provides the R
8728 library implementing most of the pipeline's features.")
8729     (home-page "https://github.com/BIMSBbioinfo/RCAS")
8730     (license license:artistic2.0)))
8731
8732 (define-public rcas-web
8733   (package
8734     (name "rcas-web")
8735     (version "0.0.5")
8736     (source
8737      (origin
8738        (method url-fetch)
8739        (uri (string-append "https://github.com/BIMSBbioinfo/rcas-web/"
8740                            "releases/download/v" version
8741                            "/rcas-web-" version ".tar.gz"))
8742        (sha256
8743         (base32
8744          "0igz7jpcf7cm9800zcag6p3gd1i649figrhbdba6cjkm8f4gfspr"))))
8745     (build-system gnu-build-system)
8746     (arguments
8747      `(#:phases
8748        (modify-phases %standard-phases
8749          (add-after 'install 'wrap-executable
8750            (lambda* (#:key inputs outputs #:allow-other-keys)
8751              (let* ((out (assoc-ref outputs "out"))
8752                     (json   (assoc-ref inputs "guile-json"))
8753                     (redis  (assoc-ref inputs "guile-redis"))
8754                     (path   (string-append
8755                              json  "/share/guile/site/2.2:"
8756                              redis "/share/guile/site/2.2")))
8757                (wrap-program (string-append out "/bin/rcas-web")
8758                  `("GUILE_LOAD_PATH" ":" = (,path))
8759                  `("GUILE_LOAD_COMPILED_PATH" ":" = (,path))
8760                  `("R_LIBS_SITE" ":" = (,(getenv "R_LIBS_SITE")))))
8761              #t)))))
8762     (inputs
8763      `(("r-minimal" ,r-minimal)
8764        ("r-rcas" ,r-rcas)
8765        ("guile-next" ,guile-2.2)
8766        ("guile-json" ,guile-json)
8767        ("guile-redis" ,guile2.2-redis)))
8768     (native-inputs
8769      `(("pkg-config" ,pkg-config)))
8770     (home-page "https://github.com/BIMSBbioinfo/rcas-web")
8771     (synopsis "Web interface for RNA-centric annotation system (RCAS)")
8772     (description "This package provides a simple web interface for the
8773 @dfn{RNA-centric annotation system} (RCAS).")
8774     (license license:agpl3+)))
8775
8776 (define-public r-mutationalpatterns
8777   (package
8778     (name "r-mutationalpatterns")
8779     (version "1.8.0")
8780     (source
8781      (origin
8782        (method url-fetch)
8783        (uri (bioconductor-uri "MutationalPatterns" version))
8784        (sha256
8785         (base32
8786          "0w9lg1zs106h6rqvy8mhikq6q6q9syw6c1prcxr38ssh85rcih12"))))
8787     (build-system r-build-system)
8788     (propagated-inputs
8789      `(("r-biocgenerics" ,r-biocgenerics)
8790        ("r-biostrings" ,r-biostrings)
8791        ;; These two packages are suggested packages
8792        ("r-bsgenome-hsapiens-1000g" ,r-bsgenome-hsapiens-1000genomes-hs37d5)
8793        ("r-bsgenome-hsapiens-ucsc-hg19" ,r-bsgenome-hsapiens-ucsc-hg19)
8794        ("r-genomicranges" ,r-genomicranges)
8795        ("r-genomeinfodb" ,r-genomeinfodb)
8796        ("r-ggplot2" ,r-ggplot2)
8797        ("r-iranges" ,r-iranges)
8798        ("r-nmf" ,r-nmf)
8799        ("r-plyr" ,r-plyr)
8800        ("r-pracma" ,r-pracma)
8801        ("r-reshape2" ,r-reshape2)
8802        ("r-cowplot" ,r-cowplot)
8803        ("r-ggdendro" ,r-ggdendro)
8804        ("r-s4vectors" ,r-s4vectors)
8805        ("r-summarizedexperiment" ,r-summarizedexperiment)
8806        ("r-variantannotation" ,r-variantannotation)))
8807     (home-page "https://bioconductor.org/packages/MutationalPatterns/")
8808     (synopsis "Extract and visualize mutational patterns in genomic data")
8809     (description "This package provides an extensive toolset for the
8810 characterization and visualization of a wide range of mutational patterns
8811 in SNV base substitution data.")
8812     (license license:expat)))
8813
8814 (define-public r-wgcna
8815   (package
8816     (name "r-wgcna")
8817     (version "1.66")
8818     (source
8819      (origin
8820        (method url-fetch)
8821        (uri (cran-uri "WGCNA" version))
8822        (sha256
8823         (base32
8824          "0rhnyhzfn93yp24jz9v6dzrmyizwzdw070a7idm0k33w1cm8sjqv"))))
8825     (properties `((upstream-name . "WGCNA")))
8826     (build-system r-build-system)
8827     (propagated-inputs
8828      `(("r-annotationdbi" ,r-annotationdbi)
8829        ("r-doparallel" ,r-doparallel)
8830        ("r-dynamictreecut" ,r-dynamictreecut)
8831        ("r-fastcluster" ,r-fastcluster)
8832        ("r-foreach" ,r-foreach)
8833        ("r-go-db" ,r-go-db)
8834        ("r-hmisc" ,r-hmisc)
8835        ("r-impute" ,r-impute)
8836        ("r-rcpp" ,r-rcpp)
8837        ("r-robust" ,r-robust)
8838        ("r-survival" ,r-survival)
8839        ("r-matrixstats" ,r-matrixstats)
8840        ("r-preprocesscore" ,r-preprocesscore)))
8841     (home-page
8842      "http://www.genetics.ucla.edu/labs/horvath/CoexpressionNetwork/Rpackages/WGCNA/")
8843     (synopsis "Weighted correlation network analysis")
8844     (description
8845      "This package provides functions necessary to perform Weighted
8846 Correlation Network Analysis on high-dimensional data.  It includes functions
8847 for rudimentary data cleaning, construction and summarization of correlation
8848 networks, module identification and functions for relating both variables and
8849 modules to sample traits.  It also includes a number of utility functions for
8850 data manipulation and visualization.")
8851     (license license:gpl2+)))
8852
8853 (define-public r-chipkernels
8854   (let ((commit "c9cfcacb626b1221094fb3490ea7bac0fd625372")
8855         (revision "1"))
8856     (package
8857       (name "r-chipkernels")
8858       (version (string-append "1.1-" revision "." (string-take commit 9)))
8859       (source
8860        (origin
8861          (method git-fetch)
8862          (uri (git-reference
8863                (url "https://github.com/ManuSetty/ChIPKernels.git")
8864                (commit commit)))
8865          (file-name (string-append name "-" version))
8866          (sha256
8867           (base32
8868            "14bj5qhjm1hsm9ay561nfbqi9wxsa7y487df2idsaaf6z10nw4v0"))))
8869       (build-system r-build-system)
8870       (propagated-inputs
8871        `(("r-iranges" ,r-iranges)
8872          ("r-xvector" ,r-xvector)
8873          ("r-biostrings" ,r-biostrings)
8874          ("r-bsgenome" ,r-bsgenome)
8875          ("r-gtools" ,r-gtools)
8876          ("r-genomicranges" ,r-genomicranges)
8877          ("r-sfsmisc" ,r-sfsmisc)
8878          ("r-kernlab" ,r-kernlab)
8879          ("r-s4vectors" ,r-s4vectors)
8880          ("r-biocgenerics" ,r-biocgenerics)))
8881       (home-page "https://github.com/ManuSetty/ChIPKernels")
8882       (synopsis "Build string kernels for DNA Sequence analysis")
8883       (description "ChIPKernels is an R package for building different string
8884 kernels used for DNA Sequence analysis.  A dictionary of the desired kernel
8885 must be built and this dictionary can be used for determining kernels for DNA
8886 Sequences.")
8887       (license license:gpl2+))))
8888
8889 (define-public r-seqgl
8890   (package
8891     (name "r-seqgl")
8892     (version "1.1.4")
8893     (source
8894      (origin
8895        (method git-fetch)
8896        (uri (git-reference
8897              (url "https://github.com/ManuSetty/SeqGL.git")
8898              (commit version)))
8899        (file-name (git-file-name name version))
8900        (sha256
8901         (base32
8902          "1r6ywvhxl3ffv48lgj7sbd582mcc6dha3ksgc2qjlvjrnkbj3799"))))
8903     (build-system r-build-system)
8904     (propagated-inputs
8905      `(("r-biostrings" ,r-biostrings)
8906        ("r-chipkernels" ,r-chipkernels)
8907        ("r-genomicranges" ,r-genomicranges)
8908        ("r-spams" ,r-spams)
8909        ("r-wgcna" ,r-wgcna)
8910        ("r-fastcluster" ,r-fastcluster)))
8911     (home-page "https://github.com/ManuSetty/SeqGL")
8912     (synopsis "Group lasso for Dnase/ChIP-seq data")
8913     (description "SeqGL is a group lasso based algorithm to extract
8914 transcription factor sequence signals from ChIP, DNase and ATAC-seq profiles.
8915 This package presents a method which uses group lasso to discriminate between
8916 bound and non bound genomic regions to accurately identify transcription
8917 factors bound at the specific regions.")
8918     (license license:gpl2+)))
8919
8920 (define-public r-gkmsvm
8921   (package
8922     (name "r-gkmsvm")
8923     (version "0.79.0")
8924     (source
8925      (origin
8926        (method url-fetch)
8927        (uri (cran-uri "gkmSVM" version))
8928        (sha256
8929         (base32
8930          "04dakbgfvfalz4rm4fvvybp506dn5fbj5g86ybfhrc6wywjllsz3"))))
8931     (properties `((upstream-name . "gkmSVM")))
8932     (build-system r-build-system)
8933     (propagated-inputs
8934      `(("r-biocgenerics" ,r-biocgenerics)
8935        ("r-biostrings" ,r-biostrings)
8936        ("r-genomeinfodb" ,r-genomeinfodb)
8937        ("r-genomicranges" ,r-genomicranges)
8938        ("r-iranges" ,r-iranges)
8939        ("r-kernlab" ,r-kernlab)
8940        ("r-rcpp" ,r-rcpp)
8941        ("r-rocr" ,r-rocr)
8942        ("r-rtracklayer" ,r-rtracklayer)
8943        ("r-s4vectors" ,r-s4vectors)
8944        ("r-seqinr" ,r-seqinr)))
8945     (home-page "https://cran.r-project.org/web/packages/gkmSVM")
8946     (synopsis "Gapped-kmer support vector machine")
8947     (description
8948      "This R package provides tools for training gapped-kmer SVM classifiers
8949 for DNA and protein sequences.  This package supports several sequence
8950 kernels, including: gkmSVM, kmer-SVM, mismatch kernel and wildcard kernel.")
8951     (license license:gpl2+)))
8952
8953 (define-public r-tximport
8954   (package
8955     (name "r-tximport")
8956     (version "1.10.0")
8957     (source (origin
8958               (method url-fetch)
8959               (uri (bioconductor-uri "tximport" version))
8960               (sha256
8961                (base32
8962                 "0za2js8hqjgz8ria09cglynffj4w9vrzg85nmn1xgpvmc1xk813h"))))
8963     (build-system r-build-system)
8964     (home-page "https://bioconductor.org/packages/tximport")
8965     (synopsis "Import and summarize transcript-level estimates for gene-level analysis")
8966     (description
8967      "This package provides tools to import transcript-level abundance,
8968 estimated counts and transcript lengths, and to summarize them into matrices
8969 for use with downstream gene-level analysis packages.  Average transcript
8970 length, weighted by sample-specific transcript abundance estimates, is
8971 provided as a matrix which can be used as an offset for different expression
8972 of gene-level counts.")
8973     (license license:gpl2+)))
8974
8975 (define-public r-rhdf5
8976   (package
8977     (name "r-rhdf5")
8978     (version "2.26.0")
8979     (source (origin
8980               (method url-fetch)
8981               (uri (bioconductor-uri "rhdf5" version))
8982               (sha256
8983                (base32
8984                 "0xmpkfdsmgl79ffffj7cf9fx3zxki2rk0xn25k778kr3s0sbmhis"))))
8985     (build-system r-build-system)
8986     (propagated-inputs
8987      `(("r-rhdf5lib" ,r-rhdf5lib)))
8988     (inputs
8989      `(("zlib" ,zlib)))
8990     (home-page "https://bioconductor.org/packages/rhdf5")
8991     (synopsis "HDF5 interface to R")
8992     (description
8993      "This R/Bioconductor package provides an interface between HDF5 and R.
8994 HDF5's main features are the ability to store and access very large and/or
8995 complex datasets and a wide variety of metadata on mass storage (disk) through
8996 a completely portable file format.  The rhdf5 package is thus suited for the
8997 exchange of large and/or complex datasets between R and other software
8998 package, and for letting R applications work on datasets that are larger than
8999 the available RAM.")
9000     (license license:artistic2.0)))
9001
9002 (define-public r-annotationfilter
9003   (package
9004     (name "r-annotationfilter")
9005     (version "1.6.0")
9006     (source (origin
9007               (method url-fetch)
9008               (uri (bioconductor-uri "AnnotationFilter" version))
9009               (sha256
9010                (base32
9011                 "0wrr10cxjzmxx46vjzq2nsf6xlqz1sqwx4xm0sk3d77ff8wmph4x"))))
9012     (properties
9013      `((upstream-name . "AnnotationFilter")))
9014     (build-system r-build-system)
9015     (propagated-inputs
9016      `(("r-genomicranges" ,r-genomicranges)
9017        ("r-lazyeval" ,r-lazyeval)))
9018     (home-page "https://github.com/Bioconductor/AnnotationFilter")
9019     (synopsis "Facilities for filtering Bioconductor annotation resources")
9020     (description
9021      "This package provides classes and other infrastructure to implement
9022 filters for manipulating Bioconductor annotation resources.  The filters are
9023 used by @code{ensembldb}, @code{Organism.dplyr}, and other packages.")
9024     (license license:artistic2.0)))
9025
9026 (define-public emboss
9027   (package
9028     (name "emboss")
9029     (version "6.5.7")
9030     (source (origin
9031               (method url-fetch)
9032               (uri (string-append "ftp://emboss.open-bio.org/pub/EMBOSS/old/"
9033                                   (version-major+minor version) ".0/"
9034                                   "EMBOSS-" version ".tar.gz"))
9035               (sha256
9036                (base32
9037                 "0vsmz96gc411yj2iyzdrsmg4l2n1nhgmp7vrgzlxx3xixv9xbf0q"))))
9038     (build-system gnu-build-system)
9039     (arguments
9040      `(#:configure-flags
9041        (list (string-append "--with-hpdf="
9042                             (assoc-ref %build-inputs "libharu")))
9043        #:phases
9044        (modify-phases %standard-phases
9045          (add-after 'unpack 'fix-checks
9046            (lambda _
9047              ;; The PNGDRIVER tests check for the presence of libgd, libpng
9048              ;; and zlib, but assume that they are all found at the same
9049              ;; prefix.
9050              (substitute* "configure.in"
9051                (("CHECK_PNGDRIVER")
9052                 "LIBS=\"$LIBS -lgd -lpng -lz -lm\"
9053 AC_DEFINE([PLD_png], [1], [Define to 1 if PNG support is available])
9054 AM_CONDITIONAL(AMPNG, true)"))
9055              #t))
9056          (add-after 'fix-checks 'disable-update-check
9057            (lambda _
9058              ;; At build time there is no connection to the Internet, so
9059              ;; looking for updates will not work.
9060              (substitute* "Makefile.am"
9061                (("\\$\\(bindir\\)/embossupdate") ""))
9062              #t))
9063          (add-after 'disable-update-check 'autogen
9064            (lambda _ (invoke "autoreconf" "-vif") #t)))))
9065     (inputs
9066      `(("perl" ,perl)
9067        ("libpng" ,libpng)
9068        ("gd" ,gd)
9069        ("libx11" ,libx11)
9070        ("libharu" ,libharu)
9071        ("zlib" ,zlib)))
9072     (native-inputs
9073      `(("autoconf" ,autoconf)
9074        ("automake" ,automake)
9075        ("libtool" ,libtool)
9076        ("pkg-config" ,pkg-config)))
9077     (home-page "http://emboss.sourceforge.net")
9078     (synopsis "Molecular biology analysis suite")
9079     (description "EMBOSS is the \"European Molecular Biology Open Software
9080 Suite\".  EMBOSS is an analysis package specially developed for the needs of
9081 the molecular biology (e.g. EMBnet) user community.  The software
9082 automatically copes with data in a variety of formats and even allows
9083 transparent retrieval of sequence data from the web.  It also provides a
9084 number of libraries for the development of software in the field of molecular
9085 biology.  EMBOSS also integrates a range of currently available packages and
9086 tools for sequence analysis into a seamless whole.")
9087     (license license:gpl2+)))
9088
9089 (define-public bits
9090   (let ((revision "1")
9091         (commit "3cc4567896d9d6442923da944beb704750a08d2d"))
9092     (package
9093       (name "bits")
9094       ;; The version is 2.13.0 even though no release archives have been
9095       ;; published as yet.
9096       (version (string-append "2.13.0-" revision "." (string-take commit 9)))
9097       (source (origin
9098                 (method git-fetch)
9099                 (uri (git-reference
9100                       (url "https://github.com/arq5x/bits.git")
9101                       (commit commit)))
9102                 (file-name (string-append name "-" version "-checkout"))
9103                 (sha256
9104                  (base32
9105                   "17n2kffk4kmhivd8c98g2vr6y1s23vbg4sxlxs689wni66797hbs"))))
9106       (build-system gnu-build-system)
9107       (arguments
9108        `(#:tests? #f ;no tests included
9109          #:phases
9110          (modify-phases %standard-phases
9111            (delete 'configure)
9112            (add-after 'unpack 'remove-cuda
9113              (lambda _
9114                (substitute* "Makefile"
9115                  ((".*_cuda") "")
9116                  (("(bits_test_intersections) \\\\" _ match) match))
9117                #t))
9118            (replace 'install
9119              (lambda* (#:key outputs #:allow-other-keys)
9120                (copy-recursively
9121                 "bin" (string-append (assoc-ref outputs "out") "/bin"))
9122                #t)))))
9123       (inputs
9124        `(("gsl" ,gsl)
9125          ("zlib" ,zlib)))
9126       (home-page "https://github.com/arq5x/bits")
9127       (synopsis "Implementation of binary interval search algorithm")
9128       (description "This package provides an implementation of the
9129 BITS (Binary Interval Search) algorithm, an approach to interval set
9130 intersection.  It is especially suited for the comparison of diverse genomic
9131 datasets and the exploration of large datasets of genome
9132 intervals (e.g. genes, sequence alignments).")
9133       (license license:gpl2))))
9134
9135 (define-public piranha
9136   ;; There is no release tarball for the latest version.  The latest commit is
9137   ;; older than one year at the time of this writing.
9138   (let ((revision "1")
9139         (commit   "0466d364b71117d01e4471b74c514436cc281233"))
9140     (package
9141       (name "piranha")
9142       (version (string-append "1.2.1-" revision "." (string-take commit 9)))
9143       (source (origin
9144                 (method git-fetch)
9145                 (uri (git-reference
9146                       (url "https://github.com/smithlabcode/piranha.git")
9147                       (commit commit)))
9148                 (file-name (git-file-name name version))
9149                 (sha256
9150                  (base32
9151                   "117dc0zf20c61jam69sk4abl57ah6yi6i7qra7d7y5zrbgk12q5n"))))
9152       (build-system gnu-build-system)
9153       (arguments
9154        `(#:test-target "test"
9155          #:phases
9156          (modify-phases %standard-phases
9157            (add-after 'unpack 'copy-smithlab-cpp
9158              (lambda* (#:key inputs #:allow-other-keys)
9159                (for-each (lambda (file)
9160                            (install-file file "./src/smithlab_cpp/"))
9161                          (find-files (assoc-ref inputs "smithlab-cpp")))
9162                #t))
9163            (add-after 'install 'install-to-store
9164              (lambda* (#:key outputs #:allow-other-keys)
9165                (let* ((out (assoc-ref outputs "out"))
9166                       (bin (string-append out "/bin")))
9167                  (for-each (lambda (file)
9168                              (install-file file bin))
9169                            (find-files "bin" ".*")))
9170                #t)))
9171          #:configure-flags
9172          (list (string-append "--with-bam_tools_headers="
9173                               (assoc-ref %build-inputs "bamtools") "/include/bamtools")
9174                (string-append "--with-bam_tools_library="
9175                               (assoc-ref %build-inputs "bamtools") "/lib/bamtools"))))
9176       (inputs
9177        `(("bamtools" ,bamtools)
9178          ("samtools" ,samtools-0.1)
9179          ("gsl" ,gsl)
9180          ("smithlab-cpp"
9181           ,(let ((commit "3723e2db438c51501d0423429ff396c3035ba46a"))
9182              (origin
9183                (method git-fetch)
9184                (uri (git-reference
9185                      (url "https://github.com/smithlabcode/smithlab_cpp.git")
9186                      (commit commit)))
9187                (file-name (string-append "smithlab_cpp-" commit "-checkout"))
9188                (sha256
9189                 (base32
9190                  "0l4gvbwslw5ngziskja41c00x1r06l3yidv7y0xw9djibhykzy0g")))))))
9191       (native-inputs
9192        `(("python" ,python-2)))
9193       (home-page "https://github.com/smithlabcode/piranha")
9194       (synopsis "Peak-caller for CLIP-seq and RIP-seq data")
9195       (description
9196        "Piranha is a peak-caller for genomic data produced by CLIP-seq and
9197 RIP-seq experiments.  It takes input in BED or BAM format and identifies
9198 regions of statistically significant read enrichment.  Additional covariates
9199 may optionally be provided to further inform the peak-calling process.")
9200       (license license:gpl3+))))
9201
9202 (define-public pepr
9203   (package
9204     (name "pepr")
9205     (version "1.0.9")
9206     (source (origin
9207               (method url-fetch)
9208               (uri (string-append "https://pypi.python.org/packages/source/P"
9209                                   "/PePr/PePr-" version ".tar.gz"))
9210               (sha256
9211                (base32
9212                 "0qxjfdpl1b1y53nccws2d85f6k74zwmx8y8sd9rszcqhfayx6gdx"))))
9213     (build-system python-build-system)
9214     (arguments
9215      `(#:python ,python-2 ; python2 only
9216        #:tests? #f)) ; no tests included
9217     (propagated-inputs
9218      `(("python2-numpy" ,python2-numpy)
9219        ("python2-scipy" ,python2-scipy)
9220        ("python2-pysam" ,python2-pysam)))
9221     (home-page "https://github.com/shawnzhangyx/PePr")
9222     (synopsis "Peak-calling and prioritization pipeline for ChIP-Seq data")
9223     (description
9224      "PePr is a ChIP-Seq peak calling or differential binding analysis tool
9225 that is primarily designed for data with biological replicates.  It uses a
9226 negative binomial distribution to model the read counts among the samples in
9227 the same group, and look for consistent differences between ChIP and control
9228 group or two ChIP groups run under different conditions.")
9229     (license license:gpl3+)))
9230
9231 (define-public filevercmp
9232   (let ((commit "1a9b779b93d0b244040274794d402106907b71b7"))
9233     (package
9234       (name "filevercmp")
9235       (version (string-append "0-1." (string-take commit 7)))
9236       (source (origin
9237                 (method git-fetch)
9238                 (uri (git-reference
9239                       (url "https://github.com/ekg/filevercmp.git")
9240                       (commit commit)))
9241                 (file-name (git-file-name name commit))
9242                 (sha256
9243                  (base32
9244                   "1j9vxsy0y050v59h0q1d6501fcw1kjvj0d18l1xk2zyg0jzj247c"))))
9245       (build-system gnu-build-system)
9246       (arguments
9247        `(#:tests? #f ; There are no tests to run.
9248          #:phases
9249          (modify-phases %standard-phases
9250            (delete 'configure) ; There is no configure phase.
9251            (replace 'install
9252              (lambda* (#:key outputs #:allow-other-keys)
9253                (let ((bin (string-append (assoc-ref outputs "out") "/bin")))
9254                  (install-file "filevercmp" bin)
9255                  #t))))))
9256       (home-page "https://github.com/ekg/filevercmp")
9257       (synopsis "This program compares version strings")
9258       (description "This program compares version strings.  It intends to be a
9259 replacement for strverscmp.")
9260       (license license:gpl3+))))
9261
9262 (define-public multiqc
9263   (package
9264     (name "multiqc")
9265     (version "1.5")
9266     (source
9267      (origin
9268        (method url-fetch)
9269        (uri (pypi-uri "multiqc" version))
9270        (sha256
9271         (base32
9272          "02iihfl0w0hpnr4pa0sbd1y9qxrg3ycyhjp5lidkcrqh1lmzs3zy"))))
9273     (build-system python-build-system)
9274     (propagated-inputs
9275      `(("python-jinja2" ,python-jinja2)
9276        ("python-simplejson" ,python-simplejson)
9277        ("python-pyyaml" ,python-pyyaml)
9278        ("python-click" ,python-click)
9279        ("python-spectra" ,python-spectra)
9280        ("python-requests" ,python-requests)
9281        ("python-markdown" ,python-markdown)
9282        ("python-lzstring" ,python-lzstring)
9283        ("python-matplotlib" ,python-matplotlib)
9284        ("python-numpy" ,python-numpy)
9285        ;; MultQC checks for the presence of nose at runtime.
9286        ("python-nose" ,python-nose)))
9287     (arguments
9288      `(#:phases
9289        (modify-phases %standard-phases
9290          (add-after 'unpack 'relax-requirements
9291            (lambda _
9292              (substitute* "setup.py"
9293                ;; MultiQC 1.5 ‘requires’ a version of python-matplotlib older
9294                ;; than the one in Guix, but should work fine with 2.2.2.
9295                ;; See <https://github.com/ewels/MultiQC/issues/725> and
9296                ;; <https://github.com/ewels/MultiQC/issues/732> for details.
9297                (("['\"]matplotlib.*?['\"]")
9298                 "'matplotlib'"))
9299              #t)))))
9300     (home-page "http://multiqc.info")
9301     (synopsis "Aggregate bioinformatics analysis reports")
9302     (description
9303      "MultiQC is a tool to aggregate bioinformatics results across many
9304 samples into a single report.  It contains modules for a large number of
9305 common bioinformatics tools.")
9306     (license license:gpl3+)))
9307
9308 (define-public r-chipseq
9309   (package
9310     (name "r-chipseq")
9311     (version "1.32.0")
9312     (source
9313      (origin
9314        (method url-fetch)
9315        (uri (bioconductor-uri "chipseq" version))
9316        (sha256
9317         (base32
9318          "1pp1rm5fs3hlar5x4dl3a3b4gara7qwf81dbvka6r1n78hrf9x1b"))))
9319     (build-system r-build-system)
9320     (propagated-inputs
9321      `(("r-biocgenerics" ,r-biocgenerics)
9322        ("r-genomicranges" ,r-genomicranges)
9323        ("r-iranges" ,r-iranges)
9324        ("r-lattice" ,r-lattice)
9325        ("r-s4vectors" ,r-s4vectors)
9326        ("r-shortread" ,r-shortread)))
9327     (home-page "https://bioconductor.org/packages/chipseq")
9328     (synopsis "Package for analyzing ChIPseq data")
9329     (description
9330      "This package provides tools for processing short read data from ChIPseq
9331 experiments.")
9332     (license license:artistic2.0)))
9333
9334 (define-public r-copyhelper
9335   (package
9336     (name "r-copyhelper")
9337     (version "1.6.0")
9338     (source
9339      (origin
9340        (method url-fetch)
9341        (uri (string-append "https://bioconductor.org/packages/release/"
9342                            "data/experiment/src/contrib/CopyhelpeR_"
9343                            version ".tar.gz"))
9344        (sha256
9345         (base32
9346          "0x7cyynjmxls9as2gg0iyp9x5fpalxmdjq914ss7i84i9zyk5bhq"))))
9347     (properties `((upstream-name . "CopyhelpeR")))
9348     (build-system r-build-system)
9349     (home-page "https://bioconductor.org/packages/CopyhelpeR/")
9350     (synopsis "Helper files for CopywriteR")
9351     (description
9352      "This package contains the helper files that are required to run the
9353 Bioconductor package CopywriteR.  It contains pre-assembled 1kb bin GC-content
9354 and mappability files for the reference genomes hg18, hg19, hg38, mm9 and
9355 mm10.  In addition, it contains a blacklist filter to remove regions that
9356 display copy number variation.  Files are stored as GRanges objects from the
9357 GenomicRanges Bioconductor package.")
9358     (license license:gpl2)))
9359
9360 (define-public r-copywriter
9361   (package
9362     (name "r-copywriter")
9363     (version "2.14.0")
9364     (source
9365      (origin
9366        (method url-fetch)
9367        (uri (bioconductor-uri "CopywriteR" version))
9368        (sha256
9369         (base32
9370          "0aamxafdk98n7s92jyqs65d6ljpnc2463vanvsw80p44qn6l6awn"))))
9371     (properties `((upstream-name . "CopywriteR")))
9372     (build-system r-build-system)
9373     (propagated-inputs
9374      `(("r-biocparallel" ,r-biocparallel)
9375        ("r-chipseq" ,r-chipseq)
9376        ("r-copyhelper" ,r-copyhelper)
9377        ("r-data-table" ,r-data-table)
9378        ("r-dnacopy" ,r-dnacopy)
9379        ("r-futile-logger" ,r-futile-logger)
9380        ("r-genomeinfodb" ,r-genomeinfodb)
9381        ("r-genomicalignments" ,r-genomicalignments)
9382        ("r-genomicranges" ,r-genomicranges)
9383        ("r-gtools" ,r-gtools)
9384        ("r-iranges" ,r-iranges)
9385        ("r-matrixstats" ,r-matrixstats)
9386        ("r-rsamtools" ,r-rsamtools)
9387        ("r-s4vectors" ,r-s4vectors)))
9388     (home-page "https://github.com/PeeperLab/CopywriteR")
9389     (synopsis "Copy number information from targeted sequencing")
9390     (description
9391      "CopywriteR extracts DNA copy number information from targeted sequencing
9392 by utilizing off-target reads.  It allows for extracting uniformly distributed
9393 copy number information, can be used without reference, and can be applied to
9394 sequencing data obtained from various techniques including chromatin
9395 immunoprecipitation and target enrichment on small gene panels.  Thereby,
9396 CopywriteR constitutes a widely applicable alternative to available copy
9397 number detection tools.")
9398     (license license:gpl2)))
9399
9400 (define-public r-methylkit
9401   (package
9402     (name "r-methylkit")
9403     (version "1.8.0")
9404     (source (origin
9405               (method url-fetch)
9406               (uri (bioconductor-uri "methylKit" version))
9407               (sha256
9408                (base32
9409                 "0mz6lil1wax931incnw5byx0v9i8ryhwq9mv0nv8s48ai33ch3x6"))))
9410     (properties `((upstream-name . "methylKit")))
9411     (build-system r-build-system)
9412     (propagated-inputs
9413      `(("r-data-table" ,r-data-table)
9414        ("r-emdbook" ,r-emdbook)
9415        ("r-fastseg" ,r-fastseg)
9416        ("r-genomeinfodb" ,r-genomeinfodb)
9417        ("r-genomicranges" ,r-genomicranges)
9418        ("r-gtools" ,r-gtools)
9419        ("r-iranges" ,r-iranges)
9420        ("r-kernsmooth" ,r-kernsmooth)
9421        ("r-limma" ,r-limma)
9422        ("r-mclust" ,r-mclust)
9423        ("r-qvalue" ,r-qvalue)
9424        ("r-r-utils" ,r-r-utils)
9425        ("r-rcpp" ,r-rcpp)
9426        ("r-rhtslib" ,r-rhtslib)
9427        ("r-rsamtools" ,r-rsamtools)
9428        ("r-rtracklayer" ,r-rtracklayer)
9429        ("r-s4vectors" ,r-s4vectors)
9430        ("r-zlibbioc" ,r-zlibbioc)))
9431     (inputs
9432      `(("zlib" ,zlib)))
9433     (home-page "https://github.com/al2na/methylKit")
9434     (synopsis
9435      "DNA methylation analysis from high-throughput bisulfite sequencing results")
9436     (description
9437      "MethylKit is an R package for DNA methylation analysis and annotation
9438 from high-throughput bisulfite sequencing.  The package is designed to deal
9439 with sequencing data from @dfn{Reduced representation bisulfite
9440 sequencing} (RRBS) and its variants, but also target-capture methods and whole
9441 genome bisulfite sequencing.  It also has functions to analyze base-pair
9442 resolution 5hmC data from experimental protocols such as oxBS-Seq and
9443 TAB-Seq.")
9444     (license license:artistic2.0)))
9445
9446 (define-public r-sva
9447   (package
9448     (name "r-sva")
9449     (version "3.30.0")
9450     (source
9451      (origin
9452        (method url-fetch)
9453        (uri (bioconductor-uri "sva" version))
9454        (sha256
9455         (base32
9456          "1xf0hlrqjxl0y3x13mrkxghiv39fd9v2g8gq3qzbf1wj7il6bph3"))))
9457     (build-system r-build-system)
9458     (propagated-inputs
9459      `(("r-genefilter" ,r-genefilter)
9460        ("r-mgcv" ,r-mgcv)
9461        ("r-biocparallel" ,r-biocparallel)
9462        ("r-matrixstats" ,r-matrixstats)
9463        ("r-limma" ,r-limma)))
9464     (home-page "https://bioconductor.org/packages/sva")
9465     (synopsis "Surrogate variable analysis")
9466     (description
9467      "This package contains functions for removing batch effects and other
9468 unwanted variation in high-throughput experiment.  It also contains functions
9469 for identifying and building surrogate variables for high-dimensional data
9470 sets.  Surrogate variables are covariates constructed directly from
9471 high-dimensional data like gene expression/RNA sequencing/methylation/brain
9472 imaging data that can be used in subsequent analyses to adjust for unknown,
9473 unmodeled, or latent sources of noise.")
