| 1 | ;;; GNU Guix --- Functional package management for GNU |
| 2 | ;;; Copyright © 2014, 2015, 2016, 2017 Ricardo Wurmus <rekado@elephly.net> |
| 3 | ;;; Copyright © 2015, 2016, 2017 Ben Woodcroft <donttrustben@gmail.com> |
| 4 | ;;; Copyright © 2015, 2016 Pjotr Prins <pjotr.guix@thebird.nl> |
| 5 | ;;; Copyright © 2015 Andreas Enge <andreas@enge.fr> |
| 6 | ;;; Copyright © 2016 Roel Janssen <roel@gnu.org> |
| 7 | ;;; Copyright © 2016, 2017 Efraim Flashner <efraim@flashner.co.il> |
| 8 | ;;; Copyright © 2016 Marius Bakke <mbakke@fastmail.com> |
| 9 | ;;; Copyright © 2016 Raoul Bonnal <ilpuccio.febo@gmail.com> |
| 10 | ;;; Copyright © 2017, 2018 Tobias Geerinckx-Rice <me@tobias.gr> |
| 11 | ;;; Copyright © 2017 Arun Isaac <arunisaac@systemreboot.net> |
| 12 | ;;; |
| 13 | ;;; This file is part of GNU Guix. |
| 14 | ;;; |
| 15 | ;;; GNU Guix is free software; you can redistribute it and/or modify it |
| 16 | ;;; under the terms of the GNU General Public License as published by |
| 17 | ;;; the Free Software Foundation; either version 3 of the License, or (at |
| 18 | ;;; your option) any later version. |
| 19 | ;;; |
| 20 | ;;; GNU Guix is distributed in the hope that it will be useful, but |
| 21 | ;;; WITHOUT ANY WARRANTY; without even the implied warranty of |
| 22 | ;;; MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the |
| 23 | ;;; GNU General Public License for more details. |
| 24 | ;;; |
| 25 | ;;; You should have received a copy of the GNU General Public License |
| 26 | ;;; along with GNU Guix. If not, see <http://www.gnu.org/licenses/>. |
| 27 | |
| 28 | (define-module (gnu packages bioinformatics) |
| 29 | #:use-module ((guix licenses) #:prefix license:) |
| 30 | #:use-module (guix packages) |
| 31 | #:use-module (guix utils) |
| 32 | #:use-module (guix download) |
| 33 | #:use-module (guix git-download) |
| 34 | #:use-module (guix hg-download) |
| 35 | #:use-module (guix build-system ant) |
| 36 | #:use-module (guix build-system gnu) |
| 37 | #:use-module (guix build-system cmake) |
| 38 | #:use-module (guix build-system ocaml) |
| 39 | #:use-module (guix build-system perl) |
| 40 | #:use-module (guix build-system python) |
| 41 | #:use-module (guix build-system r) |
| 42 | #:use-module (guix build-system ruby) |
| 43 | #:use-module (guix build-system scons) |
| 44 | #:use-module (guix build-system trivial) |
| 45 | #:use-module (gnu packages) |
| 46 | #:use-module (gnu packages autotools) |
| 47 | #:use-module (gnu packages algebra) |
| 48 | #:use-module (gnu packages base) |
| 49 | #:use-module (gnu packages bash) |
| 50 | #:use-module (gnu packages bison) |
| 51 | #:use-module (gnu packages boost) |
| 52 | #:use-module (gnu packages check) |
| 53 | #:use-module (gnu packages compression) |
| 54 | #:use-module (gnu packages cpio) |
| 55 | #:use-module (gnu packages cran) |
| 56 | #:use-module (gnu packages curl) |
| 57 | #:use-module (gnu packages documentation) |
| 58 | #:use-module (gnu packages databases) |
| 59 | #:use-module (gnu packages datastructures) |
| 60 | #:use-module (gnu packages file) |
| 61 | #:use-module (gnu packages flex) |
| 62 | #:use-module (gnu packages gawk) |
| 63 | #:use-module (gnu packages gcc) |
| 64 | #:use-module (gnu packages gd) |
| 65 | #:use-module (gnu packages gtk) |
| 66 | #:use-module (gnu packages glib) |
| 67 | #:use-module (gnu packages graph) |
| 68 | #:use-module (gnu packages groff) |
| 69 | #:use-module (gnu packages guile) |
| 70 | #:use-module (gnu packages haskell) |
| 71 | #:use-module (gnu packages image) |
| 72 | #:use-module (gnu packages imagemagick) |
| 73 | #:use-module (gnu packages java) |
| 74 | #:use-module (gnu packages ldc) |
| 75 | #:use-module (gnu packages linux) |
| 76 | #:use-module (gnu packages logging) |
| 77 | #:use-module (gnu packages machine-learning) |
| 78 | #:use-module (gnu packages man) |
| 79 | #:use-module (gnu packages maths) |
| 80 | #:use-module (gnu packages mpi) |
| 81 | #:use-module (gnu packages ncurses) |
| 82 | #:use-module (gnu packages ocaml) |
| 83 | #:use-module (gnu packages pcre) |
| 84 | #:use-module (gnu packages parallel) |
| 85 | #:use-module (gnu packages pdf) |
| 86 | #:use-module (gnu packages perl) |
| 87 | #:use-module (gnu packages perl-check) |
| 88 | #:use-module (gnu packages pkg-config) |
| 89 | #:use-module (gnu packages popt) |
| 90 | #:use-module (gnu packages protobuf) |
| 91 | #:use-module (gnu packages python) |
| 92 | #:use-module (gnu packages python-web) |
| 93 | #:use-module (gnu packages readline) |
| 94 | #:use-module (gnu packages ruby) |
| 95 | #:use-module (gnu packages serialization) |
| 96 | #:use-module (gnu packages shells) |
| 97 | #:use-module (gnu packages statistics) |
| 98 | #:use-module (gnu packages swig) |
| 99 | #:use-module (gnu packages tbb) |
| 100 | #:use-module (gnu packages tex) |
| 101 | #:use-module (gnu packages texinfo) |
| 102 | #:use-module (gnu packages textutils) |
| 103 | #:use-module (gnu packages time) |
| 104 | #:use-module (gnu packages tls) |
| 105 | #:use-module (gnu packages vim) |
| 106 | #:use-module (gnu packages web) |
| 107 | #:use-module (gnu packages xml) |
| 108 | #:use-module (gnu packages xorg) |
| 109 | #:use-module (srfi srfi-1) |
| 110 | #:use-module (ice-9 match)) |
| 111 | |
| 112 | (define-public r-ape |
| 113 | (package |
| 114 | (name "r-ape") |
| 115 | (version "5.0") |
| 116 | (source |
| 117 | (origin |
| 118 | (method url-fetch) |
| 119 | (uri (cran-uri "ape" version)) |
| 120 | (sha256 |
| 121 | (base32 |
| 122 | "0q59pmxawz498cb9mv5m49lhiwxib8ak94yyydz7qg8b6lpd4bn3")))) |
| 123 | (build-system r-build-system) |
| 124 | (propagated-inputs |
| 125 | `(("r-lattice" ,r-lattice) |
| 126 | ("r-nlme" ,r-nlme) |
| 127 | ("r-rcpp" ,r-rcpp))) |
| 128 | (home-page "http://ape-package.ird.fr/") |
| 129 | (synopsis "Analyses of phylogenetics and evolution") |
| 130 | (description |
| 131 | "This package provides functions for reading, writing, plotting, and |
| 132 | manipulating phylogenetic trees, analyses of comparative data in a |
| 133 | phylogenetic framework, ancestral character analyses, analyses of |
| 134 | diversification and macroevolution, computing distances from DNA sequences, |
| 135 | and several other tools.") |
| 136 | (license license:gpl2+))) |
| 137 | |
| 138 | (define-public aragorn |
| 139 | (package |
| 140 | (name "aragorn") |
| 141 | (version "1.2.38") |
| 142 | (source (origin |
| 143 | (method url-fetch) |
| 144 | (uri (string-append |
| 145 | "http://mbio-serv2.mbioekol.lu.se/ARAGORN/Downloads/aragorn" |
| 146 | version ".tgz")) |
| 147 | (sha256 |
| 148 | (base32 |
| 149 | "09i1rg716smlbnixfm7q1ml2mfpaa2fpn3hwjg625ysmfwwy712b")))) |
| 150 | (build-system gnu-build-system) |
| 151 | (arguments |
| 152 | `(#:tests? #f ; there are no tests |
| 153 | #:phases |
| 154 | (modify-phases %standard-phases |
| 155 | (delete 'configure) |
| 156 | (replace 'build |
| 157 | (lambda _ |
| 158 | (zero? (system* "gcc" |
| 159 | "-O3" |
| 160 | "-ffast-math" |
| 161 | "-finline-functions" |
| 162 | "-o" |
| 163 | "aragorn" |
| 164 | (string-append "aragorn" ,version ".c"))))) |
| 165 | (replace 'install |
| 166 | (lambda* (#:key outputs #:allow-other-keys) |
| 167 | (let* ((out (assoc-ref outputs "out")) |
| 168 | (bin (string-append out "/bin")) |
| 169 | (man (string-append out "/share/man/man1"))) |
| 170 | (mkdir-p bin) |
| 171 | (install-file "aragorn" bin) |
| 172 | (mkdir-p man) |
| 173 | (install-file "aragorn.1" man)) |
| 174 | #t))))) |
| 175 | (home-page "http://mbio-serv2.mbioekol.lu.se/ARAGORN") |
| 176 | (synopsis "Detect tRNA, mtRNA and tmRNA genes in nucleotide sequences") |
| 177 | (description |
| 178 | "Aragorn identifies transfer RNA, mitochondrial RNA and |
| 179 | transfer-messenger RNA from nucleotide sequences, based on homology to known |
| 180 | tRNA consensus sequences and RNA structure. It also outputs the secondary |
| 181 | structure of the predicted RNA.") |
| 182 | (license license:gpl2))) |
| 183 | |
| 184 | (define-public bamm |
| 185 | (package |
| 186 | (name "bamm") |
| 187 | (version "1.7.3") |
| 188 | (source (origin |
| 189 | (method url-fetch) |
| 190 | ;; BamM is not available on pypi. |
| 191 | (uri (string-append |
| 192 | "https://github.com/Ecogenomics/BamM/archive/" |
| 193 | version ".tar.gz")) |
| 194 | (file-name (string-append name "-" version ".tar.gz")) |
| 195 | (sha256 |
| 196 | (base32 |
| 197 | "1f35yxp4pc8aadsvbpg6r4kg2jh4fkjci0iby4iyljm6980sac0s")) |
| 198 | (modules '((guix build utils))) |
| 199 | (snippet |
| 200 | `(begin |
| 201 | ;; Delete bundled htslib. |
| 202 | (delete-file-recursively "c/htslib-1.3.1") |
| 203 | #t)))) |
| 204 | (build-system python-build-system) |
| 205 | (arguments |
| 206 | `(#:python ,python-2 ; BamM is Python 2 only. |
| 207 | ;; Do not use bundled libhts. Do use the bundled libcfu because it has |
| 208 | ;; been modified from its original form. |
| 209 | #:configure-flags |
| 210 | (let ((htslib (assoc-ref %build-inputs "htslib"))) |
| 211 | (list "--with-libhts-lib" (string-append htslib "/lib") |
| 212 | "--with-libhts-inc" (string-append htslib "/include/htslib"))) |
| 213 | #:phases |
| 214 | (modify-phases %standard-phases |
| 215 | (add-after 'unpack 'autogen |
| 216 | (lambda _ |
| 217 | (with-directory-excursion "c" |
| 218 | (let ((sh (which "sh"))) |
| 219 | ;; Use autogen so that 'configure' works. |
| 220 | (substitute* "autogen.sh" (("/bin/sh") sh)) |
| 221 | (setenv "CONFIG_SHELL" sh) |
| 222 | (substitute* "configure" (("/bin/sh") sh)) |
| 223 | (zero? (system* "./autogen.sh")))))) |
| 224 | (delete 'build) |
| 225 | ;; Run tests after installation so compilation only happens once. |
| 226 | (delete 'check) |
| 227 | (add-after 'install 'wrap-executable |
| 228 | (lambda* (#:key outputs #:allow-other-keys) |
| 229 | (let* ((out (assoc-ref outputs "out")) |
| 230 | (path (getenv "PATH"))) |
| 231 | (wrap-program (string-append out "/bin/bamm") |
| 232 | `("PATH" ":" prefix (,path)))) |
| 233 | #t)) |
| 234 | (add-after 'wrap-executable 'post-install-check |
| 235 | (lambda* (#:key inputs outputs #:allow-other-keys) |
| 236 | (setenv "PATH" |
| 237 | (string-append (assoc-ref outputs "out") |
| 238 | "/bin:" |
| 239 | (getenv "PATH"))) |
| 240 | (setenv "PYTHONPATH" |
| 241 | (string-append |
| 242 | (assoc-ref outputs "out") |
| 243 | "/lib/python" |
| 244 | (string-take (string-take-right |
| 245 | (assoc-ref inputs "python") 5) 3) |
| 246 | "/site-packages:" |
| 247 | (getenv "PYTHONPATH"))) |
| 248 | ;; There are 2 errors printed, but they are safe to ignore: |
| 249 | ;; 1) [E::hts_open_format] fail to open file ... |
| 250 | ;; 2) samtools view: failed to open ... |
| 251 | (zero? (system* "nosetests"))))))) |
| 252 | (native-inputs |
| 253 | `(("autoconf" ,autoconf) |
| 254 | ("automake" ,automake) |
| 255 | ("libtool" ,libtool) |
| 256 | ("zlib" ,zlib) |
| 257 | ("python-nose" ,python2-nose) |
| 258 | ("python-pysam" ,python2-pysam))) |
| 259 | (inputs |
| 260 | `(("htslib" ,htslib-1.3) ; At least one test fails on htslib-1.4+. |
| 261 | ("samtools" ,samtools) |
| 262 | ("bwa" ,bwa) |
| 263 | ("grep" ,grep) |
| 264 | ("sed" ,sed) |
| 265 | ("coreutils" ,coreutils))) |
| 266 | (propagated-inputs |
| 267 | `(("python-numpy" ,python2-numpy))) |
| 268 | (home-page "http://ecogenomics.github.io/BamM/") |
| 269 | (synopsis "Metagenomics-focused BAM file manipulator") |
| 270 | (description |
| 271 | "BamM is a C library, wrapped in python, to efficiently generate and |
| 272 | parse BAM files, specifically for the analysis of metagenomic data. For |
| 273 | instance, it implements several methods to assess contig-wise read coverage.") |
| 274 | (license license:lgpl3+))) |
| 275 | |
| 276 | (define-public bamtools |
| 277 | (package |
| 278 | (name "bamtools") |
| 279 | (version "2.4.1") |
| 280 | (source (origin |
| 281 | (method url-fetch) |
| 282 | (uri (string-append |
| 283 | "https://github.com/pezmaster31/bamtools/archive/v" |
| 284 | version ".tar.gz")) |
| 285 | (file-name (string-append name "-" version ".tar.gz")) |
| 286 | (sha256 |
| 287 | (base32 |
| 288 | "0jr024kcrhjb82cm69i7p5fcg5375zlc1h3qh2n1v368hcd0qflk")))) |
| 289 | (build-system cmake-build-system) |
| 290 | (arguments |
| 291 | `(#:tests? #f ;no "check" target |
| 292 | #:phases |
| 293 | (modify-phases %standard-phases |
| 294 | (add-before |
| 295 | 'configure 'set-ldflags |
| 296 | (lambda* (#:key outputs #:allow-other-keys) |
| 297 | (setenv "LDFLAGS" |
| 298 | (string-append |
| 299 | "-Wl,-rpath=" |
| 300 | (assoc-ref outputs "out") "/lib/bamtools"))))))) |
| 301 | (inputs `(("zlib" ,zlib))) |
| 302 | (home-page "https://github.com/pezmaster31/bamtools") |
| 303 | (synopsis "C++ API and command-line toolkit for working with BAM data") |
| 304 | (description |
| 305 | "BamTools provides both a C++ API and a command-line toolkit for handling |
| 306 | BAM files.") |
| 307 | (license license:expat))) |
| 308 | |
| 309 | (define-public bcftools |
| 310 | (package |
| 311 | (name "bcftools") |
| 312 | (version "1.5") |
| 313 | (source (origin |
| 314 | (method url-fetch) |
| 315 | (uri (string-append |
| 316 | "https://github.com/samtools/bcftools/releases/download/" |
| 317 | version "/bcftools-" version ".tar.bz2")) |
| 318 | (sha256 |
| 319 | (base32 |
| 320 | "0093hkkvxmbwfaa7905s6185jymynvg42kq6sxv7fili11l5mxwz")) |
| 321 | (patches (search-patches "bcftools-regidx-unsigned-char.patch")) |
| 322 | (modules '((guix build utils))) |
| 323 | (snippet |
| 324 | ;; Delete bundled htslib. |
| 325 | '(delete-file-recursively "htslib-1.5")))) |
| 326 | (build-system gnu-build-system) |
| 327 | (arguments |
| 328 | `(#:test-target "test" |
| 329 | #:configure-flags (list "--with-htslib=system") |
| 330 | #:make-flags |
| 331 | (list |
| 332 | "USE_GPL=1" |
| 333 | "LIBS=-lgsl -lgslcblas" |
| 334 | (string-append "prefix=" (assoc-ref %outputs "out")) |
| 335 | (string-append "HTSDIR=" (assoc-ref %build-inputs "htslib") "/include") |
| 336 | (string-append "HTSLIB=" (assoc-ref %build-inputs "htslib") "/lib/libhts.so") |
| 337 | (string-append "BGZIP=" (assoc-ref %build-inputs "htslib") "/bin/bgzip") |
| 338 | (string-append "TABIX=" (assoc-ref %build-inputs "htslib") "/bin/tabix") |
| 339 | (string-append "PACKAGE_VERSION=" ,version)) |
| 340 | #:phases |
| 341 | (modify-phases %standard-phases |
| 342 | (add-before 'check 'patch-tests |
| 343 | (lambda _ |
| 344 | (substitute* "test/test.pl" |
| 345 | (("/bin/bash") (which "bash"))) |
| 346 | #t))))) |
| 347 | (native-inputs |
| 348 | `(("htslib" ,htslib) |
| 349 | ("perl" ,perl))) |
| 350 | (inputs |
| 351 | `(("gsl" ,gsl) |
| 352 | ("zlib" ,zlib))) |
| 353 | (home-page "https://samtools.github.io/bcftools/") |
| 354 | (synopsis "Utilities for variant calling and manipulating VCFs and BCFs") |
| 355 | (description |
| 356 | "BCFtools is a set of utilities that manipulate variant calls in the |
| 357 | Variant Call Format (VCF) and its binary counterpart BCF. All commands work |
| 358 | transparently with both VCFs and BCFs, both uncompressed and BGZF-compressed.") |
| 359 | ;; The sources are dual MIT/GPL, but becomes GPL-only when USE_GPL=1. |
| 360 | (license (list license:gpl3+ license:expat)))) |
| 361 | |
| 362 | (define-public bedops |
| 363 | (package |
| 364 | (name "bedops") |
| 365 | (version "2.4.14") |
| 366 | (source (origin |
| 367 | (method url-fetch) |
| 368 | (uri (string-append "https://github.com/bedops/bedops/archive/v" |
| 369 | version ".tar.gz")) |
| 370 | (file-name (string-append name "-" version ".tar.gz")) |
| 371 | (sha256 |
| 372 | (base32 |
| 373 | "1kqbac547wyqma81cyky9n7mkgikjpsfd3nnmcm6hpqwanqgh10v")))) |
| 374 | (build-system gnu-build-system) |
| 375 | (arguments |
| 376 | '(#:tests? #f |
| 377 | #:make-flags (list (string-append "BINDIR=" %output "/bin")) |
| 378 | #:phases |
| 379 | (modify-phases %standard-phases |
| 380 | (add-after 'unpack 'unpack-tarballs |
| 381 | (lambda _ |
| 382 | ;; FIXME: Bedops includes tarballs of minimally patched upstream |
| 383 | ;; libraries jansson, zlib, and bzip2. We cannot just use stock |
| 384 | ;; libraries because at least one of the libraries (zlib) is |
| 385 | ;; patched to add a C++ function definition (deflateInit2cpp). |
| 386 | ;; Until the Bedops developers offer a way to link against system |
| 387 | ;; libraries we have to build the in-tree copies of these three |
| 388 | ;; libraries. |
| 389 | |
| 390 | ;; See upstream discussion: |
| 391 | ;; https://github.com/bedops/bedops/issues/124 |
| 392 | |
| 393 | ;; Unpack the tarballs to benefit from shebang patching. |
| 394 | (with-directory-excursion "third-party" |
| 395 | (and (zero? (system* "tar" "xvf" "jansson-2.6.tar.bz2")) |
| 396 | (zero? (system* "tar" "xvf" "zlib-1.2.7.tar.bz2")) |
| 397 | (zero? (system* "tar" "xvf" "bzip2-1.0.6.tar.bz2")))) |
| 398 | ;; Disable unpacking of tarballs in Makefile. |
| 399 | (substitute* "system.mk/Makefile.linux" |
| 400 | (("^\tbzcat .*") "\t@echo \"not unpacking\"\n") |
| 401 | (("\\./configure") "CONFIG_SHELL=bash ./configure")) |
| 402 | (substitute* "third-party/zlib-1.2.7/Makefile.in" |
| 403 | (("^SHELL=.*$") "SHELL=bash\n")) |
| 404 | #t)) |
| 405 | (delete 'configure)))) |
| 406 | (home-page "https://github.com/bedops/bedops") |
| 407 | (synopsis "Tools for high-performance genomic feature operations") |
| 408 | (description |
| 409 | "BEDOPS is a suite of tools to address common questions raised in genomic |
| 410 | studies---mostly with regard to overlap and proximity relationships between |
| 411 | data sets. It aims to be scalable and flexible, facilitating the efficient |
| 412 | and accurate analysis and management of large-scale genomic data. |
| 413 | |
| 414 | BEDOPS provides tools that perform highly efficient and scalable Boolean and |
| 415 | other set operations, statistical calculations, archiving, conversion and |
| 416 | other management of genomic data of arbitrary scale. Tasks can be easily |
| 417 | split by chromosome for distributing whole-genome analyses across a |
| 418 | computational cluster.") |
| 419 | (license license:gpl2+))) |
| 420 | |
| 421 | (define-public bedtools |
| 422 | (package |
| 423 | (name "bedtools") |
| 424 | (version "2.27.1") |
| 425 | (source (origin |
| 426 | (method url-fetch) |
| 427 | (uri (string-append "https://github.com/arq5x/bedtools2/releases/" |
| 428 | "download/v" version "/" |
| 429 | "bedtools-" version ".tar.gz")) |
| 430 | (sha256 |
| 431 | (base32 |
| 432 | "1ndg5yknrxl4djx8ddzgk12rrbiidfpmkkg5z3f95jzryfxarhn8")))) |
| 433 | (build-system gnu-build-system) |
| 434 | (arguments |
| 435 | '(#:test-target "test" |
| 436 | #:make-flags |
| 437 | (list (string-append "prefix=" (assoc-ref %outputs "out"))) |
| 438 | #:phases |
| 439 | (modify-phases %standard-phases |
| 440 | (delete 'configure)))) |
| 441 | (native-inputs `(("python" ,python-2))) |
| 442 | (inputs |
| 443 | `(("samtools" ,samtools) |
| 444 | ("zlib" ,zlib))) |
| 445 | (home-page "https://github.com/arq5x/bedtools2") |
| 446 | (synopsis "Tools for genome analysis and arithmetic") |
| 447 | (description |
| 448 | "Collectively, the bedtools utilities are a swiss-army knife of tools for |
| 449 | a wide-range of genomics analysis tasks. The most widely-used tools enable |
| 450 | genome arithmetic: that is, set theory on the genome. For example, bedtools |
| 451 | allows one to intersect, merge, count, complement, and shuffle genomic |
| 452 | intervals from multiple files in widely-used genomic file formats such as BAM, |
| 453 | BED, GFF/GTF, VCF.") |
| 454 | (license license:gpl2))) |
| 455 | |
| 456 | ;; Later releases of bedtools produce files with more columns than |
| 457 | ;; what Ribotaper expects. |
| 458 | (define-public bedtools-2.18 |
| 459 | (package (inherit bedtools) |
| 460 | (name "bedtools") |
| 461 | (version "2.18.0") |
| 462 | (source (origin |
| 463 | (method url-fetch) |
| 464 | (uri (string-append "https://github.com/arq5x/bedtools2/" |
| 465 | "archive/v" version ".tar.gz")) |
| 466 | (file-name (string-append name "-" version ".tar.gz")) |
| 467 | (sha256 |
| 468 | (base32 |
| 469 | "05vrnr8yp7swfagshzpgqmzk1blnwnq8pq5pckzi1m26w98d63vf")))) |
| 470 | (arguments |
| 471 | '(#:test-target "test" |
| 472 | #:phases |
| 473 | (modify-phases %standard-phases |
| 474 | (delete 'configure) |
| 475 | (replace 'install |
| 476 | (lambda* (#:key outputs #:allow-other-keys) |
| 477 | (let ((bin (string-append (assoc-ref outputs "out") "/bin/"))) |
| 478 | (for-each (lambda (file) |
| 479 | (install-file file bin)) |
| 480 | (find-files "bin" ".*"))) |
| 481 | #t))))))) |
| 482 | |
| 483 | (define-public ribotaper |
| 484 | (package |
| 485 | (name "ribotaper") |
| 486 | (version "1.3.1") |
| 487 | (source (origin |
| 488 | (method url-fetch) |
| 489 | (uri (string-append "https://ohlerlab.mdc-berlin.de/" |
| 490 | "files/RiboTaper/RiboTaper_Version_" |
| 491 | version ".tar.gz")) |
| 492 | (sha256 |
| 493 | (base32 |
| 494 | "0ykjbps1y3z3085q94npw8i9x5gldc6shy8vlc08v76zljsm07hv")))) |
| 495 | (build-system gnu-build-system) |
| 496 | (inputs |
| 497 | `(("bedtools" ,bedtools-2.18) |
| 498 | ("samtools" ,samtools-0.1) |
| 499 | ("r-minimal" ,r-minimal) |
| 500 | ("r-foreach" ,r-foreach) |
| 501 | ("r-xnomial" ,r-xnomial) |
| 502 | ("r-domc" ,r-domc) |
| 503 | ("r-multitaper" ,r-multitaper) |
| 504 | ("r-seqinr" ,r-seqinr))) |
| 505 | (home-page "https://ohlerlab.mdc-berlin.de/software/RiboTaper_126/") |
| 506 | (synopsis "Define translated ORFs using ribosome profiling data") |
| 507 | (description |
| 508 | "Ribotaper is a method for defining translated @dfn{open reading |
| 509 | frames} (ORFs) using ribosome profiling (ribo-seq) data. This package |
| 510 | provides the Ribotaper pipeline.") |
| 511 | (license license:gpl3+))) |
| 512 | |
| 513 | (define-public ribodiff |
| 514 | (package |
| 515 | (name "ribodiff") |
| 516 | (version "0.2.2") |
| 517 | (source |
| 518 | (origin |
| 519 | (method url-fetch) |
| 520 | (uri (string-append "https://github.com/ratschlab/RiboDiff/" |
| 521 | "archive/v" version ".tar.gz")) |
| 522 | (file-name (string-append name "-" version ".tar.gz")) |
| 523 | (sha256 |
| 524 | (base32 |
| 525 | "0wpbwmfv05wdjxv7ikm664f7s7p7cqr8jnw99zrda0q67rl50aaj")))) |
| 526 | (build-system python-build-system) |
| 527 | (arguments |
| 528 | `(#:python ,python-2 |
| 529 | #:phases |
| 530 | (modify-phases %standard-phases |
| 531 | ;; Generate an installable executable script wrapper. |
| 532 | (add-after 'unpack 'patch-setup.py |
| 533 | (lambda _ |
| 534 | (substitute* "setup.py" |
| 535 | (("^(.*)packages=.*" line prefix) |
| 536 | (string-append line "\n" |
| 537 | prefix "scripts=['scripts/TE.py'],\n"))) |
| 538 | #t))))) |
| 539 | (inputs |
| 540 | `(("python-numpy" ,python2-numpy) |
| 541 | ("python-matplotlib" ,python2-matplotlib) |
| 542 | ("python-scipy" ,python2-scipy) |
| 543 | ("python-statsmodels" ,python2-statsmodels))) |
| 544 | (native-inputs |
| 545 | `(("python-mock" ,python2-mock) |
| 546 | ("python-nose" ,python2-nose))) |
| 547 | (home-page "http://public.bmi.inf.ethz.ch/user/zhongy/RiboDiff/") |
| 548 | (synopsis "Detect translation efficiency changes from ribosome footprints") |
| 549 | (description "RiboDiff is a statistical tool that detects the protein |
| 550 | translational efficiency change from Ribo-Seq (ribosome footprinting) and |
| 551 | RNA-Seq data. It uses a generalized linear model to detect genes showing |
| 552 | difference in translational profile taking mRNA abundance into account. It |
| 553 | facilitates us to decipher the translational regulation that behave |
| 554 | independently with transcriptional regulation.") |
| 555 | (license license:gpl3+))) |
| 556 | |
| 557 | (define-public bioawk |
| 558 | (package |
| 559 | (name "bioawk") |
| 560 | (version "1.0") |
| 561 | (source (origin |
| 562 | (method url-fetch) |
| 563 | (uri (string-append "https://github.com/lh3/bioawk/archive/v" |
| 564 | version ".tar.gz")) |
| 565 | (file-name (string-append name "-" version ".tar.gz")) |
| 566 | (sha256 |
| 567 | (base32 "1daizxsk17ahi9n58fj8vpgwyhzrzh54bzqhanjanp88kgrz7gjw")))) |
| 568 | (build-system gnu-build-system) |
| 569 | (inputs |
| 570 | `(("zlib" ,zlib))) |
| 571 | (native-inputs |
| 572 | `(("bison" ,bison))) |
| 573 | (arguments |
| 574 | `(#:tests? #f ; There are no tests to run. |
| 575 | ;; Bison must generate files, before other targets can build. |
| 576 | #:parallel-build? #f |
| 577 | #:phases |
| 578 | (modify-phases %standard-phases |
| 579 | (delete 'configure) ; There is no configure phase. |
| 580 | (replace 'install |
| 581 | (lambda* (#:key outputs #:allow-other-keys) |
| 582 | (let* ((out (assoc-ref outputs "out")) |
| 583 | (bin (string-append out "/bin")) |
| 584 | (man (string-append out "/share/man/man1"))) |
| 585 | (mkdir-p man) |
| 586 | (copy-file "awk.1" (string-append man "/bioawk.1")) |
| 587 | (install-file "bioawk" bin))))))) |
| 588 | (home-page "https://github.com/lh3/bioawk") |
| 589 | (synopsis "AWK with bioinformatics extensions") |
| 590 | (description "Bioawk is an extension to Brian Kernighan's awk, adding the |
| 591 | support of several common biological data formats, including optionally gzip'ed |
| 592 | BED, GFF, SAM, VCF, FASTA/Q and TAB-delimited formats with column names. It |
| 593 | also adds a few built-in functions and a command line option to use TAB as the |
| 594 | input/output delimiter. When the new functionality is not used, bioawk is |
| 595 | intended to behave exactly the same as the original BWK awk.") |
| 596 | (license license:x11))) |
| 597 | |
| 598 | (define-public python2-pybedtools |
| 599 | (package |
| 600 | (name "python2-pybedtools") |
| 601 | (version "0.6.9") |
| 602 | (source (origin |
| 603 | (method url-fetch) |
| 604 | (uri (string-append |
| 605 | "https://pypi.python.org/packages/source/p/pybedtools/pybedtools-" |
| 606 | version ".tar.gz")) |
| 607 | (sha256 |
| 608 | (base32 |
| 609 | "1ldzdxw1p4y3g2ignmggsdypvqkcwqwzhdha4rbgpih048z5p4an")))) |
| 610 | (build-system python-build-system) |
| 611 | (arguments `(#:python ,python-2)) ; no Python 3 support |
| 612 | (inputs |
| 613 | `(("python-matplotlib" ,python2-matplotlib))) |
| 614 | (propagated-inputs |
| 615 | `(("bedtools" ,bedtools) |
| 616 | ("samtools" ,samtools))) |
| 617 | (native-inputs |
| 618 | `(("python-cython" ,python2-cython) |
| 619 | ("python-pyyaml" ,python2-pyyaml) |
| 620 | ("python-nose" ,python2-nose))) |
| 621 | (home-page "https://pythonhosted.org/pybedtools/") |
| 622 | (synopsis "Python wrapper for BEDtools programs") |
| 623 | (description |
| 624 | "pybedtools is a Python wrapper for Aaron Quinlan's BEDtools programs, |
| 625 | which are widely used for genomic interval manipulation or \"genome algebra\". |
| 626 | pybedtools extends BEDTools by offering feature-level manipulations from with |
| 627 | Python.") |
| 628 | (license license:gpl2+))) |
| 629 | |
| 630 | (define-public python-biom-format |
| 631 | (package |
| 632 | (name "python-biom-format") |
| 633 | (version "2.1.6") |
| 634 | (source |
| 635 | (origin |
| 636 | (method url-fetch) |
| 637 | ;; Use GitHub as source because PyPI distribution does not contain |
| 638 | ;; test data: https://github.com/biocore/biom-format/issues/693 |
| 639 | (uri (string-append "https://github.com/biocore/biom-format/archive/" |
| 640 | version ".tar.gz")) |
| 641 | (file-name (string-append name "-" version ".tar.gz")) |
| 642 | (sha256 |
| 643 | (base32 |
| 644 | "08cr7wpahk6zb31h4bs7jmzpvxcqv9s13xz40h6y2h656jvdvnpj")))) |
| 645 | (build-system python-build-system) |
| 646 | (propagated-inputs |
| 647 | `(("python-numpy" ,python-numpy) |
| 648 | ("python-scipy" ,python-scipy) |
| 649 | ("python-future" ,python-future) |
| 650 | ("python-click" ,python-click) |
| 651 | ("python-h5py" ,python-h5py) |
| 652 | ("python-pandas" ,python-pandas))) |
| 653 | (native-inputs |
| 654 | `(("python-nose" ,python-nose))) |
| 655 | (home-page "http://www.biom-format.org") |
| 656 | (synopsis "Biological Observation Matrix (BIOM) format utilities") |
| 657 | (description |
| 658 | "The BIOM file format is designed to be a general-use format for |
| 659 | representing counts of observations e.g. operational taxonomic units, KEGG |
| 660 | orthology groups or lipid types, in one or more biological samples |
| 661 | e.g. microbiome samples, genomes, metagenomes.") |
| 662 | (license license:bsd-3) |
| 663 | (properties `((python2-variant . ,(delay python2-biom-format)))))) |
| 664 | |
| 665 | (define-public python2-biom-format |
| 666 | (let ((base (package-with-python2 (strip-python2-variant python-biom-format)))) |
| 667 | (package |
| 668 | (inherit base) |
| 669 | (arguments |
| 670 | `(#:phases |
| 671 | (modify-phases %standard-phases |
| 672 | ;; Do not require the unmaintained pyqi library. |
| 673 | (add-after 'unpack 'remove-pyqi |
| 674 | (lambda _ |
| 675 | (substitute* "setup.py" |
| 676 | (("install_requires.append\\(\"pyqi\"\\)") "pass")) |
| 677 | #t))) |
| 678 | ,@(package-arguments base)))))) |
| 679 | |
| 680 | (define-public bioperl-minimal |
| 681 | (let* ((inputs `(("perl-module-build" ,perl-module-build) |
| 682 | ("perl-data-stag" ,perl-data-stag) |
| 683 | ("perl-libwww" ,perl-libwww) |
| 684 | ("perl-uri" ,perl-uri))) |
| 685 | (transitive-inputs |
| 686 | (map (compose package-name cadr) |
| 687 | (delete-duplicates |
| 688 | (concatenate |
| 689 | (map (compose package-transitive-target-inputs cadr) inputs)))))) |
| 690 | (package |
| 691 | (name "bioperl-minimal") |
| 692 | (version "1.7.0") |
| 693 | (source |
| 694 | (origin |
| 695 | (method url-fetch) |
| 696 | (uri (string-append "https://github.com/bioperl/bioperl-live/" |
| 697 | "archive/release-" |
| 698 | (string-map (lambda (c) |
| 699 | (if (char=? c #\.) |
| 700 | #\- c)) version) |
| 701 | ".tar.gz")) |
| 702 | (sha256 |
| 703 | (base32 |
| 704 | "12phgpxwgkqflkwfb9dcqg7a31dpjlfhar8wcgv0aj5ln4akfz06")))) |
| 705 | (build-system perl-build-system) |
| 706 | (arguments |
| 707 | `(#:phases |
| 708 | (modify-phases %standard-phases |
| 709 | (add-after |
| 710 | 'install 'wrap-programs |
| 711 | (lambda* (#:key outputs #:allow-other-keys) |
| 712 | ;; Make sure all executables in "bin" find the required Perl |
| 713 | ;; modules at runtime. As the PERL5LIB variable contains also |
| 714 | ;; the paths of native inputs, we pick the transitive target |
| 715 | ;; inputs from %build-inputs. |
| 716 | (let* ((out (assoc-ref outputs "out")) |
| 717 | (bin (string-append out "/bin/")) |
| 718 | (path (string-join |
| 719 | (cons (string-append out "/lib/perl5/site_perl") |
| 720 | (map (lambda (name) |
| 721 | (assoc-ref %build-inputs name)) |
| 722 | ',transitive-inputs)) |
| 723 | ":"))) |
| 724 | (for-each (lambda (file) |
| 725 | (wrap-program file |
| 726 | `("PERL5LIB" ":" prefix (,path)))) |
| 727 | (find-files bin "\\.pl$")) |
| 728 | #t)))))) |
| 729 | (inputs inputs) |
| 730 | (native-inputs |
| 731 | `(("perl-test-most" ,perl-test-most))) |
| 732 | (home-page "http://search.cpan.org/dist/BioPerl") |
| 733 | (synopsis "Bioinformatics toolkit") |
| 734 | (description |
| 735 | "BioPerl is the product of a community effort to produce Perl code which |
| 736 | is useful in biology. Examples include Sequence objects, Alignment objects |
| 737 | and database searching objects. These objects not only do what they are |
| 738 | advertised to do in the documentation, but they also interact - Alignment |
| 739 | objects are made from the Sequence objects, Sequence objects have access to |
| 740 | Annotation and SeqFeature objects and databases, Blast objects can be |
| 741 | converted to Alignment objects, and so on. This means that the objects |
| 742 | provide a coordinated and extensible framework to do computational biology.") |
| 743 | (license license:perl-license)))) |
| 744 | |
| 745 | (define-public python-biopython |
| 746 | (package |
| 747 | (name "python-biopython") |
| 748 | (version "1.70") |
| 749 | (source (origin |
| 750 | (method url-fetch) |
| 751 | ;; use PyPi rather than biopython.org to ease updating |
| 752 | (uri (pypi-uri "biopython" version)) |
| 753 | (sha256 |
| 754 | (base32 |
| 755 | "0nz4n9d2y2dg849gn1z0vjlkwcpzzkzy3fij7x94a6ixy2c54z2a")))) |
| 756 | (build-system python-build-system) |
| 757 | (arguments |
| 758 | `(#:phases |
| 759 | (modify-phases %standard-phases |
| 760 | (add-before 'check 'set-home |
| 761 | ;; Some tests require a home directory to be set. |
| 762 | (lambda _ (setenv "HOME" "/tmp") #t))))) |
| 763 | (propagated-inputs |
| 764 | `(("python-numpy" ,python-numpy))) |
| 765 | (home-page "http://biopython.org/") |
| 766 | (synopsis "Tools for biological computation in Python") |
| 767 | (description |
| 768 | "Biopython is a set of tools for biological computation including parsers |
| 769 | for bioinformatics files into Python data structures; interfaces to common |
| 770 | bioinformatics programs; a standard sequence class and tools for performing |
| 771 | common operations on them; code to perform data classification; code for |
| 772 | dealing with alignments; code making it easy to split up parallelizable tasks |
| 773 | into separate processes; and more.") |
| 774 | (license (license:non-copyleft "http://www.biopython.org/DIST/LICENSE")))) |
| 775 | |
| 776 | (define-public python2-biopython |
| 777 | (package-with-python2 python-biopython)) |
| 778 | |
| 779 | ;; An outdated version of biopython is required for seqmagick, see |
| 780 | ;; https://github.com/fhcrc/seqmagick/issues/59 |
| 781 | ;; When that issue has been resolved this package should be removed. |
| 782 | (define python2-biopython-1.66 |
| 783 | (package |
| 784 | (inherit python2-biopython) |
| 785 | (version "1.66") |
| 786 | (source (origin |
| 787 | (method url-fetch) |
| 788 | (uri (pypi-uri "biopython" version)) |
| 789 | (sha256 |
| 790 | (base32 |
| 791 | "1gdv92593klimg22icf5j9by7xiq86jnwzkpz4abaa05ylkdf6hp")))))) |
| 792 | |
| 793 | (define-public bpp-core |
| 794 | ;; The last release was in 2014 and the recommended way to install from source |
| 795 | ;; is to clone the git repository, so we do this. |
| 796 | ;; http://biopp.univ-montp2.fr/wiki/index.php/Main_Page |
| 797 | (let ((commit "7d8bced0d1a87291ea8dd7046b7fb5ff9c35c582")) |
| 798 | (package |
| 799 | (name "bpp-core") |
| 800 | (version (string-append "2.2.0-1." (string-take commit 7))) |
| 801 | (source (origin |
| 802 | (method git-fetch) |
| 803 | (uri (git-reference |
| 804 | (url "http://biopp.univ-montp2.fr/git/bpp-core") |
| 805 | (commit commit))) |
| 806 | (file-name (string-append name "-" version "-checkout")) |
| 807 | (sha256 |
| 808 | (base32 |
| 809 | "10djsq5vlnkilv436gnmh4irpk49v29pa69r6xiryg32xmvn909j")))) |
| 810 | (build-system cmake-build-system) |
| 811 | (arguments |
| 812 | `(#:parallel-build? #f)) |
| 813 | (inputs |
| 814 | `(("gcc" ,gcc-5))) ; Compilation of bpp-phyl fails with GCC 4.9 so we |
| 815 | ; compile all of the bpp packages with GCC 5. |
| 816 | (home-page "http://biopp.univ-montp2.fr") |
| 817 | (synopsis "C++ libraries for Bioinformatics") |
| 818 | (description |
| 819 | "Bio++ is a set of C++ libraries for Bioinformatics, including sequence |
| 820 | analysis, phylogenetics, molecular evolution and population genetics. It is |
| 821 | Object Oriented and is designed to be both easy to use and computer efficient. |
| 822 | Bio++ intends to help programmers to write computer expensive programs, by |
| 823 | providing them a set of re-usable tools.") |
| 824 | (license license:cecill-c)))) |
| 825 | |
| 826 | (define-public bpp-phyl |
| 827 | ;; The last release was in 2014 and the recommended way to install from source |
| 828 | ;; is to clone the git repository, so we do this. |
| 829 | ;; http://biopp.univ-montp2.fr/wiki/index.php/Main_Page |
| 830 | (let ((commit "0c07167b629f68b569bf274d1ad0c4af83276ae2")) |
| 831 | (package |
| 832 | (name "bpp-phyl") |
| 833 | (version (string-append "2.2.0-1." (string-take commit 7))) |
| 834 | (source (origin |
| 835 | (method git-fetch) |
| 836 | (uri (git-reference |
| 837 | (url "http://biopp.univ-montp2.fr/git/bpp-phyl") |
| 838 | (commit commit))) |
| 839 | (file-name (string-append name "-" version "-checkout")) |
| 840 | (sha256 |
| 841 | (base32 |
| 842 | "1ssjgchzwj3iai26kyly7gwkdv8sk59nqhkb1wpap3sf5m6kyllh")))) |
| 843 | (build-system cmake-build-system) |
| 844 | (arguments |
| 845 | `(#:parallel-build? #f |
| 846 | ;; If out-of-source, test data is not copied into the build directory |
| 847 | ;; so the tests fail. |
| 848 | #:out-of-source? #f)) |
| 849 | (inputs |
| 850 | `(("bpp-core" ,bpp-core) |
| 851 | ("bpp-seq" ,bpp-seq) |
| 852 | ;; GCC 4.8 fails due to an 'internal compiler error', so we use a more |
| 853 | ;; modern GCC. |
| 854 | ("gcc" ,gcc-5))) |
| 855 | (home-page "http://biopp.univ-montp2.fr") |
| 856 | (synopsis "Bio++ phylogenetic Library") |
| 857 | (description |
| 858 | "Bio++ is a set of C++ libraries for Bioinformatics, including sequence |
| 859 | analysis, phylogenetics, molecular evolution and population genetics. This |
| 860 | library provides phylogenetics-related modules.") |
| 861 | (license license:cecill-c)))) |
| 862 | |
| 863 | (define-public bpp-popgen |
| 864 | ;; The last release was in 2014 and the recommended way to install from source |
| 865 | ;; is to clone the git repository, so we do this. |
| 866 | ;; http://biopp.univ-montp2.fr/wiki/index.php/Main_Page |
| 867 | (let ((commit "e472bac9b1a148803895d747cd6d0c5904f85d9f")) |
| 868 | (package |
| 869 | (name "bpp-popgen") |
| 870 | (version (string-append "2.2.0-1." (string-take commit 7))) |
| 871 | (source (origin |
| 872 | (method git-fetch) |
| 873 | (uri (git-reference |
| 874 | (url "http://biopp.univ-montp2.fr/git/bpp-popgen") |
| 875 | (commit commit))) |
| 876 | (file-name (string-append name "-" version "-checkout")) |
| 877 | (sha256 |
| 878 | (base32 |
| 879 | "0yn82dzn1n5629nzja68xfrhi655709rjanyryb36vzkmymy6dw5")))) |
| 880 | (build-system cmake-build-system) |
| 881 | (arguments |
| 882 | `(#:parallel-build? #f |
| 883 | #:tests? #f)) ; There are no tests. |
| 884 | (inputs |
| 885 | `(("bpp-core" ,bpp-core) |
| 886 | ("bpp-seq" ,bpp-seq) |
| 887 | ("gcc" ,gcc-5))) |
| 888 | (home-page "http://biopp.univ-montp2.fr") |
| 889 | (synopsis "Bio++ population genetics library") |
| 890 | (description |
| 891 | "Bio++ is a set of C++ libraries for Bioinformatics, including sequence |
| 892 | analysis, phylogenetics, molecular evolution and population genetics. This |
| 893 | library provides population genetics-related modules.") |
| 894 | (license license:cecill-c)))) |
| 895 | |
| 896 | (define-public bpp-seq |
| 897 | ;; The last release was in 2014 and the recommended way to install from source |
| 898 | ;; is to clone the git repository, so we do this. |
| 899 | ;; http://biopp.univ-montp2.fr/wiki/index.php/Main_Page |
| 900 | (let ((commit "6cfa07965ce152e5598a89df2fa80a75973bfa33")) |
| 901 | (package |
| 902 | (name "bpp-seq") |
| 903 | (version (string-append "2.2.0-1." (string-take commit 7))) |
| 904 | (source (origin |
| 905 | (method git-fetch) |
| 906 | (uri (git-reference |
| 907 | (url "http://biopp.univ-montp2.fr/git/bpp-seq") |
| 908 | (commit commit))) |
| 909 | (file-name (string-append name "-" version "-checkout")) |
| 910 | (sha256 |
| 911 | (base32 |
| 912 | "1nys5jq7jqvdg40d91wsmj3q2yzy4276cp7sp44n67p468f27zf2")))) |
| 913 | (build-system cmake-build-system) |
| 914 | (arguments |
| 915 | `(#:parallel-build? #f |
| 916 | ;; If out-of-source, test data is not copied into the build directory |
| 917 | ;; so the tests fail. |
| 918 | #:out-of-source? #f)) |
| 919 | (inputs |
| 920 | `(("bpp-core" ,bpp-core) |
| 921 | ("gcc" ,gcc-5))) ; Use GCC 5 as per 'bpp-core'. |
| 922 | (home-page "http://biopp.univ-montp2.fr") |
| 923 | (synopsis "Bio++ sequence library") |
| 924 | (description |
| 925 | "Bio++ is a set of C++ libraries for Bioinformatics, including sequence |
| 926 | analysis, phylogenetics, molecular evolution and population genetics. This |
| 927 | library provides sequence-related modules.") |
| 928 | (license license:cecill-c)))) |
| 929 | |
| 930 | (define-public bppsuite |
| 931 | ;; The last release was in 2014 and the recommended way to install from source |
| 932 | ;; is to clone the git repository, so we do this. |
| 933 | ;; http://biopp.univ-montp2.fr/wiki/index.php/Main_Page |
| 934 | (let ((commit "c516147f57aa50961121cd505bed52cd7603698b")) |
| 935 | (package |
| 936 | (name "bppsuite") |
| 937 | (version (string-append "2.2.0-1." (string-take commit 7))) |
| 938 | (source (origin |
| 939 | (method git-fetch) |
| 940 | (uri (git-reference |
| 941 | (url "http://biopp.univ-montp2.fr/git/bppsuite") |
| 942 | (commit commit))) |
| 943 | (file-name (string-append name "-" version "-checkout")) |
| 944 | (sha256 |
| 945 | (base32 |
| 946 | "1y87pxvw0jxjizhq2dr9g2r91md45k1p9ih2sl1yy1y3p934l2kb")))) |
| 947 | (build-system cmake-build-system) |
| 948 | (arguments |
| 949 | `(#:parallel-build? #f |
| 950 | #:tests? #f)) ; There are no tests. |
| 951 | (native-inputs |
| 952 | `(("groff" ,groff) |
| 953 | ("man-db" ,man-db) |
| 954 | ("texinfo" ,texinfo))) |
| 955 | (inputs |
| 956 | `(("bpp-core" ,bpp-core) |
| 957 | ("bpp-seq" ,bpp-seq) |
| 958 | ("bpp-phyl" ,bpp-phyl) |
| 959 | ("bpp-phyl" ,bpp-popgen) |
| 960 | ("gcc" ,gcc-5))) |
| 961 | (home-page "http://biopp.univ-montp2.fr") |
| 962 | (synopsis "Bioinformatics tools written with the Bio++ libraries") |
| 963 | (description |
| 964 | "Bio++ is a set of C++ libraries for Bioinformatics, including sequence |
| 965 | analysis, phylogenetics, molecular evolution and population genetics. This |
| 966 | package provides command line tools using the Bio++ library.") |
| 967 | (license license:cecill-c)))) |
| 968 | |
| 969 | (define-public blast+ |
| 970 | (package |
| 971 | (name "blast+") |
| 972 | (version "2.6.0") |
| 973 | (source (origin |
| 974 | (method url-fetch) |
| 975 | (uri (string-append |
| 976 | "ftp://ftp.ncbi.nlm.nih.gov/blast/executables/blast+/" |
| 977 | version "/ncbi-blast-" version "+-src.tar.gz")) |
| 978 | (sha256 |
| 979 | (base32 |
| 980 | "15n937pw5aqmyfjb6l387d18grqbb96l63d5xj4l7yyh0zbf2405")) |
| 981 | (patches (search-patches "blast+-fix-makefile.patch")) |
| 982 | (modules '((guix build utils))) |
| 983 | (snippet |
| 984 | '(begin |
| 985 | ;; Remove bundled bzip2, zlib and pcre. |
| 986 | (delete-file-recursively "c++/src/util/compress/bzip2") |
| 987 | (delete-file-recursively "c++/src/util/compress/zlib") |
| 988 | (delete-file-recursively "c++/src/util/regexp") |
| 989 | (substitute* "c++/src/util/compress/Makefile.in" |
| 990 | (("bzip2 zlib api") "api")) |
| 991 | ;; Remove useless msbuild directory |
| 992 | (delete-file-recursively |
| 993 | "c++/src/build-system/project_tree_builder/msbuild") |
| 994 | #t)))) |
| 995 | (build-system gnu-build-system) |
| 996 | (arguments |
| 997 | `(;; There are two(!) tests for this massive library, and both fail with |
| 998 | ;; "unparsable timing stats". |
| 999 | ;; ERR [127] -- [serial/datatool] datatool.sh (unparsable timing stats) |
| 1000 | ;; ERR [127] -- [serial/datatool] datatool_xml.sh (unparsable timing stats) |
| 1001 | #:tests? #f |
| 1002 | #:out-of-source? #t |
| 1003 | #:parallel-build? #f ; not supported |
| 1004 | #:phases |
| 1005 | (modify-phases %standard-phases |
| 1006 | (add-before |
| 1007 | 'configure 'set-HOME |
| 1008 | ;; $HOME needs to be set at some point during the configure phase |
| 1009 | (lambda _ (setenv "HOME" "/tmp") #t)) |
| 1010 | (add-after |
| 1011 | 'unpack 'enter-dir |
| 1012 | (lambda _ (chdir "c++") #t)) |
| 1013 | (add-after |
| 1014 | 'enter-dir 'fix-build-system |
| 1015 | (lambda _ |
| 1016 | (define (which* cmd) |
| 1017 | (cond ((string=? cmd "date") |
| 1018 | ;; make call to "date" deterministic |
| 1019 | "date -d @0") |
| 1020 | ((which cmd) |
| 1021 | => identity) |
| 1022 | (else |
| 1023 | (format (current-error-port) |
| 1024 | "WARNING: Unable to find absolute path for ~s~%" |
| 1025 | cmd) |
| 1026 | #f))) |
| 1027 | |
| 1028 | ;; Rewrite hardcoded paths to various tools |
| 1029 | (substitute* (append '("src/build-system/configure.ac" |
| 1030 | "src/build-system/configure" |
| 1031 | "src/build-system/helpers/run_with_lock.c" |
| 1032 | "scripts/common/impl/if_diff.sh" |
| 1033 | "scripts/common/impl/run_with_lock.sh" |
| 1034 | "src/build-system/Makefile.configurables.real" |
| 1035 | "src/build-system/Makefile.in.top" |
| 1036 | "src/build-system/Makefile.meta.gmake=no" |
| 1037 | "src/build-system/Makefile.meta.in" |
| 1038 | "src/build-system/Makefile.meta_l" |
| 1039 | "src/build-system/Makefile.meta_p" |
| 1040 | "src/build-system/Makefile.meta_r" |
| 1041 | "src/build-system/Makefile.mk.in" |
| 1042 | "src/build-system/Makefile.requirements" |
| 1043 | "src/build-system/Makefile.rules_with_autodep.in") |
| 1044 | (find-files "scripts/common/check" "\\.sh$")) |
| 1045 | (("(/usr/bin/|/bin/)([a-z][-_.a-z]*)" all dir cmd) |
| 1046 | (or (which* cmd) all))) |
| 1047 | |
| 1048 | (substitute* (find-files "src/build-system" "^config.*") |
| 1049 | (("LN_S=/bin/\\$LN_S") (string-append "LN_S=" (which "ln"))) |
| 1050 | (("^PATH=.*") "")) |
| 1051 | |
| 1052 | ;; rewrite "/var/tmp" in check script |
| 1053 | (substitute* "scripts/common/check/check_make_unix.sh" |
| 1054 | (("/var/tmp") "/tmp")) |
| 1055 | |
| 1056 | ;; do not reset PATH |
| 1057 | (substitute* (find-files "scripts/common/impl/" "\\.sh$") |
| 1058 | (("^ *PATH=.*") "") |
| 1059 | (("action=/bin/") "action=") |
| 1060 | (("export PATH") ":")) |
| 1061 | #t)) |
| 1062 | (replace |
| 1063 | 'configure |
| 1064 | (lambda* (#:key inputs outputs #:allow-other-keys) |
| 1065 | (let ((out (assoc-ref outputs "out")) |
| 1066 | (lib (string-append (assoc-ref outputs "lib") "/lib")) |
| 1067 | (include (string-append (assoc-ref outputs "include") |
| 1068 | "/include/ncbi-tools++"))) |
| 1069 | ;; The 'configure' script doesn't recognize things like |
| 1070 | ;; '--enable-fast-install'. |
| 1071 | (zero? (system* "./configure.orig" |
| 1072 | (string-append "--with-build-root=" (getcwd) "/build") |
| 1073 | (string-append "--prefix=" out) |
| 1074 | (string-append "--libdir=" lib) |
| 1075 | (string-append "--includedir=" include) |
| 1076 | (string-append "--with-bz2=" |
| 1077 | (assoc-ref inputs "bzip2")) |
| 1078 | (string-append "--with-z=" |
| 1079 | (assoc-ref inputs "zlib")) |
| 1080 | (string-append "--with-pcre=" |
| 1081 | (assoc-ref inputs "pcre")) |
| 1082 | ;; Each library is built twice by default, once |
| 1083 | ;; with "-static" in its name, and again |
| 1084 | ;; without. |
| 1085 | "--without-static" |
| 1086 | "--with-dll")))))))) |
| 1087 | (outputs '("out" ; 21 MB |
| 1088 | "lib" ; 226 MB |
| 1089 | "include")) ; 33 MB |
| 1090 | (inputs |
| 1091 | `(("bzip2" ,bzip2) |
| 1092 | ("zlib" ,zlib) |
| 1093 | ("pcre" ,pcre) |
| 1094 | ("perl" ,perl) |
| 1095 | ("python" ,python-wrapper))) |
| 1096 | (native-inputs |
| 1097 | `(("cpio" ,cpio))) |
| 1098 | (home-page "http://blast.ncbi.nlm.nih.gov") |
| 1099 | (synopsis "Basic local alignment search tool") |
| 1100 | (description |
| 1101 | "BLAST is a popular method of performing a DNA or protein sequence |
| 1102 | similarity search, using heuristics to produce results quickly. It also |
| 1103 | calculates an “expect value” that estimates how many matches would have |
| 1104 | occurred at a given score by chance, which can aid a user in judging how much |
| 1105 | confidence to have in an alignment.") |
| 1106 | ;; Most of the sources are in the public domain, with the following |
| 1107 | ;; exceptions: |
| 1108 | ;; * Expat: |
| 1109 | ;; * ./c++/include/util/bitset/ |
| 1110 | ;; * ./c++/src/html/ncbi_menu*.js |
| 1111 | ;; * Boost license: |
| 1112 | ;; * ./c++/include/util/impl/floating_point_comparison.hpp |
| 1113 | ;; * LGPL 2+: |
| 1114 | ;; * ./c++/include/dbapi/driver/odbc/unix_odbc/ |
| 1115 | ;; * ASL 2.0: |
| 1116 | ;; * ./c++/src/corelib/teamcity_* |
| 1117 | (license (list license:public-domain |
| 1118 | license:expat |
| 1119 | license:boost1.0 |
| 1120 | license:lgpl2.0+ |
| 1121 | license:asl2.0)))) |
| 1122 | |
| 1123 | (define-public bless |
| 1124 | (package |
| 1125 | (name "bless") |
| 1126 | (version "1p02") |
| 1127 | (source (origin |
| 1128 | (method url-fetch) |
| 1129 | (uri (string-append "mirror://sourceforge/bless-ec/bless.v" |
| 1130 | version ".tgz")) |
| 1131 | (sha256 |
| 1132 | (base32 |
| 1133 | "0rm0gw2s18dqwzzpl3c2x1z05ni2v0xz5dmfk3d33j6g4cgrlrdd")) |
| 1134 | (modules '((guix build utils))) |
| 1135 | (snippet |
| 1136 | `(begin |
| 1137 | ;; Remove bundled boost, pigz, zlib, and .git directory |
| 1138 | ;; FIXME: also remove bundled sources for murmurhash3 and |
| 1139 | ;; kmc once packaged. |
| 1140 | (delete-file-recursively "boost") |
| 1141 | (delete-file-recursively "pigz") |
| 1142 | (delete-file-recursively "google-sparsehash") |
| 1143 | (delete-file-recursively "zlib") |
| 1144 | (delete-file-recursively ".git") |
| 1145 | #t)))) |
| 1146 | (build-system gnu-build-system) |
| 1147 | (arguments |
| 1148 | '(#:tests? #f ;no "check" target |
| 1149 | #:make-flags |
| 1150 | (list (string-append "ZLIB=" |
| 1151 | (assoc-ref %build-inputs "zlib") |
| 1152 | "/lib/libz.a") |
| 1153 | (string-append "LDFLAGS=" |
| 1154 | (string-join '("-lboost_filesystem" |
| 1155 | "-lboost_system" |
| 1156 | "-lboost_iostreams" |
| 1157 | "-lz" |
| 1158 | "-fopenmp" |
| 1159 | "-std=c++11")))) |
| 1160 | #:phases |
| 1161 | (modify-phases %standard-phases |
| 1162 | (add-after 'unpack 'do-not-build-bundled-pigz |
| 1163 | (lambda* (#:key inputs outputs #:allow-other-keys) |
| 1164 | (substitute* "Makefile" |
| 1165 | (("cd pigz/pigz-2.3.3; make") "")) |
| 1166 | #t)) |
| 1167 | (add-after 'unpack 'patch-paths-to-executables |
| 1168 | (lambda* (#:key inputs outputs #:allow-other-keys) |
| 1169 | (substitute* "parse_args.cpp" |
| 1170 | (("kmc_binary = .*") |
| 1171 | (string-append "kmc_binary = \"" |
| 1172 | (assoc-ref outputs "out") |
| 1173 | "/bin/kmc\";")) |
| 1174 | (("pigz_binary = .*") |
| 1175 | (string-append "pigz_binary = \"" |
| 1176 | (assoc-ref inputs "pigz") |
| 1177 | "/bin/pigz\";"))) |
| 1178 | #t)) |
| 1179 | (replace 'install |
| 1180 | (lambda* (#:key outputs #:allow-other-keys) |
| 1181 | (let ((bin (string-append (assoc-ref outputs "out") "/bin/"))) |
| 1182 | (for-each (lambda (file) |
| 1183 | (install-file file bin)) |
| 1184 | '("bless" "kmc/bin/kmc")) |
| 1185 | #t))) |
| 1186 | (delete 'configure)))) |
| 1187 | (native-inputs |
| 1188 | `(("perl" ,perl))) |
| 1189 | (inputs |
| 1190 | `(("openmpi" ,openmpi) |
| 1191 | ("boost" ,boost) |
| 1192 | ("sparsehash" ,sparsehash) |
| 1193 | ("pigz" ,pigz) |
| 1194 | ("zlib" ,zlib))) |
| 1195 | (supported-systems '("x86_64-linux")) |
| 1196 | (home-page "https://sourceforge.net/p/bless-ec/wiki/Home/") |
| 1197 | (synopsis "Bloom-filter-based error correction tool for NGS reads") |
| 1198 | (description |
| 1199 | "@dfn{Bloom-filter-based error correction solution for high-throughput |
| 1200 | sequencing reads} (BLESS) uses a single minimum-sized bloom filter is a |
| 1201 | correction tool for genomic reads produced by @dfn{Next-generation |
| 1202 | sequencing} (NGS). BLESS produces accurate correction results with much less |
| 1203 | memory compared with previous solutions and is also able to tolerate a higher |
| 1204 | false-positive rate. BLESS can extend reads like DNA assemblers to correct |
| 1205 | errors at the end of reads.") |
| 1206 | (license license:gpl3+))) |
| 1207 | |
| 1208 | (define-public bowtie |
| 1209 | (package |
| 1210 | (name "bowtie") |
| 1211 | (version "2.3.2") |
| 1212 | (source (origin |
| 1213 | (method url-fetch) |
| 1214 | (uri (string-append "https://github.com/BenLangmead/bowtie2/archive/v" |
| 1215 | version ".tar.gz")) |
| 1216 | (file-name (string-append name "-" version ".tar.gz")) |
| 1217 | (sha256 |
| 1218 | (base32 |
| 1219 | "0hwa5r9qbglppb7sz5z79rlmmddr3n51n468jb3wh8rwjgn3yr90")) |
| 1220 | (modules '((guix build utils))) |
| 1221 | (snippet |
| 1222 | '(substitute* "Makefile" |
| 1223 | ;; replace BUILD_HOST and BUILD_TIME for deterministic build |
| 1224 | (("-DBUILD_HOST=.*") "-DBUILD_HOST=\"\\\"guix\\\"\"") |
| 1225 | (("-DBUILD_TIME=.*") "-DBUILD_TIME=\"\\\"0\\\"\""))))) |
| 1226 | (build-system gnu-build-system) |
| 1227 | (inputs |
| 1228 | `(("perl" ,perl) |
| 1229 | ("perl-clone" ,perl-clone) |
| 1230 | ("perl-test-deep" ,perl-test-deep) |
| 1231 | ("perl-test-simple" ,perl-test-simple) |
| 1232 | ("python" ,python-2) |
| 1233 | ("tbb" ,tbb) |
| 1234 | ("zlib" ,zlib))) |
| 1235 | (arguments |
| 1236 | '(#:make-flags |
| 1237 | (list "allall" |
| 1238 | "WITH_TBB=1" |
| 1239 | (string-append "prefix=" (assoc-ref %outputs "out"))) |
| 1240 | #:phases |
| 1241 | (modify-phases %standard-phases |
| 1242 | (delete 'configure) |
| 1243 | (replace 'check |
| 1244 | (lambda* (#:key outputs #:allow-other-keys) |
| 1245 | (zero? (system* "perl" |
| 1246 | "scripts/test/simple_tests.pl" |
| 1247 | "--bowtie2=./bowtie2" |
| 1248 | "--bowtie2-build=./bowtie2-build"))))))) |
| 1249 | (home-page "http://bowtie-bio.sourceforge.net/bowtie2/index.shtml") |
| 1250 | (synopsis "Fast and sensitive nucleotide sequence read aligner") |
| 1251 | (description |
| 1252 | "Bowtie 2 is a fast and memory-efficient tool for aligning sequencing |
| 1253 | reads to long reference sequences. It is particularly good at aligning reads |
| 1254 | of about 50 up to 100s or 1,000s of characters, and particularly good at |
| 1255 | aligning to relatively long (e.g. mammalian) genomes. Bowtie 2 indexes the |
| 1256 | genome with an FM Index to keep its memory footprint small: for the human |
| 1257 | genome, its memory footprint is typically around 3.2 GB. Bowtie 2 supports |
| 1258 | gapped, local, and paired-end alignment modes.") |
| 1259 | (supported-systems '("x86_64-linux")) |
| 1260 | (license license:gpl3+))) |
| 1261 | |
| 1262 | (define-public tophat |
| 1263 | (package |
| 1264 | (name "tophat") |
| 1265 | (version "2.1.0") |
| 1266 | (source (origin |
| 1267 | (method url-fetch) |
| 1268 | (uri (string-append |
| 1269 | "http://ccb.jhu.edu/software/tophat/downloads/tophat-" |
| 1270 | version ".tar.gz")) |
| 1271 | (sha256 |
| 1272 | (base32 |
| 1273 | "168zlzykq622zbgkh90a90f1bdgsxkscq2zxzbj8brq80hbjpyp7")) |
| 1274 | (patches (search-patches "tophat-build-with-later-seqan.patch")) |
| 1275 | (modules '((guix build utils))) |
| 1276 | (snippet |
| 1277 | '(begin |
| 1278 | ;; Remove bundled SeqAn and samtools |
| 1279 | (delete-file-recursively "src/SeqAn-1.3") |
| 1280 | (delete-file-recursively "src/samtools-0.1.18") |
| 1281 | #t)))) |
| 1282 | (build-system gnu-build-system) |
| 1283 | (arguments |
| 1284 | '(#:parallel-build? #f ; not supported |
| 1285 | #:phases |
| 1286 | (modify-phases %standard-phases |
| 1287 | (add-after 'unpack 'use-system-samtools |
| 1288 | (lambda* (#:key inputs #:allow-other-keys) |
| 1289 | (substitute* "src/Makefile.in" |
| 1290 | (("(noinst_LIBRARIES = )\\$\\(SAMLIB\\)" _ prefix) prefix) |
| 1291 | (("\\$\\(SAMPROG\\): \\$\\(SAMLIB\\)") "") |
| 1292 | (("SAMPROG = samtools_0\\.1\\.18") "") |
| 1293 | (("\\$\\(samtools_0_1_18_SOURCES\\)") "") |
| 1294 | (("am__EXEEXT_1 = samtools_0\\.1\\.18\\$\\(EXEEXT\\)") "")) |
| 1295 | (substitute* '("src/common.cpp" |
| 1296 | "src/tophat.py") |
| 1297 | (("samtools_0.1.18") (which "samtools"))) |
| 1298 | (substitute* '("src/common.h" |
| 1299 | "src/bam2fastx.cpp") |
| 1300 | (("#include \"bam.h\"") "#include <samtools/bam.h>") |
| 1301 | (("#include \"sam.h\"") "#include <samtools/sam.h>")) |
| 1302 | (substitute* '("src/bwt_map.h" |
| 1303 | "src/map2gtf.h" |
| 1304 | "src/align_status.h") |
| 1305 | (("#include <bam.h>") "#include <samtools/bam.h>") |
| 1306 | (("#include <sam.h>") "#include <samtools/sam.h>")) |
| 1307 | #t))))) |
| 1308 | (inputs |
| 1309 | `(("boost" ,boost) |
| 1310 | ("bowtie" ,bowtie) |
| 1311 | ("samtools" ,samtools-0.1) |
| 1312 | ("ncurses" ,ncurses) |
| 1313 | ("python" ,python-2) |
| 1314 | ("perl" ,perl) |
| 1315 | ("zlib" ,zlib) |
| 1316 | ("seqan" ,seqan))) |
| 1317 | (home-page "http://ccb.jhu.edu/software/tophat/index.shtml") |
| 1318 | (synopsis "Spliced read mapper for RNA-Seq data") |
| 1319 | (description |
| 1320 | "TopHat is a fast splice junction mapper for nucleotide sequence |
| 1321 | reads produced by the RNA-Seq method. It aligns RNA-Seq reads to |
| 1322 | mammalian-sized genomes using the ultra high-throughput short read |
| 1323 | aligner Bowtie, and then analyzes the mapping results to identify |
| 1324 | splice junctions between exons.") |
| 1325 | ;; TopHat is released under the Boost Software License, Version 1.0 |
| 1326 | ;; See https://github.com/infphilo/tophat/issues/11#issuecomment-121589893 |
| 1327 | (license license:boost1.0))) |
| 1328 | |
| 1329 | (define-public bwa |
| 1330 | (package |
| 1331 | (name "bwa") |
| 1332 | (version "0.7.17") |
| 1333 | (source (origin |
| 1334 | (method url-fetch) |
| 1335 | (uri (string-append |
| 1336 | "https://github.com/lh3/bwa/releases/download/v" |
| 1337 | version "/bwa-" version ".tar.bz2")) |
| 1338 | (sha256 |
| 1339 | (base32 |
| 1340 | "1zfhv2zg9v1icdlq4p9ssc8k01mca5d1bd87w71py2swfi74s6yy")))) |
| 1341 | (build-system gnu-build-system) |
| 1342 | (arguments |
| 1343 | '(#:tests? #f ;no "check" target |
| 1344 | #:phases |
| 1345 | (modify-phases %standard-phases |
| 1346 | (replace 'install |
| 1347 | (lambda* (#:key outputs #:allow-other-keys) |
| 1348 | (let ((bin (string-append |
| 1349 | (assoc-ref outputs "out") "/bin")) |
| 1350 | (doc (string-append |
| 1351 | (assoc-ref outputs "out") "/share/doc/bwa")) |
| 1352 | (man (string-append |
| 1353 | (assoc-ref outputs "out") "/share/man/man1"))) |
| 1354 | (install-file "bwa" bin) |
| 1355 | (install-file "README.md" doc) |
| 1356 | (install-file "bwa.1" man)) |
| 1357 | #t)) |
| 1358 | ;; no "configure" script |
| 1359 | (delete 'configure)))) |
| 1360 | (inputs `(("zlib" ,zlib))) |
| 1361 | ;; Non-portable SSE instructions are used so building fails on platforms |
| 1362 | ;; other than x86_64. |
| 1363 | (supported-systems '("x86_64-linux")) |
| 1364 | (home-page "http://bio-bwa.sourceforge.net/") |
| 1365 | (synopsis "Burrows-Wheeler sequence aligner") |
| 1366 | (description |
| 1367 | "BWA is a software package for mapping low-divergent sequences against a |
| 1368 | large reference genome, such as the human genome. It consists of three |
| 1369 | algorithms: BWA-backtrack, BWA-SW and BWA-MEM. The first algorithm is |
| 1370 | designed for Illumina sequence reads up to 100bp, while the rest two for |
| 1371 | longer sequences ranged from 70bp to 1Mbp. BWA-MEM and BWA-SW share similar |
| 1372 | features such as long-read support and split alignment, but BWA-MEM, which is |
| 1373 | the latest, is generally recommended for high-quality queries as it is faster |
| 1374 | and more accurate. BWA-MEM also has better performance than BWA-backtrack for |
| 1375 | 70-100bp Illumina reads.") |
| 1376 | (license license:gpl3+))) |
| 1377 | |
| 1378 | (define-public bwa-pssm |
| 1379 | (package (inherit bwa) |
| 1380 | (name "bwa-pssm") |
| 1381 | (version "0.5.11") |
| 1382 | (source (origin |
| 1383 | (method url-fetch) |
| 1384 | (uri (string-append "https://github.com/pkerpedjiev/bwa-pssm/" |
| 1385 | "archive/" version ".tar.gz")) |
