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gnu: multiqc: Add python-nose to inputs.
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4e10a221 1;;; GNU Guix --- Functional package management for GNU
6193563a 2;;; Copyright © 2014, 2015, 2016, 2017 Ricardo Wurmus <rekado@elephly.net>
9b9b7ffd 3;;; Copyright © 2015, 2016 Ben Woodcroft <donttrustben@gmail.com>
8921841d 4;;; Copyright © 2015, 2016 Pjotr Prins <pjotr.guix@thebird.nl>
a5002ae7 5;;; Copyright © 2015 Andreas Enge <andreas@enge.fr>
a0a71439 6;;; Copyright © 2016 Roel Janssen <roel@gnu.org>
ddb83129 7;;; Copyright © 2016 Efraim Flashner <efraim@flashner.co.il>
318c0aee 8;;; Copyright © 2016 Marius Bakke <mbakke@fastmail.com>
3fffabce 9;;; Copyright © 2016 Raoul Bonnal <ilpuccio.febo@gmail.com>
4e10a221
RW		 10;;;
11;;; This file is part of GNU Guix.
12;;;
13;;; GNU Guix is free software; you can redistribute it and/or modify it
14;;; under the terms of the GNU General Public License as published by
15;;; the Free Software Foundation; either version 3 of the License, or (at
16;;; your option) any later version.
17;;;
18;;; GNU Guix is distributed in the hope that it will be useful, but
19;;; WITHOUT ANY WARRANTY; without even the implied warranty of
20;;; MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
21;;; GNU General Public License for more details.
22;;;
23;;; You should have received a copy of the GNU General Public License
24;;; along with GNU Guix. If not, see <http://www.gnu.org/licenses/>.
25
26(define-module (gnu packages bioinformatics)
27 #:use-module ((guix licenses) #:prefix license:)
28 #:use-module (guix packages)
8e913213 29 #:use-module (guix utils)
4e10a221 30 #:use-module (guix download)
2c16316e 31 #:use-module (guix git-download)
ec946638 32 #:use-module (guix hg-download)
10b4a969 33 #:use-module (guix build-system ant)
4e10a221 34 #:use-module (guix build-system gnu)
d7678942 35 #:use-module (guix build-system cmake)
365c8153 36 #:use-module (guix build-system perl)
8622a072 37 #:use-module (guix build-system python)
a5002ae7 38 #:use-module (guix build-system r)
9c38b540 39 #:use-module (guix build-system ruby)
d3517eda 40 #:use-module (guix build-system trivial)
4e10a221 41 #:use-module (gnu packages)
a2950fa4 42 #:use-module (gnu packages autotools)
684bf7c7 43 #:use-module (gnu packages algebra)
d3517eda 44 #:use-module (gnu packages base)
318c0aee 45 #:use-module (gnu packages bash)
a0a71439 46 #:use-module (gnu packages bison)
e4e5a4d8 47 #:use-module (gnu packages boost)
4e10a221 48 #:use-module (gnu packages compression)
82c370de 49 #:use-module (gnu packages cpio)
1baee943 50 #:use-module (gnu packages curl)
99828fa7 51 #:use-module (gnu packages documentation)
d29150b5 52 #:use-module (gnu packages datastructures)
75dd2424 53 #:use-module (gnu packages file)
99268755 54 #:use-module (gnu packages flex)
02f35bb5 55 #:use-module (gnu packages gawk)
2409f37f 56 #:use-module (gnu packages gcc)
66e40e00 57 #:use-module (gnu packages gd)
97b9da68 58 #:use-module (gnu packages gtk)
b16728b0 59 #:use-module (gnu packages glib)
db7a3444 60 #:use-module (gnu packages groff)
50937297 61 #:use-module (gnu packages guile)
89984be4 62 #:use-module (gnu packages haskell)
66e40e00 63 #:use-module (gnu packages image)
97b9da68 64 #:use-module (gnu packages imagemagick)
15a3c3d4 65 #:use-module (gnu packages java)
51c64999 66 #:use-module (gnu packages linux)
ec946638 67 #:use-module (gnu packages logging)
36742f43 68 #:use-module (gnu packages machine-learning)
db7a3444 69 #:use-module (gnu packages man)
c833ab55 70 #:use-module (gnu packages maths)
6c2b26e2 71 #:use-module (gnu packages mpi)
4e10a221 72 #:use-module (gnu packages ncurses)
81f3e0c1 73 #:use-module (gnu packages pcre)
ceb62d54 74 #:use-module (gnu packages parallel)
66e40e00 75 #:use-module (gnu packages pdf)
4e10a221
RW		 76 #:use-module (gnu packages perl)
77 #:use-module (gnu packages pkg-config)
bfe3c685 78 #:use-module (gnu packages popt)
e4e5a4d8 79 #:use-module (gnu packages protobuf)
346a829a 80 #:use-module (gnu packages python)
ec946638 81 #:use-module (gnu packages readline)
9c38b540 82 #:use-module (gnu packages ruby)
84be3b99 83 #:use-module (gnu packages serialization)
c833ab55 84 #:use-module (gnu packages statistics)
d7678942 85 #:use-module (gnu packages tbb)
97b9da68 86 #:use-module (gnu packages tex)
db7a3444 87 #:use-module (gnu packages texinfo)
2127cedb 88 #:use-module (gnu packages textutils)
43c565d2 89 #:use-module (gnu packages time)
a2950fa4 90 #:use-module (gnu packages tls)
ce7155d5 91 #:use-module (gnu packages vim)
365c8153 92 #:use-module (gnu packages web)
c833ab55 93 #:use-module (gnu packages xml)
66e40e00 94 #:use-module (gnu packages xorg)
f7283db3
RW		 95 #:use-module (gnu packages zip)
96 #:use-module (srfi srfi-1))
4e10a221 97
8dc797fa
BW		 98(define-public aragorn
99 (package
100 (name "aragorn")
e990c81d 101 (version "1.2.38")
8dc797fa
BW		 102 (source (origin
103 (method url-fetch)
104 (uri (string-append
105 "http://mbio-serv2.mbioekol.lu.se/ARAGORN/Downloads/aragorn"
106 version ".tgz"))
107 (sha256
108 (base32
e990c81d 109 "09i1rg716smlbnixfm7q1ml2mfpaa2fpn3hwjg625ysmfwwy712b"))))
8dc797fa
BW		 110 (build-system gnu-build-system)
111 (arguments
112 `(#:tests? #f ; there are no tests
113 #:phases
114 (modify-phases %standard-phases
115 (delete 'configure)
116 (replace 'build
117 (lambda _
118 (zero? (system* "gcc"
119 "-O3"
120 "-ffast-math"
121 "-finline-functions"
122 "-o"
123 "aragorn"
124 (string-append "aragorn" ,version ".c")))))
125 (replace 'install
126 (lambda* (#:key outputs #:allow-other-keys)
127 (let* ((out (assoc-ref outputs "out"))
128 (bin (string-append out "/bin"))
129 (man (string-append out "/share/man/man1")))
130 (mkdir-p bin)
131 (copy-file "aragorn"
132 (string-append bin "/aragorn"))
133 (mkdir-p man)
134 (copy-file "aragorn.1"
135 (string-append man "/aragorn.1")))
136 #t)))))
137 (home-page "http://mbio-serv2.mbioekol.lu.se/ARAGORN")
138 (synopsis "Detect tRNA, mtRNA and tmRNA genes in nucleotide sequences")
139 (description
140 "Aragorn identifies transfer RNA, mitochondrial RNA and
141transfer-messenger RNA from nucleotide sequences, based on homology to known
142tRNA consensus sequences and RNA structure. It also outputs the secondary
143structure of the predicted RNA.")
144 (license license:gpl2)))
145
a12ba6e8
BW		 146(define-public bamm
147 (package
148 (name "bamm")
4b6da268 149 (version "1.7.3")
a12ba6e8
BW		 150 (source (origin
151 (method url-fetch)
152 ;; BamM is not available on pypi.
153 (uri (string-append
4b6da268 154 "https://github.com/Ecogenomics/BamM/archive/"
a12ba6e8
BW		 155 version ".tar.gz"))
156 (file-name (string-append name "-" version ".tar.gz"))
157 (sha256
158 (base32
4b6da268 159 "1f35yxp4pc8aadsvbpg6r4kg2jh4fkjci0iby4iyljm6980sac0s"))
a12ba6e8
BW		 160 (modules '((guix build utils)))
161 (snippet
162 `(begin
163 ;; Delete bundled htslib.
164 (delete-file-recursively "c/htslib-1.3.1")
165 #t))))
166 (build-system python-build-system)
167 (arguments
168 `(#:python ,python-2 ; BamM is Python 2 only.
169 ;; Do not use bundled libhts. Do use the bundled libcfu because it has
170 ;; been modified from its original form.
171 #:configure-flags
172 (let ((htslib (assoc-ref %build-inputs "htslib")))
173 (list "--with-libhts-lib" (string-append htslib "/lib")
174 "--with-libhts-inc" (string-append htslib "/include/htslib")))
175 #:phases
176 (modify-phases %standard-phases
177 (add-after 'unpack 'autogen
178 (lambda _
179 (with-directory-excursion "c"
180 (let ((sh (which "sh")))
181 ;; Use autogen so that 'configure' works.
182 (substitute* "autogen.sh" (("/bin/sh") sh))
183 (setenv "CONFIG_SHELL" sh)
184 (substitute* "configure" (("/bin/sh") sh))
185 (zero? (system* "./autogen.sh"))))))
186 (delete 'build)
187 ;; Run tests after installation so compilation only happens once.
188 (delete 'check)
189 (add-after 'install 'wrap-executable
190 (lambda* (#:key outputs #:allow-other-keys)
191 (let* ((out (assoc-ref outputs "out"))
192 (path (getenv "PATH")))
193 (wrap-program (string-append out "/bin/bamm")
194 `("PATH" ":" prefix (,path))))
195 #t))
196 (add-after 'wrap-executable 'post-install-check
197 (lambda* (#:key inputs outputs #:allow-other-keys)
198 (setenv "PATH"
199 (string-append (assoc-ref outputs "out")
200 "/bin:"
201 (getenv "PATH")))
202 (setenv "PYTHONPATH"
203 (string-append
204 (assoc-ref outputs "out")
205 "/lib/python"
206 (string-take (string-take-right
207 (assoc-ref inputs "python") 5) 3)
208 "/site-packages:"
209 (getenv "PYTHONPATH")))
210 ;; There are 2 errors printed, but they are safe to ignore:
211 ;; 1) [E::hts_open_format] fail to open file ...
212 ;; 2) samtools view: failed to open ...
213 (zero? (system* "nosetests")))))))
214 (native-inputs
215 `(("autoconf" ,autoconf)
216 ("automake" ,automake)
217 ("libtool" ,libtool)
218 ("zlib" ,zlib)
219 ("python-nose" ,python2-nose)
f3b98f4f 220 ("python-pysam" ,python2-pysam)))
a12ba6e8
BW		 221 (inputs
222 `(("htslib" ,htslib)
223 ("samtools" ,samtools)
224 ("bwa" ,bwa)
225 ("grep" ,grep)
226 ("sed" ,sed)
227 ("coreutils" ,coreutils)))
228 (propagated-inputs
229 `(("python-numpy" ,python2-numpy)))
230 (home-page "http://ecogenomics.github.io/BamM/")
231 (synopsis "Metagenomics-focused BAM file manipulator")
232 (description
233 "BamM is a C library, wrapped in python, to efficiently generate and
234parse BAM files, specifically for the analysis of metagenomic data. For
235instance, it implements several methods to assess contig-wise read coverage.")
236 (license license:lgpl3+)))
237
9794180d
RW		 238(define-public bamtools
239 (package
240 (name "bamtools")
241 (version "2.3.0")
242 (source (origin
243 (method url-fetch)
244 (uri (string-append
245 "https://github.com/pezmaster31/bamtools/archive/v"
246 version ".tar.gz"))
247 (file-name (string-append name "-" version ".tar.gz"))
248 (sha256
249 (base32
250 "1brry29bw2xr2l9pqn240rkqwayg85b8qq78zk2zs6nlspk4d018"))))
251 (build-system cmake-build-system)
4702cec2
RW		 252 (arguments
253 `(#:tests? #f ;no "check" target
254 #:phases
255 (modify-phases %standard-phases
256 (add-before
257 'configure 'set-ldflags
258 (lambda* (#:key outputs #:allow-other-keys)
259 (setenv "LDFLAGS"
260 (string-append
261 "-Wl,-rpath="
262 (assoc-ref outputs "out") "/lib/bamtools")))))))
9794180d
RW		 263 (inputs `(("zlib" ,zlib)))
264 (home-page "https://github.com/pezmaster31/bamtools")
265 (synopsis "C++ API and command-line toolkit for working with BAM data")
266 (description
267 "BamTools provides both a C++ API and a command-line toolkit for handling
268BAM files.")
269 (license license:expat)))
270
bdc7be59
MB		 271(define-public bcftools
272 (package
273 (name "bcftools")
274 (version "1.3.1")
275 (source (origin
276 (method url-fetch)
277 (uri (string-append
278 "https://github.com/samtools/bcftools/releases/download/"
279 version "/bcftools-" version ".tar.bz2"))
280 (sha256
281 (base32
282 "095ry68vmz9q5s1scjsa698dhgyvgw5aicz24c19iwfbai07mhqj"))
283 (modules '((guix build utils)))
284 (snippet
285 ;; Delete bundled htslib.
286 '(delete-file-recursively "htslib-1.3.1"))))
287 (build-system gnu-build-system)
288 (arguments
289 `(#:test-target "test"
290 #:make-flags
291 (list
292 "USE_GPL=1"
293 (string-append "prefix=" (assoc-ref %outputs "out"))
294 (string-append "HTSDIR=" (assoc-ref %build-inputs "htslib") "/include")
295 (string-append "HTSLIB=" (assoc-ref %build-inputs "htslib") "/lib/libhts.a")
296 (string-append "BGZIP=" (assoc-ref %build-inputs "htslib") "/bin/bgzip")
297 (string-append "TABIX=" (assoc-ref %build-inputs "htslib") "/bin/tabix"))
298 #:phases
299 (modify-phases %standard-phases
300 (add-after 'unpack 'patch-Makefile
301 (lambda _
302 (substitute* "Makefile"
303 ;; Do not attempt to build htslib.
304 (("^include \\$\\(HTSDIR\\)/htslib\\.mk") "")
305 ;; Link against GSL cblas.
306 (("-lcblas") "-lgslcblas"))
307 #t))
308 (delete 'configure)
309 (add-before 'check 'patch-tests
310 (lambda _
311 (substitute* "test/test.pl"
312 (("/bin/bash") (which "bash")))
313 #t)))))
314 (native-inputs
315 `(("htslib" ,htslib)
316 ("perl" ,perl)))
317 (inputs
318 `(("gsl" ,gsl)
319 ("zlib" ,zlib)))
320 (home-page "https://samtools.github.io/bcftools/")
321 (synopsis "Utilities for variant calling and manipulating VCFs and BCFs")
322 (description
323 "BCFtools is a set of utilities that manipulate variant calls in the
324Variant Call Format (VCF) and its binary counterpart BCF. All commands work
325transparently with both VCFs and BCFs, both uncompressed and BGZF-compressed.")
326 ;; The sources are dual MIT/GPL, but becomes GPL-only when USE_GPL=1.
327 (license (list license:gpl3+ license:expat))))
328
8dd4ff11
RW		 329(define-public bedops
330 (package
331 (name "bedops")
1bbc3b1d 332 (version "2.4.14")
8dd4ff11
RW		 333 (source (origin
334 (method url-fetch)
335 (uri (string-append "https://github.com/bedops/bedops/archive/v"
336 version ".tar.gz"))
f586c877 337 (file-name (string-append name "-" version ".tar.gz"))
8dd4ff11
RW		 338 (sha256
339 (base32
1bbc3b1d 340 "1kqbac547wyqma81cyky9n7mkgikjpsfd3nnmcm6hpqwanqgh10v"))))
8dd4ff11
RW		 341 (build-system gnu-build-system)
342 (arguments
343 '(#:tests? #f
344 #:make-flags (list (string-append "BINDIR=" %output "/bin"))
345 #:phases
346 (alist-cons-after
347 'unpack 'unpack-tarballs
348 (lambda _
349 ;; FIXME: Bedops includes tarballs of minimally patched upstream
350 ;; libraries jansson, zlib, and bzip2. We cannot just use stock
351 ;; libraries because at least one of the libraries (zlib) is
352 ;; patched to add a C++ function definition (deflateInit2cpp).
353 ;; Until the Bedops developers offer a way to link against system
354 ;; libraries we have to build the in-tree copies of these three
355 ;; libraries.
356
357 ;; See upstream discussion:
358 ;; https://github.com/bedops/bedops/issues/124
359
360 ;; Unpack the tarballs to benefit from shebang patching.
361 (with-directory-excursion "third-party"
362 (and (zero? (system* "tar" "xvf" "jansson-2.6.tar.bz2"))
363 (zero? (system* "tar" "xvf" "zlib-1.2.7.tar.bz2"))
364 (zero? (system* "tar" "xvf" "bzip2-1.0.6.tar.bz2"))))
365 ;; Disable unpacking of tarballs in Makefile.
366 (substitute* "system.mk/Makefile.linux"
367 (("^\tbzcat .*") "\t@echo \"not unpacking\"\n")
368 (("\\./configure") "CONFIG_SHELL=bash ./configure"))
369 (substitute* "third-party/zlib-1.2.7/Makefile.in"
370 (("^SHELL=.*$") "SHELL=bash\n")))
371 (alist-delete 'configure %standard-phases))))
372 (home-page "https://github.com/bedops/bedops")
373 (synopsis "Tools for high-performance genomic feature operations")
374 (description
375 "BEDOPS is a suite of tools to address common questions raised in genomic
376studies---mostly with regard to overlap and proximity relationships between
377data sets. It aims to be scalable and flexible, facilitating the efficient
378and accurate analysis and management of large-scale genomic data.
379
380BEDOPS provides tools that perform highly efficient and scalable Boolean and
381other set operations, statistical calculations, archiving, conversion and
382other management of genomic data of arbitrary scale. Tasks can be easily
383split by chromosome for distributing whole-genome analyses across a
384computational cluster.")
385 (license license:gpl2+)))
386
81de5647
RW		 387(define-public bedtools
388 (package
389 (name "bedtools")
d285657e 390 (version "2.26.0")
81de5647
RW		 391 (source (origin
392 (method url-fetch)
393 (uri (string-append "https://github.com/arq5x/bedtools2/archive/v"
394 version ".tar.gz"))
f586c877 395 (file-name (string-append name "-" version ".tar.gz"))
81de5647
RW		 396 (sha256
397 (base32
d285657e 398 "0xvri5hnp2iim1cx6mcd5d9f102p5ql41x69rd6106x1c17pinqm"))))
81de5647
RW		 399 (build-system gnu-build-system)
400 (native-inputs `(("python" ,python-2)))
401 (inputs `(("samtools" ,samtools)
402 ("zlib" ,zlib)))
403 (arguments
404 '(#:test-target "test"
405 #:phases
6573ac82 406 (modify-phases %standard-phases
6573ac82
BW		 407 (delete 'configure)
408 (replace 'install
409 (lambda* (#:key outputs #:allow-other-keys)
410 (let ((bin (string-append (assoc-ref outputs "out") "/bin/")))
411 (for-each (lambda (file)
412 (install-file file bin))
413 (find-files "bin" ".*")))
414 #t)))))
81de5647
RW		 415 (home-page "https://github.com/arq5x/bedtools2")
416 (synopsis "Tools for genome analysis and arithmetic")
417 (description
418 "Collectively, the bedtools utilities are a swiss-army knife of tools for
419a wide-range of genomics analysis tasks. The most widely-used tools enable
420genome arithmetic: that is, set theory on the genome. For example, bedtools
421allows one to intersect, merge, count, complement, and shuffle genomic
422intervals from multiple files in widely-used genomic file formats such as BAM,
423BED, GFF/GTF, VCF.")
424 (license license:gpl2)))
425
9a8f309c
RW		 426;; Later releases of bedtools produce files with more columns than
427;; what Ribotaper expects.
428(define-public bedtools-2.18
429 (package (inherit bedtools)
430 (name "bedtools")
431 (version "2.18.0")
432 (source (origin
433 (method url-fetch)
434 (uri (string-append "https://github.com/arq5x/bedtools2/"
435 "archive/v" version ".tar.gz"))
436 (file-name (string-append name "-" version ".tar.gz"))
437 (sha256
438 (base32
439 "05vrnr8yp7swfagshzpgqmzk1blnwnq8pq5pckzi1m26w98d63vf"))))))
440
17dc32a4
RW		 441(define-public ribotaper
442 (package
443 (name "ribotaper")
444 (version "1.3.1")
445 (source (origin
446 (method url-fetch)
447 (uri (string-append "https://ohlerlab.mdc-berlin.de/"
448 "files/RiboTaper/RiboTaper_Version_"
449 version ".tar.gz"))
450 (sha256
451 (base32
452 "0ykjbps1y3z3085q94npw8i9x5gldc6shy8vlc08v76zljsm07hv"))))
453 (build-system gnu-build-system)
454 (inputs
455 `(("bedtools" ,bedtools-2.18)
456 ("samtools" ,samtools-0.1)
457 ("r" ,r)
458 ("r-foreach" ,r-foreach)
459 ("r-xnomial" ,r-xnomial)
460 ("r-domc" ,r-domc)
461 ("r-multitaper" ,r-multitaper)
462 ("r-seqinr" ,r-seqinr)))
463 (home-page "https://ohlerlab.mdc-berlin.de/software/RiboTaper_126/")
464 (synopsis "Define translated ORFs using ribosome profiling data")
465 (description
466 "Ribotaper is a method for defining translated @dfn{open reading
467frames} (ORFs) using ribosome profiling (ribo-seq) data. This package
468provides the Ribotaper pipeline.")
469 (license license:gpl3+)))
470
769fc6bb
RW		 471(define-public ribodiff
472 (package
473 (name "ribodiff")
474 (version "0.2.2")
475 (source
476 (origin
477 (method url-fetch)
478 (uri (string-append "https://github.com/ratschlab/RiboDiff/"
479 "archive/v" version ".tar.gz"))
480 (file-name (string-append name "-" version ".tar.gz"))
481 (sha256
482 (base32
483 "0wpbwmfv05wdjxv7ikm664f7s7p7cqr8jnw99zrda0q67rl50aaj"))))
484 (build-system python-build-system)
485 (arguments
486 `(#:python ,python-2
487 #:phases
488 (modify-phases %standard-phases
489 ;; Generate an installable executable script wrapper.
490 (add-after 'unpack 'patch-setup.py
491 (lambda _
492 (substitute* "setup.py"
493 (("^(.*)packages=.*" line prefix)
494 (string-append line "\n"
495 prefix "scripts=['scripts/TE.py'],\n")))
496 #t)))))
497 (inputs
498 `(("python-numpy" ,python2-numpy)
499 ("python-matplotlib" ,python2-matplotlib)
500 ("python-scipy" ,python2-scipy)
501 ("python-statsmodels" ,python2-statsmodels)))
502 (home-page "http://public.bmi.inf.ethz.ch/user/zhongy/RiboDiff/")
503 (synopsis "Detect translation efficiency changes from ribosome footprints")
504 (description "RiboDiff is a statistical tool that detects the protein
505translational efficiency change from Ribo-Seq (ribosome footprinting) and
506RNA-Seq data. It uses a generalized linear model to detect genes showing
507difference in translational profile taking mRNA abundance into account. It
508facilitates us to decipher the translational regulation that behave
509independently with transcriptional regulation.")
510 (license license:gpl3+)))
511
a0a71439
RJ		 512(define-public bioawk
513 (package
514 (name "bioawk")
515 (version "1.0")
516 (source (origin
517 (method url-fetch)
518 (uri (string-append "https://github.com/lh3/bioawk/archive/v"
519 version ".tar.gz"))
520 (file-name (string-append name "-" version ".tar.gz"))
521 (sha256
522 (base32 "1daizxsk17ahi9n58fj8vpgwyhzrzh54bzqhanjanp88kgrz7gjw"))))
523 (build-system gnu-build-system)
524 (inputs
525 `(("zlib" ,zlib)))
526 (native-inputs
527 `(("bison" ,bison)))
528 (arguments
529 `(#:tests? #f ; There are no tests to run.
530 ;; Bison must generate files, before other targets can build.
531 #:parallel-build? #f
532 #:phases
533 (modify-phases %standard-phases
534 (delete 'configure) ; There is no configure phase.
535 (replace 'install
536 (lambda* (#:key outputs #:allow-other-keys)
537 (let* ((out (assoc-ref outputs "out"))
538 (bin (string-append out "/bin"))
539 (man (string-append out "/share/man/man1")))
540 (mkdir-p man)
541 (copy-file "awk.1" (string-append man "/bioawk.1"))
542 (install-file "bioawk" bin)))))))
543 (home-page "https://github.com/lh3/bioawk")
544 (synopsis "AWK with bioinformatics extensions")
545 (description "Bioawk is an extension to Brian Kernighan's awk, adding the
546support of several common biological data formats, including optionally gzip'ed
547BED, GFF, SAM, VCF, FASTA/Q and TAB-delimited formats with column names. It
548also adds a few built-in functions and a command line option to use TAB as the
549input/output delimiter. When the new functionality is not used, bioawk is
550intended to behave exactly the same as the original BWK awk.")
551 (license license:x11)))
552
a2fb1492
RW		 553(define-public python2-pybedtools
554 (package
555 (name "python2-pybedtools")
556 (version "0.6.9")
557 (source (origin
558 (method url-fetch)
559 (uri (string-append
560 "https://pypi.python.org/packages/source/p/pybedtools/pybedtools-"
561 version ".tar.gz"))
562 (sha256
563 (base32
564 "1ldzdxw1p4y3g2ignmggsdypvqkcwqwzhdha4rbgpih048z5p4an"))))
565 (build-system python-build-system)
566 (arguments `(#:python ,python-2)) ; no Python 3 support
567 (inputs
f2516de2 568 `(("python-matplotlib" ,python2-matplotlib)))
a2fb1492
RW		 569 (propagated-inputs
570 `(("bedtools" ,bedtools)
571 ("samtools" ,samtools)))
572 (native-inputs
f2516de2
HG		 573 `(("python-cython" ,python2-cython)
574 ("python-pyyaml" ,python2-pyyaml)
f3b98f4f 575 ("python-nose" ,python2-nose)))
a2fb1492
RW		 576 (home-page "https://pythonhosted.org/pybedtools/")
577 (synopsis "Python wrapper for BEDtools programs")
578 (description
579 "pybedtools is a Python wrapper for Aaron Quinlan's BEDtools programs,
580which are widely used for genomic interval manipulation or \"genome algebra\".
581pybedtools extends BEDTools by offering feature-level manipulations from with
582Python.")
583 (license license:gpl2+)))
584
9e12eba8
BW		 585(define-public python-biom-format
586 (package
587 (name "python-biom-format")
588 (version "2.1.5")
589 (source
590 (origin
591 (method url-fetch)
592 ;; Use GitHub as source because PyPI distribution does not contain
593 ;; test data: https://github.com/biocore/biom-format/issues/693
594 (uri (string-append "https://github.com/biocore/biom-format/archive/"
595 version ".tar.gz"))
596 (file-name (string-append name "-" version ".tar.gz"))
597 (sha256
598 (base32
599 "1n25w3p1rixbpac8iysmzcja6m4ip5r6sz19l8y6wlwi49hxn278"))))
600 (build-system python-build-system)
de96ea28 601 (propagated-inputs
9e12eba8
BW		 602 `(("python-numpy" ,python-numpy)
603 ("python-scipy" ,python-scipy)
604 ("python-future" ,python-future)
605 ("python-click" ,python-click)
606 ("python-h5py" ,python-h5py)))
607 (home-page "http://www.biom-format.org")
608 (synopsis "Biological Observation Matrix (BIOM) format utilities")
609 (description
610 "The BIOM file format is designed to be a general-use format for
611representing counts of observations e.g. operational taxonomic units, KEGG
612orthology groups or lipid types, in one or more biological samples
613e.g. microbiome samples, genomes, metagenomes.")
614 (license license:bsd-3)
615 (properties `((python2-variant . ,(delay python2-biom-format))))))
616
617(define-public python2-biom-format
618 (let ((base (package-with-python2 (strip-python2-variant python-biom-format))))
619 (package
620 (inherit base)
621 (arguments
622 `(#:phases
623 (modify-phases %standard-phases
624 ;; Do not require the unmaintained pyqi library.
625 (add-after 'unpack 'remove-pyqi
626 (lambda _
627 (substitute* "setup.py"
628 (("install_requires.append\\(\"pyqi\"\\)") "pass"))
629 #t)))
00e10c6e 630 ,@(package-arguments base))))))
9e12eba8 631
f7283db3
RW		 632(define-public bioperl-minimal
633 (let* ((inputs `(("perl-module-build" ,perl-module-build)
634 ("perl-data-stag" ,perl-data-stag)
635 ("perl-libwww" ,perl-libwww)
636 ("perl-uri" ,perl-uri)))
637 (transitive-inputs
638 (map (compose package-name cadr)
639 (delete-duplicates
640 (concatenate
641 (map (compose package-transitive-target-inputs cadr) inputs))))))
642 (package
643 (name "bioperl-minimal")
c70271ec 644 (version "1.7.0")
f7283db3
RW		 645 (source
646 (origin
647 (method url-fetch)
c70271ec
RW		 648 (uri (string-append "https://github.com/bioperl/bioperl-live/"
649 "archive/release-"
650 (string-map (lambda (c)
651 (if (char=? c #\.)
652 #\- c)) version)
653 ".tar.gz"))
f7283db3
RW		 654 (sha256
655 (base32
c70271ec 656 "12phgpxwgkqflkwfb9dcqg7a31dpjlfhar8wcgv0aj5ln4akfz06"))))
f7283db3
RW		 657 (build-system perl-build-system)
658 (arguments
659 `(#:phases
660 (modify-phases %standard-phases
661 (add-after
662 'install 'wrap-programs
663 (lambda* (#:key outputs #:allow-other-keys)
664 ;; Make sure all executables in "bin" find the required Perl
665 ;; modules at runtime. As the PERL5LIB variable contains also
666 ;; the paths of native inputs, we pick the transitive target
667 ;; inputs from %build-inputs.
668 (let* ((out (assoc-ref outputs "out"))
669 (bin (string-append out "/bin/"))
670 (path (string-join
671 (cons (string-append out "/lib/perl5/site_perl")
672 (map (lambda (name)
673 (assoc-ref %build-inputs name))
674 ',transitive-inputs))
675 ":")))
676 (for-each (lambda (file)
677 (wrap-program file
678 `("PERL5LIB" ":" prefix (,path))))
679 (find-files bin "\\.pl$"))
680 #t))))))
681 (inputs inputs)
682 (native-inputs
683 `(("perl-test-most" ,perl-test-most)))
684 (home-page "http://search.cpan.org/dist/BioPerl")
685 (synopsis "Bioinformatics toolkit")
686 (description
687 "BioPerl is the product of a community effort to produce Perl code which
688is useful in biology. Examples include Sequence objects, Alignment objects
689and database searching objects. These objects not only do what they are
690advertised to do in the documentation, but they also interact - Alignment
691objects are made from the Sequence objects, Sequence objects have access to
692Annotation and SeqFeature objects and databases, Blast objects can be
693converted to Alignment objects, and so on. This means that the objects
694provide a coordinated and extensible framework to do computational biology.")
695 (license (package-license perl)))))
696
85c37e29
RW		 697(define-public python-biopython
698 (package
699 (name "python-biopython")
4ce60305 700 (version "1.68")
85c37e29
RW		 701 (source (origin
702 (method url-fetch)
e815c094
BW		 703 ;; use PyPi rather than biopython.org to ease updating
704 (uri (pypi-uri "biopython" version))
85c37e29
RW		 705 (sha256
706 (base32
4ce60305 707 "07qc7nz0k77y8hf8s18rscvibvm91zw0kkq7ylrhisf8vp8hkp6i"))))
85c37e29 708 (build-system python-build-system)
4ce60305
BW		 709 (arguments
710 `(#:phases
711 (modify-phases %standard-phases
712 (add-before 'check 'set-home
713 ;; Some tests require a home directory to be set.
714 (lambda _ (setenv "HOME" "/tmp") #t)))))
f22efa01 715 (propagated-inputs
85c37e29 716 `(("python-numpy" ,python-numpy)))
85c37e29
RW		 717 (home-page "http://biopython.org/")
718 (synopsis "Tools for biological computation in Python")
719 (description
720 "Biopython is a set of tools for biological computation including parsers
721for bioinformatics files into Python data structures; interfaces to common
722bioinformatics programs; a standard sequence class and tools for performing
723common operations on them; code to perform data classification; code for
724dealing with alignments; code making it easy to split up parallelizable tasks
725into separate processes; and more.")
5c31f4aa 726 (license (license:non-copyleft "http://www.biopython.org/DIST/LICENSE"))))
85c37e29
RW		 727
728(define-public python2-biopython
5c31f4aa 729 (package-with-python2 python-biopython))
85c37e29 730
4b1a1528
BW		 731;; An outdated version of biopython is required for seqmagick, see
732;; https://github.com/fhcrc/seqmagick/issues/59
733;; When that issue has been resolved this package should be removed.
734(define python2-biopython-1.66
735 (package
736 (inherit python2-biopython)
737 (version "1.66")
738 (source (origin
739 (method url-fetch)
740 (uri (pypi-uri "biopython" version))
741 (sha256
742 (base32
743 "1gdv92593klimg22icf5j9by7xiq86jnwzkpz4abaa05ylkdf6hp"))))))
744
985d8411
BW		 745(define-public bpp-core
746 ;; The last release was in 2014 and the recommended way to install from source
747 ;; is to clone the git repository, so we do this.
748 ;; http://biopp.univ-montp2.fr/wiki/index.php/Main_Page
749 (let ((commit "7d8bced0d1a87291ea8dd7046b7fb5ff9c35c582"))
750 (package
751 (name "bpp-core")
752 (version (string-append "2.2.0-1." (string-take commit 7)))
753 (source (origin
754 (method git-fetch)
755 (uri (git-reference
756 (url "http://biopp.univ-montp2.fr/git/bpp-core")
757 (commit commit)))
758 (file-name (string-append name "-" version "-checkout"))
759 (sha256
760 (base32
761 "10djsq5vlnkilv436gnmh4irpk49v29pa69r6xiryg32xmvn909j"))))
762 (build-system cmake-build-system)
763 (arguments
764 `(#:parallel-build? #f))
765 (inputs
766 `(("gcc" ,gcc-5))) ; Compilation of bpp-phyl fails with GCC 4.9 so we
767 ; compile all of the bpp packages with GCC 5.
768 (home-page "http://biopp.univ-montp2.fr")
769 (synopsis "C++ libraries for Bioinformatics")
770 (description
771 "Bio++ is a set of C++ libraries for Bioinformatics, including sequence
772analysis, phylogenetics, molecular evolution and population genetics. It is
773Object Oriented and is designed to be both easy to use and computer efficient.
774Bio++ intends to help programmers to write computer expensive programs, by
775providing them a set of re-usable tools.")
776 (license license:cecill-c))))
777
8b5f4d57
BW		 778(define-public bpp-phyl
779 ;; The last release was in 2014 and the recommended way to install from source
780 ;; is to clone the git repository, so we do this.
781 ;; http://biopp.univ-montp2.fr/wiki/index.php/Main_Page
782 (let ((commit "0c07167b629f68b569bf274d1ad0c4af83276ae2"))
783 (package
784 (name "bpp-phyl")
785 (version (string-append "2.2.0-1." (string-take commit 7)))
786 (source (origin
787 (method git-fetch)
788 (uri (git-reference
789 (url "http://biopp.univ-montp2.fr/git/bpp-phyl")
790 (commit commit)))
791 (file-name (string-append name "-" version "-checkout"))
792 (sha256
793 (base32
794 "1ssjgchzwj3iai26kyly7gwkdv8sk59nqhkb1wpap3sf5m6kyllh"))))
795 (build-system cmake-build-system)
796 (arguments
797 `(#:parallel-build? #f
798 ;; If out-of-source, test data is not copied into the build directory
799 ;; so the tests fail.
800 #:out-of-source? #f))
801 (inputs
802 `(("bpp-core" ,bpp-core)
803 ("bpp-seq" ,bpp-seq)
804 ;; GCC 4.8 fails due to an 'internal compiler error', so we use a more
805 ;; modern GCC.
806 ("gcc" ,gcc-5)))
807 (home-page "http://biopp.univ-montp2.fr")
808 (synopsis "Bio++ phylogenetic Library")
809 (description
810 "Bio++ is a set of C++ libraries for Bioinformatics, including sequence
811analysis, phylogenetics, molecular evolution and population genetics. This
812library provides phylogenetics-related modules.")
813 (license license:cecill-c))))
814
159a7016
BW		 815(define-public bpp-popgen
816 ;; The last release was in 2014 and the recommended way to install from source
817 ;; is to clone the git repository, so we do this.
818 ;; http://biopp.univ-montp2.fr/wiki/index.php/Main_Page
819 (let ((commit "e472bac9b1a148803895d747cd6d0c5904f85d9f"))
820 (package
821 (name "bpp-popgen")
822 (version (string-append "2.2.0-1." (string-take commit 7)))
823 (source (origin
824 (method git-fetch)
825 (uri (git-reference
826 (url "http://biopp.univ-montp2.fr/git/bpp-popgen")
827 (commit commit)))
828 (file-name (string-append name "-" version "-checkout"))
829 (sha256
830 (base32
831 "0yn82dzn1n5629nzja68xfrhi655709rjanyryb36vzkmymy6dw5"))))
832 (build-system cmake-build-system)
833 (arguments
834 `(#:parallel-build? #f
835 #:tests? #f)) ; There are no tests.
836 (inputs
837 `(("bpp-core" ,bpp-core)
838 ("bpp-seq" ,bpp-seq)
839 ("gcc" ,gcc-5)))
840 (home-page "http://biopp.univ-montp2.fr")
841 (synopsis "Bio++ population genetics library")
842 (description
843 "Bio++ is a set of C++ libraries for Bioinformatics, including sequence
844analysis, phylogenetics, molecular evolution and population genetics. This
845library provides population genetics-related modules.")
846 (license license:cecill-c))))
847
70f1bc05
BW		 848(define-public bpp-seq
849 ;; The last release was in 2014 and the recommended way to install from source
850 ;; is to clone the git repository, so we do this.
851 ;; http://biopp.univ-montp2.fr/wiki/index.php/Main_Page
852 (let ((commit "6cfa07965ce152e5598a89df2fa80a75973bfa33"))
853 (package
854 (name "bpp-seq")
855 (version (string-append "2.2.0-1." (string-take commit 7)))
856 (source (origin
857 (method git-fetch)
858 (uri (git-reference
859 (url "http://biopp.univ-montp2.fr/git/bpp-seq")
860 (commit commit)))
861 (file-name (string-append name "-" version "-checkout"))
862 (sha256
863 (base32
864 "1nys5jq7jqvdg40d91wsmj3q2yzy4276cp7sp44n67p468f27zf2"))))
865 (build-system cmake-build-system)
866 (arguments
867 `(#:parallel-build? #f
868 ;; If out-of-source, test data is not copied into the build directory
869 ;; so the tests fail.
870 #:out-of-source? #f))
871 (inputs
872 `(("bpp-core" ,bpp-core)
873 ("gcc" ,gcc-5))) ; Use GCC 5 as per 'bpp-core'.
874 (home-page "http://biopp.univ-montp2.fr")
875 (synopsis "Bio++ sequence library")
876 (description
877 "Bio++ is a set of C++ libraries for Bioinformatics, including sequence
878analysis, phylogenetics, molecular evolution and population genetics. This
879library provides sequence-related modules.")
880 (license license:cecill-c))))
881
db7a3444
BW		 882(define-public bppsuite
883 ;; The last release was in 2014 and the recommended way to install from source
884 ;; is to clone the git repository, so we do this.
885 ;; http://biopp.univ-montp2.fr/wiki/index.php/Main_Page
886 (let ((commit "c516147f57aa50961121cd505bed52cd7603698b"))
887 (package
888 (name "bppsuite")
889 (version (string-append "2.2.0-1." (string-take commit 7)))
890 (source (origin
891 (method git-fetch)
892 (uri (git-reference
893 (url "http://biopp.univ-montp2.fr/git/bppsuite")
894 (commit commit)))
895 (file-name (string-append name "-" version "-checkout"))
896 (sha256
897 (base32
898 "1y87pxvw0jxjizhq2dr9g2r91md45k1p9ih2sl1yy1y3p934l2kb"))))
899 (build-system cmake-build-system)
900 (arguments
901 `(#:parallel-build? #f
902 #:tests? #f)) ; There are no tests.
903 (native-inputs
904 `(("groff" ,groff)
905 ("man-db" ,man-db)
906 ("texinfo" ,texinfo)))
907 (inputs
908 `(("bpp-core" ,bpp-core)
909 ("bpp-seq" ,bpp-seq)
910 ("bpp-phyl" ,bpp-phyl)
911 ("bpp-phyl" ,bpp-popgen)
912 ("gcc" ,gcc-5)))
913 (home-page "http://biopp.univ-montp2.fr")
914 (synopsis "Bioinformatics tools written with the Bio++ libraries")
915 (description
916 "Bio++ is a set of C++ libraries for Bioinformatics, including sequence
917analysis, phylogenetics, molecular evolution and population genetics. This
918package provides command line tools using the Bio++ library.")
919 (license license:cecill-c))))
920
82c370de
RW		 921(define-public blast+
922 (package
923 (name "blast+")
8dec2229 924 (version "2.4.0")
82c370de
RW		 925 (source (origin
926 (method url-fetch)
927 (uri (string-append
928 "ftp://ftp.ncbi.nlm.nih.gov/blast/executables/blast+/"
929 version "/ncbi-blast-" version "+-src.tar.gz"))
930 (sha256
931 (base32
8dec2229 932 "14n9jik6vhiwjd3m7bach4xj1pzfn0szbsbyfxybd9l9cc43b6mb"))
82c370de
RW		 933 (modules '((guix build utils)))
934 (snippet
935 '(begin
936 ;; Remove bundled bzip2 and zlib
937 (delete-file-recursively "c++/src/util/compress/bzip2")
938 (delete-file-recursively "c++/src/util/compress/zlib")
939 (substitute* "c++/src/util/compress/Makefile.in"
940 (("bzip2 zlib api") "api"))
941 ;; Remove useless msbuild directory
942 (delete-file-recursively
943 "c++/src/build-system/project_tree_builder/msbuild")
944 #t))))
945 (build-system gnu-build-system)
946 (arguments
947 `(;; There are three(!) tests for this massive library, and all fail with
948 ;; "unparsable timing stats".
949 ;; ERR [127] -- [util/regexp] test_pcre.sh (unparsable timing stats)
950 ;; ERR [127] -- [serial/datatool] datatool.sh (unparsable timing stats)
951 ;; ERR [127] -- [serial/datatool] datatool_xml.sh (unparsable timing stats)
952 #:tests? #f
953 #:out-of-source? #t
954 #:parallel-build? #f ; not supported
955 #:phases
956 (modify-phases %standard-phases
957 (add-before
958 'configure 'set-HOME
959 ;; $HOME needs to be set at some point during the configure phase
960 (lambda _ (setenv "HOME" "/tmp") #t))
961 (add-after
962 'unpack 'enter-dir
963 (lambda _ (chdir "c++") #t))
964 (add-after
965 'enter-dir 'fix-build-system
966 (lambda _
967 (define (which* cmd)
968 (cond ((string=? cmd "date")
969 ;; make call to "date" deterministic
970 "date -d @0")
971 ((which cmd)
972 => identity)
973 (else
974 (format (current-error-port)
975 "WARNING: Unable to find absolute path for ~s~%"
976 cmd)
977 #f)))
978
979 ;; Rewrite hardcoded paths to various tools
980 (substitute* (append '("src/build-system/configure.ac"
981 "src/build-system/configure"
982 "scripts/common/impl/if_diff.sh"
983 "scripts/common/impl/run_with_lock.sh"
984 "src/build-system/Makefile.configurables.real"
985 "src/build-system/Makefile.in.top"
986 "src/build-system/Makefile.meta.gmake=no"
987 "src/build-system/Makefile.meta.in"
988 "src/build-system/Makefile.meta_l"
989 "src/build-system/Makefile.meta_p"
990 "src/build-system/Makefile.meta_r"
991 "src/build-system/Makefile.mk.in"
992 "src/build-system/Makefile.requirements"
993 "src/build-system/Makefile.rules_with_autodep.in")
994 (find-files "scripts/common/check" "\\.sh$"))
995 (("(/usr/bin/|/bin/)([a-z][-_.a-z]*)" all dir cmd)
996 (or (which* cmd) all)))
997
998 (substitute* (find-files "src/build-system" "^config.*")
999 (("LN_S=/bin/\\$LN_S") (string-append "LN_S=" (which "ln")))
1000 (("^PATH=.*") ""))
1001
1002 ;; rewrite "/var/tmp" in check script
1003 (substitute* "scripts/common/check/check_make_unix.sh"
1004 (("/var/tmp") "/tmp"))
1005
1006 ;; do not reset PATH
1007 (substitute* (find-files "scripts/common/impl/" "\\.sh$")
1008 (("^ *PATH=.*") "")
1009 (("action=/bin/") "action=")
1010 (("export PATH") ":"))
1011 #t))
1012 (replace
1013 'configure
1014 (lambda* (#:key inputs outputs #:allow-other-keys)
1015 (let ((out (assoc-ref outputs "out"))
1016 (lib (string-append (assoc-ref outputs "lib") "/lib"))
1017 (include (string-append (assoc-ref outputs "include")
1018 "/include/ncbi-tools++")))
1019 ;; The 'configure' script doesn't recognize things like
1020 ;; '--enable-fast-install'.
1021 (zero? (system* "./configure.orig"
1022 (string-append "--with-build-root=" (getcwd) "/build")
1023 (string-append "--prefix=" out)
1024 (string-append "--libdir=" lib)
1025 (string-append "--includedir=" include)
1026 (string-append "--with-bz2="
1027 (assoc-ref inputs "bzip2"))
1028 (string-append "--with-z="
1029 (assoc-ref inputs "zlib"))
1030 ;; Each library is built twice by default, once
1031 ;; with "-static" in its name, and again
1032 ;; without.
1033 "--without-static"
1034 "--with-dll"))))))))
1035 (outputs '("out" ; 19 MB
1036 "lib" ; 203 MB
1037 "include")) ; 32 MB
1038 (inputs
1039 `(("bzip2" ,bzip2)
1040 ("zlib" ,zlib)))
1041 (native-inputs
1042 `(("cpio" ,cpio)))
1043 (home-page "http://blast.ncbi.nlm.nih.gov")
1044 (synopsis "Basic local alignment search tool")
1045 (description
1046 "BLAST is a popular method of performing a DNA or protein sequence
1047similarity search, using heuristics to produce results quickly. It also
1048calculates an “expect value” that estimates how many matches would have
1049occurred at a given score by chance, which can aid a user in judging how much
1050confidence to have in an alignment.")
1051 ;; Most of the sources are in the public domain, with the following
1052 ;; exceptions:
1053 ;; * Expat:
1054 ;; * ./c++/include/util/bitset/
1055 ;; * ./c++/src/html/ncbi_menu*.js
1056 ;; * Boost license:
1057 ;; * ./c++/include/util/impl/floating_point_comparison.hpp
1058 ;; * LGPL 2+:
1059 ;; * ./c++/include/dbapi/driver/odbc/unix_odbc/
1060 ;; * ASL 2.0:
1061 ;; * ./c++/src/corelib/teamcity_*
1062 (license (list license:public-domain
1063 license:expat
1064 license:boost1.0
1065 license:lgpl2.0+
1066 license:asl2.0))))
1067
6c2b26e2
RW		 1068(define-public bless
1069 (package
1070 (name "bless")
1071 (version "1p02")
1072 (source (origin
1073 (method url-fetch)
1074 (uri (string-append "mirror://sourceforge/bless-ec/bless.v"
1075 version ".tgz"))
1076 (sha256
1077 (base32
4d75e03a
RW		 1078 "0rm0gw2s18dqwzzpl3c2x1z05ni2v0xz5dmfk3d33j6g4cgrlrdd"))
1079 (modules '((guix build utils)))
6c2b26e2
RW		 1080 (snippet
1081 `(begin
1082 ;; Remove bundled boost, pigz, zlib, and .git directory
953c1223
RW		 1083 ;; FIXME: also remove bundled sources for murmurhash3 and
1084 ;; kmc once packaged.