9474     (license license:artistic2.0)))
9475
9476 (define-public r-seqminer
9477   (package
9478     (name "r-seqminer")
9479     (version "6.1")
9480     (source
9481      (origin
9482        (method url-fetch)
9483        (uri (cran-uri "seqminer" version))
9484        (sha256
9485         (base32
9486          "15yhg4vfc7jg1jnqb3371j00pgbmbyc9l1xx63hq1l3p34lazq2l"))))
9487     (build-system r-build-system)
9488     (inputs
9489      `(("zlib" ,zlib)))
9490     (home-page "http://seqminer.genomic.codes")
9491     (synopsis "Read nucleotide sequence data (VCF, BCF, and METAL formats)")
9492     (description
9493      "This package provides tools to integrate nucleotide sequencing
9494 data (variant call format, e.g. VCF or BCF) or meta-analysis results in R.")
9495     ;; Any version of the GPL is acceptable
9496     (license (list license:gpl2+ license:gpl3+))))
9497
9498 (define-public r-raremetals2
9499   (package
9500     (name "r-raremetals2")
9501     (version "0.1")
9502     (source
9503      (origin
9504        (method url-fetch)
9505        (uri (string-append "http://genome.sph.umich.edu/w/images/"
9506                            "b/b7/RareMETALS2_" version ".tar.gz"))
9507        (sha256
9508         (base32
9509          "0z5ljcgvnm06ja9lm85a3cniq7slxcy37aqqkxrdidr79an5fs4s"))))
9510     (properties `((upstream-name . "RareMETALS2")))
9511     (build-system r-build-system)
9512     (propagated-inputs
9513      `(("r-seqminer" ,r-seqminer)
9514        ("r-mvtnorm" ,r-mvtnorm)
9515        ("r-mass" ,r-mass)
9516        ("r-compquadform" ,r-compquadform)
9517        ("r-getopt" ,r-getopt)))
9518     (home-page "http://genome.sph.umich.edu/wiki/RareMETALS2")
9519     (synopsis "Analyze gene-level association tests for binary trait")
9520     (description
9521      "The R package rareMETALS2 is an extension of the R package rareMETALS.
9522 It was designed to meta-analyze gene-level association tests for binary trait.
9523 While rareMETALS offers a near-complete solution for meta-analysis of
9524 gene-level tests for quantitative trait, it does not offer the optimal
9525 solution for binary trait.  The package rareMETALS2 offers improved features
9526 for analyzing gene-level association tests in meta-analyses for binary
9527 trait.")
9528     (license license:gpl3)))
9529
9530 (define-public r-maldiquant
9531   (package
9532     (name "r-maldiquant")
9533     (version "1.18")
9534     (source
9535      (origin
9536        (method url-fetch)
9537        (uri (cran-uri "MALDIquant" version))
9538        (sha256
9539         (base32
9540          "18nl214xjsxkcpbg79jkmw0yznwm5szyh2qb84n7ip46mm779ha6"))))
9541     (properties `((upstream-name . "MALDIquant")))
9542     (build-system r-build-system)
9543     (home-page "https://cran.r-project.org/web/packages/MALDIquant")
9544     (synopsis "Quantitative analysis of mass spectrometry data")
9545     (description
9546      "This package provides a complete analysis pipeline for matrix-assisted
9547 laser desorption/ionization-time-of-flight (MALDI-TOF) and other
9548 two-dimensional mass spectrometry data.  In addition to commonly used plotting
9549 and processing methods it includes distinctive features, namely baseline
9550 subtraction methods such as morphological filters (TopHat) or the
9551 statistics-sensitive non-linear iterative peak-clipping algorithm (SNIP), peak
9552 alignment using warping functions, handling of replicated measurements as well
9553 as allowing spectra with different resolutions.")
9554     (license license:gpl3+)))
9555
9556 (define-public r-protgenerics
9557   (package
9558     (name "r-protgenerics")
9559     (version "1.14.0")
9560     (source
9561      (origin
9562        (method url-fetch)
9563        (uri (bioconductor-uri "ProtGenerics" version))
9564        (sha256
9565         (base32
9566          "053mmxhzncqgigl2iqjlq56qzimlw2zzw31wpzw19rf7rld1vi3b"))))
9567     (properties `((upstream-name . "ProtGenerics")))
9568     (build-system r-build-system)
9569     (home-page "https://github.com/lgatto/ProtGenerics")
9570     (synopsis "S4 generic functions for proteomics infrastructure")
9571     (description
9572      "This package provides S4 generic functions needed by Bioconductor
9573 proteomics packages.")
9574     (license license:artistic2.0)))
9575
9576 (define-public r-mzr
9577   (package
9578     (name "r-mzr")
9579     (version "2.16.0")
9580     (source
9581      (origin
9582        (method url-fetch)
9583        (uri (bioconductor-uri "mzR" version))
9584        (sha256
9585         (base32
9586          "0li1y6p95ljiva4lvfmql9sipn4dq42sknbh60b36ycjppnf8lj5"))
9587        (modules '((guix build utils)))
9588        (snippet
9589         '(begin
9590            (delete-file-recursively "src/boost")
9591            #t))))
9592     (properties `((upstream-name . "mzR")))
9593     (build-system r-build-system)
9594     (arguments
9595      `(#:phases
9596        (modify-phases %standard-phases
9597          (add-after 'unpack 'use-system-boost
9598            (lambda _
9599              (substitute* "src/Makevars"
9600                (("\\./boost/libs.*") "")
9601                (("ARCH_OBJS=" line)
9602                 (string-append line
9603                                "\nARCH_LIBS=-lboost_system -lboost_regex \
9604 -lboost_iostreams -lboost_thread -lboost_filesystem -lboost_chrono\n")))
9605              #t)))))
9606     (inputs
9607      `(("boost" ,boost) ; use this instead of the bundled boost sources
9608        ("zlib" ,zlib)))
9609     (propagated-inputs
9610      `(("r-biobase" ,r-biobase)
9611        ("r-biocgenerics" ,r-biocgenerics)
9612        ("r-ncdf4" ,r-ncdf4)
9613        ("r-protgenerics" ,r-protgenerics)
9614        ("r-rcpp" ,r-rcpp)
9615        ("r-rhdf5lib" ,r-rhdf5lib)
9616        ("r-zlibbioc" ,r-zlibbioc)))
9617     (home-page "https://github.com/sneumann/mzR/")
9618     (synopsis "Parser for mass spectrometry data files")
9619     (description
9620      "The mzR package provides a unified API to the common file formats and
9621 parsers available for mass spectrometry data.  It comes with a wrapper for the
9622 ISB random access parser for mass spectrometry mzXML, mzData and mzML files.
9623 The package contains the original code written by the ISB, and a subset of the
9624 proteowizard library for mzML and mzIdentML.  The netCDF reading code has
9625 previously been used in XCMS.")
9626     (license license:artistic2.0)))
9627
9628 (define-public r-affyio
9629   (package
9630     (name "r-affyio")
9631     (version "1.52.0")
9632     (source
9633      (origin
9634        (method url-fetch)
9635        (uri (bioconductor-uri "affyio" version))
9636        (sha256
9637         (base32
9638          "1s4zp1211vf0krxzch9v3q3r6vs8hihqppq18i2fpvwlknfja7c1"))))
9639     (build-system r-build-system)
9640     (propagated-inputs
9641      `(("r-zlibbioc" ,r-zlibbioc)))
9642     (inputs
9643      `(("zlib" ,zlib)))
9644     (home-page "https://github.com/bmbolstad/affyio")
9645     (synopsis "Tools for parsing Affymetrix data files")
9646     (description
9647      "This package provides routines for parsing Affymetrix data files based
9648 upon file format information.  The primary focus is on accessing the CEL and
9649 CDF file formats.")
9650     (license license:lgpl2.0+)))
9651
9652 (define-public r-affy
9653   (package
9654     (name "r-affy")
9655     (version "1.60.0")
9656     (source
9657      (origin
9658        (method url-fetch)
9659        (uri (bioconductor-uri "affy" version))
9660        (sha256
9661         (base32
9662          "0x8h4fk2igv7vykqfvf6v9whmx3344v5rf3gyfajd431xkjldz6k"))))
9663     (build-system r-build-system)
9664     (propagated-inputs
9665      `(("r-affyio" ,r-affyio)
9666        ("r-biobase" ,r-biobase)
9667        ("r-biocgenerics" ,r-biocgenerics)
9668        ("r-biocmanager" ,r-biocmanager)
9669        ("r-preprocesscore" ,r-preprocesscore)
9670        ("r-zlibbioc" ,r-zlibbioc)))
9671     (inputs
9672      `(("zlib" ,zlib)))
9673     (home-page "https://bioconductor.org/packages/affy")
9674     (synopsis "Methods for affymetrix oligonucleotide arrays")
9675     (description
9676      "This package contains functions for exploratory oligonucleotide array
9677 analysis.")
9678     (license license:lgpl2.0+)))
9679
9680 (define-public r-vsn
9681   (package
9682     (name "r-vsn")
9683     (version "3.50.0")
9684     (source
9685      (origin
9686        (method url-fetch)
9687        (uri (bioconductor-uri "vsn" version))
9688        (sha256
9689         (base32
9690          "1g6qkpykw99jm2wv2i61dg2ffwk0n8fm4s5pm2q4c024vw5c9b69"))))
9691     (build-system r-build-system)
9692     (propagated-inputs
9693      `(("r-affy" ,r-affy)
9694        ("r-biobase" ,r-biobase)
9695        ("r-ggplot2" ,r-ggplot2)
9696        ("r-lattice" ,r-lattice)
9697        ("r-limma" ,r-limma)))
9698     (home-page "https://bioconductor.org/packages/release/bioc/html/vsn.html")
9699     (synopsis "Variance stabilization and calibration for microarray data")
9700     (description
9701      "The package implements a method for normalising microarray intensities,
9702 and works for single- and multiple-color arrays.  It can also be used for data
9703 from other technologies, as long as they have similar format.  The method uses
9704 a robust variant of the maximum-likelihood estimator for an
9705 additive-multiplicative error model and affine calibration.  The model
9706 incorporates data calibration step (a.k.a.  normalization), a model for the
9707 dependence of the variance on the mean intensity and a variance stabilizing
9708 data transformation.  Differences between transformed intensities are
9709 analogous to \"normalized log-ratios\".  However, in contrast to the latter,
9710 their variance is independent of the mean, and they are usually more sensitive
9711 and specific in detecting differential transcription.")
9712     (license license:artistic2.0)))
9713
9714 (define-public r-mzid
9715   (package
9716     (name "r-mzid")
9717     (version "1.20.0")
9718     (source
9719      (origin
9720        (method url-fetch)
9721        (uri (bioconductor-uri "mzID" version))
9722        (sha256
9723         (base32
9724          "08jbq223viwknsmsi30hyxyxslvmb0l4wx3vmqlkl6qk4vfmxzjz"))))
9725     (properties `((upstream-name . "mzID")))
9726     (build-system r-build-system)
9727     (propagated-inputs
9728      `(("r-doparallel" ,r-doparallel)
9729        ("r-foreach" ,r-foreach)
9730        ("r-iterators" ,r-iterators)
9731        ("r-plyr" ,r-plyr)
9732        ("r-protgenerics" ,r-protgenerics)
9733        ("r-rcpp" ,r-rcpp)
9734        ("r-xml" ,r-xml)))
9735     (home-page "https://bioconductor.org/packages/mzID")
9736     (synopsis "Parser for mzIdentML files")
9737     (description
9738      "This package provides a parser for mzIdentML files implemented using the
9739 XML package.  The parser tries to be general and able to handle all types of
9740 mzIdentML files with the drawback of having less pretty output than a vendor
9741 specific parser.")
9742     (license license:gpl2+)))
9743
9744 (define-public r-pcamethods
9745   (package
9746     (name "r-pcamethods")
9747     (version "1.74.0")
9748     (source
9749      (origin
9750        (method url-fetch)
9751        (uri (bioconductor-uri "pcaMethods" version))
9752        (sha256
9753         (base32
9754          "0ik82s9bsdj4a1mmv0a3k6yisa92mxx7maf3dvip1r8gqlm3dyng"))))
9755     (properties `((upstream-name . "pcaMethods")))
9756     (build-system r-build-system)
9757     (propagated-inputs
9758      `(("r-biobase" ,r-biobase)
9759        ("r-biocgenerics" ,r-biocgenerics)
9760        ("r-mass" ,r-mass)
9761        ("r-rcpp" ,r-rcpp)))
9762     (home-page "https://github.com/hredestig/pcamethods")
9763     (synopsis "Collection of PCA methods")
9764     (description
9765      "This package provides Bayesian PCA, Probabilistic PCA, Nipals PCA,
9766 Inverse Non-Linear PCA and the conventional SVD PCA.  A cluster based method
9767 for missing value estimation is included for comparison.  BPCA, PPCA and
9768 NipalsPCA may be used to perform PCA on incomplete data as well as for
9769 accurate missing value estimation.  A set of methods for printing and plotting
9770 the results is also provided.  All PCA methods make use of the same data
9771 structure (pcaRes) to provide a common interface to the PCA results.")
9772     (license license:gpl3+)))
9773
9774 (define-public r-msnbase
9775   (package
9776     (name "r-msnbase")
9777     (version "2.8.1")
9778     (source
9779      (origin
9780        (method url-fetch)
9781        (uri (bioconductor-uri "MSnbase" version))
9782        (sha256
9783         (base32
9784          "0y658anh06vnvbkfs7r8q40gqgyqr2r8kj7jlpnp33fy1lvp1nv7"))))
9785     (properties `((upstream-name . "MSnbase")))
9786     (build-system r-build-system)
9787     (propagated-inputs
9788      `(("r-affy" ,r-affy)
9789        ("r-biobase" ,r-biobase)
9790        ("r-biocgenerics" ,r-biocgenerics)
9791        ("r-biocparallel" ,r-biocparallel)
9792        ("r-digest" ,r-digest)
9793        ("r-ggplot2" ,r-ggplot2)
9794        ("r-impute" ,r-impute)
9795        ("r-iranges" ,r-iranges)
9796        ("r-lattice" ,r-lattice)
9797        ("r-maldiquant" ,r-maldiquant)
9798        ("r-mass" ,r-mass)
9799        ("r-mzid" ,r-mzid)
9800        ("r-mzr" ,r-mzr)
9801        ("r-pcamethods" ,r-pcamethods)
9802        ("r-plyr" ,r-plyr)
9803        ("r-preprocesscore" ,r-preprocesscore)
9804        ("r-protgenerics" ,r-protgenerics)
9805        ("r-rcpp" ,r-rcpp)
9806        ("r-s4vectors" ,r-s4vectors)
9807        ("r-scales" ,r-scales)
9808        ("r-vsn" ,r-vsn)
9809        ("r-xml" ,r-xml)))
9810     (home-page "https://github.com/lgatto/MSnbase")
9811     (synopsis "Base functions and classes for MS-based proteomics")
9812     (description
9813      "This package provides basic plotting, data manipulation and processing
9814 of mass spectrometry based proteomics data.")
9815     (license license:artistic2.0)))
9816
9817 (define-public r-msnid
9818   (package
9819     (name "r-msnid")
9820     (version "1.16.0")
9821     (source
9822      (origin
9823        (method url-fetch)
9824        (uri (bioconductor-uri "MSnID" version))
9825        (sha256
9826         (base32
9827          "0hgq4argllhh5hvxqi8vkf1blc3nibsslhx4zsv2mcv4yj75bv4n"))))
9828     (properties `((upstream-name . "MSnID")))
9829     (build-system r-build-system)
9830     (propagated-inputs
9831      `(("r-biobase" ,r-biobase)
9832        ("r-data-table" ,r-data-table)
9833        ("r-doparallel" ,r-doparallel)
9834        ("r-dplyr" ,r-dplyr)
9835        ("r-foreach" ,r-foreach)
9836        ("r-iterators" ,r-iterators)
9837        ("r-msnbase" ,r-msnbase)
9838        ("r-mzid" ,r-mzid)
9839        ("r-mzr" ,r-mzr)
9840        ("r-protgenerics" ,r-protgenerics)
9841        ("r-r-cache" ,r-r-cache)
9842        ("r-rcpp" ,r-rcpp)
9843        ("r-reshape2" ,r-reshape2)))
9844     (home-page "https://bioconductor.org/packages/MSnID")
9845     (synopsis "Utilities for LC-MSn proteomics identifications")
9846     (description
9847      "This package extracts @dfn{tandem mass spectrometry} (MS/MS) ID data
9848 from mzIdentML (leveraging the mzID package) or text files.  After collating
9849 the search results from multiple datasets it assesses their identification
9850 quality and optimize filtering criteria to achieve the maximum number of
9851 identifications while not exceeding a specified false discovery rate.  It also
9852 contains a number of utilities to explore the MS/MS results and assess missed
9853 and irregular enzymatic cleavages, mass measurement accuracy, etc.")
9854     (license license:artistic2.0)))
9855
9856 (define-public r-seurat
9857   (package
9858     (name "r-seurat")
9859     (version "2.3.4")
9860     (source (origin
9861               (method url-fetch)
9862               (uri (cran-uri "Seurat" version))
9863               (sha256
9864                (base32
9865                 "0l8bv4i9nzz26mirnva10mq6pimibj24vk7vpvfypgn7xk4942hd"))))
9866     (properties `((upstream-name . "Seurat")))
9867     (build-system r-build-system)
9868     (propagated-inputs
9869      `(("r-ape" ,r-ape)
9870        ("r-cluster" ,r-cluster)
9871        ("r-cowplot" ,r-cowplot)
9872        ("r-dosnow" ,r-dosnow)
9873        ("r-dplyr" ,r-dplyr)
9874        ("r-dtw" ,r-dtw)
9875        ("r-fitdistrplus" ,r-fitdistrplus)
9876        ("r-foreach" ,r-foreach)
9877        ("r-fpc" ,r-fpc)
9878        ("r-ggplot2" ,r-ggplot2)
9879        ("r-ggridges" ,r-ggridges)
9880        ("r-gplots" ,r-gplots)
9881        ("r-hdf5r" ,r-hdf5r)
9882        ("r-hmisc" ,r-hmisc)
9883        ("r-httr" ,r-httr)
9884        ("r-ica" ,r-ica)
9885        ("r-igraph" ,r-igraph)
9886        ("r-irlba" ,r-irlba)
9887        ("r-lars" ,r-lars)
9888        ("r-lmtest" ,r-lmtest)
9889        ("r-mass" ,r-mass)
9890        ("r-matrix" ,r-matrix)
9891        ("r-metap" ,r-metap)
9892        ("r-mixtools" ,r-mixtools)
9893        ("r-pbapply" ,r-pbapply)
9894        ("r-plotly" ,r-plotly)
9895        ("r-png" ,r-png)
9896        ("r-rann" ,r-rann)
9897        ("r-rcolorbrewer" ,r-rcolorbrewer)
9898        ("r-rcpp" ,r-rcpp)
9899        ("r-rcppeigen" ,r-rcppeigen)
9900        ("r-rcppprogress" ,r-rcppprogress)
9901        ("r-reshape2" ,r-reshape2)
9902        ("r-reticulate" ,r-reticulate)
9903        ("r-rocr" ,r-rocr)
9904        ("r-rtsne" ,r-rtsne)
9905        ("r-sdmtools" ,r-sdmtools)
9906        ("r-tidyr" ,r-tidyr)
9907        ("r-tsne" ,r-tsne)))
9908     (home-page "http://www.satijalab.org/seurat")
9909     (synopsis "Seurat is an R toolkit for single cell genomics")
9910     (description
9911      "This package is an R package designed for QC, analysis, and
9912 exploration of single cell RNA-seq data.  It easily enables widely-used
9913 analytical techniques, including the identification of highly variable genes,
9914 dimensionality reduction; PCA, ICA, t-SNE, standard unsupervised clustering
9915 algorithms; density clustering, hierarchical clustering, k-means, and the
9916 discovery of differentially expressed genes and markers.")
9917     (license license:gpl3)))
9918
9919 (define-public r-aroma-light
9920   (package
9921     (name "r-aroma-light")
9922     (version "3.12.0")
9923     (source
9924      (origin
9925        (method url-fetch)
9926        (uri (bioconductor-uri "aroma.light" version))
9927        (sha256
9928         (base32
9929          "0vfifgpqxjjncbiv6gvlk9jmj14j90r9f30bqk3ks9v1csjnjhrb"))))
9930     (properties `((upstream-name . "aroma.light")))
9931     (build-system r-build-system)
9932     (propagated-inputs
9933      `(("r-matrixstats" ,r-matrixstats)
9934        ("r-r-methodss3" ,r-r-methodss3)
9935        ("r-r-oo" ,r-r-oo)
9936        ("r-r-utils" ,r-r-utils)))
9937     (home-page "https://github.com/HenrikBengtsson/aroma.light")
9938     (synopsis "Methods for normalization and visualization of microarray data")
9939     (description
9940      "This package provides methods for microarray analysis that take basic
9941 data types such as matrices and lists of vectors.  These methods can be used
9942 standalone, be utilized in other packages, or be wrapped up in higher-level
9943 classes.")
9944     (license license:gpl2+)))
9945
9946 (define-public r-deseq
9947   (package
9948     (name "r-deseq")
9949     (version "1.34.0")
9950     (source
9951      (origin
9952        (method url-fetch)
9953        (uri (bioconductor-uri "DESeq" version))
9954        (sha256
9955         (base32
9956          "1klv1xrh3173srywr6dnq6i7m9djn4gc9aflr1p3a6yjlqcq6fya"))))
9957     (properties `((upstream-name . "DESeq")))
9958     (build-system r-build-system)
9959     (propagated-inputs
9960      `(("r-biobase" ,r-biobase)
9961        ("r-biocgenerics" ,r-biocgenerics)
9962        ("r-genefilter" ,r-genefilter)
9963        ("r-geneplotter" ,r-geneplotter)
9964        ("r-lattice" ,r-lattice)
9965        ("r-locfit" ,r-locfit)
9966        ("r-mass" ,r-mass)
9967        ("r-rcolorbrewer" ,r-rcolorbrewer)))
9968     (home-page "http://www-huber.embl.de/users/anders/DESeq")
9969     (synopsis "Differential gene expression analysis")
9970     (description
9971      "This package provides tools for estimating variance-mean dependence in
9972 count data from high-throughput genetic sequencing assays and for testing for
9973 differential expression based on a model using the negative binomial
9974 distribution.")
9975     (license license:gpl3+)))
9976
9977 (define-public r-edaseq
9978   (package
9979     (name "r-edaseq")
9980     (version "2.16.0")
9981     (source
9982      (origin
9983        (method url-fetch)
9984        (uri (bioconductor-uri "EDASeq" version))
9985        (sha256
9986         (base32
9987          "1gjqzn1kg9qwyz2gwjyy9xzzr1lnc7xd5zwdyvzkadz97gckzxwf"))))
9988     (properties `((upstream-name . "EDASeq")))
9989     (build-system r-build-system)
9990     (propagated-inputs
9991      `(("r-annotationdbi" ,r-annotationdbi)
9992        ("r-aroma-light" ,r-aroma-light)
9993        ("r-biobase" ,r-biobase)
9994        ("r-biocgenerics" ,r-biocgenerics)
9995        ("r-biomart" ,r-biomart)
9996        ("r-biostrings" ,r-biostrings)
9997        ("r-deseq" ,r-deseq)
9998        ("r-genomicfeatures" ,r-genomicfeatures)
9999        ("r-genomicranges" ,r-genomicranges)
10000        ("r-iranges" ,r-iranges)
10001        ("r-rsamtools" ,r-rsamtools)
10002        ("r-shortread" ,r-shortread)))
10003     (home-page "https://github.com/drisso/EDASeq")
10004     (synopsis "Exploratory data analysis and normalization for RNA-Seq")
10005     (description
10006      "This package provides support for numerical and graphical summaries of
10007 RNA-Seq genomic read data.  Provided within-lane normalization procedures to
10008 adjust for GC-content effect (or other gene-level effects) on read counts:
10009 loess robust local regression, global-scaling, and full-quantile
10010 normalization.  Between-lane normalization procedures to adjust for
10011 distributional differences between lanes (e.g., sequencing depth):
10012 global-scaling and full-quantile normalization.")
10013     (license license:artistic2.0)))
10014
10015 (define-public r-interactivedisplaybase
10016   (package
10017     (name "r-interactivedisplaybase")
10018     (version "1.20.0")
10019     (source
10020      (origin
10021        (method url-fetch)
10022        (uri (bioconductor-uri "interactiveDisplayBase" version))
10023        (sha256
10024         (base32
10025          "04xz3dkwan2s5ic1mwkdfnggm0l41mgqfagx160bcsrpkw6z7ark"))))
10026     (properties
10027      `((upstream-name . "interactiveDisplayBase")))
10028     (build-system r-build-system)
10029     (propagated-inputs
10030      `(("r-biocgenerics" ,r-biocgenerics)
10031        ("r-shiny" ,r-shiny)))
10032     (home-page "https://bioconductor.org/packages/interactiveDisplayBase")
10033     (synopsis "Base package for web displays of Bioconductor objects")
10034     (description
10035      "This package contains the basic methods needed to generate interactive
10036 Shiny-based display methods for Bioconductor objects.")
10037     (license license:artistic2.0)))
10038
10039 (define-public r-annotationhub
10040   (package
10041     (name "r-annotationhub")
10042     (version "2.14.1")
10043     (source
10044      (origin
10045        (method url-fetch)
10046        (uri (bioconductor-uri "AnnotationHub" version))
10047        (sha256
10048         (base32
10049          "00288x3na0izpmbcvsqac1br1qwry86vwc2slj1l47crdfb7za6c"))))
10050     (properties `((upstream-name . "AnnotationHub")))
10051     (build-system r-build-system)
10052     (propagated-inputs
10053      `(("r-annotationdbi" ,r-annotationdbi)
10054        ("r-biocgenerics" ,r-biocgenerics)
10055        ("r-biocmanager" ,r-biocmanager)
10056        ("r-curl" ,r-curl)
10057        ("r-httr" ,r-httr)
10058        ("r-interactivedisplaybase" ,r-interactivedisplaybase)
10059        ("r-rsqlite" ,r-rsqlite)
10060        ("r-s4vectors" ,r-s4vectors)
10061        ("r-yaml" ,r-yaml)))
10062     (home-page "https://bioconductor.org/packages/AnnotationHub")
10063     (synopsis "Client to access AnnotationHub resources")
10064     (description
10065      "This package provides a client for the Bioconductor AnnotationHub web
10066 resource.  The AnnotationHub web resource provides a central location where
10067 genomic files (e.g. VCF, bed, wig) and other resources from standard
10068 locations (e.g. UCSC, Ensembl) can be discovered.  The resource includes
10069 metadata about each resource, e.g., a textual description, tags, and date of
10070 modification.  The client creates and manages a local cache of files retrieved
10071 by the user, helping with quick and reproducible access.")
10072     (license license:artistic2.0)))
10073
10074 (define-public r-fastseg
10075   (package
10076     (name "r-fastseg")
10077     (version "1.28.0")
10078     (source
10079      (origin
10080        (method url-fetch)
10081        (uri (bioconductor-uri "fastseg" version))
10082        (sha256
10083         (base32
10084          "1l8mdjpfpgwqdss2ywjkb8b4h55wf8v6kmyxdlvy04ds2hj16sb1"))))
10085     (build-system r-build-system)
10086     (propagated-inputs
10087      `(("r-biobase" ,r-biobase)
10088        ("r-biocgenerics" ,r-biocgenerics)
10089        ("r-genomicranges" ,r-genomicranges)
10090        ("r-iranges" ,r-iranges)
10091        ("r-s4vectors" ,r-s4vectors)))
10092     (home-page "http://www.bioinf.jku.at/software/fastseg/index.html")
10093     (synopsis "Fast segmentation algorithm for genetic sequencing data")
10094     (description
10095      "Fastseg implements a very fast and efficient segmentation algorithm.
10096 It can segment data from DNA microarrays and data from next generation
10097 sequencing for example to detect copy number segments.  Further it can segment
10098 data from RNA microarrays like tiling arrays to identify transcripts.  Most
10099 generally, it can segment data given as a matrix or as a vector.  Various data
10100 formats can be used as input to fastseg like expression set objects for
10101 microarrays or GRanges for sequencing data.")
10102     (license license:lgpl2.0+)))
10103
10104 (define-public r-keggrest
10105   (package
10106     (name "r-keggrest")
10107     (version "1.22.0")
10108     (source
10109      (origin
10110        (method url-fetch)
10111        (uri (bioconductor-uri "KEGGREST" version))
10112        (sha256
10113         (base32
10114          "0blpd5a7whd2sswfhqd17h58hg06ymaf80gapdr9ja43hnnlj309"))))
10115     (properties `((upstream-name . "KEGGREST")))
10116     (build-system r-build-system)
10117     (propagated-inputs
10118      `(("r-biostrings" ,r-biostrings)
10119        ("r-httr" ,r-httr)
10120        ("r-png" ,r-png)))
10121     (home-page "https://bioconductor.org/packages/KEGGREST")
10122     (synopsis "Client-side REST access to KEGG")
10123     (description
10124      "This package provides a package that provides a client interface to the
10125 @dfn{Kyoto Encyclopedia of Genes and Genomes} (KEGG) REST server.")
10126     (license license:artistic2.0)))
10127
10128 (define-public r-gage
10129   (package
10130     (name "r-gage")
10131     (version "2.32.0")
10132     (source
10133      (origin
10134        (method url-fetch)
10135        (uri (bioconductor-uri "gage" version))
10136        (sha256
10137         (base32
10138          "07b098wvryxf0zd423nk6h52s3gyngwjcx2vplqybpbpgl8h2931"))))
10139     (build-system r-build-system)
10140     (propagated-inputs
10141      `(("r-annotationdbi" ,r-annotationdbi)
10142        ("r-graph" ,r-graph)
10143        ("r-keggrest" ,r-keggrest)))
10144     (home-page "http://www.biomedcentral.com/1471-2105/10/161")
10145     (synopsis "Generally applicable gene-set enrichment for pathway analysis")
10146     (description
10147      "GAGE is a published method for gene set (enrichment or GSEA) or pathway
10148 analysis.  GAGE is generally applicable independent of microarray or RNA-Seq
10149 data attributes including sample sizes, experimental designs, assay platforms,
10150 and other types of heterogeneity.  The gage package provides functions for
10151 basic GAGE analysis, result processing and presentation.  In addition, it
10152 provides demo microarray data and commonly used gene set data based on KEGG
10153 pathways and GO terms.  These funtions and data are also useful for gene set
10154 analysis using other methods.")
10155     (license license:gpl2+)))
10156
10157 (define-public r-genomicfiles
10158   (package
10159     (name "r-genomicfiles")
10160     (version "1.18.0")
10161     (source
10162      (origin
10163        (method url-fetch)
10164        (uri (bioconductor-uri "GenomicFiles" version))
10165        (sha256
10166         (base32
10167          "0qf2yj4lfnnk64fk125n8sqms01shfqiik04nasx2z3k129ykpxp"))))
10168     (properties `((upstream-name . "GenomicFiles")))
10169     (build-system r-build-system)
10170     (propagated-inputs
10171      `(("r-biocgenerics" ,r-biocgenerics)
10172        ("r-biocparallel" ,r-biocparallel)
10173        ("r-genomeinfodb" ,r-genomeinfodb)
10174        ("r-genomicalignments" ,r-genomicalignments)
10175        ("r-genomicranges" ,r-genomicranges)
10176        ("r-iranges" ,r-iranges)
10177        ("r-rsamtools" ,r-rsamtools)
10178        ("r-rtracklayer" ,r-rtracklayer)
10179        ("r-s4vectors" ,r-s4vectors)
10180        ("r-summarizedexperiment" ,r-summarizedexperiment)
10181        ("r-variantannotation" ,r-variantannotation)))
10182     (home-page "https://bioconductor.org/packages/GenomicFiles")
10183     (synopsis "Distributed computing by file or by range")
10184     (description
10185      "This package provides infrastructure for parallel computations
10186 distributed by file or by range.  User defined mapper and reducer functions
10187 provide added flexibility for data combination and manipulation.")
