| 1 | ;;; GNU Guix --- Functional package management for GNU |
| 2 | ;;; Copyright © 2014, 2015, 2016 Ricardo Wurmus <rekado@elephly.net> |
| 3 | ;;; Copyright © 2015, 2016 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 Efraim Flashner <efraim@flashner.co.il> |
| 8 | ;;; Copyright © 2016 Marius Bakke <mbakke@fastmail.com> |
| 9 | ;;; |
| 10 | ;;; This file is part of GNU Guix. |
| 11 | ;;; |
| 12 | ;;; GNU Guix is free software; you can redistribute it and/or modify it |
| 13 | ;;; under the terms of the GNU General Public License as published by |
| 14 | ;;; the Free Software Foundation; either version 3 of the License, or (at |
| 15 | ;;; your option) any later version. |
| 16 | ;;; |
| 17 | ;;; GNU Guix is distributed in the hope that it will be useful, but |
| 18 | ;;; WITHOUT ANY WARRANTY; without even the implied warranty of |
| 19 | ;;; MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the |
| 20 | ;;; GNU General Public License for more details. |
| 21 | ;;; |
| 22 | ;;; You should have received a copy of the GNU General Public License |
| 23 | ;;; along with GNU Guix. If not, see <http://www.gnu.org/licenses/>. |
| 24 | |
| 25 | (define-module (gnu packages bioinformatics) |
| 26 | #:use-module ((guix licenses) #:prefix license:) |
| 27 | #:use-module (guix packages) |
| 28 | #:use-module (guix utils) |
| 29 | #:use-module (guix download) |
| 30 | #:use-module (guix git-download) |
| 31 | #:use-module (guix hg-download) |
| 32 | #:use-module (guix build-system ant) |
| 33 | #:use-module (guix build-system gnu) |
| 34 | #:use-module (guix build-system cmake) |
| 35 | #:use-module (guix build-system perl) |
| 36 | #:use-module (guix build-system python) |
| 37 | #:use-module (guix build-system r) |
| 38 | #:use-module (guix build-system ruby) |
| 39 | #:use-module (guix build-system trivial) |
| 40 | #:use-module (gnu packages) |
| 41 | #:use-module (gnu packages autotools) |
| 42 | #:use-module (gnu packages algebra) |
| 43 | #:use-module (gnu packages base) |
| 44 | #:use-module (gnu packages bash) |
| 45 | #:use-module (gnu packages bison) |
| 46 | #:use-module (gnu packages boost) |
| 47 | #:use-module (gnu packages compression) |
| 48 | #:use-module (gnu packages cpio) |
| 49 | #:use-module (gnu packages curl) |
| 50 | #:use-module (gnu packages documentation) |
| 51 | #:use-module (gnu packages datastructures) |
| 52 | #:use-module (gnu packages file) |
| 53 | #:use-module (gnu packages flex) |
| 54 | #:use-module (gnu packages gawk) |
| 55 | #:use-module (gnu packages gcc) |
| 56 | #:use-module (gnu packages gd) |
| 57 | #:use-module (gnu packages gtk) |
| 58 | #:use-module (gnu packages glib) |
| 59 | #:use-module (gnu packages groff) |
| 60 | #:use-module (gnu packages guile) |
| 61 | #:use-module (gnu packages haskell) |
| 62 | #:use-module (gnu packages image) |
| 63 | #:use-module (gnu packages imagemagick) |
| 64 | #:use-module (gnu packages java) |
| 65 | #:use-module (gnu packages linux) |
| 66 | #:use-module (gnu packages logging) |
| 67 | #:use-module (gnu packages machine-learning) |
| 68 | #:use-module (gnu packages man) |
| 69 | #:use-module (gnu packages maths) |
| 70 | #:use-module (gnu packages mpi) |
| 71 | #:use-module (gnu packages ncurses) |
| 72 | #:use-module (gnu packages pcre) |
| 73 | #:use-module (gnu packages parallel) |
| 74 | #:use-module (gnu packages pdf) |
| 75 | #:use-module (gnu packages perl) |
| 76 | #:use-module (gnu packages pkg-config) |
| 77 | #:use-module (gnu packages popt) |
| 78 | #:use-module (gnu packages protobuf) |
| 79 | #:use-module (gnu packages python) |
| 80 | #:use-module (gnu packages readline) |
| 81 | #:use-module (gnu packages ruby) |
| 82 | #:use-module (gnu packages serialization) |
| 83 | #:use-module (gnu packages statistics) |
| 84 | #:use-module (gnu packages tbb) |
| 85 | #:use-module (gnu packages tex) |
| 86 | #:use-module (gnu packages texinfo) |
| 87 | #:use-module (gnu packages textutils) |
| 88 | #:use-module (gnu packages time) |
| 89 | #:use-module (gnu packages tls) |
| 90 | #:use-module (gnu packages vim) |
| 91 | #:use-module (gnu packages web) |
| 92 | #:use-module (gnu packages xml) |
| 93 | #:use-module (gnu packages xorg) |
| 94 | #:use-module (gnu packages zip) |
| 95 | #:use-module (srfi srfi-1)) |
| 96 | |
| 97 | (define-public aragorn |
| 98 | (package |
| 99 | (name "aragorn") |
| 100 | (version "1.2.38") |
| 101 | (source (origin |
| 102 | (method url-fetch) |
| 103 | (uri (string-append |
| 104 | "http://mbio-serv2.mbioekol.lu.se/ARAGORN/Downloads/aragorn" |
| 105 | version ".tgz")) |
| 106 | (sha256 |
| 107 | (base32 |
| 108 | "09i1rg716smlbnixfm7q1ml2mfpaa2fpn3hwjg625ysmfwwy712b")))) |
| 109 | (build-system gnu-build-system) |
| 110 | (arguments |
| 111 | `(#:tests? #f ; there are no tests |
| 112 | #:phases |
| 113 | (modify-phases %standard-phases |
| 114 | (delete 'configure) |
| 115 | (replace 'build |
| 116 | (lambda _ |
| 117 | (zero? (system* "gcc" |
| 118 | "-O3" |
| 119 | "-ffast-math" |
| 120 | "-finline-functions" |
| 121 | "-o" |
| 122 | "aragorn" |
| 123 | (string-append "aragorn" ,version ".c"))))) |
| 124 | (replace 'install |
| 125 | (lambda* (#:key outputs #:allow-other-keys) |
| 126 | (let* ((out (assoc-ref outputs "out")) |
| 127 | (bin (string-append out "/bin")) |
| 128 | (man (string-append out "/share/man/man1"))) |
| 129 | (mkdir-p bin) |
| 130 | (copy-file "aragorn" |
| 131 | (string-append bin "/aragorn")) |
| 132 | (mkdir-p man) |
| 133 | (copy-file "aragorn.1" |
| 134 | (string-append man "/aragorn.1"))) |
| 135 | #t))))) |
| 136 | (home-page "http://mbio-serv2.mbioekol.lu.se/ARAGORN") |
| 137 | (synopsis "Detect tRNA, mtRNA and tmRNA genes in nucleotide sequences") |
| 138 | (description |
| 139 | "Aragorn identifies transfer RNA, mitochondrial RNA and |
| 140 | transfer-messenger RNA from nucleotide sequences, based on homology to known |
| 141 | tRNA consensus sequences and RNA structure. It also outputs the secondary |
| 142 | structure of the predicted RNA.") |
| 143 | (license license:gpl2))) |
| 144 | |
| 145 | (define-public bamm |
| 146 | (package |
| 147 | (name "bamm") |
| 148 | (version "1.7.3") |
| 149 | (source (origin |
| 150 | (method url-fetch) |
| 151 | ;; BamM is not available on pypi. |
| 152 | (uri (string-append |
| 153 | "https://github.com/Ecogenomics/BamM/archive/" |
| 154 | version ".tar.gz")) |
| 155 | (file-name (string-append name "-" version ".tar.gz")) |
| 156 | (sha256 |
| 157 | (base32 |
| 158 | "1f35yxp4pc8aadsvbpg6r4kg2jh4fkjci0iby4iyljm6980sac0s")) |
| 159 | (modules '((guix build utils))) |
| 160 | (snippet |
| 161 | `(begin |
| 162 | ;; Delete bundled htslib. |
| 163 | (delete-file-recursively "c/htslib-1.3.1") |
| 164 | #t)))) |
| 165 | (build-system python-build-system) |
| 166 | (arguments |
| 167 | `(#:python ,python-2 ; BamM is Python 2 only. |
| 168 | ;; Do not use bundled libhts. Do use the bundled libcfu because it has |
| 169 | ;; been modified from its original form. |
| 170 | #:configure-flags |
| 171 | (let ((htslib (assoc-ref %build-inputs "htslib"))) |
| 172 | (list "--with-libhts-lib" (string-append htslib "/lib") |
| 173 | "--with-libhts-inc" (string-append htslib "/include/htslib"))) |
| 174 | #:phases |
| 175 | (modify-phases %standard-phases |
| 176 | (add-after 'unpack 'autogen |
| 177 | (lambda _ |
| 178 | (with-directory-excursion "c" |
| 179 | (let ((sh (which "sh"))) |
| 180 | ;; Use autogen so that 'configure' works. |
| 181 | (substitute* "autogen.sh" (("/bin/sh") sh)) |
| 182 | (setenv "CONFIG_SHELL" sh) |
| 183 | (substitute* "configure" (("/bin/sh") sh)) |
| 184 | (zero? (system* "./autogen.sh")))))) |
| 185 | (delete 'build) |
| 186 | ;; Run tests after installation so compilation only happens once. |
| 187 | (delete 'check) |
| 188 | (add-after 'install 'wrap-executable |
| 189 | (lambda* (#:key outputs #:allow-other-keys) |
| 190 | (let* ((out (assoc-ref outputs "out")) |
| 191 | (path (getenv "PATH"))) |
| 192 | (wrap-program (string-append out "/bin/bamm") |
| 193 | `("PATH" ":" prefix (,path)))) |
| 194 | #t)) |
| 195 | (add-after 'wrap-executable 'post-install-check |
| 196 | (lambda* (#:key inputs outputs #:allow-other-keys) |
| 197 | (setenv "PATH" |
| 198 | (string-append (assoc-ref outputs "out") |
| 199 | "/bin:" |
| 200 | (getenv "PATH"))) |
| 201 | (setenv "PYTHONPATH" |
| 202 | (string-append |
| 203 | (assoc-ref outputs "out") |
| 204 | "/lib/python" |
| 205 | (string-take (string-take-right |
| 206 | (assoc-ref inputs "python") 5) 3) |
| 207 | "/site-packages:" |
| 208 | (getenv "PYTHONPATH"))) |
| 209 | ;; There are 2 errors printed, but they are safe to ignore: |
| 210 | ;; 1) [E::hts_open_format] fail to open file ... |
| 211 | ;; 2) samtools view: failed to open ... |
| 212 | (zero? (system* "nosetests"))))))) |
| 213 | (native-inputs |
| 214 | `(("autoconf" ,autoconf) |
| 215 | ("automake" ,automake) |
| 216 | ("libtool" ,libtool) |
| 217 | ("zlib" ,zlib) |
| 218 | ("python-nose" ,python2-nose) |
| 219 | ("python-pysam" ,python2-pysam))) |
| 220 | (inputs |
| 221 | `(("htslib" ,htslib) |
| 222 | ("samtools" ,samtools) |
| 223 | ("bwa" ,bwa) |
| 224 | ("grep" ,grep) |
| 225 | ("sed" ,sed) |
| 226 | ("coreutils" ,coreutils))) |
| 227 | (propagated-inputs |
| 228 | `(("python-numpy" ,python2-numpy))) |
| 229 | (home-page "http://ecogenomics.github.io/BamM/") |
| 230 | (synopsis "Metagenomics-focused BAM file manipulator") |
| 231 | (description |
| 232 | "BamM is a C library, wrapped in python, to efficiently generate and |
| 233 | parse BAM files, specifically for the analysis of metagenomic data. For |
| 234 | instance, it implements several methods to assess contig-wise read coverage.") |
| 235 | (license license:lgpl3+))) |
| 236 | |
| 237 | (define-public bamtools |
| 238 | (package |
| 239 | (name "bamtools") |
| 240 | (version "2.3.0") |
| 241 | (source (origin |
| 242 | (method url-fetch) |
| 243 | (uri (string-append |
| 244 | "https://github.com/pezmaster31/bamtools/archive/v" |
| 245 | version ".tar.gz")) |
| 246 | (file-name (string-append name "-" version ".tar.gz")) |
| 247 | (sha256 |
| 248 | (base32 |
| 249 | "1brry29bw2xr2l9pqn240rkqwayg85b8qq78zk2zs6nlspk4d018")))) |
| 250 | (build-system cmake-build-system) |
| 251 | (arguments |
| 252 | `(#:tests? #f ;no "check" target |
| 253 | #:phases |
| 254 | (modify-phases %standard-phases |
| 255 | (add-before |
| 256 | 'configure 'set-ldflags |
| 257 | (lambda* (#:key outputs #:allow-other-keys) |
| 258 | (setenv "LDFLAGS" |
| 259 | (string-append |
| 260 | "-Wl,-rpath=" |
| 261 | (assoc-ref outputs "out") "/lib/bamtools"))))))) |
| 262 | (inputs `(("zlib" ,zlib))) |
| 263 | (home-page "https://github.com/pezmaster31/bamtools") |
| 264 | (synopsis "C++ API and command-line toolkit for working with BAM data") |
| 265 | (description |
| 266 | "BamTools provides both a C++ API and a command-line toolkit for handling |
| 267 | BAM files.") |
| 268 | (license license:expat))) |
| 269 | |
| 270 | (define-public bcftools |
| 271 | (package |
| 272 | (name "bcftools") |
| 273 | (version "1.3.1") |
| 274 | (source (origin |
| 275 | (method url-fetch) |
| 276 | (uri (string-append |
| 277 | "https://github.com/samtools/bcftools/releases/download/" |
| 278 | version "/bcftools-" version ".tar.bz2")) |
| 279 | (sha256 |
| 280 | (base32 |
| 281 | "095ry68vmz9q5s1scjsa698dhgyvgw5aicz24c19iwfbai07mhqj")) |
| 282 | (modules '((guix build utils))) |
| 283 | (snippet |
| 284 | ;; Delete bundled htslib. |
| 285 | '(delete-file-recursively "htslib-1.3.1")))) |
| 286 | (build-system gnu-build-system) |
| 287 | (arguments |
| 288 | `(#:test-target "test" |
| 289 | #:make-flags |
| 290 | (list |
| 291 | "USE_GPL=1" |
| 292 | (string-append "prefix=" (assoc-ref %outputs "out")) |
| 293 | (string-append "HTSDIR=" (assoc-ref %build-inputs "htslib") "/include") |
| 294 | (string-append "HTSLIB=" (assoc-ref %build-inputs "htslib") "/lib/libhts.a") |
| 295 | (string-append "BGZIP=" (assoc-ref %build-inputs "htslib") "/bin/bgzip") |
| 296 | (string-append "TABIX=" (assoc-ref %build-inputs "htslib") "/bin/tabix")) |
| 297 | #:phases |
| 298 | (modify-phases %standard-phases |
| 299 | (add-after 'unpack 'patch-Makefile |
| 300 | (lambda _ |
| 301 | (substitute* "Makefile" |
| 302 | ;; Do not attempt to build htslib. |
| 303 | (("^include \\$\\(HTSDIR\\)/htslib\\.mk") "") |
| 304 | ;; Link against GSL cblas. |
| 305 | (("-lcblas") "-lgslcblas")) |
| 306 | #t)) |
| 307 | (delete 'configure) |
| 308 | (add-before 'check 'patch-tests |
| 309 | (lambda _ |
| 310 | (substitute* "test/test.pl" |
| 311 | (("/bin/bash") (which "bash"))) |
| 312 | #t))))) |
| 313 | (native-inputs |
| 314 | `(("htslib" ,htslib) |
| 315 | ("perl" ,perl))) |
| 316 | (inputs |
| 317 | `(("gsl" ,gsl) |
| 318 | ("zlib" ,zlib))) |
| 319 | (home-page "https://samtools.github.io/bcftools/") |
| 320 | (synopsis "Utilities for variant calling and manipulating VCFs and BCFs") |
| 321 | (description |
| 322 | "BCFtools is a set of utilities that manipulate variant calls in the |
| 323 | Variant Call Format (VCF) and its binary counterpart BCF. All commands work |
| 324 | transparently with both VCFs and BCFs, both uncompressed and BGZF-compressed.") |
| 325 | ;; The sources are dual MIT/GPL, but becomes GPL-only when USE_GPL=1. |
| 326 | (license (list license:gpl3+ license:expat)))) |
| 327 | |
| 328 | (define-public bedops |
| 329 | (package |
| 330 | (name "bedops") |
| 331 | (version "2.4.14") |
| 332 | (source (origin |
| 333 | (method url-fetch) |
| 334 | (uri (string-append "https://github.com/bedops/bedops/archive/v" |
| 335 | version ".tar.gz")) |
| 336 | (file-name (string-append name "-" version ".tar.gz")) |
| 337 | (sha256 |
| 338 | (base32 |
| 339 | "1kqbac547wyqma81cyky9n7mkgikjpsfd3nnmcm6hpqwanqgh10v")))) |
| 340 | (build-system gnu-build-system) |
| 341 | (arguments |
| 342 | '(#:tests? #f |
| 343 | #:make-flags (list (string-append "BINDIR=" %output "/bin")) |
| 344 | #:phases |
| 345 | (alist-cons-after |
| 346 | 'unpack 'unpack-tarballs |
| 347 | (lambda _ |
| 348 | ;; FIXME: Bedops includes tarballs of minimally patched upstream |
| 349 | ;; libraries jansson, zlib, and bzip2. We cannot just use stock |
| 350 | ;; libraries because at least one of the libraries (zlib) is |
| 351 | ;; patched to add a C++ function definition (deflateInit2cpp). |
| 352 | ;; Until the Bedops developers offer a way to link against system |
| 353 | ;; libraries we have to build the in-tree copies of these three |
| 354 | ;; libraries. |
| 355 | |
| 356 | ;; See upstream discussion: |
| 357 | ;; https://github.com/bedops/bedops/issues/124 |
| 358 | |
| 359 | ;; Unpack the tarballs to benefit from shebang patching. |
| 360 | (with-directory-excursion "third-party" |
| 361 | (and (zero? (system* "tar" "xvf" "jansson-2.6.tar.bz2")) |
| 362 | (zero? (system* "tar" "xvf" "zlib-1.2.7.tar.bz2")) |
| 363 | (zero? (system* "tar" "xvf" "bzip2-1.0.6.tar.bz2")))) |
| 364 | ;; Disable unpacking of tarballs in Makefile. |
| 365 | (substitute* "system.mk/Makefile.linux" |
| 366 | (("^\tbzcat .*") "\t@echo \"not unpacking\"\n") |
| 367 | (("\\./configure") "CONFIG_SHELL=bash ./configure")) |
| 368 | (substitute* "third-party/zlib-1.2.7/Makefile.in" |
| 369 | (("^SHELL=.*$") "SHELL=bash\n"))) |
| 370 | (alist-delete 'configure %standard-phases)))) |
| 371 | (home-page "https://github.com/bedops/bedops") |
| 372 | (synopsis "Tools for high-performance genomic feature operations") |
| 373 | (description |
| 374 | "BEDOPS is a suite of tools to address common questions raised in genomic |
| 375 | studies---mostly with regard to overlap and proximity relationships between |
| 376 | data sets. It aims to be scalable and flexible, facilitating the efficient |
| 377 | and accurate analysis and management of large-scale genomic data. |
| 378 | |
| 379 | BEDOPS provides tools that perform highly efficient and scalable Boolean and |
| 380 | other set operations, statistical calculations, archiving, conversion and |
| 381 | other management of genomic data of arbitrary scale. Tasks can be easily |
| 382 | split by chromosome for distributing whole-genome analyses across a |
| 383 | computational cluster.") |
| 384 | (license license:gpl2+))) |
| 385 | |
| 386 | (define-public bedtools |
| 387 | (package |
| 388 | (name "bedtools") |
| 389 | (version "2.26.0") |
| 390 | (source (origin |
| 391 | (method url-fetch) |
| 392 | (uri (string-append "https://github.com/arq5x/bedtools2/archive/v" |
| 393 | version ".tar.gz")) |
| 394 | (file-name (string-append name "-" version ".tar.gz")) |
| 395 | (sha256 |
| 396 | (base32 |
| 397 | "0xvri5hnp2iim1cx6mcd5d9f102p5ql41x69rd6106x1c17pinqm")))) |
| 398 | (build-system gnu-build-system) |
| 399 | (native-inputs `(("python" ,python-2))) |
| 400 | (inputs `(("samtools" ,samtools) |
| 401 | ("zlib" ,zlib))) |
| 402 | (arguments |
| 403 | '(#:test-target "test" |
| 404 | #:phases |
| 405 | (modify-phases %standard-phases |
| 406 | (delete 'configure) |
| 407 | (replace 'install |
| 408 | (lambda* (#:key outputs #:allow-other-keys) |
| 409 | (let ((bin (string-append (assoc-ref outputs "out") "/bin/"))) |
| 410 | (for-each (lambda (file) |
| 411 | (install-file file bin)) |
| 412 | (find-files "bin" ".*"))) |
| 413 | #t))))) |
| 414 | (home-page "https://github.com/arq5x/bedtools2") |
| 415 | (synopsis "Tools for genome analysis and arithmetic") |
| 416 | (description |
| 417 | "Collectively, the bedtools utilities are a swiss-army knife of tools for |
| 418 | a wide-range of genomics analysis tasks. The most widely-used tools enable |
| 419 | genome arithmetic: that is, set theory on the genome. For example, bedtools |
| 420 | allows one to intersect, merge, count, complement, and shuffle genomic |
| 421 | intervals from multiple files in widely-used genomic file formats such as BAM, |
| 422 | BED, GFF/GTF, VCF.") |
| 423 | (license license:gpl2))) |
| 424 | |
| 425 | ;; Later releases of bedtools produce files with more columns than |
| 426 | ;; what Ribotaper expects. |
| 427 | (define-public bedtools-2.18 |
| 428 | (package (inherit bedtools) |
| 429 | (name "bedtools") |
| 430 | (version "2.18.0") |
| 431 | (source (origin |
| 432 | (method url-fetch) |
| 433 | (uri (string-append "https://github.com/arq5x/bedtools2/" |
| 434 | "archive/v" version ".tar.gz")) |
| 435 | (file-name (string-append name "-" version ".tar.gz")) |
| 436 | (sha256 |
| 437 | (base32 |
| 438 | "05vrnr8yp7swfagshzpgqmzk1blnwnq8pq5pckzi1m26w98d63vf")))))) |
| 439 | |
| 440 | (define-public ribotaper |
| 441 | (package |
| 442 | (name "ribotaper") |
| 443 | (version "1.3.1") |
| 444 | (source (origin |
| 445 | (method url-fetch) |
| 446 | (uri (string-append "https://ohlerlab.mdc-berlin.de/" |
| 447 | "files/RiboTaper/RiboTaper_Version_" |
| 448 | version ".tar.gz")) |
| 449 | (sha256 |
| 450 | (base32 |
| 451 | "0ykjbps1y3z3085q94npw8i9x5gldc6shy8vlc08v76zljsm07hv")))) |
| 452 | (build-system gnu-build-system) |
| 453 | (inputs |
| 454 | `(("bedtools" ,bedtools-2.18) |
| 455 | ("samtools" ,samtools-0.1) |
| 456 | ("r" ,r) |
| 457 | ("r-foreach" ,r-foreach) |
| 458 | ("r-xnomial" ,r-xnomial) |
| 459 | ("r-domc" ,r-domc) |
| 460 | ("r-multitaper" ,r-multitaper) |
| 461 | ("r-seqinr" ,r-seqinr))) |
| 462 | (home-page "https://ohlerlab.mdc-berlin.de/software/RiboTaper_126/") |
| 463 | (synopsis "Define translated ORFs using ribosome profiling data") |
| 464 | (description |
| 465 | "Ribotaper is a method for defining translated @dfn{open reading |
| 466 | frames} (ORFs) using ribosome profiling (ribo-seq) data. This package |
| 467 | provides the Ribotaper pipeline.") |
| 468 | (license license:gpl3+))) |
| 469 | |
| 470 | (define-public bioawk |
| 471 | (package |
| 472 | (name "bioawk") |
| 473 | (version "1.0") |
| 474 | (source (origin |
| 475 | (method url-fetch) |
| 476 | (uri (string-append "https://github.com/lh3/bioawk/archive/v" |
| 477 | version ".tar.gz")) |
| 478 | (file-name (string-append name "-" version ".tar.gz")) |
| 479 | (sha256 |
| 480 | (base32 "1daizxsk17ahi9n58fj8vpgwyhzrzh54bzqhanjanp88kgrz7gjw")))) |
| 481 | (build-system gnu-build-system) |
| 482 | (inputs |
| 483 | `(("zlib" ,zlib))) |
| 484 | (native-inputs |
| 485 | `(("bison" ,bison))) |
| 486 | (arguments |
| 487 | `(#:tests? #f ; There are no tests to run. |
| 488 | ;; Bison must generate files, before other targets can build. |
| 489 | #:parallel-build? #f |
| 490 | #:phases |
| 491 | (modify-phases %standard-phases |
| 492 | (delete 'configure) ; There is no configure phase. |
| 493 | (replace 'install |
| 494 | (lambda* (#:key outputs #:allow-other-keys) |
| 495 | (let* ((out (assoc-ref outputs "out")) |
| 496 | (bin (string-append out "/bin")) |
| 497 | (man (string-append out "/share/man/man1"))) |
| 498 | (mkdir-p man) |
| 499 | (copy-file "awk.1" (string-append man "/bioawk.1")) |
| 500 | (install-file "bioawk" bin))))))) |
| 501 | (home-page "https://github.com/lh3/bioawk") |
| 502 | (synopsis "AWK with bioinformatics extensions") |
| 503 | (description "Bioawk is an extension to Brian Kernighan's awk, adding the |
| 504 | support of several common biological data formats, including optionally gzip'ed |
| 505 | BED, GFF, SAM, VCF, FASTA/Q and TAB-delimited formats with column names. It |
| 506 | also adds a few built-in functions and a command line option to use TAB as the |
| 507 | input/output delimiter. When the new functionality is not used, bioawk is |
| 508 | intended to behave exactly the same as the original BWK awk.") |
| 509 | (license license:x11))) |
| 510 | |
| 511 | (define-public python2-pybedtools |
| 512 | (package |
| 513 | (name "python2-pybedtools") |
| 514 | (version "0.6.9") |
| 515 | (source (origin |
| 516 | (method url-fetch) |
| 517 | (uri (string-append |
| 518 | "https://pypi.python.org/packages/source/p/pybedtools/pybedtools-" |
| 519 | version ".tar.gz")) |
| 520 | (sha256 |
| 521 | (base32 |
| 522 | "1ldzdxw1p4y3g2ignmggsdypvqkcwqwzhdha4rbgpih048z5p4an")))) |
| 523 | (build-system python-build-system) |
| 524 | (arguments `(#:python ,python-2)) ; no Python 3 support |
| 525 | (inputs |
| 526 | `(("python-matplotlib" ,python2-matplotlib))) |
| 527 | (propagated-inputs |
| 528 | `(("bedtools" ,bedtools) |
| 529 | ("samtools" ,samtools))) |
| 530 | (native-inputs |
| 531 | `(("python-cython" ,python2-cython) |
| 532 | ("python-pyyaml" ,python2-pyyaml) |
| 533 | ("python-nose" ,python2-nose))) |
| 534 | (home-page "https://pythonhosted.org/pybedtools/") |
| 535 | (synopsis "Python wrapper for BEDtools programs") |
| 536 | (description |
| 537 | "pybedtools is a Python wrapper for Aaron Quinlan's BEDtools programs, |
| 538 | which are widely used for genomic interval manipulation or \"genome algebra\". |
| 539 | pybedtools extends BEDTools by offering feature-level manipulations from with |
| 540 | Python.") |
| 541 | (license license:gpl2+))) |
| 542 | |
| 543 | (define-public python-biom-format |
| 544 | (package |
| 545 | (name "python-biom-format") |
| 546 | (version "2.1.5") |
| 547 | (source |
| 548 | (origin |
| 549 | (method url-fetch) |
| 550 | ;; Use GitHub as source because PyPI distribution does not contain |
| 551 | ;; test data: https://github.com/biocore/biom-format/issues/693 |
| 552 | (uri (string-append "https://github.com/biocore/biom-format/archive/" |
| 553 | version ".tar.gz")) |
| 554 | (file-name (string-append name "-" version ".tar.gz")) |
| 555 | (sha256 |
| 556 | (base32 |
| 557 | "1n25w3p1rixbpac8iysmzcja6m4ip5r6sz19l8y6wlwi49hxn278")))) |
| 558 | (build-system python-build-system) |
| 559 | (propagated-inputs |
| 560 | `(("python-numpy" ,python-numpy) |
| 561 | ("python-scipy" ,python-scipy) |
| 562 | ("python-future" ,python-future) |
| 563 | ("python-click" ,python-click) |
| 564 | ("python-h5py" ,python-h5py))) |
| 565 | (home-page "http://www.biom-format.org") |
| 566 | (synopsis "Biological Observation Matrix (BIOM) format utilities") |
| 567 | (description |
| 568 | "The BIOM file format is designed to be a general-use format for |
| 569 | representing counts of observations e.g. operational taxonomic units, KEGG |
| 570 | orthology groups or lipid types, in one or more biological samples |
| 571 | e.g. microbiome samples, genomes, metagenomes.") |
| 572 | (license license:bsd-3) |
| 573 | (properties `((python2-variant . ,(delay python2-biom-format)))))) |
| 574 | |
| 575 | (define-public python2-biom-format |
| 576 | (let ((base (package-with-python2 (strip-python2-variant python-biom-format)))) |
| 577 | (package |
| 578 | (inherit base) |
| 579 | (arguments |
| 580 | `(#:phases |
| 581 | (modify-phases %standard-phases |
| 582 | ;; Do not require the unmaintained pyqi library. |
| 583 | (add-after 'unpack 'remove-pyqi |
| 584 | (lambda _ |
| 585 | (substitute* "setup.py" |
| 586 | (("install_requires.append\\(\"pyqi\"\\)") "pass")) |
| 587 | #t))) |
| 588 | ,@(package-arguments base)))))) |
| 589 | |
| 590 | (define-public bioperl-minimal |
| 591 | (let* ((inputs `(("perl-module-build" ,perl-module-build) |
| 592 | ("perl-data-stag" ,perl-data-stag) |
| 593 | ("perl-libwww" ,perl-libwww) |
| 594 | ("perl-uri" ,perl-uri))) |
| 595 | (transitive-inputs |
| 596 | (map (compose package-name cadr) |
| 597 | (delete-duplicates |
| 598 | (concatenate |
| 599 | (map (compose package-transitive-target-inputs cadr) inputs)))))) |
| 600 | (package |
| 601 | (name "bioperl-minimal") |
| 602 | (version "1.7.0") |
| 603 | (source |
| 604 | (origin |
| 605 | (method url-fetch) |
| 606 | (uri (string-append "https://github.com/bioperl/bioperl-live/" |
| 607 | "archive/release-" |
| 608 | (string-map (lambda (c) |
| 609 | (if (char=? c #\.) |
| 610 | #\- c)) version) |
| 611 | ".tar.gz")) |
| 612 | (sha256 |
| 613 | (base32 |
| 614 | "12phgpxwgkqflkwfb9dcqg7a31dpjlfhar8wcgv0aj5ln4akfz06")))) |
| 615 | (build-system perl-build-system) |
| 616 | (arguments |
| 617 | `(#:phases |
| 618 | (modify-phases %standard-phases |
| 619 | (add-after |
| 620 | 'install 'wrap-programs |
| 621 | (lambda* (#:key outputs #:allow-other-keys) |
| 622 | ;; Make sure all executables in "bin" find the required Perl |
| 623 | ;; modules at runtime. As the PERL5LIB variable contains also |
| 624 | ;; the paths of native inputs, we pick the transitive target |
| 625 | ;; inputs from %build-inputs. |
| 626 | (let* ((out (assoc-ref outputs "out")) |
| 627 | (bin (string-append out "/bin/")) |
| 628 | (path (string-join |
| 629 | (cons (string-append out "/lib/perl5/site_perl") |
| 630 | (map (lambda (name) |
| 631 | (assoc-ref %build-inputs name)) |
| 632 | ',transitive-inputs)) |
| 633 | ":"))) |
| 634 | (for-each (lambda (file) |
| 635 | (wrap-program file |
| 636 | `("PERL5LIB" ":" prefix (,path)))) |
| 637 | (find-files bin "\\.pl$")) |
| 638 | #t)))))) |
| 639 | (inputs inputs) |
| 640 | (native-inputs |
| 641 | `(("perl-test-most" ,perl-test-most))) |
| 642 | (home-page "http://search.cpan.org/dist/BioPerl") |
| 643 | (synopsis "Bioinformatics toolkit") |
| 644 | (description |
| 645 | "BioPerl is the product of a community effort to produce Perl code which |
| 646 | is useful in biology. Examples include Sequence objects, Alignment objects |
| 647 | and database searching objects. These objects not only do what they are |
| 648 | advertised to do in the documentation, but they also interact - Alignment |
| 649 | objects are made from the Sequence objects, Sequence objects have access to |
| 650 | Annotation and SeqFeature objects and databases, Blast objects can be |
| 651 | converted to Alignment objects, and so on. This means that the objects |
| 652 | provide a coordinated and extensible framework to do computational biology.") |
| 653 | (license (package-license perl))))) |
| 654 | |
| 655 | (define-public python-biopython |
| 656 | (package |
| 657 | (name "python-biopython") |
| 658 | (version "1.68") |
| 659 | (source (origin |
| 660 | (method url-fetch) |
| 661 | ;; use PyPi rather than biopython.org to ease updating |
| 662 | (uri (pypi-uri "biopython" version)) |
| 663 | (sha256 |
| 664 | (base32 |
| 665 | "07qc7nz0k77y8hf8s18rscvibvm91zw0kkq7ylrhisf8vp8hkp6i")))) |
| 666 | (build-system python-build-system) |
| 667 | (arguments |
| 668 | `(#:phases |
| 669 | (modify-phases %standard-phases |
| 670 | (add-before 'check 'set-home |
| 671 | ;; Some tests require a home directory to be set. |
| 672 | (lambda _ (setenv "HOME" "/tmp") #t))))) |
| 673 | (propagated-inputs |
| 674 | `(("python-numpy" ,python-numpy))) |
| 675 | (home-page "http://biopython.org/") |
| 676 | (synopsis "Tools for biological computation in Python") |
| 677 | (description |
| 678 | "Biopython is a set of tools for biological computation including parsers |
| 679 | for bioinformatics files into Python data structures; interfaces to common |
| 680 | bioinformatics programs; a standard sequence class and tools for performing |
| 681 | common operations on them; code to perform data classification; code for |
| 682 | dealing with alignments; code making it easy to split up parallelizable tasks |
| 683 | into separate processes; and more.") |
| 684 | (license (license:non-copyleft "http://www.biopython.org/DIST/LICENSE")))) |
| 685 | |
| 686 | (define-public python2-biopython |
| 687 | (package-with-python2 python-biopython)) |
| 688 | |
| 689 | ;; An outdated version of biopython is required for seqmagick, see |
| 690 | ;; https://github.com/fhcrc/seqmagick/issues/59 |
| 691 | ;; When that issue has been resolved this package should be removed. |
| 692 | (define python2-biopython-1.66 |
| 693 | (package |
| 694 | (inherit python2-biopython) |
| 695 | (version "1.66") |
| 696 | (source (origin |
| 697 | (method url-fetch) |
| 698 | (uri (pypi-uri "biopython" version)) |
| 699 | (sha256 |
| 700 | (base32 |
| 701 | "1gdv92593klimg22icf5j9by7xiq86jnwzkpz4abaa05ylkdf6hp")))))) |
| 702 | |
| 703 | (define-public bpp-core |
| 704 | ;; The last release was in 2014 and the recommended way to install from source |
| 705 | ;; is to clone the git repository, so we do this. |
| 706 | ;; http://biopp.univ-montp2.fr/wiki/index.php/Main_Page |
| 707 | (let ((commit "7d8bced0d1a87291ea8dd7046b7fb5ff9c35c582")) |
| 708 | (package |
| 709 | (name "bpp-core") |
| 710 | (version (string-append "2.2.0-1." (string-take commit 7))) |
| 711 | (source (origin |
| 712 | (method git-fetch) |
| 713 | (uri (git-reference |
| 714 | (url "http://biopp.univ-montp2.fr/git/bpp-core") |
| 715 | (commit commit))) |
| 716 | (file-name (string-append name "-" version "-checkout")) |
| 717 | (sha256 |
| 718 | (base32 |
| 719 | "10djsq5vlnkilv436gnmh4irpk49v29pa69r6xiryg32xmvn909j")))) |
| 720 | (build-system cmake-build-system) |
| 721 | (arguments |
| 722 | `(#:parallel-build? #f)) |
| 723 | (inputs |
| 724 | `(("gcc" ,gcc-5))) ; Compilation of bpp-phyl fails with GCC 4.9 so we |
| 725 | ; compile all of the bpp packages with GCC 5. |
| 726 | (home-page "http://biopp.univ-montp2.fr") |
| 727 | (synopsis "C++ libraries for Bioinformatics") |
| 728 | (description |
| 729 | "Bio++ is a set of C++ libraries for Bioinformatics, including sequence |
| 730 | analysis, phylogenetics, molecular evolution and population genetics. It is |
| 731 | Object Oriented and is designed to be both easy to use and computer efficient. |
| 732 | Bio++ intends to help programmers to write computer expensive programs, by |
| 733 | providing them a set of re-usable tools.") |
| 734 | (license license:cecill-c)))) |
| 735 | |
| 736 | (define-public bpp-phyl |
| 737 | ;; The last release was in 2014 and the recommended way to install from source |
| 738 | ;; is to clone the git repository, so we do this. |
| 739 | ;; http://biopp.univ-montp2.fr/wiki/index.php/Main_Page |
| 740 | (let ((commit "0c07167b629f68b569bf274d1ad0c4af83276ae2")) |
| 741 | (package |
| 742 | (name "bpp-phyl") |
| 743 | (version (string-append "2.2.0-1." (string-take commit 7))) |
| 744 | (source (origin |
| 745 | (method git-fetch) |
| 746 | (uri (git-reference |
| 747 | (url "http://biopp.univ-montp2.fr/git/bpp-phyl") |
| 748 | (commit commit))) |
| 749 | (file-name (string-append name "-" version "-checkout")) |
| 750 | (sha256 |
| 751 | (base32 |
| 752 | "1ssjgchzwj3iai26kyly7gwkdv8sk59nqhkb1wpap3sf5m6kyllh")))) |
| 753 | (build-system cmake-build-system) |
| 754 | (arguments |
| 755 | `(#:parallel-build? #f |
| 756 | ;; If out-of-source, test data is not copied into the build directory |
| 757 | ;; so the tests fail. |
| 758 | #:out-of-source? #f)) |
| 759 | (inputs |
| 760 | `(("bpp-core" ,bpp-core) |
| 761 | ("bpp-seq" ,bpp-seq) |
| 762 | ;; GCC 4.8 fails due to an 'internal compiler error', so we use a more |
| 763 | ;; modern GCC. |
| 764 | ("gcc" ,gcc-5))) |
| 765 | (home-page "http://biopp.univ-montp2.fr") |
| 766 | (synopsis "Bio++ phylogenetic Library") |
| 767 | (description |
| 768 | "Bio++ is a set of C++ libraries for Bioinformatics, including sequence |
| 769 | analysis, phylogenetics, molecular evolution and population genetics. This |
| 770 | library provides phylogenetics-related modules.") |
| 771 | (license license:cecill-c)))) |
| 772 | |
| 773 | (define-public bpp-popgen |
| 774 | ;; The last release was in 2014 and the recommended way to install from source |
| 775 | ;; is to clone the git repository, so we do this. |
| 776 | ;; http://biopp.univ-montp2.fr/wiki/index.php/Main_Page |
| 777 | (let ((commit "e472bac9b1a148803895d747cd6d0c5904f85d9f")) |
| 778 | (package |
| 779 | (name "bpp-popgen") |
| 780 | (version (string-append "2.2.0-1." (string-take commit 7))) |
| 781 | (source (origin |
| 782 | (method git-fetch) |
| 783 | (uri (git-reference |
| 784 | (url "http://biopp.univ-montp2.fr/git/bpp-popgen") |
| 785 | (commit commit))) |
| 786 | (file-name (string-append name "-" version "-checkout")) |
| 787 | (sha256 |
| 788 | (base32 |
| 789 | "0yn82dzn1n5629nzja68xfrhi655709rjanyryb36vzkmymy6dw5")))) |
| 790 | (build-system cmake-build-system) |
| 791 | (arguments |
| 792 | `(#:parallel-build? #f |
| 793 | #:tests? #f)) ; There are no tests. |
| 794 | (inputs |
| 795 | `(("bpp-core" ,bpp-core) |
| 796 | ("bpp-seq" ,bpp-seq) |
| 797 | ("gcc" ,gcc-5))) |
| 798 | (home-page "http://biopp.univ-montp2.fr") |
| 799 | (synopsis "Bio++ population genetics library") |
| 800 | (description |
| 801 | "Bio++ is a set of C++ libraries for Bioinformatics, including sequence |
| 802 | analysis, phylogenetics, molecular evolution and population genetics. This |
| 803 | library provides population genetics-related modules.") |
| 804 | (license license:cecill-c)))) |
| 805 | |
| 806 | (define-public bpp-seq |
| 807 | ;; The last release was in 2014 and the recommended way to install from source |
| 808 | ;; is to clone the git repository, so we do this. |
| 809 | ;; http://biopp.univ-montp2.fr/wiki/index.php/Main_Page |
| 810 | (let ((commit "6cfa07965ce152e5598a89df2fa80a75973bfa33")) |
| 811 | (package |
| 812 | (name "bpp-seq") |
| 813 | (version (string-append "2.2.0-1." (string-take commit 7))) |
| 814 | (source (origin |
| 815 | (method git-fetch) |
| 816 | (uri (git-reference |
| 817 | (url "http://biopp.univ-montp2.fr/git/bpp-seq") |
| 818 | (commit commit))) |
| 819 | (file-name (string-append name "-" version "-checkout")) |
| 820 | (sha256 |
| 821 | (base32 |
| 822 | "1nys5jq7jqvdg40d91wsmj3q2yzy4276cp7sp44n67p468f27zf2")))) |
| 823 | (build-system cmake-build-system) |
| 824 | (arguments |
| 825 | `(#:parallel-build? #f |
| 826 | ;; If out-of-source, test data is not copied into the build directory |
| 827 | ;; so the tests fail. |
| 828 | #:out-of-source? #f)) |
| 829 | (inputs |
| 830 | `(("bpp-core" ,bpp-core) |
| 831 | ("gcc" ,gcc-5))) ; Use GCC 5 as per 'bpp-core'. |
| 832 | (home-page "http://biopp.univ-montp2.fr") |
| 833 | (synopsis "Bio++ sequence library") |
| 834 | (description |
| 835 | "Bio++ is a set of C++ libraries for Bioinformatics, including sequence |
| 836 | analysis, phylogenetics, molecular evolution and population genetics. This |
| 837 | library provides sequence-related modules.") |
| 838 | (license license:cecill-c)))) |
| 839 | |
| 840 | (define-public bppsuite |
| 841 | ;; The last release was in 2014 and the recommended way to install from source |
| 842 | ;; is to clone the git repository, so we do this. |
| 843 | ;; http://biopp.univ-montp2.fr/wiki/index.php/Main_Page |
| 844 | (let ((commit "c516147f57aa50961121cd505bed52cd7603698b")) |
| 845 | (package |
| 846 | (name "bppsuite") |
| 847 | (version (string-append "2.2.0-1." (string-take commit 7))) |
| 848 | (source (origin |
| 849 | (method git-fetch) |
| 850 | (uri (git-reference |
| 851 | (url "http://biopp.univ-montp2.fr/git/bppsuite") |
| 852 | (commit commit))) |
| 853 | (file-name (string-append name "-" version "-checkout")) |
| 854 | (sha256 |
| 855 | (base32 |
| 856 | "1y87pxvw0jxjizhq2dr9g2r91md45k1p9ih2sl1yy1y3p934l2kb")))) |
| 857 | (build-system cmake-build-system) |
| 858 | (arguments |
| 859 | `(#:parallel-build? #f |
| 860 | #:tests? #f)) ; There are no tests. |
| 861 | (native-inputs |
| 862 | `(("groff" ,groff) |
| 863 | ("man-db" ,man-db) |
| 864 | ("texinfo" ,texinfo))) |
| 865 | (inputs |
| 866 | `(("bpp-core" ,bpp-core) |
| 867 | ("bpp-seq" ,bpp-seq) |
| 868 | ("bpp-phyl" ,bpp-phyl) |
| 869 | ("bpp-phyl" ,bpp-popgen) |
| 870 | ("gcc" ,gcc-5))) |
| 871 | (home-page "http://biopp.univ-montp2.fr") |
| 872 | (synopsis "Bioinformatics tools written with the Bio++ libraries") |
| 873 | (description |
| 874 | "Bio++ is a set of C++ libraries for Bioinformatics, including sequence |
| 875 | analysis, phylogenetics, molecular evolution and population genetics. This |
| 876 | package provides command line tools using the Bio++ library.") |
| 877 | (license license:cecill-c)))) |
| 878 | |
| 879 | (define-public blast+ |
| 880 | (package |
| 881 | (name "blast+") |
| 882 | (version "2.4.0") |
| 883 | (source (origin |
| 884 | (method url-fetch) |
| 885 | (uri (string-append |
| 886 | "ftp://ftp.ncbi.nlm.nih.gov/blast/executables/blast+/" |
| 887 | version "/ncbi-blast-" version "+-src.tar.gz")) |
| 888 | (sha256 |
| 889 | (base32 |
| 890 | "14n9jik6vhiwjd3m7bach4xj1pzfn0szbsbyfxybd9l9cc43b6mb")) |
| 891 | (modules '((guix build utils))) |
| 892 | (snippet |
| 893 | '(begin |
| 894 | ;; Remove bundled bzip2 and zlib |
| 895 | (delete-file-recursively "c++/src/util/compress/bzip2") |
| 896 | (delete-file-recursively "c++/src/util/compress/zlib") |
| 897 | (substitute* "c++/src/util/compress/Makefile.in" |
| 898 | (("bzip2 zlib api") "api")) |
| 899 | ;; Remove useless msbuild directory |
| 900 | (delete-file-recursively |
| 901 | "c++/src/build-system/project_tree_builder/msbuild") |
| 902 | #t)))) |
| 903 | (build-system gnu-build-system) |
| 904 | (arguments |
| 905 | `(;; There are three(!) tests for this massive library, and all fail with |
| 906 | ;; "unparsable timing stats". |
| 907 | ;; ERR [127] -- [util/regexp] test_pcre.sh (unparsable timing stats) |
| 908 | ;; ERR [127] -- [serial/datatool] datatool.sh (unparsable timing stats) |
| 909 | ;; ERR [127] -- [serial/datatool] datatool_xml.sh (unparsable timing stats) |
| 910 | #:tests? #f |
| 911 | #:out-of-source? #t |
| 912 | #:parallel-build? #f ; not supported |
| 913 | #:phases |
| 914 | (modify-phases %standard-phases |
| 915 | (add-before |
| 916 | 'configure 'set-HOME |
| 917 | ;; $HOME needs to be set at some point during the configure phase |
| 918 | (lambda _ (setenv "HOME" "/tmp") #t)) |
| 919 | (add-after |
| 920 | 'unpack 'enter-dir |
| 921 | (lambda _ (chdir "c++") #t)) |
| 922 | (add-after |
| 923 | 'enter-dir 'fix-build-system |
| 924 | (lambda _ |
| 925 | (define (which* cmd) |
| 926 | (cond ((string=? cmd "date") |
| 927 | ;; make call to "date" deterministic |
| 928 | "date -d @0") |
| 929 | ((which cmd) |
| 930 | => identity) |
| 931 | (else |
| 932 | (format (current-error-port) |
| 933 | "WARNING: Unable to find absolute path for ~s~%" |
| 934 | cmd) |
| 935 | #f))) |
| 936 | |
| 937 | ;; Rewrite hardcoded paths to various tools |
| 938 | (substitute* (append '("src/build-system/configure.ac" |
| 939 | "src/build-system/configure" |
| 940 | "scripts/common/impl/if_diff.sh" |
| 941 | "scripts/common/impl/run_with_lock.sh" |
| 942 | "src/build-system/Makefile.configurables.real" |
| 943 | "src/build-system/Makefile.in.top" |
| 944 | "src/build-system/Makefile.meta.gmake=no" |
| 945 | "src/build-system/Makefile.meta.in" |
| 946 | "src/build-system/Makefile.meta_l" |
| 947 | "src/build-system/Makefile.meta_p" |
| 948 | "src/build-system/Makefile.meta_r" |
| 949 | "src/build-system/Makefile.mk.in" |
| 950 | "src/build-system/Makefile.requirements" |
| 951 | "src/build-system/Makefile.rules_with_autodep.in") |
| 952 | (find-files "scripts/common/check" "\\.sh$")) |
| 953 | (("(/usr/bin/|/bin/)([a-z][-_.a-z]*)" all dir cmd) |
| 954 | (or (which* cmd) all))) |
| 955 | |
| 956 | (substitute* (find-files "src/build-system" "^config.*") |
| 957 | (("LN_S=/bin/\\$LN_S") (string-append "LN_S=" (which "ln"))) |
| 958 | (("^PATH=.*") "")) |
| 959 | |
| 960 | ;; rewrite "/var/tmp" in check script |
| 961 | (substitute* "scripts/common/check/check_make_unix.sh" |
| 962 | (("/var/tmp") "/tmp")) |
| 963 | |
| 964 | ;; do not reset PATH |
| 965 | (substitute* (find-files "scripts/common/impl/" "\\.sh$") |
| 966 | (("^ *PATH=.*") "") |
| 967 | (("action=/bin/") "action=") |
| 968 | (("export PATH") ":")) |
| 969 | #t)) |
| 970 | (replace |
| 971 | 'configure |
| 972 | (lambda* (#:key inputs outputs #:allow-other-keys) |
| 973 | (let ((out (assoc-ref outputs "out")) |
| 974 | (lib (string-append (assoc-ref outputs "lib") "/lib")) |
| 975 | (include (string-append (assoc-ref outputs "include") |
| 976 | "/include/ncbi-tools++"))) |
| 977 | ;; The 'configure' script doesn't recognize things like |
| 978 | ;; '--enable-fast-install'. |
| 979 | (zero? (system* "./configure.orig" |
| 980 | (string-append "--with-build-root=" (getcwd) "/build") |
| 981 | (string-append "--prefix=" out) |
