Commit | Line | Data |
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4e10a221 | 1 | ;;; GNU Guix --- Functional package management for GNU |
6193563a | 2 | ;;; Copyright © 2014, 2015, 2016, 2017 Ricardo Wurmus <rekado@elephly.net> |
a9f754d7 | 3 | ;;; Copyright © 2015, 2016, 2017 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> |
ce7e361f | 7 | ;;; Copyright © 2016, 2017 Efraim Flashner <efraim@flashner.co.il> |
318c0aee | 8 | ;;; Copyright © 2016 Marius Bakke <mbakke@fastmail.com> |
3fffabce | 9 | ;;; Copyright © 2016 Raoul Bonnal <ilpuccio.febo@gmail.com> |
4e10a221 RW |
10 | ;;; |
11 | ;;; This file is part of GNU Guix. | |
12 | ;;; | |
13 | ;;; GNU Guix is free software; you can redistribute it and/or modify it | |
14 | ;;; under the terms of the GNU General Public License as published by | |
15 | ;;; the Free Software Foundation; either version 3 of the License, or (at | |
16 | ;;; your option) any later version. | |
17 | ;;; | |
18 | ;;; GNU Guix is distributed in the hope that it will be useful, but | |
19 | ;;; WITHOUT ANY WARRANTY; without even the implied warranty of | |
20 | ;;; MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the | |
21 | ;;; GNU General Public License for more details. | |
22 | ;;; | |
23 | ;;; You should have received a copy of the GNU General Public License | |
24 | ;;; along with GNU Guix. If not, see <http://www.gnu.org/licenses/>. | |
25 | ||
26 | (define-module (gnu packages bioinformatics) | |
27 | #:use-module ((guix licenses) #:prefix license:) | |
28 | #:use-module (guix packages) | |
8e913213 | 29 | #:use-module (guix utils) |
4e10a221 | 30 | #:use-module (guix download) |
2c16316e | 31 | #:use-module (guix git-download) |
ec946638 | 32 | #:use-module (guix hg-download) |
10b4a969 | 33 | #:use-module (guix build-system ant) |
4e10a221 | 34 | #:use-module (guix build-system gnu) |
d7678942 | 35 | #:use-module (guix build-system cmake) |
c033f5d6 | 36 | #:use-module (guix build-system ocaml) |
365c8153 | 37 | #:use-module (guix build-system perl) |
8622a072 | 38 | #:use-module (guix build-system python) |
a5002ae7 | 39 | #:use-module (guix build-system r) |
9c38b540 | 40 | #:use-module (guix build-system ruby) |
d3517eda | 41 | #:use-module (guix build-system trivial) |
4e10a221 | 42 | #:use-module (gnu packages) |
a2950fa4 | 43 | #:use-module (gnu packages autotools) |
684bf7c7 | 44 | #:use-module (gnu packages algebra) |
d3517eda | 45 | #:use-module (gnu packages base) |
318c0aee | 46 | #:use-module (gnu packages bash) |
a0a71439 | 47 | #:use-module (gnu packages bison) |
e4e5a4d8 | 48 | #:use-module (gnu packages boost) |
4e10a221 | 49 | #:use-module (gnu packages compression) |
82c370de | 50 | #:use-module (gnu packages cpio) |
1baee943 | 51 | #:use-module (gnu packages curl) |
99828fa7 | 52 | #:use-module (gnu packages documentation) |
94820951 | 53 | #:use-module (gnu packages databases) |
d29150b5 | 54 | #:use-module (gnu packages datastructures) |
75dd2424 | 55 | #:use-module (gnu packages file) |
99268755 | 56 | #:use-module (gnu packages flex) |
02f35bb5 | 57 | #:use-module (gnu packages gawk) |
2409f37f | 58 | #:use-module (gnu packages gcc) |
66e40e00 | 59 | #:use-module (gnu packages gd) |
97b9da68 | 60 | #:use-module (gnu packages gtk) |
b16728b0 | 61 | #:use-module (gnu packages glib) |
db7a3444 | 62 | #:use-module (gnu packages groff) |
50937297 | 63 | #:use-module (gnu packages guile) |
89984be4 | 64 | #:use-module (gnu packages haskell) |
66e40e00 | 65 | #:use-module (gnu packages image) |
97b9da68 | 66 | #:use-module (gnu packages imagemagick) |
15a3c3d4 | 67 | #:use-module (gnu packages java) |
5ded35d8 | 68 | #:use-module (gnu packages ldc) |
51c64999 | 69 | #:use-module (gnu packages linux) |
ec946638 | 70 | #:use-module (gnu packages logging) |
36742f43 | 71 | #:use-module (gnu packages machine-learning) |
db7a3444 | 72 | #:use-module (gnu packages man) |
c833ab55 | 73 | #:use-module (gnu packages maths) |
6c2b26e2 | 74 | #:use-module (gnu packages mpi) |
4e10a221 | 75 | #:use-module (gnu packages ncurses) |
c033f5d6 | 76 | #:use-module (gnu packages ocaml) |
81f3e0c1 | 77 | #:use-module (gnu packages pcre) |
ceb62d54 | 78 | #:use-module (gnu packages parallel) |
66e40e00 | 79 | #:use-module (gnu packages pdf) |
4e10a221 RW |
80 | #:use-module (gnu packages perl) |
81 | #:use-module (gnu packages pkg-config) | |
bfe3c685 | 82 | #:use-module (gnu packages popt) |
e4e5a4d8 | 83 | #:use-module (gnu packages protobuf) |
346a829a | 84 | #:use-module (gnu packages python) |
ec946638 | 85 | #:use-module (gnu packages readline) |
9c38b540 | 86 | #:use-module (gnu packages ruby) |
84be3b99 | 87 | #:use-module (gnu packages serialization) |
94820951 | 88 | #:use-module (gnu packages shells) |
c833ab55 | 89 | #:use-module (gnu packages statistics) |
aa163424 | 90 | #:use-module (gnu packages swig) |
d7678942 | 91 | #:use-module (gnu packages tbb) |
97b9da68 | 92 | #:use-module (gnu packages tex) |
db7a3444 | 93 | #:use-module (gnu packages texinfo) |
2127cedb | 94 | #:use-module (gnu packages textutils) |
43c565d2 | 95 | #:use-module (gnu packages time) |
a2950fa4 | 96 | #:use-module (gnu packages tls) |
ce7155d5 | 97 | #:use-module (gnu packages vim) |
365c8153 | 98 | #:use-module (gnu packages web) |
c833ab55 | 99 | #:use-module (gnu packages xml) |
66e40e00 | 100 | #:use-module (gnu packages xorg) |
2c9232ae | 101 | #:use-module (srfi srfi-1) |
ce7e361f | 102 | #:use-module (ice-9 match)) |
4e10a221 | 103 | |
036cd0cb RJPB |
104 | (define-public r-ape |
105 | (package | |
106 | (name "r-ape") | |
107 | (version "4.1") | |
108 | (source | |
109 | (origin | |
110 | (method url-fetch) | |
111 | (uri (cran-uri "ape" version)) | |
112 | (sha256 | |
113 | (base32 | |
114 | "0959fiiy11rzfzrzaknmgrx64bhszj02l0ycz79k5a6bmpfzanlk")))) | |
115 | (build-system r-build-system) | |
aeb64f3c RW |
116 | (propagated-inputs |
117 | `(("r-lattice" ,r-lattice) | |
118 | ("r-nlme" ,r-nlme))) | |
036cd0cb RJPB |
119 | (home-page "http://ape-package.ird.fr/") |
120 | (synopsis "Analyses of phylogenetics and evolution") | |
121 | (description | |
122 | "This package provides functions for reading, writing, plotting, and | |
123 | manipulating phylogenetic trees, analyses of comparative data in a | |
124 | phylogenetic framework, ancestral character analyses, analyses of | |
125 | diversification and macroevolution, computing distances from DNA sequences, | |
126 | and several other tools.") | |
127 | (license license:gpl2+))) | |
128 | ||
8dc797fa BW |
129 | (define-public aragorn |
130 | (package | |
131 | (name "aragorn") | |
e990c81d | 132 | (version "1.2.38") |
8dc797fa BW |
133 | (source (origin |
134 | (method url-fetch) | |
135 | (uri (string-append | |
136 | "http://mbio-serv2.mbioekol.lu.se/ARAGORN/Downloads/aragorn" | |
137 | version ".tgz")) | |
138 | (sha256 | |
139 | (base32 | |
e990c81d | 140 | "09i1rg716smlbnixfm7q1ml2mfpaa2fpn3hwjg625ysmfwwy712b")))) |
8dc797fa BW |
141 | (build-system gnu-build-system) |
142 | (arguments | |
143 | `(#:tests? #f ; there are no tests | |
144 | #:phases | |
145 | (modify-phases %standard-phases | |
146 | (delete 'configure) | |
147 | (replace 'build | |
148 | (lambda _ | |
149 | (zero? (system* "gcc" | |
150 | "-O3" | |
151 | "-ffast-math" | |
152 | "-finline-functions" | |
153 | "-o" | |
154 | "aragorn" | |
155 | (string-append "aragorn" ,version ".c"))))) | |
156 | (replace 'install | |
157 | (lambda* (#:key outputs #:allow-other-keys) | |
158 | (let* ((out (assoc-ref outputs "out")) | |
159 | (bin (string-append out "/bin")) | |
160 | (man (string-append out "/share/man/man1"))) | |
161 | (mkdir-p bin) | |
f3860753 | 162 | (install-file "aragorn" bin) |
8dc797fa | 163 | (mkdir-p man) |
f3860753 | 164 | (install-file "aragorn.1" man)) |
8dc797fa BW |
165 | #t))))) |
166 | (home-page "http://mbio-serv2.mbioekol.lu.se/ARAGORN") | |
167 | (synopsis "Detect tRNA, mtRNA and tmRNA genes in nucleotide sequences") | |
168 | (description | |
169 | "Aragorn identifies transfer RNA, mitochondrial RNA and | |
170 | transfer-messenger RNA from nucleotide sequences, based on homology to known | |
171 | tRNA consensus sequences and RNA structure. It also outputs the secondary | |
172 | structure of the predicted RNA.") | |
173 | (license license:gpl2))) | |
174 | ||
a12ba6e8 BW |
175 | (define-public bamm |
176 | (package | |
177 | (name "bamm") | |
4b6da268 | 178 | (version "1.7.3") |
a12ba6e8 BW |
179 | (source (origin |
180 | (method url-fetch) | |
181 | ;; BamM is not available on pypi. | |
182 | (uri (string-append | |
4b6da268 | 183 | "https://github.com/Ecogenomics/BamM/archive/" |
a12ba6e8 BW |
184 | version ".tar.gz")) |
185 | (file-name (string-append name "-" version ".tar.gz")) | |
186 | (sha256 | |
187 | (base32 | |
4b6da268 | 188 | "1f35yxp4pc8aadsvbpg6r4kg2jh4fkjci0iby4iyljm6980sac0s")) |
a12ba6e8 BW |
189 | (modules '((guix build utils))) |
190 | (snippet | |
191 | `(begin | |
192 | ;; Delete bundled htslib. | |
193 | (delete-file-recursively "c/htslib-1.3.1") | |
194 | #t)))) | |
195 | (build-system python-build-system) | |
196 | (arguments | |
197 | `(#:python ,python-2 ; BamM is Python 2 only. | |
198 | ;; Do not use bundled libhts. Do use the bundled libcfu because it has | |
199 | ;; been modified from its original form. | |
200 | #:configure-flags | |
201 | (let ((htslib (assoc-ref %build-inputs "htslib"))) | |
202 | (list "--with-libhts-lib" (string-append htslib "/lib") | |
203 | "--with-libhts-inc" (string-append htslib "/include/htslib"))) | |
204 | #:phases | |
205 | (modify-phases %standard-phases | |
206 | (add-after 'unpack 'autogen | |
207 | (lambda _ | |
208 | (with-directory-excursion "c" | |
209 | (let ((sh (which "sh"))) | |
210 | ;; Use autogen so that 'configure' works. | |
211 | (substitute* "autogen.sh" (("/bin/sh") sh)) | |
212 | (setenv "CONFIG_SHELL" sh) | |
213 | (substitute* "configure" (("/bin/sh") sh)) | |
214 | (zero? (system* "./autogen.sh")))))) | |
215 | (delete 'build) | |
216 | ;; Run tests after installation so compilation only happens once. | |
217 | (delete 'check) | |
218 | (add-after 'install 'wrap-executable | |
219 | (lambda* (#:key outputs #:allow-other-keys) | |
220 | (let* ((out (assoc-ref outputs "out")) | |
221 | (path (getenv "PATH"))) | |
222 | (wrap-program (string-append out "/bin/bamm") | |
223 | `("PATH" ":" prefix (,path)))) | |
224 | #t)) | |
225 | (add-after 'wrap-executable 'post-install-check | |
226 | (lambda* (#:key inputs outputs #:allow-other-keys) | |
227 | (setenv "PATH" | |
228 | (string-append (assoc-ref outputs "out") | |
229 | "/bin:" | |
230 | (getenv "PATH"))) | |
231 | (setenv "PYTHONPATH" | |
232 | (string-append | |
233 | (assoc-ref outputs "out") | |
234 | "/lib/python" | |
235 | (string-take (string-take-right | |
236 | (assoc-ref inputs "python") 5) 3) | |
237 | "/site-packages:" | |
238 | (getenv "PYTHONPATH"))) | |
239 | ;; There are 2 errors printed, but they are safe to ignore: | |
240 | ;; 1) [E::hts_open_format] fail to open file ... | |
241 | ;; 2) samtools view: failed to open ... | |
242 | (zero? (system* "nosetests"))))))) | |
243 | (native-inputs | |
244 | `(("autoconf" ,autoconf) | |
245 | ("automake" ,automake) | |
246 | ("libtool" ,libtool) | |
247 | ("zlib" ,zlib) | |
248 | ("python-nose" ,python2-nose) | |
f3b98f4f | 249 | ("python-pysam" ,python2-pysam))) |
a12ba6e8 | 250 | (inputs |
bca2c576 | 251 | `(("htslib" ,htslib-1.3) ; At least one test fails on htslib-1.4+. |
a12ba6e8 BW |
252 | ("samtools" ,samtools) |
253 | ("bwa" ,bwa) | |
254 | ("grep" ,grep) | |
255 | ("sed" ,sed) | |
256 | ("coreutils" ,coreutils))) | |
257 | (propagated-inputs | |
258 | `(("python-numpy" ,python2-numpy))) | |
259 | (home-page "http://ecogenomics.github.io/BamM/") | |
260 | (synopsis "Metagenomics-focused BAM file manipulator") | |
261 | (description | |
262 | "BamM is a C library, wrapped in python, to efficiently generate and | |
263 | parse BAM files, specifically for the analysis of metagenomic data. For | |
264 | instance, it implements several methods to assess contig-wise read coverage.") | |
265 | (license license:lgpl3+))) | |
266 | ||
9794180d RW |
267 | (define-public bamtools |
268 | (package | |
269 | (name "bamtools") | |
48d66a9c | 270 | (version "2.4.1") |
9794180d RW |
271 | (source (origin |
272 | (method url-fetch) | |
273 | (uri (string-append | |
274 | "https://github.com/pezmaster31/bamtools/archive/v" | |
275 | version ".tar.gz")) | |
276 | (file-name (string-append name "-" version ".tar.gz")) | |
277 | (sha256 | |
278 | (base32 | |
48d66a9c | 279 | "0jr024kcrhjb82cm69i7p5fcg5375zlc1h3qh2n1v368hcd0qflk")))) |
9794180d | 280 | (build-system cmake-build-system) |
4702cec2 RW |
281 | (arguments |
282 | `(#:tests? #f ;no "check" target | |
283 | #:phases | |
284 | (modify-phases %standard-phases | |
285 | (add-before | |
286 | 'configure 'set-ldflags | |
287 | (lambda* (#:key outputs #:allow-other-keys) | |
288 | (setenv "LDFLAGS" | |
289 | (string-append | |
290 | "-Wl,-rpath=" | |
291 | (assoc-ref outputs "out") "/lib/bamtools"))))))) | |
9794180d RW |
292 | (inputs `(("zlib" ,zlib))) |
293 | (home-page "https://github.com/pezmaster31/bamtools") | |
294 | (synopsis "C++ API and command-line toolkit for working with BAM data") | |
295 | (description | |
296 | "BamTools provides both a C++ API and a command-line toolkit for handling | |
297 | BAM files.") | |
298 | (license license:expat))) | |
299 | ||
bdc7be59 MB |
300 | (define-public bcftools |
301 | (package | |
302 | (name "bcftools") | |
0620387a | 303 | (version "1.5") |
bdc7be59 MB |
304 | (source (origin |
305 | (method url-fetch) | |
306 | (uri (string-append | |
307 | "https://github.com/samtools/bcftools/releases/download/" | |
308 | version "/bcftools-" version ".tar.bz2")) | |
309 | (sha256 | |
310 | (base32 | |
0620387a | 311 | "0093hkkvxmbwfaa7905s6185jymynvg42kq6sxv7fili11l5mxwz")) |
bdc7be59 MB |
312 | (modules '((guix build utils))) |
313 | (snippet | |
314 | ;; Delete bundled htslib. | |
0620387a | 315 | '(delete-file-recursively "htslib-1.5")))) |
bdc7be59 MB |
316 | (build-system gnu-build-system) |
317 | (arguments | |
318 | `(#:test-target "test" | |
0620387a | 319 | #:configure-flags (list "--with-htslib=system") |
bdc7be59 MB |
320 | #:make-flags |
321 | (list | |
322 | "USE_GPL=1" | |
0620387a | 323 | "LIBS=-lgsl -lgslcblas" |
bdc7be59 MB |
324 | (string-append "prefix=" (assoc-ref %outputs "out")) |
325 | (string-append "HTSDIR=" (assoc-ref %build-inputs "htslib") "/include") | |
98593f9f | 326 | (string-append "HTSLIB=" (assoc-ref %build-inputs "htslib") "/lib/libhts.so") |
bdc7be59 | 327 | (string-append "BGZIP=" (assoc-ref %build-inputs "htslib") "/bin/bgzip") |
98593f9f BW |
328 | (string-append "TABIX=" (assoc-ref %build-inputs "htslib") "/bin/tabix") |
329 | (string-append "PACKAGE_VERSION=" ,version)) | |
bdc7be59 MB |
330 | #:phases |
331 | (modify-phases %standard-phases | |
bdc7be59 MB |
332 | (add-before 'check 'patch-tests |
333 | (lambda _ | |
334 | (substitute* "test/test.pl" | |
335 | (("/bin/bash") (which "bash"))) | |
336 | #t))))) | |
337 | (native-inputs | |
338 | `(("htslib" ,htslib) | |
339 | ("perl" ,perl))) | |
340 | (inputs | |
341 | `(("gsl" ,gsl) | |
342 | ("zlib" ,zlib))) | |
343 | (home-page "https://samtools.github.io/bcftools/") | |
344 | (synopsis "Utilities for variant calling and manipulating VCFs and BCFs") | |
345 | (description | |
346 | "BCFtools is a set of utilities that manipulate variant calls in the | |
347 | Variant Call Format (VCF) and its binary counterpart BCF. All commands work | |
348 | transparently with both VCFs and BCFs, both uncompressed and BGZF-compressed.") | |
349 | ;; The sources are dual MIT/GPL, but becomes GPL-only when USE_GPL=1. | |
350 | (license (list license:gpl3+ license:expat)))) | |
351 | ||
8dd4ff11 RW |
352 | (define-public bedops |
353 | (package | |
354 | (name "bedops") | |
1bbc3b1d | 355 | (version "2.4.14") |
8dd4ff11 RW |
356 | (source (origin |
357 | (method url-fetch) | |
358 | (uri (string-append "https://github.com/bedops/bedops/archive/v" | |
359 | version ".tar.gz")) | |
f586c877 | 360 | (file-name (string-append name "-" version ".tar.gz")) |
8dd4ff11 RW |
361 | (sha256 |
362 | (base32 | |
1bbc3b1d | 363 | "1kqbac547wyqma81cyky9n7mkgikjpsfd3nnmcm6hpqwanqgh10v")))) |
8dd4ff11 RW |
364 | (build-system gnu-build-system) |
365 | (arguments | |
366 | '(#:tests? #f | |
367 | #:make-flags (list (string-append "BINDIR=" %output "/bin")) | |
368 | #:phases | |
369 | (alist-cons-after | |
370 | 'unpack 'unpack-tarballs | |
371 | (lambda _ | |
372 | ;; FIXME: Bedops includes tarballs of minimally patched upstream | |
373 | ;; libraries jansson, zlib, and bzip2. We cannot just use stock | |
374 | ;; libraries because at least one of the libraries (zlib) is | |
375 | ;; patched to add a C++ function definition (deflateInit2cpp). | |
376 | ;; Until the Bedops developers offer a way to link against system | |
377 | ;; libraries we have to build the in-tree copies of these three | |
378 | ;; libraries. | |
379 | ||
380 | ;; See upstream discussion: | |
381 | ;; https://github.com/bedops/bedops/issues/124 | |
382 | ||
383 | ;; Unpack the tarballs to benefit from shebang patching. | |
384 | (with-directory-excursion "third-party" | |
385 | (and (zero? (system* "tar" "xvf" "jansson-2.6.tar.bz2")) | |
386 | (zero? (system* "tar" "xvf" "zlib-1.2.7.tar.bz2")) | |
387 | (zero? (system* "tar" "xvf" "bzip2-1.0.6.tar.bz2")))) | |
388 | ;; Disable unpacking of tarballs in Makefile. | |
389 | (substitute* "system.mk/Makefile.linux" | |
390 | (("^\tbzcat .*") "\t@echo \"not unpacking\"\n") | |
391 | (("\\./configure") "CONFIG_SHELL=bash ./configure")) | |
392 | (substitute* "third-party/zlib-1.2.7/Makefile.in" | |
393 | (("^SHELL=.*$") "SHELL=bash\n"))) | |
394 | (alist-delete 'configure %standard-phases)))) | |
395 | (home-page "https://github.com/bedops/bedops") | |
396 | (synopsis "Tools for high-performance genomic feature operations") | |
397 | (description | |
398 | "BEDOPS is a suite of tools to address common questions raised in genomic | |
399 | studies---mostly with regard to overlap and proximity relationships between | |
400 | data sets. It aims to be scalable and flexible, facilitating the efficient | |
401 | and accurate analysis and management of large-scale genomic data. | |
402 | ||
403 | BEDOPS provides tools that perform highly efficient and scalable Boolean and | |
404 | other set operations, statistical calculations, archiving, conversion and | |
405 | other management of genomic data of arbitrary scale. Tasks can be easily | |
406 | split by chromosome for distributing whole-genome analyses across a | |
407 | computational cluster.") | |
408 | (license license:gpl2+))) | |
409 | ||
81de5647 RW |
410 | (define-public bedtools |
411 | (package | |
412 | (name "bedtools") | |
d285657e | 413 | (version "2.26.0") |
81de5647 RW |
414 | (source (origin |
415 | (method url-fetch) | |
416 | (uri (string-append "https://github.com/arq5x/bedtools2/archive/v" | |
417 | version ".tar.gz")) | |
f586c877 | 418 | (file-name (string-append name "-" version ".tar.gz")) |
81de5647 RW |
419 | (sha256 |
420 | (base32 | |
d285657e | 421 | "0xvri5hnp2iim1cx6mcd5d9f102p5ql41x69rd6106x1c17pinqm")))) |
81de5647 RW |
422 | (build-system gnu-build-system) |
423 | (native-inputs `(("python" ,python-2))) | |
424 | (inputs `(("samtools" ,samtools) | |
425 | ("zlib" ,zlib))) | |
426 | (arguments | |
427 | '(#:test-target "test" | |
428 | #:phases | |
6573ac82 | 429 | (modify-phases %standard-phases |
6573ac82 BW |
430 | (delete 'configure) |
431 | (replace 'install | |
432 | (lambda* (#:key outputs #:allow-other-keys) | |
433 | (let ((bin (string-append (assoc-ref outputs "out") "/bin/"))) | |
434 | (for-each (lambda (file) | |
435 | (install-file file bin)) | |
436 | (find-files "bin" ".*"))) | |
437 | #t))))) | |
81de5647 RW |
438 | (home-page "https://github.com/arq5x/bedtools2") |
439 | (synopsis "Tools for genome analysis and arithmetic") | |
440 | (description | |
441 | "Collectively, the bedtools utilities are a swiss-army knife of tools for | |
442 | a wide-range of genomics analysis tasks. The most widely-used tools enable | |
443 | genome arithmetic: that is, set theory on the genome. For example, bedtools | |
444 | allows one to intersect, merge, count, complement, and shuffle genomic | |
445 | intervals from multiple files in widely-used genomic file formats such as BAM, | |
446 | BED, GFF/GTF, VCF.") | |
447 | (license license:gpl2))) | |
448 | ||
9a8f309c RW |
449 | ;; Later releases of bedtools produce files with more columns than |
450 | ;; what Ribotaper expects. | |
451 | (define-public bedtools-2.18 | |
452 | (package (inherit bedtools) | |
453 | (name "bedtools") | |
454 | (version "2.18.0") | |
455 | (source (origin | |
456 | (method url-fetch) | |
457 | (uri (string-append "https://github.com/arq5x/bedtools2/" | |
458 | "archive/v" version ".tar.gz")) | |
459 | (file-name (string-append name "-" version ".tar.gz")) | |
460 | (sha256 | |
461 | (base32 | |
462 | "05vrnr8yp7swfagshzpgqmzk1blnwnq8pq5pckzi1m26w98d63vf")))))) | |
463 | ||
17dc32a4 RW |
464 | (define-public ribotaper |
465 | (package | |
466 | (name "ribotaper") | |
467 | (version "1.3.1") | |
468 | (source (origin | |
469 | (method url-fetch) | |
470 | (uri (string-append "https://ohlerlab.mdc-berlin.de/" | |
471 | "files/RiboTaper/RiboTaper_Version_" | |
472 | version ".tar.gz")) | |
473 | (sha256 | |
474 | (base32 | |
475 | "0ykjbps1y3z3085q94npw8i9x5gldc6shy8vlc08v76zljsm07hv")))) | |
476 | (build-system gnu-build-system) | |
477 | (inputs | |
478 | `(("bedtools" ,bedtools-2.18) | |
479 | ("samtools" ,samtools-0.1) | |
2d7c4ae3 | 480 | ("r-minimal" ,r-minimal) |
17dc32a4 RW |
481 | ("r-foreach" ,r-foreach) |
482 | ("r-xnomial" ,r-xnomial) | |
483 | ("r-domc" ,r-domc) | |
484 | ("r-multitaper" ,r-multitaper) | |
485 | ("r-seqinr" ,r-seqinr))) | |
486 | (home-page "https://ohlerlab.mdc-berlin.de/software/RiboTaper_126/") | |
487 | (synopsis "Define translated ORFs using ribosome profiling data") | |
488 | (description | |
489 | "Ribotaper is a method for defining translated @dfn{open reading | |
490 | frames} (ORFs) using ribosome profiling (ribo-seq) data. This package | |
491 | provides the Ribotaper pipeline.") | |
492 | (license license:gpl3+))) | |
493 | ||
769fc6bb RW |
494 | (define-public ribodiff |
495 | (package | |
496 | (name "ribodiff") | |
497 | (version "0.2.2") | |
498 | (source | |
499 | (origin | |
500 | (method url-fetch) | |
501 | (uri (string-append "https://github.com/ratschlab/RiboDiff/" | |
502 | "archive/v" version ".tar.gz")) | |
503 | (file-name (string-append name "-" version ".tar.gz")) | |
504 | (sha256 | |
505 | (base32 | |
506 | "0wpbwmfv05wdjxv7ikm664f7s7p7cqr8jnw99zrda0q67rl50aaj")))) | |
507 | (build-system python-build-system) | |
508 | (arguments | |
509 | `(#:python ,python-2 | |
510 | #:phases | |
511 | (modify-phases %standard-phases | |
512 | ;; Generate an installable executable script wrapper. | |
513 | (add-after 'unpack 'patch-setup.py | |
514 | (lambda _ | |
515 | (substitute* "setup.py" | |
516 | (("^(.*)packages=.*" line prefix) | |
517 | (string-append line "\n" | |
518 | prefix "scripts=['scripts/TE.py'],\n"))) | |
519 | #t))))) | |
520 | (inputs | |
521 | `(("python-numpy" ,python2-numpy) | |
522 | ("python-matplotlib" ,python2-matplotlib) | |
523 | ("python-scipy" ,python2-scipy) | |
524 | ("python-statsmodels" ,python2-statsmodels))) | |
2bb12f5a MB |
525 | (native-inputs |
526 | `(("python-mock" ,python2-mock) | |
527 | ("python-nose" ,python2-nose))) | |
769fc6bb RW |
528 | (home-page "http://public.bmi.inf.ethz.ch/user/zhongy/RiboDiff/") |
529 | (synopsis "Detect translation efficiency changes from ribosome footprints") | |
530 | (description "RiboDiff is a statistical tool that detects the protein | |
531 | translational efficiency change from Ribo-Seq (ribosome footprinting) and | |
532 | RNA-Seq data. It uses a generalized linear model to detect genes showing | |
533 | difference in translational profile taking mRNA abundance into account. It | |
534 | facilitates us to decipher the translational regulation that behave | |
535 | independently with transcriptional regulation.") | |
536 | (license license:gpl3+))) | |
537 | ||
a0a71439 RJ |
538 | (define-public bioawk |
539 | (package | |
540 | (name "bioawk") | |
541 | (version "1.0") | |
542 | (source (origin | |
543 | (method url-fetch) | |
544 | (uri (string-append "https://github.com/lh3/bioawk/archive/v" | |
545 | version ".tar.gz")) | |
546 | (file-name (string-append name "-" version ".tar.gz")) | |
547 | (sha256 | |
548 | (base32 "1daizxsk17ahi9n58fj8vpgwyhzrzh54bzqhanjanp88kgrz7gjw")))) | |
549 | (build-system gnu-build-system) | |
550 | (inputs | |
551 | `(("zlib" ,zlib))) | |
552 | (native-inputs | |
553 | `(("bison" ,bison))) | |
554 | (arguments | |
555 | `(#:tests? #f ; There are no tests to run. | |
556 | ;; Bison must generate files, before other targets can build. | |
557 | #:parallel-build? #f | |
558 | #:phases | |
559 | (modify-phases %standard-phases | |
560 | (delete 'configure) ; There is no configure phase. | |
561 | (replace 'install | |
562 | (lambda* (#:key outputs #:allow-other-keys) | |
563 | (let* ((out (assoc-ref outputs "out")) | |
564 | (bin (string-append out "/bin")) | |
565 | (man (string-append out "/share/man/man1"))) | |
566 | (mkdir-p man) | |
567 | (copy-file "awk.1" (string-append man "/bioawk.1")) | |
568 | (install-file "bioawk" bin))))))) | |
569 | (home-page "https://github.com/lh3/bioawk") | |
570 | (synopsis "AWK with bioinformatics extensions") | |
571 | (description "Bioawk is an extension to Brian Kernighan's awk, adding the | |
572 | support of several common biological data formats, including optionally gzip'ed | |
573 | BED, GFF, SAM, VCF, FASTA/Q and TAB-delimited formats with column names. It | |
574 | also adds a few built-in functions and a command line option to use TAB as the | |
575 | input/output delimiter. When the new functionality is not used, bioawk is | |
576 | intended to behave exactly the same as the original BWK awk.") | |
577 | (license license:x11))) | |
578 | ||
a2fb1492 RW |
579 | (define-public python2-pybedtools |
580 | (package | |
581 | (name "python2-pybedtools") | |
582 | (version "0.6.9") | |
583 | (source (origin | |
584 | (method url-fetch) | |
585 | (uri (string-append | |
586 | "https://pypi.python.org/packages/source/p/pybedtools/pybedtools-" | |
587 | version ".tar.gz")) | |
588 | (sha256 | |
589 | (base32 | |
590 | "1ldzdxw1p4y3g2ignmggsdypvqkcwqwzhdha4rbgpih048z5p4an")))) | |
591 | (build-system python-build-system) | |
592 | (arguments `(#:python ,python-2)) ; no Python 3 support | |
593 | (inputs | |
f2516de2 | 594 | `(("python-matplotlib" ,python2-matplotlib))) |
a2fb1492 RW |
595 | (propagated-inputs |
596 | `(("bedtools" ,bedtools) | |
597 | ("samtools" ,samtools))) | |
598 | (native-inputs | |
f2516de2 HG |
599 | `(("python-cython" ,python2-cython) |
600 | ("python-pyyaml" ,python2-pyyaml) | |
f3b98f4f | 601 | ("python-nose" ,python2-nose))) |
a2fb1492 RW |
602 | (home-page "https://pythonhosted.org/pybedtools/") |
603 | (synopsis "Python wrapper for BEDtools programs") | |
604 | (description | |
605 | "pybedtools is a Python wrapper for Aaron Quinlan's BEDtools programs, | |
606 | which are widely used for genomic interval manipulation or \"genome algebra\". | |
607 | pybedtools extends BEDTools by offering feature-level manipulations from with | |
608 | Python.") | |
609 | (license license:gpl2+))) | |
610 | ||
9e12eba8 BW |
611 | (define-public python-biom-format |
612 | (package | |
613 | (name "python-biom-format") | |
abc08cba | 614 | (version "2.1.6") |
9e12eba8 BW |
615 | (source |
616 | (origin | |
617 | (method url-fetch) | |
618 | ;; Use GitHub as source because PyPI distribution does not contain | |
619 | ;; test data: https://github.com/biocore/biom-format/issues/693 | |
620 | (uri (string-append "https://github.com/biocore/biom-format/archive/" | |
621 | version ".tar.gz")) | |
622 | (file-name (string-append name "-" version ".tar.gz")) | |
623 | (sha256 | |
624 | (base32 | |
abc08cba | 625 | "08cr7wpahk6zb31h4bs7jmzpvxcqv9s13xz40h6y2h656jvdvnpj")))) |
9e12eba8 | 626 | (build-system python-build-system) |
de96ea28 | 627 | (propagated-inputs |
9e12eba8 BW |
628 | `(("python-numpy" ,python-numpy) |
629 | ("python-scipy" ,python-scipy) | |
630 | ("python-future" ,python-future) | |
631 | ("python-click" ,python-click) | |
abc08cba BW |
632 | ("python-h5py" ,python-h5py) |
633 | ("python-pandas" ,python-pandas))) | |
da5ebd10 MB |
634 | (native-inputs |
635 | `(("python-nose" ,python-nose))) | |
9e12eba8 BW |
636 | (home-page "http://www.biom-format.org") |
637 | (synopsis "Biological Observation Matrix (BIOM) format utilities") | |
638 | (description | |
639 | "The BIOM file format is designed to be a general-use format for | |
640 | representing counts of observations e.g. operational taxonomic units, KEGG | |
641 | orthology groups or lipid types, in one or more biological samples | |
642 | e.g. microbiome samples, genomes, metagenomes.") | |
643 | (license license:bsd-3) | |
644 | (properties `((python2-variant . ,(delay python2-biom-format)))))) | |
645 | ||
646 | (define-public python2-biom-format | |
647 | (let ((base (package-with-python2 (strip-python2-variant python-biom-format)))) | |
648 | (package | |
649 | (inherit base) | |
650 | (arguments | |
651 | `(#:phases | |
652 | (modify-phases %standard-phases | |
653 | ;; Do not require the unmaintained pyqi library. | |
654 | (add-after 'unpack 'remove-pyqi | |
655 | (lambda _ | |
656 | (substitute* "setup.py" | |
657 | (("install_requires.append\\(\"pyqi\"\\)") "pass")) | |
658 | #t))) | |
00e10c6e | 659 | ,@(package-arguments base)))))) |
9e12eba8 | 660 | |
f7283db3 RW |
661 | (define-public bioperl-minimal |
662 | (let* ((inputs `(("perl-module-build" ,perl-module-build) | |
663 | ("perl-data-stag" ,perl-data-stag) | |
664 | ("perl-libwww" ,perl-libwww) | |
665 | ("perl-uri" ,perl-uri))) | |
666 | (transitive-inputs | |
667 | (map (compose package-name cadr) | |
668 | (delete-duplicates | |
669 | (concatenate | |
670 | (map (compose package-transitive-target-inputs cadr) inputs)))))) | |
671 | (package | |
672 | (name "bioperl-minimal") | |
c70271ec | 673 | (version "1.7.0") |
f7283db3 RW |
674 | (source |
675 | (origin | |
676 | (method url-fetch) | |
c70271ec RW |
677 | (uri (string-append "https://github.com/bioperl/bioperl-live/" |
678 | "archive/release-" | |
679 | (string-map (lambda (c) | |
680 | (if (char=? c #\.) | |
681 | #\- c)) version) | |
682 | ".tar.gz")) | |
f7283db3 RW |
683 | (sha256 |
684 | (base32 | |
c70271ec | 685 | "12phgpxwgkqflkwfb9dcqg7a31dpjlfhar8wcgv0aj5ln4akfz06")))) |
f7283db3 RW |
686 | (build-system perl-build-system) |
687 | (arguments | |
688 | `(#:phases | |
689 | (modify-phases %standard-phases | |
690 | (add-after | |
691 | 'install 'wrap-programs | |
692 | (lambda* (#:key outputs #:allow-other-keys) | |
693 | ;; Make sure all executables in "bin" find the required Perl | |
694 | ;; modules at runtime. As the PERL5LIB variable contains also | |
695 | ;; the paths of native inputs, we pick the transitive target | |
696 | ;; inputs from %build-inputs. | |
697 | (let* ((out (assoc-ref outputs "out")) | |
698 | (bin (string-append out "/bin/")) | |
699 | (path (string-join | |
700 | (cons (string-append out "/lib/perl5/site_perl") | |
701 | (map (lambda (name) | |
702 | (assoc-ref %build-inputs name)) | |
703 | ',transitive-inputs)) | |
704 | ":"))) | |
705 | (for-each (lambda (file) | |
706 | (wrap-program file | |
707 | `("PERL5LIB" ":" prefix (,path)))) | |
708 | (find-files bin "\\.pl$")) | |
709 | #t)))))) | |
710 | (inputs inputs) | |
711 | (native-inputs | |
712 | `(("perl-test-most" ,perl-test-most))) | |
713 | (home-page "http://search.cpan.org/dist/BioPerl") | |
714 | (synopsis "Bioinformatics toolkit") | |
715 | (description | |
716 | "BioPerl is the product of a community effort to produce Perl code which | |
717 | is useful in biology. Examples include Sequence objects, Alignment objects | |
718 | and database searching objects. These objects not only do what they are | |
719 | advertised to do in the documentation, but they also interact - Alignment | |
720 | objects are made from the Sequence objects, Sequence objects have access to | |
721 | Annotation and SeqFeature objects and databases, Blast objects can be | |
722 | converted to Alignment objects, and so on. This means that the objects | |
723 | provide a coordinated and extensible framework to do computational biology.") | |
2f3108ad | 724 | (license license:perl-license)))) |
f7283db3 | 725 | |
85c37e29 RW |
726 | (define-public python-biopython |
727 | (package | |
728 | (name "python-biopython") | |
4ce60305 | 729 | (version "1.68") |
85c37e29 RW |
730 | (source (origin |
731 | (method url-fetch) | |
e815c094 BW |
732 | ;; use PyPi rather than biopython.org to ease updating |
733 | (uri (pypi-uri "biopython" version)) | |
85c37e29 RW |
734 | (sha256 |
735 | (base32 | |
4ce60305 | 736 | "07qc7nz0k77y8hf8s18rscvibvm91zw0kkq7ylrhisf8vp8hkp6i")))) |
85c37e29 | 737 | (build-system python-build-system) |
4ce60305 BW |
738 | (arguments |
739 | `(#:phases | |
740 | (modify-phases %standard-phases | |
741 | (add-before 'check 'set-home | |
742 | ;; Some tests require a home directory to be set. | |
743 | (lambda _ (setenv "HOME" "/tmp") #t))))) | |
f22efa01 | 744 | (propagated-inputs |
85c37e29 | 745 | `(("python-numpy" ,python-numpy))) |
85c37e29 RW |
746 | (home-page "http://biopython.org/") |
747 | (synopsis "Tools for biological computation in Python") | |
748 | (description | |
749 | "Biopython is a set of tools for biological computation including parsers | |
750 | for bioinformatics files into Python data structures; interfaces to common | |
751 | bioinformatics programs; a standard sequence class and tools for performing | |
752 | common operations on them; code to perform data classification; code for | |
753 | dealing with alignments; code making it easy to split up parallelizable tasks | |
754 | into separate processes; and more.") | |
5c31f4aa | 755 | (license (license:non-copyleft "http://www.biopython.org/DIST/LICENSE")))) |
85c37e29 RW |
756 | |
757 | (define-public python2-biopython | |
5c31f4aa | 758 | (package-with-python2 python-biopython)) |
85c37e29 | 759 | |
4b1a1528 BW |
760 | ;; An outdated version of biopython is required for seqmagick, see |
761 | ;; https://github.com/fhcrc/seqmagick/issues/59 | |
762 | ;; When that issue has been resolved this package should be removed. | |
763 | (define python2-biopython-1.66 | |
764 | (package | |
765 | (inherit python2-biopython) | |
766 | (version "1.66") | |
767 | (source (origin | |
768 | (method url-fetch) | |
769 | (uri (pypi-uri "biopython" version)) | |
770 | (sha256 | |
771 | (base32 | |
772 | "1gdv92593klimg22icf5j9by7xiq86jnwzkpz4abaa05ylkdf6hp")))))) | |
773 | ||
985d8411 BW |
774 | (define-public bpp-core |
775 | ;; The last release was in 2014 and the recommended way to install from source | |
776 | ;; is to clone the git repository, so we do this. | |
777 | ;; http://biopp.univ-montp2.fr/wiki/index.php/Main_Page | |
778 | (let ((commit "7d8bced0d1a87291ea8dd7046b7fb5ff9c35c582")) | |
779 | (package | |
780 | (name "bpp-core") | |
781 | (version (string-append "2.2.0-1." (string-take commit 7))) | |
782 | (source (origin | |
783 | (method git-fetch) | |
784 | (uri (git-reference | |
785 | (url "http://biopp.univ-montp2.fr/git/bpp-core") | |
786 | (commit commit))) | |
787 | (file-name (string-append name "-" version "-checkout")) | |
788 | (sha256 | |
789 | (base32 | |
790 | "10djsq5vlnkilv436gnmh4irpk49v29pa69r6xiryg32xmvn909j")))) | |
791 | (build-system cmake-build-system) | |
792 | (arguments | |
793 | `(#:parallel-build? #f)) | |
794 | (inputs | |
795 | `(("gcc" ,gcc-5))) ; Compilation of bpp-phyl fails with GCC 4.9 so we | |
796 | ; compile all of the bpp packages with GCC 5. | |
797 | (home-page "http://biopp.univ-montp2.fr") | |
798 | (synopsis "C++ libraries for Bioinformatics") | |
799 | (description | |
800 | "Bio++ is a set of C++ libraries for Bioinformatics, including sequence | |
801 | analysis, phylogenetics, molecular evolution and population genetics. It is | |
802 | Object Oriented and is designed to be both easy to use and computer efficient. | |
803 | Bio++ intends to help programmers to write computer expensive programs, by | |
804 | providing them a set of re-usable tools.") | |
805 | (license license:cecill-c)))) | |
806 | ||
8b5f4d57 BW |
807 | (define-public bpp-phyl |
808 | ;; The last release was in 2014 and the recommended way to install from source | |
809 | ;; is to clone the git repository, so we do this. | |
810 | ;; http://biopp.univ-montp2.fr/wiki/index.php/Main_Page | |
811 | (let ((commit "0c07167b629f68b569bf274d1ad0c4af83276ae2")) | |
812 | (package | |
813 | (name "bpp-phyl") | |
814 | (version (string-append "2.2.0-1." (string-take commit 7))) | |
815 | (source (origin | |
816 | (method git-fetch) | |
817 | (uri (git-reference | |
818 | (url "http://biopp.univ-montp2.fr/git/bpp-phyl") | |
819 | (commit commit))) | |
820 | (file-name (string-append name "-" version "-checkout")) | |
821 | (sha256 | |
822 | (base32 | |
823 | "1ssjgchzwj3iai26kyly7gwkdv8sk59nqhkb1wpap3sf5m6kyllh")))) | |
824 | (build-system cmake-build-system) | |
825 | (arguments | |
826 | `(#:parallel-build? #f | |
827 | ;; If out-of-source, test data is not copied into the build directory | |
828 | ;; so the tests fail. | |
829 | #:out-of-source? #f)) | |
830 | (inputs | |
831 | `(("bpp-core" ,bpp-core) | |
832 | ("bpp-seq" ,bpp-seq) | |
833 | ;; GCC 4.8 fails due to an 'internal compiler error', so we use a more | |
834 | ;; modern GCC. | |
835 | ("gcc" ,gcc-5))) | |
836 | (home-page "http://biopp.univ-montp2.fr") | |
837 | (synopsis "Bio++ phylogenetic Library") | |
838 | (description | |
839 | "Bio++ is a set of C++ libraries for Bioinformatics, including sequence | |
840 | analysis, phylogenetics, molecular evolution and population genetics. This | |
841 | library provides phylogenetics-related modules.") | |
842 | (license license:cecill-c)))) | |
843 | ||
159a7016 BW |
844 | (define-public bpp-popgen |
845 | ;; The last release was in 2014 and the recommended way to install from source | |
846 | ;; is to clone the git repository, so we do this. | |
847 | ;; http://biopp.univ-montp2.fr/wiki/index.php/Main_Page | |
848 | (let ((commit "e472bac9b1a148803895d747cd6d0c5904f85d9f")) | |
849 | (package | |
850 | (name "bpp-popgen") | |
851 | (version (string-append "2.2.0-1." (string-take commit 7))) | |
852 | (source (origin | |
853 | (method git-fetch) | |
854 | (uri (git-reference | |
855 | (url "http://biopp.univ-montp2.fr/git/bpp-popgen") | |
856 | (commit commit))) | |
857 | (file-name (string-append name "-" version "-checkout")) | |
858 | (sha256 | |
859 | (base32 | |
860 | "0yn82dzn1n5629nzja68xfrhi655709rjanyryb36vzkmymy6dw5")))) | |
861 | (build-system cmake-build-system) | |
862 | (arguments | |
863 | `(#:parallel-build? #f | |
864 | #:tests? #f)) ; There are no tests. | |
865 | (inputs | |
866 | `(("bpp-core" ,bpp-core) | |
867 | ("bpp-seq" ,bpp-seq) | |
868 | ("gcc" ,gcc-5))) | |
869 | (home-page "http://biopp.univ-montp2.fr") | |
870 | (synopsis "Bio++ population genetics library") | |
871 | (description | |
872 | "Bio++ is a set of C++ libraries for Bioinformatics, including sequence | |
873 | analysis, phylogenetics, molecular evolution and population genetics. This | |
874 | library provides population genetics-related modules.") | |
875 | (license license:cecill-c)))) | |
876 | ||
70f1bc05 BW |
877 | (define-public bpp-seq |
878 | ;; The last release was in 2014 and the recommended way to install from source | |
879 | ;; is to clone the git repository, so we do this. | |
880 | ;; http://biopp.univ-montp2.fr/wiki/index.php/Main_Page | |
881 | (let ((commit "6cfa07965ce152e5598a89df2fa80a75973bfa33")) | |
882 | (package | |
883 | (name "bpp-seq") | |
884 | (version (string-append "2.2.0-1." (string-take commit 7))) | |
885 | (source (origin | |
886 | (method git-fetch) | |
887 | (uri (git-reference | |
888 | (url "http://biopp.univ-montp2.fr/git/bpp-seq") | |
889 | (commit commit))) | |
890 | (file-name (string-append name "-" version "-checkout")) | |
891 | (sha256 | |
892 | (base32 | |
893 | "1nys5jq7jqvdg40d91wsmj3q2yzy4276cp7sp44n67p468f27zf2")))) | |
894 | (build-system cmake-build-system) | |
895 | (arguments | |
896 | `(#:parallel-build? #f | |
897 | ;; If out-of-source, test data is not copied into the build directory | |
898 | ;; so the tests fail. | |
899 | #:out-of-source? #f)) | |
900 | (inputs | |
901 | `(("bpp-core" ,bpp-core) | |
902 | ("gcc" ,gcc-5))) ; Use GCC 5 as per 'bpp-core'. | |
903 | (home-page "http://biopp.univ-montp2.fr") | |
904 | (synopsis "Bio++ sequence library") | |
905 | (description | |
906 | "Bio++ is a set of C++ libraries for Bioinformatics, including sequence | |
907 | analysis, phylogenetics, molecular evolution and population genetics. This | |
908 | library provides sequence-related modules.") | |
909 | (license license:cecill-c)))) | |
910 | ||
db7a3444 BW |
911 | (define-public bppsuite |
912 | ;; The last release was in 2014 and the recommended way to install from source | |
913 | ;; is to clone the git repository, so we do this. | |
914 | ;; http://biopp.univ-montp2.fr/wiki/index.php/Main_Page | |
915 | (let ((commit "c516147f57aa50961121cd505bed52cd7603698b")) | |
916 | (package | |
917 | (name "bppsuite") | |
918 | (version (string-append "2.2.0-1." (string-take commit 7))) | |
919 | (source (origin | |
920 | (method git-fetch) | |
921 | (uri (git-reference | |
922 | (url "http://biopp.univ-montp2.fr/git/bppsuite") | |
923 | (commit commit))) | |
924 | (file-name (string-append name "-" version "-checkout")) | |
925 | (sha256 | |
926 | (base32 | |
927 | "1y87pxvw0jxjizhq2dr9g2r91md45k1p9ih2sl1yy1y3p934l2kb")))) | |
928 | (build-system cmake-build-system) | |
929 | (arguments | |
930 | `(#:parallel-build? #f | |
931 | #:tests? #f)) ; There are no tests. | |
932 | (native-inputs | |
933 | `(("groff" ,groff) | |
934 | ("man-db" ,man-db) | |
935 | ("texinfo" ,texinfo))) | |
936 | (inputs | |
937 | `(("bpp-core" ,bpp-core) | |
938 | ("bpp-seq" ,bpp-seq) | |
939 | ("bpp-phyl" ,bpp-phyl) | |
940 | ("bpp-phyl" ,bpp-popgen) | |
941 | ("gcc" ,gcc-5))) | |
942 | (home-page "http://biopp.univ-montp2.fr") | |
943 | (synopsis "Bioinformatics tools written with the Bio++ libraries") | |
944 | (description | |
945 | "Bio++ is a set of C++ libraries for Bioinformatics, including sequence | |
946 | analysis, phylogenetics, molecular evolution and population genetics. This | |
947 | package provides command line tools using the Bio++ library.") | |
948 | (license license:cecill-c)))) | |
949 | ||
82c370de RW |
950 | (define-public blast+ |
951 | (package | |
952 | (name "blast+") | |
4732e6ee | 953 | (version "2.6.0") |
82c370de RW |
954 | (source (origin |
955 | (method url-fetch) | |
956 | (uri (string-append | |
957 | "ftp://ftp.ncbi.nlm.nih.gov/blast/executables/blast+/" | |
958 | version "/ncbi-blast-" version "+-src.tar.gz")) | |
959 | (sha256 | |
960 | (base32 | |
4732e6ee BW |
961 | "15n937pw5aqmyfjb6l387d18grqbb96l63d5xj4l7yyh0zbf2405")) |
962 | (patches (search-patches "blast+-fix-makefile.patch")) | |
82c370de RW |
963 | (modules '((guix build utils))) |
964 | (snippet | |
965 | '(begin | |
4732e6ee | 966 | ;; Remove bundled bzip2, zlib and pcre. |
82c370de RW |
967 | (delete-file-recursively "c++/src/util/compress/bzip2") |
968 | (delete-file-recursively "c++/src/util/compress/zlib") | |
4732e6ee | 969 | (delete-file-recursively "c++/src/util/regexp") |
82c370de RW |
970 | (substitute* "c++/src/util/compress/Makefile.in" |
971 | (("bzip2 zlib api") "api")) | |
972 | ;; Remove useless msbuild directory | |
973 | (delete-file-recursively | |
974 | "c++/src/build-system/project_tree_builder/msbuild") | |
975 | #t)))) | |
976 | (build-system gnu-build-system) | |
977 | (arguments | |
4732e6ee | 978 | `(;; There are two(!) tests for this massive library, and both fail with |
82c370de | 979 | ;; "unparsable timing stats". |
82c370de RW |
980 | ;; ERR [127] -- [serial/datatool] datatool.sh (unparsable timing stats) |
981 | ;; ERR [127] -- [serial/datatool] datatool_xml.sh (unparsable timing stats) | |
982 | #:tests? #f | |
983 | #:out-of-source? #t | |
984 | #:parallel-build? #f ; not supported | |
985 | #:phases | |
986 | (modify-phases %standard-phases | |
987 | (add-before | |
988 | 'configure 'set-HOME | |
989 | ;; $HOME needs to be set at some point during the configure phase | |
990 | (lambda _ (setenv "HOME" "/tmp") #t)) | |
991 | (add-after | |
992 | 'unpack 'enter-dir | |
993 | (lambda _ (chdir "c++") #t)) | |
994 | (add-after | |
995 | 'enter-dir 'fix-build-system | |
996 | (lambda _ | |
997 | (define (which* cmd) | |
998 | (cond ((string=? cmd "date") | |
999 | ;; make call to "date" deterministic | |
1000 | "date -d @0") | |
1001 | ((which cmd) | |
1002 | => identity) | |
1003 | (else | |
1004 | (format (current-error-port) | |
1005 | "WARNING: Unable to find absolute path for ~s~%" | |
1006 | cmd) | |
1007 | #f))) | |
1008 | ||
1009 | ;; Rewrite hardcoded paths to various tools | |
1010 | (substitute* (append '("src/build-system/configure.ac" | |
1011 | "src/build-system/configure" | |
4732e6ee | 1012 | "src/build-system/helpers/run_with_lock.c" |
82c370de RW |
1013 | "scripts/common/impl/if_diff.sh" |
1014 | "scripts/common/impl/run_with_lock.sh" | |
1015 | "src/build-system/Makefile.configurables.real" | |
1016 | "src/build-system/Makefile.in.top" | |
1017 | "src/build-system/Makefile.meta.gmake=no" | |
1018 | "src/build-system/Makefile.meta.in" | |
1019 | "src/build-system/Makefile.meta_l" | |
1020 | "src/build-system/Makefile.meta_p" | |
1021 | "src/build-system/Makefile.meta_r" | |
1022 | "src/build-system/Makefile.mk.in" | |
1023 | "src/build-system/Makefile.requirements" | |
1024 | "src/build-system/Makefile.rules_with_autodep.in") | |
1025 | (find-files "scripts/common/check" "\\.sh$")) | |
1026 | (("(/usr/bin/|/bin/)([a-z][-_.a-z]*)" all dir cmd) | |
1027 | (or (which* cmd) all))) | |
1028 | ||
1029 | (substitute* (find-files "src/build-system" "^config.*") | |
1030 | (("LN_S=/bin/\\$LN_S") (string-append "LN_S=" (which "ln"))) | |
1031 | (("^PATH=.*") "")) | |
1032 | ||
1033 | ;; rewrite "/var/tmp" in check script | |
1034 | (substitute* "scripts/common/check/check_make_unix.sh" | |
1035 | (("/var/tmp") "/tmp")) | |
1036 | ||
1037 | ;; do not reset PATH | |
1038 | (substitute* (find-files "scripts/common/impl/" "\\.sh$") | |
1039 | (("^ *PATH=.*") "") | |
1040 | (("action=/bin/") "action=") | |
1041 | (("export PATH") ":")) | |
1042 | #t)) | |
1043 | (replace | |
1044 | 'configure | |
1045 | (lambda* (#:key inputs outputs #:allow-other-keys) | |
1046 | (let ((out (assoc-ref outputs "out")) | |
1047 | (lib (string-append (assoc-ref outputs "lib") "/lib")) | |
1048 | (include (string-append (assoc-ref outputs "include") | |
1049 | "/include/ncbi-tools++"))) | |
1050 | ;; The 'configure' script doesn't recognize things like | |
1051 | ;; '--enable-fast-install'. | |
1052 | (zero? (system* "./configure.orig" | |
1053 | (string-append "--with-build-root=" (getcwd) "/build") | |
1054 | (string-append "--prefix=" out) | |
1055 | (string-append "--libdir=" lib) | |
1056 | (string-append "--includedir=" include) | |
1057 | (string-append "--with-bz2=" | |
1058 | (assoc-ref inputs "bzip2")) | |
1059 | (string-append "--with-z=" | |
1060 | (assoc-ref inputs "zlib")) | |
4732e6ee BW |
1061 | (string-append "--with-pcre=" |
1062 | (assoc-ref inputs "pcre")) | |
82c370de RW |
1063 | ;; Each library is built twice by default, once |
1064 | ;; with "-static" in its name, and again | |
1065 | ;; without. | |
1066 | "--without-static" | |
1067 | "--with-dll")))))))) | |
4732e6ee BW |
1068 | (outputs '("out" ; 21 MB |
1069 | "lib" ; 226 MB | |
1070 | "include")) ; 33 MB | |
82c370de RW |
1071 | (inputs |
1072 | `(("bzip2" ,bzip2) | |
4732e6ee BW |
1073 | ("zlib" ,zlib) |
1074 | ("pcre" ,pcre) | |
1075 | ("perl" ,perl) | |
1076 | ("python" ,python-wrapper))) | |
82c370de RW |
1077 | (native-inputs |
1078 | `(("cpio" ,cpio))) | |
1079 | (home-page "http://blast.ncbi.nlm.nih.gov") | |
1080 | (synopsis "Basic local alignment search tool") | |
1081 | (description | |
1082 | "BLAST is a popular method of performing a DNA or protein sequence | |
1083 | similarity search, using heuristics to produce results quickly. It also | |
1084 | calculates an “expect value” that estimates how many matches would have | |
1085 | occurred at a given score by chance, which can aid a user in judging how much | |
1086 | confidence to have in an alignment.") | |
1087 | ;; Most of the sources are in the public domain, with the following | |
1088 | ;; exceptions: | |
1089 | ;; * Expat: | |
1090 | ;; * ./c++/include/util/bitset/ | |
1091 | ;; * ./c++/src/html/ncbi_menu*.js | |
1092 | ;; * Boost license: | |
1093 | ;; * ./c++/include/util/impl/floating_point_comparison.hpp | |
1094 | ;; * LGPL 2+: | |
1095 | ;; * ./c++/include/dbapi/driver/odbc/unix_odbc/ | |
1096 | ;; * ASL 2.0: | |
1097 | ;; * ./c++/src/corelib/teamcity_* | |
1098 | (license (list license:public-domain | |
1099 | license:expat | |
1100 | license:boost1.0 | |
1101 | license:lgpl2.0+ | |
1102 | license:asl2.0)))) | |
1103 | ||
6c2b26e2 RW |
1104 | (define-public bless |
1105 | (package | |
1106 | (name "bless") | |
1107 | (version "1p02") | |
1108 | (source (origin | |
1109 | (method url-fetch) | |
1110 | (uri (string-append "mirror://sourceforge/bless-ec/bless.v" | |
1111 | version ".tgz")) | |
1112 | (sha256 | |
1113 | (base32 | |
4d75e03a RW |
1114 | "0rm0gw2s18dqwzzpl3c2x1z05ni2v0xz5dmfk3d33j6g4cgrlrdd")) |
1115 | (modules '((guix build utils))) | |
6c2b26e2 RW |
1116 | (snippet |
1117 | `(begin | |
1118 | ;; Remove bundled boost, pigz, zlib, and .git directory | |
953c1223 RW |
1119 | ;; FIXME: also remove bundled sources for murmurhash3 and |
1120 | ;; kmc once packaged. | |
6c2b26e2 RW |
1121 | (delete-file-recursively "boost") |
1122 | (delete-file-recursively "pigz") | |
953c1223 | 1123 | (delete-file-recursively "google-sparsehash") |
6c2b26e2 RW |
1124 | (delete-file-recursively "zlib") |
1125 | (delete-file-recursively ".git") | |
1126 | #t)))) | |
1127 | (build-system gnu-build-system) | |
1128 | (arguments | |
1129 | '(#:tests? #f ;no "check" target | |
1130 | #:make-flags | |
1131 | (list (string-append "ZLIB=" | |
1132 | (assoc-ref %build-inputs "zlib") | |
1133 | "/lib/libz.a") | |
1134 | (string-append "LDFLAGS=" | |
1135 | (string-join '("-lboost_filesystem" | |
1136 | "-lboost_system" | |
1137 | "-lboost_iostreams" | |
1138 | "-lz" | |
1139 | "-fopenmp" | |
1140 | "-std=c++11")))) | |
1141 | #:phases | |
1142 | (modify-phases %standard-phases | |
1143 | (add-after 'unpack 'do-not-build-bundled-pigz | |
1144 | (lambda* (#:key inputs outputs #:allow-other-keys) | |
1145 | (substitute* "Makefile" | |
1146 | (("cd pigz/pigz-2.3.3; make") "")) | |
1147 | #t)) | |
1148 | (add-after 'unpack 'patch-paths-to-executables | |
1149 | (lambda* (#:key inputs outputs #:allow-other-keys) | |
1150 | (substitute* "parse_args.cpp" | |
1151 | (("kmc_binary = .*") | |
1152 | (string-append "kmc_binary = \"" | |
1153 | (assoc-ref outputs "out") | |
1154 | "/bin/kmc\";")) | |
1155 | (("pigz_binary = .*") | |
1156 | (string-append "pigz_binary = \"" | |
1157 | (assoc-ref inputs "pigz") | |
1158 | "/bin/pigz\";"))) | |
1159 | #t)) | |
1160 | (replace 'install | |
1161 | (lambda* (#:key outputs #:allow-other-keys) | |
1162 | (let ((bin (string-append (assoc-ref outputs "out") "/bin/"))) | |
1163 | (for-each (lambda (file) | |
1164 | (install-file file bin)) | |
1165 | '("bless" "kmc/bin/kmc")) | |
1166 | #t))) | |
1167 | (delete 'configure)))) | |
1168 | (native-inputs | |
1169 | `(("perl" ,perl))) | |
1170 | (inputs | |
1171 | `(("openmpi" ,openmpi) | |
1172 | ("boost" ,boost) | |
953c1223 | 1173 | ("sparsehash" ,sparsehash) |
6c2b26e2 RW |
1174 | ("pigz" ,pigz) |
1175 | ("zlib" ,zlib))) | |
9641a899 | 1176 | (supported-systems '("x86_64-linux")) |
3b3b60d0 | 1177 | (home-page "https://sourceforge.net/p/bless-ec/wiki/Home/") |
6c2b26e2 RW |
1178 | (synopsis "Bloom-filter-based error correction tool for NGS reads") |
1179 | (description | |
1180 | "@dfn{Bloom-filter-based error correction solution for high-throughput | |
1181 | sequencing reads} (BLESS) uses a single minimum-sized bloom filter is a | |
1182 | correction tool for genomic reads produced by @dfn{Next-generation | |
1183 | sequencing} (NGS). BLESS produces accurate correction results with much less | |
1184 | memory compared with previous solutions and is also able to tolerate a higher | |
1185 | false-positive rate. BLESS can extend reads like DNA assemblers to correct | |
1186 | errors at the end of reads.") | |
1187 | (license license:gpl3+))) | |
1188 | ||
2c7ee167 RW |
1189 | (define-public bowtie |
1190 | (package | |
1191 | (name "bowtie") | |
d6e63cf3 | 1192 | (version "2.3.2") |
2c7ee167 RW |
1193 | (source (origin |
1194 | (method url-fetch) | |
1195 | (uri (string-append "https://github.com/BenLangmead/bowtie2/archive/v" | |
1196 | version ".tar.gz")) | |
f586c877 | 1197 | (file-name (string-append name "-" version ".tar.gz")) |
2c7ee167 RW |
1198 | (sha256 |
1199 | (base32 | |
d6e63cf3 | 1200 | "0hwa5r9qbglppb7sz5z79rlmmddr3n51n468jb3wh8rwjgn3yr90")) |
2c7ee167 RW |
1201 | (modules '((guix build utils))) |
1202 | (snippet | |
1203 | '(substitute* "Makefile" | |
2c7ee167 RW |
1204 | ;; replace BUILD_HOST and BUILD_TIME for deterministic build |
1205 | (("-DBUILD_HOST=.*") "-DBUILD_HOST=\"\\\"guix\\\"\"") | |
0047d26a | 1206 | (("-DBUILD_TIME=.*") "-DBUILD_TIME=\"\\\"0\\\"\""))))) |
2c7ee167 | 1207 | (build-system gnu-build-system) |