| 1386 | (file-name (string-append name "-" version ".tar.gz")) |
| 1387 | (sha256 |
| 1388 | (base32 |
| 1389 | "02p7mpbs4mlxmn84g2x4ghak638vbj4lqix2ipx5g84pz9bhdavg")))) |
| 1390 | (build-system gnu-build-system) |
| 1391 | (inputs |
| 1392 | `(("gdsl" ,gdsl) |
| 1393 | ("zlib" ,zlib) |
| 1394 | ("perl" ,perl))) |
| 1395 | (home-page "http://bwa-pssm.binf.ku.dk/") |
| 1396 | (synopsis "Burrows-Wheeler transform-based probabilistic short read mapper") |
| 1397 | (description |
| 1398 | "BWA-PSSM is a probabilistic short genomic sequence read aligner based on |
| 1399 | the use of @dfn{position specific scoring matrices} (PSSM). Like many of the |
| 1400 | existing aligners it is fast and sensitive. Unlike most other aligners, |
| 1401 | however, it is also adaptible in the sense that one can direct the alignment |
| 1402 | based on known biases within the data set. It is coded as a modification of |
| 1403 | the original BWA alignment program and shares the genome index structure as |
| 1404 | well as many of the command line options.") |
| 1405 | (license license:gpl3+))) |
| 1406 | |
| 1407 | (define-public python2-bx-python |
| 1408 | (package |
| 1409 | (name "python2-bx-python") |
| 1410 | (version "0.7.3") |
| 1411 | (source (origin |
| 1412 | (method url-fetch) |
| 1413 | (uri (pypi-uri "bx-python" version)) |
| 1414 | (sha256 |
| 1415 | (base32 |
| 1416 | "15z2w3bvnc0n4qmb9bd6d8ylc2h2nj883x2w9iixf4x3vki9b22i")) |
| 1417 | (modules '((guix build utils))) |
| 1418 | (snippet |
| 1419 | '(substitute* "setup.py" |
| 1420 | ;; remove dependency on outdated "distribute" module |
| 1421 | (("^from distribute_setup import use_setuptools") "") |
| 1422 | (("^use_setuptools\\(\\)") ""))))) |
| 1423 | (build-system python-build-system) |
| 1424 | (arguments |
| 1425 | `(#:tests? #f ;tests fail because test data are not included |
| 1426 | #:python ,python-2)) |
| 1427 | (inputs |
| 1428 | `(("python-numpy" ,python2-numpy) |
| 1429 | ("zlib" ,zlib))) |
| 1430 | (native-inputs |
| 1431 | `(("python-nose" ,python2-nose))) |
| 1432 | (home-page "http://bitbucket.org/james_taylor/bx-python/") |
| 1433 | (synopsis "Tools for manipulating biological data") |
| 1434 | (description |
| 1435 | "bx-python provides tools for manipulating biological data, particularly |
| 1436 | multiple sequence alignments.") |
| 1437 | (license license:expat))) |
| 1438 | |
| 1439 | (define-public python-pysam |
| 1440 | (package |
| 1441 | (name "python-pysam") |
| 1442 | (version "0.13.0") |
| 1443 | (source (origin |
| 1444 | (method url-fetch) |
| 1445 | ;; Test data is missing on PyPi. |
| 1446 | (uri (string-append |
| 1447 | "https://github.com/pysam-developers/pysam/archive/v" |
| 1448 | version ".tar.gz")) |
| 1449 | (file-name (string-append name "-" version ".tar.gz")) |
| 1450 | (sha256 |
| 1451 | (base32 |
| 1452 | "0dzap2axin9cbbl0d825w294bpn00zagfm1sigamm4v2pm5bj9lp")) |
| 1453 | (modules '((guix build utils))) |
| 1454 | (snippet |
| 1455 | ;; Drop bundled htslib. TODO: Also remove samtools and bcftools. |
| 1456 | '(delete-file-recursively "htslib")))) |
| 1457 | (build-system python-build-system) |
| 1458 | (arguments |
| 1459 | `(#:modules ((ice-9 ftw) |
| 1460 | (srfi srfi-26) |
| 1461 | (guix build python-build-system) |
| 1462 | (guix build utils)) |
| 1463 | #:phases |
| 1464 | (modify-phases %standard-phases |
| 1465 | (add-before 'build 'set-flags |
| 1466 | (lambda* (#:key inputs #:allow-other-keys) |
| 1467 | (setenv "HTSLIB_MODE" "external") |
| 1468 | (setenv "HTSLIB_LIBRARY_DIR" |
| 1469 | (string-append (assoc-ref inputs "htslib") "/lib")) |
| 1470 | (setenv "HTSLIB_INCLUDE_DIR" |
| 1471 | (string-append (assoc-ref inputs "htslib") "/include")) |
| 1472 | (setenv "LDFLAGS" "-lncurses") |
| 1473 | (setenv "CFLAGS" "-D_CURSES_LIB=1") |
| 1474 | #t)) |
| 1475 | (replace 'check |
| 1476 | (lambda* (#:key inputs outputs #:allow-other-keys) |
| 1477 | ;; Add first subdirectory of "build" directory to PYTHONPATH. |
| 1478 | (setenv "PYTHONPATH" |
| 1479 | (string-append |
| 1480 | (getenv "PYTHONPATH") |
| 1481 | ":" (getcwd) "/build/" |
| 1482 | (car (scandir "build" |
| 1483 | (negate (cut string-prefix? "." <>)))))) |
| 1484 | ;; Step out of source dir so python does not import from CWD. |
| 1485 | (with-directory-excursion "tests" |
| 1486 | (setenv "HOME" "/tmp") |
| 1487 | (and (zero? (system* "make" "-C" "pysam_data")) |
| 1488 | (zero? (system* "make" "-C" "cbcf_data")) |
| 1489 | ;; Running nosetests without explicitly asking for a |
| 1490 | ;; single process leads to a crash. Running with multiple |
| 1491 | ;; processes fails because the tests are not designed to |
| 1492 | ;; run in parallel. |
| 1493 | |
| 1494 | ;; FIXME: tests keep timing out on some systems. |
| 1495 | ;; (zero? (system* "nosetests" "-v" |
| 1496 | ;; "--processes" "1")) |
| 1497 | ))))))) |
| 1498 | (propagated-inputs |
| 1499 | `(("htslib" ,htslib))) ; Included from installed header files. |
| 1500 | (inputs |
| 1501 | `(("ncurses" ,ncurses) |
| 1502 | ("zlib" ,zlib))) |
| 1503 | (native-inputs |
| 1504 | `(("python-cython" ,python-cython) |
| 1505 | ;; Dependencies below are are for tests only. |
| 1506 | ("samtools" ,samtools) |
| 1507 | ("bcftools" ,bcftools) |
| 1508 | ("python-nose" ,python-nose))) |
| 1509 | (home-page "https://github.com/pysam-developers/pysam") |
| 1510 | (synopsis "Python bindings to the SAMtools C API") |
| 1511 | (description |
| 1512 | "Pysam is a Python module for reading and manipulating files in the |
| 1513 | SAM/BAM format. Pysam is a lightweight wrapper of the SAMtools C API. It |
| 1514 | also includes an interface for tabix.") |
| 1515 | (license license:expat))) |
| 1516 | |
| 1517 | (define-public python2-pysam |
| 1518 | (package-with-python2 python-pysam)) |
| 1519 | |
| 1520 | (define-public python-twobitreader |
| 1521 | (package |
| 1522 | (name "python-twobitreader") |
| 1523 | (version "3.1.4") |
| 1524 | (source (origin |
| 1525 | (method url-fetch) |
| 1526 | (uri (pypi-uri "twobitreader" version)) |
| 1527 | (sha256 |
| 1528 | (base32 |
| 1529 | "1q8wnj2kga9nz1lwc4w7qv52smfm536hp6mc8w6s53lhyj0mpi22")))) |
| 1530 | (build-system python-build-system) |
| 1531 | (arguments |
| 1532 | '(;; Tests are not distributed in the PyPi release. |
| 1533 | ;; TODO Try building from the Git repo or asking the upstream maintainer |
| 1534 | ;; to distribute the tests on PyPi. |
| 1535 | #:tests? #f)) |
| 1536 | (native-inputs |
| 1537 | `(("python-sphinx" ,python-sphinx))) |
| 1538 | (home-page "https://github.com/benjschiller/twobitreader") |
| 1539 | (synopsis "Python library for reading .2bit files") |
| 1540 | (description |
| 1541 | "twobitreader is a Python library for reading .2bit files as used by the |
| 1542 | UCSC genome browser.") |
| 1543 | (license license:artistic2.0))) |
| 1544 | |
| 1545 | (define-public python2-twobitreader |
| 1546 | (package-with-python2 python-twobitreader)) |
| 1547 | |
| 1548 | (define-public python-plastid |
| 1549 | (package |
| 1550 | (name "python-plastid") |
| 1551 | (version "0.4.8") |
| 1552 | (source (origin |
| 1553 | (method url-fetch) |
| 1554 | (uri (pypi-uri "plastid" version)) |
| 1555 | (sha256 |
| 1556 | (base32 |
| 1557 | "0l24dd3q66if8yj042m4s0g95n6acn7im1imqd3p6h8ns43kxhj8")))) |
| 1558 | (build-system python-build-system) |
| 1559 | (arguments |
| 1560 | ;; Some test files are not included. |
| 1561 | `(#:tests? #f)) |
| 1562 | (propagated-inputs |
| 1563 | `(("python-numpy" ,python-numpy) |
| 1564 | ("python-scipy" ,python-scipy) |
| 1565 | ("python-pandas" ,python-pandas) |
| 1566 | ("python-pysam" ,python-pysam) |
| 1567 | ("python-matplotlib" ,python-matplotlib) |
| 1568 | ("python-biopython" ,python-biopython) |
| 1569 | ("python-twobitreader" ,python-twobitreader) |
| 1570 | ("python-termcolor" ,python-termcolor))) |
| 1571 | (native-inputs |
| 1572 | `(("python-cython" ,python-cython) |
| 1573 | ("python-nose" ,python-nose))) |
| 1574 | (home-page "https://github.com/joshuagryphon/plastid") |
| 1575 | (synopsis "Python library for genomic analysis") |
| 1576 | (description |
| 1577 | "plastid is a Python library for genomic analysis – in particular, |
| 1578 | high-throughput sequencing data – with an emphasis on simplicity.") |
| 1579 | (license license:bsd-3))) |
| 1580 | |
| 1581 | (define-public python2-plastid |
| 1582 | (package-with-python2 python-plastid)) |
| 1583 | |
| 1584 | (define-public cd-hit |
| 1585 | (package |
| 1586 | (name "cd-hit") |
| 1587 | (version "4.6.8") |
| 1588 | (source (origin |
| 1589 | (method url-fetch) |
| 1590 | (uri (string-append "https://github.com/weizhongli/cdhit" |
| 1591 | "/releases/download/V" version |
| 1592 | "/cd-hit-v" version |
| 1593 | "-2017-0621-source.tar.gz")) |
| 1594 | (sha256 |
| 1595 | (base32 |
| 1596 | "1b4mwm2520ixjbw57sil20f9iixzw4bkdqqwgg1fc3pzm6rz4zmn")))) |
| 1597 | (build-system gnu-build-system) |
| 1598 | (arguments |
| 1599 | `(#:tests? #f ; there are no tests |
| 1600 | #:make-flags |
| 1601 | ;; Executables are copied directly to the PREFIX. |
| 1602 | (list (string-append "PREFIX=" (assoc-ref %outputs "out") "/bin")) |
| 1603 | #:phases |
| 1604 | (modify-phases %standard-phases |
| 1605 | ;; No "configure" script |
| 1606 | (delete 'configure) |
| 1607 | ;; Remove sources of non-determinism |
| 1608 | (add-after 'unpack 'be-timeless |
| 1609 | (lambda _ |
| 1610 | (substitute* "cdhit-utility.c++" |
| 1611 | ((" \\(built on \" __DATE__ \"\\)") "")) |
| 1612 | (substitute* "cdhit-common.c++" |
| 1613 | (("__DATE__") "\"0\"") |
| 1614 | (("\", %s, \" __TIME__ \"\\\\n\", date") "")) |
| 1615 | #t)) |
| 1616 | ;; The "install" target does not create the target directory. |
| 1617 | (add-before 'install 'create-target-dir |
| 1618 | (lambda* (#:key outputs #:allow-other-keys) |
| 1619 | (mkdir-p (string-append (assoc-ref outputs "out") "/bin")) |
| 1620 | #t))))) |
| 1621 | (inputs |
| 1622 | `(("perl" ,perl))) |
| 1623 | (home-page "http://weizhongli-lab.org/cd-hit/") |
| 1624 | (synopsis "Cluster and compare protein or nucleotide sequences") |
| 1625 | (description |
| 1626 | "CD-HIT is a program for clustering and comparing protein or nucleotide |
| 1627 | sequences. CD-HIT is designed to be fast and handle extremely large |
| 1628 | databases.") |
| 1629 | ;; The manual says: "It can be copied under the GNU General Public License |
| 1630 | ;; version 2 (GPLv2)." |
| 1631 | (license license:gpl2))) |
| 1632 | |
| 1633 | (define-public clipper |
| 1634 | (package |
| 1635 | (name "clipper") |
| 1636 | (version "1.1") |
| 1637 | (source (origin |
| 1638 | (method url-fetch) |
| 1639 | (uri (string-append |
| 1640 | "https://github.com/YeoLab/clipper/archive/" |
| 1641 | version ".tar.gz")) |
| 1642 | (file-name (string-append name "-" version ".tar.gz")) |
| 1643 | (sha256 |
| 1644 | (base32 |
| 1645 | "0pflmsvhbf8izbgwhbhj1i7349sw1f55qpqj8ljmapp16hb0p0qi")) |
| 1646 | (modules '((guix build utils))) |
| 1647 | (snippet |
| 1648 | '(begin |
| 1649 | ;; remove unnecessary setup dependency |
| 1650 | (substitute* "setup.py" |
| 1651 | (("setup_requires = .*") "")) |
| 1652 | (for-each delete-file |
| 1653 | '("clipper/src/peaks.so" |
| 1654 | "clipper/src/readsToWiggle.so")) |
| 1655 | (delete-file-recursively "dist/") |
| 1656 | #t)))) |
| 1657 | (build-system python-build-system) |
| 1658 | (arguments `(#:python ,python-2)) ; only Python 2 is supported |
| 1659 | (inputs |
| 1660 | `(("htseq" ,python2-htseq) |
| 1661 | ("python-pybedtools" ,python2-pybedtools) |
| 1662 | ("python-cython" ,python2-cython) |
| 1663 | ("python-scikit-learn" ,python2-scikit-learn) |
| 1664 | ("python-matplotlib" ,python2-matplotlib) |
| 1665 | ("python-pandas" ,python2-pandas) |
| 1666 | ("python-pysam" ,python2-pysam) |
| 1667 | ("python-numpy" ,python2-numpy) |
| 1668 | ("python-scipy" ,python2-scipy))) |
| 1669 | (native-inputs |
| 1670 | `(("python-mock" ,python2-mock) ; for tests |
| 1671 | ("python-nose" ,python2-nose) ; for tests |
| 1672 | ("python-pytz" ,python2-pytz))) ; for tests |
| 1673 | (home-page "https://github.com/YeoLab/clipper") |
| 1674 | (synopsis "CLIP peak enrichment recognition") |
| 1675 | (description |
| 1676 | "CLIPper is a tool to define peaks in CLIP-seq datasets.") |
| 1677 | (license license:gpl2))) |
| 1678 | |
| 1679 | (define-public codingquarry |
| 1680 | (package |
| 1681 | (name "codingquarry") |
| 1682 | (version "2.0") |
| 1683 | (source (origin |
| 1684 | (method url-fetch) |
| 1685 | (uri (string-append |
| 1686 | "mirror://sourceforge/codingquarry/CodingQuarry_v" |
| 1687 | version ".tar.gz")) |
| 1688 | (sha256 |
| 1689 | (base32 |
| 1690 | "0115hkjflsnfzn36xppwf9h9avfxlavr43djqmshkkzbgjzsz60i")))) |
| 1691 | (build-system gnu-build-system) |
| 1692 | (arguments |
| 1693 | '(#:tests? #f ; no "check" target |
| 1694 | #:phases |
| 1695 | (modify-phases %standard-phases |
| 1696 | (delete 'configure) |
| 1697 | (replace 'install |
| 1698 | (lambda* (#:key outputs #:allow-other-keys) |
| 1699 | (let* ((out (assoc-ref outputs "out")) |
| 1700 | (bin (string-append out "/bin")) |
| 1701 | (doc (string-append out "/share/doc/codingquarry"))) |
| 1702 | (install-file "INSTRUCTIONS.pdf" doc) |
| 1703 | (copy-recursively "QuarryFiles" |
| 1704 | (string-append out "/QuarryFiles")) |
| 1705 | (install-file "CodingQuarry" bin) |
| 1706 | (install-file "CufflinksGTF_to_CodingQuarryGFF3.py" bin))))))) |
| 1707 | (inputs `(("openmpi" ,openmpi))) |
| 1708 | (native-search-paths |
| 1709 | (list (search-path-specification |
| 1710 | (variable "QUARRY_PATH") |
| 1711 | (files '("QuarryFiles"))))) |
| 1712 | (native-inputs `(("python" ,python-2))) ; Only Python 2 is supported |
| 1713 | (synopsis "Fungal gene predictor") |
| 1714 | (description "CodingQuarry is a highly accurate, self-training GHMM fungal |
| 1715 | gene predictor designed to work with assembled, aligned RNA-seq transcripts.") |
| 1716 | (home-page "https://sourceforge.net/projects/codingquarry/") |
| 1717 | (license license:gpl3+))) |
| 1718 | |
| 1719 | (define-public couger |
| 1720 | (package |
| 1721 | (name "couger") |
| 1722 | (version "1.8.2") |
| 1723 | (source (origin |
| 1724 | (method url-fetch) |
| 1725 | (uri (string-append |
| 1726 | "http://couger.oit.duke.edu/static/assets/COUGER" |
| 1727 | version ".zip")) |
| 1728 | (sha256 |
| 1729 | (base32 |
| 1730 | "04p2b14nmhzxw5h72mpzdhalv21bx4w9b87z0wpw0xzxpysyncmq")))) |
| 1731 | (build-system gnu-build-system) |
| 1732 | (arguments |
| 1733 | `(#:tests? #f |
| 1734 | #:phases |
| 1735 | (modify-phases %standard-phases |
| 1736 | (delete 'configure) |
| 1737 | (delete 'build) |
| 1738 | (replace |
| 1739 | 'install |
| 1740 | (lambda* (#:key outputs #:allow-other-keys) |
| 1741 | (let* ((out (assoc-ref outputs "out")) |
| 1742 | (bin (string-append out "/bin"))) |
| 1743 | (copy-recursively "src" (string-append out "/src")) |
| 1744 | (mkdir bin) |
| 1745 | ;; Add "src" directory to module lookup path. |
| 1746 | (substitute* "couger" |
| 1747 | (("from argparse") |
| 1748 | (string-append "import sys\nsys.path.append(\"" |
| 1749 | out "\")\nfrom argparse"))) |
| 1750 | (install-file "couger" bin)) |
| 1751 | #t)) |
| 1752 | (add-after |
| 1753 | 'install 'wrap-program |
| 1754 | (lambda* (#:key inputs outputs #:allow-other-keys) |
| 1755 | ;; Make sure 'couger' runs with the correct PYTHONPATH. |
| 1756 | (let* ((out (assoc-ref outputs "out")) |
| 1757 | (path (getenv "PYTHONPATH"))) |
| 1758 | (wrap-program (string-append out "/bin/couger") |
| 1759 | `("PYTHONPATH" ":" prefix (,path)))) |
| 1760 | #t))))) |
| 1761 | (inputs |
| 1762 | `(("python" ,python-2) |
| 1763 | ("python2-pillow" ,python2-pillow) |
| 1764 | ("python2-numpy" ,python2-numpy) |
| 1765 | ("python2-scipy" ,python2-scipy) |
| 1766 | ("python2-matplotlib" ,python2-matplotlib))) |
| 1767 | (propagated-inputs |
| 1768 | `(("r-minimal" ,r-minimal) |
| 1769 | ("libsvm" ,libsvm) |
| 1770 | ("randomjungle" ,randomjungle))) |
| 1771 | (native-inputs |
| 1772 | `(("unzip" ,unzip))) |
| 1773 | (home-page "http://couger.oit.duke.edu") |
| 1774 | (synopsis "Identify co-factors in sets of genomic regions") |
| 1775 | (description |
| 1776 | "COUGER can be applied to any two sets of genomic regions bound by |
| 1777 | paralogous TFs (e.g., regions derived from ChIP-seq experiments) to identify |
| 1778 | putative co-factors that provide specificity to each TF. The framework |
| 1779 | determines the genomic targets uniquely-bound by each TF, and identifies a |
| 1780 | small set of co-factors that best explain the in vivo binding differences |
| 1781 | between the two TFs. |
| 1782 | |
| 1783 | COUGER uses classification algorithms (support vector machines and random |
| 1784 | forests) with features that reflect the DNA binding specificities of putative |
| 1785 | co-factors. The features are generated either from high-throughput TF-DNA |
| 1786 | binding data (from protein binding microarray experiments), or from large |
| 1787 | collections of DNA motifs.") |
| 1788 | (license license:gpl3+))) |
| 1789 | |
| 1790 | (define-public clustal-omega |
| 1791 | (package |
| 1792 | (name "clustal-omega") |
| 1793 | (version "1.2.4") |
| 1794 | (source (origin |
| 1795 | (method url-fetch) |
| 1796 | (uri (string-append "http://www.clustal.org/omega/clustal-omega-" |
| 1797 | version ".tar.gz")) |
| 1798 | (sha256 |
| 1799 | (base32 |
| 1800 | "1vm30mzncwdv881vrcwg11vzvrsmwy4wg80j5i0lcfk6dlld50w6")))) |
| 1801 | (build-system gnu-build-system) |
| 1802 | (inputs |
| 1803 | `(("argtable" ,argtable))) |
| 1804 | (home-page "http://www.clustal.org/omega/") |
| 1805 | (synopsis "Multiple sequence aligner for protein and DNA/RNA") |
| 1806 | (description |
| 1807 | "Clustal-Omega is a general purpose multiple sequence alignment (MSA) |
| 1808 | program for protein and DNA/RNA. It produces high quality MSAs and is capable |
| 1809 | of handling data-sets of hundreds of thousands of sequences in reasonable |
| 1810 | time.") |
| 1811 | (license license:gpl2+))) |
| 1812 | |
| 1813 | (define-public crossmap |
| 1814 | (package |
| 1815 | (name "crossmap") |
| 1816 | (version "0.2.1") |
| 1817 | (source (origin |
| 1818 | (method url-fetch) |
| 1819 | (uri (string-append "mirror://sourceforge/crossmap/CrossMap-" |
| 1820 | version ".tar.gz")) |
| 1821 | (sha256 |
| 1822 | (base32 |
| 1823 | "07y179f63d7qnzdvkqcziwk9bs3k4zhp81q392fp1hwszjdvy22f")) |
| 1824 | ;; This patch has been sent upstream already and is available |
| 1825 | ;; for download from Sourceforge, but it has not been merged. |
| 1826 | (patches (search-patches "crossmap-allow-system-pysam.patch")) |
| 1827 | (modules '((guix build utils))) |
| 1828 | ;; remove bundled copy of pysam |
| 1829 | (snippet |
| 1830 | '(delete-file-recursively "lib/pysam")))) |
| 1831 | (build-system python-build-system) |
| 1832 | (arguments |
| 1833 | `(#:python ,python-2 |
| 1834 | #:phases |
| 1835 | (modify-phases %standard-phases |
| 1836 | (add-after 'unpack 'set-env |
| 1837 | (lambda _ (setenv "CROSSMAP_USE_SYSTEM_PYSAM" "1") #t))))) |
| 1838 | (inputs |
| 1839 | `(("python-numpy" ,python2-numpy) |
| 1840 | ("python-pysam" ,python2-pysam) |
| 1841 | ("zlib" ,zlib))) |
| 1842 | (native-inputs |
| 1843 | `(("python-cython" ,python2-cython) |
| 1844 | ("python-nose" ,python2-nose))) |
| 1845 | (home-page "http://crossmap.sourceforge.net/") |
| 1846 | (synopsis "Convert genome coordinates between assemblies") |
| 1847 | (description |
| 1848 | "CrossMap is a program for conversion of genome coordinates or annotation |
| 1849 | files between different genome assemblies. It supports most commonly used |
| 1850 | file formats including SAM/BAM, Wiggle/BigWig, BED, GFF/GTF, VCF.") |
| 1851 | (license license:gpl2+))) |
| 1852 | |
| 1853 | (define-public cutadapt |
| 1854 | (package |
| 1855 | (name "cutadapt") |
| 1856 | (version "1.14") |
| 1857 | (source (origin |
| 1858 | (method url-fetch) |
| 1859 | (uri (string-append |
| 1860 | "https://github.com/marcelm/cutadapt/archive/v" |
| 1861 | version ".tar.gz")) |
| 1862 | (file-name (string-append name "-" version ".tar.gz")) |
| 1863 | (sha256 |
| 1864 | (base32 |
| 1865 | "16gbpiwy4m48vq2h5wqar3i8vr6vcj9gcl2qvqim19x6ya9dp8kd")))) |
| 1866 | (build-system python-build-system) |
| 1867 | (arguments |
| 1868 | `(#:phases |
| 1869 | (modify-phases %standard-phases |
| 1870 | ;; The tests must be run after installation. |
| 1871 | (delete 'check) |
| 1872 | (add-after 'install 'check |
| 1873 | (lambda* (#:key inputs outputs #:allow-other-keys) |
| 1874 | (setenv "PYTHONPATH" |
| 1875 | (string-append |
| 1876 | (getenv "PYTHONPATH") |
| 1877 | ":" (assoc-ref outputs "out") |
| 1878 | "/lib/python" |
| 1879 | (string-take (string-take-right |
| 1880 | (assoc-ref inputs "python") 5) 3) |
| 1881 | "/site-packages")) |
| 1882 | (zero? (system* "nosetests" "-P" "tests"))))))) |
| 1883 | (inputs |
| 1884 | `(("python-xopen" ,python-xopen))) |
| 1885 | (native-inputs |
| 1886 | `(("python-cython" ,python-cython) |
| 1887 | ("python-nose" ,python-nose))) |
| 1888 | (home-page "https://cutadapt.readthedocs.io/en/stable/") |
| 1889 | (synopsis "Remove adapter sequences from nucleotide sequencing reads") |
| 1890 | (description |
| 1891 | "Cutadapt finds and removes adapter sequences, primers, poly-A tails and |
| 1892 | other types of unwanted sequence from high-throughput sequencing reads.") |
| 1893 | (license license:expat))) |
| 1894 | |
| 1895 | (define-public libbigwig |
| 1896 | (package |
| 1897 | (name "libbigwig") |
| 1898 | (version "0.1.4") |
| 1899 | (source (origin |
| 1900 | (method url-fetch) |
| 1901 | (uri (string-append "https://github.com/dpryan79/libBigWig/" |
| 1902 | "archive/" version ".tar.gz")) |
| 1903 | (file-name (string-append name "-" version ".tar.gz")) |
| 1904 | (sha256 |
| 1905 | (base32 |
| 1906 | "098rjh35pi4a9q83n8wiwvyzykjqj6l8q189p1xgfw4ghywdlvw1")))) |
| 1907 | (build-system gnu-build-system) |
| 1908 | (arguments |
| 1909 | `(#:test-target "test" |
| 1910 | #:make-flags |
| 1911 | (list "CC=gcc" |
| 1912 | (string-append "prefix=" (assoc-ref %outputs "out"))) |
| 1913 | #:phases |
| 1914 | (modify-phases %standard-phases |
| 1915 | (delete 'configure) |
| 1916 | (add-before 'check 'disable-curl-test |
| 1917 | (lambda _ |
| 1918 | (substitute* "Makefile" |
| 1919 | (("./test/testRemote.*") "")) |
| 1920 | #t)) |
| 1921 | ;; This has been fixed with the upstream commit 4ff6959cd8a0, but |
| 1922 | ;; there has not yet been a release containing this change. |
| 1923 | (add-before 'install 'create-target-dirs |
| 1924 | (lambda* (#:key outputs #:allow-other-keys) |
| 1925 | (let ((out (assoc-ref outputs "out"))) |
| 1926 | (mkdir-p (string-append out "/lib")) |
| 1927 | (mkdir-p (string-append out "/include")) |
| 1928 | #t)))))) |
| 1929 | (inputs |
| 1930 | `(("zlib" ,zlib) |
| 1931 | ("curl" ,curl))) |
| 1932 | (native-inputs |
| 1933 | `(("doxygen" ,doxygen))) |
| 1934 | (home-page "https://github.com/dpryan79/libBigWig") |
| 1935 | (synopsis "C library for handling bigWig files") |
| 1936 | (description |
| 1937 | "This package provides a C library for parsing local and remote BigWig |
| 1938 | files.") |
| 1939 | (license license:expat))) |
| 1940 | |
| 1941 | (define-public python-pybigwig |
| 1942 | (package |
| 1943 | (name "python-pybigwig") |
| 1944 | (version "0.2.5") |
| 1945 | (source (origin |
| 1946 | (method url-fetch) |
| 1947 | (uri (pypi-uri "pyBigWig" version)) |
| 1948 | (sha256 |
| 1949 | (base32 |
| 1950 | "0yrpdxg3y0sny25x4w22lv1k47jzccqjmg7j4bp0hywklvp0hg7d")) |
| 1951 | (modules '((guix build utils))) |
| 1952 | (snippet |
| 1953 | '(begin |
| 1954 | ;; Delete bundled libBigWig sources |
| 1955 | (delete-file-recursively "libBigWig"))))) |
| 1956 | (build-system python-build-system) |
| 1957 | (arguments |
| 1958 | `(#:phases |
| 1959 | (modify-phases %standard-phases |
| 1960 | (add-after 'unpack 'link-with-libBigWig |
| 1961 | (lambda* (#:key inputs #:allow-other-keys) |
| 1962 | (substitute* "setup.py" |
| 1963 | (("libs=\\[") "libs=[\"BigWig\", ")) |
| 1964 | #t))))) |
| 1965 | (inputs |
| 1966 | `(("libbigwig" ,libbigwig) |
| 1967 | ("zlib" ,zlib) |
| 1968 | ("curl" ,curl))) |
| 1969 | (home-page "https://github.com/dpryan79/pyBigWig") |
| 1970 | (synopsis "Access bigWig files in Python using libBigWig") |
| 1971 | (description |
| 1972 | "This package provides Python bindings to the libBigWig library for |
| 1973 | accessing bigWig files.") |
| 1974 | (license license:expat))) |
| 1975 | |
| 1976 | (define-public python2-pybigwig |
| 1977 | (package-with-python2 python-pybigwig)) |
| 1978 | |
| 1979 | (define-public python-dendropy |
| 1980 | (package |
| 1981 | (name "python-dendropy") |
| 1982 | (version "4.2.0") |
| 1983 | (source |
| 1984 | (origin |
| 1985 | (method url-fetch) |
| 1986 | (uri (pypi-uri "DendroPy" version)) |
| 1987 | (sha256 |
| 1988 | (base32 |
| 1989 | "15c7s3d5gf19ljsxvq5advaa752wfi7pwrdjyhzmg85hccyvp47p")) |
| 1990 | (patches (search-patches "python-dendropy-fix-tests.patch")))) |
| 1991 | (build-system python-build-system) |
| 1992 | (home-page "http://packages.python.org/DendroPy/") |
| 1993 | (synopsis "Library for phylogenetics and phylogenetic computing") |
| 1994 | (description |
| 1995 | "DendroPy is a library for phylogenetics and phylogenetic computing: reading, |
| 1996 | writing, simulation, processing and manipulation of phylogenetic |
| 1997 | trees (phylogenies) and characters.") |
| 1998 | (license license:bsd-3) |
| 1999 | (properties `((python2-variant . ,(delay python2-dendropy)))))) |
| 2000 | |
| 2001 | (define-public python2-dendropy |
| 2002 | (let ((base (package-with-python2 (strip-python2-variant python-dendropy)))) |
| 2003 | (package |
| 2004 | (inherit base) |
| 2005 | (arguments |
| 2006 | `(#:python ,python-2 |
| 2007 | #:phases |
| 2008 | (modify-phases %standard-phases |
| 2009 | (replace 'check |
| 2010 | ;; There is currently a test failure that only happens on some |
| 2011 | ;; systems, and only using "setup.py test" |
| 2012 | (lambda _ (zero? (system* "nosetests"))))))) |
| 2013 | (native-inputs `(("python2-nose" ,python2-nose) |
| 2014 | ,@(package-native-inputs base)))))) |
| 2015 | |
| 2016 | (define-public python-py2bit |
| 2017 | (package |
| 2018 | (name "python-py2bit") |
| 2019 | (version "0.2.1") |
| 2020 | (source |
| 2021 | (origin |
| 2022 | (method url-fetch) |
| 2023 | (uri (pypi-uri "py2bit" version)) |
| 2024 | (sha256 |
| 2025 | (base32 |
| 2026 | "1cdf4qlmgwsh1f4k0wdv2sr8x9qn4366p0k3614vbd0fpqiarxrl")))) |
| 2027 | (build-system python-build-system) |
| 2028 | (home-page "https://github.com/dpryan79/py2bit") |
| 2029 | (synopsis "Access 2bit files using lib2bit") |
| 2030 | (description |
| 2031 | "This package provides Python bindings for lib2bit to access 2bit files |
| 2032 | with Python.") |
| 2033 | (license license:expat))) |
| 2034 | |
| 2035 | (define-public deeptools |
| 2036 | (package |
| 2037 | (name "deeptools") |
| 2038 | (version "2.5.1") |
| 2039 | (source (origin |
| 2040 | (method url-fetch) |
| 2041 | (uri (string-append "https://github.com/fidelram/deepTools/" |
| 2042 | "archive/" version ".tar.gz")) |
| 2043 | (file-name (string-append name "-" version ".tar.gz")) |
| 2044 | (sha256 |
| 2045 | (base32 |
| 2046 | "1q8i12l2gvk4n2s8lhyzwhh9g4qbc8lrk5l7maz00yvd5g6z5540")))) |
| 2047 | (build-system python-build-system) |
| 2048 | (inputs |
| 2049 | `(("python-scipy" ,python-scipy) |
| 2050 | ("python-numpy" ,python-numpy) |
| 2051 | ("python-numpydoc" ,python-numpydoc) |
| 2052 | ("python-matplotlib" ,python-matplotlib) |
| 2053 | ("python-pysam" ,python-pysam) |
| 2054 | ("python-py2bit" ,python-py2bit) |
| 2055 | ("python-pybigwig" ,python-pybigwig))) |
| 2056 | (native-inputs |
| 2057 | `(("python-mock" ,python-mock) ;for tests |
| 2058 | ("python-nose" ,python-nose) ;for tests |
| 2059 | ("python-pytz" ,python-pytz))) ;for tests |
| 2060 | (home-page "https://github.com/fidelram/deepTools") |
| 2061 | (synopsis "Tools for normalizing and visualizing deep-sequencing data") |
| 2062 | (description |
| 2063 | "DeepTools addresses the challenge of handling the large amounts of data |
| 2064 | that are now routinely generated from DNA sequencing centers. To do so, |
| 2065 | deepTools contains useful modules to process the mapped reads data to create |
| 2066 | coverage files in standard bedGraph and bigWig file formats. By doing so, |
| 2067 | deepTools allows the creation of normalized coverage files or the comparison |
| 2068 | between two files (for example, treatment and control). Finally, using such |
| 2069 | normalized and standardized files, multiple visualizations can be created to |
| 2070 | identify enrichments with functional annotations of the genome.") |
| 2071 | (license license:gpl3+))) |
| 2072 | |
| 2073 | (define-public diamond |
| 2074 | (package |
| 2075 | (name "diamond") |
| 2076 | (version "0.9.14") |
| 2077 | (source (origin |
| 2078 | (method url-fetch) |
| 2079 | (uri (string-append |
| 2080 | "https://github.com/bbuchfink/diamond/archive/v" |
| 2081 | version ".tar.gz")) |
| 2082 | (file-name (string-append name "-" version ".tar.gz")) |
| 2083 | (sha256 |
| 2084 | (base32 |
| 2085 | "07li3chjdna0wjyh680j3bhwiqh1fbfq9dy9jxxs82mc0rw0m1yy")))) |
| 2086 | (build-system cmake-build-system) |
| 2087 | (arguments |
| 2088 | '(#:tests? #f ; no "check" target |
| 2089 | #:phases |
| 2090 | (modify-phases %standard-phases |
| 2091 | (add-after 'unpack 'remove-native-compilation |
| 2092 | (lambda _ |
| 2093 | (substitute* "CMakeLists.txt" (("-march=native") "")) |
| 2094 | #t))))) |
| 2095 | (inputs |
| 2096 | `(("zlib" ,zlib))) |
| 2097 | (home-page "https://github.com/bbuchfink/diamond") |
| 2098 | (synopsis "Accelerated BLAST compatible local sequence aligner") |
| 2099 | (description |
| 2100 | "DIAMOND is a BLAST-compatible local aligner for mapping protein and |
| 2101 | translated DNA query sequences against a protein reference database (BLASTP |
| 2102 | and BLASTX alignment mode). The speedup over BLAST is up to 20,000 on short |
| 2103 | reads at a typical sensitivity of 90-99% relative to BLAST depending on the |
| 2104 | data and settings.") |
| 2105 | (license license:agpl3+))) |
| 2106 | |
| 2107 | (define-public discrover |
| 2108 | (package |
| 2109 | (name "discrover") |
| 2110 | (version "1.6.0") |
| 2111 | (source |
| 2112 | (origin |
| 2113 | (method url-fetch) |
| 2114 | (uri (string-append "https://github.com/maaskola/discrover/archive/" |
| 2115 | version ".tar.gz")) |
| 2116 | (file-name (string-append name "-" version ".tar.gz")) |
| 2117 | (sha256 |
| 2118 | (base32 |
| 2119 | "0rah9ja4m0rl5mldd6vag9rwrivw1zrqxssfq8qx64m7961fp68k")))) |
| 2120 | (build-system cmake-build-system) |
| 2121 | (arguments |
| 2122 | `(#:tests? #f ; there are no tests |
| 2123 | #:phases |
| 2124 | (modify-phases %standard-phases |
| 2125 | (add-after 'unpack 'add-missing-includes |
| 2126 | (lambda _ |
| 2127 | (substitute* "src/executioninformation.hpp" |
| 2128 | (("#define EXECUTIONINFORMATION_HPP" line) |
| 2129 | (string-append line "\n#include <random>"))) |
| 2130 | (substitute* "src/plasma/fasta.hpp" |
| 2131 | (("#define FASTA_HPP" line) |
| 2132 | (string-append line "\n#include <random>"))) |
| 2133 | #t))))) |
| 2134 | (inputs |
| 2135 | `(("boost" ,boost) |
| 2136 | ("cairo" ,cairo))) |
| 2137 | (native-inputs |
| 2138 | `(("texlive" ,texlive) |
| 2139 | ("imagemagick" ,imagemagick))) |
| 2140 | (home-page "http://dorina.mdc-berlin.de/public/rajewsky/discrover/") |
| 2141 | (synopsis "Discover discriminative nucleotide sequence motifs") |
| 2142 | (description "Discrover is a motif discovery method to find binding sites |
| 2143 | of nucleic acid binding proteins.") |
| 2144 | (license license:gpl3+))) |
| 2145 | |
| 2146 | (define-public eigensoft |
| 2147 | (let ((revision "1") |
| 2148 | (commit "b14d1e202e21e532536ff8004f0419cd5e259dc7")) |
| 2149 | (package |
| 2150 | (name "eigensoft") |
| 2151 | (version (string-append "6.1.2-" |
| 2152 | revision "." |
| 2153 | (string-take commit 9))) |
| 2154 | (source |
| 2155 | (origin |
| 2156 | (method git-fetch) |
| 2157 | (uri (git-reference |
| 2158 | (url "https://github.com/DReichLab/EIG.git") |
| 2159 | (commit commit))) |
| 2160 | (file-name (string-append "eigensoft-" commit "-checkout")) |
| 2161 | (sha256 |
| 2162 | (base32 |
| 2163 | "0f5m6k2j5c16xc3xbywcs989xyc26ncy1zfzp9j9n55n9r4xcaiq")) |
| 2164 | (modules '((guix build utils))) |
| 2165 | ;; Remove pre-built binaries. |
| 2166 | (snippet '(begin |
| 2167 | (delete-file-recursively "bin") |
| 2168 | (mkdir "bin") |
| 2169 | #t)))) |
| 2170 | (build-system gnu-build-system) |
| 2171 | (arguments |
| 2172 | `(#:tests? #f ; There are no tests. |
| 2173 | #:make-flags '("CC=gcc") |
| 2174 | #:phases |
| 2175 | (modify-phases %standard-phases |
| 2176 | ;; There is no configure phase, but the Makefile is in a |
| 2177 | ;; sub-directory. |
| 2178 | (replace 'configure |
| 2179 | (lambda _ |
| 2180 | (chdir "src") |
| 2181 | ;; The link flags are incomplete. |
| 2182 | (substitute* "Makefile" |
| 2183 | (("-lgsl") "-lgsl -lm -llapack -llapacke -lpthread")) |
| 2184 | #t)) |
| 2185 | ;; The provided install target only copies executables to |
| 2186 | ;; the "bin" directory in the build root. |
| 2187 | (add-after 'install 'actually-install |
| 2188 | (lambda* (#:key outputs #:allow-other-keys) |
| 2189 | (let* ((out (assoc-ref outputs "out")) |
| 2190 | (bin (string-append out "/bin"))) |
| 2191 | (for-each (lambda (file) |
| 2192 | (install-file file bin)) |
| 2193 | (find-files "../bin" ".*")) |
| 2194 | #t)))))) |
| 2195 | (inputs |
| 2196 | `(("gsl" ,gsl) |
| 2197 | ("lapack" ,lapack) |
| 2198 | ("openblas" ,openblas) |
| 2199 | ("perl" ,perl) |
| 2200 | ("gfortran" ,gfortran "lib"))) |
| 2201 | (home-page "https://github.com/DReichLab/EIG") |
| 2202 | (synopsis "Tools for population genetics") |
| 2203 | (description "The EIGENSOFT package provides tools for population |
| 2204 | genetics and stratification correction. EIGENSOFT implements methods commonly |
| 2205 | used in population genetics analyses such as PCA, computation of Tracy-Widom |
| 2206 | statistics, and finding related individuals in structured populations. It |
| 2207 | comes with a built-in plotting script and supports multiple file formats and |
| 2208 | quantitative phenotypes.") |
| 2209 | ;; The license of the eigensoft tools is Expat, but since it's |
| 2210 | ;; linking with the GNU Scientific Library (GSL) the effective |
| 2211 | ;; license is the GPL. |
| 2212 | (license license:gpl3+)))) |
| 2213 | |
| 2214 | (define-public edirect |
| 2215 | (package |
| 2216 | (name "edirect") |
| 2217 | (version "4.10") |
| 2218 | (source (origin |
| 2219 | (method url-fetch) |
| 2220 | (uri (string-append "ftp://ftp.ncbi.nlm.nih.gov/entrez/entrezdirect/" |
| 2221 | "versions/2016-05-03/edirect.tar.gz")) |
| 2222 | (sha256 |
| 2223 | (base32 |
| 2224 | "15zsprak5yh8c1yrz4r1knmb5s8qcmdid4xdhkh3lqcv64l60hli")))) |
| 2225 | (build-system perl-build-system) |
| 2226 | (arguments |
| 2227 | `(#:tests? #f ;no "check" target |
| 2228 | #:phases |
| 2229 | (modify-phases %standard-phases |
| 2230 | (delete 'configure) |
| 2231 | (delete 'build) |
| 2232 | (replace 'install |
| 2233 | (lambda* (#:key outputs #:allow-other-keys) |
| 2234 | (let ((target (string-append (assoc-ref outputs "out") |
| 2235 | "/bin"))) |
| 2236 | (mkdir-p target) |
| 2237 | (install-file "edirect.pl" target) |
| 2238 | #t))) |
| 2239 | (add-after |
| 2240 | 'install 'wrap-program |
| 2241 | (lambda* (#:key inputs outputs #:allow-other-keys) |
| 2242 | ;; Make sure 'edirect.pl' finds all perl inputs at runtime. |
| 2243 | (let* ((out (assoc-ref outputs "out")) |
| 2244 | (path (getenv "PERL5LIB"))) |
| 2245 | (wrap-program (string-append out "/bin/edirect.pl") |
| 2246 | `("PERL5LIB" ":" prefix (,path))))))))) |
| 2247 | (inputs |
| 2248 | `(("perl-html-parser" ,perl-html-parser) |
| 2249 | ("perl-encode-locale" ,perl-encode-locale) |
| 2250 | ("perl-file-listing" ,perl-file-listing) |
| 2251 | ("perl-html-tagset" ,perl-html-tagset) |
| 2252 | ("perl-html-tree" ,perl-html-tree) |
| 2253 | ("perl-http-cookies" ,perl-http-cookies) |
| 2254 | ("perl-http-date" ,perl-http-date) |
| 2255 | ("perl-http-message" ,perl-http-message) |
| 2256 | ("perl-http-negotiate" ,perl-http-negotiate) |
| 2257 | ("perl-lwp-mediatypes" ,perl-lwp-mediatypes) |
| 2258 | ("perl-lwp-protocol-https" ,perl-lwp-protocol-https) |
| 2259 | ("perl-net-http" ,perl-net-http) |
| 2260 | ("perl-uri" ,perl-uri) |
| 2261 | ("perl-www-robotrules" ,perl-www-robotrules) |
| 2262 | ("perl" ,perl))) |
| 2263 | (home-page "http://www.ncbi.nlm.nih.gov/books/NBK179288/") |
| 2264 | (synopsis "Tools for accessing the NCBI's set of databases") |
| 2265 | (description |
| 2266 | "Entrez Direct (EDirect) is a method for accessing the National Center |
| 2267 | for Biotechnology Information's (NCBI) set of interconnected |
| 2268 | databases (publication, sequence, structure, gene, variation, expression, |
| 2269 | etc.) from a terminal. Functions take search terms from command-line |
| 2270 | arguments. Individual operations are combined to build multi-step queries. |
| 2271 | Record retrieval and formatting normally complete the process. |
| 2272 | |
| 2273 | EDirect also provides an argument-driven function that simplifies the |
| 2274 | extraction of data from document summaries or other results that are returned |
| 2275 | in structured XML format. This can eliminate the need for writing custom |
| 2276 | software to answer ad hoc questions.") |
| 2277 | (license license:public-domain))) |
| 2278 | |
| 2279 | (define-public exonerate |
| 2280 | (package |
| 2281 | (name "exonerate") |
| 2282 | (version "2.4.0") |
| 2283 | (source |
| 2284 | (origin |
| 2285 | (method url-fetch) |
| 2286 | (uri |
| 2287 | (string-append |
| 2288 | "http://ftp.ebi.ac.uk/pub/software/vertebrategenomics/exonerate/" |
| 2289 | "exonerate-" version ".tar.gz")) |
| 2290 | (sha256 |
| 2291 | (base32 |
| 2292 | "0hj0m9xygiqsdxvbg79wq579kbrx1mdrabi2bzqz2zn9qwfjcjgq")))) |
| 2293 | (build-system gnu-build-system) |
| 2294 | (arguments |
| 2295 | `(#:parallel-build? #f)) ; Building in parallel fails on some machines. |
| 2296 | (native-inputs |
| 2297 | `(("pkg-config" ,pkg-config))) |
| 2298 | (inputs |
| 2299 | `(("glib" ,glib))) |
| 2300 | (home-page |
| 2301 | "https://www.ebi.ac.uk/about/vertebrate-genomics/software/exonerate") |
| 2302 | (synopsis "Generic tool for biological sequence alignment") |
| 2303 | (description |
| 2304 | "Exonerate is a generic tool for pairwise sequence comparison. It allows |
| 2305 | the alignment of sequences using a many alignment models, either exhaustive |
| 2306 | dynamic programming or a variety of heuristics.") |
| 2307 | (license license:gpl3))) |
| 2308 | |
| 2309 | (define-public express |
| 2310 | (package |
| 2311 | (name "express") |
| 2312 | (version "1.5.1") |
| 2313 | (source (origin |
| 2314 | (method url-fetch) |
| 2315 | (uri |
| 2316 | (string-append |
| 2317 | "http://bio.math.berkeley.edu/eXpress/downloads/express-" |
| 2318 | version "/express-" version "-src.tgz")) |
| 2319 | (sha256 |
| 2320 | (base32 |
| 2321 | "03rczxd0gjp2l1jxcmjfmf5j94j77zqyxa6x063zsc585nj40n0c")))) |
| 2322 | (build-system cmake-build-system) |
| 2323 | (arguments |
| 2324 | `(#:tests? #f ;no "check" target |
| 2325 | #:phases |
| 2326 | (modify-phases %standard-phases |
| 2327 | (add-after 'unpack 'use-shared-boost-libs-and-set-bamtools-paths |
| 2328 | (lambda* (#:key inputs #:allow-other-keys) |
| 2329 | (substitute* "CMakeLists.txt" |
| 2330 | (("set\\(Boost_USE_STATIC_LIBS ON\\)") |
| 2331 | "set(Boost_USE_STATIC_LIBS OFF)") |
| 2332 | (("\\$\\{CMAKE_CURRENT_SOURCE_DIR\\}/bamtools/include") |
| 2333 | (string-append (assoc-ref inputs "bamtools") "/include/bamtools"))) |
| 2334 | (substitute* "src/CMakeLists.txt" |
| 2335 | (("\\$\\{CMAKE_CURRENT_SOURCE_DIR\\}/\\.\\./bamtools/lib") |
| 2336 | (string-append (assoc-ref inputs "bamtools") "/lib/bamtools"))) |
| 2337 | #t))))) |
| 2338 | (inputs |
| 2339 | `(("boost" ,boost) |
| 2340 | ("bamtools" ,bamtools) |
| 2341 | ("protobuf" ,protobuf) |
| 2342 | ("zlib" ,zlib))) |
| 2343 | (home-page "http://bio.math.berkeley.edu/eXpress") |
| 2344 | (synopsis "Streaming quantification for high-throughput genomic sequencing") |
| 2345 | (description |
| 2346 | "eXpress is a streaming tool for quantifying the abundances of a set of |
| 2347 | target sequences from sampled subsequences. Example applications include |
| 2348 | transcript-level RNA-Seq quantification, allele-specific/haplotype expression |
| 2349 | analysis (from RNA-Seq), transcription factor binding quantification in |
| 2350 | ChIP-Seq, and analysis of metagenomic data.") |
| 2351 | (license license:artistic2.0))) |
| 2352 | |
| 2353 | (define-public express-beta-diversity |
| 2354 | (package |
| 2355 | (name "express-beta-diversity") |
| 2356 | (version "1.0.7") |
| 2357 | (source (origin |
| 2358 | (method url-fetch) |
| 2359 | (uri |
| 2360 | (string-append |
| 2361 | "https://github.com/dparks1134/ExpressBetaDiversity/archive/v" |
| 2362 | version ".tar.gz")) |
| 2363 | (file-name (string-append name "-" version ".tar.gz")) |
| 2364 | (sha256 |
| 2365 | (base32 |
| 2366 | "1djvdlmqvjf6h0zq7w36y8cl5cli6rgj86x65znl48agnwmzxfxr")))) |
| 2367 | (build-system gnu-build-system) |
| 2368 | (arguments |
| 2369 | `(#:phases |
| 2370 | (modify-phases %standard-phases |
| 2371 | (delete 'configure) |
| 2372 | (add-before 'build 'enter-source (lambda _ (chdir "source") #t)) |
| 2373 | (replace 'check |
| 2374 | (lambda _ (zero? (system* "../bin/ExpressBetaDiversity" |
| 2375 | "-u")))) |
| 2376 | (add-after 'check 'exit-source (lambda _ (chdir "..") #t)) |
| 2377 | (replace 'install |
| 2378 | (lambda* (#:key outputs #:allow-other-keys) |
| 2379 | (let ((bin (string-append (assoc-ref outputs "out") |
| 2380 | "/bin"))) |
| 2381 | (mkdir-p bin) |
| 2382 | (install-file "scripts/convertToEBD.py" bin) |
| 2383 | (install-file "bin/ExpressBetaDiversity" bin) |
| 2384 | #t)))))) |
| 2385 | (inputs |
| 2386 | `(("python" ,python-2))) |
| 2387 | (home-page "http://kiwi.cs.dal.ca/Software/ExpressBetaDiversity") |
| 2388 | (synopsis "Taxon- and phylogenetic-based beta diversity measures") |
| 2389 | (description |
| 2390 | "Express Beta Diversity (EBD) calculates ecological beta diversity |
| 2391 | (dissimilarity) measures between biological communities. EBD implements a |
| 2392 | variety of diversity measures including those that make use of phylogenetic |
| 2393 | similarity of community members.") |
| 2394 | (license license:gpl3+))) |
| 2395 | |
| 2396 | (define-public fasttree |
| 2397 | (package |
| 2398 | (name "fasttree") |
| 2399 | (version "2.1.10") |
| 2400 | (source (origin |
| 2401 | (method url-fetch) |
| 2402 | (uri (string-append |
| 2403 | "http://www.microbesonline.org/fasttree/FastTree-" |
| 2404 | version ".c")) |
| 2405 | (sha256 |
| 2406 | (base32 |
| 2407 | "0vcjdvy1j4m702vmak4svbfkrpcw63k7wymfksjp9a982zy8kjsl")))) |
| 2408 | (build-system gnu-build-system) |
| 2409 | (arguments |
| 2410 | `(#:tests? #f ; no "check" target |
| 2411 | #:phases |
| 2412 | (modify-phases %standard-phases |
| 2413 | (delete 'unpack) |
| 2414 | (delete 'configure) |
| 2415 | (replace 'build |
| 2416 | (lambda* (#:key source #:allow-other-keys) |
| 2417 | (and (zero? (system* "gcc" |
| 2418 | "-O3" |
| 2419 | "-finline-functions" |
| 2420 | "-funroll-loops" |
| 2421 | "-Wall" |
| 2422 | "-o" |
| 2423 | "FastTree" |
| 2424 | source |
| 2425 | "-lm")) |
| 2426 | (zero? (system* "gcc" |
| 2427 | "-DOPENMP" |
| 2428 | "-fopenmp" |
| 2429 | "-O3" |
| 2430 | "-finline-functions" |
| 2431 | "-funroll-loops" |
| 2432 | "-Wall" |
| 2433 | "-o" |
| 2434 | "FastTreeMP" |
| 2435 | source |
| 2436 | "-lm"))))) |
| 2437 | (replace 'install |
| 2438 | (lambda* (#:key outputs #:allow-other-keys) |
| 2439 | (let ((bin (string-append (assoc-ref outputs "out") |
| 2440 | "/bin"))) |
| 2441 | (mkdir-p bin) |
| 2442 | (install-file "FastTree" bin) |
| 2443 | (install-file "FastTreeMP" bin) |
| 2444 | #t)))))) |
| 2445 | (home-page "http://www.microbesonline.org/fasttree") |
| 2446 | (synopsis "Infers approximately-maximum-likelihood phylogenetic trees") |
| 2447 | (description |
| 2448 | "FastTree can handle alignments with up to a million of sequences in a |
| 2449 | reasonable amount of time and memory. For large alignments, FastTree is |
| 2450 | 100-1,000 times faster than PhyML 3.0 or RAxML 7.") |
| 2451 | (license license:gpl2+))) |
| 2452 | |
| 2453 | (define-public fastx-toolkit |
| 2454 | (package |
| 2455 | (name "fastx-toolkit") |
| 2456 | (version "0.0.14") |
| 2457 | (source (origin |
| 2458 | (method url-fetch) |
| 2459 | (uri |
| 2460 | (string-append |
| 2461 | "https://github.com/agordon/fastx_toolkit/releases/download/" |
| 2462 | version "/fastx_toolkit-" version ".tar.bz2")) |
| 2463 | (sha256 |
| 2464 | (base32 |
| 2465 | "01jqzw386873sr0pjp1wr4rn8fsga2vxs1qfmicvx1pjr72007wy")))) |
| 2466 | (build-system gnu-build-system) |
| 2467 | (inputs |
| 2468 | `(("libgtextutils" ,libgtextutils))) |
| 2469 | (native-inputs |
| 2470 | `(("pkg-config" ,pkg-config))) |
| 2471 | (home-page "http://hannonlab.cshl.edu/fastx_toolkit/") |
| 2472 | (synopsis "Tools for FASTA/FASTQ file preprocessing") |
| 2473 | (description |
| 2474 | "The FASTX-Toolkit is a collection of command line tools for Short-Reads |
| 2475 | FASTA/FASTQ files preprocessing. |
| 2476 | |
| 2477 | Next-Generation sequencing machines usually produce FASTA or FASTQ files, |
| 2478 | containing multiple short-reads sequences. The main processing of such |
| 2479 | FASTA/FASTQ files is mapping the sequences to reference genomes. However, it |
| 2480 | is sometimes more productive to preprocess the files before mapping the |
| 2481 | sequences to the genome---manipulating the sequences to produce better mapping |
| 2482 | results. The FASTX-Toolkit tools perform some of these preprocessing tasks.") |
| 2483 | (license license:agpl3+))) |
| 2484 | |
| 2485 | (define-public flexbar |
| 2486 | (package |
| 2487 | (name "flexbar") |
| 2488 | (version "2.5") |
| 2489 | (source (origin |
| 2490 | (method url-fetch) |
| 2491 | (uri |
| 2492 | (string-append "mirror://sourceforge/flexbar/" |
| 2493 | version "/flexbar_v" version "_src.tgz")) |
| 2494 | (sha256 |
| 2495 | (base32 |
| 2496 | "13jaykc3y1x8y5nn9j8ljnb79s5y51kyxz46hdmvvjj6qhyympmf")))) |
| 2497 | (build-system cmake-build-system) |
| 2498 | (arguments |
| 2499 | `(#:configure-flags (list |
| 2500 | (string-append "-DFLEXBAR_BINARY_DIR=" |
| 2501 | (assoc-ref %outputs "out") |
| 2502 | "/bin/")) |
| 2503 | #:phases |
| 2504 | (modify-phases %standard-phases |
| 2505 | (replace 'check |
| 2506 | (lambda* (#:key outputs #:allow-other-keys) |
| 2507 | (setenv "PATH" (string-append |
| 2508 | (assoc-ref outputs "out") "/bin:" |
| 2509 | (getenv "PATH"))) |
| 2510 | (chdir "../flexbar_v2.5_src/test") |
| 2511 | (zero? (system* "bash" "flexbar_validate.sh")))) |
| 2512 | (delete 'install)))) |
| 2513 | (inputs |
| 2514 | `(("tbb" ,tbb) |
| 2515 | ("zlib" ,zlib))) |
| 2516 | (native-inputs |
| 2517 | `(("pkg-config" ,pkg-config) |
| 2518 | ("seqan" ,seqan))) |
| 2519 | (home-page "http://flexbar.sourceforge.net") |
| 2520 | (synopsis "Barcode and adapter removal tool for sequencing platforms") |
| 2521 | (description |
| 2522 | "Flexbar preprocesses high-throughput nucleotide sequencing data |
| 2523 | efficiently. It demultiplexes barcoded runs and removes adapter sequences. |
| 2524 | Moreover, trimming and filtering features are provided. Flexbar increases |
| 2525 | read mapping rates and improves genome and transcriptome assemblies. It |
| 2526 | supports next-generation sequencing data in fasta/q and csfasta/q format from |
| 2527 | Illumina, Roche 454, and the SOLiD platform.") |
| 2528 | (license license:gpl3))) |
| 2529 | |
| 2530 | (define-public fraggenescan |
| 2531 | (package |
| 2532 | (name "fraggenescan") |
| 2533 | (version "1.30") |
| 2534 | (source |
| 2535 | (origin |
| 2536 | (method url-fetch) |
| 2537 | (uri |
| 2538 | (string-append "mirror://sourceforge/fraggenescan/" |
| 2539 | "FragGeneScan" version ".tar.gz")) |
| 2540 | (sha256 |
| 2541 | (base32 "158dcnwczgcyhwm4qlx19sanrwgdpzf6bn2y57mbpx55lkgz1mzj")))) |
| 2542 | (build-system gnu-build-system) |
| 2543 | (arguments |
| 2544 | `(#:phases |
| 2545 | (modify-phases %standard-phases |
| 2546 | (delete 'configure) |
| 2547 | (add-before 'build 'patch-paths |
| 2548 | (lambda* (#:key outputs #:allow-other-keys) |
| 2549 | (let* ((out (string-append (assoc-ref outputs "out"))) |
| 2550 | (share (string-append out "/share/fraggenescan/"))) |
| 2551 | (substitute* "run_FragGeneScan.pl" |
| 2552 | (("system\\(\"rm") |
| 2553 | (string-append "system(\"" (which "rm"))) |
| 2554 | (("system\\(\"mv") |
| 2555 | (string-append "system(\"" (which "mv"))) |
| 2556 | (("\\\"awk") (string-append "\"" (which "awk"))) |
| 2557 | ;; This script and other programs expect the training files |
| 2558 | ;; to be in the non-standard location bin/train/XXX. Change |
| 2559 | ;; this to be share/fraggenescan/train/XXX instead. |
| 2560 | (("^\\$train.file = \\$dir.*") |
| 2561 | (string-append "$train_file = \"" |
| 2562 | share |
| 2563 | "train/\".$FGS_train_file;"))) |
| 2564 | (substitute* "run_hmm.c" |
| 2565 | (("^ strcat\\(train_dir, \\\"train/\\\"\\);") |
| 2566 | (string-append " strcpy(train_dir, \"" share "/train/\");")))) |
| 2567 | #t)) |
| 2568 | (replace 'build |
| 2569 | (lambda _ (and (zero? (system* "make" "clean")) |
| 2570 | (zero? (system* "make" "fgs"))))) |
| 2571 | (replace 'install |
| 2572 | (lambda* (#:key outputs #:allow-other-keys) |
| 2573 | (let* ((out (string-append (assoc-ref outputs "out"))) |
| 2574 | (bin (string-append out "/bin/")) |
| 2575 | (share (string-append out "/share/fraggenescan/train"))) |
| 2576 | (install-file "run_FragGeneScan.pl" bin) |
| 2577 | (install-file "FragGeneScan" bin) |
| 2578 | (copy-recursively "train" share)))) |
| 2579 | (delete 'check) |
| 2580 | (add-after 'install 'post-install-check |
| 2581 | ;; In lieu of 'make check', run one of the examples and check the |
| 2582 | ;; output files gets created. |
| 2583 | (lambda* (#:key outputs #:allow-other-keys) |
| 2584 | (let* ((out (string-append (assoc-ref outputs "out"))) |
| 2585 | (bin (string-append out "/bin/")) |
| 2586 | (frag (string-append bin "run_FragGeneScan.pl"))) |
| 2587 | (and (zero? (system* frag ; Test complete genome. |
| 2588 | "-genome=./example/NC_000913.fna" |
| 2589 | "-out=./test2" |
| 2590 | "-complete=1" |
| 2591 | "-train=complete")) |
| 2592 | (file-exists? "test2.faa") |
| 2593 | (file-exists? "test2.ffn") |
| 2594 | (file-exists? "test2.gff") |
| 2595 | (file-exists? "test2.out") |
| 2596 | (zero? (system* ; Test incomplete sequences. |
| 2597 | frag |
| 2598 | "-genome=./example/NC_000913-fgs.ffn" |
| 2599 | "-out=out" |
| 2600 | "-complete=0" |
| 2601 | "-train=454_30"))))))))) |
| 2602 | (inputs |
| 2603 | `(("perl" ,perl) |
| 2604 | ("python" ,python-2))) ;not compatible with python 3. |
| 2605 | (home-page "https://sourceforge.net/projects/fraggenescan/") |
| 2606 | (synopsis "Finds potentially fragmented genes in short reads") |
| 2607 | (description |
| 2608 | "FragGeneScan is a program for predicting bacterial and archaeal genes in |
| 2609 | short and error-prone DNA sequencing reads. It can also be applied to predict |
| 2610 | genes in incomplete assemblies or complete genomes.") |
| 2611 | ;; GPL3+ according to private correspondense with the authors. |
| 2612 | (license license:gpl3+))) |
| 2613 | |
| 2614 | (define-public fxtract |
| 2615 | (let ((util-commit "776ca85a18a47492af3794745efcb4a905113115")) |
| 2616 | (package |
| 2617 | (name "fxtract") |
| 2618 | (version "2.3") |
| 2619 | (source |
| 2620 | (origin |
| 2621 | (method url-fetch) |
| 2622 | (uri (string-append |
| 2623 | "https://github.com/ctSkennerton/fxtract/archive/" |
| 2624 | version ".tar.gz")) |
| 2625 | (file-name (string-append "ctstennerton-util-" |
| 2626 | (string-take util-commit 7) |
| 2627 | "-checkout")) |
| 2628 | (sha256 |
| 2629 | (base32 |
| 2630 | "0275cfdhis8517hm01is62062swmi06fxzifq7mr3knbbxjlaiwj")))) |
| 2631 | (build-system gnu-build-system) |
| 2632 | (arguments |
| 2633 | `(#:make-flags (list |
| 2634 | (string-append "PREFIX=" (assoc-ref %outputs "out")) |
| 2635 | "CC=gcc") |
| 2636 | #:test-target "fxtract_test" |
| 2637 | #:phases |
| 2638 | (modify-phases %standard-phases |
| 2639 | (delete 'configure) |
| 2640 | (add-before 'build 'copy-util |
| 2641 | (lambda* (#:key inputs #:allow-other-keys) |
| 2642 | (rmdir "util") |
| 2643 | (copy-recursively (assoc-ref inputs "ctskennerton-util") "util") |
| 2644 | #t)) |
| 2645 | ;; Do not use make install as this requires additional dependencies. |
| 2646 | (replace 'install |
| 2647 | (lambda* (#:key outputs #:allow-other-keys) |
| 2648 | (let* ((out (assoc-ref outputs "out")) |
| 2649 | (bin (string-append out"/bin"))) |
| 2650 | (install-file "fxtract" bin) |
| 2651 | #t)))))) |
| 2652 | (inputs |
| 2653 | `(("pcre" ,pcre) |
| 2654 | ("zlib" ,zlib))) |
| 2655 | (native-inputs |
| 2656 | ;; ctskennerton-util is licensed under GPL2. |
| 2657 | `(("ctskennerton-util" |
| 2658 | ,(origin |
| 2659 | (method git-fetch) |
| 2660 | (uri (git-reference |
| 2661 | (url "https://github.com/ctSkennerton/util.git") |
| 2662 | (commit util-commit))) |
| 2663 | (file-name (string-append |
| 2664 | "ctstennerton-util-" util-commit "-checkout")) |
| 2665 | (sha256 |
| 2666 | (base32 |
| 2667 | "0cls1hd4vgj3f36fpzzg4xc77d6f3hpc60cbpfmn2gdr7ykzzad7")))))) |
| 2668 | (home-page "https://github.com/ctSkennerton/fxtract") |
| 2669 | (synopsis "Extract sequences from FASTA and FASTQ files") |
| 2670 | (description |
| 2671 | "Fxtract extracts sequences from a protein or nucleotide fastx (FASTA |
| 2672 | or FASTQ) file given a subsequence. It uses a simple substring search for |
| 2673 | basic tasks but can change to using POSIX regular expressions, PCRE, hash |
| 2674 | lookups or multi-pattern searching as required. By default fxtract looks in |
| 2675 | the sequence of each record but can also be told to look in the header, |
| 2676 | comment or quality sections.") |
| 2677 | ;; 'util' requires SSE instructions. |
| 2678 | (supported-systems '("x86_64-linux")) |
| 2679 | (license license:expat)))) |
| 2680 | |
| 2681 | (define-public gemma |
| 2682 | (package |
| 2683 | (name "gemma") |
| 2684 | (version "0.96") |
| 2685 | (source (origin |
| 2686 | (method url-fetch) |
| 2687 | (uri (string-append "https://github.com/xiangzhou/GEMMA/archive/v" |
| 2688 | version ".tar.gz")) |
| 2689 | (file-name (string-append name "-" version ".tar.gz")) |
| 2690 | (sha256 |
| 2691 | (base32 |
| 2692 | "055ynn16gd12pf78n4vr2a9jlwsbwzajpdnf2y2yilg1krfff222")) |
| 2693 | (patches (search-patches "gemma-intel-compat.patch")))) |
| 2694 | (inputs |
| 2695 | `(("gsl" ,gsl) |
| 2696 | ("lapack" ,lapack) |
| 2697 | ("zlib" ,zlib))) |
| 2698 | (build-system gnu-build-system) |
| 2699 | (arguments |
| 2700 | `(#:make-flags |
| 2701 | '(,@(match (%current-system) |
| 2702 | ("x86_64-linux" |
| 2703 | '("FORCE_DYNAMIC=1")) |
| 2704 | ("i686-linux" |
| 2705 | '("FORCE_DYNAMIC=1" "FORCE_32BIT=1")) |
| 2706 | (_ |
| 2707 | '("FORCE_DYNAMIC=1" "NO_INTEL_COMPAT=1")))) |
| 2708 | #:phases |
| 2709 | (modify-phases %standard-phases |
| 2710 | (delete 'configure) |
| 2711 | (add-before 'build 'bin-mkdir |
| 2712 | (lambda _ |
| 2713 | (mkdir-p "bin") |
| 2714 | #t)) |
| 2715 | (replace 'install |
| 2716 | (lambda* (#:key outputs #:allow-other-keys) |
| 2717 | (let ((out (assoc-ref outputs "out"))) |
| 2718 | (install-file "bin/gemma" |
| 2719 | (string-append |
| 2720 | out "/bin"))) |
| 2721 | #t))) |
| 2722 | #:tests? #f)) ; no tests included yet |
| 2723 | (home-page "https://github.com/xiangzhou/GEMMA") |
| 2724 | (synopsis "Tool for genome-wide efficient mixed model association") |
| 2725 | (description |
| 2726 | "Genome-wide Efficient Mixed Model Association (GEMMA) provides a |
| 2727 | standard linear mixed model resolver with application in genome-wide |
| 2728 | association studies (GWAS).") |
| 2729 | (license license:gpl3))) |
| 2730 | |
| 2731 | (define-public grit |
| 2732 | (package |
| 2733 | (name "grit") |
| 2734 | (version "2.0.2") |
| 2735 | (source (origin |
| 2736 | (method url-fetch) |
| 2737 | (uri (string-append |
| 2738 | "https://github.com/nboley/grit/archive/" |
| 2739 | version ".tar.gz")) |
| 2740 | (file-name (string-append name "-" version ".tar.gz")) |
| 2741 | (sha256 |
| 2742 | (base32 |
| 2743 | "157in84dj70wimbind3x7sy1whs3h57qfgcnj2s6lrd38fbrb7mj")))) |
| 2744 | (build-system python-build-system) |
| 2745 | (arguments |
| 2746 | `(#:python ,python-2 |
| 2747 | #:phases |
| 2748 | (modify-phases %standard-phases |
| 2749 | (add-after 'unpack 'generate-from-cython-sources |
| 2750 | (lambda* (#:key inputs outputs #:allow-other-keys) |
| 2751 | ;; Delete these C files to force fresh generation from pyx sources. |
| 2752 | (delete-file "grit/sparsify_support_fns.c") |
| 2753 | (delete-file "grit/call_peaks_support_fns.c") |
| 2754 | (substitute* "setup.py" |
| 2755 | (("Cython.Setup") "Cython.Build") |
| 2756 | ;; Add numpy include path to fix compilation |
| 2757 | (("pyx\", \\]") |
| 2758 | (string-append "pyx\", ], include_dirs = ['" |
| 2759 | (assoc-ref inputs "python-numpy") |
| 2760 | "/lib/python2.7/site-packages/numpy/core/include/" |
| 2761 | "']"))) |
| 2762 | #t))))) |
| 2763 | (inputs |
| 2764 | `(("python-scipy" ,python2-scipy) |
| 2765 | ("python-numpy" ,python2-numpy) |
| 2766 | ("python-pysam" ,python2-pysam) |
| 2767 | ("python-networkx" ,python2-networkx))) |
| 2768 | (native-inputs |
| 2769 | `(("python-cython" ,python2-cython))) |
| 2770 | (home-page "http://grit-bio.org") |
| 2771 | (synopsis "Tool for integrative analysis of RNA-seq type assays") |
| 2772 | (description |
| 2773 | "GRIT is designed to use RNA-seq, TES, and TSS data to build and quantify |
| 2774 | full length transcript models. When none of these data sources are available, |
| 2775 | GRIT can be run by providing a candidate set of TES or TSS sites. In |
| 2776 | addition, GRIT can merge in reference junctions and gene boundaries. GRIT can |
| 2777 | also be run in quantification mode, where it uses a provided GTF file and just |
| 2778 | estimates transcript expression.") |
| 2779 | (license license:gpl3+))) |
| 2780 | |
| 2781 | (define-public hisat |
| 2782 | (package |
| 2783 | (name "hisat") |
| 2784 | (version "0.1.4") |
| 2785 | (source (origin |
| 2786 | (method url-fetch) |
| 2787 | (uri (string-append |
| 2788 | "http://ccb.jhu.edu/software/hisat/downloads/hisat-" |
| 2789 | version "-beta-source.zip")) |
| 2790 | (sha256 |
| 2791 | (base32 |
| 2792 | "1k381ydranqxp09yf2y7w1d0chz5d59vb6jchi89hbb0prq19lk5")))) |
| 2793 | (build-system gnu-build-system) |
| 2794 | (arguments |
| 2795 | `(#:tests? #f ;no check target |
| 2796 | #:make-flags '("allall" |
| 2797 | ;; Disable unsupported `popcnt' instructions on |
| 2798 | ;; architectures other than x86_64 |
| 2799 | ,@(if (string-prefix? "x86_64" |
| 2800 | (or (%current-target-system) |
| 2801 | (%current-system))) |
| 2802 | '() |
| 2803 | '("POPCNT_CAPABILITY=0"))) |
| 2804 | #:phases |
| 2805 | (modify-phases %standard-phases |