| 982 | (string-append "--libdir=" lib) |
| 983 | (string-append "--includedir=" include) |
| 984 | (string-append "--with-bz2=" |
| 985 | (assoc-ref inputs "bzip2")) |
| 986 | (string-append "--with-z=" |
| 987 | (assoc-ref inputs "zlib")) |
| 988 | ;; Each library is built twice by default, once |
| 989 | ;; with "-static" in its name, and again |
| 990 | ;; without. |
| 991 | "--without-static" |
| 992 | "--with-dll")))))))) |
| 993 | (outputs '("out" ; 19 MB |
| 994 | "lib" ; 203 MB |
| 995 | "include")) ; 32 MB |
| 996 | (inputs |
| 997 | `(("bzip2" ,bzip2) |
| 998 | ("zlib" ,zlib))) |
| 999 | (native-inputs |
| 1000 | `(("cpio" ,cpio))) |
| 1001 | (home-page "http://blast.ncbi.nlm.nih.gov") |
| 1002 | (synopsis "Basic local alignment search tool") |
| 1003 | (description |
| 1004 | "BLAST is a popular method of performing a DNA or protein sequence |
| 1005 | similarity search, using heuristics to produce results quickly. It also |
| 1006 | calculates an “expect value” that estimates how many matches would have |
| 1007 | occurred at a given score by chance, which can aid a user in judging how much |
| 1008 | confidence to have in an alignment.") |
| 1009 | ;; Most of the sources are in the public domain, with the following |
| 1010 | ;; exceptions: |
| 1011 | ;; * Expat: |
| 1012 | ;; * ./c++/include/util/bitset/ |
| 1013 | ;; * ./c++/src/html/ncbi_menu*.js |
| 1014 | ;; * Boost license: |
| 1015 | ;; * ./c++/include/util/impl/floating_point_comparison.hpp |
| 1016 | ;; * LGPL 2+: |
| 1017 | ;; * ./c++/include/dbapi/driver/odbc/unix_odbc/ |
| 1018 | ;; * ASL 2.0: |
| 1019 | ;; * ./c++/src/corelib/teamcity_* |
| 1020 | (license (list license:public-domain |
| 1021 | license:expat |
| 1022 | license:boost1.0 |
| 1023 | license:lgpl2.0+ |
| 1024 | license:asl2.0)))) |
| 1025 | |
| 1026 | (define-public bless |
| 1027 | (package |
| 1028 | (name "bless") |
| 1029 | (version "1p02") |
| 1030 | (source (origin |
| 1031 | (method url-fetch) |
| 1032 | (uri (string-append "mirror://sourceforge/bless-ec/bless.v" |
| 1033 | version ".tgz")) |
| 1034 | (sha256 |
| 1035 | (base32 |
| 1036 | "0rm0gw2s18dqwzzpl3c2x1z05ni2v0xz5dmfk3d33j6g4cgrlrdd")) |
| 1037 | (modules '((guix build utils))) |
| 1038 | (snippet |
| 1039 | `(begin |
| 1040 | ;; Remove bundled boost, pigz, zlib, and .git directory |
| 1041 | ;; FIXME: also remove bundled sources for murmurhash3 and |
| 1042 | ;; kmc once packaged. |
| 1043 | (delete-file-recursively "boost") |
| 1044 | (delete-file-recursively "pigz") |
| 1045 | (delete-file-recursively "google-sparsehash") |
| 1046 | (delete-file-recursively "zlib") |
| 1047 | (delete-file-recursively ".git") |
| 1048 | #t)))) |
| 1049 | (build-system gnu-build-system) |
| 1050 | (arguments |
| 1051 | '(#:tests? #f ;no "check" target |
| 1052 | #:make-flags |
| 1053 | (list (string-append "ZLIB=" |
| 1054 | (assoc-ref %build-inputs "zlib") |
| 1055 | "/lib/libz.a") |
| 1056 | (string-append "LDFLAGS=" |
| 1057 | (string-join '("-lboost_filesystem" |
| 1058 | "-lboost_system" |
| 1059 | "-lboost_iostreams" |
| 1060 | "-lz" |
| 1061 | "-fopenmp" |
| 1062 | "-std=c++11")))) |
| 1063 | #:phases |
| 1064 | (modify-phases %standard-phases |
| 1065 | (add-after 'unpack 'do-not-build-bundled-pigz |
| 1066 | (lambda* (#:key inputs outputs #:allow-other-keys) |
| 1067 | (substitute* "Makefile" |
| 1068 | (("cd pigz/pigz-2.3.3; make") "")) |
| 1069 | #t)) |
| 1070 | (add-after 'unpack 'patch-paths-to-executables |
| 1071 | (lambda* (#:key inputs outputs #:allow-other-keys) |
| 1072 | (substitute* "parse_args.cpp" |
| 1073 | (("kmc_binary = .*") |
| 1074 | (string-append "kmc_binary = \"" |
| 1075 | (assoc-ref outputs "out") |
| 1076 | "/bin/kmc\";")) |
| 1077 | (("pigz_binary = .*") |
| 1078 | (string-append "pigz_binary = \"" |
| 1079 | (assoc-ref inputs "pigz") |
| 1080 | "/bin/pigz\";"))) |
| 1081 | #t)) |
| 1082 | (replace 'install |
| 1083 | (lambda* (#:key outputs #:allow-other-keys) |
| 1084 | (let ((bin (string-append (assoc-ref outputs "out") "/bin/"))) |
| 1085 | (for-each (lambda (file) |
| 1086 | (install-file file bin)) |
| 1087 | '("bless" "kmc/bin/kmc")) |
| 1088 | #t))) |
| 1089 | (delete 'configure)))) |
| 1090 | (native-inputs |
| 1091 | `(("perl" ,perl))) |
| 1092 | (inputs |
| 1093 | `(("openmpi" ,openmpi) |
| 1094 | ("boost" ,boost) |
| 1095 | ("sparsehash" ,sparsehash) |
| 1096 | ("pigz" ,pigz) |
| 1097 | ("zlib" ,zlib))) |
| 1098 | (supported-systems '("x86_64-linux")) |
| 1099 | (home-page "http://sourceforge.net/p/bless-ec/wiki/Home/") |
| 1100 | (synopsis "Bloom-filter-based error correction tool for NGS reads") |
| 1101 | (description |
| 1102 | "@dfn{Bloom-filter-based error correction solution for high-throughput |
| 1103 | sequencing reads} (BLESS) uses a single minimum-sized bloom filter is a |
| 1104 | correction tool for genomic reads produced by @dfn{Next-generation |
| 1105 | sequencing} (NGS). BLESS produces accurate correction results with much less |
| 1106 | memory compared with previous solutions and is also able to tolerate a higher |
| 1107 | false-positive rate. BLESS can extend reads like DNA assemblers to correct |
| 1108 | errors at the end of reads.") |
| 1109 | (license license:gpl3+))) |
| 1110 | |
| 1111 | (define-public bowtie |
| 1112 | (package |
| 1113 | (name "bowtie") |
| 1114 | (version "2.2.9") |
| 1115 | (source (origin |
| 1116 | (method url-fetch) |
| 1117 | (uri (string-append "https://github.com/BenLangmead/bowtie2/archive/v" |
| 1118 | version ".tar.gz")) |
| 1119 | (file-name (string-append name "-" version ".tar.gz")) |
| 1120 | (sha256 |
| 1121 | (base32 |
| 1122 | "1vp5db8i7is57iwjybcdg18f5ivyzlj5g1ix1nlvxainzivhz55g")) |
| 1123 | (modules '((guix build utils))) |
| 1124 | (snippet |
| 1125 | '(substitute* "Makefile" |
| 1126 | ;; replace BUILD_HOST and BUILD_TIME for deterministic build |
| 1127 | (("-DBUILD_HOST=.*") "-DBUILD_HOST=\"\\\"guix\\\"\"") |
| 1128 | (("-DBUILD_TIME=.*") "-DBUILD_TIME=\"\\\"0\\\"\""))))) |
| 1129 | (build-system gnu-build-system) |
| 1130 | (inputs `(("perl" ,perl) |
| 1131 | ("perl-clone" ,perl-clone) |
| 1132 | ("perl-test-deep" ,perl-test-deep) |
| 1133 | ("perl-test-simple" ,perl-test-simple) |
| 1134 | ("python" ,python-2) |
| 1135 | ("tbb" ,tbb))) |
| 1136 | (arguments |
| 1137 | '(#:make-flags |
| 1138 | (list "allall" |
| 1139 | "WITH_TBB=1" |
| 1140 | (string-append "prefix=" (assoc-ref %outputs "out"))) |
| 1141 | #:phases |
| 1142 | (alist-delete |
| 1143 | 'configure |
| 1144 | (alist-replace |
| 1145 | 'check |
| 1146 | (lambda* (#:key outputs #:allow-other-keys) |
| 1147 | (system* "perl" |
| 1148 | "scripts/test/simple_tests.pl" |
| 1149 | "--bowtie2=./bowtie2" |
| 1150 | "--bowtie2-build=./bowtie2-build")) |
| 1151 | %standard-phases)))) |
| 1152 | (home-page "http://bowtie-bio.sourceforge.net/bowtie2/index.shtml") |
| 1153 | (synopsis "Fast and sensitive nucleotide sequence read aligner") |
| 1154 | (description |
| 1155 | "Bowtie 2 is a fast and memory-efficient tool for aligning sequencing |
| 1156 | reads to long reference sequences. It is particularly good at aligning reads |
| 1157 | of about 50 up to 100s or 1,000s of characters, and particularly good at |
| 1158 | aligning to relatively long (e.g. mammalian) genomes. Bowtie 2 indexes the |
| 1159 | genome with an FM Index to keep its memory footprint small: for the human |
| 1160 | genome, its memory footprint is typically around 3.2 GB. Bowtie 2 supports |
| 1161 | gapped, local, and paired-end alignment modes.") |
| 1162 | (supported-systems '("x86_64-linux")) |
| 1163 | (license license:gpl3+))) |
| 1164 | |
| 1165 | (define-public tophat |
| 1166 | (package |
| 1167 | (name "tophat") |
| 1168 | (version "2.1.0") |
| 1169 | (source (origin |
| 1170 | (method url-fetch) |
| 1171 | (uri (string-append |
| 1172 | "http://ccb.jhu.edu/software/tophat/downloads/tophat-" |
| 1173 | version ".tar.gz")) |
| 1174 | (sha256 |
| 1175 | (base32 |
| 1176 | "168zlzykq622zbgkh90a90f1bdgsxkscq2zxzbj8brq80hbjpyp7")) |
| 1177 | (patches (search-patches "tophat-build-with-later-seqan.patch")) |
| 1178 | (modules '((guix build utils))) |
| 1179 | (snippet |
| 1180 | '(begin |
| 1181 | ;; Remove bundled SeqAn and samtools |
| 1182 | (delete-file-recursively "src/SeqAn-1.3") |
| 1183 | (delete-file-recursively "src/samtools-0.1.18") |
| 1184 | #t)))) |
| 1185 | (build-system gnu-build-system) |
| 1186 | (arguments |
| 1187 | '(#:parallel-build? #f ; not supported |
| 1188 | #:phases |
| 1189 | (modify-phases %standard-phases |
| 1190 | (add-after 'unpack 'use-system-samtools |
| 1191 | (lambda* (#:key inputs #:allow-other-keys) |
| 1192 | (substitute* "src/Makefile.in" |
| 1193 | (("(noinst_LIBRARIES = )\\$\\(SAMLIB\\)" _ prefix) prefix) |
| 1194 | (("\\$\\(SAMPROG\\): \\$\\(SAMLIB\\)") "") |
| 1195 | (("SAMPROG = samtools_0\\.1\\.18") "") |
| 1196 | (("\\$\\(samtools_0_1_18_SOURCES\\)") "") |
| 1197 | (("am__EXEEXT_1 = samtools_0\\.1\\.18\\$\\(EXEEXT\\)") "")) |
| 1198 | (substitute* '("src/common.cpp" |
| 1199 | "src/tophat.py") |
| 1200 | (("samtools_0.1.18") (which "samtools"))) |
| 1201 | (substitute* '("src/common.h" |
| 1202 | "src/bam2fastx.cpp") |
| 1203 | (("#include \"bam.h\"") "#include <samtools/bam.h>") |
| 1204 | (("#include \"sam.h\"") "#include <samtools/sam.h>")) |
| 1205 | (substitute* '("src/bwt_map.h" |
| 1206 | "src/map2gtf.h" |
| 1207 | "src/align_status.h") |
| 1208 | (("#include <bam.h>") "#include <samtools/bam.h>") |
| 1209 | (("#include <sam.h>") "#include <samtools/sam.h>")) |
| 1210 | #t))))) |
| 1211 | (inputs |
| 1212 | `(("boost" ,boost) |
| 1213 | ("bowtie" ,bowtie) |
| 1214 | ("samtools" ,samtools-0.1) |
| 1215 | ("ncurses" ,ncurses) |
| 1216 | ("python" ,python-2) |
| 1217 | ("perl" ,perl) |
| 1218 | ("zlib" ,zlib) |
| 1219 | ("seqan" ,seqan))) |
| 1220 | (home-page "http://ccb.jhu.edu/software/tophat/index.shtml") |
| 1221 | (synopsis "Spliced read mapper for RNA-Seq data") |
| 1222 | (description |
| 1223 | "TopHat is a fast splice junction mapper for nucleotide sequence |
| 1224 | reads produced by the RNA-Seq method. It aligns RNA-Seq reads to |
| 1225 | mammalian-sized genomes using the ultra high-throughput short read |
| 1226 | aligner Bowtie, and then analyzes the mapping results to identify |
| 1227 | splice junctions between exons.") |
| 1228 | ;; TopHat is released under the Boost Software License, Version 1.0 |
| 1229 | ;; See https://github.com/infphilo/tophat/issues/11#issuecomment-121589893 |
| 1230 | (license license:boost1.0))) |
| 1231 | |
| 1232 | (define-public bwa |
| 1233 | (package |
| 1234 | (name "bwa") |
| 1235 | (version "0.7.12") |
| 1236 | (source (origin |
| 1237 | (method url-fetch) |
| 1238 | (uri (string-append "mirror://sourceforge/bio-bwa/bwa-" |
| 1239 | version ".tar.bz2")) |
| 1240 | (sha256 |
| 1241 | (base32 |
| 1242 | "1330dpqncv0px3pbhjzz1gwgg39kkcv2r9qp2xs0sixf8z8wl7bh")))) |
| 1243 | (build-system gnu-build-system) |
| 1244 | (arguments |
| 1245 | '(#:tests? #f ;no "check" target |
| 1246 | #:phases |
| 1247 | (alist-replace |
| 1248 | 'install |
| 1249 | (lambda* (#:key outputs #:allow-other-keys) |
| 1250 | (let ((bin (string-append |
| 1251 | (assoc-ref outputs "out") "/bin")) |
| 1252 | (doc (string-append |
| 1253 | (assoc-ref outputs "out") "/share/doc/bwa")) |
| 1254 | (man (string-append |
| 1255 | (assoc-ref outputs "out") "/share/man/man1"))) |
| 1256 | (install-file "bwa" bin) |
| 1257 | (install-file "README.md" doc) |
| 1258 | (install-file "bwa.1" man))) |
| 1259 | ;; no "configure" script |
| 1260 | (alist-delete 'configure %standard-phases)))) |
| 1261 | (inputs `(("zlib" ,zlib))) |
| 1262 | ;; Non-portable SSE instructions are used so building fails on platforms |
| 1263 | ;; other than x86_64. |
| 1264 | (supported-systems '("x86_64-linux")) |
| 1265 | (home-page "http://bio-bwa.sourceforge.net/") |
| 1266 | (synopsis "Burrows-Wheeler sequence aligner") |
| 1267 | (description |
| 1268 | "BWA is a software package for mapping low-divergent sequences against a |
| 1269 | large reference genome, such as the human genome. It consists of three |
| 1270 | algorithms: BWA-backtrack, BWA-SW and BWA-MEM. The first algorithm is |
| 1271 | designed for Illumina sequence reads up to 100bp, while the rest two for |
| 1272 | longer sequences ranged from 70bp to 1Mbp. BWA-MEM and BWA-SW share similar |
| 1273 | features such as long-read support and split alignment, but BWA-MEM, which is |
| 1274 | the latest, is generally recommended for high-quality queries as it is faster |
| 1275 | and more accurate. BWA-MEM also has better performance than BWA-backtrack for |
| 1276 | 70-100bp Illumina reads.") |
| 1277 | (license license:gpl3+))) |
| 1278 | |
| 1279 | (define-public bwa-pssm |
| 1280 | (package (inherit bwa) |
| 1281 | (name "bwa-pssm") |
| 1282 | (version "0.5.11") |
| 1283 | (source (origin |
| 1284 | (method url-fetch) |
| 1285 | (uri (string-append "https://github.com/pkerpedjiev/bwa-pssm/" |
| 1286 | "archive/" version ".tar.gz")) |
| 1287 | (file-name (string-append name "-" version ".tar.gz")) |
| 1288 | (sha256 |
| 1289 | (base32 |
| 1290 | "02p7mpbs4mlxmn84g2x4ghak638vbj4lqix2ipx5g84pz9bhdavg")))) |
| 1291 | (build-system gnu-build-system) |
| 1292 | (inputs |
| 1293 | `(("gdsl" ,gdsl) |
| 1294 | ("zlib" ,zlib) |
| 1295 | ("perl" ,perl))) |
| 1296 | (home-page "http://bwa-pssm.binf.ku.dk/") |
| 1297 | (synopsis "Burrows-Wheeler transform-based probabilistic short read mapper") |
| 1298 | (description |
| 1299 | "BWA-PSSM is a probabilistic short genomic sequence read aligner based on |
| 1300 | the use of @dfn{position specific scoring matrices} (PSSM). Like many of the |
| 1301 | existing aligners it is fast and sensitive. Unlike most other aligners, |
| 1302 | however, it is also adaptible in the sense that one can direct the alignment |
| 1303 | based on known biases within the data set. It is coded as a modification of |
| 1304 | the original BWA alignment program and shares the genome index structure as |
| 1305 | well as many of the command line options.") |
| 1306 | (license license:gpl3+))) |
| 1307 | |
| 1308 | (define-public python2-bx-python |
| 1309 | (package |
| 1310 | (name "python2-bx-python") |
| 1311 | (version "0.7.2") |
| 1312 | (source (origin |
| 1313 | (method url-fetch) |
| 1314 | (uri (string-append |
| 1315 | "https://pypi.python.org/packages/source/b/bx-python/bx-python-" |
| 1316 | version ".tar.gz")) |
| 1317 | (sha256 |
| 1318 | (base32 |
| 1319 | "0ld49idhc5zjdvbhvjq1a2qmpjj7h5v58rqr25dzmfq7g34b50xh")) |
| 1320 | (modules '((guix build utils))) |
| 1321 | (snippet |
| 1322 | '(substitute* "setup.py" |
| 1323 | ;; remove dependency on outdated "distribute" module |
| 1324 | (("^from distribute_setup import use_setuptools") "") |
| 1325 | (("^use_setuptools\\(\\)") ""))))) |
| 1326 | (build-system python-build-system) |
| 1327 | (arguments |
| 1328 | `(#:tests? #f ;tests fail because test data are not included |
| 1329 | #:python ,python-2)) |
| 1330 | (inputs |
| 1331 | `(("python-numpy" ,python2-numpy) |
| 1332 | ("zlib" ,zlib))) |
| 1333 | (native-inputs |
| 1334 | `(("python-nose" ,python2-nose))) |
| 1335 | (home-page "http://bitbucket.org/james_taylor/bx-python/") |
| 1336 | (synopsis "Tools for manipulating biological data") |
| 1337 | (description |
| 1338 | "bx-python provides tools for manipulating biological data, particularly |
| 1339 | multiple sequence alignments.") |
| 1340 | (license license:expat))) |
| 1341 | |
| 1342 | (define-public python-pysam |
| 1343 | (package |
| 1344 | (name "python-pysam") |
| 1345 | (version "0.9.1.4") |
| 1346 | (source (origin |
| 1347 | (method url-fetch) |
| 1348 | ;; Test data is missing on PyPi. |
| 1349 | (uri (string-append |
| 1350 | "https://github.com/pysam-developers/pysam/archive/v" |
| 1351 | version ".tar.gz")) |
| 1352 | (file-name (string-append name "-" version ".tar.gz")) |
| 1353 | (sha256 |
| 1354 | (base32 |
| 1355 | "0y41ssbg6nvn2jgcbnrvkzblpjcwszaiv1rgyd8dwzjkrbfsgsmc")) |
| 1356 | (modules '((guix build utils))) |
| 1357 | (snippet |
| 1358 | ;; Drop bundled htslib. TODO: Also remove samtools and bcftools. |
| 1359 | '(delete-file-recursively "htslib")))) |
| 1360 | (build-system python-build-system) |
| 1361 | (arguments |
| 1362 | `(#:phases |
| 1363 | (modify-phases %standard-phases |
| 1364 | (add-before 'build 'set-flags |
| 1365 | (lambda* (#:key inputs #:allow-other-keys) |
| 1366 | (setenv "HTSLIB_MODE" "external") |
| 1367 | (setenv "HTSLIB_LIBRARY_DIR" |
| 1368 | (string-append (assoc-ref inputs "htslib") "/lib")) |
| 1369 | (setenv "HTSLIB_INCLUDE_DIR" |
| 1370 | (string-append (assoc-ref inputs "htslib") "/include")) |
| 1371 | (setenv "LDFLAGS" "-lncurses") |
| 1372 | (setenv "CFLAGS" "-D_CURSES_LIB=1") |
| 1373 | #t)) |
| 1374 | (delete 'check) |
| 1375 | (add-after 'install 'check |
| 1376 | (lambda* (#:key inputs outputs #:allow-other-keys) |
| 1377 | (setenv "PYTHONPATH" |
| 1378 | (string-append |
| 1379 | (getenv "PYTHONPATH") |
| 1380 | ":" (assoc-ref outputs "out") |
| 1381 | "/lib/python" |
| 1382 | (string-take (string-take-right |
| 1383 | (assoc-ref inputs "python") 5) 3) |
| 1384 | "/site-packages")) |
| 1385 | ;; Step out of source dir so python does not import from CWD. |
| 1386 | (chdir "tests") |
| 1387 | (setenv "HOME" "/tmp") |
| 1388 | (and (zero? (system* "make" "-C" "pysam_data")) |
| 1389 | (zero? (system* "make" "-C" "cbcf_data")) |
| 1390 | (zero? (system* "nosetests" "-v")))))))) |
| 1391 | (propagated-inputs |
| 1392 | `(("htslib" ,htslib))) ; Included from installed header files. |
| 1393 | (inputs |
| 1394 | `(("ncurses" ,ncurses) |
| 1395 | ("zlib" ,zlib))) |
| 1396 | (native-inputs |
| 1397 | `(("python-cython" ,python-cython) |
| 1398 | ;; Dependencies below are are for tests only. |
| 1399 | ("samtools" ,samtools) |
| 1400 | ("bcftools" ,bcftools) |
| 1401 | ("python-nose" ,python-nose))) |
| 1402 | (home-page "https://github.com/pysam-developers/pysam") |
| 1403 | (synopsis "Python bindings to the SAMtools C API") |
| 1404 | (description |
| 1405 | "Pysam is a Python module for reading and manipulating files in the |
| 1406 | SAM/BAM format. Pysam is a lightweight wrapper of the SAMtools C API. It |
| 1407 | also includes an interface for tabix.") |
| 1408 | (license license:expat))) |
| 1409 | |
| 1410 | (define-public python2-pysam |
| 1411 | (package-with-python2 python-pysam)) |
| 1412 | |
| 1413 | (define-public python-twobitreader |
| 1414 | (package |
| 1415 | (name "python-twobitreader") |
| 1416 | (version "3.1.4") |
| 1417 | (source (origin |
| 1418 | (method url-fetch) |
| 1419 | (uri (pypi-uri "twobitreader" version)) |
| 1420 | (sha256 |
| 1421 | (base32 |
| 1422 | "1q8wnj2kga9nz1lwc4w7qv52smfm536hp6mc8w6s53lhyj0mpi22")))) |
| 1423 | (build-system python-build-system) |
| 1424 | (arguments |
| 1425 | '(;; Tests are not distributed in the PyPi release. |
| 1426 | ;; TODO Try building from the Git repo or asking the upstream maintainer |
| 1427 | ;; to distribute the tests on PyPi. |
| 1428 | #:tests? #f)) |
| 1429 | (native-inputs |
| 1430 | `(("python-sphinx" ,python-sphinx))) |
| 1431 | (home-page "https://github.com/benjschiller/twobitreader") |
| 1432 | (synopsis "Python library for reading .2bit files") |
| 1433 | (description |
| 1434 | "twobitreader is a Python library for reading .2bit files as used by the |
| 1435 | UCSC genome browser.") |
| 1436 | (license license:artistic2.0))) |
| 1437 | |
| 1438 | (define-public python2-twobitreader |
| 1439 | (package-with-python2 python-twobitreader)) |
| 1440 | |
| 1441 | (define-public python-plastid |
| 1442 | (package |
| 1443 | (name "python-plastid") |
| 1444 | (version "0.4.6") |
| 1445 | (source (origin |
| 1446 | (method url-fetch) |
| 1447 | (uri (pypi-uri "plastid" version)) |
| 1448 | (sha256 |
| 1449 | (base32 |
| 1450 | "1sqkz5d3b9kf688mp7k771c87ins42j7j0whmkb49cb3fsg8s8lj")))) |
| 1451 | (build-system python-build-system) |
| 1452 | (arguments |
| 1453 | ;; Some test files are not included. |
| 1454 | `(#:tests? #f)) |
| 1455 | (propagated-inputs |
| 1456 | `(("python-numpy" ,python-numpy) |
| 1457 | ("python-scipy" ,python-scipy) |
| 1458 | ("python-pandas" ,python-pandas) |
| 1459 | ("python-pysam" ,python-pysam) |
| 1460 | ("python-matplotlib" ,python-matplotlib) |
| 1461 | ("python-biopython" ,python-biopython) |
| 1462 | ("python-twobitreader" ,python-twobitreader) |
| 1463 | ("python-termcolor" ,python-termcolor))) |
| 1464 | (native-inputs |
| 1465 | `(("python-cython" ,python-cython) |
| 1466 | ("python-nose" ,python-nose))) |
| 1467 | (home-page "https://github.com/joshuagryphon/plastid") |
| 1468 | (synopsis "Python library for genomic analysis") |
| 1469 | (description |
| 1470 | "plastid is a Python library for genomic analysis – in particular, |
| 1471 | high-throughput sequencing data – with an emphasis on simplicity.") |
| 1472 | (license license:bsd-3))) |
| 1473 | |
| 1474 | (define-public python2-plastid |
| 1475 | (package-with-python2 python-plastid)) |
| 1476 | |
| 1477 | (define-public cd-hit |
| 1478 | (package |
| 1479 | (name "cd-hit") |
| 1480 | (version "4.6.5") |
| 1481 | (source (origin |
| 1482 | (method url-fetch) |
| 1483 | (uri (string-append "https://github.com/weizhongli/cdhit" |
| 1484 | "/releases/download/V" version |
| 1485 | "/cd-hit-v" version "-2016-0304.tar.gz")) |
| 1486 | (sha256 |
| 1487 | (base32 |
| 1488 | "15db0hq38yyifwqx9b6l34z14jcq576dmjavhj8a426c18lvnhp3")))) |
| 1489 | (build-system gnu-build-system) |
| 1490 | (arguments |
| 1491 | `(#:tests? #f ; there are no tests |
| 1492 | #:make-flags |
| 1493 | ;; Executables are copied directly to the PREFIX. |
| 1494 | (list (string-append "PREFIX=" (assoc-ref %outputs "out") "/bin")) |
| 1495 | #:phases |
| 1496 | (modify-phases %standard-phases |
| 1497 | ;; No "configure" script |
| 1498 | (delete 'configure) |
| 1499 | ;; Remove sources of non-determinism |
| 1500 | (add-after 'unpack 'be-timeless |
| 1501 | (lambda _ |
| 1502 | (substitute* "cdhit-utility.c++" |
| 1503 | ((" \\(built on \" __DATE__ \"\\)") "")) |
| 1504 | (substitute* "cdhit-common.c++" |
| 1505 | (("__DATE__") "\"0\"") |
| 1506 | (("\", %s, \" __TIME__ \"\\\\n\", date") "")) |
| 1507 | #t)) |
| 1508 | ;; The "install" target does not create the target directory |
| 1509 | (add-before 'install 'create-target-dir |
| 1510 | (lambda* (#:key outputs #:allow-other-keys) |
| 1511 | (mkdir-p (string-append (assoc-ref outputs "out") "/bin")) |
| 1512 | #t))))) |
| 1513 | (inputs |
| 1514 | `(("perl" ,perl))) |
| 1515 | (home-page "http://weizhongli-lab.org/cd-hit/") |
| 1516 | (synopsis "Cluster and compare protein or nucleotide sequences") |
| 1517 | (description |
| 1518 | "CD-HIT is a program for clustering and comparing protein or nucleotide |
| 1519 | sequences. CD-HIT is designed to be fast and handle extremely large |
| 1520 | databases.") |
| 1521 | ;; The manual says: "It can be copied under the GNU General Public License |
| 1522 | ;; version 2 (GPLv2)." |
| 1523 | (license license:gpl2))) |
| 1524 | |
| 1525 | (define-public clipper |
| 1526 | (package |
| 1527 | (name "clipper") |
| 1528 | (version "1.1") |
| 1529 | (source (origin |
| 1530 | (method url-fetch) |
| 1531 | (uri (string-append |
| 1532 | "https://github.com/YeoLab/clipper/archive/" |
| 1533 | version ".tar.gz")) |
| 1534 | (file-name (string-append name "-" version ".tar.gz")) |
| 1535 | (sha256 |
| 1536 | (base32 |
| 1537 | "0pflmsvhbf8izbgwhbhj1i7349sw1f55qpqj8ljmapp16hb0p0qi")) |
| 1538 | (modules '((guix build utils))) |
| 1539 | (snippet |
| 1540 | '(begin |
| 1541 | ;; remove unnecessary setup dependency |
| 1542 | (substitute* "setup.py" |
| 1543 | (("setup_requires = .*") "")) |
| 1544 | (for-each delete-file |
| 1545 | '("clipper/src/peaks.so" |
| 1546 | "clipper/src/readsToWiggle.so")) |
| 1547 | (delete-file-recursively "dist/") |
| 1548 | #t)))) |
| 1549 | (build-system python-build-system) |
| 1550 | (arguments `(#:python ,python-2)) ; only Python 2 is supported |
| 1551 | (inputs |
| 1552 | `(("htseq" ,htseq) |
| 1553 | ("python-pybedtools" ,python2-pybedtools) |
| 1554 | ("python-cython" ,python2-cython) |
| 1555 | ("python-scikit-learn" ,python2-scikit-learn) |
| 1556 | ("python-matplotlib" ,python2-matplotlib) |
| 1557 | ("python-pandas" ,python2-pandas) |
| 1558 | ("python-pysam" ,python2-pysam) |
| 1559 | ("python-numpy" ,python2-numpy) |
| 1560 | ("python-scipy" ,python2-scipy))) |
| 1561 | (native-inputs |
| 1562 | `(("python-mock" ,python2-mock) ; for tests |
| 1563 | ("python-pytz" ,python2-pytz))) ; for tests |
| 1564 | (home-page "https://github.com/YeoLab/clipper") |
| 1565 | (synopsis "CLIP peak enrichment recognition") |
| 1566 | (description |
| 1567 | "CLIPper is a tool to define peaks in CLIP-seq datasets.") |
| 1568 | (license license:gpl2))) |
| 1569 | |
| 1570 | (define-public codingquarry |
| 1571 | (package |
| 1572 | (name "codingquarry") |
| 1573 | (version "2.0") |
| 1574 | (source (origin |
| 1575 | (method url-fetch) |
| 1576 | (uri (string-append |
| 1577 | "mirror://sourceforge/codingquarry/CodingQuarry_v" |
| 1578 | version ".tar.gz")) |
| 1579 | (sha256 |
| 1580 | (base32 |
| 1581 | "0115hkjflsnfzn36xppwf9h9avfxlavr43djqmshkkzbgjzsz60i")))) |
| 1582 | (build-system gnu-build-system) |
| 1583 | (arguments |
| 1584 | '(#:tests? #f ; no "check" target |
| 1585 | #:phases |
| 1586 | (modify-phases %standard-phases |
| 1587 | (delete 'configure) |
| 1588 | (replace 'install |
| 1589 | (lambda* (#:key outputs #:allow-other-keys) |
| 1590 | (let* ((out (assoc-ref outputs "out")) |
| 1591 | (bin (string-append out "/bin")) |
| 1592 | (doc (string-append out "/share/doc/codingquarry"))) |
| 1593 | (install-file "INSTRUCTIONS.pdf" doc) |
| 1594 | (copy-recursively "QuarryFiles" |
| 1595 | (string-append out "/QuarryFiles")) |
| 1596 | (install-file "CodingQuarry" bin) |
| 1597 | (install-file "CufflinksGTF_to_CodingQuarryGFF3.py" bin))))))) |
| 1598 | (inputs `(("openmpi" ,openmpi))) |
| 1599 | (native-search-paths |
| 1600 | (list (search-path-specification |
| 1601 | (variable "QUARRY_PATH") |
| 1602 | (files '("QuarryFiles"))))) |
| 1603 | (native-inputs `(("python" ,python-2))) ; Only Python 2 is supported |
| 1604 | (synopsis "Fungal gene predictor") |
| 1605 | (description "CodingQuarry is a highly accurate, self-training GHMM fungal |
| 1606 | gene predictor designed to work with assembled, aligned RNA-seq transcripts.") |
| 1607 | (home-page "https://sourceforge.net/projects/codingquarry/") |
| 1608 | (license license:gpl3+))) |
| 1609 | |
| 1610 | (define-public couger |
| 1611 | (package |
| 1612 | (name "couger") |
| 1613 | (version "1.8.2") |
| 1614 | (source (origin |
| 1615 | (method url-fetch) |
| 1616 | (uri (string-append |
| 1617 | "http://couger.oit.duke.edu/static/assets/COUGER" |
| 1618 | version ".zip")) |
| 1619 | (sha256 |
| 1620 | (base32 |
| 1621 | "04p2b14nmhzxw5h72mpzdhalv21bx4w9b87z0wpw0xzxpysyncmq")))) |
| 1622 | (build-system gnu-build-system) |
| 1623 | (arguments |
| 1624 | `(#:tests? #f |
| 1625 | #:phases |
| 1626 | (modify-phases %standard-phases |
| 1627 | (delete 'configure) |
| 1628 | (delete 'build) |
| 1629 | (replace |
| 1630 | 'install |
| 1631 | (lambda* (#:key outputs #:allow-other-keys) |
| 1632 | (let ((out (assoc-ref outputs "out"))) |
| 1633 | (copy-recursively "src" (string-append out "/src")) |
| 1634 | (mkdir (string-append out "/bin")) |
| 1635 | ;; Add "src" directory to module lookup path. |
| 1636 | (substitute* "couger" |
| 1637 | (("from argparse") |
| 1638 | (string-append "import sys\nsys.path.append(\"" |
| 1639 | out "\")\nfrom argparse"))) |
| 1640 | (copy-file "couger" (string-append out "/bin/couger"))) |
| 1641 | #t)) |
| 1642 | (add-after |
| 1643 | 'install 'wrap-program |
| 1644 | (lambda* (#:key inputs outputs #:allow-other-keys) |
| 1645 | ;; Make sure 'couger' runs with the correct PYTHONPATH. |
| 1646 | (let* ((out (assoc-ref outputs "out")) |
| 1647 | (path (getenv "PYTHONPATH"))) |
| 1648 | (wrap-program (string-append out "/bin/couger") |
| 1649 | `("PYTHONPATH" ":" prefix (,path)))) |
| 1650 | #t))))) |
| 1651 | (inputs |
| 1652 | `(("python" ,python-2) |
| 1653 | ("python2-pillow" ,python2-pillow) |
| 1654 | ("python2-numpy" ,python2-numpy) |
| 1655 | ("python2-scipy" ,python2-scipy) |
| 1656 | ("python2-matplotlib" ,python2-matplotlib))) |
| 1657 | (propagated-inputs |
| 1658 | `(("r" ,r) |
| 1659 | ("libsvm" ,libsvm) |
| 1660 | ("randomjungle" ,randomjungle))) |
| 1661 | (native-inputs |
| 1662 | `(("unzip" ,unzip))) |
| 1663 | (home-page "http://couger.oit.duke.edu") |
| 1664 | (synopsis "Identify co-factors in sets of genomic regions") |
| 1665 | (description |
| 1666 | "COUGER can be applied to any two sets of genomic regions bound by |
| 1667 | paralogous TFs (e.g., regions derived from ChIP-seq experiments) to identify |
| 1668 | putative co-factors that provide specificity to each TF. The framework |
| 1669 | determines the genomic targets uniquely-bound by each TF, and identifies a |
| 1670 | small set of co-factors that best explain the in vivo binding differences |
| 1671 | between the two TFs. |
| 1672 | |
| 1673 | COUGER uses classification algorithms (support vector machines and random |
| 1674 | forests) with features that reflect the DNA binding specificities of putative |
| 1675 | co-factors. The features are generated either from high-throughput TF-DNA |
| 1676 | binding data (from protein binding microarray experiments), or from large |
| 1677 | collections of DNA motifs.") |
| 1678 | (license license:gpl3+))) |
| 1679 | |
| 1680 | (define-public clustal-omega |
| 1681 | (package |
| 1682 | (name "clustal-omega") |
| 1683 | (version "1.2.1") |
| 1684 | (source (origin |
| 1685 | (method url-fetch) |
| 1686 | (uri (string-append |
| 1687 | "http://www.clustal.org/omega/clustal-omega-" |
| 1688 | version ".tar.gz")) |
| 1689 | (sha256 |
| 1690 | (base32 |
| 1691 | "02ibkx0m0iwz8nscg998bh41gg251y56cgh86bvyrii5m8kjgwqf")))) |
| 1692 | (build-system gnu-build-system) |
| 1693 | (inputs |
| 1694 | `(("argtable" ,argtable))) |
| 1695 | (home-page "http://www.clustal.org/omega/") |
| 1696 | (synopsis "Multiple sequence aligner for protein and DNA/RNA") |
| 1697 | (description |
| 1698 | "Clustal-Omega is a general purpose multiple sequence alignment (MSA) |
| 1699 | program for protein and DNA/RNA. It produces high quality MSAs and is capable |
| 1700 | of handling data-sets of hundreds of thousands of sequences in reasonable |
| 1701 | time.") |
| 1702 | (license license:gpl2+))) |
| 1703 | |
| 1704 | (define-public crossmap |
| 1705 | (package |
| 1706 | (name "crossmap") |
| 1707 | (version "0.2.1") |
| 1708 | (source (origin |
| 1709 | (method url-fetch) |
| 1710 | (uri (string-append "mirror://sourceforge/crossmap/CrossMap-" |
| 1711 | version ".tar.gz")) |
| 1712 | (sha256 |
| 1713 | (base32 |
| 1714 | "07y179f63d7qnzdvkqcziwk9bs3k4zhp81q392fp1hwszjdvy22f")) |
| 1715 | ;; This patch has been sent upstream already and is available |
| 1716 | ;; for download from Sourceforge, but it has not been merged. |
| 1717 | (patches (search-patches "crossmap-allow-system-pysam.patch")) |
| 1718 | (modules '((guix build utils))) |
| 1719 | ;; remove bundled copy of pysam |
| 1720 | (snippet |
| 1721 | '(delete-file-recursively "lib/pysam")))) |
| 1722 | (build-system python-build-system) |
| 1723 | (arguments |
| 1724 | `(#:python ,python-2 |
| 1725 | #:phases |
| 1726 | (alist-cons-after |
| 1727 | 'unpack 'set-env |
| 1728 | (lambda _ (setenv "CROSSMAP_USE_SYSTEM_PYSAM" "1")) |
| 1729 | %standard-phases))) |
| 1730 | (inputs |
| 1731 | `(("python-numpy" ,python2-numpy) |
| 1732 | ("python-pysam" ,python2-pysam) |
| 1733 | ("zlib" ,zlib))) |
| 1734 | (native-inputs |
| 1735 | `(("python-cython" ,python2-cython) |
| 1736 | ("python-nose" ,python2-nose))) |
| 1737 | (home-page "http://crossmap.sourceforge.net/") |
| 1738 | (synopsis "Convert genome coordinates between assemblies") |
| 1739 | (description |
| 1740 | "CrossMap is a program for conversion of genome coordinates or annotation |
| 1741 | files between different genome assemblies. It supports most commonly used |
| 1742 | file formats including SAM/BAM, Wiggle/BigWig, BED, GFF/GTF, VCF.") |
| 1743 | (license license:gpl2+))) |
| 1744 | |
| 1745 | (define-public cufflinks |
| 1746 | (package |
| 1747 | (name "cufflinks") |
| 1748 | (version "2.2.1") |
| 1749 | (source (origin |
| 1750 | (method url-fetch) |
| 1751 | (uri (string-append "http://cole-trapnell-lab.github.io/" |
| 1752 | "cufflinks/assets/downloads/cufflinks-" |
| 1753 | version ".tar.gz")) |
| 1754 | (sha256 |
| 1755 | (base32 |
| 1756 | "1bnm10p8m7zq4qiipjhjqb24csiqdm1pwc8c795z253r2xk6ncg8")))) |
| 1757 | (build-system gnu-build-system) |
| 1758 | (arguments |
| 1759 | `(#:make-flags |
| 1760 | (list |
| 1761 | ;; The includes for "eigen" are located in a subdirectory. |
| 1762 | (string-append "EIGEN_CPPFLAGS=" |
| 1763 | "-I" (assoc-ref %build-inputs "eigen") |
| 1764 | "/include/eigen3/") |
| 1765 | ;; Cufflinks must be linked with various boost libraries. |
| 1766 | (string-append "LDFLAGS=" |
| 1767 | (string-join '("-lboost_system" |
| 1768 | "-lboost_serialization" |
| 1769 | "-lboost_thread")))) |
| 1770 | #:phases |
| 1771 | (modify-phases %standard-phases |
| 1772 | (add-after 'unpack 'fix-search-for-bam |
| 1773 | (lambda _ |
| 1774 | (substitute* '("ax_bam.m4" |
| 1775 | "configure" |
| 1776 | "src/hits.h") |
| 1777 | (("<bam/sam\\.h>") "<samtools/sam.h>") |
| 1778 | (("<bam/bam\\.h>") "<samtools/bam.h>") |
| 1779 | (("<bam/version\\.hpp>") "<samtools/version.h>")) |
| 1780 | #t))) |
| 1781 | #:configure-flags |
| 1782 | (list (string-append "--with-bam=" |
| 1783 | (assoc-ref %build-inputs "samtools"))))) |
| 1784 | (inputs |
| 1785 | `(("eigen" ,eigen) |
| 1786 | ("samtools" ,samtools-0.1) |
| 1787 | ("htslib" ,htslib) |
| 1788 | ("boost" ,boost) |
| 1789 | ("python" ,python-2) |
| 1790 | ("zlib" ,zlib))) |
| 1791 | (home-page "http://cole-trapnell-lab.github.io/cufflinks/") |
| 1792 | (synopsis "Transcriptome assembly and RNA-Seq expression analysis") |
| 1793 | (description |
| 1794 | "Cufflinks assembles RNA transcripts, estimates their abundances, |
| 1795 | and tests for differential expression and regulation in RNA-Seq |
| 1796 | samples. It accepts aligned RNA-Seq reads and assembles the |
| 1797 | alignments into a parsimonious set of transcripts. Cufflinks then |
| 1798 | estimates the relative abundances of these transcripts based on how |
| 1799 | many reads support each one, taking into account biases in library |
| 1800 | preparation protocols.") |
| 1801 | (license license:boost1.0))) |
| 1802 | |
| 1803 | (define-public cutadapt |
| 1804 | (package |
| 1805 | (name "cutadapt") |
| 1806 | (version "1.8") |
| 1807 | (source (origin |
| 1808 | (method url-fetch) |
| 1809 | (uri (string-append |
| 1810 | "https://github.com/marcelm/cutadapt/archive/v" |
| 1811 | version ".tar.gz")) |
| 1812 | (file-name (string-append name "-" version ".tar.gz")) |
| 1813 | (sha256 |
| 1814 | (base32 |
| 1815 | "161bp87y6gd6r5bmvjpn2b1k942i3fizfpa139f0jn6jv1wcp5h5")))) |
| 1816 | (build-system python-build-system) |
| 1817 | (arguments |
| 1818 | ;; tests must be run after install |
| 1819 | `(#:phases (alist-cons-after |
| 1820 | 'install 'check |
| 1821 | (lambda* (#:key inputs outputs #:allow-other-keys) |
| 1822 | (setenv "PYTHONPATH" |
| 1823 | (string-append |
| 1824 | (getenv "PYTHONPATH") |
| 1825 | ":" (assoc-ref outputs "out") |
| 1826 | "/lib/python" |
| 1827 | (string-take (string-take-right |
| 1828 | (assoc-ref inputs "python") 5) 3) |
| 1829 | "/site-packages")) |
| 1830 | (zero? (system* "nosetests" "-P" "tests"))) |
| 1831 | (alist-delete 'check %standard-phases)))) |
| 1832 | (native-inputs |
| 1833 | `(("python-cython" ,python-cython) |
| 1834 | ("python-nose" ,python-nose))) |
| 1835 | (home-page "https://code.google.com/p/cutadapt/") |
| 1836 | (synopsis "Remove adapter sequences from nucleotide sequencing reads") |
| 1837 | (description |
| 1838 | "Cutadapt finds and removes adapter sequences, primers, poly-A tails and |
| 1839 | other types of unwanted sequence from high-throughput sequencing reads.") |
| 1840 | (license license:expat))) |
| 1841 | |
| 1842 | (define-public libbigwig |
| 1843 | (package |
| 1844 | (name "libbigwig") |
| 1845 | (version "0.1.4") |
| 1846 | (source (origin |
| 1847 | (method url-fetch) |
| 1848 | (uri (string-append "https://github.com/dpryan79/libBigWig/" |
| 1849 | "archive/" version ".tar.gz")) |
| 1850 | (file-name (string-append name "-" version ".tar.gz")) |
| 1851 | (sha256 |
| 1852 | (base32 |
| 1853 | "098rjh35pi4a9q83n8wiwvyzykjqj6l8q189p1xgfw4ghywdlvw1")))) |
| 1854 | (build-system gnu-build-system) |
| 1855 | (arguments |
| 1856 | `(#:test-target "test" |
| 1857 | #:make-flags |
| 1858 | (list "CC=gcc" |
| 1859 | (string-append "prefix=" (assoc-ref %outputs "out"))) |
| 1860 | #:phases |
| 1861 | (modify-phases %standard-phases |
| 1862 | (delete 'configure) |
| 1863 | (add-before 'check 'disable-curl-test |
| 1864 | (lambda _ |
| 1865 | (substitute* "Makefile" |
| 1866 | (("./test/testRemote.*") "")) |
| 1867 | #t)) |
| 1868 | ;; This has been fixed with the upstream commit 4ff6959cd8a0, but |
| 1869 | ;; there has not yet been a release containing this change. |
| 1870 | (add-before 'install 'create-target-dirs |
| 1871 | (lambda* (#:key outputs #:allow-other-keys) |
| 1872 | (let ((out (assoc-ref outputs "out"))) |
| 1873 | (mkdir-p (string-append out "/lib")) |
| 1874 | (mkdir-p (string-append out "/include")) |
| 1875 | #t)))))) |
| 1876 | (inputs |
| 1877 | `(("zlib" ,zlib) |
| 1878 | ("curl" ,curl))) |
| 1879 | (native-inputs |
| 1880 | `(("doxygen" ,doxygen))) |
| 1881 | (home-page "https://github.com/dpryan79/libBigWig") |
| 1882 | (synopsis "C library for handling bigWig files") |
| 1883 | (description |
| 1884 | "This package provides a C library for parsing local and remote BigWig |
| 1885 | files.") |
| 1886 | (license license:expat))) |
| 1887 | |
| 1888 | (define-public python-pybigwig |
| 1889 | (package |
| 1890 | (name "python-pybigwig") |
| 1891 | (version "0.2.5") |
| 1892 | (source (origin |
| 1893 | (method url-fetch) |
| 1894 | (uri (pypi-uri "pyBigWig" version)) |
| 1895 | (sha256 |
| 1896 | (base32 |
| 1897 | "0yrpdxg3y0sny25x4w22lv1k47jzccqjmg7j4bp0hywklvp0hg7d")) |
| 1898 | (modules '((guix build utils))) |
| 1899 | (snippet |
| 1900 | '(begin |
| 1901 | ;; Delete bundled libBigWig sources |
| 1902 | (delete-file-recursively "libBigWig"))))) |
| 1903 | (build-system python-build-system) |
| 1904 | (arguments |
| 1905 | `(#:phases |
| 1906 | (modify-phases %standard-phases |
| 1907 | (add-after 'unpack 'link-with-libBigWig |
| 1908 | (lambda* (#:key inputs #:allow-other-keys) |
| 1909 | (substitute* "setup.py" |
| 1910 | (("libs=\\[") "libs=[\"BigWig\", ")) |
| 1911 | #t))))) |
| 1912 | (inputs |
| 1913 | `(("libbigwig" ,libbigwig) |
| 1914 | ("zlib" ,zlib) |
| 1915 | ("curl" ,curl))) |
| 1916 | (home-page "https://github.com/dpryan79/pyBigWig") |
| 1917 | (synopsis "Access bigWig files in Python using libBigWig") |
| 1918 | (description |
| 1919 | "This package provides Python bindings to the libBigWig library for |
| 1920 | accessing bigWig files.") |
| 1921 | (license license:expat))) |
| 1922 | |
| 1923 | (define-public python2-pybigwig |
| 1924 | (package-with-python2 python-pybigwig)) |
| 1925 | |
| 1926 | (define-public python-dendropy |
| 1927 | (package |
| 1928 | (name "python-dendropy") |
| 1929 | (version "4.1.0") |
| 1930 | (source |
| 1931 | (origin |
| 1932 | (method url-fetch) |
| 1933 | (uri (pypi-uri "DendroPy" version)) |
| 1934 | (sha256 |
| 1935 | (base32 |
| 1936 | "1jfz7gp18wph311w1yygbvjanb3n5mdqal439bb6myw41dwb5m63")) |
| 1937 | ;; There are two known test failures that will be fixed in the next |
| 1938 | ;; release after 4.1.0. |
| 1939 | ;; https://github.com/jeetsukumaran/DendroPy/issues/48 |
| 1940 | (patches (search-patches |
| 1941 | "python-dendropy-exclude-failing-tests.patch")))) |
| 1942 | (build-system python-build-system) |
| 1943 | (home-page "http://packages.python.org/DendroPy/") |
| 1944 | (synopsis "Library for phylogenetics and phylogenetic computing") |
| 1945 | (description |
| 1946 | "DendroPy is a library for phylogenetics and phylogenetic computing: reading, |
| 1947 | writing, simulation, processing and manipulation of phylogenetic |
| 1948 | trees (phylogenies) and characters.") |
| 1949 | (license license:bsd-3) |
| 1950 | (properties `((python2-variant . ,(delay python2-dendropy)))))) |
| 1951 | |
| 1952 | (define-public python2-dendropy |
| 1953 | (let ((base (package-with-python2 (strip-python2-variant python-dendropy)))) |
| 1954 | (package |
| 1955 | (inherit base) |
| 1956 | ;; Do not use same source as 'python-dendropy' because the patched |
| 1957 | ;; failing tests do not occur on Python 2. |
| 1958 | (source |
| 1959 | (origin |
| 1960 | (method url-fetch) |
| 1961 | (uri (pypi-uri "DendroPy" (package-version base))) |
| 1962 | (sha256 |
| 1963 | (base32 |
| 1964 | "1jfz7gp18wph311w1yygbvjanb3n5mdqal439bb6myw41dwb5m63")))) |
| 1965 | (arguments |
| 1966 | `(#:python ,python-2 |
| 1967 | #:phases |
| 1968 | (modify-phases %standard-phases |
| 1969 | (replace 'check |
| 1970 | ;; There is currently a test failure that only happens on some |
| 1971 | ;; systems, and only using "setup.py test" |
| 1972 | (lambda _ (zero? (system* "nosetests"))))))) |
| 1973 | (native-inputs `(("python2-nose" ,python2-nose) |
| 1974 | ,@(package-native-inputs base)))))) |
| 1975 | |
| 1976 | |
| 1977 | (define-public deeptools |
| 1978 | (package |
| 1979 | (name "deeptools") |
| 1980 | (version "2.1.1") |
| 1981 | (source (origin |
| 1982 | (method url-fetch) |
| 1983 | (uri (string-append "https://github.com/fidelram/deepTools/" |
| 1984 | "archive/" version ".tar.gz")) |
| 1985 | (file-name (string-append name "-" version ".tar.gz")) |
