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gnu: python-webencodings: Fix typo in description.
[jackhill/guix/guix.git] / gnu / packages / bioinformatics.scm
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4e10a221 1;;; GNU Guix --- Functional package management for GNU
c3b2ab9d 2;;; Copyright © 2014, 2015, 2016, 2017, 2018 Ricardo Wurmus <rekado@elephly.net>
7502badb 3;;; Copyright © 2015, 2016, 2017, 2018 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>
3df57b3a 7;;; Copyright © 2016, 2017, 2018 Efraim Flashner <efraim@flashner.co.il>
318c0aee 8;;; Copyright © 2016 Marius Bakke <mbakke@fastmail.com>
658ab21d 9;;; Copyright © 2016, 2018 Raoul Bonnal <ilpuccio.febo@gmail.com>
ddf38ece 10;;; Copyright © 2017, 2018 Tobias Geerinckx-Rice <me@tobias.gr>
9364a520 11;;; Copyright © 2017 Arun Isaac <arunisaac@systemreboot.net>
4e10a221
RW		 12;;;
13;;; This file is part of GNU Guix.
14;;;
15;;; GNU Guix is free software; you can redistribute it and/or modify it
16;;; under the terms of the GNU General Public License as published by
17;;; the Free Software Foundation; either version 3 of the License, or (at
18;;; your option) any later version.
19;;;
20;;; GNU Guix is distributed in the hope that it will be useful, but
21;;; WITHOUT ANY WARRANTY; without even the implied warranty of
22;;; MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
23;;; GNU General Public License for more details.
24;;;
25;;; You should have received a copy of the GNU General Public License
26;;; along with GNU Guix. If not, see <http://www.gnu.org/licenses/>.
27
28(define-module (gnu packages bioinformatics)
29 #:use-module ((guix licenses) #:prefix license:)
30 #:use-module (guix packages)
8e913213 31 #:use-module (guix utils)
4e10a221 32 #:use-module (guix download)
2c16316e 33 #:use-module (guix git-download)
ec946638 34 #:use-module (guix hg-download)
10b4a969 35 #:use-module (guix build-system ant)
4e10a221 36 #:use-module (guix build-system gnu)
d7678942 37 #:use-module (guix build-system cmake)
c033f5d6 38 #:use-module (guix build-system ocaml)
365c8153 39 #:use-module (guix build-system perl)
8622a072 40 #:use-module (guix build-system python)
a5002ae7 41 #:use-module (guix build-system r)
9c38b540 42 #:use-module (guix build-system ruby)
9364a520 43 #:use-module (guix build-system scons)
d3517eda 44 #:use-module (guix build-system trivial)
4e10a221 45 #:use-module (gnu packages)
a2950fa4 46 #:use-module (gnu packages autotools)
684bf7c7 47 #:use-module (gnu packages algebra)
d3517eda 48 #:use-module (gnu packages base)
318c0aee 49 #:use-module (gnu packages bash)
a0a71439 50 #:use-module (gnu packages bison)
e4e5a4d8 51 #:use-module (gnu packages boost)
ac257f12 52 #:use-module (gnu packages check)
4e10a221 53 #:use-module (gnu packages compression)
82c370de 54 #:use-module (gnu packages cpio)
7cb61550 55 #:use-module (gnu packages cran)
1baee943 56 #:use-module (gnu packages curl)
99828fa7 57 #:use-module (gnu packages documentation)
94820951 58 #:use-module (gnu packages databases)
d29150b5 59 #:use-module (gnu packages datastructures)
75dd2424 60 #:use-module (gnu packages file)
99268755 61 #:use-module (gnu packages flex)
02f35bb5 62 #:use-module (gnu packages gawk)
2409f37f 63 #:use-module (gnu packages gcc)
66e40e00 64 #:use-module (gnu packages gd)
97b9da68 65 #:use-module (gnu packages gtk)
b16728b0 66 #:use-module (gnu packages glib)
18f5d2a7 67 #:use-module (gnu packages graph)
db7a3444 68 #:use-module (gnu packages groff)
50937297 69 #:use-module (gnu packages guile)
89984be4 70 #:use-module (gnu packages haskell)
66e40e00 71 #:use-module (gnu packages image)
97b9da68 72 #:use-module (gnu packages imagemagick)
15a3c3d4 73 #:use-module (gnu packages java)
8d77a085 74 #:use-module (gnu packages jemalloc)
5ded35d8 75 #:use-module (gnu packages ldc)
51c64999 76 #:use-module (gnu packages linux)
ec946638 77 #:use-module (gnu packages logging)
36742f43 78 #:use-module (gnu packages machine-learning)
db7a3444 79 #:use-module (gnu packages man)
c833ab55 80 #:use-module (gnu packages maths)
6c2b26e2 81 #:use-module (gnu packages mpi)
4e10a221 82 #:use-module (gnu packages ncurses)
c033f5d6 83 #:use-module (gnu packages ocaml)
81f3e0c1 84 #:use-module (gnu packages pcre)
ceb62d54 85 #:use-module (gnu packages parallel)
66e40e00 86 #:use-module (gnu packages pdf)
4e10a221 87 #:use-module (gnu packages perl)
5ccde207 88 #:use-module (gnu packages perl-check)
4e10a221 89 #:use-module (gnu packages pkg-config)
bfe3c685 90 #:use-module (gnu packages popt)
e4e5a4d8 91 #:use-module (gnu packages protobuf)
346a829a 92 #:use-module (gnu packages python)
589e3f4e 93 #:use-module (gnu packages python-web)
ec946638 94 #:use-module (gnu packages readline)
9c38b540 95 #:use-module (gnu packages ruby)
84be3b99 96 #:use-module (gnu packages serialization)
94820951 97 #:use-module (gnu packages shells)
c833ab55 98 #:use-module (gnu packages statistics)
aa163424 99 #:use-module (gnu packages swig)
d7678942 100 #:use-module (gnu packages tbb)
97b9da68 101 #:use-module (gnu packages tex)
db7a3444 102 #:use-module (gnu packages texinfo)
2127cedb 103 #:use-module (gnu packages textutils)
43c565d2 104 #:use-module (gnu packages time)
a2950fa4 105 #:use-module (gnu packages tls)
ce7155d5 106 #:use-module (gnu packages vim)
365c8153 107 #:use-module (gnu packages web)
c833ab55 108 #:use-module (gnu packages xml)
66e40e00 109 #:use-module (gnu packages xorg)
2c9232ae 110 #:use-module (srfi srfi-1)
ce7e361f 111 #:use-module (ice-9 match))
4e10a221 112
036cd0cb
RJPB		 113(define-public r-ape
114 (package
115 (name "r-ape")
b12c6a66 116 (version "5.0")
036cd0cb
RJPB		 117 (source
118 (origin
119 (method url-fetch)
120 (uri (cran-uri "ape" version))
121 (sha256
122 (base32
b12c6a66 123 "0q59pmxawz498cb9mv5m49lhiwxib8ak94yyydz7qg8b6lpd4bn3"))))
036cd0cb 124 (build-system r-build-system)
aeb64f3c
RW		 125 (propagated-inputs
126 `(("r-lattice" ,r-lattice)
b12c6a66
RW		 127 ("r-nlme" ,r-nlme)
128 ("r-rcpp" ,r-rcpp)))
036cd0cb
RJPB		 129 (home-page "http://ape-package.ird.fr/")
130 (synopsis "Analyses of phylogenetics and evolution")
131 (description
132 "This package provides functions for reading, writing, plotting, and
133manipulating phylogenetic trees, analyses of comparative data in a
134phylogenetic framework, ancestral character analyses, analyses of
135diversification and macroevolution, computing distances from DNA sequences,
136and several other tools.")
137 (license license:gpl2+)))
138
8dc797fa
BW		 139(define-public aragorn
140 (package
141 (name "aragorn")
e990c81d 142 (version "1.2.38")
8dc797fa
BW		 143 (source (origin
144 (method url-fetch)
145 (uri (string-append
146 "http://mbio-serv2.mbioekol.lu.se/ARAGORN/Downloads/aragorn"
147 version ".tgz"))
148 (sha256
149 (base32
e990c81d 150 "09i1rg716smlbnixfm7q1ml2mfpaa2fpn3hwjg625ysmfwwy712b"))))
8dc797fa
BW		 151 (build-system gnu-build-system)
152 (arguments
153 `(#:tests? #f ; there are no tests
154 #:phases
155 (modify-phases %standard-phases
156 (delete 'configure)
157 (replace 'build
158 (lambda _
159 (zero? (system* "gcc"
160 "-O3"
161 "-ffast-math"
162 "-finline-functions"
163 "-o"
164 "aragorn"
165 (string-append "aragorn" ,version ".c")))))
166 (replace 'install
167 (lambda* (#:key outputs #:allow-other-keys)
168 (let* ((out (assoc-ref outputs "out"))
169 (bin (string-append out "/bin"))
170 (man (string-append out "/share/man/man1")))
171 (mkdir-p bin)
f3860753 172 (install-file "aragorn" bin)
8dc797fa 173 (mkdir-p man)
f3860753 174 (install-file "aragorn.1" man))
8dc797fa
BW		 175 #t)))))
176 (home-page "http://mbio-serv2.mbioekol.lu.se/ARAGORN")
177 (synopsis "Detect tRNA, mtRNA and tmRNA genes in nucleotide sequences")
178 (description
179 "Aragorn identifies transfer RNA, mitochondrial RNA and
180transfer-messenger RNA from nucleotide sequences, based on homology to known
181tRNA consensus sequences and RNA structure. It also outputs the secondary
182structure of the predicted RNA.")
183 (license license:gpl2)))
184
a12ba6e8
BW		 185(define-public bamm
186 (package
187 (name "bamm")
4b6da268 188 (version "1.7.3")
a12ba6e8
BW		 189 (source (origin
190 (method url-fetch)
191 ;; BamM is not available on pypi.
192 (uri (string-append
4b6da268 193 "https://github.com/Ecogenomics/BamM/archive/"
a12ba6e8
BW		 194 version ".tar.gz"))
195 (file-name (string-append name "-" version ".tar.gz"))
196 (sha256
197 (base32
4b6da268 198 "1f35yxp4pc8aadsvbpg6r4kg2jh4fkjci0iby4iyljm6980sac0s"))
a12ba6e8
BW		 199 (modules '((guix build utils)))
200 (snippet
201 `(begin
202 ;; Delete bundled htslib.
203 (delete-file-recursively "c/htslib-1.3.1")
204 #t))))
205 (build-system python-build-system)
206 (arguments
207 `(#:python ,python-2 ; BamM is Python 2 only.
208 ;; Do not use bundled libhts. Do use the bundled libcfu because it has
209 ;; been modified from its original form.
210 #:configure-flags
211 (let ((htslib (assoc-ref %build-inputs "htslib")))
212 (list "--with-libhts-lib" (string-append htslib "/lib")
213 "--with-libhts-inc" (string-append htslib "/include/htslib")))
214 #:phases
215 (modify-phases %standard-phases
216 (add-after 'unpack 'autogen
217 (lambda _
218 (with-directory-excursion "c"
219 (let ((sh (which "sh")))
220 ;; Use autogen so that 'configure' works.
221 (substitute* "autogen.sh" (("/bin/sh") sh))
222 (setenv "CONFIG_SHELL" sh)
223 (substitute* "configure" (("/bin/sh") sh))
224 (zero? (system* "./autogen.sh"))))))
225 (delete 'build)
226 ;; Run tests after installation so compilation only happens once.
227 (delete 'check)
228 (add-after 'install 'wrap-executable
229 (lambda* (#:key outputs #:allow-other-keys)
230 (let* ((out (assoc-ref outputs "out"))
231 (path (getenv "PATH")))
232 (wrap-program (string-append out "/bin/bamm")
233 `("PATH" ":" prefix (,path))))
234 #t))
235 (add-after 'wrap-executable 'post-install-check
236 (lambda* (#:key inputs outputs #:allow-other-keys)
237 (setenv "PATH"
238 (string-append (assoc-ref outputs "out")
239 "/bin:"
240 (getenv "PATH")))
241 (setenv "PYTHONPATH"
242 (string-append
243 (assoc-ref outputs "out")
244 "/lib/python"
245 (string-take (string-take-right
246 (assoc-ref inputs "python") 5) 3)
247 "/site-packages:"
248 (getenv "PYTHONPATH")))
249 ;; There are 2 errors printed, but they are safe to ignore:
250 ;; 1) [E::hts_open_format] fail to open file ...
251 ;; 2) samtools view: failed to open ...
252 (zero? (system* "nosetests")))))))
253 (native-inputs
254 `(("autoconf" ,autoconf)
255 ("automake" ,automake)
256 ("libtool" ,libtool)
257 ("zlib" ,zlib)
258 ("python-nose" ,python2-nose)
f3b98f4f 259 ("python-pysam" ,python2-pysam)))
a12ba6e8 260 (inputs
bca2c576 261 `(("htslib" ,htslib-1.3) ; At least one test fails on htslib-1.4+.
a12ba6e8
BW		 262 ("samtools" ,samtools)
263 ("bwa" ,bwa)
264 ("grep" ,grep)
265 ("sed" ,sed)
266 ("coreutils" ,coreutils)))
267 (propagated-inputs
268 `(("python-numpy" ,python2-numpy)))
269 (home-page "http://ecogenomics.github.io/BamM/")
270 (synopsis "Metagenomics-focused BAM file manipulator")
271 (description
272 "BamM is a C library, wrapped in python, to efficiently generate and
273parse BAM files, specifically for the analysis of metagenomic data. For
274instance, it implements several methods to assess contig-wise read coverage.")
275 (license license:lgpl3+)))
276
9794180d
RW		 277(define-public bamtools
278 (package
279 (name "bamtools")
48d66a9c 280 (version "2.4.1")
9794180d
RW		 281 (source (origin
282 (method url-fetch)
283 (uri (string-append
284 "https://github.com/pezmaster31/bamtools/archive/v"
285 version ".tar.gz"))
286 (file-name (string-append name "-" version ".tar.gz"))
287 (sha256
288 (base32
48d66a9c 289 "0jr024kcrhjb82cm69i7p5fcg5375zlc1h3qh2n1v368hcd0qflk"))))
9794180d 290 (build-system cmake-build-system)
4702cec2
RW		 291 (arguments
292 `(#:tests? #f ;no "check" target
293 #:phases
294 (modify-phases %standard-phases
295 (add-before
296 'configure 'set-ldflags
297 (lambda* (#:key outputs #:allow-other-keys)
298 (setenv "LDFLAGS"
299 (string-append
300 "-Wl,-rpath="
301 (assoc-ref outputs "out") "/lib/bamtools")))))))
9794180d
RW		 302 (inputs `(("zlib" ,zlib)))
303 (home-page "https://github.com/pezmaster31/bamtools")
304 (synopsis "C++ API and command-line toolkit for working with BAM data")
305 (description
306 "BamTools provides both a C++ API and a command-line toolkit for handling
307BAM files.")
308 (license license:expat)))
309
bdc7be59
MB		 310(define-public bcftools
311 (package
312 (name "bcftools")
0620387a 313 (version "1.5")
bdc7be59
MB		 314 (source (origin
315 (method url-fetch)
316 (uri (string-append
317 "https://github.com/samtools/bcftools/releases/download/"
318 version "/bcftools-" version ".tar.bz2"))
319 (sha256
320 (base32
0620387a 321 "0093hkkvxmbwfaa7905s6185jymynvg42kq6sxv7fili11l5mxwz"))
3837108e 322 (patches (search-patches "bcftools-regidx-unsigned-char.patch"))
bdc7be59
MB		 323 (modules '((guix build utils)))
324 (snippet
325 ;; Delete bundled htslib.
0620387a 326 '(delete-file-recursively "htslib-1.5"))))
bdc7be59
MB		 327 (build-system gnu-build-system)
328 (arguments
329 `(#:test-target "test"
0620387a 330 #:configure-flags (list "--with-htslib=system")
bdc7be59
MB		 331 #:make-flags
332 (list
333 "USE_GPL=1"
0620387a 334 "LIBS=-lgsl -lgslcblas"
bdc7be59
MB		 335 (string-append "prefix=" (assoc-ref %outputs "out"))
336 (string-append "HTSDIR=" (assoc-ref %build-inputs "htslib") "/include")
98593f9f 337 (string-append "HTSLIB=" (assoc-ref %build-inputs "htslib") "/lib/libhts.so")
bdc7be59 338 (string-append "BGZIP=" (assoc-ref %build-inputs "htslib") "/bin/bgzip")
98593f9f
BW		 339 (string-append "TABIX=" (assoc-ref %build-inputs "htslib") "/bin/tabix")
340 (string-append "PACKAGE_VERSION=" ,version))
bdc7be59
MB		 341 #:phases
342 (modify-phases %standard-phases
bdc7be59
MB		 343 (add-before 'check 'patch-tests
344 (lambda _
345 (substitute* "test/test.pl"
346 (("/bin/bash") (which "bash")))
347 #t)))))
348 (native-inputs
349 `(("htslib" ,htslib)
350 ("perl" ,perl)))
351 (inputs
352 `(("gsl" ,gsl)
353 ("zlib" ,zlib)))
354 (home-page "https://samtools.github.io/bcftools/")
355 (synopsis "Utilities for variant calling and manipulating VCFs and BCFs")
356 (description
357 "BCFtools is a set of utilities that manipulate variant calls in the
358Variant Call Format (VCF) and its binary counterpart BCF. All commands work
359transparently with both VCFs and BCFs, both uncompressed and BGZF-compressed.")
360 ;; The sources are dual MIT/GPL, but becomes GPL-only when USE_GPL=1.
361 (license (list license:gpl3+ license:expat))))
362
8dd4ff11
RW		 363(define-public bedops
364 (package
365 (name "bedops")
1bbc3b1d 366 (version "2.4.14")
8dd4ff11
RW		 367 (source (origin
368 (method url-fetch)
369 (uri (string-append "https://github.com/bedops/bedops/archive/v"
370 version ".tar.gz"))
f586c877 371 (file-name (string-append name "-" version ".tar.gz"))
8dd4ff11
RW		 372 (sha256
373 (base32
1bbc3b1d 374 "1kqbac547wyqma81cyky9n7mkgikjpsfd3nnmcm6hpqwanqgh10v"))))
8dd4ff11
RW		 375 (build-system gnu-build-system)
376 (arguments
377 '(#:tests? #f
378 #:make-flags (list (string-append "BINDIR=" %output "/bin"))
379 #:phases
dc1d3cde
KK		 380 (modify-phases %standard-phases
381 (add-after 'unpack 'unpack-tarballs
382 (lambda _
383 ;; FIXME: Bedops includes tarballs of minimally patched upstream
384 ;; libraries jansson, zlib, and bzip2. We cannot just use stock
385 ;; libraries because at least one of the libraries (zlib) is
386 ;; patched to add a C++ function definition (deflateInit2cpp).
387 ;; Until the Bedops developers offer a way to link against system
388 ;; libraries we have to build the in-tree copies of these three
389 ;; libraries.
390
391 ;; See upstream discussion:
392 ;; https://github.com/bedops/bedops/issues/124
393
394 ;; Unpack the tarballs to benefit from shebang patching.
395 (with-directory-excursion "third-party"
396 (and (zero? (system* "tar" "xvf" "jansson-2.6.tar.bz2"))
397 (zero? (system* "tar" "xvf" "zlib-1.2.7.tar.bz2"))
398 (zero? (system* "tar" "xvf" "bzip2-1.0.6.tar.bz2"))))
399 ;; Disable unpacking of tarballs in Makefile.
400 (substitute* "system.mk/Makefile.linux"
401 (("^\tbzcat .*") "\t@echo \"not unpacking\"\n")
402 (("\\./configure") "CONFIG_SHELL=bash ./configure"))
403 (substitute* "third-party/zlib-1.2.7/Makefile.in"
404 (("^SHELL=.*$") "SHELL=bash\n"))
405 #t))
406 (delete 'configure))))
8dd4ff11
RW		 407 (home-page "https://github.com/bedops/bedops")
408 (synopsis "Tools for high-performance genomic feature operations")
409 (description
410 "BEDOPS is a suite of tools to address common questions raised in genomic
411studies---mostly with regard to overlap and proximity relationships between
412data sets. It aims to be scalable and flexible, facilitating the efficient
413and accurate analysis and management of large-scale genomic data.
414
415BEDOPS provides tools that perform highly efficient and scalable Boolean and
416other set operations, statistical calculations, archiving, conversion and
417other management of genomic data of arbitrary scale. Tasks can be easily
418split by chromosome for distributing whole-genome analyses across a
419computational cluster.")
420 (license license:gpl2+)))
421
81de5647
RW		 422(define-public bedtools
423 (package
424 (name "bedtools")
6098a386 425 (version "2.27.1")
81de5647
RW		 426 (source (origin
427 (method url-fetch)
0d9824cc
RW		 428 (uri (string-append "https://github.com/arq5x/bedtools2/releases/"
429 "download/v" version "/"
430 "bedtools-" version ".tar.gz"))
81de5647
RW		 431 (sha256
432 (base32
6098a386 433 "1ndg5yknrxl4djx8ddzgk12rrbiidfpmkkg5z3f95jzryfxarhn8"))))
81de5647 434 (build-system gnu-build-system)
81de5647
RW		 435 (arguments
436 '(#:test-target "test"
0d9824cc
RW		 437 #:make-flags
438 (list (string-append "prefix=" (assoc-ref %outputs "out")))
81de5647 439 #:phases
6573ac82 440 (modify-phases %standard-phases
0d9824cc
RW		 441 (delete 'configure))))
442 (native-inputs `(("python" ,python-2)))
443 (inputs
444 `(("samtools" ,samtools)
445 ("zlib" ,zlib)))
81de5647
RW		 446 (home-page "https://github.com/arq5x/bedtools2")
447 (synopsis "Tools for genome analysis and arithmetic")
448 (description
449 "Collectively, the bedtools utilities are a swiss-army knife of tools for
450a wide-range of genomics analysis tasks. The most widely-used tools enable
451genome arithmetic: that is, set theory on the genome. For example, bedtools
452allows one to intersect, merge, count, complement, and shuffle genomic
453intervals from multiple files in widely-used genomic file formats such as BAM,
454BED, GFF/GTF, VCF.")
455 (license license:gpl2)))
456
9a8f309c
RW		 457;; Later releases of bedtools produce files with more columns than
458;; what Ribotaper expects.
459(define-public bedtools-2.18
460 (package (inherit bedtools)
461 (name "bedtools")
462 (version "2.18.0")
463 (source (origin
464 (method url-fetch)
465 (uri (string-append "https://github.com/arq5x/bedtools2/"
466 "archive/v" version ".tar.gz"))
467 (file-name (string-append name "-" version ".tar.gz"))
468 (sha256
469 (base32
83b9d121
RW		 470 "05vrnr8yp7swfagshzpgqmzk1blnwnq8pq5pckzi1m26w98d63vf"))))
471 (arguments
472 '(#:test-target "test"
473 #:phases
474 (modify-phases %standard-phases
475 (delete 'configure)
476 (replace 'install
477 (lambda* (#:key outputs #:allow-other-keys)
478 (let ((bin (string-append (assoc-ref outputs "out") "/bin/")))
479 (for-each (lambda (file)
480 (install-file file bin))
481 (find-files "bin" ".*")))
482 #t)))))))
9a8f309c 483
17dc32a4
RW		 484(define-public ribotaper
485 (package
486 (name "ribotaper")
487 (version "1.3.1")
488 (source (origin
489 (method url-fetch)
490 (uri (string-append "https://ohlerlab.mdc-berlin.de/"
491 "files/RiboTaper/RiboTaper_Version_"
492 version ".tar.gz"))
493 (sha256
494 (base32
495 "0ykjbps1y3z3085q94npw8i9x5gldc6shy8vlc08v76zljsm07hv"))))
496 (build-system gnu-build-system)
7edee344
RW		 497 (arguments
498 `(#:phases
499 (modify-phases %standard-phases
500 (add-after 'install 'wrap-executables
501 (lambda* (#:key inputs outputs #:allow-other-keys)
502 (let* ((out (assoc-ref outputs "out")))
503 (for-each
504 (lambda (script)
505 (wrap-program (string-append out "/bin/" script)
506 `("R_LIBS_SITE" ":" = (,(getenv "R_LIBS_SITE")))))
507 '("create_annotations_files.bash"
508 "create_metaplots.bash"
509 "Ribotaper_ORF_find.sh"
510 "Ribotaper.sh"))))))))
17dc32a4
RW		 511 (inputs
512 `(("bedtools" ,bedtools-2.18)
513 ("samtools" ,samtools-0.1)
2d7c4ae3 514 ("r-minimal" ,r-minimal)
17dc32a4
RW		 515 ("r-foreach" ,r-foreach)
516 ("r-xnomial" ,r-xnomial)
517 ("r-domc" ,r-domc)
518 ("r-multitaper" ,r-multitaper)
519 ("r-seqinr" ,r-seqinr)))
520 (home-page "https://ohlerlab.mdc-berlin.de/software/RiboTaper_126/")
521 (synopsis "Define translated ORFs using ribosome profiling data")
522 (description
523 "Ribotaper is a method for defining translated @dfn{open reading
524frames} (ORFs) using ribosome profiling (ribo-seq) data. This package
525provides the Ribotaper pipeline.")
526 (license license:gpl3+)))
527
769fc6bb
RW		 528(define-public ribodiff
529 (package
530 (name "ribodiff")
531 (version "0.2.2")
532 (source
533 (origin
534 (method url-fetch)
535 (uri (string-append "https://github.com/ratschlab/RiboDiff/"
536 "archive/v" version ".tar.gz"))
537 (file-name (string-append name "-" version ".tar.gz"))
538 (sha256
539 (base32
540 "0wpbwmfv05wdjxv7ikm664f7s7p7cqr8jnw99zrda0q67rl50aaj"))))
541 (build-system python-build-system)
542 (arguments
543 `(#:python ,python-2
544 #:phases
545 (modify-phases %standard-phases
546 ;; Generate an installable executable script wrapper.
547 (add-after 'unpack 'patch-setup.py
548 (lambda _
549 (substitute* "setup.py"
550 (("^(.*)packages=.*" line prefix)
551 (string-append line "\n"
552 prefix "scripts=['scripts/TE.py'],\n")))
553 #t)))))
554 (inputs
555 `(("python-numpy" ,python2-numpy)
556 ("python-matplotlib" ,python2-matplotlib)
557 ("python-scipy" ,python2-scipy)
558 ("python-statsmodels" ,python2-statsmodels)))
2bb12f5a
MB		 559 (native-inputs
560 `(("python-mock" ,python2-mock)
561 ("python-nose" ,python2-nose)))
769fc6bb
RW		 562 (home-page "http://public.bmi.inf.ethz.ch/user/zhongy/RiboDiff/")
563 (synopsis "Detect translation efficiency changes from ribosome footprints")
564 (description "RiboDiff is a statistical tool that detects the protein
565translational efficiency change from Ribo-Seq (ribosome footprinting) and
566RNA-Seq data. It uses a generalized linear model to detect genes showing
567difference in translational profile taking mRNA abundance into account. It
568facilitates us to decipher the translational regulation that behave
569independently with transcriptional regulation.")
570 (license license:gpl3+)))
571
a0a71439
RJ		 572(define-public bioawk
573 (package
574 (name "bioawk")
575 (version "1.0")
576 (source (origin
577 (method url-fetch)
578 (uri (string-append "https://github.com/lh3/bioawk/archive/v"
579 version ".tar.gz"))
580 (file-name (string-append name "-" version ".tar.gz"))
581 (sha256
582 (base32 "1daizxsk17ahi9n58fj8vpgwyhzrzh54bzqhanjanp88kgrz7gjw"))))
583 (build-system gnu-build-system)
584 (inputs
585 `(("zlib" ,zlib)))
586 (native-inputs
587 `(("bison" ,bison)))
588 (arguments
589 `(#:tests? #f ; There are no tests to run.
590 ;; Bison must generate files, before other targets can build.
591 #:parallel-build? #f
592 #:phases
593 (modify-phases %standard-phases
594 (delete 'configure) ; There is no configure phase.
595 (replace 'install
596 (lambda* (#:key outputs #:allow-other-keys)
597 (let* ((out (assoc-ref outputs "out"))
598 (bin (string-append out "/bin"))
599 (man (string-append out "/share/man/man1")))
600 (mkdir-p man)
601 (copy-file "awk.1" (string-append man "/bioawk.1"))
602 (install-file "bioawk" bin)))))))
603 (home-page "https://github.com/lh3/bioawk")
604 (synopsis "AWK with bioinformatics extensions")
605 (description "Bioawk is an extension to Brian Kernighan's awk, adding the
606support of several common biological data formats, including optionally gzip'ed
607BED, GFF, SAM, VCF, FASTA/Q and TAB-delimited formats with column names. It
608also adds a few built-in functions and a command line option to use TAB as the
609input/output delimiter. When the new functionality is not used, bioawk is
610intended to behave exactly the same as the original BWK awk.")
611 (license license:x11)))
612
a2fb1492
RW		 613(define-public python2-pybedtools
614 (package
615 (name "python2-pybedtools")
616 (version "0.6.9")
617 (source (origin
618 (method url-fetch)
619 (uri (string-append
620 "https://pypi.python.org/packages/source/p/pybedtools/pybedtools-"
621 version ".tar.gz"))
622 (sha256
623 (base32
624 "1ldzdxw1p4y3g2ignmggsdypvqkcwqwzhdha4rbgpih048z5p4an"))))
625 (build-system python-build-system)
626 (arguments `(#:python ,python-2)) ; no Python 3 support
627 (inputs
f2516de2 628 `(("python-matplotlib" ,python2-matplotlib)))
a2fb1492
RW		 629 (propagated-inputs
630 `(("bedtools" ,bedtools)
631 ("samtools" ,samtools)))
632 (native-inputs
f2516de2
HG		 633 `(("python-cython" ,python2-cython)
634 ("python-pyyaml" ,python2-pyyaml)
f3b98f4f 635 ("python-nose" ,python2-nose)))
a2fb1492
RW		 636 (home-page "https://pythonhosted.org/pybedtools/")
637 (synopsis "Python wrapper for BEDtools programs")
638 (description
639 "pybedtools is a Python wrapper for Aaron Quinlan's BEDtools programs,
640which are widely used for genomic interval manipulation or \"genome algebra\".
641pybedtools extends BEDTools by offering feature-level manipulations from with
642Python.")
643 (license license:gpl2+)))
644
9e12eba8
BW		 645(define-public python-biom-format
646 (package
647 (name "python-biom-format")
abc08cba 648 (version "2.1.6")
9e12eba8
BW		 649 (source
650 (origin
651 (method url-fetch)
652 ;; Use GitHub as source because PyPI distribution does not contain
653 ;; test data: https://github.com/biocore/biom-format/issues/693
654 (uri (string-append "https://github.com/biocore/biom-format/archive/"
655 version ".tar.gz"))
656 (file-name (string-append name "-" version ".tar.gz"))
657 (sha256
658 (base32
abc08cba 659 "08cr7wpahk6zb31h4bs7jmzpvxcqv9s13xz40h6y2h656jvdvnpj"))))
9e12eba8 660 (build-system python-build-system)
de96ea28 661 (propagated-inputs
9e12eba8
BW		 662 `(("python-numpy" ,python-numpy)
663 ("python-scipy" ,python-scipy)
664 ("python-future" ,python-future)
665 ("python-click" ,python-click)
abc08cba
BW		 666 ("python-h5py" ,python-h5py)
667 ("python-pandas" ,python-pandas)))
da5ebd10
MB		 668 (native-inputs
669 `(("python-nose" ,python-nose)))
9e12eba8
BW		 670 (home-page "http://www.biom-format.org")
671 (synopsis "Biological Observation Matrix (BIOM) format utilities")
672 (description
673 "The BIOM file format is designed to be a general-use format for
674representing counts of observations e.g. operational taxonomic units, KEGG
675orthology groups or lipid types, in one or more biological samples
676e.g. microbiome samples, genomes, metagenomes.")
677 (license license:bsd-3)
678 (properties `((python2-variant . ,(delay python2-biom-format))))))
679
680(define-public python2-biom-format
681 (let ((base (package-with-python2 (strip-python2-variant python-biom-format))))
682 (package
683 (inherit base)
684 (arguments
685 `(#:phases
686 (modify-phases %standard-phases
687 ;; Do not require the unmaintained pyqi library.
688 (add-after 'unpack 'remove-pyqi
689 (lambda _
690 (substitute* "setup.py"
691 (("install_requires.append\\(\"pyqi\"\\)") "pass"))
692 #t)))
00e10c6e 693 ,@(package-arguments base))))))
9e12eba8 694
f7283db3
RW		 695(define-public bioperl-minimal
696 (let* ((inputs `(("perl-module-build" ,perl-module-build)
697 ("perl-data-stag" ,perl-data-stag)
698 ("perl-libwww" ,perl-libwww)
699 ("perl-uri" ,perl-uri)))
700 (transitive-inputs
701 (map (compose package-name cadr)
702 (delete-duplicates
703 (concatenate
704 (map (compose package-transitive-target-inputs cadr) inputs))))))
705 (package
706 (name "bioperl-minimal")
c70271ec 707 (version "1.7.0")
f7283db3
RW		 708 (source
709 (origin
710 (method url-fetch)
c70271ec
RW		 711 (uri (string-append "https://github.com/bioperl/bioperl-live/"
712 "archive/release-"
713 (string-map (lambda (c)
714 (if (char=? c #\.)
715 #\- c)) version)
716 ".tar.gz"))
f7283db3
RW		 717 (sha256
718 (base32
c70271ec 719 "12phgpxwgkqflkwfb9dcqg7a31dpjlfhar8wcgv0aj5ln4akfz06"))))
f7283db3
RW		 720 (build-system perl-build-system)
721 (arguments
722 `(#:phases
723 (modify-phases %standard-phases
724 (add-after
725 'install 'wrap-programs
726 (lambda* (#:key outputs #:allow-other-keys)
727 ;; Make sure all executables in "bin" find the required Perl
728 ;; modules at runtime. As the PERL5LIB variable contains also
729 ;; the paths of native inputs, we pick the transitive target
730 ;; inputs from %build-inputs.
731 (let* ((out (assoc-ref outputs "out"))
732 (bin (string-append out "/bin/"))
733 (path (string-join
734 (cons (string-append out "/lib/perl5/site_perl")
735 (map (lambda (name)
736 (assoc-ref %build-inputs name))
737 ',transitive-inputs))
738 ":")))
739 (for-each (lambda (file)
740 (wrap-program file
741 `("PERL5LIB" ":" prefix (,path))))
742 (find-files bin "\\.pl$"))
743 #t))))))
744 (inputs inputs)
745 (native-inputs
746 `(("perl-test-most" ,perl-test-most)))
747 (home-page "http://search.cpan.org/dist/BioPerl")
748 (synopsis "Bioinformatics toolkit")
749 (description
750 "BioPerl is the product of a community effort to produce Perl code which
751is useful in biology. Examples include Sequence objects, Alignment objects
752and database searching objects. These objects not only do what they are
753advertised to do in the documentation, but they also interact - Alignment
754objects are made from the Sequence objects, Sequence objects have access to
755Annotation and SeqFeature objects and databases, Blast objects can be
756converted to Alignment objects, and so on. This means that the objects
757provide a coordinated and extensible framework to do computational biology.")
2f3108ad 758 (license license:perl-license))))
f7283db3 759
85c37e29
RW		 760(define-public python-biopython
761 (package
762 (name "python-biopython")
af6ce610 763 (version "1.70")
85c37e29
RW		 764 (source (origin
765 (method url-fetch)
e815c094
BW		 766 ;; use PyPi rather than biopython.org to ease updating
767 (uri (pypi-uri "biopython" version))
85c37e29
RW		 768 (sha256
769 (base32
af6ce610 770 "0nz4n9d2y2dg849gn1z0vjlkwcpzzkzy3fij7x94a6ixy2c54z2a"))))
85c37e29 771 (build-system python-build-system)
4ce60305
BW		 772 (arguments
773 `(#:phases
774 (modify-phases %standard-phases
775 (add-before 'check 'set-home
776 ;; Some tests require a home directory to be set.
777 (lambda _ (setenv "HOME" "/tmp") #t)))))
f22efa01 778 (propagated-inputs
85c37e29 779 `(("python-numpy" ,python-numpy)))
85c37e29
RW		 780 (home-page "http://biopython.org/")
781 (synopsis "Tools for biological computation in Python")
782 (description
783 "Biopython is a set of tools for biological computation including parsers
784for bioinformatics files into Python data structures; interfaces to common
785bioinformatics programs; a standard sequence class and tools for performing
786common operations on them; code to perform data classification; code for
787dealing with alignments; code making it easy to split up parallelizable tasks
788into separate processes; and more.")
5c31f4aa 789 (license (license:non-copyleft "http://www.biopython.org/DIST/LICENSE"))))
85c37e29
RW		 790
791(define-public python2-biopython
5c31f4aa 792 (package-with-python2 python-biopython))
85c37e29 793
985d8411
BW		 794(define-public bpp-core
795 ;; The last release was in 2014 and the recommended way to install from source
796 ;; is to clone the git repository, so we do this.
797 ;; http://biopp.univ-montp2.fr/wiki/index.php/Main_Page
798 (let ((commit "7d8bced0d1a87291ea8dd7046b7fb5ff9c35c582"))
799 (package
800 (name "bpp-core")
801 (version (string-append "2.2.0-1." (string-take commit 7)))
802 (source (origin
803 (method git-fetch)
804 (uri (git-reference
805 (url "http://biopp.univ-montp2.fr/git/bpp-core")
806 (commit commit)))
807 (file-name (string-append name "-" version "-checkout"))
808 (sha256
809 (base32
810 "10djsq5vlnkilv436gnmh4irpk49v29pa69r6xiryg32xmvn909j"))))
811 (build-system cmake-build-system)
812 (arguments
813 `(#:parallel-build? #f))
814 (inputs
815 `(("gcc" ,gcc-5))) ; Compilation of bpp-phyl fails with GCC 4.9 so we
816 ; compile all of the bpp packages with GCC 5.
817 (home-page "http://biopp.univ-montp2.fr")
818 (synopsis "C++ libraries for Bioinformatics")
819 (description
820 "Bio++ is a set of C++ libraries for Bioinformatics, including sequence
821analysis, phylogenetics, molecular evolution and population genetics. It is
822Object Oriented and is designed to be both easy to use and computer efficient.
823Bio++ intends to help programmers to write computer expensive programs, by
824providing them a set of re-usable tools.")
825 (license license:cecill-c))))
826
8b5f4d57
BW		 827(define-public bpp-phyl
828 ;; The last release was in 2014 and the recommended way to install from source
829 ;; is to clone the git repository, so we do this.
830 ;; http://biopp.univ-montp2.fr/wiki/index.php/Main_Page
831 (let ((commit "0c07167b629f68b569bf274d1ad0c4af83276ae2"))
832 (package
833 (name "bpp-phyl")
834 (version (string-append "2.2.0-1." (string-take commit 7)))
835 (source (origin
836 (method git-fetch)
837 (uri (git-reference
838 (url "http://biopp.univ-montp2.fr/git/bpp-phyl")
839 (commit commit)))
840 (file-name (string-append name "-" version "-checkout"))
841 (sha256
842 (base32
843 "1ssjgchzwj3iai26kyly7gwkdv8sk59nqhkb1wpap3sf5m6kyllh"))))
844 (build-system cmake-build-system)
845 (arguments
846 `(#:parallel-build? #f
847 ;; If out-of-source, test data is not copied into the build directory
848 ;; so the tests fail.
849 #:out-of-source? #f))
850 (inputs
851 `(("bpp-core" ,bpp-core)
852 ("bpp-seq" ,bpp-seq)
853 ;; GCC 4.8 fails due to an 'internal compiler error', so we use a more
854 ;; modern GCC.
855 ("gcc" ,gcc-5)))
856 (home-page "http://biopp.univ-montp2.fr")
857 (synopsis "Bio++ phylogenetic Library")
858 (description
859 "Bio++ is a set of C++ libraries for Bioinformatics, including sequence
860analysis, phylogenetics, molecular evolution and population genetics. This
861library provides phylogenetics-related modules.")
862 (license license:cecill-c))))
863
159a7016
BW		 864(define-public bpp-popgen
865 ;; The last release was in 2014 and the recommended way to install from source
866 ;; is to clone the git repository, so we do this.
867 ;; http://biopp.univ-montp2.fr/wiki/index.php/Main_Page
868 (let ((commit "e472bac9b1a148803895d747cd6d0c5904f85d9f"))
869 (package
870 (name "bpp-popgen")
871 (version (string-append "2.2.0-1." (string-take commit 7)))
872 (source (origin
873 (method git-fetch)
874 (uri (git-reference
875 (url "http://biopp.univ-montp2.fr/git/bpp-popgen")
876 (commit commit)))
877 (file-name (string-append name "-" version "-checkout"))
878 (sha256
879 (base32
880 "0yn82dzn1n5629nzja68xfrhi655709rjanyryb36vzkmymy6dw5"))))
881 (build-system cmake-build-system)
882 (arguments
883 `(#:parallel-build? #f
884 #:tests? #f)) ; There are no tests.
885 (inputs
886 `(("bpp-core" ,bpp-core)
887 ("bpp-seq" ,bpp-seq)
888 ("gcc" ,gcc-5)))
889 (home-page "http://biopp.univ-montp2.fr")
890 (synopsis "Bio++ population genetics library")
891 (description
892 "Bio++ is a set of C++ libraries for Bioinformatics, including sequence
893analysis, phylogenetics, molecular evolution and population genetics. This
894library provides population genetics-related modules.")
895 (license license:cecill-c))))
896
70f1bc05
BW		 897(define-public bpp-seq
898 ;; The last release was in 2014 and the recommended way to install from source
899 ;; is to clone the git repository, so we do this.
900 ;; http://biopp.univ-montp2.fr/wiki/index.php/Main_Page
901 (let ((commit "6cfa07965ce152e5598a89df2fa80a75973bfa33"))
902 (package
903 (name "bpp-seq")
904 (version (string-append "2.2.0-1." (string-take commit 7)))
905 (source (origin
906 (method git-fetch)
907 (uri (git-reference
908 (url "http://biopp.univ-montp2.fr/git/bpp-seq")
909 (commit commit)))
910 (file-name (string-append name "-" version "-checkout"))
911 (sha256
912 (base32
913 "1nys5jq7jqvdg40d91wsmj3q2yzy4276cp7sp44n67p468f27zf2"))))
914 (build-system cmake-build-system)
915 (arguments
916 `(#:parallel-build? #f
917 ;; If out-of-source, test data is not copied into the build directory
918 ;; so the tests fail.
919 #:out-of-source? #f))
920 (inputs
921 `(("bpp-core" ,bpp-core)
922 ("gcc" ,gcc-5))) ; Use GCC 5 as per 'bpp-core'.
923 (home-page "http://biopp.univ-montp2.fr")
924 (synopsis "Bio++ sequence library")
925 (description
926 "Bio++ is a set of C++ libraries for Bioinformatics, including sequence
927analysis, phylogenetics, molecular evolution and population genetics. This
928library provides sequence-related modules.")
929 (license license:cecill-c))))
930
db7a3444
BW		 931(define-public bppsuite
932 ;; The last release was in 2014 and the recommended way to install from source
933 ;; is to clone the git repository, so we do this.
934 ;; http://biopp.univ-montp2.fr/wiki/index.php/Main_Page
935 (let ((commit "c516147f57aa50961121cd505bed52cd7603698b"))
936 (package
937 (name "bppsuite")
938 (version (string-append "2.2.0-1." (string-take commit 7)))
939 (source (origin
940 (method git-fetch)
941 (uri (git-reference
942 (url "http://biopp.univ-montp2.fr/git/bppsuite")
943 (commit commit)))
944 (file-name (string-append name "-" version "-checkout"))
945 (sha256
946 (base32
947 "1y87pxvw0jxjizhq2dr9g2r91md45k1p9ih2sl1yy1y3p934l2kb"))))
948 (build-system cmake-build-system)
949 (arguments
950 `(#:parallel-build? #f
951 #:tests? #f)) ; There are no tests.
952 (native-inputs
953 `(("groff" ,groff)
954 ("man-db" ,man-db)
955 ("texinfo" ,texinfo)))
956 (inputs
957 `(("bpp-core" ,bpp-core)
958 ("bpp-seq" ,bpp-seq)
959 ("bpp-phyl" ,bpp-phyl)
960 ("bpp-phyl" ,bpp-popgen)
961 ("gcc" ,gcc-5)))
962 (home-page "http://biopp.univ-montp2.fr")
963 (synopsis "Bioinformatics tools written with the Bio++ libraries")
964 (description
965 "Bio++ is a set of C++ libraries for Bioinformatics, including sequence
966analysis, phylogenetics, molecular evolution and population genetics. This
967package provides command line tools using the Bio++ library.")
968 (license license:cecill-c))))
969
82c370de
RW		 970(define-public blast+
971 (package
972 (name "blast+")
4732e6ee 973 (version "2.6.0")
82c370de
RW		 974 (source (origin
975 (method url-fetch)
976 (uri (string-append
977 "ftp://ftp.ncbi.nlm.nih.gov/blast/executables/blast+/"
978 version "/ncbi-blast-" version "+-src.tar.gz"))
979 (sha256
980 (base32
4732e6ee
BW		 981 "15n937pw5aqmyfjb6l387d18grqbb96l63d5xj4l7yyh0zbf2405"))
982 (patches (search-patches "blast+-fix-makefile.patch"))
82c370de
RW		 983 (modules '((guix build utils)))
984 (snippet
985 '(begin
4732e6ee 986 ;; Remove bundled bzip2, zlib and pcre.
82c370de
RW		 987 (delete-file-recursively "c++/src/util/compress/bzip2")
988 (delete-file-recursively "c++/src/util/compress/zlib")
4732e6ee 989 (delete-file-recursively "c++/src/util/regexp")
82c370de
RW		 990 (substitute* "c++/src/util/compress/Makefile.in"
991 (("bzip2 zlib api") "api"))
992 ;; Remove useless msbuild directory
993 (delete-file-recursively
994 "c++/src/build-system/project_tree_builder/msbuild")
995 #t))))
996 (build-system gnu-build-system)
997 (arguments
4732e6ee 998 `(;; There are two(!) tests for this massive library, and both fail with
82c370de 999 ;; "unparsable timing stats".
82c370de
RW		 1000 ;; ERR [127] -- [serial/datatool] datatool.sh (unparsable timing stats)
1001 ;; ERR [127] -- [serial/datatool] datatool_xml.sh (unparsable timing stats)
1002 #:tests? #f
1003 #:out-of-source? #t
1004 #:parallel-build? #f ; not supported
1005 #:phases
1006 (modify-phases %standard-phases
1007 (add-before
1008 'configure 'set-HOME
1009 ;; $HOME needs to be set at some point during the configure phase
1010 (lambda _ (setenv "HOME" "/tmp") #t))
1011 (add-after
1012 'unpack 'enter-dir
1013 (lambda _ (chdir "c++") #t))
1014 (add-after
1015 'enter-dir 'fix-build-system
1016 (lambda _
1017 (define (which* cmd)
1018 (cond ((string=? cmd "date")
1019 ;; make call to "date" deterministic
1020 "date -d @0")
1021 ((which cmd)
1022 => identity)
1023 (else
1024 (format (current-error-port)
1025 "WARNING: Unable to find absolute path for ~s~%"
1026 cmd)
1027 #f)))
1028
1029 ;; Rewrite hardcoded paths to various tools
1030 (substitute* (append '("src/build-system/configure.ac"
1031 "src/build-system/configure"
4732e6ee 1032 "src/build-system/helpers/run_with_lock.c"
82c370de
RW		 1033 "scripts/common/impl/if_diff.sh"
1034 "scripts/common/impl/run_with_lock.sh"
1035 "src/build-system/Makefile.configurables.real"
1036 "src/build-system/Makefile.in.top"
1037 "src/build-system/Makefile.meta.gmake=no"
1038 "src/build-system/Makefile.meta.in"
1039 "src/build-system/Makefile.meta_l"
1040 "src/build-system/Makefile.meta_p"
1041 "src/build-system/Makefile.meta_r"
1042 "src/build-system/Makefile.mk.in"
1043 "src/build-system/Makefile.requirements"
1044 "src/build-system/Makefile.rules_with_autodep.in")
1045 (find-files "scripts/common/check" "\\.sh$"))
1046 (("(/usr/bin/|/bin/)([a-z][-_.a-z]*)" all dir cmd)
1047 (or (which* cmd) all)))
1048
1049 (substitute* (find-files "src/build-system" "^config.*")
1050 (("LN_S=/bin/\\$LN_S") (string-append "LN_S=" (which "ln")))
1051 (("^PATH=.*") ""))
1052
1053 ;; rewrite "/var/tmp" in check script
1054 (substitute* "scripts/common/check/check_make_unix.sh"
1055 (("/var/tmp") "/tmp"))
1056
1057 ;; do not reset PATH
1058 (substitute* (find-files "scripts/common/impl/" "\\.sh$")
1059 (("^ *PATH=.*") "")
1060 (("action=/bin/") "action=")
1061 (("export PATH") ":"))
1062 #t))
1063 (replace
1064 'configure
1065 (lambda* (#:key inputs outputs #:allow-other-keys)
1066 (let ((out (assoc-ref outputs "out"))
1067 (lib (string-append (assoc-ref outputs "lib") "/lib"))
1068 (include (string-append (assoc-ref outputs "include")
1069 "/include/ncbi-tools++")))
1070 ;; The 'configure' script doesn't recognize things like
1071 ;; '--enable-fast-install'.
1072 (zero? (system* "./configure.orig"
1073 (string-append "--with-build-root=" (getcwd) "/build")
1074 (string-append "--prefix=" out)
1075 (string-append "--libdir=" lib)
1076 (string-append "--includedir=" include)
1077 (string-append "--with-bz2="
1078 (assoc-ref inputs "bzip2"))
1079 (string-append "--with-z="
1080 (assoc-ref inputs "zlib"))
4732e6ee
BW		 1081 (string-append "--with-pcre="
1082 (assoc-ref inputs "pcre"))
82c370de
RW		 1083 ;; Each library is built twice by default, once
1084 ;; with "-static" in its name, and again
1085 ;; without.
1086 "--without-static"
1087 "--with-dll"))))))))
4732e6ee
BW		 1088 (outputs '("out" ; 21 MB
1089 "lib" ; 226 MB
1090 "include")) ; 33 MB
82c370de
RW		 1091 (inputs
1092 `(("bzip2" ,bzip2)
4732e6ee
BW		 1093 ("zlib" ,zlib)
1094 ("pcre" ,pcre)
1095 ("perl" ,perl)
1096 ("python" ,python-wrapper)))
82c370de
RW		 1097 (native-inputs
1098 `(("cpio" ,cpio)))
1099 (home-page "http://blast.ncbi.nlm.nih.gov")
1100 (synopsis "Basic local alignment search tool")
1101 (description
1102 "BLAST is a popular method of performing a DNA or protein sequence
1103similarity search, using heuristics to produce results quickly. It also
1104calculates an “expect value” that estimates how many matches would have
1105occurred at a given score by chance, which can aid a user in judging how much
1106confidence to have in an alignment.")
1107 ;; Most of the sources are in the public domain, with the following
1108 ;; exceptions:
1109 ;; * Expat:
1110 ;; * ./c++/include/util/bitset/
1111 ;; * ./c++/src/html/ncbi_menu*.js
1112 ;; * Boost license:
1113 ;; * ./c++/include/util/impl/floating_point_comparison.hpp
1114 ;; * LGPL 2+:
1115 ;; * ./c++/include/dbapi/driver/odbc/unix_odbc/
1116 ;; * ASL 2.0:
1117 ;; * ./c++/src/corelib/teamcity_*
1118 (license (list license:public-domain
1119 license:expat
1120 license:boost1.0
1121 license:lgpl2.0+
1122 license:asl2.0))))
1123
6c2b26e2
RW		 1124(define-public bless
1125 (package
1126 (name "bless")
1127 (version "1p02")
1128 (source (origin
1129 (method url-fetch)
1130 (uri (string-append "mirror://sourceforge/bless-ec/bless.v"
1131 version ".tgz"))
1132 (sha256
1133 (base32
4d75e03a
RW		 1134 "0rm0gw2s18dqwzzpl3c2x1z05ni2v0xz5dmfk3d33j6g4cgrlrdd"))
1135 (modules '((guix build utils)))
6c2b26e2
RW		 1136 (snippet
1137 `(begin
1138 ;; Remove bundled boost, pigz, zlib, and .git directory
953c1223
RW		 1139 ;; FIXME: also remove bundled sources for murmurhash3 and
1140 ;; kmc once packaged.
6c2b26e2
RW		 1141 (delete-file-recursively "boost")
1142 (delete-file-recursively "pigz")
953c1223 1143 (delete-file-recursively "google-sparsehash")
6c2b26e2
RW		 1144 (delete-file-recursively "zlib")
1145 (delete-file-recursively ".git")
1146 #t))))
1147 (build-system gnu-build-system)
1148 (arguments
1149 '(#:tests? #f ;no "check" target
1150 #:make-flags
1151 (list (string-append "ZLIB="
1152 (assoc-ref %build-inputs "zlib")
1153 "/lib/libz.a")
1154 (string-append "LDFLAGS="
1155 (string-join '("-lboost_filesystem"
1156 "-lboost_system"
1157 "-lboost_iostreams"
1158 "-lz"
1159 "-fopenmp"
1160 "-std=c++11"))))
1161 #:phases
1162 (modify-phases %standard-phases
1163 (add-after 'unpack 'do-not-build-bundled-pigz
1164 (lambda* (#:key inputs outputs #:allow-other-keys)
1165 (substitute* "Makefile"
1166 (("cd pigz/pigz-2.3.3; make") ""))
1167 #t))
1168 (add-after 'unpack 'patch-paths-to-executables
1169 (lambda* (#:key inputs outputs #:allow-other-keys)
1170 (substitute* "parse_args.cpp"
1171 (("kmc_binary = .*")
1172 (string-append "kmc_binary = \""
1173 (assoc-ref outputs "out")
1174 "/bin/kmc\";"))
1175 (("pigz_binary = .*")
1176 (string-append "pigz_binary = \""
1177 (assoc-ref inputs "pigz")
1178 "/bin/pigz\";")))
1179 #t))
1180 (replace 'install
1181 (lambda* (#:key outputs #:allow-other-keys)
1182 (let ((bin (string-append (assoc-ref outputs "out") "/bin/")))
1183 (for-each (lambda (file)
1184 (install-file file bin))
1185 '("bless" "kmc/bin/kmc"))
1186 #t)))
1187 (delete 'configure))))
1188 (native-inputs
1189 `(("perl" ,perl)))
1190 (inputs
1191 `(("openmpi" ,openmpi)
1192 ("boost" ,boost)
953c1223 1193 ("sparsehash" ,sparsehash)
6c2b26e2
RW		 1194 ("pigz" ,pigz)
1195 ("zlib" ,zlib)))
9641a899 1196 (supported-systems '("x86_64-linux"))
3b3b60d0 1197 (home-page "https://sourceforge.net/p/bless-ec/wiki/Home/")
6c2b26e2
RW		 1198 (synopsis "Bloom-filter-based error correction tool for NGS reads")
1199 (description
1200 "@dfn{Bloom-filter-based error correction solution for high-throughput
1201sequencing reads} (BLESS) uses a single minimum-sized bloom filter is a
1202correction tool for genomic reads produced by @dfn{Next-generation
1203sequencing} (NGS). BLESS produces accurate correction results with much less
1204memory compared with previous solutions and is also able to tolerate a higher
1205false-positive rate. BLESS can extend reads like DNA assemblers to correct
1206errors at the end of reads.")
1207 (license license:gpl3+)))
1208
2c7ee167
RW		 1209(define-public bowtie
1210 (package
1211 (name "bowtie")
d6e63cf3 1212 (version "2.3.2")
2c7ee167
RW		 1213 (source (origin
1214 (method url-fetch)
1215 (uri (string-append "https://github.com/BenLangmead/bowtie2/archive/v"
1216 version ".tar.gz"))
f586c877 1217 (file-name (string-append name "-" version ".tar.gz"))
2c7ee167
RW		 1218 (sha256
1219 (base32
d6e63cf3 1220 "0hwa5r9qbglppb7sz5z79rlmmddr3n51n468jb3wh8rwjgn3yr90"))
2c7ee167
RW		 1221 (modules '((guix build utils)))
1222 (snippet
1223 '(substitute* "Makefile"
2c7ee167
RW		 1224 ;; replace BUILD_HOST and BUILD_TIME for deterministic build
1225 (("-DBUILD_HOST=.*") "-DBUILD_HOST=\"\\\"guix\\\"\"")
0047d26a 1226 (("-DBUILD_TIME=.*") "-DBUILD_TIME=\"\\\"0\\\"\"")))))
2c7ee167 1227 (build-system gnu-build-system)
d6e63cf3
BW		 1228 (inputs
1229 `(("perl" ,perl)
1230 ("perl-clone" ,perl-clone)
1231 ("perl-test-deep" ,perl-test-deep)
1232 ("perl-test-simple" ,perl-test-simple)
1233 ("python" ,python-2)
1234 ("tbb" ,tbb)
1235 ("zlib" ,zlib)))
2c7ee167 1236 (arguments
0047d26a
RW		 1237 '(#:make-flags
1238 (list "allall"
1239 "WITH_TBB=1"
1240 (string-append "prefix=" (assoc-ref %outputs "out")))
2c7ee167 1241 #:phases
06e37236
BW		 1242 (modify-phases %standard-phases
1243 (delete 'configure)
1244 (replace 'check
1245 (lambda* (#:key outputs #:allow-other-keys)
1246 (zero? (system* "perl"
1247 "scripts/test/simple_tests.pl"
1248 "--bowtie2=./bowtie2"
1249 "--bowtie2-build=./bowtie2-build")))))))
2c7ee167
RW		 1250 (home-page "http://bowtie-bio.sourceforge.net/bowtie2/index.shtml")
1251 (synopsis "Fast and sensitive nucleotide sequence read aligner")
1252 (description
1253 "Bowtie 2 is a fast and memory-efficient tool for aligning sequencing
1254reads to long reference sequences. It is particularly good at aligning reads
1255of about 50 up to 100s or 1,000s of characters, and particularly good at
1256aligning to relatively long (e.g. mammalian) genomes. Bowtie 2 indexes the
1257genome with an FM Index to keep its memory footprint small: for the human
1258genome, its memory footprint is typically around 3.2 GB. Bowtie 2 supports
1259gapped, local, and paired-end alignment modes.")
241e1221 1260 (supported-systems '("x86_64-linux"))
2c7ee167
RW		 1261 (license license:gpl3+)))
1262
94ce537e
RW		 1263(define-public tophat
1264 (package
1265 (name "tophat")
1266 (version "2.1.0")
1267 (source (origin
1268 (method url-fetch)
1269 (uri (string-append
1270 "http://ccb.jhu.edu/software/tophat/downloads/tophat-"
1271 version ".tar.gz"))
1272 (sha256
1273 (base32
1274 "168zlzykq622zbgkh90a90f1bdgsxkscq2zxzbj8brq80hbjpyp7"))
fc1adab1 1275 (patches (search-patches "tophat-build-with-later-seqan.patch"))
94ce537e
RW		 1276 (modules '((guix build utils)))
1277 (snippet
1278 '(begin
1279 ;; Remove bundled SeqAn and samtools
1280 (delete-file-recursively "src/SeqAn-1.3")
1281 (delete-file-recursively "src/samtools-0.1.18")
1282 #t))))
1283 (build-system gnu-build-system)
1284 (arguments
1285 '(#:parallel-build? #f ; not supported
1286 #:phases
1287 (modify-phases %standard-phases
1288 (add-after 'unpack 'use-system-samtools
1289 (lambda* (#:key inputs #:allow-other-keys)
1290 (substitute* "src/Makefile.in"
1291 (("(noinst_LIBRARIES = )\\$\\(SAMLIB\\)" _ prefix) prefix)
1292 (("\\$\\(SAMPROG\\): \\$\\(SAMLIB\\)") "")
1293 (("SAMPROG = samtools_0\\.1\\.18") "")
1294 (("\\$\\(samtools_0_1_18_SOURCES\\)") "")
1295 (("am__EXEEXT_1 = samtools_0\\.1\\.18\\$\\(EXEEXT\\)") ""))
1296 (substitute* '("src/common.cpp"
1297 "src/tophat.py")
1298 (("samtools_0.1.18") (which "samtools")))
1299 (substitute* '("src/common.h"
1300 "src/bam2fastx.cpp")
1301 (("#include \"bam.h\"") "#include <samtools/bam.h>")
1302 (("#include \"sam.h\"") "#include <samtools/sam.h>"))
1303 (substitute* '("src/bwt_map.h"
1304 "src/map2gtf.h"
1305 "src/align_status.h")
1306 (("#include <bam.h>") "#include <samtools/bam.h>")
1307 (("#include <sam.h>") "#include <samtools/sam.h>"))
1308 #t)))))
1309 (inputs
1310 `(("boost" ,boost)
1311 ("bowtie" ,bowtie)
1312 ("samtools" ,samtools-0.1)
1313 ("ncurses" ,ncurses)
1314 ("python" ,python-2)
1315 ("perl" ,perl)
1316 ("zlib" ,zlib)
1317 ("seqan" ,seqan)))
1318 (home-page "http://ccb.jhu.edu/software/tophat/index.shtml")
1319 (synopsis "Spliced read mapper for RNA-Seq data")
1320 (description
1321 "TopHat is a fast splice junction mapper for nucleotide sequence
1322reads produced by the RNA-Seq method. It aligns RNA-Seq reads to
1323mammalian-sized genomes using the ultra high-throughput short read
1324aligner Bowtie, and then analyzes the mapping results to identify
1325splice junctions between exons.")
1326 ;; TopHat is released under the Boost Software License, Version 1.0
1327 ;; See https://github.com/infphilo/tophat/issues/11#issuecomment-121589893
1328 (license license:boost1.0)))
1329
9a8336d8
RW		 1330(define-public bwa
1331 (package
1332 (name "bwa")
6f141eff 1333 (version "0.7.17")
9a8336d8
RW		 1334 (source (origin
1335 (method url-fetch)
ae6e00f6
BW		 1336 (uri (string-append
1337 "https://github.com/lh3/bwa/releases/download/v"
1338 version "/bwa-" version ".tar.bz2"))
9a8336d8
RW		 1339 (sha256
1340 (base32
6f141eff 1341 "1zfhv2zg9v1icdlq4p9ssc8k01mca5d1bd87w71py2swfi74s6yy"))))
9a8336d8
RW		 1342 (build-system gnu-build-system)
1343 (arguments
1344 '(#:tests? #f ;no "check" target
1345 #:phases
dc1d3cde
KK		 1346 (modify-phases %standard-phases
1347 (replace 'install
1348 (lambda* (#:key outputs #:allow-other-keys)
1349 (let ((bin (string-append
1350 (assoc-ref outputs "out") "/bin"))
1351 (doc (string-append
1352 (assoc-ref outputs "out") "/share/doc/bwa"))
1353 (man (string-append
1354 (assoc-ref outputs "out") "/share/man/man1")))
1355 (install-file "bwa" bin)
1356 (install-file "README.md" doc)
1357 (install-file "bwa.1" man))
1358 #t))
1359 ;; no "configure" script
1360 (delete 'configure))))
9a8336d8 1361 (inputs `(("zlib" ,zlib)))
db94f8c7
RW		 1362 ;; Non-portable SSE instructions are used so building fails on platforms
1363 ;; other than x86_64.
1364 (supported-systems '("x86_64-linux"))
9a8336d8
RW		 1365 (home-page "http://bio-bwa.sourceforge.net/")
1366 (synopsis "Burrows-Wheeler sequence aligner")
1367 (description
1368 "BWA is a software package for mapping low-divergent sequences against a
1369large reference genome, such as the human genome. It consists of three
1370algorithms: BWA-backtrack, BWA-SW and BWA-MEM. The first algorithm is
1371designed for Illumina sequence reads up to 100bp, while the rest two for
1372longer sequences ranged from 70bp to 1Mbp. BWA-MEM and BWA-SW share similar
1373features such as long-read support and split alignment, but BWA-MEM, which is
1374the latest, is generally recommended for high-quality queries as it is faster
1375and more accurate. BWA-MEM also has better performance than BWA-backtrack for
137670-100bp Illumina reads.")
1377 (license license:gpl3+)))
1378
d29150b5
RW		 1379(define-public bwa-pssm
1380 (package (inherit bwa)
1381 (name "bwa-pssm")
1382 (version "0.5.11")
1383 (source (origin
1384 (method url-fetch)
1385 (uri (string-append "https://github.com/pkerpedjiev/bwa-pssm/"
1386 "archive/" version ".tar.gz"))
1387 (file-name (string-append name "-" version ".tar.gz"))
1388 (sha256
1389 (base32
1390 "02p7mpbs4mlxmn84g2x4ghak638vbj4lqix2ipx5g84pz9bhdavg"))))
1391 (build-system gnu-build-system)
1392 (inputs
1393 `(("gdsl" ,gdsl)
1394 ("zlib" ,zlib)
1395 ("perl" ,perl)))
1396 (home-page "http://bwa-pssm.binf.ku.dk/")
1397 (synopsis "Burrows-Wheeler transform-based probabilistic short read mapper")
1398 (description
1399 "BWA-PSSM is a probabilistic short genomic sequence read aligner based on
1400the use of @dfn{position specific scoring matrices} (PSSM). Like many of the
1401existing aligners it is fast and sensitive. Unlike most other aligners,
1402however, it is also adaptible in the sense that one can direct the alignment
1403based on known biases within the data set. It is coded as a modification of
1404the original BWA alignment program and shares the genome index structure as
1405well as many of the command line options.")
1406 (license license:gpl3+)))
1407
ad641d53
RW		 1408(define-public python2-bx-python
1409 (package
1410 (name "python2-bx-python")
c1dfe8c3 1411 (version "0.7.3")
ad641d53
RW		 1412 (source (origin
1413 (method url-fetch)
c1dfe8c3 1414 (uri (pypi-uri "bx-python" version))
ad641d53
RW		 1415 (sha256
1416 (base32
c1dfe8c3 1417 "15z2w3bvnc0n4qmb9bd6d8ylc2h2nj883x2w9iixf4x3vki9b22i"))
ad641d53
RW		 1418 (modules '((guix build utils)))
1419 (snippet
1420 '(substitute* "setup.py"
1421 ;; remove dependency on outdated "distribute" module
1422 (("^from distribute_setup import use_setuptools") "")
1423 (("^use_setuptools\\(\\)") "")))))
1424 (build-system python-build-system)
1425 (arguments
1426 `(#:tests? #f ;tests fail because test data are not included
1427 #:python ,python-2))
1428 (inputs
1429 `(("python-numpy" ,python2-numpy)
1430 ("zlib" ,zlib)))
1431 (native-inputs
f3b98f4f 1432 `(("python-nose" ,python2-nose)))
ad641d53
RW		 1433 (home-page "http://bitbucket.org/james_taylor/bx-python/")
1434 (synopsis "Tools for manipulating biological data")
1435 (description
1436 "bx-python provides tools for manipulating biological data, particularly
1437multiple sequence alignments.")
1438 (license license:expat)))
1439
55a9a8c2
RW		 1440(define-public python-pysam
1441 (package
1442 (name "python-pysam")
68565184 1443 (version "0.13.0")
d454640c
RW		 1444 (source (origin
1445 (method url-fetch)
f536dce5
MB		 1446 ;; Test data is missing on PyPi.
1447 (uri (string-append
1448 "https://github.com/pysam-developers/pysam/archive/v"
1449 version ".tar.gz"))
1450 (file-name (string-append name "-" version ".tar.gz"))
d454640c
RW		 1451 (sha256
1452 (base32
68565184 1453 "0dzap2axin9cbbl0d825w294bpn00zagfm1sigamm4v2pm5bj9lp"))
dff26b23
MB		 1454 (modules '((guix build utils)))
1455 (snippet
1456 ;; Drop bundled htslib. TODO: Also remove samtools and bcftools.
1457 '(delete-file-recursively "htslib"))))
55a9a8c2
RW		 1458 (build-system python-build-system)
1459 (arguments
71dbf592
RW		 1460 `(#:modules ((ice-9 ftw)
1461 (srfi srfi-26)
1462 (guix build python-build-system)
1463 (guix build utils))
1464 #:phases
397d463a
MB		 1465 (modify-phases %standard-phases
1466 (add-before 'build 'set-flags
dff26b23
MB		 1467 (lambda* (#:key inputs #:allow-other-keys)
1468 (setenv "HTSLIB_MODE" "external")
1469 (setenv "HTSLIB_LIBRARY_DIR"
1470 (string-append (assoc-ref inputs "htslib") "/lib"))
1471 (setenv "HTSLIB_INCLUDE_DIR"
1472 (string-append (assoc-ref inputs "htslib") "/include"))
397d463a
MB		 1473 (setenv "LDFLAGS" "-lncurses")
1474 (setenv "CFLAGS" "-D_CURSES_LIB=1")
f536dce5 1475 #t))
71dbf592 1476 (replace 'check
f536dce5 1477 (lambda* (#:key inputs outputs #:allow-other-keys)
71dbf592 1478 ;; Add first subdirectory of "build" directory to PYTHONPATH.
f536dce5
MB		 1479 (setenv "PYTHONPATH"
1480 (string-append
1481 (getenv "PYTHONPATH")
71dbf592
RW		 1482 ":" (getcwd) "/build/"
1483 (car (scandir "build"
e1f02f92 1484 (negate (cut string-prefix? "." <>))))))
f536dce5 1485 ;; Step out of source dir so python does not import from CWD.
71dbf592
RW		 1486 (with-directory-excursion "tests"
1487 (setenv "HOME" "/tmp")
1488 (and (zero? (system* "make" "-C" "pysam_data"))
1489 (zero? (system* "make" "-C" "cbcf_data"))
b2955e22
RW		 1490 ;; Running nosetests without explicitly asking for a
1491 ;; single process leads to a crash. Running with multiple
1492 ;; processes fails because the tests are not designed to
1493 ;; run in parallel.
31c374e0
RW		 1494
1495 ;; FIXME: tests keep timing out on some systems.
1496 ;; (zero? (system* "nosetests" "-v"
1497 ;; "--processes" "1"))
1498 )))))))
dff26b23
MB		 1499 (propagated-inputs
1500 `(("htslib" ,htslib))) ; Included from installed header files.