| 2806 | (add-after 'unpack 'patch-sources |
| 2807 | (lambda _ |
| 2808 | ;; XXX Cannot use snippet because zip files are not supported |
| 2809 | (substitute* "Makefile" |
| 2810 | (("^CC = .*$") "CC = gcc") |
| 2811 | (("^CPP = .*$") "CPP = g++") |
| 2812 | ;; replace BUILD_HOST and BUILD_TIME for deterministic build |
| 2813 | (("-DBUILD_HOST=.*") "-DBUILD_HOST=\"\\\"guix\\\"\"") |
| 2814 | (("-DBUILD_TIME=.*") "-DBUILD_TIME=\"\\\"0\\\"\"")) |
| 2815 | (substitute* '("hisat-build" "hisat-inspect") |
| 2816 | (("/usr/bin/env") (which "env"))) |
| 2817 | #t)) |
| 2818 | (replace 'install |
| 2819 | (lambda* (#:key outputs #:allow-other-keys) |
| 2820 | (let ((bin (string-append (assoc-ref outputs "out") "/bin/"))) |
| 2821 | (for-each (lambda (file) |
| 2822 | (install-file file bin)) |
| 2823 | (find-files |
| 2824 | "." |
| 2825 | "hisat(-(build|align|inspect)(-(s|l)(-debug)*)*)*$"))) |
| 2826 | #t)) |
| 2827 | (delete 'configure)))) |
| 2828 | (native-inputs |
| 2829 | `(("unzip" ,unzip))) |
| 2830 | (inputs |
| 2831 | `(("perl" ,perl) |
| 2832 | ("python" ,python) |
| 2833 | ("zlib" ,zlib))) |
| 2834 | ;; Non-portable SSE instructions are used so building fails on platforms |
| 2835 | ;; other than x86_64. |
| 2836 | (supported-systems '("x86_64-linux")) |
| 2837 | (home-page "http://ccb.jhu.edu/software/hisat/index.shtml") |
| 2838 | (synopsis "Hierarchical indexing for spliced alignment of transcripts") |
| 2839 | (description |
| 2840 | "HISAT is a fast and sensitive spliced alignment program for mapping |
| 2841 | RNA-seq reads. In addition to one global FM index that represents a whole |
| 2842 | genome, HISAT uses a large set of small FM indexes that collectively cover the |
| 2843 | whole genome. These small indexes (called local indexes) combined with |
| 2844 | several alignment strategies enable effective alignment of RNA-seq reads, in |
| 2845 | particular, reads spanning multiple exons.") |
| 2846 | (license license:gpl3+))) |
| 2847 | |
| 2848 | (define-public hisat2 |
| 2849 | (package |
| 2850 | (name "hisat2") |
| 2851 | (version "2.0.5") |
| 2852 | (source |
| 2853 | (origin |
| 2854 | (method url-fetch) |
| 2855 | ;; FIXME: a better source URL is |
| 2856 | ;; (string-append "ftp://ftp.ccb.jhu.edu/pub/infphilo/hisat2" |
| 2857 | ;; "/downloads/hisat2-" version "-source.zip") |
| 2858 | ;; with hash "0lywnr8kijwsc2aw10dwxic0n0yvip6fl3rjlvc8zzwahamy4x7g" |
| 2859 | ;; but it is currently unavailable. |
| 2860 | (uri "https://github.com/infphilo/hisat2/archive/cba6e8cb.tar.gz") |
| 2861 | (file-name (string-append name "-" version ".tar.gz")) |
| 2862 | (sha256 |
| 2863 | (base32 |
| 2864 | "1mf2hdsyv7cd97xm9mp9a4qws02yrj95y6w6f6cdwnq0klp81r50")))) |
| 2865 | (build-system gnu-build-system) |
| 2866 | (arguments |
| 2867 | `(#:tests? #f ; no check target |
| 2868 | #:make-flags (list "CC=gcc" "CXX=g++" "allall") |
| 2869 | #:modules ((guix build gnu-build-system) |
| 2870 | (guix build utils) |
| 2871 | (srfi srfi-26)) |
| 2872 | #:phases |
| 2873 | (modify-phases %standard-phases |
| 2874 | (add-after 'unpack 'make-deterministic |
| 2875 | (lambda _ |
| 2876 | (substitute* "Makefile" |
| 2877 | (("`date`") "0")) |
| 2878 | #t)) |
| 2879 | (delete 'configure) |
| 2880 | (replace 'install |
| 2881 | (lambda* (#:key outputs #:allow-other-keys) |
| 2882 | (let* ((out (assoc-ref outputs "out")) |
| 2883 | (bin (string-append out "/bin/")) |
| 2884 | (doc (string-append out "/share/doc/hisat2/"))) |
| 2885 | (for-each |
| 2886 | (cut install-file <> bin) |
| 2887 | (find-files "." |
| 2888 | "hisat2(-(build|align|inspect)(-(s|l)(-debug)*)*)*$")) |
| 2889 | (mkdir-p doc) |
| 2890 | (install-file "doc/manual.inc.html" doc)) |
| 2891 | #t))))) |
| 2892 | (native-inputs |
| 2893 | `(("unzip" ,unzip) ; needed for archive from ftp |
| 2894 | ("perl" ,perl) |
| 2895 | ("pandoc" ,ghc-pandoc))) ; for documentation |
| 2896 | (home-page "http://ccb.jhu.edu/software/hisat2/index.shtml") |
| 2897 | (synopsis "Graph-based alignment of genomic sequencing reads") |
| 2898 | (description "HISAT2 is a fast and sensitive alignment program for mapping |
| 2899 | next-generation sequencing reads (both DNA and RNA) to a population of human |
| 2900 | genomes (as well as to a single reference genome). In addition to using one |
| 2901 | global @dfn{graph FM} (GFM) index that represents a population of human |
| 2902 | genomes, HISAT2 uses a large set of small GFM indexes that collectively cover |
| 2903 | the whole genome. These small indexes, combined with several alignment |
| 2904 | strategies, enable rapid and accurate alignment of sequencing reads. This new |
| 2905 | indexing scheme is called a @dfn{Hierarchical Graph FM index} (HGFM).") |
| 2906 | ;; HISAT2 contains files from Bowtie2, which is released under |
| 2907 | ;; GPLv2 or later. The HISAT2 source files are released under |
| 2908 | ;; GPLv3 or later. |
| 2909 | (license license:gpl3+))) |
| 2910 | |
| 2911 | (define-public hmmer |
| 2912 | (package |
| 2913 | (name "hmmer") |
| 2914 | (version "3.1b2") |
| 2915 | (source |
| 2916 | (origin |
| 2917 | (method url-fetch) |
| 2918 | (uri (string-append |
| 2919 | "http://eddylab.org/software/hmmer" |
| 2920 | (version-major version) "/" |
| 2921 | version "/hmmer-" version ".tar.gz")) |
| 2922 | (sha256 |
| 2923 | (base32 |
| 2924 | "0djmgc0pfli0jilfx8hql1axhwhqxqb8rxg2r5rg07aw73sfs5nx")) |
| 2925 | (patches (search-patches "hmmer-remove-cpu-specificity.patch")))) |
| 2926 | (build-system gnu-build-system) |
| 2927 | (native-inputs `(("perl" ,perl))) |
| 2928 | (home-page "http://hmmer.org/") |
| 2929 | (synopsis "Biosequence analysis using profile hidden Markov models") |
| 2930 | (description |
| 2931 | "HMMER is used for searching sequence databases for homologs of protein |
| 2932 | sequences, and for making protein sequence alignments. It implements methods |
| 2933 | using probabilistic models called profile hidden Markov models (profile |
| 2934 | HMMs).") |
| 2935 | (license (list license:gpl3+ |
| 2936 | ;; The bundled library 'easel' is distributed |
| 2937 | ;; under The Janelia Farm Software License. |
| 2938 | (license:non-copyleft |
| 2939 | "file://easel/LICENSE" |
| 2940 | "See easel/LICENSE in the distribution."))))) |
| 2941 | |
| 2942 | (define-public htseq |
| 2943 | (package |
| 2944 | (name "htseq") |
| 2945 | (version "0.9.1") |
| 2946 | (source (origin |
| 2947 | (method url-fetch) |
| 2948 | (uri (pypi-uri "HTSeq" version)) |
| 2949 | (sha256 |
| 2950 | (base32 |
| 2951 | "11flgb1381xdhk43bzbfm3vhnszkpqg6jk76rpa5xd1zbrvvlnxg")))) |
| 2952 | (build-system python-build-system) |
| 2953 | (native-inputs |
| 2954 | `(("python-cython" ,python-cython))) |
| 2955 | ;; Numpy needs to be propagated when htseq is used as a Python library. |
| 2956 | (propagated-inputs |
| 2957 | `(("python-numpy" ,python-numpy))) |
| 2958 | (inputs |
| 2959 | `(("python-pysam" ,python-pysam) |
| 2960 | ("python-matplotlib" ,python-matplotlib))) |
| 2961 | (home-page "http://www-huber.embl.de/users/anders/HTSeq/") |
| 2962 | (synopsis "Analysing high-throughput sequencing data with Python") |
| 2963 | (description |
| 2964 | "HTSeq is a Python package that provides infrastructure to process data |
| 2965 | from high-throughput sequencing assays.") |
| 2966 | (license license:gpl3+))) |
| 2967 | |
| 2968 | (define-public python2-htseq |
| 2969 | (package-with-python2 htseq)) |
| 2970 | |
| 2971 | (define-public java-htsjdk |
| 2972 | (package |
| 2973 | (name "java-htsjdk") |
| 2974 | (version "2.3.0") ; last version without build dependency on gradle |
| 2975 | (source (origin |
| 2976 | (method url-fetch) |
| 2977 | (uri (string-append |
| 2978 | "https://github.com/samtools/htsjdk/archive/" |
| 2979 | version ".tar.gz")) |
| 2980 | (file-name (string-append name "-" version ".tar.gz")) |
| 2981 | (sha256 |
| 2982 | (base32 |
| 2983 | "1ibhzzxsfc38nqyk9r8zqj6blfc1kh26iirypd4q6n90hs2m6nyq")) |
| 2984 | (modules '((guix build utils))) |
| 2985 | (snippet |
| 2986 | ;; Delete pre-built binaries |
| 2987 | '(begin |
| 2988 | (delete-file-recursively "lib") |
| 2989 | (mkdir-p "lib") |
| 2990 | #t)))) |
| 2991 | (build-system ant-build-system) |
| 2992 | (arguments |
| 2993 | `(#:tests? #f ; test require Internet access |
| 2994 | #:jdk ,icedtea-8 |
| 2995 | #:make-flags |
| 2996 | (list (string-append "-Ddist=" (assoc-ref %outputs "out") |
| 2997 | "/share/java/htsjdk/")) |
| 2998 | #:build-target "all" |
| 2999 | #:phases |
| 3000 | (modify-phases %standard-phases |
| 3001 | ;; The build phase also installs the jars |
| 3002 | (delete 'install)))) |
| 3003 | (inputs |
| 3004 | `(("java-ngs" ,java-ngs) |
| 3005 | ("java-snappy-1" ,java-snappy-1) |
| 3006 | ("java-commons-compress" ,java-commons-compress) |
| 3007 | ("java-commons-logging-minimal" ,java-commons-logging-minimal) |
| 3008 | ("java-commons-jexl-2" ,java-commons-jexl-2) |
| 3009 | ("java-xz" ,java-xz))) |
| 3010 | (native-inputs |
| 3011 | `(("java-testng" ,java-testng))) |
| 3012 | (home-page "http://samtools.github.io/htsjdk/") |
| 3013 | (synopsis "Java API for high-throughput sequencing data (HTS) formats") |
| 3014 | (description |
| 3015 | "HTSJDK is an implementation of a unified Java library for accessing |
| 3016 | common file formats, such as SAM and VCF, used for high-throughput |
| 3017 | sequencing (HTS) data. There are also an number of useful utilities for |
| 3018 | manipulating HTS data.") |
| 3019 | (license license:expat))) |
| 3020 | |
| 3021 | ;; This version matches java-htsjdk 2.3.0. Later versions also require a more |
| 3022 | ;; recent version of java-htsjdk, which depends on gradle. |
| 3023 | (define-public java-picard |
| 3024 | (package |
| 3025 | (name "java-picard") |
| 3026 | (version "2.3.0") |
| 3027 | (source (origin |
| 3028 | (method git-fetch) |
| 3029 | (uri (git-reference |
| 3030 | (url "https://github.com/broadinstitute/picard.git") |
| 3031 | (commit version))) |
| 3032 | (file-name (string-append "java-picard-" version "-checkout")) |
| 3033 | (sha256 |
| 3034 | (base32 |
| 3035 | "1ll7mf4r3by92w2nhlmpa591xd1f46xlkwh59mq6fvbb5pdwzvx6")) |
| 3036 | (modules '((guix build utils))) |
| 3037 | (snippet |
| 3038 | '(begin |
| 3039 | ;; Delete pre-built binaries. |
| 3040 | (delete-file-recursively "lib") |
| 3041 | (mkdir-p "lib") |
| 3042 | (substitute* "build.xml" |
| 3043 | ;; Remove build-time dependency on git. |
| 3044 | (("failifexecutionfails=\"true\"") |
| 3045 | "failifexecutionfails=\"false\"") |
| 3046 | ;; Use our htsjdk. |
| 3047 | (("depends=\"compile-htsjdk, ") |
| 3048 | "depends=\"") |
| 3049 | (("depends=\"compile-htsjdk-tests, ") |
| 3050 | "depends=\"") |
| 3051 | ;; Build picard-lib.jar before building picard.jar |
| 3052 | (("name=\"picard-jar\" depends=\"" line) |
| 3053 | (string-append line "picard-lib-jar, "))) |
| 3054 | #t)))) |
| 3055 | (build-system ant-build-system) |
| 3056 | (arguments |
| 3057 | `(#:build-target "picard-jar" |
| 3058 | #:test-target "test" |
| 3059 | ;; Tests require jacoco:coverage. |
| 3060 | #:tests? #f |
| 3061 | #:make-flags |
| 3062 | (list (string-append "-Dhtsjdk_lib_dir=" |
| 3063 | (assoc-ref %build-inputs "java-htsjdk") |
| 3064 | "/share/java/htsjdk/") |
| 3065 | "-Dhtsjdk-classes=dist/tmp" |
| 3066 | (string-append "-Dhtsjdk-version=" |
| 3067 | ,(package-version java-htsjdk))) |
| 3068 | #:jdk ,icedtea-8 |
| 3069 | #:phases |
| 3070 | (modify-phases %standard-phases |
| 3071 | (add-after 'unpack 'use-our-htsjdk |
| 3072 | (lambda* (#:key inputs #:allow-other-keys) |
| 3073 | (substitute* "build.xml" |
| 3074 | (("\\$\\{htsjdk\\}/lib") |
| 3075 | (string-append (assoc-ref inputs "java-htsjdk") |
| 3076 | "/share/java/htsjdk/"))) |
| 3077 | #t)) |
| 3078 | (add-after 'unpack 'make-test-target-independent |
| 3079 | (lambda* (#:key inputs #:allow-other-keys) |
| 3080 | (substitute* "build.xml" |
| 3081 | (("name=\"test\" depends=\"compile, ") |
| 3082 | "name=\"test\" depends=\"")) |
| 3083 | #t)) |
| 3084 | (replace 'install (install-jars "dist"))))) |
| 3085 | (inputs |
| 3086 | `(("java-htsjdk" ,java-htsjdk) |
| 3087 | ("java-guava" ,java-guava))) |
| 3088 | (native-inputs |
| 3089 | `(("java-testng" ,java-testng))) |
| 3090 | (home-page "http://broadinstitute.github.io/picard/") |
| 3091 | (synopsis "Tools for manipulating high-throughput sequencing data and formats") |
| 3092 | (description "Picard is a set of Java command line tools for manipulating |
| 3093 | high-throughput sequencing (HTS) data and formats. Picard is implemented |
| 3094 | using the HTSJDK Java library to support accessing file formats that are |
| 3095 | commonly used for high-throughput sequencing data such as SAM, BAM, CRAM and |
| 3096 | VCF.") |
| 3097 | (license license:expat))) |
| 3098 | |
| 3099 | ;; This is the last version of Picard to provide net.sf.samtools |
| 3100 | (define-public java-picard-1.113 |
| 3101 | (package (inherit java-picard) |
| 3102 | (name "java-picard") |
| 3103 | (version "1.113") |
| 3104 | (source (origin |
| 3105 | (method git-fetch) |
| 3106 | (uri (git-reference |
| 3107 | (url "https://github.com/broadinstitute/picard.git") |
| 3108 | (commit version))) |
| 3109 | (file-name (string-append "java-picard-" version "-checkout")) |
| 3110 | (sha256 |
| 3111 | (base32 |
| 3112 | "0lkpvin2fz3hhly4l02kk56fqy8lmlgyzr9kmvljk6ry6l1hw973")) |
| 3113 | (modules '((guix build utils))) |
| 3114 | (snippet |
| 3115 | '(begin |
| 3116 | ;; Delete pre-built binaries. |
| 3117 | (delete-file-recursively "lib") |
| 3118 | (mkdir-p "lib") |
| 3119 | #t)))) |
| 3120 | (build-system ant-build-system) |
| 3121 | (arguments |
| 3122 | `(#:build-target "picard-jar" |
| 3123 | #:test-target "test" |
| 3124 | ;; FIXME: the class path at test time is wrong. |
| 3125 | ;; [testng] Error: A JNI error has occurred, please check your installation and try again |
| 3126 | ;; [testng] Exception in thread "main" java.lang.NoClassDefFoundError: com/beust/jcommander/ParameterException |
| 3127 | #:tests? #f |
| 3128 | #:jdk ,icedtea-8 |
| 3129 | ;; This is only used for tests. |
| 3130 | #:make-flags |
| 3131 | (list "-Dsamjdk.intel_deflater_so_path=lib/jni/libIntelDeflater.so") |
| 3132 | #:phases |
| 3133 | (modify-phases %standard-phases |
| 3134 | ;; Do not use bundled ant bzip2. |
| 3135 | (add-after 'unpack 'use-ant-bzip |
| 3136 | (lambda* (#:key inputs #:allow-other-keys) |
| 3137 | (substitute* "build.xml" |
| 3138 | (("\\$\\{lib\\}/apache-ant-1.8.2-bzip2.jar") |
| 3139 | (string-append (assoc-ref inputs "ant") |
| 3140 | "/lib/ant.jar"))) |
| 3141 | #t)) |
| 3142 | (add-after 'unpack 'make-test-target-independent |
| 3143 | (lambda* (#:key inputs #:allow-other-keys) |
| 3144 | (substitute* "build.xml" |
| 3145 | (("name=\"test\" depends=\"compile, ") |
| 3146 | "name=\"test\" depends=\"compile-tests, ") |
| 3147 | (("name=\"compile\" depends=\"compile-src, compile-tests\"") |
| 3148 | "name=\"compile\" depends=\"compile-src\"")) |
| 3149 | #t)) |
| 3150 | (add-after 'unpack 'fix-deflater-path |
| 3151 | (lambda* (#:key outputs #:allow-other-keys) |
| 3152 | (substitute* "src/java/net/sf/samtools/Defaults.java" |
| 3153 | (("getStringProperty\\(\"intel_deflater_so_path\", null\\)") |
| 3154 | (string-append "getStringProperty(\"intel_deflater_so_path\", \"" |
| 3155 | (assoc-ref outputs "out") |
| 3156 | "/lib/jni/libIntelDeflater.so" |
| 3157 | "\")"))) |
| 3158 | #t)) |
| 3159 | ;; Build the deflater library, because we've previously deleted the |
| 3160 | ;; pre-built one. This can only be built with access to the JDK |
| 3161 | ;; sources. |
| 3162 | (add-after 'build 'build-jni |
| 3163 | (lambda* (#:key inputs #:allow-other-keys) |
| 3164 | (mkdir-p "lib/jni") |
| 3165 | (mkdir-p "jdk-src") |
| 3166 | (and (zero? (system* "tar" "--strip-components=1" "-C" "jdk-src" |
| 3167 | "-xf" (assoc-ref inputs "jdk-src"))) |
| 3168 | (zero? (system* "javah" "-jni" |
| 3169 | "-classpath" "classes" |
| 3170 | "-d" "lib/" |
| 3171 | "net.sf.samtools.util.zip.IntelDeflater")) |
| 3172 | (with-directory-excursion "src/c/inteldeflater" |
| 3173 | (zero? (system* "gcc" "-I../../../lib" "-I." |
| 3174 | (string-append "-I" (assoc-ref inputs "jdk") |
| 3175 | "/include/linux") |
| 3176 | "-I../../../jdk-src/src/share/native/common/" |
| 3177 | "-I../../../jdk-src/src/solaris/native/common/" |
| 3178 | "-c" "-O3" "-fPIC" "IntelDeflater.c")) |
| 3179 | (zero? (system* "gcc" "-shared" |
| 3180 | "-o" "../../../lib/jni/libIntelDeflater.so" |
| 3181 | "IntelDeflater.o" "-lz" "-lstdc++")))))) |
| 3182 | ;; We can only build everything else after building the JNI library. |
| 3183 | (add-after 'build-jni 'build-rest |
| 3184 | (lambda* (#:key make-flags #:allow-other-keys) |
| 3185 | (zero? (apply system* `("ant" "all" ,@make-flags))))) |
| 3186 | (add-before 'build 'set-JAVA6_HOME |
| 3187 | (lambda _ |
| 3188 | (setenv "JAVA6_HOME" (getenv "JAVA_HOME")) |
| 3189 | #t)) |
| 3190 | (replace 'install (install-jars "dist")) |
| 3191 | (add-after 'install 'install-jni-lib |
| 3192 | (lambda* (#:key outputs #:allow-other-keys) |
| 3193 | (let ((jni (string-append (assoc-ref outputs "out") |
| 3194 | "/lib/jni"))) |
| 3195 | (mkdir-p jni) |
| 3196 | (install-file "lib/jni/libIntelDeflater.so" jni) |
| 3197 | #t)))))) |
| 3198 | (inputs |
| 3199 | `(("java-snappy-1" ,java-snappy-1) |
| 3200 | ("java-commons-jexl-2" ,java-commons-jexl-2) |
| 3201 | ("java-cofoja" ,java-cofoja) |
| 3202 | ("ant" ,ant) ; for bzip2 support at runtime |
| 3203 | ("zlib" ,zlib))) |
| 3204 | (native-inputs |
| 3205 | `(("ant-apache-bcel" ,ant-apache-bcel) |
| 3206 | ("ant-junit" ,ant-junit) |
| 3207 | ("java-testng" ,java-testng) |
| 3208 | ("java-commons-bcel" ,java-commons-bcel) |
| 3209 | ("java-jcommander" ,java-jcommander) |
| 3210 | ("jdk" ,icedtea-8 "jdk") |
| 3211 | ("jdk-src" ,(car (assoc-ref (package-native-inputs icedtea-8) "jdk-drop"))))))) |
| 3212 | |
| 3213 | (define-public htslib |
| 3214 | (package |
| 3215 | (name "htslib") |
| 3216 | (version "1.6") |
| 3217 | (source (origin |
| 3218 | (method url-fetch) |
| 3219 | (uri (string-append |
| 3220 | "https://github.com/samtools/htslib/releases/download/" |
| 3221 | version "/htslib-" version ".tar.bz2")) |
| 3222 | (sha256 |
| 3223 | (base32 |
| 3224 | "1jsca3hg4rbr6iqq6imkj4lsvgl8g9768bcmny3hlff2w25vx24m")))) |
| 3225 | (build-system gnu-build-system) |
| 3226 | (arguments |
| 3227 | `(#:phases |
| 3228 | (modify-phases %standard-phases |
| 3229 | (add-after |
| 3230 | 'unpack 'patch-tests |
| 3231 | (lambda _ |
| 3232 | (substitute* "test/test.pl" |
| 3233 | (("/bin/bash") (which "bash"))) |
| 3234 | #t))))) |
| 3235 | (inputs |
| 3236 | `(("openssl" ,openssl) |
| 3237 | ("curl" ,curl) |
| 3238 | ("zlib" ,zlib))) |
| 3239 | (native-inputs |
| 3240 | `(("perl" ,perl))) |
| 3241 | (home-page "http://www.htslib.org") |
| 3242 | (synopsis "C library for reading/writing high-throughput sequencing data") |
| 3243 | (description |
| 3244 | "HTSlib is a C library for reading/writing high-throughput sequencing |
| 3245 | data. It also provides the bgzip, htsfile, and tabix utilities.") |
| 3246 | ;; Files under cram/ are released under the modified BSD license; |
| 3247 | ;; the rest is released under the Expat license |
| 3248 | (license (list license:expat license:bsd-3)))) |
| 3249 | |
| 3250 | ;; This package should be removed once no packages rely upon it. |
| 3251 | (define htslib-1.3 |
| 3252 | (package |
| 3253 | (inherit htslib) |
| 3254 | (version "1.3.1") |
| 3255 | (source (origin |
| 3256 | (method url-fetch) |
| 3257 | (uri (string-append |
| 3258 | "https://github.com/samtools/htslib/releases/download/" |
| 3259 | version "/htslib-" version ".tar.bz2")) |
| 3260 | (sha256 |
| 3261 | (base32 |
| 3262 | "1rja282fwdc25ql6izkhdyh8ppw8x2fs0w0js78zgkmqjlikmma9")))))) |
| 3263 | |
| 3264 | (define-public idr |
| 3265 | (package |
| 3266 | (name "idr") |
| 3267 | (version "2.0.3") |
| 3268 | (source (origin |
| 3269 | (method url-fetch) |
| 3270 | (uri (string-append |
| 3271 | "https://github.com/nboley/idr/archive/" |
| 3272 | version ".tar.gz")) |
| 3273 | (file-name (string-append name "-" version ".tar.gz")) |
| 3274 | (sha256 |
| 3275 | (base32 |
| 3276 | "1rjdly6daslw66r43g9md8znizlscn1sphycqyldzsidkc4vxqv3")) |
| 3277 | ;; Delete generated C code. |
| 3278 | (snippet |
| 3279 | '(begin (delete-file "idr/inv_cdf.c") #t)))) |
| 3280 | (build-system python-build-system) |
| 3281 | ;; There is only one test ("test_inv_cdf.py") and it tests features that |
| 3282 | ;; are no longer part of this package. It also asserts False, which |
| 3283 | ;; causes the tests to always fail. |
| 3284 | (arguments `(#:tests? #f)) |
| 3285 | (propagated-inputs |
| 3286 | `(("python-scipy" ,python-scipy) |
| 3287 | ("python-sympy" ,python-sympy) |
| 3288 | ("python-numpy" ,python-numpy) |
| 3289 | ("python-matplotlib" ,python-matplotlib))) |
| 3290 | (native-inputs |
| 3291 | `(("python-cython" ,python-cython))) |
| 3292 | (home-page "https://github.com/nboley/idr") |
| 3293 | (synopsis "Tool to measure the irreproducible discovery rate (IDR)") |
| 3294 | (description |
| 3295 | "The IDR (Irreproducible Discovery Rate) framework is a unified approach |
| 3296 | to measure the reproducibility of findings identified from replicate |
| 3297 | experiments and provide highly stable thresholds based on reproducibility.") |
| 3298 | (license license:gpl2+))) |
| 3299 | |
| 3300 | (define-public jellyfish |
| 3301 | (package |
| 3302 | (name "jellyfish") |
| 3303 | (version "2.2.7") |
| 3304 | (source (origin |
| 3305 | (method url-fetch) |
| 3306 | (uri (string-append "https://github.com/gmarcais/Jellyfish/" |
| 3307 | "releases/download/v" version |
| 3308 | "/jellyfish-" version ".tar.gz")) |
| 3309 | (sha256 |
| 3310 | (base32 |
| 3311 | "1a1iwq9pq54k2m9ypvwl5s0bqfl64gwh9dx5af9i382ajas2016q")))) |
| 3312 | (build-system gnu-build-system) |
| 3313 | (outputs '("out" ;for library |
| 3314 | "ruby" ;for Ruby bindings |
| 3315 | "python")) ;for Python bindings |
| 3316 | (arguments |
| 3317 | `(#:configure-flags |
| 3318 | (list (string-append "--enable-ruby-binding=" |
| 3319 | (assoc-ref %outputs "ruby")) |
| 3320 | (string-append "--enable-python-binding=" |
| 3321 | (assoc-ref %outputs "python"))) |
| 3322 | #:phases |
| 3323 | (modify-phases %standard-phases |
| 3324 | (add-before 'check 'set-SHELL-variable |
| 3325 | (lambda _ |
| 3326 | ;; generator_manager.hpp either uses /bin/sh or $SHELL |
| 3327 | ;; to run tests. |
| 3328 | (setenv "SHELL" (which "bash")) |
| 3329 | #t))))) |
| 3330 | (native-inputs |
| 3331 | `(("bc" ,bc) |
| 3332 | ("time" ,time) |
| 3333 | ("ruby" ,ruby) |
| 3334 | ("python" ,python-2) |
| 3335 | ("pkg-config" ,pkg-config))) |
| 3336 | (inputs |
| 3337 | `(("htslib" ,htslib))) |
| 3338 | (synopsis "Tool for fast counting of k-mers in DNA") |
| 3339 | (description |
| 3340 | "Jellyfish is a tool for fast, memory-efficient counting of k-mers in |
| 3341 | DNA. A k-mer is a substring of length k, and counting the occurrences of all |
| 3342 | such substrings is a central step in many analyses of DNA sequence. Jellyfish |
| 3343 | is a command-line program that reads FASTA and multi-FASTA files containing |
| 3344 | DNA sequences. It outputs its k-mer counts in a binary format, which can be |
| 3345 | translated into a human-readable text format using the @code{jellyfish dump} |
| 3346 | command, or queried for specific k-mers with @code{jellyfish query}.") |
| 3347 | (home-page "http://www.genome.umd.edu/jellyfish.html") |
| 3348 | ;; From their website: JELLYFISH runs on 64-bit Intel-compatible processors |
| 3349 | (supported-systems '("x86_64-linux")) |
| 3350 | ;; The combined work is published under the GPLv3 or later. Individual |
| 3351 | ;; files such as lib/jsoncpp.cpp are released under the Expat license. |
| 3352 | (license (list license:gpl3+ license:expat)))) |
| 3353 | |
| 3354 | (define-public khmer |
| 3355 | (package |
| 3356 | (name "khmer") |
| 3357 | (version "2.0") |
| 3358 | (source |
| 3359 | (origin |
| 3360 | (method url-fetch) |
| 3361 | (uri (pypi-uri "khmer" version)) |
| 3362 | (sha256 |
| 3363 | (base32 |
| 3364 | "0wb05shqh77v00256qlm68vbbx3kl76fyzihszbz5nhanl4ni33a")) |
| 3365 | (patches (search-patches "khmer-use-libraries.patch")))) |
| 3366 | (build-system python-build-system) |
| 3367 | (arguments |
| 3368 | `(#:phases |
| 3369 | (modify-phases %standard-phases |
| 3370 | (add-after 'unpack 'set-paths |
| 3371 | (lambda* (#:key inputs outputs #:allow-other-keys) |
| 3372 | ;; Delete bundled libraries. |
| 3373 | (delete-file-recursively "third-party/zlib") |
| 3374 | (delete-file-recursively "third-party/bzip2") |
| 3375 | ;; Replace bundled seqan. |
| 3376 | (let* ((seqan-all "third-party/seqan") |
| 3377 | (seqan-include (string-append |
| 3378 | seqan-all "/core/include"))) |
| 3379 | (delete-file-recursively seqan-all) |
| 3380 | (copy-recursively (string-append (assoc-ref inputs "seqan") |
| 3381 | "/include/seqan") |
| 3382 | (string-append seqan-include "/seqan"))) |
| 3383 | ;; We do not replace the bundled MurmurHash as the canonical |
| 3384 | ;; repository for this code 'SMHasher' is unsuitable for |
| 3385 | ;; providing a library. See |
| 3386 | ;; https://lists.gnu.org/archive/html/guix-devel/2016-06/msg00977.html |
| 3387 | #t)) |
| 3388 | (add-after 'unpack 'set-cc |
| 3389 | (lambda _ |
| 3390 | (setenv "CC" "gcc") |
| 3391 | #t)) |
| 3392 | ;; It is simpler to test after installation. |
| 3393 | (delete 'check) |
| 3394 | (add-after 'install 'post-install-check |
| 3395 | (lambda* (#:key inputs outputs #:allow-other-keys) |
| 3396 | (let ((out (assoc-ref outputs "out"))) |
| 3397 | (setenv "PATH" |
| 3398 | (string-append |
| 3399 | (getenv "PATH") |
| 3400 | ":" |
| 3401 | (assoc-ref outputs "out") |
| 3402 | "/bin")) |
| 3403 | (setenv "PYTHONPATH" |
| 3404 | (string-append |
| 3405 | (getenv "PYTHONPATH") |
| 3406 | ":" |
| 3407 | out |
| 3408 | "/lib/python" |
| 3409 | (string-take (string-take-right |
| 3410 | (assoc-ref inputs "python") 5) 3) |
| 3411 | "/site-packages")) |
| 3412 | (with-directory-excursion "build" |
| 3413 | (zero? (system* "nosetests" "khmer" "--attr" |
| 3414 | "!known_failing"))))))))) |
| 3415 | (native-inputs |
| 3416 | `(("seqan" ,seqan) |
| 3417 | ("python-nose" ,python-nose))) |
| 3418 | (inputs |
| 3419 | `(("zlib" ,zlib) |
| 3420 | ("bzip2" ,bzip2) |
| 3421 | ("python-screed" ,python-screed) |
| 3422 | ("python-bz2file" ,python-bz2file) |
| 3423 | ;; Tests fail when gcc-5 is used for compilation. Use gcc-4.9 at least |
| 3424 | ;; until the next version of khmer (likely 2.1) is released. |
| 3425 | ("gcc" ,gcc-4.9))) |
| 3426 | (home-page "https://khmer.readthedocs.org/") |
| 3427 | (synopsis "K-mer counting, filtering and graph traversal library") |
| 3428 | (description "The khmer software is a set of command-line tools for |
| 3429 | working with DNA shotgun sequencing data from genomes, transcriptomes, |
| 3430 | metagenomes and single cells. Khmer can make de novo assemblies faster, and |
| 3431 | sometimes better. Khmer can also identify and fix problems with shotgun |
| 3432 | data.") |
| 3433 | ;; When building on i686, armhf and mips64el, we get the following error: |
| 3434 | ;; error: ['khmer', 'khmer.tests', 'oxli'] require 64-bit operating system |
| 3435 | (supported-systems '("x86_64-linux")) |
| 3436 | (license license:bsd-3))) |
| 3437 | |
| 3438 | (define-public kaiju |
| 3439 | (package |
| 3440 | (name "kaiju") |
| 3441 | (version "1.5.0") |
| 3442 | (source (origin |
| 3443 | (method url-fetch) |
| 3444 | (uri (string-append |
| 3445 | "https://github.com/bioinformatics-centre/kaiju/archive/v" |
| 3446 | version ".tar.gz")) |
| 3447 | (file-name (string-append name "-" version ".tar.gz")) |
| 3448 | (sha256 |
| 3449 | (base32 |
| 3450 | "0afbfalfw9y39bkwnqjrh9bghs118ws1pzj5h8l0nblgn3mbjdks")))) |
| 3451 | (build-system gnu-build-system) |
| 3452 | (arguments |
| 3453 | `(#:tests? #f ; There are no tests. |
| 3454 | #:phases |
| 3455 | (modify-phases %standard-phases |
| 3456 | (delete 'configure) |
| 3457 | (add-before 'build 'move-to-src-dir |
| 3458 | (lambda _ (chdir "src") #t)) |
| 3459 | (replace 'install |
| 3460 | (lambda* (#:key inputs outputs #:allow-other-keys) |
| 3461 | (let ((bin (string-append (assoc-ref outputs "out") "/bin"))) |
| 3462 | (mkdir-p bin) |
| 3463 | (chdir "..") |
| 3464 | (copy-recursively "bin" bin) |
| 3465 | (copy-recursively "util" bin)) |
| 3466 | #t))))) |
| 3467 | (inputs |
| 3468 | `(("perl" ,perl))) |
| 3469 | (home-page "http://kaiju.binf.ku.dk/") |
| 3470 | (synopsis "Fast and sensitive taxonomic classification for metagenomics") |
| 3471 | (description "Kaiju is a program for sensitive taxonomic classification |
| 3472 | of high-throughput sequencing reads from metagenomic whole genome sequencing |
| 3473 | experiments.") |
| 3474 | (license license:gpl3+))) |
| 3475 | |
| 3476 | (define-public macs |
| 3477 | (package |
| 3478 | (name "macs") |
| 3479 | (version "2.1.0.20151222") |
| 3480 | (source (origin |
| 3481 | (method url-fetch) |
| 3482 | (uri (pypi-uri "MACS2" version)) |
| 3483 | (sha256 |
| 3484 | (base32 |
| 3485 | "1r2hcz6irhcq7lwbafjks98jbn34hv05avgbdjnp6w6mlfjkf8x5")))) |
| 3486 | (build-system python-build-system) |
| 3487 | (arguments |
| 3488 | `(#:python ,python-2 ; only compatible with Python 2.7 |
| 3489 | #:tests? #f)) ; no test target |
| 3490 | (inputs |
| 3491 | `(("python-numpy" ,python2-numpy))) |
| 3492 | (home-page "https://github.com/taoliu/MACS/") |
| 3493 | (synopsis "Model based analysis for ChIP-Seq data") |
| 3494 | (description |
| 3495 | "MACS is an implementation of a ChIP-Seq analysis algorithm for |
| 3496 | identifying transcript factor binding sites named Model-based Analysis of |
| 3497 | ChIP-Seq (MACS). MACS captures the influence of genome complexity to evaluate |
| 3498 | the significance of enriched ChIP regions and it improves the spatial |
| 3499 | resolution of binding sites through combining the information of both |
| 3500 | sequencing tag position and orientation.") |
| 3501 | (license license:bsd-3))) |
| 3502 | |
| 3503 | (define-public mafft |
| 3504 | (package |
| 3505 | (name "mafft") |
| 3506 | (version "7.310") |
| 3507 | (source (origin |
| 3508 | (method url-fetch) |
| 3509 | (uri (string-append |
| 3510 | "http://mafft.cbrc.jp/alignment/software/mafft-" version |
| 3511 | "-without-extensions-src.tgz")) |
| 3512 | (file-name (string-append name "-" version ".tgz")) |
| 3513 | (sha256 |
| 3514 | (base32 |
| 3515 | "0gbsaz6z2qa307kd7wfb06c3y4ikmv1hsdvlns11f6zq4w1z9pwc")))) |
| 3516 | (build-system gnu-build-system) |
| 3517 | (arguments |
| 3518 | `(#:tests? #f ; no automated tests, though there are tests in the read me |
| 3519 | #:make-flags (let ((out (assoc-ref %outputs "out"))) |
| 3520 | (list (string-append "PREFIX=" out) |
| 3521 | (string-append "BINDIR=" |
| 3522 | (string-append out "/bin")))) |
| 3523 | #:phases |
| 3524 | (modify-phases %standard-phases |
| 3525 | (add-after 'unpack 'enter-dir |
| 3526 | (lambda _ (chdir "core") #t)) |
| 3527 | (add-after 'enter-dir 'patch-makefile |
| 3528 | (lambda _ |
| 3529 | ;; on advice from the MAFFT authors, there is no need to |
| 3530 | ;; distribute mafft-profile, mafft-distance, or |
| 3531 | ;; mafft-homologs.rb as they are too "specialised". |
| 3532 | (substitute* "Makefile" |
| 3533 | ;; remove mafft-homologs.rb from SCRIPTS |
| 3534 | (("^SCRIPTS = mafft mafft-homologs.rb") |
| 3535 | "SCRIPTS = mafft") |
| 3536 | ;; remove mafft-homologs from MANPAGES |
| 3537 | (("^MANPAGES = mafft.1 mafft-homologs.1") |
| 3538 | "MANPAGES = mafft.1") |
| 3539 | ;; remove mafft-distance from PROGS |
| 3540 | (("^PROGS = dvtditr dndfast7 dndblast sextet5 mafft-distance") |
| 3541 | "PROGS = dvtditr dndfast7 dndblast sextet5") |
| 3542 | ;; remove mafft-profile from PROGS |
| 3543 | (("splittbfast disttbfast tbfast mafft-profile 2cl mccaskillwrap") |
| 3544 | "splittbfast disttbfast tbfast f2cl mccaskillwrap") |
| 3545 | (("^rm -f mafft-profile mafft-profile.exe") "#") |
| 3546 | (("^rm -f mafft-distance mafft-distance.exe") ")#") |
| 3547 | ;; do not install MAN pages in libexec folder |
| 3548 | (("^\t\\$\\(INSTALL\\) -m 644 \\$\\(MANPAGES\\) \ |
| 3549 | \\$\\(DESTDIR\\)\\$\\(LIBDIR\\)") "#")) |
| 3550 | #t)) |
| 3551 | (add-after 'enter-dir 'patch-paths |
| 3552 | (lambda* (#:key inputs #:allow-other-keys) |
| 3553 | (substitute* '("pairash.c" |
| 3554 | "mafft.tmpl") |
| 3555 | (("perl") (which "perl")) |
| 3556 | (("([\"`| ])awk" _ prefix) |
| 3557 | (string-append prefix (which "awk"))) |
| 3558 | (("grep") (which "grep"))) |
| 3559 | #t)) |
| 3560 | (delete 'configure) |
| 3561 | (add-after 'install 'wrap-programs |
| 3562 | (lambda* (#:key outputs #:allow-other-keys) |
| 3563 | (let* ((out (assoc-ref outputs "out")) |
| 3564 | (bin (string-append out "/bin")) |
| 3565 | (path (string-append |
| 3566 | (assoc-ref %build-inputs "coreutils") "/bin:"))) |
| 3567 | (for-each (lambda (file) |
| 3568 | (wrap-program file |
| 3569 | `("PATH" ":" prefix (,path)))) |
| 3570 | (find-files bin))) |
| 3571 | #t))))) |
| 3572 | (inputs |
| 3573 | `(("perl" ,perl) |
| 3574 | ("ruby" ,ruby) |
| 3575 | ("gawk" ,gawk) |
| 3576 | ("grep" ,grep) |
| 3577 | ("coreutils" ,coreutils))) |
| 3578 | (home-page "http://mafft.cbrc.jp/alignment/software/") |
| 3579 | (synopsis "Multiple sequence alignment program") |
| 3580 | (description |
| 3581 | "MAFFT offers a range of multiple alignment methods for nucleotide and |
| 3582 | protein sequences. For instance, it offers L-INS-i (accurate; for alignment |
| 3583 | of <~200 sequences) and FFT-NS-2 (fast; for alignment of <~30,000 |
| 3584 | sequences).") |
| 3585 | (license (license:non-copyleft |
| 3586 | "http://mafft.cbrc.jp/alignment/software/license.txt" |
| 3587 | "BSD-3 with different formatting")))) |
| 3588 | |
| 3589 | (define-public mash |
| 3590 | (package |
| 3591 | (name "mash") |
| 3592 | (version "1.1.1") |
| 3593 | (source (origin |
| 3594 | (method url-fetch) |
| 3595 | (uri (string-append |
| 3596 | "https://github.com/marbl/mash/archive/v" |
| 3597 | version ".tar.gz")) |
| 3598 | (file-name (string-append name "-" version ".tar.gz")) |
| 3599 | (sha256 |
| 3600 | (base32 |
| 3601 | "08znbvqq5xknfhmpp3wcj574zvi4p7i8zifi67c9qw9a6ikp42fj")) |
| 3602 | (modules '((guix build utils))) |
| 3603 | (snippet |
| 3604 | ;; Delete bundled kseq. |
| 3605 | ;; TODO: Also delete bundled murmurhash and open bloom filter. |
| 3606 | '(delete-file "src/mash/kseq.h")))) |
| 3607 | (build-system gnu-build-system) |
| 3608 | (arguments |
| 3609 | `(#:tests? #f ; No tests. |
| 3610 | #:configure-flags |
| 3611 | (list |
| 3612 | (string-append "--with-capnp=" (assoc-ref %build-inputs "capnproto")) |
| 3613 | (string-append "--with-gsl=" (assoc-ref %build-inputs "gsl"))) |
| 3614 | #:make-flags (list "CC=gcc") |
| 3615 | #:phases |
| 3616 | (modify-phases %standard-phases |
| 3617 | (add-after 'unpack 'fix-includes |
| 3618 | (lambda _ |
| 3619 | (substitute* '("src/mash/Sketch.cpp" "src/mash/CommandFind.cpp") |
| 3620 | (("^#include \"kseq\\.h\"") |
| 3621 | "#include \"htslib/kseq.h\"")) |
| 3622 | #t)) |
| 3623 | (add-after 'fix-includes 'autoconf |
| 3624 | (lambda _ (zero? (system* "autoconf"))))))) |
| 3625 | (native-inputs |
| 3626 | `(("autoconf" ,autoconf) |
| 3627 | ;; Capnproto and htslib are statically embedded in the final |
| 3628 | ;; application. Therefore we also list their licenses, below. |
| 3629 | ("capnproto" ,capnproto) |
| 3630 | ("htslib" ,htslib))) |
| 3631 | (inputs |
| 3632 | `(("gsl" ,gsl) |
| 3633 | ("zlib" ,zlib))) |
| 3634 | (supported-systems '("x86_64-linux")) |
| 3635 | (home-page "https://mash.readthedocs.io") |
| 3636 | (synopsis "Fast genome and metagenome distance estimation using MinHash") |
| 3637 | (description "Mash is a fast sequence distance estimator that uses the |
| 3638 | MinHash algorithm and is designed to work with genomes and metagenomes in the |
| 3639 | form of assemblies or reads.") |
| 3640 | (license (list license:bsd-3 ; Mash |
| 3641 | license:expat ; HTSlib and capnproto |
| 3642 | license:public-domain ; MurmurHash 3 |
| 3643 | license:cpl1.0)))) ; Open Bloom Filter |
| 3644 | |
| 3645 | (define-public metabat |
| 3646 | (package |
| 3647 | (name "metabat") |
| 3648 | (version "2.12.1") |
| 3649 | (source |
| 3650 | (origin |
| 3651 | (method url-fetch) |
| 3652 | (uri (string-append "https://bitbucket.org/berkeleylab/metabat/get/v" |
| 3653 | version ".tar.gz")) |
| 3654 | (file-name (string-append name "-" version ".tar.gz")) |
| 3655 | (sha256 |
| 3656 | (base32 |
| 3657 | "1hmvdalz3zj5sqqklg0l4npjdv37cv2hsdi1al9iby2ndxjs1b73")) |
| 3658 | (patches (search-patches "metabat-fix-compilation.patch")))) |
| 3659 | (build-system scons-build-system) |
| 3660 | (arguments |
| 3661 | `(#:scons ,scons-python2 |
| 3662 | #:scons-flags |
| 3663 | (list (string-append "PREFIX=" (assoc-ref %outputs "out")) |
| 3664 | (string-append "BOOST_ROOT=" (assoc-ref %build-inputs "boost"))) |
| 3665 | #:tests? #f ;; Tests are run during the build phase. |
| 3666 | #:phases |
| 3667 | (modify-phases %standard-phases |
| 3668 | (add-after 'unpack 'fix-includes |
| 3669 | (lambda _ |
| 3670 | (substitute* "src/BamUtils.h" |
| 3671 | (("^#include \"bam/bam\\.h\"") |
| 3672 | "#include \"samtools/bam.h\"") |
| 3673 | (("^#include \"bam/sam\\.h\"") |
| 3674 | "#include \"samtools/sam.h\"")) |
| 3675 | (substitute* "src/KseqReader.h" |
| 3676 | (("^#include \"bam/kseq\\.h\"") |
| 3677 | "#include \"htslib/kseq.h\"")) |
| 3678 | #t)) |
| 3679 | (add-after 'unpack 'fix-scons |
| 3680 | (lambda* (#:key inputs #:allow-other-keys) |
| 3681 | (substitute* "SConstruct" |
| 3682 | (("^htslib_dir += 'samtools'") |
| 3683 | (string-append "htslib_dir = '" |
| 3684 | (assoc-ref inputs "htslib") |
| 3685 | "'")) |
| 3686 | (("^samtools_dir = 'samtools'") |
| 3687 | (string-append "samtools_dir = '" |
| 3688 | (assoc-ref inputs "samtools") |
| 3689 | "'")) |
| 3690 | (("^findStaticOrShared\\('bam', hts_lib") |
| 3691 | (string-append "findStaticOrShared('bam', '" |
| 3692 | (assoc-ref inputs "samtools") |
| 3693 | "/lib'")) |
| 3694 | ;; Do not distribute README. |
| 3695 | (("^env\\.Install\\(idir_prefix, 'README\\.md'\\)") "")) |
| 3696 | #t))))) |
| 3697 | (inputs |
| 3698 | `(("zlib" ,zlib) |
| 3699 | ("perl" ,perl) |
| 3700 | ("samtools" ,samtools) |
| 3701 | ("htslib" ,htslib) |
| 3702 | ("boost" ,boost))) |
| 3703 | (home-page "https://bitbucket.org/berkeleylab/metabat") |
| 3704 | (synopsis |
| 3705 | "Reconstruction of single genomes from complex microbial communities") |
| 3706 | (description |
| 3707 | "Grouping large genomic fragments assembled from shotgun metagenomic |
| 3708 | sequences to deconvolute complex microbial communities, or metagenome binning, |
| 3709 | enables the study of individual organisms and their interactions. MetaBAT is |
| 3710 | an automated metagenome binning software, which integrates empirical |
| 3711 | probabilistic distances of genome abundance and tetranucleotide frequency.") |
| 3712 | ;; The source code contains inline assembly. |
| 3713 | (supported-systems '("x86_64-linux" "i686-linux")) |
| 3714 | (license (license:non-copyleft "file://license.txt" |
| 3715 | "See license.txt in the distribution.")))) |
| 3716 | |
| 3717 | (define-public minced |
| 3718 | (package |
| 3719 | (name "minced") |
| 3720 | (version "0.2.0") |
| 3721 | (source (origin |
| 3722 | (method url-fetch) |
| 3723 | (uri (string-append |
| 3724 | "https://github.com/ctSkennerton/minced/archive/" |
| 3725 | version ".tar.gz")) |
| 3726 | (file-name (string-append name "-" version ".tar.gz")) |
| 3727 | (sha256 |
| 3728 | (base32 |
| 3729 | "0wxmlsapxfpxfd3ps9636h7i2xy6la8i42mwh0j2lsky63h63jp1")))) |
| 3730 | (build-system gnu-build-system) |
| 3731 | (arguments |
| 3732 | `(#:test-target "test" |
| 3733 | #:phases |
| 3734 | (modify-phases %standard-phases |
| 3735 | (delete 'configure) |
| 3736 | (add-before 'check 'fix-test |
| 3737 | (lambda _ |
| 3738 | ;; Fix test for latest version. |
| 3739 | (substitute* "t/Aquifex_aeolicus_VF5.expected" |
| 3740 | (("minced:0.1.6") "minced:0.2.0")) |
| 3741 | #t)) |
| 3742 | (replace 'install ; No install target. |
| 3743 | (lambda* (#:key inputs outputs #:allow-other-keys) |
| 3744 | (let* ((out (assoc-ref outputs "out")) |
| 3745 | (bin (string-append out "/bin")) |
| 3746 | (wrapper (string-append bin "/minced"))) |
| 3747 | ;; Minced comes with a wrapper script that tries to figure out where |
| 3748 | ;; it is located before running the JAR. Since these paths are known |
| 3749 | ;; to us, we build our own wrapper to avoid coreutils dependency. |
| 3750 | (install-file "minced.jar" bin) |
| 3751 | (with-output-to-file wrapper |
| 3752 | (lambda _ |
| 3753 | (display |
| 3754 | (string-append |
| 3755 | "#!" (assoc-ref inputs "bash") "/bin/sh\n\n" |
| 3756 | (assoc-ref inputs "jre") "/bin/java -jar " |
| 3757 | bin "/minced.jar \"$@\"\n")))) |
| 3758 | (chmod wrapper #o555))))))) |
| 3759 | (native-inputs |
| 3760 | `(("jdk" ,icedtea "jdk"))) |
| 3761 | (inputs |
| 3762 | `(("bash" ,bash) |
| 3763 | ("jre" ,icedtea "out"))) |
| 3764 | (home-page "https://github.com/ctSkennerton/minced") |
| 3765 | (synopsis "Mining CRISPRs in Environmental Datasets") |
| 3766 | (description |
| 3767 | "MinCED is a program to find Clustered Regularly Interspaced Short |
| 3768 | Palindromic Repeats (CRISPRs) in DNA sequences. It can be used for |
| 3769 | unassembled metagenomic reads, but is mainly designed for full genomes and |
| 3770 | assembled metagenomic sequence.") |
| 3771 | (license license:gpl3+))) |
| 3772 | |
| 3773 | (define-public miso |
| 3774 | (package |
| 3775 | (name "miso") |
| 3776 | (version "0.5.4") |
| 3777 | (source (origin |
| 3778 | (method url-fetch) |
| 3779 | (uri (pypi-uri "misopy" version)) |
| 3780 | (sha256 |
| 3781 | (base32 |
| 3782 | "1z3x0vd8ma7pdrnywj7i3kgwl89sdkwrrn62zl7r5calqaq2hyip")) |
| 3783 | (modules '((guix build utils))) |
| 3784 | (snippet |
| 3785 | '(substitute* "setup.py" |
| 3786 | ;; Use setuptools, or else the executables are not |
| 3787 | ;; installed. |
| 3788 | (("distutils.core") "setuptools") |
| 3789 | ;; use "gcc" instead of "cc" for compilation |
| 3790 | (("^defines") |
| 3791 | "cc.set_executables( |
| 3792 | compiler='gcc', |
| 3793 | compiler_so='gcc', |
| 3794 | linker_exe='gcc', |
| 3795 | linker_so='gcc -shared'); defines"))))) |
| 3796 | (build-system python-build-system) |
| 3797 | (arguments |
| 3798 | `(#:python ,python-2 ; only Python 2 is supported |
| 3799 | #:tests? #f)) ; no "test" target |
| 3800 | (inputs |
| 3801 | `(("samtools" ,samtools) |
| 3802 | ("python-numpy" ,python2-numpy) |
| 3803 | ("python-pysam" ,python2-pysam) |
| 3804 | ("python-scipy" ,python2-scipy) |
| 3805 | ("python-matplotlib" ,python2-matplotlib))) |
| 3806 | (native-inputs |
| 3807 | `(("python-mock" ,python2-mock) ;for tests |
| 3808 | ("python-pytz" ,python2-pytz))) ;for tests |
| 3809 | (home-page "http://genes.mit.edu/burgelab/miso/index.html") |
| 3810 | (synopsis "Mixture of Isoforms model for RNA-Seq isoform quantitation") |
| 3811 | (description |
| 3812 | "MISO (Mixture-of-Isoforms) is a probabilistic framework that quantitates |
| 3813 | the expression level of alternatively spliced genes from RNA-Seq data, and |
| 3814 | identifies differentially regulated isoforms or exons across samples. By |
| 3815 | modeling the generative process by which reads are produced from isoforms in |
| 3816 | RNA-Seq, the MISO model uses Bayesian inference to compute the probability |
| 3817 | that a read originated from a particular isoform.") |
| 3818 | (license license:gpl2))) |
| 3819 | |
| 3820 | (define-public muscle |
| 3821 | (package |
| 3822 | (name "muscle") |
| 3823 | (version "3.8.1551") |
| 3824 | (source (origin |
| 3825 | (method url-fetch/tarbomb) |
| 3826 | (uri (string-append |
| 3827 | "http://www.drive5.com/muscle/muscle_src_" |
| 3828 | version ".tar.gz")) |
| 3829 | (sha256 |
| 3830 | (base32 |
| 3831 | "0bj8kj7sdizy3987zx6w7axihk40fk8rn76mpbqqjcnd64i5a367")))) |
| 3832 | (build-system gnu-build-system) |
| 3833 | (arguments |
| 3834 | `(#:make-flags (list "LDLIBS = -lm") |
| 3835 | #:phases |
| 3836 | (modify-phases %standard-phases |
| 3837 | (delete 'configure) |
| 3838 | (replace 'check |
| 3839 | ;; There are no tests, so just test if it runs. |
| 3840 | (lambda _ (zero? (system* "./muscle" "-version")))) |
| 3841 | (replace 'install |
| 3842 | (lambda* (#:key outputs #:allow-other-keys) |
| 3843 | (let* ((out (assoc-ref outputs "out")) |
| 3844 | (bin (string-append out "/bin"))) |
| 3845 | (install-file "muscle" bin))))))) |
| 3846 | (home-page "http://www.drive5.com/muscle") |
| 3847 | (synopsis "Multiple sequence alignment program") |
| 3848 | (description |
| 3849 | "MUSCLE aims to be a fast and accurate multiple sequence alignment |
| 3850 | program for nucleotide and protein sequences.") |
| 3851 | ;; License information found in 'muscle -h' and usage.cpp. |
| 3852 | (license license:public-domain))) |
| 3853 | |
| 3854 | (define-public newick-utils |
| 3855 | ;; There are no recent releases so we package from git. |
| 3856 | (let ((commit "da121155a977197cab9fbb15953ca1b40b11eb87")) |
| 3857 | (package |
| 3858 | (name "newick-utils") |
| 3859 | (version (string-append "1.6-1." (string-take commit 8))) |
| 3860 | (source (origin |
| 3861 | (method git-fetch) |
| 3862 | (uri (git-reference |
| 3863 | (url "https://github.com/tjunier/newick_utils.git") |
| 3864 | (commit commit))) |
| 3865 | (file-name (string-append name "-" version "-checkout")) |
| 3866 | (sha256 |
| 3867 | (base32 |
| 3868 | "1hkw21rq1mwf7xp0rmbb2gqc0i6p11108m69i7mr7xcjl268pxnb")))) |
| 3869 | (build-system gnu-build-system) |
| 3870 | (arguments |
| 3871 | `(#:phases |
| 3872 | (modify-phases %standard-phases |
| 3873 | (add-after 'unpack 'autoconf |
| 3874 | (lambda _ (zero? (system* "autoreconf" "-vif"))))))) |
| 3875 | (inputs |
| 3876 | ;; XXX: TODO: Enable Lua and Guile bindings. |
| 3877 | ;; https://github.com/tjunier/newick_utils/issues/13 |
| 3878 | `(("libxml2" ,libxml2) |
| 3879 | ("flex" ,flex) |
| 3880 | ("bison" ,bison))) |
| 3881 | (native-inputs |
| 3882 | `(("autoconf" ,autoconf) |
| 3883 | ("automake" ,automake) |
| 3884 | ("libtool" ,libtool))) |
| 3885 | (synopsis "Programs for working with newick format phylogenetic trees") |
| 3886 | (description |
| 3887 | "Newick-utils is a suite of utilities for processing phylogenetic trees |
| 3888 | in Newick format. Functions include re-rooting, extracting subtrees, |
| 3889 | trimming, pruning, condensing, drawing (ASCII graphics or SVG).") |
| 3890 | (home-page "https://github.com/tjunier/newick_utils") |
| 3891 | (license license:bsd-3)))) |
| 3892 | |
| 3893 | (define-public orfm |
| 3894 | (package |
| 3895 | (name "orfm") |
| 3896 | (version "0.7.1") |
| 3897 | (source (origin |
| 3898 | (method url-fetch) |
| 3899 | (uri (string-append |
| 3900 | "https://github.com/wwood/OrfM/releases/download/v" |
| 3901 | version "/orfm-" version ".tar.gz")) |
| 3902 | (sha256 |
| 3903 | (base32 |
| 3904 | "16iigyr2gd8x0imzkk1dr3k5xsds9bpmwg31ayvjg0f4pir9rwqr")))) |
| 3905 | (build-system gnu-build-system) |
| 3906 | (inputs `(("zlib" ,zlib))) |
| 3907 | (native-inputs |
| 3908 | `(("ruby-bio-commandeer" ,ruby-bio-commandeer) |
| 3909 | ("ruby-rspec" ,ruby-rspec) |
| 3910 | ("ruby" ,ruby))) |
| 3911 | (synopsis "Simple and not slow open reading frame (ORF) caller") |
| 3912 | (description |
| 3913 | "An ORF caller finds stretches of DNA that, when translated, are not |
| 3914 | interrupted by stop codons. OrfM finds and prints these ORFs.") |
| 3915 | (home-page "https://github.com/wwood/OrfM") |
| 3916 | (license license:lgpl3+))) |
| 3917 | |
| 3918 | (define-public pplacer |
| 3919 | (let ((commit "g807f6f3")) |
| 3920 | (package |
| 3921 | (name "pplacer") |
| 3922 | ;; The commit should be updated with each version change. |
| 3923 | (version "1.1.alpha19") |
| 3924 | (source |
| 3925 | (origin |
| 3926 | (method url-fetch) |
| 3927 | (uri (string-append "https://github.com/matsen/pplacer/archive/v" |
| 3928 | version ".tar.gz")) |
| 3929 | (file-name (string-append name "-" version ".tar.gz")) |
| 3930 | (sha256 |
| 3931 | (base32 "0z1lnd2s8sh6kpzg106wzbh2szw7h0hvq8syd5a6wv4rmyyz6x0f")))) |
| 3932 | (build-system ocaml-build-system) |
| 3933 | (arguments |
| 3934 | `(#:ocaml ,ocaml-4.01 |
| 3935 | #:findlib ,ocaml4.01-findlib |
| 3936 | #:modules ((guix build ocaml-build-system) |
| 3937 | (guix build utils) |
| 3938 | (ice-9 ftw)) |
| 3939 | #:phases |
| 3940 | (modify-phases %standard-phases |
| 3941 | (delete 'configure) |
| 3942 | (add-after 'unpack 'replace-bundled-cddlib |
| 3943 | (lambda* (#:key inputs #:allow-other-keys) |
| 3944 | (let* ((cddlib-src (assoc-ref inputs "cddlib-src")) |
| 3945 | (local-dir "cddlib_guix")) |
| 3946 | (mkdir local-dir) |
| 3947 | (with-directory-excursion local-dir |
| 3948 | (system* "tar" "xvf" cddlib-src)) |
| 3949 | (let ((cddlib-src-folder |
| 3950 | (string-append local-dir "/" |
| 3951 | (list-ref (scandir local-dir) 2) |
| 3952 | "/lib-src"))) |
| 3953 | (for-each |
| 3954 | (lambda (file) |
| 3955 | (copy-file file |
| 3956 | (string-append "cdd_src/" (basename file)))) |
| 3957 | (find-files cddlib-src-folder ".*[ch]$"))) |
| 3958 | #t))) |
| 3959 | (add-after 'unpack 'fix-makefile |
| 3960 | (lambda _ |
| 3961 | ;; Remove system calls to 'git'. |
| 3962 | (substitute* "Makefile" |
| 3963 | (("^DESCRIPT:=pplacer-.*") |
| 3964 | (string-append |
| 3965 | "DESCRIPT:=pplacer-$(shell uname)-v" ,version "\n"))) |
| 3966 | (substitute* "myocamlbuild.ml" |
| 3967 | (("git describe --tags --long .*\\\" with") |
| 3968 | (string-append |
| 3969 | "echo -n v" ,version "-" ,commit "\" with"))) |
| 3970 | #t)) |
| 3971 | (replace 'install |
| 3972 | (lambda* (#:key outputs #:allow-other-keys) |
| 3973 | (let* ((out (assoc-ref outputs "out")) |
| 3974 | (bin (string-append out "/bin"))) |
| 3975 | (copy-recursively "bin" bin)) |
| 3976 | #t))))) |
| 3977 | (native-inputs |
| 3978 | `(("zlib" ,zlib) |
| 3979 | ("gsl" ,gsl) |
| 3980 | ("ocaml-ounit" ,ocaml4.01-ounit) |
| 3981 | ("ocaml-batteries" ,ocaml4.01-batteries) |
| 3982 | ("ocaml-camlzip" ,ocaml4.01-camlzip) |
| 3983 | ("ocaml-csv" ,ocaml4.01-csv) |
| 3984 | ("ocaml-sqlite3" ,ocaml4.01-sqlite3) |
| 3985 | ("ocaml-xmlm" ,ocaml4.01-xmlm) |
| 3986 | ("ocaml-mcl" ,ocaml4.01-mcl) |
| 3987 | ("ocaml-gsl" ,ocaml4.01-gsl) |
| 3988 | ("cddlib-src" ,(package-source cddlib)))) |
| 3989 | (propagated-inputs |
| 3990 | `(("pplacer-scripts" ,pplacer-scripts))) |
| 3991 | (synopsis "Phylogenetic placement of biological sequences") |
| 3992 | (description |
| 3993 | "Pplacer places query sequences on a fixed reference phylogenetic tree |
| 3994 | to maximize phylogenetic likelihood or posterior probability according to a |
| 3995 | reference alignment. Pplacer is designed to be fast, to give useful |
| 3996 | information about uncertainty, and to offer advanced visualization and |
| 3997 | downstream analysis.") |
| 3998 | (home-page "http://matsen.fhcrc.org/pplacer") |
| 3999 | (license license:gpl3)))) |
| 4000 | |
| 4001 | ;; This package is installed alongside 'pplacer'. It is a separate package so |
| 4002 | ;; that it can use the python-build-system for the scripts that are |
| 4003 | ;; distributed alongside the main OCaml binaries. |
| 4004 | (define pplacer-scripts |
| 4005 | (package |
| 4006 | (inherit pplacer) |
| 4007 | (name "pplacer-scripts") |
| 4008 | (build-system python-build-system) |
| 4009 | (arguments |
| 4010 | `(#:python ,python-2 |
| 4011 | #:phases |
| 4012 | (modify-phases %standard-phases |
| 4013 | (add-after 'unpack 'enter-scripts-dir |
| 4014 | (lambda _ (chdir "scripts"))) |
| 4015 | (replace 'check |
| 4016 | (lambda _ |
| 4017 | (zero? (system* "python" "-m" "unittest" "discover" "-v")))) |
| 4018 | (add-after 'install 'wrap-executables |
| 4019 | (lambda* (#:key inputs outputs #:allow-other-keys) |
| 4020 | (let* ((out (assoc-ref outputs "out")) |
| 4021 | (bin (string-append out "/bin"))) |
| 4022 | (let ((path (string-append |
| 4023 | (assoc-ref inputs "hmmer") "/bin:" |
| 4024 | (assoc-ref inputs "infernal") "/bin"))) |
| 4025 | (display path) |
| 4026 | (wrap-program (string-append bin "/refpkg_align.py") |
| 4027 | `("PATH" ":" prefix (,path)))) |
| 4028 | (let ((path (string-append |
| 4029 | (assoc-ref inputs "hmmer") "/bin"))) |
| 4030 | (wrap-program (string-append bin "/hrefpkg_query.py") |
| 4031 | `("PATH" ":" prefix (,path))))) |
| 4032 | #t))))) |
| 4033 | (inputs |
| 4034 | `(("infernal" ,infernal) |
| 4035 | ("hmmer" ,hmmer))) |
| 4036 | (propagated-inputs |
| 4037 | `(("python-biopython" ,python2-biopython) |
| 4038 | ("taxtastic" ,taxtastic))) |
| 4039 | (synopsis "Pplacer Python scripts"))) |
| 4040 | |
| 4041 | (define-public python2-pbcore |
| 4042 | (package |
| 4043 | (name "python2-pbcore") |
| 4044 | (version "1.2.10") |
| 4045 | (source (origin |
| 4046 | (method url-fetch) |
| 4047 | (uri (pypi-uri "pbcore" version)) |
| 4048 | (sha256 |
| 4049 | (base32 |
| 4050 | "1kjmv891d6qbpp4shhhvkl02ff4q5xlpnls2513sm2cjcrs52f1i")))) |
| 4051 | (build-system python-build-system) |
| 4052 | (arguments `(#:python ,python-2)) ; pbcore requires Python 2.7 |
| 4053 | (propagated-inputs |
| 4054 | `(("python-cython" ,python2-cython) |
| 4055 | ("python-numpy" ,python2-numpy) |
| 4056 | ("python-pysam" ,python2-pysam) |
| 4057 | ("python-h5py" ,python2-h5py))) |
| 4058 | (native-inputs |
| 4059 | `(("python-nose" ,python2-nose) |
| 4060 | ("python-sphinx" ,python2-sphinx) |
| 4061 | ("python-pyxb" ,python2-pyxb))) |
| 4062 | (home-page "http://pacificbiosciences.github.io/pbcore/") |
| 4063 | (synopsis "Library for reading and writing PacBio data files") |
| 4064 | (description |
| 4065 | "The pbcore package provides Python APIs for interacting with PacBio data |
| 4066 | files and writing bioinformatics applications.") |
| 4067 | (license license:bsd-3))) |
| 4068 | |
| 4069 | (define-public python2-warpedlmm |
| 4070 | (package |
| 4071 | (name "python2-warpedlmm") |
| 4072 | (version "0.21") |
| 4073 | (source |
| 4074 | (origin |
| 4075 | (method url-fetch) |
| 4076 | (uri (string-append |
| 4077 | "https://pypi.python.org/packages/source/W/WarpedLMM/WarpedLMM-" |
| 4078 | version ".zip")) |
| 4079 | (sha256 |
| 4080 | (base32 |
| 4081 | "1agfz6zqa8nc6cw47yh0s3y14gkpa9wqazwcj7mwwj3ffnw39p3j")))) |
| 4082 | (build-system python-build-system) |
| 4083 | (arguments |
| 4084 | `(#:python ,python-2)) ; requires Python 2.7 |
| 4085 | (propagated-inputs |
| 4086 | `(("python-scipy" ,python2-scipy) |
| 4087 | ("python-numpy" ,python2-numpy) |
| 4088 | ("python-matplotlib" ,python2-matplotlib) |
| 4089 | ("python-fastlmm" ,python2-fastlmm) |
| 4090 | ("python-pandas" ,python2-pandas) |
| 4091 | ("python-pysnptools" ,python2-pysnptools))) |
| 4092 | (native-inputs |
| 4093 | `(("python-mock" ,python2-mock) |
| 4094 | ("python-nose" ,python2-nose) |
| 4095 | ("unzip" ,unzip))) |
| 4096 | (home-page "https://github.com/PMBio/warpedLMM") |
| 4097 | (synopsis "Implementation of warped linear mixed models") |
| 4098 | (description |
| 4099 | "WarpedLMM is a Python implementation of the warped linear mixed model, |
| 4100 | which automatically learns an optimal warping function (or transformation) for |
| 4101 | the phenotype as it models the data.") |
| 4102 | (license license:asl2.0))) |
| 4103 | |
| 4104 | (define-public pbtranscript-tofu |
| 4105 | (let ((commit "8f5467fe6a4472bcfb4226c8720993c8507adfe4")) |
| 4106 | (package |
| 4107 | (name "pbtranscript-tofu") |
| 4108 | (version (string-append "2.2.3." (string-take commit 7))) |
| 4109 | (source (origin |
| 4110 | (method git-fetch) |
| 4111 | (uri (git-reference |
| 4112 | (url "https://github.com/PacificBiosciences/cDNA_primer.git") |
| 4113 | (commit commit))) |
| 4114 | (file-name (string-append name "-" version "-checkout")) |
| 4115 | (sha256 |
| 4116 | (base32 |
| 4117 | "1lgnpi35ihay42qx0b6yl3kkgra723i413j33kvs0kvs61h82w0f")) |
| 4118 | (modules '((guix build utils))) |
| 4119 | (snippet |
| 4120 | '(begin |
| 4121 | ;; remove bundled Cython sources |
| 4122 | (delete-file "pbtranscript-tofu/pbtranscript/Cython-0.20.1.tar.gz") |
| 4123 | #t)))) |
| 4124 | (build-system python-build-system) |
| 4125 | (arguments |
| 4126 | `(#:python ,python-2 |
| 4127 | ;; FIXME: Tests fail with "No such file or directory: |
| 4128 | ;; pbtools/pbtranscript/modified_bx_intervals/intersection_unique.so" |
| 4129 | #:tests? #f |
| 4130 | #:phases |
| 4131 | (modify-phases %standard-phases |
| 4132 | (add-after 'unpack 'enter-directory |
| 4133 | (lambda _ |
| 4134 | (chdir "pbtranscript-tofu/pbtranscript/") |
| 4135 | #t)) |
| 4136 | ;; With setuptools version 18.0 and later this setup.py hack causes |
| 4137 | ;; a build error, so we disable it. |
| 4138 | (add-after 'enter-directory 'patch-setuppy |
| 4139 | (lambda _ |
| 4140 | (substitute* "setup.py" |
| 4141 | (("if 'setuptools.extension' in sys.modules:") |
| 4142 | "if False:")) |
| 4143 | #t))))) |
| 4144 | (inputs |
| 4145 | `(("python-numpy" ,python2-numpy) |
| 4146 | ("python-bx-python" ,python2-bx-python) |
| 4147 | ("python-networkx" ,python2-networkx) |
| 4148 | ("python-scipy" ,python2-scipy) |
| 4149 | ("python-pbcore" ,python2-pbcore) |
| 4150 | ("python-h5py" ,python2-h5py))) |
| 4151 | (native-inputs |
| 4152 | `(("python-cython" ,python2-cython) |
| 4153 | ("python-nose" ,python2-nose))) |
| 4154 | (home-page "https://github.com/PacificBiosciences/cDNA_primer") |
| 4155 | (synopsis "Analyze transcriptome data generated with the Iso-Seq protocol") |
| 4156 | (description |
| 4157 | "pbtranscript-tofu contains scripts to analyze transcriptome data |
| 4158 | generated using the PacBio Iso-Seq protocol.") |
| 4159 | (license license:bsd-3)))) |
| 4160 | |
| 4161 | (define-public prank |
| 4162 | (package |
| 4163 | (name "prank") |
| 4164 | (version "150803") |
| 4165 | (source (origin |
| 4166 | (method url-fetch) |
| 4167 | (uri (string-append |
| 4168 | "http://wasabiapp.org/download/prank/prank.source." |
| 4169 | version ".tgz")) |
| 4170 | (sha256 |
| 4171 | (base32 |
| 4172 | "0am4z94fs3w2n5xpfls9zda61vq7qqz4q2i7b9hlsxz5q4j3kfm4")))) |
| 4173 | (build-system gnu-build-system) |
| 4174 | (arguments |
| 4175 | `(#:phases |
| 4176 | (modify-phases %standard-phases |
| 4177 | (add-after 'unpack 'enter-src-dir |
| 4178 | (lambda _ |
| 4179 | (chdir "src") |
| 4180 | #t)) |
| 4181 | (add-after 'unpack 'remove-m64-flag |
| 4182 | ;; Prank will build with the correct 'bit-ness' without this flag |
| 4183 | ;; and this allows building on 32-bit machines. |
| 4184 | (lambda _ (substitute* "src/Makefile" |
| 4185 | (("-m64") "")) |
| 4186 | #t)) |
| 4187 | (delete 'configure) |
| 4188 | (replace 'install |
| 4189 | (lambda* (#:key outputs #:allow-other-keys) |
| 4190 | (let* ((out (assoc-ref outputs "out")) |
| 4191 | (bin (string-append out "/bin")) |
| 4192 | (man (string-append out "/share/man/man1")) |
| 4193 | (path (string-append |
| 4194 | (assoc-ref %build-inputs "mafft") "/bin:" |
| 4195 | (assoc-ref %build-inputs "exonerate") "/bin:" |
| 4196 | (assoc-ref %build-inputs "bppsuite") "/bin"))) |
| 4197 | (install-file "prank" bin) |
| 4198 | (wrap-program (string-append bin "/prank") |
| 4199 | `("PATH" ":" prefix (,path))) |
| 4200 | (install-file "prank.1" man)) |
| 4201 | #t))))) |