| 1986 | (sha256 |
| 1987 | (base32 |
| 1988 | "1nmfin0zjdby3vay3r4flvz94dr6qjhj41ax4yz3vx13j6wz8izd")))) |
| 1989 | (build-system python-build-system) |
| 1990 | (arguments |
| 1991 | `(#:python ,python-2)) |
| 1992 | (inputs |
| 1993 | `(("python-scipy" ,python2-scipy) |
| 1994 | ("python-numpy" ,python2-numpy) |
| 1995 | ("python-numpydoc" ,python2-numpydoc) |
| 1996 | ("python-matplotlib" ,python2-matplotlib) |
| 1997 | ("python-bx-python" ,python2-bx-python) |
| 1998 | ("python-pysam" ,python2-pysam) |
| 1999 | ("python-pybigwig" ,python2-pybigwig))) |
| 2000 | (native-inputs |
| 2001 | `(("python-mock" ,python2-mock) ;for tests |
| 2002 | ("python-pytz" ,python2-pytz))) ;for tests |
| 2003 | (home-page "https://github.com/fidelram/deepTools") |
| 2004 | (synopsis "Tools for normalizing and visualizing deep-sequencing data") |
| 2005 | (description |
| 2006 | "DeepTools addresses the challenge of handling the large amounts of data |
| 2007 | that are now routinely generated from DNA sequencing centers. To do so, |
| 2008 | deepTools contains useful modules to process the mapped reads data to create |
| 2009 | coverage files in standard bedGraph and bigWig file formats. By doing so, |
| 2010 | deepTools allows the creation of normalized coverage files or the comparison |
| 2011 | between two files (for example, treatment and control). Finally, using such |
| 2012 | normalized and standardized files, multiple visualizations can be created to |
| 2013 | identify enrichments with functional annotations of the genome.") |
| 2014 | (license license:gpl3+))) |
| 2015 | |
| 2016 | (define-public diamond |
| 2017 | (package |
| 2018 | (name "diamond") |
| 2019 | (version "0.8.27") |
| 2020 | (source (origin |
| 2021 | (method url-fetch) |
| 2022 | (uri (string-append |
| 2023 | "https://github.com/bbuchfink/diamond/archive/v" |
| 2024 | version ".tar.gz")) |
| 2025 | (file-name (string-append name "-" version ".tar.gz")) |
| 2026 | (sha256 |
| 2027 | (base32 |
| 2028 | "0g0zdyfnri9v7nfbh8f7zqs4af1xydqkiw8m0cx4jc2ql4chpf6a")))) |
| 2029 | (build-system cmake-build-system) |
| 2030 | (arguments |
| 2031 | '(#:tests? #f ; no "check" target |
| 2032 | #:phases |
| 2033 | (modify-phases %standard-phases |
| 2034 | (add-after 'unpack 'remove-native-compilation |
| 2035 | (lambda _ |
| 2036 | (substitute* "CMakeLists.txt" (("-march=native") "")) |
| 2037 | #t))))) |
| 2038 | (inputs |
| 2039 | `(("zlib" ,zlib))) |
| 2040 | (home-page "https://github.com/bbuchfink/diamond") |
| 2041 | (synopsis "Accelerated BLAST compatible local sequence aligner") |
| 2042 | (description |
| 2043 | "DIAMOND is a BLAST-compatible local aligner for mapping protein and |
| 2044 | translated DNA query sequences against a protein reference database (BLASTP |
| 2045 | and BLASTX alignment mode). The speedup over BLAST is up to 20,000 on short |
| 2046 | reads at a typical sensitivity of 90-99% relative to BLAST depending on the |
| 2047 | data and settings.") |
| 2048 | ;; diamond fails to build on other platforms |
| 2049 | ;; https://github.com/bbuchfink/diamond/issues/18 |
| 2050 | (supported-systems '("x86_64-linux")) |
| 2051 | (license (license:non-copyleft "file://src/COPYING" |
| 2052 | "See src/COPYING in the distribution.")))) |
| 2053 | |
| 2054 | (define-public discrover |
| 2055 | (package |
| 2056 | (name "discrover") |
| 2057 | (version "1.6.0") |
| 2058 | (source |
| 2059 | (origin |
| 2060 | (method url-fetch) |
| 2061 | (uri (string-append "https://github.com/maaskola/discrover/archive/" |
| 2062 | version ".tar.gz")) |
| 2063 | (file-name (string-append name "-" version ".tar.gz")) |
| 2064 | (sha256 |
| 2065 | (base32 |
| 2066 | "0rah9ja4m0rl5mldd6vag9rwrivw1zrqxssfq8qx64m7961fp68k")))) |
| 2067 | (build-system cmake-build-system) |
| 2068 | (arguments `(#:tests? #f)) ; there are no tests |
| 2069 | (inputs |
| 2070 | `(("boost" ,boost) |
| 2071 | ("cairo" ,cairo))) |
| 2072 | (native-inputs |
| 2073 | `(("texlive" ,texlive) |
| 2074 | ("imagemagick" ,imagemagick))) |
| 2075 | (home-page "http://dorina.mdc-berlin.de/public/rajewsky/discrover/") |
| 2076 | (synopsis "Discover discriminative nucleotide sequence motifs") |
| 2077 | (description "Discrover is a motif discovery method to find binding sites |
| 2078 | of nucleic acid binding proteins.") |
| 2079 | (license license:gpl3+))) |
| 2080 | |
| 2081 | (define-public eigensoft |
| 2082 | (let ((revision "1") |
| 2083 | (commit "b14d1e202e21e532536ff8004f0419cd5e259dc7")) |
| 2084 | (package |
| 2085 | (name "eigensoft") |
| 2086 | (version (string-append "6.1.2-" |
| 2087 | revision "." |
| 2088 | (string-take commit 9))) |
| 2089 | (source |
| 2090 | (origin |
| 2091 | (method git-fetch) |
| 2092 | (uri (git-reference |
| 2093 | (url "https://github.com/DReichLab/EIG.git") |
| 2094 | (commit commit))) |
| 2095 | (file-name (string-append "eigensoft-" commit "-checkout")) |
| 2096 | (sha256 |
| 2097 | (base32 |
| 2098 | "0f5m6k2j5c16xc3xbywcs989xyc26ncy1zfzp9j9n55n9r4xcaiq")) |
| 2099 | (modules '((guix build utils))) |
| 2100 | ;; Remove pre-built binaries. |
| 2101 | (snippet '(begin |
| 2102 | (delete-file-recursively "bin") |
| 2103 | (mkdir "bin") |
| 2104 | #t)))) |
| 2105 | (build-system gnu-build-system) |
| 2106 | (arguments |
| 2107 | `(#:tests? #f ; There are no tests. |
| 2108 | #:make-flags '("CC=gcc") |
| 2109 | #:phases |
| 2110 | (modify-phases %standard-phases |
| 2111 | ;; There is no configure phase, but the Makefile is in a |
| 2112 | ;; sub-directory. |
| 2113 | (replace 'configure |
| 2114 | (lambda _ |
| 2115 | (chdir "src") |
| 2116 | ;; The link flags are incomplete. |
| 2117 | (substitute* "Makefile" |
| 2118 | (("-lgsl") "-lgsl -lm -llapack -llapacke -lpthread")) |
| 2119 | #t)) |
| 2120 | ;; The provided install target only copies executables to |
| 2121 | ;; the "bin" directory in the build root. |
| 2122 | (add-after 'install 'actually-install |
| 2123 | (lambda* (#:key outputs #:allow-other-keys) |
| 2124 | (let* ((out (assoc-ref outputs "out")) |
| 2125 | (bin (string-append out "/bin"))) |
| 2126 | (for-each (lambda (file) |
| 2127 | (install-file file bin)) |
| 2128 | (find-files "../bin" ".*")) |
| 2129 | #t)))))) |
| 2130 | (inputs |
| 2131 | `(("gsl" ,gsl) |
| 2132 | ("lapack" ,lapack) |
| 2133 | ("openblas" ,openblas) |
| 2134 | ("perl" ,perl) |
| 2135 | ("gfortran" ,gfortran "lib"))) |
| 2136 | (home-page "https://github.com/DReichLab/EIG") |
| 2137 | (synopsis "Tools for population genetics") |
| 2138 | (description "The EIGENSOFT package provides tools for population |
| 2139 | genetics and stratification correction. EIGENSOFT implements methods commonly |
| 2140 | used in population genetics analyses such as PCA, computation of Tracy-Widom |
| 2141 | statistics, and finding related individuals in structured populations. It |
| 2142 | comes with a built-in plotting script and supports multiple file formats and |
| 2143 | quantitative phenotypes.") |
| 2144 | ;; The license of the eigensoft tools is Expat, but since it's |
| 2145 | ;; linking with the GNU Scientific Library (GSL) the effective |
| 2146 | ;; license is the GPL. |
| 2147 | (license license:gpl3+)))) |
| 2148 | |
| 2149 | (define-public edirect |
| 2150 | (package |
| 2151 | (name "edirect") |
| 2152 | (version "4.10") |
| 2153 | (source (origin |
| 2154 | (method url-fetch) |
| 2155 | (uri (string-append "ftp://ftp.ncbi.nlm.nih.gov/entrez/entrezdirect/" |
| 2156 | "versions/2016-05-03/edirect.tar.gz")) |
| 2157 | (sha256 |
| 2158 | (base32 |
| 2159 | "15zsprak5yh8c1yrz4r1knmb5s8qcmdid4xdhkh3lqcv64l60hli")))) |
| 2160 | (build-system perl-build-system) |
| 2161 | (arguments |
| 2162 | `(#:tests? #f ;no "check" target |
| 2163 | #:phases |
| 2164 | (modify-phases %standard-phases |
| 2165 | (delete 'configure) |
| 2166 | (delete 'build) |
| 2167 | (replace 'install |
| 2168 | (lambda* (#:key outputs #:allow-other-keys) |
| 2169 | (let ((target (string-append (assoc-ref outputs "out") |
| 2170 | "/bin"))) |
| 2171 | (mkdir-p target) |
| 2172 | (copy-file "edirect.pl" |
| 2173 | (string-append target "/edirect.pl")) |
| 2174 | #t))) |
| 2175 | (add-after |
| 2176 | 'install 'wrap-program |
| 2177 | (lambda* (#:key inputs outputs #:allow-other-keys) |
| 2178 | ;; Make sure 'edirect.pl' finds all perl inputs at runtime. |
| 2179 | (let* ((out (assoc-ref outputs "out")) |
| 2180 | (path (getenv "PERL5LIB"))) |
| 2181 | (wrap-program (string-append out "/bin/edirect.pl") |
| 2182 | `("PERL5LIB" ":" prefix (,path))))))))) |
| 2183 | (inputs |
| 2184 | `(("perl-html-parser" ,perl-html-parser) |
| 2185 | ("perl-encode-locale" ,perl-encode-locale) |
| 2186 | ("perl-file-listing" ,perl-file-listing) |
| 2187 | ("perl-html-tagset" ,perl-html-tagset) |
| 2188 | ("perl-html-tree" ,perl-html-tree) |
| 2189 | ("perl-http-cookies" ,perl-http-cookies) |
| 2190 | ("perl-http-date" ,perl-http-date) |
| 2191 | ("perl-http-message" ,perl-http-message) |
| 2192 | ("perl-http-negotiate" ,perl-http-negotiate) |
| 2193 | ("perl-lwp-mediatypes" ,perl-lwp-mediatypes) |
| 2194 | ("perl-lwp-protocol-https" ,perl-lwp-protocol-https) |
| 2195 | ("perl-net-http" ,perl-net-http) |
| 2196 | ("perl-uri" ,perl-uri) |
| 2197 | ("perl-www-robotrules" ,perl-www-robotrules) |
| 2198 | ("perl" ,perl))) |
| 2199 | (home-page "http://www.ncbi.nlm.nih.gov/books/NBK179288/") |
| 2200 | (synopsis "Tools for accessing the NCBI's set of databases") |
| 2201 | (description |
| 2202 | "Entrez Direct (EDirect) is a method for accessing the National Center |
| 2203 | for Biotechnology Information's (NCBI) set of interconnected |
| 2204 | databases (publication, sequence, structure, gene, variation, expression, |
| 2205 | etc.) from a terminal. Functions take search terms from command-line |
| 2206 | arguments. Individual operations are combined to build multi-step queries. |
| 2207 | Record retrieval and formatting normally complete the process. |
| 2208 | |
| 2209 | EDirect also provides an argument-driven function that simplifies the |
| 2210 | extraction of data from document summaries or other results that are returned |
| 2211 | in structured XML format. This can eliminate the need for writing custom |
| 2212 | software to answer ad hoc questions.") |
| 2213 | (license license:public-domain))) |
| 2214 | |
| 2215 | (define-public exonerate |
| 2216 | (package |
| 2217 | (name "exonerate") |
| 2218 | (version "2.4.0") |
| 2219 | (source |
| 2220 | (origin |
| 2221 | (method url-fetch) |
| 2222 | (uri |
| 2223 | (string-append |
| 2224 | "http://ftp.ebi.ac.uk/pub/software/vertebrategenomics/exonerate/" |
| 2225 | "exonerate-" version ".tar.gz")) |
| 2226 | (sha256 |
| 2227 | (base32 |
| 2228 | "0hj0m9xygiqsdxvbg79wq579kbrx1mdrabi2bzqz2zn9qwfjcjgq")))) |
| 2229 | (build-system gnu-build-system) |
| 2230 | (arguments |
| 2231 | `(#:parallel-build? #f)) ; Building in parallel fails on some machines. |
| 2232 | (native-inputs |
| 2233 | `(("pkg-config" ,pkg-config))) |
| 2234 | (inputs |
| 2235 | `(("glib" ,glib))) |
| 2236 | (home-page |
| 2237 | "https://www.ebi.ac.uk/about/vertebrate-genomics/software/exonerate") |
| 2238 | (synopsis "Generic tool for biological sequence alignment") |
| 2239 | (description |
| 2240 | "Exonerate is a generic tool for pairwise sequence comparison. It allows |
| 2241 | the alignment of sequences using a many alignment models, either exhaustive |
| 2242 | dynamic programming or a variety of heuristics.") |
| 2243 | (license license:gpl3))) |
| 2244 | |
| 2245 | (define-public express |
| 2246 | (package |
| 2247 | (name "express") |
| 2248 | (version "1.5.1") |
| 2249 | (source (origin |
| 2250 | (method url-fetch) |
| 2251 | (uri |
| 2252 | (string-append |
| 2253 | "http://bio.math.berkeley.edu/eXpress/downloads/express-" |
| 2254 | version "/express-" version "-src.tgz")) |
| 2255 | (sha256 |
| 2256 | (base32 |
| 2257 | "03rczxd0gjp2l1jxcmjfmf5j94j77zqyxa6x063zsc585nj40n0c")))) |
| 2258 | (build-system cmake-build-system) |
| 2259 | (arguments |
| 2260 | `(#:tests? #f ;no "check" target |
| 2261 | #:phases |
| 2262 | (alist-cons-after |
| 2263 | 'unpack 'use-shared-boost-libs-and-set-bamtools-paths |
| 2264 | (lambda* (#:key inputs #:allow-other-keys) |
| 2265 | (substitute* "CMakeLists.txt" |
| 2266 | (("set\\(Boost_USE_STATIC_LIBS ON\\)") |
| 2267 | "set(Boost_USE_STATIC_LIBS OFF)") |
| 2268 | (("\\$\\{CMAKE_CURRENT_SOURCE_DIR\\}/bamtools/include") |
| 2269 | (string-append (assoc-ref inputs "bamtools") "/include/bamtools"))) |
| 2270 | (substitute* "src/CMakeLists.txt" |
| 2271 | (("\\$\\{CMAKE_CURRENT_SOURCE_DIR\\}/\\.\\./bamtools/lib") |
| 2272 | (string-append (assoc-ref inputs "bamtools") "/lib/bamtools"))) |
| 2273 | #t) |
| 2274 | %standard-phases))) |
| 2275 | (inputs |
| 2276 | `(("boost" ,boost) |
| 2277 | ("bamtools" ,bamtools) |
| 2278 | ("protobuf" ,protobuf) |
| 2279 | ("zlib" ,zlib))) |
| 2280 | (home-page "http://bio.math.berkeley.edu/eXpress") |
| 2281 | (synopsis "Streaming quantification for high-throughput genomic sequencing") |
| 2282 | (description |
| 2283 | "eXpress is a streaming tool for quantifying the abundances of a set of |
| 2284 | target sequences from sampled subsequences. Example applications include |
| 2285 | transcript-level RNA-Seq quantification, allele-specific/haplotype expression |
| 2286 | analysis (from RNA-Seq), transcription factor binding quantification in |
| 2287 | ChIP-Seq, and analysis of metagenomic data.") |
| 2288 | (license license:artistic2.0))) |
| 2289 | |
| 2290 | (define-public express-beta-diversity |
| 2291 | (package |
| 2292 | (name "express-beta-diversity") |
| 2293 | (version "1.0.7") |
| 2294 | (source (origin |
| 2295 | (method url-fetch) |
| 2296 | (uri |
| 2297 | (string-append |
| 2298 | "https://github.com/dparks1134/ExpressBetaDiversity/archive/v" |
| 2299 | version ".tar.gz")) |
| 2300 | (file-name (string-append name "-" version ".tar.gz")) |
| 2301 | (sha256 |
| 2302 | (base32 |
| 2303 | "1djvdlmqvjf6h0zq7w36y8cl5cli6rgj86x65znl48agnwmzxfxr")))) |
| 2304 | (build-system gnu-build-system) |
| 2305 | (arguments |
| 2306 | `(#:phases |
| 2307 | (modify-phases %standard-phases |
| 2308 | (delete 'configure) |
| 2309 | (add-before 'build 'enter-source (lambda _ (chdir "source") #t)) |
| 2310 | (replace 'check |
| 2311 | (lambda _ (zero? (system* "../bin/ExpressBetaDiversity" |
| 2312 | "-u")))) |
| 2313 | (add-after 'check 'exit-source (lambda _ (chdir "..") #t)) |
| 2314 | (replace 'install |
| 2315 | (lambda* (#:key outputs #:allow-other-keys) |
| 2316 | (let ((bin (string-append (assoc-ref outputs "out") |
| 2317 | "/bin"))) |
| 2318 | (mkdir-p bin) |
| 2319 | (copy-file "scripts/convertToEBD.py" |
| 2320 | (string-append bin "/convertToEBD.py")) |
| 2321 | (copy-file "bin/ExpressBetaDiversity" |
| 2322 | (string-append bin "/ExpressBetaDiversity")) |
| 2323 | #t)))))) |
| 2324 | (inputs |
| 2325 | `(("python" ,python-2))) |
| 2326 | (home-page "http://kiwi.cs.dal.ca/Software/ExpressBetaDiversity") |
| 2327 | (synopsis "Taxon- and phylogenetic-based beta diversity measures") |
| 2328 | (description |
| 2329 | "Express Beta Diversity (EBD) calculates ecological beta diversity |
| 2330 | (dissimilarity) measures between biological communities. EBD implements a |
| 2331 | variety of diversity measures including those that make use of phylogenetic |
| 2332 | similarity of community members.") |
| 2333 | (license license:gpl3+))) |
| 2334 | |
| 2335 | (define-public fasttree |
| 2336 | (package |
| 2337 | (name "fasttree") |
| 2338 | (version "2.1.9") |
| 2339 | (source (origin |
| 2340 | (method url-fetch) |
| 2341 | (uri (string-append |
| 2342 | "http://www.microbesonline.org/fasttree/FastTree-" |
| 2343 | version ".c")) |
| 2344 | (sha256 |
| 2345 | (base32 |
| 2346 | "0ljvvw8i1als1wbfzvrf15c3ii2vw9db20a259g6pzg34xyyb97k")))) |
| 2347 | (build-system gnu-build-system) |
| 2348 | (arguments |
| 2349 | `(#:tests? #f ; no "check" target |
| 2350 | #:phases |
| 2351 | (modify-phases %standard-phases |
| 2352 | (delete 'unpack) |
| 2353 | (delete 'configure) |
| 2354 | (replace 'build |
| 2355 | (lambda* (#:key source #:allow-other-keys) |
| 2356 | (and (zero? (system* "gcc" |
| 2357 | "-O3" |
| 2358 | "-finline-functions" |
| 2359 | "-funroll-loops" |
| 2360 | "-Wall" |
| 2361 | "-o" |
| 2362 | "FastTree" |
| 2363 | source |
| 2364 | "-lm")) |
| 2365 | (zero? (system* "gcc" |
| 2366 | "-DOPENMP" |
| 2367 | "-fopenmp" |
| 2368 | "-O3" |
| 2369 | "-finline-functions" |
| 2370 | "-funroll-loops" |
| 2371 | "-Wall" |
| 2372 | "-o" |
| 2373 | "FastTreeMP" |
| 2374 | source |
| 2375 | "-lm"))))) |
| 2376 | (replace 'install |
| 2377 | (lambda* (#:key outputs #:allow-other-keys) |
| 2378 | (let ((bin (string-append (assoc-ref outputs "out") |
| 2379 | "/bin"))) |
| 2380 | (mkdir-p bin) |
| 2381 | (copy-file "FastTree" |
| 2382 | (string-append bin "/FastTree")) |
| 2383 | (copy-file "FastTreeMP" |
| 2384 | (string-append bin "/FastTreeMP")) |
| 2385 | #t)))))) |
| 2386 | (home-page "http://www.microbesonline.org/fasttree") |
| 2387 | (synopsis "Infers approximately-maximum-likelihood phylogenetic trees") |
| 2388 | (description |
| 2389 | "FastTree can handle alignments with up to a million of sequences in a |
| 2390 | reasonable amount of time and memory. For large alignments, FastTree is |
| 2391 | 100-1,000 times faster than PhyML 3.0 or RAxML 7.") |
| 2392 | (license license:gpl2+))) |
| 2393 | |
| 2394 | (define-public fastx-toolkit |
| 2395 | (package |
| 2396 | (name "fastx-toolkit") |
| 2397 | (version "0.0.14") |
| 2398 | (source (origin |
| 2399 | (method url-fetch) |
| 2400 | (uri |
| 2401 | (string-append |
| 2402 | "https://github.com/agordon/fastx_toolkit/releases/download/" |
| 2403 | version "/fastx_toolkit-" version ".tar.bz2")) |
| 2404 | (sha256 |
| 2405 | (base32 |
| 2406 | "01jqzw386873sr0pjp1wr4rn8fsga2vxs1qfmicvx1pjr72007wy")))) |
| 2407 | (build-system gnu-build-system) |
| 2408 | (inputs |
| 2409 | `(("libgtextutils" ,libgtextutils))) |
| 2410 | (native-inputs |
| 2411 | `(("pkg-config" ,pkg-config))) |
| 2412 | (home-page "http://hannonlab.cshl.edu/fastx_toolkit/") |
| 2413 | (synopsis "Tools for FASTA/FASTQ file preprocessing") |
| 2414 | (description |
| 2415 | "The FASTX-Toolkit is a collection of command line tools for Short-Reads |
| 2416 | FASTA/FASTQ files preprocessing. |
| 2417 | |
| 2418 | Next-Generation sequencing machines usually produce FASTA or FASTQ files, |
| 2419 | containing multiple short-reads sequences. The main processing of such |
| 2420 | FASTA/FASTQ files is mapping the sequences to reference genomes. However, it |
| 2421 | is sometimes more productive to preprocess the files before mapping the |
| 2422 | sequences to the genome---manipulating the sequences to produce better mapping |
| 2423 | results. The FASTX-Toolkit tools perform some of these preprocessing tasks.") |
| 2424 | (license license:agpl3+))) |
| 2425 | |
| 2426 | (define-public flexbar |
| 2427 | (package |
| 2428 | (name "flexbar") |
| 2429 | (version "2.5") |
| 2430 | (source (origin |
| 2431 | (method url-fetch) |
| 2432 | (uri |
| 2433 | (string-append "mirror://sourceforge/flexbar/" |
| 2434 | version "/flexbar_v" version "_src.tgz")) |
| 2435 | (sha256 |
| 2436 | (base32 |
| 2437 | "13jaykc3y1x8y5nn9j8ljnb79s5y51kyxz46hdmvvjj6qhyympmf")))) |
| 2438 | (build-system cmake-build-system) |
| 2439 | (arguments |
| 2440 | `(#:configure-flags (list |
| 2441 | (string-append "-DFLEXBAR_BINARY_DIR=" |
| 2442 | (assoc-ref %outputs "out") |
| 2443 | "/bin/")) |
| 2444 | #:phases |
| 2445 | (alist-replace |
| 2446 | 'check |
| 2447 | (lambda* (#:key outputs #:allow-other-keys) |
| 2448 | (setenv "PATH" (string-append |
| 2449 | (assoc-ref outputs "out") "/bin:" |
| 2450 | (getenv "PATH"))) |
| 2451 | (chdir "../flexbar_v2.5_src/test") |
| 2452 | (zero? (system* "bash" "flexbar_validate.sh"))) |
| 2453 | (alist-delete 'install %standard-phases)))) |
| 2454 | (inputs |
| 2455 | `(("tbb" ,tbb) |
| 2456 | ("zlib" ,zlib))) |
| 2457 | (native-inputs |
| 2458 | `(("pkg-config" ,pkg-config) |
| 2459 | ("seqan" ,seqan))) |
| 2460 | (home-page "http://flexbar.sourceforge.net") |
| 2461 | (synopsis "Barcode and adapter removal tool for sequencing platforms") |
| 2462 | (description |
| 2463 | "Flexbar preprocesses high-throughput nucleotide sequencing data |
| 2464 | efficiently. It demultiplexes barcoded runs and removes adapter sequences. |
| 2465 | Moreover, trimming and filtering features are provided. Flexbar increases |
| 2466 | read mapping rates and improves genome and transcriptome assemblies. It |
| 2467 | supports next-generation sequencing data in fasta/q and csfasta/q format from |
| 2468 | Illumina, Roche 454, and the SOLiD platform.") |
| 2469 | (license license:gpl3))) |
| 2470 | |
| 2471 | (define-public fraggenescan |
| 2472 | (package |
| 2473 | (name "fraggenescan") |
| 2474 | (version "1.20") |
| 2475 | (source |
| 2476 | (origin |
| 2477 | (method url-fetch) |
| 2478 | (uri |
| 2479 | (string-append "mirror://sourceforge/fraggenescan/" |
| 2480 | "FragGeneScan" version ".tar.gz")) |
| 2481 | (sha256 |
| 2482 | (base32 "1zzigqmvqvjyqv4945kv6nc5ah2xxm1nxgrlsnbzav3f5c0n0pyj")))) |
| 2483 | (build-system gnu-build-system) |
| 2484 | (arguments |
| 2485 | `(#:phases |
| 2486 | (modify-phases %standard-phases |
| 2487 | (delete 'configure) |
| 2488 | (add-before 'build 'patch-paths |
| 2489 | (lambda* (#:key outputs #:allow-other-keys) |
| 2490 | (let* ((out (string-append (assoc-ref outputs "out"))) |
| 2491 | (share (string-append out "/share/fraggenescan/"))) |
| 2492 | (substitute* "run_FragGeneScan.pl" |
| 2493 | (("system\\(\"rm") |
| 2494 | (string-append "system(\"" (which "rm"))) |
| 2495 | (("system\\(\"mv") |
| 2496 | (string-append "system(\"" (which "mv"))) |
| 2497 | ;; This script and other programs expect the training files |
| 2498 | ;; to be in the non-standard location bin/train/XXX. Change |
| 2499 | ;; this to be share/fraggenescan/train/XXX instead. |
| 2500 | (("^\\$train.file = \\$dir.*") |
| 2501 | (string-append "$train_file = \"" |
| 2502 | share |
| 2503 | "train/\".$FGS_train_file;"))) |
| 2504 | (substitute* "run_hmm.c" |
| 2505 | (("^ strcat\\(train_dir, \\\"train/\\\"\\);") |
| 2506 | (string-append " strcpy(train_dir, \"" share "/train/\");"))) |
| 2507 | (substitute* "post_process.pl" |
| 2508 | (("^my \\$dir = substr.*") |
| 2509 | (string-append "my $dir = \"" share "\";")))) |
| 2510 | #t)) |
| 2511 | (replace 'build |
| 2512 | (lambda _ (and (zero? (system* "make" "clean")) |
| 2513 | (zero? (system* "make" "fgs"))))) |
| 2514 | (replace 'install |
| 2515 | (lambda* (#:key outputs #:allow-other-keys) |
| 2516 | (let* ((out (string-append (assoc-ref outputs "out"))) |
| 2517 | (bin (string-append out "/bin/")) |
| 2518 | (share (string-append out "/share/fraggenescan/train"))) |
| 2519 | (install-file "run_FragGeneScan.pl" bin) |
| 2520 | (install-file "FragGeneScan" bin) |
| 2521 | (install-file "FGS_gff.py" bin) |
| 2522 | (install-file "post_process.pl" bin) |
| 2523 | (copy-recursively "train" share)))) |
| 2524 | (delete 'check) |
| 2525 | (add-after 'install 'post-install-check |
| 2526 | ;; In lieu of 'make check', run one of the examples and check the |
| 2527 | ;; output files gets created. |
| 2528 | (lambda* (#:key outputs #:allow-other-keys) |
| 2529 | (let* ((out (string-append (assoc-ref outputs "out"))) |
| 2530 | (bin (string-append out "/bin/"))) |
| 2531 | (and (zero? (system* (string-append bin "run_FragGeneScan.pl") |
| 2532 | "-genome=./example/NC_000913.fna" |
| 2533 | "-out=./test2" |
| 2534 | "-complete=1" |
| 2535 | "-train=complete")) |
| 2536 | (file-exists? "test2.faa") |
| 2537 | (file-exists? "test2.ffn") |
| 2538 | (file-exists? "test2.gff") |
| 2539 | (file-exists? "test2.out")))))))) |
| 2540 | (inputs |
| 2541 | `(("perl" ,perl) |
| 2542 | ("python" ,python-2))) ;not compatible with python 3. |
| 2543 | (home-page "https://sourceforge.net/projects/fraggenescan/") |
| 2544 | (synopsis "Finds potentially fragmented genes in short reads") |
| 2545 | (description |
| 2546 | "FragGeneScan is a program for predicting bacterial and archaeal genes in |
| 2547 | short and error-prone DNA sequencing reads. It can also be applied to predict |
| 2548 | genes in incomplete assemblies or complete genomes.") |
| 2549 | ;; GPL3+ according to private correspondense with the authors. |
| 2550 | (license license:gpl3+))) |
| 2551 | |
| 2552 | (define-public fxtract |
| 2553 | (let ((util-commit "776ca85a18a47492af3794745efcb4a905113115")) |
| 2554 | (package |
| 2555 | (name "fxtract") |
| 2556 | (version "2.3") |
| 2557 | (source |
| 2558 | (origin |
| 2559 | (method url-fetch) |
| 2560 | (uri (string-append |
| 2561 | "https://github.com/ctSkennerton/fxtract/archive/" |
| 2562 | version ".tar.gz")) |
| 2563 | (file-name (string-append "ctstennerton-util-" |
| 2564 | (string-take util-commit 7) |
| 2565 | "-checkout")) |
| 2566 | (sha256 |
| 2567 | (base32 |
| 2568 | "0275cfdhis8517hm01is62062swmi06fxzifq7mr3knbbxjlaiwj")))) |
| 2569 | (build-system gnu-build-system) |
| 2570 | (arguments |
| 2571 | `(#:make-flags (list |
| 2572 | (string-append "PREFIX=" (assoc-ref %outputs "out")) |
| 2573 | "CC=gcc") |
| 2574 | #:test-target "fxtract_test" |
| 2575 | #:phases |
| 2576 | (modify-phases %standard-phases |
| 2577 | (delete 'configure) |
| 2578 | (add-before 'build 'copy-util |
| 2579 | (lambda* (#:key inputs #:allow-other-keys) |
| 2580 | (rmdir "util") |
| 2581 | (copy-recursively (assoc-ref inputs "ctskennerton-util") "util") |
| 2582 | #t)) |
| 2583 | ;; Do not use make install as this requires additional dependencies. |
| 2584 | (replace 'install |
| 2585 | (lambda* (#:key outputs #:allow-other-keys) |
| 2586 | (let* ((out (assoc-ref outputs "out")) |
| 2587 | (bin (string-append out"/bin"))) |
| 2588 | (install-file "fxtract" bin) |
| 2589 | #t)))))) |
| 2590 | (inputs |
| 2591 | `(("pcre" ,pcre) |
| 2592 | ("zlib" ,zlib))) |
| 2593 | (native-inputs |
| 2594 | ;; ctskennerton-util is licensed under GPL2. |
| 2595 | `(("ctskennerton-util" |
| 2596 | ,(origin |
| 2597 | (method git-fetch) |
| 2598 | (uri (git-reference |
| 2599 | (url "https://github.com/ctSkennerton/util.git") |
| 2600 | (commit util-commit))) |
| 2601 | (file-name (string-append |
| 2602 | "ctstennerton-util-" util-commit "-checkout")) |
| 2603 | (sha256 |
| 2604 | (base32 |
| 2605 | "0cls1hd4vgj3f36fpzzg4xc77d6f3hpc60cbpfmn2gdr7ykzzad7")))))) |
| 2606 | (home-page "https://github.com/ctSkennerton/fxtract") |
| 2607 | (synopsis "Extract sequences from FASTA and FASTQ files") |
| 2608 | (description |
| 2609 | "Fxtract extracts sequences from a protein or nucleotide fastx (FASTA |
| 2610 | or FASTQ) file given a subsequence. It uses a simple substring search for |
| 2611 | basic tasks but can change to using POSIX regular expressions, PCRE, hash |
| 2612 | lookups or multi-pattern searching as required. By default fxtract looks in |
| 2613 | the sequence of each record but can also be told to look in the header, |
| 2614 | comment or quality sections.") |
| 2615 | ;; 'util' requires SSE instructions. |
| 2616 | (supported-systems '("x86_64-linux")) |
| 2617 | (license license:expat)))) |
| 2618 | |
| 2619 | (define-public grit |
| 2620 | (package |
| 2621 | (name "grit") |
| 2622 | (version "2.0.2") |
| 2623 | (source (origin |
| 2624 | (method url-fetch) |
| 2625 | (uri (string-append |
| 2626 | "https://github.com/nboley/grit/archive/" |
| 2627 | version ".tar.gz")) |
| 2628 | (file-name (string-append name "-" version ".tar.gz")) |
| 2629 | (sha256 |
| 2630 | (base32 |
| 2631 | "157in84dj70wimbind3x7sy1whs3h57qfgcnj2s6lrd38fbrb7mj")))) |
| 2632 | (build-system python-build-system) |
| 2633 | (arguments |
| 2634 | `(#:python ,python-2 |
| 2635 | #:phases |
| 2636 | (alist-cons-after |
| 2637 | 'unpack 'generate-from-cython-sources |
| 2638 | (lambda* (#:key inputs outputs #:allow-other-keys) |
| 2639 | ;; Delete these C files to force fresh generation from pyx sources. |
| 2640 | (delete-file "grit/sparsify_support_fns.c") |
| 2641 | (delete-file "grit/call_peaks_support_fns.c") |
| 2642 | (substitute* "setup.py" |
| 2643 | (("Cython.Setup") "Cython.Build") |
| 2644 | ;; Add numpy include path to fix compilation |
| 2645 | (("pyx\", \\]") |
| 2646 | (string-append "pyx\", ], include_dirs = ['" |
| 2647 | (assoc-ref inputs "python-numpy") |
| 2648 | "/lib/python2.7/site-packages/numpy/core/include/" |
| 2649 | "']"))) #t) |
| 2650 | %standard-phases))) |
| 2651 | (inputs |
| 2652 | `(("python-scipy" ,python2-scipy) |
| 2653 | ("python-numpy" ,python2-numpy) |
| 2654 | ("python-pysam" ,python2-pysam) |
| 2655 | ("python-networkx" ,python2-networkx))) |
| 2656 | (native-inputs |
| 2657 | `(("python-cython" ,python2-cython))) |
| 2658 | (home-page "http://grit-bio.org") |
| 2659 | (synopsis "Tool for integrative analysis of RNA-seq type assays") |
| 2660 | (description |
| 2661 | "GRIT is designed to use RNA-seq, TES, and TSS data to build and quantify |
| 2662 | full length transcript models. When none of these data sources are available, |
| 2663 | GRIT can be run by providing a candidate set of TES or TSS sites. In |
| 2664 | addition, GRIT can merge in reference junctions and gene boundaries. GRIT can |
| 2665 | also be run in quantification mode, where it uses a provided GTF file and just |
| 2666 | estimates transcript expression.") |
| 2667 | (license license:gpl3+))) |
| 2668 | |
| 2669 | (define-public hisat |
| 2670 | (package |
| 2671 | (name "hisat") |
| 2672 | (version "0.1.4") |
| 2673 | (source (origin |
| 2674 | (method url-fetch) |
| 2675 | (uri (string-append |
| 2676 | "http://ccb.jhu.edu/software/hisat/downloads/hisat-" |
| 2677 | version "-beta-source.zip")) |
| 2678 | (sha256 |
| 2679 | (base32 |
| 2680 | "1k381ydranqxp09yf2y7w1d0chz5d59vb6jchi89hbb0prq19lk5")))) |
| 2681 | (build-system gnu-build-system) |
| 2682 | (arguments |
| 2683 | `(#:tests? #f ;no check target |
| 2684 | #:make-flags '("allall" |
| 2685 | ;; Disable unsupported `popcnt' instructions on |
| 2686 | ;; architectures other than x86_64 |
| 2687 | ,@(if (string-prefix? "x86_64" |
| 2688 | (or (%current-target-system) |
| 2689 | (%current-system))) |
| 2690 | '() |
| 2691 | '("POPCNT_CAPABILITY=0"))) |
| 2692 | #:phases |
| 2693 | (alist-cons-after |
| 2694 | 'unpack 'patch-sources |
| 2695 | (lambda _ |
| 2696 | ;; XXX Cannot use snippet because zip files are not supported |
| 2697 | (substitute* "Makefile" |
| 2698 | (("^CC = .*$") "CC = gcc") |
| 2699 | (("^CPP = .*$") "CPP = g++") |
| 2700 | ;; replace BUILD_HOST and BUILD_TIME for deterministic build |
| 2701 | (("-DBUILD_HOST=.*") "-DBUILD_HOST=\"\\\"guix\\\"\"") |
| 2702 | (("-DBUILD_TIME=.*") "-DBUILD_TIME=\"\\\"0\\\"\"")) |
| 2703 | (substitute* '("hisat-build" "hisat-inspect") |
| 2704 | (("/usr/bin/env") (which "env")))) |
| 2705 | (alist-replace |
| 2706 | 'install |
| 2707 | (lambda* (#:key outputs #:allow-other-keys) |
| 2708 | (let ((bin (string-append (assoc-ref outputs "out") "/bin/"))) |
| 2709 | (for-each (lambda (file) |
| 2710 | (install-file file bin)) |
| 2711 | (find-files |
| 2712 | "." |
| 2713 | "hisat(-(build|align|inspect)(-(s|l)(-debug)*)*)*$")))) |
| 2714 | (alist-delete 'configure %standard-phases))))) |
| 2715 | (native-inputs |
| 2716 | `(("unzip" ,unzip))) |
| 2717 | (inputs |
| 2718 | `(("perl" ,perl) |
| 2719 | ("python" ,python) |
| 2720 | ("zlib" ,zlib))) |
| 2721 | ;; Non-portable SSE instructions are used so building fails on platforms |
| 2722 | ;; other than x86_64. |
| 2723 | (supported-systems '("x86_64-linux")) |
| 2724 | (home-page "http://ccb.jhu.edu/software/hisat/index.shtml") |
| 2725 | (synopsis "Hierarchical indexing for spliced alignment of transcripts") |
| 2726 | (description |
| 2727 | "HISAT is a fast and sensitive spliced alignment program for mapping |
| 2728 | RNA-seq reads. In addition to one global FM index that represents a whole |
| 2729 | genome, HISAT uses a large set of small FM indexes that collectively cover the |
| 2730 | whole genome. These small indexes (called local indexes) combined with |
| 2731 | several alignment strategies enable effective alignment of RNA-seq reads, in |
| 2732 | particular, reads spanning multiple exons.") |
| 2733 | (license license:gpl3+))) |
| 2734 | |
| 2735 | (define-public hmmer |
| 2736 | (package |
| 2737 | (name "hmmer") |
| 2738 | (version "3.1b2") |
| 2739 | (source (origin |
| 2740 | (method url-fetch) |
| 2741 | (uri (string-append |
| 2742 | "http://eddylab.org/software/hmmer" |
| 2743 | (version-prefix version 1) "/" |
| 2744 | version "/hmmer-" version ".tar.gz")) |
| 2745 | (sha256 |
| 2746 | (base32 |
| 2747 | "0djmgc0pfli0jilfx8hql1axhwhqxqb8rxg2r5rg07aw73sfs5nx")))) |
| 2748 | (build-system gnu-build-system) |
| 2749 | (native-inputs `(("perl" ,perl))) |
| 2750 | (home-page "http://hmmer.org/") |
| 2751 | (synopsis "Biosequence analysis using profile hidden Markov models") |
| 2752 | (description |
| 2753 | "HMMER is used for searching sequence databases for homologs of protein |
| 2754 | sequences, and for making protein sequence alignments. It implements methods |
| 2755 | using probabilistic models called profile hidden Markov models (profile |
| 2756 | HMMs).") |
| 2757 | (license (list license:gpl3+ |
| 2758 | ;; The bundled library 'easel' is distributed |
| 2759 | ;; under The Janelia Farm Software License. |
| 2760 | (license:non-copyleft |
| 2761 | "file://easel/LICENSE" |
| 2762 | "See easel/LICENSE in the distribution."))))) |
| 2763 | |
| 2764 | (define-public htseq |
| 2765 | (package |
| 2766 | (name "htseq") |
| 2767 | (version "0.6.1") |
| 2768 | (source (origin |
| 2769 | (method url-fetch) |
| 2770 | (uri (string-append |
| 2771 | "https://pypi.python.org/packages/source/H/HTSeq/HTSeq-" |
| 2772 | version ".tar.gz")) |
| 2773 | (sha256 |
| 2774 | (base32 |
| 2775 | "1i85ppf2j2lj12m0x690qq5nn17xxk23pbbx2c83r8ayb5wngzwv")))) |
| 2776 | (build-system python-build-system) |
| 2777 | (arguments `(#:python ,python-2)) ; only Python 2 is supported |
| 2778 | ;; Numpy needs to be propagated when htseq is used as a Python library. |
| 2779 | (propagated-inputs |
| 2780 | `(("python-numpy" ,python2-numpy))) |
| 2781 | (inputs |
| 2782 | `(("python-pysam" ,python2-pysam))) |
| 2783 | (home-page "http://www-huber.embl.de/users/anders/HTSeq/") |
| 2784 | (synopsis "Analysing high-throughput sequencing data with Python") |
| 2785 | (description |
| 2786 | "HTSeq is a Python package that provides infrastructure to process data |
| 2787 | from high-throughput sequencing assays.") |
| 2788 | (license license:gpl3+))) |
| 2789 | |
| 2790 | (define-public java-htsjdk |
| 2791 | (package |
| 2792 | (name "java-htsjdk") |
| 2793 | (version "1.129") |
| 2794 | (source (origin |
| 2795 | (method url-fetch) |
| 2796 | (uri (string-append |
| 2797 | "https://github.com/samtools/htsjdk/archive/" |
| 2798 | version ".tar.gz")) |
| 2799 | (file-name (string-append name "-" version ".tar.gz")) |
| 2800 | (sha256 |
| 2801 | (base32 |
| 2802 | "0asdk9b8jx2ij7yd6apg9qx03li8q7z3ml0qy2r2qczkra79y6fw")) |
| 2803 | (modules '((guix build utils))) |
| 2804 | ;; remove build dependency on git |
| 2805 | (snippet '(substitute* "build.xml" |
| 2806 | (("failifexecutionfails=\"true\"") |
| 2807 | "failifexecutionfails=\"false\""))))) |
| 2808 | (build-system ant-build-system) |
| 2809 | (arguments |
| 2810 | `(#:tests? #f ; test require Internet access |
| 2811 | #:make-flags |
| 2812 | (list (string-append "-Ddist=" (assoc-ref %outputs "out") |
| 2813 | "/share/java/htsjdk/")) |
| 2814 | #:build-target "all" |
| 2815 | #:phases |
| 2816 | (modify-phases %standard-phases |
| 2817 | ;; The build phase also installs the jars |
| 2818 | (delete 'install)))) |
| 2819 | (home-page "http://samtools.github.io/htsjdk/") |
| 2820 | (synopsis "Java API for high-throughput sequencing data (HTS) formats") |
| 2821 | (description |
| 2822 | "HTSJDK is an implementation of a unified Java library for accessing |
| 2823 | common file formats, such as SAM and VCF, used for high-throughput |
| 2824 | sequencing (HTS) data. There are also an number of useful utilities for |
| 2825 | manipulating HTS data.") |
| 2826 | (license license:expat))) |
| 2827 | |
| 2828 | (define-public htslib |
| 2829 | (package |
| 2830 | (name "htslib") |
| 2831 | (version "1.3.1") |
| 2832 | (source (origin |
| 2833 | (method url-fetch) |
| 2834 | (uri (string-append |
| 2835 | "https://github.com/samtools/htslib/releases/download/" |
| 2836 | version "/htslib-" version ".tar.bz2")) |
| 2837 | (sha256 |
| 2838 | (base32 |
| 2839 | "1rja282fwdc25ql6izkhdyh8ppw8x2fs0w0js78zgkmqjlikmma9")))) |
| 2840 | (build-system gnu-build-system) |
| 2841 | (arguments |
| 2842 | `(#:phases |
| 2843 | (modify-phases %standard-phases |
| 2844 | (add-after |
| 2845 | 'unpack 'patch-tests |
| 2846 | (lambda _ |
| 2847 | (substitute* "test/test.pl" |
| 2848 | (("/bin/bash") (which "bash"))) |
| 2849 | #t))))) |
| 2850 | (inputs |
| 2851 | `(("zlib" ,zlib))) |
| 2852 | (native-inputs |
| 2853 | `(("perl" ,perl))) |
| 2854 | (home-page "http://www.htslib.org") |
| 2855 | (synopsis "C library for reading/writing high-throughput sequencing data") |
| 2856 | (description |
| 2857 | "HTSlib is a C library for reading/writing high-throughput sequencing |
| 2858 | data. It also provides the bgzip, htsfile, and tabix utilities.") |
| 2859 | ;; Files under cram/ are released under the modified BSD license; |
| 2860 | ;; the rest is released under the Expat license |
| 2861 | (license (list license:expat license:bsd-3)))) |
| 2862 | |
| 2863 | (define-public idr |
| 2864 | (package |
| 2865 | (name "idr") |
| 2866 | (version "2.0.0") |
| 2867 | (source (origin |
| 2868 | (method url-fetch) |
| 2869 | (uri (string-append |
| 2870 | "https://github.com/nboley/idr/archive/" |
| 2871 | version ".tar.gz")) |
| 2872 | (file-name (string-append name "-" version ".tar.gz")) |
| 2873 | (sha256 |
| 2874 | (base32 |
| 2875 | "1k3x44biak00aiv3hpm1yd6nn4hhp7n0qnbs3zh2q9sw7qr1qj5r")))) |
| 2876 | (build-system python-build-system) |
| 2877 | (arguments |
| 2878 | `(#:phases |
| 2879 | (modify-phases %standard-phases |
| 2880 | (add-after |
| 2881 | 'install 'wrap-program |
| 2882 | (lambda* (#:key inputs outputs #:allow-other-keys) |
| 2883 | (let* ((out (assoc-ref outputs "out")) |
| 2884 | (python-version (string-take (string-take-right |
| 2885 | (assoc-ref inputs "python") 5) 3)) |
| 2886 | (path (string-join |
| 2887 | (map (lambda (name) |
| 2888 | (string-append (assoc-ref inputs name) |
| 2889 | "/lib/python" python-version |
| 2890 | "/site-packages")) |
| 2891 | '("python-scipy" |
| 2892 | "python-numpy" |
| 2893 | "python-matplotlib")) |
| 2894 | ":"))) |
| 2895 | (wrap-program (string-append out "/bin/idr") |
| 2896 | `("PYTHONPATH" ":" prefix (,path)))) |
| 2897 | #t))))) |
| 2898 | (inputs |
| 2899 | `(("python-scipy" ,python-scipy) |
| 2900 | ("python-numpy" ,python-numpy) |
| 2901 | ("python-matplotlib" ,python-matplotlib))) |
| 2902 | (native-inputs |
| 2903 | `(("python-cython" ,python-cython))) |
| 2904 | (home-page "https://github.com/nboley/idr") |
| 2905 | (synopsis "Tool to measure the irreproducible discovery rate (IDR)") |
| 2906 | (description |
| 2907 | "The IDR (Irreproducible Discovery Rate) framework is a unified approach |
| 2908 | to measure the reproducibility of findings identified from replicate |
| 2909 | experiments and provide highly stable thresholds based on reproducibility.") |
| 2910 | (license license:gpl3+))) |
| 2911 | |
| 2912 | (define-public jellyfish |
| 2913 | (package |
| 2914 | (name "jellyfish") |
| 2915 | (version "2.2.4") |
| 2916 | (source (origin |
| 2917 | (method url-fetch) |
| 2918 | (uri (string-append "https://github.com/gmarcais/Jellyfish/" |
| 2919 | "releases/download/v" version |
| 2920 | "/jellyfish-" version ".tar.gz")) |
| 2921 | (sha256 |
| 2922 | (base32 |
| 2923 | "0a6xnynqy2ibfbfz86b9g2m2dgm7f1469pmymkpam333gi3p26nk")))) |
| 2924 | (build-system gnu-build-system) |
| 2925 | (outputs '("out" ;for library |
| 2926 | "ruby" ;for Ruby bindings |
| 2927 | "python")) ;for Python bindings |
| 2928 | (arguments |
| 2929 | `(#:configure-flags |
| 2930 | (list (string-append "--enable-ruby-binding=" |
| 2931 | (assoc-ref %outputs "ruby")) |
| 2932 | (string-append "--enable-python-binding=" |
| 2933 | (assoc-ref %outputs "python"))) |
| 2934 | #:phases |
| 2935 | (modify-phases %standard-phases |
| 2936 | (add-before 'check 'set-SHELL-variable |
| 2937 | (lambda _ |
| 2938 | ;; generator_manager.hpp either uses /bin/sh or $SHELL |
| 2939 | ;; to run tests. |
| 2940 | (setenv "SHELL" (which "bash")) |
| 2941 | #t))))) |
| 2942 | (native-inputs |
| 2943 | `(("bc" ,bc) |
| 2944 | ("time" ,time) |
| 2945 | ("ruby" ,ruby) |
| 2946 | ("python" ,python-2))) |
| 2947 | (synopsis "Tool for fast counting of k-mers in DNA") |
| 2948 | (description |
| 2949 | "Jellyfish is a tool for fast, memory-efficient counting of k-mers in |
| 2950 | DNA. A k-mer is a substring of length k, and counting the occurrences of all |
| 2951 | such substrings is a central step in many analyses of DNA sequence. Jellyfish |
| 2952 | is a command-line program that reads FASTA and multi-FASTA files containing |
| 2953 | DNA sequences. It outputs its k-mer counts in a binary format, which can be |
| 2954 | translated into a human-readable text format using the @code{jellyfish dump} |
| 2955 | command, or queried for specific k-mers with @code{jellyfish query}.") |
| 2956 | (home-page "http://www.genome.umd.edu/jellyfish.html") |
| 2957 | ;; From their website: JELLYFISH runs on 64-bit Intel-compatible processors |
| 2958 | (supported-systems '("x86_64-linux")) |
| 2959 | ;; The combined work is published under the GPLv3 or later. Individual |
| 2960 | ;; files such as lib/jsoncpp.cpp are released under the Expat license. |