6c2b26e2
RW		 1085 (delete-file-recursively "boost")
1086 (delete-file-recursively "pigz")
953c1223 1087 (delete-file-recursively "google-sparsehash")
6c2b26e2
RW		 1088 (delete-file-recursively "zlib")
1089 (delete-file-recursively ".git")
1090 #t))))
1091 (build-system gnu-build-system)
1092 (arguments
1093 '(#:tests? #f ;no "check" target
1094 #:make-flags
1095 (list (string-append "ZLIB="
1096 (assoc-ref %build-inputs "zlib")
1097 "/lib/libz.a")
1098 (string-append "LDFLAGS="
1099 (string-join '("-lboost_filesystem"
1100 "-lboost_system"
1101 "-lboost_iostreams"
1102 "-lz"
1103 "-fopenmp"
1104 "-std=c++11"))))
1105 #:phases
1106 (modify-phases %standard-phases
1107 (add-after 'unpack 'do-not-build-bundled-pigz
1108 (lambda* (#:key inputs outputs #:allow-other-keys)
1109 (substitute* "Makefile"
1110 (("cd pigz/pigz-2.3.3; make") ""))
1111 #t))
1112 (add-after 'unpack 'patch-paths-to-executables
1113 (lambda* (#:key inputs outputs #:allow-other-keys)
1114 (substitute* "parse_args.cpp"
1115 (("kmc_binary = .*")
1116 (string-append "kmc_binary = \""
1117 (assoc-ref outputs "out")
1118 "/bin/kmc\";"))
1119 (("pigz_binary = .*")
1120 (string-append "pigz_binary = \""
1121 (assoc-ref inputs "pigz")
1122 "/bin/pigz\";")))
1123 #t))
1124 (replace 'install
1125 (lambda* (#:key outputs #:allow-other-keys)
1126 (let ((bin (string-append (assoc-ref outputs "out") "/bin/")))
1127 (for-each (lambda (file)
1128 (install-file file bin))
1129 '("bless" "kmc/bin/kmc"))
1130 #t)))
1131 (delete 'configure))))
1132 (native-inputs
1133 `(("perl" ,perl)))
1134 (inputs
1135 `(("openmpi" ,openmpi)
1136 ("boost" ,boost)
953c1223 1137 ("sparsehash" ,sparsehash)
6c2b26e2
RW		 1138 ("pigz" ,pigz)
1139 ("zlib" ,zlib)))
9641a899 1140 (supported-systems '("x86_64-linux"))
3b3b60d0 1141 (home-page "https://sourceforge.net/p/bless-ec/wiki/Home/")
6c2b26e2
RW		 1142 (synopsis "Bloom-filter-based error correction tool for NGS reads")
1143 (description
1144 "@dfn{Bloom-filter-based error correction solution for high-throughput
1145sequencing reads} (BLESS) uses a single minimum-sized bloom filter is a
1146correction tool for genomic reads produced by @dfn{Next-generation
1147sequencing} (NGS). BLESS produces accurate correction results with much less
1148memory compared with previous solutions and is also able to tolerate a higher
1149false-positive rate. BLESS can extend reads like DNA assemblers to correct
1150errors at the end of reads.")
1151 (license license:gpl3+)))
1152
2c7ee167
RW		 1153(define-public bowtie
1154 (package
1155 (name "bowtie")
2642231b 1156 (version "2.2.9")
2c7ee167
RW		 1157 (source (origin
1158 (method url-fetch)
1159 (uri (string-append "https://github.com/BenLangmead/bowtie2/archive/v"
1160 version ".tar.gz"))
f586c877 1161 (file-name (string-append name "-" version ".tar.gz"))
2c7ee167
RW		 1162 (sha256
1163 (base32
2642231b 1164 "1vp5db8i7is57iwjybcdg18f5ivyzlj5g1ix1nlvxainzivhz55g"))
2c7ee167
RW		 1165 (modules '((guix build utils)))
1166 (snippet
1167 '(substitute* "Makefile"
2c7ee167
RW		 1168 ;; replace BUILD_HOST and BUILD_TIME for deterministic build
1169 (("-DBUILD_HOST=.*") "-DBUILD_HOST=\"\\\"guix\\\"\"")
0047d26a 1170 (("-DBUILD_TIME=.*") "-DBUILD_TIME=\"\\\"0\\\"\"")))))
2c7ee167
RW		 1171 (build-system gnu-build-system)
1172 (inputs `(("perl" ,perl)
1173 ("perl-clone" ,perl-clone)
1174 ("perl-test-deep" ,perl-test-deep)
1175 ("perl-test-simple" ,perl-test-simple)
0047d26a
RW		 1176 ("python" ,python-2)
1177 ("tbb" ,tbb)))
2c7ee167 1178 (arguments
0047d26a
RW		 1179 '(#:make-flags
1180 (list "allall"
1181 "WITH_TBB=1"
1182 (string-append "prefix=" (assoc-ref %outputs "out")))
2c7ee167
RW		 1183 #:phases
1184 (alist-delete
1185 'configure
1186 (alist-replace
0047d26a 1187 'check
2c7ee167 1188 (lambda* (#:key outputs #:allow-other-keys)
0047d26a
RW		 1189 (system* "perl"
1190 "scripts/test/simple_tests.pl"
1191 "--bowtie2=./bowtie2"
1192 "--bowtie2-build=./bowtie2-build"))
1193 %standard-phases))))
2c7ee167
RW		 1194 (home-page "http://bowtie-bio.sourceforge.net/bowtie2/index.shtml")
1195 (synopsis "Fast and sensitive nucleotide sequence read aligner")
1196 (description
1197 "Bowtie 2 is a fast and memory-efficient tool for aligning sequencing
1198reads to long reference sequences. It is particularly good at aligning reads
1199of about 50 up to 100s or 1,000s of characters, and particularly good at
1200aligning to relatively long (e.g. mammalian) genomes. Bowtie 2 indexes the
1201genome with an FM Index to keep its memory footprint small: for the human
1202genome, its memory footprint is typically around 3.2 GB. Bowtie 2 supports
1203gapped, local, and paired-end alignment modes.")
241e1221 1204 (supported-systems '("x86_64-linux"))
2c7ee167
RW		 1205 (license license:gpl3+)))
1206
94ce537e
RW		 1207(define-public tophat
1208 (package
1209 (name "tophat")
1210 (version "2.1.0")
1211 (source (origin
1212 (method url-fetch)
1213 (uri (string-append
1214 "http://ccb.jhu.edu/software/tophat/downloads/tophat-"
1215 version ".tar.gz"))
1216 (sha256
1217 (base32
1218 "168zlzykq622zbgkh90a90f1bdgsxkscq2zxzbj8brq80hbjpyp7"))
fc1adab1 1219 (patches (search-patches "tophat-build-with-later-seqan.patch"))
94ce537e
RW		 1220 (modules '((guix build utils)))
1221 (snippet
1222 '(begin
1223 ;; Remove bundled SeqAn and samtools
1224 (delete-file-recursively "src/SeqAn-1.3")
1225 (delete-file-recursively "src/samtools-0.1.18")
1226 #t))))
1227 (build-system gnu-build-system)
1228 (arguments
1229 '(#:parallel-build? #f ; not supported
1230 #:phases
1231 (modify-phases %standard-phases
1232 (add-after 'unpack 'use-system-samtools
1233 (lambda* (#:key inputs #:allow-other-keys)
1234 (substitute* "src/Makefile.in"
1235 (("(noinst_LIBRARIES = )\\$\\(SAMLIB\\)" _ prefix) prefix)
1236 (("\\$\\(SAMPROG\\): \\$\\(SAMLIB\\)") "")
1237 (("SAMPROG = samtools_0\\.1\\.18") "")
1238 (("\\$\\(samtools_0_1_18_SOURCES\\)") "")
1239 (("am__EXEEXT_1 = samtools_0\\.1\\.18\\$\\(EXEEXT\\)") ""))
1240 (substitute* '("src/common.cpp"
1241 "src/tophat.py")
1242 (("samtools_0.1.18") (which "samtools")))
1243 (substitute* '("src/common.h"
1244 "src/bam2fastx.cpp")
1245 (("#include \"bam.h\"") "#include <samtools/bam.h>")
1246 (("#include \"sam.h\"") "#include <samtools/sam.h>"))
1247 (substitute* '("src/bwt_map.h"
1248 "src/map2gtf.h"
1249 "src/align_status.h")
1250 (("#include <bam.h>") "#include <samtools/bam.h>")
1251 (("#include <sam.h>") "#include <samtools/sam.h>"))
1252 #t)))))
1253 (inputs
1254 `(("boost" ,boost)
1255 ("bowtie" ,bowtie)
1256 ("samtools" ,samtools-0.1)
1257 ("ncurses" ,ncurses)
1258 ("python" ,python-2)
1259 ("perl" ,perl)
1260 ("zlib" ,zlib)
1261 ("seqan" ,seqan)))
1262 (home-page "http://ccb.jhu.edu/software/tophat/index.shtml")
1263 (synopsis "Spliced read mapper for RNA-Seq data")
1264 (description
1265 "TopHat is a fast splice junction mapper for nucleotide sequence
1266reads produced by the RNA-Seq method. It aligns RNA-Seq reads to
1267mammalian-sized genomes using the ultra high-throughput short read
1268aligner Bowtie, and then analyzes the mapping results to identify
1269splice junctions between exons.")
1270 ;; TopHat is released under the Boost Software License, Version 1.0
1271 ;; See https://github.com/infphilo/tophat/issues/11#issuecomment-121589893
1272 (license license:boost1.0)))
1273
9a8336d8
RW		 1274(define-public bwa
1275 (package
1276 (name "bwa")
1277 (version "0.7.12")
1278 (source (origin
1279 (method url-fetch)
1280 (uri (string-append "mirror://sourceforge/bio-bwa/bwa-"
1281 version ".tar.bz2"))
1282 (sha256
1283 (base32
1284 "1330dpqncv0px3pbhjzz1gwgg39kkcv2r9qp2xs0sixf8z8wl7bh"))))
1285 (build-system gnu-build-system)
1286 (arguments
1287 '(#:tests? #f ;no "check" target
1288 #:phases
1289 (alist-replace
1290 'install
1291 (lambda* (#:key outputs #:allow-other-keys)
1292 (let ((bin (string-append
1293 (assoc-ref outputs "out") "/bin"))
1294 (doc (string-append
1295 (assoc-ref outputs "out") "/share/doc/bwa"))
1296 (man (string-append
1297 (assoc-ref outputs "out") "/share/man/man1")))
96c46210
LC		 1298 (install-file "bwa" bin)
1299 (install-file "README.md" doc)
1300 (install-file "bwa.1" man)))
9a8336d8
RW		 1301 ;; no "configure" script
1302 (alist-delete 'configure %standard-phases))))
1303 (inputs `(("zlib" ,zlib)))
db94f8c7
RW		 1304 ;; Non-portable SSE instructions are used so building fails on platforms
1305 ;; other than x86_64.
1306 (supported-systems '("x86_64-linux"))
9a8336d8
RW		 1307 (home-page "http://bio-bwa.sourceforge.net/")
1308 (synopsis "Burrows-Wheeler sequence aligner")
1309 (description
1310 "BWA is a software package for mapping low-divergent sequences against a
1311large reference genome, such as the human genome. It consists of three
1312algorithms: BWA-backtrack, BWA-SW and BWA-MEM. The first algorithm is
1313designed for Illumina sequence reads up to 100bp, while the rest two for
1314longer sequences ranged from 70bp to 1Mbp. BWA-MEM and BWA-SW share similar
1315features such as long-read support and split alignment, but BWA-MEM, which is
1316the latest, is generally recommended for high-quality queries as it is faster
1317and more accurate. BWA-MEM also has better performance than BWA-backtrack for
131870-100bp Illumina reads.")
1319 (license license:gpl3+)))
1320
d29150b5
RW		 1321(define-public bwa-pssm
1322 (package (inherit bwa)
1323 (name "bwa-pssm")
1324 (version "0.5.11")
1325 (source (origin
1326 (method url-fetch)
1327 (uri (string-append "https://github.com/pkerpedjiev/bwa-pssm/"
1328 "archive/" version ".tar.gz"))
1329 (file-name (string-append name "-" version ".tar.gz"))
1330 (sha256
1331 (base32
1332 "02p7mpbs4mlxmn84g2x4ghak638vbj4lqix2ipx5g84pz9bhdavg"))))
1333 (build-system gnu-build-system)
1334 (inputs
1335 `(("gdsl" ,gdsl)
1336 ("zlib" ,zlib)
1337 ("perl" ,perl)))
1338 (home-page "http://bwa-pssm.binf.ku.dk/")
1339 (synopsis "Burrows-Wheeler transform-based probabilistic short read mapper")
1340 (description
1341 "BWA-PSSM is a probabilistic short genomic sequence read aligner based on
1342the use of @dfn{position specific scoring matrices} (PSSM). Like many of the
1343existing aligners it is fast and sensitive. Unlike most other aligners,
1344however, it is also adaptible in the sense that one can direct the alignment
1345based on known biases within the data set. It is coded as a modification of
1346the original BWA alignment program and shares the genome index structure as
1347well as many of the command line options.")
1348 (license license:gpl3+)))
1349
ad641d53
RW		 1350(define-public python2-bx-python
1351 (package
1352 (name "python2-bx-python")
1353 (version "0.7.2")
1354 (source (origin
1355 (method url-fetch)
1356 (uri (string-append
1357 "https://pypi.python.org/packages/source/b/bx-python/bx-python-"
1358 version ".tar.gz"))
1359 (sha256
1360 (base32
1361 "0ld49idhc5zjdvbhvjq1a2qmpjj7h5v58rqr25dzmfq7g34b50xh"))
1362 (modules '((guix build utils)))
1363 (snippet
1364 '(substitute* "setup.py"
1365 ;; remove dependency on outdated "distribute" module
1366 (("^from distribute_setup import use_setuptools") "")
1367 (("^use_setuptools\\(\\)") "")))))
1368 (build-system python-build-system)
1369 (arguments
1370 `(#:tests? #f ;tests fail because test data are not included
1371 #:python ,python-2))
1372 (inputs
1373 `(("python-numpy" ,python2-numpy)
1374 ("zlib" ,zlib)))
1375 (native-inputs
f3b98f4f 1376 `(("python-nose" ,python2-nose)))
ad641d53
RW		 1377 (home-page "http://bitbucket.org/james_taylor/bx-python/")
1378 (synopsis "Tools for manipulating biological data")
1379 (description
1380 "bx-python provides tools for manipulating biological data, particularly
1381multiple sequence alignments.")
1382 (license license:expat)))
1383
55a9a8c2
RW		 1384(define-public python-pysam
1385 (package
1386 (name "python-pysam")
fd49eb21 1387 (version "0.9.1.4")
d454640c
RW		 1388 (source (origin
1389 (method url-fetch)
f536dce5
MB		 1390 ;; Test data is missing on PyPi.
1391 (uri (string-append
1392 "https://github.com/pysam-developers/pysam/archive/v"
1393 version ".tar.gz"))
1394 (file-name (string-append name "-" version ".tar.gz"))
d454640c
RW		 1395 (sha256
1396 (base32
f536dce5 1397 "0y41ssbg6nvn2jgcbnrvkzblpjcwszaiv1rgyd8dwzjkrbfsgsmc"))
dff26b23
MB		 1398 (modules '((guix build utils)))
1399 (snippet
1400 ;; Drop bundled htslib. TODO: Also remove samtools and bcftools.
1401 '(delete-file-recursively "htslib"))))
55a9a8c2
RW		 1402 (build-system python-build-system)
1403 (arguments
f536dce5 1404 `(#:phases
397d463a
MB		 1405 (modify-phases %standard-phases
1406 (add-before 'build 'set-flags
dff26b23
MB		 1407 (lambda* (#:key inputs #:allow-other-keys)
1408 (setenv "HTSLIB_MODE" "external")
1409 (setenv "HTSLIB_LIBRARY_DIR"
1410 (string-append (assoc-ref inputs "htslib") "/lib"))
1411 (setenv "HTSLIB_INCLUDE_DIR"
1412 (string-append (assoc-ref inputs "htslib") "/include"))
397d463a
MB		 1413 (setenv "LDFLAGS" "-lncurses")
1414 (setenv "CFLAGS" "-D_CURSES_LIB=1")
f536dce5
MB		 1415 #t))
1416 (delete 'check)
1417 (add-after 'install 'check
1418 (lambda* (#:key inputs outputs #:allow-other-keys)
1419 (setenv "PYTHONPATH"
1420 (string-append
1421 (getenv "PYTHONPATH")
1422 ":" (assoc-ref outputs "out")
1423 "/lib/python"
1424 (string-take (string-take-right
1425 (assoc-ref inputs "python") 5) 3)
1426 "/site-packages"))
1427 ;; Step out of source dir so python does not import from CWD.
1428 (chdir "tests")
1429 (setenv "HOME" "/tmp")
1430 (and (zero? (system* "make" "-C" "pysam_data"))
1431 (zero? (system* "make" "-C" "cbcf_data"))
1432 (zero? (system* "nosetests" "-v"))))))))
dff26b23
MB		 1433 (propagated-inputs
1434 `(("htslib" ,htslib))) ; Included from installed header files.
55a9a8c2 1435 (inputs
649e9b3b 1436 `(("ncurses" ,ncurses)
55a9a8c2 1437 ("zlib" ,zlib)))
649e9b3b
RW		 1438 (native-inputs
1439 `(("python-cython" ,python-cython)
f536dce5
MB		 1440 ;; Dependencies below are are for tests only.
1441 ("samtools" ,samtools)
1442 ("bcftools" ,bcftools)
1443 ("python-nose" ,python-nose)))
55a9a8c2
RW		 1444 (home-page "https://github.com/pysam-developers/pysam")
1445 (synopsis "Python bindings to the SAMtools C API")
1446 (description
1447 "Pysam is a Python module for reading and manipulating files in the
1448SAM/BAM format. Pysam is a lightweight wrapper of the SAMtools C API. It
1449also includes an interface for tabix.")
1450 (license license:expat)))
1451
1452(define-public python2-pysam
1453 (package-with-python2 python-pysam))
1454
4db9433a
RW		 1455(define-public python-twobitreader
1456 (package
1457 (name "python-twobitreader")
044ac8d2 1458 (version "3.1.4")
4db9433a
RW		 1459 (source (origin
1460 (method url-fetch)
1461 (uri (pypi-uri "twobitreader" version))
1462 (sha256
1463 (base32
044ac8d2 1464 "1q8wnj2kga9nz1lwc4w7qv52smfm536hp6mc8w6s53lhyj0mpi22"))))
4db9433a 1465 (build-system python-build-system)
900fb8d0
LF		 1466 (arguments
1467 '(;; Tests are not distributed in the PyPi release.
1468 ;; TODO Try building from the Git repo or asking the upstream maintainer
1469 ;; to distribute the tests on PyPi.
1470 #:tests? #f))
4db9433a
RW		 1471 (native-inputs
1472 `(("python-sphinx" ,python-sphinx)))
1473 (home-page "https://github.com/benjschiller/twobitreader")
1474 (synopsis "Python library for reading .2bit files")
1475 (description
1476 "twobitreader is a Python library for reading .2bit files as used by the
1477UCSC genome browser.")
1478 (license license:artistic2.0)))
1479
1480(define-public python2-twobitreader
5c31f4aa 1481 (package-with-python2 python-twobitreader))
4db9433a 1482
f94bf198
RW		 1483(define-public python-plastid
1484 (package
1485 (name "python-plastid")
99caa6f7 1486 (version "0.4.6")
f94bf198
RW		 1487 (source (origin
1488 (method url-fetch)
1489 (uri (pypi-uri "plastid" version))
1490 (sha256
1491 (base32
99caa6f7 1492 "1sqkz5d3b9kf688mp7k771c87ins42j7j0whmkb49cb3fsg8s8lj"))))
f94bf198
RW		 1493 (build-system python-build-system)
1494 (arguments
1495 ;; Some test files are not included.
1496 `(#:tests? #f))
1497 (propagated-inputs
1498 `(("python-numpy" ,python-numpy)
1499 ("python-scipy" ,python-scipy)
1500 ("python-pandas" ,python-pandas)
1501 ("python-pysam" ,python-pysam)
1502 ("python-matplotlib" ,python-matplotlib)
1503 ("python-biopython" ,python-biopython)
99caa6f7
BW		 1504 ("python-twobitreader" ,python-twobitreader)
1505 ("python-termcolor" ,python-termcolor)))
f94bf198
RW		 1506 (native-inputs
1507 `(("python-cython" ,python-cython)
1508 ("python-nose" ,python-nose)))
1509 (home-page "https://github.com/joshuagryphon/plastid")
1510 (synopsis "Python library for genomic analysis")
1511 (description
1512 "plastid is a Python library for genomic analysis – in particular,
1513high-throughput sequencing data – with an emphasis on simplicity.")
1514 (license license:bsd-3)))
1515
1516(define-public python2-plastid
5c31f4aa 1517 (package-with-python2 python-plastid))
f94bf198 1518
6c1305f9
RW		 1519(define-public cd-hit
1520 (package
1521 (name "cd-hit")
0c37e2a3 1522 (version "4.6.6")
6c1305f9
RW		 1523 (source (origin
1524 (method url-fetch)
1525 (uri (string-append "https://github.com/weizhongli/cdhit"
1526 "/releases/download/V" version
0c37e2a3 1527 "/cd-hit-v" version "-2016-0711.tar.gz"))
6c1305f9
RW		 1528 (sha256
1529 (base32
0c37e2a3 1530 "1w8hd4fszgg29nqiz569fldwy012la77nljcmlhglgicws56z54p"))))
6c1305f9
RW		 1531 (build-system gnu-build-system)
1532 (arguments
1533 `(#:tests? #f ; there are no tests
1534 #:make-flags
1535 ;; Executables are copied directly to the PREFIX.
1536 (list (string-append "PREFIX=" (assoc-ref %outputs "out") "/bin"))
1537 #:phases
1538 (modify-phases %standard-phases
1539 ;; No "configure" script
1540 (delete 'configure)
1541 ;; Remove sources of non-determinism
1542 (add-after 'unpack 'be-timeless
1543 (lambda _
1544 (substitute* "cdhit-utility.c++"
1545 ((" \\(built on \" __DATE__ \"\\)") ""))
1546 (substitute* "cdhit-common.c++"
1547 (("__DATE__") "\"0\"")
1548 (("\", %s, \" __TIME__ \"\\\\n\", date") ""))
1549 #t))
1550 ;; The "install" target does not create the target directory
1551 (add-before 'install 'create-target-dir
1552 (lambda* (#:key outputs #:allow-other-keys)
1553 (mkdir-p (string-append (assoc-ref outputs "out") "/bin"))
1554 #t)))))
1555 (inputs
1556 `(("perl" ,perl)))
1557 (home-page "http://weizhongli-lab.org/cd-hit/")
1558 (synopsis "Cluster and compare protein or nucleotide sequences")
1559 (description
1560 "CD-HIT is a program for clustering and comparing protein or nucleotide
1561sequences. CD-HIT is designed to be fast and handle extremely large
1562databases.")
1563 ;; The manual says: "It can be copied under the GNU General Public License
1564 ;; version 2 (GPLv2)."
1565 (license license:gpl2)))
1566
810cff85
RW		 1567(define-public clipper
1568 (package
1569 (name "clipper")
433530a5 1570 (version "1.1")
810cff85
RW		 1571 (source (origin
1572 (method url-fetch)
1573 (uri (string-append
1574 "https://github.com/YeoLab/clipper/archive/"
1575 version ".tar.gz"))
9ab5ea44 1576 (file-name (string-append name "-" version ".tar.gz"))
810cff85
RW		 1577 (sha256
1578 (base32
433530a5 1579 "0pflmsvhbf8izbgwhbhj1i7349sw1f55qpqj8ljmapp16hb0p0qi"))
810cff85
RW		 1580 (modules '((guix build utils)))
1581 (snippet
433530a5
RW		 1582 '(begin
1583 ;; remove unnecessary setup dependency
1584 (substitute* "setup.py"
1585 (("setup_requires = .*") ""))
1586 (for-each delete-file
1587 '("clipper/src/peaks.so"
1588 "clipper/src/readsToWiggle.so"))
1589 (delete-file-recursively "dist/")
1590 #t))))
810cff85
RW		 1591 (build-system python-build-system)
1592 (arguments `(#:python ,python-2)) ; only Python 2 is supported
1593 (inputs
1594 `(("htseq" ,htseq)
1595 ("python-pybedtools" ,python2-pybedtools)
1596 ("python-cython" ,python2-cython)
1597 ("python-scikit-learn" ,python2-scikit-learn)
1598 ("python-matplotlib" ,python2-matplotlib)
433530a5 1599 ("python-pandas" ,python2-pandas)
810cff85
RW		 1600 ("python-pysam" ,python2-pysam)
1601 ("python-numpy" ,python2-numpy)
1602 ("python-scipy" ,python2-scipy)))
1603 (native-inputs
f3b98f4f
HG		 1604 `(("python-mock" ,python2-mock) ; for tests
1605 ("python-pytz" ,python2-pytz))) ; for tests
810cff85
RW		 1606 (home-page "https://github.com/YeoLab/clipper")
1607 (synopsis "CLIP peak enrichment recognition")
1608 (description
1609 "CLIPper is a tool to define peaks in CLIP-seq datasets.")
1610 (license license:gpl2)))
1611
6a35566d
RS		 1612(define-public codingquarry
1613 (package
1614 (name "codingquarry")
1615 (version "2.0")
1616 (source (origin
1617 (method url-fetch)
1618 (uri (string-append
1619 "mirror://sourceforge/codingquarry/CodingQuarry_v"
1620 version ".tar.gz"))
1621 (sha256
1622 (base32
1623 "0115hkjflsnfzn36xppwf9h9avfxlavr43djqmshkkzbgjzsz60i"))))
1624 (build-system gnu-build-system)
1625 (arguments
1626 '(#:tests? #f ; no "check" target
1627 #:phases
1628 (modify-phases %standard-phases
1629 (delete 'configure)
1630 (replace 'install
1631 (lambda* (#:key outputs #:allow-other-keys)
1632 (let* ((out (assoc-ref outputs "out"))
1633 (bin (string-append out "/bin"))
1634 (doc (string-append out "/share/doc/codingquarry")))
1635 (install-file "INSTRUCTIONS.pdf" doc)
1636 (copy-recursively "QuarryFiles"
1637 (string-append out "/QuarryFiles"))
1638 (install-file "CodingQuarry" bin)
1639 (install-file "CufflinksGTF_to_CodingQuarryGFF3.py" bin)))))))
1640 (inputs `(("openmpi" ,openmpi)))
1641 (native-search-paths
1642 (list (search-path-specification
1643 (variable "QUARRY_PATH")
1644 (files '("QuarryFiles")))))
1645 (native-inputs `(("python" ,python-2))) ; Only Python 2 is supported
1646 (synopsis "Fungal gene predictor")
1647 (description "CodingQuarry is a highly accurate, self-training GHMM fungal
1648gene predictor designed to work with assembled, aligned RNA-seq transcripts.")
1649 (home-page "https://sourceforge.net/projects/codingquarry/")
1650 (license license:gpl3+)))
1651
36742f43
RW		 1652(define-public couger
1653 (package
1654 (name "couger")
1655 (version "1.8.2")
1656 (source (origin
1657 (method url-fetch)
1658 (uri (string-append
1659 "http://couger.oit.duke.edu/static/assets/COUGER"
1660 version ".zip"))
1661 (sha256
1662 (base32
1663 "04p2b14nmhzxw5h72mpzdhalv21bx4w9b87z0wpw0xzxpysyncmq"))))
1664 (build-system gnu-build-system)
1665 (arguments
1666 `(#:tests? #f
1667 #:phases
1668 (modify-phases %standard-phases
1669 (delete 'configure)
1670 (delete 'build)
1671 (replace
1672 'install
1673 (lambda* (#:key outputs #:allow-other-keys)
1674 (let ((out (assoc-ref outputs "out")))
1675 (copy-recursively "src" (string-append out "/src"))
1676 (mkdir (string-append out "/bin"))
1677 ;; Add "src" directory to module lookup path.
1678 (substitute* "couger"
1679 (("from argparse")
1680 (string-append "import sys\nsys.path.append(\""
1681 out "\")\nfrom argparse")))
1682 (copy-file "couger" (string-append out "/bin/couger")))
1683 #t))
1684 (add-after
1685 'install 'wrap-program
1686 (lambda* (#:key inputs outputs #:allow-other-keys)
1687 ;; Make sure 'couger' runs with the correct PYTHONPATH.
1688 (let* ((out (assoc-ref outputs "out"))
1689 (path (getenv "PYTHONPATH")))
1690 (wrap-program (string-append out "/bin/couger")
1691 `("PYTHONPATH" ":" prefix (,path))))
1692 #t)))))
1693 (inputs
1694 `(("python" ,python-2)
1695 ("python2-pillow" ,python2-pillow)
1696 ("python2-numpy" ,python2-numpy)
1697 ("python2-scipy" ,python2-scipy)
1698 ("python2-matplotlib" ,python2-matplotlib)))
1699 (propagated-inputs
1700 `(("r" ,r)
1701 ("libsvm" ,libsvm)
1702 ("randomjungle" ,randomjungle)))
1703 (native-inputs
1704 `(("unzip" ,unzip)))
1705 (home-page "http://couger.oit.duke.edu")
1706 (synopsis "Identify co-factors in sets of genomic regions")
1707 (description
1708 "COUGER can be applied to any two sets of genomic regions bound by
1709paralogous TFs (e.g., regions derived from ChIP-seq experiments) to identify
1710putative co-factors that provide specificity to each TF. The framework
1711determines the genomic targets uniquely-bound by each TF, and identifies a
1712small set of co-factors that best explain the in vivo binding differences
1713between the two TFs.
1714
1715COUGER uses classification algorithms (support vector machines and random
1716forests) with features that reflect the DNA binding specificities of putative
1717co-factors. The features are generated either from high-throughput TF-DNA
1718binding data (from protein binding microarray experiments), or from large
1719collections of DNA motifs.")
1720 (license license:gpl3+)))
1721
bfe3c685
RW		 1722(define-public clustal-omega
1723 (package
1724 (name "clustal-omega")
1725 (version "1.2.1")
1726 (source (origin
1727 (method url-fetch)
1728 (uri (string-append
1729 "http://www.clustal.org/omega/clustal-omega-"
1730 version ".tar.gz"))
1731 (sha256
1732 (base32
1733 "02ibkx0m0iwz8nscg998bh41gg251y56cgh86bvyrii5m8kjgwqf"))))
1734 (build-system gnu-build-system)
1735 (inputs
1736 `(("argtable" ,argtable)))
1737 (home-page "http://www.clustal.org/omega/")
1738 (synopsis "Multiple sequence aligner for protein and DNA/RNA")
1739 (description
1740 "Clustal-Omega is a general purpose multiple sequence alignment (MSA)
1741program for protein and DNA/RNA. It produces high quality MSAs and is capable
1742of handling data-sets of hundreds of thousands of sequences in reasonable
1743time.")
1744 (license license:gpl2+)))
1745
191c7101
RW		 1746(define-public crossmap
1747 (package
1748 (name "crossmap")
61d5fd03 1749 (version "0.2.1")
191c7101
RW		 1750 (source (origin
1751 (method url-fetch)
1752 (uri (string-append "mirror://sourceforge/crossmap/CrossMap-"
1753 version ".tar.gz"))
1754 (sha256
1755 (base32
61d5fd03
RW		 1756 "07y179f63d7qnzdvkqcziwk9bs3k4zhp81q392fp1hwszjdvy22f"))
1757 ;; This patch has been sent upstream already and is available
1758 ;; for download from Sourceforge, but it has not been merged.
fc1adab1 1759 (patches (search-patches "crossmap-allow-system-pysam.patch"))
191c7101
RW		 1760 (modules '((guix build utils)))
1761 ;; remove bundled copy of pysam
1762 (snippet
1763 '(delete-file-recursively "lib/pysam"))))
1764 (build-system python-build-system)
1765 (arguments
1766 `(#:python ,python-2
1767 #:phases
1768 (alist-cons-after
1769 'unpack 'set-env
1770 (lambda _ (setenv "CROSSMAP_USE_SYSTEM_PYSAM" "1"))
1771 %standard-phases)))
1772 (inputs
1773 `(("python-numpy" ,python2-numpy)
1774 ("python-pysam" ,python2-pysam)
1775 ("zlib" ,zlib)))
1776 (native-inputs
1777 `(("python-cython" ,python2-cython)
f3b98f4f 1778 ("python-nose" ,python2-nose)))
191c7101
RW		 1779 (home-page "http://crossmap.sourceforge.net/")
1780 (synopsis "Convert genome coordinates between assemblies")
1781 (description
1782 "CrossMap is a program for conversion of genome coordinates or annotation
1783files between different genome assemblies. It supports most commonly used
1784file formats including SAM/BAM, Wiggle/BigWig, BED, GFF/GTF, VCF.")
1785 (license license:gpl2+)))
1786
3a40a92c
RW		 1787(define-public cufflinks
1788 (package
1789 (name "cufflinks")
1790 (version "2.2.1")
1791 (source (origin
1792 (method url-fetch)
1793 (uri (string-append "http://cole-trapnell-lab.github.io/"
1794 "cufflinks/assets/downloads/cufflinks-"
1795 version ".tar.gz"))
1796 (sha256
1797 (base32
1798 "1bnm10p8m7zq4qiipjhjqb24csiqdm1pwc8c795z253r2xk6ncg8"))))
1799 (build-system gnu-build-system)
1800 (arguments
1801 `(#:make-flags
1802 (list
1803 ;; The includes for "eigen" are located in a subdirectory.
1804 (string-append "EIGEN_CPPFLAGS="
1805 "-I" (assoc-ref %build-inputs "eigen")
1806 "/include/eigen3/")
1807 ;; Cufflinks must be linked with various boost libraries.
1808 (string-append "LDFLAGS="
1809 (string-join '("-lboost_system"
1810 "-lboost_serialization"
1811 "-lboost_thread"))))
1812 #:phases
1813 (modify-phases %standard-phases
1814 (add-after 'unpack 'fix-search-for-bam
1815 (lambda _
1816 (substitute* '("ax_bam.m4"
1817 "configure"
1818 "src/hits.h")
1819 (("<bam/sam\\.h>") "<samtools/sam.h>")
1820 (("<bam/bam\\.h>") "<samtools/bam.h>")
1821 (("<bam/version\\.hpp>") "<samtools/version.h>"))
1822 #t)))
1823 #:configure-flags
1824 (list (string-append "--with-bam="
1825 (assoc-ref %build-inputs "samtools")))))
1826 (inputs
1827 `(("eigen" ,eigen)
1828 ("samtools" ,samtools-0.1)
1829 ("htslib" ,htslib)
1830 ("boost" ,boost)
1831 ("python" ,python-2)
1832 ("zlib" ,zlib)))
1833 (home-page "http://cole-trapnell-lab.github.io/cufflinks/")
1834 (synopsis "Transcriptome assembly and RNA-Seq expression analysis")
1835 (description
1836 "Cufflinks assembles RNA transcripts, estimates their abundances,
1837and tests for differential expression and regulation in RNA-Seq
1838samples. It accepts aligned RNA-Seq reads and assembles the
1839alignments into a parsimonious set of transcripts. Cufflinks then
1840estimates the relative abundances of these transcripts based on how
1841many reads support each one, taking into account biases in library
1842preparation protocols.")
1843 (license license:boost1.0)))
1844
8e913213
RW		 1845(define-public cutadapt
1846 (package
1847 (name "cutadapt")
1f94bff2 1848 (version "1.12")
8e913213
RW		 1849 (source (origin
1850 (method url-fetch)
1851 (uri (string-append
1852 "https://github.com/marcelm/cutadapt/archive/v"
1853 version ".tar.gz"))
1854 (file-name (string-append name "-" version ".tar.gz"))
1855 (sha256
1856 (base32
1f94bff2 1857 "19smhh6444ikn4jlmyhvffw4m5aw7yg07rqsk7arg8dkwyga1i4v"))))
8e913213
RW		 1858 (build-system python-build-system)
1859 (arguments
33d5b246
TGR		 1860 `(#:phases
1861 (modify-phases %standard-phases
1862 ;; The tests must be run after installation.
1863 (delete 'check)
1864 (add-after 'install 'check
1865 (lambda* (#:key inputs outputs #:allow-other-keys)
1866 (setenv "PYTHONPATH"
1867 (string-append
1868 (getenv "PYTHONPATH")
1869 ":" (assoc-ref outputs "out")
1870 "/lib/python"
1871 (string-take (string-take-right
1872 (assoc-ref inputs "python") 5) 3)
1873 "/site-packages"))
1874 (zero? (system* "nosetests" "-P" "tests")))))))
1f94bff2
TGR		 1875 (inputs
1876 `(("python-xopen" ,python-xopen)))
8e913213
RW		 1877 (native-inputs
1878 `(("python-cython" ,python-cython)
f3b98f4f 1879 ("python-nose" ,python-nose)))
0c6c9c00 1880 (home-page "https://cutadapt.readthedocs.io/en/stable/")
8e913213
RW		 1881 (synopsis "Remove adapter sequences from nucleotide sequencing reads")
1882 (description
1883 "Cutadapt finds and removes adapter sequences, primers, poly-A tails and
1884other types of unwanted sequence from high-throughput sequencing reads.")
1885 (license license:expat)))
1886
1baee943
RW		 1887(define-public libbigwig
1888 (package
1889 (name "libbigwig")
1890 (version "0.1.4")
1891 (source (origin
1892 (method url-fetch)
1893 (uri (string-append "https://github.com/dpryan79/libBigWig/"
1894 "archive/" version ".tar.gz"))
1895 (file-name (string-append name "-" version ".tar.gz"))
1896 (sha256
1897 (base32
1898 "098rjh35pi4a9q83n8wiwvyzykjqj6l8q189p1xgfw4ghywdlvw1"))))
1899 (build-system gnu-build-system)
1900 (arguments
1901 `(#:test-target "test"
1902 #:make-flags
1903 (list "CC=gcc"
1904 (string-append "prefix=" (assoc-ref %outputs "out")))
1905 #:phases
1906 (modify-phases %standard-phases
1907 (delete 'configure)
1908 (add-before 'check 'disable-curl-test
1909 (lambda _
1910 (substitute* "Makefile"
1911 (("./test/testRemote.*") ""))
1912 #t))
1913 ;; This has been fixed with the upstream commit 4ff6959cd8a0, but
1914 ;; there has not yet been a release containing this change.
1915 (add-before 'install 'create-target-dirs
1916 (lambda* (#:key outputs #:allow-other-keys)
1917 (let ((out (assoc-ref outputs "out")))
1918 (mkdir-p (string-append out "/lib"))
1919 (mkdir-p (string-append out "/include"))
1920 #t))))))
1921 (inputs
1922 `(("zlib" ,zlib)
1923 ("curl" ,curl)))
1924 (native-inputs
1925 `(("doxygen" ,doxygen)))
1926 (home-page "https://github.com/dpryan79/libBigWig")
1927 (synopsis "C library for handling bigWig files")
1928 (description
1929 "This package provides a C library for parsing local and remote BigWig
1930files.")
1931 (license license:expat)))
1932
69e0e03c
RW		 1933(define-public python-pybigwig
1934 (package
1935 (name "python-pybigwig")
1936 (version "0.2.5")
1937 (source (origin
1938 (method url-fetch)
1939 (uri (pypi-uri "pyBigWig" version))
1940 (sha256
1941 (base32
1942 "0yrpdxg3y0sny25x4w22lv1k47jzccqjmg7j4bp0hywklvp0hg7d"))
1943 (modules '((guix build utils)))
1944 (snippet
1945 '(begin
1946 ;; Delete bundled libBigWig sources
1947 (delete-file-recursively "libBigWig")))))
1948 (build-system python-build-system)
1949 (arguments
1950 `(#:phases
1951 (modify-phases %standard-phases
1952 (add-after 'unpack 'link-with-libBigWig
1953 (lambda* (#:key inputs #:allow-other-keys)
1954 (substitute* "setup.py"
1955 (("libs=\\[") "libs=[\"BigWig\", "))
1956 #t)))))
1957 (inputs
1958 `(("libbigwig" ,libbigwig)
1959 ("zlib" ,zlib)
1960 ("curl" ,curl)))
1961 (home-page "https://github.com/dpryan79/pyBigWig")
1962 (synopsis "Access bigWig files in Python using libBigWig")
1963 (description
1964 "This package provides Python bindings to the libBigWig library for
1965accessing bigWig files.")
1966 (license license:expat)))
1967
1968(define-public python2-pybigwig
5c31f4aa 1969 (package-with-python2 python-pybigwig))
69e0e03c 1970
ec2a67de
BW		 1971(define-public python-dendropy
1972 (package
1973 (name "python-dendropy")
25d84d31 1974 (version "4.2.0")
ec2a67de
BW		 1975 (source
1976 (origin
1977 (method url-fetch)
1978 (uri (pypi-uri "DendroPy" version))
1979 (sha256
1980 (base32
25d84d31 1981 "15c7s3d5gf19ljsxvq5advaa752wfi7pwrdjyhzmg85hccyvp47p"))))
ec2a67de
BW		 1982 (build-system python-build-system)
1983 (home-page "http://packages.python.org/DendroPy/")
1984 (synopsis "Library for phylogenetics and phylogenetic computing")
1985 (description
1986 "DendroPy is a library for phylogenetics and phylogenetic computing: reading,
1987writing, simulation, processing and manipulation of phylogenetic
1988trees (phylogenies) and characters.")
1989 (license license:bsd-3)
1990 (properties `((python2-variant . ,(delay python2-dendropy))))))
1991
1992(define-public python2-dendropy
1993 (let ((base (package-with-python2 (strip-python2-variant python-dendropy))))
1994 (package
1995 (inherit base)
9602e3cc
BW		 1996 (arguments
1997 `(#:python ,python-2
1998 #:phases
1999 (modify-phases %standard-phases
2000 (replace 'check
2001 ;; There is currently a test failure that only happens on some
2002 ;; systems, and only using "setup.py test"
2003 (lambda _ (zero? (system* "nosetests")))))))
f3b98f4f 2004 (native-inputs `(("python2-nose" ,python2-nose)
ec2a67de
BW		 2005 ,@(package-native-inputs base))))))
2006
2007
1921b1de
RW		 2008(define-public deeptools
2009 (package
2010 (name "deeptools")
3acb8c85 2011 (version "2.1.1")
1921b1de
RW		 2012 (source (origin
2013 (method url-fetch)
3acb8c85
RW		 2014 (uri (string-append "https://github.com/fidelram/deepTools/"
2015 "archive/" version ".tar.gz"))
1921b1de
RW		 2016 (file-name (string-append name "-" version ".tar.gz"))
2017 (sha256
2018 (base32
3acb8c85 2019 "1nmfin0zjdby3vay3r4flvz94dr6qjhj41ax4yz3vx13j6wz8izd"))))
1921b1de
RW		 2020 (build-system python-build-system)
2021 (arguments
2022 `(#:python ,python-2))
14bda1ff 2023 (inputs
1921b1de
RW		 2024 `(("python-scipy" ,python2-scipy)
2025 ("python-numpy" ,python2-numpy)
3acb8c85 2026 ("python-numpydoc" ,python2-numpydoc)
1921b1de
RW		 2027 ("python-matplotlib" ,python2-matplotlib)
2028 ("python-bx-python" ,python2-bx-python)
3acb8c85
RW		 2029 ("python-pysam" ,python2-pysam)
2030 ("python-pybigwig" ,python2-pybigwig)))
1921b1de 2031 (native-inputs
f3b98f4f
HG		 2032 `(("python-mock" ,python2-mock) ;for tests
2033 ("python-pytz" ,python2-pytz))) ;for tests
1921b1de
RW		 2034 (home-page "https://github.com/fidelram/deepTools")
2035 (synopsis "Tools for normalizing and visualizing deep-sequencing data")
2036 (description
2037 "DeepTools addresses the challenge of handling the large amounts of data
2038that are now routinely generated from DNA sequencing centers. To do so,
2039deepTools contains useful modules to process the mapped reads data to create
2040coverage files in standard bedGraph and bigWig file formats. By doing so,
2041deepTools allows the creation of normalized coverage files or the comparison
2042between two files (for example, treatment and control). Finally, using such
2043normalized and standardized files, multiple visualizations can be created to
2044identify enrichments with functional annotations of the genome.")
2045 (license license:gpl3+)))
2046
684bf7c7
BW		 2047(define-public diamond
2048 (package
2049 (name "diamond")
322a583f 2050 (version "0.8.31")
684bf7c7
BW		 2051 (source (origin
2052 (method url-fetch)
2053 (uri (string-append
2054 "https://github.com/bbuchfink/diamond/archive/v"
2055 version ".tar.gz"))
2056 (file-name (string-append name "-" version ".tar.gz"))
2057 (sha256
2058 (base32
322a583f 2059 "0nh79f4rpgq8vmlga743r7vd0z0ik6spy34f7vfq0v9lcmvfr7xq"))))
122395f9 2060 (build-system cmake-build-system)
684bf7c7 2061 (arguments
7c544991
BW		 2062 '(#:tests? #f ; no "check" target
2063 #:phases
2064 (modify-phases %standard-phases
2065 (add-after 'unpack 'remove-native-compilation
2066 (lambda _
2067 (substitute* "CMakeLists.txt" (("-march=native") ""))
2068 #t)))))
684bf7c7 2069 (inputs
122395f9 2070 `(("zlib" ,zlib)))
684bf7c7
BW		 2071 (home-page "https://github.com/bbuchfink/diamond")
2072 (synopsis "Accelerated BLAST compatible local sequence aligner")
2073 (description
2074 "DIAMOND is a BLAST-compatible local aligner for mapping protein and
2075translated DNA query sequences against a protein reference database (BLASTP
2076and BLASTX alignment mode). The speedup over BLAST is up to 20,000 on short
2077reads at a typical sensitivity of 90-99% relative to BLAST depending on the
2078data and settings.")
d9c44e9c
BW		 2079 ;; diamond fails to build on other platforms
2080 ;; https://github.com/bbuchfink/diamond/issues/18
2081 (supported-systems '("x86_64-linux"))
684bf7c7
BW		 2082 (license (license:non-copyleft "file://src/COPYING"
2083 "See src/COPYING in the distribution."))))
2084
97b9da68
RW		 2085(define-public discrover
2086 (package
2087 (name "discrover")
2088 (version "1.6.0")
2089 (source
2090 (origin
2091 (method url-fetch)
2092 (uri (string-append "https://github.com/maaskola/discrover/archive/"
2093 version ".tar.gz"))
2094 (file-name (string-append name "-" version ".tar.gz"))
2095 (sha256
2096 (base32
2097 "0rah9ja4m0rl5mldd6vag9rwrivw1zrqxssfq8qx64m7961fp68k"))))
2098 (build-system cmake-build-system)
2099 (arguments `(#:tests? #f)) ; there are no tests
2100 (inputs
2101 `(("boost" ,boost)
2102 ("cairo" ,cairo)))
2103 (native-inputs
2104 `(("texlive" ,texlive)
2105 ("imagemagick" ,imagemagick)))
2106 (home-page "http://dorina.mdc-berlin.de/public/rajewsky/discrover/")
2107 (synopsis "Discover discriminative nucleotide sequence motifs")
2108 (description "Discrover is a motif discovery method to find binding sites
2109of nucleic acid binding proteins.")
2110 (license license:gpl3+)))
2111
6619f9c7
RW		 2112(define-public eigensoft
2113 (let ((revision "1")
2114 (commit "b14d1e202e21e532536ff8004f0419cd5e259dc7"))
2115 (package
2116 (name "eigensoft")
2117 (version (string-append "6.1.2-"
2118 revision "."
2119 (string-take commit 9)))
2120 (source
2121 (origin
2122 (method git-fetch)
2123 (uri (git-reference
2124 (url "https://github.com/DReichLab/EIG.git")
2125 (commit commit)))
2126 (file-name (string-append "eigensoft-" commit "-checkout"))
2127 (sha256
2128 (base32
2129 "0f5m6k2j5c16xc3xbywcs989xyc26ncy1zfzp9j9n55n9r4xcaiq"))
2130 (modules '((guix build utils)))
2131 ;; Remove pre-built binaries.
2132 (snippet '(begin
2133 (delete-file-recursively "bin")
2134 (mkdir "bin")
2135 #t))))
2136 (build-system gnu-build-system)
2137 (arguments
2138 `(#:tests? #f ; There are no tests.
2139 #:make-flags '("CC=gcc")
2140 #:phases
2141 (modify-phases %standard-phases
2142 ;; There is no configure phase, but the Makefile is in a
2143 ;; sub-directory.
2144 (replace 'configure
2145 (lambda _
2146 (chdir "src")
2147 ;; The link flags are incomplete.
2148 (substitute* "Makefile"
2149 (("-lgsl") "-lgsl -lm -llapack -llapacke -lpthread"))
2150 #t))
2151 ;; The provided install target only copies executables to
2152 ;; the "bin" directory in the build root.
2153 (add-after 'install 'actually-install
2154 (lambda* (#:key outputs #:allow-other-keys)
2155 (let* ((out (assoc-ref outputs "out"))
2156 (bin (string-append out "/bin")))
6619f9c7
RW		 2157 (for-each (lambda (file)
2158 (install-file file bin))
2159 (find-files "../bin" ".*"))
2160 #t))))))
2161 (inputs
2162 `(("gsl" ,gsl)
2163 ("lapack" ,lapack)
6619f9c7
RW		 2164 ("openblas" ,openblas)
2165 ("perl" ,perl)
2166 ("gfortran" ,gfortran "lib")))
2167 (home-page "https://github.com/DReichLab/EIG")
2168 (synopsis "Tools for population genetics")
2169 (description "The EIGENSOFT package provides tools for population
2170genetics and stratification correction. EIGENSOFT implements methods commonly
2171used in population genetics analyses such as PCA, computation of Tracy-Widom
2172statistics, and finding related individuals in structured populations. It
2173comes with a built-in plotting script and supports multiple file formats and
2174quantitative phenotypes.")
