Commit | Line | Data |
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4e10a221 | 1 | ;;; GNU Guix --- Functional package management for GNU |
c3b2ab9d | 2 | ;;; Copyright © 2014, 2015, 2016, 2017, 2018 Ricardo Wurmus <rekado@elephly.net> |
7502badb | 3 | ;;; Copyright © 2015, 2016, 2017, 2018 Ben Woodcroft <donttrustben@gmail.com> |
8921841d | 4 | ;;; Copyright © 2015, 2016 Pjotr Prins <pjotr.guix@thebird.nl> |
a5002ae7 | 5 | ;;; Copyright © 2015 Andreas Enge <andreas@enge.fr> |
a0a71439 | 6 | ;;; Copyright © 2016 Roel Janssen <roel@gnu.org> |
3df57b3a | 7 | ;;; Copyright © 2016, 2017, 2018 Efraim Flashner <efraim@flashner.co.il> |
318c0aee | 8 | ;;; Copyright © 2016 Marius Bakke <mbakke@fastmail.com> |
658ab21d | 9 | ;;; Copyright © 2016, 2018 Raoul Bonnal <ilpuccio.febo@gmail.com> |
ddf38ece | 10 | ;;; Copyright © 2017, 2018 Tobias Geerinckx-Rice <me@tobias.gr> |
9364a520 | 11 | ;;; Copyright © 2017 Arun Isaac <arunisaac@systemreboot.net> |
32cbbac1 | 12 | ;;; Copyright © 2018 Joshua Sierles, Nextjournal <joshua@nextjournal.com> |
4e10a221 RW |
13 | ;;; |
14 | ;;; This file is part of GNU Guix. | |
15 | ;;; | |
16 | ;;; GNU Guix is free software; you can redistribute it and/or modify it | |
17 | ;;; under the terms of the GNU General Public License as published by | |
18 | ;;; the Free Software Foundation; either version 3 of the License, or (at | |
19 | ;;; your option) any later version. | |
20 | ;;; | |
21 | ;;; GNU Guix is distributed in the hope that it will be useful, but | |
22 | ;;; WITHOUT ANY WARRANTY; without even the implied warranty of | |
23 | ;;; MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the | |
24 | ;;; GNU General Public License for more details. | |
25 | ;;; | |
26 | ;;; You should have received a copy of the GNU General Public License | |
27 | ;;; along with GNU Guix. If not, see <http://www.gnu.org/licenses/>. | |
28 | ||
29 | (define-module (gnu packages bioinformatics) | |
30 | #:use-module ((guix licenses) #:prefix license:) | |
31 | #:use-module (guix packages) | |
8e913213 | 32 | #:use-module (guix utils) |
4e10a221 | 33 | #:use-module (guix download) |
2c16316e | 34 | #:use-module (guix git-download) |
ec946638 | 35 | #:use-module (guix hg-download) |
10b4a969 | 36 | #:use-module (guix build-system ant) |
4e10a221 | 37 | #:use-module (guix build-system gnu) |
d7678942 | 38 | #:use-module (guix build-system cmake) |
c033f5d6 | 39 | #:use-module (guix build-system ocaml) |
365c8153 | 40 | #:use-module (guix build-system perl) |
8622a072 | 41 | #:use-module (guix build-system python) |
a5002ae7 | 42 | #:use-module (guix build-system r) |
9c38b540 | 43 | #:use-module (guix build-system ruby) |
9364a520 | 44 | #:use-module (guix build-system scons) |
d3517eda | 45 | #:use-module (guix build-system trivial) |
4e10a221 | 46 | #:use-module (gnu packages) |
a2950fa4 | 47 | #:use-module (gnu packages autotools) |
684bf7c7 | 48 | #:use-module (gnu packages algebra) |
d3517eda | 49 | #:use-module (gnu packages base) |
318c0aee | 50 | #:use-module (gnu packages bash) |
a0a71439 | 51 | #:use-module (gnu packages bison) |
e4e5a4d8 | 52 | #:use-module (gnu packages boost) |
ac257f12 | 53 | #:use-module (gnu packages check) |
4e10a221 | 54 | #:use-module (gnu packages compression) |
82c370de | 55 | #:use-module (gnu packages cpio) |
7cb61550 | 56 | #:use-module (gnu packages cran) |
1baee943 | 57 | #:use-module (gnu packages curl) |
99828fa7 | 58 | #:use-module (gnu packages documentation) |
94820951 | 59 | #:use-module (gnu packages databases) |
d29150b5 | 60 | #:use-module (gnu packages datastructures) |
75dd2424 | 61 | #:use-module (gnu packages file) |
99268755 | 62 | #:use-module (gnu packages flex) |
02f35bb5 | 63 | #:use-module (gnu packages gawk) |
2409f37f | 64 | #:use-module (gnu packages gcc) |
66e40e00 | 65 | #:use-module (gnu packages gd) |
97b9da68 | 66 | #:use-module (gnu packages gtk) |
b16728b0 | 67 | #:use-module (gnu packages glib) |
18f5d2a7 | 68 | #:use-module (gnu packages graph) |
db7a3444 | 69 | #:use-module (gnu packages groff) |
50937297 | 70 | #:use-module (gnu packages guile) |
89984be4 | 71 | #:use-module (gnu packages haskell) |
66e40e00 | 72 | #:use-module (gnu packages image) |
97b9da68 | 73 | #:use-module (gnu packages imagemagick) |
15a3c3d4 | 74 | #:use-module (gnu packages java) |
8d77a085 | 75 | #:use-module (gnu packages jemalloc) |
5ded35d8 | 76 | #:use-module (gnu packages ldc) |
51c64999 | 77 | #:use-module (gnu packages linux) |
ec946638 | 78 | #:use-module (gnu packages logging) |
36742f43 | 79 | #:use-module (gnu packages machine-learning) |
db7a3444 | 80 | #:use-module (gnu packages man) |
c833ab55 | 81 | #:use-module (gnu packages maths) |
6c2b26e2 | 82 | #:use-module (gnu packages mpi) |
4e10a221 | 83 | #:use-module (gnu packages ncurses) |
c033f5d6 | 84 | #:use-module (gnu packages ocaml) |
81f3e0c1 | 85 | #:use-module (gnu packages pcre) |
ceb62d54 | 86 | #:use-module (gnu packages parallel) |
66e40e00 | 87 | #:use-module (gnu packages pdf) |
4e10a221 | 88 | #:use-module (gnu packages perl) |
5ccde207 | 89 | #:use-module (gnu packages perl-check) |
4e10a221 | 90 | #:use-module (gnu packages pkg-config) |
bfe3c685 | 91 | #:use-module (gnu packages popt) |
e4e5a4d8 | 92 | #:use-module (gnu packages protobuf) |
346a829a | 93 | #:use-module (gnu packages python) |
589e3f4e | 94 | #:use-module (gnu packages python-web) |
ec946638 | 95 | #:use-module (gnu packages readline) |
9c38b540 | 96 | #:use-module (gnu packages ruby) |
84be3b99 | 97 | #:use-module (gnu packages serialization) |
94820951 | 98 | #:use-module (gnu packages shells) |
c833ab55 | 99 | #:use-module (gnu packages statistics) |
aa163424 | 100 | #:use-module (gnu packages swig) |
d7678942 | 101 | #:use-module (gnu packages tbb) |
97b9da68 | 102 | #:use-module (gnu packages tex) |
db7a3444 | 103 | #:use-module (gnu packages texinfo) |
2127cedb | 104 | #:use-module (gnu packages textutils) |
43c565d2 | 105 | #:use-module (gnu packages time) |
a2950fa4 | 106 | #:use-module (gnu packages tls) |
ce7155d5 | 107 | #:use-module (gnu packages vim) |
365c8153 | 108 | #:use-module (gnu packages web) |
c833ab55 | 109 | #:use-module (gnu packages xml) |
66e40e00 | 110 | #:use-module (gnu packages xorg) |
2c9232ae | 111 | #:use-module (srfi srfi-1) |
ce7e361f | 112 | #:use-module (ice-9 match)) |
4e10a221 | 113 | |
8dc797fa BW |
114 | (define-public aragorn |
115 | (package | |
116 | (name "aragorn") | |
e990c81d | 117 | (version "1.2.38") |
8dc797fa BW |
118 | (source (origin |
119 | (method url-fetch) | |
120 | (uri (string-append | |
121 | "http://mbio-serv2.mbioekol.lu.se/ARAGORN/Downloads/aragorn" | |
122 | version ".tgz")) | |
123 | (sha256 | |
124 | (base32 | |
e990c81d | 125 | "09i1rg716smlbnixfm7q1ml2mfpaa2fpn3hwjg625ysmfwwy712b")))) |
8dc797fa BW |
126 | (build-system gnu-build-system) |
127 | (arguments | |
128 | `(#:tests? #f ; there are no tests | |
129 | #:phases | |
130 | (modify-phases %standard-phases | |
131 | (delete 'configure) | |
132 | (replace 'build | |
133 | (lambda _ | |
134 | (zero? (system* "gcc" | |
135 | "-O3" | |
136 | "-ffast-math" | |
137 | "-finline-functions" | |
138 | "-o" | |
139 | "aragorn" | |
140 | (string-append "aragorn" ,version ".c"))))) | |
141 | (replace 'install | |
142 | (lambda* (#:key outputs #:allow-other-keys) | |
143 | (let* ((out (assoc-ref outputs "out")) | |
144 | (bin (string-append out "/bin")) | |
145 | (man (string-append out "/share/man/man1"))) | |
146 | (mkdir-p bin) | |
f3860753 | 147 | (install-file "aragorn" bin) |
8dc797fa | 148 | (mkdir-p man) |
f3860753 | 149 | (install-file "aragorn.1" man)) |
8dc797fa BW |
150 | #t))))) |
151 | (home-page "http://mbio-serv2.mbioekol.lu.se/ARAGORN") | |
152 | (synopsis "Detect tRNA, mtRNA and tmRNA genes in nucleotide sequences") | |
153 | (description | |
154 | "Aragorn identifies transfer RNA, mitochondrial RNA and | |
155 | transfer-messenger RNA from nucleotide sequences, based on homology to known | |
156 | tRNA consensus sequences and RNA structure. It also outputs the secondary | |
157 | structure of the predicted RNA.") | |
158 | (license license:gpl2))) | |
159 | ||
a12ba6e8 BW |
160 | (define-public bamm |
161 | (package | |
162 | (name "bamm") | |
4b6da268 | 163 | (version "1.7.3") |
a12ba6e8 BW |
164 | (source (origin |
165 | (method url-fetch) | |
166 | ;; BamM is not available on pypi. | |
167 | (uri (string-append | |
4b6da268 | 168 | "https://github.com/Ecogenomics/BamM/archive/" |
a12ba6e8 BW |
169 | version ".tar.gz")) |
170 | (file-name (string-append name "-" version ".tar.gz")) | |
171 | (sha256 | |
172 | (base32 | |
4b6da268 | 173 | "1f35yxp4pc8aadsvbpg6r4kg2jh4fkjci0iby4iyljm6980sac0s")) |
a12ba6e8 BW |
174 | (modules '((guix build utils))) |
175 | (snippet | |
176 | `(begin | |
177 | ;; Delete bundled htslib. | |
178 | (delete-file-recursively "c/htslib-1.3.1") | |
179 | #t)))) | |
180 | (build-system python-build-system) | |
181 | (arguments | |
182 | `(#:python ,python-2 ; BamM is Python 2 only. | |
183 | ;; Do not use bundled libhts. Do use the bundled libcfu because it has | |
184 | ;; been modified from its original form. | |
185 | #:configure-flags | |
186 | (let ((htslib (assoc-ref %build-inputs "htslib"))) | |
187 | (list "--with-libhts-lib" (string-append htslib "/lib") | |
188 | "--with-libhts-inc" (string-append htslib "/include/htslib"))) | |
189 | #:phases | |
190 | (modify-phases %standard-phases | |
191 | (add-after 'unpack 'autogen | |
192 | (lambda _ | |
193 | (with-directory-excursion "c" | |
194 | (let ((sh (which "sh"))) | |
195 | ;; Use autogen so that 'configure' works. | |
196 | (substitute* "autogen.sh" (("/bin/sh") sh)) | |
197 | (setenv "CONFIG_SHELL" sh) | |
198 | (substitute* "configure" (("/bin/sh") sh)) | |
199 | (zero? (system* "./autogen.sh")))))) | |
200 | (delete 'build) | |
201 | ;; Run tests after installation so compilation only happens once. | |
202 | (delete 'check) | |
203 | (add-after 'install 'wrap-executable | |
204 | (lambda* (#:key outputs #:allow-other-keys) | |
205 | (let* ((out (assoc-ref outputs "out")) | |
206 | (path (getenv "PATH"))) | |
207 | (wrap-program (string-append out "/bin/bamm") | |
208 | `("PATH" ":" prefix (,path)))) | |
209 | #t)) | |
210 | (add-after 'wrap-executable 'post-install-check | |
211 | (lambda* (#:key inputs outputs #:allow-other-keys) | |
212 | (setenv "PATH" | |
213 | (string-append (assoc-ref outputs "out") | |
214 | "/bin:" | |
215 | (getenv "PATH"))) | |
216 | (setenv "PYTHONPATH" | |
217 | (string-append | |
218 | (assoc-ref outputs "out") | |
219 | "/lib/python" | |
220 | (string-take (string-take-right | |
221 | (assoc-ref inputs "python") 5) 3) | |
222 | "/site-packages:" | |
223 | (getenv "PYTHONPATH"))) | |
224 | ;; There are 2 errors printed, but they are safe to ignore: | |
225 | ;; 1) [E::hts_open_format] fail to open file ... | |
226 | ;; 2) samtools view: failed to open ... | |
227 | (zero? (system* "nosetests"))))))) | |
228 | (native-inputs | |
229 | `(("autoconf" ,autoconf) | |
230 | ("automake" ,automake) | |
231 | ("libtool" ,libtool) | |
232 | ("zlib" ,zlib) | |
233 | ("python-nose" ,python2-nose) | |
f3b98f4f | 234 | ("python-pysam" ,python2-pysam))) |
a12ba6e8 | 235 | (inputs |
bca2c576 | 236 | `(("htslib" ,htslib-1.3) ; At least one test fails on htslib-1.4+. |
a12ba6e8 BW |
237 | ("samtools" ,samtools) |
238 | ("bwa" ,bwa) | |
239 | ("grep" ,grep) | |
240 | ("sed" ,sed) | |
241 | ("coreutils" ,coreutils))) | |
242 | (propagated-inputs | |
243 | `(("python-numpy" ,python2-numpy))) | |
244 | (home-page "http://ecogenomics.github.io/BamM/") | |
245 | (synopsis "Metagenomics-focused BAM file manipulator") | |
246 | (description | |
247 | "BamM is a C library, wrapped in python, to efficiently generate and | |
248 | parse BAM files, specifically for the analysis of metagenomic data. For | |
249 | instance, it implements several methods to assess contig-wise read coverage.") | |
250 | (license license:lgpl3+))) | |
251 | ||
9794180d RW |
252 | (define-public bamtools |
253 | (package | |
254 | (name "bamtools") | |
48d66a9c | 255 | (version "2.4.1") |
9794180d RW |
256 | (source (origin |
257 | (method url-fetch) | |
258 | (uri (string-append | |
259 | "https://github.com/pezmaster31/bamtools/archive/v" | |
260 | version ".tar.gz")) | |
261 | (file-name (string-append name "-" version ".tar.gz")) | |
262 | (sha256 | |
263 | (base32 | |
48d66a9c | 264 | "0jr024kcrhjb82cm69i7p5fcg5375zlc1h3qh2n1v368hcd0qflk")))) |
9794180d | 265 | (build-system cmake-build-system) |
4702cec2 RW |
266 | (arguments |
267 | `(#:tests? #f ;no "check" target | |
268 | #:phases | |
269 | (modify-phases %standard-phases | |
270 | (add-before | |
271 | 'configure 'set-ldflags | |
272 | (lambda* (#:key outputs #:allow-other-keys) | |
273 | (setenv "LDFLAGS" | |
274 | (string-append | |
275 | "-Wl,-rpath=" | |
276 | (assoc-ref outputs "out") "/lib/bamtools"))))))) | |
9794180d RW |
277 | (inputs `(("zlib" ,zlib))) |
278 | (home-page "https://github.com/pezmaster31/bamtools") | |
279 | (synopsis "C++ API and command-line toolkit for working with BAM data") | |
280 | (description | |
281 | "BamTools provides both a C++ API and a command-line toolkit for handling | |
282 | BAM files.") | |
283 | (license license:expat))) | |
284 | ||
bdc7be59 MB |
285 | (define-public bcftools |
286 | (package | |
287 | (name "bcftools") | |
0620387a | 288 | (version "1.5") |
bdc7be59 MB |
289 | (source (origin |
290 | (method url-fetch) | |
291 | (uri (string-append | |
292 | "https://github.com/samtools/bcftools/releases/download/" | |
293 | version "/bcftools-" version ".tar.bz2")) | |
294 | (sha256 | |
295 | (base32 | |
0620387a | 296 | "0093hkkvxmbwfaa7905s6185jymynvg42kq6sxv7fili11l5mxwz")) |
3837108e | 297 | (patches (search-patches "bcftools-regidx-unsigned-char.patch")) |
bdc7be59 MB |
298 | (modules '((guix build utils))) |
299 | (snippet | |
300 | ;; Delete bundled htslib. | |
0620387a | 301 | '(delete-file-recursively "htslib-1.5")))) |
bdc7be59 MB |
302 | (build-system gnu-build-system) |
303 | (arguments | |
304 | `(#:test-target "test" | |
0620387a | 305 | #:configure-flags (list "--with-htslib=system") |
bdc7be59 MB |
306 | #:make-flags |
307 | (list | |
308 | "USE_GPL=1" | |
0620387a | 309 | "LIBS=-lgsl -lgslcblas" |
bdc7be59 MB |
310 | (string-append "prefix=" (assoc-ref %outputs "out")) |
311 | (string-append "HTSDIR=" (assoc-ref %build-inputs "htslib") "/include") | |
98593f9f | 312 | (string-append "HTSLIB=" (assoc-ref %build-inputs "htslib") "/lib/libhts.so") |
bdc7be59 | 313 | (string-append "BGZIP=" (assoc-ref %build-inputs "htslib") "/bin/bgzip") |
98593f9f BW |
314 | (string-append "TABIX=" (assoc-ref %build-inputs "htslib") "/bin/tabix") |
315 | (string-append "PACKAGE_VERSION=" ,version)) | |
bdc7be59 MB |
316 | #:phases |
317 | (modify-phases %standard-phases | |
bdc7be59 MB |
318 | (add-before 'check 'patch-tests |
319 | (lambda _ | |
320 | (substitute* "test/test.pl" | |
321 | (("/bin/bash") (which "bash"))) | |
322 | #t))))) | |
323 | (native-inputs | |
324 | `(("htslib" ,htslib) | |
325 | ("perl" ,perl))) | |
326 | (inputs | |
327 | `(("gsl" ,gsl) | |
328 | ("zlib" ,zlib))) | |
329 | (home-page "https://samtools.github.io/bcftools/") | |
330 | (synopsis "Utilities for variant calling and manipulating VCFs and BCFs") | |
331 | (description | |
332 | "BCFtools is a set of utilities that manipulate variant calls in the | |
333 | Variant Call Format (VCF) and its binary counterpart BCF. All commands work | |
334 | transparently with both VCFs and BCFs, both uncompressed and BGZF-compressed.") | |
335 | ;; The sources are dual MIT/GPL, but becomes GPL-only when USE_GPL=1. | |
336 | (license (list license:gpl3+ license:expat)))) | |
337 | ||
8dd4ff11 RW |
338 | (define-public bedops |
339 | (package | |
340 | (name "bedops") | |
1bbc3b1d | 341 | (version "2.4.14") |
8dd4ff11 RW |
342 | (source (origin |
343 | (method url-fetch) | |
344 | (uri (string-append "https://github.com/bedops/bedops/archive/v" | |
345 | version ".tar.gz")) | |
f586c877 | 346 | (file-name (string-append name "-" version ".tar.gz")) |
8dd4ff11 RW |
347 | (sha256 |
348 | (base32 | |
1bbc3b1d | 349 | "1kqbac547wyqma81cyky9n7mkgikjpsfd3nnmcm6hpqwanqgh10v")))) |
8dd4ff11 RW |
350 | (build-system gnu-build-system) |
351 | (arguments | |
352 | '(#:tests? #f | |
353 | #:make-flags (list (string-append "BINDIR=" %output "/bin")) | |
354 | #:phases | |
dc1d3cde KK |
355 | (modify-phases %standard-phases |
356 | (add-after 'unpack 'unpack-tarballs | |
357 | (lambda _ | |
358 | ;; FIXME: Bedops includes tarballs of minimally patched upstream | |
359 | ;; libraries jansson, zlib, and bzip2. We cannot just use stock | |
360 | ;; libraries because at least one of the libraries (zlib) is | |
361 | ;; patched to add a C++ function definition (deflateInit2cpp). | |
362 | ;; Until the Bedops developers offer a way to link against system | |
363 | ;; libraries we have to build the in-tree copies of these three | |
364 | ;; libraries. | |
365 | ||
366 | ;; See upstream discussion: | |
367 | ;; https://github.com/bedops/bedops/issues/124 | |
368 | ||
369 | ;; Unpack the tarballs to benefit from shebang patching. | |
370 | (with-directory-excursion "third-party" | |
371 | (and (zero? (system* "tar" "xvf" "jansson-2.6.tar.bz2")) | |
372 | (zero? (system* "tar" "xvf" "zlib-1.2.7.tar.bz2")) | |
373 | (zero? (system* "tar" "xvf" "bzip2-1.0.6.tar.bz2")))) | |
374 | ;; Disable unpacking of tarballs in Makefile. | |
375 | (substitute* "system.mk/Makefile.linux" | |
376 | (("^\tbzcat .*") "\t@echo \"not unpacking\"\n") | |
377 | (("\\./configure") "CONFIG_SHELL=bash ./configure")) | |
378 | (substitute* "third-party/zlib-1.2.7/Makefile.in" | |
379 | (("^SHELL=.*$") "SHELL=bash\n")) | |
380 | #t)) | |
381 | (delete 'configure)))) | |
8dd4ff11 RW |
382 | (home-page "https://github.com/bedops/bedops") |
383 | (synopsis "Tools for high-performance genomic feature operations") | |
384 | (description | |
385 | "BEDOPS is a suite of tools to address common questions raised in genomic | |
386 | studies---mostly with regard to overlap and proximity relationships between | |
387 | data sets. It aims to be scalable and flexible, facilitating the efficient | |
388 | and accurate analysis and management of large-scale genomic data. | |
389 | ||
390 | BEDOPS provides tools that perform highly efficient and scalable Boolean and | |
391 | other set operations, statistical calculations, archiving, conversion and | |
392 | other management of genomic data of arbitrary scale. Tasks can be easily | |
393 | split by chromosome for distributing whole-genome analyses across a | |
394 | computational cluster.") | |
395 | (license license:gpl2+))) | |
396 | ||
81de5647 RW |
397 | (define-public bedtools |
398 | (package | |
399 | (name "bedtools") | |
6098a386 | 400 | (version "2.27.1") |
81de5647 RW |
401 | (source (origin |
402 | (method url-fetch) | |
0d9824cc RW |
403 | (uri (string-append "https://github.com/arq5x/bedtools2/releases/" |
404 | "download/v" version "/" | |
405 | "bedtools-" version ".tar.gz")) | |
81de5647 RW |
406 | (sha256 |
407 | (base32 | |
6098a386 | 408 | "1ndg5yknrxl4djx8ddzgk12rrbiidfpmkkg5z3f95jzryfxarhn8")))) |
81de5647 | 409 | (build-system gnu-build-system) |
81de5647 RW |
410 | (arguments |
411 | '(#:test-target "test" | |
0d9824cc RW |
412 | #:make-flags |
413 | (list (string-append "prefix=" (assoc-ref %outputs "out"))) | |
81de5647 | 414 | #:phases |
6573ac82 | 415 | (modify-phases %standard-phases |
0d9824cc RW |
416 | (delete 'configure)))) |
417 | (native-inputs `(("python" ,python-2))) | |
418 | (inputs | |
419 | `(("samtools" ,samtools) | |
420 | ("zlib" ,zlib))) | |
81de5647 RW |
421 | (home-page "https://github.com/arq5x/bedtools2") |
422 | (synopsis "Tools for genome analysis and arithmetic") | |
423 | (description | |
424 | "Collectively, the bedtools utilities are a swiss-army knife of tools for | |
425 | a wide-range of genomics analysis tasks. The most widely-used tools enable | |
426 | genome arithmetic: that is, set theory on the genome. For example, bedtools | |
427 | allows one to intersect, merge, count, complement, and shuffle genomic | |
428 | intervals from multiple files in widely-used genomic file formats such as BAM, | |
429 | BED, GFF/GTF, VCF.") | |
430 | (license license:gpl2))) | |
431 | ||
9a8f309c RW |
432 | ;; Later releases of bedtools produce files with more columns than |
433 | ;; what Ribotaper expects. | |
434 | (define-public bedtools-2.18 | |
435 | (package (inherit bedtools) | |
436 | (name "bedtools") | |
437 | (version "2.18.0") | |
438 | (source (origin | |
439 | (method url-fetch) | |
440 | (uri (string-append "https://github.com/arq5x/bedtools2/" | |
441 | "archive/v" version ".tar.gz")) | |
442 | (file-name (string-append name "-" version ".tar.gz")) | |
443 | (sha256 | |
444 | (base32 | |
83b9d121 RW |
445 | "05vrnr8yp7swfagshzpgqmzk1blnwnq8pq5pckzi1m26w98d63vf")))) |
446 | (arguments | |
447 | '(#:test-target "test" | |
448 | #:phases | |
449 | (modify-phases %standard-phases | |
450 | (delete 'configure) | |
451 | (replace 'install | |
452 | (lambda* (#:key outputs #:allow-other-keys) | |
453 | (let ((bin (string-append (assoc-ref outputs "out") "/bin/"))) | |
454 | (for-each (lambda (file) | |
455 | (install-file file bin)) | |
456 | (find-files "bin" ".*"))) | |
457 | #t))))))) | |
9a8f309c | 458 | |
17dc32a4 RW |
459 | (define-public ribotaper |
460 | (package | |
461 | (name "ribotaper") | |
462 | (version "1.3.1") | |
463 | (source (origin | |
464 | (method url-fetch) | |
465 | (uri (string-append "https://ohlerlab.mdc-berlin.de/" | |
466 | "files/RiboTaper/RiboTaper_Version_" | |
467 | version ".tar.gz")) | |
468 | (sha256 | |
469 | (base32 | |
470 | "0ykjbps1y3z3085q94npw8i9x5gldc6shy8vlc08v76zljsm07hv")))) | |
471 | (build-system gnu-build-system) | |
7edee344 RW |
472 | (arguments |
473 | `(#:phases | |
474 | (modify-phases %standard-phases | |
475 | (add-after 'install 'wrap-executables | |
476 | (lambda* (#:key inputs outputs #:allow-other-keys) | |
477 | (let* ((out (assoc-ref outputs "out"))) | |
478 | (for-each | |
479 | (lambda (script) | |
480 | (wrap-program (string-append out "/bin/" script) | |
481 | `("R_LIBS_SITE" ":" = (,(getenv "R_LIBS_SITE"))))) | |
482 | '("create_annotations_files.bash" | |
483 | "create_metaplots.bash" | |
484 | "Ribotaper_ORF_find.sh" | |
485 | "Ribotaper.sh")))))))) | |
17dc32a4 RW |
486 | (inputs |
487 | `(("bedtools" ,bedtools-2.18) | |
488 | ("samtools" ,samtools-0.1) | |
2d7c4ae3 | 489 | ("r-minimal" ,r-minimal) |
17dc32a4 RW |
490 | ("r-foreach" ,r-foreach) |
491 | ("r-xnomial" ,r-xnomial) | |
492 | ("r-domc" ,r-domc) | |
493 | ("r-multitaper" ,r-multitaper) | |
494 | ("r-seqinr" ,r-seqinr))) | |
495 | (home-page "https://ohlerlab.mdc-berlin.de/software/RiboTaper_126/") | |
496 | (synopsis "Define translated ORFs using ribosome profiling data") | |
497 | (description | |
498 | "Ribotaper is a method for defining translated @dfn{open reading | |
499 | frames} (ORFs) using ribosome profiling (ribo-seq) data. This package | |
500 | provides the Ribotaper pipeline.") | |
501 | (license license:gpl3+))) | |
502 | ||
769fc6bb RW |
503 | (define-public ribodiff |
504 | (package | |
505 | (name "ribodiff") | |
506 | (version "0.2.2") | |
507 | (source | |
508 | (origin | |
509 | (method url-fetch) | |
510 | (uri (string-append "https://github.com/ratschlab/RiboDiff/" | |
511 | "archive/v" version ".tar.gz")) | |
512 | (file-name (string-append name "-" version ".tar.gz")) | |
513 | (sha256 | |
514 | (base32 | |
515 | "0wpbwmfv05wdjxv7ikm664f7s7p7cqr8jnw99zrda0q67rl50aaj")))) | |
516 | (build-system python-build-system) | |
517 | (arguments | |
518 | `(#:python ,python-2 | |
519 | #:phases | |
520 | (modify-phases %standard-phases | |
521 | ;; Generate an installable executable script wrapper. | |
522 | (add-after 'unpack 'patch-setup.py | |
523 | (lambda _ | |
524 | (substitute* "setup.py" | |
525 | (("^(.*)packages=.*" line prefix) | |
526 | (string-append line "\n" | |
527 | prefix "scripts=['scripts/TE.py'],\n"))) | |
528 | #t))))) | |
529 | (inputs | |
530 | `(("python-numpy" ,python2-numpy) | |
531 | ("python-matplotlib" ,python2-matplotlib) | |
532 | ("python-scipy" ,python2-scipy) | |
533 | ("python-statsmodels" ,python2-statsmodels))) | |
2bb12f5a MB |
534 | (native-inputs |
535 | `(("python-mock" ,python2-mock) | |
536 | ("python-nose" ,python2-nose))) | |
769fc6bb RW |
537 | (home-page "http://public.bmi.inf.ethz.ch/user/zhongy/RiboDiff/") |
538 | (synopsis "Detect translation efficiency changes from ribosome footprints") | |
539 | (description "RiboDiff is a statistical tool that detects the protein | |
540 | translational efficiency change from Ribo-Seq (ribosome footprinting) and | |
541 | RNA-Seq data. It uses a generalized linear model to detect genes showing | |
542 | difference in translational profile taking mRNA abundance into account. It | |
543 | facilitates us to decipher the translational regulation that behave | |
544 | independently with transcriptional regulation.") | |
545 | (license license:gpl3+))) | |
546 | ||
a0a71439 RJ |
547 | (define-public bioawk |
548 | (package | |
549 | (name "bioawk") | |
550 | (version "1.0") | |
551 | (source (origin | |
552 | (method url-fetch) | |
553 | (uri (string-append "https://github.com/lh3/bioawk/archive/v" | |
554 | version ".tar.gz")) | |
555 | (file-name (string-append name "-" version ".tar.gz")) | |
556 | (sha256 | |
557 | (base32 "1daizxsk17ahi9n58fj8vpgwyhzrzh54bzqhanjanp88kgrz7gjw")))) | |
558 | (build-system gnu-build-system) | |
559 | (inputs | |
560 | `(("zlib" ,zlib))) | |
561 | (native-inputs | |
562 | `(("bison" ,bison))) | |
563 | (arguments | |
564 | `(#:tests? #f ; There are no tests to run. | |
565 | ;; Bison must generate files, before other targets can build. | |
566 | #:parallel-build? #f | |
567 | #:phases | |
568 | (modify-phases %standard-phases | |
569 | (delete 'configure) ; There is no configure phase. | |
570 | (replace 'install | |
571 | (lambda* (#:key outputs #:allow-other-keys) | |
572 | (let* ((out (assoc-ref outputs "out")) | |
573 | (bin (string-append out "/bin")) | |
574 | (man (string-append out "/share/man/man1"))) | |
575 | (mkdir-p man) | |
576 | (copy-file "awk.1" (string-append man "/bioawk.1")) | |
577 | (install-file "bioawk" bin))))))) | |
578 | (home-page "https://github.com/lh3/bioawk") | |
579 | (synopsis "AWK with bioinformatics extensions") | |
580 | (description "Bioawk is an extension to Brian Kernighan's awk, adding the | |
581 | support of several common biological data formats, including optionally gzip'ed | |
582 | BED, GFF, SAM, VCF, FASTA/Q and TAB-delimited formats with column names. It | |
583 | also adds a few built-in functions and a command line option to use TAB as the | |
584 | input/output delimiter. When the new functionality is not used, bioawk is | |
585 | intended to behave exactly the same as the original BWK awk.") | |
586 | (license license:x11))) | |
587 | ||
a2fb1492 RW |
588 | (define-public python2-pybedtools |
589 | (package | |
590 | (name "python2-pybedtools") | |
591 | (version "0.6.9") | |
592 | (source (origin | |
593 | (method url-fetch) | |
594 | (uri (string-append | |