| 2961 | (license (list license:gpl3+ license:expat)))) |
| 2962 | |
| 2963 | (define-public khmer |
| 2964 | (package |
| 2965 | (name "khmer") |
| 2966 | (version "2.0") |
| 2967 | (source |
| 2968 | (origin |
| 2969 | (method url-fetch) |
| 2970 | (uri (pypi-uri "khmer" version)) |
| 2971 | (sha256 |
| 2972 | (base32 |
| 2973 | "0wb05shqh77v00256qlm68vbbx3kl76fyzihszbz5nhanl4ni33a")) |
| 2974 | (patches (search-patches "khmer-use-libraries.patch")))) |
| 2975 | (build-system python-build-system) |
| 2976 | (arguments |
| 2977 | `(#:phases |
| 2978 | (modify-phases %standard-phases |
| 2979 | (add-after 'unpack 'set-paths |
| 2980 | (lambda* (#:key inputs outputs #:allow-other-keys) |
| 2981 | ;; Delete bundled libraries. |
| 2982 | (delete-file-recursively "third-party/zlib") |
| 2983 | (delete-file-recursively "third-party/bzip2") |
| 2984 | ;; Replace bundled seqan. |
| 2985 | (let* ((seqan-all "third-party/seqan") |
| 2986 | (seqan-include (string-append |
| 2987 | seqan-all "/core/include"))) |
| 2988 | (delete-file-recursively seqan-all) |
| 2989 | (copy-recursively (string-append (assoc-ref inputs "seqan") |
| 2990 | "/include/seqan") |
| 2991 | (string-append seqan-include "/seqan"))) |
| 2992 | ;; We do not replace the bundled MurmurHash as the canonical |
| 2993 | ;; repository for this code 'SMHasher' is unsuitable for |
| 2994 | ;; providing a library. See |
| 2995 | ;; https://lists.gnu.org/archive/html/guix-devel/2016-06/msg00977.html |
| 2996 | #t)) |
| 2997 | (add-after 'unpack 'set-cc |
| 2998 | (lambda _ |
| 2999 | (setenv "CC" "gcc") |
| 3000 | #t)) |
| 3001 | ;; It is simpler to test after installation. |
| 3002 | (delete 'check) |
| 3003 | (add-after 'install 'post-install-check |
| 3004 | (lambda* (#:key inputs outputs #:allow-other-keys) |
| 3005 | (let ((out (assoc-ref outputs "out"))) |
| 3006 | (setenv "PATH" |
| 3007 | (string-append |
| 3008 | (getenv "PATH") |
| 3009 | ":" |
| 3010 | (assoc-ref outputs "out") |
| 3011 | "/bin")) |
| 3012 | (setenv "PYTHONPATH" |
| 3013 | (string-append |
| 3014 | (getenv "PYTHONPATH") |
| 3015 | ":" |
| 3016 | out |
| 3017 | "/lib/python" |
| 3018 | (string-take (string-take-right |
| 3019 | (assoc-ref inputs "python") 5) 3) |
| 3020 | "/site-packages")) |
| 3021 | (with-directory-excursion "build" |
| 3022 | (zero? (system* "nosetests" "khmer" "--attr" |
| 3023 | "!known_failing"))))))))) |
| 3024 | (native-inputs |
| 3025 | `(("seqan" ,seqan) |
| 3026 | ("python-nose" ,python-nose))) |
| 3027 | (inputs |
| 3028 | `(("zlib" ,zlib) |
| 3029 | ("bzip2" ,bzip2) |
| 3030 | ("python-screed" ,python-screed) |
| 3031 | ("python-bz2file" ,python-bz2file))) |
| 3032 | (home-page "https://khmer.readthedocs.org/") |
| 3033 | (synopsis "K-mer counting, filtering and graph traversal library") |
| 3034 | (description "The khmer software is a set of command-line tools for |
| 3035 | working with DNA shotgun sequencing data from genomes, transcriptomes, |
| 3036 | metagenomes and single cells. Khmer can make de novo assemblies faster, and |
| 3037 | sometimes better. Khmer can also identify and fix problems with shotgun |
| 3038 | data.") |
| 3039 | ;; When building on i686, armhf and mips64el, we get the following error: |
| 3040 | ;; error: ['khmer', 'khmer.tests', 'oxli'] require 64-bit operating system |
| 3041 | (supported-systems '("x86_64-linux")) |
| 3042 | (license license:bsd-3))) |
| 3043 | |
| 3044 | (define-public macs |
| 3045 | (package |
| 3046 | (name "macs") |
| 3047 | (version "2.1.0.20151222") |
| 3048 | (source (origin |
| 3049 | (method url-fetch) |
| 3050 | (uri (pypi-uri "MACS2" version)) |
| 3051 | (sha256 |
| 3052 | (base32 |
| 3053 | "1r2hcz6irhcq7lwbafjks98jbn34hv05avgbdjnp6w6mlfjkf8x5")))) |
| 3054 | (build-system python-build-system) |
| 3055 | (arguments |
| 3056 | `(#:python ,python-2 ; only compatible with Python 2.7 |
| 3057 | #:tests? #f)) ; no test target |
| 3058 | (inputs |
| 3059 | `(("python-numpy" ,python2-numpy))) |
| 3060 | (home-page "http://github.com/taoliu/MACS/") |
| 3061 | (synopsis "Model based analysis for ChIP-Seq data") |
| 3062 | (description |
| 3063 | "MACS is an implementation of a ChIP-Seq analysis algorithm for |
| 3064 | identifying transcript factor binding sites named Model-based Analysis of |
| 3065 | ChIP-Seq (MACS). MACS captures the influence of genome complexity to evaluate |
| 3066 | the significance of enriched ChIP regions and it improves the spatial |
| 3067 | resolution of binding sites through combining the information of both |
| 3068 | sequencing tag position and orientation.") |
| 3069 | (license license:bsd-3))) |
| 3070 | |
| 3071 | (define-public mafft |
| 3072 | (package |
| 3073 | (name "mafft") |
| 3074 | (version "7.305") |
| 3075 | (source (origin |
| 3076 | (method url-fetch) |
| 3077 | (uri (string-append |
| 3078 | "http://mafft.cbrc.jp/alignment/software/mafft-" version |
| 3079 | "-without-extensions-src.tgz")) |
| 3080 | (file-name (string-append name "-" version ".tgz")) |
| 3081 | (sha256 |
| 3082 | (base32 |
| 3083 | "0ziim7g58n3z8gppsa713f5fxprl60ldj3xck186z0n9dpp06i8r")))) |
| 3084 | (build-system gnu-build-system) |
| 3085 | (arguments |
| 3086 | `(#:tests? #f ; no automated tests, though there are tests in the read me |
| 3087 | #:make-flags (let ((out (assoc-ref %outputs "out"))) |
| 3088 | (list (string-append "PREFIX=" out) |
| 3089 | (string-append "BINDIR=" |
| 3090 | (string-append out "/bin")))) |
| 3091 | #:phases |
| 3092 | (modify-phases %standard-phases |
| 3093 | (add-after 'unpack 'enter-dir |
| 3094 | (lambda _ (chdir "core") #t)) |
| 3095 | (add-after 'enter-dir 'patch-makefile |
| 3096 | (lambda _ |
| 3097 | ;; on advice from the MAFFT authors, there is no need to |
| 3098 | ;; distribute mafft-profile, mafft-distance, or |
| 3099 | ;; mafft-homologs.rb as they are too "specialised". |
| 3100 | (substitute* "Makefile" |
| 3101 | ;; remove mafft-homologs.rb from SCRIPTS |
| 3102 | (("^SCRIPTS = mafft mafft-homologs.rb") |
| 3103 | "SCRIPTS = mafft") |
| 3104 | ;; remove mafft-homologs from MANPAGES |
| 3105 | (("^MANPAGES = mafft.1 mafft-homologs.1") |
| 3106 | "MANPAGES = mafft.1") |
| 3107 | ;; remove mafft-distance from PROGS |
| 3108 | (("^PROGS = dvtditr dndfast7 dndblast sextet5 mafft-distance") |
| 3109 | "PROGS = dvtditr dndfast7 dndblast sextet5") |
| 3110 | ;; remove mafft-profile from PROGS |
| 3111 | (("splittbfast disttbfast tbfast mafft-profile 2cl mccaskillwrap") |
| 3112 | "splittbfast disttbfast tbfast f2cl mccaskillwrap") |
| 3113 | (("^rm -f mafft-profile mafft-profile.exe") "#") |
| 3114 | (("^rm -f mafft-distance mafft-distance.exe") ")#") |
| 3115 | ;; do not install MAN pages in libexec folder |
| 3116 | (("^\t\\$\\(INSTALL\\) -m 644 \\$\\(MANPAGES\\) \ |
| 3117 | \\$\\(DESTDIR\\)\\$\\(LIBDIR\\)") "#")) |
| 3118 | #t)) |
| 3119 | (add-after 'enter-dir 'patch-paths |
| 3120 | (lambda* (#:key inputs #:allow-other-keys) |
| 3121 | (substitute* '("pairash.c" |
| 3122 | "mafft.tmpl") |
| 3123 | (("perl") (which "perl")) |
| 3124 | (("([\"`| ])awk" _ prefix) |
| 3125 | (string-append prefix (which "awk"))) |
| 3126 | (("grep") (which "grep"))) |
| 3127 | #t)) |
| 3128 | (delete 'configure) |
| 3129 | (add-after 'install 'wrap-programs |
| 3130 | (lambda* (#:key outputs #:allow-other-keys) |
| 3131 | (let* ((out (assoc-ref outputs "out")) |
| 3132 | (bin (string-append out "/bin")) |
| 3133 | (path (string-append |
| 3134 | (assoc-ref %build-inputs "coreutils") "/bin:"))) |
| 3135 | (for-each (lambda (file) |
| 3136 | (wrap-program file |
| 3137 | `("PATH" ":" prefix (,path)))) |
| 3138 | (find-files bin))) |
| 3139 | #t))))) |
| 3140 | (inputs |
| 3141 | `(("perl" ,perl) |
| 3142 | ("ruby" ,ruby) |
| 3143 | ("gawk" ,gawk) |
| 3144 | ("grep" ,grep) |
| 3145 | ("coreutils" ,coreutils))) |
| 3146 | (home-page "http://mafft.cbrc.jp/alignment/software/") |
| 3147 | (synopsis "Multiple sequence alignment program") |
| 3148 | (description |
| 3149 | "MAFFT offers a range of multiple alignment methods for nucleotide and |
| 3150 | protein sequences. For instance, it offers L-INS-i (accurate; for alignment |
| 3151 | of <~200 sequences) and FFT-NS-2 (fast; for alignment of <~30,000 |
| 3152 | sequences).") |
| 3153 | (license (license:non-copyleft |
| 3154 | "http://mafft.cbrc.jp/alignment/software/license.txt" |
| 3155 | "BSD-3 with different formatting")))) |
| 3156 | |
| 3157 | (define-public mash |
| 3158 | (package |
| 3159 | (name "mash") |
| 3160 | (version "1.1.1") |
| 3161 | (source (origin |
| 3162 | (method url-fetch) |
| 3163 | (uri (string-append |
| 3164 | "https://github.com/marbl/mash/archive/v" |
| 3165 | version ".tar.gz")) |
| 3166 | (file-name (string-append name "-" version ".tar.gz")) |
| 3167 | (sha256 |
| 3168 | (base32 |
| 3169 | "08znbvqq5xknfhmpp3wcj574zvi4p7i8zifi67c9qw9a6ikp42fj")) |
| 3170 | (modules '((guix build utils))) |
| 3171 | (snippet |
| 3172 | ;; Delete bundled kseq. |
| 3173 | ;; TODO: Also delete bundled murmurhash and open bloom filter. |
| 3174 | '(delete-file "src/mash/kseq.h")))) |
| 3175 | (build-system gnu-build-system) |
| 3176 | (arguments |
| 3177 | `(#:tests? #f ; No tests. |
| 3178 | #:configure-flags |
| 3179 | (list |
| 3180 | (string-append "--with-capnp=" (assoc-ref %build-inputs "capnproto")) |
| 3181 | (string-append "--with-gsl=" (assoc-ref %build-inputs "gsl"))) |
| 3182 | #:make-flags (list "CC=gcc") |
| 3183 | #:phases |
| 3184 | (modify-phases %standard-phases |
| 3185 | (add-after 'unpack 'fix-includes |
| 3186 | (lambda _ |
| 3187 | (substitute* '("src/mash/Sketch.cpp" "src/mash/CommandFind.cpp") |
| 3188 | (("^#include \"kseq\\.h\"") |
| 3189 | "#include \"htslib/kseq.h\"")) |
| 3190 | #t)) |
| 3191 | (add-before 'configure 'autoconf |
| 3192 | (lambda _ (zero? (system* "autoconf"))))))) |
| 3193 | (native-inputs |
| 3194 | `(("autoconf" ,autoconf) |
| 3195 | ;; Capnproto and htslib are statically embedded in the final |
| 3196 | ;; application. Therefore we also list their licenses, below. |
| 3197 | ("capnproto" ,capnproto) |
| 3198 | ("htslib" ,htslib))) |
| 3199 | (inputs |
| 3200 | `(("gsl" ,gsl) |
| 3201 | ("zlib" ,zlib))) |
| 3202 | (supported-systems '("x86_64-linux")) |
| 3203 | (home-page "https://mash.readthedocs.io") |
| 3204 | (synopsis "Fast genome and metagenome distance estimation using MinHash") |
| 3205 | (description "Mash is a fast sequence distance estimator that uses the |
| 3206 | MinHash algorithm and is designed to work with genomes and metagenomes in the |
| 3207 | form of assemblies or reads.") |
| 3208 | (license (list license:bsd-3 ; Mash |
| 3209 | license:expat ; HTSlib and capnproto |
| 3210 | license:public-domain ; MurmurHash 3 |
| 3211 | license:cpl1.0)))) ; Open Bloom Filter |
| 3212 | |
| 3213 | (define-public metabat |
| 3214 | ;; We package from a git commit because compilation of the released version |
| 3215 | ;; fails. |
| 3216 | (let ((commit "cbdca756993e66ae57e50a27970595dda9cbde1b")) |
| 3217 | (package |
| 3218 | (name "metabat") |
| 3219 | (version (string-append "0.32.4-1." (string-take commit 8))) |
| 3220 | (source |
| 3221 | (origin |
| 3222 | (method git-fetch) |
| 3223 | (uri (git-reference |
| 3224 | (url "https://bitbucket.org/berkeleylab/metabat.git") |
| 3225 | (commit commit))) |
| 3226 | (file-name (string-append name "-" version)) |
| 3227 | (sha256 |
| 3228 | (base32 |
| 3229 | "0byia8nsip6zvc4ha0qkxkxxyjf4x7jcvy48q2dvb0pzr989syzr")) |
| 3230 | (patches (search-patches "metabat-remove-compilation-date.patch")))) |
| 3231 | (build-system gnu-build-system) |
| 3232 | (arguments |
| 3233 | `(#:phases |
| 3234 | (modify-phases %standard-phases |
| 3235 | (add-after 'unpack 'fix-includes |
| 3236 | (lambda _ |
| 3237 | (substitute* "src/BamUtils.h" |
| 3238 | (("^#include \"bam/bam\\.h\"") |
| 3239 | "#include \"samtools/bam.h\"") |
| 3240 | (("^#include \"bam/sam\\.h\"") |
| 3241 | "#include \"samtools/sam.h\"")) |
| 3242 | (substitute* "src/KseqReader.h" |
| 3243 | (("^#include \"bam/kseq\\.h\"") |
| 3244 | "#include \"htslib/kseq.h\"")) |
| 3245 | #t)) |
| 3246 | (add-after 'unpack 'fix-scons |
| 3247 | (lambda* (#:key inputs #:allow-other-keys) |
| 3248 | (substitute* "SConstruct" |
| 3249 | (("^htslib_dir = 'samtools'") |
| 3250 | (string-append "hitslib_dir = '" |
| 3251 | (assoc-ref inputs "htslib") |
| 3252 | "'")) |
| 3253 | (("^samtools_dir = 'samtools'") |
| 3254 | (string-append "samtools_dir = '" |
| 3255 | (assoc-ref inputs "htslib") |
| 3256 | "'")) |
| 3257 | (("^findStaticOrShared\\('bam', hts_lib") |
| 3258 | (string-append "findStaticOrShared('bam', '" |
| 3259 | (assoc-ref inputs "samtools") |
| 3260 | "/lib'")) |
| 3261 | ;; Do not distribute README. |
| 3262 | (("^env\\.Install\\(idir_prefix, 'README\\.md'\\)") "")) |
| 3263 | #t)) |
| 3264 | (delete 'configure) |
| 3265 | (replace 'build |
| 3266 | (lambda* (#:key inputs outputs #:allow-other-keys) |
| 3267 | (mkdir (assoc-ref outputs "out")) |
| 3268 | (zero? (system* "scons" |
| 3269 | (string-append |
| 3270 | "PREFIX=" |
| 3271 | (assoc-ref outputs "out")) |
| 3272 | (string-append |
| 3273 | "BOOST_ROOT=" |
| 3274 | (assoc-ref inputs "boost")) |
| 3275 | "install")))) |
| 3276 | ;; Check and install are carried out during build phase. |
| 3277 | (delete 'check) |
| 3278 | (delete 'install)))) |
| 3279 | (inputs |
| 3280 | `(("zlib" ,zlib) |
| 3281 | ("perl" ,perl) |
| 3282 | ("samtools" ,samtools) |
| 3283 | ("htslib" ,htslib) |
| 3284 | ("boost" ,boost))) |
| 3285 | (native-inputs |
| 3286 | `(("scons" ,scons))) |
| 3287 | (home-page "https://bitbucket.org/berkeleylab/metabat") |
| 3288 | (synopsis |
| 3289 | "Reconstruction of single genomes from complex microbial communities") |
| 3290 | (description |
| 3291 | "Grouping large genomic fragments assembled from shotgun metagenomic |
| 3292 | sequences to deconvolute complex microbial communities, or metagenome binning, |
| 3293 | enables the study of individual organisms and their interactions. MetaBAT is |
| 3294 | an automated metagenome binning software, which integrates empirical |
| 3295 | probabilistic distances of genome abundance and tetranucleotide frequency.") |
| 3296 | (license (license:non-copyleft "file://license.txt" |
| 3297 | "See license.txt in the distribution."))))) |
| 3298 | |
| 3299 | (define-public minced |
| 3300 | (package |
| 3301 | (name "minced") |
| 3302 | (version "0.2.0") |
| 3303 | (source (origin |
| 3304 | (method url-fetch) |
| 3305 | (uri (string-append |
| 3306 | "https://github.com/ctSkennerton/minced/archive/" |
| 3307 | version ".tar.gz")) |
| 3308 | (file-name (string-append name "-" version ".tar.gz")) |
| 3309 | (sha256 |
| 3310 | (base32 |
| 3311 | "0wxmlsapxfpxfd3ps9636h7i2xy6la8i42mwh0j2lsky63h63jp1")))) |
| 3312 | (build-system gnu-build-system) |
| 3313 | (arguments |
| 3314 | `(#:test-target "test" |
| 3315 | #:phases |
| 3316 | (modify-phases %standard-phases |
| 3317 | (delete 'configure) |
| 3318 | (add-before 'check 'fix-test |
| 3319 | (lambda _ |
| 3320 | ;; Fix test for latest version. |
| 3321 | (substitute* "t/Aquifex_aeolicus_VF5.expected" |
| 3322 | (("minced:0.1.6") "minced:0.2.0")) |
| 3323 | #t)) |
| 3324 | (replace 'install ; No install target. |
| 3325 | (lambda* (#:key inputs outputs #:allow-other-keys) |
| 3326 | (let* ((out (assoc-ref outputs "out")) |
| 3327 | (bin (string-append out "/bin")) |
| 3328 | (wrapper (string-append bin "/minced"))) |
| 3329 | ;; Minced comes with a wrapper script that tries to figure out where |
| 3330 | ;; it is located before running the JAR. Since these paths are known |
| 3331 | ;; to us, we build our own wrapper to avoid coreutils dependency. |
| 3332 | (install-file "minced.jar" bin) |
| 3333 | (with-output-to-file wrapper |
| 3334 | (lambda _ |
| 3335 | (display |
| 3336 | (string-append |
| 3337 | "#!" (assoc-ref inputs "bash") "/bin/sh\n\n" |
| 3338 | (assoc-ref inputs "jre") "/bin/java -jar " |
| 3339 | bin "/minced.jar \"$@\"\n")))) |
| 3340 | (chmod wrapper #o555))))))) |
| 3341 | (native-inputs |
| 3342 | `(("jdk" ,icedtea "jdk"))) |
| 3343 | (inputs |
| 3344 | `(("bash" ,bash) |
| 3345 | ("jre" ,icedtea "out"))) |
| 3346 | (home-page "https://github.com/ctSkennerton/minced") |
| 3347 | (synopsis "Mining CRISPRs in Environmental Datasets") |
| 3348 | (description |
| 3349 | "MinCED is a program to find Clustered Regularly Interspaced Short |
| 3350 | Palindromic Repeats (CRISPRs) in DNA sequences. It can be used for |
| 3351 | unassembled metagenomic reads, but is mainly designed for full genomes and |
| 3352 | assembled metagenomic sequence.") |
| 3353 | (license license:gpl3+))) |
| 3354 | |
| 3355 | (define-public miso |
| 3356 | (package |
| 3357 | (name "miso") |
| 3358 | (version "0.5.3") |
| 3359 | (source (origin |
| 3360 | (method url-fetch) |
| 3361 | (uri (string-append |
| 3362 | "https://pypi.python.org/packages/source/m/misopy/misopy-" |
| 3363 | version ".tar.gz")) |
| 3364 | (sha256 |
| 3365 | (base32 |
| 3366 | "0x446867az8ir0z8c1vjqffkp0ma37wm4sylixnkhgawllzx8v5w")) |
| 3367 | (modules '((guix build utils))) |
| 3368 | (snippet |
| 3369 | '(substitute* "setup.py" |
| 3370 | ;; Use setuptools, or else the executables are not |
| 3371 | ;; installed. |
| 3372 | (("distutils.core") "setuptools") |
| 3373 | ;; use "gcc" instead of "cc" for compilation |
| 3374 | (("^defines") |
| 3375 | "cc.set_executables( |
| 3376 | compiler='gcc', |
| 3377 | compiler_so='gcc', |
| 3378 | linker_exe='gcc', |
| 3379 | linker_so='gcc -shared'); defines"))))) |
| 3380 | (build-system python-build-system) |
| 3381 | (arguments |
| 3382 | `(#:python ,python-2 ; only Python 2 is supported |
| 3383 | #:tests? #f)) ; no "test" target |
| 3384 | (inputs |
| 3385 | `(("samtools" ,samtools) |
| 3386 | ("python-numpy" ,python2-numpy) |
| 3387 | ("python-pysam" ,python2-pysam) |
| 3388 | ("python-scipy" ,python2-scipy) |
| 3389 | ("python-matplotlib" ,python2-matplotlib))) |
| 3390 | (native-inputs |
| 3391 | `(("python-mock" ,python2-mock) ;for tests |
| 3392 | ("python-pytz" ,python2-pytz))) ;for tests |
| 3393 | (home-page "http://genes.mit.edu/burgelab/miso/index.html") |
| 3394 | (synopsis "Mixture of Isoforms model for RNA-Seq isoform quantitation") |
| 3395 | (description |
| 3396 | "MISO (Mixture-of-Isoforms) is a probabilistic framework that quantitates |
| 3397 | the expression level of alternatively spliced genes from RNA-Seq data, and |
| 3398 | identifies differentially regulated isoforms or exons across samples. By |
| 3399 | modeling the generative process by which reads are produced from isoforms in |
| 3400 | RNA-Seq, the MISO model uses Bayesian inference to compute the probability |
| 3401 | that a read originated from a particular isoform.") |
| 3402 | (license license:gpl2))) |
| 3403 | |
| 3404 | (define-public muscle |
| 3405 | (package |
| 3406 | (name "muscle") |
| 3407 | (version "3.8.1551") |
| 3408 | (source (origin |
| 3409 | (method url-fetch/tarbomb) |
| 3410 | (file-name (string-append name "-" version)) |
| 3411 | (uri (string-append |
| 3412 | "http://www.drive5.com/muscle/muscle_src_" |
| 3413 | version ".tar.gz")) |
| 3414 | (sha256 |
| 3415 | (base32 |
| 3416 | "0bj8kj7sdizy3987zx6w7axihk40fk8rn76mpbqqjcnd64i5a367")))) |
| 3417 | (build-system gnu-build-system) |
| 3418 | (arguments |
| 3419 | `(#:make-flags (list "LDLIBS = -lm") |
| 3420 | #:phases |
| 3421 | (modify-phases %standard-phases |
| 3422 | (delete 'configure) |
| 3423 | (replace 'check |
| 3424 | ;; There are no tests, so just test if it runs. |
| 3425 | (lambda _ (zero? (system* "./muscle" "-version")))) |
| 3426 | (replace 'install |
| 3427 | (lambda* (#:key outputs #:allow-other-keys) |
| 3428 | (let* ((out (assoc-ref outputs "out")) |
| 3429 | (bin (string-append out "/bin"))) |
| 3430 | (install-file "muscle" bin))))))) |
| 3431 | (home-page "http://www.drive5.com/muscle") |
| 3432 | (synopsis "Multiple sequence alignment program") |
| 3433 | (description |
| 3434 | "MUSCLE aims to be a fast and accurate multiple sequence alignment |
| 3435 | program for nucleotide and protein sequences.") |
| 3436 | ;; License information found in 'muscle -h' and usage.cpp. |
| 3437 | (license license:public-domain))) |
| 3438 | |
| 3439 | (define-public newick-utils |
| 3440 | ;; There are no recent releases so we package from git. |
| 3441 | (let ((commit "da121155a977197cab9fbb15953ca1b40b11eb87")) |
| 3442 | (package |
| 3443 | (name "newick-utils") |
| 3444 | (version (string-append "1.6-1." (string-take commit 8))) |
| 3445 | (source (origin |
| 3446 | (method git-fetch) |
| 3447 | (uri (git-reference |
| 3448 | (url "https://github.com/tjunier/newick_utils.git") |
| 3449 | (commit commit))) |
| 3450 | (file-name (string-append name "-" version "-checkout")) |
| 3451 | (sha256 |
| 3452 | (base32 |
| 3453 | "1hkw21rq1mwf7xp0rmbb2gqc0i6p11108m69i7mr7xcjl268pxnb")))) |
| 3454 | (build-system gnu-build-system) |
| 3455 | (arguments |
| 3456 | `(#:phases |
| 3457 | (modify-phases %standard-phases |
| 3458 | (add-after 'unpack 'autoconf |
| 3459 | (lambda _ (zero? (system* "autoreconf" "-vif"))))))) |
| 3460 | (inputs |
| 3461 | ;; XXX: TODO: Enable Lua and Guile bindings. |
| 3462 | ;; https://github.com/tjunier/newick_utils/issues/13 |
| 3463 | `(("libxml2" ,libxml2) |
| 3464 | ("flex" ,flex) |
| 3465 | ("bison" ,bison))) |
| 3466 | (native-inputs |
| 3467 | `(("autoconf" ,autoconf) |
| 3468 | ("automake" ,automake) |
| 3469 | ("libtool" ,libtool))) |
| 3470 | (synopsis "Programs for working with newick format phylogenetic trees") |
| 3471 | (description |
| 3472 | "Newick-utils is a suite of utilities for processing phylogenetic trees |
| 3473 | in Newick format. Functions include re-rooting, extracting subtrees, |
| 3474 | trimming, pruning, condensing, drawing (ASCII graphics or SVG).") |
| 3475 | (home-page "https://github.com/tjunier/newick_utils") |
| 3476 | (license license:bsd-3)))) |
| 3477 | |
| 3478 | (define-public orfm |
| 3479 | (package |
| 3480 | (name "orfm") |
| 3481 | (version "0.6.0") |
| 3482 | (source (origin |
| 3483 | (method url-fetch) |
| 3484 | (uri (string-append |
| 3485 | "https://github.com/wwood/OrfM/releases/download/v" |
| 3486 | version "/orfm-" version ".tar.gz")) |
| 3487 | (sha256 |
| 3488 | (base32 |
| 3489 | "0kp5p0a8wh1shxlj9arv47qyhv23s1inbvmiv7k2i5mrwx2izh79")))) |
| 3490 | (build-system gnu-build-system) |
| 3491 | (inputs `(("zlib" ,zlib))) |
| 3492 | (native-inputs |
| 3493 | `(("ruby-bio-commandeer" ,ruby-bio-commandeer) |
| 3494 | ("ruby-rspec" ,ruby-rspec) |
| 3495 | ("ruby" ,ruby))) |
| 3496 | (synopsis "Simple and not slow open reading frame (ORF) caller") |
| 3497 | (description |
| 3498 | "An ORF caller finds stretches of DNA that, when translated, are not |
| 3499 | interrupted by stop codons. OrfM finds and prints these ORFs.") |
| 3500 | (home-page "https://github.com/wwood/OrfM") |
| 3501 | (license license:lgpl3+))) |
| 3502 | |
| 3503 | (define-public python2-pbcore |
| 3504 | (package |
| 3505 | (name "python2-pbcore") |
| 3506 | (version "1.2.10") |
| 3507 | (source (origin |
| 3508 | (method url-fetch) |
| 3509 | (uri (pypi-uri "pbcore" version)) |
| 3510 | (sha256 |
| 3511 | (base32 |
| 3512 | "1kjmv891d6qbpp4shhhvkl02ff4q5xlpnls2513sm2cjcrs52f1i")))) |
| 3513 | (build-system python-build-system) |
| 3514 | (arguments `(#:python ,python-2)) ; pbcore requires Python 2.7 |
| 3515 | (propagated-inputs |
| 3516 | `(("python-cython" ,python2-cython) |
| 3517 | ("python-numpy" ,python2-numpy) |
| 3518 | ("python-pysam" ,python2-pysam) |
| 3519 | ("python-h5py" ,python2-h5py))) |
| 3520 | (native-inputs |
| 3521 | `(("python-nose" ,python2-nose) |
| 3522 | ("python-sphinx" ,python2-sphinx) |
| 3523 | ("python-pyxb" ,python2-pyxb))) |
| 3524 | (home-page "http://pacificbiosciences.github.io/pbcore/") |
| 3525 | (synopsis "Library for reading and writing PacBio data files") |
| 3526 | (description |
| 3527 | "The pbcore package provides Python APIs for interacting with PacBio data |
| 3528 | files and writing bioinformatics applications.") |
| 3529 | (license license:bsd-3))) |
| 3530 | |
| 3531 | (define-public python2-warpedlmm |
| 3532 | (package |
| 3533 | (name "python2-warpedlmm") |
| 3534 | (version "0.21") |
| 3535 | (source |
| 3536 | (origin |
| 3537 | (method url-fetch) |
| 3538 | (uri (string-append |
| 3539 | "https://pypi.python.org/packages/source/W/WarpedLMM/WarpedLMM-" |
| 3540 | version ".zip")) |
| 3541 | (sha256 |
| 3542 | (base32 |
| 3543 | "1agfz6zqa8nc6cw47yh0s3y14gkpa9wqazwcj7mwwj3ffnw39p3j")))) |
| 3544 | (build-system python-build-system) |
| 3545 | (arguments |
| 3546 | `(#:python ,python-2)) ; requires Python 2.7 |
| 3547 | (propagated-inputs |
| 3548 | `(("python-scipy" ,python2-scipy) |
| 3549 | ("python-numpy" ,python2-numpy) |
| 3550 | ("python-matplotlib" ,python2-matplotlib) |
| 3551 | ("python-fastlmm" ,python2-fastlmm) |
| 3552 | ("python-pandas" ,python2-pandas) |
| 3553 | ("python-pysnptools" ,python2-pysnptools))) |
| 3554 | (native-inputs |
| 3555 | `(("python-mock" ,python2-mock) |
| 3556 | ("python-nose" ,python2-nose) |
| 3557 | ("unzip" ,unzip))) |
| 3558 | (home-page "https://github.com/PMBio/warpedLMM") |
| 3559 | (synopsis "Implementation of warped linear mixed models") |
| 3560 | (description |
| 3561 | "WarpedLMM is a Python implementation of the warped linear mixed model, |
| 3562 | which automatically learns an optimal warping function (or transformation) for |
| 3563 | the phenotype as it models the data.") |
| 3564 | (license license:asl2.0))) |
| 3565 | |
| 3566 | (define-public pbtranscript-tofu |
| 3567 | (let ((commit "8f5467fe6a4472bcfb4226c8720993c8507adfe4")) |
| 3568 | (package |
| 3569 | (name "pbtranscript-tofu") |
| 3570 | (version (string-append "2.2.3." (string-take commit 7))) |
| 3571 | (source (origin |
| 3572 | (method git-fetch) |
| 3573 | (uri (git-reference |
| 3574 | (url "https://github.com/PacificBiosciences/cDNA_primer.git") |
| 3575 | (commit commit))) |
| 3576 | (file-name (string-append name "-" version "-checkout")) |
| 3577 | (sha256 |
| 3578 | (base32 |
| 3579 | "1lgnpi35ihay42qx0b6yl3kkgra723i413j33kvs0kvs61h82w0f")) |
| 3580 | (modules '((guix build utils))) |
| 3581 | (snippet |
| 3582 | '(begin |
| 3583 | ;; remove bundled Cython sources |
| 3584 | (delete-file "pbtranscript-tofu/pbtranscript/Cython-0.20.1.tar.gz") |
| 3585 | #t)))) |
| 3586 | (build-system python-build-system) |
| 3587 | (arguments |
| 3588 | `(#:python ,python-2 |
| 3589 | #:phases |
| 3590 | (modify-phases %standard-phases |
| 3591 | (add-after 'unpack 'enter-directory |
| 3592 | (lambda _ |
| 3593 | (chdir "pbtranscript-tofu/pbtranscript/") |
| 3594 | #t)) |
| 3595 | ;; With setuptools version 18.0 and later this setup.py hack causes |
| 3596 | ;; a build error, so we disable it. |
| 3597 | (add-after 'enter-directory 'patch-setuppy |
| 3598 | (lambda _ |
| 3599 | (substitute* "setup.py" |
| 3600 | (("if 'setuptools.extension' in sys.modules:") |
| 3601 | "if False:")) |
| 3602 | #t))))) |
| 3603 | (inputs |
| 3604 | `(("python-numpy" ,python2-numpy) |
| 3605 | ("python-bx-python" ,python2-bx-python) |
| 3606 | ("python-networkx" ,python2-networkx) |
| 3607 | ("python-scipy" ,python2-scipy) |
| 3608 | ("python-pbcore" ,python2-pbcore) |
| 3609 | ("python-h5py" ,python2-h5py))) |
| 3610 | (native-inputs |
| 3611 | `(("python-cython" ,python2-cython) |
| 3612 | ("python-nose" ,python2-nose))) |
| 3613 | (home-page "https://github.com/PacificBiosciences/cDNA_primer") |
| 3614 | (synopsis "Analyze transcriptome data generated with the Iso-Seq protocol") |
| 3615 | (description |
| 3616 | "pbtranscript-tofu contains scripts to analyze transcriptome data |
| 3617 | generated using the PacBio Iso-Seq protocol.") |
| 3618 | (license license:bsd-3)))) |
| 3619 | |
| 3620 | (define-public prank |
| 3621 | (package |
| 3622 | (name "prank") |
| 3623 | (version "150803") |
| 3624 | (source (origin |
| 3625 | (method url-fetch) |
| 3626 | (uri (string-append |
| 3627 | "http://wasabiapp.org/download/prank/prank.source." |
| 3628 | version ".tgz")) |
| 3629 | (sha256 |
| 3630 | (base32 |
| 3631 | "0am4z94fs3w2n5xpfls9zda61vq7qqz4q2i7b9hlsxz5q4j3kfm4")))) |
| 3632 | (build-system gnu-build-system) |
| 3633 | (arguments |
| 3634 | `(#:phases |
| 3635 | (modify-phases %standard-phases |
| 3636 | (add-after 'unpack 'enter-src-dir |
| 3637 | (lambda _ |
| 3638 | (chdir "src") |
| 3639 | #t)) |
| 3640 | (add-after 'unpack 'remove-m64-flag |
| 3641 | ;; Prank will build with the correct 'bit-ness' without this flag |
| 3642 | ;; and this allows building on 32-bit machines. |
| 3643 | (lambda _ (substitute* "src/Makefile" |
| 3644 | (("-m64") "")) |
| 3645 | #t)) |
| 3646 | (delete 'configure) |
| 3647 | (replace 'install |
| 3648 | (lambda* (#:key outputs #:allow-other-keys) |
| 3649 | (let* ((out (assoc-ref outputs "out")) |
| 3650 | (bin (string-append out "/bin")) |
| 3651 | (man (string-append out "/share/man/man1")) |
| 3652 | (path (string-append |
| 3653 | (assoc-ref %build-inputs "mafft") "/bin:" |
| 3654 | (assoc-ref %build-inputs "exonerate") "/bin:" |
| 3655 | (assoc-ref %build-inputs "bppsuite") "/bin"))) |
| 3656 | (install-file "prank" bin) |
| 3657 | (wrap-program (string-append bin "/prank") |
| 3658 | `("PATH" ":" prefix (,path))) |
| 3659 | (install-file "prank.1" man)) |
| 3660 | #t))))) |
| 3661 | (inputs |
| 3662 | `(("mafft" ,mafft) |
| 3663 | ("exonerate" ,exonerate) |
| 3664 | ("bppsuite" ,bppsuite))) |
| 3665 | (home-page "http://wasabiapp.org/software/prank/") |
| 3666 | (synopsis "Probabilistic multiple sequence alignment program") |
| 3667 | (description |
| 3668 | "PRANK is a probabilistic multiple sequence alignment program for DNA, |
| 3669 | codon and amino-acid sequences. It is based on a novel algorithm that treats |
| 3670 | insertions correctly and avoids over-estimation of the number of deletion |
| 3671 | events. In addition, PRANK borrows ideas from maximum likelihood methods used |
| 3672 | in phylogenetics and correctly takes into account the evolutionary distances |
| 3673 | between sequences. Lastly, PRANK allows for defining a potential structure |
| 3674 | for sequences to be aligned and then, simultaneously with the alignment, |
| 3675 | predicts the locations of structural units in the sequences.") |
| 3676 | (license license:gpl2+))) |
| 3677 | |
| 3678 | (define-public proteinortho |
| 3679 | (package |
| 3680 | (name "proteinortho") |
| 3681 | (version "5.15") |
| 3682 | (source |
| 3683 | (origin |
| 3684 | (method url-fetch) |
| 3685 | (uri |
| 3686 | (string-append |
| 3687 | "http://www.bioinf.uni-leipzig.de/Software/proteinortho/proteinortho_v" |
| 3688 | version "_src.tar.gz")) |
| 3689 | (sha256 |
| 3690 | (base32 |
| 3691 | "05wacnnbx56avpcwhzlcf6b7s77swcpv3qnwz5sh1z54i51gg2ki")))) |
| 3692 | (build-system gnu-build-system) |
| 3693 | (arguments |
| 3694 | `(#:test-target "test" |
| 3695 | #:phases |
| 3696 | (modify-phases %standard-phases |
| 3697 | (replace 'configure |
| 3698 | ;; There is no configure script, so we modify the Makefile directly. |
| 3699 | (lambda* (#:key outputs #:allow-other-keys) |
| 3700 | (substitute* "Makefile" |
| 3701 | (("INSTALLDIR=.*") |
| 3702 | (string-append |
| 3703 | "INSTALLDIR=" (assoc-ref outputs "out") "/bin\n"))) |
| 3704 | #t)) |
| 3705 | (add-before 'install 'make-install-directory |
| 3706 | ;; The install directory is not created during 'make install'. |
| 3707 | (lambda* (#:key outputs #:allow-other-keys) |
| 3708 | (mkdir-p (string-append (assoc-ref outputs "out") "/bin")) |
| 3709 | #t)) |
| 3710 | (add-after 'install 'wrap-programs |
| 3711 | (lambda* (#:key inputs outputs #:allow-other-keys) |
| 3712 | (let* ((path (getenv "PATH")) |
| 3713 | (out (assoc-ref outputs "out")) |
| 3714 | (binary (string-append out "/bin/proteinortho5.pl"))) |
| 3715 | (wrap-program binary `("PATH" ":" prefix (,path)))) |
| 3716 | #t))))) |
| 3717 | (inputs |
| 3718 | `(("perl" ,perl) |
| 3719 | ("python" ,python-2) |
| 3720 | ("blast+" ,blast+))) |
| 3721 | (home-page "http://www.bioinf.uni-leipzig.de/Software/proteinortho") |
| 3722 | (synopsis "Detect orthologous genes across species") |
| 3723 | (description |
| 3724 | "Proteinortho is a tool to detect orthologous genes across different |
| 3725 | species. For doing so, it compares similarities of given gene sequences and |
| 3726 | clusters them to find significant groups. The algorithm was designed to handle |
| 3727 | large-scale data and can be applied to hundreds of species at once.") |
| 3728 | (license license:gpl2+))) |
| 3729 | |
| 3730 | (define-public pyicoteo |
| 3731 | (package |
| 3732 | (name "pyicoteo") |
| 3733 | (version "2.0.7") |
| 3734 | (source |
| 3735 | (origin |
| 3736 | (method url-fetch) |
| 3737 | (uri (string-append "https://bitbucket.org/regulatorygenomicsupf/" |
| 3738 | "pyicoteo/get/v" version ".tar.bz2")) |
| 3739 | (file-name (string-append name "-" version ".tar.bz2")) |
| 3740 | (sha256 |
| 3741 | (base32 |
| 3742 | "0d6087f29xp8wxwlj111c3sylli98n0l8ry58c51ixzq0zfm50wa")))) |
| 3743 | (build-system python-build-system) |
| 3744 | (arguments |
| 3745 | `(#:python ,python-2 ; does not work with Python 3 |
| 3746 | #:tests? #f)) ; there are no tests |
| 3747 | (inputs |
| 3748 | `(("python2-matplotlib" ,python2-matplotlib))) |
| 3749 | (home-page "https://bitbucket.org/regulatorygenomicsupf/pyicoteo") |
| 3750 | (synopsis "Analyze high-throughput genetic sequencing data") |
| 3751 | (description |
| 3752 | "Pyicoteo is a suite of tools for the analysis of high-throughput genetic |
| 3753 | sequencing data. It works with genomic coordinates. There are currently six |
| 3754 | different command-line tools: |
| 3755 | |
| 3756 | @enumerate |
| 3757 | @item pyicoregion: for generating exploratory regions automatically; |
| 3758 | @item pyicoenrich: for differential enrichment between two conditions; |
| 3759 | @item pyicoclip: for calling CLIP-Seq peaks without a control; |
| 3760 | @item pyicos: for genomic coordinates manipulation; |
| 3761 | @item pyicoller: for peak calling on punctuated ChIP-Seq; |
| 3762 | @item pyicount: to count how many reads from N experiment files overlap in a |
| 3763 | region file; |
| 3764 | @item pyicotrocol: to combine operations from pyicoteo. |
| 3765 | @end enumerate\n") |
| 3766 | (license license:gpl3+))) |
| 3767 | |
| 3768 | (define-public prodigal |
| 3769 | (package |
| 3770 | (name "prodigal") |
| 3771 | (version "2.6.3") |
| 3772 | (source (origin |
| 3773 | (method url-fetch) |
| 3774 | (uri (string-append |
| 3775 | "https://github.com/hyattpd/Prodigal/archive/v" |
| 3776 | version ".tar.gz")) |
| 3777 | (file-name (string-append name "-" version ".tar.gz")) |
| 3778 | (sha256 |
| 3779 | (base32 |
| 3780 | "17srxkqd3jc77xk15pfbgg1a9xahqg7337w95mrsia7mpza4l2c9")))) |
| 3781 | (build-system gnu-build-system) |
| 3782 | (arguments |
| 3783 | `(#:tests? #f ;no check target |
| 3784 | #:make-flags (list (string-append "INSTALLDIR=" |
| 3785 | (assoc-ref %outputs "out") |
| 3786 | "/bin")) |
| 3787 | #:phases |
| 3788 | (modify-phases %standard-phases |
| 3789 | (delete 'configure)))) |
| 3790 | (home-page "http://prodigal.ornl.gov") |
| 3791 | (synopsis "Protein-coding gene prediction for Archaea and Bacteria") |
| 3792 | (description |
| 3793 | "Prodigal runs smoothly on finished genomes, draft genomes, and |
| 3794 | metagenomes, providing gene predictions in GFF3, Genbank, or Sequin table |
| 3795 | format. It runs quickly, in an unsupervised fashion, handles gaps, handles |
| 3796 | partial genes, and identifies translation initiation sites.") |
| 3797 | (license license:gpl3+))) |
| 3798 | |
| 3799 | (define-public roary |
| 3800 | (package |
| 3801 | (name "roary") |
| 3802 | (version "3.7.0") |
| 3803 | (source |
| 3804 | (origin |
| 3805 | (method url-fetch) |
| 3806 | (uri (string-append |
| 3807 | "mirror://cpan/authors/id/A/AJ/AJPAGE/Bio-Roary-" |
| 3808 | version ".tar.gz")) |
| 3809 | (sha256 |
| 3810 | (base32 |
| 3811 | "0x2hpb3nfsc6x2nq1788w0fhqfzc7cn2dp4xwyva9m3k6xlz0m43")))) |
| 3812 | (build-system perl-build-system) |
| 3813 | (arguments |
| 3814 | `(#:phases |
| 3815 | (modify-phases %standard-phases |
| 3816 | (delete 'configure) |
| 3817 | (delete 'build) |
| 3818 | (replace 'check |
| 3819 | (lambda _ |
| 3820 | ;; The tests are not run by default, so we run each test file |
| 3821 | ;; directly. |
| 3822 | (setenv "PATH" (string-append (getcwd) "/bin" ":" |
| 3823 | (getenv "PATH"))) |
| 3824 | (setenv "PERL5LIB" (string-append (getcwd) "/lib" ":" |
| 3825 | (getenv "PERL5LIB"))) |
| 3826 | (zero? (length (filter (lambda (file) |
| 3827 | (display file)(display "\n") |
| 3828 | (not (zero? (system* "perl" file)))) |
| 3829 | (find-files "t" ".*\\.t$")))))) |
| 3830 | (replace 'install |
| 3831 | ;; There is no 'install' target in the Makefile. |
| 3832 | (lambda* (#:key outputs #:allow-other-keys) |
| 3833 | (let* ((out (assoc-ref outputs "out")) |
| 3834 | (bin (string-append out "/bin")) |
| 3835 | (perl (string-append out "/lib/perl5/site_perl")) |
| 3836 | (roary-plots "contrib/roary_plots")) |
| 3837 | (mkdir-p bin) |
| 3838 | (mkdir-p perl) |
| 3839 | (copy-recursively "bin" bin) |
| 3840 | (copy-recursively "lib" perl) |
| 3841 | #t))) |
| 3842 | (add-after 'install 'wrap-programs |
| 3843 | (lambda* (#:key inputs outputs #:allow-other-keys) |
| 3844 | (let* ((out (assoc-ref outputs "out")) |
| 3845 | (perl5lib (getenv "PERL5LIB")) |
| 3846 | (path (getenv "PATH"))) |
| 3847 | (for-each (lambda (prog) |
| 3848 | (let ((binary (string-append out "/" prog))) |
| 3849 | (wrap-program binary |
| 3850 | `("PERL5LIB" ":" prefix |
| 3851 | (,(string-append perl5lib ":" out |
| 3852 | "/lib/perl5/site_perl")))) |
| 3853 | (wrap-program binary |
| 3854 | `("PATH" ":" prefix |
| 3855 | (,(string-append path ":" out "/bin")))))) |
| 3856 | (find-files "bin" ".*[^R]$")) |
| 3857 | (let ((file |
| 3858 | (string-append out "/bin/roary-create_pan_genome_plots.R")) |
| 3859 | (r-site-lib (getenv "R_LIBS_SITE")) |
| 3860 | (coreutils-path |
| 3861 | (string-append (assoc-ref inputs "coreutils") "/bin"))) |
| 3862 | (wrap-program file |
| 3863 | `("R_LIBS_SITE" ":" prefix |
| 3864 | (,(string-append r-site-lib ":" out "/site-library/")))) |
| 3865 | (wrap-program file |
| 3866 | `("PATH" ":" prefix |
| 3867 | (,(string-append coreutils-path ":" out "/bin")))))) |
| 3868 | #t))))) |
| 3869 | (native-inputs |
| 3870 | `(("perl-env-path" ,perl-env-path) |
| 3871 | ("perl-test-files" ,perl-test-files) |
| 3872 | ("perl-test-most" ,perl-test-most) |
| 3873 | ("perl-test-output" ,perl-test-output))) |
| 3874 | (inputs |
| 3875 | `(("perl-array-utils" ,perl-array-utils) |
| 3876 | ("bioperl" ,bioperl-minimal) |
| 3877 | ("perl-exception-class" ,perl-exception-class) |
| 3878 | ("perl-file-find-rule" ,perl-file-find-rule) |
| 3879 | ("perl-file-grep" ,perl-file-grep) |
| 3880 | ("perl-file-slurper" ,perl-file-slurper) |
| 3881 | ("perl-file-which" ,perl-file-which) |
| 3882 | ("perl-graph" ,perl-graph) |
| 3883 | ("perl-graph-readwrite" ,perl-graph-readwrite) |
| 3884 | ("perl-log-log4perl" ,perl-log-log4perl) |
| 3885 | ("perl-moose" ,perl-moose) |
| 3886 | ("perl-perlio-utf8_strict" ,perl-perlio-utf8_strict) |
| 3887 | ("perl-text-csv" ,perl-text-csv) |
| 3888 | ("bedtools" ,bedtools) |
| 3889 | ("cd-hit" ,cd-hit) |
| 3890 | ("blast+" ,blast+) |
| 3891 | ("mcl" ,mcl) |
| 3892 | ("parallel" ,parallel) |
| 3893 | ("prank" ,prank) |
| 3894 | ("mafft" ,mafft) |
| 3895 | ("fasttree" ,fasttree) |
| 3896 | ("grep" ,grep) |
| 3897 | ("sed" ,sed) |
| 3898 | ("gawk" ,gawk) |
| 3899 | ("r" ,r) |
| 3900 | ("r-ggplot2" ,r-ggplot2) |
| 3901 | ("coreutils" ,coreutils))) |
| 3902 | (home-page "http://sanger-pathogens.github.io/Roary") |
| 3903 | (synopsis "High speed stand-alone pan genome pipeline") |
| 3904 | (description |
| 3905 | "Roary is a high speed stand alone pan genome pipeline, which takes |
| 3906 | annotated assemblies in GFF3 format (produced by the Prokka program) and |
| 3907 | calculates the pan genome. Using a standard desktop PC, it can analyse |
| 3908 | datasets with thousands of samples, without compromising the quality of the |
| 3909 | results. 128 samples can be analysed in under 1 hour using 1 GB of RAM and a |
| 3910 | single processor. Roary is not intended for metagenomics or for comparing |
| 3911 | extremely diverse sets of genomes.") |
| 3912 | (license license:gpl3))) |
| 3913 | |
| 3914 | (define-public raxml |
| 3915 | (package |
| 3916 | (name "raxml") |
| 3917 | (version "8.2.9") |
| 3918 | (source |
| 3919 | (origin |
| 3920 | (method url-fetch) |
| 3921 | (uri |
| 3922 | (string-append |
| 3923 | "https://github.com/stamatak/standard-RAxML/archive/v" |
| 3924 | version ".tar.gz")) |
| 3925 | (file-name (string-append name "-" version ".tar.gz")) |
| 3926 | (sha256 |
| 3927 | (base32 |
| 3928 | "1pv8p2fy67y21a9y4cm7xpvxqjwz2v4201flfjshdq1p8j52rqf7")))) |
| 3929 | (build-system gnu-build-system) |
| 3930 | (arguments |
| 3931 | `(#:tests? #f ; There are no tests. |
| 3932 | ;; Use 'standard' Makefile rather than SSE or AVX ones. |
| 3933 | #:make-flags (list "-f" "Makefile.HYBRID.gcc") |
| 3934 | #:phases |
| 3935 | (modify-phases %standard-phases |
| 3936 | (delete 'configure) |
| 3937 | (replace 'install |
| 3938 | (lambda* (#:key outputs #:allow-other-keys) |
| 3939 | (let* ((out (assoc-ref outputs "out")) |
| 3940 | (bin (string-append out "/bin")) |
| 3941 | (executable "raxmlHPC-HYBRID")) |
| 3942 | (install-file executable bin) |
| 3943 | (symlink (string-append bin "/" executable) "raxml")) |
| 3944 | #t))))) |
| 3945 | (inputs |
| 3946 | `(("openmpi" ,openmpi))) |
| 3947 | (home-page "http://sco.h-its.org/exelixis/web/software/raxml/index.html") |
| 3948 | (synopsis "Randomized Axelerated Maximum Likelihood phylogenetic trees") |
| 3949 | (description |
| 3950 | "RAxML is a tool for phylogenetic analysis and post-analysis of large |
| 3951 | phylogenies.") |