2175 ;; The license of the eigensoft tools is Expat, but since it's
2176 ;; linking with the GNU Scientific Library (GSL) the effective
2177 ;; license is the GPL.
2178 (license license:gpl3+))))
2179
365c8153
RW		 2180(define-public edirect
2181 (package
2182 (name "edirect")
83b84fa8 2183 (version "4.10")
365c8153
RW		 2184 (source (origin
2185 (method url-fetch)
83b84fa8
RW		 2186 (uri (string-append "ftp://ftp.ncbi.nlm.nih.gov/entrez/entrezdirect/"
2187 "versions/2016-05-03/edirect.tar.gz"))
365c8153
RW		 2188 (sha256
2189 (base32
83b84fa8 2190 "15zsprak5yh8c1yrz4r1knmb5s8qcmdid4xdhkh3lqcv64l60hli"))))
365c8153
RW		 2191 (build-system perl-build-system)
2192 (arguments
2193 `(#:tests? #f ;no "check" target
2194 #:phases
2195 (modify-phases %standard-phases
2196 (delete 'configure)
2197 (delete 'build)
2198 (replace 'install
2199 (lambda* (#:key outputs #:allow-other-keys)
2200 (let ((target (string-append (assoc-ref outputs "out")
2201 "/bin")))
2202 (mkdir-p target)
2203 (copy-file "edirect.pl"
2204 (string-append target "/edirect.pl"))
2205 #t)))
2206 (add-after
2207 'install 'wrap-program
2208 (lambda* (#:key inputs outputs #:allow-other-keys)
2209 ;; Make sure 'edirect.pl' finds all perl inputs at runtime.
2210 (let* ((out (assoc-ref outputs "out"))
2211 (path (getenv "PERL5LIB")))
2212 (wrap-program (string-append out "/bin/edirect.pl")
2213 `("PERL5LIB" ":" prefix (,path)))))))))
2214 (inputs
2215 `(("perl-html-parser" ,perl-html-parser)
2216 ("perl-encode-locale" ,perl-encode-locale)
2217 ("perl-file-listing" ,perl-file-listing)
2218 ("perl-html-tagset" ,perl-html-tagset)
2219 ("perl-html-tree" ,perl-html-tree)
2220 ("perl-http-cookies" ,perl-http-cookies)
2221 ("perl-http-date" ,perl-http-date)
2222 ("perl-http-message" ,perl-http-message)
2223 ("perl-http-negotiate" ,perl-http-negotiate)
2224 ("perl-lwp-mediatypes" ,perl-lwp-mediatypes)
2225 ("perl-lwp-protocol-https" ,perl-lwp-protocol-https)
2226 ("perl-net-http" ,perl-net-http)
2227 ("perl-uri" ,perl-uri)
2228 ("perl-www-robotrules" ,perl-www-robotrules)
2229 ("perl" ,perl)))
3d51ec91 2230 (home-page "http://www.ncbi.nlm.nih.gov/books/NBK179288/")
365c8153
RW		 2231 (synopsis "Tools for accessing the NCBI's set of databases")
2232 (description
2233 "Entrez Direct (EDirect) is a method for accessing the National Center
2234for Biotechnology Information's (NCBI) set of interconnected
2235databases (publication, sequence, structure, gene, variation, expression,
2236etc.) from a terminal. Functions take search terms from command-line
2237arguments. Individual operations are combined to build multi-step queries.
2238Record retrieval and formatting normally complete the process.
2239
2240EDirect also provides an argument-driven function that simplifies the
2241extraction of data from document summaries or other results that are returned
2242in structured XML format. This can eliminate the need for writing custom
2243software to answer ad hoc questions.")
2244 (license license:public-domain)))
2245
b16728b0
BW		 2246(define-public exonerate
2247 (package
2248 (name "exonerate")
2249 (version "2.4.0")
2250 (source
2251 (origin
2252 (method url-fetch)
2253 (uri
2254 (string-append
2255 "http://ftp.ebi.ac.uk/pub/software/vertebrategenomics/exonerate/"
2256 "exonerate-" version ".tar.gz"))
2257 (sha256
2258 (base32
2259 "0hj0m9xygiqsdxvbg79wq579kbrx1mdrabi2bzqz2zn9qwfjcjgq"))))
2260 (build-system gnu-build-system)
2261 (arguments
2262 `(#:parallel-build? #f)) ; Building in parallel fails on some machines.
2263 (native-inputs
2264 `(("pkg-config" ,pkg-config)))
2265 (inputs
2266 `(("glib" ,glib)))
2267 (home-page
2268 "https://www.ebi.ac.uk/about/vertebrate-genomics/software/exonerate")
2269 (synopsis "Generic tool for biological sequence alignment")
2270 (description
2271 "Exonerate is a generic tool for pairwise sequence comparison. It allows
2272the alignment of sequences using a many alignment models, either exhaustive
2273dynamic programming or a variety of heuristics.")
2274 (license license:gpl3)))
2275
e4e5a4d8
RW		 2276(define-public express
2277 (package
2278 (name "express")
2279 (version "1.5.1")
2280 (source (origin
2281 (method url-fetch)
2282 (uri
2283 (string-append
2284 "http://bio.math.berkeley.edu/eXpress/downloads/express-"
2285 version "/express-" version "-src.tgz"))
2286 (sha256
2287 (base32
2288 "03rczxd0gjp2l1jxcmjfmf5j94j77zqyxa6x063zsc585nj40n0c"))))
2289 (build-system cmake-build-system)
2290 (arguments
2291 `(#:tests? #f ;no "check" target
2292 #:phases
2293 (alist-cons-after
2294 'unpack 'use-shared-boost-libs-and-set-bamtools-paths
2295 (lambda* (#:key inputs #:allow-other-keys)
2296 (substitute* "CMakeLists.txt"
2297 (("set\\(Boost_USE_STATIC_LIBS ON\\)")
2298 "set(Boost_USE_STATIC_LIBS OFF)")
2299 (("\\$\\{CMAKE_CURRENT_SOURCE_DIR\\}/bamtools/include")
2300 (string-append (assoc-ref inputs "bamtools") "/include/bamtools")))
2301 (substitute* "src/CMakeLists.txt"
2302 (("\\$\\{CMAKE_CURRENT_SOURCE_DIR\\}/\\.\\./bamtools/lib")
2303 (string-append (assoc-ref inputs "bamtools") "/lib/bamtools")))
2304 #t)
2305 %standard-phases)))
2306 (inputs
2307 `(("boost" ,boost)
2308 ("bamtools" ,bamtools)
2309 ("protobuf" ,protobuf)
2310 ("zlib" ,zlib)))
2311 (home-page "http://bio.math.berkeley.edu/eXpress")
2312 (synopsis "Streaming quantification for high-throughput genomic sequencing")
2313 (description
2314 "eXpress is a streaming tool for quantifying the abundances of a set of
2315target sequences from sampled subsequences. Example applications include
2316transcript-level RNA-Seq quantification, allele-specific/haplotype expression
2317analysis (from RNA-Seq), transcription factor binding quantification in
2318ChIP-Seq, and analysis of metagenomic data.")
2319 (license license:artistic2.0)))
2320
f3674b1c
BW		 2321(define-public express-beta-diversity
2322 (package
2323 (name "express-beta-diversity")
2324 (version "1.0.7")
2325 (source (origin
2326 (method url-fetch)
2327 (uri
2328 (string-append
2329 "https://github.com/dparks1134/ExpressBetaDiversity/archive/v"
2330 version ".tar.gz"))
2331 (file-name (string-append name "-" version ".tar.gz"))
2332 (sha256
2333 (base32
2334 "1djvdlmqvjf6h0zq7w36y8cl5cli6rgj86x65znl48agnwmzxfxr"))))
2335 (build-system gnu-build-system)
2336 (arguments
2337 `(#:phases
2338 (modify-phases %standard-phases
2339 (delete 'configure)
2340 (add-before 'build 'enter-source (lambda _ (chdir "source") #t))
2341 (replace 'check
2342 (lambda _ (zero? (system* "../bin/ExpressBetaDiversity"
2343 "-u"))))
2344 (add-after 'check 'exit-source (lambda _ (chdir "..") #t))
2345 (replace 'install
2346 (lambda* (#:key outputs #:allow-other-keys)
2347 (let ((bin (string-append (assoc-ref outputs "out")
2348 "/bin")))
2349 (mkdir-p bin)
2350 (copy-file "scripts/convertToEBD.py"
2351 (string-append bin "/convertToEBD.py"))
2352 (copy-file "bin/ExpressBetaDiversity"
2353 (string-append bin "/ExpressBetaDiversity"))
2354 #t))))))
2355 (inputs
2356 `(("python" ,python-2)))
2357 (home-page "http://kiwi.cs.dal.ca/Software/ExpressBetaDiversity")
2358 (synopsis "Taxon- and phylogenetic-based beta diversity measures")
2359 (description
2360 "Express Beta Diversity (EBD) calculates ecological beta diversity
2361(dissimilarity) measures between biological communities. EBD implements a
2362variety of diversity measures including those that make use of phylogenetic
2363similarity of community members.")
2364 (license license:gpl3+)))
2365
12b04cbe
BW		 2366(define-public fasttree
2367 (package
2368 (name "fasttree")
e03a5153 2369 (version "2.1.9")
12b04cbe
BW		 2370 (source (origin
2371 (method url-fetch)
2372 (uri (string-append
2373 "http://www.microbesonline.org/fasttree/FastTree-"
2374 version ".c"))
2375 (sha256
2376 (base32
e03a5153 2377 "0ljvvw8i1als1wbfzvrf15c3ii2vw9db20a259g6pzg34xyyb97k"))))
12b04cbe
BW		 2378 (build-system gnu-build-system)
2379 (arguments
2380 `(#:tests? #f ; no "check" target
2381 #:phases
2382 (modify-phases %standard-phases
2383 (delete 'unpack)
2384 (delete 'configure)
2385 (replace 'build
e03a5153
BW		 2386 (lambda* (#:key source #:allow-other-keys)
2387 (and (zero? (system* "gcc"
2388 "-O3"
2389 "-finline-functions"
2390 "-funroll-loops"
2391 "-Wall"
2392 "-o"
2393 "FastTree"
2394 source
2395 "-lm"))
2396 (zero? (system* "gcc"
2397 "-DOPENMP"
2398 "-fopenmp"
2399 "-O3"
2400 "-finline-functions"
2401 "-funroll-loops"
2402 "-Wall"
2403 "-o"
2404 "FastTreeMP"
2405 source
2406 "-lm")))))
12b04cbe 2407 (replace 'install
e03a5153
BW		 2408 (lambda* (#:key outputs #:allow-other-keys)
2409 (let ((bin (string-append (assoc-ref outputs "out")
2410 "/bin")))
2411 (mkdir-p bin)
2412 (copy-file "FastTree"
2413 (string-append bin "/FastTree"))
2414 (copy-file "FastTreeMP"
2415 (string-append bin "/FastTreeMP"))
2416 #t))))))
12b04cbe
BW		 2417 (home-page "http://www.microbesonline.org/fasttree")
2418 (synopsis "Infers approximately-maximum-likelihood phylogenetic trees")
2419 (description
2420 "FastTree can handle alignments with up to a million of sequences in a
2421reasonable amount of time and memory. For large alignments, FastTree is
2422100-1,000 times faster than PhyML 3.0 or RAxML 7.")
2423 (license license:gpl2+)))
2424
2127cedb
RW		 2425(define-public fastx-toolkit
2426 (package
2427 (name "fastx-toolkit")
2428 (version "0.0.14")
2429 (source (origin
2430 (method url-fetch)
2431 (uri
2432 (string-append
2433 "https://github.com/agordon/fastx_toolkit/releases/download/"
2434 version "/fastx_toolkit-" version ".tar.bz2"))
2435 (sha256
2436 (base32
2437 "01jqzw386873sr0pjp1wr4rn8fsga2vxs1qfmicvx1pjr72007wy"))))
2438 (build-system gnu-build-system)
2439 (inputs
2440 `(("libgtextutils" ,libgtextutils)))
2441 (native-inputs
2442 `(("pkg-config" ,pkg-config)))
2443 (home-page "http://hannonlab.cshl.edu/fastx_toolkit/")
2444 (synopsis "Tools for FASTA/FASTQ file preprocessing")
2445 (description
2446 "The FASTX-Toolkit is a collection of command line tools for Short-Reads
2447FASTA/FASTQ files preprocessing.
2448
2449Next-Generation sequencing machines usually produce FASTA or FASTQ files,
2450containing multiple short-reads sequences. The main processing of such
2451FASTA/FASTQ files is mapping the sequences to reference genomes. However, it
2452is sometimes more productive to preprocess the files before mapping the
2453sequences to the genome---manipulating the sequences to produce better mapping
2454results. The FASTX-Toolkit tools perform some of these preprocessing tasks.")
2455 (license license:agpl3+)))
2456
d7678942
RW		 2457(define-public flexbar
2458 (package
2459 (name "flexbar")
2460 (version "2.5")
2461 (source (origin
2462 (method url-fetch)
2463 (uri
2464 (string-append "mirror://sourceforge/flexbar/"
2465 version "/flexbar_v" version "_src.tgz"))
2466 (sha256
2467 (base32
2468 "13jaykc3y1x8y5nn9j8ljnb79s5y51kyxz46hdmvvjj6qhyympmf"))))
2469 (build-system cmake-build-system)
2470 (arguments
4ca009c0 2471 `(#:configure-flags (list
d7678942
RW		 2472 (string-append "-DFLEXBAR_BINARY_DIR="
2473 (assoc-ref %outputs "out")
2474 "/bin/"))
2475 #:phases
4ca009c0
RW		 2476 (alist-replace
2477 'check
2478 (lambda* (#:key outputs #:allow-other-keys)
2479 (setenv "PATH" (string-append
2480 (assoc-ref outputs "out") "/bin:"
2481 (getenv "PATH")))
2482 (chdir "../flexbar_v2.5_src/test")
2483 (zero? (system* "bash" "flexbar_validate.sh")))
2484 (alist-delete 'install %standard-phases))))
d7678942
RW		 2485 (inputs
2486 `(("tbb" ,tbb)
2487 ("zlib" ,zlib)))
2488 (native-inputs
2489 `(("pkg-config" ,pkg-config)
2490 ("seqan" ,seqan)))
2491 (home-page "http://flexbar.sourceforge.net")
2492 (synopsis "Barcode and adapter removal tool for sequencing platforms")
2493 (description
2494 "Flexbar preprocesses high-throughput nucleotide sequencing data
2495efficiently. It demultiplexes barcoded runs and removes adapter sequences.
2496Moreover, trimming and filtering features are provided. Flexbar increases
2497read mapping rates and improves genome and transcriptome assemblies. It
2498supports next-generation sequencing data in fasta/q and csfasta/q format from
2499Illumina, Roche 454, and the SOLiD platform.")
2500 (license license:gpl3)))
2501
19f4554c
BW		 2502(define-public fraggenescan
2503 (package
2504 (name "fraggenescan")
2505 (version "1.20")
2506 (source
2507 (origin
2508 (method url-fetch)
2509 (uri
2510 (string-append "mirror://sourceforge/fraggenescan/"
2511 "FragGeneScan" version ".tar.gz"))
2512 (sha256
2513 (base32 "1zzigqmvqvjyqv4945kv6nc5ah2xxm1nxgrlsnbzav3f5c0n0pyj"))))
2514 (build-system gnu-build-system)
2515 (arguments
2516 `(#:phases
2517 (modify-phases %standard-phases
2518 (delete 'configure)
2519 (add-before 'build 'patch-paths
2520 (lambda* (#:key outputs #:allow-other-keys)
2521 (let* ((out (string-append (assoc-ref outputs "out")))
2522 (share (string-append out "/share/fraggenescan/")))
2523 (substitute* "run_FragGeneScan.pl"
2524 (("system\\(\"rm")
2525 (string-append "system(\"" (which "rm")))
2526 (("system\\(\"mv")
2527 (string-append "system(\"" (which "mv")))
2528 ;; This script and other programs expect the training files
2529 ;; to be in the non-standard location bin/train/XXX. Change
2530 ;; this to be share/fraggenescan/train/XXX instead.
2531 (("^\\$train.file = \\$dir.*")
2532 (string-append "$train_file = \""
2533 share
2534 "train/\".$FGS_train_file;")))
2535 (substitute* "run_hmm.c"
2536 (("^ strcat\\(train_dir, \\\"train/\\\"\\);")
2537 (string-append " strcpy(train_dir, \"" share "/train/\");")))
2538 (substitute* "post_process.pl"
2539 (("^my \\$dir = substr.*")
2540 (string-append "my $dir = \"" share "\";"))))
2541 #t))
2542 (replace 'build
2543 (lambda _ (and (zero? (system* "make" "clean"))
2544 (zero? (system* "make" "fgs")))))
2545 (replace 'install
2546 (lambda* (#:key outputs #:allow-other-keys)
2547 (let* ((out (string-append (assoc-ref outputs "out")))
2548 (bin (string-append out "/bin/"))
2549 (share (string-append out "/share/fraggenescan/train")))
2550 (install-file "run_FragGeneScan.pl" bin)
2551 (install-file "FragGeneScan" bin)
2552 (install-file "FGS_gff.py" bin)
2553 (install-file "post_process.pl" bin)
2554 (copy-recursively "train" share))))
2555 (delete 'check)
2556 (add-after 'install 'post-install-check
2557 ;; In lieu of 'make check', run one of the examples and check the
2558 ;; output files gets created.
2559 (lambda* (#:key outputs #:allow-other-keys)
2560 (let* ((out (string-append (assoc-ref outputs "out")))
2561 (bin (string-append out "/bin/")))
2562 (and (zero? (system* (string-append bin "run_FragGeneScan.pl")
2563 "-genome=./example/NC_000913.fna"
2564 "-out=./test2"
2565 "-complete=1"
2566 "-train=complete"))
2567 (file-exists? "test2.faa")
2568 (file-exists? "test2.ffn")
2569 (file-exists? "test2.gff")
2570 (file-exists? "test2.out"))))))))
2571 (inputs
2572 `(("perl" ,perl)
2573 ("python" ,python-2))) ;not compatible with python 3.
2574 (home-page "https://sourceforge.net/projects/fraggenescan/")
2575 (synopsis "Finds potentially fragmented genes in short reads")
2576 (description
2577 "FragGeneScan is a program for predicting bacterial and archaeal genes in
2578short and error-prone DNA sequencing reads. It can also be applied to predict
2579genes in incomplete assemblies or complete genomes.")
2580 ;; GPL3+ according to private correspondense with the authors.
2581 (license license:gpl3+)))
2582
81f3e0c1
BW		 2583(define-public fxtract
2584 (let ((util-commit "776ca85a18a47492af3794745efcb4a905113115"))
2585 (package
2586 (name "fxtract")
2587 (version "2.3")
2588 (source
2589 (origin
2590 (method url-fetch)
2591 (uri (string-append
2592 "https://github.com/ctSkennerton/fxtract/archive/"
2593 version ".tar.gz"))
2594 (file-name (string-append "ctstennerton-util-"
2595 (string-take util-commit 7)
2596 "-checkout"))
2597 (sha256
2598 (base32
2599 "0275cfdhis8517hm01is62062swmi06fxzifq7mr3knbbxjlaiwj"))))
2600 (build-system gnu-build-system)
2601 (arguments
2602 `(#:make-flags (list
2603 (string-append "PREFIX=" (assoc-ref %outputs "out"))
2604 "CC=gcc")
2605 #:test-target "fxtract_test"
2606 #:phases
2607 (modify-phases %standard-phases
2608 (delete 'configure)
2609 (add-before 'build 'copy-util
2610 (lambda* (#:key inputs #:allow-other-keys)
2611 (rmdir "util")
2612 (copy-recursively (assoc-ref inputs "ctskennerton-util") "util")
2613 #t))
2614 ;; Do not use make install as this requires additional dependencies.
2615 (replace 'install
2616 (lambda* (#:key outputs #:allow-other-keys)
2617 (let* ((out (assoc-ref outputs "out"))
2618 (bin (string-append out"/bin")))
2619 (install-file "fxtract" bin)
2620 #t))))))
2621 (inputs
2622 `(("pcre" ,pcre)
2623 ("zlib" ,zlib)))
2624 (native-inputs
2625 ;; ctskennerton-util is licensed under GPL2.
2626 `(("ctskennerton-util"
2627 ,(origin
2628 (method git-fetch)
2629 (uri (git-reference
2630 (url "https://github.com/ctSkennerton/util.git")
2631 (commit util-commit)))
2632 (file-name (string-append
2633 "ctstennerton-util-" util-commit "-checkout"))
2634 (sha256
2635 (base32
2636 "0cls1hd4vgj3f36fpzzg4xc77d6f3hpc60cbpfmn2gdr7ykzzad7"))))))
2637 (home-page "https://github.com/ctSkennerton/fxtract")
2638 (synopsis "Extract sequences from FASTA and FASTQ files")
2639 (description
2640 "Fxtract extracts sequences from a protein or nucleotide fastx (FASTA
2641or FASTQ) file given a subsequence. It uses a simple substring search for
2642basic tasks but can change to using POSIX regular expressions, PCRE, hash
2643lookups or multi-pattern searching as required. By default fxtract looks in
2644the sequence of each record but can also be told to look in the header,
2645comment or quality sections.")
afde1a26
BW		 2646 ;; 'util' requires SSE instructions.
2647 (supported-systems '("x86_64-linux"))
81f3e0c1
BW		 2648 (license license:expat))))
2649
5854f685
RW		 2650(define-public grit
2651 (package
2652 (name "grit")
2653 (version "2.0.2")
2654 (source (origin
2655 (method url-fetch)
2656 (uri (string-append
2657 "https://github.com/nboley/grit/archive/"
2658 version ".tar.gz"))
2659 (file-name (string-append name "-" version ".tar.gz"))
2660 (sha256
2661 (base32
2662 "157in84dj70wimbind3x7sy1whs3h57qfgcnj2s6lrd38fbrb7mj"))))
2663 (build-system python-build-system)
2664 (arguments
2665 `(#:python ,python-2
2666 #:phases
2667 (alist-cons-after
2668 'unpack 'generate-from-cython-sources
2669 (lambda* (#:key inputs outputs #:allow-other-keys)
2670 ;; Delete these C files to force fresh generation from pyx sources.
2671 (delete-file "grit/sparsify_support_fns.c")
2672 (delete-file "grit/call_peaks_support_fns.c")
2673 (substitute* "setup.py"
2674 (("Cython.Setup") "Cython.Build")
2675 ;; Add numpy include path to fix compilation
2676 (("pyx\", \\]")
2677 (string-append "pyx\", ], include_dirs = ['"
2678 (assoc-ref inputs "python-numpy")
2679 "/lib/python2.7/site-packages/numpy/core/include/"
2680 "']"))) #t)
2681 %standard-phases)))
2682 (inputs
2683 `(("python-scipy" ,python2-scipy)
2684 ("python-numpy" ,python2-numpy)
2685 ("python-pysam" ,python2-pysam)
2686 ("python-networkx" ,python2-networkx)))
2687 (native-inputs
f3b98f4f 2688 `(("python-cython" ,python2-cython)))
5854f685
RW		 2689 (home-page "http://grit-bio.org")
2690 (synopsis "Tool for integrative analysis of RNA-seq type assays")
2691 (description
2692 "GRIT is designed to use RNA-seq, TES, and TSS data to build and quantify
2693full length transcript models. When none of these data sources are available,
2694GRIT can be run by providing a candidate set of TES or TSS sites. In
2695addition, GRIT can merge in reference junctions and gene boundaries. GRIT can
2696also be run in quantification mode, where it uses a provided GTF file and just
2697estimates transcript expression.")
2698 (license license:gpl3+)))
2699
346a829a
RW		 2700(define-public hisat
2701 (package
2702 (name "hisat")
2703 (version "0.1.4")
2704 (source (origin
2705 (method url-fetch)
2706 (uri (string-append
2707 "http://ccb.jhu.edu/software/hisat/downloads/hisat-"
2708 version "-beta-source.zip"))
2709 (sha256
2710 (base32
2711 "1k381ydranqxp09yf2y7w1d0chz5d59vb6jchi89hbb0prq19lk5"))))
2712 (build-system gnu-build-system)
2713 (arguments
e58d01fa
RW		 2714 `(#:tests? #f ;no check target
2715 #:make-flags '("allall"
2716 ;; Disable unsupported `popcnt' instructions on
2717 ;; architectures other than x86_64
2718 ,@(if (string-prefix? "x86_64"
2719 (or (%current-target-system)
2720 (%current-system)))
2721 '()
2722 '("POPCNT_CAPABILITY=0")))
346a829a 2723 #:phases
da6dd842
LC		 2724 (alist-cons-after
2725 'unpack 'patch-sources
2726 (lambda _
2727 ;; XXX Cannot use snippet because zip files are not supported
2728 (substitute* "Makefile"
2729 (("^CC = .*$") "CC = gcc")
2730 (("^CPP = .*$") "CPP = g++")
2731 ;; replace BUILD_HOST and BUILD_TIME for deterministic build
2732 (("-DBUILD_HOST=.*") "-DBUILD_HOST=\"\\\"guix\\\"\"")
2733 (("-DBUILD_TIME=.*") "-DBUILD_TIME=\"\\\"0\\\"\""))
2734 (substitute* '("hisat-build" "hisat-inspect")
2735 (("/usr/bin/env") (which "env"))))
2736 (alist-replace
2737 'install
2738 (lambda* (#:key outputs #:allow-other-keys)
84590149 2739 (let ((bin (string-append (assoc-ref outputs "out") "/bin/")))
96c46210
LC		 2740 (for-each (lambda (file)
2741 (install-file file bin))
2742 (find-files
2743 "."
2744 "hisat(-(build|align|inspect)(-(s|l)(-debug)*)*)*$"))))
da6dd842 2745 (alist-delete 'configure %standard-phases)))))
346a829a
RW		 2746 (native-inputs
2747 `(("unzip" ,unzip)))
2748 (inputs
2749 `(("perl" ,perl)
2750 ("python" ,python)
2751 ("zlib" ,zlib)))
60af3d82
RW		 2752 ;; Non-portable SSE instructions are used so building fails on platforms
2753 ;; other than x86_64.
2754 (supported-systems '("x86_64-linux"))
346a829a
RW		 2755 (home-page "http://ccb.jhu.edu/software/hisat/index.shtml")
2756 (synopsis "Hierarchical indexing for spliced alignment of transcripts")
2757 (description
2758 "HISAT is a fast and sensitive spliced alignment program for mapping
2759RNA-seq reads. In addition to one global FM index that represents a whole
2760genome, HISAT uses a large set of small FM indexes that collectively cover the
2761whole genome. These small indexes (called local indexes) combined with
2762several alignment strategies enable effective alignment of RNA-seq reads, in
2763particular, reads spanning multiple exons.")
2764 (license license:gpl3+)))
2765
e84efc50
RW		 2766(define-public hisat2
2767 (package
2768 (name "hisat2")
2769 (version "2.0.5")
2770 (source
2771 (origin
2772 (method url-fetch)
2773 ;; FIXME: a better source URL is
2774 ;; (string-append "ftp://ftp.ccb.jhu.edu/pub/infphilo/hisat2"
2775 ;; "/downloads/hisat2-" version "-source.zip")
2776 ;; with hash "0lywnr8kijwsc2aw10dwxic0n0yvip6fl3rjlvc8zzwahamy4x7g"
2777 ;; but it is currently unavailable.
2778 (uri "https://github.com/infphilo/hisat2/archive/cba6e8cb.tar.gz")
2779 (file-name (string-append name "-" version ".tar.gz"))
2780 (sha256
2781 (base32
2782 "1mf2hdsyv7cd97xm9mp9a4qws02yrj95y6w6f6cdwnq0klp81r50"))))
2783 (build-system gnu-build-system)
2784 (arguments
2785 `(#:tests? #f ; no check target
2786 #:make-flags (list "CC=gcc" "CXX=g++" "allall")
2787 #:modules ((guix build gnu-build-system)
2788 (guix build utils)
2789 (srfi srfi-26))
2790 #:phases
2791 (modify-phases %standard-phases
2792 (add-after 'unpack 'make-deterministic
2793 (lambda _
2794 (substitute* "Makefile"
2795 (("`date`") "0"))
2796 #t))
2797 (delete 'configure)
2798 (replace 'install
2799 (lambda* (#:key outputs #:allow-other-keys)
2800 (let* ((out (assoc-ref outputs "out"))
2801 (bin (string-append out "/bin/"))
2802 (doc (string-append out "/share/doc/hisat2/")))
2803 (for-each
2804 (cut install-file <> bin)
2805 (find-files "."
2806 "hisat2(-(build|align|inspect)(-(s|l)(-debug)*)*)*$"))
2807 (mkdir-p doc)
2808 (install-file "doc/manual.inc.html" doc))
2809 #t)))))
2810 (native-inputs
2811 `(("unzip" ,unzip) ; needed for archive from ftp
2812 ("perl" ,perl)
2813 ("pandoc" ,ghc-pandoc))) ; for documentation
2814 (home-page "http://ccb.jhu.edu/software/hisat2/index.shtml")
2815 (synopsis "Graph-based alignment of genomic sequencing reads")
2816 (description "HISAT2 is a fast and sensitive alignment program for mapping
2817next-generation sequencing reads (both DNA and RNA) to a population of human
2818genomes (as well as to a single reference genome). In addition to using one
2819global @dfn{graph FM} (GFM) index that represents a population of human
2820genomes, HISAT2 uses a large set of small GFM indexes that collectively cover
2821the whole genome. These small indexes, combined with several alignment
2822strategies, enable rapid and accurate alignment of sequencing reads. This new
2823indexing scheme is called a @dfn{Hierarchical Graph FM index} (HGFM).")
2824 ;; HISAT2 contains files from Bowtie2, which is released under
2825 ;; GPLv2 or later. The HISAT2 source files are released under
2826 ;; GPLv3 or later.
2827 (license license:gpl3+)))
2828
c684629f
BW		 2829(define-public hmmer
2830 (package
2831 (name "hmmer")
2832 (version "3.1b2")
2833 (source (origin
2834 (method url-fetch)
2835 (uri (string-append
a83e6046 2836 "http://eddylab.org/software/hmmer"
c684629f
BW		 2837 (version-prefix version 1) "/"
2838 version "/hmmer-" version ".tar.gz"))
2839 (sha256
2840 (base32
2841 "0djmgc0pfli0jilfx8hql1axhwhqxqb8rxg2r5rg07aw73sfs5nx"))))
2842 (build-system gnu-build-system)
b3546174 2843 (native-inputs `(("perl" ,perl)))
a83e6046 2844 (home-page "http://hmmer.org/")
c684629f
BW		 2845 (synopsis "Biosequence analysis using profile hidden Markov models")
2846 (description
2847 "HMMER is used for searching sequence databases for homologs of protein
2848sequences, and for making protein sequence alignments. It implements methods
2849using probabilistic models called profile hidden Markov models (profile
2850HMMs).")
2851 (license (list license:gpl3+
2852 ;; The bundled library 'easel' is distributed
2853 ;; under The Janelia Farm Software License.
2854 (license:non-copyleft
2855 "file://easel/LICENSE"
2856 "See easel/LICENSE in the distribution.")))))
2857
85652f59
RW		 2858(define-public htseq
2859 (package
2860 (name "htseq")
2861 (version "0.6.1")
2862 (source (origin
2863 (method url-fetch)
2864 (uri (string-append
2865 "https://pypi.python.org/packages/source/H/HTSeq/HTSeq-"
2866 version ".tar.gz"))
2867 (sha256
2868 (base32
2869 "1i85ppf2j2lj12m0x690qq5nn17xxk23pbbx2c83r8ayb5wngzwv"))))
2870 (build-system python-build-system)
2871 (arguments `(#:python ,python-2)) ; only Python 2 is supported
0536727e
RW		 2872 ;; Numpy needs to be propagated when htseq is used as a Python library.
2873 (propagated-inputs
2874 `(("python-numpy" ,python2-numpy)))
578b05d9
RW		 2875 (inputs
2876 `(("python-pysam" ,python2-pysam)))
85652f59
RW		 2877 (home-page "http://www-huber.embl.de/users/anders/HTSeq/")
2878 (synopsis "Analysing high-throughput sequencing data with Python")
2879 (description
2880 "HTSeq is a Python package that provides infrastructure to process data
2881from high-throughput sequencing assays.")
2882 (license license:gpl3+)))
2883
1ad15c16 2884(define-public java-htsjdk
15a3c3d4 2885 (package
1ad15c16 2886 (name "java-htsjdk")
15a3c3d4
RW		 2887 (version "1.129")
2888 (source (origin
2889 (method url-fetch)
2890 (uri (string-append
2891 "https://github.com/samtools/htsjdk/archive/"
2892 version ".tar.gz"))
2893 (file-name (string-append name "-" version ".tar.gz"))
2894 (sha256
2895 (base32
2896 "0asdk9b8jx2ij7yd6apg9qx03li8q7z3ml0qy2r2qczkra79y6fw"))
2897 (modules '((guix build utils)))
2898 ;; remove build dependency on git
2899 (snippet '(substitute* "build.xml"
2900 (("failifexecutionfails=\"true\"")
2901 "failifexecutionfails=\"false\"")))))
10b4a969 2902 (build-system ant-build-system)
15a3c3d4 2903 (arguments
10b4a969
RW		 2904 `(#:tests? #f ; test require Internet access
2905 #:make-flags
2906 (list (string-append "-Ddist=" (assoc-ref %outputs "out")
2907 "/share/java/htsjdk/"))
2908 #:build-target "all"
2909 #:phases
2910 (modify-phases %standard-phases
2911 ;; The build phase also installs the jars
2912 (delete 'install))))
15a3c3d4
RW		 2913 (home-page "http://samtools.github.io/htsjdk/")
2914 (synopsis "Java API for high-throughput sequencing data (HTS) formats")
2915 (description
2916 "HTSJDK is an implementation of a unified Java library for accessing
2917common file formats, such as SAM and VCF, used for high-throughput
2918sequencing (HTS) data. There are also an number of useful utilities for
2919manipulating HTS data.")
2920 (license license:expat)))
2921
e7c09730
RW		 2922(define-public htslib
2923 (package
2924 (name "htslib")
6c737963 2925 (version "1.3.1")
e7c09730
RW		 2926 (source (origin
2927 (method url-fetch)
2928 (uri (string-append
2929 "https://github.com/samtools/htslib/releases/download/"
2930 version "/htslib-" version ".tar.bz2"))
2931 (sha256
2932 (base32
6c737963 2933 "1rja282fwdc25ql6izkhdyh8ppw8x2fs0w0js78zgkmqjlikmma9"))))
e7c09730
RW		 2934 (build-system gnu-build-system)
2935 (arguments
2936 `(#:phases
2937 (modify-phases %standard-phases
2938 (add-after
2939 'unpack 'patch-tests
2940 (lambda _
2941 (substitute* "test/test.pl"
2942 (("/bin/bash") (which "bash")))
2943 #t)))))
2944 (inputs
2945 `(("zlib" ,zlib)))
2946 (native-inputs
2947 `(("perl" ,perl)))
2948 (home-page "http://www.htslib.org")
2949 (synopsis "C library for reading/writing high-throughput sequencing data")
2950 (description
2951 "HTSlib is a C library for reading/writing high-throughput sequencing
2952data. It also provides the bgzip, htsfile, and tabix utilities.")
2953 ;; Files under cram/ are released under the modified BSD license;
2954 ;; the rest is released under the Expat license
2955 (license (list license:expat license:bsd-3))))
2956
c4325f62
RW		 2957(define-public idr
2958 (package
2959 (name "idr")
2960 (version "2.0.0")
2961 (source (origin
2962 (method url-fetch)
2963 (uri (string-append
2964 "https://github.com/nboley/idr/archive/"
2965 version ".tar.gz"))
2966 (file-name (string-append name "-" version ".tar.gz"))
2967 (sha256
2968 (base32
2969 "1k3x44biak00aiv3hpm1yd6nn4hhp7n0qnbs3zh2q9sw7qr1qj5r"))))
2970 (build-system python-build-system)
2971 (arguments
2972 `(#:phases
2973 (modify-phases %standard-phases
2974 (add-after
2975 'install 'wrap-program
2976 (lambda* (#:key inputs outputs #:allow-other-keys)
2977 (let* ((out (assoc-ref outputs "out"))
2978 (python-version (string-take (string-take-right
2979 (assoc-ref inputs "python") 5) 3))
2980 (path (string-join
2981 (map (lambda (name)
2982 (string-append (assoc-ref inputs name)
2983 "/lib/python" python-version
2984 "/site-packages"))
2985 '("python-scipy"
2986 "python-numpy"
2987 "python-matplotlib"))
2988 ":")))
2989 (wrap-program (string-append out "/bin/idr")
2990 `("PYTHONPATH" ":" prefix (,path))))
2991 #t)))))
2992 (inputs
2993 `(("python-scipy" ,python-scipy)
2994 ("python-numpy" ,python-numpy)
2995 ("python-matplotlib" ,python-matplotlib)))
2996 (native-inputs
f3b98f4f 2997 `(("python-cython" ,python-cython)))
c4325f62
RW		 2998 (home-page "https://github.com/nboley/idr")
2999 (synopsis "Tool to measure the irreproducible discovery rate (IDR)")
3000 (description
3001 "The IDR (Irreproducible Discovery Rate) framework is a unified approach
3002to measure the reproducibility of findings identified from replicate
3003experiments and provide highly stable thresholds based on reproducibility.")
3004 (license license:gpl3+)))
3005
43c565d2
RW		 3006(define-public jellyfish
3007 (package
3008 (name "jellyfish")
3009 (version "2.2.4")
3010 (source (origin
3011 (method url-fetch)
3012 (uri (string-append "https://github.com/gmarcais/Jellyfish/"
3013 "releases/download/v" version
3014 "/jellyfish-" version ".tar.gz"))
3015 (sha256
3016 (base32
3017 "0a6xnynqy2ibfbfz86b9g2m2dgm7f1469pmymkpam333gi3p26nk"))))
3018 (build-system gnu-build-system)
3019 (outputs '("out" ;for library
3020 "ruby" ;for Ruby bindings
3021 "python")) ;for Python bindings
3022 (arguments
3023 `(#:configure-flags
3024 (list (string-append "--enable-ruby-binding="
3025 (assoc-ref %outputs "ruby"))
3026 (string-append "--enable-python-binding="
3027 (assoc-ref %outputs "python")))
3028 #:phases
3029 (modify-phases %standard-phases
3030 (add-before 'check 'set-SHELL-variable
3031 (lambda _
3032 ;; generator_manager.hpp either uses /bin/sh or $SHELL
3033 ;; to run tests.
3034 (setenv "SHELL" (which "bash"))
3035 #t)))))
3036 (native-inputs
3037 `(("bc" ,bc)
3038 ("time" ,time)
3039 ("ruby" ,ruby)
3040 ("python" ,python-2)))
3041 (synopsis "Tool for fast counting of k-mers in DNA")
3042 (description
3043 "Jellyfish is a tool for fast, memory-efficient counting of k-mers in
3044DNA. A k-mer is a substring of length k, and counting the occurrences of all
3045such substrings is a central step in many analyses of DNA sequence. Jellyfish
3046is a command-line program that reads FASTA and multi-FASTA files containing
3047DNA sequences. It outputs its k-mer counts in a binary format, which can be
3048translated into a human-readable text format using the @code{jellyfish dump}
3049command, or queried for specific k-mers with @code{jellyfish query}.")
3050 (home-page "http://www.genome.umd.edu/jellyfish.html")
6e8faf77
EF		 3051 ;; From their website: JELLYFISH runs on 64-bit Intel-compatible processors
3052 (supported-systems '("x86_64-linux"))
43c565d2
RW		 3053 ;; The combined work is published under the GPLv3 or later. Individual
3054 ;; files such as lib/jsoncpp.cpp are released under the Expat license.
3055 (license (list license:gpl3+ license:expat))))
3056
94ff3157
BW		 3057(define-public khmer
3058 (package
3059 (name "khmer")
3060 (version "2.0")
3061 (source
3062 (origin
3063 (method url-fetch)
3064 (uri (pypi-uri "khmer" version))
3065 (sha256
3066 (base32
3067 "0wb05shqh77v00256qlm68vbbx3kl76fyzihszbz5nhanl4ni33a"))
3068 (patches (search-patches "khmer-use-libraries.patch"))))
3069 (build-system python-build-system)
3070 (arguments
3071 `(#:phases
3072 (modify-phases %standard-phases
3073 (add-after 'unpack 'set-paths
3074 (lambda* (#:key inputs outputs #:allow-other-keys)
3075 ;; Delete bundled libraries.
3076 (delete-file-recursively "third-party/zlib")
3077 (delete-file-recursively "third-party/bzip2")
3078 ;; Replace bundled seqan.
3079 (let* ((seqan-all "third-party/seqan")
3080 (seqan-include (string-append
3081 seqan-all "/core/include")))
3082 (delete-file-recursively seqan-all)
3083 (copy-recursively (string-append (assoc-ref inputs "seqan")
3084 "/include/seqan")
3085 (string-append seqan-include "/seqan")))
3086 ;; We do not replace the bundled MurmurHash as the canonical
3087 ;; repository for this code 'SMHasher' is unsuitable for
3088 ;; providing a library. See
3089 ;; https://lists.gnu.org/archive/html/guix-devel/2016-06/msg00977.html
3090 #t))
3091 (add-after 'unpack 'set-cc
3092 (lambda _
3093 (setenv "CC" "gcc")
3094 #t))
3095 ;; It is simpler to test after installation.
3096 (delete 'check)
3097 (add-after 'install 'post-install-check
3098 (lambda* (#:key inputs outputs #:allow-other-keys)
3099 (let ((out (assoc-ref outputs "out")))
3100 (setenv "PATH"
3101 (string-append
3102 (getenv "PATH")
3103 ":"
3104 (assoc-ref outputs "out")
3105 "/bin"))
3106 (setenv "PYTHONPATH"
3107 (string-append
3108 (getenv "PYTHONPATH")
3109 ":"
3110 out
3111 "/lib/python"
3112 (string-take (string-take-right
3113 (assoc-ref inputs "python") 5) 3)
3114 "/site-packages"))
3115 (with-directory-excursion "build"
3116 (zero? (system* "nosetests" "khmer" "--attr"
3117 "!known_failing")))))))))
3118 (native-inputs
3119 `(("seqan" ,seqan)
3120 ("python-nose" ,python-nose)))
3121 (inputs
3122 `(("zlib" ,zlib)
3123 ("bzip2" ,bzip2)
3124 ("python-screed" ,python-screed)
3125 ("python-bz2file" ,python-bz2file)))
3126 (home-page "https://khmer.readthedocs.org/")
3127 (synopsis "K-mer counting, filtering and graph traversal library")
3128 (description "The khmer software is a set of command-line tools for
3129working with DNA shotgun sequencing data from genomes, transcriptomes,
3130metagenomes and single cells. Khmer can make de novo assemblies faster, and
3131sometimes better. Khmer can also identify and fix problems with shotgun
3132data.")
8157af2e
EF		 3133 ;; When building on i686, armhf and mips64el, we get the following error:
3134 ;; error: ['khmer', 'khmer.tests', 'oxli'] require 64-bit operating system
3135 (supported-systems '("x86_64-linux"))
94ff3157
BW		 3136 (license license:bsd-3)))
3137
d57e6d0f
RW		 3138(define-public macs
3139 (package
3140 (name "macs")
0d0bcaa0 3141 (version "2.1.0.20151222")
d57e6d0f
RW		 3142 (source (origin
3143 (method url-fetch)
43ec07f1 3144 (uri (pypi-uri "MACS2" version))
d57e6d0f
RW		 3145 (sha256
3146 (base32
0d0bcaa0 3147 "1r2hcz6irhcq7lwbafjks98jbn34hv05avgbdjnp6w6mlfjkf8x5"))))
d57e6d0f
RW		 3148 (build-system python-build-system)
3149 (arguments
3150 `(#:python ,python-2 ; only compatible with Python 2.7
3151 #:tests? #f)) ; no test target
3152 (inputs
3153 `(("python-numpy" ,python2-numpy)))
d57e6d0f
RW		 3154 (home-page "http://github.com/taoliu/MACS/")
3155 (synopsis "Model based analysis for ChIP-Seq data")
3156 (description
3157 "MACS is an implementation of a ChIP-Seq analysis algorithm for
3158identifying transcript factor binding sites named Model-based Analysis of
3159ChIP-Seq (MACS). MACS captures the influence of genome complexity to evaluate
3160the significance of enriched ChIP regions and it improves the spatial
3161resolution of binding sites through combining the information of both
3162sequencing tag position and orientation.")
3163 (license license:bsd-3)))
3164
41ddebdd
BW		 3165(define-public mafft
3166 (package
3167 (name "mafft")
71461f88 3168 (version "7.305")
41ddebdd
BW		 3169 (source (origin
3170 (method url-fetch)
3171 (uri (string-append
3172 "http://mafft.cbrc.jp/alignment/software/mafft-" version
3173 "-without-extensions-src.tgz"))
3174 (file-name (string-append name "-" version ".tgz"))
3175 (sha256
3176 (base32
71461f88 3177 "0ziim7g58n3z8gppsa713f5fxprl60ldj3xck186z0n9dpp06i8r"))))
41ddebdd
BW		 3178 (build-system gnu-build-system)
3179 (arguments
3180 `(#:tests? #f ; no automated tests, though there are tests in the read me
3181 #:make-flags (let ((out (assoc-ref %outputs "out")))
3182 (list (string-append "PREFIX=" out)
3183 (string-append "BINDIR="
3184 (string-append out "/bin"))))
3185 #:phases
3186 (modify-phases %standard-phases
3187 (add-after 'unpack 'enter-dir
101e8f71 3188 (lambda _ (chdir "core") #t))
41ddebdd 3189 (add-after 'enter-dir 'patch-makefile
101e8f71
BW		 3190 (lambda _
3191 ;; on advice from the MAFFT authors, there is no need to
3192 ;; distribute mafft-profile, mafft-distance, or
3193 ;; mafft-homologs.rb as they are too "specialised".
3194 (substitute* "Makefile"
3195 ;; remove mafft-homologs.rb from SCRIPTS
3196 (("^SCRIPTS = mafft mafft-homologs.rb")
3197 "SCRIPTS = mafft")
3198 ;; remove mafft-homologs from MANPAGES
3199 (("^MANPAGES = mafft.1 mafft-homologs.1")
3200 "MANPAGES = mafft.1")
3201 ;; remove mafft-distance from PROGS
3202 (("^PROGS = dvtditr dndfast7 dndblast sextet5 mafft-distance")
3203 "PROGS = dvtditr dndfast7 dndblast sextet5")
3204 ;; remove mafft-profile from PROGS
3205 (("splittbfast disttbfast tbfast mafft-profile 2cl mccaskillwrap")
3206 "splittbfast disttbfast tbfast f2cl mccaskillwrap")
3207 (("^rm -f mafft-profile mafft-profile.exe") "#")
3208 (("^rm -f mafft-distance mafft-distance.exe") ")#")
3209 ;; do not install MAN pages in libexec folder
3210 (("^\t\\$\\(INSTALL\\) -m 644 \\$\\(MANPAGES\\) \
41ddebdd 3211\\$\\(DESTDIR\\)\\$\\(LIBDIR\\)") "#"))
101e8f71 3212 #t))
02f35bb5
BW		 3213 (add-after 'enter-dir 'patch-paths
3214 (lambda* (#:key inputs #:allow-other-keys)
3215 (substitute* '("pairash.c"
3216 "mafft.tmpl")
3217 (("perl") (which "perl"))
3218 (("([\"`| ])awk" _ prefix)
3219 (string-append prefix (which "awk")))
3220 (("grep") (which "grep")))
3221 #t))
101e8f71
BW		 3222 (delete 'configure)
3223 (add-after 'install 'wrap-programs
3224 (lambda* (#:key outputs #:allow-other-keys)
3225 (let* ((out (assoc-ref outputs "out"))
3226 (bin (string-append out "/bin"))
3227 (path (string-append
3228 (assoc-ref %build-inputs "coreutils") "/bin:")))
3229 (for-each (lambda (file)
3230 (wrap-program file
3231 `("PATH" ":" prefix (,path))))
3232 (find-files bin)))
3233 #t)))))
41ddebdd 3234 (inputs
02f35bb5 3235 `(("perl" ,perl)
71461f88 3236 ("ruby" ,ruby)
02f35bb5 3237 ("gawk" ,gawk)
101e8f71
BW		 3238 ("grep" ,grep)
3239 ("coreutils" ,coreutils)))
41ddebdd
BW		 3240 (home-page "http://mafft.cbrc.jp/alignment/software/")
3241 (synopsis "Multiple sequence alignment program")
3242 (description
3243 "MAFFT offers a range of multiple alignment methods for nucleotide and
3244protein sequences. For instance, it offers L-INS-i (accurate; for alignment
3245of <~200 sequences) and FFT-NS-2 (fast; for alignment of <~30,000
3246sequences).")