55a9a8c2 1501 (inputs
649e9b3b 1502 `(("ncurses" ,ncurses)
55a9a8c2 1503 ("zlib" ,zlib)))
649e9b3b
RW		 1504 (native-inputs
1505 `(("python-cython" ,python-cython)
f536dce5
MB		 1506 ;; Dependencies below are are for tests only.
1507 ("samtools" ,samtools)
1508 ("bcftools" ,bcftools)
1509 ("python-nose" ,python-nose)))
55a9a8c2
RW		 1510 (home-page "https://github.com/pysam-developers/pysam")
1511 (synopsis "Python bindings to the SAMtools C API")
1512 (description
1513 "Pysam is a Python module for reading and manipulating files in the
1514SAM/BAM format. Pysam is a lightweight wrapper of the SAMtools C API. It
1515also includes an interface for tabix.")
1516 (license license:expat)))
1517
1518(define-public python2-pysam
1519 (package-with-python2 python-pysam))
1520
4db9433a
RW		 1521(define-public python-twobitreader
1522 (package
1523 (name "python-twobitreader")
044ac8d2 1524 (version "3.1.4")
4db9433a
RW		 1525 (source (origin
1526 (method url-fetch)
1527 (uri (pypi-uri "twobitreader" version))
1528 (sha256
1529 (base32
044ac8d2 1530 "1q8wnj2kga9nz1lwc4w7qv52smfm536hp6mc8w6s53lhyj0mpi22"))))
4db9433a 1531 (build-system python-build-system)
900fb8d0
LF		 1532 (arguments
1533 '(;; Tests are not distributed in the PyPi release.
1534 ;; TODO Try building from the Git repo or asking the upstream maintainer
1535 ;; to distribute the tests on PyPi.
1536 #:tests? #f))
4db9433a
RW		 1537 (native-inputs
1538 `(("python-sphinx" ,python-sphinx)))
1539 (home-page "https://github.com/benjschiller/twobitreader")
1540 (synopsis "Python library for reading .2bit files")
1541 (description
1542 "twobitreader is a Python library for reading .2bit files as used by the
1543UCSC genome browser.")
1544 (license license:artistic2.0)))
1545
1546(define-public python2-twobitreader
5c31f4aa 1547 (package-with-python2 python-twobitreader))
4db9433a 1548
f94bf198
RW		 1549(define-public python-plastid
1550 (package
1551 (name "python-plastid")
897ab082 1552 (version "0.4.8")
f94bf198
RW		 1553 (source (origin
1554 (method url-fetch)
1555 (uri (pypi-uri "plastid" version))
1556 (sha256
1557 (base32
897ab082 1558 "0l24dd3q66if8yj042m4s0g95n6acn7im1imqd3p6h8ns43kxhj8"))))
f94bf198
RW		 1559 (build-system python-build-system)
1560 (arguments
1561 ;; Some test files are not included.
1562 `(#:tests? #f))
1563 (propagated-inputs
1564 `(("python-numpy" ,python-numpy)
1565 ("python-scipy" ,python-scipy)
1566 ("python-pandas" ,python-pandas)
1567 ("python-pysam" ,python-pysam)
1568 ("python-matplotlib" ,python-matplotlib)
1569 ("python-biopython" ,python-biopython)
99caa6f7
BW		 1570 ("python-twobitreader" ,python-twobitreader)
1571 ("python-termcolor" ,python-termcolor)))
f94bf198
RW		 1572 (native-inputs
1573 `(("python-cython" ,python-cython)
1574 ("python-nose" ,python-nose)))
1575 (home-page "https://github.com/joshuagryphon/plastid")
1576 (synopsis "Python library for genomic analysis")
1577 (description
1578 "plastid is a Python library for genomic analysis – in particular,
1579high-throughput sequencing data – with an emphasis on simplicity.")
1580 (license license:bsd-3)))
1581
1582(define-public python2-plastid
5c31f4aa 1583 (package-with-python2 python-plastid))
f94bf198 1584
6c1305f9
RW		 1585(define-public cd-hit
1586 (package
1587 (name "cd-hit")
ba773f65 1588 (version "4.6.8")
6c1305f9
RW		 1589 (source (origin
1590 (method url-fetch)
1591 (uri (string-append "https://github.com/weizhongli/cdhit"
1592 "/releases/download/V" version
ba773f65
BW		 1593 "/cd-hit-v" version
1594 "-2017-0621-source.tar.gz"))
6c1305f9
RW		 1595 (sha256
1596 (base32
d4735e8c 1597 "1b4mwm2520ixjbw57sil20f9iixzw4bkdqqwgg1fc3pzm6rz4zmn"))))
6c1305f9
RW		 1598 (build-system gnu-build-system)
1599 (arguments
1600 `(#:tests? #f ; there are no tests
1601 #:make-flags
1602 ;; Executables are copied directly to the PREFIX.
1603 (list (string-append "PREFIX=" (assoc-ref %outputs "out") "/bin"))
1604 #:phases
1605 (modify-phases %standard-phases
1606 ;; No "configure" script
1607 (delete 'configure)
1608 ;; Remove sources of non-determinism
1609 (add-after 'unpack 'be-timeless
1610 (lambda _
1611 (substitute* "cdhit-utility.c++"
1612 ((" \\(built on \" __DATE__ \"\\)") ""))
1613 (substitute* "cdhit-common.c++"
1614 (("__DATE__") "\"0\"")
1615 (("\", %s, \" __TIME__ \"\\\\n\", date") ""))
1616 #t))
ba773f65 1617 ;; The "install" target does not create the target directory.
6c1305f9
RW		 1618 (add-before 'install 'create-target-dir
1619 (lambda* (#:key outputs #:allow-other-keys)
1620 (mkdir-p (string-append (assoc-ref outputs "out") "/bin"))
1621 #t)))))
1622 (inputs
1623 `(("perl" ,perl)))
1624 (home-page "http://weizhongli-lab.org/cd-hit/")
1625 (synopsis "Cluster and compare protein or nucleotide sequences")
1626 (description
1627 "CD-HIT is a program for clustering and comparing protein or nucleotide
1628sequences. CD-HIT is designed to be fast and handle extremely large
1629databases.")
1630 ;; The manual says: "It can be copied under the GNU General Public License
1631 ;; version 2 (GPLv2)."
1632 (license license:gpl2)))
1633
810cff85
RW		 1634(define-public clipper
1635 (package
1636 (name "clipper")
433530a5 1637 (version "1.1")
810cff85
RW		 1638 (source (origin
1639 (method url-fetch)
1640 (uri (string-append
1641 "https://github.com/YeoLab/clipper/archive/"
1642 version ".tar.gz"))
9ab5ea44 1643 (file-name (string-append name "-" version ".tar.gz"))
810cff85
RW		 1644 (sha256
1645 (base32
433530a5 1646 "0pflmsvhbf8izbgwhbhj1i7349sw1f55qpqj8ljmapp16hb0p0qi"))
810cff85
RW		 1647 (modules '((guix build utils)))
1648 (snippet
433530a5
RW		 1649 '(begin
1650 ;; remove unnecessary setup dependency
1651 (substitute* "setup.py"
1652 (("setup_requires = .*") ""))
1653 (for-each delete-file
1654 '("clipper/src/peaks.so"
1655 "clipper/src/readsToWiggle.so"))
1656 (delete-file-recursively "dist/")
1657 #t))))
810cff85
RW		 1658 (build-system python-build-system)
1659 (arguments `(#:python ,python-2)) ; only Python 2 is supported
1660 (inputs
92971d68 1661 `(("htseq" ,python2-htseq)
810cff85
RW		 1662 ("python-pybedtools" ,python2-pybedtools)
1663 ("python-cython" ,python2-cython)
1664 ("python-scikit-learn" ,python2-scikit-learn)
1665 ("python-matplotlib" ,python2-matplotlib)
433530a5 1666 ("python-pandas" ,python2-pandas)
810cff85
RW		 1667 ("python-pysam" ,python2-pysam)
1668 ("python-numpy" ,python2-numpy)
1669 ("python-scipy" ,python2-scipy)))
1670 (native-inputs
f3b98f4f 1671 `(("python-mock" ,python2-mock) ; for tests
d281be18 1672 ("python-nose" ,python2-nose) ; for tests
f3b98f4f 1673 ("python-pytz" ,python2-pytz))) ; for tests
810cff85
RW		 1674 (home-page "https://github.com/YeoLab/clipper")
1675 (synopsis "CLIP peak enrichment recognition")
1676 (description
1677 "CLIPper is a tool to define peaks in CLIP-seq datasets.")
1678 (license license:gpl2)))
1679
6a35566d
RS		 1680(define-public codingquarry
1681 (package
1682 (name "codingquarry")
1683 (version "2.0")
1684 (source (origin
1685 (method url-fetch)
1686 (uri (string-append
1687 "mirror://sourceforge/codingquarry/CodingQuarry_v"
1688 version ".tar.gz"))
1689 (sha256
1690 (base32
1691 "0115hkjflsnfzn36xppwf9h9avfxlavr43djqmshkkzbgjzsz60i"))))
1692 (build-system gnu-build-system)
1693 (arguments
1694 '(#:tests? #f ; no "check" target
1695 #:phases
1696 (modify-phases %standard-phases
1697 (delete 'configure)
1698 (replace 'install
1699 (lambda* (#:key outputs #:allow-other-keys)
1700 (let* ((out (assoc-ref outputs "out"))
1701 (bin (string-append out "/bin"))
1702 (doc (string-append out "/share/doc/codingquarry")))
1703 (install-file "INSTRUCTIONS.pdf" doc)
1704 (copy-recursively "QuarryFiles"
1705 (string-append out "/QuarryFiles"))
1706 (install-file "CodingQuarry" bin)
1707 (install-file "CufflinksGTF_to_CodingQuarryGFF3.py" bin)))))))
1708 (inputs `(("openmpi" ,openmpi)))
1709 (native-search-paths
1710 (list (search-path-specification
1711 (variable "QUARRY_PATH")
1712 (files '("QuarryFiles")))))
1713 (native-inputs `(("python" ,python-2))) ; Only Python 2 is supported
1714 (synopsis "Fungal gene predictor")
1715 (description "CodingQuarry is a highly accurate, self-training GHMM fungal
1716gene predictor designed to work with assembled, aligned RNA-seq transcripts.")
1717 (home-page "https://sourceforge.net/projects/codingquarry/")
1718 (license license:gpl3+)))
1719
36742f43
RW		 1720(define-public couger
1721 (package
1722 (name "couger")
1723 (version "1.8.2")
1724 (source (origin
1725 (method url-fetch)
1726 (uri (string-append
1727 "http://couger.oit.duke.edu/static/assets/COUGER"
1728 version ".zip"))
1729 (sha256
1730 (base32
1731 "04p2b14nmhzxw5h72mpzdhalv21bx4w9b87z0wpw0xzxpysyncmq"))))
1732 (build-system gnu-build-system)
1733 (arguments
1734 `(#:tests? #f
1735 #:phases
1736 (modify-phases %standard-phases
1737 (delete 'configure)
1738 (delete 'build)
1739 (replace
1740 'install
1741 (lambda* (#:key outputs #:allow-other-keys)
f3860753
TGR		 1742 (let* ((out (assoc-ref outputs "out"))
1743 (bin (string-append out "/bin")))
36742f43 1744 (copy-recursively "src" (string-append out "/src"))
f3860753 1745 (mkdir bin)
36742f43
RW		 1746 ;; Add "src" directory to module lookup path.
1747 (substitute* "couger"
1748 (("from argparse")
1749 (string-append "import sys\nsys.path.append(\""
1750 out "\")\nfrom argparse")))
f3860753 1751 (install-file "couger" bin))
36742f43
RW		 1752 #t))
1753 (add-after
1754 'install 'wrap-program
1755 (lambda* (#:key inputs outputs #:allow-other-keys)
1756 ;; Make sure 'couger' runs with the correct PYTHONPATH.
1757 (let* ((out (assoc-ref outputs "out"))
1758 (path (getenv "PYTHONPATH")))
1759 (wrap-program (string-append out "/bin/couger")
1760 `("PYTHONPATH" ":" prefix (,path))))
1761 #t)))))
1762 (inputs
1763 `(("python" ,python-2)
1764 ("python2-pillow" ,python2-pillow)
1765 ("python2-numpy" ,python2-numpy)
1766 ("python2-scipy" ,python2-scipy)
1767 ("python2-matplotlib" ,python2-matplotlib)))
1768 (propagated-inputs
2d7c4ae3 1769 `(("r-minimal" ,r-minimal)
36742f43
RW		 1770 ("libsvm" ,libsvm)
1771 ("randomjungle" ,randomjungle)))
1772 (native-inputs
1773 `(("unzip" ,unzip)))
1774 (home-page "http://couger.oit.duke.edu")
1775 (synopsis "Identify co-factors in sets of genomic regions")
1776 (description
1777 "COUGER can be applied to any two sets of genomic regions bound by
1778paralogous TFs (e.g., regions derived from ChIP-seq experiments) to identify
1779putative co-factors that provide specificity to each TF. The framework
1780determines the genomic targets uniquely-bound by each TF, and identifies a
1781small set of co-factors that best explain the in vivo binding differences
1782between the two TFs.
1783
1784COUGER uses classification algorithms (support vector machines and random
1785forests) with features that reflect the DNA binding specificities of putative
1786co-factors. The features are generated either from high-throughput TF-DNA
1787binding data (from protein binding microarray experiments), or from large
1788collections of DNA motifs.")
1789 (license license:gpl3+)))
1790
bfe3c685
RW		 1791(define-public clustal-omega
1792 (package
1793 (name "clustal-omega")
b3936f35 1794 (version "1.2.4")
bfe3c685
RW		 1795 (source (origin
1796 (method url-fetch)
b3936f35
RW		 1797 (uri (string-append "http://www.clustal.org/omega/clustal-omega-"
1798 version ".tar.gz"))
bfe3c685
RW		 1799 (sha256
1800 (base32
b3936f35 1801 "1vm30mzncwdv881vrcwg11vzvrsmwy4wg80j5i0lcfk6dlld50w6"))))
bfe3c685
RW		 1802 (build-system gnu-build-system)
1803 (inputs
1804 `(("argtable" ,argtable)))
1805 (home-page "http://www.clustal.org/omega/")
1806 (synopsis "Multiple sequence aligner for protein and DNA/RNA")
1807 (description
1808 "Clustal-Omega is a general purpose multiple sequence alignment (MSA)
1809program for protein and DNA/RNA. It produces high quality MSAs and is capable
1810of handling data-sets of hundreds of thousands of sequences in reasonable
1811time.")
1812 (license license:gpl2+)))
1813
191c7101
RW		 1814(define-public crossmap
1815 (package
1816 (name "crossmap")
61d5fd03 1817 (version "0.2.1")
191c7101
RW		 1818 (source (origin
1819 (method url-fetch)
1820 (uri (string-append "mirror://sourceforge/crossmap/CrossMap-"
1821 version ".tar.gz"))
1822 (sha256
1823 (base32
61d5fd03
RW		 1824 "07y179f63d7qnzdvkqcziwk9bs3k4zhp81q392fp1hwszjdvy22f"))
1825 ;; This patch has been sent upstream already and is available
1826 ;; for download from Sourceforge, but it has not been merged.
fc1adab1 1827 (patches (search-patches "crossmap-allow-system-pysam.patch"))
191c7101
RW		 1828 (modules '((guix build utils)))
1829 ;; remove bundled copy of pysam
1830 (snippet
1831 '(delete-file-recursively "lib/pysam"))))
1832 (build-system python-build-system)
1833 (arguments
1834 `(#:python ,python-2
1835 #:phases
dc1d3cde
KK		 1836 (modify-phases %standard-phases
1837 (add-after 'unpack 'set-env
1838 (lambda _ (setenv "CROSSMAP_USE_SYSTEM_PYSAM" "1") #t)))))
191c7101
RW		 1839 (inputs
1840 `(("python-numpy" ,python2-numpy)
1841 ("python-pysam" ,python2-pysam)
1842 ("zlib" ,zlib)))
1843 (native-inputs
1844 `(("python-cython" ,python2-cython)
f3b98f4f 1845 ("python-nose" ,python2-nose)))
191c7101
RW		 1846 (home-page "http://crossmap.sourceforge.net/")
1847 (synopsis "Convert genome coordinates between assemblies")
1848 (description
1849 "CrossMap is a program for conversion of genome coordinates or annotation
1850files between different genome assemblies. It supports most commonly used
1851file formats including SAM/BAM, Wiggle/BigWig, BED, GFF/GTF, VCF.")
1852 (license license:gpl2+)))
1853
8e913213
RW		 1854(define-public cutadapt
1855 (package
1856 (name "cutadapt")
0af4df7e 1857 (version "1.14")
8e913213
RW		 1858 (source (origin
1859 (method url-fetch)
1860 (uri (string-append
1861 "https://github.com/marcelm/cutadapt/archive/v"
1862 version ".tar.gz"))
1863 (file-name (string-append name "-" version ".tar.gz"))
1864 (sha256
1865 (base32
0af4df7e 1866 "16gbpiwy4m48vq2h5wqar3i8vr6vcj9gcl2qvqim19x6ya9dp8kd"))))
8e913213
RW		 1867 (build-system python-build-system)
1868 (arguments
33d5b246
TGR		 1869 `(#:phases
1870 (modify-phases %standard-phases
1871 ;; The tests must be run after installation.
1872 (delete 'check)
1873 (add-after 'install 'check
1874 (lambda* (#:key inputs outputs #:allow-other-keys)
1875 (setenv "PYTHONPATH"
1876 (string-append
1877 (getenv "PYTHONPATH")
1878 ":" (assoc-ref outputs "out")
1879 "/lib/python"
1880 (string-take (string-take-right
1881 (assoc-ref inputs "python") 5) 3)
1882 "/site-packages"))
1883 (zero? (system* "nosetests" "-P" "tests")))))))
1f94bff2
TGR		 1884 (inputs
1885 `(("python-xopen" ,python-xopen)))
8e913213
RW		 1886 (native-inputs
1887 `(("python-cython" ,python-cython)
f3b98f4f 1888 ("python-nose" ,python-nose)))
0c6c9c00 1889 (home-page "https://cutadapt.readthedocs.io/en/stable/")
8e913213
RW		 1890 (synopsis "Remove adapter sequences from nucleotide sequencing reads")
1891 (description
1892 "Cutadapt finds and removes adapter sequences, primers, poly-A tails and
1893other types of unwanted sequence from high-throughput sequencing reads.")
1894 (license license:expat)))
1895
1baee943
RW		 1896(define-public libbigwig
1897 (package
1898 (name "libbigwig")
1899 (version "0.1.4")
1900 (source (origin
1901 (method url-fetch)
1902 (uri (string-append "https://github.com/dpryan79/libBigWig/"
1903 "archive/" version ".tar.gz"))
1904 (file-name (string-append name "-" version ".tar.gz"))
1905 (sha256
1906 (base32
1907 "098rjh35pi4a9q83n8wiwvyzykjqj6l8q189p1xgfw4ghywdlvw1"))))
1908 (build-system gnu-build-system)
1909 (arguments
1910 `(#:test-target "test"
1911 #:make-flags
1912 (list "CC=gcc"
1913 (string-append "prefix=" (assoc-ref %outputs "out")))
1914 #:phases
1915 (modify-phases %standard-phases
1916 (delete 'configure)
1917 (add-before 'check 'disable-curl-test
1918 (lambda _
1919 (substitute* "Makefile"
1920 (("./test/testRemote.*") ""))
1921 #t))
1922 ;; This has been fixed with the upstream commit 4ff6959cd8a0, but
1923 ;; there has not yet been a release containing this change.
1924 (add-before 'install 'create-target-dirs
1925 (lambda* (#:key outputs #:allow-other-keys)
1926 (let ((out (assoc-ref outputs "out")))
1927 (mkdir-p (string-append out "/lib"))
1928 (mkdir-p (string-append out "/include"))
1929 #t))))))
1930 (inputs
1931 `(("zlib" ,zlib)
1932 ("curl" ,curl)))
1933 (native-inputs
1934 `(("doxygen" ,doxygen)))
1935 (home-page "https://github.com/dpryan79/libBigWig")
1936 (synopsis "C library for handling bigWig files")
1937 (description
1938 "This package provides a C library for parsing local and remote BigWig
1939files.")
1940 (license license:expat)))
1941
69e0e03c
RW		 1942(define-public python-pybigwig
1943 (package
1944 (name "python-pybigwig")
1945 (version "0.2.5")
1946 (source (origin
1947 (method url-fetch)
1948 (uri (pypi-uri "pyBigWig" version))
1949 (sha256
1950 (base32
1951 "0yrpdxg3y0sny25x4w22lv1k47jzccqjmg7j4bp0hywklvp0hg7d"))
1952 (modules '((guix build utils)))
1953 (snippet
1954 '(begin
1955 ;; Delete bundled libBigWig sources
1956 (delete-file-recursively "libBigWig")))))
1957 (build-system python-build-system)
1958 (arguments
1959 `(#:phases
1960 (modify-phases %standard-phases
1961 (add-after 'unpack 'link-with-libBigWig
1962 (lambda* (#:key inputs #:allow-other-keys)
1963 (substitute* "setup.py"
1964 (("libs=\\[") "libs=[\"BigWig\", "))
1965 #t)))))
1966 (inputs
1967 `(("libbigwig" ,libbigwig)
1968 ("zlib" ,zlib)
1969 ("curl" ,curl)))
1970 (home-page "https://github.com/dpryan79/pyBigWig")
1971 (synopsis "Access bigWig files in Python using libBigWig")
1972 (description
1973 "This package provides Python bindings to the libBigWig library for
1974accessing bigWig files.")
1975 (license license:expat)))
1976
1977(define-public python2-pybigwig
5c31f4aa 1978 (package-with-python2 python-pybigwig))
69e0e03c 1979
ec2a67de
BW		 1980(define-public python-dendropy
1981 (package
1982 (name "python-dendropy")
25d84d31 1983 (version "4.2.0")
ec2a67de
BW		 1984 (source
1985 (origin
1986 (method url-fetch)
1987 (uri (pypi-uri "DendroPy" version))
1988 (sha256
1989 (base32
1885bb0c
RW		 1990 "15c7s3d5gf19ljsxvq5advaa752wfi7pwrdjyhzmg85hccyvp47p"))
1991 (patches (search-patches "python-dendropy-fix-tests.patch"))))
ec2a67de
BW		 1992 (build-system python-build-system)
1993 (home-page "http://packages.python.org/DendroPy/")
1994 (synopsis "Library for phylogenetics and phylogenetic computing")
1995 (description
1996 "DendroPy is a library for phylogenetics and phylogenetic computing: reading,
1997writing, simulation, processing and manipulation of phylogenetic
1998trees (phylogenies) and characters.")
1999 (license license:bsd-3)
2000 (properties `((python2-variant . ,(delay python2-dendropy))))))
2001
2002(define-public python2-dendropy
2003 (let ((base (package-with-python2 (strip-python2-variant python-dendropy))))
2004 (package
2005 (inherit base)
9602e3cc
BW		 2006 (arguments
2007 `(#:python ,python-2
2008 #:phases
2009 (modify-phases %standard-phases
2010 (replace 'check
2011 ;; There is currently a test failure that only happens on some
2012 ;; systems, and only using "setup.py test"
2013 (lambda _ (zero? (system* "nosetests")))))))
f3b98f4f 2014 (native-inputs `(("python2-nose" ,python2-nose)
ec2a67de
BW		 2015 ,@(package-native-inputs base))))))
2016
eb2200f3
RW		 2017(define-public python-py2bit
2018 (package
2019 (name "python-py2bit")
2020 (version "0.2.1")
2021 (source
2022 (origin
2023 (method url-fetch)
2024 (uri (pypi-uri "py2bit" version))
2025 (sha256
2026 (base32
2027 "1cdf4qlmgwsh1f4k0wdv2sr8x9qn4366p0k3614vbd0fpqiarxrl"))))
2028 (build-system python-build-system)
2029 (home-page "https://github.com/dpryan79/py2bit")
2030 (synopsis "Access 2bit files using lib2bit")
2031 (description
2032 "This package provides Python bindings for lib2bit to access 2bit files
2033with Python.")
2034 (license license:expat)))
ec2a67de 2035
1921b1de
RW		 2036(define-public deeptools
2037 (package
2038 (name "deeptools")
fed72008 2039 (version "2.5.1")
1921b1de
RW		 2040 (source (origin
2041 (method url-fetch)
cd70f9bd 2042 (uri (string-append "https://github.com/deeptools/deepTools/"
3acb8c85 2043 "archive/" version ".tar.gz"))
1921b1de
RW		 2044 (file-name (string-append name "-" version ".tar.gz"))
2045 (sha256
2046 (base32
fed72008 2047 "1q8i12l2gvk4n2s8lhyzwhh9g4qbc8lrk5l7maz00yvd5g6z5540"))))
1921b1de 2048 (build-system python-build-system)
14bda1ff 2049 (inputs
fed72008
RW		 2050 `(("python-scipy" ,python-scipy)
2051 ("python-numpy" ,python-numpy)
2052 ("python-numpydoc" ,python-numpydoc)
2053 ("python-matplotlib" ,python-matplotlib)
2054 ("python-pysam" ,python-pysam)
2055 ("python-py2bit" ,python-py2bit)
2056 ("python-pybigwig" ,python-pybigwig)))
1921b1de 2057 (native-inputs
fed72008
RW		 2058 `(("python-mock" ,python-mock) ;for tests
2059 ("python-nose" ,python-nose) ;for tests
2060 ("python-pytz" ,python-pytz))) ;for tests
cd70f9bd 2061 (home-page "https://github.com/deeptools/deepTools")
1921b1de
RW		 2062 (synopsis "Tools for normalizing and visualizing deep-sequencing data")
2063 (description
2064 "DeepTools addresses the challenge of handling the large amounts of data
2065that are now routinely generated from DNA sequencing centers. To do so,
2066deepTools contains useful modules to process the mapped reads data to create
2067coverage files in standard bedGraph and bigWig file formats. By doing so,
2068deepTools allows the creation of normalized coverage files or the comparison
2069between two files (for example, treatment and control). Finally, using such
2070normalized and standardized files, multiple visualizations can be created to
2071identify enrichments with functional annotations of the genome.")
2072 (license license:gpl3+)))
2073
684bf7c7
BW		 2074(define-public diamond
2075 (package
2076 (name "diamond")
5ebc8e7f 2077 (version "0.9.18")
684bf7c7
BW		 2078 (source (origin
2079 (method url-fetch)
2080 (uri (string-append
2081 "https://github.com/bbuchfink/diamond/archive/v"
2082 version ".tar.gz"))
2083 (file-name (string-append name "-" version ".tar.gz"))
2084 (sha256
2085 (base32
5ebc8e7f 2086 "1vi2nddmy7knrv8gsprwqp6a40k63n3f2dfvx22ipjhrg9xir96f"))))
122395f9 2087 (build-system cmake-build-system)
684bf7c7 2088 (arguments
7c544991
BW		 2089 '(#:tests? #f ; no "check" target
2090 #:phases
2091 (modify-phases %standard-phases
2092 (add-after 'unpack 'remove-native-compilation
2093 (lambda _
2094 (substitute* "CMakeLists.txt" (("-march=native") ""))
2095 #t)))))
684bf7c7 2096 (inputs
122395f9 2097 `(("zlib" ,zlib)))
684bf7c7
BW		 2098 (home-page "https://github.com/bbuchfink/diamond")
2099 (synopsis "Accelerated BLAST compatible local sequence aligner")
2100 (description
2101 "DIAMOND is a BLAST-compatible local aligner for mapping protein and
2102translated DNA query sequences against a protein reference database (BLASTP
2103and BLASTX alignment mode). The speedup over BLAST is up to 20,000 on short
2104reads at a typical sensitivity of 90-99% relative to BLAST depending on the
2105data and settings.")
ef81341f 2106 (license license:agpl3+)))
684bf7c7 2107
97b9da68
RW		 2108(define-public discrover
2109 (package
2110 (name "discrover")
2111 (version "1.6.0")
2112 (source
2113 (origin
2114 (method url-fetch)
2115 (uri (string-append "https://github.com/maaskola/discrover/archive/"
2116 version ".tar.gz"))
2117 (file-name (string-append name "-" version ".tar.gz"))
2118 (sha256
2119 (base32
2120 "0rah9ja4m0rl5mldd6vag9rwrivw1zrqxssfq8qx64m7961fp68k"))))
2121 (build-system cmake-build-system)
fa702e1a
RW		 2122 (arguments
2123 `(#:tests? #f ; there are no tests
2124 #:phases
2125 (modify-phases %standard-phases
2126 (add-after 'unpack 'add-missing-includes
2127 (lambda _
2128 (substitute* "src/executioninformation.hpp"
2129 (("#define EXECUTIONINFORMATION_HPP" line)
2130 (string-append line "\n#include <random>")))
2131 (substitute* "src/plasma/fasta.hpp"
2132 (("#define FASTA_HPP" line)
2133 (string-append line "\n#include <random>")))
2134 #t)))))
97b9da68
RW		 2135 (inputs
2136 `(("boost" ,boost)
2137 ("cairo" ,cairo)))
2138 (native-inputs
2139 `(("texlive" ,texlive)
2140 ("imagemagick" ,imagemagick)))
2141 (home-page "http://dorina.mdc-berlin.de/public/rajewsky/discrover/")
2142 (synopsis "Discover discriminative nucleotide sequence motifs")
2143 (description "Discrover is a motif discovery method to find binding sites
2144of nucleic acid binding proteins.")
2145 (license license:gpl3+)))
2146
6619f9c7
RW		 2147(define-public eigensoft
2148 (let ((revision "1")
2149 (commit "b14d1e202e21e532536ff8004f0419cd5e259dc7"))
2150 (package
2151 (name "eigensoft")
2152 (version (string-append "6.1.2-"
2153 revision "."
2154 (string-take commit 9)))
2155 (source
2156 (origin
2157 (method git-fetch)
2158 (uri (git-reference
2159 (url "https://github.com/DReichLab/EIG.git")
2160 (commit commit)))
2161 (file-name (string-append "eigensoft-" commit "-checkout"))
2162 (sha256
2163 (base32
2164 "0f5m6k2j5c16xc3xbywcs989xyc26ncy1zfzp9j9n55n9r4xcaiq"))
2165 (modules '((guix build utils)))
2166 ;; Remove pre-built binaries.
2167 (snippet '(begin
2168 (delete-file-recursively "bin")
2169 (mkdir "bin")
2170 #t))))
2171 (build-system gnu-build-system)
2172 (arguments
2173 `(#:tests? #f ; There are no tests.
2174 #:make-flags '("CC=gcc")
2175 #:phases
2176 (modify-phases %standard-phases
2177 ;; There is no configure phase, but the Makefile is in a
2178 ;; sub-directory.
2179 (replace 'configure
2180 (lambda _
2181 (chdir "src")
2182 ;; The link flags are incomplete.
2183 (substitute* "Makefile"
2184 (("-lgsl") "-lgsl -lm -llapack -llapacke -lpthread"))
2185 #t))
2186 ;; The provided install target only copies executables to
2187 ;; the "bin" directory in the build root.
2188 (add-after 'install 'actually-install
2189 (lambda* (#:key outputs #:allow-other-keys)
2190 (let* ((out (assoc-ref outputs "out"))
2191 (bin (string-append out "/bin")))
6619f9c7
RW		 2192 (for-each (lambda (file)
2193 (install-file file bin))
2194 (find-files "../bin" ".*"))
2195 #t))))))
2196 (inputs
2197 `(("gsl" ,gsl)
2198 ("lapack" ,lapack)
6619f9c7
RW		 2199 ("openblas" ,openblas)
2200 ("perl" ,perl)
2201 ("gfortran" ,gfortran "lib")))
2202 (home-page "https://github.com/DReichLab/EIG")
2203 (synopsis "Tools for population genetics")
2204 (description "The EIGENSOFT package provides tools for population
2205genetics and stratification correction. EIGENSOFT implements methods commonly
2206used in population genetics analyses such as PCA, computation of Tracy-Widom
2207statistics, and finding related individuals in structured populations. It
2208comes with a built-in plotting script and supports multiple file formats and
2209quantitative phenotypes.")
2210 ;; The license of the eigensoft tools is Expat, but since it's
2211 ;; linking with the GNU Scientific Library (GSL) the effective
2212 ;; license is the GPL.
2213 (license license:gpl3+))))
2214
365c8153
RW		 2215(define-public edirect
2216 (package
2217 (name "edirect")
83b84fa8 2218 (version "4.10")
365c8153
RW		 2219 (source (origin
2220 (method url-fetch)
83b84fa8
RW		 2221 (uri (string-append "ftp://ftp.ncbi.nlm.nih.gov/entrez/entrezdirect/"
2222 "versions/2016-05-03/edirect.tar.gz"))
365c8153
RW		 2223 (sha256
2224 (base32
83b84fa8 2225 "15zsprak5yh8c1yrz4r1knmb5s8qcmdid4xdhkh3lqcv64l60hli"))))
365c8153
RW		 2226 (build-system perl-build-system)
2227 (arguments
2228 `(#:tests? #f ;no "check" target
2229 #:phases
2230 (modify-phases %standard-phases
2231 (delete 'configure)
2232 (delete 'build)
2233 (replace 'install
2234 (lambda* (#:key outputs #:allow-other-keys)
2235 (let ((target (string-append (assoc-ref outputs "out")
2236 "/bin")))
2237 (mkdir-p target)
f3860753 2238 (install-file "edirect.pl" target)
365c8153
RW		 2239 #t)))
2240 (add-after
2241 'install 'wrap-program
2242 (lambda* (#:key inputs outputs #:allow-other-keys)
2243 ;; Make sure 'edirect.pl' finds all perl inputs at runtime.
2244 (let* ((out (assoc-ref outputs "out"))
2245 (path (getenv "PERL5LIB")))
2246 (wrap-program (string-append out "/bin/edirect.pl")
2247 `("PERL5LIB" ":" prefix (,path)))))))))
2248 (inputs
2249 `(("perl-html-parser" ,perl-html-parser)
2250 ("perl-encode-locale" ,perl-encode-locale)
2251 ("perl-file-listing" ,perl-file-listing)
2252 ("perl-html-tagset" ,perl-html-tagset)
2253 ("perl-html-tree" ,perl-html-tree)
2254 ("perl-http-cookies" ,perl-http-cookies)
2255 ("perl-http-date" ,perl-http-date)
2256 ("perl-http-message" ,perl-http-message)
2257 ("perl-http-negotiate" ,perl-http-negotiate)
2258 ("perl-lwp-mediatypes" ,perl-lwp-mediatypes)
2259 ("perl-lwp-protocol-https" ,perl-lwp-protocol-https)
2260 ("perl-net-http" ,perl-net-http)
2261 ("perl-uri" ,perl-uri)
2262 ("perl-www-robotrules" ,perl-www-robotrules)
2263 ("perl" ,perl)))
3d51ec91 2264 (home-page "http://www.ncbi.nlm.nih.gov/books/NBK179288/")
365c8153
RW		 2265 (synopsis "Tools for accessing the NCBI's set of databases")
2266 (description
2267 "Entrez Direct (EDirect) is a method for accessing the National Center
2268for Biotechnology Information's (NCBI) set of interconnected
2269databases (publication, sequence, structure, gene, variation, expression,
2270etc.) from a terminal. Functions take search terms from command-line
2271arguments. Individual operations are combined to build multi-step queries.
2272Record retrieval and formatting normally complete the process.
2273
2274EDirect also provides an argument-driven function that simplifies the
2275extraction of data from document summaries or other results that are returned
2276in structured XML format. This can eliminate the need for writing custom
2277software to answer ad hoc questions.")
2278 (license license:public-domain)))
2279
b16728b0
BW		 2280(define-public exonerate
2281 (package
2282 (name "exonerate")
2283 (version "2.4.0")
2284 (source
2285 (origin
2286 (method url-fetch)
2287 (uri
2288 (string-append
2289 "http://ftp.ebi.ac.uk/pub/software/vertebrategenomics/exonerate/"
2290 "exonerate-" version ".tar.gz"))
2291 (sha256
2292 (base32
2293 "0hj0m9xygiqsdxvbg79wq579kbrx1mdrabi2bzqz2zn9qwfjcjgq"))))
2294 (build-system gnu-build-system)
2295 (arguments
2296 `(#:parallel-build? #f)) ; Building in parallel fails on some machines.
2297 (native-inputs
2298 `(("pkg-config" ,pkg-config)))
2299 (inputs
2300 `(("glib" ,glib)))
2301 (home-page
2302 "https://www.ebi.ac.uk/about/vertebrate-genomics/software/exonerate")
2303 (synopsis "Generic tool for biological sequence alignment")
2304 (description
2305 "Exonerate is a generic tool for pairwise sequence comparison. It allows
2306the alignment of sequences using a many alignment models, either exhaustive
2307dynamic programming or a variety of heuristics.")
2308 (license license:gpl3)))
2309
e4e5a4d8
RW		 2310(define-public express
2311 (package
2312 (name "express")
2313 (version "1.5.1")
2314 (source (origin
2315 (method url-fetch)
2316 (uri
2317 (string-append
2318 "http://bio.math.berkeley.edu/eXpress/downloads/express-"
2319 version "/express-" version "-src.tgz"))
2320 (sha256
2321 (base32
2322 "03rczxd0gjp2l1jxcmjfmf5j94j77zqyxa6x063zsc585nj40n0c"))))
2323 (build-system cmake-build-system)
2324 (arguments
2325 `(#:tests? #f ;no "check" target
2326 #:phases
dc1d3cde
KK		 2327 (modify-phases %standard-phases
2328 (add-after 'unpack 'use-shared-boost-libs-and-set-bamtools-paths
2329 (lambda* (#:key inputs #:allow-other-keys)
2330 (substitute* "CMakeLists.txt"
2331 (("set\\(Boost_USE_STATIC_LIBS ON\\)")
2332 "set(Boost_USE_STATIC_LIBS OFF)")
2333 (("\\$\\{CMAKE_CURRENT_SOURCE_DIR\\}/bamtools/include")
2334 (string-append (assoc-ref inputs "bamtools") "/include/bamtools")))
2335 (substitute* "src/CMakeLists.txt"
2336 (("\\$\\{CMAKE_CURRENT_SOURCE_DIR\\}/\\.\\./bamtools/lib")
2337 (string-append (assoc-ref inputs "bamtools") "/lib/bamtools")))
2338 #t)))))
e4e5a4d8
RW		 2339 (inputs
2340 `(("boost" ,boost)
2341 ("bamtools" ,bamtools)
2342 ("protobuf" ,protobuf)
2343 ("zlib" ,zlib)))
2344 (home-page "http://bio.math.berkeley.edu/eXpress")
2345 (synopsis "Streaming quantification for high-throughput genomic sequencing")
2346 (description
2347 "eXpress is a streaming tool for quantifying the abundances of a set of
2348target sequences from sampled subsequences. Example applications include
2349transcript-level RNA-Seq quantification, allele-specific/haplotype expression
2350analysis (from RNA-Seq), transcription factor binding quantification in
2351ChIP-Seq, and analysis of metagenomic data.")
2352 (license license:artistic2.0)))
2353
f3674b1c
BW		 2354(define-public express-beta-diversity
2355 (package
2356 (name "express-beta-diversity")
2357 (version "1.0.7")
2358 (source (origin
2359 (method url-fetch)
2360 (uri
2361 (string-append
2362 "https://github.com/dparks1134/ExpressBetaDiversity/archive/v"
2363 version ".tar.gz"))
2364 (file-name (string-append name "-" version ".tar.gz"))
2365 (sha256
2366 (base32
2367 "1djvdlmqvjf6h0zq7w36y8cl5cli6rgj86x65znl48agnwmzxfxr"))))
2368 (build-system gnu-build-system)
2369 (arguments
2370 `(#:phases
2371 (modify-phases %standard-phases
2372 (delete 'configure)
2373 (add-before 'build 'enter-source (lambda _ (chdir "source") #t))
2374 (replace 'check
2375 (lambda _ (zero? (system* "../bin/ExpressBetaDiversity"
2376 "-u"))))
2377 (add-after 'check 'exit-source (lambda _ (chdir "..") #t))
2378 (replace 'install
2379 (lambda* (#:key outputs #:allow-other-keys)
2380 (let ((bin (string-append (assoc-ref outputs "out")
2381 "/bin")))
2382 (mkdir-p bin)
f3860753
TGR		 2383 (install-file "scripts/convertToEBD.py" bin)
2384 (install-file "bin/ExpressBetaDiversity" bin)
f3674b1c
BW		 2385 #t))))))
2386 (inputs
2387 `(("python" ,python-2)))
2388 (home-page "http://kiwi.cs.dal.ca/Software/ExpressBetaDiversity")
2389 (synopsis "Taxon- and phylogenetic-based beta diversity measures")
2390 (description
2391 "Express Beta Diversity (EBD) calculates ecological beta diversity
2392(dissimilarity) measures between biological communities. EBD implements a
2393variety of diversity measures including those that make use of phylogenetic
2394similarity of community members.")
2395 (license license:gpl3+)))
2396
12b04cbe
BW		 2397(define-public fasttree
2398 (package
2399 (name "fasttree")
88682c9a 2400 (version "2.1.10")
12b04cbe
BW		 2401 (source (origin
2402 (method url-fetch)
2403 (uri (string-append
2404 "http://www.microbesonline.org/fasttree/FastTree-"
2405 version ".c"))
2406 (sha256
2407 (base32
88682c9a 2408 "0vcjdvy1j4m702vmak4svbfkrpcw63k7wymfksjp9a982zy8kjsl"))))
12b04cbe
BW		 2409 (build-system gnu-build-system)
2410 (arguments
2411 `(#:tests? #f ; no "check" target
2412 #:phases
2413 (modify-phases %standard-phases
2414 (delete 'unpack)
2415 (delete 'configure)
2416 (replace 'build
e03a5153
BW		 2417 (lambda* (#:key source #:allow-other-keys)
2418 (and (zero? (system* "gcc"
2419 "-O3"
2420 "-finline-functions"
2421 "-funroll-loops"
2422 "-Wall"
2423 "-o"
2424 "FastTree"
2425 source
2426 "-lm"))
2427 (zero? (system* "gcc"
2428 "-DOPENMP"
2429 "-fopenmp"
2430 "-O3"
2431 "-finline-functions"
2432 "-funroll-loops"
2433 "-Wall"
2434 "-o"
2435 "FastTreeMP"
2436 source
2437 "-lm")))))
12b04cbe 2438 (replace 'install
e03a5153
BW		 2439 (lambda* (#:key outputs #:allow-other-keys)
2440 (let ((bin (string-append (assoc-ref outputs "out")
2441 "/bin")))
2442 (mkdir-p bin)
f3860753
TGR		 2443 (install-file "FastTree" bin)
2444 (install-file "FastTreeMP" bin)
e03a5153 2445 #t))))))
12b04cbe
BW		 2446 (home-page "http://www.microbesonline.org/fasttree")
2447 (synopsis "Infers approximately-maximum-likelihood phylogenetic trees")
2448 (description
2449 "FastTree can handle alignments with up to a million of sequences in a
2450reasonable amount of time and memory. For large alignments, FastTree is
2451100-1,000 times faster than PhyML 3.0 or RAxML 7.")
2452 (license license:gpl2+)))
2453
2127cedb
RW		 2454(define-public fastx-toolkit
2455 (package
2456 (name "fastx-toolkit")
2457 (version "0.0.14")
2458 (source (origin
2459 (method url-fetch)
2460 (uri
2461 (string-append
2462 "https://github.com/agordon/fastx_toolkit/releases/download/"
2463 version "/fastx_toolkit-" version ".tar.bz2"))
2464 (sha256
2465 (base32
2466 "01jqzw386873sr0pjp1wr4rn8fsga2vxs1qfmicvx1pjr72007wy"))))
2467 (build-system gnu-build-system)
2468 (inputs
2469 `(("libgtextutils" ,libgtextutils)))
2470 (native-inputs
2471 `(("pkg-config" ,pkg-config)))
2472 (home-page "http://hannonlab.cshl.edu/fastx_toolkit/")
2473 (synopsis "Tools for FASTA/FASTQ file preprocessing")
2474 (description
2475 "The FASTX-Toolkit is a collection of command line tools for Short-Reads
2476FASTA/FASTQ files preprocessing.
2477
2478Next-Generation sequencing machines usually produce FASTA or FASTQ files,
2479containing multiple short-reads sequences. The main processing of such
2480FASTA/FASTQ files is mapping the sequences to reference genomes. However, it
2481is sometimes more productive to preprocess the files before mapping the
2482sequences to the genome---manipulating the sequences to produce better mapping
2483results. The FASTX-Toolkit tools perform some of these preprocessing tasks.")
2484 (license license:agpl3+)))
2485
d7678942
RW		 2486(define-public flexbar
2487 (package
2488 (name "flexbar")
2489 (version "2.5")
2490 (source (origin
2491 (method url-fetch)
2492 (uri
2493 (string-append "mirror://sourceforge/flexbar/"
2494 version "/flexbar_v" version "_src.tgz"))
2495 (sha256
2496 (base32
2497 "13jaykc3y1x8y5nn9j8ljnb79s5y51kyxz46hdmvvjj6qhyympmf"))))
2498 (build-system cmake-build-system)
2499 (arguments
4ca009c0 2500 `(#:configure-flags (list
d7678942
RW		 2501 (string-append "-DFLEXBAR_BINARY_DIR="
2502 (assoc-ref %outputs "out")
2503 "/bin/"))
2504 #:phases
dc1d3cde
KK		 2505 (modify-phases %standard-phases
2506 (replace 'check
2507 (lambda* (#:key outputs #:allow-other-keys)
2508 (setenv "PATH" (string-append
2509 (assoc-ref outputs "out") "/bin:"
2510 (getenv "PATH")))
2511 (chdir "../flexbar_v2.5_src/test")
2512 (zero? (system* "bash" "flexbar_validate.sh"))))
2513 (delete 'install))))
d7678942
RW		 2514 (inputs
2515 `(("tbb" ,tbb)
2516 ("zlib" ,zlib)))
2517 (native-inputs
2518 `(("pkg-config" ,pkg-config)
2519 ("seqan" ,seqan)))
2520 (home-page "http://flexbar.sourceforge.net")
2521 (synopsis "Barcode and adapter removal tool for sequencing platforms")
2522 (description
2523 "Flexbar preprocesses high-throughput nucleotide sequencing data
2524efficiently. It demultiplexes barcoded runs and removes adapter sequences.
2525Moreover, trimming and filtering features are provided. Flexbar increases
2526read mapping rates and improves genome and transcriptome assemblies. It
2527supports next-generation sequencing data in fasta/q and csfasta/q format from
2528Illumina, Roche 454, and the SOLiD platform.")
2529 (license license:gpl3)))
2530
19f4554c
BW		 2531(define-public fraggenescan
2532 (package
2533 (name "fraggenescan")
74297231 2534 (version "1.30")
19f4554c
BW		 2535 (source
2536 (origin
2537 (method url-fetch)
2538 (uri
2539 (string-append "mirror://sourceforge/fraggenescan/"
2540 "FragGeneScan" version ".tar.gz"))
2541 (sha256
74297231 2542 (base32 "158dcnwczgcyhwm4qlx19sanrwgdpzf6bn2y57mbpx55lkgz1mzj"))))
19f4554c
BW		 2543 (build-system gnu-build-system)
2544 (arguments
2545 `(#:phases
2546 (modify-phases %standard-phases
2547 (delete 'configure)
2548 (add-before 'build 'patch-paths
2549 (lambda* (#:key outputs #:allow-other-keys)
2550 (let* ((out (string-append (assoc-ref outputs "out")))
2551 (share (string-append out "/share/fraggenescan/")))
2552 (substitute* "run_FragGeneScan.pl"
2553 (("system\\(\"rm")
2554 (string-append "system(\"" (which "rm")))
2555 (("system\\(\"mv")
2556 (string-append "system(\"" (which "mv")))
74297231 2557 (("\\\"awk") (string-append "\"" (which "awk")))
19f4554c
BW		 2558 ;; This script and other programs expect the training files
2559 ;; to be in the non-standard location bin/train/XXX. Change
2560 ;; this to be share/fraggenescan/train/XXX instead.
2561 (("^\\$train.file = \\$dir.*")
2562 (string-append "$train_file = \""
2563 share
2564 "train/\".$FGS_train_file;")))
2565 (substitute* "run_hmm.c"
2566 (("^ strcat\\(train_dir, \\\"train/\\\"\\);")
74297231 2567 (string-append " strcpy(train_dir, \"" share "/train/\");"))))
19f4554c
BW		 2568 #t))
2569 (replace 'build
2570 (lambda _ (and (zero? (system* "make" "clean"))
2571 (zero? (system* "make" "fgs")))))
2572 (replace 'install
2573 (lambda* (#:key outputs #:allow-other-keys)
2574 (let* ((out (string-append (assoc-ref outputs "out")))
2575 (bin (string-append out "/bin/"))
2576 (share (string-append out "/share/fraggenescan/train")))
2577 (install-file "run_FragGeneScan.pl" bin)
2578 (install-file "FragGeneScan" bin)
19f4554c
BW		 2579 (copy-recursively "train" share))))
2580 (delete 'check)
2581 (add-after 'install 'post-install-check
2582 ;; In lieu of 'make check', run one of the examples and check the
2583 ;; output files gets created.
2584 (lambda* (#:key outputs #:allow-other-keys)
2585 (let* ((out (string-append (assoc-ref outputs "out")))
74297231
BW		 2586 (bin (string-append out "/bin/"))
2587 (frag (string-append bin "run_FragGeneScan.pl")))
2588 (and (zero? (system* frag ; Test complete genome.
19f4554c
BW		 2589 "-genome=./example/NC_000913.fna"
2590 "-out=./test2"
2591 "-complete=1"
2592 "-train=complete"))
2593 (file-exists? "test2.faa")
2594 (file-exists? "test2.ffn")
2595 (file-exists? "test2.gff")
74297231
BW		 2596 (file-exists? "test2.out")
2597 (zero? (system* ; Test incomplete sequences.
2598 frag
2599 "-genome=./example/NC_000913-fgs.ffn"
2600 "-out=out"
2601 "-complete=0"
2602 "-train=454_30")))))))))
19f4554c
BW		 2603 (inputs
2604 `(("perl" ,perl)
2605 ("python" ,python-2))) ;not compatible with python 3.
2606 (home-page "https://sourceforge.net/projects/fraggenescan/")
2607 (synopsis "Finds potentially fragmented genes in short reads")
2608 (description
2609 "FragGeneScan is a program for predicting bacterial and archaeal genes in
2610short and error-prone DNA sequencing reads. It can also be applied to predict
2611genes in incomplete assemblies or complete genomes.")
2612 ;; GPL3+ according to private correspondense with the authors.
2613 (license license:gpl3+)))
2614
81f3e0c1
BW		 2615(define-public fxtract
2616 (let ((util-commit "776ca85a18a47492af3794745efcb4a905113115"))
2617 (package
2618 (name "fxtract")
2619 (version "2.3")
2620 (source
2621 (origin
2622 (method url-fetch)
2623 (uri (string-append
2624 "https://github.com/ctSkennerton/fxtract/archive/"
2625 version ".tar.gz"))
2626 (file-name (string-append "ctstennerton-util-"
2627 (string-take util-commit 7)
2628 "-checkout"))
2629 (sha256
2630 (base32
2631 "0275cfdhis8517hm01is62062swmi06fxzifq7mr3knbbxjlaiwj"))))
2632 (build-system gnu-build-system)
2633 (arguments
2634 `(#:make-flags (list
2635 (string-append "PREFIX=" (assoc-ref %outputs "out"))
2636 "CC=gcc")
2637 #:test-target "fxtract_test"
2638 #:phases
2639 (modify-phases %standard-phases
2640 (delete 'configure)
2641 (add-before 'build 'copy-util
2642 (lambda* (#:key inputs #:allow-other-keys)
2643 (rmdir "util")
2644 (copy-recursively (assoc-ref inputs "ctskennerton-util") "util")
2645 #t))
2646 ;; Do not use make install as this requires additional dependencies.
2647 (replace 'install
2648 (lambda* (#:key outputs #:allow-other-keys)
2649 (let* ((out (assoc-ref outputs "out"))
2650 (bin (string-append out"/bin")))
2651 (install-file "fxtract" bin)
2652 #t))))))
2653 (inputs
2654 `(("pcre" ,pcre)
2655 ("zlib" ,zlib)))
2656 (native-inputs
2657 ;; ctskennerton-util is licensed under GPL2.
2658 `(("ctskennerton-util"
2659 ,(origin
2660 (method git-fetch)
2661 (uri (git-reference
2662 (url "https://github.com/ctSkennerton/util.git")
2663 (commit util-commit)))
2664 (file-name (string-append
2665 "ctstennerton-util-" util-commit "-checkout"))
2666 (sha256
2667 (base32
2668 "0cls1hd4vgj3f36fpzzg4xc77d6f3hpc60cbpfmn2gdr7ykzzad7"))))))
2669 (home-page "https://github.com/ctSkennerton/fxtract")
2670 (synopsis "Extract sequences from FASTA and FASTQ files")
2671 (description
2672 "Fxtract extracts sequences from a protein or nucleotide fastx (FASTA
2673or FASTQ) file given a subsequence. It uses a simple substring search for
2674basic tasks but can change to using POSIX regular expressions, PCRE, hash
2675lookups or multi-pattern searching as required. By default fxtract looks in
2676the sequence of each record but can also be told to look in the header,
2677comment or quality sections.")
afde1a26
BW		 2678 ;; 'util' requires SSE instructions.
2679 (supported-systems '("x86_64-linux"))
81f3e0c1
BW		 2680 (license license:expat))))
2681
2b18ad05
PP		 2682(define-public gemma
2683 (package
2684 (name "gemma")
2685 (version "0.96")
2686 (source (origin
2687 (method url-fetch)
2688 (uri (string-append "https://github.com/xiangzhou/GEMMA/archive/v"
2689 version ".tar.gz"))
2690 (file-name (string-append name "-" version ".tar.gz"))
2691 (sha256
2692 (base32
ce7e361f
EF		 2693 "055ynn16gd12pf78n4vr2a9jlwsbwzajpdnf2y2yilg1krfff222"))
2694 (patches (search-patches "gemma-intel-compat.patch"))))
2b18ad05
PP		 2695 (inputs
2696 `(("gsl" ,gsl)
2697 ("lapack" ,lapack)
2698 ("zlib" ,zlib)))
2699 (build-system gnu-build-system)
2700 (arguments
2c9232ae 2701 `(#:make-flags
ce7e361f
EF		 2702 '(,@(match (%current-system)
2703 ("x86_64-linux"
2704 '("FORCE_DYNAMIC=1"))
2705 ("i686-linux"
2706 '("FORCE_DYNAMIC=1" "FORCE_32BIT=1"))
2707 (_
2708 '("FORCE_DYNAMIC=1" "NO_INTEL_COMPAT=1"))))
2b18ad05
PP		 2709 #:phases
2710 (modify-phases %standard-phases
2711 (delete 'configure)
2712 (add-before 'build 'bin-mkdir
07bf6929
EF		 2713 (lambda _
2714 (mkdir-p "bin")
2715 #t))
2b18ad05 2716 (replace 'install
07bf6929
EF		 2717 (lambda* (#:key outputs #:allow-other-keys)
2718 (let ((out (assoc-ref outputs "out")))
2719 (install-file "bin/gemma"
2720 (string-append
2721 out "/bin")))
2722 #t)))
2b18ad05
PP		 2723 #:tests? #f)) ; no tests included yet
2724 (home-page "https://github.com/xiangzhou/GEMMA")
2725 (synopsis "Tool for genome-wide efficient mixed model association")
2726 (description
2727 "Genome-wide Efficient Mixed Model Association (GEMMA) provides a
2728standard linear mixed model resolver with application in genome-wide
2729association studies (GWAS).")
2730 (license license:gpl3)))
2731
5854f685
RW		 2732(define-public grit
2733 (package
2734 (name "grit")
2735 (version "2.0.2")
2736 (source (origin
2737 (method url-fetch)
2738 (uri (string-append
2739 "https://github.com/nboley/grit/archive/"
2740 version ".tar.gz"))
2741 (file-name (string-append name "-" version ".tar.gz"))
2742 (sha256
2743 (base32
2744 "157in84dj70wimbind3x7sy1whs3h57qfgcnj2s6lrd38fbrb7mj"))))
2745 (build-system python-build-system)
2746 (arguments
2747 `(#:python ,python-2
2748 #:phases
dc1d3cde
KK		 2749 (modify-phases %standard-phases
2750 (add-after 'unpack 'generate-from-cython-sources
2751 (lambda* (#:key inputs outputs #:allow-other-keys)
2752 ;; Delete these C files to force fresh generation from pyx sources.
2753 (delete-file "grit/sparsify_support_fns.c")
2754 (delete-file "grit/call_peaks_support_fns.c")
2755 (substitute* "setup.py"
2756 (("Cython.Setup") "Cython.Build")
2757 ;; Add numpy include path to fix compilation
2758 (("pyx\", \\]")
2759 (string-append "pyx\", ], include_dirs = ['"
2760 (assoc-ref inputs "python-numpy")
2761 "/lib/python2.7/site-packages/numpy/core/include/"
2762 "']")))
2763 #t)))))
5854f685
RW		 2764 (inputs
2765 `(("python-scipy" ,python2-scipy)
2766 ("python-numpy" ,python2-numpy)
2767 ("python-pysam" ,python2-pysam)
2768 ("python-networkx" ,python2-networkx)))
2769 (native-inputs
f3b98f4f 2770 `(("python-cython" ,python2-cython)))
5854f685
RW		 2771 (home-page "http://grit-bio.org")
2772 (synopsis "Tool for integrative analysis of RNA-seq type assays")
2773 (description
2774 "GRIT is designed to use RNA-seq, TES, and TSS data to build and quantify
2775full length transcript models. When none of these data sources are available,
2776GRIT can be run by providing a candidate set of TES or TSS sites. In
2777addition, GRIT can merge in reference junctions and gene boundaries. GRIT can
2778also be run in quantification mode, where it uses a provided GTF file and just
2779estimates transcript expression.")
2780 (license license:gpl3+)))
2781
346a829a
RW		 2782(define-public hisat
2783 (package
2784 (name "hisat")
2785 (version "0.1.4")
2786 (source (origin
2787 (method url-fetch)
2788 (uri (string-append
2789 "http://ccb.jhu.edu/software/hisat/downloads/hisat-"
2790 version "-beta-source.zip"))
2791 (sha256
2792 (base32
2793 "1k381ydranqxp09yf2y7w1d0chz5d59vb6jchi89hbb0prq19lk5"))))
2794 (build-system gnu-build-system)
2795 (arguments
e58d01fa
RW		 2796 `(#:tests? #f ;no check target
2797 #:make-flags '("allall"
2798 ;; Disable unsupported `popcnt' instructions on
2799 ;; architectures other than x86_64
2800 ,@(if (string-prefix? "x86_64"
2801 (or (%current-target-system)
2802 (%current-system)))
2803 '()
2804 '("POPCNT_CAPABILITY=0")))
346a829a 2805 #:phases
dc1d3cde
KK		 2806 (modify-phases %standard-phases
2807 (add-after 'unpack 'patch-sources
2808 (lambda _
2809 ;; XXX Cannot use snippet because zip files are not supported
2810 (substitute* "Makefile"
2811 (("^CC = .*$") "CC = gcc")
2812 (("^CPP = .*$") "CPP = g++")
2813 ;; replace BUILD_HOST and BUILD_TIME for deterministic build
2814 (("-DBUILD_HOST=.*") "-DBUILD_HOST=\"\\\"guix\\\"\"")
2815 (("-DBUILD_TIME=.*") "-DBUILD_TIME=\"\\\"0\\\"\""))
2816 (substitute* '("hisat-build" "hisat-inspect")
2817 (("/usr/bin/env") (which "env")))
2818 #t))
2819 (replace 'install
2820 (lambda* (#:key outputs #:allow-other-keys)
2821 (let ((bin (string-append (assoc-ref outputs "out") "/bin/")))
2822 (for-each (lambda (file)
2823 (install-file file bin))
2824 (find-files
2825 "."
2826 "hisat(-(build|align|inspect)(-(s|l)(-debug)*)*)*$")))
2827 #t))
2828 (delete 'configure))))
346a829a
RW		 2829 (native-inputs
2830 `(("unzip" ,unzip)))
2831 (inputs
2832 `(("perl" ,perl)
2833 ("python" ,python)
2834 ("zlib" ,zlib)))
60af3d82
RW		 2835 ;; Non-portable SSE instructions are used so building fails on platforms
2836 ;; other than x86_64.
2837 (supported-systems '("x86_64-linux"))
346a829a
RW		 2838 (home-page "http://ccb.jhu.edu/software/hisat/index.shtml")
2839 (synopsis "Hierarchical indexing for spliced alignment of transcripts")
2840 (description
2841 "HISAT is a fast and sensitive spliced alignment program for mapping
2842RNA-seq reads. In addition to one global FM index that represents a whole
2843genome, HISAT uses a large set of small FM indexes that collectively cover the
2844whole genome. These small indexes (called local indexes) combined with
2845several alignment strategies enable effective alignment of RNA-seq reads, in
2846particular, reads spanning multiple exons.")
2847 (license license:gpl3+)))
2848
e84efc50
RW		 2849(define-public hisat2
2850 (package
2851 (name "hisat2")
2852 (version "2.0.5")
2853 (source
2854 (origin
2855 (method url-fetch)
2856 ;; FIXME: a better source URL is
2857 ;; (string-append "ftp://ftp.ccb.jhu.edu/pub/infphilo/hisat2"
2858 ;; "/downloads/hisat2-" version "-source.zip")
2859 ;; with hash "0lywnr8kijwsc2aw10dwxic0n0yvip6fl3rjlvc8zzwahamy4x7g"
2860 ;; but it is currently unavailable.
2861 (uri "https://github.com/infphilo/hisat2/archive/cba6e8cb.tar.gz")
2862 (file-name (string-append name "-" version ".tar.gz"))
2863 (sha256
2864 (base32
2865 "1mf2hdsyv7cd97xm9mp9a4qws02yrj95y6w6f6cdwnq0klp81r50"))))
2866 (build-system gnu-build-system)
2867 (arguments
2868 `(#:tests? #f ; no check target
2869 #:make-flags (list "CC=gcc" "CXX=g++" "allall")
2870 #:modules ((guix build gnu-build-system)
2871 (guix build utils)
2872 (srfi srfi-26))
2873 #:phases
2874 (modify-phases %standard-phases
2875 (add-after 'unpack 'make-deterministic
2876 (lambda _
2877 (substitute* "Makefile"
2878 (("`date`") "0"))
2879 #t))
2880 (delete 'configure)
2881 (replace 'install
2882 (lambda* (#:key outputs #:allow-other-keys)
2883 (let* ((out (assoc-ref outputs "out"))
2884 (bin (string-append out "/bin/"))
2885 (doc (string-append out "/share/doc/hisat2/")))
2886 (for-each
2887 (cut install-file <> bin)
2888 (find-files "."
2889 "hisat2(-(build|align|inspect)(-(s|l)(-debug)*)*)*$"))
2890 (mkdir-p doc)
2891 (install-file "doc/manual.inc.html" doc))
2892 #t)))))
2893 (native-inputs
2894 `(("unzip" ,unzip) ; needed for archive from ftp
2895 ("perl" ,perl)
2896 ("pandoc" ,ghc-pandoc))) ; for documentation
2897 (home-page "http://ccb.jhu.edu/software/hisat2/index.shtml")
2898 (synopsis "Graph-based alignment of genomic sequencing reads")
2899 (description "HISAT2 is a fast and sensitive alignment program for mapping
2900next-generation sequencing reads (both DNA and RNA) to a population of human
2901genomes (as well as to a single reference genome). In addition to using one
2902global @dfn{graph FM} (GFM) index that represents a population of human
2903genomes, HISAT2 uses a large set of small GFM indexes that collectively cover
2904the whole genome. These small indexes, combined with several alignment
2905strategies, enable rapid and accurate alignment of sequencing reads. This new
2906indexing scheme is called a @dfn{Hierarchical Graph FM index} (HGFM).")
2907 ;; HISAT2 contains files from Bowtie2, which is released under
2908 ;; GPLv2 or later. The HISAT2 source files are released under
2909 ;; GPLv3 or later.
2910 (license license:gpl3+)))
2911
c684629f
BW		 2912(define-public hmmer
2913 (package
2914 (name "hmmer")
2915 (version "3.1b2")
79f09fa2
BW		 2916 (source
2917 (origin
2918 (method url-fetch)
2919 (uri (string-append
2920 "http://eddylab.org/software/hmmer"
9cf5f134 2921 (version-major version) "/"
79f09fa2
BW		 2922 version "/hmmer-" version ".tar.gz"))
2923 (sha256
2924 (base32
2925 "0djmgc0pfli0jilfx8hql1axhwhqxqb8rxg2r5rg07aw73sfs5nx"))
2926 (patches (search-patches "hmmer-remove-cpu-specificity.patch"))))
c684629f 2927 (build-system gnu-build-system)
b3546174 2928 (native-inputs `(("perl" ,perl)))
a83e6046 2929 (home-page "http://hmmer.org/")
c684629f
BW		 2930 (synopsis "Biosequence analysis using profile hidden Markov models")
2931 (description
2932 "HMMER is used for searching sequence databases for homologs of protein
2933sequences, and for making protein sequence alignments. It implements methods
2934using probabilistic models called profile hidden Markov models (profile
2935HMMs).")
2936 (license (list license:gpl3+
2937 ;; The bundled library 'easel' is distributed
2938 ;; under The Janelia Farm Software License.
2939 (license:non-copyleft
2940 "file://easel/LICENSE"
2941 "See easel/LICENSE in the distribution.")))))
2942
85652f59
RW		 2943(define-public htseq
2944 (package
2945 (name "htseq")
92971d68 2946 (version "0.9.1")
85652f59
RW		 2947 (source (origin
2948 (method url-fetch)
75e6639f 2949 (uri (pypi-uri "HTSeq" version))
85652f59
RW		 2950 (sha256
2951 (base32
92971d68 2952 "11flgb1381xdhk43bzbfm3vhnszkpqg6jk76rpa5xd1zbrvvlnxg"))))
85652f59 2953 (build-system python-build-system)
92971d68
BW		 2954 (native-inputs
2955 `(("python-cython" ,python-cython)))
0536727e
RW		 2956 ;; Numpy needs to be propagated when htseq is used as a Python library.
2957 (propagated-inputs
92971d68 2958 `(("python-numpy" ,python-numpy)))
578b05d9 2959 (inputs
92971d68
BW		 2960 `(("python-pysam" ,python-pysam)
2961 ("python-matplotlib" ,python-matplotlib)))
85652f59
RW		 2962 (home-page "http://www-huber.embl.de/users/anders/HTSeq/")
2963 (synopsis "Analysing high-throughput sequencing data with Python")
2964 (description
2965 "HTSeq is a Python package that provides infrastructure to process data
2966from high-throughput sequencing assays.")
2967 (license license:gpl3+)))
2968
92971d68
BW		 2969(define-public python2-htseq
2970 (package-with-python2 htseq))
2971
1ad15c16 2972(define-public java-htsjdk
15a3c3d4 2973 (package
1ad15c16 2974 (name "java-htsjdk")
bd94b6f8 2975 (version "2.3.0") ; last version without build dependency on gradle
15a3c3d4
RW		 2976 (source (origin
2977 (method url-fetch)
2978 (uri (string-append
2979 "https://github.com/samtools/htsjdk/archive/"
2980 version ".tar.gz"))
2981 (file-name (string-append name "-" version ".tar.gz"))
2982 (sha256
2983 (base32
bd94b6f8 2984 "1ibhzzxsfc38nqyk9r8zqj6blfc1kh26iirypd4q6n90hs2m6nyq"))
15a3c3d4 2985 (modules '((guix build utils)))
bd94b6f8
RW		 2986 (snippet
2987 ;; Delete pre-built binaries
2988 '(begin
2989 (delete-file-recursively "lib")
2990 (mkdir-p "lib")
2991 #t))))
10b4a969 2992 (build-system ant-build-system)
15a3c3d4 2993 (arguments
10b4a969 2994 `(#:tests? #f ; test require Internet access
bd94b6f8 2995 #:jdk ,icedtea-8
10b4a969
RW		 2996 #:make-flags
2997 (list (string-append "-Ddist=" (assoc-ref %outputs "out")
2998 "/share/java/htsjdk/"))
2999 #:build-target "all"
3000 #:phases
3001 (modify-phases %standard-phases
3002 ;; The build phase also installs the jars
3003 (delete 'install))))
bd94b6f8
RW		 3004 (inputs
3005 `(("java-ngs" ,java-ngs)
3006 ("java-snappy-1" ,java-snappy-1)
3007 ("java-commons-compress" ,java-commons-compress)
3008 ("java-commons-logging-minimal" ,java-commons-logging-minimal)
3009 ("java-commons-jexl-2" ,java-commons-jexl-2)
3010 ("java-xz" ,java-xz)))
3011 (native-inputs
3012 `(("java-testng" ,java-testng)))
15a3c3d4
RW		 3013 (home-page "http://samtools.github.io/htsjdk/")
3014 (synopsis "Java API for high-throughput sequencing data (HTS) formats")
3015 (description
3016 "HTSJDK is an implementation of a unified Java library for accessing
3017common file formats, such as SAM and VCF, used for high-throughput
3018sequencing (HTS) data. There are also an number of useful utilities for
3019manipulating HTS data.")
3020 (license license:expat)))
3021
d7fed31a
RW		 3022;; This version matches java-htsjdk 2.3.0. Later versions also require a more
3023;; recent version of java-htsjdk, which depends on gradle.
3024(define-public java-picard
3025 (package
3026 (name "java-picard")
3027 (version "2.3.0")
3028 (source (origin
3029 (method git-fetch)
3030 (uri (git-reference
3031 (url "https://github.com/broadinstitute/picard.git")
3032 (commit version)))
3033 (file-name (string-append "java-picard-" version "-checkout"))
3034 (sha256
3035 (base32
3036 "1ll7mf4r3by92w2nhlmpa591xd1f46xlkwh59mq6fvbb5pdwzvx6"))
3037 (modules '((guix build utils)))
3038 (snippet
3039 '(begin
3040 ;; Delete pre-built binaries.