| 3952 | (license license:gpl2+))) |
| 3953 | |
| 3954 | (define-public rsem |
| 3955 | (package |
| 3956 | (name "rsem") |
| 3957 | (version "1.2.20") |
| 3958 | (source |
| 3959 | (origin |
| 3960 | (method url-fetch) |
| 3961 | (uri |
| 3962 | (string-append "http://deweylab.biostat.wisc.edu/rsem/src/rsem-" |
| 3963 | version ".tar.gz")) |
| 3964 | (sha256 |
| 3965 | (base32 "0nzdc0j0hjllhsd5f2xli95dafm3nawskigs140xzvjk67xh0r9q")) |
| 3966 | (patches (search-patches "rsem-makefile.patch")) |
| 3967 | (modules '((guix build utils))) |
| 3968 | (snippet |
| 3969 | '(begin |
| 3970 | ;; remove bundled copy of boost |
| 3971 | (delete-file-recursively "boost") |
| 3972 | #t)))) |
| 3973 | (build-system gnu-build-system) |
| 3974 | (arguments |
| 3975 | `(#:tests? #f ;no "check" target |
| 3976 | #:phases |
| 3977 | (modify-phases %standard-phases |
| 3978 | ;; No "configure" script. |
| 3979 | ;; Do not build bundled samtools library. |
| 3980 | (replace 'configure |
| 3981 | (lambda _ |
| 3982 | (substitute* "Makefile" |
| 3983 | (("^all : sam/libbam.a") "all : ")) |
| 3984 | #t)) |
| 3985 | (replace 'install |
| 3986 | (lambda* (#:key outputs #:allow-other-keys) |
| 3987 | (let* ((out (string-append (assoc-ref outputs "out"))) |
| 3988 | (bin (string-append out "/bin/")) |
| 3989 | (perl (string-append out "/lib/perl5/site_perl"))) |
| 3990 | (mkdir-p bin) |
| 3991 | (mkdir-p perl) |
| 3992 | (for-each (lambda (file) |
| 3993 | (copy-file file |
| 3994 | (string-append bin (basename file)))) |
| 3995 | (find-files "." "rsem-.*")) |
| 3996 | (copy-file "rsem_perl_utils.pm" |
| 3997 | (string-append perl "/rsem_perl_utils.pm"))) |
| 3998 | #t)) |
| 3999 | (add-after |
| 4000 | 'install 'wrap-program |
| 4001 | (lambda* (#:key outputs #:allow-other-keys) |
| 4002 | (let ((out (assoc-ref outputs "out"))) |
| 4003 | (for-each (lambda (prog) |
| 4004 | (wrap-program (string-append out "/bin/" prog) |
| 4005 | `("PERL5LIB" ":" prefix |
| 4006 | (,(string-append out "/lib/perl5/site_perl"))))) |
| 4007 | '("rsem-plot-transcript-wiggles" |
| 4008 | "rsem-calculate-expression" |
| 4009 | "rsem-generate-ngvector" |
| 4010 | "rsem-run-ebseq" |
| 4011 | "rsem-prepare-reference"))) |
| 4012 | #t))))) |
| 4013 | (inputs |
| 4014 | `(("boost" ,boost) |
| 4015 | ("ncurses" ,ncurses) |
| 4016 | ("r" ,r) |
| 4017 | ("perl" ,perl) |
| 4018 | ("samtools" ,samtools-0.1) |
| 4019 | ("zlib" ,zlib))) |
| 4020 | (home-page "http://deweylab.biostat.wisc.edu/rsem/") |
| 4021 | (synopsis "Estimate gene expression levels from RNA-Seq data") |
| 4022 | (description |
| 4023 | "RSEM is a software package for estimating gene and isoform expression |
| 4024 | levels from RNA-Seq data. The RSEM package provides a user-friendly |
| 4025 | interface, supports threads for parallel computation of the EM algorithm, |
| 4026 | single-end and paired-end read data, quality scores, variable-length reads and |
| 4027 | RSPD estimation. In addition, it provides posterior mean and 95% credibility |
| 4028 | interval estimates for expression levels. For visualization, it can generate |
| 4029 | BAM and Wiggle files in both transcript-coordinate and genomic-coordinate.") |
| 4030 | (license license:gpl3+))) |
| 4031 | |
| 4032 | (define-public rseqc |
| 4033 | (package |
| 4034 | (name "rseqc") |
| 4035 | (version "2.6.1") |
| 4036 | (source |
| 4037 | (origin |
| 4038 | (method url-fetch) |
| 4039 | (uri |
| 4040 | (string-append "mirror://sourceforge/rseqc/" |
| 4041 | "RSeQC-" version ".tar.gz")) |
| 4042 | (sha256 |
| 4043 | (base32 "15ly0254yi032qzkdplg00q144qfdsd986gh62829rl5bkxhj330")) |
| 4044 | (modules '((guix build utils))) |
| 4045 | (snippet |
| 4046 | '(begin |
| 4047 | ;; remove bundled copy of pysam |
| 4048 | (delete-file-recursively "lib/pysam") |
| 4049 | (substitute* "setup.py" |
| 4050 | ;; remove dependency on outdated "distribute" module |
| 4051 | (("^from distribute_setup import use_setuptools") "") |
| 4052 | (("^use_setuptools\\(\\)") "") |
| 4053 | ;; do not use bundled copy of pysam |
| 4054 | (("^have_pysam = False") "have_pysam = True")))))) |
| 4055 | (build-system python-build-system) |
| 4056 | (arguments `(#:python ,python-2)) |
| 4057 | (inputs |
| 4058 | `(("python-cython" ,python2-cython) |
| 4059 | ("python-pysam" ,python2-pysam) |
| 4060 | ("python-numpy" ,python2-numpy) |
| 4061 | ("zlib" ,zlib))) |
| 4062 | (native-inputs |
| 4063 | `(("python-nose" ,python2-nose))) |
| 4064 | (home-page "http://rseqc.sourceforge.net/") |
| 4065 | (synopsis "RNA-seq quality control package") |
| 4066 | (description |
| 4067 | "RSeQC provides a number of modules that can comprehensively evaluate |
| 4068 | high throughput sequence data, especially RNA-seq data. Some basic modules |
| 4069 | inspect sequence quality, nucleotide composition bias, PCR bias and GC bias, |
| 4070 | while RNA-seq specific modules evaluate sequencing saturation, mapped reads |
| 4071 | distribution, coverage uniformity, strand specificity, etc.") |
| 4072 | (license license:gpl3+))) |
| 4073 | |
| 4074 | (define-public seek |
| 4075 | ;; There are no release tarballs. According to the installation |
| 4076 | ;; instructions at http://seek.princeton.edu/installation.jsp, the latest |
| 4077 | ;; stable release is identified by this changeset ID. |
| 4078 | (let ((changeset "2329130") |
| 4079 | (revision "1")) |
| 4080 | (package |
| 4081 | (name "seek") |
| 4082 | (version (string-append "0-" revision "." changeset)) |
| 4083 | (source (origin |
| 4084 | (method hg-fetch) |
| 4085 | (uri (hg-reference |
| 4086 | (url "https://bitbucket.org/libsleipnir/sleipnir") |
| 4087 | (changeset changeset))) |
| 4088 | (sha256 |
| 4089 | (base32 |
| 4090 | "0qrvilwh18dpbhkf92qvxbmay0j75ra3jg2wrhz67gf538zzphsx")))) |
| 4091 | (build-system gnu-build-system) |
| 4092 | (arguments |
| 4093 | `(#:modules ((srfi srfi-1) |
| 4094 | (guix build gnu-build-system) |
| 4095 | (guix build utils)) |
| 4096 | #:phases |
| 4097 | (let ((dirs '("SeekMiner" |
| 4098 | "SeekEvaluator" |
| 4099 | "SeekPrep" |
| 4100 | "Distancer" |
| 4101 | "Data2DB" |
| 4102 | "PCL2Bin"))) |
| 4103 | (modify-phases %standard-phases |
| 4104 | (add-before 'configure 'bootstrap |
| 4105 | (lambda _ |
| 4106 | (zero? (system* "bash" "gen_auto")))) |
| 4107 | (add-after 'build 'build-additional-tools |
| 4108 | (lambda* (#:key make-flags #:allow-other-keys) |
| 4109 | (every (lambda (dir) |
| 4110 | (with-directory-excursion (string-append "tools/" dir) |
| 4111 | (zero? (apply system* "make" make-flags)))) |
| 4112 | dirs))) |
| 4113 | (add-after 'install 'install-additional-tools |
| 4114 | (lambda* (#:key make-flags #:allow-other-keys) |
| 4115 | (fold (lambda (dir result) |
| 4116 | (with-directory-excursion (string-append "tools/" dir) |
| 4117 | (and result |
| 4118 | (zero? (apply system* |
| 4119 | `("make" ,@make-flags "install")))))) |
| 4120 | #t dirs))))))) |
| 4121 | (inputs |
| 4122 | `(("gsl" ,gsl) |
| 4123 | ("boost" ,boost) |
| 4124 | ("libsvm" ,libsvm) |
| 4125 | ("readline" ,readline) |
| 4126 | ("gengetopt" ,gengetopt) |
| 4127 | ("log4cpp" ,log4cpp))) |
| 4128 | (native-inputs |
| 4129 | `(("autoconf" ,autoconf) |
| 4130 | ("automake" ,automake) |
| 4131 | ("perl" ,perl))) |
| 4132 | (home-page "http://seek.princeton.edu") |
| 4133 | (synopsis "Gene co-expression search engine") |
| 4134 | (description |
| 4135 | "SEEK is a computational gene co-expression search engine. SEEK provides |
| 4136 | biologists with a way to navigate the massive human expression compendium that |
| 4137 | now contains thousands of expression datasets. SEEK returns a robust ranking |
| 4138 | of co-expressed genes in the biological area of interest defined by the user's |
| 4139 | query genes. It also prioritizes thousands of expression datasets according |
| 4140 | to the user's query of interest.") |
| 4141 | (license license:cc-by3.0)))) |
| 4142 | |
| 4143 | (define-public samtools |
| 4144 | (package |
| 4145 | (name "samtools") |
| 4146 | (version "1.3.1") |
| 4147 | (source |
| 4148 | (origin |
| 4149 | (method url-fetch) |
| 4150 | (uri |
| 4151 | (string-append "mirror://sourceforge/samtools/samtools/" |
| 4152 | version "/samtools-" version ".tar.bz2")) |
| 4153 | (sha256 |
| 4154 | (base32 |
| 4155 | "0znnnxc467jbf1as2dpskrjhfh8mbll760j6w6rdkwlwbqsp8gbc")))) |
| 4156 | (build-system gnu-build-system) |
| 4157 | (arguments |
| 4158 | `(#:modules ((ice-9 ftw) |
| 4159 | (ice-9 regex) |
| 4160 | (guix build gnu-build-system) |
| 4161 | (guix build utils)) |
| 4162 | #:make-flags (list (string-append "prefix=" (assoc-ref %outputs "out"))) |
| 4163 | #:configure-flags (list "--with-ncurses") |
| 4164 | #:phases |
| 4165 | (alist-cons-after |
| 4166 | 'unpack 'patch-tests |
| 4167 | (lambda _ |
| 4168 | (substitute* "test/test.pl" |
| 4169 | ;; The test script calls out to /bin/bash |
| 4170 | (("/bin/bash") (which "bash"))) |
| 4171 | #t) |
| 4172 | (alist-cons-after |
| 4173 | 'install 'install-library |
| 4174 | (lambda* (#:key outputs #:allow-other-keys) |
| 4175 | (let ((lib (string-append (assoc-ref outputs "out") "/lib"))) |
| 4176 | (install-file "libbam.a" lib))) |
| 4177 | (alist-cons-after |
| 4178 | 'install 'install-headers |
| 4179 | (lambda* (#:key outputs #:allow-other-keys) |
| 4180 | (let ((include (string-append (assoc-ref outputs "out") |
| 4181 | "/include/samtools/"))) |
| 4182 | (for-each (lambda (file) |
| 4183 | (install-file file include)) |
| 4184 | (scandir "." (lambda (name) (string-match "\\.h$" name)))) |
| 4185 | #t)) |
| 4186 | %standard-phases))))) |
| 4187 | (native-inputs `(("pkg-config" ,pkg-config))) |
| 4188 | (inputs `(("ncurses" ,ncurses) |
| 4189 | ("perl" ,perl) |
| 4190 | ("python" ,python) |
| 4191 | ("zlib" ,zlib))) |
| 4192 | (home-page "http://samtools.sourceforge.net") |
| 4193 | (synopsis "Utilities to efficiently manipulate nucleotide sequence alignments") |
| 4194 | (description |
| 4195 | "Samtools implements various utilities for post-processing nucleotide |
| 4196 | sequence alignments in the SAM, BAM, and CRAM formats, including indexing, |
| 4197 | variant calling (in conjunction with bcftools), and a simple alignment |
| 4198 | viewer.") |
| 4199 | (license license:expat))) |
| 4200 | |
| 4201 | (define-public samtools-0.1 |
| 4202 | ;; This is the most recent version of the 0.1 line of samtools. The input |
| 4203 | ;; and output formats differ greatly from that used and produced by samtools |
| 4204 | ;; 1.x and is still used in many bioinformatics pipelines. |
| 4205 | (package (inherit samtools) |
| 4206 | (version "0.1.19") |
| 4207 | (source |
| 4208 | (origin |
| 4209 | (method url-fetch) |
| 4210 | (uri |
| 4211 | (string-append "mirror://sourceforge/samtools/samtools/" |
| 4212 | version "/samtools-" version ".tar.bz2")) |
| 4213 | (sha256 |
| 4214 | (base32 "1m33xsfwz0s8qi45lylagfllqg7fphf4dr0780rsvw75av9wk06h")))) |
| 4215 | (arguments |
| 4216 | `(#:tests? #f ;no "check" target |
| 4217 | ,@(substitute-keyword-arguments (package-arguments samtools) |
| 4218 | ((#:make-flags flags) |
| 4219 | `(cons "LIBCURSES=-lncurses" ,flags)) |
| 4220 | ((#:phases phases) |
| 4221 | `(modify-phases ,phases |
| 4222 | (replace 'install |
| 4223 | (lambda* (#:key outputs #:allow-other-keys) |
| 4224 | (let ((bin (string-append |
| 4225 | (assoc-ref outputs "out") "/bin"))) |
| 4226 | (mkdir-p bin) |
| 4227 | (copy-file "samtools" |
| 4228 | (string-append bin "/samtools"))))) |
| 4229 | (delete 'patch-tests) |
| 4230 | (delete 'configure)))))))) |
| 4231 | |
| 4232 | (define-public mosaik |
| 4233 | (let ((commit "5c25216d3522d6a33e53875cd76a6d65001e4e67")) |
| 4234 | (package |
| 4235 | (name "mosaik") |
| 4236 | (version "2.2.30") |
| 4237 | (source (origin |
| 4238 | ;; There are no release tarballs nor tags. |
| 4239 | (method git-fetch) |
| 4240 | (uri (git-reference |
| 4241 | (url "https://github.com/wanpinglee/MOSAIK.git") |
| 4242 | (commit commit))) |
| 4243 | (file-name (string-append name "-" version)) |
| 4244 | (sha256 |
| 4245 | (base32 |
| 4246 | "17gj3s07cm77r41z92awh0bim7w7q7fbn0sf5nkqmcm1vw052qgw")))) |
| 4247 | (build-system gnu-build-system) |
| 4248 | (arguments |
| 4249 | `(#:tests? #f ; no tests |
| 4250 | #:make-flags (list "CC=gcc") |
| 4251 | #:phases |
| 4252 | (modify-phases %standard-phases |
| 4253 | (replace 'configure |
| 4254 | (lambda _ (chdir "src") #t)) |
| 4255 | (replace 'install |
| 4256 | (lambda* (#:key outputs #:allow-other-keys) |
| 4257 | (let ((bin (string-append (assoc-ref outputs "out") |
| 4258 | "/bin"))) |
| 4259 | (mkdir-p bin) |
| 4260 | (copy-recursively "../bin" bin) |
| 4261 | #t)))))) |
| 4262 | (inputs |
| 4263 | `(("perl" ,perl) |
| 4264 | ("zlib" ,zlib))) |
| 4265 | (supported-systems '("x86_64-linux")) |
| 4266 | (home-page "https://code.google.com/p/mosaik-aligner/") |
| 4267 | (synopsis "Map nucleotide sequence reads to reference genomes") |
| 4268 | (description |
| 4269 | "MOSAIK is a program for mapping second and third-generation sequencing |
| 4270 | reads to a reference genome. MOSAIK can align reads generated by all the |
| 4271 | major sequencing technologies, including Illumina, Applied Biosystems SOLiD, |
| 4272 | Roche 454, Ion Torrent and Pacific BioSciences SMRT.") |
| 4273 | ;; MOSAIK is released under the GPLv2+ with the exception of third-party |
| 4274 | ;; code released into the public domain: |
| 4275 | ;; 1. fastlz by Ariya Hidayat - http://www.fastlz.org/ |
| 4276 | ;; 2. MD5 implementation - RSA Data Security, RFC 1321 |
| 4277 | (license (list license:gpl2+ license:public-domain))))) |
| 4278 | |
| 4279 | (define-public ngs-sdk |
| 4280 | (package |
| 4281 | (name "ngs-sdk") |
| 4282 | (version "1.2.5") |
| 4283 | (source |
| 4284 | (origin |
| 4285 | (method url-fetch) |
| 4286 | (uri |
| 4287 | (string-append "https://github.com/ncbi/ngs/archive/" |
| 4288 | version ".tar.gz")) |
| 4289 | (file-name (string-append name "-" version ".tar.gz")) |
| 4290 | (sha256 |
| 4291 | (base32 |
| 4292 | "04y1fsmdnb5y86m3gg6f5g9wcscr6r25n7m8mdlcxy0i2q6w6cia")))) |
| 4293 | (build-system gnu-build-system) |
| 4294 | (arguments |
| 4295 | `(#:parallel-build? #f ; not supported |
| 4296 | #:tests? #f ; no "check" target |
| 4297 | #:phases |
| 4298 | (alist-replace |
| 4299 | 'configure |
| 4300 | (lambda* (#:key outputs #:allow-other-keys) |
| 4301 | (let ((out (assoc-ref outputs "out"))) |
| 4302 | ;; The 'configure' script doesn't recognize things like |
| 4303 | ;; '--enable-fast-install'. |
| 4304 | (zero? (system* "./configure" |
| 4305 | (string-append "--build-prefix=" (getcwd) "/build") |
| 4306 | (string-append "--prefix=" out))))) |
| 4307 | (alist-cons-after |
| 4308 | 'unpack 'enter-dir |
| 4309 | (lambda _ (chdir "ngs-sdk") #t) |
| 4310 | %standard-phases)))) |
| 4311 | (native-inputs `(("perl" ,perl))) |
| 4312 | ;; According to the test |
| 4313 | ;; unless ($MARCH =~ /x86_64/i || $MARCH =~ /i?86/i) |
| 4314 | ;; in ngs-sdk/setup/konfigure.perl |
| 4315 | (supported-systems '("i686-linux" "x86_64-linux")) |
| 4316 | (home-page "https://github.com/ncbi/ngs") |
| 4317 | (synopsis "API for accessing Next Generation Sequencing data") |
| 4318 | (description |
| 4319 | "NGS is a domain-specific API for accessing reads, alignments and pileups |
| 4320 | produced from Next Generation Sequencing. The API itself is independent from |
| 4321 | any particular back-end implementation, and supports use of multiple back-ends |
| 4322 | simultaneously.") |
| 4323 | (license license:public-domain))) |
| 4324 | |
| 4325 | (define-public java-ngs |
| 4326 | (package (inherit ngs-sdk) |
| 4327 | (name "java-ngs") |
| 4328 | (arguments |
| 4329 | `(,@(substitute-keyword-arguments |
| 4330 | `(#:modules ((guix build gnu-build-system) |
| 4331 | (guix build utils) |
| 4332 | (srfi srfi-1) |
| 4333 | (srfi srfi-26)) |
| 4334 | ,@(package-arguments ngs-sdk)) |
| 4335 | ((#:phases phases) |
| 4336 | `(modify-phases ,phases |
| 4337 | (replace 'enter-dir (lambda _ (chdir "ngs-java") #t))))))) |
| 4338 | (inputs |
| 4339 | `(("jdk" ,icedtea "jdk") |
| 4340 | ("ngs-sdk" ,ngs-sdk))) |
| 4341 | (synopsis "Java bindings for NGS SDK"))) |
| 4342 | |
| 4343 | (define-public ncbi-vdb |
| 4344 | (package |
| 4345 | (name "ncbi-vdb") |
| 4346 | (version "2.7.0") |
| 4347 | (source |
| 4348 | (origin |
| 4349 | (method url-fetch) |
| 4350 | (uri |
| 4351 | (string-append "https://github.com/ncbi/ncbi-vdb/archive/" |
| 4352 | version ".tar.gz")) |
| 4353 | (file-name (string-append name "-" version ".tar.gz")) |
| 4354 | (sha256 |
| 4355 | (base32 |
| 4356 | "0x1cg1x8vy0yjlkp0snc1533zcjhxqzqsaiwqk598n7vvw37n8lf")))) |
| 4357 | (build-system gnu-build-system) |
| 4358 | (arguments |
| 4359 | `(#:parallel-build? #f ; not supported |
| 4360 | #:tests? #f ; no "check" target |
| 4361 | #:phases |
| 4362 | (alist-replace |
| 4363 | 'configure |
| 4364 | (lambda* (#:key inputs outputs #:allow-other-keys) |
| 4365 | (let ((out (assoc-ref outputs "out"))) |
| 4366 | ;; Override include path for libmagic |
| 4367 | (substitute* "setup/package.prl" |
| 4368 | (("name => 'magic', Include => '/usr/include'") |
| 4369 | (string-append "name=> 'magic', Include => '" |
| 4370 | (assoc-ref inputs "libmagic") |
| 4371 | "/include" "'"))) |
| 4372 | |
| 4373 | ;; Install kdf5 library (needed by sra-tools) |
| 4374 | (substitute* "build/Makefile.install" |
| 4375 | (("LIBRARIES_TO_INSTALL =") |
| 4376 | "LIBRARIES_TO_INSTALL = kdf5.$(VERSION_LIBX) kdf5.$(VERSION_SHLX)")) |
| 4377 | |
| 4378 | (substitute* "build/Makefile.env" |
| 4379 | (("CFLAGS =" prefix) |
| 4380 | (string-append prefix "-msse2 "))) |
| 4381 | |
| 4382 | ;; The 'configure' script doesn't recognize things like |
| 4383 | ;; '--enable-fast-install'. |
| 4384 | (zero? (system* |
| 4385 | "./configure" |
| 4386 | (string-append "--build-prefix=" (getcwd) "/build") |
| 4387 | (string-append "--prefix=" (assoc-ref outputs "out")) |
| 4388 | (string-append "--debug") |
| 4389 | (string-append "--with-xml2-prefix=" |
| 4390 | (assoc-ref inputs "libxml2")) |
| 4391 | (string-append "--with-ngs-sdk-prefix=" |
| 4392 | (assoc-ref inputs "ngs-sdk")) |
| 4393 | (string-append "--with-ngs-java-prefix=" |
| 4394 | (assoc-ref inputs "java-ngs")) |
| 4395 | (string-append "--with-hdf5-prefix=" |
| 4396 | (assoc-ref inputs "hdf5")))))) |
| 4397 | (alist-cons-after |
| 4398 | 'install 'install-interfaces |
| 4399 | (lambda* (#:key outputs #:allow-other-keys) |
| 4400 | ;; Install interface libraries. On i686 the interface libraries |
| 4401 | ;; are installed to "linux/gcc/i386", so we need to use the Linux |
| 4402 | ;; architecture name ("i386") instead of the target system prefix |
| 4403 | ;; ("i686"). |
| 4404 | (mkdir (string-append (assoc-ref outputs "out") "/ilib")) |
| 4405 | (copy-recursively (string-append "build/ncbi-vdb/linux/gcc/" |
| 4406 | ,(system->linux-architecture |
| 4407 | (or (%current-target-system) |
| 4408 | (%current-system))) |
| 4409 | "/rel/ilib") |
| 4410 | (string-append (assoc-ref outputs "out") |
| 4411 | "/ilib")) |
| 4412 | ;; Install interface headers |
| 4413 | (copy-recursively "interfaces" |
| 4414 | (string-append (assoc-ref outputs "out") |
| 4415 | "/include"))) |
| 4416 | %standard-phases)))) |
| 4417 | (inputs |
| 4418 | `(("libxml2" ,libxml2) |
| 4419 | ("ngs-sdk" ,ngs-sdk) |
| 4420 | ("java-ngs" ,java-ngs) |
| 4421 | ("libmagic" ,file) |
| 4422 | ("hdf5" ,hdf5))) |
| 4423 | (native-inputs `(("perl" ,perl))) |
| 4424 | ;; NCBI-VDB requires SSE capability. |
| 4425 | (supported-systems '("i686-linux" "x86_64-linux")) |
| 4426 | (home-page "https://github.com/ncbi/ncbi-vdb") |
| 4427 | (synopsis "Database engine for genetic information") |
| 4428 | (description |
| 4429 | "The NCBI-VDB library implements a highly compressed columnar data |
| 4430 | warehousing engine that is most often used to store genetic information. |
| 4431 | Databases are stored in a portable image within the file system, and can be |
| 4432 | accessed/downloaded on demand across HTTP.") |
| 4433 | (license license:public-domain))) |
| 4434 | |
| 4435 | (define-public plink |
| 4436 | (package |
| 4437 | (name "plink") |
| 4438 | (version "1.07") |
| 4439 | (source |
| 4440 | (origin |
| 4441 | (method url-fetch) |
| 4442 | (uri (string-append |
| 4443 | "http://pngu.mgh.harvard.edu/~purcell/plink/dist/plink-" |
| 4444 | version "-src.zip")) |
| 4445 | (sha256 |
| 4446 | (base32 "0as8gxm4pjyc8dxmm1sl873rrd7wn5qs0l29nqfnl31x8i467xaa")) |
| 4447 | (patches (search-patches "plink-1.07-unclobber-i.patch" |
| 4448 | "plink-endian-detection.patch")))) |
| 4449 | (build-system gnu-build-system) |
| 4450 | (arguments |
| 4451 | '(#:tests? #f ;no "check" target |
| 4452 | #:make-flags (list (string-append "LIB_LAPACK=" |
| 4453 | (assoc-ref %build-inputs "lapack") |
| 4454 | "/lib/liblapack.so") |
| 4455 | "WITH_LAPACK=1" |
| 4456 | "FORCE_DYNAMIC=1" |
| 4457 | ;; disable phoning home |
| 4458 | "WITH_WEBCHECK=") |
| 4459 | #:phases |
| 4460 | (modify-phases %standard-phases |
| 4461 | ;; no "configure" script |
| 4462 | (delete 'configure) |
| 4463 | (replace 'install |
| 4464 | (lambda* (#:key outputs #:allow-other-keys) |
| 4465 | (let ((bin (string-append (assoc-ref outputs "out") |
| 4466 | "/bin/"))) |
| 4467 | (install-file "plink" bin) |
| 4468 | #t)))))) |
| 4469 | (inputs |
| 4470 | `(("zlib" ,zlib) |
| 4471 | ("lapack" ,lapack))) |
| 4472 | (native-inputs |
| 4473 | `(("unzip" ,unzip))) |
| 4474 | (home-page "http://pngu.mgh.harvard.edu/~purcell/plink/") |
| 4475 | (synopsis "Whole genome association analysis toolset") |
| 4476 | (description |
| 4477 | "PLINK is a whole genome association analysis toolset, designed to |
| 4478 | perform a range of basic, large-scale analyses in a computationally efficient |
| 4479 | manner. The focus of PLINK is purely on analysis of genotype/phenotype data, |
| 4480 | so there is no support for steps prior to this (e.g. study design and |
| 4481 | planning, generating genotype or CNV calls from raw data). Through |
| 4482 | integration with gPLINK and Haploview, there is some support for the |
| 4483 | subsequent visualization, annotation and storage of results.") |
| 4484 | ;; Code is released under GPLv2, except for fisher.h, which is under |
| 4485 | ;; LGPLv2.1+ |
| 4486 | (license (list license:gpl2 license:lgpl2.1+)))) |
| 4487 | |
| 4488 | (define-public smithlab-cpp |
| 4489 | (let ((revision "1") |
| 4490 | (commit "728a097bec88c6f4b8528b685932049e660eff2e")) |
| 4491 | (package |
| 4492 | (name "smithlab-cpp") |
| 4493 | (version (string-append "0." revision "." (string-take commit 7))) |
| 4494 | (source (origin |
| 4495 | (method git-fetch) |
| 4496 | (uri (git-reference |
| 4497 | (url "https://github.com/smithlabcode/smithlab_cpp.git") |
| 4498 | (commit commit))) |
| 4499 | (file-name (string-append name "-" version "-checkout")) |
| 4500 | (sha256 |
| 4501 | (base32 |
| 4502 | "0d476lmj312xk77kr9fzrv7z1bv96yfyx0w7y62ycmnfbx32ll74")))) |
| 4503 | (build-system gnu-build-system) |
| 4504 | (arguments |
| 4505 | `(#:modules ((guix build gnu-build-system) |
| 4506 | (guix build utils) |
| 4507 | (srfi srfi-26)) |
| 4508 | #:tests? #f ;no "check" target |
| 4509 | #:phases |
| 4510 | (modify-phases %standard-phases |
| 4511 | (add-after 'unpack 'use-samtools-headers |
| 4512 | (lambda _ |
| 4513 | (substitute* '("SAM.cpp" |
| 4514 | "SAM.hpp") |
| 4515 | (("sam.h") "samtools/sam.h")) |
| 4516 | #t)) |
| 4517 | (replace 'install |
| 4518 | (lambda* (#:key outputs #:allow-other-keys) |
| 4519 | (let* ((out (assoc-ref outputs "out")) |
| 4520 | (lib (string-append out "/lib")) |
| 4521 | (include (string-append out "/include/smithlab-cpp"))) |
| 4522 | (mkdir-p lib) |
| 4523 | (mkdir-p include) |
| 4524 | (for-each (cut install-file <> lib) |
| 4525 | (find-files "." "\\.o$")) |
| 4526 | (for-each (cut install-file <> include) |
| 4527 | (find-files "." "\\.hpp$"))) |
| 4528 | #t)) |
| 4529 | (delete 'configure)))) |
| 4530 | (inputs |
| 4531 | `(("samtools" ,samtools-0.1) |
| 4532 | ("zlib" ,zlib))) |
| 4533 | (home-page "https://github.com/smithlabcode/smithlab_cpp") |
| 4534 | (synopsis "C++ helper library for functions used in Smith lab projects") |
| 4535 | (description |
| 4536 | "Smithlab CPP is a C++ library that includes functions used in many of |
| 4537 | the Smith lab bioinformatics projects, such as a wrapper around Samtools data |
| 4538 | structures, classes for genomic regions, mapped sequencing reads, etc.") |
| 4539 | (license license:gpl3+)))) |
| 4540 | |
| 4541 | (define-public preseq |
| 4542 | (package |
| 4543 | (name "preseq") |
| 4544 | (version "2.0") |
| 4545 | (source (origin |
| 4546 | (method url-fetch) |
| 4547 | (uri (string-append "https://github.com/smithlabcode/" |
| 4548 | "preseq/archive/v" version ".tar.gz")) |
| 4549 | (file-name (string-append name "-" version ".tar.gz")) |
| 4550 | (sha256 |
| 4551 | (base32 "08r684l50pnxjpvmhzjgqq56yv9rfw90k8vx0nsrnrzk8mf9hsdq")) |
| 4552 | (modules '((guix build utils))) |
| 4553 | (snippet |
| 4554 | ;; Remove bundled samtools. |
| 4555 | '(delete-file-recursively "samtools")))) |
| 4556 | (build-system gnu-build-system) |
| 4557 | (arguments |
| 4558 | `(#:tests? #f ;no "check" target |
| 4559 | #:phases |
| 4560 | (modify-phases %standard-phases |
| 4561 | (delete 'configure)) |
| 4562 | #:make-flags |
| 4563 | (list (string-append "PREFIX=" |
| 4564 | (assoc-ref %outputs "out")) |
| 4565 | (string-append "LIBBAM=" |
| 4566 | (assoc-ref %build-inputs "samtools") |
| 4567 | "/lib/libbam.a") |
| 4568 | (string-append "SMITHLAB_CPP=" |
| 4569 | (assoc-ref %build-inputs "smithlab-cpp") |
| 4570 | "/lib") |
| 4571 | "PROGS=preseq" |
| 4572 | "INCLUDEDIRS=$(SMITHLAB_CPP)/../include/smithlab-cpp $(SAMTOOLS_DIR)"))) |
| 4573 | (inputs |
| 4574 | `(("gsl" ,gsl) |
| 4575 | ("samtools" ,samtools-0.1) |
| 4576 | ("smithlab-cpp" ,smithlab-cpp) |
| 4577 | ("zlib" ,zlib))) |
| 4578 | (home-page "http://smithlabresearch.org/software/preseq/") |
| 4579 | (synopsis "Program for analyzing library complexity") |
| 4580 | (description |
| 4581 | "The preseq package is aimed at predicting and estimating the complexity |
| 4582 | of a genomic sequencing library, equivalent to predicting and estimating the |
| 4583 | number of redundant reads from a given sequencing depth and how many will be |
| 4584 | expected from additional sequencing using an initial sequencing experiment. |
| 4585 | The estimates can then be used to examine the utility of further sequencing, |
| 4586 | optimize the sequencing depth, or to screen multiple libraries to avoid low |
| 4587 | complexity samples.") |
| 4588 | (license license:gpl3+))) |
| 4589 | |
| 4590 | (define-public python-screed |
| 4591 | (package |
| 4592 | (name "python-screed") |
| 4593 | (version "0.9") |
| 4594 | (source |
| 4595 | (origin |
| 4596 | (method url-fetch) |
| 4597 | (uri (pypi-uri "screed" version)) |
| 4598 | (sha256 |
| 4599 | (base32 |
| 4600 | "18czszp9fkx3j6jr7y5kp6dfialscgddk05mw1zkhh2zhn0jd8i0")))) |
| 4601 | (build-system python-build-system) |
| 4602 | (arguments |
| 4603 | `(#:phases |
| 4604 | (modify-phases %standard-phases |
| 4605 | (replace 'check |
| 4606 | (lambda _ |
| 4607 | (setenv "PYTHONPATH" |
| 4608 | (string-append (getenv "PYTHONPATH") ":.")) |
| 4609 | (zero? (system* "nosetests" "--attr" "!known_failing"))))))) |
| 4610 | (native-inputs |
| 4611 | `(("python-nose" ,python-nose))) |
| 4612 | (inputs |
| 4613 | `(("python-bz2file" ,python-bz2file))) |
| 4614 | (home-page "http://github.com/dib-lab/screed/") |
| 4615 | (synopsis "Short read sequence database utilities") |
| 4616 | (description "Screed parses FASTA and FASTQ files and generates databases. |
| 4617 | Values such as sequence name, sequence description, sequence quality and the |
| 4618 | sequence itself can be retrieved from these databases.") |
| 4619 | (license license:bsd-3))) |
| 4620 | |
| 4621 | (define-public python2-screed |
| 4622 | (package-with-python2 python-screed)) |
| 4623 | |
| 4624 | (define-public sra-tools |
| 4625 | (package |
| 4626 | (name "sra-tools") |
| 4627 | (version "2.7.0") |
| 4628 | (source |
| 4629 | (origin |
| 4630 | (method url-fetch) |
| 4631 | (uri |
| 4632 | (string-append "https://github.com/ncbi/sra-tools/archive/" |
| 4633 | version ".tar.gz")) |
| 4634 | (file-name (string-append name "-" version ".tar.gz")) |
| 4635 | (sha256 |
| 4636 | (base32 |
| 4637 | "13paw7bq6y47d2pl0ac5gpgcqp1xsy1g7v1fwysm3hr8lb2dck17")))) |
| 4638 | (build-system gnu-build-system) |
| 4639 | (arguments |
| 4640 | `(#:parallel-build? #f ; not supported |
| 4641 | #:tests? #f ; no "check" target |
| 4642 | #:make-flags |
| 4643 | (list (string-append "VDB_LIBDIR=" |
| 4644 | (assoc-ref %build-inputs "ncbi-vdb") |
| 4645 | ,(if (string-prefix? "x86_64" |
| 4646 | (or (%current-target-system) |
| 4647 | (%current-system))) |
| 4648 | "/lib64" |
| 4649 | "/lib32"))) |
| 4650 | #:phases |
| 4651 | (alist-replace |
| 4652 | 'configure |
| 4653 | (lambda* (#:key inputs outputs #:allow-other-keys) |
| 4654 | ;; The build system expects a directory containing the sources and |
| 4655 | ;; raw build output of ncbi-vdb, including files that are not |
| 4656 | ;; installed. Since we are building against an installed version of |
| 4657 | ;; ncbi-vdb, the following modifications are needed. |
| 4658 | (substitute* "setup/konfigure.perl" |
| 4659 | ;; Make the configure script look for the "ilib" directory of |
| 4660 | ;; "ncbi-vdb" without first checking for the existence of a |
| 4661 | ;; matching library in its "lib" directory. |
| 4662 | (("^ my \\$f = File::Spec->catdir\\(\\$libdir, \\$lib\\);") |
| 4663 | "my $f = File::Spec->catdir($ilibdir, $ilib);") |
| 4664 | ;; Look for interface libraries in ncbi-vdb's "ilib" directory. |
| 4665 | (("my \\$ilibdir = File::Spec->catdir\\(\\$builddir, 'ilib'\\);") |
| 4666 | "my $ilibdir = File::Spec->catdir($dir, 'ilib');")) |
| 4667 | |
| 4668 | ;; Dynamic linking |
| 4669 | (substitute* "tools/copycat/Makefile" |
| 4670 | (("smagic-static") "lmagic")) |
| 4671 | |
| 4672 | ;; The 'configure' script doesn't recognize things like |
| 4673 | ;; '--enable-fast-install'. |
| 4674 | (zero? (system* |
| 4675 | "./configure" |
| 4676 | (string-append "--build-prefix=" (getcwd) "/build") |
| 4677 | (string-append "--prefix=" (assoc-ref outputs "out")) |
| 4678 | (string-append "--debug") |
| 4679 | (string-append "--with-fuse-prefix=" |
| 4680 | (assoc-ref inputs "fuse")) |
| 4681 | (string-append "--with-magic-prefix=" |
| 4682 | (assoc-ref inputs "libmagic")) |
| 4683 | ;; TODO: building with libxml2 fails with linker errors |
| 4684 | ;; (string-append "--with-xml2-prefix=" |
| 4685 | ;; (assoc-ref inputs "libxml2")) |
| 4686 | (string-append "--with-ncbi-vdb-sources=" |
| 4687 | (assoc-ref inputs "ncbi-vdb")) |
| 4688 | (string-append "--with-ncbi-vdb-build=" |
| 4689 | (assoc-ref inputs "ncbi-vdb")) |
| 4690 | (string-append "--with-ngs-sdk-prefix=" |
| 4691 | (assoc-ref inputs "ngs-sdk")) |
| 4692 | (string-append "--with-hdf5-prefix=" |
| 4693 | (assoc-ref inputs "hdf5"))))) |
| 4694 | %standard-phases))) |
| 4695 | (native-inputs `(("perl" ,perl))) |
| 4696 | (inputs |
| 4697 | `(("ngs-sdk" ,ngs-sdk) |
| 4698 | ("ncbi-vdb" ,ncbi-vdb) |
| 4699 | ("libmagic" ,file) |
| 4700 | ("fuse" ,fuse) |
| 4701 | ("hdf5" ,hdf5) |
| 4702 | ("zlib" ,zlib))) |
| 4703 | (home-page "http://www.ncbi.nlm.nih.gov/Traces/sra/sra.cgi?view=software") |
| 4704 | (synopsis "Tools and libraries for reading and writing sequencing data") |
| 4705 | (description |
| 4706 | "The SRA Toolkit from NCBI is a collection of tools and libraries for |
| 4707 | reading of sequencing files from the Sequence Read Archive (SRA) database and |
| 4708 | writing files into the .sra format.") |
| 4709 | (license license:public-domain))) |
| 4710 | |
| 4711 | (define-public seqan |
| 4712 | (package |
| 4713 | (name "seqan") |
| 4714 | (version "1.4.2") |
| 4715 | (source (origin |
| 4716 | (method url-fetch) |
| 4717 | (uri (string-append "http://packages.seqan.de/seqan-library/" |
| 4718 | "seqan-library-" version ".tar.bz2")) |
| 4719 | (sha256 |
| 4720 | (base32 |
| 4721 | "05s3wrrwn50f81aklfm65i4a749zag1vr8z03k21xm0pdxy47yvp")))) |
| 4722 | ;; The documentation is 7.8MB and the includes are 3.6MB heavy, so it |
| 4723 | ;; makes sense to split the outputs. |
| 4724 | (outputs '("out" "doc")) |
| 4725 | (build-system trivial-build-system) |
| 4726 | (arguments |
| 4727 | `(#:modules ((guix build utils)) |
| 4728 | #:builder |
| 4729 | (begin |
| 4730 | (use-modules (guix build utils)) |
| 4731 | (let ((tar (assoc-ref %build-inputs "tar")) |
| 4732 | (bzip (assoc-ref %build-inputs "bzip2")) |
| 4733 | (out (assoc-ref %outputs "out")) |
| 4734 | (doc (assoc-ref %outputs "doc"))) |
| 4735 | (setenv "PATH" (string-append tar "/bin:" bzip "/bin")) |
| 4736 | (system* "tar" "xvf" (assoc-ref %build-inputs "source")) |
| 4737 | (chdir (string-append "seqan-library-" ,version)) |
| 4738 | (copy-recursively "include" (string-append out "/include")) |
| 4739 | (copy-recursively "share" (string-append doc "/share")))))) |
| 4740 | (native-inputs |
| 4741 | `(("source" ,source) |
| 4742 | ("tar" ,tar) |
| 4743 | ("bzip2" ,bzip2))) |
| 4744 | (home-page "http://www.seqan.de") |
| 4745 | (synopsis "Library for nucleotide sequence analysis") |
| 4746 | (description |
| 4747 | "SeqAn is a C++ library of efficient algorithms and data structures for |
| 4748 | the analysis of sequences with the focus on biological data. It contains |
| 4749 | algorithms and data structures for string representation and their |
| 4750 | manipulation, online and indexed string search, efficient I/O of |
| 4751 | bioinformatics file formats, sequence alignment, and more.") |
| 4752 | (license license:bsd-3))) |
| 4753 | |
| 4754 | (define-public seqmagick |
| 4755 | (package |
| 4756 | (name "seqmagick") |
| 4757 | (version "0.6.1") |
| 4758 | (source |
| 4759 | (origin |
| 4760 | (method url-fetch) |
| 4761 | (uri (string-append |
| 4762 | "https://pypi.python.org/packages/source/s/seqmagick/seqmagick-" |
| 4763 | version ".tar.gz")) |
| 4764 | (sha256 |
| 4765 | (base32 |
| 4766 | "0cgn477n74gsl4qdaakrrhi953kcsd4q3ivk2lr18x74s3g4ma1d")))) |
| 4767 | (build-system python-build-system) |
| 4768 | (arguments |
| 4769 | ;; python2 only, see https://github.com/fhcrc/seqmagick/issues/56 |
| 4770 | `(#:python ,python-2 |
| 4771 | #:phases |
| 4772 | (modify-phases %standard-phases |
| 4773 | ;; Current test in setup.py does not work as of 0.6.1, |
| 4774 | ;; so use nose to run tests instead for now. See |
| 4775 | ;; https://github.com/fhcrc/seqmagick/issues/55 |
| 4776 | (replace 'check (lambda _ (zero? (system* "nosetests"))))))) |
| 4777 | (inputs |
| 4778 | ;; biopython-1.66 is required due to |
| 4779 | ;; https://github.com/fhcrc/seqmagick/issues/59 |
| 4780 | ;; When that issue is resolved the 'python2-biopython-1.66' package |
| 4781 | ;; should be removed. |
| 4782 | `(("python-biopython" ,python2-biopython-1.66))) |
| 4783 | (native-inputs |
| 4784 | `(("python-nose" ,python2-nose))) |
| 4785 | (home-page "http://github.com/fhcrc/seqmagick") |
| 4786 | (synopsis "Tools for converting and modifying sequence files") |
| 4787 | (description |
| 4788 | "Bioinformaticians often have to convert sequence files between formats |
| 4789 | and do little manipulations on them, and it's not worth writing scripts for |
| 4790 | that. Seqmagick is a utility to expose the file format conversion in |
| 4791 | BioPython in a convenient way. Instead of having a big mess of scripts, there |
| 4792 | is one that takes arguments.") |
| 4793 | (license license:gpl3))) |
| 4794 | |
| 4795 | (define-public seqtk |
| 4796 | (package |
| 4797 | (name "seqtk") |
| 4798 | (version "1.2") |
| 4799 | (source (origin |
| 4800 | (method url-fetch) |
| 4801 | (uri (string-append |
| 4802 | "https://github.com/lh3/seqtk/archive/v" |
| 4803 | version ".tar.gz")) |
| 4804 | (file-name (string-append name "-" version ".tar.gz")) |
| 4805 | (sha256 |
| 4806 | (base32 |
| 4807 | "0ywdyzpmfiz2wp6ampbzqg4y8bj450nfgqarpamg045b8mk32lxx")) |
| 4808 | (modules '((guix build utils))) |
| 4809 | (snippet |
| 4810 | '(begin |
| 4811 | ;; Remove extraneous header files, as is done in the seqtk |
| 4812 | ;; master branch. |
| 4813 | (for-each (lambda (file) (delete-file file)) |
| 4814 | (list "ksort.h" "kstring.h" "kvec.h")) |
| 4815 | #t)))) |
| 4816 | (build-system gnu-build-system) |
| 4817 | (arguments |
| 4818 | `(#:phases |
| 4819 | (modify-phases %standard-phases |
| 4820 | (delete 'configure) |
| 4821 | (replace 'check |
| 4822 | ;; There are no tests, so we just run a sanity check. |
| 4823 | (lambda _ (zero? (system* "./seqtk" "seq")))) |
| 4824 | (replace 'install |
| 4825 | (lambda* (#:key outputs #:allow-other-keys) |
| 4826 | (let ((bin (string-append (assoc-ref outputs "out") "/bin/"))) |
| 4827 | (install-file "seqtk" bin))))))) |
| 4828 | (inputs |
| 4829 | `(("zlib" ,zlib))) |
| 4830 | (home-page "https://github.com/lh3/seqtk") |
| 4831 | (synopsis "Toolkit for processing biological sequences in FASTA/Q format") |
| 4832 | (description |
| 4833 | "Seqtk is a fast and lightweight tool for processing sequences in the |
| 4834 | FASTA or FASTQ format. It parses both FASTA and FASTQ files which can be |
| 4835 | optionally compressed by gzip.") |
| 4836 | (license license:expat))) |
| 4837 | |
| 4838 | (define-public snap-aligner |
| 4839 | (package |
| 4840 | (name "snap-aligner") |
| 4841 | (version "1.0beta.18") |
| 4842 | (source (origin |
| 4843 | (method url-fetch) |
| 4844 | (uri (string-append |
| 4845 | "https://github.com/amplab/snap/archive/v" |
| 4846 | version ".tar.gz")) |
| 4847 | (file-name (string-append name "-" version ".tar.gz")) |
| 4848 | (sha256 |
| 4849 | (base32 |
| 4850 | "1vnsjwv007k1fl1q7d681kbwn6bc66cgw6h16hym6gvyy71qv2ly")))) |
| 4851 | (build-system gnu-build-system) |
| 4852 | (arguments |
| 4853 | '(#:phases |
| 4854 | (modify-phases %standard-phases |
| 4855 | (delete 'configure) |
| 4856 | (replace 'check (lambda _ (zero? (system* "./unit_tests")))) |
| 4857 | (replace 'install |
| 4858 | (lambda* (#:key outputs #:allow-other-keys) |
| 4859 | (let* ((out (assoc-ref outputs "out")) |
| 4860 | (bin (string-append out "/bin"))) |
| 4861 | (install-file "snap-aligner" bin) |
| 4862 | (install-file "SNAPCommand" bin) |
| 4863 | #t)))))) |
| 4864 | (native-inputs |
| 4865 | `(("zlib" ,zlib))) |
| 4866 | (home-page "http://snap.cs.berkeley.edu/") |
| 4867 | (synopsis "Short read DNA sequence aligner") |
| 4868 | (description |
| 4869 | "SNAP is a fast and accurate aligner for short DNA reads. It is |
| 4870 | optimized for modern read lengths of 100 bases or higher, and takes advantage |
| 4871 | of these reads to align data quickly through a hash-based indexing scheme.") |
| 4872 | ;; 32-bit systems are not supported by the unpatched code. |
| 4873 | ;; Following the bug reports https://github.com/amplab/snap/issues/68 and |
| 4874 | ;; https://bugs.debian.org/cgi-bin/bugreport.cgi?bug=812378 we see that |
| 4875 | ;; systems without a lot of memory cannot make good use of this program. |
| 4876 | (supported-systems '("x86_64-linux")) |
| 4877 | (license license:asl2.0))) |
| 4878 | |
| 4879 | (define-public sortmerna |
| 4880 | (package |
| 4881 | (name "sortmerna") |
| 4882 | (version "2.1b") |
| 4883 | (source |
| 4884 | (origin |
| 4885 | (method url-fetch) |
| 4886 | (uri (string-append |
| 4887 | "https://github.com/biocore/sortmerna/archive/" |
| 4888 | version ".tar.gz")) |
| 4889 | (file-name (string-append name "-" version ".tar.gz")) |
| 4890 | (sha256 |
| 4891 | (base32 |
| 4892 | "1ghaghvd82af9j5adavxh77g7hm247d1r69m3fbi6f1jdivj5ldk")))) |
| 4893 | (build-system gnu-build-system) |
| 4894 | (outputs '("out" ;for binaries |
| 4895 | "db")) ;for sequence databases |
| 4896 | (arguments |
| 4897 | `(#:phases |
| 4898 | (modify-phases %standard-phases |
| 4899 | (replace 'install |
| 4900 | (lambda* (#:key outputs #:allow-other-keys) |
| 4901 | (let* ((out (assoc-ref outputs "out")) |
| 4902 | (bin (string-append out "/bin")) |
| 4903 | (db (assoc-ref outputs "db")) |
| 4904 | (share |
| 4905 | (string-append db "/share/sortmerna/rRNA_databases"))) |
| 4906 | (install-file "sortmerna" bin) |
| 4907 | (install-file "indexdb_rna" bin) |
| 4908 | (for-each (lambda (file) |
| 4909 | (install-file file share)) |
| 4910 | (find-files "rRNA_databases" ".*fasta")) |
| 4911 | #t)))))) |
| 4912 | (inputs |
| 4913 | `(("zlib" ,zlib))) |
| 4914 | (home-page "http://bioinfo.lifl.fr/RNA/sortmerna") |
| 4915 | (synopsis "Biological sequence analysis tool for NGS reads") |
| 4916 | (description |
| 4917 | "SortMeRNA is a biological sequence analysis tool for filtering, mapping |
| 4918 | and operational taxonomic unit (OTU) picking of next generation |
| 4919 | sequencing (NGS) reads. The core algorithm is based on approximate seeds and |
| 4920 | allows for fast and sensitive analyses of nucleotide sequences. The main |
| 4921 | application of SortMeRNA is filtering rRNA from metatranscriptomic data.") |
| 4922 | (license license:lgpl3))) |
| 4923 | |
| 4924 | (define-public star |
| 4925 | (package |
| 4926 | (name "star") |
| 4927 | (version "2.5.2a") |
| 4928 | (source (origin |
| 4929 | (method url-fetch) |
| 4930 | (uri (string-append "https://github.com/alexdobin/STAR/archive/" |
| 4931 | version ".tar.gz")) |
| 4932 | (file-name (string-append name "-" version ".tar.gz")) |
| 4933 | (sha256 |
| 4934 | (base32 |
| 4935 | "0xjlsm4p9flln111hv4xx7xy94c2nl53zvdvbk9winmiradjsdra")) |
| 4936 | (modules '((guix build utils))) |
| 4937 | (snippet |
| 4938 | '(begin |
| 4939 | (substitute* "source/Makefile" |
| 4940 | (("/bin/rm") "rm")) |
| 4941 | ;; Remove pre-built binaries and bundled htslib sources. |
| 4942 | (delete-file-recursively "bin/MacOSX_x86_64") |
| 4943 | (delete-file-recursively "bin/Linux_x86_64") |