3247 (license (license:non-copyleft
3248 "http://mafft.cbrc.jp/alignment/software/license.txt"
3249 "BSD-3 with different formatting"))))
8fd790eb 3250
84be3b99
MB		 3251(define-public mash
3252 (package
3253 (name "mash")
3254 (version "1.1.1")
3255 (source (origin
3256 (method url-fetch)
3257 (uri (string-append
3258 "https://github.com/marbl/mash/archive/v"
3259 version ".tar.gz"))
3260 (file-name (string-append name "-" version ".tar.gz"))
3261 (sha256
3262 (base32
3263 "08znbvqq5xknfhmpp3wcj574zvi4p7i8zifi67c9qw9a6ikp42fj"))
3264 (modules '((guix build utils)))
3265 (snippet
3266 ;; Delete bundled kseq.
3267 ;; TODO: Also delete bundled murmurhash and open bloom filter.
3268 '(delete-file "src/mash/kseq.h"))))
3269 (build-system gnu-build-system)
3270 (arguments
3271 `(#:tests? #f ; No tests.
3272 #:configure-flags
3273 (list
3274 (string-append "--with-capnp=" (assoc-ref %build-inputs "capnproto"))
3275 (string-append "--with-gsl=" (assoc-ref %build-inputs "gsl")))
3276 #:make-flags (list "CC=gcc")
3277 #:phases
3278 (modify-phases %standard-phases
3279 (add-after 'unpack 'fix-includes
3280 (lambda _
3281 (substitute* '("src/mash/Sketch.cpp" "src/mash/CommandFind.cpp")
3282 (("^#include \"kseq\\.h\"")
3283 "#include \"htslib/kseq.h\""))
3284 #t))
3285 (add-before 'configure 'autoconf
3286 (lambda _ (zero? (system* "autoconf")))))))
3287 (native-inputs
3288 `(("autoconf" ,autoconf)
3289 ;; Capnproto and htslib are statically embedded in the final
3290 ;; application. Therefore we also list their licenses, below.
3291 ("capnproto" ,capnproto)
3292 ("htslib" ,htslib)))
3293 (inputs
3294 `(("gsl" ,gsl)
3295 ("zlib" ,zlib)))
3296 (supported-systems '("x86_64-linux"))
3297 (home-page "https://mash.readthedocs.io")
3298 (synopsis "Fast genome and metagenome distance estimation using MinHash")
3299 (description "Mash is a fast sequence distance estimator that uses the
3300MinHash algorithm and is designed to work with genomes and metagenomes in the
3301form of assemblies or reads.")
3302 (license (list license:bsd-3 ; Mash
3303 license:expat ; HTSlib and capnproto
3304 license:public-domain ; MurmurHash 3
3305 license:cpl1.0)))) ; Open Bloom Filter
3306
8fd790eb 3307(define-public metabat
2c3eb4b8
BW		 3308 ;; We package from a git commit because compilation of the released version
3309 ;; fails.
3310 (let ((commit "cbdca756993e66ae57e50a27970595dda9cbde1b"))
3311 (package
3312 (name "metabat")
3313 (version (string-append "0.32.4-1." (string-take commit 8)))
3314 (source
3315 (origin
3316 (method git-fetch)
3317 (uri (git-reference
3318 (url "https://bitbucket.org/berkeleylab/metabat.git")
3319 (commit commit)))
3320 (file-name (string-append name "-" version))
3321 (sha256
3322 (base32
3323 "0byia8nsip6zvc4ha0qkxkxxyjf4x7jcvy48q2dvb0pzr989syzr"))
3324 (patches (search-patches "metabat-remove-compilation-date.patch"))))
8fd790eb
BW		 3325 (build-system gnu-build-system)
3326 (arguments
3327 `(#:phases
3328 (modify-phases %standard-phases
3329 (add-after 'unpack 'fix-includes
45469ebe
BW		 3330 (lambda _
3331 (substitute* "src/BamUtils.h"
3332 (("^#include \"bam/bam\\.h\"")
3333 "#include \"samtools/bam.h\"")
3334 (("^#include \"bam/sam\\.h\"")
3335 "#include \"samtools/sam.h\""))
3336 (substitute* "src/KseqReader.h"
3337 (("^#include \"bam/kseq\\.h\"")
3338 "#include \"htslib/kseq.h\""))
3339 #t))
8fd790eb 3340 (add-after 'unpack 'fix-scons
45469ebe
BW		 3341 (lambda* (#:key inputs #:allow-other-keys)
3342 (substitute* "SConstruct"
3343 (("^htslib_dir = 'samtools'")
3344 (string-append "hitslib_dir = '"
3345 (assoc-ref inputs "htslib")
3346 "'"))
3347 (("^samtools_dir = 'samtools'")
3348 (string-append "samtools_dir = '"
3349 (assoc-ref inputs "htslib")
3350 "'"))
3351 (("^findStaticOrShared\\('bam', hts_lib")
3352 (string-append "findStaticOrShared('bam', '"
3353 (assoc-ref inputs "samtools")
3354 "/lib'"))
3355 ;; Do not distribute README.
3356 (("^env\\.Install\\(idir_prefix, 'README\\.md'\\)") ""))
3357 #t))
8fd790eb
BW		 3358 (delete 'configure)
3359 (replace 'build
3360 (lambda* (#:key inputs outputs #:allow-other-keys)
3361 (mkdir (assoc-ref outputs "out"))
3362 (zero? (system* "scons"
3363 (string-append
3364 "PREFIX="
3365 (assoc-ref outputs "out"))
8fd790eb
BW		 3366 (string-append
3367 "BOOST_ROOT="
3368 (assoc-ref inputs "boost"))
3369 "install"))))
45469ebe 3370 ;; Check and install are carried out during build phase.
8fd790eb
BW		 3371 (delete 'check)
3372 (delete 'install))))
3373 (inputs
3374 `(("zlib" ,zlib)
3375 ("perl" ,perl)
3376 ("samtools" ,samtools)
3377 ("htslib" ,htslib)
3378 ("boost" ,boost)))
3379 (native-inputs
3380 `(("scons" ,scons)))
3381 (home-page "https://bitbucket.org/berkeleylab/metabat")
3382 (synopsis
3383 "Reconstruction of single genomes from complex microbial communities")
3384 (description
3385 "Grouping large genomic fragments assembled from shotgun metagenomic
3386sequences to deconvolute complex microbial communities, or metagenome binning,
3387enables the study of individual organisms and their interactions. MetaBAT is
3388an automated metagenome binning software, which integrates empirical
3389probabilistic distances of genome abundance and tetranucleotide frequency.")
3390 (license (license:non-copyleft "file://license.txt"
2c3eb4b8 3391 "See license.txt in the distribution.")))))
8fd790eb 3392
318c0aee
MB		 3393(define-public minced
3394 (package
3395 (name "minced")
3396 (version "0.2.0")
3397 (source (origin
3398 (method url-fetch)
3399 (uri (string-append
3400 "https://github.com/ctSkennerton/minced/archive/"
3401 version ".tar.gz"))
3402 (file-name (string-append name "-" version ".tar.gz"))
3403 (sha256
3404 (base32
3405 "0wxmlsapxfpxfd3ps9636h7i2xy6la8i42mwh0j2lsky63h63jp1"))))
3406 (build-system gnu-build-system)
3407 (arguments
3408 `(#:test-target "test"
3409 #:phases
3410 (modify-phases %standard-phases
3411 (delete 'configure)
3412 (add-before 'check 'fix-test
3413 (lambda _
3414 ;; Fix test for latest version.
3415 (substitute* "t/Aquifex_aeolicus_VF5.expected"
3416 (("minced:0.1.6") "minced:0.2.0"))
3417 #t))
3418 (replace 'install ; No install target.
3419 (lambda* (#:key inputs outputs #:allow-other-keys)
3420 (let* ((out (assoc-ref outputs "out"))
3421 (bin (string-append out "/bin"))
3422 (wrapper (string-append bin "/minced")))
3423 ;; Minced comes with a wrapper script that tries to figure out where
3424 ;; it is located before running the JAR. Since these paths are known
3425 ;; to us, we build our own wrapper to avoid coreutils dependency.
3426 (install-file "minced.jar" bin)
3427 (with-output-to-file wrapper
3428 (lambda _
3429 (display
3430 (string-append
3431 "#!" (assoc-ref inputs "bash") "/bin/sh\n\n"
3432 (assoc-ref inputs "jre") "/bin/java -jar "
3433 bin "/minced.jar \"$@\"\n"))))
3434 (chmod wrapper #o555)))))))
3435 (native-inputs
3436 `(("jdk" ,icedtea "jdk")))
3437 (inputs
3438 `(("bash" ,bash)
3439 ("jre" ,icedtea "out")))
3440 (home-page "https://github.com/ctSkennerton/minced")
3441 (synopsis "Mining CRISPRs in Environmental Datasets")
3442 (description
3443 "MinCED is a program to find Clustered Regularly Interspaced Short
3444Palindromic Repeats (CRISPRs) in DNA sequences. It can be used for
3445unassembled metagenomic reads, but is mainly designed for full genomes and
3446assembled metagenomic sequence.")
3447 (license license:gpl3+)))
3448
ddd82e0e
RW		 3449(define-public miso
3450 (package
3451 (name "miso")
3452 (version "0.5.3")
3453 (source (origin
3454 (method url-fetch)
3455 (uri (string-append
86517de6 3456 "https://pypi.python.org/packages/source/m/misopy/misopy-"
ddd82e0e
RW		 3457 version ".tar.gz"))
3458 (sha256
3459 (base32
3460 "0x446867az8ir0z8c1vjqffkp0ma37wm4sylixnkhgawllzx8v5w"))
3461 (modules '((guix build utils)))
ddd82e0e
RW		 3462 (snippet
3463 '(substitute* "setup.py"
0ec8b206
RW		 3464 ;; Use setuptools, or else the executables are not
3465 ;; installed.
3466 (("distutils.core") "setuptools")
3467 ;; use "gcc" instead of "cc" for compilation
ddd82e0e
RW		 3468 (("^defines")
3469 "cc.set_executables(
3470compiler='gcc',
3471compiler_so='gcc',
3472linker_exe='gcc',
3473linker_so='gcc -shared'); defines")))))
3474 (build-system python-build-system)
3475 (arguments
3476 `(#:python ,python-2 ; only Python 2 is supported
3477 #:tests? #f)) ; no "test" target
3478 (inputs
3479 `(("samtools" ,samtools)
3480 ("python-numpy" ,python2-numpy)
3481 ("python-pysam" ,python2-pysam)
3482 ("python-scipy" ,python2-scipy)
3483 ("python-matplotlib" ,python2-matplotlib)))
3484 (native-inputs
f3b98f4f
HG		 3485 `(("python-mock" ,python2-mock) ;for tests
3486 ("python-pytz" ,python2-pytz))) ;for tests
ddd82e0e
RW		 3487 (home-page "http://genes.mit.edu/burgelab/miso/index.html")
3488 (synopsis "Mixture of Isoforms model for RNA-Seq isoform quantitation")
3489 (description
3490 "MISO (Mixture-of-Isoforms) is a probabilistic framework that quantitates
3491the expression level of alternatively spliced genes from RNA-Seq data, and
3492identifies differentially regulated isoforms or exons across samples. By
3493modeling the generative process by which reads are produced from isoforms in
3494RNA-Seq, the MISO model uses Bayesian inference to compute the probability
3495that a read originated from a particular isoform.")
3496 (license license:gpl2)))
3497
324efb88
BW		 3498(define-public muscle
3499 (package
3500 (name "muscle")
3501 (version "3.8.1551")
3502 (source (origin
3503 (method url-fetch/tarbomb)
3504 (file-name (string-append name "-" version))
3505 (uri (string-append
3506 "http://www.drive5.com/muscle/muscle_src_"
3507 version ".tar.gz"))
3508 (sha256
3509 (base32
3510 "0bj8kj7sdizy3987zx6w7axihk40fk8rn76mpbqqjcnd64i5a367"))))
3511 (build-system gnu-build-system)
3512 (arguments
3513 `(#:make-flags (list "LDLIBS = -lm")
3514 #:phases
3515 (modify-phases %standard-phases
3516 (delete 'configure)
3517 (replace 'check
3518 ;; There are no tests, so just test if it runs.
3519 (lambda _ (zero? (system* "./muscle" "-version"))))
3520 (replace 'install
3521 (lambda* (#:key outputs #:allow-other-keys)
3522 (let* ((out (assoc-ref outputs "out"))
3523 (bin (string-append out "/bin")))
3524 (install-file "muscle" bin)))))))
3525 (home-page "http://www.drive5.com/muscle")
3526 (synopsis "Multiple sequence alignment program")
3527 (description
3528 "MUSCLE aims to be a fast and accurate multiple sequence alignment
3529program for nucleotide and protein sequences.")
3530 ;; License information found in 'muscle -h' and usage.cpp.
3531 (license license:public-domain)))
3532
99268755
BW		 3533(define-public newick-utils
3534 ;; There are no recent releases so we package from git.
3535 (let ((commit "da121155a977197cab9fbb15953ca1b40b11eb87"))
3536 (package
3537 (name "newick-utils")
3538 (version (string-append "1.6-1." (string-take commit 8)))
3539 (source (origin
3540 (method git-fetch)
3541 (uri (git-reference
3542 (url "https://github.com/tjunier/newick_utils.git")
3543 (commit commit)))
3544 (file-name (string-append name "-" version "-checkout"))
3545 (sha256
3546 (base32
3547 "1hkw21rq1mwf7xp0rmbb2gqc0i6p11108m69i7mr7xcjl268pxnb"))))
3548 (build-system gnu-build-system)
3549 (arguments
3550 `(#:phases
3551 (modify-phases %standard-phases
3552 (add-after 'unpack 'autoconf
3553 (lambda _ (zero? (system* "autoreconf" "-vif")))))))
3554 (inputs
3555 ;; XXX: TODO: Enable Lua and Guile bindings.
3556 ;; https://github.com/tjunier/newick_utils/issues/13
3557 `(("libxml2" ,libxml2)
3558 ("flex" ,flex)
3559 ("bison" ,bison)))
3560 (native-inputs
3561 `(("autoconf" ,autoconf)
3562 ("automake" ,automake)
3563 ("libtool" ,libtool)))
3564 (synopsis "Programs for working with newick format phylogenetic trees")
3565 (description
3566 "Newick-utils is a suite of utilities for processing phylogenetic trees
3567in Newick format. Functions include re-rooting, extracting subtrees,
3568trimming, pruning, condensing, drawing (ASCII graphics or SVG).")
3569 (home-page "https://github.com/tjunier/newick_utils")
3570 (license license:bsd-3))))
3571
1e44cf8b
BW		 3572(define-public orfm
3573 (package
3574 (name "orfm")
ced1c496 3575 (version "0.6.1")
1e44cf8b
BW		 3576 (source (origin
3577 (method url-fetch)
3578 (uri (string-append
3579 "https://github.com/wwood/OrfM/releases/download/v"
3580 version "/orfm-" version ".tar.gz"))
3581 (sha256
3582 (base32
ced1c496 3583 "19hwp13n82isdvk16710l9m35cmzf0q3fsrcn3r8c5r67biiz39s"))))
1e44cf8b
BW		 3584 (build-system gnu-build-system)
3585 (inputs `(("zlib" ,zlib)))
6b6f7d6a
BW		 3586 (native-inputs
3587 `(("ruby-bio-commandeer" ,ruby-bio-commandeer)
3588 ("ruby-rspec" ,ruby-rspec)
3589 ("ruby" ,ruby)))
1e44cf8b
BW		 3590 (synopsis "Simple and not slow open reading frame (ORF) caller")
3591 (description
6b6f7d6a 3592 "An ORF caller finds stretches of DNA that, when translated, are not
1e44cf8b
BW		 3593interrupted by stop codons. OrfM finds and prints these ORFs.")
3594 (home-page "https://github.com/wwood/OrfM")
3595 (license license:lgpl3+)))
3596
19ee9201
RW		 3597(define-public python2-pbcore
3598 (package
3599 (name "python2-pbcore")
e301bfc8 3600 (version "1.2.10")
19ee9201
RW		 3601 (source (origin
3602 (method url-fetch)
ddb83129 3603 (uri (pypi-uri "pbcore" version))
19ee9201
RW		 3604 (sha256
3605 (base32
e301bfc8 3606 "1kjmv891d6qbpp4shhhvkl02ff4q5xlpnls2513sm2cjcrs52f1i"))))
19ee9201
RW		 3607 (build-system python-build-system)
3608 (arguments `(#:python ,python-2)) ; pbcore requires Python 2.7
de5bc890 3609 (propagated-inputs
19ee9201
RW		 3610 `(("python-cython" ,python2-cython)
3611 ("python-numpy" ,python2-numpy)
3612 ("python-pysam" ,python2-pysam)
3613 ("python-h5py" ,python2-h5py)))
3614 (native-inputs
de5bc890
HG		 3615 `(("python-nose" ,python2-nose)
3616 ("python-sphinx" ,python2-sphinx)
3617 ("python-pyxb" ,python2-pyxb)))
19ee9201
RW		 3618 (home-page "http://pacificbiosciences.github.io/pbcore/")
3619 (synopsis "Library for reading and writing PacBio data files")
3620 (description
3621 "The pbcore package provides Python APIs for interacting with PacBio data
3622files and writing bioinformatics applications.")
3623 (license license:bsd-3)))
3624
c61fe02c
RW		 3625(define-public python2-warpedlmm
3626 (package
3627 (name "python2-warpedlmm")
3628 (version "0.21")
3629 (source
3630 (origin
3631 (method url-fetch)
3632 (uri (string-append
3633 "https://pypi.python.org/packages/source/W/WarpedLMM/WarpedLMM-"
3634 version ".zip"))
3635 (sha256
3636 (base32
3637 "1agfz6zqa8nc6cw47yh0s3y14gkpa9wqazwcj7mwwj3ffnw39p3j"))))
3638 (build-system python-build-system)
3639 (arguments
54c85e12 3640 `(#:python ,python-2)) ; requires Python 2.7
c61fe02c
RW		 3641 (propagated-inputs
3642 `(("python-scipy" ,python2-scipy)
3643 ("python-numpy" ,python2-numpy)
3644 ("python-matplotlib" ,python2-matplotlib)
3645 ("python-fastlmm" ,python2-fastlmm)
3646 ("python-pandas" ,python2-pandas)
3647 ("python-pysnptools" ,python2-pysnptools)))
3648 (native-inputs
f3b98f4f 3649 `(("python-mock" ,python2-mock)
c61fe02c
RW		 3650 ("python-nose" ,python2-nose)
3651 ("unzip" ,unzip)))
3652 (home-page "https://github.com/PMBio/warpedLMM")
3653 (synopsis "Implementation of warped linear mixed models")
3654 (description
3655 "WarpedLMM is a Python implementation of the warped linear mixed model,
3656which automatically learns an optimal warping function (or transformation) for
3657the phenotype as it models the data.")
3658 (license license:asl2.0)))
3659
2c16316e 3660(define-public pbtranscript-tofu
698bd297 3661 (let ((commit "8f5467fe6a4472bcfb4226c8720993c8507adfe4"))
2c16316e
RW		 3662 (package
3663 (name "pbtranscript-tofu")
698bd297 3664 (version (string-append "2.2.3." (string-take commit 7)))
2c16316e
RW		 3665 (source (origin
3666 (method git-fetch)
3667 (uri (git-reference
3668 (url "https://github.com/PacificBiosciences/cDNA_primer.git")
3669 (commit commit)))
9a067efd 3670 (file-name (string-append name "-" version "-checkout"))
2c16316e
RW		 3671 (sha256
3672 (base32
9a067efd
RW		 3673 "1lgnpi35ihay42qx0b6yl3kkgra723i413j33kvs0kvs61h82w0f"))
3674 (modules '((guix build utils)))
3675 (snippet
3676 '(begin
3677 ;; remove bundled Cython sources
3678 (delete-file "pbtranscript-tofu/pbtranscript/Cython-0.20.1.tar.gz")
3679 #t))))
2c16316e
RW		 3680 (build-system python-build-system)
3681 (arguments
3682 `(#:python ,python-2
2c16316e 3683 #:phases
9a067efd
RW		 3684 (modify-phases %standard-phases
3685 (add-after 'unpack 'enter-directory
3686 (lambda _
3687 (chdir "pbtranscript-tofu/pbtranscript/")
3688 #t))
3689 ;; With setuptools version 18.0 and later this setup.py hack causes
3690 ;; a build error, so we disable it.
3691 (add-after 'enter-directory 'patch-setuppy
3692 (lambda _
3693 (substitute* "setup.py"
3694 (("if 'setuptools.extension' in sys.modules:")
3695 "if False:"))
3696 #t)))))
2c16316e 3697 (inputs
9a067efd 3698 `(("python-numpy" ,python2-numpy)
2c16316e 3699 ("python-bx-python" ,python2-bx-python)
c5372108
RW		 3700 ("python-networkx" ,python2-networkx)
3701 ("python-scipy" ,python2-scipy)
9a067efd
RW		 3702 ("python-pbcore" ,python2-pbcore)
3703 ("python-h5py" ,python2-h5py)))
2c16316e 3704 (native-inputs
9a067efd 3705 `(("python-cython" ,python2-cython)
f3b98f4f 3706 ("python-nose" ,python2-nose)))
2c16316e
RW		 3707 (home-page "https://github.com/PacificBiosciences/cDNA_primer")
3708 (synopsis "Analyze transcriptome data generated with the Iso-Seq protocol")
3709 (description
3710 "pbtranscript-tofu contains scripts to analyze transcriptome data
3711generated using the PacBio Iso-Seq protocol.")
3712 (license license:bsd-3))))
3713
024130d2
BW		 3714(define-public prank
3715 (package
3716 (name "prank")
3717 (version "150803")
3718 (source (origin
3719 (method url-fetch)
3720 (uri (string-append
3721 "http://wasabiapp.org/download/prank/prank.source."
3722 version ".tgz"))
3723 (sha256
3724 (base32
3725 "0am4z94fs3w2n5xpfls9zda61vq7qqz4q2i7b9hlsxz5q4j3kfm4"))))
3726 (build-system gnu-build-system)
3727 (arguments
3728 `(#:phases
3729 (modify-phases %standard-phases
3730 (add-after 'unpack 'enter-src-dir
3731 (lambda _
3732 (chdir "src")
3733 #t))
62d00095
EF		 3734 (add-after 'unpack 'remove-m64-flag
3735 ;; Prank will build with the correct 'bit-ness' without this flag
3736 ;; and this allows building on 32-bit machines.
3737 (lambda _ (substitute* "src/Makefile"
3738 (("-m64") ""))
3739 #t))
024130d2
BW		 3740 (delete 'configure)
3741 (replace 'install
3742 (lambda* (#:key outputs #:allow-other-keys)
3743 (let* ((out (assoc-ref outputs "out"))
3744 (bin (string-append out "/bin"))
3745 (man (string-append out "/share/man/man1"))
3746 (path (string-append
3747 (assoc-ref %build-inputs "mafft") "/bin:"
3748 (assoc-ref %build-inputs "exonerate") "/bin:"
3749 (assoc-ref %build-inputs "bppsuite") "/bin")))
3750 (install-file "prank" bin)
3751 (wrap-program (string-append bin "/prank")
3752 `("PATH" ":" prefix (,path)))
3753 (install-file "prank.1" man))
3754 #t)))))
3755 (inputs
3756 `(("mafft" ,mafft)
3757 ("exonerate" ,exonerate)
3758 ("bppsuite" ,bppsuite)))
3759 (home-page "http://wasabiapp.org/software/prank/")
3760 (synopsis "Probabilistic multiple sequence alignment program")
3761 (description
3762 "PRANK is a probabilistic multiple sequence alignment program for DNA,
3763codon and amino-acid sequences. It is based on a novel algorithm that treats
3764insertions correctly and avoids over-estimation of the number of deletion
3765events. In addition, PRANK borrows ideas from maximum likelihood methods used
3766in phylogenetics and correctly takes into account the evolutionary distances
3767between sequences. Lastly, PRANK allows for defining a potential structure
3768for sequences to be aligned and then, simultaneously with the alignment,
3769predicts the locations of structural units in the sequences.")
3770 (license license:gpl2+)))
3771
31a9d653
BW		 3772(define-public proteinortho
3773 (package
3774 (name "proteinortho")
3775 (version "5.15")
3776 (source
3777 (origin
3778 (method url-fetch)
3779 (uri
3780 (string-append
3781 "http://www.bioinf.uni-leipzig.de/Software/proteinortho/proteinortho_v"
3782 version "_src.tar.gz"))
3783 (sha256
3784 (base32
3785 "05wacnnbx56avpcwhzlcf6b7s77swcpv3qnwz5sh1z54i51gg2ki"))))
3786 (build-system gnu-build-system)
3787 (arguments
3788 `(#:test-target "test"
3789 #:phases
3790 (modify-phases %standard-phases
3791 (replace 'configure
3792 ;; There is no configure script, so we modify the Makefile directly.
3793 (lambda* (#:key outputs #:allow-other-keys)
3794 (substitute* "Makefile"
3795 (("INSTALLDIR=.*")
3796 (string-append
3797 "INSTALLDIR=" (assoc-ref outputs "out") "/bin\n")))
3798 #t))
3799 (add-before 'install 'make-install-directory
3800 ;; The install directory is not created during 'make install'.
3801 (lambda* (#:key outputs #:allow-other-keys)
3802 (mkdir-p (string-append (assoc-ref outputs "out") "/bin"))
3803 #t))
3804 (add-after 'install 'wrap-programs
3805 (lambda* (#:key inputs outputs #:allow-other-keys)
3806 (let* ((path (getenv "PATH"))
3807 (out (assoc-ref outputs "out"))
3808 (binary (string-append out "/bin/proteinortho5.pl")))
3809 (wrap-program binary `("PATH" ":" prefix (,path))))
3810 #t)))))
3811 (inputs
3812 `(("perl" ,perl)
3813 ("python" ,python-2)
3814 ("blast+" ,blast+)))
3815 (home-page "http://www.bioinf.uni-leipzig.de/Software/proteinortho")
3816 (synopsis "Detect orthologous genes across species")
3817 (description
3818 "Proteinortho is a tool to detect orthologous genes across different
3819species. For doing so, it compares similarities of given gene sequences and
3820clusters them to find significant groups. The algorithm was designed to handle
3821large-scale data and can be applied to hundreds of species at once.")
3822 (license license:gpl2+)))
3823
846e3409
RW		 3824(define-public pyicoteo
3825 (package
3826 (name "pyicoteo")
3827 (version "2.0.7")
3828 (source
3829 (origin
3830 (method url-fetch)
3831 (uri (string-append "https://bitbucket.org/regulatorygenomicsupf/"
3832 "pyicoteo/get/v" version ".tar.bz2"))
3833 (file-name (string-append name "-" version ".tar.bz2"))
3834 (sha256
3835 (base32
3836 "0d6087f29xp8wxwlj111c3sylli98n0l8ry58c51ixzq0zfm50wa"))))
3837 (build-system python-build-system)
3838 (arguments
3839 `(#:python ,python-2 ; does not work with Python 3
3840 #:tests? #f)) ; there are no tests
3841 (inputs
3842 `(("python2-matplotlib" ,python2-matplotlib)))
3843 (home-page "https://bitbucket.org/regulatorygenomicsupf/pyicoteo")
3844 (synopsis "Analyze high-throughput genetic sequencing data")
3845 (description
3846 "Pyicoteo is a suite of tools for the analysis of high-throughput genetic
3847sequencing data. It works with genomic coordinates. There are currently six
3848different command-line tools:
3849
3850@enumerate
3851@item pyicoregion: for generating exploratory regions automatically;
3852@item pyicoenrich: for differential enrichment between two conditions;
3853@item pyicoclip: for calling CLIP-Seq peaks without a control;
3854@item pyicos: for genomic coordinates manipulation;
3855@item pyicoller: for peak calling on punctuated ChIP-Seq;
3856@item pyicount: to count how many reads from N experiment files overlap in a
3857 region file;
3858@item pyicotrocol: to combine operations from pyicoteo.
3859@end enumerate\n")
3860 (license license:gpl3+)))
3861
af860475
BW		 3862(define-public prodigal
3863 (package
3864 (name "prodigal")
e70f7a23 3865 (version "2.6.3")
af860475
BW		 3866 (source (origin
3867 (method url-fetch)
3868 (uri (string-append
3869 "https://github.com/hyattpd/Prodigal/archive/v"
3870 version ".tar.gz"))
3871 (file-name (string-append name "-" version ".tar.gz"))
3872 (sha256
3873 (base32
e70f7a23 3874 "17srxkqd3jc77xk15pfbgg1a9xahqg7337w95mrsia7mpza4l2c9"))))
af860475
BW		 3875 (build-system gnu-build-system)
3876 (arguments
3877 `(#:tests? #f ;no check target
3878 #:make-flags (list (string-append "INSTALLDIR="
3879 (assoc-ref %outputs "out")
3880 "/bin"))
3881 #:phases
3882 (modify-phases %standard-phases
3883 (delete 'configure))))
3884 (home-page "http://prodigal.ornl.gov")
3885 (synopsis "Protein-coding gene prediction for Archaea and Bacteria")
3886 (description
3887 "Prodigal runs smoothly on finished genomes, draft genomes, and
3888metagenomes, providing gene predictions in GFF3, Genbank, or Sequin table
3889format. It runs quickly, in an unsupervised fashion, handles gaps, handles
3890partial genes, and identifies translation initiation sites.")
3891 (license license:gpl3+)))
608dd932 3892
ceb62d54
BW		 3893(define-public roary
3894 (package
3895 (name "roary")
5e0a0f42 3896 (version "3.7.0")
ceb62d54
BW		 3897 (source
3898 (origin
3899 (method url-fetch)
3900 (uri (string-append
3901 "mirror://cpan/authors/id/A/AJ/AJPAGE/Bio-Roary-"
3902 version ".tar.gz"))
3903 (sha256
3904 (base32
5e0a0f42 3905 "0x2hpb3nfsc6x2nq1788w0fhqfzc7cn2dp4xwyva9m3k6xlz0m43"))))
ceb62d54
BW		 3906 (build-system perl-build-system)
3907 (arguments
3908 `(#:phases
3909 (modify-phases %standard-phases
3910 (delete 'configure)
3911 (delete 'build)
3912 (replace 'check
3913 (lambda _
3914 ;; The tests are not run by default, so we run each test file
3915 ;; directly.
3916 (setenv "PATH" (string-append (getcwd) "/bin" ":"
3917 (getenv "PATH")))
3918 (setenv "PERL5LIB" (string-append (getcwd) "/lib" ":"
3919 (getenv "PERL5LIB")))
3920 (zero? (length (filter (lambda (file)
3921 (display file)(display "\n")
3922 (not (zero? (system* "perl" file))))
3923 (find-files "t" ".*\\.t$"))))))
3924 (replace 'install
3925 ;; There is no 'install' target in the Makefile.
3926 (lambda* (#:key outputs #:allow-other-keys)
3927 (let* ((out (assoc-ref outputs "out"))
3928 (bin (string-append out "/bin"))
3929 (perl (string-append out "/lib/perl5/site_perl"))
3930 (roary-plots "contrib/roary_plots"))
3931 (mkdir-p bin)
3932 (mkdir-p perl)
3933 (copy-recursively "bin" bin)
3934 (copy-recursively "lib" perl)
3935 #t)))
3936 (add-after 'install 'wrap-programs
3937 (lambda* (#:key inputs outputs #:allow-other-keys)
3938 (let* ((out (assoc-ref outputs "out"))
3939 (perl5lib (getenv "PERL5LIB"))
3940 (path (getenv "PATH")))
3941 (for-each (lambda (prog)
3942 (let ((binary (string-append out "/" prog)))
3943 (wrap-program binary
3944 `("PERL5LIB" ":" prefix
3945 (,(string-append perl5lib ":" out
3946 "/lib/perl5/site_perl"))))
3947 (wrap-program binary
3948 `("PATH" ":" prefix
3949 (,(string-append path ":" out "/bin"))))))
3950 (find-files "bin" ".*[^R]$"))
3951 (let ((file
3952 (string-append out "/bin/roary-create_pan_genome_plots.R"))
3953 (r-site-lib (getenv "R_LIBS_SITE"))
3954 (coreutils-path
3955 (string-append (assoc-ref inputs "coreutils") "/bin")))
3956 (wrap-program file
3957 `("R_LIBS_SITE" ":" prefix
3958 (,(string-append r-site-lib ":" out "/site-library/"))))
3959 (wrap-program file
3960 `("PATH" ":" prefix
3961 (,(string-append coreutils-path ":" out "/bin"))))))
3962 #t)))))
3963 (native-inputs
3964 `(("perl-env-path" ,perl-env-path)
3965 ("perl-test-files" ,perl-test-files)
3966 ("perl-test-most" ,perl-test-most)
3967 ("perl-test-output" ,perl-test-output)))
3968 (inputs
3969 `(("perl-array-utils" ,perl-array-utils)
3970 ("bioperl" ,bioperl-minimal)
3971 ("perl-exception-class" ,perl-exception-class)
3972 ("perl-file-find-rule" ,perl-file-find-rule)
3973 ("perl-file-grep" ,perl-file-grep)
3974 ("perl-file-slurper" ,perl-file-slurper)
3975 ("perl-file-which" ,perl-file-which)
3976 ("perl-graph" ,perl-graph)
3977 ("perl-graph-readwrite" ,perl-graph-readwrite)
3978 ("perl-log-log4perl" ,perl-log-log4perl)
3979 ("perl-moose" ,perl-moose)
3980 ("perl-perlio-utf8_strict" ,perl-perlio-utf8_strict)
3981 ("perl-text-csv" ,perl-text-csv)
3982 ("bedtools" ,bedtools)
3983 ("cd-hit" ,cd-hit)
3984 ("blast+" ,blast+)
3985 ("mcl" ,mcl)
3986 ("parallel" ,parallel)
3987 ("prank" ,prank)
3988 ("mafft" ,mafft)
3989 ("fasttree" ,fasttree)
3990 ("grep" ,grep)
3991 ("sed" ,sed)
3992 ("gawk" ,gawk)
3993 ("r" ,r)
3994 ("r-ggplot2" ,r-ggplot2)
3995 ("coreutils" ,coreutils)))
3996 (home-page "http://sanger-pathogens.github.io/Roary")
3997 (synopsis "High speed stand-alone pan genome pipeline")
3998 (description
3999 "Roary is a high speed stand alone pan genome pipeline, which takes
4000annotated assemblies in GFF3 format (produced by the Prokka program) and
4001calculates the pan genome. Using a standard desktop PC, it can analyse
4002datasets with thousands of samples, without compromising the quality of the
4003results. 128 samples can be analysed in under 1 hour using 1 GB of RAM and a
4004single processor. Roary is not intended for metagenomics or for comparing
4005extremely diverse sets of genomes.")
4006 (license license:gpl3)))
4007
608dd932
BW		 4008(define-public raxml
4009 (package
4010 (name "raxml")
4011 (version "8.2.9")
4012 (source
4013 (origin
4014 (method url-fetch)
4015 (uri
4016 (string-append
4017 "https://github.com/stamatak/standard-RAxML/archive/v"
4018 version ".tar.gz"))
4019 (file-name (string-append name "-" version ".tar.gz"))
4020 (sha256
4021 (base32
4022 "1pv8p2fy67y21a9y4cm7xpvxqjwz2v4201flfjshdq1p8j52rqf7"))))
4023 (build-system gnu-build-system)
4024 (arguments
4025 `(#:tests? #f ; There are no tests.
4026 ;; Use 'standard' Makefile rather than SSE or AVX ones.
4027 #:make-flags (list "-f" "Makefile.HYBRID.gcc")
4028 #:phases
4029 (modify-phases %standard-phases
4030 (delete 'configure)
4031 (replace 'install
4032 (lambda* (#:key outputs #:allow-other-keys)
4033 (let* ((out (assoc-ref outputs "out"))
4034 (bin (string-append out "/bin"))
4035 (executable "raxmlHPC-HYBRID"))
4036 (install-file executable bin)
4037 (symlink (string-append bin "/" executable) "raxml"))
4038 #t)))))
4039 (inputs
4040 `(("openmpi" ,openmpi)))
4041 (home-page "http://sco.h-its.org/exelixis/web/software/raxml/index.html")
4042 (synopsis "Randomized Axelerated Maximum Likelihood phylogenetic trees")
4043 (description
4044 "RAxML is a tool for phylogenetic analysis and post-analysis of large
4045phylogenies.")
4046 (license license:gpl2+)))
af860475 4047
66e3eff1
RW		 4048(define-public rsem
4049 (package
4050 (name "rsem")
4051 (version "1.2.20")
4052 (source
4053 (origin
4054 (method url-fetch)
4055 (uri
4056 (string-append "http://deweylab.biostat.wisc.edu/rsem/src/rsem-"
4057 version ".tar.gz"))
4058 (sha256
4059 (base32 "0nzdc0j0hjllhsd5f2xli95dafm3nawskigs140xzvjk67xh0r9q"))
fc1adab1 4060 (patches (search-patches "rsem-makefile.patch"))
66e3eff1
RW		 4061 (modules '((guix build utils)))
4062 (snippet
4063 '(begin
4064 ;; remove bundled copy of boost
4065 (delete-file-recursively "boost")
4066 #t))))
4067 (build-system gnu-build-system)
4068 (arguments
4069 `(#:tests? #f ;no "check" target
4070 #:phases
4071 (modify-phases %standard-phases
4072 ;; No "configure" script.
4073 ;; Do not build bundled samtools library.
4074 (replace 'configure
4075 (lambda _
4076 (substitute* "Makefile"
4077 (("^all : sam/libbam.a") "all : "))
4078 #t))
4079 (replace 'install
4080 (lambda* (#:key outputs #:allow-other-keys)
4081 (let* ((out (string-append (assoc-ref outputs "out")))
4082 (bin (string-append out "/bin/"))
4083 (perl (string-append out "/lib/perl5/site_perl")))
4084 (mkdir-p bin)
4085 (mkdir-p perl)
4086 (for-each (lambda (file)
4087 (copy-file file
4088 (string-append bin (basename file))))
4089 (find-files "." "rsem-.*"))
4090 (copy-file "rsem_perl_utils.pm"
4091 (string-append perl "/rsem_perl_utils.pm")))
4092 #t))
4093 (add-after
4094 'install 'wrap-program
4095 (lambda* (#:key outputs #:allow-other-keys)
4096 (let ((out (assoc-ref outputs "out")))
4097 (for-each (lambda (prog)
4098 (wrap-program (string-append out "/bin/" prog)
4099 `("PERL5LIB" ":" prefix
4100 (,(string-append out "/lib/perl5/site_perl")))))
4101 '("rsem-plot-transcript-wiggles"
4102 "rsem-calculate-expression"
4103 "rsem-generate-ngvector"
4104 "rsem-run-ebseq"
4105 "rsem-prepare-reference")))
4106 #t)))))
4107 (inputs
4108 `(("boost" ,boost)
4109 ("ncurses" ,ncurses)
4110 ("r" ,r)
4111 ("perl" ,perl)
4112 ("samtools" ,samtools-0.1)
4113 ("zlib" ,zlib)))
4114 (home-page "http://deweylab.biostat.wisc.edu/rsem/")
4115 (synopsis "Estimate gene expression levels from RNA-Seq data")
4116 (description
4117 "RSEM is a software package for estimating gene and isoform expression
4118levels from RNA-Seq data. The RSEM package provides a user-friendly
4119interface, supports threads for parallel computation of the EM algorithm,
4120single-end and paired-end read data, quality scores, variable-length reads and
4121RSPD estimation. In addition, it provides posterior mean and 95% credibility
4122interval estimates for expression levels. For visualization, it can generate
4123BAM and Wiggle files in both transcript-coordinate and genomic-coordinate.")
4124 (license license:gpl3+)))
4125
8622a072
RW		 4126(define-public rseqc
4127 (package
4128 (name "rseqc")
4129 (version "2.6.1")
4130 (source
4131 (origin
4132 (method url-fetch)
4133 (uri
4134 (string-append "mirror://sourceforge/rseqc/"
de67e922 4135 "RSeQC-" version ".tar.gz"))
8622a072 4136 (sha256
8214b7fb 4137 (base32 "15ly0254yi032qzkdplg00q144qfdsd986gh62829rl5bkxhj330"))
8622a072
RW		 4138 (modules '((guix build utils)))
4139 (snippet
4140 '(begin
4141 ;; remove bundled copy of pysam
4142 (delete-file-recursively "lib/pysam")
4143 (substitute* "setup.py"
4144 ;; remove dependency on outdated "distribute" module
4145 (("^from distribute_setup import use_setuptools") "")
4146 (("^use_setuptools\\(\\)") "")
4147 ;; do not use bundled copy of pysam
4148 (("^have_pysam = False") "have_pysam = True"))))))
4149 (build-system python-build-system)
4150 (arguments `(#:python ,python-2))
4151 (inputs
4152 `(("python-cython" ,python2-cython)
4153 ("python-pysam" ,python2-pysam)
4154 ("python-numpy" ,python2-numpy)
8622a072
RW		 4155 ("zlib" ,zlib)))
4156 (native-inputs
4157 `(("python-nose" ,python2-nose)))
4158 (home-page "http://rseqc.sourceforge.net/")
4159 (synopsis "RNA-seq quality control package")
4160 (description
4161 "RSeQC provides a number of modules that can comprehensively evaluate
4162high throughput sequence data, especially RNA-seq data. Some basic modules
4163inspect sequence quality, nucleotide composition bias, PCR bias and GC bias,
4164while RNA-seq specific modules evaluate sequencing saturation, mapped reads
4165distribution, coverage uniformity, strand specificity, etc.")
4166 (license license:gpl3+)))
4167
ec946638
RW		 4168(define-public seek
4169 ;; There are no release tarballs. According to the installation
4170 ;; instructions at http://seek.princeton.edu/installation.jsp, the latest
4171 ;; stable release is identified by this changeset ID.
4172 (let ((changeset "2329130")
4173 (revision "1"))
4174 (package
4175 (name "seek")
4176 (version (string-append "0-" revision "." changeset))
4177 (source (origin
4178 (method hg-fetch)
4179 (uri (hg-reference
4180 (url "https://bitbucket.org/libsleipnir/sleipnir")
4181 (changeset changeset)))
4182 (sha256
4183 (base32
4184 "0qrvilwh18dpbhkf92qvxbmay0j75ra3jg2wrhz67gf538zzphsx"))))
4185 (build-system gnu-build-system)
4186 (arguments
4187 `(#:modules ((srfi srfi-1)
4188 (guix build gnu-build-system)
4189 (guix build utils))
4190 #:phases
4191 (let ((dirs '("SeekMiner"
4192 "SeekEvaluator"
4193 "SeekPrep"
4194 "Distancer"
4195 "Data2DB"
4196 "PCL2Bin")))
4197 (modify-phases %standard-phases
4198 (add-before 'configure 'bootstrap
4199 (lambda _
4200 (zero? (system* "bash" "gen_auto"))))
4201 (add-after 'build 'build-additional-tools
4202 (lambda* (#:key make-flags #:allow-other-keys)
4203 (every (lambda (dir)
4204 (with-directory-excursion (string-append "tools/" dir)
4205 (zero? (apply system* "make" make-flags))))
4206 dirs)))
4207 (add-after 'install 'install-additional-tools
4208 (lambda* (#:key make-flags #:allow-other-keys)
4209 (fold (lambda (dir result)
4210 (with-directory-excursion (string-append "tools/" dir)
4211 (and result
4212 (zero? (apply system*
4213 `("make" ,@make-flags "install"))))))
4214 #t dirs)))))))
4215 (inputs
4216 `(("gsl" ,gsl)
4217 ("boost" ,boost)
4218 ("libsvm" ,libsvm)
4219 ("readline" ,readline)
4220 ("gengetopt" ,gengetopt)
4221 ("log4cpp" ,log4cpp)))
4222 (native-inputs
4223 `(("autoconf" ,autoconf)
4224 ("automake" ,automake)
4225 ("perl" ,perl)))
4226 (home-page "http://seek.princeton.edu")
4227 (synopsis "Gene co-expression search engine")
4228 (description
4229 "SEEK is a computational gene co-expression search engine. SEEK provides
4230biologists with a way to navigate the massive human expression compendium that
4231now contains thousands of expression datasets. SEEK returns a robust ranking
4232of co-expressed genes in the biological area of interest defined by the user's
4233query genes. It also prioritizes thousands of expression datasets according
4234to the user's query of interest.")
4235 (license license:cc-by3.0))))
4236
4e10a221
RW		 4237(define-public samtools
4238 (package
4239 (name "samtools")
79b555ed 4240 (version "1.3.1")
4e10a221
RW		 4241 (source
4242 (origin
4243 (method url-fetch)
4244 (uri
de67e922 4245 (string-append "mirror://sourceforge/samtools/samtools/"
4e10a221
RW		 4246 version "/samtools-" version ".tar.bz2"))
4247 (sha256
4248 (base32
79b555ed 4249 "0znnnxc467jbf1as2dpskrjhfh8mbll760j6w6rdkwlwbqsp8gbc"))))
4e10a221
RW		 4250 (build-system gnu-build-system)
4251 (arguments
c4473411 4252 `(#:modules ((ice-9 ftw)
5bdda30b
RW		 4253 (ice-9 regex)
4254 (guix build gnu-build-system)
4255 (guix build utils))
c4473411
RW		 4256 #:make-flags (list (string-append "prefix=" (assoc-ref %outputs "out")))
4257 #:configure-flags (list "--with-ncurses")
4e10a221
RW		 4258 #:phases
4259 (alist-cons-after
c4473411
RW		 4260 'unpack 'patch-tests
4261 (lambda _
4262 (substitute* "test/test.pl"
4263 ;; The test script calls out to /bin/bash
4264 (("/bin/bash") (which "bash")))
4265 #t)
41dd7126
RW		 4266 (alist-cons-after
4267 'install 'install-library
4268 (lambda* (#:key outputs #:allow-other-keys)
4269 (let ((lib (string-append (assoc-ref outputs "out") "/lib")))
96c46210 4270 (install-file "libbam.a" lib)))
5bdda30b
RW		 4271 (alist-cons-after
4272 'install 'install-headers
4273 (lambda* (#:key outputs #:allow-other-keys)
4274 (let ((include (string-append (assoc-ref outputs "out")
4275 "/include/samtools/")))
5bdda30b 4276 (for-each (lambda (file)
96c46210 4277 (install-file file include))
5bdda30b
RW		 4278 (scandir "." (lambda (name) (string-match "\\.h$" name))))
4279 #t))
c4473411 4280 %standard-phases)))))
4e10a221
RW		 4281 (native-inputs `(("pkg-config" ,pkg-config)))
4282 (inputs `(("ncurses" ,ncurses)
4283 ("perl" ,perl)
4284 ("python" ,python)
4285 ("zlib" ,zlib)))
4286 (home-page "http://samtools.sourceforge.net")
4287 (synopsis "Utilities to efficiently manipulate nucleotide sequence alignments")
4288 (description
4289 "Samtools implements various utilities for post-processing nucleotide
4290sequence alignments in the SAM, BAM, and CRAM formats, including indexing,
4291variant calling (in conjunction with bcftools), and a simple alignment
4292viewer.")
4293 (license license:expat)))
d3517eda 4294
0b84a0aa
RW		 4295(define-public samtools-0.1
4296 ;; This is the most recent version of the 0.1 line of samtools. The input
4297 ;; and output formats differ greatly from that used and produced by samtools
4298 ;; 1.x and is still used in many bioinformatics pipelines.
4299 (package (inherit samtools)
4300 (version "0.1.19")
4301 (source
4302 (origin
4303 (method url-fetch)
4304 (uri
de67e922 4305 (string-append "mirror://sourceforge/samtools/samtools/"
0b84a0aa
RW		 4306 version "/samtools-" version ".tar.bz2"))
4307 (sha256
4308 (base32 "1m33xsfwz0s8qi45lylagfllqg7fphf4dr0780rsvw75av9wk06h"))))
4309 (arguments
2309ed68
RW		 4310 `(#:tests? #f ;no "check" target
4311 ,@(substitute-keyword-arguments (package-arguments samtools)
4312 ((#:make-flags flags)
4313 `(cons "LIBCURSES=-lncurses" ,flags))
4314 ((#:phases phases)
4315 `(modify-phases ,phases
4316 (replace 'install
4317 (lambda* (#:key outputs #:allow-other-keys)
4318 (let ((bin (string-append
4319 (assoc-ref outputs "out") "/bin")))
4320 (mkdir-p bin)
4321 (copy-file "samtools"
4322 (string-append bin "/samtools")))))
4323 (delete 'patch-tests)
4324 (delete 'configure))))))))
0b84a0aa 4325
fe4c37c2 4326(define-public mosaik
698bd297 4327 (let ((commit "5c25216d3522d6a33e53875cd76a6d65001e4e67"))
fe4c37c2
RW		 4328 (package
4329 (name "mosaik")
4330 (version "2.2.30")
4331 (source (origin
4332 ;; There are no release tarballs nor tags.