3041 (delete-file-recursively "lib")
3042 (mkdir-p "lib")
3043 (substitute* "build.xml"
3044 ;; Remove build-time dependency on git.
3045 (("failifexecutionfails=\"true\"")
3046 "failifexecutionfails=\"false\"")
3047 ;; Use our htsjdk.
3048 (("depends=\"compile-htsjdk, ")
3049 "depends=\"")
3050 (("depends=\"compile-htsjdk-tests, ")
3051 "depends=\"")
3052 ;; Build picard-lib.jar before building picard.jar
3053 (("name=\"picard-jar\" depends=\"" line)
3054 (string-append line "picard-lib-jar, ")))
3055 #t))))
3056 (build-system ant-build-system)
3057 (arguments
3058 `(#:build-target "picard-jar"
3059 #:test-target "test"
3060 ;; Tests require jacoco:coverage.
3061 #:tests? #f
3062 #:make-flags
3063 (list (string-append "-Dhtsjdk_lib_dir="
3064 (assoc-ref %build-inputs "java-htsjdk")
3065 "/share/java/htsjdk/")
3066 "-Dhtsjdk-classes=dist/tmp"
3067 (string-append "-Dhtsjdk-version="
3068 ,(package-version java-htsjdk)))
3069 #:jdk ,icedtea-8
3070 #:phases
3071 (modify-phases %standard-phases
3072 (add-after 'unpack 'use-our-htsjdk
3073 (lambda* (#:key inputs #:allow-other-keys)
3074 (substitute* "build.xml"
3075 (("\\$\\{htsjdk\\}/lib")
3076 (string-append (assoc-ref inputs "java-htsjdk")
3077 "/share/java/htsjdk/")))
3078 #t))
3079 (add-after 'unpack 'make-test-target-independent
3080 (lambda* (#:key inputs #:allow-other-keys)
3081 (substitute* "build.xml"
3082 (("name=\"test\" depends=\"compile, ")
3083 "name=\"test\" depends=\""))
3084 #t))
3085 (replace 'install (install-jars "dist")))))
3086 (inputs
3087 `(("java-htsjdk" ,java-htsjdk)
3088 ("java-guava" ,java-guava)))
3089 (native-inputs
3090 `(("java-testng" ,java-testng)))
3091 (home-page "http://broadinstitute.github.io/picard/")
3092 (synopsis "Tools for manipulating high-throughput sequencing data and formats")
3093 (description "Picard is a set of Java command line tools for manipulating
3094high-throughput sequencing (HTS) data and formats. Picard is implemented
3095using the HTSJDK Java library to support accessing file formats that are
3096commonly used for high-throughput sequencing data such as SAM, BAM, CRAM and
3097VCF.")
3098 (license license:expat)))
3099
d7f24778
RW		 3100;; This is the last version of Picard to provide net.sf.samtools
3101(define-public java-picard-1.113
3102 (package (inherit java-picard)
3103 (name "java-picard")
3104 (version "1.113")
3105 (source (origin
3106 (method git-fetch)
3107 (uri (git-reference
3108 (url "https://github.com/broadinstitute/picard.git")
3109 (commit version)))
3110 (file-name (string-append "java-picard-" version "-checkout"))
3111 (sha256
3112 (base32
3113 "0lkpvin2fz3hhly4l02kk56fqy8lmlgyzr9kmvljk6ry6l1hw973"))
3114 (modules '((guix build utils)))
3115 (snippet
3116 '(begin
3117 ;; Delete pre-built binaries.
3118 (delete-file-recursively "lib")
3119 (mkdir-p "lib")
3120 #t))))
3121 (build-system ant-build-system)
3122 (arguments
3123 `(#:build-target "picard-jar"
3124 #:test-target "test"
3125 ;; FIXME: the class path at test time is wrong.
3126 ;; [testng] Error: A JNI error has occurred, please check your installation and try again
3127 ;; [testng] Exception in thread "main" java.lang.NoClassDefFoundError: com/beust/jcommander/ParameterException
3128 #:tests? #f
3129 #:jdk ,icedtea-8
3130 ;; This is only used for tests.
3131 #:make-flags
3132 (list "-Dsamjdk.intel_deflater_so_path=lib/jni/libIntelDeflater.so")
3133 #:phases
3134 (modify-phases %standard-phases
3135 ;; Do not use bundled ant bzip2.
3136 (add-after 'unpack 'use-ant-bzip
3137 (lambda* (#:key inputs #:allow-other-keys)
3138 (substitute* "build.xml"
3139 (("\\$\\{lib\\}/apache-ant-1.8.2-bzip2.jar")
3140 (string-append (assoc-ref inputs "ant")
3141 "/lib/ant.jar")))
3142 #t))
3143 (add-after 'unpack 'make-test-target-independent
3144 (lambda* (#:key inputs #:allow-other-keys)
3145 (substitute* "build.xml"
3146 (("name=\"test\" depends=\"compile, ")
3147 "name=\"test\" depends=\"compile-tests, ")
3148 (("name=\"compile\" depends=\"compile-src, compile-tests\"")
3149 "name=\"compile\" depends=\"compile-src\""))
3150 #t))
3151 (add-after 'unpack 'fix-deflater-path
3152 (lambda* (#:key outputs #:allow-other-keys)
3153 (substitute* "src/java/net/sf/samtools/Defaults.java"
3154 (("getStringProperty\\(\"intel_deflater_so_path\", null\\)")
3155 (string-append "getStringProperty(\"intel_deflater_so_path\", \""
3156 (assoc-ref outputs "out")
3157 "/lib/jni/libIntelDeflater.so"
3158 "\")")))
3159 #t))
3160 ;; Build the deflater library, because we've previously deleted the
3161 ;; pre-built one. This can only be built with access to the JDK
3162 ;; sources.
3163 (add-after 'build 'build-jni
3164 (lambda* (#:key inputs #:allow-other-keys)
3165 (mkdir-p "lib/jni")
3166 (mkdir-p "jdk-src")
3167 (and (zero? (system* "tar" "--strip-components=1" "-C" "jdk-src"
3168 "-xf" (assoc-ref inputs "jdk-src")))
3169 (zero? (system* "javah" "-jni"
3170 "-classpath" "classes"
3171 "-d" "lib/"
3172 "net.sf.samtools.util.zip.IntelDeflater"))
3173 (with-directory-excursion "src/c/inteldeflater"
3174 (zero? (system* "gcc" "-I../../../lib" "-I."
3175 (string-append "-I" (assoc-ref inputs "jdk")
3176 "/include/linux")
3177 "-I../../../jdk-src/src/share/native/common/"
3178 "-I../../../jdk-src/src/solaris/native/common/"
3179 "-c" "-O3" "-fPIC" "IntelDeflater.c"))
3180 (zero? (system* "gcc" "-shared"
3181 "-o" "../../../lib/jni/libIntelDeflater.so"
3182 "IntelDeflater.o" "-lz" "-lstdc++"))))))
3183 ;; We can only build everything else after building the JNI library.
3184 (add-after 'build-jni 'build-rest
3185 (lambda* (#:key make-flags #:allow-other-keys)
3186 (zero? (apply system* `("ant" "all" ,@make-flags)))))
3187 (add-before 'build 'set-JAVA6_HOME
3188 (lambda _
3189 (setenv "JAVA6_HOME" (getenv "JAVA_HOME"))
3190 #t))
3191 (replace 'install (install-jars "dist"))
3192 (add-after 'install 'install-jni-lib
3193 (lambda* (#:key outputs #:allow-other-keys)
3194 (let ((jni (string-append (assoc-ref outputs "out")
3195 "/lib/jni")))
3196 (mkdir-p jni)
3197 (install-file "lib/jni/libIntelDeflater.so" jni)
3198 #t))))))
3199 (inputs
3200 `(("java-snappy-1" ,java-snappy-1)
3201 ("java-commons-jexl-2" ,java-commons-jexl-2)
3202 ("java-cofoja" ,java-cofoja)
3203 ("ant" ,ant) ; for bzip2 support at runtime
3204 ("zlib" ,zlib)))
3205 (native-inputs
3206 `(("ant-apache-bcel" ,ant-apache-bcel)
3207 ("ant-junit" ,ant-junit)
3208 ("java-testng" ,java-testng)
3209 ("java-commons-bcel" ,java-commons-bcel)
3210 ("java-jcommander" ,java-jcommander)
3211 ("jdk" ,icedtea-8 "jdk")
3212 ("jdk-src" ,(car (assoc-ref (package-native-inputs icedtea-8) "jdk-drop")))))))
3213
e7c09730
RW		 3214(define-public htslib
3215 (package
3216 (name "htslib")
ddf38ece 3217 (version "1.6")
e7c09730
RW		 3218 (source (origin
3219 (method url-fetch)
3220 (uri (string-append
3221 "https://github.com/samtools/htslib/releases/download/"
3222 version "/htslib-" version ".tar.bz2"))
3223 (sha256
3224 (base32
ddf38ece 3225 "1jsca3hg4rbr6iqq6imkj4lsvgl8g9768bcmny3hlff2w25vx24m"))))
e7c09730
RW		 3226 (build-system gnu-build-system)
3227 (arguments
3228 `(#:phases
3229 (modify-phases %standard-phases
3230 (add-after
3231 'unpack 'patch-tests
3232 (lambda _
3233 (substitute* "test/test.pl"
3234 (("/bin/bash") (which "bash")))
3235 #t)))))
3236 (inputs
a9e4a1e6
BW		 3237 `(("openssl" ,openssl)
3238 ("curl" ,curl)
3239 ("zlib" ,zlib)))
e7c09730
RW		 3240 (native-inputs
3241 `(("perl" ,perl)))
3242 (home-page "http://www.htslib.org")
3243 (synopsis "C library for reading/writing high-throughput sequencing data")
3244 (description
3245 "HTSlib is a C library for reading/writing high-throughput sequencing
8057dee1
TGR		 3246data. It also provides the @command{bgzip}, @command{htsfile}, and
3247@command{tabix} utilities.")
e7c09730
RW		 3248 ;; Files under cram/ are released under the modified BSD license;
3249 ;; the rest is released under the Expat license
3250 (license (list license:expat license:bsd-3))))
3251
bca2c576
BW		 3252;; This package should be removed once no packages rely upon it.
3253(define htslib-1.3
3254 (package
3255 (inherit htslib)
3256 (version "1.3.1")
3257 (source (origin
3258 (method url-fetch)
3259 (uri (string-append
3260 "https://github.com/samtools/htslib/releases/download/"
3261 version "/htslib-" version ".tar.bz2"))
3262 (sha256
3263 (base32
3264 "1rja282fwdc25ql6izkhdyh8ppw8x2fs0w0js78zgkmqjlikmma9"))))))
3265
c4325f62
RW		 3266(define-public idr
3267 (package
3268 (name "idr")
aa33cc29 3269 (version "2.0.3")
c4325f62
RW		 3270 (source (origin
3271 (method url-fetch)
3272 (uri (string-append
3273 "https://github.com/nboley/idr/archive/"
3274 version ".tar.gz"))
3275 (file-name (string-append name "-" version ".tar.gz"))
3276 (sha256
3277 (base32
aa33cc29
RW		 3278 "1rjdly6daslw66r43g9md8znizlscn1sphycqyldzsidkc4vxqv3"))
3279 ;; Delete generated C code.
3280 (snippet
3281 '(begin (delete-file "idr/inv_cdf.c") #t))))
c4325f62 3282 (build-system python-build-system)
aa33cc29
RW		 3283 ;; There is only one test ("test_inv_cdf.py") and it tests features that
3284 ;; are no longer part of this package. It also asserts False, which
3285 ;; causes the tests to always fail.
3286 (arguments `(#:tests? #f))
b7a820fc 3287 (propagated-inputs
c4325f62 3288 `(("python-scipy" ,python-scipy)
b7a820fc 3289 ("python-sympy" ,python-sympy)
c4325f62
RW		 3290 ("python-numpy" ,python-numpy)
3291 ("python-matplotlib" ,python-matplotlib)))
3292 (native-inputs
f3b98f4f 3293 `(("python-cython" ,python-cython)))
c4325f62
RW		 3294 (home-page "https://github.com/nboley/idr")
3295 (synopsis "Tool to measure the irreproducible discovery rate (IDR)")
3296 (description
3297 "The IDR (Irreproducible Discovery Rate) framework is a unified approach
3298to measure the reproducibility of findings identified from replicate
3299experiments and provide highly stable thresholds based on reproducibility.")
40590caf 3300 (license license:gpl2+)))
c4325f62 3301
43c565d2
RW		 3302(define-public jellyfish
3303 (package
3304 (name "jellyfish")
117d8cc4 3305 (version "2.2.7")
43c565d2
RW		 3306 (source (origin
3307 (method url-fetch)
3308 (uri (string-append "https://github.com/gmarcais/Jellyfish/"
3309 "releases/download/v" version
3310 "/jellyfish-" version ".tar.gz"))
3311 (sha256
3312 (base32
117d8cc4 3313 "1a1iwq9pq54k2m9ypvwl5s0bqfl64gwh9dx5af9i382ajas2016q"))))
43c565d2
RW		 3314 (build-system gnu-build-system)
3315 (outputs '("out" ;for library
3316 "ruby" ;for Ruby bindings
3317 "python")) ;for Python bindings
3318 (arguments
3319 `(#:configure-flags
3320 (list (string-append "--enable-ruby-binding="
3321 (assoc-ref %outputs "ruby"))
3322 (string-append "--enable-python-binding="
3323 (assoc-ref %outputs "python")))
3324 #:phases
3325 (modify-phases %standard-phases
3326 (add-before 'check 'set-SHELL-variable
3327 (lambda _
3328 ;; generator_manager.hpp either uses /bin/sh or $SHELL
3329 ;; to run tests.
3330 (setenv "SHELL" (which "bash"))
3331 #t)))))
3332 (native-inputs
3333 `(("bc" ,bc)
3334 ("time" ,time)
3335 ("ruby" ,ruby)
117d8cc4
RW		 3336 ("python" ,python-2)
3337 ("pkg-config" ,pkg-config)))
3338 (inputs
3339 `(("htslib" ,htslib)))
43c565d2
RW		 3340 (synopsis "Tool for fast counting of k-mers in DNA")
3341 (description
3342 "Jellyfish is a tool for fast, memory-efficient counting of k-mers in
3343DNA. A k-mer is a substring of length k, and counting the occurrences of all
3344such substrings is a central step in many analyses of DNA sequence. Jellyfish
3345is a command-line program that reads FASTA and multi-FASTA files containing
3346DNA sequences. It outputs its k-mer counts in a binary format, which can be
3347translated into a human-readable text format using the @code{jellyfish dump}
3348command, or queried for specific k-mers with @code{jellyfish query}.")
3349 (home-page "http://www.genome.umd.edu/jellyfish.html")
6e8faf77
EF		 3350 ;; From their website: JELLYFISH runs on 64-bit Intel-compatible processors
3351 (supported-systems '("x86_64-linux"))
43c565d2
RW		 3352 ;; The combined work is published under the GPLv3 or later. Individual
3353 ;; files such as lib/jsoncpp.cpp are released under the Expat license.
3354 (license (list license:gpl3+ license:expat))))
3355
94ff3157
BW		 3356(define-public khmer
3357 (package
3358 (name "khmer")
3359 (version "2.0")
3360 (source
3361 (origin
3362 (method url-fetch)
3363 (uri (pypi-uri "khmer" version))
3364 (sha256
3365 (base32
3366 "0wb05shqh77v00256qlm68vbbx3kl76fyzihszbz5nhanl4ni33a"))
3367 (patches (search-patches "khmer-use-libraries.patch"))))
3368 (build-system python-build-system)
3369 (arguments
3370 `(#:phases
3371 (modify-phases %standard-phases
3372 (add-after 'unpack 'set-paths
3373 (lambda* (#:key inputs outputs #:allow-other-keys)
3374 ;; Delete bundled libraries.
3375 (delete-file-recursively "third-party/zlib")
3376 (delete-file-recursively "third-party/bzip2")
3377 ;; Replace bundled seqan.
3378 (let* ((seqan-all "third-party/seqan")
3379 (seqan-include (string-append
3380 seqan-all "/core/include")))
3381 (delete-file-recursively seqan-all)
3382 (copy-recursively (string-append (assoc-ref inputs "seqan")
3383 "/include/seqan")
3384 (string-append seqan-include "/seqan")))
3385 ;; We do not replace the bundled MurmurHash as the canonical
3386 ;; repository for this code 'SMHasher' is unsuitable for
3387 ;; providing a library. See
3388 ;; https://lists.gnu.org/archive/html/guix-devel/2016-06/msg00977.html
3389 #t))
3390 (add-after 'unpack 'set-cc
3391 (lambda _
3392 (setenv "CC" "gcc")
3393 #t))
3394 ;; It is simpler to test after installation.
3395 (delete 'check)
3396 (add-after 'install 'post-install-check
3397 (lambda* (#:key inputs outputs #:allow-other-keys)
3398 (let ((out (assoc-ref outputs "out")))
3399 (setenv "PATH"
3400 (string-append
3401 (getenv "PATH")
3402 ":"
3403 (assoc-ref outputs "out")
3404 "/bin"))
3405 (setenv "PYTHONPATH"
3406 (string-append
3407 (getenv "PYTHONPATH")
3408 ":"
3409 out
3410 "/lib/python"
3411 (string-take (string-take-right
3412 (assoc-ref inputs "python") 5) 3)
3413 "/site-packages"))
3414 (with-directory-excursion "build"
3415 (zero? (system* "nosetests" "khmer" "--attr"
3416 "!known_failing")))))))))
3417 (native-inputs
3418 `(("seqan" ,seqan)
3419 ("python-nose" ,python-nose)))
3420 (inputs
3421 `(("zlib" ,zlib)
3422 ("bzip2" ,bzip2)
3423 ("python-screed" ,python-screed)
cf1d5814
BW		 3424 ("python-bz2file" ,python-bz2file)
3425 ;; Tests fail when gcc-5 is used for compilation. Use gcc-4.9 at least
3426 ;; until the next version of khmer (likely 2.1) is released.
3427 ("gcc" ,gcc-4.9)))
94ff3157
BW		 3428 (home-page "https://khmer.readthedocs.org/")
3429 (synopsis "K-mer counting, filtering and graph traversal library")
3430 (description "The khmer software is a set of command-line tools for
3431working with DNA shotgun sequencing data from genomes, transcriptomes,
3432metagenomes and single cells. Khmer can make de novo assemblies faster, and
3433sometimes better. Khmer can also identify and fix problems with shotgun
3434data.")
8157af2e
EF		 3435 ;; When building on i686, armhf and mips64el, we get the following error:
3436 ;; error: ['khmer', 'khmer.tests', 'oxli'] require 64-bit operating system
3df57b3a 3437 (supported-systems '("x86_64-linux" "aarch64-linux"))
94ff3157
BW		 3438 (license license:bsd-3)))
3439
b9a601d9
RJ		 3440(define-public kaiju
3441 (package
3442 (name "kaiju")
3443 (version "1.5.0")
3444 (source (origin
3445 (method url-fetch)
3446 (uri (string-append
3447 "https://github.com/bioinformatics-centre/kaiju/archive/v"
3448 version ".tar.gz"))
3449 (file-name (string-append name "-" version ".tar.gz"))
3450 (sha256
3451 (base32
3452 "0afbfalfw9y39bkwnqjrh9bghs118ws1pzj5h8l0nblgn3mbjdks"))))
3453 (build-system gnu-build-system)
3454 (arguments
3455 `(#:tests? #f ; There are no tests.
3456 #:phases
3457 (modify-phases %standard-phases
3458 (delete 'configure)
3459 (add-before 'build 'move-to-src-dir
3460 (lambda _ (chdir "src") #t))
3461 (replace 'install
3462 (lambda* (#:key inputs outputs #:allow-other-keys)
3463 (let ((bin (string-append (assoc-ref outputs "out") "/bin")))
3464 (mkdir-p bin)
3465 (chdir "..")
3466 (copy-recursively "bin" bin)
3467 (copy-recursively "util" bin))
3468 #t)))))
3469 (inputs
3470 `(("perl" ,perl)))
3471 (home-page "http://kaiju.binf.ku.dk/")
3472 (synopsis "Fast and sensitive taxonomic classification for metagenomics")
3473 (description "Kaiju is a program for sensitive taxonomic classification
3474of high-throughput sequencing reads from metagenomic whole genome sequencing
3475experiments.")
3476 (license license:gpl3+)))
3477
d57e6d0f
RW		 3478(define-public macs
3479 (package
3480 (name "macs")
0d0bcaa0 3481 (version "2.1.0.20151222")
d57e6d0f
RW		 3482 (source (origin
3483 (method url-fetch)
43ec07f1 3484 (uri (pypi-uri "MACS2" version))
d57e6d0f
RW		 3485 (sha256
3486 (base32
0d0bcaa0 3487 "1r2hcz6irhcq7lwbafjks98jbn34hv05avgbdjnp6w6mlfjkf8x5"))))
d57e6d0f
RW		 3488 (build-system python-build-system)
3489 (arguments
3490 `(#:python ,python-2 ; only compatible with Python 2.7
3491 #:tests? #f)) ; no test target
3492 (inputs
3493 `(("python-numpy" ,python2-numpy)))
7bf837fd 3494 (home-page "https://github.com/taoliu/MACS/")
d57e6d0f
RW		 3495 (synopsis "Model based analysis for ChIP-Seq data")
3496 (description
3497 "MACS is an implementation of a ChIP-Seq analysis algorithm for
3498identifying transcript factor binding sites named Model-based Analysis of
3499ChIP-Seq (MACS). MACS captures the influence of genome complexity to evaluate
3500the significance of enriched ChIP regions and it improves the spatial
3501resolution of binding sites through combining the information of both
3502sequencing tag position and orientation.")
3503 (license license:bsd-3)))
3504
41ddebdd
BW		 3505(define-public mafft
3506 (package
3507 (name "mafft")
3146f22d 3508 (version "7.313")
41ddebdd
BW		 3509 (source (origin
3510 (method url-fetch)
3511 (uri (string-append
3146f22d 3512 "https://mafft.cbrc.jp/alignment/software/mafft-" version
41ddebdd
BW		 3513 "-without-extensions-src.tgz"))
3514 (file-name (string-append name "-" version ".tgz"))
3515 (sha256
3516 (base32
3146f22d 3517 "0r83qmg2if8mi6jyx3xdf8ar2gcxl7r9nmj98jr7lxym97v61a2k"))))
41ddebdd
BW		 3518 (build-system gnu-build-system)
3519 (arguments
3520 `(#:tests? #f ; no automated tests, though there are tests in the read me
3521 #:make-flags (let ((out (assoc-ref %outputs "out")))
3522 (list (string-append "PREFIX=" out)
3523 (string-append "BINDIR="
3524 (string-append out "/bin"))))
3525 #:phases
3526 (modify-phases %standard-phases
3527 (add-after 'unpack 'enter-dir
101e8f71 3528 (lambda _ (chdir "core") #t))
41ddebdd 3529 (add-after 'enter-dir 'patch-makefile
101e8f71
BW		 3530 (lambda _
3531 ;; on advice from the MAFFT authors, there is no need to
3532 ;; distribute mafft-profile, mafft-distance, or
3533 ;; mafft-homologs.rb as they are too "specialised".
3534 (substitute* "Makefile"
3535 ;; remove mafft-homologs.rb from SCRIPTS
3536 (("^SCRIPTS = mafft mafft-homologs.rb")
3537 "SCRIPTS = mafft")
3538 ;; remove mafft-homologs from MANPAGES
3539 (("^MANPAGES = mafft.1 mafft-homologs.1")
3540 "MANPAGES = mafft.1")
3541 ;; remove mafft-distance from PROGS
3542 (("^PROGS = dvtditr dndfast7 dndblast sextet5 mafft-distance")
3543 "PROGS = dvtditr dndfast7 dndblast sextet5")
3544 ;; remove mafft-profile from PROGS
3545 (("splittbfast disttbfast tbfast mafft-profile 2cl mccaskillwrap")
3546 "splittbfast disttbfast tbfast f2cl mccaskillwrap")
3547 (("^rm -f mafft-profile mafft-profile.exe") "#")
3548 (("^rm -f mafft-distance mafft-distance.exe") ")#")
3549 ;; do not install MAN pages in libexec folder
3550 (("^\t\\$\\(INSTALL\\) -m 644 \\$\\(MANPAGES\\) \
41ddebdd 3551\\$\\(DESTDIR\\)\\$\\(LIBDIR\\)") "#"))
101e8f71 3552 #t))
02f35bb5
BW		 3553 (add-after 'enter-dir 'patch-paths
3554 (lambda* (#:key inputs #:allow-other-keys)
3555 (substitute* '("pairash.c"
3556 "mafft.tmpl")
3557 (("perl") (which "perl"))
3558 (("([\"`| ])awk" _ prefix)
3559 (string-append prefix (which "awk")))
3560 (("grep") (which "grep")))
3561 #t))
101e8f71
BW		 3562 (delete 'configure)
3563 (add-after 'install 'wrap-programs
3564 (lambda* (#:key outputs #:allow-other-keys)
3565 (let* ((out (assoc-ref outputs "out"))
3566 (bin (string-append out "/bin"))
3567 (path (string-append
3568 (assoc-ref %build-inputs "coreutils") "/bin:")))
3569 (for-each (lambda (file)
3570 (wrap-program file
3571 `("PATH" ":" prefix (,path))))
3572 (find-files bin)))
3573 #t)))))
41ddebdd 3574 (inputs
02f35bb5 3575 `(("perl" ,perl)
71461f88 3576 ("ruby" ,ruby)
02f35bb5 3577 ("gawk" ,gawk)
101e8f71
BW		 3578 ("grep" ,grep)
3579 ("coreutils" ,coreutils)))
41ddebdd
BW		 3580 (home-page "http://mafft.cbrc.jp/alignment/software/")
3581 (synopsis "Multiple sequence alignment program")
3582 (description
3583 "MAFFT offers a range of multiple alignment methods for nucleotide and
3584protein sequences. For instance, it offers L-INS-i (accurate; for alignment
3585of <~200 sequences) and FFT-NS-2 (fast; for alignment of <~30,000
3586sequences).")
3587 (license (license:non-copyleft
3588 "http://mafft.cbrc.jp/alignment/software/license.txt"
3589 "BSD-3 with different formatting"))))
8fd790eb 3590
84be3b99
MB		 3591(define-public mash
3592 (package
3593 (name "mash")
3594 (version "1.1.1")
3595 (source (origin
3596 (method url-fetch)
3597 (uri (string-append
3598 "https://github.com/marbl/mash/archive/v"
3599 version ".tar.gz"))
3600 (file-name (string-append name "-" version ".tar.gz"))
3601 (sha256
3602 (base32
3603 "08znbvqq5xknfhmpp3wcj574zvi4p7i8zifi67c9qw9a6ikp42fj"))
3604 (modules '((guix build utils)))
3605 (snippet
3606 ;; Delete bundled kseq.
3607 ;; TODO: Also delete bundled murmurhash and open bloom filter.
3608 '(delete-file "src/mash/kseq.h"))))
3609 (build-system gnu-build-system)
3610 (arguments
3611 `(#:tests? #f ; No tests.
3612 #:configure-flags
3613 (list
3614 (string-append "--with-capnp=" (assoc-ref %build-inputs "capnproto"))
3615 (string-append "--with-gsl=" (assoc-ref %build-inputs "gsl")))
3616 #:make-flags (list "CC=gcc")
3617 #:phases
3618 (modify-phases %standard-phases
3619 (add-after 'unpack 'fix-includes
3620 (lambda _
3621 (substitute* '("src/mash/Sketch.cpp" "src/mash/CommandFind.cpp")
3622 (("^#include \"kseq\\.h\"")
3623 "#include \"htslib/kseq.h\""))
3624 #t))
d10092b8 3625 (add-after 'fix-includes 'autoconf
84be3b99
MB		 3626 (lambda _ (zero? (system* "autoconf")))))))
3627 (native-inputs
3628 `(("autoconf" ,autoconf)
3629 ;; Capnproto and htslib are statically embedded in the final
3630 ;; application. Therefore we also list their licenses, below.
3631 ("capnproto" ,capnproto)
3632 ("htslib" ,htslib)))
3633 (inputs
3634 `(("gsl" ,gsl)
3635 ("zlib" ,zlib)))
3636 (supported-systems '("x86_64-linux"))
3637 (home-page "https://mash.readthedocs.io")
3638 (synopsis "Fast genome and metagenome distance estimation using MinHash")
3639 (description "Mash is a fast sequence distance estimator that uses the
3640MinHash algorithm and is designed to work with genomes and metagenomes in the
3641form of assemblies or reads.")
3642 (license (list license:bsd-3 ; Mash
3643 license:expat ; HTSlib and capnproto
3644 license:public-domain ; MurmurHash 3
3645 license:cpl1.0)))) ; Open Bloom Filter
3646
8fd790eb 3647(define-public metabat
f3f68a44
BW		 3648 (package
3649 (name "metabat")
25bd1fc1 3650 (version "2.12.1")
f3f68a44
BW		 3651 (source
3652 (origin
25bd1fc1
BW		 3653 (method url-fetch)
3654 (uri (string-append "https://bitbucket.org/berkeleylab/metabat/get/v"
3655 version ".tar.gz"))
3656 (file-name (string-append name "-" version ".tar.gz"))
f3f68a44
BW		 3657 (sha256
3658 (base32
25bd1fc1
BW		 3659 "1hmvdalz3zj5sqqklg0l4npjdv37cv2hsdi1al9iby2ndxjs1b73"))
3660 (patches (search-patches "metabat-fix-compilation.patch"))))
9364a520 3661 (build-system scons-build-system)
8fd790eb 3662 (arguments
9364a520
AI		 3663 `(#:scons ,scons-python2
3664 #:scons-flags
3665 (list (string-append "PREFIX=" (assoc-ref %outputs "out"))
3666 (string-append "BOOST_ROOT=" (assoc-ref %build-inputs "boost")))
3667 #:tests? #f ;; Tests are run during the build phase.
3668 #:phases
8fd790eb
BW		 3669 (modify-phases %standard-phases
3670 (add-after 'unpack 'fix-includes
45469ebe
BW		 3671 (lambda _
3672 (substitute* "src/BamUtils.h"
3673 (("^#include \"bam/bam\\.h\"")
3674 "#include \"samtools/bam.h\"")
3675 (("^#include \"bam/sam\\.h\"")
3676 "#include \"samtools/sam.h\""))
3677 (substitute* "src/KseqReader.h"
3678 (("^#include \"bam/kseq\\.h\"")
3679 "#include \"htslib/kseq.h\""))
3680 #t))
8fd790eb 3681 (add-after 'unpack 'fix-scons
f3f68a44
BW		 3682 (lambda* (#:key inputs #:allow-other-keys)
3683 (substitute* "SConstruct"
3684 (("^htslib_dir += 'samtools'")
3685 (string-append "htslib_dir = '"
3686 (assoc-ref inputs "htslib")
3687 "'"))
3688 (("^samtools_dir = 'samtools'")
3689 (string-append "samtools_dir = '"
3690 (assoc-ref inputs "samtools")
3691 "'"))
3692 (("^findStaticOrShared\\('bam', hts_lib")
3693 (string-append "findStaticOrShared('bam', '"
3694 (assoc-ref inputs "samtools")
3695 "/lib'"))
3696 ;; Do not distribute README.
3697 (("^env\\.Install\\(idir_prefix, 'README\\.md'\\)") ""))
9364a520 3698 #t)))))
8fd790eb
BW		 3699 (inputs
3700 `(("zlib" ,zlib)
3701 ("perl" ,perl)
3702 ("samtools" ,samtools)
3703 ("htslib" ,htslib)
3704 ("boost" ,boost)))
8fd790eb
BW		 3705 (home-page "https://bitbucket.org/berkeleylab/metabat")
3706 (synopsis
3707 "Reconstruction of single genomes from complex microbial communities")
3708 (description
3709 "Grouping large genomic fragments assembled from shotgun metagenomic
3710sequences to deconvolute complex microbial communities, or metagenome binning,
3711enables the study of individual organisms and their interactions. MetaBAT is
3712an automated metagenome binning software, which integrates empirical
3713probabilistic distances of genome abundance and tetranucleotide frequency.")
d931a4bb
EF		 3714 ;; The source code contains inline assembly.
3715 (supported-systems '("x86_64-linux" "i686-linux"))
f3f68a44
BW		 3716 (license (license:non-copyleft "file://license.txt"
3717 "See license.txt in the distribution."))))
8fd790eb 3718
318c0aee
MB		 3719(define-public minced
3720 (package
3721 (name "minced")
3722 (version "0.2.0")
3723 (source (origin
3724 (method url-fetch)
3725 (uri (string-append
3726 "https://github.com/ctSkennerton/minced/archive/"
3727 version ".tar.gz"))
3728 (file-name (string-append name "-" version ".tar.gz"))
3729 (sha256
3730 (base32
3731 "0wxmlsapxfpxfd3ps9636h7i2xy6la8i42mwh0j2lsky63h63jp1"))))
3732 (build-system gnu-build-system)
3733 (arguments
3734 `(#:test-target "test"
3735 #:phases
3736 (modify-phases %standard-phases
3737 (delete 'configure)
3738 (add-before 'check 'fix-test
3739 (lambda _
3740 ;; Fix test for latest version.
3741 (substitute* "t/Aquifex_aeolicus_VF5.expected"
3742 (("minced:0.1.6") "minced:0.2.0"))
3743 #t))
3744 (replace 'install ; No install target.
3745 (lambda* (#:key inputs outputs #:allow-other-keys)
3746 (let* ((out (assoc-ref outputs "out"))
3747 (bin (string-append out "/bin"))
3748 (wrapper (string-append bin "/minced")))
3749 ;; Minced comes with a wrapper script that tries to figure out where
3750 ;; it is located before running the JAR. Since these paths are known
3751 ;; to us, we build our own wrapper to avoid coreutils dependency.
3752 (install-file "minced.jar" bin)
3753 (with-output-to-file wrapper
3754 (lambda _
3755 (display
3756 (string-append
3757 "#!" (assoc-ref inputs "bash") "/bin/sh\n\n"
3758 (assoc-ref inputs "jre") "/bin/java -jar "
3759 bin "/minced.jar \"$@\"\n"))))
3760 (chmod wrapper #o555)))))))
3761 (native-inputs
3762 `(("jdk" ,icedtea "jdk")))
3763 (inputs
3764 `(("bash" ,bash)
3765 ("jre" ,icedtea "out")))
3766 (home-page "https://github.com/ctSkennerton/minced")
3767 (synopsis "Mining CRISPRs in Environmental Datasets")
3768 (description
3769 "MinCED is a program to find Clustered Regularly Interspaced Short
3770Palindromic Repeats (CRISPRs) in DNA sequences. It can be used for
3771unassembled metagenomic reads, but is mainly designed for full genomes and
3772assembled metagenomic sequence.")
3773 (license license:gpl3+)))
3774
ddd82e0e
RW		 3775(define-public miso
3776 (package
3777 (name "miso")
ce4dfde0 3778 (version "0.5.4")
ddd82e0e
RW		 3779 (source (origin
3780 (method url-fetch)
34260a10 3781 (uri (pypi-uri "misopy" version))
ddd82e0e
RW		 3782 (sha256
3783 (base32
ce4dfde0 3784 "1z3x0vd8ma7pdrnywj7i3kgwl89sdkwrrn62zl7r5calqaq2hyip"))
ddd82e0e 3785 (modules '((guix build utils)))
ddd82e0e
RW		 3786 (snippet
3787 '(substitute* "setup.py"
0ec8b206
RW		 3788 ;; Use setuptools, or else the executables are not
3789 ;; installed.
3790 (("distutils.core") "setuptools")
3791 ;; use "gcc" instead of "cc" for compilation
ddd82e0e
RW		 3792 (("^defines")
3793 "cc.set_executables(
3794compiler='gcc',
3795compiler_so='gcc',
3796linker_exe='gcc',
3797linker_so='gcc -shared'); defines")))))
3798 (build-system python-build-system)
3799 (arguments
3800 `(#:python ,python-2 ; only Python 2 is supported
3801 #:tests? #f)) ; no "test" target
3802 (inputs
3803 `(("samtools" ,samtools)
3804 ("python-numpy" ,python2-numpy)
3805 ("python-pysam" ,python2-pysam)
3806 ("python-scipy" ,python2-scipy)
3807 ("python-matplotlib" ,python2-matplotlib)))
3808 (native-inputs
f3b98f4f
HG		 3809 `(("python-mock" ,python2-mock) ;for tests
3810 ("python-pytz" ,python2-pytz))) ;for tests
ddd82e0e
RW		 3811 (home-page "http://genes.mit.edu/burgelab/miso/index.html")
3812 (synopsis "Mixture of Isoforms model for RNA-Seq isoform quantitation")
3813 (description
3814 "MISO (Mixture-of-Isoforms) is a probabilistic framework that quantitates
3815the expression level of alternatively spliced genes from RNA-Seq data, and
3816identifies differentially regulated isoforms or exons across samples. By
3817modeling the generative process by which reads are produced from isoforms in
3818RNA-Seq, the MISO model uses Bayesian inference to compute the probability
3819that a read originated from a particular isoform.")
3820 (license license:gpl2)))
3821
324efb88
BW		 3822(define-public muscle
3823 (package
3824 (name "muscle")
3825 (version "3.8.1551")
3826 (source (origin
3827 (method url-fetch/tarbomb)
324efb88
BW		 3828 (uri (string-append
3829 "http://www.drive5.com/muscle/muscle_src_"
3830 version ".tar.gz"))
3831 (sha256
3832 (base32
3833 "0bj8kj7sdizy3987zx6w7axihk40fk8rn76mpbqqjcnd64i5a367"))))
3834 (build-system gnu-build-system)
3835 (arguments
3836 `(#:make-flags (list "LDLIBS = -lm")
3837 #:phases
3838 (modify-phases %standard-phases
3839 (delete 'configure)
3840 (replace 'check
3841 ;; There are no tests, so just test if it runs.
3842 (lambda _ (zero? (system* "./muscle" "-version"))))
3843 (replace 'install
3844 (lambda* (#:key outputs #:allow-other-keys)
3845 (let* ((out (assoc-ref outputs "out"))
3846 (bin (string-append out "/bin")))
3847 (install-file "muscle" bin)))))))
3848 (home-page "http://www.drive5.com/muscle")
3849 (synopsis "Multiple sequence alignment program")
3850 (description
3851 "MUSCLE aims to be a fast and accurate multiple sequence alignment
3852program for nucleotide and protein sequences.")
3853 ;; License information found in 'muscle -h' and usage.cpp.
3854 (license license:public-domain)))
3855
99268755
BW		 3856(define-public newick-utils
3857 ;; There are no recent releases so we package from git.
3858 (let ((commit "da121155a977197cab9fbb15953ca1b40b11eb87"))
3859 (package
3860 (name "newick-utils")
3861 (version (string-append "1.6-1." (string-take commit 8)))
3862 (source (origin
3863 (method git-fetch)
3864 (uri (git-reference
3865 (url "https://github.com/tjunier/newick_utils.git")
3866 (commit commit)))
3867 (file-name (string-append name "-" version "-checkout"))
3868 (sha256
3869 (base32
3870 "1hkw21rq1mwf7xp0rmbb2gqc0i6p11108m69i7mr7xcjl268pxnb"))))
3871 (build-system gnu-build-system)
3872 (arguments
3873 `(#:phases
3874 (modify-phases %standard-phases
3875 (add-after 'unpack 'autoconf
3876 (lambda _ (zero? (system* "autoreconf" "-vif")))))))
3877 (inputs
3878 ;; XXX: TODO: Enable Lua and Guile bindings.
3879 ;; https://github.com/tjunier/newick_utils/issues/13
3880 `(("libxml2" ,libxml2)
3881 ("flex" ,flex)
3882 ("bison" ,bison)))
3883 (native-inputs
3884 `(("autoconf" ,autoconf)
3885 ("automake" ,automake)
3886 ("libtool" ,libtool)))
3887 (synopsis "Programs for working with newick format phylogenetic trees")
3888 (description
3889 "Newick-utils is a suite of utilities for processing phylogenetic trees
3890in Newick format. Functions include re-rooting, extracting subtrees,
3891trimming, pruning, condensing, drawing (ASCII graphics or SVG).")
3892 (home-page "https://github.com/tjunier/newick_utils")
3893 (license license:bsd-3))))
3894
1e44cf8b
BW		 3895(define-public orfm
3896 (package
3897 (name "orfm")
dfc83ead 3898 (version "0.7.1")
1e44cf8b
BW		 3899 (source (origin
3900 (method url-fetch)
3901 (uri (string-append
3902 "https://github.com/wwood/OrfM/releases/download/v"
3903 version "/orfm-" version ".tar.gz"))
3904 (sha256
3905 (base32
dfc83ead 3906 "16iigyr2gd8x0imzkk1dr3k5xsds9bpmwg31ayvjg0f4pir9rwqr"))))
1e44cf8b
BW		 3907 (build-system gnu-build-system)
3908 (inputs `(("zlib" ,zlib)))
6b6f7d6a
BW		 3909 (native-inputs
3910 `(("ruby-bio-commandeer" ,ruby-bio-commandeer)
3911 ("ruby-rspec" ,ruby-rspec)
3912 ("ruby" ,ruby)))
1e44cf8b
BW		 3913 (synopsis "Simple and not slow open reading frame (ORF) caller")
3914 (description
6b6f7d6a 3915 "An ORF caller finds stretches of DNA that, when translated, are not
1e44cf8b
BW		 3916interrupted by stop codons. OrfM finds and prints these ORFs.")
3917 (home-page "https://github.com/wwood/OrfM")
3918 (license license:lgpl3+)))
3919
c033f5d6
BW		 3920(define-public pplacer
3921 (let ((commit "g807f6f3"))
3922 (package
3923 (name "pplacer")
3924 ;; The commit should be updated with each version change.
3925 (version "1.1.alpha19")
3926 (source
3927 (origin
3928 (method url-fetch)
3929 (uri (string-append "https://github.com/matsen/pplacer/archive/v"
3930 version ".tar.gz"))
3931 (file-name (string-append name "-" version ".tar.gz"))
3932 (sha256
3933 (base32 "0z1lnd2s8sh6kpzg106wzbh2szw7h0hvq8syd5a6wv4rmyyz6x0f"))))
3934 (build-system ocaml-build-system)
3935 (arguments
3936 `(#:ocaml ,ocaml-4.01
3937 #:findlib ,ocaml4.01-findlib
3938 #:modules ((guix build ocaml-build-system)
3939 (guix build utils)
3940 (ice-9 ftw))
3941 #:phases
3942 (modify-phases %standard-phases
3943 (delete 'configure)
3944 (add-after 'unpack 'replace-bundled-cddlib
3945 (lambda* (#:key inputs #:allow-other-keys)
3946 (let* ((cddlib-src (assoc-ref inputs "cddlib-src"))
3947 (local-dir "cddlib_guix"))
3948 (mkdir local-dir)
3949 (with-directory-excursion local-dir
3950 (system* "tar" "xvf" cddlib-src))
3951 (let ((cddlib-src-folder
3952 (string-append local-dir "/"
3953 (list-ref (scandir local-dir) 2)
3954 "/lib-src")))
3955 (for-each
3956 (lambda (file)
3957 (copy-file file
3958 (string-append "cdd_src/" (basename file))))
3959 (find-files cddlib-src-folder ".*[ch]$")))
3960 #t)))
3961 (add-after 'unpack 'fix-makefile
3962 (lambda _
3963 ;; Remove system calls to 'git'.
3964 (substitute* "Makefile"
3965 (("^DESCRIPT:=pplacer-.*")
3966 (string-append
3967 "DESCRIPT:=pplacer-$(shell uname)-v" ,version "\n")))
3968 (substitute* "myocamlbuild.ml"
3969 (("git describe --tags --long .*\\\" with")
3970 (string-append
3971 "echo -n v" ,version "-" ,commit "\" with")))
3972 #t))
3973 (replace 'install
3974 (lambda* (#:key outputs #:allow-other-keys)
3975 (let* ((out (assoc-ref outputs "out"))
3976 (bin (string-append out "/bin")))
3977 (copy-recursively "bin" bin))
3978 #t)))))
3979 (native-inputs
3980 `(("zlib" ,zlib)
3981 ("gsl" ,gsl)
3982 ("ocaml-ounit" ,ocaml4.01-ounit)
3983 ("ocaml-batteries" ,ocaml4.01-batteries)
3984 ("ocaml-camlzip" ,ocaml4.01-camlzip)
3985 ("ocaml-csv" ,ocaml4.01-csv)
3986 ("ocaml-sqlite3" ,ocaml4.01-sqlite3)
3987 ("ocaml-xmlm" ,ocaml4.01-xmlm)
3988 ("ocaml-mcl" ,ocaml4.01-mcl)
3989 ("ocaml-gsl" ,ocaml4.01-gsl)
3990 ("cddlib-src" ,(package-source cddlib))))
3991 (propagated-inputs
3992 `(("pplacer-scripts" ,pplacer-scripts)))
3993 (synopsis "Phylogenetic placement of biological sequences")
3994 (description
3995 "Pplacer places query sequences on a fixed reference phylogenetic tree
3996to maximize phylogenetic likelihood or posterior probability according to a
3997reference alignment. Pplacer is designed to be fast, to give useful
3998information about uncertainty, and to offer advanced visualization and
3999downstream analysis.")
4000 (home-page "http://matsen.fhcrc.org/pplacer")
4001 (license license:gpl3))))
4002
4003;; This package is installed alongside 'pplacer'. It is a separate package so
4004;; that it can use the python-build-system for the scripts that are
4005;; distributed alongside the main OCaml binaries.
4006(define pplacer-scripts
4007 (package
4008 (inherit pplacer)
4009 (name "pplacer-scripts")
4010 (build-system python-build-system)
4011 (arguments
4012 `(#:python ,python-2
4013 #:phases
4014 (modify-phases %standard-phases
4015 (add-after 'unpack 'enter-scripts-dir
4016 (lambda _ (chdir "scripts")))
4017 (replace 'check
4018 (lambda _
4019 (zero? (system* "python" "-m" "unittest" "discover" "-v"))))
4020 (add-after 'install 'wrap-executables
4021 (lambda* (#:key inputs outputs #:allow-other-keys)
4022 (let* ((out (assoc-ref outputs "out"))
4023 (bin (string-append out "/bin")))
4024 (let ((path (string-append
4025 (assoc-ref inputs "hmmer") "/bin:"
4026 (assoc-ref inputs "infernal") "/bin")))
4027 (display path)
4028 (wrap-program (string-append bin "/refpkg_align.py")
4029 `("PATH" ":" prefix (,path))))
4030 (let ((path (string-append
4031 (assoc-ref inputs "hmmer") "/bin")))
4032 (wrap-program (string-append bin "/hrefpkg_query.py")
4033 `("PATH" ":" prefix (,path)))))
4034 #t)))))
4035 (inputs
4036 `(("infernal" ,infernal)
4037 ("hmmer" ,hmmer)))
4038 (propagated-inputs
4039 `(("python-biopython" ,python2-biopython)
4040 ("taxtastic" ,taxtastic)))
4041 (synopsis "Pplacer Python scripts")))
4042
19ee9201
RW		 4043(define-public python2-pbcore
4044 (package
4045 (name "python2-pbcore")
e301bfc8 4046 (version "1.2.10")
19ee9201
RW		 4047 (source (origin
4048 (method url-fetch)
ddb83129 4049 (uri (pypi-uri "pbcore" version))
19ee9201
RW		 4050 (sha256
4051 (base32
e301bfc8 4052 "1kjmv891d6qbpp4shhhvkl02ff4q5xlpnls2513sm2cjcrs52f1i"))))
19ee9201
RW		 4053 (build-system python-build-system)
4054 (arguments `(#:python ,python-2)) ; pbcore requires Python 2.7
de5bc890 4055 (propagated-inputs
19ee9201
RW		 4056 `(("python-cython" ,python2-cython)
4057 ("python-numpy" ,python2-numpy)
4058 ("python-pysam" ,python2-pysam)
4059 ("python-h5py" ,python2-h5py)))
4060 (native-inputs
de5bc890
HG		 4061 `(("python-nose" ,python2-nose)
4062 ("python-sphinx" ,python2-sphinx)
4063 ("python-pyxb" ,python2-pyxb)))
19ee9201
RW		 4064 (home-page "http://pacificbiosciences.github.io/pbcore/")
4065 (synopsis "Library for reading and writing PacBio data files")
4066 (description
4067 "The pbcore package provides Python APIs for interacting with PacBio data
4068files and writing bioinformatics applications.")
4069 (license license:bsd-3)))
4070
c61fe02c
RW		 4071(define-public python2-warpedlmm
4072 (package
4073 (name "python2-warpedlmm")
4074 (version "0.21")
4075 (source
4076 (origin
4077 (method url-fetch)
4078 (uri (string-append
4079 "https://pypi.python.org/packages/source/W/WarpedLMM/WarpedLMM-"
4080 version ".zip"))
4081 (sha256
4082 (base32
4083 "1agfz6zqa8nc6cw47yh0s3y14gkpa9wqazwcj7mwwj3ffnw39p3j"))))
4084 (build-system python-build-system)
4085 (arguments
54c85e12 4086 `(#:python ,python-2)) ; requires Python 2.7
c61fe02c
RW		 4087 (propagated-inputs
4088 `(("python-scipy" ,python2-scipy)
4089 ("python-numpy" ,python2-numpy)
4090 ("python-matplotlib" ,python2-matplotlib)
4091 ("python-fastlmm" ,python2-fastlmm)
4092 ("python-pandas" ,python2-pandas)
4093 ("python-pysnptools" ,python2-pysnptools)))
4094 (native-inputs
f3b98f4f 4095 `(("python-mock" ,python2-mock)
c61fe02c
RW		 4096 ("python-nose" ,python2-nose)
4097 ("unzip" ,unzip)))
4098 (home-page "https://github.com/PMBio/warpedLMM")
4099 (synopsis "Implementation of warped linear mixed models")
4100 (description
4101 "WarpedLMM is a Python implementation of the warped linear mixed model,
4102which automatically learns an optimal warping function (or transformation) for
4103the phenotype as it models the data.")
4104 (license license:asl2.0)))
4105
2c16316e 4106(define-public pbtranscript-tofu
698bd297 4107 (let ((commit "8f5467fe6a4472bcfb4226c8720993c8507adfe4"))
2c16316e
RW		 4108 (package
4109 (name "pbtranscript-tofu")
698bd297 4110 (version (string-append "2.2.3." (string-take commit 7)))
2c16316e
RW		 4111 (source (origin
4112 (method git-fetch)
4113 (uri (git-reference
4114 (url "https://github.com/PacificBiosciences/cDNA_primer.git")
4115 (commit commit)))
9a067efd 4116 (file-name (string-append name "-" version "-checkout"))
2c16316e
RW		 4117 (sha256
4118 (base32
9a067efd
RW		 4119 "1lgnpi35ihay42qx0b6yl3kkgra723i413j33kvs0kvs61h82w0f"))
4120 (modules '((guix build utils)))
4121 (snippet
4122 '(begin
4123 ;; remove bundled Cython sources
4124 (delete-file "pbtranscript-tofu/pbtranscript/Cython-0.20.1.tar.gz")
4125 #t))))
2c16316e
RW		 4126 (build-system python-build-system)
4127 (arguments
4128 `(#:python ,python-2
cdc2bb50
MB		 4129 ;; FIXME: Tests fail with "No such file or directory:
4130 ;; pbtools/pbtranscript/modified_bx_intervals/intersection_unique.so"
4131 #:tests? #f
2c16316e 4132 #:phases
9a067efd
RW		 4133 (modify-phases %standard-phases
4134 (add-after 'unpack 'enter-directory
4135 (lambda _
4136 (chdir "pbtranscript-tofu/pbtranscript/")
4137 #t))
4138 ;; With setuptools version 18.0 and later this setup.py hack causes
4139 ;; a build error, so we disable it.
4140 (add-after 'enter-directory 'patch-setuppy
4141 (lambda _
4142 (substitute* "setup.py"
4143 (("if 'setuptools.extension' in sys.modules:")
4144 "if False:"))
4145 #t)))))
2c16316e 4146 (inputs
9a067efd 4147 `(("python-numpy" ,python2-numpy)
2c16316e 4148 ("python-bx-python" ,python2-bx-python)
c5372108
RW		 4149 ("python-networkx" ,python2-networkx)
4150 ("python-scipy" ,python2-scipy)
9a067efd
RW		 4151 ("python-pbcore" ,python2-pbcore)
4152 ("python-h5py" ,python2-h5py)))
2c16316e 4153 (native-inputs
9a067efd 4154 `(("python-cython" ,python2-cython)
f3b98f4f 4155 ("python-nose" ,python2-nose)))
2c16316e
RW		 4156 (home-page "https://github.com/PacificBiosciences/cDNA_primer")
4157 (synopsis "Analyze transcriptome data generated with the Iso-Seq protocol")
4158 (description
4159 "pbtranscript-tofu contains scripts to analyze transcriptome data
4160generated using the PacBio Iso-Seq protocol.")
4161 (license license:bsd-3))))
4162
024130d2
BW		 4163(define-public prank
4164 (package
4165 (name "prank")
4166 (version "150803")
4167 (source (origin
4168 (method url-fetch)
4169 (uri (string-append
4170 "http://wasabiapp.org/download/prank/prank.source."
4171 version ".tgz"))
4172 (sha256
4173 (base32
4174 "0am4z94fs3w2n5xpfls9zda61vq7qqz4q2i7b9hlsxz5q4j3kfm4"))))
4175 (build-system gnu-build-system)
4176 (arguments
4177 `(#:phases
4178 (modify-phases %standard-phases
4179 (add-after 'unpack 'enter-src-dir
4180 (lambda _
4181 (chdir "src")
4182 #t))
62d00095
EF		 4183 (add-after 'unpack 'remove-m64-flag
4184 ;; Prank will build with the correct 'bit-ness' without this flag
4185 ;; and this allows building on 32-bit machines.
4186 (lambda _ (substitute* "src/Makefile"
4187 (("-m64") ""))
4188 #t))
024130d2
BW		 4189 (delete 'configure)
4190 (replace 'install
4191 (lambda* (#:key outputs #:allow-other-keys)
4192 (let* ((out (assoc-ref outputs "out"))
4193 (bin (string-append out "/bin"))
4194 (man (string-append out "/share/man/man1"))
4195 (path (string-append
4196 (assoc-ref %build-inputs "mafft") "/bin:"
4197 (assoc-ref %build-inputs "exonerate") "/bin:"
4198 (assoc-ref %build-inputs "bppsuite") "/bin")))
4199 (install-file "prank" bin)
4200 (wrap-program (string-append bin "/prank")
4201 `("PATH" ":" prefix (,path)))
4202 (install-file "prank.1" man))
4203 #t)))))
4204 (inputs
4205 `(("mafft" ,mafft)
4206 ("exonerate" ,exonerate)
4207 ("bppsuite" ,bppsuite)))
4208 (home-page "http://wasabiapp.org/software/prank/")
4209 (synopsis "Probabilistic multiple sequence alignment program")
4210 (description
4211 "PRANK is a probabilistic multiple sequence alignment program for DNA,
4212codon and amino-acid sequences. It is based on a novel algorithm that treats
4213insertions correctly and avoids over-estimation of the number of deletion
4214events. In addition, PRANK borrows ideas from maximum likelihood methods used
4215in phylogenetics and correctly takes into account the evolutionary distances
4216between sequences. Lastly, PRANK allows for defining a potential structure
4217for sequences to be aligned and then, simultaneously with the alignment,
4218predicts the locations of structural units in the sequences.")
4219 (license license:gpl2+)))
4220
31a9d653
BW		 4221(define-public proteinortho
4222 (package
4223 (name "proteinortho")
8c864901 4224 (version "5.16b")
31a9d653
BW		 4225 (source
4226 (origin
4227 (method url-fetch)
4228 (uri
4229 (string-append
4230 "http://www.bioinf.uni-leipzig.de/Software/proteinortho/proteinortho_v"
4231 version "_src.tar.gz"))
4232 (sha256
4233 (base32
8c864901 4234 "1wl0dawpssqwfjvr651r4wlww8hhjin8nba6xh71ks7sbypx886j"))))
31a9d653
BW		 4235 (build-system gnu-build-system)
4236 (arguments
4237 `(#:test-target "test"
4238 #:phases
4239 (modify-phases %standard-phases
4240 (replace 'configure
4241 ;; There is no configure script, so we modify the Makefile directly.
4242 (lambda* (#:key outputs #:allow-other-keys)
4243 (substitute* "Makefile"
4244 (("INSTALLDIR=.*")
4245 (string-append
4246 "INSTALLDIR=" (assoc-ref outputs "out") "/bin\n")))
4247 #t))
4248 (add-before 'install 'make-install-directory
4249 ;; The install directory is not created during 'make install'.
4250 (lambda* (#:key outputs #:allow-other-keys)
4251 (mkdir-p (string-append (assoc-ref outputs "out") "/bin"))
4252 #t))
4253 (add-after 'install 'wrap-programs
4254 (lambda* (#:key inputs outputs #:allow-other-keys)
4255 (let* ((path (getenv "PATH"))
4256 (out (assoc-ref outputs "out"))
4257 (binary (string-append out "/bin/proteinortho5.pl")))
4258 (wrap-program binary `("PATH" ":" prefix (,path))))
4259 #t)))))
4260 (inputs
4261 `(("perl" ,perl)
4262 ("python" ,python-2)
4263 ("blast+" ,blast+)))
4264 (home-page "http://www.bioinf.uni-leipzig.de/Software/proteinortho")
4265 (synopsis "Detect orthologous genes across species")
4266 (description
4267 "Proteinortho is a tool to detect orthologous genes across different
4268species. For doing so, it compares similarities of given gene sequences and
4269clusters them to find significant groups. The algorithm was designed to handle
4270large-scale data and can be applied to hundreds of species at once.")
4271 (license license:gpl2+)))
4272
846e3409
RW		 4273(define-public pyicoteo
4274 (package
4275 (name "pyicoteo")
4276 (version "2.0.7")
4277 (source
4278 (origin
4279 (method url-fetch)
4280 (uri (string-append "https://bitbucket.org/regulatorygenomicsupf/"
4281 "pyicoteo/get/v" version ".tar.bz2"))
4282 (file-name (string-append name "-" version ".tar.bz2"))
4283 (sha256
4284 (base32
4285 "0d6087f29xp8wxwlj111c3sylli98n0l8ry58c51ixzq0zfm50wa"))))
4286 (build-system python-build-system)
4287 (arguments
4288 `(#:python ,python-2 ; does not work with Python 3
4289 #:tests? #f)) ; there are no tests
4290 (inputs
4291 `(("python2-matplotlib" ,python2-matplotlib)))
4292 (home-page "https://bitbucket.org/regulatorygenomicsupf/pyicoteo")
4293 (synopsis "Analyze high-throughput genetic sequencing data")
4294 (description
4295 "Pyicoteo is a suite of tools for the analysis of high-throughput genetic
4296sequencing data. It works with genomic coordinates. There are currently six
4297different command-line tools:
4298
4299@enumerate
4300@item pyicoregion: for generating exploratory regions automatically;
4301@item pyicoenrich: for differential enrichment between two conditions;
4302@item pyicoclip: for calling CLIP-Seq peaks without a control;
4303@item pyicos: for genomic coordinates manipulation;
4304@item pyicoller: for peak calling on punctuated ChIP-Seq;
4305@item pyicount: to count how many reads from N experiment files overlap in a
4306 region file;
4307@item pyicotrocol: to combine operations from pyicoteo.
4308@end enumerate\n")
4309 (license license:gpl3+)))
4310
af860475
BW		 4311(define-public prodigal
4312 (package
4313 (name "prodigal")
e70f7a23 4314 (version "2.6.3")
af860475
BW		 4315 (source (origin
4316 (method url-fetch)
4317 (uri (string-append
4318 "https://github.com/hyattpd/Prodigal/archive/v"
4319 version ".tar.gz"))
4320 (file-name (string-append name "-" version ".tar.gz"))
4321 (sha256
4322 (base32
e70f7a23 4323 "17srxkqd3jc77xk15pfbgg1a9xahqg7337w95mrsia7mpza4l2c9"))))
af860475
BW		 4324 (build-system gnu-build-system)
4325 (arguments
4326 `(#:tests? #f ;no check target
4327 #:make-flags (list (string-append "INSTALLDIR="
4328 (assoc-ref %outputs "out")
4329 "/bin"))
4330 #:phases
4331 (modify-phases %standard-phases
4332 (delete 'configure))))
4333 (home-page "http://prodigal.ornl.gov")
4334 (synopsis "Protein-coding gene prediction for Archaea and Bacteria")
4335 (description
4336 "Prodigal runs smoothly on finished genomes, draft genomes, and
4337metagenomes, providing gene predictions in GFF3, Genbank, or Sequin table
4338format. It runs quickly, in an unsupervised fashion, handles gaps, handles
4339partial genes, and identifies translation initiation sites.")
4340 (license license:gpl3+)))
608dd932 4341
ceb62d54
BW		 4342(define-public roary
4343 (package
4344 (name "roary")
da4a707c 4345 (version "3.11.0")
ceb62d54
BW		 4346 (source
4347 (origin
4348 (method url-fetch)
4349 (uri (string-append
4350 "mirror://cpan/authors/id/A/AJ/AJPAGE/Bio-Roary-"
4351 version ".tar.gz"))
4352 (sha256
4353 (base32
da4a707c 4354 "10lw78x1xzvn7xzvnmh4bm3cak3ah5cssapl0yidvhaj1f44h29i"))))
ceb62d54
BW		 4355 (build-system perl-build-system)
4356 (arguments
4357 `(#:phases
4358 (modify-phases %standard-phases
4359 (delete 'configure)
4360 (delete 'build)
4361 (replace 'check
4362 (lambda _
4363 ;; The tests are not run by default, so we run each test file
4364 ;; directly.
4365 (setenv "PATH" (string-append (getcwd) "/bin" ":"
4366 (getenv "PATH")))
4367 (setenv "PERL5LIB" (string-append (getcwd) "/lib" ":"
4368 (getenv "PERL5LIB")))
4369 (zero? (length (filter (lambda (file)
4370 (display file)(display "\n")
4371 (not (zero? (system* "perl" file))))
4372 (find-files "t" ".*\\.t$"))))))
4373 (replace 'install
4374 ;; There is no 'install' target in the Makefile.
4375 (lambda* (#:key outputs #:allow-other-keys)
4376 (let* ((out (assoc-ref outputs "out"))
4377 (bin (string-append out "/bin"))
4378 (perl (string-append out "/lib/perl5/site_perl"))
4379 (roary-plots "contrib/roary_plots"))
4380 (mkdir-p bin)
4381 (mkdir-p perl)
4382 (copy-recursively "bin" bin)
4383 (copy-recursively "lib" perl)
4384 #t)))
4385 (add-after 'install 'wrap-programs
4386 (lambda* (#:key inputs outputs #:allow-other-keys)
4387 (let* ((out (assoc-ref outputs "out"))
4388 (perl5lib (getenv "PERL5LIB"))
4389 (path (getenv "PATH")))
4390 (for-each (lambda (prog)
4391 (let ((binary (string-append out "/" prog)))
4392 (wrap-program binary
4393 `("PERL5LIB" ":" prefix
4394 (,(string-append perl5lib ":" out
4395 "/lib/perl5/site_perl"))))
4396 (wrap-program binary
4397 `("PATH" ":" prefix
4398 (,(string-append path ":" out "/bin"))))))
4399 (find-files "bin" ".*[^R]$"))
4400 (let ((file
4401 (string-append out "/bin/roary-create_pan_genome_plots.R"))
4402 (r-site-lib (getenv "R_LIBS_SITE"))
4403 (coreutils-path
4404 (string-append (assoc-ref inputs "coreutils") "/bin")))
4405 (wrap-program file
4406 `("R_LIBS_SITE" ":" prefix
4407 (,(string-append r-site-lib ":" out "/site-library/"))))
4408 (wrap-program file
4409 `("PATH" ":" prefix
4410 (,(string-append coreutils-path ":" out "/bin"))))))
4411 #t)))))
4412 (native-inputs
4413 `(("perl-env-path" ,perl-env-path)
4414 ("perl-test-files" ,perl-test-files)
4415 ("perl-test-most" ,perl-test-most)
4416 ("perl-test-output" ,perl-test-output)))
4417 (inputs
4418 `(("perl-array-utils" ,perl-array-utils)
4419 ("bioperl" ,bioperl-minimal)
da4a707c 4420 ("perl-digest-md5-file" ,perl-digest-md5-file)
ceb62d54
BW		 4421 ("perl-exception-class" ,perl-exception-class)
4422 ("perl-file-find-rule" ,perl-file-find-rule)
4423 ("perl-file-grep" ,perl-file-grep)
4424 ("perl-file-slurper" ,perl-file-slurper)
4425 ("perl-file-which" ,perl-file-which)
4426 ("perl-graph" ,perl-graph)
4427 ("perl-graph-readwrite" ,perl-graph-readwrite)
4428 ("perl-log-log4perl" ,perl-log-log4perl)
4429 ("perl-moose" ,perl-moose)
4430 ("perl-perlio-utf8_strict" ,perl-perlio-utf8_strict)
4431 ("perl-text-csv" ,perl-text-csv)
4432 ("bedtools" ,bedtools)
4433 ("cd-hit" ,cd-hit)
4434 ("blast+" ,blast+)
4435 ("mcl" ,mcl)
4436 ("parallel" ,parallel)
4437 ("prank" ,prank)
4438 ("mafft" ,mafft)
4439 ("fasttree" ,fasttree)
4440 ("grep" ,grep)
4441 ("sed" ,sed)
4442 ("gawk" ,gawk)
2d7c4ae3 4443 ("r-minimal" ,r-minimal)
ceb62d54
BW		 4444 ("r-ggplot2" ,r-ggplot2)
4445 ("coreutils" ,coreutils)))
4446 (home-page "http://sanger-pathogens.github.io/Roary")
4447 (synopsis "High speed stand-alone pan genome pipeline")
4448 (description
4449 "Roary is a high speed stand alone pan genome pipeline, which takes
4450annotated assemblies in GFF3 format (produced by the Prokka program) and
4451calculates the pan genome. Using a standard desktop PC, it can analyse
4452datasets with thousands of samples, without compromising the quality of the
4453results. 128 samples can be analysed in under 1 hour using 1 GB of RAM and a
4454single processor. Roary is not intended for metagenomics or for comparing
4455extremely diverse sets of genomes.")
4456 (license license:gpl3)))
4457
608dd932
BW		 4458(define-public raxml
4459 (package
4460 (name "raxml")
e9e0fab0 4461 (version "8.2.10")
608dd932
BW		 4462 (source
4463 (origin
4464 (method url-fetch)
4465 (uri
4466 (string-append
4467 "https://github.com/stamatak/standard-RAxML/archive/v"
4468 version ".tar.gz"))
4469 (file-name (string-append name "-" version ".tar.gz"))
4470 (sha256
4471 (base32
e9e0fab0 4472 "13s7aspfdcfr6asynwdg1x6vznys6pzap5f8wsffbnnwpkkg9ya8"))))
608dd932
BW		 4473 (build-system gnu-build-system)
4474 (arguments
4475 `(#:tests? #f ; There are no tests.
4476 ;; Use 'standard' Makefile rather than SSE or AVX ones.
4477 #:make-flags (list "-f" "Makefile.HYBRID.gcc")
4478 #:phases
4479 (modify-phases %standard-phases
4480 (delete 'configure)
4481 (replace 'install
4482 (lambda* (#:key outputs #:allow-other-keys)
4483 (let* ((out (assoc-ref outputs "out"))
4484 (bin (string-append out "/bin"))
4485 (executable "raxmlHPC-HYBRID"))
4486 (install-file executable bin)
4487 (symlink (string-append bin "/" executable) "raxml"))
4488 #t)))))
4489 (inputs
4490 `(("openmpi" ,openmpi)))
4491 (home-page "http://sco.h-its.org/exelixis/web/software/raxml/index.html")
4492 (synopsis "Randomized Axelerated Maximum Likelihood phylogenetic trees")
4493 (description
4494 "RAxML is a tool for phylogenetic analysis and post-analysis of large
4495phylogenies.")
2805f9b2
EF		 4496 ;; The source includes x86 specific code
4497 (supported-systems '("x86_64-linux" "i686-linux"))
608dd932 4498 (license license:gpl2+)))
af860475 4499
66e3eff1
RW		 4500(define-public rsem
4501 (package
4502 (name "rsem")
4503 (version "1.2.20")
4504 (source
4505 (origin
4506 (method url-fetch)
4507 (uri
4508 (string-append "http://deweylab.biostat.wisc.edu/rsem/src/rsem-"
4509 version ".tar.gz"))
4510 (sha256
4511 (base32 "0nzdc0j0hjllhsd5f2xli95dafm3nawskigs140xzvjk67xh0r9q"))
fc1adab1 4512 (patches (search-patches "rsem-makefile.patch"))
66e3eff1
RW		 4513 (modules '((guix build utils)))
4514 (snippet
4515 '(begin
4516 ;; remove bundled copy of boost
4517 (delete-file-recursively "boost")
4518 #t))))
4519 (build-system gnu-build-system)
4520 (arguments
4521 `(#:tests? #f ;no "check" target
4522 #:phases
4523 (modify-phases %standard-phases
4524 ;; No "configure" script.
4525 ;; Do not build bundled samtools library.
