gnu/packages/bioinformatics.scm

   1 ;;; GNU Guix --- Functional package management for GNU
   2 ;;; Copyright © 2014, 2015 Ricardo Wurmus <rekado@elephly.net>
   3 ;;; Copyright © 2015 Ben Woodcroft <donttrustben@gmail.com>
   4 ;;;
   5 ;;; This file is part of GNU Guix.
   6 ;;;
   7 ;;; GNU Guix is free software; you can redistribute it and/or modify it
   8 ;;; under the terms of the GNU General Public License as published by
   9 ;;; the Free Software Foundation; either version 3 of the License, or (at
  10 ;;; your option) any later version.
  11 ;;;
  12 ;;; GNU Guix is distributed in the hope that it will be useful, but
  13 ;;; WITHOUT ANY WARRANTY; without even the implied warranty of
  14 ;;; MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
  15 ;;; GNU General Public License for more details.
  16 ;;;
  17 ;;; You should have received a copy of the GNU General Public License
  18 ;;; along with GNU Guix.  If not, see <http://www.gnu.org/licenses/>.
  19
  20 (define-module (gnu packages bioinformatics)
  21   #:use-module ((guix licenses) #:prefix license:)
  22   #:use-module (guix packages)
  23   #:use-module (guix utils)
  24   #:use-module (guix download)
  25   #:use-module (guix git-download)
  26   #:use-module (guix build-system gnu)
  27   #:use-module (guix build-system cmake)
  28   #:use-module (guix build-system perl)
  29   #:use-module (guix build-system python)
  30   #:use-module (guix build-system trivial)
  31   #:use-module (gnu packages)
  32   #:use-module (gnu packages algebra)
  33   #:use-module (gnu packages base)
  34   #:use-module (gnu packages boost)
  35   #:use-module (gnu packages compression)
  36   #:use-module (gnu packages cpio)
  37   #:use-module (gnu packages file)
  38   #:use-module (gnu packages java)
  39   #:use-module (gnu packages linux)
  40   #:use-module (gnu packages machine-learning)
  41   #:use-module (gnu packages maths)
  42   #:use-module (gnu packages ncurses)
  43   #:use-module (gnu packages perl)
  44   #:use-module (gnu packages pkg-config)
  45   #:use-module (gnu packages popt)
  46   #:use-module (gnu packages protobuf)
  47   #:use-module (gnu packages python)
  48   #:use-module (gnu packages statistics)
  49   #:use-module (gnu packages tbb)
  50   #:use-module (gnu packages textutils)
  51   #:use-module (gnu packages vim)
  52   #:use-module (gnu packages web)
  53   #:use-module (gnu packages xml)
  54   #:use-module (gnu packages zip)
  55   #:use-module (srfi srfi-1))
  56
  57 (define-public aragorn
  58   (package
  59     (name "aragorn")
  60     (version "1.2.36")
  61     (source (origin
  62               (method url-fetch)
  63               (uri (string-append
  64                     "http://mbio-serv2.mbioekol.lu.se/ARAGORN/Downloads/aragorn"
  65                     version ".tgz"))
  66               (sha256
  67                (base32
  68                 "1dg7jlz1qpqy88igjxd6ncs11ccsirb36qv1z01a0np4i4jh61mb"))))
  69     (build-system gnu-build-system)
  70     (arguments
  71      `(#:tests? #f ; there are no tests
  72        #:phases
  73        (modify-phases %standard-phases
  74          (delete 'configure)
  75          (replace 'build
  76                   (lambda _
  77                     (zero? (system* "gcc"
  78                                     "-O3"
  79                                     "-ffast-math"
  80                                     "-finline-functions"
  81                                     "-o"
  82                                     "aragorn"
  83                                     (string-append "aragorn" ,version ".c")))))
  84          (replace 'install
  85                   (lambda* (#:key outputs #:allow-other-keys)
  86                     (let* ((out (assoc-ref outputs "out"))
  87                            (bin (string-append out "/bin"))
  88                            (man (string-append out "/share/man/man1")))
  89                       (mkdir-p bin)
  90                       (copy-file "aragorn"
  91                                  (string-append bin "/aragorn"))
  92                       (mkdir-p man)
  93                       (copy-file "aragorn.1"
  94                                  (string-append man "/aragorn.1")))
  95                     #t)))))
  96     (home-page "http://mbio-serv2.mbioekol.lu.se/ARAGORN")
  97     (synopsis "Detect tRNA, mtRNA and tmRNA genes in nucleotide sequences")
  98     (description
  99      "Aragorn identifies transfer RNA, mitochondrial RNA and
 100 transfer-messenger RNA from nucleotide sequences, based on homology to known
 101 tRNA consensus sequences and RNA structure.  It also outputs the secondary
 102 structure of the predicted RNA.")
 103     (license license:gpl2)))
 104
 105 (define-public bamtools
 106   (package
 107     (name "bamtools")
 108     (version "2.3.0")
 109     (source (origin
 110               (method url-fetch)
 111               (uri (string-append
 112                     "https://github.com/pezmaster31/bamtools/archive/v"
 113                     version ".tar.gz"))
 114               (file-name (string-append name "-" version ".tar.gz"))
 115               (sha256
 116                (base32
 117                 "1brry29bw2xr2l9pqn240rkqwayg85b8qq78zk2zs6nlspk4d018"))))
 118     (build-system cmake-build-system)
 119     (arguments
 120      `(#:tests? #f ;no "check" target
 121        #:phases
 122        (modify-phases %standard-phases
 123          (add-before
 124           'configure 'set-ldflags
 125           (lambda* (#:key outputs #:allow-other-keys)
 126             (setenv "LDFLAGS"
 127                     (string-append
 128                      "-Wl,-rpath="
 129                      (assoc-ref outputs "out") "/lib/bamtools")))))))
 130     (inputs `(("zlib" ,zlib)))
 131     (home-page "https://github.com/pezmaster31/bamtools")
 132     (synopsis "C++ API and command-line toolkit for working with BAM data")
 133     (description
 134      "BamTools provides both a C++ API and a command-line toolkit for handling
 135 BAM files.")
 136     (license license:expat)))
 137
 138 (define-public bedops
 139   (package
 140     (name "bedops")
 141     (version "2.4.14")
 142     (source (origin
 143               (method url-fetch)
 144               (uri (string-append "https://github.com/bedops/bedops/archive/v"
 145                                   version ".tar.gz"))
 146               (file-name (string-append name "-" version ".tar.gz"))
 147               (sha256
 148                (base32
 149                 "1kqbac547wyqma81cyky9n7mkgikjpsfd3nnmcm6hpqwanqgh10v"))))
 150     (build-system gnu-build-system)
 151     (arguments
 152      '(#:tests? #f
 153        #:make-flags (list (string-append "BINDIR=" %output "/bin"))
 154        #:phases
 155        (alist-cons-after
 156          'unpack 'unpack-tarballs
 157          (lambda _
 158            ;; FIXME: Bedops includes tarballs of minimally patched upstream
 159            ;; libraries jansson, zlib, and bzip2.  We cannot just use stock
 160            ;; libraries because at least one of the libraries (zlib) is
 161            ;; patched to add a C++ function definition (deflateInit2cpp).
 162            ;; Until the Bedops developers offer a way to link against system
 163            ;; libraries we have to build the in-tree copies of these three
 164            ;; libraries.
 165
 166            ;; See upstream discussion:
 167            ;; https://github.com/bedops/bedops/issues/124
 168
 169            ;; Unpack the tarballs to benefit from shebang patching.
 170            (with-directory-excursion "third-party"
 171              (and (zero? (system* "tar" "xvf" "jansson-2.6.tar.bz2"))
 172                   (zero? (system* "tar" "xvf" "zlib-1.2.7.tar.bz2"))
 173                   (zero? (system* "tar" "xvf" "bzip2-1.0.6.tar.bz2"))))
 174            ;; Disable unpacking of tarballs in Makefile.
 175            (substitute* "system.mk/Makefile.linux"
 176              (("^\tbzcat .*") "\t@echo \"not unpacking\"\n")
 177              (("\\./configure") "CONFIG_SHELL=bash ./configure"))
 178            (substitute* "third-party/zlib-1.2.7/Makefile.in"
 179              (("^SHELL=.*$") "SHELL=bash\n")))
 180          (alist-delete 'configure %standard-phases))))
 181     (home-page "https://github.com/bedops/bedops")
 182     (synopsis "Tools for high-performance genomic feature operations")
 183     (description
 184      "BEDOPS is a suite of tools to address common questions raised in genomic
 185 studies---mostly with regard to overlap and proximity relationships between
 186 data sets.  It aims to be scalable and flexible, facilitating the efficient
 187 and accurate analysis and management of large-scale genomic data.
 188
 189 BEDOPS provides tools that perform highly efficient and scalable Boolean and
 190 other set operations, statistical calculations, archiving, conversion and
 191 other management of genomic data of arbitrary scale.  Tasks can be easily
 192 split by chromosome for distributing whole-genome analyses across a
 193 computational cluster.")
 194     (license license:gpl2+)))
 195
 196 (define-public bedtools
 197   (package
 198     (name "bedtools")
 199     (version "2.24.0")
 200     (source (origin
 201               (method url-fetch)
 202               (uri (string-append "https://github.com/arq5x/bedtools2/archive/v"
 203                                   version ".tar.gz"))
 204               (file-name (string-append name "-" version ".tar.gz"))
 205               (sha256
 206                (base32
 207                 "0lnxrjvs3nnmb4bmskag1wg3h2hd80przz5q3xd0bvs7vyxrvpbl"))
 208               (patches (list (search-patch "bedtools-32bit-compilation.patch")))))
 209     (build-system gnu-build-system)
 210     (native-inputs `(("python" ,python-2)))
 211     (inputs `(("samtools" ,samtools)
 212               ("zlib" ,zlib)))
 213     (arguments
 214      '(#:test-target "test"
 215        #:phases
 216        (alist-cons-after
 217         'unpack 'patch-makefile-SHELL-definition
 218         (lambda _
 219           ;; patch-makefile-SHELL cannot be used here as it does not
 220           ;; yet patch definitions with `:='.  Since changes to
 221           ;; patch-makefile-SHELL result in a full rebuild, features
 222           ;; of patch-makefile-SHELL are reimplemented here.
 223           (substitute* "Makefile"
 224             (("^SHELL := .*$") (string-append "SHELL := " (which "bash") " -e \n"))))
 225         (alist-delete
 226          'configure
 227          (alist-replace
 228           'install
 229           (lambda* (#:key outputs #:allow-other-keys)
 230             (let ((bin (string-append (assoc-ref outputs "out") "/bin/")))
 231               (mkdir-p bin)
 232               (for-each (lambda (file)
 233                           (copy-file file (string-append bin (basename file))))
 234                         (find-files "bin" ".*"))))
 235           %standard-phases)))))
 236     (home-page "https://github.com/arq5x/bedtools2")
 237     (synopsis "Tools for genome analysis and arithmetic")
 238     (description
 239      "Collectively, the bedtools utilities are a swiss-army knife of tools for
 240 a wide-range of genomics analysis tasks.  The most widely-used tools enable
 241 genome arithmetic: that is, set theory on the genome.  For example, bedtools
 242 allows one to intersect, merge, count, complement, and shuffle genomic
 243 intervals from multiple files in widely-used genomic file formats such as BAM,
 244 BED, GFF/GTF, VCF.")
 245     (license license:gpl2)))
 246
 247 (define-public python2-pybedtools
 248   (package
 249     (name "python2-pybedtools")
 250     (version "0.6.9")
 251     (source (origin
 252               (method url-fetch)
 253               (uri (string-append
 254                     "https://pypi.python.org/packages/source/p/pybedtools/pybedtools-"
 255                     version ".tar.gz"))
 256               (sha256
 257                (base32
 258                 "1ldzdxw1p4y3g2ignmggsdypvqkcwqwzhdha4rbgpih048z5p4an"))))
 259     (build-system python-build-system)
 260     (arguments `(#:python ,python-2)) ; no Python 3 support
 261     (inputs
 262      `(("python-cython" ,python2-cython)
 263        ("python-matplotlib" ,python2-matplotlib)))
 264     (propagated-inputs
 265      `(("bedtools" ,bedtools)
 266        ("samtools" ,samtools)))
 267     (native-inputs
 268      `(("python-pyyaml" ,python2-pyyaml)
 269        ("python-nose" ,python2-nose)
 270        ("python-setuptools" ,python2-setuptools)))
 271     (home-page "https://pythonhosted.org/pybedtools/")
 272     (synopsis "Python wrapper for BEDtools programs")
 273     (description
 274      "pybedtools is a Python wrapper for Aaron Quinlan's BEDtools programs,
 275 which are widely used for genomic interval manipulation or \"genome algebra\".
 276 pybedtools extends BEDTools by offering feature-level manipulations from with
 277 Python.")
 278     (license license:gpl2+)))
 279
 280 (define-public bioperl-minimal
 281   (let* ((inputs `(("perl-module-build" ,perl-module-build)
 282                    ("perl-data-stag" ,perl-data-stag)
 283                    ("perl-libwww" ,perl-libwww)
 284                    ("perl-uri" ,perl-uri)))
 285          (transitive-inputs
 286           (map (compose package-name cadr)
 287                (delete-duplicates
 288                 (concatenate
 289                  (map (compose package-transitive-target-inputs cadr) inputs))))))
 290     (package
 291       (name "bioperl-minimal")
 292       (version "1.6.924")
 293       (source
 294        (origin
 295          (method url-fetch)
 296          (uri (string-append "mirror://cpan/authors/id/C/CJ/CJFIELDS/BioPerl-"
 297                              version ".tar.gz"))
 298          (sha256
 299           (base32
 300            "1l3npcvvvwjlhkna9dndpfv1hklhrgva013kw96m0n1wpd37ask1"))))
 301       (build-system perl-build-system)
 302       (arguments
 303        `(#:phases
 304          (modify-phases %standard-phases
 305            (add-after
 306             'install 'wrap-programs
 307             (lambda* (#:key outputs #:allow-other-keys)
 308               ;; Make sure all executables in "bin" find the required Perl
 309               ;; modules at runtime.  As the PERL5LIB variable contains also
 310               ;; the paths of native inputs, we pick the transitive target
 311               ;; inputs from %build-inputs.