595 | "https://pypi.python.org/packages/source/p/pybedtools/pybedtools-" | |
596 | version ".tar.gz")) | |
597 | (sha256 | |
598 | (base32 | |
599 | "1ldzdxw1p4y3g2ignmggsdypvqkcwqwzhdha4rbgpih048z5p4an")))) | |
600 | (build-system python-build-system) | |
601 | (arguments `(#:python ,python-2)) ; no Python 3 support | |
602 | (inputs | |
f2516de2 | 603 | `(("python-matplotlib" ,python2-matplotlib))) |
a2fb1492 RW |
604 | (propagated-inputs |
605 | `(("bedtools" ,bedtools) | |
606 | ("samtools" ,samtools))) | |
607 | (native-inputs | |
f2516de2 HG |
608 | `(("python-cython" ,python2-cython) |
609 | ("python-pyyaml" ,python2-pyyaml) | |
f3b98f4f | 610 | ("python-nose" ,python2-nose))) |
a2fb1492 RW |
611 | (home-page "https://pythonhosted.org/pybedtools/") |
612 | (synopsis "Python wrapper for BEDtools programs") | |
613 | (description | |
614 | "pybedtools is a Python wrapper for Aaron Quinlan's BEDtools programs, | |
615 | which are widely used for genomic interval manipulation or \"genome algebra\". | |
616 | pybedtools extends BEDTools by offering feature-level manipulations from with | |
617 | Python.") | |
618 | (license license:gpl2+))) | |
619 | ||
9e12eba8 BW |
620 | (define-public python-biom-format |
621 | (package | |
622 | (name "python-biom-format") | |
abc08cba | 623 | (version "2.1.6") |
9e12eba8 BW |
624 | (source |
625 | (origin | |
626 | (method url-fetch) | |
627 | ;; Use GitHub as source because PyPI distribution does not contain | |
628 | ;; test data: https://github.com/biocore/biom-format/issues/693 | |
629 | (uri (string-append "https://github.com/biocore/biom-format/archive/" | |
630 | version ".tar.gz")) | |
631 | (file-name (string-append name "-" version ".tar.gz")) | |
632 | (sha256 | |
633 | (base32 | |
abc08cba | 634 | "08cr7wpahk6zb31h4bs7jmzpvxcqv9s13xz40h6y2h656jvdvnpj")))) |
9e12eba8 | 635 | (build-system python-build-system) |
de96ea28 | 636 | (propagated-inputs |
9e12eba8 BW |
637 | `(("python-numpy" ,python-numpy) |
638 | ("python-scipy" ,python-scipy) | |
639 | ("python-future" ,python-future) | |
640 | ("python-click" ,python-click) | |
abc08cba BW |
641 | ("python-h5py" ,python-h5py) |
642 | ("python-pandas" ,python-pandas))) | |
da5ebd10 MB |
643 | (native-inputs |
644 | `(("python-nose" ,python-nose))) | |
9e12eba8 BW |
645 | (home-page "http://www.biom-format.org") |
646 | (synopsis "Biological Observation Matrix (BIOM) format utilities") | |
647 | (description | |
648 | "The BIOM file format is designed to be a general-use format for | |
649 | representing counts of observations e.g. operational taxonomic units, KEGG | |
650 | orthology groups or lipid types, in one or more biological samples | |
651 | e.g. microbiome samples, genomes, metagenomes.") | |
652 | (license license:bsd-3) | |
653 | (properties `((python2-variant . ,(delay python2-biom-format)))))) | |
654 | ||
655 | (define-public python2-biom-format | |
656 | (let ((base (package-with-python2 (strip-python2-variant python-biom-format)))) | |
657 | (package | |
658 | (inherit base) | |
659 | (arguments | |
660 | `(#:phases | |
661 | (modify-phases %standard-phases | |
662 | ;; Do not require the unmaintained pyqi library. | |
663 | (add-after 'unpack 'remove-pyqi | |
664 | (lambda _ | |
665 | (substitute* "setup.py" | |
666 | (("install_requires.append\\(\"pyqi\"\\)") "pass")) | |
667 | #t))) | |
00e10c6e | 668 | ,@(package-arguments base)))))) |
9e12eba8 | 669 | |
f7283db3 RW |
670 | (define-public bioperl-minimal |
671 | (let* ((inputs `(("perl-module-build" ,perl-module-build) | |
672 | ("perl-data-stag" ,perl-data-stag) | |
673 | ("perl-libwww" ,perl-libwww) | |
674 | ("perl-uri" ,perl-uri))) | |
675 | (transitive-inputs | |
676 | (map (compose package-name cadr) | |
677 | (delete-duplicates | |
678 | (concatenate | |
679 | (map (compose package-transitive-target-inputs cadr) inputs)))))) | |
680 | (package | |
681 | (name "bioperl-minimal") | |
c70271ec | 682 | (version "1.7.0") |
f7283db3 RW |
683 | (source |
684 | (origin | |
685 | (method url-fetch) | |
c70271ec RW |
686 | (uri (string-append "https://github.com/bioperl/bioperl-live/" |
687 | "archive/release-" | |
688 | (string-map (lambda (c) | |
689 | (if (char=? c #\.) | |
690 | #\- c)) version) | |
691 | ".tar.gz")) | |
f7283db3 RW |
692 | (sha256 |
693 | (base32 | |
c70271ec | 694 | "12phgpxwgkqflkwfb9dcqg7a31dpjlfhar8wcgv0aj5ln4akfz06")))) |
f7283db3 RW |
695 | (build-system perl-build-system) |
696 | (arguments | |
697 | `(#:phases | |
698 | (modify-phases %standard-phases | |
699 | (add-after | |
700 | 'install 'wrap-programs | |
701 | (lambda* (#:key outputs #:allow-other-keys) | |
702 | ;; Make sure all executables in "bin" find the required Perl | |
703 | ;; modules at runtime. As the PERL5LIB variable contains also | |
704 | ;; the paths of native inputs, we pick the transitive target | |
705 | ;; inputs from %build-inputs. | |
706 | (let* ((out (assoc-ref outputs "out")) | |
707 | (bin (string-append out "/bin/")) | |
708 | (path (string-join | |
709 | (cons (string-append out "/lib/perl5/site_perl") | |
710 | (map (lambda (name) | |
711 | (assoc-ref %build-inputs name)) | |
712 | ',transitive-inputs)) | |
713 | ":"))) | |
714 | (for-each (lambda (file) | |
715 | (wrap-program file | |
716 | `("PERL5LIB" ":" prefix (,path)))) | |
717 | (find-files bin "\\.pl$")) | |
718 | #t)))))) | |
719 | (inputs inputs) | |
720 | (native-inputs | |
721 | `(("perl-test-most" ,perl-test-most))) | |
722 | (home-page "http://search.cpan.org/dist/BioPerl") | |
723 | (synopsis "Bioinformatics toolkit") | |
724 | (description | |
725 | "BioPerl is the product of a community effort to produce Perl code which | |
726 | is useful in biology. Examples include Sequence objects, Alignment objects | |
727 | and database searching objects. These objects not only do what they are | |
728 | advertised to do in the documentation, but they also interact - Alignment | |
729 | objects are made from the Sequence objects, Sequence objects have access to | |
730 | Annotation and SeqFeature objects and databases, Blast objects can be | |
731 | converted to Alignment objects, and so on. This means that the objects | |
732 | provide a coordinated and extensible framework to do computational biology.") | |
2f3108ad | 733 | (license license:perl-license)))) |
f7283db3 | 734 | |
85c37e29 RW |
735 | (define-public python-biopython |
736 | (package | |
737 | (name "python-biopython") | |
af6ce610 | 738 | (version "1.70") |
85c37e29 RW |
739 | (source (origin |
740 | (method url-fetch) | |
e815c094 BW |
741 | ;; use PyPi rather than biopython.org to ease updating |
742 | (uri (pypi-uri "biopython" version)) | |
85c37e29 RW |
743 | (sha256 |
744 | (base32 | |
af6ce610 | 745 | "0nz4n9d2y2dg849gn1z0vjlkwcpzzkzy3fij7x94a6ixy2c54z2a")))) |
85c37e29 | 746 | (build-system python-build-system) |
4ce60305 BW |
747 | (arguments |
748 | `(#:phases | |
749 | (modify-phases %standard-phases | |
750 | (add-before 'check 'set-home | |
751 | ;; Some tests require a home directory to be set. | |
752 | (lambda _ (setenv "HOME" "/tmp") #t))))) | |
f22efa01 | 753 | (propagated-inputs |
85c37e29 | 754 | `(("python-numpy" ,python-numpy))) |
85c37e29 RW |
755 | (home-page "http://biopython.org/") |
756 | (synopsis "Tools for biological computation in Python") | |
757 | (description | |
758 | "Biopython is a set of tools for biological computation including parsers | |
759 | for bioinformatics files into Python data structures; interfaces to common | |
760 | bioinformatics programs; a standard sequence class and tools for performing | |
761 | common operations on them; code to perform data classification; code for | |
762 | dealing with alignments; code making it easy to split up parallelizable tasks | |
763 | into separate processes; and more.") | |
5c31f4aa | 764 | (license (license:non-copyleft "http://www.biopython.org/DIST/LICENSE")))) |
85c37e29 RW |
765 | |
766 | (define-public python2-biopython | |
5c31f4aa | 767 | (package-with-python2 python-biopython)) |
85c37e29 | 768 | |
985d8411 BW |
769 | (define-public bpp-core |
770 | ;; The last release was in 2014 and the recommended way to install from source | |
771 | ;; is to clone the git repository, so we do this. | |
772 | ;; http://biopp.univ-montp2.fr/wiki/index.php/Main_Page | |
773 | (let ((commit "7d8bced0d1a87291ea8dd7046b7fb5ff9c35c582")) | |
774 | (package | |
775 | (name "bpp-core") | |
776 | (version (string-append "2.2.0-1." (string-take commit 7))) | |
777 | (source (origin | |
778 | (method git-fetch) | |
779 | (uri (git-reference | |
780 | (url "http://biopp.univ-montp2.fr/git/bpp-core") | |
781 | (commit commit))) | |
782 | (file-name (string-append name "-" version "-checkout")) | |
783 | (sha256 | |
784 | (base32 | |
785 | "10djsq5vlnkilv436gnmh4irpk49v29pa69r6xiryg32xmvn909j")))) | |
786 | (build-system cmake-build-system) | |
787 | (arguments | |
788 | `(#:parallel-build? #f)) | |
789 | (inputs | |
790 | `(("gcc" ,gcc-5))) ; Compilation of bpp-phyl fails with GCC 4.9 so we | |
791 | ; compile all of the bpp packages with GCC 5. | |
792 | (home-page "http://biopp.univ-montp2.fr") | |
793 | (synopsis "C++ libraries for Bioinformatics") | |
794 | (description | |
795 | "Bio++ is a set of C++ libraries for Bioinformatics, including sequence | |
796 | analysis, phylogenetics, molecular evolution and population genetics. It is | |
797 | Object Oriented and is designed to be both easy to use and computer efficient. | |
798 | Bio++ intends to help programmers to write computer expensive programs, by | |
799 | providing them a set of re-usable tools.") | |
800 | (license license:cecill-c)))) | |
801 | ||
8b5f4d57 BW |
802 | (define-public bpp-phyl |
803 | ;; The last release was in 2014 and the recommended way to install from source | |
804 | ;; is to clone the git repository, so we do this. | |
805 | ;; http://biopp.univ-montp2.fr/wiki/index.php/Main_Page | |
806 | (let ((commit "0c07167b629f68b569bf274d1ad0c4af83276ae2")) | |
807 | (package | |
808 | (name "bpp-phyl") | |
809 | (version (string-append "2.2.0-1." (string-take commit 7))) | |
810 | (source (origin | |
811 | (method git-fetch) | |
812 | (uri (git-reference | |
813 | (url "http://biopp.univ-montp2.fr/git/bpp-phyl") | |
814 | (commit commit))) | |
815 | (file-name (string-append name "-" version "-checkout")) | |
816 | (sha256 | |
817 | (base32 | |
818 | "1ssjgchzwj3iai26kyly7gwkdv8sk59nqhkb1wpap3sf5m6kyllh")))) | |
819 | (build-system cmake-build-system) | |
820 | (arguments | |
821 | `(#:parallel-build? #f | |
822 | ;; If out-of-source, test data is not copied into the build directory | |
823 | ;; so the tests fail. | |
824 | #:out-of-source? #f)) | |
825 | (inputs | |
826 | `(("bpp-core" ,bpp-core) | |
827 | ("bpp-seq" ,bpp-seq) | |
828 | ;; GCC 4.8 fails due to an 'internal compiler error', so we use a more | |
829 | ;; modern GCC. | |
830 | ("gcc" ,gcc-5))) | |
831 | (home-page "http://biopp.univ-montp2.fr") | |
832 | (synopsis "Bio++ phylogenetic Library") | |
833 | (description | |
834 | "Bio++ is a set of C++ libraries for Bioinformatics, including sequence | |
835 | analysis, phylogenetics, molecular evolution and population genetics. This | |
836 | library provides phylogenetics-related modules.") | |
837 | (license license:cecill-c)))) | |
838 | ||
159a7016 BW |
839 | (define-public bpp-popgen |
840 | ;; The last release was in 2014 and the recommended way to install from source | |
841 | ;; is to clone the git repository, so we do this. | |
842 | ;; http://biopp.univ-montp2.fr/wiki/index.php/Main_Page | |
843 | (let ((commit "e472bac9b1a148803895d747cd6d0c5904f85d9f")) | |
844 | (package | |
845 | (name "bpp-popgen") | |
846 | (version (string-append "2.2.0-1." (string-take commit 7))) | |
847 | (source (origin | |
848 | (method git-fetch) | |
849 | (uri (git-reference | |
850 | (url "http://biopp.univ-montp2.fr/git/bpp-popgen") | |
851 | (commit commit))) | |
852 | (file-name (string-append name "-" version "-checkout")) | |
853 | (sha256 | |
854 | (base32 | |
855 | "0yn82dzn1n5629nzja68xfrhi655709rjanyryb36vzkmymy6dw5")))) | |
856 | (build-system cmake-build-system) | |
857 | (arguments | |
858 | `(#:parallel-build? #f | |
859 | #:tests? #f)) ; There are no tests. | |
860 | (inputs | |
861 | `(("bpp-core" ,bpp-core) | |
862 | ("bpp-seq" ,bpp-seq) | |
863 | ("gcc" ,gcc-5))) | |
864 | (home-page "http://biopp.univ-montp2.fr") | |
865 | (synopsis "Bio++ population genetics library") | |
866 | (description | |
867 | "Bio++ is a set of C++ libraries for Bioinformatics, including sequence | |
868 | analysis, phylogenetics, molecular evolution and population genetics. This | |
869 | library provides population genetics-related modules.") | |
870 | (license license:cecill-c)))) | |
871 | ||
70f1bc05 BW |
872 | (define-public bpp-seq |
873 | ;; The last release was in 2014 and the recommended way to install from source | |
874 | ;; is to clone the git repository, so we do this. | |
875 | ;; http://biopp.univ-montp2.fr/wiki/index.php/Main_Page | |
876 | (let ((commit "6cfa07965ce152e5598a89df2fa80a75973bfa33")) | |
877 | (package | |
878 | (name "bpp-seq") | |
879 | (version (string-append "2.2.0-1." (string-take commit 7))) | |
880 | (source (origin | |
881 | (method git-fetch) | |
882 | (uri (git-reference | |
883 | (url "http://biopp.univ-montp2.fr/git/bpp-seq") | |
884 | (commit commit))) | |
885 | (file-name (string-append name "-" version "-checkout")) | |
886 | (sha256 | |
887 | (base32 | |
888 | "1nys5jq7jqvdg40d91wsmj3q2yzy4276cp7sp44n67p468f27zf2")))) | |
889 | (build-system cmake-build-system) | |
890 | (arguments | |
891 | `(#:parallel-build? #f | |
892 | ;; If out-of-source, test data is not copied into the build directory | |
893 | ;; so the tests fail. | |
894 | #:out-of-source? #f)) | |
895 | (inputs | |
896 | `(("bpp-core" ,bpp-core) | |
897 | ("gcc" ,gcc-5))) ; Use GCC 5 as per 'bpp-core'. | |
898 | (home-page "http://biopp.univ-montp2.fr") | |
899 | (synopsis "Bio++ sequence library") | |
900 | (description | |
901 | "Bio++ is a set of C++ libraries for Bioinformatics, including sequence | |
902 | analysis, phylogenetics, molecular evolution and population genetics. This | |
903 | library provides sequence-related modules.") | |
904 | (license license:cecill-c)))) | |
905 | ||
db7a3444 BW |
906 | (define-public bppsuite |
907 | ;; The last release was in 2014 and the recommended way to install from source | |
908 | ;; is to clone the git repository, so we do this. | |
909 | ;; http://biopp.univ-montp2.fr/wiki/index.php/Main_Page | |
910 | (let ((commit "c516147f57aa50961121cd505bed52cd7603698b")) | |
911 | (package | |
912 | (name "bppsuite") | |
913 | (version (string-append "2.2.0-1." (string-take commit 7))) | |
914 | (source (origin | |
915 | (method git-fetch) | |
916 | (uri (git-reference | |
917 | (url "http://biopp.univ-montp2.fr/git/bppsuite") | |
918 | (commit commit))) | |
919 | (file-name (string-append name "-" version "-checkout")) | |
920 | (sha256 | |
921 | (base32 | |
922 | "1y87pxvw0jxjizhq2dr9g2r91md45k1p9ih2sl1yy1y3p934l2kb")))) | |
923 | (build-system cmake-build-system) | |
924 | (arguments | |
925 | `(#:parallel-build? #f | |
926 | #:tests? #f)) ; There are no tests. | |
927 | (native-inputs | |
928 | `(("groff" ,groff) | |
929 | ("man-db" ,man-db) | |
930 | ("texinfo" ,texinfo))) | |
931 | (inputs | |
932 | `(("bpp-core" ,bpp-core) | |
933 | ("bpp-seq" ,bpp-seq) | |
934 | ("bpp-phyl" ,bpp-phyl) | |
935 | ("bpp-phyl" ,bpp-popgen) | |
936 | ("gcc" ,gcc-5))) | |
937 | (home-page "http://biopp.univ-montp2.fr") | |
938 | (synopsis "Bioinformatics tools written with the Bio++ libraries") | |
939 | (description | |
940 | "Bio++ is a set of C++ libraries for Bioinformatics, including sequence | |
941 | analysis, phylogenetics, molecular evolution and population genetics. This | |
942 | package provides command line tools using the Bio++ library.") | |
943 | (license license:cecill-c)))) | |
944 | ||
82c370de RW |
945 | (define-public blast+ |
946 | (package | |
947 | (name "blast+") | |
4732e6ee | 948 | (version "2.6.0") |
82c370de RW |
949 | (source (origin |
950 | (method url-fetch) | |
951 | (uri (string-append | |
952 | "ftp://ftp.ncbi.nlm.nih.gov/blast/executables/blast+/" | |
953 | version "/ncbi-blast-" version "+-src.tar.gz")) | |
954 | (sha256 | |
955 | (base32 | |
4732e6ee BW |
956 | "15n937pw5aqmyfjb6l387d18grqbb96l63d5xj4l7yyh0zbf2405")) |
957 | (patches (search-patches "blast+-fix-makefile.patch")) | |
82c370de RW |
958 | (modules '((guix build utils))) |
959 | (snippet | |
960 | '(begin | |
4732e6ee | 961 | ;; Remove bundled bzip2, zlib and pcre. |
82c370de RW |
962 | (delete-file-recursively "c++/src/util/compress/bzip2") |
963 | (delete-file-recursively "c++/src/util/compress/zlib") | |
4732e6ee | 964 | (delete-file-recursively "c++/src/util/regexp") |
82c370de RW |
965 | (substitute* "c++/src/util/compress/Makefile.in" |
966 | (("bzip2 zlib api") "api")) | |
967 | ;; Remove useless msbuild directory | |
968 | (delete-file-recursively | |
969 | "c++/src/build-system/project_tree_builder/msbuild") | |
970 | #t)))) | |
971 | (build-system gnu-build-system) | |
972 | (arguments | |
4732e6ee | 973 | `(;; There are two(!) tests for this massive library, and both fail with |
82c370de | 974 | ;; "unparsable timing stats". |
82c370de RW |
975 | ;; ERR [127] -- [serial/datatool] datatool.sh (unparsable timing stats) |
976 | ;; ERR [127] -- [serial/datatool] datatool_xml.sh (unparsable timing stats) | |
977 | #:tests? #f | |
978 | #:out-of-source? #t | |
979 | #:parallel-build? #f ; not supported | |
980 | #:phases | |
981 | (modify-phases %standard-phases | |
982 | (add-before | |
983 | 'configure 'set-HOME | |
984 | ;; $HOME needs to be set at some point during the configure phase | |
985 | (lambda _ (setenv "HOME" "/tmp") #t)) | |
986 | (add-after | |
987 | 'unpack 'enter-dir | |
988 | (lambda _ (chdir "c++") #t)) | |
989 | (add-after | |
990 | 'enter-dir 'fix-build-system | |
991 | (lambda _ | |
992 | (define (which* cmd) | |
993 | (cond ((string=? cmd "date") | |
994 | ;; make call to "date" deterministic | |
995 | "date -d @0") | |
996 | ((which cmd) | |
997 | => identity) | |
998 | (else | |
999 | (format (current-error-port) | |
1000 | "WARNING: Unable to find absolute path for ~s~%" | |
1001 | cmd) | |
1002 | #f))) | |
1003 | ||
1004 | ;; Rewrite hardcoded paths to various tools | |
1005 | (substitute* (append '("src/build-system/configure.ac" | |
1006 | "src/build-system/configure" | |
4732e6ee | 1007 | "src/build-system/helpers/run_with_lock.c" |
82c370de RW |
1008 | "scripts/common/impl/if_diff.sh" |
1009 | "scripts/common/impl/run_with_lock.sh" | |
1010 | "src/build-system/Makefile.configurables.real" | |
1011 | "src/build-system/Makefile.in.top" | |
1012 | "src/build-system/Makefile.meta.gmake=no" | |
1013 | "src/build-system/Makefile.meta.in" | |
1014 | "src/build-system/Makefile.meta_l" | |
1015 | "src/build-system/Makefile.meta_p" | |
1016 | "src/build-system/Makefile.meta_r" | |
1017 | "src/build-system/Makefile.mk.in" | |
1018 | "src/build-system/Makefile.requirements" | |
1019 | "src/build-system/Makefile.rules_with_autodep.in") | |
1020 | (find-files "scripts/common/check" "\\.sh$")) | |
1021 | (("(/usr/bin/|/bin/)([a-z][-_.a-z]*)" all dir cmd) | |
1022 | (or (which* cmd) all))) | |
1023 | ||
1024 | (substitute* (find-files "src/build-system" "^config.*") | |
1025 | (("LN_S=/bin/\\$LN_S") (string-append "LN_S=" (which "ln"))) | |
1026 | (("^PATH=.*") "")) | |
1027 | ||
1028 | ;; rewrite "/var/tmp" in check script | |
1029 | (substitute* "scripts/common/check/check_make_unix.sh" | |
1030 | (("/var/tmp") "/tmp")) | |
1031 | ||
1032 | ;; do not reset PATH | |
1033 | (substitute* (find-files "scripts/common/impl/" "\\.sh$") | |
1034 | (("^ *PATH=.*") "") | |
1035 | (("action=/bin/") "action=") | |
1036 | (("export PATH") ":")) | |
1037 | #t)) | |
1038 | (replace | |
1039 | 'configure | |
1040 | (lambda* (#:key inputs outputs #:allow-other-keys) | |
1041 | (let ((out (assoc-ref outputs "out")) | |
1042 | (lib (string-append (assoc-ref outputs "lib") "/lib")) | |
1043 | (include (string-append (assoc-ref outputs "include") | |
1044 | "/include/ncbi-tools++"))) | |
1045 | ;; The 'configure' script doesn't recognize things like | |
1046 | ;; '--enable-fast-install'. | |
1047 | (zero? (system* "./configure.orig" | |
1048 | (string-append "--with-build-root=" (getcwd) "/build") | |
1049 | (string-append "--prefix=" out) | |
1050 | (string-append "--libdir=" lib) | |
1051 | (string-append "--includedir=" include) | |
1052 | (string-append "--with-bz2=" | |
1053 | (assoc-ref inputs "bzip2")) | |
1054 | (string-append "--with-z=" | |
1055 | (assoc-ref inputs "zlib")) | |
4732e6ee BW |
1056 | (string-append "--with-pcre=" |
1057 | (assoc-ref inputs "pcre")) | |
82c370de RW |
1058 | ;; Each library is built twice by default, once |
1059 | ;; with "-static" in its name, and again | |
1060 | ;; without. | |
1061 | "--without-static" | |
1062 | "--with-dll")))))))) | |
4732e6ee BW |
1063 | (outputs '("out" ; 21 MB |
1064 | "lib" ; 226 MB | |
1065 | "include")) ; 33 MB | |
82c370de RW |
1066 | (inputs |
1067 | `(("bzip2" ,bzip2) | |
4732e6ee BW |
1068 | ("zlib" ,zlib) |
1069 | ("pcre" ,pcre) | |
1070 | ("perl" ,perl) | |
1071 | ("python" ,python-wrapper))) | |
82c370de RW |
1072 | (native-inputs |
1073 | `(("cpio" ,cpio))) | |
1074 | (home-page "http://blast.ncbi.nlm.nih.gov") | |
1075 | (synopsis "Basic local alignment search tool") | |
1076 | (description | |
1077 | "BLAST is a popular method of performing a DNA or protein sequence | |
1078 | similarity search, using heuristics to produce results quickly. It also | |
1079 | calculates an “expect value” that estimates how many matches would have | |
1080 | occurred at a given score by chance, which can aid a user in judging how much | |
1081 | confidence to have in an alignment.") | |
1082 | ;; Most of the sources are in the public domain, with the following | |
1083 | ;; exceptions: | |
1084 | ;; * Expat: | |
1085 | ;; * ./c++/include/util/bitset/ | |
1086 | ;; * ./c++/src/html/ncbi_menu*.js | |
1087 | ;; * Boost license: | |
1088 | ;; * ./c++/include/util/impl/floating_point_comparison.hpp | |
1089 | ;; * LGPL 2+: | |
1090 | ;; * ./c++/include/dbapi/driver/odbc/unix_odbc/ | |
1091 | ;; * ASL 2.0: | |
1092 | ;; * ./c++/src/corelib/teamcity_* | |
1093 | (license (list license:public-domain | |
1094 | license:expat | |
1095 | license:boost1.0 | |
1096 | license:lgpl2.0+ | |
1097 | license:asl2.0)))) | |
1098 | ||
6c2b26e2 RW |
1099 | (define-public bless |
1100 | (package | |
1101 | (name "bless") | |
1102 | (version "1p02") | |
1103 | (source (origin | |
1104 | (method url-fetch) | |
1105 | (uri (string-append "mirror://sourceforge/bless-ec/bless.v" | |
1106 | version ".tgz")) | |
1107 | (sha256 | |
1108 | (base32 | |
4d75e03a RW |
1109 | "0rm0gw2s18dqwzzpl3c2x1z05ni2v0xz5dmfk3d33j6g4cgrlrdd")) |
1110 | (modules '((guix build utils))) | |
6c2b26e2 RW |
1111 | (snippet |
1112 | `(begin | |
1113 | ;; Remove bundled boost, pigz, zlib, and .git directory | |
953c1223 RW |
1114 | ;; FIXME: also remove bundled sources for murmurhash3 and |
1115 | ;; kmc once packaged. | |
6c2b26e2 RW |
1116 | (delete-file-recursively "boost") |
1117 | (delete-file-recursively "pigz") | |
953c1223 | 1118 | (delete-file-recursively "google-sparsehash") |
6c2b26e2 RW |
1119 | (delete-file-recursively "zlib") |
1120 | (delete-file-recursively ".git") | |
1121 | #t)))) | |
1122 | (build-system gnu-build-system) | |
1123 | (arguments | |
1124 | '(#:tests? #f ;no "check" target | |
1125 | #:make-flags | |
1126 | (list (string-append "ZLIB=" | |
1127 | (assoc-ref %build-inputs "zlib") | |
1128 | "/lib/libz.a") | |
1129 | (string-append "LDFLAGS=" | |
1130 | (string-join '("-lboost_filesystem" | |
1131 | "-lboost_system" | |
1132 | "-lboost_iostreams" | |
1133 | "-lz" | |
1134 | "-fopenmp" | |
1135 | "-std=c++11")))) | |
1136 | #:phases | |
1137 | (modify-phases %standard-phases | |
1138 | (add-after 'unpack 'do-not-build-bundled-pigz | |
1139 | (lambda* (#:key inputs outputs #:allow-other-keys) | |
1140 | (substitute* "Makefile" | |
1141 | (("cd pigz/pigz-2.3.3; make") "")) | |
1142 | #t)) | |
1143 | (add-after 'unpack 'patch-paths-to-executables | |
1144 | (lambda* (#:key inputs outputs #:allow-other-keys) | |
1145 | (substitute* "parse_args.cpp" | |
1146 | (("kmc_binary = .*") | |
1147 | (string-append "kmc_binary = \"" | |
1148 | (assoc-ref outputs "out") | |
1149 | "/bin/kmc\";")) | |
1150 | (("pigz_binary = .*") | |
1151 | (string-append "pigz_binary = \"" | |
1152 | (assoc-ref inputs "pigz") | |
1153 | "/bin/pigz\";"))) | |
1154 | #t)) | |
1155 | (replace 'install | |
1156 | (lambda* (#:key outputs #:allow-other-keys) | |
1157 | (let ((bin (string-append (assoc-ref outputs "out") "/bin/"))) | |
1158 | (for-each (lambda (file) | |
1159 | (install-file file bin)) | |
1160 | '("bless" "kmc/bin/kmc")) | |
1161 | #t))) | |
1162 | (delete 'configure)))) | |
1163 | (native-inputs | |
1164 | `(("perl" ,perl))) | |
1165 | (inputs | |
1166 | `(("openmpi" ,openmpi) | |
1167 | ("boost" ,boost) | |
953c1223 | 1168 | ("sparsehash" ,sparsehash) |
6c2b26e2 RW |
1169 | ("pigz" ,pigz) |
1170 | ("zlib" ,zlib))) | |
9641a899 | 1171 | (supported-systems '("x86_64-linux")) |
3b3b60d0 | 1172 | (home-page "https://sourceforge.net/p/bless-ec/wiki/Home/") |
6c2b26e2 RW |
1173 | (synopsis "Bloom-filter-based error correction tool for NGS reads") |
1174 | (description | |
1175 | "@dfn{Bloom-filter-based error correction solution for high-throughput | |
1176 | sequencing reads} (BLESS) uses a single minimum-sized bloom filter is a | |
1177 | correction tool for genomic reads produced by @dfn{Next-generation | |
1178 | sequencing} (NGS). BLESS produces accurate correction results with much less | |
1179 | memory compared with previous solutions and is also able to tolerate a higher | |
1180 | false-positive rate. BLESS can extend reads like DNA assemblers to correct | |
1181 | errors at the end of reads.") | |
1182 | (license license:gpl3+))) | |
1183 | ||
2c7ee167 RW |
1184 | (define-public bowtie |
1185 | (package | |
1186 | (name "bowtie") | |
d6e63cf3 | 1187 | (version "2.3.2") |
2c7ee167 RW |
1188 | (source (origin |
1189 | (method url-fetch) | |
1190 | (uri (string-append "https://github.com/BenLangmead/bowtie2/archive/v" | |
1191 | version ".tar.gz")) | |
f586c877 | 1192 | (file-name (string-append name "-" version ".tar.gz")) |
2c7ee167 RW |
1193 | (sha256 |
1194 | (base32 | |
d6e63cf3 | 1195 | "0hwa5r9qbglppb7sz5z79rlmmddr3n51n468jb3wh8rwjgn3yr90")) |
2c7ee167 RW |
1196 | (modules '((guix build utils))) |
1197 | (snippet | |
1198 | '(substitute* "Makefile" | |
2c7ee167 RW |
1199 | ;; replace BUILD_HOST and BUILD_TIME for deterministic build |
1200 | (("-DBUILD_HOST=.*") "-DBUILD_HOST=\"\\\"guix\\\"\"") | |
0047d26a | 1201 | (("-DBUILD_TIME=.*") "-DBUILD_TIME=\"\\\"0\\\"\""))))) |
2c7ee167 | 1202 | (build-system gnu-build-system) |
d6e63cf3 BW |
1203 | (inputs |
1204 | `(("perl" ,perl) | |
1205 | ("perl-clone" ,perl-clone) | |
1206 | ("perl-test-deep" ,perl-test-deep) | |
1207 | ("perl-test-simple" ,perl-test-simple) | |
1208 | ("python" ,python-2) | |
1209 | ("tbb" ,tbb) | |
1210 | ("zlib" ,zlib))) | |