4526 (replace 'configure
4527 (lambda _
4528 (substitute* "Makefile"
4529 (("^all : sam/libbam.a") "all : "))
4530 #t))
4531 (replace 'install
4532 (lambda* (#:key outputs #:allow-other-keys)
4533 (let* ((out (string-append (assoc-ref outputs "out")))
4534 (bin (string-append out "/bin/"))
4535 (perl (string-append out "/lib/perl5/site_perl")))
4536 (mkdir-p bin)
4537 (mkdir-p perl)
4538 (for-each (lambda (file)
f3860753 4539 (install-file file bin))
66e3eff1 4540 (find-files "." "rsem-.*"))
f3860753 4541 (install-file "rsem_perl_utils.pm" perl))
66e3eff1
RW		 4542 #t))
4543 (add-after
4544 'install 'wrap-program
4545 (lambda* (#:key outputs #:allow-other-keys)
4546 (let ((out (assoc-ref outputs "out")))
4547 (for-each (lambda (prog)
4548 (wrap-program (string-append out "/bin/" prog)
4549 `("PERL5LIB" ":" prefix
4550 (,(string-append out "/lib/perl5/site_perl")))))
4551 '("rsem-plot-transcript-wiggles"
4552 "rsem-calculate-expression"
4553 "rsem-generate-ngvector"
4554 "rsem-run-ebseq"
4555 "rsem-prepare-reference")))
4556 #t)))))
4557 (inputs
4558 `(("boost" ,boost)
4559 ("ncurses" ,ncurses)
2d7c4ae3 4560 ("r-minimal" ,r-minimal)
66e3eff1
RW		 4561 ("perl" ,perl)
4562 ("samtools" ,samtools-0.1)
4563 ("zlib" ,zlib)))
4564 (home-page "http://deweylab.biostat.wisc.edu/rsem/")
4565 (synopsis "Estimate gene expression levels from RNA-Seq data")
4566 (description
4567 "RSEM is a software package for estimating gene and isoform expression
4568levels from RNA-Seq data. The RSEM package provides a user-friendly
4569interface, supports threads for parallel computation of the EM algorithm,
4570single-end and paired-end read data, quality scores, variable-length reads and
4571RSPD estimation. In addition, it provides posterior mean and 95% credibility
4572interval estimates for expression levels. For visualization, it can generate
4573BAM and Wiggle files in both transcript-coordinate and genomic-coordinate.")
4574 (license license:gpl3+)))
4575
8622a072
RW		 4576(define-public rseqc
4577 (package
4578 (name "rseqc")
4579 (version "2.6.1")
4580 (source
4581 (origin
4582 (method url-fetch)
4583 (uri
4584 (string-append "mirror://sourceforge/rseqc/"
de67e922 4585 "RSeQC-" version ".tar.gz"))
8622a072 4586 (sha256
8214b7fb 4587 (base32 "15ly0254yi032qzkdplg00q144qfdsd986gh62829rl5bkxhj330"))
8622a072
RW		 4588 (modules '((guix build utils)))
4589 (snippet
4590 '(begin
4591 ;; remove bundled copy of pysam
4592 (delete-file-recursively "lib/pysam")
4593 (substitute* "setup.py"
4594 ;; remove dependency on outdated "distribute" module
4595 (("^from distribute_setup import use_setuptools") "")
4596 (("^use_setuptools\\(\\)") "")
4597 ;; do not use bundled copy of pysam
4598 (("^have_pysam = False") "have_pysam = True"))))))
4599 (build-system python-build-system)
4600 (arguments `(#:python ,python-2))
4601 (inputs
4602 `(("python-cython" ,python2-cython)
4603 ("python-pysam" ,python2-pysam)
4604 ("python-numpy" ,python2-numpy)
8622a072
RW		 4605 ("zlib" ,zlib)))
4606 (native-inputs
4607 `(("python-nose" ,python2-nose)))
4608 (home-page "http://rseqc.sourceforge.net/")
4609 (synopsis "RNA-seq quality control package")
4610 (description
4611 "RSeQC provides a number of modules that can comprehensively evaluate
4612high throughput sequence data, especially RNA-seq data. Some basic modules
4613inspect sequence quality, nucleotide composition bias, PCR bias and GC bias,
4614while RNA-seq specific modules evaluate sequencing saturation, mapped reads
4615distribution, coverage uniformity, strand specificity, etc.")
4616 (license license:gpl3+)))
4617
ec946638
RW		 4618(define-public seek
4619 ;; There are no release tarballs. According to the installation
4620 ;; instructions at http://seek.princeton.edu/installation.jsp, the latest
4621 ;; stable release is identified by this changeset ID.
4622 (let ((changeset "2329130")
4623 (revision "1"))
4624 (package
4625 (name "seek")
4626 (version (string-append "0-" revision "." changeset))
4627 (source (origin
4628 (method hg-fetch)
4629 (uri (hg-reference
4630 (url "https://bitbucket.org/libsleipnir/sleipnir")
4631 (changeset changeset)))
4632 (sha256
4633 (base32
4634 "0qrvilwh18dpbhkf92qvxbmay0j75ra3jg2wrhz67gf538zzphsx"))))
4635 (build-system gnu-build-system)
4636 (arguments
4637 `(#:modules ((srfi srfi-1)
4638 (guix build gnu-build-system)
4639 (guix build utils))
4640 #:phases
4641 (let ((dirs '("SeekMiner"
4642 "SeekEvaluator"
4643 "SeekPrep"
4644 "Distancer"
4645 "Data2DB"
4646 "PCL2Bin")))
4647 (modify-phases %standard-phases
4561498e 4648 (add-before 'configure 'bootstrap
ec946638
RW		 4649 (lambda _
4650 (zero? (system* "bash" "gen_auto"))))
4651 (add-after 'build 'build-additional-tools
4652 (lambda* (#:key make-flags #:allow-other-keys)
4653 (every (lambda (dir)
4654 (with-directory-excursion (string-append "tools/" dir)
4655 (zero? (apply system* "make" make-flags))))
4656 dirs)))
4657 (add-after 'install 'install-additional-tools
4658 (lambda* (#:key make-flags #:allow-other-keys)
4659 (fold (lambda (dir result)
4660 (with-directory-excursion (string-append "tools/" dir)
4661 (and result
4662 (zero? (apply system*
4663 `("make" ,@make-flags "install"))))))
4664 #t dirs)))))))
4665 (inputs
4666 `(("gsl" ,gsl)
4667 ("boost" ,boost)
4668 ("libsvm" ,libsvm)
4669 ("readline" ,readline)
4670 ("gengetopt" ,gengetopt)
4671 ("log4cpp" ,log4cpp)))
4672 (native-inputs
4673 `(("autoconf" ,autoconf)
4674 ("automake" ,automake)
4675 ("perl" ,perl)))
4676 (home-page "http://seek.princeton.edu")
4677 (synopsis "Gene co-expression search engine")
4678 (description
4679 "SEEK is a computational gene co-expression search engine. SEEK provides
4680biologists with a way to navigate the massive human expression compendium that
4681now contains thousands of expression datasets. SEEK returns a robust ranking
4682of co-expressed genes in the biological area of interest defined by the user's
4683query genes. It also prioritizes thousands of expression datasets according
4684to the user's query of interest.")
4685 (license license:cc-by3.0))))
4686
4e10a221
RW		 4687(define-public samtools
4688 (package
4689 (name "samtools")
63fa0ffc 4690 (version "1.5")
4e10a221
RW		 4691 (source
4692 (origin
4693 (method url-fetch)
4694 (uri
de67e922 4695 (string-append "mirror://sourceforge/samtools/samtools/"
4e10a221
RW		 4696 version "/samtools-" version ".tar.bz2"))
4697 (sha256
4698 (base32
63fa0ffc 4699 "1xidmv0jmfy7l0kb32hdnlshcxgzi1hmygvig0cqrq1fhckdlhl5"))))
4e10a221
RW		 4700 (build-system gnu-build-system)
4701 (arguments
c4473411 4702 `(#:modules ((ice-9 ftw)
5bdda30b
RW		 4703 (ice-9 regex)
4704 (guix build gnu-build-system)
4705 (guix build utils))
c4473411 4706 #:make-flags (list (string-append "prefix=" (assoc-ref %outputs "out")))
4ab16440 4707 #:configure-flags (list "--with-ncurses" "--with-htslib=system")
4e10a221 4708 #:phases
c842d425
BW		 4709 (modify-phases %standard-phases
4710 (add-after 'unpack 'patch-tests
4711 (lambda _
4712 (substitute* "test/test.pl"
4713 ;; The test script calls out to /bin/bash
4714 (("/bin/bash") (which "bash")))
b2d748ed 4715 #t))
c842d425
BW		 4716 (add-after 'install 'install-library
4717 (lambda* (#:key outputs #:allow-other-keys)
4718 (let ((lib (string-append (assoc-ref outputs "out") "/lib")))
4719 (install-file "libbam.a" lib)
4720 #t)))
4721 (add-after 'install 'install-headers
4722 (lambda* (#:key outputs #:allow-other-keys)
4723 (let ((include (string-append (assoc-ref outputs "out")
4724 "/include/samtools/")))
4725 (for-each (lambda (file)
4726 (install-file file include))
4727 (scandir "." (lambda (name) (string-match "\\.h$" name))))
4728 #t))))))
4e10a221 4729 (native-inputs `(("pkg-config" ,pkg-config)))
4ab16440
BW		 4730 (inputs
4731 `(("htslib" ,htslib)
4732 ("ncurses" ,ncurses)
4733 ("perl" ,perl)
4734 ("python" ,python)
4735 ("zlib" ,zlib)))
4e10a221
RW		 4736 (home-page "http://samtools.sourceforge.net")
4737 (synopsis "Utilities to efficiently manipulate nucleotide sequence alignments")
4738 (description
4739 "Samtools implements various utilities for post-processing nucleotide
4740sequence alignments in the SAM, BAM, and CRAM formats, including indexing,
4741variant calling (in conjunction with bcftools), and a simple alignment
4742viewer.")
4743 (license license:expat)))
d3517eda 4744
0b84a0aa
RW		 4745(define-public samtools-0.1
4746 ;; This is the most recent version of the 0.1 line of samtools. The input
4747 ;; and output formats differ greatly from that used and produced by samtools
4748 ;; 1.x and is still used in many bioinformatics pipelines.
4749 (package (inherit samtools)
4750 (version "0.1.19")
4751 (source
4752 (origin
4753 (method url-fetch)
4754 (uri
de67e922 4755 (string-append "mirror://sourceforge/samtools/samtools/"
0b84a0aa
RW		 4756 version "/samtools-" version ".tar.bz2"))
4757 (sha256
4758 (base32 "1m33xsfwz0s8qi45lylagfllqg7fphf4dr0780rsvw75av9wk06h"))))
4759 (arguments
2309ed68
RW		 4760 `(#:tests? #f ;no "check" target
4761 ,@(substitute-keyword-arguments (package-arguments samtools)
4762 ((#:make-flags flags)
4763 `(cons "LIBCURSES=-lncurses" ,flags))
4764 ((#:phases phases)
4765 `(modify-phases ,phases
4766 (replace 'install
4767 (lambda* (#:key outputs #:allow-other-keys)
4768 (let ((bin (string-append
4769 (assoc-ref outputs "out") "/bin")))
4770 (mkdir-p bin)
f3860753 4771 (install-file "samtools" bin)
b2d748ed 4772 #t)))
2309ed68
RW		 4773 (delete 'patch-tests)
4774 (delete 'configure))))))))
0b84a0aa 4775
fe4c37c2 4776(define-public mosaik
698bd297 4777 (let ((commit "5c25216d3522d6a33e53875cd76a6d65001e4e67"))
fe4c37c2
RW		 4778 (package
4779 (name "mosaik")
4780 (version "2.2.30")
4781 (source (origin
4782 ;; There are no release tarballs nor tags.
4783 (method git-fetch)
4784 (uri (git-reference
4785 (url "https://github.com/wanpinglee/MOSAIK.git")
4786 (commit commit)))
4787 (file-name (string-append name "-" version))
4788 (sha256
4789 (base32
4790 "17gj3s07cm77r41z92awh0bim7w7q7fbn0sf5nkqmcm1vw052qgw"))))
4791 (build-system gnu-build-system)
4792 (arguments
4793 `(#:tests? #f ; no tests
4794 #:make-flags (list "CC=gcc")
4795 #:phases
4796 (modify-phases %standard-phases
4797 (replace 'configure
4798 (lambda _ (chdir "src") #t))
4799 (replace 'install
4800 (lambda* (#:key outputs #:allow-other-keys)
4801 (let ((bin (string-append (assoc-ref outputs "out")
4802 "/bin")))
4803 (mkdir-p bin)
4804 (copy-recursively "../bin" bin)
4805 #t))))))
4806 (inputs
4807 `(("perl" ,perl)
4808 ("zlib" ,zlib)))
029d9f77 4809 (supported-systems '("x86_64-linux"))
0c6c9c00 4810 (home-page "https://github.com/wanpinglee/MOSAIK")
fe4c37c2
RW		 4811 (synopsis "Map nucleotide sequence reads to reference genomes")
4812 (description
4813 "MOSAIK is a program for mapping second and third-generation sequencing
4814reads to a reference genome. MOSAIK can align reads generated by all the
4815major sequencing technologies, including Illumina, Applied Biosystems SOLiD,
4816Roche 454, Ion Torrent and Pacific BioSciences SMRT.")
4817 ;; MOSAIK is released under the GPLv2+ with the exception of third-party
4818 ;; code released into the public domain:
4819 ;; 1. fastlz by Ariya Hidayat - http://www.fastlz.org/
4820 ;; 2. MD5 implementation - RSA Data Security, RFC 1321
4821 (license (list license:gpl2+ license:public-domain)))))
4822
282c5087
RW		 4823(define-public ngs-sdk
4824 (package
4825 (name "ngs-sdk")
6c4ccf32 4826 (version "1.3.0")
282c5087
RW		 4827 (source
4828 (origin
4829 (method url-fetch)
4830 (uri
4831 (string-append "https://github.com/ncbi/ngs/archive/"
4832 version ".tar.gz"))
4833 (file-name (string-append name "-" version ".tar.gz"))
4834 (sha256
4835 (base32
6c4ccf32 4836 "1wiyf4c6nm2j87pv015cbi0qny5byf3pbvcw3likifz5dl56ag40"))))
282c5087
RW		 4837 (build-system gnu-build-system)
4838 (arguments
4839 `(#:parallel-build? #f ; not supported
4840 #:tests? #f ; no "check" target
4841 #:phases
dc1d3cde
KK		 4842 (modify-phases %standard-phases
4843 (replace 'configure
4844 (lambda* (#:key outputs #:allow-other-keys)
4845 (let ((out (assoc-ref outputs "out")))
4846 ;; Allow 'konfigure.perl' to find 'package.prl'.
4847 (setenv "PERL5LIB"
4848 (string-append ".:" (getenv "PERL5LIB")))
4849
4850 ;; The 'configure' script doesn't recognize things like
4851 ;; '--enable-fast-install'.
4852 (zero? (system* "./configure"
4853 (string-append "--build-prefix=" (getcwd) "/build")
4854 (string-append "--prefix=" out))))))
4855 (add-after 'unpack 'enter-dir
4856 (lambda _ (chdir "ngs-sdk") #t)))))
282c5087 4857 (native-inputs `(("perl" ,perl)))
a0dadf0c
AE		 4858 ;; According to the test
4859 ;; unless ($MARCH =~ /x86_64/i || $MARCH =~ /i?86/i)
4860 ;; in ngs-sdk/setup/konfigure.perl
ab29be81 4861 (supported-systems '("i686-linux" "x86_64-linux"))
282c5087
RW		 4862 (home-page "https://github.com/ncbi/ngs")
4863 (synopsis "API for accessing Next Generation Sequencing data")
4864 (description
4865 "NGS is a domain-specific API for accessing reads, alignments and pileups
4866produced from Next Generation Sequencing. The API itself is independent from
4867any particular back-end implementation, and supports use of multiple back-ends
4868simultaneously.")
4869 (license license:public-domain)))
4870
1ad15c16 4871(define-public java-ngs
2651a5e6 4872 (package (inherit ngs-sdk)
1ad15c16 4873 (name "java-ngs")
2651a5e6
RW		 4874 (arguments
4875 `(,@(substitute-keyword-arguments
4876 `(#:modules ((guix build gnu-build-system)
4877 (guix build utils)
4878 (srfi srfi-1)
4879 (srfi srfi-26))
4880 ,@(package-arguments ngs-sdk))
4881 ((#:phases phases)
614a8977
RW		 4882 `(modify-phases ,phases
4883 (replace 'enter-dir (lambda _ (chdir "ngs-java") #t)))))))
2651a5e6 4884 (inputs
d2540f80 4885 `(("jdk" ,icedtea "jdk")
2651a5e6
RW		 4886 ("ngs-sdk" ,ngs-sdk)))
4887 (synopsis "Java bindings for NGS SDK")))
4888
75dd2424
RW		 4889(define-public ncbi-vdb
4890 (package
4891 (name "ncbi-vdb")
5021f547 4892 (version "2.8.2")
75dd2424
RW		 4893 (source
4894 (origin
4895 (method url-fetch)
4896 (uri
4897 (string-append "https://github.com/ncbi/ncbi-vdb/archive/"
4898 version ".tar.gz"))
4899 (file-name (string-append name "-" version ".tar.gz"))
4900 (sha256
4901 (base32
5021f547 4902 "1acn4bv81mfl137qnbn9995mjjhwd36pm0b7qli1iw5skrxa9j8m"))))
75dd2424
RW		 4903 (build-system gnu-build-system)
4904 (arguments
4905 `(#:parallel-build? #f ; not supported
4906 #:tests? #f ; no "check" target
4907 #:phases
70111198 4908 (modify-phases %standard-phases
0691851a
BW		 4909 (add-before 'configure 'set-perl-search-path
4910 (lambda _
4911 ;; Work around "dotless @INC" build failure.
4912 (setenv "PERL5LIB"
4913 (string-append (getcwd) "/setup:"
4914 (getenv "PERL5LIB")))
4915 #t))
70111198
RW		 4916 (replace 'configure
4917 (lambda* (#:key inputs outputs #:allow-other-keys)
4918 (let ((out (assoc-ref outputs "out")))
4919 ;; Override include path for libmagic
4920 (substitute* "setup/package.prl"
4921 (("name => 'magic', Include => '/usr/include'")
4922 (string-append "name=> 'magic', Include => '"
4923 (assoc-ref inputs "libmagic")
4924 "/include" "'")))
75dd2424 4925
70111198
RW		 4926 ;; Install kdf5 library (needed by sra-tools)
4927 (substitute* "build/Makefile.install"
4928 (("LIBRARIES_TO_INSTALL =")
4929 "LIBRARIES_TO_INSTALL = kdf5.$(VERSION_LIBX) kdf5.$(VERSION_SHLX)"))
75dd2424 4930
70111198
RW		 4931 (substitute* "build/Makefile.env"
4932 (("CFLAGS =" prefix)
4933 (string-append prefix "-msse2 ")))
675d7ae2 4934
558e2307
RW		 4935 ;; Override search path for ngs-java
4936 (substitute* "setup/package.prl"
4937 (("/usr/local/ngs/ngs-java")
4938 (assoc-ref inputs "java-ngs")))
4939
70111198
RW		 4940 ;; The 'configure' script doesn't recognize things like
4941 ;; '--enable-fast-install'.
4942 (zero? (system*
4943 "./configure"
4944 (string-append "--build-prefix=" (getcwd) "/build")
4945 (string-append "--prefix=" (assoc-ref outputs "out"))
4946 (string-append "--debug")
4947 (string-append "--with-xml2-prefix="
4948 (assoc-ref inputs "libxml2"))
4949 (string-append "--with-ngs-sdk-prefix="
4950 (assoc-ref inputs "ngs-sdk"))
70111198
RW		 4951 (string-append "--with-hdf5-prefix="
4952 (assoc-ref inputs "hdf5")))))))
4953 (add-after 'install 'install-interfaces
4954 (lambda* (#:key outputs #:allow-other-keys)
4955 ;; Install interface libraries. On i686 the interface libraries
4956 ;; are installed to "linux/gcc/i386", so we need to use the Linux
4957 ;; architecture name ("i386") instead of the target system prefix
4958 ;; ("i686").
4959 (mkdir (string-append (assoc-ref outputs "out") "/ilib"))
4960 (copy-recursively (string-append "build/ncbi-vdb/linux/gcc/"
4961 ,(system->linux-architecture
4962 (or (%current-target-system)
4963 (%current-system)))
4964 "/rel/ilib")
4965 (string-append (assoc-ref outputs "out")
4966 "/ilib"))
4967 ;; Install interface headers
4968 (copy-recursively "interfaces"
4969 (string-append (assoc-ref outputs "out")
4970 "/include"))
d5e17162
RW		 4971 #t))
4972 ;; These files are needed by sra-tools.
4973 (add-after 'install 'install-configuration-files
4974 (lambda* (#:key outputs #:allow-other-keys)
4975 (let ((target (string-append (assoc-ref outputs "out") "/kfg")))
4976 (mkdir target)
4977 (install-file "libs/kfg/default.kfg" target)
4978 (install-file "libs/kfg/certs.kfg" target))
70111198 4979 #t)))))
75dd2424
RW		 4980 (inputs
4981 `(("libxml2" ,libxml2)
4982 ("ngs-sdk" ,ngs-sdk)
1ad15c16 4983 ("java-ngs" ,java-ngs)
75dd2424
RW		 4984 ("libmagic" ,file)
4985 ("hdf5" ,hdf5)))
4986 (native-inputs `(("perl" ,perl)))
675d7ae2
RW		 4987 ;; NCBI-VDB requires SSE capability.
4988 (supported-systems '("i686-linux" "x86_64-linux"))
75dd2424
RW		 4989 (home-page "https://github.com/ncbi/ncbi-vdb")
4990 (synopsis "Database engine for genetic information")
4991 (description
4992 "The NCBI-VDB library implements a highly compressed columnar data
4993warehousing engine that is most often used to store genetic information.
4994Databases are stored in a portable image within the file system, and can be
4995accessed/downloaded on demand across HTTP.")
4996 (license license:public-domain)))
4997
cc6ed477
RW		 4998(define-public plink
4999 (package
5000 (name "plink")
5001 (version "1.07")
5002 (source
5003 (origin
5004 (method url-fetch)
5005 (uri (string-append
5006 "http://pngu.mgh.harvard.edu/~purcell/plink/dist/plink-"
5007 version "-src.zip"))
5008 (sha256
5009 (base32 "0as8gxm4pjyc8dxmm1sl873rrd7wn5qs0l29nqfnl31x8i467xaa"))
0dbb7ac2
EF		 5010 (patches (search-patches "plink-1.07-unclobber-i.patch"
5011 "plink-endian-detection.patch"))))
cc6ed477
RW		 5012 (build-system gnu-build-system)
5013 (arguments
5014 '(#:tests? #f ;no "check" target
5015 #:make-flags (list (string-append "LIB_LAPACK="
5016 (assoc-ref %build-inputs "lapack")
5017 "/lib/liblapack.so")
5018 "WITH_LAPACK=1"
5019 "FORCE_DYNAMIC=1"
5020 ;; disable phoning home
5021 "WITH_WEBCHECK=")
5022 #:phases
5023 (modify-phases %standard-phases
5024 ;; no "configure" script
5025 (delete 'configure)
5026 (replace 'install
5027 (lambda* (#:key outputs #:allow-other-keys)
5028 (let ((bin (string-append (assoc-ref outputs "out")
5029 "/bin/")))
96c46210 5030 (install-file "plink" bin)
cc6ed477
RW		 5031 #t))))))
5032 (inputs
5033 `(("zlib" ,zlib)
5034 ("lapack" ,lapack)))
5035 (native-inputs
5036 `(("unzip" ,unzip)))
5037 (home-page "http://pngu.mgh.harvard.edu/~purcell/plink/")
5038 (synopsis "Whole genome association analysis toolset")
5039 (description
5040 "PLINK is a whole genome association analysis toolset, designed to
5041perform a range of basic, large-scale analyses in a computationally efficient
5042manner. The focus of PLINK is purely on analysis of genotype/phenotype data,
5043so there is no support for steps prior to this (e.g. study design and
5044planning, generating genotype or CNV calls from raw data). Through
5045integration with gPLINK and Haploview, there is some support for the
5046subsequent visualization, annotation and storage of results.")
5047 ;; Code is released under GPLv2, except for fisher.h, which is under
5048 ;; LGPLv2.1+
5049 (license (list license:gpl2 license:lgpl2.1+))))
5050
dad66da4
RW		 5051(define-public plink-ng
5052 (package (inherit plink)
5053 (name "plink-ng")
5054 (version "1.90b4")
5055 (source
5056 (origin
5057 (method url-fetch)
5058 (uri (string-append "https://github.com/chrchang/plink-ng/archive/v"
5059 version ".tar.gz"))
5060 (file-name (string-append name "-" version ".tar.gz"))
5061 (sha256
5062 (base32 "09ixrds009aczjswxr2alcb774mksq5g0v78dgjjn1h4dky0kf9a"))))
5063 (build-system gnu-build-system)
5064 (arguments
5065 '(#:tests? #f ;no "check" target
5066 #:make-flags (list "BLASFLAGS=-llapack -lopenblas"
5067 "CFLAGS=-Wall -O2 -DDYNAMIC_ZLIB=1"
5068 "ZLIB=-lz"
5069 "-f" "Makefile.std")
5070 #:phases
5071 (modify-phases %standard-phases
5072 (add-after 'unpack 'chdir
5073 (lambda _ (chdir "1.9") #t))
5074 (delete 'configure) ; no "configure" script
5075 (replace 'install
5076 (lambda* (#:key outputs #:allow-other-keys)
5077 (let ((bin (string-append (assoc-ref outputs "out")
5078 "/bin/")))
5079 (install-file "plink" bin)
5080 #t))))))
5081 (inputs
5082 `(("zlib" ,zlib)
5083 ("lapack" ,lapack)
5084 ("openblas" ,openblas)))
5085 (home-page "https://www.cog-genomics.org/plink/")
5086 (license license:gpl3+)))
5087
c6a24d6e
RW		 5088(define-public smithlab-cpp
5089 (let ((revision "1")
698bd297 5090 (commit "728a097bec88c6f4b8528b685932049e660eff2e"))
c6a24d6e
RW		 5091 (package
5092 (name "smithlab-cpp")
698bd297 5093 (version (string-append "0." revision "." (string-take commit 7)))
c6a24d6e
RW		 5094 (source (origin
5095 (method git-fetch)
5096 (uri (git-reference
5097 (url "https://github.com/smithlabcode/smithlab_cpp.git")
5098 (commit commit)))
5099 (file-name (string-append name "-" version "-checkout"))
5100 (sha256
5101 (base32
5102 "0d476lmj312xk77kr9fzrv7z1bv96yfyx0w7y62ycmnfbx32ll74"))))
5103 (build-system gnu-build-system)
5104 (arguments
5105 `(#:modules ((guix build gnu-build-system)
5106 (guix build utils)
5107 (srfi srfi-26))
5108 #:tests? #f ;no "check" target
5109 #:phases
5110 (modify-phases %standard-phases
5111 (add-after 'unpack 'use-samtools-headers
5112 (lambda _
5113 (substitute* '("SAM.cpp"
5114 "SAM.hpp")
5115 (("sam.h") "samtools/sam.h"))
5116 #t))
5117 (replace 'install
5118 (lambda* (#:key outputs #:allow-other-keys)
5119 (let* ((out (assoc-ref outputs "out"))
5120 (lib (string-append out "/lib"))
5121 (include (string-append out "/include/smithlab-cpp")))
5122 (mkdir-p lib)
5123 (mkdir-p include)
5124 (for-each (cut install-file <> lib)
5125 (find-files "." "\\.o$"))
5126 (for-each (cut install-file <> include)
5127 (find-files "." "\\.hpp$")))
5128 #t))
5129 (delete 'configure))))
5130 (inputs
5131 `(("samtools" ,samtools-0.1)
5132 ("zlib" ,zlib)))
5133 (home-page "https://github.com/smithlabcode/smithlab_cpp")
5134 (synopsis "C++ helper library for functions used in Smith lab projects")
5135 (description
5136 "Smithlab CPP is a C++ library that includes functions used in many of
5137the Smith lab bioinformatics projects, such as a wrapper around Samtools data
5138structures, classes for genomic regions, mapped sequencing reads, etc.")
5139 (license license:gpl3+))))
5140
56e373ef
RW		 5141(define-public preseq
5142 (package
5143 (name "preseq")
b49c5a58 5144 (version "2.0")
56e373ef
RW		 5145 (source (origin
5146 (method url-fetch)
b49c5a58
RW		 5147 (uri (string-append "https://github.com/smithlabcode/"
5148 "preseq/archive/v" version ".tar.gz"))
5149 (file-name (string-append name "-" version ".tar.gz"))
56e373ef 5150 (sha256
b49c5a58 5151 (base32 "08r684l50pnxjpvmhzjgqq56yv9rfw90k8vx0nsrnrzk8mf9hsdq"))
56e373ef
RW		 5152 (modules '((guix build utils)))
5153 (snippet
5154 ;; Remove bundled samtools.
b49c5a58 5155 '(delete-file-recursively "samtools"))))
56e373ef
RW		 5156 (build-system gnu-build-system)
5157 (arguments
5158 `(#:tests? #f ;no "check" target
5159 #:phases
5160 (modify-phases %standard-phases
56e373ef 5161 (delete 'configure))
b49c5a58
RW		 5162 #:make-flags
5163 (list (string-append "PREFIX="
5164 (assoc-ref %outputs "out"))
5165 (string-append "LIBBAM="
5166 (assoc-ref %build-inputs "samtools")
5167 "/lib/libbam.a")
5168 (string-append "SMITHLAB_CPP="
5169 (assoc-ref %build-inputs "smithlab-cpp")
5170 "/lib")
5171 "PROGS=preseq"
5172 "INCLUDEDIRS=$(SMITHLAB_CPP)/../include/smithlab-cpp $(SAMTOOLS_DIR)")))
56e373ef
RW		 5173 (inputs
5174 `(("gsl" ,gsl)
5175 ("samtools" ,samtools-0.1)
b49c5a58 5176 ("smithlab-cpp" ,smithlab-cpp)
56e373ef
RW		 5177 ("zlib" ,zlib)))
5178 (home-page "http://smithlabresearch.org/software/preseq/")
5179 (synopsis "Program for analyzing library complexity")
5180 (description
5181 "The preseq package is aimed at predicting and estimating the complexity
5182of a genomic sequencing library, equivalent to predicting and estimating the
5183number of redundant reads from a given sequencing depth and how many will be
5184expected from additional sequencing using an initial sequencing experiment.
5185The estimates can then be used to examine the utility of further sequencing,
5186optimize the sequencing depth, or to screen multiple libraries to avoid low
5187complexity samples.")
5188 (license license:gpl3+)))
5189
9ded1457
BW		 5190(define-public python-screed
5191 (package
5192 (name "python-screed")
5193 (version "0.9")
5194 (source
5195 (origin
5196 (method url-fetch)
5197 (uri (pypi-uri "screed" version))
5198 (sha256
5199 (base32
5200 "18czszp9fkx3j6jr7y5kp6dfialscgddk05mw1zkhh2zhn0jd8i0"))))
5201 (build-system python-build-system)
5202 (arguments
5203 `(#:phases
5204 (modify-phases %standard-phases
5205 (replace 'check
5206 (lambda _
5207 (setenv "PYTHONPATH"
5208 (string-append (getenv "PYTHONPATH") ":."))
5209 (zero? (system* "nosetests" "--attr" "!known_failing")))))))
5210 (native-inputs
5211 `(("python-nose" ,python-nose)))
5212 (inputs
5213 `(("python-bz2file" ,python-bz2file)))
7bf837fd 5214 (home-page "https://github.com/dib-lab/screed/")
9ded1457
BW		 5215 (synopsis "Short read sequence database utilities")
5216 (description "Screed parses FASTA and FASTQ files and generates databases.
5217Values such as sequence name, sequence description, sequence quality and the
5218sequence itself can be retrieved from these databases.")
5219 (license license:bsd-3)))
5220
5221(define-public python2-screed
5c31f4aa 5222 (package-with-python2 python-screed))
9ded1457 5223
51c64999
RW		 5224(define-public sra-tools
5225 (package
5226 (name "sra-tools")
79849358 5227 (version "2.8.2-1")
51c64999
RW		 5228 (source
5229 (origin
5230 (method url-fetch)
5231 (uri
5232 (string-append "https://github.com/ncbi/sra-tools/archive/"
5233 version ".tar.gz"))
5234 (file-name (string-append name "-" version ".tar.gz"))
5235 (sha256
5236 (base32
79849358 5237 "1camsijmvv2s45mb4iyf44ghl4gkd4rl0viphpcgl3ccchy32a0g"))))
51c64999
RW		 5238 (build-system gnu-build-system)
5239 (arguments
5240 `(#:parallel-build? #f ; not supported
5241 #:tests? #f ; no "check" target
2320e76b 5242 #:make-flags
79849358
RW		 5243 (list (string-append "DEFAULT_CRT="
5244 (assoc-ref %build-inputs "ncbi-vdb")
5245 "/kfg/certs.kfg")
5246 (string-append "DEFAULT_KFG="
5247 (assoc-ref %build-inputs "ncbi-vdb")
5248 "/kfg/default.kfg")
5249 (string-append "VDB_LIBDIR="
2320e76b
RW		 5250 (assoc-ref %build-inputs "ncbi-vdb")
5251 ,(if (string-prefix? "x86_64"
5252 (or (%current-target-system)
5253 (%current-system)))
5254 "/lib64"
5255 "/lib32")))
51c64999 5256 #:phases
beebe431 5257 (modify-phases %standard-phases
0691851a
BW		 5258 (add-before 'configure 'set-perl-search-path
5259 (lambda _
5260 ;; Work around "dotless @INC" build failure.
5261 (setenv "PERL5LIB"
5262 (string-append (getcwd) "/setup:"
5263 (getenv "PERL5LIB")))
5264 #t))
beebe431
RW		 5265 (replace 'configure
5266 (lambda* (#:key inputs outputs #:allow-other-keys)
5267 ;; The build system expects a directory containing the sources and
5268 ;; raw build output of ncbi-vdb, including files that are not
5269 ;; installed. Since we are building against an installed version of
5270 ;; ncbi-vdb, the following modifications are needed.
5271 (substitute* "setup/konfigure.perl"
5272 ;; Make the configure script look for the "ilib" directory of
5273 ;; "ncbi-vdb" without first checking for the existence of a
5274 ;; matching library in its "lib" directory.
5275 (("^ my \\$f = File::Spec->catdir\\(\\$libdir, \\$lib\\);")
5276 "my $f = File::Spec->catdir($ilibdir, $ilib);")
5277 ;; Look for interface libraries in ncbi-vdb's "ilib" directory.
5278 (("my \\$ilibdir = File::Spec->catdir\\(\\$builddir, 'ilib'\\);")
5279 "my $ilibdir = File::Spec->catdir($dir, 'ilib');"))
51c64999 5280
beebe431
RW		 5281 ;; Dynamic linking
5282 (substitute* "tools/copycat/Makefile"
5283 (("smagic-static") "lmagic"))
2320e76b 5284
beebe431
RW		 5285 ;; The 'configure' script doesn't recognize things like
5286 ;; '--enable-fast-install'.
5287 (zero? (system*
5288 "./configure"
5289 (string-append "--build-prefix=" (getcwd) "/build")
5290 (string-append "--prefix=" (assoc-ref outputs "out"))
5291 (string-append "--debug")
5292 (string-append "--with-fuse-prefix="
5293 (assoc-ref inputs "fuse"))
5294 (string-append "--with-magic-prefix="
5295 (assoc-ref inputs "libmagic"))
5296 ;; TODO: building with libxml2 fails with linker errors
5297 ;; (string-append "--with-xml2-prefix="
5298 ;; (assoc-ref inputs "libxml2"))
5299 (string-append "--with-ncbi-vdb-sources="
5300 (assoc-ref inputs "ncbi-vdb"))
5301 (string-append "--with-ncbi-vdb-build="
5302 (assoc-ref inputs "ncbi-vdb"))
5303 (string-append "--with-ngs-sdk-prefix="
5304 (assoc-ref inputs "ngs-sdk"))
5305 (string-append "--with-hdf5-prefix="
1108a920
RW		 5306 (assoc-ref inputs "hdf5"))))))
5307 ;; This version of sra-tools fails to build with glibc because of a
5308 ;; naming conflict. glibc-2.25/include/bits/mathcalls.h already
5309 ;; contains a definition of "canonicalize", so we rename it.
5310 ;;
5311 ;; See upstream bug report:
5312 ;; https://github.com/ncbi/sra-tools/issues/67
5313 (add-after 'unpack 'patch-away-glibc-conflict
5314 (lambda _
5315 (substitute* "tools/bam-loader/bam.c"
5316 (("canonicalize\\(" line)
5317 (string-append "sra_tools_" line)))
5318 #t)))))
51c64999
RW		 5319 (native-inputs `(("perl" ,perl)))
5320 (inputs
5321 `(("ngs-sdk" ,ngs-sdk)
5322 ("ncbi-vdb" ,ncbi-vdb)
5323 ("libmagic" ,file)
5324 ("fuse" ,fuse)
5325 ("hdf5" ,hdf5)
5326 ("zlib" ,zlib)))
5327 (home-page "http://www.ncbi.nlm.nih.gov/Traces/sra/sra.cgi?view=software")
5328 (synopsis "Tools and libraries for reading and writing sequencing data")
5329 (description
5330 "The SRA Toolkit from NCBI is a collection of tools and libraries for
5331reading of sequencing files from the Sequence Read Archive (SRA) database and
5332writing files into the .sra format.")
5333 (license license:public-domain)))
5334
d3517eda
RW		 5335(define-public seqan
5336 (package
5337 (name "seqan")
5338 (version "1.4.2")
5339 (source (origin
5340 (method url-fetch)
5341 (uri (string-append "http://packages.seqan.de/seqan-library/"
5342 "seqan-library-" version ".tar.bz2"))
5343 (sha256
5344 (base32
5345 "05s3wrrwn50f81aklfm65i4a749zag1vr8z03k21xm0pdxy47yvp"))))
5346 ;; The documentation is 7.8MB and the includes are 3.6MB heavy, so it
5347 ;; makes sense to split the outputs.
5348 (outputs '("out" "doc"))
5349 (build-system trivial-build-system)
5350 (arguments
5351 `(#:modules ((guix build utils))
5352 #:builder
5353 (begin
5354 (use-modules (guix build utils))
5355 (let ((tar (assoc-ref %build-inputs "tar"))
5356 (bzip (assoc-ref %build-inputs "bzip2"))
5357 (out (assoc-ref %outputs "out"))
5358 (doc (assoc-ref %outputs "doc")))
5359 (setenv "PATH" (string-append tar "/bin:" bzip "/bin"))
5360 (system* "tar" "xvf" (assoc-ref %build-inputs "source"))
5361 (chdir (string-append "seqan-library-" ,version))
5362 (copy-recursively "include" (string-append out "/include"))
5363 (copy-recursively "share" (string-append doc "/share"))))))
5364 (native-inputs
5365 `(("source" ,source)
5366 ("tar" ,tar)
5367 ("bzip2" ,bzip2)))
5368 (home-page "http://www.seqan.de")
5369 (synopsis "Library for nucleotide sequence analysis")
5370 (description
5371 "SeqAn is a C++ library of efficient algorithms and data structures for
5372the analysis of sequences with the focus on biological data. It contains
5373algorithms and data structures for string representation and their
5374manipulation, online and indexed string search, efficient I/O of
5375bioinformatics file formats, sequence alignment, and more.")
5376 (license license:bsd-3)))
ce7155d5 5377
d708b7a9
BW		 5378(define-public seqmagick
5379 (package
5380 (name "seqmagick")
39fb853a 5381 (version "0.7.0")
d708b7a9
BW		 5382 (source
5383 (origin
5384 (method url-fetch)
f6e2d86f 5385 (uri (pypi-uri "seqmagick" version))
d708b7a9
BW		 5386 (sha256
5387 (base32
39fb853a 5388 "12bfyp8nqi0hd36rmj450aygafp01qy3hkbvlwn3bk39pyjjkgg5"))))
d708b7a9 5389 (build-system python-build-system)
d708b7a9 5390 (inputs
39fb853a 5391 `(("python-biopython" ,python-biopython)))
d708b7a9 5392 (native-inputs
39fb853a 5393 `(("python-nose" ,python-nose)))
7bf837fd 5394 (home-page "https://github.com/fhcrc/seqmagick")
d708b7a9
BW		 5395 (synopsis "Tools for converting and modifying sequence files")
5396 (description
5397 "Bioinformaticians often have to convert sequence files between formats
5398and do little manipulations on them, and it's not worth writing scripts for
5399that. Seqmagick is a utility to expose the file format conversion in
5400BioPython in a convenient way. Instead of having a big mess of scripts, there
5401is one that takes arguments.")
5402 (license license:gpl3)))
5403
66daf78c
BW		 5404(define-public seqtk
5405 (package
5406 (name "seqtk")
5407 (version "1.2")
5408 (source (origin
5409 (method url-fetch)
5410 (uri (string-append
5411 "https://github.com/lh3/seqtk/archive/v"
5412 version ".tar.gz"))
5413 (file-name (string-append name "-" version ".tar.gz"))
5414 (sha256
5415 (base32
5416 "0ywdyzpmfiz2wp6ampbzqg4y8bj450nfgqarpamg045b8mk32lxx"))
5417 (modules '((guix build utils)))
5418 (snippet
5419 '(begin
5420 ;; Remove extraneous header files, as is done in the seqtk
5421 ;; master branch.
5422 (for-each (lambda (file) (delete-file file))
5423 (list "ksort.h" "kstring.h" "kvec.h"))
5424 #t))))
5425 (build-system gnu-build-system)
5426 (arguments
5427 `(#:phases
5428 (modify-phases %standard-phases
5429 (delete 'configure)
5430 (replace 'check
5431 ;; There are no tests, so we just run a sanity check.
5432 (lambda _ (zero? (system* "./seqtk" "seq"))))
5433 (replace 'install
5434 (lambda* (#:key outputs #:allow-other-keys)
5435 (let ((bin (string-append (assoc-ref outputs "out") "/bin/")))
5436 (install-file "seqtk" bin)))))))
5437 (inputs
5438 `(("zlib" ,zlib)))
5439 (home-page "https://github.com/lh3/seqtk")
5440 (synopsis "Toolkit for processing biological sequences in FASTA/Q format")
5441 (description
5442 "Seqtk is a fast and lightweight tool for processing sequences in the
5443FASTA or FASTQ format. It parses both FASTA and FASTQ files which can be
5444optionally compressed by gzip.")
5445 (license license:expat)))
5446
5f7e17be
BW		 5447(define-public snap-aligner
5448 (package
5449 (name "snap-aligner")
5450 (version "1.0beta.18")
5451 (source (origin
5452 (method url-fetch)
5453 (uri (string-append
5454 "https://github.com/amplab/snap/archive/v"
5455 version ".tar.gz"))
5456 (file-name (string-append name "-" version ".tar.gz"))
5457 (sha256
5458 (base32
5459 "1vnsjwv007k1fl1q7d681kbwn6bc66cgw6h16hym6gvyy71qv2ly"))))
5460 (build-system gnu-build-system)
5461 (arguments
5462 '(#:phases
5463 (modify-phases %standard-phases
5464 (delete 'configure)
5465 (replace 'check (lambda _ (zero? (system* "./unit_tests"))))
5466 (replace 'install
5467 (lambda* (#:key outputs #:allow-other-keys)
5468 (let* ((out (assoc-ref outputs "out"))
5469 (bin (string-append out "/bin")))
5f7e17be
BW		 5470 (install-file "snap-aligner" bin)
5471 (install-file "SNAPCommand" bin)
5472 #t))))))
5473 (native-inputs
5474 `(("zlib" ,zlib)))
5475 (home-page "http://snap.cs.berkeley.edu/")
5476 (synopsis "Short read DNA sequence aligner")
5477 (description
5478 "SNAP is a fast and accurate aligner for short DNA reads. It is
5479optimized for modern read lengths of 100 bases or higher, and takes advantage
5480of these reads to align data quickly through a hash-based indexing scheme.")
3e6fdd5f
EF		 5481 ;; 32-bit systems are not supported by the unpatched code.
5482 ;; Following the bug reports https://github.com/amplab/snap/issues/68 and
5483 ;; https://bugs.debian.org/cgi-bin/bugreport.cgi?bug=812378 we see that
5484 ;; systems without a lot of memory cannot make good use of this program.
5485 (supported-systems '("x86_64-linux"))
5f7e17be
BW		 5486 (license license:asl2.0)))
5487
bcadaf00
BW		 5488(define-public sortmerna
5489 (package
5490 (name "sortmerna")
849485f5 5491 (version "2.1b")
bcadaf00
BW		 5492 (source
5493 (origin
5494 (method url-fetch)
5495 (uri (string-append
5496 "https://github.com/biocore/sortmerna/archive/"
5497 version ".tar.gz"))
5498 (file-name (string-append name "-" version ".tar.gz"))
5499 (sha256
5500 (base32
849485f5 5501 "1ghaghvd82af9j5adavxh77g7hm247d1r69m3fbi6f1jdivj5ldk"))))
bcadaf00
BW		 5502 (build-system gnu-build-system)
5503 (outputs '("out" ;for binaries
5504 "db")) ;for sequence databases
5505 (arguments
5506 `(#:phases
5507 (modify-phases %standard-phases
5508 (replace 'install
5509 (lambda* (#:key outputs #:allow-other-keys)
5510 (let* ((out (assoc-ref outputs "out"))
5511 (bin (string-append out "/bin"))
5512 (db (assoc-ref outputs "db"))
5513 (share
5514 (string-append db "/share/sortmerna/rRNA_databases")))
5515 (install-file "sortmerna" bin)
5516 (install-file "indexdb_rna" bin)
5517 (for-each (lambda (file)
5518 (install-file file share))
5519 (find-files "rRNA_databases" ".*fasta"))
5520 #t))))))
849485f5
BW		 5521 (inputs
5522 `(("zlib" ,zlib)))
bcadaf00
BW		 5523 (home-page "http://bioinfo.lifl.fr/RNA/sortmerna")
5524 (synopsis "Biological sequence analysis tool for NGS reads")
5525 (description
5526 "SortMeRNA is a biological sequence analysis tool for filtering, mapping
5527and operational taxonomic unit (OTU) picking of next generation
5528sequencing (NGS) reads. The core algorithm is based on approximate seeds and
5529allows for fast and sensitive analyses of nucleotide sequences. The main
5530application of SortMeRNA is filtering rRNA from metatranscriptomic data.")
2324541b
EF		 5531 ;; The source includes x86 specific code
5532 (supported-systems '("x86_64-linux" "i686-linux"))
bcadaf00
BW		 5533 (license license:lgpl3)))
5534
ce7155d5
RW		 5535(define-public star
5536 (package
5537 (name "star")
939b6b11 5538 (version "2.5.3a")
ce7155d5
RW		 5539 (source (origin
5540 (method url-fetch)
3062d750
RW		 5541 (uri (string-append "https://github.com/alexdobin/STAR/archive/"
5542 version ".tar.gz"))
5543 (file-name (string-append name "-" version ".tar.gz"))
ce7155d5
RW		 5544 (sha256
5545 (base32
939b6b11 5546 "013wirlz8lllgjyagl48l75n1isxyabqb3sj7qlsl0x1rmvqw99a"))
ce7155d5
RW		 5547 (modules '((guix build utils)))
5548 (snippet
3062d750
RW		 5549 '(begin
5550 (substitute* "source/Makefile"
5551 (("/bin/rm") "rm"))
5552 ;; Remove pre-built binaries and bundled htslib sources.
5553 (delete-file-recursively "bin/MacOSX_x86_64")
5554 (delete-file-recursively "bin/Linux_x86_64")
c9e9154e 5555 (delete-file-recursively "bin/Linux_x86_64_static")
3062d750
RW		 5556 (delete-file-recursively "source/htslib")
5557 #t))))
ce7155d5
RW		 5558 (build-system gnu-build-system)
5559 (arguments
5560 '(#:tests? #f ;no check target
5561 #:make-flags '("STAR")
5562 #:phases
c0266e8d
RW		 5563 (modify-phases %standard-phases
5564 (add-after 'unpack 'enter-source-dir
5565 (lambda _ (chdir "source") #t))
625cdc3f
RW		 5566 (add-after 'enter-source-dir 'make-reproducible
5567 (lambda _
5568 (substitute* "Makefile"
5569 (("(COMPILATION_TIME_PLACE=\")(.*)(\")" _ pre mid post)
5570 (string-append pre "Built with Guix" post)))))
3062d750
RW		 5571 (add-after 'enter-source-dir 'do-not-use-bundled-htslib
5572 (lambda _
5573 (substitute* "Makefile"
5574 (("(Depend.list: \\$\\(SOURCES\\) parametersDefault\\.xxd) htslib"
5575 _ prefix) prefix))
5576 (substitute* '("BAMfunctions.cpp"
5577 "signalFromBAM.h"
5578 "bam_cat.h"
5579 "bam_cat.c"
5580 "STAR.cpp"
5581 "bamRemoveDuplicates.cpp")
5582 (("#include \"htslib/([^\"]+\\.h)\"" _ header)
5583 (string-append "#include <" header ">")))
5584 (substitute* "IncludeDefine.h"
5585 (("\"htslib/(htslib/[^\"]+.h)\"" _ header)
5586 (string-append "<" header ">")))
5587 #t))
c0266e8d
RW		 5588 (replace 'install
5589 (lambda* (#:key outputs #:allow-other-keys)
5590 (let ((bin (string-append (assoc-ref outputs "out") "/bin/")))
5591 (install-file "STAR" bin))
5592 #t))
5593 (delete 'configure))))
ce7155d5 5594 (native-inputs
9fc513ad 5595 `(("xxd" ,xxd)))
ce7155d5 5596 (inputs
3062d750
RW		 5597 `(("htslib" ,htslib)
5598 ("zlib" ,zlib)))
ce7155d5
RW		 5599 (home-page "https://github.com/alexdobin/STAR")
5600 (synopsis "Universal RNA-seq aligner")
5601 (description
5602 "The Spliced Transcripts Alignment to a Reference (STAR) software is
5603based on a previously undescribed RNA-seq alignment algorithm that uses
5604sequential maximum mappable seed search in uncompressed suffix arrays followed
5605by seed clustering and stitching procedure. In addition to unbiased de novo
5606detection of canonical junctions, STAR can discover non-canonical splices and
5607chimeric (fusion) transcripts, and is also capable of mapping full-length RNA
5608sequences.")
c11f79a4
BW		 5609 ;; Only 64-bit systems are supported according to the README.
5610 (supported-systems '("x86_64-linux" "mips64el-linux"))
ce7155d5
RW		 5611 ;; STAR is licensed under GPLv3 or later; htslib is MIT-licensed.
5612 (license license:gpl3+)))
de07c0db 5613
dbf4ed7c
RW		 5614(define-public subread
5615 (package
5616 (name "subread")
e6debcaf 5617 (version "1.6.0")
dbf4ed7c
RW		 5618 (source (origin
5619 (method url-fetch)
de67e922
LF		 5620 (uri (string-append "mirror://sourceforge/subread/subread-"
5621 version "/subread-" version "-source.tar.gz"))
dbf4ed7c
RW		 5622 (sha256
5623 (base32
e6debcaf 5624 "0ah0n4jx6ksk2m2j7xk385x2qzmk1y4rfc6a4mfrdqrlq721w99i"))))
dbf4ed7c
RW		 5625 (build-system gnu-build-system)
5626 (arguments
5627 `(#:tests? #f ;no "check" target
104c1986
RW		 5628 ;; The CC and CCFLAGS variables are set to contain a lot of x86_64
5629 ;; optimizations by default, so we override these flags such that x86_64
5630 ;; flags are only added when the build target is an x86_64 system.
5631 #:make-flags
5632 (list (let ((system ,(or (%current-target-system)
5633 (%current-system)))
5634 (flags '("-ggdb" "-fomit-frame-pointer"
5635 "-ffast-math" "-funroll-loops"
5636 "-fmessage-length=0"
5637 "-O9" "-Wall" "-DMAKE_FOR_EXON"
5638 "-DMAKE_STANDALONE"
5639 "-DSUBREAD_VERSION=\\\"${SUBREAD_VERSION}\\\""))
5640 (flags64 '("-mmmx" "-msse" "-msse2" "-msse3")))
5641 (if (string-prefix? "x86_64" system)
5642 (string-append "CCFLAGS=" (string-join (append flags flags64)))
5643 (string-append "CCFLAGS=" (string-join flags))))
5644 "-f" "Makefile.Linux"
5645 "CC=gcc ${CCFLAGS}")
dbf4ed7c 5646 #:phases
dc1d3cde
KK		 5647 (modify-phases %standard-phases
5648 (add-after 'unpack 'enter-dir
5649 (lambda _ (chdir "src") #t))
5650 (replace 'install
5651 (lambda* (#:key outputs #:allow-other-keys)
5652 (let ((bin (string-append (assoc-ref outputs "out") "/bin/")))
5653 (mkdir-p bin)
5654 (copy-recursively "../bin" bin))))
dbf4ed7c 5655 ;; no "configure" script
dc1d3cde 5656 (delete 'configure))))
dbf4ed7c
RW		 5657 (inputs `(("zlib" ,zlib)))
5658 (home-page "http://bioinf.wehi.edu.au/subread-package/")
5659 (synopsis "Tool kit for processing next-gen sequencing data")
5660 (description
5661 "The subread package contains the following tools: subread aligner, a
5662general-purpose read aligner; subjunc aligner: detecting exon-exon junctions
5663and mapping RNA-seq reads; featureCounts: counting mapped reads for genomic
5664features; exactSNP: a SNP caller that discovers SNPs by testing signals
5665against local background noises.")
5666 (license license:gpl3+)))
5667
d15d981e
RW		 5668(define-public stringtie
5669 (package
5670 (name "stringtie")
5671 (version "1.2.1")
5672 (source (origin
5673 (method url-fetch)
5674 (uri (string-append "http://ccb.jhu.edu/software/stringtie/dl/"
5675 "stringtie-" version ".tar.gz"))
5676 (sha256
5677 (base32
5678 "1cqllsc1maq4kh92isi8yadgzbmnf042hlnalpk3y59aph1z3bfz"))
5679 (modules '((guix build utils)))
5680 (snippet
5681 '(begin
5682 (delete-file-recursively "samtools-0.1.18")
5683 #t))))
5684 (build-system gnu-build-system)
5685 (arguments
5686 `(#:tests? #f ;no test suite
5687 #:phases
5688 (modify-phases %standard-phases
5689 ;; no configure script
5690 (delete 'configure)
5691 (add-before 'build 'use-system-samtools
5692 (lambda _
5693 (substitute* "Makefile"
5694 (("stringtie: \\$\\{BAM\\}/libbam\\.a")
5695 "stringtie: "))
5696 (substitute* '("gclib/GBam.h"
5697 "gclib/GBam.cpp")
5698 (("#include \"(bam|sam|kstring).h\"" _ header)
5699 (string-append "#include <samtools/" header ".h>")))
5700 #t))
0d2c0562
RW		 5701 (add-after 'unpack 'remove-duplicate-typedef
5702 (lambda _
5703 ;; This typedef conflicts with the typedef in
5704 ;; glibc-2.25/include/bits/types.h
5705 (substitute* "gclib/GThreads.h"
5706 (("typedef long long __intmax_t;") ""))
5707 #t))
d15d981e
RW		 5708 (replace 'install
5709 (lambda* (#:key outputs #:allow-other-keys)
5710 (let ((bin (string-append (assoc-ref outputs "out") "/bin/")))
5711 (install-file "stringtie" bin)
5712 #t))))))
5713 (inputs
5714 `(("samtools" ,samtools-0.1)
5715 ("zlib" ,zlib)))
5716 (home-page "http://ccb.jhu.edu/software/stringtie/")
5717 (synopsis "Transcript assembly and quantification for RNA-Seq data")
5718 (description
5719 "StringTie is a fast and efficient assembler of RNA-Seq sequence
5720alignments into potential transcripts. It uses a novel network flow algorithm
5721as well as an optional de novo assembly step to assemble and quantitate
5722full-length transcripts representing multiple splice variants for each gene
5723locus. Its input can include not only the alignments of raw reads used by
5724other transcript assemblers, but also alignments of longer sequences that have
5725been assembled from those reads. To identify differentially expressed genes
5726between experiments, StringTie's output can be processed either by the
5727Cuffdiff or Ballgown programs.")
5728 (license license:artistic2.0)))
5729
ad0ae297
BW		 5730(define-public taxtastic
5731 (package
5732 (name "taxtastic")
3cbfc149 5733 (version "0.6.4")
ad0ae297
BW		 5734 (source (origin
5735 (method url-fetch)
3cbfc149 5736 (uri (pypi-uri "taxtastic" version))
ad0ae297
BW		 5737 (sha256
5738 (base32
3cbfc149 5739 "0s79z8kfl853x7l4h8ms05k31q87aw62nrchlk20w9n227j35929"))))
ad0ae297
BW		 5740 (build-system python-build-system)
5741 (arguments
5742 `(#:python ,python-2
5743 #:phases
5744 (modify-phases %standard-phases
5745 (replace 'check
5746 (lambda _
5747 (zero? (system* "python" "-m" "unittest" "discover" "-v")))))))
5748 (propagated-inputs
5749 `(("python-sqlalchemy" ,python2-sqlalchemy)
5750 ("python-decorator" ,python2-decorator)
5751 ("python-biopython" ,python2-biopython)
5752 ("python-pandas" ,python2-pandas)))
5753 (home-page "https://github.com/fhcrc/taxtastic")
5754 (synopsis "Tools for taxonomic naming and annotation")
5755 (description
5756 "Taxtastic is software written in python used to build and maintain
5757reference packages i.e. collections of reference trees, reference alignments,
5758profiles, and associated taxonomic information.")
5759 (license license:gpl3+)))
5760
de07c0db
RW		 5761(define-public vcftools
5762 (package
5763 (name "vcftools")
f4322542 5764 (version "0.1.15")
de07c0db
RW		 5765 (source (origin
5766 (method url-fetch)
5767 (uri (string-append
9b36e256
RJ		 5768 "https://github.com/vcftools/vcftools/releases/download/v"
5769 version "/vcftools-" version ".tar.gz"))
de07c0db
RW		 5770 (sha256
5771 (base32
f4322542 5772 "1qw30c45wihgy632rbz4rh3njnwj4msj46l1rsgdhyg6bgypmr1i"))))
de07c0db
RW		 5773 (build-system gnu-build-system)
5774 (arguments
5775 `(#:tests? #f ; no "check" target
5776 #:make-flags (list
7c3958e1 5777 "CFLAGS=-O2" ; override "-m64" flag
de07c0db
RW		 5778 (string-append "PREFIX=" (assoc-ref %outputs "out"))
5779 (string-append "MANDIR=" (assoc-ref %outputs "out")
9b36e256
RJ		 5780 "/share/man/man1"))))
5781 (native-inputs
5782 `(("pkg-config" ,pkg-config)))
de07c0db
RW		 5783 (inputs
5784 `(("perl" ,perl)
5785 ("zlib" ,zlib)))
9b36e256 5786 (home-page "https://vcftools.github.io/")
de07c0db
RW		 5787 (synopsis "Tools for working with VCF files")
5788 (description
5789 "VCFtools is a program package designed for working with VCF files, such
5790as those generated by the 1000 Genomes Project. The aim of VCFtools is to
5791provide easily accessible methods for working with complex genetic variation
5792data in the form of VCF files.")
5793 ;; The license is declared as LGPLv3 in the README and
9b36e256 5794 ;; at https://vcftools.github.io/license.html
de07c0db 5795 (license license:lgpl3)))
9c38b540 5796
35aa90a1
RW		 5797(define-public infernal
5798 (package
5799 (name "infernal")
5800 (version "1.1.2")
5801 (source (origin
5802 (method url-fetch)
5803 (uri (string-append "http://eddylab.org/software/infernal/"
5804 "infernal-" version ".tar.gz"))
5805 (sha256
5806 (base32
5807 "0sr2hiz3qxfwqpz3whxr6n82p3x27336v3f34iqznp10hks2935c"))))
5808 (build-system gnu-build-system)
5809 (native-inputs
5810 `(("perl" ,perl))) ; for tests
5811 (home-page "http://eddylab.org/infernal/")
5812 (synopsis "Inference of RNA alignments")
5813 (description "Infernal (\"INFERence of RNA ALignment\") is a tool for
5814searching DNA sequence databases for RNA structure and sequence similarities.
5815It is an implementation of a special case of profile stochastic context-free
5816grammars called @dfn{covariance models} (CMs). A CM is like a sequence
5817profile, but it scores a combination of sequence consensus and RNA secondary
5818structure consensus, so in many cases, it is more capable of identifying RNA
5819homologs that conserve their secondary structure more than their primary
5820sequence.")
48409ef2
EF		 5821 ;; Infernal 1.1.2 requires VMX or SSE capability for parallel instructions.
5822 (supported-systems '("i686-linux" "x86_64-linux"))
35aa90a1
RW		 5823 (license license:bsd-3)))
5824
b91cfa22
RW		 5825(define-public r-centipede
5826 (package
5827 (name "r-centipede")
5828 (version "1.2")
5829 (source (origin
5830 (method url-fetch)
5831 (uri (string-append "http://download.r-forge.r-project.org/"
5832 "src/contrib/CENTIPEDE_" version ".tar.gz"))
5833 (sha256
5834 (base32
5835 "1hsx6qgwr0i67fhy9257zj7s0ppncph2hjgbia5nn6nfmj0ax6l9"))))
5836 (build-system r-build-system)
5837 (home-page "http://centipede.uchicago.edu/")
5838 (synopsis "Predict transcription factor binding sites")
5839 (description
5840 "CENTIPEDE applies a hierarchical Bayesian mixture model to infer regions
5841of the genome that are bound by particular transcription factors. It starts
5842by identifying a set of candidate binding sites, and then aims to classify the
5843sites according to whether each site is bound or not bound by a transcription
5844factor. CENTIPEDE is an unsupervised learning algorithm that discriminates
5845between two different types of motif instances using as much relevant
5846information as possible.")
5847 (license (list license:gpl2+ license:gpl3+))))
5848
7b3df1e5
BW		 5849(define-public r-vegan
5850 (package
5851 (name "r-vegan")
2e9da339 5852 (version "2.4-6")
7b3df1e5
BW		 5853 (source
5854 (origin
5855 (method url-fetch)
5856 (uri (cran-uri "vegan" version))
5857 (sha256
5858 (base32
2e9da339 5859 "175mqr42mmxy98gpf3rky8alnkw3w1k90ggdw3cispl36841p76w"))))
7b3df1e5 5860 (build-system r-build-system)
7b3df1e5 5861 (native-inputs
db2e4386 5862 `(("gfortran" ,gfortran)))
7b3df1e5
BW		 5863 (propagated-inputs
5864 `(("r-cluster" ,r-cluster)
5865 ("r-lattice" ,r-lattice)
aeb64f3c 5866 ("r-mass" ,r-mass)
7b3df1e5
BW		 5867 ("r-mgcv" ,r-mgcv)
5868 ("r-permute" ,r-permute)))
5869 (home-page "https://cran.r-project.org/web/packages/vegan")
5870 (synopsis "Functions for community ecology")
5871 (description
5872 "The vegan package provides tools for descriptive community ecology. It
5873has most basic functions of diversity analysis, community ordination and
5874dissimilarity analysis. Most of its multivariate tools can be used for other
5875data types as well.")
5876 (license license:gpl2+)))
5877
8c6de588
RW		 5878(define-public r-annotate
5879 (package
5880 (name "r-annotate")
654c29ac 5881 (version "1.56.1")
8c6de588
RW		 5882 (source
5883 (origin
5884 (method url-fetch)
5885 (uri (bioconductor-uri "annotate" version))
5886 (sha256
5887 (base32
654c29ac 5888 "14c5xd9kasvcwg5gbjys2c1vizxhlqlzxakqc2kml0kw97hmx0rq"))))
8c6de588
RW		 5889 (build-system r-build-system)
5890 (propagated-inputs
5891 `(("r-annotationdbi" ,r-annotationdbi)
5892 ("r-biobase" ,r-biobase)
5893 ("r-biocgenerics" ,r-biocgenerics)
5894 ("r-dbi" ,r-dbi)
d0f0579e 5895 ("r-rcurl" ,r-rcurl)
8c6de588
RW		 5896 ("r-xml" ,r-xml)
5897 ("r-xtable" ,r-xtable)))
5898 (home-page
5713bbf1 5899 "https://bioconductor.org/packages/annotate")
8c6de588 5900 (synopsis "Annotation for microarrays")
d1e4ad1b 5901 (description "This package provides R environments for the annotation of
8c6de588
RW		 5902microarrays.")
5903 (license license:artistic2.0)))
5904
efa6a1dd
RJ		 5905(define-public r-copynumber
5906 (package
5907 (name "r-copynumber")
5908 (version "1.18.0")
5909 (source (origin
5910 (method url-fetch)
5911 (uri (bioconductor-uri "copynumber" version))
5912 (sha256
5913 (base32
5914 "01kcwzl485yjrkgyg8117b1il957ss0v6rq4bbxf4ksd5fzcjmyx"))))
5915 (build-system r-build-system)
5916 (propagated-inputs
5917 `(("r-s4vectors" ,r-s4vectors)
5918 ("r-iranges" ,r-iranges)
5919 ("r-genomicranges" ,r-genomicranges)
5920 ("r-biocgenerics" ,r-biocgenerics)))
5921 (home-page "https://bioconductor.org/packages/copynumber")
5922 (synopsis "Segmentation of single- and multi-track copy number data")
5923 (description
5924 "This package segments single- and multi-track copy number data by a
5925penalized least squares regression method.")
5926 (license license:artistic2.0)))
5927
07a664cd
RW		 5928(define-public r-geneplotter
5929 (package
5930 (name "r-geneplotter")
cb4d3ff2 5931 (version "1.56.0")
07a664cd
RW		 5932 (source
5933 (origin
5934 (method url-fetch)
5935 (uri (bioconductor-uri "geneplotter" version))
5936 (sha256
5937 (base32
cb4d3ff2 5938 "1z3g7frc1iviwrsv2dlm4nqvkc0685h4va0388yfxn102ln8wwma"))))
07a664cd
RW		 5939 (build-system r-build-system)
5940 (propagated-inputs
5941 `(("r-annotate" ,r-annotate)
5942 ("r-annotationdbi" ,r-annotationdbi)
5943 ("r-biobase" ,r-biobase)
5944 ("r-biocgenerics" ,r-biocgenerics)
5945 ("r-lattice" ,r-lattice)
5946 ("r-rcolorbrewer" ,r-rcolorbrewer)))
5713bbf1 5947 (home-page "https://bioconductor.org/packages/geneplotter")
07a664cd
RW		 5948 (synopsis "Graphics functions for genomic data")
5949 (description
5950 "This package provides functions for plotting genomic data.")
5951 (license license:artistic2.0)))
5952
2301fd3e
RW		 5953(define-public r-genefilter
5954 (package
5955 (name "r-genefilter")
554fac74 5956 (version "1.60.0")
2301fd3e
RW		 5957 (source
5958 (origin
5959 (method url-fetch)
5960 (uri (bioconductor-uri "genefilter" version))
5961 (sha256
5962 (base32
554fac74 5963 "173swlg6gj4kdllbqvyiw5dggbcxiwlwpqmllsv4dxzn7h25i3g7"))))
2301fd3e
RW		 5964 (build-system r-build-system)
5965 (native-inputs
5966 `(("gfortran" ,gfortran)))
5967 (propagated-inputs
5968 `(("r-annotate" ,r-annotate)
5969 ("r-annotationdbi" ,r-annotationdbi)
5970 ("r-biobase" ,r-biobase)
aeb64f3c
RW		 5971 ("r-s4vectors" ,r-s4vectors)
5972 ("r-survival" ,r-survival)))
5713bbf1 5973 (home-page "https://bioconductor.org/packages/genefilter")
2301fd3e
RW		 5974 (synopsis "Filter genes from high-throughput experiments")
5975 (description
5976 "This package provides basic functions for filtering genes from
5977high-throughput sequencing experiments.")
5978 (license license:artistic2.0)))
5979
ad34f0ac
RW		 5980(define-public r-deseq2
5981 (package
5982 (name "r-deseq2")
058644c0 5983 (version "1.18.1")
ad34f0ac
RW		 5984 (source
5985 (origin
5986 (method url-fetch)
5987 (uri (bioconductor-uri "DESeq2" version))
5988 (sha256
5989 (base32
058644c0 5990 "1iyimg1s0x5pdmvl8x08s8h0v019y0nhjzs50chagbpk2x91fsmv"))))
ad34f0ac
RW		 5991 (properties `((upstream-name . "DESeq2")))
5992 (build-system r-build-system)
ad34f0ac
RW		 5993 (propagated-inputs
5994 `(("r-biobase" ,r-biobase)
5995 ("r-biocgenerics" ,r-biocgenerics)
5996 ("r-biocparallel" ,r-biocparallel)
5997 ("r-genefilter" ,r-genefilter)
5998 ("r-geneplotter" ,r-geneplotter)
5999 ("r-genomicranges" ,r-genomicranges)
6000 ("r-ggplot2" ,r-ggplot2)
6001 ("r-hmisc" ,r-hmisc)
6002 ("r-iranges" ,r-iranges)
6003 ("r-locfit" ,r-locfit)
6004 ("r-rcpp" ,r-rcpp)
6005 ("r-rcpparmadillo" ,r-rcpparmadillo)
6006 ("r-s4vectors" ,r-s4vectors)
6007 ("r-summarizedexperiment" ,r-summarizedexperiment)))
5713bbf1 6008 (home-page "https://bioconductor.org/packages/DESeq2")
ad34f0ac
RW		 6009 (synopsis "Differential gene expression analysis")
6010 (description
6011 "This package provides functions to estimate variance-mean dependence in
6012count data from high-throughput nucleotide sequencing assays and test for
6013differential expression based on a model using the negative binomial
6014distribution.")