| 4202 | (inputs |
| 4203 | `(("mafft" ,mafft) |
| 4204 | ("exonerate" ,exonerate) |
| 4205 | ("bppsuite" ,bppsuite))) |
| 4206 | (home-page "http://wasabiapp.org/software/prank/") |
| 4207 | (synopsis "Probabilistic multiple sequence alignment program") |
| 4208 | (description |
| 4209 | "PRANK is a probabilistic multiple sequence alignment program for DNA, |
| 4210 | codon and amino-acid sequences. It is based on a novel algorithm that treats |
| 4211 | insertions correctly and avoids over-estimation of the number of deletion |
| 4212 | events. In addition, PRANK borrows ideas from maximum likelihood methods used |
| 4213 | in phylogenetics and correctly takes into account the evolutionary distances |
| 4214 | between sequences. Lastly, PRANK allows for defining a potential structure |
| 4215 | for sequences to be aligned and then, simultaneously with the alignment, |
| 4216 | predicts the locations of structural units in the sequences.") |
| 4217 | (license license:gpl2+))) |
| 4218 | |
| 4219 | (define-public proteinortho |
| 4220 | (package |
| 4221 | (name "proteinortho") |
| 4222 | (version "5.16b") |
| 4223 | (source |
| 4224 | (origin |
| 4225 | (method url-fetch) |
| 4226 | (uri |
| 4227 | (string-append |
| 4228 | "http://www.bioinf.uni-leipzig.de/Software/proteinortho/proteinortho_v" |
| 4229 | version "_src.tar.gz")) |
| 4230 | (sha256 |
| 4231 | (base32 |
| 4232 | "1wl0dawpssqwfjvr651r4wlww8hhjin8nba6xh71ks7sbypx886j")))) |
| 4233 | (build-system gnu-build-system) |
| 4234 | (arguments |
| 4235 | `(#:test-target "test" |
| 4236 | #:phases |
| 4237 | (modify-phases %standard-phases |
| 4238 | (replace 'configure |
| 4239 | ;; There is no configure script, so we modify the Makefile directly. |
| 4240 | (lambda* (#:key outputs #:allow-other-keys) |
| 4241 | (substitute* "Makefile" |
| 4242 | (("INSTALLDIR=.*") |
| 4243 | (string-append |
| 4244 | "INSTALLDIR=" (assoc-ref outputs "out") "/bin\n"))) |
| 4245 | #t)) |
| 4246 | (add-before 'install 'make-install-directory |
| 4247 | ;; The install directory is not created during 'make install'. |
| 4248 | (lambda* (#:key outputs #:allow-other-keys) |
| 4249 | (mkdir-p (string-append (assoc-ref outputs "out") "/bin")) |
| 4250 | #t)) |
| 4251 | (add-after 'install 'wrap-programs |
| 4252 | (lambda* (#:key inputs outputs #:allow-other-keys) |
| 4253 | (let* ((path (getenv "PATH")) |
| 4254 | (out (assoc-ref outputs "out")) |
| 4255 | (binary (string-append out "/bin/proteinortho5.pl"))) |
| 4256 | (wrap-program binary `("PATH" ":" prefix (,path)))) |
| 4257 | #t))))) |
| 4258 | (inputs |
| 4259 | `(("perl" ,perl) |
| 4260 | ("python" ,python-2) |
| 4261 | ("blast+" ,blast+))) |
| 4262 | (home-page "http://www.bioinf.uni-leipzig.de/Software/proteinortho") |
| 4263 | (synopsis "Detect orthologous genes across species") |
| 4264 | (description |
| 4265 | "Proteinortho is a tool to detect orthologous genes across different |
| 4266 | species. For doing so, it compares similarities of given gene sequences and |
| 4267 | clusters them to find significant groups. The algorithm was designed to handle |
| 4268 | large-scale data and can be applied to hundreds of species at once.") |
| 4269 | (license license:gpl2+))) |
| 4270 | |
| 4271 | (define-public pyicoteo |
| 4272 | (package |
| 4273 | (name "pyicoteo") |
| 4274 | (version "2.0.7") |
| 4275 | (source |
| 4276 | (origin |
| 4277 | (method url-fetch) |
| 4278 | (uri (string-append "https://bitbucket.org/regulatorygenomicsupf/" |
| 4279 | "pyicoteo/get/v" version ".tar.bz2")) |
| 4280 | (file-name (string-append name "-" version ".tar.bz2")) |
| 4281 | (sha256 |
| 4282 | (base32 |
| 4283 | "0d6087f29xp8wxwlj111c3sylli98n0l8ry58c51ixzq0zfm50wa")))) |
| 4284 | (build-system python-build-system) |
| 4285 | (arguments |
| 4286 | `(#:python ,python-2 ; does not work with Python 3 |
| 4287 | #:tests? #f)) ; there are no tests |
| 4288 | (inputs |
| 4289 | `(("python2-matplotlib" ,python2-matplotlib))) |
| 4290 | (home-page "https://bitbucket.org/regulatorygenomicsupf/pyicoteo") |
| 4291 | (synopsis "Analyze high-throughput genetic sequencing data") |
| 4292 | (description |
| 4293 | "Pyicoteo is a suite of tools for the analysis of high-throughput genetic |
| 4294 | sequencing data. It works with genomic coordinates. There are currently six |
| 4295 | different command-line tools: |
| 4296 | |
| 4297 | @enumerate |
| 4298 | @item pyicoregion: for generating exploratory regions automatically; |
| 4299 | @item pyicoenrich: for differential enrichment between two conditions; |
| 4300 | @item pyicoclip: for calling CLIP-Seq peaks without a control; |
| 4301 | @item pyicos: for genomic coordinates manipulation; |
| 4302 | @item pyicoller: for peak calling on punctuated ChIP-Seq; |
| 4303 | @item pyicount: to count how many reads from N experiment files overlap in a |
| 4304 | region file; |
| 4305 | @item pyicotrocol: to combine operations from pyicoteo. |
| 4306 | @end enumerate\n") |
| 4307 | (license license:gpl3+))) |
| 4308 | |
| 4309 | (define-public prodigal |
| 4310 | (package |
| 4311 | (name "prodigal") |
| 4312 | (version "2.6.3") |
| 4313 | (source (origin |
| 4314 | (method url-fetch) |
| 4315 | (uri (string-append |
| 4316 | "https://github.com/hyattpd/Prodigal/archive/v" |
| 4317 | version ".tar.gz")) |
| 4318 | (file-name (string-append name "-" version ".tar.gz")) |
| 4319 | (sha256 |
| 4320 | (base32 |
| 4321 | "17srxkqd3jc77xk15pfbgg1a9xahqg7337w95mrsia7mpza4l2c9")))) |
| 4322 | (build-system gnu-build-system) |
| 4323 | (arguments |
| 4324 | `(#:tests? #f ;no check target |
| 4325 | #:make-flags (list (string-append "INSTALLDIR=" |
| 4326 | (assoc-ref %outputs "out") |
| 4327 | "/bin")) |
| 4328 | #:phases |
| 4329 | (modify-phases %standard-phases |
| 4330 | (delete 'configure)))) |
| 4331 | (home-page "http://prodigal.ornl.gov") |
| 4332 | (synopsis "Protein-coding gene prediction for Archaea and Bacteria") |
| 4333 | (description |
| 4334 | "Prodigal runs smoothly on finished genomes, draft genomes, and |
| 4335 | metagenomes, providing gene predictions in GFF3, Genbank, or Sequin table |
| 4336 | format. It runs quickly, in an unsupervised fashion, handles gaps, handles |
| 4337 | partial genes, and identifies translation initiation sites.") |
| 4338 | (license license:gpl3+))) |
| 4339 | |
| 4340 | (define-public roary |
| 4341 | (package |
| 4342 | (name "roary") |
| 4343 | (version "3.11.0") |
| 4344 | (source |
| 4345 | (origin |
| 4346 | (method url-fetch) |
| 4347 | (uri (string-append |
| 4348 | "mirror://cpan/authors/id/A/AJ/AJPAGE/Bio-Roary-" |
| 4349 | version ".tar.gz")) |
| 4350 | (sha256 |
| 4351 | (base32 |
| 4352 | "10lw78x1xzvn7xzvnmh4bm3cak3ah5cssapl0yidvhaj1f44h29i")))) |
| 4353 | (build-system perl-build-system) |
| 4354 | (arguments |
| 4355 | `(#:phases |
| 4356 | (modify-phases %standard-phases |
| 4357 | (delete 'configure) |
| 4358 | (delete 'build) |
| 4359 | (replace 'check |
| 4360 | (lambda _ |
| 4361 | ;; The tests are not run by default, so we run each test file |
| 4362 | ;; directly. |
| 4363 | (setenv "PATH" (string-append (getcwd) "/bin" ":" |
| 4364 | (getenv "PATH"))) |
| 4365 | (setenv "PERL5LIB" (string-append (getcwd) "/lib" ":" |
| 4366 | (getenv "PERL5LIB"))) |
| 4367 | (zero? (length (filter (lambda (file) |
| 4368 | (display file)(display "\n") |
| 4369 | (not (zero? (system* "perl" file)))) |
| 4370 | (find-files "t" ".*\\.t$")))))) |
| 4371 | (replace 'install |
| 4372 | ;; There is no 'install' target in the Makefile. |
| 4373 | (lambda* (#:key outputs #:allow-other-keys) |
| 4374 | (let* ((out (assoc-ref outputs "out")) |
| 4375 | (bin (string-append out "/bin")) |
| 4376 | (perl (string-append out "/lib/perl5/site_perl")) |
| 4377 | (roary-plots "contrib/roary_plots")) |
| 4378 | (mkdir-p bin) |
| 4379 | (mkdir-p perl) |
| 4380 | (copy-recursively "bin" bin) |
| 4381 | (copy-recursively "lib" perl) |
| 4382 | #t))) |
| 4383 | (add-after 'install 'wrap-programs |
| 4384 | (lambda* (#:key inputs outputs #:allow-other-keys) |
| 4385 | (let* ((out (assoc-ref outputs "out")) |
| 4386 | (perl5lib (getenv "PERL5LIB")) |
| 4387 | (path (getenv "PATH"))) |
| 4388 | (for-each (lambda (prog) |
| 4389 | (let ((binary (string-append out "/" prog))) |
| 4390 | (wrap-program binary |
| 4391 | `("PERL5LIB" ":" prefix |
| 4392 | (,(string-append perl5lib ":" out |
| 4393 | "/lib/perl5/site_perl")))) |
| 4394 | (wrap-program binary |
| 4395 | `("PATH" ":" prefix |
| 4396 | (,(string-append path ":" out "/bin")))))) |
| 4397 | (find-files "bin" ".*[^R]$")) |
| 4398 | (let ((file |
| 4399 | (string-append out "/bin/roary-create_pan_genome_plots.R")) |
| 4400 | (r-site-lib (getenv "R_LIBS_SITE")) |
| 4401 | (coreutils-path |
| 4402 | (string-append (assoc-ref inputs "coreutils") "/bin"))) |
| 4403 | (wrap-program file |
| 4404 | `("R_LIBS_SITE" ":" prefix |
| 4405 | (,(string-append r-site-lib ":" out "/site-library/")))) |
| 4406 | (wrap-program file |
| 4407 | `("PATH" ":" prefix |
| 4408 | (,(string-append coreutils-path ":" out "/bin")))))) |
| 4409 | #t))))) |
| 4410 | (native-inputs |
| 4411 | `(("perl-env-path" ,perl-env-path) |
| 4412 | ("perl-test-files" ,perl-test-files) |
| 4413 | ("perl-test-most" ,perl-test-most) |
| 4414 | ("perl-test-output" ,perl-test-output))) |
| 4415 | (inputs |
| 4416 | `(("perl-array-utils" ,perl-array-utils) |
| 4417 | ("bioperl" ,bioperl-minimal) |
| 4418 | ("perl-digest-md5-file" ,perl-digest-md5-file) |
| 4419 | ("perl-exception-class" ,perl-exception-class) |
| 4420 | ("perl-file-find-rule" ,perl-file-find-rule) |
| 4421 | ("perl-file-grep" ,perl-file-grep) |
| 4422 | ("perl-file-slurper" ,perl-file-slurper) |
| 4423 | ("perl-file-which" ,perl-file-which) |
| 4424 | ("perl-graph" ,perl-graph) |
| 4425 | ("perl-graph-readwrite" ,perl-graph-readwrite) |
| 4426 | ("perl-log-log4perl" ,perl-log-log4perl) |
| 4427 | ("perl-moose" ,perl-moose) |
| 4428 | ("perl-perlio-utf8_strict" ,perl-perlio-utf8_strict) |
| 4429 | ("perl-text-csv" ,perl-text-csv) |
| 4430 | ("bedtools" ,bedtools) |
| 4431 | ("cd-hit" ,cd-hit) |
| 4432 | ("blast+" ,blast+) |
| 4433 | ("mcl" ,mcl) |
| 4434 | ("parallel" ,parallel) |
| 4435 | ("prank" ,prank) |
| 4436 | ("mafft" ,mafft) |
| 4437 | ("fasttree" ,fasttree) |
| 4438 | ("grep" ,grep) |
| 4439 | ("sed" ,sed) |
| 4440 | ("gawk" ,gawk) |
| 4441 | ("r-minimal" ,r-minimal) |
| 4442 | ("r-ggplot2" ,r-ggplot2) |
| 4443 | ("coreutils" ,coreutils))) |
| 4444 | (home-page "http://sanger-pathogens.github.io/Roary") |
| 4445 | (synopsis "High speed stand-alone pan genome pipeline") |
| 4446 | (description |
| 4447 | "Roary is a high speed stand alone pan genome pipeline, which takes |
| 4448 | annotated assemblies in GFF3 format (produced by the Prokka program) and |
| 4449 | calculates the pan genome. Using a standard desktop PC, it can analyse |
| 4450 | datasets with thousands of samples, without compromising the quality of the |
| 4451 | results. 128 samples can be analysed in under 1 hour using 1 GB of RAM and a |
| 4452 | single processor. Roary is not intended for metagenomics or for comparing |
| 4453 | extremely diverse sets of genomes.") |
| 4454 | (license license:gpl3))) |
| 4455 | |
| 4456 | (define-public raxml |
| 4457 | (package |
| 4458 | (name "raxml") |
| 4459 | (version "8.2.10") |
| 4460 | (source |
| 4461 | (origin |
| 4462 | (method url-fetch) |
| 4463 | (uri |
| 4464 | (string-append |
| 4465 | "https://github.com/stamatak/standard-RAxML/archive/v" |
| 4466 | version ".tar.gz")) |
| 4467 | (file-name (string-append name "-" version ".tar.gz")) |
| 4468 | (sha256 |
| 4469 | (base32 |
| 4470 | "13s7aspfdcfr6asynwdg1x6vznys6pzap5f8wsffbnnwpkkg9ya8")))) |
| 4471 | (build-system gnu-build-system) |
| 4472 | (arguments |
| 4473 | `(#:tests? #f ; There are no tests. |
| 4474 | ;; Use 'standard' Makefile rather than SSE or AVX ones. |
| 4475 | #:make-flags (list "-f" "Makefile.HYBRID.gcc") |
| 4476 | #:phases |
| 4477 | (modify-phases %standard-phases |
| 4478 | (delete 'configure) |
| 4479 | (replace 'install |
| 4480 | (lambda* (#:key outputs #:allow-other-keys) |
| 4481 | (let* ((out (assoc-ref outputs "out")) |
| 4482 | (bin (string-append out "/bin")) |
| 4483 | (executable "raxmlHPC-HYBRID")) |
| 4484 | (install-file executable bin) |
| 4485 | (symlink (string-append bin "/" executable) "raxml")) |
| 4486 | #t))))) |
| 4487 | (inputs |
| 4488 | `(("openmpi" ,openmpi))) |
| 4489 | (home-page "http://sco.h-its.org/exelixis/web/software/raxml/index.html") |
| 4490 | (synopsis "Randomized Axelerated Maximum Likelihood phylogenetic trees") |
| 4491 | (description |
| 4492 | "RAxML is a tool for phylogenetic analysis and post-analysis of large |
| 4493 | phylogenies.") |
| 4494 | ;; The source includes x86 specific code |
| 4495 | (supported-systems '("x86_64-linux" "i686-linux")) |
| 4496 | (license license:gpl2+))) |
| 4497 | |
| 4498 | (define-public rsem |
| 4499 | (package |
| 4500 | (name "rsem") |
| 4501 | (version "1.2.20") |
| 4502 | (source |
| 4503 | (origin |
| 4504 | (method url-fetch) |
| 4505 | (uri |
| 4506 | (string-append "http://deweylab.biostat.wisc.edu/rsem/src/rsem-" |
| 4507 | version ".tar.gz")) |
| 4508 | (sha256 |
| 4509 | (base32 "0nzdc0j0hjllhsd5f2xli95dafm3nawskigs140xzvjk67xh0r9q")) |
| 4510 | (patches (search-patches "rsem-makefile.patch")) |
| 4511 | (modules '((guix build utils))) |
| 4512 | (snippet |
| 4513 | '(begin |
| 4514 | ;; remove bundled copy of boost |
| 4515 | (delete-file-recursively "boost") |
| 4516 | #t)))) |
| 4517 | (build-system gnu-build-system) |
| 4518 | (arguments |
| 4519 | `(#:tests? #f ;no "check" target |
| 4520 | #:phases |
| 4521 | (modify-phases %standard-phases |
| 4522 | ;; No "configure" script. |
| 4523 | ;; Do not build bundled samtools library. |
| 4524 | (replace 'configure |
| 4525 | (lambda _ |
| 4526 | (substitute* "Makefile" |
| 4527 | (("^all : sam/libbam.a") "all : ")) |
| 4528 | #t)) |
| 4529 | (replace 'install |
| 4530 | (lambda* (#:key outputs #:allow-other-keys) |
| 4531 | (let* ((out (string-append (assoc-ref outputs "out"))) |
| 4532 | (bin (string-append out "/bin/")) |
| 4533 | (perl (string-append out "/lib/perl5/site_perl"))) |
| 4534 | (mkdir-p bin) |
| 4535 | (mkdir-p perl) |
| 4536 | (for-each (lambda (file) |
| 4537 | (install-file file bin)) |
| 4538 | (find-files "." "rsem-.*")) |
| 4539 | (install-file "rsem_perl_utils.pm" perl)) |
| 4540 | #t)) |
| 4541 | (add-after |
| 4542 | 'install 'wrap-program |
| 4543 | (lambda* (#:key outputs #:allow-other-keys) |
| 4544 | (let ((out (assoc-ref outputs "out"))) |
| 4545 | (for-each (lambda (prog) |
| 4546 | (wrap-program (string-append out "/bin/" prog) |
| 4547 | `("PERL5LIB" ":" prefix |
| 4548 | (,(string-append out "/lib/perl5/site_perl"))))) |
| 4549 | '("rsem-plot-transcript-wiggles" |
| 4550 | "rsem-calculate-expression" |
| 4551 | "rsem-generate-ngvector" |
| 4552 | "rsem-run-ebseq" |
| 4553 | "rsem-prepare-reference"))) |
| 4554 | #t))))) |
| 4555 | (inputs |
| 4556 | `(("boost" ,boost) |
| 4557 | ("ncurses" ,ncurses) |
| 4558 | ("r-minimal" ,r-minimal) |
| 4559 | ("perl" ,perl) |
| 4560 | ("samtools" ,samtools-0.1) |
| 4561 | ("zlib" ,zlib))) |
| 4562 | (home-page "http://deweylab.biostat.wisc.edu/rsem/") |
| 4563 | (synopsis "Estimate gene expression levels from RNA-Seq data") |
| 4564 | (description |
| 4565 | "RSEM is a software package for estimating gene and isoform expression |
| 4566 | levels from RNA-Seq data. The RSEM package provides a user-friendly |
| 4567 | interface, supports threads for parallel computation of the EM algorithm, |
| 4568 | single-end and paired-end read data, quality scores, variable-length reads and |
| 4569 | RSPD estimation. In addition, it provides posterior mean and 95% credibility |
| 4570 | interval estimates for expression levels. For visualization, it can generate |
| 4571 | BAM and Wiggle files in both transcript-coordinate and genomic-coordinate.") |
| 4572 | (license license:gpl3+))) |
| 4573 | |
| 4574 | (define-public rseqc |
| 4575 | (package |
| 4576 | (name "rseqc") |
| 4577 | (version "2.6.1") |
| 4578 | (source |
| 4579 | (origin |
| 4580 | (method url-fetch) |
| 4581 | (uri |
| 4582 | (string-append "mirror://sourceforge/rseqc/" |
| 4583 | "RSeQC-" version ".tar.gz")) |
| 4584 | (sha256 |
| 4585 | (base32 "15ly0254yi032qzkdplg00q144qfdsd986gh62829rl5bkxhj330")) |
| 4586 | (modules '((guix build utils))) |
| 4587 | (snippet |
| 4588 | '(begin |
| 4589 | ;; remove bundled copy of pysam |
| 4590 | (delete-file-recursively "lib/pysam") |
| 4591 | (substitute* "setup.py" |
| 4592 | ;; remove dependency on outdated "distribute" module |
| 4593 | (("^from distribute_setup import use_setuptools") "") |
| 4594 | (("^use_setuptools\\(\\)") "") |
| 4595 | ;; do not use bundled copy of pysam |
| 4596 | (("^have_pysam = False") "have_pysam = True")))))) |
| 4597 | (build-system python-build-system) |
| 4598 | (arguments `(#:python ,python-2)) |
| 4599 | (inputs |
| 4600 | `(("python-cython" ,python2-cython) |
| 4601 | ("python-pysam" ,python2-pysam) |
| 4602 | ("python-numpy" ,python2-numpy) |
| 4603 | ("zlib" ,zlib))) |
| 4604 | (native-inputs |
| 4605 | `(("python-nose" ,python2-nose))) |
| 4606 | (home-page "http://rseqc.sourceforge.net/") |
| 4607 | (synopsis "RNA-seq quality control package") |
| 4608 | (description |
| 4609 | "RSeQC provides a number of modules that can comprehensively evaluate |
| 4610 | high throughput sequence data, especially RNA-seq data. Some basic modules |
| 4611 | inspect sequence quality, nucleotide composition bias, PCR bias and GC bias, |
| 4612 | while RNA-seq specific modules evaluate sequencing saturation, mapped reads |
| 4613 | distribution, coverage uniformity, strand specificity, etc.") |
| 4614 | (license license:gpl3+))) |
| 4615 | |
| 4616 | (define-public seek |
| 4617 | ;; There are no release tarballs. According to the installation |
| 4618 | ;; instructions at http://seek.princeton.edu/installation.jsp, the latest |
| 4619 | ;; stable release is identified by this changeset ID. |
| 4620 | (let ((changeset "2329130") |
| 4621 | (revision "1")) |
| 4622 | (package |
| 4623 | (name "seek") |
| 4624 | (version (string-append "0-" revision "." changeset)) |
| 4625 | (source (origin |
| 4626 | (method hg-fetch) |
| 4627 | (uri (hg-reference |
| 4628 | (url "https://bitbucket.org/libsleipnir/sleipnir") |
| 4629 | (changeset changeset))) |
| 4630 | (sha256 |
| 4631 | (base32 |
| 4632 | "0qrvilwh18dpbhkf92qvxbmay0j75ra3jg2wrhz67gf538zzphsx")))) |
| 4633 | (build-system gnu-build-system) |
| 4634 | (arguments |
| 4635 | `(#:modules ((srfi srfi-1) |
| 4636 | (guix build gnu-build-system) |
| 4637 | (guix build utils)) |
| 4638 | #:phases |
| 4639 | (let ((dirs '("SeekMiner" |
| 4640 | "SeekEvaluator" |
| 4641 | "SeekPrep" |
| 4642 | "Distancer" |
| 4643 | "Data2DB" |
| 4644 | "PCL2Bin"))) |
| 4645 | (modify-phases %standard-phases |
| 4646 | (add-before 'configure 'bootstrap |
| 4647 | (lambda _ |
| 4648 | (zero? (system* "bash" "gen_auto")))) |
| 4649 | (add-after 'build 'build-additional-tools |
| 4650 | (lambda* (#:key make-flags #:allow-other-keys) |
| 4651 | (every (lambda (dir) |
| 4652 | (with-directory-excursion (string-append "tools/" dir) |
| 4653 | (zero? (apply system* "make" make-flags)))) |
| 4654 | dirs))) |
| 4655 | (add-after 'install 'install-additional-tools |
| 4656 | (lambda* (#:key make-flags #:allow-other-keys) |
| 4657 | (fold (lambda (dir result) |
| 4658 | (with-directory-excursion (string-append "tools/" dir) |
| 4659 | (and result |
| 4660 | (zero? (apply system* |
| 4661 | `("make" ,@make-flags "install")))))) |
| 4662 | #t dirs))))))) |
| 4663 | (inputs |
| 4664 | `(("gsl" ,gsl) |
| 4665 | ("boost" ,boost) |
| 4666 | ("libsvm" ,libsvm) |
| 4667 | ("readline" ,readline) |
| 4668 | ("gengetopt" ,gengetopt) |
| 4669 | ("log4cpp" ,log4cpp))) |
| 4670 | (native-inputs |
| 4671 | `(("autoconf" ,autoconf) |
| 4672 | ("automake" ,automake) |
| 4673 | ("perl" ,perl))) |
| 4674 | (home-page "http://seek.princeton.edu") |
| 4675 | (synopsis "Gene co-expression search engine") |
| 4676 | (description |
| 4677 | "SEEK is a computational gene co-expression search engine. SEEK provides |
| 4678 | biologists with a way to navigate the massive human expression compendium that |
| 4679 | now contains thousands of expression datasets. SEEK returns a robust ranking |
| 4680 | of co-expressed genes in the biological area of interest defined by the user's |
| 4681 | query genes. It also prioritizes thousands of expression datasets according |
| 4682 | to the user's query of interest.") |
| 4683 | (license license:cc-by3.0)))) |
| 4684 | |
| 4685 | (define-public samtools |
| 4686 | (package |
| 4687 | (name "samtools") |
| 4688 | (version "1.5") |
| 4689 | (source |
| 4690 | (origin |
| 4691 | (method url-fetch) |
| 4692 | (uri |
| 4693 | (string-append "mirror://sourceforge/samtools/samtools/" |
| 4694 | version "/samtools-" version ".tar.bz2")) |
| 4695 | (sha256 |
| 4696 | (base32 |
| 4697 | "1xidmv0jmfy7l0kb32hdnlshcxgzi1hmygvig0cqrq1fhckdlhl5")))) |
| 4698 | (build-system gnu-build-system) |
| 4699 | (arguments |
| 4700 | `(#:modules ((ice-9 ftw) |
| 4701 | (ice-9 regex) |
| 4702 | (guix build gnu-build-system) |
| 4703 | (guix build utils)) |
| 4704 | #:make-flags (list (string-append "prefix=" (assoc-ref %outputs "out"))) |
| 4705 | #:configure-flags (list "--with-ncurses" "--with-htslib=system") |
| 4706 | #:phases |
| 4707 | (modify-phases %standard-phases |
| 4708 | (add-after 'unpack 'patch-tests |
| 4709 | (lambda _ |
| 4710 | (substitute* "test/test.pl" |
| 4711 | ;; The test script calls out to /bin/bash |
| 4712 | (("/bin/bash") (which "bash"))) |
| 4713 | #t)) |
| 4714 | (add-after 'install 'install-library |
| 4715 | (lambda* (#:key outputs #:allow-other-keys) |
| 4716 | (let ((lib (string-append (assoc-ref outputs "out") "/lib"))) |
| 4717 | (install-file "libbam.a" lib) |
| 4718 | #t))) |
| 4719 | (add-after 'install 'install-headers |
| 4720 | (lambda* (#:key outputs #:allow-other-keys) |
| 4721 | (let ((include (string-append (assoc-ref outputs "out") |
| 4722 | "/include/samtools/"))) |
| 4723 | (for-each (lambda (file) |
| 4724 | (install-file file include)) |
| 4725 | (scandir "." (lambda (name) (string-match "\\.h$" name)))) |
| 4726 | #t)))))) |
| 4727 | (native-inputs `(("pkg-config" ,pkg-config))) |
| 4728 | (inputs |
| 4729 | `(("htslib" ,htslib) |
| 4730 | ("ncurses" ,ncurses) |
| 4731 | ("perl" ,perl) |
| 4732 | ("python" ,python) |
| 4733 | ("zlib" ,zlib))) |
| 4734 | (home-page "http://samtools.sourceforge.net") |
| 4735 | (synopsis "Utilities to efficiently manipulate nucleotide sequence alignments") |
| 4736 | (description |
| 4737 | "Samtools implements various utilities for post-processing nucleotide |
| 4738 | sequence alignments in the SAM, BAM, and CRAM formats, including indexing, |
| 4739 | variant calling (in conjunction with bcftools), and a simple alignment |
| 4740 | viewer.") |
| 4741 | (license license:expat))) |
| 4742 | |
| 4743 | (define-public samtools-0.1 |
| 4744 | ;; This is the most recent version of the 0.1 line of samtools. The input |
| 4745 | ;; and output formats differ greatly from that used and produced by samtools |
| 4746 | ;; 1.x and is still used in many bioinformatics pipelines. |
| 4747 | (package (inherit samtools) |
| 4748 | (version "0.1.19") |
| 4749 | (source |
| 4750 | (origin |
| 4751 | (method url-fetch) |
| 4752 | (uri |
| 4753 | (string-append "mirror://sourceforge/samtools/samtools/" |
| 4754 | version "/samtools-" version ".tar.bz2")) |
| 4755 | (sha256 |
| 4756 | (base32 "1m33xsfwz0s8qi45lylagfllqg7fphf4dr0780rsvw75av9wk06h")))) |
| 4757 | (arguments |
| 4758 | `(#:tests? #f ;no "check" target |
| 4759 | ,@(substitute-keyword-arguments (package-arguments samtools) |
| 4760 | ((#:make-flags flags) |
| 4761 | `(cons "LIBCURSES=-lncurses" ,flags)) |
| 4762 | ((#:phases phases) |
| 4763 | `(modify-phases ,phases |
| 4764 | (replace 'install |
| 4765 | (lambda* (#:key outputs #:allow-other-keys) |
| 4766 | (let ((bin (string-append |
| 4767 | (assoc-ref outputs "out") "/bin"))) |
| 4768 | (mkdir-p bin) |
| 4769 | (install-file "samtools" bin) |
| 4770 | #t))) |
| 4771 | (delete 'patch-tests) |
| 4772 | (delete 'configure)))))))) |
| 4773 | |
| 4774 | (define-public mosaik |
| 4775 | (let ((commit "5c25216d3522d6a33e53875cd76a6d65001e4e67")) |
| 4776 | (package |
| 4777 | (name "mosaik") |
| 4778 | (version "2.2.30") |
| 4779 | (source (origin |
| 4780 | ;; There are no release tarballs nor tags. |
| 4781 | (method git-fetch) |
| 4782 | (uri (git-reference |
| 4783 | (url "https://github.com/wanpinglee/MOSAIK.git") |
| 4784 | (commit commit))) |
| 4785 | (file-name (string-append name "-" version)) |
| 4786 | (sha256 |
| 4787 | (base32 |
| 4788 | "17gj3s07cm77r41z92awh0bim7w7q7fbn0sf5nkqmcm1vw052qgw")))) |
| 4789 | (build-system gnu-build-system) |
| 4790 | (arguments |
| 4791 | `(#:tests? #f ; no tests |
| 4792 | #:make-flags (list "CC=gcc") |
| 4793 | #:phases |
| 4794 | (modify-phases %standard-phases |
| 4795 | (replace 'configure |
| 4796 | (lambda _ (chdir "src") #t)) |
| 4797 | (replace 'install |
| 4798 | (lambda* (#:key outputs #:allow-other-keys) |
| 4799 | (let ((bin (string-append (assoc-ref outputs "out") |
| 4800 | "/bin"))) |
| 4801 | (mkdir-p bin) |
| 4802 | (copy-recursively "../bin" bin) |
| 4803 | #t)))))) |
| 4804 | (inputs |
| 4805 | `(("perl" ,perl) |
| 4806 | ("zlib" ,zlib))) |
| 4807 | (supported-systems '("x86_64-linux")) |
| 4808 | (home-page "https://github.com/wanpinglee/MOSAIK") |
| 4809 | (synopsis "Map nucleotide sequence reads to reference genomes") |
| 4810 | (description |
| 4811 | "MOSAIK is a program for mapping second and third-generation sequencing |
| 4812 | reads to a reference genome. MOSAIK can align reads generated by all the |
| 4813 | major sequencing technologies, including Illumina, Applied Biosystems SOLiD, |
| 4814 | Roche 454, Ion Torrent and Pacific BioSciences SMRT.") |
| 4815 | ;; MOSAIK is released under the GPLv2+ with the exception of third-party |
| 4816 | ;; code released into the public domain: |
| 4817 | ;; 1. fastlz by Ariya Hidayat - http://www.fastlz.org/ |
| 4818 | ;; 2. MD5 implementation - RSA Data Security, RFC 1321 |
| 4819 | (license (list license:gpl2+ license:public-domain))))) |
| 4820 | |
| 4821 | (define-public ngs-sdk |
| 4822 | (package |
| 4823 | (name "ngs-sdk") |
| 4824 | (version "1.3.0") |
| 4825 | (source |
| 4826 | (origin |
| 4827 | (method url-fetch) |
| 4828 | (uri |
| 4829 | (string-append "https://github.com/ncbi/ngs/archive/" |
| 4830 | version ".tar.gz")) |
| 4831 | (file-name (string-append name "-" version ".tar.gz")) |
| 4832 | (sha256 |
| 4833 | (base32 |
| 4834 | "1wiyf4c6nm2j87pv015cbi0qny5byf3pbvcw3likifz5dl56ag40")))) |
| 4835 | (build-system gnu-build-system) |
| 4836 | (arguments |
| 4837 | `(#:parallel-build? #f ; not supported |
| 4838 | #:tests? #f ; no "check" target |
| 4839 | #:phases |
| 4840 | (modify-phases %standard-phases |
| 4841 | (replace 'configure |
| 4842 | (lambda* (#:key outputs #:allow-other-keys) |
| 4843 | (let ((out (assoc-ref outputs "out"))) |
| 4844 | ;; Allow 'konfigure.perl' to find 'package.prl'. |
| 4845 | (setenv "PERL5LIB" |
| 4846 | (string-append ".:" (getenv "PERL5LIB"))) |
| 4847 | |
| 4848 | ;; The 'configure' script doesn't recognize things like |
| 4849 | ;; '--enable-fast-install'. |
| 4850 | (zero? (system* "./configure" |
| 4851 | (string-append "--build-prefix=" (getcwd) "/build") |
| 4852 | (string-append "--prefix=" out)))))) |
| 4853 | (add-after 'unpack 'enter-dir |
| 4854 | (lambda _ (chdir "ngs-sdk") #t))))) |
| 4855 | (native-inputs `(("perl" ,perl))) |
| 4856 | ;; According to the test |
| 4857 | ;; unless ($MARCH =~ /x86_64/i || $MARCH =~ /i?86/i) |
| 4858 | ;; in ngs-sdk/setup/konfigure.perl |
| 4859 | (supported-systems '("i686-linux" "x86_64-linux")) |
| 4860 | (home-page "https://github.com/ncbi/ngs") |
| 4861 | (synopsis "API for accessing Next Generation Sequencing data") |
| 4862 | (description |
| 4863 | "NGS is a domain-specific API for accessing reads, alignments and pileups |
| 4864 | produced from Next Generation Sequencing. The API itself is independent from |
| 4865 | any particular back-end implementation, and supports use of multiple back-ends |
| 4866 | simultaneously.") |
| 4867 | (license license:public-domain))) |
| 4868 | |
| 4869 | (define-public java-ngs |
| 4870 | (package (inherit ngs-sdk) |
| 4871 | (name "java-ngs") |
| 4872 | (arguments |
| 4873 | `(,@(substitute-keyword-arguments |
| 4874 | `(#:modules ((guix build gnu-build-system) |
| 4875 | (guix build utils) |
| 4876 | (srfi srfi-1) |
| 4877 | (srfi srfi-26)) |
| 4878 | ,@(package-arguments ngs-sdk)) |
| 4879 | ((#:phases phases) |
| 4880 | `(modify-phases ,phases |
| 4881 | (replace 'enter-dir (lambda _ (chdir "ngs-java") #t))))))) |
| 4882 | (inputs |
| 4883 | `(("jdk" ,icedtea "jdk") |
| 4884 | ("ngs-sdk" ,ngs-sdk))) |
| 4885 | (synopsis "Java bindings for NGS SDK"))) |
| 4886 | |
| 4887 | (define-public ncbi-vdb |
| 4888 | (package |
| 4889 | (name "ncbi-vdb") |
| 4890 | (version "2.8.2") |
| 4891 | (source |
| 4892 | (origin |
| 4893 | (method url-fetch) |
| 4894 | (uri |
| 4895 | (string-append "https://github.com/ncbi/ncbi-vdb/archive/" |
| 4896 | version ".tar.gz")) |
| 4897 | (file-name (string-append name "-" version ".tar.gz")) |
| 4898 | (sha256 |
| 4899 | (base32 |
| 4900 | "1acn4bv81mfl137qnbn9995mjjhwd36pm0b7qli1iw5skrxa9j8m")))) |
| 4901 | (build-system gnu-build-system) |
| 4902 | (arguments |
| 4903 | `(#:parallel-build? #f ; not supported |
| 4904 | #:tests? #f ; no "check" target |
| 4905 | #:phases |
| 4906 | (modify-phases %standard-phases |
| 4907 | (add-before 'configure 'set-perl-search-path |
| 4908 | (lambda _ |
| 4909 | ;; Work around "dotless @INC" build failure. |
| 4910 | (setenv "PERL5LIB" |
| 4911 | (string-append (getcwd) "/setup:" |
| 4912 | (getenv "PERL5LIB"))) |
| 4913 | #t)) |
| 4914 | (replace 'configure |
| 4915 | (lambda* (#:key inputs outputs #:allow-other-keys) |
| 4916 | (let ((out (assoc-ref outputs "out"))) |
| 4917 | ;; Override include path for libmagic |
| 4918 | (substitute* "setup/package.prl" |
| 4919 | (("name => 'magic', Include => '/usr/include'") |
| 4920 | (string-append "name=> 'magic', Include => '" |
| 4921 | (assoc-ref inputs "libmagic") |
| 4922 | "/include" "'"))) |
| 4923 | |
| 4924 | ;; Install kdf5 library (needed by sra-tools) |
| 4925 | (substitute* "build/Makefile.install" |
| 4926 | (("LIBRARIES_TO_INSTALL =") |
| 4927 | "LIBRARIES_TO_INSTALL = kdf5.$(VERSION_LIBX) kdf5.$(VERSION_SHLX)")) |
| 4928 | |
| 4929 | (substitute* "build/Makefile.env" |
| 4930 | (("CFLAGS =" prefix) |
| 4931 | (string-append prefix "-msse2 "))) |
| 4932 | |
| 4933 | ;; Override search path for ngs-java |
| 4934 | (substitute* "setup/package.prl" |
| 4935 | (("/usr/local/ngs/ngs-java") |
| 4936 | (assoc-ref inputs "java-ngs"))) |
| 4937 | |
| 4938 | ;; The 'configure' script doesn't recognize things like |
| 4939 | ;; '--enable-fast-install'. |
| 4940 | (zero? (system* |
| 4941 | "./configure" |
| 4942 | (string-append "--build-prefix=" (getcwd) "/build") |
| 4943 | (string-append "--prefix=" (assoc-ref outputs "out")) |
| 4944 | (string-append "--debug") |
| 4945 | (string-append "--with-xml2-prefix=" |
| 4946 | (assoc-ref inputs "libxml2")) |
| 4947 | (string-append "--with-ngs-sdk-prefix=" |
| 4948 | (assoc-ref inputs "ngs-sdk")) |
| 4949 | (string-append "--with-hdf5-prefix=" |
| 4950 | (assoc-ref inputs "hdf5"))))))) |
| 4951 | (add-after 'install 'install-interfaces |
| 4952 | (lambda* (#:key outputs #:allow-other-keys) |
| 4953 | ;; Install interface libraries. On i686 the interface libraries |
| 4954 | ;; are installed to "linux/gcc/i386", so we need to use the Linux |
| 4955 | ;; architecture name ("i386") instead of the target system prefix |
| 4956 | ;; ("i686"). |
| 4957 | (mkdir (string-append (assoc-ref outputs "out") "/ilib")) |
| 4958 | (copy-recursively (string-append "build/ncbi-vdb/linux/gcc/" |
| 4959 | ,(system->linux-architecture |
| 4960 | (or (%current-target-system) |
| 4961 | (%current-system))) |
| 4962 | "/rel/ilib") |
| 4963 | (string-append (assoc-ref outputs "out") |
| 4964 | "/ilib")) |
| 4965 | ;; Install interface headers |
| 4966 | (copy-recursively "interfaces" |
| 4967 | (string-append (assoc-ref outputs "out") |
| 4968 | "/include")) |
| 4969 | #t)) |
| 4970 | ;; These files are needed by sra-tools. |
| 4971 | (add-after 'install 'install-configuration-files |
| 4972 | (lambda* (#:key outputs #:allow-other-keys) |
| 4973 | (let ((target (string-append (assoc-ref outputs "out") "/kfg"))) |
| 4974 | (mkdir target) |
| 4975 | (install-file "libs/kfg/default.kfg" target) |
| 4976 | (install-file "libs/kfg/certs.kfg" target)) |
| 4977 | #t))))) |
| 4978 | (inputs |
| 4979 | `(("libxml2" ,libxml2) |
| 4980 | ("ngs-sdk" ,ngs-sdk) |
| 4981 | ("java-ngs" ,java-ngs) |
| 4982 | ("libmagic" ,file) |
| 4983 | ("hdf5" ,hdf5))) |
| 4984 | (native-inputs `(("perl" ,perl))) |
| 4985 | ;; NCBI-VDB requires SSE capability. |
| 4986 | (supported-systems '("i686-linux" "x86_64-linux")) |
| 4987 | (home-page "https://github.com/ncbi/ncbi-vdb") |
| 4988 | (synopsis "Database engine for genetic information") |
| 4989 | (description |
| 4990 | "The NCBI-VDB library implements a highly compressed columnar data |
| 4991 | warehousing engine that is most often used to store genetic information. |
| 4992 | Databases are stored in a portable image within the file system, and can be |
| 4993 | accessed/downloaded on demand across HTTP.") |
| 4994 | (license license:public-domain))) |
| 4995 | |
| 4996 | (define-public plink |
| 4997 | (package |
| 4998 | (name "plink") |
| 4999 | (version "1.07") |
| 5000 | (source |
| 5001 | (origin |
| 5002 | (method url-fetch) |
| 5003 | (uri (string-append |
| 5004 | "http://pngu.mgh.harvard.edu/~purcell/plink/dist/plink-" |
| 5005 | version "-src.zip")) |
| 5006 | (sha256 |
| 5007 | (base32 "0as8gxm4pjyc8dxmm1sl873rrd7wn5qs0l29nqfnl31x8i467xaa")) |
| 5008 | (patches (search-patches "plink-1.07-unclobber-i.patch" |
| 5009 | "plink-endian-detection.patch")))) |
| 5010 | (build-system gnu-build-system) |
| 5011 | (arguments |
| 5012 | '(#:tests? #f ;no "check" target |
| 5013 | #:make-flags (list (string-append "LIB_LAPACK=" |
| 5014 | (assoc-ref %build-inputs "lapack") |
| 5015 | "/lib/liblapack.so") |
| 5016 | "WITH_LAPACK=1" |
| 5017 | "FORCE_DYNAMIC=1" |
| 5018 | ;; disable phoning home |
| 5019 | "WITH_WEBCHECK=") |
| 5020 | #:phases |
| 5021 | (modify-phases %standard-phases |
| 5022 | ;; no "configure" script |
| 5023 | (delete 'configure) |
| 5024 | (replace 'install |
| 5025 | (lambda* (#:key outputs #:allow-other-keys) |
| 5026 | (let ((bin (string-append (assoc-ref outputs "out") |
| 5027 | "/bin/"))) |
| 5028 | (install-file "plink" bin) |
| 5029 | #t)))))) |
| 5030 | (inputs |
| 5031 | `(("zlib" ,zlib) |
| 5032 | ("lapack" ,lapack))) |
| 5033 | (native-inputs |
| 5034 | `(("unzip" ,unzip))) |
| 5035 | (home-page "http://pngu.mgh.harvard.edu/~purcell/plink/") |
| 5036 | (synopsis "Whole genome association analysis toolset") |
| 5037 | (description |
| 5038 | "PLINK is a whole genome association analysis toolset, designed to |
| 5039 | perform a range of basic, large-scale analyses in a computationally efficient |
| 5040 | manner. The focus of PLINK is purely on analysis of genotype/phenotype data, |
| 5041 | so there is no support for steps prior to this (e.g. study design and |
| 5042 | planning, generating genotype or CNV calls from raw data). Through |
| 5043 | integration with gPLINK and Haploview, there is some support for the |
| 5044 | subsequent visualization, annotation and storage of results.") |
| 5045 | ;; Code is released under GPLv2, except for fisher.h, which is under |
| 5046 | ;; LGPLv2.1+ |
| 5047 | (license (list license:gpl2 license:lgpl2.1+)))) |
| 5048 | |
| 5049 | (define-public plink-ng |
| 5050 | (package (inherit plink) |
| 5051 | (name "plink-ng") |
| 5052 | (version "1.90b4") |
| 5053 | (source |
| 5054 | (origin |
| 5055 | (method url-fetch) |
| 5056 | (uri (string-append "https://github.com/chrchang/plink-ng/archive/v" |
| 5057 | version ".tar.gz")) |
| 5058 | (file-name (string-append name "-" version ".tar.gz")) |
| 5059 | (sha256 |
| 5060 | (base32 "09ixrds009aczjswxr2alcb774mksq5g0v78dgjjn1h4dky0kf9a")))) |
| 5061 | (build-system gnu-build-system) |
| 5062 | (arguments |
| 5063 | '(#:tests? #f ;no "check" target |
| 5064 | #:make-flags (list "BLASFLAGS=-llapack -lopenblas" |
| 5065 | "CFLAGS=-Wall -O2 -DDYNAMIC_ZLIB=1" |
| 5066 | "ZLIB=-lz" |
| 5067 | "-f" "Makefile.std") |
| 5068 | #:phases |
| 5069 | (modify-phases %standard-phases |
| 5070 | (add-after 'unpack 'chdir |
| 5071 | (lambda _ (chdir "1.9") #t)) |
| 5072 | (delete 'configure) ; no "configure" script |
| 5073 | (replace 'install |
| 5074 | (lambda* (#:key outputs #:allow-other-keys) |
| 5075 | (let ((bin (string-append (assoc-ref outputs "out") |
| 5076 | "/bin/"))) |
| 5077 | (install-file "plink" bin) |
| 5078 | #t)))))) |
| 5079 | (inputs |
| 5080 | `(("zlib" ,zlib) |
| 5081 | ("lapack" ,lapack) |
| 5082 | ("openblas" ,openblas))) |
| 5083 | (home-page "https://www.cog-genomics.org/plink/") |
| 5084 | (license license:gpl3+))) |
| 5085 | |
| 5086 | (define-public smithlab-cpp |
| 5087 | (let ((revision "1") |
| 5088 | (commit "728a097bec88c6f4b8528b685932049e660eff2e")) |
| 5089 | (package |
| 5090 | (name "smithlab-cpp") |
| 5091 | (version (string-append "0." revision "." (string-take commit 7))) |
| 5092 | (source (origin |
| 5093 | (method git-fetch) |
| 5094 | (uri (git-reference |
| 5095 | (url "https://github.com/smithlabcode/smithlab_cpp.git") |
| 5096 | (commit commit))) |
| 5097 | (file-name (string-append name "-" version "-checkout")) |
| 5098 | (sha256 |
| 5099 | (base32 |
| 5100 | "0d476lmj312xk77kr9fzrv7z1bv96yfyx0w7y62ycmnfbx32ll74")))) |
| 5101 | (build-system gnu-build-system) |
| 5102 | (arguments |
| 5103 | `(#:modules ((guix build gnu-build-system) |
| 5104 | (guix build utils) |
| 5105 | (srfi srfi-26)) |
| 5106 | #:tests? #f ;no "check" target |
| 5107 | #:phases |
| 5108 | (modify-phases %standard-phases |
| 5109 | (add-after 'unpack 'use-samtools-headers |
| 5110 | (lambda _ |
| 5111 | (substitute* '("SAM.cpp" |
| 5112 | "SAM.hpp") |
| 5113 | (("sam.h") "samtools/sam.h")) |
| 5114 | #t)) |
| 5115 | (replace 'install |
| 5116 | (lambda* (#:key outputs #:allow-other-keys) |
| 5117 | (let* ((out (assoc-ref outputs "out")) |
| 5118 | (lib (string-append out "/lib")) |
| 5119 | (include (string-append out "/include/smithlab-cpp"))) |
| 5120 | (mkdir-p lib) |
| 5121 | (mkdir-p include) |
| 5122 | (for-each (cut install-file <> lib) |
| 5123 | (find-files "." "\\.o$")) |
| 5124 | (for-each (cut install-file <> include) |
| 5125 | (find-files "." "\\.hpp$"))) |
| 5126 | #t)) |
| 5127 | (delete 'configure)))) |
| 5128 | (inputs |
| 5129 | `(("samtools" ,samtools-0.1) |
| 5130 | ("zlib" ,zlib))) |
| 5131 | (home-page "https://github.com/smithlabcode/smithlab_cpp") |
| 5132 | (synopsis "C++ helper library for functions used in Smith lab projects") |
| 5133 | (description |
| 5134 | "Smithlab CPP is a C++ library that includes functions used in many of |
| 5135 | the Smith lab bioinformatics projects, such as a wrapper around Samtools data |
| 5136 | structures, classes for genomic regions, mapped sequencing reads, etc.") |
| 5137 | (license license:gpl3+)))) |
| 5138 | |
| 5139 | (define-public preseq |
| 5140 | (package |
| 5141 | (name "preseq") |
| 5142 | (version "2.0") |
| 5143 | (source (origin |
| 5144 | (method url-fetch) |
| 5145 | (uri (string-append "https://github.com/smithlabcode/" |
| 5146 | "preseq/archive/v" version ".tar.gz")) |
| 5147 | (file-name (string-append name "-" version ".tar.gz")) |
| 5148 | (sha256 |
| 5149 | (base32 "08r684l50pnxjpvmhzjgqq56yv9rfw90k8vx0nsrnrzk8mf9hsdq")) |
| 5150 | (modules '((guix build utils))) |
| 5151 | (snippet |
| 5152 | ;; Remove bundled samtools. |
| 5153 | '(delete-file-recursively "samtools")))) |
| 5154 | (build-system gnu-build-system) |
| 5155 | (arguments |
| 5156 | `(#:tests? #f ;no "check" target |
| 5157 | #:phases |
| 5158 | (modify-phases %standard-phases |
| 5159 | (delete 'configure)) |
| 5160 | #:make-flags |
| 5161 | (list (string-append "PREFIX=" |
| 5162 | (assoc-ref %outputs "out")) |
| 5163 | (string-append "LIBBAM=" |
| 5164 | (assoc-ref %build-inputs "samtools") |
| 5165 | "/lib/libbam.a") |
| 5166 | (string-append "SMITHLAB_CPP=" |
| 5167 | (assoc-ref %build-inputs "smithlab-cpp") |
| 5168 | "/lib") |
| 5169 | "PROGS=preseq" |
| 5170 | "INCLUDEDIRS=$(SMITHLAB_CPP)/../include/smithlab-cpp $(SAMTOOLS_DIR)"))) |
| 5171 | (inputs |
| 5172 | `(("gsl" ,gsl) |
| 5173 | ("samtools" ,samtools-0.1) |
| 5174 | ("smithlab-cpp" ,smithlab-cpp) |
| 5175 | ("zlib" ,zlib))) |
| 5176 | (home-page "http://smithlabresearch.org/software/preseq/") |
| 5177 | (synopsis "Program for analyzing library complexity") |
| 5178 | (description |
| 5179 | "The preseq package is aimed at predicting and estimating the complexity |
| 5180 | of a genomic sequencing library, equivalent to predicting and estimating the |
| 5181 | number of redundant reads from a given sequencing depth and how many will be |
| 5182 | expected from additional sequencing using an initial sequencing experiment. |
| 5183 | The estimates can then be used to examine the utility of further sequencing, |
| 5184 | optimize the sequencing depth, or to screen multiple libraries to avoid low |
| 5185 | complexity samples.") |
| 5186 | (license license:gpl3+))) |
| 5187 | |
| 5188 | (define-public python-screed |
| 5189 | (package |
| 5190 | (name "python-screed") |
| 5191 | (version "0.9") |
| 5192 | (source |
| 5193 | (origin |
| 5194 | (method url-fetch) |
| 5195 | (uri (pypi-uri "screed" version)) |
| 5196 | (sha256 |
| 5197 | (base32 |
| 5198 | "18czszp9fkx3j6jr7y5kp6dfialscgddk05mw1zkhh2zhn0jd8i0")))) |
| 5199 | (build-system python-build-system) |
| 5200 | (arguments |
| 5201 | `(#:phases |
| 5202 | (modify-phases %standard-phases |
| 5203 | (replace 'check |
| 5204 | (lambda _ |
| 5205 | (setenv "PYTHONPATH" |
| 5206 | (string-append (getenv "PYTHONPATH") ":.")) |
| 5207 | (zero? (system* "nosetests" "--attr" "!known_failing"))))))) |
| 5208 | (native-inputs |
| 5209 | `(("python-nose" ,python-nose))) |
| 5210 | (inputs |
| 5211 | `(("python-bz2file" ,python-bz2file))) |
| 5212 | (home-page "https://github.com/dib-lab/screed/") |
| 5213 | (synopsis "Short read sequence database utilities") |
| 5214 | (description "Screed parses FASTA and FASTQ files and generates databases. |
| 5215 | Values such as sequence name, sequence description, sequence quality and the |
| 5216 | sequence itself can be retrieved from these databases.") |
| 5217 | (license license:bsd-3))) |
| 5218 | |
| 5219 | (define-public python2-screed |
| 5220 | (package-with-python2 python-screed)) |
| 5221 | |
| 5222 | (define-public sra-tools |
| 5223 | (package |
| 5224 | (name "sra-tools") |
| 5225 | (version "2.8.2-1") |
| 5226 | (source |
| 5227 | (origin |
| 5228 | (method url-fetch) |
| 5229 | (uri |
| 5230 | (string-append "https://github.com/ncbi/sra-tools/archive/" |
| 5231 | version ".tar.gz")) |
| 5232 | (file-name (string-append name "-" version ".tar.gz")) |
| 5233 | (sha256 |
| 5234 | (base32 |
| 5235 | "1camsijmvv2s45mb4iyf44ghl4gkd4rl0viphpcgl3ccchy32a0g")))) |
| 5236 | (build-system gnu-build-system) |
| 5237 | (arguments |
| 5238 | `(#:parallel-build? #f ; not supported |
| 5239 | #:tests? #f ; no "check" target |
| 5240 | #:make-flags |
| 5241 | (list (string-append "DEFAULT_CRT=" |
| 5242 | (assoc-ref %build-inputs "ncbi-vdb") |
| 5243 | "/kfg/certs.kfg") |
| 5244 | (string-append "DEFAULT_KFG=" |
| 5245 | (assoc-ref %build-inputs "ncbi-vdb") |
| 5246 | "/kfg/default.kfg") |
| 5247 | (string-append "VDB_LIBDIR=" |
| 5248 | (assoc-ref %build-inputs "ncbi-vdb") |
| 5249 | ,(if (string-prefix? "x86_64" |
| 5250 | (or (%current-target-system) |
| 5251 | (%current-system))) |
| 5252 | "/lib64" |
| 5253 | "/lib32"))) |
| 5254 | #:phases |
| 5255 | (modify-phases %standard-phases |
| 5256 | (add-before 'configure 'set-perl-search-path |
| 5257 | (lambda _ |
| 5258 | ;; Work around "dotless @INC" build failure. |
| 5259 | (setenv "PERL5LIB" |
| 5260 | (string-append (getcwd) "/setup:" |
| 5261 | (getenv "PERL5LIB"))) |
| 5262 | #t)) |
| 5263 | (replace 'configure |
| 5264 | (lambda* (#:key inputs outputs #:allow-other-keys) |
| 5265 | ;; The build system expects a directory containing the sources and |
| 5266 | ;; raw build output of ncbi-vdb, including files that are not |
| 5267 | ;; installed. Since we are building against an installed version of |
| 5268 | ;; ncbi-vdb, the following modifications are needed. |
| 5269 | (substitute* "setup/konfigure.perl" |
| 5270 | ;; Make the configure script look for the "ilib" directory of |
| 5271 | ;; "ncbi-vdb" without first checking for the existence of a |
| 5272 | ;; matching library in its "lib" directory. |
| 5273 | (("^ my \\$f = File::Spec->catdir\\(\\$libdir, \\$lib\\);") |
| 5274 | "my $f = File::Spec->catdir($ilibdir, $ilib);") |
| 5275 | ;; Look for interface libraries in ncbi-vdb's "ilib" directory. |
| 5276 | (("my \\$ilibdir = File::Spec->catdir\\(\\$builddir, 'ilib'\\);") |
| 5277 | "my $ilibdir = File::Spec->catdir($dir, 'ilib');")) |
| 5278 | |
| 5279 | ;; Dynamic linking |
| 5280 | (substitute* "tools/copycat/Makefile" |
| 5281 | (("smagic-static") "lmagic")) |
| 5282 | |
| 5283 | ;; The 'configure' script doesn't recognize things like |
| 5284 | ;; '--enable-fast-install'. |
| 5285 | (zero? (system* |
| 5286 | "./configure" |
| 5287 | (string-append "--build-prefix=" (getcwd) "/build") |
| 5288 | (string-append "--prefix=" (assoc-ref outputs "out")) |
| 5289 | (string-append "--debug") |
| 5290 | (string-append "--with-fuse-prefix=" |
| 5291 | (assoc-ref inputs "fuse")) |
| 5292 | (string-append "--with-magic-prefix=" |
| 5293 | (assoc-ref inputs "libmagic")) |
| 5294 | ;; TODO: building with libxml2 fails with linker errors |
| 5295 | ;; (string-append "--with-xml2-prefix=" |
| 5296 | ;; (assoc-ref inputs "libxml2")) |
| 5297 | (string-append "--with-ncbi-vdb-sources=" |
| 5298 | (assoc-ref inputs "ncbi-vdb")) |
| 5299 | (string-append "--with-ncbi-vdb-build=" |
| 5300 | (assoc-ref inputs "ncbi-vdb")) |
| 5301 | (string-append "--with-ngs-sdk-prefix=" |
| 5302 | (assoc-ref inputs "ngs-sdk")) |
| 5303 | (string-append "--with-hdf5-prefix=" |
| 5304 | (assoc-ref inputs "hdf5")))))) |
| 5305 | ;; This version of sra-tools fails to build with glibc because of a |
| 5306 | ;; naming conflict. glibc-2.25/include/bits/mathcalls.h already |
| 5307 | ;; contains a definition of "canonicalize", so we rename it. |
| 5308 | ;; |
| 5309 | ;; See upstream bug report: |
| 5310 | ;; https://github.com/ncbi/sra-tools/issues/67 |
| 5311 | (add-after 'unpack 'patch-away-glibc-conflict |
| 5312 | (lambda _ |
| 5313 | (substitute* "tools/bam-loader/bam.c" |
| 5314 | (("canonicalize\\(" line) |
| 5315 | (string-append "sra_tools_" line))) |
| 5316 | #t))))) |
| 5317 | (native-inputs `(("perl" ,perl))) |
| 5318 | (inputs |
| 5319 | `(("ngs-sdk" ,ngs-sdk) |
| 5320 | ("ncbi-vdb" ,ncbi-vdb) |
| 5321 | ("libmagic" ,file) |
| 5322 | ("fuse" ,fuse) |
| 5323 | ("hdf5" ,hdf5) |
| 5324 | ("zlib" ,zlib))) |
| 5325 | (home-page "http://www.ncbi.nlm.nih.gov/Traces/sra/sra.cgi?view=software") |
| 5326 | (synopsis "Tools and libraries for reading and writing sequencing data") |
| 5327 | (description |
| 5328 | "The SRA Toolkit from NCBI is a collection of tools and libraries for |
| 5329 | reading of sequencing files from the Sequence Read Archive (SRA) database and |
| 5330 | writing files into the .sra format.") |
| 5331 | (license license:public-domain))) |
| 5332 | |
| 5333 | (define-public seqan |
| 5334 | (package |
| 5335 | (name "seqan") |
| 5336 | (version "1.4.2") |
| 5337 | (source (origin |
| 5338 | (method url-fetch) |
| 5339 | (uri (string-append "http://packages.seqan.de/seqan-library/" |
| 5340 | "seqan-library-" version ".tar.bz2")) |
| 5341 | (sha256 |
| 5342 | (base32 |
| 5343 | "05s3wrrwn50f81aklfm65i4a749zag1vr8z03k21xm0pdxy47yvp")))) |
| 5344 | ;; The documentation is 7.8MB and the includes are 3.6MB heavy, so it |
| 5345 | ;; makes sense to split the outputs. |
| 5346 | (outputs '("out" "doc")) |
| 5347 | (build-system trivial-build-system) |
| 5348 | (arguments |
| 5349 | `(#:modules ((guix build utils)) |
| 5350 | #:builder |
| 5351 | (begin |
| 5352 | (use-modules (guix build utils)) |
| 5353 | (let ((tar (assoc-ref %build-inputs "tar")) |
| 5354 | (bzip (assoc-ref %build-inputs "bzip2")) |
| 5355 | (out (assoc-ref %outputs "out")) |
| 5356 | (doc (assoc-ref %outputs "doc"))) |
| 5357 | (setenv "PATH" (string-append tar "/bin:" bzip "/bin")) |
| 5358 | (system* "tar" "xvf" (assoc-ref %build-inputs "source")) |
| 5359 | (chdir (string-append "seqan-library-" ,version)) |
| 5360 | (copy-recursively "include" (string-append out "/include")) |
| 5361 | (copy-recursively "share" (string-append doc "/share")))))) |
| 5362 | (native-inputs |
| 5363 | `(("source" ,source) |
| 5364 | ("tar" ,tar) |
| 5365 | ("bzip2" ,bzip2))) |
| 5366 | (home-page "http://www.seqan.de") |
| 5367 | (synopsis "Library for nucleotide sequence analysis") |
| 5368 | (description |
| 5369 | "SeqAn is a C++ library of efficient algorithms and data structures for |
| 5370 | the analysis of sequences with the focus on biological data. It contains |
| 5371 | algorithms and data structures for string representation and their |
| 5372 | manipulation, online and indexed string search, efficient I/O of |
| 5373 | bioinformatics file formats, sequence alignment, and more.") |
| 5374 | (license license:bsd-3))) |
| 5375 | |
| 5376 | (define-public seqmagick |
| 5377 | (package |
| 5378 | (name "seqmagick") |
| 5379 | (version "0.6.1") |
| 5380 | (source |
| 5381 | (origin |
| 5382 | (method url-fetch) |
| 5383 | (uri (string-append |
| 5384 | "https://pypi.python.org/packages/source/s/seqmagick/seqmagick-" |
| 5385 | version ".tar.gz")) |
| 5386 | (sha256 |
| 5387 | (base32 |
| 5388 | "0cgn477n74gsl4qdaakrrhi953kcsd4q3ivk2lr18x74s3g4ma1d")))) |
| 5389 | (build-system python-build-system) |
| 5390 | (arguments |
| 5391 | ;; python2 only, see https://github.com/fhcrc/seqmagick/issues/56 |
| 5392 | `(#:python ,python-2 |
| 5393 | #:phases |
| 5394 | (modify-phases %standard-phases |
| 5395 | ;; Current test in setup.py does not work as of 0.6.1, |
| 5396 | ;; so use nose to run tests instead for now. See |
| 5397 | ;; https://github.com/fhcrc/seqmagick/issues/55 |
| 5398 | (replace 'check (lambda _ (zero? (system* "nosetests"))))))) |
| 5399 | (inputs |
| 5400 | ;; biopython-1.66 is required due to |
| 5401 | ;; https://github.com/fhcrc/seqmagick/issues/59 |
| 5402 | ;; When that issue is resolved the 'python2-biopython-1.66' package |
| 5403 | ;; should be removed. |
| 5404 | `(("python-biopython" ,python2-biopython-1.66))) |
| 5405 | (native-inputs |
| 5406 | `(("python-nose" ,python2-nose))) |
| 5407 | (home-page "https://github.com/fhcrc/seqmagick") |
| 5408 | (synopsis "Tools for converting and modifying sequence files") |
| 5409 | (description |
| 5410 | "Bioinformaticians often have to convert sequence files between formats |
| 5411 | and do little manipulations on them, and it's not worth writing scripts for |
| 5412 | that. Seqmagick is a utility to expose the file format conversion in |
| 5413 | BioPython in a convenient way. Instead of having a big mess of scripts, there |
| 5414 | is one that takes arguments.") |
| 5415 | (license license:gpl3))) |
| 5416 | |
| 5417 | (define-public seqtk |
| 5418 | (package |
| 5419 | (name "seqtk") |
| 5420 | (version "1.2") |
| 5421 | (source (origin |
| 5422 | (method url-fetch) |
| 5423 | (uri (string-append |
| 5424 | "https://github.com/lh3/seqtk/archive/v" |
| 5425 | version ".tar.gz")) |
| 5426 | (file-name (string-append name "-" version ".tar.gz")) |
| 5427 | (sha256 |
| 5428 | (base32 |
| 5429 | "0ywdyzpmfiz2wp6ampbzqg4y8bj450nfgqarpamg045b8mk32lxx")) |
| 5430 | (modules '((guix build utils))) |
| 5431 | (snippet |
| 5432 | '(begin |
| 5433 | ;; Remove extraneous header files, as is done in the seqtk |
| 5434 | ;; master branch. |
| 5435 | (for-each (lambda (file) (delete-file file)) |
| 5436 | (list "ksort.h" "kstring.h" "kvec.h")) |
| 5437 | #t)))) |
| 5438 | (build-system gnu-build-system) |
| 5439 | (arguments |
| 5440 | `(#:phases |
| 5441 | (modify-phases %standard-phases |
| 5442 | (delete 'configure) |
| 5443 | (replace 'check |
| 5444 | ;; There are no tests, so we just run a sanity check. |
| 5445 | (lambda _ (zero? (system* "./seqtk" "seq")))) |
| 5446 | (replace 'install |
| 5447 | (lambda* (#:key outputs #:allow-other-keys) |
| 5448 | (let ((bin (string-append (assoc-ref outputs "out") "/bin/"))) |
| 5449 | (install-file "seqtk" bin))))))) |
| 5450 | (inputs |
| 5451 | `(("zlib" ,zlib))) |
| 5452 | (home-page "https://github.com/lh3/seqtk") |
| 5453 | (synopsis "Toolkit for processing biological sequences in FASTA/Q format") |
| 5454 | (description |
| 5455 | "Seqtk is a fast and lightweight tool for processing sequences in the |
| 5456 | FASTA or FASTQ format. It parses both FASTA and FASTQ files which can be |
| 5457 | optionally compressed by gzip.") |
| 5458 | (license license:expat))) |
| 5459 | |
| 5460 | (define-public snap-aligner |
| 5461 | (package |
| 5462 | (name "snap-aligner") |
| 5463 | (version "1.0beta.18") |
| 5464 | (source (origin |
| 5465 | (method url-fetch) |
| 5466 | (uri (string-append |
| 5467 | "https://github.com/amplab/snap/archive/v" |
| 5468 | version ".tar.gz")) |
| 5469 | (file-name (string-append name "-" version ".tar.gz")) |
| 5470 | (sha256 |
| 5471 | (base32 |
| 5472 | "1vnsjwv007k1fl1q7d681kbwn6bc66cgw6h16hym6gvyy71qv2ly")))) |
| 5473 | (build-system gnu-build-system) |
| 5474 | (arguments |
| 5475 | '(#:phases |
| 5476 | (modify-phases %standard-phases |
| 5477 | (delete 'configure) |
| 5478 | (replace 'check (lambda _ (zero? (system* "./unit_tests")))) |
| 5479 | (replace 'install |
| 5480 | (lambda* (#:key outputs #:allow-other-keys) |
| 5481 | (let* ((out (assoc-ref outputs "out")) |
| 5482 | (bin (string-append out "/bin"))) |
| 5483 | (install-file "snap-aligner" bin) |
| 5484 | (install-file "SNAPCommand" bin) |
| 5485 | #t)))))) |
| 5486 | (native-inputs |
| 5487 | `(("zlib" ,zlib))) |
| 5488 | (home-page "http://snap.cs.berkeley.edu/") |
| 5489 | (synopsis "Short read DNA sequence aligner") |
| 5490 | (description |
| 5491 | "SNAP is a fast and accurate aligner for short DNA reads. It is |
| 5492 | optimized for modern read lengths of 100 bases or higher, and takes advantage |
| 5493 | of these reads to align data quickly through a hash-based indexing scheme.") |
| 5494 | ;; 32-bit systems are not supported by the unpatched code. |
| 5495 | ;; Following the bug reports https://github.com/amplab/snap/issues/68 and |
| 5496 | ;; https://bugs.debian.org/cgi-bin/bugreport.cgi?bug=812378 we see that |
| 5497 | ;; systems without a lot of memory cannot make good use of this program. |
| 5498 | (supported-systems '("x86_64-linux")) |
| 5499 | (license license:asl2.0))) |
| 5500 | |
| 5501 | (define-public sortmerna |
| 5502 | (package |
| 5503 | (name "sortmerna") |
| 5504 | (version "2.1b") |
| 5505 | (source |
| 5506 | (origin |
| 5507 | (method url-fetch) |
| 5508 | (uri (string-append |
| 5509 | "https://github.com/biocore/sortmerna/archive/" |
| 5510 | version ".tar.gz")) |
| 5511 | (file-name (string-append name "-" version ".tar.gz")) |
| 5512 | (sha256 |
| 5513 | (base32 |
| 5514 | "1ghaghvd82af9j5adavxh77g7hm247d1r69m3fbi6f1jdivj5ldk")))) |
| 5515 | (build-system gnu-build-system) |
| 5516 | (outputs '("out" ;for binaries |
| 5517 | "db")) ;for sequence databases |
| 5518 | (arguments |
| 5519 | `(#:phases |
| 5520 | (modify-phases %standard-phases |
| 5521 | (replace 'install |
| 5522 | (lambda* (#:key outputs #:allow-other-keys) |
| 5523 | (let* ((out (assoc-ref outputs "out")) |
| 5524 | (bin (string-append out "/bin")) |
| 5525 | (db (assoc-ref outputs "db")) |
| 5526 | (share |
| 5527 | (string-append db "/share/sortmerna/rRNA_databases"))) |
| 5528 | (install-file "sortmerna" bin) |
| 5529 | (install-file "indexdb_rna" bin) |
| 5530 | (for-each (lambda (file) |
| 5531 | (install-file file share)) |
| 5532 | (find-files "rRNA_databases" ".*fasta")) |
| 5533 | #t)))))) |
| 5534 | (inputs |
| 5535 | `(("zlib" ,zlib))) |
| 5536 | (home-page "http://bioinfo.lifl.fr/RNA/sortmerna") |
| 5537 | (synopsis "Biological sequence analysis tool for NGS reads") |
| 5538 | (description |
| 5539 | "SortMeRNA is a biological sequence analysis tool for filtering, mapping |
| 5540 | and operational taxonomic unit (OTU) picking of next generation |
| 5541 | sequencing (NGS) reads. The core algorithm is based on approximate seeds and |
| 5542 | allows for fast and sensitive analyses of nucleotide sequences. The main |
| 5543 | application of SortMeRNA is filtering rRNA from metatranscriptomic data.") |
| 5544 | ;; The source includes x86 specific code |
| 5545 | (supported-systems '("x86_64-linux" "i686-linux")) |
| 5546 | (license license:lgpl3))) |
| 5547 | |
| 5548 | (define-public star |
| 5549 | (package |
| 5550 | (name "star") |
| 5551 | (version "2.5.3a") |
| 5552 | (source (origin |
| 5553 | (method url-fetch) |
| 5554 | (uri (string-append "https://github.com/alexdobin/STAR/archive/" |
| 5555 | version ".tar.gz")) |
| 5556 | (file-name (string-append name "-" version ".tar.gz")) |
| 5557 | (sha256 |
| 5558 | (base32 |
| 5559 | "013wirlz8lllgjyagl48l75n1isxyabqb3sj7qlsl0x1rmvqw99a")) |
| 5560 | (modules '((guix build utils))) |
| 5561 | (snippet |
| 5562 | '(begin |
| 5563 | (substitute* "source/Makefile" |
| 5564 | (("/bin/rm") "rm")) |
| 5565 | ;; Remove pre-built binaries and bundled htslib sources. |
| 5566 | (delete-file-recursively "bin/MacOSX_x86_64") |
| 5567 | (delete-file-recursively "bin/Linux_x86_64") |
| 5568 | (delete-file-recursively "bin/Linux_x86_64_static") |
| 5569 | (delete-file-recursively "source/htslib") |
| 5570 | #t)))) |
| 5571 | (build-system gnu-build-system) |
| 5572 | (arguments |
| 5573 | '(#:tests? #f ;no check target |
| 5574 | #:make-flags '("STAR") |
| 5575 | #:phases |
| 5576 | (modify-phases %standard-phases |
| 5577 | (add-after 'unpack 'enter-source-dir |
| 5578 | (lambda _ (chdir "source") #t)) |
| 5579 | (add-after 'enter-source-dir 'do-not-use-bundled-htslib |
| 5580 | (lambda _ |
| 5581 | (substitute* "Makefile" |
| 5582 | (("(Depend.list: \\$\\(SOURCES\\) parametersDefault\\.xxd) htslib" |
| 5583 | _ prefix) prefix)) |
| 5584 | (substitute* '("BAMfunctions.cpp" |
| 5585 | "signalFromBAM.h" |
| 5586 | "bam_cat.h" |
| 5587 | "bam_cat.c" |
| 5588 | "STAR.cpp" |
| 5589 | "bamRemoveDuplicates.cpp") |
| 5590 | (("#include \"htslib/([^\"]+\\.h)\"" _ header) |
| 5591 | (string-append "#include <" header ">"))) |
| 5592 | (substitute* "IncludeDefine.h" |
| 5593 | (("\"htslib/(htslib/[^\"]+.h)\"" _ header) |
| 5594 | (string-append "<" header ">"))) |
| 5595 | #t)) |
| 5596 | (replace 'install |
| 5597 | (lambda* (#:key outputs #:allow-other-keys) |
| 5598 | (let ((bin (string-append (assoc-ref outputs "out") "/bin/"))) |
| 5599 | (install-file "STAR" bin)) |
| 5600 | #t)) |
| 5601 | (delete 'configure)))) |
| 5602 | (native-inputs |