d6e63cf3 BW |
1208 | (inputs |
1209 | `(("perl" ,perl) | |
1210 | ("perl-clone" ,perl-clone) | |
1211 | ("perl-test-deep" ,perl-test-deep) | |
1212 | ("perl-test-simple" ,perl-test-simple) | |
1213 | ("python" ,python-2) | |
1214 | ("tbb" ,tbb) | |
1215 | ("zlib" ,zlib))) | |
2c7ee167 | 1216 | (arguments |
0047d26a RW |
1217 | '(#:make-flags |
1218 | (list "allall" | |
1219 | "WITH_TBB=1" | |
1220 | (string-append "prefix=" (assoc-ref %outputs "out"))) | |
2c7ee167 | 1221 | #:phases |
06e37236 BW |
1222 | (modify-phases %standard-phases |
1223 | (delete 'configure) | |
1224 | (replace 'check | |
1225 | (lambda* (#:key outputs #:allow-other-keys) | |
1226 | (zero? (system* "perl" | |
1227 | "scripts/test/simple_tests.pl" | |
1228 | "--bowtie2=./bowtie2" | |
1229 | "--bowtie2-build=./bowtie2-build"))))))) | |
2c7ee167 RW |
1230 | (home-page "http://bowtie-bio.sourceforge.net/bowtie2/index.shtml") |
1231 | (synopsis "Fast and sensitive nucleotide sequence read aligner") | |
1232 | (description | |
1233 | "Bowtie 2 is a fast and memory-efficient tool for aligning sequencing | |
1234 | reads to long reference sequences. It is particularly good at aligning reads | |
1235 | of about 50 up to 100s or 1,000s of characters, and particularly good at | |
1236 | aligning to relatively long (e.g. mammalian) genomes. Bowtie 2 indexes the | |
1237 | genome with an FM Index to keep its memory footprint small: for the human | |
1238 | genome, its memory footprint is typically around 3.2 GB. Bowtie 2 supports | |
1239 | gapped, local, and paired-end alignment modes.") | |
241e1221 | 1240 | (supported-systems '("x86_64-linux")) |
2c7ee167 RW |
1241 | (license license:gpl3+))) |
1242 | ||
94ce537e RW |
1243 | (define-public tophat |
1244 | (package | |
1245 | (name "tophat") | |
1246 | (version "2.1.0") | |
1247 | (source (origin | |
1248 | (method url-fetch) | |
1249 | (uri (string-append | |
1250 | "http://ccb.jhu.edu/software/tophat/downloads/tophat-" | |
1251 | version ".tar.gz")) | |
1252 | (sha256 | |
1253 | (base32 | |
1254 | "168zlzykq622zbgkh90a90f1bdgsxkscq2zxzbj8brq80hbjpyp7")) | |
fc1adab1 | 1255 | (patches (search-patches "tophat-build-with-later-seqan.patch")) |
94ce537e RW |
1256 | (modules '((guix build utils))) |
1257 | (snippet | |
1258 | '(begin | |
1259 | ;; Remove bundled SeqAn and samtools | |
1260 | (delete-file-recursively "src/SeqAn-1.3") | |
1261 | (delete-file-recursively "src/samtools-0.1.18") | |
1262 | #t)))) | |
1263 | (build-system gnu-build-system) | |
1264 | (arguments | |
1265 | '(#:parallel-build? #f ; not supported | |
1266 | #:phases | |
1267 | (modify-phases %standard-phases | |
1268 | (add-after 'unpack 'use-system-samtools | |
1269 | (lambda* (#:key inputs #:allow-other-keys) | |
1270 | (substitute* "src/Makefile.in" | |
1271 | (("(noinst_LIBRARIES = )\\$\\(SAMLIB\\)" _ prefix) prefix) | |
1272 | (("\\$\\(SAMPROG\\): \\$\\(SAMLIB\\)") "") | |
1273 | (("SAMPROG = samtools_0\\.1\\.18") "") | |
1274 | (("\\$\\(samtools_0_1_18_SOURCES\\)") "") | |
1275 | (("am__EXEEXT_1 = samtools_0\\.1\\.18\\$\\(EXEEXT\\)") "")) | |
1276 | (substitute* '("src/common.cpp" | |
1277 | "src/tophat.py") | |
1278 | (("samtools_0.1.18") (which "samtools"))) | |
1279 | (substitute* '("src/common.h" | |
1280 | "src/bam2fastx.cpp") | |
1281 | (("#include \"bam.h\"") "#include <samtools/bam.h>") | |
1282 | (("#include \"sam.h\"") "#include <samtools/sam.h>")) | |
1283 | (substitute* '("src/bwt_map.h" | |
1284 | "src/map2gtf.h" | |
1285 | "src/align_status.h") | |
1286 | (("#include <bam.h>") "#include <samtools/bam.h>") | |
1287 | (("#include <sam.h>") "#include <samtools/sam.h>")) | |
1288 | #t))))) | |
1289 | (inputs | |
1290 | `(("boost" ,boost) | |
1291 | ("bowtie" ,bowtie) | |
1292 | ("samtools" ,samtools-0.1) | |
1293 | ("ncurses" ,ncurses) | |
1294 | ("python" ,python-2) | |
1295 | ("perl" ,perl) | |
1296 | ("zlib" ,zlib) | |
1297 | ("seqan" ,seqan))) | |
1298 | (home-page "http://ccb.jhu.edu/software/tophat/index.shtml") | |
1299 | (synopsis "Spliced read mapper for RNA-Seq data") | |
1300 | (description | |
1301 | "TopHat is a fast splice junction mapper for nucleotide sequence | |
1302 | reads produced by the RNA-Seq method. It aligns RNA-Seq reads to | |
1303 | mammalian-sized genomes using the ultra high-throughput short read | |
1304 | aligner Bowtie, and then analyzes the mapping results to identify | |
1305 | splice junctions between exons.") | |
1306 | ;; TopHat is released under the Boost Software License, Version 1.0 | |
1307 | ;; See https://github.com/infphilo/tophat/issues/11#issuecomment-121589893 | |
1308 | (license license:boost1.0))) | |
1309 | ||
9a8336d8 RW |
1310 | (define-public bwa |
1311 | (package | |
1312 | (name "bwa") | |
fd99d95b | 1313 | (version "0.7.15") |
9a8336d8 RW |
1314 | (source (origin |
1315 | (method url-fetch) | |
1316 | (uri (string-append "mirror://sourceforge/bio-bwa/bwa-" | |
1317 | version ".tar.bz2")) | |
1318 | (sha256 | |
1319 | (base32 | |
fd99d95b | 1320 | "0585ikg0gv0mpyw9iq0bq9n0hr95867bbv8jbzs9pk4slkpsymig")))) |
9a8336d8 RW |
1321 | (build-system gnu-build-system) |
1322 | (arguments | |
1323 | '(#:tests? #f ;no "check" target | |
1324 | #:phases | |
1325 | (alist-replace | |
1326 | 'install | |
1327 | (lambda* (#:key outputs #:allow-other-keys) | |
1328 | (let ((bin (string-append | |
1329 | (assoc-ref outputs "out") "/bin")) | |
1330 | (doc (string-append | |
1331 | (assoc-ref outputs "out") "/share/doc/bwa")) | |
1332 | (man (string-append | |
1333 | (assoc-ref outputs "out") "/share/man/man1"))) | |
96c46210 LC |
1334 | (install-file "bwa" bin) |
1335 | (install-file "README.md" doc) | |
1336 | (install-file "bwa.1" man))) | |
9a8336d8 RW |
1337 | ;; no "configure" script |
1338 | (alist-delete 'configure %standard-phases)))) | |
1339 | (inputs `(("zlib" ,zlib))) | |
db94f8c7 RW |
1340 | ;; Non-portable SSE instructions are used so building fails on platforms |
1341 | ;; other than x86_64. | |
1342 | (supported-systems '("x86_64-linux")) | |
9a8336d8 RW |
1343 | (home-page "http://bio-bwa.sourceforge.net/") |
1344 | (synopsis "Burrows-Wheeler sequence aligner") | |
1345 | (description | |
1346 | "BWA is a software package for mapping low-divergent sequences against a | |
1347 | large reference genome, such as the human genome. It consists of three | |
1348 | algorithms: BWA-backtrack, BWA-SW and BWA-MEM. The first algorithm is | |
1349 | designed for Illumina sequence reads up to 100bp, while the rest two for | |
1350 | longer sequences ranged from 70bp to 1Mbp. BWA-MEM and BWA-SW share similar | |
1351 | features such as long-read support and split alignment, but BWA-MEM, which is | |
1352 | the latest, is generally recommended for high-quality queries as it is faster | |
1353 | and more accurate. BWA-MEM also has better performance than BWA-backtrack for | |
1354 | 70-100bp Illumina reads.") | |
1355 | (license license:gpl3+))) | |
1356 | ||
d29150b5 RW |
1357 | (define-public bwa-pssm |
1358 | (package (inherit bwa) | |
1359 | (name "bwa-pssm") | |
1360 | (version "0.5.11") | |
1361 | (source (origin | |
1362 | (method url-fetch) | |
1363 | (uri (string-append "https://github.com/pkerpedjiev/bwa-pssm/" | |
1364 | "archive/" version ".tar.gz")) | |
1365 | (file-name (string-append name "-" version ".tar.gz")) | |
1366 | (sha256 | |
1367 | (base32 | |
1368 | "02p7mpbs4mlxmn84g2x4ghak638vbj4lqix2ipx5g84pz9bhdavg")))) | |
1369 | (build-system gnu-build-system) | |
1370 | (inputs | |
1371 | `(("gdsl" ,gdsl) | |
1372 | ("zlib" ,zlib) | |
1373 | ("perl" ,perl))) | |
1374 | (home-page "http://bwa-pssm.binf.ku.dk/") | |
1375 | (synopsis "Burrows-Wheeler transform-based probabilistic short read mapper") | |
1376 | (description | |
1377 | "BWA-PSSM is a probabilistic short genomic sequence read aligner based on | |
1378 | the use of @dfn{position specific scoring matrices} (PSSM). Like many of the | |
1379 | existing aligners it is fast and sensitive. Unlike most other aligners, | |
1380 | however, it is also adaptible in the sense that one can direct the alignment | |
1381 | based on known biases within the data set. It is coded as a modification of | |
1382 | the original BWA alignment program and shares the genome index structure as | |
1383 | well as many of the command line options.") | |
1384 | (license license:gpl3+))) | |
1385 | ||
ad641d53 RW |
1386 | (define-public python2-bx-python |
1387 | (package | |
1388 | (name "python2-bx-python") | |
c1dfe8c3 | 1389 | (version "0.7.3") |
ad641d53 RW |
1390 | (source (origin |
1391 | (method url-fetch) | |
c1dfe8c3 | 1392 | (uri (pypi-uri "bx-python" version)) |
ad641d53 RW |
1393 | (sha256 |
1394 | (base32 | |
c1dfe8c3 | 1395 | "15z2w3bvnc0n4qmb9bd6d8ylc2h2nj883x2w9iixf4x3vki9b22i")) |
ad641d53 RW |
1396 | (modules '((guix build utils))) |
1397 | (snippet | |
1398 | '(substitute* "setup.py" | |
1399 | ;; remove dependency on outdated "distribute" module | |
1400 | (("^from distribute_setup import use_setuptools") "") | |
1401 | (("^use_setuptools\\(\\)") ""))))) | |
1402 | (build-system python-build-system) | |
1403 | (arguments | |
1404 | `(#:tests? #f ;tests fail because test data are not included | |
1405 | #:python ,python-2)) | |
1406 | (inputs | |
1407 | `(("python-numpy" ,python2-numpy) | |
1408 | ("zlib" ,zlib))) | |
1409 | (native-inputs | |
f3b98f4f | 1410 | `(("python-nose" ,python2-nose))) |
ad641d53 RW |
1411 | (home-page "http://bitbucket.org/james_taylor/bx-python/") |
1412 | (synopsis "Tools for manipulating biological data") | |
1413 | (description | |
1414 | "bx-python provides tools for manipulating biological data, particularly | |
1415 | multiple sequence alignments.") | |
1416 | (license license:expat))) | |
1417 | ||
55a9a8c2 RW |
1418 | (define-public python-pysam |
1419 | (package | |
1420 | (name "python-pysam") | |
60739965 | 1421 | (version "0.11.2.2") |
d454640c RW |
1422 | (source (origin |
1423 | (method url-fetch) | |
f536dce5 MB |
1424 | ;; Test data is missing on PyPi. |
1425 | (uri (string-append | |
1426 | "https://github.com/pysam-developers/pysam/archive/v" | |
1427 | version ".tar.gz")) | |
1428 | (file-name (string-append name "-" version ".tar.gz")) | |
d454640c RW |
1429 | (sha256 |
1430 | (base32 | |
60739965 | 1431 | "1cfqdxsqs3xhacns9n0271ck6wkc76px66ddjm91wfw2jxxfklvc")) |
dff26b23 MB |
1432 | (modules '((guix build utils))) |
1433 | (snippet | |
1434 | ;; Drop bundled htslib. TODO: Also remove samtools and bcftools. | |
1435 | '(delete-file-recursively "htslib")))) | |
55a9a8c2 RW |
1436 | (build-system python-build-system) |
1437 | (arguments | |
71dbf592 RW |
1438 | `(#:modules ((ice-9 ftw) |
1439 | (srfi srfi-26) | |
1440 | (guix build python-build-system) | |
1441 | (guix build utils)) | |
1442 | #:phases | |
397d463a MB |
1443 | (modify-phases %standard-phases |
1444 | (add-before 'build 'set-flags | |
dff26b23 MB |
1445 | (lambda* (#:key inputs #:allow-other-keys) |
1446 | (setenv "HTSLIB_MODE" "external") | |
1447 | (setenv "HTSLIB_LIBRARY_DIR" | |
1448 | (string-append (assoc-ref inputs "htslib") "/lib")) | |
1449 | (setenv "HTSLIB_INCLUDE_DIR" | |
1450 | (string-append (assoc-ref inputs "htslib") "/include")) | |
397d463a MB |
1451 | (setenv "LDFLAGS" "-lncurses") |
1452 | (setenv "CFLAGS" "-D_CURSES_LIB=1") | |
f536dce5 | 1453 | #t)) |
71dbf592 | 1454 | (replace 'check |
f536dce5 | 1455 | (lambda* (#:key inputs outputs #:allow-other-keys) |
71dbf592 | 1456 | ;; Add first subdirectory of "build" directory to PYTHONPATH. |
f536dce5 MB |
1457 | (setenv "PYTHONPATH" |
1458 | (string-append | |
1459 | (getenv "PYTHONPATH") | |
71dbf592 RW |
1460 | ":" (getcwd) "/build/" |
1461 | (car (scandir "build" | |
e1f02f92 | 1462 | (negate (cut string-prefix? "." <>)))))) |
f536dce5 | 1463 | ;; Step out of source dir so python does not import from CWD. |
71dbf592 RW |
1464 | (with-directory-excursion "tests" |
1465 | (setenv "HOME" "/tmp") | |
1466 | (and (zero? (system* "make" "-C" "pysam_data")) | |
1467 | (zero? (system* "make" "-C" "cbcf_data")) | |
b2955e22 RW |
1468 | ;; Running nosetests without explicitly asking for a |
1469 | ;; single process leads to a crash. Running with multiple | |
1470 | ;; processes fails because the tests are not designed to | |
1471 | ;; run in parallel. | |
31c374e0 RW |
1472 | |
1473 | ;; FIXME: tests keep timing out on some systems. | |
1474 | ;; (zero? (system* "nosetests" "-v" | |
1475 | ;; "--processes" "1")) | |
1476 | ))))))) | |
dff26b23 MB |
1477 | (propagated-inputs |
1478 | `(("htslib" ,htslib))) ; Included from installed header files. | |
55a9a8c2 | 1479 | (inputs |
649e9b3b | 1480 | `(("ncurses" ,ncurses) |
55a9a8c2 | 1481 | ("zlib" ,zlib))) |
649e9b3b RW |
1482 | (native-inputs |
1483 | `(("python-cython" ,python-cython) | |
f536dce5 MB |
1484 | ;; Dependencies below are are for tests only. |
1485 | ("samtools" ,samtools) | |
1486 | ("bcftools" ,bcftools) | |
1487 | ("python-nose" ,python-nose))) | |
55a9a8c2 RW |
1488 | (home-page "https://github.com/pysam-developers/pysam") |
1489 | (synopsis "Python bindings to the SAMtools C API") | |
1490 | (description | |
1491 | "Pysam is a Python module for reading and manipulating files in the | |
1492 | SAM/BAM format. Pysam is a lightweight wrapper of the SAMtools C API. It | |
1493 | also includes an interface for tabix.") | |
1494 | (license license:expat))) | |
1495 | ||
1496 | (define-public python2-pysam | |
1497 | (package-with-python2 python-pysam)) | |
1498 | ||
4db9433a RW |
1499 | (define-public python-twobitreader |
1500 | (package | |
1501 | (name "python-twobitreader") | |
044ac8d2 | 1502 | (version "3.1.4") |
4db9433a RW |
1503 | (source (origin |
1504 | (method url-fetch) | |
1505 | (uri (pypi-uri "twobitreader" version)) | |
1506 | (sha256 | |
1507 | (base32 | |
044ac8d2 | 1508 | "1q8wnj2kga9nz1lwc4w7qv52smfm536hp6mc8w6s53lhyj0mpi22")))) |
4db9433a | 1509 | (build-system python-build-system) |
900fb8d0 LF |
1510 | (arguments |
1511 | '(;; Tests are not distributed in the PyPi release. | |
1512 | ;; TODO Try building from the Git repo or asking the upstream maintainer | |
1513 | ;; to distribute the tests on PyPi. | |
1514 | #:tests? #f)) | |
4db9433a RW |
1515 | (native-inputs |
1516 | `(("python-sphinx" ,python-sphinx))) | |
1517 | (home-page "https://github.com/benjschiller/twobitreader") | |
1518 | (synopsis "Python library for reading .2bit files") | |
1519 | (description | |
1520 | "twobitreader is a Python library for reading .2bit files as used by the | |
1521 | UCSC genome browser.") | |
1522 | (license license:artistic2.0))) | |
1523 | ||
1524 | (define-public python2-twobitreader | |
5c31f4aa | 1525 | (package-with-python2 python-twobitreader)) |
4db9433a | 1526 | |
f94bf198 RW |
1527 | (define-public python-plastid |
1528 | (package | |
1529 | (name "python-plastid") | |
897ab082 | 1530 | (version "0.4.8") |
f94bf198 RW |
1531 | (source (origin |
1532 | (method url-fetch) | |
1533 | (uri (pypi-uri "plastid" version)) | |
1534 | (sha256 | |
1535 | (base32 | |
897ab082 | 1536 | "0l24dd3q66if8yj042m4s0g95n6acn7im1imqd3p6h8ns43kxhj8")))) |
f94bf198 RW |
1537 | (build-system python-build-system) |
1538 | (arguments | |
1539 | ;; Some test files are not included. | |
1540 | `(#:tests? #f)) | |
1541 | (propagated-inputs | |
1542 | `(("python-numpy" ,python-numpy) | |
1543 | ("python-scipy" ,python-scipy) | |
1544 | ("python-pandas" ,python-pandas) | |
1545 | ("python-pysam" ,python-pysam) | |
1546 | ("python-matplotlib" ,python-matplotlib) | |
1547 | ("python-biopython" ,python-biopython) | |
99caa6f7 BW |
1548 | ("python-twobitreader" ,python-twobitreader) |
1549 | ("python-termcolor" ,python-termcolor))) | |
f94bf198 RW |
1550 | (native-inputs |
1551 | `(("python-cython" ,python-cython) | |
1552 | ("python-nose" ,python-nose))) | |
1553 | (home-page "https://github.com/joshuagryphon/plastid") | |
1554 | (synopsis "Python library for genomic analysis") | |
1555 | (description | |
1556 | "plastid is a Python library for genomic analysis – in particular, | |
1557 | high-throughput sequencing data – with an emphasis on simplicity.") | |
1558 | (license license:bsd-3))) | |
1559 | ||
1560 | (define-public python2-plastid | |
5c31f4aa | 1561 | (package-with-python2 python-plastid)) |
f94bf198 | 1562 | |
6c1305f9 RW |
1563 | (define-public cd-hit |
1564 | (package | |
1565 | (name "cd-hit") | |
ba773f65 | 1566 | (version "4.6.8") |
6c1305f9 RW |
1567 | (source (origin |
1568 | (method url-fetch) | |
1569 | (uri (string-append "https://github.com/weizhongli/cdhit" | |
1570 | "/releases/download/V" version | |
ba773f65 BW |
1571 | "/cd-hit-v" version |
1572 | "-2017-0621-source.tar.gz")) | |
6c1305f9 RW |
1573 | (sha256 |
1574 | (base32 | |
ba773f65 | 1575 | "1386dg2npx8p62wmv08mjzsd2z3waknb9j1gg3gkvblcy57hymnn")))) |
6c1305f9 RW |
1576 | (build-system gnu-build-system) |
1577 | (arguments | |
1578 | `(#:tests? #f ; there are no tests | |
1579 | #:make-flags | |
1580 | ;; Executables are copied directly to the PREFIX. | |
1581 | (list (string-append "PREFIX=" (assoc-ref %outputs "out") "/bin")) | |
1582 | #:phases | |
1583 | (modify-phases %standard-phases | |
1584 | ;; No "configure" script | |
1585 | (delete 'configure) | |
1586 | ;; Remove sources of non-determinism | |
1587 | (add-after 'unpack 'be-timeless | |
1588 | (lambda _ | |
1589 | (substitute* "cdhit-utility.c++" | |
1590 | ((" \\(built on \" __DATE__ \"\\)") "")) | |
1591 | (substitute* "cdhit-common.c++" | |
1592 | (("__DATE__") "\"0\"") | |
1593 | (("\", %s, \" __TIME__ \"\\\\n\", date") "")) | |
1594 | #t)) | |
ba773f65 | 1595 | ;; The "install" target does not create the target directory. |
6c1305f9 RW |
1596 | (add-before 'install 'create-target-dir |
1597 | (lambda* (#:key outputs #:allow-other-keys) | |
1598 | (mkdir-p (string-append (assoc-ref outputs "out") "/bin")) | |
1599 | #t))))) | |
1600 | (inputs | |
1601 | `(("perl" ,perl))) | |
1602 | (home-page "http://weizhongli-lab.org/cd-hit/") | |
1603 | (synopsis "Cluster and compare protein or nucleotide sequences") | |
1604 | (description | |
1605 | "CD-HIT is a program for clustering and comparing protein or nucleotide | |
1606 | sequences. CD-HIT is designed to be fast and handle extremely large | |
1607 | databases.") | |
1608 | ;; The manual says: "It can be copied under the GNU General Public License | |
1609 | ;; version 2 (GPLv2)." | |
1610 | (license license:gpl2))) | |
1611 | ||
810cff85 RW |
1612 | (define-public clipper |
1613 | (package | |
1614 | (name "clipper") | |
433530a5 | 1615 | (version "1.1") |
810cff85 RW |
1616 | (source (origin |
1617 | (method url-fetch) | |
1618 | (uri (string-append | |
1619 | "https://github.com/YeoLab/clipper/archive/" | |
1620 | version ".tar.gz")) | |
9ab5ea44 | 1621 | (file-name (string-append name "-" version ".tar.gz")) |
810cff85 RW |
1622 | (sha256 |
1623 | (base32 | |
433530a5 | 1624 | "0pflmsvhbf8izbgwhbhj1i7349sw1f55qpqj8ljmapp16hb0p0qi")) |
810cff85 RW |
1625 | (modules '((guix build utils))) |
1626 | (snippet | |
433530a5 RW |
1627 | '(begin |
1628 | ;; remove unnecessary setup dependency | |
1629 | (substitute* "setup.py" | |
1630 | (("setup_requires = .*") "")) | |
1631 | (for-each delete-file | |
1632 | '("clipper/src/peaks.so" | |
1633 | "clipper/src/readsToWiggle.so")) | |
1634 | (delete-file-recursively "dist/") | |
1635 | #t)))) | |
810cff85 RW |
1636 | (build-system python-build-system) |
1637 | (arguments `(#:python ,python-2)) ; only Python 2 is supported | |
1638 | (inputs | |
1639 | `(("htseq" ,htseq) | |
1640 | ("python-pybedtools" ,python2-pybedtools) | |
1641 | ("python-cython" ,python2-cython) | |
1642 | ("python-scikit-learn" ,python2-scikit-learn) | |
1643 | ("python-matplotlib" ,python2-matplotlib) | |
433530a5 | 1644 | ("python-pandas" ,python2-pandas) |
810cff85 RW |
1645 | ("python-pysam" ,python2-pysam) |
1646 | ("python-numpy" ,python2-numpy) | |
1647 | ("python-scipy" ,python2-scipy))) | |
1648 | (native-inputs | |
f3b98f4f | 1649 | `(("python-mock" ,python2-mock) ; for tests |
d281be18 | 1650 | ("python-nose" ,python2-nose) ; for tests |
f3b98f4f | 1651 | ("python-pytz" ,python2-pytz))) ; for tests |
810cff85 RW |
1652 | (home-page "https://github.com/YeoLab/clipper") |
1653 | (synopsis "CLIP peak enrichment recognition") | |
1654 | (description | |
1655 | "CLIPper is a tool to define peaks in CLIP-seq datasets.") | |
1656 | (license license:gpl2))) | |
1657 | ||
6a35566d RS |
1658 | (define-public codingquarry |
1659 | (package | |
1660 | (name "codingquarry") | |
1661 | (version "2.0") | |
1662 | (source (origin | |
1663 | (method url-fetch) | |
1664 | (uri (string-append | |
1665 | "mirror://sourceforge/codingquarry/CodingQuarry_v" | |
1666 | version ".tar.gz")) | |
1667 | (sha256 | |
1668 | (base32 | |
1669 | "0115hkjflsnfzn36xppwf9h9avfxlavr43djqmshkkzbgjzsz60i")))) | |
1670 | (build-system gnu-build-system) | |
1671 | (arguments | |
1672 | '(#:tests? #f ; no "check" target | |
1673 | #:phases | |
1674 | (modify-phases %standard-phases | |
1675 | (delete 'configure) | |
1676 | (replace 'install | |
1677 | (lambda* (#:key outputs #:allow-other-keys) | |
1678 | (let* ((out (assoc-ref outputs "out")) | |
1679 | (bin (string-append out "/bin")) | |
1680 | (doc (string-append out "/share/doc/codingquarry"))) | |
1681 | (install-file "INSTRUCTIONS.pdf" doc) | |
1682 | (copy-recursively "QuarryFiles" | |
1683 | (string-append out "/QuarryFiles")) | |
1684 | (install-file "CodingQuarry" bin) | |
1685 | (install-file "CufflinksGTF_to_CodingQuarryGFF3.py" bin))))))) | |
1686 | (inputs `(("openmpi" ,openmpi))) | |
1687 | (native-search-paths | |
1688 | (list (search-path-specification | |
1689 | (variable "QUARRY_PATH") | |
1690 | (files '("QuarryFiles"))))) | |
1691 | (native-inputs `(("python" ,python-2))) ; Only Python 2 is supported | |
1692 | (synopsis "Fungal gene predictor") | |
1693 | (description "CodingQuarry is a highly accurate, self-training GHMM fungal | |
1694 | gene predictor designed to work with assembled, aligned RNA-seq transcripts.") | |
1695 | (home-page "https://sourceforge.net/projects/codingquarry/") | |
1696 | (license license:gpl3+))) | |
1697 | ||
36742f43 RW |
1698 | (define-public couger |
1699 | (package | |
1700 | (name "couger") | |
1701 | (version "1.8.2") | |
1702 | (source (origin | |
1703 | (method url-fetch) | |
1704 | (uri (string-append | |
1705 | "http://couger.oit.duke.edu/static/assets/COUGER" | |
1706 | version ".zip")) | |
1707 | (sha256 | |
1708 | (base32 | |
1709 | "04p2b14nmhzxw5h72mpzdhalv21bx4w9b87z0wpw0xzxpysyncmq")))) | |
1710 | (build-system gnu-build-system) | |
1711 | (arguments | |
1712 | `(#:tests? #f | |
1713 | #:phases | |
1714 | (modify-phases %standard-phases | |
1715 | (delete 'configure) | |
1716 | (delete 'build) | |
1717 | (replace | |
1718 | 'install | |
1719 | (lambda* (#:key outputs #:allow-other-keys) | |
f3860753 TGR |
1720 | (let* ((out (assoc-ref outputs "out")) |
1721 | (bin (string-append out "/bin"))) | |
36742f43 | 1722 | (copy-recursively "src" (string-append out "/src")) |
f3860753 | 1723 | (mkdir bin) |
36742f43 RW |
1724 | ;; Add "src" directory to module lookup path. |
1725 | (substitute* "couger" | |
1726 | (("from argparse") | |
1727 | (string-append "import sys\nsys.path.append(\"" | |
1728 | out "\")\nfrom argparse"))) | |
f3860753 | 1729 | (install-file "couger" bin)) |
36742f43 RW |
1730 | #t)) |
1731 | (add-after | |
1732 | 'install 'wrap-program | |
1733 | (lambda* (#:key inputs outputs #:allow-other-keys) | |
1734 | ;; Make sure 'couger' runs with the correct PYTHONPATH. | |
1735 | (let* ((out (assoc-ref outputs "out")) | |
1736 | (path (getenv "PYTHONPATH"))) | |
1737 | (wrap-program (string-append out "/bin/couger") | |
1738 | `("PYTHONPATH" ":" prefix (,path)))) | |
1739 | #t))))) | |
1740 | (inputs | |
1741 | `(("python" ,python-2) | |
1742 | ("python2-pillow" ,python2-pillow) | |
1743 | ("python2-numpy" ,python2-numpy) | |
1744 | ("python2-scipy" ,python2-scipy) | |
1745 | ("python2-matplotlib" ,python2-matplotlib))) | |
1746 | (propagated-inputs | |
2d7c4ae3 | 1747 | `(("r-minimal" ,r-minimal) |
36742f43 RW |
1748 | ("libsvm" ,libsvm) |
1749 | ("randomjungle" ,randomjungle))) | |
1750 | (native-inputs | |
1751 | `(("unzip" ,unzip))) | |
1752 | (home-page "http://couger.oit.duke.edu") | |
1753 | (synopsis "Identify co-factors in sets of genomic regions") | |
1754 | (description | |
1755 | "COUGER can be applied to any two sets of genomic regions bound by | |
1756 | paralogous TFs (e.g., regions derived from ChIP-seq experiments) to identify | |
1757 | putative co-factors that provide specificity to each TF. The framework | |
1758 | determines the genomic targets uniquely-bound by each TF, and identifies a | |
1759 | small set of co-factors that best explain the in vivo binding differences | |
1760 | between the two TFs. | |
1761 | ||
1762 | COUGER uses classification algorithms (support vector machines and random | |
1763 | forests) with features that reflect the DNA binding specificities of putative | |
1764 | co-factors. The features are generated either from high-throughput TF-DNA | |
1765 | binding data (from protein binding microarray experiments), or from large | |
1766 | collections of DNA motifs.") | |
1767 | (license license:gpl3+))) | |
1768 | ||
bfe3c685 RW |
1769 | (define-public clustal-omega |
1770 | (package | |
1771 | (name "clustal-omega") | |
1772 | (version "1.2.1") | |
1773 | (source (origin | |
1774 | (method url-fetch) | |
1775 | (uri (string-append | |
1776 | "http://www.clustal.org/omega/clustal-omega-" | |
1777 | version ".tar.gz")) | |
1778 | (sha256 | |
1779 | (base32 | |
1780 | "02ibkx0m0iwz8nscg998bh41gg251y56cgh86bvyrii5m8kjgwqf")))) | |
1781 | (build-system gnu-build-system) | |
1782 | (inputs | |
1783 | `(("argtable" ,argtable))) | |
1784 | (home-page "http://www.clustal.org/omega/") | |
1785 | (synopsis "Multiple sequence aligner for protein and DNA/RNA") | |
1786 | (description | |
1787 | "Clustal-Omega is a general purpose multiple sequence alignment (MSA) | |
1788 | program for protein and DNA/RNA. It produces high quality MSAs and is capable | |
1789 | of handling data-sets of hundreds of thousands of sequences in reasonable | |
1790 | time.") | |
1791 | (license license:gpl2+))) | |
1792 | ||
191c7101 RW |
1793 | (define-public crossmap |
1794 | (package | |
1795 | (name "crossmap") | |
61d5fd03 | 1796 | (version "0.2.1") |
191c7101 RW |
1797 | (source (origin |
1798 | (method url-fetch) | |
1799 | (uri (string-append "mirror://sourceforge/crossmap/CrossMap-" | |
1800 | version ".tar.gz")) | |
1801 | (sha256 | |
1802 | (base32 | |
61d5fd03 RW |
1803 | "07y179f63d7qnzdvkqcziwk9bs3k4zhp81q392fp1hwszjdvy22f")) |
1804 | ;; This patch has been sent upstream already and is available | |
1805 | ;; for download from Sourceforge, but it has not been merged. | |
fc1adab1 | 1806 | (patches (search-patches "crossmap-allow-system-pysam.patch")) |
191c7101 RW |
1807 | (modules '((guix build utils))) |
1808 | ;; remove bundled copy of pysam | |
1809 | (snippet | |
1810 | '(delete-file-recursively "lib/pysam")))) | |
1811 | (build-system python-build-system) | |
1812 | (arguments | |
1813 | `(#:python ,python-2 | |
1814 | #:phases | |
1815 | (alist-cons-after | |
1816 | 'unpack 'set-env | |
1817 | (lambda _ (setenv "CROSSMAP_USE_SYSTEM_PYSAM" "1")) | |
1818 | %standard-phases))) | |
1819 | (inputs | |
1820 | `(("python-numpy" ,python2-numpy) | |
1821 | ("python-pysam" ,python2-pysam) | |
1822 | ("zlib" ,zlib))) | |
1823 | (native-inputs | |
1824 | `(("python-cython" ,python2-cython) | |
f3b98f4f | 1825 | ("python-nose" ,python2-nose))) |
191c7101 RW |
1826 | (home-page "http://crossmap.sourceforge.net/") |
1827 | (synopsis "Convert genome coordinates between assemblies") | |
1828 | (description | |
1829 | "CrossMap is a program for conversion of genome coordinates or annotation | |
1830 | files between different genome assemblies. It supports most commonly used | |
1831 | file formats including SAM/BAM, Wiggle/BigWig, BED, GFF/GTF, VCF.") | |
1832 | (license license:gpl2+))) | |
1833 | ||
3a40a92c RW |
1834 | (define-public cufflinks |
1835 | (package | |
1836 | (name "cufflinks") | |
1837 | (version "2.2.1") | |
1838 | (source (origin | |
1839 | (method url-fetch) | |
1840 | (uri (string-append "http://cole-trapnell-lab.github.io/" | |
1841 | "cufflinks/assets/downloads/cufflinks-" | |
1842 | version ".tar.gz")) | |
1843 | (sha256 | |
1844 | (base32 | |
1845 | "1bnm10p8m7zq4qiipjhjqb24csiqdm1pwc8c795z253r2xk6ncg8")))) | |
1846 | (build-system gnu-build-system) | |
1847 | (arguments | |
1848 | `(#:make-flags | |
1849 | (list | |
1850 | ;; The includes for "eigen" are located in a subdirectory. | |
1851 | (string-append "EIGEN_CPPFLAGS=" | |
1852 | "-I" (assoc-ref %build-inputs "eigen") | |
1853 | "/include/eigen3/") | |
1854 | ;; Cufflinks must be linked with various boost libraries. | |
1855 | (string-append "LDFLAGS=" | |
1856 | (string-join '("-lboost_system" | |
1857 | "-lboost_serialization" | |
1858 | "-lboost_thread")))) | |
1859 | #:phases | |
1860 | (modify-phases %standard-phases | |
1861 | (add-after 'unpack 'fix-search-for-bam | |
1862 | (lambda _ | |
1863 | (substitute* '("ax_bam.m4" | |
1864 | "configure" | |
1865 | "src/hits.h") | |
1866 | (("<bam/sam\\.h>") "<samtools/sam.h>") | |
1867 | (("<bam/bam\\.h>") "<samtools/bam.h>") | |
1868 | (("<bam/version\\.hpp>") "<samtools/version.h>")) | |
1869 | #t))) | |
1870 | #:configure-flags | |
1871 | (list (string-append "--with-bam=" | |
1872 | (assoc-ref %build-inputs "samtools"))))) | |
1873 | (inputs | |
1874 | `(("eigen" ,eigen) | |
1875 | ("samtools" ,samtools-0.1) | |
1876 | ("htslib" ,htslib) | |
1877 | ("boost" ,boost) | |
1878 | ("python" ,python-2) | |
1879 | ("zlib" ,zlib))) | |
1880 | (home-page "http://cole-trapnell-lab.github.io/cufflinks/") | |
1881 | (synopsis "Transcriptome assembly and RNA-Seq expression analysis") | |
1882 | (description | |
1883 | "Cufflinks assembles RNA transcripts, estimates their abundances, | |
1884 | and tests for differential expression and regulation in RNA-Seq | |
1885 | samples. It accepts aligned RNA-Seq reads and assembles the | |
1886 | alignments into a parsimonious set of transcripts. Cufflinks then | |
1887 | estimates the relative abundances of these transcripts based on how | |
1888 | many reads support each one, taking into account biases in library | |
1889 | preparation protocols.") | |
1890 | (license license:boost1.0))) | |
1891 | ||
8e913213 RW |
1892 | (define-public cutadapt |
1893 | (package | |
1894 | (name "cutadapt") | |
1f94bff2 | 1895 | (version "1.12") |
8e913213 RW |
1896 | (source (origin |
1897 | (method url-fetch) | |
1898 | (uri (string-append | |
1899 | "https://github.com/marcelm/cutadapt/archive/v" | |
1900 | version ".tar.gz")) | |
1901 | (file-name (string-append name "-" version ".tar.gz")) | |
1902 | (sha256 | |
1903 | (base32 | |
1f94bff2 | 1904 | "19smhh6444ikn4jlmyhvffw4m5aw7yg07rqsk7arg8dkwyga1i4v")))) |
8e913213 RW |
1905 | (build-system python-build-system) |
1906 | (arguments | |
33d5b246 TGR |
1907 | `(#:phases |
1908 | (modify-phases %standard-phases | |
1909 | ;; The tests must be run after installation. | |
1910 | (delete 'check) | |
1911 | (add-after 'install 'check | |
1912 | (lambda* (#:key inputs outputs #:allow-other-keys) | |
1913 | (setenv "PYTHONPATH" | |
1914 | (string-append | |
1915 | (getenv "PYTHONPATH") | |
1916 | ":" (assoc-ref outputs "out") | |
1917 | "/lib/python" | |
1918 | (string-take (string-take-right | |
1919 | (assoc-ref inputs "python") 5) 3) | |
1920 | "/site-packages")) | |
1921 | (zero? (system* "nosetests" "-P" "tests"))))))) | |
1f94bff2 TGR |
1922 | (inputs |
1923 | `(("python-xopen" ,python-xopen))) | |
8e913213 RW |
1924 | (native-inputs |
1925 | `(("python-cython" ,python-cython) | |
f3b98f4f | 1926 | ("python-nose" ,python-nose))) |
0c6c9c00 | 1927 | (home-page "https://cutadapt.readthedocs.io/en/stable/") |
8e913213 RW |
1928 | (synopsis "Remove adapter sequences from nucleotide sequencing reads") |
1929 | (description | |
1930 | "Cutadapt finds and removes adapter sequences, primers, poly-A tails and | |
1931 | other types of unwanted sequence from high-throughput sequencing reads.") | |
1932 | (license license:expat))) | |
1933 | ||
1baee943 RW |
1934 | (define-public libbigwig |
1935 | (package | |
1936 | (name "libbigwig") | |
1937 | (version "0.1.4") | |
1938 | (source (origin | |
1939 | (method url-fetch) | |
1940 | (uri (string-append "https://github.com/dpryan79/libBigWig/" | |
1941 | "archive/" version ".tar.gz")) | |
1942 | (file-name (string-append name "-" version ".tar.gz")) | |
1943 | (sha256 | |
1944 | (base32 | |
1945 | "098rjh35pi4a9q83n8wiwvyzykjqj6l8q189p1xgfw4ghywdlvw1")))) | |
1946 | (build-system gnu-build-system) | |
1947 | (arguments | |
1948 | `(#:test-target "test" | |
1949 | #:make-flags | |
1950 | (list "CC=gcc" | |
1951 | (string-append "prefix=" (assoc-ref %outputs "out"))) | |
1952 | #:phases | |
1953 | (modify-phases %standard-phases | |
1954 | (delete 'configure) | |
1955 | (add-before 'check 'disable-curl-test | |
1956 | (lambda _ | |
1957 | (substitute* "Makefile" | |
1958 | (("./test/testRemote.*") "")) | |
1959 | #t)) | |
1960 | ;; This has been fixed with the upstream commit 4ff6959cd8a0, but | |
1961 | ;; there has not yet been a release containing this change. | |
1962 | (add-before 'install 'create-target-dirs | |
1963 | (lambda* (#:key outputs #:allow-other-keys) | |
1964 | (let ((out (assoc-ref outputs "out"))) | |
1965 | (mkdir-p (string-append out "/lib")) | |
1966 | (mkdir-p (string-append out "/include")) | |
1967 | #t)))))) | |
1968 | (inputs | |
1969 | `(("zlib" ,zlib) | |
1970 | ("curl" ,curl))) | |
1971 | (native-inputs | |
1972 | `(("doxygen" ,doxygen))) | |
1973 | (home-page "https://github.com/dpryan79/libBigWig") | |
1974 | (synopsis "C library for handling bigWig files") | |
1975 | (description | |
1976 | "This package provides a C library for parsing local and remote BigWig | |
1977 | files.") | |
1978 | (license license:expat))) | |
1979 | ||
69e0e03c RW |
1980 | (define-public python-pybigwig |
1981 | (package | |
1982 | (name "python-pybigwig") | |
1983 | (version "0.2.5") | |
1984 | (source (origin | |
1985 | (method url-fetch) | |
1986 | (uri (pypi-uri "pyBigWig" version)) | |
1987 | (sha256 | |
1988 | (base32 | |
1989 | "0yrpdxg3y0sny25x4w22lv1k47jzccqjmg7j4bp0hywklvp0hg7d")) | |
1990 | (modules '((guix build utils))) | |
1991 | (snippet | |
1992 | '(begin | |
1993 | ;; Delete bundled libBigWig sources | |
1994 | (delete-file-recursively "libBigWig"))))) | |
1995 | (build-system python-build-system) | |
1996 | (arguments | |
1997 | `(#:phases | |
1998 | (modify-phases %standard-phases | |
1999 | (add-after 'unpack 'link-with-libBigWig | |
2000 | (lambda* (#:key inputs #:allow-other-keys) | |
2001 | (substitute* "setup.py" | |
2002 | (("libs=\\[") "libs=[\"BigWig\", ")) | |
2003 | #t))))) | |
2004 | (inputs | |
2005 | `(("libbigwig" ,libbigwig) | |
2006 | ("zlib" ,zlib) | |
2007 | ("curl" ,curl))) | |
2008 | (home-page "https://github.com/dpryan79/pyBigWig") | |
2009 | (synopsis "Access bigWig files in Python using libBigWig") | |
2010 | (description | |
2011 | "This package provides Python bindings to the libBigWig library for | |
2012 | accessing bigWig files.") | |
2013 | (license license:expat))) | |
2014 | ||
2015 | (define-public python2-pybigwig | |
5c31f4aa | 2016 | (package-with-python2 python-pybigwig)) |
69e0e03c | 2017 | |
ec2a67de BW |
2018 | (define-public python-dendropy |
2019 | (package | |
2020 | (name "python-dendropy") | |
25d84d31 | 2021 | (version "4.2.0") |
ec2a67de BW |
2022 | (source |
2023 | (origin | |
2024 | (method url-fetch) | |
2025 | (uri (pypi-uri "DendroPy" version)) | |
2026 | (sha256 | |
2027 | (base32 | |
1885bb0c RW |
2028 | "15c7s3d5gf19ljsxvq5advaa752wfi7pwrdjyhzmg85hccyvp47p")) |
2029 | (patches (search-patches "python-dendropy-fix-tests.patch")))) | |
ec2a67de BW |
2030 | (build-system python-build-system) |
2031 | (home-page "http://packages.python.org/DendroPy/") | |
2032 | (synopsis "Library for phylogenetics and phylogenetic computing") | |
2033 | (description | |
2034 | "DendroPy is a library for phylogenetics and phylogenetic computing: reading, | |
2035 | writing, simulation, processing and manipulation of phylogenetic | |
2036 | trees (phylogenies) and characters.") | |
2037 | (license license:bsd-3) | |
2038 | (properties `((python2-variant . ,(delay python2-dendropy)))))) | |
2039 | ||
2040 | (define-public python2-dendropy | |
2041 | (let ((base (package-with-python2 (strip-python2-variant python-dendropy)))) | |
2042 | (package | |
2043 | (inherit base) | |
9602e3cc BW |
2044 | (arguments |
2045 | `(#:python ,python-2 | |
2046 | #:phases | |
2047 | (modify-phases %standard-phases | |
2048 | (replace 'check | |
2049 | ;; There is currently a test failure that only happens on some | |
2050 | ;; systems, and only using "setup.py test" | |
2051 | (lambda _ (zero? (system* "nosetests"))))))) | |
f3b98f4f | 2052 | (native-inputs `(("python2-nose" ,python2-nose) |
ec2a67de BW |
2053 | ,@(package-native-inputs base)))))) |
2054 | ||
eb2200f3 RW |
2055 | (define-public python-py2bit |
2056 | (package | |
2057 | (name "python-py2bit") | |
2058 | (version "0.2.1") | |
2059 | (source | |
2060 | (origin | |
2061 | (method url-fetch) | |
2062 | (uri (pypi-uri "py2bit" version)) | |
2063 | (sha256 | |
2064 | (base32 | |
2065 | "1cdf4qlmgwsh1f4k0wdv2sr8x9qn4366p0k3614vbd0fpqiarxrl")))) | |
2066 | (build-system python-build-system) | |
2067 | (home-page "https://github.com/dpryan79/py2bit") | |
2068 | (synopsis "Access 2bit files using lib2bit") | |
2069 | (description | |
2070 | "This package provides Python bindings for lib2bit to access 2bit files | |
2071 | with Python.") | |
2072 | (license license:expat))) | |
ec2a67de | 2073 | |
1921b1de RW |
2074 | (define-public deeptools |
2075 | (package | |
2076 | (name "deeptools") | |
fed72008 | 2077 | (version "2.5.1") |
1921b1de RW |
2078 | (source (origin |
2079 | (method url-fetch) | |
3acb8c85 RW |
2080 | (uri (string-append "https://github.com/fidelram/deepTools/" |
2081 | "archive/" version ".tar.gz")) | |
1921b1de RW |
2082 | (file-name (string-append name "-" version ".tar.gz")) |
2083 | (sha256 | |
2084 | (base32 | |
fed72008 | 2085 | "1q8i12l2gvk4n2s8lhyzwhh9g4qbc8lrk5l7maz00yvd5g6z5540")))) |
1921b1de | 2086 | (build-system python-build-system) |
14bda1ff | 2087 | (inputs |
fed72008 RW |
2088 | `(("python-scipy" ,python-scipy) |
2089 | ("python-numpy" ,python-numpy) | |
2090 | ("python-numpydoc" ,python-numpydoc) | |
2091 | ("python-matplotlib" ,python-matplotlib) | |
2092 | ("python-pysam" ,python-pysam) | |
2093 | ("python-py2bit" ,python-py2bit) | |
2094 | ("python-pybigwig" ,python-pybigwig))) | |
1921b1de | 2095 | (native-inputs |
fed72008 RW |
2096 | `(("python-mock" ,python-mock) ;for tests |
2097 | ("python-nose" ,python-nose) ;for tests | |
2098 | ("python-pytz" ,python-pytz))) ;for tests | |
1921b1de RW |
2099 | (home-page "https://github.com/fidelram/deepTools") |
2100 | (synopsis "Tools for normalizing and visualizing deep-sequencing data") | |
2101 | (description | |
2102 | "DeepTools addresses the challenge of handling the large amounts of data | |
2103 | that are now routinely generated from DNA sequencing centers. To do so, | |
2104 | deepTools contains useful modules to process the mapped reads data to create | |
2105 | coverage files in standard bedGraph and bigWig file formats. By doing so, | |
2106 | deepTools allows the creation of normalized coverage files or the comparison | |
2107 | between two files (for example, treatment and control). Finally, using such | |
2108 | normalized and standardized files, multiple visualizations can be created to | |
2109 | identify enrichments with functional annotations of the genome.") | |
2110 | (license license:gpl3+))) | |
2111 | ||
684bf7c7 BW |
2112 | (define-public diamond |
2113 | (package | |
2114 | (name "diamond") | |
a522517c | 2115 | (version "0.9.9") |
684bf7c7 BW |
2116 | (source (origin |
2117 | (method url-fetch) | |
2118 | (uri (string-append | |
2119 | "https://github.com/bbuchfink/diamond/archive/v" | |
2120 | version ".tar.gz")) | |
2121 | (file-name (string-append name "-" version ".tar.gz")) | |
2122 | (sha256 | |
2123 | (base32 | |
a522517c | 2124 | "04i03046g3l2vk9722z47r1p7j415g97vvz6d76ywmbawyiihcb1")))) |
122395f9 | 2125 | (build-system cmake-build-system) |
684bf7c7 | 2126 | (arguments |
7c544991 BW |
2127 | '(#:tests? #f ; no "check" target |
2128 | #:phases | |
2129 | (modify-phases %standard-phases | |
2130 | (add-after 'unpack 'remove-native-compilation | |
2131 | (lambda _ | |
2132 | (substitute* "CMakeLists.txt" (("-march=native") "")) | |
2133 | #t))))) | |
684bf7c7 | 2134 | (inputs |
122395f9 | 2135 | `(("zlib" ,zlib))) |
684bf7c7 BW |
2136 | (home-page "https://github.com/bbuchfink/diamond") |
2137 | (synopsis "Accelerated BLAST compatible local sequence aligner") | |
2138 | (description | |
2139 | "DIAMOND is a BLAST-compatible local aligner for mapping protein and | |
2140 | translated DNA query sequences against a protein reference database (BLASTP | |
2141 | and BLASTX alignment mode). The speedup over BLAST is up to 20,000 on short | |
2142 | reads at a typical sensitivity of 90-99% relative to BLAST depending on the | |
2143 | data and settings.") | |
ef81341f | 2144 | (license license:agpl3+))) |
684bf7c7 | 2145 | |
97b9da68 RW |
2146 | (define-public discrover |
2147 | (package | |
2148 | (name "discrover") | |
2149 | (version "1.6.0") | |
2150 | (source | |
2151 | (origin | |
2152 | (method url-fetch) | |
2153 | (uri (string-append "https://github.com/maaskola/discrover/archive/" | |
2154 | version ".tar.gz")) | |
2155 | (file-name (string-append name "-" version ".tar.gz")) | |
2156 | (sha256 | |
2157 | (base32 | |
2158 | "0rah9ja4m0rl5mldd6vag9rwrivw1zrqxssfq8qx64m7961fp68k")))) | |
2159 | (build-system cmake-build-system) | |
fa702e1a RW |
2160 | (arguments |
2161 | `(#:tests? #f ; there are no tests | |
2162 | #:phases | |
2163 | (modify-phases %standard-phases | |
2164 | (add-after 'unpack 'add-missing-includes | |
2165 | (lambda _ | |
2166 | (substitute* "src/executioninformation.hpp" | |
2167 | (("#define EXECUTIONINFORMATION_HPP" line) | |
2168 | (string-append line "\n#include <random>"))) | |
2169 | (substitute* "src/plasma/fasta.hpp" | |
2170 | (("#define FASTA_HPP" line) | |
2171 | (string-append line "\n#include <random>"))) | |
2172 | #t))))) | |
97b9da68 RW |
2173 | (inputs |
2174 | `(("boost" ,boost) | |
2175 | ("cairo" ,cairo))) | |
2176 | (native-inputs | |
2177 | `(("texlive" ,texlive) | |
2178 | ("imagemagick" ,imagemagick))) | |
2179 | (home-page "http://dorina.mdc-berlin.de/public/rajewsky/discrover/") | |
2180 | (synopsis "Discover discriminative nucleotide sequence motifs") | |
2181 | (description "Discrover is a motif discovery method to find binding sites | |
2182 | of nucleic acid binding proteins.") | |
2183 | (license license:gpl3+))) | |
2184 | ||
6619f9c7 RW |
2185 | (define-public eigensoft |
2186 | (let ((revision "1") | |
2187 | (commit "b14d1e202e21e532536ff8004f0419cd5e259dc7")) | |
2188 | (package | |
2189 | (name "eigensoft") | |
2190 | (version (string-append "6.1.2-" | |
2191 | revision "." | |
2192 | (string-take commit 9))) | |
2193 | (source | |
2194 | (origin | |
2195 | (method git-fetch) | |
2196 | (uri (git-reference | |
2197 | (url "https://github.com/DReichLab/EIG.git") | |
2198 | (commit commit))) | |
2199 | (file-name (string-append "eigensoft-" commit "-checkout")) | |
2200 | (sha256 | |
2201 | (base32 | |
2202 | "0f5m6k2j5c16xc3xbywcs989xyc26ncy1zfzp9j9n55n9r4xcaiq")) | |
2203 | (modules '((guix build utils))) | |
2204 | ;; Remove pre-built binaries. | |
2205 | (snippet '(begin | |
2206 | (delete-file-recursively "bin") | |
2207 | (mkdir "bin") | |
2208 | #t)))) | |
2209 | (build-system gnu-build-system) | |
2210 | (arguments | |
2211 | `(#:tests? #f ; There are no tests. | |
2212 | #:make-flags '("CC=gcc") | |
2213 | #:phases | |
2214 | (modify-phases %standard-phases | |
2215 | ;; There is no configure phase, but the Makefile is in a | |
2216 | ;; sub-directory. | |
2217 | (replace 'configure | |
2218 | (lambda _ | |
2219 | (chdir "src") | |
2220 | ;; The link flags are incomplete. | |
2221 | (substitute* "Makefile" | |
2222 | (("-lgsl") "-lgsl -lm -llapack -llapacke -lpthread")) | |
2223 | #t)) | |
2224 | ;; The provided install target only copies executables to | |
2225 | ;; the "bin" directory in the build root. | |
2226 | (add-after 'install 'actually-install | |
2227 | (lambda* (#:key outputs #:allow-other-keys) | |
2228 | (let* ((out (assoc-ref outputs "out")) | |
2229 | (bin (string-append out "/bin"))) | |
6619f9c7 RW |
2230 | (for-each (lambda (file) |
2231 | (install-file file bin)) | |
2232 | (find-files "../bin" ".*")) | |
2233 | #t)))))) | |
2234 | (inputs | |
2235 | `(("gsl" ,gsl) | |
2236 | ("lapack" ,lapack) | |
6619f9c7 RW |
2237 | ("openblas" ,openblas) |
2238 | ("perl" ,perl) | |
2239 | ("gfortran" ,gfortran "lib"))) | |
2240 | (home-page "https://github.com/DReichLab/EIG") | |
2241 | (synopsis "Tools for population genetics") | |
2242 | (description "The EIGENSOFT package provides tools for population | |
2243 | genetics and stratification correction. EIGENSOFT implements methods commonly | |
2244 | used in population genetics analyses such as PCA, computation of Tracy-Widom | |
2245 | statistics, and finding related individuals in structured populations. It | |
2246 | comes with a built-in plotting script and supports multiple file formats and | |
2247 | quantitative phenotypes.") | |
2248 | ;; The license of the eigensoft tools is Expat, but since it's | |
2249 | ;; linking with the GNU Scientific Library (GSL) the effective | |
2250 | ;; license is the GPL. | |
2251 | (license license:gpl3+)))) | |
2252 | ||
365c8153 RW |
2253 | (define-public edirect |
2254 | (package | |
2255 | (name "edirect") | |
83b84fa8 | 2256 | (version "4.10") |
365c8153 RW |
2257 | (source (origin |
2258 | (method url-fetch) | |
83b84fa8 RW |
2259 | (uri (string-append "ftp://ftp.ncbi.nlm.nih.gov/entrez/entrezdirect/" |
2260 | "versions/2016-05-03/edirect.tar.gz")) | |
365c8153 RW |
2261 | (sha256 |
2262 | (base32 | |
83b84fa8 | 2263 | "15zsprak5yh8c1yrz4r1knmb5s8qcmdid4xdhkh3lqcv64l60hli")))) |
365c8153 RW |
2264 | (build-system perl-build-system) |
2265 | (arguments | |
2266 | `(#:tests? #f ;no "check" target | |
2267 | #:phases | |
2268 | (modify-phases %standard-phases | |
2269 | (delete 'configure) | |
2270 | (delete 'build) | |
2271 | (replace 'install | |
2272 | (lambda* (#:key outputs #:allow-other-keys) | |
2273 | (let ((target (string-append (assoc-ref outputs "out") | |
2274 | "/bin"))) | |
2275 | (mkdir-p target) | |
f3860753 | 2276 | (install-file "edirect.pl" target) |
365c8153 RW |
2277 | #t))) |
2278 | (add-after | |
2279 | 'install 'wrap-program | |
2280 | (lambda* (#:key inputs outputs #:allow-other-keys) | |
2281 | ;; Make sure 'edirect.pl' finds all perl inputs at runtime. | |
2282 | (let* ((out (assoc-ref outputs "out")) | |
2283 | (path (getenv "PERL5LIB"))) | |
2284 | (wrap-program (string-append out "/bin/edirect.pl") | |
2285 | `("PERL5LIB" ":" prefix (,path))))))))) | |
2286 | (inputs | |
2287 | `(("perl-html-parser" ,perl-html-parser) | |
2288 | ("perl-encode-locale" ,perl-encode-locale) | |
2289 | ("perl-file-listing" ,perl-file-listing) | |
2290 | ("perl-html-tagset" ,perl-html-tagset) | |
2291 | ("perl-html-tree" ,perl-html-tree) | |
2292 | ("perl-http-cookies" ,perl-http-cookies) | |
2293 | ("perl-http-date" ,perl-http-date) | |
2294 | ("perl-http-message" ,perl-http-message) | |
2295 | ("perl-http-negotiate" ,perl-http-negotiate) | |
2296 | ("perl-lwp-mediatypes" ,perl-lwp-mediatypes) | |
2297 | ("perl-lwp-protocol-https" ,perl-lwp-protocol-https) | |
2298 | ("perl-net-http" ,perl-net-http) | |
2299 | ("perl-uri" ,perl-uri) | |
2300 | ("perl-www-robotrules" ,perl-www-robotrules) | |
2301 | ("perl" ,perl))) | |
3d51ec91 | 2302 | (home-page "http://www.ncbi.nlm.nih.gov/books/NBK179288/") |
365c8153 RW |
2303 | (synopsis "Tools for accessing the NCBI's set of databases") |
2304 | (description | |
2305 | "Entrez Direct (EDirect) is a method for accessing the National Center | |
2306 | for Biotechnology Information's (NCBI) set of interconnected | |
2307 | databases (publication, sequence, structure, gene, variation, expression, | |
2308 | etc.) from a terminal. Functions take search terms from command-line | |
2309 | arguments. Individual operations are combined to build multi-step queries. | |
2310 | Record retrieval and formatting normally complete the process. | |
2311 | ||
2312 | EDirect also provides an argument-driven function that simplifies the | |
2313 | extraction of data from document summaries or other results that are returned | |
2314 | in structured XML format. This can eliminate the need for writing custom | |
2315 | software to answer ad hoc questions.") | |
2316 | (license license:public-domain))) | |
2317 | ||
b16728b0 BW |
2318 | (define-public exonerate |
2319 | (package | |
2320 | (name "exonerate") | |
2321 | (version "2.4.0") | |
2322 | (source | |
2323 | (origin | |
2324 | (method url-fetch) | |
2325 | (uri | |
2326 | (string-append | |
2327 | "http://ftp.ebi.ac.uk/pub/software/vertebrategenomics/exonerate/" | |
2328 | "exonerate-" version ".tar.gz")) | |
2329 | (sha256 | |
2330 | (base32 | |
2331 | "0hj0m9xygiqsdxvbg79wq579kbrx1mdrabi2bzqz2zn9qwfjcjgq")))) | |
2332 | (build-system gnu-build-system) | |
2333 | (arguments | |
2334 | `(#:parallel-build? #f)) ; Building in parallel fails on some machines. | |
2335 | (native-inputs | |
2336 | `(("pkg-config" ,pkg-config))) | |
2337 | (inputs | |
2338 | `(("glib" ,glib))) | |
2339 | (home-page | |
2340 | "https://www.ebi.ac.uk/about/vertebrate-genomics/software/exonerate") | |
2341 | (synopsis "Generic tool for biological sequence alignment") | |
2342 | (description | |
2343 | "Exonerate is a generic tool for pairwise sequence comparison. It allows | |
2344 | the alignment of sequences using a many alignment models, either exhaustive | |
2345 | dynamic programming or a variety of heuristics.") | |
2346 | (license license:gpl3))) | |
2347 | ||
e4e5a4d8 RW |
2348 | (define-public express |
2349 | (package | |
2350 | (name "express") | |
2351 | (version "1.5.1") | |
2352 | (source (origin | |
2353 | (method url-fetch) | |
2354 | (uri | |
2355 | (string-append | |
2356 | "http://bio.math.berkeley.edu/eXpress/downloads/express-" | |
2357 | version "/express-" version "-src.tgz")) | |
2358 | (sha256 | |
2359 | (base32 | |
2360 | "03rczxd0gjp2l1jxcmjfmf5j94j77zqyxa6x063zsc585nj40n0c")))) | |
2361 | (build-system cmake-build-system) | |
2362 | (arguments | |
2363 | `(#:tests? #f ;no "check" target | |
2364 | #:phases | |
2365 | (alist-cons-after | |
2366 | 'unpack 'use-shared-boost-libs-and-set-bamtools-paths | |
2367 | (lambda* (#:key inputs #:allow-other-keys) | |
2368 | (substitute* "CMakeLists.txt" | |
2369 | (("set\\(Boost_USE_STATIC_LIBS ON\\)") | |
2370 | "set(Boost_USE_STATIC_LIBS OFF)") | |
2371 | (("\\$\\{CMAKE_CURRENT_SOURCE_DIR\\}/bamtools/include") | |
2372 | (string-append (assoc-ref inputs "bamtools") "/include/bamtools"))) | |
2373 | (substitute* "src/CMakeLists.txt" | |
2374 | (("\\$\\{CMAKE_CURRENT_SOURCE_DIR\\}/\\.\\./bamtools/lib") | |
2375 | (string-append (assoc-ref inputs "bamtools") "/lib/bamtools"))) | |
2376 | #t) | |
2377 | %standard-phases))) | |
2378 | (inputs | |
2379 | `(("boost" ,boost) | |
2380 | ("bamtools" ,bamtools) | |
2381 | ("protobuf" ,protobuf) | |
2382 | ("zlib" ,zlib))) | |
2383 | (home-page "http://bio.math.berkeley.edu/eXpress") | |
2384 | (synopsis "Streaming quantification for high-throughput genomic sequencing") | |
2385 | (description | |
2386 | "eXpress is a streaming tool for quantifying the abundances of a set of | |
2387 | target sequences from sampled subsequences. Example applications include | |
2388 | transcript-level RNA-Seq quantification, allele-specific/haplotype expression | |
2389 | analysis (from RNA-Seq), transcription factor binding quantification in | |
2390 | ChIP-Seq, and analysis of metagenomic data.") | |
2391 | (license license:artistic2.0))) | |
2392 | ||
f3674b1c BW |
2393 | (define-public express-beta-diversity |
2394 | (package | |
2395 | (name "express-beta-diversity") | |
2396 | (version "1.0.7") | |
2397 | (source (origin | |
2398 | (method url-fetch) | |
2399 | (uri | |
2400 | (string-append | |
2401 | "https://github.com/dparks1134/ExpressBetaDiversity/archive/v" | |
2402 | version ".tar.gz")) | |
2403 | (file-name (string-append name "-" version ".tar.gz")) | |
2404 | (sha256 | |
2405 | (base32 | |
2406 | "1djvdlmqvjf6h0zq7w36y8cl5cli6rgj86x65znl48agnwmzxfxr")))) | |
2407 | (build-system gnu-build-system) | |
2408 | (arguments | |
2409 | `(#:phases | |
2410 | (modify-phases %standard-phases | |
2411 | (delete 'configure) | |
2412 | (add-before 'build 'enter-source (lambda _ (chdir "source") #t)) | |
2413 | (replace 'check | |
2414 | (lambda _ (zero? (system* "../bin/ExpressBetaDiversity" | |
2415 | "-u")))) | |
2416 | (add-after 'check 'exit-source (lambda _ (chdir "..") #t)) | |
2417 | (replace 'install | |
2418 | (lambda* (#:key outputs #:allow-other-keys) | |
2419 | (let ((bin (string-append (assoc-ref outputs "out") | |
2420 | "/bin"))) | |
2421 | (mkdir-p bin) | |
f3860753 TGR |
2422 | (install-file "scripts/convertToEBD.py" bin) |
2423 | (install-file "bin/ExpressBetaDiversity" bin) | |
f3674b1c BW |
2424 | #t)))))) |
2425 | (inputs | |
2426 | `(("python" ,python-2))) | |
2427 | (home-page "http://kiwi.cs.dal.ca/Software/ExpressBetaDiversity") | |
2428 | (synopsis "Taxon- and phylogenetic-based beta diversity measures") | |
2429 | (description | |
2430 | "Express Beta Diversity (EBD) calculates ecological beta diversity | |
2431 | (dissimilarity) measures between biological communities. EBD implements a | |