6015 (license license:lgpl3+)))
6016
86763fdd
RW		 6017(define-public r-dexseq
6018 (package
6019 (name "r-dexseq")
b1808932 6020 (version "1.24.3")
86763fdd
RW		 6021 (source
6022 (origin
6023 (method url-fetch)
6024 (uri (bioconductor-uri "DEXSeq" version))
6025 (sha256
6026 (base32
b1808932 6027 "0xip73hlbr3zry9d7ly9vvvsbb3xjcmfa09lr9fdy528dwjrf084"))))
86763fdd
RW		 6028 (properties `((upstream-name . "DEXSeq")))
6029 (build-system r-build-system)
6030 (propagated-inputs
6031 `(("r-annotationdbi" ,r-annotationdbi)
6032 ("r-biobase" ,r-biobase)
6033 ("r-biocgenerics" ,r-biocgenerics)
6034 ("r-biocparallel" ,r-biocparallel)
6035 ("r-biomart" ,r-biomart)
6036 ("r-deseq2" ,r-deseq2)
6037 ("r-genefilter" ,r-genefilter)
6038 ("r-geneplotter" ,r-geneplotter)
6039 ("r-genomicranges" ,r-genomicranges)
6040 ("r-hwriter" ,r-hwriter)
6041 ("r-iranges" ,r-iranges)
6042 ("r-rcolorbrewer" ,r-rcolorbrewer)
6043 ("r-rsamtools" ,r-rsamtools)
6044 ("r-s4vectors" ,r-s4vectors)
6045 ("r-statmod" ,r-statmod)
6046 ("r-stringr" ,r-stringr)
6047 ("r-summarizedexperiment" ,r-summarizedexperiment)))
5713bbf1 6048 (home-page "https://bioconductor.org/packages/DEXSeq")
86763fdd
RW		 6049 (synopsis "Inference of differential exon usage in RNA-Seq")
6050 (description
6051 "This package is focused on finding differential exon usage using RNA-seq
6052exon counts between samples with different experimental designs. It provides
6053functions that allows the user to make the necessary statistical tests based
6054on a model that uses the negative binomial distribution to estimate the
6055variance between biological replicates and generalized linear models for
6056testing. The package also provides functions for the visualization and
6057exploration of the results.")
6058 (license license:gpl3+)))
6059
e8163773
RW		 6060(define-public r-annotationforge
6061 (package
6062 (name "r-annotationforge")
727706ad 6063 (version "1.20.0")
e8163773
RW		 6064 (source
6065 (origin
6066 (method url-fetch)
6067 (uri (bioconductor-uri "AnnotationForge" version))
6068 (sha256
6069 (base32
727706ad 6070 "01vbrf76vqfvxh6vpfxkjwccxggnha3byqzj333glqz2b6kwx5q1"))))
e8163773
RW		 6071 (properties
6072 `((upstream-name . "AnnotationForge")))
6073 (build-system r-build-system)
6074 (propagated-inputs
6075 `(("r-annotationdbi" ,r-annotationdbi)
6076 ("r-biobase" ,r-biobase)
6077 ("r-biocgenerics" ,r-biocgenerics)
6078 ("r-dbi" ,r-dbi)
55cd914c 6079 ("r-rcurl" ,r-rcurl)
e8163773
RW		 6080 ("r-rsqlite" ,r-rsqlite)
6081 ("r-s4vectors" ,r-s4vectors)
6082 ("r-xml" ,r-xml)))
5713bbf1 6083 (home-page "https://bioconductor.org/packages/AnnotationForge")
e8163773
RW		 6084 (synopsis "Code for building annotation database packages")
6085 (description
6086 "This package provides code for generating Annotation packages and their
6087databases. Packages produced are intended to be used with AnnotationDbi.")
6088 (license license:artistic2.0)))
6089
cd9e7dc7
RW		 6090(define-public r-rbgl
6091 (package
6092 (name "r-rbgl")
c25154e5 6093 (version "1.54.0")
cd9e7dc7
RW		 6094 (source
6095 (origin
6096 (method url-fetch)
6097 (uri (bioconductor-uri "RBGL" version))
6098 (sha256
6099 (base32
c25154e5 6100 "18jad23i3899ypv4bg3l47cvvs3qnj1pqis2p9x0135yv5y6wnv7"))))
cd9e7dc7
RW		 6101 (properties `((upstream-name . "RBGL")))
6102 (build-system r-build-system)
6103 (propagated-inputs `(("r-graph" ,r-graph)))
5713bbf1 6104 (home-page "https://www.bioconductor.org/packages/RBGL")
cd9e7dc7
RW		 6105 (synopsis "Interface to the Boost graph library")
6106 (description
6107 "This package provides a fairly extensive and comprehensive interface to
6108the graph algorithms contained in the Boost library.")
6109 (license license:artistic2.0)))
6110
ad740ff8
RW		 6111(define-public r-gseabase
6112 (package
6113 (name "r-gseabase")
4220ab0c 6114 (version "1.40.1")
ad740ff8
RW		 6115 (source
6116 (origin
6117 (method url-fetch)
6118 (uri (bioconductor-uri "GSEABase" version))
6119 (sha256
6120 (base32
4220ab0c 6121 "10cmjxahg2plwacfan6g0k8cwyzya96ypc7m1r79gwqkyykxw5fz"))))
ad740ff8
RW		 6122 (properties `((upstream-name . "GSEABase")))
6123 (build-system r-build-system)
6124 (propagated-inputs
6125 `(("r-annotate" ,r-annotate)
6126 ("r-annotationdbi" ,r-annotationdbi)
6127 ("r-biobase" ,r-biobase)
6128 ("r-biocgenerics" ,r-biocgenerics)
6129 ("r-graph" ,r-graph)
6130 ("r-xml" ,r-xml)))
5713bbf1 6131 (home-page "https://bioconductor.org/packages/GSEABase")
ad740ff8
RW		 6132 (synopsis "Gene set enrichment data structures and methods")
6133 (description
6134 "This package provides classes and methods to support @dfn{Gene Set
6135Enrichment Analysis} (GSEA).")
6136 (license license:artistic2.0)))
6137
1a1931f7
RW		 6138(define-public r-category
6139 (package
6140 (name "r-category")
2404cc42 6141 (version "2.44.0")
1a1931f7
RW		 6142 (source
6143 (origin
6144 (method url-fetch)
6145 (uri (bioconductor-uri "Category" version))
6146 (sha256
6147 (base32
2404cc42 6148 "0mkav04vbla0xfa0dssxdd0rjs589sxi83xklf5iq5hj3dm8y0i8"))))
1a1931f7
RW		 6149 (properties `((upstream-name . "Category")))
6150 (build-system r-build-system)
6151 (propagated-inputs
6152 `(("r-annotate" ,r-annotate)
6153 ("r-annotationdbi" ,r-annotationdbi)
6154 ("r-biobase" ,r-biobase)
6155 ("r-biocgenerics" ,r-biocgenerics)
6156 ("r-genefilter" ,r-genefilter)
6157 ("r-graph" ,r-graph)
6158 ("r-gseabase" ,r-gseabase)
6159 ("r-matrix" ,r-matrix)
6160 ("r-rbgl" ,r-rbgl)
2404cc42 6161 ("r-dbi" ,r-dbi)))
5713bbf1 6162 (home-page "https://bioconductor.org/packages/Category")
1a1931f7
RW		 6163 (synopsis "Category analysis")
6164 (description
6165 "This package provides a collection of tools for performing category
6166analysis.")
6167 (license license:artistic2.0)))
6168
89f40c5e
RW		 6169(define-public r-gostats
6170 (package
6171 (name "r-gostats")
eb3f5cc7 6172 (version "2.44.0")
89f40c5e
RW		 6173 (source
6174 (origin
6175 (method url-fetch)
6176 (uri (bioconductor-uri "GOstats" version))
6177 (sha256
6178 (base32
eb3f5cc7 6179 "04gqfdlx9fxf97qf0l28x4aaqvl10n6v58qiz5fiaw05sbj1pf1i"))))
89f40c5e
RW		 6180 (properties `((upstream-name . "GOstats")))
6181 (build-system r-build-system)
6182 (propagated-inputs
6183 `(("r-annotate" ,r-annotate)
6184 ("r-annotationdbi" ,r-annotationdbi)
6185 ("r-annotationforge" ,r-annotationforge)
6186 ("r-biobase" ,r-biobase)
6187 ("r-category" ,r-category)
6188 ("r-go-db" ,r-go-db)
6189 ("r-graph" ,r-graph)
eb3f5cc7 6190 ("r-rgraphviz" ,r-rgraphviz)
89f40c5e 6191 ("r-rbgl" ,r-rbgl)))
5713bbf1 6192 (home-page "https://bioconductor.org/packages/GOstats")
89f40c5e
RW		 6193 (synopsis "Tools for manipulating GO and microarrays")
6194 (description
6195 "This package provides a set of tools for interacting with GO and
6196microarray data. A variety of basic manipulation tools for graphs, hypothesis
6197testing and other simple calculations.")
6198 (license license:artistic2.0)))
6199
cb99d457
RW		 6200(define-public r-shortread
6201 (package
6202 (name "r-shortread")
99e4b11d 6203 (version "1.36.1")
cb99d457
RW		 6204 (source
6205 (origin
6206 (method url-fetch)
6207 (uri (bioconductor-uri "ShortRead" version))
6208 (sha256
6209 (base32
99e4b11d 6210 "1cyv47632m9ljkxfsvnvmd19sb607ys5kz8fwh6v39dnw16g0a6m"))))
cb99d457
RW		 6211 (properties `((upstream-name . "ShortRead")))
6212 (build-system r-build-system)
6213 (inputs
6214 `(("zlib" ,zlib)))
6215 (propagated-inputs
6216 `(("r-biobase" ,r-biobase)
6217 ("r-biocgenerics" ,r-biocgenerics)
6218 ("r-biocparallel" ,r-biocparallel)
6219 ("r-biostrings" ,r-biostrings)
6220 ("r-genomeinfodb" ,r-genomeinfodb)
6221 ("r-genomicalignments" ,r-genomicalignments)
6222 ("r-genomicranges" ,r-genomicranges)
6223 ("r-hwriter" ,r-hwriter)
6224 ("r-iranges" ,r-iranges)
6225 ("r-lattice" ,r-lattice)
6226 ("r-latticeextra" ,r-latticeextra)
6227 ("r-rsamtools" ,r-rsamtools)
6228 ("r-s4vectors" ,r-s4vectors)
6229 ("r-xvector" ,r-xvector)
6230 ("r-zlibbioc" ,r-zlibbioc)))
5713bbf1 6231 (home-page "https://bioconductor.org/packages/ShortRead")
cb99d457
RW		 6232 (synopsis "FASTQ input and manipulation tools")
6233 (description
6234 "This package implements sampling, iteration, and input of FASTQ files.
6235It includes functions for filtering and trimming reads, and for generating a
6236quality assessment report. Data are represented as
6237@code{DNAStringSet}-derived objects, and easily manipulated for a diversity of
6238purposes. The package also contains legacy support for early single-end,
6239ungapped alignment formats.")
6240 (license license:artistic2.0)))
6241
7f903d73
RW		 6242(define-public r-systempiper
6243 (package
6244 (name "r-systempiper")
b5375525 6245 (version "1.12.0")
7f903d73
RW		 6246 (source
6247 (origin
6248 (method url-fetch)
6249 (uri (bioconductor-uri "systemPipeR" version))
6250 (sha256
6251 (base32
b5375525 6252 "11mj8pjq5vj25768vmagpzv74fvi3p3kdk5zdlznqyiaggri04cv"))))
7f903d73
RW		 6253 (properties `((upstream-name . "systemPipeR")))
6254 (build-system r-build-system)
6255 (propagated-inputs
6256 `(("r-annotate" ,r-annotate)
6257 ("r-batchjobs" ,r-batchjobs)
6258 ("r-biocgenerics" ,r-biocgenerics)
6259 ("r-biostrings" ,r-biostrings)
6260 ("r-deseq2" ,r-deseq2)
6261 ("r-edger" ,r-edger)
6262 ("r-genomicfeatures" ,r-genomicfeatures)
6263 ("r-genomicranges" ,r-genomicranges)
6264 ("r-ggplot2" ,r-ggplot2)
6265 ("r-go-db" ,r-go-db)
6266 ("r-gostats" ,r-gostats)
6267 ("r-limma" ,r-limma)
6268 ("r-pheatmap" ,r-pheatmap)
6269 ("r-rjson" ,r-rjson)
6270 ("r-rsamtools" ,r-rsamtools)
6271 ("r-shortread" ,r-shortread)
6272 ("r-summarizedexperiment" ,r-summarizedexperiment)
6273 ("r-variantannotation" ,r-variantannotation)))
6274 (home-page "https://github.com/tgirke/systemPipeR")
6275 (synopsis "Next generation sequencing workflow and reporting environment")
6276 (description
6277 "This R package provides tools for building and running automated
6278end-to-end analysis workflows for a wide range of @dfn{next generation
6279sequence} (NGS) applications such as RNA-Seq, ChIP-Seq, VAR-Seq and Ribo-Seq.
6280Important features include a uniform workflow interface across different NGS
6281applications, automated report generation, and support for running both R and
6282command-line software, such as NGS aligners or peak/variant callers, on local
6283computers or compute clusters. Efficient handling of complex sample sets and
6284experimental designs is facilitated by a consistently implemented sample
6285annotation infrastructure.")
6286 (license license:artistic2.0)))
6287
684f29bd
RW		 6288(define-public r-grohmm
6289 (package
6290 (name "r-grohmm")
704fe4d1 6291 (version "1.12.0")
684f29bd
RW		 6292 (source
6293 (origin
6294 (method url-fetch)
6295 (uri (bioconductor-uri "groHMM" version))
6296 (sha256
6297 (base32
704fe4d1 6298 "0cjkj0ypyc4dfi9s8dh88kh6q4xlpnc0wal7njg4b4gqj0l2hva7"))))
684f29bd
RW		 6299 (properties `((upstream-name . "groHMM")))
6300 (build-system r-build-system)
6301 (propagated-inputs
6302 `(("r-genomeinfodb" ,r-genomeinfodb)
6303 ("r-genomicalignments" ,r-genomicalignments)
6304 ("r-genomicranges" ,r-genomicranges)
6305 ("r-iranges" ,r-iranges)
aeb64f3c 6306 ("r-mass" ,r-mass)
684f29bd
RW		 6307 ("r-rtracklayer" ,r-rtracklayer)
6308 ("r-s4vectors" ,r-s4vectors)))
6309 (home-page "https://github.com/Kraus-Lab/groHMM")
6310 (synopsis "GRO-seq analysis pipeline")
6311 (description
6312 "This package provides a pipeline for the analysis of GRO-seq data.")
6313 (license license:gpl3+)))
6314
f3cfe451
RW		 6315(define-public r-txdb-hsapiens-ucsc-hg19-knowngene
6316 (package
6317 (name "r-txdb-hsapiens-ucsc-hg19-knowngene")
6318 (version "3.2.2")
6319 (source (origin
6320 (method url-fetch)
6321 ;; We cannot use bioconductor-uri here because this tarball is
6322 ;; located under "data/annotation/" instead of "bioc/".
5713bbf1 6323 (uri (string-append "https://bioconductor.org/packages/"
f3cfe451
RW		 6324 "release/data/annotation/src/contrib"
6325 "/TxDb.Hsapiens.UCSC.hg19.knownGene_"
6326 version ".tar.gz"))
6327 (sha256
6328 (base32
6329 "1sajhcqqwazgz2lqbik7rd935i7kpnh08zxbp2ra10j72yqy4g86"))))
6330 (properties
6331 `((upstream-name . "TxDb.Hsapiens.UCSC.hg19.knownGene")))
6332 (build-system r-build-system)
6333 ;; As this package provides little more than a very large data file it
6334 ;; doesn't make sense to build substitutes.
6335 (arguments `(#:substitutable? #f))
6336 (propagated-inputs
6337 `(("r-genomicfeatures" ,r-genomicfeatures)))
6338 (home-page
5713bbf1 6339 "https://bioconductor.org/packages/TxDb.Hsapiens.UCSC.hg19.knownGene/")
f3cfe451
RW		 6340 (synopsis "Annotation package for human genome in TxDb format")
6341 (description
6342 "This package provides an annotation database of Homo sapiens genome
6343data. It is derived from the UCSC hg19 genome and based on the \"knownGene\"
6344track. The database is exposed as a @code{TxDb} object.")
6345 (license license:artistic2.0)))
6346
325c039c
RJ		 6347(define-public r-sparql
6348 (package
6349 (name "r-sparql")
6350 (version "1.16")
6351 (source (origin
6352 (method url-fetch)
6353 (uri (cran-uri "SPARQL" version))
6354 (sha256
6355 (base32
6356 "0gak1q06yyhdmcxb2n3v0h9gr1vqd0viqji52wpw211qp6r6dcrc"))))
6357 (properties `((upstream-name . "SPARQL")))
6358 (build-system r-build-system)
6359 (propagated-inputs
6360 `(("r-rcurl" ,r-rcurl)
6361 ("r-xml" ,r-xml)))
e9960d8c 6362 (home-page "https://cran.r-project.org/web/packages/SPARQL")
325c039c
RJ		 6363 (synopsis "SPARQL client for R")
6364 (description "This package provides an interface to use SPARQL to pose
6365SELECT or UPDATE queries to an end-point.")
6366 ;; The only license indication is found in the DESCRIPTION file,
6367 ;; which states GPL-3. So we cannot assume GPLv3+.
6368 (license license:gpl3)))
6369
a2950fa4
BW		 6370(define-public vsearch
6371 (package
6372 (name "vsearch")
369eee87 6373 (version "2.7.1")
a2950fa4
BW		 6374 (source
6375 (origin
6376 (method url-fetch)
6377 (uri (string-append
6378 "https://github.com/torognes/vsearch/archive/v"
6379 version ".tar.gz"))
6380 (file-name (string-append name "-" version ".tar.gz"))
6381 (sha256
6382 (base32
369eee87 6383 "0jlzfgh79fzmb4g7sngzdjjsjyc37icvs1k7vmc2ksxglj6x5i7f"))
206af46f 6384 (patches (search-patches "vsearch-unbundle-cityhash.patch"))
a2950fa4
BW		 6385 (snippet
6386 '(begin
206af46f
BW		 6387 ;; Remove bundled cityhash sources. The vsearch source is adjusted
6388 ;; for this in the patch.
cf6edaba
BW		 6389 (delete-file "src/city.h")
6390 (delete-file "src/citycrc.h")
6391 (delete-file "src/city.cc")
a2950fa4
BW		 6392 #t))))
6393 (build-system gnu-build-system)
6394 (arguments
6395 `(#:phases
6396 (modify-phases %standard-phases
d10092b8
KK		 6397 (add-after 'unpack 'autogen
6398 (lambda _ (zero? (system* "autoreconf" "-vif")))))))
a2950fa4
BW		 6399 (inputs
6400 `(("zlib" ,zlib)
6401 ("bzip2" ,bzip2)
6402 ("cityhash" ,cityhash)))
6403 (native-inputs
6404 `(("autoconf" ,autoconf)
6405 ("automake" ,automake)))
6406 (synopsis "Sequence search tools for metagenomics")
6407 (description
6408 "VSEARCH supports DNA sequence searching, clustering, chimera detection,
6409dereplication, pairwise alignment, shuffling, subsampling, sorting and
6410masking. The tool takes advantage of parallelism in the form of SIMD
6411vectorization as well as multiple threads to perform accurate alignments at
6412high speed. VSEARCH uses an optimal global aligner (full dynamic programming
6413Needleman-Wunsch).")
6414 (home-page "https://github.com/torognes/vsearch")
6f04e515
BW		 6415 ;; vsearch uses non-portable SSE intrinsics so building fails on other
6416 ;; platforms.
6417 (supported-systems '("x86_64-linux"))
a2950fa4
BW		 6418 ;; Dual licensed; also includes public domain source.
6419 (license (list license:gpl3 license:bsd-2))))
6420
07837874
RW		 6421(define-public pardre
6422 (package
6423 (name "pardre")
7922ab8f
BW		 6424 ;; The source of 1.1.5 changed in place, so we append "-1" to the version.
6425 (version "1.1.5-1")
07837874
RW		 6426 (source
6427 (origin
6428 (method url-fetch)
6429 (uri (string-append "mirror://sourceforge/pardre/ParDRe-rel"
7922ab8f 6430 "1.1.5" ".tar.gz"))
07837874
RW		 6431 (sha256
6432 (base32
7922ab8f 6433 "17j73nc0viq4f6qj50nrndsrif5d6b71q8fl87m54psiv0ilns2b"))))
07837874
RW		 6434 (build-system gnu-build-system)
6435 (arguments
6436 `(#:tests? #f ; no tests included
6437 #:phases
6438 (modify-phases %standard-phases
6439 (delete 'configure)
6440 (replace 'install
6441 (lambda* (#:key outputs #:allow-other-keys)
6442 (let ((bin (string-append (assoc-ref outputs "out") "/bin")))
07837874
RW		 6443 (install-file "ParDRe" bin)
6444 #t))))))
6445 (inputs
6446 `(("openmpi" ,openmpi)
6447 ("zlib" ,zlib)))
6448 (synopsis "Parallel tool to remove duplicate DNA reads")
6449 (description
6450 "ParDRe is a parallel tool to remove duplicate genetic sequence reads.
6451Duplicate reads can be seen as identical or nearly identical sequences with
6452some mismatches. This tool lets users avoid the analysis of unnecessary
6453reads, reducing the time of subsequent procedures with the
6454dataset (e.g. assemblies, mappings, etc.). The tool is implemented with MPI
6455in order to exploit the parallel capabilities of multicore clusters. It is
6456faster than multithreaded counterparts (end of 2015) for the same number of
6457cores and, thanks to the message-passing technology, it can be executed on
6458clusters.")
6459 (home-page "https://sourceforge.net/projects/pardre/")
6460 (license license:gpl3+)))
6461
e4a44a6a
BW		 6462(define-public ruby-bio-kseq
6463 (package
6464 (name "ruby-bio-kseq")
6465 (version "0.0.2")
6466 (source
6467 (origin
6468 (method url-fetch)
6469 (uri (rubygems-uri "bio-kseq" version))
6470 (sha256
6471 (base32
6472 "1xyaha46khb5jc6wzkbf7040jagac49jbimn0vcrzid0j8jdikrz"))))
6473 (build-system ruby-build-system)
6474 (arguments
6475 `(#:test-target "spec"))
6476 (native-inputs
6477 `(("bundler" ,bundler)
6478 ("ruby-rspec" ,ruby-rspec)
6479 ("ruby-rake-compiler" ,ruby-rake-compiler)))
6480 (inputs
6481 `(("zlib" ,zlib)))
6482 (synopsis "Ruby bindings for the kseq.h FASTA/Q parser")
6483 (description
6484 "@code{Bio::Kseq} provides ruby bindings to the @code{kseq.h} FASTA and
6485FASTQ parsing code. It provides a fast iterator over sequences and their
6486quality scores.")
6487 (home-page "https://github.com/gusevfe/bio-kseq")
6488 (license license:expat)))
6489
9c38b540
PP		 6490(define-public bio-locus
6491 (package
6492 (name "bio-locus")
6493 (version "0.0.7")
6494 (source
6495 (origin
6496 (method url-fetch)
6497 (uri (rubygems-uri "bio-locus" version))
6498 (sha256
6499 (base32
6500 "02vmrxyimkj9sahsp4zhfhnmbvz6dbbqz1y01vglf8cbwvkajfl0"))))
6501 (build-system ruby-build-system)
6502 (native-inputs
6503 `(("ruby-rspec" ,ruby-rspec)))
6504 (synopsis "Tool for fast querying of genome locations")
6505 (description
6506 "Bio-locus is a tabix-like tool for fast querying of genome
6507locations. Many file formats in bioinformatics contain records that
6508start with a chromosome name and a position for a SNP, or a start-end
6509position for indels. Bio-locus allows users to store this chr+pos or
6510chr+pos+alt information in a database.")
6511 (home-page "https://github.com/pjotrp/bio-locus")
6512 (license license:expat)))
edb15985 6513
b2bddb07
PP		 6514(define-public bio-blastxmlparser
6515 (package
6516 (name "bio-blastxmlparser")
6517 (version "2.0.4")
6518 (source (origin
6519 (method url-fetch)
6520 (uri (rubygems-uri "bio-blastxmlparser" version))
6521 (sha256
6522 (base32
6523 "1wf4qygcmdjgcqm6flmvsagfr1gs9lf63mj32qv3z1f481zc5692"))))
6524 (build-system ruby-build-system)
6525 (propagated-inputs
6526 `(("ruby-bio-logger" ,ruby-bio-logger)
6527 ("ruby-nokogiri" ,ruby-nokogiri)))
6528 (inputs
6529 `(("ruby-rspec" ,ruby-rspec)))
6530 (synopsis "Fast big data BLAST XML parser and library")
6531 (description
6532 "Very fast parallel big-data BLAST XML file parser which can be used as
6533command line utility. Use blastxmlparser to: Parse BLAST XML; filter output;
6534generate FASTA, JSON, YAML, RDF, JSON-LD, HTML, CSV, tabular output etc.")
7bf837fd 6535 (home-page "https://github.com/pjotrp/blastxmlparser")
b2bddb07
PP		 6536 (license license:expat)))
6537
edb15985
PP		 6538(define-public bioruby
6539 (package
6540 (name "bioruby")
dbf9d371 6541 (version "1.5.1")
edb15985
PP		 6542 (source
6543 (origin
6544 (method url-fetch)
6545 (uri (rubygems-uri "bio" version))
6546 (sha256
6547 (base32
dbf9d371 6548 "0hdl0789c9n4mprnx5pgd46bfwl8d000rqpamj5h6kkjgspijv49"))))
edb15985
PP		 6549 (build-system ruby-build-system)
6550 (propagated-inputs
6551 `(("ruby-libxml" ,ruby-libxml)))
6552 (native-inputs
6553 `(("which" ,which))) ; required for test phase
6554 (arguments
6555 `(#:phases
6556 (modify-phases %standard-phases
6557 (add-before 'build 'patch-test-command
6558 (lambda _
6559 (substitute* '("test/functional/bio/test_command.rb")
6560 (("/bin/sh") (which "sh")))
6561 (substitute* '("test/functional/bio/test_command.rb")
6562 (("/bin/ls") (which "ls")))
6563 (substitute* '("test/functional/bio/test_command.rb")
6564 (("which") (which "which")))
6565 (substitute* '("test/functional/bio/test_command.rb",
6566 "test/data/command/echoarg2.sh")
6567 (("/bin/echo") (which "echo")))
6568 #t)))))
6569 (synopsis "Ruby library, shell and utilities for bioinformatics")
6570 (description "BioRuby comes with a comprehensive set of Ruby development
6571tools and libraries for bioinformatics and molecular biology. BioRuby has
6572components for sequence analysis, pathway analysis, protein modelling and
6573phylogenetic analysis; it supports many widely used data formats and provides
6574easy access to databases, external programs and public web services, including
6575BLAST, KEGG, GenBank, MEDLINE and GO.")
6576 (home-page "http://bioruby.org/")
6577 ;; Code is released under Ruby license, except for setup
6578 ;; (LGPLv2.1+) and scripts in samples (which have GPL2 and GPL2+)
6579 (license (list license:ruby license:lgpl2.1+ license:gpl2+ ))))
a5002ae7 6580
9fba89e8
RW		 6581(define-public r-acsnminer
6582 (package
6583 (name "r-acsnminer")
0b54b4c9 6584 (version "0.16.8.25")
9fba89e8
RW		 6585 (source (origin
6586 (method url-fetch)
6587 (uri (cran-uri "ACSNMineR" version))
6588 (sha256
6589 (base32
0b54b4c9 6590 "0gh604s8qall6zfjlwcg2ilxjvz08dplf9k5g47idhv43scm748l"))))
9fba89e8
RW		 6591 (properties `((upstream-name . "ACSNMineR")))
6592 (build-system r-build-system)
6593 (propagated-inputs
6594 `(("r-ggplot2" ,r-ggplot2)
6595 ("r-gridextra" ,r-gridextra)))
e9960d8c 6596 (home-page "https://cran.r-project.org/web/packages/ACSNMineR")
9fba89e8
RW		 6597 (synopsis "Gene enrichment analysis")
6598 (description
6599 "This package provides tools to compute and represent gene set enrichment
6600or depletion from your data based on pre-saved maps from the @dfn{Atlas of
6601Cancer Signalling Networks} (ACSN) or user imported maps. The gene set
6602enrichment can be run with hypergeometric test or Fisher exact test, and can
6603use multiple corrections. Visualization of data can be done either by
6604barplots or heatmaps.")
6605 (license license:gpl2+)))
6606
d29b25c4
RW		 6607(define-public r-biocgenerics
6608 (package
6609 (name "r-biocgenerics")
d61fc4e1 6610 (version "0.24.0")
d29b25c4
RW		 6611 (source (origin
6612 (method url-fetch)
6613 (uri (bioconductor-uri "BiocGenerics" version))
6614 (sha256
6615 (base32
d61fc4e1 6616 "03wxvhxyrhipbgcg83lqlfn7p9gbzzrnl48y0dq7303xgp232zai"))))
d29b25c4 6617 (properties
1d216b6e 6618 `((upstream-name . "BiocGenerics")))
d29b25c4 6619 (build-system r-build-system)
5713bbf1 6620 (home-page "https://bioconductor.org/packages/BiocGenerics")
d29b25c4
RW		 6621 (synopsis "S4 generic functions for Bioconductor")
6622 (description
6623 "This package provides S4 generic functions needed by many Bioconductor
6624packages.")
6625 (license license:artistic2.0)))
6626
eb24341f
RJ		 6627(define-public r-biocinstaller
6628 (package
6629 (name "r-biocinstaller")
32414616 6630 (version "1.28.0")
eb24341f
RJ		 6631 (source (origin
6632 (method url-fetch)
6633 (uri (bioconductor-uri "BiocInstaller" version))
6634 (sha256
6635 (base32
32414616 6636 "19fga27bv6q9v5mpil74y76lahmnwvpg2h33rdx1r79nvljkd19d"))))
eb24341f
RJ		 6637 (properties
6638 `((upstream-name . "BiocInstaller")))
6639 (build-system r-build-system)
5713bbf1 6640 (home-page "https://bioconductor.org/packages/BiocInstaller")
eb24341f
RJ		 6641 (synopsis "Install Bioconductor packages")
6642 (description "This package is used to install and update R packages from
6643Bioconductor, CRAN, and Github.")
6644 (license license:artistic2.0)))
6645
207ce8fb
RJ		 6646(define-public r-biocviews
6647 (package
6648 (name "r-biocviews")
c7782c3f 6649 (version "1.46.0")
207ce8fb
RJ		 6650 (source (origin
6651 (method url-fetch)
6652 (uri (bioconductor-uri "biocViews" version))
6653 (sha256
6654 (base32
c7782c3f 6655 "09zyqj1kqc089lmh9sliy0acanx9zimcasvp71dsrg2bqm08r1md"))))
207ce8fb
RJ		 6656 (properties
6657 `((upstream-name . "biocViews")))
6658 (build-system r-build-system)
6659 (propagated-inputs
6660 `(("r-biobase" ,r-biobase)
6661 ("r-graph" ,r-graph)
6662 ("r-rbgl" ,r-rbgl)
6663 ("r-rcurl" ,r-rcurl)
6664 ("r-xml" ,r-xml)
207ce8fb 6665 ("r-runit" ,r-runit)))
5713bbf1 6666 (home-page "https://bioconductor.org/packages/biocViews")
207ce8fb
RJ		 6667 (synopsis "Bioconductor package categorization helper")
6668 (description "The purpose of biocViews is to create HTML pages that
6669categorize packages in a Bioconductor package repository according to keywords,
6670also known as views, in a controlled vocabulary.")
6671 (license license:artistic2.0)))
6672
2abfc5b8
RJ		 6673(define-public r-bookdown
6674 (package
9800f7d9
RW		 6675 (name "r-bookdown")
6676 (version "0.7")
6677 (source (origin
6678 (method url-fetch)
6679 (uri (cran-uri "bookdown" version))
6680 (sha256
6681 (base32
6682 "1b3fw1f41zph5yw3kynb47aijq53vhaa6mnnvxly72zamyzdf95q"))))
6683 (build-system r-build-system)
6684 (propagated-inputs
6685 `(("r-htmltools" ,r-htmltools)
6686 ("r-knitr" ,r-knitr)
6687 ("r-rmarkdown" ,r-rmarkdown)
6688 ("r-tinytex" ,r-tinytex)
6689 ("r-yaml" ,r-yaml)
6690 ("r-xfun" ,r-xfun)
6691 ("ghc-pandoc" ,ghc-pandoc)))
6692 (home-page "https://github.com/rstudio/bookdown")
6693 (synopsis "Authoring books and technical documents with R markdown")
6694 (description "This package provides output formats and utilities for
2abfc5b8 6695authoring books and technical documents with R Markdown.")
9800f7d9 6696 (license license:gpl3)))
2abfc5b8 6697
99df12cd
RJ		 6698(define-public r-biocstyle
6699 (package
6700 (name "r-biocstyle")
7665fb39 6701 (version "2.6.1")
99df12cd
RJ		 6702 (source (origin
6703 (method url-fetch)
6704 (uri (bioconductor-uri "BiocStyle" version))
6705 (sha256
6706 (base32
7665fb39 6707 "03pp04pkcq99kdv2spzr995h2cxsza7l6w3d4gp4112m06prcybm"))))
99df12cd
RJ		 6708 (properties
6709 `((upstream-name . "BiocStyle")))
6710 (build-system r-build-system)
3bef24c9
RJ		 6711 (propagated-inputs
6712 `(("r-bookdown" ,r-bookdown)
6713 ("r-knitr" ,r-knitr)
6714 ("r-rmarkdown" ,r-rmarkdown)
6715 ("r-yaml" ,r-yaml)))
5713bbf1 6716 (home-page "https://bioconductor.org/packages/BiocStyle")
99df12cd
RJ		 6717 (synopsis "Bioconductor formatting styles")
6718 (description "This package provides standard formatting styles for
6719Bioconductor PDF and HTML documents. Package vignettes illustrate use and
6720functionality.")
6721 (license license:artistic2.0)))
6722
4644644a
RJ		 6723(define-public r-bioccheck
6724 (package
6725 (name "r-bioccheck")
7373b416 6726 (version "1.14.0")
4644644a
RJ		 6727 (source (origin
6728 (method url-fetch)
6729 (uri (bioconductor-uri "BiocCheck" version))
6730 (sha256
6731 (base32
7373b416 6732 "1nzp8kgw13z9pgf885rplj6k37jcldfhbz0adqclxr2gq0yalmyx"))))
4644644a
RJ		 6733 (properties
6734 `((upstream-name . "BiocCheck")))
6735 (build-system r-build-system)
6736 (arguments
6737 '(#:phases
6738 (modify-phases %standard-phases
6739 ;; This package can be used by calling BiocCheck(<package>) from
6740 ;; within R, or by running R CMD BiocCheck <package>. This phase
6741 ;; makes sure the latter works. For this to work, the BiocCheck
6742 ;; script must be somewhere on the PATH (not the R bin directory).
6743 (add-after 'install 'install-bioccheck-subcommand
6744 (lambda* (#:key outputs #:allow-other-keys)
6745 (let* ((out (assoc-ref outputs "out"))
6746 (dest-dir (string-append out "/bin"))
6747 (script-dir
6748 (string-append out "/site-library/BiocCheck/script/")))
6749 (mkdir-p dest-dir)
6750 (symlink (string-append script-dir "/checkBadDeps.R")
6751 (string-append dest-dir "/checkBadDeps.R"))
6752 (symlink (string-append script-dir "/BiocCheck")
6753 (string-append dest-dir "/BiocCheck")))
6754 #t)))))
4644644a 6755 (propagated-inputs
aeb64f3c
RW		 6756 `(("r-codetools" ,r-codetools)
6757 ("r-graph" ,r-graph)
4644644a
RJ		 6758 ("r-httr" ,r-httr)
6759 ("r-optparse" ,r-optparse)
4644644a 6760 ("r-biocinstaller" ,r-biocinstaller)
7373b416
RW		 6761 ("r-biocviews" ,r-biocviews)
6762 ("r-stringdist" ,r-stringdist)))
5713bbf1 6763 (home-page "https://bioconductor.org/packages/BiocCheck")
4644644a
RJ		 6764 (synopsis "Executes Bioconductor-specific package checks")
6765 (description "This package contains tools to perform additional quality
6766checks on R packages that are to be submitted to the Bioconductor repository.")
6767 (license license:artistic2.0)))
6768
2acaaee5
RJ		 6769(define-public r-getopt
6770 (package
6771 (name "r-getopt")
e8484711 6772 (version "1.20.2")
2acaaee5
RJ		 6773 (source
6774 (origin
6775 (method url-fetch)
6776 (uri (cran-uri "getopt" version))
6777 (sha256
6778 (base32
e8484711 6779 "13p35lbpy7i578752fa71sbfvcsqw5qfa9p6kf8b5m3c5p9i4v1x"))))
2acaaee5
RJ		 6780 (build-system r-build-system)
6781 (home-page "https://github.com/trevorld/getopt")
6782 (synopsis "Command-line option processor for R")
6783 (description
6784 "This package is designed to be used with Rscript to write shebang
6785scripts that accept short and long options. Many users will prefer to
6786use the packages @code{optparse} or @code{argparse} which add extra
6787features like automatically generated help options and usage texts,
6788support for default values, positional argument support, etc.")
6789 (license license:gpl2+)))
6790
c79ad57a
RJ		 6791(define-public r-optparse
6792 (package
6793 (name "r-optparse")
7150f1c3 6794 (version "1.4.4")
c79ad57a
RJ		 6795 (source
6796 (origin
6797 (method url-fetch)
6798 (uri (cran-uri "optparse" version))
6799 (sha256
6800 (base32
7150f1c3 6801 "1ff4wmsszrb3spwfp7ynfs8w11qpy1sdzfxm1wk8dqqvdwris7qb"))))
c79ad57a
RJ		 6802 (build-system r-build-system)
6803 (propagated-inputs
6804 `(("r-getopt" ,r-getopt)))
6805 (home-page
6806 "https://github.com/trevorld/optparse")
6807 (synopsis "Command line option parser")
6808 (description
6809 "This package provides a command line parser inspired by Python's
6810@code{optparse} library to be used with Rscript to write shebang scripts
6811that accept short and long options.")
6812 (license license:gpl2+)))
6813
247d498a
RJ		 6814(define-public r-dnacopy
6815 (package
6816 (name "r-dnacopy")
94fd86e5 6817 (version "1.52.0")
247d498a
RJ		 6818 (source (origin
6819 (method url-fetch)
6820 (uri (bioconductor-uri "DNAcopy" version))
6821 (sha256
6822 (base32
94fd86e5 6823 "127il5rlg1hzjlhwhs64x3nm18p00q1pd9ckb2b9ifl0rax95wai"))))
247d498a
RJ		 6824 (properties
6825 `((upstream-name . "DNAcopy")))
6826 (build-system r-build-system)
6827 (inputs
6828 `(("gfortran" ,gfortran)))
5697fdc3 6829 (home-page "https://bioconductor.org/packages/DNAcopy")
247d498a
RJ		 6830 (synopsis "Implementation of a circular binary segmentation algorithm")
6831 (description "This package implements the circular binary segmentation (CBS)
6832algorithm to segment DNA copy number data and identify genomic regions with
6833abnormal copy number.")
6834 (license license:gpl2+)))
6835
7485129e
RW		 6836(define-public r-s4vectors
6837 (package
6838 (name "r-s4vectors")
41f0f949 6839 (version "0.16.0")
7485129e
RW		 6840 (source (origin
6841 (method url-fetch)
6842 (uri (bioconductor-uri "S4Vectors" version))
6843 (sha256
6844 (base32
41f0f949 6845 "03s8vz33nl6mivjb7dbvj702dkypi340lji1sjban03fyyls0hw0"))))
7485129e 6846 (properties
1d216b6e 6847 `((upstream-name . "S4Vectors")))
7485129e
RW		 6848 (build-system r-build-system)
6849 (propagated-inputs
6850 `(("r-biocgenerics" ,r-biocgenerics)))
5713bbf1 6851 (home-page "https://bioconductor.org/packages/S4Vectors")
7485129e
RW		 6852 (synopsis "S4 implementation of vectors and lists")
6853 (description
6854 "The S4Vectors package defines the @code{Vector} and @code{List} virtual
6855classes and a set of generic functions that extend the semantic of ordinary
6856vectors and lists in R. Package developers can easily implement vector-like
6857or list-like objects as concrete subclasses of @code{Vector} or @code{List}.
6858In addition, a few low-level concrete subclasses of general interest (e.g.
6859@code{DataFrame}, @code{Rle}, and @code{Hits}) are implemented in the
6860S4Vectors package itself.")
6861 (license license:artistic2.0)))
6862
274da826
RW		 6863(define-public r-seqinr
6864 (package
6865 (name "r-seqinr")
023aa8ff 6866 (version "3.4-5")
274da826
RW		 6867 (source
6868 (origin
6869 (method url-fetch)
6870 (uri (cran-uri "seqinr" version))
6871 (sha256
6872 (base32
023aa8ff 6873 "17zv0n5cji17izwmwg0jcbxbjl3w5rls91w15svcnlpxjms38ahn"))))
274da826
RW		 6874 (build-system r-build-system)
6875 (propagated-inputs
3b851cd4
RW		 6876 `(("r-ade4" ,r-ade4)
6877 ("r-segmented" ,r-segmented)))
274da826
RW		 6878 (inputs
6879 `(("zlib" ,zlib)))
6880 (home-page "http://seqinr.r-forge.r-project.org/")
6881 (synopsis "Biological sequences retrieval and analysis")
6882 (description
6883 "This package provides tools for exploratory data analysis and data
6884visualization of biological sequence (DNA and protein) data. It also includes
6885utilities for sequence data management under the ACNUC system.")
6886 (license license:gpl2+)))
6887
78addcb0
RW		 6888(define-public r-iranges
6889 (package
6890 (name "r-iranges")
9e482c20 6891 (version "2.12.0")
78addcb0
RW		 6892 (source (origin
6893 (method url-fetch)
6894 (uri (bioconductor-uri "IRanges" version))
6895 (sha256
6896 (base32
9e482c20 6897 "1vqczb9wlxsmpwpqig6j1dmiblcfpq6mgnq8qwzcrvddm4cp47m5"))))
78addcb0 6898 (properties
1d216b6e 6899 `((upstream-name . "IRanges")))
78addcb0
RW		 6900 (build-system r-build-system)
6901 (propagated-inputs
6902 `(("r-biocgenerics" ,r-biocgenerics)
6903 ("r-s4vectors" ,r-s4vectors)))
5713bbf1 6904 (home-page "https://bioconductor.org/packages/IRanges")
78addcb0
RW		 6905 (synopsis "Infrastructure for manipulating intervals on sequences")
6906 (description
6907 "This package provides efficient low-level and highly reusable S4 classes
6908for storing ranges of integers, RLE vectors (Run-Length Encoding), and, more
6909generally, data that can be organized sequentially (formally defined as
6910@code{Vector} objects), as well as views on these @code{Vector} objects.
6911Efficient list-like classes are also provided for storing big collections of
6912instances of the basic classes. All classes in the package use consistent
6913naming and share the same rich and consistent \"Vector API\" as much as
6914possible.")
6915 (license license:artistic2.0)))
6916
ffef27f3
RJ		 6917(define-public r-genomeinfodbdata
6918 (package
6919 (name "r-genomeinfodbdata")
261b38a9 6920 (version "0.99.1")
ffef27f3
RJ		 6921 (source (origin
6922 (method url-fetch)
90f83099
EF		 6923 ;; We cannot use bioconductor-uri here because this tarball is
6924 ;; located under "data/annotation/" instead of "bioc/".
6925 (uri (string-append "https://bioconductor.org/packages/release/"
6926 "data/annotation/src/contrib/GenomeInfoDbData_"
6927 version ".tar.gz"))
ffef27f3
RJ		 6928 (sha256
6929 (base32
261b38a9 6930 "0hipipvyvrh75n68hsjg35sxbcfzrghzxv547vnkk2f8ya99g01r"))))
ffef27f3
RJ		 6931 (properties
6932 `((upstream-name . "GenomeInfoDbData")))
6933 (build-system r-build-system)
5713bbf1 6934 (home-page "https://bioconductor.org/packages/GenomeInfoDbData")
ffef27f3
RJ		 6935 (synopsis "Species and taxonomy ID look up tables for GenomeInfoDb")
6936 (description "This package contains data for mapping between NCBI taxonomy
6937ID and species. It is used by functions in the GenomeInfoDb package.")
6938 (license license:artistic2.0)))
6939
bf7764b7
RW		 6940(define-public r-genomeinfodb
6941 (package
6942 (name "r-genomeinfodb")
8aab0235 6943 (version "1.14.0")
bf7764b7
RW		 6944 (source (origin
6945 (method url-fetch)
6946 (uri (bioconductor-uri "GenomeInfoDb" version))
6947 (sha256
6948 (base32
8aab0235 6949 "1jhm0imkac4gvchbjxj408aakk39xdv2fyh818d3lk295bz6bnyp"))))
bf7764b7 6950 (properties
1d216b6e 6951 `((upstream-name . "GenomeInfoDb")))
bf7764b7
RW		 6952 (build-system r-build-system)
6953 (propagated-inputs
6954 `(("r-biocgenerics" ,r-biocgenerics)
38b99ccc 6955 ("r-genomeinfodbdata" ,r-genomeinfodbdata)
bf7764b7 6956 ("r-iranges" ,r-iranges)
4cd07e48 6957 ("r-rcurl" ,r-rcurl)
bf7764b7 6958 ("r-s4vectors" ,r-s4vectors)))
5713bbf1 6959 (home-page "https://bioconductor.org/packages/GenomeInfoDb")
bf7764b7
RW		 6960 (synopsis "Utilities for manipulating chromosome identifiers")
6961 (description
6962 "This package contains data and functions that define and allow
6963translation between different chromosome sequence naming conventions (e.g.,
6964\"chr1\" versus \"1\"), including a function that attempts to place sequence
6965names in their natural, rather than lexicographic, order.")
6966 (license license:artistic2.0)))
6967
744004a3
RJ		 6968(define-public r-edger
6969 (package
6970 (name "r-edger")
22d96920 6971 (version "3.20.9")
744004a3
RJ		 6972 (source (origin
6973 (method url-fetch)
6974 (uri (bioconductor-uri "edgeR" version))
6975 (sha256
6976 (base32
22d96920 6977 "0y52snwbz37xzdd7gihdkqczbndlfzmmypv6hri3ymjyfmlx6qaw"))))
744004a3
RJ		 6978 (properties `((upstream-name . "edgeR")))
6979 (build-system r-build-system)
6980 (propagated-inputs
5e48005f 6981 `(("r-limma" ,r-limma)
47055b27 6982 ("r-locfit" ,r-locfit)
010ab2ff 6983 ("r-rcpp" ,r-rcpp)
47055b27 6984 ("r-statmod" ,r-statmod))) ;for estimateDisp
744004a3
RJ		 6985 (home-page "http://bioinf.wehi.edu.au/edgeR")
6986 (synopsis "EdgeR does empirical analysis of digital gene expression data")
6987 (description "This package can do differential expression analysis of
6988RNA-seq expression profiles with biological replication. It implements a range
6989of statistical methodology based on the negative binomial distributions,
6990including empirical Bayes estimation, exact tests, generalized linear models
6991and quasi-likelihood tests. It be applied to differential signal analysis of
6992other types of genomic data that produce counts, including ChIP-seq, SAGE and
6993CAGE.")
6994 (license license:gpl2+)))
6995
b669d9c4
RJ		 6996(define-public r-variantannotation
6997 (package
6998 (name "r-variantannotation")
5fb1fee6 6999 (version "1.24.5")
b669d9c4
RJ		 7000 (source (origin
7001 (method url-fetch)
7002 (uri (bioconductor-uri "VariantAnnotation" version))
7003 (sha256
7004 (base32
5fb1fee6 7005 "07ywn3c4w83l3sr76d0z3b1nv9icgdh3phsjlc6cfx7i6nfmvxw2"))))
b669d9c4
RJ		 7006 (properties
7007 `((upstream-name . "VariantAnnotation")))
7008 (inputs
7009 `(("zlib" ,zlib)))
7010 (propagated-inputs
7011 `(("r-annotationdbi" ,r-annotationdbi)
37d96f1d 7012 ("r-biobase" ,r-biobase)
b669d9c4 7013 ("r-biocgenerics" ,r-biocgenerics)
37d96f1d 7014 ("r-biostrings" ,r-biostrings)
b669d9c4
RJ		 7015 ("r-bsgenome" ,r-bsgenome)
7016 ("r-dbi" ,r-dbi)
7017 ("r-genomeinfodb" ,r-genomeinfodb)
7018 ("r-genomicfeatures" ,r-genomicfeatures)
7019 ("r-genomicranges" ,r-genomicranges)
37d96f1d 7020 ("r-iranges" ,r-iranges)
b669d9c4
RJ		 7021 ("r-summarizedexperiment" ,r-summarizedexperiment)
7022 ("r-rsamtools" ,r-rsamtools)
37d96f1d
RW		 7023 ("r-rtracklayer" ,r-rtracklayer)
7024 ("r-s4vectors" ,r-s4vectors)
7025 ("r-xvector" ,r-xvector)
b669d9c4
RJ		 7026 ("r-zlibbioc" ,r-zlibbioc)))
7027 (build-system r-build-system)
7028 (home-page "https://bioconductor.org/packages/VariantAnnotation")
7029 (synopsis "Package for annotation of genetic variants")
7030 (description "This R package can annotate variants, compute amino acid
7031coding changes and predict coding outcomes.")
7032 (license license:artistic2.0)))
7033
7d4224d7
RJ		 7034(define-public r-limma
7035 (package
7036 (name "r-limma")
eb8971b7 7037 (version "3.34.9")
7d4224d7
RJ		 7038 (source (origin
7039 (method url-fetch)
7040 (uri (bioconductor-uri "limma" version))
7041 (sha256
7042 (base32
eb8971b7 7043 "1y2fm61g5i0fn0j3l31xvwh9zww9bpkc4nwzb1d0yv1cag20jkdc"))))
7d4224d7
RJ		 7044 (build-system r-build-system)
7045 (home-page "http://bioinf.wehi.edu.au/limma")
7046 (synopsis "Package for linear models for microarray and RNA-seq data")
7047 (description "This package can be used for the analysis of gene expression
7048studies, especially the use of linear models for analysing designed experiments
7049and the assessment of differential expression. The analysis methods apply to
7050different technologies, including microarrays, RNA-seq, and quantitative PCR.")
7051 (license license:gpl2+)))
7052
0e7d5560
RW		 7053(define-public r-xvector
7054 (package
7055 (name "r-xvector")
2b6ae8bf 7056 (version "0.18.0")
0e7d5560
RW		 7057 (source (origin
7058 (method url-fetch)
7059 (uri (bioconductor-uri "XVector" version))
7060 (sha256
7061 (base32
2b6ae8bf 7062 "1i4i3kdxr78lr1kcxq657p11ybi7kq10c8kyaqyh6gfc8i9rhvmk"))))
0e7d5560 7063 (properties
1d216b6e 7064 `((upstream-name . "XVector")))
0e7d5560
RW		 7065 (build-system r-build-system)
7066 (arguments
7067 `(#:phases
7068 (modify-phases %standard-phases
7069 (add-after 'unpack 'use-system-zlib
7070 (lambda _
7071 (substitute* "DESCRIPTION"
7072 (("zlibbioc, ") ""))
7073 (substitute* "NAMESPACE"
7074 (("import\\(zlibbioc\\)") ""))
7075 #t)))))
7076 (inputs
7077 `(("zlib" ,zlib)))
7078 (propagated-inputs
7079 `(("r-biocgenerics" ,r-biocgenerics)
7080 ("r-iranges" ,r-iranges)
7081 ("r-s4vectors" ,r-s4vectors)))
5713bbf1 7082 (home-page "https://bioconductor.org/packages/XVector")
0e7d5560
RW		 7083 (synopsis "Representation and manpulation of external sequences")
7084 (description
7085 "This package provides memory efficient S4 classes for storing sequences
7086\"externally\" (behind an R external pointer, or on disk).")
7087 (license license:artistic2.0)))
7088
e2cd1d0f
RW		 7089(define-public r-genomicranges
7090 (package
7091 (name "r-genomicranges")
535014ce 7092 (version "1.30.3")
e2cd1d0f
RW		 7093 (source (origin
7094 (method url-fetch)
7095 (uri (bioconductor-uri "GenomicRanges" version))
7096 (sha256
7097 (base32
535014ce 7098 "07cszc9ri94nzk4dffwnsj247ih6pchnrzrvnb0q4dkk33gwy8n1"))))
e2cd1d0f 7099 (properties
1d216b6e 7100 `((upstream-name . "GenomicRanges")))
e2cd1d0f
RW		 7101 (build-system r-build-system)
7102 (propagated-inputs
7103 `(("r-biocgenerics" ,r-biocgenerics)
7104 ("r-genomeinfodb" ,r-genomeinfodb)
92a740af
RW		 7105 ("r-iranges" ,r-iranges)
7106 ("r-s4vectors" ,r-s4vectors)
e2cd1d0f 7107 ("r-xvector" ,r-xvector)))
5713bbf1 7108 (home-page "https://bioconductor.org/packages/GenomicRanges")
e2cd1d0f
RW		 7109 (synopsis "Representation and manipulation of genomic intervals")
7110 (description
7111 "This package provides tools to efficiently represent and manipulate
7112genomic annotations and alignments is playing a central role when it comes to
7113analyzing high-throughput sequencing data (a.k.a. NGS data). The
7114GenomicRanges package defines general purpose containers for storing and
7115manipulating genomic intervals and variables defined along a genome.")
7116 (license license:artistic2.0)))
7117
555e3399
RW		 7118(define-public r-biobase
7119 (package
7120 (name "r-biobase")
ca521236 7121 (version "2.38.0")
555e3399
RW		 7122 (source (origin
7123 (method url-fetch)
7124 (uri (bioconductor-uri "Biobase" version))
7125 (sha256
7126 (base32
ca521236 7127 "1cgm1ja1kp56zdlzyy9ggbkfn8r2vbsd4hncmz8g4hjd47fg18kg"))))
555e3399
RW		 7128 (properties
7129 `((upstream-name . "Biobase")))
7130 (build-system r-build-system)
7131 (propagated-inputs
7132 `(("r-biocgenerics" ,r-biocgenerics)))
5713bbf1 7133 (home-page "https://bioconductor.org/packages/Biobase")
555e3399
RW		 7134 (synopsis "Base functions for Bioconductor")
7135 (description
7136 "This package provides functions that are needed by many other packages
7137on Bioconductor or which replace R functions.")
7138 (license license:artistic2.0)))
7139
8b7bce74
RW		 7140(define-public r-annotationdbi
7141 (package
7142 (name "r-annotationdbi")
0f8d98f2 7143 (version "1.40.0")
8b7bce74
RW		 7144 (source (origin
7145 (method url-fetch)
7146 (uri (bioconductor-uri "AnnotationDbi" version))
7147 (sha256
7148 (base32
0f8d98f2 7149 "1dh4qs1a757n640gs34lf6z2glc96nan86x0sqaw5csadl2rhnlc"))))
8b7bce74
RW		 7150 (properties
7151 `((upstream-name . "AnnotationDbi")))
7152 (build-system r-build-system)
7153 (propagated-inputs
7154 `(("r-biobase" ,r-biobase)
7155 ("r-biocgenerics" ,r-biocgenerics)
7156 ("r-dbi" ,r-dbi)
7157 ("r-iranges" ,r-iranges)
7158 ("r-rsqlite" ,r-rsqlite)
7159 ("r-s4vectors" ,r-s4vectors)))
5713bbf1 7160 (home-page "https://bioconductor.org/packages/AnnotationDbi")
8b7bce74
RW		 7161 (synopsis "Annotation database interface")
7162 (description
7163 "This package provides user interface and database connection code for
7164annotation data packages using SQLite data storage.")
7165 (license license:artistic2.0)))
7166
c465fa72
RW		 7167(define-public r-biomart
7168 (package
7169 (name "r-biomart")
37343067 7170 (version "2.34.2")
c465fa72
RW		 7171 (source (origin
7172 (method url-fetch)
7173 (uri (bioconductor-uri "biomaRt" version))
7174 (sha256
7175 (base32
37343067 7176 "1zlgs2zg0lmnk572p55n7m34nkxka8w10x8f2ndssjkffl2csy79"))))
c465fa72
RW		 7177 (properties
7178 `((upstream-name . "biomaRt")))
7179 (build-system r-build-system)
7180 (propagated-inputs
7181 `(("r-annotationdbi" ,r-annotationdbi)
b9e8a5c5 7182 ("r-httr" ,r-httr)
42e11d33 7183 ("r-progress" ,r-progress)
c465fa72 7184 ("r-rcurl" ,r-rcurl)
42e11d33 7185 ("r-stringr" ,r-stringr)
c465fa72 7186 ("r-xml" ,r-xml)))
5713bbf1 7187 (home-page "https://bioconductor.org/packages/biomaRt")
c465fa72
RW		 7188 (synopsis "Interface to BioMart databases")
7189 (description
7190 "biomaRt provides an interface to a growing collection of databases
7191implementing the @url{BioMart software suite, http://www.biomart.org}. The
7192package enables retrieval of large amounts of data in a uniform way without
7193the need to know the underlying database schemas or write complex SQL queries.
7194Examples of BioMart databases are Ensembl, COSMIC, Uniprot, HGNC, Gramene,
7195Wormbase and dbSNP mapped to Ensembl. These major databases give biomaRt
7196users direct access to a diverse set of data and enable a wide range of
7197powerful online queries from gene annotation to database mining.")
7198 (license license:artistic2.0)))
7199
e91d362e
RW		 7200(define-public r-biocparallel
7201 (package
7202 (name "r-biocparallel")
a044c7f4 7203 (version "1.12.0")
e91d362e
RW		 7204 (source (origin
7205 (method url-fetch)
7206 (uri (bioconductor-uri "BiocParallel" version))
7207 (sha256
7208 (base32
a044c7f4 7209 "13ng3n2wsgl3fh0v6jnz3vg51k5c1sh44pqdvblcrcd1qyjmmqhd"))))
e91d362e
RW		 7210 (properties
7211 `((upstream-name . "BiocParallel")))
7212 (build-system r-build-system)
7213 (propagated-inputs
7214 `(("r-futile-logger" ,r-futile-logger)
a044c7f4
RW		 7215 ("r-snow" ,r-snow)
7216 ("r-bh" ,r-bh)))
5713bbf1 7217 (home-page "https://bioconductor.org/packages/BiocParallel")
e91d362e
RW		 7218 (synopsis "Bioconductor facilities for parallel evaluation")
7219 (description
7220 "This package provides modified versions and novel implementation of
7221functions for parallel evaluation, tailored to use with Bioconductor
7222objects.")
7223 (license (list license:gpl2+ license:gpl3+))))
7224
bf159353
RW		 7225(define-public r-biostrings
7226 (package
7227 (name "r-biostrings")
b719435e 7228 (version "2.46.0")
bf159353
RW		 7229 (source (origin
7230 (method url-fetch)
7231 (uri (bioconductor-uri "Biostrings" version))
7232 (sha256
7233 (base32
b719435e 7234 "0vg50qdlxqcm2d6axjnzg8wh8pr4c5gz03l8bdl0llmwzp0zclzk"))))
bf159353
RW		 7235 (properties
7236 `((upstream-name . "Biostrings")))
7237 (build-system r-build-system)
7238 (propagated-inputs
7239 `(("r-biocgenerics" ,r-biocgenerics)
7240 ("r-iranges" ,r-iranges)
7241 ("r-s4vectors" ,r-s4vectors)
7242 ("r-xvector" ,r-xvector)))
5713bbf1 7243 (home-page "https://bioconductor.org/packages/Biostrings")
bf159353
RW		 7244 (synopsis "String objects and algorithms for biological sequences")
7245 (description
7246 "This package provides memory efficient string containers, string
7247matching algorithms, and other utilities, for fast manipulation of large
7248biological sequences or sets of sequences.")
7249 (license license:artistic2.0)))
7250
f8d74f70
RW		 7251(define-public r-rsamtools
7252 (package
7253 (name "r-rsamtools")
f8068419 7254 (version "1.30.0")
f8d74f70
RW		 7255 (source (origin
7256 (method url-fetch)
7257 (uri (bioconductor-uri "Rsamtools" version))
7258 (sha256
7259 (base32
f8068419 7260 "0pjny5fjvbnfdyhl3bwxin678sha2drvs00sivxh3l772cn6yams"))))
f8d74f70
RW		 7261 (properties
7262 `((upstream-name . "Rsamtools")))
7263 (build-system r-build-system)
7264 (arguments
7265 `(#:phases
7266 (modify-phases %standard-phases
7267 (add-after 'unpack 'use-system-zlib
7268 (lambda _
7269 (substitute* "DESCRIPTION"
7270 (("zlibbioc, ") ""))
7271 (substitute* "NAMESPACE"
7272 (("import\\(zlibbioc\\)") ""))
7273 #t)))))
7274 (inputs
7275 `(("zlib" ,zlib)))
7276 (propagated-inputs
7277 `(("r-biocgenerics" ,r-biocgenerics)
7278 ("r-biocparallel" ,r-biocparallel)
7279 ("r-biostrings" ,r-biostrings)
7280 ("r-bitops" ,r-bitops)
7281 ("r-genomeinfodb" ,r-genomeinfodb)
7282 ("r-genomicranges" ,r-genomicranges)
7283 ("r-iranges" ,r-iranges)
7284 ("r-s4vectors" ,r-s4vectors)
7285 ("r-xvector" ,r-xvector)))
5713bbf1 7286 (home-page "https://bioconductor.org/packages/release/bioc/html/Rsamtools.html")
f8d74f70
RW		 7287 (synopsis "Interface to samtools, bcftools, and tabix")
7288 (description
7289 "This package provides an interface to the 'samtools', 'bcftools', and
7290'tabix' utilities for manipulating SAM (Sequence Alignment / Map), FASTA,
7291binary variant call (BCF) and compressed indexed tab-delimited (tabix)
7292files.")
7293 (license license:expat)))
7294
71e34e6b
RJ		 7295(define-public r-delayedarray
7296 (package
7297 (name "r-delayedarray")
cb0a9a74 7298 (version "0.4.1")
71e34e6b
RJ		 7299 (source (origin
7300 (method url-fetch)
7301 (uri (bioconductor-uri "DelayedArray" version))
7302 (sha256
7303 (base32
cb0a9a74 7304 "0s7h2giyvz04cg6248kbbzpwhxdrpnsvl2s8k5c8ricisd9aaz4b"))))
71e34e6b
RJ		 7305 (properties
7306 `((upstream-name . "DelayedArray")))
7307 (build-system r-build-system)
7308 (propagated-inputs
7309 `(("r-biocgenerics" ,r-biocgenerics)
7310 ("r-s4vectors" ,r-s4vectors)
7311 ("r-iranges" ,r-iranges)
7312 ("r-matrixstats" ,r-matrixstats)))
5713bbf1 7313 (home-page "https://bioconductor.org/packages/DelayedArray")
71e34e6b
RJ		 7314 (synopsis "Delayed operations on array-like objects")
7315 (description
7316 "Wrapping an array-like object (typically an on-disk object) in a
7317@code{DelayedArray} object allows one to perform common array operations on it
7318without loading the object in memory. In order to reduce memory usage and
7319optimize performance, operations on the object are either delayed or executed
7320using a block processing mechanism. Note that this also works on in-memory
7321array-like objects like @code{DataFrame} objects (typically with Rle columns),
7322@code{Matrix} objects, and ordinary arrays and data frames.")
7323 (license license:artistic2.0)))
7324
6e76dda2
RW		 7325(define-public r-summarizedexperiment
7326 (package
7327 (name "r-summarizedexperiment")
c37b361e 7328 (version "1.8.1")
6e76dda2
RW		 7329 (source (origin
7330 (method url-fetch)
7331 (uri (bioconductor-uri "SummarizedExperiment" version))
7332 (sha256
7333 (base32
c37b361e 7334 "19vlwnby83fqjrilsxvnvgz0gvby7mrxvlmx18nb3p1w591ddfjh"))))
6e76dda2
RW		 7335 (properties
7336 `((upstream-name . "SummarizedExperiment")))
7337 (build-system r-build-system)
7338 (propagated-inputs
7339 `(("r-biobase" ,r-biobase)
7340 ("r-biocgenerics" ,r-biocgenerics)
d006ee31 7341 ("r-delayedarray" ,r-delayedarray)
6e76dda2
RW		 7342 ("r-genomeinfodb" ,r-genomeinfodb)
7343 ("r-genomicranges" ,r-genomicranges)
7344 ("r-iranges" ,r-iranges)
aeb64f3c 7345 ("r-matrix" ,r-matrix)
6e76dda2 7346 ("r-s4vectors" ,r-s4vectors)))
5713bbf1 7347 (home-page "https://bioconductor.org/packages/SummarizedExperiment")
6e76dda2
RW		 7348 (synopsis "Container for representing genomic ranges by sample")
7349 (description
7350 "The SummarizedExperiment container contains one or more assays, each
7351represented by a matrix-like object of numeric or other mode. The rows
7352typically represent genomic ranges of interest and the columns represent
7353samples.")
7354 (license license:artistic2.0)))
7355
d8a828af
RW		 7356(define-public r-genomicalignments
7357 (package
7358 (name "r-genomicalignments")
06e8e0fc 7359 (version "1.14.1")
d8a828af
RW		 7360 (source (origin
7361 (method url-fetch)
7362 (uri (bioconductor-uri "GenomicAlignments" version))
7363 (sha256
7364 (base32
06e8e0fc 7365 "033p6fw46sn7w2yyn14nb9qcnkf30cl0nv6zh014ixflm3iifz39"))))
d8a828af
RW		 7366 (properties
7367 `((upstream-name . "GenomicAlignments")))
7368 (build-system r-build-system)
7369 (propagated-inputs
7370 `(("r-biocgenerics" ,r-biocgenerics)
7371 ("r-biocparallel" ,r-biocparallel)
7372 ("r-biostrings" ,r-biostrings)
7373 ("r-genomeinfodb" ,r-genomeinfodb)
7374 ("r-genomicranges" ,r-genomicranges)
7375 ("r-iranges" ,r-iranges)
7376 ("r-rsamtools" ,r-rsamtools)
7377 ("r-s4vectors" ,r-s4vectors)
7378 ("r-summarizedexperiment" ,r-summarizedexperiment)))
5713bbf1 7379 (home-page "https://bioconductor.org/packages/GenomicAlignments")
d8a828af
RW		 7380 (synopsis "Representation and manipulation of short genomic alignments")
7381 (description
7382 "This package provides efficient containers for storing and manipulating
7383short genomic alignments (typically obtained by aligning short reads to a
7384reference genome). This includes read counting, computing the coverage,
7385junction detection, and working with the nucleotide content of the
7386alignments.")
7387 (license license:artistic2.0)))
7388
317755ff
RW		 7389(define-public r-rtracklayer
7390 (package
7391 (name "r-rtracklayer")
99b3236e 7392 (version "1.38.3")
317755ff
RW		 7393 (source (origin
7394 (method url-fetch)
7395 (uri (bioconductor-uri "rtracklayer" version))
7396 (sha256
7397 (base32
99b3236e 7398 "1khzfczm35k5lq9h0jlqrq01192spzjyh8s6is89spj006flwn4k"))))
317755ff
RW		 7399 (build-system r-build-system)
7400 (arguments
7401 `(#:phases
7402 (modify-phases %standard-phases
7403 (add-after 'unpack 'use-system-zlib
7404 (lambda _
7405 (substitute* "DESCRIPTION"
4dd469ef 7406 ((" zlibbioc,") ""))
317755ff
RW		 7407 (substitute* "NAMESPACE"
7408 (("import\\(zlibbioc\\)") ""))
7409 #t)))))
7410 (inputs
7411 `(("zlib" ,zlib)))
7412 (propagated-inputs
7413 `(("r-biocgenerics" ,r-biocgenerics)
7414 ("r-biostrings" ,r-biostrings)
7415 ("r-genomeinfodb" ,r-genomeinfodb)
7416 ("r-genomicalignments" ,r-genomicalignments)
7417 ("r-genomicranges" ,r-genomicranges)
7418 ("r-iranges" ,r-iranges)
7419 ("r-rcurl" ,r-rcurl)
7420 ("r-rsamtools" ,r-rsamtools)
7421 ("r-s4vectors" ,r-s4vectors)
7422 ("r-xml" ,r-xml)
7423 ("r-xvector" ,r-xvector)))
5713bbf1 7424 (home-page "https://bioconductor.org/packages/rtracklayer")
317755ff
RW		 7425 (synopsis "R interface to genome browsers and their annotation tracks")
7426 (description
7427 "rtracklayer is an extensible framework for interacting with multiple
7428genome browsers (currently UCSC built-in) and manipulating annotation tracks
7429in various formats (currently GFF, BED, bedGraph, BED15, WIG, BigWig and 2bit
7430built-in). The user may export/import tracks to/from the supported browsers,
7431as well as query and modify the browser state, such as the current viewport.")
7432 (license license:artistic2.0)))
7433
2fd7c049
RW		 7434(define-public r-genomicfeatures
7435 (package
7436 (name "r-genomicfeatures")
0b188565 7437 (version "1.30.3")
2fd7c049
RW		 7438 (source (origin
7439 (method url-fetch)
7440 (uri (bioconductor-uri "GenomicFeatures" version))
7441 (sha256
7442 (base32
0b188565 7443 "010vn8hlwbnw12pd1d8pv6m12yp3xwx557gba5rbjq9p4qypnn3z"))))
2fd7c049
RW		 7444 (properties
7445 `((upstream-name . "GenomicFeatures")))
7446 (build-system r-build-system)
7447 (propagated-inputs
7448 `(("r-annotationdbi" ,r-annotationdbi)
7449 ("r-biobase" ,r-biobase)
7450 ("r-biocgenerics" ,r-biocgenerics)
7451 ("r-biomart" ,r-biomart)
7452 ("r-biostrings" ,r-biostrings)
7453 ("r-dbi" ,r-dbi)
7454 ("r-genomeinfodb" ,r-genomeinfodb)
7455 ("r-genomicranges" ,r-genomicranges)
7456 ("r-iranges" ,r-iranges)
7457 ("r-rcurl" ,r-rcurl)
7458 ("r-rsqlite" ,r-rsqlite)
158b6743 7459 ("r-rmysql" ,r-rmysql)
2fd7c049
RW		 7460 ("r-rtracklayer" ,r-rtracklayer)
7461 ("r-s4vectors" ,r-s4vectors)
7462 ("r-xvector" ,r-xvector)))
5713bbf1 7463 (home-page "https://bioconductor.org/packages/GenomicFeatures")
2fd7c049
RW		 7464 (synopsis "Tools for working with transcript centric annotations")
7465 (description
7466 "This package provides a set of tools and methods for making and
7467manipulating transcript centric annotations. With these tools the user can
7468easily download the genomic locations of the transcripts, exons and cds of a
7469given organism, from either the UCSC Genome Browser or a BioMart
7470database (more sources will be supported in the future). This information is
7471then stored in a local database that keeps track of the relationship between
7472transcripts, exons, cds and genes. Flexible methods are provided for
7473extracting the desired features in a convenient format.")