 312               (let* ((out  (assoc-ref outputs "out"))
 313                      (bin  (string-append out "/bin/"))
 314                      (path (string-join
 315                             (cons (string-append out "/lib/perl5/site_perl")
 316                                   (map (lambda (name)
 317                                          (assoc-ref %build-inputs name))
 318                                        ',transitive-inputs))
 319                             ":")))
 320                 (for-each (lambda (file)
 321                             (wrap-program file
 322                               `("PERL5LIB" ":" prefix (,path))))
 323                           (find-files bin "\\.pl$"))
 324                 #t))))))
 325       (inputs inputs)
 326       (native-inputs
 327        `(("perl-test-most" ,perl-test-most)))
 328       (home-page "http://search.cpan.org/dist/BioPerl")
 329       (synopsis "Bioinformatics toolkit")
 330       (description
 331        "BioPerl is the product of a community effort to produce Perl code which
 332 is useful in biology.  Examples include Sequence objects, Alignment objects
 333 and database searching objects.  These objects not only do what they are
 334 advertised to do in the documentation, but they also interact - Alignment
 335 objects are made from the Sequence objects, Sequence objects have access to
 336 Annotation and SeqFeature objects and databases, Blast objects can be
 337 converted to Alignment objects, and so on.  This means that the objects
 338 provide a coordinated and extensible framework to do computational biology.")
 339       (license (package-license perl)))))
 340
 341 (define-public python-biopython
 342   (package
 343     (name "python-biopython")
 344     (version "1.65")
 345     (source (origin
 346               (method url-fetch)
 347               (uri (string-append
 348                     "http://biopython.org/DIST/biopython-"
 349                     version ".tar.gz"))
 350               (sha256
 351                (base32
 352                 "13m8s9jkrw40zvdp1rl709n6lmgdh4f52aann7gzr6sfp0fwhg26"))))
 353     (build-system python-build-system)
 354     (inputs
 355      `(("python-numpy" ,python-numpy)))
 356     (native-inputs
 357      `(("python-setuptools" ,python2-setuptools)))
 358     (home-page "http://biopython.org/")
 359     (synopsis "Tools for biological computation in Python")
 360     (description
 361      "Biopython is a set of tools for biological computation including parsers
 362 for bioinformatics files into Python data structures; interfaces to common
 363 bioinformatics programs; a standard sequence class and tools for performing
 364 common operations on them; code to perform data classification; code for
 365 dealing with alignments; code making it easy to split up parallelizable tasks
 366 into separate processes; and more.")
 367     (license (license:non-copyleft "http://www.biopython.org/DIST/LICENSE"))))
 368
 369 (define-public python2-biopython
 370   (package (inherit (package-with-python2 python-biopython))
 371     (inputs
 372      `(("python2-numpy" ,python2-numpy)))))
 373
 374 (define-public blast+
 375   (package
 376     (name "blast+")
 377     (version "2.2.31")
 378     (source (origin
 379               (method url-fetch)
 380               (uri (string-append
 381                     "ftp://ftp.ncbi.nlm.nih.gov/blast/executables/blast+/"
 382                     version "/ncbi-blast-" version "+-src.tar.gz"))
 383               (sha256
 384                (base32
 385                 "19gq6as4k1jrgsd26158ads6h7v4jca3h4r5dzg1y0m6ya50x5ph"))
 386               (modules '((guix build utils)))
 387               (snippet
 388                '(begin
 389                   ;; Remove bundled bzip2 and zlib
 390                   (delete-file-recursively "c++/src/util/compress/bzip2")
 391                   (delete-file-recursively "c++/src/util/compress/zlib")
 392                   (substitute* "c++/src/util/compress/Makefile.in"
 393                     (("bzip2 zlib api") "api"))
 394                   ;; Remove useless msbuild directory
 395                   (delete-file-recursively
 396                    "c++/src/build-system/project_tree_builder/msbuild")
 397                   #t))))
 398     (build-system gnu-build-system)
 399     (arguments
 400      `(;; There are three(!) tests for this massive library, and all fail with
 401        ;; "unparsable timing stats".
 402        ;; ERR [127] --  [util/regexp] test_pcre.sh     (unparsable timing stats)
 403        ;; ERR [127] --  [serial/datatool] datatool.sh     (unparsable timing stats)
 404        ;; ERR [127] --  [serial/datatool] datatool_xml.sh     (unparsable timing stats)
 405        #:tests? #f
 406        #:out-of-source? #t
 407        #:parallel-build? #f ; not supported
 408        #:phases
 409        (modify-phases %standard-phases
 410          (add-before
 411           'configure 'set-HOME
 412           ;; $HOME needs to be set at some point during the configure phase
 413           (lambda _ (setenv "HOME" "/tmp") #t))
 414          (add-after
 415           'unpack 'enter-dir
 416           (lambda _ (chdir "c++") #t))
 417          (add-after
 418           'enter-dir 'fix-build-system
 419           (lambda _
 420             (define (which* cmd)
 421               (cond ((string=? cmd "date")
 422                      ;; make call to "date" deterministic
 423                      "date -d @0")
 424                     ((which cmd)
 425                      => identity)
 426                     (else
 427                      (format (current-error-port)
 428                              "WARNING: Unable to find absolute path for ~s~%"
 429                              cmd)
 430                      #f)))
 431
 432             ;; Rewrite hardcoded paths to various tools
 433             (substitute* (append '("src/build-system/configure.ac"
 434                                    "src/build-system/configure"
 435                                    "scripts/common/impl/if_diff.sh"
 436                                    "scripts/common/impl/run_with_lock.sh"
 437                                    "src/build-system/Makefile.configurables.real"
 438                                    "src/build-system/Makefile.in.top"
 439                                    "src/build-system/Makefile.meta.gmake=no"
 440                                    "src/build-system/Makefile.meta.in"
 441                                    "src/build-system/Makefile.meta_l"
 442                                    "src/build-system/Makefile.meta_p"
 443                                    "src/build-system/Makefile.meta_r"
 444                                    "src/build-system/Makefile.mk.in"
 445                                    "src/build-system/Makefile.requirements"
 446                                    "src/build-system/Makefile.rules_with_autodep.in")
 447                                  (find-files "scripts/common/check" "\\.sh$"))
 448               (("(/usr/bin/|/bin/)([a-z][-_.a-z]*)" all dir cmd)
 449                (or (which* cmd) all)))
 450
 451             (substitute* (find-files "src/build-system" "^config.*")
 452               (("LN_S=/bin/\\$LN_S") (string-append "LN_S=" (which "ln")))
 453               (("^PATH=.*") ""))
 454
 455             ;; rewrite "/var/tmp" in check script
 456             (substitute* "scripts/common/check/check_make_unix.sh"
 457               (("/var/tmp") "/tmp"))
 458
 459             ;; do not reset PATH
 460             (substitute* (find-files "scripts/common/impl/" "\\.sh$")
 461               (("^ *PATH=.*") "")
 462               (("action=/bin/") "action=")
 463               (("export PATH") ":"))
 464             #t))
 465          (replace
 466           'configure
 467           (lambda* (#:key inputs outputs #:allow-other-keys)
 468             (let ((out     (assoc-ref outputs "out"))
 469                   (lib     (string-append (assoc-ref outputs "lib") "/lib"))
 470                   (include (string-append (assoc-ref outputs "include")
 471                                           "/include/ncbi-tools++")))
 472               ;; The 'configure' script doesn't recognize things like
 473               ;; '--enable-fast-install'.
 474               (zero? (system* "./configure.orig"
 475                               (string-append "--with-build-root=" (getcwd) "/build")
 476                               (string-append "--prefix=" out)
 477                               (string-append "--libdir=" lib)
 478                               (string-append "--includedir=" include)
 479                               (string-append "--with-bz2="
 480                                              (assoc-ref inputs "bzip2"))
 481                               (string-append "--with-z="
 482                                              (assoc-ref inputs "zlib"))
 483                               ;; Each library is built twice by default, once
 484                               ;; with "-static" in its name, and again
 485                               ;; without.
 486                               "--without-static"
 487                               "--with-dll"))))))))
 488     (outputs '("out"       ;  19 MB
 489                "lib"       ; 203 MB
 490                "include")) ;  32 MB
 491     (inputs
 492      `(("bzip2" ,bzip2)
 493        ("zlib" ,zlib)))
 494     (native-inputs
 495      `(("cpio" ,cpio)))
 496     (home-page "http://blast.ncbi.nlm.nih.gov")
 497     (synopsis "Basic local alignment search tool")
 498     (description
 499      "BLAST is a popular method of performing a DNA or protein sequence
 500 similarity search, using heuristics to produce results quickly.  It also
 501 calculates an “expect value” that estimates how many matches would have
 502 occurred at a given score by chance, which can aid a user in judging how much
 503 confidence to have in an alignment.")
 504     ;; Most of the sources are in the public domain, with the following
 505     ;; exceptions:
 506     ;;   * Expat:
 507     ;;     * ./c++/include/util/bitset/
 508     ;;     * ./c++/src/html/ncbi_menu*.js
 509     ;;   * Boost license:
 510     ;;     * ./c++/include/util/impl/floating_point_comparison.hpp
 511     ;;   * LGPL 2+:
 512     ;;     * ./c++/include/dbapi/driver/odbc/unix_odbc/
 513     ;;   * ASL 2.0:
 514     ;;     * ./c++/src/corelib/teamcity_*
 515     (license (list license:public-domain
 516                    license:expat
 517                    license:boost1.0
 518                    license:lgpl2.0+
 519                    license:asl2.0))))
 520
 521 (define-public bowtie
 522   (package
 523     (name "bowtie")
 524     (version "2.2.4")
 525     (source (origin
 526               (method url-fetch)
 527               (uri (string-append "https://github.com/BenLangmead/bowtie2/archive/v"
 528                                   version ".tar.gz"))
 529               (file-name (string-append name "-" version ".tar.gz"))
 530               (sha256
 531                (base32
 532                 "15dnbqippwvhyh9zqjhaxkabk7lm1xbh1nvar1x4b5kwm117zijn"))
 533               (modules '((guix build utils)))
 534               (snippet
 535                '(substitute* "Makefile"
 536                   (("^CC = .*$") "CC = gcc")
 537                   (("^CPP = .*$") "CPP = g++")
 538                   ;; replace BUILD_HOST and BUILD_TIME for deterministic build
 539                   (("-DBUILD_HOST=.*") "-DBUILD_HOST=\"\\\"guix\\\"\"")
 540                   (("-DBUILD_TIME=.*") "-DBUILD_TIME=\"\\\"0\\\"\"")))
 541               (patches (list (search-patch "bowtie-fix-makefile.patch")))))
 542     (build-system gnu-build-system)
 543     (inputs `(("perl" ,perl)
 544               ("perl-clone" ,perl-clone)
 545               ("perl-test-deep" ,perl-test-deep)
 546               ("perl-test-simple" ,perl-test-simple)
 547               ("python" ,python-2)))
 548     (arguments
 549      '(#:make-flags '("allall")
 550        #:phases
 551        (alist-delete
 552         'configure
 553         (alist-replace
 554          'install
 555          (lambda* (#:key outputs #:allow-other-keys)
 556            (let ((bin (string-append (assoc-ref outputs "out") "/bin/")))
 557              (mkdir-p bin)
 558              (for-each (lambda (file)
 559                          (copy-file file (string-append bin file)))
 560                        (find-files "." "bowtie2.*"))))
 561          (alist-replace
 562           'check
 563           (lambda* (#:key outputs #:allow-other-keys)
 564             (system* "perl"
 565                      "scripts/test/simple_tests.pl"
 566                      "--bowtie2=./bowtie2"
 567                      "--bowtie2-build=./bowtie2-build"))
 568           %standard-phases)))))
 569     (home-page "http://bowtie-bio.sourceforge.net/bowtie2/index.shtml")
 570     (synopsis "Fast and sensitive nucleotide sequence read aligner")
 571     (description
 572      "Bowtie 2 is a fast and memory-efficient tool for aligning sequencing
 573 reads to long reference sequences.  It is particularly good at aligning reads
 574 of about 50 up to 100s or 1,000s of characters, and particularly good at
 575 aligning to relatively long (e.g. mammalian) genomes.  Bowtie 2 indexes the
 576 genome with an FM Index to keep its memory footprint small: for the human
 577 genome, its memory footprint is typically around 3.2 GB.  Bowtie 2 supports
 578 gapped, local, and paired-end alignment modes.")
 579     (supported-systems '("x86_64-linux"))
 580     (license license:gpl3+)))
 581
 582 (define-public bwa
 583   (package
 584     (name "bwa")
 585     (version "0.7.12")
 586     (source (origin
 587               (method url-fetch)
 588               (uri (string-append "mirror://sourceforge/bio-bwa/bwa-"
 589                                   version ".tar.bz2"))
 590               (sha256
 591                (base32
 592                 "1330dpqncv0px3pbhjzz1gwgg39kkcv2r9qp2xs0sixf8z8wl7bh"))))
 593     (build-system gnu-build-system)
 594     (arguments
 595      '(#:tests? #f ;no "check" target
 596        #:phases
 597        (alist-replace
 598         'install
 599         (lambda* (#:key outputs #:allow-other-keys)
 600           (let ((bin (string-append
 601                       (assoc-ref outputs "out") "/bin"))
 602                 (doc (string-append
 603                       (assoc-ref outputs "out") "/share/doc/bwa"))
 604                 (man (string-append
 605                       (assoc-ref outputs "out") "/share/man/man1")))
 606             (mkdir-p bin)
 607             (mkdir-p doc)
 608             (mkdir-p man)
 609             (copy-file "bwa" (string-append bin "/bwa"))
 610             (copy-file "README.md" (string-append doc "/README.md"))
 611             (copy-file "bwa.1" (string-append man "/bwa.1"))))
 612         ;; no "configure" script
 613         (alist-delete 'configure %standard-phases))))
 614     (inputs `(("zlib" ,zlib)))
 615     (home-page "http://bio-bwa.sourceforge.net/")
 616     (synopsis "Burrows-Wheeler sequence aligner")
 617     (description
 618      "BWA is a software package for mapping low-divergent sequences against a
 619 large reference genome, such as the human genome.  It consists of three
 620 algorithms: BWA-backtrack, BWA-SW and BWA-MEM.  The first algorithm is
 621 designed for Illumina sequence reads up to 100bp, while the rest two for
 622 longer sequences ranged from 70bp to 1Mbp.  BWA-MEM and BWA-SW share similar
 623 features such as long-read support and split alignment, but BWA-MEM, which is
 624 the latest, is generally recommended for high-quality queries as it is faster
 625 and more accurate.  BWA-MEM also has better performance than BWA-backtrack for
 626 70-100bp Illumina reads.")