| 5603 | `(("xxd" ,xxd))) |
| 5604 | (inputs |
| 5605 | `(("htslib" ,htslib) |
| 5606 | ("zlib" ,zlib))) |
| 5607 | (home-page "https://github.com/alexdobin/STAR") |
| 5608 | (synopsis "Universal RNA-seq aligner") |
| 5609 | (description |
| 5610 | "The Spliced Transcripts Alignment to a Reference (STAR) software is |
| 5611 | based on a previously undescribed RNA-seq alignment algorithm that uses |
| 5612 | sequential maximum mappable seed search in uncompressed suffix arrays followed |
| 5613 | by seed clustering and stitching procedure. In addition to unbiased de novo |
| 5614 | detection of canonical junctions, STAR can discover non-canonical splices and |
| 5615 | chimeric (fusion) transcripts, and is also capable of mapping full-length RNA |
| 5616 | sequences.") |
| 5617 | ;; Only 64-bit systems are supported according to the README. |
| 5618 | (supported-systems '("x86_64-linux" "mips64el-linux")) |
| 5619 | ;; STAR is licensed under GPLv3 or later; htslib is MIT-licensed. |
| 5620 | (license license:gpl3+))) |
| 5621 | |
| 5622 | (define-public subread |
| 5623 | (package |
| 5624 | (name "subread") |
| 5625 | (version "1.6.0") |
| 5626 | (source (origin |
| 5627 | (method url-fetch) |
| 5628 | (uri (string-append "mirror://sourceforge/subread/subread-" |
| 5629 | version "/subread-" version "-source.tar.gz")) |
| 5630 | (sha256 |
| 5631 | (base32 |
| 5632 | "0ah0n4jx6ksk2m2j7xk385x2qzmk1y4rfc6a4mfrdqrlq721w99i")))) |
| 5633 | (build-system gnu-build-system) |
| 5634 | (arguments |
| 5635 | `(#:tests? #f ;no "check" target |
| 5636 | ;; The CC and CCFLAGS variables are set to contain a lot of x86_64 |
| 5637 | ;; optimizations by default, so we override these flags such that x86_64 |
| 5638 | ;; flags are only added when the build target is an x86_64 system. |
| 5639 | #:make-flags |
| 5640 | (list (let ((system ,(or (%current-target-system) |
| 5641 | (%current-system))) |
| 5642 | (flags '("-ggdb" "-fomit-frame-pointer" |
| 5643 | "-ffast-math" "-funroll-loops" |
| 5644 | "-fmessage-length=0" |
| 5645 | "-O9" "-Wall" "-DMAKE_FOR_EXON" |
| 5646 | "-DMAKE_STANDALONE" |
| 5647 | "-DSUBREAD_VERSION=\\\"${SUBREAD_VERSION}\\\"")) |
| 5648 | (flags64 '("-mmmx" "-msse" "-msse2" "-msse3"))) |
| 5649 | (if (string-prefix? "x86_64" system) |
| 5650 | (string-append "CCFLAGS=" (string-join (append flags flags64))) |
| 5651 | (string-append "CCFLAGS=" (string-join flags)))) |
| 5652 | "-f" "Makefile.Linux" |
| 5653 | "CC=gcc ${CCFLAGS}") |
| 5654 | #:phases |
| 5655 | (modify-phases %standard-phases |
| 5656 | (add-after 'unpack 'enter-dir |
| 5657 | (lambda _ (chdir "src") #t)) |
| 5658 | (replace 'install |
| 5659 | (lambda* (#:key outputs #:allow-other-keys) |
| 5660 | (let ((bin (string-append (assoc-ref outputs "out") "/bin/"))) |
| 5661 | (mkdir-p bin) |
| 5662 | (copy-recursively "../bin" bin)))) |
| 5663 | ;; no "configure" script |
| 5664 | (delete 'configure)))) |
| 5665 | (inputs `(("zlib" ,zlib))) |
| 5666 | (home-page "http://bioinf.wehi.edu.au/subread-package/") |
| 5667 | (synopsis "Tool kit for processing next-gen sequencing data") |
| 5668 | (description |
| 5669 | "The subread package contains the following tools: subread aligner, a |
| 5670 | general-purpose read aligner; subjunc aligner: detecting exon-exon junctions |
| 5671 | and mapping RNA-seq reads; featureCounts: counting mapped reads for genomic |
| 5672 | features; exactSNP: a SNP caller that discovers SNPs by testing signals |
| 5673 | against local background noises.") |
| 5674 | (license license:gpl3+))) |
| 5675 | |
| 5676 | (define-public stringtie |
| 5677 | (package |
| 5678 | (name "stringtie") |
| 5679 | (version "1.2.1") |
| 5680 | (source (origin |
| 5681 | (method url-fetch) |
| 5682 | (uri (string-append "http://ccb.jhu.edu/software/stringtie/dl/" |
| 5683 | "stringtie-" version ".tar.gz")) |
| 5684 | (sha256 |
| 5685 | (base32 |
| 5686 | "1cqllsc1maq4kh92isi8yadgzbmnf042hlnalpk3y59aph1z3bfz")) |
| 5687 | (modules '((guix build utils))) |
| 5688 | (snippet |
| 5689 | '(begin |
| 5690 | (delete-file-recursively "samtools-0.1.18") |
| 5691 | #t)))) |
| 5692 | (build-system gnu-build-system) |
| 5693 | (arguments |
| 5694 | `(#:tests? #f ;no test suite |
| 5695 | #:phases |
| 5696 | (modify-phases %standard-phases |
| 5697 | ;; no configure script |
| 5698 | (delete 'configure) |
| 5699 | (add-before 'build 'use-system-samtools |
| 5700 | (lambda _ |
| 5701 | (substitute* "Makefile" |
| 5702 | (("stringtie: \\$\\{BAM\\}/libbam\\.a") |
| 5703 | "stringtie: ")) |
| 5704 | (substitute* '("gclib/GBam.h" |
| 5705 | "gclib/GBam.cpp") |
| 5706 | (("#include \"(bam|sam|kstring).h\"" _ header) |
| 5707 | (string-append "#include <samtools/" header ".h>"))) |
| 5708 | #t)) |
| 5709 | (add-after 'unpack 'remove-duplicate-typedef |
| 5710 | (lambda _ |
| 5711 | ;; This typedef conflicts with the typedef in |
| 5712 | ;; glibc-2.25/include/bits/types.h |
| 5713 | (substitute* "gclib/GThreads.h" |
| 5714 | (("typedef long long __intmax_t;") "")) |
| 5715 | #t)) |
| 5716 | (replace 'install |
| 5717 | (lambda* (#:key outputs #:allow-other-keys) |
| 5718 | (let ((bin (string-append (assoc-ref outputs "out") "/bin/"))) |
| 5719 | (install-file "stringtie" bin) |
| 5720 | #t)))))) |
| 5721 | (inputs |
| 5722 | `(("samtools" ,samtools-0.1) |
| 5723 | ("zlib" ,zlib))) |
| 5724 | (home-page "http://ccb.jhu.edu/software/stringtie/") |
| 5725 | (synopsis "Transcript assembly and quantification for RNA-Seq data") |
| 5726 | (description |
| 5727 | "StringTie is a fast and efficient assembler of RNA-Seq sequence |
| 5728 | alignments into potential transcripts. It uses a novel network flow algorithm |
| 5729 | as well as an optional de novo assembly step to assemble and quantitate |
| 5730 | full-length transcripts representing multiple splice variants for each gene |
| 5731 | locus. Its input can include not only the alignments of raw reads used by |
| 5732 | other transcript assemblers, but also alignments of longer sequences that have |
| 5733 | been assembled from those reads. To identify differentially expressed genes |
| 5734 | between experiments, StringTie's output can be processed either by the |
| 5735 | Cuffdiff or Ballgown programs.") |
| 5736 | (license license:artistic2.0))) |
| 5737 | |
| 5738 | (define-public taxtastic |
| 5739 | (package |
| 5740 | (name "taxtastic") |
| 5741 | (version "0.6.4") |
| 5742 | (source (origin |
| 5743 | (method url-fetch) |
| 5744 | (uri (pypi-uri "taxtastic" version)) |
| 5745 | (sha256 |
| 5746 | (base32 |
| 5747 | "0s79z8kfl853x7l4h8ms05k31q87aw62nrchlk20w9n227j35929")))) |
| 5748 | (build-system python-build-system) |
| 5749 | (arguments |
| 5750 | `(#:python ,python-2 |
| 5751 | #:phases |
| 5752 | (modify-phases %standard-phases |
| 5753 | (replace 'check |
| 5754 | (lambda _ |
| 5755 | (zero? (system* "python" "-m" "unittest" "discover" "-v"))))))) |
| 5756 | (propagated-inputs |
| 5757 | `(("python-sqlalchemy" ,python2-sqlalchemy) |
| 5758 | ("python-decorator" ,python2-decorator) |
| 5759 | ("python-biopython" ,python2-biopython) |
| 5760 | ("python-pandas" ,python2-pandas))) |
| 5761 | (home-page "https://github.com/fhcrc/taxtastic") |
| 5762 | (synopsis "Tools for taxonomic naming and annotation") |
| 5763 | (description |
| 5764 | "Taxtastic is software written in python used to build and maintain |
| 5765 | reference packages i.e. collections of reference trees, reference alignments, |
| 5766 | profiles, and associated taxonomic information.") |
| 5767 | (license license:gpl3+))) |
| 5768 | |
| 5769 | (define-public vcftools |
| 5770 | (package |
| 5771 | (name "vcftools") |
| 5772 | (version "0.1.15") |
| 5773 | (source (origin |
| 5774 | (method url-fetch) |
| 5775 | (uri (string-append |
| 5776 | "https://github.com/vcftools/vcftools/releases/download/v" |
| 5777 | version "/vcftools-" version ".tar.gz")) |
| 5778 | (sha256 |
| 5779 | (base32 |
| 5780 | "1qw30c45wihgy632rbz4rh3njnwj4msj46l1rsgdhyg6bgypmr1i")))) |
| 5781 | (build-system gnu-build-system) |
| 5782 | (arguments |
| 5783 | `(#:tests? #f ; no "check" target |
| 5784 | #:make-flags (list |
| 5785 | "CFLAGS=-O2" ; override "-m64" flag |
| 5786 | (string-append "PREFIX=" (assoc-ref %outputs "out")) |
| 5787 | (string-append "MANDIR=" (assoc-ref %outputs "out") |
| 5788 | "/share/man/man1")))) |
| 5789 | (native-inputs |
| 5790 | `(("pkg-config" ,pkg-config))) |
| 5791 | (inputs |
| 5792 | `(("perl" ,perl) |
| 5793 | ("zlib" ,zlib))) |
| 5794 | (home-page "https://vcftools.github.io/") |
| 5795 | (synopsis "Tools for working with VCF files") |
| 5796 | (description |
| 5797 | "VCFtools is a program package designed for working with VCF files, such |
| 5798 | as those generated by the 1000 Genomes Project. The aim of VCFtools is to |
| 5799 | provide easily accessible methods for working with complex genetic variation |
| 5800 | data in the form of VCF files.") |
| 5801 | ;; The license is declared as LGPLv3 in the README and |
| 5802 | ;; at https://vcftools.github.io/license.html |
| 5803 | (license license:lgpl3))) |
| 5804 | |
| 5805 | (define-public infernal |
| 5806 | (package |
| 5807 | (name "infernal") |
| 5808 | (version "1.1.2") |
| 5809 | (source (origin |
| 5810 | (method url-fetch) |
| 5811 | (uri (string-append "http://eddylab.org/software/infernal/" |
| 5812 | "infernal-" version ".tar.gz")) |
| 5813 | (sha256 |
| 5814 | (base32 |
| 5815 | "0sr2hiz3qxfwqpz3whxr6n82p3x27336v3f34iqznp10hks2935c")))) |
| 5816 | (build-system gnu-build-system) |
| 5817 | (native-inputs |
| 5818 | `(("perl" ,perl))) ; for tests |
| 5819 | (home-page "http://eddylab.org/infernal/") |
| 5820 | (synopsis "Inference of RNA alignments") |
| 5821 | (description "Infernal (\"INFERence of RNA ALignment\") is a tool for |
| 5822 | searching DNA sequence databases for RNA structure and sequence similarities. |
| 5823 | It is an implementation of a special case of profile stochastic context-free |
| 5824 | grammars called @dfn{covariance models} (CMs). A CM is like a sequence |
| 5825 | profile, but it scores a combination of sequence consensus and RNA secondary |
| 5826 | structure consensus, so in many cases, it is more capable of identifying RNA |
| 5827 | homologs that conserve their secondary structure more than their primary |
| 5828 | sequence.") |
| 5829 | ;; Infernal 1.1.2 requires VMX or SSE capability for parallel instructions. |
| 5830 | (supported-systems '("i686-linux" "x86_64-linux")) |
| 5831 | (license license:bsd-3))) |
| 5832 | |
| 5833 | (define-public r-centipede |
| 5834 | (package |
| 5835 | (name "r-centipede") |
| 5836 | (version "1.2") |
| 5837 | (source (origin |
| 5838 | (method url-fetch) |
| 5839 | (uri (string-append "http://download.r-forge.r-project.org/" |
| 5840 | "src/contrib/CENTIPEDE_" version ".tar.gz")) |
| 5841 | (sha256 |
| 5842 | (base32 |
| 5843 | "1hsx6qgwr0i67fhy9257zj7s0ppncph2hjgbia5nn6nfmj0ax6l9")))) |
| 5844 | (build-system r-build-system) |
| 5845 | (home-page "http://centipede.uchicago.edu/") |
| 5846 | (synopsis "Predict transcription factor binding sites") |
| 5847 | (description |
| 5848 | "CENTIPEDE applies a hierarchical Bayesian mixture model to infer regions |
| 5849 | of the genome that are bound by particular transcription factors. It starts |
| 5850 | by identifying a set of candidate binding sites, and then aims to classify the |
| 5851 | sites according to whether each site is bound or not bound by a transcription |
| 5852 | factor. CENTIPEDE is an unsupervised learning algorithm that discriminates |
| 5853 | between two different types of motif instances using as much relevant |
| 5854 | information as possible.") |
| 5855 | (license (list license:gpl2+ license:gpl3+)))) |
| 5856 | |
| 5857 | (define-public r-vegan |
| 5858 | (package |
| 5859 | (name "r-vegan") |
| 5860 | (version "2.4-5") |
| 5861 | (source |
| 5862 | (origin |
| 5863 | (method url-fetch) |
| 5864 | (uri (cran-uri "vegan" version)) |
| 5865 | (sha256 |
| 5866 | (base32 |
| 5867 | "0cyyvn3xsjn24w590jn6z4xajafv7yzvj6c51vqi9q6m8v5831ya")))) |
| 5868 | (build-system r-build-system) |
| 5869 | (native-inputs |
| 5870 | `(("gfortran" ,gfortran))) |
| 5871 | (propagated-inputs |
| 5872 | `(("r-cluster" ,r-cluster) |
| 5873 | ("r-lattice" ,r-lattice) |
| 5874 | ("r-mass" ,r-mass) |
| 5875 | ("r-mgcv" ,r-mgcv) |
| 5876 | ("r-permute" ,r-permute))) |
| 5877 | (home-page "https://cran.r-project.org/web/packages/vegan") |
| 5878 | (synopsis "Functions for community ecology") |
| 5879 | (description |
| 5880 | "The vegan package provides tools for descriptive community ecology. It |
| 5881 | has most basic functions of diversity analysis, community ordination and |
| 5882 | dissimilarity analysis. Most of its multivariate tools can be used for other |
| 5883 | data types as well.") |
| 5884 | (license license:gpl2+))) |
| 5885 | |
| 5886 | (define-public r-annotate |
| 5887 | (package |
| 5888 | (name "r-annotate") |
| 5889 | (version "1.56.1") |
| 5890 | (source |
| 5891 | (origin |
| 5892 | (method url-fetch) |
| 5893 | (uri (bioconductor-uri "annotate" version)) |
| 5894 | (sha256 |
| 5895 | (base32 |
| 5896 | "14c5xd9kasvcwg5gbjys2c1vizxhlqlzxakqc2kml0kw97hmx0rq")))) |
| 5897 | (build-system r-build-system) |
| 5898 | (propagated-inputs |
| 5899 | `(("r-annotationdbi" ,r-annotationdbi) |
| 5900 | ("r-biobase" ,r-biobase) |
| 5901 | ("r-biocgenerics" ,r-biocgenerics) |
| 5902 | ("r-dbi" ,r-dbi) |
| 5903 | ("r-rcurl" ,r-rcurl) |
| 5904 | ("r-xml" ,r-xml) |
| 5905 | ("r-xtable" ,r-xtable))) |
| 5906 | (home-page |
| 5907 | "https://bioconductor.org/packages/annotate") |
| 5908 | (synopsis "Annotation for microarrays") |
| 5909 | (description "This package provides R environments for the annotation of |
| 5910 | microarrays.") |
| 5911 | (license license:artistic2.0))) |
| 5912 | |
| 5913 | (define-public r-copynumber |
| 5914 | (package |
| 5915 | (name "r-copynumber") |
| 5916 | (version "1.18.0") |
| 5917 | (source (origin |
| 5918 | (method url-fetch) |
| 5919 | (uri (bioconductor-uri "copynumber" version)) |
| 5920 | (sha256 |
| 5921 | (base32 |
| 5922 | "01kcwzl485yjrkgyg8117b1il957ss0v6rq4bbxf4ksd5fzcjmyx")))) |
| 5923 | (build-system r-build-system) |
| 5924 | (propagated-inputs |
| 5925 | `(("r-s4vectors" ,r-s4vectors) |
| 5926 | ("r-iranges" ,r-iranges) |
| 5927 | ("r-genomicranges" ,r-genomicranges) |
| 5928 | ("r-biocgenerics" ,r-biocgenerics))) |
| 5929 | (home-page "https://bioconductor.org/packages/copynumber") |
| 5930 | (synopsis "Segmentation of single- and multi-track copy number data") |
| 5931 | (description |
| 5932 | "This package segments single- and multi-track copy number data by a |
| 5933 | penalized least squares regression method.") |
| 5934 | (license license:artistic2.0))) |
| 5935 | |
| 5936 | (define-public r-geneplotter |
| 5937 | (package |
| 5938 | (name "r-geneplotter") |
| 5939 | (version "1.56.0") |
| 5940 | (source |
| 5941 | (origin |
| 5942 | (method url-fetch) |
| 5943 | (uri (bioconductor-uri "geneplotter" version)) |
| 5944 | (sha256 |
| 5945 | (base32 |
| 5946 | "1z3g7frc1iviwrsv2dlm4nqvkc0685h4va0388yfxn102ln8wwma")))) |
| 5947 | (build-system r-build-system) |
| 5948 | (propagated-inputs |
| 5949 | `(("r-annotate" ,r-annotate) |
| 5950 | ("r-annotationdbi" ,r-annotationdbi) |
| 5951 | ("r-biobase" ,r-biobase) |
| 5952 | ("r-biocgenerics" ,r-biocgenerics) |
| 5953 | ("r-lattice" ,r-lattice) |
| 5954 | ("r-rcolorbrewer" ,r-rcolorbrewer))) |
| 5955 | (home-page "https://bioconductor.org/packages/geneplotter") |
| 5956 | (synopsis "Graphics functions for genomic data") |
| 5957 | (description |
| 5958 | "This package provides functions for plotting genomic data.") |
| 5959 | (license license:artistic2.0))) |
| 5960 | |
| 5961 | (define-public r-genefilter |
| 5962 | (package |
| 5963 | (name "r-genefilter") |
| 5964 | (version "1.60.0") |
| 5965 | (source |
| 5966 | (origin |
| 5967 | (method url-fetch) |
| 5968 | (uri (bioconductor-uri "genefilter" version)) |
| 5969 | (sha256 |
| 5970 | (base32 |
| 5971 | "173swlg6gj4kdllbqvyiw5dggbcxiwlwpqmllsv4dxzn7h25i3g7")))) |
| 5972 | (build-system r-build-system) |
| 5973 | (native-inputs |
| 5974 | `(("gfortran" ,gfortran))) |
| 5975 | (propagated-inputs |
| 5976 | `(("r-annotate" ,r-annotate) |
| 5977 | ("r-annotationdbi" ,r-annotationdbi) |
| 5978 | ("r-biobase" ,r-biobase) |
| 5979 | ("r-s4vectors" ,r-s4vectors) |
| 5980 | ("r-survival" ,r-survival))) |
| 5981 | (home-page "https://bioconductor.org/packages/genefilter") |
| 5982 | (synopsis "Filter genes from high-throughput experiments") |
| 5983 | (description |
| 5984 | "This package provides basic functions for filtering genes from |
| 5985 | high-throughput sequencing experiments.") |
| 5986 | (license license:artistic2.0))) |
| 5987 | |
| 5988 | (define-public r-deseq2 |
| 5989 | (package |
| 5990 | (name "r-deseq2") |
| 5991 | (version "1.18.1") |
| 5992 | (source |
| 5993 | (origin |
| 5994 | (method url-fetch) |
| 5995 | (uri (bioconductor-uri "DESeq2" version)) |
| 5996 | (sha256 |
| 5997 | (base32 |
| 5998 | "1iyimg1s0x5pdmvl8x08s8h0v019y0nhjzs50chagbpk2x91fsmv")))) |
| 5999 | (properties `((upstream-name . "DESeq2"))) |
| 6000 | (build-system r-build-system) |
| 6001 | (propagated-inputs |
| 6002 | `(("r-biobase" ,r-biobase) |
| 6003 | ("r-biocgenerics" ,r-biocgenerics) |
| 6004 | ("r-biocparallel" ,r-biocparallel) |
| 6005 | ("r-genefilter" ,r-genefilter) |
| 6006 | ("r-geneplotter" ,r-geneplotter) |
| 6007 | ("r-genomicranges" ,r-genomicranges) |
| 6008 | ("r-ggplot2" ,r-ggplot2) |
| 6009 | ("r-hmisc" ,r-hmisc) |
| 6010 | ("r-iranges" ,r-iranges) |
| 6011 | ("r-locfit" ,r-locfit) |
| 6012 | ("r-rcpp" ,r-rcpp) |
| 6013 | ("r-rcpparmadillo" ,r-rcpparmadillo) |
| 6014 | ("r-s4vectors" ,r-s4vectors) |
| 6015 | ("r-summarizedexperiment" ,r-summarizedexperiment))) |
| 6016 | (home-page "https://bioconductor.org/packages/DESeq2") |
| 6017 | (synopsis "Differential gene expression analysis") |
| 6018 | (description |
| 6019 | "This package provides functions to estimate variance-mean dependence in |
| 6020 | count data from high-throughput nucleotide sequencing assays and test for |
| 6021 | differential expression based on a model using the negative binomial |
| 6022 | distribution.") |
| 6023 | (license license:lgpl3+))) |
| 6024 | |
| 6025 | (define-public r-dexseq |
| 6026 | (package |
| 6027 | (name "r-dexseq") |
| 6028 | (version "1.24.2") |
| 6029 | (source |
| 6030 | (origin |
| 6031 | (method url-fetch) |
| 6032 | (uri (bioconductor-uri "DEXSeq" version)) |
| 6033 | (sha256 |
| 6034 | (base32 |
| 6035 | "18nh8ynxirfwkmc4sawdxgl7w1sl9ny5zpv8zbhv9vi5vgb8pxmj")))) |
| 6036 | (properties `((upstream-name . "DEXSeq"))) |
| 6037 | (build-system r-build-system) |
| 6038 | (propagated-inputs |
| 6039 | `(("r-annotationdbi" ,r-annotationdbi) |
| 6040 | ("r-biobase" ,r-biobase) |
| 6041 | ("r-biocgenerics" ,r-biocgenerics) |
| 6042 | ("r-biocparallel" ,r-biocparallel) |
| 6043 | ("r-biomart" ,r-biomart) |
| 6044 | ("r-deseq2" ,r-deseq2) |
| 6045 | ("r-genefilter" ,r-genefilter) |
| 6046 | ("r-geneplotter" ,r-geneplotter) |
| 6047 | ("r-genomicranges" ,r-genomicranges) |
| 6048 | ("r-hwriter" ,r-hwriter) |
| 6049 | ("r-iranges" ,r-iranges) |
| 6050 | ("r-rcolorbrewer" ,r-rcolorbrewer) |
| 6051 | ("r-rsamtools" ,r-rsamtools) |
| 6052 | ("r-s4vectors" ,r-s4vectors) |
| 6053 | ("r-statmod" ,r-statmod) |
| 6054 | ("r-stringr" ,r-stringr) |
| 6055 | ("r-summarizedexperiment" ,r-summarizedexperiment))) |
| 6056 | (home-page "https://bioconductor.org/packages/DEXSeq") |
| 6057 | (synopsis "Inference of differential exon usage in RNA-Seq") |
| 6058 | (description |
| 6059 | "This package is focused on finding differential exon usage using RNA-seq |
| 6060 | exon counts between samples with different experimental designs. It provides |
| 6061 | functions that allows the user to make the necessary statistical tests based |
| 6062 | on a model that uses the negative binomial distribution to estimate the |
| 6063 | variance between biological replicates and generalized linear models for |
| 6064 | testing. The package also provides functions for the visualization and |
| 6065 | exploration of the results.") |
| 6066 | (license license:gpl3+))) |
| 6067 | |
| 6068 | (define-public r-annotationforge |
| 6069 | (package |
| 6070 | (name "r-annotationforge") |
| 6071 | (version "1.20.0") |
| 6072 | (source |
| 6073 | (origin |
| 6074 | (method url-fetch) |
| 6075 | (uri (bioconductor-uri "AnnotationForge" version)) |
| 6076 | (sha256 |
| 6077 | (base32 |
| 6078 | "01vbrf76vqfvxh6vpfxkjwccxggnha3byqzj333glqz2b6kwx5q1")))) |
| 6079 | (properties |
| 6080 | `((upstream-name . "AnnotationForge"))) |
| 6081 | (build-system r-build-system) |
| 6082 | (propagated-inputs |
| 6083 | `(("r-annotationdbi" ,r-annotationdbi) |
| 6084 | ("r-biobase" ,r-biobase) |
| 6085 | ("r-biocgenerics" ,r-biocgenerics) |
| 6086 | ("r-dbi" ,r-dbi) |
| 6087 | ("r-rcurl" ,r-rcurl) |
| 6088 | ("r-rsqlite" ,r-rsqlite) |
| 6089 | ("r-s4vectors" ,r-s4vectors) |
| 6090 | ("r-xml" ,r-xml))) |
| 6091 | (home-page "https://bioconductor.org/packages/AnnotationForge") |
| 6092 | (synopsis "Code for building annotation database packages") |
| 6093 | (description |
| 6094 | "This package provides code for generating Annotation packages and their |
| 6095 | databases. Packages produced are intended to be used with AnnotationDbi.") |
| 6096 | (license license:artistic2.0))) |
| 6097 | |
| 6098 | (define-public r-rbgl |
| 6099 | (package |
| 6100 | (name "r-rbgl") |
| 6101 | (version "1.54.0") |
| 6102 | (source |
| 6103 | (origin |
| 6104 | (method url-fetch) |
| 6105 | (uri (bioconductor-uri "RBGL" version)) |
| 6106 | (sha256 |
| 6107 | (base32 |
| 6108 | "18jad23i3899ypv4bg3l47cvvs3qnj1pqis2p9x0135yv5y6wnv7")))) |
| 6109 | (properties `((upstream-name . "RBGL"))) |
| 6110 | (build-system r-build-system) |
| 6111 | (propagated-inputs `(("r-graph" ,r-graph))) |
| 6112 | (home-page "https://www.bioconductor.org/packages/RBGL") |
| 6113 | (synopsis "Interface to the Boost graph library") |
| 6114 | (description |
| 6115 | "This package provides a fairly extensive and comprehensive interface to |
| 6116 | the graph algorithms contained in the Boost library.") |
| 6117 | (license license:artistic2.0))) |
| 6118 | |
| 6119 | (define-public r-gseabase |
| 6120 | (package |
| 6121 | (name "r-gseabase") |
| 6122 | (version "1.40.1") |
| 6123 | (source |
| 6124 | (origin |
| 6125 | (method url-fetch) |
| 6126 | (uri (bioconductor-uri "GSEABase" version)) |
| 6127 | (sha256 |
| 6128 | (base32 |
| 6129 | "10cmjxahg2plwacfan6g0k8cwyzya96ypc7m1r79gwqkyykxw5fz")))) |
| 6130 | (properties `((upstream-name . "GSEABase"))) |
| 6131 | (build-system r-build-system) |
| 6132 | (propagated-inputs |
| 6133 | `(("r-annotate" ,r-annotate) |
| 6134 | ("r-annotationdbi" ,r-annotationdbi) |
| 6135 | ("r-biobase" ,r-biobase) |
| 6136 | ("r-biocgenerics" ,r-biocgenerics) |
| 6137 | ("r-graph" ,r-graph) |
| 6138 | ("r-xml" ,r-xml))) |
| 6139 | (home-page "https://bioconductor.org/packages/GSEABase") |
| 6140 | (synopsis "Gene set enrichment data structures and methods") |
| 6141 | (description |
| 6142 | "This package provides classes and methods to support @dfn{Gene Set |
| 6143 | Enrichment Analysis} (GSEA).") |
| 6144 | (license license:artistic2.0))) |
| 6145 | |
| 6146 | (define-public r-category |
| 6147 | (package |
| 6148 | (name "r-category") |
| 6149 | (version "2.44.0") |
| 6150 | (source |
| 6151 | (origin |
| 6152 | (method url-fetch) |
| 6153 | (uri (bioconductor-uri "Category" version)) |
| 6154 | (sha256 |
| 6155 | (base32 |
| 6156 | "0mkav04vbla0xfa0dssxdd0rjs589sxi83xklf5iq5hj3dm8y0i8")))) |
| 6157 | (properties `((upstream-name . "Category"))) |
| 6158 | (build-system r-build-system) |
| 6159 | (propagated-inputs |
| 6160 | `(("r-annotate" ,r-annotate) |
| 6161 | ("r-annotationdbi" ,r-annotationdbi) |
| 6162 | ("r-biobase" ,r-biobase) |
| 6163 | ("r-biocgenerics" ,r-biocgenerics) |
| 6164 | ("r-genefilter" ,r-genefilter) |
| 6165 | ("r-graph" ,r-graph) |
| 6166 | ("r-gseabase" ,r-gseabase) |
| 6167 | ("r-matrix" ,r-matrix) |
| 6168 | ("r-rbgl" ,r-rbgl) |
| 6169 | ("r-dbi" ,r-dbi))) |
| 6170 | (home-page "https://bioconductor.org/packages/Category") |
| 6171 | (synopsis "Category analysis") |
| 6172 | (description |
| 6173 | "This package provides a collection of tools for performing category |
| 6174 | analysis.") |
| 6175 | (license license:artistic2.0))) |
| 6176 | |
| 6177 | (define-public r-gostats |
| 6178 | (package |
| 6179 | (name "r-gostats") |
| 6180 | (version "2.44.0") |
| 6181 | (source |
| 6182 | (origin |
| 6183 | (method url-fetch) |
| 6184 | (uri (bioconductor-uri "GOstats" version)) |
| 6185 | (sha256 |
| 6186 | (base32 |
| 6187 | "04gqfdlx9fxf97qf0l28x4aaqvl10n6v58qiz5fiaw05sbj1pf1i")))) |
| 6188 | (properties `((upstream-name . "GOstats"))) |
| 6189 | (build-system r-build-system) |
| 6190 | (propagated-inputs |
| 6191 | `(("r-annotate" ,r-annotate) |
| 6192 | ("r-annotationdbi" ,r-annotationdbi) |
| 6193 | ("r-annotationforge" ,r-annotationforge) |
| 6194 | ("r-biobase" ,r-biobase) |
| 6195 | ("r-category" ,r-category) |
| 6196 | ("r-go-db" ,r-go-db) |
| 6197 | ("r-graph" ,r-graph) |
| 6198 | ("r-rgraphviz" ,r-rgraphviz) |
| 6199 | ("r-rbgl" ,r-rbgl))) |
| 6200 | (home-page "https://bioconductor.org/packages/GOstats") |
| 6201 | (synopsis "Tools for manipulating GO and microarrays") |
| 6202 | (description |
| 6203 | "This package provides a set of tools for interacting with GO and |
| 6204 | microarray data. A variety of basic manipulation tools for graphs, hypothesis |
| 6205 | testing and other simple calculations.") |
| 6206 | (license license:artistic2.0))) |
| 6207 | |
| 6208 | (define-public r-shortread |
| 6209 | (package |
| 6210 | (name "r-shortread") |
| 6211 | (version "1.36.0") |
| 6212 | (source |
| 6213 | (origin |
| 6214 | (method url-fetch) |
| 6215 | (uri (bioconductor-uri "ShortRead" version)) |
| 6216 | (sha256 |
| 6217 | (base32 |
| 6218 | "06mknlsmd4hnaxzdjapgvp2kgdnf9w103y500dsac5jgsz4vwzcz")))) |
| 6219 | (properties `((upstream-name . "ShortRead"))) |
| 6220 | (build-system r-build-system) |
| 6221 | (inputs |
| 6222 | `(("zlib" ,zlib))) |
| 6223 | (propagated-inputs |
| 6224 | `(("r-biobase" ,r-biobase) |
| 6225 | ("r-biocgenerics" ,r-biocgenerics) |
| 6226 | ("r-biocparallel" ,r-biocparallel) |
| 6227 | ("r-biostrings" ,r-biostrings) |
| 6228 | ("r-genomeinfodb" ,r-genomeinfodb) |
| 6229 | ("r-genomicalignments" ,r-genomicalignments) |
| 6230 | ("r-genomicranges" ,r-genomicranges) |
| 6231 | ("r-hwriter" ,r-hwriter) |
| 6232 | ("r-iranges" ,r-iranges) |
| 6233 | ("r-lattice" ,r-lattice) |
| 6234 | ("r-latticeextra" ,r-latticeextra) |
| 6235 | ("r-rsamtools" ,r-rsamtools) |
| 6236 | ("r-s4vectors" ,r-s4vectors) |
| 6237 | ("r-xvector" ,r-xvector) |
| 6238 | ("r-zlibbioc" ,r-zlibbioc))) |
| 6239 | (home-page "https://bioconductor.org/packages/ShortRead") |
| 6240 | (synopsis "FASTQ input and manipulation tools") |
| 6241 | (description |
| 6242 | "This package implements sampling, iteration, and input of FASTQ files. |
| 6243 | It includes functions for filtering and trimming reads, and for generating a |
| 6244 | quality assessment report. Data are represented as |
| 6245 | @code{DNAStringSet}-derived objects, and easily manipulated for a diversity of |
| 6246 | purposes. The package also contains legacy support for early single-end, |
| 6247 | ungapped alignment formats.") |
| 6248 | (license license:artistic2.0))) |
| 6249 | |
| 6250 | (define-public r-systempiper |
| 6251 | (package |
| 6252 | (name "r-systempiper") |
| 6253 | (version "1.12.0") |
| 6254 | (source |
| 6255 | (origin |
| 6256 | (method url-fetch) |
| 6257 | (uri (bioconductor-uri "systemPipeR" version)) |
| 6258 | (sha256 |
| 6259 | (base32 |
| 6260 | "11mj8pjq5vj25768vmagpzv74fvi3p3kdk5zdlznqyiaggri04cv")))) |
| 6261 | (properties `((upstream-name . "systemPipeR"))) |
| 6262 | (build-system r-build-system) |
| 6263 | (propagated-inputs |
| 6264 | `(("r-annotate" ,r-annotate) |
| 6265 | ("r-batchjobs" ,r-batchjobs) |
| 6266 | ("r-biocgenerics" ,r-biocgenerics) |
| 6267 | ("r-biostrings" ,r-biostrings) |
| 6268 | ("r-deseq2" ,r-deseq2) |
| 6269 | ("r-edger" ,r-edger) |
| 6270 | ("r-genomicfeatures" ,r-genomicfeatures) |
| 6271 | ("r-genomicranges" ,r-genomicranges) |
| 6272 | ("r-ggplot2" ,r-ggplot2) |
| 6273 | ("r-go-db" ,r-go-db) |
| 6274 | ("r-gostats" ,r-gostats) |
| 6275 | ("r-limma" ,r-limma) |
| 6276 | ("r-pheatmap" ,r-pheatmap) |
| 6277 | ("r-rjson" ,r-rjson) |
| 6278 | ("r-rsamtools" ,r-rsamtools) |
| 6279 | ("r-shortread" ,r-shortread) |
| 6280 | ("r-summarizedexperiment" ,r-summarizedexperiment) |
| 6281 | ("r-variantannotation" ,r-variantannotation))) |
| 6282 | (home-page "https://github.com/tgirke/systemPipeR") |
| 6283 | (synopsis "Next generation sequencing workflow and reporting environment") |
| 6284 | (description |
| 6285 | "This R package provides tools for building and running automated |
| 6286 | end-to-end analysis workflows for a wide range of @dfn{next generation |
| 6287 | sequence} (NGS) applications such as RNA-Seq, ChIP-Seq, VAR-Seq and Ribo-Seq. |
| 6288 | Important features include a uniform workflow interface across different NGS |
| 6289 | applications, automated report generation, and support for running both R and |
| 6290 | command-line software, such as NGS aligners or peak/variant callers, on local |
| 6291 | computers or compute clusters. Efficient handling of complex sample sets and |
| 6292 | experimental designs is facilitated by a consistently implemented sample |
| 6293 | annotation infrastructure.") |
| 6294 | (license license:artistic2.0))) |
| 6295 | |
| 6296 | (define-public r-grohmm |
| 6297 | (package |
| 6298 | (name "r-grohmm") |
| 6299 | (version "1.12.0") |
| 6300 | (source |
| 6301 | (origin |
| 6302 | (method url-fetch) |
| 6303 | (uri (bioconductor-uri "groHMM" version)) |
| 6304 | (sha256 |
| 6305 | (base32 |
| 6306 | "0cjkj0ypyc4dfi9s8dh88kh6q4xlpnc0wal7njg4b4gqj0l2hva7")))) |
| 6307 | (properties `((upstream-name . "groHMM"))) |
| 6308 | (build-system r-build-system) |
| 6309 | (propagated-inputs |
| 6310 | `(("r-genomeinfodb" ,r-genomeinfodb) |
| 6311 | ("r-genomicalignments" ,r-genomicalignments) |
| 6312 | ("r-genomicranges" ,r-genomicranges) |
| 6313 | ("r-iranges" ,r-iranges) |
| 6314 | ("r-mass" ,r-mass) |
| 6315 | ("r-rtracklayer" ,r-rtracklayer) |
| 6316 | ("r-s4vectors" ,r-s4vectors))) |
| 6317 | (home-page "https://github.com/Kraus-Lab/groHMM") |
| 6318 | (synopsis "GRO-seq analysis pipeline") |
| 6319 | (description |
| 6320 | "This package provides a pipeline for the analysis of GRO-seq data.") |
| 6321 | (license license:gpl3+))) |
| 6322 | |
| 6323 | (define-public r-txdb-hsapiens-ucsc-hg19-knowngene |
| 6324 | (package |
| 6325 | (name "r-txdb-hsapiens-ucsc-hg19-knowngene") |
| 6326 | (version "3.2.2") |
| 6327 | (source (origin |
| 6328 | (method url-fetch) |
| 6329 | ;; We cannot use bioconductor-uri here because this tarball is |
| 6330 | ;; located under "data/annotation/" instead of "bioc/". |
| 6331 | (uri (string-append "https://bioconductor.org/packages/" |
| 6332 | "release/data/annotation/src/contrib" |
| 6333 | "/TxDb.Hsapiens.UCSC.hg19.knownGene_" |
| 6334 | version ".tar.gz")) |
| 6335 | (sha256 |
| 6336 | (base32 |
| 6337 | "1sajhcqqwazgz2lqbik7rd935i7kpnh08zxbp2ra10j72yqy4g86")))) |
| 6338 | (properties |
| 6339 | `((upstream-name . "TxDb.Hsapiens.UCSC.hg19.knownGene"))) |
| 6340 | (build-system r-build-system) |
| 6341 | ;; As this package provides little more than a very large data file it |
| 6342 | ;; doesn't make sense to build substitutes. |
| 6343 | (arguments `(#:substitutable? #f)) |
| 6344 | (propagated-inputs |
| 6345 | `(("r-genomicfeatures" ,r-genomicfeatures))) |
| 6346 | (home-page |
| 6347 | "https://bioconductor.org/packages/TxDb.Hsapiens.UCSC.hg19.knownGene/") |
| 6348 | (synopsis "Annotation package for human genome in TxDb format") |
| 6349 | (description |
| 6350 | "This package provides an annotation database of Homo sapiens genome |
| 6351 | data. It is derived from the UCSC hg19 genome and based on the \"knownGene\" |
| 6352 | track. The database is exposed as a @code{TxDb} object.") |
| 6353 | (license license:artistic2.0))) |
| 6354 | |
| 6355 | (define-public r-sparql |
| 6356 | (package |
| 6357 | (name "r-sparql") |
| 6358 | (version "1.16") |
| 6359 | (source (origin |
| 6360 | (method url-fetch) |
| 6361 | (uri (cran-uri "SPARQL" version)) |
| 6362 | (sha256 |
| 6363 | (base32 |
| 6364 | "0gak1q06yyhdmcxb2n3v0h9gr1vqd0viqji52wpw211qp6r6dcrc")))) |
| 6365 | (properties `((upstream-name . "SPARQL"))) |
| 6366 | (build-system r-build-system) |
| 6367 | (propagated-inputs |
| 6368 | `(("r-rcurl" ,r-rcurl) |
| 6369 | ("r-xml" ,r-xml))) |
| 6370 | (home-page "https://cran.r-project.org/web/packages/SPARQL") |
| 6371 | (synopsis "SPARQL client for R") |
| 6372 | (description "This package provides an interface to use SPARQL to pose |
| 6373 | SELECT or UPDATE queries to an end-point.") |
| 6374 | ;; The only license indication is found in the DESCRIPTION file, |
| 6375 | ;; which states GPL-3. So we cannot assume GPLv3+. |
| 6376 | (license license:gpl3))) |
| 6377 | |
| 6378 | (define-public vsearch |
| 6379 | (package |
| 6380 | (name "vsearch") |
| 6381 | (version "2.6.2") |
| 6382 | (source |
| 6383 | (origin |
| 6384 | (method url-fetch) |
| 6385 | (uri (string-append |
| 6386 | "https://github.com/torognes/vsearch/archive/v" |
| 6387 | version ".tar.gz")) |
| 6388 | (file-name (string-append name "-" version ".tar.gz")) |
| 6389 | (sha256 |
| 6390 | (base32 |
| 6391 | "02khrgh8hm11cgww2f9mqc6886zqli9ss4pd4kfpqzd0d31vbzv5")) |
| 6392 | (patches (search-patches "vsearch-unbundle-cityhash.patch")) |
| 6393 | (snippet |
| 6394 | '(begin |
| 6395 | ;; Remove bundled cityhash sources. The vsearch source is adjusted |
| 6396 | ;; for this in the patch. |
| 6397 | (delete-file "src/city.h") |
| 6398 | (delete-file "src/citycrc.h") |
| 6399 | (delete-file "src/city.cc") |
| 6400 | #t)))) |
| 6401 | (build-system gnu-build-system) |
| 6402 | (arguments |
| 6403 | `(#:phases |
| 6404 | (modify-phases %standard-phases |
| 6405 | (add-after 'unpack 'autogen |
| 6406 | (lambda _ (zero? (system* "autoreconf" "-vif"))))))) |
| 6407 | (inputs |
| 6408 | `(("zlib" ,zlib) |
| 6409 | ("bzip2" ,bzip2) |
| 6410 | ("cityhash" ,cityhash))) |
| 6411 | (native-inputs |
| 6412 | `(("autoconf" ,autoconf) |
| 6413 | ("automake" ,automake))) |
| 6414 | (synopsis "Sequence search tools for metagenomics") |
| 6415 | (description |
| 6416 | "VSEARCH supports DNA sequence searching, clustering, chimera detection, |
| 6417 | dereplication, pairwise alignment, shuffling, subsampling, sorting and |
| 6418 | masking. The tool takes advantage of parallelism in the form of SIMD |
| 6419 | vectorization as well as multiple threads to perform accurate alignments at |
| 6420 | high speed. VSEARCH uses an optimal global aligner (full dynamic programming |
| 6421 | Needleman-Wunsch).") |
| 6422 | (home-page "https://github.com/torognes/vsearch") |
| 6423 | ;; vsearch uses non-portable SSE intrinsics so building fails on other |
| 6424 | ;; platforms. |
| 6425 | (supported-systems '("x86_64-linux")) |
| 6426 | ;; Dual licensed; also includes public domain source. |
| 6427 | (license (list license:gpl3 license:bsd-2)))) |
| 6428 | |
| 6429 | (define-public pardre |
| 6430 | (package |
| 6431 | (name "pardre") |
| 6432 | ;; The source of 1.1.5 changed in place, so we append "-1" to the version. |
| 6433 | (version "1.1.5-1") |
| 6434 | (source |
| 6435 | (origin |
| 6436 | (method url-fetch) |
| 6437 | (uri (string-append "mirror://sourceforge/pardre/ParDRe-rel" |
| 6438 | "1.1.5" ".tar.gz")) |
| 6439 | (sha256 |
| 6440 | (base32 |
| 6441 | "17j73nc0viq4f6qj50nrndsrif5d6b71q8fl87m54psiv0ilns2b")))) |
| 6442 | (build-system gnu-build-system) |
| 6443 | (arguments |
| 6444 | `(#:tests? #f ; no tests included |
| 6445 | #:phases |
| 6446 | (modify-phases %standard-phases |
| 6447 | (delete 'configure) |
| 6448 | (replace 'install |
| 6449 | (lambda* (#:key outputs #:allow-other-keys) |
| 6450 | (let ((bin (string-append (assoc-ref outputs "out") "/bin"))) |
| 6451 | (install-file "ParDRe" bin) |
| 6452 | #t)))))) |
| 6453 | (inputs |
| 6454 | `(("openmpi" ,openmpi) |
| 6455 | ("zlib" ,zlib))) |
| 6456 | (synopsis "Parallel tool to remove duplicate DNA reads") |
| 6457 | (description |
| 6458 | "ParDRe is a parallel tool to remove duplicate genetic sequence reads. |
| 6459 | Duplicate reads can be seen as identical or nearly identical sequences with |
| 6460 | some mismatches. This tool lets users avoid the analysis of unnecessary |
| 6461 | reads, reducing the time of subsequent procedures with the |
| 6462 | dataset (e.g. assemblies, mappings, etc.). The tool is implemented with MPI |
| 6463 | in order to exploit the parallel capabilities of multicore clusters. It is |
| 6464 | faster than multithreaded counterparts (end of 2015) for the same number of |
| 6465 | cores and, thanks to the message-passing technology, it can be executed on |
| 6466 | clusters.") |
| 6467 | (home-page "https://sourceforge.net/projects/pardre/") |
| 6468 | (license license:gpl3+))) |
| 6469 | |
| 6470 | (define-public ruby-bio-kseq |
| 6471 | (package |
| 6472 | (name "ruby-bio-kseq") |
| 6473 | (version "0.0.2") |
| 6474 | (source |
| 6475 | (origin |
| 6476 | (method url-fetch) |
| 6477 | (uri (rubygems-uri "bio-kseq" version)) |
| 6478 | (sha256 |
| 6479 | (base32 |
| 6480 | "1xyaha46khb5jc6wzkbf7040jagac49jbimn0vcrzid0j8jdikrz")))) |
| 6481 | (build-system ruby-build-system) |
| 6482 | (arguments |
| 6483 | `(#:test-target "spec")) |
| 6484 | (native-inputs |
| 6485 | `(("bundler" ,bundler) |
| 6486 | ("ruby-rspec" ,ruby-rspec) |
| 6487 | ("ruby-rake-compiler" ,ruby-rake-compiler))) |
| 6488 | (inputs |
| 6489 | `(("zlib" ,zlib))) |
| 6490 | (synopsis "Ruby bindings for the kseq.h FASTA/Q parser") |
| 6491 | (description |
| 6492 | "@code{Bio::Kseq} provides ruby bindings to the @code{kseq.h} FASTA and |
| 6493 | FASTQ parsing code. It provides a fast iterator over sequences and their |
| 6494 | quality scores.") |
| 6495 | (home-page "https://github.com/gusevfe/bio-kseq") |
| 6496 | (license license:expat))) |
| 6497 | |
| 6498 | (define-public bio-locus |
| 6499 | (package |
| 6500 | (name "bio-locus") |
| 6501 | (version "0.0.7") |
| 6502 | (source |
| 6503 | (origin |
| 6504 | (method url-fetch) |
| 6505 | (uri (rubygems-uri "bio-locus" version)) |
| 6506 | (sha256 |
| 6507 | (base32 |
| 6508 | "02vmrxyimkj9sahsp4zhfhnmbvz6dbbqz1y01vglf8cbwvkajfl0")))) |
| 6509 | (build-system ruby-build-system) |
| 6510 | (native-inputs |
| 6511 | `(("ruby-rspec" ,ruby-rspec))) |
| 6512 | (synopsis "Tool for fast querying of genome locations") |
| 6513 | (description |
| 6514 | "Bio-locus is a tabix-like tool for fast querying of genome |
| 6515 | locations. Many file formats in bioinformatics contain records that |
| 6516 | start with a chromosome name and a position for a SNP, or a start-end |
| 6517 | position for indels. Bio-locus allows users to store this chr+pos or |
| 6518 | chr+pos+alt information in a database.") |
| 6519 | (home-page "https://github.com/pjotrp/bio-locus") |
| 6520 | (license license:expat))) |
| 6521 | |
| 6522 | (define-public bio-blastxmlparser |
| 6523 | (package |
| 6524 | (name "bio-blastxmlparser") |
| 6525 | (version "2.0.4") |
| 6526 | (source (origin |
| 6527 | (method url-fetch) |
| 6528 | (uri (rubygems-uri "bio-blastxmlparser" version)) |
| 6529 | (sha256 |
| 6530 | (base32 |
| 6531 | "1wf4qygcmdjgcqm6flmvsagfr1gs9lf63mj32qv3z1f481zc5692")))) |
| 6532 | (build-system ruby-build-system) |
| 6533 | (propagated-inputs |
| 6534 | `(("ruby-bio-logger" ,ruby-bio-logger) |
| 6535 | ("ruby-nokogiri" ,ruby-nokogiri))) |
| 6536 | (inputs |
| 6537 | `(("ruby-rspec" ,ruby-rspec))) |
| 6538 | (synopsis "Fast big data BLAST XML parser and library") |
| 6539 | (description |
| 6540 | "Very fast parallel big-data BLAST XML file parser which can be used as |
| 6541 | command line utility. Use blastxmlparser to: Parse BLAST XML; filter output; |
| 6542 | generate FASTA, JSON, YAML, RDF, JSON-LD, HTML, CSV, tabular output etc.") |
| 6543 | (home-page "https://github.com/pjotrp/blastxmlparser") |
| 6544 | (license license:expat))) |
| 6545 | |
| 6546 | (define-public bioruby |
| 6547 | (package |
| 6548 | (name "bioruby") |
| 6549 | (version "1.5.1") |
| 6550 | (source |
| 6551 | (origin |
| 6552 | (method url-fetch) |
| 6553 | (uri (rubygems-uri "bio" version)) |
| 6554 | (sha256 |
| 6555 | (base32 |
| 6556 | "0hdl0789c9n4mprnx5pgd46bfwl8d000rqpamj5h6kkjgspijv49")))) |
| 6557 | (build-system ruby-build-system) |
| 6558 | (propagated-inputs |
| 6559 | `(("ruby-libxml" ,ruby-libxml))) |
| 6560 | (native-inputs |
| 6561 | `(("which" ,which))) ; required for test phase |
| 6562 | (arguments |
| 6563 | `(#:phases |
| 6564 | (modify-phases %standard-phases |
| 6565 | (add-before 'build 'patch-test-command |
| 6566 | (lambda _ |
| 6567 | (substitute* '("test/functional/bio/test_command.rb") |
| 6568 | (("/bin/sh") (which "sh"))) |
| 6569 | (substitute* '("test/functional/bio/test_command.rb") |
| 6570 | (("/bin/ls") (which "ls"))) |
| 6571 | (substitute* '("test/functional/bio/test_command.rb") |
| 6572 | (("which") (which "which"))) |
| 6573 | (substitute* '("test/functional/bio/test_command.rb", |
| 6574 | "test/data/command/echoarg2.sh") |
| 6575 | (("/bin/echo") (which "echo"))) |
| 6576 | #t))))) |
| 6577 | (synopsis "Ruby library, shell and utilities for bioinformatics") |
| 6578 | (description "BioRuby comes with a comprehensive set of Ruby development |
| 6579 | tools and libraries for bioinformatics and molecular biology. BioRuby has |
| 6580 | components for sequence analysis, pathway analysis, protein modelling and |
| 6581 | phylogenetic analysis; it supports many widely used data formats and provides |
| 6582 | easy access to databases, external programs and public web services, including |
| 6583 | BLAST, KEGG, GenBank, MEDLINE and GO.") |
| 6584 | (home-page "http://bioruby.org/") |
| 6585 | ;; Code is released under Ruby license, except for setup |
| 6586 | ;; (LGPLv2.1+) and scripts in samples (which have GPL2 and GPL2+) |
| 6587 | (license (list license:ruby license:lgpl2.1+ license:gpl2+ )))) |
| 6588 | |
| 6589 | (define-public r-acsnminer |
| 6590 | (package |
| 6591 | (name "r-acsnminer") |
| 6592 | (version "0.16.8.25") |
| 6593 | (source (origin |
| 6594 | (method url-fetch) |
| 6595 | (uri (cran-uri "ACSNMineR" version)) |
| 6596 | (sha256 |
| 6597 | (base32 |
| 6598 | "0gh604s8qall6zfjlwcg2ilxjvz08dplf9k5g47idhv43scm748l")))) |
| 6599 | (properties `((upstream-name . "ACSNMineR"))) |
| 6600 | (build-system r-build-system) |
| 6601 | (propagated-inputs |
| 6602 | `(("r-ggplot2" ,r-ggplot2) |
| 6603 | ("r-gridextra" ,r-gridextra))) |
| 6604 | (home-page "https://cran.r-project.org/web/packages/ACSNMineR") |
| 6605 | (synopsis "Gene enrichment analysis") |
| 6606 | (description |
| 6607 | "This package provides tools to compute and represent gene set enrichment |
| 6608 | or depletion from your data based on pre-saved maps from the @dfn{Atlas of |
| 6609 | Cancer Signalling Networks} (ACSN) or user imported maps. The gene set |
| 6610 | enrichment can be run with hypergeometric test or Fisher exact test, and can |
| 6611 | use multiple corrections. Visualization of data can be done either by |
| 6612 | barplots or heatmaps.") |
| 6613 | (license license:gpl2+))) |
| 6614 | |
| 6615 | (define-public r-biocgenerics |
| 6616 | (package |
| 6617 | (name "r-biocgenerics") |
| 6618 | (version "0.24.0") |
| 6619 | (source (origin |
| 6620 | (method url-fetch) |
| 6621 | (uri (bioconductor-uri "BiocGenerics" version)) |
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| 6626 | `((upstream-name . "BiocGenerics"))) |
| 6627 | (build-system r-build-system) |
| 6628 | (home-page "https://bioconductor.org/packages/BiocGenerics") |
| 6629 | (synopsis "S4 generic functions for Bioconductor") |
| 6630 | (description |
| 6631 | "This package provides S4 generic functions needed by many Bioconductor |
| 6632 | packages.") |
| 6633 | (license license:artistic2.0))) |
| 6634 | |
| 6635 | (define-public r-biocinstaller |
| 6636 | (package |
| 6637 | (name "r-biocinstaller") |
| 6638 | (version "1.28.0") |
| 6639 | (source (origin |
| 6640 | (method url-fetch) |
| 6641 | (uri (bioconductor-uri "BiocInstaller" version)) |
| 6642 | (sha256 |
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| 6645 | (properties |
| 6646 | `((upstream-name . "BiocInstaller"))) |
| 6647 | (build-system r-build-system) |
| 6648 | (home-page "https://bioconductor.org/packages/BiocInstaller") |
| 6649 | (synopsis "Install Bioconductor packages") |
| 6650 | (description "This package is used to install and update R packages from |
| 6651 | Bioconductor, CRAN, and Github.") |
| 6652 | (license license:artistic2.0))) |
| 6653 | |
| 6654 | (define-public r-biocviews |
| 6655 | (package |
| 6656 | (name "r-biocviews") |
| 6657 | (version "1.46.0") |
| 6658 | (source (origin |
| 6659 | (method url-fetch) |
| 6660 | (uri (bioconductor-uri "biocViews" version)) |
| 6661 | (sha256 |
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| 6664 | (properties |
| 6665 | `((upstream-name . "biocViews"))) |
| 6666 | (build-system r-build-system) |
| 6667 | (propagated-inputs |
| 6668 | `(("r-biobase" ,r-biobase) |
| 6669 | ("r-graph" ,r-graph) |
| 6670 | ("r-rbgl" ,r-rbgl) |
| 6671 | ("r-rcurl" ,r-rcurl) |
| 6672 | ("r-xml" ,r-xml) |
| 6673 | ("r-runit" ,r-runit))) |
| 6674 | (home-page "https://bioconductor.org/packages/biocViews") |
| 6675 | (synopsis "Bioconductor package categorization helper") |
| 6676 | (description "The purpose of biocViews is to create HTML pages that |
| 6677 | categorize packages in a Bioconductor package repository according to keywords, |
| 6678 | also known as views, in a controlled vocabulary.") |
| 6679 | (license license:artistic2.0))) |
| 6680 | |
| 6681 | (define-public r-bookdown |
| 6682 | (package |
| 6683 | (name "r-bookdown") |
| 6684 | (version "0.5") |
| 6685 | (source (origin |
| 6686 | (method url-fetch) |
| 6687 | (uri (cran-uri "bookdown" version)) |
| 6688 | (sha256 |
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| 6691 | (build-system r-build-system) |
| 6692 | (propagated-inputs |
| 6693 | `(("r-htmltools" ,r-htmltools) |
| 6694 | ("r-knitr" ,r-knitr) |
| 6695 | ("r-rmarkdown" ,r-rmarkdown) |
| 6696 | ("r-yaml" ,r-yaml))) |
| 6697 | (home-page "https://github.com/rstudio/bookdown") |
| 6698 | (synopsis "Authoring books and technical documents with R markdown") |
| 6699 | (description "This package provides output formats and utilities for |
| 6700 | authoring books and technical documents with R Markdown.") |
| 6701 | (license license:gpl3))) |
| 6702 | |
| 6703 | (define-public r-biocstyle |
| 6704 | (package |
| 6705 | (name "r-biocstyle") |
| 6706 | (version "2.6.1") |
| 6707 | (source (origin |
| 6708 | (method url-fetch) |
| 6709 | (uri (bioconductor-uri "BiocStyle" version)) |
| 6710 | (sha256 |
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| 6713 | (properties |
| 6714 | `((upstream-name . "BiocStyle"))) |
| 6715 | (build-system r-build-system) |
| 6716 | (propagated-inputs |
| 6717 | `(("r-bookdown" ,r-bookdown) |
| 6718 | ("r-knitr" ,r-knitr) |
| 6719 | ("r-rmarkdown" ,r-rmarkdown) |
| 6720 | ("r-yaml" ,r-yaml))) |
| 6721 | (home-page "https://bioconductor.org/packages/BiocStyle") |
| 6722 | (synopsis "Bioconductor formatting styles") |
| 6723 | (description "This package provides standard formatting styles for |
| 6724 | Bioconductor PDF and HTML documents. Package vignettes illustrate use and |
| 6725 | functionality.") |
| 6726 | (license license:artistic2.0))) |
| 6727 | |
| 6728 | (define-public r-bioccheck |
| 6729 | (package |
| 6730 | (name "r-bioccheck") |
| 6731 | (version "1.14.0") |
| 6732 | (source (origin |
| 6733 | (method url-fetch) |
| 6734 | (uri (bioconductor-uri "BiocCheck" version)) |
| 6735 | (sha256 |
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| 6738 | (properties |
| 6739 | `((upstream-name . "BiocCheck"))) |
| 6740 | (build-system r-build-system) |
| 6741 | (arguments |
| 6742 | '(#:phases |
| 6743 | (modify-phases %standard-phases |
| 6744 | ;; This package can be used by calling BiocCheck(<package>) from |
| 6745 | ;; within R, or by running R CMD BiocCheck <package>. This phase |
| 6746 | ;; makes sure the latter works. For this to work, the BiocCheck |
| 6747 | ;; script must be somewhere on the PATH (not the R bin directory). |
| 6748 | (add-after 'install 'install-bioccheck-subcommand |
| 6749 | (lambda* (#:key outputs #:allow-other-keys) |
| 6750 | (let* ((out (assoc-ref outputs "out")) |
| 6751 | (dest-dir (string-append out "/bin")) |
| 6752 | (script-dir |
| 6753 | (string-append out "/site-library/BiocCheck/script/"))) |
| 6754 | (mkdir-p dest-dir) |
| 6755 | (symlink (string-append script-dir "/checkBadDeps.R") |
| 6756 | (string-append dest-dir "/checkBadDeps.R")) |
| 6757 | (symlink (string-append script-dir "/BiocCheck") |
| 6758 | (string-append dest-dir "/BiocCheck"))) |
| 6759 | #t))))) |
| 6760 | (propagated-inputs |
| 6761 | `(("r-codetools" ,r-codetools) |
| 6762 | ("r-graph" ,r-graph) |
| 6763 | ("r-httr" ,r-httr) |
| 6764 | ("r-optparse" ,r-optparse) |
| 6765 | ("r-biocinstaller" ,r-biocinstaller) |
| 6766 | ("r-biocviews" ,r-biocviews) |
| 6767 | ("r-stringdist" ,r-stringdist))) |
| 6768 | (home-page "https://bioconductor.org/packages/BiocCheck") |
| 6769 | (synopsis "Executes Bioconductor-specific package checks") |
| 6770 | (description "This package contains tools to perform additional quality |
| 6771 | checks on R packages that are to be submitted to the Bioconductor repository.") |
| 6772 | (license license:artistic2.0))) |
| 6773 | |
| 6774 | (define-public r-getopt |
| 6775 | (package |
| 6776 | (name "r-getopt") |
| 6777 | (version "1.20.1") |
| 6778 | (source |
| 6779 | (origin |
| 6780 | (method url-fetch) |
| 6781 | (uri (cran-uri "getopt" version)) |
| 6782 | (sha256 |
| 6783 | (base32 |
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| 6785 | (build-system r-build-system) |
| 6786 | (home-page "https://github.com/trevorld/getopt") |
| 6787 | (synopsis "Command-line option processor for R") |
| 6788 | (description |
| 6789 | "This package is designed to be used with Rscript to write shebang |
| 6790 | scripts that accept short and long options. Many users will prefer to |
| 6791 | use the packages @code{optparse} or @code{argparse} which add extra |
| 6792 | features like automatically generated help options and usage texts, |
| 6793 | support for default values, positional argument support, etc.") |
| 6794 | (license license:gpl2+))) |
| 6795 | |
| 6796 | (define-public r-optparse |
| 6797 | (package |
| 6798 | (name "r-optparse") |
| 6799 | (version "1.4.4") |
| 6800 | (source |
| 6801 | (origin |
| 6802 | (method url-fetch) |
| 6803 | (uri (cran-uri "optparse" version)) |
| 6804 | (sha256 |
| 6805 | (base32 |
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| 6807 | (build-system r-build-system) |
| 6808 | (propagated-inputs |
| 6809 | `(("r-getopt" ,r-getopt))) |
| 6810 | (home-page |
| 6811 | "https://github.com/trevorld/optparse") |
| 6812 | (synopsis "Command line option parser") |
| 6813 | (description |
| 6814 | "This package provides a command line parser inspired by Python's |
| 6815 | @code{optparse} library to be used with Rscript to write shebang scripts |
| 6816 | that accept short and long options.") |
| 6817 | (license license:gpl2+))) |
| 6818 | |
| 6819 | (define-public r-dnacopy |
| 6820 | (package |
| 6821 | (name "r-dnacopy") |
| 6822 | (version "1.52.0") |
| 6823 | (source (origin |
| 6824 | (method url-fetch) |
| 6825 | (uri (bioconductor-uri "DNAcopy" version)) |
| 6826 | (sha256 |
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| 6829 | (properties |
| 6830 | `((upstream-name . "DNAcopy"))) |
| 6831 | (build-system r-build-system) |
| 6832 | (inputs |
| 6833 | `(("gfortran" ,gfortran))) |
| 6834 | (home-page "https://bioconductor.org/packages/DNAcopy") |
| 6835 | (synopsis "Implementation of a circular binary segmentation algorithm") |
| 6836 | (description "This package implements the circular binary segmentation (CBS) |
| 6837 | algorithm to segment DNA copy number data and identify genomic regions with |
| 6838 | abnormal copy number.") |
| 6839 | (license license:gpl2+))) |
| 6840 | |
| 6841 | (define-public r-s4vectors |
| 6842 | (package |
| 6843 | (name "r-s4vectors") |
| 6844 | (version "0.16.0") |
| 6845 | (source (origin |
| 6846 | (method url-fetch) |
| 6847 | (uri (bioconductor-uri "S4Vectors" version)) |
| 6848 | (sha256 |
| 6849 | (base32 |
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| 6851 | (properties |
| 6852 | `((upstream-name . "S4Vectors"))) |
| 6853 | (build-system r-build-system) |
| 6854 | (propagated-inputs |
| 6855 | `(("r-biocgenerics" ,r-biocgenerics))) |
| 6856 | (home-page "https://bioconductor.org/packages/S4Vectors") |
| 6857 | (synopsis "S4 implementation of vectors and lists") |
| 6858 | (description |
| 6859 | "The S4Vectors package defines the @code{Vector} and @code{List} virtual |
| 6860 | classes and a set of generic functions that extend the semantic of ordinary |
| 6861 | vectors and lists in R. Package developers can easily implement vector-like |
| 6862 | or list-like objects as concrete subclasses of @code{Vector} or @code{List}. |
| 6863 | In addition, a few low-level concrete subclasses of general interest (e.g. |
| 6864 | @code{DataFrame}, @code{Rle}, and @code{Hits}) are implemented in the |
| 6865 | S4Vectors package itself.") |
| 6866 | (license license:artistic2.0))) |
| 6867 | |
| 6868 | (define-public r-seqinr |
| 6869 | (package |
| 6870 | (name "r-seqinr") |
| 6871 | (version "3.4-5") |
| 6872 | (source |
| 6873 | (origin |
| 6874 | (method url-fetch) |
| 6875 | (uri (cran-uri "seqinr" version)) |
| 6876 | (sha256 |
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| 6879 | (build-system r-build-system) |
| 6880 | (propagated-inputs |
| 6881 | `(("r-ade4" ,r-ade4) |
| 6882 | ("r-segmented" ,r-segmented))) |
| 6883 | (inputs |
| 6884 | `(("zlib" ,zlib))) |
| 6885 | (home-page "http://seqinr.r-forge.r-project.org/") |
| 6886 | (synopsis "Biological sequences retrieval and analysis") |
| 6887 | (description |
| 6888 | "This package provides tools for exploratory data analysis and data |
| 6889 | visualization of biological sequence (DNA and protein) data. It also includes |
| 6890 | utilities for sequence data management under the ACNUC system.") |
| 6891 | (license license:gpl2+))) |
| 6892 | |
| 6893 | (define-public r-iranges |
| 6894 | (package |
| 6895 | (name "r-iranges") |
| 6896 | (version "2.12.0") |
| 6897 | (source (origin |
| 6898 | (method url-fetch) |
| 6899 | (uri (bioconductor-uri "IRanges" version)) |
| 6900 | (sha256 |
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| 6904 | `((upstream-name . "IRanges"))) |
| 6905 | (build-system r-build-system) |
| 6906 | (propagated-inputs |
| 6907 | `(("r-biocgenerics" ,r-biocgenerics) |
| 6908 | ("r-s4vectors" ,r-s4vectors))) |
| 6909 | (home-page "https://bioconductor.org/packages/IRanges") |
| 6910 | (synopsis "Infrastructure for manipulating intervals on sequences") |
| 6911 | (description |
| 6912 | "This package provides efficient low-level and highly reusable S4 classes |
| 6913 | for storing ranges of integers, RLE vectors (Run-Length Encoding), and, more |
| 6914 | generally, data that can be organized sequentially (formally defined as |
| 6915 | @code{Vector} objects), as well as views on these @code{Vector} objects. |
| 6916 | Efficient list-like classes are also provided for storing big collections of |
| 6917 | instances of the basic classes. All classes in the package use consistent |
| 6918 | naming and share the same rich and consistent \"Vector API\" as much as |
| 6919 | possible.") |
| 6920 | (license license:artistic2.0))) |
| 6921 | |
| 6922 | (define-public r-genomeinfodbdata |
| 6923 | (package |
| 6924 | (name "r-genomeinfodbdata") |
| 6925 | (version "0.99.1") |
| 6926 | (source (origin |
| 6927 | (method url-fetch) |
| 6928 | ;; We cannot use bioconductor-uri here because this tarball is |
| 6929 | ;; located under "data/annotation/" instead of "bioc/". |
| 6930 | (uri (string-append "https://bioconductor.org/packages/release/" |
| 6931 | "data/annotation/src/contrib/GenomeInfoDbData_" |
| 6932 | version ".tar.gz")) |
| 6933 | (sha256 |
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| 6936 | (properties |
| 6937 | `((upstream-name . "GenomeInfoDbData"))) |
| 6938 | (build-system r-build-system) |
| 6939 | (home-page "https://bioconductor.org/packages/GenomeInfoDbData") |
| 6940 | (synopsis "Species and taxonomy ID look up tables for GenomeInfoDb") |
| 6941 | (description "This package contains data for mapping between NCBI taxonomy |
| 6942 | ID and species. It is used by functions in the GenomeInfoDb package.") |
| 6943 | (license license:artistic2.0))) |
| 6944 | |
| 6945 | (define-public r-genomeinfodb |
| 6946 | (package |
| 6947 | (name "r-genomeinfodb") |
| 6948 | (version "1.14.0") |
| 6949 | (source (origin |
| 6950 | (method url-fetch) |
| 6951 | (uri (bioconductor-uri "GenomeInfoDb" version)) |
| 6952 | (sha256 |
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| 6955 | (properties |
| 6956 | `((upstream-name . "GenomeInfoDb"))) |
| 6957 | (build-system r-build-system) |
| 6958 | (propagated-inputs |
| 6959 | `(("r-biocgenerics" ,r-biocgenerics) |
| 6960 | ("r-genomeinfodbdata" ,r-genomeinfodbdata) |
| 6961 | ("r-iranges" ,r-iranges) |
| 6962 | ("r-rcurl" ,r-rcurl) |
| 6963 | ("r-s4vectors" ,r-s4vectors))) |
| 6964 | (home-page "https://bioconductor.org/packages/GenomeInfoDb") |
| 6965 | (synopsis "Utilities for manipulating chromosome identifiers") |
| 6966 | (description |
| 6967 | "This package contains data and functions that define and allow |
| 6968 | translation between different chromosome sequence naming conventions (e.g., |
| 6969 | \"chr1\" versus \"1\"), including a function that attempts to place sequence |
| 6970 | names in their natural, rather than lexicographic, order.") |
| 6971 | (license license:artistic2.0))) |
| 6972 | |
| 6973 | (define-public r-edger |
| 6974 | (package |
| 6975 | (name "r-edger") |
| 6976 | (version "3.20.2") |
| 6977 | (source (origin |
| 6978 | (method url-fetch) |
| 6979 | (uri (bioconductor-uri "edgeR" version)) |
| 6980 | (sha256 |
| 6981 | (base32 |
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| 6983 | (properties `((upstream-name . "edgeR"))) |
| 6984 | (build-system r-build-system) |
| 6985 | (propagated-inputs |
| 6986 | `(("r-limma" ,r-limma) |
| 6987 | ("r-locfit" ,r-locfit) |
| 6988 | ("r-rcpp" ,r-rcpp) |
| 6989 | ("r-statmod" ,r-statmod))) ;for estimateDisp |
| 6990 | (home-page "http://bioinf.wehi.edu.au/edgeR") |
| 6991 | (synopsis "EdgeR does empirical analysis of digital gene expression data") |
| 6992 | (description "This package can do differential expression analysis of |
| 6993 | RNA-seq expression profiles with biological replication. It implements a range |
| 6994 | of statistical methodology based on the negative binomial distributions, |
| 6995 | including empirical Bayes estimation, exact tests, generalized linear models |