7474 (license license:artistic2.0)))
7475
fb25d880
RW		 7476(define-public r-go-db
7477 (package
7478 (name "r-go-db")
592f4a94 7479 (version "3.5.0")
fb25d880
RW		 7480 (source (origin
7481 (method url-fetch)
5713bbf1 7482 (uri (string-append "https://www.bioconductor.org/packages/"
f82c8c3c
PP		 7483 "release/data/annotation/src/contrib/GO.db_"
7484 version ".tar.gz"))
fb25d880
RW		 7485 (sha256
7486 (base32
592f4a94 7487 "02d1mn1al3q7qvhx1ylrr3ar4w4iw0qyi5d89v2336rzwk9maq35"))))
fb25d880
RW		 7488 (properties
7489 `((upstream-name . "GO.db")))
7490 (build-system r-build-system)
3141b83d
RW		 7491 (propagated-inputs
7492 `(("r-annotationdbi" ,r-annotationdbi)))
5713bbf1 7493 (home-page "https://bioconductor.org/packages/GO.db")
fb25d880
RW		 7494 (synopsis "Annotation maps describing the entire Gene Ontology")
7495 (description
7496 "The purpose of this GO.db annotation package is to provide detailed
7497information about the latest version of the Gene Ontologies.")
7498 (license license:artistic2.0)))
7499
d1dbde6a
RW		 7500(define-public r-graph
7501 (package
7502 (name "r-graph")
aeb73879 7503 (version "1.56.0")
d1dbde6a
RW		 7504 (source (origin
7505 (method url-fetch)
7506 (uri (bioconductor-uri "graph" version))
7507 (sha256
7508 (base32
aeb73879 7509 "15aajjp8h2z14p80c8hyd4rrmr9vqsm7bvwb989jxjl4k6g52an1"))))
d1dbde6a
RW		 7510 (build-system r-build-system)
7511 (propagated-inputs
7512 `(("r-biocgenerics" ,r-biocgenerics)))
5713bbf1 7513 (home-page "https://bioconductor.org/packages/graph")
d1dbde6a
RW		 7514 (synopsis "Handle graph data structures in R")
7515 (description
7516 "This package implements some simple graph handling capabilities for R.")
7517 (license license:artistic2.0)))
7518
d547ce5e
RW		 7519(define-public r-topgo
7520 (package
7521 (name "r-topgo")
61cbd49b 7522 (version "2.30.1")
d547ce5e
RW		 7523 (source (origin
7524 (method url-fetch)
7525 (uri (bioconductor-uri "topGO" version))
7526 (sha256
7527 (base32
61cbd49b 7528 "1cgz4knxr328xfqlhl6ypxl6x86rfrlqz748kn94ainxjzz55i6x"))))
d547ce5e
RW		 7529 (properties
7530 `((upstream-name . "topGO")))
7531 (build-system r-build-system)
7532 (propagated-inputs
7533 `(("r-annotationdbi" ,r-annotationdbi)
30ec4de7 7534 ("r-dbi" ,r-dbi)
d547ce5e
RW		 7535 ("r-biobase" ,r-biobase)
7536 ("r-biocgenerics" ,r-biocgenerics)
7537 ("r-go-db" ,r-go-db)
6d415db2 7538 ("r-graph" ,r-graph)
aeb64f3c
RW		 7539 ("r-lattice" ,r-lattice)
7540 ("r-matrixstats" ,r-matrixstats)
d547ce5e 7541 ("r-sparsem" ,r-sparsem)))
5713bbf1 7542 (home-page "https://bioconductor.org/packages/topGO")
d547ce5e
RW		 7543 (synopsis "Enrichment analysis for gene ontology")
7544 (description
7545 "The topGO package provides tools for testing @dfn{gene ontology} (GO)
7546terms while accounting for the topology of the GO graph. Different test
7547statistics and different methods for eliminating local similarities and
7548dependencies between GO terms can be implemented and applied.")
7549 ;; Any version of the LGPL applies.
7550 (license license:lgpl2.1+)))
7551
c63cef66
RW		 7552(define-public r-bsgenome
7553 (package
7554 (name "r-bsgenome")
e67850b4 7555 (version "1.46.0")
c63cef66
RW		 7556 (source (origin
7557 (method url-fetch)
7558 (uri (bioconductor-uri "BSgenome" version))
7559 (sha256
7560 (base32
e67850b4 7561 "1jbzq7lm2iajajn2bifxnkss0k9fdvgqr30mral17cbhp5f6w4lq"))))
c63cef66
RW		 7562 (properties
7563 `((upstream-name . "BSgenome")))
7564 (build-system r-build-system)
7565 (propagated-inputs
7566 `(("r-biocgenerics" ,r-biocgenerics)
7567 ("r-biostrings" ,r-biostrings)
7568 ("r-genomeinfodb" ,r-genomeinfodb)
7569 ("r-genomicranges" ,r-genomicranges)
7570 ("r-iranges" ,r-iranges)
7571 ("r-rsamtools" ,r-rsamtools)
7572 ("r-rtracklayer" ,r-rtracklayer)
7573 ("r-s4vectors" ,r-s4vectors)
7574 ("r-xvector" ,r-xvector)))
5713bbf1 7575 (home-page "https://bioconductor.org/packages/BSgenome")
c63cef66
RW		 7576 (synopsis "Infrastructure for Biostrings-based genome data packages")
7577 (description
7578 "This package provides infrastructure shared by all Biostrings-based
7579genome data packages and support for efficient SNP representation.")
7580 (license license:artistic2.0)))
7581
aa3eeeb5
RJ		 7582(define-public r-bsgenome-hsapiens-1000genomes-hs37d5
7583 (package
7584 (name "r-bsgenome-hsapiens-1000genomes-hs37d5")
7585 (version "0.99.1")
7586 (source (origin
7587 (method url-fetch)
7588 ;; We cannot use bioconductor-uri here because this tarball is
7589 ;; located under "data/annotation/" instead of "bioc/".
5713bbf1 7590 (uri (string-append "https://www.bioconductor.org/packages/"
aa3eeeb5
RJ		 7591 "release/data/annotation/src/contrib/"
7592 "BSgenome.Hsapiens.1000genomes.hs37d5_"
7593 version ".tar.gz"))
7594 (sha256
7595 (base32
7596 "1cg0g5fqmsvwyw2p9hp2yy4ilk21jkbbrnpgqvb5c36ihjwvc7sr"))))
7597 (properties
7598 `((upstream-name . "BSgenome.Hsapiens.1000genomes.hs37d5")))
7599 (build-system r-build-system)
7600 ;; As this package provides little more than a very large data file it
7601 ;; doesn't make sense to build substitutes.
7602 (arguments `(#:substitutable? #f))
7603 (propagated-inputs
7604 `(("r-bsgenome" ,r-bsgenome)))
7605 (home-page
5713bbf1 7606 "https://www.bioconductor.org/packages/BSgenome.Hsapiens.1000genomes.hs37d5/")
aa3eeeb5
RJ		 7607 (synopsis "Full genome sequences for Homo sapiens")
7608 (description
7609 "This package provides full genome sequences for Homo sapiens from
76101000genomes phase2 reference genome sequence (hs37d5), based on NCBI GRCh37.")
7611 (license license:artistic2.0)))
7612
c43a011d
RW		 7613(define-public r-impute
7614 (package
7615 (name "r-impute")
e6ce4bf0 7616 (version "1.52.0")
c43a011d
RW		 7617 (source (origin
7618 (method url-fetch)
7619 (uri (bioconductor-uri "impute" version))
7620 (sha256
7621 (base32
e6ce4bf0 7622 "0b8r4swvyx3cjcc2ky8yn0ncpzlbi1pgfsn3wpbjmhh7sqrffm2n"))))
c43a011d
RW		 7623 (inputs
7624 `(("gfortran" ,gfortran)))
7625 (build-system r-build-system)
5713bbf1 7626 (home-page "https://bioconductor.org/packages/impute")
c43a011d
RW		 7627 (synopsis "Imputation for microarray data")
7628 (description
7629 "This package provides a function to impute missing gene expression
7630microarray data, using nearest neighbor averaging.")
7631 (license license:gpl2+)))
7632
03ea5a35
RW		 7633(define-public r-seqpattern
7634 (package
7635 (name "r-seqpattern")
0f948b11 7636 (version "1.10.0")
03ea5a35
RW		 7637 (source (origin
7638 (method url-fetch)
7639 (uri (bioconductor-uri "seqPattern" version))
7640 (sha256
7641 (base32
0f948b11 7642 "1kcm5w83q7w0v0vs7nyp4gq5z86c6n6pqy9zmyyhxcrns7f597pm"))))
03ea5a35
RW		 7643 (properties
7644 `((upstream-name . "seqPattern")))
7645 (build-system r-build-system)
7646 (propagated-inputs
7647 `(("r-biostrings" ,r-biostrings)
7648 ("r-genomicranges" ,r-genomicranges)
7649 ("r-iranges" ,r-iranges)
e92dd6f5 7650 ("r-kernsmooth" ,r-kernsmooth)
03ea5a35 7651 ("r-plotrix" ,r-plotrix)))
5713bbf1 7652 (home-page "https://bioconductor.org/packages/seqPattern")
03ea5a35
RW		 7653 (synopsis "Visualising oligonucleotide patterns and motif occurrences")
7654 (description
7655 "This package provides tools to visualize oligonucleotide patterns and
7656sequence motif occurrences across a large set of sequences centred at a common
7657reference point and sorted by a user defined feature.")
7658 (license license:gpl3+)))
7659
cb933df6
RW		 7660(define-public r-genomation
7661 (package
7662 (name "r-genomation")
e1129446 7663 (version "1.11.3")
cb933df6
RW		 7664 (source (origin
7665 (method url-fetch)
7666 (uri (bioconductor-uri "genomation" version))
7667 (sha256
7668 (base32
e1129446 7669 "1d2g1v6xhrf3gm86pv8ln22df5g6v6k6i4i39v4j82zn4apany6v"))))
cb933df6
RW		 7670 (build-system r-build-system)
7671 (propagated-inputs
7672 `(("r-biostrings" ,r-biostrings)
7673 ("r-bsgenome" ,r-bsgenome)
7674 ("r-data-table" ,r-data-table)
7675 ("r-genomeinfodb" ,r-genomeinfodb)
7676 ("r-genomicalignments" ,r-genomicalignments)
7677 ("r-genomicranges" ,r-genomicranges)
7678 ("r-ggplot2" ,r-ggplot2)
7679 ("r-gridbase" ,r-gridbase)
7680 ("r-impute" ,r-impute)
7681 ("r-iranges" ,r-iranges)
7682 ("r-matrixstats" ,r-matrixstats)
7683 ("r-plotrix" ,r-plotrix)
7684 ("r-plyr" ,r-plyr)
51c3c490 7685 ("r-rcpp" ,r-rcpp)
cb933df6
RW		 7686 ("r-readr" ,r-readr)
7687 ("r-reshape2" ,r-reshape2)
7688 ("r-rsamtools" ,r-rsamtools)
7689 ("r-rtracklayer" ,r-rtracklayer)
51c3c490
RW		 7690 ("r-runit" ,r-runit)
7691 ("r-s4vectors" ,r-s4vectors)
cb933df6
RW		 7692 ("r-seqpattern" ,r-seqpattern)))
7693 (home-page "http://bioinformatics.mdc-berlin.de/genomation/")
7694 (synopsis "Summary, annotation and visualization of genomic data")
7695 (description
7696 "This package provides a package for summary and annotation of genomic
7697intervals. Users can visualize and quantify genomic intervals over
7698pre-defined functional regions, such as promoters, exons, introns, etc. The
7699genomic intervals represent regions with a defined chromosome position, which
7700may be associated with a score, such as aligned reads from HT-seq experiments,
7701TF binding sites, methylation scores, etc. The package can use any tabular
7702genomic feature data as long as it has minimal information on the locations of
7703genomic intervals. In addition, it can use BAM or BigWig files as input.")
7704 (license license:artistic2.0)))
7705
64efa307
RW		 7706(define-public r-genomationdata
7707 (package
7708 (name "r-genomationdata")
57dc9b58 7709 (version "1.10.0")
64efa307
RW		 7710 (source (origin
7711 (method url-fetch)
7712 ;; We cannot use bioconductor-uri here because this tarball is
7713 ;; located under "data/annotation/" instead of "bioc/".
7714 (uri (string-append "https://bioconductor.org/packages/"
7715 "release/data/experiment/src/contrib/"
7716 "genomationData_" version ".tar.gz"))
7717 (sha256
7718 (base32
57dc9b58 7719 "0h7g5x3kyb50qlblz5hc85lfm6n6f5nb68i146way3ggs04sqvla"))))
64efa307
RW		 7720 (build-system r-build-system)
7721 ;; As this package provides little more than large data files, it doesn't
7722 ;; make sense to build substitutes.
7723 (arguments `(#:substitutable? #f))
7724 (native-inputs
7725 `(("r-knitr" ,r-knitr)))
7726 (home-page "http://bioinformatics.mdc-berlin.de/genomation/")
7727 (synopsis "Experimental data for use with the genomation package")
7728 (description
7729 "This package contains experimental genetic data for use with the
7730genomation package. Included are Chip Seq, Methylation and Cage data,
7731downloaded from Encode.")
7732 (license license:gpl3+)))
7733
486da491
RW		 7734(define-public r-org-hs-eg-db
7735 (package
7736 (name "r-org-hs-eg-db")
d595fed3 7737 (version "3.5.0")
486da491
RW		 7738 (source (origin
7739 (method url-fetch)
7740 ;; We cannot use bioconductor-uri here because this tarball is
7741 ;; located under "data/annotation/" instead of "bioc/".
5713bbf1 7742 (uri (string-append "https://www.bioconductor.org/packages/"
486da491
RW		 7743 "release/data/annotation/src/contrib/"
7744 "org.Hs.eg.db_" version ".tar.gz"))
7745 (sha256
7746 (base32
d595fed3 7747 "1v6wa5613cjq59xd7x1qz8lr9nb2abm9abl2cci1khrnrlpla927"))))
486da491
RW		 7748 (properties
7749 `((upstream-name . "org.Hs.eg.db")))
7750 (build-system r-build-system)
7751 (propagated-inputs
7752 `(("r-annotationdbi" ,r-annotationdbi)))
5713bbf1 7753 (home-page "https://www.bioconductor.org/packages/org.Hs.eg.db/")
486da491
RW		 7754 (synopsis "Genome wide annotation for Human")
7755 (description
676507e3
RW		 7756 "This package contains genome-wide annotations for Human, primarily based
7757on mapping using Entrez Gene identifiers.")
486da491
RW		 7758 (license license:artistic2.0)))
7759
fefedf98
RW		 7760(define-public r-org-ce-eg-db
7761 (package
7762 (name "r-org-ce-eg-db")
e4664290 7763 (version "3.5.0")
fefedf98
RW		 7764 (source (origin
7765 (method url-fetch)
7766 ;; We cannot use bioconductor-uri here because this tarball is
7767 ;; located under "data/annotation/" instead of "bioc/".
5713bbf1 7768 (uri (string-append "https://www.bioconductor.org/packages/"
fefedf98
RW		 7769 "release/data/annotation/src/contrib/"
7770 "org.Ce.eg.db_" version ".tar.gz"))
7771 (sha256
7772 (base32
e4664290 7773 "02ggchixlmzywhsbr0h2ms4dravv7m5964cjxqcjxqs16vjwlbk9"))))
fefedf98
RW		 7774 (properties
7775 `((upstream-name . "org.Ce.eg.db")))
7776 (build-system r-build-system)
7777 (propagated-inputs
7778 `(("r-annotationdbi" ,r-annotationdbi)))
5713bbf1 7779 (home-page "https://www.bioconductor.org/packages/org.Ce.eg.db/")
fefedf98
RW		 7780 (synopsis "Genome wide annotation for Worm")
7781 (description
7782 "This package provides mappings from Entrez gene identifiers to various
7783annotations for the genome of the model worm Caenorhabditis elegans.")
7784 (license license:artistic2.0)))
7785
16c53a1e
RW		 7786(define-public r-org-dm-eg-db
7787 (package
7788 (name "r-org-dm-eg-db")
19fc299f 7789 (version "3.5.0")
16c53a1e
RW		 7790 (source (origin
7791 (method url-fetch)
7792 ;; We cannot use bioconductor-uri here because this tarball is
7793 ;; located under "data/annotation/" instead of "bioc/".
5713bbf1 7794 (uri (string-append "https://www.bioconductor.org/packages/"
16c53a1e
RW		 7795 "release/data/annotation/src/contrib/"
7796 "org.Dm.eg.db_" version ".tar.gz"))
7797 (sha256
7798 (base32
19fc299f 7799 "033qak1d3wwz17va0bh8z8p8arx0aw2va6gm1qfwsvdkj9cd9d7d"))))
16c53a1e
RW		 7800 (properties
7801 `((upstream-name . "org.Dm.eg.db")))
7802 (build-system r-build-system)
7803 (propagated-inputs
7804 `(("r-annotationdbi" ,r-annotationdbi)))
5713bbf1 7805 (home-page "https://www.bioconductor.org/packages/org.Dm.eg.db/")
16c53a1e
RW		 7806 (synopsis "Genome wide annotation for Fly")
7807 (description
7808 "This package provides mappings from Entrez gene identifiers to various
7809annotations for the genome of the model fruit fly Drosophila melanogaster.")
7810 (license license:artistic2.0)))
7811
e761beb9
RW		 7812(define-public r-org-mm-eg-db
7813 (package
7814 (name "r-org-mm-eg-db")
f3569f52 7815 (version "3.5.0")
e761beb9
RW		 7816 (source (origin
7817 (method url-fetch)
7818 ;; We cannot use bioconductor-uri here because this tarball is
7819 ;; located under "data/annotation/" instead of "bioc/".
5713bbf1 7820 (uri (string-append "https://www.bioconductor.org/packages/"
e761beb9
RW		 7821 "release/data/annotation/src/contrib/"
7822 "org.Mm.eg.db_" version ".tar.gz"))
7823 (sha256
7824 (base32
f3569f52 7825 "11q21p3ki4bn4hb3aix0g775l45l66jmas6m94nfhqqnpjhv4d6g"))))
e761beb9
RW		 7826 (properties
7827 `((upstream-name . "org.Mm.eg.db")))
7828 (build-system r-build-system)
7829 (propagated-inputs
7830 `(("r-annotationdbi" ,r-annotationdbi)))
5713bbf1 7831 (home-page "https://www.bioconductor.org/packages/org.Mm.eg.db/")
e761beb9
RW		 7832 (synopsis "Genome wide annotation for Mouse")
7833 (description
7834 "This package provides mappings from Entrez gene identifiers to various
7835annotations for the genome of the model mouse Mus musculus.")
7836 (license license:artistic2.0)))
7837
936e7d67
RW		 7838(define-public r-seqlogo
7839 (package
7840 (name "r-seqlogo")
61770089 7841 (version "1.44.0")
936e7d67
RW		 7842 (source
7843 (origin
7844 (method url-fetch)
7845 (uri (bioconductor-uri "seqLogo" version))
7846 (sha256
7847 (base32
61770089 7848 "1ql4q4vx0j61a893dqc3c8zxmgs8sqhy3j1qhyfdvbd01vw9w1kq"))))
936e7d67
RW		 7849 (properties `((upstream-name . "seqLogo")))
7850 (build-system r-build-system)
5713bbf1 7851 (home-page "https://bioconductor.org/packages/seqLogo")
936e7d67
RW		 7852 (synopsis "Sequence logos for DNA sequence alignments")
7853 (description
7854 "seqLogo takes the position weight matrix of a DNA sequence motif and
7855plots the corresponding sequence logo as introduced by Schneider and
7856Stephens (1990).")
7857 (license license:lgpl2.0+)))
7858
c90a4baf
RW		 7859(define-public r-bsgenome-hsapiens-ucsc-hg19
7860 (package
7861 (name "r-bsgenome-hsapiens-ucsc-hg19")
7862 (version "1.4.0")
7863 (source (origin
7864 (method url-fetch)
7865 ;; We cannot use bioconductor-uri here because this tarball is
7866 ;; located under "data/annotation/" instead of "bioc/".
5713bbf1 7867 (uri (string-append "https://www.bioconductor.org/packages/"
c90a4baf
RW		 7868 "release/data/annotation/src/contrib/"
7869 "BSgenome.Hsapiens.UCSC.hg19_"
7870 version ".tar.gz"))
7871 (sha256
7872 (base32
9d217d27 7873 "1y0nqpk8cw5a34sd9hmin3z4v7iqm6hf6l22cl81vlbxqbjibxc8"))))
c90a4baf
RW		 7874 (properties
7875 `((upstream-name . "BSgenome.Hsapiens.UCSC.hg19")))
7876 (build-system r-build-system)
7877 ;; As this package provides little more than a very large data file it
7878 ;; doesn't make sense to build substitutes.
7879 (arguments `(#:substitutable? #f))
7880 (propagated-inputs
7881 `(("r-bsgenome" ,r-bsgenome)))
7882 (home-page
5713bbf1 7883 "https://www.bioconductor.org/packages/BSgenome.Hsapiens.UCSC.hg19/")
c90a4baf
RW		 7884 (synopsis "Full genome sequences for Homo sapiens")
7885 (description
7886 "This package provides full genome sequences for Homo sapiens as provided
7887by UCSC (hg19, February 2009) and stored in Biostrings objects.")
7888 (license license:artistic2.0)))
7889
a3e90287
RW		 7890(define-public r-bsgenome-mmusculus-ucsc-mm9
7891 (package
7892 (name "r-bsgenome-mmusculus-ucsc-mm9")
7893 (version "1.4.0")
7894 (source (origin
7895 (method url-fetch)
7896 ;; We cannot use bioconductor-uri here because this tarball is
7897 ;; located under "data/annotation/" instead of "bioc/".
5713bbf1 7898 (uri (string-append "https://www.bioconductor.org/packages/"
a3e90287
RW		 7899 "release/data/annotation/src/contrib/"
7900 "BSgenome.Mmusculus.UCSC.mm9_"
7901 version ".tar.gz"))
7902 (sha256
7903 (base32
7904 "1birqw30g2azimxpnjfzmkphan7x131yy8b9h85lfz5fjdg7841i"))))
7905 (properties
7906 `((upstream-name . "BSgenome.Mmusculus.UCSC.mm9")))
7907 (build-system r-build-system)
7908 ;; As this package provides little more than a very large data file it
7909 ;; doesn't make sense to build substitutes.
7910 (arguments `(#:substitutable? #f))
7911 (propagated-inputs
7912 `(("r-bsgenome" ,r-bsgenome)))
7913 (home-page
5713bbf1 7914 "https://www.bioconductor.org/packages/BSgenome.Mmusculus.UCSC.mm9/")
a3e90287
RW		 7915 (synopsis "Full genome sequences for Mouse")
7916 (description
7917 "This package provides full genome sequences for Mus musculus (Mouse) as
7918provided by UCSC (mm9, July 2007) and stored in Biostrings objects.")
7919 (license license:artistic2.0)))
7920
4714d521
RW		 7921(define-public r-bsgenome-mmusculus-ucsc-mm10
7922 (package
7923 (name "r-bsgenome-mmusculus-ucsc-mm10")
7924 (version "1.4.0")
7925 (source (origin
7926 (method url-fetch)
7927 ;; We cannot use bioconductor-uri here because this tarball is
7928 ;; located under "data/annotation/" instead of "bioc/".
5713bbf1 7929 (uri (string-append "https://www.bioconductor.org/packages/"
4714d521
RW		 7930 "release/data/annotation/src/contrib/"
7931 "BSgenome.Mmusculus.UCSC.mm10_"
7932 version ".tar.gz"))
7933 (sha256
7934 (base32
7935 "12s0nm2na9brjad4rn9l7d3db2aj8qa1xvz0y1k7gk08wayb6bkf"))))
7936 (properties
7937 `((upstream-name . "BSgenome.Mmusculus.UCSC.mm10")))
7938 (build-system r-build-system)
7939 ;; As this package provides little more than a very large data file it
7940 ;; doesn't make sense to build substitutes.
7941 (arguments `(#:substitutable? #f))
7942 (propagated-inputs
7943 `(("r-bsgenome" ,r-bsgenome)))
7944 (home-page
5713bbf1 7945 "https://www.bioconductor.org/packages/BSgenome.Mmusculus.UCSC.mm10/")
4714d521
RW		 7946 (synopsis "Full genome sequences for Mouse")
7947 (description
7948 "This package provides full genome sequences for Mus
7949musculus (Mouse) as provided by UCSC (mm10, December 2011) and stored
7950in Biostrings objects.")
7951 (license license:artistic2.0)))
7952
c5173d74
RJ		 7953(define-public r-txdb-mmusculus-ucsc-mm10-knowngene
7954 (package
7955 (name "r-txdb-mmusculus-ucsc-mm10-knowngene")
7956 (version "3.4.0")
7957 (source (origin
7958 (method url-fetch)
7959 ;; We cannot use bioconductor-uri here because this tarball is
7960 ;; located under "data/annotation/" instead of "bioc/".
5713bbf1 7961 (uri (string-append "https://www.bioconductor.org/packages/"
c5173d74
RJ		 7962 "release/data/annotation/src/contrib/"
7963 "TxDb.Mmusculus.UCSC.mm10.knownGene_"
7964 version ".tar.gz"))
7965 (sha256
7966 (base32
7967 "08gava9wsvpcqz51k2sni3pj03n5155v32d9riqbf305nbirqbkb"))))
7968 (properties
7969 `((upstream-name . "TxDb.Mmusculus.UCSC.mm10.knownGene")))
7970 (build-system r-build-system)
7971 ;; As this package provides little more than a very large data file it
7972 ;; doesn't make sense to build substitutes.
7973 (arguments `(#:substitutable? #f))
7974 (propagated-inputs
7975 `(("r-bsgenome" ,r-bsgenome)
7976 ("r-genomicfeatures" ,r-genomicfeatures)
7977 ("r-annotationdbi" ,r-annotationdbi)))
7978 (home-page
5713bbf1 7979 "https://bioconductor.org/packages/TxDb.Mmusculus.UCSC.mm10.knownGene/")
c5173d74
RJ		 7980 (synopsis "Annotation package for TxDb knownGene object(s) for Mouse")
7981 (description
7982 "This package loads a TxDb object, which is an R interface to
7983prefabricated databases contained in this package. This package provides
7984the TxDb object of Mouse data as provided by UCSC (mm10, December 2011)
7985based on the knownGene track.")
7986 (license license:artistic2.0)))
7987
943bd627
RW		 7988(define-public r-bsgenome-celegans-ucsc-ce6
7989 (package
7990 (name "r-bsgenome-celegans-ucsc-ce6")
7991 (version "1.4.0")
7992 (source (origin
7993 (method url-fetch)
7994 ;; We cannot use bioconductor-uri here because this tarball is
7995 ;; located under "data/annotation/" instead of "bioc/".
5713bbf1 7996 (uri (string-append "https://www.bioconductor.org/packages/"
943bd627
RW		 7997 "release/data/annotation/src/contrib/"
7998 "BSgenome.Celegans.UCSC.ce6_"
7999 version ".tar.gz"))
8000 (sha256
8001 (base32
8002 "0mqzb353xv2c3m3vkb315dkmnxkgczp7ndnknyhpgjlybyf715v9"))))
8003 (properties
8004 `((upstream-name . "BSgenome.Celegans.UCSC.ce6")))
8005 (build-system r-build-system)
8006 ;; As this package provides little more than a very large data file it
8007 ;; doesn't make sense to build substitutes.
8008 (arguments `(#:substitutable? #f))
8009 (propagated-inputs
8010 `(("r-bsgenome" ,r-bsgenome)))
8011 (home-page
5713bbf1 8012 "https://www.bioconductor.org/packages/BSgenome.Celegans.UCSC.ce6/")
943bd627
RW		 8013 (synopsis "Full genome sequences for Worm")
8014 (description
8015 "This package provides full genome sequences for Caenorhabditis
8016elegans (Worm) as provided by UCSC (ce6, May 2008) and stored in Biostrings
8017objects.")
8018 (license license:artistic2.0)))
8019
fc47c7d6
RW		 8020(define-public r-bsgenome-celegans-ucsc-ce10
8021 (package
8022 (name "r-bsgenome-celegans-ucsc-ce10")
8023 (version "1.4.0")
8024 (source (origin
8025 (method url-fetch)
8026 ;; We cannot use bioconductor-uri here because this tarball is
8027 ;; located under "data/annotation/" instead of "bioc/".
5713bbf1 8028 (uri (string-append "https://www.bioconductor.org/packages/"
fc47c7d6
RW		 8029 "release/data/annotation/src/contrib/"
8030 "BSgenome.Celegans.UCSC.ce10_"
8031 version ".tar.gz"))
8032 (sha256
8033 (base32
8034 "1zaym97jk4npxk14ifvwz2rvhm4zx9xgs33r9vvx9rlynp0gydrk"))))
8035 (properties
8036 `((upstream-name . "BSgenome.Celegans.UCSC.ce10")))
8037 (build-system r-build-system)
8038 ;; As this package provides little more than a very large data file it
8039 ;; doesn't make sense to build substitutes.
8040 (arguments `(#:substitutable? #f))
8041 (propagated-inputs
8042 `(("r-bsgenome" ,r-bsgenome)))
8043 (home-page
5713bbf1 8044 "https://www.bioconductor.org/packages/BSgenome.Celegans.UCSC.ce10/")
fc47c7d6
RW		 8045 (synopsis "Full genome sequences for Worm")
8046 (description
8047 "This package provides full genome sequences for Caenorhabditis
8048elegans (Worm) as provided by UCSC (ce10, Oct 2010) and stored in Biostrings
8049objects.")
8050 (license license:artistic2.0)))
8051
6dc60998
RW		 8052(define-public r-bsgenome-dmelanogaster-ucsc-dm3
8053 (package
8054 (name "r-bsgenome-dmelanogaster-ucsc-dm3")
8055 (version "1.4.0")
8056 (source (origin
8057 (method url-fetch)
8058 ;; We cannot use bioconductor-uri here because this tarball is
8059 ;; located under "data/annotation/" instead of "bioc/".
5713bbf1 8060 (uri (string-append "https://www.bioconductor.org/packages/"
6dc60998
RW		 8061 "release/data/annotation/src/contrib/"
8062 "BSgenome.Dmelanogaster.UCSC.dm3_"
8063 version ".tar.gz"))
8064 (sha256
8065 (base32
8066 "19bm3lkhhkag3gnwp419211fh0cnr0x6fa0r1lr0ycwrikxdxsv8"))))
8067 (properties
8068 `((upstream-name . "BSgenome.Dmelanogaster.UCSC.dm3")))
8069 (build-system r-build-system)
8070 ;; As this package provides little more than a very large data file it
8071 ;; doesn't make sense to build substitutes.
8072 (arguments `(#:substitutable? #f))
8073 (propagated-inputs
8074 `(("r-bsgenome" ,r-bsgenome)))
8075 (home-page
5713bbf1 8076 "https://www.bioconductor.org/packages/BSgenome.Dmelanogaster.UCSC.dm3/")
6dc60998
RW		 8077 (synopsis "Full genome sequences for Fly")
8078 (description
8079 "This package provides full genome sequences for Drosophila
8080melanogaster (Fly) as provided by UCSC (dm3, April 2006) and stored in
8081Biostrings objects.")
8082 (license license:artistic2.0)))
8083
ae2462f7
RW		 8084(define-public r-motifrg
8085 (package
8086 (name "r-motifrg")
ce59d625 8087 (version "1.22.0")
ae2462f7
RW		 8088 (source
8089 (origin
8090 (method url-fetch)
8091 (uri (bioconductor-uri "motifRG" version))
8092 (sha256
8093 (base32
ce59d625 8094 "193zl2rlzwxv9p9q5i7rilj3w05ndqfyp9bdpvagp5s5cin4hf44"))))
ae2462f7
RW		 8095 (properties `((upstream-name . "motifRG")))
8096 (build-system r-build-system)
8097 (propagated-inputs
8098 `(("r-biostrings" ,r-biostrings)
8099 ("r-bsgenome" ,r-bsgenome)
007424b5 8100 ("r-bsgenome-hsapiens-ucsc-hg19" ,r-bsgenome-hsapiens-ucsc-hg19)
ae2462f7
RW		 8101 ("r-iranges" ,r-iranges)
8102 ("r-seqlogo" ,r-seqlogo)
8103 ("r-xvector" ,r-xvector)))
5713bbf1 8104 (home-page "https://bioconductor.org/packages/motifRG")
ae2462f7
RW		 8105 (synopsis "Discover motifs in high throughput sequencing data")
8106 (description
8107 "This package provides tools for discriminative motif discovery in high
8108throughput genetic sequencing data sets using regression methods.")
8109 (license license:artistic2.0)))
8110
a5002ae7
AE		 8111(define-public r-qtl
8112 (package
8113 (name "r-qtl")
65c9d257 8114 (version "1.42-8")
a5002ae7
AE		 8115 (source
8116 (origin
8117 (method url-fetch)
8118 (uri (string-append "mirror://cran/src/contrib/qtl_"
8119 version ".tar.gz"))
8120 (sha256
8121 (base32
65c9d257 8122 "1l528dwvfpdlr05imrrm4rq32axp6hld9nqm6mm43kn5n7z2f5k6"))))
a5002ae7
AE		 8123 (build-system r-build-system)
8124 (home-page "http://rqtl.org/")
8125 (synopsis "R package for analyzing QTL experiments in genetics")
8126 (description "R/qtl is an extension library for the R statistics
8127system. It is used to analyze experimental crosses for identifying
8128genes contributing to variation in quantitative traits (so-called
8129quantitative trait loci, QTLs).
8130
8131Using a hidden Markov model, R/qtl allows to estimate genetic maps, to
8132identify genotyping errors, and to perform single-QTL and two-QTL,
8133two-dimensional genome scans.")
8134 (license license:gpl3)))
d1e32822 8135
9e3ba31c
RJ		 8136(define-public r-zlibbioc
8137 (package
8138 (name "r-zlibbioc")
5c184700 8139 (version "1.24.0")
9e3ba31c
RJ		 8140 (source (origin
8141 (method url-fetch)
8142 (uri (bioconductor-uri "zlibbioc" version))
8143 (sha256
8144 (base32
5c184700 8145 "1zr9hbh55hglfpy15cpxwmddxblhyb0an15953l3rbhmlh2vpy92"))))
9e3ba31c
RJ		 8146 (properties
8147 `((upstream-name . "zlibbioc")))
8148 (build-system r-build-system)
8149 (home-page "https://bioconductor.org/packages/zlibbioc")
8150 (synopsis "Provider for zlib-1.2.5 to R packages")
8151 (description "This package uses the source code of zlib-1.2.5 to create
8152libraries for systems that do not have these available via other means.")
8153 (license license:artistic2.0)))
8154
e619a5c2
RW		 8155(define-public r-r4rna
8156 (package
8157 (name "r-r4rna")
8158 (version "0.1.4")
8159 (source
8160 (origin
8161 (method url-fetch)
8162 (uri (string-append "http://www.e-rna.org/r-chie/files/R4RNA_"
8163 version ".tar.gz"))
8164 (sha256
8165 (base32
8166 "1p0i78wh76jfgmn9jphbwwaz6yy6pipzfg08xs54cxavxg2j81p5"))))
8167 (build-system r-build-system)
8168 (propagated-inputs
8169 `(("r-optparse" ,r-optparse)
8170 ("r-rcolorbrewer" ,r-rcolorbrewer)))
8171 (home-page "http://www.e-rna.org/r-chie/index.cgi")
8172 (synopsis "Analysis framework for RNA secondary structure")
8173 (description
8174 "The R4RNA package aims to be a general framework for the analysis of RNA
8175secondary structure and comparative analysis in R.")
8176 (license license:gpl3+)))
8177
52765a63
RW		 8178(define-public r-rhtslib
8179 (package
8180 (name "r-rhtslib")
1d0263b4 8181 (version "1.10.0")
52765a63
RW		 8182 (source
8183 (origin
8184 (method url-fetch)
8185 (uri (bioconductor-uri "Rhtslib" version))
8186 (sha256
8187 (base32
1d0263b4 8188 "1dw3p44bfr0m7w39ckc2k37sjcp1zz0b9g12mr8am15jaj6v0q2j"))))
52765a63
RW		 8189 (properties `((upstream-name . "Rhtslib")))
8190 (build-system r-build-system)
8191 (propagated-inputs
8192 `(("r-zlibbioc" ,r-zlibbioc)))
8193 (inputs
8194 `(("zlib" ,zlib)))
53ca52f0
RW		 8195 (native-inputs
8196 `(("autoconf" ,autoconf)))
52765a63
RW		 8197 (home-page "https://github.com/nhayden/Rhtslib")
8198 (synopsis "High-throughput sequencing library as an R package")
8199 (description
8200 "This package provides the HTSlib C library for high-throughput
8201nucleotide sequence analysis. The package is primarily useful to developers
8202of other R packages who wish to make use of HTSlib.")
8203 (license license:lgpl2.0+)))
8204
fe02c4c9
RW		 8205(define-public r-bamsignals
8206 (package
8207 (name "r-bamsignals")
da153b7f 8208 (version "1.10.0")
fe02c4c9
RW		 8209 (source
8210 (origin
8211 (method url-fetch)
8212 (uri (bioconductor-uri "bamsignals" version))
8213 (sha256
8214 (base32
da153b7f 8215 "15id6mkj95skb4kfafvfs2j7ylydal60c3pspcl7llhwpq6vcqvl"))))
fe02c4c9
RW		 8216 (build-system r-build-system)
8217 (propagated-inputs
8218 `(("r-biocgenerics" ,r-biocgenerics)
8219 ("r-genomicranges" ,r-genomicranges)
8220 ("r-iranges" ,r-iranges)
8221 ("r-rcpp" ,r-rcpp)
8222 ("r-rhtslib" ,r-rhtslib)
8223 ("r-zlibbioc" ,r-zlibbioc)))
8224 (inputs
8225 `(("zlib" ,zlib)))
5713bbf1 8226 (home-page "https://bioconductor.org/packages/bamsignals")
fe02c4c9
RW		 8227 (synopsis "Extract read count signals from bam files")
8228 (description
8229 "This package allows to efficiently obtain count vectors from indexed bam
8230files. It counts the number of nucleotide sequence reads in given genomic
8231ranges and it computes reads profiles and coverage profiles. It also handles
8232paired-end data.")
8233 (license license:gpl2+)))
8234
89984be4
RW		 8235(define-public r-rcas
8236 (package
8237 (name "r-rcas")
d82937fb 8238 (version "1.3.4")
89984be4
RW		 8239 (source (origin
8240 (method url-fetch)
8241 (uri (string-append "https://github.com/BIMSBbioinfo/RCAS/archive/v"
8242 version ".tar.gz"))
8243 (file-name (string-append name "-" version ".tar.gz"))
8244 (sha256
8245 (base32
d82937fb 8246 "1qgc7vi6fpzl440yg7jhiycg5q336kd4pxqzx10yx2zcq3bq3msg"))))
89984be4
RW		 8247 (build-system r-build-system)
8248 (native-inputs
8249 `(("r-knitr" ,r-knitr)
8250 ("r-testthat" ,r-testthat)
8251 ;; During vignette building knitr checks that "pandoc-citeproc"
8252 ;; is in the PATH.
8253 ("ghc-pandoc-citeproc" ,ghc-pandoc-citeproc)))
8254 (propagated-inputs
8255 `(("r-data-table" ,r-data-table)
8256 ("r-biomart" ,r-biomart)
8257 ("r-org-hs-eg-db" ,r-org-hs-eg-db)
8258 ("r-org-ce-eg-db" ,r-org-ce-eg-db)
8259 ("r-org-dm-eg-db" ,r-org-dm-eg-db)
8260 ("r-org-mm-eg-db" ,r-org-mm-eg-db)
8261 ("r-bsgenome-hsapiens-ucsc-hg19" ,r-bsgenome-hsapiens-ucsc-hg19)
8262 ("r-bsgenome-mmusculus-ucsc-mm9" ,r-bsgenome-mmusculus-ucsc-mm9)
8263 ("r-bsgenome-celegans-ucsc-ce10" ,r-bsgenome-celegans-ucsc-ce10)
8264 ("r-bsgenome-dmelanogaster-ucsc-dm3" ,r-bsgenome-dmelanogaster-ucsc-dm3)
8265 ("r-topgo" ,r-topgo)
8266 ("r-dt" ,r-dt)
ebfd6a71 8267 ("r-pbapply" ,r-pbapply)
89984be4 8268 ("r-plotly" ,r-plotly)
2c8d6c0b 8269 ("r-plotrix" ,r-plotrix)
89984be4
RW		 8270 ("r-motifrg" ,r-motifrg)
8271 ("r-genomation" ,r-genomation)
8272 ("r-genomicfeatures" ,r-genomicfeatures)
8273 ("r-rtracklayer" ,r-rtracklayer)
8274 ("r-rmarkdown" ,r-rmarkdown)))
8275 (synopsis "RNA-centric annotation system")
8276 (description
8277 "RCAS aims to be a standalone RNA-centric annotation system that provides
8278intuitive reports and publication-ready graphics. This package provides the R
8279library implementing most of the pipeline's features.")
8280 (home-page "https://github.com/BIMSBbioinfo/RCAS")
75690c9f 8281 (license license:artistic2.0)))
89984be4 8282
50937297
RW		 8283(define-public rcas-web
8284 (package
8285 (name "rcas-web")
01d87d3c 8286 (version "0.0.4")
50937297
RW		 8287 (source
8288 (origin
8289 (method url-fetch)
8290 (uri (string-append "https://github.com/BIMSBbioinfo/rcas-web/"
8291 "releases/download/v" version
8292 "/rcas-web-" version ".tar.gz"))
8293 (sha256
8294 (base32
01d87d3c 8295 "1p16frfys41a8yaa4gkm457nzkqhqs2pc3lkac0ds457w9w5j1gm"))))
50937297
RW		 8296 (build-system gnu-build-system)
8297 (arguments
8298 `(#:phases
8299 (modify-phases %standard-phases
8300 (add-after 'install 'wrap-executable
8301 (lambda* (#:key inputs outputs #:allow-other-keys)
8302 (let* ((out (assoc-ref outputs "out"))
8303 (json (assoc-ref inputs "guile-json"))
8304 (redis (assoc-ref inputs "guile-redis"))
8305 (path (string-append
8306 json "/share/guile/site/2.2:"
8307 redis "/share/guile/site/2.2")))
8308 (wrap-program (string-append out "/bin/rcas-web")
8309 `("GUILE_LOAD_PATH" ":" = (,path))
8310 `("GUILE_LOAD_COMPILED_PATH" ":" = (,path))
8311 `("R_LIBS_SITE" ":" = (,(getenv "R_LIBS_SITE")))))
8312 #t)))))
8313 (inputs
2d7c4ae3 8314 `(("r-minimal" ,r-minimal)
50937297 8315 ("r-rcas" ,r-rcas)
f6396d86 8316 ("guile-next" ,guile-2.2)
2252f087 8317 ("guile-json" ,guile-json)
50937297
RW		 8318 ("guile-redis" ,guile2.2-redis)))
8319 (native-inputs
8320 `(("pkg-config" ,pkg-config)))
8321 (home-page "https://github.com/BIMSBbioinfo/rcas-web")
8322 (synopsis "Web interface for RNA-centric annotation system (RCAS)")
8323 (description "This package provides a simple web interface for the
8324@dfn{RNA-centric annotation system} (RCAS).")
8325 (license license:agpl3+)))
8326
7500e42b
RJ		 8327(define-public r-mutationalpatterns
8328 (package
8329 (name "r-mutationalpatterns")
b9bf2b89 8330 (version "1.4.2")
7500e42b
RJ		 8331 (source
8332 (origin
8333 (method url-fetch)
8334 (uri (bioconductor-uri "MutationalPatterns" version))
8335 (sha256
8336 (base32
b9bf2b89 8337 "08ay9h5cqsi8ypb6r0g4rfa5l1g06jgfzl64wmhgz134yqbl7vfv"))))
7500e42b
RJ		 8338 (build-system r-build-system)
8339 (propagated-inputs
8340 `(("r-biocgenerics" ,r-biocgenerics)
8341 ("r-biostrings" ,r-biostrings)
cf4ac4e4
RJ		 8342 ("r-bsgenome-hsapiens-1000g" ,r-bsgenome-hsapiens-1000genomes-hs37d5)
8343 ("r-bsgenome-hsapiens-ucsc-hg19" ,r-bsgenome-hsapiens-ucsc-hg19)
7500e42b
RJ		 8344 ("r-genomicranges" ,r-genomicranges)
8345 ("r-genomeinfodb" ,r-genomeinfodb)
8346 ("r-ggplot2" ,r-ggplot2)
8347 ("r-gridextra" ,r-gridextra)
8348 ("r-iranges" ,r-iranges)
8349 ("r-nmf" ,r-nmf)
8350 ("r-plyr" ,r-plyr)
8351 ("r-pracma" ,r-pracma)
8352 ("r-reshape2" ,r-reshape2)
39d9098d
RW		 8353 ("r-cowplot" ,r-cowplot)
8354 ("r-ggdendro" ,r-ggdendro)
8355 ("r-s4vectors" ,r-s4vectors)
7500e42b
RJ		 8356 ("r-summarizedexperiment" ,r-summarizedexperiment)
8357 ("r-variantannotation" ,r-variantannotation)))
5713bbf1 8358 (home-page "https://bioconductor.org/packages/MutationalPatterns/")
7500e42b
RJ		 8359 (synopsis "Extract and visualize mutational patterns in genomic data")
8360 (description "This package provides an extensive toolset for the
8361characterization and visualization of a wide range of mutational patterns
8362in SNV base substitution data.")
8363 (license license:expat)))
8364
d7160529
RW		 8365(define-public r-wgcna
8366 (package
8367 (name "r-wgcna")
6a0e1390 8368 (version "1.63")
d7160529
RW		 8369 (source
8370 (origin
8371 (method url-fetch)
8372 (uri (cran-uri "WGCNA" version))
8373 (sha256
8374 (base32
6a0e1390 8375 "1225dqm68bynkmklnsxdqdd3zqrpzbvqwyly8ibxmk75z33xz309"))))
d7160529
RW		 8376 (properties `((upstream-name . "WGCNA")))
8377 (build-system r-build-system)
8378 (propagated-inputs
8379 `(("r-annotationdbi" ,r-annotationdbi)
8380 ("r-doparallel" ,r-doparallel)
8381 ("r-dynamictreecut" ,r-dynamictreecut)
8382 ("r-fastcluster" ,r-fastcluster)
8383 ("r-foreach" ,r-foreach)
8384 ("r-go-db" ,r-go-db)
8385 ("r-hmisc" ,r-hmisc)
8386 ("r-impute" ,r-impute)
1b22ecda
RW		 8387 ("r-rcpp" ,r-rcpp)
8388 ("r-robust" ,r-robust)
8389 ("r-survival" ,r-survival)
d7160529
RW		 8390 ("r-matrixstats" ,r-matrixstats)
8391 ("r-preprocesscore" ,r-preprocesscore)))
8392 (home-page
8393 "http://www.genetics.ucla.edu/labs/horvath/CoexpressionNetwork/Rpackages/WGCNA/")
8394 (synopsis "Weighted correlation network analysis")
8395 (description
8396 "This package provides functions necessary to perform Weighted
8397Correlation Network Analysis on high-dimensional data. It includes functions
8398for rudimentary data cleaning, construction and summarization of correlation
8399networks, module identification and functions for relating both variables and
8400modules to sample traits. It also includes a number of utility functions for
8401data manipulation and visualization.")
8402 (license license:gpl2+)))
8403
c827f202
RW		 8404(define-public r-chipkernels
8405 (let ((commit "c9cfcacb626b1221094fb3490ea7bac0fd625372")
8406 (revision "1"))
8407 (package
8408 (name "r-chipkernels")
8409 (version (string-append "1.1-" revision "." (string-take commit 9)))
8410 (source
8411 (origin
8412 (method git-fetch)
8413 (uri (git-reference
8414 (url "https://github.com/ManuSetty/ChIPKernels.git")
8415 (commit commit)))
8416 (file-name (string-append name "-" version))
8417 (sha256
8418 (base32
8419 "14bj5qhjm1hsm9ay561nfbqi9wxsa7y487df2idsaaf6z10nw4v0"))))
8420 (build-system r-build-system)
8421 (propagated-inputs
8422 `(("r-iranges" ,r-iranges)
8423 ("r-xvector" ,r-xvector)
8424 ("r-biostrings" ,r-biostrings)
8425 ("r-bsgenome" ,r-bsgenome)
8426 ("r-gtools" ,r-gtools)
8427 ("r-genomicranges" ,r-genomicranges)
8428 ("r-sfsmisc" ,r-sfsmisc)
8429 ("r-kernlab" ,r-kernlab)
8430 ("r-s4vectors" ,r-s4vectors)
8431 ("r-biocgenerics" ,r-biocgenerics)))
8432 (home-page "https://github.com/ManuSetty/ChIPKernels")
8433 (synopsis "Build string kernels for DNA Sequence analysis")
8434 (description "ChIPKernels is an R package for building different string
8435kernels used for DNA Sequence analysis. A dictionary of the desired kernel
8436must be built and this dictionary can be used for determining kernels for DNA
8437Sequences.")
8438 (license license:gpl2+))))
8439
2d9fb170
RW		 8440(define-public r-seqgl
8441 (package
8442 (name "r-seqgl")
8443 (version "1.1.4")
8444 (source
8445 (origin
8446 (method url-fetch)
8447 (uri (string-append "https://github.com/ManuSetty/SeqGL/"
8448 "archive/" version ".tar.gz"))
8449 (file-name (string-append name "-" version ".tar.gz"))
8450 (sha256
8451 (base32
8452 "0pnk1p3sci5yipyc8xnb6jbmydpl80fld927xgnbcv104hy8h8yh"))))
8453 (build-system r-build-system)
8454 (propagated-inputs
8455 `(("r-biostrings" ,r-biostrings)
8456 ("r-chipkernels" ,r-chipkernels)
8457 ("r-genomicranges" ,r-genomicranges)
8458 ("r-spams" ,r-spams)
8459 ("r-wgcna" ,r-wgcna)
8460 ("r-fastcluster" ,r-fastcluster)))
8461 (home-page "https://github.com/ManuSetty/SeqGL")
8462 (synopsis "Group lasso for Dnase/ChIP-seq data")
8463 (description "SeqGL is a group lasso based algorithm to extract
8464transcription factor sequence signals from ChIP, DNase and ATAC-seq profiles.
8465This package presents a method which uses group lasso to discriminate between
8466bound and non bound genomic regions to accurately identify transcription
8467factors bound at the specific regions.")
8468 (license license:gpl2+)))
8469
bd3be46e
RW		 8470(define-public r-gkmsvm
8471 (package
8472 (name "r-gkmsvm")
5ef76bc2 8473 (version "0.79.0")
bd3be46e
RW		 8474 (source
8475 (origin
8476 (method url-fetch)
8477 (uri (cran-uri "gkmSVM" version))
8478 (sha256
8479 (base32
5ef76bc2 8480 "04dakbgfvfalz4rm4fvvybp506dn5fbj5g86ybfhrc6wywjllsz3"))))
bd3be46e
RW		 8481 (properties `((upstream-name . "gkmSVM")))
8482 (build-system r-build-system)
8483 (propagated-inputs
8484 `(("r-biocgenerics" ,r-biocgenerics)
8485 ("r-biostrings" ,r-biostrings)
8486 ("r-genomeinfodb" ,r-genomeinfodb)
8487 ("r-genomicranges" ,r-genomicranges)
8488 ("r-iranges" ,r-iranges)
8489 ("r-kernlab" ,r-kernlab)
8490 ("r-rcpp" ,r-rcpp)
8491 ("r-rocr" ,r-rocr)
8492 ("r-rtracklayer" ,r-rtracklayer)
8493 ("r-s4vectors" ,r-s4vectors)
8494 ("r-seqinr" ,r-seqinr)))
e9960d8c 8495 (home-page "https://cran.r-project.org/web/packages/gkmSVM")
bd3be46e
RW		 8496 (synopsis "Gapped-kmer support vector machine")
8497 (description
8498 "This R package provides tools for training gapped-kmer SVM classifiers
8499for DNA and protein sequences. This package supports several sequence
8500kernels, including: gkmSVM, kmer-SVM, mismatch kernel and wildcard kernel.")
8501 (license license:gpl2+)))
8502
d4af25b5
RJPB		 8503(define-public r-tximport
8504 (package
8505 (name "r-tximport")
19e8929c 8506 (version "1.6.0")
d4af25b5
RJPB		 8507 (source (origin
8508 (method url-fetch)
8509 (uri (bioconductor-uri "tximport" version))
8510 (sha256
8511 (base32
19e8929c 8512 "1gyqcm91hxg1kgjqcz2qw1n56yp9pymjzs50rwcpb2893dr8sp2h"))))
d4af25b5 8513 (build-system r-build-system)
5713bbf1 8514 (home-page "https://bioconductor.org/packages/tximport")
d4af25b5
RJPB		 8515 (synopsis "Import and summarize transcript-level estimates for gene-level analysis")
8516 (description
8517 "This package provides tools to import transcript-level abundance,
8518estimated counts and transcript lengths, and to summarize them into matrices
8519for use with downstream gene-level analysis packages. Average transcript
8520length, weighted by sample-specific transcript abundance estimates, is
8521provided as a matrix which can be used as an offset for different expression
8522of gene-level counts.")
8523 (license license:gpl2+)))
8524
69f2b3bd
RJPB		 8525(define-public r-rhdf5
8526 (package
8527 (name "r-rhdf5")
e6b332d4 8528 (version "2.22.0")
69f2b3bd
RJPB		 8529 (source (origin
8530 (method url-fetch)
8531 (uri (bioconductor-uri "rhdf5" version))
8532 (sha256
8533 (base32
e6b332d4 8534 "145858qg1xan6imxcbprzq3yn3mdf532aahdr6cibvdjg47hs4c1"))))
69f2b3bd
RJPB		 8535 (build-system r-build-system)
8536 (arguments
8537 `(#:phases
8538 (modify-phases %standard-phases
8539 (add-after 'unpack 'unpack-smallhdf5
8540 (lambda* (#:key outputs #:allow-other-keys)
8541 (system* "tar" "-xzvf"
8542 "src/hdf5source/hdf5small.tgz" "-C" "src/" )
69f2b3bd
RJPB		 8543 (substitute* "src/hdf5/configure"
8544 (("/bin/mv") "mv"))
8545 #t)))))
8546 (propagated-inputs
8547 `(("r-zlibbioc" ,r-zlibbioc)))
8548 (inputs
8549 `(("perl" ,perl)
8550 ("zlib" ,zlib)))
5713bbf1 8551 (home-page "https://bioconductor.org/packages/rhdf5")
69f2b3bd
RJPB		 8552 (synopsis "HDF5 interface to R")
8553 (description
8554 "This R/Bioconductor package provides an interface between HDF5 and R.
8555HDF5's main features are the ability to store and access very large and/or
8556complex datasets and a wide variety of metadata on mass storage (disk) through
8557a completely portable file format. The rhdf5 package is thus suited for the
8558exchange of large and/or complex datasets between R and other software
8559package, and for letting R applications work on datasets that are larger than
8560the available RAM.")
8561 (license license:artistic2.0)))
8562
17cddc17
RW		 8563(define-public r-annotationfilter
8564 (package
8565 (name "r-annotationfilter")
598dacf6 8566 (version "1.2.0")
17cddc17
RW		 8567 (source (origin
8568 (method url-fetch)
8569 (uri (bioconductor-uri "AnnotationFilter" version))
8570 (sha256
8571 (base32
598dacf6 8572 "04zf864c1fvdlaay2r5cn30fc1n5i3czh31fs62qlrvs61wjiscs"))))
17cddc17
RW		 8573 (properties
8574 `((upstream-name . "AnnotationFilter")))
8575 (build-system r-build-system)
8576 (propagated-inputs
8577 `(("r-genomicranges" ,r-genomicranges)
8578 ("r-lazyeval" ,r-lazyeval)))
8579 (home-page "https://github.com/Bioconductor/AnnotationFilter")
8580 (synopsis "Facilities for filtering Bioconductor annotation resources")
8581 (description
8582 "This package provides classes and other infrastructure to implement
8583filters for manipulating Bioconductor annotation resources. The filters are
8584used by @code{ensembldb}, @code{Organism.dplyr}, and other packages.")
8585 (license license:artistic2.0)))
8586
66e40e00
RW		 8587(define-public emboss
8588 (package
8589 (name "emboss")
8590 (version "6.5.7")
8591 (source (origin
8592 (method url-fetch)
8593 (uri (string-append "ftp://emboss.open-bio.org/pub/EMBOSS/old/"
8594 (version-major+minor version) ".0/"
8595 "EMBOSS-" version ".tar.gz"))
8596 (sha256
8597 (base32
8598 "0vsmz96gc411yj2iyzdrsmg4l2n1nhgmp7vrgzlxx3xixv9xbf0q"))))
8599 (build-system gnu-build-system)
8600 (arguments
8601 `(#:configure-flags
8602 (list (string-append "--with-hpdf="
8603 (assoc-ref %build-inputs "libharu")))
8604 #:phases
8605 (modify-phases %standard-phases
8606 (add-after 'unpack 'fix-checks
8607 (lambda _
8608 ;; The PNGDRIVER tests check for the presence of libgd, libpng
8609 ;; and zlib, but assume that they are all found at the same
8610 ;; prefix.
8611 (substitute* "configure.in"
8612 (("CHECK_PNGDRIVER")
8613 "LIBS=\"$LIBS -lgd -lpng -lz -lm\"
8614AC_DEFINE([PLD_png], [1], [Define to 1 if PNG support is available])
8615AM_CONDITIONAL(AMPNG, true)"))
8616 #t))
d10092b8 8617 (add-after 'fix-checks 'disable-update-check
66e40e00
RW		 8618 (lambda _
8619 ;; At build time there is no connection to the Internet, so
8620 ;; looking for updates will not work.
8621 (substitute* "Makefile.am"
8622 (("\\$\\(bindir\\)/embossupdate") ""))
8623 #t))
d10092b8 8624 (add-after 'disable-update-check 'autogen
66e40e00
RW		 8625 (lambda _ (zero? (system* "autoreconf" "-vif")))))))
8626 (inputs
8627 `(("perl" ,perl)
8628 ("libpng" ,libpng)
8629 ("gd" ,gd)
8630 ("libx11" ,libx11)
8631 ("libharu" ,libharu)
8632 ("zlib" ,zlib)))
8633 (native-inputs
8634 `(("autoconf" ,autoconf)
8635 ("automake" ,automake)
8636 ("libtool" ,libtool)
8637 ("pkg-config" ,pkg-config)))
8638 (home-page "http://emboss.sourceforge.net")
8639 (synopsis "Molecular biology analysis suite")
8640 (description "EMBOSS is the \"European Molecular Biology Open Software
8641Suite\". EMBOSS is an analysis package specially developed for the needs of
8642the molecular biology (e.g. EMBnet) user community. The software
8643automatically copes with data in a variety of formats and even allows
8644transparent retrieval of sequence data from the web. It also provides a
8645number of libraries for the development of software in the field of molecular
8646biology. EMBOSS also integrates a range of currently available packages and
8647tools for sequence analysis into a seamless whole.")
8648 (license license:gpl2+)))
8649
1f1b20b8
RW		 8650(define-public bits
8651 (let ((revision "1")
8652 (commit "3cc4567896d9d6442923da944beb704750a08d2d"))
8653 (package
8654 (name "bits")
8655 ;; The version is 2.13.0 even though no release archives have been
8656 ;; published as yet.
8657 (version (string-append "2.13.0-" revision "." (string-take commit 9)))
8658 (source (origin
8659 (method git-fetch)
8660 (uri (git-reference
8661 (url "https://github.com/arq5x/bits.git")
8662 (commit commit)))
8663 (file-name (string-append name "-" version "-checkout"))
8664 (sha256
8665 (base32
8666 "17n2kffk4kmhivd8c98g2vr6y1s23vbg4sxlxs689wni66797hbs"))))
8667 (build-system gnu-build-system)
8668 (arguments
8669 `(#:tests? #f ;no tests included
8670 #:phases
8671 (modify-phases %standard-phases
8672 (delete 'configure)
8673 (add-after 'unpack 'remove-cuda
8674 (lambda _
8675 (substitute* "Makefile"
8676 ((".*_cuda") "")
8677 (("(bits_test_intersections) \\\\" _ match) match))
8678 #t))
8679 (replace 'install
8680 (lambda* (#:key outputs #:allow-other-keys)
8681 (copy-recursively
8682 "bin" (string-append (assoc-ref outputs "out") "/bin"))
8683 #t)))))
8684 (inputs
8685 `(("gsl" ,gsl)
8686 ("zlib" ,zlib)))
8687 (home-page "https://github.com/arq5x/bits")
8688 (synopsis "Implementation of binary interval search algorithm")
8689 (description "This package provides an implementation of the
8690BITS (Binary Interval Search) algorithm, an approach to interval set
8691intersection. It is especially suited for the comparison of diverse genomic
8692datasets and the exploration of large datasets of genome
8693intervals (e.g. genes, sequence alignments).")
8694 (license license:gpl2))))
8695
e62ffce5 8696(define-public piranha
883302da
RW		 8697 ;; There is no release tarball for the latest version. The latest commit is
8698 ;; older than one year at the time of this writing.
8699 (let ((revision "1")
8700 (commit "0466d364b71117d01e4471b74c514436cc281233"))
8701 (package
8702 (name "piranha")
8703 (version (string-append "1.2.1-" revision "." (string-take commit 9)))
8704 (source (origin
8705 (method git-fetch)
8706 (uri (git-reference
8707 (url "https://github.com/smithlabcode/piranha.git")
8708 (commit commit)))
8709 (sha256
8710 (base32
8711 "117dc0zf20c61jam69sk4abl57ah6yi6i7qra7d7y5zrbgk12q5n"))))
8712 (build-system gnu-build-system)
8713 (arguments
8714 `(#:test-target "test"
8715 #:phases
8716 (modify-phases %standard-phases
8717 (add-after 'unpack 'copy-smithlab-cpp
8718 (lambda* (#:key inputs #:allow-other-keys)
e62ffce5 8719 (for-each (lambda (file)
883302da
RW		 8720 (install-file file "./src/smithlab_cpp/"))
8721 (find-files (assoc-ref inputs "smithlab-cpp")))
8722 #t))
8723 (add-after 'install 'install-to-store
8724 (lambda* (#:key outputs #:allow-other-keys)
8725 (let* ((out (assoc-ref outputs "out"))
8726 (bin (string-append out "/bin")))
883302da
RW		 8727 (for-each (lambda (file)
8728 (install-file file bin))
8729 (find-files "bin" ".*")))
8730 #t)))
8731 #:configure-flags
8732 (list (string-append "--with-bam_tools_headers="
8733 (assoc-ref %build-inputs "bamtools") "/include/bamtools")
8734 (string-append "--with-bam_tools_library="
8735 (assoc-ref %build-inputs "bamtools") "/lib/bamtools"))))
8736 (inputs
8737 `(("bamtools" ,bamtools)
8738 ("samtools" ,samtools-0.1)
8739 ("gsl" ,gsl)
8740 ("smithlab-cpp"
8741 ,(let ((commit "3723e2db438c51501d0423429ff396c3035ba46a"))
8742 (origin
8743 (method git-fetch)
8744 (uri (git-reference
8745 (url "https://github.com/smithlabcode/smithlab_cpp.git")
8746 (commit commit)))
8747 (file-name (string-append "smithlab_cpp-" commit "-checkout"))
8748 (sha256
8749 (base32
8750 "0l4gvbwslw5ngziskja41c00x1r06l3yidv7y0xw9djibhykzy0g")))))))
8751 (native-inputs
8752 `(("python" ,python-2)))
8753 (home-page "https://github.com/smithlabcode/piranha")
8754 (synopsis "Peak-caller for CLIP-seq and RIP-seq data")
8755 (description
8756 "Piranha is a peak-caller for genomic data produced by CLIP-seq and
e62ffce5
RW		 8757RIP-seq experiments. It takes input in BED or BAM format and identifies
8758regions of statistically significant read enrichment. Additional covariates
8759may optionally be provided to further inform the peak-calling process.")
883302da 8760 (license license:gpl3+))))
e62ffce5 8761
d1e32822
RW		 8762(define-public pepr
8763 (package
8764 (name "pepr")
8765 (version "1.0.9")
8766 (source (origin
8767 (method url-fetch)
8768 (uri (string-append "https://pypi.python.org/packages/source/P"
8769 "/PePr/PePr-" version ".tar.gz"))
8770 (sha256
8771 (base32
8772 "0qxjfdpl1b1y53nccws2d85f6k74zwmx8y8sd9rszcqhfayx6gdx"))))
8773 (build-system python-build-system)
8774 (arguments
8775 `(#:python ,python-2 ; python2 only
b41a05ce 8776 #:tests? #f)) ; no tests included
d1e32822
RW		 8777 (propagated-inputs
8778 `(("python2-numpy" ,python2-numpy)
8779 ("python2-scipy" ,python2-scipy)
8780 ("python2-pysam" ,python2-pysam)))
0c6c9c00 8781 (home-page "https://github.com/shawnzhangyx/PePr")
d1e32822
RW		 8782 (synopsis "Peak-calling and prioritization pipeline for ChIP-Seq data")
8783 (description
8784 "PePr is a ChIP-Seq peak calling or differential binding analysis tool
8785that is primarily designed for data with biological replicates. It uses a
8786negative binomial distribution to model the read counts among the samples in
8787the same group, and look for consistent differences between ChIP and control
8788group or two ChIP groups run under different conditions.")
8789 (license license:gpl3+)))
6b49a37e
RJ		 8790
8791(define-public filevercmp
8792 (let ((commit "1a9b779b93d0b244040274794d402106907b71b7"))
8793 (package
8794 (name "filevercmp")
8795 (version (string-append "0-1." (string-take commit 7)))
8796 (source (origin
8797 (method url-fetch)
8798 (uri (string-append "https://github.com/ekg/filevercmp/archive/"
8799 commit ".tar.gz"))
8800 (file-name (string-append name "-" version ".tar.gz"))
8801 (sha256
8802 (base32 "0yp5jswf5j2pqc6517x277s4s6h1ss99v57kxw9gy0jkfl3yh450"))))
8803 (build-system gnu-build-system)
8804 (arguments
8805 `(#:tests? #f ; There are no tests to run.
8806 #:phases
8807 (modify-phases %standard-phases
8808 (delete 'configure) ; There is no configure phase.
8809 (replace 'install
8810 (lambda* (#:key outputs #:allow-other-keys)
8811 (let ((bin (string-append (assoc-ref outputs "out") "/bin")))
8812 (install-file "filevercmp" bin)))))))
8813 (home-page "https://github.com/ekg/filevercmp")
8814 (synopsis "This program compares version strings")
8815 (description "This program compares version strings. It intends to be a
8816replacement for strverscmp.")
8817 (license license:gpl3+))))
5fb5dffb
RW		 8818
8819(define-public multiqc
8820 (package
8821 (name "multiqc")
9e94d063 8822 (version "1.4")
5fb5dffb
RW		 8823 (source
8824 (origin
8825 (method url-fetch)
8826 (uri (pypi-uri "multiqc" version))
8827 (sha256
8828 (base32
9e94d063 8829 "0ihx4rzmsfphv4byn05qv6f1y95g2dxs6viwziipl4wjk96acgm8"))))
5fb5dffb
RW		 8830 (build-system python-build-system)
8831 (propagated-inputs
9e94d063 8832 `(("python-jinja2" ,python-jinja2)
5fb5dffb
RW		 8833 ("python-simplejson" ,python-simplejson)
8834 ("python-pyyaml" ,python-pyyaml)
8835 ("python-click" ,python-click)
799247d2
RW		 8836 ("python-spectra" ,python-spectra)
8837 ("python-requests" ,python-requests)
8838 ("python-markdown" ,python-markdown)
8839 ("python-lzstring" ,python-lzstring)
5fb5dffb 8840 ("python-matplotlib" ,python-matplotlib)
1778ea74
RW		 8841 ("python-numpy" ,python-numpy)
8842 ;; MultQC checks for the presence of nose at runtime.
8843 ("python-nose" ,python-nose)))
5fb5dffb
RW		 8844 (home-page "http://multiqc.info")
8845 (synopsis "Aggregate bioinformatics analysis reports")
8846 (description
8847 "MultiQC is a tool to aggregate bioinformatics results across many
8848samples into a single report. It contains modules for a large number of
8849common bioinformatics tools.")
66865ab8 8850 (license license:gpl3+)))
6193563a
RW		 8851
8852(define-public r-chipseq
8853 (package
8854 (name "r-chipseq")
eeaa6967 8855 (version "1.28.0")
6193563a
RW		 8856 (source
8857 (origin
8858 (method url-fetch)
8859 (uri (bioconductor-uri "chipseq" version))
8860 (sha256
8861 (base32
eeaa6967 8862 "1ymcq77krwjzrkzzcw7i9909cmkqa7c0675z9wzvrrk81hgdssfq"))))
6193563a
RW		 8863 (build-system r-build-system)
8864 (propagated-inputs
8865 `(("r-biocgenerics" ,r-biocgenerics)
8866 ("r-genomicranges" ,r-genomicranges)
8867 ("r-iranges" ,r-iranges)
eeaa6967 8868 ("r-lattice" ,r-lattice)
6193563a
RW		 8869 ("r-s4vectors" ,r-s4vectors)
8870 ("r-shortread" ,r-shortread)))
5713bbf1 8871 (home-page "https://bioconductor.org/packages/chipseq")
6193563a
RW		 8872 (synopsis "Package for analyzing ChIPseq data")
8873 (description
8874 "This package provides tools for processing short read data from ChIPseq
8875experiments.")