2c7ee167 | 1211 | (arguments |
0047d26a RW |
1212 | '(#:make-flags |
1213 | (list "allall" | |
1214 | "WITH_TBB=1" | |
1215 | (string-append "prefix=" (assoc-ref %outputs "out"))) | |
2c7ee167 | 1216 | #:phases |
06e37236 BW |
1217 | (modify-phases %standard-phases |
1218 | (delete 'configure) | |
1219 | (replace 'check | |
1220 | (lambda* (#:key outputs #:allow-other-keys) | |
1221 | (zero? (system* "perl" | |
1222 | "scripts/test/simple_tests.pl" | |
1223 | "--bowtie2=./bowtie2" | |
1224 | "--bowtie2-build=./bowtie2-build"))))))) | |
2c7ee167 RW |
1225 | (home-page "http://bowtie-bio.sourceforge.net/bowtie2/index.shtml") |
1226 | (synopsis "Fast and sensitive nucleotide sequence read aligner") | |
1227 | (description | |
1228 | "Bowtie 2 is a fast and memory-efficient tool for aligning sequencing | |
1229 | reads to long reference sequences. It is particularly good at aligning reads | |
1230 | of about 50 up to 100s or 1,000s of characters, and particularly good at | |
1231 | aligning to relatively long (e.g. mammalian) genomes. Bowtie 2 indexes the | |
1232 | genome with an FM Index to keep its memory footprint small: for the human | |
1233 | genome, its memory footprint is typically around 3.2 GB. Bowtie 2 supports | |
1234 | gapped, local, and paired-end alignment modes.") | |
241e1221 | 1235 | (supported-systems '("x86_64-linux")) |
2c7ee167 RW |
1236 | (license license:gpl3+))) |
1237 | ||
94ce537e RW |
1238 | (define-public tophat |
1239 | (package | |
1240 | (name "tophat") | |
1241 | (version "2.1.0") | |
1242 | (source (origin | |
1243 | (method url-fetch) | |
1244 | (uri (string-append | |
1245 | "http://ccb.jhu.edu/software/tophat/downloads/tophat-" | |
1246 | version ".tar.gz")) | |
1247 | (sha256 | |
1248 | (base32 | |
1249 | "168zlzykq622zbgkh90a90f1bdgsxkscq2zxzbj8brq80hbjpyp7")) | |
fc1adab1 | 1250 | (patches (search-patches "tophat-build-with-later-seqan.patch")) |
94ce537e RW |
1251 | (modules '((guix build utils))) |
1252 | (snippet | |
1253 | '(begin | |
1254 | ;; Remove bundled SeqAn and samtools | |
1255 | (delete-file-recursively "src/SeqAn-1.3") | |
1256 | (delete-file-recursively "src/samtools-0.1.18") | |
1257 | #t)))) | |
1258 | (build-system gnu-build-system) | |
1259 | (arguments | |
1260 | '(#:parallel-build? #f ; not supported | |
1261 | #:phases | |
1262 | (modify-phases %standard-phases | |
1263 | (add-after 'unpack 'use-system-samtools | |
1264 | (lambda* (#:key inputs #:allow-other-keys) | |
1265 | (substitute* "src/Makefile.in" | |
1266 | (("(noinst_LIBRARIES = )\\$\\(SAMLIB\\)" _ prefix) prefix) | |
1267 | (("\\$\\(SAMPROG\\): \\$\\(SAMLIB\\)") "") | |
1268 | (("SAMPROG = samtools_0\\.1\\.18") "") | |
1269 | (("\\$\\(samtools_0_1_18_SOURCES\\)") "") | |
1270 | (("am__EXEEXT_1 = samtools_0\\.1\\.18\\$\\(EXEEXT\\)") "")) | |
1271 | (substitute* '("src/common.cpp" | |
1272 | "src/tophat.py") | |
1273 | (("samtools_0.1.18") (which "samtools"))) | |
1274 | (substitute* '("src/common.h" | |
1275 | "src/bam2fastx.cpp") | |
1276 | (("#include \"bam.h\"") "#include <samtools/bam.h>") | |
1277 | (("#include \"sam.h\"") "#include <samtools/sam.h>")) | |
1278 | (substitute* '("src/bwt_map.h" | |
1279 | "src/map2gtf.h" | |
1280 | "src/align_status.h") | |
1281 | (("#include <bam.h>") "#include <samtools/bam.h>") | |
1282 | (("#include <sam.h>") "#include <samtools/sam.h>")) | |
1283 | #t))))) | |
1284 | (inputs | |
1285 | `(("boost" ,boost) | |
1286 | ("bowtie" ,bowtie) | |
1287 | ("samtools" ,samtools-0.1) | |
1288 | ("ncurses" ,ncurses) | |
1289 | ("python" ,python-2) | |
1290 | ("perl" ,perl) | |
1291 | ("zlib" ,zlib) | |
1292 | ("seqan" ,seqan))) | |
1293 | (home-page "http://ccb.jhu.edu/software/tophat/index.shtml") | |
1294 | (synopsis "Spliced read mapper for RNA-Seq data") | |
1295 | (description | |
1296 | "TopHat is a fast splice junction mapper for nucleotide sequence | |
1297 | reads produced by the RNA-Seq method. It aligns RNA-Seq reads to | |
1298 | mammalian-sized genomes using the ultra high-throughput short read | |
1299 | aligner Bowtie, and then analyzes the mapping results to identify | |
1300 | splice junctions between exons.") | |
1301 | ;; TopHat is released under the Boost Software License, Version 1.0 | |
1302 | ;; See https://github.com/infphilo/tophat/issues/11#issuecomment-121589893 | |
1303 | (license license:boost1.0))) | |
1304 | ||
9a8336d8 RW |
1305 | (define-public bwa |
1306 | (package | |
1307 | (name "bwa") | |
6f141eff | 1308 | (version "0.7.17") |
9a8336d8 RW |
1309 | (source (origin |
1310 | (method url-fetch) | |
ae6e00f6 BW |
1311 | (uri (string-append |
1312 | "https://github.com/lh3/bwa/releases/download/v" | |
1313 | version "/bwa-" version ".tar.bz2")) | |
9a8336d8 RW |
1314 | (sha256 |
1315 | (base32 | |
6f141eff | 1316 | "1zfhv2zg9v1icdlq4p9ssc8k01mca5d1bd87w71py2swfi74s6yy")))) |
9a8336d8 RW |
1317 | (build-system gnu-build-system) |
1318 | (arguments | |
1319 | '(#:tests? #f ;no "check" target | |
1320 | #:phases | |
dc1d3cde KK |
1321 | (modify-phases %standard-phases |
1322 | (replace 'install | |
1323 | (lambda* (#:key outputs #:allow-other-keys) | |
1324 | (let ((bin (string-append | |
1325 | (assoc-ref outputs "out") "/bin")) | |
1326 | (doc (string-append | |
1327 | (assoc-ref outputs "out") "/share/doc/bwa")) | |
1328 | (man (string-append | |
1329 | (assoc-ref outputs "out") "/share/man/man1"))) | |
1330 | (install-file "bwa" bin) | |
1331 | (install-file "README.md" doc) | |
1332 | (install-file "bwa.1" man)) | |
1333 | #t)) | |
1334 | ;; no "configure" script | |
1335 | (delete 'configure)))) | |
9a8336d8 | 1336 | (inputs `(("zlib" ,zlib))) |
db94f8c7 RW |
1337 | ;; Non-portable SSE instructions are used so building fails on platforms |
1338 | ;; other than x86_64. | |
1339 | (supported-systems '("x86_64-linux")) | |
9a8336d8 RW |
1340 | (home-page "http://bio-bwa.sourceforge.net/") |
1341 | (synopsis "Burrows-Wheeler sequence aligner") | |
1342 | (description | |
1343 | "BWA is a software package for mapping low-divergent sequences against a | |
1344 | large reference genome, such as the human genome. It consists of three | |
1345 | algorithms: BWA-backtrack, BWA-SW and BWA-MEM. The first algorithm is | |
1346 | designed for Illumina sequence reads up to 100bp, while the rest two for | |
1347 | longer sequences ranged from 70bp to 1Mbp. BWA-MEM and BWA-SW share similar | |
1348 | features such as long-read support and split alignment, but BWA-MEM, which is | |
1349 | the latest, is generally recommended for high-quality queries as it is faster | |
1350 | and more accurate. BWA-MEM also has better performance than BWA-backtrack for | |
1351 | 70-100bp Illumina reads.") | |
1352 | (license license:gpl3+))) | |
1353 | ||
d29150b5 RW |
1354 | (define-public bwa-pssm |
1355 | (package (inherit bwa) | |
1356 | (name "bwa-pssm") | |
1357 | (version "0.5.11") | |
1358 | (source (origin | |
1359 | (method url-fetch) | |
1360 | (uri (string-append "https://github.com/pkerpedjiev/bwa-pssm/" | |
1361 | "archive/" version ".tar.gz")) | |
1362 | (file-name (string-append name "-" version ".tar.gz")) | |
1363 | (sha256 | |
1364 | (base32 | |
1365 | "02p7mpbs4mlxmn84g2x4ghak638vbj4lqix2ipx5g84pz9bhdavg")))) | |
1366 | (build-system gnu-build-system) | |
1367 | (inputs | |
1368 | `(("gdsl" ,gdsl) | |
1369 | ("zlib" ,zlib) | |
1370 | ("perl" ,perl))) | |
1371 | (home-page "http://bwa-pssm.binf.ku.dk/") | |
1372 | (synopsis "Burrows-Wheeler transform-based probabilistic short read mapper") | |
1373 | (description | |
1374 | "BWA-PSSM is a probabilistic short genomic sequence read aligner based on | |
1375 | the use of @dfn{position specific scoring matrices} (PSSM). Like many of the | |
1376 | existing aligners it is fast and sensitive. Unlike most other aligners, | |
1377 | however, it is also adaptible in the sense that one can direct the alignment | |
1378 | based on known biases within the data set. It is coded as a modification of | |
1379 | the original BWA alignment program and shares the genome index structure as | |
1380 | well as many of the command line options.") | |
1381 | (license license:gpl3+))) | |
1382 | ||
ad641d53 RW |
1383 | (define-public python2-bx-python |
1384 | (package | |
1385 | (name "python2-bx-python") | |
c1dfe8c3 | 1386 | (version "0.7.3") |
ad641d53 RW |
1387 | (source (origin |
1388 | (method url-fetch) | |
c1dfe8c3 | 1389 | (uri (pypi-uri "bx-python" version)) |
ad641d53 RW |
1390 | (sha256 |
1391 | (base32 | |
c1dfe8c3 | 1392 | "15z2w3bvnc0n4qmb9bd6d8ylc2h2nj883x2w9iixf4x3vki9b22i")) |
ad641d53 RW |
1393 | (modules '((guix build utils))) |
1394 | (snippet | |
1395 | '(substitute* "setup.py" | |
1396 | ;; remove dependency on outdated "distribute" module | |
1397 | (("^from distribute_setup import use_setuptools") "") | |
1398 | (("^use_setuptools\\(\\)") ""))))) | |
1399 | (build-system python-build-system) | |
1400 | (arguments | |
1401 | `(#:tests? #f ;tests fail because test data are not included | |
1402 | #:python ,python-2)) | |
1403 | (inputs | |
1404 | `(("python-numpy" ,python2-numpy) | |
1405 | ("zlib" ,zlib))) | |
1406 | (native-inputs | |
f3b98f4f | 1407 | `(("python-nose" ,python2-nose))) |
ad641d53 RW |
1408 | (home-page "http://bitbucket.org/james_taylor/bx-python/") |
1409 | (synopsis "Tools for manipulating biological data") | |
1410 | (description | |
1411 | "bx-python provides tools for manipulating biological data, particularly | |
1412 | multiple sequence alignments.") | |
1413 | (license license:expat))) | |
1414 | ||
55a9a8c2 RW |
1415 | (define-public python-pysam |
1416 | (package | |
1417 | (name "python-pysam") | |
68565184 | 1418 | (version "0.13.0") |
d454640c RW |
1419 | (source (origin |
1420 | (method url-fetch) | |
f536dce5 MB |
1421 | ;; Test data is missing on PyPi. |
1422 | (uri (string-append | |
1423 | "https://github.com/pysam-developers/pysam/archive/v" | |
1424 | version ".tar.gz")) | |
1425 | (file-name (string-append name "-" version ".tar.gz")) | |
d454640c RW |
1426 | (sha256 |
1427 | (base32 | |
68565184 | 1428 | "0dzap2axin9cbbl0d825w294bpn00zagfm1sigamm4v2pm5bj9lp")) |
dff26b23 MB |
1429 | (modules '((guix build utils))) |
1430 | (snippet | |
1431 | ;; Drop bundled htslib. TODO: Also remove samtools and bcftools. | |
1432 | '(delete-file-recursively "htslib")))) | |
55a9a8c2 RW |
1433 | (build-system python-build-system) |
1434 | (arguments | |
71dbf592 RW |
1435 | `(#:modules ((ice-9 ftw) |
1436 | (srfi srfi-26) | |
1437 | (guix build python-build-system) | |
1438 | (guix build utils)) | |
1439 | #:phases | |
397d463a MB |
1440 | (modify-phases %standard-phases |
1441 | (add-before 'build 'set-flags | |
dff26b23 MB |
1442 | (lambda* (#:key inputs #:allow-other-keys) |
1443 | (setenv "HTSLIB_MODE" "external") | |
1444 | (setenv "HTSLIB_LIBRARY_DIR" | |
1445 | (string-append (assoc-ref inputs "htslib") "/lib")) | |
1446 | (setenv "HTSLIB_INCLUDE_DIR" | |
1447 | (string-append (assoc-ref inputs "htslib") "/include")) | |
397d463a MB |
1448 | (setenv "LDFLAGS" "-lncurses") |
1449 | (setenv "CFLAGS" "-D_CURSES_LIB=1") | |
f536dce5 | 1450 | #t)) |
71dbf592 | 1451 | (replace 'check |
f536dce5 | 1452 | (lambda* (#:key inputs outputs #:allow-other-keys) |
71dbf592 | 1453 | ;; Add first subdirectory of "build" directory to PYTHONPATH. |
f536dce5 MB |
1454 | (setenv "PYTHONPATH" |
1455 | (string-append | |
1456 | (getenv "PYTHONPATH") | |
71dbf592 RW |
1457 | ":" (getcwd) "/build/" |
1458 | (car (scandir "build" | |
e1f02f92 | 1459 | (negate (cut string-prefix? "." <>)))))) |
f536dce5 | 1460 | ;; Step out of source dir so python does not import from CWD. |
71dbf592 RW |
1461 | (with-directory-excursion "tests" |
1462 | (setenv "HOME" "/tmp") | |
1463 | (and (zero? (system* "make" "-C" "pysam_data")) | |
1464 | (zero? (system* "make" "-C" "cbcf_data")) | |
b2955e22 RW |
1465 | ;; Running nosetests without explicitly asking for a |
1466 | ;; single process leads to a crash. Running with multiple | |
1467 | ;; processes fails because the tests are not designed to | |
1468 | ;; run in parallel. | |
31c374e0 RW |
1469 | |
1470 | ;; FIXME: tests keep timing out on some systems. | |
1471 | ;; (zero? (system* "nosetests" "-v" | |
1472 | ;; "--processes" "1")) | |
1473 | ))))))) | |
dff26b23 MB |
1474 | (propagated-inputs |
1475 | `(("htslib" ,htslib))) ; Included from installed header files. | |
55a9a8c2 | 1476 | (inputs |
649e9b3b | 1477 | `(("ncurses" ,ncurses) |
55a9a8c2 | 1478 | ("zlib" ,zlib))) |
649e9b3b RW |
1479 | (native-inputs |
1480 | `(("python-cython" ,python-cython) | |
f536dce5 MB |
1481 | ;; Dependencies below are are for tests only. |
1482 | ("samtools" ,samtools) | |
1483 | ("bcftools" ,bcftools) | |
1484 | ("python-nose" ,python-nose))) | |
55a9a8c2 RW |
1485 | (home-page "https://github.com/pysam-developers/pysam") |
1486 | (synopsis "Python bindings to the SAMtools C API") | |
1487 | (description | |
1488 | "Pysam is a Python module for reading and manipulating files in the | |
1489 | SAM/BAM format. Pysam is a lightweight wrapper of the SAMtools C API. It | |
1490 | also includes an interface for tabix.") | |
1491 | (license license:expat))) | |
1492 | ||
1493 | (define-public python2-pysam | |
1494 | (package-with-python2 python-pysam)) | |
1495 | ||
4db9433a RW |
1496 | (define-public python-twobitreader |
1497 | (package | |
1498 | (name "python-twobitreader") | |
044ac8d2 | 1499 | (version "3.1.4") |
4db9433a RW |
1500 | (source (origin |
1501 | (method url-fetch) | |
1502 | (uri (pypi-uri "twobitreader" version)) | |
1503 | (sha256 | |
1504 | (base32 | |
044ac8d2 | 1505 | "1q8wnj2kga9nz1lwc4w7qv52smfm536hp6mc8w6s53lhyj0mpi22")))) |
4db9433a | 1506 | (build-system python-build-system) |
900fb8d0 LF |
1507 | (arguments |
1508 | '(;; Tests are not distributed in the PyPi release. | |
1509 | ;; TODO Try building from the Git repo or asking the upstream maintainer | |
1510 | ;; to distribute the tests on PyPi. | |
1511 | #:tests? #f)) | |
4db9433a RW |
1512 | (native-inputs |
1513 | `(("python-sphinx" ,python-sphinx))) | |
1514 | (home-page "https://github.com/benjschiller/twobitreader") | |
1515 | (synopsis "Python library for reading .2bit files") | |
1516 | (description | |
1517 | "twobitreader is a Python library for reading .2bit files as used by the | |
1518 | UCSC genome browser.") | |
1519 | (license license:artistic2.0))) | |
1520 | ||
1521 | (define-public python2-twobitreader | |
5c31f4aa | 1522 | (package-with-python2 python-twobitreader)) |
4db9433a | 1523 | |
f94bf198 RW |
1524 | (define-public python-plastid |
1525 | (package | |
1526 | (name "python-plastid") | |
897ab082 | 1527 | (version "0.4.8") |
f94bf198 RW |
1528 | (source (origin |
1529 | (method url-fetch) | |
1530 | (uri (pypi-uri "plastid" version)) | |
1531 | (sha256 | |
1532 | (base32 | |
897ab082 | 1533 | "0l24dd3q66if8yj042m4s0g95n6acn7im1imqd3p6h8ns43kxhj8")))) |
f94bf198 RW |
1534 | (build-system python-build-system) |
1535 | (arguments | |
1536 | ;; Some test files are not included. | |
1537 | `(#:tests? #f)) | |
1538 | (propagated-inputs | |
1539 | `(("python-numpy" ,python-numpy) | |
1540 | ("python-scipy" ,python-scipy) | |
1541 | ("python-pandas" ,python-pandas) | |
1542 | ("python-pysam" ,python-pysam) | |
1543 | ("python-matplotlib" ,python-matplotlib) | |
1544 | ("python-biopython" ,python-biopython) | |
99caa6f7 BW |
1545 | ("python-twobitreader" ,python-twobitreader) |
1546 | ("python-termcolor" ,python-termcolor))) | |
f94bf198 RW |
1547 | (native-inputs |
1548 | `(("python-cython" ,python-cython) | |
1549 | ("python-nose" ,python-nose))) | |
1550 | (home-page "https://github.com/joshuagryphon/plastid") | |
1551 | (synopsis "Python library for genomic analysis") | |
1552 | (description | |
1553 | "plastid is a Python library for genomic analysis – in particular, | |
1554 | high-throughput sequencing data – with an emphasis on simplicity.") | |
1555 | (license license:bsd-3))) | |
1556 | ||
1557 | (define-public python2-plastid | |
5c31f4aa | 1558 | (package-with-python2 python-plastid)) |
f94bf198 | 1559 | |
6c1305f9 RW |
1560 | (define-public cd-hit |
1561 | (package | |
1562 | (name "cd-hit") | |
ba773f65 | 1563 | (version "4.6.8") |
6c1305f9 RW |
1564 | (source (origin |
1565 | (method url-fetch) | |
1566 | (uri (string-append "https://github.com/weizhongli/cdhit" | |
1567 | "/releases/download/V" version | |
ba773f65 BW |
1568 | "/cd-hit-v" version |
1569 | "-2017-0621-source.tar.gz")) | |
6c1305f9 RW |
1570 | (sha256 |
1571 | (base32 | |
d4735e8c | 1572 | "1b4mwm2520ixjbw57sil20f9iixzw4bkdqqwgg1fc3pzm6rz4zmn")))) |
6c1305f9 RW |
1573 | (build-system gnu-build-system) |
1574 | (arguments | |
1575 | `(#:tests? #f ; there are no tests | |
1576 | #:make-flags | |
1577 | ;; Executables are copied directly to the PREFIX. | |
1578 | (list (string-append "PREFIX=" (assoc-ref %outputs "out") "/bin")) | |
1579 | #:phases | |
1580 | (modify-phases %standard-phases | |
1581 | ;; No "configure" script | |
1582 | (delete 'configure) | |
1583 | ;; Remove sources of non-determinism | |
1584 | (add-after 'unpack 'be-timeless | |
1585 | (lambda _ | |
1586 | (substitute* "cdhit-utility.c++" | |
1587 | ((" \\(built on \" __DATE__ \"\\)") "")) | |
1588 | (substitute* "cdhit-common.c++" | |
1589 | (("__DATE__") "\"0\"") | |
1590 | (("\", %s, \" __TIME__ \"\\\\n\", date") "")) | |
1591 | #t)) | |
ba773f65 | 1592 | ;; The "install" target does not create the target directory. |
6c1305f9 RW |
1593 | (add-before 'install 'create-target-dir |
1594 | (lambda* (#:key outputs #:allow-other-keys) | |
1595 | (mkdir-p (string-append (assoc-ref outputs "out") "/bin")) | |
1596 | #t))))) | |
1597 | (inputs | |
1598 | `(("perl" ,perl))) | |
1599 | (home-page "http://weizhongli-lab.org/cd-hit/") | |
1600 | (synopsis "Cluster and compare protein or nucleotide sequences") | |
1601 | (description | |
1602 | "CD-HIT is a program for clustering and comparing protein or nucleotide | |
1603 | sequences. CD-HIT is designed to be fast and handle extremely large | |
1604 | databases.") | |
1605 | ;; The manual says: "It can be copied under the GNU General Public License | |
1606 | ;; version 2 (GPLv2)." | |
1607 | (license license:gpl2))) | |
1608 | ||
810cff85 RW |
1609 | (define-public clipper |
1610 | (package | |
1611 | (name "clipper") | |
433530a5 | 1612 | (version "1.1") |
810cff85 RW |
1613 | (source (origin |
1614 | (method url-fetch) | |
1615 | (uri (string-append | |
1616 | "https://github.com/YeoLab/clipper/archive/" | |
1617 | version ".tar.gz")) | |
9ab5ea44 | 1618 | (file-name (string-append name "-" version ".tar.gz")) |
810cff85 RW |
1619 | (sha256 |
1620 | (base32 | |
433530a5 | 1621 | "0pflmsvhbf8izbgwhbhj1i7349sw1f55qpqj8ljmapp16hb0p0qi")) |
810cff85 RW |
1622 | (modules '((guix build utils))) |
1623 | (snippet | |
433530a5 RW |
1624 | '(begin |
1625 | ;; remove unnecessary setup dependency | |
1626 | (substitute* "setup.py" | |
1627 | (("setup_requires = .*") "")) | |
1628 | (for-each delete-file | |
1629 | '("clipper/src/peaks.so" | |
1630 | "clipper/src/readsToWiggle.so")) | |
1631 | (delete-file-recursively "dist/") | |
1632 | #t)))) | |
810cff85 RW |
1633 | (build-system python-build-system) |
1634 | (arguments `(#:python ,python-2)) ; only Python 2 is supported | |
1635 | (inputs | |
92971d68 | 1636 | `(("htseq" ,python2-htseq) |
810cff85 RW |
1637 | ("python-pybedtools" ,python2-pybedtools) |
1638 | ("python-cython" ,python2-cython) | |
1639 | ("python-scikit-learn" ,python2-scikit-learn) | |
1640 | ("python-matplotlib" ,python2-matplotlib) | |
433530a5 | 1641 | ("python-pandas" ,python2-pandas) |
810cff85 RW |
1642 | ("python-pysam" ,python2-pysam) |
1643 | ("python-numpy" ,python2-numpy) | |
1644 | ("python-scipy" ,python2-scipy))) | |
1645 | (native-inputs | |
f3b98f4f | 1646 | `(("python-mock" ,python2-mock) ; for tests |
d281be18 | 1647 | ("python-nose" ,python2-nose) ; for tests |
f3b98f4f | 1648 | ("python-pytz" ,python2-pytz))) ; for tests |
810cff85 RW |
1649 | (home-page "https://github.com/YeoLab/clipper") |
1650 | (synopsis "CLIP peak enrichment recognition") | |
1651 | (description | |
1652 | "CLIPper is a tool to define peaks in CLIP-seq datasets.") | |
1653 | (license license:gpl2))) | |
1654 | ||
6a35566d RS |
1655 | (define-public codingquarry |
1656 | (package | |
1657 | (name "codingquarry") | |
1658 | (version "2.0") | |
1659 | (source (origin | |
1660 | (method url-fetch) | |
1661 | (uri (string-append | |
1662 | "mirror://sourceforge/codingquarry/CodingQuarry_v" | |
1663 | version ".tar.gz")) | |
1664 | (sha256 | |
1665 | (base32 | |
1666 | "0115hkjflsnfzn36xppwf9h9avfxlavr43djqmshkkzbgjzsz60i")))) | |
1667 | (build-system gnu-build-system) | |
1668 | (arguments | |
1669 | '(#:tests? #f ; no "check" target | |
1670 | #:phases | |
1671 | (modify-phases %standard-phases | |
1672 | (delete 'configure) | |
1673 | (replace 'install | |
1674 | (lambda* (#:key outputs #:allow-other-keys) | |
1675 | (let* ((out (assoc-ref outputs "out")) | |
1676 | (bin (string-append out "/bin")) | |
1677 | (doc (string-append out "/share/doc/codingquarry"))) | |
1678 | (install-file "INSTRUCTIONS.pdf" doc) | |
1679 | (copy-recursively "QuarryFiles" | |
1680 | (string-append out "/QuarryFiles")) | |
1681 | (install-file "CodingQuarry" bin) | |
1682 | (install-file "CufflinksGTF_to_CodingQuarryGFF3.py" bin))))))) | |
1683 | (inputs `(("openmpi" ,openmpi))) | |
1684 | (native-search-paths | |
1685 | (list (search-path-specification | |
1686 | (variable "QUARRY_PATH") | |
1687 | (files '("QuarryFiles"))))) | |
1688 | (native-inputs `(("python" ,python-2))) ; Only Python 2 is supported | |
1689 | (synopsis "Fungal gene predictor") | |
1690 | (description "CodingQuarry is a highly accurate, self-training GHMM fungal | |
1691 | gene predictor designed to work with assembled, aligned RNA-seq transcripts.") | |
1692 | (home-page "https://sourceforge.net/projects/codingquarry/") | |
1693 | (license license:gpl3+))) | |
1694 | ||
36742f43 RW |
1695 | (define-public couger |
1696 | (package | |
1697 | (name "couger") | |
1698 | (version "1.8.2") | |
1699 | (source (origin | |
1700 | (method url-fetch) | |
1701 | (uri (string-append | |
1702 | "http://couger.oit.duke.edu/static/assets/COUGER" | |
1703 | version ".zip")) | |
1704 | (sha256 | |
1705 | (base32 | |
1706 | "04p2b14nmhzxw5h72mpzdhalv21bx4w9b87z0wpw0xzxpysyncmq")))) | |
1707 | (build-system gnu-build-system) | |
1708 | (arguments | |
1709 | `(#:tests? #f | |
1710 | #:phases | |
1711 | (modify-phases %standard-phases | |
1712 | (delete 'configure) | |
1713 | (delete 'build) | |
1714 | (replace | |
1715 | 'install | |
1716 | (lambda* (#:key outputs #:allow-other-keys) | |
f3860753 TGR |
1717 | (let* ((out (assoc-ref outputs "out")) |
1718 | (bin (string-append out "/bin"))) | |
36742f43 | 1719 | (copy-recursively "src" (string-append out "/src")) |
f3860753 | 1720 | (mkdir bin) |
36742f43 RW |
1721 | ;; Add "src" directory to module lookup path. |
1722 | (substitute* "couger" | |
1723 | (("from argparse") | |
1724 | (string-append "import sys\nsys.path.append(\"" | |
1725 | out "\")\nfrom argparse"))) | |
f3860753 | 1726 | (install-file "couger" bin)) |
36742f43 RW |
1727 | #t)) |
1728 | (add-after | |
1729 | 'install 'wrap-program | |
1730 | (lambda* (#:key inputs outputs #:allow-other-keys) | |
1731 | ;; Make sure 'couger' runs with the correct PYTHONPATH. | |
1732 | (let* ((out (assoc-ref outputs "out")) | |
1733 | (path (getenv "PYTHONPATH"))) | |
1734 | (wrap-program (string-append out "/bin/couger") | |
1735 | `("PYTHONPATH" ":" prefix (,path)))) | |
1736 | #t))))) | |
1737 | (inputs | |
1738 | `(("python" ,python-2) | |
1739 | ("python2-pillow" ,python2-pillow) | |
1740 | ("python2-numpy" ,python2-numpy) | |
1741 | ("python2-scipy" ,python2-scipy) | |
1742 | ("python2-matplotlib" ,python2-matplotlib))) | |
1743 | (propagated-inputs | |
2d7c4ae3 | 1744 | `(("r-minimal" ,r-minimal) |
36742f43 RW |
1745 | ("libsvm" ,libsvm) |
1746 | ("randomjungle" ,randomjungle))) | |
1747 | (native-inputs | |
1748 | `(("unzip" ,unzip))) | |
1749 | (home-page "http://couger.oit.duke.edu") | |
1750 | (synopsis "Identify co-factors in sets of genomic regions") | |
1751 | (description | |
1752 | "COUGER can be applied to any two sets of genomic regions bound by | |
1753 | paralogous TFs (e.g., regions derived from ChIP-seq experiments) to identify | |
1754 | putative co-factors that provide specificity to each TF. The framework | |
1755 | determines the genomic targets uniquely-bound by each TF, and identifies a | |
1756 | small set of co-factors that best explain the in vivo binding differences | |
1757 | between the two TFs. | |
1758 | ||
1759 | COUGER uses classification algorithms (support vector machines and random | |
1760 | forests) with features that reflect the DNA binding specificities of putative | |
1761 | co-factors. The features are generated either from high-throughput TF-DNA | |
1762 | binding data (from protein binding microarray experiments), or from large | |
1763 | collections of DNA motifs.") | |
1764 | (license license:gpl3+))) | |
1765 | ||
bfe3c685 RW |
1766 | (define-public clustal-omega |
1767 | (package | |
1768 | (name "clustal-omega") | |
b3936f35 | 1769 | (version "1.2.4") |
bfe3c685 RW |
1770 | (source (origin |
1771 | (method url-fetch) | |
b3936f35 RW |
1772 | (uri (string-append "http://www.clustal.org/omega/clustal-omega-" |
1773 | version ".tar.gz")) | |
bfe3c685 RW |
1774 | (sha256 |
1775 | (base32 | |
b3936f35 | 1776 | "1vm30mzncwdv881vrcwg11vzvrsmwy4wg80j5i0lcfk6dlld50w6")))) |
bfe3c685 RW |
1777 | (build-system gnu-build-system) |
1778 | (inputs | |
1779 | `(("argtable" ,argtable))) | |
1780 | (home-page "http://www.clustal.org/omega/") | |
1781 | (synopsis "Multiple sequence aligner for protein and DNA/RNA") | |
1782 | (description | |
1783 | "Clustal-Omega is a general purpose multiple sequence alignment (MSA) | |
1784 | program for protein and DNA/RNA. It produces high quality MSAs and is capable | |
1785 | of handling data-sets of hundreds of thousands of sequences in reasonable | |
1786 | time.") | |
1787 | (license license:gpl2+))) | |
1788 | ||
191c7101 RW |
1789 | (define-public crossmap |
1790 | (package | |
1791 | (name "crossmap") | |
61d5fd03 | 1792 | (version "0.2.1") |
191c7101 RW |
1793 | (source (origin |
1794 | (method url-fetch) | |
1795 | (uri (string-append "mirror://sourceforge/crossmap/CrossMap-" | |
1796 | version ".tar.gz")) | |
1797 | (sha256 | |
1798 | (base32 | |
61d5fd03 RW |
1799 | "07y179f63d7qnzdvkqcziwk9bs3k4zhp81q392fp1hwszjdvy22f")) |
1800 | ;; This patch has been sent upstream already and is available | |
1801 | ;; for download from Sourceforge, but it has not been merged. | |
fc1adab1 | 1802 | (patches (search-patches "crossmap-allow-system-pysam.patch")) |
191c7101 RW |
1803 | (modules '((guix build utils))) |
1804 | ;; remove bundled copy of pysam | |
1805 | (snippet | |
1806 | '(delete-file-recursively "lib/pysam")))) | |
1807 | (build-system python-build-system) | |
1808 | (arguments | |
1809 | `(#:python ,python-2 | |
1810 | #:phases | |
dc1d3cde KK |
1811 | (modify-phases %standard-phases |
1812 | (add-after 'unpack 'set-env | |
1813 | (lambda _ (setenv "CROSSMAP_USE_SYSTEM_PYSAM" "1") #t))))) | |
191c7101 RW |
1814 | (inputs |
1815 | `(("python-numpy" ,python2-numpy) | |