4333 (method git-fetch)
4334 (uri (git-reference
4335 (url "https://github.com/wanpinglee/MOSAIK.git")
4336 (commit commit)))
4337 (file-name (string-append name "-" version))
4338 (sha256
4339 (base32
4340 "17gj3s07cm77r41z92awh0bim7w7q7fbn0sf5nkqmcm1vw052qgw"))))
4341 (build-system gnu-build-system)
4342 (arguments
4343 `(#:tests? #f ; no tests
4344 #:make-flags (list "CC=gcc")
4345 #:phases
4346 (modify-phases %standard-phases
4347 (replace 'configure
4348 (lambda _ (chdir "src") #t))
4349 (replace 'install
4350 (lambda* (#:key outputs #:allow-other-keys)
4351 (let ((bin (string-append (assoc-ref outputs "out")
4352 "/bin")))
4353 (mkdir-p bin)
4354 (copy-recursively "../bin" bin)
4355 #t))))))
4356 (inputs
4357 `(("perl" ,perl)
4358 ("zlib" ,zlib)))
029d9f77 4359 (supported-systems '("x86_64-linux"))
0c6c9c00 4360 (home-page "https://github.com/wanpinglee/MOSAIK")
fe4c37c2
RW		 4361 (synopsis "Map nucleotide sequence reads to reference genomes")
4362 (description
4363 "MOSAIK is a program for mapping second and third-generation sequencing
4364reads to a reference genome. MOSAIK can align reads generated by all the
4365major sequencing technologies, including Illumina, Applied Biosystems SOLiD,
4366Roche 454, Ion Torrent and Pacific BioSciences SMRT.")
4367 ;; MOSAIK is released under the GPLv2+ with the exception of third-party
4368 ;; code released into the public domain:
4369 ;; 1. fastlz by Ariya Hidayat - http://www.fastlz.org/
4370 ;; 2. MD5 implementation - RSA Data Security, RFC 1321
4371 (license (list license:gpl2+ license:public-domain)))))
4372
282c5087
RW		 4373(define-public ngs-sdk
4374 (package
4375 (name "ngs-sdk")
48b419eb 4376 (version "1.2.5")
282c5087
RW		 4377 (source
4378 (origin
4379 (method url-fetch)
4380 (uri
4381 (string-append "https://github.com/ncbi/ngs/archive/"
4382 version ".tar.gz"))
4383 (file-name (string-append name "-" version ".tar.gz"))
4384 (sha256
4385 (base32
48b419eb 4386 "04y1fsmdnb5y86m3gg6f5g9wcscr6r25n7m8mdlcxy0i2q6w6cia"))))
282c5087
RW		 4387 (build-system gnu-build-system)
4388 (arguments
4389 `(#:parallel-build? #f ; not supported
4390 #:tests? #f ; no "check" target
4391 #:phases
4392 (alist-replace
4393 'configure
4394 (lambda* (#:key outputs #:allow-other-keys)
4395 (let ((out (assoc-ref outputs "out")))
282c5087
RW		 4396 ;; The 'configure' script doesn't recognize things like
4397 ;; '--enable-fast-install'.
4398 (zero? (system* "./configure"
4399 (string-append "--build-prefix=" (getcwd) "/build")
4400 (string-append "--prefix=" out)))))
4401 (alist-cons-after
4402 'unpack 'enter-dir
4403 (lambda _ (chdir "ngs-sdk") #t)
4404 %standard-phases))))
4405 (native-inputs `(("perl" ,perl)))
a0dadf0c
AE		 4406 ;; According to the test
4407 ;; unless ($MARCH =~ /x86_64/i || $MARCH =~ /i?86/i)
4408 ;; in ngs-sdk/setup/konfigure.perl
ab29be81 4409 (supported-systems '("i686-linux" "x86_64-linux"))
282c5087
RW		 4410 (home-page "https://github.com/ncbi/ngs")
4411 (synopsis "API for accessing Next Generation Sequencing data")
4412 (description
4413 "NGS is a domain-specific API for accessing reads, alignments and pileups
4414produced from Next Generation Sequencing. The API itself is independent from
4415any particular back-end implementation, and supports use of multiple back-ends
4416simultaneously.")
4417 (license license:public-domain)))
4418
1ad15c16 4419(define-public java-ngs
2651a5e6 4420 (package (inherit ngs-sdk)
1ad15c16 4421 (name "java-ngs")
2651a5e6
RW		 4422 (arguments
4423 `(,@(substitute-keyword-arguments
4424 `(#:modules ((guix build gnu-build-system)
4425 (guix build utils)
4426 (srfi srfi-1)
4427 (srfi srfi-26))
4428 ,@(package-arguments ngs-sdk))
4429 ((#:phases phases)
614a8977
RW		 4430 `(modify-phases ,phases
4431 (replace 'enter-dir (lambda _ (chdir "ngs-java") #t)))))))
2651a5e6 4432 (inputs
d2540f80 4433 `(("jdk" ,icedtea "jdk")
2651a5e6
RW		 4434 ("ngs-sdk" ,ngs-sdk)))
4435 (synopsis "Java bindings for NGS SDK")))
4436
75dd2424
RW		 4437(define-public ncbi-vdb
4438 (package
4439 (name "ncbi-vdb")
40974c93 4440 (version "2.7.0")
75dd2424
RW		 4441 (source
4442 (origin
4443 (method url-fetch)
4444 (uri
4445 (string-append "https://github.com/ncbi/ncbi-vdb/archive/"
4446 version ".tar.gz"))
4447 (file-name (string-append name "-" version ".tar.gz"))
4448 (sha256
4449 (base32
40974c93 4450 "0x1cg1x8vy0yjlkp0snc1533zcjhxqzqsaiwqk598n7vvw37n8lf"))))
75dd2424
RW		 4451 (build-system gnu-build-system)
4452 (arguments
4453 `(#:parallel-build? #f ; not supported
4454 #:tests? #f ; no "check" target
4455 #:phases
4456 (alist-replace
4457 'configure
4458 (lambda* (#:key inputs outputs #:allow-other-keys)
4459 (let ((out (assoc-ref outputs "out")))
75dd2424
RW		 4460 ;; Override include path for libmagic
4461 (substitute* "setup/package.prl"
4462 (("name => 'magic', Include => '/usr/include'")
4463 (string-append "name=> 'magic', Include => '"
4464 (assoc-ref inputs "libmagic")
4465 "/include" "'")))
4466
4467 ;; Install kdf5 library (needed by sra-tools)
4468 (substitute* "build/Makefile.install"
4469 (("LIBRARIES_TO_INSTALL =")
4470 "LIBRARIES_TO_INSTALL = kdf5.$(VERSION_LIBX) kdf5.$(VERSION_SHLX)"))
4471
675d7ae2
RW		 4472 (substitute* "build/Makefile.env"
4473 (("CFLAGS =" prefix)
4474 (string-append prefix "-msse2 ")))
4475
75dd2424
RW		 4476 ;; The 'configure' script doesn't recognize things like
4477 ;; '--enable-fast-install'.
4478 (zero? (system*
4479 "./configure"
4480 (string-append "--build-prefix=" (getcwd) "/build")
4481 (string-append "--prefix=" (assoc-ref outputs "out"))
4482 (string-append "--debug")
4483 (string-append "--with-xml2-prefix="
4484 (assoc-ref inputs "libxml2"))
4485 (string-append "--with-ngs-sdk-prefix="
4486 (assoc-ref inputs "ngs-sdk"))
4487 (string-append "--with-ngs-java-prefix="
1ad15c16 4488 (assoc-ref inputs "java-ngs"))
75dd2424
RW		 4489 (string-append "--with-hdf5-prefix="
4490 (assoc-ref inputs "hdf5"))))))
4491 (alist-cons-after
4492 'install 'install-interfaces
132b4c8c
RW		 4493 (lambda* (#:key outputs #:allow-other-keys)
4494 ;; Install interface libraries. On i686 the interface libraries
4495 ;; are installed to "linux/gcc/i386", so we need to use the Linux
4496 ;; architecture name ("i386") instead of the target system prefix
4497 ;; ("i686").
75dd2424
RW		 4498 (mkdir (string-append (assoc-ref outputs "out") "/ilib"))
4499 (copy-recursively (string-append "build/ncbi-vdb/linux/gcc/"
132b4c8c
RW		 4500 ,(system->linux-architecture
4501 (or (%current-target-system)
4502 (%current-system)))
75dd2424
RW		 4503 "/rel/ilib")
4504 (string-append (assoc-ref outputs "out")
4505 "/ilib"))
4506 ;; Install interface headers
4507 (copy-recursively "interfaces"
4508 (string-append (assoc-ref outputs "out")
4509 "/include")))
4510 %standard-phases))))
4511 (inputs
4512 `(("libxml2" ,libxml2)
4513 ("ngs-sdk" ,ngs-sdk)
1ad15c16 4514 ("java-ngs" ,java-ngs)
75dd2424
RW		 4515 ("libmagic" ,file)
4516 ("hdf5" ,hdf5)))
4517 (native-inputs `(("perl" ,perl)))
675d7ae2
RW		 4518 ;; NCBI-VDB requires SSE capability.
4519 (supported-systems '("i686-linux" "x86_64-linux"))
75dd2424
RW		 4520 (home-page "https://github.com/ncbi/ncbi-vdb")
4521 (synopsis "Database engine for genetic information")
4522 (description
4523 "The NCBI-VDB library implements a highly compressed columnar data
4524warehousing engine that is most often used to store genetic information.
4525Databases are stored in a portable image within the file system, and can be
4526accessed/downloaded on demand across HTTP.")
4527 (license license:public-domain)))
4528
cc6ed477
RW		 4529(define-public plink
4530 (package
4531 (name "plink")
4532 (version "1.07")
4533 (source
4534 (origin
4535 (method url-fetch)
4536 (uri (string-append
4537 "http://pngu.mgh.harvard.edu/~purcell/plink/dist/plink-"
4538 version "-src.zip"))
4539 (sha256
4540 (base32 "0as8gxm4pjyc8dxmm1sl873rrd7wn5qs0l29nqfnl31x8i467xaa"))
0dbb7ac2
EF		 4541 (patches (search-patches "plink-1.07-unclobber-i.patch"
4542 "plink-endian-detection.patch"))))
cc6ed477
RW		 4543 (build-system gnu-build-system)
4544 (arguments
4545 '(#:tests? #f ;no "check" target
4546 #:make-flags (list (string-append "LIB_LAPACK="
4547 (assoc-ref %build-inputs "lapack")
4548 "/lib/liblapack.so")
4549 "WITH_LAPACK=1"
4550 "FORCE_DYNAMIC=1"
4551 ;; disable phoning home
4552 "WITH_WEBCHECK=")
4553 #:phases
4554 (modify-phases %standard-phases
4555 ;; no "configure" script
4556 (delete 'configure)
4557 (replace 'install
4558 (lambda* (#:key outputs #:allow-other-keys)
4559 (let ((bin (string-append (assoc-ref outputs "out")
4560 "/bin/")))
96c46210 4561 (install-file "plink" bin)
cc6ed477
RW		 4562 #t))))))
4563 (inputs
4564 `(("zlib" ,zlib)
4565 ("lapack" ,lapack)))
4566 (native-inputs
4567 `(("unzip" ,unzip)))
4568 (home-page "http://pngu.mgh.harvard.edu/~purcell/plink/")
4569 (synopsis "Whole genome association analysis toolset")
4570 (description
4571 "PLINK is a whole genome association analysis toolset, designed to
4572perform a range of basic, large-scale analyses in a computationally efficient
4573manner. The focus of PLINK is purely on analysis of genotype/phenotype data,
4574so there is no support for steps prior to this (e.g. study design and
4575planning, generating genotype or CNV calls from raw data). Through
4576integration with gPLINK and Haploview, there is some support for the
4577subsequent visualization, annotation and storage of results.")
4578 ;; Code is released under GPLv2, except for fisher.h, which is under
4579 ;; LGPLv2.1+
4580 (license (list license:gpl2 license:lgpl2.1+))))
4581
c6a24d6e
RW		 4582(define-public smithlab-cpp
4583 (let ((revision "1")
698bd297 4584 (commit "728a097bec88c6f4b8528b685932049e660eff2e"))
c6a24d6e
RW		 4585 (package
4586 (name "smithlab-cpp")
698bd297 4587 (version (string-append "0." revision "." (string-take commit 7)))
c6a24d6e
RW		 4588 (source (origin
4589 (method git-fetch)
4590 (uri (git-reference
4591 (url "https://github.com/smithlabcode/smithlab_cpp.git")
4592 (commit commit)))
4593 (file-name (string-append name "-" version "-checkout"))
4594 (sha256
4595 (base32
4596 "0d476lmj312xk77kr9fzrv7z1bv96yfyx0w7y62ycmnfbx32ll74"))))
4597 (build-system gnu-build-system)
4598 (arguments
4599 `(#:modules ((guix build gnu-build-system)
4600 (guix build utils)
4601 (srfi srfi-26))
4602 #:tests? #f ;no "check" target
4603 #:phases
4604 (modify-phases %standard-phases
4605 (add-after 'unpack 'use-samtools-headers
4606 (lambda _
4607 (substitute* '("SAM.cpp"
4608 "SAM.hpp")
4609 (("sam.h") "samtools/sam.h"))
4610 #t))
4611 (replace 'install
4612 (lambda* (#:key outputs #:allow-other-keys)
4613 (let* ((out (assoc-ref outputs "out"))
4614 (lib (string-append out "/lib"))
4615 (include (string-append out "/include/smithlab-cpp")))
4616 (mkdir-p lib)
4617 (mkdir-p include)
4618 (for-each (cut install-file <> lib)
4619 (find-files "." "\\.o$"))
4620 (for-each (cut install-file <> include)
4621 (find-files "." "\\.hpp$")))
4622 #t))
4623 (delete 'configure))))
4624 (inputs
4625 `(("samtools" ,samtools-0.1)
4626 ("zlib" ,zlib)))
4627 (home-page "https://github.com/smithlabcode/smithlab_cpp")
4628 (synopsis "C++ helper library for functions used in Smith lab projects")
4629 (description
4630 "Smithlab CPP is a C++ library that includes functions used in many of
4631the Smith lab bioinformatics projects, such as a wrapper around Samtools data
4632structures, classes for genomic regions, mapped sequencing reads, etc.")
4633 (license license:gpl3+))))
4634
56e373ef
RW		 4635(define-public preseq
4636 (package
4637 (name "preseq")
b49c5a58 4638 (version "2.0")
56e373ef
RW		 4639 (source (origin
4640 (method url-fetch)
b49c5a58
RW		 4641 (uri (string-append "https://github.com/smithlabcode/"
4642 "preseq/archive/v" version ".tar.gz"))
4643 (file-name (string-append name "-" version ".tar.gz"))
56e373ef 4644 (sha256
b49c5a58 4645 (base32 "08r684l50pnxjpvmhzjgqq56yv9rfw90k8vx0nsrnrzk8mf9hsdq"))
56e373ef
RW		 4646 (modules '((guix build utils)))
4647 (snippet
4648 ;; Remove bundled samtools.
b49c5a58 4649 '(delete-file-recursively "samtools"))))
56e373ef
RW		 4650 (build-system gnu-build-system)
4651 (arguments
4652 `(#:tests? #f ;no "check" target
4653 #:phases
4654 (modify-phases %standard-phases
56e373ef 4655 (delete 'configure))
b49c5a58
RW		 4656 #:make-flags
4657 (list (string-append "PREFIX="
4658 (assoc-ref %outputs "out"))
4659 (string-append "LIBBAM="
4660 (assoc-ref %build-inputs "samtools")
4661 "/lib/libbam.a")
4662 (string-append "SMITHLAB_CPP="
4663 (assoc-ref %build-inputs "smithlab-cpp")
4664 "/lib")
4665 "PROGS=preseq"
4666 "INCLUDEDIRS=$(SMITHLAB_CPP)/../include/smithlab-cpp $(SAMTOOLS_DIR)")))
56e373ef
RW		 4667 (inputs
4668 `(("gsl" ,gsl)
4669 ("samtools" ,samtools-0.1)
b49c5a58 4670 ("smithlab-cpp" ,smithlab-cpp)
56e373ef
RW		 4671 ("zlib" ,zlib)))
4672 (home-page "http://smithlabresearch.org/software/preseq/")
4673 (synopsis "Program for analyzing library complexity")
4674 (description
4675 "The preseq package is aimed at predicting and estimating the complexity
4676of a genomic sequencing library, equivalent to predicting and estimating the
4677number of redundant reads from a given sequencing depth and how many will be
4678expected from additional sequencing using an initial sequencing experiment.
4679The estimates can then be used to examine the utility of further sequencing,
4680optimize the sequencing depth, or to screen multiple libraries to avoid low
4681complexity samples.")
4682 (license license:gpl3+)))
4683
9ded1457
BW		 4684(define-public python-screed
4685 (package
4686 (name "python-screed")
4687 (version "0.9")
4688 (source
4689 (origin
4690 (method url-fetch)
4691 (uri (pypi-uri "screed" version))
4692 (sha256
4693 (base32
4694 "18czszp9fkx3j6jr7y5kp6dfialscgddk05mw1zkhh2zhn0jd8i0"))))
4695 (build-system python-build-system)
4696 (arguments
4697 `(#:phases
4698 (modify-phases %standard-phases
4699 (replace 'check
4700 (lambda _
4701 (setenv "PYTHONPATH"
4702 (string-append (getenv "PYTHONPATH") ":."))
4703 (zero? (system* "nosetests" "--attr" "!known_failing")))))))
4704 (native-inputs
4705 `(("python-nose" ,python-nose)))
4706 (inputs
4707 `(("python-bz2file" ,python-bz2file)))
4708 (home-page "http://github.com/dib-lab/screed/")
4709 (synopsis "Short read sequence database utilities")
4710 (description "Screed parses FASTA and FASTQ files and generates databases.
4711Values such as sequence name, sequence description, sequence quality and the
4712sequence itself can be retrieved from these databases.")
4713 (license license:bsd-3)))
4714
4715(define-public python2-screed
5c31f4aa 4716 (package-with-python2 python-screed))
9ded1457 4717
51c64999
RW		 4718(define-public sra-tools
4719 (package
4720 (name "sra-tools")
646a8433 4721 (version "2.7.0")
51c64999
RW		 4722 (source
4723 (origin
4724 (method url-fetch)
4725 (uri
4726 (string-append "https://github.com/ncbi/sra-tools/archive/"
4727 version ".tar.gz"))
4728 (file-name (string-append name "-" version ".tar.gz"))
4729 (sha256
4730 (base32
646a8433 4731 "13paw7bq6y47d2pl0ac5gpgcqp1xsy1g7v1fwysm3hr8lb2dck17"))))
51c64999
RW		 4732 (build-system gnu-build-system)
4733 (arguments
4734 `(#:parallel-build? #f ; not supported
4735 #:tests? #f ; no "check" target
2320e76b
RW		 4736 #:make-flags
4737 (list (string-append "VDB_LIBDIR="
4738 (assoc-ref %build-inputs "ncbi-vdb")
4739 ,(if (string-prefix? "x86_64"
4740 (or (%current-target-system)
4741 (%current-system)))
4742 "/lib64"
4743 "/lib32")))
51c64999
RW		 4744 #:phases
4745 (alist-replace
4746 'configure
4747 (lambda* (#:key inputs outputs #:allow-other-keys)
4748 ;; The build system expects a directory containing the sources and
4749 ;; raw build output of ncbi-vdb, including files that are not
4750 ;; installed. Since we are building against an installed version of
4751 ;; ncbi-vdb, the following modifications are needed.
4752 (substitute* "setup/konfigure.perl"
4753 ;; Make the configure script look for the "ilib" directory of
4754 ;; "ncbi-vdb" without first checking for the existence of a
4755 ;; matching library in its "lib" directory.
4756 (("^ my \\$f = File::Spec->catdir\\(\\$libdir, \\$lib\\);")
4757 "my $f = File::Spec->catdir($ilibdir, $ilib);")
4758 ;; Look for interface libraries in ncbi-vdb's "ilib" directory.
4759 (("my \\$ilibdir = File::Spec->catdir\\(\\$builddir, 'ilib'\\);")
4760 "my $ilibdir = File::Spec->catdir($dir, 'ilib');"))
4761
2320e76b
RW		 4762 ;; Dynamic linking
4763 (substitute* "tools/copycat/Makefile"
4764 (("smagic-static") "lmagic"))
4765
51c64999
RW		 4766 ;; The 'configure' script doesn't recognize things like
4767 ;; '--enable-fast-install'.
4768 (zero? (system*
4769 "./configure"
4770 (string-append "--build-prefix=" (getcwd) "/build")
4771 (string-append "--prefix=" (assoc-ref outputs "out"))
4772 (string-append "--debug")
4773 (string-append "--with-fuse-prefix="
4774 (assoc-ref inputs "fuse"))
4775 (string-append "--with-magic-prefix="
4776 (assoc-ref inputs "libmagic"))
4777 ;; TODO: building with libxml2 fails with linker errors
4778 ;; (string-append "--with-xml2-prefix="
4779 ;; (assoc-ref inputs "libxml2"))
4780 (string-append "--with-ncbi-vdb-sources="
4781 (assoc-ref inputs "ncbi-vdb"))
4782 (string-append "--with-ncbi-vdb-build="
4783 (assoc-ref inputs "ncbi-vdb"))
4784 (string-append "--with-ngs-sdk-prefix="
4785 (assoc-ref inputs "ngs-sdk"))
4786 (string-append "--with-hdf5-prefix="
4787 (assoc-ref inputs "hdf5")))))
4788 %standard-phases)))
4789 (native-inputs `(("perl" ,perl)))
4790 (inputs
4791 `(("ngs-sdk" ,ngs-sdk)
4792 ("ncbi-vdb" ,ncbi-vdb)
4793 ("libmagic" ,file)
4794 ("fuse" ,fuse)
4795 ("hdf5" ,hdf5)
4796 ("zlib" ,zlib)))
4797 (home-page "http://www.ncbi.nlm.nih.gov/Traces/sra/sra.cgi?view=software")
4798 (synopsis "Tools and libraries for reading and writing sequencing data")
4799 (description
4800 "The SRA Toolkit from NCBI is a collection of tools and libraries for
4801reading of sequencing files from the Sequence Read Archive (SRA) database and
4802writing files into the .sra format.")
4803 (license license:public-domain)))
4804
d3517eda
RW		 4805(define-public seqan
4806 (package
4807 (name "seqan")
4808 (version "1.4.2")
4809 (source (origin
4810 (method url-fetch)
4811 (uri (string-append "http://packages.seqan.de/seqan-library/"
4812 "seqan-library-" version ".tar.bz2"))
4813 (sha256
4814 (base32
4815 "05s3wrrwn50f81aklfm65i4a749zag1vr8z03k21xm0pdxy47yvp"))))
4816 ;; The documentation is 7.8MB and the includes are 3.6MB heavy, so it
4817 ;; makes sense to split the outputs.
4818 (outputs '("out" "doc"))
4819 (build-system trivial-build-system)
4820 (arguments
4821 `(#:modules ((guix build utils))
4822 #:builder
4823 (begin
4824 (use-modules (guix build utils))
4825 (let ((tar (assoc-ref %build-inputs "tar"))
4826 (bzip (assoc-ref %build-inputs "bzip2"))
4827 (out (assoc-ref %outputs "out"))
4828 (doc (assoc-ref %outputs "doc")))
4829 (setenv "PATH" (string-append tar "/bin:" bzip "/bin"))
4830 (system* "tar" "xvf" (assoc-ref %build-inputs "source"))
4831 (chdir (string-append "seqan-library-" ,version))
4832 (copy-recursively "include" (string-append out "/include"))
4833 (copy-recursively "share" (string-append doc "/share"))))))
4834 (native-inputs
4835 `(("source" ,source)
4836 ("tar" ,tar)
4837 ("bzip2" ,bzip2)))
4838 (home-page "http://www.seqan.de")
4839 (synopsis "Library for nucleotide sequence analysis")
4840 (description
4841 "SeqAn is a C++ library of efficient algorithms and data structures for
4842the analysis of sequences with the focus on biological data. It contains
4843algorithms and data structures for string representation and their
4844manipulation, online and indexed string search, efficient I/O of
4845bioinformatics file formats, sequence alignment, and more.")
4846 (license license:bsd-3)))
ce7155d5 4847
d708b7a9
BW		 4848(define-public seqmagick
4849 (package
4850 (name "seqmagick")
4851 (version "0.6.1")
4852 (source
4853 (origin
4854 (method url-fetch)
4855 (uri (string-append
4856 "https://pypi.python.org/packages/source/s/seqmagick/seqmagick-"
4857 version ".tar.gz"))
4858 (sha256
4859 (base32
4860 "0cgn477n74gsl4qdaakrrhi953kcsd4q3ivk2lr18x74s3g4ma1d"))))
4861 (build-system python-build-system)
4862 (arguments
4863 ;; python2 only, see https://github.com/fhcrc/seqmagick/issues/56
4864 `(#:python ,python-2
4865 #:phases
4866 (modify-phases %standard-phases
4867 ;; Current test in setup.py does not work as of 0.6.1,
4868 ;; so use nose to run tests instead for now. See
4869 ;; https://github.com/fhcrc/seqmagick/issues/55
4870 (replace 'check (lambda _ (zero? (system* "nosetests")))))))
4871 (inputs
7bba95b7
BW		 4872 ;; biopython-1.66 is required due to
4873 ;; https://github.com/fhcrc/seqmagick/issues/59
4874 ;; When that issue is resolved the 'python2-biopython-1.66' package
4875 ;; should be removed.
4876 `(("python-biopython" ,python2-biopython-1.66)))
d708b7a9 4877 (native-inputs
f3b98f4f 4878 `(("python-nose" ,python2-nose)))
d708b7a9
BW		 4879 (home-page "http://github.com/fhcrc/seqmagick")
4880 (synopsis "Tools for converting and modifying sequence files")
4881 (description
4882 "Bioinformaticians often have to convert sequence files between formats
4883and do little manipulations on them, and it's not worth writing scripts for
4884that. Seqmagick is a utility to expose the file format conversion in
4885BioPython in a convenient way. Instead of having a big mess of scripts, there
4886is one that takes arguments.")
4887 (license license:gpl3)))
4888
66daf78c
BW		 4889(define-public seqtk
4890 (package
4891 (name "seqtk")
4892 (version "1.2")
4893 (source (origin
4894 (method url-fetch)
4895 (uri (string-append
4896 "https://github.com/lh3/seqtk/archive/v"
4897 version ".tar.gz"))
4898 (file-name (string-append name "-" version ".tar.gz"))
4899 (sha256
4900 (base32
4901 "0ywdyzpmfiz2wp6ampbzqg4y8bj450nfgqarpamg045b8mk32lxx"))
4902 (modules '((guix build utils)))
4903 (snippet
4904 '(begin
4905 ;; Remove extraneous header files, as is done in the seqtk
4906 ;; master branch.
4907 (for-each (lambda (file) (delete-file file))
4908 (list "ksort.h" "kstring.h" "kvec.h"))
4909 #t))))
4910 (build-system gnu-build-system)
4911 (arguments
4912 `(#:phases
4913 (modify-phases %standard-phases
4914 (delete 'configure)
4915 (replace 'check
4916 ;; There are no tests, so we just run a sanity check.
4917 (lambda _ (zero? (system* "./seqtk" "seq"))))
4918 (replace 'install
4919 (lambda* (#:key outputs #:allow-other-keys)
4920 (let ((bin (string-append (assoc-ref outputs "out") "/bin/")))
4921 (install-file "seqtk" bin)))))))
4922 (inputs
4923 `(("zlib" ,zlib)))
4924 (home-page "https://github.com/lh3/seqtk")
4925 (synopsis "Toolkit for processing biological sequences in FASTA/Q format")
4926 (description
4927 "Seqtk is a fast and lightweight tool for processing sequences in the
4928FASTA or FASTQ format. It parses both FASTA and FASTQ files which can be
4929optionally compressed by gzip.")
4930 (license license:expat)))
4931
5f7e17be
BW		 4932(define-public snap-aligner
4933 (package
4934 (name "snap-aligner")
4935 (version "1.0beta.18")
4936 (source (origin
4937 (method url-fetch)
4938 (uri (string-append
4939 "https://github.com/amplab/snap/archive/v"
4940 version ".tar.gz"))
4941 (file-name (string-append name "-" version ".tar.gz"))
4942 (sha256
4943 (base32
4944 "1vnsjwv007k1fl1q7d681kbwn6bc66cgw6h16hym6gvyy71qv2ly"))))
4945 (build-system gnu-build-system)
4946 (arguments
4947 '(#:phases
4948 (modify-phases %standard-phases
4949 (delete 'configure)
4950 (replace 'check (lambda _ (zero? (system* "./unit_tests"))))
4951 (replace 'install
4952 (lambda* (#:key outputs #:allow-other-keys)
4953 (let* ((out (assoc-ref outputs "out"))
4954 (bin (string-append out "/bin")))
5f7e17be
BW		 4955 (install-file "snap-aligner" bin)
4956 (install-file "SNAPCommand" bin)
4957 #t))))))
4958 (native-inputs
4959 `(("zlib" ,zlib)))
4960 (home-page "http://snap.cs.berkeley.edu/")
4961 (synopsis "Short read DNA sequence aligner")
4962 (description
4963 "SNAP is a fast and accurate aligner for short DNA reads. It is
4964optimized for modern read lengths of 100 bases or higher, and takes advantage
4965of these reads to align data quickly through a hash-based indexing scheme.")
3e6fdd5f
EF		 4966 ;; 32-bit systems are not supported by the unpatched code.
4967 ;; Following the bug reports https://github.com/amplab/snap/issues/68 and
4968 ;; https://bugs.debian.org/cgi-bin/bugreport.cgi?bug=812378 we see that
4969 ;; systems without a lot of memory cannot make good use of this program.
4970 (supported-systems '("x86_64-linux"))
5f7e17be
BW		 4971 (license license:asl2.0)))
4972
bcadaf00
BW		 4973(define-public sortmerna
4974 (package
4975 (name "sortmerna")
849485f5 4976 (version "2.1b")
bcadaf00
BW		 4977 (source
4978 (origin
4979 (method url-fetch)
4980 (uri (string-append
4981 "https://github.com/biocore/sortmerna/archive/"
4982 version ".tar.gz"))
4983 (file-name (string-append name "-" version ".tar.gz"))
4984 (sha256
4985 (base32
849485f5 4986 "1ghaghvd82af9j5adavxh77g7hm247d1r69m3fbi6f1jdivj5ldk"))))
bcadaf00
BW		 4987 (build-system gnu-build-system)
4988 (outputs '("out" ;for binaries
4989 "db")) ;for sequence databases
4990 (arguments
4991 `(#:phases
4992 (modify-phases %standard-phases
4993 (replace 'install
4994 (lambda* (#:key outputs #:allow-other-keys)
4995 (let* ((out (assoc-ref outputs "out"))
4996 (bin (string-append out "/bin"))
4997 (db (assoc-ref outputs "db"))
4998 (share
4999 (string-append db "/share/sortmerna/rRNA_databases")))
5000 (install-file "sortmerna" bin)
5001 (install-file "indexdb_rna" bin)
5002 (for-each (lambda (file)
5003 (install-file file share))
5004 (find-files "rRNA_databases" ".*fasta"))
5005 #t))))))
849485f5
BW		 5006 (inputs
5007 `(("zlib" ,zlib)))
bcadaf00
BW		 5008 (home-page "http://bioinfo.lifl.fr/RNA/sortmerna")
5009 (synopsis "Biological sequence analysis tool for NGS reads")
5010 (description
5011 "SortMeRNA is a biological sequence analysis tool for filtering, mapping
5012and operational taxonomic unit (OTU) picking of next generation
5013sequencing (NGS) reads. The core algorithm is based on approximate seeds and
5014allows for fast and sensitive analyses of nucleotide sequences. The main
5015application of SortMeRNA is filtering rRNA from metatranscriptomic data.")
5016 (license license:lgpl3)))
5017
ce7155d5
RW		 5018(define-public star
5019 (package
5020 (name "star")
c9e9154e 5021 (version "2.5.2b")
ce7155d5
RW		 5022 (source (origin
5023 (method url-fetch)
3062d750
RW		 5024 (uri (string-append "https://github.com/alexdobin/STAR/archive/"
5025 version ".tar.gz"))
5026 (file-name (string-append name "-" version ".tar.gz"))
ce7155d5
RW		 5027 (sha256
5028 (base32
c9e9154e 5029 "1na6np880r1zaamiy00hy8bid5anpy0kgf63587v2yl080krk2zq"))
ce7155d5
RW		 5030 (modules '((guix build utils)))
5031 (snippet
3062d750
RW		 5032 '(begin
5033 (substitute* "source/Makefile"
5034 (("/bin/rm") "rm"))
5035 ;; Remove pre-built binaries and bundled htslib sources.
5036 (delete-file-recursively "bin/MacOSX_x86_64")
5037 (delete-file-recursively "bin/Linux_x86_64")
c9e9154e 5038 (delete-file-recursively "bin/Linux_x86_64_static")
3062d750
RW		 5039 (delete-file-recursively "source/htslib")
5040 #t))))
ce7155d5
RW		 5041 (build-system gnu-build-system)
5042 (arguments
5043 '(#:tests? #f ;no check target
5044 #:make-flags '("STAR")
5045 #:phases
c0266e8d
RW		 5046 (modify-phases %standard-phases
5047 (add-after 'unpack 'enter-source-dir
5048 (lambda _ (chdir "source") #t))
3062d750
RW		 5049 (add-after 'enter-source-dir 'do-not-use-bundled-htslib
5050 (lambda _
5051 (substitute* "Makefile"
5052 (("(Depend.list: \\$\\(SOURCES\\) parametersDefault\\.xxd) htslib"
5053 _ prefix) prefix))
5054 (substitute* '("BAMfunctions.cpp"
5055 "signalFromBAM.h"
5056 "bam_cat.h"
5057 "bam_cat.c"
5058 "STAR.cpp"
5059 "bamRemoveDuplicates.cpp")
5060 (("#include \"htslib/([^\"]+\\.h)\"" _ header)
5061 (string-append "#include <" header ">")))
5062 (substitute* "IncludeDefine.h"
5063 (("\"htslib/(htslib/[^\"]+.h)\"" _ header)
5064 (string-append "<" header ">")))
5065 #t))
c0266e8d
RW		 5066 (replace 'install
5067 (lambda* (#:key outputs #:allow-other-keys)
5068 (let ((bin (string-append (assoc-ref outputs "out") "/bin/")))
5069 (install-file "STAR" bin))
5070 #t))
5071 (delete 'configure))))
ce7155d5
RW		 5072 (native-inputs
5073 `(("vim" ,vim))) ; for xxd
5074 (inputs
3062d750
RW		 5075 `(("htslib" ,htslib)
5076 ("zlib" ,zlib)))
ce7155d5
RW		 5077 (home-page "https://github.com/alexdobin/STAR")
5078 (synopsis "Universal RNA-seq aligner")
5079 (description
5080 "The Spliced Transcripts Alignment to a Reference (STAR) software is
5081based on a previously undescribed RNA-seq alignment algorithm that uses
5082sequential maximum mappable seed search in uncompressed suffix arrays followed
5083by seed clustering and stitching procedure. In addition to unbiased de novo
5084detection of canonical junctions, STAR can discover non-canonical splices and
5085chimeric (fusion) transcripts, and is also capable of mapping full-length RNA
5086sequences.")
c11f79a4
BW		 5087 ;; Only 64-bit systems are supported according to the README.
5088 (supported-systems '("x86_64-linux" "mips64el-linux"))
ce7155d5
RW		 5089 ;; STAR is licensed under GPLv3 or later; htslib is MIT-licensed.
5090 (license license:gpl3+)))
de07c0db 5091
dbf4ed7c
RW		 5092(define-public subread
5093 (package
5094 (name "subread")
c180533b 5095 (version "1.5.1")
dbf4ed7c
RW		 5096 (source (origin
5097 (method url-fetch)
de67e922
LF		 5098 (uri (string-append "mirror://sourceforge/subread/subread-"
5099 version "/subread-" version "-source.tar.gz"))
dbf4ed7c
RW		 5100 (sha256
5101 (base32
c180533b 5102 "0gn5zhbvllks0mmdg3qlmsbg91p2mpdc2wixwfqpi85yzfrh8hcy"))))
dbf4ed7c
RW		 5103 (build-system gnu-build-system)
5104 (arguments
5105 `(#:tests? #f ;no "check" target
104c1986
RW		 5106 ;; The CC and CCFLAGS variables are set to contain a lot of x86_64
5107 ;; optimizations by default, so we override these flags such that x86_64
5108 ;; flags are only added when the build target is an x86_64 system.
5109 #:make-flags
5110 (list (let ((system ,(or (%current-target-system)
5111 (%current-system)))
5112 (flags '("-ggdb" "-fomit-frame-pointer"
5113 "-ffast-math" "-funroll-loops"
5114 "-fmessage-length=0"
5115 "-O9" "-Wall" "-DMAKE_FOR_EXON"
5116 "-DMAKE_STANDALONE"
5117 "-DSUBREAD_VERSION=\\\"${SUBREAD_VERSION}\\\""))
5118 (flags64 '("-mmmx" "-msse" "-msse2" "-msse3")))
5119 (if (string-prefix? "x86_64" system)
5120 (string-append "CCFLAGS=" (string-join (append flags flags64)))
5121 (string-append "CCFLAGS=" (string-join flags))))
5122 "-f" "Makefile.Linux"
5123 "CC=gcc ${CCFLAGS}")
dbf4ed7c
RW		 5124 #:phases
5125 (alist-cons-after
5126 'unpack 'enter-dir
5127 (lambda _ (chdir "src") #t)
5128 (alist-replace
5129 'install
5130 (lambda* (#:key outputs #:allow-other-keys)
5131 (let ((bin (string-append (assoc-ref outputs "out") "/bin/")))
5132 (mkdir-p bin)
5133 (copy-recursively "../bin" bin)))
5134 ;; no "configure" script
5135 (alist-delete 'configure %standard-phases)))))
5136 (inputs `(("zlib" ,zlib)))
5137 (home-page "http://bioinf.wehi.edu.au/subread-package/")
5138 (synopsis "Tool kit for processing next-gen sequencing data")
5139 (description
5140 "The subread package contains the following tools: subread aligner, a
5141general-purpose read aligner; subjunc aligner: detecting exon-exon junctions
5142and mapping RNA-seq reads; featureCounts: counting mapped reads for genomic
5143features; exactSNP: a SNP caller that discovers SNPs by testing signals
5144against local background noises.")
5145 (license license:gpl3+)))
5146
d15d981e
RW		 5147(define-public stringtie
5148 (package
5149 (name "stringtie")
5150 (version "1.2.1")
5151 (source (origin
5152 (method url-fetch)
5153 (uri (string-append "http://ccb.jhu.edu/software/stringtie/dl/"
5154 "stringtie-" version ".tar.gz"))
5155 (sha256
5156 (base32
5157 "1cqllsc1maq4kh92isi8yadgzbmnf042hlnalpk3y59aph1z3bfz"))
5158 (modules '((guix build utils)))
5159 (snippet
5160 '(begin
5161 (delete-file-recursively "samtools-0.1.18")
5162 #t))))
5163 (build-system gnu-build-system)
5164 (arguments
5165 `(#:tests? #f ;no test suite
5166 #:phases
5167 (modify-phases %standard-phases
5168 ;; no configure script
5169 (delete 'configure)
5170 (add-before 'build 'use-system-samtools
5171 (lambda _
5172 (substitute* "Makefile"
5173 (("stringtie: \\$\\{BAM\\}/libbam\\.a")
5174 "stringtie: "))
5175 (substitute* '("gclib/GBam.h"
5176 "gclib/GBam.cpp")
5177 (("#include \"(bam|sam|kstring).h\"" _ header)
5178 (string-append "#include <samtools/" header ".h>")))
5179 #t))
5180 (replace 'install
5181 (lambda* (#:key outputs #:allow-other-keys)
5182 (let ((bin (string-append (assoc-ref outputs "out") "/bin/")))
5183 (install-file "stringtie" bin)
5184 #t))))))
5185 (inputs
5186 `(("samtools" ,samtools-0.1)
5187 ("zlib" ,zlib)))
5188 (home-page "http://ccb.jhu.edu/software/stringtie/")
5189 (synopsis "Transcript assembly and quantification for RNA-Seq data")
5190 (description
5191 "StringTie is a fast and efficient assembler of RNA-Seq sequence
5192alignments into potential transcripts. It uses a novel network flow algorithm
5193as well as an optional de novo assembly step to assemble and quantitate
5194full-length transcripts representing multiple splice variants for each gene
5195locus. Its input can include not only the alignments of raw reads used by
5196other transcript assemblers, but also alignments of longer sequences that have
5197been assembled from those reads. To identify differentially expressed genes
5198between experiments, StringTie's output can be processed either by the
5199Cuffdiff or Ballgown programs.")
5200 (license license:artistic2.0)))
5201
de07c0db
RW		 5202(define-public vcftools
5203 (package
5204 (name "vcftools")
9b36e256 5205 (version "0.1.14")
de07c0db
RW		 5206 (source (origin
5207 (method url-fetch)
5208 (uri (string-append
9b36e256
RJ		 5209 "https://github.com/vcftools/vcftools/releases/download/v"
5210 version "/vcftools-" version ".tar.gz"))
de07c0db
RW		 5211 (sha256
5212 (base32
9b36e256 5213 "10l5c07z9p4i9pr4gl54b2c9h6ndhqlbq1rashg2zcgwkbfrkmvn"))))
de07c0db
RW		 5214 (build-system gnu-build-system)
5215 (arguments
5216 `(#:tests? #f ; no "check" target
5217 #:make-flags (list
7c3958e1 5218 "CFLAGS=-O2" ; override "-m64" flag
de07c0db
RW		 5219 (string-append "PREFIX=" (assoc-ref %outputs "out"))
5220 (string-append "MANDIR=" (assoc-ref %outputs "out")
9b36e256
RJ		 5221 "/share/man/man1"))))
5222 (native-inputs
5223 `(("pkg-config" ,pkg-config)))
de07c0db
RW		 5224 (inputs
5225 `(("perl" ,perl)
5226 ("zlib" ,zlib)))
9b36e256 5227 (home-page "https://vcftools.github.io/")
de07c0db
RW		 5228 (synopsis "Tools for working with VCF files")
5229 (description
5230 "VCFtools is a program package designed for working with VCF files, such
5231as those generated by the 1000 Genomes Project. The aim of VCFtools is to
5232provide easily accessible methods for working with complex genetic variation
5233data in the form of VCF files.")
5234 ;; The license is declared as LGPLv3 in the README and
9b36e256 5235 ;; at https://vcftools.github.io/license.html
de07c0db 5236 (license license:lgpl3)))
9c38b540 5237
35aa90a1
RW		 5238(define-public infernal
5239 (package
5240 (name "infernal")
5241 (version "1.1.2")
5242 (source (origin
5243 (method url-fetch)
5244 (uri (string-append "http://eddylab.org/software/infernal/"
5245 "infernal-" version ".tar.gz"))
5246 (sha256
5247 (base32
5248 "0sr2hiz3qxfwqpz3whxr6n82p3x27336v3f34iqznp10hks2935c"))))
5249 (build-system gnu-build-system)
5250 (native-inputs
5251 `(("perl" ,perl))) ; for tests
5252 (home-page "http://eddylab.org/infernal/")
5253 (synopsis "Inference of RNA alignments")
5254 (description "Infernal (\"INFERence of RNA ALignment\") is a tool for
5255searching DNA sequence databases for RNA structure and sequence similarities.
5256It is an implementation of a special case of profile stochastic context-free
5257grammars called @dfn{covariance models} (CMs). A CM is like a sequence
5258profile, but it scores a combination of sequence consensus and RNA secondary
5259structure consensus, so in many cases, it is more capable of identifying RNA
5260homologs that conserve their secondary structure more than their primary
5261sequence.")
48409ef2
EF		 5262 ;; Infernal 1.1.2 requires VMX or SSE capability for parallel instructions.
5263 (supported-systems '("i686-linux" "x86_64-linux"))
35aa90a1
RW		 5264 (license license:bsd-3)))
5265
b91cfa22
RW		 5266(define-public r-centipede
5267 (package
5268 (name "r-centipede")
5269 (version "1.2")
5270 (source (origin
5271 (method url-fetch)
5272 (uri (string-append "http://download.r-forge.r-project.org/"
5273 "src/contrib/CENTIPEDE_" version ".tar.gz"))
5274 (sha256
5275 (base32
5276 "1hsx6qgwr0i67fhy9257zj7s0ppncph2hjgbia5nn6nfmj0ax6l9"))))
5277 (build-system r-build-system)
5278 (home-page "http://centipede.uchicago.edu/")
5279 (synopsis "Predict transcription factor binding sites")
5280 (description
5281 "CENTIPEDE applies a hierarchical Bayesian mixture model to infer regions
5282of the genome that are bound by particular transcription factors. It starts
5283by identifying a set of candidate binding sites, and then aims to classify the
5284sites according to whether each site is bound or not bound by a transcription
5285factor. CENTIPEDE is an unsupervised learning algorithm that discriminates
5286between two different types of motif instances using as much relevant
5287information as possible.")
5288 (license (list license:gpl2+ license:gpl3+))))
5289
7b3df1e5
BW		 5290(define-public r-vegan
5291 (package
5292 (name "r-vegan")
2c575bb9 5293 (version "2.4-1")
7b3df1e5
BW		 5294 (source
5295 (origin
5296 (method url-fetch)
5297 (uri (cran-uri "vegan" version))
5298 (sha256
5299 (base32
2c575bb9 5300 "0i0c7rc0nzgbysd1nlxzxd2rvy75qcnw3yc7nggzqjzzj5d7yzsd"))))
7b3df1e5
BW		 5301 (build-system r-build-system)
5302 (arguments
5303 `(#:phases
5304 (modify-phases %standard-phases
5305 (add-after 'unpack 'revert-test-deletion
5306 ;; The distributed sources do not include tests with the CRAN
5307 ;; package. Here we revert the commit
5308 ;; `591d0e8ba1deaaf82445474ec6619c0b43db4e63' which deletes these
5309 ;; tests. There are plans to not delete tests in future as
5310 ;; documented at https://github.com/vegandevs/vegan/issues/181.
5311 (lambda* (#:key inputs #:allow-other-keys)
5312 (zero?
5313 (system* "patch" "-R" "-p1" "-i"
5314 (assoc-ref inputs "r-vegan-delete-tests-patch"))))))))
5315 (native-inputs
5316 `(("gfortran" ,gfortran)
5317 ("r-knitr" ,r-knitr)
5318 ("r-vegan-delete-tests-patch"
5319 ,(origin
5320 (method url-fetch)
5321 (uri (string-append
5322 "https://github.com/vegandevs/vegan/commit/"
5323 "591d0e8ba1deaaf82445474ec6619c0b43db4e63.patch"))
5324 (sha256
5325 (base32
5326 "0b1bi7y4jjdl3ph721vm9apm51dr2z9piwvhy4355sf2b4kyyj5a"))))))
5327 (propagated-inputs
5328 `(("r-cluster" ,r-cluster)
5329 ("r-lattice" ,r-lattice)
5330 ("r-mgcv" ,r-mgcv)
5331 ("r-permute" ,r-permute)))
5332 (home-page "https://cran.r-project.org/web/packages/vegan")
5333 (synopsis "Functions for community ecology")
5334 (description
5335 "The vegan package provides tools for descriptive community ecology. It
5336has most basic functions of diversity analysis, community ordination and
5337dissimilarity analysis. Most of its multivariate tools can be used for other
5338data types as well.")
5339 (license license:gpl2+)))
5340
8c6de588
RW		 5341(define-public r-annotate
5342 (package
5343 (name "r-annotate")
d0f0579e 5344 (version "1.52.1")
8c6de588
RW		 5345 (source
5346 (origin
5347 (method url-fetch)
5348 (uri (bioconductor-uri "annotate" version))
5349 (sha256
5350 (base32
d0f0579e 5351 "0yymz8qxgnbybvfhqrgkd1hh9dhwxdii1yxkhr1zicjgb35xixxb"))))
8c6de588
RW		 5352 (build-system r-build-system)
5353 (propagated-inputs
5354 `(("r-annotationdbi" ,r-annotationdbi)
5355 ("r-biobase" ,r-biobase)
5356 ("r-biocgenerics" ,r-biocgenerics)
5357 ("r-dbi" ,r-dbi)
d0f0579e 5358 ("r-rcurl" ,r-rcurl)
8c6de588
RW		 5359 ("r-xml" ,r-xml)
5360 ("r-xtable" ,r-xtable)))
5361 (home-page
5362 "http://bioconductor.org/packages/annotate")
5363 (synopsis "Annotation for microarrays")
5364 (description "This package provides R enviroments for the annotation of
5365microarrays.")