10188     (license license:artistic2.0)))
10189
10190 (define-public r-complexheatmap
10191   (package
10192     (name "r-complexheatmap")
10193     (version "1.20.0")
10194     (source
10195      (origin
10196        (method url-fetch)
10197        (uri (bioconductor-uri "ComplexHeatmap" version))
10198        (sha256
10199         (base32
10200          "0s01dzcfj1lmpqfpsbqw7r4858krfzy499lz4cwx4fq3mbyvy2aj"))))
10201     (properties
10202      `((upstream-name . "ComplexHeatmap")))
10203     (build-system r-build-system)
10204     (propagated-inputs
10205      `(("r-circlize" ,r-circlize)
10206        ("r-colorspace" ,r-colorspace)
10207        ("r-getoptlong" ,r-getoptlong)
10208        ("r-globaloptions" ,r-globaloptions)
10209        ("r-rcolorbrewer" ,r-rcolorbrewer)))
10210     (home-page
10211      "https://github.com/jokergoo/ComplexHeatmap")
10212     (synopsis "Making Complex Heatmaps")
10213     (description
10214      "Complex heatmaps are efficient to visualize associations between
10215 different sources of data sets and reveal potential structures.  This package
10216 provides a highly flexible way to arrange multiple heatmaps and supports
10217 self-defined annotation graphics.")
10218     (license license:gpl2+)))
10219
10220 (define-public r-dirichletmultinomial
10221   (package
10222     (name "r-dirichletmultinomial")
10223     (version "1.24.0")
10224     (source
10225      (origin
10226        (method url-fetch)
10227        (uri (bioconductor-uri "DirichletMultinomial" version))
10228        (sha256
10229         (base32
10230          "19bzn0a5jal1xv0ad6wikxc7wrk582hczqamlln0vb2ffwkj1z3f"))))
10231     (properties
10232      `((upstream-name . "DirichletMultinomial")))
10233     (build-system r-build-system)
10234     (inputs
10235      `(("gsl" ,gsl)))
10236     (propagated-inputs
10237      `(("r-biocgenerics" ,r-biocgenerics)
10238        ("r-iranges" ,r-iranges)
10239        ("r-s4vectors" ,r-s4vectors)))
10240     (home-page "https://bioconductor.org/packages/DirichletMultinomial")
10241     (synopsis "Dirichlet-Multinomial mixture models for microbiome data")
10242     (description
10243      "Dirichlet-multinomial mixture models can be used to describe variability
10244 in microbial metagenomic data.  This package is an interface to code
10245 originally made available by Holmes, Harris, and Quince, 2012, PLoS ONE 7(2):
10246 1-15.")
10247     (license license:lgpl3)))
10248
10249 (define-public r-ensembldb
10250   (package
10251     (name "r-ensembldb")
10252     (version "2.6.2")
10253     (source
10254      (origin
10255        (method url-fetch)
10256        (uri (bioconductor-uri "ensembldb" version))
10257        (sha256
10258         (base32
10259          "0hdz1f34v7sas2v4225icwl3wd4sf17ykpd5dkbx1hc7wcy4w3np"))))
10260     (build-system r-build-system)
10261     (propagated-inputs
10262      `(("r-annotationdbi" ,r-annotationdbi)
10263        ("r-annotationfilter" ,r-annotationfilter)
10264        ("r-biobase" ,r-biobase)
10265        ("r-biocgenerics" ,r-biocgenerics)
10266        ("r-biostrings" ,r-biostrings)
10267        ("r-curl" ,r-curl)
10268        ("r-dbi" ,r-dbi)
10269        ("r-genomeinfodb" ,r-genomeinfodb)
10270        ("r-genomicfeatures" ,r-genomicfeatures)
10271        ("r-genomicranges" ,r-genomicranges)
10272        ("r-iranges" ,r-iranges)
10273        ("r-protgenerics" ,r-protgenerics)
10274        ("r-rsamtools" ,r-rsamtools)
10275        ("r-rsqlite" ,r-rsqlite)
10276        ("r-rtracklayer" ,r-rtracklayer)
10277        ("r-s4vectors" ,r-s4vectors)))
10278     (home-page "https://github.com/jotsetung/ensembldb")
10279     (synopsis "Utilities to create and use Ensembl-based annotation databases")
10280     (description
10281      "The package provides functions to create and use transcript-centric
10282 annotation databases/packages.  The annotation for the databases are directly
10283 fetched from Ensembl using their Perl API.  The functionality and data is
10284 similar to that of the TxDb packages from the @code{GenomicFeatures} package,
10285 but, in addition to retrieve all gene/transcript models and annotations from
10286 the database, the @code{ensembldb} package also provides a filter framework
10287 allowing to retrieve annotations for specific entries like genes encoded on a
10288 chromosome region or transcript models of lincRNA genes.")
10289     ;; No version specified
10290     (license license:lgpl3+)))
10291
10292 (define-public r-organismdbi
10293   (package
10294     (name "r-organismdbi")
10295     (version "1.24.0")
10296     (source
10297      (origin
10298        (method url-fetch)
10299        (uri (bioconductor-uri "OrganismDbi" version))
10300        (sha256
10301         (base32
10302          "11pyv56cy4iy095h40k6k0mpjdlh6gsb4ld3s57nfa9nd4ypx3yi"))))
10303     (properties `((upstream-name . "OrganismDbi")))
10304     (build-system r-build-system)
10305     (propagated-inputs
10306      `(("r-annotationdbi" ,r-annotationdbi)
10307        ("r-biobase" ,r-biobase)
10308        ("r-biocgenerics" ,r-biocgenerics)
10309        ("r-biocmanager" ,r-biocmanager)
10310        ("r-dbi" ,r-dbi)
10311        ("r-genomicfeatures" ,r-genomicfeatures)
10312        ("r-genomicranges" ,r-genomicranges)
10313        ("r-graph" ,r-graph)
10314        ("r-iranges" ,r-iranges)
10315        ("r-rbgl" ,r-rbgl)
10316        ("r-s4vectors" ,r-s4vectors)))
10317     (home-page "https://bioconductor.org/packages/OrganismDbi")
10318     (synopsis "Software to enable the smooth interfacing of database packages")
10319     (description "The package enables a simple unified interface to several
10320 annotation packages each of which has its own schema by taking advantage of
10321 the fact that each of these packages implements a select methods.")
10322     (license license:artistic2.0)))
10323
10324 (define-public r-biovizbase
10325   (package
10326     (name "r-biovizbase")
10327     (version "1.30.0")
10328     (source
10329      (origin
10330        (method url-fetch)
10331        (uri (bioconductor-uri "biovizBase" version))
10332        (sha256
10333         (base32
10334          "0v54mcn3rnnfx8dmcrms5z3rgq19n3hp4r23azlgzwq6hjw7cccx"))))
10335     (properties `((upstream-name . "biovizBase")))
10336     (build-system r-build-system)
10337     (propagated-inputs
10338      `(("r-annotationdbi" ,r-annotationdbi)
10339        ("r-annotationfilter" ,r-annotationfilter)
10340        ("r-biocgenerics" ,r-biocgenerics)
10341        ("r-biostrings" ,r-biostrings)
10342        ("r-dichromat" ,r-dichromat)
10343        ("r-ensembldb" ,r-ensembldb)
10344        ("r-genomeinfodb" ,r-genomeinfodb)
10345        ("r-genomicalignments" ,r-genomicalignments)
10346        ("r-genomicfeatures" ,r-genomicfeatures)
10347        ("r-genomicranges" ,r-genomicranges)
10348        ("r-hmisc" ,r-hmisc)
10349        ("r-iranges" ,r-iranges)
10350        ("r-rcolorbrewer" ,r-rcolorbrewer)
10351        ("r-rlang" ,r-rlang)
10352        ("r-rsamtools" ,r-rsamtools)
10353        ("r-s4vectors" ,r-s4vectors)
10354        ("r-scales" ,r-scales)
10355        ("r-summarizedexperiment" ,r-summarizedexperiment)
10356        ("r-variantannotation" ,r-variantannotation)))
10357     (home-page "https://bioconductor.org/packages/biovizBase")
10358     (synopsis "Basic graphic utilities for visualization of genomic data")
10359     (description
10360      "The biovizBase package is designed to provide a set of utilities, color
10361 schemes and conventions for genomic data.  It serves as the base for various
10362 high-level packages for biological data visualization.  This saves development
10363 effort and encourages consistency.")
10364     (license license:artistic2.0)))
10365
10366 (define-public r-ggbio
10367   (package
10368     (name "r-ggbio")
10369     (version "1.30.0")
10370     (source
10371      (origin
10372        (method url-fetch)
10373        (uri (bioconductor-uri "ggbio" version))
10374        (sha256
10375         (base32
10376          "0wq49qqzkcn8s19xgaxf2s1j1a563d7pbhhvris6fhxfdjsz4934"))))
10377     (build-system r-build-system)
10378     (propagated-inputs
10379      `(("r-annotationdbi" ,r-annotationdbi)
10380        ("r-annotationfilter" ,r-annotationfilter)
10381        ("r-biobase" ,r-biobase)
10382        ("r-biocgenerics" ,r-biocgenerics)
10383        ("r-biostrings" ,r-biostrings)
10384        ("r-biovizbase" ,r-biovizbase)
10385        ("r-bsgenome" ,r-bsgenome)
10386        ("r-ensembldb" ,r-ensembldb)
10387        ("r-genomeinfodb" ,r-genomeinfodb)
10388        ("r-genomicalignments" ,r-genomicalignments)
10389        ("r-genomicfeatures" ,r-genomicfeatures)
10390        ("r-genomicranges" ,r-genomicranges)
10391        ("r-ggally" ,r-ggally)
10392        ("r-ggplot2" ,r-ggplot2)
10393        ("r-gridextra" ,r-gridextra)
10394        ("r-gtable" ,r-gtable)
10395        ("r-hmisc" ,r-hmisc)
10396        ("r-iranges" ,r-iranges)
10397        ("r-organismdbi" ,r-organismdbi)
10398        ("r-reshape2" ,r-reshape2)
10399        ("r-rlang" ,r-rlang)
10400        ("r-rsamtools" ,r-rsamtools)
10401        ("r-rtracklayer" ,r-rtracklayer)
10402        ("r-s4vectors" ,r-s4vectors)
10403        ("r-scales" ,r-scales)
10404        ("r-summarizedexperiment" ,r-summarizedexperiment)
10405        ("r-variantannotation" ,r-variantannotation)))
10406     (home-page "http://www.tengfei.name/ggbio/")
10407     (synopsis "Visualization tools for genomic data")
10408     (description
10409      "The ggbio package extends and specializes the grammar of graphics for
10410 biological data.  The graphics are designed to answer common scientific
10411 questions, in particular those often asked of high throughput genomics data.
10412 All core Bioconductor data structures are supported, where appropriate.  The
10413 package supports detailed views of particular genomic regions, as well as
10414 genome-wide overviews.  Supported overviews include ideograms and grand linear
10415 views.  High-level plots include sequence fragment length, edge-linked
10416 interval to data view, mismatch pileup, and several splicing summaries.")
10417     (license license:artistic2.0)))
10418
10419 (define-public r-gprofiler
10420   (package
10421     (name "r-gprofiler")
10422     (version "0.6.7")
10423     (source
10424      (origin
10425        (method url-fetch)
10426        (uri (cran-uri "gProfileR" version))
10427        (sha256
10428         (base32
10429          "12nwidbnqmnfy5dnqga26byslvdnkrpz2fi19qfcby6xx0wbndk7"))))
10430     (properties `((upstream-name . "gProfileR")))
10431     (build-system r-build-system)
10432     (propagated-inputs
10433      `(("r-plyr" ,r-plyr)
10434        ("r-rcurl" ,r-rcurl)))
10435     (home-page "https://cran.r-project.org/web/packages/gProfileR/")
10436     (synopsis "Interface to the g:Profiler toolkit")
10437     (description
10438      "This package provides tools for functional enrichment analysis,
10439 gene identifier conversion and mapping homologous genes across related
10440 organisms via the @code{g:Profiler} toolkit.")
10441     (license license:gpl2+)))
10442
10443 (define-public r-gqtlbase
10444   (package
10445     (name "r-gqtlbase")
10446     (version "1.14.0")
10447     (source
10448      (origin
10449        (method url-fetch)
10450        (uri (bioconductor-uri "gQTLBase" version))
10451        (sha256
10452         (base32
10453          "1lbk1m1mkvbk30flk5pf3pcrnm2s0sj5r48kbjgad39dsvd8zgqx"))))
10454     (properties `((upstream-name . "gQTLBase")))
10455     (build-system r-build-system)
10456     (propagated-inputs
10457      `(("r-batchjobs" ,r-batchjobs)
10458        ("r-bbmisc" ,r-bbmisc)
10459        ("r-biocgenerics" ,r-biocgenerics)
10460        ("r-bit" ,r-bit)
10461        ("r-doparallel" ,r-doparallel)
10462        ("r-ff" ,r-ff)
10463        ("r-ffbase" ,r-ffbase)
10464        ("r-foreach" ,r-foreach)
10465        ("r-genomicfiles" ,r-genomicfiles)
10466        ("r-genomicranges" ,r-genomicranges)
10467        ("r-rtracklayer" ,r-rtracklayer)
10468        ("r-s4vectors" ,r-s4vectors)
10469        ("r-summarizedexperiment" ,r-summarizedexperiment)))
10470     (home-page "https://bioconductor.org/packages/gQTLBase")
10471     (synopsis "Infrastructure for eQTL, mQTL and similar studies")
10472     (description
10473      "The purpose of this package is to simplify the storage and interrogation
10474 of @dfn{quantitative trait loci} (QTL) archives, such as eQTL, mQTL, dsQTL,
10475 and more.")
10476     (license license:artistic2.0)))
10477
10478 (define-public r-snpstats
10479   (package
10480     (name "r-snpstats")
10481     (version "1.32.0")
10482     (source
10483      (origin
10484        (method url-fetch)
10485        (uri (bioconductor-uri "snpStats" version))
10486        (sha256
10487         (base32
10488          "1pplx4pf9bqi7v5v1l74yknc1s61carvbqkf327ky7vbvp0bck33"))))
10489     (properties `((upstream-name . "snpStats")))
10490     (build-system r-build-system)
10491     (inputs `(("zlib" ,zlib)))
10492     (propagated-inputs
10493      `(("r-biocgenerics" ,r-biocgenerics)
10494        ("r-matrix" ,r-matrix)
10495        ("r-survival" ,r-survival)
10496        ("r-zlibbioc" ,r-zlibbioc)))
10497     (home-page "https://bioconductor.org/packages/snpStats")
10498     (synopsis "Methods for SNP association studies")
10499     (description
10500      "This package provides classes and statistical methods for large
10501 @dfn{single-nucleotide polymorphism} (SNP) association studies.  This extends
10502 the earlier snpMatrix package, allowing for uncertainty in genotypes.")
10503     (license license:gpl3)))
10504
10505 (define-public r-homo-sapiens
10506   (package
10507     (name "r-homo-sapiens")
10508     (version "1.3.1")
10509     (source (origin
10510               (method url-fetch)
10511               ;; We cannot use bioconductor-uri here because this tarball is
10512               ;; located under "data/annotation/" instead of "bioc/".
10513               (uri (string-append "http://www.bioconductor.org/packages/"
10514                                   "release/data/annotation/src/contrib/"
10515                                   "Homo.sapiens_"
10516                                   version ".tar.gz"))
10517               (sha256
10518                (base32
10519                 "151vj7h5p1c8yd5swrchk46z469p135wk50hvkl0nhgndvy0jj01"))))
10520     (properties
10521      `((upstream-name . "Homo.sapiens")))
10522     (build-system r-build-system)
10523     (propagated-inputs
10524      `(("r-genomicfeatures" ,r-genomicfeatures)
10525        ("r-go-db" ,r-go-db)
10526        ("r-org-hs-eg-db" ,r-org-hs-eg-db)
10527        ("r-txdb-hsapiens-ucsc-hg19-knowngene" ,r-txdb-hsapiens-ucsc-hg19-knowngene)
10528        ("r-organismdbi" ,r-organismdbi)
10529        ("r-annotationdbi" ,r-annotationdbi)))
10530     (home-page "https://bioconductor.org/packages/Homo.sapiens/")
10531     (synopsis "Annotation package for the Homo.sapiens object")
10532     (description
10533      "This package contains the Homo.sapiens object to access data from
10534 several related annotation packages.")
10535     (license license:artistic2.0)))
10536
10537 (define-public r-erma
10538   (package
10539     (name "r-erma")
10540     (version "0.14.0")
10541     (source
10542      (origin
10543        (method url-fetch)
10544        (uri (bioconductor-uri "erma" version))
10545        (sha256
10546         (base32
10547          "0hj9iz904rr1y66442lkxjywkw1ydyxxlhmjirawbf09ic5ad4g9"))))
10548     (build-system r-build-system)
10549     (propagated-inputs
10550      `(("r-annotationdbi" ,r-annotationdbi)
10551        ("r-biobase" ,r-biobase)
10552        ("r-biocgenerics" ,r-biocgenerics)
10553        ("r-biocparallel" ,r-biocparallel)
10554        ("r-genomeinfodb" ,r-genomeinfodb)
10555        ("r-genomicfiles" ,r-genomicfiles)
10556        ("r-genomicranges" ,r-genomicranges)
10557        ("r-ggplot2" ,r-ggplot2)
10558        ("r-homo-sapiens" ,r-homo-sapiens)
10559        ("r-iranges" ,r-iranges)
10560        ("r-rtracklayer" ,r-rtracklayer)
10561        ("r-s4vectors" ,r-s4vectors)
10562        ("r-shiny" ,r-shiny)
10563        ("r-summarizedexperiment" ,r-summarizedexperiment)))
10564     (home-page "https://bioconductor.org/packages/erma")
10565     (synopsis "Epigenomic road map adventures")
10566     (description
10567      "The epigenomics road map describes locations of epigenetic marks in DNA
10568 from a variety of cell types.  Of interest are locations of histone
10569 modifications, sites of DNA methylation, and regions of accessible chromatin.
10570 This package presents a selection of elements of the road map including
10571 metadata and outputs of the ChromImpute procedure applied to ENCODE cell lines
10572 by Ernst and Kellis.")
10573     (license license:artistic2.0)))
10574
10575 (define-public r-ldblock
10576   (package
10577     (name "r-ldblock")
10578     (version "1.12.0")
10579     (source
10580      (origin
10581        (method url-fetch)
10582        (uri (bioconductor-uri "ldblock" version))
10583        (sha256
10584         (base32
10585          "0xbf4pmhrk5fnd1iz5wzjvdr75v114bwpznhcig4wiqmxc27sips"))))
10586     (build-system r-build-system)
10587     (propagated-inputs
10588      `(("r-biocgenerics" ,r-biocgenerics)
10589        ("r-erma" ,r-erma)
10590        ("r-genomeinfodb" ,r-genomeinfodb)
10591        ("r-genomicfiles" ,r-genomicfiles)
10592        ("r-go-db" ,r-go-db)
10593        ("r-homo-sapiens" ,r-homo-sapiens)
10594        ("r-matrix" ,r-matrix)
10595        ("r-rsamtools" ,r-rsamtools)
10596        ("r-snpstats" ,r-snpstats)
10597        ("r-variantannotation" ,r-variantannotation)))
10598     (home-page "https://bioconductor.org/packages/ldblock")
10599     (synopsis "Data structures for linkage disequilibrium measures in populations")
10600     (description
10601      "This package defines data structures for @dfn{linkage
10602 disequilibrium} (LD) measures in populations.  Its purpose is to simplify
10603 handling of existing population-level data for the purpose of flexibly
10604 defining LD blocks.")
10605     (license license:artistic2.0)))
10606
10607 (define-public r-gqtlstats
10608   (package
10609     (name "r-gqtlstats")
10610     (version "1.14.0")
10611     (source
10612      (origin
10613        (method url-fetch)
10614        (uri (bioconductor-uri "gQTLstats" version))
10615        (sha256
10616         (base32
10617          "1sg9kw59dlayj7qxql9pd93d4hmml504sa3kkfpzfh3xri7m5pxf"))))
10618     (properties `((upstream-name . "gQTLstats")))
10619     (build-system r-build-system)
10620     (propagated-inputs
10621      `(("r-annotationdbi" ,r-annotationdbi)
10622        ("r-batchjobs" ,r-batchjobs)
10623        ("r-bbmisc" ,r-bbmisc)
10624        ("r-beeswarm" ,r-beeswarm)
10625        ("r-biobase" ,r-biobase)
10626        ("r-biocgenerics" ,r-biocgenerics)
10627        ("r-doparallel" ,r-doparallel)
10628        ("r-dplyr" ,r-dplyr)
10629        ("r-erma" ,r-erma)
10630        ("r-ffbase" ,r-ffbase)
10631        ("r-foreach" ,r-foreach)
10632        ("r-genomeinfodb" ,r-genomeinfodb)
10633        ("r-genomicfeatures" ,r-genomicfeatures)
10634        ("r-genomicfiles" ,r-genomicfiles)
10635        ("r-genomicranges" ,r-genomicranges)
10636        ("r-ggbeeswarm" ,r-ggbeeswarm)
10637        ("r-ggplot2" ,r-ggplot2)
10638        ("r-gqtlbase" ,r-gqtlbase)
10639        ("r-hardyweinberg" ,r-hardyweinberg)
10640        ("r-homo-sapiens" ,r-homo-sapiens)
10641        ("r-iranges" ,r-iranges)
10642        ("r-limma" ,r-limma)
10643        ("r-mgcv" ,r-mgcv)
10644        ("r-plotly" ,r-plotly)
10645        ("r-reshape2" ,r-reshape2)
10646        ("r-s4vectors" ,r-s4vectors)
10647        ("r-shiny" ,r-shiny)
10648        ("r-snpstats" ,r-snpstats)
10649        ("r-summarizedexperiment" ,r-summarizedexperiment)
10650        ("r-variantannotation" ,r-variantannotation)))
10651     (home-page "https://bioconductor.org/packages/gQTLstats")
10652     (synopsis "Computationally efficient analysis for eQTL and allied studies")
10653     (description
10654      "This package provides tools for the computationally efficient analysis
10655 of @dfn{quantitative trait loci} (QTL) data, including eQTL, mQTL, dsQTL, etc.
10656 The software in this package aims to support refinements and functional
10657 interpretation of members of a collection of association statistics on a
10658 family of feature/genome hypotheses.")
10659     (license license:artistic2.0)))
10660
10661 (define-public r-gviz
10662   (package
10663     (name "r-gviz")
10664     (version "1.26.0")
10665     (source
10666      (origin
10667        (method url-fetch)
10668        (uri (bioconductor-uri "Gviz" version))
10669        (sha256
10670         (base32
10671          "05zk9hf30afg6rjg97lzn5v8xij90v8zm09y9vcz0asmc3c8xs0a"))))
10672     (properties `((upstream-name . "Gviz")))
10673     (build-system r-build-system)
10674     (propagated-inputs
10675      `(("r-annotationdbi" ,r-annotationdbi)
10676        ("r-biobase" ,r-biobase)
10677        ("r-biocgenerics" ,r-biocgenerics)
10678        ("r-biomart" ,r-biomart)
10679        ("r-biostrings" ,r-biostrings)
10680        ("r-biovizbase" ,r-biovizbase)
10681        ("r-bsgenome" ,r-bsgenome)
10682        ("r-digest" ,r-digest)
10683        ("r-genomeinfodb" ,r-genomeinfodb)
10684        ("r-genomicalignments" ,r-genomicalignments)
10685        ("r-genomicfeatures" ,r-genomicfeatures)
10686        ("r-genomicranges" ,r-genomicranges)
10687        ("r-iranges" ,r-iranges)
10688        ("r-lattice" ,r-lattice)
10689        ("r-latticeextra" ,r-latticeextra)
10690        ("r-matrixstats" ,r-matrixstats)
10691        ("r-rcolorbrewer" ,r-rcolorbrewer)
10692        ("r-rsamtools" ,r-rsamtools)
10693        ("r-rtracklayer" ,r-rtracklayer)
10694        ("r-s4vectors" ,r-s4vectors)
10695        ("r-xvector" ,r-xvector)))
10696     (home-page "https://bioconductor.org/packages/Gviz")
10697     (synopsis "Plotting data and annotation information along genomic coordinates")
10698     (description
10699      "Genomic data analyses requires integrated visualization of known genomic
10700 information and new experimental data.  Gviz uses the biomaRt and the
10701 rtracklayer packages to perform live annotation queries to Ensembl and UCSC
10702 and translates this to e.g. gene/transcript structures in viewports of the
10703 grid graphics package.  This results in genomic information plotted together
10704 with your data.")
10705     (license license:artistic2.0)))
10706
10707 (define-public r-gwascat
10708   (package
10709     (name "r-gwascat")
10710     (version "2.14.0")
10711     (source
10712      (origin
10713        (method url-fetch)
10714        (uri (bioconductor-uri "gwascat" version))
10715        (sha256
10716         (base32
10717          "1fnyjydhicq4ayrv0lqjv48h9bd72h40s6l82g1h2ng0icwz38g0"))))
10718     (build-system r-build-system)
10719     (propagated-inputs
10720      `(("r-annotationdbi" ,r-annotationdbi)
10721        ("r-annotationhub" ,r-annotationhub)
10722        ("r-biocgenerics" ,r-biocgenerics)
10723        ("r-biostrings" ,r-biostrings)
10724        ("r-genomeinfodb" ,r-genomeinfodb)
10725        ("r-genomicfeatures" ,r-genomicfeatures)
10726        ("r-genomicranges" ,r-genomicranges)
10727        ("r-ggbio" ,r-ggbio)
10728        ("r-ggplot2" ,r-ggplot2)
10729        ("r-gqtlstats" ,r-gqtlstats)
10730        ("r-graph" ,r-graph)
10731        ("r-gviz" ,r-gviz)
10732        ("r-homo-sapiens" ,r-homo-sapiens)
10733        ("r-iranges" ,r-iranges)
10734        ("r-rsamtools" ,r-rsamtools)
10735        ("r-rtracklayer" ,r-rtracklayer)
10736        ("r-s4vectors" ,r-s4vectors)
10737        ("r-snpstats" ,r-snpstats)
10738        ("r-summarizedexperiment" ,r-summarizedexperiment)
10739        ("r-variantannotation" ,r-variantannotation)))
10740     (home-page "https://bioconductor.org/packages/gwascat")
10741     (synopsis "Tools for data in the EMBL-EBI GWAS catalog")
10742     (description
10743      "This package provides tools for representing and modeling data in the
10744 EMBL-EBI GWAS catalog.")
10745     (license license:artistic2.0)))
10746
10747 (define-public r-sushi
10748   (package
10749     (name "r-sushi")
10750     (version "1.20.0")
10751     (source (origin
10752               (method url-fetch)
10753               (uri (bioconductor-uri "Sushi" version))
10754               (sha256
10755                (base32
10756                 "0dv5di0hgbvk9cxnqhyf18mdjl50k6bk00a89r6zgp83rbxwr1r8"))))
10757     (properties `((upstream-name . "Sushi")))
10758     (build-system r-build-system)
10759     (propagated-inputs
10760      `(("r-biomart" ,r-biomart)
10761        ("r-zoo" ,r-zoo)))
10762     (home-page "https://bioconductor.org/packages/Sushi")
10763     (synopsis "Tools for visualizing genomics data")
10764     (description
10765      "This package provides flexible, quantitative, and integrative genomic
10766 visualizations for publication-quality multi-panel figures.")
10767     (license license:gpl2+)))
10768
10769 (define-public r-fithic
10770   (package
10771     (name "r-fithic")
10772     (version "1.8.0")
10773     (source (origin
10774               (method url-fetch)
10775               (uri (bioconductor-uri "FitHiC" version))
10776               (sha256
10777                (base32
10778                 "15xd8mz7660q4zr9p74mq1pqps4iz7pxp8f9ifn21gwg94aq1avn"))))
10779     (properties `((upstream-name . "FitHiC")))
10780     (build-system r-build-system)
10781     (propagated-inputs
10782      `(("r-data-table" ,r-data-table)
10783        ("r-fdrtool" ,r-fdrtool)
10784        ("r-rcpp" ,r-rcpp)))
10785     (home-page "https://bioconductor.org/packages/FitHiC")
10786     (synopsis "Confidence estimation for intra-chromosomal contact maps")
10787     (description
10788      "Fit-Hi-C is a tool for assigning statistical confidence estimates to
10789 intra-chromosomal contact maps produced by genome-wide genome architecture
10790 assays such as Hi-C.")
10791     (license license:gpl2+)))
10792
10793 (define-public r-hitc
10794   (package
10795     (name "r-hitc")
10796     (version "1.26.0")
10797     (source (origin
10798               (method url-fetch)
10799               (uri (bioconductor-uri "HiTC" version))
10800               (sha256
10801                (base32
10802                 "11f96k1707g6milpjgnrjf3b5r42hsrxhb5d8znkcr3y3mrskdbj"))))
10803     (properties `((upstream-name . "HiTC")))
10804     (build-system r-build-system)
10805     (propagated-inputs
10806      `(("r-biostrings" ,r-biostrings)
10807        ("r-genomeinfodb" ,r-genomeinfodb)
10808        ("r-genomicranges" ,r-genomicranges)
10809        ("r-iranges" ,r-iranges)
10810        ("r-matrix" ,r-matrix)
10811        ("r-rcolorbrewer" ,r-rcolorbrewer)
10812        ("r-rtracklayer" ,r-rtracklayer)))
10813     (home-page "https://bioconductor.org/packages/HiTC")
10814     (synopsis "High throughput chromosome conformation capture analysis")
10815     (description
10816      "The HiTC package was developed to explore high-throughput \"C\" data
10817 such as 5C or Hi-C.  Dedicated R classes as well as standard methods for
10818 quality controls, normalization, visualization, and further analysis are also
10819 provided.")
10820     (license license:artistic2.0)))
10821
10822 (define-public r-qvalue
10823   (package
10824     (name "r-qvalue")
10825     (version "2.14.0")
10826     (source
10827      (origin
10828        (method url-fetch)
10829        (uri (bioconductor-uri "qvalue" version))
10830        (sha256
10831         (base32
10832          "03qxshqwwq1rj23p6pjrz08jm3ziikvy9badi4mz2rcwy2nz783a"))))
10833     (build-system r-build-system)
10834     (propagated-inputs
10835      `(("r-ggplot2" ,r-ggplot2)
10836        ("r-reshape2" ,r-reshape2)))
10837     (home-page "http://github.com/jdstorey/qvalue")
10838     (synopsis "Q-value estimation for false discovery rate control")
10839     (description
10840      "This package takes a list of p-values resulting from the simultaneous
10841 testing of many hypotheses and estimates their q-values and local @dfn{false
10842 discovery rate} (FDR) values.  The q-value of a test measures the proportion
10843 of false positives incurred when that particular test is called significant.
10844 The local FDR measures the posterior probability the null hypothesis is true
10845 given the test's p-value.  Various plots are automatically generated, allowing
10846 one to make sensible significance cut-offs.  The software can be applied to
10847 problems in genomics, brain imaging, astrophysics, and data mining.")
10848     ;; Any version of the LGPL.
10849     (license license:lgpl3+)))
10850
10851 (define-public r-hdf5array
10852   (package
10853     (name "r-hdf5array")
10854     (version "1.10.0")
10855     (source
10856      (origin
10857        (method url-fetch)
10858        (uri (bioconductor-uri "HDF5Array" version))
10859        (sha256
10860         (base32
10861          "1w7ad8cfsbh5xx82m3l4lc0vbmj9lcsqxxpiy3ana2ycgn1bqv3g"))))
10862     (properties `((upstream-name . "HDF5Array")))
10863     (build-system r-build-system)
10864     (propagated-inputs
10865      `(("r-biocgenerics" ,r-biocgenerics)
10866        ("r-delayedarray" ,r-delayedarray)
10867        ("r-iranges" ,r-iranges)
10868        ("r-rhdf5" ,r-rhdf5)
10869        ("r-s4vectors" ,r-s4vectors)))
10870     (home-page "https://bioconductor.org/packages/HDF5Array")
10871     (synopsis "HDF5 back end for DelayedArray objects")
10872     (description "This package provides an array-like container for convenient
10873 access and manipulation of HDF5 datasets.  It supports delayed operations and
10874 block processing.")
10875     (license license:artistic2.0)))
10876
10877 (define-public r-rhdf5lib
10878   (package
10879     (name "r-rhdf5lib")
10880     (version "1.4.0")
10881     (source
10882      (origin
10883        (method url-fetch)
10884        (uri (bioconductor-uri "Rhdf5lib" version))
10885        (sha256
10886         (base32
10887          "01gpz780g850ql20b2ql6pvr678ydk4nq4sn5iiih94a4crb9lz1"))
10888        (modules '((guix build utils)))
10889        (snippet
10890         '(begin
10891            ;; Delete bundled binaries
10892            (delete-file-recursively "src/winlib/")
10893            #t))))
10894     (properties `((upstream-name . "Rhdf5lib")))
10895     (build-system r-build-system)
10896     (arguments
10897      `(#:phases
10898        (modify-phases %standard-phases
10899          (add-after 'unpack 'do-not-use-bundled-hdf5
10900            (lambda* (#:key inputs #:allow-other-keys)
10901              (for-each delete-file '("configure" "configure.ac"))
10902              ;; Do not make other packages link with the proprietary libsz.