1816 | ("python-pysam" ,python2-pysam) | |
1817 | ("zlib" ,zlib))) | |
1818 | (native-inputs | |
1819 | `(("python-cython" ,python2-cython) | |
f3b98f4f | 1820 | ("python-nose" ,python2-nose))) |
191c7101 RW |
1821 | (home-page "http://crossmap.sourceforge.net/") |
1822 | (synopsis "Convert genome coordinates between assemblies") | |
1823 | (description | |
1824 | "CrossMap is a program for conversion of genome coordinates or annotation | |
1825 | files between different genome assemblies. It supports most commonly used | |
1826 | file formats including SAM/BAM, Wiggle/BigWig, BED, GFF/GTF, VCF.") | |
1827 | (license license:gpl2+))) | |
1828 | ||
8e913213 RW |
1829 | (define-public cutadapt |
1830 | (package | |
1831 | (name "cutadapt") | |
3ede1550 | 1832 | (version "1.16") |
8e913213 | 1833 | (source (origin |
3ede1550 RW |
1834 | (method git-fetch) |
1835 | (uri (git-reference | |
1836 | (url "https://github.com/marcelm/cutadapt.git") | |
1837 | (commit (string-append "v" version)))) | |
1838 | (file-name (string-append name "-" version "-checkout")) | |
8e913213 RW |
1839 | (sha256 |
1840 | (base32 | |
3ede1550 | 1841 | "09pr02067jiks19nc0aby4xp70hhgvb554i2y1c04rv1m401w7q8")))) |
8e913213 | 1842 | (build-system python-build-system) |
1f94bff2 TGR |
1843 | (inputs |
1844 | `(("python-xopen" ,python-xopen))) | |
8e913213 RW |
1845 | (native-inputs |
1846 | `(("python-cython" ,python-cython) | |
3ede1550 | 1847 | ("python-pytest" ,python-pytest))) |
0c6c9c00 | 1848 | (home-page "https://cutadapt.readthedocs.io/en/stable/") |
8e913213 RW |
1849 | (synopsis "Remove adapter sequences from nucleotide sequencing reads") |
1850 | (description | |
1851 | "Cutadapt finds and removes adapter sequences, primers, poly-A tails and | |
1852 | other types of unwanted sequence from high-throughput sequencing reads.") | |
1853 | (license license:expat))) | |
1854 | ||
1baee943 RW |
1855 | (define-public libbigwig |
1856 | (package | |
1857 | (name "libbigwig") | |
1858 | (version "0.1.4") | |
1859 | (source (origin | |
1860 | (method url-fetch) | |
1861 | (uri (string-append "https://github.com/dpryan79/libBigWig/" | |
1862 | "archive/" version ".tar.gz")) | |
1863 | (file-name (string-append name "-" version ".tar.gz")) | |
1864 | (sha256 | |
1865 | (base32 | |
1866 | "098rjh35pi4a9q83n8wiwvyzykjqj6l8q189p1xgfw4ghywdlvw1")))) | |
1867 | (build-system gnu-build-system) | |
1868 | (arguments | |
1869 | `(#:test-target "test" | |
1870 | #:make-flags | |
1871 | (list "CC=gcc" | |
1872 | (string-append "prefix=" (assoc-ref %outputs "out"))) | |
1873 | #:phases | |
1874 | (modify-phases %standard-phases | |
1875 | (delete 'configure) | |
1876 | (add-before 'check 'disable-curl-test | |
1877 | (lambda _ | |
1878 | (substitute* "Makefile" | |
1879 | (("./test/testRemote.*") "")) | |
1880 | #t)) | |
1881 | ;; This has been fixed with the upstream commit 4ff6959cd8a0, but | |
1882 | ;; there has not yet been a release containing this change. | |
1883 | (add-before 'install 'create-target-dirs | |
1884 | (lambda* (#:key outputs #:allow-other-keys) | |
1885 | (let ((out (assoc-ref outputs "out"))) | |
1886 | (mkdir-p (string-append out "/lib")) | |
1887 | (mkdir-p (string-append out "/include")) | |
1888 | #t)))))) | |
1889 | (inputs | |
1890 | `(("zlib" ,zlib) | |
1891 | ("curl" ,curl))) | |
1892 | (native-inputs | |
1893 | `(("doxygen" ,doxygen))) | |
1894 | (home-page "https://github.com/dpryan79/libBigWig") | |
1895 | (synopsis "C library for handling bigWig files") | |
1896 | (description | |
1897 | "This package provides a C library for parsing local and remote BigWig | |
1898 | files.") | |
1899 | (license license:expat))) | |
1900 | ||
69e0e03c RW |
1901 | (define-public python-pybigwig |
1902 | (package | |
1903 | (name "python-pybigwig") | |
1904 | (version "0.2.5") | |
1905 | (source (origin | |
1906 | (method url-fetch) | |
1907 | (uri (pypi-uri "pyBigWig" version)) | |
1908 | (sha256 | |
1909 | (base32 | |
1910 | "0yrpdxg3y0sny25x4w22lv1k47jzccqjmg7j4bp0hywklvp0hg7d")) | |
1911 | (modules '((guix build utils))) | |
1912 | (snippet | |
1913 | '(begin | |
1914 | ;; Delete bundled libBigWig sources | |
1915 | (delete-file-recursively "libBigWig"))))) | |
1916 | (build-system python-build-system) | |
1917 | (arguments | |
1918 | `(#:phases | |
1919 | (modify-phases %standard-phases | |
1920 | (add-after 'unpack 'link-with-libBigWig | |
1921 | (lambda* (#:key inputs #:allow-other-keys) | |
1922 | (substitute* "setup.py" | |
1923 | (("libs=\\[") "libs=[\"BigWig\", ")) | |
1924 | #t))))) | |
1925 | (inputs | |
1926 | `(("libbigwig" ,libbigwig) | |
1927 | ("zlib" ,zlib) | |
1928 | ("curl" ,curl))) | |
1929 | (home-page "https://github.com/dpryan79/pyBigWig") | |
1930 | (synopsis "Access bigWig files in Python using libBigWig") | |
1931 | (description | |
1932 | "This package provides Python bindings to the libBigWig library for | |
1933 | accessing bigWig files.") | |
1934 | (license license:expat))) | |
1935 | ||
1936 | (define-public python2-pybigwig | |
5c31f4aa | 1937 | (package-with-python2 python-pybigwig)) |
69e0e03c | 1938 | |
ec2a67de BW |
1939 | (define-public python-dendropy |
1940 | (package | |
1941 | (name "python-dendropy") | |
25d84d31 | 1942 | (version "4.2.0") |
ec2a67de BW |
1943 | (source |
1944 | (origin | |
1945 | (method url-fetch) | |
1946 | (uri (pypi-uri "DendroPy" version)) | |
1947 | (sha256 | |
1948 | (base32 | |
1885bb0c RW |
1949 | "15c7s3d5gf19ljsxvq5advaa752wfi7pwrdjyhzmg85hccyvp47p")) |
1950 | (patches (search-patches "python-dendropy-fix-tests.patch")))) | |
ec2a67de BW |
1951 | (build-system python-build-system) |
1952 | (home-page "http://packages.python.org/DendroPy/") | |
1953 | (synopsis "Library for phylogenetics and phylogenetic computing") | |
1954 | (description | |
1955 | "DendroPy is a library for phylogenetics and phylogenetic computing: reading, | |
1956 | writing, simulation, processing and manipulation of phylogenetic | |
1957 | trees (phylogenies) and characters.") | |
1958 | (license license:bsd-3) | |
1959 | (properties `((python2-variant . ,(delay python2-dendropy)))))) | |
1960 | ||
1961 | (define-public python2-dendropy | |
1962 | (let ((base (package-with-python2 (strip-python2-variant python-dendropy)))) | |
1963 | (package | |
1964 | (inherit base) | |
9602e3cc BW |
1965 | (arguments |
1966 | `(#:python ,python-2 | |
1967 | #:phases | |
1968 | (modify-phases %standard-phases | |
1969 | (replace 'check | |
1970 | ;; There is currently a test failure that only happens on some | |
1971 | ;; systems, and only using "setup.py test" | |
1972 | (lambda _ (zero? (system* "nosetests"))))))) | |
f3b98f4f | 1973 | (native-inputs `(("python2-nose" ,python2-nose) |
ec2a67de BW |
1974 | ,@(package-native-inputs base)))))) |
1975 | ||
eb2200f3 RW |
1976 | (define-public python-py2bit |
1977 | (package | |
1978 | (name "python-py2bit") | |
1979 | (version "0.2.1") | |
1980 | (source | |
1981 | (origin | |
1982 | (method url-fetch) | |
1983 | (uri (pypi-uri "py2bit" version)) | |
1984 | (sha256 | |
1985 | (base32 | |
1986 | "1cdf4qlmgwsh1f4k0wdv2sr8x9qn4366p0k3614vbd0fpqiarxrl")))) | |
1987 | (build-system python-build-system) | |
1988 | (home-page "https://github.com/dpryan79/py2bit") | |
1989 | (synopsis "Access 2bit files using lib2bit") | |
1990 | (description | |
1991 | "This package provides Python bindings for lib2bit to access 2bit files | |
1992 | with Python.") | |
1993 | (license license:expat))) | |
ec2a67de | 1994 | |
1921b1de RW |
1995 | (define-public deeptools |
1996 | (package | |
1997 | (name "deeptools") | |
fed72008 | 1998 | (version "2.5.1") |
1921b1de RW |
1999 | (source (origin |
2000 | (method url-fetch) | |
cd70f9bd | 2001 | (uri (string-append "https://github.com/deeptools/deepTools/" |
3acb8c85 | 2002 | "archive/" version ".tar.gz")) |
1921b1de RW |
2003 | (file-name (string-append name "-" version ".tar.gz")) |
2004 | (sha256 | |
2005 | (base32 | |
fed72008 | 2006 | "1q8i12l2gvk4n2s8lhyzwhh9g4qbc8lrk5l7maz00yvd5g6z5540")))) |
1921b1de | 2007 | (build-system python-build-system) |
14bda1ff | 2008 | (inputs |
fed72008 RW |
2009 | `(("python-scipy" ,python-scipy) |
2010 | ("python-numpy" ,python-numpy) | |
2011 | ("python-numpydoc" ,python-numpydoc) | |
2012 | ("python-matplotlib" ,python-matplotlib) | |
2013 | ("python-pysam" ,python-pysam) | |
2014 | ("python-py2bit" ,python-py2bit) | |
2015 | ("python-pybigwig" ,python-pybigwig))) | |
1921b1de | 2016 | (native-inputs |
fed72008 RW |
2017 | `(("python-mock" ,python-mock) ;for tests |
2018 | ("python-nose" ,python-nose) ;for tests | |
2019 | ("python-pytz" ,python-pytz))) ;for tests | |
cd70f9bd | 2020 | (home-page "https://github.com/deeptools/deepTools") |
1921b1de RW |
2021 | (synopsis "Tools for normalizing and visualizing deep-sequencing data") |
2022 | (description | |
2023 | "DeepTools addresses the challenge of handling the large amounts of data | |
2024 | that are now routinely generated from DNA sequencing centers. To do so, | |
2025 | deepTools contains useful modules to process the mapped reads data to create | |
2026 | coverage files in standard bedGraph and bigWig file formats. By doing so, | |
2027 | deepTools allows the creation of normalized coverage files or the comparison | |
2028 | between two files (for example, treatment and control). Finally, using such | |
2029 | normalized and standardized files, multiple visualizations can be created to | |
2030 | identify enrichments with functional annotations of the genome.") | |
2031 | (license license:gpl3+))) | |
2032 | ||
684bf7c7 BW |
2033 | (define-public diamond |
2034 | (package | |
2035 | (name "diamond") | |
5ebc8e7f | 2036 | (version "0.9.18") |
684bf7c7 BW |
2037 | (source (origin |
2038 | (method url-fetch) | |
2039 | (uri (string-append | |
2040 | "https://github.com/bbuchfink/diamond/archive/v" | |
2041 | version ".tar.gz")) | |
2042 | (file-name (string-append name "-" version ".tar.gz")) | |
2043 | (sha256 | |
2044 | (base32 | |
5ebc8e7f | 2045 | "1vi2nddmy7knrv8gsprwqp6a40k63n3f2dfvx22ipjhrg9xir96f")))) |
122395f9 | 2046 | (build-system cmake-build-system) |
684bf7c7 | 2047 | (arguments |
7c544991 BW |
2048 | '(#:tests? #f ; no "check" target |
2049 | #:phases | |
2050 | (modify-phases %standard-phases | |
2051 | (add-after 'unpack 'remove-native-compilation | |
2052 | (lambda _ | |
2053 | (substitute* "CMakeLists.txt" (("-march=native") "")) | |
2054 | #t))))) | |
684bf7c7 | 2055 | (inputs |
122395f9 | 2056 | `(("zlib" ,zlib))) |
684bf7c7 BW |
2057 | (home-page "https://github.com/bbuchfink/diamond") |
2058 | (synopsis "Accelerated BLAST compatible local sequence aligner") | |
2059 | (description | |
2060 | "DIAMOND is a BLAST-compatible local aligner for mapping protein and | |
2061 | translated DNA query sequences against a protein reference database (BLASTP | |
2062 | and BLASTX alignment mode). The speedup over BLAST is up to 20,000 on short | |
2063 | reads at a typical sensitivity of 90-99% relative to BLAST depending on the | |
2064 | data and settings.") | |
ef81341f | 2065 | (license license:agpl3+))) |
684bf7c7 | 2066 | |
97b9da68 RW |
2067 | (define-public discrover |
2068 | (package | |
2069 | (name "discrover") | |
2070 | (version "1.6.0") | |
2071 | (source | |
2072 | (origin | |
2073 | (method url-fetch) | |
2074 | (uri (string-append "https://github.com/maaskola/discrover/archive/" | |
2075 | version ".tar.gz")) | |
2076 | (file-name (string-append name "-" version ".tar.gz")) | |
2077 | (sha256 | |
2078 | (base32 | |
2079 | "0rah9ja4m0rl5mldd6vag9rwrivw1zrqxssfq8qx64m7961fp68k")))) | |
2080 | (build-system cmake-build-system) | |
fa702e1a RW |
2081 | (arguments |
2082 | `(#:tests? #f ; there are no tests | |
2083 | #:phases | |
2084 | (modify-phases %standard-phases | |
2085 | (add-after 'unpack 'add-missing-includes | |
2086 | (lambda _ | |
2087 | (substitute* "src/executioninformation.hpp" | |
2088 | (("#define EXECUTIONINFORMATION_HPP" line) | |
2089 | (string-append line "\n#include <random>"))) | |
2090 | (substitute* "src/plasma/fasta.hpp" | |
2091 | (("#define FASTA_HPP" line) | |
2092 | (string-append line "\n#include <random>"))) | |
2093 | #t))))) | |
97b9da68 RW |
2094 | (inputs |
2095 | `(("boost" ,boost) | |
2096 | ("cairo" ,cairo))) | |
2097 | (native-inputs | |
2098 | `(("texlive" ,texlive) | |
2099 | ("imagemagick" ,imagemagick))) | |
2100 | (home-page "http://dorina.mdc-berlin.de/public/rajewsky/discrover/") | |
2101 | (synopsis "Discover discriminative nucleotide sequence motifs") | |
2102 | (description "Discrover is a motif discovery method to find binding sites | |
2103 | of nucleic acid binding proteins.") | |
2104 | (license license:gpl3+))) | |
2105 | ||
6619f9c7 RW |
2106 | (define-public eigensoft |
2107 | (let ((revision "1") | |
2108 | (commit "b14d1e202e21e532536ff8004f0419cd5e259dc7")) | |
2109 | (package | |
2110 | (name "eigensoft") | |
2111 | (version (string-append "6.1.2-" | |
2112 | revision "." | |
2113 | (string-take commit 9))) | |
2114 | (source | |
2115 | (origin | |
2116 | (method git-fetch) | |
2117 | (uri (git-reference | |
2118 | (url "https://github.com/DReichLab/EIG.git") | |
2119 | (commit commit))) | |
2120 | (file-name (string-append "eigensoft-" commit "-checkout")) | |
2121 | (sha256 | |
2122 | (base32 | |
2123 | "0f5m6k2j5c16xc3xbywcs989xyc26ncy1zfzp9j9n55n9r4xcaiq")) | |
2124 | (modules '((guix build utils))) | |
2125 | ;; Remove pre-built binaries. | |
2126 | (snippet '(begin | |
2127 | (delete-file-recursively "bin") | |
2128 | (mkdir "bin") | |
2129 | #t)))) | |
2130 | (build-system gnu-build-system) | |
2131 | (arguments | |
2132 | `(#:tests? #f ; There are no tests. | |
2133 | #:make-flags '("CC=gcc") | |
2134 | #:phases | |
2135 | (modify-phases %standard-phases | |
2136 | ;; There is no configure phase, but the Makefile is in a | |
2137 | ;; sub-directory. | |
2138 | (replace 'configure | |
2139 | (lambda _ | |
2140 | (chdir "src") | |
2141 | ;; The link flags are incomplete. | |
2142 | (substitute* "Makefile" | |
2143 | (("-lgsl") "-lgsl -lm -llapack -llapacke -lpthread")) | |
2144 | #t)) | |
2145 | ;; The provided install target only copies executables to | |
2146 | ;; the "bin" directory in the build root. | |
2147 | (add-after 'install 'actually-install | |
2148 | (lambda* (#:key outputs #:allow-other-keys) | |
2149 | (let* ((out (assoc-ref outputs "out")) | |
2150 | (bin (string-append out "/bin"))) | |
6619f9c7 RW |
2151 | (for-each (lambda (file) |
2152 | (install-file file bin)) | |
2153 | (find-files "../bin" ".*")) | |
2154 | #t)))))) | |
2155 | (inputs | |
2156 | `(("gsl" ,gsl) | |
2157 | ("lapack" ,lapack) | |
6619f9c7 RW |
2158 | ("openblas" ,openblas) |
2159 | ("perl" ,perl) | |
2160 | ("gfortran" ,gfortran "lib"))) | |
2161 | (home-page "https://github.com/DReichLab/EIG") | |
2162 | (synopsis "Tools for population genetics") | |
2163 | (description "The EIGENSOFT package provides tools for population | |
2164 | genetics and stratification correction. EIGENSOFT implements methods commonly | |
2165 | used in population genetics analyses such as PCA, computation of Tracy-Widom | |
2166 | statistics, and finding related individuals in structured populations. It | |
2167 | comes with a built-in plotting script and supports multiple file formats and | |
2168 | quantitative phenotypes.") | |
2169 | ;; The license of the eigensoft tools is Expat, but since it's | |
2170 | ;; linking with the GNU Scientific Library (GSL) the effective | |
2171 | ;; license is the GPL. | |
2172 | (license license:gpl3+)))) | |
2173 | ||
365c8153 RW |
2174 | (define-public edirect |
2175 | (package | |
2176 | (name "edirect") | |
83b84fa8 | 2177 | (version "4.10") |
365c8153 RW |
2178 | (source (origin |
2179 | (method url-fetch) | |
83b84fa8 RW |
2180 | (uri (string-append "ftp://ftp.ncbi.nlm.nih.gov/entrez/entrezdirect/" |
2181 | "versions/2016-05-03/edirect.tar.gz")) | |
365c8153 RW |
2182 | (sha256 |
2183 | (base32 | |
83b84fa8 | 2184 | "15zsprak5yh8c1yrz4r1knmb5s8qcmdid4xdhkh3lqcv64l60hli")))) |
365c8153 RW |
2185 | (build-system perl-build-system) |
2186 | (arguments | |
2187 | `(#:tests? #f ;no "check" target | |
2188 | #:phases | |
2189 | (modify-phases %standard-phases | |
2190 | (delete 'configure) | |
2191 | (delete 'build) | |
2192 | (replace 'install | |
2193 | (lambda* (#:key outputs #:allow-other-keys) | |
2194 | (let ((target (string-append (assoc-ref outputs "out") | |
2195 | "/bin"))) | |
2196 | (mkdir-p target) | |
f3860753 | 2197 | (install-file "edirect.pl" target) |
365c8153 RW |
2198 | #t))) |
2199 | (add-after | |
2200 | 'install 'wrap-program | |
2201 | (lambda* (#:key inputs outputs #:allow-other-keys) | |
2202 | ;; Make sure 'edirect.pl' finds all perl inputs at runtime. | |
2203 | (let* ((out (assoc-ref outputs "out")) | |
2204 | (path (getenv "PERL5LIB"))) | |
2205 | (wrap-program (string-append out "/bin/edirect.pl") | |
2206 | `("PERL5LIB" ":" prefix (,path))))))))) | |
2207 | (inputs | |
2208 | `(("perl-html-parser" ,perl-html-parser) | |
2209 | ("perl-encode-locale" ,perl-encode-locale) | |
2210 | ("perl-file-listing" ,perl-file-listing) | |
2211 | ("perl-html-tagset" ,perl-html-tagset) | |
2212 | ("perl-html-tree" ,perl-html-tree) | |
2213 | ("perl-http-cookies" ,perl-http-cookies) | |
2214 | ("perl-http-date" ,perl-http-date) | |
2215 | ("perl-http-message" ,perl-http-message) | |
2216 | ("perl-http-negotiate" ,perl-http-negotiate) | |
2217 | ("perl-lwp-mediatypes" ,perl-lwp-mediatypes) | |
2218 | ("perl-lwp-protocol-https" ,perl-lwp-protocol-https) | |
2219 | ("perl-net-http" ,perl-net-http) | |
2220 | ("perl-uri" ,perl-uri) | |
2221 | ("perl-www-robotrules" ,perl-www-robotrules) | |
2222 | ("perl" ,perl))) | |
3d51ec91 | 2223 | (home-page "http://www.ncbi.nlm.nih.gov/books/NBK179288/") |
365c8153 RW |
2224 | (synopsis "Tools for accessing the NCBI's set of databases") |
2225 | (description | |
2226 | "Entrez Direct (EDirect) is a method for accessing the National Center | |
2227 | for Biotechnology Information's (NCBI) set of interconnected | |
2228 | databases (publication, sequence, structure, gene, variation, expression, | |
2229 | etc.) from a terminal. Functions take search terms from command-line | |
2230 | arguments. Individual operations are combined to build multi-step queries. | |
2231 | Record retrieval and formatting normally complete the process. | |
2232 | ||
2233 | EDirect also provides an argument-driven function that simplifies the | |
2234 | extraction of data from document summaries or other results that are returned | |
2235 | in structured XML format. This can eliminate the need for writing custom | |
2236 | software to answer ad hoc questions.") | |
2237 | (license license:public-domain))) | |
2238 | ||
b16728b0 BW |
2239 | (define-public exonerate |
2240 | (package | |
2241 | (name "exonerate") | |
2242 | (version "2.4.0") | |
2243 | (source | |
2244 | (origin | |
2245 | (method url-fetch) | |
2246 | (uri | |
2247 | (string-append | |
2248 | "http://ftp.ebi.ac.uk/pub/software/vertebrategenomics/exonerate/" | |
2249 | "exonerate-" version ".tar.gz")) | |
2250 | (sha256 | |
2251 | (base32 | |
2252 | "0hj0m9xygiqsdxvbg79wq579kbrx1mdrabi2bzqz2zn9qwfjcjgq")))) | |
2253 | (build-system gnu-build-system) | |
2254 | (arguments | |
2255 | `(#:parallel-build? #f)) ; Building in parallel fails on some machines. | |
2256 | (native-inputs | |
2257 | `(("pkg-config" ,pkg-config))) | |
2258 | (inputs | |
2259 | `(("glib" ,glib))) | |
2260 | (home-page | |
2261 | "https://www.ebi.ac.uk/about/vertebrate-genomics/software/exonerate") | |
2262 | (synopsis "Generic tool for biological sequence alignment") | |
2263 | (description | |
2264 | "Exonerate is a generic tool for pairwise sequence comparison. It allows | |
2265 | the alignment of sequences using a many alignment models, either exhaustive | |
2266 | dynamic programming or a variety of heuristics.") | |
2267 | (license license:gpl3))) | |
2268 | ||
e4e5a4d8 RW |
2269 | (define-public express |
2270 | (package | |
2271 | (name "express") | |
2272 | (version "1.5.1") | |
2273 | (source (origin | |
2274 | (method url-fetch) | |
2275 | (uri | |
2276 | (string-append | |
2277 | "http://bio.math.berkeley.edu/eXpress/downloads/express-" | |
2278 | version "/express-" version "-src.tgz")) | |
2279 | (sha256 | |
2280 | (base32 | |
2281 | "03rczxd0gjp2l1jxcmjfmf5j94j77zqyxa6x063zsc585nj40n0c")))) | |
2282 | (build-system cmake-build-system) | |
2283 | (arguments | |
2284 | `(#:tests? #f ;no "check" target | |
2285 | #:phases | |
dc1d3cde KK |
2286 | (modify-phases %standard-phases |
2287 | (add-after 'unpack 'use-shared-boost-libs-and-set-bamtools-paths | |
2288 | (lambda* (#:key inputs #:allow-other-keys) | |
2289 | (substitute* "CMakeLists.txt" | |
2290 | (("set\\(Boost_USE_STATIC_LIBS ON\\)") | |
2291 | "set(Boost_USE_STATIC_LIBS OFF)") | |
2292 | (("\\$\\{CMAKE_CURRENT_SOURCE_DIR\\}/bamtools/include") | |
2293 | (string-append (assoc-ref inputs "bamtools") "/include/bamtools"))) | |
2294 | (substitute* "src/CMakeLists.txt" | |
2295 | (("\\$\\{CMAKE_CURRENT_SOURCE_DIR\\}/\\.\\./bamtools/lib") | |
2296 | (string-append (assoc-ref inputs "bamtools") "/lib/bamtools"))) | |
2297 | #t))))) | |
e4e5a4d8 RW |
2298 | (inputs |
2299 | `(("boost" ,boost) | |
2300 | ("bamtools" ,bamtools) | |
2301 | ("protobuf" ,protobuf) | |
2302 | ("zlib" ,zlib))) | |
2303 | (home-page "http://bio.math.berkeley.edu/eXpress") | |
2304 | (synopsis "Streaming quantification for high-throughput genomic sequencing") | |
2305 | (description | |
2306 | "eXpress is a streaming tool for quantifying the abundances of a set of | |
2307 | target sequences from sampled subsequences. Example applications include | |
2308 | transcript-level RNA-Seq quantification, allele-specific/haplotype expression | |
2309 | analysis (from RNA-Seq), transcription factor binding quantification in | |
2310 | ChIP-Seq, and analysis of metagenomic data.") | |
2311 | (license license:artistic2.0))) | |
2312 | ||
f3674b1c BW |
2313 | (define-public express-beta-diversity |
2314 | (package | |
2315 | (name "express-beta-diversity") | |
2316 | (version "1.0.7") | |
2317 | (source (origin | |
2318 | (method url-fetch) | |
2319 | (uri | |
2320 | (string-append | |
2321 | "https://github.com/dparks1134/ExpressBetaDiversity/archive/v" | |
2322 | version ".tar.gz")) | |
2323 | (file-name (string-append name "-" version ".tar.gz")) | |
2324 | (sha256 | |
2325 | (base32 | |
2326 | "1djvdlmqvjf6h0zq7w36y8cl5cli6rgj86x65znl48agnwmzxfxr")))) | |
2327 | (build-system gnu-build-system) | |
2328 | (arguments | |
2329 | `(#:phases | |
2330 | (modify-phases %standard-phases | |
2331 | (delete 'configure) | |
2332 | (add-before 'build 'enter-source (lambda _ (chdir "source") #t)) | |
2333 | (replace 'check | |
2334 | (lambda _ (zero? (system* "../bin/ExpressBetaDiversity" | |
2335 | "-u")))) | |
2336 | (add-after 'check 'exit-source (lambda _ (chdir "..") #t)) | |
2337 | (replace 'install | |
2338 | (lambda* (#:key outputs #:allow-other-keys) | |
2339 | (let ((bin (string-append (assoc-ref outputs "out") | |
2340 | "/bin"))) | |
2341 | (mkdir-p bin) | |
f3860753 TGR |
2342 | (install-file "scripts/convertToEBD.py" bin) |
2343 | (install-file "bin/ExpressBetaDiversity" bin) | |
f3674b1c BW |
2344 | #t)))))) |
2345 | (inputs | |
2346 | `(("python" ,python-2))) | |
2347 | (home-page "http://kiwi.cs.dal.ca/Software/ExpressBetaDiversity") | |
2348 | (synopsis "Taxon- and phylogenetic-based beta diversity measures") | |
2349 | (description | |
2350 | "Express Beta Diversity (EBD) calculates ecological beta diversity | |
2351 | (dissimilarity) measures between biological communities. EBD implements a | |
2352 | variety of diversity measures including those that make use of phylogenetic | |
2353 | similarity of community members.") | |
2354 | (license license:gpl3+))) | |
2355 | ||
12b04cbe BW |
2356 | (define-public fasttree |
2357 | (package | |
2358 | (name "fasttree") | |
88682c9a | 2359 | (version "2.1.10") |
12b04cbe BW |
2360 | (source (origin |
2361 | (method url-fetch) | |
2362 | (uri (string-append | |
2363 | "http://www.microbesonline.org/fasttree/FastTree-" | |
2364 | version ".c")) | |
2365 | (sha256 | |
2366 | (base32 | |
88682c9a | 2367 | "0vcjdvy1j4m702vmak4svbfkrpcw63k7wymfksjp9a982zy8kjsl")))) |
12b04cbe BW |
2368 | (build-system gnu-build-system) |
2369 | (arguments | |
2370 | `(#:tests? #f ; no "check" target | |
2371 | #:phases | |
2372 | (modify-phases %standard-phases | |
2373 | (delete 'unpack) | |
2374 | (delete 'configure) | |
2375 | (replace 'build | |
e03a5153 BW |
2376 | (lambda* (#:key source #:allow-other-keys) |
2377 | (and (zero? (system* "gcc" | |
2378 | "-O3" | |
2379 | "-finline-functions" | |
2380 | "-funroll-loops" | |
2381 | "-Wall" | |
2382 | "-o" | |
2383 | "FastTree" | |
2384 | source | |
2385 | "-lm")) | |
2386 | (zero? (system* "gcc" | |
2387 | "-DOPENMP" | |
2388 | "-fopenmp" | |
2389 | "-O3" | |
2390 | "-finline-functions" | |
2391 | "-funroll-loops" | |
2392 | "-Wall" | |
2393 | "-o" | |
2394 | "FastTreeMP" | |
2395 | source | |
2396 | "-lm"))))) | |
12b04cbe | 2397 | (replace 'install |
e03a5153 BW |
2398 | (lambda* (#:key outputs #:allow-other-keys) |
2399 | (let ((bin (string-append (assoc-ref outputs "out") | |
2400 | "/bin"))) | |
2401 | (mkdir-p bin) | |
f3860753 TGR |
2402 | (install-file "FastTree" bin) |
2403 | (install-file "FastTreeMP" bin) | |
e03a5153 | 2404 | #t)))))) |
12b04cbe BW |
2405 | (home-page "http://www.microbesonline.org/fasttree") |
2406 | (synopsis "Infers approximately-maximum-likelihood phylogenetic trees") | |
2407 | (description | |
2408 | "FastTree can handle alignments with up to a million of sequences in a | |
2409 | reasonable amount of time and memory. For large alignments, FastTree is | |
2410 | 100-1,000 times faster than PhyML 3.0 or RAxML 7.") | |
2411 | (license license:gpl2+))) | |
2412 | ||
2127cedb RW |
2413 | (define-public fastx-toolkit |
2414 | (package | |
2415 | (name "fastx-toolkit") | |
2416 | (version "0.0.14") | |
2417 | (source (origin | |
2418 | (method url-fetch) | |
2419 | (uri | |
2420 | (string-append | |
2421 | "https://github.com/agordon/fastx_toolkit/releases/download/" | |
2422 | version "/fastx_toolkit-" version ".tar.bz2")) | |
2423 | (sha256 | |
2424 | (base32 | |
2425 | "01jqzw386873sr0pjp1wr4rn8fsga2vxs1qfmicvx1pjr72007wy")))) | |
2426 | (build-system gnu-build-system) | |
2427 | (inputs | |
2428 | `(("libgtextutils" ,libgtextutils))) | |
2429 | (native-inputs | |
2430 | `(("pkg-config" ,pkg-config))) | |
2431 | (home-page "http://hannonlab.cshl.edu/fastx_toolkit/") | |
2432 | (synopsis "Tools for FASTA/FASTQ file preprocessing") | |
2433 | (description | |
2434 | "The FASTX-Toolkit is a collection of command line tools for Short-Reads | |
2435 | FASTA/FASTQ files preprocessing. | |
2436 | ||
2437 | Next-Generation sequencing machines usually produce FASTA or FASTQ files, | |
2438 | containing multiple short-reads sequences. The main processing of such | |
2439 | FASTA/FASTQ files is mapping the sequences to reference genomes. However, it | |
2440 | is sometimes more productive to preprocess the files before mapping the | |
2441 | sequences to the genome---manipulating the sequences to produce better mapping | |