 627     (license license:gpl3+)))
 628
 629 (define-public python2-bx-python
 630   (package
 631     (name "python2-bx-python")
 632     (version "0.7.2")
 633     (source (origin
 634               (method url-fetch)
 635               (uri (string-append
 636                     "https://pypi.python.org/packages/source/b/bx-python/bx-python-"
 637                     version ".tar.gz"))
 638               (sha256
 639                (base32
 640                 "0ld49idhc5zjdvbhvjq1a2qmpjj7h5v58rqr25dzmfq7g34b50xh"))
 641               (modules '((guix build utils)))
 642               (snippet
 643                '(substitute* "setup.py"
 644                   ;; remove dependency on outdated "distribute" module
 645                   (("^from distribute_setup import use_setuptools") "")
 646                   (("^use_setuptools\\(\\)") "")))))
 647     (build-system python-build-system)
 648     (arguments
 649      `(#:tests? #f ;tests fail because test data are not included
 650        #:python ,python-2))
 651     (inputs
 652      `(("python-numpy" ,python2-numpy)
 653        ("zlib" ,zlib)))
 654     (native-inputs
 655      `(("python-nose" ,python2-nose)
 656        ("python-setuptools" ,python2-setuptools)))
 657     (home-page "http://bitbucket.org/james_taylor/bx-python/")
 658     (synopsis "Tools for manipulating biological data")
 659     (description
 660      "bx-python provides tools for manipulating biological data, particularly
 661 multiple sequence alignments.")
 662     (license license:expat)))
 663
 664 (define-public clipper
 665   (package
 666     (name "clipper")
 667     (version "0.3.0")
 668     (source (origin
 669               (method url-fetch)
 670               (uri (string-append
 671                     "https://github.com/YeoLab/clipper/archive/"
 672                     version ".tar.gz"))
 673               (sha256
 674                (base32
 675                 "1q7jpimsqln7ic44i8v2rx2haj5wvik8hc1s2syd31zcn0xk1iyq"))
 676               (modules '((guix build utils)))
 677               (snippet
 678                ;; remove unnecessary setup dependency
 679                '(substitute* "setup.py"
 680                   (("setup_requires = .*") "")))))
 681     (build-system python-build-system)
 682     (arguments `(#:python ,python-2)) ; only Python 2 is supported
 683     (inputs
 684      `(("htseq" ,htseq)
 685        ("python-pybedtools" ,python2-pybedtools)
 686        ("python-cython" ,python2-cython)
 687        ("python-scikit-learn" ,python2-scikit-learn)
 688        ("python-matplotlib" ,python2-matplotlib)
 689        ("python-pysam" ,python2-pysam)
 690        ("python-numpy" ,python2-numpy)
 691        ("python-scipy" ,python2-scipy)))
 692     (native-inputs
 693      `(("python-mock" ,python2-mock) ; for tests
 694        ("python-pytz" ,python2-pytz) ; for tests
 695        ("python-setuptools" ,python2-setuptools)))
 696     (home-page "https://github.com/YeoLab/clipper")
 697     (synopsis "CLIP peak enrichment recognition")
 698     (description
 699      "CLIPper is a tool to define peaks in CLIP-seq datasets.")
 700     (license license:gpl2)))
 701
 702 (define-public couger
 703   (package
 704     (name "couger")
 705     (version "1.8.2")
 706     (source (origin
 707               (method url-fetch)
 708               (uri (string-append
 709                     "http://couger.oit.duke.edu/static/assets/COUGER"
 710                     version ".zip"))
 711               (sha256
 712                (base32
 713                 "04p2b14nmhzxw5h72mpzdhalv21bx4w9b87z0wpw0xzxpysyncmq"))))
 714     (build-system gnu-build-system)
 715     (arguments
 716      `(#:tests? #f
 717        #:phases
 718        (modify-phases %standard-phases
 719          (delete 'configure)
 720          (delete 'build)
 721          (replace
 722           'install
 723           (lambda* (#:key outputs #:allow-other-keys)
 724             (let ((out (assoc-ref outputs "out")))
 725               (copy-recursively "src" (string-append out "/src"))
 726               (mkdir (string-append out "/bin"))
 727               ;; Add "src" directory to module lookup path.
 728               (substitute* "couger"
 729                 (("from argparse")
 730                  (string-append "import sys\nsys.path.append(\""
 731                                 out "\")\nfrom argparse")))
 732               (copy-file "couger" (string-append out "/bin/couger")))
 733             #t))
 734          (add-after
 735           'install 'wrap-program
 736           (lambda* (#:key inputs outputs #:allow-other-keys)
 737             ;; Make sure 'couger' runs with the correct PYTHONPATH.
 738             (let* ((out (assoc-ref outputs "out"))
 739                    (path (getenv "PYTHONPATH")))
 740               (wrap-program (string-append out "/bin/couger")
 741                 `("PYTHONPATH" ":" prefix (,path))))
 742             #t)))))
 743     (inputs
 744      `(("python" ,python-2)
 745        ("python2-pillow" ,python2-pillow)
 746        ("python2-numpy" ,python2-numpy)
 747        ("python2-scipy" ,python2-scipy)
 748        ("python2-matplotlib" ,python2-matplotlib)))
 749     (propagated-inputs
 750      `(("r" ,r)
 751        ("libsvm" ,libsvm)
 752        ("randomjungle" ,randomjungle)))
 753     (native-inputs
 754      `(("unzip" ,unzip)))
 755     (home-page "http://couger.oit.duke.edu")
 756     (synopsis "Identify co-factors in sets of genomic regions")
 757     (description
 758      "COUGER can be applied to any two sets of genomic regions bound by
 759 paralogous TFs (e.g., regions derived from ChIP-seq experiments) to identify
 760 putative co-factors that provide specificity to each TF.  The framework
 761 determines the genomic targets uniquely-bound by each TF, and identifies a
 762 small set of co-factors that best explain the in vivo binding differences
 763 between the two TFs.
 764
 765 COUGER uses classification algorithms (support vector machines and random
 766 forests) with features that reflect the DNA binding specificities of putative
 767 co-factors.  The features are generated either from high-throughput TF-DNA
 768 binding data (from protein binding microarray experiments), or from large
 769 collections of DNA motifs.")
 770     (license license:gpl3+)))
 771
 772 (define-public clustal-omega
 773   (package
 774     (name "clustal-omega")
 775     (version "1.2.1")
 776     (source (origin
 777               (method url-fetch)
 778               (uri (string-append
 779                     "http://www.clustal.org/omega/clustal-omega-"
 780                     version ".tar.gz"))
 781               (sha256
 782                (base32
 783                 "02ibkx0m0iwz8nscg998bh41gg251y56cgh86bvyrii5m8kjgwqf"))))
 784     (build-system gnu-build-system)
 785     (inputs
 786      `(("argtable" ,argtable)))
 787     (home-page "http://www.clustal.org/omega/")
 788     (synopsis "Multiple sequence aligner for protein and DNA/RNA")
 789     (description
 790      "Clustal-Omega is a general purpose multiple sequence alignment (MSA)
 791 program for protein and DNA/RNA.  It produces high quality MSAs and is capable
 792 of handling data-sets of hundreds of thousands of sequences in reasonable
 793 time.")
 794     (license license:gpl2+)))
 795
 796 (define-public crossmap
 797   (package
 798     (name "crossmap")
 799     (version "0.1.6")
 800     (source (origin
 801               (method url-fetch)
 802               (uri (string-append "mirror://sourceforge/crossmap/CrossMap-"
 803                                   version ".tar.gz"))
 804               (sha256
 805                (base32
 806                 "163hi5gjgij6cndxlvbkp5jjwr0k4wbm9im6d2210278q7k9kpnp"))
 807               ;; patch has been sent upstream already
 808               (patches (list
 809                         (search-patch "crossmap-allow-system-pysam.patch")))
 810               (modules '((guix build utils)))
 811               ;; remove bundled copy of pysam
 812               (snippet
 813                '(delete-file-recursively "lib/pysam"))))
 814     (build-system python-build-system)
 815     (arguments
 816      `(#:python ,python-2
 817        #:phases
 818        (alist-cons-after
 819         'unpack 'set-env
 820         (lambda _ (setenv "CROSSMAP_USE_SYSTEM_PYSAM" "1"))
 821         %standard-phases)))
 822     (inputs
 823      `(("python-numpy" ,python2-numpy)
 824        ("python-pysam" ,python2-pysam)
 825        ("zlib" ,zlib)))
 826     (native-inputs
 827      `(("python-cython" ,python2-cython)
 828        ("python-nose" ,python2-nose)
 829        ("python-setuptools" ,python2-setuptools)))
 830     (home-page "http://crossmap.sourceforge.net/")
 831     (synopsis "Convert genome coordinates between assemblies")
 832     (description
 833      "CrossMap is a program for conversion of genome coordinates or annotation
 834 files between different genome assemblies.  It supports most commonly used
 835 file formats including SAM/BAM, Wiggle/BigWig, BED, GFF/GTF, VCF.")
 836     (license license:gpl2+)))
 837
 838 (define-public cutadapt
 839   (package
 840     (name "cutadapt")
 841     (version "1.8")
 842     (source (origin
 843               (method url-fetch)
 844               (uri (string-append
 845                     "https://github.com/marcelm/cutadapt/archive/v"
 846                     version ".tar.gz"))
 847               (file-name (string-append name "-" version ".tar.gz"))
 848               (sha256
 849                (base32
 850                 "161bp87y6gd6r5bmvjpn2b1k942i3fizfpa139f0jn6jv1wcp5h5"))))
 851     (build-system python-build-system)
 852     (arguments
 853      ;; tests must be run after install
 854      `(#:phases (alist-cons-after
 855                  'install 'check
 856                  (lambda* (#:key inputs outputs #:allow-other-keys)
 857                    (setenv "PYTHONPATH"
 858                            (string-append
 859                             (getenv "PYTHONPATH")
 860                             ":" (assoc-ref outputs "out")
 861                             "/lib/python"
 862                             (string-take (string-take-right
 863                                           (assoc-ref inputs "python") 5) 3)
 864                             "/site-packages"))
 865                    (zero? (system* "nosetests" "-P" "tests")))
 866                  (alist-delete 'check %standard-phases))))
 867     (native-inputs
 868      `(("python-cython" ,python-cython)
 869        ("python-nose" ,python-nose)
 870        ("python-setuptools" ,python-setuptools)))
 871     (home-page "https://code.google.com/p/cutadapt/")
 872     (synopsis "Remove adapter sequences from nucleotide sequencing reads")
 873     (description
 874      "Cutadapt finds and removes adapter sequences, primers, poly-A tails and
 875 other types of unwanted sequence from high-throughput sequencing reads.")
 876     (license license:expat)))
 877
 878 (define-public deeptools
 879   (package
 880     (name "deeptools")
 881     (version "1.5.11")
 882     (source (origin
 883               (method url-fetch)
 884               (uri (string-append
 885                     "https://github.com/fidelram/deepTools/archive/"
 886                     version ".tar.gz"))
 887               (file-name (string-append name "-" version ".tar.gz"))
 888               (sha256
 889                (base32
 890                 "1kaagygcbvjs9sxd9cqmskd02wcfp9imvb735r087w7hwqpvz6fs"))))
 891     (build-system python-build-system)
 892     (arguments
 893      `(#:python ,python-2))
 894     (propagated-inputs
 895      `(("python-scipy" ,python2-scipy)
 896        ("python-numpy" ,python2-numpy)
 897        ("python-matplotlib" ,python2-matplotlib)
 898        ("python-bx-python" ,python2-bx-python)
 899        ("python-pysam" ,python2-pysam)))
 900     (native-inputs
 901      `(("python-mock" ,python2-mock) ;for tests
 902        ("python-pytz" ,python2-pytz) ;for tests
 903        ("python-setuptools" ,python2-setuptools)))
 904     (home-page "https://github.com/fidelram/deepTools")
 905     (synopsis "Tools for normalizing and visualizing deep-sequencing data")
 906     (description
 907      "DeepTools addresses the challenge of handling the large amounts of data
 908 that are now routinely generated from DNA sequencing centers.  To do so,
 909 deepTools contains useful modules to process the mapped reads data to create
 910 coverage files in standard bedGraph and bigWig file formats.  By doing so,
 911 deepTools allows the creation of normalized coverage files or the comparison
 912 between two files (for example, treatment and control).  Finally, using such
 913 normalized and standardized files, multiple visualizations can be created to
 914 identify enrichments with functional annotations of the genome.")
 915     (license license:gpl3+)))
 916
 917 (define-public diamond
 918   (package
 919     (name "diamond")
 920     (version "0.7.9")
 921     (source (origin
 922               (method url-fetch)
 923               (uri (string-append
 924                     "https://github.com/bbuchfink/diamond/archive/v"
 925                     version ".tar.gz"))
 926               (file-name (string-append name "-" version ".tar.gz"))
 927               (sha256
 928                (base32
 929                 "0hfkcfv9f76h5brbyw9fyvmc0l9cmbsxrcdqk0fa9xv82zj47p15"))
 930               (snippet '(begin
 931                           (delete-file "bin/diamond")
 932                           #t))))
 933     (build-system gnu-build-system)
 934     (arguments
 935      '(#:tests? #f  ;no "check" target
 936        #:phases
 937        (modify-phases %standard-phases
 938          (add-after 'unpack 'enter-source-dir
 939                     (lambda _
 940                       (chdir "src")
 941                       #t))
 942          (delete 'configure)
 943          (replace 'install
 944                   (lambda* (#:key outputs #:allow-other-keys)
 945                     (let ((bin (string-append (assoc-ref outputs "out")
 946                                               "/bin")))
 947                       (mkdir-p bin)
 948                       (copy-file "../bin/diamond"
 949                                  (string-append bin "/diamond"))
 950                       #t))))))
 951     (native-inputs
 952      `(("bc" ,bc)))
 953     (inputs
 954      `(("boost" ,boost)
 955        ("zlib" ,zlib)))
 956     (home-page "https://github.com/bbuchfink/diamond")
 957     (synopsis "Accelerated BLAST compatible local sequence aligner")
 958     (description
 959      "DIAMOND is a BLAST-compatible local aligner for mapping protein and
 960 translated DNA query sequences against a protein reference database (BLASTP
 961 and BLASTX alignment mode).  The speedup over BLAST is up to 20,000 on short
 962 reads at a typical sensitivity of 90-99% relative to BLAST depending on the
 963 data and settings.")
 964     (license (license:non-copyleft "file://src/COPYING"
 965                                    "See src/COPYING in the distribution."))))
 966
 967 (define-public edirect
 968   (package
 969     (name "edirect")
 970     (version "2.50")
 971     (source (origin
 972               (method url-fetch)
 973               ;; Note: older versions are not retained.