10903              (substitute* "R/zzz.R"
10904                (("'%s/libhdf5_cpp.a %s/libhdf5.a %s/libsz.a -lz'")
10905                 "'%s/libhdf5_cpp.a %s/libhdf5.a %s/libhdf5.a -lz'")
10906                (("'%s/libhdf5.a %s/libsz.a -lz'")
10907                 "'%s/libhdf5.a %s/libhdf5.a -lz'"))
10908              (with-directory-excursion "src"
10909                (invoke "tar" "xvf" (assoc-ref inputs "hdf5-source"))
10910                (rename-file (string-append "hdf5-" ,(package-version hdf5-1.10))
10911                             "hdf5")
10912                ;; Remove timestamp and host system information to make
10913                ;; the build reproducible.
10914                (substitute* "hdf5/src/libhdf5.settings.in"
10915                  (("Configured on: @CONFIG_DATE@")
10916                   "Configured on: Guix")
10917                  (("Uname information:.*")
10918                   "Uname information: Linux\n")
10919                  ;; Remove unnecessary store reference.
10920                  (("C Compiler:.*")
10921                   "C Compiler: GCC\n"))
10922                (rename-file "Makevars.in" "Makevars")
10923                (substitute* "Makevars"
10924                  (("HDF5_CXX_LIB=.*")
10925                   (string-append "HDF5_CXX_LIB="
10926                                  (assoc-ref inputs "hdf5") "/lib/libhdf5_cpp.a\n"))
10927                  (("HDF5_LIB=.*")
10928                   (string-append "HDF5_LIB="
10929                                  (assoc-ref inputs "hdf5") "/lib/libhdf5.a\n"))
10930                  (("HDF5_CXX_INCLUDE=.*") "HDF5_CXX_INCLUDE=./hdf5/c++/src\n")
10931                  (("HDF5_INCLUDE=.*") "HDF5_INCLUDE=./hdf5/src\n")
10932                  ;; szip is non-free software
10933                  (("cp \\$\\{SZIP_LIB\\}.*") "")
10934                  (("\\$\\{USER_LIB_DIR\\}libsz.a") "")))
10935              #t)))))
10936     (inputs
10937      `(("zlib" ,zlib)))
10938     (propagated-inputs
10939      `(("hdf5" ,hdf5-1.10)))
10940     (native-inputs
10941      `(("hdf5-source" ,(package-source hdf5-1.10))))
10942     (home-page "https://bioconductor.org/packages/Rhdf5lib")
10943     (synopsis "HDF5 library as an R package")
10944     (description "This package provides C and C++ HDF5 libraries for use in R
10945 packages.")
10946     (license license:artistic2.0)))
10947
10948 (define-public r-beachmat
10949   (package
10950     (name "r-beachmat")
10951     (version "1.4.0")
10952     (source
10953      (origin
10954        (method url-fetch)
10955        (uri (bioconductor-uri "beachmat" version))
10956        (sha256
10957         (base32
10958          "07zgmms0qg8gw7x0js46965bbhpfj2aa1h5ixdz9r332bxv9cdmr"))))
10959     (build-system r-build-system)
10960     (inputs
10961      `(("hdf5" ,hdf5)
10962        ("zlib" ,zlib)))
10963     (propagated-inputs
10964      `(("r-biocgenerics" ,r-biocgenerics)
10965        ("r-delayedarray" ,r-delayedarray)
10966        ("r-hdf5array" ,r-hdf5array)
10967        ("r-rcpp" ,r-rcpp)
10968        ("r-rhdf5" ,r-rhdf5)
10969        ("r-rhdf5lib" ,r-rhdf5lib)))
10970     (home-page "https://bioconductor.org/packages/beachmat")
10971     (synopsis "Compiling Bioconductor to handle each matrix type")
10972     (description "This package provides a consistent C++ class interface for a
10973 variety of commonly used matrix types, including sparse and HDF5-backed
10974 matrices.")
10975     (license license:gpl3)))
10976
10977 (define-public r-singlecellexperiment
10978   (package
10979     (name "r-singlecellexperiment")
10980     (version "1.4.0")
10981     (source
10982      (origin
10983        (method url-fetch)
10984        (uri (bioconductor-uri "SingleCellExperiment" version))
10985        (sha256
10986         (base32
10987          "19r4r7djrn46qlijkj1g926vcklxzcrxjlxv6cg43m9j9jgfs3dj"))))
10988     (properties
10989      `((upstream-name . "SingleCellExperiment")))
10990     (build-system r-build-system)
10991     (propagated-inputs
10992      `(("r-biocgenerics" ,r-biocgenerics)
10993        ("r-s4vectors" ,r-s4vectors)
10994        ("r-summarizedexperiment" ,r-summarizedexperiment)))
10995     (home-page "https://bioconductor.org/packages/SingleCellExperiment")
10996     (synopsis "S4 classes for single cell data")
10997     (description "This package defines an S4 class for storing data from
10998 single-cell experiments.  This includes specialized methods to store and
10999 retrieve spike-in information, dimensionality reduction coordinates and size
11000 factors for each cell, along with the usual metadata for genes and
11001 libraries.")
11002     (license license:gpl3)))
11003
11004 (define-public r-scater
11005   (package
11006     (name "r-scater")
11007     (version "1.10.0")
11008     (source (origin
11009               (method url-fetch)
11010               (uri (bioconductor-uri "scater" version))
11011               (sha256
11012                (base32
11013                 "1kwa9n70c5j0xcj6nkmlkzjr63cnj78mp8nhg58n07fq1ijm4ns3"))))
11014     (build-system r-build-system)
11015     (propagated-inputs
11016      `(("r-beachmat" ,r-beachmat)
11017        ("r-biocgenerics" ,r-biocgenerics)
11018        ("r-biocparallel" ,r-biocparallel)
11019        ("r-delayedarray" ,r-delayedarray)
11020        ("r-delayedmatrixstats" ,r-delayedmatrixstats)
11021        ("r-dplyr" ,r-dplyr)
11022        ("r-ggbeeswarm" ,r-ggbeeswarm)
11023        ("r-ggplot2" ,r-ggplot2)
11024        ("r-matrix" ,r-matrix)
11025        ("r-plyr" ,r-plyr)
11026        ("r-rcpp" ,r-rcpp)
11027        ("r-reshape2" ,r-reshape2)
11028        ("r-rhdf5lib" ,r-rhdf5lib)
11029        ("r-s4vectors" ,r-s4vectors)
11030        ("r-singlecellexperiment" ,r-singlecellexperiment)
11031        ("r-summarizedexperiment" ,r-summarizedexperiment)
11032        ("r-viridis" ,r-viridis)))
11033     (home-page "https://github.com/davismcc/scater")
11034     (synopsis "Single-cell analysis toolkit for gene expression data in R")
11035     (description "This package provides a collection of tools for doing
11036 various analyses of single-cell RNA-seq gene expression data, with a focus on
11037 quality control.")
11038     (license license:gpl2+)))
11039
11040 (define-public r-scran
11041   (package
11042     (name "r-scran")
11043     (version "1.10.1")
11044     (source
11045      (origin
11046        (method url-fetch)
11047        (uri (bioconductor-uri "scran" version))
11048        (sha256
11049         (base32
11050          "1viyzrwfm9vccsf54c6g7k1dn7skkfx4ml1jy12q67wa20sx8l03"))))
11051     (build-system r-build-system)
11052     (propagated-inputs
11053      `(("r-beachmat" ,r-beachmat)
11054        ("r-biocgenerics" ,r-biocgenerics)
11055        ("r-biocneighbors" ,r-biocneighbors)
11056        ("r-biocparallel" ,r-biocparallel)
11057        ("r-delayedarray" ,r-delayedarray)
11058        ("r-delayedmatrixstats" ,r-delayedmatrixstats)
11059        ("r-dynamictreecut" ,r-dynamictreecut)
11060        ("r-edger" ,r-edger)
11061        ("r-igraph" ,r-igraph)
11062        ("r-limma" ,r-limma)
11063        ("r-matrix" ,r-matrix)
11064        ("r-rcpp" ,r-rcpp)
11065        ("r-rhdf5lib" ,r-rhdf5lib)
11066        ("r-s4vectors" ,r-s4vectors)
11067        ("r-scater" ,r-scater)
11068        ("r-singlecellexperiment" ,r-singlecellexperiment)
11069        ("r-statmod" ,r-statmod)
11070        ("r-summarizedexperiment" ,r-summarizedexperiment)))
11071     (home-page "https://bioconductor.org/packages/scran")
11072     (synopsis "Methods for single-cell RNA-Seq data analysis")
11073     (description "This package implements a variety of low-level analyses of
11074 single-cell RNA-seq data.  Methods are provided for normalization of
11075 cell-specific biases, assignment of cell cycle phase, and detection of highly
11076 variable and significantly correlated genes.")
11077     (license license:gpl3)))
11078
11079 (define-public r-delayedmatrixstats
11080   (package
11081     (name "r-delayedmatrixstats")
11082     (version "1.4.0")
11083     (source
11084      (origin
11085        (method url-fetch)
11086        (uri (bioconductor-uri "DelayedMatrixStats" version))
11087        (sha256
11088         (base32
11089          "03fk2avl1vyjv2wslczkc82qr0zmp1ra8iimd47pbmnnm839ly4w"))))
11090     (properties
11091      `((upstream-name . "DelayedMatrixStats")))
11092     (build-system r-build-system)
11093     (propagated-inputs
11094      `(("r-biocparallel" ,r-biocparallel)
11095        ("r-delayedarray" ,r-delayedarray)
11096        ("r-hdf5array" ,r-hdf5array)
11097        ("r-iranges" ,r-iranges)
11098        ("r-matrix" ,r-matrix)
11099        ("r-matrixstats" ,r-matrixstats)
11100        ("r-s4vectors" ,r-s4vectors)))
11101     (home-page "https://github.com/PeteHaitch/DelayedMatrixStats")
11102     (synopsis "Functions that apply to rows and columns of DelayedMatrix objects")
11103     (description
11104      "This package provides a port of the @code{matrixStats} API for use with
11105 @code{DelayedMatrix} objects from the @code{DelayedArray} package.  It
11106 contains high-performing functions operating on rows and columns of
11107 @code{DelayedMatrix} objects, e.g. @code{colMedians}, @code{rowMedians},
11108 @code{colRanks}, @code{rowRanks}, @code{colSds}, and @code{rowSds}.  Functions
11109 are optimized per data type and for subsetted calculations such that both
11110 memory usage and processing time is minimized.")
11111     (license license:expat)))
11112
11113 (define-public r-phangorn
11114   (package
11115     (name "r-phangorn")
11116     (version "2.4.0")
11117     (source
11118      (origin
11119        (method url-fetch)
11120        (uri (cran-uri "phangorn" version))
11121        (sha256
11122         (base32
11123          "0xc8k552nxczy19jr0xjjagrzc8x6lafasgk2c099ls8bc1yml1i"))))
11124     (build-system r-build-system)
11125     (propagated-inputs
11126      `(("r-ape" ,r-ape)
11127        ("r-fastmatch" ,r-fastmatch)
11128        ("r-igraph" ,r-igraph)
11129        ("r-magrittr" ,r-magrittr)
11130        ("r-matrix" ,r-matrix)
11131        ("r-quadprog" ,r-quadprog)
11132        ("r-rcpp" ,r-rcpp)))
11133     (home-page "https://github.com/KlausVigo/phangorn")
11134     (synopsis "Phylogenetic analysis in R")
11135     (description
11136      "Phangorn is a package for phylogenetic analysis in R.  It supports
11137 estimation of phylogenetic trees and networks using Maximum Likelihood,
11138 Maximum Parsimony, distance methods and Hadamard conjugation.")
11139     (license license:gpl2+)))
11140
11141 (define-public r-dropbead
11142   (let ((commit "d746c6f3b32110428ea56d6a0001ce52a251c247")
11143         (revision "2"))
11144     (package
11145       (name "r-dropbead")
11146       (version (string-append "0-" revision "." (string-take commit 7)))
11147       (source
11148        (origin
11149          (method git-fetch)
11150          (uri (git-reference
11151                (url "https://github.com/rajewsky-lab/dropbead.git")
11152                (commit commit)))
11153          (file-name (git-file-name name version))
11154          (sha256
11155           (base32
11156            "0sbzma49aiiyw8b0jpr7fnhzys9nsqmp4hy4hdz1gzyg1lhnca26"))))
11157       (build-system r-build-system)
11158       (propagated-inputs
11159        `(("r-ggplot2" ,r-ggplot2)
11160          ("r-rcolorbrewer" ,r-rcolorbrewer)
11161          ("r-gridextra" ,r-gridextra)
11162          ("r-gplots" ,r-gplots)
11163          ("r-plyr" ,r-plyr)))
11164       (home-page "https://github.com/rajewsky-lab/dropbead")
11165       (synopsis "Basic exploration and analysis of Drop-seq data")
11166       (description "This package offers a quick and straight-forward way to
11167 explore and perform basic analysis of single cell sequencing data coming from
11168 droplet sequencing.  It has been particularly tailored for Drop-seq.")
11169       (license license:gpl3))))
11170
11171 (define htslib-for-sambamba
11172   (let ((commit "2f3c3ea7b301f9b45737a793c0b2dcf0240e5ee5"))
11173     (package
11174       (inherit htslib)
11175       (name "htslib-for-sambamba")
11176       (version (string-append "1.3.1-1." (string-take commit 9)))
11177       (source
11178        (origin
11179          (method git-fetch)
11180          (uri (git-reference
11181                (url "https://github.com/lomereiter/htslib.git")
11182                (commit commit)))
11183          (file-name (string-append "htslib-" version "-checkout"))
11184          (sha256
11185           (base32
11186            "0g38g8s3npr0gjm9fahlbhiskyfws9l5i0x1ml3rakzj7az5l9c9"))))
11187       (native-inputs
11188        `(("autoconf" ,autoconf)
11189          ("automake" ,automake)
11190          ,@(package-native-inputs htslib))))))
11191
11192 (define-public sambamba
11193   (package
11194     (name "sambamba")
11195     (version "0.6.8")
11196     (source
11197      (origin
11198        (method git-fetch)
11199        (uri (git-reference
11200              (url "https://github.com/lomereiter/sambamba.git")
11201              (commit (string-append "v" version))))
11202        (file-name (string-append name "-" version "-checkout"))
11203        (sha256
11204         (base32
11205          "0k0cz3qcv98p6cq09zlbgnjsggxcqbcmzxg5zikgcgbr2nfq4lry"))))
11206     (build-system gnu-build-system)
11207     (arguments
11208      `(#:tests? #f                      ; there is no test target
11209        #:parallel-build? #f             ; not supported
11210        #:phases
11211        (modify-phases %standard-phases
11212          (delete 'configure)
11213          (add-after 'unpack 'fix-ldc-version
11214            (lambda _
11215              (substitute* "gen_ldc_version_info.py"
11216                (("/usr/bin/env.*") (which "python3")))
11217              (substitute* "Makefile"
11218                ;; We use ldc2 instead of ldmd2 to compile sambamba.
11219                (("\\$\\(shell which ldmd2\\)") (which "ldc2")))
11220              #t))
11221          (add-after 'unpack 'place-biod-and-undead
11222            (lambda* (#:key inputs #:allow-other-keys)
11223              (copy-recursively (assoc-ref inputs "biod") "BioD")
11224              (copy-recursively (assoc-ref inputs "undead") "undeaD")
11225              #t))
11226          (add-after 'unpack 'unbundle-prerequisites
11227            (lambda _
11228              (substitute* "Makefile"
11229                (("htslib/libhts.a lz4/lib/liblz4.a")
11230                 "-L-lhts -L-llz4")
11231                ((" lz4-static htslib-static") ""))
11232              #t))
11233          (replace 'install
11234            (lambda* (#:key outputs #:allow-other-keys)
11235              (let* ((out   (assoc-ref outputs "out"))
11236                     (bin   (string-append out "/bin")))
11237                (mkdir-p bin)
11238                (install-file "bin/sambamba" bin)
11239                #t))))))
11240     (native-inputs
11241      `(("ldc" ,ldc)
11242        ("rdmd" ,rdmd)
11243        ("python" ,python-minimal)
11244        ("biod"
11245         ,(let ((commit "4f1a7d2fb7ef3dfe962aa357d672f354ebfbe42e"))
11246            (origin
11247              (method git-fetch)
11248              (uri (git-reference
11249                    (url "https://github.com/biod/BioD.git")
11250                    (commit commit)))
11251              (file-name (string-append "biod-"
11252                                        (string-take commit 9)
11253                                        "-checkout"))
11254              (sha256
11255               (base32
11256                "1k5pdjv1qvi0a3rwd1sfq6zbj37l86i7bf710m4c0y6737lxj426")))))
11257        ("undead"
11258         ,(let ((commit "9be93876982b5f14fcca60832563b3cd767dd84d"))
11259            (origin
11260              (method git-fetch)
11261              (uri (git-reference
11262                    (url "https://github.com/biod/undeaD.git")
11263                    (commit commit)))
11264              (file-name (string-append "undead-"
11265                                        (string-take commit 9)
11266                                        "-checkout"))
11267              (sha256
11268               (base32
11269                "1xfarj0nqlmi5jd1vmcmm7pabzaf9hxyvk6hp0d6jslb5k9r8r3d")))))))
11270     (inputs
11271      `(("lz4" ,lz4)
11272        ("htslib" ,htslib-for-sambamba)))
11273     (home-page "http://lomereiter.github.io/sambamba")
11274     (synopsis "Tools for working with SAM/BAM data")
11275     (description "Sambamba is a high performance modern robust and
11276 fast tool (and library), written in the D programming language, for
11277 working with SAM and BAM files.  Current parallelised functionality is
11278 an important subset of samtools functionality, including view, index,
11279 sort, markdup, and depth.")
11280     (license license:gpl2+)))
11281
11282 (define-public ritornello
11283   (package
11284     (name "ritornello")
11285     (version "2.0.1")
11286     (source (origin
11287               (method git-fetch)
11288               (uri (git-reference
11289                     (url "https://github.com/KlugerLab/Ritornello.git")
11290                     (commit (string-append "v" version))))
11291               (file-name (git-file-name name version))
11292               (sha256
11293                (base32
11294                 "1xahvq215qld7x1w8vpa5zbrsj6p9crb9shqa2x89sb0aaxa02jk"))))
11295     (build-system gnu-build-system)
11296     (arguments
11297      `(#:tests? #f                      ; there are no tests
11298        #:phases
11299        (modify-phases %standard-phases
11300          (add-after 'unpack 'patch-samtools-references
11301            (lambda* (#:key inputs #:allow-other-keys)
11302              (substitute* '("src/SamStream.h"
11303                             "src/FLD.cpp")
11304                (("<sam.h>") "<samtools/sam.h>"))
11305              #t))
11306          (delete 'configure)
11307          (replace 'install
11308            (lambda* (#:key inputs outputs #:allow-other-keys)
11309              (let* ((out    (assoc-ref outputs "out"))
11310                     (bin    (string-append out "/bin/")))
11311                (mkdir-p bin)
11312                (install-file "bin/Ritornello" bin)
11313                #t))))))
11314     (inputs
11315      `(("samtools" ,samtools-0.1)
11316        ("fftw" ,fftw)
11317        ("boost" ,boost)
11318        ("zlib" ,zlib)))
11319     (home-page "https://github.com/KlugerLab/Ritornello")
11320     (synopsis "Control-free peak caller for ChIP-seq data")
11321     (description "Ritornello is a ChIP-seq peak calling algorithm based on
11322 signal processing that can accurately call binding events without the need to
11323 do a pair total DNA input or IgG control sample.  It has been tested for use
11324 with narrow binding events such as transcription factor ChIP-seq.")
11325     (license license:gpl3+)))
11326
11327 (define-public trim-galore
11328   (package
11329     (name "trim-galore")
11330     (version "0.4.5")
11331     (source
11332      (origin
11333        (method git-fetch)
11334        (uri (git-reference
11335              (url "https://github.com/FelixKrueger/TrimGalore.git")
11336              (commit version)))
11337        (file-name (string-append name "-" version "-checkout"))
11338        (sha256
11339         (base32
11340          "0x5892l48c816pf00wmnz5vq0zq6170d3xc8zrxncd4jcz7h1p71"))))
11341     (build-system gnu-build-system)
11342     (arguments
11343      `(#:tests? #f                      ; no tests
11344        #:phases
11345        (modify-phases %standard-phases
11346          (delete 'configure)
11347          (delete 'build)
11348          (add-after 'unpack 'hardcode-tool-references
11349            (lambda* (#:key inputs #:allow-other-keys)
11350              (substitute* "trim_galore"
11351                (("\\$path_to_cutadapt = 'cutadapt'")
11352                 (string-append "$path_to_cutadapt = '"
11353                                (assoc-ref inputs "cutadapt")
11354                                "/bin/cutadapt'"))
11355                (("\\| gzip")
11356                 (string-append "| "
11357                                (assoc-ref inputs "gzip")
11358                                "/bin/gzip"))
11359                (("\"gunzip")
11360                 (string-append "\""
11361                                (assoc-ref inputs "gzip")
11362                                "/bin/gunzip")))
11363              #t))
11364          (replace 'install
11365            (lambda* (#:key outputs #:allow-other-keys)
11366              (let ((bin (string-append (assoc-ref outputs "out")
11367                                        "/bin")))
11368                (mkdir-p bin)
11369                (install-file "trim_galore" bin)
11370                #t))))))
11371     (inputs
11372      `(("gzip" ,gzip)
11373        ("perl" ,perl)
11374        ("cutadapt" ,cutadapt)))
11375     (native-inputs
11376      `(("unzip" ,unzip)))
11377     (home-page "http://www.bioinformatics.babraham.ac.uk/projects/trim_galore/")
11378     (synopsis "Wrapper around Cutadapt and FastQC")
11379     (description "Trim Galore! is a wrapper script to automate quality and
11380 adapter trimming as well as quality control, with some added functionality to
11381 remove biased methylation positions for RRBS sequence files.")
11382     (license license:gpl3+)))
11383
11384 (define-public gess
11385   (package
11386     (name "gess")
11387     (version "1.0")
11388     (source (origin
11389               (method url-fetch)
11390               (uri (string-append "http://compbio.uthscsa.edu/"
11391                                   "GESS_Web/files/"
11392                                   "gess-" version ".src.tar.gz"))
11393               (sha256
11394                (base32
11395                 "0hyk403kxscclzfs24pvdgiv0wm03kjcziqdrp5w46cb049gz0d7"))))
11396     (build-system gnu-build-system)
11397     (arguments
11398      `(#:tests? #f                      ; no tests
11399        #:phases
11400        (modify-phases %standard-phases
11401          (delete 'configure)
11402          (delete 'build)
11403          (replace 'install
11404            (lambda* (#:key inputs outputs #:allow-other-keys)
11405              (let* ((python (assoc-ref inputs "python"))
11406                     (out    (assoc-ref outputs "out"))
11407                     (bin    (string-append out "/bin/"))
11408                     (target (string-append
11409                              out "/lib/python"
11410                              ,(version-major+minor
11411                                 (package-version python))
11412                              "/site-packages/gess/")))
11413                (mkdir-p target)
11414                (copy-recursively "." target)
11415                ;; Make GESS.py executable
11416                (chmod (string-append target "GESS.py") #o555)
11417                ;; Add Python shebang to the top and make Matplotlib
11418                ;; usable.
11419                (substitute* (string-append target "GESS.py")
11420                  (("\"\"\"Description:" line)
11421                   (string-append "#!" (which "python") "
11422 import matplotlib
11423 matplotlib.use('Agg')
11424 " line)))
11425                ;; Make sure GESS has all modules in its path
11426                (wrap-program (string-append target "GESS.py")
11427                  `("PYTHONPATH" ":" prefix (,target ,(getenv "PYTHONPATH"))))
11428                (mkdir-p bin)
11429                (symlink (string-append target "GESS.py")
11430                         (string-append bin "GESS.py"))
11431                #t))))))
11432     (inputs
11433      `(("python" ,python-2)
11434        ("python2-pysam" ,python2-pysam)
11435        ("python2-scipy" ,python2-scipy)
11436        ("python2-numpy" ,python2-numpy)
11437        ("python2-networkx" ,python2-networkx)
11438        ("python2-biopython" ,python2-biopython)))
11439     (home-page "http://compbio.uthscsa.edu/GESS_Web/")
11440     (synopsis "Detect exon-skipping events from raw RNA-seq data")
11441     (description
11442      "GESS is an implementation of a novel computational method to detect de
11443 novo exon-skipping events directly from raw RNA-seq data without the prior
11444 knowledge of gene annotation information.  GESS stands for the graph-based
11445 exon-skipping scanner detection scheme.")
11446     (license license:bsd-3)))
11447
11448 (define-public phylip
11449   (package
11450     (name "phylip")
11451     (version "3.696")
11452     (source
11453      (origin
11454        (method url-fetch)
11455        (uri (string-append "http://evolution.gs.washington.edu/phylip/"
11456                            "download/phylip-" version ".tar.gz"))
11457        (sha256
11458         (base32
11459          "01jar1rayhr2gba2pgbw49m56rc5z4p5wn3ds0m188hrlln4a2nd"))))
11460     (build-system gnu-build-system)
11461     (arguments
11462      `(#:tests? #f                      ; no check target
11463        #:make-flags (list "-f" "Makefile.unx" "install")
11464        #:parallel-build? #f             ; not supported
11465        #:phases
11466        (modify-phases %standard-phases
11467          (add-after 'unpack 'enter-dir
11468            (lambda _ (chdir "src") #t))
11469          (delete 'configure)
11470          (replace 'install
11471            (lambda* (#:key inputs outputs #:allow-other-keys)
11472              (let ((target (string-append (assoc-ref outputs "out")
11473                                           "/bin")))
11474                (mkdir-p target)
11475                (for-each (lambda (file)
11476                            (install-file file target))
11477                          (find-files "../exe" ".*")))
11478              #t)))))
11479     (home-page "http://evolution.genetics.washington.edu/phylip/")
11480     (synopsis "Tools for inferring phylogenies")
11481     (description "PHYLIP (the PHYLogeny Inference Package) is a package of
11482 programs for inferring phylogenies (evolutionary trees).")
11483     (license license:bsd-2)))
11484
11485 (define-public imp
11486   (package
11487     (name "imp")
11488     (version "2.6.2")
11489     (source
11490      (origin
11491        (method url-fetch)
11492        (uri (string-append "https://integrativemodeling.org/"
11493                            version "/download/imp-" version ".tar.gz"))
11494        (sha256
11495         (base32
11496          "0lxqx7vh79d771svr611dkilp6sn30qrbw8zvscbrm37v38d2j6h"))))
11497     (build-system cmake-build-system)
11498     (arguments
11499      `(;; FIXME: Some tests fail because they produce warnings, others fail
11500        ;; because the PYTHONPATH does not include the modeller's directory.
11501        #:tests? #f))
11502     (inputs
11503      `(("boost" ,boost)
11504        ("gsl" ,gsl)
11505        ("swig" ,swig)
11506        ("hdf5" ,hdf5)
11507        ("fftw" ,fftw)
11508        ("python" ,python-2)))
11509     (propagated-inputs
11510      `(("python2-numpy" ,python2-numpy)
11511        ("python2-scipy" ,python2-scipy)
11512        ("python2-pandas" ,python2-pandas)
11513        ("python2-scikit-learn" ,python2-scikit-learn)
11514        ("python2-networkx" ,python2-networkx)))
11515     (home-page "https://integrativemodeling.org")
11516     (synopsis "Integrative modeling platform")
11517     (description "IMP's broad goal is to contribute to a comprehensive
11518 structural characterization of biomolecules ranging in size and complexity
11519 from small peptides to large macromolecular assemblies, by integrating data
11520 from diverse biochemical and biophysical experiments.  IMP provides a C++ and
11521 Python toolbox for solving complex modeling problems, and a number of
11522 applications for tackling some common problems in a user-friendly way.")
11523     ;; IMP is largely available under the GNU Lesser GPL; see the file
11524     ;; COPYING.LGPL for the full text of this license. Some IMP modules are
11525     ;; available under the GNU GPL (see the file COPYING.GPL).
11526     (license (list license:lgpl2.1+
11527                    license:gpl3+))))
11528
11529 (define-public tadbit
11530   (package
11531     (name "tadbit")
11532     (version "0.2.0")
11533     (source (origin
11534               (method git-fetch)
11535               (uri (git-reference
11536                     (url "https://github.com/3DGenomes/TADbit.git")
11537                     (commit (string-append "v" version))))
11538               (file-name (git-file-name name version))
11539               (sha256
11540                (base32
11541                 "07g3aj648prmsvxp9caz5yl41k0y0647vxh0f5p3w8376mfiljd0"))))
11542     (build-system python-build-system)
11543     (arguments
11544      `(;; Tests are included and must be run after installation, but
11545        ;; they are incomplete and thus cannot be run.
11546        #:tests? #f
11547        #:python ,python-2
11548        #:phases
11549        (modify-phases %standard-phases
11550          (add-after 'unpack 'fix-problems-with-setup.py
11551            (lambda* (#:key outputs #:allow-other-keys)
11552              ;; setup.py opens these files for writing
11553              (chmod "_pytadbit/_version.py" #o664)
11554              (chmod "README.rst" #o664)
11555
11556              ;; Don't attempt to install the bash completions to
11557              ;; the home directory.
11558              (rename-file "extras/.bash_completion"
11559                           "extras/tadbit")
11560              (substitute* "setup.py"
11561                (("\\(path.expanduser\\('~'\\)")
11562                 (string-append "(\""
11563                                (assoc-ref outputs "out")
11564                                "/etc/bash_completion.d\""))
11565                (("extras/\\.bash_completion")
11566                 "extras/tadbit"))
11567              #t)))))
11568     (inputs
11569      ;; TODO: add Chimera for visualization
11570      `(("imp" ,imp)
11571        ("mcl" ,mcl)
11572        ("python2-scipy" ,python2-scipy)
11573        ("python2-numpy" ,python2-numpy)
11574        ("python2-matplotlib" ,python2-matplotlib)
11575        ("python2-pysam" ,python2-pysam)))
11576     (home-page "https://3dgenomes.github.io/TADbit/")
11577     (synopsis "Analyze, model, and explore 3C-based data")
11578     (description
11579      "TADbit is a complete Python library to deal with all steps to analyze,
11580 model, and explore 3C-based data.  With TADbit the user can map FASTQ files to
11581 obtain raw interaction binned matrices (Hi-C like matrices), normalize and
11582 correct interaction matrices, identify and compare the so-called
11583 @dfn{Topologically Associating Domains} (TADs), build 3D models from the
11584 interaction matrices, and finally, extract structural properties from the
11585 models.  TADbit is complemented by TADkit for visualizing 3D models.")
11586     (license license:gpl3+)))
11587
11588 (define-public kentutils
11589   (package
11590     (name "kentutils")
11591     ;; 302.1.0 is out, but the only difference is the inclusion of
11592     ;; pre-built binaries.
11593     (version "302.0.0")
11594     (source
11595      (origin
11596        (method git-fetch)
11597        (uri (git-reference
11598              (url "https://github.com/ENCODE-DCC/kentUtils.git")
11599              (commit (string-append "v" version))))
11600        (file-name (git-file-name name version))
11601        (sha256
11602         (base32
11603          "0n1wbyjpzii2b9qhyp9r1q76j623cggpg3y8fmw78ld3z4y7ivha"))
11604        (modules '((guix build utils)
11605                   (srfi srfi-26)
11606                   (ice-9 ftw)))
11607        (snippet
11608         '(begin
11609            ;; Only the contents of the specified directories are free
11610            ;; for all uses, so we remove the rest.  "hg/autoSql" and
11611            ;; "hg/autoXml" are nominally free, but they depend on a
11612            ;; library that is built from the sources in "hg/lib",
11613            ;; which is nonfree.
11614            (let ((free (list "." ".."
11615                              "utils" "lib" "inc" "tagStorm"
11616                              "parasol" "htslib"))
11617                  (directory? (lambda (file)
11618                                (eq? 'directory (stat:type (stat file))))))
11619              (for-each (lambda (file)
11620                          (and (directory? file)
11621                               (delete-file-recursively file)))
11622                        (map (cut string-append "src/" <>)
11623                             (scandir "src"
11624                                      (lambda (file)
11625                                        (not (member file free)))))))
11626            ;; Only make the utils target, not the userApps target,
11627            ;; because that requires libraries we won't build.
11628            (substitute* "Makefile"
11629              ((" userApps") " utils"))
11630            ;; Only build libraries that are free.
11631            (substitute* "src/makefile"
11632              (("DIRS =.*") "DIRS =\n")
11633              (("cd jkOwnLib.*") "")
11634              ((" hgLib") "")
11635              (("cd hg.*") ""))
11636            (substitute* "src/utils/makefile"
11637              ;; These tools depend on "jkhgap.a", which is part of the
11638              ;; nonfree "src/hg/lib" directory.