2442 | results. The FASTX-Toolkit tools perform some of these preprocessing tasks.") | |
2443 | (license license:agpl3+))) | |
2444 | ||
d7678942 RW |
2445 | (define-public flexbar |
2446 | (package | |
2447 | (name "flexbar") | |
2448 | (version "2.5") | |
2449 | (source (origin | |
2450 | (method url-fetch) | |
2451 | (uri | |
2452 | (string-append "mirror://sourceforge/flexbar/" | |
2453 | version "/flexbar_v" version "_src.tgz")) | |
2454 | (sha256 | |
2455 | (base32 | |
2456 | "13jaykc3y1x8y5nn9j8ljnb79s5y51kyxz46hdmvvjj6qhyympmf")))) | |
2457 | (build-system cmake-build-system) | |
2458 | (arguments | |
4ca009c0 | 2459 | `(#:configure-flags (list |
d7678942 RW |
2460 | (string-append "-DFLEXBAR_BINARY_DIR=" |
2461 | (assoc-ref %outputs "out") | |
2462 | "/bin/")) | |
2463 | #:phases | |
dc1d3cde KK |
2464 | (modify-phases %standard-phases |
2465 | (replace 'check | |
2466 | (lambda* (#:key outputs #:allow-other-keys) | |
2467 | (setenv "PATH" (string-append | |
2468 | (assoc-ref outputs "out") "/bin:" | |
2469 | (getenv "PATH"))) | |
2470 | (chdir "../flexbar_v2.5_src/test") | |
2471 | (zero? (system* "bash" "flexbar_validate.sh")))) | |
2472 | (delete 'install)))) | |
d7678942 RW |
2473 | (inputs |
2474 | `(("tbb" ,tbb) | |
2475 | ("zlib" ,zlib))) | |
2476 | (native-inputs | |
2477 | `(("pkg-config" ,pkg-config) | |
2478 | ("seqan" ,seqan))) | |
2479 | (home-page "http://flexbar.sourceforge.net") | |
2480 | (synopsis "Barcode and adapter removal tool for sequencing platforms") | |
2481 | (description | |
2482 | "Flexbar preprocesses high-throughput nucleotide sequencing data | |
2483 | efficiently. It demultiplexes barcoded runs and removes adapter sequences. | |
2484 | Moreover, trimming and filtering features are provided. Flexbar increases | |
2485 | read mapping rates and improves genome and transcriptome assemblies. It | |
2486 | supports next-generation sequencing data in fasta/q and csfasta/q format from | |
2487 | Illumina, Roche 454, and the SOLiD platform.") | |
2488 | (license license:gpl3))) | |
2489 | ||
19f4554c BW |
2490 | (define-public fraggenescan |
2491 | (package | |
2492 | (name "fraggenescan") | |
74297231 | 2493 | (version "1.30") |
19f4554c BW |
2494 | (source |
2495 | (origin | |
2496 | (method url-fetch) | |
2497 | (uri | |
2498 | (string-append "mirror://sourceforge/fraggenescan/" | |
2499 | "FragGeneScan" version ".tar.gz")) | |
2500 | (sha256 | |
74297231 | 2501 | (base32 "158dcnwczgcyhwm4qlx19sanrwgdpzf6bn2y57mbpx55lkgz1mzj")))) |
19f4554c BW |
2502 | (build-system gnu-build-system) |
2503 | (arguments | |
2504 | `(#:phases | |
2505 | (modify-phases %standard-phases | |
2506 | (delete 'configure) | |
2507 | (add-before 'build 'patch-paths | |
2508 | (lambda* (#:key outputs #:allow-other-keys) | |
2509 | (let* ((out (string-append (assoc-ref outputs "out"))) | |
2510 | (share (string-append out "/share/fraggenescan/"))) | |
2511 | (substitute* "run_FragGeneScan.pl" | |
2512 | (("system\\(\"rm") | |
2513 | (string-append "system(\"" (which "rm"))) | |
2514 | (("system\\(\"mv") | |
2515 | (string-append "system(\"" (which "mv"))) | |
74297231 | 2516 | (("\\\"awk") (string-append "\"" (which "awk"))) |
19f4554c BW |
2517 | ;; This script and other programs expect the training files |
2518 | ;; to be in the non-standard location bin/train/XXX. Change | |
2519 | ;; this to be share/fraggenescan/train/XXX instead. | |
2520 | (("^\\$train.file = \\$dir.*") | |
2521 | (string-append "$train_file = \"" | |
2522 | share | |
2523 | "train/\".$FGS_train_file;"))) | |
2524 | (substitute* "run_hmm.c" | |
2525 | (("^ strcat\\(train_dir, \\\"train/\\\"\\);") | |
74297231 | 2526 | (string-append " strcpy(train_dir, \"" share "/train/\");")))) |
19f4554c BW |
2527 | #t)) |
2528 | (replace 'build | |
2529 | (lambda _ (and (zero? (system* "make" "clean")) | |
2530 | (zero? (system* "make" "fgs"))))) | |
2531 | (replace 'install | |
2532 | (lambda* (#:key outputs #:allow-other-keys) | |
2533 | (let* ((out (string-append (assoc-ref outputs "out"))) | |
2534 | (bin (string-append out "/bin/")) | |
2535 | (share (string-append out "/share/fraggenescan/train"))) | |
2536 | (install-file "run_FragGeneScan.pl" bin) | |
2537 | (install-file "FragGeneScan" bin) | |
19f4554c BW |
2538 | (copy-recursively "train" share)))) |
2539 | (delete 'check) | |
2540 | (add-after 'install 'post-install-check | |
2541 | ;; In lieu of 'make check', run one of the examples and check the | |
2542 | ;; output files gets created. | |
2543 | (lambda* (#:key outputs #:allow-other-keys) | |
2544 | (let* ((out (string-append (assoc-ref outputs "out"))) | |
74297231 BW |
2545 | (bin (string-append out "/bin/")) |
2546 | (frag (string-append bin "run_FragGeneScan.pl"))) | |
2547 | (and (zero? (system* frag ; Test complete genome. | |
19f4554c BW |
2548 | "-genome=./example/NC_000913.fna" |
2549 | "-out=./test2" | |
2550 | "-complete=1" | |
2551 | "-train=complete")) | |
2552 | (file-exists? "test2.faa") | |
2553 | (file-exists? "test2.ffn") | |
2554 | (file-exists? "test2.gff") | |
74297231 BW |
2555 | (file-exists? "test2.out") |
2556 | (zero? (system* ; Test incomplete sequences. | |
2557 | frag | |
2558 | "-genome=./example/NC_000913-fgs.ffn" | |
2559 | "-out=out" | |
2560 | "-complete=0" | |
2561 | "-train=454_30"))))))))) | |
19f4554c BW |
2562 | (inputs |
2563 | `(("perl" ,perl) | |
2564 | ("python" ,python-2))) ;not compatible with python 3. | |
2565 | (home-page "https://sourceforge.net/projects/fraggenescan/") | |
2566 | (synopsis "Finds potentially fragmented genes in short reads") | |
2567 | (description | |
2568 | "FragGeneScan is a program for predicting bacterial and archaeal genes in | |
2569 | short and error-prone DNA sequencing reads. It can also be applied to predict | |
2570 | genes in incomplete assemblies or complete genomes.") | |
2571 | ;; GPL3+ according to private correspondense with the authors. | |
2572 | (license license:gpl3+))) | |
2573 | ||
81f3e0c1 BW |
2574 | (define-public fxtract |
2575 | (let ((util-commit "776ca85a18a47492af3794745efcb4a905113115")) | |
2576 | (package | |
2577 | (name "fxtract") | |
2578 | (version "2.3") | |
2579 | (source | |
2580 | (origin | |
2581 | (method url-fetch) | |
2582 | (uri (string-append | |
2583 | "https://github.com/ctSkennerton/fxtract/archive/" | |
2584 | version ".tar.gz")) | |
2585 | (file-name (string-append "ctstennerton-util-" | |
2586 | (string-take util-commit 7) | |
2587 | "-checkout")) | |
2588 | (sha256 | |
2589 | (base32 | |
2590 | "0275cfdhis8517hm01is62062swmi06fxzifq7mr3knbbxjlaiwj")))) | |
2591 | (build-system gnu-build-system) | |
2592 | (arguments | |
2593 | `(#:make-flags (list | |
2594 | (string-append "PREFIX=" (assoc-ref %outputs "out")) | |
2595 | "CC=gcc") | |
2596 | #:test-target "fxtract_test" | |
2597 | #:phases | |
2598 | (modify-phases %standard-phases | |
2599 | (delete 'configure) | |
2600 | (add-before 'build 'copy-util | |
2601 | (lambda* (#:key inputs #:allow-other-keys) | |
2602 | (rmdir "util") | |
2603 | (copy-recursively (assoc-ref inputs "ctskennerton-util") "util") | |
2604 | #t)) | |
2605 | ;; Do not use make install as this requires additional dependencies. | |
2606 | (replace 'install | |
2607 | (lambda* (#:key outputs #:allow-other-keys) | |
2608 | (let* ((out (assoc-ref outputs "out")) | |
2609 | (bin (string-append out"/bin"))) | |
2610 | (install-file "fxtract" bin) | |
2611 | #t)))))) | |
2612 | (inputs | |
2613 | `(("pcre" ,pcre) | |
2614 | ("zlib" ,zlib))) | |
2615 | (native-inputs | |
2616 | ;; ctskennerton-util is licensed under GPL2. | |
2617 | `(("ctskennerton-util" | |
2618 | ,(origin | |
2619 | (method git-fetch) | |
2620 | (uri (git-reference | |
2621 | (url "https://github.com/ctSkennerton/util.git") | |
2622 | (commit util-commit))) | |
2623 | (file-name (string-append | |
2624 | "ctstennerton-util-" util-commit "-checkout")) | |
2625 | (sha256 | |
2626 | (base32 | |
2627 | "0cls1hd4vgj3f36fpzzg4xc77d6f3hpc60cbpfmn2gdr7ykzzad7")))))) | |
2628 | (home-page "https://github.com/ctSkennerton/fxtract") | |
2629 | (synopsis "Extract sequences from FASTA and FASTQ files") | |
2630 | (description | |
2631 | "Fxtract extracts sequences from a protein or nucleotide fastx (FASTA | |
2632 | or FASTQ) file given a subsequence. It uses a simple substring search for | |
2633 | basic tasks but can change to using POSIX regular expressions, PCRE, hash | |
2634 | lookups or multi-pattern searching as required. By default fxtract looks in | |
2635 | the sequence of each record but can also be told to look in the header, | |
2636 | comment or quality sections.") | |
afde1a26 BW |
2637 | ;; 'util' requires SSE instructions. |
2638 | (supported-systems '("x86_64-linux")) | |
81f3e0c1 BW |
2639 | (license license:expat)))) |
2640 | ||
2b18ad05 PP |
2641 | (define-public gemma |
2642 | (package | |
2643 | (name "gemma") | |
2644 | (version "0.96") | |
2645 | (source (origin | |
2646 | (method url-fetch) | |
2647 | (uri (string-append "https://github.com/xiangzhou/GEMMA/archive/v" | |
2648 | version ".tar.gz")) | |
2649 | (file-name (string-append name "-" version ".tar.gz")) | |
2650 | (sha256 | |
2651 | (base32 | |
ce7e361f EF |
2652 | "055ynn16gd12pf78n4vr2a9jlwsbwzajpdnf2y2yilg1krfff222")) |
2653 | (patches (search-patches "gemma-intel-compat.patch")))) | |
2b18ad05 PP |
2654 | (inputs |
2655 | `(("gsl" ,gsl) | |
2656 | ("lapack" ,lapack) | |
2657 | ("zlib" ,zlib))) | |
2658 | (build-system gnu-build-system) | |
2659 | (arguments | |
2c9232ae | 2660 | `(#:make-flags |
ce7e361f EF |
2661 | '(,@(match (%current-system) |
2662 | ("x86_64-linux" | |
2663 | '("FORCE_DYNAMIC=1")) | |
2664 | ("i686-linux" | |
2665 | '("FORCE_DYNAMIC=1" "FORCE_32BIT=1")) | |
2666 | (_ | |
2667 | '("FORCE_DYNAMIC=1" "NO_INTEL_COMPAT=1")))) | |
2b18ad05 PP |
2668 | #:phases |
2669 | (modify-phases %standard-phases | |
2670 | (delete 'configure) | |
2671 | (add-before 'build 'bin-mkdir | |
07bf6929 EF |
2672 | (lambda _ |
2673 | (mkdir-p "bin") | |
2674 | #t)) | |
2b18ad05 | 2675 | (replace 'install |
07bf6929 EF |
2676 | (lambda* (#:key outputs #:allow-other-keys) |
2677 | (let ((out (assoc-ref outputs "out"))) | |
2678 | (install-file "bin/gemma" | |
2679 | (string-append | |
2680 | out "/bin"))) | |
2681 | #t))) | |
2b18ad05 PP |
2682 | #:tests? #f)) ; no tests included yet |
2683 | (home-page "https://github.com/xiangzhou/GEMMA") | |
2684 | (synopsis "Tool for genome-wide efficient mixed model association") | |
2685 | (description | |
2686 | "Genome-wide Efficient Mixed Model Association (GEMMA) provides a | |
2687 | standard linear mixed model resolver with application in genome-wide | |
2688 | association studies (GWAS).") | |
2689 | (license license:gpl3))) | |
2690 | ||
5854f685 RW |
2691 | (define-public grit |
2692 | (package | |
2693 | (name "grit") | |
2694 | (version "2.0.2") | |
2695 | (source (origin | |
2696 | (method url-fetch) | |
2697 | (uri (string-append | |
2698 | "https://github.com/nboley/grit/archive/" | |
2699 | version ".tar.gz")) | |
2700 | (file-name (string-append name "-" version ".tar.gz")) | |
2701 | (sha256 | |
2702 | (base32 | |
2703 | "157in84dj70wimbind3x7sy1whs3h57qfgcnj2s6lrd38fbrb7mj")))) | |
2704 | (build-system python-build-system) | |
2705 | (arguments | |
2706 | `(#:python ,python-2 | |
2707 | #:phases | |
dc1d3cde KK |
2708 | (modify-phases %standard-phases |
2709 | (add-after 'unpack 'generate-from-cython-sources | |
2710 | (lambda* (#:key inputs outputs #:allow-other-keys) | |
2711 | ;; Delete these C files to force fresh generation from pyx sources. | |
2712 | (delete-file "grit/sparsify_support_fns.c") | |
2713 | (delete-file "grit/call_peaks_support_fns.c") | |
2714 | (substitute* "setup.py" | |
2715 | (("Cython.Setup") "Cython.Build") | |
2716 | ;; Add numpy include path to fix compilation | |
2717 | (("pyx\", \\]") | |
2718 | (string-append "pyx\", ], include_dirs = ['" | |
2719 | (assoc-ref inputs "python-numpy") | |
2720 | "/lib/python2.7/site-packages/numpy/core/include/" | |
2721 | "']"))) | |
2722 | #t))))) | |
5854f685 RW |
2723 | (inputs |
2724 | `(("python-scipy" ,python2-scipy) | |
2725 | ("python-numpy" ,python2-numpy) | |
2726 | ("python-pysam" ,python2-pysam) | |
2727 | ("python-networkx" ,python2-networkx))) | |
2728 | (native-inputs | |
f3b98f4f | 2729 | `(("python-cython" ,python2-cython))) |
5854f685 RW |
2730 | (home-page "http://grit-bio.org") |
2731 | (synopsis "Tool for integrative analysis of RNA-seq type assays") | |
2732 | (description | |
2733 | "GRIT is designed to use RNA-seq, TES, and TSS data to build and quantify | |
2734 | full length transcript models. When none of these data sources are available, | |
2735 | GRIT can be run by providing a candidate set of TES or TSS sites. In | |
2736 | addition, GRIT can merge in reference junctions and gene boundaries. GRIT can | |
2737 | also be run in quantification mode, where it uses a provided GTF file and just | |
2738 | estimates transcript expression.") | |
2739 | (license license:gpl3+))) | |
2740 | ||
346a829a RW |
2741 | (define-public hisat |
2742 | (package | |
2743 | (name "hisat") | |
2744 | (version "0.1.4") | |
2745 | (source (origin | |
2746 | (method url-fetch) | |
2747 | (uri (string-append | |
2748 | "http://ccb.jhu.edu/software/hisat/downloads/hisat-" | |
2749 | version "-beta-source.zip")) | |
2750 | (sha256 | |
2751 | (base32 | |
2752 | "1k381ydranqxp09yf2y7w1d0chz5d59vb6jchi89hbb0prq19lk5")))) | |
2753 | (build-system gnu-build-system) | |
2754 | (arguments | |
e58d01fa RW |
2755 | `(#:tests? #f ;no check target |
2756 | #:make-flags '("allall" | |
2757 | ;; Disable unsupported `popcnt' instructions on | |
2758 | ;; architectures other than x86_64 | |
2759 | ,@(if (string-prefix? "x86_64" | |
2760 | (or (%current-target-system) | |
2761 | (%current-system))) | |
2762 | '() | |
2763 | '("POPCNT_CAPABILITY=0"))) | |
346a829a | 2764 | #:phases |
dc1d3cde KK |
2765 | (modify-phases %standard-phases |
2766 | (add-after 'unpack 'patch-sources | |
2767 | (lambda _ | |
2768 | ;; XXX Cannot use snippet because zip files are not supported | |
2769 | (substitute* "Makefile" | |
2770 | (("^CC = .*$") "CC = gcc") | |
2771 | (("^CPP = .*$") "CPP = g++") | |
2772 | ;; replace BUILD_HOST and BUILD_TIME for deterministic build | |
2773 | (("-DBUILD_HOST=.*") "-DBUILD_HOST=\"\\\"guix\\\"\"") | |
2774 | (("-DBUILD_TIME=.*") "-DBUILD_TIME=\"\\\"0\\\"\"")) | |
2775 | (substitute* '("hisat-build" "hisat-inspect") | |
2776 | (("/usr/bin/env") (which "env"))) | |
2777 | #t)) | |
2778 | (replace 'install | |
2779 | (lambda* (#:key outputs #:allow-other-keys) | |
2780 | (let ((bin (string-append (assoc-ref outputs "out") "/bin/"))) | |
2781 | (for-each (lambda (file) | |
2782 | (install-file file bin)) | |
2783 | (find-files | |
2784 | "." | |
2785 | "hisat(-(build|align|inspect)(-(s|l)(-debug)*)*)*$"))) | |
2786 | #t)) | |
2787 | (delete 'configure)))) | |
346a829a RW |
2788 | (native-inputs |
2789 | `(("unzip" ,unzip))) | |
2790 | (inputs | |
2791 | `(("perl" ,perl) | |
2792 | ("python" ,python) | |
2793 | ("zlib" ,zlib))) | |
60af3d82 RW |
2794 | ;; Non-portable SSE instructions are used so building fails on platforms |
2795 | ;; other than x86_64. | |
2796 | (supported-systems '("x86_64-linux")) | |
346a829a RW |
2797 | (home-page "http://ccb.jhu.edu/software/hisat/index.shtml") |
2798 | (synopsis "Hierarchical indexing for spliced alignment of transcripts") | |
2799 | (description | |
2800 | "HISAT is a fast and sensitive spliced alignment program for mapping | |
2801 | RNA-seq reads. In addition to one global FM index that represents a whole | |
2802 | genome, HISAT uses a large set of small FM indexes that collectively cover the | |
2803 | whole genome. These small indexes (called local indexes) combined with | |
2804 | several alignment strategies enable effective alignment of RNA-seq reads, in | |
2805 | particular, reads spanning multiple exons.") | |
2806 | (license license:gpl3+))) | |
2807 | ||
e84efc50 RW |
2808 | (define-public hisat2 |
2809 | (package | |
2810 | (name "hisat2") | |
2811 | (version "2.0.5") | |
2812 | (source | |
2813 | (origin | |
2814 | (method url-fetch) | |
2815 | ;; FIXME: a better source URL is | |
2816 | ;; (string-append "ftp://ftp.ccb.jhu.edu/pub/infphilo/hisat2" | |
2817 | ;; "/downloads/hisat2-" version "-source.zip") | |
2818 | ;; with hash "0lywnr8kijwsc2aw10dwxic0n0yvip6fl3rjlvc8zzwahamy4x7g" | |
2819 | ;; but it is currently unavailable. | |
2820 | (uri "https://github.com/infphilo/hisat2/archive/cba6e8cb.tar.gz") | |
2821 | (file-name (string-append name "-" version ".tar.gz")) | |
2822 | (sha256 | |
2823 | (base32 | |
2824 | "1mf2hdsyv7cd97xm9mp9a4qws02yrj95y6w6f6cdwnq0klp81r50")))) | |
2825 | (build-system gnu-build-system) | |
2826 | (arguments | |
2827 | `(#:tests? #f ; no check target | |
2828 | #:make-flags (list "CC=gcc" "CXX=g++" "allall") | |
2829 | #:modules ((guix build gnu-build-system) | |
2830 | (guix build utils) | |
2831 | (srfi srfi-26)) | |
2832 | #:phases | |
2833 | (modify-phases %standard-phases | |
2834 | (add-after 'unpack 'make-deterministic | |
2835 | (lambda _ | |
2836 | (substitute* "Makefile" | |
2837 | (("`date`") "0")) | |
2838 | #t)) | |
2839 | (delete 'configure) | |
2840 | (replace 'install | |
2841 | (lambda* (#:key outputs #:allow-other-keys) | |
2842 | (let* ((out (assoc-ref outputs "out")) | |
2843 | (bin (string-append out "/bin/")) | |
2844 | (doc (string-append out "/share/doc/hisat2/"))) | |
2845 | (for-each | |
2846 | (cut install-file <> bin) | |
2847 | (find-files "." | |
2848 | "hisat2(-(build|align|inspect)(-(s|l)(-debug)*)*)*$")) | |
2849 | (mkdir-p doc) | |
2850 | (install-file "doc/manual.inc.html" doc)) | |
2851 | #t))))) | |
2852 | (native-inputs | |
2853 | `(("unzip" ,unzip) ; needed for archive from ftp | |
2854 | ("perl" ,perl) | |
2855 | ("pandoc" ,ghc-pandoc))) ; for documentation | |
2856 | (home-page "http://ccb.jhu.edu/software/hisat2/index.shtml") | |
2857 | (synopsis "Graph-based alignment of genomic sequencing reads") | |
2858 | (description "HISAT2 is a fast and sensitive alignment program for mapping | |
2859 | next-generation sequencing reads (both DNA and RNA) to a population of human | |
2860 | genomes (as well as to a single reference genome). In addition to using one | |
2861 | global @dfn{graph FM} (GFM) index that represents a population of human | |
2862 | genomes, HISAT2 uses a large set of small GFM indexes that collectively cover | |
2863 | the whole genome. These small indexes, combined with several alignment | |
2864 | strategies, enable rapid and accurate alignment of sequencing reads. This new | |
2865 | indexing scheme is called a @dfn{Hierarchical Graph FM index} (HGFM).") | |
2866 | ;; HISAT2 contains files from Bowtie2, which is released under | |
2867 | ;; GPLv2 or later. The HISAT2 source files are released under | |
2868 | ;; GPLv3 or later. | |
2869 | (license license:gpl3+))) | |
2870 | ||
c684629f BW |
2871 | (define-public hmmer |
2872 | (package | |
2873 | (name "hmmer") | |
2874 | (version "3.1b2") | |
79f09fa2 BW |
2875 | (source |
2876 | (origin | |
2877 | (method url-fetch) | |
2878 | (uri (string-append | |
2879 | "http://eddylab.org/software/hmmer" | |
9cf5f134 | 2880 | (version-major version) "/" |
79f09fa2 BW |
2881 | version "/hmmer-" version ".tar.gz")) |
2882 | (sha256 | |
2883 | (base32 | |
2884 | "0djmgc0pfli0jilfx8hql1axhwhqxqb8rxg2r5rg07aw73sfs5nx")) | |
2885 | (patches (search-patches "hmmer-remove-cpu-specificity.patch")))) | |
c684629f | 2886 | (build-system gnu-build-system) |
b3546174 | 2887 | (native-inputs `(("perl" ,perl))) |
a83e6046 | 2888 | (home-page "http://hmmer.org/") |
c684629f BW |
2889 | (synopsis "Biosequence analysis using profile hidden Markov models") |
2890 | (description | |
2891 | "HMMER is used for searching sequence databases for homologs of protein | |
2892 | sequences, and for making protein sequence alignments. It implements methods | |
2893 | using probabilistic models called profile hidden Markov models (profile | |
2894 | HMMs).") | |
2895 | (license (list license:gpl3+ | |
2896 | ;; The bundled library 'easel' is distributed | |
2897 | ;; under The Janelia Farm Software License. | |
2898 | (license:non-copyleft | |
2899 | "file://easel/LICENSE" | |
2900 | "See easel/LICENSE in the distribution."))))) | |
2901 | ||
85652f59 RW |
2902 | (define-public htseq |
2903 | (package | |
2904 | (name "htseq") | |
92971d68 | 2905 | (version "0.9.1") |
85652f59 RW |
2906 | (source (origin |
2907 | (method url-fetch) | |
75e6639f | 2908 | (uri (pypi-uri "HTSeq" version)) |
85652f59 RW |
2909 | (sha256 |
2910 | (base32 | |
92971d68 | 2911 | "11flgb1381xdhk43bzbfm3vhnszkpqg6jk76rpa5xd1zbrvvlnxg")))) |
85652f59 | 2912 | (build-system python-build-system) |
92971d68 BW |
2913 | (native-inputs |
2914 | `(("python-cython" ,python-cython))) | |
0536727e RW |
2915 | ;; Numpy needs to be propagated when htseq is used as a Python library. |
2916 | (propagated-inputs | |
92971d68 | 2917 | `(("python-numpy" ,python-numpy))) |
578b05d9 | 2918 | (inputs |
92971d68 BW |
2919 | `(("python-pysam" ,python-pysam) |
2920 | ("python-matplotlib" ,python-matplotlib))) | |
85652f59 RW |
2921 | (home-page "http://www-huber.embl.de/users/anders/HTSeq/") |
2922 | (synopsis "Analysing high-throughput sequencing data with Python") | |
2923 | (description | |
2924 | "HTSeq is a Python package that provides infrastructure to process data | |
2925 | from high-throughput sequencing assays.") | |
2926 | (license license:gpl3+))) | |
2927 | ||
92971d68 BW |
2928 | (define-public python2-htseq |
2929 | (package-with-python2 htseq)) | |
2930 | ||
1ad15c16 | 2931 | (define-public java-htsjdk |
15a3c3d4 | 2932 | (package |
1ad15c16 | 2933 | (name "java-htsjdk") |
bd94b6f8 | 2934 | (version "2.3.0") ; last version without build dependency on gradle |
15a3c3d4 RW |
2935 | (source (origin |
2936 | (method url-fetch) | |
2937 | (uri (string-append | |
2938 | "https://github.com/samtools/htsjdk/archive/" | |
2939 | version ".tar.gz")) | |
2940 | (file-name (string-append name "-" version ".tar.gz")) | |
2941 | (sha256 | |
2942 | (base32 | |
bd94b6f8 | 2943 | "1ibhzzxsfc38nqyk9r8zqj6blfc1kh26iirypd4q6n90hs2m6nyq")) |
15a3c3d4 | 2944 | (modules '((guix build utils))) |
bd94b6f8 RW |
2945 | (snippet |
2946 | ;; Delete pre-built binaries | |
2947 | '(begin | |
2948 | (delete-file-recursively "lib") | |
2949 | (mkdir-p "lib") | |
2950 | #t)))) | |
10b4a969 | 2951 | (build-system ant-build-system) |
15a3c3d4 | 2952 | (arguments |
10b4a969 | 2953 | `(#:tests? #f ; test require Internet access |
bd94b6f8 | 2954 | #:jdk ,icedtea-8 |
10b4a969 RW |
2955 | #:make-flags |
2956 | (list (string-append "-Ddist=" (assoc-ref %outputs "out") | |
2957 | "/share/java/htsjdk/")) | |
2958 | #:build-target "all" | |
2959 | #:phases | |
2960 | (modify-phases %standard-phases | |
2961 | ;; The build phase also installs the jars | |
2962 | (delete 'install)))) | |
bd94b6f8 RW |
2963 | (inputs |
2964 | `(("java-ngs" ,java-ngs) | |
2965 | ("java-snappy-1" ,java-snappy-1) | |
2966 | ("java-commons-compress" ,java-commons-compress) | |
2967 | ("java-commons-logging-minimal" ,java-commons-logging-minimal) | |
2968 | ("java-commons-jexl-2" ,java-commons-jexl-2) | |
2969 | ("java-xz" ,java-xz))) | |
2970 | (native-inputs | |
2971 | `(("java-testng" ,java-testng))) | |
15a3c3d4 | 2972 | (home-page "http://samtools.github.io/htsjdk/") |
9a599c17 RW |
2973 | (synopsis "Java API for high-throughput sequencing data (HTS) formats") |
2974 | (description | |
2975 | "HTSJDK is an implementation of a unified Java library for accessing | |
2976 | common file formats, such as SAM and VCF, used for high-throughput | |
2977 | sequencing (HTS) data. There are also an number of useful utilities for | |
2978 | manipulating HTS data.") | |
2979 | (license license:expat))) | |
2980 | ||
2981 | (define-public java-htsjdk-latest | |
2982 | (package | |
2983 | (name "java-htsjdk") | |
2984 | (version "2.14.3") | |
2985 | (source (origin | |
2986 | (method git-fetch) | |
2987 | (uri (git-reference | |
2988 | (url "https://github.com/samtools/htsjdk.git") | |
2989 | (commit version))) | |
2990 | (file-name (string-append name "-" version "-checkout")) | |
2991 | (sha256 | |
2992 | (base32 | |
2993 | "1lmya1fdjy03mz6zmdmd86j9v9vfhqb3952mqq075navx1i6g4bc")))) | |
2994 | (build-system ant-build-system) | |
2995 | (arguments | |
2996 | `(#:tests? #f ; test require Scala | |
2997 | #:jdk ,icedtea-8 | |
2998 | #:jar-name "htsjdk.jar" | |
2999 | #:phases | |
3000 | (modify-phases %standard-phases | |
3001 | (add-after 'unpack 'remove-useless-build.xml | |
3002 | (lambda _ (delete-file "build.xml") #t)) | |
3003 | ;; The tests require the scalatest package. | |
3004 | (add-after 'unpack 'remove-tests | |
3005 | (lambda _ (delete-file-recursively "src/test") #t))))) | |
3006 | (inputs | |
3007 | `(("java-ngs" ,java-ngs) | |
3008 | ("java-snappy-1" ,java-snappy-1) | |
3009 | ("java-commons-compress" ,java-commons-compress) | |
3010 | ("java-commons-logging-minimal" ,java-commons-logging-minimal) | |
3011 | ("java-commons-jexl-2" ,java-commons-jexl-2) | |
3012 | ("java-xz" ,java-xz))) | |
3013 | (native-inputs | |
3014 | `(("java-junit" ,java-junit))) | |
3015 | (home-page "http://samtools.github.io/htsjdk/") | |
15a3c3d4 RW |
3016 | (synopsis "Java API for high-throughput sequencing data (HTS) formats") |
3017 | (description | |
3018 | "HTSJDK is an implementation of a unified Java library for accessing | |
3019 | common file formats, such as SAM and VCF, used for high-throughput | |
3020 | sequencing (HTS) data. There are also an number of useful utilities for | |
3021 | manipulating HTS data.") | |
3022 | (license license:expat))) | |
3023 | ||
719fa958 RW |
3024 | ;; This is needed for picard 2.10.3 |
3025 | (define-public java-htsjdk-2.10.1 | |
3026 | (package (inherit java-htsjdk-latest) | |
3027 | (name "java-htsjdk") | |
3028 | (version "2.10.1") | |
3029 | (source (origin | |
3030 | (method git-fetch) | |
3031 | (uri (git-reference | |
3032 | (url "https://github.com/samtools/htsjdk.git") | |
3033 | (commit version))) | |
3034 | (file-name (string-append name "-" version "-checkout")) | |
3035 | (sha256 | |
3036 | (base32 | |
3037 | "1kxh7slm2pm3x9p6jxa1wqsq9a31dhiiflhxnxqcisan4k3rwia2")))) | |
3038 | (build-system ant-build-system) | |
3039 | (arguments | |
3040 | `(#:tests? #f ; tests require Scala | |
3041 | #:jdk ,icedtea-8 | |
3042 | #:jar-name "htsjdk.jar" | |
3043 | #:phases | |
3044 | (modify-phases %standard-phases | |
3045 | (add-after 'unpack 'remove-useless-build.xml | |
3046 | (lambda _ (delete-file "build.xml") #t)) | |
3047 | ;; The tests require the scalatest package. | |
3048 | (add-after 'unpack 'remove-tests | |
3049 | (lambda _ (delete-file-recursively "src/test") #t))))))) | |
3050 | ||
d7fed31a RW |
3051 | ;; This version matches java-htsjdk 2.3.0. Later versions also require a more |
3052 | ;; recent version of java-htsjdk, which depends on gradle. | |
3053 | (define-public java-picard | |
3054 | (package | |
3055 | (name "java-picard") | |
3056 | (version "2.3.0") | |
3057 | (source (origin | |
3058 | (method git-fetch) | |
3059 | (uri (git-reference | |
3060 | (url "https://github.com/broadinstitute/picard.git") | |