2432 | variety of diversity measures including those that make use of phylogenetic | |
2433 | similarity of community members.") | |
2434 | (license license:gpl3+))) | |
2435 | ||
12b04cbe BW |
2436 | (define-public fasttree |
2437 | (package | |
2438 | (name "fasttree") | |
88682c9a | 2439 | (version "2.1.10") |
12b04cbe BW |
2440 | (source (origin |
2441 | (method url-fetch) | |
2442 | (uri (string-append | |
2443 | "http://www.microbesonline.org/fasttree/FastTree-" | |
2444 | version ".c")) | |
2445 | (sha256 | |
2446 | (base32 | |
88682c9a | 2447 | "0vcjdvy1j4m702vmak4svbfkrpcw63k7wymfksjp9a982zy8kjsl")))) |
12b04cbe BW |
2448 | (build-system gnu-build-system) |
2449 | (arguments | |
2450 | `(#:tests? #f ; no "check" target | |
2451 | #:phases | |
2452 | (modify-phases %standard-phases | |
2453 | (delete 'unpack) | |
2454 | (delete 'configure) | |
2455 | (replace 'build | |
e03a5153 BW |
2456 | (lambda* (#:key source #:allow-other-keys) |
2457 | (and (zero? (system* "gcc" | |
2458 | "-O3" | |
2459 | "-finline-functions" | |
2460 | "-funroll-loops" | |
2461 | "-Wall" | |
2462 | "-o" | |
2463 | "FastTree" | |
2464 | source | |
2465 | "-lm")) | |
2466 | (zero? (system* "gcc" | |
2467 | "-DOPENMP" | |
2468 | "-fopenmp" | |
2469 | "-O3" | |
2470 | "-finline-functions" | |
2471 | "-funroll-loops" | |
2472 | "-Wall" | |
2473 | "-o" | |
2474 | "FastTreeMP" | |
2475 | source | |
2476 | "-lm"))))) | |
12b04cbe | 2477 | (replace 'install |
e03a5153 BW |
2478 | (lambda* (#:key outputs #:allow-other-keys) |
2479 | (let ((bin (string-append (assoc-ref outputs "out") | |
2480 | "/bin"))) | |
2481 | (mkdir-p bin) | |
f3860753 TGR |
2482 | (install-file "FastTree" bin) |
2483 | (install-file "FastTreeMP" bin) | |
e03a5153 | 2484 | #t)))))) |
12b04cbe BW |
2485 | (home-page "http://www.microbesonline.org/fasttree") |
2486 | (synopsis "Infers approximately-maximum-likelihood phylogenetic trees") | |
2487 | (description | |
2488 | "FastTree can handle alignments with up to a million of sequences in a | |
2489 | reasonable amount of time and memory. For large alignments, FastTree is | |
2490 | 100-1,000 times faster than PhyML 3.0 or RAxML 7.") | |
2491 | (license license:gpl2+))) | |
2492 | ||
2127cedb RW |
2493 | (define-public fastx-toolkit |
2494 | (package | |
2495 | (name "fastx-toolkit") | |
2496 | (version "0.0.14") | |
2497 | (source (origin | |
2498 | (method url-fetch) | |
2499 | (uri | |
2500 | (string-append | |
2501 | "https://github.com/agordon/fastx_toolkit/releases/download/" | |
2502 | version "/fastx_toolkit-" version ".tar.bz2")) | |
2503 | (sha256 | |
2504 | (base32 | |
2505 | "01jqzw386873sr0pjp1wr4rn8fsga2vxs1qfmicvx1pjr72007wy")))) | |
2506 | (build-system gnu-build-system) | |
2507 | (inputs | |
2508 | `(("libgtextutils" ,libgtextutils))) | |
2509 | (native-inputs | |
2510 | `(("pkg-config" ,pkg-config))) | |
2511 | (home-page "http://hannonlab.cshl.edu/fastx_toolkit/") | |
2512 | (synopsis "Tools for FASTA/FASTQ file preprocessing") | |
2513 | (description | |
2514 | "The FASTX-Toolkit is a collection of command line tools for Short-Reads | |
2515 | FASTA/FASTQ files preprocessing. | |
2516 | ||
2517 | Next-Generation sequencing machines usually produce FASTA or FASTQ files, | |
2518 | containing multiple short-reads sequences. The main processing of such | |
2519 | FASTA/FASTQ files is mapping the sequences to reference genomes. However, it | |
2520 | is sometimes more productive to preprocess the files before mapping the | |
2521 | sequences to the genome---manipulating the sequences to produce better mapping | |
2522 | results. The FASTX-Toolkit tools perform some of these preprocessing tasks.") | |
2523 | (license license:agpl3+))) | |
2524 | ||
d7678942 RW |
2525 | (define-public flexbar |
2526 | (package | |
2527 | (name "flexbar") | |
2528 | (version "2.5") | |
2529 | (source (origin | |
2530 | (method url-fetch) | |
2531 | (uri | |
2532 | (string-append "mirror://sourceforge/flexbar/" | |
2533 | version "/flexbar_v" version "_src.tgz")) | |
2534 | (sha256 | |
2535 | (base32 | |
2536 | "13jaykc3y1x8y5nn9j8ljnb79s5y51kyxz46hdmvvjj6qhyympmf")))) | |
2537 | (build-system cmake-build-system) | |
2538 | (arguments | |
4ca009c0 | 2539 | `(#:configure-flags (list |
d7678942 RW |
2540 | (string-append "-DFLEXBAR_BINARY_DIR=" |
2541 | (assoc-ref %outputs "out") | |
2542 | "/bin/")) | |
2543 | #:phases | |
4ca009c0 RW |
2544 | (alist-replace |
2545 | 'check | |
2546 | (lambda* (#:key outputs #:allow-other-keys) | |
2547 | (setenv "PATH" (string-append | |
2548 | (assoc-ref outputs "out") "/bin:" | |
2549 | (getenv "PATH"))) | |
2550 | (chdir "../flexbar_v2.5_src/test") | |
2551 | (zero? (system* "bash" "flexbar_validate.sh"))) | |
2552 | (alist-delete 'install %standard-phases)))) | |
d7678942 RW |
2553 | (inputs |
2554 | `(("tbb" ,tbb) | |
2555 | ("zlib" ,zlib))) | |
2556 | (native-inputs | |
2557 | `(("pkg-config" ,pkg-config) | |
2558 | ("seqan" ,seqan))) | |
2559 | (home-page "http://flexbar.sourceforge.net") | |
2560 | (synopsis "Barcode and adapter removal tool for sequencing platforms") | |
2561 | (description | |
2562 | "Flexbar preprocesses high-throughput nucleotide sequencing data | |
2563 | efficiently. It demultiplexes barcoded runs and removes adapter sequences. | |
2564 | Moreover, trimming and filtering features are provided. Flexbar increases | |
2565 | read mapping rates and improves genome and transcriptome assemblies. It | |
2566 | supports next-generation sequencing data in fasta/q and csfasta/q format from | |
2567 | Illumina, Roche 454, and the SOLiD platform.") | |
2568 | (license license:gpl3))) | |
2569 | ||
19f4554c BW |
2570 | (define-public fraggenescan |
2571 | (package | |
2572 | (name "fraggenescan") | |
74297231 | 2573 | (version "1.30") |
19f4554c BW |
2574 | (source |
2575 | (origin | |
2576 | (method url-fetch) | |
2577 | (uri | |
2578 | (string-append "mirror://sourceforge/fraggenescan/" | |
2579 | "FragGeneScan" version ".tar.gz")) | |
2580 | (sha256 | |
74297231 | 2581 | (base32 "158dcnwczgcyhwm4qlx19sanrwgdpzf6bn2y57mbpx55lkgz1mzj")))) |
19f4554c BW |
2582 | (build-system gnu-build-system) |
2583 | (arguments | |
2584 | `(#:phases | |
2585 | (modify-phases %standard-phases | |
2586 | (delete 'configure) | |
2587 | (add-before 'build 'patch-paths | |
2588 | (lambda* (#:key outputs #:allow-other-keys) | |
2589 | (let* ((out (string-append (assoc-ref outputs "out"))) | |
2590 | (share (string-append out "/share/fraggenescan/"))) | |
2591 | (substitute* "run_FragGeneScan.pl" | |
2592 | (("system\\(\"rm") | |
2593 | (string-append "system(\"" (which "rm"))) | |
2594 | (("system\\(\"mv") | |
2595 | (string-append "system(\"" (which "mv"))) | |
74297231 | 2596 | (("\\\"awk") (string-append "\"" (which "awk"))) |
19f4554c BW |
2597 | ;; This script and other programs expect the training files |
2598 | ;; to be in the non-standard location bin/train/XXX. Change | |
2599 | ;; this to be share/fraggenescan/train/XXX instead. | |
2600 | (("^\\$train.file = \\$dir.*") | |
2601 | (string-append "$train_file = \"" | |
2602 | share | |
2603 | "train/\".$FGS_train_file;"))) | |
2604 | (substitute* "run_hmm.c" | |
2605 | (("^ strcat\\(train_dir, \\\"train/\\\"\\);") | |
74297231 | 2606 | (string-append " strcpy(train_dir, \"" share "/train/\");")))) |
19f4554c BW |
2607 | #t)) |
2608 | (replace 'build | |
2609 | (lambda _ (and (zero? (system* "make" "clean")) | |
2610 | (zero? (system* "make" "fgs"))))) | |
2611 | (replace 'install | |
2612 | (lambda* (#:key outputs #:allow-other-keys) | |
2613 | (let* ((out (string-append (assoc-ref outputs "out"))) | |
2614 | (bin (string-append out "/bin/")) | |
2615 | (share (string-append out "/share/fraggenescan/train"))) | |
2616 | (install-file "run_FragGeneScan.pl" bin) | |
2617 | (install-file "FragGeneScan" bin) | |
19f4554c BW |
2618 | (copy-recursively "train" share)))) |
2619 | (delete 'check) | |
2620 | (add-after 'install 'post-install-check | |
2621 | ;; In lieu of 'make check', run one of the examples and check the | |
2622 | ;; output files gets created. | |
2623 | (lambda* (#:key outputs #:allow-other-keys) | |
2624 | (let* ((out (string-append (assoc-ref outputs "out"))) | |
74297231 BW |
2625 | (bin (string-append out "/bin/")) |
2626 | (frag (string-append bin "run_FragGeneScan.pl"))) | |
2627 | (and (zero? (system* frag ; Test complete genome. | |
19f4554c BW |
2628 | "-genome=./example/NC_000913.fna" |
2629 | "-out=./test2" | |
2630 | "-complete=1" | |
2631 | "-train=complete")) | |
2632 | (file-exists? "test2.faa") | |
2633 | (file-exists? "test2.ffn") | |
2634 | (file-exists? "test2.gff") | |
74297231 BW |
2635 | (file-exists? "test2.out") |
2636 | (zero? (system* ; Test incomplete sequences. | |
2637 | frag | |
2638 | "-genome=./example/NC_000913-fgs.ffn" | |
2639 | "-out=out" | |
2640 | "-complete=0" | |
2641 | "-train=454_30"))))))))) | |
19f4554c BW |
2642 | (inputs |
2643 | `(("perl" ,perl) | |
2644 | ("python" ,python-2))) ;not compatible with python 3. | |
2645 | (home-page "https://sourceforge.net/projects/fraggenescan/") | |
2646 | (synopsis "Finds potentially fragmented genes in short reads") | |
2647 | (description | |
2648 | "FragGeneScan is a program for predicting bacterial and archaeal genes in | |
2649 | short and error-prone DNA sequencing reads. It can also be applied to predict | |
2650 | genes in incomplete assemblies or complete genomes.") | |
2651 | ;; GPL3+ according to private correspondense with the authors. | |
2652 | (license license:gpl3+))) | |
2653 | ||
81f3e0c1 BW |
2654 | (define-public fxtract |
2655 | (let ((util-commit "776ca85a18a47492af3794745efcb4a905113115")) | |
2656 | (package | |
2657 | (name "fxtract") | |
2658 | (version "2.3") | |
2659 | (source | |
2660 | (origin | |
2661 | (method url-fetch) | |
2662 | (uri (string-append | |
2663 | "https://github.com/ctSkennerton/fxtract/archive/" | |
2664 | version ".tar.gz")) | |
2665 | (file-name (string-append "ctstennerton-util-" | |
2666 | (string-take util-commit 7) | |
2667 | "-checkout")) | |
2668 | (sha256 | |
2669 | (base32 | |
2670 | "0275cfdhis8517hm01is62062swmi06fxzifq7mr3knbbxjlaiwj")))) | |
2671 | (build-system gnu-build-system) | |
2672 | (arguments | |
2673 | `(#:make-flags (list | |
2674 | (string-append "PREFIX=" (assoc-ref %outputs "out")) | |
2675 | "CC=gcc") | |
2676 | #:test-target "fxtract_test" | |
2677 | #:phases | |
2678 | (modify-phases %standard-phases | |
2679 | (delete 'configure) | |
2680 | (add-before 'build 'copy-util | |
2681 | (lambda* (#:key inputs #:allow-other-keys) | |
2682 | (rmdir "util") | |
2683 | (copy-recursively (assoc-ref inputs "ctskennerton-util") "util") | |
2684 | #t)) | |
2685 | ;; Do not use make install as this requires additional dependencies. | |
2686 | (replace 'install | |
2687 | (lambda* (#:key outputs #:allow-other-keys) | |
2688 | (let* ((out (assoc-ref outputs "out")) | |
2689 | (bin (string-append out"/bin"))) | |
2690 | (install-file "fxtract" bin) | |
2691 | #t)))))) | |
2692 | (inputs | |
2693 | `(("pcre" ,pcre) | |
2694 | ("zlib" ,zlib))) | |
2695 | (native-inputs | |
2696 | ;; ctskennerton-util is licensed under GPL2. | |
2697 | `(("ctskennerton-util" | |
2698 | ,(origin | |
2699 | (method git-fetch) | |
2700 | (uri (git-reference | |
2701 | (url "https://github.com/ctSkennerton/util.git") | |
2702 | (commit util-commit))) | |
2703 | (file-name (string-append | |
2704 | "ctstennerton-util-" util-commit "-checkout")) | |
2705 | (sha256 | |
2706 | (base32 | |
2707 | "0cls1hd4vgj3f36fpzzg4xc77d6f3hpc60cbpfmn2gdr7ykzzad7")))))) | |
2708 | (home-page "https://github.com/ctSkennerton/fxtract") | |
2709 | (synopsis "Extract sequences from FASTA and FASTQ files") | |
2710 | (description | |
2711 | "Fxtract extracts sequences from a protein or nucleotide fastx (FASTA | |
2712 | or FASTQ) file given a subsequence. It uses a simple substring search for | |
2713 | basic tasks but can change to using POSIX regular expressions, PCRE, hash | |
2714 | lookups or multi-pattern searching as required. By default fxtract looks in | |
2715 | the sequence of each record but can also be told to look in the header, | |
2716 | comment or quality sections.") | |
afde1a26 BW |
2717 | ;; 'util' requires SSE instructions. |
2718 | (supported-systems '("x86_64-linux")) | |
81f3e0c1 BW |
2719 | (license license:expat)))) |
2720 | ||
2b18ad05 PP |
2721 | (define-public gemma |
2722 | (package | |
2723 | (name "gemma") | |
2724 | (version "0.96") | |
2725 | (source (origin | |
2726 | (method url-fetch) | |
2727 | (uri (string-append "https://github.com/xiangzhou/GEMMA/archive/v" | |
2728 | version ".tar.gz")) | |
2729 | (file-name (string-append name "-" version ".tar.gz")) | |
2730 | (sha256 | |
2731 | (base32 | |
ce7e361f EF |
2732 | "055ynn16gd12pf78n4vr2a9jlwsbwzajpdnf2y2yilg1krfff222")) |
2733 | (patches (search-patches "gemma-intel-compat.patch")))) | |
2b18ad05 PP |
2734 | (inputs |
2735 | `(("gsl" ,gsl) | |
2736 | ("lapack" ,lapack) | |
2737 | ("zlib" ,zlib))) | |
2738 | (build-system gnu-build-system) | |
2739 | (arguments | |
2c9232ae | 2740 | `(#:make-flags |
ce7e361f EF |
2741 | '(,@(match (%current-system) |
2742 | ("x86_64-linux" | |
2743 | '("FORCE_DYNAMIC=1")) | |
2744 | ("i686-linux" | |
2745 | '("FORCE_DYNAMIC=1" "FORCE_32BIT=1")) | |
2746 | (_ | |
2747 | '("FORCE_DYNAMIC=1" "NO_INTEL_COMPAT=1")))) | |
2b18ad05 PP |
2748 | #:phases |
2749 | (modify-phases %standard-phases | |
2750 | (delete 'configure) | |
2751 | (add-before 'build 'bin-mkdir | |
07bf6929 EF |
2752 | (lambda _ |
2753 | (mkdir-p "bin") | |
2754 | #t)) | |
2b18ad05 | 2755 | (replace 'install |
07bf6929 EF |
2756 | (lambda* (#:key outputs #:allow-other-keys) |
2757 | (let ((out (assoc-ref outputs "out"))) | |
2758 | (install-file "bin/gemma" | |
2759 | (string-append | |
2760 | out "/bin"))) | |
2761 | #t))) | |
2b18ad05 PP |
2762 | #:tests? #f)) ; no tests included yet |
2763 | (home-page "https://github.com/xiangzhou/GEMMA") | |
2764 | (synopsis "Tool for genome-wide efficient mixed model association") | |
2765 | (description | |
2766 | "Genome-wide Efficient Mixed Model Association (GEMMA) provides a | |
2767 | standard linear mixed model resolver with application in genome-wide | |
2768 | association studies (GWAS).") | |
2769 | (license license:gpl3))) | |
2770 | ||
5854f685 RW |
2771 | (define-public grit |
2772 | (package | |
2773 | (name "grit") | |
2774 | (version "2.0.2") | |
2775 | (source (origin | |
2776 | (method url-fetch) | |
2777 | (uri (string-append | |
2778 | "https://github.com/nboley/grit/archive/" | |
2779 | version ".tar.gz")) | |
2780 | (file-name (string-append name "-" version ".tar.gz")) | |
2781 | (sha256 | |
2782 | (base32 | |
2783 | "157in84dj70wimbind3x7sy1whs3h57qfgcnj2s6lrd38fbrb7mj")))) | |
2784 | (build-system python-build-system) | |
2785 | (arguments | |
2786 | `(#:python ,python-2 | |
2787 | #:phases | |
2788 | (alist-cons-after | |
2789 | 'unpack 'generate-from-cython-sources | |
2790 | (lambda* (#:key inputs outputs #:allow-other-keys) | |
2791 | ;; Delete these C files to force fresh generation from pyx sources. | |
2792 | (delete-file "grit/sparsify_support_fns.c") | |
2793 | (delete-file "grit/call_peaks_support_fns.c") | |
2794 | (substitute* "setup.py" | |
2795 | (("Cython.Setup") "Cython.Build") | |
2796 | ;; Add numpy include path to fix compilation | |
2797 | (("pyx\", \\]") | |
2798 | (string-append "pyx\", ], include_dirs = ['" | |
2799 | (assoc-ref inputs "python-numpy") | |
2800 | "/lib/python2.7/site-packages/numpy/core/include/" | |
2801 | "']"))) #t) | |
2802 | %standard-phases))) | |
2803 | (inputs | |
2804 | `(("python-scipy" ,python2-scipy) | |
2805 | ("python-numpy" ,python2-numpy) | |
2806 | ("python-pysam" ,python2-pysam) | |
2807 | ("python-networkx" ,python2-networkx))) | |
2808 | (native-inputs | |
f3b98f4f | 2809 | `(("python-cython" ,python2-cython))) |
5854f685 RW |
2810 | (home-page "http://grit-bio.org") |
2811 | (synopsis "Tool for integrative analysis of RNA-seq type assays") | |
2812 | (description | |
2813 | "GRIT is designed to use RNA-seq, TES, and TSS data to build and quantify | |
2814 | full length transcript models. When none of these data sources are available, | |
2815 | GRIT can be run by providing a candidate set of TES or TSS sites. In | |
2816 | addition, GRIT can merge in reference junctions and gene boundaries. GRIT can | |
2817 | also be run in quantification mode, where it uses a provided GTF file and just | |
2818 | estimates transcript expression.") | |
2819 | (license license:gpl3+))) | |
2820 | ||
346a829a RW |
2821 | (define-public hisat |
2822 | (package | |
2823 | (name "hisat") | |
2824 | (version "0.1.4") | |
2825 | (source (origin | |
2826 | (method url-fetch) | |
2827 | (uri (string-append | |
2828 | "http://ccb.jhu.edu/software/hisat/downloads/hisat-" | |
2829 | version "-beta-source.zip")) | |
2830 | (sha256 | |
2831 | (base32 | |
2832 | "1k381ydranqxp09yf2y7w1d0chz5d59vb6jchi89hbb0prq19lk5")))) | |
2833 | (build-system gnu-build-system) | |
2834 | (arguments | |
e58d01fa RW |
2835 | `(#:tests? #f ;no check target |
2836 | #:make-flags '("allall" | |
2837 | ;; Disable unsupported `popcnt' instructions on | |
2838 | ;; architectures other than x86_64 | |
2839 | ,@(if (string-prefix? "x86_64" | |
2840 | (or (%current-target-system) | |
2841 | (%current-system))) | |
2842 | '() | |
2843 | '("POPCNT_CAPABILITY=0"))) | |
346a829a | 2844 | #:phases |
da6dd842 LC |
2845 | (alist-cons-after |
2846 | 'unpack 'patch-sources | |
2847 | (lambda _ | |
2848 | ;; XXX Cannot use snippet because zip files are not supported | |
2849 | (substitute* "Makefile" | |
2850 | (("^CC = .*$") "CC = gcc") | |
2851 | (("^CPP = .*$") "CPP = g++") | |
2852 | ;; replace BUILD_HOST and BUILD_TIME for deterministic build | |
2853 | (("-DBUILD_HOST=.*") "-DBUILD_HOST=\"\\\"guix\\\"\"") | |
2854 | (("-DBUILD_TIME=.*") "-DBUILD_TIME=\"\\\"0\\\"\"")) | |
2855 | (substitute* '("hisat-build" "hisat-inspect") | |
2856 | (("/usr/bin/env") (which "env")))) | |
2857 | (alist-replace | |
2858 | 'install | |
2859 | (lambda* (#:key outputs #:allow-other-keys) | |
84590149 | 2860 | (let ((bin (string-append (assoc-ref outputs "out") "/bin/"))) |
96c46210 LC |
2861 | (for-each (lambda (file) |
2862 | (install-file file bin)) | |
2863 | (find-files | |
2864 | "." | |
2865 | "hisat(-(build|align|inspect)(-(s|l)(-debug)*)*)*$")))) | |
da6dd842 | 2866 | (alist-delete 'configure %standard-phases))))) |
346a829a RW |
2867 | (native-inputs |
2868 | `(("unzip" ,unzip))) | |
2869 | (inputs | |
2870 | `(("perl" ,perl) | |
2871 | ("python" ,python) | |
2872 | ("zlib" ,zlib))) | |
60af3d82 RW |
2873 | ;; Non-portable SSE instructions are used so building fails on platforms |
2874 | ;; other than x86_64. | |
2875 | (supported-systems '("x86_64-linux")) | |
346a829a RW |
2876 | (home-page "http://ccb.jhu.edu/software/hisat/index.shtml") |
2877 | (synopsis "Hierarchical indexing for spliced alignment of transcripts") | |
2878 | (description | |
2879 | "HISAT is a fast and sensitive spliced alignment program for mapping | |
2880 | RNA-seq reads. In addition to one global FM index that represents a whole | |
2881 | genome, HISAT uses a large set of small FM indexes that collectively cover the | |
2882 | whole genome. These small indexes (called local indexes) combined with | |
2883 | several alignment strategies enable effective alignment of RNA-seq reads, in | |
2884 | particular, reads spanning multiple exons.") | |
2885 | (license license:gpl3+))) | |
2886 | ||
e84efc50 RW |
2887 | (define-public hisat2 |
2888 | (package | |
2889 | (name "hisat2") | |
2890 | (version "2.0.5") | |
2891 | (source | |
2892 | (origin | |
2893 | (method url-fetch) | |
2894 | ;; FIXME: a better source URL is | |
2895 | ;; (string-append "ftp://ftp.ccb.jhu.edu/pub/infphilo/hisat2" | |
2896 | ;; "/downloads/hisat2-" version "-source.zip") | |
2897 | ;; with hash "0lywnr8kijwsc2aw10dwxic0n0yvip6fl3rjlvc8zzwahamy4x7g" | |
2898 | ;; but it is currently unavailable. | |
2899 | (uri "https://github.com/infphilo/hisat2/archive/cba6e8cb.tar.gz") | |
2900 | (file-name (string-append name "-" version ".tar.gz")) | |
2901 | (sha256 | |
2902 | (base32 | |
2903 | "1mf2hdsyv7cd97xm9mp9a4qws02yrj95y6w6f6cdwnq0klp81r50")))) | |
2904 | (build-system gnu-build-system) | |
2905 | (arguments | |
2906 | `(#:tests? #f ; no check target | |
2907 | #:make-flags (list "CC=gcc" "CXX=g++" "allall") | |
2908 | #:modules ((guix build gnu-build-system) | |
2909 | (guix build utils) | |
2910 | (srfi srfi-26)) | |
2911 | #:phases | |
2912 | (modify-phases %standard-phases | |
2913 | (add-after 'unpack 'make-deterministic | |
2914 | (lambda _ | |
2915 | (substitute* "Makefile" | |
2916 | (("`date`") "0")) | |
2917 | #t)) | |
2918 | (delete 'configure) | |
2919 | (replace 'install | |
2920 | (lambda* (#:key outputs #:allow-other-keys) | |
2921 | (let* ((out (assoc-ref outputs "out")) | |
2922 | (bin (string-append out "/bin/")) | |
2923 | (doc (string-append out "/share/doc/hisat2/"))) | |
2924 | (for-each | |
2925 | (cut install-file <> bin) | |
2926 | (find-files "." | |
2927 | "hisat2(-(build|align|inspect)(-(s|l)(-debug)*)*)*$")) | |
2928 | (mkdir-p doc) | |
2929 | (install-file "doc/manual.inc.html" doc)) | |
2930 | #t))))) | |
2931 | (native-inputs | |
2932 | `(("unzip" ,unzip) ; needed for archive from ftp | |
2933 | ("perl" ,perl) | |
2934 | ("pandoc" ,ghc-pandoc))) ; for documentation | |
2935 | (home-page "http://ccb.jhu.edu/software/hisat2/index.shtml") | |
2936 | (synopsis "Graph-based alignment of genomic sequencing reads") | |
2937 | (description "HISAT2 is a fast and sensitive alignment program for mapping | |
2938 | next-generation sequencing reads (both DNA and RNA) to a population of human | |
2939 | genomes (as well as to a single reference genome). In addition to using one | |
2940 | global @dfn{graph FM} (GFM) index that represents a population of human | |
2941 | genomes, HISAT2 uses a large set of small GFM indexes that collectively cover | |
2942 | the whole genome. These small indexes, combined with several alignment | |
2943 | strategies, enable rapid and accurate alignment of sequencing reads. This new | |
2944 | indexing scheme is called a @dfn{Hierarchical Graph FM index} (HGFM).") | |
2945 | ;; HISAT2 contains files from Bowtie2, which is released under | |
2946 | ;; GPLv2 or later. The HISAT2 source files are released under | |
2947 | ;; GPLv3 or later. | |
2948 | (license license:gpl3+))) | |
2949 | ||
c684629f BW |
2950 | (define-public hmmer |
2951 | (package | |
2952 | (name "hmmer") | |
2953 | (version "3.1b2") | |
79f09fa2 BW |
2954 | (source |
2955 | (origin | |
2956 | (method url-fetch) | |
2957 | (uri (string-append | |
2958 | "http://eddylab.org/software/hmmer" | |
2959 | (version-prefix version 1) "/" | |
2960 | version "/hmmer-" version ".tar.gz")) | |
2961 | (sha256 | |
2962 | (base32 | |
2963 | "0djmgc0pfli0jilfx8hql1axhwhqxqb8rxg2r5rg07aw73sfs5nx")) | |
2964 | (patches (search-patches "hmmer-remove-cpu-specificity.patch")))) | |
c684629f | 2965 | (build-system gnu-build-system) |
b3546174 | 2966 | (native-inputs `(("perl" ,perl))) |
a83e6046 | 2967 | (home-page "http://hmmer.org/") |
c684629f BW |
2968 | (synopsis "Biosequence analysis using profile hidden Markov models") |
2969 | (description | |
2970 | "HMMER is used for searching sequence databases for homologs of protein | |
2971 | sequences, and for making protein sequence alignments. It implements methods | |
2972 | using probabilistic models called profile hidden Markov models (profile | |
2973 | HMMs).") | |
2974 | (license (list license:gpl3+ | |
2975 | ;; The bundled library 'easel' is distributed | |
2976 | ;; under The Janelia Farm Software License. | |
2977 | (license:non-copyleft | |
2978 | "file://easel/LICENSE" | |
2979 | "See easel/LICENSE in the distribution."))))) | |
2980 | ||
85652f59 RW |
2981 | (define-public htseq |
2982 | (package | |
2983 | (name "htseq") | |
2984 | (version "0.6.1") | |
2985 | (source (origin | |
2986 | (method url-fetch) | |
2987 | (uri (string-append | |
2988 | "https://pypi.python.org/packages/source/H/HTSeq/HTSeq-" | |
2989 | version ".tar.gz")) | |
2990 | (sha256 | |
2991 | (base32 | |
2992 | "1i85ppf2j2lj12m0x690qq5nn17xxk23pbbx2c83r8ayb5wngzwv")))) | |
2993 | (build-system python-build-system) | |
2994 | (arguments `(#:python ,python-2)) ; only Python 2 is supported | |
0536727e RW |
2995 | ;; Numpy needs to be propagated when htseq is used as a Python library. |
2996 | (propagated-inputs | |
2997 | `(("python-numpy" ,python2-numpy))) | |
578b05d9 RW |
2998 | (inputs |
2999 | `(("python-pysam" ,python2-pysam))) | |
85652f59 RW |
3000 | (home-page "http://www-huber.embl.de/users/anders/HTSeq/") |
3001 | (synopsis "Analysing high-throughput sequencing data with Python") | |
3002 | (description | |
3003 | "HTSeq is a Python package that provides infrastructure to process data | |
3004 | from high-throughput sequencing assays.") | |
3005 | (license license:gpl3+))) | |
3006 | ||
1ad15c16 | 3007 | (define-public java-htsjdk |
15a3c3d4 | 3008 | (package |
1ad15c16 | 3009 | (name "java-htsjdk") |
15a3c3d4 RW |
3010 | (version "1.129") |
3011 | (source (origin | |
3012 | (method url-fetch) | |
3013 | (uri (string-append | |
3014 | "https://github.com/samtools/htsjdk/archive/" | |
3015 | version ".tar.gz")) | |
3016 | (file-name (string-append name "-" version ".tar.gz")) | |
3017 | (sha256 | |
3018 | (base32 | |
3019 | "0asdk9b8jx2ij7yd6apg9qx03li8q7z3ml0qy2r2qczkra79y6fw")) | |
3020 | (modules '((guix build utils))) | |
3021 | ;; remove build dependency on git | |
3022 | (snippet '(substitute* "build.xml" | |
3023 | (("failifexecutionfails=\"true\"") | |
3024 | "failifexecutionfails=\"false\""))))) | |
10b4a969 | 3025 | (build-system ant-build-system) |
15a3c3d4 | 3026 | (arguments |
10b4a969 RW |
3027 | `(#:tests? #f ; test require Internet access |
3028 | #:make-flags | |
3029 | (list (string-append "-Ddist=" (assoc-ref %outputs "out") | |
3030 | "/share/java/htsjdk/")) | |
3031 | #:build-target "all" | |
3032 | #:phases | |
3033 | (modify-phases %standard-phases | |
3034 | ;; The build phase also installs the jars | |
3035 | (delete 'install)))) | |
15a3c3d4 RW |
3036 | (home-page "http://samtools.github.io/htsjdk/") |
3037 | (synopsis "Java API for high-throughput sequencing data (HTS) formats") | |
3038 | (description | |
3039 | "HTSJDK is an implementation of a unified Java library for accessing | |
3040 | common file formats, such as SAM and VCF, used for high-throughput | |
3041 | sequencing (HTS) data. There are also an number of useful utilities for | |
3042 | manipulating HTS data.") | |
3043 | (license license:expat))) | |
3044 | ||
e7c09730 RW |
3045 | (define-public htslib |
3046 | (package | |
3047 | (name "htslib") | |
4fb6d128 | 3048 | (version "1.5") |
e7c09730 RW |
3049 | (source (origin |
3050 | (method url-fetch) | |
3051 | (uri (string-append | |
3052 | "https://github.com/samtools/htslib/releases/download/" | |
3053 | version "/htslib-" version ".tar.bz2")) | |
3054 | (sha256 | |
3055 | (base32 | |
4fb6d128 | 3056 | "0bcjmnbwp2bib1z1bkrp95w9v2syzdwdfqww10mkb1hxlmg52ax0")))) |
e7c09730 RW |
3057 | (build-system gnu-build-system) |
3058 | (arguments | |
3059 | `(#:phases | |
3060 | (modify-phases %standard-phases | |
3061 | (add-after | |
3062 | 'unpack 'patch-tests | |
3063 | (lambda _ | |
3064 | (substitute* "test/test.pl" | |
3065 | (("/bin/bash") (which "bash"))) | |
3066 | #t))))) | |
3067 | (inputs | |
a9e4a1e6 BW |
3068 | `(("openssl" ,openssl) |
3069 | ("curl" ,curl) | |
3070 | ("zlib" ,zlib))) | |
e7c09730 RW |
3071 | (native-inputs |
3072 | `(("perl" ,perl))) | |
3073 | (home-page "http://www.htslib.org") | |
3074 | (synopsis "C library for reading/writing high-throughput sequencing data") | |
3075 | (description | |
3076 | "HTSlib is a C library for reading/writing high-throughput sequencing | |
3077 | data. It also provides the bgzip, htsfile, and tabix utilities.") | |
3078 | ;; Files under cram/ are released under the modified BSD license; | |
3079 | ;; the rest is released under the Expat license | |
3080 | (license (list license:expat license:bsd-3)))) | |
3081 | ||
bca2c576 BW |
3082 | ;; This package should be removed once no packages rely upon it. |
3083 | (define htslib-1.3 | |
3084 | (package | |
3085 | (inherit htslib) | |
3086 | (version "1.3.1") | |
3087 | (source (origin | |
3088 | (method url-fetch) | |
3089 | (uri (string-append | |
3090 | "https://github.com/samtools/htslib/releases/download/" | |
3091 | version "/htslib-" version ".tar.bz2")) | |
3092 | (sha256 | |
3093 | (base32 | |
3094 | "1rja282fwdc25ql6izkhdyh8ppw8x2fs0w0js78zgkmqjlikmma9")))))) | |
3095 | ||
c4325f62 RW |
3096 | (define-public idr |
3097 | (package | |
3098 | (name "idr") | |
3099 | (version "2.0.0") | |
3100 | (source (origin | |
3101 | (method url-fetch) | |
3102 | (uri (string-append | |
3103 | "https://github.com/nboley/idr/archive/" | |
3104 | version ".tar.gz")) | |
3105 | (file-name (string-append name "-" version ".tar.gz")) | |
3106 | (sha256 | |
3107 | (base32 | |
3108 | "1k3x44biak00aiv3hpm1yd6nn4hhp7n0qnbs3zh2q9sw7qr1qj5r")))) | |
3109 | (build-system python-build-system) | |
3110 | (arguments | |
14386fc7 | 3111 | `(#:tests? #f)) ; FIXME: "ImportError: No module named 'utility'" |
b7a820fc | 3112 | (propagated-inputs |
c4325f62 | 3113 | `(("python-scipy" ,python-scipy) |
b7a820fc | 3114 | ("python-sympy" ,python-sympy) |
c4325f62 RW |
3115 | ("python-numpy" ,python-numpy) |
3116 | ("python-matplotlib" ,python-matplotlib))) | |
3117 | (native-inputs | |
f3b98f4f | 3118 | `(("python-cython" ,python-cython))) |
c4325f62 RW |
3119 | (home-page "https://github.com/nboley/idr") |
3120 | (synopsis "Tool to measure the irreproducible discovery rate (IDR)") | |
3121 | (description | |
3122 | "The IDR (Irreproducible Discovery Rate) framework is a unified approach | |
3123 | to measure the reproducibility of findings identified from replicate | |
3124 | experiments and provide highly stable thresholds based on reproducibility.") | |
3125 | (license license:gpl3+))) | |
3126 | ||
43c565d2 RW |
3127 | (define-public jellyfish |
3128 | (package | |
3129 | (name "jellyfish") | |
3130 | (version "2.2.4") | |
3131 | (source (origin | |
3132 | (method url-fetch) | |
3133 | (uri (string-append "https://github.com/gmarcais/Jellyfish/" | |
3134 | "releases/download/v" version | |
3135 | "/jellyfish-" version ".tar.gz")) | |
3136 | (sha256 | |
3137 | (base32 | |
3138 | "0a6xnynqy2ibfbfz86b9g2m2dgm7f1469pmymkpam333gi3p26nk")))) | |
3139 | (build-system gnu-build-system) | |
3140 | (outputs '("out" ;for library | |
3141 | "ruby" ;for Ruby bindings | |
3142 | "python")) ;for Python bindings | |
3143 | (arguments | |
3144 | `(#:configure-flags | |
3145 | (list (string-append "--enable-ruby-binding=" | |
3146 | (assoc-ref %outputs "ruby")) | |
3147 | (string-append "--enable-python-binding=" | |
3148 | (assoc-ref %outputs "python"))) | |
3149 | #:phases | |
3150 | (modify-phases %standard-phases | |
3151 | (add-before 'check 'set-SHELL-variable | |
3152 | (lambda _ | |
3153 | ;; generator_manager.hpp either uses /bin/sh or $SHELL | |
3154 | ;; to run tests. | |
3155 | (setenv "SHELL" (which "bash")) | |
3156 | #t))))) | |
3157 | (native-inputs | |
3158 | `(("bc" ,bc) | |
3159 | ("time" ,time) | |
3160 | ("ruby" ,ruby) | |
3161 | ("python" ,python-2))) | |
3162 | (synopsis "Tool for fast counting of k-mers in DNA") | |
3163 | (description | |
3164 | "Jellyfish is a tool for fast, memory-efficient counting of k-mers in | |
3165 | DNA. A k-mer is a substring of length k, and counting the occurrences of all | |
3166 | such substrings is a central step in many analyses of DNA sequence. Jellyfish | |
3167 | is a command-line program that reads FASTA and multi-FASTA files containing | |
3168 | DNA sequences. It outputs its k-mer counts in a binary format, which can be | |
3169 | translated into a human-readable text format using the @code{jellyfish dump} | |
3170 | command, or queried for specific k-mers with @code{jellyfish query}.") | |
3171 | (home-page "http://www.genome.umd.edu/jellyfish.html") | |
6e8faf77 EF |
3172 | ;; From their website: JELLYFISH runs on 64-bit Intel-compatible processors |
3173 | (supported-systems '("x86_64-linux")) | |
43c565d2 RW |
3174 | ;; The combined work is published under the GPLv3 or later. Individual |
3175 | ;; files such as lib/jsoncpp.cpp are released under the Expat license. | |
3176 | (license (list license:gpl3+ license:expat)))) | |
3177 | ||
94ff3157 BW |
3178 | (define-public khmer |
3179 | (package | |
3180 | (name "khmer") | |
3181 | (version "2.0") | |
3182 | (source | |
3183 | (origin | |
3184 | (method url-fetch) | |
3185 | (uri (pypi-uri "khmer" version)) | |
3186 | (sha256 | |
3187 | (base32 | |
3188 | "0wb05shqh77v00256qlm68vbbx3kl76fyzihszbz5nhanl4ni33a")) | |
3189 | (patches (search-patches "khmer-use-libraries.patch")))) | |
3190 | (build-system python-build-system) | |
3191 | (arguments | |
3192 | `(#:phases | |
3193 | (modify-phases %standard-phases | |
3194 | (add-after 'unpack 'set-paths | |
3195 | (lambda* (#:key inputs outputs #:allow-other-keys) | |
3196 | ;; Delete bundled libraries. | |
3197 | (delete-file-recursively "third-party/zlib") | |
3198 | (delete-file-recursively "third-party/bzip2") | |
3199 | ;; Replace bundled seqan. | |
3200 | (let* ((seqan-all "third-party/seqan") | |
3201 | (seqan-include (string-append | |
3202 | seqan-all "/core/include"))) | |
3203 | (delete-file-recursively seqan-all) | |
3204 | (copy-recursively (string-append (assoc-ref inputs "seqan") | |
3205 | "/include/seqan") | |
3206 | (string-append seqan-include "/seqan"))) | |
3207 | ;; We do not replace the bundled MurmurHash as the canonical | |
3208 | ;; repository for this code 'SMHasher' is unsuitable for | |
3209 | ;; providing a library. See | |
3210 | ;; https://lists.gnu.org/archive/html/guix-devel/2016-06/msg00977.html | |
3211 | #t)) | |
3212 | (add-after 'unpack 'set-cc | |
3213 | (lambda _ | |
3214 | (setenv "CC" "gcc") | |
3215 | #t)) | |
3216 | ;; It is simpler to test after installation. | |
3217 | (delete 'check) | |
3218 | (add-after 'install 'post-install-check | |
3219 | (lambda* (#:key inputs outputs #:allow-other-keys) | |
3220 | (let ((out (assoc-ref outputs "out"))) | |
3221 | (setenv "PATH" | |
3222 | (string-append | |
3223 | (getenv "PATH") | |
3224 | ":" | |
3225 | (assoc-ref outputs "out") | |
3226 | "/bin")) | |
3227 | (setenv "PYTHONPATH" | |
3228 | (string-append | |
3229 | (getenv "PYTHONPATH") | |
3230 | ":" | |
3231 | out | |
3232 | "/lib/python" | |
3233 | (string-take (string-take-right | |
3234 | (assoc-ref inputs "python") 5) 3) | |
3235 | "/site-packages")) | |
3236 | (with-directory-excursion "build" | |
3237 | (zero? (system* "nosetests" "khmer" "--attr" | |
3238 | "!known_failing"))))))))) | |
3239 | (native-inputs | |
3240 | `(("seqan" ,seqan) | |
3241 | ("python-nose" ,python-nose))) | |
3242 | (inputs | |
3243 | `(("zlib" ,zlib) | |
3244 | ("bzip2" ,bzip2) | |
3245 | ("python-screed" ,python-screed) | |
cf1d5814 BW |
3246 | ("python-bz2file" ,python-bz2file) |
3247 | ;; Tests fail when gcc-5 is used for compilation. Use gcc-4.9 at least | |
3248 | ;; until the next version of khmer (likely 2.1) is released. | |
3249 | ("gcc" ,gcc-4.9))) | |
94ff3157 BW |
3250 | (home-page "https://khmer.readthedocs.org/") |
3251 | (synopsis "K-mer counting, filtering and graph traversal library") | |
3252 | (description "The khmer software is a set of command-line tools for | |
3253 | working with DNA shotgun sequencing data from genomes, transcriptomes, | |
3254 | metagenomes and single cells. Khmer can make de novo assemblies faster, and | |
3255 | sometimes better. Khmer can also identify and fix problems with shotgun | |
3256 | data.") | |
8157af2e EF |
3257 | ;; When building on i686, armhf and mips64el, we get the following error: |
3258 | ;; error: ['khmer', 'khmer.tests', 'oxli'] require 64-bit operating system | |
3259 | (supported-systems '("x86_64-linux")) | |
94ff3157 BW |
3260 | (license license:bsd-3))) |
3261 | ||
b9a601d9 RJ |
3262 | (define-public kaiju |
3263 | (package | |
3264 | (name "kaiju") | |
3265 | (version "1.5.0") | |
3266 | (source (origin | |
3267 | (method url-fetch) | |
3268 | (uri (string-append | |
3269 | "https://github.com/bioinformatics-centre/kaiju/archive/v" | |
3270 | version ".tar.gz")) | |
3271 | (file-name (string-append name "-" version ".tar.gz")) | |
3272 | (sha256 | |
3273 | (base32 | |
3274 | "0afbfalfw9y39bkwnqjrh9bghs118ws1pzj5h8l0nblgn3mbjdks")))) | |
3275 | (build-system gnu-build-system) | |
3276 | (arguments | |
3277 | `(#:tests? #f ; There are no tests. | |
3278 | #:phases | |
3279 | (modify-phases %standard-phases | |
3280 | (delete 'configure) | |
3281 | (add-before 'build 'move-to-src-dir | |
3282 | (lambda _ (chdir "src") #t)) | |
3283 | (replace 'install | |
3284 | (lambda* (#:key inputs outputs #:allow-other-keys) | |
3285 | (let ((bin (string-append (assoc-ref outputs "out") "/bin"))) | |
3286 | (mkdir-p bin) | |
3287 | (chdir "..") | |
3288 | (copy-recursively "bin" bin) | |
3289 | (copy-recursively "util" bin)) | |
3290 | #t))))) | |
3291 | (inputs | |
3292 | `(("perl" ,perl))) | |
3293 | (home-page "http://kaiju.binf.ku.dk/") | |
3294 | (synopsis "Fast and sensitive taxonomic classification for metagenomics") | |
3295 | (description "Kaiju is a program for sensitive taxonomic classification | |
3296 | of high-throughput sequencing reads from metagenomic whole genome sequencing | |
3297 | experiments.") | |
3298 | (license license:gpl3+))) | |
3299 | ||
d57e6d0f RW |
3300 | (define-public macs |
3301 | (package | |
3302 | (name "macs") | |
0d0bcaa0 | 3303 | (version "2.1.0.20151222") |
d57e6d0f RW |
3304 | (source (origin |
3305 | (method url-fetch) | |
43ec07f1 | 3306 | (uri (pypi-uri "MACS2" version)) |
d57e6d0f RW |
3307 | (sha256 |
3308 | (base32 | |
0d0bcaa0 | 3309 | "1r2hcz6irhcq7lwbafjks98jbn34hv05avgbdjnp6w6mlfjkf8x5")))) |
d57e6d0f RW |
3310 | (build-system python-build-system) |
3311 | (arguments | |
3312 | `(#:python ,python-2 ; only compatible with Python 2.7 | |
3313 | #:tests? #f)) ; no test target | |
3314 | (inputs | |
3315 | `(("python-numpy" ,python2-numpy))) | |
7bf837fd | 3316 | (home-page "https://github.com/taoliu/MACS/") |
d57e6d0f RW |
3317 | (synopsis "Model based analysis for ChIP-Seq data") |
3318 | (description | |
3319 | "MACS is an implementation of a ChIP-Seq analysis algorithm for | |
3320 | identifying transcript factor binding sites named Model-based Analysis of | |
3321 | ChIP-Seq (MACS). MACS captures the influence of genome complexity to evaluate | |
3322 | the significance of enriched ChIP regions and it improves the spatial | |
3323 | resolution of binding sites through combining the information of both | |
3324 | sequencing tag position and orientation.") | |
3325 | (license license:bsd-3))) | |
3326 | ||
41ddebdd BW |
3327 | (define-public mafft |
3328 | (package | |
3329 | (name "mafft") | |
88eb119f | 3330 | (version "7.310") |
41ddebdd BW |
3331 | (source (origin |
3332 | (method url-fetch) | |
3333 | (uri (string-append | |
3334 | "http://mafft.cbrc.jp/alignment/software/mafft-" version | |
3335 | "-without-extensions-src.tgz")) | |
3336 | (file-name (string-append name "-" version ".tgz")) | |
3337 | (sha256 | |
3338 | (base32 | |
88eb119f | 3339 | "0gbsaz6z2qa307kd7wfb06c3y4ikmv1hsdvlns11f6zq4w1z9pwc")))) |
41ddebdd BW |
3340 | (build-system gnu-build-system) |
3341 | (arguments | |
3342 | `(#:tests? #f ; no automated tests, though there are tests in the read me | |
3343 | #:make-flags (let ((out (assoc-ref %outputs "out"))) | |
3344 | (list (string-append "PREFIX=" out) | |
3345 | (string-append "BINDIR=" | |
3346 | (string-append out "/bin")))) | |
3347 | #:phases | |
3348 | (modify-phases %standard-phases | |
3349 | (add-after 'unpack 'enter-dir | |
101e8f71 | 3350 | (lambda _ (chdir "core") #t)) |
41ddebdd | 3351 | (add-after 'enter-dir 'patch-makefile |
101e8f71 BW |
3352 | (lambda _ |
3353 | ;; on advice from the MAFFT authors, there is no need to | |
3354 | ;; distribute mafft-profile, mafft-distance, or | |
3355 | ;; mafft-homologs.rb as they are too "specialised". | |
3356 | (substitute* "Makefile" | |
3357 | ;; remove mafft-homologs.rb from SCRIPTS | |
3358 | (("^SCRIPTS = mafft mafft-homologs.rb") | |
3359 | "SCRIPTS = mafft") | |
3360 | ;; remove mafft-homologs from MANPAGES | |
3361 | (("^MANPAGES = mafft.1 mafft-homologs.1") | |
3362 | "MANPAGES = mafft.1") | |
3363 | ;; remove mafft-distance from PROGS | |
3364 | (("^PROGS = dvtditr dndfast7 dndblast sextet5 mafft-distance") | |
3365 | "PROGS = dvtditr dndfast7 dndblast sextet5") | |
3366 | ;; remove mafft-profile from PROGS | |
3367 | (("splittbfast disttbfast tbfast mafft-profile 2cl mccaskillwrap") | |
3368 | "splittbfast disttbfast tbfast f2cl mccaskillwrap") | |
3369 | (("^rm -f mafft-profile mafft-profile.exe") "#") | |
3370 | (("^rm -f mafft-distance mafft-distance.exe") ")#") | |
3371 | ;; do not install MAN pages in libexec folder | |
3372 | (("^\t\\$\\(INSTALL\\) -m 644 \\$\\(MANPAGES\\) \ | |
41ddebdd | 3373 | \\$\\(DESTDIR\\)\\$\\(LIBDIR\\)") "#")) |
101e8f71 | 3374 | #t)) |
02f35bb5 BW |
3375 | (add-after 'enter-dir 'patch-paths |
3376 | (lambda* (#:key inputs #:allow-other-keys) | |
3377 | (substitute* '("pairash.c" | |
3378 | "mafft.tmpl") | |
3379 | (("perl") (which "perl")) | |
3380 | (("([\"`| ])awk" _ prefix) | |
3381 | (string-append prefix (which "awk"))) | |
3382 | (("grep") (which "grep"))) | |
3383 | #t)) | |
101e8f71 BW |
3384 | (delete 'configure) |
3385 | (add-after 'install 'wrap-programs | |
3386 | (lambda* (#:key outputs #:allow-other-keys) | |
3387 | (let* ((out (assoc-ref outputs "out")) | |
3388 | (bin (string-append out "/bin")) | |
3389 | (path (string-append | |
3390 | (assoc-ref %build-inputs "coreutils") "/bin:"))) | |
3391 | (for-each (lambda (file) | |
3392 | (wrap-program file | |
3393 | `("PATH" ":" prefix (,path)))) | |
3394 | (find-files bin))) | |
3395 | #t))))) | |
41ddebdd | 3396 | (inputs |
02f35bb5 | 3397 | `(("perl" ,perl) |
71461f88 | 3398 | ("ruby" ,ruby) |
02f35bb5 | 3399 | ("gawk" ,gawk) |
101e8f71 BW |
3400 | ("grep" ,grep) |
3401 | ("coreutils" ,coreutils))) | |
41ddebdd BW |
3402 | (home-page "http://mafft.cbrc.jp/alignment/software/") |
3403 | (synopsis "Multiple sequence alignment program") | |
3404 | (description | |
3405 | "MAFFT offers a range of multiple alignment methods for nucleotide and | |
3406 | protein sequences. For instance, it offers L-INS-i (accurate; for alignment | |
3407 | of <~200 sequences) and FFT-NS-2 (fast; for alignment of <~30,000 | |
3408 | sequences).") | |
3409 | (license (license:non-copyleft | |
3410 | "http://mafft.cbrc.jp/alignment/software/license.txt" | |
3411 | "BSD-3 with different formatting")))) | |
8fd790eb | 3412 | |
84be3b99 MB |
3413 | (define-public mash |
3414 | (package | |
3415 | (name "mash") | |
3416 | (version "1.1.1") | |
3417 | (source (origin | |
3418 | (method url-fetch) | |
3419 | (uri (string-append | |
3420 | "https://github.com/marbl/mash/archive/v" | |
3421 | version ".tar.gz")) | |
3422 | (file-name (string-append name "-" version ".tar.gz")) | |
3423 | (sha256 | |
3424 | (base32 | |
3425 | "08znbvqq5xknfhmpp3wcj574zvi4p7i8zifi67c9qw9a6ikp42fj")) | |
3426 | (modules '((guix build utils))) | |
3427 | (snippet | |
3428 | ;; Delete bundled kseq. | |
3429 | ;; TODO: Also delete bundled murmurhash and open bloom filter. | |
3430 | '(delete-file "src/mash/kseq.h")))) | |
3431 | (build-system gnu-build-system) | |
3432 | (arguments | |
3433 | `(#:tests? #f ; No tests. | |
3434 | #:configure-flags | |
3435 | (list | |
3436 | (string-append "--with-capnp=" (assoc-ref %build-inputs "capnproto")) | |
3437 | (string-append "--with-gsl=" (assoc-ref %build-inputs "gsl"))) | |
3438 | #:make-flags (list "CC=gcc") | |
3439 | #:phases | |
3440 | (modify-phases %standard-phases | |
3441 | (add-after 'unpack 'fix-includes | |
3442 | (lambda _ | |
3443 | (substitute* '("src/mash/Sketch.cpp" "src/mash/CommandFind.cpp") | |
3444 | (("^#include \"kseq\\.h\"") | |
3445 | "#include \"htslib/kseq.h\"")) | |
3446 | #t)) | |
3447 | (add-before 'configure 'autoconf | |
3448 | (lambda _ (zero? (system* "autoconf"))))))) | |
3449 | (native-inputs | |
3450 | `(("autoconf" ,autoconf) | |
3451 | ;; Capnproto and htslib are statically embedded in the final | |
3452 | ;; application. Therefore we also list their licenses, below. | |
3453 | ("capnproto" ,capnproto) | |
3454 | ("htslib" ,htslib))) | |
3455 | (inputs | |
3456 | `(("gsl" ,gsl) | |
3457 | ("zlib" ,zlib))) | |
3458 | (supported-systems '("x86_64-linux")) | |
3459 | (home-page "https://mash.readthedocs.io") | |
3460 | (synopsis "Fast genome and metagenome distance estimation using MinHash") | |
3461 | (description "Mash is a fast sequence distance estimator that uses the | |
3462 | MinHash algorithm and is designed to work with genomes and metagenomes in the | |
3463 | form of assemblies or reads.") | |
3464 | (license (list license:bsd-3 ; Mash | |
3465 | license:expat ; HTSlib and capnproto | |
3466 | license:public-domain ; MurmurHash 3 | |
3467 | license:cpl1.0)))) ; Open Bloom Filter | |
3468 | ||
8fd790eb | 3469 | (define-public metabat |
f3f68a44 BW |
3470 | (package |
3471 | (name "metabat") | |
a9085f0c | 3472 | (version "2.11.2") |
f3f68a44 BW |
3473 | (source |
3474 | (origin | |
3475 | (method url-fetch) | |
3476 | (uri (string-append "https://bitbucket.org/berkeleylab/metabat/get/v" | |
3477 | version ".tar.gz")) | |
3478 | (file-name (string-append name "-" version ".tar.gz")) | |
3479 | (sha256 | |
3480 | (base32 | |
a9085f0c | 3481 | "0rws9r1ziv6way8cf49jg8bzj7x2131kfqkhj8byf0z5hnrq3bwv")) |
f3f68a44 BW |
3482 | (patches (search-patches "metabat-remove-compilation-date.patch" |
3483 | "metabat-fix-compilation.patch")))) | |
8fd790eb BW |
3484 | (build-system gnu-build-system) |
3485 | (arguments | |
3486 | `(#:phases | |
3487 | (modify-phases %standard-phases | |
3488 | (add-after 'unpack 'fix-includes | |
45469ebe BW |
3489 | (lambda _ |
3490 | (substitute* "src/BamUtils.h" | |
3491 | (("^#include \"bam/bam\\.h\"") | |
3492 | "#include \"samtools/bam.h\"") | |
3493 | (("^#include \"bam/sam\\.h\"") | |
3494 | "#include \"samtools/sam.h\"")) | |
3495 | (substitute* "src/KseqReader.h" | |
3496 | (("^#include \"bam/kseq\\.h\"") | |
3497 | "#include \"htslib/kseq.h\"")) | |
3498 | #t)) | |
8fd790eb | 3499 | (add-after 'unpack 'fix-scons |
f3f68a44 BW |
3500 | (lambda* (#:key inputs #:allow-other-keys) |
3501 | (substitute* "SConstruct" | |
3502 | (("^htslib_dir += 'samtools'") | |
3503 | (string-append "htslib_dir = '" | |
3504 | (assoc-ref inputs "htslib") | |
3505 | "'")) | |
3506 | (("^samtools_dir = 'samtools'") | |
3507 | (string-append "samtools_dir = '" | |
3508 | (assoc-ref inputs "samtools") | |
3509 | "'")) | |
3510 | (("^findStaticOrShared\\('bam', hts_lib") | |
3511 | (string-append "findStaticOrShared('bam', '" | |
3512 | (assoc-ref inputs "samtools") | |
3513 | "/lib'")) | |
3514 | ;; Do not distribute README. | |
3515 | (("^env\\.Install\\(idir_prefix, 'README\\.md'\\)") "")) | |
3516 | #t)) | |
8fd790eb BW |
3517 | (delete 'configure) |
3518 | (replace 'build | |
f3f68a44 BW |
3519 | (lambda* (#:key inputs outputs #:allow-other-keys) |
3520 | (mkdir (assoc-ref outputs "out")) | |
3521 | (zero? (system* "scons" | |
3522 | (string-append | |
3523 | "PREFIX=" | |
3524 | (assoc-ref outputs "out")) | |
3525 | (string-append | |
3526 | "BOOST_ROOT=" | |
3527 | (assoc-ref inputs "boost")) | |
3528 | "install")))) | |
45469ebe | 3529 | ;; Check and install are carried out during build phase. |
8fd790eb BW |
3530 | (delete 'check) |
3531 | (delete 'install)))) | |
3532 | (inputs | |
3533 | `(("zlib" ,zlib) | |
3534 | ("perl" ,perl) | |
3535 | ("samtools" ,samtools) | |
3536 | ("htslib" ,htslib) | |
3537 | ("boost" ,boost))) | |
3538 | (native-inputs | |
3539 | `(("scons" ,scons))) | |
3540 | (home-page "https://bitbucket.org/berkeleylab/metabat") | |
3541 | (synopsis | |
3542 | "Reconstruction of single genomes from complex microbial communities") | |
3543 | (description | |
3544 | "Grouping large genomic fragments assembled from shotgun metagenomic | |
3545 | sequences to deconvolute complex microbial communities, or metagenome binning, | |
3546 | enables the study of individual organisms and their interactions. MetaBAT is | |
3547 | an automated metagenome binning software, which integrates empirical | |
3548 | probabilistic distances of genome abundance and tetranucleotide frequency.") | |
d931a4bb EF |
3549 | ;; The source code contains inline assembly. |
3550 | (supported-systems '("x86_64-linux" "i686-linux")) | |
f3f68a44 BW |
3551 | (license (license:non-copyleft "file://license.txt" |
3552 | "See license.txt in the distribution.")))) | |
8fd790eb | 3553 | |
318c0aee MB |
3554 | (define-public minced |
3555 | (package | |
3556 | (name "minced") | |
3557 | (version "0.2.0") | |
3558 | (source (origin | |
3559 | (method url-fetch) | |
3560 | (uri (string-append | |
3561 | "https://github.com/ctSkennerton/minced/archive/" | |
3562 | version ".tar.gz")) | |
3563 | (file-name (string-append name "-" version ".tar.gz")) | |
3564 | (sha256 | |
3565 | (base32 | |
3566 | "0wxmlsapxfpxfd3ps9636h7i2xy6la8i42mwh0j2lsky63h63jp1")))) | |
3567 | (build-system gnu-build-system) | |
3568 | (arguments | |
3569 | `(#:test-target "test" | |
3570 | #:phases | |
3571 | (modify-phases %standard-phases | |
3572 | (delete 'configure) | |
3573 | (add-before 'check 'fix-test | |
3574 | (lambda _ | |
3575 | ;; Fix test for latest version. | |
3576 | (substitute* "t/Aquifex_aeolicus_VF5.expected" | |
3577 | (("minced:0.1.6") "minced:0.2.0")) | |
3578 | #t)) | |
3579 | (replace 'install ; No install target. | |
3580 | (lambda* (#:key inputs outputs #:allow-other-keys) | |
3581 | (let* ((out (assoc-ref outputs "out")) | |
3582 | (bin (string-append out "/bin")) | |
3583 | (wrapper (string-append bin "/minced"))) | |
3584 | ;; Minced comes with a wrapper script that tries to figure out where | |
3585 | ;; it is located before running the JAR. Since these paths are known | |
3586 | ;; to us, we build our own wrapper to avoid coreutils dependency. | |
3587 | (install-file "minced.jar" bin) | |
3588 | (with-output-to-file wrapper | |
3589 | (lambda _ | |
3590 | (display | |
3591 | (string-append | |
3592 | "#!" (assoc-ref inputs "bash") "/bin/sh\n\n" | |
3593 | (assoc-ref inputs "jre") "/bin/java -jar " | |
3594 | bin "/minced.jar \"$@\"\n")))) | |
3595 | (chmod wrapper #o555))))))) | |
3596 | (native-inputs | |
3597 | `(("jdk" ,icedtea "jdk"))) | |
3598 | (inputs | |
3599 | `(("bash" ,bash) | |
3600 | ("jre" ,icedtea "out"))) | |
3601 | (home-page "https://github.com/ctSkennerton/minced") | |
3602 | (synopsis "Mining CRISPRs in Environmental Datasets") | |
3603 | (description | |
3604 | "MinCED is a program to find Clustered Regularly Interspaced Short | |
3605 | Palindromic Repeats (CRISPRs) in DNA sequences. It can be used for | |
3606 | unassembled metagenomic reads, but is mainly designed for full genomes and | |
3607 | assembled metagenomic sequence.") | |
3608 | (license license:gpl3+))) | |
3609 | ||
ddd82e0e RW |
3610 | (define-public miso |
3611 | (package | |
3612 | (name "miso") | |
3613 | (version "0.5.3") | |
3614 | (source (origin | |
3615 | (method url-fetch) | |
3616 | (uri (string-append | |
86517de6 | 3617 | "https://pypi.python.org/packages/source/m/misopy/misopy-" |
ddd82e0e RW |
3618 | version ".tar.gz")) |
3619 | (sha256 | |
3620 | (base32 | |
3621 | "0x446867az8ir0z8c1vjqffkp0ma37wm4sylixnkhgawllzx8v5w")) | |
3622 | (modules '((guix build utils))) | |
ddd82e0e RW |
3623 | (snippet |
3624 | '(substitute* "setup.py" | |
0ec8b206 RW |
3625 | ;; Use setuptools, or else the executables are not |
3626 | ;; installed. | |
3627 | (("distutils.core") "setuptools") | |
3628 | ;; use "gcc" instead of "cc" for compilation | |
ddd82e0e RW |
3629 | (("^defines") |
3630 | "cc.set_executables( | |
3631 | compiler='gcc', | |
3632 | compiler_so='gcc', | |
3633 | linker_exe='gcc', | |
3634 | linker_so='gcc -shared'); defines"))))) | |
3635 | (build-system python-build-system) | |
3636 | (arguments | |
3637 | `(#:python ,python-2 ; only Python 2 is supported | |
3638 | #:tests? #f)) ; no "test" target | |
3639 | (inputs | |
3640 | `(("samtools" ,samtools) | |
3641 | ("python-numpy" ,python2-numpy) | |
3642 | ("python-pysam" ,python2-pysam) | |
3643 | ("python-scipy" ,python2-scipy) | |
3644 | ("python-matplotlib" ,python2-matplotlib))) | |
3645 | (native-inputs | |
f3b98f4f HG |
3646 | `(("python-mock" ,python2-mock) ;for tests |
3647 | ("python-pytz" ,python2-pytz))) ;for tests | |
ddd82e0e RW |
3648 | (home-page "http://genes.mit.edu/burgelab/miso/index.html") |
3649 | (synopsis "Mixture of Isoforms model for RNA-Seq isoform quantitation") | |
3650 | (description | |
3651 | "MISO (Mixture-of-Isoforms) is a probabilistic framework that quantitates | |
3652 | the expression level of alternatively spliced genes from RNA-Seq data, and | |
3653 | identifies differentially regulated isoforms or exons across samples. By | |
3654 | modeling the generative process by which reads are produced from isoforms in | |
3655 | RNA-Seq, the MISO model uses Bayesian inference to compute the probability | |
3656 | that a read originated from a particular isoform.") | |
3657 | (license license:gpl2))) | |
3658 | ||
324efb88 BW |
3659 | (define-public muscle |
3660 | (package | |
3661 | (name "muscle") | |
3662 | (version "3.8.1551") | |
3663 | (source (origin | |
3664 | (method url-fetch/tarbomb) | |
324efb88 BW |
3665 | (uri (string-append |
3666 | "http://www.drive5.com/muscle/muscle_src_" | |
3667 | version ".tar.gz")) | |
3668 | (sha256 | |
3669 | (base32 | |
3670 | "0bj8kj7sdizy3987zx6w7axihk40fk8rn76mpbqqjcnd64i5a367")))) | |