 974               (uri "ftp://ftp.ncbi.nlm.nih.gov/entrez/entrezdirect/edirect.zip")
 975               (sha256
 976                (base32
 977                 "08afhz2ph66h8h381hl1mqyxkdi5nbvzsyj9gfw3jfbdijnpi4qj"))))
 978     (build-system perl-build-system)
 979     (arguments
 980      `(#:tests? #f ;no "check" target
 981        #:phases
 982        (modify-phases %standard-phases
 983          (delete 'configure)
 984          (delete 'build)
 985          (replace 'install
 986                   (lambda* (#:key outputs #:allow-other-keys)
 987                     (let ((target (string-append (assoc-ref outputs "out")
 988                                                  "/bin")))
 989                       (mkdir-p target)
 990                       (copy-file "edirect.pl"
 991                                  (string-append target "/edirect.pl"))
 992                       #t)))
 993          (add-after
 994           'install 'wrap-program
 995           (lambda* (#:key inputs outputs #:allow-other-keys)
 996             ;; Make sure 'edirect.pl' finds all perl inputs at runtime.
 997             (let* ((out (assoc-ref outputs "out"))
 998                    (path (getenv "PERL5LIB")))
 999               (wrap-program (string-append out "/bin/edirect.pl")
1000                 `("PERL5LIB" ":" prefix (,path)))))))))
1001     (inputs
1002      `(("perl-html-parser" ,perl-html-parser)
1003        ("perl-encode-locale" ,perl-encode-locale)
1004        ("perl-file-listing" ,perl-file-listing)
1005        ("perl-html-tagset" ,perl-html-tagset)
1006        ("perl-html-tree" ,perl-html-tree)
1007        ("perl-http-cookies" ,perl-http-cookies)
1008        ("perl-http-date" ,perl-http-date)
1009        ("perl-http-message" ,perl-http-message)
1010        ("perl-http-negotiate" ,perl-http-negotiate)
1011        ("perl-lwp-mediatypes" ,perl-lwp-mediatypes)
1012        ("perl-lwp-protocol-https" ,perl-lwp-protocol-https)
1013        ("perl-net-http" ,perl-net-http)
1014        ("perl-uri" ,perl-uri)
1015        ("perl-www-robotrules" ,perl-www-robotrules)
1016        ("perl" ,perl)))
1017     (native-inputs
1018      `(("unzip" ,unzip)))
1019     (home-page "http://www.ncbi.nlm.nih.gov/books/NBK179288")
1020     (synopsis "Tools for accessing the NCBI's set of databases")
1021     (description
1022      "Entrez Direct (EDirect) is a method for accessing the National Center
1023 for Biotechnology Information's (NCBI) set of interconnected
1024 databases (publication, sequence, structure, gene, variation, expression,
1025 etc.) from a terminal.  Functions take search terms from command-line
1026 arguments.  Individual operations are combined to build multi-step queries.
1027 Record retrieval and formatting normally complete the process.
1028
1029 EDirect also provides an argument-driven function that simplifies the
1030 extraction of data from document summaries or other results that are returned
1031 in structured XML format.  This can eliminate the need for writing custom
1032 software to answer ad hoc questions.")
1033     (license license:public-domain)))
1034
1035 (define-public express
1036   (package
1037     (name "express")
1038     (version "1.5.1")
1039     (source (origin
1040               (method url-fetch)
1041               (uri
1042                (string-append
1043                 "http://bio.math.berkeley.edu/eXpress/downloads/express-"
1044                 version "/express-" version "-src.tgz"))
1045               (sha256
1046                (base32
1047                 "03rczxd0gjp2l1jxcmjfmf5j94j77zqyxa6x063zsc585nj40n0c"))))
1048     (build-system cmake-build-system)
1049     (arguments
1050      `(#:tests? #f ;no "check" target
1051        #:phases
1052        (alist-cons-after
1053         'unpack 'use-shared-boost-libs-and-set-bamtools-paths
1054         (lambda* (#:key inputs #:allow-other-keys)
1055           (substitute* "CMakeLists.txt"
1056             (("set\\(Boost_USE_STATIC_LIBS ON\\)")
1057              "set(Boost_USE_STATIC_LIBS OFF)")
1058             (("\\$\\{CMAKE_CURRENT_SOURCE_DIR\\}/bamtools/include")
1059              (string-append (assoc-ref inputs "bamtools") "/include/bamtools")))
1060           (substitute* "src/CMakeLists.txt"
1061             (("\\$\\{CMAKE_CURRENT_SOURCE_DIR\\}/\\.\\./bamtools/lib")
1062              (string-append (assoc-ref inputs "bamtools") "/lib/bamtools")))
1063           #t)
1064         %standard-phases)))
1065     (inputs
1066      `(("boost" ,boost)
1067        ("bamtools" ,bamtools)
1068        ("protobuf" ,protobuf)
1069        ("zlib" ,zlib)))
1070     (home-page "http://bio.math.berkeley.edu/eXpress")
1071     (synopsis "Streaming quantification for high-throughput genomic sequencing")
1072     (description
1073      "eXpress is a streaming tool for quantifying the abundances of a set of
1074 target sequences from sampled subsequences.  Example applications include
1075 transcript-level RNA-Seq quantification, allele-specific/haplotype expression
1076 analysis (from RNA-Seq), transcription factor binding quantification in
1077 ChIP-Seq, and analysis of metagenomic data.")
1078     (license license:artistic2.0)))
1079
1080 (define-public fasttree
1081   (package
1082    (name "fasttree")
1083    (version "2.1.8")
1084    (source (origin
1085              (method url-fetch)
1086              (uri (string-append
1087                    "http://www.microbesonline.org/fasttree/FastTree-"
1088                    version ".c"))
1089              (sha256
1090               (base32
1091                "0dzqc9vr9iiiw21y159xfjl2z90vw0y7r4x6456pcaxiy5hd2wmi"))))
1092    (build-system gnu-build-system)
1093    (arguments
1094     `(#:tests? #f ; no "check" target
1095       #:phases
1096       (modify-phases %standard-phases
1097         (delete 'unpack)
1098         (delete 'configure)
1099         (replace 'build
1100                  (lambda* (#:key source #:allow-other-keys)
1101                    (and (zero? (system* "gcc"
1102                                         "-O3"
1103                                         "-finline-functions"
1104                                         "-funroll-loops"
1105                                         "-Wall"
1106                                         "-o"
1107                                         "FastTree"
1108                                         source
1109                                         "-lm"))
1110                         (zero? (system* "gcc"
1111                                         "-DOPENMP"
1112                                         "-fopenmp"
1113                                         "-O3"
1114                                         "-finline-functions"
1115                                         "-funroll-loops"
1116                                         "-Wall"
1117                                         "-o"
1118                                         "FastTreeMP"
1119                                         source
1120                                         "-lm")))))
1121         (replace 'install
1122                  (lambda* (#:key outputs #:allow-other-keys)
1123                    (let ((bin (string-append (assoc-ref outputs "out")
1124                                              "/bin")))
1125                      (mkdir-p bin)
1126                      (copy-file "FastTree"
1127                                 (string-append bin "/FastTree"))
1128                      (copy-file "FastTreeMP"
1129                                 (string-append bin "/FastTreeMP"))
1130                      #t))))))
1131    (home-page "http://www.microbesonline.org/fasttree")
1132    (synopsis "Infers approximately-maximum-likelihood phylogenetic trees")
1133    (description
1134     "FastTree can handle alignments with up to a million of sequences in a
1135 reasonable amount of time and memory.  For large alignments, FastTree is
1136 100-1,000 times faster than PhyML 3.0 or RAxML 7.")
1137    (license license:gpl2+)))
1138
1139 (define-public fastx-toolkit
1140   (package
1141     (name "fastx-toolkit")
1142     (version "0.0.14")
1143     (source (origin
1144               (method url-fetch)
1145               (uri
1146                (string-append
1147                 "https://github.com/agordon/fastx_toolkit/releases/download/"
1148                 version "/fastx_toolkit-" version ".tar.bz2"))
1149               (sha256
1150                (base32
1151                 "01jqzw386873sr0pjp1wr4rn8fsga2vxs1qfmicvx1pjr72007wy"))))
1152     (build-system gnu-build-system)
1153     (inputs
1154      `(("libgtextutils" ,libgtextutils)))
1155     (native-inputs
1156      `(("pkg-config" ,pkg-config)))
1157     (home-page "http://hannonlab.cshl.edu/fastx_toolkit/")
1158     (synopsis "Tools for FASTA/FASTQ file preprocessing")
1159     (description
1160      "The FASTX-Toolkit is a collection of command line tools for Short-Reads
1161 FASTA/FASTQ files preprocessing.
1162
1163 Next-Generation sequencing machines usually produce FASTA or FASTQ files,
1164 containing multiple short-reads sequences.  The main processing of such
1165 FASTA/FASTQ files is mapping the sequences to reference genomes.  However, it
1166 is sometimes more productive to preprocess the files before mapping the
1167 sequences to the genome---manipulating the sequences to produce better mapping
1168 results.  The FASTX-Toolkit tools perform some of these preprocessing tasks.")
1169     (license license:agpl3+)))
1170
1171 (define-public flexbar
1172   (package
1173     (name "flexbar")
1174     (version "2.5")
1175     (source (origin
1176               (method url-fetch)
1177               (uri
1178                (string-append "mirror://sourceforge/flexbar/"
1179                               version "/flexbar_v" version "_src.tgz"))
1180               (sha256
1181                (base32
1182                 "13jaykc3y1x8y5nn9j8ljnb79s5y51kyxz46hdmvvjj6qhyympmf"))))
1183     (build-system cmake-build-system)
1184     (arguments
1185      `(#:configure-flags (list
1186                           (string-append "-DFLEXBAR_BINARY_DIR="
1187                                          (assoc-ref %outputs "out")
1188                                          "/bin/"))
1189        #:phases
1190        (alist-replace
1191         'check
1192         (lambda* (#:key outputs #:allow-other-keys)
1193           (setenv "PATH" (string-append
1194                           (assoc-ref outputs "out") "/bin:"
1195                           (getenv "PATH")))
1196           (chdir "../flexbar_v2.5_src/test")
1197           (zero? (system* "bash" "flexbar_validate.sh")))
1198         (alist-delete 'install %standard-phases))))
1199     (inputs
1200      `(("tbb" ,tbb)
1201        ("zlib" ,zlib)))
1202     (native-inputs
1203      `(("pkg-config" ,pkg-config)
1204        ("seqan" ,seqan)))
1205     (home-page "http://flexbar.sourceforge.net")
1206     (synopsis "Barcode and adapter removal tool for sequencing platforms")
1207     (description
1208      "Flexbar preprocesses high-throughput nucleotide sequencing data
1209 efficiently.  It demultiplexes barcoded runs and removes adapter sequences.
1210 Moreover, trimming and filtering features are provided.  Flexbar increases
1211 read mapping rates and improves genome and transcriptome assemblies.  It
1212 supports next-generation sequencing data in fasta/q and csfasta/q format from
1213 Illumina, Roche 454, and the SOLiD platform.")
1214     (license license:gpl3)))
1215
1216 (define-public grit
1217   (package
1218     (name "grit")
1219     (version "2.0.2")
1220     (source (origin
1221               (method url-fetch)
1222               (uri (string-append
1223                     "https://github.com/nboley/grit/archive/"
1224                     version ".tar.gz"))
1225               (file-name (string-append name "-" version ".tar.gz"))
1226               (sha256
1227                (base32
1228                 "157in84dj70wimbind3x7sy1whs3h57qfgcnj2s6lrd38fbrb7mj"))))
1229     (build-system python-build-system)
1230     (arguments
1231      `(#:python ,python-2
1232        #:phases
1233        (alist-cons-after
1234         'unpack 'generate-from-cython-sources
1235         (lambda* (#:key inputs outputs #:allow-other-keys)
1236           ;; Delete these C files to force fresh generation from pyx sources.
1237           (delete-file "grit/sparsify_support_fns.c")
1238           (delete-file "grit/call_peaks_support_fns.c")
1239           (substitute* "setup.py"
1240             (("Cython.Setup") "Cython.Build")
1241             ;; Add numpy include path to fix compilation
1242             (("pyx\", \\]")
1243              (string-append "pyx\", ], include_dirs = ['"
1244                             (assoc-ref inputs "python-numpy")
1245                             "/lib/python2.7/site-packages/numpy/core/include/"
1246                             "']"))) #t)
1247         %standard-phases)))
1248     (inputs
1249      `(("python-scipy" ,python2-scipy)
1250        ("python-numpy" ,python2-numpy)
1251        ("python-pysam" ,python2-pysam)
1252        ("python-networkx" ,python2-networkx)))
1253     (native-inputs
1254      `(("python-cython" ,python2-cython)
1255        ("python-setuptools" ,python2-setuptools)))
1256     (home-page "http://grit-bio.org")
1257     (synopsis "Tool for integrative analysis of RNA-seq type assays")
1258     (description
1259      "GRIT is designed to use RNA-seq, TES, and TSS data to build and quantify
1260 full length transcript models.  When none of these data sources are available,
1261 GRIT can be run by providing a candidate set of TES or TSS sites.  In
1262 addition, GRIT can merge in reference junctions and gene boundaries.  GRIT can
1263 also be run in quantification mode, where it uses a provided GTF file and just
1264 estimates transcript expression.")
1265     (license license:gpl3+)))
1266
1267 (define-public hisat
1268   (package
1269     (name "hisat")
1270     (version "0.1.4")
1271     (source (origin
1272               (method url-fetch)
1273               (uri (string-append
1274                     "http://ccb.jhu.edu/software/hisat/downloads/hisat-"
1275                     version "-beta-source.zip"))
1276               (sha256
1277                (base32
1278                 "1k381ydranqxp09yf2y7w1d0chz5d59vb6jchi89hbb0prq19lk5"))))
1279     (build-system gnu-build-system)
1280     (arguments
1281      `(#:tests? #f ;no check target
1282        #:make-flags '("allall"
1283                       ;; Disable unsupported `popcnt' instructions on
1284                       ;; architectures other than x86_64
1285                       ,@(if (string-prefix? "x86_64"
1286                                             (or (%current-target-system)
1287                                                 (%current-system)))
1288                             '()
1289                             '("POPCNT_CAPABILITY=0")))
1290        #:phases
1291        (alist-cons-after
1292         'unpack 'patch-sources
1293         (lambda _
1294           ;; XXX Cannot use snippet because zip files are not supported
1295           (substitute* "Makefile"
1296             (("^CC = .*$") "CC = gcc")
1297             (("^CPP = .*$") "CPP = g++")
1298             ;; replace BUILD_HOST and BUILD_TIME for deterministic build
1299             (("-DBUILD_HOST=.*") "-DBUILD_HOST=\"\\\"guix\\\"\"")
1300             (("-DBUILD_TIME=.*") "-DBUILD_TIME=\"\\\"0\\\"\""))
1301           (substitute* '("hisat-build" "hisat-inspect")
1302             (("/usr/bin/env") (which "env"))))
1303         (alist-replace
1304          'install
1305          (lambda* (#:key outputs #:allow-other-keys)
1306            (let ((bin (string-append (assoc-ref outputs "out") "/bin/")))
1307              (mkdir-p bin)
1308              (for-each
1309               (lambda (file)
1310                 (copy-file file (string-append bin file)))
1311               (find-files
1312                "."