3061 | (commit version))) | |
3062 | (file-name (string-append "java-picard-" version "-checkout")) | |
3063 | (sha256 | |
3064 | (base32 | |
3065 | "1ll7mf4r3by92w2nhlmpa591xd1f46xlkwh59mq6fvbb5pdwzvx6")) | |
3066 | (modules '((guix build utils))) | |
3067 | (snippet | |
3068 | '(begin | |
3069 | ;; Delete pre-built binaries. | |
3070 | (delete-file-recursively "lib") | |
3071 | (mkdir-p "lib") | |
3072 | (substitute* "build.xml" | |
3073 | ;; Remove build-time dependency on git. | |
3074 | (("failifexecutionfails=\"true\"") | |
3075 | "failifexecutionfails=\"false\"") | |
3076 | ;; Use our htsjdk. | |
3077 | (("depends=\"compile-htsjdk, ") | |
3078 | "depends=\"") | |
3079 | (("depends=\"compile-htsjdk-tests, ") | |
3080 | "depends=\"") | |
3081 | ;; Build picard-lib.jar before building picard.jar | |
3082 | (("name=\"picard-jar\" depends=\"" line) | |
3083 | (string-append line "picard-lib-jar, "))) | |
3084 | #t)))) | |
3085 | (build-system ant-build-system) | |
3086 | (arguments | |
3087 | `(#:build-target "picard-jar" | |
3088 | #:test-target "test" | |
3089 | ;; Tests require jacoco:coverage. | |
3090 | #:tests? #f | |
3091 | #:make-flags | |
3092 | (list (string-append "-Dhtsjdk_lib_dir=" | |
3093 | (assoc-ref %build-inputs "java-htsjdk") | |
3094 | "/share/java/htsjdk/") | |
3095 | "-Dhtsjdk-classes=dist/tmp" | |
3096 | (string-append "-Dhtsjdk-version=" | |
3097 | ,(package-version java-htsjdk))) | |
3098 | #:jdk ,icedtea-8 | |
3099 | #:phases | |
3100 | (modify-phases %standard-phases | |
3101 | (add-after 'unpack 'use-our-htsjdk | |
3102 | (lambda* (#:key inputs #:allow-other-keys) | |
3103 | (substitute* "build.xml" | |
3104 | (("\\$\\{htsjdk\\}/lib") | |
3105 | (string-append (assoc-ref inputs "java-htsjdk") | |
3106 | "/share/java/htsjdk/"))) | |
3107 | #t)) | |
3108 | (add-after 'unpack 'make-test-target-independent | |
3109 | (lambda* (#:key inputs #:allow-other-keys) | |
3110 | (substitute* "build.xml" | |
3111 | (("name=\"test\" depends=\"compile, ") | |
3112 | "name=\"test\" depends=\"")) | |
3113 | #t)) | |
3114 | (replace 'install (install-jars "dist"))))) | |
3115 | (inputs | |
3116 | `(("java-htsjdk" ,java-htsjdk) | |
3117 | ("java-guava" ,java-guava))) | |
3118 | (native-inputs | |
3119 | `(("java-testng" ,java-testng))) | |
3120 | (home-page "http://broadinstitute.github.io/picard/") | |
3121 | (synopsis "Tools for manipulating high-throughput sequencing data and formats") | |
3122 | (description "Picard is a set of Java command line tools for manipulating | |
3123 | high-throughput sequencing (HTS) data and formats. Picard is implemented | |
3124 | using the HTSJDK Java library to support accessing file formats that are | |
3125 | commonly used for high-throughput sequencing data such as SAM, BAM, CRAM and | |
3126 | VCF.") | |
3127 | (license license:expat))) | |
3128 | ||
72299db9 RW |
3129 | ;; This is needed for dropseq-tools |
3130 | (define-public java-picard-2.10.3 | |
3131 | (package | |
3132 | (name "java-picard") | |
3133 | (version "2.10.3") | |
3134 | (source (origin | |
3135 | (method git-fetch) | |
3136 | (uri (git-reference | |
3137 | (url "https://github.com/broadinstitute/picard.git") | |
3138 | (commit version))) | |
3139 | (file-name (string-append "java-picard-" version "-checkout")) | |
3140 | (sha256 | |
3141 | (base32 | |
3142 | "1ajlx31l6i1k3y2rhnmgq07sz99g2czqfqgkr9mihmdjp3gwjhvi")))) | |
3143 | (build-system ant-build-system) | |
3144 | (arguments | |
3145 | `(#:jar-name "picard.jar" | |
3146 | ;; Tests require jacoco:coverage. | |
3147 | #:tests? #f | |
3148 | #:jdk ,icedtea-8 | |
3149 | #:main-class "picard.cmdline.PicardCommandLine" | |
3150 | #:modules ((guix build ant-build-system) | |
3151 | (guix build utils) | |
3152 | (guix build java-utils) | |
3153 | (sxml simple) | |
3154 | (sxml transform) | |
3155 | (sxml xpath)) | |
3156 | #:phases | |
3157 | (modify-phases %standard-phases | |
3158 | (add-after 'unpack 'remove-useless-build.xml | |
3159 | (lambda _ (delete-file "build.xml") #t)) | |
3160 | ;; This is necessary to ensure that htsjdk is found when using | |
3161 | ;; picard.jar as an executable. | |
3162 | (add-before 'build 'edit-classpath-in-manifest | |
3163 | (lambda* (#:key inputs #:allow-other-keys) | |
3164 | (chmod "build.xml" #o664) | |
3165 | (call-with-output-file "build.xml.new" | |
3166 | (lambda (port) | |
3167 | (sxml->xml | |
3168 | (pre-post-order | |
3169 | (with-input-from-file "build.xml" | |
3170 | (lambda _ (xml->sxml #:trim-whitespace? #t))) | |
3171 | `((target . ,(lambda (tag . kids) | |
3172 | (let ((name ((sxpath '(name *text*)) | |
3173 | (car kids))) | |
3174 | ;; FIXME: We're breaking the line | |
3175 | ;; early with a dummy path to | |
3176 | ;; ensure that the store reference | |
3177 | ;; isn't broken apart and can still | |
3178 | ;; be found by the reference | |
3179 | ;; scanner. | |
3180 | (msg (format #f | |
3181 | "\ | |
3182 | Class-Path: /~a \ | |
3183 | ~a/share/java/htsjdk.jar${line.separator}" | |
3184 | ;; maximum line length is 70 | |
3185 | (string-tabulate (const #\b) 57) | |
3186 | (assoc-ref inputs "java-htsjdk")))) | |
3187 | (if (member "manifest" name) | |
3188 | `(,tag ,@kids | |
3189 | (echo | |
3190 | (@ (message ,msg) | |
3191 | (file "${manifest.file}") | |
3192 | (append "true")))) | |
3193 | `(,tag ,@kids))))) | |
3194 | (*default* . ,(lambda (tag . kids) `(,tag ,@kids))) | |
3195 | (*text* . ,(lambda (_ txt) txt)))) | |
3196 | port))) | |
3197 | (rename-file "build.xml.new" "build.xml") | |
3198 | #t))))) | |
3199 | (propagated-inputs | |
3200 | `(("java-htsjdk" ,java-htsjdk-2.10.1))) | |
3201 | (native-inputs | |
3202 | `(("java-testng" ,java-testng) | |
3203 | ("java-guava" ,java-guava))) | |
3204 | (home-page "http://broadinstitute.github.io/picard/") | |
3205 | (synopsis "Tools for manipulating high-throughput sequencing data and formats") | |
3206 | (description "Picard is a set of Java command line tools for manipulating | |
3207 | high-throughput sequencing (HTS) data and formats. Picard is implemented | |
3208 | using the HTSJDK Java library to support accessing file formats that are | |
3209 | commonly used for high-throughput sequencing data such as SAM, BAM, CRAM and | |
3210 | VCF.") | |
3211 | (license license:expat))) | |
3212 | ||
d7f24778 RW |
3213 | ;; This is the last version of Picard to provide net.sf.samtools |
3214 | (define-public java-picard-1.113 | |
3215 | (package (inherit java-picard) | |
3216 | (name "java-picard") | |
3217 | (version "1.113") | |
3218 | (source (origin | |
3219 | (method git-fetch) | |
3220 | (uri (git-reference | |
3221 | (url "https://github.com/broadinstitute/picard.git") | |
3222 | (commit version))) | |
3223 | (file-name (string-append "java-picard-" version "-checkout")) | |
3224 | (sha256 | |
3225 | (base32 | |
3226 | "0lkpvin2fz3hhly4l02kk56fqy8lmlgyzr9kmvljk6ry6l1hw973")) | |
3227 | (modules '((guix build utils))) | |
3228 | (snippet | |
3229 | '(begin | |
3230 | ;; Delete pre-built binaries. | |
3231 | (delete-file-recursively "lib") | |
3232 | (mkdir-p "lib") | |
3233 | #t)))) | |
3234 | (build-system ant-build-system) | |
3235 | (arguments | |
3236 | `(#:build-target "picard-jar" | |
3237 | #:test-target "test" | |
3238 | ;; FIXME: the class path at test time is wrong. | |
3239 | ;; [testng] Error: A JNI error has occurred, please check your installation and try again | |
3240 | ;; [testng] Exception in thread "main" java.lang.NoClassDefFoundError: com/beust/jcommander/ParameterException | |
3241 | #:tests? #f | |
3242 | #:jdk ,icedtea-8 | |
3243 | ;; This is only used for tests. | |
3244 | #:make-flags | |
3245 | (list "-Dsamjdk.intel_deflater_so_path=lib/jni/libIntelDeflater.so") | |
3246 | #:phases | |
3247 | (modify-phases %standard-phases | |
3248 | ;; Do not use bundled ant bzip2. | |
3249 | (add-after 'unpack 'use-ant-bzip | |
3250 | (lambda* (#:key inputs #:allow-other-keys) | |
3251 | (substitute* "build.xml" | |
3252 | (("\\$\\{lib\\}/apache-ant-1.8.2-bzip2.jar") | |
3253 | (string-append (assoc-ref inputs "ant") | |
3254 | "/lib/ant.jar"))) | |
3255 | #t)) | |
3256 | (add-after 'unpack 'make-test-target-independent | |
3257 | (lambda* (#:key inputs #:allow-other-keys) | |
3258 | (substitute* "build.xml" | |
3259 | (("name=\"test\" depends=\"compile, ") | |
3260 | "name=\"test\" depends=\"compile-tests, ") | |
3261 | (("name=\"compile\" depends=\"compile-src, compile-tests\"") | |
3262 | "name=\"compile\" depends=\"compile-src\"")) | |
3263 | #t)) | |
3264 | (add-after 'unpack 'fix-deflater-path | |
3265 | (lambda* (#:key outputs #:allow-other-keys) | |
3266 | (substitute* "src/java/net/sf/samtools/Defaults.java" | |
3267 | (("getStringProperty\\(\"intel_deflater_so_path\", null\\)") | |
3268 | (string-append "getStringProperty(\"intel_deflater_so_path\", \"" | |
3269 | (assoc-ref outputs "out") | |
3270 | "/lib/jni/libIntelDeflater.so" | |
3271 | "\")"))) | |
3272 | #t)) | |
3273 | ;; Build the deflater library, because we've previously deleted the | |
3274 | ;; pre-built one. This can only be built with access to the JDK | |
3275 | ;; sources. | |
3276 | (add-after 'build 'build-jni | |
3277 | (lambda* (#:key inputs #:allow-other-keys) | |
3278 | (mkdir-p "lib/jni") | |
3279 | (mkdir-p "jdk-src") | |
3280 | (and (zero? (system* "tar" "--strip-components=1" "-C" "jdk-src" | |
3281 | "-xf" (assoc-ref inputs "jdk-src"))) | |
3282 | (zero? (system* "javah" "-jni" | |
3283 | "-classpath" "classes" | |
3284 | "-d" "lib/" | |
3285 | "net.sf.samtools.util.zip.IntelDeflater")) | |
3286 | (with-directory-excursion "src/c/inteldeflater" | |
3287 | (zero? (system* "gcc" "-I../../../lib" "-I." | |
3288 | (string-append "-I" (assoc-ref inputs "jdk") | |
3289 | "/include/linux") | |
3290 | "-I../../../jdk-src/src/share/native/common/" | |
3291 | "-I../../../jdk-src/src/solaris/native/common/" | |
3292 | "-c" "-O3" "-fPIC" "IntelDeflater.c")) | |
3293 | (zero? (system* "gcc" "-shared" | |
3294 | "-o" "../../../lib/jni/libIntelDeflater.so" | |
3295 | "IntelDeflater.o" "-lz" "-lstdc++")))))) | |
3296 | ;; We can only build everything else after building the JNI library. | |
3297 | (add-after 'build-jni 'build-rest | |
3298 | (lambda* (#:key make-flags #:allow-other-keys) | |
3299 | (zero? (apply system* `("ant" "all" ,@make-flags))))) | |
3300 | (add-before 'build 'set-JAVA6_HOME | |
3301 | (lambda _ | |
3302 | (setenv "JAVA6_HOME" (getenv "JAVA_HOME")) | |
3303 | #t)) | |
3304 | (replace 'install (install-jars "dist")) | |
3305 | (add-after 'install 'install-jni-lib | |
3306 | (lambda* (#:key outputs #:allow-other-keys) | |
3307 | (let ((jni (string-append (assoc-ref outputs "out") | |
3308 | "/lib/jni"))) | |
3309 | (mkdir-p jni) | |
3310 | (install-file "lib/jni/libIntelDeflater.so" jni) | |
3311 | #t)))))) | |
3312 | (inputs | |
3313 | `(("java-snappy-1" ,java-snappy-1) | |
3314 | ("java-commons-jexl-2" ,java-commons-jexl-2) | |
3315 | ("java-cofoja" ,java-cofoja) | |
3316 | ("ant" ,ant) ; for bzip2 support at runtime | |
3317 | ("zlib" ,zlib))) | |
3318 | (native-inputs | |
3319 | `(("ant-apache-bcel" ,ant-apache-bcel) | |
3320 | ("ant-junit" ,ant-junit) | |
3321 | ("java-testng" ,java-testng) | |
3322 | ("java-commons-bcel" ,java-commons-bcel) | |
3323 | ("java-jcommander" ,java-jcommander) | |
3324 | ("jdk" ,icedtea-8 "jdk") | |
3325 | ("jdk-src" ,(car (assoc-ref (package-native-inputs icedtea-8) "jdk-drop"))))))) | |
3326 | ||
bd975831 RW |
3327 | (define-public fastqc |
3328 | (package | |
3329 | (name "fastqc") | |
3330 | (version "0.11.5") | |
3331 | (source | |
3332 | (origin | |
3333 | (method url-fetch) | |
3334 | (uri (string-append "http://www.bioinformatics.babraham.ac.uk/" | |
3335 | "projects/fastqc/fastqc_v" | |
3336 | version "_source.zip")) | |
3337 | (sha256 | |
3338 | (base32 | |
3339 | "18rrlkhcrxvvvlapch4dpj6xc6mpayzys8qfppybi8jrpgx5cc5f")))) | |
3340 | (build-system ant-build-system) | |
3341 | (arguments | |
3342 | `(#:tests? #f ; there are no tests | |
3343 | #:build-target "build" | |
3344 | #:phases | |
3345 | (modify-phases %standard-phases | |
3346 | (add-after 'unpack 'fix-dependencies | |
3347 | (lambda* (#:key inputs #:allow-other-keys) | |
3348 | (substitute* "build.xml" | |
3349 | (("jbzip2-0.9.jar") | |
3350 | (string-append (assoc-ref inputs "java-jbzip2") | |
3351 | "/share/java/jbzip2.jar")) | |
3352 | (("sam-1.103.jar") | |
3353 | (string-append (assoc-ref inputs "java-picard-1.113") | |
3354 | "/share/java/sam-1.112.jar")) | |
3355 | (("cisd-jhdf5.jar") | |
3356 | (string-append (assoc-ref inputs "java-cisd-jhdf5") | |
3357 | "/share/java/sis-jhdf5.jar"))) | |
3358 | #t)) | |
3359 | ;; There is no installation target | |
3360 | (replace 'install | |
3361 | (lambda* (#:key inputs outputs #:allow-other-keys) | |
3362 | (let* ((out (assoc-ref outputs "out")) | |
3363 | (bin (string-append out "/bin")) | |
3364 | (share (string-append out "/share/fastqc/")) | |
3365 | (exe (string-append share "/fastqc"))) | |
3366 | (for-each mkdir-p (list bin share)) | |
3367 | (copy-recursively "bin" share) | |
3368 | (substitute* exe | |
3369 | (("my \\$java_bin = 'java';") | |
3370 | (string-append "my $java_bin = '" | |
3371 | (assoc-ref inputs "java") | |
3372 | "/bin/java';"))) | |
3373 | (chmod exe #o555) | |
3374 | (symlink exe (string-append bin "/fastqc")) | |
3375 | #t)))))) | |
3376 | (inputs | |
3377 | `(("java" ,icedtea) | |
3378 | ("perl" ,perl) ; needed for the wrapper script | |
3379 | ("java-cisd-jhdf5" ,java-cisd-jhdf5) | |
3380 | ("java-picard-1.113" ,java-picard-1.113) | |
3381 | ("java-jbzip2" ,java-jbzip2))) | |
3382 | (native-inputs | |
3383 | `(("unzip" ,unzip))) | |
3384 | (home-page "http://www.bioinformatics.babraham.ac.uk/projects/fastqc/") | |
3385 | (synopsis "Quality control tool for high throughput sequence data") | |
3386 | (description | |
3387 | "FastQC aims to provide a simple way to do some quality control | |
3388 | checks on raw sequence data coming from high throughput sequencing | |
3389 | pipelines. It provides a modular set of analyses which you can use to | |
3390 | give a quick impression of whether your data has any problems of which | |
3391 | you should be aware before doing any further analysis. | |
3392 | ||
3393 | The main functions of FastQC are: | |
3394 | ||
3395 | @itemize | |
3396 | @item Import of data from BAM, SAM or FastQ files (any variant); | |
3397 | @item Providing a quick overview to tell you in which areas there may | |
3398 | be problems; | |
3399 | @item Summary graphs and tables to quickly assess your data; | |
3400 | @item Export of results to an HTML based permanent report; | |
3401 | @item Offline operation to allow automated generation of reports | |
3402 | without running the interactive application. | |
3403 | @end itemize\n") | |
3404 | (license license:gpl3+))) | |
3405 | ||
e7c09730 RW |
3406 | (define-public htslib |
3407 | (package | |
3408 | (name "htslib") | |
727d8479 | 3409 | (version "1.7") |
e7c09730 RW |
3410 | (source (origin |
3411 | (method url-fetch) | |
3412 | (uri (string-append | |
3413 | "https://github.com/samtools/htslib/releases/download/" | |
3414 | version "/htslib-" version ".tar.bz2")) | |
3415 | (sha256 | |
3416 | (base32 | |
727d8479 | 3417 | "1il6i2p84b0y9c93dhvzzki1ifw9bvapm2mvpr0xvb2nq8jlwgdy")))) |
e7c09730 | 3418 | (build-system gnu-build-system) |
e7c09730 | 3419 | (inputs |
a9e4a1e6 BW |
3420 | `(("openssl" ,openssl) |
3421 | ("curl" ,curl) | |
3422 | ("zlib" ,zlib))) | |
e7c09730 RW |
3423 | (native-inputs |
3424 | `(("perl" ,perl))) | |
3425 | (home-page "http://www.htslib.org") | |
3426 | (synopsis "C library for reading/writing high-throughput sequencing data") | |
3427 | (description | |
3428 | "HTSlib is a C library for reading/writing high-throughput sequencing | |
8057dee1 TGR |
3429 | data. It also provides the @command{bgzip}, @command{htsfile}, and |
3430 | @command{tabix} utilities.") | |
e7c09730 RW |
3431 | ;; Files under cram/ are released under the modified BSD license; |
3432 | ;; the rest is released under the Expat license | |
3433 | (license (list license:expat license:bsd-3)))) | |
3434 | ||
bca2c576 BW |
3435 | ;; This package should be removed once no packages rely upon it. |
3436 | (define htslib-1.3 | |
3437 | (package | |
3438 | (inherit htslib) | |
3439 | (version "1.3.1") | |
3440 | (source (origin | |
3441 | (method url-fetch) | |
3442 | (uri (string-append | |
3443 | "https://github.com/samtools/htslib/releases/download/" | |
3444 | version "/htslib-" version ".tar.bz2")) | |
3445 | (sha256 | |
3446 | (base32 | |
3447 | "1rja282fwdc25ql6izkhdyh8ppw8x2fs0w0js78zgkmqjlikmma9")))))) | |
3448 | ||
c4325f62 RW |
3449 | (define-public idr |
3450 | (package | |
3451 | (name "idr") | |
aa33cc29 | 3452 | (version "2.0.3") |
c4325f62 RW |
3453 | (source (origin |
3454 | (method url-fetch) | |
3455 | (uri (string-append | |
3456 | "https://github.com/nboley/idr/archive/" | |
3457 | version ".tar.gz")) | |
3458 | (file-name (string-append name "-" version ".tar.gz")) | |
3459 | (sha256 | |
3460 | (base32 | |
aa33cc29 RW |
3461 | "1rjdly6daslw66r43g9md8znizlscn1sphycqyldzsidkc4vxqv3")) |
3462 | ;; Delete generated C code. | |
3463 | (snippet | |
3464 | '(begin (delete-file "idr/inv_cdf.c") #t)))) | |
c4325f62 | 3465 | (build-system python-build-system) |
aa33cc29 RW |
3466 | ;; There is only one test ("test_inv_cdf.py") and it tests features that |
3467 | ;; are no longer part of this package. It also asserts False, which | |
3468 | ;; causes the tests to always fail. | |
3469 | (arguments `(#:tests? #f)) | |
b7a820fc | 3470 | (propagated-inputs |
c4325f62 | 3471 | `(("python-scipy" ,python-scipy) |
b7a820fc | 3472 | ("python-sympy" ,python-sympy) |
c4325f62 RW |
3473 | ("python-numpy" ,python-numpy) |
3474 | ("python-matplotlib" ,python-matplotlib))) | |
3475 | (native-inputs | |
f3b98f4f | 3476 | `(("python-cython" ,python-cython))) |
c4325f62 RW |
3477 | (home-page "https://github.com/nboley/idr") |
3478 | (synopsis "Tool to measure the irreproducible discovery rate (IDR)") | |
3479 | (description | |
3480 | "The IDR (Irreproducible Discovery Rate) framework is a unified approach | |
3481 | to measure the reproducibility of findings identified from replicate | |
3482 | experiments and provide highly stable thresholds based on reproducibility.") | |
40590caf | 3483 | (license license:gpl2+))) |
c4325f62 | 3484 | |
43c565d2 RW |
3485 | (define-public jellyfish |
3486 | (package | |
3487 | (name "jellyfish") | |
117d8cc4 | 3488 | (version "2.2.7") |
43c565d2 RW |
3489 | (source (origin |
3490 | (method url-fetch) | |
3491 | (uri (string-append "https://github.com/gmarcais/Jellyfish/" | |
3492 | "releases/download/v" version | |
3493 | "/jellyfish-" version ".tar.gz")) | |
3494 | (sha256 | |
3495 | (base32 | |
117d8cc4 | 3496 | "1a1iwq9pq54k2m9ypvwl5s0bqfl64gwh9dx5af9i382ajas2016q")))) |
43c565d2 RW |
3497 | (build-system gnu-build-system) |
3498 | (outputs '("out" ;for library | |
3499 | "ruby" ;for Ruby bindings | |
3500 | "python")) ;for Python bindings | |
3501 | (arguments | |
3502 | `(#:configure-flags | |
3503 | (list (string-append "--enable-ruby-binding=" | |
3504 | (assoc-ref %outputs "ruby")) | |
3505 | (string-append "--enable-python-binding=" | |
3506 | (assoc-ref %outputs "python"))) | |
3507 | #:phases | |
3508 | (modify-phases %standard-phases | |
3509 | (add-before 'check 'set-SHELL-variable | |
3510 | (lambda _ | |
3511 | ;; generator_manager.hpp either uses /bin/sh or $SHELL | |
3512 | ;; to run tests. | |
3513 | (setenv "SHELL" (which "bash")) | |
3514 | #t))))) | |
3515 | (native-inputs | |
3516 | `(("bc" ,bc) | |
3517 | ("time" ,time) | |
3518 | ("ruby" ,ruby) | |
117d8cc4 RW |
3519 | ("python" ,python-2) |
3520 | ("pkg-config" ,pkg-config))) | |
3521 | (inputs | |
3522 | `(("htslib" ,htslib))) | |
43c565d2 RW |
3523 | (synopsis "Tool for fast counting of k-mers in DNA") |
3524 | (description | |
3525 | "Jellyfish is a tool for fast, memory-efficient counting of k-mers in | |
3526 | DNA. A k-mer is a substring of length k, and counting the occurrences of all | |
3527 | such substrings is a central step in many analyses of DNA sequence. Jellyfish | |
3528 | is a command-line program that reads FASTA and multi-FASTA files containing | |
3529 | DNA sequences. It outputs its k-mer counts in a binary format, which can be | |
3530 | translated into a human-readable text format using the @code{jellyfish dump} | |
3531 | command, or queried for specific k-mers with @code{jellyfish query}.") | |
3532 | (home-page "http://www.genome.umd.edu/jellyfish.html") | |
6e8faf77 EF |
3533 | ;; From their website: JELLYFISH runs on 64-bit Intel-compatible processors |
3534 | (supported-systems '("x86_64-linux")) | |
43c565d2 RW |
3535 | ;; The combined work is published under the GPLv3 or later. Individual |
3536 | ;; files such as lib/jsoncpp.cpp are released under the Expat license. | |
3537 | (license (list license:gpl3+ license:expat)))) | |
3538 | ||
94ff3157 BW |
3539 | (define-public khmer |
3540 | (package | |
3541 | (name "khmer") | |
3542 | (version "2.0") | |
3543 | (source | |
3544 | (origin | |
3545 | (method url-fetch) | |
3546 | (uri (pypi-uri "khmer" version)) | |
3547 | (sha256 | |
3548 | (base32 | |
3549 | "0wb05shqh77v00256qlm68vbbx3kl76fyzihszbz5nhanl4ni33a")) | |
3550 | (patches (search-patches "khmer-use-libraries.patch")))) | |
3551 | (build-system python-build-system) | |
3552 | (arguments | |
3553 | `(#:phases | |
3554 | (modify-phases %standard-phases | |
3555 | (add-after 'unpack 'set-paths | |
3556 | (lambda* (#:key inputs outputs #:allow-other-keys) | |
3557 | ;; Delete bundled libraries. | |
3558 | (delete-file-recursively "third-party/zlib") | |
3559 | (delete-file-recursively "third-party/bzip2") | |
3560 | ;; Replace bundled seqan. | |
3561 | (let* ((seqan-all "third-party/seqan") | |
3562 | (seqan-include (string-append | |
3563 | seqan-all "/core/include"))) | |
3564 | (delete-file-recursively seqan-all) | |
3565 | (copy-recursively (string-append (assoc-ref inputs "seqan") | |
3566 | "/include/seqan") | |
3567 | (string-append seqan-include "/seqan"))) | |
3568 | ;; We do not replace the bundled MurmurHash as the canonical | |
3569 | ;; repository for this code 'SMHasher' is unsuitable for | |
3570 | ;; providing a library. See | |
3571 | ;; https://lists.gnu.org/archive/html/guix-devel/2016-06/msg00977.html | |
3572 | #t)) | |
3573 | (add-after 'unpack 'set-cc | |
3574 | (lambda _ | |
3575 | (setenv "CC" "gcc") | |
3576 | #t)) | |
3577 | ;; It is simpler to test after installation. | |
3578 | (delete 'check) | |
3579 | (add-after 'install 'post-install-check | |
3580 | (lambda* (#:key inputs outputs #:allow-other-keys) | |
3581 | (let ((out (assoc-ref outputs "out"))) | |
3582 | (setenv "PATH" | |
3583 | (string-append | |
3584 | (getenv "PATH") | |
3585 | ":" | |
3586 | (assoc-ref outputs "out") | |
3587 | "/bin")) | |
3588 | (setenv "PYTHONPATH" | |
3589 | (string-append | |
3590 | (getenv "PYTHONPATH") | |
3591 | ":" | |
3592 | out | |
3593 | "/lib/python" | |
3594 | (string-take (string-take-right | |
3595 | (assoc-ref inputs "python") 5) 3) | |
3596 | "/site-packages")) | |
3597 | (with-directory-excursion "build" | |
3598 | (zero? (system* "nosetests" "khmer" "--attr" | |
3599 | "!known_failing"))))))))) | |
3600 | (native-inputs | |
3601 | `(("seqan" ,seqan) | |
3602 | ("python-nose" ,python-nose))) | |
3603 | (inputs | |
3604 | `(("zlib" ,zlib) | |
3605 | ("bzip2" ,bzip2) | |
3606 | ("python-screed" ,python-screed) | |
cf1d5814 BW |
3607 | ("python-bz2file" ,python-bz2file) |
3608 | ;; Tests fail when gcc-5 is used for compilation. Use gcc-4.9 at least | |
3609 | ;; until the next version of khmer (likely 2.1) is released. | |
3610 | ("gcc" ,gcc-4.9))) | |
94ff3157 BW |
3611 | (home-page "https://khmer.readthedocs.org/") |
3612 | (synopsis "K-mer counting, filtering and graph traversal library") | |
3613 | (description "The khmer software is a set of command-line tools for | |
3614 | working with DNA shotgun sequencing data from genomes, transcriptomes, | |
3615 | metagenomes and single cells. Khmer can make de novo assemblies faster, and | |
3616 | sometimes better. Khmer can also identify and fix problems with shotgun | |
3617 | data.") | |
8157af2e EF |
3618 | ;; When building on i686, armhf and mips64el, we get the following error: |
3619 | ;; error: ['khmer', 'khmer.tests', 'oxli'] require 64-bit operating system | |
3df57b3a | 3620 | (supported-systems '("x86_64-linux" "aarch64-linux")) |
94ff3157 BW |
3621 | (license license:bsd-3))) |
3622 | ||
b9a601d9 RJ |
3623 | (define-public kaiju |
3624 | (package | |
3625 | (name "kaiju") | |
3626 | (version "1.5.0") | |
3627 | (source (origin | |
3628 | (method url-fetch) | |
3629 | (uri (string-append | |
3630 | "https://github.com/bioinformatics-centre/kaiju/archive/v" | |
3631 | version ".tar.gz")) | |
3632 | (file-name (string-append name "-" version ".tar.gz")) | |
3633 | (sha256 | |
3634 | (base32 | |
3635 | "0afbfalfw9y39bkwnqjrh9bghs118ws1pzj5h8l0nblgn3mbjdks")))) | |
3636 | (build-system gnu-build-system) | |
3637 | (arguments | |
3638 | `(#:tests? #f ; There are no tests. | |
3639 | #:phases | |
3640 | (modify-phases %standard-phases | |
3641 | (delete 'configure) | |
3642 | (add-before 'build 'move-to-src-dir | |
3643 | (lambda _ (chdir "src") #t)) | |
3644 | (replace 'install | |
3645 | (lambda* (#:key inputs outputs #:allow-other-keys) | |
3646 | (let ((bin (string-append (assoc-ref outputs "out") "/bin"))) | |
3647 | (mkdir-p bin) | |
3648 | (chdir "..") | |
3649 | (copy-recursively "bin" bin) | |
3650 | (copy-recursively "util" bin)) | |
3651 | #t))))) | |
3652 | (inputs | |
3653 | `(("perl" ,perl))) | |
3654 | (home-page "http://kaiju.binf.ku.dk/") | |
3655 | (synopsis "Fast and sensitive taxonomic classification for metagenomics") | |
3656 | (description "Kaiju is a program for sensitive taxonomic classification | |
3657 | of high-throughput sequencing reads from metagenomic whole genome sequencing | |
3658 | experiments.") | |
3659 | (license license:gpl3+))) | |
3660 | ||
d57e6d0f RW |
3661 | (define-public macs |
3662 | (package | |
3663 | (name "macs") | |
0d0bcaa0 | 3664 | (version "2.1.0.20151222") |
d57e6d0f RW |
3665 | (source (origin |
3666 | (method url-fetch) | |
43ec07f1 | 3667 | (uri (pypi-uri "MACS2" version)) |
d57e6d0f RW |
3668 | (sha256 |
3669 | (base32 | |
0d0bcaa0 | 3670 | "1r2hcz6irhcq7lwbafjks98jbn34hv05avgbdjnp6w6mlfjkf8x5")))) |
d57e6d0f RW |
3671 | (build-system python-build-system) |
3672 | (arguments | |
3673 | `(#:python ,python-2 ; only compatible with Python 2.7 | |
3674 | #:tests? #f)) ; no test target | |
3675 | (inputs | |
3676 | `(("python-numpy" ,python2-numpy))) | |
7bf837fd | 3677 | (home-page "https://github.com/taoliu/MACS/") |
d57e6d0f RW |
3678 | (synopsis "Model based analysis for ChIP-Seq data") |
3679 | (description | |
3680 | "MACS is an implementation of a ChIP-Seq analysis algorithm for | |
3681 | identifying transcript factor binding sites named Model-based Analysis of | |
3682 | ChIP-Seq (MACS). MACS captures the influence of genome complexity to evaluate | |
3683 | the significance of enriched ChIP regions and it improves the spatial | |
3684 | resolution of binding sites through combining the information of both | |