3671 | (build-system gnu-build-system) | |
3672 | (arguments | |
3673 | `(#:make-flags (list "LDLIBS = -lm") | |
3674 | #:phases | |
3675 | (modify-phases %standard-phases | |
3676 | (delete 'configure) | |
3677 | (replace 'check | |
3678 | ;; There are no tests, so just test if it runs. | |
3679 | (lambda _ (zero? (system* "./muscle" "-version")))) | |
3680 | (replace 'install | |
3681 | (lambda* (#:key outputs #:allow-other-keys) | |
3682 | (let* ((out (assoc-ref outputs "out")) | |
3683 | (bin (string-append out "/bin"))) | |
3684 | (install-file "muscle" bin))))))) | |
3685 | (home-page "http://www.drive5.com/muscle") | |
3686 | (synopsis "Multiple sequence alignment program") | |
3687 | (description | |
3688 | "MUSCLE aims to be a fast and accurate multiple sequence alignment | |
3689 | program for nucleotide and protein sequences.") | |
3690 | ;; License information found in 'muscle -h' and usage.cpp. | |
3691 | (license license:public-domain))) | |
3692 | ||
99268755 BW |
3693 | (define-public newick-utils |
3694 | ;; There are no recent releases so we package from git. | |
3695 | (let ((commit "da121155a977197cab9fbb15953ca1b40b11eb87")) | |
3696 | (package | |
3697 | (name "newick-utils") | |
3698 | (version (string-append "1.6-1." (string-take commit 8))) | |
3699 | (source (origin | |
3700 | (method git-fetch) | |
3701 | (uri (git-reference | |
3702 | (url "https://github.com/tjunier/newick_utils.git") | |
3703 | (commit commit))) | |
3704 | (file-name (string-append name "-" version "-checkout")) | |
3705 | (sha256 | |
3706 | (base32 | |
3707 | "1hkw21rq1mwf7xp0rmbb2gqc0i6p11108m69i7mr7xcjl268pxnb")))) | |
3708 | (build-system gnu-build-system) | |
3709 | (arguments | |
3710 | `(#:phases | |
3711 | (modify-phases %standard-phases | |
3712 | (add-after 'unpack 'autoconf | |
3713 | (lambda _ (zero? (system* "autoreconf" "-vif"))))))) | |
3714 | (inputs | |
3715 | ;; XXX: TODO: Enable Lua and Guile bindings. | |
3716 | ;; https://github.com/tjunier/newick_utils/issues/13 | |
3717 | `(("libxml2" ,libxml2) | |
3718 | ("flex" ,flex) | |
3719 | ("bison" ,bison))) | |
3720 | (native-inputs | |
3721 | `(("autoconf" ,autoconf) | |
3722 | ("automake" ,automake) | |
3723 | ("libtool" ,libtool))) | |
3724 | (synopsis "Programs for working with newick format phylogenetic trees") | |
3725 | (description | |
3726 | "Newick-utils is a suite of utilities for processing phylogenetic trees | |
3727 | in Newick format. Functions include re-rooting, extracting subtrees, | |
3728 | trimming, pruning, condensing, drawing (ASCII graphics or SVG).") | |
3729 | (home-page "https://github.com/tjunier/newick_utils") | |
3730 | (license license:bsd-3)))) | |
3731 | ||
1e44cf8b BW |
3732 | (define-public orfm |
3733 | (package | |
3734 | (name "orfm") | |
dfc83ead | 3735 | (version "0.7.1") |
1e44cf8b BW |
3736 | (source (origin |
3737 | (method url-fetch) | |
3738 | (uri (string-append | |
3739 | "https://github.com/wwood/OrfM/releases/download/v" | |
3740 | version "/orfm-" version ".tar.gz")) | |
3741 | (sha256 | |
3742 | (base32 | |
dfc83ead | 3743 | "16iigyr2gd8x0imzkk1dr3k5xsds9bpmwg31ayvjg0f4pir9rwqr")))) |
1e44cf8b BW |
3744 | (build-system gnu-build-system) |
3745 | (inputs `(("zlib" ,zlib))) | |
6b6f7d6a BW |
3746 | (native-inputs |
3747 | `(("ruby-bio-commandeer" ,ruby-bio-commandeer) | |
3748 | ("ruby-rspec" ,ruby-rspec) | |
3749 | ("ruby" ,ruby))) | |
1e44cf8b BW |
3750 | (synopsis "Simple and not slow open reading frame (ORF) caller") |
3751 | (description | |
6b6f7d6a | 3752 | "An ORF caller finds stretches of DNA that, when translated, are not |
1e44cf8b BW |
3753 | interrupted by stop codons. OrfM finds and prints these ORFs.") |
3754 | (home-page "https://github.com/wwood/OrfM") | |
3755 | (license license:lgpl3+))) | |
3756 | ||
c033f5d6 BW |
3757 | (define-public pplacer |
3758 | (let ((commit "g807f6f3")) | |
3759 | (package | |
3760 | (name "pplacer") | |
3761 | ;; The commit should be updated with each version change. | |
3762 | (version "1.1.alpha19") | |
3763 | (source | |
3764 | (origin | |
3765 | (method url-fetch) | |
3766 | (uri (string-append "https://github.com/matsen/pplacer/archive/v" | |
3767 | version ".tar.gz")) | |
3768 | (file-name (string-append name "-" version ".tar.gz")) | |
3769 | (sha256 | |
3770 | (base32 "0z1lnd2s8sh6kpzg106wzbh2szw7h0hvq8syd5a6wv4rmyyz6x0f")))) | |
3771 | (build-system ocaml-build-system) | |
3772 | (arguments | |
3773 | `(#:ocaml ,ocaml-4.01 | |
3774 | #:findlib ,ocaml4.01-findlib | |
3775 | #:modules ((guix build ocaml-build-system) | |
3776 | (guix build utils) | |
3777 | (ice-9 ftw)) | |
3778 | #:phases | |
3779 | (modify-phases %standard-phases | |
3780 | (delete 'configure) | |
3781 | (add-after 'unpack 'replace-bundled-cddlib | |
3782 | (lambda* (#:key inputs #:allow-other-keys) | |
3783 | (let* ((cddlib-src (assoc-ref inputs "cddlib-src")) | |
3784 | (local-dir "cddlib_guix")) | |
3785 | (mkdir local-dir) | |
3786 | (with-directory-excursion local-dir | |
3787 | (system* "tar" "xvf" cddlib-src)) | |
3788 | (let ((cddlib-src-folder | |
3789 | (string-append local-dir "/" | |
3790 | (list-ref (scandir local-dir) 2) | |
3791 | "/lib-src"))) | |
3792 | (for-each | |
3793 | (lambda (file) | |
3794 | (copy-file file | |
3795 | (string-append "cdd_src/" (basename file)))) | |
3796 | (find-files cddlib-src-folder ".*[ch]$"))) | |
3797 | #t))) | |
3798 | (add-after 'unpack 'fix-makefile | |
3799 | (lambda _ | |
3800 | ;; Remove system calls to 'git'. | |
3801 | (substitute* "Makefile" | |
3802 | (("^DESCRIPT:=pplacer-.*") | |
3803 | (string-append | |
3804 | "DESCRIPT:=pplacer-$(shell uname)-v" ,version "\n"))) | |
3805 | (substitute* "myocamlbuild.ml" | |
3806 | (("git describe --tags --long .*\\\" with") | |
3807 | (string-append | |
3808 | "echo -n v" ,version "-" ,commit "\" with"))) | |
3809 | #t)) | |
3810 | (replace 'install | |
3811 | (lambda* (#:key outputs #:allow-other-keys) | |
3812 | (let* ((out (assoc-ref outputs "out")) | |
3813 | (bin (string-append out "/bin"))) | |
3814 | (copy-recursively "bin" bin)) | |
3815 | #t))))) | |
3816 | (native-inputs | |
3817 | `(("zlib" ,zlib) | |
3818 | ("gsl" ,gsl) | |
3819 | ("ocaml-ounit" ,ocaml4.01-ounit) | |
3820 | ("ocaml-batteries" ,ocaml4.01-batteries) | |
3821 | ("ocaml-camlzip" ,ocaml4.01-camlzip) | |
3822 | ("ocaml-csv" ,ocaml4.01-csv) | |
3823 | ("ocaml-sqlite3" ,ocaml4.01-sqlite3) | |
3824 | ("ocaml-xmlm" ,ocaml4.01-xmlm) | |
3825 | ("ocaml-mcl" ,ocaml4.01-mcl) | |
3826 | ("ocaml-gsl" ,ocaml4.01-gsl) | |
3827 | ("cddlib-src" ,(package-source cddlib)))) | |
3828 | (propagated-inputs | |
3829 | `(("pplacer-scripts" ,pplacer-scripts))) | |
3830 | (synopsis "Phylogenetic placement of biological sequences") | |
3831 | (description | |
3832 | "Pplacer places query sequences on a fixed reference phylogenetic tree | |
3833 | to maximize phylogenetic likelihood or posterior probability according to a | |
3834 | reference alignment. Pplacer is designed to be fast, to give useful | |
3835 | information about uncertainty, and to offer advanced visualization and | |
3836 | downstream analysis.") | |
3837 | (home-page "http://matsen.fhcrc.org/pplacer") | |
3838 | (license license:gpl3)))) | |
3839 | ||
3840 | ;; This package is installed alongside 'pplacer'. It is a separate package so | |
3841 | ;; that it can use the python-build-system for the scripts that are | |
3842 | ;; distributed alongside the main OCaml binaries. | |
3843 | (define pplacer-scripts | |
3844 | (package | |
3845 | (inherit pplacer) | |
3846 | (name "pplacer-scripts") | |
3847 | (build-system python-build-system) | |
3848 | (arguments | |
3849 | `(#:python ,python-2 | |
3850 | #:phases | |
3851 | (modify-phases %standard-phases | |
3852 | (add-after 'unpack 'enter-scripts-dir | |
3853 | (lambda _ (chdir "scripts"))) | |
3854 | (replace 'check | |
3855 | (lambda _ | |
3856 | (zero? (system* "python" "-m" "unittest" "discover" "-v")))) | |
3857 | (add-after 'install 'wrap-executables | |
3858 | (lambda* (#:key inputs outputs #:allow-other-keys) | |
3859 | (let* ((out (assoc-ref outputs "out")) | |
3860 | (bin (string-append out "/bin"))) | |
3861 | (let ((path (string-append | |
3862 | (assoc-ref inputs "hmmer") "/bin:" | |
3863 | (assoc-ref inputs "infernal") "/bin"))) | |
3864 | (display path) | |
3865 | (wrap-program (string-append bin "/refpkg_align.py") | |
3866 | `("PATH" ":" prefix (,path)))) | |
3867 | (let ((path (string-append | |
3868 | (assoc-ref inputs "hmmer") "/bin"))) | |
3869 | (wrap-program (string-append bin "/hrefpkg_query.py") | |
3870 | `("PATH" ":" prefix (,path))))) | |
3871 | #t))))) | |
3872 | (inputs | |
3873 | `(("infernal" ,infernal) | |
3874 | ("hmmer" ,hmmer))) | |
3875 | (propagated-inputs | |
3876 | `(("python-biopython" ,python2-biopython) | |
3877 | ("taxtastic" ,taxtastic))) | |
3878 | (synopsis "Pplacer Python scripts"))) | |
3879 | ||
19ee9201 RW |
3880 | (define-public python2-pbcore |
3881 | (package | |
3882 | (name "python2-pbcore") | |
e301bfc8 | 3883 | (version "1.2.10") |
19ee9201 RW |
3884 | (source (origin |
3885 | (method url-fetch) | |
ddb83129 | 3886 | (uri (pypi-uri "pbcore" version)) |
19ee9201 RW |
3887 | (sha256 |
3888 | (base32 | |
e301bfc8 | 3889 | "1kjmv891d6qbpp4shhhvkl02ff4q5xlpnls2513sm2cjcrs52f1i")))) |
19ee9201 RW |
3890 | (build-system python-build-system) |
3891 | (arguments `(#:python ,python-2)) ; pbcore requires Python 2.7 | |
de5bc890 | 3892 | (propagated-inputs |
19ee9201 RW |
3893 | `(("python-cython" ,python2-cython) |
3894 | ("python-numpy" ,python2-numpy) | |
3895 | ("python-pysam" ,python2-pysam) | |
3896 | ("python-h5py" ,python2-h5py))) | |
3897 | (native-inputs | |
de5bc890 HG |
3898 | `(("python-nose" ,python2-nose) |
3899 | ("python-sphinx" ,python2-sphinx) | |
3900 | ("python-pyxb" ,python2-pyxb))) | |
19ee9201 RW |
3901 | (home-page "http://pacificbiosciences.github.io/pbcore/") |
3902 | (synopsis "Library for reading and writing PacBio data files") | |
3903 | (description | |
3904 | "The pbcore package provides Python APIs for interacting with PacBio data | |
3905 | files and writing bioinformatics applications.") | |
3906 | (license license:bsd-3))) | |
3907 | ||
c61fe02c RW |
3908 | (define-public python2-warpedlmm |
3909 | (package | |
3910 | (name "python2-warpedlmm") | |
3911 | (version "0.21") | |
3912 | (source | |
3913 | (origin | |
3914 | (method url-fetch) | |
3915 | (uri (string-append | |
3916 | "https://pypi.python.org/packages/source/W/WarpedLMM/WarpedLMM-" | |
3917 | version ".zip")) | |
3918 | (sha256 | |
3919 | (base32 | |
3920 | "1agfz6zqa8nc6cw47yh0s3y14gkpa9wqazwcj7mwwj3ffnw39p3j")))) | |
3921 | (build-system python-build-system) | |
3922 | (arguments | |
54c85e12 | 3923 | `(#:python ,python-2)) ; requires Python 2.7 |
c61fe02c RW |
3924 | (propagated-inputs |
3925 | `(("python-scipy" ,python2-scipy) | |
3926 | ("python-numpy" ,python2-numpy) | |
3927 | ("python-matplotlib" ,python2-matplotlib) | |
3928 | ("python-fastlmm" ,python2-fastlmm) | |
3929 | ("python-pandas" ,python2-pandas) | |
3930 | ("python-pysnptools" ,python2-pysnptools))) | |
3931 | (native-inputs | |
f3b98f4f | 3932 | `(("python-mock" ,python2-mock) |
c61fe02c RW |
3933 | ("python-nose" ,python2-nose) |
3934 | ("unzip" ,unzip))) | |
3935 | (home-page "https://github.com/PMBio/warpedLMM") | |
3936 | (synopsis "Implementation of warped linear mixed models") | |
3937 | (description | |
3938 | "WarpedLMM is a Python implementation of the warped linear mixed model, | |
3939 | which automatically learns an optimal warping function (or transformation) for | |
3940 | the phenotype as it models the data.") | |
3941 | (license license:asl2.0))) | |
3942 | ||
2c16316e | 3943 | (define-public pbtranscript-tofu |
698bd297 | 3944 | (let ((commit "8f5467fe6a4472bcfb4226c8720993c8507adfe4")) |
2c16316e RW |
3945 | (package |
3946 | (name "pbtranscript-tofu") | |
698bd297 | 3947 | (version (string-append "2.2.3." (string-take commit 7))) |
2c16316e RW |
3948 | (source (origin |
3949 | (method git-fetch) | |
3950 | (uri (git-reference | |
3951 | (url "https://github.com/PacificBiosciences/cDNA_primer.git") | |
3952 | (commit commit))) | |
9a067efd | 3953 | (file-name (string-append name "-" version "-checkout")) |
2c16316e RW |
3954 | (sha256 |
3955 | (base32 | |
9a067efd RW |
3956 | "1lgnpi35ihay42qx0b6yl3kkgra723i413j33kvs0kvs61h82w0f")) |
3957 | (modules '((guix build utils))) | |
3958 | (snippet | |
3959 | '(begin | |
3960 | ;; remove bundled Cython sources | |
3961 | (delete-file "pbtranscript-tofu/pbtranscript/Cython-0.20.1.tar.gz") | |
3962 | #t)))) | |
2c16316e RW |
3963 | (build-system python-build-system) |
3964 | (arguments | |
3965 | `(#:python ,python-2 | |
cdc2bb50 MB |
3966 | ;; FIXME: Tests fail with "No such file or directory: |
3967 | ;; pbtools/pbtranscript/modified_bx_intervals/intersection_unique.so" | |
3968 | #:tests? #f | |
2c16316e | 3969 | #:phases |
9a067efd RW |
3970 | (modify-phases %standard-phases |
3971 | (add-after 'unpack 'enter-directory | |
3972 | (lambda _ | |
3973 | (chdir "pbtranscript-tofu/pbtranscript/") | |
3974 | #t)) | |
3975 | ;; With setuptools version 18.0 and later this setup.py hack causes | |
3976 | ;; a build error, so we disable it. | |
3977 | (add-after 'enter-directory 'patch-setuppy | |
3978 | (lambda _ | |
3979 | (substitute* "setup.py" | |
3980 | (("if 'setuptools.extension' in sys.modules:") | |
3981 | "if False:")) | |
3982 | #t))))) | |
2c16316e | 3983 | (inputs |
9a067efd | 3984 | `(("python-numpy" ,python2-numpy) |
2c16316e | 3985 | ("python-bx-python" ,python2-bx-python) |
c5372108 RW |
3986 | ("python-networkx" ,python2-networkx) |
3987 | ("python-scipy" ,python2-scipy) | |
9a067efd RW |
3988 | ("python-pbcore" ,python2-pbcore) |
3989 | ("python-h5py" ,python2-h5py))) | |
2c16316e | 3990 | (native-inputs |
9a067efd | 3991 | `(("python-cython" ,python2-cython) |
f3b98f4f | 3992 | ("python-nose" ,python2-nose))) |
2c16316e RW |
3993 | (home-page "https://github.com/PacificBiosciences/cDNA_primer") |
3994 | (synopsis "Analyze transcriptome data generated with the Iso-Seq protocol") | |
3995 | (description | |
3996 | "pbtranscript-tofu contains scripts to analyze transcriptome data | |
3997 | generated using the PacBio Iso-Seq protocol.") | |
3998 | (license license:bsd-3)))) | |
3999 | ||
024130d2 BW |
4000 | (define-public prank |
4001 | (package | |
4002 | (name "prank") | |
4003 | (version "150803") | |
4004 | (source (origin | |
4005 | (method url-fetch) | |
4006 | (uri (string-append | |
4007 | "http://wasabiapp.org/download/prank/prank.source." | |
4008 | version ".tgz")) | |
4009 | (sha256 | |
4010 | (base32 | |
4011 | "0am4z94fs3w2n5xpfls9zda61vq7qqz4q2i7b9hlsxz5q4j3kfm4")))) | |
4012 | (build-system gnu-build-system) | |
4013 | (arguments | |
4014 | `(#:phases | |
4015 | (modify-phases %standard-phases | |
4016 | (add-after 'unpack 'enter-src-dir | |
4017 | (lambda _ | |
4018 | (chdir "src") | |
4019 | #t)) | |
62d00095 EF |
4020 | (add-after 'unpack 'remove-m64-flag |
4021 | ;; Prank will build with the correct 'bit-ness' without this flag | |
4022 | ;; and this allows building on 32-bit machines. | |
4023 | (lambda _ (substitute* "src/Makefile" | |
4024 | (("-m64") "")) | |
4025 | #t)) | |
024130d2 BW |
4026 | (delete 'configure) |
4027 | (replace 'install | |
4028 | (lambda* (#:key outputs #:allow-other-keys) | |
4029 | (let* ((out (assoc-ref outputs "out")) | |
4030 | (bin (string-append out "/bin")) | |
4031 | (man (string-append out "/share/man/man1")) | |
4032 | (path (string-append | |
4033 | (assoc-ref %build-inputs "mafft") "/bin:" | |
4034 | (assoc-ref %build-inputs "exonerate") "/bin:" | |
4035 | (assoc-ref %build-inputs "bppsuite") "/bin"))) | |
4036 | (install-file "prank" bin) | |
4037 | (wrap-program (string-append bin "/prank") | |
4038 | `("PATH" ":" prefix (,path))) | |
4039 | (install-file "prank.1" man)) | |
4040 | #t))))) | |
4041 | (inputs | |
4042 | `(("mafft" ,mafft) | |
4043 | ("exonerate" ,exonerate) | |
4044 | ("bppsuite" ,bppsuite))) | |
4045 | (home-page "http://wasabiapp.org/software/prank/") | |
4046 | (synopsis "Probabilistic multiple sequence alignment program") | |
4047 | (description | |
4048 | "PRANK is a probabilistic multiple sequence alignment program for DNA, | |
4049 | codon and amino-acid sequences. It is based on a novel algorithm that treats | |
4050 | insertions correctly and avoids over-estimation of the number of deletion | |
4051 | events. In addition, PRANK borrows ideas from maximum likelihood methods used | |
4052 | in phylogenetics and correctly takes into account the evolutionary distances | |
4053 | between sequences. Lastly, PRANK allows for defining a potential structure | |
4054 | for sequences to be aligned and then, simultaneously with the alignment, | |
4055 | predicts the locations of structural units in the sequences.") | |
4056 | (license license:gpl2+))) | |
4057 | ||
31a9d653 BW |
4058 | (define-public proteinortho |
4059 | (package | |
4060 | (name "proteinortho") | |
a7d12a9e | 4061 | (version "5.16") |
31a9d653 BW |
4062 | (source |
4063 | (origin | |
4064 | (method url-fetch) | |
4065 | (uri | |
4066 | (string-append | |
4067 | "http://www.bioinf.uni-leipzig.de/Software/proteinortho/proteinortho_v" | |
4068 | version "_src.tar.gz")) | |
4069 | (sha256 | |
4070 | (base32 | |
a7d12a9e | 4071 | "0z4f5cg0cs8ai62hfvp4q6w66q2phcc55nhs4xj5cyhxxivjv2ai")))) |
31a9d653 BW |
4072 | (build-system gnu-build-system) |
4073 | (arguments | |
4074 | `(#:test-target "test" | |
4075 | #:phases | |
4076 | (modify-phases %standard-phases | |
4077 | (replace 'configure | |
4078 | ;; There is no configure script, so we modify the Makefile directly. | |
4079 | (lambda* (#:key outputs #:allow-other-keys) | |
4080 | (substitute* "Makefile" | |
4081 | (("INSTALLDIR=.*") | |
4082 | (string-append | |
4083 | "INSTALLDIR=" (assoc-ref outputs "out") "/bin\n"))) | |
4084 | #t)) | |
4085 | (add-before 'install 'make-install-directory | |
4086 | ;; The install directory is not created during 'make install'. | |
4087 | (lambda* (#:key outputs #:allow-other-keys) | |
4088 | (mkdir-p (string-append (assoc-ref outputs "out") "/bin")) | |
4089 | #t)) | |
4090 | (add-after 'install 'wrap-programs | |
4091 | (lambda* (#:key inputs outputs #:allow-other-keys) | |
4092 | (let* ((path (getenv "PATH")) | |
4093 | (out (assoc-ref outputs "out")) | |
4094 | (binary (string-append out "/bin/proteinortho5.pl"))) | |
4095 | (wrap-program binary `("PATH" ":" prefix (,path)))) | |
4096 | #t))))) | |
4097 | (inputs | |
4098 | `(("perl" ,perl) | |
4099 | ("python" ,python-2) | |
4100 | ("blast+" ,blast+))) | |
4101 | (home-page "http://www.bioinf.uni-leipzig.de/Software/proteinortho") | |
4102 | (synopsis "Detect orthologous genes across species") | |
4103 | (description | |
4104 | "Proteinortho is a tool to detect orthologous genes across different | |
4105 | species. For doing so, it compares similarities of given gene sequences and | |
4106 | clusters them to find significant groups. The algorithm was designed to handle | |
4107 | large-scale data and can be applied to hundreds of species at once.") | |
4108 | (license license:gpl2+))) | |
4109 | ||
846e3409 RW |
4110 | (define-public pyicoteo |
4111 | (package | |
4112 | (name "pyicoteo") | |
4113 | (version "2.0.7") | |
4114 | (source | |
4115 | (origin | |
4116 | (method url-fetch) | |
4117 | (uri (string-append "https://bitbucket.org/regulatorygenomicsupf/" | |
4118 | "pyicoteo/get/v" version ".tar.bz2")) | |
4119 | (file-name (string-append name "-" version ".tar.bz2")) | |
4120 | (sha256 | |
4121 | (base32 | |
4122 | "0d6087f29xp8wxwlj111c3sylli98n0l8ry58c51ixzq0zfm50wa")))) | |
4123 | (build-system python-build-system) | |
4124 | (arguments | |
4125 | `(#:python ,python-2 ; does not work with Python 3 | |
4126 | #:tests? #f)) ; there are no tests | |
4127 | (inputs | |
4128 | `(("python2-matplotlib" ,python2-matplotlib))) | |
4129 | (home-page "https://bitbucket.org/regulatorygenomicsupf/pyicoteo") | |
4130 | (synopsis "Analyze high-throughput genetic sequencing data") | |
4131 | (description | |
4132 | "Pyicoteo is a suite of tools for the analysis of high-throughput genetic | |
4133 | sequencing data. It works with genomic coordinates. There are currently six | |
4134 | different command-line tools: | |
4135 | ||
4136 | @enumerate | |
4137 | @item pyicoregion: for generating exploratory regions automatically; | |
4138 | @item pyicoenrich: for differential enrichment between two conditions; | |
4139 | @item pyicoclip: for calling CLIP-Seq peaks without a control; | |
4140 | @item pyicos: for genomic coordinates manipulation; | |
4141 | @item pyicoller: for peak calling on punctuated ChIP-Seq; | |
4142 | @item pyicount: to count how many reads from N experiment files overlap in a | |
4143 | region file; | |
4144 | @item pyicotrocol: to combine operations from pyicoteo. | |
4145 | @end enumerate\n") | |
4146 | (license license:gpl3+))) | |
4147 | ||
af860475 BW |
4148 | (define-public prodigal |
4149 | (package | |
4150 | (name "prodigal") | |
e70f7a23 | 4151 | (version "2.6.3") |
af860475 BW |
4152 | (source (origin |
4153 | (method url-fetch) | |
4154 | (uri (string-append | |
4155 | "https://github.com/hyattpd/Prodigal/archive/v" | |
4156 | version ".tar.gz")) | |
4157 | (file-name (string-append name "-" version ".tar.gz")) | |
4158 | (sha256 | |
4159 | (base32 | |
e70f7a23 | 4160 | "17srxkqd3jc77xk15pfbgg1a9xahqg7337w95mrsia7mpza4l2c9")))) |
af860475 BW |
4161 | (build-system gnu-build-system) |
4162 | (arguments | |
4163 | `(#:tests? #f ;no check target | |
4164 | #:make-flags (list (string-append "INSTALLDIR=" | |
4165 | (assoc-ref %outputs "out") | |
4166 | "/bin")) | |
4167 | #:phases | |
4168 | (modify-phases %standard-phases | |
4169 | (delete 'configure)))) | |
4170 | (home-page "http://prodigal.ornl.gov") | |
4171 | (synopsis "Protein-coding gene prediction for Archaea and Bacteria") | |
4172 | (description | |
4173 | "Prodigal runs smoothly on finished genomes, draft genomes, and | |
4174 | metagenomes, providing gene predictions in GFF3, Genbank, or Sequin table | |
4175 | format. It runs quickly, in an unsupervised fashion, handles gaps, handles | |
4176 | partial genes, and identifies translation initiation sites.") | |
4177 | (license license:gpl3+))) | |
608dd932 | 4178 | |
ceb62d54 BW |
4179 | (define-public roary |
4180 | (package | |
4181 | (name "roary") | |
75696130 | 4182 | (version "3.8.2") |
ceb62d54 BW |
4183 | (source |
4184 | (origin | |
4185 | (method url-fetch) | |
4186 | (uri (string-append | |
4187 | "mirror://cpan/authors/id/A/AJ/AJPAGE/Bio-Roary-" | |
4188 | version ".tar.gz")) | |
4189 | (sha256 | |
4190 | (base32 | |
75696130 | 4191 | "03dfr2cd5fp80bcr65923zpdzrasvcxl7c2vgh8373v25a1yfap7")))) |
ceb62d54 BW |
4192 | (build-system perl-build-system) |
4193 | (arguments | |
4194 | `(#:phases | |
4195 | (modify-phases %standard-phases | |
4196 | (delete 'configure) | |
4197 | (delete 'build) | |
4198 | (replace 'check | |
4199 | (lambda _ | |
4200 | ;; The tests are not run by default, so we run each test file | |
4201 | ;; directly. | |
4202 | (setenv "PATH" (string-append (getcwd) "/bin" ":" | |
4203 | (getenv "PATH"))) | |
4204 | (setenv "PERL5LIB" (string-append (getcwd) "/lib" ":" | |
4205 | (getenv "PERL5LIB"))) | |
4206 | (zero? (length (filter (lambda (file) | |
4207 | (display file)(display "\n") | |
4208 | (not (zero? (system* "perl" file)))) | |
4209 | (find-files "t" ".*\\.t$")))))) | |
4210 | (replace 'install | |
4211 | ;; There is no 'install' target in the Makefile. | |
4212 | (lambda* (#:key outputs #:allow-other-keys) | |
4213 | (let* ((out (assoc-ref outputs "out")) | |
4214 | (bin (string-append out "/bin")) | |
4215 | (perl (string-append out "/lib/perl5/site_perl")) | |
4216 | (roary-plots "contrib/roary_plots")) | |
4217 | (mkdir-p bin) | |
4218 | (mkdir-p perl) | |
4219 | (copy-recursively "bin" bin) | |
4220 | (copy-recursively "lib" perl) | |
4221 | #t))) | |
4222 | (add-after 'install 'wrap-programs | |
4223 | (lambda* (#:key inputs outputs #:allow-other-keys) | |
4224 | (let* ((out (assoc-ref outputs "out")) | |
4225 | (perl5lib (getenv "PERL5LIB")) | |
4226 | (path (getenv "PATH"))) | |
4227 | (for-each (lambda (prog) | |
4228 | (let ((binary (string-append out "/" prog))) | |
4229 | (wrap-program binary | |
4230 | `("PERL5LIB" ":" prefix | |
4231 | (,(string-append perl5lib ":" out | |
4232 | "/lib/perl5/site_perl")))) | |
4233 | (wrap-program binary | |
4234 | `("PATH" ":" prefix | |
4235 | (,(string-append path ":" out "/bin")))))) | |
4236 | (find-files "bin" ".*[^R]$")) | |
4237 | (let ((file | |
4238 | (string-append out "/bin/roary-create_pan_genome_plots.R")) | |
4239 | (r-site-lib (getenv "R_LIBS_SITE")) | |
4240 | (coreutils-path | |
4241 | (string-append (assoc-ref inputs "coreutils") "/bin"))) | |
4242 | (wrap-program file | |
4243 | `("R_LIBS_SITE" ":" prefix | |
4244 | (,(string-append r-site-lib ":" out "/site-library/")))) | |
4245 | (wrap-program file | |
4246 | `("PATH" ":" prefix | |
4247 | (,(string-append coreutils-path ":" out "/bin")))))) | |
4248 | #t))))) | |
4249 | (native-inputs | |
4250 | `(("perl-env-path" ,perl-env-path) | |
4251 | ("perl-test-files" ,perl-test-files) | |
4252 | ("perl-test-most" ,perl-test-most) | |
4253 | ("perl-test-output" ,perl-test-output))) | |
4254 | (inputs | |
4255 | `(("perl-array-utils" ,perl-array-utils) | |
4256 | ("bioperl" ,bioperl-minimal) | |
4257 | ("perl-exception-class" ,perl-exception-class) | |
4258 | ("perl-file-find-rule" ,perl-file-find-rule) | |
4259 | ("perl-file-grep" ,perl-file-grep) | |
4260 | ("perl-file-slurper" ,perl-file-slurper) | |
4261 | ("perl-file-which" ,perl-file-which) | |
4262 | ("perl-graph" ,perl-graph) | |
4263 | ("perl-graph-readwrite" ,perl-graph-readwrite) | |
4264 | ("perl-log-log4perl" ,perl-log-log4perl) | |
4265 | ("perl-moose" ,perl-moose) | |
4266 | ("perl-perlio-utf8_strict" ,perl-perlio-utf8_strict) | |
4267 | ("perl-text-csv" ,perl-text-csv) | |
4268 | ("bedtools" ,bedtools) | |
4269 | ("cd-hit" ,cd-hit) | |
4270 | ("blast+" ,blast+) | |
4271 | ("mcl" ,mcl) | |
4272 | ("parallel" ,parallel) | |
4273 | ("prank" ,prank) | |
4274 | ("mafft" ,mafft) | |
4275 | ("fasttree" ,fasttree) | |
4276 | ("grep" ,grep) | |
4277 | ("sed" ,sed) | |
4278 | ("gawk" ,gawk) | |
2d7c4ae3 | 4279 | ("r-minimal" ,r-minimal) |
ceb62d54 BW |
4280 | ("r-ggplot2" ,r-ggplot2) |
4281 | ("coreutils" ,coreutils))) | |
4282 | (home-page "http://sanger-pathogens.github.io/Roary") | |
4283 | (synopsis "High speed stand-alone pan genome pipeline") | |
4284 | (description | |
4285 | "Roary is a high speed stand alone pan genome pipeline, which takes | |
4286 | annotated assemblies in GFF3 format (produced by the Prokka program) and | |
4287 | calculates the pan genome. Using a standard desktop PC, it can analyse | |
4288 | datasets with thousands of samples, without compromising the quality of the | |
4289 | results. 128 samples can be analysed in under 1 hour using 1 GB of RAM and a | |
4290 | single processor. Roary is not intended for metagenomics or for comparing | |
4291 | extremely diverse sets of genomes.") | |
4292 | (license license:gpl3))) | |
4293 | ||
608dd932 BW |
4294 | (define-public raxml |
4295 | (package | |
4296 | (name "raxml") | |
e9e0fab0 | 4297 | (version "8.2.10") |
608dd932 BW |
4298 | (source |
4299 | (origin | |
4300 | (method url-fetch) | |
4301 | (uri | |
4302 | (string-append | |
4303 | "https://github.com/stamatak/standard-RAxML/archive/v" | |
4304 | version ".tar.gz")) | |
4305 | (file-name (string-append name "-" version ".tar.gz")) | |
4306 | (sha256 | |
4307 | (base32 | |
e9e0fab0 | 4308 | "13s7aspfdcfr6asynwdg1x6vznys6pzap5f8wsffbnnwpkkg9ya8")))) |
608dd932 BW |
4309 | (build-system gnu-build-system) |
4310 | (arguments | |
4311 | `(#:tests? #f ; There are no tests. | |
4312 | ;; Use 'standard' Makefile rather than SSE or AVX ones. | |
4313 | #:make-flags (list "-f" "Makefile.HYBRID.gcc") | |
4314 | #:phases | |
4315 | (modify-phases %standard-phases | |
4316 | (delete 'configure) | |
4317 | (replace 'install | |
4318 | (lambda* (#:key outputs #:allow-other-keys) | |
4319 | (let* ((out (assoc-ref outputs "out")) | |
4320 | (bin (string-append out "/bin")) | |
4321 | (executable "raxmlHPC-HYBRID")) | |
4322 | (install-file executable bin) | |
4323 | (symlink (string-append bin "/" executable) "raxml")) | |
4324 | #t))))) | |
4325 | (inputs | |
4326 | `(("openmpi" ,openmpi))) | |
4327 | (home-page "http://sco.h-its.org/exelixis/web/software/raxml/index.html") | |
4328 | (synopsis "Randomized Axelerated Maximum Likelihood phylogenetic trees") | |
4329 | (description | |
4330 | "RAxML is a tool for phylogenetic analysis and post-analysis of large | |
4331 | phylogenies.") | |
2805f9b2 EF |
4332 | ;; The source includes x86 specific code |
4333 | (supported-systems '("x86_64-linux" "i686-linux")) | |
608dd932 | 4334 | (license license:gpl2+))) |
af860475 | 4335 | |
66e3eff1 RW |
4336 | (define-public rsem |
4337 | (package | |
4338 | (name "rsem") | |
4339 | (version "1.2.20") | |
4340 | (source | |
4341 | (origin | |
4342 | (method url-fetch) | |
4343 | (uri | |
4344 | (string-append "http://deweylab.biostat.wisc.edu/rsem/src/rsem-" | |
4345 | version ".tar.gz")) | |
4346 | (sha256 | |
4347 | (base32 "0nzdc0j0hjllhsd5f2xli95dafm3nawskigs140xzvjk67xh0r9q")) | |
fc1adab1 | 4348 | (patches (search-patches "rsem-makefile.patch")) |
66e3eff1 RW |
4349 | (modules '((guix build utils))) |
4350 | (snippet | |
4351 | '(begin | |
4352 | ;; remove bundled copy of boost | |
4353 | (delete-file-recursively "boost") | |
4354 | #t)))) | |
4355 | (build-system gnu-build-system) | |
4356 | (arguments | |
4357 | `(#:tests? #f ;no "check" target | |
4358 | #:phases | |
4359 | (modify-phases %standard-phases | |
4360 | ;; No "configure" script. | |
4361 | ;; Do not build bundled samtools library. | |
4362 | (replace 'configure | |
4363 | (lambda _ | |
4364 | (substitute* "Makefile" | |
4365 | (("^all : sam/libbam.a") "all : ")) | |
4366 | #t)) | |
4367 | (replace 'install | |
4368 | (lambda* (#:key outputs #:allow-other-keys) | |
4369 | (let* ((out (string-append (assoc-ref outputs "out"))) | |
4370 | (bin (string-append out "/bin/")) | |
4371 | (perl (string-append out "/lib/perl5/site_perl"))) | |
4372 | (mkdir-p bin) | |
4373 | (mkdir-p perl) | |
4374 | (for-each (lambda (file) | |
f3860753 | 4375 | (install-file file bin)) |
66e3eff1 | 4376 | (find-files "." "rsem-.*")) |
f3860753 | 4377 | (install-file "rsem_perl_utils.pm" perl)) |
66e3eff1 RW |
4378 | #t)) |
4379 | (add-after | |
4380 | 'install 'wrap-program | |
4381 | (lambda* (#:key outputs #:allow-other-keys) | |
4382 | (let ((out (assoc-ref outputs "out"))) | |
4383 | (for-each (lambda (prog) | |
4384 | (wrap-program (string-append out "/bin/" prog) | |
4385 | `("PERL5LIB" ":" prefix | |
4386 | (,(string-append out "/lib/perl5/site_perl"))))) | |
4387 | '("rsem-plot-transcript-wiggles" | |
4388 | "rsem-calculate-expression" | |
4389 | "rsem-generate-ngvector" | |
4390 | "rsem-run-ebseq" | |
4391 | "rsem-prepare-reference"))) | |
4392 | #t))))) | |
4393 | (inputs | |
4394 | `(("boost" ,boost) | |
4395 | ("ncurses" ,ncurses) | |
2d7c4ae3 | 4396 | ("r-minimal" ,r-minimal) |
66e3eff1 RW |
4397 | ("perl" ,perl) |
4398 | ("samtools" ,samtools-0.1) | |
4399 | ("zlib" ,zlib))) | |
4400 | (home-page "http://deweylab.biostat.wisc.edu/rsem/") | |
4401 | (synopsis "Estimate gene expression levels from RNA-Seq data") | |
4402 | (description | |
4403 | "RSEM is a software package for estimating gene and isoform expression | |
4404 | levels from RNA-Seq data. The RSEM package provides a user-friendly | |
4405 | interface, supports threads for parallel computation of the EM algorithm, | |
4406 | single-end and paired-end read data, quality scores, variable-length reads and | |
4407 | RSPD estimation. In addition, it provides posterior mean and 95% credibility | |
4408 | interval estimates for expression levels. For visualization, it can generate | |
4409 | BAM and Wiggle files in both transcript-coordinate and genomic-coordinate.") | |
4410 | (license license:gpl3+))) | |
4411 | ||
8622a072 RW |
4412 | (define-public rseqc |
4413 | (package | |
4414 | (name "rseqc") | |
4415 | (version "2.6.1") | |
4416 | (source | |
4417 | (origin | |
4418 | (method url-fetch) | |
4419 | (uri | |
4420 | (string-append "mirror://sourceforge/rseqc/" | |
de67e922 | 4421 | "RSeQC-" version ".tar.gz")) |
8622a072 | 4422 | (sha256 |
8214b7fb | 4423 | (base32 "15ly0254yi032qzkdplg00q144qfdsd986gh62829rl5bkxhj330")) |
8622a072 RW |
4424 | (modules '((guix build utils))) |
4425 | (snippet | |
4426 | '(begin | |
4427 | ;; remove bundled copy of pysam | |
4428 | (delete-file-recursively "lib/pysam") | |
4429 | (substitute* "setup.py" | |
4430 | ;; remove dependency on outdated "distribute" module | |
4431 | (("^from distribute_setup import use_setuptools") "") | |
4432 | (("^use_setuptools\\(\\)") "") | |
4433 | ;; do not use bundled copy of pysam | |
4434 | (("^have_pysam = False") "have_pysam = True")))))) | |
4435 | (build-system python-build-system) | |
4436 | (arguments `(#:python ,python-2)) | |
4437 | (inputs | |
4438 | `(("python-cython" ,python2-cython) | |
4439 | ("python-pysam" ,python2-pysam) | |
4440 | ("python-numpy" ,python2-numpy) | |
8622a072 RW |
4441 | ("zlib" ,zlib))) |
4442 | (native-inputs | |
4443 | `(("python-nose" ,python2-nose))) | |
4444 | (home-page "http://rseqc.sourceforge.net/") | |
4445 | (synopsis "RNA-seq quality control package") | |
4446 | (description | |
4447 | "RSeQC provides a number of modules that can comprehensively evaluate | |
4448 | high throughput sequence data, especially RNA-seq data. Some basic modules | |
4449 | inspect sequence quality, nucleotide composition bias, PCR bias and GC bias, | |
4450 | while RNA-seq specific modules evaluate sequencing saturation, mapped reads | |
4451 | distribution, coverage uniformity, strand specificity, etc.") | |
4452 | (license license:gpl3+))) | |
4453 | ||
ec946638 RW |
4454 | (define-public seek |
4455 | ;; There are no release tarballs. According to the installation | |
4456 | ;; instructions at http://seek.princeton.edu/installation.jsp, the latest | |
4457 | ;; stable release is identified by this changeset ID. | |
4458 | (let ((changeset "2329130") | |
4459 | (revision "1")) | |
4460 | (package | |
4461 | (name "seek") | |
4462 | (version (string-append "0-" revision "." changeset)) | |
4463 | (source (origin | |
4464 | (method hg-fetch) | |
4465 | (uri (hg-reference | |
4466 | (url "https://bitbucket.org/libsleipnir/sleipnir") | |
4467 | (changeset changeset))) | |
4468 | (sha256 | |
4469 | (base32 | |
4470 | "0qrvilwh18dpbhkf92qvxbmay0j75ra3jg2wrhz67gf538zzphsx")))) | |
4471 | (build-system gnu-build-system) | |
4472 | (arguments | |
4473 | `(#:modules ((srfi srfi-1) | |
4474 | (guix build gnu-build-system) | |
4475 | (guix build utils)) | |
4476 | #:phases | |
4477 | (let ((dirs '("SeekMiner" | |
4478 | "SeekEvaluator" | |
4479 | "SeekPrep" | |
4480 | "Distancer" | |
4481 | "Data2DB" | |
4482 | "PCL2Bin"))) | |
4483 | (modify-phases %standard-phases | |
4484 | (add-before 'configure 'bootstrap | |
4485 | (lambda _ | |
4486 | (zero? (system* "bash" "gen_auto")))) | |
4487 | (add-after 'build 'build-additional-tools | |
4488 | (lambda* (#:key make-flags #:allow-other-keys) | |
4489 | (every (lambda (dir) | |
4490 | (with-directory-excursion (string-append "tools/" dir) | |
4491 | (zero? (apply system* "make" make-flags)))) | |
4492 | dirs))) | |
4493 | (add-after 'install 'install-additional-tools | |
4494 | (lambda* (#:key make-flags #:allow-other-keys) | |
4495 | (fold (lambda (dir result) | |
4496 | (with-directory-excursion (string-append "tools/" dir) | |
4497 | (and result | |
4498 | (zero? (apply system* | |
4499 | `("make" ,@make-flags "install")))))) | |
4500 | #t dirs))))))) | |
4501 | (inputs | |
4502 | `(("gsl" ,gsl) | |
4503 | ("boost" ,boost) | |
4504 | ("libsvm" ,libsvm) | |
4505 | ("readline" ,readline) | |
4506 | ("gengetopt" ,gengetopt) | |
4507 | ("log4cpp" ,log4cpp))) | |
4508 | (native-inputs | |
4509 | `(("autoconf" ,autoconf) | |
4510 | ("automake" ,automake) | |
4511 | ("perl" ,perl))) | |
4512 | (home-page "http://seek.princeton.edu") | |
4513 | (synopsis "Gene co-expression search engine") | |
4514 | (description | |
4515 | "SEEK is a computational gene co-expression search engine. SEEK provides | |
4516 | biologists with a way to navigate the massive human expression compendium that | |
4517 | now contains thousands of expression datasets. SEEK returns a robust ranking | |
4518 | of co-expressed genes in the biological area of interest defined by the user's | |
4519 | query genes. It also prioritizes thousands of expression datasets according | |
4520 | to the user's query of interest.") | |
4521 | (license license:cc-by3.0)))) | |
4522 | ||
4e10a221 RW |
4523 | (define-public samtools |
4524 | (package | |
4525 | (name "samtools") | |
63fa0ffc | 4526 | (version "1.5") |
4e10a221 RW |
4527 | (source |
4528 | (origin | |
4529 | (method url-fetch) | |
4530 | (uri | |
de67e922 | 4531 | (string-append "mirror://sourceforge/samtools/samtools/" |
4e10a221 RW |
4532 | version "/samtools-" version ".tar.bz2")) |
4533 | (sha256 | |
4534 | (base32 | |
63fa0ffc | 4535 | "1xidmv0jmfy7l0kb32hdnlshcxgzi1hmygvig0cqrq1fhckdlhl5")))) |
4e10a221 RW |
4536 | (build-system gnu-build-system) |
4537 | (arguments | |
c4473411 | 4538 | `(#:modules ((ice-9 ftw) |
5bdda30b RW |
4539 | (ice-9 regex) |
4540 | (guix build gnu-build-system) | |
4541 | (guix build utils)) | |
c4473411 | 4542 | #:make-flags (list (string-append "prefix=" (assoc-ref %outputs "out"))) |
4ab16440 | 4543 | #:configure-flags (list "--with-ncurses" "--with-htslib=system") |
4e10a221 | 4544 | #:phases |
c842d425 BW |
4545 | (modify-phases %standard-phases |
4546 | (add-after 'unpack 'patch-tests | |
4547 | (lambda _ | |
4548 | (substitute* "test/test.pl" | |
4549 | ;; The test script calls out to /bin/bash | |
4550 | (("/bin/bash") (which "bash"))) | |
b2d748ed | 4551 | #t)) |
c842d425 BW |
4552 | (add-after 'install 'install-library |
4553 | (lambda* (#:key outputs #:allow-other-keys) | |
4554 | (let ((lib (string-append (assoc-ref outputs "out") "/lib"))) | |
4555 | (install-file "libbam.a" lib) | |
4556 | #t))) | |
4557 | (add-after 'install 'install-headers | |
4558 | (lambda* (#:key outputs #:allow-other-keys) | |
4559 | (let ((include (string-append (assoc-ref outputs "out") | |
4560 | "/include/samtools/"))) | |
4561 | (for-each (lambda (file) | |
4562 | (install-file file include)) | |
4563 | (scandir "." (lambda (name) (string-match "\\.h$" name)))) | |
4564 | #t)))))) | |
4e10a221 | 4565 | (native-inputs `(("pkg-config" ,pkg-config))) |
4ab16440 BW |
4566 | (inputs |
4567 | `(("htslib" ,htslib) | |
4568 | ("ncurses" ,ncurses) | |
4569 | ("perl" ,perl) | |
4570 | ("python" ,python) | |
4571 | ("zlib" ,zlib))) | |
4e10a221 RW |
4572 | (home-page "http://samtools.sourceforge.net") |
4573 | (synopsis "Utilities to efficiently manipulate nucleotide sequence alignments") | |
4574 | (description | |
4575 | "Samtools implements various utilities for post-processing nucleotide | |
4576 | sequence alignments in the SAM, BAM, and CRAM formats, including indexing, | |
4577 | variant calling (in conjunction with bcftools), and a simple alignment | |
4578 | viewer.") | |
4579 | (license license:expat))) | |
d3517eda | 4580 | |
0b84a0aa RW |
4581 | (define-public samtools-0.1 |
4582 | ;; This is the most recent version of the 0.1 line of samtools. The input | |
4583 | ;; and output formats differ greatly from that used and produced by samtools | |
4584 | ;; 1.x and is still used in many bioinformatics pipelines. | |
4585 | (package (inherit samtools) | |
4586 | (version "0.1.19") | |
4587 | (source | |
4588 | (origin | |
4589 | (method url-fetch) | |
4590 | (uri | |
de67e922 | 4591 | (string-append "mirror://sourceforge/samtools/samtools/" |
0b84a0aa RW |
4592 | version "/samtools-" version ".tar.bz2")) |
4593 | (sha256 | |
4594 | (base32 "1m33xsfwz0s8qi45lylagfllqg7fphf4dr0780rsvw75av9wk06h")))) | |
4595 | (arguments | |
2309ed68 RW |
4596 | `(#:tests? #f ;no "check" target |
4597 | ,@(substitute-keyword-arguments (package-arguments samtools) | |
4598 | ((#:make-flags flags) | |
4599 | `(cons "LIBCURSES=-lncurses" ,flags)) | |
4600 | ((#:phases phases) | |
4601 | `(modify-phases ,phases | |
4602 | (replace 'install | |
4603 | (lambda* (#:key outputs #:allow-other-keys) | |
4604 | (let ((bin (string-append | |
4605 | (assoc-ref outputs "out") "/bin"))) | |
4606 | (mkdir-p bin) | |
f3860753 | 4607 | (install-file "samtools" bin) |
b2d748ed | 4608 | #t))) |
2309ed68 RW |
4609 | (delete 'patch-tests) |
4610 | (delete 'configure)))))))) | |
0b84a0aa | 4611 | |
fe4c37c2 | 4612 | (define-public mosaik |
698bd297 | 4613 | (let ((commit "5c25216d3522d6a33e53875cd76a6d65001e4e67")) |
fe4c37c2 RW |
4614 | (package |
4615 | (name "mosaik") | |
4616 | (version "2.2.30") | |
4617 | (source (origin | |
4618 | ;; There are no release tarballs nor tags. | |
4619 | (method git-fetch) | |
4620 | (uri (git-reference | |
4621 | (url "https://github.com/wanpinglee/MOSAIK.git") | |
4622 | (commit commit))) | |
4623 | (file-name (string-append name "-" version)) | |
4624 | (sha256 | |
4625 | (base32 | |
4626 | "17gj3s07cm77r41z92awh0bim7w7q7fbn0sf5nkqmcm1vw052qgw")))) | |
4627 | (build-system gnu-build-system) | |
4628 | (arguments | |
4629 | `(#:tests? #f ; no tests | |
4630 | #:make-flags (list "CC=gcc") | |
4631 | #:phases | |
4632 | (modify-phases %standard-phases | |
4633 | (replace 'configure | |
4634 | (lambda _ (chdir "src") #t)) | |
4635 | (replace 'install | |
4636 | (lambda* (#:key outputs #:allow-other-keys) | |
4637 | (let ((bin (string-append (assoc-ref outputs "out") | |
4638 | "/bin"))) | |
4639 | (mkdir-p bin) | |
4640 | (copy-recursively "../bin" bin) | |
4641 | #t)))))) | |
4642 | (inputs | |
4643 | `(("perl" ,perl) | |
4644 | ("zlib" ,zlib))) | |
029d9f77 | 4645 | (supported-systems '("x86_64-linux")) |
0c6c9c00 | 4646 | (home-page "https://github.com/wanpinglee/MOSAIK") |
fe4c37c2 RW |
4647 | (synopsis "Map nucleotide sequence reads to reference genomes") |
4648 | (description | |
4649 | "MOSAIK is a program for mapping second and third-generation sequencing | |
4650 | reads to a reference genome. MOSAIK can align reads generated by all the | |
4651 | major sequencing technologies, including Illumina, Applied Biosystems SOLiD, | |
4652 | Roche 454, Ion Torrent and Pacific BioSciences SMRT.") | |
4653 | ;; MOSAIK is released under the GPLv2+ with the exception of third-party | |
4654 | ;; code released into the public domain: | |
4655 | ;; 1. fastlz by Ariya Hidayat - http://www.fastlz.org/ | |
4656 | ;; 2. MD5 implementation - RSA Data Security, RFC 1321 | |
4657 | (license (list license:gpl2+ license:public-domain))))) | |
4658 | ||
282c5087 RW |
4659 | (define-public ngs-sdk |
4660 | (package | |
4661 | (name "ngs-sdk") | |
6c4ccf32 | 4662 | (version "1.3.0") |
282c5087 RW |
4663 | (source |
4664 | (origin | |
4665 | (method url-fetch) | |
4666 | (uri | |
4667 | (string-append "https://github.com/ncbi/ngs/archive/" | |
4668 | version ".tar.gz")) | |
4669 | (file-name (string-append name "-" version ".tar.gz")) | |
4670 | (sha256 | |
4671 | (base32 | |
6c4ccf32 | 4672 | "1wiyf4c6nm2j87pv015cbi0qny5byf3pbvcw3likifz5dl56ag40")))) |
282c5087 RW |
4673 | (build-system gnu-build-system) |
4674 | (arguments | |
4675 | `(#:parallel-build? #f ; not supported | |
4676 | #:tests? #f ; no "check" target | |
4677 | #:phases | |
4678 | (alist-replace | |
4679 | 'configure | |
4680 | (lambda* (#:key outputs #:allow-other-keys) | |
4681 | (let ((out (assoc-ref outputs "out"))) | |
282c5087 RW |
4682 | ;; The 'configure' script doesn't recognize things like |
4683 | ;; '--enable-fast-install'. | |
4684 | (zero? (system* "./configure" | |
4685 | (string-append "--build-prefix=" (getcwd) "/build") | |
4686 | (string-append "--prefix=" out))))) | |
4687 | (alist-cons-after | |
4688 | 'unpack 'enter-dir | |
4689 | (lambda _ (chdir "ngs-sdk") #t) | |
4690 | %standard-phases)))) | |
4691 | (native-inputs `(("perl" ,perl))) | |
a0dadf0c AE |
4692 | ;; According to the test |
4693 | ;; unless ($MARCH =~ /x86_64/i || $MARCH =~ /i?86/i) | |
4694 | ;; in ngs-sdk/setup/konfigure.perl | |
ab29be81 | 4695 | (supported-systems '("i686-linux" "x86_64-linux")) |
282c5087 RW |
4696 | (home-page "https://github.com/ncbi/ngs") |
4697 | (synopsis "API for accessing Next Generation Sequencing data") | |
4698 | (description | |
4699 | "NGS is a domain-specific API for accessing reads, alignments and pileups | |
4700 | produced from Next Generation Sequencing. The API itself is independent from | |
4701 | any particular back-end implementation, and supports use of multiple back-ends | |
4702 | simultaneously.") | |
4703 | (license license:public-domain))) | |
4704 | ||
1ad15c16 | 4705 | (define-public java-ngs |
2651a5e6 | 4706 | (package (inherit ngs-sdk) |
1ad15c16 | 4707 | (name "java-ngs") |
2651a5e6 RW |
4708 | (arguments |
4709 | `(,@(substitute-keyword-arguments | |
4710 | `(#:modules ((guix build gnu-build-system) | |
4711 | (guix build utils) | |
4712 | (srfi srfi-1) | |
4713 | (srfi srfi-26)) | |
4714 | ,@(package-arguments ngs-sdk)) | |
4715 | ((#:phases phases) | |
614a8977 RW |
4716 | `(modify-phases ,phases |
4717 | (replace 'enter-dir (lambda _ (chdir "ngs-java") #t))))))) | |
2651a5e6 | 4718 | (inputs |
d2540f80 | 4719 | `(("jdk" ,icedtea "jdk") |
2651a5e6 RW |
4720 | ("ngs-sdk" ,ngs-sdk))) |
4721 | (synopsis "Java bindings for NGS SDK"))) | |
4722 | ||
75dd2424 RW |
4723 | (define-public ncbi-vdb |
4724 | (package | |
4725 | (name "ncbi-vdb") | |
5021f547 | 4726 | (version "2.8.2") |
75dd2424 RW |
4727 | (source |
4728 | (origin | |
4729 | (method url-fetch) | |
4730 | (uri | |
4731 | (string-append "https://github.com/ncbi/ncbi-vdb/archive/" | |
4732 | version ".tar.gz")) | |
4733 | (file-name (string-append name "-" version ".tar.gz")) | |
4734 | (sha256 | |
4735 | (base32 | |
5021f547 | 4736 | "1acn4bv81mfl137qnbn9995mjjhwd36pm0b7qli1iw5skrxa9j8m")))) |
75dd2424 RW |
4737 | (build-system gnu-build-system) |
4738 | (arguments | |
4739 | `(#:parallel-build? #f ; not supported | |
4740 | #:tests? #f ; no "check" target | |
4741 | #:phases | |
70111198 RW |
4742 | (modify-phases %standard-phases |
4743 | (replace 'configure | |
4744 | (lambda* (#:key inputs outputs #:allow-other-keys) | |
4745 | (let ((out (assoc-ref outputs "out"))) | |
4746 | ;; Override include path for libmagic | |
4747 | (substitute* "setup/package.prl" | |
4748 | (("name => 'magic', Include => '/usr/include'") | |
4749 | (string-append "name=> 'magic', Include => '" | |
4750 | (assoc-ref inputs "libmagic") | |
4751 | "/include" "'"))) | |
75dd2424 | 4752 | |
70111198 RW |
4753 | ;; Install kdf5 library (needed by sra-tools) |
4754 | (substitute* "build/Makefile.install" | |
4755 | (("LIBRARIES_TO_INSTALL =") | |
4756 | "LIBRARIES_TO_INSTALL = kdf5.$(VERSION_LIBX) kdf5.$(VERSION_SHLX)")) | |
75dd2424 | 4757 | |
70111198 RW |
4758 | (substitute* "build/Makefile.env" |
4759 | (("CFLAGS =" prefix) | |
4760 | (string-append prefix "-msse2 "))) | |
675d7ae2 | 4761 | |
558e2307 RW |
4762 | ;; Override search path for ngs-java |
4763 | (substitute* "setup/package.prl" | |
4764 | (("/usr/local/ngs/ngs-java") | |
4765 | (assoc-ref inputs "java-ngs"))) | |
4766 | ||
70111198 RW |
4767 | ;; The 'configure' script doesn't recognize things like |
4768 | ;; '--enable-fast-install'. | |
4769 | (zero? (system* | |
4770 | "./configure" | |
4771 | (string-append "--build-prefix=" (getcwd) "/build") | |
4772 | (string-append "--prefix=" (assoc-ref outputs "out")) | |
4773 | (string-append "--debug") | |
4774 | (string-append "--with-xml2-prefix=" | |
4775 | (assoc-ref inputs "libxml2")) | |
4776 | (string-append "--with-ngs-sdk-prefix=" | |
4777 | (assoc-ref inputs "ngs-sdk")) | |
70111198 RW |
4778 | (string-append "--with-hdf5-prefix=" |
4779 | (assoc-ref inputs "hdf5"))))))) | |
4780 | (add-after 'install 'install-interfaces | |
4781 | (lambda* (#:key outputs #:allow-other-keys) | |
4782 | ;; Install interface libraries. On i686 the interface libraries | |
4783 | ;; are installed to "linux/gcc/i386", so we need to use the Linux | |
4784 | ;; architecture name ("i386") instead of the target system prefix | |
4785 | ;; ("i686"). | |
4786 | (mkdir (string-append (assoc-ref outputs "out") "/ilib")) | |
4787 | (copy-recursively (string-append "build/ncbi-vdb/linux/gcc/" | |
4788 | ,(system->linux-architecture | |
4789 | (or (%current-target-system) | |
4790 | (%current-system))) | |
4791 | "/rel/ilib") | |
4792 | (string-append (assoc-ref outputs "out") | |
4793 | "/ilib")) | |
4794 | ;; Install interface headers | |
4795 | (copy-recursively "interfaces" | |
4796 | (string-append (assoc-ref outputs "out") | |
4797 | "/include")) | |
d5e17162 RW |
4798 | #t)) |
4799 | ;; These files are needed by sra-tools. | |
4800 | (add-after 'install 'install-configuration-files | |
4801 | (lambda* (#:key outputs #:allow-other-keys) | |
4802 | (let ((target (string-append (assoc-ref outputs "out") "/kfg"))) | |
4803 | (mkdir target) | |
4804 | (install-file "libs/kfg/default.kfg" target) | |
4805 | (install-file "libs/kfg/certs.kfg" target)) | |
70111198 | 4806 | #t))))) |
75dd2424 RW |
4807 | (inputs |
4808 | `(("libxml2" ,libxml2) | |
4809 | ("ngs-sdk" ,ngs-sdk) | |
1ad15c16 | 4810 | ("java-ngs" ,java-ngs) |
75dd2424 RW |
4811 | ("libmagic" ,file) |
4812 | ("hdf5" ,hdf5))) | |
4813 | (native-inputs `(("perl" ,perl))) | |
675d7ae2 RW |
4814 | ;; NCBI-VDB requires SSE capability. |
4815 | (supported-systems '("i686-linux" "x86_64-linux")) | |
75dd2424 RW |
4816 | (home-page "https://github.com/ncbi/ncbi-vdb") |
4817 | (synopsis "Database engine for genetic information") | |
4818 | (description | |
4819 | "The NCBI-VDB library implements a highly compressed columnar data | |
4820 | warehousing engine that is most often used to store genetic information. | |
4821 | Databases are stored in a portable image within the file system, and can be | |
4822 | accessed/downloaded on demand across HTTP.") | |
4823 | (license license:public-domain))) | |
4824 | ||
cc6ed477 RW |
4825 | (define-public plink |
4826 | (package | |
4827 | (name "plink") | |
4828 | (version "1.07") | |
4829 | (source | |
4830 | (origin | |
4831 | (method url-fetch) | |
4832 | (uri (string-append | |
4833 | "http://pngu.mgh.harvard.edu/~purcell/plink/dist/plink-" | |
4834 | version "-src.zip")) | |
4835 | (sha256 | |
4836 | (base32 "0as8gxm4pjyc8dxmm1sl873rrd7wn5qs0l29nqfnl31x8i467xaa")) | |
0dbb7ac2 EF |
4837 | (patches (search-patches "plink-1.07-unclobber-i.patch" |
4838 | "plink-endian-detection.patch")))) | |
cc6ed477 RW |
4839 | (build-system gnu-build-system) |
4840 | (arguments | |
4841 | '(#:tests? #f ;no "check" target | |
4842 | #:make-flags (list (string-append "LIB_LAPACK=" | |
4843 | (assoc-ref %build-inputs "lapack") | |
4844 | "/lib/liblapack.so") | |
4845 | "WITH_LAPACK=1" | |
4846 | "FORCE_DYNAMIC=1" | |
4847 | ;; disable phoning home | |
4848 | "WITH_WEBCHECK=") | |
4849 | #:phases | |
4850 | (modify-phases %standard-phases | |
4851 | ;; no "configure" script | |
4852 | (delete 'configure) | |
4853 | (replace 'install | |
4854 | (lambda* (#:key outputs #:allow-other-keys) | |
4855 | (let ((bin (string-append (assoc-ref outputs "out") | |
4856 | "/bin/"))) | |
96c46210 | 4857 | (install-file "plink" bin) |
cc6ed477 RW |
4858 | #t)))))) |
4859 | (inputs | |
4860 | `(("zlib" ,zlib) | |
4861 | ("lapack" ,lapack))) | |
4862 | (native-inputs | |
4863 | `(("unzip" ,unzip))) | |
4864 | (home-page "http://pngu.mgh.harvard.edu/~purcell/plink/") | |
4865 | (synopsis "Whole genome association analysis toolset") | |
4866 | (description | |
4867 | "PLINK is a whole genome association analysis toolset, designed to | |
4868 | perform a range of basic, large-scale analyses in a computationally efficient | |
4869 | manner. The focus of PLINK is purely on analysis of genotype/phenotype data, | |
4870 | so there is no support for steps prior to this (e.g. study design and | |
4871 | planning, generating genotype or CNV calls from raw data). Through | |
4872 | integration with gPLINK and Haploview, there is some support for the | |
4873 | subsequent visualization, annotation and storage of results.") | |
4874 | ;; Code is released under GPLv2, except for fisher.h, which is under | |
4875 | ;; LGPLv2.1+ | |
4876 | (license (list license:gpl2 license:lgpl2.1+)))) | |
4877 | ||
c6a24d6e RW |
4878 | (define-public smithlab-cpp |
4879 | (let ((revision "1") | |
698bd297 | 4880 | (commit "728a097bec88c6f4b8528b685932049e660eff2e")) |
c6a24d6e RW |
4881 | (package |
4882 | (name "smithlab-cpp") | |
698bd297 | 4883 | (version (string-append "0." revision "." (string-take commit 7))) |
c6a24d6e RW |
4884 | (source (origin |
4885 | (method git-fetch) | |
4886 | (uri (git-reference | |
4887 | (url "https://github.com/smithlabcode/smithlab_cpp.git") | |
4888 | (commit commit))) | |
4889 | (file-name (string-append name "-" version "-checkout")) | |
4890 | (sha256 | |
4891 | (base32 | |
4892 | "0d476lmj312xk77kr9fzrv7z1bv96yfyx0w7y62ycmnfbx32ll74")))) | |
4893 | (build-system gnu-build-system) | |
4894 | (arguments | |
4895 | `(#:modules ((guix build gnu-build-system) | |
4896 | (guix build utils) | |
4897 | (srfi srfi-26)) | |
4898 | #:tests? #f ;no "check" target | |
4899 | #:phases | |
4900 | (modify-phases %standard-phases | |
4901 | (add-after 'unpack 'use-samtools-headers | |
4902 | (lambda _ | |
4903 | (substitute* '("SAM.cpp" | |
4904 | "SAM.hpp") | |
4905 | (("sam.h") "samtools/sam.h")) | |
4906 | #t)) | |
4907 | (replace 'install | |
4908 | (lambda* (#:key outputs #:allow-other-keys) | |
4909 | (let* ((out (assoc-ref outputs "out")) | |
4910 | (lib (string-append out "/lib")) | |