1313                "hisat(-(build|align|inspect)(-(s|l)(-debug)*)*)*$"))))
1314          (alist-delete 'configure %standard-phases)))))
1315     (native-inputs
1316      `(("unzip" ,unzip)))
1317     (inputs
1318      `(("perl" ,perl)
1319        ("python" ,python)
1320        ("zlib" ,zlib)))
1321     (home-page "http://ccb.jhu.edu/software/hisat/index.shtml")
1322     (synopsis "Hierarchical indexing for spliced alignment of transcripts")
1323     (description
1324      "HISAT is a fast and sensitive spliced alignment program for mapping
1325 RNA-seq reads.  In addition to one global FM index that represents a whole
1326 genome, HISAT uses a large set of small FM indexes that collectively cover the
1327 whole genome.  These small indexes (called local indexes) combined with
1328 several alignment strategies enable effective alignment of RNA-seq reads, in
1329 particular, reads spanning multiple exons.")
1330     (license license:gpl3+)))
1331
1332 (define-public hmmer
1333   (package
1334     (name "hmmer")
1335     (version "3.1b2")
1336     (source (origin
1337               (method url-fetch)
1338               (uri (string-append
1339                     "http://selab.janelia.org/software/hmmer"
1340                     (version-prefix version 1) "/"
1341                     version "/hmmer-" version ".tar.gz"))
1342               (sha256
1343                (base32
1344                 "0djmgc0pfli0jilfx8hql1axhwhqxqb8rxg2r5rg07aw73sfs5nx"))))
1345     (build-system gnu-build-system)
1346     (native-inputs `(("perl", perl)))
1347     (home-page "http://hmmer.janelia.org")
1348     (synopsis "Biosequence analysis using profile hidden Markov models")
1349     (description
1350      "HMMER is used for searching sequence databases for homologs of protein
1351 sequences, and for making protein sequence alignments.  It implements methods
1352 using probabilistic models called profile hidden Markov models (profile
1353 HMMs).")
1354     (license (list license:gpl3+
1355                    ;; The bundled library 'easel' is distributed
1356                    ;; under The Janelia Farm Software License.
1357                    (license:non-copyleft
1358                     "file://easel/LICENSE"
1359                     "See easel/LICENSE in the distribution.")))))
1360
1361 (define-public htseq
1362   (package
1363     (name "htseq")
1364     (version "0.6.1")
1365     (source (origin
1366               (method url-fetch)
1367               (uri (string-append
1368                     "https://pypi.python.org/packages/source/H/HTSeq/HTSeq-"
1369                     version ".tar.gz"))
1370               (sha256
1371                (base32
1372                 "1i85ppf2j2lj12m0x690qq5nn17xxk23pbbx2c83r8ayb5wngzwv"))))
1373     (build-system python-build-system)
1374     (arguments `(#:python ,python-2)) ; only Python 2 is supported
1375     (inputs
1376      `(("python-numpy" ,python2-numpy)
1377        ("python-setuptools" ,python2-setuptools)))
1378     (home-page "http://www-huber.embl.de/users/anders/HTSeq/")
1379     (synopsis "Analysing high-throughput sequencing data with Python")
1380     (description
1381      "HTSeq is a Python package that provides infrastructure to process data
1382 from high-throughput sequencing assays.")
1383     (license license:gpl3+)))
1384
1385 (define-public htsjdk
1386   (package
1387     (name "htsjdk")
1388     (version "1.129")
1389     (source (origin
1390               (method url-fetch)
1391               (uri (string-append
1392                     "https://github.com/samtools/htsjdk/archive/"
1393                     version ".tar.gz"))
1394               (file-name (string-append name "-" version ".tar.gz"))
1395               (sha256
1396                (base32
1397                 "0asdk9b8jx2ij7yd6apg9qx03li8q7z3ml0qy2r2qczkra79y6fw"))
1398               (modules '((guix build utils)))
1399               ;; remove build dependency on git
1400               (snippet '(substitute* "build.xml"
1401                           (("failifexecutionfails=\"true\"")
1402                            "failifexecutionfails=\"false\"")))))
1403     (build-system gnu-build-system)
1404     (arguments
1405      `(#:modules ((srfi srfi-1)
1406                   (guix build gnu-build-system)
1407                   (guix build utils))
1408        #:phases (alist-replace
1409                  'build
1410                  (lambda _
1411                    (setenv "JAVA_HOME" (assoc-ref %build-inputs "jdk"))
1412                    (zero? (system* "ant" "all"
1413                                    (string-append "-Ddist="
1414                                                   (assoc-ref %outputs "out")
1415                                                   "/share/java/htsjdk/"))))
1416                  (fold alist-delete %standard-phases
1417                        '(configure install check)))))
1418     (native-inputs
1419      `(("ant" ,ant)
1420        ("jdk" ,icedtea6 "jdk")))
1421     (home-page "http://samtools.github.io/htsjdk/")
1422     (synopsis "Java API for high-throughput sequencing data (HTS) formats")
1423     (description
1424      "HTSJDK is an implementation of a unified Java library for accessing
1425 common file formats, such as SAM and VCF, used for high-throughput
1426 sequencing (HTS) data.  There are also an number of useful utilities for
1427 manipulating HTS data.")
1428     (license license:expat)))
1429
1430 (define-public htslib
1431   (package
1432     (name "htslib")
1433     (version "1.2.1")
1434     (source (origin
1435               (method url-fetch)
1436               (uri (string-append
1437                     "https://github.com/samtools/htslib/releases/download/"
1438                     version "/htslib-" version ".tar.bz2"))
1439               (sha256
1440                (base32
1441                 "1c32ssscbnjwfw3dra140fq7riarp2x990qxybh34nr1p5r17nxx"))))
1442     (build-system gnu-build-system)
1443     (arguments
1444      `(#:phases
1445        (modify-phases %standard-phases
1446          (add-after
1447           'unpack 'patch-tests
1448           (lambda _
1449             (substitute* "test/test.pl"
1450               (("/bin/bash") (which "bash")))
1451             #t)))))
1452     (inputs
1453      `(("zlib" ,zlib)))
1454     (native-inputs
1455      `(("perl" ,perl)))
1456     (home-page "http://www.htslib.org")
1457     (synopsis "C library for reading/writing high-throughput sequencing data")
1458     (description
1459      "HTSlib is a C library for reading/writing high-throughput sequencing
1460 data.  It also provides the bgzip, htsfile, and tabix utilities.")
1461     ;; Files under cram/ are released under the modified BSD license;
1462     ;; the rest is released under the Expat license
1463     (license (list license:expat license:bsd-3))))
1464
1465 (define-public idr
1466   (package
1467     (name "idr")
1468     (version "2.0.0")
1469     (source (origin
1470               (method url-fetch)
1471               (uri (string-append
1472                     "https://github.com/nboley/idr/archive/"
1473                     version ".tar.gz"))
1474               (file-name (string-append name "-" version ".tar.gz"))
1475               (sha256
1476                (base32
1477                 "1k3x44biak00aiv3hpm1yd6nn4hhp7n0qnbs3zh2q9sw7qr1qj5r"))))
1478     (build-system python-build-system)
1479     (arguments
1480      `(#:phases
1481        (modify-phases %standard-phases
1482          (add-after
1483           'install 'wrap-program
1484           (lambda* (#:key inputs outputs #:allow-other-keys)
1485             (let* ((out (assoc-ref outputs "out"))
1486                    (python-version (string-take (string-take-right
1487                                                  (assoc-ref inputs "python") 5) 3))
1488                    (path (string-join
1489                           (map (lambda (name)
1490                                  (string-append (assoc-ref inputs name)
1491                                                 "/lib/python" python-version
1492                                                 "/site-packages"))
1493                                '("python-scipy"
1494                                  "python-numpy"
1495                                  "python-matplotlib"))
1496                           ":")))
1497               (wrap-program (string-append out "/bin/idr")
1498                 `("PYTHONPATH" ":" prefix (,path))))
1499             #t)))))
1500     (inputs
1501      `(("python-scipy" ,python-scipy)
1502        ("python-numpy" ,python-numpy)
1503        ("python-matplotlib" ,python-matplotlib)))
1504     (native-inputs
1505      `(("python-cython" ,python-cython)
1506        ("python-setuptools" ,python-setuptools)))
1507     (home-page "https://github.com/nboley/idr")
1508     (synopsis "Tool to measure the irreproducible discovery rate (IDR)")
1509     (description
1510      "The IDR (Irreproducible Discovery Rate) framework is a unified approach
1511 to measure the reproducibility of findings identified from replicate
1512 experiments and provide highly stable thresholds based on reproducibility.")
1513     (license license:gpl3+)))
1514
1515 (define-public macs
1516   (package
1517     (name "macs")
1518     (version "2.1.0.20140616")
1519     (source (origin
1520               (method url-fetch)
1521               (uri (string-append
1522                     "https://pypi.python.org/packages/source/M/MACS2/MACS2-"
1523                     version ".tar.gz"))
1524               (sha256
1525                (base32
1526                 "11lmiw6avqhwn75sn59g4lfkrr2kk20r3rgfbx9xfqb8rg9mi2n6"))))
1527     (build-system python-build-system)
1528     (arguments
1529      `(#:python ,python-2 ; only compatible with Python 2.7
1530        #:tests? #f)) ; no test target
1531     (inputs
1532      `(("python-numpy" ,python2-numpy)))
1533     (native-inputs
1534      `(("python-setuptools" ,python2-setuptools)))
1535     (home-page "http://github.com/taoliu/MACS/")
1536     (synopsis "Model based analysis for ChIP-Seq data")
1537     (description
1538      "MACS is an implementation of a ChIP-Seq analysis algorithm for
1539 identifying transcript factor binding sites named Model-based Analysis of
1540 ChIP-Seq (MACS).  MACS captures the influence of genome complexity to evaluate
1541 the significance of enriched ChIP regions and it improves the spatial
1542 resolution of binding sites through combining the information of both
1543 sequencing tag position and orientation.")
1544     (license license:bsd-3)))
1545
1546
1547 (define-public metabat
1548   (package
1549     (name "metabat")
1550     (version "0.26.1")
1551     (source (origin
1552               (method url-fetch)
1553               (uri (string-append
1554                     "https://bitbucket.org/berkeleylab/metabat/get/"
1555                     version ".tar.bz2"))
1556               (file-name (string-append name "-" version ".tar.bz2"))
1557               (sha256
1558                (base32
1559                 "0vgrhbaxg4dkxyax2kbigak7w0arhqvw0szwp6gd9wmyilc44kfa"))))
1560     (build-system gnu-build-system)
1561     (arguments
1562      `(#:phases
1563        (modify-phases %standard-phases
1564          (add-after 'unpack 'fix-includes
1565                     (lambda _
1566                       (substitute* "SConstruct"
1567                         (("/include/bam/bam.h")
1568                          "/include/samtools/bam.h"))
1569                       (substitute* "src/BamUtils.h"
1570                         (("^#include \"bam/bam\\.h\"")
1571                          "#include \"samtools/bam.h\"")
1572                         (("^#include \"bam/sam\\.h\"")
1573                          "#include \"samtools/sam.h\""))
1574                       (substitute* "src/KseqReader.h"
1575                         (("^#include \"bam/kseq\\.h\"")
1576                          "#include \"samtools/kseq.h\""))
1577                       #t))
1578          (add-after 'unpack 'fix-scons
1579                     (lambda _
1580                       (substitute* "SConstruct" ; Do not distribute README
1581                         (("^env\\.Install\\(idir_prefix, 'README\\.md'\\)")
1582                          ""))
1583                       #t))
1584          (delete 'configure)
1585          (replace 'build
1586                   (lambda* (#:key inputs outputs #:allow-other-keys)
1587                     (mkdir (assoc-ref outputs "out"))
1588                     (zero? (system* "scons"
1589                                     (string-append
1590                                      "PREFIX="
1591                                      (assoc-ref outputs "out"))
1592                                     (string-append
1593                                      "HTSLIB_DIR="
1594                                      (assoc-ref inputs "htslib"))
1595                                     (string-append
1596                                      "SAMTOOLS_DIR="
1597                                      (assoc-ref inputs "samtools"))
1598                                     (string-append
1599                                      "BOOST_ROOT="
1600                                      (assoc-ref inputs "boost"))
1601                                     "install"))))
1602          ;; check and install carried out during build phase
1603          (delete 'check)
1604          (delete 'install))))
1605     (inputs
1606      `(("zlib" ,zlib)
1607        ("perl" ,perl)
1608        ("samtools" ,samtools)
1609        ("htslib" ,htslib)
1610        ("boost" ,boost)))
1611     (native-inputs
1612      `(("scons" ,scons)))
1613     (home-page "https://bitbucket.org/berkeleylab/metabat")
1614     (synopsis
1615      "Reconstruction of single genomes from complex microbial communities")
1616     (description
1617      "Grouping large genomic fragments assembled from shotgun metagenomic
1618 sequences to deconvolute complex microbial communities, or metagenome binning,
1619 enables the study of individual organisms and their interactions.  MetaBAT is
1620 an automated metagenome binning software, which integrates empirical
1621 probabilistic distances of genome abundance and tetranucleotide frequency.")
1622    (license (license:non-copyleft "file://license.txt"
1623                                   "See license.txt in the distribution."))))
1624
1625 (define-public miso
1626   (package
1627     (name "miso")
1628     (version "0.5.3")
1629     (source (origin
1630               (method url-fetch)
1631               (uri (string-append
1632                     "https://pypi.python.org/packages/source/m/misopy/misopy-"
1633                     version ".tar.gz"))
1634               (sha256
1635                (base32
1636                 "0x446867az8ir0z8c1vjqffkp0ma37wm4sylixnkhgawllzx8v5w"))
1637               (modules '((guix build utils)))
1638               (snippet
1639                '(substitute* "setup.py"
1640                   ;; Use setuptools, or else the executables are not
1641                   ;; installed.