3685 | sequencing tag position and orientation.") | |
3686 | (license license:bsd-3))) | |
3687 | ||
41ddebdd BW |
3688 | (define-public mafft |
3689 | (package | |
3690 | (name "mafft") | |
3146f22d | 3691 | (version "7.313") |
41ddebdd BW |
3692 | (source (origin |
3693 | (method url-fetch) | |
3694 | (uri (string-append | |
3146f22d | 3695 | "https://mafft.cbrc.jp/alignment/software/mafft-" version |
41ddebdd BW |
3696 | "-without-extensions-src.tgz")) |
3697 | (file-name (string-append name "-" version ".tgz")) | |
3698 | (sha256 | |
3699 | (base32 | |
3146f22d | 3700 | "0r83qmg2if8mi6jyx3xdf8ar2gcxl7r9nmj98jr7lxym97v61a2k")))) |
41ddebdd BW |
3701 | (build-system gnu-build-system) |
3702 | (arguments | |
3703 | `(#:tests? #f ; no automated tests, though there are tests in the read me | |
3704 | #:make-flags (let ((out (assoc-ref %outputs "out"))) | |
3705 | (list (string-append "PREFIX=" out) | |
3706 | (string-append "BINDIR=" | |
3707 | (string-append out "/bin")))) | |
3708 | #:phases | |
3709 | (modify-phases %standard-phases | |
3710 | (add-after 'unpack 'enter-dir | |
101e8f71 | 3711 | (lambda _ (chdir "core") #t)) |
41ddebdd | 3712 | (add-after 'enter-dir 'patch-makefile |
101e8f71 BW |
3713 | (lambda _ |
3714 | ;; on advice from the MAFFT authors, there is no need to | |
3715 | ;; distribute mafft-profile, mafft-distance, or | |
3716 | ;; mafft-homologs.rb as they are too "specialised". | |
3717 | (substitute* "Makefile" | |
3718 | ;; remove mafft-homologs.rb from SCRIPTS | |
3719 | (("^SCRIPTS = mafft mafft-homologs.rb") | |
3720 | "SCRIPTS = mafft") | |
3721 | ;; remove mafft-homologs from MANPAGES | |
3722 | (("^MANPAGES = mafft.1 mafft-homologs.1") | |
3723 | "MANPAGES = mafft.1") | |
3724 | ;; remove mafft-distance from PROGS | |
3725 | (("^PROGS = dvtditr dndfast7 dndblast sextet5 mafft-distance") | |
3726 | "PROGS = dvtditr dndfast7 dndblast sextet5") | |
3727 | ;; remove mafft-profile from PROGS | |
3728 | (("splittbfast disttbfast tbfast mafft-profile 2cl mccaskillwrap") | |
3729 | "splittbfast disttbfast tbfast f2cl mccaskillwrap") | |
3730 | (("^rm -f mafft-profile mafft-profile.exe") "#") | |
3731 | (("^rm -f mafft-distance mafft-distance.exe") ")#") | |
3732 | ;; do not install MAN pages in libexec folder | |
3733 | (("^\t\\$\\(INSTALL\\) -m 644 \\$\\(MANPAGES\\) \ | |
41ddebdd | 3734 | \\$\\(DESTDIR\\)\\$\\(LIBDIR\\)") "#")) |
101e8f71 | 3735 | #t)) |
02f35bb5 BW |
3736 | (add-after 'enter-dir 'patch-paths |
3737 | (lambda* (#:key inputs #:allow-other-keys) | |
3738 | (substitute* '("pairash.c" | |
3739 | "mafft.tmpl") | |
3740 | (("perl") (which "perl")) | |
3741 | (("([\"`| ])awk" _ prefix) | |
3742 | (string-append prefix (which "awk"))) | |
3743 | (("grep") (which "grep"))) | |
3744 | #t)) | |
101e8f71 BW |
3745 | (delete 'configure) |
3746 | (add-after 'install 'wrap-programs | |
3747 | (lambda* (#:key outputs #:allow-other-keys) | |
3748 | (let* ((out (assoc-ref outputs "out")) | |
3749 | (bin (string-append out "/bin")) | |
3750 | (path (string-append | |
3751 | (assoc-ref %build-inputs "coreutils") "/bin:"))) | |
3752 | (for-each (lambda (file) | |
3753 | (wrap-program file | |
3754 | `("PATH" ":" prefix (,path)))) | |
3755 | (find-files bin))) | |
3756 | #t))))) | |
41ddebdd | 3757 | (inputs |
02f35bb5 | 3758 | `(("perl" ,perl) |
71461f88 | 3759 | ("ruby" ,ruby) |
02f35bb5 | 3760 | ("gawk" ,gawk) |
101e8f71 BW |
3761 | ("grep" ,grep) |
3762 | ("coreutils" ,coreutils))) | |
41ddebdd BW |
3763 | (home-page "http://mafft.cbrc.jp/alignment/software/") |
3764 | (synopsis "Multiple sequence alignment program") | |
3765 | (description | |
3766 | "MAFFT offers a range of multiple alignment methods for nucleotide and | |
3767 | protein sequences. For instance, it offers L-INS-i (accurate; for alignment | |
3768 | of <~200 sequences) and FFT-NS-2 (fast; for alignment of <~30,000 | |
3769 | sequences).") | |
3770 | (license (license:non-copyleft | |
3771 | "http://mafft.cbrc.jp/alignment/software/license.txt" | |
3772 | "BSD-3 with different formatting")))) | |
8fd790eb | 3773 | |
84be3b99 MB |
3774 | (define-public mash |
3775 | (package | |
3776 | (name "mash") | |
3777 | (version "1.1.1") | |
3778 | (source (origin | |
3779 | (method url-fetch) | |
3780 | (uri (string-append | |
3781 | "https://github.com/marbl/mash/archive/v" | |
3782 | version ".tar.gz")) | |
3783 | (file-name (string-append name "-" version ".tar.gz")) | |
3784 | (sha256 | |
3785 | (base32 | |
3786 | "08znbvqq5xknfhmpp3wcj574zvi4p7i8zifi67c9qw9a6ikp42fj")) | |
3787 | (modules '((guix build utils))) | |
3788 | (snippet | |
3789 | ;; Delete bundled kseq. | |
3790 | ;; TODO: Also delete bundled murmurhash and open bloom filter. | |
3791 | '(delete-file "src/mash/kseq.h")))) | |
3792 | (build-system gnu-build-system) | |
3793 | (arguments | |
3794 | `(#:tests? #f ; No tests. | |
3795 | #:configure-flags | |
3796 | (list | |
3797 | (string-append "--with-capnp=" (assoc-ref %build-inputs "capnproto")) | |
3798 | (string-append "--with-gsl=" (assoc-ref %build-inputs "gsl"))) | |
3799 | #:make-flags (list "CC=gcc") | |
3800 | #:phases | |
3801 | (modify-phases %standard-phases | |
3802 | (add-after 'unpack 'fix-includes | |
3803 | (lambda _ | |
3804 | (substitute* '("src/mash/Sketch.cpp" "src/mash/CommandFind.cpp") | |
3805 | (("^#include \"kseq\\.h\"") | |
3806 | "#include \"htslib/kseq.h\"")) | |
3807 | #t)) | |
d10092b8 | 3808 | (add-after 'fix-includes 'autoconf |
84be3b99 MB |
3809 | (lambda _ (zero? (system* "autoconf"))))))) |
3810 | (native-inputs | |
3811 | `(("autoconf" ,autoconf) | |
3812 | ;; Capnproto and htslib are statically embedded in the final | |
3813 | ;; application. Therefore we also list their licenses, below. | |
3814 | ("capnproto" ,capnproto) | |
3815 | ("htslib" ,htslib))) | |
3816 | (inputs | |
3817 | `(("gsl" ,gsl) | |
3818 | ("zlib" ,zlib))) | |
3819 | (supported-systems '("x86_64-linux")) | |
3820 | (home-page "https://mash.readthedocs.io") | |
3821 | (synopsis "Fast genome and metagenome distance estimation using MinHash") | |
3822 | (description "Mash is a fast sequence distance estimator that uses the | |
3823 | MinHash algorithm and is designed to work with genomes and metagenomes in the | |
3824 | form of assemblies or reads.") | |
3825 | (license (list license:bsd-3 ; Mash | |
3826 | license:expat ; HTSlib and capnproto | |
3827 | license:public-domain ; MurmurHash 3 | |
3828 | license:cpl1.0)))) ; Open Bloom Filter | |
3829 | ||
8fd790eb | 3830 | (define-public metabat |
f3f68a44 BW |
3831 | (package |
3832 | (name "metabat") | |
25bd1fc1 | 3833 | (version "2.12.1") |
f3f68a44 BW |
3834 | (source |
3835 | (origin | |
25bd1fc1 BW |
3836 | (method url-fetch) |
3837 | (uri (string-append "https://bitbucket.org/berkeleylab/metabat/get/v" | |
3838 | version ".tar.gz")) | |
3839 | (file-name (string-append name "-" version ".tar.gz")) | |
f3f68a44 BW |
3840 | (sha256 |
3841 | (base32 | |
25bd1fc1 BW |
3842 | "1hmvdalz3zj5sqqklg0l4npjdv37cv2hsdi1al9iby2ndxjs1b73")) |
3843 | (patches (search-patches "metabat-fix-compilation.patch")))) | |
9364a520 | 3844 | (build-system scons-build-system) |
8fd790eb | 3845 | (arguments |
9364a520 AI |
3846 | `(#:scons ,scons-python2 |
3847 | #:scons-flags | |
3848 | (list (string-append "PREFIX=" (assoc-ref %outputs "out")) | |
3849 | (string-append "BOOST_ROOT=" (assoc-ref %build-inputs "boost"))) | |
3850 | #:tests? #f ;; Tests are run during the build phase. | |
3851 | #:phases | |
8fd790eb BW |
3852 | (modify-phases %standard-phases |
3853 | (add-after 'unpack 'fix-includes | |
45469ebe BW |
3854 | (lambda _ |
3855 | (substitute* "src/BamUtils.h" | |
3856 | (("^#include \"bam/bam\\.h\"") | |
3857 | "#include \"samtools/bam.h\"") | |
3858 | (("^#include \"bam/sam\\.h\"") | |
3859 | "#include \"samtools/sam.h\"")) | |
3860 | (substitute* "src/KseqReader.h" | |
3861 | (("^#include \"bam/kseq\\.h\"") | |
3862 | "#include \"htslib/kseq.h\"")) | |
3863 | #t)) | |
8fd790eb | 3864 | (add-after 'unpack 'fix-scons |
f3f68a44 BW |
3865 | (lambda* (#:key inputs #:allow-other-keys) |
3866 | (substitute* "SConstruct" | |
3867 | (("^htslib_dir += 'samtools'") | |
3868 | (string-append "htslib_dir = '" | |
3869 | (assoc-ref inputs "htslib") | |
3870 | "'")) | |
3871 | (("^samtools_dir = 'samtools'") | |
3872 | (string-append "samtools_dir = '" | |
3873 | (assoc-ref inputs "samtools") | |
3874 | "'")) | |
3875 | (("^findStaticOrShared\\('bam', hts_lib") | |
3876 | (string-append "findStaticOrShared('bam', '" | |
3877 | (assoc-ref inputs "samtools") | |
3878 | "/lib'")) | |
3879 | ;; Do not distribute README. | |
3880 | (("^env\\.Install\\(idir_prefix, 'README\\.md'\\)") "")) | |
9364a520 | 3881 | #t))))) |
8fd790eb BW |
3882 | (inputs |
3883 | `(("zlib" ,zlib) | |
3884 | ("perl" ,perl) | |
3885 | ("samtools" ,samtools) | |
3886 | ("htslib" ,htslib) | |
3887 | ("boost" ,boost))) | |
8fd790eb BW |
3888 | (home-page "https://bitbucket.org/berkeleylab/metabat") |
3889 | (synopsis | |
3890 | "Reconstruction of single genomes from complex microbial communities") | |
3891 | (description | |
3892 | "Grouping large genomic fragments assembled from shotgun metagenomic | |
3893 | sequences to deconvolute complex microbial communities, or metagenome binning, | |
3894 | enables the study of individual organisms and their interactions. MetaBAT is | |
3895 | an automated metagenome binning software, which integrates empirical | |
3896 | probabilistic distances of genome abundance and tetranucleotide frequency.") | |
d931a4bb EF |
3897 | ;; The source code contains inline assembly. |
3898 | (supported-systems '("x86_64-linux" "i686-linux")) | |
f3f68a44 BW |
3899 | (license (license:non-copyleft "file://license.txt" |
3900 | "See license.txt in the distribution.")))) | |
8fd790eb | 3901 | |
318c0aee MB |
3902 | (define-public minced |
3903 | (package | |
3904 | (name "minced") | |
3905 | (version "0.2.0") | |
3906 | (source (origin | |
3907 | (method url-fetch) | |
3908 | (uri (string-append | |
3909 | "https://github.com/ctSkennerton/minced/archive/" | |
3910 | version ".tar.gz")) | |
3911 | (file-name (string-append name "-" version ".tar.gz")) | |
3912 | (sha256 | |
3913 | (base32 | |
3914 | "0wxmlsapxfpxfd3ps9636h7i2xy6la8i42mwh0j2lsky63h63jp1")))) | |
3915 | (build-system gnu-build-system) | |
3916 | (arguments | |
3917 | `(#:test-target "test" | |
3918 | #:phases | |
3919 | (modify-phases %standard-phases | |
3920 | (delete 'configure) | |
3921 | (add-before 'check 'fix-test | |
3922 | (lambda _ | |
3923 | ;; Fix test for latest version. | |
3924 | (substitute* "t/Aquifex_aeolicus_VF5.expected" | |
3925 | (("minced:0.1.6") "minced:0.2.0")) | |
3926 | #t)) | |
3927 | (replace 'install ; No install target. | |
3928 | (lambda* (#:key inputs outputs #:allow-other-keys) | |
3929 | (let* ((out (assoc-ref outputs "out")) | |
3930 | (bin (string-append out "/bin")) | |
3931 | (wrapper (string-append bin "/minced"))) | |
3932 | ;; Minced comes with a wrapper script that tries to figure out where | |
3933 | ;; it is located before running the JAR. Since these paths are known | |
3934 | ;; to us, we build our own wrapper to avoid coreutils dependency. | |
3935 | (install-file "minced.jar" bin) | |
3936 | (with-output-to-file wrapper | |
3937 | (lambda _ | |
3938 | (display | |
3939 | (string-append | |
3940 | "#!" (assoc-ref inputs "bash") "/bin/sh\n\n" | |
3941 | (assoc-ref inputs "jre") "/bin/java -jar " | |
3942 | bin "/minced.jar \"$@\"\n")))) | |
3943 | (chmod wrapper #o555))))))) | |
3944 | (native-inputs | |
3945 | `(("jdk" ,icedtea "jdk"))) | |
3946 | (inputs | |
3947 | `(("bash" ,bash) | |
3948 | ("jre" ,icedtea "out"))) | |
3949 | (home-page "https://github.com/ctSkennerton/minced") | |
3950 | (synopsis "Mining CRISPRs in Environmental Datasets") | |
3951 | (description | |
3952 | "MinCED is a program to find Clustered Regularly Interspaced Short | |
3953 | Palindromic Repeats (CRISPRs) in DNA sequences. It can be used for | |
3954 | unassembled metagenomic reads, but is mainly designed for full genomes and | |
3955 | assembled metagenomic sequence.") | |
3956 | (license license:gpl3+))) | |
3957 | ||
ddd82e0e RW |
3958 | (define-public miso |
3959 | (package | |
3960 | (name "miso") | |
ce4dfde0 | 3961 | (version "0.5.4") |
ddd82e0e RW |
3962 | (source (origin |
3963 | (method url-fetch) | |
34260a10 | 3964 | (uri (pypi-uri "misopy" version)) |
ddd82e0e RW |
3965 | (sha256 |
3966 | (base32 | |
ce4dfde0 | 3967 | "1z3x0vd8ma7pdrnywj7i3kgwl89sdkwrrn62zl7r5calqaq2hyip")) |
ddd82e0e | 3968 | (modules '((guix build utils))) |
ddd82e0e RW |
3969 | (snippet |
3970 | '(substitute* "setup.py" | |
0ec8b206 RW |
3971 | ;; Use setuptools, or else the executables are not |
3972 | ;; installed. | |
3973 | (("distutils.core") "setuptools") | |
3974 | ;; use "gcc" instead of "cc" for compilation | |
ddd82e0e RW |
3975 | (("^defines") |
3976 | "cc.set_executables( | |
3977 | compiler='gcc', | |
3978 | compiler_so='gcc', | |
3979 | linker_exe='gcc', | |
3980 | linker_so='gcc -shared'); defines"))))) | |
3981 | (build-system python-build-system) | |
3982 | (arguments | |
3983 | `(#:python ,python-2 ; only Python 2 is supported | |
3984 | #:tests? #f)) ; no "test" target | |
3985 | (inputs | |
3986 | `(("samtools" ,samtools) | |
3987 | ("python-numpy" ,python2-numpy) | |
3988 | ("python-pysam" ,python2-pysam) | |
3989 | ("python-scipy" ,python2-scipy) | |
3990 | ("python-matplotlib" ,python2-matplotlib))) | |
3991 | (native-inputs | |
f3b98f4f HG |
3992 | `(("python-mock" ,python2-mock) ;for tests |
3993 | ("python-pytz" ,python2-pytz))) ;for tests | |
ddd82e0e RW |
3994 | (home-page "http://genes.mit.edu/burgelab/miso/index.html") |
3995 | (synopsis "Mixture of Isoforms model for RNA-Seq isoform quantitation") | |
3996 | (description | |
3997 | "MISO (Mixture-of-Isoforms) is a probabilistic framework that quantitates | |
3998 | the expression level of alternatively spliced genes from RNA-Seq data, and | |
3999 | identifies differentially regulated isoforms or exons across samples. By | |
4000 | modeling the generative process by which reads are produced from isoforms in | |
4001 | RNA-Seq, the MISO model uses Bayesian inference to compute the probability | |
4002 | that a read originated from a particular isoform.") | |
4003 | (license license:gpl2))) | |
4004 | ||
324efb88 BW |
4005 | (define-public muscle |
4006 | (package | |
4007 | (name "muscle") | |
4008 | (version "3.8.1551") | |
4009 | (source (origin | |
4010 | (method url-fetch/tarbomb) | |
324efb88 BW |
4011 | (uri (string-append |
4012 | "http://www.drive5.com/muscle/muscle_src_" | |
4013 | version ".tar.gz")) | |
4014 | (sha256 | |
4015 | (base32 | |
4016 | "0bj8kj7sdizy3987zx6w7axihk40fk8rn76mpbqqjcnd64i5a367")))) | |
4017 | (build-system gnu-build-system) | |
4018 | (arguments | |
4019 | `(#:make-flags (list "LDLIBS = -lm") | |
4020 | #:phases | |
4021 | (modify-phases %standard-phases | |
4022 | (delete 'configure) | |
4023 | (replace 'check | |
4024 | ;; There are no tests, so just test if it runs. | |
4025 | (lambda _ (zero? (system* "./muscle" "-version")))) | |
4026 | (replace 'install | |
4027 | (lambda* (#:key outputs #:allow-other-keys) | |
4028 | (let* ((out (assoc-ref outputs "out")) | |
4029 | (bin (string-append out "/bin"))) | |
4030 | (install-file "muscle" bin))))))) | |
4031 | (home-page "http://www.drive5.com/muscle") | |
4032 | (synopsis "Multiple sequence alignment program") | |
4033 | (description | |
4034 | "MUSCLE aims to be a fast and accurate multiple sequence alignment | |
4035 | program for nucleotide and protein sequences.") | |
4036 | ;; License information found in 'muscle -h' and usage.cpp. | |
4037 | (license license:public-domain))) | |
4038 | ||
99268755 BW |
4039 | (define-public newick-utils |
4040 | ;; There are no recent releases so we package from git. | |
4041 | (let ((commit "da121155a977197cab9fbb15953ca1b40b11eb87")) | |
4042 | (package | |
4043 | (name "newick-utils") | |
4044 | (version (string-append "1.6-1." (string-take commit 8))) | |
4045 | (source (origin | |
4046 | (method git-fetch) | |
4047 | (uri (git-reference | |
4048 | (url "https://github.com/tjunier/newick_utils.git") | |
4049 | (commit commit))) | |
4050 | (file-name (string-append name "-" version "-checkout")) | |
4051 | (sha256 | |
4052 | (base32 | |
4053 | "1hkw21rq1mwf7xp0rmbb2gqc0i6p11108m69i7mr7xcjl268pxnb")))) | |
4054 | (build-system gnu-build-system) | |
4055 | (arguments | |
4056 | `(#:phases | |
4057 | (modify-phases %standard-phases | |
4058 | (add-after 'unpack 'autoconf | |
4059 | (lambda _ (zero? (system* "autoreconf" "-vif"))))))) | |
4060 | (inputs | |
4061 | ;; XXX: TODO: Enable Lua and Guile bindings. | |
4062 | ;; https://github.com/tjunier/newick_utils/issues/13 | |
4063 | `(("libxml2" ,libxml2) | |
4064 | ("flex" ,flex) | |
4065 | ("bison" ,bison))) | |
4066 | (native-inputs | |
4067 | `(("autoconf" ,autoconf) | |
4068 | ("automake" ,automake) | |
4069 | ("libtool" ,libtool))) | |
4070 | (synopsis "Programs for working with newick format phylogenetic trees") | |
4071 | (description | |
4072 | "Newick-utils is a suite of utilities for processing phylogenetic trees | |
4073 | in Newick format. Functions include re-rooting, extracting subtrees, | |
4074 | trimming, pruning, condensing, drawing (ASCII graphics or SVG).") | |
4075 | (home-page "https://github.com/tjunier/newick_utils") | |
4076 | (license license:bsd-3)))) | |
4077 | ||
1e44cf8b BW |
4078 | (define-public orfm |
4079 | (package | |
4080 | (name "orfm") | |
dfc83ead | 4081 | (version "0.7.1") |
1e44cf8b BW |
4082 | (source (origin |
4083 | (method url-fetch) | |
4084 | (uri (string-append | |
4085 | "https://github.com/wwood/OrfM/releases/download/v" | |
4086 | version "/orfm-" version ".tar.gz")) | |
4087 | (sha256 | |
4088 | (base32 | |
dfc83ead | 4089 | "16iigyr2gd8x0imzkk1dr3k5xsds9bpmwg31ayvjg0f4pir9rwqr")))) |
1e44cf8b BW |
4090 | (build-system gnu-build-system) |
4091 | (inputs `(("zlib" ,zlib))) | |
6b6f7d6a BW |
4092 | (native-inputs |
4093 | `(("ruby-bio-commandeer" ,ruby-bio-commandeer) | |
4094 | ("ruby-rspec" ,ruby-rspec) | |
4095 | ("ruby" ,ruby))) | |
1e44cf8b BW |
4096 | (synopsis "Simple and not slow open reading frame (ORF) caller") |
4097 | (description | |
6b6f7d6a | 4098 | "An ORF caller finds stretches of DNA that, when translated, are not |
1e44cf8b BW |
4099 | interrupted by stop codons. OrfM finds and prints these ORFs.") |
4100 | (home-page "https://github.com/wwood/OrfM") | |
4101 | (license license:lgpl3+))) | |
4102 | ||
c033f5d6 BW |
4103 | (define-public pplacer |
4104 | (let ((commit "g807f6f3")) | |
4105 | (package | |
4106 | (name "pplacer") | |
4107 | ;; The commit should be updated with each version change. | |
4108 | (version "1.1.alpha19") | |
4109 | (source | |
4110 | (origin | |
4111 | (method url-fetch) | |
4112 | (uri (string-append "https://github.com/matsen/pplacer/archive/v" | |
4113 | version ".tar.gz")) | |
4114 | (file-name (string-append name "-" version ".tar.gz")) | |
4115 | (sha256 | |
4116 | (base32 "0z1lnd2s8sh6kpzg106wzbh2szw7h0hvq8syd5a6wv4rmyyz6x0f")))) | |
4117 | (build-system ocaml-build-system) | |
4118 | (arguments | |
4119 | `(#:ocaml ,ocaml-4.01 | |
4120 | #:findlib ,ocaml4.01-findlib | |
4121 | #:modules ((guix build ocaml-build-system) | |
4122 | (guix build utils) | |
4123 | (ice-9 ftw)) | |
4124 | #:phases | |
4125 | (modify-phases %standard-phases | |
4126 | (delete 'configure) | |
4127 | (add-after 'unpack 'replace-bundled-cddlib | |
4128 | (lambda* (#:key inputs #:allow-other-keys) | |
4129 | (let* ((cddlib-src (assoc-ref inputs "cddlib-src")) | |
4130 | (local-dir "cddlib_guix")) | |
4131 | (mkdir local-dir) | |
4132 | (with-directory-excursion local-dir | |
4133 | (system* "tar" "xvf" cddlib-src)) | |
4134 | (let ((cddlib-src-folder | |
4135 | (string-append local-dir "/" | |
4136 | (list-ref (scandir local-dir) 2) | |
4137 | "/lib-src"))) | |
4138 | (for-each | |
4139 | (lambda (file) | |
4140 | (copy-file file | |
4141 | (string-append "cdd_src/" (basename file)))) | |
4142 | (find-files cddlib-src-folder ".*[ch]$"))) | |
4143 | #t))) | |
4144 | (add-after 'unpack 'fix-makefile | |
4145 | (lambda _ | |
4146 | ;; Remove system calls to 'git'. | |
4147 | (substitute* "Makefile" | |
4148 | (("^DESCRIPT:=pplacer-.*") | |
4149 | (string-append | |
4150 | "DESCRIPT:=pplacer-$(shell uname)-v" ,version "\n"))) | |
4151 | (substitute* "myocamlbuild.ml" | |
4152 | (("git describe --tags --long .*\\\" with") | |
4153 | (string-append | |
4154 | "echo -n v" ,version "-" ,commit "\" with"))) | |
4155 | #t)) | |
4156 | (replace 'install | |
4157 | (lambda* (#:key outputs #:allow-other-keys) | |
4158 | (let* ((out (assoc-ref outputs "out")) | |
4159 | (bin (string-append out "/bin"))) | |
4160 | (copy-recursively "bin" bin)) | |
4161 | #t))))) | |
4162 | (native-inputs | |
4163 | `(("zlib" ,zlib) | |
4164 | ("gsl" ,gsl) | |
4165 | ("ocaml-ounit" ,ocaml4.01-ounit) | |
4166 | ("ocaml-batteries" ,ocaml4.01-batteries) | |
4167 | ("ocaml-camlzip" ,ocaml4.01-camlzip) | |
4168 | ("ocaml-csv" ,ocaml4.01-csv) | |
4169 | ("ocaml-sqlite3" ,ocaml4.01-sqlite3) | |
4170 | ("ocaml-xmlm" ,ocaml4.01-xmlm) | |
4171 | ("ocaml-mcl" ,ocaml4.01-mcl) | |
4172 | ("ocaml-gsl" ,ocaml4.01-gsl) | |
4173 | ("cddlib-src" ,(package-source cddlib)))) | |
4174 | (propagated-inputs | |
4175 | `(("pplacer-scripts" ,pplacer-scripts))) | |
4176 | (synopsis "Phylogenetic placement of biological sequences") | |
4177 | (description | |
4178 | "Pplacer places query sequences on a fixed reference phylogenetic tree | |
4179 | to maximize phylogenetic likelihood or posterior probability according to a | |
4180 | reference alignment. Pplacer is designed to be fast, to give useful | |
4181 | information about uncertainty, and to offer advanced visualization and | |
4182 | downstream analysis.") | |
4183 | (home-page "http://matsen.fhcrc.org/pplacer") | |
4184 | (license license:gpl3)))) | |
4185 | ||
4186 | ;; This package is installed alongside 'pplacer'. It is a separate package so | |
4187 | ;; that it can use the python-build-system for the scripts that are | |
4188 | ;; distributed alongside the main OCaml binaries. | |
4189 | (define pplacer-scripts | |
4190 | (package | |
4191 | (inherit pplacer) | |
4192 | (name "pplacer-scripts") | |
4193 | (build-system python-build-system) | |
4194 | (arguments | |
4195 | `(#:python ,python-2 | |
4196 | #:phases | |
4197 | (modify-phases %standard-phases | |
4198 | (add-after 'unpack 'enter-scripts-dir | |
4199 | (lambda _ (chdir "scripts"))) | |
4200 | (replace 'check | |
4201 | (lambda _ | |
4202 | (zero? (system* "python" "-m" "unittest" "discover" "-v")))) | |
4203 | (add-after 'install 'wrap-executables | |
4204 | (lambda* (#:key inputs outputs #:allow-other-keys) | |
4205 | (let* ((out (assoc-ref outputs "out")) | |
4206 | (bin (string-append out "/bin"))) | |
4207 | (let ((path (string-append | |
4208 | (assoc-ref inputs "hmmer") "/bin:" | |
4209 | (assoc-ref inputs "infernal") "/bin"))) | |
4210 | (display path) | |
4211 | (wrap-program (string-append bin "/refpkg_align.py") | |
4212 | `("PATH" ":" prefix (,path)))) | |
4213 | (let ((path (string-append | |
4214 | (assoc-ref inputs "hmmer") "/bin"))) | |
4215 | (wrap-program (string-append bin "/hrefpkg_query.py") | |
4216 | `("PATH" ":" prefix (,path))))) | |
4217 | #t))))) | |
4218 | (inputs | |
4219 | `(("infernal" ,infernal) | |
4220 | ("hmmer" ,hmmer))) | |
4221 | (propagated-inputs | |
4222 | `(("python-biopython" ,python2-biopython) | |
4223 | ("taxtastic" ,taxtastic))) | |
4224 | (synopsis "Pplacer Python scripts"))) | |
4225 | ||
19ee9201 RW |
4226 | (define-public python2-pbcore |
4227 | (package | |
4228 | (name "python2-pbcore") | |
e301bfc8 | 4229 | (version "1.2.10") |
19ee9201 RW |
4230 | (source (origin |
4231 | (method url-fetch) | |
ddb83129 | 4232 | (uri (pypi-uri "pbcore" version)) |
19ee9201 RW |
4233 | (sha256 |
4234 | (base32 | |
e301bfc8 | 4235 | "1kjmv891d6qbpp4shhhvkl02ff4q5xlpnls2513sm2cjcrs52f1i")))) |
19ee9201 RW |
4236 | (build-system python-build-system) |
4237 | (arguments `(#:python ,python-2)) ; pbcore requires Python 2.7 | |
de5bc890 | 4238 | (propagated-inputs |
19ee9201 RW |
4239 | `(("python-cython" ,python2-cython) |
4240 | ("python-numpy" ,python2-numpy) | |
4241 | ("python-pysam" ,python2-pysam) | |
4242 | ("python-h5py" ,python2-h5py))) | |
4243 | (native-inputs | |
de5bc890 HG |
4244 | `(("python-nose" ,python2-nose) |
4245 | ("python-sphinx" ,python2-sphinx) | |
4246 | ("python-pyxb" ,python2-pyxb))) | |
19ee9201 RW |
4247 | (home-page "http://pacificbiosciences.github.io/pbcore/") |
4248 | (synopsis "Library for reading and writing PacBio data files") | |
4249 | (description | |
4250 | "The pbcore package provides Python APIs for interacting with PacBio data | |
4251 | files and writing bioinformatics applications.") | |
4252 | (license license:bsd-3))) | |
4253 | ||
c61fe02c RW |
4254 | (define-public python2-warpedlmm |
4255 | (package | |
4256 | (name "python2-warpedlmm") | |
4257 | (version "0.21") | |
4258 | (source | |
4259 | (origin | |
4260 | (method url-fetch) | |
4261 | (uri (string-append | |
4262 | "https://pypi.python.org/packages/source/W/WarpedLMM/WarpedLMM-" | |
4263 | version ".zip")) | |
4264 | (sha256 | |
4265 | (base32 | |
4266 | "1agfz6zqa8nc6cw47yh0s3y14gkpa9wqazwcj7mwwj3ffnw39p3j")))) | |
4267 | (build-system python-build-system) | |
4268 | (arguments | |
54c85e12 | 4269 | `(#:python ,python-2)) ; requires Python 2.7 |
c61fe02c RW |
4270 | (propagated-inputs |
4271 | `(("python-scipy" ,python2-scipy) | |
4272 | ("python-numpy" ,python2-numpy) | |
4273 | ("python-matplotlib" ,python2-matplotlib) | |
4274 | ("python-fastlmm" ,python2-fastlmm) | |
4275 | ("python-pandas" ,python2-pandas) | |
4276 | ("python-pysnptools" ,python2-pysnptools))) | |
4277 | (native-inputs | |
f3b98f4f | 4278 | `(("python-mock" ,python2-mock) |
c61fe02c RW |
4279 | ("python-nose" ,python2-nose) |
4280 | ("unzip" ,unzip))) | |
4281 | (home-page "https://github.com/PMBio/warpedLMM") | |
4282 | (synopsis "Implementation of warped linear mixed models") | |
4283 | (description | |
4284 | "WarpedLMM is a Python implementation of the warped linear mixed model, | |
4285 | which automatically learns an optimal warping function (or transformation) for | |
4286 | the phenotype as it models the data.") | |
4287 | (license license:asl2.0))) | |
4288 | ||
2c16316e | 4289 | (define-public pbtranscript-tofu |
698bd297 | 4290 | (let ((commit "8f5467fe6a4472bcfb4226c8720993c8507adfe4")) |
2c16316e RW |
4291 | (package |
4292 | (name "pbtranscript-tofu") | |
698bd297 | 4293 | (version (string-append "2.2.3." (string-take commit 7))) |
2c16316e RW |
4294 | (source (origin |
4295 | (method git-fetch) | |
4296 | (uri (git-reference | |
4297 | (url "https://github.com/PacificBiosciences/cDNA_primer.git") | |
4298 | (commit commit))) | |
9a067efd | 4299 | (file-name (string-append name "-" version "-checkout")) |
2c16316e RW |
4300 | (sha256 |
4301 | (base32 | |
9a067efd RW |
4302 | "1lgnpi35ihay42qx0b6yl3kkgra723i413j33kvs0kvs61h82w0f")) |
4303 | (modules '((guix build utils))) | |
4304 | (snippet | |
4305 | '(begin | |
4306 | ;; remove bundled Cython sources | |