8876 (license license:artistic2.0)))
d407bdb9
RW		 8877
8878(define-public r-copyhelper
8879 (package
8880 (name "r-copyhelper")
8881 (version "1.6.0")
8882 (source
8883 (origin
8884 (method url-fetch)
5713bbf1 8885 (uri (string-append "https://bioconductor.org/packages/release/"
d407bdb9
RW		 8886 "data/experiment/src/contrib/CopyhelpeR_"
8887 version ".tar.gz"))
8888 (sha256
8889 (base32
8890 "0x7cyynjmxls9as2gg0iyp9x5fpalxmdjq914ss7i84i9zyk5bhq"))))
8891 (properties `((upstream-name . "CopyhelpeR")))
8892 (build-system r-build-system)
5713bbf1 8893 (home-page "https://bioconductor.org/packages/CopyhelpeR/")
d407bdb9
RW		 8894 (synopsis "Helper files for CopywriteR")
8895 (description
8896 "This package contains the helper files that are required to run the
8897Bioconductor package CopywriteR. It contains pre-assembled 1kb bin GC-content
8898and mappability files for the reference genomes hg18, hg19, hg38, mm9 and
8899mm10. In addition, it contains a blacklist filter to remove regions that
8900display copy number variation. Files are stored as GRanges objects from the
8901GenomicRanges Bioconductor package.")
8902 (license license:gpl2)))
3a3bf2f8
RW		 8903
8904(define-public r-copywriter
8905 (package
8906 (name "r-copywriter")
c126ba69 8907 (version "2.10.0")
3a3bf2f8
RW		 8908 (source
8909 (origin
8910 (method url-fetch)
8911 (uri (bioconductor-uri "CopywriteR" version))
8912 (sha256
8913 (base32
c126ba69 8914 "17fy2lc5yf3nh6v077kv87h53n263hqz2540lzrl0vjiqrl2plca"))))
3a3bf2f8
RW		 8915 (properties `((upstream-name . "CopywriteR")))
8916 (build-system r-build-system)
8917 (propagated-inputs
8918 `(("r-biocparallel" ,r-biocparallel)
8919 ("r-chipseq" ,r-chipseq)
8920 ("r-copyhelper" ,r-copyhelper)
8921 ("r-data-table" ,r-data-table)
8922 ("r-dnacopy" ,r-dnacopy)
8923 ("r-futile-logger" ,r-futile-logger)
8924 ("r-genomeinfodb" ,r-genomeinfodb)
8925 ("r-genomicalignments" ,r-genomicalignments)
8926 ("r-genomicranges" ,r-genomicranges)
8927 ("r-gtools" ,r-gtools)
8928 ("r-iranges" ,r-iranges)
8929 ("r-matrixstats" ,r-matrixstats)
8930 ("r-rsamtools" ,r-rsamtools)
8931 ("r-s4vectors" ,r-s4vectors)))
8932 (home-page "https://github.com/PeeperLab/CopywriteR")
8933 (synopsis "Copy number information from targeted sequencing")
8934 (description
8935 "CopywriteR extracts DNA copy number information from targeted sequencing
8936by utilizing off-target reads. It allows for extracting uniformly distributed
8937copy number information, can be used without reference, and can be applied to
8938sequencing data obtained from various techniques including chromatin
8939immunoprecipitation and target enrichment on small gene panels. Thereby,
8940CopywriteR constitutes a widely applicable alternative to available copy
8941number detection tools.")
8942 (license license:gpl2)))
dd42a330 8943
bf3fa996
RW		 8944(define-public r-methylkit
8945 (package
8946 (name "r-methylkit")
b1f27536 8947 (version "1.4.1")
bf3fa996
RW		 8948 (source (origin
8949 (method url-fetch)
8950 (uri (bioconductor-uri "methylKit" version))
8951 (sha256
8952 (base32
b1f27536 8953 "1k0nfn9318sgwm4z963bhnbp4c3zv85v3f9886vc5hgaisr0yvai"))))
bf3fa996
RW		 8954 (properties `((upstream-name . "methylKit")))
8955 (build-system r-build-system)
8956 (propagated-inputs
8957 `(("r-data-table" ,r-data-table)
8958 ("r-emdbook" ,r-emdbook)
8959 ("r-fastseg" ,r-fastseg)
8960 ("r-genomeinfodb" ,r-genomeinfodb)
8961 ("r-genomicranges" ,r-genomicranges)
8962 ("r-gtools" ,r-gtools)
8963 ("r-iranges" ,r-iranges)
8964 ("r-kernsmooth" ,r-kernsmooth)
8965 ("r-limma" ,r-limma)
8966 ("r-mclust" ,r-mclust)
8967 ("r-qvalue" ,r-qvalue)
8968 ("r-r-utils" ,r-r-utils)
8969 ("r-rcpp" ,r-rcpp)
8970 ("r-rhtslib" ,r-rhtslib)
8971 ("r-rsamtools" ,r-rsamtools)
8972 ("r-rtracklayer" ,r-rtracklayer)
8973 ("r-s4vectors" ,r-s4vectors)
8974 ("r-zlibbioc" ,r-zlibbioc)))
8975 (inputs
8976 `(("zlib" ,zlib)))
11ed4108 8977 (home-page "https://github.com/al2na/methylKit")
bf3fa996
RW		 8978 (synopsis
8979 "DNA methylation analysis from high-throughput bisulfite sequencing results")
8980 (description
8981 "MethylKit is an R package for DNA methylation analysis and annotation
8982from high-throughput bisulfite sequencing. The package is designed to deal
8983with sequencing data from @dfn{Reduced representation bisulfite
8984sequencing} (RRBS) and its variants, but also target-capture methods and whole
8985genome bisulfite sequencing. It also has functions to analyze base-pair
8986resolution 5hmC data from experimental protocols such as oxBS-Seq and
8987TAB-Seq.")
8988 (license license:artistic2.0)))
8989
dd42a330
RJPB		 8990(define-public r-sva
8991 (package
8992 (name "r-sva")
fad7c0c7 8993 (version "3.26.0")
dd42a330
RJPB		 8994 (source
8995 (origin
8996 (method url-fetch)
8997 (uri (bioconductor-uri "sva" version))
8998 (sha256
8999 (base32
fad7c0c7 9000 "0q5xb68wfcnchy8rkv5ma67pmz1i91lsnvmwmj8f1c3w4xan3pgw"))))
dd42a330
RJPB		 9001 (build-system r-build-system)
9002 (propagated-inputs
aeb64f3c 9003 `(("r-genefilter" ,r-genefilter)
bfa0d1e7
RJ		 9004 ("r-mgcv" ,r-mgcv)
9005 ("r-biocparallel" ,r-biocparallel)
9006 ("r-matrixstats" ,r-matrixstats)
9007 ("r-limma" ,r-limma)))
5713bbf1 9008 (home-page "https://bioconductor.org/packages/sva")
dd42a330
RJPB		 9009 (synopsis "Surrogate variable analysis")
9010 (description
9011 "This package contains functions for removing batch effects and other
9012unwanted variation in high-throughput experiment. It also contains functions
9013for identifying and building surrogate variables for high-dimensional data
9014sets. Surrogate variables are covariates constructed directly from
9015high-dimensional data like gene expression/RNA sequencing/methylation/brain
9016imaging data that can be used in subsequent analyses to adjust for unknown,
9017unmodeled, or latent sources of noise.")
9018 (license license:artistic2.0)))
fb1e528e
RW		 9019
9020(define-public r-seqminer
9021 (package
9022 (name "r-seqminer")
5e0de298 9023 (version "6.0")
fb1e528e
RW		 9024 (source
9025 (origin
9026 (method url-fetch)
9027 (uri (cran-uri "seqminer" version))
9028 (sha256
9029 (base32
5e0de298 9030 "057j1l6dip35l1aivilapl2zv9db677b3di2pb3sfgq2sxg0ps3l"))))
fb1e528e
RW		 9031 (build-system r-build-system)
9032 (inputs
9033 `(("zlib" ,zlib)))
9034 (home-page "http://seqminer.genomic.codes")
9035 (synopsis "Read nucleotide sequence data (VCF, BCF, and METAL formats)")
9036 (description
9037 "This package provides tools to integrate nucleotide sequencing
9038data (variant call format, e.g. VCF or BCF) or meta-analysis results in R.")
9039 ;; Any version of the GPL is acceptable
9040 (license (list license:gpl2+ license:gpl3+))))
1f40e73c
RW		 9041
9042(define-public r-raremetals2
9043 (package
9044 (name "r-raremetals2")
9045 (version "0.1")
9046 (source
9047 (origin
9048 (method url-fetch)
9049 (uri (string-append "http://genome.sph.umich.edu/w/images/"
9050 "b/b7/RareMETALS2_" version ".tar.gz"))
9051 (sha256
9052 (base32
9053 "0z5ljcgvnm06ja9lm85a3cniq7slxcy37aqqkxrdidr79an5fs4s"))))
9054 (properties `((upstream-name . "RareMETALS2")))
9055 (build-system r-build-system)
9056 (propagated-inputs
9057 `(("r-seqminer" ,r-seqminer)
9058 ("r-mvtnorm" ,r-mvtnorm)
aeb64f3c 9059 ("r-mass" ,r-mass)
1f40e73c
RW		 9060 ("r-compquadform" ,r-compquadform)
9061 ("r-getopt" ,r-getopt)))
9062 (home-page "http://genome.sph.umich.edu/wiki/RareMETALS2")
9063 (synopsis "Analyze gene-level association tests for binary trait")
9064 (description
9065 "The R package rareMETALS2 is an extension of the R package rareMETALS.
9066It was designed to meta-analyze gene-level association tests for binary trait.
9067While rareMETALS offers a near-complete solution for meta-analysis of
9068gene-level tests for quantitative trait, it does not offer the optimal
9069solution for binary trait. The package rareMETALS2 offers improved features
9070for analyzing gene-level association tests in meta-analyses for binary
9071trait.")
9072 (license license:gpl3)))
0e7d058e
RW		 9073
9074(define-public r-maldiquant
9075 (package
9076 (name "r-maldiquant")
43949265 9077 (version "1.17")
0e7d058e
RW		 9078 (source
9079 (origin
9080 (method url-fetch)
9081 (uri (cran-uri "MALDIquant" version))
9082 (sha256
9083 (base32
43949265 9084 "047s6007ydc38x8wm027mlb4mngz15n0d4238fr8h43wyll5zy0z"))))
0e7d058e
RW		 9085 (properties `((upstream-name . "MALDIquant")))
9086 (build-system r-build-system)
e9960d8c 9087 (home-page "https://cran.r-project.org/web/packages/MALDIquant")
0e7d058e
RW		 9088 (synopsis "Quantitative analysis of mass spectrometry data")
9089 (description
9090 "This package provides a complete analysis pipeline for matrix-assisted
9091laser desorption/ionization-time-of-flight (MALDI-TOF) and other
9092two-dimensional mass spectrometry data. In addition to commonly used plotting
9093and processing methods it includes distinctive features, namely baseline
9094subtraction methods such as morphological filters (TopHat) or the
9095statistics-sensitive non-linear iterative peak-clipping algorithm (SNIP), peak
9096alignment using warping functions, handling of replicated measurements as well
9097as allowing spectra with different resolutions.")
9098 (license license:gpl3+)))
ae262174
RW		 9099
9100(define-public r-protgenerics
9101 (package
9102 (name "r-protgenerics")
9a665dfb 9103 (version "1.10.0")
ae262174
RW		 9104 (source
9105 (origin
9106 (method url-fetch)
9107 (uri (bioconductor-uri "ProtGenerics" version))
9108 (sha256
9109 (base32
9a665dfb 9110 "16ijp50448wnabp43klx943rhdvh7x45hvy7cnpq1s4dckxhhyni"))))
ae262174
RW		 9111 (properties `((upstream-name . "ProtGenerics")))
9112 (build-system r-build-system)
9113 (home-page "https://github.com/lgatto/ProtGenerics")
9114 (synopsis "S4 generic functions for proteomics infrastructure")
9115 (description
9116 "This package provides S4 generic functions needed by Bioconductor
9117proteomics packages.")
9118 (license license:artistic2.0)))
71676a1f
RW		 9119
9120(define-public r-mzr
9121 (package
9122 (name "r-mzr")
34b96754 9123 (version "2.12.0")
71676a1f
RW		 9124 (source
9125 (origin
9126 (method url-fetch)
9127 (uri (bioconductor-uri "mzR" version))
9128 (sha256
9129 (base32
15ca1959
RW		 9130 "1x3gp30sfxz2v3k3swih9kff9b2rvk7hzhnlkp6ywlnn2wgb0q8c"))
9131 (modules '((guix build utils)))
9132 (snippet
9133 '(begin
9134 (delete-file-recursively "src/boost")
9135 #t))))
71676a1f
RW		 9136 (properties `((upstream-name . "mzR")))
9137 (build-system r-build-system)
15ca1959
RW		 9138 (arguments
9139 `(#:phases
9140 (modify-phases %standard-phases
9141 (add-after 'unpack 'use-system-boost
9142 (lambda _
9143 (substitute* "src/Makevars"
9144 (("\\./boost/libs.*") "")
9145 (("ARCH_OBJS=" line)
9146 (string-append line
9147 "\nARCH_LIBS=-lboost_system -lboost_regex \
9148-lboost_iostreams -lboost_thread -lboost_filesystem -lboost_chrono\n")))
9149 #t)))))
71676a1f 9150 (inputs
34b96754 9151 `(("boost" ,boost) ; use this instead of the bundled boost sources
d534f3a4 9152 ("netcdf" ,netcdf)))
71676a1f
RW		 9153 (propagated-inputs
9154 `(("r-biobase" ,r-biobase)
9155 ("r-biocgenerics" ,r-biocgenerics)
9156 ("r-protgenerics" ,r-protgenerics)
9157 ("r-rcpp" ,r-rcpp)
9158 ("r-zlibbioc" ,r-zlibbioc)))
9159 (home-page "https://github.com/sneumann/mzR/")
9160 (synopsis "Parser for mass spectrometry data files")
9161 (description
9162 "The mzR package provides a unified API to the common file formats and
9163parsers available for mass spectrometry data. It comes with a wrapper for the
9164ISB random access parser for mass spectrometry mzXML, mzData and mzML files.
9165The package contains the original code written by the ISB, and a subset of the
9166proteowizard library for mzML and mzIdentML. The netCDF reading code has
9167previously been used in XCMS.")
9168 (license license:artistic2.0)))
5c9d1505
RW		 9169
9170(define-public r-affyio
9171 (package
9172 (name "r-affyio")
8a8138d2 9173 (version "1.48.0")
5c9d1505
RW		 9174 (source
9175 (origin
9176 (method url-fetch)
9177 (uri (bioconductor-uri "affyio" version))
9178 (sha256
9179 (base32
8a8138d2 9180 "1pzzp3d3dbmyf34gvivfiprkpscn36rgvhrq853a1d3avcwr5ak9"))))
5c9d1505
RW		 9181 (build-system r-build-system)
9182 (propagated-inputs
9183 `(("r-zlibbioc" ,r-zlibbioc)))
9184 (inputs
9185 `(("zlib" ,zlib)))
9186 (home-page "https://github.com/bmbolstad/affyio")
9187 (synopsis "Tools for parsing Affymetrix data files")
9188 (description
9189 "This package provides routines for parsing Affymetrix data files based
9190upon file format information. The primary focus is on accessing the CEL and
9191CDF file formats.")
9192 (license license:lgpl2.0+)))
05c7e5fb
RW		 9193
9194(define-public r-affy
9195 (package
9196 (name "r-affy")
dad5f838 9197 (version "1.56.0")
05c7e5fb
RW		 9198 (source
9199 (origin
9200 (method url-fetch)
9201 (uri (bioconductor-uri "affy" version))
9202 (sha256
9203 (base32
dad5f838 9204 "0jmbkimma5ffsdkk3xp03g4lpz84gd95nkqakif2nqq6wmx0syrj"))))
05c7e5fb
RW		 9205 (build-system r-build-system)
9206 (propagated-inputs
9207 `(("r-affyio" ,r-affyio)
9208 ("r-biobase" ,r-biobase)
9209 ("r-biocgenerics" ,r-biocgenerics)
9210 ("r-biocinstaller" ,r-biocinstaller)
9211 ("r-preprocesscore" ,r-preprocesscore)
9212 ("r-zlibbioc" ,r-zlibbioc)))
5713bbf1 9213 (home-page "https://bioconductor.org/packages/affy")
05c7e5fb
RW		 9214 (synopsis "Methods for affymetrix oligonucleotide arrays")
9215 (description
9216 "This package contains functions for exploratory oligonucleotide array
9217analysis.")
9218 (license license:lgpl2.0+)))
7c08afaf
RW		 9219
9220(define-public r-vsn
9221 (package
9222 (name "r-vsn")
1be0f536 9223 (version "3.46.0")
7c08afaf
RW		 9224 (source
9225 (origin
9226 (method url-fetch)
9227 (uri (bioconductor-uri "vsn" version))
9228 (sha256
9229 (base32
1be0f536 9230 "18y62phzirj75gg6v5l41jwybmk23ia6w7qhch0kxc4bl2rysw6j"))))
7c08afaf
RW		 9231 (build-system r-build-system)
9232 (propagated-inputs
9233 `(("r-affy" ,r-affy)
9234 ("r-biobase" ,r-biobase)
9235 ("r-ggplot2" ,r-ggplot2)
aeb64f3c 9236 ("r-lattice" ,r-lattice)
7c08afaf 9237 ("r-limma" ,r-limma)))
5713bbf1 9238 (home-page "https://bioconductor.org/packages/release/bioc/html/vsn.html")
7c08afaf
RW		 9239 (synopsis "Variance stabilization and calibration for microarray data")
9240 (description
9241 "The package implements a method for normalising microarray intensities,
9242and works for single- and multiple-color arrays. It can also be used for data
9243from other technologies, as long as they have similar format. The method uses
9244a robust variant of the maximum-likelihood estimator for an
9245additive-multiplicative error model and affine calibration. The model
9246incorporates data calibration step (a.k.a. normalization), a model for the
9247dependence of the variance on the mean intensity and a variance stabilizing
9248data transformation. Differences between transformed intensities are
9249analogous to \"normalized log-ratios\". However, in contrast to the latter,
9250their variance is independent of the mean, and they are usually more sensitive
9251and specific in detecting differential transcription.")
9252 (license license:artistic2.0)))
4aa7d592
RW		 9253
9254(define-public r-mzid
9255 (package
9256 (name "r-mzid")
b500dbcd 9257 (version "1.16.0")
4aa7d592
RW		 9258 (source
9259 (origin
9260 (method url-fetch)
9261 (uri (bioconductor-uri "mzID" version))
9262 (sha256
9263 (base32
b500dbcd 9264 "0yk70dka56zd8w62f03ggx3mandj91gfa767h9ajj0sd3mjmfqb9"))))
4aa7d592
RW		 9265 (properties `((upstream-name . "mzID")))
9266 (build-system r-build-system)
9267 (propagated-inputs
9268 `(("r-doparallel" ,r-doparallel)
9269 ("r-foreach" ,r-foreach)
9270 ("r-iterators" ,r-iterators)
9271 ("r-plyr" ,r-plyr)
9272 ("r-protgenerics" ,r-protgenerics)
9273 ("r-rcpp" ,r-rcpp)
9274 ("r-xml" ,r-xml)))
5713bbf1 9275 (home-page "https://bioconductor.org/packages/mzID")
4aa7d592
RW		 9276 (synopsis "Parser for mzIdentML files")
9277 (description
9278 "This package provides a parser for mzIdentML files implemented using the
9279XML package. The parser tries to be general and able to handle all types of
9280mzIdentML files with the drawback of having less pretty output than a vendor
9281specific parser.")
9282 (license license:gpl2+)))
6a67e181
RW		 9283
9284(define-public r-pcamethods
9285 (package
9286 (name "r-pcamethods")
a998c9a4 9287 (version "1.70.0")
6a67e181
RW		 9288 (source
9289 (origin
9290 (method url-fetch)
9291 (uri (bioconductor-uri "pcaMethods" version))
9292 (sha256
9293 (base32
a998c9a4 9294 "0ii235g0x0492kh8cfrf28ni0b6vd6fh7kizkqmczzqggd6b1bk8"))))
6a67e181
RW		 9295 (properties `((upstream-name . "pcaMethods")))
9296 (build-system r-build-system)
9297 (propagated-inputs
9298 `(("r-biobase" ,r-biobase)
9299 ("r-biocgenerics" ,r-biocgenerics)
aeb64f3c 9300 ("r-mass" ,r-mass)
6a67e181
RW		 9301 ("r-rcpp" ,r-rcpp)))
9302 (home-page "https://github.com/hredestig/pcamethods")
9303 (synopsis "Collection of PCA methods")
9304 (description
9305 "This package provides Bayesian PCA, Probabilistic PCA, Nipals PCA,
9306Inverse Non-Linear PCA and the conventional SVD PCA. A cluster based method
9307for missing value estimation is included for comparison. BPCA, PPCA and
9308NipalsPCA may be used to perform PCA on incomplete data as well as for
9309accurate missing value estimation. A set of methods for printing and plotting
9310the results is also provided. All PCA methods make use of the same data
9311structure (pcaRes) to provide a common interface to the PCA results.")
9312 (license license:gpl3+)))
11879284
RW		 9313
9314(define-public r-msnbase
9315 (package
9316 (name "r-msnbase")
53f0dea9 9317 (version "2.4.2")
11879284
RW		 9318 (source
9319 (origin
9320 (method url-fetch)
9321 (uri (bioconductor-uri "MSnbase" version))
9322 (sha256
9323 (base32
53f0dea9 9324 "1ig64bf881p118dwqfr0ry41m7yhnyv165smv8fdwfv7sb6sagif"))))
11879284
RW		 9325 (properties `((upstream-name . "MSnbase")))
9326 (build-system r-build-system)
9327 (propagated-inputs
9328 `(("r-affy" ,r-affy)
9329 ("r-biobase" ,r-biobase)
9330 ("r-biocgenerics" ,r-biocgenerics)
9331 ("r-biocparallel" ,r-biocparallel)
9332 ("r-digest" ,r-digest)
9333 ("r-ggplot2" ,r-ggplot2)
9334 ("r-impute" ,r-impute)
9335 ("r-iranges" ,r-iranges)
baa00ee9 9336 ("r-lattice" ,r-lattice)
11879284
RW		 9337 ("r-maldiquant" ,r-maldiquant)
9338 ("r-mzid" ,r-mzid)
9339 ("r-mzr" ,r-mzr)
9340 ("r-pcamethods" ,r-pcamethods)
9341 ("r-plyr" ,r-plyr)
9342 ("r-preprocesscore" ,r-preprocesscore)
9343 ("r-protgenerics" ,r-protgenerics)
9344 ("r-rcpp" ,r-rcpp)
11879284
RW		 9345 ("r-s4vectors" ,r-s4vectors)
9346 ("r-vsn" ,r-vsn)
9347 ("r-xml" ,r-xml)))
9348 (home-page "https://github.com/lgatto/MSnbase")
9349 (synopsis "Base functions and classes for MS-based proteomics")
9350 (description
9351 "This package provides basic plotting, data manipulation and processing
e614d639 9352of mass spectrometry based proteomics data.")
11879284 9353 (license license:artistic2.0)))
66da3a9f
RW		 9354
9355(define-public r-msnid
9356 (package
9357 (name "r-msnid")
87e91a9f 9358 (version "1.12.1")
66da3a9f
RW		 9359 (source
9360 (origin
9361 (method url-fetch)
9362 (uri (bioconductor-uri "MSnID" version))
9363 (sha256
9364 (base32
87e91a9f 9365 "1zw508kk4f8brg69674wp18gqkpx2kpya5f6x9cl3qng7v4h5pxx"))))
66da3a9f
RW		 9366 (properties `((upstream-name . "MSnID")))
9367 (build-system r-build-system)
9368 (propagated-inputs
9369 `(("r-biobase" ,r-biobase)
9370 ("r-data-table" ,r-data-table)
9371 ("r-doparallel" ,r-doparallel)
9372 ("r-dplyr" ,r-dplyr)
9373 ("r-foreach" ,r-foreach)
9374 ("r-iterators" ,r-iterators)
9375 ("r-msnbase" ,r-msnbase)
9376 ("r-mzid" ,r-mzid)
9377 ("r-mzr" ,r-mzr)
9378 ("r-protgenerics" ,r-protgenerics)
9379 ("r-r-cache" ,r-r-cache)
9380 ("r-rcpp" ,r-rcpp)
9381 ("r-reshape2" ,r-reshape2)))
5713bbf1 9382 (home-page "https://bioconductor.org/packages/MSnID")
66da3a9f
RW		 9383 (synopsis "Utilities for LC-MSn proteomics identifications")
9384 (description
2923f3e5
RW		 9385 "This package extracts @dfn{tandem mass spectrometry} (MS/MS) ID data
9386from mzIdentML (leveraging the mzID package) or text files. After collating
9387the search results from multiple datasets it assesses their identification
9388quality and optimize filtering criteria to achieve the maximum number of
9389identifications while not exceeding a specified false discovery rate. It also
9390contains a number of utilities to explore the MS/MS results and assess missed
9391and irregular enzymatic cleavages, mass measurement accuracy, etc.")
66da3a9f 9392 (license license:artistic2.0)))
5ded35d8 9393
2441c284 9394(define-public r-seurat
f1a2b1cb
RW		 9395 (package
9396 (name "r-seurat")
ebec98ae 9397 (version "2.2.1")
f1a2b1cb
RW		 9398 (source (origin
9399 (method url-fetch)
9400 (uri (cran-uri "Seurat" version))
9401 (sha256
9402 (base32
ebec98ae 9403 "1sr82nf38hq07avrfn8vlrzjq7dfm4pcr8l1nh6mnglcql2bk9z2"))
f1a2b1cb
RW		 9404 ;; Delete pre-built jar.
9405 (snippet
9406 '(begin (delete-file "inst/java/ModularityOptimizer.jar")
9407 #t))))
9408 (properties `((upstream-name . "Seurat")))
9409 (build-system r-build-system)
9410 (arguments
9411 `(#:phases
9412 (modify-phases %standard-phases
9413 (add-after 'unpack 'build-jar
9414 (lambda* (#:key inputs #:allow-other-keys)
9415 (let ((classesdir "tmp-classes"))
9416 (setenv "JAVA_HOME" (assoc-ref inputs "jdk"))
9417 (mkdir classesdir)
9418 (with-output-to-file "manifest"
8271b8d2
RW		 9419 (lambda _
9420 (display "Manifest-Version: 1.0
9421Main-Class: ModularityOptimizer\n")))
9422 (and (zero? (apply system* `("javac" "-d" ,classesdir
9423 ,@(find-files "java" "\\.java$"))))
9424 (zero? (system* "jar"
9425 "-cmf" "manifest"
9426 "inst/java/ModularityOptimizer.jar"
f1a2b1cb
RW		 9427 "-C" classesdir ".")))))))))
9428 (native-inputs
9429 `(("jdk" ,icedtea "jdk")))
9430 (propagated-inputs
9431 `(("r-ape" ,r-ape)
9432 ("r-caret" ,r-caret)
9433 ("r-cowplot" ,r-cowplot)
9434 ("r-diffusionmap" ,r-diffusionmap)
9435 ("r-dplyr" ,r-dplyr)
9436 ("r-dtw" ,r-dtw)
9437 ("r-fnn" ,r-fnn)
9438 ("r-fpc" ,r-fpc)
9439 ("r-gdata" ,r-gdata)
f1a2b1cb 9440 ("r-ggplot2" ,r-ggplot2)
26e3e28c 9441 ("r-ggridges" ,r-ggridges)
f1a2b1cb
RW		 9442 ("r-gplots" ,r-gplots)
9443 ("r-gridextra" ,r-gridextra)
9444 ("r-hmisc" ,r-hmisc)
9445 ("r-ica" ,r-ica)
9446 ("r-igraph" ,r-igraph)
9447 ("r-irlba" ,r-irlba)
9448 ("r-lars" ,r-lars)
9449 ("r-mass" ,r-mass)
9450 ("r-matrix" ,r-matrix)
ebec98ae 9451 ("r-metap" ,r-metap)
f1a2b1cb 9452 ("r-mixtools" ,r-mixtools)
f1a2b1cb
RW		 9453 ("r-pbapply" ,r-pbapply)
9454 ("r-plotly" ,r-plotly)
9455 ("r-ranger" ,r-ranger)
9456 ("r-rcolorbrewer" ,r-rcolorbrewer)
9457 ("r-rcpp" ,r-rcpp)
26e3e28c 9458 ("r-rcppeigen" ,r-rcppeigen)
f1a2b1cb
RW		 9459 ("r-rcppprogress" ,r-rcppprogress)
9460 ("r-reshape2" ,r-reshape2)
9461 ("r-rocr" ,r-rocr)
9462 ("r-rtsne" ,r-rtsne)
9463 ("r-sdmtools" ,r-sdmtools)
9464 ("r-stringr" ,r-stringr)
9465 ("r-tclust" ,r-tclust)
9466 ("r-tidyr" ,r-tidyr)
9467 ("r-tsne" ,r-tsne)
9468 ("r-vgam" ,r-vgam)))
9469 (home-page "http://www.satijalab.org/seurat")
9470 (synopsis "Seurat is an R toolkit for single cell genomics")
9471 (description
9472 "This package is an R package designed for QC, analysis, and
2441c284
RJPB		 9473exploration of single cell RNA-seq data. It easily enables widely-used
9474analytical techniques, including the identification of highly variable genes,
9475dimensionality reduction; PCA, ICA, t-SNE, standard unsupervised clustering
9476algorithms; density clustering, hierarchical clustering, k-means, and the
9477discovery of differentially expressed genes and markers.")
f1a2b1cb 9478 (license license:gpl3)))
2441c284 9479
d4b83651
RW		 9480(define-public r-aroma-light
9481 (package
9482 (name "r-aroma-light")
531e8090 9483 (version "3.8.0")
d4b83651
RW		 9484 (source
9485 (origin
9486 (method url-fetch)
9487 (uri (bioconductor-uri "aroma.light" version))
9488 (sha256
9489 (base32
531e8090 9490 "0crnk6851jwypqr5l5jcbbay0vi5vvdjyisaf6z2d69c39wmr6sc"))))
d4b83651
RW		 9491 (properties `((upstream-name . "aroma.light")))
9492 (build-system r-build-system)
9493 (propagated-inputs
9494 `(("r-matrixstats" ,r-matrixstats)
9495 ("r-r-methodss3" ,r-r-methodss3)
9496 ("r-r-oo" ,r-r-oo)
9497 ("r-r-utils" ,r-r-utils)))
9498 (home-page "https://github.com/HenrikBengtsson/aroma.light")
9499 (synopsis "Methods for normalization and visualization of microarray data")
9500 (description
9501 "This package provides methods for microarray analysis that take basic
9502data types such as matrices and lists of vectors. These methods can be used
9503standalone, be utilized in other packages, or be wrapped up in higher-level
9504classes.")
9505 (license license:gpl2+)))
9506
7b465327
RW		 9507(define-public r-deseq
9508 (package
9509 (name "r-deseq")
8140f680 9510 (version "1.30.0")
7b465327
RW		 9511 (source
9512 (origin
9513 (method url-fetch)
9514 (uri (bioconductor-uri "DESeq" version))
9515 (sha256
9516 (base32
8140f680 9517 "0mn5w3cy16iwwk8zxs7za6aa6cnrca75z0g45zd5zh1py5d7nfv9"))))
7b465327
RW		 9518 (properties `((upstream-name . "DESeq")))
9519 (build-system r-build-system)
9520 (propagated-inputs
9521 `(("r-biobase" ,r-biobase)
9522 ("r-biocgenerics" ,r-biocgenerics)
9523 ("r-genefilter" ,r-genefilter)
9524 ("r-geneplotter" ,r-geneplotter)
9525 ("r-lattice" ,r-lattice)
9526 ("r-locfit" ,r-locfit)
9527 ("r-mass" ,r-mass)
9528 ("r-rcolorbrewer" ,r-rcolorbrewer)))
9529 (home-page "http://www-huber.embl.de/users/anders/DESeq")
9530 (synopsis "Differential gene expression analysis")
9531 (description
9532 "This package provides tools for estimating variance-mean dependence in
9533count data from high-throughput genetic sequencing assays and for testing for
9534differential expression based on a model using the negative binomial
9535distribution.")
9536 (license license:gpl3+)))
9537
296b3c63
RW		 9538(define-public r-edaseq
9539 (package
9540 (name "r-edaseq")
00961279 9541 (version "2.12.0")
296b3c63
RW		 9542 (source
9543 (origin
9544 (method url-fetch)
9545 (uri (bioconductor-uri "EDASeq" version))
9546 (sha256
9547 (base32
00961279 9548 "07zm89zcivyn2261aq9grqmly8ji482kr9h9dyfknfdfrpv7jpwv"))))
296b3c63
RW		 9549 (properties `((upstream-name . "EDASeq")))
9550 (build-system r-build-system)
9551 (propagated-inputs
9552 `(("r-annotationdbi" ,r-annotationdbi)
9553 ("r-aroma-light" ,r-aroma-light)
9554 ("r-biobase" ,r-biobase)
9555 ("r-biocgenerics" ,r-biocgenerics)
9556 ("r-biomart" ,r-biomart)
9557 ("r-biostrings" ,r-biostrings)
9558 ("r-deseq" ,r-deseq)
9559 ("r-genomicfeatures" ,r-genomicfeatures)
9560 ("r-genomicranges" ,r-genomicranges)
9561 ("r-iranges" ,r-iranges)
9562 ("r-rsamtools" ,r-rsamtools)
9563 ("r-shortread" ,r-shortread)))
9564 (home-page "https://github.com/drisso/EDASeq")
9565 (synopsis "Exploratory data analysis and normalization for RNA-Seq")
9566 (description
9567 "This package provides support for numerical and graphical summaries of
9568RNA-Seq genomic read data. Provided within-lane normalization procedures to
9569adjust for GC-content effect (or other gene-level effects) on read counts:
9570loess robust local regression, global-scaling, and full-quantile
9571normalization. Between-lane normalization procedures to adjust for
9572distributional differences between lanes (e.g., sequencing depth):
9573global-scaling and full-quantile normalization.")
9574 (license license:artistic2.0)))
9575
5f96f30f
RW		 9576(define-public r-interactivedisplaybase
9577 (package
9578 (name "r-interactivedisplaybase")
1567c8d9 9579 (version "1.16.0")
5f96f30f
RW		 9580 (source
9581 (origin
9582 (method url-fetch)
9583 (uri (bioconductor-uri "interactiveDisplayBase" version))
9584 (sha256
9585 (base32
1567c8d9 9586 "01yb945jqqimwjgriza6yy4dnp303cdirxrhl4hjyprfdlmnz5p5"))))
5f96f30f
RW		 9587 (properties
9588 `((upstream-name . "interactiveDisplayBase")))
9589 (build-system r-build-system)
9590 (propagated-inputs
9591 `(("r-biocgenerics" ,r-biocgenerics)
9592 ("r-shiny" ,r-shiny)))
5713bbf1 9593 (home-page "https://bioconductor.org/packages/interactiveDisplayBase")
5f96f30f
RW		 9594 (synopsis "Base package for web displays of Bioconductor objects")
9595 (description
9596 "This package contains the basic methods needed to generate interactive
9597Shiny-based display methods for Bioconductor objects.")
9598 (license license:artistic2.0)))
9599
4a007ffa
RW		 9600(define-public r-annotationhub
9601 (package
9602 (name "r-annotationhub")
9b8d0201 9603 (version "2.10.1")
4a007ffa
RW		 9604 (source
9605 (origin
9606 (method url-fetch)
9607 (uri (bioconductor-uri "AnnotationHub" version))
9608 (sha256
9609 (base32
9b8d0201 9610 "14v8g44a6zg9j2rwn9x9y8509k0wr2cw8yccliz24glplb40wva4"))))
4a007ffa
RW		 9611 (properties `((upstream-name . "AnnotationHub")))
9612 (build-system r-build-system)
9613 (propagated-inputs
9614 `(("r-annotationdbi" ,r-annotationdbi)
9615 ("r-biocgenerics" ,r-biocgenerics)
9616 ("r-biocinstaller" ,r-biocinstaller)
14b3c719 9617 ("r-curl" ,r-curl)
4a007ffa
RW		 9618 ("r-httr" ,r-httr)
9619 ("r-interactivedisplaybase" ,r-interactivedisplaybase)
9620 ("r-rsqlite" ,r-rsqlite)
9621 ("r-s4vectors" ,r-s4vectors)
9622 ("r-yaml" ,r-yaml)))
5713bbf1 9623 (home-page "https://bioconductor.org/packages/AnnotationHub")
4a007ffa
RW		 9624 (synopsis "Client to access AnnotationHub resources")
9625 (description
9626 "This package provides a client for the Bioconductor AnnotationHub web
9627resource. The AnnotationHub web resource provides a central location where
9628genomic files (e.g. VCF, bed, wig) and other resources from standard
9629locations (e.g. UCSC, Ensembl) can be discovered. The resource includes
9630metadata about each resource, e.g., a textual description, tags, and date of
9631modification. The client creates and manages a local cache of files retrieved
9632by the user, helping with quick and reproducible access.")
9633 (license license:artistic2.0)))
9634
d4a1e918
RW		 9635(define-public r-fastseg
9636 (package
9637 (name "r-fastseg")
87fa5afa 9638 (version "1.24.0")
d4a1e918
RW		 9639 (source
9640 (origin
9641 (method url-fetch)
9642 (uri (bioconductor-uri "fastseg" version))
9643 (sha256
9644 (base32
87fa5afa 9645 "0dd7nr3klwz9ailwshnbynhd62lwb8zbbpj6jf3igpb94yi6x2jp"))))
d4a1e918
RW		 9646 (build-system r-build-system)
9647 (propagated-inputs
9648 `(("r-biobase" ,r-biobase)
9649 ("r-biocgenerics" ,r-biocgenerics)
9650 ("r-genomicranges" ,r-genomicranges)
9651 ("r-iranges" ,r-iranges)
9652 ("r-s4vectors" ,r-s4vectors)))
9653 (home-page "http://www.bioinf.jku.at/software/fastseg/index.html")
9654 (synopsis "Fast segmentation algorithm for genetic sequencing data")
9655 (description
9656 "Fastseg implements a very fast and efficient segmentation algorithm.
9657It can segment data from DNA microarrays and data from next generation
9658sequencing for example to detect copy number segments. Further it can segment
9659data from RNA microarrays like tiling arrays to identify transcripts. Most
9660generally, it can segment data given as a matrix or as a vector. Various data
9661formats can be used as input to fastseg like expression set objects for
9662microarrays or GRanges for sequencing data.")
9663 (license license:lgpl2.0+)))
9664
3121814e
RW		 9665(define-public r-keggrest
9666 (package
9667 (name "r-keggrest")
f5f94427 9668 (version "1.18.1")
3121814e
RW		 9669 (source
9670 (origin
9671 (method url-fetch)
9672 (uri (bioconductor-uri "KEGGREST" version))
9673 (sha256
9674 (base32
f5f94427 9675 "02gwmm79djj55a90dzc80hlgwc6bafl7xd7fnx2q59pk945k3z9c"))))
3121814e
RW		 9676 (properties `((upstream-name . "KEGGREST")))
9677 (build-system r-build-system)
9678 (propagated-inputs
9679 `(("r-biostrings" ,r-biostrings)
9680 ("r-httr" ,r-httr)
9681 ("r-png" ,r-png)))
9682 (home-page "https://bioconductor.org/packages/KEGGREST")
9683 (synopsis "Client-side REST access to KEGG")
9684 (description
9685 "This package provides a package that provides a client interface to the
9686@dfn{Kyoto Encyclopedia of Genes and Genomes} (KEGG) REST server.")
9687 (license license:artistic2.0)))
9688
e160aa1f
RW		 9689(define-public r-gage
9690 (package
9691 (name "r-gage")
34d077b8 9692 (version "2.28.2")
e160aa1f
RW		 9693 (source
9694 (origin
9695 (method url-fetch)
9696 (uri (bioconductor-uri "gage" version))
9697 (sha256
9698 (base32
34d077b8 9699 "0h0mlhns9j7cpfksvdlvx9jb7szm3r1dwqb3s4s8p8hmkb9byyii"))))
e160aa1f
RW		 9700 (build-system r-build-system)
9701 (propagated-inputs
9702 `(("r-annotationdbi" ,r-annotationdbi)
9703 ("r-graph" ,r-graph)
9704 ("r-keggrest" ,r-keggrest)))
9705 (home-page "http://www.biomedcentral.com/1471-2105/10/161")
9706 (synopsis "Generally applicable gene-set enrichment for pathway analysis")
9707 (description
9708 "GAGE is a published method for gene set (enrichment or GSEA) or pathway
9709analysis. GAGE is generally applicable independent of microarray or RNA-Seq
9710data attributes including sample sizes, experimental designs, assay platforms,
9711and other types of heterogeneity. The gage package provides functions for
9712basic GAGE analysis, result processing and presentation. In addition, it
9713provides demo microarray data and commonly used gene set data based on KEGG
9714pathways and GO terms. These funtions and data are also useful for gene set
9715analysis using other methods.")
9716 (license license:gpl2+)))
9717
902fb15d
RW		 9718(define-public r-genomicfiles
9719 (package
9720 (name "r-genomicfiles")
9721 (version "1.14.0")
9722 (source
9723 (origin
9724 (method url-fetch)
9725 (uri (bioconductor-uri "GenomicFiles" version))
9726 (sha256
9727 (base32
9728 "0r0wmrs5jycf1kckhnc2sgjmp336srlcjdkpbb1ymm7kazdd0s9n"))))
9729 (properties `((upstream-name . "GenomicFiles")))
9730 (build-system r-build-system)
9731 (propagated-inputs
9732 `(("r-biocgenerics" ,r-biocgenerics)
9733 ("r-biocparallel" ,r-biocparallel)
9734 ("r-genomeinfodb" ,r-genomeinfodb)
9735 ("r-genomicalignments" ,r-genomicalignments)
9736 ("r-genomicranges" ,r-genomicranges)
9737 ("r-iranges" ,r-iranges)
9738 ("r-rsamtools" ,r-rsamtools)
9739 ("r-rtracklayer" ,r-rtracklayer)
9740 ("r-s4vectors" ,r-s4vectors)
9741 ("r-summarizedexperiment" ,r-summarizedexperiment)
9742 ("r-variantannotation" ,r-variantannotation)))
9743 (home-page "https://bioconductor.org/packages/GenomicFiles")
9744 (synopsis "Distributed computing by file or by range")
9745 (description
9746 "This package provides infrastructure for parallel computations
9747distributed by file or by range. User defined mapper and reducer functions
9748provide added flexibility for data combination and manipulation.")
9749 (license license:artistic2.0)))
9750
3af149f5
RW		 9751(define-public r-complexheatmap
9752 (package
9753 (name "r-complexheatmap")
9754 (version "1.17.1")
9755 (source
9756 (origin
9757 (method url-fetch)
9758 (uri (bioconductor-uri "ComplexHeatmap" version))
9759 (sha256
9760 (base32
9761 "1x6kp55iqqsd8bhdl3qch95nfiy2y46ldbbsx1sj1v8f0b0ywwcy"))))
9762 (properties
9763 `((upstream-name . "ComplexHeatmap")))
9764 (build-system r-build-system)
9765 (propagated-inputs
9766 `(("r-circlize" ,r-circlize)
9767 ("r-colorspace" ,r-colorspace)
9768 ("r-getoptlong" ,r-getoptlong)
9769 ("r-globaloptions" ,r-globaloptions)
9770 ("r-rcolorbrewer" ,r-rcolorbrewer)))
9771 (home-page
9772 "https://github.com/jokergoo/ComplexHeatmap")
9773 (synopsis "Making Complex Heatmaps")
9774 (description
9775 "Complex heatmaps are efficient to visualize associations between
9776different sources of data sets and reveal potential structures. This package
9777provides a highly flexible way to arrange multiple heatmaps and supports
9778self-defined annotation graphics.")
9779 (license license:gpl2+)))
9780
04e2a2e9
RW		 9781(define-public r-dirichletmultinomial
9782 (package
9783 (name "r-dirichletmultinomial")
9784 (version "1.20.0")
9785 (source
9786 (origin
9787 (method url-fetch)
9788 (uri (bioconductor-uri "DirichletMultinomial" version))
9789 (sha256
9790 (base32
9791 "1c4s6x0qm20556grcd1xys9kkpnlzpasaai474malwcg6qvgi4x1"))))
9792 (properties
9793 `((upstream-name . "DirichletMultinomial")))
9794 (build-system r-build-system)
9795 (inputs
9796 `(("gsl" ,gsl)))
9797 (propagated-inputs
9798 `(("r-biocgenerics" ,r-biocgenerics)
9799 ("r-iranges" ,r-iranges)
9800 ("r-s4vectors" ,r-s4vectors)))
9801 (home-page "https://bioconductor.org/packages/DirichletMultinomial")
9802 (synopsis "Dirichlet-Multinomial mixture models for microbiome data")
9803 (description
9804 "Dirichlet-multinomial mixture models can be used to describe variability
9805in microbial metagenomic data. This package is an interface to code
9806originally made available by Holmes, Harris, and Quince, 2012, PLoS ONE 7(2):
98071-15.")
9808 (license license:lgpl3)))
9809
aa30ab5a
RW		 9810(define-public r-ensembldb
9811 (package
9812 (name "r-ensembldb")
8877ab43 9813 (version "2.2.2")
aa30ab5a
RW		 9814 (source
9815 (origin
9816 (method url-fetch)
9817 (uri (bioconductor-uri "ensembldb" version))
9818 (sha256
9819 (base32
8877ab43 9820 "1yngndkf3588z91z0a2fvkg423p26ajm6xv1p27x0l9mzhhaqq3k"))))
aa30ab5a
RW		 9821 (build-system r-build-system)
9822 (propagated-inputs
9823 `(("r-annotationdbi" ,r-annotationdbi)
9824 ("r-annotationfilter" ,r-annotationfilter)
9825 ("r-annotationhub" ,r-annotationhub)
9826 ("r-biobase" ,r-biobase)
9827 ("r-biocgenerics" ,r-biocgenerics)
9828 ("r-biostrings" ,r-biostrings)
9829 ("r-curl" ,r-curl)
9830 ("r-dbi" ,r-dbi)
9831 ("r-genomeinfodb" ,r-genomeinfodb)
9832 ("r-genomicfeatures" ,r-genomicfeatures)
9833 ("r-genomicranges" ,r-genomicranges)
9834 ("r-iranges" ,r-iranges)
9835 ("r-protgenerics" ,r-protgenerics)
9836 ("r-rsamtools" ,r-rsamtools)
9837 ("r-rsqlite" ,r-rsqlite)
9838 ("r-rtracklayer" ,r-rtracklayer)
9839 ("r-s4vectors" ,r-s4vectors)))
9840 (home-page "https://github.com/jotsetung/ensembldb")
9841 (synopsis "Utilities to create and use Ensembl-based annotation databases")
9842 (description
9843 "The package provides functions to create and use transcript-centric
9844annotation databases/packages. The annotation for the databases are directly
9845fetched from Ensembl using their Perl API. The functionality and data is
9846similar to that of the TxDb packages from the @code{GenomicFeatures} package,
9847but, in addition to retrieve all gene/transcript models and annotations from
9848the database, the @code{ensembldb} package also provides a filter framework
9849allowing to retrieve annotations for specific entries like genes encoded on a
9850chromosome region or transcript models of lincRNA genes.")
9851 ;; No version specified
9852 (license license:lgpl3+)))
9853
2f6f61fd
RW		 9854(define-public r-organismdbi
9855 (package
9856 (name "r-organismdbi")
9857 (version "1.20.0")
9858 (source
9859 (origin
9860 (method url-fetch)
9861 (uri (bioconductor-uri "OrganismDbi" version))
9862 (sha256
9863 (base32
9864 "0yxvhwn0m53wfwp0zi81x96argdf7cf1lpymc2as51apvfcnjdl8"))))
9865 (properties `((upstream-name . "OrganismDbi")))
9866 (build-system r-build-system)
9867 (propagated-inputs
9868 `(("r-annotationdbi" ,r-annotationdbi)
9869 ("r-biobase" ,r-biobase)
9870 ("r-biocgenerics" ,r-biocgenerics)
9871 ("r-biocinstaller" ,r-biocinstaller)
9872 ("r-dbi" ,r-dbi)
9873 ("r-genomicfeatures" ,r-genomicfeatures)
9874 ("r-genomicranges" ,r-genomicranges)
9875 ("r-graph" ,r-graph)
9876 ("r-iranges" ,r-iranges)
9877 ("r-rbgl" ,r-rbgl)
9878 ("r-s4vectors" ,r-s4vectors)))
9879 (home-page "https://bioconductor.org/packages/OrganismDbi")
9880 (synopsis "Software to enable the smooth interfacing of database packages")
9881 (description "The package enables a simple unified interface to several
9882annotation packages each of which has its own schema by taking advantage of
9883the fact that each of these packages implements a select methods.")
9884 (license license:artistic2.0)))
9885
7af1f403
RW		 9886(define-public r-biovizbase
9887 (package
9888 (name "r-biovizbase")
9889 (version "1.26.0")
9890 (source
9891 (origin
9892 (method url-fetch)
9893 (uri (bioconductor-uri "biovizBase" version))
9894 (sha256
9895 (base32
9896 "14l4vhj0a4ssr9m9zdzz3qpd4qw1mhgq5bmxq7jhrq3j9kmd6i2f"))))
9897 (properties `((upstream-name . "biovizBase")))
9898 (build-system r-build-system)
9899 (propagated-inputs
9900 `(("r-annotationdbi" ,r-annotationdbi)
9901 ("r-annotationfilter" ,r-annotationfilter)
9902 ("r-biocgenerics" ,r-biocgenerics)
9903 ("r-biostrings" ,r-biostrings)
9904 ("r-dichromat" ,r-dichromat)
9905 ("r-ensembldb" ,r-ensembldb)
9906 ("r-genomeinfodb" ,r-genomeinfodb)
9907 ("r-genomicalignments" ,r-genomicalignments)
9908 ("r-genomicfeatures" ,r-genomicfeatures)
9909 ("r-genomicranges" ,r-genomicranges)
9910 ("r-hmisc" ,r-hmisc)
9911 ("r-iranges" ,r-iranges)
9912 ("r-rcolorbrewer" ,r-rcolorbrewer)
9913 ("r-rsamtools" ,r-rsamtools)
9914 ("r-s4vectors" ,r-s4vectors)
9915 ("r-scales" ,r-scales)
9916 ("r-summarizedexperiment" ,r-summarizedexperiment)
9917 ("r-variantannotation" ,r-variantannotation)))
9918 (home-page "https://bioconductor.org/packages/biovizBase")
9919 (synopsis "Basic graphic utilities for visualization of genomic data")
9920 (description
9921 "The biovizBase package is designed to provide a set of utilities, color
9922schemes and conventions for genomic data. It serves as the base for various
9923high-level packages for biological data visualization. This saves development
9924effort and encourages consistency.")
9925 (license license:artistic2.0)))
9926
60faf945
RW		 9927(define-public r-ggbio
9928 (package
9929 (name "r-ggbio")
9930 (version "1.26.0")
9931 (source
9932 (origin
9933 (method url-fetch)
9934 (uri (bioconductor-uri "ggbio" version))
9935 (sha256
9936 (base32
9937 "1bqxfqy0hff87ax92z4lfbjz01ndrz7x8pzm6dlkdmi52p30krm9"))))
9938 (build-system r-build-system)
9939 (propagated-inputs
9940 `(("r-annotationdbi" ,r-annotationdbi)
9941 ("r-annotationfilter" ,r-annotationfilter)
9942 ("r-biobase" ,r-biobase)
9943 ("r-biocgenerics" ,r-biocgenerics)
9944 ("r-biostrings" ,r-biostrings)
9945 ("r-biovizbase" ,r-biovizbase)
9946 ("r-bsgenome" ,r-bsgenome)
9947 ("r-ensembldb" ,r-ensembldb)
9948 ("r-genomeinfodb" ,r-genomeinfodb)
9949 ("r-genomicalignments" ,r-genomicalignments)
9950 ("r-genomicfeatures" ,r-genomicfeatures)
9951 ("r-genomicranges" ,r-genomicranges)
9952 ("r-ggally" ,r-ggally)
9953 ("r-ggplot2" ,r-ggplot2)
9954 ("r-gridextra" ,r-gridextra)
9955 ("r-gtable" ,r-gtable)
9956 ("r-hmisc" ,r-hmisc)
9957 ("r-iranges" ,r-iranges)
9958 ("r-organismdbi" ,r-organismdbi)
9959 ("r-reshape2" ,r-reshape2)
9960 ("r-rsamtools" ,r-rsamtools)
9961 ("r-rtracklayer" ,r-rtracklayer)
9962 ("r-s4vectors" ,r-s4vectors)
9963 ("r-scales" ,r-scales)
9964 ("r-summarizedexperiment" ,r-summarizedexperiment)
9965 ("r-variantannotation" ,r-variantannotation)))
9966 (home-page "http://www.tengfei.name/ggbio/")
9967 (synopsis "Visualization tools for genomic data")
9968 (description
9969 "The ggbio package extends and specializes the grammar of graphics for
9970biological data. The graphics are designed to answer common scientific
9971questions, in particular those often asked of high throughput genomics data.
9972All core Bioconductor data structures are supported, where appropriate. The
9973package supports detailed views of particular genomic regions, as well as
9974genome-wide overviews. Supported overviews include ideograms and grand linear
9975views. High-level plots include sequence fragment length, edge-linked
9976interval to data view, mismatch pileup, and several splicing summaries.")
9977 (license license:artistic2.0)))
9978
96a392a0
RW		 9979(define-public r-gprofiler
9980 (package
9981 (name "r-gprofiler")
ca7855fc 9982 (version "0.6.4")
96a392a0
RW		 9983 (source
9984 (origin
9985 (method url-fetch)
9986 (uri (cran-uri "gProfileR" version))
9987 (sha256
9988 (base32
ca7855fc 9989 "1cka02zbz1rbppm782qpxk1xn9qxbrv2gp5rgf970j906hxm2y0b"))))
96a392a0
RW		 9990 (properties `((upstream-name . "gProfileR")))
9991 (build-system r-build-system)
9992 (propagated-inputs
9993 `(("r-plyr" ,r-plyr)
9994 ("r-rcurl" ,r-rcurl)))
e9960d8c 9995 (home-page "https://cran.r-project.org/web/packages/gProfileR/")
96a392a0
RW		 9996 (synopsis "Interface to the g:Profiler toolkit")
9997 (description
9998 "This package provides tools for functional enrichment analysis,
9999gene identifier conversion and mapping homologous genes across related
10000organisms via the @code{g:Profiler} toolkit.")
10001 (license license:gpl2+)))
10002
e2b92799
RW		 10003(define-public r-gqtlbase
10004 (package
10005 (name "r-gqtlbase")
10006 (version "1.10.0")
10007 (source
10008 (origin
10009 (method url-fetch)
10010 (uri (bioconductor-uri "gQTLBase" version))
10011 (sha256
10012 (base32
10013 "1756vfcj2dkkgcmfkkg7qdaig36dv9gfvpypn9rbrky56wm1p035"))))
10014 (properties `((upstream-name . "gQTLBase")))
10015 (build-system r-build-system)
10016 (propagated-inputs
10017 `(("r-batchjobs" ,r-batchjobs)
10018 ("r-bbmisc" ,r-bbmisc)
10019 ("r-biocgenerics" ,r-biocgenerics)
10020 ("r-bit" ,r-bit)
10021 ("r-doparallel" ,r-doparallel)
10022 ("r-ff" ,r-ff)
10023 ("r-ffbase" ,r-ffbase)
10024 ("r-foreach" ,r-foreach)
10025 ("r-genomicfiles" ,r-genomicfiles)
10026 ("r-genomicranges" ,r-genomicranges)
10027 ("r-rtracklayer" ,r-rtracklayer)
10028 ("r-s4vectors" ,r-s4vectors)
10029 ("r-summarizedexperiment" ,r-summarizedexperiment)))
10030 (home-page "https://bioconductor.org/packages/gQTLBase")
10031 (synopsis "Infrastructure for eQTL, mQTL and similar studies")
10032 (description
10033 "The purpose of this package is to simplify the storage and interrogation
10034of @dfn{quantitative trait loci} (QTL) archives, such as eQTL, mQTL, dsQTL,
10035and more.")
10036 (license license:artistic2.0)))
10037
dd5fc8b7
RW		 10038(define-public r-snpstats
10039 (package
10040 (name "r-snpstats")
10041 (version "1.28.0")
10042 (source
10043 (origin
10044 (method url-fetch)
10045 (uri (bioconductor-uri "snpStats" version))
10046 (sha256
10047 (base32
10048 "1x9qwynh2hwl24vq02naf4mchpch7xi2pkdrlgw896k28kx0lvir"))))
10049 (properties `((upstream-name . "snpStats")))
10050 (build-system r-build-system)
10051 (inputs `(("zlib" ,zlib)))
10052 (propagated-inputs
10053 `(("r-biocgenerics" ,r-biocgenerics)
10054 ("r-matrix" ,r-matrix)
10055 ("r-survival" ,r-survival)
10056 ("r-zlibbioc" ,r-zlibbioc)))
10057 (home-page "https://bioconductor.org/packages/snpStats")
10058 (synopsis "Methods for SNP association studies")
10059 (description
10060 "This package provides classes and statistical methods for large
10061@dfn{single-nucleotide polymorphism} (SNP) association studies. This extends
10062the earlier snpMatrix package, allowing for uncertainty in genotypes.")
10063 (license license:gpl3)))
10064
421c68e3
RW		 10065(define-public r-homo-sapiens
10066 (package
10067 (name "r-homo-sapiens")
10068 (version "1.3.1")
10069 (source (origin
10070 (method url-fetch)
10071 ;; We cannot use bioconductor-uri here because this tarball is
10072 ;; located under "data/annotation/" instead of "bioc/".
10073 (uri (string-append "http://www.bioconductor.org/packages/"
10074 "release/data/annotation/src/contrib/"
10075 "Homo.sapiens_"
10076 version ".tar.gz"))
10077 (sha256
10078 (base32
10079 "151vj7h5p1c8yd5swrchk46z469p135wk50hvkl0nhgndvy0jj01"))))
10080 (properties
10081 `((upstream-name . "Homo.sapiens")))
10082 (build-system r-build-system)
10083 (propagated-inputs
10084 `(("r-genomicfeatures" ,r-genomicfeatures)
10085 ("r-go-db" ,r-go-db)
10086 ("r-org-hs-eg-db" ,r-org-hs-eg-db)
10087 ("r-txdb-hsapiens-ucsc-hg19-knowngene" ,r-txdb-hsapiens-ucsc-hg19-knowngene)
10088 ("r-organismdbi" ,r-organismdbi)
10089 ("r-annotationdbi" ,r-annotationdbi)))
10090 (home-page "https://bioconductor.org/packages/Homo.sapiens/")
10091 (synopsis "Annotation package for the Homo.sapiens object")
10092 (description
10093 "This package contains the Homo.sapiens object to access data from
10094several related annotation packages.")
10095 (license license:artistic2.0)))
10096
15f98b0d
RW		 10097(define-public r-erma
10098 (package
10099 (name "r-erma")
10100 (version "0.10.0")
10101 (source
10102 (origin
10103 (method url-fetch)
10104 (uri (bioconductor-uri "erma" version))
10105 (sha256
10106 (base32
10107 "0gcfs9g8vvdv5vmq9b21kd8sq5mizjj49nfzd4in9zvp4b9v7x1g"))))
10108 (build-system r-build-system)
10109 (propagated-inputs
10110 `(("r-annotationdbi" ,r-annotationdbi)
10111 ("r-biobase" ,r-biobase)
10112 ("r-biocgenerics" ,r-biocgenerics)
10113 ("r-foreach" ,r-foreach)
10114 ("r-genomicfiles" ,r-genomicfiles)
10115 ("r-genomicranges" ,r-genomicranges)
10116 ("r-ggplot2" ,r-ggplot2)
10117 ("r-homo-sapiens" ,r-homo-sapiens)
10118 ("r-rtracklayer" ,r-rtracklayer)
10119 ("r-s4vectors" ,r-s4vectors)
10120 ("r-shiny" ,r-shiny)
10121 ("r-summarizedexperiment" ,r-summarizedexperiment)))
10122 (home-page "https://bioconductor.org/packages/erma")
10123 (synopsis "Epigenomic road map adventures")
10124 (description
10125 "The epigenomics road map describes locations of epigenetic marks in DNA
10126from a variety of cell types. Of interest are locations of histone
10127modifications, sites of DNA methylation, and regions of accessible chromatin.
10128This package presents a selection of elements of the road map including
10129metadata and outputs of the ChromImpute procedure applied to ENCODE cell lines
10130by Ernst and Kellis.")
10131 (license license:artistic2.0)))
10132
66c39102
RW		 10133(define-public r-ldblock
10134 (package
10135 (name "r-ldblock")
10136 (version "1.8.0")
10137 (source
10138 (origin
10139 (method url-fetch)
10140 (uri (bioconductor-uri "ldblock" version))
10141 (sha256
10142 (base32
10143 "18nfsixh6d2wfrb9laqsgly5w1frzihhak683k0p8fdf51h4aqba"))))
10144 (build-system r-build-system)
10145 (propagated-inputs
10146 `(("r-erma" ,r-erma)
10147 ("r-genomeinfodb" ,r-genomeinfodb)
10148 ("r-genomicfiles" ,r-genomicfiles)
10149 ("r-go-db" ,r-go-db)
10150 ("r-homo-sapiens" ,r-homo-sapiens)
10151 ("r-matrix" ,r-matrix)
10152 ("r-rsamtools" ,r-rsamtools)
10153 ("r-snpstats" ,r-snpstats)
10154 ("r-variantannotation" ,r-variantannotation)))
10155 (home-page "https://bioconductor.org/packages/ldblock")
10156 (synopsis "Data structures for linkage disequilibrium measures in populations")
10157 (description
10158 "This package defines data structures for @dfn{linkage
10159disequilibrium} (LD) measures in populations. Its purpose is to simplify
10160handling of existing population-level data for the purpose of flexibly
10161defining LD blocks.")
10162 (license license:artistic2.0)))
10163
794ff347
RW		 10164(define-public r-gqtlstats
10165 (package
10166 (name "r-gqtlstats")
2ccd8501 10167 (version "1.10.1")
794ff347
RW		 10168 (source
10169 (origin
10170 (method url-fetch)
10171 (uri (bioconductor-uri "gQTLstats" version))
10172 (sha256
10173 (base32
2ccd8501 10174 "0gvq1sf2zjbkk431x40z6wql3c1rpclnnwa2f1hvykb8mmw70kmq"))))
794ff347
RW		 10175 (properties `((upstream-name . "gQTLstats")))
10176 (build-system r-build-system)
10177 (propagated-inputs
10178 `(("r-annotationdbi" ,r-annotationdbi)
10179 ("r-batchjobs" ,r-batchjobs)
10180 ("r-bbmisc" ,r-bbmisc)
10181 ("r-beeswarm" ,r-beeswarm)
10182 ("r-biobase" ,r-biobase)
10183 ("r-biocgenerics" ,r-biocgenerics)
10184 ("r-doparallel" ,r-doparallel)
10185 ("r-dplyr" ,r-dplyr)
10186 ("r-erma" ,r-erma)
10187 ("r-ffbase" ,r-ffbase)
10188 ("r-foreach" ,r-foreach)
10189 ("r-genomeinfodb" ,r-genomeinfodb)
10190 ("r-genomicfeatures" ,r-genomicfeatures)
10191 ("r-genomicfiles" ,r-genomicfiles)
10192 ("r-genomicranges" ,r-genomicranges)
10193 ("r-ggbeeswarm" ,r-ggbeeswarm)
10194 ("r-ggplot2" ,r-ggplot2)
10195 ("r-gqtlbase" ,r-gqtlbase)
10196 ("r-hardyweinberg" ,r-hardyweinberg)
10197 ("r-iranges" ,r-iranges)
10198 ("r-ldblock" ,r-ldblock)
10199 ("r-limma" ,r-limma)
10200 ("r-mgcv" ,r-mgcv)
10201 ("r-plotly" ,r-plotly)
10202 ("r-reshape2" ,r-reshape2)
10203 ("r-s4vectors" ,r-s4vectors)
10204 ("r-shiny" ,r-shiny)
10205 ("r-snpstats" ,r-snpstats)
10206 ("r-summarizedexperiment" ,r-summarizedexperiment)
10207 ("r-variantannotation" ,r-variantannotation)))
10208 (home-page "https://bioconductor.org/packages/gQTLstats")
10209 (synopsis "Computationally efficient analysis for eQTL and allied studies")
10210 (description
10211 "This package provides tools for the computationally efficient analysis
10212of @dfn{quantitative trait loci} (QTL) data, including eQTL, mQTL, dsQTL, etc.
10213The software in this package aims to support refinements and functional
10214interpretation of members of a collection of association statistics on a
10215family of feature/genome hypotheses.")
10216 (license license:artistic2.0)))
10217
42720006
RW		 10218(define-public r-gviz
10219 (package
10220 (name "r-gviz")
d578278e 10221 (version "1.22.3")
42720006
RW		 10222 (source
10223 (origin
10224 (method url-fetch)
10225 (uri (bioconductor-uri "Gviz" version))
10226 (sha256
10227 (base32
d578278e 10228 "1grjzrjpzkw572pbvpsvdnfkfgwybl0cnjd7nnk2xdr26wnbsi9a"))))
42720006
RW		 10229 (properties `((upstream-name . "Gviz")))
10230 (build-system r-build-system)
10231 (propagated-inputs
10232 `(("r-annotationdbi" ,r-annotationdbi)
10233 ("r-biobase" ,r-biobase)
10234 ("r-biocgenerics" ,r-biocgenerics)
10235 ("r-biomart" ,r-biomart)
10236 ("r-biostrings" ,r-biostrings)
10237 ("r-biovizbase" ,r-biovizbase)
10238 ("r-bsgenome" ,r-bsgenome)
10239 ("r-digest" ,r-digest)
10240 ("r-genomeinfodb" ,r-genomeinfodb)
10241 ("r-genomicalignments" ,r-genomicalignments)
10242 ("r-genomicfeatures" ,r-genomicfeatures)
10243 ("r-genomicranges" ,r-genomicranges)
10244 ("r-iranges" ,r-iranges)
10245 ("r-lattice" ,r-lattice)
10246 ("r-latticeextra" ,r-latticeextra)
10247 ("r-matrixstats" ,r-matrixstats)
10248 ("r-rcolorbrewer" ,r-rcolorbrewer)
10249 ("r-rsamtools" ,r-rsamtools)
10250 ("r-rtracklayer" ,r-rtracklayer)
10251 ("r-s4vectors" ,r-s4vectors)
10252 ("r-xvector" ,r-xvector)))
10253 (home-page "https://bioconductor.org/packages/Gviz")
10254 (synopsis "Plotting data and annotation information along genomic coordinates")
10255 (description
10256 "Genomic data analyses requires integrated visualization of known genomic
10257information and new experimental data. Gviz uses the biomaRt and the
10258rtracklayer packages to perform live annotation queries to Ensembl and UCSC
10259and translates this to e.g. gene/transcript structures in viewports of the
10260grid graphics package. This results in genomic information plotted together
10261with your data.")
10262 (license license:artistic2.0)))
10263
2e4ce60e
RW		 10264(define-public r-gwascat
10265 (package
10266 (name "r-gwascat")
10267 (version "2.10.0")
10268 (source
10269 (origin
10270 (method url-fetch)
10271 (uri (bioconductor-uri "gwascat" version))
10272 (sha256
10273 (base32
10274 "0n5x5i5v6a8wpn5mxmlpkl34b4kyypmymiwww6g61zch7xqrgywi"))))
10275 (build-system r-build-system)
10276 (propagated-inputs
10277 `(("r-annotationdbi" ,r-annotationdbi)
10278 ("r-annotationhub" ,r-annotationhub)
10279 ("r-biocgenerics" ,r-biocgenerics)
10280 ("r-biostrings" ,r-biostrings)
10281 ("r-genomeinfodb" ,r-genomeinfodb)
10282 ("r-genomicfeatures" ,r-genomicfeatures)
10283 ("r-genomicranges" ,r-genomicranges)
10284 ("r-ggbio" ,r-ggbio)
10285 ("r-ggplot2" ,r-ggplot2)
10286 ("r-gqtlstats" ,r-gqtlstats)
10287 ("r-graph" ,r-graph)
10288 ("r-gviz" ,r-gviz)
10289 ("r-homo-sapiens" ,r-homo-sapiens)
10290 ("r-iranges" ,r-iranges)
10291 ("r-rsamtools" ,r-rsamtools)
10292 ("r-rtracklayer" ,r-rtracklayer)
10293 ("r-s4vectors" ,r-s4vectors)
10294 ("r-snpstats" ,r-snpstats)
10295 ("r-summarizedexperiment" ,r-summarizedexperiment)
10296 ("r-variantannotation" ,r-variantannotation)))
10297 (home-page "https://bioconductor.org/packages/gwascat")
10298 (synopsis "Tools for data in the EMBL-EBI GWAS catalog")
10299 (description
10300 "This package provides tools for representing and modeling data in the
10301EMBL-EBI GWAS catalog.")
10302 (license license:artistic2.0)))
10303
fbf54406
RW		 10304(define-public r-sushi
10305 (package
10306 (name "r-sushi")
10307 (version "1.16.0")
10308 (source (origin
10309 (method url-fetch)
10310 (uri (bioconductor-uri "Sushi" version))
10311 (sha256
10312 (base32
10313 "0axaqm480z8d0b2ldgxwm0swava1p4irc62bpl17p2k8k78g687g"))))
10314 (properties `((upstream-name . "Sushi")))
10315 (build-system r-build-system)
10316 (propagated-inputs
10317 `(("r-biomart" ,r-biomart)
10318 ("r-zoo" ,r-zoo)))
10319 (home-page "https://bioconductor.org/packages/Sushi")
10320 (synopsis "Tools for visualizing genomics data")
10321 (description
10322 "This package provides flexible, quantitative, and integrative genomic
10323visualizations for publication-quality multi-panel figures.")
10324 (license license:gpl2+)))
10325
30eb4e37
RW		 10326(define-public r-fithic
10327 (package
10328 (name "r-fithic")
10329 (version "1.4.0")
10330 (source (origin
10331 (method url-fetch)
10332 (uri (bioconductor-uri "FitHiC" version))
10333 (sha256
10334 (base32
10335 "12ylhrppi051m7nqsgq95kzd9g9wmp34i0zzfi55cjqawlpx7c6n"))))
10336 (properties `((upstream-name . "FitHiC")))
10337 (build-system r-build-system)
10338 (propagated-inputs
10339 `(("r-data-table" ,r-data-table)
10340 ("r-fdrtool" ,r-fdrtool)
10341 ("r-rcpp" ,r-rcpp)))
10342 (home-page "https://bioconductor.org/packages/FitHiC")
10343 (synopsis "Confidence estimation for intra-chromosomal contact maps")
10344 (description
10345 "Fit-Hi-C is a tool for assigning statistical confidence estimates to
10346intra-chromosomal contact maps produced by genome-wide genome architecture
10347assays such as Hi-C.")