1642                   (("distutils.core") "setuptools")
1643                   ;; use "gcc" instead of "cc" for compilation
1644                   (("^defines")
1645                    "cc.set_executables(
1646 compiler='gcc',
1647 compiler_so='gcc',
1648 linker_exe='gcc',
1649 linker_so='gcc -shared'); defines")))))
1650     (build-system python-build-system)
1651     (arguments
1652      `(#:python ,python-2 ; only Python 2 is supported
1653        #:tests? #f)) ; no "test" target
1654     (inputs
1655      `(("samtools" ,samtools)
1656        ("python-numpy" ,python2-numpy)
1657        ("python-pysam" ,python2-pysam)
1658        ("python-scipy" ,python2-scipy)
1659        ("python-matplotlib" ,python2-matplotlib)))
1660     (native-inputs
1661      `(("python-mock" ,python2-mock) ;for tests
1662        ("python-pytz" ,python2-pytz) ;for tests
1663        ("python-setuptools" ,python2-setuptools)))
1664     (home-page "http://genes.mit.edu/burgelab/miso/index.html")
1665     (synopsis "Mixture of Isoforms model for RNA-Seq isoform quantitation")
1666     (description
1667      "MISO (Mixture-of-Isoforms) is a probabilistic framework that quantitates
1668 the expression level of alternatively spliced genes from RNA-Seq data, and
1669 identifies differentially regulated isoforms or exons across samples.  By
1670 modeling the generative process by which reads are produced from isoforms in
1671 RNA-Seq, the MISO model uses Bayesian inference to compute the probability
1672 that a read originated from a particular isoform.")
1673     (license license:gpl2)))
1674
1675 (define-public orfm
1676   (package
1677     (name "orfm")
1678     (version "0.4.1")
1679     (source (origin
1680               (method url-fetch)
1681               (uri (string-append
1682                     "https://github.com/wwood/OrfM/releases/download/v"
1683                     version "/orfm-" version ".tar.gz"))
1684               (sha256
1685                (base32
1686                 "05fmw145snk646ly076zby0fjav0k7ysbclck5d4s9pmgcfpijc2"))))
1687     (build-system gnu-build-system)
1688     (inputs `(("zlib" ,zlib)))
1689     (synopsis "Simple and not slow open reading frame (ORF) caller")
1690     (description
1691      "An ORF caller finds stretches of DNA that when translated are not
1692 interrupted by stop codons.  OrfM finds and prints these ORFs.")
1693     (home-page "https://github.com/wwood/OrfM")
1694     (license license:lgpl3+)))
1695
1696 (define-public python2-pbcore
1697   (package
1698     (name "python2-pbcore")
1699     (version "0.9.3")
1700     (source (origin
1701               (method url-fetch)
1702               (uri (string-append
1703                     "https://github.com/PacificBiosciences/pbcore/archive/"
1704                     version ".tar.gz"))
1705               (file-name (string-append name "-" version ".tar.gz"))
1706               (sha256
1707                (base32
1708                 "1z46rwjac93jm87cbj2zgjg6qvsgs65140wkbbxsvxps7ai4pm09"))))
1709     (build-system python-build-system)
1710     (arguments `(#:python ,python-2)) ; pbcore requires Python 2.7
1711     (inputs
1712      `(("python-cython" ,python2-cython)
1713        ("python-numpy" ,python2-numpy)
1714        ("python-pysam" ,python2-pysam)
1715        ("python-h5py" ,python2-h5py)))
1716     (native-inputs
1717      `(("python-setuptools" ,python2-setuptools)))
1718     (home-page "http://pacificbiosciences.github.io/pbcore/")
1719     (synopsis "Library for reading and writing PacBio data files")
1720     (description
1721      "The pbcore package provides Python APIs for interacting with PacBio data
1722 files and writing bioinformatics applications.")
1723     (license license:bsd-3)))
1724
1725 (define-public python2-warpedlmm
1726   (package
1727     (name "python2-warpedlmm")
1728     (version "0.21")
1729     (source
1730      (origin
1731        (method url-fetch)
1732        (uri (string-append
1733              "https://pypi.python.org/packages/source/W/WarpedLMM/WarpedLMM-"
1734              version ".zip"))
1735        (sha256
1736         (base32
1737          "1agfz6zqa8nc6cw47yh0s3y14gkpa9wqazwcj7mwwj3ffnw39p3j"))))
1738     (build-system python-build-system)
1739     (arguments
1740      `(#:python ,python-2  ; requires Python 2.7
1741        #:phases
1742        (modify-phases %standard-phases
1743          (add-after
1744           'install 'remove-bin-directory
1745           (lambda* (#:key outputs #:allow-other-keys)
1746             ;; The "bin" directory only contains wrappers for running
1747             ;; the module tests.  They are not needed after the
1748             ;; "check" phase.
1749             (delete-file-recursively
1750              (string-append (assoc-ref outputs "out") "/bin"))
1751             #t)))))
1752     (propagated-inputs
1753      `(("python-scipy" ,python2-scipy)
1754        ("python-numpy" ,python2-numpy)
1755        ("python-matplotlib" ,python2-matplotlib)
1756        ("python-fastlmm" ,python2-fastlmm)
1757        ("python-pandas" ,python2-pandas)
1758        ("python-pysnptools" ,python2-pysnptools)))
1759     (native-inputs
1760      `(("python-setuptools" ,python2-setuptools)
1761        ("python-mock" ,python2-mock)
1762        ("python-nose" ,python2-nose)
1763        ("unzip" ,unzip)))
1764     (home-page "https://github.com/PMBio/warpedLMM")
1765     (synopsis "Implementation of warped linear mixed models")
1766     (description
1767      "WarpedLMM is a Python implementation of the warped linear mixed model,
1768 which automatically learns an optimal warping function (or transformation) for
1769 the phenotype as it models the data.")
1770     (license license:asl2.0)))
1771
1772 (define-public pbtranscript-tofu
1773   (let ((commit "c7bbd5472"))
1774     (package
1775       (name "pbtranscript-tofu")
1776       (version (string-append "0.4.1." commit))
1777       (source (origin
1778                 (method git-fetch)
1779                 (uri (git-reference
1780                       (url "https://github.com/PacificBiosciences/cDNA_primer.git")
1781                       (commit commit)))
1782                 (file-name (string-append name "-" version ".tar.gz"))
1783                 (sha256
1784                  (base32
1785                   "148xkzi689c49g6fdhckp6mnmj2qhjdf1j4wifm6ja7ij95d7fxx"))))
1786       (build-system python-build-system)
1787       (arguments
1788        `(#:python ,python-2
1789          ;; With standard flags, the install phase attempts to create a zip'd
1790          ;; egg file, and fails with an error: 'ZIP does not support timestamps
1791          ;; before 1980'
1792          #:configure-flags '("--single-version-externally-managed"
1793                              "--record=pbtranscript-tofu.txt")
1794          #:phases
1795          (alist-cons-after
1796           'unpack 'enter-directory-and-clean-up
1797           (lambda _
1798             (chdir "pbtranscript-tofu/pbtranscript/")
1799             ;; Delete clutter
1800             (delete-file-recursively "dist/")
1801             (delete-file-recursively "build/")
1802             (delete-file-recursively "setuptools_cython-0.2.1-py2.6.egg/")
1803             (delete-file-recursively "pbtools.pbtranscript.egg-info")
1804             (delete-file "Cython-0.20.1.tar.gz")
1805             (delete-file "setuptools_cython-0.2.1-py2.7.egg")
1806             (delete-file "setuptools_cython-0.2.1.tar.gz")
1807             (delete-file "setup.cfg")
1808             (for-each delete-file
1809                       (find-files "." "\\.so$"))
1810             ;; files should be writable for install phase
1811             (for-each (lambda (f) (chmod f #o755))
1812                       (find-files "." "\\.py$")))
1813           %standard-phases)))
1814       (inputs
1815        `(("python-cython" ,python2-cython)
1816          ("python-numpy" ,python2-numpy)
1817          ("python-bx-python" ,python2-bx-python)
1818          ("python-networkx" ,python2-networkx)
1819          ("python-scipy" ,python2-scipy)
1820          ("python-pbcore" ,python2-pbcore)))
1821       (native-inputs
1822        `(("python-nose" ,python2-nose)
1823          ("python-setuptools" ,python2-setuptools)))
1824       (home-page "https://github.com/PacificBiosciences/cDNA_primer")
1825       (synopsis "Analyze transcriptome data generated with the Iso-Seq protocol")
1826       (description
1827        "pbtranscript-tofu contains scripts to analyze transcriptome data
1828 generated using the PacBio Iso-Seq protocol.")
1829       (license license:bsd-3))))
1830
1831 (define-public prodigal
1832   (package
1833     (name "prodigal")
1834     (version "2.6.2")
1835     (source (origin
1836               (method url-fetch)
1837               (uri (string-append
1838                     "https://github.com/hyattpd/Prodigal/archive/v"
1839                     version ".tar.gz"))
1840               (file-name (string-append name "-" version ".tar.gz"))
1841               (sha256
1842                (base32
1843                 "0m8sb0fg6lmxrlpzna0am6svbnlmd3dckrhgzxxgb3gxr5fyj284"))))
1844     (build-system gnu-build-system)
1845     (arguments
1846      `(#:tests? #f ;no check target
1847        #:make-flags (list (string-append "INSTALLDIR="
1848                                          (assoc-ref %outputs "out")
1849                                          "/bin"))
1850        #:phases
1851        (modify-phases %standard-phases
1852          (delete 'configure))))
1853     (home-page "http://prodigal.ornl.gov")
1854     (synopsis "Protein-coding gene prediction for Archaea and Bacteria")
1855     (description
1856      "Prodigal runs smoothly on finished genomes, draft genomes, and
1857 metagenomes, providing gene predictions in GFF3, Genbank, or Sequin table
1858 format.  It runs quickly, in an unsupervised fashion, handles gaps, handles
1859 partial genes, and identifies translation initiation sites.")
1860     (license license:gpl3+)))
1861
1862 (define-public rsem
1863   (package
1864     (name "rsem")
1865     (version "1.2.20")
1866     (source
1867      (origin
1868        (method url-fetch)
1869        (uri
1870         (string-append "http://deweylab.biostat.wisc.edu/rsem/src/rsem-"
1871                        version ".tar.gz"))
1872        (sha256
1873         (base32 "0nzdc0j0hjllhsd5f2xli95dafm3nawskigs140xzvjk67xh0r9q"))
1874        (patches (list (search-patch "rsem-makefile.patch")))
1875        (modules '((guix build utils)))
1876        (snippet
1877         '(begin
1878            ;; remove bundled copy of boost
1879            (delete-file-recursively "boost")
1880            #t))))
1881     (build-system gnu-build-system)
1882     (arguments
1883      `(#:tests? #f ;no "check" target
1884        #:phases
1885        (modify-phases %standard-phases
1886          ;; No "configure" script.
1887          ;; Do not build bundled samtools library.
1888          (replace 'configure
1889                   (lambda _
1890                     (substitute* "Makefile"
1891                       (("^all : sam/libbam.a") "all : "))
1892                     #t))
1893          (replace 'install
1894                   (lambda* (#:key outputs #:allow-other-keys)
1895                     (let* ((out (string-append (assoc-ref outputs "out")))
1896                            (bin (string-append out "/bin/"))
1897                            (perl (string-append out "/lib/perl5/site_perl")))
1898                       (mkdir-p bin)
1899                       (mkdir-p perl)
1900                       (for-each (lambda (file)
1901                                   (copy-file file
1902                                              (string-append bin (basename file))))
1903                                 (find-files "." "rsem-.*"))
1904                       (copy-file "rsem_perl_utils.pm"
1905                                  (string-append perl "/rsem_perl_utils.pm")))
1906                     #t))
1907          (add-after
1908           'install 'wrap-program
1909           (lambda* (#:key outputs #:allow-other-keys)
1910             (let ((out (assoc-ref outputs "out")))
1911               (for-each (lambda (prog)
1912                           (wrap-program (string-append out "/bin/" prog)
1913                             `("PERL5LIB" ":" prefix
1914                               (,(string-append out "/lib/perl5/site_perl")))))
1915                         '("rsem-plot-transcript-wiggles"
1916                           "rsem-calculate-expression"
1917                           "rsem-generate-ngvector"
1918                           "rsem-run-ebseq"
1919                           "rsem-prepare-reference")))
1920             #t)))))
1921     (inputs
1922      `(("boost" ,boost)
1923        ("ncurses" ,ncurses)
1924        ("r" ,r)
1925        ("perl" ,perl)
1926        ("samtools" ,samtools-0.1)
1927        ("zlib" ,zlib)))
1928     (home-page "http://deweylab.biostat.wisc.edu/rsem/")
1929     (synopsis "Estimate gene expression levels from RNA-Seq data")
1930     (description
1931      "RSEM is a software package for estimating gene and isoform expression
1932 levels from RNA-Seq data.  The RSEM package provides a user-friendly
1933 interface, supports threads for parallel computation of the EM algorithm,
1934 single-end and paired-end read data, quality scores, variable-length reads and
1935 RSPD estimation.  In addition, it provides posterior mean and 95% credibility
1936 interval estimates for expression levels.  For visualization, it can generate
1937 BAM and Wiggle files in both transcript-coordinate and genomic-coordinate.")
1938     (license license:gpl3+)))
1939
1940 (define-public rseqc
1941   (package
1942     (name "rseqc")
1943     (version "2.6.1")
1944     (source
1945      (origin
1946        (method url-fetch)
1947        (uri
1948         (string-append "mirror://sourceforge/rseqc/"
1949                        version "/RSeQC-" version ".tar.gz"))
1950        (sha256
1951         (base32 "15ly0254yi032qzkdplg00q144qfdsd986gh62829rl5bkxhj330"))
1952        (modules '((guix build utils)))
1953        (snippet
1954         '(begin
1955            ;; remove bundled copy of pysam
1956            (delete-file-recursively "lib/pysam")
1957            (substitute* "setup.py"
1958              ;; remove dependency on outdated "distribute" module
1959              (("^from distribute_setup import use_setuptools") "")
1960              (("^use_setuptools\\(\\)") "")
1961              ;; do not use bundled copy of pysam
1962              (("^have_pysam = False") "have_pysam = True"))))))
1963     (build-system python-build-system)
1964     (arguments `(#:python ,python-2))
1965     (inputs
1966      `(("python-cython" ,python2-cython)
1967        ("python-pysam" ,python2-pysam)
1968        ("python-numpy" ,python2-numpy)
1969        ("python-setuptools" ,python2-setuptools)
1970        ("zlib" ,zlib)))
1971     (native-inputs
1972      `(("python-nose" ,python2-nose)))
1973     (home-page "http://rseqc.sourceforge.net/")
1974     (synopsis "RNA-seq quality control package")
1975     (description
1976      "RSeQC provides a number of modules that can comprehensively evaluate
1977 high throughput sequence data, especially RNA-seq data.  Some basic modules
1978 inspect sequence quality, nucleotide composition bias, PCR bias and GC bias,
1979 while RNA-seq specific modules evaluate sequencing saturation, mapped reads
1980 distribution, coverage uniformity, strand specificity, etc.")