4911 | (include (string-append out "/include/smithlab-cpp"))) | |
4912 | (mkdir-p lib) | |
4913 | (mkdir-p include) | |
4914 | (for-each (cut install-file <> lib) | |
4915 | (find-files "." "\\.o$")) | |
4916 | (for-each (cut install-file <> include) | |
4917 | (find-files "." "\\.hpp$"))) | |
4918 | #t)) | |
4919 | (delete 'configure)))) | |
4920 | (inputs | |
4921 | `(("samtools" ,samtools-0.1) | |
4922 | ("zlib" ,zlib))) | |
4923 | (home-page "https://github.com/smithlabcode/smithlab_cpp") | |
4924 | (synopsis "C++ helper library for functions used in Smith lab projects") | |
4925 | (description | |
4926 | "Smithlab CPP is a C++ library that includes functions used in many of | |
4927 | the Smith lab bioinformatics projects, such as a wrapper around Samtools data | |
4928 | structures, classes for genomic regions, mapped sequencing reads, etc.") | |
4929 | (license license:gpl3+)))) | |
4930 | ||
56e373ef RW |
4931 | (define-public preseq |
4932 | (package | |
4933 | (name "preseq") | |
b49c5a58 | 4934 | (version "2.0") |
56e373ef RW |
4935 | (source (origin |
4936 | (method url-fetch) | |
b49c5a58 RW |
4937 | (uri (string-append "https://github.com/smithlabcode/" |
4938 | "preseq/archive/v" version ".tar.gz")) | |
4939 | (file-name (string-append name "-" version ".tar.gz")) | |
56e373ef | 4940 | (sha256 |
b49c5a58 | 4941 | (base32 "08r684l50pnxjpvmhzjgqq56yv9rfw90k8vx0nsrnrzk8mf9hsdq")) |
56e373ef RW |
4942 | (modules '((guix build utils))) |
4943 | (snippet | |
4944 | ;; Remove bundled samtools. | |
b49c5a58 | 4945 | '(delete-file-recursively "samtools")))) |
56e373ef RW |
4946 | (build-system gnu-build-system) |
4947 | (arguments | |
4948 | `(#:tests? #f ;no "check" target | |
4949 | #:phases | |
4950 | (modify-phases %standard-phases | |
56e373ef | 4951 | (delete 'configure)) |
b49c5a58 RW |
4952 | #:make-flags |
4953 | (list (string-append "PREFIX=" | |
4954 | (assoc-ref %outputs "out")) | |
4955 | (string-append "LIBBAM=" | |
4956 | (assoc-ref %build-inputs "samtools") | |
4957 | "/lib/libbam.a") | |
4958 | (string-append "SMITHLAB_CPP=" | |
4959 | (assoc-ref %build-inputs "smithlab-cpp") | |
4960 | "/lib") | |
4961 | "PROGS=preseq" | |
4962 | "INCLUDEDIRS=$(SMITHLAB_CPP)/../include/smithlab-cpp $(SAMTOOLS_DIR)"))) | |
56e373ef RW |
4963 | (inputs |
4964 | `(("gsl" ,gsl) | |
4965 | ("samtools" ,samtools-0.1) | |
b49c5a58 | 4966 | ("smithlab-cpp" ,smithlab-cpp) |
56e373ef RW |
4967 | ("zlib" ,zlib))) |
4968 | (home-page "http://smithlabresearch.org/software/preseq/") | |
4969 | (synopsis "Program for analyzing library complexity") | |
4970 | (description | |
4971 | "The preseq package is aimed at predicting and estimating the complexity | |
4972 | of a genomic sequencing library, equivalent to predicting and estimating the | |
4973 | number of redundant reads from a given sequencing depth and how many will be | |
4974 | expected from additional sequencing using an initial sequencing experiment. | |
4975 | The estimates can then be used to examine the utility of further sequencing, | |
4976 | optimize the sequencing depth, or to screen multiple libraries to avoid low | |
4977 | complexity samples.") | |
4978 | (license license:gpl3+))) | |
4979 | ||
9ded1457 BW |
4980 | (define-public python-screed |
4981 | (package | |
4982 | (name "python-screed") | |
4983 | (version "0.9") | |
4984 | (source | |
4985 | (origin | |
4986 | (method url-fetch) | |
4987 | (uri (pypi-uri "screed" version)) | |
4988 | (sha256 | |
4989 | (base32 | |
4990 | "18czszp9fkx3j6jr7y5kp6dfialscgddk05mw1zkhh2zhn0jd8i0")))) | |
4991 | (build-system python-build-system) | |
4992 | (arguments | |
4993 | `(#:phases | |
4994 | (modify-phases %standard-phases | |
4995 | (replace 'check | |
4996 | (lambda _ | |
4997 | (setenv "PYTHONPATH" | |
4998 | (string-append (getenv "PYTHONPATH") ":.")) | |
4999 | (zero? (system* "nosetests" "--attr" "!known_failing"))))))) | |
5000 | (native-inputs | |
5001 | `(("python-nose" ,python-nose))) | |
5002 | (inputs | |
5003 | `(("python-bz2file" ,python-bz2file))) | |
7bf837fd | 5004 | (home-page "https://github.com/dib-lab/screed/") |
9ded1457 BW |
5005 | (synopsis "Short read sequence database utilities") |
5006 | (description "Screed parses FASTA and FASTQ files and generates databases. | |
5007 | Values such as sequence name, sequence description, sequence quality and the | |
5008 | sequence itself can be retrieved from these databases.") | |
5009 | (license license:bsd-3))) | |
5010 | ||
5011 | (define-public python2-screed | |
5c31f4aa | 5012 | (package-with-python2 python-screed)) |
9ded1457 | 5013 | |
51c64999 RW |
5014 | (define-public sra-tools |
5015 | (package | |
5016 | (name "sra-tools") | |
79849358 | 5017 | (version "2.8.2-1") |
51c64999 RW |
5018 | (source |
5019 | (origin | |
5020 | (method url-fetch) | |
5021 | (uri | |
5022 | (string-append "https://github.com/ncbi/sra-tools/archive/" | |
5023 | version ".tar.gz")) | |
5024 | (file-name (string-append name "-" version ".tar.gz")) | |
5025 | (sha256 | |
5026 | (base32 | |
79849358 | 5027 | "1camsijmvv2s45mb4iyf44ghl4gkd4rl0viphpcgl3ccchy32a0g")))) |
51c64999 RW |
5028 | (build-system gnu-build-system) |
5029 | (arguments | |
5030 | `(#:parallel-build? #f ; not supported | |
5031 | #:tests? #f ; no "check" target | |
2320e76b | 5032 | #:make-flags |
79849358 RW |
5033 | (list (string-append "DEFAULT_CRT=" |
5034 | (assoc-ref %build-inputs "ncbi-vdb") | |
5035 | "/kfg/certs.kfg") | |
5036 | (string-append "DEFAULT_KFG=" | |
5037 | (assoc-ref %build-inputs "ncbi-vdb") | |
5038 | "/kfg/default.kfg") | |
5039 | (string-append "VDB_LIBDIR=" | |
2320e76b RW |
5040 | (assoc-ref %build-inputs "ncbi-vdb") |
5041 | ,(if (string-prefix? "x86_64" | |
5042 | (or (%current-target-system) | |
5043 | (%current-system))) | |
5044 | "/lib64" | |
5045 | "/lib32"))) | |
51c64999 | 5046 | #:phases |
beebe431 RW |
5047 | (modify-phases %standard-phases |
5048 | (replace 'configure | |
5049 | (lambda* (#:key inputs outputs #:allow-other-keys) | |
5050 | ;; The build system expects a directory containing the sources and | |
5051 | ;; raw build output of ncbi-vdb, including files that are not | |
5052 | ;; installed. Since we are building against an installed version of | |
5053 | ;; ncbi-vdb, the following modifications are needed. | |
5054 | (substitute* "setup/konfigure.perl" | |
5055 | ;; Make the configure script look for the "ilib" directory of | |
5056 | ;; "ncbi-vdb" without first checking for the existence of a | |
5057 | ;; matching library in its "lib" directory. | |
5058 | (("^ my \\$f = File::Spec->catdir\\(\\$libdir, \\$lib\\);") | |
5059 | "my $f = File::Spec->catdir($ilibdir, $ilib);") | |
5060 | ;; Look for interface libraries in ncbi-vdb's "ilib" directory. | |
5061 | (("my \\$ilibdir = File::Spec->catdir\\(\\$builddir, 'ilib'\\);") | |
5062 | "my $ilibdir = File::Spec->catdir($dir, 'ilib');")) | |
51c64999 | 5063 | |
beebe431 RW |
5064 | ;; Dynamic linking |
5065 | (substitute* "tools/copycat/Makefile" | |
5066 | (("smagic-static") "lmagic")) | |
2320e76b | 5067 | |
beebe431 RW |
5068 | ;; The 'configure' script doesn't recognize things like |
5069 | ;; '--enable-fast-install'. | |
5070 | (zero? (system* | |
5071 | "./configure" | |
5072 | (string-append "--build-prefix=" (getcwd) "/build") | |
5073 | (string-append "--prefix=" (assoc-ref outputs "out")) | |
5074 | (string-append "--debug") | |
5075 | (string-append "--with-fuse-prefix=" | |
5076 | (assoc-ref inputs "fuse")) | |
5077 | (string-append "--with-magic-prefix=" | |
5078 | (assoc-ref inputs "libmagic")) | |
5079 | ;; TODO: building with libxml2 fails with linker errors | |
5080 | ;; (string-append "--with-xml2-prefix=" | |
5081 | ;; (assoc-ref inputs "libxml2")) | |
5082 | (string-append "--with-ncbi-vdb-sources=" | |
5083 | (assoc-ref inputs "ncbi-vdb")) | |
5084 | (string-append "--with-ncbi-vdb-build=" | |
5085 | (assoc-ref inputs "ncbi-vdb")) | |
5086 | (string-append "--with-ngs-sdk-prefix=" | |
5087 | (assoc-ref inputs "ngs-sdk")) | |
5088 | (string-append "--with-hdf5-prefix=" | |
1108a920 RW |
5089 | (assoc-ref inputs "hdf5")))))) |
5090 | ;; This version of sra-tools fails to build with glibc because of a | |
5091 | ;; naming conflict. glibc-2.25/include/bits/mathcalls.h already | |
5092 | ;; contains a definition of "canonicalize", so we rename it. | |
5093 | ;; | |
5094 | ;; See upstream bug report: | |
5095 | ;; https://github.com/ncbi/sra-tools/issues/67 | |
5096 | (add-after 'unpack 'patch-away-glibc-conflict | |
5097 | (lambda _ | |
5098 | (substitute* "tools/bam-loader/bam.c" | |
5099 | (("canonicalize\\(" line) | |
5100 | (string-append "sra_tools_" line))) | |
5101 | #t))))) | |
51c64999 RW |
5102 | (native-inputs `(("perl" ,perl))) |
5103 | (inputs | |
5104 | `(("ngs-sdk" ,ngs-sdk) | |
5105 | ("ncbi-vdb" ,ncbi-vdb) | |
5106 | ("libmagic" ,file) | |
5107 | ("fuse" ,fuse) | |
5108 | ("hdf5" ,hdf5) | |
5109 | ("zlib" ,zlib))) | |
5110 | (home-page "http://www.ncbi.nlm.nih.gov/Traces/sra/sra.cgi?view=software") | |
5111 | (synopsis "Tools and libraries for reading and writing sequencing data") | |
5112 | (description | |
5113 | "The SRA Toolkit from NCBI is a collection of tools and libraries for | |
5114 | reading of sequencing files from the Sequence Read Archive (SRA) database and | |
5115 | writing files into the .sra format.") | |
5116 | (license license:public-domain))) | |
5117 | ||
d3517eda RW |
5118 | (define-public seqan |
5119 | (package | |
5120 | (name "seqan") | |
5121 | (version "1.4.2") | |
5122 | (source (origin | |
5123 | (method url-fetch) | |
5124 | (uri (string-append "http://packages.seqan.de/seqan-library/" | |
5125 | "seqan-library-" version ".tar.bz2")) | |
5126 | (sha256 | |
5127 | (base32 | |
5128 | "05s3wrrwn50f81aklfm65i4a749zag1vr8z03k21xm0pdxy47yvp")))) | |
5129 | ;; The documentation is 7.8MB and the includes are 3.6MB heavy, so it | |
5130 | ;; makes sense to split the outputs. | |
5131 | (outputs '("out" "doc")) | |
5132 | (build-system trivial-build-system) | |
5133 | (arguments | |
5134 | `(#:modules ((guix build utils)) | |
5135 | #:builder | |
5136 | (begin | |
5137 | (use-modules (guix build utils)) | |
5138 | (let ((tar (assoc-ref %build-inputs "tar")) | |
5139 | (bzip (assoc-ref %build-inputs "bzip2")) | |
5140 | (out (assoc-ref %outputs "out")) | |
5141 | (doc (assoc-ref %outputs "doc"))) | |
5142 | (setenv "PATH" (string-append tar "/bin:" bzip "/bin")) | |
5143 | (system* "tar" "xvf" (assoc-ref %build-inputs "source")) | |
5144 | (chdir (string-append "seqan-library-" ,version)) | |
5145 | (copy-recursively "include" (string-append out "/include")) | |
5146 | (copy-recursively "share" (string-append doc "/share")))))) | |
5147 | (native-inputs | |
5148 | `(("source" ,source) | |
5149 | ("tar" ,tar) | |
5150 | ("bzip2" ,bzip2))) | |
5151 | (home-page "http://www.seqan.de") | |
5152 | (synopsis "Library for nucleotide sequence analysis") | |
5153 | (description | |
5154 | "SeqAn is a C++ library of efficient algorithms and data structures for | |
5155 | the analysis of sequences with the focus on biological data. It contains | |
5156 | algorithms and data structures for string representation and their | |
5157 | manipulation, online and indexed string search, efficient I/O of | |
5158 | bioinformatics file formats, sequence alignment, and more.") | |
5159 | (license license:bsd-3))) | |
ce7155d5 | 5160 | |
d708b7a9 BW |
5161 | (define-public seqmagick |
5162 | (package | |
5163 | (name "seqmagick") | |
5164 | (version "0.6.1") | |
5165 | (source | |
5166 | (origin | |
5167 | (method url-fetch) | |
5168 | (uri (string-append | |
5169 | "https://pypi.python.org/packages/source/s/seqmagick/seqmagick-" | |
5170 | version ".tar.gz")) | |
5171 | (sha256 | |
5172 | (base32 | |
5173 | "0cgn477n74gsl4qdaakrrhi953kcsd4q3ivk2lr18x74s3g4ma1d")))) | |
5174 | (build-system python-build-system) | |
5175 | (arguments | |
5176 | ;; python2 only, see https://github.com/fhcrc/seqmagick/issues/56 | |
5177 | `(#:python ,python-2 | |
5178 | #:phases | |
5179 | (modify-phases %standard-phases | |
5180 | ;; Current test in setup.py does not work as of 0.6.1, | |
5181 | ;; so use nose to run tests instead for now. See | |
5182 | ;; https://github.com/fhcrc/seqmagick/issues/55 | |
5183 | (replace 'check (lambda _ (zero? (system* "nosetests"))))))) | |
5184 | (inputs | |
7bba95b7 BW |
5185 | ;; biopython-1.66 is required due to |
5186 | ;; https://github.com/fhcrc/seqmagick/issues/59 | |
5187 | ;; When that issue is resolved the 'python2-biopython-1.66' package | |
5188 | ;; should be removed. | |
5189 | `(("python-biopython" ,python2-biopython-1.66))) | |
d708b7a9 | 5190 | (native-inputs |
f3b98f4f | 5191 | `(("python-nose" ,python2-nose))) |
7bf837fd | 5192 | (home-page "https://github.com/fhcrc/seqmagick") |
d708b7a9 BW |
5193 | (synopsis "Tools for converting and modifying sequence files") |
5194 | (description | |
5195 | "Bioinformaticians often have to convert sequence files between formats | |
5196 | and do little manipulations on them, and it's not worth writing scripts for | |
5197 | that. Seqmagick is a utility to expose the file format conversion in | |
5198 | BioPython in a convenient way. Instead of having a big mess of scripts, there | |
5199 | is one that takes arguments.") | |
5200 | (license license:gpl3))) | |
5201 | ||
66daf78c BW |
5202 | (define-public seqtk |
5203 | (package | |
5204 | (name "seqtk") | |
5205 | (version "1.2") | |
5206 | (source (origin | |
5207 | (method url-fetch) | |
5208 | (uri (string-append | |
5209 | "https://github.com/lh3/seqtk/archive/v" | |
5210 | version ".tar.gz")) | |
5211 | (file-name (string-append name "-" version ".tar.gz")) | |
5212 | (sha256 | |
5213 | (base32 | |
5214 | "0ywdyzpmfiz2wp6ampbzqg4y8bj450nfgqarpamg045b8mk32lxx")) | |
5215 | (modules '((guix build utils))) | |
5216 | (snippet | |
5217 | '(begin | |
5218 | ;; Remove extraneous header files, as is done in the seqtk | |
5219 | ;; master branch. | |
5220 | (for-each (lambda (file) (delete-file file)) | |
5221 | (list "ksort.h" "kstring.h" "kvec.h")) | |
5222 | #t)))) | |
5223 | (build-system gnu-build-system) | |
5224 | (arguments | |
5225 | `(#:phases | |
5226 | (modify-phases %standard-phases | |
5227 | (delete 'configure) | |
5228 | (replace 'check | |
5229 | ;; There are no tests, so we just run a sanity check. | |
5230 | (lambda _ (zero? (system* "./seqtk" "seq")))) | |
5231 | (replace 'install | |
5232 | (lambda* (#:key outputs #:allow-other-keys) | |
5233 | (let ((bin (string-append (assoc-ref outputs "out") "/bin/"))) | |
5234 | (install-file "seqtk" bin))))))) | |
5235 | (inputs | |
5236 | `(("zlib" ,zlib))) | |
5237 | (home-page "https://github.com/lh3/seqtk") | |
5238 | (synopsis "Toolkit for processing biological sequences in FASTA/Q format") | |
5239 | (description | |
5240 | "Seqtk is a fast and lightweight tool for processing sequences in the | |
5241 | FASTA or FASTQ format. It parses both FASTA and FASTQ files which can be | |
5242 | optionally compressed by gzip.") | |
5243 | (license license:expat))) | |
5244 | ||
5f7e17be BW |
5245 | (define-public snap-aligner |
5246 | (package | |
5247 | (name "snap-aligner") | |
5248 | (version "1.0beta.18") | |
5249 | (source (origin | |
5250 | (method url-fetch) | |
5251 | (uri (string-append | |
5252 | "https://github.com/amplab/snap/archive/v" | |
5253 | version ".tar.gz")) | |
5254 | (file-name (string-append name "-" version ".tar.gz")) | |
5255 | (sha256 | |
5256 | (base32 | |
5257 | "1vnsjwv007k1fl1q7d681kbwn6bc66cgw6h16hym6gvyy71qv2ly")))) | |
5258 | (build-system gnu-build-system) | |
5259 | (arguments | |
5260 | '(#:phases | |
5261 | (modify-phases %standard-phases | |
5262 | (delete 'configure) | |
5263 | (replace 'check (lambda _ (zero? (system* "./unit_tests")))) | |
5264 | (replace 'install | |
5265 | (lambda* (#:key outputs #:allow-other-keys) | |
5266 | (let* ((out (assoc-ref outputs "out")) | |
5267 | (bin (string-append out "/bin"))) | |
5f7e17be BW |
5268 | (install-file "snap-aligner" bin) |
5269 | (install-file "SNAPCommand" bin) | |
5270 | #t)))))) | |
5271 | (native-inputs | |
5272 | `(("zlib" ,zlib))) | |
5273 | (home-page "http://snap.cs.berkeley.edu/") | |
5274 | (synopsis "Short read DNA sequence aligner") | |
5275 | (description | |
5276 | "SNAP is a fast and accurate aligner for short DNA reads. It is | |
5277 | optimized for modern read lengths of 100 bases or higher, and takes advantage | |
5278 | of these reads to align data quickly through a hash-based indexing scheme.") | |
3e6fdd5f EF |
5279 | ;; 32-bit systems are not supported by the unpatched code. |
5280 | ;; Following the bug reports https://github.com/amplab/snap/issues/68 and | |
5281 | ;; https://bugs.debian.org/cgi-bin/bugreport.cgi?bug=812378 we see that | |
5282 | ;; systems without a lot of memory cannot make good use of this program. | |
5283 | (supported-systems '("x86_64-linux")) | |
5f7e17be BW |
5284 | (license license:asl2.0))) |
5285 | ||
bcadaf00 BW |
5286 | (define-public sortmerna |
5287 | (package | |
5288 | (name "sortmerna") | |
849485f5 | 5289 | (version "2.1b") |
bcadaf00 BW |
5290 | (source |
5291 | (origin | |
5292 | (method url-fetch) | |
5293 | (uri (string-append | |
5294 | "https://github.com/biocore/sortmerna/archive/" | |
5295 | version ".tar.gz")) | |
5296 | (file-name (string-append name "-" version ".tar.gz")) | |
5297 | (sha256 | |
5298 | (base32 | |
849485f5 | 5299 | "1ghaghvd82af9j5adavxh77g7hm247d1r69m3fbi6f1jdivj5ldk")))) |
bcadaf00 BW |
5300 | (build-system gnu-build-system) |
5301 | (outputs '("out" ;for binaries | |
5302 | "db")) ;for sequence databases | |
5303 | (arguments | |
5304 | `(#:phases | |
5305 | (modify-phases %standard-phases | |
5306 | (replace 'install | |
5307 | (lambda* (#:key outputs #:allow-other-keys) | |
5308 | (let* ((out (assoc-ref outputs "out")) | |
5309 | (bin (string-append out "/bin")) | |
5310 | (db (assoc-ref outputs "db")) | |
5311 | (share | |
5312 | (string-append db "/share/sortmerna/rRNA_databases"))) | |
5313 | (install-file "sortmerna" bin) | |
5314 | (install-file "indexdb_rna" bin) | |
5315 | (for-each (lambda (file) | |
5316 | (install-file file share)) | |
5317 | (find-files "rRNA_databases" ".*fasta")) | |
5318 | #t)))))) | |
849485f5 BW |
5319 | (inputs |
5320 | `(("zlib" ,zlib))) | |
bcadaf00 BW |
5321 | (home-page "http://bioinfo.lifl.fr/RNA/sortmerna") |
5322 | (synopsis "Biological sequence analysis tool for NGS reads") | |
5323 | (description | |
5324 | "SortMeRNA is a biological sequence analysis tool for filtering, mapping | |
5325 | and operational taxonomic unit (OTU) picking of next generation | |
5326 | sequencing (NGS) reads. The core algorithm is based on approximate seeds and | |
5327 | allows for fast and sensitive analyses of nucleotide sequences. The main | |
5328 | application of SortMeRNA is filtering rRNA from metatranscriptomic data.") | |
2324541b EF |
5329 | ;; The source includes x86 specific code |
5330 | (supported-systems '("x86_64-linux" "i686-linux")) | |
bcadaf00 BW |
5331 | (license license:lgpl3))) |
5332 | ||
ce7155d5 RW |
5333 | (define-public star |
5334 | (package | |
5335 | (name "star") | |
939b6b11 | 5336 | (version "2.5.3a") |
ce7155d5 RW |
5337 | (source (origin |
5338 | (method url-fetch) | |
3062d750 RW |
5339 | (uri (string-append "https://github.com/alexdobin/STAR/archive/" |
5340 | version ".tar.gz")) | |
5341 | (file-name (string-append name "-" version ".tar.gz")) | |
ce7155d5 RW |
5342 | (sha256 |
5343 | (base32 | |
939b6b11 | 5344 | "013wirlz8lllgjyagl48l75n1isxyabqb3sj7qlsl0x1rmvqw99a")) |
ce7155d5 RW |
5345 | (modules '((guix build utils))) |
5346 | (snippet | |
3062d750 RW |
5347 | '(begin |
5348 | (substitute* "source/Makefile" | |
5349 | (("/bin/rm") "rm")) | |
5350 | ;; Remove pre-built binaries and bundled htslib sources. | |
5351 | (delete-file-recursively "bin/MacOSX_x86_64") | |
5352 | (delete-file-recursively "bin/Linux_x86_64") | |
c9e9154e | 5353 | (delete-file-recursively "bin/Linux_x86_64_static") |
3062d750 RW |
5354 | (delete-file-recursively "source/htslib") |
5355 | #t)))) | |
ce7155d5 RW |
5356 | (build-system gnu-build-system) |
5357 | (arguments | |
5358 | '(#:tests? #f ;no check target | |
5359 | #:make-flags '("STAR") | |
5360 | #:phases | |
c0266e8d RW |
5361 | (modify-phases %standard-phases |
5362 | (add-after 'unpack 'enter-source-dir | |
5363 | (lambda _ (chdir "source") #t)) | |
3062d750 RW |
5364 | (add-after 'enter-source-dir 'do-not-use-bundled-htslib |
5365 | (lambda _ | |
5366 | (substitute* "Makefile" | |
5367 | (("(Depend.list: \\$\\(SOURCES\\) parametersDefault\\.xxd) htslib" | |
5368 | _ prefix) prefix)) | |
5369 | (substitute* '("BAMfunctions.cpp" | |
5370 | "signalFromBAM.h" | |
5371 | "bam_cat.h" | |
5372 | "bam_cat.c" | |
5373 | "STAR.cpp" | |
5374 | "bamRemoveDuplicates.cpp") | |
5375 | (("#include \"htslib/([^\"]+\\.h)\"" _ header) | |
5376 | (string-append "#include <" header ">"))) | |
5377 | (substitute* "IncludeDefine.h" | |
5378 | (("\"htslib/(htslib/[^\"]+.h)\"" _ header) | |
5379 | (string-append "<" header ">"))) | |
5380 | #t)) | |
c0266e8d RW |
5381 | (replace 'install |
5382 | (lambda* (#:key outputs #:allow-other-keys) | |
5383 | (let ((bin (string-append (assoc-ref outputs "out") "/bin/"))) | |
5384 | (install-file "STAR" bin)) | |
5385 | #t)) | |
5386 | (delete 'configure)))) | |
ce7155d5 RW |
5387 | (native-inputs |
5388 | `(("vim" ,vim))) ; for xxd | |
5389 | (inputs | |
3062d750 RW |
5390 | `(("htslib" ,htslib) |
5391 | ("zlib" ,zlib))) | |
ce7155d5 RW |
5392 | (home-page "https://github.com/alexdobin/STAR") |
5393 | (synopsis "Universal RNA-seq aligner") | |
5394 | (description | |
5395 | "The Spliced Transcripts Alignment to a Reference (STAR) software is | |
5396 | based on a previously undescribed RNA-seq alignment algorithm that uses | |
5397 | sequential maximum mappable seed search in uncompressed suffix arrays followed | |
5398 | by seed clustering and stitching procedure. In addition to unbiased de novo | |
5399 | detection of canonical junctions, STAR can discover non-canonical splices and | |
5400 | chimeric (fusion) transcripts, and is also capable of mapping full-length RNA | |
5401 | sequences.") | |
c11f79a4 BW |
5402 | ;; Only 64-bit systems are supported according to the README. |
5403 | (supported-systems '("x86_64-linux" "mips64el-linux")) | |
ce7155d5 RW |
5404 | ;; STAR is licensed under GPLv3 or later; htslib is MIT-licensed. |
5405 | (license license:gpl3+))) | |
de07c0db | 5406 | |
dbf4ed7c RW |
5407 | (define-public subread |
5408 | (package | |
5409 | (name "subread") | |
c180533b | 5410 | (version "1.5.1") |
dbf4ed7c RW |
5411 | (source (origin |
5412 | (method url-fetch) | |
de67e922 LF |
5413 | (uri (string-append "mirror://sourceforge/subread/subread-" |
5414 | version "/subread-" version "-source.tar.gz")) | |
dbf4ed7c RW |
5415 | (sha256 |
5416 | (base32 | |
c180533b | 5417 | "0gn5zhbvllks0mmdg3qlmsbg91p2mpdc2wixwfqpi85yzfrh8hcy")))) |
dbf4ed7c RW |
5418 | (build-system gnu-build-system) |
5419 | (arguments | |
5420 | `(#:tests? #f ;no "check" target | |
104c1986 RW |
5421 | ;; The CC and CCFLAGS variables are set to contain a lot of x86_64 |
5422 | ;; optimizations by default, so we override these flags such that x86_64 | |
5423 | ;; flags are only added when the build target is an x86_64 system. | |
5424 | #:make-flags | |
5425 | (list (let ((system ,(or (%current-target-system) | |
5426 | (%current-system))) | |
5427 | (flags '("-ggdb" "-fomit-frame-pointer" | |
5428 | "-ffast-math" "-funroll-loops" | |
5429 | "-fmessage-length=0" | |
5430 | "-O9" "-Wall" "-DMAKE_FOR_EXON" | |
5431 | "-DMAKE_STANDALONE" | |
5432 | "-DSUBREAD_VERSION=\\\"${SUBREAD_VERSION}\\\"")) | |
5433 | (flags64 '("-mmmx" "-msse" "-msse2" "-msse3"))) | |
5434 | (if (string-prefix? "x86_64" system) | |
5435 | (string-append "CCFLAGS=" (string-join (append flags flags64))) | |
5436 | (string-append "CCFLAGS=" (string-join flags)))) | |
5437 | "-f" "Makefile.Linux" | |
5438 | "CC=gcc ${CCFLAGS}") | |
dbf4ed7c RW |
5439 | #:phases |
5440 | (alist-cons-after | |
5441 | 'unpack 'enter-dir | |
5442 | (lambda _ (chdir "src") #t) | |
5443 | (alist-replace | |
5444 | 'install | |
5445 | (lambda* (#:key outputs #:allow-other-keys) | |
5446 | (let ((bin (string-append (assoc-ref outputs "out") "/bin/"))) | |
5447 | (mkdir-p bin) | |
5448 | (copy-recursively "../bin" bin))) | |
5449 | ;; no "configure" script | |
5450 | (alist-delete 'configure %standard-phases))))) | |
5451 | (inputs `(("zlib" ,zlib))) | |
5452 | (home-page "http://bioinf.wehi.edu.au/subread-package/") | |
5453 | (synopsis "Tool kit for processing next-gen sequencing data") | |
5454 | (description | |
5455 | "The subread package contains the following tools: subread aligner, a | |
5456 | general-purpose read aligner; subjunc aligner: detecting exon-exon junctions | |
5457 | and mapping RNA-seq reads; featureCounts: counting mapped reads for genomic | |
5458 | features; exactSNP: a SNP caller that discovers SNPs by testing signals | |
5459 | against local background noises.") | |
5460 | (license license:gpl3+))) | |
5461 | ||
d15d981e RW |
5462 | (define-public stringtie |
5463 | (package | |
5464 | (name "stringtie") | |
5465 | (version "1.2.1") | |
5466 | (source (origin | |
5467 | (method url-fetch) | |
5468 | (uri (string-append "http://ccb.jhu.edu/software/stringtie/dl/" | |
5469 | "stringtie-" version ".tar.gz")) | |
5470 | (sha256 | |
5471 | (base32 | |
5472 | "1cqllsc1maq4kh92isi8yadgzbmnf042hlnalpk3y59aph1z3bfz")) | |
5473 | (modules '((guix build utils))) | |
5474 | (snippet | |
5475 | '(begin | |
5476 | (delete-file-recursively "samtools-0.1.18") | |
5477 | #t)))) | |
5478 | (build-system gnu-build-system) | |
5479 | (arguments | |
5480 | `(#:tests? #f ;no test suite | |
5481 | #:phases | |
5482 | (modify-phases %standard-phases | |
5483 | ;; no configure script | |
5484 | (delete 'configure) | |
5485 | (add-before 'build 'use-system-samtools | |
5486 | (lambda _ | |
5487 | (substitute* "Makefile" | |
5488 | (("stringtie: \\$\\{BAM\\}/libbam\\.a") | |
5489 | "stringtie: ")) | |
5490 | (substitute* '("gclib/GBam.h" | |
5491 | "gclib/GBam.cpp") | |
5492 | (("#include \"(bam|sam|kstring).h\"" _ header) | |
5493 | (string-append "#include <samtools/" header ".h>"))) | |
5494 | #t)) | |
0d2c0562 RW |
5495 | (add-after 'unpack 'remove-duplicate-typedef |
5496 | (lambda _ | |
5497 | ;; This typedef conflicts with the typedef in | |
5498 | ;; glibc-2.25/include/bits/types.h | |
5499 | (substitute* "gclib/GThreads.h" | |
5500 | (("typedef long long __intmax_t;") "")) | |
5501 | #t)) | |
d15d981e RW |
5502 | (replace 'install |
5503 | (lambda* (#:key outputs #:allow-other-keys) | |
5504 | (let ((bin (string-append (assoc-ref outputs "out") "/bin/"))) | |
5505 | (install-file "stringtie" bin) | |
5506 | #t)))))) | |
5507 | (inputs | |
5508 | `(("samtools" ,samtools-0.1) | |
5509 | ("zlib" ,zlib))) | |
5510 | (home-page "http://ccb.jhu.edu/software/stringtie/") | |
5511 | (synopsis "Transcript assembly and quantification for RNA-Seq data") | |
5512 | (description | |
5513 | "StringTie is a fast and efficient assembler of RNA-Seq sequence | |
5514 | alignments into potential transcripts. It uses a novel network flow algorithm | |
5515 | as well as an optional de novo assembly step to assemble and quantitate | |
5516 | full-length transcripts representing multiple splice variants for each gene | |
5517 | locus. Its input can include not only the alignments of raw reads used by | |
5518 | other transcript assemblers, but also alignments of longer sequences that have | |
5519 | been assembled from those reads. To identify differentially expressed genes | |
5520 | between experiments, StringTie's output can be processed either by the | |
5521 | Cuffdiff or Ballgown programs.") | |
5522 | (license license:artistic2.0))) | |
5523 | ||
ad0ae297 BW |
5524 | (define-public taxtastic |
5525 | (package | |
5526 | (name "taxtastic") | |
3cbfc149 | 5527 | (version "0.6.4") |
ad0ae297 BW |
5528 | (source (origin |
5529 | (method url-fetch) | |
3cbfc149 | 5530 | (uri (pypi-uri "taxtastic" version)) |
ad0ae297 BW |
5531 | (sha256 |
5532 | (base32 | |
3cbfc149 | 5533 | "0s79z8kfl853x7l4h8ms05k31q87aw62nrchlk20w9n227j35929")))) |
ad0ae297 BW |
5534 | (build-system python-build-system) |
5535 | (arguments | |
5536 | `(#:python ,python-2 | |
5537 | #:phases | |
5538 | (modify-phases %standard-phases | |
5539 | (replace 'check | |
5540 | (lambda _ | |
5541 | (zero? (system* "python" "-m" "unittest" "discover" "-v"))))))) | |
5542 | (propagated-inputs | |
5543 | `(("python-sqlalchemy" ,python2-sqlalchemy) | |
5544 | ("python-decorator" ,python2-decorator) | |
5545 | ("python-biopython" ,python2-biopython) | |
5546 | ("python-pandas" ,python2-pandas))) | |
5547 | (home-page "https://github.com/fhcrc/taxtastic") | |
5548 | (synopsis "Tools for taxonomic naming and annotation") | |
5549 | (description | |
5550 | "Taxtastic is software written in python used to build and maintain | |
5551 | reference packages i.e. collections of reference trees, reference alignments, | |
5552 | profiles, and associated taxonomic information.") | |
5553 | (license license:gpl3+))) | |
5554 | ||
de07c0db RW |
5555 | (define-public vcftools |
5556 | (package | |
5557 | (name "vcftools") | |
f4322542 | 5558 | (version "0.1.15") |
de07c0db RW |
5559 | (source (origin |
5560 | (method url-fetch) | |
5561 | (uri (string-append | |
9b36e256 RJ |
5562 | "https://github.com/vcftools/vcftools/releases/download/v" |
5563 | version "/vcftools-" version ".tar.gz")) | |
de07c0db RW |
5564 | (sha256 |
5565 | (base32 | |
f4322542 | 5566 | "1qw30c45wihgy632rbz4rh3njnwj4msj46l1rsgdhyg6bgypmr1i")))) |
de07c0db RW |
5567 | (build-system gnu-build-system) |
5568 | (arguments | |
5569 | `(#:tests? #f ; no "check" target | |
5570 | #:make-flags (list | |
7c3958e1 | 5571 | "CFLAGS=-O2" ; override "-m64" flag |
de07c0db RW |
5572 | (string-append "PREFIX=" (assoc-ref %outputs "out")) |
5573 | (string-append "MANDIR=" (assoc-ref %outputs "out") | |
9b36e256 RJ |
5574 | "/share/man/man1")))) |
5575 | (native-inputs | |
5576 | `(("pkg-config" ,pkg-config))) | |
de07c0db RW |
5577 | (inputs |
5578 | `(("perl" ,perl) | |
5579 | ("zlib" ,zlib))) | |
9b36e256 | 5580 | (home-page "https://vcftools.github.io/") |
de07c0db RW |
5581 | (synopsis "Tools for working with VCF files") |
5582 | (description | |
5583 | "VCFtools is a program package designed for working with VCF files, such | |
5584 | as those generated by the 1000 Genomes Project. The aim of VCFtools is to | |
5585 | provide easily accessible methods for working with complex genetic variation | |
5586 | data in the form of VCF files.") | |
5587 | ;; The license is declared as LGPLv3 in the README and | |
9b36e256 | 5588 | ;; at https://vcftools.github.io/license.html |
de07c0db | 5589 | (license license:lgpl3))) |
9c38b540 | 5590 | |
35aa90a1 RW |
5591 | (define-public infernal |
5592 | (package | |
5593 | (name "infernal") | |
5594 | (version "1.1.2") | |
5595 | (source (origin | |
5596 | (method url-fetch) | |
5597 | (uri (string-append "http://eddylab.org/software/infernal/" | |
5598 | "infernal-" version ".tar.gz")) | |
5599 | (sha256 | |
5600 | (base32 | |
5601 | "0sr2hiz3qxfwqpz3whxr6n82p3x27336v3f34iqznp10hks2935c")))) | |
5602 | (build-system gnu-build-system) | |
5603 | (native-inputs | |
5604 | `(("perl" ,perl))) ; for tests | |
5605 | (home-page "http://eddylab.org/infernal/") | |
5606 | (synopsis "Inference of RNA alignments") | |
5607 | (description "Infernal (\"INFERence of RNA ALignment\") is a tool for | |
5608 | searching DNA sequence databases for RNA structure and sequence similarities. | |
5609 | It is an implementation of a special case of profile stochastic context-free | |
5610 | grammars called @dfn{covariance models} (CMs). A CM is like a sequence | |
5611 | profile, but it scores a combination of sequence consensus and RNA secondary | |
5612 | structure consensus, so in many cases, it is more capable of identifying RNA | |
5613 | homologs that conserve their secondary structure more than their primary | |
5614 | sequence.") | |
48409ef2 EF |
5615 | ;; Infernal 1.1.2 requires VMX or SSE capability for parallel instructions. |
5616 | (supported-systems '("i686-linux" "x86_64-linux")) | |
35aa90a1 RW |
5617 | (license license:bsd-3))) |
5618 | ||
b91cfa22 RW |
5619 | (define-public r-centipede |
5620 | (package | |
5621 | (name "r-centipede") | |
5622 | (version "1.2") | |
5623 | (source (origin | |
5624 | (method url-fetch) | |
5625 | (uri (string-append "http://download.r-forge.r-project.org/" | |
5626 | "src/contrib/CENTIPEDE_" version ".tar.gz")) | |
5627 | (sha256 | |
5628 | (base32 | |
5629 | "1hsx6qgwr0i67fhy9257zj7s0ppncph2hjgbia5nn6nfmj0ax6l9")))) | |
5630 | (build-system r-build-system) | |
5631 | (home-page "http://centipede.uchicago.edu/") | |
5632 | (synopsis "Predict transcription factor binding sites") | |
5633 | (description | |
5634 | "CENTIPEDE applies a hierarchical Bayesian mixture model to infer regions | |
5635 | of the genome that are bound by particular transcription factors. It starts | |
5636 | by identifying a set of candidate binding sites, and then aims to classify the | |
5637 | sites according to whether each site is bound or not bound by a transcription | |
5638 | factor. CENTIPEDE is an unsupervised learning algorithm that discriminates | |
5639 | between two different types of motif instances using as much relevant | |
5640 | information as possible.") | |
5641 | (license (list license:gpl2+ license:gpl3+)))) | |
5642 | ||
7b3df1e5 BW |
5643 | (define-public r-vegan |
5644 | (package | |
5645 | (name "r-vegan") | |
1d65b537 | 5646 | (version "2.4-3") |
7b3df1e5 BW |
5647 | (source |
5648 | (origin | |
5649 | (method url-fetch) | |
5650 | (uri (cran-uri "vegan" version)) | |
5651 | (sha256 | |
5652 | (base32 | |
1d65b537 | 5653 | "15zcxfix2d854897k1lr0sfmj2n00339nlsppcr3zrb238lb2mi5")))) |
7b3df1e5 | 5654 | (build-system r-build-system) |
7b3df1e5 BW |
5655 | (native-inputs |
5656 | `(("gfortran" ,gfortran) | |
1d65b537 | 5657 | ("r-knitr" ,r-knitr))) |
7b3df1e5 BW |
5658 | (propagated-inputs |
5659 | `(("r-cluster" ,r-cluster) | |
5660 | ("r-lattice" ,r-lattice) | |
aeb64f3c | 5661 | ("r-mass" ,r-mass) |
7b3df1e5 BW |
5662 | ("r-mgcv" ,r-mgcv) |
5663 | ("r-permute" ,r-permute))) | |
5664 | (home-page "https://cran.r-project.org/web/packages/vegan") | |
5665 | (synopsis "Functions for community ecology") | |
5666 | (description | |
5667 | "The vegan package provides tools for descriptive community ecology. It | |
5668 | has most basic functions of diversity analysis, community ordination and | |
5669 | dissimilarity analysis. Most of its multivariate tools can be used for other | |
5670 | data types as well.") | |
5671 | (license license:gpl2+))) | |
5672 | ||
8c6de588 RW |
5673 | (define-public r-annotate |
5674 | (package | |
5675 | (name "r-annotate") | |
dbab99b6 | 5676 | (version "1.54.0") |
8c6de588 RW |
5677 | (source |
5678 | (origin | |
5679 | (method url-fetch) | |
5680 | (uri (bioconductor-uri "annotate" version)) | |
5681 | (sha256 | |
5682 | (base32 | |
dbab99b6 | 5683 | "03hmbvp3i6lvd307fqdg7akxi2qp322rlky3bzw0zccgm0i0221g")))) |
8c6de588 RW |
5684 | (build-system r-build-system) |
5685 | (propagated-inputs | |
5686 | `(("r-annotationdbi" ,r-annotationdbi) | |
5687 | ("r-biobase" ,r-biobase) | |
5688 | ("r-biocgenerics" ,r-biocgenerics) | |
5689 | ("r-dbi" ,r-dbi) | |
d0f0579e | 5690 | ("r-rcurl" ,r-rcurl) |
8c6de588 RW |
5691 | ("r-xml" ,r-xml) |
5692 | ("r-xtable" ,r-xtable))) | |
5693 | (home-page | |
5694 | "http://bioconductor.org/packages/annotate") | |
5695 | (synopsis "Annotation for microarrays") | |
d1e4ad1b | 5696 | (description "This package provides R environments for the annotation of |
8c6de588 RW |
5697 | microarrays.") |
5698 | (license license:artistic2.0))) | |
5699 | ||
07a664cd RW |
5700 | (define-public r-geneplotter |
5701 | (package | |
5702 | (name "r-geneplotter") | |
97a50e4f | 5703 | (version "1.54.0") |
07a664cd RW |
5704 | (source |
5705 | (origin | |
5706 | (method url-fetch) | |
5707 | (uri (bioconductor-uri "geneplotter" version)) | |
5708 | (sha256 | |
5709 | (base32 | |
97a50e4f | 5710 | "0a0ajns21db5rrjl16bq6wawggsnxr00fg184pc38nmfghv4z4b6")))) |
07a664cd RW |
5711 | (build-system r-build-system) |
5712 | (propagated-inputs | |
5713 | `(("r-annotate" ,r-annotate) | |
5714 | ("r-annotationdbi" ,r-annotationdbi) | |
5715 | ("r-biobase" ,r-biobase) | |
5716 | ("r-biocgenerics" ,r-biocgenerics) | |
5717 | ("r-lattice" ,r-lattice) | |
5718 | ("r-rcolorbrewer" ,r-rcolorbrewer))) | |
5719 | (home-page "http://bioconductor.org/packages/geneplotter") | |
5720 | (synopsis "Graphics functions for genomic data") | |
5721 | (description | |
5722 | "This package provides functions for plotting genomic data.") | |
5723 | (license license:artistic2.0))) | |
5724 | ||
2301fd3e RW |
5725 | (define-public r-genefilter |
5726 | (package | |
5727 | (name "r-genefilter") | |
b5bc3a39 | 5728 | (version "1.58.0") |
2301fd3e RW |
5729 | (source |
5730 | (origin | |
5731 | (method url-fetch) | |
5732 | (uri (bioconductor-uri "genefilter" version)) | |
5733 | (sha256 | |
5734 | (base32 | |
b5bc3a39 | 5735 | "0sf2hdi9nv6r83vn1y65m4jiba8pffddpj46d6yjn5rlsixplmqg")))) |
2301fd3e RW |
5736 | (build-system r-build-system) |
5737 | (native-inputs | |
5738 | `(("gfortran" ,gfortran))) | |
5739 | (propagated-inputs | |
5740 | `(("r-annotate" ,r-annotate) | |
5741 | ("r-annotationdbi" ,r-annotationdbi) | |
5742 | ("r-biobase" ,r-biobase) | |
aeb64f3c RW |
5743 | ("r-s4vectors" ,r-s4vectors) |
5744 | ("r-survival" ,r-survival))) | |
2301fd3e RW |
5745 | (home-page "http://bioconductor.org/packages/genefilter") |
5746 | (synopsis "Filter genes from high-throughput experiments") | |
5747 | (description | |
5748 | "This package provides basic functions for filtering genes from | |
5749 | high-throughput sequencing experiments.") | |
5750 | (license license:artistic2.0))) | |
5751 | ||
ad34f0ac RW |
5752 | (define-public r-deseq2 |
5753 | (package | |
5754 | (name "r-deseq2") | |
3ae74e45 | 5755 | (version "1.16.0") |
ad34f0ac RW |
5756 | (source |
5757 | (origin | |
5758 | (method url-fetch) | |
5759 | (uri (bioconductor-uri "DESeq2" version)) | |
5760 | (sha256 | |
5761 | (base32 | |
3ae74e45 | 5762 | "0m0apn3xi4kdkinsj4xkw5cwysicyjr6xxlxhpa4scyv589am1s5")))) |
ad34f0ac RW |
5763 | (properties `((upstream-name . "DESeq2"))) |
5764 | (build-system r-build-system) | |
ad34f0ac RW |
5765 | (propagated-inputs |
5766 | `(("r-biobase" ,r-biobase) | |
5767 | ("r-biocgenerics" ,r-biocgenerics) | |
5768 | ("r-biocparallel" ,r-biocparallel) | |
5769 | ("r-genefilter" ,r-genefilter) | |
5770 | ("r-geneplotter" ,r-geneplotter) | |
5771 | ("r-genomicranges" ,r-genomicranges) | |
5772 | ("r-ggplot2" ,r-ggplot2) | |
5773 | ("r-hmisc" ,r-hmisc) | |
5774 | ("r-iranges" ,r-iranges) | |
5775 | ("r-locfit" ,r-locfit) | |
5776 | ("r-rcpp" ,r-rcpp) | |
5777 | ("r-rcpparmadillo" ,r-rcpparmadillo) | |
5778 | ("r-s4vectors" ,r-s4vectors) | |
5779 | ("r-summarizedexperiment" ,r-summarizedexperiment))) | |
5780 | (home-page "http://bioconductor.org/packages/DESeq2") | |
5781 | (synopsis "Differential gene expression analysis") | |
5782 | (description | |
5783 | "This package provides functions to estimate variance-mean dependence in | |
5784 | count data from high-throughput nucleotide sequencing assays and test for | |
5785 | differential expression based on a model using the negative binomial | |
5786 | distribution.") | |
5787 | (license license:lgpl3+))) | |
5788 | ||
e8163773 RW |
5789 | (define-public r-annotationforge |
5790 | (package | |
5791 | (name "r-annotationforge") | |
46972a44 | 5792 | (version "1.18.0") |
e8163773 RW |
5793 | (source |
5794 | (origin | |
5795 | (method url-fetch) | |
5796 | (uri (bioconductor-uri "AnnotationForge" version)) | |
5797 | (sha256 | |
5798 | (base32 | |
46972a44 | 5799 | "01kd86vvgpa4a5zivcy4g6z8rhcykasdskrz8yqsqz211sd1xsr3")))) |
e8163773 RW |
5800 | (properties |
5801 | `((upstream-name . "AnnotationForge"))) | |
5802 | (build-system r-build-system) | |
5803 | (propagated-inputs | |
5804 | `(("r-annotationdbi" ,r-annotationdbi) | |
5805 | ("r-biobase" ,r-biobase) | |
5806 | ("r-biocgenerics" ,r-biocgenerics) | |
5807 | ("r-dbi" ,r-dbi) | |
55cd914c | 5808 | ("r-rcurl" ,r-rcurl) |
e8163773 RW |
5809 | ("r-rsqlite" ,r-rsqlite) |
5810 | ("r-s4vectors" ,r-s4vectors) | |
5811 | ("r-xml" ,r-xml))) | |
5812 | (home-page "http://bioconductor.org/packages/AnnotationForge") | |
5813 | (synopsis "Code for building annotation database packages") | |
5814 | (description | |
5815 | "This package provides code for generating Annotation packages and their | |
5816 | databases. Packages produced are intended to be used with AnnotationDbi.") | |
5817 | (license license:artistic2.0))) | |
5818 | ||
cd9e7dc7 RW |
5819 | (define-public r-rbgl |
5820 | (package | |
5821 | (name "r-rbgl") | |
8ab6f241 | 5822 | (version "1.52.0") |
cd9e7dc7 RW |
5823 | (source |
5824 | (origin | |
5825 | (method url-fetch) | |
5826 | (uri (bioconductor-uri "RBGL" version)) | |
5827 | (sha256 | |
5828 | (base32 | |
8ab6f241 | 5829 | "11db6kvz453ypj9ds3xpjqzwrrjck84ijn4wlhkfyz2dzdgd5ryv")))) |
cd9e7dc7 RW |
5830 | (properties `((upstream-name . "RBGL"))) |
5831 | (build-system r-build-system) | |
5832 | (propagated-inputs `(("r-graph" ,r-graph))) | |
5833 | (home-page "http://www.bioconductor.org/packages/RBGL") | |
5834 | (synopsis "Interface to the Boost graph library") | |
5835 | (description | |
5836 | "This package provides a fairly extensive and comprehensive interface to | |
5837 | the graph algorithms contained in the Boost library.") | |
5838 | (license license:artistic2.0))) | |
5839 | ||
ad740ff8 RW |
5840 | (define-public r-gseabase |
5841 | (package | |
5842 | (name "r-gseabase") | |
c584a07f | 5843 | (version "1.38.0") |
ad740ff8 RW |
5844 | (source |
5845 | (origin | |
5846 | (method url-fetch) | |
5847 | (uri (bioconductor-uri "GSEABase" version)) | |
5848 | (sha256 | |
5849 | (base32 | |
c584a07f | 5850 | "1c6i6g4fj3b8wjyxyygr7i3v8sxrq1ffb2bbicya5ah2gdaclfad")))) |
ad740ff8 RW |
5851 | (properties `((upstream-name . "GSEABase"))) |
5852 | (build-system r-build-system) | |
5853 | (propagated-inputs | |
5854 | `(("r-annotate" ,r-annotate) | |
5855 | ("r-annotationdbi" ,r-annotationdbi) | |
5856 | ("r-biobase" ,r-biobase) | |
5857 | ("r-biocgenerics" ,r-biocgenerics) | |
5858 | ("r-graph" ,r-graph) | |
5859 | ("r-xml" ,r-xml))) | |
5860 | (home-page "http://bioconductor.org/packages/GSEABase") | |
5861 | (synopsis "Gene set enrichment data structures and methods") | |
5862 | (description | |
5863 | "This package provides classes and methods to support @dfn{Gene Set | |
5864 | Enrichment Analysis} (GSEA).") | |
5865 | (license license:artistic2.0))) | |
5866 | ||
1a1931f7 RW |
5867 | (define-public r-category |
5868 | (package | |
5869 | (name "r-category") | |
ca0289ae | 5870 | (version "2.42.0") |
1a1931f7 RW |
5871 | (source |
5872 | (origin | |
5873 | (method url-fetch) | |
5874 | (uri (bioconductor-uri "Category" version)) | |
5875 | (sha256 | |
5876 | (base32 | |
ca0289ae | 5877 | "0swcmihyjg0fhaaydl9hm24aj9zffw3bibza9y6sqs6jaqd97f09")))) |
1a1931f7 RW |
5878 | (properties `((upstream-name . "Category"))) |
5879 | (build-system r-build-system) | |
5880 | (propagated-inputs | |
5881 | `(("r-annotate" ,r-annotate) | |
5882 | ("r-annotationdbi" ,r-annotationdbi) | |
5883 | ("r-biobase" ,r-biobase) | |
5884 | ("r-biocgenerics" ,r-biocgenerics) | |
5885 | ("r-genefilter" ,r-genefilter) | |
5886 | ("r-graph" ,r-graph) | |
5887 | ("r-gseabase" ,r-gseabase) | |
5888 | ("r-matrix" ,r-matrix) | |
5889 | ("r-rbgl" ,r-rbgl) | |
5890 | ("r-rsqlite" ,r-rsqlite))) | |
5891 | (home-page "http://bioconductor.org/packages/Category") | |
5892 | (synopsis "Category analysis") | |
5893 | (description | |
5894 | "This package provides a collection of tools for performing category | |
5895 | analysis.") | |
5896 | (license license:artistic2.0))) | |
5897 | ||
89f40c5e RW |
5898 | (define-public r-gostats |
5899 | (package | |
5900 | (name "r-gostats") | |
95117734 | 5901 | (version "2.42.0") |
89f40c5e RW |
5902 | (source |
5903 | (origin | |
5904 | (method url-fetch) | |
5905 | (uri (bioconductor-uri "GOstats" version)) | |
5906 | (sha256 | |
5907 | (base32 | |
95117734 | 5908 | "0qvqjgfnd9ap4rikvyxa9p4dhcnccvkw8phzv88vghh6pq463d62")))) |
89f40c5e RW |
5909 | (properties `((upstream-name . "GOstats"))) |
5910 | (build-system r-build-system) | |
5911 | (propagated-inputs | |
5912 | `(("r-annotate" ,r-annotate) | |
5913 | ("r-annotationdbi" ,r-annotationdbi) | |
5914 | ("r-annotationforge" ,r-annotationforge) | |
5915 | ("r-biobase" ,r-biobase) | |
5916 | ("r-category" ,r-category) | |
5917 | ("r-go-db" ,r-go-db) | |
5918 | ("r-graph" ,r-graph) | |
5919 | ("r-rbgl" ,r-rbgl))) | |
5920 | (home-page "http://bioconductor.org/packages/GOstats") | |
5921 | (synopsis "Tools for manipulating GO and microarrays") | |
5922 | (description | |
5923 | "This package provides a set of tools for interacting with GO and | |
5924 | microarray data. A variety of basic manipulation tools for graphs, hypothesis | |
5925 | testing and other simple calculations.") | |
5926 | (license license:artistic2.0))) | |
5927 | ||
cb99d457 RW |
5928 | (define-public r-shortread |
5929 | (package | |
5930 | (name "r-shortread") | |
34c276f7 | 5931 | (version "1.34.0") |
cb99d457 RW |
5932 | (source |
5933 | (origin | |
5934 | (method url-fetch) | |
5935 | (uri (bioconductor-uri "ShortRead" version)) | |
5936 | (sha256 | |
5937 | (base32 | |
34c276f7 | 5938 | "0ayk3d5625ymb5g2gycq6banzqmyd642xrwjzhdshz2dwid7kly8")))) |
cb99d457 RW |
5939 | (properties `((upstream-name . "ShortRead"))) |
5940 | (build-system r-build-system) | |
5941 | (inputs | |
5942 | `(("zlib" ,zlib))) | |
5943 | (propagated-inputs | |
5944 | `(("r-biobase" ,r-biobase) | |
5945 | ("r-biocgenerics" ,r-biocgenerics) | |
5946 | ("r-biocparallel" ,r-biocparallel) | |
5947 | ("r-biostrings" ,r-biostrings) | |
5948 | ("r-genomeinfodb" ,r-genomeinfodb) | |
5949 | ("r-genomicalignments" ,r-genomicalignments) | |
5950 | ("r-genomicranges" ,r-genomicranges) | |
5951 | ("r-hwriter" ,r-hwriter) | |
5952 | ("r-iranges" ,r-iranges) | |
5953 | ("r-lattice" ,r-lattice) | |
5954 | ("r-latticeextra" ,r-latticeextra) | |
5955 | ("r-rsamtools" ,r-rsamtools) | |
5956 | ("r-s4vectors" ,r-s4vectors) | |
5957 | ("r-xvector" ,r-xvector) | |
5958 | ("r-zlibbioc" ,r-zlibbioc))) | |
5959 | (home-page "http://bioconductor.org/packages/ShortRead") | |
5960 | (synopsis "FASTQ input and manipulation tools") | |
5961 | (description | |
5962 | "This package implements sampling, iteration, and input of FASTQ files. | |
5963 | It includes functions for filtering and trimming reads, and for generating a | |
5964 | quality assessment report. Data are represented as | |
5965 | @code{DNAStringSet}-derived objects, and easily manipulated for a diversity of | |
5966 | purposes. The package also contains legacy support for early single-end, | |
5967 | ungapped alignment formats.") | |
5968 | (license license:artistic2.0))) | |
5969 | ||
7f903d73 RW |
5970 | (define-public r-systempiper |
5971 | (package | |
5972 | (name "r-systempiper") | |
026dc7e4 | 5973 | (version "1.10.0") |
7f903d73 RW |
5974 | (source |
5975 | (origin | |
5976 | (method url-fetch) | |
5977 | (uri (bioconductor-uri "systemPipeR" version)) | |
5978 | (sha256 | |
5979 | (base32 | |
026dc7e4 | 5980 | "0c3m5rq63ypv15yca97yag5d4vgd7xj9by2a4sd8z0pcmpajz0hw")))) |
7f903d73 RW |
5981 | (properties `((upstream-name . "systemPipeR"))) |
5982 | (build-system r-build-system) | |
5983 | (propagated-inputs | |
5984 | `(("r-annotate" ,r-annotate) | |
5985 | ("r-batchjobs" ,r-batchjobs) | |
5986 | ("r-biocgenerics" ,r-biocgenerics) | |
5987 | ("r-biostrings" ,r-biostrings) | |
5988 | ("r-deseq2" ,r-deseq2) | |
5989 | ("r-edger" ,r-edger) | |
5990 | ("r-genomicfeatures" ,r-genomicfeatures) | |
5991 | ("r-genomicranges" ,r-genomicranges) | |
5992 | ("r-ggplot2" ,r-ggplot2) | |
5993 | ("r-go-db" ,r-go-db) | |
5994 | ("r-gostats" ,r-gostats) | |
5995 | ("r-limma" ,r-limma) | |
5996 | ("r-pheatmap" ,r-pheatmap) | |
5997 | ("r-rjson" ,r-rjson) | |
5998 | ("r-rsamtools" ,r-rsamtools) | |
5999 | ("r-shortread" ,r-shortread) | |
6000 | ("r-summarizedexperiment" ,r-summarizedexperiment) | |
6001 | ("r-variantannotation" ,r-variantannotation))) | |
6002 | (home-page "https://github.com/tgirke/systemPipeR") | |
6003 | (synopsis "Next generation sequencing workflow and reporting environment") | |
6004 | (description | |
6005 | "This R package provides tools for building and running automated | |
6006 | end-to-end analysis workflows for a wide range of @dfn{next generation | |
6007 | sequence} (NGS) applications such as RNA-Seq, ChIP-Seq, VAR-Seq and Ribo-Seq. | |
6008 | Important features include a uniform workflow interface across different NGS | |
6009 | applications, automated report generation, and support for running both R and | |
6010 | command-line software, such as NGS aligners or peak/variant callers, on local | |
6011 | computers or compute clusters. Efficient handling of complex sample sets and | |
6012 | experimental designs is facilitated by a consistently implemented sample | |
6013 | annotation infrastructure.") | |
6014 | (license license:artistic2.0))) | |
6015 | ||
684f29bd RW |
6016 | (define-public r-grohmm |
6017 | (package | |
6018 | (name "r-grohmm") | |
795a6045 | 6019 | (version "1.10.0") |
684f29bd RW |
6020 | (source |
6021 | (origin | |
6022 | (method url-fetch) | |
6023 | (uri (bioconductor-uri "groHMM" version)) | |
6024 | (sha256 | |
6025 | (base32 | |
795a6045 | 6026 | "16k1kp4sbhh0vp7dzywafq52csq42ksqfrqfy4bdv1qbd7536dpd")))) |
684f29bd RW |
6027 | (properties `((upstream-name . "groHMM"))) |
6028 | (build-system r-build-system) | |
6029 | (propagated-inputs | |
6030 | `(("r-genomeinfodb" ,r-genomeinfodb) | |
6031 | ("r-genomicalignments" ,r-genomicalignments) | |
6032 | ("r-genomicranges" ,r-genomicranges) | |
6033 | ("r-iranges" ,r-iranges) | |
aeb64f3c | 6034 | ("r-mass" ,r-mass) |
684f29bd RW |
6035 | ("r-rtracklayer" ,r-rtracklayer) |
6036 | ("r-s4vectors" ,r-s4vectors))) | |
6037 | (home-page "https://github.com/Kraus-Lab/groHMM") | |
6038 | (synopsis "GRO-seq analysis pipeline") | |
6039 | (description | |
6040 | "This package provides a pipeline for the analysis of GRO-seq data.") | |
6041 | (license license:gpl3+))) | |
6042 | ||
f3cfe451 RW |
6043 | (define-public r-txdb-hsapiens-ucsc-hg19-knowngene |
6044 | (package | |
6045 | (name "r-txdb-hsapiens-ucsc-hg19-knowngene") | |
6046 | (version "3.2.2") | |
6047 | (source (origin | |
6048 | (method url-fetch) | |
6049 | ;; We cannot use bioconductor-uri here because this tarball is | |
6050 | ;; located under "data/annotation/" instead of "bioc/". | |
6051 | (uri (string-append "http://bioconductor.org/packages/" | |
6052 | "release/data/annotation/src/contrib" | |
6053 | "/TxDb.Hsapiens.UCSC.hg19.knownGene_" | |
6054 | version ".tar.gz")) | |
6055 | (sha256 | |
6056 | (base32 | |
6057 | "1sajhcqqwazgz2lqbik7rd935i7kpnh08zxbp2ra10j72yqy4g86")))) | |
6058 | (properties | |
6059 | `((upstream-name . "TxDb.Hsapiens.UCSC.hg19.knownGene"))) | |
6060 | (build-system r-build-system) | |
6061 | ;; As this package provides little more than a very large data file it | |
6062 | ;; doesn't make sense to build substitutes. | |
6063 | (arguments `(#:substitutable? #f)) | |
6064 | (propagated-inputs | |
6065 | `(("r-genomicfeatures" ,r-genomicfeatures))) | |
6066 | (home-page | |
6067 | "http://bioconductor.org/packages/TxDb.Hsapiens.UCSC.hg19.knownGene/") | |
6068 | (synopsis "Annotation package for human genome in TxDb format") | |
6069 | (description | |
6070 | "This package provides an annotation database of Homo sapiens genome | |
6071 | data. It is derived from the UCSC hg19 genome and based on the \"knownGene\" | |
6072 | track. The database is exposed as a @code{TxDb} object.") | |
6073 | (license license:artistic2.0))) | |
6074 | ||
a2950fa4 BW |
6075 | (define-public vsearch |
6076 | (package | |
6077 | (name "vsearch") | |
37982693 | 6078 | (version "2.4.3") |
a2950fa4 BW |
6079 | (source |
6080 | (origin | |
6081 | (method url-fetch) | |
6082 | (uri (string-append | |
6083 | "https://github.com/torognes/vsearch/archive/v" | |
6084 | version ".tar.gz")) | |
6085 | (file-name (string-append name "-" version ".tar.gz")) | |
6086 | (sha256 | |
6087 | (base32 | |
37982693 | 6088 | "0hc110ycqpa54nr6x173qg7190hk08qp7yz7zzqxlsypqnpc5zzp")) |
206af46f | 6089 | (patches (search-patches "vsearch-unbundle-cityhash.patch")) |
a2950fa4 BW |
6090 | (snippet |
6091 | '(begin | |
206af46f BW |
6092 | ;; Remove bundled cityhash sources. The vsearch source is adjusted |
6093 | ;; for this in the patch. | |
cf6edaba BW |
6094 | (delete-file "src/city.h") |
6095 | (delete-file "src/citycrc.h") | |
6096 | (delete-file "src/city.cc") | |
a2950fa4 BW |
6097 | #t)))) |
6098 | (build-system gnu-build-system) | |
6099 | (arguments | |
6100 | `(#:phases | |
6101 | (modify-phases %standard-phases | |
6102 | (add-before 'configure 'autogen | |
6103 | (lambda _ (zero? (system* "autoreconf" "-vif"))))))) | |
6104 | (inputs | |
6105 | `(("zlib" ,zlib) | |
6106 | ("bzip2" ,bzip2) | |
6107 | ("cityhash" ,cityhash))) | |
6108 | (native-inputs | |
6109 | `(("autoconf" ,autoconf) | |
6110 | ("automake" ,automake))) | |
6111 | (synopsis "Sequence search tools for metagenomics") | |
6112 | (description | |
6113 | "VSEARCH supports DNA sequence searching, clustering, chimera detection, | |
6114 | dereplication, pairwise alignment, shuffling, subsampling, sorting and | |
6115 | masking. The tool takes advantage of parallelism in the form of SIMD | |
6116 | vectorization as well as multiple threads to perform accurate alignments at | |