11639              (("raSqlQuery") "")
11640              (("pslLiftSubrangeBlat") "")
11641
11642              ;; Do not build UCSC tools, which may require nonfree
11643              ;; components.
11644              (("ALL_APPS =.*") "ALL_APPS = $(UTILS_APPLIST)\n"))
11645            #t))))
11646     (build-system gnu-build-system)
11647     (arguments
11648      `( ;; There is no global test target and the test target for
11649        ;; individual tools depends on input files that are not
11650        ;; included.
11651        #:tests? #f
11652        #:phases
11653        (modify-phases %standard-phases
11654          (add-after 'unpack 'fix-permissions
11655            (lambda _ (make-file-writable "src/inc/localEnvironment.mk") #t))
11656          (add-after 'unpack 'fix-paths
11657            (lambda _
11658              (substitute* "Makefile"
11659                (("/bin/echo") (which "echo")))
11660              #t))
11661          (add-after 'unpack 'prepare-samtabix
11662            (lambda* (#:key inputs #:allow-other-keys)
11663              (copy-recursively (assoc-ref inputs "samtabix")
11664                                "samtabix")
11665              #t))
11666          (delete 'configure)
11667          (replace 'install
11668            (lambda* (#:key outputs #:allow-other-keys)
11669              (let ((bin (string-append (assoc-ref outputs "out")
11670                                        "/bin")))
11671                (copy-recursively "bin" bin))
11672              #t)))))
11673     (native-inputs
11674      `(("samtabix"
11675         ,(origin
11676            (method git-fetch)
11677            (uri (git-reference
11678                  (url "http://genome-source.cse.ucsc.edu/samtabix.git")
11679                  (commit "10fd107909c1ac4d679299908be4262a012965ba")))
11680            (sha256
11681             (base32
11682              "0c1nj64l42v395sa84n7az43xiap4i6f9n9dfz4058aqiwkhkmma"))))))
11683     (inputs
11684      `(("zlib" ,zlib)
11685        ("tcsh" ,tcsh)
11686        ("perl" ,perl)
11687        ("libpng" ,libpng)
11688        ("mariadb" ,mariadb)
11689        ("openssl" ,openssl)))
11690     (home-page "http://genome.cse.ucsc.edu/index.html")
11691     (synopsis "Assorted bioinformatics utilities")
11692     (description "This package provides the kentUtils, a selection of
11693 bioinformatics utilities used in combination with the UCSC genome
11694 browser.")
11695     ;; Only a subset of the sources are released under a non-copyleft
11696     ;; free software license.  All other sources are removed in a
11697     ;; snippet.  See this bug report for an explanation of how the
11698     ;; license statements apply:
11699     ;; https://github.com/ENCODE-DCC/kentUtils/issues/12
11700     (license (license:non-copyleft
11701               "http://genome.ucsc.edu/license/"
11702               "The contents of this package are free for all uses."))))
11703
11704 (define-public f-seq
11705   (let ((commit "6ccded34cff38cf432deed8503648b4a66953f9b")
11706         (revision "1"))
11707     (package
11708       (name "f-seq")
11709       (version (string-append "1.1-" revision "." (string-take commit 7)))
11710       (source (origin
11711                 (method git-fetch)
11712                 (uri (git-reference
11713                       (url "https://github.com/aboyle/F-seq.git")
11714                       (commit commit)))
11715                 (file-name (string-append name "-" version))
11716                 (sha256
11717                  (base32
11718                   "1nk33k0yajg2id4g59bc4szr58r2q6pdq42vgcw054m8ip9wv26h"))
11719                 (modules '((guix build utils)))
11720                 ;; Remove bundled Java library archives.
11721                 (snippet
11722                  '(begin
11723                     (for-each delete-file (find-files "lib" ".*"))
11724                     #t))))
11725       (build-system ant-build-system)
11726       (arguments
11727        `(#:tests? #f ; no tests included
11728          #:phases
11729          (modify-phases %standard-phases
11730            (replace 'install
11731              (lambda* (#:key inputs outputs #:allow-other-keys)
11732                (let* ((target (assoc-ref outputs "out"))
11733                       (bin (string-append target "/bin"))
11734                       (doc (string-append target "/share/doc/f-seq"))
11735                       (lib (string-append target "/lib")))
11736                  (mkdir-p target)
11737                  (mkdir-p doc)
11738                  (substitute* "bin/linux/fseq"
11739                    (("java") (which "java"))
11740                    (("\\$REALDIR/../lib/commons-cli-1.1.jar")
11741                     (string-append (assoc-ref inputs "java-commons-cli")
11742                                    "/share/java/commons-cli.jar"))
11743                    (("REALDIR=.*")
11744                     (string-append "REALDIR=" bin "\n")))
11745                  (install-file "README.txt" doc)
11746                  (install-file "bin/linux/fseq" bin)
11747                  (install-file "build~/fseq.jar" lib)
11748                  (copy-recursively "lib" lib)
11749                  #t))))))
11750       (inputs
11751        `(("perl" ,perl)
11752          ("java-commons-cli" ,java-commons-cli)))
11753       (home-page "http://fureylab.web.unc.edu/software/fseq/")
11754       (synopsis "Feature density estimator for high-throughput sequence tags")
11755       (description
11756        "F-Seq is a software package that generates a continuous tag sequence
11757 density estimation allowing identification of biologically meaningful sites
11758 such as transcription factor binding sites (ChIP-seq) or regions of open
11759 chromatin (DNase-seq).  Output can be displayed directly in the UCSC Genome
11760 Browser.")
11761       (license license:gpl3+))))
11762
11763 (define-public bismark
11764   (package
11765     (name "bismark")
11766     (version "0.19.1")
11767     (source
11768      (origin
11769        (method git-fetch)
11770        (uri (git-reference
11771              (url "https://github.com/FelixKrueger/Bismark.git")
11772              (commit version)))
11773        (file-name (string-append name "-" version "-checkout"))
11774        (sha256
11775         (base32
11776          "0yb5l36slwg02fp4b1jdlplgljcsxgqfzvzihzdnphd87dghcc84"))
11777        (snippet
11778         '(begin
11779            ;; highcharts.js is non-free software.  The code is available under
11780            ;; CC-BY-NC or proprietary licenses only.
11781            (delete-file "bismark_sitrep/highcharts.js")
11782            #t))))
11783     (build-system perl-build-system)
11784     (arguments
11785      `(#:tests? #f                      ; there are no tests
11786        #:phases
11787        (modify-phases %standard-phases
11788          (delete 'configure)
11789          (delete 'build)
11790          (replace 'install
11791            (lambda* (#:key inputs outputs #:allow-other-keys)
11792              (let* ((out (assoc-ref outputs "out"))
11793                     (bin (string-append out "/bin"))
11794                     (share   (string-append out "/share/bismark"))
11795                     (docdir  (string-append out "/share/doc/bismark"))
11796                     (docs    '("Docs/Bismark_User_Guide.html"))
11797                     (scripts '("bismark"
11798                                "bismark_genome_preparation"
11799                                "bismark_methylation_extractor"
11800                                "bismark2bedGraph"
11801                                "bismark2report"
11802                                "coverage2cytosine"
11803                                "deduplicate_bismark"
11804                                "filter_non_conversion"
11805                                "bam2nuc"
11806                                "bismark2summary")))
11807                (substitute* "bismark2report"
11808                  (("\\$RealBin/bismark_sitrep")
11809                   (string-append share "/bismark_sitrep")))
11810                (mkdir-p share)
11811                (mkdir-p docdir)
11812                (mkdir-p bin)
11813                (for-each (lambda (file) (install-file file bin))
11814                          scripts)
11815                (for-each (lambda (file) (install-file file docdir))
11816                          docs)
11817                (copy-recursively "Docs/Images" (string-append docdir "/Images"))
11818                (copy-recursively "bismark_sitrep"
11819                                  (string-append share "/bismark_sitrep"))
11820
11821                ;; Fix references to gunzip
11822                (substitute* (map (lambda (file)
11823                                    (string-append bin "/" file))
11824                                  scripts)
11825                  (("\"gunzip -c")
11826                   (string-append "\"" (assoc-ref inputs "gzip")
11827                                  "/bin/gunzip -c")))
11828                #t))))))
11829     (inputs
11830      `(("gzip" ,gzip)))
11831     (home-page "http://www.bioinformatics.babraham.ac.uk/projects/bismark/")
11832     (synopsis "Map bisulfite treated sequence reads and analyze methylation")
11833     (description "Bismark is a program to map bisulfite treated sequencing
11834 reads to a genome of interest and perform methylation calls in a single step.
11835 The output can be easily imported into a genome viewer, such as SeqMonk, and
11836 enables a researcher to analyse the methylation levels of their samples
11837 straight away.  Its main features are:
11838
11839 @itemize
11840 @item Bisulfite mapping and methylation calling in one single step
11841 @item Supports single-end and paired-end read alignments
11842 @item Supports ungapped and gapped alignments
11843 @item Alignment seed length, number of mismatches etc are adjustable
11844 @item Output discriminates between cytosine methylation in CpG, CHG
11845   and CHH context
11846 @end itemize\n")
11847     (license license:gpl3+)))
11848
11849 (define-public paml
11850   (package
11851     (name "paml")
11852     (version "4.9e")
11853     (source (origin
11854               (method url-fetch)
11855               (uri (string-append "http://abacus.gene.ucl.ac.uk/software/"
11856                                   "paml" version ".tgz"))
11857               (sha256
11858                (base32
11859                 "13zf6h9fiqghwhch2h06x1zdr6s42plsnqahflp5g7myr3han3s6"))
11860               (modules '((guix build utils)))
11861               ;; Remove Windows binaries
11862               (snippet
11863                '(begin
11864                   (for-each delete-file (find-files "." "\\.exe$"))
11865                   #t))))
11866     (build-system gnu-build-system)
11867     (arguments
11868      `(#:tests? #f ; there are no tests
11869        #:make-flags '("CC=gcc")
11870        #:phases
11871        (modify-phases %standard-phases
11872          (replace 'configure
11873            (lambda _
11874              (substitute* "src/BFdriver.c"
11875                (("/bin/bash") (which "bash")))
11876              (chdir "src")
11877              #t))
11878          (replace 'install
11879            (lambda* (#:key outputs #:allow-other-keys)
11880              (let ((tools '("baseml" "basemlg" "codeml"
11881                             "pamp" "evolver" "yn00" "chi2"))
11882                    (bin    (string-append (assoc-ref outputs "out") "/bin"))
11883                    (docdir (string-append (assoc-ref outputs "out")
11884                                            "/share/doc/paml")))
11885                (mkdir-p bin)
11886                (for-each (lambda (file) (install-file file bin)) tools)
11887                (copy-recursively "../doc" docdir)
11888                #t))))))
11889     (home-page "http://abacus.gene.ucl.ac.uk/software/paml.html")
11890     (synopsis "Phylogentic analysis by maximum likelihood")
11891     (description "PAML (for Phylogentic Analysis by Maximum Likelihood)
11892 contains a few programs for model fitting and phylogenetic tree reconstruction
11893 using nucleotide or amino-acid sequence data.")
11894     ;; GPLv3 only
11895     (license license:gpl3)))
11896
11897 (define-public kallisto
11898   (package
11899     (name "kallisto")
11900     (version "0.44.0")
11901     (source (origin
11902               (method git-fetch)
11903               (uri (git-reference
11904                     (url "https://github.com/pachterlab/kallisto.git")
11905                     (commit (string-append "v" version))))
11906               (file-name (git-file-name name version))
11907               (sha256
11908                (base32
11909                 "0nj382jiywqnpgvyhichajpkkh5r0bapn43f4dx40zdaq5v4m40m"))))
11910     (build-system cmake-build-system)
11911     (arguments
11912      `(#:tests? #f          ; no "check" target
11913        #:phases
11914        (modify-phases %standard-phases
11915          (add-after 'unpack 'do-not-use-bundled-htslib
11916            (lambda _
11917              (substitute* "CMakeLists.txt"
11918                (("^ExternalProject_Add" m)
11919                 (string-append "if (NEVER)\n" m))
11920                (("^\\)")
11921                 (string-append ")\nendif(NEVER)"))
11922                (("include_directories\\(\\$\\{htslib_PREFIX.*" m)
11923                 (string-append "# " m)))
11924              (substitute* "src/CMakeLists.txt"
11925                (("target_link_libraries\\(kallisto kallisto_core pthread \
11926 \\$\\{CMAKE_CURRENT_SOURCE_DIR\\}/../ext/htslib/libhts.a\\)")
11927                 "target_link_libraries(kallisto kallisto_core pthread hts)")
11928                (("include_directories\\(\\.\\./ext/htslib\\)") ""))
11929              #t)))))
11930     (inputs
11931      `(("hdf5" ,hdf5)
11932        ("htslib" ,htslib)
11933        ("zlib" ,zlib)))
11934     (home-page "http://pachterlab.github.io/kallisto/")
11935     (synopsis "Near-optimal RNA-Seq quantification")
11936     (description
11937      "Kallisto is a program for quantifying abundances of transcripts from
11938 RNA-Seq data, or more generally of target sequences using high-throughput
11939 sequencing reads.  It is based on the novel idea of pseudoalignment for
11940 rapidly determining the compatibility of reads with targets, without the need
11941 for alignment.  Pseudoalignment of reads preserves the key information needed
11942 for quantification, and kallisto is therefore not only fast, but also as
11943 accurate as existing quantification tools.")
11944     (license license:bsd-2)))
11945
11946 (define-public libgff
11947   (package
11948     (name "libgff")
11949     (version "1.0")
11950     (source (origin
11951               (method git-fetch)
11952               (uri (git-reference
11953                     (url "https://github.com/Kingsford-Group/libgff.git")
11954                     (commit (string-append "v" version))))
11955               (file-name (git-file-name name version))
11956               (sha256
11957                (base32
11958                 "0n6vfjnq7a2mianipscbshrvbncss8z4zkgkbjw754p9043nfkps"))))
11959     (build-system cmake-build-system)
11960     (arguments `(#:tests? #f))          ; no tests included
11961     (home-page "https://github.com/Kingsford-Group/libgff")
11962     (synopsis "Parser library for reading/writing GFF files")
11963     (description "This is a simple \"libraryfication\" of the GFF/GTF parsing
11964 code that is used in the Cufflinks codebase.  The goal of this library is to
11965 provide this functionality without the necessity of drawing in a heavy-weight
11966 dependency like SeqAn.")
11967     (license (license:x11-style "https://www.boost.org/LICENSE_1_0.txt"))))
11968
11969 (define-public libdivsufsort
11970   (package
11971     (name "libdivsufsort")
11972     (version "2.0.1")
11973     (source (origin
11974               (method git-fetch)
11975               (uri (git-reference
11976                     (url "https://github.com/y-256/libdivsufsort.git")
11977                     (commit version)))
11978               (file-name (git-file-name name version))
11979               (sha256
11980                (base32
11981                 "0fgdz9fzihlvjjrxy01md1bv9vh12rkgkwbm90b1hj5xpbaqp7z2"))))
11982     (build-system cmake-build-system)
11983     (arguments
11984      '(#:tests? #f                      ; there are no tests
11985        #:configure-flags
11986        ;; Needed for rapmap and sailfish.
11987        '("-DBUILD_DIVSUFSORT64=ON")))
11988     (home-page "https://github.com/y-256/libdivsufsort")
11989     (synopsis "Lightweight suffix-sorting library")
11990     (description "libdivsufsort is a software library that implements a
11991 lightweight suffix array construction algorithm.  This library provides a
11992 simple and an efficient C API to construct a suffix array and a
11993 Burrows-Wheeler transformed string from a given string over a constant-size
11994 alphabet.  The algorithm runs in O(n log n) worst-case time using only 5n+O(1)
11995 bytes of memory space, where n is the length of the string.")
11996     (license license:expat)))
11997
11998 (define-public sailfish
11999   (package
12000     (name "sailfish")
12001     (version "0.10.1")
12002     (source (origin
12003               (method git-fetch)
12004               (uri (git-reference
12005                     (url "https://github.com/kingsfordgroup/sailfish.git")
12006                     (commit (string-append "v" version))))
12007               (file-name (git-file-name name version))
12008               (sha256
12009                (base32
12010                 "1amcc5hqvsl42hg4x19bi9vy47cl874s0lw1fmi0hwsdk9i8c03v"))
12011               (modules '((guix build utils)))
12012               (snippet
12013                '(begin
12014                   ;; Delete bundled headers for eigen3.
12015                   (delete-file-recursively "include/eigen3/")
12016                   #t))))
12017     (build-system cmake-build-system)
12018     (arguments
12019      `(#:configure-flags
12020        (list (string-append "-DBOOST_INCLUDEDIR="
12021                             (assoc-ref %build-inputs "boost")
12022                             "/include/")
12023              (string-append "-DBOOST_LIBRARYDIR="
12024                             (assoc-ref %build-inputs "boost")
12025                             "/lib/")
12026              (string-append "-DBoost_LIBRARIES="
12027                             "-lboost_iostreams "
12028                             "-lboost_filesystem "
12029                             "-lboost_system "
12030                             "-lboost_thread "
12031                             "-lboost_timer "
12032                             "-lboost_chrono "
12033                             "-lboost_program_options")
12034              "-DBoost_FOUND=TRUE"
12035              ;; Don't download RapMap---we already have it!
12036              "-DFETCHED_RAPMAP=1")
12037        ;; Tests must be run after installation and the location of the test
12038        ;; data file must be overridden.  But the tests fail.  It looks like
12039        ;; they are not really meant to be run.
12040        #:tests? #f
12041        #:phases
12042        (modify-phases %standard-phases
12043          ;; Boost cannot be found, even though it's right there.
12044          (add-after 'unpack 'do-not-look-for-boost
12045            (lambda* (#:key inputs #:allow-other-keys)
12046              (substitute* "CMakeLists.txt"
12047                (("find_package\\(Boost 1\\.53\\.0") "#"))
12048              #t))
12049          (add-after 'unpack 'do-not-assign-to-macro
12050            (lambda _
12051              (substitute* "include/spdlog/details/format.cc"
12052                (("const unsigned CHAR_WIDTH = 1;") ""))
12053              #t))
12054          (add-after 'unpack 'prepare-rapmap
12055            (lambda* (#:key inputs #:allow-other-keys)
12056              (let ((src "external/install/src/rapmap/")
12057                    (include "external/install/include/rapmap/")
12058                    (rapmap (assoc-ref inputs "rapmap")))
12059                (mkdir-p "/tmp/rapmap")
12060                (invoke "tar" "xf"
12061                        (assoc-ref inputs "rapmap")
12062                        "-C" "/tmp/rapmap"
12063                        "--strip-components=1")
12064                (mkdir-p src)
12065                (mkdir-p include)
12066                (for-each (lambda (file)
12067                            (install-file file src))
12068                          (find-files "/tmp/rapmap/src" "\\.(c|cpp)"))
12069                (copy-recursively "/tmp/rapmap/include" include))
12070              #t))
12071          (add-after 'unpack 'use-system-libraries
12072            (lambda* (#:key inputs #:allow-other-keys)
12073              (substitute* '("src/SailfishIndexer.cpp"
12074                             "src/SailfishUtils.cpp"
12075                             "src/SailfishQuantify.cpp"
12076                             "src/FASTAParser.cpp"
12077                             "include/PCA.hpp"
12078                             "include/SailfishUtils.hpp"
12079                             "include/SailfishIndex.hpp"
12080                             "include/CollapsedEMOptimizer.hpp"
12081                             "src/CollapsedEMOptimizer.cpp")
12082                (("#include \"jellyfish/config.h\"") ""))
12083              (substitute* "src/CMakeLists.txt"
12084                (("\\$\\{GAT_SOURCE_DIR\\}/external/install/include/jellyfish-2.2..")
12085                 (string-append (assoc-ref inputs "jellyfish")
12086                                "/include/jellyfish-" ,(package-version jellyfish)))
12087                (("\\$\\{GAT_SOURCE_DIR\\}/external/install/lib/libjellyfish-2.0.a")
12088                 (string-append (assoc-ref inputs "jellyfish")
12089                                "/lib/libjellyfish-2.0.a"))
12090                (("\\$\\{GAT_SOURCE_DIR\\}/external/install/lib/libdivsufsort.a")
12091                 (string-append (assoc-ref inputs "libdivsufsort")
12092                                "/lib/libdivsufsort.so"))
12093                (("\\$\\{GAT_SOURCE_DIR\\}/external/install/lib/libdivsufsort64.a")
12094                 (string-append (assoc-ref inputs "libdivsufsort")
12095                                "/lib/libdivsufsort64.so")))
12096              (substitute* "CMakeLists.txt"
12097                ;; Don't prefer static libs
12098                (("SET\\(CMAKE_FIND_LIBRARY_SUFFIXES.*") "")
12099                (("find_package\\(Jellyfish.*") "")
12100                (("ExternalProject_Add\\(libjellyfish") "message(")
12101                (("ExternalProject_Add\\(libgff") "message(")
12102                (("ExternalProject_Add\\(libsparsehash") "message(")
12103                (("ExternalProject_Add\\(libdivsufsort") "message("))
12104
12105              ;; Ensure that Eigen headers can be found
12106              (setenv "CPLUS_INCLUDE_PATH"
12107                      (string-append (getenv "CPLUS_INCLUDE_PATH")
12108                                     ":"
12109                                     (assoc-ref inputs "eigen")
12110                                     "/include/eigen3"))
12111              #t)))))
12112     (inputs
12113      `(("boost" ,boost)
12114        ("eigen" ,eigen)
12115        ("jemalloc" ,jemalloc)
12116        ("jellyfish" ,jellyfish)
12117        ("sparsehash" ,sparsehash)
12118        ("rapmap" ,(origin
12119                     (method git-fetch)
12120                     (uri (git-reference
12121                           (url "https://github.com/COMBINE-lab/RapMap.git")
12122                           (commit (string-append "sf-v" version))))
12123                     (file-name (string-append "rapmap-sf-v" version "-checkout"))
12124                     (sha256
12125                      (base32
12126                       "1hv79l5i576ykv5a1srj2p0q36yvyl5966m0fcy2lbi169ipjakf"))
12127                     (modules '((guix build utils)))
12128                     ;; These files are expected to be excluded.
12129                     (snippet
12130                      '(begin (delete-file-recursively "include/spdlog")
12131                              (for-each delete-file '("include/xxhash.h"
12132                                                      "src/xxhash.c"))
12133                              #t))))
12134        ("libdivsufsort" ,libdivsufsort)
12135        ("libgff" ,libgff)
12136        ("tbb" ,tbb)
12137        ("zlib" ,zlib)))
12138     (native-inputs
12139      `(("pkg-config" ,pkg-config)))
12140     (home-page "http://www.cs.cmu.edu/~ckingsf/software/sailfish")
12141     (synopsis "Mapping-based isoform quantification from RNA-Seq reads")
12142     (description "Sailfish is a tool for genomic transcript quantification
12143 from RNA-seq data.  It requires a set of target transcripts (either from a
12144 reference or de-novo assembly) to quantify.  All you need to run sailfish is a
12145 fasta file containing your reference transcripts and a (set of) fasta/fastq
12146 file(s) containing your reads.")
12147     (license license:gpl3+)))
12148
12149 (define libstadenio-for-salmon
12150   (package
12151     (name "libstadenio")
12152     (version "1.14.8")
12153     (source (origin
12154               (method git-fetch)
12155               (uri (git-reference
12156                     (url "https://github.com/COMBINE-lab/staden-io_lib.git")
12157                     (commit (string-append "v" version))))
12158               (file-name (string-append name "-" version "-checkout"))
12159               (sha256
12160                (base32
12161                 "1x8kxxqxl892vwfbprlbyfwkkv7c34ggkc94892x9x0g37x5nbwx"))))
12162     (build-system gnu-build-system)
12163     (arguments '(#:parallel-tests? #f)) ; not supported
12164     (inputs
12165      `(("zlib" ,zlib)))
12166     (native-inputs
12167      `(("perl" ,perl)))                 ; for tests
12168     (home-page "https://github.com/COMBINE-lab/staden-io_lib")
12169     (synopsis "General purpose trace and experiment file library")
12170     (description "This package provides a library of file reading and writing
12171 code to provide a general purpose Trace file (and Experiment File) reading
12172 interface.
12173
12174 The following file formats are supported:
12175
12176 @enumerate
12177 @item SCF trace files
12178 @item ABI trace files
12179 @item ALF trace files
12180 @item ZTR trace files
12181 @item SFF trace archives
12182 @item SRF trace archives
12183 @item Experiment files
12184 @item Plain text files
12185 @item SAM/BAM sequence files
12186 @item CRAM sequence files
12187 @end enumerate\n")
12188     (license license:bsd-3)))
12189
12190 (define spdlog-for-salmon
12191   (package
12192     (name "spdlog")
12193     (version "0.14.0")
12194     (source (origin
12195               (method git-fetch)
12196               (uri (git-reference
12197                     (url "https://github.com/COMBINE-lab/spdlog.git")
12198                     (commit (string-append "v" version))))
12199               (file-name (string-append name "-" version "-checkout"))
12200               (sha256
12201                (base32
12202                 "13730429gwlabi432ilpnja3sfvy0nn2719vnhhmii34xcdyc57q"))))
12203     (build-system cmake-build-system)
12204     (home-page "https://github.com/COMBINE-lab/spdlog")
12205     (synopsis "Very fast C++ logging library")
12206     (description "Spdlog is a very fast header-only C++ logging library with
12207 performance as its primary goal.")
12208     (license license:expat)))
12209
12210 ;; This is a modified variant of bwa for use with Salmon. It installs a
12211 ;; library to avoid having to build this as part of Salmon.
12212 (define bwa-for-salmon
12213   (package (inherit bwa)
12214     (name "bwa")
12215     (version "0.7.12.5")
12216     (source (origin
12217               (method git-fetch)
12218               (uri (git-reference
12219                     (url "https://github.com/COMBINE-lab/bwa.git")
12220                     (commit (string-append "v" version))))
12221               (file-name (string-append "bwa-for-salmon-" version "-checkout"))
12222               (sha256
12223                (base32
12224                 "1z2qa64y0c5hky10510x137mnzlhz6k8qf27csw4w9j6qihq95gb"))))
12225     (build-system gnu-build-system)
12226     (arguments
12227      '(#:tests? #f ;no "check" target
12228        #:phases
12229        (modify-phases %standard-phases
12230          (replace 'install
12231            (lambda* (#:key outputs #:allow-other-keys)
12232              (let* ((out (assoc-ref outputs "out"))
12233                     (bin (string-append out "/bin"))
12234                     (lib (string-append out "/lib"))
12235                     (doc (string-append out "/share/doc/bwa"))
12236                     (man (string-append out "/share/man/man1"))
12237                     (inc (string-append out "/include/bwa")))
12238                (install-file "bwa" bin)
12239                (install-file "README.md" doc)
12240                (install-file "bwa.1" man)
12241                (install-file "libbwa.a" lib)
12242                (mkdir-p lib)
12243                (mkdir-p inc)
12244                (for-each (lambda (file)
12245                            (install-file file inc))
12246                          (find-files "." "\\.h$")))
12247              #t))
12248          ;; no "configure" script
12249          (delete 'configure))))))
12250
12251 (define-public salmon
12252   (package
12253     (name "salmon")
12254     (version "0.9.1")
12255     (source (origin
12256               (method git-fetch)
12257               (uri (git-reference
12258                     (url "https://github.com/COMBINE-lab/salmon.git")
12259                     (commit (string-append "v" version))))
12260               (file-name (string-append name "-" version "-checkout"))
12261               (sha256
12262                (base32
12263                 "1zi1ff4i7y2ykk0vdzysgwzzzv166vg2x77pj1mf4baclavxj87a"))
12264               (modules '((guix build utils)))
12265               (snippet
12266                '(begin
12267                   ;; Delete bundled headers for eigen3.
12268                   (delete-file-recursively "include/eigen3/")
12269                   #t))))
12270     (build-system cmake-build-system)
12271     (arguments
12272      `(#:configure-flags
12273        (list (string-append "-DBOOST_INCLUDEDIR="
12274                             (assoc-ref %build-inputs "boost")
12275                             "/include/")
12276              (string-append "-DBOOST_LIBRARYDIR="
12277                             (assoc-ref %build-inputs "boost")
12278                             "/lib/")
12279              (string-append "-DBoost_LIBRARIES="
12280                             "-lboost_iostreams "
12281                             "-lboost_filesystem "
12282                             "-lboost_system "
12283                             "-lboost_thread "
12284                             "-lboost_timer "
12285                             "-lboost_chrono "
12286                             "-lboost_program_options")
12287              "-DBoost_FOUND=TRUE"
12288              "-DTBB_LIBRARIES=tbb tbbmalloc"
12289              ;; Don't download RapMap---we already have it!
12290              "-DFETCHED_RAPMAP=1")
12291        #:phases
12292        (modify-phases %standard-phases
12293          ;; Boost cannot be found, even though it's right there.
12294          (add-after 'unpack 'do-not-look-for-boost
12295            (lambda* (#:key inputs #:allow-other-keys)
12296              (substitute* "CMakeLists.txt"
12297                (("find_package\\(Boost 1\\.53\\.0") "#"))
12298              #t))
12299          (add-after 'unpack 'do-not-phone-home
12300            (lambda _
12301              (substitute* "src/Salmon.cpp"
12302                (("getVersionMessage\\(\\)") "\"\""))
12303              #t))
12304          (add-after 'unpack 'prepare-rapmap
12305            (lambda* (#:key inputs #:allow-other-keys)
12306              (let ((src "external/install/src/rapmap/")
12307                    (include "external/install/include/rapmap/")
12308                    (rapmap (assoc-ref inputs "rapmap")))
12309                (mkdir-p src)
12310                (mkdir-p include)
12311                (for-each (lambda (file)
12312                            (install-file file src))
12313                          (find-files (string-append rapmap "/src") "\\.(c|cpp)"))
12314                (copy-recursively (string-append rapmap "/include") include)
12315                (for-each delete-file '("external/install/include/rapmap/xxhash.h"
12316                                        "external/install/include/rapmap/FastxParser.hpp"
12317                                        "external/install/include/rapmap/concurrentqueue.h"
12318                                        "external/install/include/rapmap/FastxParserThreadUtils.hpp"
12319                                        "external/install/src/rapmap/FastxParser.cpp"
12320                                        "external/install/src/rapmap/xxhash.c")))
12321              #t))
12322          (add-after 'unpack 'use-system-libraries
12323            (lambda* (#:key inputs #:allow-other-keys)
12324              (substitute* "src/CMakeLists.txt"
12325                (("\\$\\{GAT_SOURCE_DIR\\}/external/install/include/jellyfish-2.2..")
12326                 (string-append (assoc-ref inputs "jellyfish")
12327                                "/include/jellyfish-" ,(package-version jellyfish)))
12328                (("\\$\\{GAT_SOURCE_DIR\\}/external/install/lib/libjellyfish-2.0.a")
12329                 (string-append (assoc-ref inputs "jellyfish")
12330                                "/lib/libjellyfish-2.0.a"))
12331                (("\\$\\{GAT_SOURCE_DIR\\}/external/install/lib/libdivsufsort.a")
12332                 (string-append (assoc-ref inputs "libdivsufsort")
12333                                "/lib/libdivsufsort.so"))
12334                (("\\$\\{GAT_SOURCE_DIR\\}/external/install/lib/libstaden-read.a")
12335                 (string-append (assoc-ref inputs "libstadenio-for-salmon")
12336                                "/lib/libstaden-read.a"))
12337                (("\\$\\{GAT_SOURCE_DIR\\}/external/install/lib/libbwa.a")
12338                 (string-append (assoc-ref inputs "bwa") "/lib/libbwa.a"))
12339                (("\\$\\{GAT_SOURCE_DIR\\}/external/install/lib/libdivsufsort64.a")
12340                 (string-append (assoc-ref inputs "libdivsufsort")
12341                                "/lib/libdivsufsort64.so")))
12342              (substitute* "CMakeLists.txt"
12343                ;; Don't prefer static libs
12344                (("SET\\(CMAKE_FIND_LIBRARY_SUFFIXES.*") "")
12345                (("set\\(TBB_LIBRARIES") "message(")
12346                (("find_package\\(Jellyfish.*") "")
12347                (("ExternalProject_Add\\(libcereal") "message(")
12348                (("ExternalProject_Add\\(libbwa") "message(")
12349                (("ExternalProject_Add\\(libjellyfish") "message(")
12350                (("ExternalProject_Add\\(libgff") "message(")
12351                (("ExternalProject_Add\\(libtbb") "message(")
12352                (("ExternalProject_Add\\(libspdlog") "message(")
12353                (("ExternalProject_Add\\(libdivsufsort") "message(")
12354                (("ExternalProject_Add\\(libstadenio") "message(")
12355                (("ExternalProject_Add_Step\\(") "message("))
12356
12357              ;; Ensure that all headers can be found
12358              (setenv "CPLUS_INCLUDE_PATH"
12359                      (string-append (getenv "CPLUS_INCLUDE_PATH")
12360                                     ":"
12361                                     (assoc-ref inputs "bwa")
12362                                     "/include/bwa"
12363                                     ":"
12364                                     (assoc-ref inputs "eigen")
12365                                     "/include/eigen3"))
12366              (setenv "CPATH"
12367                      (string-append (assoc-ref inputs "bwa")
12368                                     "/include/bwa"
12369                                     ":"
12370                                     (assoc-ref inputs "eigen")
12371                                     "/include/eigen3"))
12372              #t))
12373          ;; CMAKE_INSTALL_PREFIX does not exist when the tests are
12374          ;; run.  It only exists after the install phase.