1981     (license license:gpl3+)))
1982
1983 (define-public samtools
1984   (package
1985     (name "samtools")
1986     (version "1.2")
1987     (source
1988      (origin
1989        (method url-fetch)
1990        (uri
1991         (string-append "mirror://sourceforge/samtools/"
1992                        version "/samtools-" version ".tar.bz2"))
1993        (sha256
1994         (base32
1995          "1akdqb685pk9xk1nb6sa9aq8xssjjhvvc06kp4cpdqvz2157l3j2"))))
1996     (build-system gnu-build-system)
1997     (arguments
1998      `(;; There are 87 test failures when building on non-64-bit architectures
1999        ;; due to invalid test data.  This has since been fixed upstream (see
2000        ;; <https://github.com/samtools/samtools/pull/307>), but as there has
2001        ;; not been a new release we disable the tests for all non-64-bit
2002        ;; systems.
2003        #:tests? ,(string=? (or (%current-system) (%current-target-system))
2004                            "x86_64-linux")
2005        #:modules ((ice-9 ftw)
2006                   (ice-9 regex)
2007                   (guix build gnu-build-system)
2008                   (guix build utils))
2009        #:make-flags (list "LIBCURSES=-lncurses"
2010                           (string-append "prefix=" (assoc-ref %outputs "out")))
2011        #:phases
2012        (alist-cons-after
2013         'unpack
2014         'patch-tests
2015         (lambda* (#:key inputs #:allow-other-keys)
2016           (let ((bash (assoc-ref inputs "bash")))
2017             (substitute* "test/test.pl"
2018               ;; The test script calls out to /bin/bash
2019               (("/bin/bash")
2020                (string-append bash "/bin/bash"))
2021               ;; There are two failing tests upstream relating to the "stats"
2022               ;; subcommand in test_usage_subcommand ("did not have Usage"
2023               ;; and "usage did not mention samtools stats"), so we disable
2024               ;; them.
2025               (("(test_usage_subcommand\\(.*\\);)" cmd)
2026                (string-append "unless ($subcommand eq 'stats') {" cmd "};")))))
2027         (alist-cons-after
2028          'install 'install-library
2029          (lambda* (#:key outputs #:allow-other-keys)
2030            (let ((lib (string-append (assoc-ref outputs "out") "/lib")))
2031              (mkdir-p lib)
2032              (copy-file "libbam.a" (string-append lib "/libbam.a"))))
2033          (alist-cons-after
2034           'install 'install-headers
2035           (lambda* (#:key outputs #:allow-other-keys)
2036             (let ((include (string-append (assoc-ref outputs "out")
2037                                           "/include/samtools/")))
2038               (mkdir-p include)
2039               (for-each (lambda (file)
2040                           (copy-file file (string-append include
2041                                                          (basename file))))
2042                         (scandir "." (lambda (name) (string-match "\\.h$" name))))
2043               #t))
2044           (alist-delete 'configure %standard-phases))))))
2045     (native-inputs `(("pkg-config" ,pkg-config)))
2046     (inputs `(("ncurses" ,ncurses)
2047               ("perl" ,perl)
2048               ("python" ,python)
2049               ("zlib" ,zlib)))
2050     (home-page "http://samtools.sourceforge.net")
2051     (synopsis "Utilities to efficiently manipulate nucleotide sequence alignments")
2052     (description
2053      "Samtools implements various utilities for post-processing nucleotide
2054 sequence alignments in the SAM, BAM, and CRAM formats, including indexing,
2055 variant calling (in conjunction with bcftools), and a simple alignment
2056 viewer.")
2057     (license license:expat)))
2058
2059 (define-public samtools-0.1
2060   ;; This is the most recent version of the 0.1 line of samtools.  The input
2061   ;; and output formats differ greatly from that used and produced by samtools
2062   ;; 1.x and is still used in many bioinformatics pipelines.
2063   (package (inherit samtools)
2064     (version "0.1.19")
2065     (source
2066      (origin
2067        (method url-fetch)
2068        (uri
2069         (string-append "mirror://sourceforge/samtools/"
2070                        version "/samtools-" version ".tar.bz2"))
2071        (sha256
2072         (base32 "1m33xsfwz0s8qi45lylagfllqg7fphf4dr0780rsvw75av9wk06h"))))
2073     (arguments
2074      (substitute-keyword-arguments (package-arguments samtools)
2075        ((#:tests? tests) #f) ;no "check" target
2076        ((#:phases phases)
2077         `(modify-phases ,phases
2078            (replace 'install
2079                     (lambda* (#:key outputs #:allow-other-keys)
2080                       (let ((bin (string-append
2081                                   (assoc-ref outputs "out") "/bin")))
2082                         (mkdir-p bin)
2083                         (copy-file "samtools"
2084                                    (string-append bin "/samtools")))))
2085            (delete 'patch-tests)))))))
2086
2087 (define-public ngs-sdk
2088   (package
2089     (name "ngs-sdk")
2090     (version "1.1.1")
2091     (source
2092      (origin
2093        (method url-fetch)
2094        (uri
2095         (string-append "https://github.com/ncbi/ngs/archive/"
2096                        version ".tar.gz"))
2097        (file-name (string-append name "-" version ".tar.gz"))
2098        (sha256
2099         (base32
2100          "1x58gpm574n0xmk2a98gmikbgycq78ia0bvnb42k5ck34fmd5v8y"))))
2101     (build-system gnu-build-system)
2102     (arguments
2103      `(#:parallel-build? #f ; not supported
2104        #:tests? #f ; no "check" target
2105        #:phases
2106        (alist-replace
2107         'configure
2108         (lambda* (#:key outputs #:allow-other-keys)
2109           (let ((out (assoc-ref outputs "out")))
2110             ;; The 'configure' script doesn't recognize things like
2111             ;; '--enable-fast-install'.
2112             (zero? (system* "./configure"
2113                             (string-append "--build-prefix=" (getcwd) "/build")
2114                             (string-append "--prefix=" out)))))
2115         (alist-cons-after
2116          'unpack 'enter-dir
2117          (lambda _ (chdir "ngs-sdk") #t)
2118          %standard-phases))))
2119     (native-inputs `(("perl" ,perl)))
2120     (home-page "https://github.com/ncbi/ngs")
2121     (synopsis "API for accessing Next Generation Sequencing data")
2122     (description
2123      "NGS is a domain-specific API for accessing reads, alignments and pileups
2124 produced from Next Generation Sequencing.  The API itself is independent from
2125 any particular back-end implementation, and supports use of multiple back-ends
2126 simultaneously.")
2127     (license license:public-domain)))
2128
2129 (define-public ngs-java
2130   (package (inherit ngs-sdk)
2131     (name "ngs-java")
2132     (arguments
2133      `(,@(substitute-keyword-arguments
2134              `(#:modules ((guix build gnu-build-system)
2135                           (guix build utils)
2136                           (srfi srfi-1)
2137                           (srfi srfi-26))
2138                          ,@(package-arguments ngs-sdk))
2139            ((#:phases phases)
2140             `(alist-cons-after
2141               'enter-dir 'fix-java-symlink-installation
2142               (lambda _
2143                 ;; Only replace the version suffix, not the version number in
2144                 ;; the directory name.  Reported here:
2145                 ;; https://github.com/ncbi/ngs/pull/4
2146                 (substitute* "Makefile.java"
2147                   (((string-append "\\$\\(subst "
2148                                    "(\\$\\(VERSION[^\\)]*\\)),"
2149                                    "(\\$\\([^\\)]+\\)),"
2150                                    "(\\$\\([^\\)]+\\)|\\$\\@)"
2151                                    "\\)")
2152                     _ pattern replacement target)
2153                    (string-append "$(patsubst "
2154                                   "%" pattern ","
2155                                   "%" replacement ","
2156                                   target ")"))))
2157               (alist-replace
2158                'enter-dir (lambda _ (chdir "ngs-java") #t)
2159                ,phases))))))
2160     (inputs
2161      `(("jdk" ,icedtea6 "jdk")
2162        ("ngs-sdk" ,ngs-sdk)))
2163     (synopsis "Java bindings for NGS SDK")))
2164
2165 (define-public ncbi-vdb
2166   (package
2167     (name "ncbi-vdb")
2168     (version "2.4.5-5")
2169     (source
2170      (origin
2171        (method url-fetch)
2172        (uri
2173         (string-append "https://github.com/ncbi/ncbi-vdb/archive/"
2174                        version ".tar.gz"))
2175        (file-name (string-append name "-" version ".tar.gz"))
2176        (sha256
2177         (base32
2178          "1cj8nk6if8sqagv20vx36v566fdvhcaadf0x1ycnbgql6chbs6vy"))))
2179     (build-system gnu-build-system)
2180     (arguments
2181      `(#:parallel-build? #f ; not supported
2182        #:tests? #f ; no "check" target
2183        #:phases
2184        (alist-replace
2185         'configure
2186         (lambda* (#:key inputs outputs #:allow-other-keys)
2187           (let ((out (assoc-ref outputs "out")))
2188             ;; Only replace the version suffix, not the version number in the
2189             ;; directory name; fixed in commit 4dbba5c6a809 (no release yet).
2190             (substitute* "setup/konfigure.perl"
2191               (((string-append "\\$\\(subst "
2192                                "(\\$\\(VERSION[^\\)]*\\)),"
2193                                "(\\$\\([^\\)]+\\)),"
2194                                "(\\$\\([^\\)]+\\)|\\$\\@)"
2195                                "\\)")
2196                 _ pattern replacement target)
2197                (string-append "$(patsubst "
2198                               "%" pattern ","
2199                               "%" replacement ","
2200                               target ")")))
2201
2202             ;; Override include path for libmagic
2203             (substitute* "setup/package.prl"
2204               (("name => 'magic', Include => '/usr/include'")
2205                (string-append "name=> 'magic', Include => '"
2206                               (assoc-ref inputs "libmagic")
2207                               "/include" "'")))
2208
2209             ;; Install kdf5 library (needed by sra-tools)
2210             (substitute* "build/Makefile.install"
2211               (("LIBRARIES_TO_INSTALL =")
2212                "LIBRARIES_TO_INSTALL = kdf5.$(VERSION_LIBX) kdf5.$(VERSION_SHLX)"))
2213
2214             ;; The 'configure' script doesn't recognize things like
2215             ;; '--enable-fast-install'.
2216             (zero? (system*
2217                     "./configure"
2218                     (string-append "--build-prefix=" (getcwd) "/build")
2219                     (string-append "--prefix=" (assoc-ref outputs "out"))
2220                     (string-append "--debug")
2221                     (string-append "--with-xml2-prefix="
2222                                    (assoc-ref inputs "libxml2"))
2223                     (string-append "--with-ngs-sdk-prefix="
2224                                    (assoc-ref inputs "ngs-sdk"))
2225                     (string-append "--with-ngs-java-prefix="
2226                                    (assoc-ref inputs "ngs-java"))
2227                     (string-append "--with-hdf5-prefix="
2228                                    (assoc-ref inputs "hdf5"))))))
2229         (alist-cons-after
2230          'install 'install-interfaces
2231          (lambda* (#:key outputs #:allow-other-keys)
2232            ;; Install interface libraries.  On i686 the interface libraries
2233            ;; are installed to "linux/gcc/i386", so we need to use the Linux
2234            ;; architecture name ("i386") instead of the target system prefix
2235            ;; ("i686").
2236            (mkdir (string-append (assoc-ref outputs "out") "/ilib"))
2237            (copy-recursively (string-append "build/ncbi-vdb/linux/gcc/"
2238                                             ,(system->linux-architecture
2239                                               (or (%current-target-system)
2240                                                   (%current-system)))
2241                                             "/rel/ilib")
2242                              (string-append (assoc-ref outputs "out")
2243                                             "/ilib"))
2244            ;; Install interface headers
2245            (copy-recursively "interfaces"
2246                              (string-append (assoc-ref outputs "out")
2247                                             "/include")))
2248          %standard-phases))))
2249     (inputs
2250      `(("libxml2" ,libxml2)
2251        ("ngs-sdk" ,ngs-sdk)
2252        ("ngs-java" ,ngs-java)
2253        ("libmagic" ,file)
2254        ("hdf5" ,hdf5)))
2255     (native-inputs `(("perl" ,perl)))
2256     (home-page "https://github.com/ncbi/ncbi-vdb")
2257     (synopsis "Database engine for genetic information")
2258     (description
2259      "The NCBI-VDB library implements a highly compressed columnar data
2260 warehousing engine that is most often used to store genetic information.
2261 Databases are stored in a portable image within the file system, and can be
2262 accessed/downloaded on demand across HTTP.")
2263     (license license:public-domain)))
2264
2265 (define-public plink
2266   (package
2267     (name "plink")
2268     (version "1.07")
2269     (source
2270      (origin
2271        (method url-fetch)
2272        (uri (string-append
2273              "http://pngu.mgh.harvard.edu/~purcell/plink/dist/plink-"
2274              version "-src.zip"))
2275        (sha256
2276         (base32 "0as8gxm4pjyc8dxmm1sl873rrd7wn5qs0l29nqfnl31x8i467xaa"))
2277        (patches (list (search-patch "plink-1.07-unclobber-i.patch")))))
2278     (build-system gnu-build-system)
2279     (arguments
2280      '(#:tests? #f ;no "check" target
2281        #:make-flags (list (string-append "LIB_LAPACK="
2282                                          (assoc-ref %build-inputs "lapack")
2283                                          "/lib/liblapack.so")
2284                           "WITH_LAPACK=1"
2285                           "FORCE_DYNAMIC=1"
2286                           ;; disable phoning home
2287                           "WITH_WEBCHECK=")
2288        #:phases
2289        (modify-phases %standard-phases
2290          ;; no "configure" script
2291          (delete 'configure)
2292          (replace 'install
2293                   (lambda* (#:key outputs #:allow-other-keys)
2294                     (let ((bin (string-append (assoc-ref outputs "out")
2295                                               "/bin/")))
2296                       (mkdir-p bin)
2297                       (copy-file "plink" (string-append bin "plink"))
2298                       #t))))))
2299     (inputs
2300      `(("zlib" ,zlib)
2301        ("lapack" ,lapack)))
2302     (native-inputs
2303      `(("unzip" ,unzip)))
2304     (home-page "http://pngu.mgh.harvard.edu/~purcell/plink/")
2305     (synopsis "Whole genome association analysis toolset")
2306     (description
2307      "PLINK is a whole genome association analysis toolset, designed to
2308 perform a range of basic, large-scale analyses in a computationally efficient
2309 manner.  The focus of PLINK is purely on analysis of genotype/phenotype data,
2310 so there is no support for steps prior to this (e.g. study design and
2311 planning, generating genotype or CNV calls from raw data).  Through
2312 integration with gPLINK and Haploview, there is some support for the
2313 subsequent visualization, annotation and storage of results.")