| 6996 | and quasi-likelihood tests. It be applied to differential signal analysis of |
| 6997 | other types of genomic data that produce counts, including ChIP-seq, SAGE and |
| 6998 | CAGE.") |
| 6999 | (license license:gpl2+))) |
| 7000 | |
| 7001 | (define-public r-variantannotation |
| 7002 | (package |
| 7003 | (name "r-variantannotation") |
| 7004 | (version "1.24.2") |
| 7005 | (source (origin |
| 7006 | (method url-fetch) |
| 7007 | (uri (bioconductor-uri "VariantAnnotation" version)) |
| 7008 | (sha256 |
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| 7011 | (properties |
| 7012 | `((upstream-name . "VariantAnnotation"))) |
| 7013 | (inputs |
| 7014 | `(("zlib" ,zlib))) |
| 7015 | (propagated-inputs |
| 7016 | `(("r-annotationdbi" ,r-annotationdbi) |
| 7017 | ("r-biobase" ,r-biobase) |
| 7018 | ("r-biocgenerics" ,r-biocgenerics) |
| 7019 | ("r-biostrings" ,r-biostrings) |
| 7020 | ("r-bsgenome" ,r-bsgenome) |
| 7021 | ("r-dbi" ,r-dbi) |
| 7022 | ("r-genomeinfodb" ,r-genomeinfodb) |
| 7023 | ("r-genomicfeatures" ,r-genomicfeatures) |
| 7024 | ("r-genomicranges" ,r-genomicranges) |
| 7025 | ("r-iranges" ,r-iranges) |
| 7026 | ("r-summarizedexperiment" ,r-summarizedexperiment) |
| 7027 | ("r-rsamtools" ,r-rsamtools) |
| 7028 | ("r-rtracklayer" ,r-rtracklayer) |
| 7029 | ("r-s4vectors" ,r-s4vectors) |
| 7030 | ("r-xvector" ,r-xvector) |
| 7031 | ("r-zlibbioc" ,r-zlibbioc))) |
| 7032 | (build-system r-build-system) |
| 7033 | (home-page "https://bioconductor.org/packages/VariantAnnotation") |
| 7034 | (synopsis "Package for annotation of genetic variants") |
| 7035 | (description "This R package can annotate variants, compute amino acid |
| 7036 | coding changes and predict coding outcomes.") |
| 7037 | (license license:artistic2.0))) |
| 7038 | |
| 7039 | (define-public r-limma |
| 7040 | (package |
| 7041 | (name "r-limma") |
| 7042 | (version "3.34.4") |
| 7043 | (source (origin |
| 7044 | (method url-fetch) |
| 7045 | (uri (bioconductor-uri "limma" version)) |
| 7046 | (sha256 |
| 7047 | (base32 |
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| 7049 | (build-system r-build-system) |
| 7050 | (home-page "http://bioinf.wehi.edu.au/limma") |
| 7051 | (synopsis "Package for linear models for microarray and RNA-seq data") |
| 7052 | (description "This package can be used for the analysis of gene expression |
| 7053 | studies, especially the use of linear models for analysing designed experiments |
| 7054 | and the assessment of differential expression. The analysis methods apply to |
| 7055 | different technologies, including microarrays, RNA-seq, and quantitative PCR.") |
| 7056 | (license license:gpl2+))) |
| 7057 | |
| 7058 | (define-public r-xvector |
| 7059 | (package |
| 7060 | (name "r-xvector") |
| 7061 | (version "0.18.0") |
| 7062 | (source (origin |
| 7063 | (method url-fetch) |
| 7064 | (uri (bioconductor-uri "XVector" version)) |
| 7065 | (sha256 |
| 7066 | (base32 |
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| 7068 | (properties |
| 7069 | `((upstream-name . "XVector"))) |
| 7070 | (build-system r-build-system) |
| 7071 | (arguments |
| 7072 | `(#:phases |
| 7073 | (modify-phases %standard-phases |
| 7074 | (add-after 'unpack 'use-system-zlib |
| 7075 | (lambda _ |
| 7076 | (substitute* "DESCRIPTION" |
| 7077 | (("zlibbioc, ") "")) |
| 7078 | (substitute* "NAMESPACE" |
| 7079 | (("import\\(zlibbioc\\)") "")) |
| 7080 | #t))))) |
| 7081 | (inputs |
| 7082 | `(("zlib" ,zlib))) |
| 7083 | (propagated-inputs |
| 7084 | `(("r-biocgenerics" ,r-biocgenerics) |
| 7085 | ("r-iranges" ,r-iranges) |
| 7086 | ("r-s4vectors" ,r-s4vectors))) |
| 7087 | (home-page "https://bioconductor.org/packages/XVector") |
| 7088 | (synopsis "Representation and manpulation of external sequences") |
| 7089 | (description |
| 7090 | "This package provides memory efficient S4 classes for storing sequences |
| 7091 | \"externally\" (behind an R external pointer, or on disk).") |
| 7092 | (license license:artistic2.0))) |
| 7093 | |
| 7094 | (define-public r-genomicranges |
| 7095 | (package |
| 7096 | (name "r-genomicranges") |
| 7097 | (version "1.30.0") |
| 7098 | (source (origin |
| 7099 | (method url-fetch) |
| 7100 | (uri (bioconductor-uri "GenomicRanges" version)) |
| 7101 | (sha256 |
| 7102 | (base32 |
| 7103 | "10ra2sjn17h6gilm9iz0cygp9ijpgbirljlc4drwrnivnw9cmi2a")))) |
| 7104 | (properties |
| 7105 | `((upstream-name . "GenomicRanges"))) |
| 7106 | (build-system r-build-system) |
| 7107 | (propagated-inputs |
| 7108 | `(("r-biocgenerics" ,r-biocgenerics) |
| 7109 | ("r-genomeinfodb" ,r-genomeinfodb) |
| 7110 | ("r-iranges" ,r-iranges) |
| 7111 | ("r-s4vectors" ,r-s4vectors) |
| 7112 | ("r-xvector" ,r-xvector))) |
| 7113 | (home-page "https://bioconductor.org/packages/GenomicRanges") |
| 7114 | (synopsis "Representation and manipulation of genomic intervals") |
| 7115 | (description |
| 7116 | "This package provides tools to efficiently represent and manipulate |
| 7117 | genomic annotations and alignments is playing a central role when it comes to |
| 7118 | analyzing high-throughput sequencing data (a.k.a. NGS data). The |
| 7119 | GenomicRanges package defines general purpose containers for storing and |
| 7120 | manipulating genomic intervals and variables defined along a genome.") |
| 7121 | (license license:artistic2.0))) |
| 7122 | |
| 7123 | (define-public r-biobase |
| 7124 | (package |
| 7125 | (name "r-biobase") |
| 7126 | (version "2.38.0") |
| 7127 | (source (origin |
| 7128 | (method url-fetch) |
| 7129 | (uri (bioconductor-uri "Biobase" version)) |
| 7130 | (sha256 |
| 7131 | (base32 |
| 7132 | "1cgm1ja1kp56zdlzyy9ggbkfn8r2vbsd4hncmz8g4hjd47fg18kg")))) |
| 7133 | (properties |
| 7134 | `((upstream-name . "Biobase"))) |
| 7135 | (build-system r-build-system) |
| 7136 | (propagated-inputs |
| 7137 | `(("r-biocgenerics" ,r-biocgenerics))) |
| 7138 | (home-page "https://bioconductor.org/packages/Biobase") |
| 7139 | (synopsis "Base functions for Bioconductor") |
| 7140 | (description |
| 7141 | "This package provides functions that are needed by many other packages |
| 7142 | on Bioconductor or which replace R functions.") |
| 7143 | (license license:artistic2.0))) |
| 7144 | |
| 7145 | (define-public r-annotationdbi |
| 7146 | (package |
| 7147 | (name "r-annotationdbi") |
| 7148 | (version "1.40.0") |
| 7149 | (source (origin |
| 7150 | (method url-fetch) |
| 7151 | (uri (bioconductor-uri "AnnotationDbi" version)) |
| 7152 | (sha256 |
| 7153 | (base32 |
| 7154 | "1dh4qs1a757n640gs34lf6z2glc96nan86x0sqaw5csadl2rhnlc")))) |
| 7155 | (properties |
| 7156 | `((upstream-name . "AnnotationDbi"))) |
| 7157 | (build-system r-build-system) |
| 7158 | (propagated-inputs |
| 7159 | `(("r-biobase" ,r-biobase) |
| 7160 | ("r-biocgenerics" ,r-biocgenerics) |
| 7161 | ("r-dbi" ,r-dbi) |
| 7162 | ("r-iranges" ,r-iranges) |
| 7163 | ("r-rsqlite" ,r-rsqlite) |
| 7164 | ("r-s4vectors" ,r-s4vectors))) |
| 7165 | (home-page "https://bioconductor.org/packages/AnnotationDbi") |
| 7166 | (synopsis "Annotation database interface") |
| 7167 | (description |
| 7168 | "This package provides user interface and database connection code for |
| 7169 | annotation data packages using SQLite data storage.") |
| 7170 | (license license:artistic2.0))) |
| 7171 | |
| 7172 | (define-public r-biomart |
| 7173 | (package |
| 7174 | (name "r-biomart") |
| 7175 | (version "2.34.1") |
| 7176 | (source (origin |
| 7177 | (method url-fetch) |
| 7178 | (uri (bioconductor-uri "biomaRt" version)) |
| 7179 | (sha256 |
| 7180 | (base32 |
| 7181 | "0jzv8b86vpvavwnzi5xf7y18xmn72zkabkn2kclg1mgl847cq13k")))) |
| 7182 | (properties |
| 7183 | `((upstream-name . "biomaRt"))) |
| 7184 | (build-system r-build-system) |
| 7185 | (propagated-inputs |
| 7186 | `(("r-annotationdbi" ,r-annotationdbi) |
| 7187 | ("r-httr" ,r-httr) |
| 7188 | ("r-progress" ,r-progress) |
| 7189 | ("r-rcurl" ,r-rcurl) |
| 7190 | ("r-stringr" ,r-stringr) |
| 7191 | ("r-xml" ,r-xml))) |
| 7192 | (home-page "https://bioconductor.org/packages/biomaRt") |
| 7193 | (synopsis "Interface to BioMart databases") |
| 7194 | (description |
| 7195 | "biomaRt provides an interface to a growing collection of databases |
| 7196 | implementing the @url{BioMart software suite, http://www.biomart.org}. The |
| 7197 | package enables retrieval of large amounts of data in a uniform way without |
| 7198 | the need to know the underlying database schemas or write complex SQL queries. |
| 7199 | Examples of BioMart databases are Ensembl, COSMIC, Uniprot, HGNC, Gramene, |
| 7200 | Wormbase and dbSNP mapped to Ensembl. These major databases give biomaRt |
| 7201 | users direct access to a diverse set of data and enable a wide range of |
| 7202 | powerful online queries from gene annotation to database mining.") |
| 7203 | (license license:artistic2.0))) |
| 7204 | |
| 7205 | (define-public r-biocparallel |
| 7206 | (package |
| 7207 | (name "r-biocparallel") |
| 7208 | (version "1.12.0") |
| 7209 | (source (origin |
| 7210 | (method url-fetch) |
| 7211 | (uri (bioconductor-uri "BiocParallel" version)) |
| 7212 | (sha256 |
| 7213 | (base32 |
| 7214 | "13ng3n2wsgl3fh0v6jnz3vg51k5c1sh44pqdvblcrcd1qyjmmqhd")))) |
| 7215 | (properties |
| 7216 | `((upstream-name . "BiocParallel"))) |
| 7217 | (build-system r-build-system) |
| 7218 | (propagated-inputs |
| 7219 | `(("r-futile-logger" ,r-futile-logger) |
| 7220 | ("r-snow" ,r-snow) |
| 7221 | ("r-bh" ,r-bh))) |
| 7222 | (home-page "https://bioconductor.org/packages/BiocParallel") |
| 7223 | (synopsis "Bioconductor facilities for parallel evaluation") |
| 7224 | (description |
| 7225 | "This package provides modified versions and novel implementation of |
| 7226 | functions for parallel evaluation, tailored to use with Bioconductor |
| 7227 | objects.") |
| 7228 | (license (list license:gpl2+ license:gpl3+)))) |
| 7229 | |
| 7230 | (define-public r-biostrings |
| 7231 | (package |
| 7232 | (name "r-biostrings") |
| 7233 | (version "2.46.0") |
| 7234 | (source (origin |
| 7235 | (method url-fetch) |
| 7236 | (uri (bioconductor-uri "Biostrings" version)) |
| 7237 | (sha256 |
| 7238 | (base32 |
| 7239 | "0vg50qdlxqcm2d6axjnzg8wh8pr4c5gz03l8bdl0llmwzp0zclzk")))) |
| 7240 | (properties |
| 7241 | `((upstream-name . "Biostrings"))) |
| 7242 | (build-system r-build-system) |
| 7243 | (propagated-inputs |
| 7244 | `(("r-biocgenerics" ,r-biocgenerics) |
| 7245 | ("r-iranges" ,r-iranges) |
| 7246 | ("r-s4vectors" ,r-s4vectors) |
| 7247 | ("r-xvector" ,r-xvector))) |
| 7248 | (home-page "https://bioconductor.org/packages/Biostrings") |
| 7249 | (synopsis "String objects and algorithms for biological sequences") |
| 7250 | (description |
| 7251 | "This package provides memory efficient string containers, string |
| 7252 | matching algorithms, and other utilities, for fast manipulation of large |
| 7253 | biological sequences or sets of sequences.") |
| 7254 | (license license:artistic2.0))) |
| 7255 | |
| 7256 | (define-public r-rsamtools |
| 7257 | (package |
| 7258 | (name "r-rsamtools") |
| 7259 | (version "1.30.0") |
| 7260 | (source (origin |
| 7261 | (method url-fetch) |
| 7262 | (uri (bioconductor-uri "Rsamtools" version)) |
| 7263 | (sha256 |
| 7264 | (base32 |
| 7265 | "0pjny5fjvbnfdyhl3bwxin678sha2drvs00sivxh3l772cn6yams")))) |
| 7266 | (properties |
| 7267 | `((upstream-name . "Rsamtools"))) |
| 7268 | (build-system r-build-system) |
| 7269 | (arguments |
| 7270 | `(#:phases |
| 7271 | (modify-phases %standard-phases |
| 7272 | (add-after 'unpack 'use-system-zlib |
| 7273 | (lambda _ |
| 7274 | (substitute* "DESCRIPTION" |
| 7275 | (("zlibbioc, ") "")) |
| 7276 | (substitute* "NAMESPACE" |
| 7277 | (("import\\(zlibbioc\\)") "")) |
| 7278 | #t))))) |
| 7279 | (inputs |
| 7280 | `(("zlib" ,zlib))) |
| 7281 | (propagated-inputs |
| 7282 | `(("r-biocgenerics" ,r-biocgenerics) |
| 7283 | ("r-biocparallel" ,r-biocparallel) |
| 7284 | ("r-biostrings" ,r-biostrings) |
| 7285 | ("r-bitops" ,r-bitops) |
| 7286 | ("r-genomeinfodb" ,r-genomeinfodb) |
| 7287 | ("r-genomicranges" ,r-genomicranges) |
| 7288 | ("r-iranges" ,r-iranges) |
| 7289 | ("r-s4vectors" ,r-s4vectors) |
| 7290 | ("r-xvector" ,r-xvector))) |
| 7291 | (home-page "https://bioconductor.org/packages/release/bioc/html/Rsamtools.html") |
| 7292 | (synopsis "Interface to samtools, bcftools, and tabix") |
| 7293 | (description |
| 7294 | "This package provides an interface to the 'samtools', 'bcftools', and |
| 7295 | 'tabix' utilities for manipulating SAM (Sequence Alignment / Map), FASTA, |
| 7296 | binary variant call (BCF) and compressed indexed tab-delimited (tabix) |
| 7297 | files.") |
| 7298 | (license license:expat))) |
| 7299 | |
| 7300 | (define-public r-delayedarray |
| 7301 | (package |
| 7302 | (name "r-delayedarray") |
| 7303 | (version "0.4.1") |
| 7304 | (source (origin |
| 7305 | (method url-fetch) |
| 7306 | (uri (bioconductor-uri "DelayedArray" version)) |
| 7307 | (sha256 |
| 7308 | (base32 |
| 7309 | "0s7h2giyvz04cg6248kbbzpwhxdrpnsvl2s8k5c8ricisd9aaz4b")))) |
| 7310 | (properties |
| 7311 | `((upstream-name . "DelayedArray"))) |
| 7312 | (build-system r-build-system) |
| 7313 | (propagated-inputs |
| 7314 | `(("r-biocgenerics" ,r-biocgenerics) |
| 7315 | ("r-s4vectors" ,r-s4vectors) |
| 7316 | ("r-iranges" ,r-iranges) |
| 7317 | ("r-matrixstats" ,r-matrixstats))) |
| 7318 | (home-page "https://bioconductor.org/packages/DelayedArray") |
| 7319 | (synopsis "Delayed operations on array-like objects") |
| 7320 | (description |
| 7321 | "Wrapping an array-like object (typically an on-disk object) in a |
| 7322 | @code{DelayedArray} object allows one to perform common array operations on it |
| 7323 | without loading the object in memory. In order to reduce memory usage and |
| 7324 | optimize performance, operations on the object are either delayed or executed |
| 7325 | using a block processing mechanism. Note that this also works on in-memory |
| 7326 | array-like objects like @code{DataFrame} objects (typically with Rle columns), |
| 7327 | @code{Matrix} objects, and ordinary arrays and data frames.") |
| 7328 | (license license:artistic2.0))) |
| 7329 | |
| 7330 | (define-public r-summarizedexperiment |
| 7331 | (package |
| 7332 | (name "r-summarizedexperiment") |
| 7333 | (version "1.8.0") |
| 7334 | (source (origin |
| 7335 | (method url-fetch) |
| 7336 | (uri (bioconductor-uri "SummarizedExperiment" version)) |
| 7337 | (sha256 |
| 7338 | (base32 |
| 7339 | "1011r8l0k8420j31bmh4xdcp6ka5bzf4bqhip84v5b6alpkcbvmf")))) |
| 7340 | (properties |
| 7341 | `((upstream-name . "SummarizedExperiment"))) |
| 7342 | (build-system r-build-system) |
| 7343 | (propagated-inputs |
| 7344 | `(("r-biobase" ,r-biobase) |
| 7345 | ("r-biocgenerics" ,r-biocgenerics) |
| 7346 | ("r-delayedarray" ,r-delayedarray) |
| 7347 | ("r-genomeinfodb" ,r-genomeinfodb) |
| 7348 | ("r-genomicranges" ,r-genomicranges) |
| 7349 | ("r-iranges" ,r-iranges) |
| 7350 | ("r-matrix" ,r-matrix) |
| 7351 | ("r-s4vectors" ,r-s4vectors))) |
| 7352 | (home-page "https://bioconductor.org/packages/SummarizedExperiment") |
| 7353 | (synopsis "Container for representing genomic ranges by sample") |
| 7354 | (description |
| 7355 | "The SummarizedExperiment container contains one or more assays, each |
| 7356 | represented by a matrix-like object of numeric or other mode. The rows |
| 7357 | typically represent genomic ranges of interest and the columns represent |
| 7358 | samples.") |
| 7359 | (license license:artistic2.0))) |
| 7360 | |
| 7361 | (define-public r-genomicalignments |
| 7362 | (package |
| 7363 | (name "r-genomicalignments") |
| 7364 | (version "1.14.1") |
| 7365 | (source (origin |
| 7366 | (method url-fetch) |
| 7367 | (uri (bioconductor-uri "GenomicAlignments" version)) |
| 7368 | (sha256 |
| 7369 | (base32 |
| 7370 | "033p6fw46sn7w2yyn14nb9qcnkf30cl0nv6zh014ixflm3iifz39")))) |
| 7371 | (properties |
| 7372 | `((upstream-name . "GenomicAlignments"))) |
| 7373 | (build-system r-build-system) |
| 7374 | (propagated-inputs |
| 7375 | `(("r-biocgenerics" ,r-biocgenerics) |
| 7376 | ("r-biocparallel" ,r-biocparallel) |
| 7377 | ("r-biostrings" ,r-biostrings) |
| 7378 | ("r-genomeinfodb" ,r-genomeinfodb) |
| 7379 | ("r-genomicranges" ,r-genomicranges) |
| 7380 | ("r-iranges" ,r-iranges) |
| 7381 | ("r-rsamtools" ,r-rsamtools) |
| 7382 | ("r-s4vectors" ,r-s4vectors) |
| 7383 | ("r-summarizedexperiment" ,r-summarizedexperiment))) |
| 7384 | (home-page "https://bioconductor.org/packages/GenomicAlignments") |
| 7385 | (synopsis "Representation and manipulation of short genomic alignments") |
| 7386 | (description |
| 7387 | "This package provides efficient containers for storing and manipulating |
| 7388 | short genomic alignments (typically obtained by aligning short reads to a |
| 7389 | reference genome). This includes read counting, computing the coverage, |
| 7390 | junction detection, and working with the nucleotide content of the |
| 7391 | alignments.") |
| 7392 | (license license:artistic2.0))) |
| 7393 | |
| 7394 | (define-public r-rtracklayer |
| 7395 | (package |
| 7396 | (name "r-rtracklayer") |
| 7397 | (version "1.38.2") |
| 7398 | (source (origin |
| 7399 | (method url-fetch) |
| 7400 | (uri (bioconductor-uri "rtracklayer" version)) |
| 7401 | (sha256 |
| 7402 | (base32 |
| 7403 | "1sjn3976f1sqvrq6jq2hgc60ffxgfr3jlklaxfrk3xad5cv2kr2d")))) |
| 7404 | (build-system r-build-system) |
| 7405 | (arguments |
| 7406 | `(#:phases |
| 7407 | (modify-phases %standard-phases |
| 7408 | (add-after 'unpack 'use-system-zlib |
| 7409 | (lambda _ |
| 7410 | (substitute* "DESCRIPTION" |
| 7411 | ((" zlibbioc,") "")) |
| 7412 | (substitute* "NAMESPACE" |
| 7413 | (("import\\(zlibbioc\\)") "")) |
| 7414 | #t))))) |
| 7415 | (inputs |
| 7416 | `(("zlib" ,zlib))) |
| 7417 | (propagated-inputs |
| 7418 | `(("r-biocgenerics" ,r-biocgenerics) |
| 7419 | ("r-biostrings" ,r-biostrings) |
| 7420 | ("r-genomeinfodb" ,r-genomeinfodb) |
| 7421 | ("r-genomicalignments" ,r-genomicalignments) |
| 7422 | ("r-genomicranges" ,r-genomicranges) |
| 7423 | ("r-iranges" ,r-iranges) |
| 7424 | ("r-rcurl" ,r-rcurl) |
| 7425 | ("r-rsamtools" ,r-rsamtools) |
| 7426 | ("r-s4vectors" ,r-s4vectors) |
| 7427 | ("r-xml" ,r-xml) |
| 7428 | ("r-xvector" ,r-xvector))) |
| 7429 | (home-page "https://bioconductor.org/packages/rtracklayer") |
| 7430 | (synopsis "R interface to genome browsers and their annotation tracks") |
| 7431 | (description |
| 7432 | "rtracklayer is an extensible framework for interacting with multiple |
| 7433 | genome browsers (currently UCSC built-in) and manipulating annotation tracks |
| 7434 | in various formats (currently GFF, BED, bedGraph, BED15, WIG, BigWig and 2bit |
| 7435 | built-in). The user may export/import tracks to/from the supported browsers, |
| 7436 | as well as query and modify the browser state, such as the current viewport.") |
| 7437 | (license license:artistic2.0))) |
| 7438 | |
| 7439 | (define-public r-genomicfeatures |
| 7440 | (package |
| 7441 | (name "r-genomicfeatures") |
| 7442 | (version "1.30.0") |
| 7443 | (source (origin |
| 7444 | (method url-fetch) |
| 7445 | (uri (bioconductor-uri "GenomicFeatures" version)) |
| 7446 | (sha256 |
| 7447 | (base32 |
| 7448 | "1khjvq1ffhqavkwf8n7bilknci60lxbg52icrcf2vnb9k8rlpghs")))) |
| 7449 | (properties |
| 7450 | `((upstream-name . "GenomicFeatures"))) |
| 7451 | (build-system r-build-system) |
| 7452 | (propagated-inputs |
| 7453 | `(("r-annotationdbi" ,r-annotationdbi) |
| 7454 | ("r-biobase" ,r-biobase) |
| 7455 | ("r-biocgenerics" ,r-biocgenerics) |
| 7456 | ("r-biomart" ,r-biomart) |
| 7457 | ("r-biostrings" ,r-biostrings) |
| 7458 | ("r-dbi" ,r-dbi) |
| 7459 | ("r-genomeinfodb" ,r-genomeinfodb) |
| 7460 | ("r-genomicranges" ,r-genomicranges) |
| 7461 | ("r-iranges" ,r-iranges) |
| 7462 | ("r-rcurl" ,r-rcurl) |
| 7463 | ("r-rsqlite" ,r-rsqlite) |
| 7464 | ("r-rmysql" ,r-rmysql) |
| 7465 | ("r-rtracklayer" ,r-rtracklayer) |
| 7466 | ("r-s4vectors" ,r-s4vectors) |
| 7467 | ("r-xvector" ,r-xvector))) |
| 7468 | (home-page "https://bioconductor.org/packages/GenomicFeatures") |
| 7469 | (synopsis "Tools for working with transcript centric annotations") |
| 7470 | (description |
| 7471 | "This package provides a set of tools and methods for making and |
| 7472 | manipulating transcript centric annotations. With these tools the user can |
| 7473 | easily download the genomic locations of the transcripts, exons and cds of a |
| 7474 | given organism, from either the UCSC Genome Browser or a BioMart |
| 7475 | database (more sources will be supported in the future). This information is |
| 7476 | then stored in a local database that keeps track of the relationship between |
| 7477 | transcripts, exons, cds and genes. Flexible methods are provided for |
| 7478 | extracting the desired features in a convenient format.") |
| 7479 | (license license:artistic2.0))) |
| 7480 | |
| 7481 | (define-public r-go-db |
| 7482 | (package |
| 7483 | (name "r-go-db") |
| 7484 | (version "3.5.0") |
| 7485 | (source (origin |
| 7486 | (method url-fetch) |
| 7487 | (uri (string-append "https://www.bioconductor.org/packages/" |
| 7488 | "release/data/annotation/src/contrib/GO.db_" |
| 7489 | version ".tar.gz")) |
| 7490 | (sha256 |
| 7491 | (base32 |
| 7492 | "02d1mn1al3q7qvhx1ylrr3ar4w4iw0qyi5d89v2336rzwk9maq35")))) |
| 7493 | (properties |
| 7494 | `((upstream-name . "GO.db"))) |
| 7495 | (build-system r-build-system) |
| 7496 | (propagated-inputs |
| 7497 | `(("r-annotationdbi" ,r-annotationdbi))) |
| 7498 | (home-page "https://bioconductor.org/packages/GO.db") |
| 7499 | (synopsis "Annotation maps describing the entire Gene Ontology") |
| 7500 | (description |
| 7501 | "The purpose of this GO.db annotation package is to provide detailed |
| 7502 | information about the latest version of the Gene Ontologies.") |
| 7503 | (license license:artistic2.0))) |
| 7504 | |
| 7505 | (define-public r-graph |
| 7506 | (package |
| 7507 | (name "r-graph") |
| 7508 | (version "1.56.0") |
| 7509 | (source (origin |
| 7510 | (method url-fetch) |
| 7511 | (uri (bioconductor-uri "graph" version)) |
| 7512 | (sha256 |
| 7513 | (base32 |
| 7514 | "15aajjp8h2z14p80c8hyd4rrmr9vqsm7bvwb989jxjl4k6g52an1")))) |
| 7515 | (build-system r-build-system) |
| 7516 | (propagated-inputs |
| 7517 | `(("r-biocgenerics" ,r-biocgenerics))) |
| 7518 | (home-page "https://bioconductor.org/packages/graph") |
| 7519 | (synopsis "Handle graph data structures in R") |
| 7520 | (description |
| 7521 | "This package implements some simple graph handling capabilities for R.") |
| 7522 | (license license:artistic2.0))) |
| 7523 | |
| 7524 | (define-public r-topgo |
| 7525 | (package |
| 7526 | (name "r-topgo") |
| 7527 | (version "2.30.0") |
| 7528 | (source (origin |
| 7529 | (method url-fetch) |
| 7530 | (uri (bioconductor-uri "topGO" version)) |
| 7531 | (sha256 |
| 7532 | (base32 |
| 7533 | "1hqffz5qp7glxdvjp37005g8qk5nam3f9wpf6d1wjnzpar04f3dz")))) |
| 7534 | (properties |
| 7535 | `((upstream-name . "topGO"))) |
| 7536 | (build-system r-build-system) |
| 7537 | (propagated-inputs |
| 7538 | `(("r-annotationdbi" ,r-annotationdbi) |
| 7539 | ("r-dbi" ,r-dbi) |
| 7540 | ("r-biobase" ,r-biobase) |
| 7541 | ("r-biocgenerics" ,r-biocgenerics) |
| 7542 | ("r-go-db" ,r-go-db) |
| 7543 | ("r-graph" ,r-graph) |
| 7544 | ("r-lattice" ,r-lattice) |
| 7545 | ("r-matrixstats" ,r-matrixstats) |
| 7546 | ("r-sparsem" ,r-sparsem))) |
| 7547 | (home-page "https://bioconductor.org/packages/topGO") |
| 7548 | (synopsis "Enrichment analysis for gene ontology") |
| 7549 | (description |
| 7550 | "The topGO package provides tools for testing @dfn{gene ontology} (GO) |
| 7551 | terms while accounting for the topology of the GO graph. Different test |
| 7552 | statistics and different methods for eliminating local similarities and |
| 7553 | dependencies between GO terms can be implemented and applied.") |
| 7554 | ;; Any version of the LGPL applies. |
| 7555 | (license license:lgpl2.1+))) |
| 7556 | |
| 7557 | (define-public r-bsgenome |
| 7558 | (package |
| 7559 | (name "r-bsgenome") |
| 7560 | (version "1.46.0") |
| 7561 | (source (origin |
| 7562 | (method url-fetch) |
| 7563 | (uri (bioconductor-uri "BSgenome" version)) |
| 7564 | (sha256 |
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| 7567 | (properties |
| 7568 | `((upstream-name . "BSgenome"))) |
| 7569 | (build-system r-build-system) |
| 7570 | (propagated-inputs |
| 7571 | `(("r-biocgenerics" ,r-biocgenerics) |
| 7572 | ("r-biostrings" ,r-biostrings) |
| 7573 | ("r-genomeinfodb" ,r-genomeinfodb) |
| 7574 | ("r-genomicranges" ,r-genomicranges) |
| 7575 | ("r-iranges" ,r-iranges) |
| 7576 | ("r-rsamtools" ,r-rsamtools) |
| 7577 | ("r-rtracklayer" ,r-rtracklayer) |
| 7578 | ("r-s4vectors" ,r-s4vectors) |
| 7579 | ("r-xvector" ,r-xvector))) |
| 7580 | (home-page "https://bioconductor.org/packages/BSgenome") |
| 7581 | (synopsis "Infrastructure for Biostrings-based genome data packages") |
| 7582 | (description |
| 7583 | "This package provides infrastructure shared by all Biostrings-based |
| 7584 | genome data packages and support for efficient SNP representation.") |
| 7585 | (license license:artistic2.0))) |
| 7586 | |
| 7587 | (define-public r-bsgenome-hsapiens-1000genomes-hs37d5 |
| 7588 | (package |
| 7589 | (name "r-bsgenome-hsapiens-1000genomes-hs37d5") |
| 7590 | (version "0.99.1") |
| 7591 | (source (origin |
| 7592 | (method url-fetch) |
| 7593 | ;; We cannot use bioconductor-uri here because this tarball is |
| 7594 | ;; located under "data/annotation/" instead of "bioc/". |
| 7595 | (uri (string-append "https://www.bioconductor.org/packages/" |
| 7596 | "release/data/annotation/src/contrib/" |
| 7597 | "BSgenome.Hsapiens.1000genomes.hs37d5_" |
| 7598 | version ".tar.gz")) |
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| 7602 | (properties |
| 7603 | `((upstream-name . "BSgenome.Hsapiens.1000genomes.hs37d5"))) |
| 7604 | (build-system r-build-system) |
| 7605 | ;; As this package provides little more than a very large data file it |
| 7606 | ;; doesn't make sense to build substitutes. |
| 7607 | (arguments `(#:substitutable? #f)) |
| 7608 | (propagated-inputs |
| 7609 | `(("r-bsgenome" ,r-bsgenome))) |
| 7610 | (home-page |
| 7611 | "https://www.bioconductor.org/packages/BSgenome.Hsapiens.1000genomes.hs37d5/") |
| 7612 | (synopsis "Full genome sequences for Homo sapiens") |
| 7613 | (description |
| 7614 | "This package provides full genome sequences for Homo sapiens from |
| 7615 | 1000genomes phase2 reference genome sequence (hs37d5), based on NCBI GRCh37.") |
| 7616 | (license license:artistic2.0))) |
| 7617 | |
| 7618 | (define-public r-impute |
| 7619 | (package |
| 7620 | (name "r-impute") |
| 7621 | (version "1.52.0") |
| 7622 | (source (origin |
| 7623 | (method url-fetch) |
| 7624 | (uri (bioconductor-uri "impute" version)) |
| 7625 | (sha256 |
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| 7628 | (inputs |
| 7629 | `(("gfortran" ,gfortran))) |
| 7630 | (build-system r-build-system) |
| 7631 | (home-page "https://bioconductor.org/packages/impute") |
| 7632 | (synopsis "Imputation for microarray data") |
| 7633 | (description |
| 7634 | "This package provides a function to impute missing gene expression |
| 7635 | microarray data, using nearest neighbor averaging.") |
| 7636 | (license license:gpl2+))) |
| 7637 | |
| 7638 | (define-public r-seqpattern |
| 7639 | (package |
| 7640 | (name "r-seqpattern") |
| 7641 | (version "1.10.0") |
| 7642 | (source (origin |
| 7643 | (method url-fetch) |
| 7644 | (uri (bioconductor-uri "seqPattern" version)) |
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| 7648 | (properties |
| 7649 | `((upstream-name . "seqPattern"))) |
| 7650 | (build-system r-build-system) |
| 7651 | (propagated-inputs |
| 7652 | `(("r-biostrings" ,r-biostrings) |
| 7653 | ("r-genomicranges" ,r-genomicranges) |
| 7654 | ("r-iranges" ,r-iranges) |
| 7655 | ("r-kernsmooth" ,r-kernsmooth) |
| 7656 | ("r-plotrix" ,r-plotrix))) |
| 7657 | (home-page "https://bioconductor.org/packages/seqPattern") |
| 7658 | (synopsis "Visualising oligonucleotide patterns and motif occurrences") |
| 7659 | (description |
| 7660 | "This package provides tools to visualize oligonucleotide patterns and |
| 7661 | sequence motif occurrences across a large set of sequences centred at a common |
| 7662 | reference point and sorted by a user defined feature.") |
| 7663 | (license license:gpl3+))) |
| 7664 | |
| 7665 | (define-public r-genomation |
| 7666 | (package |
| 7667 | (name "r-genomation") |
| 7668 | (version "1.10.0") |
| 7669 | (source (origin |
| 7670 | (method url-fetch) |
| 7671 | (uri (bioconductor-uri "genomation" version)) |
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| 7675 | (build-system r-build-system) |
| 7676 | (propagated-inputs |
| 7677 | `(("r-biostrings" ,r-biostrings) |
| 7678 | ("r-bsgenome" ,r-bsgenome) |
| 7679 | ("r-data-table" ,r-data-table) |
| 7680 | ("r-genomeinfodb" ,r-genomeinfodb) |
| 7681 | ("r-genomicalignments" ,r-genomicalignments) |
| 7682 | ("r-genomicranges" ,r-genomicranges) |
| 7683 | ("r-ggplot2" ,r-ggplot2) |
| 7684 | ("r-gridbase" ,r-gridbase) |
| 7685 | ("r-impute" ,r-impute) |
| 7686 | ("r-iranges" ,r-iranges) |
| 7687 | ("r-matrixstats" ,r-matrixstats) |
| 7688 | ("r-plotrix" ,r-plotrix) |
| 7689 | ("r-plyr" ,r-plyr) |
| 7690 | ("r-rcpp" ,r-rcpp) |
| 7691 | ("r-readr" ,r-readr) |
| 7692 | ("r-reshape2" ,r-reshape2) |
| 7693 | ("r-rsamtools" ,r-rsamtools) |
| 7694 | ("r-rtracklayer" ,r-rtracklayer) |
| 7695 | ("r-runit" ,r-runit) |
| 7696 | ("r-s4vectors" ,r-s4vectors) |
| 7697 | ("r-seqpattern" ,r-seqpattern))) |
| 7698 | (home-page "http://bioinformatics.mdc-berlin.de/genomation/") |
| 7699 | (synopsis "Summary, annotation and visualization of genomic data") |
| 7700 | (description |
| 7701 | "This package provides a package for summary and annotation of genomic |
| 7702 | intervals. Users can visualize and quantify genomic intervals over |
| 7703 | pre-defined functional regions, such as promoters, exons, introns, etc. The |
| 7704 | genomic intervals represent regions with a defined chromosome position, which |
| 7705 | may be associated with a score, such as aligned reads from HT-seq experiments, |
| 7706 | TF binding sites, methylation scores, etc. The package can use any tabular |
| 7707 | genomic feature data as long as it has minimal information on the locations of |
| 7708 | genomic intervals. In addition, it can use BAM or BigWig files as input.") |
| 7709 | (license license:artistic2.0))) |
| 7710 | |
| 7711 | (define-public r-genomationdata |
| 7712 | (package |
| 7713 | (name "r-genomationdata") |
| 7714 | (version "1.10.0") |
| 7715 | (source (origin |
| 7716 | (method url-fetch) |
| 7717 | ;; We cannot use bioconductor-uri here because this tarball is |
| 7718 | ;; located under "data/annotation/" instead of "bioc/". |
| 7719 | (uri (string-append "https://bioconductor.org/packages/" |
| 7720 | "release/data/experiment/src/contrib/" |
| 7721 | "genomationData_" version ".tar.gz")) |
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| 7725 | (build-system r-build-system) |
| 7726 | ;; As this package provides little more than large data files, it doesn't |
| 7727 | ;; make sense to build substitutes. |
| 7728 | (arguments `(#:substitutable? #f)) |
| 7729 | (native-inputs |
| 7730 | `(("r-knitr" ,r-knitr))) |
| 7731 | (home-page "http://bioinformatics.mdc-berlin.de/genomation/") |
| 7732 | (synopsis "Experimental data for use with the genomation package") |
| 7733 | (description |
| 7734 | "This package contains experimental genetic data for use with the |
| 7735 | genomation package. Included are Chip Seq, Methylation and Cage data, |
| 7736 | downloaded from Encode.") |
| 7737 | (license license:gpl3+))) |
| 7738 | |
| 7739 | (define-public r-org-hs-eg-db |
| 7740 | (package |
| 7741 | (name "r-org-hs-eg-db") |
| 7742 | (version "3.5.0") |
| 7743 | (source (origin |
| 7744 | (method url-fetch) |
| 7745 | ;; We cannot use bioconductor-uri here because this tarball is |
| 7746 | ;; located under "data/annotation/" instead of "bioc/". |
| 7747 | (uri (string-append "https://www.bioconductor.org/packages/" |
| 7748 | "release/data/annotation/src/contrib/" |
| 7749 | "org.Hs.eg.db_" version ".tar.gz")) |
| 7750 | (sha256 |
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| 7753 | (properties |
| 7754 | `((upstream-name . "org.Hs.eg.db"))) |
| 7755 | (build-system r-build-system) |
| 7756 | (propagated-inputs |
| 7757 | `(("r-annotationdbi" ,r-annotationdbi))) |
| 7758 | (home-page "https://www.bioconductor.org/packages/org.Hs.eg.db/") |
| 7759 | (synopsis "Genome wide annotation for Human") |
| 7760 | (description |
| 7761 | "This package contains genome-wide annotations for Human, primarily based |
| 7762 | on mapping using Entrez Gene identifiers.") |
| 7763 | (license license:artistic2.0))) |
| 7764 | |
| 7765 | (define-public r-org-ce-eg-db |
| 7766 | (package |
| 7767 | (name "r-org-ce-eg-db") |
| 7768 | (version "3.5.0") |
| 7769 | (source (origin |
| 7770 | (method url-fetch) |
| 7771 | ;; We cannot use bioconductor-uri here because this tarball is |
| 7772 | ;; located under "data/annotation/" instead of "bioc/". |
| 7773 | (uri (string-append "https://www.bioconductor.org/packages/" |
| 7774 | "release/data/annotation/src/contrib/" |
| 7775 | "org.Ce.eg.db_" version ".tar.gz")) |
| 7776 | (sha256 |
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| 7779 | (properties |
| 7780 | `((upstream-name . "org.Ce.eg.db"))) |
| 7781 | (build-system r-build-system) |
| 7782 | (propagated-inputs |
| 7783 | `(("r-annotationdbi" ,r-annotationdbi))) |
| 7784 | (home-page "https://www.bioconductor.org/packages/org.Ce.eg.db/") |
| 7785 | (synopsis "Genome wide annotation for Worm") |
| 7786 | (description |
| 7787 | "This package provides mappings from Entrez gene identifiers to various |
| 7788 | annotations for the genome of the model worm Caenorhabditis elegans.") |
| 7789 | (license license:artistic2.0))) |
| 7790 | |
| 7791 | (define-public r-org-dm-eg-db |
| 7792 | (package |
| 7793 | (name "r-org-dm-eg-db") |
| 7794 | (version "3.5.0") |
| 7795 | (source (origin |
| 7796 | (method url-fetch) |
| 7797 | ;; We cannot use bioconductor-uri here because this tarball is |
| 7798 | ;; located under "data/annotation/" instead of "bioc/". |
| 7799 | (uri (string-append "https://www.bioconductor.org/packages/" |
| 7800 | "release/data/annotation/src/contrib/" |
| 7801 | "org.Dm.eg.db_" version ".tar.gz")) |
| 7802 | (sha256 |
| 7803 | (base32 |
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| 7805 | (properties |
| 7806 | `((upstream-name . "org.Dm.eg.db"))) |
| 7807 | (build-system r-build-system) |
| 7808 | (propagated-inputs |
| 7809 | `(("r-annotationdbi" ,r-annotationdbi))) |
| 7810 | (home-page "https://www.bioconductor.org/packages/org.Dm.eg.db/") |
| 7811 | (synopsis "Genome wide annotation for Fly") |
| 7812 | (description |
| 7813 | "This package provides mappings from Entrez gene identifiers to various |
| 7814 | annotations for the genome of the model fruit fly Drosophila melanogaster.") |
| 7815 | (license license:artistic2.0))) |
| 7816 | |
| 7817 | (define-public r-org-mm-eg-db |
| 7818 | (package |
| 7819 | (name "r-org-mm-eg-db") |
| 7820 | (version "3.5.0") |
| 7821 | (source (origin |
| 7822 | (method url-fetch) |
| 7823 | ;; We cannot use bioconductor-uri here because this tarball is |
| 7824 | ;; located under "data/annotation/" instead of "bioc/". |
| 7825 | (uri (string-append "https://www.bioconductor.org/packages/" |
| 7826 | "release/data/annotation/src/contrib/" |
| 7827 | "org.Mm.eg.db_" version ".tar.gz")) |
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| 7831 | (properties |
| 7832 | `((upstream-name . "org.Mm.eg.db"))) |
| 7833 | (build-system r-build-system) |
| 7834 | (propagated-inputs |
| 7835 | `(("r-annotationdbi" ,r-annotationdbi))) |
| 7836 | (home-page "https://www.bioconductor.org/packages/org.Mm.eg.db/") |
| 7837 | (synopsis "Genome wide annotation for Mouse") |
| 7838 | (description |
| 7839 | "This package provides mappings from Entrez gene identifiers to various |
| 7840 | annotations for the genome of the model mouse Mus musculus.") |
| 7841 | (license license:artistic2.0))) |
| 7842 | |
| 7843 | (define-public r-seqlogo |
| 7844 | (package |
| 7845 | (name "r-seqlogo") |
| 7846 | (version "1.44.0") |
| 7847 | (source |
| 7848 | (origin |
| 7849 | (method url-fetch) |
| 7850 | (uri (bioconductor-uri "seqLogo" version)) |
| 7851 | (sha256 |
| 7852 | (base32 |
| 7853 | "1ql4q4vx0j61a893dqc3c8zxmgs8sqhy3j1qhyfdvbd01vw9w1kq")))) |
| 7854 | (properties `((upstream-name . "seqLogo"))) |
| 7855 | (build-system r-build-system) |
| 7856 | (home-page "https://bioconductor.org/packages/seqLogo") |
| 7857 | (synopsis "Sequence logos for DNA sequence alignments") |
| 7858 | (description |
| 7859 | "seqLogo takes the position weight matrix of a DNA sequence motif and |
| 7860 | plots the corresponding sequence logo as introduced by Schneider and |
| 7861 | Stephens (1990).") |
| 7862 | (license license:lgpl2.0+))) |
| 7863 | |
| 7864 | (define-public r-bsgenome-hsapiens-ucsc-hg19 |
| 7865 | (package |
| 7866 | (name "r-bsgenome-hsapiens-ucsc-hg19") |
| 7867 | (version "1.4.0") |
| 7868 | (source (origin |
| 7869 | (method url-fetch) |
| 7870 | ;; We cannot use bioconductor-uri here because this tarball is |
| 7871 | ;; located under "data/annotation/" instead of "bioc/". |
| 7872 | (uri (string-append "https://www.bioconductor.org/packages/" |
| 7873 | "release/data/annotation/src/contrib/" |
| 7874 | "BSgenome.Hsapiens.UCSC.hg19_" |
| 7875 | version ".tar.gz")) |
| 7876 | (sha256 |
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| 7879 | (properties |
| 7880 | `((upstream-name . "BSgenome.Hsapiens.UCSC.hg19"))) |
| 7881 | (build-system r-build-system) |
| 7882 | ;; As this package provides little more than a very large data file it |
| 7883 | ;; doesn't make sense to build substitutes. |
| 7884 | (arguments `(#:substitutable? #f)) |
| 7885 | (propagated-inputs |
| 7886 | `(("r-bsgenome" ,r-bsgenome))) |
| 7887 | (home-page |
| 7888 | "https://www.bioconductor.org/packages/BSgenome.Hsapiens.UCSC.hg19/") |
| 7889 | (synopsis "Full genome sequences for Homo sapiens") |
| 7890 | (description |
| 7891 | "This package provides full genome sequences for Homo sapiens as provided |
| 7892 | by UCSC (hg19, February 2009) and stored in Biostrings objects.") |
| 7893 | (license license:artistic2.0))) |
| 7894 | |
| 7895 | (define-public r-bsgenome-mmusculus-ucsc-mm9 |
| 7896 | (package |
| 7897 | (name "r-bsgenome-mmusculus-ucsc-mm9") |
| 7898 | (version "1.4.0") |
| 7899 | (source (origin |
| 7900 | (method url-fetch) |
| 7901 | ;; We cannot use bioconductor-uri here because this tarball is |
| 7902 | ;; located under "data/annotation/" instead of "bioc/". |
| 7903 | (uri (string-append "https://www.bioconductor.org/packages/" |
| 7904 | "release/data/annotation/src/contrib/" |
| 7905 | "BSgenome.Mmusculus.UCSC.mm9_" |
| 7906 | version ".tar.gz")) |
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| 7910 | (properties |
| 7911 | `((upstream-name . "BSgenome.Mmusculus.UCSC.mm9"))) |
| 7912 | (build-system r-build-system) |
| 7913 | ;; As this package provides little more than a very large data file it |
| 7914 | ;; doesn't make sense to build substitutes. |
| 7915 | (arguments `(#:substitutable? #f)) |
| 7916 | (propagated-inputs |
| 7917 | `(("r-bsgenome" ,r-bsgenome))) |
| 7918 | (home-page |
| 7919 | "https://www.bioconductor.org/packages/BSgenome.Mmusculus.UCSC.mm9/") |
| 7920 | (synopsis "Full genome sequences for Mouse") |
| 7921 | (description |
| 7922 | "This package provides full genome sequences for Mus musculus (Mouse) as |
| 7923 | provided by UCSC (mm9, July 2007) and stored in Biostrings objects.") |
| 7924 | (license license:artistic2.0))) |
| 7925 | |
| 7926 | (define-public r-bsgenome-mmusculus-ucsc-mm10 |
| 7927 | (package |
| 7928 | (name "r-bsgenome-mmusculus-ucsc-mm10") |
| 7929 | (version "1.4.0") |
| 7930 | (source (origin |
| 7931 | (method url-fetch) |
| 7932 | ;; We cannot use bioconductor-uri here because this tarball is |
| 7933 | ;; located under "data/annotation/" instead of "bioc/". |
| 7934 | (uri (string-append "https://www.bioconductor.org/packages/" |
| 7935 | "release/data/annotation/src/contrib/" |
| 7936 | "BSgenome.Mmusculus.UCSC.mm10_" |
| 7937 | version ".tar.gz")) |
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| 7941 | (properties |
| 7942 | `((upstream-name . "BSgenome.Mmusculus.UCSC.mm10"))) |
| 7943 | (build-system r-build-system) |
| 7944 | ;; As this package provides little more than a very large data file it |
| 7945 | ;; doesn't make sense to build substitutes. |
| 7946 | (arguments `(#:substitutable? #f)) |
| 7947 | (propagated-inputs |
| 7948 | `(("r-bsgenome" ,r-bsgenome))) |
| 7949 | (home-page |
| 7950 | "https://www.bioconductor.org/packages/BSgenome.Mmusculus.UCSC.mm10/") |
| 7951 | (synopsis "Full genome sequences for Mouse") |
| 7952 | (description |
| 7953 | "This package provides full genome sequences for Mus |
| 7954 | musculus (Mouse) as provided by UCSC (mm10, December 2011) and stored |
| 7955 | in Biostrings objects.") |
| 7956 | (license license:artistic2.0))) |
| 7957 | |
| 7958 | (define-public r-txdb-mmusculus-ucsc-mm10-knowngene |
| 7959 | (package |
| 7960 | (name "r-txdb-mmusculus-ucsc-mm10-knowngene") |
| 7961 | (version "3.4.0") |
| 7962 | (source (origin |
| 7963 | (method url-fetch) |
| 7964 | ;; We cannot use bioconductor-uri here because this tarball is |
| 7965 | ;; located under "data/annotation/" instead of "bioc/". |
| 7966 | (uri (string-append "https://www.bioconductor.org/packages/" |
| 7967 | "release/data/annotation/src/contrib/" |
| 7968 | "TxDb.Mmusculus.UCSC.mm10.knownGene_" |
| 7969 | version ".tar.gz")) |
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| 7973 | (properties |
| 7974 | `((upstream-name . "TxDb.Mmusculus.UCSC.mm10.knownGene"))) |
| 7975 | (build-system r-build-system) |
| 7976 | ;; As this package provides little more than a very large data file it |
| 7977 | ;; doesn't make sense to build substitutes. |
| 7978 | (arguments `(#:substitutable? #f)) |
| 7979 | (propagated-inputs |
| 7980 | `(("r-bsgenome" ,r-bsgenome) |
| 7981 | ("r-genomicfeatures" ,r-genomicfeatures) |
| 7982 | ("r-annotationdbi" ,r-annotationdbi))) |
| 7983 | (home-page |
| 7984 | "https://bioconductor.org/packages/TxDb.Mmusculus.UCSC.mm10.knownGene/") |
| 7985 | (synopsis "Annotation package for TxDb knownGene object(s) for Mouse") |
| 7986 | (description |
| 7987 | "This package loads a TxDb object, which is an R interface to |
| 7988 | prefabricated databases contained in this package. This package provides |
| 7989 | the TxDb object of Mouse data as provided by UCSC (mm10, December 2011) |
| 7990 | based on the knownGene track.") |
| 7991 | (license license:artistic2.0))) |
| 7992 | |
| 7993 | (define-public r-bsgenome-celegans-ucsc-ce6 |
| 7994 | (package |
| 7995 | (name "r-bsgenome-celegans-ucsc-ce6") |
| 7996 | (version "1.4.0") |
| 7997 | (source (origin |
| 7998 | (method url-fetch) |
| 7999 | ;; We cannot use bioconductor-uri here because this tarball is |
| 8000 | ;; located under "data/annotation/" instead of "bioc/". |
| 8001 | (uri (string-append "https://www.bioconductor.org/packages/" |
| 8002 | "release/data/annotation/src/contrib/" |
| 8003 | "BSgenome.Celegans.UCSC.ce6_" |
| 8004 | version ".tar.gz")) |
| 8005 | (sha256 |
| 8006 | (base32 |
| 8007 | "0mqzb353xv2c3m3vkb315dkmnxkgczp7ndnknyhpgjlybyf715v9")))) |
| 8008 | (properties |
| 8009 | `((upstream-name . "BSgenome.Celegans.UCSC.ce6"))) |
| 8010 | (build-system r-build-system) |
| 8011 | ;; As this package provides little more than a very large data file it |
| 8012 | ;; doesn't make sense to build substitutes. |
| 8013 | (arguments `(#:substitutable? #f)) |
| 8014 | (propagated-inputs |
| 8015 | `(("r-bsgenome" ,r-bsgenome))) |
| 8016 | (home-page |
| 8017 | "https://www.bioconductor.org/packages/BSgenome.Celegans.UCSC.ce6/") |
| 8018 | (synopsis "Full genome sequences for Worm") |
| 8019 | (description |
| 8020 | "This package provides full genome sequences for Caenorhabditis |
| 8021 | elegans (Worm) as provided by UCSC (ce6, May 2008) and stored in Biostrings |
| 8022 | objects.") |
| 8023 | (license license:artistic2.0))) |
| 8024 | |
| 8025 | (define-public r-bsgenome-celegans-ucsc-ce10 |
| 8026 | (package |
| 8027 | (name "r-bsgenome-celegans-ucsc-ce10") |
| 8028 | (version "1.4.0") |
| 8029 | (source (origin |
| 8030 | (method url-fetch) |
| 8031 | ;; We cannot use bioconductor-uri here because this tarball is |
| 8032 | ;; located under "data/annotation/" instead of "bioc/". |
| 8033 | (uri (string-append "https://www.bioconductor.org/packages/" |
| 8034 | "release/data/annotation/src/contrib/" |
| 8035 | "BSgenome.Celegans.UCSC.ce10_" |
| 8036 | version ".tar.gz")) |
| 8037 | (sha256 |
| 8038 | (base32 |
| 8039 | "1zaym97jk4npxk14ifvwz2rvhm4zx9xgs33r9vvx9rlynp0gydrk")))) |
| 8040 | (properties |
| 8041 | `((upstream-name . "BSgenome.Celegans.UCSC.ce10"))) |
| 8042 | (build-system r-build-system) |
| 8043 | ;; As this package provides little more than a very large data file it |
| 8044 | ;; doesn't make sense to build substitutes. |
| 8045 | (arguments `(#:substitutable? #f)) |
| 8046 | (propagated-inputs |
| 8047 | `(("r-bsgenome" ,r-bsgenome))) |
| 8048 | (home-page |
| 8049 | "https://www.bioconductor.org/packages/BSgenome.Celegans.UCSC.ce10/") |
| 8050 | (synopsis "Full genome sequences for Worm") |
| 8051 | (description |
| 8052 | "This package provides full genome sequences for Caenorhabditis |
| 8053 | elegans (Worm) as provided by UCSC (ce10, Oct 2010) and stored in Biostrings |
| 8054 | objects.") |
| 8055 | (license license:artistic2.0))) |
| 8056 | |
| 8057 | (define-public r-bsgenome-dmelanogaster-ucsc-dm3 |
| 8058 | (package |
| 8059 | (name "r-bsgenome-dmelanogaster-ucsc-dm3") |
| 8060 | (version "1.4.0") |
| 8061 | (source (origin |
| 8062 | (method url-fetch) |
| 8063 | ;; We cannot use bioconductor-uri here because this tarball is |
| 8064 | ;; located under "data/annotation/" instead of "bioc/". |
| 8065 | (uri (string-append "https://www.bioconductor.org/packages/" |
| 8066 | "release/data/annotation/src/contrib/" |
| 8067 | "BSgenome.Dmelanogaster.UCSC.dm3_" |
| 8068 | version ".tar.gz")) |
| 8069 | (sha256 |
| 8070 | (base32 |
| 8071 | "19bm3lkhhkag3gnwp419211fh0cnr0x6fa0r1lr0ycwrikxdxsv8")))) |
| 8072 | (properties |
| 8073 | `((upstream-name . "BSgenome.Dmelanogaster.UCSC.dm3"))) |
| 8074 | (build-system r-build-system) |
| 8075 | ;; As this package provides little more than a very large data file it |
| 8076 | ;; doesn't make sense to build substitutes. |
| 8077 | (arguments `(#:substitutable? #f)) |
| 8078 | (propagated-inputs |
| 8079 | `(("r-bsgenome" ,r-bsgenome))) |
| 8080 | (home-page |
| 8081 | "https://www.bioconductor.org/packages/BSgenome.Dmelanogaster.UCSC.dm3/") |
| 8082 | (synopsis "Full genome sequences for Fly") |
| 8083 | (description |
| 8084 | "This package provides full genome sequences for Drosophila |
| 8085 | melanogaster (Fly) as provided by UCSC (dm3, April 2006) and stored in |
| 8086 | Biostrings objects.") |
| 8087 | (license license:artistic2.0))) |
| 8088 | |
| 8089 | (define-public r-motifrg |
| 8090 | (package |
| 8091 | (name "r-motifrg") |
| 8092 | (version "1.22.0") |
| 8093 | (source |
| 8094 | (origin |
| 8095 | (method url-fetch) |
| 8096 | (uri (bioconductor-uri "motifRG" version)) |
| 8097 | (sha256 |
| 8098 | (base32 |
| 8099 | "193zl2rlzwxv9p9q5i7rilj3w05ndqfyp9bdpvagp5s5cin4hf44")))) |
| 8100 | (properties `((upstream-name . "motifRG"))) |
| 8101 | (build-system r-build-system) |
| 8102 | (propagated-inputs |
| 8103 | `(("r-biostrings" ,r-biostrings) |
| 8104 | ("r-bsgenome" ,r-bsgenome) |
| 8105 | ("r-bsgenome-hsapiens-ucsc-hg19" ,r-bsgenome-hsapiens-ucsc-hg19) |
| 8106 | ("r-iranges" ,r-iranges) |
| 8107 | ("r-seqlogo" ,r-seqlogo) |
| 8108 | ("r-xvector" ,r-xvector))) |
| 8109 | (home-page "https://bioconductor.org/packages/motifRG") |
| 8110 | (synopsis "Discover motifs in high throughput sequencing data") |
| 8111 | (description |
| 8112 | "This package provides tools for discriminative motif discovery in high |
| 8113 | throughput genetic sequencing data sets using regression methods.") |
| 8114 | (license license:artistic2.0))) |
| 8115 | |
| 8116 | (define-public r-qtl |
| 8117 | (package |
| 8118 | (name "r-qtl") |
| 8119 | (version "1.41-6") |
| 8120 | (source |
| 8121 | (origin |
| 8122 | (method url-fetch) |
| 8123 | (uri (string-append "mirror://cran/src/contrib/qtl_" |
| 8124 | version ".tar.gz")) |
| 8125 | (sha256 |
| 8126 | (base32 |
| 8127 | "067az4v432zxp6lxck8d7vlh9w4r13r0mvw5zsglyaqwsh3d9sad")))) |
| 8128 | (build-system r-build-system) |
| 8129 | (home-page "http://rqtl.org/") |
| 8130 | (synopsis "R package for analyzing QTL experiments in genetics") |
| 8131 | (description "R/qtl is an extension library for the R statistics |
| 8132 | system. It is used to analyze experimental crosses for identifying |
| 8133 | genes contributing to variation in quantitative traits (so-called |
| 8134 | quantitative trait loci, QTLs). |
| 8135 | |
| 8136 | Using a hidden Markov model, R/qtl allows to estimate genetic maps, to |
| 8137 | identify genotyping errors, and to perform single-QTL and two-QTL, |
| 8138 | two-dimensional genome scans.") |
| 8139 | (license license:gpl3))) |
| 8140 | |
| 8141 | (define-public r-zlibbioc |
| 8142 | (package |
| 8143 | (name "r-zlibbioc") |
| 8144 | (version "1.24.0") |
| 8145 | (source (origin |
| 8146 | (method url-fetch) |
| 8147 | (uri (bioconductor-uri "zlibbioc" version)) |
| 8148 | (sha256 |
| 8149 | (base32 |
| 8150 | "1zr9hbh55hglfpy15cpxwmddxblhyb0an15953l3rbhmlh2vpy92")))) |
| 8151 | (properties |
| 8152 | `((upstream-name . "zlibbioc"))) |
| 8153 | (build-system r-build-system) |
| 8154 | (home-page "https://bioconductor.org/packages/zlibbioc") |
| 8155 | (synopsis "Provider for zlib-1.2.5 to R packages") |
| 8156 | (description "This package uses the source code of zlib-1.2.5 to create |
| 8157 | libraries for systems that do not have these available via other means.") |
| 8158 | (license license:artistic2.0))) |
| 8159 | |
| 8160 | (define-public r-r4rna |
| 8161 | (package |
| 8162 | (name "r-r4rna") |
| 8163 | (version "0.1.4") |
| 8164 | (source |
| 8165 | (origin |
| 8166 | (method url-fetch) |
| 8167 | (uri (string-append "http://www.e-rna.org/r-chie/files/R4RNA_" |
| 8168 | version ".tar.gz")) |
| 8169 | (sha256 |
| 8170 | (base32 |
| 8171 | "1p0i78wh76jfgmn9jphbwwaz6yy6pipzfg08xs54cxavxg2j81p5")))) |
| 8172 | (build-system r-build-system) |
| 8173 | (propagated-inputs |
| 8174 | `(("r-optparse" ,r-optparse) |
| 8175 | ("r-rcolorbrewer" ,r-rcolorbrewer))) |
| 8176 | (home-page "http://www.e-rna.org/r-chie/index.cgi") |
| 8177 | (synopsis "Analysis framework for RNA secondary structure") |
| 8178 | (description |
| 8179 | "The R4RNA package aims to be a general framework for the analysis of RNA |
| 8180 | secondary structure and comparative analysis in R.") |
| 8181 | (license license:gpl3+))) |
| 8182 | |
| 8183 | (define-public r-rhtslib |
| 8184 | (package |
| 8185 | (name "r-rhtslib") |
| 8186 | (version "1.10.0") |
| 8187 | (source |
| 8188 | (origin |
| 8189 | (method url-fetch) |
| 8190 | (uri (bioconductor-uri "Rhtslib" version)) |
| 8191 | (sha256 |
| 8192 | (base32 |
| 8193 | "1dw3p44bfr0m7w39ckc2k37sjcp1zz0b9g12mr8am15jaj6v0q2j")))) |
| 8194 | (properties `((upstream-name . "Rhtslib"))) |
| 8195 | (build-system r-build-system) |
| 8196 | (propagated-inputs |
| 8197 | `(("r-zlibbioc" ,r-zlibbioc))) |
| 8198 | (inputs |
| 8199 | `(("zlib" ,zlib))) |
| 8200 | (native-inputs |
| 8201 | `(("autoconf" ,autoconf))) |
| 8202 | (home-page "https://github.com/nhayden/Rhtslib") |
| 8203 | (synopsis "High-throughput sequencing library as an R package") |
| 8204 | (description |
| 8205 | "This package provides the HTSlib C library for high-throughput |
| 8206 | nucleotide sequence analysis. The package is primarily useful to developers |
| 8207 | of other R packages who wish to make use of HTSlib.") |
| 8208 | (license license:lgpl2.0+))) |
| 8209 | |
| 8210 | (define-public r-bamsignals |
| 8211 | (package |
| 8212 | (name "r-bamsignals") |
| 8213 | (version "1.10.0") |
| 8214 | (source |
| 8215 | (origin |
| 8216 | (method url-fetch) |
| 8217 | (uri (bioconductor-uri "bamsignals" version)) |
| 8218 | (sha256 |
| 8219 | (base32 |
| 8220 | "15id6mkj95skb4kfafvfs2j7ylydal60c3pspcl7llhwpq6vcqvl")))) |
| 8221 | (build-system r-build-system) |
| 8222 | (propagated-inputs |
| 8223 | `(("r-biocgenerics" ,r-biocgenerics) |
| 8224 | ("r-genomicranges" ,r-genomicranges) |
| 8225 | ("r-iranges" ,r-iranges) |
| 8226 | ("r-rcpp" ,r-rcpp) |
| 8227 | ("r-rhtslib" ,r-rhtslib) |
| 8228 | ("r-zlibbioc" ,r-zlibbioc))) |
| 8229 | (inputs |
| 8230 | `(("zlib" ,zlib))) |
| 8231 | (home-page "https://bioconductor.org/packages/bamsignals") |
| 8232 | (synopsis "Extract read count signals from bam files") |
| 8233 | (description |
| 8234 | "This package allows to efficiently obtain count vectors from indexed bam |
| 8235 | files. It counts the number of nucleotide sequence reads in given genomic |
| 8236 | ranges and it computes reads profiles and coverage profiles. It also handles |
| 8237 | paired-end data.") |
| 8238 | (license license:gpl2+))) |
| 8239 | |
| 8240 | (define-public r-rcas |
| 8241 | (package |
| 8242 | (name "r-rcas") |
| 8243 | (version "1.3.4") |
| 8244 | (source (origin |
| 8245 | (method url-fetch) |
| 8246 | (uri (string-append "https://github.com/BIMSBbioinfo/RCAS/archive/v" |
| 8247 | version ".tar.gz")) |
| 8248 | (file-name (string-append name "-" version ".tar.gz")) |
| 8249 | (sha256 |
| 8250 | (base32 |
| 8251 | "1qgc7vi6fpzl440yg7jhiycg5q336kd4pxqzx10yx2zcq3bq3msg")))) |
| 8252 | (build-system r-build-system) |
| 8253 | (native-inputs |
| 8254 | `(("r-knitr" ,r-knitr) |
| 8255 | ("r-testthat" ,r-testthat) |
| 8256 | ;; During vignette building knitr checks that "pandoc-citeproc" |
| 8257 | ;; is in the PATH. |
| 8258 | ("ghc-pandoc-citeproc" ,ghc-pandoc-citeproc))) |
| 8259 | (propagated-inputs |
| 8260 | `(("r-data-table" ,r-data-table) |
| 8261 | ("r-biomart" ,r-biomart) |
| 8262 | ("r-org-hs-eg-db" ,r-org-hs-eg-db) |
| 8263 | ("r-org-ce-eg-db" ,r-org-ce-eg-db) |
| 8264 | ("r-org-dm-eg-db" ,r-org-dm-eg-db) |
| 8265 | ("r-org-mm-eg-db" ,r-org-mm-eg-db) |
| 8266 | ("r-bsgenome-hsapiens-ucsc-hg19" ,r-bsgenome-hsapiens-ucsc-hg19) |
| 8267 | ("r-bsgenome-mmusculus-ucsc-mm9" ,r-bsgenome-mmusculus-ucsc-mm9) |
| 8268 | ("r-bsgenome-celegans-ucsc-ce10" ,r-bsgenome-celegans-ucsc-ce10) |
| 8269 | ("r-bsgenome-dmelanogaster-ucsc-dm3" ,r-bsgenome-dmelanogaster-ucsc-dm3) |
| 8270 | ("r-topgo" ,r-topgo) |
| 8271 | ("r-dt" ,r-dt) |
| 8272 | ("r-pbapply" ,r-pbapply) |
| 8273 | ("r-plotly" ,r-plotly) |
| 8274 | ("r-plotrix" ,r-plotrix) |
| 8275 | ("r-motifrg" ,r-motifrg) |
| 8276 | ("r-genomation" ,r-genomation) |
| 8277 | ("r-genomicfeatures" ,r-genomicfeatures) |
| 8278 | ("r-rtracklayer" ,r-rtracklayer) |
| 8279 | ("r-rmarkdown" ,r-rmarkdown))) |
| 8280 | (synopsis "RNA-centric annotation system") |
| 8281 | (description |
| 8282 | "RCAS aims to be a standalone RNA-centric annotation system that provides |
| 8283 | intuitive reports and publication-ready graphics. This package provides the R |
| 8284 | library implementing most of the pipeline's features.") |
| 8285 | (home-page "https://github.com/BIMSBbioinfo/RCAS") |
| 8286 | (license license:artistic2.0))) |
| 8287 | |
| 8288 | (define-public rcas-web |
| 8289 | (package |
| 8290 | (name "rcas-web") |
| 8291 | (version "0.0.4") |
| 8292 | (source |
| 8293 | (origin |
| 8294 | (method url-fetch) |
| 8295 | (uri (string-append "https://github.com/BIMSBbioinfo/rcas-web/" |
| 8296 | "releases/download/v" version |
| 8297 | "/rcas-web-" version ".tar.gz")) |
| 8298 | (sha256 |
| 8299 | (base32 |
| 8300 | "1p16frfys41a8yaa4gkm457nzkqhqs2pc3lkac0ds457w9w5j1gm")))) |
| 8301 | (build-system gnu-build-system) |
| 8302 | (arguments |
| 8303 | `(#:phases |
| 8304 | (modify-phases %standard-phases |
| 8305 | (add-after 'install 'wrap-executable |
| 8306 | (lambda* (#:key inputs outputs #:allow-other-keys) |
| 8307 | (let* ((out (assoc-ref outputs "out")) |
| 8308 | (json (assoc-ref inputs "guile-json")) |
| 8309 | (redis (assoc-ref inputs "guile-redis")) |
| 8310 | (path (string-append |
| 8311 | json "/share/guile/site/2.2:" |
| 8312 | redis "/share/guile/site/2.2"))) |
| 8313 | (wrap-program (string-append out "/bin/rcas-web") |
| 8314 | `("GUILE_LOAD_PATH" ":" = (,path)) |
| 8315 | `("GUILE_LOAD_COMPILED_PATH" ":" = (,path)) |
| 8316 | `("R_LIBS_SITE" ":" = (,(getenv "R_LIBS_SITE"))))) |
| 8317 | #t))))) |
| 8318 | (inputs |
| 8319 | `(("r-minimal" ,r-minimal) |
| 8320 | ("r-rcas" ,r-rcas) |
| 8321 | ("guile-next" ,guile-2.2) |
| 8322 | ("guile-json" ,guile-json) |
| 8323 | ("guile-redis" ,guile2.2-redis))) |
| 8324 | (native-inputs |
| 8325 | `(("pkg-config" ,pkg-config))) |
| 8326 | (home-page "https://github.com/BIMSBbioinfo/rcas-web") |
| 8327 | (synopsis "Web interface for RNA-centric annotation system (RCAS)") |
| 8328 | (description "This package provides a simple web interface for the |
| 8329 | @dfn{RNA-centric annotation system} (RCAS).") |
| 8330 | (license license:agpl3+))) |
| 8331 | |
| 8332 | (define-public r-mutationalpatterns |
| 8333 | (package |
| 8334 | (name "r-mutationalpatterns") |
| 8335 | (version "1.4.2") |
| 8336 | (source |
| 8337 | (origin |
| 8338 | (method url-fetch) |
| 8339 | (uri (bioconductor-uri "MutationalPatterns" version)) |
| 8340 | (sha256 |
| 8341 | (base32 |
| 8342 | "08ay9h5cqsi8ypb6r0g4rfa5l1g06jgfzl64wmhgz134yqbl7vfv")))) |
| 8343 | (build-system r-build-system) |
| 8344 | (propagated-inputs |
| 8345 | `(("r-biocgenerics" ,r-biocgenerics) |
| 8346 | ("r-biostrings" ,r-biostrings) |
| 8347 | ("r-bsgenome-hsapiens-1000g" ,r-bsgenome-hsapiens-1000genomes-hs37d5) |
| 8348 | ("r-bsgenome-hsapiens-ucsc-hg19" ,r-bsgenome-hsapiens-ucsc-hg19) |
| 8349 | ("r-genomicranges" ,r-genomicranges) |
| 8350 | ("r-genomeinfodb" ,r-genomeinfodb) |
| 8351 | ("r-ggplot2" ,r-ggplot2) |
| 8352 | ("r-gridextra" ,r-gridextra) |
| 8353 | ("r-iranges" ,r-iranges) |
| 8354 | ("r-nmf" ,r-nmf) |
| 8355 | ("r-plyr" ,r-plyr) |
| 8356 | ("r-pracma" ,r-pracma) |
| 8357 | ("r-reshape2" ,r-reshape2) |
| 8358 | ("r-cowplot" ,r-cowplot) |
| 8359 | ("r-ggdendro" ,r-ggdendro) |
| 8360 | ("r-s4vectors" ,r-s4vectors) |
| 8361 | ("r-summarizedexperiment" ,r-summarizedexperiment) |
| 8362 | ("r-variantannotation" ,r-variantannotation))) |
| 8363 | (home-page "https://bioconductor.org/packages/MutationalPatterns/") |
| 8364 | (synopsis "Extract and visualize mutational patterns in genomic data") |
| 8365 | (description "This package provides an extensive toolset for the |
| 8366 | characterization and visualization of a wide range of mutational patterns |
| 8367 | in SNV base substitution data.") |
| 8368 | (license license:expat))) |
| 8369 | |
| 8370 | (define-public r-wgcna |
| 8371 | (package |
| 8372 | (name "r-wgcna") |
| 8373 | (version "1.61") |
| 8374 | (source |
| 8375 | (origin |
| 8376 | (method url-fetch) |
| 8377 | (uri (cran-uri "WGCNA" version)) |
| 8378 | (sha256 |
| 8379 | (base32 |