6117 | high speed. VSEARCH uses an optimal global aligner (full dynamic programming | |
6118 | Needleman-Wunsch).") | |
6119 | (home-page "https://github.com/torognes/vsearch") | |
6f04e515 BW |
6120 | ;; vsearch uses non-portable SSE intrinsics so building fails on other |
6121 | ;; platforms. | |
6122 | (supported-systems '("x86_64-linux")) | |
a2950fa4 BW |
6123 | ;; Dual licensed; also includes public domain source. |
6124 | (license (list license:gpl3 license:bsd-2)))) | |
6125 | ||
07837874 RW |
6126 | (define-public pardre |
6127 | (package | |
6128 | (name "pardre") | |
7922ab8f BW |
6129 | ;; The source of 1.1.5 changed in place, so we append "-1" to the version. |
6130 | (version "1.1.5-1") | |
07837874 RW |
6131 | (source |
6132 | (origin | |
6133 | (method url-fetch) | |
6134 | (uri (string-append "mirror://sourceforge/pardre/ParDRe-rel" | |
7922ab8f | 6135 | "1.1.5" ".tar.gz")) |
07837874 RW |
6136 | (sha256 |
6137 | (base32 | |
7922ab8f | 6138 | "17j73nc0viq4f6qj50nrndsrif5d6b71q8fl87m54psiv0ilns2b")))) |
07837874 RW |
6139 | (build-system gnu-build-system) |
6140 | (arguments | |
6141 | `(#:tests? #f ; no tests included | |
6142 | #:phases | |
6143 | (modify-phases %standard-phases | |
6144 | (delete 'configure) | |
6145 | (replace 'install | |
6146 | (lambda* (#:key outputs #:allow-other-keys) | |
6147 | (let ((bin (string-append (assoc-ref outputs "out") "/bin"))) | |
07837874 RW |
6148 | (install-file "ParDRe" bin) |
6149 | #t)))))) | |
6150 | (inputs | |
6151 | `(("openmpi" ,openmpi) | |
6152 | ("zlib" ,zlib))) | |
6153 | (synopsis "Parallel tool to remove duplicate DNA reads") | |
6154 | (description | |
6155 | "ParDRe is a parallel tool to remove duplicate genetic sequence reads. | |
6156 | Duplicate reads can be seen as identical or nearly identical sequences with | |
6157 | some mismatches. This tool lets users avoid the analysis of unnecessary | |
6158 | reads, reducing the time of subsequent procedures with the | |
6159 | dataset (e.g. assemblies, mappings, etc.). The tool is implemented with MPI | |
6160 | in order to exploit the parallel capabilities of multicore clusters. It is | |
6161 | faster than multithreaded counterparts (end of 2015) for the same number of | |
6162 | cores and, thanks to the message-passing technology, it can be executed on | |
6163 | clusters.") | |
6164 | (home-page "https://sourceforge.net/projects/pardre/") | |
6165 | (license license:gpl3+))) | |
6166 | ||
e4a44a6a BW |
6167 | (define-public ruby-bio-kseq |
6168 | (package | |
6169 | (name "ruby-bio-kseq") | |
6170 | (version "0.0.2") | |
6171 | (source | |
6172 | (origin | |
6173 | (method url-fetch) | |
6174 | (uri (rubygems-uri "bio-kseq" version)) | |
6175 | (sha256 | |
6176 | (base32 | |
6177 | "1xyaha46khb5jc6wzkbf7040jagac49jbimn0vcrzid0j8jdikrz")))) | |
6178 | (build-system ruby-build-system) | |
6179 | (arguments | |
6180 | `(#:test-target "spec")) | |
6181 | (native-inputs | |
6182 | `(("bundler" ,bundler) | |
6183 | ("ruby-rspec" ,ruby-rspec) | |
6184 | ("ruby-rake-compiler" ,ruby-rake-compiler))) | |
6185 | (inputs | |
6186 | `(("zlib" ,zlib))) | |
6187 | (synopsis "Ruby bindings for the kseq.h FASTA/Q parser") | |
6188 | (description | |
6189 | "@code{Bio::Kseq} provides ruby bindings to the @code{kseq.h} FASTA and | |
6190 | FASTQ parsing code. It provides a fast iterator over sequences and their | |
6191 | quality scores.") | |
6192 | (home-page "https://github.com/gusevfe/bio-kseq") | |
6193 | (license license:expat))) | |
6194 | ||
9c38b540 PP |
6195 | (define-public bio-locus |
6196 | (package | |
6197 | (name "bio-locus") | |
6198 | (version "0.0.7") | |
6199 | (source | |
6200 | (origin | |
6201 | (method url-fetch) | |
6202 | (uri (rubygems-uri "bio-locus" version)) | |
6203 | (sha256 | |
6204 | (base32 | |
6205 | "02vmrxyimkj9sahsp4zhfhnmbvz6dbbqz1y01vglf8cbwvkajfl0")))) | |
6206 | (build-system ruby-build-system) | |
6207 | (native-inputs | |
6208 | `(("ruby-rspec" ,ruby-rspec))) | |
6209 | (synopsis "Tool for fast querying of genome locations") | |
6210 | (description | |
6211 | "Bio-locus is a tabix-like tool for fast querying of genome | |
6212 | locations. Many file formats in bioinformatics contain records that | |
6213 | start with a chromosome name and a position for a SNP, or a start-end | |
6214 | position for indels. Bio-locus allows users to store this chr+pos or | |
6215 | chr+pos+alt information in a database.") | |
6216 | (home-page "https://github.com/pjotrp/bio-locus") | |
6217 | (license license:expat))) | |
edb15985 | 6218 | |
b2bddb07 PP |
6219 | (define-public bio-blastxmlparser |
6220 | (package | |
6221 | (name "bio-blastxmlparser") | |
6222 | (version "2.0.4") | |
6223 | (source (origin | |
6224 | (method url-fetch) | |
6225 | (uri (rubygems-uri "bio-blastxmlparser" version)) | |
6226 | (sha256 | |
6227 | (base32 | |
6228 | "1wf4qygcmdjgcqm6flmvsagfr1gs9lf63mj32qv3z1f481zc5692")))) | |
6229 | (build-system ruby-build-system) | |
6230 | (propagated-inputs | |
6231 | `(("ruby-bio-logger" ,ruby-bio-logger) | |
6232 | ("ruby-nokogiri" ,ruby-nokogiri))) | |
6233 | (inputs | |
6234 | `(("ruby-rspec" ,ruby-rspec))) | |
6235 | (synopsis "Fast big data BLAST XML parser and library") | |
6236 | (description | |
6237 | "Very fast parallel big-data BLAST XML file parser which can be used as | |
6238 | command line utility. Use blastxmlparser to: Parse BLAST XML; filter output; | |
6239 | generate FASTA, JSON, YAML, RDF, JSON-LD, HTML, CSV, tabular output etc.") | |
7bf837fd | 6240 | (home-page "https://github.com/pjotrp/blastxmlparser") |
b2bddb07 PP |
6241 | (license license:expat))) |
6242 | ||
edb15985 PP |
6243 | (define-public bioruby |
6244 | (package | |
6245 | (name "bioruby") | |
dbf9d371 | 6246 | (version "1.5.1") |
edb15985 PP |
6247 | (source |
6248 | (origin | |
6249 | (method url-fetch) | |
6250 | (uri (rubygems-uri "bio" version)) | |
6251 | (sha256 | |
6252 | (base32 | |
dbf9d371 | 6253 | "0hdl0789c9n4mprnx5pgd46bfwl8d000rqpamj5h6kkjgspijv49")))) |
edb15985 PP |
6254 | (build-system ruby-build-system) |
6255 | (propagated-inputs | |
6256 | `(("ruby-libxml" ,ruby-libxml))) | |
6257 | (native-inputs | |
6258 | `(("which" ,which))) ; required for test phase | |
6259 | (arguments | |
6260 | `(#:phases | |
6261 | (modify-phases %standard-phases | |
6262 | (add-before 'build 'patch-test-command | |
6263 | (lambda _ | |
6264 | (substitute* '("test/functional/bio/test_command.rb") | |
6265 | (("/bin/sh") (which "sh"))) | |
6266 | (substitute* '("test/functional/bio/test_command.rb") | |
6267 | (("/bin/ls") (which "ls"))) | |
6268 | (substitute* '("test/functional/bio/test_command.rb") | |
6269 | (("which") (which "which"))) | |
6270 | (substitute* '("test/functional/bio/test_command.rb", | |
6271 | "test/data/command/echoarg2.sh") | |
6272 | (("/bin/echo") (which "echo"))) | |
6273 | #t))))) | |
6274 | (synopsis "Ruby library, shell and utilities for bioinformatics") | |
6275 | (description "BioRuby comes with a comprehensive set of Ruby development | |
6276 | tools and libraries for bioinformatics and molecular biology. BioRuby has | |
6277 | components for sequence analysis, pathway analysis, protein modelling and | |
6278 | phylogenetic analysis; it supports many widely used data formats and provides | |
6279 | easy access to databases, external programs and public web services, including | |
6280 | BLAST, KEGG, GenBank, MEDLINE and GO.") | |
6281 | (home-page "http://bioruby.org/") | |
6282 | ;; Code is released under Ruby license, except for setup | |
6283 | ;; (LGPLv2.1+) and scripts in samples (which have GPL2 and GPL2+) | |
6284 | (license (list license:ruby license:lgpl2.1+ license:gpl2+ )))) | |
a5002ae7 | 6285 | |
9fba89e8 RW |
6286 | (define-public r-acsnminer |
6287 | (package | |
6288 | (name "r-acsnminer") | |
0b54b4c9 | 6289 | (version "0.16.8.25") |
9fba89e8 RW |
6290 | (source (origin |
6291 | (method url-fetch) | |
6292 | (uri (cran-uri "ACSNMineR" version)) | |
6293 | (sha256 | |
6294 | (base32 | |
0b54b4c9 | 6295 | "0gh604s8qall6zfjlwcg2ilxjvz08dplf9k5g47idhv43scm748l")))) |
9fba89e8 RW |
6296 | (properties `((upstream-name . "ACSNMineR"))) |
6297 | (build-system r-build-system) | |
6298 | (propagated-inputs | |
6299 | `(("r-ggplot2" ,r-ggplot2) | |
6300 | ("r-gridextra" ,r-gridextra))) | |
6301 | (home-page "http://cran.r-project.org/web/packages/ACSNMineR") | |
6302 | (synopsis "Gene enrichment analysis") | |
6303 | (description | |
6304 | "This package provides tools to compute and represent gene set enrichment | |
6305 | or depletion from your data based on pre-saved maps from the @dfn{Atlas of | |
6306 | Cancer Signalling Networks} (ACSN) or user imported maps. The gene set | |
6307 | enrichment can be run with hypergeometric test or Fisher exact test, and can | |
6308 | use multiple corrections. Visualization of data can be done either by | |
6309 | barplots or heatmaps.") | |
6310 | (license license:gpl2+))) | |
6311 | ||
d29b25c4 RW |
6312 | (define-public r-biocgenerics |
6313 | (package | |
6314 | (name "r-biocgenerics") | |
28a5b3f2 | 6315 | (version "0.22.0") |
d29b25c4 RW |
6316 | (source (origin |
6317 | (method url-fetch) | |
6318 | (uri (bioconductor-uri "BiocGenerics" version)) | |
6319 | (sha256 | |
6320 | (base32 | |
28a5b3f2 | 6321 | "0qbmz2qxwwi30xpxpvp2h1h7l494rbbz5d9pls5cfhqdv3wnpzsv")))) |
d29b25c4 | 6322 | (properties |
1d216b6e | 6323 | `((upstream-name . "BiocGenerics"))) |
d29b25c4 RW |
6324 | (build-system r-build-system) |
6325 | (home-page "http://bioconductor.org/packages/BiocGenerics") | |
6326 | (synopsis "S4 generic functions for Bioconductor") | |
6327 | (description | |
6328 | "This package provides S4 generic functions needed by many Bioconductor | |
6329 | packages.") | |
6330 | (license license:artistic2.0))) | |
6331 | ||
eb24341f RJ |
6332 | (define-public r-biocinstaller |
6333 | (package | |
6334 | (name "r-biocinstaller") | |
3bef1528 | 6335 | (version "1.26.0") |
eb24341f RJ |
6336 | (source (origin |
6337 | (method url-fetch) | |
6338 | (uri (bioconductor-uri "BiocInstaller" version)) | |
6339 | (sha256 | |
6340 | (base32 | |
3bef1528 | 6341 | "0njw2q3lq1rrjx8qzw5d2130l72bmd3g2z8qlxqmkdcbmmgliyj2")))) |
eb24341f RJ |
6342 | (properties |
6343 | `((upstream-name . "BiocInstaller"))) | |
6344 | (build-system r-build-system) | |
6345 | (home-page "http://bioconductor.org/packages/BiocInstaller") | |
6346 | (synopsis "Install Bioconductor packages") | |
6347 | (description "This package is used to install and update R packages from | |
6348 | Bioconductor, CRAN, and Github.") | |
6349 | (license license:artistic2.0))) | |
6350 | ||
207ce8fb RJ |
6351 | (define-public r-biocviews |
6352 | (package | |
6353 | (name "r-biocviews") | |
68eac349 | 6354 | (version "1.44.0") |
207ce8fb RJ |
6355 | (source (origin |
6356 | (method url-fetch) | |
6357 | (uri (bioconductor-uri "biocViews" version)) | |
6358 | (sha256 | |
6359 | (base32 | |
68eac349 | 6360 | "17hi8w0w63f5yc43kid5pbld3ca78sj6n8x9dmkbl8h48818xbga")))) |
207ce8fb RJ |
6361 | (properties |
6362 | `((upstream-name . "biocViews"))) | |
6363 | (build-system r-build-system) | |
6364 | (propagated-inputs | |
6365 | `(("r-biobase" ,r-biobase) | |
6366 | ("r-graph" ,r-graph) | |
6367 | ("r-rbgl" ,r-rbgl) | |
6368 | ("r-rcurl" ,r-rcurl) | |
6369 | ("r-xml" ,r-xml) | |
6370 | ("r-knitr" ,r-knitr) | |
6371 | ("r-runit" ,r-runit))) | |
6372 | (home-page "http://bioconductor.org/packages/biocViews") | |
6373 | (synopsis "Bioconductor package categorization helper") | |
6374 | (description "The purpose of biocViews is to create HTML pages that | |
6375 | categorize packages in a Bioconductor package repository according to keywords, | |
6376 | also known as views, in a controlled vocabulary.") | |
6377 | (license license:artistic2.0))) | |
6378 | ||
2abfc5b8 RJ |
6379 | (define-public r-bookdown |
6380 | (package | |
6381 | (name "r-bookdown") | |
6382 | (version "0.3") | |
6383 | (source (origin | |
6384 | (method url-fetch) | |
6385 | (uri (cran-uri "bookdown" version)) | |
6386 | (sha256 | |
6387 | (base32 | |
6388 | "0r9bchzg7im6psc3jphvshzbidc5bv5xaih1qg7b5518jy4iyvb9")))) | |
6389 | (build-system r-build-system) | |
6390 | (propagated-inputs | |
6391 | `(("r-htmltools" ,r-htmltools) | |
6392 | ("r-knitr" ,r-knitr) | |
6393 | ("r-rmarkdown" ,r-rmarkdown) | |
6394 | ("r-yaml" ,r-yaml))) | |
6395 | (home-page "https://github.com/rstudio/bookdown") | |
6396 | (synopsis "Authoring books and technical documents with R markdown") | |
6397 | (description "This package provides output formats and utilities for | |
6398 | authoring books and technical documents with R Markdown.") | |
6399 | (license license:gpl3))) | |
6400 | ||
99df12cd RJ |
6401 | (define-public r-biocstyle |
6402 | (package | |
6403 | (name "r-biocstyle") | |
3bef24c9 | 6404 | (version "2.4.0") |
99df12cd RJ |
6405 | (source (origin |
6406 | (method url-fetch) | |
6407 | (uri (bioconductor-uri "BiocStyle" version)) | |
6408 | (sha256 | |
6409 | (base32 | |
3bef24c9 | 6410 | "1n2c8rj920wmk3q2khmjfnhn5i4b3lmhx1whnghk0zk3jf88hvbi")))) |
99df12cd RJ |
6411 | (properties |
6412 | `((upstream-name . "BiocStyle"))) | |
6413 | (build-system r-build-system) | |
3bef24c9 RJ |
6414 | (propagated-inputs |
6415 | `(("r-bookdown" ,r-bookdown) | |
6416 | ("r-knitr" ,r-knitr) | |
6417 | ("r-rmarkdown" ,r-rmarkdown) | |
6418 | ("r-yaml" ,r-yaml))) | |
99df12cd RJ |
6419 | (home-page "http://bioconductor.org/packages/BiocStyle") |
6420 | (synopsis "Bioconductor formatting styles") | |
6421 | (description "This package provides standard formatting styles for | |
6422 | Bioconductor PDF and HTML documents. Package vignettes illustrate use and | |
6423 | functionality.") | |
6424 | (license license:artistic2.0))) | |
6425 | ||
4644644a RJ |
6426 | (define-public r-bioccheck |
6427 | (package | |
6428 | (name "r-bioccheck") | |
2e11beec | 6429 | (version "1.12.0") |
4644644a RJ |
6430 | (source (origin |
6431 | (method url-fetch) | |
6432 | (uri (bioconductor-uri "BiocCheck" version)) | |
6433 | (sha256 | |
6434 | (base32 | |
2e11beec | 6435 | "01zkw5hggzvn0wj4msac71k1mknq4h2inn1c2hwqgw4cy1675wl0")))) |
4644644a RJ |
6436 | (properties |
6437 | `((upstream-name . "BiocCheck"))) | |
6438 | (build-system r-build-system) | |
6439 | (arguments | |
6440 | '(#:phases | |
6441 | (modify-phases %standard-phases | |
6442 | ;; This package can be used by calling BiocCheck(<package>) from | |
6443 | ;; within R, or by running R CMD BiocCheck <package>. This phase | |
6444 | ;; makes sure the latter works. For this to work, the BiocCheck | |
6445 | ;; script must be somewhere on the PATH (not the R bin directory). | |
6446 | (add-after 'install 'install-bioccheck-subcommand | |
6447 | (lambda* (#:key outputs #:allow-other-keys) | |
6448 | (let* ((out (assoc-ref outputs "out")) | |
6449 | (dest-dir (string-append out "/bin")) | |
6450 | (script-dir | |
6451 | (string-append out "/site-library/BiocCheck/script/"))) | |
6452 | (mkdir-p dest-dir) | |
6453 | (symlink (string-append script-dir "/checkBadDeps.R") | |
6454 | (string-append dest-dir "/checkBadDeps.R")) | |
6455 | (symlink (string-append script-dir "/BiocCheck") | |
6456 | (string-append dest-dir "/BiocCheck"))) | |
6457 | #t))))) | |
6458 | (native-inputs | |
6459 | `(("which" ,which))) | |
6460 | (propagated-inputs | |
aeb64f3c RW |
6461 | `(("r-codetools" ,r-codetools) |
6462 | ("r-graph" ,r-graph) | |
4644644a RJ |
6463 | ("r-httr" ,r-httr) |
6464 | ("r-optparse" ,r-optparse) | |
4644644a RJ |
6465 | ("r-biocinstaller" ,r-biocinstaller) |
6466 | ("r-biocviews" ,r-biocviews))) | |
6467 | (home-page "http://bioconductor.org/packages/BiocCheck") | |
6468 | (synopsis "Executes Bioconductor-specific package checks") | |
6469 | (description "This package contains tools to perform additional quality | |
6470 | checks on R packages that are to be submitted to the Bioconductor repository.") | |
6471 | (license license:artistic2.0))) | |
6472 | ||
2acaaee5 RJ |
6473 | (define-public r-getopt |
6474 | (package | |
6475 | (name "r-getopt") | |
6476 | (version "1.20.0") | |
6477 | (source | |
6478 | (origin | |
6479 | (method url-fetch) | |
6480 | (uri (cran-uri "getopt" version)) | |
6481 | (sha256 | |
6482 | (base32 | |
6483 | "00f57vgnzmg7cz80rjmjz1556xqcmx8nhrlbbhaq4w7gl2ibl87r")))) | |
6484 | (build-system r-build-system) | |
6485 | (home-page "https://github.com/trevorld/getopt") | |
6486 | (synopsis "Command-line option processor for R") | |
6487 | (description | |
6488 | "This package is designed to be used with Rscript to write shebang | |
6489 | scripts that accept short and long options. Many users will prefer to | |
6490 | use the packages @code{optparse} or @code{argparse} which add extra | |
6491 | features like automatically generated help options and usage texts, | |
6492 | support for default values, positional argument support, etc.") | |
6493 | (license license:gpl2+))) | |
6494 | ||
c79ad57a RJ |
6495 | (define-public r-optparse |
6496 | (package | |
6497 | (name "r-optparse") | |
6498 | (version "1.3.2") | |
6499 | (source | |
6500 | (origin | |
6501 | (method url-fetch) | |
6502 | (uri (cran-uri "optparse" version)) | |
6503 | (sha256 | |
6504 | (base32 | |
6505 | "1g8as89r91xxi5j5azsd6vrfrhg84mnfx2683j7pacdp8s33radw")))) | |
6506 | (build-system r-build-system) | |
6507 | (propagated-inputs | |
6508 | `(("r-getopt" ,r-getopt))) | |
6509 | (home-page | |
6510 | "https://github.com/trevorld/optparse") | |
6511 | (synopsis "Command line option parser") | |
6512 | (description | |
6513 | "This package provides a command line parser inspired by Python's | |
6514 | @code{optparse} library to be used with Rscript to write shebang scripts | |
6515 | that accept short and long options.") | |
6516 | (license license:gpl2+))) | |
6517 | ||
247d498a RJ |
6518 | (define-public r-dnacopy |
6519 | (package | |
6520 | (name "r-dnacopy") | |
9b02d49c | 6521 | (version "1.50.0") |
247d498a RJ |
6522 | (source (origin |
6523 | (method url-fetch) | |
6524 | (uri (bioconductor-uri "DNAcopy" version)) | |
6525 | (sha256 | |
6526 | (base32 | |
9b02d49c | 6527 | "0112ry62z18m7rdyrn3gvbxq2f6m44cawhcfb1f02z9xzlsj0k28")))) |
247d498a RJ |
6528 | (properties |
6529 | `((upstream-name . "DNAcopy"))) | |
6530 | (build-system r-build-system) | |
6531 | (inputs | |
6532 | `(("gfortran" ,gfortran))) | |
5697fdc3 | 6533 | (home-page "https://bioconductor.org/packages/DNAcopy") |
247d498a RJ |
6534 | (synopsis "Implementation of a circular binary segmentation algorithm") |
6535 | (description "This package implements the circular binary segmentation (CBS) | |
6536 | algorithm to segment DNA copy number data and identify genomic regions with | |
6537 | abnormal copy number.") | |
6538 | (license license:gpl2+))) | |
6539 | ||
7485129e RW |
6540 | (define-public r-s4vectors |
6541 | (package | |
6542 | (name "r-s4vectors") | |
3a4b0b12 | 6543 | (version "0.14.3") |
7485129e RW |
6544 | (source (origin |
6545 | (method url-fetch) | |
6546 | (uri (bioconductor-uri "S4Vectors" version)) | |
6547 | (sha256 | |
6548 | (base32 | |
3a4b0b12 | 6549 | "1r7s4pfw026qazzic090mhk8d9m39j2nwl87dyqcpdylyq7gq5qs")))) |
7485129e | 6550 | (properties |
1d216b6e | 6551 | `((upstream-name . "S4Vectors"))) |
7485129e RW |
6552 | (build-system r-build-system) |
6553 | (propagated-inputs | |
6554 | `(("r-biocgenerics" ,r-biocgenerics))) | |
6555 | (home-page "http://bioconductor.org/packages/S4Vectors") | |
6556 | (synopsis "S4 implementation of vectors and lists") | |
6557 | (description | |
6558 | "The S4Vectors package defines the @code{Vector} and @code{List} virtual | |
6559 | classes and a set of generic functions that extend the semantic of ordinary | |
6560 | vectors and lists in R. Package developers can easily implement vector-like | |
6561 | or list-like objects as concrete subclasses of @code{Vector} or @code{List}. | |
6562 | In addition, a few low-level concrete subclasses of general interest (e.g. | |
6563 | @code{DataFrame}, @code{Rle}, and @code{Hits}) are implemented in the | |
6564 | S4Vectors package itself.") | |
6565 | (license license:artistic2.0))) | |
6566 | ||
274da826 RW |
6567 | (define-public r-seqinr |
6568 | (package | |
6569 | (name "r-seqinr") | |
e18c731b | 6570 | (version "3.3-6") |
274da826 RW |
6571 | (source |
6572 | (origin | |
6573 | (method url-fetch) | |
6574 | (uri (cran-uri "seqinr" version)) | |
6575 | (sha256 | |
6576 | (base32 | |
e18c731b | 6577 | "13d0qxm2244wgdl2dy2s8vnrnf5fx4n47if9gkb49dqx6c0sx8s2")))) |
274da826 RW |
6578 | (build-system r-build-system) |
6579 | (propagated-inputs | |
3b851cd4 RW |
6580 | `(("r-ade4" ,r-ade4) |
6581 | ("r-segmented" ,r-segmented))) | |
274da826 RW |
6582 | (inputs |
6583 | `(("zlib" ,zlib))) | |
6584 | (home-page "http://seqinr.r-forge.r-project.org/") | |
6585 | (synopsis "Biological sequences retrieval and analysis") | |
6586 | (description | |
6587 | "This package provides tools for exploratory data analysis and data | |
6588 | visualization of biological sequence (DNA and protein) data. It also includes | |
6589 | utilities for sequence data management under the ACNUC system.") | |
6590 | (license license:gpl2+))) | |
6591 | ||
78addcb0 RW |
6592 | (define-public r-iranges |
6593 | (package | |
6594 | (name "r-iranges") | |
7d9ab5d9 | 6595 | (version "2.10.0") |
78addcb0 RW |
6596 | (source (origin |
6597 | (method url-fetch) | |
6598 | (uri (bioconductor-uri "IRanges" version)) | |
6599 | (sha256 | |
6600 | (base32 | |
7d9ab5d9 | 6601 | "0zp4mxm9h1p4krj7m7cinkvwa2ibqkq59jwpan97yvhb4z8q0d6n")))) |
78addcb0 | 6602 | (properties |
1d216b6e | 6603 | `((upstream-name . "IRanges"))) |
78addcb0 RW |
6604 | (build-system r-build-system) |
6605 | (propagated-inputs | |
6606 | `(("r-biocgenerics" ,r-biocgenerics) | |
6607 | ("r-s4vectors" ,r-s4vectors))) | |
6608 | (home-page "http://bioconductor.org/packages/IRanges") | |
6609 | (synopsis "Infrastructure for manipulating intervals on sequences") | |
6610 | (description | |
6611 | "This package provides efficient low-level and highly reusable S4 classes | |
6612 | for storing ranges of integers, RLE vectors (Run-Length Encoding), and, more | |
6613 | generally, data that can be organized sequentially (formally defined as | |
6614 | @code{Vector} objects), as well as views on these @code{Vector} objects. | |
6615 | Efficient list-like classes are also provided for storing big collections of | |
6616 | instances of the basic classes. All classes in the package use consistent | |
6617 | naming and share the same rich and consistent \"Vector API\" as much as | |
6618 | possible.") | |
6619 | (license license:artistic2.0))) | |
6620 | ||
ffef27f3 RJ |
6621 | (define-public r-genomeinfodbdata |
6622 | (package | |
6623 | (name "r-genomeinfodbdata") | |
6624 | (version "0.99.0") | |
6625 | (source (origin | |
6626 | (method url-fetch) | |
90f83099 EF |
6627 | ;; We cannot use bioconductor-uri here because this tarball is |
6628 | ;; located under "data/annotation/" instead of "bioc/". | |
6629 | (uri (string-append "https://bioconductor.org/packages/release/" | |
6630 | "data/annotation/src/contrib/GenomeInfoDbData_" | |
6631 | version ".tar.gz")) | |
ffef27f3 RJ |
6632 | (sha256 |
6633 | (base32 | |
6634 | "120qvhb0pvkzd65lsgja62vyrgc37si6fh68q4cg4w5x9f04jw25")))) | |
6635 | (properties | |
6636 | `((upstream-name . "GenomeInfoDbData"))) | |
6637 | (build-system r-build-system) | |
6638 | (home-page "http://bioconductor.org/packages/GenomeInfoDbData") | |
6639 | (synopsis "Species and taxonomy ID look up tables for GenomeInfoDb") | |
6640 | (description "This package contains data for mapping between NCBI taxonomy | |
6641 | ID and species. It is used by functions in the GenomeInfoDb package.") | |
6642 | (license license:artistic2.0))) | |
6643 | ||
bf7764b7 RW |
6644 | (define-public r-genomeinfodb |
6645 | (package | |
6646 | (name "r-genomeinfodb") | |
38b99ccc | 6647 | (version "1.12.0") |
bf7764b7 RW |
6648 | (source (origin |
6649 | (method url-fetch) | |
6650 | (uri (bioconductor-uri "GenomeInfoDb" version)) | |
6651 | (sha256 | |
6652 | (base32 | |
38b99ccc | 6653 | "1bwwhscjl376a5p43mx8ijrqajxmgypbqhv049pgagl22hkkf0y3")))) |
bf7764b7 | 6654 | (properties |
1d216b6e | 6655 | `((upstream-name . "GenomeInfoDb"))) |
bf7764b7 RW |
6656 | (build-system r-build-system) |
6657 | (propagated-inputs | |
6658 | `(("r-biocgenerics" ,r-biocgenerics) | |
38b99ccc | 6659 | ("r-genomeinfodbdata" ,r-genomeinfodbdata) |
bf7764b7 | 6660 | ("r-iranges" ,r-iranges) |
4cd07e48 | 6661 | ("r-rcurl" ,r-rcurl) |
bf7764b7 RW |
6662 | ("r-s4vectors" ,r-s4vectors))) |
6663 | (home-page "http://bioconductor.org/packages/GenomeInfoDb") | |
6664 | (synopsis "Utilities for manipulating chromosome identifiers") | |
6665 | (description | |
6666 | "This package contains data and functions that define and allow | |
6667 | translation between different chromosome sequence naming conventions (e.g., | |
6668 | \"chr1\" versus \"1\"), including a function that attempts to place sequence | |
6669 | names in their natural, rather than lexicographic, order.") | |
6670 | (license license:artistic2.0))) | |
6671 | ||
744004a3 RJ |
6672 | (define-public r-edger |
6673 | (package | |
6674 | (name "r-edger") | |
00ffd55f | 6675 | (version "3.18.0") |
744004a3 RJ |
6676 | (source (origin |
6677 | (method url-fetch) | |
6678 | (uri (bioconductor-uri "edgeR" version)) | |
6679 | (sha256 | |
6680 | (base32 | |
00ffd55f | 6681 | "02l17i6xh33dv10swwvyfxrmv5kp23iv278iwvkfq2mnipasfnb9")))) |
744004a3 RJ |
6682 | (properties `((upstream-name . "edgeR"))) |
6683 | (build-system r-build-system) | |
6684 | (propagated-inputs | |
5e48005f | 6685 | `(("r-limma" ,r-limma) |
47055b27 RW |
6686 | ("r-locfit" ,r-locfit) |
6687 | ("r-statmod" ,r-statmod))) ;for estimateDisp | |
744004a3 RJ |
6688 | (home-page "http://bioinf.wehi.edu.au/edgeR") |
6689 | (synopsis "EdgeR does empirical analysis of digital gene expression data") | |
6690 | (description "This package can do differential expression analysis of | |
6691 | RNA-seq expression profiles with biological replication. It implements a range | |
6692 | of statistical methodology based on the negative binomial distributions, | |
6693 | including empirical Bayes estimation, exact tests, generalized linear models | |
6694 | and quasi-likelihood tests. It be applied to differential signal analysis of | |
6695 | other types of genomic data that produce counts, including ChIP-seq, SAGE and | |
6696 | CAGE.") | |
6697 | (license license:gpl2+))) | |
6698 | ||
b669d9c4 RJ |
6699 | (define-public r-variantannotation |
6700 | (package | |
6701 | (name "r-variantannotation") | |
d2d7af98 | 6702 | (version "1.22.0") |
b669d9c4 RJ |
6703 | (source (origin |
6704 | (method url-fetch) | |
6705 | (uri (bioconductor-uri "VariantAnnotation" version)) | |
6706 | (sha256 | |
6707 | (base32 | |
d2d7af98 | 6708 | "05hpm4as36kvpiqhgnkfjwfx0a05p304c21ggba29iac4nanm8b3")))) |
b669d9c4 RJ |
6709 | (properties |
6710 | `((upstream-name . "VariantAnnotation"))) | |
6711 | (inputs | |
6712 | `(("zlib" ,zlib))) | |
6713 | (propagated-inputs | |
6714 | `(("r-annotationdbi" ,r-annotationdbi) | |
37d96f1d | 6715 | ("r-biobase" ,r-biobase) |
b669d9c4 | 6716 | ("r-biocgenerics" ,r-biocgenerics) |
37d96f1d | 6717 | ("r-biostrings" ,r-biostrings) |
b669d9c4 RJ |
6718 | ("r-bsgenome" ,r-bsgenome) |
6719 | ("r-dbi" ,r-dbi) | |
6720 | ("r-genomeinfodb" ,r-genomeinfodb) | |
6721 | ("r-genomicfeatures" ,r-genomicfeatures) | |
6722 | ("r-genomicranges" ,r-genomicranges) | |
37d96f1d | 6723 | ("r-iranges" ,r-iranges) |
b669d9c4 RJ |
6724 | ("r-summarizedexperiment" ,r-summarizedexperiment) |
6725 | ("r-rsamtools" ,r-rsamtools) | |
37d96f1d RW |
6726 | ("r-rtracklayer" ,r-rtracklayer) |
6727 | ("r-s4vectors" ,r-s4vectors) | |
6728 | ("r-xvector" ,r-xvector) | |
b669d9c4 RJ |
6729 | ("r-zlibbioc" ,r-zlibbioc))) |
6730 | (build-system r-build-system) | |
6731 | (home-page "https://bioconductor.org/packages/VariantAnnotation") | |
6732 | (synopsis "Package for annotation of genetic variants") | |
6733 | (description "This R package can annotate variants, compute amino acid | |
6734 | coding changes and predict coding outcomes.") | |
6735 | (license license:artistic2.0))) | |
6736 | ||
7d4224d7 RJ |
6737 | (define-public r-limma |
6738 | (package | |
6739 | (name "r-limma") | |
abf5a14e | 6740 | (version "3.32.0") |
7d4224d7 RJ |
6741 | (source (origin |
6742 | (method url-fetch) | |
6743 | (uri (bioconductor-uri "limma" version)) | |
6744 | (sha256 | |
6745 | (base32 | |
abf5a14e | 6746 | "0q7rqm86nwq0rg4fjggfr7xqybjrxj425vni3cva70b4c8d1h425")))) |
7d4224d7 RJ |
6747 | (build-system r-build-system) |
6748 | (home-page "http://bioinf.wehi.edu.au/limma") | |
6749 | (synopsis "Package for linear models for microarray and RNA-seq data") | |
6750 | (description "This package can be used for the analysis of gene expression | |
6751 | studies, especially the use of linear models for analysing designed experiments | |
6752 | and the assessment of differential expression. The analysis methods apply to | |
6753 | different technologies, including microarrays, RNA-seq, and quantitative PCR.") | |
6754 | (license license:gpl2+))) | |
6755 | ||
0e7d5560 RW |
6756 | (define-public r-xvector |
6757 | (package | |
6758 | (name "r-xvector") | |
17a02f51 | 6759 | (version "0.16.0") |
0e7d5560 RW |
6760 | (source (origin |
6761 | (method url-fetch) | |
6762 | (uri (bioconductor-uri "XVector" version)) | |
6763 | (sha256 | |
6764 | (base32 | |
17a02f51 | 6765 | "01n09f4jdm60684lzikp02zf9gjan8bdrjx740vggr21q9fa69wn")))) |
0e7d5560 | 6766 | (properties |
1d216b6e | 6767 | `((upstream-name . "XVector"))) |
0e7d5560 RW |
6768 | (build-system r-build-system) |
6769 | (arguments | |
6770 | `(#:phases | |
6771 | (modify-phases %standard-phases | |
6772 | (add-after 'unpack 'use-system-zlib | |
6773 | (lambda _ | |
6774 | (substitute* "DESCRIPTION" | |
6775 | (("zlibbioc, ") "")) | |
6776 | (substitute* "NAMESPACE" | |
6777 | (("import\\(zlibbioc\\)") "")) | |
6778 | #t))))) | |
6779 | (inputs | |
6780 | `(("zlib" ,zlib))) | |
6781 | (propagated-inputs | |
6782 | `(("r-biocgenerics" ,r-biocgenerics) | |
6783 | ("r-iranges" ,r-iranges) | |
6784 | ("r-s4vectors" ,r-s4vectors))) | |
6785 | (home-page "http://bioconductor.org/packages/XVector") | |
6786 | (synopsis "Representation and manpulation of external sequences") | |
6787 | (description | |
6788 | "This package provides memory efficient S4 classes for storing sequences | |
6789 | \"externally\" (behind an R external pointer, or on disk).") | |
6790 | (license license:artistic2.0))) | |
6791 | ||
e2cd1d0f RW |
6792 | (define-public r-genomicranges |
6793 | (package | |
6794 | (name "r-genomicranges") | |
a35a1e9c | 6795 | (version "1.28.4") |
e2cd1d0f RW |
6796 | (source (origin |
6797 | (method url-fetch) | |
6798 | (uri (bioconductor-uri "GenomicRanges" version)) | |
6799 | (sha256 | |
6800 | (base32 | |
a35a1e9c | 6801 | "1y15kg1q81h8rmga83ljiwr8whkajcargfjiljr212d6if17ys1z")))) |
e2cd1d0f | 6802 | (properties |
1d216b6e | 6803 | `((upstream-name . "GenomicRanges"))) |
e2cd1d0f RW |
6804 | (build-system r-build-system) |
6805 | (propagated-inputs | |
6806 | `(("r-biocgenerics" ,r-biocgenerics) | |
6807 | ("r-genomeinfodb" ,r-genomeinfodb) | |
92a740af RW |
6808 | ("r-iranges" ,r-iranges) |
6809 | ("r-s4vectors" ,r-s4vectors) | |
e2cd1d0f RW |
6810 | ("r-xvector" ,r-xvector))) |
6811 | (home-page "http://bioconductor.org/packages/GenomicRanges") | |
6812 | (synopsis "Representation and manipulation of genomic intervals") | |
6813 | (description | |
6814 | "This package provides tools to efficiently represent and manipulate | |
6815 | genomic annotations and alignments is playing a central role when it comes to | |
6816 | analyzing high-throughput sequencing data (a.k.a. NGS data). The | |
6817 | GenomicRanges package defines general purpose containers for storing and | |
6818 | manipulating genomic intervals and variables defined along a genome.") | |
6819 | (license license:artistic2.0))) | |
6820 | ||
555e3399 RW |
6821 | (define-public r-biobase |
6822 | (package | |
6823 | (name "r-biobase") | |
b2fff403 | 6824 | (version "2.36.0") |
555e3399 RW |
6825 | (source (origin |
6826 | (method url-fetch) | |
6827 | (uri (bioconductor-uri "Biobase" version)) | |
6828 | (sha256 | |
6829 | (base32 | |
b2fff403 | 6830 | "0x7pf5xsdcj12dbf5qqki2c6bd5madqg2fbiq5xgisarpc9v6c1m")))) |
555e3399 RW |
6831 | (properties |
6832 | `((upstream-name . "Biobase"))) | |
6833 | (build-system r-build-system) | |
6834 | (propagated-inputs | |
6835 | `(("r-biocgenerics" ,r-biocgenerics))) | |
6836 | (home-page "http://bioconductor.org/packages/Biobase") | |
6837 | (synopsis "Base functions for Bioconductor") | |
6838 | (description | |
6839 | "This package provides functions that are needed by many other packages | |
6840 | on Bioconductor or which replace R functions.") | |
6841 | (license license:artistic2.0))) | |
6842 | ||
8b7bce74 RW |
6843 | (define-public r-annotationdbi |
6844 | (package | |
6845 | (name "r-annotationdbi") | |
aafaab22 | 6846 | (version "1.38.0") |
8b7bce74 RW |
6847 | (source (origin |
6848 | (method url-fetch) | |
6849 | (uri (bioconductor-uri "AnnotationDbi" version)) | |
6850 | (sha256 | |
6851 | (base32 | |
aafaab22 | 6852 | "1xffm98s817mfc827cnr0by6167nlrl1glxzjawzz0rkghs41g27")))) |
8b7bce74 RW |
6853 | (properties |
6854 | `((upstream-name . "AnnotationDbi"))) | |
6855 | (build-system r-build-system) | |
6856 | (propagated-inputs | |
6857 | `(("r-biobase" ,r-biobase) | |
6858 | ("r-biocgenerics" ,r-biocgenerics) | |
6859 | ("r-dbi" ,r-dbi) | |
6860 | ("r-iranges" ,r-iranges) | |
6861 | ("r-rsqlite" ,r-rsqlite) | |
6862 | ("r-s4vectors" ,r-s4vectors))) | |
6863 | (home-page "http://bioconductor.org/packages/AnnotationDbi") | |
6864 | (synopsis "Annotation database interface") | |
6865 | (description | |
6866 | "This package provides user interface and database connection code for | |
6867 | annotation data packages using SQLite data storage.") | |
6868 | (license license:artistic2.0))) | |
6869 | ||
c465fa72 RW |
6870 | (define-public r-biomart |
6871 | (package | |
6872 | (name "r-biomart") | |
78e7a589 | 6873 | (version "2.32.0") |
c465fa72 RW |
6874 | (source (origin |
6875 | (method url-fetch) | |
6876 | (uri (bioconductor-uri "biomaRt" version)) | |
6877 | (sha256 | |
6878 | (base32 | |
78e7a589 | 6879 | "0knkxh23vl9pa0by03xr6dy9aiah714cmf54jl828k51l9wv5l2j")))) |
c465fa72 RW |
6880 | (properties |
6881 | `((upstream-name . "biomaRt"))) | |
6882 | (build-system r-build-system) | |
6883 | (propagated-inputs | |
6884 | `(("r-annotationdbi" ,r-annotationdbi) | |
6885 | ("r-rcurl" ,r-rcurl) | |
6886 | ("r-xml" ,r-xml))) | |
6887 | (home-page "http://bioconductor.org/packages/biomaRt") | |
6888 | (synopsis "Interface to BioMart databases") | |
6889 | (description | |
6890 | "biomaRt provides an interface to a growing collection of databases | |
6891 | implementing the @url{BioMart software suite, http://www.biomart.org}. The | |
6892 | package enables retrieval of large amounts of data in a uniform way without | |
6893 | the need to know the underlying database schemas or write complex SQL queries. | |
6894 | Examples of BioMart databases are Ensembl, COSMIC, Uniprot, HGNC, Gramene, | |
6895 | Wormbase and dbSNP mapped to Ensembl. These major databases give biomaRt | |
6896 | users direct access to a diverse set of data and enable a wide range of | |
6897 | powerful online queries from gene annotation to database mining.") | |
6898 | (license license:artistic2.0))) | |
6899 | ||
e91d362e RW |
6900 | (define-public r-biocparallel |
6901 | (package | |
6902 | (name "r-biocparallel") | |
502da6ff | 6903 | (version "1.10.0") |
e91d362e RW |
6904 | (source (origin |
6905 | (method url-fetch) | |
6906 | (uri (bioconductor-uri "BiocParallel" version)) | |
6907 | (sha256 | |
6908 | (base32 | |
502da6ff | 6909 | "01ph0kq70b5gkd7n6a4myjlvwzgc0hi4xfwz8h17h06n9p5sdwa9")))) |
e91d362e RW |
6910 | (properties |
6911 | `((upstream-name . "BiocParallel"))) | |
6912 | (build-system r-build-system) | |
6913 | (propagated-inputs | |
6914 | `(("r-futile-logger" ,r-futile-logger) | |
6915 | ("r-snow" ,r-snow))) | |
6916 | (home-page "http://bioconductor.org/packages/BiocParallel") | |
6917 | (synopsis "Bioconductor facilities for parallel evaluation") | |
6918 | (description | |
6919 | "This package provides modified versions and novel implementation of | |
6920 | functions for parallel evaluation, tailored to use with Bioconductor | |
6921 | objects.") | |
6922 | (license (list license:gpl2+ license:gpl3+)))) | |
6923 | ||
bf159353 RW |
6924 | (define-public r-biostrings |
6925 | (package | |
6926 | (name "r-biostrings") | |
3ed41af6 | 6927 | (version "2.44.0") |
bf159353 RW |
6928 | (source (origin |
6929 | (method url-fetch) | |
6930 | (uri (bioconductor-uri "Biostrings" version)) | |
6931 | (sha256 | |
6932 | (base32 | |
3ed41af6 | 6933 | "0ixgx12cx2z4n2khxq83crz9gc21qckj2v78y2p31567kfsw7clg")))) |
bf159353 RW |
6934 | (properties |
6935 | `((upstream-name . "Biostrings"))) | |
6936 | (build-system r-build-system) | |
6937 | (propagated-inputs | |
6938 | `(("r-biocgenerics" ,r-biocgenerics) | |
6939 | ("r-iranges" ,r-iranges) | |
6940 | ("r-s4vectors" ,r-s4vectors) | |
6941 | ("r-xvector" ,r-xvector))) | |
6942 | (home-page "http://bioconductor.org/packages/Biostrings") | |
6943 | (synopsis "String objects and algorithms for biological sequences") | |
6944 | (description | |
6945 | "This package provides memory efficient string containers, string | |
6946 | matching algorithms, and other utilities, for fast manipulation of large | |
6947 | biological sequences or sets of sequences.") | |
6948 | (license license:artistic2.0))) | |
6949 | ||
f8d74f70 RW |
6950 | (define-public r-rsamtools |
6951 | (package | |
6952 | (name "r-rsamtools") | |
6bf5543b | 6953 | (version "1.28.0") |
f8d74f70 RW |
6954 | (source (origin |
6955 | (method url-fetch) | |
6956 | (uri (bioconductor-uri "Rsamtools" version)) | |
6957 | (sha256 | |
6958 | (base32 | |
6bf5543b | 6959 | "1zx6vhdz3lksbfy98jj3qzl7cxgspigm2pbsd5835b12r6mc5w6d")))) |
f8d74f70 RW |
6960 | (properties |
6961 | `((upstream-name . "Rsamtools"))) | |
6962 | (build-system r-build-system) | |
6963 | (arguments | |
6964 | `(#:phases | |
6965 | (modify-phases %standard-phases | |
6966 | (add-after 'unpack 'use-system-zlib | |
6967 | (lambda _ | |
6968 | (substitute* "DESCRIPTION" | |
6969 | (("zlibbioc, ") "")) | |
6970 | (substitute* "NAMESPACE" | |
6971 | (("import\\(zlibbioc\\)") "")) | |
6972 | #t))))) | |
6973 | (inputs | |
6974 | `(("zlib" ,zlib))) | |
6975 | (propagated-inputs | |
6976 | `(("r-biocgenerics" ,r-biocgenerics) | |
6977 | ("r-biocparallel" ,r-biocparallel) | |
6978 | ("r-biostrings" ,r-biostrings) | |
6979 | ("r-bitops" ,r-bitops) | |
6980 | ("r-genomeinfodb" ,r-genomeinfodb) | |
6981 | ("r-genomicranges" ,r-genomicranges) | |
6982 | ("r-iranges" ,r-iranges) | |
6983 | ("r-s4vectors" ,r-s4vectors) | |
6984 | ("r-xvector" ,r-xvector))) | |
6985 | (home-page "http://bioconductor.org/packages/release/bioc/html/Rsamtools.html") | |
6986 | (synopsis "Interface to samtools, bcftools, and tabix") | |
6987 | (description | |
6988 | "This package provides an interface to the 'samtools', 'bcftools', and | |
6989 | 'tabix' utilities for manipulating SAM (Sequence Alignment / Map), FASTA, | |
6990 | binary variant call (BCF) and compressed indexed tab-delimited (tabix) | |
6991 | files.") | |
6992 | (license license:expat))) | |
6993 | ||
71e34e6b RJ |
6994 | (define-public r-delayedarray |
6995 | (package | |
6996 | (name "r-delayedarray") | |
adf5d0a0 | 6997 | (version "0.2.7") |
71e34e6b RJ |
6998 | (source (origin |
6999 | (method url-fetch) | |
7000 | (uri (bioconductor-uri "DelayedArray" version)) | |
7001 | (sha256 | |
7002 | (base32 | |
adf5d0a0 | 7003 | "02dfqp4md9xaqjj712ijc3jswghmipr5hwkd5hr0x1xi6l2fb69g")))) |
71e34e6b RJ |
7004 | (properties |
7005 | `((upstream-name . "DelayedArray"))) | |
7006 | (build-system r-build-system) | |
7007 | (propagated-inputs | |
7008 | `(("r-biocgenerics" ,r-biocgenerics) | |
7009 | ("r-s4vectors" ,r-s4vectors) | |
7010 | ("r-iranges" ,r-iranges) | |
7011 | ("r-matrixstats" ,r-matrixstats))) | |
7012 | (home-page "http://bioconductor.org/packages/DelayedArray") | |
7013 | (synopsis "Delayed operations on array-like objects") | |
7014 | (description | |
7015 | "Wrapping an array-like object (typically an on-disk object) in a | |
7016 | @code{DelayedArray} object allows one to perform common array operations on it | |
7017 | without loading the object in memory. In order to reduce memory usage and | |
7018 | optimize performance, operations on the object are either delayed or executed | |
7019 | using a block processing mechanism. Note that this also works on in-memory | |
7020 | array-like objects like @code{DataFrame} objects (typically with Rle columns), | |
7021 | @code{Matrix} objects, and ordinary arrays and data frames.") | |
7022 | (license license:artistic2.0))) | |
7023 | ||
6e76dda2 RW |
7024 | (define-public r-summarizedexperiment |
7025 | (package | |
7026 | (name "r-summarizedexperiment") | |
f41150f1 | 7027 | (version "1.6.3") |
6e76dda2 RW |
7028 | (source (origin |
7029 | (method url-fetch) | |
7030 | (uri (bioconductor-uri "SummarizedExperiment" version)) | |
7031 | (sha256 | |
7032 | (base32 | |
f41150f1 | 7033 | "0j7xn7pk52d383fb1wplcggacl2586c4zi0alkgfc3wz7qq9w13s")))) |
6e76dda2 RW |
7034 | (properties |
7035 | `((upstream-name . "SummarizedExperiment"))) | |
7036 | (build-system r-build-system) | |
7037 | (propagated-inputs | |
7038 | `(("r-biobase" ,r-biobase) | |
7039 | ("r-biocgenerics" ,r-biocgenerics) | |
d006ee31 | 7040 | ("r-delayedarray" ,r-delayedarray) |
6e76dda2 RW |
7041 | ("r-genomeinfodb" ,r-genomeinfodb) |
7042 | ("r-genomicranges" ,r-genomicranges) | |
7043 | ("r-iranges" ,r-iranges) | |
aeb64f3c | 7044 | ("r-matrix" ,r-matrix) |
6e76dda2 RW |
7045 | ("r-s4vectors" ,r-s4vectors))) |
7046 | (home-page "http://bioconductor.org/packages/SummarizedExperiment") | |
7047 | (synopsis "Container for representing genomic ranges by sample") | |
7048 | (description | |
7049 | "The SummarizedExperiment container contains one or more assays, each | |
7050 | represented by a matrix-like object of numeric or other mode. The rows | |
7051 | typically represent genomic ranges of interest and the columns represent | |
7052 | samples.") | |
7053 | (license license:artistic2.0))) | |
7054 | ||
d8a828af RW |
7055 | (define-public r-genomicalignments |
7056 | (package | |
7057 | (name "r-genomicalignments") | |
26760c80 | 7058 | (version "1.12.1") |
d8a828af RW |
7059 | (source (origin |
7060 | (method url-fetch) | |
7061 | (uri (bioconductor-uri "GenomicAlignments" version)) | |
7062 | (sha256 | |
7063 | (base32 | |
26760c80 | 7064 | "127690sys4i5q3l4vxnjg4xg8q19qlw2258vgs5d1156w9ypp04h")))) |
d8a828af RW |
7065 | (properties |
7066 | `((upstream-name . "GenomicAlignments"))) | |
7067 | (build-system r-build-system) | |
7068 | (propagated-inputs | |
7069 | `(("r-biocgenerics" ,r-biocgenerics) | |
7070 | ("r-biocparallel" ,r-biocparallel) | |
7071 | ("r-biostrings" ,r-biostrings) | |
7072 | ("r-genomeinfodb" ,r-genomeinfodb) | |
7073 | ("r-genomicranges" ,r-genomicranges) | |
7074 | ("r-iranges" ,r-iranges) | |
7075 | ("r-rsamtools" ,r-rsamtools) | |
7076 | ("r-s4vectors" ,r-s4vectors) | |
7077 | ("r-summarizedexperiment" ,r-summarizedexperiment))) | |
7078 | (home-page "http://bioconductor.org/packages/GenomicAlignments") | |
7079 | (synopsis "Representation and manipulation of short genomic alignments") | |
7080 | (description | |
7081 | "This package provides efficient containers for storing and manipulating | |
7082 | short genomic alignments (typically obtained by aligning short reads to a | |
7083 | reference genome). This includes read counting, computing the coverage, | |
7084 | junction detection, and working with the nucleotide content of the | |
7085 | alignments.") | |
7086 | (license license:artistic2.0))) | |
7087 | ||
317755ff RW |
7088 | (define-public r-rtracklayer |
7089 | (package | |
7090 | (name "r-rtracklayer") | |
15afa9bf | 7091 | (version "1.36.4") |
317755ff RW |
7092 | (source (origin |
7093 | (method url-fetch) | |
7094 | (uri (bioconductor-uri "rtracklayer" version)) | |
7095 | (sha256 | |
7096 | (base32 | |
15afa9bf | 7097 | "050q1rv04w31168ljr975vxva31n9lqdx84rnmsk6zcr6p640ffp")))) |
317755ff RW |
7098 | (build-system r-build-system) |
7099 | (arguments | |
7100 | `(#:phases | |
7101 | (modify-phases %standard-phases | |
7102 | (add-after 'unpack 'use-system-zlib | |
7103 | (lambda _ | |
7104 | (substitute* "DESCRIPTION" | |
7105 | (("zlibbioc, ") "")) | |
7106 | (substitute* "NAMESPACE" | |
7107 | (("import\\(zlibbioc\\)") "")) | |
7108 | #t))))) | |
7109 | (inputs | |
7110 | `(("zlib" ,zlib))) | |
7111 | (propagated-inputs | |
7112 | `(("r-biocgenerics" ,r-biocgenerics) | |
7113 | ("r-biostrings" ,r-biostrings) | |
7114 | ("r-genomeinfodb" ,r-genomeinfodb) | |
7115 | ("r-genomicalignments" ,r-genomicalignments) | |
7116 | ("r-genomicranges" ,r-genomicranges) | |
7117 | ("r-iranges" ,r-iranges) | |
7118 | ("r-rcurl" ,r-rcurl) | |
7119 | ("r-rsamtools" ,r-rsamtools) | |
7120 | ("r-s4vectors" ,r-s4vectors) | |
7121 | ("r-xml" ,r-xml) | |
7122 | ("r-xvector" ,r-xvector))) | |
7123 | (home-page "http://bioconductor.org/packages/rtracklayer") | |
7124 | (synopsis "R interface to genome browsers and their annotation tracks") | |
7125 | (description | |
7126 | "rtracklayer is an extensible framework for interacting with multiple | |
7127 | genome browsers (currently UCSC built-in) and manipulating annotation tracks | |
7128 | in various formats (currently GFF, BED, bedGraph, BED15, WIG, BigWig and 2bit | |
7129 | built-in). The user may export/import tracks to/from the supported browsers, | |
7130 | as well as query and modify the browser state, such as the current viewport.") | |
7131 | (license license:artistic2.0))) | |
7132 | ||
2fd7c049 RW |
7133 | (define-public r-genomicfeatures |
7134 | (package | |
7135 | (name "r-genomicfeatures") | |
8cfaa9ab | 7136 | (version "1.28.4") |
2fd7c049 RW |
7137 | (source (origin |
7138 | (method url-fetch) | |
7139 | (uri (bioconductor-uri "GenomicFeatures" version)) | |
7140 | (sha256 | |
7141 | (base32 | |
8cfaa9ab | 7142 | "01ylvg275iy0cvsbxkbfxcf9pi9al597v5wnlqi2xdpmrcxyc3q0")))) |
2fd7c049 RW |
7143 | (properties |
7144 | `((upstream-name . "GenomicFeatures"))) | |
7145 | (build-system r-build-system) | |
7146 | (propagated-inputs | |
7147 | `(("r-annotationdbi" ,r-annotationdbi) | |
7148 | ("r-biobase" ,r-biobase) | |
7149 | ("r-biocgenerics" ,r-biocgenerics) | |
7150 | ("r-biomart" ,r-biomart) | |
7151 | ("r-biostrings" ,r-biostrings) | |
7152 | ("r-dbi" ,r-dbi) | |
7153 | ("r-genomeinfodb" ,r-genomeinfodb) | |
7154 | ("r-genomicranges" ,r-genomicranges) | |
7155 | ("r-iranges" ,r-iranges) | |
7156 | ("r-rcurl" ,r-rcurl) | |
7157 | ("r-rsqlite" ,r-rsqlite) | |
7158 | ("r-rtracklayer" ,r-rtracklayer) | |
7159 | ("r-s4vectors" ,r-s4vectors) | |
7160 | ("r-xvector" ,r-xvector))) | |
7161 | (home-page "http://bioconductor.org/packages/GenomicFeatures") | |
7162 | (synopsis "Tools for working with transcript centric annotations") | |
7163 | (description | |
7164 | "This package provides a set of tools and methods for making and | |
7165 | manipulating transcript centric annotations. With these tools the user can | |
7166 | easily download the genomic locations of the transcripts, exons and cds of a | |
7167 | given organism, from either the UCSC Genome Browser or a BioMart | |
7168 | database (more sources will be supported in the future). This information is | |
7169 | then stored in a local database that keeps track of the relationship between | |
7170 | transcripts, exons, cds and genes. Flexible methods are provided for | |
7171 | extracting the desired features in a convenient format.") | |
7172 | (license license:artistic2.0))) | |
7173 | ||
fb25d880 RW |
7174 | (define-public r-go-db |
7175 | (package | |
7176 | (name "r-go-db") | |
d1b1587c | 7177 | (version "3.4.0") |
fb25d880 RW |
7178 | (source (origin |
7179 | (method url-fetch) | |
f82c8c3c PP |
7180 | (uri (string-append "http://www.bioconductor.org/packages/" |
7181 | "release/data/annotation/src/contrib/GO.db_" | |
7182 | version ".tar.gz")) | |
fb25d880 RW |
7183 | (sha256 |
7184 | (base32 | |
d1b1587c | 7185 | "02cj8kqi5w39jwcs8gp1dgj08sah262ppxnkz4h3qd0w191y8yyl")))) |
fb25d880 RW |
7186 | (properties |
7187 | `((upstream-name . "GO.db"))) | |
7188 | (build-system r-build-system) | |
3141b83d RW |
7189 | (propagated-inputs |
7190 | `(("r-annotationdbi" ,r-annotationdbi))) | |
fb25d880 RW |
7191 | (home-page "http://bioconductor.org/packages/GO.db") |
7192 | (synopsis "Annotation maps describing the entire Gene Ontology") | |
7193 | (description | |
7194 | "The purpose of this GO.db annotation package is to provide detailed | |
7195 | information about the latest version of the Gene Ontologies.") | |
7196 | (license license:artistic2.0))) | |
7197 | ||
d1dbde6a RW |
7198 | (define-public r-graph |
7199 | (package | |
7200 | (name "r-graph") | |
56373771 | 7201 | (version "1.54.0") |
d1dbde6a RW |
7202 | (source (origin |
7203 | (method url-fetch) | |
7204 | (uri (bioconductor-uri "graph" version)) | |
7205 | (sha256 | |
7206 | (base32 | |
56373771 | 7207 | "0hx9wslnrci7c5i1gd1zlpjmgrkdnx9gabfgmzzwfnykk1mdvvna")))) |
d1dbde6a RW |
7208 | (build-system r-build-system) |
7209 | (propagated-inputs | |
7210 | `(("r-biocgenerics" ,r-biocgenerics))) | |
7211 | (home-page "http://bioconductor.org/packages/graph") | |
7212 | (synopsis "Handle graph data structures in R") | |
7213 | (description | |
7214 | "This package implements some simple graph handling capabilities for R.") | |
7215 | (license license:artistic2.0))) | |
7216 | ||
d547ce5e RW |
7217 | (define-public r-topgo |
7218 | (package | |
7219 | (name "r-topgo") | |
6e70b6d6 | 7220 | (version "2.28.0") |
d547ce5e RW |
7221 | (source (origin |
7222 | (method url-fetch) | |
7223 | (uri (bioconductor-uri "topGO" version)) | |
7224 | (sha256 | |
7225 | (base32 | |
6e70b6d6 | 7226 | "04kvxz9qsxfz0np7wlrzp4r95nykz94x7mqpyyk76f90g6m66vcc")))) |
d547ce5e RW |
7227 | (properties |
7228 | `((upstream-name . "topGO"))) | |
7229 | (build-system r-build-system) | |
7230 | (propagated-inputs | |
7231 | `(("r-annotationdbi" ,r-annotationdbi) | |
30ec4de7 | 7232 | ("r-dbi" ,r-dbi) |
d547ce5e RW |
7233 | ("r-biobase" ,r-biobase) |
7234 | ("r-biocgenerics" ,r-biocgenerics) | |
7235 | ("r-go-db" ,r-go-db) | |
6d415db2 | 7236 | ("r-graph" ,r-graph) |
aeb64f3c RW |
7237 | ("r-lattice" ,r-lattice) |
7238 | ("r-matrixstats" ,r-matrixstats) | |
d547ce5e RW |
7239 | ("r-sparsem" ,r-sparsem))) |
7240 | (home-page "http://bioconductor.org/packages/topGO") | |
7241 | (synopsis "Enrichment analysis for gene ontology") | |
7242 | (description | |
7243 | "The topGO package provides tools for testing @dfn{gene ontology} (GO) | |
7244 | terms while accounting for the topology of the GO graph. Different test | |
7245 | statistics and different methods for eliminating local similarities and | |
7246 | dependencies between GO terms can be implemented and applied.") | |
7247 | ;; Any version of the LGPL applies. | |
7248 | (license license:lgpl2.1+))) | |
7249 | ||
c63cef66 RW |
7250 | (define-public r-bsgenome |
7251 | (package | |
7252 | (name "r-bsgenome") | |
c54a702a | 7253 | (version "1.44.0") |
c63cef66 RW |
7254 | (source (origin |
7255 | (method url-fetch) | |
7256 | (uri (bioconductor-uri "BSgenome" version)) | |
7257 | (sha256 | |
7258 | (base32 | |
c54a702a | 7259 | "18dlknwk3xvi52hamxf9pl5bjc5806mpw98xwvx5xajn8mrxiy5h")))) |
c63cef66 RW |
7260 | (properties |
7261 | `((upstream-name . "BSgenome"))) | |
7262 | (build-system r-build-system) | |
7263 | (propagated-inputs | |
7264 | `(("r-biocgenerics" ,r-biocgenerics) | |
7265 | ("r-biostrings" ,r-biostrings) | |
7266 | ("r-genomeinfodb" ,r-genomeinfodb) | |
7267 | ("r-genomicranges" ,r-genomicranges) | |
7268 | ("r-iranges" ,r-iranges) | |
7269 | ("r-rsamtools" ,r-rsamtools) | |
7270 | ("r-rtracklayer" ,r-rtracklayer) | |
7271 | ("r-s4vectors" ,r-s4vectors) | |
7272 | ("r-xvector" ,r-xvector))) | |
7273 | (home-page "http://bioconductor.org/packages/BSgenome") | |
7274 | (synopsis "Infrastructure for Biostrings-based genome data packages") | |
7275 | (description | |
7276 | "This package provides infrastructure shared by all Biostrings-based | |
7277 | genome data packages and support for efficient SNP representation.") | |
7278 | (license license:artistic2.0))) | |
7279 | ||
aa3eeeb5 RJ |
7280 | (define-public r-bsgenome-hsapiens-1000genomes-hs37d5 |
7281 | (package | |
7282 | (name "r-bsgenome-hsapiens-1000genomes-hs37d5") | |
7283 | (version "0.99.1") | |
7284 | (source (origin | |
7285 | (method url-fetch) | |
7286 | ;; We cannot use bioconductor-uri here because this tarball is | |
7287 | ;; located under "data/annotation/" instead of "bioc/". | |
7288 | (uri (string-append "http://www.bioconductor.org/packages/" | |
7289 | "release/data/annotation/src/contrib/" | |
7290 | "BSgenome.Hsapiens.1000genomes.hs37d5_" | |
7291 | version ".tar.gz")) | |
7292 | (sha256 | |
7293 | (base32 | |
7294 | "1cg0g5fqmsvwyw2p9hp2yy4ilk21jkbbrnpgqvb5c36ihjwvc7sr")))) | |
7295 | (properties | |
7296 | `((upstream-name . "BSgenome.Hsapiens.1000genomes.hs37d5"))) | |
7297 | (build-system r-build-system) | |
7298 | ;; As this package provides little more than a very large data file it | |
7299 | ;; doesn't make sense to build substitutes. | |
7300 | (arguments `(#:substitutable? #f)) | |
7301 | (propagated-inputs | |
7302 | `(("r-bsgenome" ,r-bsgenome))) | |
7303 | (home-page | |
7304 | "http://www.bioconductor.org/packages/BSgenome.Hsapiens.1000genomes.hs37d5/") | |
7305 | (synopsis "Full genome sequences for Homo sapiens") | |
7306 | (description | |