2314     ;; Code is released under GPLv2, except for fisher.h, which is under
2315     ;; LGPLv2.1+
2316     (license (list license:gpl2 license:lgpl2.1+))))
2317
2318 (define-public preseq
2319   (package
2320     (name "preseq")
2321     (version "1.0.2")
2322     (source (origin
2323               (method url-fetch)
2324               (uri
2325                (string-append "http://smithlabresearch.org/downloads/preseq-"
2326                               version ".tar.bz2"))
2327               (sha256
2328                (base32 "0r7sw07p6nv8ygvc17gd78lisbw5336v3vhs86b5wv8mw3pwqksc"))
2329               (patches (list (search-patch "preseq-1.0.2-install-to-PREFIX.patch")
2330                              (search-patch "preseq-1.0.2-link-with-libbam.patch")))
2331               (modules '((guix build utils)))
2332               (snippet
2333                ;; Remove bundled samtools.
2334                '(delete-file-recursively "preseq-master/samtools"))))
2335     (build-system gnu-build-system)
2336     (arguments
2337      `(#:tests? #f ;no "check" target
2338        #:phases
2339        (modify-phases %standard-phases
2340          (add-after
2341           'unpack 'enter-dir
2342           (lambda _
2343             (chdir "preseq-master")
2344             #t))
2345          (add-after
2346           'enter-dir 'use-samtools-headers
2347           (lambda _
2348             (substitute* '("smithlab_cpp/SAM.cpp"
2349                            "smithlab_cpp/SAM.hpp")
2350               (("sam.h") "samtools/sam.h"))
2351             #t))
2352          (delete 'configure))
2353        #:make-flags (list (string-append "PREFIX="
2354                                          (assoc-ref %outputs "out"))
2355                           (string-append "LIBBAM="
2356                                          (assoc-ref %build-inputs "samtools")
2357                                          "/lib/libbam.a"))))
2358     (inputs
2359      `(("gsl" ,gsl)
2360        ("samtools" ,samtools-0.1)
2361        ("zlib" ,zlib)))
2362     (home-page "http://smithlabresearch.org/software/preseq/")
2363     (synopsis "Program for analyzing library complexity")
2364     (description
2365      "The preseq package is aimed at predicting and estimating the complexity
2366 of a genomic sequencing library, equivalent to predicting and estimating the
2367 number of redundant reads from a given sequencing depth and how many will be
2368 expected from additional sequencing using an initial sequencing experiment.
2369 The estimates can then be used to examine the utility of further sequencing,
2370 optimize the sequencing depth, or to screen multiple libraries to avoid low
2371 complexity samples.")
2372     (license license:gpl3+)))
2373
2374 (define-public sra-tools
2375   (package
2376     (name "sra-tools")
2377     (version "2.4.5-5")
2378     (source
2379      (origin
2380        (method url-fetch)
2381        (uri
2382         (string-append "https://github.com/ncbi/sra-tools/archive/"
2383                        version ".tar.gz"))
2384        (file-name (string-append name "-" version ".tar.gz"))
2385        (sha256
2386         (base32
2387          "11nrnvz7a012f4iryf0wiwrid0h111grsfxbxa9j51h3f2xbvgns"))))
2388     (build-system gnu-build-system)
2389     (arguments
2390      `(#:parallel-build? #f ; not supported
2391        #:tests? #f ; no "check" target
2392        #:phases
2393        (alist-replace
2394         'configure
2395         (lambda* (#:key inputs outputs #:allow-other-keys)
2396           ;; The build system expects a directory containing the sources and
2397           ;; raw build output of ncbi-vdb, including files that are not
2398           ;; installed.  Since we are building against an installed version of
2399           ;; ncbi-vdb, the following modifications are needed.
2400           (substitute* "setup/konfigure.perl"
2401             ;; Make the configure script look for the "ilib" directory of
2402             ;; "ncbi-vdb" without first checking for the existence of a
2403             ;; matching library in its "lib" directory.
2404             (("^            my \\$f = File::Spec->catdir\\(\\$libdir, \\$lib\\);")
2405              "my $f = File::Spec->catdir($ilibdir, $ilib);")
2406             ;; Look for interface libraries in ncbi-vdb's "ilib" directory.
2407             (("my \\$ilibdir = File::Spec->catdir\\(\\$builddir, 'ilib'\\);")
2408              "my $ilibdir = File::Spec->catdir($dir, 'ilib');"))
2409
2410           ;; The 'configure' script doesn't recognize things like
2411           ;; '--enable-fast-install'.
2412           (zero? (system*
2413                   "./configure"
2414                   (string-append "--build-prefix=" (getcwd) "/build")
2415                   (string-append "--prefix=" (assoc-ref outputs "out"))
2416                   (string-append "--debug")
2417                   (string-append "--with-fuse-prefix="
2418                                  (assoc-ref inputs "fuse"))
2419                   (string-append "--with-magic-prefix="
2420                                  (assoc-ref inputs "libmagic"))
2421                   ;; TODO: building with libxml2 fails with linker errors
2422                   ;; (string-append "--with-xml2-prefix="
2423                   ;;                (assoc-ref inputs "libxml2"))
2424                   (string-append "--with-ncbi-vdb-sources="
2425                                  (assoc-ref inputs "ncbi-vdb"))
2426                   (string-append "--with-ncbi-vdb-build="
2427                                  (assoc-ref inputs "ncbi-vdb"))
2428                   (string-append "--with-ngs-sdk-prefix="
2429                                  (assoc-ref inputs "ngs-sdk"))
2430                   (string-append "--with-hdf5-prefix="
2431                                  (assoc-ref inputs "hdf5")))))
2432         %standard-phases)))
2433     (native-inputs `(("perl" ,perl)))
2434     (inputs
2435      `(("ngs-sdk" ,ngs-sdk)
2436        ("ncbi-vdb" ,ncbi-vdb)
2437        ("libmagic" ,file)
2438        ("fuse" ,fuse)
2439        ("hdf5" ,hdf5)
2440        ("zlib" ,zlib)))
2441     (home-page "http://www.ncbi.nlm.nih.gov/Traces/sra/sra.cgi?view=software")
2442     (synopsis "Tools and libraries for reading and writing sequencing data")
2443     (description
2444      "The SRA Toolkit from NCBI is a collection of tools and libraries for
2445 reading of sequencing files from the Sequence Read Archive (SRA) database and
2446 writing files into the .sra format.")
2447     (license license:public-domain)))
2448
2449 (define-public seqan
2450   (package
2451     (name "seqan")
2452     (version "1.4.2")
2453     (source (origin
2454               (method url-fetch)
2455               (uri (string-append "http://packages.seqan.de/seqan-library/"
2456                                   "seqan-library-" version ".tar.bz2"))
2457               (sha256
2458                (base32
2459                 "05s3wrrwn50f81aklfm65i4a749zag1vr8z03k21xm0pdxy47yvp"))))
2460     ;; The documentation is 7.8MB and the includes are 3.6MB heavy, so it
2461     ;; makes sense to split the outputs.
2462     (outputs '("out" "doc"))
2463     (build-system trivial-build-system)
2464     (arguments
2465      `(#:modules ((guix build utils))
2466        #:builder
2467        (begin
2468          (use-modules (guix build utils))
2469          (let ((tar  (assoc-ref %build-inputs "tar"))
2470                (bzip (assoc-ref %build-inputs "bzip2"))
2471                (out  (assoc-ref %outputs "out"))
2472                (doc  (assoc-ref %outputs "doc")))
2473            (setenv "PATH" (string-append tar "/bin:" bzip "/bin"))
2474            (system* "tar" "xvf" (assoc-ref %build-inputs "source"))
2475            (chdir (string-append "seqan-library-" ,version))
2476            (copy-recursively "include" (string-append out "/include"))
2477            (copy-recursively "share"  (string-append doc "/share"))))))
2478     (native-inputs
2479      `(("source" ,source)
2480        ("tar" ,tar)
2481        ("bzip2" ,bzip2)))
2482     (home-page "http://www.seqan.de")
2483     (synopsis "Library for nucleotide sequence analysis")
2484     (description
2485      "SeqAn is a C++ library of efficient algorithms and data structures for
2486 the analysis of sequences with the focus on biological data.  It contains
2487 algorithms and data structures for string representation and their
2488 manipulation, online and indexed string search, efficient I/O of
2489 bioinformatics file formats, sequence alignment, and more.")
2490     (license license:bsd-3)))
2491
2492 (define-public star
2493   (package
2494     (name "star")
2495     (version "2.4.2a")
2496     (source (origin
2497               (method url-fetch)
2498               (uri (string-append
2499                     "https://github.com/alexdobin/STAR/archive/STAR_"
2500                     version ".tar.gz"))
2501               (sha256
2502                (base32
2503                 "1c3rnm7r5l0kl3d04gl1g7938xqf1c2l0mla87rlplqg1hcns5mc"))
2504               (modules '((guix build utils)))
2505               (snippet
2506                '(substitute* "source/Makefile"
2507                   (("/bin/rm") "rm")))))
2508     (build-system gnu-build-system)
2509     (arguments
2510      '(#:tests? #f ;no check target
2511        #:make-flags '("STAR")
2512        #:phases
2513        (alist-cons-after
2514         'unpack 'enter-source-dir (lambda _ (chdir "source"))
2515         (alist-replace
2516          'install
2517          (lambda* (#:key outputs #:allow-other-keys)
2518            (let ((bin (string-append (assoc-ref outputs "out") "/bin/")))
2519              (mkdir-p bin)
2520              (copy-file "STAR" (string-append bin "STAR"))))
2521          (alist-delete
2522           'configure %standard-phases)))))
2523     (native-inputs
2524      `(("vim" ,vim))) ; for xxd
2525     (inputs
2526      `(("zlib" ,zlib)))
2527     (home-page "https://github.com/alexdobin/STAR")
2528     (synopsis "Universal RNA-seq aligner")
2529     (description
2530      "The Spliced Transcripts Alignment to a Reference (STAR) software is
2531 based on a previously undescribed RNA-seq alignment algorithm that uses
2532 sequential maximum mappable seed search in uncompressed suffix arrays followed
2533 by seed clustering and stitching procedure.  In addition to unbiased de novo
2534 detection of canonical junctions, STAR can discover non-canonical splices and
2535 chimeric (fusion) transcripts, and is also capable of mapping full-length RNA
2536 sequences.")
2537     ;; STAR is licensed under GPLv3 or later; htslib is MIT-licensed.
2538     (license license:gpl3+)))
2539
2540 (define-public subread
2541   (package
2542     (name "subread")
2543     (version "1.4.6-p2")
2544     (source (origin
2545               (method url-fetch)
2546               (uri (string-append
2547                     "mirror://sourceforge/subread/subread-"
2548                     version "-source.tar.gz"))
2549               (sha256
2550                (base32
2551                 "06sv9mpcsdj6p68y15d6gi70lca3lxmzk0dn61hg0kfsa7rxmsr3"))))
2552     (build-system gnu-build-system)
2553     (arguments
2554      `(#:tests? #f ;no "check" target
2555        #:make-flags '("-f" "Makefile.Linux")
2556        #:phases
2557        (alist-cons-after
2558         'unpack 'enter-dir
2559         (lambda _ (chdir "src") #t)
2560         (alist-replace
2561          'install
2562          (lambda* (#:key outputs #:allow-other-keys)
2563            (let ((bin (string-append (assoc-ref outputs "out") "/bin/")))
2564              (mkdir-p bin)
2565              (copy-recursively "../bin" bin)))
2566          ;; no "configure" script
2567          (alist-delete 'configure %standard-phases)))))
2568     (inputs `(("zlib" ,zlib)))
2569     (home-page "http://bioinf.wehi.edu.au/subread-package/")
2570     (synopsis "Tool kit for processing next-gen sequencing data")
2571     (description
2572      "The subread package contains the following tools: subread aligner, a
2573 general-purpose read aligner; subjunc aligner: detecting exon-exon junctions
2574 and mapping RNA-seq reads; featureCounts: counting mapped reads for genomic
2575 features; exactSNP: a SNP caller that discovers SNPs by testing signals
2576 against local background noises.")
2577     (license license:gpl3+)))
2578
2579 (define-public vcftools
2580   (package
2581     (name "vcftools")
2582     (version "0.1.12b")
2583     (source (origin
2584               (method url-fetch)
2585               (uri (string-append
2586                     "mirror://sourceforge/vcftools/vcftools_"
2587                      version ".tar.gz"))
2588               (sha256
2589                (base32
2590                 "148al9h7f8g8my2qdnpax51kdd2yjrivlx6frvakf4lz5r8j88wx"))))
2591     (build-system gnu-build-system)
2592     (arguments
2593      `(#:tests? #f ; no "check" target
2594        #:make-flags (list
2595                      "CFLAGS=-O2" ; override "-m64" flag
2596                      (string-append "PREFIX=" (assoc-ref %outputs "out"))
2597                      (string-append "MANDIR=" (assoc-ref %outputs "out")
2598                                     "/share/man/man1"))
2599        #:phases
2600        (alist-cons-after
2601         'unpack 'patch-manpage-install
2602         (lambda _
2603           (substitute* "Makefile"
2604             (("cp \\$\\{PREFIX\\}/cpp/vcftools.1") "cp ./cpp/vcftools.1")))
2605         (alist-delete 'configure %standard-phases))))
2606     (inputs
2607      `(("perl" ,perl)
2608        ("zlib" ,zlib)))
2609     (home-page "http://vcftools.sourceforge.net/")
2610     (synopsis "Tools for working with VCF files")
2611     (description
2612      "VCFtools is a program package designed for working with VCF files, such
2613 as those generated by the 1000 Genomes Project.  The aim of VCFtools is to
2614 provide easily accessible methods for working with complex genetic variation
2615 data in the form of VCF files.")
2616     ;; The license is declared as LGPLv3 in the README and
2617     ;; at http://vcftools.sourceforge.net/license.html
2618     (license license:lgpl3)))