10348 (license license:gpl2+)))
10349
c49102ec
RW		 10350(define-public r-hitc
10351 (package
10352 (name "r-hitc")
10353 (version "1.22.0")
10354 (source (origin
10355 (method url-fetch)
10356 (uri (bioconductor-uri "HiTC" version))
10357 (sha256
10358 (base32
10359 "0288xa1jy6nzvz2ha07csmp6dirjw5r7p9vy69q2wsbyzr02ymkp"))))
10360 (properties `((upstream-name . "HiTC")))
10361 (build-system r-build-system)
10362 (propagated-inputs
10363 `(("r-biostrings" ,r-biostrings)
10364 ("r-genomeinfodb" ,r-genomeinfodb)
10365 ("r-genomicranges" ,r-genomicranges)
10366 ("r-iranges" ,r-iranges)
10367 ("r-matrix" ,r-matrix)
10368 ("r-rcolorbrewer" ,r-rcolorbrewer)
10369 ("r-rtracklayer" ,r-rtracklayer)))
10370 (home-page "https://bioconductor.org/packages/HiTC")
10371 (synopsis "High throughput chromosome conformation capture analysis")
10372 (description
10373 "The HiTC package was developed to explore high-throughput \"C\" data
10374such as 5C or Hi-C. Dedicated R classes as well as standard methods for
10375quality controls, normalization, visualization, and further analysis are also
10376provided.")
10377 (license license:artistic2.0)))
10378
212f6120
RW		 10379(define-public r-qvalue
10380 (package
10381 (name "r-qvalue")
98791c25 10382 (version "2.10.0")
212f6120
RW		 10383 (source
10384 (origin
10385 (method url-fetch)
10386 (uri (bioconductor-uri "qvalue" version))
10387 (sha256
10388 (base32
98791c25 10389 "1rd9rnf16kh8wc076kahd9hsb9rfwsbzmz3kjmp0pj6rbiq0051i"))))
212f6120
RW		 10390 (build-system r-build-system)
10391 (propagated-inputs
10392 `(("r-ggplot2" ,r-ggplot2)
10393 ("r-reshape2" ,r-reshape2)))
10394 (home-page "http://github.com/jdstorey/qvalue")
10395 (synopsis "Q-value estimation for false discovery rate control")
10396 (description
10397 "This package takes a list of p-values resulting from the simultaneous
10398testing of many hypotheses and estimates their q-values and local @dfn{false
10399discovery rate} (FDR) values. The q-value of a test measures the proportion
10400of false positives incurred when that particular test is called significant.
10401The local FDR measures the posterior probability the null hypothesis is true
10402given the test's p-value. Various plots are automatically generated, allowing
10403one to make sensible significance cut-offs. The software can be applied to
10404problems in genomics, brain imaging, astrophysics, and data mining.")
10405 ;; Any version of the LGPL.
10406 (license license:lgpl3+)))
10407
aba3e482
RW		 10408(define-public r-hdf5array
10409 (package
10410 (name "r-hdf5array")
10411 (version "1.6.0")
10412 (source
10413 (origin
10414 (method url-fetch)
10415 (uri (bioconductor-uri "HDF5Array" version))
10416 (sha256
10417 (base32
10418 "0kcdza41saqv6vlpvqd841awbiwkg84lh0plx6c7fmfgbqv7a0jh"))))
10419 (properties `((upstream-name . "HDF5Array")))
10420 (build-system r-build-system)
10421 (propagated-inputs
10422 `(("r-biocgenerics" ,r-biocgenerics)
10423 ("r-delayedarray" ,r-delayedarray)
10424 ("r-iranges" ,r-iranges)
10425 ("r-rhdf5" ,r-rhdf5)
10426 ("r-s4vectors" ,r-s4vectors)))
10427 (home-page "https://bioconductor.org/packages/HDF5Array")
10428 (synopsis "HDF5 back end for DelayedArray objects")
10429 (description "This package provides an array-like container for convenient
10430access and manipulation of HDF5 datasets. It supports delayed operations and
10431block processing.")
10432 (license license:artistic2.0)))
10433
748e9f16
RW		 10434(define-public r-rhdf5lib
10435 (package
10436 (name "r-rhdf5lib")
10437 (version "1.0.0")
10438 (source
10439 (origin
10440 (method url-fetch)
10441 (uri (bioconductor-uri "Rhdf5lib" version))
10442 (sha256
10443 (base32
10444 "0kkc4rprjbqn2wvbx4d49kk9l91vihccxbl4843qr1wqk6v33r1w"))))
10445 (properties `((upstream-name . "Rhdf5lib")))
10446 (build-system r-build-system)
10447 (arguments
10448 `(#:phases
10449 (modify-phases %standard-phases
10450 (add-after 'unpack 'do-not-use-bundled-hdf5
10451 (lambda* (#:key inputs #:allow-other-keys)
10452 (for-each delete-file '("configure" "configure.ac"))
10453 ;; Do not make other packages link with the proprietary libsz.
10454 (substitute* "R/zzz.R"
10455 (("'%s/libhdf5_cpp.a %s/libhdf5.a %s/libsz.a'")
10456 "'%s/libhdf5_cpp.a %s/libhdf5.a %s/libhdf5.a'")
10457 (("'%s/libhdf5.a %s/libsz.a'")
10458 "'%s/libhdf5.a %s/libhdf5.a'"))
10459 (with-directory-excursion "src"
10460 (invoke "tar" "xvf" (assoc-ref inputs "hdf5-source"))
10461 (rename-file (string-append "hdf5-" ,(package-version hdf5))
10462 "hdf5")
10463 (rename-file "Makevars.in" "Makevars")
10464 (substitute* "Makevars"
10465 (("HDF5_CXX_LIB=.*")
10466 (string-append "HDF5_CXX_LIB="
10467 (assoc-ref inputs "hdf5") "/lib/libhdf5_cpp.a\n"))
10468 (("HDF5_LIB=.*")
10469 (string-append "HDF5_LIB="
10470 (assoc-ref inputs "hdf5") "/lib/libhdf5.a\n"))
10471 (("HDF5_CXX_INCLUDE=.*") "HDF5_CXX_INCLUDE=./hdf5/c++/src\n")
10472 (("HDF5_INCLUDE=.*") "HDF5_INCLUDE=./hdf5/src\n")
10473 ;; szip is non-free software
10474 (("cp \\$\\{SZIP_LIB\\}.*") "")
10475 (("PKG_LIBS = \\$\\{HDF5_LIB\\} \\$\\{SZIP_LIB\\}")
10476 "PKG_LIBS = ${HDF5_LIB}\n")))
10477 #t)))))
10478 (inputs
10479 `(("zlib" ,zlib)))
10480 (propagated-inputs
10481 `(("hdf5" ,hdf5)))
10482 (native-inputs
10483 `(("hdf5-source" ,(package-source hdf5))))
10484 (home-page "https://bioconductor.org/packages/Rhdf5lib")
10485 (synopsis "HDF5 library as an R package")
10486 (description "This package provides C and C++ HDF5 libraries for use in R
10487packages.")
10488 (license license:artistic2.0)))
10489
9ec08988
RW		 10490(define-public r-beachmat
10491 (package
10492 (name "r-beachmat")
10493 (version "1.0.2")
10494 (source
10495 (origin
10496 (method url-fetch)
10497 (uri (bioconductor-uri "beachmat" version))
10498 (sha256
10499 (base32
10500 "0b6dzja5fbx4dawb7ixj67mlhw4fy62pfp20mfp918fy96zmdwqz"))))
10501 (build-system r-build-system)
10502 (inputs
10503 `(("hdf5" ,hdf5)))
10504 (propagated-inputs
10505 `(("r-delayedarray" ,r-delayedarray)
10506 ("r-hdf5array" ,r-hdf5array)
10507 ("r-rcpp" ,r-rcpp)
10508 ("r-rhdf5" ,r-rhdf5)
10509 ("r-rhdf5lib" ,r-rhdf5lib)))
10510 (home-page "https://bioconductor.org/packages/beachmat")
10511 (synopsis "Compiling Bioconductor to handle each matrix type")
10512 (description "This package provides a consistent C++ class interface for a
10513variety of commonly used matrix types, including sparse and HDF5-backed
10514matrices.")
10515 (license license:gpl3)))
10516
6fb1dc17
RW		 10517(define-public r-singlecellexperiment
10518 (package
10519 (name "r-singlecellexperiment")
10520 (version "1.0.0")
10521 (source
10522 (origin
10523 (method url-fetch)
10524 (uri (bioconductor-uri "SingleCellExperiment" version))
10525 (sha256
10526 (base32
10527 "1r276i97w64a5vdlg6952gkj7bls909p42zl8fn8yz87cdwyaars"))))
10528 (properties
10529 `((upstream-name . "SingleCellExperiment")))
10530 (build-system r-build-system)
10531 (propagated-inputs
10532 `(("r-biocgenerics" ,r-biocgenerics)
10533 ("r-s4vectors" ,r-s4vectors)
10534 ("r-summarizedexperiment" ,r-summarizedexperiment)))
10535 (home-page "https://bioconductor.org/packages/SingleCellExperiment")
10536 (synopsis "S4 classes for single cell data")
10537 (description "This package defines an S4 class for storing data from
10538single-cell experiments. This includes specialized methods to store and
10539retrieve spike-in information, dimensionality reduction coordinates and size
10540factors for each cell, along with the usual metadata for genes and
10541libraries.")
10542 (license license:gpl3)))
10543
658ab21d
RW		 10544(define-public r-scater
10545 (package
10546 (name "r-scater")
59b2864d 10547 (version "1.6.3")
658ab21d
RW		 10548 (source (origin
10549 (method url-fetch)
10550 (uri (bioconductor-uri "scater" version))
10551 (sha256
10552 (base32
59b2864d 10553 "0q3s96gf8saa1dq2fvmpl0jyj7bx3wrdfck3hanb8pxkcir2p7dn"))))
658ab21d
RW		 10554 (build-system r-build-system)
10555 (propagated-inputs
10556 `(("r-beachmat" ,r-beachmat)
10557 ("r-biobase" ,r-biobase)
10558 ("r-biocgenerics" ,r-biocgenerics)
10559 ("r-biomart" ,r-biomart)
10560 ("r-data-table" ,r-data-table)
10561 ("r-dplyr" ,r-dplyr)
10562 ("r-edger" ,r-edger)
10563 ("r-ggbeeswarm" ,r-ggbeeswarm)
10564 ("r-ggplot2" ,r-ggplot2)
10565 ("r-limma" ,r-limma)
10566 ("r-matrix" ,r-matrix)
10567 ("r-matrixstats" ,r-matrixstats)
10568 ("r-plyr" ,r-plyr)
10569 ("r-rcpp" ,r-rcpp)
10570 ("r-reshape2" ,r-reshape2)
10571 ("r-rhdf5" ,r-rhdf5)
10572 ("r-rhdf5lib" ,r-rhdf5lib)
10573 ("r-rjson" ,r-rjson)
10574 ("r-s4vectors" ,r-s4vectors)
10575 ("r-shiny" ,r-shiny)
10576 ("r-shinydashboard" ,r-shinydashboard)
10577 ("r-singlecellexperiment" ,r-singlecellexperiment)
10578 ("r-summarizedexperiment" ,r-summarizedexperiment)
10579 ("r-tximport" ,r-tximport)
10580 ("r-viridis" ,r-viridis)))
10581 (home-page "https://github.com/davismcc/scater")
10582 (synopsis "Single-cell analysis toolkit for gene expression data in R")
10583 (description "This package provides a collection of tools for doing
10584various analyses of single-cell RNA-seq gene expression data, with a focus on
10585quality control.")
10586 (license license:gpl2+)))
10587
7f1d9bef
RW		 10588(define-public r-scran
10589 (package
10590 (name "r-scran")
9aaf2813 10591 (version "1.6.8")
7f1d9bef
RW		 10592 (source
10593 (origin
10594 (method url-fetch)
10595 (uri (bioconductor-uri "scran" version))
10596 (sha256
10597 (base32
9aaf2813 10598 "07wniyrh2fhhkz28v0bfgpvpi1hkkn2cvhacrvvvck142j79944x"))))
7f1d9bef
RW		 10599 (build-system r-build-system)
10600 (propagated-inputs
10601 `(("r-beachmat" ,r-beachmat)
10602 ("r-biocgenerics" ,r-biocgenerics)
10603 ("r-biocparallel" ,r-biocparallel)
10604 ("r-dt" ,r-dt)
10605 ("r-dynamictreecut" ,r-dynamictreecut)
10606 ("r-edger" ,r-edger)
10607 ("r-fnn" ,r-fnn)
10608 ("r-ggplot2" ,r-ggplot2)
10609 ("r-igraph" ,r-igraph)
10610 ("r-limma" ,r-limma)
10611 ("r-matrix" ,r-matrix)
10612 ("r-rcpp" ,r-rcpp)
10613 ("r-rhdf5lib" ,r-rhdf5lib)
10614 ("r-s4vectors" ,r-s4vectors)
10615 ("r-scater" ,r-scater)
10616 ("r-shiny" ,r-shiny)
10617 ("r-singlecellexperiment" ,r-singlecellexperiment)
10618 ("r-statmod" ,r-statmod)
10619 ("r-summarizedexperiment" ,r-summarizedexperiment)
10620 ("r-viridis" ,r-viridis)
10621 ("r-zoo" ,r-zoo)))
10622 (home-page "https://bioconductor.org/packages/scran")
10623 (synopsis "Methods for single-cell RNA-Seq data analysis")
10624 (description "This package implements a variety of low-level analyses of
10625single-cell RNA-seq data. Methods are provided for normalization of
10626cell-specific biases, assignment of cell cycle phase, and detection of highly
10627variable and significantly correlated genes.")
10628 (license license:gpl3)))
10629
05f72960
RW		 10630(define-public r-delayedmatrixstats
10631 (package
10632 (name "r-delayedmatrixstats")
79c6af13 10633 (version "1.0.3")
05f72960
RW		 10634 (source
10635 (origin
10636 (method url-fetch)
10637 (uri (bioconductor-uri "DelayedMatrixStats" version))
10638 (sha256
10639 (base32
79c6af13 10640 "1cxjbjdq9hg9cm95rci0al7a4pk2h73ym276ahw9q4977zbg6381"))))
05f72960
RW		 10641 (properties
10642 `((upstream-name . "DelayedMatrixStats")))
10643 (build-system r-build-system)
10644 (propagated-inputs
10645 `(("r-delayedarray" ,r-delayedarray)
10646 ("r-iranges" ,r-iranges)
10647 ("r-matrix" ,r-matrix)
10648 ("r-matrixstats" ,r-matrixstats)
10649 ("r-s4vectors" ,r-s4vectors)))
10650 (home-page "https://github.com/PeteHaitch/DelayedMatrixStats")
10651 (synopsis "Functions that apply to rows and columns of DelayedMatrix objects")
10652 (description
10653 "This package provides a port of the @code{matrixStats} API for use with
10654@code{DelayedMatrix} objects from the @code{DelayedArray} package. It
10655contains high-performing functions operating on rows and columns of
10656@code{DelayedMatrix} objects, e.g. @code{colMedians}, @code{rowMedians},
10657@code{colRanks}, @code{rowRanks}, @code{colSds}, and @code{rowSds}. Functions
10658are optimized per data type and for subsetted calculations such that both
10659memory usage and processing time is minimized.")
10660 (license license:expat)))
10661
3082de04
RW		 10662(define-public r-dropbead
10663 (let ((commit "cf0be5ae5302684bd03e78ab65b142900bbbb840")
10664 (revision "1"))
10665 (package
10666 (name "r-dropbead")
10667 (version (string-append "0-" revision "." (string-take commit 7)))
10668 (source
10669 (origin
10670 (method git-fetch)
10671 (uri (git-reference
10672 (url "https://github.com/rajewsky-lab/dropbead.git")
10673 (commit commit)))
10674 (sha256
10675 (base32
10676 "1b2lphsc236s1rdzlijxg8yl1jnqpwcvj4x938r89rqpj93jb780"))))
10677 (build-system r-build-system)
10678 (propagated-inputs
10679 `(("r-ggplot2" ,r-ggplot2)
10680 ("r-rcolorbrewer" ,r-rcolorbrewer)
10681 ("r-gridextra" ,r-gridextra)
10682 ("r-gplots" ,r-gplots)
10683 ("r-plyr" ,r-plyr)))
10684 (home-page "https://github.com/rajewsky-lab/dropbead")
10685 (synopsis "Basic exploration and analysis of Drop-seq data")
10686 (description "This package offers a quick and straight-forward way to
10687explore and perform basic analysis of single cell sequencing data coming from
10688droplet sequencing. It has been particularly tailored for Drop-seq.")
10689 (license license:gpl3))))
10690
5ded35d8
RW		 10691(define htslib-for-sambamba
10692 (let ((commit "2f3c3ea7b301f9b45737a793c0b2dcf0240e5ee5"))
10693 (package
10694 (inherit htslib)
10695 (name "htslib-for-sambamba")
10696 (version (string-append "1.3.1-1." (string-take commit 9)))
10697 (source
10698 (origin
10699 (method git-fetch)
10700 (uri (git-reference
10701 (url "https://github.com/lomereiter/htslib.git")
10702 (commit commit)))
10703 (file-name (string-append "htslib-" version "-checkout"))
10704 (sha256
10705 (base32
10706 "0g38g8s3npr0gjm9fahlbhiskyfws9l5i0x1ml3rakzj7az5l9c9"))))
10707 (arguments
10708 (substitute-keyword-arguments (package-arguments htslib)
10709 ((#:phases phases)
10710 `(modify-phases ,phases
d10092b8 10711 (add-after 'unpack 'bootstrap
5ded35d8
RW		 10712 (lambda _
10713 (zero? (system* "autoreconf" "-vif"))))))))
10714 (native-inputs
10715 `(("autoconf" ,autoconf)
10716 ("automake" ,automake)
10717 ,@(package-native-inputs htslib))))))
10718
10719(define-public sambamba
10720 (package
10721 (name "sambamba")
10722 (version "0.6.5")
10723 (source
10724 (origin
10725 (method url-fetch)
10726 (uri (string-append "https://github.com/lomereiter/sambamba/"
10727 "archive/v" version ".tar.gz"))
10728 (file-name (string-append name "-" version ".tar.gz"))
10729 (sha256
10730 (base32
10731 "17076gijd65a3f07zns2gvbgahiz5lriwsa6dq353ss3jl85d8vy"))))
10732 (build-system gnu-build-system)
10733 (arguments
10734 `(#:tests? #f ; there is no test target
10735 #:make-flags
10736 '("D_COMPILER=ldc2"
10737 ;; Override "--compiler" flag only.
10738 "D_FLAGS=--compiler=ldc2 -IBioD -g -d"
10739 "sambamba-ldmd2-64")
10740 #:phases
10741 (modify-phases %standard-phases
10742 (delete 'configure)
10743 (add-after 'unpack 'place-biod
10744 (lambda* (#:key inputs #:allow-other-keys)
10745 (copy-recursively (assoc-ref inputs "biod") "BioD")
10746 #t))
10747 (add-after 'unpack 'unbundle-prerequisites
10748 (lambda _
10749 (substitute* "Makefile"
10750 ((" htslib-static lz4-static") ""))
10751 #t))
10752 (replace 'install
10753 (lambda* (#:key outputs #:allow-other-keys)
10754 (let* ((out (assoc-ref outputs "out"))
10755 (bin (string-append out "/bin")))
10756 (mkdir-p bin)
10757 (install-file "build/sambamba" bin)
10758 #t))))))
10759 (native-inputs
10760 `(("ldc" ,ldc)
10761 ("rdmd" ,rdmd)
10762 ("biod"
10763 ,(let ((commit "1248586b54af4bd4dfb28ebfebfc6bf012e7a587"))
10764 (origin
10765 (method git-fetch)
10766 (uri (git-reference
10767 (url "https://github.com/biod/BioD.git")
10768 (commit commit)))
10769 (file-name (string-append "biod-"
10770 (string-take commit 9)
10771 "-checkout"))
10772 (sha256
10773 (base32
10774 "1m8hi1n7x0ri4l6s9i0x6jg4z4v94xrfdzp7mbizdipfag0m17g3")))))))
10775 (inputs
10776 `(("lz4" ,lz4)
10777 ("htslib" ,htslib-for-sambamba)))
10778 (home-page "http://lomereiter.github.io/sambamba")
10779 (synopsis "Tools for working with SAM/BAM data")
10780 (description "Sambamba is a high performance modern robust and
10781fast tool (and library), written in the D programming language, for
10782working with SAM and BAM files. Current parallelised functionality is
10783an important subset of samtools functionality, including view, index,
10784sort, markdup, and depth.")
10785 (license license:gpl2+)))
b8fffd3a
RW		 10786
10787(define-public ritornello
10788 (package
10789 (name "ritornello")
10790 (version "1.0.0")
10791 (source (origin
10792 (method url-fetch)
10793 (uri (string-append "https://github.com/KlugerLab/"
10794 "Ritornello/archive/v"
10795 version ".tar.gz"))
10796 (file-name (string-append name "-" version ".tar.gz"))
10797 (sha256
10798 (base32
10799 "02nik86gq9ljjriv6pamwlmqnfky3ads1fpklx6mc3hx6k40pg38"))))
10800 (build-system gnu-build-system)
10801 (arguments
10802 `(#:tests? #f ; there are no tests
10803 #:phases
10804 (modify-phases %standard-phases
10805 (add-after 'unpack 'patch-samtools-references
10806 (lambda* (#:key inputs #:allow-other-keys)
10807 (substitute* '("src/SamStream.h"
10808 "src/BufferedGenomeReader.h")
10809 (("<sam.h>") "<samtools/sam.h>"))
10810 #t))
10811 (delete 'configure)
10812 (replace 'install
10813 (lambda* (#:key inputs outputs #:allow-other-keys)
10814 (let* ((out (assoc-ref outputs "out"))
10815 (bin (string-append out "/bin/")))
10816 (mkdir-p bin)
10817 (install-file "bin/Ritornello" bin)
10818 #t))))))
10819 (inputs
10820 `(("samtools" ,samtools-0.1)
10821 ("fftw" ,fftw)
10822 ("boost" ,boost)
10823 ("zlib" ,zlib)))
10824 (home-page "https://github.com/KlugerLab/Ritornello")
10825 (synopsis "Control-free peak caller for ChIP-seq data")
10826 (description "Ritornello is a ChIP-seq peak calling algorithm based on
10827signal processing that can accurately call binding events without the need to
10828do a pair total DNA input or IgG control sample. It has been tested for use
10829with narrow binding events such as transcription factor ChIP-seq.")
10830 (license license:gpl3+)))
44f6c889
RW		 10831
10832(define-public trim-galore
10833 (package
10834 (name "trim-galore")
10835 (version "0.4.2")
10836 (source
10837 (origin
10838 (method url-fetch)
10839 (uri (string-append "http://www.bioinformatics.babraham.ac.uk/"
10840 "projects/trim_galore/trim_galore_v"
10841 version ".zip"))
10842 (sha256
10843 (base32
10844 "0b9qdxi4521gsrjvbhgky8g7kry9b5nx3byzaxkgxz7p4k8bn1mn"))))
10845 (build-system gnu-build-system)
10846 (arguments
10847 `(#:tests? #f ; no tests
10848 #:phases
10849 (modify-phases %standard-phases
10850 ;; The archive contains plain files.
10851 (replace 'unpack
10852 (lambda* (#:key source #:allow-other-keys)
10853 (zero? (system* "unzip" source))))
10854 (delete 'configure)
10855 (delete 'build)
10856 (add-after 'unpack 'hardcode-tool-references
10857 (lambda* (#:key inputs #:allow-other-keys)
10858 (substitute* "trim_galore"
10859 (("\\$path_to_cutadapt = 'cutadapt'")
10860 (string-append "$path_to_cutadapt = '"
10861 (assoc-ref inputs "cutadapt")
10862 "/bin/cutadapt'"))
10863 (("\\| gzip")
10864 (string-append "| "
10865 (assoc-ref inputs "gzip")
10866 "/bin/gzip"))
10867 (("\"gunzip")
10868 (string-append "\""
10869 (assoc-ref inputs "gzip")
10870 "/bin/gunzip")))
10871 #t))
10872 (replace 'install
10873 (lambda* (#:key outputs #:allow-other-keys)
10874 (let ((bin (string-append (assoc-ref outputs "out")
10875 "/bin")))
10876 (mkdir-p bin)
10877 (install-file "trim_galore" bin)
10878 #t))))))
10879 (inputs
10880 `(("gzip" ,gzip)
10881 ("perl" ,perl)
10882 ("cutadapt" ,cutadapt)))
10883 (native-inputs
10884 `(("unzip" ,unzip)))
10885 (home-page "http://www.bioinformatics.babraham.ac.uk/projects/trim_galore/")
10886 (synopsis "Wrapper around Cutadapt and FastQC")
10887 (description "Trim Galore! is a wrapper script to automate quality and
10888adapter trimming as well as quality control, with some added functionality to
10889remove biased methylation positions for RRBS sequence files.")
10890 (license license:gpl3+)))
3420c905
RW		 10891
10892(define-public gess
10893 (package
10894 (name "gess")
10895 (version "1.0")
10896 (source (origin
10897 (method url-fetch)
10898 (uri (string-append "http://compbio.uthscsa.edu/"
10899 "GESS_Web/files/"
10900 "gess-" version ".src.tar.gz"))
10901 (sha256
10902 (base32
10903 "0hyk403kxscclzfs24pvdgiv0wm03kjcziqdrp5w46cb049gz0d7"))))
10904 (build-system gnu-build-system)
10905 (arguments
10906 `(#:tests? #f ; no tests
10907 #:phases
10908 (modify-phases %standard-phases
10909 (delete 'configure)
10910 (delete 'build)
10911 (replace 'install
10912 (lambda* (#:key inputs outputs #:allow-other-keys)
10913 (let* ((python (assoc-ref inputs "python"))
10914 (out (assoc-ref outputs "out"))
10915 (bin (string-append out "/bin/"))
10916 (target (string-append
10917 out "/lib/python2.7/site-packages/gess/")))
10918 (mkdir-p target)
10919 (copy-recursively "." target)
10920 ;; Make GESS.py executable
10921 (chmod (string-append target "GESS.py") #o555)
10922 ;; Add Python shebang to the top and make Matplotlib
10923 ;; usable.
10924 (substitute* (string-append target "GESS.py")
10925 (("\"\"\"Description:" line)
10926 (string-append "#!" (which "python") "
10927import matplotlib
10928matplotlib.use('Agg')
10929" line)))
10930 ;; Make sure GESS has all modules in its path
10931 (wrap-program (string-append target "GESS.py")
10932 `("PYTHONPATH" ":" prefix (,target ,(getenv "PYTHONPATH"))))
10933 (mkdir-p bin)
10934 (symlink (string-append target "GESS.py")
10935 (string-append bin "GESS.py"))
10936 #t))))))
10937 (inputs
10938 `(("python" ,python-2)
10939 ("python2-pysam" ,python2-pysam)
10940 ("python2-scipy" ,python2-scipy)
10941 ("python2-numpy" ,python2-numpy)
10942 ("python2-networkx" ,python2-networkx)
10943 ("python2-biopython" ,python2-biopython)))
10944 (home-page "http://compbio.uthscsa.edu/GESS_Web/")
10945 (synopsis "Detect exon-skipping events from raw RNA-seq data")
10946 (description
10947 "GESS is an implementation of a novel computational method to detect de
10948novo exon-skipping events directly from raw RNA-seq data without the prior
10949knowledge of gene annotation information. GESS stands for the graph-based
10950exon-skipping scanner detection scheme.")
10951 (license license:bsd-3)))
282b0151
RW		 10952
10953(define-public phylip
10954 (package
10955 (name "phylip")
10956 (version "3.696")
10957 (source
10958 (origin
10959 (method url-fetch)
10960 (uri (string-append "http://evolution.gs.washington.edu/phylip/"
10961 "download/phylip-" version ".tar.gz"))
10962 (sha256
10963 (base32
10964 "01jar1rayhr2gba2pgbw49m56rc5z4p5wn3ds0m188hrlln4a2nd"))))
10965 (build-system gnu-build-system)
10966 (arguments
10967 `(#:tests? #f ; no check target
10968 #:make-flags (list "-f" "Makefile.unx" "install")
10969 #:parallel-build? #f ; not supported
10970 #:phases
10971 (modify-phases %standard-phases
10972 (add-after 'unpack 'enter-dir
10973 (lambda _ (chdir "src") #t))
10974 (delete 'configure)
10975 (replace 'install
10976 (lambda* (#:key inputs outputs #:allow-other-keys)
10977 (let ((target (string-append (assoc-ref outputs "out")
10978 "/bin")))
10979 (mkdir-p target)
10980 (for-each (lambda (file)
10981 (install-file file target))
10982 (find-files "../exe" ".*")))
10983 #t)))))
10984 (home-page "http://evolution.genetics.washington.edu/phylip/")
10985 (synopsis "Tools for inferring phylogenies")
10986 (description "PHYLIP (the PHYLogeny Inference Package) is a package of
10987programs for inferring phylogenies (evolutionary trees).")
10988 (license license:bsd-2)))
aa163424
RW		 10989
10990(define-public imp
10991 (package
10992 (name "imp")
10993 (version "2.6.2")
10994 (source
10995 (origin
10996 (method url-fetch)
10997 (uri (string-append "https://integrativemodeling.org/"
10998 version "/download/imp-" version ".tar.gz"))
10999 (sha256
11000 (base32
11001 "0lxqx7vh79d771svr611dkilp6sn30qrbw8zvscbrm37v38d2j6h"))))
11002 (build-system cmake-build-system)
11003 (arguments
11004 `(;; FIXME: Some tests fail because they produce warnings, others fail
11005 ;; because the PYTHONPATH does not include the modeller's directory.
677bc34d 11006 #:tests? #f))
aa163424
RW		 11007 (inputs
11008 `(("boost" ,boost)
11009 ("gsl" ,gsl)
11010 ("swig" ,swig)
11011 ("hdf5" ,hdf5)
11012 ("fftw" ,fftw)
11013 ("python" ,python-2)))
11014 (propagated-inputs
11015 `(("python2-numpy" ,python2-numpy)
11016 ("python2-scipy" ,python2-scipy)
11017 ("python2-pandas" ,python2-pandas)
11018 ("python2-scikit-learn" ,python2-scikit-learn)
11019 ("python2-networkx" ,python2-networkx)))
11020 (home-page "https://integrativemodeling.org")
11021 (synopsis "Integrative modeling platform")
11022 (description "IMP's broad goal is to contribute to a comprehensive
11023structural characterization of biomolecules ranging in size and complexity
11024from small peptides to large macromolecular assemblies, by integrating data
11025from diverse biochemical and biophysical experiments. IMP provides a C++ and
11026Python toolbox for solving complex modeling problems, and a number of
11027applications for tackling some common problems in a user-friendly way.")
11028 ;; IMP is largely available under the GNU Lesser GPL; see the file
11029 ;; COPYING.LGPL for the full text of this license. Some IMP modules are
11030 ;; available under the GNU GPL (see the file COPYING.GPL).
11031 (license (list license:lgpl2.1+
11032 license:gpl3+))))
8befd094
RW		 11033
11034(define-public tadbit
11035 (package
11036 (name "tadbit")
11037 (version "0.2")
11038 (source (origin
11039 (method url-fetch)
11040 (uri (string-append "https://github.com/3DGenomes/TADbit/"
11041 "archive/v" version ".tar.gz"))
11042 (file-name (string-append name "-" version ".tar.gz"))
11043 (sha256
11044 (base32
11045 "1cnfqrl4685zar4nnw94j94nhvl2h29jm448nadqi1h05z6fdk4f"))))
11046 (build-system python-build-system)
11047 (arguments
11048 `(;; Tests are included and must be run after installation, but
11049 ;; they are incomplete and thus cannot be run.
11050 #:tests? #f
11051 #:python ,python-2
11052 #:phases
11053 (modify-phases %standard-phases
11054 (add-after 'unpack 'fix-problems-with-setup.py
11055 (lambda* (#:key outputs #:allow-other-keys)
11056 ;; setup.py opens these files for writing
11057 (chmod "_pytadbit/_version.py" #o664)
11058 (chmod "README.rst" #o664)
11059
11060 ;; Don't attempt to install the bash completions to
11061 ;; the home directory.
11062 (rename-file "extras/.bash_completion"
11063 "extras/tadbit")
11064 (substitute* "setup.py"
11065 (("\\(path.expanduser\\('~'\\)")
11066 (string-append "(\""
11067 (assoc-ref outputs "out")
11068 "/etc/bash_completion.d\""))
11069 (("extras/\\.bash_completion")
11070 "extras/tadbit"))
11071 #t)))))
11072 (inputs
11073 ;; TODO: add Chimera for visualization
11074 `(("imp" ,imp)
11075 ("mcl" ,mcl)
11076 ("python2-scipy" ,python2-scipy)
11077 ("python2-numpy" ,python2-numpy)
11078 ("python2-matplotlib" ,python2-matplotlib)
11079 ("python2-pysam" ,python2-pysam)))
11080 (home-page "http://3dgenomes.github.io/TADbit/")
11081 (synopsis "Analyze, model, and explore 3C-based data")
11082 (description
11083 "TADbit is a complete Python library to deal with all steps to analyze,
11084model, and explore 3C-based data. With TADbit the user can map FASTQ files to
11085obtain raw interaction binned matrices (Hi-C like matrices), normalize and
a147fadd 11086correct interaction matrices, identify and compare the so-called
8befd094
RW		 11087@dfn{Topologically Associating Domains} (TADs), build 3D models from the
11088interaction matrices, and finally, extract structural properties from the
11089models. TADbit is complemented by TADkit for visualizing 3D models.")
11090 (license license:gpl3+)))
94820951
RW		 11091
11092(define-public kentutils
11093 (package
11094 (name "kentutils")
11095 ;; 302.1.0 is out, but the only difference is the inclusion of
11096 ;; pre-built binaries.
11097 (version "302.0.0")
11098 (source
11099 (origin
11100 (method url-fetch)
11101 (uri (string-append "https://github.com/ENCODE-DCC/kentUtils/"
11102 "archive/v" version ".tar.gz"))
11103 (file-name (string-append name "-" version ".tar.gz"))
11104 (sha256
11105 (base32
11106 "134aja3k1cj32kbk1nnw0q9gxjb2krr15q6sga8qldzvc0585rmm"))
11107 (modules '((guix build utils)
11108 (srfi srfi-26)
11109 (ice-9 ftw)))
11110 (snippet
11111 '(begin
11112 ;; Only the contents of the specified directories are free
11113 ;; for all uses, so we remove the rest. "hg/autoSql" and
11114 ;; "hg/autoXml" are nominally free, but they depend on a
11115 ;; library that is built from the sources in "hg/lib",
11116 ;; which is nonfree.
11117 (let ((free (list "." ".."
11118 "utils" "lib" "inc" "tagStorm"
11119 "parasol" "htslib"))
11120 (directory? (lambda (file)
11121 (eq? 'directory (stat:type (stat file))))))
11122 (for-each (lambda (file)
11123 (and (directory? file)
11124 (delete-file-recursively file)))
11125 (map (cut string-append "src/" <>)
11126 (scandir "src"
11127 (lambda (file)
11128 (not (member file free)))))))
11129 ;; Only make the utils target, not the userApps target,
11130 ;; because that requires libraries we won't build.
11131 (substitute* "Makefile"
11132 ((" userApps") " utils"))
11133 ;; Only build libraries that are free.
11134 (substitute* "src/makefile"
11135 (("DIRS =.*") "DIRS =\n")
11136 (("cd jkOwnLib.*") "")
11137 ((" hgLib") "")
11138 (("cd hg.*") ""))
11139 (substitute* "src/utils/makefile"
11140 ;; These tools depend on "jkhgap.a", which is part of the
11141 ;; nonfree "src/hg/lib" directory.
11142 (("raSqlQuery") "")
11143 (("pslLiftSubrangeBlat") "")
11144
11145 ;; Do not build UCSC tools, which may require nonfree
11146 ;; components.
11147 (("ALL_APPS =.*") "ALL_APPS = $(UTILS_APPLIST)\n"))
11148 #t))))
11149 (build-system gnu-build-system)
11150 (arguments
11151 `( ;; There is no global test target and the test target for
11152 ;; individual tools depends on input files that are not
11153 ;; included.
11154 #:tests? #f
11155 #:phases
11156 (modify-phases %standard-phases
11157 (add-after 'unpack 'fix-paths
11158 (lambda _
11159 (substitute* "Makefile"
11160 (("/bin/echo") (which "echo")))
11161 #t))
11162 (add-after 'unpack 'prepare-samtabix
11163 (lambda* (#:key inputs #:allow-other-keys)
11164 (copy-recursively (assoc-ref inputs "samtabix")
11165 "samtabix")
11166 #t))
11167 (delete 'configure)
11168 (replace 'install
11169 (lambda* (#:key outputs #:allow-other-keys)
11170 (let ((bin (string-append (assoc-ref outputs "out")
11171 "/bin")))
11172 (copy-recursively "bin" bin))
11173 #t)))))
11174 (native-inputs
11175 `(("samtabix"
11176 ,(origin
11177 (method git-fetch)
11178 (uri (git-reference
11179 (url "http://genome-source.cse.ucsc.edu/samtabix.git")
11180 (commit "10fd107909c1ac4d679299908be4262a012965ba")))
11181 (sha256
11182 (base32
11183 "0c1nj64l42v395sa84n7az43xiap4i6f9n9dfz4058aqiwkhkmma"))))))
11184 (inputs
11185 `(("zlib" ,zlib)
11186 ("tcsh" ,tcsh)
11187 ("perl" ,perl)
11188 ("libpng" ,libpng)
11189 ("mysql" ,mysql)
11190 ("openssl" ,openssl)))
11191 (home-page "http://genome.cse.ucsc.edu/index.html")
11192 (synopsis "Assorted bioinformatics utilities")
11193 (description "This package provides the kentUtils, a selection of
11194bioinformatics utilities used in combination with the UCSC genome
11195browser.")
11196 ;; Only a subset of the sources are released under a non-copyleft
11197 ;; free software license. All other sources are removed in a
11198 ;; snippet. See this bug report for an explanation of how the
11199 ;; license statements apply:
11200 ;; https://github.com/ENCODE-DCC/kentUtils/issues/12
11201 (license (license:non-copyleft
11202 "http://genome.ucsc.edu/license/"
11203 "The contents of this package are free for all uses."))))
7ceb0a83
RW		 11204
11205(define-public f-seq
11206 (let ((commit "6ccded34cff38cf432deed8503648b4a66953f9b")
11207 (revision "1"))
11208 (package
11209 (name "f-seq")
c6643f2d 11210 (version (string-append "1.1-" revision "." (string-take commit 7)))
7ceb0a83
RW		 11211 (source (origin
11212 (method git-fetch)
11213 (uri (git-reference
11214 (url "https://github.com/aboyle/F-seq.git")
11215 (commit commit)))
11216 (file-name (string-append name "-" version))
11217 (sha256
11218 (base32
11219 "1nk33k0yajg2id4g59bc4szr58r2q6pdq42vgcw054m8ip9wv26h"))
11220 (modules '((guix build utils)))
11221 ;; Remove bundled Java library archives.
11222 (snippet
11223 '(begin
11224 (for-each delete-file (find-files "lib" ".*"))
11225 #t))))
11226 (build-system ant-build-system)
11227 (arguments
11228 `(#:tests? #f ; no tests included
11229 #:phases
11230 (modify-phases %standard-phases
11231 (replace 'install
c0770fee 11232 (lambda* (#:key inputs outputs #:allow-other-keys)
7ceb0a83
RW		 11233 (let* ((target (assoc-ref outputs "out"))
11234 (doc (string-append target "/share/doc/f-seq/")))
11235 (mkdir-p target)
11236 (mkdir-p doc)
11237 (substitute* "bin/linux/fseq"
c0770fee
RW		 11238 (("java") (which "java"))
11239 (("\\$REALDIR/../lib/commons-cli-1.1.jar")
11240 (string-append (assoc-ref inputs "java-commons-cli")
11241 "/share/java/commons-cli.jar"))
11242 (("REALDIR=.*")
11243 (string-append "REALDIR=" target "/bin\n")))
7ceb0a83
RW		 11244 (install-file "README.txt" doc)
11245 (install-file "bin/linux/fseq" (string-append target "/bin"))
11246 (install-file "build~/fseq.jar" (string-append target "/lib"))
11247 (copy-recursively "lib" (string-append target "/lib"))
11248 #t))))))
11249 (inputs
11250 `(("perl" ,perl)
11251 ("java-commons-cli" ,java-commons-cli)))
11252 (home-page "http://fureylab.web.unc.edu/software/fseq/")
11253 (synopsis "Feature density estimator for high-throughput sequence tags")
11254 (description
11255 "F-Seq is a software package that generates a continuous tag sequence
11256density estimation allowing identification of biologically meaningful sites
11257such as transcription factor binding sites (ChIP-seq) or regions of open
11258chromatin (DNase-seq). Output can be displayed directly in the UCSC Genome
11259Browser.")
11260 (license license:gpl3+))))
96348048
RW		 11261
11262(define-public bismark
11263 (package
11264 (name "bismark")
11265 (version "0.16.3")
11266 (source
11267 (origin
11268 (method url-fetch)
11269 (uri (string-append "https://github.com/FelixKrueger/Bismark/"
11270 "archive/" version ".tar.gz"))
11271 (file-name (string-append name "-" version ".tar.gz"))
11272 (sha256
11273 (base32
11274 "1204i0pa02ll2jn5pnxypkclnskvv7a2nwh5nxhagmhxk9wfv9sq"))))
11275 (build-system perl-build-system)
11276 (arguments
11277 `(#:tests? #f ; there are no tests
11278 #:phases
11279 (modify-phases %standard-phases
11280 (delete 'configure)
11281 (delete 'build)
11282 (replace 'install
11283 (lambda* (#:key outputs #:allow-other-keys)
11284 (let ((bin (string-append (assoc-ref outputs "out")
11285 "/bin"))
11286 (docdir (string-append (assoc-ref outputs "out")
11287 "/share/doc/bismark"))
11288 (docs '("Bismark_User_Guide.pdf"
11289 "RELEASE_NOTES.txt"))
11290 (scripts '("bismark"
11291 "bismark_genome_preparation"
11292 "bismark_methylation_extractor"
11293 "bismark2bedGraph"
11294 "bismark2report"
11295 "coverage2cytosine"
11296 "deduplicate_bismark"
11297 "bismark_sitrep.tpl"
11298 "bam2nuc"
11299 "bismark2summary")))
11300 (mkdir-p docdir)
11301 (mkdir-p bin)
11302 (for-each (lambda (file) (install-file file bin))
11303 scripts)
11304 (for-each (lambda (file) (install-file file docdir))
11305 docs)
11306 #t))))))
11307 (home-page "http://www.bioinformatics.babraham.ac.uk/projects/bismark/")
11308 (synopsis "Map bisulfite treated sequence reads and analyze methylation")
11309 (description "Bismark is a program to map bisulfite treated sequencing
11310reads to a genome of interest and perform methylation calls in a single step.
11311The output can be easily imported into a genome viewer, such as SeqMonk, and
11312enables a researcher to analyse the methylation levels of their samples
11313straight away. Its main features are:
11314
11315@itemize
11316@item Bisulfite mapping and methylation calling in one single step
11317@item Supports single-end and paired-end read alignments
11318@item Supports ungapped and gapped alignments
11319@item Alignment seed length, number of mismatches etc are adjustable
11320@item Output discriminates between cytosine methylation in CpG, CHG
11321 and CHH context
11322@end itemize\n")
11323 (license license:gpl3+)))
dc8ddbfb
RW		 11324
11325(define-public paml
11326 (package
11327 (name "paml")
11328 (version "4.9e")
11329 (source (origin
11330 (method url-fetch)
11331 (uri (string-append "http://abacus.gene.ucl.ac.uk/software/"
11332 "paml" version ".tgz"))
11333 (sha256
11334 (base32
11335 "13zf6h9fiqghwhch2h06x1zdr6s42plsnqahflp5g7myr3han3s6"))
11336 (modules '((guix build utils)))
11337 ;; Remove Windows binaries
11338 (snippet
11339 '(begin
11340 (for-each delete-file (find-files "." "\\.exe$"))
11341 #t))))
11342 (build-system gnu-build-system)
11343 (arguments
11344 `(#:tests? #f ; there are no tests
11345 #:make-flags '("CC=gcc")
11346 #:phases
11347 (modify-phases %standard-phases
11348 (replace 'configure
11349 (lambda _
11350 (substitute* "src/BFdriver.c"
11351 (("/bin/bash") (which "bash")))
11352 (chdir "src")
11353 #t))
11354 (replace 'install
11355 (lambda* (#:key outputs #:allow-other-keys)
11356 (let ((tools '("baseml" "basemlg" "codeml"
11357 "pamp" "evolver" "yn00" "chi2"))
11358 (bin (string-append (assoc-ref outputs "out") "/bin"))
11359 (docdir (string-append (assoc-ref outputs "out")
11360 "/share/doc/paml")))
11361 (mkdir-p bin)
11362 (for-each (lambda (file) (install-file file bin)) tools)
11363 (copy-recursively "../doc" docdir)
11364 #t))))))
11365 (home-page "http://abacus.gene.ucl.ac.uk/software/paml.html")
11366 (synopsis "Phylogentic analysis by maximum likelihood")
11367 (description "PAML (for Phylogentic Analysis by Maximum Likelihood)
11368contains a few programs for model fitting and phylogenetic tree reconstruction
11369using nucleotide or amino-acid sequence data.")
11370 ;; GPLv3 only
11371 (license license:gpl3)))
d112e5a8
RW		 11372
11373(define-public kallisto
11374 (package
11375 (name "kallisto")
11376 (version "0.43.1")
11377 (source (origin
11378 (method url-fetch)
11379 (uri (string-append "https://github.com/pachterlab/"
11380 "kallisto/archive/v" version ".tar.gz"))
11381 (file-name (string-append name "-" version ".tar.gz"))
11382 (sha256
11383 (base32
11384 "03j3iqhvq7ya3c91gidly3k3jvgm97vjq4scihrlxh315j696r11"))))
11385 (build-system cmake-build-system)
11386 (arguments `(#:tests? #f)) ; no "check" target
11387 (inputs
11388 `(("hdf5" ,hdf5)
11389 ("zlib" ,zlib)))
11390 (home-page "http://pachterlab.github.io/kallisto/")
11391 (synopsis "Near-optimal RNA-Seq quantification")
11392 (description
11393 "Kallisto is a program for quantifying abundances of transcripts from
11394RNA-Seq data, or more generally of target sequences using high-throughput
11395sequencing reads. It is based on the novel idea of pseudoalignment for
11396rapidly determining the compatibility of reads with targets, without the need
11397for alignment. Pseudoalignment of reads preserves the key information needed
11398for quantification, and kallisto is therefore not only fast, but also as
11399accurate as existing quantification tools.")
11400 (license license:bsd-2)))
c3b2ab9d
RW		 11401
11402(define-public libgff
11403 (package
11404 (name "libgff")
11405 (version "1.0")
11406 (source (origin
11407 (method url-fetch)
11408 (uri (string-append
11409 "https://github.com/Kingsford-Group/"
11410 "libgff/archive/v" version ".tar.gz"))
11411 (file-name (string-append name "-" version ".tar.gz"))
11412 (sha256
11413 (base32
11414 "0vc4nxyhlm6g9vvmx5l4lfs5pnvixsv1hiiy4kddf2y3p6jna8ls"))))
11415 (build-system cmake-build-system)
11416 (arguments `(#:tests? #f)) ; no tests included
11417 (home-page "https://github.com/Kingsford-Group/libgff")
11418 (synopsis "Parser library for reading/writing GFF files")
11419 (description "This is a simple \"libraryfication\" of the GFF/GTF parsing
11420code that is used in the Cufflinks codebase. The goal of this library is to
11421provide this functionality without the necessity of drawing in a heavy-weight
11422dependency like SeqAn.")
11423 (license (license:x11-style "http://www.boost.org/LICENSE_1_0.txt"))))
1fe0bde3
RW		 11424
11425(define-public libdivsufsort
11426 (package
11427 (name "libdivsufsort")
11428 (version "2.0.1")
11429 (source (origin
11430 (method git-fetch)
11431 (uri (git-reference
11432 (url "https://github.com/y-256/libdivsufsort.git")
11433 (commit version)))
11434 (sha256
11435 (base32
11436 "0fgdz9fzihlvjjrxy01md1bv9vh12rkgkwbm90b1hj5xpbaqp7z2"))))
11437 (build-system cmake-build-system)
11438 (arguments
11439 '(#:tests? #f ; there are no tests
11440 #:configure-flags
11441 ;; Needed for rapmap and sailfish.
11442 '("-DBUILD_DIVSUFSORT64=ON")))
11443 (home-page "https://github.com/y-256/libdivsufsort")
11444 (synopsis "Lightweight suffix-sorting library")
11445 (description "libdivsufsort is a software library that implements a
11446lightweight suffix array construction algorithm. This library provides a
11447simple and an efficient C API to construct a suffix array and a
11448Burrows-Wheeler transformed string from a given string over a constant-size
11449alphabet. The algorithm runs in O(n log n) worst-case time using only 5n+O(1)
11450bytes of memory space, where n is the length of the string.")
11451 (license license:expat)))
8d77a085
RW		 11452
11453(define-public sailfish
11454 (package
11455 (name "sailfish")
11456 (version "0.10.1")
11457 (source (origin
11458 (method url-fetch)
11459 (uri
11460 (string-append "https://github.com/kingsfordgroup/"
11461 "sailfish/archive/v" version ".tar.gz"))
11462 (file-name (string-append name "-" version ".tar.gz"))
11463 (sha256
11464 (base32
11465 "1inn60dxiwsz8g9w7kvfhjxj4bwfb0r12dyhpzzhfbig712dkmm0"))
11466 (modules '((guix build utils)))
11467 (snippet
11468 '(begin
11469 ;; Delete bundled headers for eigen3.
11470 (delete-file-recursively "include/eigen3/")
11471 #t))))
11472 (build-system cmake-build-system)
11473 (arguments
11474 `(#:configure-flags
11475 (list (string-append "-DBOOST_INCLUDEDIR="
11476 (assoc-ref %build-inputs "boost")
11477 "/include/")
11478 (string-append "-DBOOST_LIBRARYDIR="
11479 (assoc-ref %build-inputs "boost")
11480 "/lib/")
11481 (string-append "-DBoost_LIBRARIES="
11482 "-lboost_iostreams "
11483 "-lboost_filesystem "
11484 "-lboost_system "
11485 "-lboost_thread "
11486 "-lboost_timer "
11487 "-lboost_chrono "
11488 "-lboost_program_options")
11489 "-DBoost_FOUND=TRUE"
11490 ;; Don't download RapMap---we already have it!
11491 "-DFETCHED_RAPMAP=1")
11492 ;; Tests must be run after installation and the location of the test
11493 ;; data file must be overridden. But the tests fail. It looks like
11494 ;; they are not really meant to be run.
11495 #:tests? #f
11496 #:phases
11497 (modify-phases %standard-phases
11498 ;; Boost cannot be found, even though it's right there.
11499 (add-after 'unpack 'do-not-look-for-boost
11500 (lambda* (#:key inputs #:allow-other-keys)
11501 (substitute* "CMakeLists.txt"
11502 (("find_package\\(Boost 1\\.53\\.0") "#"))))
11503 (add-after 'unpack 'do-not-assign-to-macro
11504 (lambda _
11505 (substitute* "include/spdlog/details/format.cc"
11506 (("const unsigned CHAR_WIDTH = 1;") ""))))
11507 (add-after 'unpack 'prepare-rapmap
11508 (lambda* (#:key inputs #:allow-other-keys)
11509 (let ((src "external/install/src/rapmap/")
11510 (include "external/install/include/rapmap/")
11511 (rapmap (assoc-ref inputs "rapmap")))
11512 (mkdir-p "/tmp/rapmap")
11513 (system* "tar" "xf"
11514 (assoc-ref inputs "rapmap")
11515 "-C" "/tmp/rapmap"
11516 "--strip-components=1")
11517 (mkdir-p src)
11518 (mkdir-p include)
11519 (for-each (lambda (file)
11520 (install-file file src))
11521 (find-files "/tmp/rapmap/src" "\\.(c|cpp)"))
11522 (copy-recursively "/tmp/rapmap/include" include))))
11523 (add-after 'unpack 'use-system-libraries
11524 (lambda* (#:key inputs #:allow-other-keys)
11525 (substitute* '("src/SailfishIndexer.cpp"
11526 "src/SailfishUtils.cpp"
11527 "src/SailfishQuantify.cpp"
11528 "src/FASTAParser.cpp"
11529 "include/PCA.hpp"
11530 "include/SailfishUtils.hpp"
11531 "include/SailfishIndex.hpp"
11532 "include/CollapsedEMOptimizer.hpp"
11533 "src/CollapsedEMOptimizer.cpp")
11534 (("#include \"jellyfish/config.h\"") ""))
11535 (substitute* "src/CMakeLists.txt"
11536 (("\\$\\{GAT_SOURCE_DIR\\}/external/install/include/jellyfish-2.2..")
11537 (string-append (assoc-ref inputs "jellyfish")
11538 "/include/jellyfish-" ,(package-version jellyfish)))
11539 (("\\$\\{GAT_SOURCE_DIR\\}/external/install/lib/libjellyfish-2.0.a")
11540 (string-append (assoc-ref inputs "jellyfish")
11541 "/lib/libjellyfish-2.0.a"))
11542 (("\\$\\{GAT_SOURCE_DIR\\}/external/install/lib/libdivsufsort.a")
11543 (string-append (assoc-ref inputs "libdivsufsort")
11544 "/lib/libdivsufsort.so"))
11545 (("\\$\\{GAT_SOURCE_DIR\\}/external/install/lib/libdivsufsort64.a")
11546 (string-append (assoc-ref inputs "libdivsufsort")
11547 "/lib/libdivsufsort64.so")))
11548 (substitute* "CMakeLists.txt"
11549 ;; Don't prefer static libs
11550 (("SET\\(CMAKE_FIND_LIBRARY_SUFFIXES.*") "")
11551 (("find_package\\(Jellyfish.*") "")
11552 (("ExternalProject_Add\\(libjellyfish") "message(")
11553 (("ExternalProject_Add\\(libgff") "message(")
11554 (("ExternalProject_Add\\(libsparsehash") "message(")
11555 (("ExternalProject_Add\\(libdivsufsort") "message("))
11556
11557 ;; Ensure that Eigen headers can be found
11558 (setenv "CPLUS_INCLUDE_PATH"
11559 (string-append (getenv "CPLUS_INCLUDE_PATH")
11560 ":"
11561 (assoc-ref inputs "eigen")
11562 "/include/eigen3")))))))
11563 (inputs
11564 `(("boost" ,boost)
11565 ("eigen" ,eigen)
11566 ("jemalloc" ,jemalloc)
11567 ("jellyfish" ,jellyfish)
11568 ("sparsehash" ,sparsehash)
11569 ("rapmap" ,(origin
11570 (method git-fetch)
11571 (uri (git-reference
11572 (url "https://github.com/COMBINE-lab/RapMap.git")
11573 (commit (string-append "sf-v" version))))
11574 (file-name (string-append "rapmap-sf-v" version "-checkout"))
11575 (sha256
11576 (base32
11577 "1hv79l5i576ykv5a1srj2p0q36yvyl5966m0fcy2lbi169ipjakf"))
11578 (modules '((guix build utils)))
11579 ;; These files are expected to be excluded.
11580 (snippet
11581 '(begin (delete-file-recursively "include/spdlog")
11582 (for-each delete-file '("include/xxhash.h"
11583 "src/xxhash.c"))))))
11584 ("libdivsufsort" ,libdivsufsort)
11585 ("libgff" ,libgff)
11586 ("tbb" ,tbb)
11587 ("zlib" ,zlib)))
11588 (native-inputs
11589 `(("pkg-config" ,pkg-config)))
11590 (home-page "http://www.cs.cmu.edu/~ckingsf/software/sailfish")
11591 (synopsis "Mapping-based isoform quantification from RNA-Seq reads")
11592 (description "Sailfish is a tool for genomic transcript quantification
11593from RNA-seq data. It requires a set of target transcripts (either from a
11594reference or de-novo assembly) to quantify. All you need to run sailfish is a
11595fasta file containing your reference transcripts and a (set of) fasta/fastq
11596file(s) containing your reads.")
11597 (license license:gpl3+)))
7762646d
RW		 11598
11599(define libstadenio-for-salmon
11600 (package
11601 (name "libstadenio")
11602 (version "1.14.8")
11603 (source (origin
11604 (method git-fetch)
11605 (uri (git-reference
11606 (url "https://github.com/COMBINE-lab/staden-io_lib.git")
11607 (commit (string-append "v" version))))
11608 (file-name (string-append name "-" version "-checkout"))
11609 (sha256
11610 (base32
11611 "1x8kxxqxl892vwfbprlbyfwkkv7c34ggkc94892x9x0g37x5nbwx"))))
11612 (build-system gnu-build-system)
11613 (arguments '(#:parallel-tests? #f)) ; not supported
11614 (inputs
11615 `(("zlib" ,zlib)))
11616 (native-inputs
11617 `(("perl" ,perl))) ; for tests
11618 (home-page "https://github.com/COMBINE-lab/staden-io_lib")
11619 (synopsis "General purpose trace and experiment file library")
11620 (description "This package provides a library of file reading and writing
11621code to provide a general purpose Trace file (and Experiment File) reading
11622interface.
11623
11624The following file formats are supported:
11625
11626@enumerate
11627@item SCF trace files
11628@item ABI trace files
11629@item ALF trace files
11630@item ZTR trace files
11631@item SFF trace archives
11632@item SRF trace archives
11633@item Experiment files
11634@item Plain text files
11635@item SAM/BAM sequence files
11636@item CRAM sequence files
11637@end enumerate\n")
11638 (license license:bsd-3)))
11639
11640(define spdlog-for-salmon
11641 (package
11642 (name "spdlog")
11643 (version "0.14.0")
11644 (source (origin
11645 (method git-fetch)
11646 (uri (git-reference
11647 (url "https://github.com/COMBINE-lab/spdlog.git")
11648 (commit (string-append "v" version))))
11649 (file-name (string-append name "-" version "-checkout"))
11650 (sha256
11651 (base32
11652 "13730429gwlabi432ilpnja3sfvy0nn2719vnhhmii34xcdyc57q"))))
11653 (build-system cmake-build-system)
11654 (home-page "https://github.com/COMBINE-lab/spdlog")
11655 (synopsis "Very fast C++ logging library")
11656 (description "Spdlog is a very fast header-only C++ logging library with
11657performance as its primary goal.")
11658 (license license:expat)))
11659
11660;; This is a modified variant of bwa for use with Salmon. It installs a
11661;; library to avoid having to build this as part of Salmon.
11662(define bwa-for-salmon
11663 (package (inherit bwa)
11664 (name "bwa")
11665 (version "0.7.12.5")
11666 (source (origin
11667 (method git-fetch)
11668 (uri (git-reference
11669 (url "https://github.com/COMBINE-lab/bwa.git")
11670 (commit (string-append "v" version))))
11671 (file-name (string-append "bwa-for-salmon-" version "-checkout"))
11672 (sha256
11673 (base32
11674 "1z2qa64y0c5hky10510x137mnzlhz6k8qf27csw4w9j6qihq95gb"))))
11675 (build-system gnu-build-system)
11676 (arguments
11677 '(#:tests? #f ;no "check" target
11678 #:phases
11679 (modify-phases %standard-phases
11680 (replace 'install
11681 (lambda* (#:key outputs #:allow-other-keys)
11682 (let* ((out (assoc-ref outputs "out"))
11683 (bin (string-append out "/bin"))
11684 (lib (string-append out "/lib"))
11685 (doc (string-append out "/share/doc/bwa"))
11686 (man (string-append out "/share/man/man1"))
11687 (inc (string-append out "/include/bwa")))
11688 (install-file "bwa" bin)
11689 (install-file "README.md" doc)
11690 (install-file "bwa.1" man)
11691 (install-file "libbwa.a" lib)
11692 (mkdir-p lib)
11693 (mkdir-p inc)
11694 (for-each (lambda (file)
11695 (install-file file inc))
11696 (find-files "." "\\.h$")))
11697 #t))
11698 ;; no "configure" script
11699 (delete 'configure))))))
11700
11701(define-public salmon
11702 (package
11703 (name "salmon")
11704 (version "0.9.1")
11705 (source (origin
11706 (method git-fetch)
11707 (uri (git-reference
11708 (url "https://github.com/COMBINE-lab/salmon.git")
11709 (commit (string-append "v" version))))
11710 (file-name (string-append name "-" version "-checkout"))
11711 (sha256
11712 (base32
11713 "1zi1ff4i7y2ykk0vdzysgwzzzv166vg2x77pj1mf4baclavxj87a"))
11714 (modules '((guix build utils)))
11715 (snippet
11716 '(begin
11717 ;; Delete bundled headers for eigen3.
11718 (delete-file-recursively "include/eigen3/")
11719 #t))))
11720 (build-system cmake-build-system)
11721 (arguments
11722 `(#:configure-flags
11723 (list (string-append "-DBOOST_INCLUDEDIR="
11724 (assoc-ref %build-inputs "boost")
11725 "/include/")
11726 (string-append "-DBOOST_LIBRARYDIR="
11727 (assoc-ref %build-inputs "boost")
11728 "/lib/")
11729 (string-append "-DBoost_LIBRARIES="
11730 "-lboost_iostreams "
11731 "-lboost_filesystem "
11732 "-lboost_system "
11733 "-lboost_thread "
11734 "-lboost_timer "
11735 "-lboost_chrono "
11736 "-lboost_program_options")
11737 "-DBoost_FOUND=TRUE"
11738 "-DTBB_LIBRARIES=tbb tbbmalloc"
11739 ;; Don't download RapMap---we already have it!
11740 "-DFETCHED_RAPMAP=1")
11741 #:phases
11742 (modify-phases %standard-phases
11743 ;; Boost cannot be found, even though it's right there.
11744 (add-after 'unpack 'do-not-look-for-boost
11745 (lambda* (#:key inputs #:allow-other-keys)
11746 (substitute* "CMakeLists.txt"
11747 (("find_package\\(Boost 1\\.53\\.0") "#"))))
11748 (add-after 'unpack 'do-not-phone-home
11749 (lambda _
11750 (substitute* "src/Salmon.cpp"
11751 (("getVersionMessage\\(\\)") "\"\""))))
11752 (add-after 'unpack 'prepare-rapmap
11753 (lambda* (#:key inputs #:allow-other-keys)
11754 (let ((src "external/install/src/rapmap/")
11755 (include "external/install/include/rapmap/")
11756 (rapmap (assoc-ref inputs "rapmap")))
11757 (mkdir-p src)
11758 (mkdir-p include)
11759 (for-each (lambda (file)
11760 (install-file file src))
11761 (find-files (string-append rapmap "/src") "\\.(c|cpp)"))
11762 (copy-recursively (string-append rapmap "/include") include)
11763 (for-each delete-file '("external/install/include/rapmap/xxhash.h"
11764 "external/install/include/rapmap/FastxParser.hpp"
11765 "external/install/include/rapmap/concurrentqueue.h"
11766 "external/install/include/rapmap/FastxParserThreadUtils.hpp"
11767 "external/install/src/rapmap/FastxParser.cpp"
11768 "external/install/src/rapmap/xxhash.c")))))
11769 (add-after 'unpack 'use-system-libraries
11770 (lambda* (#:key inputs #:allow-other-keys)
11771 (substitute* "src/CMakeLists.txt"
11772 (("\\$\\{GAT_SOURCE_DIR\\}/external/install/include/jellyfish-2.2..")
11773 (string-append (assoc-ref inputs "jellyfish")
11774 "/include/jellyfish-" ,(package-version jellyfish)))
11775 (("\\$\\{GAT_SOURCE_DIR\\}/external/install/lib/libjellyfish-2.0.a")
11776 (string-append (assoc-ref inputs "jellyfish")
11777 "/lib/libjellyfish-2.0.a"))
11778 (("\\$\\{GAT_SOURCE_DIR\\}/external/install/lib/libdivsufsort.a")
11779 (string-append (assoc-ref inputs "libdivsufsort")
11780 "/lib/libdivsufsort.so"))
11781 (("\\$\\{GAT_SOURCE_DIR\\}/external/install/lib/libstaden-read.a")
11782 (string-append (assoc-ref inputs "libstadenio-for-salmon")
11783 "/lib/libstaden-read.a"))
11784 (("\\$\\{GAT_SOURCE_DIR\\}/external/install/lib/libbwa.a")
11785 (string-append (assoc-ref inputs "bwa") "/lib/libbwa.a"))
11786 (("\\$\\{GAT_SOURCE_DIR\\}/external/install/lib/libdivsufsort64.a")
11787 (string-append (assoc-ref inputs "libdivsufsort")
11788 "/lib/libdivsufsort64.so")))
11789 (substitute* "CMakeLists.txt"
11790 ;; Don't prefer static libs
11791 (("SET\\(CMAKE_FIND_LIBRARY_SUFFIXES.*") "")
11792 (("set\\(TBB_LIBRARIES") "message(")
11793 (("find_package\\(Jellyfish.*") "")
11794 (("ExternalProject_Add\\(libcereal") "message(")
11795 (("ExternalProject_Add\\(libbwa") "message(")
11796 (("ExternalProject_Add\\(libjellyfish") "message(")
11797 (("ExternalProject_Add\\(libgff") "message(")
11798 (("ExternalProject_Add\\(libtbb") "message(")
11799 (("ExternalProject_Add\\(libspdlog") "message(")
11800 (("ExternalProject_Add\\(libdivsufsort") "message(")
11801 (("ExternalProject_Add\\(libstadenio") "message(")
11802 (("ExternalProject_Add_Step\\(") "message("))
11803
11804 ;; Ensure that all headers can be found
11805 (setenv "CPLUS_INCLUDE_PATH"
11806 (string-append (getenv "CPLUS_INCLUDE_PATH")
11807 ":"
11808 (assoc-ref inputs "bwa")
11809 "/include/bwa"
11810 ":"
11811 (assoc-ref inputs "eigen")
11812 "/include/eigen3"))
11813 (setenv "CPATH"
11814 (string-append (assoc-ref inputs "bwa")
11815 "/include/bwa"
11816 ":"
11817 (assoc-ref inputs "eigen")
11818 "/include/eigen3"))
11819 #t))
11820 ;; CMAKE_INSTALL_PREFIX does not exist when the tests are
11821 ;; run. It only exists after the install phase.
11822 (add-after 'unpack 'fix-tests
11823 (lambda _
11824 (substitute* "src/CMakeLists.txt"
11825 (("DTOPLEVEL_DIR=\\$\\{CMAKE_INSTALL_PREFIX")
11826 "DTOPLEVEL_DIR=${GAT_SOURCE_DIR"))
11827 #t)))))
11828 (inputs
11829 `(("boost" ,boost)
11830 ("bwa" ,bwa-for-salmon)
11831 ("bzip2" ,bzip2)
11832 ("cereal" ,cereal)
11833 ("eigen" ,eigen)
11834 ("rapmap" ,(origin
11835 (method git-fetch)
11836 (uri (git-reference
11837 (url "https://github.com/COMBINE-lab/RapMap.git")
11838 (commit (string-append "salmon-v" version))))
11839 (file-name (string-append "rapmap-salmon-v" version "-checkout"))
11840 (sha256
11841 (base32
11842 "1yc12yqsz6f0r8sg1qnk57xg34aqwc9jbqq6gd5ys28xw3plj98p"))))
11843 ("jemalloc" ,jemalloc)
11844 ("jellyfish" ,jellyfish)
11845 ("libgff" ,libgff)
11846 ("tbb" ,tbb)
11847 ("libdivsufsort" ,libdivsufsort)
11848 ("libstadenio-for-salmon" ,libstadenio-for-salmon)
11849 ("spdlog-for-salmon" ,spdlog-for-salmon)
11850 ("xz" ,xz)
11851 ("zlib" ,zlib)))
11852 (home-page "https://github.com/COMBINE-lab/salmon")
11853 (synopsis "Quantification from RNA-seq reads using lightweight alignments")
11854 (description "Salmon is a program to produce highly-accurate,
11855transcript-level quantification estimates from RNA-seq data. Salmon achieves
11856its accuracy and speed via a number of different innovations, including the
11857use of lightweight alignments (accurate but fast-to-compute proxies for
11858traditional read alignments) and massively-parallel stochastic collapsed
11859variational inference.")
11860 (license license:gpl3+)))
152d30c3
RW		 11861
11862(define-public python-loompy
11863 (package
11864 (name "python-loompy")
11865 (version "2.0.2")
11866 (source
11867 (origin
11868 (method url-fetch)
11869 (uri (pypi-uri "loompy" version))
11870 (sha256
11871 (base32
11872 "1drgv8j1hxqzzpnfg272x9djb6j8qr798w1pc2x8ikmfgyd9gh51"))))
11873 (build-system python-build-system)
11874 ;; There are no tests
11875 (arguments '(#:tests? #f))
11876 (propagated-inputs
11877 `(("python-h5py" ,python-h5py)
11878 ("python-numpy" ,python-numpy)
11879 ("python-scipy" ,python-scipy)
11880 ("python-typing" ,python-typing)))
11881 (home-page "https://github.com/linnarsson-lab/loompy")
11882 (synopsis "Work with .loom files for single-cell RNA-seq data")
11883 (description "The loom file format is an efficient format for very large
11884omics datasets, consisting of a main matrix, optional additional layers, a
11885variable number of row and column annotations. Loom also supports sparse
11886graphs. This library makes it easy to work with @file{.loom} files for
11887single-cell RNA-seq data.")
11888 (license license:bsd-3)))
jackhill's copy of GNU Guix: https://guix.gnu.org/