5366 (license license:artistic2.0)))
5367
07a664cd
RW		 5368(define-public r-geneplotter
5369 (package
5370 (name "r-geneplotter")
6faa2a48 5371 (version "1.52.0")
07a664cd
RW		 5372 (source
5373 (origin
5374 (method url-fetch)
5375 (uri (bioconductor-uri "geneplotter" version))
5376 (sha256
5377 (base32
6faa2a48 5378 "1p6yvxi243irhjxwm97hp73abhwampj0myyf8z00ij166674pc7h"))))
07a664cd
RW		 5379 (build-system r-build-system)
5380 (propagated-inputs
5381 `(("r-annotate" ,r-annotate)
5382 ("r-annotationdbi" ,r-annotationdbi)
5383 ("r-biobase" ,r-biobase)
5384 ("r-biocgenerics" ,r-biocgenerics)
5385 ("r-lattice" ,r-lattice)
5386 ("r-rcolorbrewer" ,r-rcolorbrewer)))
5387 (home-page "http://bioconductor.org/packages/geneplotter")
5388 (synopsis "Graphics functions for genomic data")
5389 (description
5390 "This package provides functions for plotting genomic data.")
5391 (license license:artistic2.0)))
5392
2301fd3e
RW		 5393(define-public r-genefilter
5394 (package
5395 (name "r-genefilter")
1e66e719 5396 (version "1.56.0")
2301fd3e
RW		 5397 (source
5398 (origin
5399 (method url-fetch)
5400 (uri (bioconductor-uri "genefilter" version))
5401 (sha256
5402 (base32
1e66e719 5403 "1vzgciqd09csqcw9qync8blsv51ylrd86a65iadgyy6j26g01fwd"))))
2301fd3e
RW		 5404 (build-system r-build-system)
5405 (native-inputs
5406 `(("gfortran" ,gfortran)))
5407 (propagated-inputs
5408 `(("r-annotate" ,r-annotate)
5409 ("r-annotationdbi" ,r-annotationdbi)
5410 ("r-biobase" ,r-biobase)
5411 ("r-s4vectors" ,r-s4vectors)))
5412 (home-page "http://bioconductor.org/packages/genefilter")
5413 (synopsis "Filter genes from high-throughput experiments")
5414 (description
5415 "This package provides basic functions for filtering genes from
5416high-throughput sequencing experiments.")
5417 (license license:artistic2.0)))
5418
ad34f0ac
RW		 5419(define-public r-deseq2
5420 (package
5421 (name "r-deseq2")
007ee802 5422 (version "1.14.1")
ad34f0ac
RW		 5423 (source
5424 (origin
5425 (method url-fetch)
5426 (uri (bioconductor-uri "DESeq2" version))
5427 (sha256
5428 (base32
007ee802 5429 "1walwkqryn1gnwz7zryr5764a0p6ia7ag4w6w9n8fskg8dkg0fqs"))))
ad34f0ac
RW		 5430 (properties `((upstream-name . "DESeq2")))
5431 (build-system r-build-system)
5432 (arguments
5433 `(#:phases
5434 (modify-phases %standard-phases
5435 (add-after 'unpack 'link-against-armadillo
5436 (lambda _
5437 (substitute* "src/Makevars"
5438 (("PKG_LIBS =" prefix)
5439 (string-append prefix "-larmadillo"))))))))
5440 (propagated-inputs
5441 `(("r-biobase" ,r-biobase)
5442 ("r-biocgenerics" ,r-biocgenerics)
5443 ("r-biocparallel" ,r-biocparallel)
5444 ("r-genefilter" ,r-genefilter)
5445 ("r-geneplotter" ,r-geneplotter)
5446 ("r-genomicranges" ,r-genomicranges)
5447 ("r-ggplot2" ,r-ggplot2)
5448 ("r-hmisc" ,r-hmisc)
5449 ("r-iranges" ,r-iranges)
5450 ("r-locfit" ,r-locfit)
5451 ("r-rcpp" ,r-rcpp)
5452 ("r-rcpparmadillo" ,r-rcpparmadillo)
5453 ("r-s4vectors" ,r-s4vectors)
5454 ("r-summarizedexperiment" ,r-summarizedexperiment)))
5455 (home-page "http://bioconductor.org/packages/DESeq2")
5456 (synopsis "Differential gene expression analysis")
5457 (description
5458 "This package provides functions to estimate variance-mean dependence in
5459count data from high-throughput nucleotide sequencing assays and test for
5460differential expression based on a model using the negative binomial
5461distribution.")
5462 (license license:lgpl3+)))
5463
e8163773
RW		 5464(define-public r-annotationforge
5465 (package
5466 (name "r-annotationforge")
55cd914c 5467 (version "1.16.0")
e8163773
RW		 5468 (source
5469 (origin
5470 (method url-fetch)
5471 (uri (bioconductor-uri "AnnotationForge" version))
5472 (sha256
5473 (base32
55cd914c 5474 "02msyb9p3hywrryx00zpjkjl126mrv827i1ah1092s0cplm6xxvf"))))
e8163773
RW		 5475 (properties
5476 `((upstream-name . "AnnotationForge")))
5477 (build-system r-build-system)
5478 (propagated-inputs
5479 `(("r-annotationdbi" ,r-annotationdbi)
5480 ("r-biobase" ,r-biobase)
5481 ("r-biocgenerics" ,r-biocgenerics)
5482 ("r-dbi" ,r-dbi)
55cd914c 5483 ("r-rcurl" ,r-rcurl)
e8163773
RW		 5484 ("r-rsqlite" ,r-rsqlite)
5485 ("r-s4vectors" ,r-s4vectors)
5486 ("r-xml" ,r-xml)))
5487 (home-page "http://bioconductor.org/packages/AnnotationForge")
5488 (synopsis "Code for building annotation database packages")
5489 (description
5490 "This package provides code for generating Annotation packages and their
5491databases. Packages produced are intended to be used with AnnotationDbi.")
5492 (license license:artistic2.0)))
5493
cd9e7dc7
RW		 5494(define-public r-rbgl
5495 (package
5496 (name "r-rbgl")
700c780d 5497 (version "1.50.0")
cd9e7dc7
RW		 5498 (source
5499 (origin
5500 (method url-fetch)
5501 (uri (bioconductor-uri "RBGL" version))
5502 (sha256
5503 (base32
700c780d 5504 "1q14m8w6ih56v680kf3d9wh1qbgp7af33kz3cxafdf1vvzx9km08"))))
cd9e7dc7
RW		 5505 (properties `((upstream-name . "RBGL")))
5506 (build-system r-build-system)
5507 (propagated-inputs `(("r-graph" ,r-graph)))
5508 (home-page "http://www.bioconductor.org/packages/RBGL")
5509 (synopsis "Interface to the Boost graph library")
5510 (description
5511 "This package provides a fairly extensive and comprehensive interface to
5512the graph algorithms contained in the Boost library.")
5513 (license license:artistic2.0)))
5514
ad740ff8
RW		 5515(define-public r-gseabase
5516 (package
5517 (name "r-gseabase")
558d02c3 5518 (version "1.36.0")
ad740ff8
RW		 5519 (source
5520 (origin
5521 (method url-fetch)
5522 (uri (bioconductor-uri "GSEABase" version))
5523 (sha256
5524 (base32
558d02c3 5525 "0l2x7yj7lfb0m2dmsav5ib026dikpgl4crdckrnj776yy08lgxpj"))))
ad740ff8
RW		 5526 (properties `((upstream-name . "GSEABase")))
5527 (build-system r-build-system)
5528 (propagated-inputs
5529 `(("r-annotate" ,r-annotate)
5530 ("r-annotationdbi" ,r-annotationdbi)
5531 ("r-biobase" ,r-biobase)
5532 ("r-biocgenerics" ,r-biocgenerics)
5533 ("r-graph" ,r-graph)
5534 ("r-xml" ,r-xml)))
5535 (home-page "http://bioconductor.org/packages/GSEABase")
5536 (synopsis "Gene set enrichment data structures and methods")
5537 (description
5538 "This package provides classes and methods to support @dfn{Gene Set
5539Enrichment Analysis} (GSEA).")
5540 (license license:artistic2.0)))
5541
1a1931f7
RW		 5542(define-public r-category
5543 (package
5544 (name "r-category")
816599c1 5545 (version "2.40.0")
1a1931f7
RW		 5546 (source
5547 (origin
5548 (method url-fetch)
5549 (uri (bioconductor-uri "Category" version))
5550 (sha256
5551 (base32
816599c1 5552 "16ncwz7b4y48k0p3fvbrbmvf7nfz63li9ysgcl8kp9kl4hg7llng"))))
1a1931f7
RW		 5553 (properties `((upstream-name . "Category")))
5554 (build-system r-build-system)
5555 (propagated-inputs
5556 `(("r-annotate" ,r-annotate)
5557 ("r-annotationdbi" ,r-annotationdbi)
5558 ("r-biobase" ,r-biobase)
5559 ("r-biocgenerics" ,r-biocgenerics)
5560 ("r-genefilter" ,r-genefilter)
5561 ("r-graph" ,r-graph)
5562 ("r-gseabase" ,r-gseabase)
5563 ("r-matrix" ,r-matrix)
5564 ("r-rbgl" ,r-rbgl)
5565 ("r-rsqlite" ,r-rsqlite)))
5566 (home-page "http://bioconductor.org/packages/Category")
5567 (synopsis "Category analysis")
5568 (description
5569 "This package provides a collection of tools for performing category
5570analysis.")
5571 (license license:artistic2.0)))
5572
89f40c5e
RW		 5573(define-public r-gostats
5574 (package
5575 (name "r-gostats")
ae6899b6 5576 (version "2.40.0")
89f40c5e
RW		 5577 (source
5578 (origin
5579 (method url-fetch)
5580 (uri (bioconductor-uri "GOstats" version))
5581 (sha256
5582 (base32
ae6899b6 5583 "0g2czm94zhzx92z7y2r4mjfxhwml7bhab2db6820ks8nkw1zvr9n"))))
89f40c5e
RW		 5584 (properties `((upstream-name . "GOstats")))
5585 (build-system r-build-system)
5586 (propagated-inputs
5587 `(("r-annotate" ,r-annotate)
5588 ("r-annotationdbi" ,r-annotationdbi)
5589 ("r-annotationforge" ,r-annotationforge)
5590 ("r-biobase" ,r-biobase)
5591 ("r-category" ,r-category)
5592 ("r-go-db" ,r-go-db)
5593 ("r-graph" ,r-graph)
5594 ("r-rbgl" ,r-rbgl)))
5595 (home-page "http://bioconductor.org/packages/GOstats")
5596 (synopsis "Tools for manipulating GO and microarrays")
5597 (description
5598 "This package provides a set of tools for interacting with GO and
5599microarray data. A variety of basic manipulation tools for graphs, hypothesis
5600testing and other simple calculations.")
5601 (license license:artistic2.0)))
5602
cb99d457
RW		 5603(define-public r-shortread
5604 (package
5605 (name "r-shortread")
b87b41a7 5606 (version "1.32.0")
cb99d457
RW		 5607 (source
5608 (origin
5609 (method url-fetch)
5610 (uri (bioconductor-uri "ShortRead" version))
5611 (sha256
5612 (base32
b87b41a7 5613 "0mjdlg92x5qw4x2djc4dv5lxwl7ai6ix56nnf86zr07jk8vc7yls"))))
cb99d457
RW		 5614 (properties `((upstream-name . "ShortRead")))
5615 (build-system r-build-system)
5616 (inputs
5617 `(("zlib" ,zlib)))
5618 (propagated-inputs
5619 `(("r-biobase" ,r-biobase)
5620 ("r-biocgenerics" ,r-biocgenerics)
5621 ("r-biocparallel" ,r-biocparallel)
5622 ("r-biostrings" ,r-biostrings)
5623 ("r-genomeinfodb" ,r-genomeinfodb)
5624 ("r-genomicalignments" ,r-genomicalignments)
5625 ("r-genomicranges" ,r-genomicranges)
5626 ("r-hwriter" ,r-hwriter)
5627 ("r-iranges" ,r-iranges)
5628 ("r-lattice" ,r-lattice)
5629 ("r-latticeextra" ,r-latticeextra)
5630 ("r-rsamtools" ,r-rsamtools)
5631 ("r-s4vectors" ,r-s4vectors)
5632 ("r-xvector" ,r-xvector)
5633 ("r-zlibbioc" ,r-zlibbioc)))
5634 (home-page "http://bioconductor.org/packages/ShortRead")
5635 (synopsis "FASTQ input and manipulation tools")
5636 (description
5637 "This package implements sampling, iteration, and input of FASTQ files.
5638It includes functions for filtering and trimming reads, and for generating a
5639quality assessment report. Data are represented as
5640@code{DNAStringSet}-derived objects, and easily manipulated for a diversity of
5641purposes. The package also contains legacy support for early single-end,
5642ungapped alignment formats.")
5643 (license license:artistic2.0)))
5644
7f903d73
RW		 5645(define-public r-systempiper
5646 (package
5647 (name "r-systempiper")
1265d387 5648 (version "1.8.1")
7f903d73
RW		 5649 (source
5650 (origin
5651 (method url-fetch)
5652 (uri (bioconductor-uri "systemPipeR" version))
5653 (sha256
5654 (base32
1265d387 5655 "0hyi841w8fm2yzpm6lwqi3jz5kc8ny8dy5p29dxynzaw5bpjw56d"))))
7f903d73
RW		 5656 (properties `((upstream-name . "systemPipeR")))
5657 (build-system r-build-system)
5658 (propagated-inputs
5659 `(("r-annotate" ,r-annotate)
5660 ("r-batchjobs" ,r-batchjobs)
5661 ("r-biocgenerics" ,r-biocgenerics)
5662 ("r-biostrings" ,r-biostrings)
5663 ("r-deseq2" ,r-deseq2)
5664 ("r-edger" ,r-edger)
5665 ("r-genomicfeatures" ,r-genomicfeatures)
5666 ("r-genomicranges" ,r-genomicranges)
5667 ("r-ggplot2" ,r-ggplot2)
5668 ("r-go-db" ,r-go-db)
5669 ("r-gostats" ,r-gostats)
5670 ("r-limma" ,r-limma)
5671 ("r-pheatmap" ,r-pheatmap)
5672 ("r-rjson" ,r-rjson)
5673 ("r-rsamtools" ,r-rsamtools)
5674 ("r-shortread" ,r-shortread)
5675 ("r-summarizedexperiment" ,r-summarizedexperiment)
5676 ("r-variantannotation" ,r-variantannotation)))
5677 (home-page "https://github.com/tgirke/systemPipeR")
5678 (synopsis "Next generation sequencing workflow and reporting environment")
5679 (description
5680 "This R package provides tools for building and running automated
5681end-to-end analysis workflows for a wide range of @dfn{next generation
5682sequence} (NGS) applications such as RNA-Seq, ChIP-Seq, VAR-Seq and Ribo-Seq.
5683Important features include a uniform workflow interface across different NGS
5684applications, automated report generation, and support for running both R and
5685command-line software, such as NGS aligners or peak/variant callers, on local
5686computers or compute clusters. Efficient handling of complex sample sets and
5687experimental designs is facilitated by a consistently implemented sample
5688annotation infrastructure.")
5689 (license license:artistic2.0)))
5690
684f29bd
RW		 5691(define-public r-grohmm
5692 (package
5693 (name "r-grohmm")
c9b5046a 5694 (version "1.8.0")
684f29bd
RW		 5695 (source
5696 (origin
5697 (method url-fetch)
5698 (uri (bioconductor-uri "groHMM" version))
5699 (sha256
5700 (base32
c9b5046a 5701 "0d91nyhqbi5hv3mgmr2z0g29wg2md26g0hyv5mgapmz20cd9zi4y"))))
684f29bd
RW		 5702 (properties `((upstream-name . "groHMM")))
5703 (build-system r-build-system)
5704 (propagated-inputs
5705 `(("r-genomeinfodb" ,r-genomeinfodb)
5706 ("r-genomicalignments" ,r-genomicalignments)
5707 ("r-genomicranges" ,r-genomicranges)
5708 ("r-iranges" ,r-iranges)
5709 ("r-rtracklayer" ,r-rtracklayer)
5710 ("r-s4vectors" ,r-s4vectors)))
5711 (home-page "https://github.com/Kraus-Lab/groHMM")
5712 (synopsis "GRO-seq analysis pipeline")
5713 (description
5714 "This package provides a pipeline for the analysis of GRO-seq data.")
5715 (license license:gpl3+)))
5716
f3cfe451
RW		 5717(define-public r-txdb-hsapiens-ucsc-hg19-knowngene
5718 (package
5719 (name "r-txdb-hsapiens-ucsc-hg19-knowngene")
5720 (version "3.2.2")
5721 (source (origin
5722 (method url-fetch)
5723 ;; We cannot use bioconductor-uri here because this tarball is
5724 ;; located under "data/annotation/" instead of "bioc/".
5725 (uri (string-append "http://bioconductor.org/packages/"
5726 "release/data/annotation/src/contrib"
5727 "/TxDb.Hsapiens.UCSC.hg19.knownGene_"
5728 version ".tar.gz"))
5729 (sha256
5730 (base32
5731 "1sajhcqqwazgz2lqbik7rd935i7kpnh08zxbp2ra10j72yqy4g86"))))
5732 (properties
5733 `((upstream-name . "TxDb.Hsapiens.UCSC.hg19.knownGene")))
5734 (build-system r-build-system)
5735 ;; As this package provides little more than a very large data file it
5736 ;; doesn't make sense to build substitutes.
5737 (arguments `(#:substitutable? #f))
5738 (propagated-inputs
5739 `(("r-genomicfeatures" ,r-genomicfeatures)))
5740 (home-page
5741 "http://bioconductor.org/packages/TxDb.Hsapiens.UCSC.hg19.knownGene/")
5742 (synopsis "Annotation package for human genome in TxDb format")
5743 (description
5744 "This package provides an annotation database of Homo sapiens genome
5745data. It is derived from the UCSC hg19 genome and based on the \"knownGene\"
5746track. The database is exposed as a @code{TxDb} object.")
5747 (license license:artistic2.0)))
5748
a2950fa4
BW		 5749(define-public vsearch
5750 (package
5751 (name "vsearch")
a225db52 5752 (version "2.3.4")
a2950fa4
BW		 5753 (source
5754 (origin
5755 (method url-fetch)
5756 (uri (string-append
5757 "https://github.com/torognes/vsearch/archive/v"
5758 version ".tar.gz"))
5759 (file-name (string-append name "-" version ".tar.gz"))
5760 (sha256
5761 (base32
a225db52 5762 "1xyraxmhyx62mxx8z7c8waygvcijwkh48ms1ar60w2cv2y2sn4al"))
a2950fa4
BW		 5763 (modules '((guix build utils)))
5764 (snippet
5765 '(begin
5766 ;; Remove bundled cityhash and '-mtune=native'.
5767 (substitute* "src/Makefile.am"
5768 (("^AM_CXXFLAGS=-I\\$\\{srcdir\\}/cityhash \
5769-O3 -mtune=native -Wall -Wsign-compare")
5770 (string-append "AM_CXXFLAGS=-lcityhash"
5771 " -O3 -Wall -Wsign-compare"))
cf6edaba 5772 (("^__top_builddir__bin_vsearch_SOURCES = city.h \\\\")
a2950fa4 5773 "__top_builddir__bin_vsearch_SOURCES = \\")
cf6edaba
BW		 5774 (("^city.h \\\\") "\\")
5775 (("^citycrc.h \\\\") "\\")
5776 (("^libcityhash_a.*") "")
5777 (("noinst_LIBRARIES = libcpu_sse2.a libcpu_ssse3.a \
5778libcityhash.a")
5779 "noinst_LIBRARIES = libcpu_sse2.a libcpu_ssse3.a")
5780 (("__top_builddir__bin_vsearch_LDADD = libcpu_ssse3.a \
5781libcpu_sse2.a libcityhash.a")
5782 "__top_builddir__bin_vsearch_LDADD = libcpu_ssse3.a \
5783libcpu_sse2.a -lcityhash"))
a2950fa4 5784 (substitute* "src/vsearch.h"
cf6edaba
BW		 5785 (("^\\#include \"city.h\"") "#include <city.h>")
5786 (("^\\#include \"citycrc.h\"") "#include <citycrc.h>"))
5787 (delete-file "src/city.h")
5788 (delete-file "src/citycrc.h")
5789 (delete-file "src/city.cc")
a2950fa4
BW		 5790 #t))))
5791 (build-system gnu-build-system)
5792 (arguments
5793 `(#:phases
5794 (modify-phases %standard-phases
5795 (add-before 'configure 'autogen
5796 (lambda _ (zero? (system* "autoreconf" "-vif")))))))
5797 (inputs
5798 `(("zlib" ,zlib)
5799 ("bzip2" ,bzip2)
5800 ("cityhash" ,cityhash)))
5801 (native-inputs
5802 `(("autoconf" ,autoconf)
5803 ("automake" ,automake)))
5804 (synopsis "Sequence search tools for metagenomics")
5805 (description
5806 "VSEARCH supports DNA sequence searching, clustering, chimera detection,
5807dereplication, pairwise alignment, shuffling, subsampling, sorting and
5808masking. The tool takes advantage of parallelism in the form of SIMD
5809vectorization as well as multiple threads to perform accurate alignments at
5810high speed. VSEARCH uses an optimal global aligner (full dynamic programming
5811Needleman-Wunsch).")
5812 (home-page "https://github.com/torognes/vsearch")
6f04e515
BW		 5813 ;; vsearch uses non-portable SSE intrinsics so building fails on other
5814 ;; platforms.
5815 (supported-systems '("x86_64-linux"))
a2950fa4
BW		 5816 ;; Dual licensed; also includes public domain source.
5817 (license (list license:gpl3 license:bsd-2))))
5818
07837874
RW		 5819(define-public pardre
5820 (package
5821 (name "pardre")
7922ab8f
BW		 5822 ;; The source of 1.1.5 changed in place, so we append "-1" to the version.
5823 (version "1.1.5-1")
07837874
RW		 5824 (source
5825 (origin
5826 (method url-fetch)
5827 (uri (string-append "mirror://sourceforge/pardre/ParDRe-rel"
7922ab8f 5828 "1.1.5" ".tar.gz"))
07837874
RW		 5829 (sha256
5830 (base32
7922ab8f 5831 "17j73nc0viq4f6qj50nrndsrif5d6b71q8fl87m54psiv0ilns2b"))))
07837874
RW		 5832 (build-system gnu-build-system)
5833 (arguments
5834 `(#:tests? #f ; no tests included
5835 #:phases
5836 (modify-phases %standard-phases
5837 (delete 'configure)
5838 (replace 'install
5839 (lambda* (#:key outputs #:allow-other-keys)
5840 (let ((bin (string-append (assoc-ref outputs "out") "/bin")))
07837874
RW		 5841 (install-file "ParDRe" bin)
5842 #t))))))
5843 (inputs
5844 `(("openmpi" ,openmpi)
5845 ("zlib" ,zlib)))
5846 (synopsis "Parallel tool to remove duplicate DNA reads")
5847 (description
5848 "ParDRe is a parallel tool to remove duplicate genetic sequence reads.
5849Duplicate reads can be seen as identical or nearly identical sequences with
5850some mismatches. This tool lets users avoid the analysis of unnecessary
5851reads, reducing the time of subsequent procedures with the
5852dataset (e.g. assemblies, mappings, etc.). The tool is implemented with MPI
5853in order to exploit the parallel capabilities of multicore clusters. It is
5854faster than multithreaded counterparts (end of 2015) for the same number of
5855cores and, thanks to the message-passing technology, it can be executed on
5856clusters.")
5857 (home-page "https://sourceforge.net/projects/pardre/")
5858 (license license:gpl3+)))
5859
e4a44a6a
BW		 5860(define-public ruby-bio-kseq
5861 (package
5862 (name "ruby-bio-kseq")
5863 (version "0.0.2")
5864 (source
5865 (origin
5866 (method url-fetch)
5867 (uri (rubygems-uri "bio-kseq" version))
5868 (sha256
5869 (base32
5870 "1xyaha46khb5jc6wzkbf7040jagac49jbimn0vcrzid0j8jdikrz"))))
5871 (build-system ruby-build-system)
5872 (arguments
5873 `(#:test-target "spec"))
5874 (native-inputs
5875 `(("bundler" ,bundler)
5876 ("ruby-rspec" ,ruby-rspec)
5877 ("ruby-rake-compiler" ,ruby-rake-compiler)))
5878 (inputs
5879 `(("zlib" ,zlib)))
5880 (synopsis "Ruby bindings for the kseq.h FASTA/Q parser")
5881 (description
5882 "@code{Bio::Kseq} provides ruby bindings to the @code{kseq.h} FASTA and
5883FASTQ parsing code. It provides a fast iterator over sequences and their
5884quality scores.")
5885 (home-page "https://github.com/gusevfe/bio-kseq")
5886 (license license:expat)))
5887
9c38b540
PP		 5888(define-public bio-locus
5889 (package
5890 (name "bio-locus")
5891 (version "0.0.7")
5892 (source
5893 (origin
5894 (method url-fetch)
5895 (uri (rubygems-uri "bio-locus" version))
5896 (sha256
5897 (base32
5898 "02vmrxyimkj9sahsp4zhfhnmbvz6dbbqz1y01vglf8cbwvkajfl0"))))
5899 (build-system ruby-build-system)
5900 (native-inputs
5901 `(("ruby-rspec" ,ruby-rspec)))
5902 (synopsis "Tool for fast querying of genome locations")
5903 (description
5904 "Bio-locus is a tabix-like tool for fast querying of genome
5905locations. Many file formats in bioinformatics contain records that
5906start with a chromosome name and a position for a SNP, or a start-end
5907position for indels. Bio-locus allows users to store this chr+pos or
5908chr+pos+alt information in a database.")
5909 (home-page "https://github.com/pjotrp/bio-locus")
5910 (license license:expat)))
edb15985 5911
b2bddb07
PP		 5912(define-public bio-blastxmlparser
5913 (package
5914 (name "bio-blastxmlparser")
5915 (version "2.0.4")
5916 (source (origin
5917 (method url-fetch)
5918 (uri (rubygems-uri "bio-blastxmlparser" version))
5919 (sha256
5920 (base32
5921 "1wf4qygcmdjgcqm6flmvsagfr1gs9lf63mj32qv3z1f481zc5692"))))
5922 (build-system ruby-build-system)
5923 (propagated-inputs
5924 `(("ruby-bio-logger" ,ruby-bio-logger)
5925 ("ruby-nokogiri" ,ruby-nokogiri)))
5926 (inputs
5927 `(("ruby-rspec" ,ruby-rspec)))
5928 (synopsis "Fast big data BLAST XML parser and library")
5929 (description
5930 "Very fast parallel big-data BLAST XML file parser which can be used as
5931command line utility. Use blastxmlparser to: Parse BLAST XML; filter output;
5932generate FASTA, JSON, YAML, RDF, JSON-LD, HTML, CSV, tabular output etc.")
5933 (home-page "http://github.com/pjotrp/blastxmlparser")
5934 (license license:expat)))
5935
edb15985
PP		 5936(define-public bioruby
5937 (package
5938 (name "bioruby")
dbf9d371 5939 (version "1.5.1")
edb15985
PP		 5940 (source
5941 (origin
5942 (method url-fetch)
5943 (uri (rubygems-uri "bio" version))
5944 (sha256
5945 (base32
dbf9d371 5946 "0hdl0789c9n4mprnx5pgd46bfwl8d000rqpamj5h6kkjgspijv49"))))
edb15985
PP		 5947 (build-system ruby-build-system)
5948 (propagated-inputs
5949 `(("ruby-libxml" ,ruby-libxml)))
5950 (native-inputs
5951 `(("which" ,which))) ; required for test phase
5952 (arguments
5953 `(#:phases
5954 (modify-phases %standard-phases
5955 (add-before 'build 'patch-test-command
5956 (lambda _
5957 (substitute* '("test/functional/bio/test_command.rb")
5958 (("/bin/sh") (which "sh")))
5959 (substitute* '("test/functional/bio/test_command.rb")
5960 (("/bin/ls") (which "ls")))
5961 (substitute* '("test/functional/bio/test_command.rb")
5962 (("which") (which "which")))
5963 (substitute* '("test/functional/bio/test_command.rb",
5964 "test/data/command/echoarg2.sh")
5965 (("/bin/echo") (which "echo")))
5966 #t)))))
5967 (synopsis "Ruby library, shell and utilities for bioinformatics")
5968 (description "BioRuby comes with a comprehensive set of Ruby development
5969tools and libraries for bioinformatics and molecular biology. BioRuby has
5970components for sequence analysis, pathway analysis, protein modelling and
5971phylogenetic analysis; it supports many widely used data formats and provides
5972easy access to databases, external programs and public web services, including
5973BLAST, KEGG, GenBank, MEDLINE and GO.")
5974 (home-page "http://bioruby.org/")
5975 ;; Code is released under Ruby license, except for setup
5976 ;; (LGPLv2.1+) and scripts in samples (which have GPL2 and GPL2+)
5977 (license (list license:ruby license:lgpl2.1+ license:gpl2+ ))))
a5002ae7 5978
9fba89e8
RW		 5979(define-public r-acsnminer
5980 (package
5981 (name "r-acsnminer")
0b54b4c9 5982 (version "0.16.8.25")
9fba89e8
RW		 5983 (source (origin
5984 (method url-fetch)
5985 (uri (cran-uri "ACSNMineR" version))
5986 (sha256
5987 (base32
0b54b4c9 5988 "0gh604s8qall6zfjlwcg2ilxjvz08dplf9k5g47idhv43scm748l"))))
9fba89e8
RW		 5989 (properties `((upstream-name . "ACSNMineR")))
5990 (build-system r-build-system)
5991 (propagated-inputs
5992 `(("r-ggplot2" ,r-ggplot2)
5993 ("r-gridextra" ,r-gridextra)))
5994 (home-page "http://cran.r-project.org/web/packages/ACSNMineR")
5995 (synopsis "Gene enrichment analysis")
5996 (description
5997 "This package provides tools to compute and represent gene set enrichment
5998or depletion from your data based on pre-saved maps from the @dfn{Atlas of
5999Cancer Signalling Networks} (ACSN) or user imported maps. The gene set
6000enrichment can be run with hypergeometric test or Fisher exact test, and can
6001use multiple corrections. Visualization of data can be done either by
6002barplots or heatmaps.")
6003 (license license:gpl2+)))
6004
d29b25c4
RW		 6005(define-public r-biocgenerics
6006 (package
6007 (name "r-biocgenerics")
f0b297e1 6008 (version "0.20.0")
d29b25c4
RW		 6009 (source (origin
6010 (method url-fetch)
6011 (uri (bioconductor-uri "BiocGenerics" version))
6012 (sha256
6013 (base32
f0b297e1 6014 "06szdz7dfs1iyv5zdl4fjzad18nnf1zf3wvglc6c6yd9mrqlf7vk"))))
d29b25c4 6015 (properties
1d216b6e 6016 `((upstream-name . "BiocGenerics")))
d29b25c4
RW		 6017 (build-system r-build-system)
6018 (home-page "http://bioconductor.org/packages/BiocGenerics")
6019 (synopsis "S4 generic functions for Bioconductor")
6020 (description
6021 "This package provides S4 generic functions needed by many Bioconductor
6022packages.")
6023 (license license:artistic2.0)))
6024
eb24341f
RJ		 6025(define-public r-biocinstaller
6026 (package
6027 (name "r-biocinstaller")
5c7b04e0 6028 (version "1.24.0")
eb24341f
RJ		 6029 (source (origin
6030 (method url-fetch)
6031 (uri (bioconductor-uri "BiocInstaller" version))
6032 (sha256
6033 (base32
5c7b04e0 6034 "0y1y5wmy6lzjqx3hdg15n91d417ccjj8dbvdkhmp99bs5aijwcpn"))))
eb24341f
RJ		 6035 (properties
6036 `((upstream-name . "BiocInstaller")))
6037 (build-system r-build-system)
6038 (home-page "http://bioconductor.org/packages/BiocInstaller")
6039 (synopsis "Install Bioconductor packages")
6040 (description "This package is used to install and update R packages from
6041Bioconductor, CRAN, and Github.")
6042 (license license:artistic2.0)))
6043
207ce8fb
RJ		 6044(define-public r-biocviews
6045 (package
6046 (name "r-biocviews")
6047 (version "1.42.0")
6048 (source (origin
6049 (method url-fetch)
6050 (uri (bioconductor-uri "biocViews" version))
6051 (sha256
6052 (base32
6053 "07rjk10b91pkriyq297w86199r2d3sfji3ggs9mq2gyalsa8y4b6"))))
6054 (properties
6055 `((upstream-name . "biocViews")))
6056 (build-system r-build-system)
6057 (propagated-inputs
6058 `(("r-biobase" ,r-biobase)
6059 ("r-graph" ,r-graph)
6060 ("r-rbgl" ,r-rbgl)
6061 ("r-rcurl" ,r-rcurl)
6062 ("r-xml" ,r-xml)
6063 ("r-knitr" ,r-knitr)
6064 ("r-runit" ,r-runit)))
6065 (home-page "http://bioconductor.org/packages/biocViews")
6066 (synopsis "Bioconductor package categorization helper")
6067 (description "The purpose of biocViews is to create HTML pages that
6068categorize packages in a Bioconductor package repository according to keywords,
6069also known as views, in a controlled vocabulary.")
6070 (license license:artistic2.0)))
6071
99df12cd
RJ		 6072(define-public r-biocstyle
6073 (package
6074 (name "r-biocstyle")
c8ad8b69 6075 (version "2.2.1")
99df12cd
RJ		 6076 (source (origin
6077 (method url-fetch)
6078 (uri (bioconductor-uri "BiocStyle" version))
6079 (sha256
6080 (base32
c8ad8b69 6081 "0sl99xw940ixrm6v24lgaw3ljh56g59a6rdz7g160hx84z9f8n2n"))))
99df12cd
RJ		 6082 (properties
6083 `((upstream-name . "BiocStyle")))
6084 (build-system r-build-system)
6085 (home-page "http://bioconductor.org/packages/BiocStyle")
6086 (synopsis "Bioconductor formatting styles")
6087 (description "This package provides standard formatting styles for
6088Bioconductor PDF and HTML documents. Package vignettes illustrate use and
6089functionality.")
6090 (license license:artistic2.0)))
6091
4644644a
RJ		 6092(define-public r-bioccheck
6093 (package
6094 (name "r-bioccheck")
6095 (version "1.10.0")
6096 (source (origin
6097 (method url-fetch)
6098 (uri (bioconductor-uri "BiocCheck" version))
6099 (sha256
6100 (base32
6101 "1rfy37xg1nc2cmgbclvzsi7sgmdcdjiahsx9crgx3yaw7kxgiack"))))
6102 (properties
6103 `((upstream-name . "BiocCheck")))
6104 (build-system r-build-system)
6105 (arguments
6106 '(#:phases
6107 (modify-phases %standard-phases
6108 ;; This package can be used by calling BiocCheck(<package>) from
6109 ;; within R, or by running R CMD BiocCheck <package>. This phase
6110 ;; makes sure the latter works. For this to work, the BiocCheck
6111 ;; script must be somewhere on the PATH (not the R bin directory).
6112 (add-after 'install 'install-bioccheck-subcommand
6113 (lambda* (#:key outputs #:allow-other-keys)
6114 (let* ((out (assoc-ref outputs "out"))
6115 (dest-dir (string-append out "/bin"))
6116 (script-dir
6117 (string-append out "/site-library/BiocCheck/script/")))
6118 (mkdir-p dest-dir)
6119 (symlink (string-append script-dir "/checkBadDeps.R")
6120 (string-append dest-dir "/checkBadDeps.R"))
6121 (symlink (string-append script-dir "/BiocCheck")
6122 (string-append dest-dir "/BiocCheck")))
6123 #t)))))
6124 (native-inputs
6125 `(("which" ,which)))
6126 (propagated-inputs
6127 `(("r-graph" ,r-graph)
6128 ("r-knitr" ,r-knitr)
6129 ("r-httr" ,r-httr)
6130 ("r-optparse" ,r-optparse)
6131 ("r-devtools" ,r-devtools)
6132 ("r-biocinstaller" ,r-biocinstaller)
6133 ("r-biocviews" ,r-biocviews)))
6134 (home-page "http://bioconductor.org/packages/BiocCheck")
6135 (synopsis "Executes Bioconductor-specific package checks")
6136 (description "This package contains tools to perform additional quality
6137checks on R packages that are to be submitted to the Bioconductor repository.")
6138 (license license:artistic2.0)))
6139
2acaaee5
RJ		 6140(define-public r-getopt
6141 (package
6142 (name "r-getopt")
6143 (version "1.20.0")
6144 (source
6145 (origin
6146 (method url-fetch)
6147 (uri (cran-uri "getopt" version))
6148 (sha256
6149 (base32
6150 "00f57vgnzmg7cz80rjmjz1556xqcmx8nhrlbbhaq4w7gl2ibl87r"))))
6151 (build-system r-build-system)
6152 (home-page "https://github.com/trevorld/getopt")
6153 (synopsis "Command-line option processor for R")
6154 (description
6155 "This package is designed to be used with Rscript to write shebang
6156scripts that accept short and long options. Many users will prefer to
6157use the packages @code{optparse} or @code{argparse} which add extra
6158features like automatically generated help options and usage texts,
6159support for default values, positional argument support, etc.")
6160 (license license:gpl2+)))
6161
c79ad57a
RJ		 6162(define-public r-optparse
6163 (package
6164 (name "r-optparse")
6165 (version "1.3.2")
6166 (source
6167 (origin
6168 (method url-fetch)
6169 (uri (cran-uri "optparse" version))
6170 (sha256
6171 (base32
6172 "1g8as89r91xxi5j5azsd6vrfrhg84mnfx2683j7pacdp8s33radw"))))
6173 (build-system r-build-system)
6174 (propagated-inputs
6175 `(("r-getopt" ,r-getopt)))
6176 (home-page
6177 "https://github.com/trevorld/optparse")
6178 (synopsis "Command line option parser")
6179 (description
6180 "This package provides a command line parser inspired by Python's
6181@code{optparse} library to be used with Rscript to write shebang scripts
6182that accept short and long options.")
6183 (license license:gpl2+)))
6184
247d498a
RJ		 6185(define-public r-dnacopy
6186 (package
6187 (name "r-dnacopy")
22c5d736 6188 (version "1.48.0")
247d498a
RJ		 6189 (source (origin
6190 (method url-fetch)
6191 (uri (bioconductor-uri "DNAcopy" version))
6192 (sha256
6193 (base32
22c5d736 6194 "1idyvfvy7xx8k9vk00y4k3819qmip8iqm809j3vpxabmsn7r9zyh"))))
247d498a
RJ		 6195 (properties
6196 `((upstream-name . "DNAcopy")))
6197 (build-system r-build-system)
6198 (inputs
6199 `(("gfortran" ,gfortran)))
5697fdc3 6200 (home-page "https://bioconductor.org/packages/DNAcopy")
247d498a
RJ		 6201 (synopsis "Implementation of a circular binary segmentation algorithm")
6202 (description "This package implements the circular binary segmentation (CBS)
6203algorithm to segment DNA copy number data and identify genomic regions with
6204abnormal copy number.")
6205 (license license:gpl2+)))
6206
7485129e
RW		 6207(define-public r-s4vectors
6208 (package
6209 (name "r-s4vectors")
86fc9c4a 6210 (version "0.12.1")
7485129e
RW		 6211 (source (origin
6212 (method url-fetch)
6213 (uri (bioconductor-uri "S4Vectors" version))
6214 (sha256
6215 (base32
86fc9c4a 6216 "0i36y3w36h3d8rmazxcrip4gvn54rd9av1wz4lygsprrjmylfhcc"))))
7485129e 6217 (properties
1d216b6e 6218 `((upstream-name . "S4Vectors")))
7485129e
RW		 6219 (build-system r-build-system)
6220 (propagated-inputs
6221 `(("r-biocgenerics" ,r-biocgenerics)))
6222 (home-page "http://bioconductor.org/packages/S4Vectors")
6223 (synopsis "S4 implementation of vectors and lists")
6224 (description
6225 "The S4Vectors package defines the @code{Vector} and @code{List} virtual
6226classes and a set of generic functions that extend the semantic of ordinary
6227vectors and lists in R. Package developers can easily implement vector-like
6228or list-like objects as concrete subclasses of @code{Vector} or @code{List}.
6229In addition, a few low-level concrete subclasses of general interest (e.g.
6230@code{DataFrame}, @code{Rle}, and @code{Hits}) are implemented in the
6231S4Vectors package itself.")
6232 (license license:artistic2.0)))
6233
274da826
RW		 6234(define-public r-seqinr
6235 (package
6236 (name "r-seqinr")
a46cc723 6237 (version "3.3-3")
274da826
RW		 6238 (source
6239 (origin
6240 (method url-fetch)
6241 (uri (cran-uri "seqinr" version))
6242 (sha256
6243 (base32
a46cc723 6244 "0rk4yba8km26c0rh1f4h474zsb5n6kjmqsi55bnzr6p8pymp18hj"))))
274da826
RW		 6245 (build-system r-build-system)
6246 (propagated-inputs
3b851cd4
RW		 6247 `(("r-ade4" ,r-ade4)
6248 ("r-segmented" ,r-segmented)))
274da826
RW		 6249 (inputs
6250 `(("zlib" ,zlib)))
6251 (home-page "http://seqinr.r-forge.r-project.org/")
6252 (synopsis "Biological sequences retrieval and analysis")
6253 (description
6254 "This package provides tools for exploratory data analysis and data
6255visualization of biological sequence (DNA and protein) data. It also includes
6256utilities for sequence data management under the ACNUC system.")
6257 (license license:gpl2+)))
6258
78addcb0
RW		 6259(define-public r-iranges
6260 (package
6261 (name "r-iranges")
54d9b568 6262 (version "2.8.1")
78addcb0
RW		 6263 (source (origin
6264 (method url-fetch)
6265 (uri (bioconductor-uri "IRanges" version))
6266 (sha256
6267 (base32
54d9b568 6268 "0cryqnpqb3p6l9jjw27hyqd550sxlljls3ka7b9rb38hkji7b5hw"))))
78addcb0 6269 (properties
1d216b6e 6270 `((upstream-name . "IRanges")))
78addcb0
RW		 6271 (build-system r-build-system)
6272 (propagated-inputs
6273 `(("r-biocgenerics" ,r-biocgenerics)
6274 ("r-s4vectors" ,r-s4vectors)))
6275 (home-page "http://bioconductor.org/packages/IRanges")
6276 (synopsis "Infrastructure for manipulating intervals on sequences")
6277 (description
6278 "This package provides efficient low-level and highly reusable S4 classes
6279for storing ranges of integers, RLE vectors (Run-Length Encoding), and, more
6280generally, data that can be organized sequentially (formally defined as
6281@code{Vector} objects), as well as views on these @code{Vector} objects.
6282Efficient list-like classes are also provided for storing big collections of
6283instances of the basic classes. All classes in the package use consistent
6284naming and share the same rich and consistent \"Vector API\" as much as
6285possible.")
6286 (license license:artistic2.0)))
6287
bf7764b7
RW		 6288(define-public r-genomeinfodb
6289 (package
6290 (name "r-genomeinfodb")
ac370a33 6291 (version "1.10.2")
bf7764b7
RW		 6292 (source (origin
6293 (method url-fetch)
6294 (uri (bioconductor-uri "GenomeInfoDb" version))
6295 (sha256
6296 (base32
ac370a33 6297 "0zh894qd1sgpjbn0wfvq6hs2dzn7y1pyicvzk2aa48y3zbidanv7"))))
bf7764b7 6298 (properties
1d216b6e 6299 `((upstream-name . "GenomeInfoDb")))
bf7764b7
RW		 6300 (build-system r-build-system)
6301 (propagated-inputs
6302 `(("r-biocgenerics" ,r-biocgenerics)
6303 ("r-iranges" ,r-iranges)
6304 ("r-s4vectors" ,r-s4vectors)))
6305 (home-page "http://bioconductor.org/packages/GenomeInfoDb")
6306 (synopsis "Utilities for manipulating chromosome identifiers")
6307 (description
6308 "This package contains data and functions that define and allow
6309translation between different chromosome sequence naming conventions (e.g.,
6310\"chr1\" versus \"1\"), including a function that attempts to place sequence
6311names in their natural, rather than lexicographic, order.")
6312 (license license:artistic2.0)))
6313
744004a3
RJ		 6314(define-public r-edger
6315 (package
6316 (name "r-edger")
5d3acc0b 6317 (version "3.16.5")
744004a3
RJ		 6318 (source (origin
6319 (method url-fetch)
6320 (uri (bioconductor-uri "edgeR" version))
6321 (sha256
6322 (base32
5d3acc0b 6323 "04vpa0a6dkkjyvvfbkmfjyaxf2ldkagi66g028qpaszd8jsk8yiv"))))
744004a3
RJ		 6324 (properties `((upstream-name . "edgeR")))
6325 (build-system r-build-system)
6326 (propagated-inputs
5e48005f
RW		 6327 `(("r-limma" ,r-limma)
6328 ("r-locfit" ,r-locfit)))
744004a3
RJ		 6329 (home-page "http://bioinf.wehi.edu.au/edgeR")
6330 (synopsis "EdgeR does empirical analysis of digital gene expression data")
6331 (description "This package can do differential expression analysis of
6332RNA-seq expression profiles with biological replication. It implements a range
6333of statistical methodology based on the negative binomial distributions,
6334including empirical Bayes estimation, exact tests, generalized linear models
6335and quasi-likelihood tests. It be applied to differential signal analysis of
6336other types of genomic data that produce counts, including ChIP-seq, SAGE and
6337CAGE.")
6338 (license license:gpl2+)))
6339
b669d9c4
RJ		 6340(define-public r-variantannotation
6341 (package
6342 (name "r-variantannotation")
5796af99 6343 (version "1.20.2")
b669d9c4
RJ		 6344 (source (origin
6345 (method url-fetch)
6346 (uri (bioconductor-uri "VariantAnnotation" version))
6347 (sha256
6348 (base32
5796af99 6349 "165wda1d2jagd907pnra4m3sla66icyqxvd60xpv09jl5agd5mn9"))))
b669d9c4
RJ		 6350 (properties
6351 `((upstream-name . "VariantAnnotation")))
6352 (inputs
6353 `(("zlib" ,zlib)))
6354 (propagated-inputs
6355 `(("r-annotationdbi" ,r-annotationdbi)
37d96f1d 6356 ("r-biobase" ,r-biobase)
b669d9c4 6357 ("r-biocgenerics" ,r-biocgenerics)
37d96f1d 6358 ("r-biostrings" ,r-biostrings)
b669d9c4
RJ		 6359 ("r-bsgenome" ,r-bsgenome)
6360 ("r-dbi" ,r-dbi)
6361 ("r-genomeinfodb" ,r-genomeinfodb)
6362 ("r-genomicfeatures" ,r-genomicfeatures)
6363 ("r-genomicranges" ,r-genomicranges)
37d96f1d 6364 ("r-iranges" ,r-iranges)
b669d9c4
RJ		 6365 ("r-summarizedexperiment" ,r-summarizedexperiment)
6366 ("r-rsamtools" ,r-rsamtools)
37d96f1d
RW		 6367 ("r-rtracklayer" ,r-rtracklayer)
6368 ("r-s4vectors" ,r-s4vectors)
6369 ("r-xvector" ,r-xvector)
b669d9c4
RJ		 6370 ("r-zlibbioc" ,r-zlibbioc)))
6371 (build-system r-build-system)
6372 (home-page "https://bioconductor.org/packages/VariantAnnotation")
6373 (synopsis "Package for annotation of genetic variants")
6374 (description "This R package can annotate variants, compute amino acid
6375coding changes and predict coding outcomes.")
6376 (license license:artistic2.0)))
6377
7d4224d7
RJ		 6378(define-public r-limma
6379 (package
6380 (name "r-limma")
72c2693b 6381 (version "3.30.7")
7d4224d7
RJ		 6382 (source (origin
6383 (method url-fetch)
6384 (uri (bioconductor-uri "limma" version))
6385 (sha256
6386 (base32
72c2693b 6387 "1xg9w4lmn9n4hwyflxiwi6g969lcy569cg4z1x47crwwg7z7qdka"))))
7d4224d7
RJ		 6388 (build-system r-build-system)
6389 (home-page "http://bioinf.wehi.edu.au/limma")
6390 (synopsis "Package for linear models for microarray and RNA-seq data")
6391 (description "This package can be used for the analysis of gene expression
6392studies, especially the use of linear models for analysing designed experiments
6393and the assessment of differential expression. The analysis methods apply to
6394different technologies, including microarrays, RNA-seq, and quantitative PCR.")
6395 (license license:gpl2+)))
6396
0e7d5560
RW		 6397(define-public r-xvector
6398 (package
6399 (name "r-xvector")
1d048589 6400 (version "0.14.0")
0e7d5560
RW		 6401 (source (origin
6402 (method url-fetch)
6403 (uri (bioconductor-uri "XVector" version))
6404 (sha256
6405 (base32
1d048589 6406 "09lbqxpqr80g0kw77mpz0p1a8cq706j33kz8194wp71il67cdzi7"))))
0e7d5560 6407 (properties
1d216b6e 6408 `((upstream-name . "XVector")))
0e7d5560
RW		 6409 (build-system r-build-system)
6410 (arguments
6411 `(#:phases
6412 (modify-phases %standard-phases
6413 (add-after 'unpack 'use-system-zlib
6414 (lambda _
6415 (substitute* "DESCRIPTION"
6416 (("zlibbioc, ") ""))
6417 (substitute* "NAMESPACE"
6418 (("import\\(zlibbioc\\)") ""))
6419 #t)))))
6420 (inputs
6421 `(("zlib" ,zlib)))
6422 (propagated-inputs
6423 `(("r-biocgenerics" ,r-biocgenerics)
6424 ("r-iranges" ,r-iranges)
6425 ("r-s4vectors" ,r-s4vectors)))
6426 (home-page "http://bioconductor.org/packages/XVector")
6427 (synopsis "Representation and manpulation of external sequences")
6428 (description
6429 "This package provides memory efficient S4 classes for storing sequences
6430\"externally\" (behind an R external pointer, or on disk).")