12375          (add-after 'unpack 'fix-tests
12376            (lambda _
12377              (substitute* "src/CMakeLists.txt"
12378                (("DTOPLEVEL_DIR=\\$\\{CMAKE_INSTALL_PREFIX")
12379                 "DTOPLEVEL_DIR=${GAT_SOURCE_DIR"))
12380              #t)))))
12381     (inputs
12382      `(("boost" ,boost)
12383        ("bwa" ,bwa-for-salmon)
12384        ("bzip2" ,bzip2)
12385        ("cereal" ,cereal)
12386        ("eigen" ,eigen)
12387        ("rapmap" ,(origin
12388                     (method git-fetch)
12389                     (uri (git-reference
12390                           (url "https://github.com/COMBINE-lab/RapMap.git")
12391                           (commit (string-append "salmon-v" version))))
12392                     (file-name (string-append "rapmap-salmon-v" version "-checkout"))
12393                     (sha256
12394                      (base32
12395                       "1yc12yqsz6f0r8sg1qnk57xg34aqwc9jbqq6gd5ys28xw3plj98p"))))
12396        ("jemalloc" ,jemalloc)
12397        ("jellyfish" ,jellyfish)
12398        ("libgff" ,libgff)
12399        ("tbb" ,tbb)
12400        ("libdivsufsort" ,libdivsufsort)
12401        ("libstadenio-for-salmon" ,libstadenio-for-salmon)
12402        ("spdlog-for-salmon" ,spdlog-for-salmon)
12403        ("xz" ,xz)
12404        ("zlib" ,zlib)))
12405     (home-page "https://github.com/COMBINE-lab/salmon")
12406     (synopsis "Quantification from RNA-seq reads using lightweight alignments")
12407     (description "Salmon is a program to produce highly-accurate,
12408 transcript-level quantification estimates from RNA-seq data.  Salmon achieves
12409 its accuracy and speed via a number of different innovations, including the
12410 use of lightweight alignments (accurate but fast-to-compute proxies for
12411 traditional read alignments) and massively-parallel stochastic collapsed
12412 variational inference.")
12413     (license license:gpl3+)))
12414
12415 (define-public python-loompy
12416   (package
12417     (name "python-loompy")
12418     (version "2.0.2")
12419     (source
12420      (origin
12421        (method url-fetch)
12422        (uri (pypi-uri "loompy" version))
12423        (sha256
12424         (base32
12425          "1drgv8j1hxqzzpnfg272x9djb6j8qr798w1pc2x8ikmfgyd9gh51"))))
12426     (build-system python-build-system)
12427     ;; There are no tests
12428     (arguments '(#:tests? #f))
12429     (propagated-inputs
12430      `(("python-h5py" ,python-h5py)
12431        ("python-numpy" ,python-numpy)
12432        ("python-scipy" ,python-scipy)))
12433     (home-page "https://github.com/linnarsson-lab/loompy")
12434     (synopsis "Work with .loom files for single-cell RNA-seq data")
12435     (description "The loom file format is an efficient format for very large
12436 omics datasets, consisting of a main matrix, optional additional layers, a
12437 variable number of row and column annotations.  Loom also supports sparse
12438 graphs.  This library makes it easy to work with @file{.loom} files for
12439 single-cell RNA-seq data.")
12440     (license license:bsd-3)))
12441
12442 ;; We cannot use the latest commit because it requires Java 9.
12443 (define-public java-forester
12444   (let ((commit "86b07efe302d5094b42deed9260f719a4c4ac2e6")
12445         (revision "1"))
12446     (package
12447       (name "java-forester")
12448       (version (string-append "0-" revision "." (string-take commit 7)))
12449       (source (origin
12450                 (method git-fetch)
12451                 (uri (git-reference
12452                       (url "https://github.com/cmzmasek/forester.git")
12453                       (commit commit)))
12454                 (file-name (string-append name "-" version "-checkout"))
12455                 (sha256
12456                  (base32
12457                   "0vxavc1yrf84yrnf20dq26hi0lglidk8d382xrxsy4qmlbjd276z"))
12458                 (modules '((guix build utils)))
12459                 (snippet
12460                  '(begin
12461                     ;; Delete bundled jars and pre-built classes
12462                     (delete-file-recursively "forester/java/resources")
12463                     (delete-file-recursively "forester/java/classes")
12464                     (for-each delete-file (find-files "forester/java/" "\\.jar$"))
12465                     ;; Delete bundled applications
12466                     (delete-file-recursively "forester_applications")
12467                     #t))))
12468       (build-system ant-build-system)
12469       (arguments
12470        `(#:tests? #f ; there are none
12471          #:jdk ,icedtea-8
12472          #:modules ((guix build ant-build-system)
12473                     (guix build utils)
12474                     (guix build java-utils)
12475                     (sxml simple)
12476                     (sxml transform))
12477          #:phases
12478          (modify-phases %standard-phases
12479            (add-after 'unpack 'chdir
12480              (lambda _ (chdir "forester/java") #t))
12481            (add-after 'chdir 'fix-dependencies
12482              (lambda _
12483                (chmod "build.xml" #o664)
12484                (call-with-output-file "build.xml.new"
12485                  (lambda (port)
12486                    (sxml->xml
12487                     (pre-post-order
12488                      (with-input-from-file "build.xml"
12489                        (lambda _ (xml->sxml #:trim-whitespace? #t)))
12490                      `(;; Remove all unjar tags to avoid repacking classes.
12491                        (unjar     . ,(lambda _ '()))
12492                        (*default* . ,(lambda (tag . kids) `(,tag ,@kids)))
12493                        (*text*    . ,(lambda (_ txt) txt))))
12494                     port)))
12495                (rename-file "build.xml.new" "build.xml")
12496                #t))
12497            ;; FIXME: itext is difficult to package as it depends on a few
12498            ;; unpackaged libraries.
12499            (add-after 'chdir 'remove-dependency-on-unpackaged-itext
12500              (lambda _
12501                (delete-file "src/org/forester/archaeopteryx/PdfExporter.java")
12502                (substitute* "src/org/forester/archaeopteryx/MainFrame.java"
12503                  (("pdf_written_to = PdfExporter.*")
12504                   "throw new IOException(\"PDF export is not available.\");"))
12505                #t))
12506            ;; There is no install target
12507            (replace 'install (install-jars ".")))))
12508       (propagated-inputs
12509        `(("java-commons-codec" ,java-commons-codec)
12510          ("java-openchart2" ,java-openchart2)))
12511       (home-page "https://sites.google.com/site/cmzmasek/home/software/forester")
12512       (synopsis "Phylogenomics libraries for Java")
12513       (description "Forester is a collection of Java libraries for
12514 phylogenomics and evolutionary biology research.  It includes support for
12515 reading, writing, and exporting phylogenetic trees.")
12516       (license license:lgpl2.1+))))
12517
12518 (define-public java-forester-1.005
12519   (package
12520     (name "java-forester")
12521     (version "1.005")
12522     (source (origin
12523               (method url-fetch)
12524               (uri (string-append "http://search.maven.org/remotecontent?"
12525                                   "filepath=org/biojava/thirdparty/forester/"
12526                                   version "/forester-" version "-sources.jar"))
12527               (file-name (string-append name "-" version ".jar"))
12528               (sha256
12529                (base32
12530                 "04r8qv4rk3p71z4ajrvp11py1z46qrx0047j3zzs79s6lnsm3lcv"))))
12531     (build-system ant-build-system)
12532     (arguments
12533      `(#:tests? #f ; there are none
12534        #:jdk ,icedtea-8
12535        #:modules ((guix build ant-build-system)
12536                   (guix build utils)
12537                   (guix build java-utils)
12538                   (sxml simple)
12539                   (sxml transform))
12540        #:phases
12541        (modify-phases %standard-phases
12542          (add-after 'unpack 'fix-dependencies
12543            (lambda* (#:key inputs #:allow-other-keys)
12544              (call-with-output-file "build.xml"
12545                (lambda (port)
12546                  (sxml->xml
12547                   (pre-post-order
12548                    (with-input-from-file "src/build.xml"
12549                      (lambda _ (xml->sxml #:trim-whitespace? #t)))
12550                    `(;; Remove all unjar tags to avoid repacking classes.
12551                      (unjar     . ,(lambda _ '()))
12552                      (*default* . ,(lambda (tag . kids) `(,tag ,@kids)))
12553                      (*text*    . ,(lambda (_ txt) txt))))
12554                   port)))
12555              (copy-file (assoc-ref inputs "synth_look_and_feel_1.xml")
12556                         "synth_look_and_feel_1.xml")
12557              (copy-file (assoc-ref inputs "phyloxml.xsd")
12558                         "phyloxml.xsd")
12559              (substitute* "build.xml"
12560                (("../resources/synth_laf/synth_look_and_feel_1.xml")
12561                 "synth_look_and_feel_1.xml")
12562                (("../resources/phyloxml_schema/1.10/phyloxml.xsd")
12563                 "phyloxml.xsd"))
12564              #t))
12565          ;; FIXME: itext is difficult to package as it depends on a few
12566          ;; unpackaged libraries.
12567          (add-after 'unpack 'remove-dependency-on-unpackaged-itext
12568            (lambda _
12569              (delete-file "src/org/forester/archaeopteryx/PdfExporter.java")
12570              (substitute* '("src/org/forester/archaeopteryx/MainFrame.java"
12571                             "src/org/forester/archaeopteryx/MainFrameApplication.java")
12572                (("pdf_written_to = PdfExporter.*")
12573                 "throw new IOException(\"PDF export is not available.\"); /*")
12574                ((".getPrintSizeX\\(\\), getOptions\\(\\).getPrintSizeY\\(\\) \\);") "*/")
12575                (("getCurrentTreePanel\\(\\).getHeight\\(\\) \\);") "*/"))
12576              #t))
12577          (add-after 'unpack 'delete-pre-built-classes
12578            (lambda _ (delete-file-recursively "src/classes") #t))
12579          ;; There is no install target
12580          (replace 'install (install-jars ".")))))
12581     (propagated-inputs
12582      `(("java-commons-codec" ,java-commons-codec)
12583        ("java-openchart2" ,java-openchart2)))
12584     ;; The source archive does not contain the resources.
12585     (native-inputs
12586      `(("phyloxml.xsd"
12587         ,(origin
12588            (method url-fetch)
12589            (uri (string-append "https://raw.githubusercontent.com/cmzmasek/forester/"
12590                                "b61cc2dcede0bede317db362472333115756b8c6/"
12591                                "forester/resources/phyloxml_schema/1.10/phyloxml.xsd"))
12592            (file-name (string-append name "-phyloxml-" version ".xsd"))
12593            (sha256
12594             (base32
12595              "1zxc4m8sn4n389nqdnpxa8d0k17qnr3pm2y5y6g6vh4k0zm52npv"))))
12596        ("synth_look_and_feel_1.xml"
12597         ,(origin
12598            (method url-fetch)
12599            (uri (string-append "https://raw.githubusercontent.com/cmzmasek/forester/"
12600                                "29e04321615da6b35c1e15c60e52caf3f21d8e6a/"
12601                                "forester/java/classes/resources/synth_look_and_feel_1.xml"))
12602            (file-name (string-append name "-synth-look-and-feel-" version ".xml"))
12603            (sha256
12604             (base32
12605              "1gv5602gv4k7y7713y75a4jvj7i9s7nildsbdl7n9q10sc2ikg8h"))))))
12606     (home-page "https://sites.google.com/site/cmzmasek/home/software/forester")
12607     (synopsis "Phylogenomics libraries for Java")
12608     (description "Forester is a collection of Java libraries for
12609 phylogenomics and evolutionary biology research.  It includes support for
12610 reading, writing, and exporting phylogenetic trees.")
12611     (license license:lgpl2.1+)))
12612
12613 (define-public java-biojava-core
12614   (package
12615     (name "java-biojava-core")
12616     (version "4.2.11")
12617     (source (origin
12618               (method git-fetch)
12619               (uri (git-reference
12620                     (url "https://github.com/biojava/biojava")
12621                     (commit (string-append "biojava-" version))))
12622               (file-name (string-append name "-" version "-checkout"))
12623               (sha256
12624                (base32
12625                 "1bvryh2bpsvash8ln79cmc9sqm8qw72hz4xzwqxcrjm8ssxszhqk"))))
12626     (build-system ant-build-system)
12627     (arguments
12628      `(#:jdk ,icedtea-8
12629        #:jar-name "biojava-core.jar"
12630        #:source-dir "biojava-core/src/main/java/"
12631        #:test-dir "biojava-core/src/test"
12632        ;; These tests seem to require internet access.
12633        #:test-exclude (list "**/SearchIOTest.java"
12634                             "**/BlastXMLParserTest.java"
12635                             "**/GenbankCookbookTest.java"
12636                             "**/GenbankProxySequenceReaderTest.java")
12637        #:phases
12638        (modify-phases %standard-phases
12639          (add-before 'build 'copy-resources
12640            (lambda _
12641              (copy-recursively "biojava-core/src/main/resources"
12642                                "build/classes")
12643              #t))
12644          (add-before 'check 'copy-test-resources
12645            (lambda _
12646              (copy-recursively "biojava-core/src/test/resources"
12647                                "build/test-classes")
12648              #t)))))
12649     (propagated-inputs
12650      `(("java-log4j-api" ,java-log4j-api)
12651        ("java-log4j-core" ,java-log4j-core)
12652        ("java-slf4j-api" ,java-slf4j-api)
12653        ("java-slf4j-simple" ,java-slf4j-simple)))
12654     (native-inputs
12655      `(("java-junit" ,java-junit)
12656        ("java-hamcrest-core" ,java-hamcrest-core)))
12657     (home-page "http://biojava.org")
12658     (synopsis "Core libraries of Java framework for processing biological data")
12659     (description "BioJava is a project dedicated to providing a Java framework
12660 for processing biological data.  It provides analytical and statistical
12661 routines, parsers for common file formats, reference implementations of
12662 popular algorithms, and allows the manipulation of sequences and 3D
12663 structures.  The goal of the biojava project is to facilitate rapid
12664 application development for bioinformatics.
12665
12666 This package provides the core libraries.")
12667     (license license:lgpl2.1+)))
12668
12669 (define-public java-biojava-phylo
12670   (package (inherit java-biojava-core)
12671     (name "java-biojava-phylo")
12672     (build-system ant-build-system)
12673     (arguments
12674      `(#:jdk ,icedtea-8
12675        #:jar-name "biojava-phylo.jar"
12676        #:source-dir "biojava-phylo/src/main/java/"
12677        #:test-dir "biojava-phylo/src/test"
12678        #:phases
12679        (modify-phases %standard-phases
12680          (add-before 'build 'copy-resources
12681            (lambda _
12682              (copy-recursively "biojava-phylo/src/main/resources"
12683                                "build/classes")
12684              #t))
12685          (add-before 'check 'copy-test-resources
12686            (lambda _
12687              (copy-recursively "biojava-phylo/src/test/resources"
12688                                "build/test-classes")
12689              #t)))))
12690     (propagated-inputs
12691      `(("java-log4j-api" ,java-log4j-api)
12692        ("java-log4j-core" ,java-log4j-core)
12693        ("java-slf4j-api" ,java-slf4j-api)
12694        ("java-slf4j-simple" ,java-slf4j-simple)
12695        ("java-biojava-core" ,java-biojava-core)
12696        ("java-forester" ,java-forester)))
12697     (native-inputs
12698      `(("java-junit" ,java-junit)
12699        ("java-hamcrest-core" ,java-hamcrest-core)))
12700     (home-page "http://biojava.org")
12701     (synopsis "Biojava interface to the forester phylogenomics library")
12702     (description "The phylo module provides a biojava interface layer to the
12703 forester phylogenomics library for constructing phylogenetic trees.")))
12704
12705 (define-public java-biojava-alignment
12706   (package (inherit java-biojava-core)
12707     (name "java-biojava-alignment")
12708     (build-system ant-build-system)
12709     (arguments
12710      `(#:jdk ,icedtea-8
12711        #:jar-name "biojava-alignment.jar"
12712        #:source-dir "biojava-alignment/src/main/java/"
12713        #:test-dir "biojava-alignment/src/test"
12714        #:phases
12715        (modify-phases %standard-phases
12716          (add-before 'build 'copy-resources
12717            (lambda _
12718              (copy-recursively "biojava-alignment/src/main/resources"
12719                                "build/classes")
12720              #t))
12721          (add-before 'check 'copy-test-resources
12722            (lambda _
12723              (copy-recursively "biojava-alignment/src/test/resources"
12724                                "build/test-classes")
12725              #t)))))
12726     (propagated-inputs
12727      `(("java-log4j-api" ,java-log4j-api)
12728        ("java-log4j-core" ,java-log4j-core)
12729        ("java-slf4j-api" ,java-slf4j-api)
12730        ("java-slf4j-simple" ,java-slf4j-simple)
12731        ("java-biojava-core" ,java-biojava-core)
12732        ("java-biojava-phylo" ,java-biojava-phylo)
12733        ("java-forester" ,java-forester)))
12734     (native-inputs
12735      `(("java-junit" ,java-junit)
12736        ("java-hamcrest-core" ,java-hamcrest-core)))
12737     (home-page "http://biojava.org")
12738     (synopsis "Biojava API for genetic sequence alignment")
12739     (description "The alignment module of BioJava provides an API that
12740 contains
12741
12742 @itemize
12743 @item implementations of dynamic programming algorithms for sequence
12744   alignment;
12745 @item reading and writing of popular alignment file formats;
12746 @item a single-, or multi- threaded multiple sequence alignment algorithm.
12747 @end itemize\n")))
12748
12749 (define-public java-biojava-core-4.0
12750   (package (inherit java-biojava-core)
12751     (name "java-biojava-core")
12752     (version "4.0.0")
12753     (source (origin
12754               (method git-fetch)
12755               (uri (git-reference
12756                     (url "https://github.com/biojava/biojava")
12757                     (commit (string-append "biojava-" version))))
12758               (file-name (string-append name "-" version "-checkout"))
12759               (sha256
12760                (base32
12761                 "13675f6y9aqi7bi2lk3s1z7a22ynccjiqwa8izh7p97xi9wsfmd8"))))))
12762
12763 (define-public java-biojava-phylo-4.0
12764   (package (inherit java-biojava-core-4.0)
12765     (name "java-biojava-phylo")
12766     (build-system ant-build-system)
12767     (arguments
12768      `(#:jdk ,icedtea-8
12769        #:jar-name "biojava-phylo.jar"
12770        #:source-dir "biojava-phylo/src/main/java/"
12771        #:test-dir "biojava-phylo/src/test"
12772        #:phases
12773        (modify-phases %standard-phases
12774          (add-before 'build 'copy-resources
12775            (lambda _
12776              (copy-recursively "biojava-phylo/src/main/resources"
12777                                "build/classes")
12778              #t))
12779          (add-before 'check 'copy-test-resources
12780            (lambda _
12781              (copy-recursively "biojava-phylo/src/test/resources"
12782                                "build/test-classes")
12783              #t)))))
12784     (propagated-inputs
12785      `(("java-log4j-api" ,java-log4j-api)
12786        ("java-log4j-core" ,java-log4j-core)
12787        ("java-slf4j-api" ,java-slf4j-api)
12788        ("java-slf4j-simple" ,java-slf4j-simple)
12789        ("java-biojava-core" ,java-biojava-core-4.0)
12790        ("java-forester" ,java-forester-1.005)))
12791     (native-inputs
12792      `(("java-junit" ,java-junit)
12793        ("java-hamcrest-core" ,java-hamcrest-core)))
12794     (home-page "http://biojava.org")
12795     (synopsis "Biojava interface to the forester phylogenomics library")
12796     (description "The phylo module provides a biojava interface layer to the
12797 forester phylogenomics library for constructing phylogenetic trees.")))
12798
12799 (define-public java-biojava-alignment-4.0
12800   (package (inherit java-biojava-core-4.0)
12801     (name "java-biojava-alignment")
12802     (build-system ant-build-system)
12803     (arguments
12804      `(#:jdk ,icedtea-8
12805        #:jar-name "biojava-alignment.jar"
12806        #:source-dir "biojava-alignment/src/main/java/"
12807        #:test-dir "biojava-alignment/src/test"
12808        #:phases
12809        (modify-phases %standard-phases
12810          (add-before 'build 'copy-resources
12811            (lambda _
12812              (copy-recursively "biojava-alignment/src/main/resources"
12813                                "build/classes")
12814              #t))
12815          (add-before 'check 'copy-test-resources
12816            (lambda _
12817              (copy-recursively "biojava-alignment/src/test/resources"
12818                                "build/test-classes")
12819              #t)))))
12820     (propagated-inputs
12821      `(("java-log4j-api" ,java-log4j-api)
12822        ("java-log4j-core" ,java-log4j-core)
12823        ("java-slf4j-api" ,java-slf4j-api)
12824        ("java-slf4j-simple" ,java-slf4j-simple)
12825        ("java-biojava-core" ,java-biojava-core-4.0)
12826        ("java-biojava-phylo" ,java-biojava-phylo-4.0)
12827        ("java-forester" ,java-forester-1.005)))
12828     (native-inputs
12829      `(("java-junit" ,java-junit)
12830        ("java-hamcrest-core" ,java-hamcrest-core)))
12831     (home-page "http://biojava.org")
12832     (synopsis "Biojava API for genetic sequence alignment")
12833     (description "The alignment module of BioJava provides an API that
12834 contains
12835
12836 @itemize
12837 @item implementations of dynamic programming algorithms for sequence
12838   alignment;
12839 @item reading and writing of popular alignment file formats;
12840 @item a single-, or multi- threaded multiple sequence alignment algorithm.
12841 @end itemize\n")))
12842
12843 (define-public dropseq-tools
12844   (package
12845     (name "dropseq-tools")
12846     (version "1.13")
12847     (source
12848      (origin
12849        (method url-fetch)
12850        (uri "http://mccarrolllab.com/download/1276/")
12851        (file-name (string-append "dropseq-tools-" version ".zip"))
12852        (sha256
12853         (base32
12854          "0yrffckxqk5l8b5xb6z4laq157zd9mdypr2p4b4vq2bhjzi1sj0s"))
12855        ;; Delete bundled libraries
12856        (modules '((guix build utils)))
12857        (snippet
12858         '(begin
12859            (for-each delete-file (find-files "jar/lib" "\\.jar$"))
12860            (delete-file-recursively "3rdParty")
12861            #t))))
12862     (build-system ant-build-system)
12863     (arguments
12864      `(#:tests? #f                      ; test data are not included
12865        #:test-target "test"
12866        #:build-target "all"
12867        #:source-dir "public/src/"
12868        #:jdk ,icedtea-8
12869        #:make-flags
12870        (list (string-append "-Dpicard.executable.dir="
12871                             (assoc-ref %build-inputs "java-picard")
12872                             "/share/java/"))
12873        #:modules ((ice-9 match)
12874                   (srfi srfi-1)
12875                   (guix build utils)
12876                   (guix build java-utils)
12877                   (guix build ant-build-system))
12878        #:phases
12879        (modify-phases %standard-phases
12880          ;; FIXME: fails with "java.io.FileNotFoundException:
12881          ;; /gnu/store/…-dropseq-tools-1.13/share/java/lib/biojava-alignment.jar"
12882          (delete 'generate-jar-indices)
12883          ;; All dependencies must be linked to "lib", because that's where
12884          ;; they will be searched for when the Class-Path property of the
12885          ;; manifest is computed.
12886          (add-after 'unpack 'record-references
12887            (lambda* (#:key inputs #:allow-other-keys)
12888              (mkdir-p "jar/lib")
12889              (let ((dirs (filter-map (match-lambda
12890                                        ((name . dir)
12891                                         (if (and (string-prefix? "java-" name)
12892                                                  (not (string=? name "java-testng")))
12893                                             dir #f)))
12894                                      inputs)))
12895                (for-each (lambda (jar)
12896                            (symlink jar (string-append "jar/lib/" (basename jar))))
12897                          (append-map (lambda (dir) (find-files dir "\\.jar$"))
12898                                      dirs)))
12899              #t))
12900          ;; There is no installation target
12901          (replace 'install
12902            (lambda* (#:key inputs outputs #:allow-other-keys)
12903              (let* ((out     (assoc-ref outputs "out"))
12904                     (bin     (string-append out "/bin"))
12905                     (share   (string-append out "/share/java/"))
12906                     (lib     (string-append share "/lib/"))
12907                     (scripts (list "BAMTagHistogram"
12908                                    "BAMTagofTagCounts"
12909                                    "BaseDistributionAtReadPosition"
12910                                    "CollapseBarcodesInPlace"
12911                                    "CollapseTagWithContext"
12912                                    "ConvertToRefFlat"
12913                                    "CreateIntervalsFiles"
12914                                    "DetectBeadSynthesisErrors"
12915                                    "DigitalExpression"
12916                                    "Drop-seq_alignment.sh"
12917                                    "FilterBAM"
12918                                    "FilterBAMByTag"
12919                                    "GatherGeneGCLength"
12920                                    "GatherMolecularBarcodeDistributionByGene"
12921                                    "GatherReadQualityMetrics"
12922                                    "PolyATrimmer"
12923                                    "ReduceGTF"
12924                                    "SelectCellsByNumTranscripts"
12925                                    "SingleCellRnaSeqMetricsCollector"
12926                                    "TagBamWithReadSequenceExtended"
12927                                    "TagReadWithGeneExon"
12928                                    "TagReadWithInterval"
12929                                    "TrimStartingSequence"
12930                                    "ValidateReference")))
12931                (for-each mkdir-p (list bin share lib))
12932                (install-file "dist/dropseq.jar" share)
12933                (for-each (lambda (script)
12934                            (chmod script #o555)
12935                            (install-file script bin))
12936                          scripts)
12937                (substitute* (map (lambda (script)
12938                                    (string-append bin "/" script))
12939                                  scripts)
12940                  (("^java") (which "java"))
12941                  (("jar_deploy_dir=.*")
12942                   (string-append "jar_deploy_dir=" share "\n"))))
12943              #t))
12944          ;; FIXME: We do this after stripping jars because we don't want it to
12945          ;; copy all these jars and strip them.  We only want to install
12946          ;; links.  Arguably, this is a problem with the ant-build-system.
12947          (add-after 'strip-jar-timestamps 'install-links
12948            (lambda* (#:key outputs #:allow-other-keys)
12949              (let* ((out     (assoc-ref outputs "out"))
12950                     (share   (string-append out "/share/java/"))
12951                     (lib     (string-append share "/lib/")))
12952                (for-each (lambda (jar)
12953                            (symlink (readlink jar)
12954                                     (string-append lib (basename jar))))
12955                          (find-files "jar/lib" "\\.jar$")))
12956              #t)))))
12957     (inputs
12958      `(("jdk" ,icedtea-8)
12959        ("java-picard" ,java-picard-2.10.3)
12960        ("java-log4j-1.2-api" ,java-log4j-1.2-api)
12961        ("java-commons-math3" ,java-commons-math3)
12962        ("java-commons-jexl2" ,java-commons-jexl-2)
12963        ("java-commons-collections4" ,java-commons-collections4)
12964        ("java-commons-lang2" ,java-commons-lang)
12965        ("java-commons-io" ,java-commons-io)
12966        ("java-snappy-1.0.3-rc3" ,java-snappy-1)
12967        ("java-guava" ,java-guava)
12968        ("java-la4j" ,java-la4j)
12969        ("java-biojava-core" ,java-biojava-core-4.0)
12970        ("java-biojava-alignment" ,java-biojava-alignment-4.0)
12971        ("java-jdistlib" ,java-jdistlib)
12972        ("java-simple-xml" ,java-simple-xml)
12973        ("java-snakeyaml" ,java-snakeyaml)))
12974     (native-inputs
12975      `(("unzip" ,unzip)
12976        ("java-testng" ,java-testng)))
12977     (home-page "http://mccarrolllab.com/dropseq/")
12978     (synopsis "Tools for Drop-seq analyses")
12979     (description "Drop-seq is a technology to enable biologists to
12980 analyze RNA expression genome-wide in thousands of individual cells at
12981 once.  This package provides tools to perform Drop-seq analyses.")
12982     (license license:expat)))
12983
12984 (define-public pigx-rnaseq
12985   (package
12986     (name "pigx-rnaseq")
12987     (version "0.0.5")
12988     (source (origin
12989               (method url-fetch)
12990               (uri (string-append "https://github.com/BIMSBbioinfo/pigx_rnaseq/"
12991                                   "releases/download/v" version
12992                                   "/pigx_rnaseq-" version ".tar.gz"))
12993               (sha256
12994                (base32
12995                 "05gn658zpj9xki5dbs728z9zxq1mcm25hkwr5vzwqxsfi15l5f2l"))))
12996     (build-system gnu-build-system)
12997     (arguments
12998      `(#:parallel-tests? #f             ; not supported
12999        #:phases
13000        (modify-phases %standard-phases
13001          ;; "test.sh" runs STAR, which requires excessive amounts of memory.
13002          (add-after 'unpack 'disable-resource-intensive-test
13003            (lambda _
13004              (substitute* "Makefile.in"
13005                (("(^  tests/test_trim_galore/test.sh).*" _ m) m)
13006                (("^  tests/test_multiqc/test.sh") "")
13007                (("^  test.sh") ""))
13008              #t)))))
13009     (inputs
13010      `(("gzip" ,gzip)
13011        ("snakemake" ,snakemake)
13012        ("fastqc" ,fastqc)
13013        ("multiqc" ,multiqc)
13014        ("star" ,star)
13015        ("trim-galore" ,trim-galore)
13016        ("htseq" ,htseq)
13017        ("samtools" ,samtools)
13018        ("bedtools" ,bedtools)
13019        ("r-minimal" ,r-minimal)
13020        ("r-rmarkdown" ,r-rmarkdown)
13021        ("r-ggplot2" ,r-ggplot2)
13022        ("r-ggrepel" ,r-ggrepel)
13023        ("r-gprofiler" ,r-gprofiler)
13024        ("r-deseq2" ,r-deseq2)
13025        ("r-dt" ,r-dt)
13026        ("r-knitr" ,r-knitr)
13027        ("r-pheatmap" ,r-pheatmap)
13028        ("r-corrplot" ,r-corrplot)
13029        ("r-reshape2" ,r-reshape2)
13030        ("r-plotly" ,r-plotly)
13031        ("r-scales" ,r-scales)
13032        ("r-summarizedexperiment" ,r-summarizedexperiment)
13033        ("r-crosstalk" ,r-crosstalk)
13034        ("r-tximport" ,r-tximport)
13035        ("r-rtracklayer" ,r-rtracklayer)
13036        ("r-rjson" ,r-rjson)
13037        ("salmon" ,salmon)
13038        ("ghc-pandoc" ,ghc-pandoc)
13039        ("ghc-pandoc-citeproc" ,ghc-pandoc-citeproc)
13040        ("python-wrapper" ,python-wrapper)
13041        ("python-pyyaml" ,python-pyyaml)))
13042     (home-page "http://bioinformatics.mdc-berlin.de/pigx/")
13043     (synopsis "Analysis pipeline for RNA sequencing experiments")
13044     (description "PiGX RNAseq is an analysis pipeline for preprocessing and
13045 reporting for RNA sequencing experiments.  It is easy to use and produces high
13046 quality reports.  The inputs are reads files from the sequencing experiment,
13047 and a configuration file which describes the experiment.  In addition to
13048 quality control of the experiment, the pipeline produces a differential
13049 expression report comparing samples in an easily configurable manner.")