7307 | "This package provides full genome sequences for Homo sapiens from | |
7308 | 1000genomes phase2 reference genome sequence (hs37d5), based on NCBI GRCh37.") | |
7309 | (license license:artistic2.0))) | |
7310 | ||
c43a011d RW |
7311 | (define-public r-impute |
7312 | (package | |
7313 | (name "r-impute") | |
5999359f | 7314 | (version "1.50.0") |
c43a011d RW |
7315 | (source (origin |
7316 | (method url-fetch) | |
7317 | (uri (bioconductor-uri "impute" version)) | |
7318 | (sha256 | |
7319 | (base32 | |
5999359f | 7320 | "0va45vfixy3np549md87h3b3rbavm54gfnmnjhpr9hf02lll6zxs")))) |
c43a011d RW |
7321 | (inputs |
7322 | `(("gfortran" ,gfortran))) | |
7323 | (build-system r-build-system) | |
7324 | (home-page "http://bioconductor.org/packages/impute") | |
7325 | (synopsis "Imputation for microarray data") | |
7326 | (description | |
7327 | "This package provides a function to impute missing gene expression | |
7328 | microarray data, using nearest neighbor averaging.") | |
7329 | (license license:gpl2+))) | |
7330 | ||
03ea5a35 RW |
7331 | (define-public r-seqpattern |
7332 | (package | |
7333 | (name "r-seqpattern") | |
08b9224d | 7334 | (version "1.8.0") |
03ea5a35 RW |
7335 | (source (origin |
7336 | (method url-fetch) | |
7337 | (uri (bioconductor-uri "seqPattern" version)) | |
7338 | (sha256 | |
7339 | (base32 | |
08b9224d | 7340 | "0yw5251sirv3283xgmfmfbf900xp8dwvqfk88mr945s3by5hx99v")))) |
03ea5a35 RW |
7341 | (properties |
7342 | `((upstream-name . "seqPattern"))) | |
7343 | (build-system r-build-system) | |
7344 | (propagated-inputs | |
7345 | `(("r-biostrings" ,r-biostrings) | |
7346 | ("r-genomicranges" ,r-genomicranges) | |
7347 | ("r-iranges" ,r-iranges) | |
e92dd6f5 | 7348 | ("r-kernsmooth" ,r-kernsmooth) |
03ea5a35 RW |
7349 | ("r-plotrix" ,r-plotrix))) |
7350 | (home-page "http://bioconductor.org/packages/seqPattern") | |
7351 | (synopsis "Visualising oligonucleotide patterns and motif occurrences") | |
7352 | (description | |
7353 | "This package provides tools to visualize oligonucleotide patterns and | |
7354 | sequence motif occurrences across a large set of sequences centred at a common | |
7355 | reference point and sorted by a user defined feature.") | |
7356 | (license license:gpl3+))) | |
7357 | ||
cb933df6 RW |
7358 | (define-public r-genomation |
7359 | (package | |
7360 | (name "r-genomation") | |
3ae82c8d | 7361 | (version "1.8.0") |
cb933df6 RW |
7362 | (source (origin |
7363 | (method url-fetch) | |
7364 | (uri (bioconductor-uri "genomation" version)) | |
7365 | (sha256 | |
7366 | (base32 | |
3ae82c8d | 7367 | "0r71nf8p3aq3yffqxg4yir1zmm7rar5a57nmy1kpqpn8kaf2svjl")))) |
cb933df6 RW |
7368 | (build-system r-build-system) |
7369 | (propagated-inputs | |
7370 | `(("r-biostrings" ,r-biostrings) | |
7371 | ("r-bsgenome" ,r-bsgenome) | |
7372 | ("r-data-table" ,r-data-table) | |
7373 | ("r-genomeinfodb" ,r-genomeinfodb) | |
7374 | ("r-genomicalignments" ,r-genomicalignments) | |
7375 | ("r-genomicranges" ,r-genomicranges) | |
7376 | ("r-ggplot2" ,r-ggplot2) | |
7377 | ("r-gridbase" ,r-gridbase) | |
7378 | ("r-impute" ,r-impute) | |
7379 | ("r-iranges" ,r-iranges) | |
7380 | ("r-matrixstats" ,r-matrixstats) | |
7381 | ("r-plotrix" ,r-plotrix) | |
7382 | ("r-plyr" ,r-plyr) | |
51c3c490 | 7383 | ("r-rcpp" ,r-rcpp) |
cb933df6 RW |
7384 | ("r-readr" ,r-readr) |
7385 | ("r-reshape2" ,r-reshape2) | |
51c3c490 | 7386 | ("r-rhtslib" ,r-rhtslib) |
cb933df6 RW |
7387 | ("r-rsamtools" ,r-rsamtools) |
7388 | ("r-rtracklayer" ,r-rtracklayer) | |
51c3c490 RW |
7389 | ("r-runit" ,r-runit) |
7390 | ("r-s4vectors" ,r-s4vectors) | |
cb933df6 | 7391 | ("r-seqpattern" ,r-seqpattern))) |
51c3c490 RW |
7392 | (inputs |
7393 | `(("zlib" ,zlib))) | |
cb933df6 RW |
7394 | (home-page "http://bioinformatics.mdc-berlin.de/genomation/") |
7395 | (synopsis "Summary, annotation and visualization of genomic data") | |
7396 | (description | |
7397 | "This package provides a package for summary and annotation of genomic | |
7398 | intervals. Users can visualize and quantify genomic intervals over | |
7399 | pre-defined functional regions, such as promoters, exons, introns, etc. The | |
7400 | genomic intervals represent regions with a defined chromosome position, which | |
7401 | may be associated with a score, such as aligned reads from HT-seq experiments, | |
7402 | TF binding sites, methylation scores, etc. The package can use any tabular | |
7403 | genomic feature data as long as it has minimal information on the locations of | |
7404 | genomic intervals. In addition, it can use BAM or BigWig files as input.") | |
7405 | (license license:artistic2.0))) | |
7406 | ||
64efa307 RW |
7407 | (define-public r-genomationdata |
7408 | (package | |
7409 | (name "r-genomationdata") | |
59198f8f | 7410 | (version "1.6.0") |
64efa307 RW |
7411 | (source (origin |
7412 | (method url-fetch) | |
7413 | ;; We cannot use bioconductor-uri here because this tarball is | |
7414 | ;; located under "data/annotation/" instead of "bioc/". | |
7415 | (uri (string-append "https://bioconductor.org/packages/" | |
7416 | "release/data/experiment/src/contrib/" | |
7417 | "genomationData_" version ".tar.gz")) | |
7418 | (sha256 | |
7419 | (base32 | |
59198f8f | 7420 | "16dqwb7wx1igx77zdbcskx5m1hs4g4gp2hl56zzm70hcagnlkz8y")))) |
64efa307 RW |
7421 | (build-system r-build-system) |
7422 | ;; As this package provides little more than large data files, it doesn't | |
7423 | ;; make sense to build substitutes. | |
7424 | (arguments `(#:substitutable? #f)) | |
7425 | (native-inputs | |
7426 | `(("r-knitr" ,r-knitr))) | |
7427 | (home-page "http://bioinformatics.mdc-berlin.de/genomation/") | |
7428 | (synopsis "Experimental data for use with the genomation package") | |
7429 | (description | |
7430 | "This package contains experimental genetic data for use with the | |
7431 | genomation package. Included are Chip Seq, Methylation and Cage data, | |
7432 | downloaded from Encode.") | |
7433 | (license license:gpl3+))) | |
7434 | ||
486da491 RW |
7435 | (define-public r-org-hs-eg-db |
7436 | (package | |
7437 | (name "r-org-hs-eg-db") | |
83f9a6fb | 7438 | (version "3.4.0") |
486da491 RW |
7439 | (source (origin |
7440 | (method url-fetch) | |
7441 | ;; We cannot use bioconductor-uri here because this tarball is | |
7442 | ;; located under "data/annotation/" instead of "bioc/". | |
7443 | (uri (string-append "http://www.bioconductor.org/packages/" | |
7444 | "release/data/annotation/src/contrib/" | |
7445 | "org.Hs.eg.db_" version ".tar.gz")) | |
7446 | (sha256 | |
7447 | (base32 | |
83f9a6fb | 7448 | "19mg64pw8zcvb9yxzzyf7caz1kvdrkfsj1hd84bzq7crrh8kc4y6")))) |
486da491 RW |
7449 | (properties |
7450 | `((upstream-name . "org.Hs.eg.db"))) | |
7451 | (build-system r-build-system) | |
7452 | (propagated-inputs | |
7453 | `(("r-annotationdbi" ,r-annotationdbi))) | |
7454 | (home-page "http://www.bioconductor.org/packages/org.Hs.eg.db/") | |
7455 | (synopsis "Genome wide annotation for Human") | |
7456 | (description | |
7457 | "This package provides mappings from Entrez gene identifiers to various | |
7458 | annotations for the human genome.") | |
7459 | (license license:artistic2.0))) | |
7460 | ||
fefedf98 RW |
7461 | (define-public r-org-ce-eg-db |
7462 | (package | |
7463 | (name "r-org-ce-eg-db") | |
f04a3eff | 7464 | (version "3.4.0") |
fefedf98 RW |
7465 | (source (origin |
7466 | (method url-fetch) | |
7467 | ;; We cannot use bioconductor-uri here because this tarball is | |
7468 | ;; located under "data/annotation/" instead of "bioc/". | |
7469 | (uri (string-append "http://www.bioconductor.org/packages/" | |
7470 | "release/data/annotation/src/contrib/" | |
7471 | "org.Ce.eg.db_" version ".tar.gz")) | |
7472 | (sha256 | |
7473 | (base32 | |
f04a3eff | 7474 | "12llfzrrc09kj2wzbisdspv38qzkzgpsbn8kv7qkwg746k3pq436")))) |
fefedf98 RW |
7475 | (properties |
7476 | `((upstream-name . "org.Ce.eg.db"))) | |
7477 | (build-system r-build-system) | |
7478 | (propagated-inputs | |
7479 | `(("r-annotationdbi" ,r-annotationdbi))) | |
7480 | (home-page "http://www.bioconductor.org/packages/org.Ce.eg.db/") | |
7481 | (synopsis "Genome wide annotation for Worm") | |
7482 | (description | |
7483 | "This package provides mappings from Entrez gene identifiers to various | |
7484 | annotations for the genome of the model worm Caenorhabditis elegans.") | |
7485 | (license license:artistic2.0))) | |
7486 | ||
16c53a1e RW |
7487 | (define-public r-org-dm-eg-db |
7488 | (package | |
7489 | (name "r-org-dm-eg-db") | |
0cfac6f2 | 7490 | (version "3.4.0") |
16c53a1e RW |
7491 | (source (origin |
7492 | (method url-fetch) | |
7493 | ;; We cannot use bioconductor-uri here because this tarball is | |
7494 | ;; located under "data/annotation/" instead of "bioc/". | |
7495 | (uri (string-append "http://www.bioconductor.org/packages/" | |
7496 | "release/data/annotation/src/contrib/" | |
7497 | "org.Dm.eg.db_" version ".tar.gz")) | |
7498 | (sha256 | |
7499 | (base32 | |
0cfac6f2 | 7500 | "1vzbphbrh1cf7xi5cksia9xy9a9l42js2z2qsajvjxvddiphrb7j")))) |
16c53a1e RW |
7501 | (properties |
7502 | `((upstream-name . "org.Dm.eg.db"))) | |
7503 | (build-system r-build-system) | |
7504 | (propagated-inputs | |
7505 | `(("r-annotationdbi" ,r-annotationdbi))) | |
7506 | (home-page "http://www.bioconductor.org/packages/org.Dm.eg.db/") | |
7507 | (synopsis "Genome wide annotation for Fly") | |
7508 | (description | |
7509 | "This package provides mappings from Entrez gene identifiers to various | |
7510 | annotations for the genome of the model fruit fly Drosophila melanogaster.") | |
7511 | (license license:artistic2.0))) | |
7512 | ||
e761beb9 RW |
7513 | (define-public r-org-mm-eg-db |
7514 | (package | |
7515 | (name "r-org-mm-eg-db") | |
7c45670b | 7516 | (version "3.4.0") |
e761beb9 RW |
7517 | (source (origin |
7518 | (method url-fetch) | |
7519 | ;; We cannot use bioconductor-uri here because this tarball is | |
7520 | ;; located under "data/annotation/" instead of "bioc/". | |
7521 | (uri (string-append "http://www.bioconductor.org/packages/" | |
7522 | "release/data/annotation/src/contrib/" | |
7523 | "org.Mm.eg.db_" version ".tar.gz")) | |
7524 | (sha256 | |
7525 | (base32 | |
7c45670b | 7526 | "1lykjqjaf01fmgg3cvfcvwd5xjq6zc5vbxnm5r4l32fzvl89q50c")))) |
e761beb9 RW |
7527 | (properties |
7528 | `((upstream-name . "org.Mm.eg.db"))) | |
7529 | (build-system r-build-system) | |
7530 | (propagated-inputs | |
7531 | `(("r-annotationdbi" ,r-annotationdbi))) | |
7532 | (home-page "http://www.bioconductor.org/packages/org.Mm.eg.db/") | |
7533 | (synopsis "Genome wide annotation for Mouse") | |
7534 | (description | |
7535 | "This package provides mappings from Entrez gene identifiers to various | |
7536 | annotations for the genome of the model mouse Mus musculus.") | |
7537 | (license license:artistic2.0))) | |
7538 | ||
936e7d67 RW |
7539 | (define-public r-seqlogo |
7540 | (package | |
7541 | (name "r-seqlogo") | |
0fce7d9b | 7542 | (version "1.42.0") |
936e7d67 RW |
7543 | (source |
7544 | (origin | |
7545 | (method url-fetch) | |
7546 | (uri (bioconductor-uri "seqLogo" version)) | |
7547 | (sha256 | |
7548 | (base32 | |
0fce7d9b | 7549 | "19d5zmy7m8svljwgbmrb4vxkq18slq0f3all6k2ayv42b8w44h6q")))) |
936e7d67 RW |
7550 | (properties `((upstream-name . "seqLogo"))) |
7551 | (build-system r-build-system) | |
7552 | (home-page "http://bioconductor.org/packages/seqLogo") | |
7553 | (synopsis "Sequence logos for DNA sequence alignments") | |
7554 | (description | |
7555 | "seqLogo takes the position weight matrix of a DNA sequence motif and | |
7556 | plots the corresponding sequence logo as introduced by Schneider and | |
7557 | Stephens (1990).") | |
7558 | (license license:lgpl2.0+))) | |
7559 | ||
c90a4baf RW |
7560 | (define-public r-bsgenome-hsapiens-ucsc-hg19 |
7561 | (package | |
7562 | (name "r-bsgenome-hsapiens-ucsc-hg19") | |
7563 | (version "1.4.0") | |
7564 | (source (origin | |
7565 | (method url-fetch) | |
7566 | ;; We cannot use bioconductor-uri here because this tarball is | |
7567 | ;; located under "data/annotation/" instead of "bioc/". | |
7568 | (uri (string-append "http://www.bioconductor.org/packages/" | |
7569 | "release/data/annotation/src/contrib/" | |
7570 | "BSgenome.Hsapiens.UCSC.hg19_" | |
7571 | version ".tar.gz")) | |
7572 | (sha256 | |
7573 | (base32 | |
fd408579 | 7574 | "0479qx4bapgcp5chj10a63chk0s28x9cx1gamz3f5m3yd7jzwcf2")))) |
c90a4baf RW |
7575 | (properties |
7576 | `((upstream-name . "BSgenome.Hsapiens.UCSC.hg19"))) | |
7577 | (build-system r-build-system) | |
7578 | ;; As this package provides little more than a very large data file it | |
7579 | ;; doesn't make sense to build substitutes. | |
7580 | (arguments `(#:substitutable? #f)) | |
7581 | (propagated-inputs | |
7582 | `(("r-bsgenome" ,r-bsgenome))) | |
7583 | (home-page | |
7584 | "http://www.bioconductor.org/packages/BSgenome.Hsapiens.UCSC.hg19/") | |
7585 | (synopsis "Full genome sequences for Homo sapiens") | |
7586 | (description | |
7587 | "This package provides full genome sequences for Homo sapiens as provided | |
7588 | by UCSC (hg19, February 2009) and stored in Biostrings objects.") | |
7589 | (license license:artistic2.0))) | |
7590 | ||
a3e90287 RW |
7591 | (define-public r-bsgenome-mmusculus-ucsc-mm9 |
7592 | (package | |
7593 | (name "r-bsgenome-mmusculus-ucsc-mm9") | |
7594 | (version "1.4.0") | |
7595 | (source (origin | |
7596 | (method url-fetch) | |
7597 | ;; We cannot use bioconductor-uri here because this tarball is | |
7598 | ;; located under "data/annotation/" instead of "bioc/". | |
7599 | (uri (string-append "http://www.bioconductor.org/packages/" | |
7600 | "release/data/annotation/src/contrib/" | |
7601 | "BSgenome.Mmusculus.UCSC.mm9_" | |
7602 | version ".tar.gz")) | |
7603 | (sha256 | |
7604 | (base32 | |
7605 | "1birqw30g2azimxpnjfzmkphan7x131yy8b9h85lfz5fjdg7841i")))) | |
7606 | (properties | |
7607 | `((upstream-name . "BSgenome.Mmusculus.UCSC.mm9"))) | |
7608 | (build-system r-build-system) | |
7609 | ;; As this package provides little more than a very large data file it | |
7610 | ;; doesn't make sense to build substitutes. | |
7611 | (arguments `(#:substitutable? #f)) | |
7612 | (propagated-inputs | |
7613 | `(("r-bsgenome" ,r-bsgenome))) | |
7614 | (home-page | |
7615 | "http://www.bioconductor.org/packages/BSgenome.Mmusculus.UCSC.mm9/") | |
7616 | (synopsis "Full genome sequences for Mouse") | |
7617 | (description | |
7618 | "This package provides full genome sequences for Mus musculus (Mouse) as | |
7619 | provided by UCSC (mm9, July 2007) and stored in Biostrings objects.") | |
7620 | (license license:artistic2.0))) | |
7621 | ||
4714d521 RW |
7622 | (define-public r-bsgenome-mmusculus-ucsc-mm10 |
7623 | (package | |
7624 | (name "r-bsgenome-mmusculus-ucsc-mm10") | |
7625 | (version "1.4.0") | |
7626 | (source (origin | |
7627 | (method url-fetch) | |
7628 | ;; We cannot use bioconductor-uri here because this tarball is | |
7629 | ;; located under "data/annotation/" instead of "bioc/". | |
7630 | (uri (string-append "http://www.bioconductor.org/packages/" | |
7631 | "release/data/annotation/src/contrib/" | |
7632 | "BSgenome.Mmusculus.UCSC.mm10_" | |
7633 | version ".tar.gz")) | |
7634 | (sha256 | |
7635 | (base32 | |
7636 | "12s0nm2na9brjad4rn9l7d3db2aj8qa1xvz0y1k7gk08wayb6bkf")))) | |
7637 | (properties | |
7638 | `((upstream-name . "BSgenome.Mmusculus.UCSC.mm10"))) | |
7639 | (build-system r-build-system) | |
7640 | ;; As this package provides little more than a very large data file it | |
7641 | ;; doesn't make sense to build substitutes. | |
7642 | (arguments `(#:substitutable? #f)) | |
7643 | (propagated-inputs | |
7644 | `(("r-bsgenome" ,r-bsgenome))) | |
7645 | (home-page | |
7646 | "http://www.bioconductor.org/packages/BSgenome.Mmusculus.UCSC.mm10/") | |
7647 | (synopsis "Full genome sequences for Mouse") | |
7648 | (description | |
7649 | "This package provides full genome sequences for Mus | |
7650 | musculus (Mouse) as provided by UCSC (mm10, December 2011) and stored | |
7651 | in Biostrings objects.") | |
7652 | (license license:artistic2.0))) | |
7653 | ||
c5173d74 RJ |
7654 | (define-public r-txdb-mmusculus-ucsc-mm10-knowngene |
7655 | (package | |
7656 | (name "r-txdb-mmusculus-ucsc-mm10-knowngene") | |
7657 | (version "3.4.0") | |
7658 | (source (origin | |
7659 | (method url-fetch) | |
7660 | ;; We cannot use bioconductor-uri here because this tarball is | |
7661 | ;; located under "data/annotation/" instead of "bioc/". | |
7662 | (uri (string-append "http://www.bioconductor.org/packages/" | |
7663 | "release/data/annotation/src/contrib/" | |
7664 | "TxDb.Mmusculus.UCSC.mm10.knownGene_" | |
7665 | version ".tar.gz")) | |
7666 | (sha256 | |
7667 | (base32 | |
7668 | "08gava9wsvpcqz51k2sni3pj03n5155v32d9riqbf305nbirqbkb")))) | |
7669 | (properties | |
7670 | `((upstream-name . "TxDb.Mmusculus.UCSC.mm10.knownGene"))) | |
7671 | (build-system r-build-system) | |
7672 | ;; As this package provides little more than a very large data file it | |
7673 | ;; doesn't make sense to build substitutes. | |
7674 | (arguments `(#:substitutable? #f)) | |
7675 | (propagated-inputs | |
7676 | `(("r-bsgenome" ,r-bsgenome) | |
7677 | ("r-genomicfeatures" ,r-genomicfeatures) | |
7678 | ("r-annotationdbi" ,r-annotationdbi))) | |
7679 | (home-page | |
7680 | "http://bioconductor.org/packages/TxDb.Mmusculus.UCSC.mm10.knownGene/") | |
7681 | (synopsis "Annotation package for TxDb knownGene object(s) for Mouse") | |
7682 | (description | |
7683 | "This package loads a TxDb object, which is an R interface to | |
7684 | prefabricated databases contained in this package. This package provides | |
7685 | the TxDb object of Mouse data as provided by UCSC (mm10, December 2011) | |
7686 | based on the knownGene track.") | |
7687 | (license license:artistic2.0))) | |
7688 | ||
943bd627 RW |
7689 | (define-public r-bsgenome-celegans-ucsc-ce6 |
7690 | (package | |
7691 | (name "r-bsgenome-celegans-ucsc-ce6") | |
7692 | (version "1.4.0") | |
7693 | (source (origin | |
7694 | (method url-fetch) | |
7695 | ;; We cannot use bioconductor-uri here because this tarball is | |
7696 | ;; located under "data/annotation/" instead of "bioc/". | |
7697 | (uri (string-append "http://www.bioconductor.org/packages/" | |
7698 | "release/data/annotation/src/contrib/" | |
7699 | "BSgenome.Celegans.UCSC.ce6_" | |
7700 | version ".tar.gz")) | |
7701 | (sha256 | |
7702 | (base32 | |
7703 | "0mqzb353xv2c3m3vkb315dkmnxkgczp7ndnknyhpgjlybyf715v9")))) | |
7704 | (properties | |
7705 | `((upstream-name . "BSgenome.Celegans.UCSC.ce6"))) | |
7706 | (build-system r-build-system) | |
7707 | ;; As this package provides little more than a very large data file it | |
7708 | ;; doesn't make sense to build substitutes. | |
7709 | (arguments `(#:substitutable? #f)) | |
7710 | (propagated-inputs | |
7711 | `(("r-bsgenome" ,r-bsgenome))) | |
7712 | (home-page | |
7713 | "http://www.bioconductor.org/packages/BSgenome.Celegans.UCSC.ce6/") | |
7714 | (synopsis "Full genome sequences for Worm") | |
7715 | (description | |
7716 | "This package provides full genome sequences for Caenorhabditis | |
7717 | elegans (Worm) as provided by UCSC (ce6, May 2008) and stored in Biostrings | |
7718 | objects.") | |
7719 | (license license:artistic2.0))) | |
7720 | ||
fc47c7d6 RW |
7721 | (define-public r-bsgenome-celegans-ucsc-ce10 |
7722 | (package | |
7723 | (name "r-bsgenome-celegans-ucsc-ce10") | |
7724 | (version "1.4.0") | |
7725 | (source (origin | |
7726 | (method url-fetch) | |
7727 | ;; We cannot use bioconductor-uri here because this tarball is | |
7728 | ;; located under "data/annotation/" instead of "bioc/". | |
7729 | (uri (string-append "http://www.bioconductor.org/packages/" | |
7730 | "release/data/annotation/src/contrib/" | |
7731 | "BSgenome.Celegans.UCSC.ce10_" | |
7732 | version ".tar.gz")) | |
7733 | (sha256 | |
7734 | (base32 | |
7735 | "1zaym97jk4npxk14ifvwz2rvhm4zx9xgs33r9vvx9rlynp0gydrk")))) | |
7736 | (properties | |
7737 | `((upstream-name . "BSgenome.Celegans.UCSC.ce10"))) | |
7738 | (build-system r-build-system) | |
7739 | ;; As this package provides little more than a very large data file it | |
7740 | ;; doesn't make sense to build substitutes. | |
7741 | (arguments `(#:substitutable? #f)) | |
7742 | (propagated-inputs | |
7743 | `(("r-bsgenome" ,r-bsgenome))) | |
7744 | (home-page | |
7745 | "http://www.bioconductor.org/packages/BSgenome.Celegans.UCSC.ce10/") | |
7746 | (synopsis "Full genome sequences for Worm") | |
7747 | (description | |
7748 | "This package provides full genome sequences for Caenorhabditis | |
7749 | elegans (Worm) as provided by UCSC (ce10, Oct 2010) and stored in Biostrings | |
7750 | objects.") | |
7751 | (license license:artistic2.0))) | |
7752 | ||
6dc60998 RW |
7753 | (define-public r-bsgenome-dmelanogaster-ucsc-dm3 |
7754 | (package | |
7755 | (name "r-bsgenome-dmelanogaster-ucsc-dm3") | |
7756 | (version "1.4.0") | |
7757 | (source (origin | |
7758 | (method url-fetch) | |
7759 | ;; We cannot use bioconductor-uri here because this tarball is | |
7760 | ;; located under "data/annotation/" instead of "bioc/". | |
7761 | (uri (string-append "http://www.bioconductor.org/packages/" | |
7762 | "release/data/annotation/src/contrib/" | |
7763 | "BSgenome.Dmelanogaster.UCSC.dm3_" | |
7764 | version ".tar.gz")) | |
7765 | (sha256 | |
7766 | (base32 | |
7767 | "19bm3lkhhkag3gnwp419211fh0cnr0x6fa0r1lr0ycwrikxdxsv8")))) | |
7768 | (properties | |
7769 | `((upstream-name . "BSgenome.Dmelanogaster.UCSC.dm3"))) | |
7770 | (build-system r-build-system) | |
7771 | ;; As this package provides little more than a very large data file it | |
7772 | ;; doesn't make sense to build substitutes. | |
7773 | (arguments `(#:substitutable? #f)) | |
7774 | (propagated-inputs | |
7775 | `(("r-bsgenome" ,r-bsgenome))) | |
7776 | (home-page | |
7777 | "http://www.bioconductor.org/packages/BSgenome.Dmelanogaster.UCSC.dm3/") | |
7778 | (synopsis "Full genome sequences for Fly") | |
7779 | (description | |
7780 | "This package provides full genome sequences for Drosophila | |
7781 | melanogaster (Fly) as provided by UCSC (dm3, April 2006) and stored in | |
7782 | Biostrings objects.") | |
7783 | (license license:artistic2.0))) | |
7784 | ||
ae2462f7 RW |
7785 | (define-public r-motifrg |
7786 | (package | |
7787 | (name "r-motifrg") | |
a7b90ea9 | 7788 | (version "1.20.0") |
ae2462f7 RW |
7789 | (source |
7790 | (origin | |
7791 | (method url-fetch) | |
7792 | (uri (bioconductor-uri "motifRG" version)) | |
7793 | (sha256 | |
7794 | (base32 | |
a7b90ea9 | 7795 | "0lxxpqyljiyk73vyq6ss46q13g81pm24q87mkzdsqlr5zx427ch6")))) |
ae2462f7 RW |
7796 | (properties `((upstream-name . "motifRG"))) |
7797 | (build-system r-build-system) | |
7798 | (propagated-inputs | |
7799 | `(("r-biostrings" ,r-biostrings) | |
7800 | ("r-bsgenome" ,r-bsgenome) | |
7801 | ("r-bsgenome.hsapiens.ucsc.hg19" ,r-bsgenome-hsapiens-ucsc-hg19) | |
7802 | ("r-iranges" ,r-iranges) | |
7803 | ("r-seqlogo" ,r-seqlogo) | |
7804 | ("r-xvector" ,r-xvector))) | |
7805 | (home-page "http://bioconductor.org/packages/motifRG") | |
7806 | (synopsis "Discover motifs in high throughput sequencing data") | |
7807 | (description | |
7808 | "This package provides tools for discriminative motif discovery in high | |
7809 | throughput genetic sequencing data sets using regression methods.") | |
7810 | (license license:artistic2.0))) | |
7811 | ||
a5002ae7 AE |
7812 | (define-public r-qtl |
7813 | (package | |
7814 | (name "r-qtl") | |
421f7772 | 7815 | (version "1.40-8") |
a5002ae7 AE |
7816 | (source |
7817 | (origin | |
7818 | (method url-fetch) | |
7819 | (uri (string-append "mirror://cran/src/contrib/qtl_" | |
7820 | version ".tar.gz")) | |
7821 | (sha256 | |
7822 | (base32 | |
421f7772 | 7823 | "05bj1x2ry0i7yqiydlswb3d2h4pxg70z8w1072az1mrv1m54k8sp")))) |
a5002ae7 AE |
7824 | (build-system r-build-system) |
7825 | (home-page "http://rqtl.org/") | |
7826 | (synopsis "R package for analyzing QTL experiments in genetics") | |
7827 | (description "R/qtl is an extension library for the R statistics | |
7828 | system. It is used to analyze experimental crosses for identifying | |
7829 | genes contributing to variation in quantitative traits (so-called | |
7830 | quantitative trait loci, QTLs). | |
7831 | ||
7832 | Using a hidden Markov model, R/qtl allows to estimate genetic maps, to | |
7833 | identify genotyping errors, and to perform single-QTL and two-QTL, | |
7834 | two-dimensional genome scans.") | |
7835 | (license license:gpl3))) | |
d1e32822 | 7836 | |
9e3ba31c RJ |
7837 | (define-public r-zlibbioc |
7838 | (package | |
7839 | (name "r-zlibbioc") | |
8444f606 | 7840 | (version "1.22.0") |
9e3ba31c RJ |
7841 | (source (origin |
7842 | (method url-fetch) | |
7843 | (uri (bioconductor-uri "zlibbioc" version)) | |
7844 | (sha256 | |
7845 | (base32 | |
8444f606 | 7846 | "1kdgwwlh39mgwzj3zq71za4iv40sq625ghnyrndv5wrivrcr2igv")))) |
9e3ba31c RJ |
7847 | (properties |
7848 | `((upstream-name . "zlibbioc"))) | |
7849 | (build-system r-build-system) | |
7850 | (home-page "https://bioconductor.org/packages/zlibbioc") | |
7851 | (synopsis "Provider for zlib-1.2.5 to R packages") | |
7852 | (description "This package uses the source code of zlib-1.2.5 to create | |
7853 | libraries for systems that do not have these available via other means.") | |
7854 | (license license:artistic2.0))) | |
7855 | ||
e619a5c2 RW |
7856 | (define-public r-r4rna |
7857 | (package | |
7858 | (name "r-r4rna") | |
7859 | (version "0.1.4") | |
7860 | (source | |
7861 | (origin | |
7862 | (method url-fetch) | |
7863 | (uri (string-append "http://www.e-rna.org/r-chie/files/R4RNA_" | |
7864 | version ".tar.gz")) | |
7865 | (sha256 | |
7866 | (base32 | |
7867 | "1p0i78wh76jfgmn9jphbwwaz6yy6pipzfg08xs54cxavxg2j81p5")))) | |
7868 | (build-system r-build-system) | |
7869 | (propagated-inputs | |
7870 | `(("r-optparse" ,r-optparse) | |
7871 | ("r-rcolorbrewer" ,r-rcolorbrewer))) | |
7872 | (home-page "http://www.e-rna.org/r-chie/index.cgi") | |
7873 | (synopsis "Analysis framework for RNA secondary structure") | |
7874 | (description | |
7875 | "The R4RNA package aims to be a general framework for the analysis of RNA | |
7876 | secondary structure and comparative analysis in R.") | |
7877 | (license license:gpl3+))) | |
7878 | ||
52765a63 RW |
7879 | (define-public r-rhtslib |
7880 | (package | |
7881 | (name "r-rhtslib") | |
37631ddc | 7882 | (version "1.8.0") |
52765a63 RW |
7883 | (source |
7884 | (origin | |
7885 | (method url-fetch) | |
7886 | (uri (bioconductor-uri "Rhtslib" version)) | |
7887 | (sha256 | |
7888 | (base32 | |
37631ddc | 7889 | "0jj5h81z5gyf4j3lp2l3zsm6pgbmalgrngr8qdpygc20phndpp0b")))) |
52765a63 RW |
7890 | (properties `((upstream-name . "Rhtslib"))) |
7891 | (build-system r-build-system) | |
7892 | (propagated-inputs | |
7893 | `(("r-zlibbioc" ,r-zlibbioc))) | |
7894 | (inputs | |
7895 | `(("zlib" ,zlib))) | |
53ca52f0 RW |
7896 | (native-inputs |
7897 | `(("autoconf" ,autoconf))) | |
52765a63 RW |
7898 | (home-page "https://github.com/nhayden/Rhtslib") |
7899 | (synopsis "High-throughput sequencing library as an R package") | |
7900 | (description | |
7901 | "This package provides the HTSlib C library for high-throughput | |
7902 | nucleotide sequence analysis. The package is primarily useful to developers | |
7903 | of other R packages who wish to make use of HTSlib.") | |
7904 | (license license:lgpl2.0+))) | |
7905 | ||
fe02c4c9 RW |
7906 | (define-public r-bamsignals |
7907 | (package | |
7908 | (name "r-bamsignals") | |
ccd2aade | 7909 | (version "1.8.0") |
fe02c4c9 RW |
7910 | (source |
7911 | (origin | |
7912 | (method url-fetch) | |
7913 | (uri (bioconductor-uri "bamsignals" version)) | |
7914 | (sha256 | |
7915 | (base32 | |
ccd2aade | 7916 | "0knx69zzdaak2sjim8k9mygmcjxpa705m8013ld5zwpgi8dag9mc")))) |
fe02c4c9 RW |
7917 | (build-system r-build-system) |
7918 | (propagated-inputs | |
7919 | `(("r-biocgenerics" ,r-biocgenerics) | |
7920 | ("r-genomicranges" ,r-genomicranges) | |
7921 | ("r-iranges" ,r-iranges) | |
7922 | ("r-rcpp" ,r-rcpp) | |
7923 | ("r-rhtslib" ,r-rhtslib) | |
7924 | ("r-zlibbioc" ,r-zlibbioc))) | |
7925 | (inputs | |
7926 | `(("zlib" ,zlib))) | |
7927 | (home-page "http://bioconductor.org/packages/bamsignals") | |
7928 | (synopsis "Extract read count signals from bam files") | |
7929 | (description | |
7930 | "This package allows to efficiently obtain count vectors from indexed bam | |
7931 | files. It counts the number of nucleotide sequence reads in given genomic | |
7932 | ranges and it computes reads profiles and coverage profiles. It also handles | |
7933 | paired-end data.") | |
7934 | (license license:gpl2+))) | |
7935 | ||
89984be4 RW |
7936 | (define-public r-rcas |
7937 | (package | |
7938 | (name "r-rcas") | |
2c8d6c0b | 7939 | (version "1.1.1") |
89984be4 RW |
7940 | (source (origin |
7941 | (method url-fetch) | |
7942 | (uri (string-append "https://github.com/BIMSBbioinfo/RCAS/archive/v" | |
7943 | version ".tar.gz")) | |
7944 | (file-name (string-append name "-" version ".tar.gz")) | |
7945 | (sha256 | |
7946 | (base32 | |
2c8d6c0b | 7947 | "1hd0r66556bxbdd82ksjklq7nfli36l4k6y88ic7kkg9873wa1nw")))) |
89984be4 RW |
7948 | (build-system r-build-system) |
7949 | (native-inputs | |
7950 | `(("r-knitr" ,r-knitr) | |
7951 | ("r-testthat" ,r-testthat) | |
7952 | ;; During vignette building knitr checks that "pandoc-citeproc" | |
7953 | ;; is in the PATH. | |
7954 | ("ghc-pandoc-citeproc" ,ghc-pandoc-citeproc))) | |
7955 | (propagated-inputs | |
7956 | `(("r-data-table" ,r-data-table) | |
7957 | ("r-biomart" ,r-biomart) | |
7958 | ("r-org-hs-eg-db" ,r-org-hs-eg-db) | |
7959 | ("r-org-ce-eg-db" ,r-org-ce-eg-db) | |
7960 | ("r-org-dm-eg-db" ,r-org-dm-eg-db) | |
7961 | ("r-org-mm-eg-db" ,r-org-mm-eg-db) | |
7962 | ("r-bsgenome-hsapiens-ucsc-hg19" ,r-bsgenome-hsapiens-ucsc-hg19) | |
7963 | ("r-bsgenome-mmusculus-ucsc-mm9" ,r-bsgenome-mmusculus-ucsc-mm9) | |
7964 | ("r-bsgenome-celegans-ucsc-ce10" ,r-bsgenome-celegans-ucsc-ce10) | |
7965 | ("r-bsgenome-dmelanogaster-ucsc-dm3" ,r-bsgenome-dmelanogaster-ucsc-dm3) | |
7966 | ("r-topgo" ,r-topgo) | |
7967 | ("r-dt" ,r-dt) | |
7968 | ("r-plotly" ,r-plotly) | |
2c8d6c0b | 7969 | ("r-plotrix" ,r-plotrix) |
89984be4 RW |
7970 | ("r-motifrg" ,r-motifrg) |
7971 | ("r-genomation" ,r-genomation) | |
7972 | ("r-genomicfeatures" ,r-genomicfeatures) | |
7973 | ("r-rtracklayer" ,r-rtracklayer) | |
7974 | ("r-rmarkdown" ,r-rmarkdown))) | |
7975 | (synopsis "RNA-centric annotation system") | |
7976 | (description | |
7977 | "RCAS aims to be a standalone RNA-centric annotation system that provides | |
7978 | intuitive reports and publication-ready graphics. This package provides the R | |
7979 | library implementing most of the pipeline's features.") | |
7980 | (home-page "https://github.com/BIMSBbioinfo/RCAS") | |
7981 | (license license:expat))) | |
7982 | ||
50937297 RW |
7983 | (define-public rcas-web |
7984 | (package | |
7985 | (name "rcas-web") | |
7986 | (version "0.0.3") | |
7987 | (source | |
7988 | (origin | |
7989 | (method url-fetch) | |
7990 | (uri (string-append "https://github.com/BIMSBbioinfo/rcas-web/" | |
7991 | "releases/download/v" version | |
7992 | "/rcas-web-" version ".tar.gz")) | |
7993 | (sha256 | |
7994 | (base32 | |
7995 | "0d3my0g8i7js59n184zzzjdki7hgmhpi4rhfvk7i6jsw01ba04qq")))) | |
7996 | (build-system gnu-build-system) | |
7997 | (arguments | |
7998 | `(#:phases | |
7999 | (modify-phases %standard-phases | |
8000 | (add-after 'install 'wrap-executable | |
8001 | (lambda* (#:key inputs outputs #:allow-other-keys) | |
8002 | (let* ((out (assoc-ref outputs "out")) | |
8003 | (json (assoc-ref inputs "guile-json")) | |
8004 | (redis (assoc-ref inputs "guile-redis")) | |
8005 | (path (string-append | |
8006 | json "/share/guile/site/2.2:" | |
8007 | redis "/share/guile/site/2.2"))) | |
8008 | (wrap-program (string-append out "/bin/rcas-web") | |
8009 | `("GUILE_LOAD_PATH" ":" = (,path)) | |
8010 | `("GUILE_LOAD_COMPILED_PATH" ":" = (,path)) | |
8011 | `("R_LIBS_SITE" ":" = (,(getenv "R_LIBS_SITE"))))) | |
8012 | #t))))) | |
8013 | (inputs | |
2d7c4ae3 | 8014 | `(("r-minimal" ,r-minimal) |
50937297 | 8015 | ("r-rcas" ,r-rcas) |
f6396d86 | 8016 | ("guile-next" ,guile-2.2) |
2252f087 | 8017 | ("guile-json" ,guile-json) |
50937297 RW |
8018 | ("guile-redis" ,guile2.2-redis))) |
8019 | (native-inputs | |
8020 | `(("pkg-config" ,pkg-config))) | |
8021 | (home-page "https://github.com/BIMSBbioinfo/rcas-web") | |
8022 | (synopsis "Web interface for RNA-centric annotation system (RCAS)") | |
8023 | (description "This package provides a simple web interface for the | |
8024 | @dfn{RNA-centric annotation system} (RCAS).") | |
8025 | (license license:agpl3+))) | |
8026 | ||
7500e42b RJ |
8027 | (define-public r-mutationalpatterns |
8028 | (package | |
8029 | (name "r-mutationalpatterns") | |
b4584137 | 8030 | (version "1.2.1") |
7500e42b RJ |
8031 | (source |
8032 | (origin | |
8033 | (method url-fetch) | |
8034 | (uri (bioconductor-uri "MutationalPatterns" version)) | |
8035 | (sha256 | |
8036 | (base32 | |
b4584137 | 8037 | "1s50diwh1j6vg3mgahh6bczvq74mfdbmwjrad4d5lh723gnc5pjg")))) |
7500e42b RJ |
8038 | (build-system r-build-system) |
8039 | (propagated-inputs | |
8040 | `(("r-biocgenerics" ,r-biocgenerics) | |
8041 | ("r-biostrings" ,r-biostrings) | |
cf4ac4e4 RJ |
8042 | ("r-bsgenome-hsapiens-1000g" ,r-bsgenome-hsapiens-1000genomes-hs37d5) |
8043 | ("r-bsgenome-hsapiens-ucsc-hg19" ,r-bsgenome-hsapiens-ucsc-hg19) | |
7500e42b RJ |
8044 | ("r-genomicranges" ,r-genomicranges) |
8045 | ("r-genomeinfodb" ,r-genomeinfodb) | |
8046 | ("r-ggplot2" ,r-ggplot2) | |
8047 | ("r-gridextra" ,r-gridextra) | |
8048 | ("r-iranges" ,r-iranges) | |
8049 | ("r-nmf" ,r-nmf) | |
8050 | ("r-plyr" ,r-plyr) | |
8051 | ("r-pracma" ,r-pracma) | |
8052 | ("r-reshape2" ,r-reshape2) | |
8053 | ("r-summarizedexperiment" ,r-summarizedexperiment) | |
8054 | ("r-variantannotation" ,r-variantannotation))) | |
8055 | (home-page "http://bioconductor.org/packages/MutationalPatterns/") | |
8056 | (synopsis "Extract and visualize mutational patterns in genomic data") | |
8057 | (description "This package provides an extensive toolset for the | |
8058 | characterization and visualization of a wide range of mutational patterns | |
8059 | in SNV base substitution data.") | |
8060 | (license license:expat))) | |
8061 | ||
d7160529 RW |
8062 | (define-public r-wgcna |
8063 | (package | |
8064 | (name "r-wgcna") | |
8065 | (version "1.51") | |
8066 | (source | |
8067 | (origin | |
8068 | (method url-fetch) | |
8069 | (uri (cran-uri "WGCNA" version)) | |
8070 | (sha256 | |
8071 | (base32 | |
8072 | "0hzvnhw76vwg8bl8x368f0c5szpwb8323bmrb3bir93i5bmfjsxx")))) | |
8073 | (properties `((upstream-name . "WGCNA"))) | |
8074 | (build-system r-build-system) | |
8075 | (propagated-inputs | |
8076 | `(("r-annotationdbi" ,r-annotationdbi) | |
8077 | ("r-doparallel" ,r-doparallel) | |
8078 | ("r-dynamictreecut" ,r-dynamictreecut) | |
8079 | ("r-fastcluster" ,r-fastcluster) | |
8080 | ("r-foreach" ,r-foreach) | |
8081 | ("r-go-db" ,r-go-db) | |
8082 | ("r-hmisc" ,r-hmisc) | |
8083 | ("r-impute" ,r-impute) | |
8084 | ("r-matrixstats" ,r-matrixstats) | |
8085 | ("r-preprocesscore" ,r-preprocesscore))) | |
8086 | (home-page | |
8087 | "http://www.genetics.ucla.edu/labs/horvath/CoexpressionNetwork/Rpackages/WGCNA/") | |
8088 | (synopsis "Weighted correlation network analysis") | |
8089 | (description | |
8090 | "This package provides functions necessary to perform Weighted | |
8091 | Correlation Network Analysis on high-dimensional data. It includes functions | |
8092 | for rudimentary data cleaning, construction and summarization of correlation | |
8093 | networks, module identification and functions for relating both variables and | |
8094 | modules to sample traits. It also includes a number of utility functions for | |
8095 | data manipulation and visualization.") | |
8096 | (license license:gpl2+))) | |
8097 | ||
c827f202 RW |
8098 | (define-public r-chipkernels |
8099 | (let ((commit "c9cfcacb626b1221094fb3490ea7bac0fd625372") | |
8100 | (revision "1")) | |
8101 | (package | |
8102 | (name "r-chipkernels") | |
8103 | (version (string-append "1.1-" revision "." (string-take commit 9))) | |
8104 | (source | |
8105 | (origin | |
8106 | (method git-fetch) | |
8107 | (uri (git-reference | |
8108 | (url "https://github.com/ManuSetty/ChIPKernels.git") | |
8109 | (commit commit))) | |
8110 | (file-name (string-append name "-" version)) | |
8111 | (sha256 | |
8112 | (base32 | |
8113 | "14bj5qhjm1hsm9ay561nfbqi9wxsa7y487df2idsaaf6z10nw4v0")))) | |
8114 | (build-system r-build-system) | |
8115 | (propagated-inputs | |
8116 | `(("r-iranges" ,r-iranges) | |
8117 | ("r-xvector" ,r-xvector) | |
8118 | ("r-biostrings" ,r-biostrings) | |
8119 | ("r-bsgenome" ,r-bsgenome) | |
8120 | ("r-gtools" ,r-gtools) | |
8121 | ("r-genomicranges" ,r-genomicranges) | |
8122 | ("r-sfsmisc" ,r-sfsmisc) | |
8123 | ("r-kernlab" ,r-kernlab) | |
8124 | ("r-s4vectors" ,r-s4vectors) | |
8125 | ("r-biocgenerics" ,r-biocgenerics))) | |
8126 | (home-page "https://github.com/ManuSetty/ChIPKernels") | |
8127 | (synopsis "Build string kernels for DNA Sequence analysis") | |
8128 | (description "ChIPKernels is an R package for building different string | |
8129 | kernels used for DNA Sequence analysis. A dictionary of the desired kernel | |
8130 | must be built and this dictionary can be used for determining kernels for DNA | |
8131 | Sequences.") | |
8132 | (license license:gpl2+)))) | |
8133 | ||
2d9fb170 RW |
8134 | (define-public r-seqgl |
8135 | (package | |
8136 | (name "r-seqgl") | |
8137 | (version "1.1.4") | |
8138 | (source | |
8139 | (origin | |
8140 | (method url-fetch) | |
8141 | (uri (string-append "https://github.com/ManuSetty/SeqGL/" | |
8142 | "archive/" version ".tar.gz")) | |
8143 | (file-name (string-append name "-" version ".tar.gz")) | |
8144 | (sha256 | |
8145 | (base32 | |
8146 | "0pnk1p3sci5yipyc8xnb6jbmydpl80fld927xgnbcv104hy8h8yh")))) | |
8147 | (build-system r-build-system) | |
8148 | (propagated-inputs | |
8149 | `(("r-biostrings" ,r-biostrings) | |
8150 | ("r-chipkernels" ,r-chipkernels) | |
8151 | ("r-genomicranges" ,r-genomicranges) | |
8152 | ("r-spams" ,r-spams) | |
8153 | ("r-wgcna" ,r-wgcna) | |
8154 | ("r-fastcluster" ,r-fastcluster))) | |
8155 | (home-page "https://github.com/ManuSetty/SeqGL") | |
8156 | (synopsis "Group lasso for Dnase/ChIP-seq data") | |
8157 | (description "SeqGL is a group lasso based algorithm to extract | |
8158 | transcription factor sequence signals from ChIP, DNase and ATAC-seq profiles. | |
8159 | This package presents a method which uses group lasso to discriminate between | |
8160 | bound and non bound genomic regions to accurately identify transcription | |
8161 | factors bound at the specific regions.") | |
8162 | (license license:gpl2+))) | |
8163 | ||
bd3be46e RW |
8164 | (define-public r-gkmsvm |
8165 | (package | |
8166 | (name "r-gkmsvm") | |
8167 | (version "0.71.0") | |
8168 | (source | |
8169 | (origin | |
8170 | (method url-fetch) | |
8171 | (uri (cran-uri "gkmSVM" version)) | |
8172 | (sha256 | |
8173 | (base32 | |
8174 | "1zpxgxmf2nd5j5wn00ps6kfxr8wxh7d1swr1rr4spq7sj5z5z0k0")))) | |
8175 | (properties `((upstream-name . "gkmSVM"))) | |
8176 | (build-system r-build-system) | |
8177 | (propagated-inputs | |
8178 | `(("r-biocgenerics" ,r-biocgenerics) | |
8179 | ("r-biostrings" ,r-biostrings) | |
8180 | ("r-genomeinfodb" ,r-genomeinfodb) | |
8181 | ("r-genomicranges" ,r-genomicranges) | |
8182 | ("r-iranges" ,r-iranges) | |
8183 | ("r-kernlab" ,r-kernlab) | |
8184 | ("r-rcpp" ,r-rcpp) | |
8185 | ("r-rocr" ,r-rocr) | |
8186 | ("r-rtracklayer" ,r-rtracklayer) | |
8187 | ("r-s4vectors" ,r-s4vectors) | |
8188 | ("r-seqinr" ,r-seqinr))) | |
8189 | (home-page "http://cran.r-project.org/web/packages/gkmSVM") | |
8190 | (synopsis "Gapped-kmer support vector machine") | |
8191 | (description | |
8192 | "This R package provides tools for training gapped-kmer SVM classifiers | |
8193 | for DNA and protein sequences. This package supports several sequence | |
8194 | kernels, including: gkmSVM, kmer-SVM, mismatch kernel and wildcard kernel.") | |
8195 | (license license:gpl2+))) | |
8196 | ||
d4af25b5 RJPB |
8197 | (define-public r-tximport |
8198 | (package | |
8199 | (name "r-tximport") | |
ff58a1af | 8200 | (version "1.4.0") |
d4af25b5 RJPB |
8201 | (source (origin |
8202 | (method url-fetch) | |
8203 | (uri (bioconductor-uri "tximport" version)) | |
8204 | (sha256 | |
8205 | (base32 | |
ff58a1af | 8206 | "1mklb02bj4gnbjlmb7vv6k4lr3w9fp3pzli9rddbrwd0y5n8fcpx")))) |
d4af25b5 RJPB |
8207 | (build-system r-build-system) |
8208 | (home-page "http://bioconductor.org/packages/tximport") | |
8209 | (synopsis "Import and summarize transcript-level estimates for gene-level analysis") | |
8210 | (description | |
8211 | "This package provides tools to import transcript-level abundance, | |
8212 | estimated counts and transcript lengths, and to summarize them into matrices | |
8213 | for use with downstream gene-level analysis packages. Average transcript | |
8214 | length, weighted by sample-specific transcript abundance estimates, is | |
8215 | provided as a matrix which can be used as an offset for different expression | |
8216 | of gene-level counts.") | |
8217 | (license license:gpl2+))) | |
8218 | ||
69f2b3bd RJPB |
8219 | (define-public r-rhdf5 |
8220 | (package | |
8221 | (name "r-rhdf5") | |
04049a5f | 8222 | (version "2.20.0") |
69f2b3bd RJPB |
8223 | (source (origin |
8224 | (method url-fetch) | |
8225 | (uri (bioconductor-uri "rhdf5" version)) | |
8226 | (sha256 | |
8227 | (base32 | |
04049a5f | 8228 | "1p6f5i6l44phl772a38x9cav2sya37bkqbkjzdc4pmyfzkv1j6hy")))) |
69f2b3bd RJPB |
8229 | (build-system r-build-system) |
8230 | (arguments | |
8231 | `(#:phases | |
8232 | (modify-phases %standard-phases | |
8233 | (add-after 'unpack 'unpack-smallhdf5 | |
8234 | (lambda* (#:key outputs #:allow-other-keys) | |
8235 | (system* "tar" "-xzvf" | |
8236 | "src/hdf5source/hdf5small.tgz" "-C" "src/" ) | |
8237 | (substitute* "src/Makevars" | |
8238 | (("^.*cd hdf5source &&.*$") "") | |
8239 | (("^.*gunzip -dc hdf5small.tgz.*$") "") | |
8240 | (("^.*rm -rf hdf5.*$") "") | |
8241 | (("^.*mv hdf5source/hdf5 ..*$") "")) | |
8242 | (substitute* "src/hdf5/configure" | |
8243 | (("/bin/mv") "mv")) | |
8244 | #t))))) | |
8245 | (propagated-inputs | |
8246 | `(("r-zlibbioc" ,r-zlibbioc))) | |
8247 | (inputs | |
8248 | `(("perl" ,perl) | |
8249 | ("zlib" ,zlib))) | |
8250 | (home-page "http://bioconductor.org/packages/rhdf5") | |
8251 | (synopsis "HDF5 interface to R") | |
8252 | (description | |
8253 | "This R/Bioconductor package provides an interface between HDF5 and R. | |
8254 | HDF5's main features are the ability to store and access very large and/or | |
8255 | complex datasets and a wide variety of metadata on mass storage (disk) through | |
8256 | a completely portable file format. The rhdf5 package is thus suited for the | |
8257 | exchange of large and/or complex datasets between R and other software | |
8258 | package, and for letting R applications work on datasets that are larger than | |
8259 | the available RAM.") | |
8260 | (license license:artistic2.0))) | |
8261 | ||
66e40e00 RW |
8262 | (define-public emboss |
8263 | (package | |
8264 | (name "emboss") | |
8265 | (version "6.5.7") | |
8266 | (source (origin | |
8267 | (method url-fetch) | |
8268 | (uri (string-append "ftp://emboss.open-bio.org/pub/EMBOSS/old/" | |
8269 | (version-major+minor version) ".0/" | |
8270 | "EMBOSS-" version ".tar.gz")) | |
8271 | (sha256 | |
8272 | (base32 | |
8273 | "0vsmz96gc411yj2iyzdrsmg4l2n1nhgmp7vrgzlxx3xixv9xbf0q")))) | |
8274 | (build-system gnu-build-system) | |
8275 | (arguments | |
8276 | `(#:configure-flags | |
8277 | (list (string-append "--with-hpdf=" | |
8278 | (assoc-ref %build-inputs "libharu"))) | |
8279 | #:phases | |
8280 | (modify-phases %standard-phases | |
8281 | (add-after 'unpack 'fix-checks | |
8282 | (lambda _ | |
8283 | ;; The PNGDRIVER tests check for the presence of libgd, libpng | |
8284 | ;; and zlib, but assume that they are all found at the same | |
8285 | ;; prefix. | |
8286 | (substitute* "configure.in" | |
8287 | (("CHECK_PNGDRIVER") | |
8288 | "LIBS=\"$LIBS -lgd -lpng -lz -lm\" | |
8289 | AC_DEFINE([PLD_png], [1], [Define to 1 if PNG support is available]) | |
8290 | AM_CONDITIONAL(AMPNG, true)")) | |
8291 | #t)) | |
8292 | (add-after 'unpack 'disable-update-check | |
8293 | (lambda _ | |
8294 | ;; At build time there is no connection to the Internet, so | |
8295 | ;; looking for updates will not work. | |
8296 | (substitute* "Makefile.am" | |
8297 | (("\\$\\(bindir\\)/embossupdate") "")) | |
8298 | #t)) | |
8299 | (add-before 'configure 'autogen | |
8300 | (lambda _ (zero? (system* "autoreconf" "-vif"))))))) | |
8301 | (inputs | |
8302 | `(("perl" ,perl) | |
8303 | ("libpng" ,libpng) | |
8304 | ("gd" ,gd) | |
8305 | ("libx11" ,libx11) | |
8306 | ("libharu" ,libharu) | |
8307 | ("zlib" ,zlib))) | |
8308 | (native-inputs | |
8309 | `(("autoconf" ,autoconf) | |
8310 | ("automake" ,automake) | |
8311 | ("libtool" ,libtool) | |
8312 | ("pkg-config" ,pkg-config))) | |
8313 | (home-page "http://emboss.sourceforge.net") | |
8314 | (synopsis "Molecular biology analysis suite") | |
8315 | (description "EMBOSS is the \"European Molecular Biology Open Software | |
8316 | Suite\". EMBOSS is an analysis package specially developed for the needs of | |
8317 | the molecular biology (e.g. EMBnet) user community. The software | |
8318 | automatically copes with data in a variety of formats and even allows | |
8319 | transparent retrieval of sequence data from the web. It also provides a | |
8320 | number of libraries for the development of software in the field of molecular | |
8321 | biology. EMBOSS also integrates a range of currently available packages and | |
8322 | tools for sequence analysis into a seamless whole.") | |
8323 | (license license:gpl2+))) | |
8324 | ||
1f1b20b8 RW |
8325 | (define-public bits |
8326 | (let ((revision "1") | |
8327 | (commit "3cc4567896d9d6442923da944beb704750a08d2d")) | |
8328 | (package | |
8329 | (name "bits") | |
8330 | ;; The version is 2.13.0 even though no release archives have been | |
8331 | ;; published as yet. | |
8332 | (version (string-append "2.13.0-" revision "." (string-take commit 9))) | |
8333 | (source (origin | |
8334 | (method git-fetch) | |
8335 | (uri (git-reference | |
8336 | (url "https://github.com/arq5x/bits.git") | |
8337 | (commit commit))) | |
8338 | (file-name (string-append name "-" version "-checkout")) | |
8339 | (sha256 | |
8340 | (base32 | |
8341 | "17n2kffk4kmhivd8c98g2vr6y1s23vbg4sxlxs689wni66797hbs")))) | |
8342 | (build-system gnu-build-system) | |
8343 | (arguments | |
8344 | `(#:tests? #f ;no tests included | |
8345 | #:phases | |
8346 | (modify-phases %standard-phases | |
8347 | (delete 'configure) | |
8348 | (add-after 'unpack 'remove-cuda | |
8349 | (lambda _ | |
8350 | (substitute* "Makefile" | |
8351 | ((".*_cuda") "") | |
8352 | (("(bits_test_intersections) \\\\" _ match) match)) | |
8353 | #t)) | |
8354 | (replace 'install | |
8355 | (lambda* (#:key outputs #:allow-other-keys) | |
8356 | (copy-recursively | |
8357 | "bin" (string-append (assoc-ref outputs "out") "/bin")) | |
8358 | #t))))) | |
8359 | (inputs | |
8360 | `(("gsl" ,gsl) | |
8361 | ("zlib" ,zlib))) | |
8362 | (home-page "https://github.com/arq5x/bits") | |
8363 | (synopsis "Implementation of binary interval search algorithm") | |
8364 | (description "This package provides an implementation of the | |
8365 | BITS (Binary Interval Search) algorithm, an approach to interval set | |
8366 | intersection. It is especially suited for the comparison of diverse genomic | |
8367 | datasets and the exploration of large datasets of genome | |
8368 | intervals (e.g. genes, sequence alignments).") | |
8369 | (license license:gpl2)))) | |
8370 | ||
e62ffce5 | 8371 | (define-public piranha |
883302da RW |
8372 | ;; There is no release tarball for the latest version. The latest commit is |
8373 | ;; older than one year at the time of this writing. | |
8374 | (let ((revision "1") | |
8375 | (commit "0466d364b71117d01e4471b74c514436cc281233")) | |
8376 | (package | |
8377 | (name "piranha") | |
8378 | (version (string-append "1.2.1-" revision "." (string-take commit 9))) | |
8379 | (source (origin | |
8380 | (method git-fetch) | |
8381 | (uri (git-reference | |
8382 | (url "https://github.com/smithlabcode/piranha.git") | |
8383 | (commit commit))) | |
8384 | (sha256 | |
8385 | (base32 | |
8386 | "117dc0zf20c61jam69sk4abl57ah6yi6i7qra7d7y5zrbgk12q5n")))) | |
8387 | (build-system gnu-build-system) | |
8388 | (arguments | |
8389 | `(#:test-target "test" | |
8390 | #:phases | |
8391 | (modify-phases %standard-phases | |
8392 | (add-after 'unpack 'copy-smithlab-cpp | |
8393 | (lambda* (#:key inputs #:allow-other-keys) | |
e62ffce5 | 8394 | (for-each (lambda (file) |
883302da RW |
8395 | (install-file file "./src/smithlab_cpp/")) |
8396 | (find-files (assoc-ref inputs "smithlab-cpp"))) | |
8397 | #t)) | |
8398 | (add-after 'install 'install-to-store | |
8399 | (lambda* (#:key outputs #:allow-other-keys) | |
8400 | (let* ((out (assoc-ref outputs "out")) | |
8401 | (bin (string-append out "/bin"))) | |
883302da RW |
8402 | (for-each (lambda (file) |
8403 | (install-file file bin)) | |
8404 | (find-files "bin" ".*"))) | |
8405 | #t))) | |
8406 | #:configure-flags | |
8407 | (list (string-append "--with-bam_tools_headers=" | |
8408 | (assoc-ref %build-inputs "bamtools") "/include/bamtools") | |
8409 | (string-append "--with-bam_tools_library=" | |
8410 | (assoc-ref %build-inputs "bamtools") "/lib/bamtools")))) | |
8411 | (inputs | |
8412 | `(("bamtools" ,bamtools) | |
8413 | ("samtools" ,samtools-0.1) | |
8414 | ("gsl" ,gsl) | |
8415 | ("smithlab-cpp" | |
8416 | ,(let ((commit "3723e2db438c51501d0423429ff396c3035ba46a")) | |
8417 | (origin | |
8418 | (method git-fetch) | |
8419 | (uri (git-reference | |
8420 | (url "https://github.com/smithlabcode/smithlab_cpp.git") | |
8421 | (commit commit))) | |
8422 | (file-name (string-append "smithlab_cpp-" commit "-checkout")) | |
8423 | (sha256 | |
8424 | (base32 | |
8425 | "0l4gvbwslw5ngziskja41c00x1r06l3yidv7y0xw9djibhykzy0g"))))))) | |
8426 | (native-inputs | |
8427 | `(("python" ,python-2))) | |
8428 | (home-page "https://github.com/smithlabcode/piranha") | |
8429 | (synopsis "Peak-caller for CLIP-seq and RIP-seq data") | |
8430 | (description | |
8431 | "Piranha is a peak-caller for genomic data produced by CLIP-seq and | |
e62ffce5 RW |
8432 | RIP-seq experiments. It takes input in BED or BAM format and identifies |
8433 | regions of statistically significant read enrichment. Additional covariates | |
8434 | may optionally be provided to further inform the peak-calling process.") | |
883302da | 8435 | (license license:gpl3+)))) |
e62ffce5 | 8436 | |
d1e32822 RW |
8437 | (define-public pepr |
8438 | (package | |
8439 | (name "pepr") | |
8440 | (version "1.0.9") | |
8441 | (source (origin | |
8442 | (method url-fetch) | |
8443 | (uri (string-append "https://pypi.python.org/packages/source/P" | |
8444 | "/PePr/PePr-" version ".tar.gz")) | |
8445 | (sha256 | |
8446 | (base32 | |
8447 | "0qxjfdpl1b1y53nccws2d85f6k74zwmx8y8sd9rszcqhfayx6gdx")))) | |
8448 | (build-system python-build-system) | |
8449 | (arguments | |
8450 | `(#:python ,python-2 ; python2 only | |
b41a05ce | 8451 | #:tests? #f)) ; no tests included |
d1e32822 RW |
8452 | (propagated-inputs |
8453 | `(("python2-numpy" ,python2-numpy) | |
8454 | ("python2-scipy" ,python2-scipy) | |
8455 | ("python2-pysam" ,python2-pysam))) | |
0c6c9c00 | 8456 | (home-page "https://github.com/shawnzhangyx/PePr") |
d1e32822 RW |
8457 | (synopsis "Peak-calling and prioritization pipeline for ChIP-Seq data") |
8458 | (description | |
8459 | "PePr is a ChIP-Seq peak calling or differential binding analysis tool | |
8460 | that is primarily designed for data with biological replicates. It uses a | |
8461 | negative binomial distribution to model the read counts among the samples in | |
8462 | the same group, and look for consistent differences between ChIP and control | |
8463 | group or two ChIP groups run under different conditions.") | |
8464 | (license license:gpl3+))) | |
6b49a37e RJ |
8465 | |
8466 | (define-public filevercmp | |
8467 | (let ((commit "1a9b779b93d0b244040274794d402106907b71b7")) | |
8468 | (package | |
8469 | (name "filevercmp") | |
8470 | (version (string-append "0-1." (string-take commit 7))) | |
8471 | (source (origin | |
8472 | (method url-fetch) | |
8473 | (uri (string-append "https://github.com/ekg/filevercmp/archive/" | |
8474 | commit ".tar.gz")) | |
8475 | (file-name (string-append name "-" version ".tar.gz")) | |
8476 | (sha256 | |
8477 | (base32 "0yp5jswf5j2pqc6517x277s4s6h1ss99v57kxw9gy0jkfl3yh450")))) | |
8478 | (build-system gnu-build-system) | |
8479 | (arguments | |
8480 | `(#:tests? #f ; There are no tests to run. | |
8481 | #:phases | |
8482 | (modify-phases %standard-phases | |
8483 | (delete 'configure) ; There is no configure phase. | |
8484 | (replace 'install | |
8485 | (lambda* (#:key outputs #:allow-other-keys) | |
8486 | (let ((bin (string-append (assoc-ref outputs "out") "/bin"))) | |
8487 | (install-file "filevercmp" bin))))))) | |
8488 | (home-page "https://github.com/ekg/filevercmp") | |
8489 | (synopsis "This program compares version strings") | |
8490 | (description "This program compares version strings. It intends to be a | |
8491 | replacement for strverscmp.") | |
8492 | (license license:gpl3+)))) | |
5fb5dffb RW |
8493 | |
8494 | (define-public multiqc | |
8495 | (package | |
8496 | (name "multiqc") | |
a29929b3 | 8497 | (version "0.9") |
5fb5dffb RW |
8498 | (source |
8499 | (origin | |
8500 | (method url-fetch) | |
8501 | (uri (pypi-uri "multiqc" version)) | |
8502 | (sha256 | |
8503 | (base32 | |
a29929b3 BW |