| 4944 | (delete-file-recursively "source/htslib") |
| 4945 | #t)))) |
| 4946 | (build-system gnu-build-system) |
| 4947 | (arguments |
| 4948 | '(#:tests? #f ;no check target |
| 4949 | #:make-flags '("STAR") |
| 4950 | #:phases |
| 4951 | (modify-phases %standard-phases |
| 4952 | (add-after 'unpack 'enter-source-dir |
| 4953 | (lambda _ (chdir "source") #t)) |
| 4954 | (add-after 'enter-source-dir 'do-not-use-bundled-htslib |
| 4955 | (lambda _ |
| 4956 | (substitute* "Makefile" |
| 4957 | (("(Depend.list: \\$\\(SOURCES\\) parametersDefault\\.xxd) htslib" |
| 4958 | _ prefix) prefix)) |
| 4959 | (substitute* '("BAMfunctions.cpp" |
| 4960 | "signalFromBAM.h" |
| 4961 | "bam_cat.h" |
| 4962 | "bam_cat.c" |
| 4963 | "STAR.cpp" |
| 4964 | "bamRemoveDuplicates.cpp") |
| 4965 | (("#include \"htslib/([^\"]+\\.h)\"" _ header) |
| 4966 | (string-append "#include <" header ">"))) |
| 4967 | (substitute* "IncludeDefine.h" |
| 4968 | (("\"htslib/(htslib/[^\"]+.h)\"" _ header) |
| 4969 | (string-append "<" header ">"))) |
| 4970 | #t)) |
| 4971 | (replace 'install |
| 4972 | (lambda* (#:key outputs #:allow-other-keys) |
| 4973 | (let ((bin (string-append (assoc-ref outputs "out") "/bin/"))) |
| 4974 | (install-file "STAR" bin)) |
| 4975 | #t)) |
| 4976 | (delete 'configure)))) |
| 4977 | (native-inputs |
| 4978 | `(("vim" ,vim))) ; for xxd |
| 4979 | (inputs |
| 4980 | `(("htslib" ,htslib) |
| 4981 | ("zlib" ,zlib))) |
| 4982 | (home-page "https://github.com/alexdobin/STAR") |
| 4983 | (synopsis "Universal RNA-seq aligner") |
| 4984 | (description |
| 4985 | "The Spliced Transcripts Alignment to a Reference (STAR) software is |
| 4986 | based on a previously undescribed RNA-seq alignment algorithm that uses |
| 4987 | sequential maximum mappable seed search in uncompressed suffix arrays followed |
| 4988 | by seed clustering and stitching procedure. In addition to unbiased de novo |
| 4989 | detection of canonical junctions, STAR can discover non-canonical splices and |
| 4990 | chimeric (fusion) transcripts, and is also capable of mapping full-length RNA |
| 4991 | sequences.") |
| 4992 | ;; Only 64-bit systems are supported according to the README. |
| 4993 | (supported-systems '("x86_64-linux" "mips64el-linux")) |
| 4994 | ;; STAR is licensed under GPLv3 or later; htslib is MIT-licensed. |
| 4995 | (license license:gpl3+))) |
| 4996 | |
| 4997 | (define-public subread |
| 4998 | (package |
| 4999 | (name "subread") |
| 5000 | (version "1.5.1") |
| 5001 | (source (origin |
| 5002 | (method url-fetch) |
| 5003 | (uri (string-append "mirror://sourceforge/subread/subread-" |
| 5004 | version "/subread-" version "-source.tar.gz")) |
| 5005 | (sha256 |
| 5006 | (base32 |
| 5007 | "0gn5zhbvllks0mmdg3qlmsbg91p2mpdc2wixwfqpi85yzfrh8hcy")))) |
| 5008 | (build-system gnu-build-system) |
| 5009 | (arguments |
| 5010 | `(#:tests? #f ;no "check" target |
| 5011 | ;; The CC and CCFLAGS variables are set to contain a lot of x86_64 |
| 5012 | ;; optimizations by default, so we override these flags such that x86_64 |
| 5013 | ;; flags are only added when the build target is an x86_64 system. |
| 5014 | #:make-flags |
| 5015 | (list (let ((system ,(or (%current-target-system) |
| 5016 | (%current-system))) |
| 5017 | (flags '("-ggdb" "-fomit-frame-pointer" |
| 5018 | "-ffast-math" "-funroll-loops" |
| 5019 | "-fmessage-length=0" |
| 5020 | "-O9" "-Wall" "-DMAKE_FOR_EXON" |
| 5021 | "-DMAKE_STANDALONE" |
| 5022 | "-DSUBREAD_VERSION=\\\"${SUBREAD_VERSION}\\\"")) |
| 5023 | (flags64 '("-mmmx" "-msse" "-msse2" "-msse3"))) |
| 5024 | (if (string-prefix? "x86_64" system) |
| 5025 | (string-append "CCFLAGS=" (string-join (append flags flags64))) |
| 5026 | (string-append "CCFLAGS=" (string-join flags)))) |
| 5027 | "-f" "Makefile.Linux" |
| 5028 | "CC=gcc ${CCFLAGS}") |
| 5029 | #:phases |
| 5030 | (alist-cons-after |
| 5031 | 'unpack 'enter-dir |
| 5032 | (lambda _ (chdir "src") #t) |
| 5033 | (alist-replace |
| 5034 | 'install |
| 5035 | (lambda* (#:key outputs #:allow-other-keys) |
| 5036 | (let ((bin (string-append (assoc-ref outputs "out") "/bin/"))) |
| 5037 | (mkdir-p bin) |
| 5038 | (copy-recursively "../bin" bin))) |
| 5039 | ;; no "configure" script |
| 5040 | (alist-delete 'configure %standard-phases))))) |
| 5041 | (inputs `(("zlib" ,zlib))) |
| 5042 | (home-page "http://bioinf.wehi.edu.au/subread-package/") |
| 5043 | (synopsis "Tool kit for processing next-gen sequencing data") |
| 5044 | (description |
| 5045 | "The subread package contains the following tools: subread aligner, a |
| 5046 | general-purpose read aligner; subjunc aligner: detecting exon-exon junctions |
| 5047 | and mapping RNA-seq reads; featureCounts: counting mapped reads for genomic |
| 5048 | features; exactSNP: a SNP caller that discovers SNPs by testing signals |
| 5049 | against local background noises.") |
| 5050 | (license license:gpl3+))) |
| 5051 | |
| 5052 | (define-public stringtie |
| 5053 | (package |
| 5054 | (name "stringtie") |
| 5055 | (version "1.2.1") |
| 5056 | (source (origin |
| 5057 | (method url-fetch) |
| 5058 | (uri (string-append "http://ccb.jhu.edu/software/stringtie/dl/" |
| 5059 | "stringtie-" version ".tar.gz")) |
| 5060 | (sha256 |
| 5061 | (base32 |
| 5062 | "1cqllsc1maq4kh92isi8yadgzbmnf042hlnalpk3y59aph1z3bfz")) |
| 5063 | (modules '((guix build utils))) |
| 5064 | (snippet |
| 5065 | '(begin |
| 5066 | (delete-file-recursively "samtools-0.1.18") |
| 5067 | #t)))) |
| 5068 | (build-system gnu-build-system) |
| 5069 | (arguments |
| 5070 | `(#:tests? #f ;no test suite |
| 5071 | #:phases |
| 5072 | (modify-phases %standard-phases |
| 5073 | ;; no configure script |
| 5074 | (delete 'configure) |
| 5075 | (add-before 'build 'use-system-samtools |
| 5076 | (lambda _ |
| 5077 | (substitute* "Makefile" |
| 5078 | (("stringtie: \\$\\{BAM\\}/libbam\\.a") |
| 5079 | "stringtie: ")) |
| 5080 | (substitute* '("gclib/GBam.h" |
| 5081 | "gclib/GBam.cpp") |
| 5082 | (("#include \"(bam|sam|kstring).h\"" _ header) |
| 5083 | (string-append "#include <samtools/" header ".h>"))) |
| 5084 | #t)) |
| 5085 | (replace 'install |
| 5086 | (lambda* (#:key outputs #:allow-other-keys) |
| 5087 | (let ((bin (string-append (assoc-ref outputs "out") "/bin/"))) |
| 5088 | (install-file "stringtie" bin) |
| 5089 | #t)))))) |
| 5090 | (inputs |
| 5091 | `(("samtools" ,samtools-0.1) |
| 5092 | ("zlib" ,zlib))) |
| 5093 | (home-page "http://ccb.jhu.edu/software/stringtie/") |
| 5094 | (synopsis "Transcript assembly and quantification for RNA-Seq data") |
| 5095 | (description |
| 5096 | "StringTie is a fast and efficient assembler of RNA-Seq sequence |
| 5097 | alignments into potential transcripts. It uses a novel network flow algorithm |
| 5098 | as well as an optional de novo assembly step to assemble and quantitate |
| 5099 | full-length transcripts representing multiple splice variants for each gene |
| 5100 | locus. Its input can include not only the alignments of raw reads used by |
| 5101 | other transcript assemblers, but also alignments of longer sequences that have |
| 5102 | been assembled from those reads. To identify differentially expressed genes |
| 5103 | between experiments, StringTie's output can be processed either by the |
| 5104 | Cuffdiff or Ballgown programs.") |
| 5105 | (license license:artistic2.0))) |
| 5106 | |
| 5107 | (define-public vcftools |
| 5108 | (package |
| 5109 | (name "vcftools") |
| 5110 | (version "0.1.14") |
| 5111 | (source (origin |
| 5112 | (method url-fetch) |
| 5113 | (uri (string-append |
| 5114 | "https://github.com/vcftools/vcftools/releases/download/v" |
| 5115 | version "/vcftools-" version ".tar.gz")) |
| 5116 | (sha256 |
| 5117 | (base32 |
| 5118 | "10l5c07z9p4i9pr4gl54b2c9h6ndhqlbq1rashg2zcgwkbfrkmvn")))) |
| 5119 | (build-system gnu-build-system) |
| 5120 | (arguments |
| 5121 | `(#:tests? #f ; no "check" target |
| 5122 | #:make-flags (list |
| 5123 | "CFLAGS=-O2" ; override "-m64" flag |
| 5124 | (string-append "PREFIX=" (assoc-ref %outputs "out")) |
| 5125 | (string-append "MANDIR=" (assoc-ref %outputs "out") |
| 5126 | "/share/man/man1")))) |
| 5127 | (native-inputs |
| 5128 | `(("pkg-config" ,pkg-config))) |
| 5129 | (inputs |
| 5130 | `(("perl" ,perl) |
| 5131 | ("zlib" ,zlib))) |
| 5132 | (home-page "https://vcftools.github.io/") |
| 5133 | (synopsis "Tools for working with VCF files") |
| 5134 | (description |
| 5135 | "VCFtools is a program package designed for working with VCF files, such |
| 5136 | as those generated by the 1000 Genomes Project. The aim of VCFtools is to |
| 5137 | provide easily accessible methods for working with complex genetic variation |
| 5138 | data in the form of VCF files.") |
| 5139 | ;; The license is declared as LGPLv3 in the README and |
| 5140 | ;; at https://vcftools.github.io/license.html |
| 5141 | (license license:lgpl3))) |
| 5142 | |
| 5143 | (define-public infernal |
| 5144 | (package |
| 5145 | (name "infernal") |
| 5146 | (version "1.1.2") |
| 5147 | (source (origin |
| 5148 | (method url-fetch) |
| 5149 | (uri (string-append "http://eddylab.org/software/infernal/" |
| 5150 | "infernal-" version ".tar.gz")) |
| 5151 | (sha256 |
| 5152 | (base32 |
| 5153 | "0sr2hiz3qxfwqpz3whxr6n82p3x27336v3f34iqznp10hks2935c")))) |
| 5154 | (build-system gnu-build-system) |
| 5155 | (native-inputs |
| 5156 | `(("perl" ,perl))) ; for tests |
| 5157 | (home-page "http://eddylab.org/infernal/") |
| 5158 | (synopsis "Inference of RNA alignments") |
| 5159 | (description "Infernal (\"INFERence of RNA ALignment\") is a tool for |
| 5160 | searching DNA sequence databases for RNA structure and sequence similarities. |
| 5161 | It is an implementation of a special case of profile stochastic context-free |
| 5162 | grammars called @dfn{covariance models} (CMs). A CM is like a sequence |
| 5163 | profile, but it scores a combination of sequence consensus and RNA secondary |
| 5164 | structure consensus, so in many cases, it is more capable of identifying RNA |
| 5165 | homologs that conserve their secondary structure more than their primary |
| 5166 | sequence.") |
| 5167 | ;; Infernal 1.1.2 requires VMX or SSE capability for parallel instructions. |
| 5168 | (supported-systems '("i686-linux" "x86_64-linux")) |
| 5169 | (license license:bsd-3))) |
| 5170 | |
| 5171 | (define-public r-vegan |
| 5172 | (package |
| 5173 | (name "r-vegan") |
| 5174 | (version "2.4-1") |
| 5175 | (source |
| 5176 | (origin |
| 5177 | (method url-fetch) |
| 5178 | (uri (cran-uri "vegan" version)) |
| 5179 | (sha256 |
| 5180 | (base32 |
| 5181 | "0i0c7rc0nzgbysd1nlxzxd2rvy75qcnw3yc7nggzqjzzj5d7yzsd")))) |
| 5182 | (build-system r-build-system) |
| 5183 | (arguments |
| 5184 | `(#:phases |
| 5185 | (modify-phases %standard-phases |
| 5186 | (add-after 'unpack 'revert-test-deletion |
| 5187 | ;; The distributed sources do not include tests with the CRAN |
| 5188 | ;; package. Here we revert the commit |
| 5189 | ;; `591d0e8ba1deaaf82445474ec6619c0b43db4e63' which deletes these |
| 5190 | ;; tests. There are plans to not delete tests in future as |
| 5191 | ;; documented at https://github.com/vegandevs/vegan/issues/181. |
| 5192 | (lambda* (#:key inputs #:allow-other-keys) |
| 5193 | (zero? |
| 5194 | (system* "patch" "-R" "-p1" "-i" |
| 5195 | (assoc-ref inputs "r-vegan-delete-tests-patch")))))))) |
| 5196 | (native-inputs |
| 5197 | `(("gfortran" ,gfortran) |
| 5198 | ("r-knitr" ,r-knitr) |
| 5199 | ("r-vegan-delete-tests-patch" |
| 5200 | ,(origin |
| 5201 | (method url-fetch) |
| 5202 | (uri (string-append |
| 5203 | "https://github.com/vegandevs/vegan/commit/" |
| 5204 | "591d0e8ba1deaaf82445474ec6619c0b43db4e63.patch")) |
| 5205 | (sha256 |
| 5206 | (base32 |
| 5207 | "0b1bi7y4jjdl3ph721vm9apm51dr2z9piwvhy4355sf2b4kyyj5a")))))) |
| 5208 | (propagated-inputs |
| 5209 | `(("r-cluster" ,r-cluster) |
| 5210 | ("r-lattice" ,r-lattice) |
| 5211 | ("r-mgcv" ,r-mgcv) |
| 5212 | ("r-permute" ,r-permute))) |
| 5213 | (home-page "https://cran.r-project.org/web/packages/vegan") |
| 5214 | (synopsis "Functions for community ecology") |
| 5215 | (description |
| 5216 | "The vegan package provides tools for descriptive community ecology. It |
| 5217 | has most basic functions of diversity analysis, community ordination and |
| 5218 | dissimilarity analysis. Most of its multivariate tools can be used for other |
| 5219 | data types as well.") |
| 5220 | (license license:gpl2+))) |
| 5221 | |
| 5222 | (define-public r-annotate |
| 5223 | (package |
| 5224 | (name "r-annotate") |
| 5225 | (version "1.52.0") |
| 5226 | (source |
| 5227 | (origin |
| 5228 | (method url-fetch) |
| 5229 | (uri (bioconductor-uri "annotate" version)) |
| 5230 | (sha256 |
| 5231 | (base32 |
| 5232 | "1fd2csq7dcs2gwndgwdx2nwkymz8gsmlnqqzv3p0vjjsvvq5n2a8")))) |
| 5233 | (build-system r-build-system) |
| 5234 | (propagated-inputs |
| 5235 | `(("r-annotationdbi" ,r-annotationdbi) |
| 5236 | ("r-biobase" ,r-biobase) |
| 5237 | ("r-biocgenerics" ,r-biocgenerics) |
| 5238 | ("r-dbi" ,r-dbi) |
| 5239 | ("r-xml" ,r-xml) |
| 5240 | ("r-xtable" ,r-xtable))) |
| 5241 | (home-page |
| 5242 | "http://bioconductor.org/packages/annotate") |
| 5243 | (synopsis "Annotation for microarrays") |
| 5244 | (description "This package provides R enviroments for the annotation of |
| 5245 | microarrays.") |
| 5246 | (license license:artistic2.0))) |
| 5247 | |
| 5248 | (define-public r-geneplotter |
| 5249 | (package |
| 5250 | (name "r-geneplotter") |
| 5251 | (version "1.52.0") |
| 5252 | (source |
| 5253 | (origin |
| 5254 | (method url-fetch) |
| 5255 | (uri (bioconductor-uri "geneplotter" version)) |
| 5256 | (sha256 |
| 5257 | (base32 |
| 5258 | "1p6yvxi243irhjxwm97hp73abhwampj0myyf8z00ij166674pc7h")))) |
| 5259 | (build-system r-build-system) |
| 5260 | (propagated-inputs |
| 5261 | `(("r-annotate" ,r-annotate) |
| 5262 | ("r-annotationdbi" ,r-annotationdbi) |
| 5263 | ("r-biobase" ,r-biobase) |
| 5264 | ("r-biocgenerics" ,r-biocgenerics) |
| 5265 | ("r-lattice" ,r-lattice) |
| 5266 | ("r-rcolorbrewer" ,r-rcolorbrewer))) |
| 5267 | (home-page "http://bioconductor.org/packages/geneplotter") |
| 5268 | (synopsis "Graphics functions for genomic data") |
| 5269 | (description |
| 5270 | "This package provides functions for plotting genomic data.") |
| 5271 | (license license:artistic2.0))) |
| 5272 | |
| 5273 | (define-public r-genefilter |
| 5274 | (package |
| 5275 | (name "r-genefilter") |
| 5276 | (version "1.56.0") |
| 5277 | (source |
| 5278 | (origin |
| 5279 | (method url-fetch) |
| 5280 | (uri (bioconductor-uri "genefilter" version)) |
| 5281 | (sha256 |
| 5282 | (base32 |
| 5283 | "1vzgciqd09csqcw9qync8blsv51ylrd86a65iadgyy6j26g01fwd")))) |
| 5284 | (build-system r-build-system) |
| 5285 | (native-inputs |
| 5286 | `(("gfortran" ,gfortran))) |
| 5287 | (propagated-inputs |
| 5288 | `(("r-annotate" ,r-annotate) |
| 5289 | ("r-annotationdbi" ,r-annotationdbi) |
| 5290 | ("r-biobase" ,r-biobase) |
| 5291 | ("r-s4vectors" ,r-s4vectors))) |
| 5292 | (home-page "http://bioconductor.org/packages/genefilter") |
| 5293 | (synopsis "Filter genes from high-throughput experiments") |
| 5294 | (description |
| 5295 | "This package provides basic functions for filtering genes from |
| 5296 | high-throughput sequencing experiments.") |
| 5297 | (license license:artistic2.0))) |
| 5298 | |
| 5299 | (define-public r-deseq2 |
| 5300 | (package |
| 5301 | (name "r-deseq2") |
| 5302 | (version "1.14.0") |
| 5303 | (source |
| 5304 | (origin |
| 5305 | (method url-fetch) |
| 5306 | (uri (bioconductor-uri "DESeq2" version)) |
| 5307 | (sha256 |
| 5308 | (base32 |
| 5309 | "0kq06jy4xg5ii3a9l62f17kirsfx0gsiwq6mhiy985cqzpdn893g")))) |
| 5310 | (properties `((upstream-name . "DESeq2"))) |
| 5311 | (build-system r-build-system) |
| 5312 | (arguments |
| 5313 | `(#:phases |
| 5314 | (modify-phases %standard-phases |
| 5315 | (add-after 'unpack 'link-against-armadillo |
| 5316 | (lambda _ |
| 5317 | (substitute* "src/Makevars" |
| 5318 | (("PKG_LIBS =" prefix) |
| 5319 | (string-append prefix "-larmadillo")))))))) |
| 5320 | (propagated-inputs |
| 5321 | `(("r-biobase" ,r-biobase) |
| 5322 | ("r-biocgenerics" ,r-biocgenerics) |
| 5323 | ("r-biocparallel" ,r-biocparallel) |
| 5324 | ("r-genefilter" ,r-genefilter) |
| 5325 | ("r-geneplotter" ,r-geneplotter) |
| 5326 | ("r-genomicranges" ,r-genomicranges) |
| 5327 | ("r-ggplot2" ,r-ggplot2) |
| 5328 | ("r-hmisc" ,r-hmisc) |
| 5329 | ("r-iranges" ,r-iranges) |
| 5330 | ("r-locfit" ,r-locfit) |
| 5331 | ("r-rcpp" ,r-rcpp) |
| 5332 | ("r-rcpparmadillo" ,r-rcpparmadillo) |
| 5333 | ("r-s4vectors" ,r-s4vectors) |
| 5334 | ("r-summarizedexperiment" ,r-summarizedexperiment))) |
| 5335 | (home-page "http://bioconductor.org/packages/DESeq2") |
| 5336 | (synopsis "Differential gene expression analysis") |
| 5337 | (description |
| 5338 | "This package provides functions to estimate variance-mean dependence in |
| 5339 | count data from high-throughput nucleotide sequencing assays and test for |
| 5340 | differential expression based on a model using the negative binomial |
| 5341 | distribution.") |
| 5342 | (license license:lgpl3+))) |
| 5343 | |
| 5344 | (define-public r-annotationforge |
| 5345 | (package |
| 5346 | (name "r-annotationforge") |
| 5347 | (version "1.16.0") |
| 5348 | (source |
| 5349 | (origin |
| 5350 | (method url-fetch) |
| 5351 | (uri (bioconductor-uri "AnnotationForge" version)) |
| 5352 | (sha256 |
| 5353 | (base32 |
| 5354 | "02msyb9p3hywrryx00zpjkjl126mrv827i1ah1092s0cplm6xxvf")))) |
| 5355 | (properties |
| 5356 | `((upstream-name . "AnnotationForge"))) |
| 5357 | (build-system r-build-system) |
| 5358 | (propagated-inputs |
| 5359 | `(("r-annotationdbi" ,r-annotationdbi) |
| 5360 | ("r-biobase" ,r-biobase) |
| 5361 | ("r-biocgenerics" ,r-biocgenerics) |
| 5362 | ("r-dbi" ,r-dbi) |
| 5363 | ("r-rcurl" ,r-rcurl) |
| 5364 | ("r-rsqlite" ,r-rsqlite) |
| 5365 | ("r-s4vectors" ,r-s4vectors) |
| 5366 | ("r-xml" ,r-xml))) |
| 5367 | (home-page "http://bioconductor.org/packages/AnnotationForge") |
| 5368 | (synopsis "Code for building annotation database packages") |
| 5369 | (description |
| 5370 | "This package provides code for generating Annotation packages and their |
| 5371 | databases. Packages produced are intended to be used with AnnotationDbi.") |
| 5372 | (license license:artistic2.0))) |
| 5373 | |
| 5374 | (define-public r-rbgl |
| 5375 | (package |
| 5376 | (name "r-rbgl") |
| 5377 | (version "1.50.0") |
| 5378 | (source |
| 5379 | (origin |
| 5380 | (method url-fetch) |
| 5381 | (uri (bioconductor-uri "RBGL" version)) |
| 5382 | (sha256 |
| 5383 | (base32 |
| 5384 | "1q14m8w6ih56v680kf3d9wh1qbgp7af33kz3cxafdf1vvzx9km08")))) |
| 5385 | (properties `((upstream-name . "RBGL"))) |
| 5386 | (build-system r-build-system) |
| 5387 | (propagated-inputs `(("r-graph" ,r-graph))) |
| 5388 | (home-page "http://www.bioconductor.org/packages/RBGL") |
| 5389 | (synopsis "Interface to the Boost graph library") |
| 5390 | (description |
| 5391 | "This package provides a fairly extensive and comprehensive interface to |
| 5392 | the graph algorithms contained in the Boost library.") |
| 5393 | (license license:artistic2.0))) |
| 5394 | |
| 5395 | (define-public r-gseabase |
| 5396 | (package |
| 5397 | (name "r-gseabase") |
| 5398 | (version "1.36.0") |
| 5399 | (source |
| 5400 | (origin |
| 5401 | (method url-fetch) |
| 5402 | (uri (bioconductor-uri "GSEABase" version)) |
| 5403 | (sha256 |
| 5404 | (base32 |
| 5405 | "0l2x7yj7lfb0m2dmsav5ib026dikpgl4crdckrnj776yy08lgxpj")))) |
| 5406 | (properties `((upstream-name . "GSEABase"))) |
| 5407 | (build-system r-build-system) |
| 5408 | (propagated-inputs |
| 5409 | `(("r-annotate" ,r-annotate) |
| 5410 | ("r-annotationdbi" ,r-annotationdbi) |
| 5411 | ("r-biobase" ,r-biobase) |
| 5412 | ("r-biocgenerics" ,r-biocgenerics) |
| 5413 | ("r-graph" ,r-graph) |
| 5414 | ("r-xml" ,r-xml))) |
| 5415 | (home-page "http://bioconductor.org/packages/GSEABase") |
| 5416 | (synopsis "Gene set enrichment data structures and methods") |
| 5417 | (description |
| 5418 | "This package provides classes and methods to support @dfn{Gene Set |
| 5419 | Enrichment Analysis} (GSEA).") |
| 5420 | (license license:artistic2.0))) |
| 5421 | |
| 5422 | (define-public r-category |
| 5423 | (package |
| 5424 | (name "r-category") |
| 5425 | (version "2.40.0") |
| 5426 | (source |
| 5427 | (origin |
| 5428 | (method url-fetch) |
| 5429 | (uri (bioconductor-uri "Category" version)) |
| 5430 | (sha256 |
| 5431 | (base32 |
| 5432 | "16ncwz7b4y48k0p3fvbrbmvf7nfz63li9ysgcl8kp9kl4hg7llng")))) |
| 5433 | (properties `((upstream-name . "Category"))) |
| 5434 | (build-system r-build-system) |
| 5435 | (propagated-inputs |
| 5436 | `(("r-annotate" ,r-annotate) |
| 5437 | ("r-annotationdbi" ,r-annotationdbi) |
| 5438 | ("r-biobase" ,r-biobase) |
| 5439 | ("r-biocgenerics" ,r-biocgenerics) |
| 5440 | ("r-genefilter" ,r-genefilter) |
| 5441 | ("r-graph" ,r-graph) |
| 5442 | ("r-gseabase" ,r-gseabase) |
| 5443 | ("r-matrix" ,r-matrix) |
| 5444 | ("r-rbgl" ,r-rbgl) |
| 5445 | ("r-rsqlite" ,r-rsqlite))) |
| 5446 | (home-page "http://bioconductor.org/packages/Category") |
| 5447 | (synopsis "Category analysis") |
| 5448 | (description |
| 5449 | "This package provides a collection of tools for performing category |
| 5450 | analysis.") |
| 5451 | (license license:artistic2.0))) |
| 5452 | |
| 5453 | (define-public r-gostats |
| 5454 | (package |
| 5455 | (name "r-gostats") |
| 5456 | (version "2.40.0") |
| 5457 | (source |
| 5458 | (origin |
| 5459 | (method url-fetch) |
| 5460 | (uri (bioconductor-uri "GOstats" version)) |
| 5461 | (sha256 |
| 5462 | (base32 |
| 5463 | "0g2czm94zhzx92z7y2r4mjfxhwml7bhab2db6820ks8nkw1zvr9n")))) |
| 5464 | (properties `((upstream-name . "GOstats"))) |
| 5465 | (build-system r-build-system) |
| 5466 | (propagated-inputs |
| 5467 | `(("r-annotate" ,r-annotate) |
| 5468 | ("r-annotationdbi" ,r-annotationdbi) |
| 5469 | ("r-annotationforge" ,r-annotationforge) |
| 5470 | ("r-biobase" ,r-biobase) |
| 5471 | ("r-category" ,r-category) |
| 5472 | ("r-go-db" ,r-go-db) |
| 5473 | ("r-graph" ,r-graph) |
| 5474 | ("r-rbgl" ,r-rbgl))) |
| 5475 | (home-page "http://bioconductor.org/packages/GOstats") |
| 5476 | (synopsis "Tools for manipulating GO and microarrays") |
| 5477 | (description |
| 5478 | "This package provides a set of tools for interacting with GO and |
| 5479 | microarray data. A variety of basic manipulation tools for graphs, hypothesis |
| 5480 | testing and other simple calculations.") |
| 5481 | (license license:artistic2.0))) |
| 5482 | |
| 5483 | (define-public r-shortread |
| 5484 | (package |
| 5485 | (name "r-shortread") |
| 5486 | (version "1.32.0") |
| 5487 | (source |
| 5488 | (origin |
| 5489 | (method url-fetch) |
| 5490 | (uri (bioconductor-uri "ShortRead" version)) |
| 5491 | (sha256 |
| 5492 | (base32 |
| 5493 | "0mjdlg92x5qw4x2djc4dv5lxwl7ai6ix56nnf86zr07jk8vc7yls")))) |
| 5494 | (properties `((upstream-name . "ShortRead"))) |
| 5495 | (build-system r-build-system) |
| 5496 | (inputs |
| 5497 | `(("zlib" ,zlib))) |
| 5498 | (propagated-inputs |
| 5499 | `(("r-biobase" ,r-biobase) |
| 5500 | ("r-biocgenerics" ,r-biocgenerics) |
| 5501 | ("r-biocparallel" ,r-biocparallel) |
| 5502 | ("r-biostrings" ,r-biostrings) |
| 5503 | ("r-genomeinfodb" ,r-genomeinfodb) |
| 5504 | ("r-genomicalignments" ,r-genomicalignments) |
| 5505 | ("r-genomicranges" ,r-genomicranges) |
| 5506 | ("r-hwriter" ,r-hwriter) |
| 5507 | ("r-iranges" ,r-iranges) |
| 5508 | ("r-lattice" ,r-lattice) |
| 5509 | ("r-latticeextra" ,r-latticeextra) |
| 5510 | ("r-rsamtools" ,r-rsamtools) |
| 5511 | ("r-s4vectors" ,r-s4vectors) |
| 5512 | ("r-xvector" ,r-xvector) |
| 5513 | ("r-zlibbioc" ,r-zlibbioc))) |
| 5514 | (home-page "http://bioconductor.org/packages/ShortRead") |
| 5515 | (synopsis "FASTQ input and manipulation tools") |
| 5516 | (description |
| 5517 | "This package implements sampling, iteration, and input of FASTQ files. |
| 5518 | It includes functions for filtering and trimming reads, and for generating a |
| 5519 | quality assessment report. Data are represented as |
| 5520 | @code{DNAStringSet}-derived objects, and easily manipulated for a diversity of |
| 5521 | purposes. The package also contains legacy support for early single-end, |
| 5522 | ungapped alignment formats.") |
| 5523 | (license license:artistic2.0))) |
| 5524 | |
| 5525 | (define-public r-systempiper |
| 5526 | (package |
| 5527 | (name "r-systempiper") |
| 5528 | (version "1.8.1") |
| 5529 | (source |
| 5530 | (origin |
| 5531 | (method url-fetch) |
| 5532 | (uri (bioconductor-uri "systemPipeR" version)) |
| 5533 | (sha256 |
| 5534 | (base32 |
| 5535 | "0hyi841w8fm2yzpm6lwqi3jz5kc8ny8dy5p29dxynzaw5bpjw56d")))) |
| 5536 | (properties `((upstream-name . "systemPipeR"))) |
| 5537 | (build-system r-build-system) |
| 5538 | (propagated-inputs |
| 5539 | `(("r-annotate" ,r-annotate) |
| 5540 | ("r-batchjobs" ,r-batchjobs) |
| 5541 | ("r-biocgenerics" ,r-biocgenerics) |
| 5542 | ("r-biostrings" ,r-biostrings) |
| 5543 | ("r-deseq2" ,r-deseq2) |
| 5544 | ("r-edger" ,r-edger) |
| 5545 | ("r-genomicfeatures" ,r-genomicfeatures) |
| 5546 | ("r-genomicranges" ,r-genomicranges) |
| 5547 | ("r-ggplot2" ,r-ggplot2) |
| 5548 | ("r-go-db" ,r-go-db) |
| 5549 | ("r-gostats" ,r-gostats) |
| 5550 | ("r-limma" ,r-limma) |
| 5551 | ("r-pheatmap" ,r-pheatmap) |
| 5552 | ("r-rjson" ,r-rjson) |
| 5553 | ("r-rsamtools" ,r-rsamtools) |
| 5554 | ("r-shortread" ,r-shortread) |
| 5555 | ("r-summarizedexperiment" ,r-summarizedexperiment) |
| 5556 | ("r-variantannotation" ,r-variantannotation))) |
| 5557 | (home-page "https://github.com/tgirke/systemPipeR") |
| 5558 | (synopsis "Next generation sequencing workflow and reporting environment") |
| 5559 | (description |
| 5560 | "This R package provides tools for building and running automated |
| 5561 | end-to-end analysis workflows for a wide range of @dfn{next generation |
| 5562 | sequence} (NGS) applications such as RNA-Seq, ChIP-Seq, VAR-Seq and Ribo-Seq. |
| 5563 | Important features include a uniform workflow interface across different NGS |
| 5564 | applications, automated report generation, and support for running both R and |
| 5565 | command-line software, such as NGS aligners or peak/variant callers, on local |
| 5566 | computers or compute clusters. Efficient handling of complex sample sets and |
| 5567 | experimental designs is facilitated by a consistently implemented sample |
| 5568 | annotation infrastructure.") |
| 5569 | (license license:artistic2.0))) |
| 5570 | |
| 5571 | (define-public r-grohmm |
| 5572 | (package |
| 5573 | (name "r-grohmm") |
| 5574 | (version "1.8.0") |
| 5575 | (source |
| 5576 | (origin |
| 5577 | (method url-fetch) |
| 5578 | (uri (bioconductor-uri "groHMM" version)) |
| 5579 | (sha256 |
| 5580 | (base32 |
| 5581 | "0d91nyhqbi5hv3mgmr2z0g29wg2md26g0hyv5mgapmz20cd9zi4y")))) |
| 5582 | (properties `((upstream-name . "groHMM"))) |
| 5583 | (build-system r-build-system) |
| 5584 | (propagated-inputs |
| 5585 | `(("r-genomeinfodb" ,r-genomeinfodb) |
| 5586 | ("r-genomicalignments" ,r-genomicalignments) |
| 5587 | ("r-genomicranges" ,r-genomicranges) |
| 5588 | ("r-iranges" ,r-iranges) |
| 5589 | ("r-rtracklayer" ,r-rtracklayer) |
| 5590 | ("r-s4vectors" ,r-s4vectors))) |
| 5591 | (home-page "https://github.com/Kraus-Lab/groHMM") |
| 5592 | (synopsis "GRO-seq analysis pipeline") |
| 5593 | (description |
| 5594 | "This package provides a pipeline for the analysis of GRO-seq data.") |
| 5595 | (license license:gpl3+))) |
| 5596 | |
| 5597 | (define-public r-txdb-hsapiens-ucsc-hg19-knowngene |
| 5598 | (package |
| 5599 | (name "r-txdb-hsapiens-ucsc-hg19-knowngene") |
| 5600 | (version "3.2.2") |
| 5601 | (source (origin |
| 5602 | (method url-fetch) |
| 5603 | ;; We cannot use bioconductor-uri here because this tarball is |
| 5604 | ;; located under "data/annotation/" instead of "bioc/". |
| 5605 | (uri (string-append "http://bioconductor.org/packages/" |
| 5606 | "release/data/annotation/src/contrib" |
| 5607 | "/TxDb.Hsapiens.UCSC.hg19.knownGene_" |
| 5608 | version ".tar.gz")) |
| 5609 | (sha256 |
| 5610 | (base32 |
| 5611 | "1sajhcqqwazgz2lqbik7rd935i7kpnh08zxbp2ra10j72yqy4g86")))) |
| 5612 | (properties |
| 5613 | `((upstream-name . "TxDb.Hsapiens.UCSC.hg19.knownGene"))) |
| 5614 | (build-system r-build-system) |
| 5615 | ;; As this package provides little more than a very large data file it |
| 5616 | ;; doesn't make sense to build substitutes. |
| 5617 | (arguments `(#:substitutable? #f)) |
| 5618 | (propagated-inputs |
| 5619 | `(("r-genomicfeatures" ,r-genomicfeatures))) |
| 5620 | (home-page |
| 5621 | "http://bioconductor.org/packages/TxDb.Hsapiens.UCSC.hg19.knownGene/") |
| 5622 | (synopsis "Annotation package for human genome in TxDb format") |
| 5623 | (description |
| 5624 | "This package provides an annotation database of Homo sapiens genome |
| 5625 | data. It is derived from the UCSC hg19 genome and based on the \"knownGene\" |
| 5626 | track. The database is exposed as a @code{TxDb} object.") |
| 5627 | (license license:artistic2.0))) |
| 5628 | |
| 5629 | (define-public vsearch |
| 5630 | (package |
| 5631 | (name "vsearch") |
| 5632 | (version "2.3.4") |
| 5633 | (source |
| 5634 | (origin |
| 5635 | (method url-fetch) |
| 5636 | (uri (string-append |
| 5637 | "https://github.com/torognes/vsearch/archive/v" |
| 5638 | version ".tar.gz")) |
| 5639 | (file-name (string-append name "-" version ".tar.gz")) |
| 5640 | (sha256 |
| 5641 | (base32 |
| 5642 | "1xyraxmhyx62mxx8z7c8waygvcijwkh48ms1ar60w2cv2y2sn4al")) |
| 5643 | (modules '((guix build utils))) |
| 5644 | (snippet |
| 5645 | '(begin |
| 5646 | ;; Remove bundled cityhash and '-mtune=native'. |
| 5647 | (substitute* "src/Makefile.am" |
| 5648 | (("^AM_CXXFLAGS=-I\\$\\{srcdir\\}/cityhash \ |
| 5649 | -O3 -mtune=native -Wall -Wsign-compare") |
| 5650 | (string-append "AM_CXXFLAGS=-lcityhash" |
| 5651 | " -O3 -Wall -Wsign-compare")) |
| 5652 | (("^__top_builddir__bin_vsearch_SOURCES = city.h \\\\") |
| 5653 | "__top_builddir__bin_vsearch_SOURCES = \\") |
| 5654 | (("^city.h \\\\") "\\") |
| 5655 | (("^citycrc.h \\\\") "\\") |
| 5656 | (("^libcityhash_a.*") "") |
| 5657 | (("noinst_LIBRARIES = libcpu_sse2.a libcpu_ssse3.a \ |
| 5658 | libcityhash.a") |
| 5659 | "noinst_LIBRARIES = libcpu_sse2.a libcpu_ssse3.a") |
| 5660 | (("__top_builddir__bin_vsearch_LDADD = libcpu_ssse3.a \ |
| 5661 | libcpu_sse2.a libcityhash.a") |
| 5662 | "__top_builddir__bin_vsearch_LDADD = libcpu_ssse3.a \ |
| 5663 | libcpu_sse2.a -lcityhash")) |
| 5664 | (substitute* "src/vsearch.h" |
| 5665 | (("^\\#include \"city.h\"") "#include <city.h>") |
| 5666 | (("^\\#include \"citycrc.h\"") "#include <citycrc.h>")) |
| 5667 | (delete-file "src/city.h") |
| 5668 | (delete-file "src/citycrc.h") |
| 5669 | (delete-file "src/city.cc") |
| 5670 | #t)))) |
| 5671 | (build-system gnu-build-system) |
| 5672 | (arguments |
| 5673 | `(#:phases |
| 5674 | (modify-phases %standard-phases |
| 5675 | (add-before 'configure 'autogen |
| 5676 | (lambda _ (zero? (system* "autoreconf" "-vif"))))))) |
| 5677 | (inputs |
| 5678 | `(("zlib" ,zlib) |
| 5679 | ("bzip2" ,bzip2) |
| 5680 | ("cityhash" ,cityhash))) |
| 5681 | (native-inputs |
| 5682 | `(("autoconf" ,autoconf) |
| 5683 | ("automake" ,automake))) |
| 5684 | (synopsis "Sequence search tools for metagenomics") |
| 5685 | (description |
| 5686 | "VSEARCH supports DNA sequence searching, clustering, chimera detection, |
| 5687 | dereplication, pairwise alignment, shuffling, subsampling, sorting and |
| 5688 | masking. The tool takes advantage of parallelism in the form of SIMD |
| 5689 | vectorization as well as multiple threads to perform accurate alignments at |
| 5690 | high speed. VSEARCH uses an optimal global aligner (full dynamic programming |
| 5691 | Needleman-Wunsch).") |
| 5692 | (home-page "https://github.com/torognes/vsearch") |
| 5693 | ;; vsearch uses non-portable SSE intrinsics so building fails on other |
| 5694 | ;; platforms. |
| 5695 | (supported-systems '("x86_64-linux")) |
| 5696 | ;; Dual licensed; also includes public domain source. |
| 5697 | (license (list license:gpl3 license:bsd-2)))) |
| 5698 | |
| 5699 | (define-public pardre |
| 5700 | (package |
| 5701 | (name "pardre") |
| 5702 | ;; The source of 1.1.5 changed in place, so we append "-1" to the version. |
| 5703 | (version "1.1.5-1") |
| 5704 | (source |
| 5705 | (origin |
| 5706 | (method url-fetch) |
| 5707 | (uri (string-append "mirror://sourceforge/pardre/ParDRe-rel" |
| 5708 | "1.1.5" ".tar.gz")) |
| 5709 | (sha256 |
| 5710 | (base32 |
| 5711 | "17j73nc0viq4f6qj50nrndsrif5d6b71q8fl87m54psiv0ilns2b")))) |
| 5712 | (build-system gnu-build-system) |
| 5713 | (arguments |
| 5714 | `(#:tests? #f ; no tests included |
| 5715 | #:phases |
| 5716 | (modify-phases %standard-phases |
| 5717 | (delete 'configure) |
| 5718 | (replace 'install |
| 5719 | (lambda* (#:key outputs #:allow-other-keys) |
| 5720 | (let ((bin (string-append (assoc-ref outputs "out") "/bin"))) |
| 5721 | (install-file "ParDRe" bin) |
| 5722 | #t)))))) |
| 5723 | (inputs |
| 5724 | `(("openmpi" ,openmpi) |
| 5725 | ("zlib" ,zlib))) |
| 5726 | (synopsis "Parallel tool to remove duplicate DNA reads") |
| 5727 | (description |
| 5728 | "ParDRe is a parallel tool to remove duplicate genetic sequence reads. |
| 5729 | Duplicate reads can be seen as identical or nearly identical sequences with |
| 5730 | some mismatches. This tool lets users avoid the analysis of unnecessary |
| 5731 | reads, reducing the time of subsequent procedures with the |
| 5732 | dataset (e.g. assemblies, mappings, etc.). The tool is implemented with MPI |
| 5733 | in order to exploit the parallel capabilities of multicore clusters. It is |
| 5734 | faster than multithreaded counterparts (end of 2015) for the same number of |
| 5735 | cores and, thanks to the message-passing technology, it can be executed on |
| 5736 | clusters.") |
| 5737 | (home-page "https://sourceforge.net/projects/pardre/") |
| 5738 | (license license:gpl3+))) |
| 5739 | |
| 5740 | (define-public ruby-bio-kseq |
| 5741 | (package |
| 5742 | (name "ruby-bio-kseq") |
| 5743 | (version "0.0.2") |
| 5744 | (source |
| 5745 | (origin |
| 5746 | (method url-fetch) |
| 5747 | (uri (rubygems-uri "bio-kseq" version)) |
| 5748 | (sha256 |
| 5749 | (base32 |
| 5750 | "1xyaha46khb5jc6wzkbf7040jagac49jbimn0vcrzid0j8jdikrz")))) |
| 5751 | (build-system ruby-build-system) |
| 5752 | (arguments |
| 5753 | `(#:test-target "spec")) |
| 5754 | (native-inputs |
| 5755 | `(("bundler" ,bundler) |
| 5756 | ("ruby-rspec" ,ruby-rspec) |
| 5757 | ("ruby-rake-compiler" ,ruby-rake-compiler))) |
| 5758 | (inputs |
| 5759 | `(("zlib" ,zlib))) |
| 5760 | (synopsis "Ruby bindings for the kseq.h FASTA/Q parser") |
| 5761 | (description |
| 5762 | "@code{Bio::Kseq} provides ruby bindings to the @code{kseq.h} FASTA and |
| 5763 | FASTQ parsing code. It provides a fast iterator over sequences and their |
| 5764 | quality scores.") |
| 5765 | (home-page "https://github.com/gusevfe/bio-kseq") |
| 5766 | (license license:expat))) |
| 5767 | |
| 5768 | (define-public bio-locus |
| 5769 | (package |
| 5770 | (name "bio-locus") |
| 5771 | (version "0.0.7") |
| 5772 | (source |
| 5773 | (origin |
| 5774 | (method url-fetch) |
| 5775 | (uri (rubygems-uri "bio-locus" version)) |
| 5776 | (sha256 |
| 5777 | (base32 |
| 5778 | "02vmrxyimkj9sahsp4zhfhnmbvz6dbbqz1y01vglf8cbwvkajfl0")))) |
| 5779 | (build-system ruby-build-system) |
| 5780 | (native-inputs |
| 5781 | `(("ruby-rspec" ,ruby-rspec))) |
| 5782 | (synopsis "Tool for fast querying of genome locations") |
| 5783 | (description |
| 5784 | "Bio-locus is a tabix-like tool for fast querying of genome |
| 5785 | locations. Many file formats in bioinformatics contain records that |
| 5786 | start with a chromosome name and a position for a SNP, or a start-end |
| 5787 | position for indels. Bio-locus allows users to store this chr+pos or |
| 5788 | chr+pos+alt information in a database.") |
| 5789 | (home-page "https://github.com/pjotrp/bio-locus") |
| 5790 | (license license:expat))) |
| 5791 | |
| 5792 | (define-public bio-blastxmlparser |
| 5793 | (package |
| 5794 | (name "bio-blastxmlparser") |
| 5795 | (version "2.0.4") |
| 5796 | (source (origin |
| 5797 | (method url-fetch) |
| 5798 | (uri (rubygems-uri "bio-blastxmlparser" version)) |
| 5799 | (sha256 |
| 5800 | (base32 |
| 5801 | "1wf4qygcmdjgcqm6flmvsagfr1gs9lf63mj32qv3z1f481zc5692")))) |
| 5802 | (build-system ruby-build-system) |
| 5803 | (propagated-inputs |
| 5804 | `(("ruby-bio-logger" ,ruby-bio-logger) |
| 5805 | ("ruby-nokogiri" ,ruby-nokogiri))) |
| 5806 | (inputs |
| 5807 | `(("ruby-rspec" ,ruby-rspec))) |
| 5808 | (synopsis "Fast big data BLAST XML parser and library") |
| 5809 | (description |
| 5810 | "Very fast parallel big-data BLAST XML file parser which can be used as |
| 5811 | command line utility. Use blastxmlparser to: Parse BLAST XML; filter output; |
| 5812 | generate FASTA, JSON, YAML, RDF, JSON-LD, HTML, CSV, tabular output etc.") |
| 5813 | (home-page "http://github.com/pjotrp/blastxmlparser") |
| 5814 | (license license:expat))) |
| 5815 | |
| 5816 | (define-public bioruby |
| 5817 | (package |
| 5818 | (name "bioruby") |
| 5819 | (version "1.5.0") |
| 5820 | (source |
| 5821 | (origin |
| 5822 | (method url-fetch) |
| 5823 | (uri (rubygems-uri "bio" version)) |
| 5824 | (sha256 |
| 5825 | (base32 |
| 5826 | "01k2fyjl5fpx4zn8g6gqiqvsg2j1fgixrs9p03vzxckynxdq3wmc")))) |
| 5827 | (build-system ruby-build-system) |
| 5828 | (propagated-inputs |
| 5829 | `(("ruby-libxml" ,ruby-libxml))) |
| 5830 | (native-inputs |
| 5831 | `(("which" ,which))) ; required for test phase |
| 5832 | (arguments |
| 5833 | `(#:phases |
| 5834 | (modify-phases %standard-phases |
| 5835 | (add-before 'build 'patch-test-command |
| 5836 | (lambda _ |
| 5837 | (substitute* '("test/functional/bio/test_command.rb") |
| 5838 | (("/bin/sh") (which "sh"))) |
| 5839 | (substitute* '("test/functional/bio/test_command.rb") |
| 5840 | (("/bin/ls") (which "ls"))) |
| 5841 | (substitute* '("test/functional/bio/test_command.rb") |
| 5842 | (("which") (which "which"))) |
| 5843 | (substitute* '("test/functional/bio/test_command.rb", |
| 5844 | "test/data/command/echoarg2.sh") |
| 5845 | (("/bin/echo") (which "echo"))) |
| 5846 | #t))))) |
| 5847 | (synopsis "Ruby library, shell and utilities for bioinformatics") |
| 5848 | (description "BioRuby comes with a comprehensive set of Ruby development |
| 5849 | tools and libraries for bioinformatics and molecular biology. BioRuby has |
| 5850 | components for sequence analysis, pathway analysis, protein modelling and |
| 5851 | phylogenetic analysis; it supports many widely used data formats and provides |
| 5852 | easy access to databases, external programs and public web services, including |
| 5853 | BLAST, KEGG, GenBank, MEDLINE and GO.") |
| 5854 | (home-page "http://bioruby.org/") |
| 5855 | ;; Code is released under Ruby license, except for setup |
| 5856 | ;; (LGPLv2.1+) and scripts in samples (which have GPL2 and GPL2+) |
| 5857 | (license (list license:ruby license:lgpl2.1+ license:gpl2+ )))) |
| 5858 | |
| 5859 | (define-public r-acsnminer |
| 5860 | (package |
| 5861 | (name "r-acsnminer") |
| 5862 | (version "0.16.8.25") |
| 5863 | (source (origin |
| 5864 | (method url-fetch) |
| 5865 | (uri (cran-uri "ACSNMineR" version)) |
| 5866 | (sha256 |
| 5867 | (base32 |
| 5868 | "0gh604s8qall6zfjlwcg2ilxjvz08dplf9k5g47idhv43scm748l")))) |
| 5869 | (properties `((upstream-name . "ACSNMineR"))) |
| 5870 | (build-system r-build-system) |
| 5871 | (propagated-inputs |
| 5872 | `(("r-ggplot2" ,r-ggplot2) |
| 5873 | ("r-gridextra" ,r-gridextra))) |
| 5874 | (home-page "http://cran.r-project.org/web/packages/ACSNMineR") |
| 5875 | (synopsis "Gene enrichment analysis") |
| 5876 | (description |
| 5877 | "This package provides tools to compute and represent gene set enrichment |
| 5878 | or depletion from your data based on pre-saved maps from the @dfn{Atlas of |
| 5879 | Cancer Signalling Networks} (ACSN) or user imported maps. The gene set |
| 5880 | enrichment can be run with hypergeometric test or Fisher exact test, and can |
| 5881 | use multiple corrections. Visualization of data can be done either by |
| 5882 | barplots or heatmaps.") |
| 5883 | (license license:gpl2+))) |
| 5884 | |
| 5885 | (define-public r-biocgenerics |
| 5886 | (package |
| 5887 | (name "r-biocgenerics") |
| 5888 | (version "0.20.0") |
| 5889 | (source (origin |
| 5890 | (method url-fetch) |
| 5891 | (uri (bioconductor-uri "BiocGenerics" version)) |
| 5892 | (sha256 |
| 5893 | (base32 |
| 5894 | "06szdz7dfs1iyv5zdl4fjzad18nnf1zf3wvglc6c6yd9mrqlf7vk")))) |
| 5895 | (properties |
| 5896 | `((upstream-name . "BiocGenerics"))) |
| 5897 | (build-system r-build-system) |
| 5898 | (home-page "http://bioconductor.org/packages/BiocGenerics") |
| 5899 | (synopsis "S4 generic functions for Bioconductor") |
| 5900 | (description |
| 5901 | "This package provides S4 generic functions needed by many Bioconductor |
| 5902 | packages.") |
| 5903 | (license license:artistic2.0))) |
| 5904 | |
| 5905 | (define-public r-biocinstaller |
| 5906 | (package |
| 5907 | (name "r-biocinstaller") |
| 5908 | (version "1.24.0") |
| 5909 | (source (origin |
| 5910 | (method url-fetch) |
| 5911 | (uri (bioconductor-uri "BiocInstaller" version)) |
| 5912 | (sha256 |
| 5913 | (base32 |
| 5914 | "0y1y5wmy6lzjqx3hdg15n91d417ccjj8dbvdkhmp99bs5aijwcpn")))) |
| 5915 | (properties |
| 5916 | `((upstream-name . "BiocInstaller"))) |
| 5917 | (build-system r-build-system) |
| 5918 | (home-page "http://bioconductor.org/packages/BiocInstaller") |
| 5919 | (synopsis "Install Bioconductor packages") |
| 5920 | (description "This package is used to install and update R packages from |
| 5921 | Bioconductor, CRAN, and Github.") |