| 8380 | "1vrc2k33a196hrrl7k0z534fp96vv0shmigcr65ny1q0v6lq0h6i")))) |
| 8381 | (properties `((upstream-name . "WGCNA"))) |
| 8382 | (build-system r-build-system) |
| 8383 | (propagated-inputs |
| 8384 | `(("r-annotationdbi" ,r-annotationdbi) |
| 8385 | ("r-doparallel" ,r-doparallel) |
| 8386 | ("r-dynamictreecut" ,r-dynamictreecut) |
| 8387 | ("r-fastcluster" ,r-fastcluster) |
| 8388 | ("r-foreach" ,r-foreach) |
| 8389 | ("r-go-db" ,r-go-db) |
| 8390 | ("r-hmisc" ,r-hmisc) |
| 8391 | ("r-impute" ,r-impute) |
| 8392 | ("r-rcpp" ,r-rcpp) |
| 8393 | ("r-robust" ,r-robust) |
| 8394 | ("r-survival" ,r-survival) |
| 8395 | ("r-matrixstats" ,r-matrixstats) |
| 8396 | ("r-preprocesscore" ,r-preprocesscore))) |
| 8397 | (home-page |
| 8398 | "http://www.genetics.ucla.edu/labs/horvath/CoexpressionNetwork/Rpackages/WGCNA/") |
| 8399 | (synopsis "Weighted correlation network analysis") |
| 8400 | (description |
| 8401 | "This package provides functions necessary to perform Weighted |
| 8402 | Correlation Network Analysis on high-dimensional data. It includes functions |
| 8403 | for rudimentary data cleaning, construction and summarization of correlation |
| 8404 | networks, module identification and functions for relating both variables and |
| 8405 | modules to sample traits. It also includes a number of utility functions for |
| 8406 | data manipulation and visualization.") |
| 8407 | (license license:gpl2+))) |
| 8408 | |
| 8409 | (define-public r-chipkernels |
| 8410 | (let ((commit "c9cfcacb626b1221094fb3490ea7bac0fd625372") |
| 8411 | (revision "1")) |
| 8412 | (package |
| 8413 | (name "r-chipkernels") |
| 8414 | (version (string-append "1.1-" revision "." (string-take commit 9))) |
| 8415 | (source |
| 8416 | (origin |
| 8417 | (method git-fetch) |
| 8418 | (uri (git-reference |
| 8419 | (url "https://github.com/ManuSetty/ChIPKernels.git") |
| 8420 | (commit commit))) |
| 8421 | (file-name (string-append name "-" version)) |
| 8422 | (sha256 |
| 8423 | (base32 |
| 8424 | "14bj5qhjm1hsm9ay561nfbqi9wxsa7y487df2idsaaf6z10nw4v0")))) |
| 8425 | (build-system r-build-system) |
| 8426 | (propagated-inputs |
| 8427 | `(("r-iranges" ,r-iranges) |
| 8428 | ("r-xvector" ,r-xvector) |
| 8429 | ("r-biostrings" ,r-biostrings) |
| 8430 | ("r-bsgenome" ,r-bsgenome) |
| 8431 | ("r-gtools" ,r-gtools) |
| 8432 | ("r-genomicranges" ,r-genomicranges) |
| 8433 | ("r-sfsmisc" ,r-sfsmisc) |
| 8434 | ("r-kernlab" ,r-kernlab) |
| 8435 | ("r-s4vectors" ,r-s4vectors) |
| 8436 | ("r-biocgenerics" ,r-biocgenerics))) |
| 8437 | (home-page "https://github.com/ManuSetty/ChIPKernels") |
| 8438 | (synopsis "Build string kernels for DNA Sequence analysis") |
| 8439 | (description "ChIPKernels is an R package for building different string |
| 8440 | kernels used for DNA Sequence analysis. A dictionary of the desired kernel |
| 8441 | must be built and this dictionary can be used for determining kernels for DNA |
| 8442 | Sequences.") |
| 8443 | (license license:gpl2+)))) |
| 8444 | |
| 8445 | (define-public r-seqgl |
| 8446 | (package |
| 8447 | (name "r-seqgl") |
| 8448 | (version "1.1.4") |
| 8449 | (source |
| 8450 | (origin |
| 8451 | (method url-fetch) |
| 8452 | (uri (string-append "https://github.com/ManuSetty/SeqGL/" |
| 8453 | "archive/" version ".tar.gz")) |
| 8454 | (file-name (string-append name "-" version ".tar.gz")) |
| 8455 | (sha256 |
| 8456 | (base32 |
| 8457 | "0pnk1p3sci5yipyc8xnb6jbmydpl80fld927xgnbcv104hy8h8yh")))) |
| 8458 | (build-system r-build-system) |
| 8459 | (propagated-inputs |
| 8460 | `(("r-biostrings" ,r-biostrings) |
| 8461 | ("r-chipkernels" ,r-chipkernels) |
| 8462 | ("r-genomicranges" ,r-genomicranges) |
| 8463 | ("r-spams" ,r-spams) |
| 8464 | ("r-wgcna" ,r-wgcna) |
| 8465 | ("r-fastcluster" ,r-fastcluster))) |
| 8466 | (home-page "https://github.com/ManuSetty/SeqGL") |
| 8467 | (synopsis "Group lasso for Dnase/ChIP-seq data") |
| 8468 | (description "SeqGL is a group lasso based algorithm to extract |
| 8469 | transcription factor sequence signals from ChIP, DNase and ATAC-seq profiles. |
| 8470 | This package presents a method which uses group lasso to discriminate between |
| 8471 | bound and non bound genomic regions to accurately identify transcription |
| 8472 | factors bound at the specific regions.") |
| 8473 | (license license:gpl2+))) |
| 8474 | |
| 8475 | (define-public r-gkmsvm |
| 8476 | (package |
| 8477 | (name "r-gkmsvm") |
| 8478 | (version "0.71.0") |
| 8479 | (source |
| 8480 | (origin |
| 8481 | (method url-fetch) |
| 8482 | (uri (cran-uri "gkmSVM" version)) |
| 8483 | (sha256 |
| 8484 | (base32 |
| 8485 | "1zpxgxmf2nd5j5wn00ps6kfxr8wxh7d1swr1rr4spq7sj5z5z0k0")))) |
| 8486 | (properties `((upstream-name . "gkmSVM"))) |
| 8487 | (build-system r-build-system) |
| 8488 | (propagated-inputs |
| 8489 | `(("r-biocgenerics" ,r-biocgenerics) |
| 8490 | ("r-biostrings" ,r-biostrings) |
| 8491 | ("r-genomeinfodb" ,r-genomeinfodb) |
| 8492 | ("r-genomicranges" ,r-genomicranges) |
| 8493 | ("r-iranges" ,r-iranges) |
| 8494 | ("r-kernlab" ,r-kernlab) |
| 8495 | ("r-rcpp" ,r-rcpp) |
| 8496 | ("r-rocr" ,r-rocr) |
| 8497 | ("r-rtracklayer" ,r-rtracklayer) |
| 8498 | ("r-s4vectors" ,r-s4vectors) |
| 8499 | ("r-seqinr" ,r-seqinr))) |
| 8500 | (home-page "https://cran.r-project.org/web/packages/gkmSVM") |
| 8501 | (synopsis "Gapped-kmer support vector machine") |
| 8502 | (description |
| 8503 | "This R package provides tools for training gapped-kmer SVM classifiers |
| 8504 | for DNA and protein sequences. This package supports several sequence |
| 8505 | kernels, including: gkmSVM, kmer-SVM, mismatch kernel and wildcard kernel.") |
| 8506 | (license license:gpl2+))) |
| 8507 | |
| 8508 | (define-public r-tximport |
| 8509 | (package |
| 8510 | (name "r-tximport") |
| 8511 | (version "1.6.0") |
| 8512 | (source (origin |
| 8513 | (method url-fetch) |
| 8514 | (uri (bioconductor-uri "tximport" version)) |
| 8515 | (sha256 |
| 8516 | (base32 |
| 8517 | "1gyqcm91hxg1kgjqcz2qw1n56yp9pymjzs50rwcpb2893dr8sp2h")))) |
| 8518 | (build-system r-build-system) |
| 8519 | (home-page "https://bioconductor.org/packages/tximport") |
| 8520 | (synopsis "Import and summarize transcript-level estimates for gene-level analysis") |
| 8521 | (description |
| 8522 | "This package provides tools to import transcript-level abundance, |
| 8523 | estimated counts and transcript lengths, and to summarize them into matrices |
| 8524 | for use with downstream gene-level analysis packages. Average transcript |
| 8525 | length, weighted by sample-specific transcript abundance estimates, is |
| 8526 | provided as a matrix which can be used as an offset for different expression |
| 8527 | of gene-level counts.") |
| 8528 | (license license:gpl2+))) |
| 8529 | |
| 8530 | (define-public r-rhdf5 |
| 8531 | (package |
| 8532 | (name "r-rhdf5") |
| 8533 | (version "2.22.0") |
| 8534 | (source (origin |
| 8535 | (method url-fetch) |
| 8536 | (uri (bioconductor-uri "rhdf5" version)) |
| 8537 | (sha256 |
| 8538 | (base32 |
| 8539 | "145858qg1xan6imxcbprzq3yn3mdf532aahdr6cibvdjg47hs4c1")))) |
| 8540 | (build-system r-build-system) |
| 8541 | (arguments |
| 8542 | `(#:phases |
| 8543 | (modify-phases %standard-phases |
| 8544 | (add-after 'unpack 'unpack-smallhdf5 |
| 8545 | (lambda* (#:key outputs #:allow-other-keys) |
| 8546 | (system* "tar" "-xzvf" |
| 8547 | "src/hdf5source/hdf5small.tgz" "-C" "src/" ) |
| 8548 | (substitute* "src/hdf5/configure" |
| 8549 | (("/bin/mv") "mv")) |
| 8550 | #t))))) |
| 8551 | (propagated-inputs |
| 8552 | `(("r-zlibbioc" ,r-zlibbioc))) |
| 8553 | (inputs |
| 8554 | `(("perl" ,perl) |
| 8555 | ("zlib" ,zlib))) |
| 8556 | (home-page "https://bioconductor.org/packages/rhdf5") |
| 8557 | (synopsis "HDF5 interface to R") |
| 8558 | (description |
| 8559 | "This R/Bioconductor package provides an interface between HDF5 and R. |
| 8560 | HDF5's main features are the ability to store and access very large and/or |
| 8561 | complex datasets and a wide variety of metadata on mass storage (disk) through |
| 8562 | a completely portable file format. The rhdf5 package is thus suited for the |
| 8563 | exchange of large and/or complex datasets between R and other software |
| 8564 | package, and for letting R applications work on datasets that are larger than |
| 8565 | the available RAM.") |
| 8566 | (license license:artistic2.0))) |
| 8567 | |
| 8568 | (define-public r-annotationfilter |
| 8569 | (package |
| 8570 | (name "r-annotationfilter") |
| 8571 | (version "1.2.0") |
| 8572 | (source (origin |
| 8573 | (method url-fetch) |
| 8574 | (uri (bioconductor-uri "AnnotationFilter" version)) |
| 8575 | (sha256 |
| 8576 | (base32 |
| 8577 | "04zf864c1fvdlaay2r5cn30fc1n5i3czh31fs62qlrvs61wjiscs")))) |
| 8578 | (properties |
| 8579 | `((upstream-name . "AnnotationFilter"))) |
| 8580 | (build-system r-build-system) |
| 8581 | (propagated-inputs |
| 8582 | `(("r-genomicranges" ,r-genomicranges) |
| 8583 | ("r-lazyeval" ,r-lazyeval))) |
| 8584 | (home-page "https://github.com/Bioconductor/AnnotationFilter") |
| 8585 | (synopsis "Facilities for filtering Bioconductor annotation resources") |
| 8586 | (description |
| 8587 | "This package provides classes and other infrastructure to implement |
| 8588 | filters for manipulating Bioconductor annotation resources. The filters are |
| 8589 | used by @code{ensembldb}, @code{Organism.dplyr}, and other packages.") |
| 8590 | (license license:artistic2.0))) |
| 8591 | |
| 8592 | (define-public emboss |
| 8593 | (package |
| 8594 | (name "emboss") |
| 8595 | (version "6.5.7") |
| 8596 | (source (origin |
| 8597 | (method url-fetch) |
| 8598 | (uri (string-append "ftp://emboss.open-bio.org/pub/EMBOSS/old/" |
| 8599 | (version-major+minor version) ".0/" |
| 8600 | "EMBOSS-" version ".tar.gz")) |
| 8601 | (sha256 |
| 8602 | (base32 |
| 8603 | "0vsmz96gc411yj2iyzdrsmg4l2n1nhgmp7vrgzlxx3xixv9xbf0q")))) |
| 8604 | (build-system gnu-build-system) |
| 8605 | (arguments |
| 8606 | `(#:configure-flags |
| 8607 | (list (string-append "--with-hpdf=" |
| 8608 | (assoc-ref %build-inputs "libharu"))) |
| 8609 | #:phases |
| 8610 | (modify-phases %standard-phases |
| 8611 | (add-after 'unpack 'fix-checks |
| 8612 | (lambda _ |
| 8613 | ;; The PNGDRIVER tests check for the presence of libgd, libpng |
| 8614 | ;; and zlib, but assume that they are all found at the same |
| 8615 | ;; prefix. |
| 8616 | (substitute* "configure.in" |
| 8617 | (("CHECK_PNGDRIVER") |
| 8618 | "LIBS=\"$LIBS -lgd -lpng -lz -lm\" |
| 8619 | AC_DEFINE([PLD_png], [1], [Define to 1 if PNG support is available]) |
| 8620 | AM_CONDITIONAL(AMPNG, true)")) |
| 8621 | #t)) |
| 8622 | (add-after 'fix-checks 'disable-update-check |
| 8623 | (lambda _ |
| 8624 | ;; At build time there is no connection to the Internet, so |
| 8625 | ;; looking for updates will not work. |
| 8626 | (substitute* "Makefile.am" |
| 8627 | (("\\$\\(bindir\\)/embossupdate") "")) |
| 8628 | #t)) |
| 8629 | (add-after 'disable-update-check 'autogen |
| 8630 | (lambda _ (zero? (system* "autoreconf" "-vif"))))))) |
| 8631 | (inputs |
| 8632 | `(("perl" ,perl) |
| 8633 | ("libpng" ,libpng) |
| 8634 | ("gd" ,gd) |
| 8635 | ("libx11" ,libx11) |
| 8636 | ("libharu" ,libharu) |
| 8637 | ("zlib" ,zlib))) |
| 8638 | (native-inputs |
| 8639 | `(("autoconf" ,autoconf) |
| 8640 | ("automake" ,automake) |
| 8641 | ("libtool" ,libtool) |
| 8642 | ("pkg-config" ,pkg-config))) |
| 8643 | (home-page "http://emboss.sourceforge.net") |
| 8644 | (synopsis "Molecular biology analysis suite") |
| 8645 | (description "EMBOSS is the \"European Molecular Biology Open Software |
| 8646 | Suite\". EMBOSS is an analysis package specially developed for the needs of |
| 8647 | the molecular biology (e.g. EMBnet) user community. The software |
| 8648 | automatically copes with data in a variety of formats and even allows |
| 8649 | transparent retrieval of sequence data from the web. It also provides a |
| 8650 | number of libraries for the development of software in the field of molecular |
| 8651 | biology. EMBOSS also integrates a range of currently available packages and |
| 8652 | tools for sequence analysis into a seamless whole.") |
| 8653 | (license license:gpl2+))) |
| 8654 | |
| 8655 | (define-public bits |
| 8656 | (let ((revision "1") |
| 8657 | (commit "3cc4567896d9d6442923da944beb704750a08d2d")) |
| 8658 | (package |
| 8659 | (name "bits") |
| 8660 | ;; The version is 2.13.0 even though no release archives have been |
| 8661 | ;; published as yet. |
| 8662 | (version (string-append "2.13.0-" revision "." (string-take commit 9))) |
| 8663 | (source (origin |
| 8664 | (method git-fetch) |
| 8665 | (uri (git-reference |
| 8666 | (url "https://github.com/arq5x/bits.git") |
| 8667 | (commit commit))) |
| 8668 | (file-name (string-append name "-" version "-checkout")) |
| 8669 | (sha256 |
| 8670 | (base32 |
| 8671 | "17n2kffk4kmhivd8c98g2vr6y1s23vbg4sxlxs689wni66797hbs")))) |
| 8672 | (build-system gnu-build-system) |
| 8673 | (arguments |
| 8674 | `(#:tests? #f ;no tests included |
| 8675 | #:phases |
| 8676 | (modify-phases %standard-phases |
| 8677 | (delete 'configure) |
| 8678 | (add-after 'unpack 'remove-cuda |
| 8679 | (lambda _ |
| 8680 | (substitute* "Makefile" |
| 8681 | ((".*_cuda") "") |
| 8682 | (("(bits_test_intersections) \\\\" _ match) match)) |
| 8683 | #t)) |
| 8684 | (replace 'install |
| 8685 | (lambda* (#:key outputs #:allow-other-keys) |
| 8686 | (copy-recursively |
| 8687 | "bin" (string-append (assoc-ref outputs "out") "/bin")) |
| 8688 | #t))))) |
| 8689 | (inputs |
| 8690 | `(("gsl" ,gsl) |
| 8691 | ("zlib" ,zlib))) |
| 8692 | (home-page "https://github.com/arq5x/bits") |
| 8693 | (synopsis "Implementation of binary interval search algorithm") |
| 8694 | (description "This package provides an implementation of the |
| 8695 | BITS (Binary Interval Search) algorithm, an approach to interval set |
| 8696 | intersection. It is especially suited for the comparison of diverse genomic |
| 8697 | datasets and the exploration of large datasets of genome |
| 8698 | intervals (e.g. genes, sequence alignments).") |
| 8699 | (license license:gpl2)))) |
| 8700 | |
| 8701 | (define-public piranha |
| 8702 | ;; There is no release tarball for the latest version. The latest commit is |
| 8703 | ;; older than one year at the time of this writing. |
| 8704 | (let ((revision "1") |
| 8705 | (commit "0466d364b71117d01e4471b74c514436cc281233")) |
| 8706 | (package |
| 8707 | (name "piranha") |
| 8708 | (version (string-append "1.2.1-" revision "." (string-take commit 9))) |
| 8709 | (source (origin |
| 8710 | (method git-fetch) |
| 8711 | (uri (git-reference |
| 8712 | (url "https://github.com/smithlabcode/piranha.git") |
| 8713 | (commit commit))) |
| 8714 | (sha256 |
| 8715 | (base32 |
| 8716 | "117dc0zf20c61jam69sk4abl57ah6yi6i7qra7d7y5zrbgk12q5n")))) |
| 8717 | (build-system gnu-build-system) |
| 8718 | (arguments |
| 8719 | `(#:test-target "test" |
| 8720 | #:phases |
| 8721 | (modify-phases %standard-phases |
| 8722 | (add-after 'unpack 'copy-smithlab-cpp |
| 8723 | (lambda* (#:key inputs #:allow-other-keys) |
| 8724 | (for-each (lambda (file) |
| 8725 | (install-file file "./src/smithlab_cpp/")) |
| 8726 | (find-files (assoc-ref inputs "smithlab-cpp"))) |
| 8727 | #t)) |
| 8728 | (add-after 'install 'install-to-store |
| 8729 | (lambda* (#:key outputs #:allow-other-keys) |
| 8730 | (let* ((out (assoc-ref outputs "out")) |
| 8731 | (bin (string-append out "/bin"))) |
| 8732 | (for-each (lambda (file) |
| 8733 | (install-file file bin)) |
| 8734 | (find-files "bin" ".*"))) |
| 8735 | #t))) |
| 8736 | #:configure-flags |
| 8737 | (list (string-append "--with-bam_tools_headers=" |
| 8738 | (assoc-ref %build-inputs "bamtools") "/include/bamtools") |
| 8739 | (string-append "--with-bam_tools_library=" |
| 8740 | (assoc-ref %build-inputs "bamtools") "/lib/bamtools")))) |
| 8741 | (inputs |
| 8742 | `(("bamtools" ,bamtools) |
| 8743 | ("samtools" ,samtools-0.1) |
| 8744 | ("gsl" ,gsl) |
| 8745 | ("smithlab-cpp" |
| 8746 | ,(let ((commit "3723e2db438c51501d0423429ff396c3035ba46a")) |
| 8747 | (origin |
| 8748 | (method git-fetch) |
| 8749 | (uri (git-reference |
| 8750 | (url "https://github.com/smithlabcode/smithlab_cpp.git") |
| 8751 | (commit commit))) |
| 8752 | (file-name (string-append "smithlab_cpp-" commit "-checkout")) |
| 8753 | (sha256 |
| 8754 | (base32 |
| 8755 | "0l4gvbwslw5ngziskja41c00x1r06l3yidv7y0xw9djibhykzy0g"))))))) |
| 8756 | (native-inputs |
| 8757 | `(("python" ,python-2))) |
| 8758 | (home-page "https://github.com/smithlabcode/piranha") |
| 8759 | (synopsis "Peak-caller for CLIP-seq and RIP-seq data") |
| 8760 | (description |
| 8761 | "Piranha is a peak-caller for genomic data produced by CLIP-seq and |
| 8762 | RIP-seq experiments. It takes input in BED or BAM format and identifies |
| 8763 | regions of statistically significant read enrichment. Additional covariates |
| 8764 | may optionally be provided to further inform the peak-calling process.") |
| 8765 | (license license:gpl3+)))) |
| 8766 | |
| 8767 | (define-public pepr |
| 8768 | (package |
| 8769 | (name "pepr") |
| 8770 | (version "1.0.9") |
| 8771 | (source (origin |
| 8772 | (method url-fetch) |
| 8773 | (uri (string-append "https://pypi.python.org/packages/source/P" |
| 8774 | "/PePr/PePr-" version ".tar.gz")) |
| 8775 | (sha256 |
| 8776 | (base32 |
| 8777 | "0qxjfdpl1b1y53nccws2d85f6k74zwmx8y8sd9rszcqhfayx6gdx")))) |
| 8778 | (build-system python-build-system) |
| 8779 | (arguments |
| 8780 | `(#:python ,python-2 ; python2 only |
| 8781 | #:tests? #f)) ; no tests included |
| 8782 | (propagated-inputs |
| 8783 | `(("python2-numpy" ,python2-numpy) |
| 8784 | ("python2-scipy" ,python2-scipy) |
| 8785 | ("python2-pysam" ,python2-pysam))) |
| 8786 | (home-page "https://github.com/shawnzhangyx/PePr") |
| 8787 | (synopsis "Peak-calling and prioritization pipeline for ChIP-Seq data") |
| 8788 | (description |
| 8789 | "PePr is a ChIP-Seq peak calling or differential binding analysis tool |
| 8790 | that is primarily designed for data with biological replicates. It uses a |
| 8791 | negative binomial distribution to model the read counts among the samples in |
| 8792 | the same group, and look for consistent differences between ChIP and control |
| 8793 | group or two ChIP groups run under different conditions.") |
| 8794 | (license license:gpl3+))) |
| 8795 | |
| 8796 | (define-public filevercmp |
| 8797 | (let ((commit "1a9b779b93d0b244040274794d402106907b71b7")) |
| 8798 | (package |
| 8799 | (name "filevercmp") |
| 8800 | (version (string-append "0-1." (string-take commit 7))) |
| 8801 | (source (origin |
| 8802 | (method url-fetch) |
| 8803 | (uri (string-append "https://github.com/ekg/filevercmp/archive/" |
| 8804 | commit ".tar.gz")) |
| 8805 | (file-name (string-append name "-" version ".tar.gz")) |
| 8806 | (sha256 |
| 8807 | (base32 "0yp5jswf5j2pqc6517x277s4s6h1ss99v57kxw9gy0jkfl3yh450")))) |
| 8808 | (build-system gnu-build-system) |
| 8809 | (arguments |
| 8810 | `(#:tests? #f ; There are no tests to run. |
| 8811 | #:phases |
| 8812 | (modify-phases %standard-phases |
| 8813 | (delete 'configure) ; There is no configure phase. |
| 8814 | (replace 'install |
| 8815 | (lambda* (#:key outputs #:allow-other-keys) |
| 8816 | (let ((bin (string-append (assoc-ref outputs "out") "/bin"))) |
| 8817 | (install-file "filevercmp" bin))))))) |
| 8818 | (home-page "https://github.com/ekg/filevercmp") |
| 8819 | (synopsis "This program compares version strings") |
| 8820 | (description "This program compares version strings. It intends to be a |
| 8821 | replacement for strverscmp.") |
| 8822 | (license license:gpl3+)))) |
| 8823 | |
| 8824 | (define-public multiqc |
| 8825 | (package |
| 8826 | (name "multiqc") |
| 8827 | (version "1.3") |
| 8828 | (source |
| 8829 | (origin |
| 8830 | (method url-fetch) |
| 8831 | (uri (pypi-uri "multiqc" version)) |
| 8832 | (sha256 |
| 8833 | (base32 |
| 8834 | "0fx1sx53znbgzfhbbiyd8j6cg5llpcsl5q5c45jy2c81d12piqfd")))) |
| 8835 | (build-system python-build-system) |
| 8836 | (propagated-inputs |
| 8837 | `(("python-enum34" ,python-enum34) |
| 8838 | ("python-jinja2" ,python-jinja2) |
| 8839 | ("python-simplejson" ,python-simplejson) |
| 8840 | ("python-pyyaml" ,python-pyyaml) |
| 8841 | ("python-click" ,python-click) |
| 8842 | ("python-spectra" ,python-spectra) |
| 8843 | ("python-requests" ,python-requests) |
| 8844 | ("python-markdown" ,python-markdown) |
| 8845 | ("python-lzstring" ,python-lzstring) |
| 8846 | ("python-matplotlib" ,python-matplotlib) |
| 8847 | ("python-numpy" ,python-numpy) |
| 8848 | ;; MultQC checks for the presence of nose at runtime. |
| 8849 | ("python-nose" ,python-nose))) |
| 8850 | (home-page "http://multiqc.info") |
| 8851 | (synopsis "Aggregate bioinformatics analysis reports") |
| 8852 | (description |
| 8853 | "MultiQC is a tool to aggregate bioinformatics results across many |
| 8854 | samples into a single report. It contains modules for a large number of |
| 8855 | common bioinformatics tools.") |
| 8856 | (license license:gpl3+))) |
| 8857 | |
| 8858 | (define-public r-chipseq |
| 8859 | (package |
| 8860 | (name "r-chipseq") |
| 8861 | (version "1.28.0") |
| 8862 | (source |
| 8863 | (origin |
| 8864 | (method url-fetch) |
| 8865 | (uri (bioconductor-uri "chipseq" version)) |
| 8866 | (sha256 |
| 8867 | (base32 |
| 8868 | "1ymcq77krwjzrkzzcw7i9909cmkqa7c0675z9wzvrrk81hgdssfq")))) |
| 8869 | (build-system r-build-system) |
| 8870 | (propagated-inputs |
| 8871 | `(("r-biocgenerics" ,r-biocgenerics) |
| 8872 | ("r-genomicranges" ,r-genomicranges) |
| 8873 | ("r-iranges" ,r-iranges) |
| 8874 | ("r-lattice" ,r-lattice) |
| 8875 | ("r-s4vectors" ,r-s4vectors) |
| 8876 | ("r-shortread" ,r-shortread))) |
| 8877 | (home-page "https://bioconductor.org/packages/chipseq") |
| 8878 | (synopsis "Package for analyzing ChIPseq data") |
| 8879 | (description |
| 8880 | "This package provides tools for processing short read data from ChIPseq |
| 8881 | experiments.") |
| 8882 | (license license:artistic2.0))) |
| 8883 | |
| 8884 | (define-public r-copyhelper |
| 8885 | (package |
| 8886 | (name "r-copyhelper") |
| 8887 | (version "1.6.0") |
| 8888 | (source |
| 8889 | (origin |
| 8890 | (method url-fetch) |
| 8891 | (uri (string-append "https://bioconductor.org/packages/release/" |
| 8892 | "data/experiment/src/contrib/CopyhelpeR_" |
| 8893 | version ".tar.gz")) |
| 8894 | (sha256 |
| 8895 | (base32 |
| 8896 | "0x7cyynjmxls9as2gg0iyp9x5fpalxmdjq914ss7i84i9zyk5bhq")))) |
| 8897 | (properties `((upstream-name . "CopyhelpeR"))) |
| 8898 | (build-system r-build-system) |
| 8899 | (home-page "https://bioconductor.org/packages/CopyhelpeR/") |
| 8900 | (synopsis "Helper files for CopywriteR") |
| 8901 | (description |
| 8902 | "This package contains the helper files that are required to run the |
| 8903 | Bioconductor package CopywriteR. It contains pre-assembled 1kb bin GC-content |
| 8904 | and mappability files for the reference genomes hg18, hg19, hg38, mm9 and |
| 8905 | mm10. In addition, it contains a blacklist filter to remove regions that |
| 8906 | display copy number variation. Files are stored as GRanges objects from the |
| 8907 | GenomicRanges Bioconductor package.") |
| 8908 | (license license:gpl2))) |
| 8909 | |
| 8910 | (define-public r-copywriter |
| 8911 | (package |
| 8912 | (name "r-copywriter") |
| 8913 | (version "2.10.0") |
| 8914 | (source |
| 8915 | (origin |
| 8916 | (method url-fetch) |
| 8917 | (uri (bioconductor-uri "CopywriteR" version)) |
| 8918 | (sha256 |
| 8919 | (base32 |
| 8920 | "17fy2lc5yf3nh6v077kv87h53n263hqz2540lzrl0vjiqrl2plca")))) |
| 8921 | (properties `((upstream-name . "CopywriteR"))) |
| 8922 | (build-system r-build-system) |
| 8923 | (propagated-inputs |
| 8924 | `(("r-biocparallel" ,r-biocparallel) |
| 8925 | ("r-chipseq" ,r-chipseq) |
| 8926 | ("r-copyhelper" ,r-copyhelper) |
| 8927 | ("r-data-table" ,r-data-table) |
| 8928 | ("r-dnacopy" ,r-dnacopy) |
| 8929 | ("r-futile-logger" ,r-futile-logger) |
| 8930 | ("r-genomeinfodb" ,r-genomeinfodb) |
| 8931 | ("r-genomicalignments" ,r-genomicalignments) |
| 8932 | ("r-genomicranges" ,r-genomicranges) |
| 8933 | ("r-gtools" ,r-gtools) |
| 8934 | ("r-iranges" ,r-iranges) |
| 8935 | ("r-matrixstats" ,r-matrixstats) |
| 8936 | ("r-rsamtools" ,r-rsamtools) |
| 8937 | ("r-s4vectors" ,r-s4vectors))) |
| 8938 | (home-page "https://github.com/PeeperLab/CopywriteR") |
| 8939 | (synopsis "Copy number information from targeted sequencing") |
| 8940 | (description |
| 8941 | "CopywriteR extracts DNA copy number information from targeted sequencing |
| 8942 | by utilizing off-target reads. It allows for extracting uniformly distributed |
| 8943 | copy number information, can be used without reference, and can be applied to |
| 8944 | sequencing data obtained from various techniques including chromatin |
| 8945 | immunoprecipitation and target enrichment on small gene panels. Thereby, |
| 8946 | CopywriteR constitutes a widely applicable alternative to available copy |
| 8947 | number detection tools.") |
| 8948 | (license license:gpl2))) |
| 8949 | |
| 8950 | (define-public r-methylkit |
| 8951 | (package |
| 8952 | (name "r-methylkit") |
| 8953 | (version "1.4.0") |
| 8954 | (source (origin |
| 8955 | (method url-fetch) |
| 8956 | (uri (bioconductor-uri "methylKit" version)) |
| 8957 | (sha256 |
| 8958 | (base32 |
| 8959 | "0h53w2mrjrg2n0ndi12k9j6cwclgwcgpy25nz7nyj971aisw02xn")))) |
| 8960 | (properties `((upstream-name . "methylKit"))) |
| 8961 | (build-system r-build-system) |
| 8962 | (propagated-inputs |
| 8963 | `(("r-data-table" ,r-data-table) |
| 8964 | ("r-emdbook" ,r-emdbook) |
| 8965 | ("r-fastseg" ,r-fastseg) |
| 8966 | ("r-genomeinfodb" ,r-genomeinfodb) |
| 8967 | ("r-genomicranges" ,r-genomicranges) |
| 8968 | ("r-gtools" ,r-gtools) |
| 8969 | ("r-iranges" ,r-iranges) |
| 8970 | ("r-kernsmooth" ,r-kernsmooth) |
| 8971 | ("r-limma" ,r-limma) |
| 8972 | ("r-mclust" ,r-mclust) |
| 8973 | ("r-qvalue" ,r-qvalue) |
| 8974 | ("r-r-utils" ,r-r-utils) |
| 8975 | ("r-rcpp" ,r-rcpp) |
| 8976 | ("r-rhtslib" ,r-rhtslib) |
| 8977 | ("r-rsamtools" ,r-rsamtools) |
| 8978 | ("r-rtracklayer" ,r-rtracklayer) |
| 8979 | ("r-s4vectors" ,r-s4vectors) |
| 8980 | ("r-zlibbioc" ,r-zlibbioc))) |
| 8981 | (inputs |
| 8982 | `(("zlib" ,zlib))) |
| 8983 | (home-page "https://github.com/al2na/methylKit") |
| 8984 | (synopsis |
| 8985 | "DNA methylation analysis from high-throughput bisulfite sequencing results") |
| 8986 | (description |
| 8987 | "MethylKit is an R package for DNA methylation analysis and annotation |
| 8988 | from high-throughput bisulfite sequencing. The package is designed to deal |
| 8989 | with sequencing data from @dfn{Reduced representation bisulfite |
| 8990 | sequencing} (RRBS) and its variants, but also target-capture methods and whole |
| 8991 | genome bisulfite sequencing. It also has functions to analyze base-pair |
| 8992 | resolution 5hmC data from experimental protocols such as oxBS-Seq and |
| 8993 | TAB-Seq.") |
| 8994 | (license license:artistic2.0))) |
| 8995 | |
| 8996 | (define-public r-sva |
| 8997 | (package |
| 8998 | (name "r-sva") |
| 8999 | (version "3.26.0") |
| 9000 | (source |
| 9001 | (origin |
| 9002 | (method url-fetch) |
| 9003 | (uri (bioconductor-uri "sva" version)) |
| 9004 | (sha256 |
| 9005 | (base32 |
| 9006 | "0q5xb68wfcnchy8rkv5ma67pmz1i91lsnvmwmj8f1c3w4xan3pgw")))) |
| 9007 | (build-system r-build-system) |
| 9008 | (propagated-inputs |
| 9009 | `(("r-genefilter" ,r-genefilter) |
| 9010 | ("r-mgcv" ,r-mgcv) |
| 9011 | ("r-biocparallel" ,r-biocparallel) |
| 9012 | ("r-matrixstats" ,r-matrixstats) |
| 9013 | ("r-limma" ,r-limma))) |
| 9014 | (home-page "https://bioconductor.org/packages/sva") |
| 9015 | (synopsis "Surrogate variable analysis") |
| 9016 | (description |
| 9017 | "This package contains functions for removing batch effects and other |
| 9018 | unwanted variation in high-throughput experiment. It also contains functions |
| 9019 | for identifying and building surrogate variables for high-dimensional data |
| 9020 | sets. Surrogate variables are covariates constructed directly from |
| 9021 | high-dimensional data like gene expression/RNA sequencing/methylation/brain |
| 9022 | imaging data that can be used in subsequent analyses to adjust for unknown, |
| 9023 | unmodeled, or latent sources of noise.") |
| 9024 | (license license:artistic2.0))) |
| 9025 | |
| 9026 | (define-public r-seqminer |
| 9027 | (package |
| 9028 | (name "r-seqminer") |
| 9029 | (version "6.0") |
| 9030 | (source |
| 9031 | (origin |
| 9032 | (method url-fetch) |
| 9033 | (uri (cran-uri "seqminer" version)) |
| 9034 | (sha256 |
| 9035 | (base32 |
| 9036 | "057j1l6dip35l1aivilapl2zv9db677b3di2pb3sfgq2sxg0ps3l")))) |
| 9037 | (build-system r-build-system) |
| 9038 | (inputs |
| 9039 | `(("zlib" ,zlib))) |
| 9040 | (home-page "http://seqminer.genomic.codes") |
| 9041 | (synopsis "Read nucleotide sequence data (VCF, BCF, and METAL formats)") |
| 9042 | (description |
| 9043 | "This package provides tools to integrate nucleotide sequencing |
| 9044 | data (variant call format, e.g. VCF or BCF) or meta-analysis results in R.") |
| 9045 | ;; Any version of the GPL is acceptable |
| 9046 | (license (list license:gpl2+ license:gpl3+)))) |
| 9047 | |
| 9048 | (define-public r-raremetals2 |
| 9049 | (package |
| 9050 | (name "r-raremetals2") |
| 9051 | (version "0.1") |
| 9052 | (source |
| 9053 | (origin |
| 9054 | (method url-fetch) |
| 9055 | (uri (string-append "http://genome.sph.umich.edu/w/images/" |
| 9056 | "b/b7/RareMETALS2_" version ".tar.gz")) |
| 9057 | (sha256 |
| 9058 | (base32 |
| 9059 | "0z5ljcgvnm06ja9lm85a3cniq7slxcy37aqqkxrdidr79an5fs4s")))) |
| 9060 | (properties `((upstream-name . "RareMETALS2"))) |
| 9061 | (build-system r-build-system) |
| 9062 | (propagated-inputs |
| 9063 | `(("r-seqminer" ,r-seqminer) |
| 9064 | ("r-mvtnorm" ,r-mvtnorm) |
| 9065 | ("r-mass" ,r-mass) |
| 9066 | ("r-compquadform" ,r-compquadform) |
| 9067 | ("r-getopt" ,r-getopt))) |
| 9068 | (home-page "http://genome.sph.umich.edu/wiki/RareMETALS2") |
| 9069 | (synopsis "Analyze gene-level association tests for binary trait") |
| 9070 | (description |
| 9071 | "The R package rareMETALS2 is an extension of the R package rareMETALS. |
| 9072 | It was designed to meta-analyze gene-level association tests for binary trait. |
| 9073 | While rareMETALS offers a near-complete solution for meta-analysis of |
| 9074 | gene-level tests for quantitative trait, it does not offer the optimal |
| 9075 | solution for binary trait. The package rareMETALS2 offers improved features |
| 9076 | for analyzing gene-level association tests in meta-analyses for binary |
| 9077 | trait.") |
| 9078 | (license license:gpl3))) |
| 9079 | |
| 9080 | (define-public r-maldiquant |
| 9081 | (package |
| 9082 | (name "r-maldiquant") |
| 9083 | (version "1.17") |
| 9084 | (source |
| 9085 | (origin |
| 9086 | (method url-fetch) |
| 9087 | (uri (cran-uri "MALDIquant" version)) |
| 9088 | (sha256 |
| 9089 | (base32 |
| 9090 | "047s6007ydc38x8wm027mlb4mngz15n0d4238fr8h43wyll5zy0z")))) |
| 9091 | (properties `((upstream-name . "MALDIquant"))) |
| 9092 | (build-system r-build-system) |
| 9093 | (home-page "https://cran.r-project.org/web/packages/MALDIquant") |
| 9094 | (synopsis "Quantitative analysis of mass spectrometry data") |
| 9095 | (description |
| 9096 | "This package provides a complete analysis pipeline for matrix-assisted |
| 9097 | laser desorption/ionization-time-of-flight (MALDI-TOF) and other |
| 9098 | two-dimensional mass spectrometry data. In addition to commonly used plotting |
| 9099 | and processing methods it includes distinctive features, namely baseline |
| 9100 | subtraction methods such as morphological filters (TopHat) or the |
| 9101 | statistics-sensitive non-linear iterative peak-clipping algorithm (SNIP), peak |
| 9102 | alignment using warping functions, handling of replicated measurements as well |
| 9103 | as allowing spectra with different resolutions.") |
| 9104 | (license license:gpl3+))) |
| 9105 | |
| 9106 | (define-public r-protgenerics |
| 9107 | (package |
| 9108 | (name "r-protgenerics") |
| 9109 | (version "1.10.0") |
| 9110 | (source |
| 9111 | (origin |
| 9112 | (method url-fetch) |
| 9113 | (uri (bioconductor-uri "ProtGenerics" version)) |
| 9114 | (sha256 |
| 9115 | (base32 |
| 9116 | "16ijp50448wnabp43klx943rhdvh7x45hvy7cnpq1s4dckxhhyni")))) |
| 9117 | (properties `((upstream-name . "ProtGenerics"))) |
| 9118 | (build-system r-build-system) |
| 9119 | (home-page "https://github.com/lgatto/ProtGenerics") |
| 9120 | (synopsis "S4 generic functions for proteomics infrastructure") |
| 9121 | (description |
| 9122 | "This package provides S4 generic functions needed by Bioconductor |
| 9123 | proteomics packages.") |
| 9124 | (license license:artistic2.0))) |
| 9125 | |
| 9126 | (define-public r-mzr |
| 9127 | (package |
| 9128 | (name "r-mzr") |
| 9129 | (version "2.12.0") |
| 9130 | (source |
| 9131 | (origin |
| 9132 | (method url-fetch) |
| 9133 | (uri (bioconductor-uri "mzR" version)) |
| 9134 | (sha256 |
| 9135 | (base32 |
| 9136 | "1x3gp30sfxz2v3k3swih9kff9b2rvk7hzhnlkp6ywlnn2wgb0q8c")) |
| 9137 | (modules '((guix build utils))) |
| 9138 | (snippet |
| 9139 | '(begin |
| 9140 | (delete-file-recursively "src/boost") |
| 9141 | #t)))) |
| 9142 | (properties `((upstream-name . "mzR"))) |
| 9143 | (build-system r-build-system) |
| 9144 | (arguments |
| 9145 | `(#:phases |
| 9146 | (modify-phases %standard-phases |
| 9147 | (add-after 'unpack 'use-system-boost |
| 9148 | (lambda _ |
| 9149 | (substitute* "src/Makevars" |
| 9150 | (("\\./boost/libs.*") "") |
| 9151 | (("ARCH_OBJS=" line) |
| 9152 | (string-append line |
| 9153 | "\nARCH_LIBS=-lboost_system -lboost_regex \ |
| 9154 | -lboost_iostreams -lboost_thread -lboost_filesystem -lboost_chrono\n"))) |
| 9155 | #t))))) |
| 9156 | (inputs |
| 9157 | `(("boost" ,boost) ; use this instead of the bundled boost sources |
| 9158 | ("netcdf" ,netcdf))) |
| 9159 | (propagated-inputs |
| 9160 | `(("r-biobase" ,r-biobase) |
| 9161 | ("r-biocgenerics" ,r-biocgenerics) |
| 9162 | ("r-protgenerics" ,r-protgenerics) |
| 9163 | ("r-rcpp" ,r-rcpp) |
| 9164 | ("r-zlibbioc" ,r-zlibbioc))) |
| 9165 | (home-page "https://github.com/sneumann/mzR/") |
| 9166 | (synopsis "Parser for mass spectrometry data files") |
| 9167 | (description |
| 9168 | "The mzR package provides a unified API to the common file formats and |
| 9169 | parsers available for mass spectrometry data. It comes with a wrapper for the |
| 9170 | ISB random access parser for mass spectrometry mzXML, mzData and mzML files. |
| 9171 | The package contains the original code written by the ISB, and a subset of the |
| 9172 | proteowizard library for mzML and mzIdentML. The netCDF reading code has |
| 9173 | previously been used in XCMS.") |
| 9174 | (license license:artistic2.0))) |
| 9175 | |
| 9176 | (define-public r-affyio |
| 9177 | (package |
| 9178 | (name "r-affyio") |
| 9179 | (version "1.48.0") |
| 9180 | (source |
| 9181 | (origin |
| 9182 | (method url-fetch) |
| 9183 | (uri (bioconductor-uri "affyio" version)) |
| 9184 | (sha256 |
| 9185 | (base32 |
| 9186 | "1pzzp3d3dbmyf34gvivfiprkpscn36rgvhrq853a1d3avcwr5ak9")))) |
| 9187 | (build-system r-build-system) |
| 9188 | (propagated-inputs |
| 9189 | `(("r-zlibbioc" ,r-zlibbioc))) |
| 9190 | (inputs |
| 9191 | `(("zlib" ,zlib))) |
| 9192 | (home-page "https://github.com/bmbolstad/affyio") |
| 9193 | (synopsis "Tools for parsing Affymetrix data files") |
| 9194 | (description |
| 9195 | "This package provides routines for parsing Affymetrix data files based |
| 9196 | upon file format information. The primary focus is on accessing the CEL and |
| 9197 | CDF file formats.") |
| 9198 | (license license:lgpl2.0+))) |
| 9199 | |
| 9200 | (define-public r-affy |
| 9201 | (package |
| 9202 | (name "r-affy") |
| 9203 | (version "1.56.0") |
| 9204 | (source |
| 9205 | (origin |
| 9206 | (method url-fetch) |
| 9207 | (uri (bioconductor-uri "affy" version)) |
| 9208 | (sha256 |
| 9209 | (base32 |
| 9210 | "0jmbkimma5ffsdkk3xp03g4lpz84gd95nkqakif2nqq6wmx0syrj")))) |
| 9211 | (build-system r-build-system) |
| 9212 | (propagated-inputs |
| 9213 | `(("r-affyio" ,r-affyio) |
| 9214 | ("r-biobase" ,r-biobase) |
| 9215 | ("r-biocgenerics" ,r-biocgenerics) |
| 9216 | ("r-biocinstaller" ,r-biocinstaller) |
| 9217 | ("r-preprocesscore" ,r-preprocesscore) |
| 9218 | ("r-zlibbioc" ,r-zlibbioc))) |
| 9219 | (home-page "https://bioconductor.org/packages/affy") |
| 9220 | (synopsis "Methods for affymetrix oligonucleotide arrays") |
| 9221 | (description |
| 9222 | "This package contains functions for exploratory oligonucleotide array |
| 9223 | analysis.") |
| 9224 | (license license:lgpl2.0+))) |
| 9225 | |
| 9226 | (define-public r-vsn |
| 9227 | (package |
| 9228 | (name "r-vsn") |
| 9229 | (version "3.46.0") |
| 9230 | (source |
| 9231 | (origin |
| 9232 | (method url-fetch) |
| 9233 | (uri (bioconductor-uri "vsn" version)) |
| 9234 | (sha256 |
| 9235 | (base32 |
| 9236 | "18y62phzirj75gg6v5l41jwybmk23ia6w7qhch0kxc4bl2rysw6j")))) |
| 9237 | (build-system r-build-system) |
| 9238 | (propagated-inputs |
| 9239 | `(("r-affy" ,r-affy) |
| 9240 | ("r-biobase" ,r-biobase) |
| 9241 | ("r-ggplot2" ,r-ggplot2) |
| 9242 | ("r-lattice" ,r-lattice) |
| 9243 | ("r-limma" ,r-limma))) |
| 9244 | (home-page "https://bioconductor.org/packages/release/bioc/html/vsn.html") |
| 9245 | (synopsis "Variance stabilization and calibration for microarray data") |
| 9246 | (description |
| 9247 | "The package implements a method for normalising microarray intensities, |
| 9248 | and works for single- and multiple-color arrays. It can also be used for data |
| 9249 | from other technologies, as long as they have similar format. The method uses |
| 9250 | a robust variant of the maximum-likelihood estimator for an |
| 9251 | additive-multiplicative error model and affine calibration. The model |
| 9252 | incorporates data calibration step (a.k.a. normalization), a model for the |
| 9253 | dependence of the variance on the mean intensity and a variance stabilizing |
| 9254 | data transformation. Differences between transformed intensities are |
| 9255 | analogous to \"normalized log-ratios\". However, in contrast to the latter, |
| 9256 | their variance is independent of the mean, and they are usually more sensitive |
| 9257 | and specific in detecting differential transcription.") |
| 9258 | (license license:artistic2.0))) |
| 9259 | |
| 9260 | (define-public r-mzid |
| 9261 | (package |
| 9262 | (name "r-mzid") |
| 9263 | (version "1.16.0") |
| 9264 | (source |
| 9265 | (origin |
| 9266 | (method url-fetch) |
| 9267 | (uri (bioconductor-uri "mzID" version)) |
| 9268 | (sha256 |
| 9269 | (base32 |
| 9270 | "0yk70dka56zd8w62f03ggx3mandj91gfa767h9ajj0sd3mjmfqb9")))) |
| 9271 | (properties `((upstream-name . "mzID"))) |
| 9272 | (build-system r-build-system) |
| 9273 | (propagated-inputs |
| 9274 | `(("r-doparallel" ,r-doparallel) |
| 9275 | ("r-foreach" ,r-foreach) |
| 9276 | ("r-iterators" ,r-iterators) |
| 9277 | ("r-plyr" ,r-plyr) |
| 9278 | ("r-protgenerics" ,r-protgenerics) |
| 9279 | ("r-rcpp" ,r-rcpp) |
| 9280 | ("r-xml" ,r-xml))) |
| 9281 | (home-page "https://bioconductor.org/packages/mzID") |
| 9282 | (synopsis "Parser for mzIdentML files") |
| 9283 | (description |
| 9284 | "This package provides a parser for mzIdentML files implemented using the |
| 9285 | XML package. The parser tries to be general and able to handle all types of |
| 9286 | mzIdentML files with the drawback of having less pretty output than a vendor |
| 9287 | specific parser.") |
| 9288 | (license license:gpl2+))) |
| 9289 | |
| 9290 | (define-public r-pcamethods |
| 9291 | (package |
| 9292 | (name "r-pcamethods") |
| 9293 | (version "1.70.0") |
| 9294 | (source |
| 9295 | (origin |
| 9296 | (method url-fetch) |
| 9297 | (uri (bioconductor-uri "pcaMethods" version)) |
| 9298 | (sha256 |
| 9299 | (base32 |
| 9300 | "0ii235g0x0492kh8cfrf28ni0b6vd6fh7kizkqmczzqggd6b1bk8")))) |
| 9301 | (properties `((upstream-name . "pcaMethods"))) |
| 9302 | (build-system r-build-system) |
| 9303 | (propagated-inputs |
| 9304 | `(("r-biobase" ,r-biobase) |
| 9305 | ("r-biocgenerics" ,r-biocgenerics) |
| 9306 | ("r-mass" ,r-mass) |
| 9307 | ("r-rcpp" ,r-rcpp))) |
| 9308 | (home-page "https://github.com/hredestig/pcamethods") |
| 9309 | (synopsis "Collection of PCA methods") |
| 9310 | (description |
| 9311 | "This package provides Bayesian PCA, Probabilistic PCA, Nipals PCA, |
| 9312 | Inverse Non-Linear PCA and the conventional SVD PCA. A cluster based method |
| 9313 | for missing value estimation is included for comparison. BPCA, PPCA and |
| 9314 | NipalsPCA may be used to perform PCA on incomplete data as well as for |
| 9315 | accurate missing value estimation. A set of methods for printing and plotting |
| 9316 | the results is also provided. All PCA methods make use of the same data |
| 9317 | structure (pcaRes) to provide a common interface to the PCA results.") |
| 9318 | (license license:gpl3+))) |
| 9319 | |
| 9320 | (define-public r-msnbase |
| 9321 | (package |
| 9322 | (name "r-msnbase") |
| 9323 | (version "2.4.0") |
| 9324 | (source |
| 9325 | (origin |
| 9326 | (method url-fetch) |
| 9327 | (uri (bioconductor-uri "MSnbase" version)) |
| 9328 | (sha256 |
| 9329 | (base32 |
| 9330 | "0dqfimljhrx3gac8d1k72gppx27lz8yckyb12v4604nbviw7xd3r")))) |
| 9331 | (properties `((upstream-name . "MSnbase"))) |
| 9332 | (build-system r-build-system) |
| 9333 | (propagated-inputs |
| 9334 | `(("r-affy" ,r-affy) |
| 9335 | ("r-biobase" ,r-biobase) |
| 9336 | ("r-biocgenerics" ,r-biocgenerics) |
| 9337 | ("r-biocparallel" ,r-biocparallel) |
| 9338 | ("r-digest" ,r-digest) |
| 9339 | ("r-ggplot2" ,r-ggplot2) |
| 9340 | ("r-impute" ,r-impute) |
| 9341 | ("r-iranges" ,r-iranges) |
| 9342 | ("r-lattice" ,r-lattice) |
| 9343 | ("r-maldiquant" ,r-maldiquant) |
| 9344 | ("r-mzid" ,r-mzid) |
| 9345 | ("r-mzr" ,r-mzr) |
| 9346 | ("r-pcamethods" ,r-pcamethods) |
| 9347 | ("r-plyr" ,r-plyr) |
| 9348 | ("r-preprocesscore" ,r-preprocesscore) |
| 9349 | ("r-protgenerics" ,r-protgenerics) |
| 9350 | ("r-rcpp" ,r-rcpp) |
| 9351 | ("r-s4vectors" ,r-s4vectors) |
| 9352 | ("r-vsn" ,r-vsn) |
| 9353 | ("r-xml" ,r-xml))) |
| 9354 | (home-page "https://github.com/lgatto/MSnbase") |
| 9355 | (synopsis "Base functions and classes for MS-based proteomics") |
| 9356 | (description |
| 9357 | "This package provides basic plotting, data manipulation and processing |
| 9358 | of mass spectrometry based proteomics data.") |
| 9359 | (license license:artistic2.0))) |
| 9360 | |
| 9361 | (define-public r-msnid |
| 9362 | (package |
| 9363 | (name "r-msnid") |
| 9364 | (version "1.12.1") |
| 9365 | (source |
| 9366 | (origin |
| 9367 | (method url-fetch) |
| 9368 | (uri (bioconductor-uri "MSnID" version)) |
| 9369 | (sha256 |
| 9370 | (base32 |
| 9371 | "1zw508kk4f8brg69674wp18gqkpx2kpya5f6x9cl3qng7v4h5pxx")))) |
| 9372 | (properties `((upstream-name . "MSnID"))) |
| 9373 | (build-system r-build-system) |
| 9374 | (propagated-inputs |
| 9375 | `(("r-biobase" ,r-biobase) |
| 9376 | ("r-data-table" ,r-data-table) |
| 9377 | ("r-doparallel" ,r-doparallel) |
| 9378 | ("r-dplyr" ,r-dplyr) |
| 9379 | ("r-foreach" ,r-foreach) |
| 9380 | ("r-iterators" ,r-iterators) |
| 9381 | ("r-msnbase" ,r-msnbase) |
| 9382 | ("r-mzid" ,r-mzid) |
| 9383 | ("r-mzr" ,r-mzr) |
| 9384 | ("r-protgenerics" ,r-protgenerics) |
| 9385 | ("r-r-cache" ,r-r-cache) |
| 9386 | ("r-rcpp" ,r-rcpp) |
| 9387 | ("r-reshape2" ,r-reshape2))) |
| 9388 | (home-page "https://bioconductor.org/packages/MSnID") |
| 9389 | (synopsis "Utilities for LC-MSn proteomics identifications") |
| 9390 | (description |
| 9391 | "This package extracts @dfn{tandem mass spectrometry} (MS/MS) ID data |
| 9392 | from mzIdentML (leveraging the mzID package) or text files. After collating |
| 9393 | the search results from multiple datasets it assesses their identification |
| 9394 | quality and optimize filtering criteria to achieve the maximum number of |
| 9395 | identifications while not exceeding a specified false discovery rate. It also |
| 9396 | contains a number of utilities to explore the MS/MS results and assess missed |
| 9397 | and irregular enzymatic cleavages, mass measurement accuracy, etc.") |
| 9398 | (license license:artistic2.0))) |
| 9399 | |
| 9400 | (define-public r-seurat |
| 9401 | (package |
| 9402 | (name "r-seurat") |
| 9403 | (version "2.1.0") |
| 9404 | (source (origin |
| 9405 | (method url-fetch) |
| 9406 | (uri (cran-uri "Seurat" version)) |
| 9407 | (sha256 |
| 9408 | (base32 |
| 9409 | "1hqaq6bciikrsyw157w8fn4jw885air7xbkxrmism93rp4qx483x")) |
| 9410 | ;; Delete pre-built jar. |
| 9411 | (snippet |
| 9412 | '(begin (delete-file "inst/java/ModularityOptimizer.jar") |
| 9413 | #t)))) |
| 9414 | (properties `((upstream-name . "Seurat"))) |
| 9415 | (build-system r-build-system) |
| 9416 | (arguments |
| 9417 | `(#:phases |
| 9418 | (modify-phases %standard-phases |
| 9419 | (add-after 'unpack 'build-jar |
| 9420 | (lambda* (#:key inputs #:allow-other-keys) |
| 9421 | (let ((classesdir "tmp-classes")) |
| 9422 | (setenv "JAVA_HOME" (assoc-ref inputs "jdk")) |
| 9423 | (mkdir classesdir) |
| 9424 | (with-output-to-file "manifest" |
| 9425 | (lambda _ |
| 9426 | (display "Manifest-Version: 1.0 |
| 9427 | Main-Class: ModularityOptimizer\n"))) |
| 9428 | (and (zero? (apply system* `("javac" "-d" ,classesdir |
| 9429 | ,@(find-files "java" "\\.java$")))) |
| 9430 | (zero? (system* "jar" |
| 9431 | "-cmf" "manifest" |
| 9432 | "inst/java/ModularityOptimizer.jar" |
| 9433 | "-C" classesdir "."))))))))) |
| 9434 | (native-inputs |
| 9435 | `(("jdk" ,icedtea "jdk"))) |
| 9436 | (propagated-inputs |
| 9437 | `(("r-ape" ,r-ape) |
| 9438 | ("r-caret" ,r-caret) |
| 9439 | ("r-cowplot" ,r-cowplot) |
| 9440 | ("r-diffusionmap" ,r-diffusionmap) |
| 9441 | ("r-dplyr" ,r-dplyr) |
| 9442 | ("r-dtw" ,r-dtw) |
| 9443 | ("r-fnn" ,r-fnn) |
| 9444 | ("r-fpc" ,r-fpc) |
| 9445 | ("r-gdata" ,r-gdata) |
| 9446 | ("r-ggjoy" ,r-ggjoy) |
| 9447 | ("r-ggplot2" ,r-ggplot2) |
| 9448 | ("r-gplots" ,r-gplots) |
| 9449 | ("r-gridextra" ,r-gridextra) |
| 9450 | ("r-hmisc" ,r-hmisc) |
| 9451 | ("r-ica" ,r-ica) |
| 9452 | ("r-igraph" ,r-igraph) |
| 9453 | ("r-irlba" ,r-irlba) |
| 9454 | ("r-lars" ,r-lars) |
| 9455 | ("r-mass" ,r-mass) |
| 9456 | ("r-matrix" ,r-matrix) |
| 9457 | ("r-mixtools" ,r-mixtools) |
| 9458 | ("r-nmf" ,r-nmf) |
| 9459 | ("r-pbapply" ,r-pbapply) |
| 9460 | ("r-plotly" ,r-plotly) |
| 9461 | ("r-ranger" ,r-ranger) |
| 9462 | ("r-rcolorbrewer" ,r-rcolorbrewer) |
| 9463 | ("r-rcpp" ,r-rcpp) |
| 9464 | ("r-rcppprogress" ,r-rcppprogress) |
| 9465 | ("r-reshape2" ,r-reshape2) |
| 9466 | ("r-rocr" ,r-rocr) |
| 9467 | ("r-rtsne" ,r-rtsne) |
| 9468 | ("r-sdmtools" ,r-sdmtools) |
| 9469 | ("r-stringr" ,r-stringr) |
| 9470 | ("r-tclust" ,r-tclust) |
| 9471 | ("r-tidyr" ,r-tidyr) |
| 9472 | ("r-tsne" ,r-tsne) |
| 9473 | ("r-vgam" ,r-vgam))) |
| 9474 | (home-page "http://www.satijalab.org/seurat") |
| 9475 | (synopsis "Seurat is an R toolkit for single cell genomics") |
| 9476 | (description |
| 9477 | "This package is an R package designed for QC, analysis, and |
| 9478 | exploration of single cell RNA-seq data. It easily enables widely-used |
| 9479 | analytical techniques, including the identification of highly variable genes, |
| 9480 | dimensionality reduction; PCA, ICA, t-SNE, standard unsupervised clustering |
| 9481 | algorithms; density clustering, hierarchical clustering, k-means, and the |
| 9482 | discovery of differentially expressed genes and markers.") |
| 9483 | (license license:gpl3))) |
| 9484 | |
| 9485 | (define-public r-aroma-light |
| 9486 | (package |
| 9487 | (name "r-aroma-light") |
| 9488 | (version "3.8.0") |
| 9489 | (source |
| 9490 | (origin |
| 9491 | (method url-fetch) |
| 9492 | (uri (bioconductor-uri "aroma.light" version)) |
| 9493 | (sha256 |
| 9494 | (base32 |
| 9495 | "0crnk6851jwypqr5l5jcbbay0vi5vvdjyisaf6z2d69c39wmr6sc")))) |
| 9496 | (properties `((upstream-name . "aroma.light"))) |
| 9497 | (build-system r-build-system) |
| 9498 | (propagated-inputs |
| 9499 | `(("r-matrixstats" ,r-matrixstats) |
| 9500 | ("r-r-methodss3" ,r-r-methodss3) |
| 9501 | ("r-r-oo" ,r-r-oo) |
| 9502 | ("r-r-utils" ,r-r-utils))) |
| 9503 | (home-page "https://github.com/HenrikBengtsson/aroma.light") |
| 9504 | (synopsis "Methods for normalization and visualization of microarray data") |
| 9505 | (description |
| 9506 | "This package provides methods for microarray analysis that take basic |
| 9507 | data types such as matrices and lists of vectors. These methods can be used |
| 9508 | standalone, be utilized in other packages, or be wrapped up in higher-level |
| 9509 | classes.") |
| 9510 | (license license:gpl2+))) |
| 9511 | |
| 9512 | (define-public r-deseq |
| 9513 | (package |
| 9514 | (name "r-deseq") |
| 9515 | (version "1.30.0") |
| 9516 | (source |
| 9517 | (origin |
| 9518 | (method url-fetch) |
| 9519 | (uri (bioconductor-uri "DESeq" version)) |
| 9520 | (sha256 |
| 9521 | (base32 |
| 9522 | "0mn5w3cy16iwwk8zxs7za6aa6cnrca75z0g45zd5zh1py5d7nfv9")))) |
| 9523 | (properties `((upstream-name . "DESeq"))) |
| 9524 | (build-system r-build-system) |
| 9525 | (propagated-inputs |
| 9526 | `(("r-biobase" ,r-biobase) |
| 9527 | ("r-biocgenerics" ,r-biocgenerics) |
| 9528 | ("r-genefilter" ,r-genefilter) |
| 9529 | ("r-geneplotter" ,r-geneplotter) |
| 9530 | ("r-lattice" ,r-lattice) |
| 9531 | ("r-locfit" ,r-locfit) |
| 9532 | ("r-mass" ,r-mass) |
| 9533 | ("r-rcolorbrewer" ,r-rcolorbrewer))) |
| 9534 | (home-page "http://www-huber.embl.de/users/anders/DESeq") |
| 9535 | (synopsis "Differential gene expression analysis") |
| 9536 | (description |
| 9537 | "This package provides tools for estimating variance-mean dependence in |
| 9538 | count data from high-throughput genetic sequencing assays and for testing for |
| 9539 | differential expression based on a model using the negative binomial |
| 9540 | distribution.") |
| 9541 | (license license:gpl3+))) |
| 9542 | |
| 9543 | (define-public r-edaseq |
| 9544 | (package |
| 9545 | (name "r-edaseq") |
| 9546 | (version "2.12.0") |
| 9547 | (source |
| 9548 | (origin |
| 9549 | (method url-fetch) |
| 9550 | (uri (bioconductor-uri "EDASeq" version)) |
| 9551 | (sha256 |
| 9552 | (base32 |
| 9553 | "07zm89zcivyn2261aq9grqmly8ji482kr9h9dyfknfdfrpv7jpwv")))) |
| 9554 | (properties `((upstream-name . "EDASeq"))) |
| 9555 | (build-system r-build-system) |
| 9556 | (propagated-inputs |
| 9557 | `(("r-annotationdbi" ,r-annotationdbi) |
| 9558 | ("r-aroma-light" ,r-aroma-light) |
| 9559 | ("r-biobase" ,r-biobase) |
| 9560 | ("r-biocgenerics" ,r-biocgenerics) |
| 9561 | ("r-biomart" ,r-biomart) |
| 9562 | ("r-biostrings" ,r-biostrings) |
| 9563 | ("r-deseq" ,r-deseq) |
| 9564 | ("r-genomicfeatures" ,r-genomicfeatures) |
| 9565 | ("r-genomicranges" ,r-genomicranges) |
| 9566 | ("r-iranges" ,r-iranges) |
| 9567 | ("r-rsamtools" ,r-rsamtools) |
| 9568 | ("r-shortread" ,r-shortread))) |
| 9569 | (home-page "https://github.com/drisso/EDASeq") |
| 9570 | (synopsis "Exploratory data analysis and normalization for RNA-Seq") |
| 9571 | (description |
| 9572 | "This package provides support for numerical and graphical summaries of |
| 9573 | RNA-Seq genomic read data. Provided within-lane normalization procedures to |
| 9574 | adjust for GC-content effect (or other gene-level effects) on read counts: |
| 9575 | loess robust local regression, global-scaling, and full-quantile |
| 9576 | normalization. Between-lane normalization procedures to adjust for |
| 9577 | distributional differences between lanes (e.g., sequencing depth): |
| 9578 | global-scaling and full-quantile normalization.") |
| 9579 | (license license:artistic2.0))) |
| 9580 | |
| 9581 | (define-public r-interactivedisplaybase |
| 9582 | (package |
| 9583 | (name "r-interactivedisplaybase") |
| 9584 | (version "1.16.0") |
| 9585 | (source |
| 9586 | (origin |
| 9587 | (method url-fetch) |
| 9588 | (uri (bioconductor-uri "interactiveDisplayBase" version)) |
| 9589 | (sha256 |
| 9590 | (base32 |
| 9591 | "01yb945jqqimwjgriza6yy4dnp303cdirxrhl4hjyprfdlmnz5p5")))) |
| 9592 | (properties |
| 9593 | `((upstream-name . "interactiveDisplayBase"))) |
| 9594 | (build-system r-build-system) |
| 9595 | (propagated-inputs |
| 9596 | `(("r-biocgenerics" ,r-biocgenerics) |
| 9597 | ("r-shiny" ,r-shiny))) |
| 9598 | (home-page "https://bioconductor.org/packages/interactiveDisplayBase") |
| 9599 | (synopsis "Base package for web displays of Bioconductor objects") |
| 9600 | (description |
| 9601 | "This package contains the basic methods needed to generate interactive |
| 9602 | Shiny-based display methods for Bioconductor objects.") |
| 9603 | (license license:artistic2.0))) |
| 9604 | |
| 9605 | (define-public r-annotationhub |
| 9606 | (package |
| 9607 | (name "r-annotationhub") |
| 9608 | (version "2.10.1") |
| 9609 | (source |
| 9610 | (origin |
| 9611 | (method url-fetch) |
| 9612 | (uri (bioconductor-uri "AnnotationHub" version)) |
| 9613 | (sha256 |
| 9614 | (base32 |
| 9615 | "14v8g44a6zg9j2rwn9x9y8509k0wr2cw8yccliz24glplb40wva4")))) |
| 9616 | (properties `((upstream-name . "AnnotationHub"))) |
| 9617 | (build-system r-build-system) |
| 9618 | (propagated-inputs |
| 9619 | `(("r-annotationdbi" ,r-annotationdbi) |
| 9620 | ("r-biocgenerics" ,r-biocgenerics) |
| 9621 | ("r-biocinstaller" ,r-biocinstaller) |
| 9622 | ("r-curl" ,r-curl) |
| 9623 | ("r-httr" ,r-httr) |
| 9624 | ("r-interactivedisplaybase" ,r-interactivedisplaybase) |
| 9625 | ("r-rsqlite" ,r-rsqlite) |
| 9626 | ("r-s4vectors" ,r-s4vectors) |
| 9627 | ("r-yaml" ,r-yaml))) |
| 9628 | (home-page "https://bioconductor.org/packages/AnnotationHub") |
| 9629 | (synopsis "Client to access AnnotationHub resources") |
| 9630 | (description |
| 9631 | "This package provides a client for the Bioconductor AnnotationHub web |
| 9632 | resource. The AnnotationHub web resource provides a central location where |
| 9633 | genomic files (e.g. VCF, bed, wig) and other resources from standard |
| 9634 | locations (e.g. UCSC, Ensembl) can be discovered. The resource includes |
| 9635 | metadata about each resource, e.g., a textual description, tags, and date of |
| 9636 | modification. The client creates and manages a local cache of files retrieved |
| 9637 | by the user, helping with quick and reproducible access.") |
| 9638 | (license license:artistic2.0))) |
| 9639 | |
| 9640 | (define-public r-fastseg |
| 9641 | (package |
| 9642 | (name "r-fastseg") |
| 9643 | (version "1.24.0") |
| 9644 | (source |
| 9645 | (origin |
| 9646 | (method url-fetch) |
| 9647 | (uri (bioconductor-uri "fastseg" version)) |
| 9648 | (sha256 |
| 9649 | (base32 |
| 9650 | "0dd7nr3klwz9ailwshnbynhd62lwb8zbbpj6jf3igpb94yi6x2jp")))) |
| 9651 | (build-system r-build-system) |
| 9652 | (propagated-inputs |
| 9653 | `(("r-biobase" ,r-biobase) |
| 9654 | ("r-biocgenerics" ,r-biocgenerics) |
| 9655 | ("r-genomicranges" ,r-genomicranges) |
| 9656 | ("r-iranges" ,r-iranges) |
| 9657 | ("r-s4vectors" ,r-s4vectors))) |
| 9658 | (home-page "http://www.bioinf.jku.at/software/fastseg/index.html") |
| 9659 | (synopsis "Fast segmentation algorithm for genetic sequencing data") |
| 9660 | (description |
| 9661 | "Fastseg implements a very fast and efficient segmentation algorithm. |
| 9662 | It can segment data from DNA microarrays and data from next generation |
| 9663 | sequencing for example to detect copy number segments. Further it can segment |
| 9664 | data from RNA microarrays like tiling arrays to identify transcripts. Most |
| 9665 | generally, it can segment data given as a matrix or as a vector. Various data |
| 9666 | formats can be used as input to fastseg like expression set objects for |
| 9667 | microarrays or GRanges for sequencing data.") |
| 9668 | (license license:lgpl2.0+))) |
| 9669 | |
| 9670 | (define-public r-keggrest |
| 9671 | (package |
| 9672 | (name "r-keggrest") |
| 9673 | (version "1.18.0") |
| 9674 | (source |
| 9675 | (origin |
| 9676 | (method url-fetch) |
| 9677 | (uri (bioconductor-uri "KEGGREST" version)) |
| 9678 | (sha256 |
| 9679 | (base32 |
| 9680 | "1i3i88lj57wvpgjf75a23msgfsjv8pr2b4j1faga276p4fsblkhj")))) |
| 9681 | (properties `((upstream-name . "KEGGREST"))) |
| 9682 | (build-system r-build-system) |
| 9683 | (propagated-inputs |
| 9684 | `(("r-biostrings" ,r-biostrings) |
| 9685 | ("r-httr" ,r-httr) |
| 9686 | ("r-png" ,r-png))) |
| 9687 | (home-page "https://bioconductor.org/packages/KEGGREST") |
| 9688 | (synopsis "Client-side REST access to KEGG") |
| 9689 | (description |
| 9690 | "This package provides a package that provides a client interface to the |
| 9691 | @dfn{Kyoto Encyclopedia of Genes and Genomes} (KEGG) REST server.") |
| 9692 | (license license:artistic2.0))) |
| 9693 | |
| 9694 | (define-public r-gage |
| 9695 | (package |
| 9696 | (name "r-gage") |
| 9697 | (version "2.28.0") |
| 9698 | (source |
| 9699 | (origin |
| 9700 | (method url-fetch) |
| 9701 | (uri (bioconductor-uri "gage" version)) |
| 9702 | (sha256 |
| 9703 | (base32 |
| 9704 | "1r14p88q3y736pkqm4pdimf1izy1xy3xgivmj3cr4dv65kjny1zk")))) |
| 9705 | (build-system r-build-system) |
| 9706 | (propagated-inputs |
| 9707 | `(("r-annotationdbi" ,r-annotationdbi) |
| 9708 | ("r-graph" ,r-graph) |
| 9709 | ("r-keggrest" ,r-keggrest))) |
| 9710 | (home-page "http://www.biomedcentral.com/1471-2105/10/161") |
| 9711 | (synopsis "Generally applicable gene-set enrichment for pathway analysis") |
| 9712 | (description |
| 9713 | "GAGE is a published method for gene set (enrichment or GSEA) or pathway |
| 9714 | analysis. GAGE is generally applicable independent of microarray or RNA-Seq |
| 9715 | data attributes including sample sizes, experimental designs, assay platforms, |
| 9716 | and other types of heterogeneity. The gage package provides functions for |
| 9717 | basic GAGE analysis, result processing and presentation. In addition, it |
| 9718 | provides demo microarray data and commonly used gene set data based on KEGG |
| 9719 | pathways and GO terms. These funtions and data are also useful for gene set |
| 9720 | analysis using other methods.") |
| 9721 | (license license:gpl2+))) |
| 9722 | |
| 9723 | (define-public r-genomicfiles |
| 9724 | (package |
| 9725 | (name "r-genomicfiles") |
| 9726 | (version "1.14.0") |
| 9727 | (source |
| 9728 | (origin |
| 9729 | (method url-fetch) |
| 9730 | (uri (bioconductor-uri "GenomicFiles" version)) |
| 9731 | (sha256 |
| 9732 | (base32 |
| 9733 | "0r0wmrs5jycf1kckhnc2sgjmp336srlcjdkpbb1ymm7kazdd0s9n")))) |
| 9734 | (properties `((upstream-name . "GenomicFiles"))) |
| 9735 | (build-system r-build-system) |
| 9736 | (propagated-inputs |
| 9737 | `(("r-biocgenerics" ,r-biocgenerics) |
| 9738 | ("r-biocparallel" ,r-biocparallel) |
| 9739 | ("r-genomeinfodb" ,r-genomeinfodb) |
| 9740 | ("r-genomicalignments" ,r-genomicalignments) |
| 9741 | ("r-genomicranges" ,r-genomicranges) |
| 9742 | ("r-iranges" ,r-iranges) |
| 9743 | ("r-rsamtools" ,r-rsamtools) |
| 9744 | ("r-rtracklayer" ,r-rtracklayer) |
| 9745 | ("r-s4vectors" ,r-s4vectors) |
| 9746 | ("r-summarizedexperiment" ,r-summarizedexperiment) |
| 9747 | ("r-variantannotation" ,r-variantannotation))) |
| 9748 | (home-page "https://bioconductor.org/packages/GenomicFiles") |
| 9749 | (synopsis "Distributed computing by file or by range") |
| 9750 | (description |