13050     (license license:gpl3+)))
13051
13052 (define-public pigx-chipseq
13053   (package
13054     (name "pigx-chipseq")
13055     (version "0.0.20")
13056     (source (origin
13057               (method url-fetch)
13058               (uri (string-append "https://github.com/BIMSBbioinfo/pigx_chipseq/"
13059                                   "releases/download/v" version
13060                                   "/pigx_chipseq-" version ".tar.gz"))
13061               (sha256
13062                (base32
13063                 "19a7dclqq0b4kqg3phiz4d4arlwfp34nm3z0rf1gkqdpsy7gghp3"))))
13064     (build-system gnu-build-system)
13065     ;; parts of the tests rely on access to the network
13066     (arguments '(#:tests? #f))
13067     (inputs
13068      `(("grep" ,grep)
13069        ("coreutils" ,coreutils)
13070        ("r-minimal" ,r-minimal)
13071        ("r-argparser" ,r-argparser)
13072        ("r-biocparallel" ,r-biocparallel)
13073        ("r-biostrings" ,r-biostrings)
13074        ("r-chipseq" ,r-chipseq)
13075        ("r-data-table" ,r-data-table)
13076        ("r-dplyr" ,r-dplyr)
13077        ("r-genomation" ,r-genomation)
13078        ("r-genomicalignments" ,r-genomicalignments)
13079        ("r-genomicranges" ,r-genomicranges)
13080        ("r-rsamtools" ,r-rsamtools)
13081        ("r-rtracklayer" ,r-rtracklayer)
13082        ("r-s4vectors" ,r-s4vectors)
13083        ("r-stringr" ,r-stringr)
13084        ("r-tibble" ,r-tibble)
13085        ("r-tidyr" ,r-tidyr)
13086        ("r-jsonlite" ,r-jsonlite)
13087        ("r-heatmaply" ,r-heatmaply)
13088        ("r-htmlwidgets" ,r-htmlwidgets)
13089        ("r-ggplot2" ,r-ggplot2)
13090        ("r-plotly" ,r-plotly)
13091        ("r-rmarkdown" ,r-rmarkdown)
13092        ("python-wrapper" ,python-wrapper)
13093        ("python-pyyaml" ,python-pyyaml)
13094        ("python-magic" ,python-magic)
13095        ("python-xlrd" ,python-xlrd)
13096        ("trim-galore" ,trim-galore)
13097        ("macs" ,macs)
13098        ("multiqc" ,multiqc)
13099        ("perl" ,perl)
13100        ("ghc-pandoc" ,ghc-pandoc)
13101        ("ghc-pandoc-citeproc" ,ghc-pandoc-citeproc)
13102        ("fastqc" ,fastqc)
13103        ("bowtie" ,bowtie)
13104        ("idr" ,idr)
13105        ("snakemake" ,snakemake)
13106        ("samtools" ,samtools)
13107        ("bedtools" ,bedtools)
13108        ("kentutils" ,kentutils)))
13109     (native-inputs
13110      `(("python-pytest" ,python-pytest)))
13111     (home-page "http://bioinformatics.mdc-berlin.de/pigx/")
13112     (synopsis "Analysis pipeline for ChIP sequencing experiments")
13113     (description "PiGX ChIPseq is an analysis pipeline for preprocessing, peak
13114 calling and reporting for ChIP sequencing experiments.  It is easy to use and
13115 produces high quality reports.  The inputs are reads files from the sequencing
13116 experiment, and a configuration file which describes the experiment.  In
13117 addition to quality control of the experiment, the pipeline enables to set up
13118 multiple peak calling analysis and allows the generation of a UCSC track hub
13119 in an easily configurable manner.")
13120     (license license:gpl3+)))
13121
13122 (define-public pigx-bsseq
13123   (package
13124     (name "pigx-bsseq")
13125     (version "0.0.10")
13126     (source (origin
13127               (method url-fetch)
13128               (uri (string-append "https://github.com/BIMSBbioinfo/pigx_bsseq/"
13129                                   "releases/download/v" version
13130                                   "/pigx_bsseq-" version ".tar.gz"))
13131               (sha256
13132                (base32
13133                 "0l97wvkq4diq8lcarraj33bby1zzf0w804jwi8mlc5qddp8idwhy"))))
13134     (build-system gnu-build-system)
13135     (arguments
13136      `(#:phases
13137        (modify-phases %standard-phases
13138          (add-before 'check 'set-timezone
13139            ;; The readr package is picky about timezones.
13140            (lambda* (#:key inputs #:allow-other-keys)
13141              (setenv "TZ" "UTC+1")
13142              (setenv "TZDIR"
13143                      (string-append (assoc-ref inputs "tzdata")
13144                                     "/share/zoneinfo"))
13145              #t)))))
13146     (native-inputs
13147      `(("tzdata" ,tzdata)))
13148     (inputs
13149      `(("coreutils" ,coreutils)
13150        ("sed" ,sed)
13151        ("grep" ,grep)
13152        ("r-minimal" ,r-minimal)
13153        ("r-annotationhub" ,r-annotationhub)
13154        ("r-dt" ,r-dt)
13155        ("r-genomation" ,r-genomation)
13156        ("r-methylkit" ,r-methylkit)
13157        ("r-rtracklayer" ,r-rtracklayer)
13158        ("r-rmarkdown" ,r-rmarkdown)
13159        ("r-bookdown" ,r-bookdown)
13160        ("r-ggplot2" ,r-ggplot2)
13161        ("r-ggbio" ,r-ggbio)
13162        ("ghc-pandoc" ,ghc-pandoc)
13163        ("ghc-pandoc-citeproc" ,ghc-pandoc-citeproc)
13164        ("python-wrapper" ,python-wrapper)
13165        ("python-pyyaml" ,python-pyyaml)
13166        ("snakemake" ,snakemake)
13167        ("bismark" ,bismark)
13168        ("fastqc" ,fastqc)
13169        ("bowtie" ,bowtie)
13170        ("trim-galore" ,trim-galore)
13171        ("cutadapt" ,cutadapt)
13172        ("samtools" ,samtools)))
13173     (home-page "http://bioinformatics.mdc-berlin.de/pigx/")
13174     (synopsis "Bisulfite sequencing pipeline from fastq to methylation reports")
13175     (description "PiGx BSseq is a data processing pipeline for raw fastq read
13176 data of bisulfite experiments; it produces reports on aggregate methylation
13177 and coverage and can be used to produce information on differential
13178 methylation and segmentation.")
13179     (license license:gpl3+)))
13180
13181 (define-public pigx-scrnaseq
13182   (package
13183     (name "pigx-scrnaseq")
13184     (version "0.0.7")
13185     (source (origin
13186               (method url-fetch)
13187               (uri (string-append "https://github.com/BIMSBbioinfo/pigx_scrnaseq/"
13188                                   "releases/download/v" version
13189                                   "/pigx_scrnaseq-" version ".tar.gz"))
13190               (sha256
13191                (base32
13192                 "131zarirv16w8653m0d66jgjnwqfsxqc0hix0rypssz4d83bl51j"))))
13193     (build-system gnu-build-system)
13194     (arguments
13195      `(#:configure-flags
13196        (list (string-append "PICARDJAR=" (assoc-ref %build-inputs "java-picard")
13197                             "/share/java/picard.jar")
13198              (string-append "DROPSEQJAR=" (assoc-ref %build-inputs "dropseq-tools")
13199                             "/share/java/dropseq.jar"))))
13200     (inputs
13201      `(("coreutils" ,coreutils)
13202        ("perl" ,perl)
13203        ("dropseq-tools" ,dropseq-tools)
13204        ("fastqc" ,fastqc)
13205        ("java-picard" ,java-picard-2.10.3) ; same as for dropseq
13206        ("java" ,icedtea-8)
13207        ("python-wrapper" ,python-wrapper)
13208        ("python-pyyaml" ,python-pyyaml)
13209        ("python-pandas" ,python-pandas)
13210        ("python-magic" ,python-magic)
13211        ("python-numpy" ,python-numpy)
13212        ("python-loompy" ,python-loompy)
13213        ("ghc-pandoc" ,ghc-pandoc)
13214        ("ghc-pandoc-citeproc" ,ghc-pandoc-citeproc)
13215        ("samtools" ,samtools)
13216        ("snakemake" ,snakemake)
13217        ("star" ,star)
13218        ("r-minimal" ,r-minimal)
13219        ("r-argparser" ,r-argparser)
13220        ("r-cowplot" ,r-cowplot)
13221        ("r-data-table" ,r-data-table)
13222        ("r-delayedarray" ,r-delayedarray)
13223        ("r-delayedmatrixstats" ,r-delayedmatrixstats)
13224        ("r-dplyr" ,r-dplyr)
13225        ("r-dropbead" ,r-dropbead)
13226        ("r-dt" ,r-dt)
13227        ("r-genomicalignments" ,r-genomicalignments)
13228        ("r-genomicfiles" ,r-genomicfiles)
13229        ("r-genomicranges" ,r-genomicranges)
13230        ("r-ggplot2" ,r-ggplot2)
13231        ("r-hdf5array" ,r-hdf5array)
13232        ("r-pheatmap" ,r-pheatmap)
13233        ("r-rmarkdown" ,r-rmarkdown)
13234        ("r-rsamtools" ,r-rsamtools)
13235        ("r-rtracklayer" ,r-rtracklayer)
13236        ("r-rtsne" ,r-rtsne)
13237        ("r-scater" ,r-scater)
13238        ("r-scran" ,r-scran)
13239        ("r-singlecellexperiment" ,r-singlecellexperiment)
13240        ("r-stringr" ,r-stringr)
13241        ("r-yaml" ,r-yaml)))
13242     (home-page "http://bioinformatics.mdc-berlin.de/pigx/")
13243     (synopsis "Analysis pipeline for single-cell RNA sequencing experiments")
13244     (description "PiGX scRNAseq is an analysis pipeline for preprocessing and
13245 quality control for single cell RNA sequencing experiments.  The inputs are
13246 read files from the sequencing experiment, and a configuration file which
13247 describes the experiment.  It produces processed files for downstream analysis
13248 and interactive quality reports.  The pipeline is designed to work with UMI
13249 based methods.")
13250     (license license:gpl3+)))
13251
13252 (define-public pigx
13253   (package
13254     (name "pigx")
13255     (version "0.0.3")
13256     (source (origin
13257               (method url-fetch)
13258               (uri (string-append "https://github.com/BIMSBbioinfo/pigx/"
13259                                   "releases/download/v" version
13260                                   "/pigx-" version ".tar.gz"))
13261               (sha256
13262                (base32
13263                 "1i5njdy1clj5ncw45d16p7mwmqvb1ilikl9n797pxklc3f4s7mq7"))))
13264     (build-system gnu-build-system)
13265     (inputs
13266      `(("python" ,python)
13267        ("pigx-bsseq" ,pigx-bsseq)
13268        ("pigx-chipseq" ,pigx-chipseq)
13269        ("pigx-rnaseq" ,pigx-rnaseq)
13270        ("pigx-scrnaseq" ,pigx-scrnaseq)))
13271     (home-page "http://bioinformatics.mdc-berlin.de/pigx/")
13272     (synopsis "Analysis pipelines for genomics")
13273     (description "PiGx is a collection of genomics pipelines.  It includes the
13274 following pipelines:
13275
13276 @itemize
13277 @item PiGx BSseq for raw fastq read data of bisulfite experiments
13278 @item PiGx RNAseq for RNAseq samples
13279 @item PiGx scRNAseq for single cell dropseq analysis
13280 @item PiGx ChIPseq for reads from ChIPseq experiments
13281 @end itemize
13282
13283 All pipelines are easily configured with a simple sample sheet and a
13284 descriptive settings file.  The result is a set of comprehensive, interactive
13285 HTML reports with interesting findings about your samples.")
13286     (license license:gpl3+)))
13287
13288 (define-public mantis
13289   (let ((commit "4ffd171632c2cb0056a86d709dfd2bf21bc69b84")
13290         (revision "1"))
13291     (package
13292       (name "mantis")
13293       (version (git-version "0" revision commit))
13294       (source (origin
13295                 (method git-fetch)
13296                 (uri (git-reference
13297                       (url "https://github.com/splatlab/mantis.git")
13298                       (commit commit)))
13299                 (file-name (git-file-name name version))
13300                 (sha256
13301                  (base32
13302                   "0iqbr0dhmlc8mzpirmm2s4pkzkwdgrcx50yx6cv3wlr2qi064p55"))))
13303       (build-system cmake-build-system)
13304       (arguments '(#:tests? #f)) ; there are none
13305       (inputs
13306        `(("sdsl-lite" ,sdsl-lite)
13307          ("openssl" ,openssl)
13308          ("zlib" ,zlib)))
13309       (home-page "https://github.com/splatlab/mantis")
13310       (synopsis "Large-scale sequence-search index data structure")
13311       (description "Mantis is a space-efficient data structure that can be
13312 used to index thousands of raw-read genomics experiments and facilitate
13313 large-scale sequence searches on those experiments.  Mantis uses counting
13314 quotient filters instead of Bloom filters, enabling rapid index builds and
13315 queries, small indexes, and exact results, i.e., no false positives or
13316 negatives.  Furthermore, Mantis is also a colored de Bruijn graph
13317 representation, so it supports fast graph traversal and other topological
13318 analyses in addition to large-scale sequence-level searches.")
13319       ;; uses __uint128_t and inline assembly
13320       (supported-systems '("x86_64-linux"))
13321       (license license:bsd-3))))
13322
13323 (define-public r-diversitree
13324   (package
13325     (name "r-diversitree")
13326     (version "0.9-10")
13327     (source
13328       (origin
13329         (method url-fetch)
13330         (uri (cran-uri "diversitree" version))
13331         (sha256
13332          (base32
13333           "0gh4rcrp0an3jh8915i1fsxlgyfk7njywgbd5ln5r2jhr085kpz7"))))
13334     (build-system r-build-system)
13335     (native-inputs
13336      `(("gfortran" ,gfortran)))
13337     (inputs `(("fftw" ,fftw) ("gsl" ,gsl)))
13338     (propagated-inputs
13339      `(("r-ape" ,r-ape)
13340        ("r-desolve" ,r-desolve)
13341        ("r-rcpp" ,r-rcpp)
13342        ("r-suplex" ,r-subplex)))
13343     (home-page "https://www.zoology.ubc.ca/prog/diversitree")
13344     (synopsis "Comparative 'phylogenetic' analyses of diversification")
13345     (description "This package contains a number of comparative \"phylogenetic\"
13346 methods, mostly focusing on analysing diversification and character evolution.
13347 Contains implementations of \"BiSSE\" (Binary State Speciation and Extinction)
13348 and its unresolved tree extensions, \"MuSSE\" (Multiple State Speciation and
13349 Extinction), \"QuaSSE\", \"GeoSSE\", and \"BiSSE-ness\" Other included methods
13350 include Markov models of discrete and continuous trait evolution and constant
13351 rate speciation and extinction.")
13352     (license license:gpl2+)))
13353
13354 (define-public sjcount
13355   ;; There is no tag for version 3.2, nor is there a release archive.
13356   (let ((commit "292d3917cadb3f6834c81e509c30e61cd7ead6e5")
13357         (revision "1"))
13358     (package
13359       (name "sjcount")
13360       (version (git-version "3.2" revision commit))
13361       (source (origin
13362                 (method git-fetch)
13363                 (uri (git-reference
13364                       (url "https://github.com/pervouchine/sjcount-full.git")
13365                       (commit commit)))
13366                 (file-name (string-append name "-" version "-checkout"))
13367                 (sha256
13368                  (base32
13369                   "0gdgj35j249f04rqgq8ymcc1xg1vi9kzbajnjqpaq2wpbh8bl234"))))
13370       (build-system gnu-build-system)
13371       (arguments
13372        `(#:tests? #f                    ; requires a 1.4G test file
13373          #:make-flags
13374          (list (string-append "SAMTOOLS_DIR="
13375                               (assoc-ref %build-inputs "samtools")
13376                               "/lib/"))
13377          #:phases
13378          (modify-phases %standard-phases
13379            (replace 'configure
13380              (lambda* (#:key inputs #:allow-other-keys)
13381                (substitute* "makefile"
13382                  (("-I \\$\\{SAMTOOLS_DIR\\}")
13383                   (string-append "-I" (assoc-ref inputs "samtools")
13384                                  "/include/samtools"))
13385                  (("-lz ") "-lz -lpthread "))
13386                #t))
13387            (replace 'install
13388              (lambda* (#:key outputs #:allow-other-keys)
13389                (for-each (lambda (tool)
13390                            (install-file tool
13391                                          (string-append (assoc-ref outputs "out")
13392                                                         "/bin")))
13393                          '("j_count" "b_count" "sjcount"))
13394                #t)))))
13395       (inputs
13396        `(("samtools" ,samtools-0.1)
13397          ("zlib" ,zlib)))
13398       (home-page "https://github.com/pervouchine/sjcount-full/")
13399       (synopsis "Annotation-agnostic splice junction counting pipeline")
13400       (description "Sjcount is a utility for fast quantification of splice
13401 junctions in RNA-seq data.  It is annotation-agnostic and offset-aware.  This
13402 version does count multisplits.")
13403       (license license:gpl3+))))
13404
13405 (define-public minimap2
13406   (package
13407     (name "minimap2")
13408     (version "2.10")
13409     (source
13410      (origin
13411        (method url-fetch)
13412        (uri (string-append "https://github.com/lh3/minimap2/"
13413                            "releases/download/v" version "/"
13414                            "minimap2-" version ".tar.bz2"))
13415        (sha256
13416         (base32
13417          "080w9066irkbhbyr4nmf19pzkdd2s4v31hpzlajgq2y0drr6zcsj"))))
13418     (build-system gnu-build-system)
13419     (arguments
13420      `(#:tests? #f                      ; there are none
13421        #:make-flags
13422        (list "CC=gcc"
13423              (let ((system ,(or (%current-target-system)
13424                                 (%current-system))))
13425                (cond
13426                 ((string-prefix? "x86_64" system)
13427                  "all")
13428                 ((or (string-prefix? "armhf" system)
13429                      (string-prefix? "aarch64" system))
13430                  "arm_neon=1")
13431                 (_ "sse2only=1"))))
13432        #:phases
13433        (modify-phases %standard-phases
13434          (delete 'configure)
13435          (replace 'install
13436            (lambda* (#:key outputs #:allow-other-keys)
13437              (let* ((out (assoc-ref outputs "out"))
13438                     (bin (string-append out "/bin"))
13439                     (man (string-append out "/share/man/man1")))
13440                (install-file "minimap2" bin)
13441                (mkdir-p man)
13442                (install-file "minimap2.1" man))
13443              #t)))))
13444     (inputs
13445      `(("zlib" ,zlib)))
13446     (home-page "https://lh3.github.io/minimap2/")
13447     (synopsis "Pairwise aligner for genomic and spliced nucleotide sequences")
13448     (description "Minimap2 is a versatile sequence alignment program that
13449 aligns DNA or mRNA sequences against a large reference database.  Typical use
13450 cases include:
13451
13452 @enumerate
13453 @item mapping PacBio or Oxford Nanopore genomic reads to the human genome;
13454 @item finding overlaps between long reads with error rate up to ~15%;
13455 @item splice-aware alignment of PacBio Iso-Seq or Nanopore cDNA or Direct RNA
13456   reads against a reference genome;
13457 @item aligning Illumina single- or paired-end reads;
13458 @item assembly-to-assembly alignment;
13459 @item full-genome alignment between two closely related species with
13460   divergence below ~15%.
13461 @end enumerate\n")
13462     (license license:expat)))
13463
13464 (define-public r-circus
13465   (package
13466     (name "r-circus")
13467     (version "0.1.5")
13468     (source
13469      (origin
13470        (method git-fetch)
13471        (uri (git-reference
13472              (url "https://github.com/BIMSBbioinfo/ciRcus.git")
13473              (commit (string-append "v" version))))
13474        (file-name (git-file-name name version))
13475        (sha256
13476         (base32
13477          "0jhjn3ilb057hbf6yzrihj13ifxxs32y7nkby8l3lkm28dg4p97h"))))
13478     (build-system r-build-system)
13479     (propagated-inputs
13480      `(("r-annotationdbi" ,r-annotationdbi)
13481        ("r-annotationhub" ,r-annotationhub)
13482        ("r-biomart" ,r-biomart)
13483        ("r-data-table" ,r-data-table)
13484        ("r-dbi" ,r-dbi)
13485        ("r-genomicfeatures" ,r-genomicfeatures)
13486        ("r-genomicranges" ,r-genomicranges)
13487        ("r-ggplot2" ,r-ggplot2)
13488        ("r-hash" ,r-hash)
13489        ("r-iranges" ,r-iranges)
13490        ("r-rcolorbrewer" ,r-rcolorbrewer)
13491        ("r-rmysql" ,r-rmysql)
13492        ("r-s4vectors" ,r-s4vectors)
13493        ("r-stringr" ,r-stringr)
13494        ("r-summarizedexperiment" ,r-summarizedexperiment)))
13495     (native-inputs
13496      `(("r-knitr" ,r-knitr)))
13497     (home-page "https://github.com/BIMSBbioinfo/ciRcus")
13498     (synopsis "Annotation, analysis and visualization of circRNA data")
13499     (description "Circus is an R package for annotation, analysis and
13500 visualization of circRNA data.  Users can annotate their circRNA candidates
13501 with host genes, gene featrues they are spliced from, and discriminate between
13502 known and yet unknown splice junctions.  Circular-to-linear ratios of circRNAs
13503 can be calculated, and a number of descriptive plots easily generated.")
13504     (license license:artistic2.0)))
13505
13506 (define-public r-loomr
13507   (let ((commit "df0144bd2bbceca6fadef9edc1bbc5ca672d4739")
13508         (revision "1"))
13509     (package
13510       (name "r-loomr")
13511       (version (git-version "0.2.0" revision commit))
13512       (source
13513        (origin
13514          (method git-fetch)
13515          (uri (git-reference
13516                (url "https://github.com/mojaveazure/loomR.git")
13517                (commit commit)))
13518          (file-name (git-file-name name version))
13519          (sha256
13520           (base32
13521            "1b1g4dlmfdyhn56bz1mkh9ymirri43wiz7rjhs7py3y7bdw1s3yr"))))
13522       (build-system r-build-system)
13523       (propagated-inputs
13524        `(("r-r6" ,r-r6)
13525          ("r-hdf5r" ,r-hdf5r)
13526          ("r-iterators" ,r-iterators)
13527          ("r-itertools" ,r-itertools)
13528          ("r-matrix" ,r-matrix)))
13529       (home-page "https://github.com/mojaveazure/loomR")
13530       (synopsis "R interface for loom files")
13531       (description "This package provides an R interface to access, create,
13532 and modify loom files.  loomR aims to be completely compatible with loompy.")
13533       (license license:gpl3))))
13534
13535 (define-public gffread
13536   ;; We cannot use the tagged release because it is not in sync with gclib.
13537   ;; See https://github.com/gpertea/gffread/issues/26
13538   (let ((commit "ba7535fcb3cea55a6e5a491d916e93b454e87fd0")
13539         (revision "1"))
13540     (package
13541       (name "gffread")
13542       (version (git-version "0.9.12" revision commit))
13543       (source
13544        (origin
13545          (method git-fetch)
13546          (uri (git-reference
13547                (url "https://github.com/gpertea/gffread.git")
13548                (commit commit)))
13549          (file-name (git-file-name name version))
13550          (sha256
13551           (base32
13552            "1dl2nbcg96lxpd0drg48ssa8343nf7pw9s9mkrc4mjjmfwsin3ki"))))
13553       (build-system gnu-build-system)
13554       (arguments
13555        `(#:tests? #f ; no check target
13556          #:make-flags
13557          (list "GCLDIR=gclib")
13558          #:phases
13559          (modify-phases %standard-phases
13560            (delete 'configure)
13561            (add-after 'unpack 'copy-gclib-source
13562              (lambda* (#:key inputs #:allow-other-keys)
13563                (mkdir-p "gclib")
13564                (copy-recursively (assoc-ref inputs "gclib-source") "gclib")
13565                #t))
13566            ;; There is no install target
13567            (replace 'install
13568              (lambda* (#:key outputs #:allow-other-keys)
13569                (let* ((out (assoc-ref outputs "out"))
13570                       (bin (string-append out "/bin")))
13571                  (install-file "gffread" bin))
13572                #t)))))
13573       (native-inputs
13574        `(("gclib-source"
13575           ,(let ((version "0.10.3")
13576                  (commit "54917d0849c1e83cfb057b5f712e5cb6a35d948f")
13577                  (revision "1"))
13578              (origin
13579                (method git-fetch)
13580                (uri (git-reference
13581                      (url "https://github.com/gpertea/gclib.git")
13582                      (commit commit)))
13583                (file-name (git-file-name "gclib" version))
13584                (sha256
13585                 (base32
13586                  "0b51lc0b8syrv7186fd7n8f15rwnf264qgfmm2palrwks1px24mr")))))))
13587       (home-page "https://github.com/gpertea/gffread/")
13588       (synopsis "Parse and convert GFF/GTF files")
13589       (description
13590        "This package provides a GFF/GTF file parsing utility providing format
13591 conversions, region filtering, FASTA sequence extraction and more.")
13592       ;; gffread is under Expat, but gclib is under Artistic 2.0
13593       (license (list license:expat
13594                      license:artistic2.0)))))
13595
13596 (define-public find-circ
13597   ;; The last release was in 2015.  The license was clarified in 2017, so we
13598   ;; take the latest commit.
13599   (let ((commit "8655dca54970fcf7e92e22fbf57e1188724dda7d")
13600         (revision "1"))
13601     (package
13602       (name "find-circ")
13603       (version (git-version "1.2" revision commit))
13604       (source
13605        (origin
13606          (method git-fetch)
13607          (uri (git-reference
13608                (url "https://github.com/marvin-jens/find_circ.git")
13609                (commit commit)))
13610          (file-name (git-file-name name version))
13611          (sha256
13612           (base32
13613            "0p77pbqbclqr4srms34y1b9b4njybfpjiknc11ki84f3p8skb3cg"))))
13614       (build-system gnu-build-system)
13615       (arguments
13616        `(#:tests? #f                    ; there are none
13617          #:phases
13618          ;; There is no actual build system.
13619          (modify-phases %standard-phases
13620            (delete 'configure)
13621            (delete 'build)
13622            (replace 'install
13623              (lambda* (#:key outputs #:allow-other-keys)
13624                (let* ((out (assoc-ref outputs "out"))
13625                       (bin (string-append out "/bin"))
13626                       (path (getenv "PYTHONPATH")))
13627                  (for-each (lambda (script)
13628                              (install-file script bin)
13629                              (wrap-program (string-append bin "/" script)
13630                                `("PYTHONPATH" ":" prefix (,path))))
13631                            '("cmp_bed.py"
13632                              "find_circ.py"
13633                              "maxlength.py"
13634                              "merge_bed.py"
13635                              "unmapped2anchors.py")))
13636                #t)))))
13637       (inputs
13638        `(("python2" ,python-2)
13639          ("python2-pysam" ,python2-pysam)
13640          ("python2-numpy" ,python2-numpy)))
13641       (home-page "https://github.com/marvin-jens/find_circ")
13642       (synopsis "circRNA detection from RNA-seq reads")
13643       (description "This package provides tools to detect head-to-tail
13644 spliced (back-spliced) sequencing reads, indicative of circular RNA (circRNA)
13645 in RNA-seq data.")
13646       (license license:gpl3))))
13647
13648 (define-public python-scanpy
13649   (package
13650     (name "python-scanpy")
13651     (version "1.2.2")
13652     (source
13653      (origin
13654        (method url-fetch)
13655        (uri (pypi-uri "scanpy" version))
13656        (sha256
13657         (base32
13658          "1ak7bxms5a0yvf65prppq2g38clkv7c7jnjbnfpkh3xxv7q512jz"))))
13659     (build-system python-build-system)
13660     (propagated-inputs
13661      `(("python-anndata" ,python-anndata)
13662        ("python-igraph" ,python-igraph)
13663        ("python-numba" ,python-numba)
13664        ("python-joblib" ,python-joblib)
13665        ("python-natsort" ,python-natsort)
13666        ("python-networkx" ,python-networkx)
13667        ("python-statsmodels" ,python-statsmodels)
13668        ("python-scikit-learn" ,python-scikit-learn)
13669        ("python-matplotlib" ,python-matplotlib)
13670        ("python-pandas" ,python-pandas)
13671        ("python-scipy" ,python-scipy)
13672        ("python-seaborn" ,python-seaborn)
13673        ("python-h5py" ,python-h5py)
13674        ("python-tables" ,python-tables)))
13675     (home-page "http://github.com/theislab/scanpy")
13676     (synopsis "Single-Cell Analysis in Python.")
13677     (description "Scanpy is a scalable toolkit for analyzing single-cell gene
13678 expression data.  It includes preprocessing, visualization, clustering,
13679 pseudotime and trajectory inference and differential expression testing.  The
13680 Python-based implementation efficiently deals with datasets of more than one
13681 million cells.")
13682     (license license:bsd-3)))
13683
13684 (define-public gffcompare
13685   (let ((commit "be56ef4349ea3966c12c6397f85e49e047361c41")
13686         (revision "1"))
13687     (package
13688       (name "gffcompare")
13689       (version (git-version "0.10.15" revision commit))
13690       (source
13691        (origin
13692          (method git-fetch)
13693          (uri (git-reference
13694                (url "https://github.com/gpertea/gffcompare/")
13695                (commit commit)))
13696          (file-name (git-file-name name version))
13697          (sha256
13698           (base32 "0cp5qpxdhw4mxpya5dld8wi3jk00zyklm6rcri426wydinrnfmkg"))))
13699       (build-system gnu-build-system)
13700       (arguments
13701        `(#:tests? #f                    ; no check target
13702          #:phases
13703          (modify-phases %standard-phases
13704            (delete 'configure)
13705            (add-before 'build 'copy-gclib-source
13706              (lambda* (#:key inputs #:allow-other-keys)
13707                (mkdir "../gclib")
13708                (copy-recursively
13709                 (assoc-ref inputs "gclib-source") "../gclib")
13710                #t))
13711            (replace 'install
13712              (lambda* (#:key outputs #:allow-other-keys)
13713                (let ((bin (string-append (assoc-ref outputs "out") "/bin")))
13714                  (install-file "gffcompare" bin)
13715                  #t))))))
13716       (native-inputs
13717        `(("gclib-source" ; see 'README.md' of gffcompare
13718           ,(let ((commit "54917d0849c1e83cfb057b5f712e5cb6a35d948f")
13719                  (revision "1")
13720                  (name "gclib")
13721                  (version (git-version "0.10.3" revision commit)))
13722              (origin
13723                (method git-fetch)
13724                (uri (git-reference
13725                      (url "https://github.com/gpertea/gclib/")
13726                      (commit commit)))
13727                (file-name (git-file-name name version))
13728                (sha256
13729                 (base32 "0b51lc0b8syrv7186fd7n8f15rwnf264qgfmm2palrwks1px24mr")))))))
13730       (home-page "https://github.com/gpertea/gffcompare/")
13731       (synopsis "Tool for comparing or classifing transcripts of RNA-Seq")
13732       (description
13733        "@code{gffcompare} is a tool that can:
13734 @enumerate
13735 @item compare and evaluate the accuracy of RNA-Seq transcript assemblers
13736 (Cufflinks, Stringtie);
13737 @item collapse (merge) duplicate transcripts from multiple GTF/GFF3 files (e.g.
13738 resulted from assembly of different samples);
13739 @item classify transcripts from one or multiple GTF/GFF3 files as they relate to
13740 reference transcripts provided in a annotation file (also in GTF/GFF3 format).
13741 @end enumerate")
13742       (license
13743        (list
13744         license:expat                   ;license for gffcompare
13745         license:artistic2.0)))))        ;license for gclib
13746
13747 (define-public python-intervaltree
13748   (package
13749     (name "python-intervaltree")
13750     (version "2.1.0")
13751     (source
13752      (origin
13753        (method url-fetch)
13754        (uri (pypi-uri "intervaltree" version))
13755        (sha256
13756         (base32
13757          "02w191m9zxkcjqr1kv2slxvhymwhj3jnsyy3a28b837pi15q19dc"))))
13758     (build-system python-build-system)
13759     ;; FIXME: error when collecting tests
13760     (arguments '(#:tests? #f))
13761     (propagated-inputs
13762      `(("python-sortedcontainers" ,python-sortedcontainers)))
13763     (native-inputs
13764      `(("python-pytest" ,python-pytest)))
13765     (home-page "https://github.com/chaimleib/intervaltree")
13766     (synopsis "Editable interval tree data structure")
13767     (description
13768      "This package provides a mutable, self-balancing interval tree
13769 implementation for Python.  Queries may be by point, by range overlap, or by
13770 range envelopment.  This library was designed to allow tagging text and time
13771 intervals, where the intervals include the lower bound but not the upper
13772 bound.")
13773     (license license:asl2.0)))
13774
13775 (define-public python-pypairix
13776   (package
13777     (name "python-pypairix")
13778     (version "0.3.6")
13779     (source
13780      (origin
13781        (method url-fetch)
13782        (uri (pypi-uri "pypairix" version))
13783        (sha256
13784         (base32
13785          "0zs92b74s5v4xy2h16s15f3z6l4nnbw8x8zyif7xx5xpafjn0xss"))))
13786     (build-system python-build-system)
13787     ;; FIXME: the tests fail because test.support cannot be loaded:
13788     ;; ImportError: cannot import name 'support'
13789     (arguments '(#:tests? #f))
13790     (inputs
13791      `(("zlib" ,zlib)))
13792     (home-page "https://github.com/4dn-dcic/pairix")
13793     (synopsis "Support for querying pairix-indexed bgzipped text files")
13794     (description
13795      "Pypairix is a Python module for fast querying on a pairix-indexed
13796 bgzipped text file that contains a pair of genomic coordinates per line.")