6431 (license license:artistic2.0)))
6432
e2cd1d0f
RW		 6433(define-public r-genomicranges
6434 (package
6435 (name "r-genomicranges")
407a2801 6436 (version "1.26.2")
e2cd1d0f
RW		 6437 (source (origin
6438 (method url-fetch)
6439 (uri (bioconductor-uri "GenomicRanges" version))
6440 (sha256
6441 (base32
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e2cd1d0f 6443 (properties
1d216b6e 6444 `((upstream-name . "GenomicRanges")))
e2cd1d0f
RW		 6445 (build-system r-build-system)
6446 (propagated-inputs
6447 `(("r-biocgenerics" ,r-biocgenerics)
6448 ("r-genomeinfodb" ,r-genomeinfodb)
92a740af
RW		 6449 ("r-iranges" ,r-iranges)
6450 ("r-s4vectors" ,r-s4vectors)
e2cd1d0f
RW		 6451 ("r-xvector" ,r-xvector)))
6452 (home-page "http://bioconductor.org/packages/GenomicRanges")
6453 (synopsis "Representation and manipulation of genomic intervals")
6454 (description
6455 "This package provides tools to efficiently represent and manipulate
6456genomic annotations and alignments is playing a central role when it comes to
6457analyzing high-throughput sequencing data (a.k.a. NGS data). The
6458GenomicRanges package defines general purpose containers for storing and
6459manipulating genomic intervals and variables defined along a genome.")
6460 (license license:artistic2.0)))
6461
555e3399
RW		 6462(define-public r-biobase
6463 (package
6464 (name "r-biobase")
464870ca 6465 (version "2.34.0")
555e3399
RW		 6466 (source (origin
6467 (method url-fetch)
6468 (uri (bioconductor-uri "Biobase" version))
6469 (sha256
6470 (base32
464870ca 6471 "0js9j9wqls8f571ifl9ylllbb9a9hwf7b7drf2grwb1fl31ldazl"))))
555e3399
RW		 6472 (properties
6473 `((upstream-name . "Biobase")))
6474 (build-system r-build-system)
6475 (propagated-inputs
6476 `(("r-biocgenerics" ,r-biocgenerics)))
6477 (home-page "http://bioconductor.org/packages/Biobase")
6478 (synopsis "Base functions for Bioconductor")
6479 (description
6480 "This package provides functions that are needed by many other packages
6481on Bioconductor or which replace R functions.")
6482 (license license:artistic2.0)))
6483
8b7bce74
RW		 6484(define-public r-annotationdbi
6485 (package
6486 (name "r-annotationdbi")
e45dc057 6487 (version "1.36.0")
8b7bce74
RW		 6488 (source (origin
6489 (method url-fetch)
6490 (uri (bioconductor-uri "AnnotationDbi" version))
6491 (sha256
6492 (base32
e45dc057 6493 "0ydrqw1k1j5p6w76bwc753cx545c055x88q87wzya93858synj6r"))))
8b7bce74
RW		 6494 (properties
6495 `((upstream-name . "AnnotationDbi")))
6496 (build-system r-build-system)
6497 (propagated-inputs
6498 `(("r-biobase" ,r-biobase)
6499 ("r-biocgenerics" ,r-biocgenerics)
6500 ("r-dbi" ,r-dbi)
6501 ("r-iranges" ,r-iranges)
6502 ("r-rsqlite" ,r-rsqlite)
6503 ("r-s4vectors" ,r-s4vectors)))
6504 (home-page "http://bioconductor.org/packages/AnnotationDbi")
6505 (synopsis "Annotation database interface")
6506 (description
6507 "This package provides user interface and database connection code for
6508annotation data packages using SQLite data storage.")
6509 (license license:artistic2.0)))
6510
c465fa72
RW		 6511(define-public r-biomart
6512 (package
6513 (name "r-biomart")
94053331 6514 (version "2.30.0")
c465fa72
RW		 6515 (source (origin
6516 (method url-fetch)
6517 (uri (bioconductor-uri "biomaRt" version))
6518 (sha256
6519 (base32
94053331 6520 "1x0flcghq71784q2l02j0g4f9jkmyb14f6i307n6c59d6ji7h7x6"))))
c465fa72
RW		 6521 (properties
6522 `((upstream-name . "biomaRt")))
6523 (build-system r-build-system)
6524 (propagated-inputs
6525 `(("r-annotationdbi" ,r-annotationdbi)
6526 ("r-rcurl" ,r-rcurl)
6527 ("r-xml" ,r-xml)))
6528 (home-page "http://bioconductor.org/packages/biomaRt")
6529 (synopsis "Interface to BioMart databases")
6530 (description
6531 "biomaRt provides an interface to a growing collection of databases
6532implementing the @url{BioMart software suite, http://www.biomart.org}. The
6533package enables retrieval of large amounts of data in a uniform way without
6534the need to know the underlying database schemas or write complex SQL queries.
6535Examples of BioMart databases are Ensembl, COSMIC, Uniprot, HGNC, Gramene,
6536Wormbase and dbSNP mapped to Ensembl. These major databases give biomaRt
6537users direct access to a diverse set of data and enable a wide range of
6538powerful online queries from gene annotation to database mining.")
6539 (license license:artistic2.0)))
6540
e91d362e
RW		 6541(define-public r-biocparallel
6542 (package
6543 (name "r-biocparallel")
c15ae9b0 6544 (version "1.8.1")
e91d362e
RW		 6545 (source (origin
6546 (method url-fetch)
6547 (uri (bioconductor-uri "BiocParallel" version))
6548 (sha256
6549 (base32
c15ae9b0 6550 "123i928rwi4h4sy4fpysv6pinw5nns0sm3myxi2ghqhm34ws8gyl"))))
e91d362e
RW		 6551 (properties
6552 `((upstream-name . "BiocParallel")))
6553 (build-system r-build-system)
6554 (propagated-inputs
6555 `(("r-futile-logger" ,r-futile-logger)
6556 ("r-snow" ,r-snow)))
6557 (home-page "http://bioconductor.org/packages/BiocParallel")
6558 (synopsis "Bioconductor facilities for parallel evaluation")
6559 (description
6560 "This package provides modified versions and novel implementation of
6561functions for parallel evaluation, tailored to use with Bioconductor
6562objects.")
6563 (license (list license:gpl2+ license:gpl3+))))
6564
bf159353
RW		 6565(define-public r-biostrings
6566 (package
6567 (name "r-biostrings")
2f642e52 6568 (version "2.42.1")
bf159353
RW		 6569 (source (origin
6570 (method url-fetch)
6571 (uri (bioconductor-uri "Biostrings" version))
6572 (sha256
6573 (base32
2f642e52 6574 "0vqgd9i6y3wj4zviqwgvwgd4qj6033fg01rmx1cw9bw5i8ans42d"))))
bf159353
RW		 6575 (properties
6576 `((upstream-name . "Biostrings")))
6577 (build-system r-build-system)
6578 (propagated-inputs
6579 `(("r-biocgenerics" ,r-biocgenerics)
6580 ("r-iranges" ,r-iranges)
6581 ("r-s4vectors" ,r-s4vectors)
6582 ("r-xvector" ,r-xvector)))
6583 (home-page "http://bioconductor.org/packages/Biostrings")
6584 (synopsis "String objects and algorithms for biological sequences")
6585 (description
6586 "This package provides memory efficient string containers, string
6587matching algorithms, and other utilities, for fast manipulation of large
6588biological sequences or sets of sequences.")
6589 (license license:artistic2.0)))
6590
f8d74f70
RW		 6591(define-public r-rsamtools
6592 (package
6593 (name "r-rsamtools")
c0ccef41 6594 (version "1.26.1")
f8d74f70
RW		 6595 (source (origin
6596 (method url-fetch)
6597 (uri (bioconductor-uri "Rsamtools" version))
6598 (sha256
6599 (base32
c0ccef41 6600 "0pf4f6brf4bl5zgjrah0f38qslazrs49ayqgyh0xfqgrh63yx4ck"))))
f8d74f70
RW		 6601 (properties
6602 `((upstream-name . "Rsamtools")))
6603 (build-system r-build-system)
6604 (arguments
6605 `(#:phases
6606 (modify-phases %standard-phases
6607 (add-after 'unpack 'use-system-zlib
6608 (lambda _
6609 (substitute* "DESCRIPTION"
6610 (("zlibbioc, ") ""))
6611 (substitute* "NAMESPACE"
6612 (("import\\(zlibbioc\\)") ""))
6613 #t)))))
6614 (inputs
6615 `(("zlib" ,zlib)))
6616 (propagated-inputs
6617 `(("r-biocgenerics" ,r-biocgenerics)
6618 ("r-biocparallel" ,r-biocparallel)
6619 ("r-biostrings" ,r-biostrings)
6620 ("r-bitops" ,r-bitops)
6621 ("r-genomeinfodb" ,r-genomeinfodb)
6622 ("r-genomicranges" ,r-genomicranges)
6623 ("r-iranges" ,r-iranges)
6624 ("r-s4vectors" ,r-s4vectors)
6625 ("r-xvector" ,r-xvector)))
6626 (home-page "http://bioconductor.org/packages/release/bioc/html/Rsamtools.html")
6627 (synopsis "Interface to samtools, bcftools, and tabix")
6628 (description
6629 "This package provides an interface to the 'samtools', 'bcftools', and
6630'tabix' utilities for manipulating SAM (Sequence Alignment / Map), FASTA,
6631binary variant call (BCF) and compressed indexed tab-delimited (tabix)
6632files.")
6633 (license license:expat)))
6634
6e76dda2
RW		 6635(define-public r-summarizedexperiment
6636 (package
6637 (name "r-summarizedexperiment")
08da08d2 6638 (version "1.4.0")
6e76dda2
RW		 6639 (source (origin
6640 (method url-fetch)
6641 (uri (bioconductor-uri "SummarizedExperiment" version))
6642 (sha256
6643 (base32
08da08d2 6644 "1kbj8sg2ik9f8d6g95wz0py62jldg01qy5rsdpg1cxw95nf7dzi3"))))
6e76dda2
RW		 6645 (properties
6646 `((upstream-name . "SummarizedExperiment")))
6647 (build-system r-build-system)
6648 (propagated-inputs
6649 `(("r-biobase" ,r-biobase)
6650 ("r-biocgenerics" ,r-biocgenerics)
6651 ("r-genomeinfodb" ,r-genomeinfodb)
6652 ("r-genomicranges" ,r-genomicranges)
6653 ("r-iranges" ,r-iranges)
6654 ("r-s4vectors" ,r-s4vectors)))
6655 (home-page "http://bioconductor.org/packages/SummarizedExperiment")
6656 (synopsis "Container for representing genomic ranges by sample")
6657 (description
6658 "The SummarizedExperiment container contains one or more assays, each
6659represented by a matrix-like object of numeric or other mode. The rows
6660typically represent genomic ranges of interest and the columns represent
6661samples.")
6662 (license license:artistic2.0)))
6663
d8a828af
RW		 6664(define-public r-genomicalignments
6665 (package
6666 (name "r-genomicalignments")
4ab32f0c 6667 (version "1.10.0")
d8a828af
RW		 6668 (source (origin
6669 (method url-fetch)
6670 (uri (bioconductor-uri "GenomicAlignments" version))
6671 (sha256
6672 (base32
4ab32f0c 6673 "11vb0a0zd36i4yhg4mfijv787v0nihn6pkjj6q7rfy19gwy61xlc"))))
d8a828af
RW		 6674 (properties
6675 `((upstream-name . "GenomicAlignments")))
6676 (build-system r-build-system)
6677 (propagated-inputs
6678 `(("r-biocgenerics" ,r-biocgenerics)
6679 ("r-biocparallel" ,r-biocparallel)
6680 ("r-biostrings" ,r-biostrings)
6681 ("r-genomeinfodb" ,r-genomeinfodb)
6682 ("r-genomicranges" ,r-genomicranges)
6683 ("r-iranges" ,r-iranges)
6684 ("r-rsamtools" ,r-rsamtools)
6685 ("r-s4vectors" ,r-s4vectors)
6686 ("r-summarizedexperiment" ,r-summarizedexperiment)))
6687 (home-page "http://bioconductor.org/packages/GenomicAlignments")
6688 (synopsis "Representation and manipulation of short genomic alignments")
6689 (description
6690 "This package provides efficient containers for storing and manipulating
6691short genomic alignments (typically obtained by aligning short reads to a
6692reference genome). This includes read counting, computing the coverage,
6693junction detection, and working with the nucleotide content of the
6694alignments.")
6695 (license license:artistic2.0)))
6696
317755ff
RW		 6697(define-public r-rtracklayer
6698 (package
6699 (name "r-rtracklayer")
16a8bd31 6700 (version "1.34.1")
317755ff
RW		 6701 (source (origin
6702 (method url-fetch)
6703 (uri (bioconductor-uri "rtracklayer" version))
6704 (sha256
6705 (base32
16a8bd31 6706 "0x59k2fd0iaqi93gy6bm58p2j2z90z1b7a6w5b4c098y98n096rc"))))
317755ff
RW		 6707 (build-system r-build-system)
6708 (arguments
6709 `(#:phases
6710 (modify-phases %standard-phases
6711 (add-after 'unpack 'use-system-zlib
6712 (lambda _
6713 (substitute* "DESCRIPTION"
6714 (("zlibbioc, ") ""))
6715 (substitute* "NAMESPACE"
6716 (("import\\(zlibbioc\\)") ""))
6717 #t)))))
6718 (inputs
6719 `(("zlib" ,zlib)))
6720 (propagated-inputs
6721 `(("r-biocgenerics" ,r-biocgenerics)
6722 ("r-biostrings" ,r-biostrings)
6723 ("r-genomeinfodb" ,r-genomeinfodb)
6724 ("r-genomicalignments" ,r-genomicalignments)
6725 ("r-genomicranges" ,r-genomicranges)
6726 ("r-iranges" ,r-iranges)
6727 ("r-rcurl" ,r-rcurl)
6728 ("r-rsamtools" ,r-rsamtools)
6729 ("r-s4vectors" ,r-s4vectors)
6730 ("r-xml" ,r-xml)
6731 ("r-xvector" ,r-xvector)))
6732 (home-page "http://bioconductor.org/packages/rtracklayer")
6733 (synopsis "R interface to genome browsers and their annotation tracks")
6734 (description
6735 "rtracklayer is an extensible framework for interacting with multiple
6736genome browsers (currently UCSC built-in) and manipulating annotation tracks
6737in various formats (currently GFF, BED, bedGraph, BED15, WIG, BigWig and 2bit
6738built-in). The user may export/import tracks to/from the supported browsers,
6739as well as query and modify the browser state, such as the current viewport.")
6740 (license license:artistic2.0)))
6741
2fd7c049
RW		 6742(define-public r-genomicfeatures
6743 (package
6744 (name "r-genomicfeatures")
76b64381 6745 (version "1.26.2")
2fd7c049
RW		 6746 (source (origin
6747 (method url-fetch)
6748 (uri (bioconductor-uri "GenomicFeatures" version))
6749 (sha256
6750 (base32
76b64381 6751 "1ybi6r3bax07wlv2qcd34y5qjdvcqcfayfvlrjc39ifrkk65wv4f"))))
2fd7c049
RW		 6752 (properties
6753 `((upstream-name . "GenomicFeatures")))
6754 (build-system r-build-system)
6755 (propagated-inputs
6756 `(("r-annotationdbi" ,r-annotationdbi)
6757 ("r-biobase" ,r-biobase)
6758 ("r-biocgenerics" ,r-biocgenerics)
6759 ("r-biomart" ,r-biomart)
6760 ("r-biostrings" ,r-biostrings)
6761 ("r-dbi" ,r-dbi)
6762 ("r-genomeinfodb" ,r-genomeinfodb)
6763 ("r-genomicranges" ,r-genomicranges)
6764 ("r-iranges" ,r-iranges)
6765 ("r-rcurl" ,r-rcurl)
6766 ("r-rsqlite" ,r-rsqlite)
6767 ("r-rtracklayer" ,r-rtracklayer)
6768 ("r-s4vectors" ,r-s4vectors)
6769 ("r-xvector" ,r-xvector)))
6770 (home-page "http://bioconductor.org/packages/GenomicFeatures")
6771 (synopsis "Tools for working with transcript centric annotations")
6772 (description
6773 "This package provides a set of tools and methods for making and
6774manipulating transcript centric annotations. With these tools the user can
6775easily download the genomic locations of the transcripts, exons and cds of a
6776given organism, from either the UCSC Genome Browser or a BioMart
6777database (more sources will be supported in the future). This information is
6778then stored in a local database that keeps track of the relationship between
6779transcripts, exons, cds and genes. Flexible methods are provided for
6780extracting the desired features in a convenient format.")
6781 (license license:artistic2.0)))
6782
fb25d880
RW		 6783(define-public r-go-db
6784 (package
6785 (name "r-go-db")
d1b1587c 6786 (version "3.4.0")
fb25d880
RW		 6787 (source (origin
6788 (method url-fetch)
f82c8c3c
PP		 6789 (uri (string-append "http://www.bioconductor.org/packages/"
6790 "release/data/annotation/src/contrib/GO.db_"
6791 version ".tar.gz"))
fb25d880
RW		 6792 (sha256
6793 (base32
d1b1587c 6794 "02cj8kqi5w39jwcs8gp1dgj08sah262ppxnkz4h3qd0w191y8yyl"))))
fb25d880
RW		 6795 (properties
6796 `((upstream-name . "GO.db")))
6797 (build-system r-build-system)
3141b83d
RW		 6798 (propagated-inputs
6799 `(("r-annotationdbi" ,r-annotationdbi)))
fb25d880
RW		 6800 (home-page "http://bioconductor.org/packages/GO.db")
6801 (synopsis "Annotation maps describing the entire Gene Ontology")
6802 (description
6803 "The purpose of this GO.db annotation package is to provide detailed
6804information about the latest version of the Gene Ontologies.")
6805 (license license:artistic2.0)))
6806
d1dbde6a
RW		 6807(define-public r-graph
6808 (package
6809 (name "r-graph")
3587b464 6810 (version "1.52.0")
d1dbde6a
RW		 6811 (source (origin
6812 (method url-fetch)
6813 (uri (bioconductor-uri "graph" version))
6814 (sha256
6815 (base32
3587b464 6816 "0g3dk5vsdp489fmyg8mifczmzgqrjlakkkr8i96dj15gghp3l135"))))
d1dbde6a
RW		 6817 (build-system r-build-system)
6818 (propagated-inputs
6819 `(("r-biocgenerics" ,r-biocgenerics)))
6820 (home-page "http://bioconductor.org/packages/graph")
6821 (synopsis "Handle graph data structures in R")
6822 (description
6823 "This package implements some simple graph handling capabilities for R.")
6824 (license license:artistic2.0)))
6825
d547ce5e
RW		 6826(define-public r-topgo
6827 (package
6828 (name "r-topgo")
30ec4de7 6829 (version "2.26.0")
d547ce5e
RW		 6830 (source (origin
6831 (method url-fetch)
6832 (uri (bioconductor-uri "topGO" version))
6833 (sha256
6834 (base32
30ec4de7 6835 "0j6sgvam4lk9348ag6pypcbkv93x4fk0di8ivhr23mz2s2yqzwrx"))))
d547ce5e
RW		 6836 (properties
6837 `((upstream-name . "topGO")))
6838 (build-system r-build-system)
6839 (propagated-inputs
6840 `(("r-annotationdbi" ,r-annotationdbi)
30ec4de7 6841 ("r-dbi" ,r-dbi)
d547ce5e
RW		 6842 ("r-biobase" ,r-biobase)
6843 ("r-biocgenerics" ,r-biocgenerics)
6844 ("r-go-db" ,r-go-db)
e48e88c2 6845 ("r-matrixstats" ,r-matrixstats)
6d415db2 6846 ("r-graph" ,r-graph)
d547ce5e
RW		 6847 ("r-sparsem" ,r-sparsem)))
6848 (home-page "http://bioconductor.org/packages/topGO")
6849 (synopsis "Enrichment analysis for gene ontology")
6850 (description
6851 "The topGO package provides tools for testing @dfn{gene ontology} (GO)
6852terms while accounting for the topology of the GO graph. Different test
6853statistics and different methods for eliminating local similarities and
6854dependencies between GO terms can be implemented and applied.")
6855 ;; Any version of the LGPL applies.
6856 (license license:lgpl2.1+)))
6857
c63cef66
RW		 6858(define-public r-bsgenome
6859 (package
6860 (name "r-bsgenome")
3d74c044 6861 (version "1.42.0")
c63cef66
RW		 6862 (source (origin
6863 (method url-fetch)
6864 (uri (bioconductor-uri "BSgenome" version))
6865 (sha256
6866 (base32
3d74c044 6867 "0hxwc02h5mzhkrk60d1jmlsfjf0ai9jxdc0128kj1sg4r2k1q94y"))))
c63cef66
RW		 6868 (properties
6869 `((upstream-name . "BSgenome")))
6870 (build-system r-build-system)
6871 (propagated-inputs
6872 `(("r-biocgenerics" ,r-biocgenerics)
6873 ("r-biostrings" ,r-biostrings)
6874 ("r-genomeinfodb" ,r-genomeinfodb)
6875 ("r-genomicranges" ,r-genomicranges)
6876 ("r-iranges" ,r-iranges)
6877 ("r-rsamtools" ,r-rsamtools)
6878 ("r-rtracklayer" ,r-rtracklayer)
6879 ("r-s4vectors" ,r-s4vectors)
6880 ("r-xvector" ,r-xvector)))
6881 (home-page "http://bioconductor.org/packages/BSgenome")
6882 (synopsis "Infrastructure for Biostrings-based genome data packages")
6883 (description
6884 "This package provides infrastructure shared by all Biostrings-based
6885genome data packages and support for efficient SNP representation.")
6886 (license license:artistic2.0)))
6887
c43a011d
RW		 6888(define-public r-impute
6889 (package
6890 (name "r-impute")
acf6f7e0 6891 (version "1.48.0")
c43a011d
RW		 6892 (source (origin
6893 (method url-fetch)
6894 (uri (bioconductor-uri "impute" version))
6895 (sha256
6896 (base32
acf6f7e0 6897 "1164zvnikbjd0ybdn9xwn520rlmdjd824vmhnl83zgv3v9lzp9bm"))))
c43a011d
RW		 6898 (inputs
6899 `(("gfortran" ,gfortran)))
6900 (build-system r-build-system)
6901 (home-page "http://bioconductor.org/packages/impute")
6902 (synopsis "Imputation for microarray data")
6903 (description
6904 "This package provides a function to impute missing gene expression
6905microarray data, using nearest neighbor averaging.")
6906 (license license:gpl2+)))
6907
03ea5a35
RW		 6908(define-public r-seqpattern
6909 (package
6910 (name "r-seqpattern")
e92dd6f5 6911 (version "1.6.0")
03ea5a35
RW		 6912 (source (origin
6913 (method url-fetch)
6914 (uri (bioconductor-uri "seqPattern" version))
6915 (sha256
6916 (base32
e92dd6f5 6917 "0lsa5pz36xapi3yiv78k3z286a5md5sm5g21pgfyg8zmhmkxr7y8"))))
03ea5a35
RW		 6918 (properties
6919 `((upstream-name . "seqPattern")))
6920 (build-system r-build-system)
6921 (propagated-inputs
6922 `(("r-biostrings" ,r-biostrings)
6923 ("r-genomicranges" ,r-genomicranges)
6924 ("r-iranges" ,r-iranges)
e92dd6f5 6925 ("r-kernsmooth" ,r-kernsmooth)
03ea5a35
RW		 6926 ("r-plotrix" ,r-plotrix)))
6927 (home-page "http://bioconductor.org/packages/seqPattern")
6928 (synopsis "Visualising oligonucleotide patterns and motif occurrences")
6929 (description
6930 "This package provides tools to visualize oligonucleotide patterns and
6931sequence motif occurrences across a large set of sequences centred at a common
6932reference point and sorted by a user defined feature.")
6933 (license license:gpl3+)))
6934
cb933df6
RW		 6935(define-public r-genomation
6936 (package
6937 (name "r-genomation")
51c3c490 6938 (version "1.6.0")
cb933df6
RW		 6939 (source (origin
6940 (method url-fetch)
6941 (uri (bioconductor-uri "genomation" version))
6942 (sha256
6943 (base32
51c3c490 6944 "1m4mz7wihj8yqivwkzw68div8ybk4rjsai3ffki7xp7sh21ax03y"))))
cb933df6
RW		 6945 (build-system r-build-system)
6946 (propagated-inputs
6947 `(("r-biostrings" ,r-biostrings)
6948 ("r-bsgenome" ,r-bsgenome)
6949 ("r-data-table" ,r-data-table)
6950 ("r-genomeinfodb" ,r-genomeinfodb)
6951 ("r-genomicalignments" ,r-genomicalignments)
6952 ("r-genomicranges" ,r-genomicranges)
6953 ("r-ggplot2" ,r-ggplot2)
6954 ("r-gridbase" ,r-gridbase)
6955 ("r-impute" ,r-impute)
6956 ("r-iranges" ,r-iranges)
6957 ("r-matrixstats" ,r-matrixstats)
6958 ("r-plotrix" ,r-plotrix)
6959 ("r-plyr" ,r-plyr)
51c3c490 6960 ("r-rcpp" ,r-rcpp)
cb933df6
RW		 6961 ("r-readr" ,r-readr)
6962 ("r-reshape2" ,r-reshape2)
51c3c490 6963 ("r-rhtslib" ,r-rhtslib)
cb933df6
RW		 6964 ("r-rsamtools" ,r-rsamtools)
6965 ("r-rtracklayer" ,r-rtracklayer)
51c3c490
RW		 6966 ("r-runit" ,r-runit)
6967 ("r-s4vectors" ,r-s4vectors)
cb933df6 6968 ("r-seqpattern" ,r-seqpattern)))
51c3c490
RW		 6969 (inputs
6970 `(("zlib" ,zlib)))
cb933df6
RW		 6971 (home-page "http://bioinformatics.mdc-berlin.de/genomation/")
6972 (synopsis "Summary, annotation and visualization of genomic data")
6973 (description
6974 "This package provides a package for summary and annotation of genomic
6975intervals. Users can visualize and quantify genomic intervals over
6976pre-defined functional regions, such as promoters, exons, introns, etc. The
6977genomic intervals represent regions with a defined chromosome position, which
6978may be associated with a score, such as aligned reads from HT-seq experiments,
6979TF binding sites, methylation scores, etc. The package can use any tabular
6980genomic feature data as long as it has minimal information on the locations of
6981genomic intervals. In addition, it can use BAM or BigWig files as input.")
6982 (license license:artistic2.0)))
6983
64efa307
RW		 6984(define-public r-genomationdata
6985 (package
6986 (name "r-genomationdata")
59198f8f 6987 (version "1.6.0")
64efa307
RW		 6988 (source (origin
6989 (method url-fetch)
6990 ;; We cannot use bioconductor-uri here because this tarball is
6991 ;; located under "data/annotation/" instead of "bioc/".
6992 (uri (string-append "https://bioconductor.org/packages/"
6993 "release/data/experiment/src/contrib/"
6994 "genomationData_" version ".tar.gz"))
6995 (sha256
6996 (base32
59198f8f 6997 "16dqwb7wx1igx77zdbcskx5m1hs4g4gp2hl56zzm70hcagnlkz8y"))))
64efa307
RW		 6998 (build-system r-build-system)
6999 ;; As this package provides little more than large data files, it doesn't
7000 ;; make sense to build substitutes.
7001 (arguments `(#:substitutable? #f))
7002 (native-inputs
7003 `(("r-knitr" ,r-knitr)))
7004 (home-page "http://bioinformatics.mdc-berlin.de/genomation/")
7005 (synopsis "Experimental data for use with the genomation package")
7006 (description
7007 "This package contains experimental genetic data for use with the
7008genomation package. Included are Chip Seq, Methylation and Cage data,
7009downloaded from Encode.")
7010 (license license:gpl3+)))
7011
486da491
RW		 7012(define-public r-org-hs-eg-db
7013 (package
7014 (name "r-org-hs-eg-db")
83f9a6fb 7015 (version "3.4.0")
486da491
RW		 7016 (source (origin
7017 (method url-fetch)
7018 ;; We cannot use bioconductor-uri here because this tarball is
7019 ;; located under "data/annotation/" instead of "bioc/".
7020 (uri (string-append "http://www.bioconductor.org/packages/"
7021 "release/data/annotation/src/contrib/"
7022 "org.Hs.eg.db_" version ".tar.gz"))
7023 (sha256
7024 (base32
83f9a6fb 7025 "19mg64pw8zcvb9yxzzyf7caz1kvdrkfsj1hd84bzq7crrh8kc4y6"))))
486da491
RW		 7026 (properties
7027 `((upstream-name . "org.Hs.eg.db")))
7028 (build-system r-build-system)
7029 (propagated-inputs
7030 `(("r-annotationdbi" ,r-annotationdbi)))
7031 (home-page "http://www.bioconductor.org/packages/org.Hs.eg.db/")
7032 (synopsis "Genome wide annotation for Human")
7033 (description
7034 "This package provides mappings from Entrez gene identifiers to various
7035annotations for the human genome.")
7036 (license license:artistic2.0)))
7037
fefedf98
RW		 7038(define-public r-org-ce-eg-db
7039 (package
7040 (name "r-org-ce-eg-db")
f04a3eff 7041 (version "3.4.0")
fefedf98
RW		 7042 (source (origin
7043 (method url-fetch)
7044 ;; We cannot use bioconductor-uri here because this tarball is
7045 ;; located under "data/annotation/" instead of "bioc/".
7046 (uri (string-append "http://www.bioconductor.org/packages/"
7047 "release/data/annotation/src/contrib/"
7048 "org.Ce.eg.db_" version ".tar.gz"))
7049 (sha256
7050 (base32
f04a3eff 7051 "12llfzrrc09kj2wzbisdspv38qzkzgpsbn8kv7qkwg746k3pq436"))))
fefedf98
RW		 7052 (properties
7053 `((upstream-name . "org.Ce.eg.db")))
7054 (build-system r-build-system)
7055 (propagated-inputs
7056 `(("r-annotationdbi" ,r-annotationdbi)))
7057 (home-page "http://www.bioconductor.org/packages/org.Ce.eg.db/")
7058 (synopsis "Genome wide annotation for Worm")
7059 (description
7060 "This package provides mappings from Entrez gene identifiers to various
7061annotations for the genome of the model worm Caenorhabditis elegans.")
7062 (license license:artistic2.0)))
7063
16c53a1e
RW		 7064(define-public r-org-dm-eg-db
7065 (package
7066 (name "r-org-dm-eg-db")
0cfac6f2 7067 (version "3.4.0")
16c53a1e
RW		 7068 (source (origin
7069 (method url-fetch)
7070 ;; We cannot use bioconductor-uri here because this tarball is
7071 ;; located under "data/annotation/" instead of "bioc/".
7072 (uri (string-append "http://www.bioconductor.org/packages/"
7073 "release/data/annotation/src/contrib/"
7074 "org.Dm.eg.db_" version ".tar.gz"))
7075 (sha256
7076 (base32
0cfac6f2 7077 "1vzbphbrh1cf7xi5cksia9xy9a9l42js2z2qsajvjxvddiphrb7j"))))
16c53a1e
RW		 7078 (properties
7079 `((upstream-name . "org.Dm.eg.db")))
7080 (build-system r-build-system)
7081 (propagated-inputs
7082 `(("r-annotationdbi" ,r-annotationdbi)))
7083 (home-page "http://www.bioconductor.org/packages/org.Dm.eg.db/")
7084 (synopsis "Genome wide annotation for Fly")
7085 (description
7086 "This package provides mappings from Entrez gene identifiers to various
7087annotations for the genome of the model fruit fly Drosophila melanogaster.")
7088 (license license:artistic2.0)))
7089
e761beb9
RW		 7090(define-public r-org-mm-eg-db
7091 (package
7092 (name "r-org-mm-eg-db")
7c45670b 7093 (version "3.4.0")
e761beb9
RW		 7094 (source (origin
7095 (method url-fetch)
7096 ;; We cannot use bioconductor-uri here because this tarball is
7097 ;; located under "data/annotation/" instead of "bioc/".
7098 (uri (string-append "http://www.bioconductor.org/packages/"
7099 "release/data/annotation/src/contrib/"
7100 "org.Mm.eg.db_" version ".tar.gz"))
7101 (sha256
7102 (base32
7c45670b 7103 "1lykjqjaf01fmgg3cvfcvwd5xjq6zc5vbxnm5r4l32fzvl89q50c"))))
e761beb9
RW		 7104 (properties
7105 `((upstream-name . "org.Mm.eg.db")))
7106 (build-system r-build-system)
7107 (propagated-inputs
7108 `(("r-annotationdbi" ,r-annotationdbi)))
7109 (home-page "http://www.bioconductor.org/packages/org.Mm.eg.db/")
7110 (synopsis "Genome wide annotation for Mouse")
7111 (description
7112 "This package provides mappings from Entrez gene identifiers to various
7113annotations for the genome of the model mouse Mus musculus.")
7114 (license license:artistic2.0)))
7115
936e7d67
RW		 7116(define-public r-seqlogo
7117 (package
7118 (name "r-seqlogo")
21d6c7a3 7119 (version "1.40.0")
936e7d67
RW		 7120 (source
7121 (origin
7122 (method url-fetch)
7123 (uri (bioconductor-uri "seqLogo" version))
7124 (sha256
7125 (base32
21d6c7a3 7126 "18bajdl75h3039559d81rgllqqvnq8ygsfxfx081xphxs0v6xggy"))))
936e7d67
RW		 7127 (properties `((upstream-name . "seqLogo")))
7128 (build-system r-build-system)
7129 (home-page "http://bioconductor.org/packages/seqLogo")
7130 (synopsis "Sequence logos for DNA sequence alignments")
7131 (description
7132 "seqLogo takes the position weight matrix of a DNA sequence motif and
7133plots the corresponding sequence logo as introduced by Schneider and
7134Stephens (1990).")
7135 (license license:lgpl2.0+)))
7136
c90a4baf
RW		 7137(define-public r-bsgenome-hsapiens-ucsc-hg19
7138 (package
7139 (name "r-bsgenome-hsapiens-ucsc-hg19")
7140 (version "1.4.0")
7141 (source (origin
7142 (method url-fetch)
7143 ;; We cannot use bioconductor-uri here because this tarball is
7144 ;; located under "data/annotation/" instead of "bioc/".
7145 (uri (string-append "http://www.bioconductor.org/packages/"
7146 "release/data/annotation/src/contrib/"
7147 "BSgenome.Hsapiens.UCSC.hg19_"
7148 version ".tar.gz"))
7149 (sha256
7150 (base32
7151 "1y0nqpk8cw5a34sd9hmin3z4v7iqm6hf6l22cl81vlbxqbjibxc8"))))
7152 (properties
7153 `((upstream-name . "BSgenome.Hsapiens.UCSC.hg19")))
7154 (build-system r-build-system)
7155 ;; As this package provides little more than a very large data file it
7156 ;; doesn't make sense to build substitutes.
7157 (arguments `(#:substitutable? #f))
7158 (propagated-inputs
7159 `(("r-bsgenome" ,r-bsgenome)))
7160 (home-page
7161 "http://www.bioconductor.org/packages/BSgenome.Hsapiens.UCSC.hg19/")
7162 (synopsis "Full genome sequences for Homo sapiens")
7163 (description
7164 "This package provides full genome sequences for Homo sapiens as provided
7165by UCSC (hg19, February 2009) and stored in Biostrings objects.")
7166 (license license:artistic2.0)))
7167
a3e90287
RW		 7168(define-public r-bsgenome-mmusculus-ucsc-mm9
7169 (package
7170 (name "r-bsgenome-mmusculus-ucsc-mm9")
7171 (version "1.4.0")
7172 (source (origin
7173 (method url-fetch)
7174 ;; We cannot use bioconductor-uri here because this tarball is
7175 ;; located under "data/annotation/" instead of "bioc/".
7176 (uri (string-append "http://www.bioconductor.org/packages/"
7177 "release/data/annotation/src/contrib/"
7178 "BSgenome.Mmusculus.UCSC.mm9_"
7179 version ".tar.gz"))
7180 (sha256
7181 (base32
7182 "1birqw30g2azimxpnjfzmkphan7x131yy8b9h85lfz5fjdg7841i"))))
7183 (properties
7184 `((upstream-name . "BSgenome.Mmusculus.UCSC.mm9")))
7185 (build-system r-build-system)
7186 ;; As this package provides little more than a very large data file it
7187 ;; doesn't make sense to build substitutes.
7188 (arguments `(#:substitutable? #f))
7189 (propagated-inputs
7190 `(("r-bsgenome" ,r-bsgenome)))
7191 (home-page
7192 "http://www.bioconductor.org/packages/BSgenome.Mmusculus.UCSC.mm9/")
7193 (synopsis "Full genome sequences for Mouse")
7194 (description
7195 "This package provides full genome sequences for Mus musculus (Mouse) as
7196provided by UCSC (mm9, July 2007) and stored in Biostrings objects.")
7197 (license license:artistic2.0)))
7198
4714d521
RW		 7199(define-public r-bsgenome-mmusculus-ucsc-mm10
7200 (package
7201 (name "r-bsgenome-mmusculus-ucsc-mm10")
7202 (version "1.4.0")
7203 (source (origin
7204 (method url-fetch)
7205 ;; We cannot use bioconductor-uri here because this tarball is
7206 ;; located under "data/annotation/" instead of "bioc/".
7207 (uri (string-append "http://www.bioconductor.org/packages/"
7208 "release/data/annotation/src/contrib/"
7209 "BSgenome.Mmusculus.UCSC.mm10_"
7210 version ".tar.gz"))
7211 (sha256
7212 (base32
7213 "12s0nm2na9brjad4rn9l7d3db2aj8qa1xvz0y1k7gk08wayb6bkf"))))
7214 (properties
7215 `((upstream-name . "BSgenome.Mmusculus.UCSC.mm10")))
7216 (build-system r-build-system)
7217 ;; As this package provides little more than a very large data file it
7218 ;; doesn't make sense to build substitutes.
7219 (arguments `(#:substitutable? #f))
7220 (propagated-inputs
7221 `(("r-bsgenome" ,r-bsgenome)))
7222 (home-page
7223 "http://www.bioconductor.org/packages/BSgenome.Mmusculus.UCSC.mm10/")
7224 (synopsis "Full genome sequences for Mouse")
7225 (description
7226 "This package provides full genome sequences for Mus
7227musculus (Mouse) as provided by UCSC (mm10, December 2011) and stored
7228in Biostrings objects.")
7229 (license license:artistic2.0)))
7230
c5173d74
RJ		 7231(define-public r-txdb-mmusculus-ucsc-mm10-knowngene
7232 (package
7233 (name "r-txdb-mmusculus-ucsc-mm10-knowngene")
7234 (version "3.4.0")
7235 (source (origin
7236 (method url-fetch)
7237 ;; We cannot use bioconductor-uri here because this tarball is
7238 ;; located under "data/annotation/" instead of "bioc/".
7239 (uri (string-append "http://www.bioconductor.org/packages/"
7240 "release/data/annotation/src/contrib/"
7241 "TxDb.Mmusculus.UCSC.mm10.knownGene_"
7242 version ".tar.gz"))
7243 (sha256
7244 (base32
7245 "08gava9wsvpcqz51k2sni3pj03n5155v32d9riqbf305nbirqbkb"))))
7246 (properties
7247 `((upstream-name . "TxDb.Mmusculus.UCSC.mm10.knownGene")))
7248 (build-system r-build-system)
7249 ;; As this package provides little more than a very large data file it
7250 ;; doesn't make sense to build substitutes.
7251 (arguments `(#:substitutable? #f))
7252 (propagated-inputs
7253 `(("r-bsgenome" ,r-bsgenome)
7254 ("r-genomicfeatures" ,r-genomicfeatures)
7255 ("r-annotationdbi" ,r-annotationdbi)))
7256 (home-page
7257 "http://bioconductor.org/packages/TxDb.Mmusculus.UCSC.mm10.knownGene/")
7258 (synopsis "Annotation package for TxDb knownGene object(s) for Mouse")
7259 (description
7260 "This package loads a TxDb object, which is an R interface to
7261prefabricated databases contained in this package. This package provides
7262the TxDb object of Mouse data as provided by UCSC (mm10, December 2011)
7263based on the knownGene track.")
7264 (license license:artistic2.0)))
7265
943bd627
RW		 7266(define-public r-bsgenome-celegans-ucsc-ce6
7267 (package
7268 (name "r-bsgenome-celegans-ucsc-ce6")
7269 (version "1.4.0")
7270 (source (origin
7271 (method url-fetch)
7272 ;; We cannot use bioconductor-uri here because this tarball is
7273 ;; located under "data/annotation/" instead of "bioc/".
7274 (uri (string-append "http://www.bioconductor.org/packages/"
7275 "release/data/annotation/src/contrib/"
7276 "BSgenome.Celegans.UCSC.ce6_"
7277 version ".tar.gz"))
7278 (sha256
7279 (base32
7280 "0mqzb353xv2c3m3vkb315dkmnxkgczp7ndnknyhpgjlybyf715v9"))))
7281 (properties
7282 `((upstream-name . "BSgenome.Celegans.UCSC.ce6")))
7283 (build-system r-build-system)
7284 ;; As this package provides little more than a very large data file it
7285 ;; doesn't make sense to build substitutes.
7286 (arguments `(#:substitutable? #f))
7287 (propagated-inputs
7288 `(("r-bsgenome" ,r-bsgenome)))
7289 (home-page
7290 "http://www.bioconductor.org/packages/BSgenome.Celegans.UCSC.ce6/")
7291 (synopsis "Full genome sequences for Worm")
7292 (description
7293 "This package provides full genome sequences for Caenorhabditis
7294elegans (Worm) as provided by UCSC (ce6, May 2008) and stored in Biostrings
7295objects.")
7296 (license license:artistic2.0)))
7297
fc47c7d6
RW		 7298(define-public r-bsgenome-celegans-ucsc-ce10
7299 (package
7300 (name "r-bsgenome-celegans-ucsc-ce10")
7301 (version "1.4.0")
7302 (source (origin
7303 (method url-fetch)
7304 ;; We cannot use bioconductor-uri here because this tarball is
7305 ;; located under "data/annotation/" instead of "bioc/".
7306 (uri (string-append "http://www.bioconductor.org/packages/"
7307 "release/data/annotation/src/contrib/"
7308 "BSgenome.Celegans.UCSC.ce10_"
7309 version ".tar.gz"))
7310 (sha256
7311 (base32
7312 "1zaym97jk4npxk14ifvwz2rvhm4zx9xgs33r9vvx9rlynp0gydrk"))))
7313 (properties
7314 `((upstream-name . "BSgenome.Celegans.UCSC.ce10")))
7315 (build-system r-build-system)
7316 ;; As this package provides little more than a very large data file it
7317 ;; doesn't make sense to build substitutes.
7318 (arguments `(#:substitutable? #f))
7319 (propagated-inputs
7320 `(("r-bsgenome" ,r-bsgenome)))
7321 (home-page
7322 "http://www.bioconductor.org/packages/BSgenome.Celegans.UCSC.ce10/")
7323 (synopsis "Full genome sequences for Worm")
7324 (description
7325 "This package provides full genome sequences for Caenorhabditis
7326elegans (Worm) as provided by UCSC (ce10, Oct 2010) and stored in Biostrings
7327objects.")
7328 (license license:artistic2.0)))
7329
6dc60998
RW		 7330(define-public r-bsgenome-dmelanogaster-ucsc-dm3
7331 (package
7332 (name "r-bsgenome-dmelanogaster-ucsc-dm3")
7333 (version "1.4.0")
7334 (source (origin
7335 (method url-fetch)
7336 ;; We cannot use bioconductor-uri here because this tarball is
7337 ;; located under "data/annotation/" instead of "bioc/".
7338 (uri (string-append "http://www.bioconductor.org/packages/"
7339 "release/data/annotation/src/contrib/"
7340 "BSgenome.Dmelanogaster.UCSC.dm3_"
7341 version ".tar.gz"))
7342 (sha256
7343 (base32
7344 "19bm3lkhhkag3gnwp419211fh0cnr0x6fa0r1lr0ycwrikxdxsv8"))))
7345 (properties
7346 `((upstream-name . "BSgenome.Dmelanogaster.UCSC.dm3")))
7347 (build-system r-build-system)
7348 ;; As this package provides little more than a very large data file it
7349 ;; doesn't make sense to build substitutes.
7350 (arguments `(#:substitutable? #f))
7351 (propagated-inputs
7352 `(("r-bsgenome" ,r-bsgenome)))
7353 (home-page
7354 "http://www.bioconductor.org/packages/BSgenome.Dmelanogaster.UCSC.dm3/")
7355 (synopsis "Full genome sequences for Fly")
7356 (description
7357 "This package provides full genome sequences for Drosophila
7358melanogaster (Fly) as provided by UCSC (dm3, April 2006) and stored in
7359Biostrings objects.")
7360 (license license:artistic2.0)))
7361
ae2462f7
RW		 7362(define-public r-motifrg
7363 (package
7364 (name "r-motifrg")
809251e1 7365 (version "1.18.0")
ae2462f7
RW		 7366 (source
7367 (origin
7368 (method url-fetch)
7369 (uri (bioconductor-uri "motifRG" version))
7370 (sha256
7371 (base32
809251e1 7372 "1pa97aj6c5f3gx4bgriw110764dj3m9h104ddi8rv2bpy41yd98d"))))
ae2462f7
RW		 7373 (properties `((upstream-name . "motifRG")))
7374 (build-system r-build-system)
7375 (propagated-inputs
7376 `(("r-biostrings" ,r-biostrings)
7377 ("r-bsgenome" ,r-bsgenome)
7378 ("r-bsgenome.hsapiens.ucsc.hg19" ,r-bsgenome-hsapiens-ucsc-hg19)
7379 ("r-iranges" ,r-iranges)
7380 ("r-seqlogo" ,r-seqlogo)
7381 ("r-xvector" ,r-xvector)))
7382 (home-page "http://bioconductor.org/packages/motifRG")
7383 (synopsis "Discover motifs in high throughput sequencing data")
7384 (description
7385 "This package provides tools for discriminative motif discovery in high
7386throughput genetic sequencing data sets using regression methods.")
7387 (license license:artistic2.0)))
7388
a5002ae7
AE		 7389(define-public r-qtl
7390 (package
7391 (name "r-qtl")
421f7772 7392 (version "1.40-8")
a5002ae7
AE		 7393 (source
7394 (origin
7395 (method url-fetch)
7396 (uri (string-append "mirror://cran/src/contrib/qtl_"
7397 version ".tar.gz"))
7398 (sha256
7399 (base32
421f7772 7400 "05bj1x2ry0i7yqiydlswb3d2h4pxg70z8w1072az1mrv1m54k8sp"))))
a5002ae7
AE		 7401 (build-system r-build-system)
7402 (home-page "http://rqtl.org/")
7403 (synopsis "R package for analyzing QTL experiments in genetics")
7404 (description "R/qtl is an extension library for the R statistics
7405system. It is used to analyze experimental crosses for identifying
7406genes contributing to variation in quantitative traits (so-called
7407quantitative trait loci, QTLs).
7408
7409Using a hidden Markov model, R/qtl allows to estimate genetic maps, to
7410identify genotyping errors, and to perform single-QTL and two-QTL,
7411two-dimensional genome scans.")
7412 (license license:gpl3)))
d1e32822 7413
9e3ba31c
RJ		 7414(define-public r-zlibbioc
7415 (package
7416 (name "r-zlibbioc")
da22da86 7417 (version "1.20.0")
9e3ba31c
RJ		 7418 (source (origin
7419 (method url-fetch)
7420 (uri (bioconductor-uri "zlibbioc" version))
7421 (sha256
7422 (base32
da22da86 7423 "0hbk90q5hl0fycfvy5nxxa4hxgglag9lzp7i0fg849bqygg5nbyq"))))
9e3ba31c
RJ		 7424 (properties
7425 `((upstream-name . "zlibbioc")))
7426 (build-system r-build-system)
7427 (home-page "https://bioconductor.org/packages/zlibbioc")
7428 (synopsis "Provider for zlib-1.2.5 to R packages")
7429 (description "This package uses the source code of zlib-1.2.5 to create
7430libraries for systems that do not have these available via other means.")