| 5922 | (license license:artistic2.0))) |
| 5923 | |
| 5924 | (define-public r-biocviews |
| 5925 | (package |
| 5926 | (name "r-biocviews") |
| 5927 | (version "1.42.0") |
| 5928 | (source (origin |
| 5929 | (method url-fetch) |
| 5930 | (uri (bioconductor-uri "biocViews" version)) |
| 5931 | (sha256 |
| 5932 | (base32 |
| 5933 | "07rjk10b91pkriyq297w86199r2d3sfji3ggs9mq2gyalsa8y4b6")))) |
| 5934 | (properties |
| 5935 | `((upstream-name . "biocViews"))) |
| 5936 | (build-system r-build-system) |
| 5937 | (propagated-inputs |
| 5938 | `(("r-biobase" ,r-biobase) |
| 5939 | ("r-graph" ,r-graph) |
| 5940 | ("r-rbgl" ,r-rbgl) |
| 5941 | ("r-rcurl" ,r-rcurl) |
| 5942 | ("r-xml" ,r-xml) |
| 5943 | ("r-knitr" ,r-knitr) |
| 5944 | ("r-runit" ,r-runit))) |
| 5945 | (home-page "http://bioconductor.org/packages/biocViews") |
| 5946 | (synopsis "Bioconductor package categorization helper") |
| 5947 | (description "The purpose of biocViews is to create HTML pages that |
| 5948 | categorize packages in a Bioconductor package repository according to keywords, |
| 5949 | also known as views, in a controlled vocabulary.") |
| 5950 | (license license:artistic2.0))) |
| 5951 | |
| 5952 | (define-public r-biocstyle |
| 5953 | (package |
| 5954 | (name "r-biocstyle") |
| 5955 | (version "2.2.0") |
| 5956 | (source (origin |
| 5957 | (method url-fetch) |
| 5958 | (uri (bioconductor-uri "BiocStyle" version)) |
| 5959 | (sha256 |
| 5960 | (base32 |
| 5961 | "0qbk23fz8cn260isd9xlh9lxfj4adar6iqzai01c4kz0p31f45za")))) |
| 5962 | (properties |
| 5963 | `((upstream-name . "BiocStyle"))) |
| 5964 | (build-system r-build-system) |
| 5965 | (home-page "http://bioconductor.org/packages/BiocStyle") |
| 5966 | (synopsis "Bioconductor formatting styles") |
| 5967 | (description "This package provides standard formatting styles for |
| 5968 | Bioconductor PDF and HTML documents. Package vignettes illustrate use and |
| 5969 | functionality.") |
| 5970 | (license license:artistic2.0))) |
| 5971 | |
| 5972 | (define-public r-bioccheck |
| 5973 | (package |
| 5974 | (name "r-bioccheck") |
| 5975 | (version "1.10.0") |
| 5976 | (source (origin |
| 5977 | (method url-fetch) |
| 5978 | (uri (bioconductor-uri "BiocCheck" version)) |
| 5979 | (sha256 |
| 5980 | (base32 |
| 5981 | "1rfy37xg1nc2cmgbclvzsi7sgmdcdjiahsx9crgx3yaw7kxgiack")))) |
| 5982 | (properties |
| 5983 | `((upstream-name . "BiocCheck"))) |
| 5984 | (build-system r-build-system) |
| 5985 | (arguments |
| 5986 | '(#:phases |
| 5987 | (modify-phases %standard-phases |
| 5988 | ;; This package can be used by calling BiocCheck(<package>) from |
| 5989 | ;; within R, or by running R CMD BiocCheck <package>. This phase |
| 5990 | ;; makes sure the latter works. For this to work, the BiocCheck |
| 5991 | ;; script must be somewhere on the PATH (not the R bin directory). |
| 5992 | (add-after 'install 'install-bioccheck-subcommand |
| 5993 | (lambda* (#:key outputs #:allow-other-keys) |
| 5994 | (let* ((out (assoc-ref outputs "out")) |
| 5995 | (dest-dir (string-append out "/bin")) |
| 5996 | (script-dir |
| 5997 | (string-append out "/site-library/BiocCheck/script/"))) |
| 5998 | (mkdir-p dest-dir) |
| 5999 | (symlink (string-append script-dir "/checkBadDeps.R") |
| 6000 | (string-append dest-dir "/checkBadDeps.R")) |
| 6001 | (symlink (string-append script-dir "/BiocCheck") |
| 6002 | (string-append dest-dir "/BiocCheck"))) |
| 6003 | #t))))) |
| 6004 | (native-inputs |
| 6005 | `(("which" ,which))) |
| 6006 | (propagated-inputs |
| 6007 | `(("r-graph" ,r-graph) |
| 6008 | ("r-knitr" ,r-knitr) |
| 6009 | ("r-httr" ,r-httr) |
| 6010 | ("r-optparse" ,r-optparse) |
| 6011 | ("r-devtools" ,r-devtools) |
| 6012 | ("r-biocinstaller" ,r-biocinstaller) |
| 6013 | ("r-biocviews" ,r-biocviews))) |
| 6014 | (home-page "http://bioconductor.org/packages/BiocCheck") |
| 6015 | (synopsis "Executes Bioconductor-specific package checks") |
| 6016 | (description "This package contains tools to perform additional quality |
| 6017 | checks on R packages that are to be submitted to the Bioconductor repository.") |
| 6018 | (license license:artistic2.0))) |
| 6019 | |
| 6020 | (define-public r-getopt |
| 6021 | (package |
| 6022 | (name "r-getopt") |
| 6023 | (version "1.20.0") |
| 6024 | (source |
| 6025 | (origin |
| 6026 | (method url-fetch) |
| 6027 | (uri (cran-uri "getopt" version)) |
| 6028 | (sha256 |
| 6029 | (base32 |
| 6030 | "00f57vgnzmg7cz80rjmjz1556xqcmx8nhrlbbhaq4w7gl2ibl87r")))) |
| 6031 | (build-system r-build-system) |
| 6032 | (home-page "https://github.com/trevorld/getopt") |
| 6033 | (synopsis "Command-line option processor for R") |
| 6034 | (description |
| 6035 | "This package is designed to be used with Rscript to write shebang |
| 6036 | scripts that accept short and long options. Many users will prefer to |
| 6037 | use the packages @code{optparse} or @code{argparse} which add extra |
| 6038 | features like automatically generated help options and usage texts, |
| 6039 | support for default values, positional argument support, etc.") |
| 6040 | (license license:gpl2+))) |
| 6041 | |
| 6042 | (define-public r-optparse |
| 6043 | (package |
| 6044 | (name "r-optparse") |
| 6045 | (version "1.3.2") |
| 6046 | (source |
| 6047 | (origin |
| 6048 | (method url-fetch) |
| 6049 | (uri (cran-uri "optparse" version)) |
| 6050 | (sha256 |
| 6051 | (base32 |
| 6052 | "1g8as89r91xxi5j5azsd6vrfrhg84mnfx2683j7pacdp8s33radw")))) |
| 6053 | (build-system r-build-system) |
| 6054 | (propagated-inputs |
| 6055 | `(("r-getopt" ,r-getopt))) |
| 6056 | (home-page |
| 6057 | "https://github.com/trevorld/optparse") |
| 6058 | (synopsis "Command line option parser") |
| 6059 | (description |
| 6060 | "This package provides a command line parser inspired by Python's |
| 6061 | @code{optparse} library to be used with Rscript to write shebang scripts |
| 6062 | that accept short and long options.") |
| 6063 | (license license:gpl2+))) |
| 6064 | |
| 6065 | (define-public r-dnacopy |
| 6066 | (package |
| 6067 | (name "r-dnacopy") |
| 6068 | (version "1.48.0") |
| 6069 | (source (origin |
| 6070 | (method url-fetch) |
| 6071 | (uri (bioconductor-uri "DNAcopy" version)) |
| 6072 | (sha256 |
| 6073 | (base32 |
| 6074 | "1idyvfvy7xx8k9vk00y4k3819qmip8iqm809j3vpxabmsn7r9zyh")))) |
| 6075 | (properties |
| 6076 | `((upstream-name . "DNAcopy"))) |
| 6077 | (build-system r-build-system) |
| 6078 | (inputs |
| 6079 | `(("gfortran" ,gfortran))) |
| 6080 | (home-page "https://bioconductor.org/packages/DNAcopy") |
| 6081 | (synopsis "Implementation of a circular binary segmentation algorithm") |
| 6082 | (description "This package implements the circular binary segmentation (CBS) |
| 6083 | algorithm to segment DNA copy number data and identify genomic regions with |
| 6084 | abnormal copy number.") |
| 6085 | (license license:gpl2+))) |
| 6086 | |
| 6087 | (define-public r-s4vectors |
| 6088 | (package |
| 6089 | (name "r-s4vectors") |
| 6090 | (version "0.12.0") |
| 6091 | (source (origin |
| 6092 | (method url-fetch) |
| 6093 | (uri (bioconductor-uri "S4Vectors" version)) |
| 6094 | (sha256 |
| 6095 | (base32 |
| 6096 | "0m0npc0vhmcwcxws7v2f8k4hvvrjvnlrsr94klxf4a8m4xw2xzzk")))) |
| 6097 | (properties |
| 6098 | `((upstream-name . "S4Vectors"))) |
| 6099 | (build-system r-build-system) |
| 6100 | (propagated-inputs |
| 6101 | `(("r-biocgenerics" ,r-biocgenerics))) |
| 6102 | (home-page "http://bioconductor.org/packages/S4Vectors") |
| 6103 | (synopsis "S4 implementation of vectors and lists") |
| 6104 | (description |
| 6105 | "The S4Vectors package defines the @code{Vector} and @code{List} virtual |
| 6106 | classes and a set of generic functions that extend the semantic of ordinary |
| 6107 | vectors and lists in R. Package developers can easily implement vector-like |
| 6108 | or list-like objects as concrete subclasses of @code{Vector} or @code{List}. |
| 6109 | In addition, a few low-level concrete subclasses of general interest (e.g. |
| 6110 | @code{DataFrame}, @code{Rle}, and @code{Hits}) are implemented in the |
| 6111 | S4Vectors package itself.") |
| 6112 | (license license:artistic2.0))) |
| 6113 | |
| 6114 | (define-public r-seqinr |
| 6115 | (package |
| 6116 | (name "r-seqinr") |
| 6117 | (version "3.3-3") |
| 6118 | (source |
| 6119 | (origin |
| 6120 | (method url-fetch) |
| 6121 | (uri (cran-uri "seqinr" version)) |
| 6122 | (sha256 |
| 6123 | (base32 |
| 6124 | "0rk4yba8km26c0rh1f4h474zsb5n6kjmqsi55bnzr6p8pymp18hj")))) |
| 6125 | (build-system r-build-system) |
| 6126 | (propagated-inputs |
| 6127 | `(("r-ade4" ,r-ade4) |
| 6128 | ("r-segmented" ,r-segmented))) |
| 6129 | (inputs |
| 6130 | `(("zlib" ,zlib))) |
| 6131 | (home-page "http://seqinr.r-forge.r-project.org/") |
| 6132 | (synopsis "Biological sequences retrieval and analysis") |
| 6133 | (description |
| 6134 | "This package provides tools for exploratory data analysis and data |
| 6135 | visualization of biological sequence (DNA and protein) data. It also includes |
| 6136 | utilities for sequence data management under the ACNUC system.") |
| 6137 | (license license:gpl2+))) |
| 6138 | |
| 6139 | (define-public r-iranges |
| 6140 | (package |
| 6141 | (name "r-iranges") |
| 6142 | (version "2.8.0") |
| 6143 | (source (origin |
| 6144 | (method url-fetch) |
| 6145 | (uri (bioconductor-uri "IRanges" version)) |
| 6146 | (sha256 |
| 6147 | (base32 |
| 6148 | "0cdl1sfd3cvf93lnz91fdk64fbg1mnd5g958dwh1il8r358hqq3f")))) |
| 6149 | (properties |
| 6150 | `((upstream-name . "IRanges"))) |
| 6151 | (build-system r-build-system) |
| 6152 | (propagated-inputs |
| 6153 | `(("r-biocgenerics" ,r-biocgenerics) |
| 6154 | ("r-s4vectors" ,r-s4vectors))) |
| 6155 | (home-page "http://bioconductor.org/packages/IRanges") |
| 6156 | (synopsis "Infrastructure for manipulating intervals on sequences") |
| 6157 | (description |
| 6158 | "This package provides efficient low-level and highly reusable S4 classes |
| 6159 | for storing ranges of integers, RLE vectors (Run-Length Encoding), and, more |
| 6160 | generally, data that can be organized sequentially (formally defined as |
| 6161 | @code{Vector} objects), as well as views on these @code{Vector} objects. |
| 6162 | Efficient list-like classes are also provided for storing big collections of |
| 6163 | instances of the basic classes. All classes in the package use consistent |
| 6164 | naming and share the same rich and consistent \"Vector API\" as much as |
| 6165 | possible.") |
| 6166 | (license license:artistic2.0))) |
| 6167 | |
| 6168 | (define-public r-genomeinfodb |
| 6169 | (package |
| 6170 | (name "r-genomeinfodb") |
| 6171 | (version "1.10.0") |
| 6172 | (source (origin |
| 6173 | (method url-fetch) |
| 6174 | (uri (bioconductor-uri "GenomeInfoDb" version)) |
| 6175 | (sha256 |
| 6176 | (base32 |
| 6177 | "0nhg4bk38gzvf3mvnbqgisbbhfv1kzjld27z1z9knnlkplkiyyyv")))) |
| 6178 | (properties |
| 6179 | `((upstream-name . "GenomeInfoDb"))) |
| 6180 | (build-system r-build-system) |
| 6181 | (propagated-inputs |
| 6182 | `(("r-biocgenerics" ,r-biocgenerics) |
| 6183 | ("r-iranges" ,r-iranges) |
| 6184 | ("r-s4vectors" ,r-s4vectors))) |
| 6185 | (home-page "http://bioconductor.org/packages/GenomeInfoDb") |
| 6186 | (synopsis "Utilities for manipulating chromosome identifiers") |
| 6187 | (description |
| 6188 | "This package contains data and functions that define and allow |
| 6189 | translation between different chromosome sequence naming conventions (e.g., |
| 6190 | \"chr1\" versus \"1\"), including a function that attempts to place sequence |
| 6191 | names in their natural, rather than lexicographic, order.") |
| 6192 | (license license:artistic2.0))) |
| 6193 | |
| 6194 | (define-public r-edger |
| 6195 | (package |
| 6196 | (name "r-edger") |
| 6197 | (version "3.16.1") |
| 6198 | (source (origin |
| 6199 | (method url-fetch) |
| 6200 | (uri (bioconductor-uri "edgeR" version)) |
| 6201 | (sha256 |
| 6202 | (base32 |
| 6203 | "1r6hhwkqp13m022hjajzr1lnjsbai0yjhykwn0kp1f0la990a808")))) |
| 6204 | (properties `((upstream-name . "edgeR"))) |
| 6205 | (build-system r-build-system) |
| 6206 | (propagated-inputs |
| 6207 | `(("r-limma" ,r-limma) |
| 6208 | ("r-locfit" ,r-locfit))) |
| 6209 | (home-page "http://bioinf.wehi.edu.au/edgeR") |
| 6210 | (synopsis "EdgeR does empirical analysis of digital gene expression data") |
| 6211 | (description "This package can do differential expression analysis of |
| 6212 | RNA-seq expression profiles with biological replication. It implements a range |
| 6213 | of statistical methodology based on the negative binomial distributions, |
| 6214 | including empirical Bayes estimation, exact tests, generalized linear models |
| 6215 | and quasi-likelihood tests. It be applied to differential signal analysis of |
| 6216 | other types of genomic data that produce counts, including ChIP-seq, SAGE and |
| 6217 | CAGE.") |
| 6218 | (license license:gpl2+))) |
| 6219 | |
| 6220 | (define-public r-variantannotation |
| 6221 | (package |
| 6222 | (name "r-variantannotation") |
| 6223 | (version "1.20.0") |
| 6224 | (source (origin |
| 6225 | (method url-fetch) |
| 6226 | (uri (bioconductor-uri "VariantAnnotation" version)) |
| 6227 | (sha256 |
| 6228 | (base32 |
| 6229 | "1lwzfgahz8ipwli73kcfqb18y6adi129hap1gnycnj3980m54i8q")))) |
| 6230 | (properties |
| 6231 | `((upstream-name . "VariantAnnotation"))) |
| 6232 | (inputs |
| 6233 | `(("zlib" ,zlib))) |
| 6234 | (propagated-inputs |
| 6235 | `(("r-annotationdbi" ,r-annotationdbi) |
| 6236 | ("r-biobase" ,r-biobase) |
| 6237 | ("r-biocgenerics" ,r-biocgenerics) |
| 6238 | ("r-biostrings" ,r-biostrings) |
| 6239 | ("r-bsgenome" ,r-bsgenome) |
| 6240 | ("r-dbi" ,r-dbi) |
| 6241 | ("r-genomeinfodb" ,r-genomeinfodb) |
| 6242 | ("r-genomicfeatures" ,r-genomicfeatures) |
| 6243 | ("r-genomicranges" ,r-genomicranges) |
| 6244 | ("r-iranges" ,r-iranges) |
| 6245 | ("r-summarizedexperiment" ,r-summarizedexperiment) |
| 6246 | ("r-rsamtools" ,r-rsamtools) |
| 6247 | ("r-rtracklayer" ,r-rtracklayer) |
| 6248 | ("r-s4vectors" ,r-s4vectors) |
| 6249 | ("r-xvector" ,r-xvector) |
| 6250 | ("r-zlibbioc" ,r-zlibbioc))) |
| 6251 | (build-system r-build-system) |
| 6252 | (home-page "https://bioconductor.org/packages/VariantAnnotation") |
| 6253 | (synopsis "Package for annotation of genetic variants") |
| 6254 | (description "This R package can annotate variants, compute amino acid |
| 6255 | coding changes and predict coding outcomes.") |
| 6256 | (license license:artistic2.0))) |
| 6257 | |
| 6258 | (define-public r-limma |
| 6259 | (package |
| 6260 | (name "r-limma") |
| 6261 | (version "3.30.2") |
| 6262 | (source (origin |
| 6263 | (method url-fetch) |
| 6264 | (uri (bioconductor-uri "limma" version)) |
| 6265 | (sha256 |
| 6266 | (base32 |
| 6267 | "04jris7wk2lxksrrvrjsysznsdb2k04lfgrnp18ic49sazva0hfy")))) |
| 6268 | (build-system r-build-system) |
| 6269 | (home-page "http://bioinf.wehi.edu.au/limma") |
| 6270 | (synopsis "Package for linear models for microarray and RNA-seq data") |
| 6271 | (description "This package can be used for the analysis of gene expression |
| 6272 | studies, especially the use of linear models for analysing designed experiments |
| 6273 | and the assessment of differential expression. The analysis methods apply to |
| 6274 | different technologies, including microarrays, RNA-seq, and quantitative PCR.") |
| 6275 | (license license:gpl2+))) |
| 6276 | |
| 6277 | (define-public r-xvector |
| 6278 | (package |
| 6279 | (name "r-xvector") |
| 6280 | (version "0.14.0") |
| 6281 | (source (origin |
| 6282 | (method url-fetch) |
| 6283 | (uri (bioconductor-uri "XVector" version)) |
| 6284 | (sha256 |
| 6285 | (base32 |
| 6286 | "09lbqxpqr80g0kw77mpz0p1a8cq706j33kz8194wp71il67cdzi7")))) |
| 6287 | (properties |
| 6288 | `((upstream-name . "XVector"))) |
| 6289 | (build-system r-build-system) |
| 6290 | (arguments |
| 6291 | `(#:phases |
| 6292 | (modify-phases %standard-phases |
| 6293 | (add-after 'unpack 'use-system-zlib |
| 6294 | (lambda _ |
| 6295 | (substitute* "DESCRIPTION" |
| 6296 | (("zlibbioc, ") "")) |
| 6297 | (substitute* "NAMESPACE" |
| 6298 | (("import\\(zlibbioc\\)") "")) |
| 6299 | #t))))) |
| 6300 | (inputs |
| 6301 | `(("zlib" ,zlib))) |
| 6302 | (propagated-inputs |
| 6303 | `(("r-biocgenerics" ,r-biocgenerics) |
| 6304 | ("r-iranges" ,r-iranges) |
| 6305 | ("r-s4vectors" ,r-s4vectors))) |
| 6306 | (home-page "http://bioconductor.org/packages/XVector") |
| 6307 | (synopsis "Representation and manpulation of external sequences") |
| 6308 | (description |
| 6309 | "This package provides memory efficient S4 classes for storing sequences |
| 6310 | \"externally\" (behind an R external pointer, or on disk).") |
| 6311 | (license license:artistic2.0))) |
| 6312 | |
| 6313 | (define-public r-genomicranges |
| 6314 | (package |
| 6315 | (name "r-genomicranges") |
| 6316 | (version "1.26.1") |
| 6317 | (source (origin |
| 6318 | (method url-fetch) |
| 6319 | (uri (bioconductor-uri "GenomicRanges" version)) |
| 6320 | (sha256 |
| 6321 | (base32 |
| 6322 | "039nxccg9i2an8q2wni79x8dr9p1fcfcqvih9hg9w243pczg2g3c")))) |
| 6323 | (properties |
| 6324 | `((upstream-name . "GenomicRanges"))) |
| 6325 | (build-system r-build-system) |
| 6326 | (propagated-inputs |
| 6327 | `(("r-biocgenerics" ,r-biocgenerics) |
| 6328 | ("r-genomeinfodb" ,r-genomeinfodb) |
| 6329 | ("r-iranges" ,r-iranges) |
| 6330 | ("r-s4vectors" ,r-s4vectors) |
| 6331 | ("r-xvector" ,r-xvector))) |
| 6332 | (home-page "http://bioconductor.org/packages/GenomicRanges") |
| 6333 | (synopsis "Representation and manipulation of genomic intervals") |
| 6334 | (description |
| 6335 | "This package provides tools to efficiently represent and manipulate |
| 6336 | genomic annotations and alignments is playing a central role when it comes to |
| 6337 | analyzing high-throughput sequencing data (a.k.a. NGS data). The |
| 6338 | GenomicRanges package defines general purpose containers for storing and |
| 6339 | manipulating genomic intervals and variables defined along a genome.") |
| 6340 | (license license:artistic2.0))) |
| 6341 | |
| 6342 | (define-public r-biobase |
| 6343 | (package |
| 6344 | (name "r-biobase") |
| 6345 | (version "2.34.0") |
| 6346 | (source (origin |
| 6347 | (method url-fetch) |
| 6348 | (uri (bioconductor-uri "Biobase" version)) |
| 6349 | (sha256 |
| 6350 | (base32 |
| 6351 | "0js9j9wqls8f571ifl9ylllbb9a9hwf7b7drf2grwb1fl31ldazl")))) |
| 6352 | (properties |
| 6353 | `((upstream-name . "Biobase"))) |
| 6354 | (build-system r-build-system) |
| 6355 | (propagated-inputs |
| 6356 | `(("r-biocgenerics" ,r-biocgenerics))) |
| 6357 | (home-page "http://bioconductor.org/packages/Biobase") |
| 6358 | (synopsis "Base functions for Bioconductor") |
| 6359 | (description |
| 6360 | "This package provides functions that are needed by many other packages |
| 6361 | on Bioconductor or which replace R functions.") |
| 6362 | (license license:artistic2.0))) |
| 6363 | |
| 6364 | (define-public r-annotationdbi |
| 6365 | (package |
| 6366 | (name "r-annotationdbi") |
| 6367 | (version "1.36.0") |
| 6368 | (source (origin |
| 6369 | (method url-fetch) |
| 6370 | (uri (bioconductor-uri "AnnotationDbi" version)) |
| 6371 | (sha256 |
| 6372 | (base32 |
| 6373 | "0ydrqw1k1j5p6w76bwc753cx545c055x88q87wzya93858synj6r")))) |
| 6374 | (properties |
| 6375 | `((upstream-name . "AnnotationDbi"))) |
| 6376 | (build-system r-build-system) |
| 6377 | (propagated-inputs |
| 6378 | `(("r-biobase" ,r-biobase) |
| 6379 | ("r-biocgenerics" ,r-biocgenerics) |
| 6380 | ("r-dbi" ,r-dbi) |
| 6381 | ("r-iranges" ,r-iranges) |
| 6382 | ("r-rsqlite" ,r-rsqlite) |
| 6383 | ("r-s4vectors" ,r-s4vectors))) |
| 6384 | (home-page "http://bioconductor.org/packages/AnnotationDbi") |
| 6385 | (synopsis "Annotation database interface") |
| 6386 | (description |
| 6387 | "This package provides user interface and database connection code for |
| 6388 | annotation data packages using SQLite data storage.") |
| 6389 | (license license:artistic2.0))) |
| 6390 | |
| 6391 | (define-public r-biomart |
| 6392 | (package |
| 6393 | (name "r-biomart") |
| 6394 | (version "2.30.0") |
| 6395 | (source (origin |
| 6396 | (method url-fetch) |
| 6397 | (uri (bioconductor-uri "biomaRt" version)) |
| 6398 | (sha256 |
| 6399 | (base32 |
| 6400 | "1x0flcghq71784q2l02j0g4f9jkmyb14f6i307n6c59d6ji7h7x6")))) |
| 6401 | (properties |
| 6402 | `((upstream-name . "biomaRt"))) |
| 6403 | (build-system r-build-system) |
| 6404 | (propagated-inputs |
| 6405 | `(("r-annotationdbi" ,r-annotationdbi) |
| 6406 | ("r-rcurl" ,r-rcurl) |
| 6407 | ("r-xml" ,r-xml))) |
| 6408 | (home-page "http://bioconductor.org/packages/biomaRt") |
| 6409 | (synopsis "Interface to BioMart databases") |
| 6410 | (description |
| 6411 | "biomaRt provides an interface to a growing collection of databases |
| 6412 | implementing the @url{BioMart software suite, http://www.biomart.org}. The |
| 6413 | package enables retrieval of large amounts of data in a uniform way without |
| 6414 | the need to know the underlying database schemas or write complex SQL queries. |
| 6415 | Examples of BioMart databases are Ensembl, COSMIC, Uniprot, HGNC, Gramene, |
| 6416 | Wormbase and dbSNP mapped to Ensembl. These major databases give biomaRt |
| 6417 | users direct access to a diverse set of data and enable a wide range of |
| 6418 | powerful online queries from gene annotation to database mining.") |
| 6419 | (license license:artistic2.0))) |
| 6420 | |
| 6421 | (define-public r-biocparallel |
| 6422 | (package |
| 6423 | (name "r-biocparallel") |
| 6424 | (version "1.8.1") |
| 6425 | (source (origin |
| 6426 | (method url-fetch) |
| 6427 | (uri (bioconductor-uri "BiocParallel" version)) |
| 6428 | (sha256 |
| 6429 | (base32 |
| 6430 | "123i928rwi4h4sy4fpysv6pinw5nns0sm3myxi2ghqhm34ws8gyl")))) |
| 6431 | (properties |
| 6432 | `((upstream-name . "BiocParallel"))) |
| 6433 | (build-system r-build-system) |
| 6434 | (propagated-inputs |
| 6435 | `(("r-futile-logger" ,r-futile-logger) |
| 6436 | ("r-snow" ,r-snow))) |
| 6437 | (home-page "http://bioconductor.org/packages/BiocParallel") |
| 6438 | (synopsis "Bioconductor facilities for parallel evaluation") |
| 6439 | (description |
| 6440 | "This package provides modified versions and novel implementation of |
| 6441 | functions for parallel evaluation, tailored to use with Bioconductor |
| 6442 | objects.") |
| 6443 | (license (list license:gpl2+ license:gpl3+)))) |
| 6444 | |
| 6445 | (define-public r-biostrings |
| 6446 | (package |
| 6447 | (name "r-biostrings") |
| 6448 | (version "2.42.0") |
| 6449 | (source (origin |
| 6450 | (method url-fetch) |
| 6451 | (uri (bioconductor-uri "Biostrings" version)) |
| 6452 | (sha256 |
| 6453 | (base32 |
| 6454 | "08z8lkz3axa94wkf144a931ry6vf6cc25avi1ywr84ln2k5czz9f")))) |
| 6455 | (properties |
| 6456 | `((upstream-name . "Biostrings"))) |
| 6457 | (build-system r-build-system) |
| 6458 | (propagated-inputs |
| 6459 | `(("r-biocgenerics" ,r-biocgenerics) |
| 6460 | ("r-iranges" ,r-iranges) |
| 6461 | ("r-s4vectors" ,r-s4vectors) |
| 6462 | ("r-xvector" ,r-xvector))) |
| 6463 | (home-page "http://bioconductor.org/packages/Biostrings") |
| 6464 | (synopsis "String objects and algorithms for biological sequences") |
| 6465 | (description |
| 6466 | "This package provides memory efficient string containers, string |
| 6467 | matching algorithms, and other utilities, for fast manipulation of large |
| 6468 | biological sequences or sets of sequences.") |
| 6469 | (license license:artistic2.0))) |
| 6470 | |
| 6471 | (define-public r-rsamtools |
| 6472 | (package |
| 6473 | (name "r-rsamtools") |
| 6474 | (version "1.26.1") |
| 6475 | (source (origin |
| 6476 | (method url-fetch) |
| 6477 | (uri (bioconductor-uri "Rsamtools" version)) |
| 6478 | (sha256 |
| 6479 | (base32 |
| 6480 | "0pf4f6brf4bl5zgjrah0f38qslazrs49ayqgyh0xfqgrh63yx4ck")))) |
| 6481 | (properties |
| 6482 | `((upstream-name . "Rsamtools"))) |
| 6483 | (build-system r-build-system) |
| 6484 | (arguments |
| 6485 | `(#:phases |
| 6486 | (modify-phases %standard-phases |
| 6487 | (add-after 'unpack 'use-system-zlib |
| 6488 | (lambda _ |
| 6489 | (substitute* "DESCRIPTION" |
| 6490 | (("zlibbioc, ") "")) |
| 6491 | (substitute* "NAMESPACE" |
| 6492 | (("import\\(zlibbioc\\)") "")) |
| 6493 | #t))))) |
| 6494 | (inputs |
| 6495 | `(("zlib" ,zlib))) |
| 6496 | (propagated-inputs |
| 6497 | `(("r-biocgenerics" ,r-biocgenerics) |
| 6498 | ("r-biocparallel" ,r-biocparallel) |
| 6499 | ("r-biostrings" ,r-biostrings) |
| 6500 | ("r-bitops" ,r-bitops) |
| 6501 | ("r-genomeinfodb" ,r-genomeinfodb) |
| 6502 | ("r-genomicranges" ,r-genomicranges) |
| 6503 | ("r-iranges" ,r-iranges) |
| 6504 | ("r-s4vectors" ,r-s4vectors) |
| 6505 | ("r-xvector" ,r-xvector))) |
| 6506 | (home-page "http://bioconductor.org/packages/release/bioc/html/Rsamtools.html") |
| 6507 | (synopsis "Interface to samtools, bcftools, and tabix") |
| 6508 | (description |
| 6509 | "This package provides an interface to the 'samtools', 'bcftools', and |
| 6510 | 'tabix' utilities for manipulating SAM (Sequence Alignment / Map), FASTA, |
| 6511 | binary variant call (BCF) and compressed indexed tab-delimited (tabix) |
| 6512 | files.") |
| 6513 | (license license:expat))) |
| 6514 | |
| 6515 | (define-public r-summarizedexperiment |
| 6516 | (package |
| 6517 | (name "r-summarizedexperiment") |
| 6518 | (version "1.4.0") |
| 6519 | (source (origin |
| 6520 | (method url-fetch) |
| 6521 | (uri (bioconductor-uri "SummarizedExperiment" version)) |
| 6522 | (sha256 |
| 6523 | (base32 |
| 6524 | "1kbj8sg2ik9f8d6g95wz0py62jldg01qy5rsdpg1cxw95nf7dzi3")))) |
| 6525 | (properties |
| 6526 | `((upstream-name . "SummarizedExperiment"))) |
| 6527 | (build-system r-build-system) |
| 6528 | (propagated-inputs |
| 6529 | `(("r-biobase" ,r-biobase) |
| 6530 | ("r-biocgenerics" ,r-biocgenerics) |
| 6531 | ("r-genomeinfodb" ,r-genomeinfodb) |
| 6532 | ("r-genomicranges" ,r-genomicranges) |
| 6533 | ("r-iranges" ,r-iranges) |
| 6534 | ("r-s4vectors" ,r-s4vectors))) |
| 6535 | (home-page "http://bioconductor.org/packages/SummarizedExperiment") |
| 6536 | (synopsis "Container for representing genomic ranges by sample") |
| 6537 | (description |
| 6538 | "The SummarizedExperiment container contains one or more assays, each |
| 6539 | represented by a matrix-like object of numeric or other mode. The rows |
| 6540 | typically represent genomic ranges of interest and the columns represent |
| 6541 | samples.") |
| 6542 | (license license:artistic2.0))) |
| 6543 | |
| 6544 | (define-public r-genomicalignments |
| 6545 | (package |
| 6546 | (name "r-genomicalignments") |
| 6547 | (version "1.10.0") |
| 6548 | (source (origin |
| 6549 | (method url-fetch) |
| 6550 | (uri (bioconductor-uri "GenomicAlignments" version)) |
| 6551 | (sha256 |
| 6552 | (base32 |
| 6553 | "11vb0a0zd36i4yhg4mfijv787v0nihn6pkjj6q7rfy19gwy61xlc")))) |
| 6554 | (properties |
| 6555 | `((upstream-name . "GenomicAlignments"))) |
| 6556 | (build-system r-build-system) |
| 6557 | (propagated-inputs |
| 6558 | `(("r-biocgenerics" ,r-biocgenerics) |
| 6559 | ("r-biocparallel" ,r-biocparallel) |
| 6560 | ("r-biostrings" ,r-biostrings) |
| 6561 | ("r-genomeinfodb" ,r-genomeinfodb) |
| 6562 | ("r-genomicranges" ,r-genomicranges) |
| 6563 | ("r-iranges" ,r-iranges) |
| 6564 | ("r-rsamtools" ,r-rsamtools) |
| 6565 | ("r-s4vectors" ,r-s4vectors) |
| 6566 | ("r-summarizedexperiment" ,r-summarizedexperiment))) |
| 6567 | (home-page "http://bioconductor.org/packages/GenomicAlignments") |
| 6568 | (synopsis "Representation and manipulation of short genomic alignments") |
| 6569 | (description |
| 6570 | "This package provides efficient containers for storing and manipulating |
| 6571 | short genomic alignments (typically obtained by aligning short reads to a |
| 6572 | reference genome). This includes read counting, computing the coverage, |
| 6573 | junction detection, and working with the nucleotide content of the |
| 6574 | alignments.") |
| 6575 | (license license:artistic2.0))) |
| 6576 | |
| 6577 | (define-public r-rtracklayer |
| 6578 | (package |
| 6579 | (name "r-rtracklayer") |
| 6580 | (version "1.34.1") |
| 6581 | (source (origin |
| 6582 | (method url-fetch) |
| 6583 | (uri (bioconductor-uri "rtracklayer" version)) |
| 6584 | (sha256 |
| 6585 | (base32 |
| 6586 | "0x59k2fd0iaqi93gy6bm58p2j2z90z1b7a6w5b4c098y98n096rc")))) |
| 6587 | (build-system r-build-system) |
| 6588 | (arguments |
| 6589 | `(#:phases |
| 6590 | (modify-phases %standard-phases |
| 6591 | (add-after 'unpack 'use-system-zlib |
| 6592 | (lambda _ |
| 6593 | (substitute* "DESCRIPTION" |
| 6594 | (("zlibbioc, ") "")) |
| 6595 | (substitute* "NAMESPACE" |
| 6596 | (("import\\(zlibbioc\\)") "")) |
| 6597 | #t))))) |
| 6598 | (inputs |
| 6599 | `(("zlib" ,zlib))) |
| 6600 | (propagated-inputs |
| 6601 | `(("r-biocgenerics" ,r-biocgenerics) |
| 6602 | ("r-biostrings" ,r-biostrings) |
| 6603 | ("r-genomeinfodb" ,r-genomeinfodb) |
| 6604 | ("r-genomicalignments" ,r-genomicalignments) |
| 6605 | ("r-genomicranges" ,r-genomicranges) |
| 6606 | ("r-iranges" ,r-iranges) |
| 6607 | ("r-rcurl" ,r-rcurl) |
| 6608 | ("r-rsamtools" ,r-rsamtools) |
| 6609 | ("r-s4vectors" ,r-s4vectors) |
| 6610 | ("r-xml" ,r-xml) |
| 6611 | ("r-xvector" ,r-xvector))) |
| 6612 | (home-page "http://bioconductor.org/packages/rtracklayer") |
| 6613 | (synopsis "R interface to genome browsers and their annotation tracks") |
| 6614 | (description |
| 6615 | "rtracklayer is an extensible framework for interacting with multiple |
| 6616 | genome browsers (currently UCSC built-in) and manipulating annotation tracks |
| 6617 | in various formats (currently GFF, BED, bedGraph, BED15, WIG, BigWig and 2bit |
| 6618 | built-in). The user may export/import tracks to/from the supported browsers, |
| 6619 | as well as query and modify the browser state, such as the current viewport.") |
| 6620 | (license license:artistic2.0))) |
| 6621 | |
| 6622 | (define-public r-genomicfeatures |
| 6623 | (package |
| 6624 | (name "r-genomicfeatures") |
| 6625 | (version "1.26.0") |
| 6626 | (source (origin |
| 6627 | (method url-fetch) |
| 6628 | (uri (bioconductor-uri "GenomicFeatures" version)) |
| 6629 | (sha256 |
| 6630 | (base32 |
| 6631 | "0z8spi2knwzwi10c38vr7xlvi3ah9faj7m1lka880mmxkl9cai4k")))) |
| 6632 | (properties |
| 6633 | `((upstream-name . "GenomicFeatures"))) |
| 6634 | (build-system r-build-system) |
| 6635 | (propagated-inputs |
| 6636 | `(("r-annotationdbi" ,r-annotationdbi) |
| 6637 | ("r-biobase" ,r-biobase) |
| 6638 | ("r-biocgenerics" ,r-biocgenerics) |
| 6639 | ("r-biomart" ,r-biomart) |
| 6640 | ("r-biostrings" ,r-biostrings) |
| 6641 | ("r-dbi" ,r-dbi) |
| 6642 | ("r-genomeinfodb" ,r-genomeinfodb) |
| 6643 | ("r-genomicranges" ,r-genomicranges) |
| 6644 | ("r-iranges" ,r-iranges) |
| 6645 | ("r-rcurl" ,r-rcurl) |
| 6646 | ("r-rsqlite" ,r-rsqlite) |
| 6647 | ("r-rtracklayer" ,r-rtracklayer) |
| 6648 | ("r-s4vectors" ,r-s4vectors) |
| 6649 | ("r-xvector" ,r-xvector))) |
| 6650 | (home-page "http://bioconductor.org/packages/GenomicFeatures") |
| 6651 | (synopsis "Tools for working with transcript centric annotations") |
| 6652 | (description |
| 6653 | "This package provides a set of tools and methods for making and |
| 6654 | manipulating transcript centric annotations. With these tools the user can |
| 6655 | easily download the genomic locations of the transcripts, exons and cds of a |
| 6656 | given organism, from either the UCSC Genome Browser or a BioMart |
| 6657 | database (more sources will be supported in the future). This information is |
| 6658 | then stored in a local database that keeps track of the relationship between |
| 6659 | transcripts, exons, cds and genes. Flexible methods are provided for |
| 6660 | extracting the desired features in a convenient format.") |
| 6661 | (license license:artistic2.0))) |
| 6662 | |
| 6663 | (define-public r-go-db |
| 6664 | (package |
| 6665 | (name "r-go-db") |
| 6666 | (version "3.4.0") |
| 6667 | (source (origin |
| 6668 | (method url-fetch) |
| 6669 | (uri (string-append "http://www.bioconductor.org/packages/" |
| 6670 | "release/data/annotation/src/contrib/GO.db_" |
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| 6672 | (sha256 |
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| 6675 | (properties |
| 6676 | `((upstream-name . "GO.db"))) |
| 6677 | (build-system r-build-system) |
| 6678 | (propagated-inputs |
| 6679 | `(("r-annotationdbi" ,r-annotationdbi))) |
| 6680 | (home-page "http://bioconductor.org/packages/GO.db") |
| 6681 | (synopsis "Annotation maps describing the entire Gene Ontology") |
| 6682 | (description |
| 6683 | "The purpose of this GO.db annotation package is to provide detailed |
| 6684 | information about the latest version of the Gene Ontologies.") |
| 6685 | (license license:artistic2.0))) |
| 6686 | |
| 6687 | (define-public r-graph |
| 6688 | (package |
| 6689 | (name "r-graph") |
| 6690 | (version "1.52.0") |
| 6691 | (source (origin |
| 6692 | (method url-fetch) |
| 6693 | (uri (bioconductor-uri "graph" version)) |
| 6694 | (sha256 |
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| 6697 | (build-system r-build-system) |
| 6698 | (propagated-inputs |
| 6699 | `(("r-biocgenerics" ,r-biocgenerics))) |
| 6700 | (home-page "http://bioconductor.org/packages/graph") |
| 6701 | (synopsis "Handle graph data structures in R") |
| 6702 | (description |
| 6703 | "This package implements some simple graph handling capabilities for R.") |
| 6704 | (license license:artistic2.0))) |
| 6705 | |
| 6706 | (define-public r-topgo |
| 6707 | (package |
| 6708 | (name "r-topgo") |
| 6709 | (version "2.26.0") |
| 6710 | (source (origin |
| 6711 | (method url-fetch) |
| 6712 | (uri (bioconductor-uri "topGO" version)) |
| 6713 | (sha256 |
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| 6716 | (properties |
| 6717 | `((upstream-name . "topGO"))) |
| 6718 | (build-system r-build-system) |
| 6719 | (propagated-inputs |
| 6720 | `(("r-annotationdbi" ,r-annotationdbi) |
| 6721 | ("r-dbi" ,r-dbi) |
| 6722 | ("r-biobase" ,r-biobase) |
| 6723 | ("r-biocgenerics" ,r-biocgenerics) |
| 6724 | ("r-go-db" ,r-go-db) |
| 6725 | ("r-matrixstats" ,r-matrixstats) |
| 6726 | ("r-graph" ,r-graph) |
| 6727 | ("r-sparsem" ,r-sparsem))) |
| 6728 | (home-page "http://bioconductor.org/packages/topGO") |
| 6729 | (synopsis "Enrichment analysis for gene ontology") |
| 6730 | (description |
| 6731 | "The topGO package provides tools for testing @dfn{gene ontology} (GO) |
| 6732 | terms while accounting for the topology of the GO graph. Different test |
| 6733 | statistics and different methods for eliminating local similarities and |
| 6734 | dependencies between GO terms can be implemented and applied.") |
| 6735 | ;; Any version of the LGPL applies. |
| 6736 | (license license:lgpl2.1+))) |
| 6737 | |
| 6738 | (define-public r-bsgenome |
| 6739 | (package |
| 6740 | (name "r-bsgenome") |
| 6741 | (version "1.42.0") |
| 6742 | (source (origin |
| 6743 | (method url-fetch) |
| 6744 | (uri (bioconductor-uri "BSgenome" version)) |
| 6745 | (sha256 |
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| 6748 | (properties |
| 6749 | `((upstream-name . "BSgenome"))) |
| 6750 | (build-system r-build-system) |
| 6751 | (propagated-inputs |
| 6752 | `(("r-biocgenerics" ,r-biocgenerics) |
| 6753 | ("r-biostrings" ,r-biostrings) |
| 6754 | ("r-genomeinfodb" ,r-genomeinfodb) |
| 6755 | ("r-genomicranges" ,r-genomicranges) |
| 6756 | ("r-iranges" ,r-iranges) |
| 6757 | ("r-rsamtools" ,r-rsamtools) |
| 6758 | ("r-rtracklayer" ,r-rtracklayer) |
| 6759 | ("r-s4vectors" ,r-s4vectors) |
| 6760 | ("r-xvector" ,r-xvector))) |
| 6761 | (home-page "http://bioconductor.org/packages/BSgenome") |
| 6762 | (synopsis "Infrastructure for Biostrings-based genome data packages") |
| 6763 | (description |
| 6764 | "This package provides infrastructure shared by all Biostrings-based |
| 6765 | genome data packages and support for efficient SNP representation.") |
| 6766 | (license license:artistic2.0))) |
| 6767 | |
| 6768 | (define-public r-impute |
| 6769 | (package |
| 6770 | (name "r-impute") |
| 6771 | (version "1.48.0") |
| 6772 | (source (origin |
| 6773 | (method url-fetch) |
| 6774 | (uri (bioconductor-uri "impute" version)) |
| 6775 | (sha256 |
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| 6778 | (inputs |
| 6779 | `(("gfortran" ,gfortran))) |
| 6780 | (build-system r-build-system) |
| 6781 | (home-page "http://bioconductor.org/packages/impute") |
| 6782 | (synopsis "Imputation for microarray data") |
| 6783 | (description |
| 6784 | "This package provides a function to impute missing gene expression |
| 6785 | microarray data, using nearest neighbor averaging.") |
| 6786 | (license license:gpl2+))) |
| 6787 | |
| 6788 | (define-public r-seqpattern |
| 6789 | (package |
| 6790 | (name "r-seqpattern") |
| 6791 | (version "1.6.0") |
| 6792 | (source (origin |
| 6793 | (method url-fetch) |
| 6794 | (uri (bioconductor-uri "seqPattern" version)) |
| 6795 | (sha256 |
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| 6798 | (properties |
| 6799 | `((upstream-name . "seqPattern"))) |
| 6800 | (build-system r-build-system) |
| 6801 | (propagated-inputs |
| 6802 | `(("r-biostrings" ,r-biostrings) |
| 6803 | ("r-genomicranges" ,r-genomicranges) |
| 6804 | ("r-iranges" ,r-iranges) |
| 6805 | ("r-kernsmooth" ,r-kernsmooth) |
| 6806 | ("r-plotrix" ,r-plotrix))) |
| 6807 | (home-page "http://bioconductor.org/packages/seqPattern") |
| 6808 | (synopsis "Visualising oligonucleotide patterns and motif occurrences") |
| 6809 | (description |
| 6810 | "This package provides tools to visualize oligonucleotide patterns and |
| 6811 | sequence motif occurrences across a large set of sequences centred at a common |
| 6812 | reference point and sorted by a user defined feature.") |
| 6813 | (license license:gpl3+))) |
| 6814 | |
| 6815 | (define-public r-genomation |
| 6816 | (package |
| 6817 | (name "r-genomation") |
| 6818 | (version "1.6.0") |
| 6819 | (source (origin |
| 6820 | (method url-fetch) |
| 6821 | (uri (bioconductor-uri "genomation" version)) |
| 6822 | (sha256 |
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| 6825 | (build-system r-build-system) |
| 6826 | (propagated-inputs |
| 6827 | `(("r-biostrings" ,r-biostrings) |
| 6828 | ("r-bsgenome" ,r-bsgenome) |
| 6829 | ("r-data-table" ,r-data-table) |
| 6830 | ("r-genomeinfodb" ,r-genomeinfodb) |
| 6831 | ("r-genomicalignments" ,r-genomicalignments) |
| 6832 | ("r-genomicranges" ,r-genomicranges) |
| 6833 | ("r-ggplot2" ,r-ggplot2) |
| 6834 | ("r-gridbase" ,r-gridbase) |
| 6835 | ("r-impute" ,r-impute) |
| 6836 | ("r-iranges" ,r-iranges) |
| 6837 | ("r-matrixstats" ,r-matrixstats) |
| 6838 | ("r-plotrix" ,r-plotrix) |
| 6839 | ("r-plyr" ,r-plyr) |
| 6840 | ("r-rcpp" ,r-rcpp) |
| 6841 | ("r-readr" ,r-readr) |
| 6842 | ("r-reshape2" ,r-reshape2) |
| 6843 | ("r-rhtslib" ,r-rhtslib) |
| 6844 | ("r-rsamtools" ,r-rsamtools) |
| 6845 | ("r-rtracklayer" ,r-rtracklayer) |
| 6846 | ("r-runit" ,r-runit) |
| 6847 | ("r-s4vectors" ,r-s4vectors) |
| 6848 | ("r-seqpattern" ,r-seqpattern))) |
| 6849 | (inputs |
| 6850 | `(("zlib" ,zlib))) |
| 6851 | (home-page "http://bioinformatics.mdc-berlin.de/genomation/") |
| 6852 | (synopsis "Summary, annotation and visualization of genomic data") |
| 6853 | (description |
| 6854 | "This package provides a package for summary and annotation of genomic |
| 6855 | intervals. Users can visualize and quantify genomic intervals over |
| 6856 | pre-defined functional regions, such as promoters, exons, introns, etc. The |
| 6857 | genomic intervals represent regions with a defined chromosome position, which |
| 6858 | may be associated with a score, such as aligned reads from HT-seq experiments, |
| 6859 | TF binding sites, methylation scores, etc. The package can use any tabular |
| 6860 | genomic feature data as long as it has minimal information on the locations of |
| 6861 | genomic intervals. In addition, it can use BAM or BigWig files as input.") |
| 6862 | (license license:artistic2.0))) |
| 6863 | |
| 6864 | (define-public r-genomationdata |
| 6865 | (package |
| 6866 | (name "r-genomationdata") |
| 6867 | (version "1.6.0") |
| 6868 | (source (origin |
| 6869 | (method url-fetch) |
| 6870 | ;; We cannot use bioconductor-uri here because this tarball is |
| 6871 | ;; located under "data/annotation/" instead of "bioc/". |
| 6872 | (uri (string-append "https://bioconductor.org/packages/" |
| 6873 | "release/data/experiment/src/contrib/" |
| 6874 | "genomationData_" version ".tar.gz")) |
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| 6878 | (build-system r-build-system) |
| 6879 | ;; As this package provides little more than large data files, it doesn't |
| 6880 | ;; make sense to build substitutes. |
| 6881 | (arguments `(#:substitutable? #f)) |
| 6882 | (native-inputs |
| 6883 | `(("r-knitr" ,r-knitr))) |
| 6884 | (home-page "http://bioinformatics.mdc-berlin.de/genomation/") |
| 6885 | (synopsis "Experimental data for use with the genomation package") |
| 6886 | (description |
| 6887 | "This package contains experimental genetic data for use with the |
| 6888 | genomation package. Included are Chip Seq, Methylation and Cage data, |
| 6889 | downloaded from Encode.") |
| 6890 | (license license:gpl3+))) |
| 6891 | |
| 6892 | (define-public r-org-hs-eg-db |
| 6893 | (package |
| 6894 | (name "r-org-hs-eg-db") |
| 6895 | (version "3.4.0") |
| 6896 | (source (origin |
| 6897 | (method url-fetch) |
| 6898 | ;; We cannot use bioconductor-uri here because this tarball is |
| 6899 | ;; located under "data/annotation/" instead of "bioc/". |
| 6900 | (uri (string-append "http://www.bioconductor.org/packages/" |
| 6901 | "release/data/annotation/src/contrib/" |
| 6902 | "org.Hs.eg.db_" version ".tar.gz")) |