13797     (license license:expat)))
13798
13799 (define-public python-pyfaidx
13800   (package
13801     (name "python-pyfaidx")
13802     (version "0.5.4.2")
13803     (source
13804      (origin
13805        (method url-fetch)
13806        (uri (pypi-uri "pyfaidx" version))
13807        (sha256
13808         (base32
13809          "0y5zyjksj1rdglj601xd2bbni5abhdh622y3ck76chyzxz9z4rx8"))))
13810     (build-system python-build-system)
13811     (propagated-inputs
13812      `(("python-setuptools" ,python-setuptools)
13813        ("python-six" ,python-six)))
13814     (home-page "http://mattshirley.com")
13815     (synopsis "Random access to fasta subsequences")
13816     (description
13817      "This package provides procedures for efficient pythonic random access to
13818 fasta subsequences.")
13819     (license license:bsd-3)))
13820
13821 (define-public python-cooler
13822   (package
13823     (name "python-cooler")
13824     (version "0.7.11")
13825     (source
13826      (origin
13827        (method url-fetch)
13828        (uri (pypi-uri "cooler" version))
13829        (sha256
13830         (base32
13831          "08k5nxnxa6qsbk15z5z0q01n28042k87wi4905hh95rzqib15mhx"))))
13832     (build-system python-build-system)
13833     (propagated-inputs
13834      `(("python-biopython" ,python-biopython)
13835        ("python-click" ,python-click)
13836        ("python-cytoolz" ,python-cytoolz)
13837        ("python-dask" ,python-dask)
13838        ("python-h5py" ,python-h5py)
13839        ("python-multiprocess" ,python-multiprocess)
13840        ("python-pandas" ,python-pandas)
13841        ("python-pyfaidx" ,python-pyfaidx)
13842        ("python-pypairix" ,python-pypairix)
13843        ("python-pysam" ,python-pysam)
13844        ("python-scipy" ,python-scipy)))
13845     (native-inputs
13846      `(("python-mock" ,python-mock)
13847        ("python-nose" ,python-nose)
13848        ("python-numpydoc" ,python-numpydoc)
13849        ("python-sphinx" ,python-sphinx)))
13850     (home-page "https://github.com/mirnylab/cooler")
13851     (synopsis "Sparse binary format for genomic interaction matrices")
13852     (description
13853      "Cooler is a support library for a sparse, compressed, binary persistent
13854 storage format, called @code{cool}, used to store genomic interaction data,
13855 such as Hi-C contact matrices.")
13856     (license license:bsd-3)))
13857
13858 (define-public python-hicexplorer
13859   (package
13860     (name "python-hicexplorer")
13861     (version "2.1.4")
13862     (source
13863      (origin
13864        ;; The latest version is not available on Pypi.
13865        (method git-fetch)
13866        (uri (git-reference
13867              (url "https://github.com/deeptools/HiCExplorer.git")
13868              (commit version)))
13869        (file-name (git-file-name name version))
13870        (sha256
13871         (base32
13872          "0q5gpbzmrkvygqgw524q36b4nrivcmyi5v194vsx0qw7b3gcmq08"))))
13873     (build-system python-build-system)
13874     (arguments
13875      `(#:phases
13876        (modify-phases %standard-phases
13877          (add-after 'unpack 'loosen-up-requirements
13878            (lambda _
13879              (substitute* "setup.py"
13880                (("==") ">="))
13881              #t)))))
13882     (propagated-inputs
13883      `(("python-biopython" ,python-biopython)
13884        ("python-configparser" ,python-configparser)
13885        ("python-cooler" ,python-cooler)
13886        ("python-future" ,python-future)
13887        ("python-intervaltree" ,python-intervaltree)
13888        ("python-jinja2" ,python-jinja2)
13889        ("python-matplotlib" ,python-matplotlib)
13890        ("python-numpy" ,python-numpy)
13891        ("python-pandas" ,python-pandas)
13892        ("python-pybigwig" ,python-pybigwig)
13893        ("python-pysam" ,python-pysam)
13894        ("python-scipy" ,python-scipy)
13895        ("python-six" ,python-six)
13896        ("python-tables" ,python-tables)
13897        ("python-unidecode" ,python-unidecode)))
13898     (home-page "http://hicexplorer.readthedocs.io")
13899     (synopsis "Process, analyze and visualize Hi-C data")
13900     (description
13901      "HiCExplorer is a powerful and easy to use set of tools to process,
13902 normalize and visualize Hi-C data.  HiCExplorer facilitates the creation of
13903 contact matrices, correction of contacts, TAD detection, A/B compartments,
13904 merging, reordering or chromosomes, conversion from different formats
13905 including cooler and detection of long-range contacts.  Moreover, it allows
13906 the visualization of multiple contact matrices along with other types of data
13907 like genes, compartments, ChIP-seq coverage tracks (and in general any type of
13908 genomic scores), long range contacts and the visualization of viewpoints.")
13909     (license license:gpl3)))
13910
13911 (define-public python-pygenometracks
13912   (package
13913     (name "python-pygenometracks")
13914     (version "2.0")
13915     (source
13916      (origin
13917        (method url-fetch)
13918        (uri (pypi-uri "pyGenomeTracks" version))
13919        (sha256
13920         (base32
13921          "1fws6bqsyy9kj3qiabhkqx4wd4i775gsxnhszqd3zg7w67sc1ic5"))))
13922     (build-system python-build-system)
13923     (propagated-inputs
13924      `(("python-configparser" ,python-configparser)
13925        ("python-future" ,python-future)
13926        ("python-hicexplorer" ,python-hicexplorer)
13927        ("python-intervaltree" ,python-intervaltree)
13928        ("python-matplotlib" ,python-matplotlib)
13929        ("python-numpy" ,python-numpy)
13930        ("python-pybigwig" ,python-pybigwig)))
13931     (native-inputs
13932      `(("python-pytest" ,python-pytest)))
13933     (home-page "https://pygenometracks.readthedocs.io")
13934     (synopsis "Program and library to plot beautiful genome browser tracks")
13935     (description
13936      "This package aims to produce high-quality genome browser tracks that
13937 are highly customizable.  Currently, it is possible to plot: bigwig, bed (many
13938 options), bedgraph, links (represented as arcs), and Hi-C matrices.
13939 pyGenomeTracks can make plots with or without Hi-C data.")
13940     (license license:gpl3+)))
13941
13942 (define-public python-hic2cool
13943   (package
13944     (name "python-hic2cool")
13945     (version "0.4.2")
13946     (source
13947      (origin
13948        (method url-fetch)
13949        (uri (pypi-uri "hic2cool" version))
13950        (sha256
13951         (base32
13952          "0xy6mhfns2lzib1kcr6419jjp6pmh0qx8z8na55lmiwn0ds8q9cl"))))
13953     (build-system python-build-system)
13954     (arguments '(#:tests? #f)) ; no tests included
13955     (propagated-inputs
13956      `(("python-cooler" ,python-cooler)))
13957     (home-page "https://github.com/4dn-dcic/hic2cool")
13958     (synopsis "Converter for .hic and .cool files")
13959     (description
13960      "This package provides a converter between @code{.hic} files (from
13961 juicer) and single-resolution or multi-resolution @code{.cool} files (for
13962 cooler).  Both @code{hic} and @code{cool} files describe Hi-C contact
13963 matrices.")
13964     (license license:expat)))
13965
13966 (define-public r-pore
13967   (package
13968     (name "r-pore")
13969     (version "0.24")
13970     (source
13971      (origin
13972        (method url-fetch)
13973        (uri
13974         (string-append "mirror://sourceforge/rpore/" version
13975                        "/poRe_" version ".tar.gz"))
13976        (sha256
13977         (base32 "0pih9nljbv8g4x8rkk29i7aqq681b782r5s5ynp4nw9yzqnmmksv"))))
13978     (properties `((upstream-name . "poRe")))
13979     (build-system r-build-system)
13980     (propagated-inputs
13981      `(("r-bit64" ,r-bit64)
13982        ("r-data-table" ,r-data-table)
13983        ("r-rhdf5" ,r-rhdf5)
13984        ("r-shiny" ,r-shiny)
13985        ("r-svdialogs" ,r-svdialogs)))
13986     (home-page "https://sourceforge.net/projects/rpore/")
13987     (synopsis "Visualize Nanopore sequencing data")
13988     (description
13989      "This package provides graphical user interfaces to organize and visualize Nanopore
13990 sequencing data.")
13991     ;; This is free software but the license variant is unclear:
13992     ;; <https://github.com/mw55309/poRe_docs/issues/10>.
13993     (license license:bsd-3)))
13994
13995 (define-public r-xbioc
13996   (let ((revision "1")
13997         (commit "f798c187e376fd1ba27abd559f47bbae7e3e466b"))
13998     (package
13999       (name "r-xbioc")
14000       (version (git-version "0.1.15" revision commit))
14001       (source (origin
14002                 (method git-fetch)
14003                 (uri (git-reference
14004                       (url "https://github.com/renozao/xbioc.git")
14005                       (commit commit)))
14006                 (file-name (git-file-name name version))
14007                 (sha256
14008                  (base32
14009                   "03hffh2f6z71y6l6dqpa5cql3hdaw7zigdi8sm2dzgx379k9rgrr"))))
14010       (build-system r-build-system)
14011       (propagated-inputs
14012        `(("r-annotationdbi" ,r-annotationdbi)
14013          ("r-assertthat" ,r-assertthat)
14014          ("r-biobase" ,r-biobase)
14015          ("r-biocinstaller" ,r-biocinstaller)
14016          ("r-digest" ,r-digest)
14017          ("r-pkgmaker" ,r-pkgmaker)
14018          ("r-plyr" ,r-plyr)
14019          ("r-reshape2" ,r-reshape2)
14020          ("r-stringr" ,r-stringr)))
14021       (home-page "https://github.com/renozao/xbioc/")
14022       (synopsis "Extra base functions for Bioconductor")
14023       (description "This package provides extra utility functions to perform
14024 common tasks in the analysis of omics data, leveraging and enhancing features
14025 provided by Bioconductor packages.")
14026       (license license:gpl3+))))
14027
14028 (define-public r-cssam
14029   (let ((revision "1")
14030         (commit "9ec58c982fa551af0d80b1a266890d92954833f2"))
14031     (package
14032       (name "r-cssam")
14033       (version (git-version "1.4" revision commit))
14034       (source (origin
14035                 (method git-fetch)
14036                 (uri (git-reference
14037                       (url "https://github.com/shenorrLab/csSAM.git")
14038                       (commit commit)))
14039                 (file-name (git-file-name name version))
14040                 (sha256
14041                  (base32
14042                   "128syf9v39gk0z3ip000qpsjbg6l1siyq6c8b0hz41dzg5achyb3"))))
14043       (build-system r-build-system)
14044       (propagated-inputs
14045        `(("r-formula" ,r-formula)
14046          ("r-ggplot2" ,r-ggplot2)
14047          ("r-pkgmaker" ,r-pkgmaker)
14048          ("r-plyr" ,r-plyr)
14049          ("r-rngtools" ,r-rngtools)
14050          ("r-scales" ,r-scales)))
14051       (home-page "https://github.com/shenorrLab/csSAM/")
14052       (synopsis "Cell type-specific statistical analysis of microarray")
14053       (description "This package implements the method csSAM that computes
14054 cell-specific differential expression from measured cell proportions using
14055 SAM.")
14056       ;; Any version
14057       (license license:lgpl2.1+))))
14058
14059 (define-public r-bseqsc
14060   (let ((revision "1")
14061         (commit "fef3f3e38dcf3df37103348b5780937982b43b98"))
14062     (package
14063       (name "r-bseqsc")
14064       (version (git-version "1.0" revision commit))
14065       (source (origin
14066                 (method git-fetch)
14067                 (uri (git-reference
14068                       (url "https://github.com/shenorrLab/bseqsc.git")
14069                       (commit commit)))
14070                 (file-name (git-file-name name version))
14071                 (sha256
14072                  (base32
14073                   "1prw13wa20f7wlc3gkkls66n1kxz8d28qrb8icfqdwdnnv8w5qg8"))))
14074       (build-system r-build-system)
14075       (propagated-inputs
14076        `(("r-abind" ,r-abind)
14077          ("r-annotationdbi" ,r-annotationdbi)
14078          ("r-biobase" ,r-biobase)
14079          ("r-cssam" ,r-cssam)
14080          ("r-dplyr" ,r-dplyr)
14081          ("r-e1071" ,r-e1071)
14082          ("r-edger" ,r-edger)
14083          ("r-ggplot2" ,r-ggplot2)
14084          ("r-nmf" ,r-nmf)
14085          ("r-openxlsx" ,r-openxlsx)
14086          ("r-pkgmaker" ,r-pkgmaker)
14087          ("r-plyr" ,r-plyr)
14088          ("r-preprocesscore" ,r-preprocesscore)
14089          ("r-rngtools" ,r-rngtools)
14090          ("r-scales" ,r-scales)
14091          ("r-stringr" ,r-stringr)
14092          ("r-xbioc" ,r-xbioc)))
14093       (home-page "https://github.com/shenorrLab/bseqsc")
14094       (synopsis "Deconvolution of bulk sequencing experiments using single cell data")
14095       (description "BSeq-sc is a bioinformatics analysis pipeline that
14096 leverages single-cell sequencing data to estimate cell type proportion and
14097 cell type-specific gene expression differences from RNA-seq data from bulk
14098 tissue samples.  This is a companion package to the publication \"A
14099 single-cell transcriptomic map of the human and mouse pancreas reveals inter-
14100 and intra-cell population structure.\" Baron et al. Cell Systems (2016)
14101 @url{https://www.ncbi.nlm.nih.gov/pubmed/27667365}.")
14102       (license license:gpl2+))))
14103
14104 (define-public porechop
14105   ;; The recommended way to install is to clone the git repository
14106   ;; https://github.com/rrwick/Porechop#installation
14107   (let ((commit "289d5dca4a5fc327f97b3f8cecb68ecaf1014861")
14108         (revision "1"))
14109     (package
14110       (name "porechop")
14111       (version (git-version "0.2.3" revision commit))
14112       (source
14113        (origin
14114          (method git-fetch)
14115          (uri (git-reference
14116                (url "https://github.com/rrwick/Porechop.git")
14117                (commit commit)))
14118          (file-name (git-file-name name version))
14119          (sha256
14120           (base32 "05ps43gig0d3ia9x5lj84lb00hbsl6ba9n7y7jz927npxbr2ym23"))))
14121       (build-system python-build-system)
14122       (home-page "https://github.com/rrwick/porechop")
14123       (synopsis "Finding, trimming or splitting adapters, in Oxford Nanopore reads")
14124       (description
14125        "The porechop package is a tool for finding and removing adapters from Oxford
14126 Nanopore reads.  Adapters on the ends of reads are trimmed off, and when a read
14127 has an adapter in its middle, it is treated as chimeric and chopped into
14128 separate reads.  Porechop performs thorough alignments to effectively find
14129 adapters, even at low sequence identity.  Porechop also supports demultiplexing
14130 of Nanopore reads that were barcoded with the Native Barcoding Kit, PCR
14131 Barcoding Kit or Rapid Barcoding Kit.")
14132       (license license:gpl3+))))
14133
14134 (define-public poretools
14135   ;; The latest release was in 2016 and the latest commit is from 2017
14136   ;; the recommended way to install is to clone the git repository
14137   ;; https://poretools.readthedocs.io/en/latest/content/installation.html
14138   (let ((commit "e426b1f09e86ac259a00c261c79df91510777407")
14139         (revision "1"))
14140     (package
14141       (name "poretools")
14142       (version (git-version "0.6.0" revision commit))
14143       (source
14144        (origin
14145          (method git-fetch)
14146          (uri (git-reference
14147                (url "https://github.com/arq5x/poretools.git")
14148                (commit commit)))
14149          (file-name (git-file-name name version))
14150          (sha256
14151           (base32 "0bglj833wxpp3cq430p1d3xp085ls221js2y90w7ir2x5ay8l7am"))))
14152       (build-system python-build-system)
14153       ;; requires python >=2.7, <3.0, and the same for python dependencies
14154       (arguments `(#:python ,python-2))
14155       (inputs
14156        `(("hdf5" ,hdf5)))
14157       (propagated-inputs
14158        `(("python-dateutil" ,python2-dateutil)
14159          ("python-h5py" ,python2-h5py)
14160          ("python-matplotlib" ,python2-matplotlib)
14161          ("python-pandas" ,python2-pandas)
14162          ("python-seaborn" ,python2-seaborn)))
14163       (home-page "https://poretools.readthedocs.io")
14164       (synopsis "Toolkit for working with nanopore sequencing data")
14165       (description
14166        "The MinION from Oxford Nanopore Technologies is a nanopore sequencer.
14167 This @code{poretools} package is a flexible toolkit for exploring datasets
14168 generated by nanopore sequencing devices for the purposes of quality control and
14169 downstream analysis.  Poretools operates directly on the native FAST5, a variant
14170 of the Hierarchical Data Format (HDF5) standard.")
14171       (license license:expat))))
14172
14173 (define-public r-absfiltergsea
14174   (package
14175     (name "r-absfiltergsea")
14176     (version "1.5.1")
14177     (source
14178      (origin
14179        (method url-fetch)
14180        (uri (cran-uri "AbsFilterGSEA" version))
14181        (sha256
14182         (base32 "15srxkxsvn38kd5frdrwfdf0ad8gskrd0h01wmdf9hglq8fjrp7w"))))
14183     (properties `((upstream-name . "AbsFilterGSEA")))
14184     (build-system r-build-system)
14185     (propagated-inputs
14186      `(("r-biobase" ,r-biobase)
14187        ("r-deseq" ,r-deseq)
14188        ("r-limma" ,r-limma)
14189        ("r-rcpp" ,r-rcpp)
14190        ("r-rcpparmadillo" ,r-rcpparmadillo)))
14191     (home-page "https://cran.r-project.org/web/packages/AbsFilterGSEA/")
14192     (synopsis "Improved false positive control of gene-permuting with absolute filtering")
14193     (description
14194      "This package provides a function that performs gene-permuting of a gene-set
14195 enrichment analysis (GSEA) calculation with or without the absolute filtering.
14196   Without filtering, users can perform (original) two-tailed or one-tailed
14197 absolute GSEA.")
14198     (license license:gpl2)))
14199
14200 (define-public jamm
14201   (package
14202     (name "jamm")
14203     (version "1.0.7.5")
14204     (source
14205      (origin
14206        (method git-fetch)
14207        (uri (git-reference
14208              (url "https://github.com/mahmoudibrahim/JAMM.git")
14209              (commit (string-append "JAMMv" version))))
14210        (file-name (git-file-name name version))
14211        (sha256
14212         (base32
14213          "0ls889jcma1ch9h21jjhnkadgszgqj41842hhcjh6cg88f85qf3i"))))
14214     (build-system gnu-build-system)
14215     (arguments
14216      `(#:tests? #f ; there are none
14217        #:phases
14218        (modify-phases %standard-phases
14219          (delete 'configure)
14220          (replace 'build
14221            (lambda* (#:key inputs outputs #:allow-other-keys)
14222              (substitute* "JAMM.sh"
14223                (("^sPath=.*")
14224                 (string-append "")))
14225              #t))
14226          (replace 'install
14227            (lambda* (#:key inputs outputs #:allow-other-keys)
14228              (let* ((out (assoc-ref outputs "out"))
14229                     (libexec (string-append out "/libexec/jamm"))
14230                     (bin (string-append out "/bin")))
14231                (substitute* '("JAMM.sh"
14232                               "SignalGenerator.sh")
14233                  (("^sPath=.*")
14234                   (string-append "sPath=\"" libexec "\"\n")))
14235                (for-each (lambda (file)
14236                            (install-file file libexec))
14237                          (list "bincalculator.r"
14238                                "peakfinder.r"
14239                                "peakhelper.r"
14240                                "signalmaker.r"
14241                                "xcorr.r"
14242                                "xcorrhelper.r"
14243                                ;; Perl scripts
14244                                "peakfilter.pl"
14245                                "readshifter.pl"))
14246
14247                (for-each
14248                 (lambda (script)
14249                   (chmod script #o555)
14250                   (install-file script bin)
14251                   (wrap-program (string-append bin "/" script)
14252                     `("PATH" ":" prefix
14253                       (,(string-append (assoc-ref inputs "coreutils") "/bin")
14254                        ,(string-append (assoc-ref inputs "gawk") "/bin")
14255                        ,(string-append (assoc-ref inputs "perl") "/bin")
14256                        ,(string-append (assoc-ref inputs "r-minimal") "/bin")))
14257                     `("PERL5LIB" ":" prefix (,(getenv "PERL5LIB")))
14258                     `("R_LIBS_SITE" ":" prefix (,(getenv "R_LIBS_SITE")))))
14259                 (list "JAMM.sh" "SignalGenerator.sh")))
14260              #t)))))
14261     (inputs
14262      `(("bash" ,bash)
14263        ("coreutils" ,coreutils)
14264        ("gawk" ,gawk)
14265        ("perl" ,perl)
14266        ("r-minimal" ,r-minimal)
14267        ;;("r-parallel" ,r-parallel)
14268        ("r-signal" ,r-signal)
14269        ("r-mclust" ,r-mclust)))
14270     (home-page "https://github.com/mahmoudibrahim/JAMM")
14271     (synopsis "Peak finder for NGS datasets")
14272     (description
14273      "JAMM is a peak finder for next generation sequencing datasets (ChIP-Seq,
14274 ATAC-Seq, DNase-Seq, etc.) that can integrate replicates and assign peak
14275 boundaries accurately.  JAMM is applicable to both broad and narrow
14276 datasets.")
14277     (license license:gpl3+)))
14278
14279 (define-public ngless
14280   (package
14281     (name "ngless")
14282     (version "0.9.1")
14283     (source
14284      (origin
14285        (method git-fetch)
14286        (uri (git-reference
14287              (url "https://gitlab.com/ngless/ngless.git")
14288              (commit (string-append "v" version))))
14289        (file-name (git-file-name name version))
14290        (sha256
14291         (base32
14292          "0mc2gi7h4lx74zylvyp76mvc0w6706j858ii9vlgzqsw6acpr117"))))
14293     (build-system haskell-build-system)
14294     (arguments
14295      `(#:haddock? #f ; The haddock phase fails with: NGLess/CmdArgs.hs:20:1:
14296                      ; error: parse error on input import
14297                      ; import Options.Applicative
14298        #:phases
14299        (modify-phases %standard-phases
14300          (add-after 'unpack 'create-cabal-file
14301            (lambda _ (invoke "hpack") #t))
14302          ;; These tools are expected to be installed alongside ngless.
14303          (add-after 'install 'link-tools
14304            (lambda* (#:key inputs outputs #:allow-other-keys)
14305              (let ((bin (string-append (assoc-ref outputs "out") "/bin/")))
14306                (symlink (string-append (assoc-ref inputs "prodigal")
14307                                        "/bin/prodigal")
14308                         (string-append bin "ngless-" ,version "-prodigal"))
14309                (symlink (string-append (assoc-ref inputs "minimap2")
14310                                        "/bin/minimap2")
14311                         (string-append bin "ngless-" ,version "-minimap2"))
14312                (symlink (string-append (assoc-ref inputs "samtools")
14313                                        "/bin/samtools")
14314                         (string-append bin "ngless-" ,version "-samtools"))
14315                (symlink (string-append (assoc-ref inputs "bwa")
14316                                        "/bin/bwa")
14317                         (string-append bin "ngless-" ,version "-bwa"))
14318                #t))))))
14319     (inputs
14320      `(("prodigal" ,prodigal)
14321        ("bwa" ,bwa)
14322        ("samtools" ,samtools)
14323        ("minimap2" ,minimap2)
14324        ("ghc-aeson" ,ghc-aeson)
14325        ("ghc-ansi-terminal" ,ghc-ansi-terminal)
14326        ("ghc-async" ,ghc-async)
14327        ("ghc-atomic-write" ,ghc-atomic-write)
14328        ("ghc-bytestring-lexing" ,ghc-bytestring-lexing)
14329        ("ghc-chart" ,ghc-chart)
14330        ("ghc-chart-cairo" ,ghc-chart-cairo)
14331        ("ghc-conduit" ,ghc-conduit)
14332        ("ghc-conduit-algorithms" ,ghc-conduit-algorithms)
14333        ("ghc-conduit-combinators" ,ghc-conduit-combinators)
14334        ("ghc-conduit-extra" ,ghc-conduit-extra)
14335        ("ghc-configurator" ,ghc-configurator)
14336        ("ghc-convertible" ,ghc-convertible)
14337        ("ghc-data-default" ,ghc-data-default)
14338        ("ghc-double-conversion" ,ghc-double-conversion)
14339        ("ghc-edit-distance" ,ghc-edit-distance)
14340        ("ghc-either" ,ghc-either)
14341        ("ghc-errors" ,ghc-errors)
14342        ("ghc-extra" ,ghc-extra)
14343        ("ghc-filemanip" ,ghc-filemanip)
14344        ("ghc-file-embed" ,ghc-file-embed)
14345        ("ghc-gitrev" ,ghc-gitrev)
14346        ("ghc-hashtables" ,ghc-hashtables)
14347        ("ghc-http-conduit" ,ghc-http-conduit)
14348        ("ghc-inline-c" ,ghc-inline-c)
14349        ("ghc-inline-c-cpp" ,ghc-inline-c-cpp)
14350        ("ghc-intervalmap" ,ghc-intervalmap)
14351        ("ghc-missingh" ,ghc-missingh)
14352        ("ghc-optparse-applicative" ,ghc-optparse-applicative)
14353        ("ghc-parsec" ,ghc-parsec)
14354        ("ghc-regex" ,ghc-regex)
14355        ("ghc-safe" ,ghc-safe)
14356        ("ghc-safeio" ,ghc-safeio)
14357        ("ghc-strict" ,ghc-strict)
14358        ("ghc-tar" ,ghc-tar)
14359        ("ghc-text" ,ghc-text)
14360        ("ghc-unliftio" ,ghc-unliftio)
14361        ("ghc-unliftio-core" ,ghc-unliftio-core)
14362        ("ghc-vector" ,ghc-vector)
14363        ("ghc-yaml" ,ghc-yaml)
14364        ("ghc-zlib" ,ghc-zlib)))
14365     (propagated-inputs
14366      `(("r-r6" ,r-r6)
14367        ("r-hdf5r" ,r-hdf5r)
14368        ("r-iterators" ,r-iterators)
14369        ("r-itertools" ,r-itertools)
14370        ("r-matrix" ,r-matrix)))
14371     (native-inputs
14372      `(("ghc-hpack" ,ghc-hpack)
14373        ("ghc-quickcheck" ,ghc-quickcheck)
14374        ("ghc-test-framework" ,ghc-test-framework)
14375        ("ghc-test-framework-hunit",ghc-test-framework-hunit)
14376        ("ghc-test-framework-quickcheck2" ,ghc-test-framework-quickcheck2)
14377        ("ghc-test-framework-th" ,ghc-test-framework-th)))
14378     (home-page "https://gitlab.com/ngless/ngless")
14379     (synopsis "DSL for processing next-generation sequencing data")
14380     (description "Ngless is a domain-specific language for
14381 @dfn{next-generation sequencing} (NGS) data processing.")
14382     (license license:expat)))
14383
14384 (define-public filtlong
14385   ;; The recommended way to install is to clone the git repository
14386   ;; https://github.com/rrwick/Filtlong#installation
14387   ;; and the lastest release is more than nine months old
14388   (let ((commit "d1bb46dfe8bc7efe6257b5ce222c04bfe8aedaab")
14389         (revision "1"))
14390     (package
14391       (name "filtlong")
14392       (version (git-version "0.2.0" revision commit))
14393       (source
14394        (origin
14395          (method git-fetch)
14396          (uri (git-reference
14397                (url "https://github.com/rrwick/Filtlong.git")
14398                (commit commit)))
14399          (file-name (git-file-name name version))
14400          (sha256
14401           (base32 "1xr92r820x8qlkcr3b57iw223yq8vjgyi42jr79w2xgw47qzr575"))))
14402       (build-system gnu-build-system)
14403       (arguments
14404        `(#:tests? #f                    ; no check target
14405          #:phases
14406          (modify-phases %standard-phases
14407            (delete 'configure)
14408            (replace 'install
14409              (lambda* (#:key outputs #:allow-other-keys)
14410                (let* ((out (assoc-ref outputs "out"))
14411                       (bin (string-append out "/bin"))
14412                       (scripts (string-append out "/share/filtlong/scripts")))
14413                  (install-file "bin/filtlong" bin)
14414                  (install-file "scripts/histogram.py" scripts)
14415                  (install-file "scripts/read_info_histograms.sh" scripts))
14416                #t))
14417            (add-after 'install 'wrap-program
14418              (lambda* (#:key inputs outputs #:allow-other-keys)
14419                (let* ((out (assoc-ref outputs "out"))
14420                       (path (getenv "PYTHONPATH")))
14421                  (wrap-program (string-append out
14422                                               "/share/filtlong/scripts/histogram.py")
14423                    `("PYTHONPATH" ":" prefix (,path))))
14424                #t))
14425            (add-before 'check 'patch-tests
14426              (lambda _
14427                (substitute* "scripts/read_info_histograms.sh"
14428                  (("awk") (which "gawk")))
14429                #t)))))
14430       (inputs
14431        `(("gawk" ,gawk)                 ;for read_info_histograms.sh
14432          ("python" ,python-2)           ;required for histogram.py
14433          ("zlib" ,zlib)))
14434       (home-page "https://github.com/rrwick/Filtlong/")
14435       (synopsis "Tool for quality filtering of Nanopore and PacBio data")
14436       (description
14437        "The Filtlong package is a tool for filtering long reads by quality.
14438 It can take a set of long reads and produce a smaller, better subset.  It uses
14439 both read length (longer is better) and read identity (higher is better) when
14440 choosing which reads pass the filter.")
14441       (license (list license:gpl3       ;filtlong
14442                      license:asl2.0))))) ;histogram.py
14443
14444 (define-public nanopolish
14445   ;; The recommended way to install is to clone the git repository
14446   ;; <https://github.com/jts/nanopolish#installing-a-particular-release>.
14447   ;; Also, the differences between release and current version seem to be
14448   ;; significant.
14449   (let ((commit "50e8b5cc62f9b46f5445f5c5e8c5ab7263ea6d9d")
14450         (revision "1"))
14451     (package
14452       (name "nanopolish")
14453       (version (git-version "0.10.2" revision commit))
14454       (source
14455        (origin
14456          (method git-fetch)
14457          (uri (git-reference
14458                (url "https://github.com/jts/nanopolish.git")
14459                (commit commit)
14460                (recursive? #t)))
14461          (file-name (git-file-name name version))
14462          (sha256
14463           (base32 "09j5gz57yr9i34a27vbl72i4g8syv2zzgmsfyjq02yshmnrvkjs6"))))
14464       (build-system gnu-build-system)
14465       (arguments
14466        `(#:make-flags
14467          `("HDF5=noinstall" "EIGEN=noinstall" "HTS=noinstall" "CC=gcc")
14468          #:tests? #f                    ; no check target
14469          #:phases
14470          (modify-phases %standard-phases
14471            (add-after 'unpack 'find-eigen
14472              (lambda* (#:key inputs #:allow-other-keys)
14473                (setenv "CPATH"
14474                        (string-append (assoc-ref inputs "eigen")
14475                                       "/include/eigen3"))
14476                #t))
14477            (delete 'configure)
14478            (replace 'install
14479              (lambda* (#:key outputs #:allow-other-keys)
14480                (let* ((out (assoc-ref outputs "out"))
14481                       (bin (string-append out "/bin"))
14482                       (scripts (string-append out "/share/nanopolish/scripts")))
14483
14484                  (install-file "nanopolish" bin)
14485                  (for-each (lambda (file) (install-file file scripts))
14486                            (find-files "scripts" ".*"))
14487                  #t)))
14488            (add-after 'install 'wrap-programs
14489              (lambda* (#:key outputs #:allow-other-keys)
14490                (for-each (lambda (file)
14491                            (wrap-program file `("PYTHONPATH" ":" prefix (,path))))
14492                          (find-files "/share/nanopolish/scripts" "\\.py"))
14493                (for-each (lambda (file)
14494                            (wrap-program file `("PERL5LIB" ":" prefix (,path))))
14495                          (find-files  "/share/nanopolish/scripts" "\\.pl"))
14496                #t)))))
14497       (inputs
14498        `(("eigen" ,eigen)
14499          ("hdf5" ,hdf5)
14500          ("htslib" ,htslib)
14501          ("perl" ,perl)
14502          ("python" ,python)
14503          ("python-biopython" ,python-biopython)
14504          ("python-numpy" ,python-numpy)
14505          ("python-pysam" ,python-pysam)
14506          ("python-scikit-learn" , python-scikit-learn)
14507          ("python-scipy" ,python-scipy)
14508          ("zlib" ,zlib)))
14509       (home-page "https://github.com/jts/nanopolish")
14510       (synopsis "Signal-level analysis of Oxford Nanopore sequencing data")
14511       (description
14512        "This package analyses the Oxford Nanopore sequencing data at signal-level.
14513 Nanopolish can calculate an improved consensus sequence for a draft genome
14514 assembly, detect base modifications, call SNPs (Single nucleotide
14515 polymorphisms) and indels with respect to a reference genome and more.")
14516       (license license:expat))))