8504 | "12gs1jw2jrxrij529rnl5kaqxfcqn15yzcsggxkfhdx634ml0cny")) |
8505 | (patches (search-patches "multiqc-fix-git-subprocess-error.patch")))) | |
5fb5dffb | 8506 | (build-system python-build-system) |
a29929b3 BW |
8507 | (arguments |
8508 | ;; Tests are to be introduced in the next version, see | |
8509 | ;; https://github.com/ewels/MultiQC/issues/376 | |
8510 | `(#:tests? #f)) | |
5fb5dffb RW |
8511 | (propagated-inputs |
8512 | `(("python-jinja2" ,python-jinja2) | |
8513 | ("python-simplejson" ,python-simplejson) | |
8514 | ("python-pyyaml" ,python-pyyaml) | |
8515 | ("python-click" ,python-click) | |
8516 | ("python-matplotlib" ,python-matplotlib) | |
1778ea74 RW |
8517 | ("python-numpy" ,python-numpy) |
8518 | ;; MultQC checks for the presence of nose at runtime. | |
8519 | ("python-nose" ,python-nose))) | |
5fb5dffb RW |
8520 | (home-page "http://multiqc.info") |
8521 | (synopsis "Aggregate bioinformatics analysis reports") | |
8522 | (description | |
8523 | "MultiQC is a tool to aggregate bioinformatics results across many | |
8524 | samples into a single report. It contains modules for a large number of | |
8525 | common bioinformatics tools.") | |
8526 | (license license:gpl3))) | |
6193563a RW |
8527 | |
8528 | (define-public r-chipseq | |
8529 | (package | |
8530 | (name "r-chipseq") | |
7d72f2a8 | 8531 | (version "1.26.0") |
6193563a RW |
8532 | (source |
8533 | (origin | |
8534 | (method url-fetch) | |
8535 | (uri (bioconductor-uri "chipseq" version)) | |
8536 | (sha256 | |
8537 | (base32 | |
7d72f2a8 | 8538 | "1hahyqiwb2ch8214xqpw0c3jpiwkmyf3dwz0xc87jx6cdnzipj3i")))) |
6193563a RW |
8539 | (build-system r-build-system) |
8540 | (propagated-inputs | |
8541 | `(("r-biocgenerics" ,r-biocgenerics) | |
8542 | ("r-genomicranges" ,r-genomicranges) | |
8543 | ("r-iranges" ,r-iranges) | |
8544 | ("r-s4vectors" ,r-s4vectors) | |
8545 | ("r-shortread" ,r-shortread))) | |
8546 | (home-page "http://bioconductor.org/packages/chipseq") | |
8547 | (synopsis "Package for analyzing ChIPseq data") | |
8548 | (description | |
8549 | "This package provides tools for processing short read data from ChIPseq | |
8550 | experiments.") | |
8551 | (license license:artistic2.0))) | |
d407bdb9 RW |
8552 | |
8553 | (define-public r-copyhelper | |
8554 | (package | |
8555 | (name "r-copyhelper") | |
8556 | (version "1.6.0") | |
8557 | (source | |
8558 | (origin | |
8559 | (method url-fetch) | |
8560 | (uri (string-append "http://bioconductor.org/packages/release/" | |
8561 | "data/experiment/src/contrib/CopyhelpeR_" | |
8562 | version ".tar.gz")) | |
8563 | (sha256 | |
8564 | (base32 | |
8565 | "0x7cyynjmxls9as2gg0iyp9x5fpalxmdjq914ss7i84i9zyk5bhq")))) | |
8566 | (properties `((upstream-name . "CopyhelpeR"))) | |
8567 | (build-system r-build-system) | |
8568 | (home-page "http://bioconductor.org/packages/CopyhelpeR/") | |
8569 | (synopsis "Helper files for CopywriteR") | |
8570 | (description | |
8571 | "This package contains the helper files that are required to run the | |
8572 | Bioconductor package CopywriteR. It contains pre-assembled 1kb bin GC-content | |
8573 | and mappability files for the reference genomes hg18, hg19, hg38, mm9 and | |
8574 | mm10. In addition, it contains a blacklist filter to remove regions that | |
8575 | display copy number variation. Files are stored as GRanges objects from the | |
8576 | GenomicRanges Bioconductor package.") | |
8577 | (license license:gpl2))) | |
3a3bf2f8 RW |
8578 | |
8579 | (define-public r-copywriter | |
8580 | (package | |
8581 | (name "r-copywriter") | |
9eb27146 | 8582 | (version "2.8.1") |
3a3bf2f8 RW |
8583 | (source |
8584 | (origin | |
8585 | (method url-fetch) | |
8586 | (uri (bioconductor-uri "CopywriteR" version)) | |
8587 | (sha256 | |
8588 | (base32 | |
9eb27146 | 8589 | "0xgqnq5v5213b3nzvlmjysjb7w1bc0iblqpmzbjqn7n0ib0qyhbm")))) |
3a3bf2f8 RW |
8590 | (properties `((upstream-name . "CopywriteR"))) |
8591 | (build-system r-build-system) | |
8592 | (propagated-inputs | |
8593 | `(("r-biocparallel" ,r-biocparallel) | |
8594 | ("r-chipseq" ,r-chipseq) | |
8595 | ("r-copyhelper" ,r-copyhelper) | |
8596 | ("r-data-table" ,r-data-table) | |
8597 | ("r-dnacopy" ,r-dnacopy) | |
8598 | ("r-futile-logger" ,r-futile-logger) | |
8599 | ("r-genomeinfodb" ,r-genomeinfodb) | |
8600 | ("r-genomicalignments" ,r-genomicalignments) | |
8601 | ("r-genomicranges" ,r-genomicranges) | |
8602 | ("r-gtools" ,r-gtools) | |
8603 | ("r-iranges" ,r-iranges) | |
8604 | ("r-matrixstats" ,r-matrixstats) | |
8605 | ("r-rsamtools" ,r-rsamtools) | |
8606 | ("r-s4vectors" ,r-s4vectors))) | |
8607 | (home-page "https://github.com/PeeperLab/CopywriteR") | |
8608 | (synopsis "Copy number information from targeted sequencing") | |
8609 | (description | |
8610 | "CopywriteR extracts DNA copy number information from targeted sequencing | |
8611 | by utilizing off-target reads. It allows for extracting uniformly distributed | |
8612 | copy number information, can be used without reference, and can be applied to | |
8613 | sequencing data obtained from various techniques including chromatin | |
8614 | immunoprecipitation and target enrichment on small gene panels. Thereby, | |
8615 | CopywriteR constitutes a widely applicable alternative to available copy | |
8616 | number detection tools.") | |
8617 | (license license:gpl2))) | |
dd42a330 RJPB |
8618 | |
8619 | (define-public r-sva | |
8620 | (package | |
8621 | (name "r-sva") | |
bfa0d1e7 | 8622 | (version "3.24.4") |
dd42a330 RJPB |
8623 | (source |
8624 | (origin | |
8625 | (method url-fetch) | |
8626 | (uri (bioconductor-uri "sva" version)) | |
8627 | (sha256 | |
8628 | (base32 | |
bfa0d1e7 | 8629 | "0wcway4ai9im81xnrzb1vij2iidq5pw24qhjfgacmhxvx3dzhbsc")))) |
dd42a330 RJPB |
8630 | (build-system r-build-system) |
8631 | (propagated-inputs | |
aeb64f3c | 8632 | `(("r-genefilter" ,r-genefilter) |
bfa0d1e7 RJ |
8633 | ("r-mgcv" ,r-mgcv) |
8634 | ("r-biocparallel" ,r-biocparallel) | |
8635 | ("r-matrixstats" ,r-matrixstats) | |
8636 | ("r-limma" ,r-limma))) | |
dd42a330 RJPB |
8637 | (home-page "http://bioconductor.org/packages/sva") |
8638 | (synopsis "Surrogate variable analysis") | |
8639 | (description | |
8640 | "This package contains functions for removing batch effects and other | |
8641 | unwanted variation in high-throughput experiment. It also contains functions | |
8642 | for identifying and building surrogate variables for high-dimensional data | |
8643 | sets. Surrogate variables are covariates constructed directly from | |
8644 | high-dimensional data like gene expression/RNA sequencing/methylation/brain | |
8645 | imaging data that can be used in subsequent analyses to adjust for unknown, | |
8646 | unmodeled, or latent sources of noise.") | |
8647 | (license license:artistic2.0))) | |
fb1e528e RW |
8648 | |
8649 | (define-public r-seqminer | |
8650 | (package | |
8651 | (name "r-seqminer") | |
1a84edeb | 8652 | (version "5.9") |
fb1e528e RW |
8653 | (source |
8654 | (origin | |
8655 | (method url-fetch) | |
8656 | (uri (cran-uri "seqminer" version)) | |
8657 | (sha256 | |
8658 | (base32 | |
1a84edeb | 8659 | "0sfkxrc9gy5a8fadzyzfzh7l5grasm8cj6cd2nnpv85ws6mqr6qd")))) |
fb1e528e RW |
8660 | (build-system r-build-system) |
8661 | (inputs | |
8662 | `(("zlib" ,zlib))) | |
8663 | (home-page "http://seqminer.genomic.codes") | |
8664 | (synopsis "Read nucleotide sequence data (VCF, BCF, and METAL formats)") | |
8665 | (description | |
8666 | "This package provides tools to integrate nucleotide sequencing | |
8667 | data (variant call format, e.g. VCF or BCF) or meta-analysis results in R.") | |
8668 | ;; Any version of the GPL is acceptable | |
8669 | (license (list license:gpl2+ license:gpl3+)))) | |
1f40e73c RW |
8670 | |
8671 | (define-public r-raremetals2 | |
8672 | (package | |
8673 | (name "r-raremetals2") | |
8674 | (version "0.1") | |
8675 | (source | |
8676 | (origin | |
8677 | (method url-fetch) | |
8678 | (uri (string-append "http://genome.sph.umich.edu/w/images/" | |
8679 | "b/b7/RareMETALS2_" version ".tar.gz")) | |
8680 | (sha256 | |
8681 | (base32 | |
8682 | "0z5ljcgvnm06ja9lm85a3cniq7slxcy37aqqkxrdidr79an5fs4s")))) | |
8683 | (properties `((upstream-name . "RareMETALS2"))) | |
8684 | (build-system r-build-system) | |
8685 | (propagated-inputs | |
8686 | `(("r-seqminer" ,r-seqminer) | |
8687 | ("r-mvtnorm" ,r-mvtnorm) | |
aeb64f3c | 8688 | ("r-mass" ,r-mass) |
1f40e73c RW |
8689 | ("r-compquadform" ,r-compquadform) |
8690 | ("r-getopt" ,r-getopt))) | |
8691 | (home-page "http://genome.sph.umich.edu/wiki/RareMETALS2") | |
8692 | (synopsis "Analyze gene-level association tests for binary trait") | |
8693 | (description | |
8694 | "The R package rareMETALS2 is an extension of the R package rareMETALS. | |
8695 | It was designed to meta-analyze gene-level association tests for binary trait. | |
8696 | While rareMETALS offers a near-complete solution for meta-analysis of | |
8697 | gene-level tests for quantitative trait, it does not offer the optimal | |
8698 | solution for binary trait. The package rareMETALS2 offers improved features | |
8699 | for analyzing gene-level association tests in meta-analyses for binary | |
8700 | trait.") | |
8701 | (license license:gpl3))) | |
0e7d058e RW |
8702 | |
8703 | (define-public r-maldiquant | |
8704 | (package | |
8705 | (name "r-maldiquant") | |
e8bec95e | 8706 | (version "1.16.2") |
0e7d058e RW |
8707 | (source |
8708 | (origin | |
8709 | (method url-fetch) | |
8710 | (uri (cran-uri "MALDIquant" version)) | |
8711 | (sha256 | |
8712 | (base32 | |
e8bec95e | 8713 | "0z5srzsfgsgi4bssr4chls4ry6d18y2g9143znqmraylppwrrqzr")))) |
0e7d058e RW |
8714 | (properties `((upstream-name . "MALDIquant"))) |
8715 | (build-system r-build-system) | |
8716 | (home-page "http://cran.r-project.org/web/packages/MALDIquant") | |
8717 | (synopsis "Quantitative analysis of mass spectrometry data") | |
8718 | (description | |
8719 | "This package provides a complete analysis pipeline for matrix-assisted | |
8720 | laser desorption/ionization-time-of-flight (MALDI-TOF) and other | |
8721 | two-dimensional mass spectrometry data. In addition to commonly used plotting | |
8722 | and processing methods it includes distinctive features, namely baseline | |
8723 | subtraction methods such as morphological filters (TopHat) or the | |
8724 | statistics-sensitive non-linear iterative peak-clipping algorithm (SNIP), peak | |
8725 | alignment using warping functions, handling of replicated measurements as well | |
8726 | as allowing spectra with different resolutions.") | |
8727 | (license license:gpl3+))) | |
ae262174 RW |
8728 | |
8729 | (define-public r-protgenerics | |
8730 | (package | |
8731 | (name "r-protgenerics") | |
5b1337cc | 8732 | (version "1.8.0") |
ae262174 RW |
8733 | (source |
8734 | (origin | |
8735 | (method url-fetch) | |
8736 | (uri (bioconductor-uri "ProtGenerics" version)) | |
8737 | (sha256 | |
8738 | (base32 | |
5b1337cc | 8739 | "08idb3rvxn4fl7rd66jasyqz47cb76dbc3968r1g26jr2ci3w1pl")))) |
ae262174 RW |
8740 | (properties `((upstream-name . "ProtGenerics"))) |
8741 | (build-system r-build-system) | |
8742 | (home-page "https://github.com/lgatto/ProtGenerics") | |
8743 | (synopsis "S4 generic functions for proteomics infrastructure") | |
8744 | (description | |
8745 | "This package provides S4 generic functions needed by Bioconductor | |
8746 | proteomics packages.") | |
8747 | (license license:artistic2.0))) | |
71676a1f RW |
8748 | |
8749 | (define-public r-mzr | |
8750 | (package | |
8751 | (name "r-mzr") | |
e440ad6d | 8752 | (version "2.10.0") |
71676a1f RW |
8753 | (source |
8754 | (origin | |
8755 | (method url-fetch) | |
8756 | (uri (bioconductor-uri "mzR" version)) | |
8757 | (sha256 | |
8758 | (base32 | |
e440ad6d | 8759 | "1zir46h320n2vbrky6q3m8l221f3wdjlfsnx4ak9xca5min24xm7")))) |
71676a1f RW |
8760 | (properties `((upstream-name . "mzR"))) |
8761 | (build-system r-build-system) | |
8762 | (inputs | |
8763 | `(("netcdf" ,netcdf))) | |
8764 | (propagated-inputs | |
8765 | `(("r-biobase" ,r-biobase) | |
8766 | ("r-biocgenerics" ,r-biocgenerics) | |
8767 | ("r-protgenerics" ,r-protgenerics) | |
8768 | ("r-rcpp" ,r-rcpp) | |
8769 | ("r-zlibbioc" ,r-zlibbioc))) | |
8770 | (home-page "https://github.com/sneumann/mzR/") | |
8771 | (synopsis "Parser for mass spectrometry data files") | |
8772 | (description | |
8773 | "The mzR package provides a unified API to the common file formats and | |
8774 | parsers available for mass spectrometry data. It comes with a wrapper for the | |
8775 | ISB random access parser for mass spectrometry mzXML, mzData and mzML files. | |
8776 | The package contains the original code written by the ISB, and a subset of the | |
8777 | proteowizard library for mzML and mzIdentML. The netCDF reading code has | |
8778 | previously been used in XCMS.") | |
8779 | (license license:artistic2.0))) | |
5c9d1505 RW |
8780 | |
8781 | (define-public r-affyio | |
8782 | (package | |
8783 | (name "r-affyio") | |
71abcc4c | 8784 | (version "1.46.0") |
5c9d1505 RW |
8785 | (source |
8786 | (origin | |
8787 | (method url-fetch) | |
8788 | (uri (bioconductor-uri "affyio" version)) | |
8789 | (sha256 | |
8790 | (base32 | |
71abcc4c | 8791 | "13w6al9296q916w0w6ngbsk25b21ahla1b6n40fcqhbvhyfii6sj")))) |
5c9d1505 RW |
8792 | (build-system r-build-system) |
8793 | (propagated-inputs | |
8794 | `(("r-zlibbioc" ,r-zlibbioc))) | |
8795 | (inputs | |
8796 | `(("zlib" ,zlib))) | |
8797 | (home-page "https://github.com/bmbolstad/affyio") | |
8798 | (synopsis "Tools for parsing Affymetrix data files") | |
8799 | (description | |
8800 | "This package provides routines for parsing Affymetrix data files based | |
8801 | upon file format information. The primary focus is on accessing the CEL and | |
8802 | CDF file formats.") | |
8803 | (license license:lgpl2.0+))) | |
05c7e5fb RW |
8804 | |
8805 | (define-public r-affy | |
8806 | (package | |
8807 | (name "r-affy") | |
bd3cc4cc | 8808 | (version "1.54.0") |
05c7e5fb RW |
8809 | (source |
8810 | (origin | |
8811 | (method url-fetch) | |
8812 | (uri (bioconductor-uri "affy" version)) | |
8813 | (sha256 | |
8814 | (base32 | |
bd3cc4cc | 8815 | "0azwg2qxzgflr1rjvbdln5i5rbcr9gs36kqlacd9cwl1szb9ad3m")))) |
05c7e5fb RW |
8816 | (build-system r-build-system) |
8817 | (propagated-inputs | |
8818 | `(("r-affyio" ,r-affyio) | |
8819 | ("r-biobase" ,r-biobase) | |
8820 | ("r-biocgenerics" ,r-biocgenerics) | |
8821 | ("r-biocinstaller" ,r-biocinstaller) | |
8822 | ("r-preprocesscore" ,r-preprocesscore) | |
8823 | ("r-zlibbioc" ,r-zlibbioc))) | |
8824 | (home-page "http://bioconductor.org/packages/affy") | |
8825 | (synopsis "Methods for affymetrix oligonucleotide arrays") | |
8826 | (description | |
8827 | "This package contains functions for exploratory oligonucleotide array | |
8828 | analysis.") | |
8829 | (license license:lgpl2.0+))) | |
7c08afaf RW |
8830 | |
8831 | (define-public r-vsn | |
8832 | (package | |
8833 | (name "r-vsn") | |
60c08b2f | 8834 | (version "3.44.0") |
7c08afaf RW |
8835 | (source |
8836 | (origin | |
8837 | (method url-fetch) | |
8838 | (uri (bioconductor-uri "vsn" version)) | |
8839 | (sha256 | |
8840 | (base32 | |
60c08b2f | 8841 | "0qhg3a4sc62pfdxcpvmk831rk138xh4zx4f1s39jhxpqqhmr7jvk")))) |
7c08afaf RW |
8842 | (build-system r-build-system) |
8843 | (propagated-inputs | |
8844 | `(("r-affy" ,r-affy) | |
8845 | ("r-biobase" ,r-biobase) | |
8846 | ("r-ggplot2" ,r-ggplot2) | |
60c08b2f | 8847 | ("r-hexbin" ,r-hexbin) |
aeb64f3c | 8848 | ("r-lattice" ,r-lattice) |
7c08afaf RW |
8849 | ("r-limma" ,r-limma))) |
8850 | (home-page "http://bioconductor.org/packages/release/bioc/html/vsn.html") | |
8851 | (synopsis "Variance stabilization and calibration for microarray data") | |
8852 | (description | |
8853 | "The package implements a method for normalising microarray intensities, | |
8854 | and works for single- and multiple-color arrays. It can also be used for data | |
8855 | from other technologies, as long as they have similar format. The method uses | |
8856 | a robust variant of the maximum-likelihood estimator for an | |
8857 | additive-multiplicative error model and affine calibration. The model | |
8858 | incorporates data calibration step (a.k.a. normalization), a model for the | |
8859 | dependence of the variance on the mean intensity and a variance stabilizing | |
8860 | data transformation. Differences between transformed intensities are | |
8861 | analogous to \"normalized log-ratios\". However, in contrast to the latter, | |
8862 | their variance is independent of the mean, and they are usually more sensitive | |
8863 | and specific in detecting differential transcription.") | |
8864 | (license license:artistic2.0))) | |
4aa7d592 RW |
8865 | |
8866 | (define-public r-mzid | |
8867 | (package | |
8868 | (name "r-mzid") | |
63bf2102 | 8869 | (version "1.14.0") |
4aa7d592 RW |
8870 | (source |
8871 | (origin | |
8872 | (method url-fetch) | |
8873 | (uri (bioconductor-uri "mzID" version)) | |
8874 | (sha256 | |
8875 | (base32 | |
63bf2102 | 8876 | "11xnild02jz24vbsfy92lb7jlqqwnrswg66a7r4rsw8d2ibrbk33")))) |
4aa7d592 RW |
8877 | (properties `((upstream-name . "mzID"))) |
8878 | (build-system r-build-system) | |
8879 | (propagated-inputs | |
8880 | `(("r-doparallel" ,r-doparallel) | |
8881 | ("r-foreach" ,r-foreach) | |
8882 | ("r-iterators" ,r-iterators) | |
8883 | ("r-plyr" ,r-plyr) | |
8884 | ("r-protgenerics" ,r-protgenerics) | |
8885 | ("r-rcpp" ,r-rcpp) | |
8886 | ("r-xml" ,r-xml))) | |
8887 | (home-page "http://bioconductor.org/packages/mzID") | |
8888 | (synopsis "Parser for mzIdentML files") | |
8889 | (description | |
8890 | "This package provides a parser for mzIdentML files implemented using the | |
8891 | XML package. The parser tries to be general and able to handle all types of | |
8892 | mzIdentML files with the drawback of having less pretty output than a vendor | |
8893 | specific parser.") | |
8894 | (license license:gpl2+))) | |
6a67e181 RW |
8895 | |
8896 | (define-public r-pcamethods | |
8897 | (package | |
8898 | (name "r-pcamethods") | |
5bfa6e09 | 8899 | (version "1.68.0") |
6a67e181 RW |
8900 | (source |
8901 | (origin | |
8902 | (method url-fetch) | |
8903 | (uri (bioconductor-uri "pcaMethods" version)) | |
8904 | (sha256 | |
8905 | (base32 | |
5bfa6e09 | 8906 | "0c4lphqyzj577ws4s172391cgv00s5nhy152zp18k2k4diyhq6n0")))) |
6a67e181 RW |
8907 | (properties `((upstream-name . "pcaMethods"))) |
8908 | (build-system r-build-system) | |
8909 | (propagated-inputs | |
8910 | `(("r-biobase" ,r-biobase) | |
8911 | ("r-biocgenerics" ,r-biocgenerics) | |
aeb64f3c | 8912 | ("r-mass" ,r-mass) |
6a67e181 RW |
8913 | ("r-rcpp" ,r-rcpp))) |
8914 | (home-page "https://github.com/hredestig/pcamethods") | |
8915 | (synopsis "Collection of PCA methods") | |
8916 | (description | |
8917 | "This package provides Bayesian PCA, Probabilistic PCA, Nipals PCA, | |
8918 | Inverse Non-Linear PCA and the conventional SVD PCA. A cluster based method | |
8919 | for missing value estimation is included for comparison. BPCA, PPCA and | |
8920 | NipalsPCA may be used to perform PCA on incomplete data as well as for | |
8921 | accurate missing value estimation. A set of methods for printing and plotting | |
8922 | the results is also provided. All PCA methods make use of the same data | |
8923 | structure (pcaRes) to provide a common interface to the PCA results.") | |
8924 | (license license:gpl3+))) | |
11879284 RW |
8925 | |
8926 | (define-public r-msnbase | |
8927 | (package | |
8928 | (name "r-msnbase") | |
82359c72 | 8929 | (version "2.2.0") |
11879284 RW |
8930 | (source |
8931 | (origin | |
8932 | (method url-fetch) | |
8933 | (uri (bioconductor-uri "MSnbase" version)) | |
8934 | (sha256 | |
8935 | (base32 | |
82359c72 | 8936 | "1n9bbdlp8d8bx2mqby0c4yylz1yil42scbkxqgyrfr9s5sn6dqff")))) |
11879284 RW |
8937 | (properties `((upstream-name . "MSnbase"))) |
8938 | (build-system r-build-system) | |
8939 | (propagated-inputs | |
8940 | `(("r-affy" ,r-affy) | |
8941 | ("r-biobase" ,r-biobase) | |
8942 | ("r-biocgenerics" ,r-biocgenerics) | |
8943 | ("r-biocparallel" ,r-biocparallel) | |
8944 | ("r-digest" ,r-digest) | |
8945 | ("r-ggplot2" ,r-ggplot2) | |
8946 | ("r-impute" ,r-impute) | |
8947 | ("r-iranges" ,r-iranges) | |
8948 | ("r-maldiquant" ,r-maldiquant) | |
8949 | ("r-mzid" ,r-mzid) | |
8950 | ("r-mzr" ,r-mzr) | |
8951 | ("r-pcamethods" ,r-pcamethods) | |
8952 | ("r-plyr" ,r-plyr) | |
8953 | ("r-preprocesscore" ,r-preprocesscore) | |
8954 | ("r-protgenerics" ,r-protgenerics) | |
8955 | ("r-rcpp" ,r-rcpp) | |
8956 | ("r-reshape2" ,r-reshape2) | |
8957 | ("r-s4vectors" ,r-s4vectors) | |
8958 | ("r-vsn" ,r-vsn) | |
8959 | ("r-xml" ,r-xml))) | |
8960 | (home-page "https://github.com/lgatto/MSnbase") | |
8961 | (synopsis "Base functions and classes for MS-based proteomics") | |
8962 | (description | |
8963 | "This package provides basic plotting, data manipulation and processing | |
e614d639 | 8964 | of mass spectrometry based proteomics data.") |
11879284 | 8965 | (license license:artistic2.0))) |
66da3a9f RW |
8966 | |
8967 | (define-public r-msnid | |
8968 | (package | |
8969 | (name "r-msnid") | |
524bfe2d | 8970 | (version "1.10.0") |
66da3a9f RW |
8971 | (source |
8972 | (origin | |
8973 | (method url-fetch) | |
8974 | (uri (bioconductor-uri "MSnID" version)) | |
8975 | (sha256 | |
8976 | (base32 | |
524bfe2d | 8977 | "0pjwargi5lif8q53fd43ql67p3yk9w10jychafd9qgbaw5k3f68k")))) |
66da3a9f RW |
8978 | (properties `((upstream-name . "MSnID"))) |
8979 | (build-system r-build-system) | |
8980 | (propagated-inputs | |
8981 | `(("r-biobase" ,r-biobase) | |
8982 | ("r-data-table" ,r-data-table) | |
8983 | ("r-doparallel" ,r-doparallel) | |
8984 | ("r-dplyr" ,r-dplyr) | |
8985 | ("r-foreach" ,r-foreach) | |
8986 | ("r-iterators" ,r-iterators) | |
8987 | ("r-msnbase" ,r-msnbase) | |
8988 | ("r-mzid" ,r-mzid) | |
8989 | ("r-mzr" ,r-mzr) | |
8990 | ("r-protgenerics" ,r-protgenerics) | |
8991 | ("r-r-cache" ,r-r-cache) | |
8992 | ("r-rcpp" ,r-rcpp) | |
8993 | ("r-reshape2" ,r-reshape2))) | |
8994 | (home-page "http://bioconductor.org/packages/MSnID") | |
8995 | (synopsis "Utilities for LC-MSn proteomics identifications") | |
8996 | (description | |
2923f3e5 RW |
8997 | "This package extracts @dfn{tandem mass spectrometry} (MS/MS) ID data |
8998 | from mzIdentML (leveraging the mzID package) or text files. After collating | |
8999 | the search results from multiple datasets it assesses their identification | |
9000 | quality and optimize filtering criteria to achieve the maximum number of | |
9001 | identifications while not exceeding a specified false discovery rate. It also | |
9002 | contains a number of utilities to explore the MS/MS results and assess missed | |
9003 | and irregular enzymatic cleavages, mass measurement accuracy, etc.") | |
66da3a9f | 9004 | (license license:artistic2.0))) |
5ded35d8 | 9005 | |
2441c284 RJPB |
9006 | (define-public r-seurat |
9007 | ;; Source releases are only made for new x.0 versions. All newer versions | |
9008 | ;; are only released as pre-built binaries. At the time of this writing the | |
9009 | ;; latest binary release is 1.4.0.12, which is equivalent to this commit. | |
9010 | (let ((commit "fccb77d1452c35ee47e47ebf8e87bddb59f3b08d") | |
9011 | (revision "1")) | |
9012 | (package | |
9013 | (name "r-seurat") | |
9014 | (version (string-append "1.4.0.12-" revision "." (string-take commit 7))) | |
9015 | (source (origin | |
9016 | (method git-fetch) | |
9017 | (uri (git-reference | |
9018 | (url "https://github.com/satijalab/seurat") | |
9019 | (commit commit))) | |
9020 | (file-name (string-append name "-" version "-checkout")) | |
9021 | (sha256 | |
9022 | (base32 | |
9023 | "101wq3aqrdmbfi3lqmq4iivk9iwbf10d4z216ss25hf7n9091cyl")) | |
9024 | ;; Delete pre-built jar. | |
9025 | (snippet | |
9026 | '(begin (delete-file "inst/java/ModularityOptimizer.jar") | |
9027 | #t)))) | |
9028 | (build-system r-build-system) | |
9029 | (arguments | |
9030 | `(#:phases | |
9031 | (modify-phases %standard-phases | |
9032 | (add-after 'unpack 'build-jar | |
9033 | (lambda* (#:key inputs #:allow-other-keys) | |
9034 | (let ((classesdir "tmp-classes")) | |
9035 | (setenv "JAVA_HOME" (assoc-ref inputs "jdk")) | |
9036 | (mkdir classesdir) | |
9037 | (and (zero? (apply system* `("javac" "-d" ,classesdir | |
9038 | ,@(find-files "java" "\\.java$")))) | |
9039 | (zero? (system* "jar" | |
9040 | "-cf" "inst/java/ModularityOptimizer.jar" | |
9041 | "-C" classesdir "."))))))))) | |
9042 | (native-inputs | |
9043 | `(("jdk" ,icedtea "jdk"))) | |
9044 | (propagated-inputs | |
9045 | `(("r-ape" ,r-ape) | |
9046 | ("r-caret" ,r-caret) | |
9047 | ("r-cowplot" ,r-cowplot) | |
9048 | ("r-dplyr" ,r-dplyr) | |
9049 | ("r-fastica" ,r-fastica) | |
9050 | ("r-fnn" ,r-fnn) | |
9051 | ("r-fpc" ,r-fpc) | |
9052 | ("r-gdata" ,r-gdata) | |
9053 | ("r-ggplot2" ,r-ggplot2) | |
9054 | ("r-gplots" ,r-gplots) | |
9055 | ("r-gridextra" ,r-gridextra) | |
9056 | ("r-igraph" ,r-igraph) | |
9057 | ("r-irlba" ,r-irlba) | |
9058 | ("r-lars" ,r-lars) | |
9059 | ("r-mixtools" ,r-mixtools) | |
9060 | ("r-pbapply" ,r-pbapply) | |
9061 | ("r-plyr" ,r-plyr) | |
9062 | ("r-ranger" ,r-ranger) | |
9063 | ("r-rcolorbrewer" ,r-rcolorbrewer) | |
9064 | ("r-rcpp" ,r-rcpp) | |
9065 | ("r-rcppeigen" ,r-rcppeigen) | |
9066 | ("r-rcppprogress" ,r-rcppprogress) | |
9067 | ("r-reshape2" ,r-reshape2) | |
9068 | ("r-rocr" ,r-rocr) | |
9069 | ("r-rtsne" ,r-rtsne) | |
9070 | ("r-stringr" ,r-stringr) | |
9071 | ("r-tclust" ,r-tclust) | |
9072 | ("r-tsne" ,r-tsne) | |
9073 | ("r-vgam" ,r-vgam))) | |
9074 | (home-page "http://www.satijalab.org/seurat") | |
9075 | (synopsis "Seurat is an R toolkit for single cell genomics") | |
9076 | (description | |
9077 | "This package is an R package designed for QC, analysis, and | |
9078 | exploration of single cell RNA-seq data. It easily enables widely-used | |
9079 | analytical techniques, including the identification of highly variable genes, | |
9080 | dimensionality reduction; PCA, ICA, t-SNE, standard unsupervised clustering | |
9081 | algorithms; density clustering, hierarchical clustering, k-means, and the | |
9082 | discovery of differentially expressed genes and markers.") | |
9083 | (license license:gpl3)))) | |
9084 | ||
d4b83651 RW |
9085 | (define-public r-aroma-light |
9086 | (package | |
9087 | (name "r-aroma-light") | |
9088 | (version "3.6.0") | |
9089 | (source | |
9090 | (origin | |
9091 | (method url-fetch) | |
9092 | (uri (bioconductor-uri "aroma.light" version)) | |
9093 | (sha256 | |
9094 | (base32 | |
9095 | "10snykmmx36qaymyf5s1n1km8hsscyzpykcpf0mzsrcv8ml9rp8a")))) | |
9096 | (properties `((upstream-name . "aroma.light"))) | |
9097 | (build-system r-build-system) | |
9098 | (propagated-inputs | |
9099 | `(("r-matrixstats" ,r-matrixstats) | |
9100 | ("r-r-methodss3" ,r-r-methodss3) | |
9101 | ("r-r-oo" ,r-r-oo) | |
9102 | ("r-r-utils" ,r-r-utils))) | |
9103 | (home-page "https://github.com/HenrikBengtsson/aroma.light") | |
9104 | (synopsis "Methods for normalization and visualization of microarray data") | |
9105 | (description | |
9106 | "This package provides methods for microarray analysis that take basic | |
9107 | data types such as matrices and lists of vectors. These methods can be used | |
9108 | standalone, be utilized in other packages, or be wrapped up in higher-level | |
9109 | classes.") | |
9110 | (license license:gpl2+))) | |
9111 | ||
7b465327 RW |
9112 | (define-public r-deseq |
9113 | (package | |
9114 | (name "r-deseq") | |
9115 | (version "1.28.0") | |
9116 | (source | |
9117 | (origin | |
9118 | (method url-fetch) | |
9119 | (uri (bioconductor-uri "DESeq" version)) | |
9120 | (sha256 | |
9121 | (base32 | |
9122 | "0j3dgcxd64m9qknmlcbdzvg4xhp981xd6nbwsvnqjfn6yypslgyw")))) | |
9123 | (properties `((upstream-name . "DESeq"))) | |
9124 | (build-system r-build-system) | |
9125 | (propagated-inputs | |
9126 | `(("r-biobase" ,r-biobase) | |
9127 | ("r-biocgenerics" ,r-biocgenerics) | |
9128 | ("r-genefilter" ,r-genefilter) | |
9129 | ("r-geneplotter" ,r-geneplotter) | |
9130 | ("r-lattice" ,r-lattice) | |
9131 | ("r-locfit" ,r-locfit) | |
9132 | ("r-mass" ,r-mass) | |
9133 | ("r-rcolorbrewer" ,r-rcolorbrewer))) | |
9134 | (home-page "http://www-huber.embl.de/users/anders/DESeq") | |
9135 | (synopsis "Differential gene expression analysis") | |
9136 | (description | |
9137 | "This package provides tools for estimating variance-mean dependence in | |
9138 | count data from high-throughput genetic sequencing assays and for testing for | |
9139 | differential expression based on a model using the negative binomial | |
9140 | distribution.") | |
9141 | (license license:gpl3+))) | |
9142 | ||
296b3c63 RW |
9143 | (define-public r-edaseq |
9144 | (package | |
9145 | (name "r-edaseq") | |
9146 | (version "2.10.0") | |
9147 | (source | |
9148 | (origin | |
9149 | (method url-fetch) | |
9150 | (uri (bioconductor-uri "EDASeq" version)) | |
9151 | (sha256 | |
9152 | (base32 | |
9153 | "0f25dfc8hdii9fjm3bf89vy9jkxv23sa62fkcga5b4gkipwrvm9a")))) | |
9154 | (properties `((upstream-name . "EDASeq"))) | |
9155 | (build-system r-build-system) | |
9156 | (propagated-inputs | |
9157 | `(("r-annotationdbi" ,r-annotationdbi) | |
9158 | ("r-aroma-light" ,r-aroma-light) | |
9159 | ("r-biobase" ,r-biobase) | |
9160 | ("r-biocgenerics" ,r-biocgenerics) | |
9161 | ("r-biomart" ,r-biomart) | |
9162 | ("r-biostrings" ,r-biostrings) | |
9163 | ("r-deseq" ,r-deseq) | |
9164 | ("r-genomicfeatures" ,r-genomicfeatures) | |
9165 | ("r-genomicranges" ,r-genomicranges) | |
9166 | ("r-iranges" ,r-iranges) | |
9167 | ("r-rsamtools" ,r-rsamtools) | |
9168 | ("r-shortread" ,r-shortread))) | |
9169 | (home-page "https://github.com/drisso/EDASeq") | |
9170 | (synopsis "Exploratory data analysis and normalization for RNA-Seq") | |
9171 | (description | |
9172 | "This package provides support for numerical and graphical summaries of | |
9173 | RNA-Seq genomic read data. Provided within-lane normalization procedures to | |
9174 | adjust for GC-content effect (or other gene-level effects) on read counts: | |
9175 | loess robust local regression, global-scaling, and full-quantile | |
9176 | normalization. Between-lane normalization procedures to adjust for | |
9177 | distributional differences between lanes (e.g., sequencing depth): | |
9178 | global-scaling and full-quantile normalization.") | |
9179 | (license license:artistic2.0))) | |
9180 | ||
5ded35d8 RW |
9181 | (define htslib-for-sambamba |
9182 | (let ((commit "2f3c3ea7b301f9b45737a793c0b2dcf0240e5ee5")) | |
9183 | (package | |
9184 | (inherit htslib) | |
9185 | (name "htslib-for-sambamba") | |
9186 | (version (string-append "1.3.1-1." (string-take commit 9))) | |
9187 | (source | |
9188 | (origin | |
9189 | (method git-fetch) | |
9190 | (uri (git-reference | |
9191 | (url "https://github.com/lomereiter/htslib.git") | |
9192 | (commit commit))) | |
9193 | (file-name (string-append "htslib-" version "-checkout")) | |
9194 | (sha256 | |
9195 | (base32 | |
9196 | "0g38g8s3npr0gjm9fahlbhiskyfws9l5i0x1ml3rakzj7az5l9c9")))) | |
9197 | (arguments | |
9198 | (substitute-keyword-arguments (package-arguments htslib) | |
9199 | ((#:phases phases) | |
9200 | `(modify-phases ,phases | |
9201 | (add-before 'configure 'bootstrap | |
9202 | (lambda _ | |
9203 | (zero? (system* "autoreconf" "-vif")))))))) | |
9204 | (native-inputs | |
9205 | `(("autoconf" ,autoconf) | |
9206 | ("automake" ,automake) | |
9207 | ,@(package-native-inputs htslib)))))) | |
9208 | ||
9209 | (define-public sambamba | |
9210 | (package | |
9211 | (name "sambamba") | |
9212 | (version "0.6.5") | |
9213 | (source | |
9214 | (origin | |
9215 | (method url-fetch) | |
9216 | (uri (string-append "https://github.com/lomereiter/sambamba/" | |
9217 | "archive/v" version ".tar.gz")) | |
9218 | (file-name (string-append name "-" version ".tar.gz")) | |
9219 | (sha256 | |
9220 | (base32 | |
9221 | "17076gijd65a3f07zns2gvbgahiz5lriwsa6dq353ss3jl85d8vy")))) | |
9222 | (build-system gnu-build-system) | |
9223 | (arguments | |
9224 | `(#:tests? #f ; there is no test target | |
9225 | #:make-flags | |
9226 | '("D_COMPILER=ldc2" | |
9227 | ;; Override "--compiler" flag only. | |
9228 | "D_FLAGS=--compiler=ldc2 -IBioD -g -d" | |
9229 | "sambamba-ldmd2-64") | |
9230 | #:phases | |
9231 | (modify-phases %standard-phases | |
9232 | (delete 'configure) | |
9233 | (add-after 'unpack 'place-biod | |
9234 | (lambda* (#:key inputs #:allow-other-keys) | |
9235 | (copy-recursively (assoc-ref inputs "biod") "BioD") | |
9236 | #t)) | |
9237 | (add-after 'unpack 'unbundle-prerequisites | |
9238 | (lambda _ | |
9239 | (substitute* "Makefile" | |
9240 | ((" htslib-static lz4-static") "")) | |
9241 | #t)) | |
9242 | (replace 'install | |
9243 | (lambda* (#:key outputs #:allow-other-keys) | |
9244 | (let* ((out (assoc-ref outputs "out")) | |
9245 | (bin (string-append out "/bin"))) | |
9246 | (mkdir-p bin) | |
9247 | (install-file "build/sambamba" bin) | |
9248 | #t)))))) | |
9249 | (native-inputs | |
9250 | `(("ldc" ,ldc) | |
9251 | ("rdmd" ,rdmd) | |
9252 | ("biod" | |
9253 | ,(let ((commit "1248586b54af4bd4dfb28ebfebfc6bf012e7a587")) | |
9254 | (origin | |
9255 | (method git-fetch) | |
9256 | (uri (git-reference | |
9257 | (url "https://github.com/biod/BioD.git") | |
9258 | (commit commit))) | |
9259 | (file-name (string-append "biod-" | |
9260 | (string-take commit 9) | |
9261 | "-checkout")) | |
9262 | (sha256 | |
9263 | (base32 | |
9264 | "1m8hi1n7x0ri4l6s9i0x6jg4z4v94xrfdzp7mbizdipfag0m17g3"))))))) | |
9265 | (inputs | |
9266 | `(("lz4" ,lz4) | |
9267 | ("htslib" ,htslib-for-sambamba))) | |
9268 | (home-page "http://lomereiter.github.io/sambamba") | |
9269 | (synopsis "Tools for working with SAM/BAM data") | |
9270 | (description "Sambamba is a high performance modern robust and | |
9271 | fast tool (and library), written in the D programming language, for | |
9272 | working with SAM and BAM files. Current parallelised functionality is | |
9273 | an important subset of samtools functionality, including view, index, | |
9274 | sort, markdup, and depth.") | |
9275 | (license license:gpl2+))) | |
b8fffd3a RW |
9276 | |
9277 | (define-public ritornello | |
9278 | (package | |
9279 | (name "ritornello") | |
9280 | (version "1.0.0") | |
9281 | (source (origin | |
9282 | (method url-fetch) | |
9283 | (uri (string-append "https://github.com/KlugerLab/" | |
9284 | "Ritornello/archive/v" | |
9285 | version ".tar.gz")) | |
9286 | (file-name (string-append name "-" version ".tar.gz")) | |
9287 | (sha256 | |
9288 | (base32 | |
9289 | "02nik86gq9ljjriv6pamwlmqnfky3ads1fpklx6mc3hx6k40pg38")))) | |
9290 | (build-system gnu-build-system) | |
9291 | (arguments | |
9292 | `(#:tests? #f ; there are no tests | |
9293 | #:phases | |
9294 | (modify-phases %standard-phases | |
9295 | (add-after 'unpack 'patch-samtools-references | |
9296 | (lambda* (#:key inputs #:allow-other-keys) | |
9297 | (substitute* '("src/SamStream.h" | |
9298 | "src/BufferedGenomeReader.h") | |
9299 | (("<sam.h>") "<samtools/sam.h>")) | |
9300 | #t)) | |
9301 | (delete 'configure) | |
9302 | (replace 'install | |
9303 | (lambda* (#:key inputs outputs #:allow-other-keys) | |
9304 | (let* ((out (assoc-ref outputs "out")) | |
9305 | (bin (string-append out "/bin/"))) | |
9306 | (mkdir-p bin) | |
9307 | (install-file "bin/Ritornello" bin) | |
9308 | #t)))))) | |
9309 | (inputs | |
9310 | `(("samtools" ,samtools-0.1) | |
9311 | ("fftw" ,fftw) | |
9312 | ("boost" ,boost) | |
9313 | ("zlib" ,zlib))) | |
9314 | (home-page "https://github.com/KlugerLab/Ritornello") | |
9315 | (synopsis "Control-free peak caller for ChIP-seq data") | |
9316 | (description "Ritornello is a ChIP-seq peak calling algorithm based on | |
9317 | signal processing that can accurately call binding events without the need to | |
9318 | do a pair total DNA input or IgG control sample. It has been tested for use | |
9319 | with narrow binding events such as transcription factor ChIP-seq.") | |
9320 | (license license:gpl3+))) | |
44f6c889 RW |
9321 | |
9322 | (define-public trim-galore | |
9323 | (package | |
9324 | (name "trim-galore") | |
9325 | (version "0.4.2") | |
9326 | (source | |
9327 | (origin | |
9328 | (method url-fetch) | |
9329 | (uri (string-append "http://www.bioinformatics.babraham.ac.uk/" | |
9330 | "projects/trim_galore/trim_galore_v" | |
9331 | version ".zip")) | |
9332 | (sha256 | |
9333 | (base32 | |
9334 | "0b9qdxi4521gsrjvbhgky8g7kry9b5nx3byzaxkgxz7p4k8bn1mn")))) | |
9335 | (build-system gnu-build-system) | |
9336 | (arguments | |
9337 | `(#:tests? #f ; no tests | |
9338 | #:phases | |
9339 | (modify-phases %standard-phases | |
9340 | ;; The archive contains plain files. | |
9341 | (replace 'unpack | |
9342 | (lambda* (#:key source #:allow-other-keys) | |
9343 | (zero? (system* "unzip" source)))) | |
9344 | (delete 'configure) | |
9345 | (delete 'build) | |
9346 | (add-after 'unpack 'hardcode-tool-references | |
9347 | (lambda* (#:key inputs #:allow-other-keys) | |
9348 | (substitute* "trim_galore" | |
9349 | (("\\$path_to_cutadapt = 'cutadapt'") | |
9350 | (string-append "$path_to_cutadapt = '" | |
9351 | (assoc-ref inputs "cutadapt") | |
9352 | "/bin/cutadapt'")) | |
9353 | (("\\| gzip") | |
9354 | (string-append "| " | |
9355 | (assoc-ref inputs "gzip") | |
9356 | "/bin/gzip")) | |
9357 | (("\"gunzip") | |
9358 | (string-append "\"" | |
9359 | (assoc-ref inputs "gzip") | |
9360 | "/bin/gunzip"))) | |
9361 | #t)) | |
9362 | (replace 'install | |
9363 | (lambda* (#:key outputs #:allow-other-keys) | |
9364 | (let ((bin (string-append (assoc-ref outputs "out") | |
9365 | "/bin"))) | |
9366 | (mkdir-p bin) | |
9367 | (install-file "trim_galore" bin) | |
9368 | #t)))))) | |
9369 | (inputs | |
9370 | `(("gzip" ,gzip) | |
9371 | ("perl" ,perl) | |
9372 | ("cutadapt" ,cutadapt))) | |
9373 | (native-inputs | |
9374 | `(("unzip" ,unzip))) | |
9375 | (home-page "http://www.bioinformatics.babraham.ac.uk/projects/trim_galore/") | |
9376 | (synopsis "Wrapper around Cutadapt and FastQC") | |
9377 | (description "Trim Galore! is a wrapper script to automate quality and | |
9378 | adapter trimming as well as quality control, with some added functionality to | |
9379 | remove biased methylation positions for RRBS sequence files.") | |
9380 | (license license:gpl3+))) | |
3420c905 RW |
9381 | |
9382 | (define-public gess | |
9383 | (package | |
9384 | (name "gess") | |
9385 | (version "1.0") | |
9386 | (source (origin | |
9387 | (method url-fetch) | |
9388 | (uri (string-append "http://compbio.uthscsa.edu/" | |
9389 | "GESS_Web/files/" | |
9390 | "gess-" version ".src.tar.gz")) | |
9391 | (sha256 | |
9392 | (base32 | |
9393 | "0hyk403kxscclzfs24pvdgiv0wm03kjcziqdrp5w46cb049gz0d7")))) | |
9394 | (build-system gnu-build-system) | |
9395 | (arguments | |
9396 | `(#:tests? #f ; no tests | |
9397 | #:phases | |
9398 | (modify-phases %standard-phases | |
9399 | (delete 'configure) | |
9400 | (delete 'build) | |
9401 | (replace 'install | |
9402 | (lambda* (#:key inputs outputs #:allow-other-keys) | |
9403 | (let* ((python (assoc-ref inputs "python")) | |
9404 | (out (assoc-ref outputs "out")) | |
9405 | (bin (string-append out "/bin/")) | |
9406 | (target (string-append | |
9407 | out "/lib/python2.7/site-packages/gess/"))) | |
9408 | (mkdir-p target) | |
9409 | (copy-recursively "." target) | |
9410 | ;; Make GESS.py executable | |
9411 | (chmod (string-append target "GESS.py") #o555) | |
9412 | ;; Add Python shebang to the top and make Matplotlib | |
9413 | ;; usable. | |
9414 | (substitute* (string-append target "GESS.py") | |
9415 | (("\"\"\"Description:" line) | |
9416 | (string-append "#!" (which "python") " | |
9417 | import matplotlib | |
9418 | matplotlib.use('Agg') | |
9419 | " line))) | |
9420 | ;; Make sure GESS has all modules in its path | |
9421 | (wrap-program (string-append target "GESS.py") | |
9422 | `("PYTHONPATH" ":" prefix (,target ,(getenv "PYTHONPATH")))) | |
9423 | (mkdir-p bin) | |
9424 | (symlink (string-append target "GESS.py") | |
9425 | (string-append bin "GESS.py")) | |
9426 | #t)))))) | |
9427 | (inputs | |
9428 | `(("python" ,python-2) | |
9429 | ("python2-pysam" ,python2-pysam) | |
9430 | ("python2-scipy" ,python2-scipy) | |
9431 | ("python2-numpy" ,python2-numpy) | |
9432 | ("python2-networkx" ,python2-networkx) | |
9433 | ("python2-biopython" ,python2-biopython))) | |
9434 | (home-page "http://compbio.uthscsa.edu/GESS_Web/") | |
9435 | (synopsis "Detect exon-skipping events from raw RNA-seq data") | |
9436 | (description | |
9437 | "GESS is an implementation of a novel computational method to detect de | |
9438 | novo exon-skipping events directly from raw RNA-seq data without the prior | |
9439 | knowledge of gene annotation information. GESS stands for the graph-based | |
9440 | exon-skipping scanner detection scheme.") | |
9441 | (license license:bsd-3))) | |
282b0151 RW |
9442 | |
9443 | (define-public phylip | |
9444 | (package | |
9445 | (name "phylip") | |
9446 | (version "3.696") | |
9447 | (source | |
9448 | (origin | |
9449 | (method url-fetch) | |
9450 | (uri (string-append "http://evolution.gs.washington.edu/phylip/" | |
9451 | "download/phylip-" version ".tar.gz")) | |
9452 | (sha256 | |
9453 | (base32 | |
9454 | "01jar1rayhr2gba2pgbw49m56rc5z4p5wn3ds0m188hrlln4a2nd")))) | |
9455 | (build-system gnu-build-system) | |
9456 | (arguments | |
9457 | `(#:tests? #f ; no check target | |
9458 | #:make-flags (list "-f" "Makefile.unx" "install") | |
9459 | #:parallel-build? #f ; not supported | |
9460 | #:phases | |
9461 | (modify-phases %standard-phases | |
9462 | (add-after 'unpack 'enter-dir | |
9463 | (lambda _ (chdir "src") #t)) | |
9464 | (delete 'configure) | |
9465 | (replace 'install | |
9466 | (lambda* (#:key inputs outputs #:allow-other-keys) | |
9467 | (let ((target (string-append (assoc-ref outputs "out") | |
9468 | "/bin"))) | |
9469 | (mkdir-p target) | |
9470 | (for-each (lambda (file) | |
9471 | (install-file file target)) | |
9472 | (find-files "../exe" ".*"))) | |
9473 | #t))))) | |
9474 | (home-page "http://evolution.genetics.washington.edu/phylip/") | |
9475 | (synopsis "Tools for inferring phylogenies") | |
9476 | (description "PHYLIP (the PHYLogeny Inference Package) is a package of | |
9477 | programs for inferring phylogenies (evolutionary trees).") | |
9478 | (license license:bsd-2))) | |
aa163424 RW |
9479 | |
9480 | (define-public imp | |
9481 | (package | |
9482 | (name "imp") | |
9483 | (version "2.6.2") | |
9484 | (source | |
9485 | (origin | |
9486 | (method url-fetch) | |
9487 | (uri (string-append "https://integrativemodeling.org/" | |
9488 | version "/download/imp-" version ".tar.gz")) | |
9489 | (sha256 | |
9490 | (base32 | |
9491 | "0lxqx7vh79d771svr611dkilp6sn30qrbw8zvscbrm37v38d2j6h")))) | |
9492 | (build-system cmake-build-system) | |
9493 | (arguments | |
9494 | `(;; FIXME: Some tests fail because they produce warnings, others fail | |
9495 | ;; because the PYTHONPATH does not include the modeller's directory. | |
9496 | #:tests? #f | |
9497 | ;; Do not place libraries in an architecture-specific directory. | |
9498 | #:configure-flags | |
9499 | (list "-DCMAKE_INSTALL_LIBDIR=lib"))) | |
9500 | (inputs | |
9501 | `(("boost" ,boost) | |
9502 | ("gsl" ,gsl) | |
9503 | ("swig" ,swig) | |
9504 | ("hdf5" ,hdf5) | |
9505 | ("fftw" ,fftw) | |
9506 | ("python" ,python-2))) | |
9507 | (propagated-inputs | |
9508 | `(("python2-numpy" ,python2-numpy) | |
9509 | ("python2-scipy" ,python2-scipy) | |
9510 | ("python2-pandas" ,python2-pandas) | |
9511 | ("python2-scikit-learn" ,python2-scikit-learn) | |
9512 | ("python2-networkx" ,python2-networkx))) | |
9513 | (home-page "https://integrativemodeling.org") | |
9514 | (synopsis "Integrative modeling platform") | |
9515 | (description "IMP's broad goal is to contribute to a comprehensive | |
9516 | structural characterization of biomolecules ranging in size and complexity | |
9517 | from small peptides to large macromolecular assemblies, by integrating data | |
9518 | from diverse biochemical and biophysical experiments. IMP provides a C++ and | |
9519 | Python toolbox for solving complex modeling problems, and a number of | |
9520 | applications for tackling some common problems in a user-friendly way.") | |
9521 | ;; IMP is largely available under the GNU Lesser GPL; see the file | |
9522 | ;; COPYING.LGPL for the full text of this license. Some IMP modules are | |
9523 | ;; available under the GNU GPL (see the file COPYING.GPL). | |
9524 | (license (list license:lgpl2.1+ | |
9525 | license:gpl3+)))) | |
8befd094 RW |
9526 | |
9527 | (define-public tadbit | |
9528 | (package | |
9529 | (name "tadbit") | |
9530 | (version "0.2") | |
9531 | (source (origin | |
9532 | (method url-fetch) | |
9533 | (uri (string-append "https://github.com/3DGenomes/TADbit/" | |
9534 | "archive/v" version ".tar.gz")) | |
9535 | (file-name (string-append name "-" version ".tar.gz")) | |
9536 | (sha256 | |
9537 | (base32 | |
9538 | "1cnfqrl4685zar4nnw94j94nhvl2h29jm448nadqi1h05z6fdk4f")))) | |
9539 | (build-system python-build-system) | |
9540 | (arguments | |
9541 | `(;; Tests are included and must be run after installation, but | |
9542 | ;; they are incomplete and thus cannot be run. | |
9543 | #:tests? #f | |
9544 | #:python ,python-2 | |
9545 | #:phases | |
9546 | (modify-phases %standard-phases | |
9547 | (add-after 'unpack 'fix-problems-with-setup.py | |
9548 | (lambda* (#:key outputs #:allow-other-keys) | |
9549 | ;; setup.py opens these files for writing | |
9550 | (chmod "_pytadbit/_version.py" #o664) | |
9551 | (chmod "README.rst" #o664) | |
9552 | ||
9553 | ;; Don't attempt to install the bash completions to | |
9554 | ;; the home directory. | |
9555 | (rename-file "extras/.bash_completion" | |
9556 | "extras/tadbit") | |
9557 | (substitute* "setup.py" | |
9558 | (("\\(path.expanduser\\('~'\\)") | |
9559 | (string-append "(\"" | |
9560 | (assoc-ref outputs "out") | |
9561 | "/etc/bash_completion.d\"")) | |
9562 | (("extras/\\.bash_completion") | |
9563 | "extras/tadbit")) | |
9564 | #t))))) | |
9565 | (inputs | |
9566 | ;; TODO: add Chimera for visualization | |
9567 | `(("imp" ,imp) | |
9568 | ("mcl" ,mcl) | |
9569 | ("python2-scipy" ,python2-scipy) | |
9570 | ("python2-numpy" ,python2-numpy) | |
9571 | ("python2-matplotlib" ,python2-matplotlib) | |
9572 | ("python2-pysam" ,python2-pysam))) | |
9573 | (home-page "http://3dgenomes.github.io/TADbit/") | |
9574 | (synopsis "Analyze, model, and explore 3C-based data") | |
9575 | (description | |
9576 | "TADbit is a complete Python library to deal with all steps to analyze, | |
9577 | model, and explore 3C-based data. With TADbit the user can map FASTQ files to | |
9578 | obtain raw interaction binned matrices (Hi-C like matrices), normalize and | |
a147fadd | 9579 | correct interaction matrices, identify and compare the so-called |
8befd094 RW |
9580 | @dfn{Topologically Associating Domains} (TADs), build 3D models from the |
9581 | interaction matrices, and finally, extract structural properties from the | |
9582 | models. TADbit is complemented by TADkit for visualizing 3D models.") | |
9583 | (license license:gpl3+))) | |
94820951 RW |
9584 | |
9585 | (define-public kentutils | |
9586 | (package | |
9587 | (name "kentutils") | |
9588 | ;; 302.1.0 is out, but the only difference is the inclusion of | |
9589 | ;; pre-built binaries. | |
9590 | (version "302.0.0") | |
9591 | (source | |
9592 | (origin | |
9593 | (method url-fetch) | |
9594 | (uri (string-append "https://github.com/ENCODE-DCC/kentUtils/" | |
9595 | "archive/v" version ".tar.gz")) | |
9596 | (file-name (string-append name "-" version ".tar.gz")) | |
9597 | (sha256 | |
9598 | (base32 | |
9599 | "134aja3k1cj32kbk1nnw0q9gxjb2krr15q6sga8qldzvc0585rmm")) | |
9600 | (modules '((guix build utils) | |
9601 | (srfi srfi-26) | |
9602 | (ice-9 ftw))) | |
9603 | (snippet | |
9604 | '(begin | |
9605 | ;; Only the contents of the specified directories are free | |
9606 | ;; for all uses, so we remove the rest. "hg/autoSql" and | |
9607 | ;; "hg/autoXml" are nominally free, but they depend on a | |
9608 | ;; library that is built from the sources in "hg/lib", | |
9609 | ;; which is nonfree. | |
9610 | (let ((free (list "." ".." | |
9611 | "utils" "lib" "inc" "tagStorm" | |
9612 | "parasol" "htslib")) | |
9613 | (directory? (lambda (file) | |
9614 | (eq? 'directory (stat:type (stat file)))))) | |
9615 | (for-each (lambda (file) | |
9616 | (and (directory? file) | |
9617 | (delete-file-recursively file))) | |
9618 | (map (cut string-append "src/" <>) | |
9619 | (scandir "src" | |
9620 | (lambda (file) | |
9621 | (not (member file free))))))) | |
9622 | ;; Only make the utils target, not the userApps target, | |
9623 | ;; because that requires libraries we won't build. | |
9624 | (substitute* "Makefile" | |
9625 | ((" userApps") " utils")) | |
9626 | ;; Only build libraries that are free. | |
9627 | (substitute* "src/makefile" | |
9628 | (("DIRS =.*") "DIRS =\n") | |
9629 | (("cd jkOwnLib.*") "") | |
9630 | ((" hgLib") "") | |
9631 | (("cd hg.*") "")) | |
9632 | (substitute* "src/utils/makefile" | |
9633 | ;; These tools depend on "jkhgap.a", which is part of the | |
9634 | ;; nonfree "src/hg/lib" directory. | |
9635 | (("raSqlQuery") "") | |
9636 | (("pslLiftSubrangeBlat") "") | |
9637 | ||
9638 | ;; Do not build UCSC tools, which may require nonfree | |
9639 | ;; components. | |
9640 | (("ALL_APPS =.*") "ALL_APPS = $(UTILS_APPLIST)\n")) | |
9641 | #t)))) | |
9642 | (build-system gnu-build-system) | |
9643 | (arguments | |
9644 | `( ;; There is no global test target and the test target for | |
9645 | ;; individual tools depends on input files that are not | |
9646 | ;; included. | |
9647 | #:tests? #f | |
9648 | #:phases | |
9649 | (modify-phases %standard-phases | |
9650 | (add-after 'unpack 'fix-paths | |
9651 | (lambda _ | |
9652 | (substitute* "Makefile" | |
9653 | (("/bin/echo") (which "echo"))) | |
9654 | #t)) | |
9655 | (add-after 'unpack 'prepare-samtabix | |
9656 | (lambda* (#:key inputs #:allow-other-keys) | |
9657 | (copy-recursively (assoc-ref inputs "samtabix") | |
9658 | "samtabix") | |
9659 | #t)) | |
9660 | (delete 'configure) | |
9661 | (replace 'install | |
9662 | (lambda* (#:key outputs #:allow-other-keys) | |
9663 | (let ((bin (string-append (assoc-ref outputs "out") | |
9664 | "/bin"))) | |
9665 | (copy-recursively "bin" bin)) | |
9666 | #t))))) | |
9667 | (native-inputs | |
9668 | `(("samtabix" | |
9669 | ,(origin | |
9670 | (method git-fetch) | |
9671 | (uri (git-reference | |
9672 | (url "http://genome-source.cse.ucsc.edu/samtabix.git") | |
9673 | (commit "10fd107909c1ac4d679299908be4262a012965ba"))) | |
9674 | (sha256 | |
9675 | (base32 | |
9676 | "0c1nj64l42v395sa84n7az43xiap4i6f9n9dfz4058aqiwkhkmma")))))) | |
9677 | (inputs | |
9678 | `(("zlib" ,zlib) | |
9679 | ("tcsh" ,tcsh) | |
9680 | ("perl" ,perl) | |
9681 | ("libpng" ,libpng) | |
9682 | ("mysql" ,mysql) | |
9683 | ("openssl" ,openssl))) | |
9684 | (home-page "http://genome.cse.ucsc.edu/index.html") | |
9685 | (synopsis "Assorted bioinformatics utilities") | |
9686 | (description "This package provides the kentUtils, a selection of | |
9687 | bioinformatics utilities used in combination with the UCSC genome | |
9688 | browser.") | |
9689 | ;; Only a subset of the sources are released under a non-copyleft | |
9690 | ;; free software license. All other sources are removed in a | |
9691 | ;; snippet. See this bug report for an explanation of how the | |
9692 | ;; license statements apply: | |
9693 | ;; https://github.com/ENCODE-DCC/kentUtils/issues/12 | |
9694 | (license (license:non-copyleft | |
9695 | "http://genome.ucsc.edu/license/" | |
9696 | "The contents of this package are free for all uses.")))) | |
7ceb0a83 RW |
9697 | |
9698 | (define-public f-seq | |
9699 | (let ((commit "6ccded34cff38cf432deed8503648b4a66953f9b") | |
9700 | (revision "1")) | |
9701 | (package | |
9702 | (name "f-seq") | |
9703 | (version (string-append "1.1-" revision "." commit)) | |
9704 | (source (origin | |
9705 | (method git-fetch) | |
9706 | (uri (git-reference | |
9707 | (url "https://github.com/aboyle/F-seq.git") | |
9708 | (commit commit))) | |
9709 | (file-name (string-append name "-" version)) | |
9710 | (sha256 | |
9711 | (base32 | |
9712 | "1nk33k0yajg2id4g59bc4szr58r2q6pdq42vgcw054m8ip9wv26h")) | |
9713 | (modules '((guix build utils))) | |
9714 | ;; Remove bundled Java library archives. | |
9715 | (snippet | |
9716 | '(begin | |
9717 | (for-each delete-file (find-files "lib" ".*")) | |
9718 | #t)))) | |
9719 | (build-system ant-build-system) | |
9720 | (arguments | |
9721 | `(#:tests? #f ; no tests included | |
9722 | #:phases | |
9723 | (modify-phases %standard-phases | |
9724 | (replace 'install | |
9725 | (lambda* (#:key outputs #:allow-other-keys) | |
9726 | (let* ((target (assoc-ref outputs "out")) | |
9727 | (doc (string-append target "/share/doc/f-seq/"))) | |
9728 | (mkdir-p target) | |
9729 | (mkdir-p doc) | |
9730 | (substitute* "bin/linux/fseq" | |
9731 | (("java") (which "java"))) | |
9732 | (install-file "README.txt" doc) | |
9733 | (install-file "bin/linux/fseq" (string-append target "/bin")) | |
9734 | (install-file "build~/fseq.jar" (string-append target "/lib")) | |
9735 | (copy-recursively "lib" (string-append target "/lib")) | |
9736 | #t)))))) | |
9737 | (inputs | |
9738 | `(("perl" ,perl) | |
9739 | ("java-commons-cli" ,java-commons-cli))) | |
9740 | (home-page "http://fureylab.web.unc.edu/software/fseq/") | |
9741 | (synopsis "Feature density estimator for high-throughput sequence tags") | |
9742 | (description | |
9743 | "F-Seq is a software package that generates a continuous tag sequence | |
9744 | density estimation allowing identification of biologically meaningful sites | |
9745 | such as transcription factor binding sites (ChIP-seq) or regions of open | |
9746 | chromatin (DNase-seq). Output can be displayed directly in the UCSC Genome | |
9747 | Browser.") | |
9748 | (license license:gpl3+)))) |