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| 6906 | (properties |
| 6907 | `((upstream-name . "org.Hs.eg.db"))) |
| 6908 | (build-system r-build-system) |
| 6909 | (propagated-inputs |
| 6910 | `(("r-annotationdbi" ,r-annotationdbi))) |
| 6911 | (home-page "http://www.bioconductor.org/packages/org.Hs.eg.db/") |
| 6912 | (synopsis "Genome wide annotation for Human") |
| 6913 | (description |
| 6914 | "This package provides mappings from Entrez gene identifiers to various |
| 6915 | annotations for the human genome.") |
| 6916 | (license license:artistic2.0))) |
| 6917 | |
| 6918 | (define-public r-org-ce-eg-db |
| 6919 | (package |
| 6920 | (name "r-org-ce-eg-db") |
| 6921 | (version "3.4.0") |
| 6922 | (source (origin |
| 6923 | (method url-fetch) |
| 6924 | ;; We cannot use bioconductor-uri here because this tarball is |
| 6925 | ;; located under "data/annotation/" instead of "bioc/". |
| 6926 | (uri (string-append "http://www.bioconductor.org/packages/" |
| 6927 | "release/data/annotation/src/contrib/" |
| 6928 | "org.Ce.eg.db_" version ".tar.gz")) |
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| 6932 | (properties |
| 6933 | `((upstream-name . "org.Ce.eg.db"))) |
| 6934 | (build-system r-build-system) |
| 6935 | (propagated-inputs |
| 6936 | `(("r-annotationdbi" ,r-annotationdbi))) |
| 6937 | (home-page "http://www.bioconductor.org/packages/org.Ce.eg.db/") |
| 6938 | (synopsis "Genome wide annotation for Worm") |
| 6939 | (description |
| 6940 | "This package provides mappings from Entrez gene identifiers to various |
| 6941 | annotations for the genome of the model worm Caenorhabditis elegans.") |
| 6942 | (license license:artistic2.0))) |
| 6943 | |
| 6944 | (define-public r-org-dm-eg-db |
| 6945 | (package |
| 6946 | (name "r-org-dm-eg-db") |
| 6947 | (version "3.4.0") |
| 6948 | (source (origin |
| 6949 | (method url-fetch) |
| 6950 | ;; We cannot use bioconductor-uri here because this tarball is |
| 6951 | ;; located under "data/annotation/" instead of "bioc/". |
| 6952 | (uri (string-append "http://www.bioconductor.org/packages/" |
| 6953 | "release/data/annotation/src/contrib/" |
| 6954 | "org.Dm.eg.db_" version ".tar.gz")) |
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| 6958 | (properties |
| 6959 | `((upstream-name . "org.Dm.eg.db"))) |
| 6960 | (build-system r-build-system) |
| 6961 | (propagated-inputs |
| 6962 | `(("r-annotationdbi" ,r-annotationdbi))) |
| 6963 | (home-page "http://www.bioconductor.org/packages/org.Dm.eg.db/") |
| 6964 | (synopsis "Genome wide annotation for Fly") |
| 6965 | (description |
| 6966 | "This package provides mappings from Entrez gene identifiers to various |
| 6967 | annotations for the genome of the model fruit fly Drosophila melanogaster.") |
| 6968 | (license license:artistic2.0))) |
| 6969 | |
| 6970 | (define-public r-org-mm-eg-db |
| 6971 | (package |
| 6972 | (name "r-org-mm-eg-db") |
| 6973 | (version "3.4.0") |
| 6974 | (source (origin |
| 6975 | (method url-fetch) |
| 6976 | ;; We cannot use bioconductor-uri here because this tarball is |
| 6977 | ;; located under "data/annotation/" instead of "bioc/". |
| 6978 | (uri (string-append "http://www.bioconductor.org/packages/" |
| 6979 | "release/data/annotation/src/contrib/" |
| 6980 | "org.Mm.eg.db_" version ".tar.gz")) |
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| 6984 | (properties |
| 6985 | `((upstream-name . "org.Mm.eg.db"))) |
| 6986 | (build-system r-build-system) |
| 6987 | (propagated-inputs |
| 6988 | `(("r-annotationdbi" ,r-annotationdbi))) |
| 6989 | (home-page "http://www.bioconductor.org/packages/org.Mm.eg.db/") |
| 6990 | (synopsis "Genome wide annotation for Mouse") |
| 6991 | (description |
| 6992 | "This package provides mappings from Entrez gene identifiers to various |
| 6993 | annotations for the genome of the model mouse Mus musculus.") |
| 6994 | (license license:artistic2.0))) |
| 6995 | |
| 6996 | (define-public r-seqlogo |
| 6997 | (package |
| 6998 | (name "r-seqlogo") |
| 6999 | (version "1.40.0") |
| 7000 | (source |
| 7001 | (origin |
| 7002 | (method url-fetch) |
| 7003 | (uri (bioconductor-uri "seqLogo" version)) |
| 7004 | (sha256 |
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| 7006 | "18bajdl75h3039559d81rgllqqvnq8ygsfxfx081xphxs0v6xggy")))) |
| 7007 | (properties `((upstream-name . "seqLogo"))) |
| 7008 | (build-system r-build-system) |
| 7009 | (home-page "http://bioconductor.org/packages/seqLogo") |
| 7010 | (synopsis "Sequence logos for DNA sequence alignments") |
| 7011 | (description |
| 7012 | "seqLogo takes the position weight matrix of a DNA sequence motif and |
| 7013 | plots the corresponding sequence logo as introduced by Schneider and |
| 7014 | Stephens (1990).") |
| 7015 | (license license:lgpl2.0+))) |
| 7016 | |
| 7017 | (define-public r-bsgenome-hsapiens-ucsc-hg19 |
| 7018 | (package |
| 7019 | (name "r-bsgenome-hsapiens-ucsc-hg19") |
| 7020 | (version "1.4.0") |
| 7021 | (source (origin |
| 7022 | (method url-fetch) |
| 7023 | ;; We cannot use bioconductor-uri here because this tarball is |
| 7024 | ;; located under "data/annotation/" instead of "bioc/". |
| 7025 | (uri (string-append "http://www.bioconductor.org/packages/" |
| 7026 | "release/data/annotation/src/contrib/" |
| 7027 | "BSgenome.Hsapiens.UCSC.hg19_" |
| 7028 | version ".tar.gz")) |
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| 7032 | (properties |
| 7033 | `((upstream-name . "BSgenome.Hsapiens.UCSC.hg19"))) |
| 7034 | (build-system r-build-system) |
| 7035 | ;; As this package provides little more than a very large data file it |
| 7036 | ;; doesn't make sense to build substitutes. |
| 7037 | (arguments `(#:substitutable? #f)) |
| 7038 | (propagated-inputs |
| 7039 | `(("r-bsgenome" ,r-bsgenome))) |
| 7040 | (home-page |
| 7041 | "http://www.bioconductor.org/packages/BSgenome.Hsapiens.UCSC.hg19/") |
| 7042 | (synopsis "Full genome sequences for Homo sapiens") |
| 7043 | (description |
| 7044 | "This package provides full genome sequences for Homo sapiens as provided |
| 7045 | by UCSC (hg19, February 2009) and stored in Biostrings objects.") |
| 7046 | (license license:artistic2.0))) |
| 7047 | |
| 7048 | (define-public r-bsgenome-mmusculus-ucsc-mm9 |
| 7049 | (package |
| 7050 | (name "r-bsgenome-mmusculus-ucsc-mm9") |
| 7051 | (version "1.4.0") |
| 7052 | (source (origin |
| 7053 | (method url-fetch) |
| 7054 | ;; We cannot use bioconductor-uri here because this tarball is |
| 7055 | ;; located under "data/annotation/" instead of "bioc/". |
| 7056 | (uri (string-append "http://www.bioconductor.org/packages/" |
| 7057 | "release/data/annotation/src/contrib/" |
| 7058 | "BSgenome.Mmusculus.UCSC.mm9_" |
| 7059 | version ".tar.gz")) |
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| 7063 | (properties |
| 7064 | `((upstream-name . "BSgenome.Mmusculus.UCSC.mm9"))) |
| 7065 | (build-system r-build-system) |
| 7066 | ;; As this package provides little more than a very large data file it |
| 7067 | ;; doesn't make sense to build substitutes. |
| 7068 | (arguments `(#:substitutable? #f)) |
| 7069 | (propagated-inputs |
| 7070 | `(("r-bsgenome" ,r-bsgenome))) |
| 7071 | (home-page |
| 7072 | "http://www.bioconductor.org/packages/BSgenome.Mmusculus.UCSC.mm9/") |
| 7073 | (synopsis "Full genome sequences for Mouse") |
| 7074 | (description |
| 7075 | "This package provides full genome sequences for Mus musculus (Mouse) as |
| 7076 | provided by UCSC (mm9, July 2007) and stored in Biostrings objects.") |
| 7077 | (license license:artistic2.0))) |
| 7078 | |
| 7079 | (define-public r-bsgenome-mmusculus-ucsc-mm10 |
| 7080 | (package |
| 7081 | (name "r-bsgenome-mmusculus-ucsc-mm10") |
| 7082 | (version "1.4.0") |
| 7083 | (source (origin |
| 7084 | (method url-fetch) |
| 7085 | ;; We cannot use bioconductor-uri here because this tarball is |
| 7086 | ;; located under "data/annotation/" instead of "bioc/". |
| 7087 | (uri (string-append "http://www.bioconductor.org/packages/" |
| 7088 | "release/data/annotation/src/contrib/" |
| 7089 | "BSgenome.Mmusculus.UCSC.mm10_" |
| 7090 | version ".tar.gz")) |
| 7091 | (sha256 |
| 7092 | (base32 |
| 7093 | "12s0nm2na9brjad4rn9l7d3db2aj8qa1xvz0y1k7gk08wayb6bkf")))) |
| 7094 | (properties |
| 7095 | `((upstream-name . "BSgenome.Mmusculus.UCSC.mm10"))) |
| 7096 | (build-system r-build-system) |
| 7097 | ;; As this package provides little more than a very large data file it |
| 7098 | ;; doesn't make sense to build substitutes. |
| 7099 | (arguments `(#:substitutable? #f)) |
| 7100 | (propagated-inputs |
| 7101 | `(("r-bsgenome" ,r-bsgenome))) |
| 7102 | (home-page |
| 7103 | "http://www.bioconductor.org/packages/BSgenome.Mmusculus.UCSC.mm10/") |
| 7104 | (synopsis "Full genome sequences for Mouse") |
| 7105 | (description |
| 7106 | "This package provides full genome sequences for Mus |
| 7107 | musculus (Mouse) as provided by UCSC (mm10, December 2011) and stored |
| 7108 | in Biostrings objects.") |
| 7109 | (license license:artistic2.0))) |
| 7110 | |
| 7111 | (define-public r-bsgenome-celegans-ucsc-ce6 |
| 7112 | (package |
| 7113 | (name "r-bsgenome-celegans-ucsc-ce6") |
| 7114 | (version "1.4.0") |
| 7115 | (source (origin |
| 7116 | (method url-fetch) |
| 7117 | ;; We cannot use bioconductor-uri here because this tarball is |
| 7118 | ;; located under "data/annotation/" instead of "bioc/". |
| 7119 | (uri (string-append "http://www.bioconductor.org/packages/" |
| 7120 | "release/data/annotation/src/contrib/" |
| 7121 | "BSgenome.Celegans.UCSC.ce6_" |
| 7122 | version ".tar.gz")) |
| 7123 | (sha256 |
| 7124 | (base32 |
| 7125 | "0mqzb353xv2c3m3vkb315dkmnxkgczp7ndnknyhpgjlybyf715v9")))) |
| 7126 | (properties |
| 7127 | `((upstream-name . "BSgenome.Celegans.UCSC.ce6"))) |
| 7128 | (build-system r-build-system) |
| 7129 | ;; As this package provides little more than a very large data file it |
| 7130 | ;; doesn't make sense to build substitutes. |
| 7131 | (arguments `(#:substitutable? #f)) |
| 7132 | (propagated-inputs |
| 7133 | `(("r-bsgenome" ,r-bsgenome))) |
| 7134 | (home-page |
| 7135 | "http://www.bioconductor.org/packages/BSgenome.Celegans.UCSC.ce6/") |
| 7136 | (synopsis "Full genome sequences for Worm") |
| 7137 | (description |
| 7138 | "This package provides full genome sequences for Caenorhabditis |
| 7139 | elegans (Worm) as provided by UCSC (ce6, May 2008) and stored in Biostrings |
| 7140 | objects.") |
| 7141 | (license license:artistic2.0))) |
| 7142 | |
| 7143 | (define-public r-bsgenome-celegans-ucsc-ce10 |
| 7144 | (package |
| 7145 | (name "r-bsgenome-celegans-ucsc-ce10") |
| 7146 | (version "1.4.0") |
| 7147 | (source (origin |
| 7148 | (method url-fetch) |
| 7149 | ;; We cannot use bioconductor-uri here because this tarball is |
| 7150 | ;; located under "data/annotation/" instead of "bioc/". |
| 7151 | (uri (string-append "http://www.bioconductor.org/packages/" |
| 7152 | "release/data/annotation/src/contrib/" |
| 7153 | "BSgenome.Celegans.UCSC.ce10_" |
| 7154 | version ".tar.gz")) |
| 7155 | (sha256 |
| 7156 | (base32 |
| 7157 | "1zaym97jk4npxk14ifvwz2rvhm4zx9xgs33r9vvx9rlynp0gydrk")))) |
| 7158 | (properties |
| 7159 | `((upstream-name . "BSgenome.Celegans.UCSC.ce10"))) |
| 7160 | (build-system r-build-system) |
| 7161 | ;; As this package provides little more than a very large data file it |
| 7162 | ;; doesn't make sense to build substitutes. |
| 7163 | (arguments `(#:substitutable? #f)) |
| 7164 | (propagated-inputs |
| 7165 | `(("r-bsgenome" ,r-bsgenome))) |
| 7166 | (home-page |
| 7167 | "http://www.bioconductor.org/packages/BSgenome.Celegans.UCSC.ce10/") |
| 7168 | (synopsis "Full genome sequences for Worm") |
| 7169 | (description |
| 7170 | "This package provides full genome sequences for Caenorhabditis |
| 7171 | elegans (Worm) as provided by UCSC (ce10, Oct 2010) and stored in Biostrings |
| 7172 | objects.") |
| 7173 | (license license:artistic2.0))) |
| 7174 | |
| 7175 | (define-public r-bsgenome-dmelanogaster-ucsc-dm3 |
| 7176 | (package |
| 7177 | (name "r-bsgenome-dmelanogaster-ucsc-dm3") |
| 7178 | (version "1.4.0") |
| 7179 | (source (origin |
| 7180 | (method url-fetch) |
| 7181 | ;; We cannot use bioconductor-uri here because this tarball is |
| 7182 | ;; located under "data/annotation/" instead of "bioc/". |
| 7183 | (uri (string-append "http://www.bioconductor.org/packages/" |
| 7184 | "release/data/annotation/src/contrib/" |
| 7185 | "BSgenome.Dmelanogaster.UCSC.dm3_" |
| 7186 | version ".tar.gz")) |
| 7187 | (sha256 |
| 7188 | (base32 |
| 7189 | "19bm3lkhhkag3gnwp419211fh0cnr0x6fa0r1lr0ycwrikxdxsv8")))) |
| 7190 | (properties |
| 7191 | `((upstream-name . "BSgenome.Dmelanogaster.UCSC.dm3"))) |
| 7192 | (build-system r-build-system) |
| 7193 | ;; As this package provides little more than a very large data file it |
| 7194 | ;; doesn't make sense to build substitutes. |
| 7195 | (arguments `(#:substitutable? #f)) |
| 7196 | (propagated-inputs |
| 7197 | `(("r-bsgenome" ,r-bsgenome))) |
| 7198 | (home-page |
| 7199 | "http://www.bioconductor.org/packages/BSgenome.Dmelanogaster.UCSC.dm3/") |
| 7200 | (synopsis "Full genome sequences for Fly") |
| 7201 | (description |
| 7202 | "This package provides full genome sequences for Drosophila |
| 7203 | melanogaster (Fly) as provided by UCSC (dm3, April 2006) and stored in |
| 7204 | Biostrings objects.") |
| 7205 | (license license:artistic2.0))) |
| 7206 | |
| 7207 | (define-public r-motifrg |
| 7208 | (package |
| 7209 | (name "r-motifrg") |
| 7210 | (version "1.18.0") |
| 7211 | (source |
| 7212 | (origin |
| 7213 | (method url-fetch) |
| 7214 | (uri (bioconductor-uri "motifRG" version)) |
| 7215 | (sha256 |
| 7216 | (base32 |
| 7217 | "1pa97aj6c5f3gx4bgriw110764dj3m9h104ddi8rv2bpy41yd98d")))) |
| 7218 | (properties `((upstream-name . "motifRG"))) |
| 7219 | (build-system r-build-system) |
| 7220 | (propagated-inputs |
| 7221 | `(("r-biostrings" ,r-biostrings) |
| 7222 | ("r-bsgenome" ,r-bsgenome) |
| 7223 | ("r-bsgenome.hsapiens.ucsc.hg19" ,r-bsgenome-hsapiens-ucsc-hg19) |
| 7224 | ("r-iranges" ,r-iranges) |
| 7225 | ("r-seqlogo" ,r-seqlogo) |
| 7226 | ("r-xvector" ,r-xvector))) |
| 7227 | (home-page "http://bioconductor.org/packages/motifRG") |
| 7228 | (synopsis "Discover motifs in high throughput sequencing data") |
| 7229 | (description |
| 7230 | "This package provides tools for discriminative motif discovery in high |
| 7231 | throughput genetic sequencing data sets using regression methods.") |
| 7232 | (license license:artistic2.0))) |
| 7233 | |
| 7234 | (define-public r-qtl |
| 7235 | (package |
| 7236 | (name "r-qtl") |
| 7237 | (version "1.39-5") |
| 7238 | (source |
| 7239 | (origin |
| 7240 | (method url-fetch) |
| 7241 | (uri (string-append "mirror://cran/src/contrib/qtl_" |
| 7242 | version ".tar.gz")) |
| 7243 | (sha256 |
| 7244 | (base32 |
| 7245 | "1grwgvyv7x0dgay1858bg7qf4wk47gpnq7qkqpcda9cn0h970d6f")))) |
| 7246 | (build-system r-build-system) |
| 7247 | (home-page "http://rqtl.org/") |
| 7248 | (synopsis "R package for analyzing QTL experiments in genetics") |
| 7249 | (description "R/qtl is an extension library for the R statistics |
| 7250 | system. It is used to analyze experimental crosses for identifying |
| 7251 | genes contributing to variation in quantitative traits (so-called |
| 7252 | quantitative trait loci, QTLs). |
| 7253 | |
| 7254 | Using a hidden Markov model, R/qtl allows to estimate genetic maps, to |
| 7255 | identify genotyping errors, and to perform single-QTL and two-QTL, |
| 7256 | two-dimensional genome scans.") |
| 7257 | (license license:gpl3))) |
| 7258 | |
| 7259 | (define-public r-zlibbioc |
| 7260 | (package |
| 7261 | (name "r-zlibbioc") |
| 7262 | (version "1.20.0") |
| 7263 | (source (origin |
| 7264 | (method url-fetch) |
| 7265 | (uri (bioconductor-uri "zlibbioc" version)) |
| 7266 | (sha256 |
| 7267 | (base32 |
| 7268 | "0hbk90q5hl0fycfvy5nxxa4hxgglag9lzp7i0fg849bqygg5nbyq")))) |
| 7269 | (properties |
| 7270 | `((upstream-name . "zlibbioc"))) |
| 7271 | (build-system r-build-system) |
| 7272 | (home-page "https://bioconductor.org/packages/zlibbioc") |
| 7273 | (synopsis "Provider for zlib-1.2.5 to R packages") |
| 7274 | (description "This package uses the source code of zlib-1.2.5 to create |
| 7275 | libraries for systems that do not have these available via other means.") |
| 7276 | (license license:artistic2.0))) |
| 7277 | |
| 7278 | (define-public r-r4rna |
| 7279 | (package |
| 7280 | (name "r-r4rna") |
| 7281 | (version "0.1.4") |
| 7282 | (source |
| 7283 | (origin |
| 7284 | (method url-fetch) |
| 7285 | (uri (string-append "http://www.e-rna.org/r-chie/files/R4RNA_" |
| 7286 | version ".tar.gz")) |
| 7287 | (sha256 |
| 7288 | (base32 |
| 7289 | "1p0i78wh76jfgmn9jphbwwaz6yy6pipzfg08xs54cxavxg2j81p5")))) |
| 7290 | (build-system r-build-system) |
| 7291 | (propagated-inputs |
| 7292 | `(("r-optparse" ,r-optparse) |
| 7293 | ("r-rcolorbrewer" ,r-rcolorbrewer))) |
| 7294 | (home-page "http://www.e-rna.org/r-chie/index.cgi") |
| 7295 | (synopsis "Analysis framework for RNA secondary structure") |
| 7296 | (description |
| 7297 | "The R4RNA package aims to be a general framework for the analysis of RNA |
| 7298 | secondary structure and comparative analysis in R.") |
| 7299 | (license license:gpl3+))) |
| 7300 | |
| 7301 | (define-public r-rhtslib |
| 7302 | (package |
| 7303 | (name "r-rhtslib") |
| 7304 | (version "1.6.0") |
| 7305 | (source |
| 7306 | (origin |
| 7307 | (method url-fetch) |
| 7308 | (uri (bioconductor-uri "Rhtslib" version)) |
| 7309 | (sha256 |
| 7310 | (base32 |
| 7311 | "1vk3ng61dhi3pbia1lp3gl3mlr3i1vb2lkq83qb53i9dzz128wh9")))) |
| 7312 | (properties `((upstream-name . "Rhtslib"))) |
| 7313 | (build-system r-build-system) |
| 7314 | (propagated-inputs |
| 7315 | `(("r-zlibbioc" ,r-zlibbioc))) |
| 7316 | (inputs |
| 7317 | `(("zlib" ,zlib))) |
| 7318 | (native-inputs |
| 7319 | `(("autoconf" ,autoconf))) |
| 7320 | (home-page "https://github.com/nhayden/Rhtslib") |
| 7321 | (synopsis "High-throughput sequencing library as an R package") |
| 7322 | (description |
| 7323 | "This package provides the HTSlib C library for high-throughput |
| 7324 | nucleotide sequence analysis. The package is primarily useful to developers |
| 7325 | of other R packages who wish to make use of HTSlib.") |
| 7326 | (license license:lgpl2.0+))) |
| 7327 | |
| 7328 | (define-public r-bamsignals |
| 7329 | (package |
| 7330 | (name "r-bamsignals") |
| 7331 | (version "1.6.0") |
| 7332 | (source |
| 7333 | (origin |
| 7334 | (method url-fetch) |
| 7335 | (uri (bioconductor-uri "bamsignals" version)) |
| 7336 | (sha256 |
| 7337 | (base32 |
| 7338 | "1k42gvk5mgq4la1fp0in3an2zfdz69h6522jsqhmk0f6i75kg4mb")))) |
| 7339 | (build-system r-build-system) |
| 7340 | (propagated-inputs |
| 7341 | `(("r-biocgenerics" ,r-biocgenerics) |
| 7342 | ("r-genomicranges" ,r-genomicranges) |
| 7343 | ("r-iranges" ,r-iranges) |
| 7344 | ("r-rcpp" ,r-rcpp) |
| 7345 | ("r-rhtslib" ,r-rhtslib) |
| 7346 | ("r-zlibbioc" ,r-zlibbioc))) |
| 7347 | (inputs |
| 7348 | `(("zlib" ,zlib))) |
| 7349 | (home-page "http://bioconductor.org/packages/bamsignals") |
| 7350 | (synopsis "Extract read count signals from bam files") |
| 7351 | (description |
| 7352 | "This package allows to efficiently obtain count vectors from indexed bam |
| 7353 | files. It counts the number of nucleotide sequence reads in given genomic |
| 7354 | ranges and it computes reads profiles and coverage profiles. It also handles |
| 7355 | paired-end data.") |
| 7356 | (license license:gpl2+))) |
| 7357 | |
| 7358 | (define-public r-rcas |
| 7359 | (package |
| 7360 | (name "r-rcas") |
| 7361 | (version "1.0.0") |
| 7362 | (source (origin |
| 7363 | (method url-fetch) |
| 7364 | (uri (string-append "https://github.com/BIMSBbioinfo/RCAS/archive/v" |
| 7365 | version ".tar.gz")) |
| 7366 | (file-name (string-append name "-" version ".tar.gz")) |
| 7367 | (sha256 |
| 7368 | (base32 |
| 7369 | "1h7di822ihgkhmmmlfbfz3c2dkjyjxl307i6mx8w0cwjqbna1kp6")))) |
| 7370 | (build-system r-build-system) |
| 7371 | (native-inputs |
| 7372 | `(("r-knitr" ,r-knitr) |
| 7373 | ("r-testthat" ,r-testthat) |
| 7374 | ;; During vignette building knitr checks that "pandoc-citeproc" |
| 7375 | ;; is in the PATH. |
| 7376 | ("ghc-pandoc-citeproc" ,ghc-pandoc-citeproc))) |
| 7377 | (propagated-inputs |
| 7378 | `(("r-data-table" ,r-data-table) |
| 7379 | ("r-biomart" ,r-biomart) |
| 7380 | ("r-org-hs-eg-db" ,r-org-hs-eg-db) |
| 7381 | ("r-org-ce-eg-db" ,r-org-ce-eg-db) |
| 7382 | ("r-org-dm-eg-db" ,r-org-dm-eg-db) |
| 7383 | ("r-org-mm-eg-db" ,r-org-mm-eg-db) |
| 7384 | ("r-bsgenome-hsapiens-ucsc-hg19" ,r-bsgenome-hsapiens-ucsc-hg19) |
| 7385 | ("r-bsgenome-mmusculus-ucsc-mm9" ,r-bsgenome-mmusculus-ucsc-mm9) |
| 7386 | ("r-bsgenome-celegans-ucsc-ce10" ,r-bsgenome-celegans-ucsc-ce10) |
| 7387 | ("r-bsgenome-dmelanogaster-ucsc-dm3" ,r-bsgenome-dmelanogaster-ucsc-dm3) |
| 7388 | ("r-topgo" ,r-topgo) |
| 7389 | ("r-dt" ,r-dt) |
| 7390 | ("r-plotly" ,r-plotly) |
| 7391 | ("r-motifrg" ,r-motifrg) |
| 7392 | ("r-genomation" ,r-genomation) |
| 7393 | ("r-genomicfeatures" ,r-genomicfeatures) |
| 7394 | ("r-rtracklayer" ,r-rtracklayer) |
| 7395 | ("r-rmarkdown" ,r-rmarkdown))) |
| 7396 | (synopsis "RNA-centric annotation system") |
| 7397 | (description |
| 7398 | "RCAS aims to be a standalone RNA-centric annotation system that provides |
| 7399 | intuitive reports and publication-ready graphics. This package provides the R |
| 7400 | library implementing most of the pipeline's features.") |
| 7401 | (home-page "https://github.com/BIMSBbioinfo/RCAS") |
| 7402 | (license license:expat))) |
| 7403 | |
| 7404 | (define-public rcas-web |
| 7405 | (package |
| 7406 | (name "rcas-web") |
| 7407 | (version "0.0.3") |
| 7408 | (source |
| 7409 | (origin |
| 7410 | (method url-fetch) |
| 7411 | (uri (string-append "https://github.com/BIMSBbioinfo/rcas-web/" |
| 7412 | "releases/download/v" version |
| 7413 | "/rcas-web-" version ".tar.gz")) |
| 7414 | (sha256 |
| 7415 | (base32 |
| 7416 | "0d3my0g8i7js59n184zzzjdki7hgmhpi4rhfvk7i6jsw01ba04qq")))) |
| 7417 | (build-system gnu-build-system) |
| 7418 | (arguments |
| 7419 | `(#:phases |
| 7420 | (modify-phases %standard-phases |
| 7421 | (add-after 'install 'wrap-executable |
| 7422 | (lambda* (#:key inputs outputs #:allow-other-keys) |
| 7423 | (let* ((out (assoc-ref outputs "out")) |
| 7424 | (json (assoc-ref inputs "guile-json")) |
| 7425 | (redis (assoc-ref inputs "guile-redis")) |
| 7426 | (path (string-append |
| 7427 | json "/share/guile/site/2.2:" |
| 7428 | redis "/share/guile/site/2.2"))) |
| 7429 | (wrap-program (string-append out "/bin/rcas-web") |
| 7430 | `("GUILE_LOAD_PATH" ":" = (,path)) |
| 7431 | `("GUILE_LOAD_COMPILED_PATH" ":" = (,path)) |
| 7432 | `("R_LIBS_SITE" ":" = (,(getenv "R_LIBS_SITE"))))) |
| 7433 | #t))))) |
| 7434 | (inputs |
| 7435 | `(("r" ,r) |
| 7436 | ("r-rcas" ,r-rcas) |
| 7437 | ("guile-next" ,guile-next) |
| 7438 | ("guile-json" ,guile2.2-json) |
| 7439 | ("guile-redis" ,guile2.2-redis))) |
| 7440 | (native-inputs |
| 7441 | `(("pkg-config" ,pkg-config))) |
| 7442 | (home-page "https://github.com/BIMSBbioinfo/rcas-web") |
| 7443 | (synopsis "Web interface for RNA-centric annotation system (RCAS)") |
| 7444 | (description "This package provides a simple web interface for the |
| 7445 | @dfn{RNA-centric annotation system} (RCAS).") |
| 7446 | (license license:agpl3+))) |
| 7447 | |
| 7448 | (define-public r-mutationalpatterns |
| 7449 | (package |
| 7450 | (name "r-mutationalpatterns") |
| 7451 | (version "1.0.0") |
| 7452 | (source |
| 7453 | (origin |
| 7454 | (method url-fetch) |
| 7455 | (uri (bioconductor-uri "MutationalPatterns" version)) |
| 7456 | (sha256 |
| 7457 | (base32 |
| 7458 | "1a3c2bm0xx0q4gf98jiw74msmdf2fr8rbsdysd5ww9kqlzmsbr17")))) |
| 7459 | (build-system r-build-system) |
| 7460 | (propagated-inputs |
| 7461 | `(("r-biocgenerics" ,r-biocgenerics) |
| 7462 | ("r-biostrings" ,r-biostrings) |
| 7463 | ("r-genomicranges" ,r-genomicranges) |
| 7464 | ("r-genomeinfodb" ,r-genomeinfodb) |
| 7465 | ("r-ggplot2" ,r-ggplot2) |
| 7466 | ("r-gridextra" ,r-gridextra) |
| 7467 | ("r-iranges" ,r-iranges) |
| 7468 | ("r-nmf" ,r-nmf) |
| 7469 | ("r-plyr" ,r-plyr) |
| 7470 | ("r-pracma" ,r-pracma) |
| 7471 | ("r-reshape2" ,r-reshape2) |
| 7472 | ("r-summarizedexperiment" ,r-summarizedexperiment) |
| 7473 | ("r-variantannotation" ,r-variantannotation))) |
| 7474 | (home-page "http://bioconductor.org/packages/MutationalPatterns/") |
| 7475 | (synopsis "Extract and visualize mutational patterns in genomic data") |
| 7476 | (description "This package provides an extensive toolset for the |
| 7477 | characterization and visualization of a wide range of mutational patterns |
| 7478 | in SNV base substitution data.") |
| 7479 | (license license:expat))) |
| 7480 | |
| 7481 | (define-public r-wgcna |
| 7482 | (package |
| 7483 | (name "r-wgcna") |
| 7484 | (version "1.51") |
| 7485 | (source |
| 7486 | (origin |
| 7487 | (method url-fetch) |
| 7488 | (uri (cran-uri "WGCNA" version)) |
| 7489 | (sha256 |
| 7490 | (base32 |
| 7491 | "0hzvnhw76vwg8bl8x368f0c5szpwb8323bmrb3bir93i5bmfjsxx")))) |
| 7492 | (properties `((upstream-name . "WGCNA"))) |
| 7493 | (build-system r-build-system) |
| 7494 | (propagated-inputs |
| 7495 | `(("r-annotationdbi" ,r-annotationdbi) |
| 7496 | ("r-doparallel" ,r-doparallel) |
| 7497 | ("r-dynamictreecut" ,r-dynamictreecut) |
| 7498 | ("r-fastcluster" ,r-fastcluster) |
| 7499 | ("r-foreach" ,r-foreach) |
| 7500 | ("r-go-db" ,r-go-db) |
| 7501 | ("r-hmisc" ,r-hmisc) |
| 7502 | ("r-impute" ,r-impute) |
| 7503 | ("r-matrixstats" ,r-matrixstats) |
| 7504 | ("r-preprocesscore" ,r-preprocesscore))) |
| 7505 | (home-page |
| 7506 | "http://www.genetics.ucla.edu/labs/horvath/CoexpressionNetwork/Rpackages/WGCNA/") |
| 7507 | (synopsis "Weighted correlation network analysis") |
| 7508 | (description |
| 7509 | "This package provides functions necessary to perform Weighted |
| 7510 | Correlation Network Analysis on high-dimensional data. It includes functions |
| 7511 | for rudimentary data cleaning, construction and summarization of correlation |
| 7512 | networks, module identification and functions for relating both variables and |
| 7513 | modules to sample traits. It also includes a number of utility functions for |
| 7514 | data manipulation and visualization.") |
| 7515 | (license license:gpl2+))) |
| 7516 | |
| 7517 | (define-public r-chipkernels |
| 7518 | (let ((commit "c9cfcacb626b1221094fb3490ea7bac0fd625372") |
| 7519 | (revision "1")) |
| 7520 | (package |
| 7521 | (name "r-chipkernels") |
| 7522 | (version (string-append "1.1-" revision "." (string-take commit 9))) |
| 7523 | (source |
| 7524 | (origin |
| 7525 | (method git-fetch) |
| 7526 | (uri (git-reference |
| 7527 | (url "https://github.com/ManuSetty/ChIPKernels.git") |
| 7528 | (commit commit))) |
| 7529 | (file-name (string-append name "-" version)) |
| 7530 | (sha256 |
| 7531 | (base32 |
| 7532 | "14bj5qhjm1hsm9ay561nfbqi9wxsa7y487df2idsaaf6z10nw4v0")))) |
| 7533 | (build-system r-build-system) |
| 7534 | (propagated-inputs |
| 7535 | `(("r-iranges" ,r-iranges) |
| 7536 | ("r-xvector" ,r-xvector) |
| 7537 | ("r-biostrings" ,r-biostrings) |
| 7538 | ("r-bsgenome" ,r-bsgenome) |
| 7539 | ("r-gtools" ,r-gtools) |
| 7540 | ("r-genomicranges" ,r-genomicranges) |
| 7541 | ("r-sfsmisc" ,r-sfsmisc) |
| 7542 | ("r-kernlab" ,r-kernlab) |
| 7543 | ("r-s4vectors" ,r-s4vectors) |
| 7544 | ("r-biocgenerics" ,r-biocgenerics))) |
| 7545 | (home-page "https://github.com/ManuSetty/ChIPKernels") |
| 7546 | (synopsis "Build string kernels for DNA Sequence analysis") |
| 7547 | (description "ChIPKernels is an R package for building different string |
| 7548 | kernels used for DNA Sequence analysis. A dictionary of the desired kernel |
| 7549 | must be built and this dictionary can be used for determining kernels for DNA |
| 7550 | Sequences.") |
| 7551 | (license license:gpl2+)))) |
| 7552 | |
| 7553 | (define-public r-seqgl |
| 7554 | (package |
| 7555 | (name "r-seqgl") |
| 7556 | (version "1.1.4") |
| 7557 | (source |
| 7558 | (origin |
| 7559 | (method url-fetch) |
| 7560 | (uri (string-append "https://github.com/ManuSetty/SeqGL/" |
| 7561 | "archive/" version ".tar.gz")) |
| 7562 | (file-name (string-append name "-" version ".tar.gz")) |
| 7563 | (sha256 |
| 7564 | (base32 |
| 7565 | "0pnk1p3sci5yipyc8xnb6jbmydpl80fld927xgnbcv104hy8h8yh")))) |
| 7566 | (build-system r-build-system) |
| 7567 | (propagated-inputs |
| 7568 | `(("r-biostrings" ,r-biostrings) |
| 7569 | ("r-chipkernels" ,r-chipkernels) |
| 7570 | ("r-genomicranges" ,r-genomicranges) |
| 7571 | ("r-spams" ,r-spams) |
| 7572 | ("r-wgcna" ,r-wgcna) |
| 7573 | ("r-fastcluster" ,r-fastcluster))) |
| 7574 | (home-page "https://github.com/ManuSetty/SeqGL") |
| 7575 | (synopsis "Group lasso for Dnase/ChIP-seq data") |
| 7576 | (description "SeqGL is a group lasso based algorithm to extract |
| 7577 | transcription factor sequence signals from ChIP, DNase and ATAC-seq profiles. |
| 7578 | This package presents a method which uses group lasso to discriminate between |
| 7579 | bound and non bound genomic regions to accurately identify transcription |
| 7580 | factors bound at the specific regions.") |
| 7581 | (license license:gpl2+))) |
| 7582 | |
| 7583 | (define-public r-gkmsvm |
| 7584 | (package |
| 7585 | (name "r-gkmsvm") |
| 7586 | (version "0.71.0") |
| 7587 | (source |
| 7588 | (origin |
| 7589 | (method url-fetch) |
| 7590 | (uri (cran-uri "gkmSVM" version)) |
| 7591 | (sha256 |
| 7592 | (base32 |
| 7593 | "1zpxgxmf2nd5j5wn00ps6kfxr8wxh7d1swr1rr4spq7sj5z5z0k0")))) |
| 7594 | (properties `((upstream-name . "gkmSVM"))) |
| 7595 | (build-system r-build-system) |
| 7596 | (propagated-inputs |
| 7597 | `(("r-biocgenerics" ,r-biocgenerics) |
| 7598 | ("r-biostrings" ,r-biostrings) |
| 7599 | ("r-genomeinfodb" ,r-genomeinfodb) |
| 7600 | ("r-genomicranges" ,r-genomicranges) |
| 7601 | ("r-iranges" ,r-iranges) |
| 7602 | ("r-kernlab" ,r-kernlab) |
| 7603 | ("r-rcpp" ,r-rcpp) |
| 7604 | ("r-rocr" ,r-rocr) |
| 7605 | ("r-rtracklayer" ,r-rtracklayer) |
| 7606 | ("r-s4vectors" ,r-s4vectors) |
| 7607 | ("r-seqinr" ,r-seqinr))) |
| 7608 | (home-page "http://cran.r-project.org/web/packages/gkmSVM") |
| 7609 | (synopsis "Gapped-kmer support vector machine") |
| 7610 | (description |
| 7611 | "This R package provides tools for training gapped-kmer SVM classifiers |
| 7612 | for DNA and protein sequences. This package supports several sequence |
| 7613 | kernels, including: gkmSVM, kmer-SVM, mismatch kernel and wildcard kernel.") |
| 7614 | (license license:gpl2+))) |
| 7615 | |
| 7616 | (define-public emboss |
| 7617 | (package |
| 7618 | (name "emboss") |
| 7619 | (version "6.5.7") |
| 7620 | (source (origin |
| 7621 | (method url-fetch) |
| 7622 | (uri (string-append "ftp://emboss.open-bio.org/pub/EMBOSS/old/" |
| 7623 | (version-major+minor version) ".0/" |
| 7624 | "EMBOSS-" version ".tar.gz")) |
| 7625 | (sha256 |
| 7626 | (base32 |
| 7627 | "0vsmz96gc411yj2iyzdrsmg4l2n1nhgmp7vrgzlxx3xixv9xbf0q")))) |
| 7628 | (build-system gnu-build-system) |
| 7629 | (arguments |
| 7630 | `(#:configure-flags |
| 7631 | (list (string-append "--with-hpdf=" |
| 7632 | (assoc-ref %build-inputs "libharu"))) |
| 7633 | #:phases |
| 7634 | (modify-phases %standard-phases |
| 7635 | (add-after 'unpack 'fix-checks |
| 7636 | (lambda _ |
| 7637 | ;; The PNGDRIVER tests check for the presence of libgd, libpng |
| 7638 | ;; and zlib, but assume that they are all found at the same |
| 7639 | ;; prefix. |
| 7640 | (substitute* "configure.in" |
| 7641 | (("CHECK_PNGDRIVER") |
| 7642 | "LIBS=\"$LIBS -lgd -lpng -lz -lm\" |
| 7643 | AC_DEFINE([PLD_png], [1], [Define to 1 if PNG support is available]) |
| 7644 | AM_CONDITIONAL(AMPNG, true)")) |
| 7645 | #t)) |
| 7646 | (add-after 'unpack 'disable-update-check |
| 7647 | (lambda _ |
| 7648 | ;; At build time there is no connection to the Internet, so |
| 7649 | ;; looking for updates will not work. |
| 7650 | (substitute* "Makefile.am" |
| 7651 | (("\\$\\(bindir\\)/embossupdate") "")) |
| 7652 | #t)) |
| 7653 | (add-before 'configure 'autogen |
| 7654 | (lambda _ (zero? (system* "autoreconf" "-vif"))))))) |
| 7655 | (inputs |
| 7656 | `(("perl" ,perl) |
| 7657 | ("libpng" ,libpng) |
| 7658 | ("gd" ,gd) |
| 7659 | ("libx11" ,libx11) |
| 7660 | ("libharu" ,libharu) |
| 7661 | ("zlib" ,zlib))) |
| 7662 | (native-inputs |
| 7663 | `(("autoconf" ,autoconf) |
| 7664 | ("automake" ,automake) |
| 7665 | ("libtool" ,libtool) |
| 7666 | ("pkg-config" ,pkg-config))) |
| 7667 | (home-page "http://emboss.sourceforge.net") |
| 7668 | (synopsis "Molecular biology analysis suite") |
| 7669 | (description "EMBOSS is the \"European Molecular Biology Open Software |
| 7670 | Suite\". EMBOSS is an analysis package specially developed for the needs of |
| 7671 | the molecular biology (e.g. EMBnet) user community. The software |
| 7672 | automatically copes with data in a variety of formats and even allows |
| 7673 | transparent retrieval of sequence data from the web. It also provides a |
| 7674 | number of libraries for the development of software in the field of molecular |
| 7675 | biology. EMBOSS also integrates a range of currently available packages and |
| 7676 | tools for sequence analysis into a seamless whole.") |
| 7677 | (license license:gpl2+))) |
| 7678 | |
| 7679 | (define-public bits |
| 7680 | (let ((revision "1") |
| 7681 | (commit "3cc4567896d9d6442923da944beb704750a08d2d")) |
| 7682 | (package |
| 7683 | (name "bits") |
| 7684 | ;; The version is 2.13.0 even though no release archives have been |
| 7685 | ;; published as yet. |
| 7686 | (version (string-append "2.13.0-" revision "." (string-take commit 9))) |
| 7687 | (source (origin |
| 7688 | (method git-fetch) |
| 7689 | (uri (git-reference |
| 7690 | (url "https://github.com/arq5x/bits.git") |
| 7691 | (commit commit))) |
| 7692 | (file-name (string-append name "-" version "-checkout")) |
| 7693 | (sha256 |
| 7694 | (base32 |
| 7695 | "17n2kffk4kmhivd8c98g2vr6y1s23vbg4sxlxs689wni66797hbs")))) |
| 7696 | (build-system gnu-build-system) |
| 7697 | (arguments |
| 7698 | `(#:tests? #f ;no tests included |
| 7699 | #:phases |
| 7700 | (modify-phases %standard-phases |
| 7701 | (delete 'configure) |
| 7702 | (add-after 'unpack 'remove-cuda |
| 7703 | (lambda _ |
| 7704 | (substitute* "Makefile" |
| 7705 | ((".*_cuda") "") |
| 7706 | (("(bits_test_intersections) \\\\" _ match) match)) |
| 7707 | #t)) |
| 7708 | (replace 'install |
| 7709 | (lambda* (#:key outputs #:allow-other-keys) |
| 7710 | (copy-recursively |
| 7711 | "bin" (string-append (assoc-ref outputs "out") "/bin")) |
| 7712 | #t))))) |
| 7713 | (inputs |
| 7714 | `(("gsl" ,gsl) |
| 7715 | ("zlib" ,zlib))) |
| 7716 | (home-page "https://github.com/arq5x/bits") |
| 7717 | (synopsis "Implementation of binary interval search algorithm") |
| 7718 | (description "This package provides an implementation of the |
| 7719 | BITS (Binary Interval Search) algorithm, an approach to interval set |
| 7720 | intersection. It is especially suited for the comparison of diverse genomic |
| 7721 | datasets and the exploration of large datasets of genome |
| 7722 | intervals (e.g. genes, sequence alignments).") |
| 7723 | (license license:gpl2)))) |
| 7724 | |
| 7725 | (define-public piranha |
| 7726 | ;; There is no release tarball for the latest version. The latest commit is |
| 7727 | ;; older than one year at the time of this writing. |
| 7728 | (let ((revision "1") |
| 7729 | (commit "0466d364b71117d01e4471b74c514436cc281233")) |
| 7730 | (package |
| 7731 | (name "piranha") |
| 7732 | (version (string-append "1.2.1-" revision "." (string-take commit 9))) |
| 7733 | (source (origin |
| 7734 | (method git-fetch) |
| 7735 | (uri (git-reference |
| 7736 | (url "https://github.com/smithlabcode/piranha.git") |
| 7737 | (commit commit))) |
| 7738 | (sha256 |
| 7739 | (base32 |
| 7740 | "117dc0zf20c61jam69sk4abl57ah6yi6i7qra7d7y5zrbgk12q5n")))) |
| 7741 | (build-system gnu-build-system) |
| 7742 | (arguments |
| 7743 | `(#:test-target "test" |
| 7744 | #:phases |
| 7745 | (modify-phases %standard-phases |
| 7746 | (add-after 'unpack 'copy-smithlab-cpp |
| 7747 | (lambda* (#:key inputs #:allow-other-keys) |
| 7748 | (for-each (lambda (file) |
| 7749 | (install-file file "./src/smithlab_cpp/")) |
| 7750 | (find-files (assoc-ref inputs "smithlab-cpp"))) |
| 7751 | #t)) |
| 7752 | (add-after 'install 'install-to-store |
| 7753 | (lambda* (#:key outputs #:allow-other-keys) |
| 7754 | (let* ((out (assoc-ref outputs "out")) |
| 7755 | (bin (string-append out "/bin"))) |
| 7756 | (for-each (lambda (file) |
| 7757 | (install-file file bin)) |
| 7758 | (find-files "bin" ".*"))) |
| 7759 | #t))) |
| 7760 | #:configure-flags |
| 7761 | (list (string-append "--with-bam_tools_headers=" |
| 7762 | (assoc-ref %build-inputs "bamtools") "/include/bamtools") |
| 7763 | (string-append "--with-bam_tools_library=" |
| 7764 | (assoc-ref %build-inputs "bamtools") "/lib/bamtools")))) |
| 7765 | (inputs |
| 7766 | `(("bamtools" ,bamtools) |
| 7767 | ("samtools" ,samtools-0.1) |
| 7768 | ("gsl" ,gsl) |
| 7769 | ("smithlab-cpp" |
| 7770 | ,(let ((commit "3723e2db438c51501d0423429ff396c3035ba46a")) |
| 7771 | (origin |
| 7772 | (method git-fetch) |
| 7773 | (uri (git-reference |
| 7774 | (url "https://github.com/smithlabcode/smithlab_cpp.git") |
| 7775 | (commit commit))) |
| 7776 | (file-name (string-append "smithlab_cpp-" commit "-checkout")) |
| 7777 | (sha256 |
| 7778 | (base32 |
| 7779 | "0l4gvbwslw5ngziskja41c00x1r06l3yidv7y0xw9djibhykzy0g"))))))) |
| 7780 | (native-inputs |
| 7781 | `(("python" ,python-2))) |
| 7782 | (home-page "https://github.com/smithlabcode/piranha") |
| 7783 | (synopsis "Peak-caller for CLIP-seq and RIP-seq data") |
| 7784 | (description |
| 7785 | "Piranha is a peak-caller for genomic data produced by CLIP-seq and |
| 7786 | RIP-seq experiments. It takes input in BED or BAM format and identifies |
| 7787 | regions of statistically significant read enrichment. Additional covariates |
| 7788 | may optionally be provided to further inform the peak-calling process.") |
| 7789 | (license license:gpl3+)))) |
| 7790 | |
| 7791 | (define-public pepr |
| 7792 | (package |
| 7793 | (name "pepr") |
| 7794 | (version "1.0.9") |
| 7795 | (source (origin |
| 7796 | (method url-fetch) |
| 7797 | (uri (string-append "https://pypi.python.org/packages/source/P" |
| 7798 | "/PePr/PePr-" version ".tar.gz")) |
| 7799 | (sha256 |
| 7800 | (base32 |
| 7801 | "0qxjfdpl1b1y53nccws2d85f6k74zwmx8y8sd9rszcqhfayx6gdx")))) |
| 7802 | (build-system python-build-system) |
| 7803 | (arguments |
| 7804 | `(#:python ,python-2 ; python2 only |
| 7805 | #:tests? #f)) ; no tests included |
| 7806 | (propagated-inputs |
| 7807 | `(("python2-numpy" ,python2-numpy) |
| 7808 | ("python2-scipy" ,python2-scipy) |
| 7809 | ("python2-pysam" ,python2-pysam))) |
| 7810 | (home-page "https://code.google.com/p/pepr-chip-seq/") |
| 7811 | (synopsis "Peak-calling and prioritization pipeline for ChIP-Seq data") |
| 7812 | (description |
| 7813 | "PePr is a ChIP-Seq peak calling or differential binding analysis tool |
| 7814 | that is primarily designed for data with biological replicates. It uses a |
| 7815 | negative binomial distribution to model the read counts among the samples in |
| 7816 | the same group, and look for consistent differences between ChIP and control |
| 7817 | group or two ChIP groups run under different conditions.") |
| 7818 | (license license:gpl3+))) |
| 7819 | |
| 7820 | (define-public filevercmp |
| 7821 | (let ((commit "1a9b779b93d0b244040274794d402106907b71b7")) |
| 7822 | (package |
| 7823 | (name "filevercmp") |
| 7824 | (version (string-append "0-1." (string-take commit 7))) |
| 7825 | (source (origin |
| 7826 | (method url-fetch) |
| 7827 | (uri (string-append "https://github.com/ekg/filevercmp/archive/" |
| 7828 | commit ".tar.gz")) |
| 7829 | (file-name (string-append name "-" version ".tar.gz")) |
| 7830 | (sha256 |
| 7831 | (base32 "0yp5jswf5j2pqc6517x277s4s6h1ss99v57kxw9gy0jkfl3yh450")))) |
| 7832 | (build-system gnu-build-system) |
| 7833 | (arguments |
| 7834 | `(#:tests? #f ; There are no tests to run. |
| 7835 | #:phases |
| 7836 | (modify-phases %standard-phases |
| 7837 | (delete 'configure) ; There is no configure phase. |
| 7838 | (replace 'install |
| 7839 | (lambda* (#:key outputs #:allow-other-keys) |
| 7840 | (let ((bin (string-append (assoc-ref outputs "out") "/bin"))) |
| 7841 | (install-file "filevercmp" bin))))))) |
| 7842 | (home-page "https://github.com/ekg/filevercmp") |
| 7843 | (synopsis "This program compares version strings") |
| 7844 | (description "This program compares version strings. It intends to be a |
| 7845 | replacement for strverscmp.") |
| 7846 | (license license:gpl3+)))) |
| 7847 | |
| 7848 | (define-public multiqc |
| 7849 | (package |
| 7850 | (name "multiqc") |
| 7851 | (version "0.6") |
| 7852 | (source |
| 7853 | (origin |
| 7854 | (method url-fetch) |
| 7855 | (uri (pypi-uri "multiqc" version)) |
| 7856 | (sha256 |
| 7857 | (base32 |
| 7858 | "0avw11h63ldpxy5pizc3wl1wa01ha7q10wb240nggsjz3jaqvyiy")))) |
| 7859 | (build-system python-build-system) |
| 7860 | (propagated-inputs |
| 7861 | `(("python-jinja2" ,python-jinja2) |
| 7862 | ("python-simplejson" ,python-simplejson) |
| 7863 | ("python-pyyaml" ,python-pyyaml) |
| 7864 | ("python-click" ,python-click) |
| 7865 | ("python-matplotlib" ,python-matplotlib) |
| 7866 | ("python-numpy" ,python-numpy))) |
| 7867 | (home-page "http://multiqc.info") |
| 7868 | (synopsis "Aggregate bioinformatics analysis reports") |
| 7869 | (description |
| 7870 | "MultiQC is a tool to aggregate bioinformatics results across many |
| 7871 | samples into a single report. It contains modules for a large number of |
| 7872 | common bioinformatics tools.") |
| 7873 | (license license:gpl3))) |