| 9751 | "This package provides infrastructure for parallel computations |
| 9752 | distributed by file or by range. User defined mapper and reducer functions |
| 9753 | provide added flexibility for data combination and manipulation.") |
| 9754 | (license license:artistic2.0))) |
| 9755 | |
| 9756 | (define-public r-complexheatmap |
| 9757 | (package |
| 9758 | (name "r-complexheatmap") |
| 9759 | (version "1.17.1") |
| 9760 | (source |
| 9761 | (origin |
| 9762 | (method url-fetch) |
| 9763 | (uri (bioconductor-uri "ComplexHeatmap" version)) |
| 9764 | (sha256 |
| 9765 | (base32 |
| 9766 | "1x6kp55iqqsd8bhdl3qch95nfiy2y46ldbbsx1sj1v8f0b0ywwcy")))) |
| 9767 | (properties |
| 9768 | `((upstream-name . "ComplexHeatmap"))) |
| 9769 | (build-system r-build-system) |
| 9770 | (propagated-inputs |
| 9771 | `(("r-circlize" ,r-circlize) |
| 9772 | ("r-colorspace" ,r-colorspace) |
| 9773 | ("r-getoptlong" ,r-getoptlong) |
| 9774 | ("r-globaloptions" ,r-globaloptions) |
| 9775 | ("r-rcolorbrewer" ,r-rcolorbrewer))) |
| 9776 | (home-page |
| 9777 | "https://github.com/jokergoo/ComplexHeatmap") |
| 9778 | (synopsis "Making Complex Heatmaps") |
| 9779 | (description |
| 9780 | "Complex heatmaps are efficient to visualize associations between |
| 9781 | different sources of data sets and reveal potential structures. This package |
| 9782 | provides a highly flexible way to arrange multiple heatmaps and supports |
| 9783 | self-defined annotation graphics.") |
| 9784 | (license license:gpl2+))) |
| 9785 | |
| 9786 | (define-public r-dirichletmultinomial |
| 9787 | (package |
| 9788 | (name "r-dirichletmultinomial") |
| 9789 | (version "1.20.0") |
| 9790 | (source |
| 9791 | (origin |
| 9792 | (method url-fetch) |
| 9793 | (uri (bioconductor-uri "DirichletMultinomial" version)) |
| 9794 | (sha256 |
| 9795 | (base32 |
| 9796 | "1c4s6x0qm20556grcd1xys9kkpnlzpasaai474malwcg6qvgi4x1")))) |
| 9797 | (properties |
| 9798 | `((upstream-name . "DirichletMultinomial"))) |
| 9799 | (build-system r-build-system) |
| 9800 | (inputs |
| 9801 | `(("gsl" ,gsl))) |
| 9802 | (propagated-inputs |
| 9803 | `(("r-biocgenerics" ,r-biocgenerics) |
| 9804 | ("r-iranges" ,r-iranges) |
| 9805 | ("r-s4vectors" ,r-s4vectors))) |
| 9806 | (home-page "https://bioconductor.org/packages/DirichletMultinomial") |
| 9807 | (synopsis "Dirichlet-Multinomial mixture models for microbiome data") |
| 9808 | (description |
| 9809 | "Dirichlet-multinomial mixture models can be used to describe variability |
| 9810 | in microbial metagenomic data. This package is an interface to code |
| 9811 | originally made available by Holmes, Harris, and Quince, 2012, PLoS ONE 7(2): |
| 9812 | 1-15.") |
| 9813 | (license license:lgpl3))) |
| 9814 | |
| 9815 | (define-public r-ensembldb |
| 9816 | (package |
| 9817 | (name "r-ensembldb") |
| 9818 | (version "2.2.0") |
| 9819 | (source |
| 9820 | (origin |
| 9821 | (method url-fetch) |
| 9822 | (uri (bioconductor-uri "ensembldb" version)) |
| 9823 | (sha256 |
| 9824 | (base32 |
| 9825 | "1w0lca3ws5j770bmls91cn93lznvv2pc8s42nybdzz3vdxjvb4m1")))) |
| 9826 | (build-system r-build-system) |
| 9827 | (propagated-inputs |
| 9828 | `(("r-annotationdbi" ,r-annotationdbi) |
| 9829 | ("r-annotationfilter" ,r-annotationfilter) |
| 9830 | ("r-annotationhub" ,r-annotationhub) |
| 9831 | ("r-biobase" ,r-biobase) |
| 9832 | ("r-biocgenerics" ,r-biocgenerics) |
| 9833 | ("r-biostrings" ,r-biostrings) |
| 9834 | ("r-curl" ,r-curl) |
| 9835 | ("r-dbi" ,r-dbi) |
| 9836 | ("r-genomeinfodb" ,r-genomeinfodb) |
| 9837 | ("r-genomicfeatures" ,r-genomicfeatures) |
| 9838 | ("r-genomicranges" ,r-genomicranges) |
| 9839 | ("r-iranges" ,r-iranges) |
| 9840 | ("r-protgenerics" ,r-protgenerics) |
| 9841 | ("r-rsamtools" ,r-rsamtools) |
| 9842 | ("r-rsqlite" ,r-rsqlite) |
| 9843 | ("r-rtracklayer" ,r-rtracklayer) |
| 9844 | ("r-s4vectors" ,r-s4vectors))) |
| 9845 | (home-page "https://github.com/jotsetung/ensembldb") |
| 9846 | (synopsis "Utilities to create and use Ensembl-based annotation databases") |
| 9847 | (description |
| 9848 | "The package provides functions to create and use transcript-centric |
| 9849 | annotation databases/packages. The annotation for the databases are directly |
| 9850 | fetched from Ensembl using their Perl API. The functionality and data is |
| 9851 | similar to that of the TxDb packages from the @code{GenomicFeatures} package, |
| 9852 | but, in addition to retrieve all gene/transcript models and annotations from |
| 9853 | the database, the @code{ensembldb} package also provides a filter framework |
| 9854 | allowing to retrieve annotations for specific entries like genes encoded on a |
| 9855 | chromosome region or transcript models of lincRNA genes.") |
| 9856 | ;; No version specified |
| 9857 | (license license:lgpl3+))) |
| 9858 | |
| 9859 | (define-public r-organismdbi |
| 9860 | (package |
| 9861 | (name "r-organismdbi") |
| 9862 | (version "1.20.0") |
| 9863 | (source |
| 9864 | (origin |
| 9865 | (method url-fetch) |
| 9866 | (uri (bioconductor-uri "OrganismDbi" version)) |
| 9867 | (sha256 |
| 9868 | (base32 |
| 9869 | "0yxvhwn0m53wfwp0zi81x96argdf7cf1lpymc2as51apvfcnjdl8")))) |
| 9870 | (properties `((upstream-name . "OrganismDbi"))) |
| 9871 | (build-system r-build-system) |
| 9872 | (propagated-inputs |
| 9873 | `(("r-annotationdbi" ,r-annotationdbi) |
| 9874 | ("r-biobase" ,r-biobase) |
| 9875 | ("r-biocgenerics" ,r-biocgenerics) |
| 9876 | ("r-biocinstaller" ,r-biocinstaller) |
| 9877 | ("r-dbi" ,r-dbi) |
| 9878 | ("r-genomicfeatures" ,r-genomicfeatures) |
| 9879 | ("r-genomicranges" ,r-genomicranges) |
| 9880 | ("r-graph" ,r-graph) |
| 9881 | ("r-iranges" ,r-iranges) |
| 9882 | ("r-rbgl" ,r-rbgl) |
| 9883 | ("r-s4vectors" ,r-s4vectors))) |
| 9884 | (home-page "https://bioconductor.org/packages/OrganismDbi") |
| 9885 | (synopsis "Software to enable the smooth interfacing of database packages") |
| 9886 | (description "The package enables a simple unified interface to several |
| 9887 | annotation packages each of which has its own schema by taking advantage of |
| 9888 | the fact that each of these packages implements a select methods.") |
| 9889 | (license license:artistic2.0))) |
| 9890 | |
| 9891 | (define-public r-biovizbase |
| 9892 | (package |
| 9893 | (name "r-biovizbase") |
| 9894 | (version "1.26.0") |
| 9895 | (source |
| 9896 | (origin |
| 9897 | (method url-fetch) |
| 9898 | (uri (bioconductor-uri "biovizBase" version)) |
| 9899 | (sha256 |
| 9900 | (base32 |
| 9901 | "14l4vhj0a4ssr9m9zdzz3qpd4qw1mhgq5bmxq7jhrq3j9kmd6i2f")))) |
| 9902 | (properties `((upstream-name . "biovizBase"))) |
| 9903 | (build-system r-build-system) |
| 9904 | (propagated-inputs |
| 9905 | `(("r-annotationdbi" ,r-annotationdbi) |
| 9906 | ("r-annotationfilter" ,r-annotationfilter) |
| 9907 | ("r-biocgenerics" ,r-biocgenerics) |
| 9908 | ("r-biostrings" ,r-biostrings) |
| 9909 | ("r-dichromat" ,r-dichromat) |
| 9910 | ("r-ensembldb" ,r-ensembldb) |
| 9911 | ("r-genomeinfodb" ,r-genomeinfodb) |
| 9912 | ("r-genomicalignments" ,r-genomicalignments) |
| 9913 | ("r-genomicfeatures" ,r-genomicfeatures) |
| 9914 | ("r-genomicranges" ,r-genomicranges) |
| 9915 | ("r-hmisc" ,r-hmisc) |
| 9916 | ("r-iranges" ,r-iranges) |
| 9917 | ("r-rcolorbrewer" ,r-rcolorbrewer) |
| 9918 | ("r-rsamtools" ,r-rsamtools) |
| 9919 | ("r-s4vectors" ,r-s4vectors) |
| 9920 | ("r-scales" ,r-scales) |
| 9921 | ("r-summarizedexperiment" ,r-summarizedexperiment) |
| 9922 | ("r-variantannotation" ,r-variantannotation))) |
| 9923 | (home-page "https://bioconductor.org/packages/biovizBase") |
| 9924 | (synopsis "Basic graphic utilities for visualization of genomic data") |
| 9925 | (description |
| 9926 | "The biovizBase package is designed to provide a set of utilities, color |
| 9927 | schemes and conventions for genomic data. It serves as the base for various |
| 9928 | high-level packages for biological data visualization. This saves development |
| 9929 | effort and encourages consistency.") |
| 9930 | (license license:artistic2.0))) |
| 9931 | |
| 9932 | (define-public r-ggbio |
| 9933 | (package |
| 9934 | (name "r-ggbio") |
| 9935 | (version "1.26.0") |
| 9936 | (source |
| 9937 | (origin |
| 9938 | (method url-fetch) |
| 9939 | (uri (bioconductor-uri "ggbio" version)) |
| 9940 | (sha256 |
| 9941 | (base32 |
| 9942 | "1bqxfqy0hff87ax92z4lfbjz01ndrz7x8pzm6dlkdmi52p30krm9")))) |
| 9943 | (build-system r-build-system) |
| 9944 | (propagated-inputs |
| 9945 | `(("r-annotationdbi" ,r-annotationdbi) |
| 9946 | ("r-annotationfilter" ,r-annotationfilter) |
| 9947 | ("r-biobase" ,r-biobase) |
| 9948 | ("r-biocgenerics" ,r-biocgenerics) |
| 9949 | ("r-biostrings" ,r-biostrings) |
| 9950 | ("r-biovizbase" ,r-biovizbase) |
| 9951 | ("r-bsgenome" ,r-bsgenome) |
| 9952 | ("r-ensembldb" ,r-ensembldb) |
| 9953 | ("r-genomeinfodb" ,r-genomeinfodb) |
| 9954 | ("r-genomicalignments" ,r-genomicalignments) |
| 9955 | ("r-genomicfeatures" ,r-genomicfeatures) |
| 9956 | ("r-genomicranges" ,r-genomicranges) |
| 9957 | ("r-ggally" ,r-ggally) |
| 9958 | ("r-ggplot2" ,r-ggplot2) |
| 9959 | ("r-gridextra" ,r-gridextra) |
| 9960 | ("r-gtable" ,r-gtable) |
| 9961 | ("r-hmisc" ,r-hmisc) |
| 9962 | ("r-iranges" ,r-iranges) |
| 9963 | ("r-organismdbi" ,r-organismdbi) |
| 9964 | ("r-reshape2" ,r-reshape2) |
| 9965 | ("r-rsamtools" ,r-rsamtools) |
| 9966 | ("r-rtracklayer" ,r-rtracklayer) |
| 9967 | ("r-s4vectors" ,r-s4vectors) |
| 9968 | ("r-scales" ,r-scales) |
| 9969 | ("r-summarizedexperiment" ,r-summarizedexperiment) |
| 9970 | ("r-variantannotation" ,r-variantannotation))) |
| 9971 | (home-page "http://www.tengfei.name/ggbio/") |
| 9972 | (synopsis "Visualization tools for genomic data") |
| 9973 | (description |
| 9974 | "The ggbio package extends and specializes the grammar of graphics for |
| 9975 | biological data. The graphics are designed to answer common scientific |
| 9976 | questions, in particular those often asked of high throughput genomics data. |
| 9977 | All core Bioconductor data structures are supported, where appropriate. The |
| 9978 | package supports detailed views of particular genomic regions, as well as |
| 9979 | genome-wide overviews. Supported overviews include ideograms and grand linear |
| 9980 | views. High-level plots include sequence fragment length, edge-linked |
| 9981 | interval to data view, mismatch pileup, and several splicing summaries.") |
| 9982 | (license license:artistic2.0))) |
| 9983 | |
| 9984 | (define-public r-gprofiler |
| 9985 | (package |
| 9986 | (name "r-gprofiler") |
| 9987 | (version "0.6.1") |
| 9988 | (source |
| 9989 | (origin |
| 9990 | (method url-fetch) |
| 9991 | (uri (cran-uri "gProfileR" version)) |
| 9992 | (sha256 |
| 9993 | (base32 |
| 9994 | "1qix15d0wa9nspdclcawml94mng4qmr2jciv7d24py315wfsvv8p")))) |
| 9995 | (properties `((upstream-name . "gProfileR"))) |
| 9996 | (build-system r-build-system) |
| 9997 | (propagated-inputs |
| 9998 | `(("r-plyr" ,r-plyr) |
| 9999 | ("r-rcurl" ,r-rcurl))) |
| 10000 | (home-page "https://cran.r-project.org/web/packages/gProfileR/") |
| 10001 | (synopsis "Interface to the g:Profiler toolkit") |
| 10002 | (description |
| 10003 | "This package provides tools for functional enrichment analysis, |
| 10004 | gene identifier conversion and mapping homologous genes across related |
| 10005 | organisms via the @code{g:Profiler} toolkit.") |
| 10006 | (license license:gpl2+))) |
| 10007 | |
| 10008 | (define-public r-gqtlbase |
| 10009 | (package |
| 10010 | (name "r-gqtlbase") |
| 10011 | (version "1.10.0") |
| 10012 | (source |
| 10013 | (origin |
| 10014 | (method url-fetch) |
| 10015 | (uri (bioconductor-uri "gQTLBase" version)) |
| 10016 | (sha256 |
| 10017 | (base32 |
| 10018 | "1756vfcj2dkkgcmfkkg7qdaig36dv9gfvpypn9rbrky56wm1p035")))) |
| 10019 | (properties `((upstream-name . "gQTLBase"))) |
| 10020 | (build-system r-build-system) |
| 10021 | (propagated-inputs |
| 10022 | `(("r-batchjobs" ,r-batchjobs) |
| 10023 | ("r-bbmisc" ,r-bbmisc) |
| 10024 | ("r-biocgenerics" ,r-biocgenerics) |
| 10025 | ("r-bit" ,r-bit) |
| 10026 | ("r-doparallel" ,r-doparallel) |
| 10027 | ("r-ff" ,r-ff) |
| 10028 | ("r-ffbase" ,r-ffbase) |
| 10029 | ("r-foreach" ,r-foreach) |
| 10030 | ("r-genomicfiles" ,r-genomicfiles) |
| 10031 | ("r-genomicranges" ,r-genomicranges) |
| 10032 | ("r-rtracklayer" ,r-rtracklayer) |
| 10033 | ("r-s4vectors" ,r-s4vectors) |
| 10034 | ("r-summarizedexperiment" ,r-summarizedexperiment))) |
| 10035 | (home-page "https://bioconductor.org/packages/gQTLBase") |
| 10036 | (synopsis "Infrastructure for eQTL, mQTL and similar studies") |
| 10037 | (description |
| 10038 | "The purpose of this package is to simplify the storage and interrogation |
| 10039 | of @dfn{quantitative trait loci} (QTL) archives, such as eQTL, mQTL, dsQTL, |
| 10040 | and more.") |
| 10041 | (license license:artistic2.0))) |
| 10042 | |
| 10043 | (define-public r-snpstats |
| 10044 | (package |
| 10045 | (name "r-snpstats") |
| 10046 | (version "1.28.0") |
| 10047 | (source |
| 10048 | (origin |
| 10049 | (method url-fetch) |
| 10050 | (uri (bioconductor-uri "snpStats" version)) |
| 10051 | (sha256 |
| 10052 | (base32 |
| 10053 | "1x9qwynh2hwl24vq02naf4mchpch7xi2pkdrlgw896k28kx0lvir")))) |
| 10054 | (properties `((upstream-name . "snpStats"))) |
| 10055 | (build-system r-build-system) |
| 10056 | (inputs `(("zlib" ,zlib))) |
| 10057 | (propagated-inputs |
| 10058 | `(("r-biocgenerics" ,r-biocgenerics) |
| 10059 | ("r-matrix" ,r-matrix) |
| 10060 | ("r-survival" ,r-survival) |
| 10061 | ("r-zlibbioc" ,r-zlibbioc))) |
| 10062 | (home-page "https://bioconductor.org/packages/snpStats") |
| 10063 | (synopsis "Methods for SNP association studies") |
| 10064 | (description |
| 10065 | "This package provides classes and statistical methods for large |
| 10066 | @dfn{single-nucleotide polymorphism} (SNP) association studies. This extends |
| 10067 | the earlier snpMatrix package, allowing for uncertainty in genotypes.") |
| 10068 | (license license:gpl3))) |
| 10069 | |
| 10070 | (define-public r-homo-sapiens |
| 10071 | (package |
| 10072 | (name "r-homo-sapiens") |
| 10073 | (version "1.3.1") |
| 10074 | (source (origin |
| 10075 | (method url-fetch) |
| 10076 | ;; We cannot use bioconductor-uri here because this tarball is |
| 10077 | ;; located under "data/annotation/" instead of "bioc/". |
| 10078 | (uri (string-append "http://www.bioconductor.org/packages/" |
| 10079 | "release/data/annotation/src/contrib/" |
| 10080 | "Homo.sapiens_" |
| 10081 | version ".tar.gz")) |
| 10082 | (sha256 |
| 10083 | (base32 |
| 10084 | "151vj7h5p1c8yd5swrchk46z469p135wk50hvkl0nhgndvy0jj01")))) |
| 10085 | (properties |
| 10086 | `((upstream-name . "Homo.sapiens"))) |
| 10087 | (build-system r-build-system) |
| 10088 | (propagated-inputs |
| 10089 | `(("r-genomicfeatures" ,r-genomicfeatures) |
| 10090 | ("r-go-db" ,r-go-db) |
| 10091 | ("r-org-hs-eg-db" ,r-org-hs-eg-db) |
| 10092 | ("r-txdb-hsapiens-ucsc-hg19-knowngene" ,r-txdb-hsapiens-ucsc-hg19-knowngene) |
| 10093 | ("r-organismdbi" ,r-organismdbi) |
| 10094 | ("r-annotationdbi" ,r-annotationdbi))) |
| 10095 | (home-page "https://bioconductor.org/packages/Homo.sapiens/") |
| 10096 | (synopsis "Annotation package for the Homo.sapiens object") |
| 10097 | (description |
| 10098 | "This package contains the Homo.sapiens object to access data from |
| 10099 | several related annotation packages.") |
| 10100 | (license license:artistic2.0))) |
| 10101 | |
| 10102 | (define-public r-erma |
| 10103 | (package |
| 10104 | (name "r-erma") |
| 10105 | (version "0.10.0") |
| 10106 | (source |
| 10107 | (origin |
| 10108 | (method url-fetch) |
| 10109 | (uri (bioconductor-uri "erma" version)) |
| 10110 | (sha256 |
| 10111 | (base32 |
| 10112 | "0gcfs9g8vvdv5vmq9b21kd8sq5mizjj49nfzd4in9zvp4b9v7x1g")))) |
| 10113 | (build-system r-build-system) |
| 10114 | (propagated-inputs |
| 10115 | `(("r-annotationdbi" ,r-annotationdbi) |
| 10116 | ("r-biobase" ,r-biobase) |
| 10117 | ("r-biocgenerics" ,r-biocgenerics) |
| 10118 | ("r-foreach" ,r-foreach) |
| 10119 | ("r-genomicfiles" ,r-genomicfiles) |
| 10120 | ("r-genomicranges" ,r-genomicranges) |
| 10121 | ("r-ggplot2" ,r-ggplot2) |
| 10122 | ("r-homo-sapiens" ,r-homo-sapiens) |
| 10123 | ("r-rtracklayer" ,r-rtracklayer) |
| 10124 | ("r-s4vectors" ,r-s4vectors) |
| 10125 | ("r-shiny" ,r-shiny) |
| 10126 | ("r-summarizedexperiment" ,r-summarizedexperiment))) |
| 10127 | (home-page "https://bioconductor.org/packages/erma") |
| 10128 | (synopsis "Epigenomic road map adventures") |
| 10129 | (description |
| 10130 | "The epigenomics road map describes locations of epigenetic marks in DNA |
| 10131 | from a variety of cell types. Of interest are locations of histone |
| 10132 | modifications, sites of DNA methylation, and regions of accessible chromatin. |
| 10133 | This package presents a selection of elements of the road map including |
| 10134 | metadata and outputs of the ChromImpute procedure applied to ENCODE cell lines |
| 10135 | by Ernst and Kellis.") |
| 10136 | (license license:artistic2.0))) |
| 10137 | |
| 10138 | (define-public r-ldblock |
| 10139 | (package |
| 10140 | (name "r-ldblock") |
| 10141 | (version "1.8.0") |
| 10142 | (source |
| 10143 | (origin |
| 10144 | (method url-fetch) |
| 10145 | (uri (bioconductor-uri "ldblock" version)) |
| 10146 | (sha256 |
| 10147 | (base32 |
| 10148 | "18nfsixh6d2wfrb9laqsgly5w1frzihhak683k0p8fdf51h4aqba")))) |
| 10149 | (build-system r-build-system) |
| 10150 | (propagated-inputs |
| 10151 | `(("r-erma" ,r-erma) |
| 10152 | ("r-genomeinfodb" ,r-genomeinfodb) |
| 10153 | ("r-genomicfiles" ,r-genomicfiles) |
| 10154 | ("r-go-db" ,r-go-db) |
| 10155 | ("r-homo-sapiens" ,r-homo-sapiens) |
| 10156 | ("r-matrix" ,r-matrix) |
| 10157 | ("r-rsamtools" ,r-rsamtools) |
| 10158 | ("r-snpstats" ,r-snpstats) |
| 10159 | ("r-variantannotation" ,r-variantannotation))) |
| 10160 | (home-page "https://bioconductor.org/packages/ldblock") |
| 10161 | (synopsis "Data structures for linkage disequilibrium measures in populations") |
| 10162 | (description |
| 10163 | "This package defines data structures for @dfn{linkage |
| 10164 | disequilibrium} (LD) measures in populations. Its purpose is to simplify |
| 10165 | handling of existing population-level data for the purpose of flexibly |
| 10166 | defining LD blocks.") |
| 10167 | (license license:artistic2.0))) |
| 10168 | |
| 10169 | (define-public r-gqtlstats |
| 10170 | (package |
| 10171 | (name "r-gqtlstats") |
| 10172 | (version "1.10.1") |
| 10173 | (source |
| 10174 | (origin |
| 10175 | (method url-fetch) |
| 10176 | (uri (bioconductor-uri "gQTLstats" version)) |
| 10177 | (sha256 |
| 10178 | (base32 |
| 10179 | "0gvq1sf2zjbkk431x40z6wql3c1rpclnnwa2f1hvykb8mmw70kmq")))) |
| 10180 | (properties `((upstream-name . "gQTLstats"))) |
| 10181 | (build-system r-build-system) |
| 10182 | (propagated-inputs |
| 10183 | `(("r-annotationdbi" ,r-annotationdbi) |
| 10184 | ("r-batchjobs" ,r-batchjobs) |
| 10185 | ("r-bbmisc" ,r-bbmisc) |
| 10186 | ("r-beeswarm" ,r-beeswarm) |
| 10187 | ("r-biobase" ,r-biobase) |
| 10188 | ("r-biocgenerics" ,r-biocgenerics) |
| 10189 | ("r-doparallel" ,r-doparallel) |
| 10190 | ("r-dplyr" ,r-dplyr) |
| 10191 | ("r-erma" ,r-erma) |
| 10192 | ("r-ffbase" ,r-ffbase) |
| 10193 | ("r-foreach" ,r-foreach) |
| 10194 | ("r-genomeinfodb" ,r-genomeinfodb) |
| 10195 | ("r-genomicfeatures" ,r-genomicfeatures) |
| 10196 | ("r-genomicfiles" ,r-genomicfiles) |
| 10197 | ("r-genomicranges" ,r-genomicranges) |
| 10198 | ("r-ggbeeswarm" ,r-ggbeeswarm) |
| 10199 | ("r-ggplot2" ,r-ggplot2) |
| 10200 | ("r-gqtlbase" ,r-gqtlbase) |
| 10201 | ("r-hardyweinberg" ,r-hardyweinberg) |
| 10202 | ("r-iranges" ,r-iranges) |
| 10203 | ("r-ldblock" ,r-ldblock) |
| 10204 | ("r-limma" ,r-limma) |
| 10205 | ("r-mgcv" ,r-mgcv) |
| 10206 | ("r-plotly" ,r-plotly) |
| 10207 | ("r-reshape2" ,r-reshape2) |
| 10208 | ("r-s4vectors" ,r-s4vectors) |
| 10209 | ("r-shiny" ,r-shiny) |
| 10210 | ("r-snpstats" ,r-snpstats) |
| 10211 | ("r-summarizedexperiment" ,r-summarizedexperiment) |
| 10212 | ("r-variantannotation" ,r-variantannotation))) |
| 10213 | (home-page "https://bioconductor.org/packages/gQTLstats") |
| 10214 | (synopsis "Computationally efficient analysis for eQTL and allied studies") |
| 10215 | (description |
| 10216 | "This package provides tools for the computationally efficient analysis |
| 10217 | of @dfn{quantitative trait loci} (QTL) data, including eQTL, mQTL, dsQTL, etc. |
| 10218 | The software in this package aims to support refinements and functional |
| 10219 | interpretation of members of a collection of association statistics on a |
| 10220 | family of feature/genome hypotheses.") |
| 10221 | (license license:artistic2.0))) |
| 10222 | |
| 10223 | (define-public r-gviz |
| 10224 | (package |
| 10225 | (name "r-gviz") |
| 10226 | (version "1.22.2") |
| 10227 | (source |
| 10228 | (origin |
| 10229 | (method url-fetch) |
| 10230 | (uri (bioconductor-uri "Gviz" version)) |
| 10231 | (sha256 |
| 10232 | (base32 |
| 10233 | "173n99mc95sij2vb8n3xd016x7mxhjs961q3l29xkg1lrnnm2sva")))) |
| 10234 | (properties `((upstream-name . "Gviz"))) |
| 10235 | (build-system r-build-system) |
| 10236 | (propagated-inputs |
| 10237 | `(("r-annotationdbi" ,r-annotationdbi) |
| 10238 | ("r-biobase" ,r-biobase) |
| 10239 | ("r-biocgenerics" ,r-biocgenerics) |
| 10240 | ("r-biomart" ,r-biomart) |
| 10241 | ("r-biostrings" ,r-biostrings) |
| 10242 | ("r-biovizbase" ,r-biovizbase) |
| 10243 | ("r-bsgenome" ,r-bsgenome) |
| 10244 | ("r-digest" ,r-digest) |
| 10245 | ("r-genomeinfodb" ,r-genomeinfodb) |
| 10246 | ("r-genomicalignments" ,r-genomicalignments) |
| 10247 | ("r-genomicfeatures" ,r-genomicfeatures) |
| 10248 | ("r-genomicranges" ,r-genomicranges) |
| 10249 | ("r-iranges" ,r-iranges) |
| 10250 | ("r-lattice" ,r-lattice) |
| 10251 | ("r-latticeextra" ,r-latticeextra) |
| 10252 | ("r-matrixstats" ,r-matrixstats) |
| 10253 | ("r-rcolorbrewer" ,r-rcolorbrewer) |
| 10254 | ("r-rsamtools" ,r-rsamtools) |
| 10255 | ("r-rtracklayer" ,r-rtracklayer) |
| 10256 | ("r-s4vectors" ,r-s4vectors) |
| 10257 | ("r-xvector" ,r-xvector))) |
| 10258 | (home-page "https://bioconductor.org/packages/Gviz") |
| 10259 | (synopsis "Plotting data and annotation information along genomic coordinates") |
| 10260 | (description |
| 10261 | "Genomic data analyses requires integrated visualization of known genomic |
| 10262 | information and new experimental data. Gviz uses the biomaRt and the |
| 10263 | rtracklayer packages to perform live annotation queries to Ensembl and UCSC |
| 10264 | and translates this to e.g. gene/transcript structures in viewports of the |
| 10265 | grid graphics package. This results in genomic information plotted together |
| 10266 | with your data.") |
| 10267 | (license license:artistic2.0))) |
| 10268 | |
| 10269 | (define-public r-gwascat |
| 10270 | (package |
| 10271 | (name "r-gwascat") |
| 10272 | (version "2.10.0") |
| 10273 | (source |
| 10274 | (origin |
| 10275 | (method url-fetch) |
| 10276 | (uri (bioconductor-uri "gwascat" version)) |
| 10277 | (sha256 |
| 10278 | (base32 |
| 10279 | "0n5x5i5v6a8wpn5mxmlpkl34b4kyypmymiwww6g61zch7xqrgywi")))) |
| 10280 | (build-system r-build-system) |
| 10281 | (propagated-inputs |
| 10282 | `(("r-annotationdbi" ,r-annotationdbi) |
| 10283 | ("r-annotationhub" ,r-annotationhub) |
| 10284 | ("r-biocgenerics" ,r-biocgenerics) |
| 10285 | ("r-biostrings" ,r-biostrings) |
| 10286 | ("r-genomeinfodb" ,r-genomeinfodb) |
| 10287 | ("r-genomicfeatures" ,r-genomicfeatures) |
| 10288 | ("r-genomicranges" ,r-genomicranges) |
| 10289 | ("r-ggbio" ,r-ggbio) |
| 10290 | ("r-ggplot2" ,r-ggplot2) |
| 10291 | ("r-gqtlstats" ,r-gqtlstats) |
| 10292 | ("r-graph" ,r-graph) |
| 10293 | ("r-gviz" ,r-gviz) |
| 10294 | ("r-homo-sapiens" ,r-homo-sapiens) |
| 10295 | ("r-iranges" ,r-iranges) |
| 10296 | ("r-rsamtools" ,r-rsamtools) |
| 10297 | ("r-rtracklayer" ,r-rtracklayer) |
| 10298 | ("r-s4vectors" ,r-s4vectors) |
| 10299 | ("r-snpstats" ,r-snpstats) |
| 10300 | ("r-summarizedexperiment" ,r-summarizedexperiment) |
| 10301 | ("r-variantannotation" ,r-variantannotation))) |
| 10302 | (home-page "https://bioconductor.org/packages/gwascat") |
| 10303 | (synopsis "Tools for data in the EMBL-EBI GWAS catalog") |
| 10304 | (description |
| 10305 | "This package provides tools for representing and modeling data in the |
| 10306 | EMBL-EBI GWAS catalog.") |
| 10307 | (license license:artistic2.0))) |
| 10308 | |
| 10309 | (define-public r-sushi |
| 10310 | (package |
| 10311 | (name "r-sushi") |
| 10312 | (version "1.16.0") |
| 10313 | (source (origin |
| 10314 | (method url-fetch) |
| 10315 | (uri (bioconductor-uri "Sushi" version)) |
| 10316 | (sha256 |
| 10317 | (base32 |
| 10318 | "0axaqm480z8d0b2ldgxwm0swava1p4irc62bpl17p2k8k78g687g")))) |
| 10319 | (properties `((upstream-name . "Sushi"))) |
| 10320 | (build-system r-build-system) |
| 10321 | (propagated-inputs |
| 10322 | `(("r-biomart" ,r-biomart) |
| 10323 | ("r-zoo" ,r-zoo))) |
| 10324 | (home-page "https://bioconductor.org/packages/Sushi") |
| 10325 | (synopsis "Tools for visualizing genomics data") |
| 10326 | (description |
| 10327 | "This package provides flexible, quantitative, and integrative genomic |
| 10328 | visualizations for publication-quality multi-panel figures.") |
| 10329 | (license license:gpl2+))) |
| 10330 | |
| 10331 | (define-public r-fithic |
| 10332 | (package |
| 10333 | (name "r-fithic") |
| 10334 | (version "1.4.0") |
| 10335 | (source (origin |
| 10336 | (method url-fetch) |
| 10337 | (uri (bioconductor-uri "FitHiC" version)) |
| 10338 | (sha256 |
| 10339 | (base32 |
| 10340 | "12ylhrppi051m7nqsgq95kzd9g9wmp34i0zzfi55cjqawlpx7c6n")))) |
| 10341 | (properties `((upstream-name . "FitHiC"))) |
| 10342 | (build-system r-build-system) |
| 10343 | (propagated-inputs |
| 10344 | `(("r-data-table" ,r-data-table) |
| 10345 | ("r-fdrtool" ,r-fdrtool) |
| 10346 | ("r-rcpp" ,r-rcpp))) |
| 10347 | (home-page "https://bioconductor.org/packages/FitHiC") |
| 10348 | (synopsis "Confidence estimation for intra-chromosomal contact maps") |
| 10349 | (description |
| 10350 | "Fit-Hi-C is a tool for assigning statistical confidence estimates to |
| 10351 | intra-chromosomal contact maps produced by genome-wide genome architecture |
| 10352 | assays such as Hi-C.") |
| 10353 | (license license:gpl2+))) |
| 10354 | |
| 10355 | (define-public r-hitc |
| 10356 | (package |
| 10357 | (name "r-hitc") |
| 10358 | (version "1.22.0") |
| 10359 | (source (origin |
| 10360 | (method url-fetch) |
| 10361 | (uri (bioconductor-uri "HiTC" version)) |
| 10362 | (sha256 |
| 10363 | (base32 |
| 10364 | "0288xa1jy6nzvz2ha07csmp6dirjw5r7p9vy69q2wsbyzr02ymkp")))) |
| 10365 | (properties `((upstream-name . "HiTC"))) |
| 10366 | (build-system r-build-system) |
| 10367 | (propagated-inputs |
| 10368 | `(("r-biostrings" ,r-biostrings) |
| 10369 | ("r-genomeinfodb" ,r-genomeinfodb) |
| 10370 | ("r-genomicranges" ,r-genomicranges) |
| 10371 | ("r-iranges" ,r-iranges) |
| 10372 | ("r-matrix" ,r-matrix) |
| 10373 | ("r-rcolorbrewer" ,r-rcolorbrewer) |
| 10374 | ("r-rtracklayer" ,r-rtracklayer))) |
| 10375 | (home-page "https://bioconductor.org/packages/HiTC") |
| 10376 | (synopsis "High throughput chromosome conformation capture analysis") |
| 10377 | (description |
| 10378 | "The HiTC package was developed to explore high-throughput \"C\" data |
| 10379 | such as 5C or Hi-C. Dedicated R classes as well as standard methods for |
| 10380 | quality controls, normalization, visualization, and further analysis are also |
| 10381 | provided.") |
| 10382 | (license license:artistic2.0))) |
| 10383 | |
| 10384 | (define-public r-qvalue |
| 10385 | (package |
| 10386 | (name "r-qvalue") |
| 10387 | (version "2.10.0") |
| 10388 | (source |
| 10389 | (origin |
| 10390 | (method url-fetch) |
| 10391 | (uri (bioconductor-uri "qvalue" version)) |
| 10392 | (sha256 |
| 10393 | (base32 |
| 10394 | "1rd9rnf16kh8wc076kahd9hsb9rfwsbzmz3kjmp0pj6rbiq0051i")))) |
| 10395 | (build-system r-build-system) |
| 10396 | (propagated-inputs |
| 10397 | `(("r-ggplot2" ,r-ggplot2) |
| 10398 | ("r-reshape2" ,r-reshape2))) |
| 10399 | (home-page "http://github.com/jdstorey/qvalue") |
| 10400 | (synopsis "Q-value estimation for false discovery rate control") |
| 10401 | (description |
| 10402 | "This package takes a list of p-values resulting from the simultaneous |
| 10403 | testing of many hypotheses and estimates their q-values and local @dfn{false |
| 10404 | discovery rate} (FDR) values. The q-value of a test measures the proportion |
| 10405 | of false positives incurred when that particular test is called significant. |
| 10406 | The local FDR measures the posterior probability the null hypothesis is true |
| 10407 | given the test's p-value. Various plots are automatically generated, allowing |
| 10408 | one to make sensible significance cut-offs. The software can be applied to |
| 10409 | problems in genomics, brain imaging, astrophysics, and data mining.") |
| 10410 | ;; Any version of the LGPL. |
| 10411 | (license license:lgpl3+))) |
| 10412 | |
| 10413 | (define htslib-for-sambamba |
| 10414 | (let ((commit "2f3c3ea7b301f9b45737a793c0b2dcf0240e5ee5")) |
| 10415 | (package |
| 10416 | (inherit htslib) |
| 10417 | (name "htslib-for-sambamba") |
| 10418 | (version (string-append "1.3.1-1." (string-take commit 9))) |
| 10419 | (source |
| 10420 | (origin |
| 10421 | (method git-fetch) |
| 10422 | (uri (git-reference |
| 10423 | (url "https://github.com/lomereiter/htslib.git") |
| 10424 | (commit commit))) |
| 10425 | (file-name (string-append "htslib-" version "-checkout")) |
| 10426 | (sha256 |
| 10427 | (base32 |
| 10428 | "0g38g8s3npr0gjm9fahlbhiskyfws9l5i0x1ml3rakzj7az5l9c9")))) |
| 10429 | (arguments |
| 10430 | (substitute-keyword-arguments (package-arguments htslib) |
| 10431 | ((#:phases phases) |
| 10432 | `(modify-phases ,phases |
| 10433 | (add-after 'unpack 'bootstrap |
| 10434 | (lambda _ |
| 10435 | (zero? (system* "autoreconf" "-vif")))))))) |
| 10436 | (native-inputs |
| 10437 | `(("autoconf" ,autoconf) |
| 10438 | ("automake" ,automake) |
| 10439 | ,@(package-native-inputs htslib)))))) |
| 10440 | |
| 10441 | (define-public sambamba |
| 10442 | (package |
| 10443 | (name "sambamba") |
| 10444 | (version "0.6.5") |
| 10445 | (source |
| 10446 | (origin |
| 10447 | (method url-fetch) |
| 10448 | (uri (string-append "https://github.com/lomereiter/sambamba/" |
| 10449 | "archive/v" version ".tar.gz")) |
| 10450 | (file-name (string-append name "-" version ".tar.gz")) |
| 10451 | (sha256 |
| 10452 | (base32 |
| 10453 | "17076gijd65a3f07zns2gvbgahiz5lriwsa6dq353ss3jl85d8vy")))) |
| 10454 | (build-system gnu-build-system) |
| 10455 | (arguments |
| 10456 | `(#:tests? #f ; there is no test target |
| 10457 | #:make-flags |
| 10458 | '("D_COMPILER=ldc2" |
| 10459 | ;; Override "--compiler" flag only. |
| 10460 | "D_FLAGS=--compiler=ldc2 -IBioD -g -d" |
| 10461 | "sambamba-ldmd2-64") |
| 10462 | #:phases |
| 10463 | (modify-phases %standard-phases |
| 10464 | (delete 'configure) |
| 10465 | (add-after 'unpack 'place-biod |
| 10466 | (lambda* (#:key inputs #:allow-other-keys) |
| 10467 | (copy-recursively (assoc-ref inputs "biod") "BioD") |
| 10468 | #t)) |
| 10469 | (add-after 'unpack 'unbundle-prerequisites |
| 10470 | (lambda _ |
| 10471 | (substitute* "Makefile" |
| 10472 | ((" htslib-static lz4-static") "")) |
| 10473 | #t)) |
| 10474 | (replace 'install |
| 10475 | (lambda* (#:key outputs #:allow-other-keys) |
| 10476 | (let* ((out (assoc-ref outputs "out")) |
| 10477 | (bin (string-append out "/bin"))) |
| 10478 | (mkdir-p bin) |
| 10479 | (install-file "build/sambamba" bin) |
| 10480 | #t)))))) |
| 10481 | (native-inputs |
| 10482 | `(("ldc" ,ldc) |
| 10483 | ("rdmd" ,rdmd) |
| 10484 | ("biod" |
| 10485 | ,(let ((commit "1248586b54af4bd4dfb28ebfebfc6bf012e7a587")) |
| 10486 | (origin |
| 10487 | (method git-fetch) |
| 10488 | (uri (git-reference |
| 10489 | (url "https://github.com/biod/BioD.git") |
| 10490 | (commit commit))) |
| 10491 | (file-name (string-append "biod-" |
| 10492 | (string-take commit 9) |
| 10493 | "-checkout")) |
| 10494 | (sha256 |
| 10495 | (base32 |
| 10496 | "1m8hi1n7x0ri4l6s9i0x6jg4z4v94xrfdzp7mbizdipfag0m17g3"))))))) |
| 10497 | (inputs |
| 10498 | `(("lz4" ,lz4) |
| 10499 | ("htslib" ,htslib-for-sambamba))) |
| 10500 | (home-page "http://lomereiter.github.io/sambamba") |
| 10501 | (synopsis "Tools for working with SAM/BAM data") |
| 10502 | (description "Sambamba is a high performance modern robust and |
| 10503 | fast tool (and library), written in the D programming language, for |
| 10504 | working with SAM and BAM files. Current parallelised functionality is |
| 10505 | an important subset of samtools functionality, including view, index, |
| 10506 | sort, markdup, and depth.") |
| 10507 | (license license:gpl2+))) |
| 10508 | |
| 10509 | (define-public ritornello |
| 10510 | (package |
| 10511 | (name "ritornello") |
| 10512 | (version "1.0.0") |
| 10513 | (source (origin |
| 10514 | (method url-fetch) |
| 10515 | (uri (string-append "https://github.com/KlugerLab/" |
| 10516 | "Ritornello/archive/v" |
| 10517 | version ".tar.gz")) |
| 10518 | (file-name (string-append name "-" version ".tar.gz")) |
| 10519 | (sha256 |
| 10520 | (base32 |
| 10521 | "02nik86gq9ljjriv6pamwlmqnfky3ads1fpklx6mc3hx6k40pg38")))) |
| 10522 | (build-system gnu-build-system) |
| 10523 | (arguments |
| 10524 | `(#:tests? #f ; there are no tests |
| 10525 | #:phases |
| 10526 | (modify-phases %standard-phases |
| 10527 | (add-after 'unpack 'patch-samtools-references |
| 10528 | (lambda* (#:key inputs #:allow-other-keys) |
| 10529 | (substitute* '("src/SamStream.h" |
| 10530 | "src/BufferedGenomeReader.h") |
| 10531 | (("<sam.h>") "<samtools/sam.h>")) |
| 10532 | #t)) |
| 10533 | (delete 'configure) |
| 10534 | (replace 'install |
| 10535 | (lambda* (#:key inputs outputs #:allow-other-keys) |
| 10536 | (let* ((out (assoc-ref outputs "out")) |
| 10537 | (bin (string-append out "/bin/"))) |
| 10538 | (mkdir-p bin) |
| 10539 | (install-file "bin/Ritornello" bin) |
| 10540 | #t)))))) |
| 10541 | (inputs |
| 10542 | `(("samtools" ,samtools-0.1) |
| 10543 | ("fftw" ,fftw) |
| 10544 | ("boost" ,boost) |
| 10545 | ("zlib" ,zlib))) |
| 10546 | (home-page "https://github.com/KlugerLab/Ritornello") |
| 10547 | (synopsis "Control-free peak caller for ChIP-seq data") |
| 10548 | (description "Ritornello is a ChIP-seq peak calling algorithm based on |
| 10549 | signal processing that can accurately call binding events without the need to |
| 10550 | do a pair total DNA input or IgG control sample. It has been tested for use |
| 10551 | with narrow binding events such as transcription factor ChIP-seq.") |
| 10552 | (license license:gpl3+))) |
| 10553 | |
| 10554 | (define-public trim-galore |
| 10555 | (package |
| 10556 | (name "trim-galore") |
| 10557 | (version "0.4.2") |
| 10558 | (source |
| 10559 | (origin |
| 10560 | (method url-fetch) |
| 10561 | (uri (string-append "http://www.bioinformatics.babraham.ac.uk/" |
| 10562 | "projects/trim_galore/trim_galore_v" |
| 10563 | version ".zip")) |
| 10564 | (sha256 |
| 10565 | (base32 |
| 10566 | "0b9qdxi4521gsrjvbhgky8g7kry9b5nx3byzaxkgxz7p4k8bn1mn")))) |
| 10567 | (build-system gnu-build-system) |
| 10568 | (arguments |
| 10569 | `(#:tests? #f ; no tests |
| 10570 | #:phases |
| 10571 | (modify-phases %standard-phases |
| 10572 | ;; The archive contains plain files. |
| 10573 | (replace 'unpack |
| 10574 | (lambda* (#:key source #:allow-other-keys) |
| 10575 | (zero? (system* "unzip" source)))) |
| 10576 | (delete 'configure) |
| 10577 | (delete 'build) |
| 10578 | (add-after 'unpack 'hardcode-tool-references |
| 10579 | (lambda* (#:key inputs #:allow-other-keys) |
| 10580 | (substitute* "trim_galore" |
| 10581 | (("\\$path_to_cutadapt = 'cutadapt'") |
| 10582 | (string-append "$path_to_cutadapt = '" |
| 10583 | (assoc-ref inputs "cutadapt") |
| 10584 | "/bin/cutadapt'")) |
| 10585 | (("\\| gzip") |
| 10586 | (string-append "| " |
| 10587 | (assoc-ref inputs "gzip") |
| 10588 | "/bin/gzip")) |
| 10589 | (("\"gunzip") |
| 10590 | (string-append "\"" |
| 10591 | (assoc-ref inputs "gzip") |
| 10592 | "/bin/gunzip"))) |
| 10593 | #t)) |
| 10594 | (replace 'install |
| 10595 | (lambda* (#:key outputs #:allow-other-keys) |
| 10596 | (let ((bin (string-append (assoc-ref outputs "out") |
| 10597 | "/bin"))) |
| 10598 | (mkdir-p bin) |
| 10599 | (install-file "trim_galore" bin) |
| 10600 | #t)))))) |
| 10601 | (inputs |
| 10602 | `(("gzip" ,gzip) |
| 10603 | ("perl" ,perl) |
| 10604 | ("cutadapt" ,cutadapt))) |
| 10605 | (native-inputs |
| 10606 | `(("unzip" ,unzip))) |
| 10607 | (home-page "http://www.bioinformatics.babraham.ac.uk/projects/trim_galore/") |
| 10608 | (synopsis "Wrapper around Cutadapt and FastQC") |
| 10609 | (description "Trim Galore! is a wrapper script to automate quality and |
| 10610 | adapter trimming as well as quality control, with some added functionality to |
| 10611 | remove biased methylation positions for RRBS sequence files.") |
| 10612 | (license license:gpl3+))) |
| 10613 | |
| 10614 | (define-public gess |
| 10615 | (package |
| 10616 | (name "gess") |
| 10617 | (version "1.0") |
| 10618 | (source (origin |
| 10619 | (method url-fetch) |
| 10620 | (uri (string-append "http://compbio.uthscsa.edu/" |
| 10621 | "GESS_Web/files/" |
| 10622 | "gess-" version ".src.tar.gz")) |
| 10623 | (sha256 |
| 10624 | (base32 |
| 10625 | "0hyk403kxscclzfs24pvdgiv0wm03kjcziqdrp5w46cb049gz0d7")))) |
| 10626 | (build-system gnu-build-system) |
| 10627 | (arguments |
| 10628 | `(#:tests? #f ; no tests |
| 10629 | #:phases |
| 10630 | (modify-phases %standard-phases |
| 10631 | (delete 'configure) |
| 10632 | (delete 'build) |
| 10633 | (replace 'install |
| 10634 | (lambda* (#:key inputs outputs #:allow-other-keys) |
| 10635 | (let* ((python (assoc-ref inputs "python")) |
| 10636 | (out (assoc-ref outputs "out")) |
| 10637 | (bin (string-append out "/bin/")) |
| 10638 | (target (string-append |
| 10639 | out "/lib/python2.7/site-packages/gess/"))) |
| 10640 | (mkdir-p target) |
| 10641 | (copy-recursively "." target) |
| 10642 | ;; Make GESS.py executable |
| 10643 | (chmod (string-append target "GESS.py") #o555) |
| 10644 | ;; Add Python shebang to the top and make Matplotlib |
| 10645 | ;; usable. |
| 10646 | (substitute* (string-append target "GESS.py") |
| 10647 | (("\"\"\"Description:" line) |
| 10648 | (string-append "#!" (which "python") " |
| 10649 | import matplotlib |
| 10650 | matplotlib.use('Agg') |
| 10651 | " line))) |
| 10652 | ;; Make sure GESS has all modules in its path |
| 10653 | (wrap-program (string-append target "GESS.py") |
| 10654 | `("PYTHONPATH" ":" prefix (,target ,(getenv "PYTHONPATH")))) |
| 10655 | (mkdir-p bin) |
| 10656 | (symlink (string-append target "GESS.py") |
| 10657 | (string-append bin "GESS.py")) |
| 10658 | #t)))))) |
| 10659 | (inputs |
| 10660 | `(("python" ,python-2) |
| 10661 | ("python2-pysam" ,python2-pysam) |
| 10662 | ("python2-scipy" ,python2-scipy) |
| 10663 | ("python2-numpy" ,python2-numpy) |
| 10664 | ("python2-networkx" ,python2-networkx) |
| 10665 | ("python2-biopython" ,python2-biopython))) |
| 10666 | (home-page "http://compbio.uthscsa.edu/GESS_Web/") |
| 10667 | (synopsis "Detect exon-skipping events from raw RNA-seq data") |
| 10668 | (description |
| 10669 | "GESS is an implementation of a novel computational method to detect de |
| 10670 | novo exon-skipping events directly from raw RNA-seq data without the prior |
| 10671 | knowledge of gene annotation information. GESS stands for the graph-based |
| 10672 | exon-skipping scanner detection scheme.") |
| 10673 | (license license:bsd-3))) |
| 10674 | |
| 10675 | (define-public phylip |
| 10676 | (package |
| 10677 | (name "phylip") |
| 10678 | (version "3.696") |
| 10679 | (source |
| 10680 | (origin |
| 10681 | (method url-fetch) |
| 10682 | (uri (string-append "http://evolution.gs.washington.edu/phylip/" |
| 10683 | "download/phylip-" version ".tar.gz")) |
| 10684 | (sha256 |
| 10685 | (base32 |
| 10686 | "01jar1rayhr2gba2pgbw49m56rc5z4p5wn3ds0m188hrlln4a2nd")))) |
| 10687 | (build-system gnu-build-system) |
| 10688 | (arguments |
| 10689 | `(#:tests? #f ; no check target |
| 10690 | #:make-flags (list "-f" "Makefile.unx" "install") |
| 10691 | #:parallel-build? #f ; not supported |
| 10692 | #:phases |
| 10693 | (modify-phases %standard-phases |
| 10694 | (add-after 'unpack 'enter-dir |
| 10695 | (lambda _ (chdir "src") #t)) |
| 10696 | (delete 'configure) |
| 10697 | (replace 'install |
| 10698 | (lambda* (#:key inputs outputs #:allow-other-keys) |
| 10699 | (let ((target (string-append (assoc-ref outputs "out") |
| 10700 | "/bin"))) |
| 10701 | (mkdir-p target) |
| 10702 | (for-each (lambda (file) |
| 10703 | (install-file file target)) |
| 10704 | (find-files "../exe" ".*"))) |
| 10705 | #t))))) |
| 10706 | (home-page "http://evolution.genetics.washington.edu/phylip/") |
| 10707 | (synopsis "Tools for inferring phylogenies") |
| 10708 | (description "PHYLIP (the PHYLogeny Inference Package) is a package of |
| 10709 | programs for inferring phylogenies (evolutionary trees).") |
| 10710 | (license license:bsd-2))) |
| 10711 | |
| 10712 | (define-public imp |
| 10713 | (package |
| 10714 | (name "imp") |
| 10715 | (version "2.6.2") |
| 10716 | (source |
| 10717 | (origin |
| 10718 | (method url-fetch) |
| 10719 | (uri (string-append "https://integrativemodeling.org/" |
| 10720 | version "/download/imp-" version ".tar.gz")) |
| 10721 | (sha256 |
| 10722 | (base32 |
| 10723 | "0lxqx7vh79d771svr611dkilp6sn30qrbw8zvscbrm37v38d2j6h")))) |
| 10724 | (build-system cmake-build-system) |
| 10725 | (arguments |
| 10726 | `(;; FIXME: Some tests fail because they produce warnings, others fail |
| 10727 | ;; because the PYTHONPATH does not include the modeller's directory. |
| 10728 | #:tests? #f |
| 10729 | ;; Do not place libraries in an architecture-specific directory. |
| 10730 | #:configure-flags |
| 10731 | (list "-DCMAKE_INSTALL_LIBDIR=lib"))) |
| 10732 | (inputs |
| 10733 | `(("boost" ,boost) |
| 10734 | ("gsl" ,gsl) |
| 10735 | ("swig" ,swig) |
| 10736 | ("hdf5" ,hdf5) |
| 10737 | ("fftw" ,fftw) |
| 10738 | ("python" ,python-2))) |
| 10739 | (propagated-inputs |
| 10740 | `(("python2-numpy" ,python2-numpy) |
| 10741 | ("python2-scipy" ,python2-scipy) |
| 10742 | ("python2-pandas" ,python2-pandas) |
| 10743 | ("python2-scikit-learn" ,python2-scikit-learn) |
| 10744 | ("python2-networkx" ,python2-networkx))) |
| 10745 | (home-page "https://integrativemodeling.org") |
| 10746 | (synopsis "Integrative modeling platform") |
| 10747 | (description "IMP's broad goal is to contribute to a comprehensive |
| 10748 | structural characterization of biomolecules ranging in size and complexity |
| 10749 | from small peptides to large macromolecular assemblies, by integrating data |
| 10750 | from diverse biochemical and biophysical experiments. IMP provides a C++ and |
| 10751 | Python toolbox for solving complex modeling problems, and a number of |
| 10752 | applications for tackling some common problems in a user-friendly way.") |
| 10753 | ;; IMP is largely available under the GNU Lesser GPL; see the file |
| 10754 | ;; COPYING.LGPL for the full text of this license. Some IMP modules are |
| 10755 | ;; available under the GNU GPL (see the file COPYING.GPL). |
| 10756 | (license (list license:lgpl2.1+ |
| 10757 | license:gpl3+)))) |
| 10758 | |
| 10759 | (define-public tadbit |
| 10760 | (package |
| 10761 | (name "tadbit") |
| 10762 | (version "0.2") |
| 10763 | (source (origin |
| 10764 | (method url-fetch) |
| 10765 | (uri (string-append "https://github.com/3DGenomes/TADbit/" |
| 10766 | "archive/v" version ".tar.gz")) |
| 10767 | (file-name (string-append name "-" version ".tar.gz")) |
| 10768 | (sha256 |
| 10769 | (base32 |
| 10770 | "1cnfqrl4685zar4nnw94j94nhvl2h29jm448nadqi1h05z6fdk4f")))) |
| 10771 | (build-system python-build-system) |
| 10772 | (arguments |
| 10773 | `(;; Tests are included and must be run after installation, but |
| 10774 | ;; they are incomplete and thus cannot be run. |
| 10775 | #:tests? #f |
| 10776 | #:python ,python-2 |
| 10777 | #:phases |
| 10778 | (modify-phases %standard-phases |
| 10779 | (add-after 'unpack 'fix-problems-with-setup.py |
| 10780 | (lambda* (#:key outputs #:allow-other-keys) |
| 10781 | ;; setup.py opens these files for writing |
| 10782 | (chmod "_pytadbit/_version.py" #o664) |
| 10783 | (chmod "README.rst" #o664) |
| 10784 | |
| 10785 | ;; Don't attempt to install the bash completions to |
| 10786 | ;; the home directory. |
| 10787 | (rename-file "extras/.bash_completion" |
| 10788 | "extras/tadbit") |
| 10789 | (substitute* "setup.py" |
| 10790 | (("\\(path.expanduser\\('~'\\)") |
| 10791 | (string-append "(\"" |
| 10792 | (assoc-ref outputs "out") |
| 10793 | "/etc/bash_completion.d\"")) |
| 10794 | (("extras/\\.bash_completion") |
| 10795 | "extras/tadbit")) |
| 10796 | #t))))) |
| 10797 | (inputs |
| 10798 | ;; TODO: add Chimera for visualization |
| 10799 | `(("imp" ,imp) |
| 10800 | ("mcl" ,mcl) |
| 10801 | ("python2-scipy" ,python2-scipy) |
| 10802 | ("python2-numpy" ,python2-numpy) |
| 10803 | ("python2-matplotlib" ,python2-matplotlib) |
| 10804 | ("python2-pysam" ,python2-pysam))) |
| 10805 | (home-page "http://3dgenomes.github.io/TADbit/") |
| 10806 | (synopsis "Analyze, model, and explore 3C-based data") |
| 10807 | (description |
| 10808 | "TADbit is a complete Python library to deal with all steps to analyze, |
| 10809 | model, and explore 3C-based data. With TADbit the user can map FASTQ files to |
| 10810 | obtain raw interaction binned matrices (Hi-C like matrices), normalize and |
| 10811 | correct interaction matrices, identify and compare the so-called |
| 10812 | @dfn{Topologically Associating Domains} (TADs), build 3D models from the |
| 10813 | interaction matrices, and finally, extract structural properties from the |
| 10814 | models. TADbit is complemented by TADkit for visualizing 3D models.") |
| 10815 | (license license:gpl3+))) |
| 10816 | |
| 10817 | (define-public kentutils |
| 10818 | (package |
| 10819 | (name "kentutils") |
| 10820 | ;; 302.1.0 is out, but the only difference is the inclusion of |
| 10821 | ;; pre-built binaries. |
| 10822 | (version "302.0.0") |
| 10823 | (source |
| 10824 | (origin |
| 10825 | (method url-fetch) |
| 10826 | (uri (string-append "https://github.com/ENCODE-DCC/kentUtils/" |
| 10827 | "archive/v" version ".tar.gz")) |
| 10828 | (file-name (string-append name "-" version ".tar.gz")) |
| 10829 | (sha256 |
| 10830 | (base32 |
| 10831 | "134aja3k1cj32kbk1nnw0q9gxjb2krr15q6sga8qldzvc0585rmm")) |
| 10832 | (modules '((guix build utils) |
| 10833 | (srfi srfi-26) |
| 10834 | (ice-9 ftw))) |
| 10835 | (snippet |
| 10836 | '(begin |
| 10837 | ;; Only the contents of the specified directories are free |
| 10838 | ;; for all uses, so we remove the rest. "hg/autoSql" and |
| 10839 | ;; "hg/autoXml" are nominally free, but they depend on a |
| 10840 | ;; library that is built from the sources in "hg/lib", |
| 10841 | ;; which is nonfree. |
| 10842 | (let ((free (list "." ".." |
| 10843 | "utils" "lib" "inc" "tagStorm" |
| 10844 | "parasol" "htslib")) |
| 10845 | (directory? (lambda (file) |
| 10846 | (eq? 'directory (stat:type (stat file)))))) |
| 10847 | (for-each (lambda (file) |
| 10848 | (and (directory? file) |
| 10849 | (delete-file-recursively file))) |
| 10850 | (map (cut string-append "src/" <>) |
| 10851 | (scandir "src" |
| 10852 | (lambda (file) |
| 10853 | (not (member file free))))))) |
| 10854 | ;; Only make the utils target, not the userApps target, |
| 10855 | ;; because that requires libraries we won't build. |
| 10856 | (substitute* "Makefile" |
| 10857 | ((" userApps") " utils")) |
| 10858 | ;; Only build libraries that are free. |
| 10859 | (substitute* "src/makefile" |
| 10860 | (("DIRS =.*") "DIRS =\n") |
| 10861 | (("cd jkOwnLib.*") "") |
| 10862 | ((" hgLib") "") |
| 10863 | (("cd hg.*") "")) |
| 10864 | (substitute* "src/utils/makefile" |
| 10865 | ;; These tools depend on "jkhgap.a", which is part of the |
| 10866 | ;; nonfree "src/hg/lib" directory. |
| 10867 | (("raSqlQuery") "") |
| 10868 | (("pslLiftSubrangeBlat") "") |
| 10869 | |
| 10870 | ;; Do not build UCSC tools, which may require nonfree |
| 10871 | ;; components. |
| 10872 | (("ALL_APPS =.*") "ALL_APPS = $(UTILS_APPLIST)\n")) |
| 10873 | #t)))) |
| 10874 | (build-system gnu-build-system) |
| 10875 | (arguments |
| 10876 | `( ;; There is no global test target and the test target for |
| 10877 | ;; individual tools depends on input files that are not |
| 10878 | ;; included. |
| 10879 | #:tests? #f |
| 10880 | #:phases |
| 10881 | (modify-phases %standard-phases |
| 10882 | (add-after 'unpack 'fix-paths |
| 10883 | (lambda _ |
| 10884 | (substitute* "Makefile" |
| 10885 | (("/bin/echo") (which "echo"))) |
| 10886 | #t)) |
| 10887 | (add-after 'unpack 'prepare-samtabix |
| 10888 | (lambda* (#:key inputs #:allow-other-keys) |
| 10889 | (copy-recursively (assoc-ref inputs "samtabix") |
| 10890 | "samtabix") |
| 10891 | #t)) |
| 10892 | (delete 'configure) |
| 10893 | (replace 'install |
| 10894 | (lambda* (#:key outputs #:allow-other-keys) |
| 10895 | (let ((bin (string-append (assoc-ref outputs "out") |
| 10896 | "/bin"))) |
| 10897 | (copy-recursively "bin" bin)) |
| 10898 | #t))))) |
| 10899 | (native-inputs |
| 10900 | `(("samtabix" |
| 10901 | ,(origin |
| 10902 | (method git-fetch) |
| 10903 | (uri (git-reference |
| 10904 | (url "http://genome-source.cse.ucsc.edu/samtabix.git") |
| 10905 | (commit "10fd107909c1ac4d679299908be4262a012965ba"))) |
| 10906 | (sha256 |
| 10907 | (base32 |
| 10908 | "0c1nj64l42v395sa84n7az43xiap4i6f9n9dfz4058aqiwkhkmma")))))) |
| 10909 | (inputs |
| 10910 | `(("zlib" ,zlib) |
| 10911 | ("tcsh" ,tcsh) |
| 10912 | ("perl" ,perl) |
| 10913 | ("libpng" ,libpng) |
| 10914 | ("mysql" ,mysql) |
| 10915 | ("openssl" ,openssl))) |
| 10916 | (home-page "http://genome.cse.ucsc.edu/index.html") |
| 10917 | (synopsis "Assorted bioinformatics utilities") |
| 10918 | (description "This package provides the kentUtils, a selection of |
| 10919 | bioinformatics utilities used in combination with the UCSC genome |
| 10920 | browser.") |
| 10921 | ;; Only a subset of the sources are released under a non-copyleft |
| 10922 | ;; free software license. All other sources are removed in a |
| 10923 | ;; snippet. See this bug report for an explanation of how the |
| 10924 | ;; license statements apply: |
| 10925 | ;; https://github.com/ENCODE-DCC/kentUtils/issues/12 |
| 10926 | (license (license:non-copyleft |
| 10927 | "http://genome.ucsc.edu/license/" |
| 10928 | "The contents of this package are free for all uses.")))) |
| 10929 | |
| 10930 | (define-public f-seq |
| 10931 | (let ((commit "6ccded34cff38cf432deed8503648b4a66953f9b") |
| 10932 | (revision "1")) |
| 10933 | (package |
| 10934 | (name "f-seq") |
| 10935 | (version (string-append "1.1-" revision "." (string-take commit 7))) |
| 10936 | (source (origin |
| 10937 | (method git-fetch) |
| 10938 | (uri (git-reference |
| 10939 | (url "https://github.com/aboyle/F-seq.git") |
| 10940 | (commit commit))) |
| 10941 | (file-name (string-append name "-" version)) |
| 10942 | (sha256 |
| 10943 | (base32 |
| 10944 | "1nk33k0yajg2id4g59bc4szr58r2q6pdq42vgcw054m8ip9wv26h")) |
| 10945 | (modules '((guix build utils))) |
| 10946 | ;; Remove bundled Java library archives. |
| 10947 | (snippet |
| 10948 | '(begin |
| 10949 | (for-each delete-file (find-files "lib" ".*")) |
| 10950 | #t)))) |
| 10951 | (build-system ant-build-system) |
| 10952 | (arguments |
| 10953 | `(#:tests? #f ; no tests included |
| 10954 | #:phases |
| 10955 | (modify-phases %standard-phases |
| 10956 | (replace 'install |
| 10957 | (lambda* (#:key inputs outputs #:allow-other-keys) |
| 10958 | (let* ((target (assoc-ref outputs "out")) |
| 10959 | (doc (string-append target "/share/doc/f-seq/"))) |
| 10960 | (mkdir-p target) |
| 10961 | (mkdir-p doc) |
| 10962 | (substitute* "bin/linux/fseq" |
| 10963 | (("java") (which "java")) |
| 10964 | (("\\$REALDIR/../lib/commons-cli-1.1.jar") |
| 10965 | (string-append (assoc-ref inputs "java-commons-cli") |
| 10966 | "/share/java/commons-cli.jar")) |
| 10967 | (("REALDIR=.*") |
| 10968 | (string-append "REALDIR=" target "/bin\n"))) |
| 10969 | (install-file "README.txt" doc) |
| 10970 | (install-file "bin/linux/fseq" (string-append target "/bin")) |
| 10971 | (install-file "build~/fseq.jar" (string-append target "/lib")) |
| 10972 | (copy-recursively "lib" (string-append target "/lib")) |
| 10973 | #t)))))) |
| 10974 | (inputs |
| 10975 | `(("perl" ,perl) |
| 10976 | ("java-commons-cli" ,java-commons-cli))) |
| 10977 | (home-page "http://fureylab.web.unc.edu/software/fseq/") |
| 10978 | (synopsis "Feature density estimator for high-throughput sequence tags") |
| 10979 | (description |
| 10980 | "F-Seq is a software package that generates a continuous tag sequence |
| 10981 | density estimation allowing identification of biologically meaningful sites |
| 10982 | such as transcription factor binding sites (ChIP-seq) or regions of open |
| 10983 | chromatin (DNase-seq). Output can be displayed directly in the UCSC Genome |
| 10984 | Browser.") |
| 10985 | (license license:gpl3+)))) |
| 10986 | |
| 10987 | (define-public bismark |
| 10988 | (package |
| 10989 | (name "bismark") |
| 10990 | (version "0.16.3") |
| 10991 | (source |
| 10992 | (origin |
| 10993 | (method url-fetch) |
| 10994 | (uri (string-append "https://github.com/FelixKrueger/Bismark/" |
| 10995 | "archive/" version ".tar.gz")) |
| 10996 | (file-name (string-append name "-" version ".tar.gz")) |
| 10997 | (sha256 |
| 10998 | (base32 |
| 10999 | "1204i0pa02ll2jn5pnxypkclnskvv7a2nwh5nxhagmhxk9wfv9sq")))) |
| 11000 | (build-system perl-build-system) |
| 11001 | (arguments |
| 11002 | `(#:tests? #f ; there are no tests |
| 11003 | #:phases |
| 11004 | (modify-phases %standard-phases |
| 11005 | (delete 'configure) |
| 11006 | (delete 'build) |
| 11007 | (replace 'install |
| 11008 | (lambda* (#:key outputs #:allow-other-keys) |
| 11009 | (let ((bin (string-append (assoc-ref outputs "out") |
| 11010 | "/bin")) |
| 11011 | (docdir (string-append (assoc-ref outputs "out") |
| 11012 | "/share/doc/bismark")) |
| 11013 | (docs '("Bismark_User_Guide.pdf" |
| 11014 | "RELEASE_NOTES.txt")) |
| 11015 | (scripts '("bismark" |
| 11016 | "bismark_genome_preparation" |
| 11017 | "bismark_methylation_extractor" |
| 11018 | "bismark2bedGraph" |
| 11019 | "bismark2report" |
| 11020 | "coverage2cytosine" |
| 11021 | "deduplicate_bismark" |
| 11022 | "bismark_sitrep.tpl" |
| 11023 | "bam2nuc" |
| 11024 | "bismark2summary"))) |
| 11025 | (mkdir-p docdir) |
| 11026 | (mkdir-p bin) |
| 11027 | (for-each (lambda (file) (install-file file bin)) |
| 11028 | scripts) |
| 11029 | (for-each (lambda (file) (install-file file docdir)) |
| 11030 | docs) |
| 11031 | #t)))))) |
| 11032 | (home-page "http://www.bioinformatics.babraham.ac.uk/projects/bismark/") |
| 11033 | (synopsis "Map bisulfite treated sequence reads and analyze methylation") |
| 11034 | (description "Bismark is a program to map bisulfite treated sequencing |
| 11035 | reads to a genome of interest and perform methylation calls in a single step. |
| 11036 | The output can be easily imported into a genome viewer, such as SeqMonk, and |
| 11037 | enables a researcher to analyse the methylation levels of their samples |
| 11038 | straight away. Its main features are: |
| 11039 | |
| 11040 | @itemize |
| 11041 | @item Bisulfite mapping and methylation calling in one single step |
| 11042 | @item Supports single-end and paired-end read alignments |
| 11043 | @item Supports ungapped and gapped alignments |
| 11044 | @item Alignment seed length, number of mismatches etc are adjustable |
| 11045 | @item Output discriminates between cytosine methylation in CpG, CHG |
| 11046 | and CHH context |
| 11047 | @end itemize\n") |
| 11048 | (license license:gpl3+))) |
| 11049 | |
| 11050 | (define-public paml |
| 11051 | (package |
| 11052 | (name "paml") |
| 11053 | (version "4.9e") |
| 11054 | (source (origin |
| 11055 | (method url-fetch) |
| 11056 | (uri (string-append "http://abacus.gene.ucl.ac.uk/software/" |
| 11057 | "paml" version ".tgz")) |
| 11058 | (sha256 |
| 11059 | (base32 |
| 11060 | "13zf6h9fiqghwhch2h06x1zdr6s42plsnqahflp5g7myr3han3s6")) |
| 11061 | (modules '((guix build utils))) |
| 11062 | ;; Remove Windows binaries |
| 11063 | (snippet |
| 11064 | '(begin |
| 11065 | (for-each delete-file (find-files "." "\\.exe$")) |
| 11066 | #t)))) |
| 11067 | (build-system gnu-build-system) |
| 11068 | (arguments |
| 11069 | `(#:tests? #f ; there are no tests |
| 11070 | #:make-flags '("CC=gcc") |
| 11071 | #:phases |
| 11072 | (modify-phases %standard-phases |
| 11073 | (replace 'configure |
| 11074 | (lambda _ |
| 11075 | (substitute* "src/BFdriver.c" |
| 11076 | (("/bin/bash") (which "bash"))) |
| 11077 | (chdir "src") |
| 11078 | #t)) |
| 11079 | (replace 'install |
| 11080 | (lambda* (#:key outputs #:allow-other-keys) |
| 11081 | (let ((tools '("baseml" "basemlg" "codeml" |
| 11082 | "pamp" "evolver" "yn00" "chi2")) |
| 11083 | (bin (string-append (assoc-ref outputs "out") "/bin")) |
| 11084 | (docdir (string-append (assoc-ref outputs "out") |
| 11085 | "/share/doc/paml"))) |
| 11086 | (mkdir-p bin) |
| 11087 | (for-each (lambda (file) (install-file file bin)) tools) |
| 11088 | (copy-recursively "../doc" docdir) |
| 11089 | #t)))))) |
| 11090 | (home-page "http://abacus.gene.ucl.ac.uk/software/paml.html") |
| 11091 | (synopsis "Phylogentic analysis by maximum likelihood") |
| 11092 | (description "PAML (for Phylogentic Analysis by Maximum Likelihood) |
| 11093 | contains a few programs for model fitting and phylogenetic tree reconstruction |
| 11094 | using nucleotide or amino-acid sequence data.") |
| 11095 | ;; GPLv3 only |
| 11096 | (license license:gpl3))) |
| 11097 | |
| 11098 | (define-public kallisto |
| 11099 | (package |
| 11100 | (name "kallisto") |
| 11101 | (version "0.43.1") |
| 11102 | (source (origin |
| 11103 | (method url-fetch) |
| 11104 | (uri (string-append "https://github.com/pachterlab/" |
| 11105 | "kallisto/archive/v" version ".tar.gz")) |
| 11106 | (file-name (string-append name "-" version ".tar.gz")) |
| 11107 | (sha256 |
| 11108 | (base32 |
| 11109 | "03j3iqhvq7ya3c91gidly3k3jvgm97vjq4scihrlxh315j696r11")))) |
| 11110 | (build-system cmake-build-system) |
| 11111 | (arguments `(#:tests? #f)) ; no "check" target |
| 11112 | (inputs |
| 11113 | `(("hdf5" ,hdf5) |
| 11114 | ("zlib" ,zlib))) |
| 11115 | (home-page "http://pachterlab.github.io/kallisto/") |
| 11116 | (synopsis "Near-optimal RNA-Seq quantification") |
| 11117 | (description |
| 11118 | "Kallisto is a program for quantifying abundances of transcripts from |
| 11119 | RNA-Seq data, or more generally of target sequences using high-throughput |
| 11120 | sequencing reads. It is based on the novel idea of pseudoalignment for |
| 11121 | rapidly determining the compatibility of reads with targets, without the need |
| 11122 | for alignment. Pseudoalignment of reads preserves the key information needed |
| 11123 | for quantification, and kallisto is therefore not only fast, but also as |
| 11124 | accurate as existing quantification tools.") |
| 11125 | (license license:bsd-2))) |