7431 (license license:artistic2.0)))
7432
e619a5c2
RW		 7433(define-public r-r4rna
7434 (package
7435 (name "r-r4rna")
7436 (version "0.1.4")
7437 (source
7438 (origin
7439 (method url-fetch)
7440 (uri (string-append "http://www.e-rna.org/r-chie/files/R4RNA_"
7441 version ".tar.gz"))
7442 (sha256
7443 (base32
7444 "1p0i78wh76jfgmn9jphbwwaz6yy6pipzfg08xs54cxavxg2j81p5"))))
7445 (build-system r-build-system)
7446 (propagated-inputs
7447 `(("r-optparse" ,r-optparse)
7448 ("r-rcolorbrewer" ,r-rcolorbrewer)))
7449 (home-page "http://www.e-rna.org/r-chie/index.cgi")
7450 (synopsis "Analysis framework for RNA secondary structure")
7451 (description
7452 "The R4RNA package aims to be a general framework for the analysis of RNA
7453secondary structure and comparative analysis in R.")
7454 (license license:gpl3+)))
7455
52765a63
RW		 7456(define-public r-rhtslib
7457 (package
7458 (name "r-rhtslib")
53ca52f0 7459 (version "1.6.0")
52765a63
RW		 7460 (source
7461 (origin
7462 (method url-fetch)
7463 (uri (bioconductor-uri "Rhtslib" version))
7464 (sha256
7465 (base32
53ca52f0 7466 "1vk3ng61dhi3pbia1lp3gl3mlr3i1vb2lkq83qb53i9dzz128wh9"))))
52765a63
RW		 7467 (properties `((upstream-name . "Rhtslib")))
7468 (build-system r-build-system)
7469 (propagated-inputs
7470 `(("r-zlibbioc" ,r-zlibbioc)))
7471 (inputs
7472 `(("zlib" ,zlib)))
53ca52f0
RW		 7473 (native-inputs
7474 `(("autoconf" ,autoconf)))
52765a63
RW		 7475 (home-page "https://github.com/nhayden/Rhtslib")
7476 (synopsis "High-throughput sequencing library as an R package")
7477 (description
7478 "This package provides the HTSlib C library for high-throughput
7479nucleotide sequence analysis. The package is primarily useful to developers
7480of other R packages who wish to make use of HTSlib.")
7481 (license license:lgpl2.0+)))
7482
fe02c4c9
RW		 7483(define-public r-bamsignals
7484 (package
7485 (name "r-bamsignals")
e357bec8 7486 (version "1.6.0")
fe02c4c9
RW		 7487 (source
7488 (origin
7489 (method url-fetch)
7490 (uri (bioconductor-uri "bamsignals" version))
7491 (sha256
7492 (base32
e357bec8 7493 "1k42gvk5mgq4la1fp0in3an2zfdz69h6522jsqhmk0f6i75kg4mb"))))
fe02c4c9
RW		 7494 (build-system r-build-system)
7495 (propagated-inputs
7496 `(("r-biocgenerics" ,r-biocgenerics)
7497 ("r-genomicranges" ,r-genomicranges)
7498 ("r-iranges" ,r-iranges)
7499 ("r-rcpp" ,r-rcpp)
7500 ("r-rhtslib" ,r-rhtslib)
7501 ("r-zlibbioc" ,r-zlibbioc)))
7502 (inputs
7503 `(("zlib" ,zlib)))
7504 (home-page "http://bioconductor.org/packages/bamsignals")
7505 (synopsis "Extract read count signals from bam files")
7506 (description
7507 "This package allows to efficiently obtain count vectors from indexed bam
7508files. It counts the number of nucleotide sequence reads in given genomic
7509ranges and it computes reads profiles and coverage profiles. It also handles
7510paired-end data.")
7511 (license license:gpl2+)))
7512
89984be4
RW		 7513(define-public r-rcas
7514 (package
7515 (name "r-rcas")
2c8d6c0b 7516 (version "1.1.1")
89984be4
RW		 7517 (source (origin
7518 (method url-fetch)
7519 (uri (string-append "https://github.com/BIMSBbioinfo/RCAS/archive/v"
7520 version ".tar.gz"))
7521 (file-name (string-append name "-" version ".tar.gz"))
7522 (sha256
7523 (base32
2c8d6c0b 7524 "1hd0r66556bxbdd82ksjklq7nfli36l4k6y88ic7kkg9873wa1nw"))))
89984be4
RW		 7525 (build-system r-build-system)
7526 (native-inputs
7527 `(("r-knitr" ,r-knitr)
7528 ("r-testthat" ,r-testthat)
7529 ;; During vignette building knitr checks that "pandoc-citeproc"
7530 ;; is in the PATH.
7531 ("ghc-pandoc-citeproc" ,ghc-pandoc-citeproc)))
7532 (propagated-inputs
7533 `(("r-data-table" ,r-data-table)
7534 ("r-biomart" ,r-biomart)
7535 ("r-org-hs-eg-db" ,r-org-hs-eg-db)
7536 ("r-org-ce-eg-db" ,r-org-ce-eg-db)
7537 ("r-org-dm-eg-db" ,r-org-dm-eg-db)
7538 ("r-org-mm-eg-db" ,r-org-mm-eg-db)
7539 ("r-bsgenome-hsapiens-ucsc-hg19" ,r-bsgenome-hsapiens-ucsc-hg19)
7540 ("r-bsgenome-mmusculus-ucsc-mm9" ,r-bsgenome-mmusculus-ucsc-mm9)
7541 ("r-bsgenome-celegans-ucsc-ce10" ,r-bsgenome-celegans-ucsc-ce10)
7542 ("r-bsgenome-dmelanogaster-ucsc-dm3" ,r-bsgenome-dmelanogaster-ucsc-dm3)
7543 ("r-topgo" ,r-topgo)
7544 ("r-dt" ,r-dt)
7545 ("r-plotly" ,r-plotly)
2c8d6c0b 7546 ("r-plotrix" ,r-plotrix)
89984be4
RW		 7547 ("r-motifrg" ,r-motifrg)
7548 ("r-genomation" ,r-genomation)
7549 ("r-genomicfeatures" ,r-genomicfeatures)
7550 ("r-rtracklayer" ,r-rtracklayer)
7551 ("r-rmarkdown" ,r-rmarkdown)))
7552 (synopsis "RNA-centric annotation system")
7553 (description
7554 "RCAS aims to be a standalone RNA-centric annotation system that provides
7555intuitive reports and publication-ready graphics. This package provides the R
7556library implementing most of the pipeline's features.")
7557 (home-page "https://github.com/BIMSBbioinfo/RCAS")
7558 (license license:expat)))
7559
50937297
RW		 7560(define-public rcas-web
7561 (package
7562 (name "rcas-web")
7563 (version "0.0.3")
7564 (source
7565 (origin
7566 (method url-fetch)
7567 (uri (string-append "https://github.com/BIMSBbioinfo/rcas-web/"
7568 "releases/download/v" version
7569 "/rcas-web-" version ".tar.gz"))
7570 (sha256
7571 (base32
7572 "0d3my0g8i7js59n184zzzjdki7hgmhpi4rhfvk7i6jsw01ba04qq"))))
7573 (build-system gnu-build-system)
7574 (arguments
7575 `(#:phases
7576 (modify-phases %standard-phases
7577 (add-after 'install 'wrap-executable
7578 (lambda* (#:key inputs outputs #:allow-other-keys)
7579 (let* ((out (assoc-ref outputs "out"))
7580 (json (assoc-ref inputs "guile-json"))
7581 (redis (assoc-ref inputs "guile-redis"))
7582 (path (string-append
7583 json "/share/guile/site/2.2:"
7584 redis "/share/guile/site/2.2")))
7585 (wrap-program (string-append out "/bin/rcas-web")
7586 `("GUILE_LOAD_PATH" ":" = (,path))
7587 `("GUILE_LOAD_COMPILED_PATH" ":" = (,path))
7588 `("R_LIBS_SITE" ":" = (,(getenv "R_LIBS_SITE")))))
7589 #t)))))
7590 (inputs
7591 `(("r" ,r)
7592 ("r-rcas" ,r-rcas)
7593 ("guile-next" ,guile-next)
7594 ("guile-json" ,guile2.2-json)
7595 ("guile-redis" ,guile2.2-redis)))
7596 (native-inputs
7597 `(("pkg-config" ,pkg-config)))
7598 (home-page "https://github.com/BIMSBbioinfo/rcas-web")
7599 (synopsis "Web interface for RNA-centric annotation system (RCAS)")
7600 (description "This package provides a simple web interface for the
7601@dfn{RNA-centric annotation system} (RCAS).")
7602 (license license:agpl3+)))
7603
7500e42b
RJ		 7604(define-public r-mutationalpatterns
7605 (package
7606 (name "r-mutationalpatterns")
7607 (version "1.0.0")
7608 (source
7609 (origin
7610 (method url-fetch)
7611 (uri (bioconductor-uri "MutationalPatterns" version))
7612 (sha256
7613 (base32
7614 "1a3c2bm0xx0q4gf98jiw74msmdf2fr8rbsdysd5ww9kqlzmsbr17"))))
7615 (build-system r-build-system)
7616 (propagated-inputs
7617 `(("r-biocgenerics" ,r-biocgenerics)
7618 ("r-biostrings" ,r-biostrings)
7619 ("r-genomicranges" ,r-genomicranges)
7620 ("r-genomeinfodb" ,r-genomeinfodb)
7621 ("r-ggplot2" ,r-ggplot2)
7622 ("r-gridextra" ,r-gridextra)
7623 ("r-iranges" ,r-iranges)
7624 ("r-nmf" ,r-nmf)
7625 ("r-plyr" ,r-plyr)
7626 ("r-pracma" ,r-pracma)
7627 ("r-reshape2" ,r-reshape2)
7628 ("r-summarizedexperiment" ,r-summarizedexperiment)
7629 ("r-variantannotation" ,r-variantannotation)))
7630 (home-page "http://bioconductor.org/packages/MutationalPatterns/")
7631 (synopsis "Extract and visualize mutational patterns in genomic data")
7632 (description "This package provides an extensive toolset for the
7633characterization and visualization of a wide range of mutational patterns
7634in SNV base substitution data.")
7635 (license license:expat)))
7636
d7160529
RW		 7637(define-public r-wgcna
7638 (package
7639 (name "r-wgcna")
7640 (version "1.51")
7641 (source
7642 (origin
7643 (method url-fetch)
7644 (uri (cran-uri "WGCNA" version))
7645 (sha256
7646 (base32
7647 "0hzvnhw76vwg8bl8x368f0c5szpwb8323bmrb3bir93i5bmfjsxx"))))
7648 (properties `((upstream-name . "WGCNA")))
7649 (build-system r-build-system)
7650 (propagated-inputs
7651 `(("r-annotationdbi" ,r-annotationdbi)
7652 ("r-doparallel" ,r-doparallel)
7653 ("r-dynamictreecut" ,r-dynamictreecut)
7654 ("r-fastcluster" ,r-fastcluster)
7655 ("r-foreach" ,r-foreach)
7656 ("r-go-db" ,r-go-db)
7657 ("r-hmisc" ,r-hmisc)
7658 ("r-impute" ,r-impute)
7659 ("r-matrixstats" ,r-matrixstats)
7660 ("r-preprocesscore" ,r-preprocesscore)))
7661 (home-page
7662 "http://www.genetics.ucla.edu/labs/horvath/CoexpressionNetwork/Rpackages/WGCNA/")
7663 (synopsis "Weighted correlation network analysis")
7664 (description
7665 "This package provides functions necessary to perform Weighted
7666Correlation Network Analysis on high-dimensional data. It includes functions
7667for rudimentary data cleaning, construction and summarization of correlation
7668networks, module identification and functions for relating both variables and
7669modules to sample traits. It also includes a number of utility functions for
7670data manipulation and visualization.")
7671 (license license:gpl2+)))
7672
c827f202
RW		 7673(define-public r-chipkernels
7674 (let ((commit "c9cfcacb626b1221094fb3490ea7bac0fd625372")
7675 (revision "1"))
7676 (package
7677 (name "r-chipkernels")
7678 (version (string-append "1.1-" revision "." (string-take commit 9)))
7679 (source
7680 (origin
7681 (method git-fetch)
7682 (uri (git-reference
7683 (url "https://github.com/ManuSetty/ChIPKernels.git")
7684 (commit commit)))
7685 (file-name (string-append name "-" version))
7686 (sha256
7687 (base32
7688 "14bj5qhjm1hsm9ay561nfbqi9wxsa7y487df2idsaaf6z10nw4v0"))))
7689 (build-system r-build-system)
7690 (propagated-inputs
7691 `(("r-iranges" ,r-iranges)
7692 ("r-xvector" ,r-xvector)
7693 ("r-biostrings" ,r-biostrings)
7694 ("r-bsgenome" ,r-bsgenome)
7695 ("r-gtools" ,r-gtools)
7696 ("r-genomicranges" ,r-genomicranges)
7697 ("r-sfsmisc" ,r-sfsmisc)
7698 ("r-kernlab" ,r-kernlab)
7699 ("r-s4vectors" ,r-s4vectors)
7700 ("r-biocgenerics" ,r-biocgenerics)))
7701 (home-page "https://github.com/ManuSetty/ChIPKernels")
7702 (synopsis "Build string kernels for DNA Sequence analysis")
7703 (description "ChIPKernels is an R package for building different string
7704kernels used for DNA Sequence analysis. A dictionary of the desired kernel
7705must be built and this dictionary can be used for determining kernels for DNA
7706Sequences.")
7707 (license license:gpl2+))))
7708
2d9fb170
RW		 7709(define-public r-seqgl
7710 (package
7711 (name "r-seqgl")
7712 (version "1.1.4")
7713 (source
7714 (origin
7715 (method url-fetch)
7716 (uri (string-append "https://github.com/ManuSetty/SeqGL/"
7717 "archive/" version ".tar.gz"))
7718 (file-name (string-append name "-" version ".tar.gz"))
7719 (sha256
7720 (base32
7721 "0pnk1p3sci5yipyc8xnb6jbmydpl80fld927xgnbcv104hy8h8yh"))))
7722 (build-system r-build-system)
7723 (propagated-inputs
7724 `(("r-biostrings" ,r-biostrings)
7725 ("r-chipkernels" ,r-chipkernels)
7726 ("r-genomicranges" ,r-genomicranges)
7727 ("r-spams" ,r-spams)
7728 ("r-wgcna" ,r-wgcna)
7729 ("r-fastcluster" ,r-fastcluster)))
7730 (home-page "https://github.com/ManuSetty/SeqGL")
7731 (synopsis "Group lasso for Dnase/ChIP-seq data")
7732 (description "SeqGL is a group lasso based algorithm to extract
7733transcription factor sequence signals from ChIP, DNase and ATAC-seq profiles.
7734This package presents a method which uses group lasso to discriminate between
7735bound and non bound genomic regions to accurately identify transcription
7736factors bound at the specific regions.")
7737 (license license:gpl2+)))
7738
bd3be46e
RW		 7739(define-public r-gkmsvm
7740 (package
7741 (name "r-gkmsvm")
7742 (version "0.71.0")
7743 (source
7744 (origin
7745 (method url-fetch)
7746 (uri (cran-uri "gkmSVM" version))
7747 (sha256
7748 (base32
7749 "1zpxgxmf2nd5j5wn00ps6kfxr8wxh7d1swr1rr4spq7sj5z5z0k0"))))
7750 (properties `((upstream-name . "gkmSVM")))
7751 (build-system r-build-system)
7752 (propagated-inputs
7753 `(("r-biocgenerics" ,r-biocgenerics)
7754 ("r-biostrings" ,r-biostrings)
7755 ("r-genomeinfodb" ,r-genomeinfodb)
7756 ("r-genomicranges" ,r-genomicranges)
7757 ("r-iranges" ,r-iranges)
7758 ("r-kernlab" ,r-kernlab)
7759 ("r-rcpp" ,r-rcpp)
7760 ("r-rocr" ,r-rocr)
7761 ("r-rtracklayer" ,r-rtracklayer)
7762 ("r-s4vectors" ,r-s4vectors)
7763 ("r-seqinr" ,r-seqinr)))
7764 (home-page "http://cran.r-project.org/web/packages/gkmSVM")
7765 (synopsis "Gapped-kmer support vector machine")
7766 (description
7767 "This R package provides tools for training gapped-kmer SVM classifiers
7768for DNA and protein sequences. This package supports several sequence
7769kernels, including: gkmSVM, kmer-SVM, mismatch kernel and wildcard kernel.")
7770 (license license:gpl2+)))
7771
66e40e00
RW		 7772(define-public emboss
7773 (package
7774 (name "emboss")
7775 (version "6.5.7")
7776 (source (origin
7777 (method url-fetch)
7778 (uri (string-append "ftp://emboss.open-bio.org/pub/EMBOSS/old/"
7779 (version-major+minor version) ".0/"
7780 "EMBOSS-" version ".tar.gz"))
7781 (sha256
7782 (base32
7783 "0vsmz96gc411yj2iyzdrsmg4l2n1nhgmp7vrgzlxx3xixv9xbf0q"))))
7784 (build-system gnu-build-system)
7785 (arguments
7786 `(#:configure-flags
7787 (list (string-append "--with-hpdf="
7788 (assoc-ref %build-inputs "libharu")))
7789 #:phases
7790 (modify-phases %standard-phases
7791 (add-after 'unpack 'fix-checks
7792 (lambda _
7793 ;; The PNGDRIVER tests check for the presence of libgd, libpng
7794 ;; and zlib, but assume that they are all found at the same
7795 ;; prefix.
7796 (substitute* "configure.in"
7797 (("CHECK_PNGDRIVER")
7798 "LIBS=\"$LIBS -lgd -lpng -lz -lm\"
7799AC_DEFINE([PLD_png], [1], [Define to 1 if PNG support is available])
7800AM_CONDITIONAL(AMPNG, true)"))
7801 #t))
7802 (add-after 'unpack 'disable-update-check
7803 (lambda _
7804 ;; At build time there is no connection to the Internet, so
7805 ;; looking for updates will not work.
7806 (substitute* "Makefile.am"
7807 (("\\$\\(bindir\\)/embossupdate") ""))
7808 #t))
7809 (add-before 'configure 'autogen
7810 (lambda _ (zero? (system* "autoreconf" "-vif")))))))
7811 (inputs
7812 `(("perl" ,perl)
7813 ("libpng" ,libpng)
7814 ("gd" ,gd)
7815 ("libx11" ,libx11)
7816 ("libharu" ,libharu)
7817 ("zlib" ,zlib)))
7818 (native-inputs
7819 `(("autoconf" ,autoconf)
7820 ("automake" ,automake)
7821 ("libtool" ,libtool)
7822 ("pkg-config" ,pkg-config)))
7823 (home-page "http://emboss.sourceforge.net")
7824 (synopsis "Molecular biology analysis suite")
7825 (description "EMBOSS is the \"European Molecular Biology Open Software
7826Suite\". EMBOSS is an analysis package specially developed for the needs of
7827the molecular biology (e.g. EMBnet) user community. The software
7828automatically copes with data in a variety of formats and even allows
7829transparent retrieval of sequence data from the web. It also provides a
7830number of libraries for the development of software in the field of molecular
7831biology. EMBOSS also integrates a range of currently available packages and
7832tools for sequence analysis into a seamless whole.")
7833 (license license:gpl2+)))
7834
1f1b20b8
RW		 7835(define-public bits
7836 (let ((revision "1")
7837 (commit "3cc4567896d9d6442923da944beb704750a08d2d"))
7838 (package
7839 (name "bits")
7840 ;; The version is 2.13.0 even though no release archives have been
7841 ;; published as yet.
7842 (version (string-append "2.13.0-" revision "." (string-take commit 9)))
7843 (source (origin
7844 (method git-fetch)
7845 (uri (git-reference
7846 (url "https://github.com/arq5x/bits.git")
7847 (commit commit)))
7848 (file-name (string-append name "-" version "-checkout"))
7849 (sha256
7850 (base32
7851 "17n2kffk4kmhivd8c98g2vr6y1s23vbg4sxlxs689wni66797hbs"))))
7852 (build-system gnu-build-system)
7853 (arguments
7854 `(#:tests? #f ;no tests included
7855 #:phases
7856 (modify-phases %standard-phases
7857 (delete 'configure)
7858 (add-after 'unpack 'remove-cuda
7859 (lambda _
7860 (substitute* "Makefile"
7861 ((".*_cuda") "")
7862 (("(bits_test_intersections) \\\\" _ match) match))
7863 #t))
7864 (replace 'install
7865 (lambda* (#:key outputs #:allow-other-keys)
7866 (copy-recursively
7867 "bin" (string-append (assoc-ref outputs "out") "/bin"))
7868 #t)))))
7869 (inputs
7870 `(("gsl" ,gsl)
7871 ("zlib" ,zlib)))
7872 (home-page "https://github.com/arq5x/bits")
7873 (synopsis "Implementation of binary interval search algorithm")
7874 (description "This package provides an implementation of the
7875BITS (Binary Interval Search) algorithm, an approach to interval set
7876intersection. It is especially suited for the comparison of diverse genomic
7877datasets and the exploration of large datasets of genome
7878intervals (e.g. genes, sequence alignments).")
7879 (license license:gpl2))))
7880
e62ffce5 7881(define-public piranha
883302da
RW		 7882 ;; There is no release tarball for the latest version. The latest commit is
7883 ;; older than one year at the time of this writing.
7884 (let ((revision "1")
7885 (commit "0466d364b71117d01e4471b74c514436cc281233"))
7886 (package
7887 (name "piranha")
7888 (version (string-append "1.2.1-" revision "." (string-take commit 9)))
7889 (source (origin
7890 (method git-fetch)
7891 (uri (git-reference
7892 (url "https://github.com/smithlabcode/piranha.git")
7893 (commit commit)))
7894 (sha256
7895 (base32
7896 "117dc0zf20c61jam69sk4abl57ah6yi6i7qra7d7y5zrbgk12q5n"))))
7897 (build-system gnu-build-system)
7898 (arguments
7899 `(#:test-target "test"
7900 #:phases
7901 (modify-phases %standard-phases
7902 (add-after 'unpack 'copy-smithlab-cpp
7903 (lambda* (#:key inputs #:allow-other-keys)
e62ffce5 7904 (for-each (lambda (file)
883302da
RW		 7905 (install-file file "./src/smithlab_cpp/"))
7906 (find-files (assoc-ref inputs "smithlab-cpp")))
7907 #t))
7908 (add-after 'install 'install-to-store
7909 (lambda* (#:key outputs #:allow-other-keys)
7910 (let* ((out (assoc-ref outputs "out"))
7911 (bin (string-append out "/bin")))
883302da
RW		 7912 (for-each (lambda (file)
7913 (install-file file bin))
7914 (find-files "bin" ".*")))
7915 #t)))
7916 #:configure-flags
7917 (list (string-append "--with-bam_tools_headers="
7918 (assoc-ref %build-inputs "bamtools") "/include/bamtools")
7919 (string-append "--with-bam_tools_library="
7920 (assoc-ref %build-inputs "bamtools") "/lib/bamtools"))))
7921 (inputs
7922 `(("bamtools" ,bamtools)
7923 ("samtools" ,samtools-0.1)
7924 ("gsl" ,gsl)
7925 ("smithlab-cpp"
7926 ,(let ((commit "3723e2db438c51501d0423429ff396c3035ba46a"))
7927 (origin
7928 (method git-fetch)
7929 (uri (git-reference
7930 (url "https://github.com/smithlabcode/smithlab_cpp.git")
7931 (commit commit)))
7932 (file-name (string-append "smithlab_cpp-" commit "-checkout"))
7933 (sha256
7934 (base32
7935 "0l4gvbwslw5ngziskja41c00x1r06l3yidv7y0xw9djibhykzy0g")))))))
7936 (native-inputs
7937 `(("python" ,python-2)))
7938 (home-page "https://github.com/smithlabcode/piranha")
7939 (synopsis "Peak-caller for CLIP-seq and RIP-seq data")
7940 (description
7941 "Piranha is a peak-caller for genomic data produced by CLIP-seq and
e62ffce5
RW		 7942RIP-seq experiments. It takes input in BED or BAM format and identifies
7943regions of statistically significant read enrichment. Additional covariates
7944may optionally be provided to further inform the peak-calling process.")
883302da 7945 (license license:gpl3+))))
e62ffce5 7946
d1e32822
RW		 7947(define-public pepr
7948 (package
7949 (name "pepr")
7950 (version "1.0.9")
7951 (source (origin
7952 (method url-fetch)
7953 (uri (string-append "https://pypi.python.org/packages/source/P"
7954 "/PePr/PePr-" version ".tar.gz"))
7955 (sha256
7956 (base32
7957 "0qxjfdpl1b1y53nccws2d85f6k74zwmx8y8sd9rszcqhfayx6gdx"))))
7958 (build-system python-build-system)
7959 (arguments
7960 `(#:python ,python-2 ; python2 only
b41a05ce 7961 #:tests? #f)) ; no tests included
d1e32822
RW		 7962 (propagated-inputs
7963 `(("python2-numpy" ,python2-numpy)
7964 ("python2-scipy" ,python2-scipy)
7965 ("python2-pysam" ,python2-pysam)))
0c6c9c00 7966 (home-page "https://github.com/shawnzhangyx/PePr")
d1e32822
RW		 7967 (synopsis "Peak-calling and prioritization pipeline for ChIP-Seq data")
7968 (description
7969 "PePr is a ChIP-Seq peak calling or differential binding analysis tool
7970that is primarily designed for data with biological replicates. It uses a
7971negative binomial distribution to model the read counts among the samples in
7972the same group, and look for consistent differences between ChIP and control
7973group or two ChIP groups run under different conditions.")
7974 (license license:gpl3+)))
6b49a37e
RJ		 7975
7976(define-public filevercmp
7977 (let ((commit "1a9b779b93d0b244040274794d402106907b71b7"))
7978 (package
7979 (name "filevercmp")
7980 (version (string-append "0-1." (string-take commit 7)))
7981 (source (origin
7982 (method url-fetch)
7983 (uri (string-append "https://github.com/ekg/filevercmp/archive/"
7984 commit ".tar.gz"))
7985 (file-name (string-append name "-" version ".tar.gz"))
7986 (sha256
7987 (base32 "0yp5jswf5j2pqc6517x277s4s6h1ss99v57kxw9gy0jkfl3yh450"))))
7988 (build-system gnu-build-system)
7989 (arguments
7990 `(#:tests? #f ; There are no tests to run.
7991 #:phases
7992 (modify-phases %standard-phases
7993 (delete 'configure) ; There is no configure phase.
7994 (replace 'install
7995 (lambda* (#:key outputs #:allow-other-keys)
7996 (let ((bin (string-append (assoc-ref outputs "out") "/bin")))
7997 (install-file "filevercmp" bin)))))))
7998 (home-page "https://github.com/ekg/filevercmp")
7999 (synopsis "This program compares version strings")
8000 (description "This program compares version strings. It intends to be a
8001replacement for strverscmp.")
8002 (license license:gpl3+))))
5fb5dffb
RW		 8003
8004(define-public multiqc
8005 (package
8006 (name "multiqc")
a29929b3 8007 (version "0.9")
5fb5dffb
RW		 8008 (source
8009 (origin
8010 (method url-fetch)
8011 (uri (pypi-uri "multiqc" version))
8012 (sha256
8013 (base32
a29929b3
BW		 8014 "12gs1jw2jrxrij529rnl5kaqxfcqn15yzcsggxkfhdx634ml0cny"))
8015 (patches (search-patches "multiqc-fix-git-subprocess-error.patch"))))
5fb5dffb 8016 (build-system python-build-system)
a29929b3
BW		 8017 (arguments
8018 ;; Tests are to be introduced in the next version, see
8019 ;; https://github.com/ewels/MultiQC/issues/376
8020 `(#:tests? #f))
5fb5dffb
RW		 8021 (propagated-inputs
8022 `(("python-jinja2" ,python-jinja2)
8023 ("python-simplejson" ,python-simplejson)
8024 ("python-pyyaml" ,python-pyyaml)
8025 ("python-click" ,python-click)
8026 ("python-matplotlib" ,python-matplotlib)
1778ea74
RW		 8027 ("python-numpy" ,python-numpy)
8028 ;; MultQC checks for the presence of nose at runtime.
8029 ("python-nose" ,python-nose)))
5fb5dffb
RW		 8030 (home-page "http://multiqc.info")
8031 (synopsis "Aggregate bioinformatics analysis reports")
8032 (description
8033 "MultiQC is a tool to aggregate bioinformatics results across many
8034samples into a single report. It contains modules for a large number of
8035common bioinformatics tools.")
8036 (license license:gpl3)))
6193563a
RW		 8037
8038(define-public r-chipseq
8039 (package
8040 (name "r-chipseq")
8041 (version "1.24.0")
8042 (source
8043 (origin
8044 (method url-fetch)
8045 (uri (bioconductor-uri "chipseq" version))
8046 (sha256
8047 (base32
8048 "115ayp82rs99iaswrx45skw1i5iacgwzz5k8rzijbp5qic0554n0"))))
8049 (build-system r-build-system)
8050 (propagated-inputs
8051 `(("r-biocgenerics" ,r-biocgenerics)
8052 ("r-genomicranges" ,r-genomicranges)
8053 ("r-iranges" ,r-iranges)
8054 ("r-s4vectors" ,r-s4vectors)
8055 ("r-shortread" ,r-shortread)))
8056 (home-page "http://bioconductor.org/packages/chipseq")
8057 (synopsis "Package for analyzing ChIPseq data")
8058 (description
8059 "This package provides tools for processing short read data from ChIPseq
8060experiments.")
8061 (license license:artistic2.0)))
d407bdb9
RW		 8062
8063(define-public r-copyhelper
8064 (package
8065 (name "r-copyhelper")
8066 (version "1.6.0")
8067 (source
8068 (origin
8069 (method url-fetch)
8070 (uri (string-append "http://bioconductor.org/packages/release/"
8071 "data/experiment/src/contrib/CopyhelpeR_"
8072 version ".tar.gz"))
8073 (sha256
8074 (base32
8075 "0x7cyynjmxls9as2gg0iyp9x5fpalxmdjq914ss7i84i9zyk5bhq"))))
8076 (properties `((upstream-name . "CopyhelpeR")))
8077 (build-system r-build-system)
8078 (home-page "http://bioconductor.org/packages/CopyhelpeR/")
8079 (synopsis "Helper files for CopywriteR")
8080 (description
8081 "This package contains the helper files that are required to run the
8082Bioconductor package CopywriteR. It contains pre-assembled 1kb bin GC-content
8083and mappability files for the reference genomes hg18, hg19, hg38, mm9 and
8084mm10. In addition, it contains a blacklist filter to remove regions that
8085display copy number variation. Files are stored as GRanges objects from the
8086GenomicRanges Bioconductor package.")
8087 (license license:gpl2)))
3a3bf2f8
RW		 8088
8089(define-public r-copywriter
8090 (package
8091 (name "r-copywriter")
8092 (version "2.6.0")
8093 (source
8094 (origin
8095 (method url-fetch)
8096 (uri (bioconductor-uri "CopywriteR" version))
8097 (sha256
8098 (base32
8099 "1bwwnsyk7cpgwkagsnn5mv6fv233b0rkhjvbadrh70h8m4anawfj"))))
8100 (properties `((upstream-name . "CopywriteR")))
8101 (build-system r-build-system)
8102 (propagated-inputs
8103 `(("r-biocparallel" ,r-biocparallel)
8104 ("r-chipseq" ,r-chipseq)
8105 ("r-copyhelper" ,r-copyhelper)
8106 ("r-data-table" ,r-data-table)
8107 ("r-dnacopy" ,r-dnacopy)
8108 ("r-futile-logger" ,r-futile-logger)
8109 ("r-genomeinfodb" ,r-genomeinfodb)
8110 ("r-genomicalignments" ,r-genomicalignments)
8111 ("r-genomicranges" ,r-genomicranges)
8112 ("r-gtools" ,r-gtools)
8113 ("r-iranges" ,r-iranges)
8114 ("r-matrixstats" ,r-matrixstats)
8115 ("r-rsamtools" ,r-rsamtools)
8116 ("r-s4vectors" ,r-s4vectors)))
8117 (home-page "https://github.com/PeeperLab/CopywriteR")
8118 (synopsis "Copy number information from targeted sequencing")
8119 (description
8120 "CopywriteR extracts DNA copy number information from targeted sequencing
8121by utilizing off-target reads. It allows for extracting uniformly distributed
8122copy number information, can be used without reference, and can be applied to
8123sequencing data obtained from various techniques including chromatin
8124immunoprecipitation and target enrichment on small gene panels. Thereby,
8125CopywriteR constitutes a widely applicable alternative to available copy
8126number detection tools.")
8127 (license license:gpl2)))
dd42a330
RJPB		 8128
8129(define-public r-sva
8130 (package
8131 (name "r-sva")
8132 (version "3.22.0")
8133 (source
8134 (origin
8135 (method url-fetch)
8136 (uri (bioconductor-uri "sva" version))
8137 (sha256
8138 (base32
8139 "1wc1fjm6dzlsqqagm43y57w8jh8nsh0r0m8z1p6ximcb5gxqh7hn"))))
8140 (build-system r-build-system)
8141 (propagated-inputs
8142 `(("r-genefilter" ,r-genefilter)))
8143 (home-page "http://bioconductor.org/packages/sva")
8144 (synopsis "Surrogate variable analysis")
8145 (description
8146 "This package contains functions for removing batch effects and other
8147unwanted variation in high-throughput experiment. It also contains functions
8148for identifying and building surrogate variables for high-dimensional data
8149sets. Surrogate variables are covariates constructed directly from
8150high-dimensional data like gene expression/RNA sequencing/methylation/brain
8151imaging data that can be used in subsequent analyses to adjust for unknown,
8152unmodeled, or latent sources of noise.")
8153 (license license:artistic2.0)))
fb1e528e
RW		 8154
8155(define-public r-seqminer
8156 (package
8157 (name "r-seqminer")
8158 (version "5.3")
8159 (source
8160 (origin
8161 (method url-fetch)
8162 (uri (cran-uri "seqminer" version))
8163 (sha256
8164 (base32
8165 "0y0gc5lws3hdxasjb84m532ics6imb7qg9sl1zy62h503jh4j9gw"))))
8166 (build-system r-build-system)
8167 (inputs
8168 `(("zlib" ,zlib)))
8169 (home-page "http://seqminer.genomic.codes")
8170 (synopsis "Read nucleotide sequence data (VCF, BCF, and METAL formats)")
8171 (description
8172 "This package provides tools to integrate nucleotide sequencing
8173data (variant call format, e.g. VCF or BCF) or meta-analysis results in R.")
8174 ;; Any version of the GPL is acceptable
8175 (license (list license:gpl2+ license:gpl3+))))
1f40e73c
RW		 8176
8177(define-public r-raremetals2
8178 (package
8179 (name "r-raremetals2")
8180 (version "0.1")
8181 (source
8182 (origin
8183 (method url-fetch)
8184 (uri (string-append "http://genome.sph.umich.edu/w/images/"
8185 "b/b7/RareMETALS2_" version ".tar.gz"))
8186 (sha256
8187 (base32
8188 "0z5ljcgvnm06ja9lm85a3cniq7slxcy37aqqkxrdidr79an5fs4s"))))
8189 (properties `((upstream-name . "RareMETALS2")))
8190 (build-system r-build-system)
8191 (propagated-inputs
8192 `(("r-seqminer" ,r-seqminer)
8193 ("r-mvtnorm" ,r-mvtnorm)
8194 ("r-compquadform" ,r-compquadform)
8195 ("r-getopt" ,r-getopt)))
8196 (home-page "http://genome.sph.umich.edu/wiki/RareMETALS2")
8197 (synopsis "Analyze gene-level association tests for binary trait")
8198 (description
8199 "The R package rareMETALS2 is an extension of the R package rareMETALS.
8200It was designed to meta-analyze gene-level association tests for binary trait.
8201While rareMETALS offers a near-complete solution for meta-analysis of
8202gene-level tests for quantitative trait, it does not offer the optimal
8203solution for binary trait. The package rareMETALS2 offers improved features
8204for analyzing gene-level association tests in meta-analyses for binary
8205trait.")
8206 (license license:gpl3)))
0e7d058e
RW		 8207
8208(define-public r-maldiquant
8209 (package
8210 (name "r-maldiquant")
8211 (version "1.16")
8212 (source
8213 (origin
8214 (method url-fetch)
8215 (uri (cran-uri "MALDIquant" version))
8216 (sha256
8217 (base32
8218 "067xbmy10mpsvmv77g62chd7wwhdhcfn5hmp5fisbnz2h5rq0q60"))))
8219 (properties `((upstream-name . "MALDIquant")))
8220 (build-system r-build-system)
8221 (home-page "http://cran.r-project.org/web/packages/MALDIquant")
8222 (synopsis "Quantitative analysis of mass spectrometry data")
8223 (description
8224 "This package provides a complete analysis pipeline for matrix-assisted
8225laser desorption/ionization-time-of-flight (MALDI-TOF) and other
8226two-dimensional mass spectrometry data. In addition to commonly used plotting
8227and processing methods it includes distinctive features, namely baseline
8228subtraction methods such as morphological filters (TopHat) or the
8229statistics-sensitive non-linear iterative peak-clipping algorithm (SNIP), peak
8230alignment using warping functions, handling of replicated measurements as well
8231as allowing spectra with different resolutions.")
8232 (license license:gpl3+)))
ae262174
RW		 8233
8234(define-public r-protgenerics
8235 (package
8236 (name "r-protgenerics")
8237 (version "1.6.0")
8238 (source
8239 (origin
8240 (method url-fetch)
8241 (uri (bioconductor-uri "ProtGenerics" version))
8242 (sha256
8243 (base32
8244 "0hb3vrrvfx6lcfalmjxm8dmigfmi5nba0pzjfgsrzd35c8mbfc6f"))))
8245 (properties `((upstream-name . "ProtGenerics")))
8246 (build-system r-build-system)
8247 (home-page "https://github.com/lgatto/ProtGenerics")
8248 (synopsis "S4 generic functions for proteomics infrastructure")
8249 (description
8250 "This package provides S4 generic functions needed by Bioconductor
8251proteomics packages.")
8252 (license license:artistic2.0)))
71676a1f
RW		 8253
8254(define-public r-mzr
8255 (package
8256 (name "r-mzr")
8257 (version "2.8.1")
8258 (source
8259 (origin
8260 (method url-fetch)
8261 (uri (bioconductor-uri "mzR" version))
8262 (sha256
8263 (base32
8264 "0ipmhg6l3pf648rdx5g2ha7l5ppd3cja6afxhdw76x8ga3633x0r"))))
8265 (properties `((upstream-name . "mzR")))
8266 (build-system r-build-system)
8267 (inputs
8268 `(("netcdf" ,netcdf)))
8269 (propagated-inputs
8270 `(("r-biobase" ,r-biobase)
8271 ("r-biocgenerics" ,r-biocgenerics)
8272 ("r-protgenerics" ,r-protgenerics)
8273 ("r-rcpp" ,r-rcpp)
8274 ("r-zlibbioc" ,r-zlibbioc)))
8275 (home-page "https://github.com/sneumann/mzR/")
8276 (synopsis "Parser for mass spectrometry data files")
8277 (description
8278 "The mzR package provides a unified API to the common file formats and
8279parsers available for mass spectrometry data. It comes with a wrapper for the
8280ISB random access parser for mass spectrometry mzXML, mzData and mzML files.
8281The package contains the original code written by the ISB, and a subset of the
8282proteowizard library for mzML and mzIdentML. The netCDF reading code has
8283previously been used in XCMS.")
8284 (license license:artistic2.0)))
5c9d1505
RW		 8285
8286(define-public r-affyio
8287 (package
8288 (name "r-affyio")
8289 (version "1.44.0")
8290 (source
8291 (origin
8292 (method url-fetch)
8293 (uri (bioconductor-uri "affyio" version))
8294 (sha256
8295 (base32
8296 "1svsl4mpk06xm505pap913x69ywks99262krag8y4ygpllj7dfyy"))))
8297 (build-system r-build-system)
8298 (propagated-inputs
8299 `(("r-zlibbioc" ,r-zlibbioc)))
8300 (inputs
8301 `(("zlib" ,zlib)))
8302 (home-page "https://github.com/bmbolstad/affyio")
8303 (synopsis "Tools for parsing Affymetrix data files")
8304 (description
8305 "This package provides routines for parsing Affymetrix data files based
8306upon file format information. The primary focus is on accessing the CEL and
8307CDF file formats.")
8308 (license license:lgpl2.0+)))
05c7e5fb
RW		 8309
8310(define-public r-affy
8311 (package
8312 (name "r-affy")
8313 (version "1.52.0")
8314 (source
8315 (origin
8316 (method url-fetch)
8317 (uri (bioconductor-uri "affy" version))
8318 (sha256
8319 (base32
8320 "1snq71ligf0wvaxa6zfrl13ydw0zfhspmhdyfk8q3ba3np4cz344"))))
8321 (build-system r-build-system)
8322 (propagated-inputs
8323 `(("r-affyio" ,r-affyio)
8324 ("r-biobase" ,r-biobase)
8325 ("r-biocgenerics" ,r-biocgenerics)
8326 ("r-biocinstaller" ,r-biocinstaller)
8327 ("r-preprocesscore" ,r-preprocesscore)
8328 ("r-zlibbioc" ,r-zlibbioc)))
8329 (home-page "http://bioconductor.org/packages/affy")
8330 (synopsis "Methods for affymetrix oligonucleotide arrays")
8331 (description
8332 "This package contains functions for exploratory oligonucleotide array
8333analysis.")
8334 (license license:lgpl2.0+)))
7c08afaf
RW		 8335
8336(define-public r-vsn
8337 (package
8338 (name "r-vsn")
8339 (version "3.42.3")
8340 (source
8341 (origin
8342 (method url-fetch)
8343 (uri (bioconductor-uri "vsn" version))
8344 (sha256
8345 (base32
8346 "0mgl0azys2g90simf8wx6jdwd7gyg3m4pf12n6w6507jixm2cg97"))))
8347 (build-system r-build-system)
8348 (propagated-inputs
8349 `(("r-affy" ,r-affy)
8350 ("r-biobase" ,r-biobase)
8351 ("r-ggplot2" ,r-ggplot2)
8352 ("r-limma" ,r-limma)))
8353 (home-page "http://bioconductor.org/packages/release/bioc/html/vsn.html")
8354 (synopsis "Variance stabilization and calibration for microarray data")
8355 (description
8356 "The package implements a method for normalising microarray intensities,
8357and works for single- and multiple-color arrays. It can also be used for data
8358from other technologies, as long as they have similar format. The method uses
8359a robust variant of the maximum-likelihood estimator for an
8360additive-multiplicative error model and affine calibration. The model
8361incorporates data calibration step (a.k.a. normalization), a model for the
8362dependence of the variance on the mean intensity and a variance stabilizing
8363data transformation. Differences between transformed intensities are
8364analogous to \"normalized log-ratios\". However, in contrast to the latter,
8365their variance is independent of the mean, and they are usually more sensitive
8366and specific in detecting differential transcription.")
8367 (license license:artistic2.0)))
4aa7d592
RW		 8368
8369(define-public r-mzid
8370 (package
8371 (name "r-mzid")
8372 (version "1.12.0")
8373 (source
8374 (origin
8375 (method url-fetch)
8376 (uri (bioconductor-uri "mzID" version))
8377 (sha256
8378 (base32
8379 "1zn896cpfvqp1qmq5c4vcj933hb8rxwb6gkck1wqvr7393rpqy1q"))))
8380 (properties `((upstream-name . "mzID")))
8381 (build-system r-build-system)
8382 (propagated-inputs
8383 `(("r-doparallel" ,r-doparallel)
8384 ("r-foreach" ,r-foreach)
8385 ("r-iterators" ,r-iterators)
8386 ("r-plyr" ,r-plyr)
8387 ("r-protgenerics" ,r-protgenerics)
8388 ("r-rcpp" ,r-rcpp)
8389 ("r-xml" ,r-xml)))
8390 (home-page "http://bioconductor.org/packages/mzID")
8391 (synopsis "Parser for mzIdentML files")
8392 (description
8393 "This package provides a parser for mzIdentML files implemented using the
8394XML package. The parser tries to be general and able to handle all types of
8395mzIdentML files with the drawback of having less pretty output than a vendor
8396specific parser.")
8397 (license license:gpl2+)))
6a67e181
RW		 8398
8399(define-public r-pcamethods
8400 (package
8401 (name "r-pcamethods")
8402 (version "1.66.0")
8403 (source
8404 (origin
8405 (method url-fetch)
8406 (uri (bioconductor-uri "pcaMethods" version))
8407 (sha256
8408 (base32
8409 "18mawhxw57pgpn87qha4mwki24gqja7wpqha8q496476vyap11xw"))))
8410 (properties `((upstream-name . "pcaMethods")))
8411 (build-system r-build-system)
8412 (propagated-inputs
8413 `(("r-biobase" ,r-biobase)
8414 ("r-biocgenerics" ,r-biocgenerics)
8415 ("r-rcpp" ,r-rcpp)))
8416 (home-page "https://github.com/hredestig/pcamethods")
8417 (synopsis "Collection of PCA methods")
8418 (description
8419 "This package provides Bayesian PCA, Probabilistic PCA, Nipals PCA,
8420Inverse Non-Linear PCA and the conventional SVD PCA. A cluster based method
8421for missing value estimation is included for comparison. BPCA, PPCA and
8422NipalsPCA may be used to perform PCA on incomplete data as well as for
8423accurate missing value estimation. A set of methods for printing and plotting
8424the results is also provided. All PCA methods make use of the same data
8425structure (pcaRes) to provide a common interface to the PCA results.")
8426 (license license:gpl3+)))
11879284
RW		 8427
8428(define-public r-msnbase
8429 (package
8430 (name "r-msnbase")
8431 (version "2.0.2")
8432 (source
8433 (origin
8434 (method url-fetch)
8435 (uri (bioconductor-uri "MSnbase" version))
8436 (sha256
8437 (base32
8438 "0jjjs29dcwsjaxzfqxy98ycpg3rwxzzchkj77my3cjgdc00sm66n"))))
8439 (properties `((upstream-name . "MSnbase")))
8440 (build-system r-build-system)
8441 (propagated-inputs
8442 `(("r-affy" ,r-affy)
8443 ("r-biobase" ,r-biobase)
8444 ("r-biocgenerics" ,r-biocgenerics)
8445 ("r-biocparallel" ,r-biocparallel)
8446 ("r-digest" ,r-digest)
8447 ("r-ggplot2" ,r-ggplot2)
8448 ("r-impute" ,r-impute)
8449 ("r-iranges" ,r-iranges)
8450 ("r-maldiquant" ,r-maldiquant)
8451 ("r-mzid" ,r-mzid)
8452 ("r-mzr" ,r-mzr)
8453 ("r-pcamethods" ,r-pcamethods)
8454 ("r-plyr" ,r-plyr)
8455 ("r-preprocesscore" ,r-preprocesscore)
8456 ("r-protgenerics" ,r-protgenerics)
8457 ("r-rcpp" ,r-rcpp)
8458 ("r-reshape2" ,r-reshape2)
8459 ("r-s4vectors" ,r-s4vectors)
8460 ("r-vsn" ,r-vsn)
8461 ("r-xml" ,r-xml)))
8462 (home-page "https://github.com/lgatto/MSnbase")
8463 (synopsis "Base functions and classes for MS-based proteomics")
8464 (description
8465 "This package provides basic plotting, data manipulation and processing
8466of MS-based proteomics data.")
8467 (license license:artistic2.0)))
66da3a9f
RW		 8468
8469(define-public r-msnid
8470 (package
8471 (name "r-msnid")
8472 (version "1.8.0")
8473 (source
8474 (origin
8475 (method url-fetch)
8476 (uri (bioconductor-uri "MSnID" version))
8477 (sha256
8478 (base32
8479 "0fkk3za39cxi0jyxmagmycjdslr2xf6vg3ylz14jyffqi0blw9d5"))))
8480 (properties `((upstream-name . "MSnID")))
8481 (build-system r-build-system)
8482 (propagated-inputs
8483 `(("r-biobase" ,r-biobase)
8484 ("r-data-table" ,r-data-table)
8485 ("r-doparallel" ,r-doparallel)
8486 ("r-dplyr" ,r-dplyr)
8487 ("r-foreach" ,r-foreach)
8488 ("r-iterators" ,r-iterators)
8489 ("r-msnbase" ,r-msnbase)
8490 ("r-mzid" ,r-mzid)
8491 ("r-mzr" ,r-mzr)
8492 ("r-protgenerics" ,r-protgenerics)
8493 ("r-r-cache" ,r-r-cache)
8494 ("r-rcpp" ,r-rcpp)
8495 ("r-reshape2" ,r-reshape2)))
8496 (home-page "http://bioconductor.org/packages/MSnID")
8497 (synopsis "Utilities for LC-MSn proteomics identifications")
8498 (description
8499 "This package extracts MS/MS ID data from mzIdentML (leveraging the mzID
8500package) or text files. After collating the search results from multiple
8501datasets it assesses their identification quality and optimize filtering
8502criteria to achieve the maximum number of identifications while not exceeding
8503a specified false discovery rate. It also contains a number of utilities to
8504explore the MS/MS results and assess missed and irregular enzymatic cleavages,
8505mass measurement accuracy, etc.")
8506 (license license:artistic2.0)))
jackhill's copy of GNU Guix: https://guix.gnu.org/