4307 | (delete-file "pbtranscript-tofu/pbtranscript/Cython-0.20.1.tar.gz") | |
4308 | #t)))) | |
2c16316e RW |
4309 | (build-system python-build-system) |
4310 | (arguments | |
4311 | `(#:python ,python-2 | |
cdc2bb50 MB |
4312 | ;; FIXME: Tests fail with "No such file or directory: |
4313 | ;; pbtools/pbtranscript/modified_bx_intervals/intersection_unique.so" | |
4314 | #:tests? #f | |
2c16316e | 4315 | #:phases |
9a067efd RW |
4316 | (modify-phases %standard-phases |
4317 | (add-after 'unpack 'enter-directory | |
4318 | (lambda _ | |
4319 | (chdir "pbtranscript-tofu/pbtranscript/") | |
4320 | #t)) | |
4321 | ;; With setuptools version 18.0 and later this setup.py hack causes | |
4322 | ;; a build error, so we disable it. | |
4323 | (add-after 'enter-directory 'patch-setuppy | |
4324 | (lambda _ | |
4325 | (substitute* "setup.py" | |
4326 | (("if 'setuptools.extension' in sys.modules:") | |
4327 | "if False:")) | |
4328 | #t))))) | |
2c16316e | 4329 | (inputs |
9a067efd | 4330 | `(("python-numpy" ,python2-numpy) |
2c16316e | 4331 | ("python-bx-python" ,python2-bx-python) |
c5372108 RW |
4332 | ("python-networkx" ,python2-networkx) |
4333 | ("python-scipy" ,python2-scipy) | |
9a067efd RW |
4334 | ("python-pbcore" ,python2-pbcore) |
4335 | ("python-h5py" ,python2-h5py))) | |
2c16316e | 4336 | (native-inputs |
9a067efd | 4337 | `(("python-cython" ,python2-cython) |
f3b98f4f | 4338 | ("python-nose" ,python2-nose))) |
2c16316e RW |
4339 | (home-page "https://github.com/PacificBiosciences/cDNA_primer") |
4340 | (synopsis "Analyze transcriptome data generated with the Iso-Seq protocol") | |
4341 | (description | |
4342 | "pbtranscript-tofu contains scripts to analyze transcriptome data | |
4343 | generated using the PacBio Iso-Seq protocol.") | |
4344 | (license license:bsd-3)))) | |
4345 | ||
024130d2 BW |
4346 | (define-public prank |
4347 | (package | |
4348 | (name "prank") | |
4349 | (version "150803") | |
4350 | (source (origin | |
4351 | (method url-fetch) | |
4352 | (uri (string-append | |
4353 | "http://wasabiapp.org/download/prank/prank.source." | |
4354 | version ".tgz")) | |
4355 | (sha256 | |
4356 | (base32 | |
4357 | "0am4z94fs3w2n5xpfls9zda61vq7qqz4q2i7b9hlsxz5q4j3kfm4")))) | |
4358 | (build-system gnu-build-system) | |
4359 | (arguments | |
4360 | `(#:phases | |
4361 | (modify-phases %standard-phases | |
4362 | (add-after 'unpack 'enter-src-dir | |
4363 | (lambda _ | |
4364 | (chdir "src") | |
4365 | #t)) | |
62d00095 EF |
4366 | (add-after 'unpack 'remove-m64-flag |
4367 | ;; Prank will build with the correct 'bit-ness' without this flag | |
4368 | ;; and this allows building on 32-bit machines. | |
4369 | (lambda _ (substitute* "src/Makefile" | |
4370 | (("-m64") "")) | |
4371 | #t)) | |
024130d2 BW |
4372 | (delete 'configure) |
4373 | (replace 'install | |
4374 | (lambda* (#:key outputs #:allow-other-keys) | |
4375 | (let* ((out (assoc-ref outputs "out")) | |
4376 | (bin (string-append out "/bin")) | |
4377 | (man (string-append out "/share/man/man1")) | |
4378 | (path (string-append | |
4379 | (assoc-ref %build-inputs "mafft") "/bin:" | |
4380 | (assoc-ref %build-inputs "exonerate") "/bin:" | |
4381 | (assoc-ref %build-inputs "bppsuite") "/bin"))) | |
4382 | (install-file "prank" bin) | |
4383 | (wrap-program (string-append bin "/prank") | |
4384 | `("PATH" ":" prefix (,path))) | |
4385 | (install-file "prank.1" man)) | |
4386 | #t))))) | |
4387 | (inputs | |
4388 | `(("mafft" ,mafft) | |
4389 | ("exonerate" ,exonerate) | |
4390 | ("bppsuite" ,bppsuite))) | |
4391 | (home-page "http://wasabiapp.org/software/prank/") | |
4392 | (synopsis "Probabilistic multiple sequence alignment program") | |
4393 | (description | |
4394 | "PRANK is a probabilistic multiple sequence alignment program for DNA, | |
4395 | codon and amino-acid sequences. It is based on a novel algorithm that treats | |
4396 | insertions correctly and avoids over-estimation of the number of deletion | |
4397 | events. In addition, PRANK borrows ideas from maximum likelihood methods used | |
4398 | in phylogenetics and correctly takes into account the evolutionary distances | |
4399 | between sequences. Lastly, PRANK allows for defining a potential structure | |
4400 | for sequences to be aligned and then, simultaneously with the alignment, | |
4401 | predicts the locations of structural units in the sequences.") | |
4402 | (license license:gpl2+))) | |
4403 | ||
31a9d653 BW |
4404 | (define-public proteinortho |
4405 | (package | |
4406 | (name "proteinortho") | |
8c864901 | 4407 | (version "5.16b") |
31a9d653 BW |
4408 | (source |
4409 | (origin | |
4410 | (method url-fetch) | |
4411 | (uri | |
4412 | (string-append | |
4413 | "http://www.bioinf.uni-leipzig.de/Software/proteinortho/proteinortho_v" | |
4414 | version "_src.tar.gz")) | |
4415 | (sha256 | |
4416 | (base32 | |
8c864901 | 4417 | "1wl0dawpssqwfjvr651r4wlww8hhjin8nba6xh71ks7sbypx886j")))) |
31a9d653 BW |
4418 | (build-system gnu-build-system) |
4419 | (arguments | |
4420 | `(#:test-target "test" | |
4421 | #:phases | |
4422 | (modify-phases %standard-phases | |
4423 | (replace 'configure | |
4424 | ;; There is no configure script, so we modify the Makefile directly. | |
4425 | (lambda* (#:key outputs #:allow-other-keys) | |
4426 | (substitute* "Makefile" | |
4427 | (("INSTALLDIR=.*") | |
4428 | (string-append | |
4429 | "INSTALLDIR=" (assoc-ref outputs "out") "/bin\n"))) | |
4430 | #t)) | |
4431 | (add-before 'install 'make-install-directory | |
4432 | ;; The install directory is not created during 'make install'. | |
4433 | (lambda* (#:key outputs #:allow-other-keys) | |
4434 | (mkdir-p (string-append (assoc-ref outputs "out") "/bin")) | |
4435 | #t)) | |
4436 | (add-after 'install 'wrap-programs | |
4437 | (lambda* (#:key inputs outputs #:allow-other-keys) | |
4438 | (let* ((path (getenv "PATH")) | |
4439 | (out (assoc-ref outputs "out")) | |
4440 | (binary (string-append out "/bin/proteinortho5.pl"))) | |
4441 | (wrap-program binary `("PATH" ":" prefix (,path)))) | |
4442 | #t))))) | |
4443 | (inputs | |
4444 | `(("perl" ,perl) | |
4445 | ("python" ,python-2) | |
4446 | ("blast+" ,blast+))) | |
4447 | (home-page "http://www.bioinf.uni-leipzig.de/Software/proteinortho") | |
4448 | (synopsis "Detect orthologous genes across species") | |
4449 | (description | |
4450 | "Proteinortho is a tool to detect orthologous genes across different | |
4451 | species. For doing so, it compares similarities of given gene sequences and | |
4452 | clusters them to find significant groups. The algorithm was designed to handle | |
4453 | large-scale data and can be applied to hundreds of species at once.") | |
4454 | (license license:gpl2+))) | |
4455 | ||
846e3409 RW |
4456 | (define-public pyicoteo |
4457 | (package | |
4458 | (name "pyicoteo") | |
4459 | (version "2.0.7") | |
4460 | (source | |
4461 | (origin | |
4462 | (method url-fetch) | |
4463 | (uri (string-append "https://bitbucket.org/regulatorygenomicsupf/" | |
4464 | "pyicoteo/get/v" version ".tar.bz2")) | |
4465 | (file-name (string-append name "-" version ".tar.bz2")) | |
4466 | (sha256 | |
4467 | (base32 | |
4468 | "0d6087f29xp8wxwlj111c3sylli98n0l8ry58c51ixzq0zfm50wa")))) | |
4469 | (build-system python-build-system) | |
4470 | (arguments | |
4471 | `(#:python ,python-2 ; does not work with Python 3 | |
4472 | #:tests? #f)) ; there are no tests | |
4473 | (inputs | |
4474 | `(("python2-matplotlib" ,python2-matplotlib))) | |
4475 | (home-page "https://bitbucket.org/regulatorygenomicsupf/pyicoteo") | |
4476 | (synopsis "Analyze high-throughput genetic sequencing data") | |
4477 | (description | |
4478 | "Pyicoteo is a suite of tools for the analysis of high-throughput genetic | |
4479 | sequencing data. It works with genomic coordinates. There are currently six | |
4480 | different command-line tools: | |
4481 | ||
4482 | @enumerate | |
4483 | @item pyicoregion: for generating exploratory regions automatically; | |
4484 | @item pyicoenrich: for differential enrichment between two conditions; | |
4485 | @item pyicoclip: for calling CLIP-Seq peaks without a control; | |
4486 | @item pyicos: for genomic coordinates manipulation; | |
4487 | @item pyicoller: for peak calling on punctuated ChIP-Seq; | |
4488 | @item pyicount: to count how many reads from N experiment files overlap in a | |
4489 | region file; | |
4490 | @item pyicotrocol: to combine operations from pyicoteo. | |
4491 | @end enumerate\n") | |
4492 | (license license:gpl3+))) | |
4493 | ||
af860475 BW |
4494 | (define-public prodigal |
4495 | (package | |
4496 | (name "prodigal") | |
e70f7a23 | 4497 | (version "2.6.3") |
af860475 BW |
4498 | (source (origin |
4499 | (method url-fetch) | |
4500 | (uri (string-append | |
4501 | "https://github.com/hyattpd/Prodigal/archive/v" | |
4502 | version ".tar.gz")) | |
4503 | (file-name (string-append name "-" version ".tar.gz")) | |
4504 | (sha256 | |
4505 | (base32 | |
e70f7a23 | 4506 | "17srxkqd3jc77xk15pfbgg1a9xahqg7337w95mrsia7mpza4l2c9")))) |
af860475 BW |
4507 | (build-system gnu-build-system) |
4508 | (arguments | |
4509 | `(#:tests? #f ;no check target | |
4510 | #:make-flags (list (string-append "INSTALLDIR=" | |
4511 | (assoc-ref %outputs "out") | |
4512 | "/bin")) | |
4513 | #:phases | |
4514 | (modify-phases %standard-phases | |
4515 | (delete 'configure)))) | |
4516 | (home-page "http://prodigal.ornl.gov") | |
4517 | (synopsis "Protein-coding gene prediction for Archaea and Bacteria") | |
4518 | (description | |
4519 | "Prodigal runs smoothly on finished genomes, draft genomes, and | |
4520 | metagenomes, providing gene predictions in GFF3, Genbank, or Sequin table | |
4521 | format. It runs quickly, in an unsupervised fashion, handles gaps, handles | |
4522 | partial genes, and identifies translation initiation sites.") | |
4523 | (license license:gpl3+))) | |
608dd932 | 4524 | |
ceb62d54 BW |
4525 | (define-public roary |
4526 | (package | |
4527 | (name "roary") | |
da4a707c | 4528 | (version "3.11.0") |
ceb62d54 BW |
4529 | (source |
4530 | (origin | |
4531 | (method url-fetch) | |
4532 | (uri (string-append | |
4533 | "mirror://cpan/authors/id/A/AJ/AJPAGE/Bio-Roary-" | |
4534 | version ".tar.gz")) | |
4535 | (sha256 | |
4536 | (base32 | |
da4a707c | 4537 | "10lw78x1xzvn7xzvnmh4bm3cak3ah5cssapl0yidvhaj1f44h29i")))) |
ceb62d54 BW |
4538 | (build-system perl-build-system) |
4539 | (arguments | |
4540 | `(#:phases | |
4541 | (modify-phases %standard-phases | |
4542 | (delete 'configure) | |
4543 | (delete 'build) | |
4544 | (replace 'check | |
4545 | (lambda _ | |
4546 | ;; The tests are not run by default, so we run each test file | |
4547 | ;; directly. | |
4548 | (setenv "PATH" (string-append (getcwd) "/bin" ":" | |
4549 | (getenv "PATH"))) | |
4550 | (setenv "PERL5LIB" (string-append (getcwd) "/lib" ":" | |
4551 | (getenv "PERL5LIB"))) | |
4552 | (zero? (length (filter (lambda (file) | |
4553 | (display file)(display "\n") | |
4554 | (not (zero? (system* "perl" file)))) | |
4555 | (find-files "t" ".*\\.t$")))))) | |
4556 | (replace 'install | |
4557 | ;; There is no 'install' target in the Makefile. | |
4558 | (lambda* (#:key outputs #:allow-other-keys) | |
4559 | (let* ((out (assoc-ref outputs "out")) | |
4560 | (bin (string-append out "/bin")) | |
4561 | (perl (string-append out "/lib/perl5/site_perl")) | |
4562 | (roary-plots "contrib/roary_plots")) | |
4563 | (mkdir-p bin) | |
4564 | (mkdir-p perl) | |
4565 | (copy-recursively "bin" bin) | |
4566 | (copy-recursively "lib" perl) | |
4567 | #t))) | |
4568 | (add-after 'install 'wrap-programs | |
4569 | (lambda* (#:key inputs outputs #:allow-other-keys) | |
4570 | (let* ((out (assoc-ref outputs "out")) | |
4571 | (perl5lib (getenv "PERL5LIB")) | |
4572 | (path (getenv "PATH"))) | |
4573 | (for-each (lambda (prog) | |
4574 | (let ((binary (string-append out "/" prog))) | |
4575 | (wrap-program binary | |
4576 | `("PERL5LIB" ":" prefix | |
4577 | (,(string-append perl5lib ":" out | |
4578 | "/lib/perl5/site_perl")))) | |
4579 | (wrap-program binary | |
4580 | `("PATH" ":" prefix | |
4581 | (,(string-append path ":" out "/bin")))))) | |
4582 | (find-files "bin" ".*[^R]$")) | |
4583 | (let ((file | |
4584 | (string-append out "/bin/roary-create_pan_genome_plots.R")) | |
4585 | (r-site-lib (getenv "R_LIBS_SITE")) | |
4586 | (coreutils-path | |
4587 | (string-append (assoc-ref inputs "coreutils") "/bin"))) | |
4588 | (wrap-program file | |
4589 | `("R_LIBS_SITE" ":" prefix | |
4590 | (,(string-append r-site-lib ":" out "/site-library/")))) | |
4591 | (wrap-program file | |
4592 | `("PATH" ":" prefix | |
4593 | (,(string-append coreutils-path ":" out "/bin")))))) | |
4594 | #t))))) | |
4595 | (native-inputs | |
4596 | `(("perl-env-path" ,perl-env-path) | |
4597 | ("perl-test-files" ,perl-test-files) | |
4598 | ("perl-test-most" ,perl-test-most) | |
4599 | ("perl-test-output" ,perl-test-output))) | |
4600 | (inputs | |
4601 | `(("perl-array-utils" ,perl-array-utils) | |
4602 | ("bioperl" ,bioperl-minimal) | |
da4a707c | 4603 | ("perl-digest-md5-file" ,perl-digest-md5-file) |
ceb62d54 BW |
4604 | ("perl-exception-class" ,perl-exception-class) |
4605 | ("perl-file-find-rule" ,perl-file-find-rule) | |
4606 | ("perl-file-grep" ,perl-file-grep) | |
4607 | ("perl-file-slurper" ,perl-file-slurper) | |
4608 | ("perl-file-which" ,perl-file-which) | |
4609 | ("perl-graph" ,perl-graph) | |
4610 | ("perl-graph-readwrite" ,perl-graph-readwrite) | |
4611 | ("perl-log-log4perl" ,perl-log-log4perl) | |
4612 | ("perl-moose" ,perl-moose) | |
4613 | ("perl-perlio-utf8_strict" ,perl-perlio-utf8_strict) | |
4614 | ("perl-text-csv" ,perl-text-csv) | |
4615 | ("bedtools" ,bedtools) | |
4616 | ("cd-hit" ,cd-hit) | |
4617 | ("blast+" ,blast+) | |
4618 | ("mcl" ,mcl) | |
4619 | ("parallel" ,parallel) | |
4620 | ("prank" ,prank) | |
4621 | ("mafft" ,mafft) | |
4622 | ("fasttree" ,fasttree) | |
4623 | ("grep" ,grep) | |
4624 | ("sed" ,sed) | |
4625 | ("gawk" ,gawk) | |
2d7c4ae3 | 4626 | ("r-minimal" ,r-minimal) |
ceb62d54 BW |
4627 | ("r-ggplot2" ,r-ggplot2) |
4628 | ("coreutils" ,coreutils))) | |
4629 | (home-page "http://sanger-pathogens.github.io/Roary") | |
4630 | (synopsis "High speed stand-alone pan genome pipeline") | |
4631 | (description | |
4632 | "Roary is a high speed stand alone pan genome pipeline, which takes | |
4633 | annotated assemblies in GFF3 format (produced by the Prokka program) and | |
4634 | calculates the pan genome. Using a standard desktop PC, it can analyse | |
4635 | datasets with thousands of samples, without compromising the quality of the | |
4636 | results. 128 samples can be analysed in under 1 hour using 1 GB of RAM and a | |
4637 | single processor. Roary is not intended for metagenomics or for comparing | |
4638 | extremely diverse sets of genomes.") | |
4639 | (license license:gpl3))) | |
4640 | ||
608dd932 BW |
4641 | (define-public raxml |
4642 | (package | |
4643 | (name "raxml") | |
e9e0fab0 | 4644 | (version "8.2.10") |
608dd932 BW |
4645 | (source |
4646 | (origin | |
4647 | (method url-fetch) | |
4648 | (uri | |
4649 | (string-append | |
4650 | "https://github.com/stamatak/standard-RAxML/archive/v" | |
4651 | version ".tar.gz")) | |
4652 | (file-name (string-append name "-" version ".tar.gz")) | |
4653 | (sha256 | |
4654 | (base32 | |
e9e0fab0 | 4655 | "13s7aspfdcfr6asynwdg1x6vznys6pzap5f8wsffbnnwpkkg9ya8")))) |
608dd932 BW |
4656 | (build-system gnu-build-system) |
4657 | (arguments | |
4658 | `(#:tests? #f ; There are no tests. | |
4659 | ;; Use 'standard' Makefile rather than SSE or AVX ones. | |
4660 | #:make-flags (list "-f" "Makefile.HYBRID.gcc") | |
4661 | #:phases | |
4662 | (modify-phases %standard-phases | |
4663 | (delete 'configure) | |
4664 | (replace 'install | |
4665 | (lambda* (#:key outputs #:allow-other-keys) | |
4666 | (let* ((out (assoc-ref outputs "out")) | |
4667 | (bin (string-append out "/bin")) | |
4668 | (executable "raxmlHPC-HYBRID")) | |
4669 | (install-file executable bin) | |
4670 | (symlink (string-append bin "/" executable) "raxml")) | |
4671 | #t))))) | |
4672 | (inputs | |
4673 | `(("openmpi" ,openmpi))) | |
4674 | (home-page "http://sco.h-its.org/exelixis/web/software/raxml/index.html") | |
4675 | (synopsis "Randomized Axelerated Maximum Likelihood phylogenetic trees") | |
4676 | (description | |
4677 | "RAxML is a tool for phylogenetic analysis and post-analysis of large | |
4678 | phylogenies.") | |
2805f9b2 EF |
4679 | ;; The source includes x86 specific code |
4680 | (supported-systems '("x86_64-linux" "i686-linux")) | |
608dd932 | 4681 | (license license:gpl2+))) |
af860475 | 4682 | |
66e3eff1 RW |
4683 | (define-public rsem |
4684 | (package | |
4685 | (name "rsem") | |
4686 | (version "1.2.20") | |
4687 | (source | |
4688 | (origin | |
4689 | (method url-fetch) | |
4690 | (uri | |
4691 | (string-append "http://deweylab.biostat.wisc.edu/rsem/src/rsem-" | |
4692 | version ".tar.gz")) | |
4693 | (sha256 | |
4694 | (base32 "0nzdc0j0hjllhsd5f2xli95dafm3nawskigs140xzvjk67xh0r9q")) | |
fc1adab1 | 4695 | (patches (search-patches "rsem-makefile.patch")) |
66e3eff1 RW |
4696 | (modules '((guix build utils))) |
4697 | (snippet | |
4698 | '(begin | |
4699 | ;; remove bundled copy of boost | |
4700 | (delete-file-recursively "boost") | |
4701 | #t)))) | |
4702 | (build-system gnu-build-system) | |
4703 | (arguments | |
4704 | `(#:tests? #f ;no "check" target | |
4705 | #:phases | |
4706 | (modify-phases %standard-phases | |
4707 | ;; No "configure" script. | |
4708 | ;; Do not build bundled samtools library. | |
4709 | (replace 'configure | |
4710 | (lambda _ | |
4711 | (substitute* "Makefile" | |
4712 | (("^all : sam/libbam.a") "all : ")) | |
4713 | #t)) | |
4714 | (replace 'install | |
4715 | (lambda* (#:key outputs #:allow-other-keys) | |
4716 | (let* ((out (string-append (assoc-ref outputs "out"))) | |
4717 | (bin (string-append out "/bin/")) | |
4718 | (perl (string-append out "/lib/perl5/site_perl"))) | |
4719 | (mkdir-p bin) | |
4720 | (mkdir-p perl) | |
4721 | (for-each (lambda (file) | |
f3860753 | 4722 | (install-file file bin)) |
66e3eff1 | 4723 | (find-files "." "rsem-.*")) |
f3860753 | 4724 | (install-file "rsem_perl_utils.pm" perl)) |
66e3eff1 RW |
4725 | #t)) |
4726 | (add-after | |
4727 | 'install 'wrap-program | |
4728 | (lambda* (#:key outputs #:allow-other-keys) | |
4729 | (let ((out (assoc-ref outputs "out"))) | |
4730 | (for-each (lambda (prog) | |
4731 | (wrap-program (string-append out "/bin/" prog) | |
4732 | `("PERL5LIB" ":" prefix | |
4733 | (,(string-append out "/lib/perl5/site_perl"))))) | |
4734 | '("rsem-plot-transcript-wiggles" | |
4735 | "rsem-calculate-expression" | |
4736 | "rsem-generate-ngvector" | |
4737 | "rsem-run-ebseq" | |
4738 | "rsem-prepare-reference"))) | |
4739 | #t))))) | |
4740 | (inputs | |
4741 | `(("boost" ,boost) | |
4742 | ("ncurses" ,ncurses) | |
2d7c4ae3 | 4743 | ("r-minimal" ,r-minimal) |
66e3eff1 RW |
4744 | ("perl" ,perl) |
4745 | ("samtools" ,samtools-0.1) | |
4746 | ("zlib" ,zlib))) | |
4747 | (home-page "http://deweylab.biostat.wisc.edu/rsem/") | |
4748 | (synopsis "Estimate gene expression levels from RNA-Seq data") | |
4749 | (description | |
4750 | "RSEM is a software package for estimating gene and isoform expression | |
4751 | levels from RNA-Seq data. The RSEM package provides a user-friendly | |
4752 | interface, supports threads for parallel computation of the EM algorithm, | |
4753 | single-end and paired-end read data, quality scores, variable-length reads and | |
4754 | RSPD estimation. In addition, it provides posterior mean and 95% credibility | |
4755 | interval estimates for expression levels. For visualization, it can generate | |
4756 | BAM and Wiggle files in both transcript-coordinate and genomic-coordinate.") | |
4757 | (license license:gpl3+))) | |
4758 | ||
8622a072 RW |
4759 | (define-public rseqc |
4760 | (package | |
4761 | (name "rseqc") | |
4762 | (version "2.6.1") | |
4763 | (source | |
4764 | (origin | |
4765 | (method url-fetch) | |
4766 | (uri | |
4767 | (string-append "mirror://sourceforge/rseqc/" | |
de67e922 | 4768 | "RSeQC-" version ".tar.gz")) |
8622a072 | 4769 | (sha256 |
8214b7fb | 4770 | (base32 "15ly0254yi032qzkdplg00q144qfdsd986gh62829rl5bkxhj330")) |
8622a072 RW |
4771 | (modules '((guix build utils))) |
4772 | (snippet | |
4773 | '(begin | |
4774 | ;; remove bundled copy of pysam | |
4775 | (delete-file-recursively "lib/pysam") | |
4776 | (substitute* "setup.py" | |
4777 | ;; remove dependency on outdated "distribute" module | |
4778 | (("^from distribute_setup import use_setuptools") "") | |
4779 | (("^use_setuptools\\(\\)") "") | |
4780 | ;; do not use bundled copy of pysam | |
4781 | (("^have_pysam = False") "have_pysam = True")))))) | |
4782 | (build-system python-build-system) | |
4783 | (arguments `(#:python ,python-2)) | |
4784 | (inputs | |
4785 | `(("python-cython" ,python2-cython) | |
4786 | ("python-pysam" ,python2-pysam) | |
4787 | ("python-numpy" ,python2-numpy) | |
8622a072 RW |
4788 | ("zlib" ,zlib))) |
4789 | (native-inputs | |
4790 | `(("python-nose" ,python2-nose))) | |
4791 | (home-page "http://rseqc.sourceforge.net/") | |
4792 | (synopsis "RNA-seq quality control package") | |
4793 | (description | |
4794 | "RSeQC provides a number of modules that can comprehensively evaluate | |
4795 | high throughput sequence data, especially RNA-seq data. Some basic modules | |
4796 | inspect sequence quality, nucleotide composition bias, PCR bias and GC bias, | |
4797 | while RNA-seq specific modules evaluate sequencing saturation, mapped reads | |
4798 | distribution, coverage uniformity, strand specificity, etc.") | |
4799 | (license license:gpl3+))) | |
4800 | ||
ec946638 RW |
4801 | (define-public seek |
4802 | ;; There are no release tarballs. According to the installation | |
4803 | ;; instructions at http://seek.princeton.edu/installation.jsp, the latest | |
4804 | ;; stable release is identified by this changeset ID. | |
4805 | (let ((changeset "2329130") | |
4806 | (revision "1")) | |
4807 | (package | |
4808 | (name "seek") | |
4809 | (version (string-append "0-" revision "." changeset)) | |
4810 | (source (origin | |
4811 | (method hg-fetch) | |
4812 | (uri (hg-reference | |
4813 | (url "https://bitbucket.org/libsleipnir/sleipnir") | |
4814 | (changeset changeset))) | |
51106724 | 4815 | (file-name (string-append name "-" version "-checkout")) |
ec946638 RW |
4816 | (sha256 |
4817 | (base32 | |
4818 | "0qrvilwh18dpbhkf92qvxbmay0j75ra3jg2wrhz67gf538zzphsx")))) | |
4819 | (build-system gnu-build-system) | |
4820 | (arguments | |
4821 | `(#:modules ((srfi srfi-1) | |
4822 | (guix build gnu-build-system) | |
4823 | (guix build utils)) | |
4824 | #:phases | |
4825 | (let ((dirs '("SeekMiner" | |
4826 | "SeekEvaluator" | |
4827 | "SeekPrep" | |
4828 | "Distancer" | |
4829 | "Data2DB" | |
4830 | "PCL2Bin"))) | |
4831 | (modify-phases %standard-phases | |
4561498e | 4832 | (add-before 'configure 'bootstrap |
ec946638 RW |
4833 | (lambda _ |
4834 | (zero? (system* "bash" "gen_auto")))) | |
4835 | (add-after 'build 'build-additional-tools | |
4836 | (lambda* (#:key make-flags #:allow-other-keys) | |
4837 | (every (lambda (dir) | |
4838 | (with-directory-excursion (string-append "tools/" dir) | |
4839 | (zero? (apply system* "make" make-flags)))) | |
4840 | dirs))) | |
4841 | (add-after 'install 'install-additional-tools | |
4842 | (lambda* (#:key make-flags #:allow-other-keys) | |
4843 | (fold (lambda (dir result) | |
4844 | (with-directory-excursion (string-append "tools/" dir) | |
4845 | (and result | |
4846 | (zero? (apply system* | |
4847 | `("make" ,@make-flags "install")))))) | |
4848 | #t dirs))))))) | |
4849 | (inputs | |
4850 | `(("gsl" ,gsl) | |
4851 | ("boost" ,boost) | |
4852 | ("libsvm" ,libsvm) | |
4853 | ("readline" ,readline) | |
4854 | ("gengetopt" ,gengetopt) | |
4855 | ("log4cpp" ,log4cpp))) | |
4856 | (native-inputs | |
4857 | `(("autoconf" ,autoconf) | |
4858 | ("automake" ,automake) | |
4859 | ("perl" ,perl))) | |
4860 | (home-page "http://seek.princeton.edu") | |
4861 | (synopsis "Gene co-expression search engine") | |
4862 | (description | |
4863 | "SEEK is a computational gene co-expression search engine. SEEK provides | |
4864 | biologists with a way to navigate the massive human expression compendium that | |
4865 | now contains thousands of expression datasets. SEEK returns a robust ranking | |
4866 | of co-expressed genes in the biological area of interest defined by the user's | |
4867 | query genes. It also prioritizes thousands of expression datasets according | |
4868 | to the user's query of interest.") | |
4869 | (license license:cc-by3.0)))) | |
4870 | ||
4e10a221 RW |
4871 | (define-public samtools |
4872 | (package | |
4873 | (name "samtools") | |
c072cf57 | 4874 | (version "1.7") |
4e10a221 RW |
4875 | (source |
4876 | (origin | |
4877 | (method url-fetch) | |
4878 | (uri | |
de67e922 | 4879 | (string-append "mirror://sourceforge/samtools/samtools/" |
4e10a221 RW |
4880 | version "/samtools-" version ".tar.bz2")) |
4881 | (sha256 | |
4882 | (base32 | |
c072cf57 | 4883 | "18acyqysbxpydlc44lqv2hpp57l06bs9a3yqmcvjk8va2xrrdc77")))) |
4e10a221 RW |
4884 | (build-system gnu-build-system) |
4885 | (arguments | |
c4473411 | 4886 | `(#:modules ((ice-9 ftw) |
5bdda30b RW |
4887 | (ice-9 regex) |
4888 | (guix build gnu-build-system) | |
4889 | (guix build utils)) | |
c4473411 | 4890 | #:make-flags (list (string-append "prefix=" (assoc-ref %outputs "out"))) |
4ab16440 | 4891 | #:configure-flags (list "--with-ncurses" "--with-htslib=system") |
4e10a221 | 4892 | #:phases |
c842d425 BW |
4893 | (modify-phases %standard-phases |
4894 | (add-after 'unpack 'patch-tests | |
4895 | (lambda _ | |
4896 | (substitute* "test/test.pl" | |
4897 | ;; The test script calls out to /bin/bash | |
4898 | (("/bin/bash") (which "bash"))) | |
b2d748ed | 4899 | #t)) |
c842d425 BW |
4900 | (add-after 'install 'install-library |
4901 | (lambda* (#:key outputs #:allow-other-keys) | |
4902 | (let ((lib (string-append (assoc-ref outputs "out") "/lib"))) | |
4903 | (install-file "libbam.a" lib) | |
4904 | #t))) | |
4905 | (add-after 'install 'install-headers | |
4906 | (lambda* (#:key outputs #:allow-other-keys) | |
4907 | (let ((include (string-append (assoc-ref outputs "out") | |
4908 | "/include/samtools/"))) | |
4909 | (for-each (lambda (file) | |
4910 | (install-file file include)) | |
4911 | (scandir "." (lambda (name) (string-match "\\.h$" name)))) | |
4912 | #t)))))) | |
4e10a221 | 4913 | (native-inputs `(("pkg-config" ,pkg-config))) |
4ab16440 BW |
4914 | (inputs |
4915 | `(("htslib" ,htslib) | |
4916 | ("ncurses" ,ncurses) | |
4917 | ("perl" ,perl) | |
4918 | ("python" ,python) | |
4919 | ("zlib" ,zlib))) | |
4e10a221 RW |
4920 | (home-page "http://samtools.sourceforge.net") |
4921 | (synopsis "Utilities to efficiently manipulate nucleotide sequence alignments") | |
4922 | (description | |
4923 | "Samtools implements various utilities for post-processing nucleotide | |
4924 | sequence alignments in the SAM, BAM, and CRAM formats, including indexing, | |
4925 | variant calling (in conjunction with bcftools), and a simple alignment | |
4926 | viewer.") | |
4927 | (license license:expat))) | |
d3517eda | 4928 | |
0b84a0aa RW |
4929 | (define-public samtools-0.1 |
4930 | ;; This is the most recent version of the 0.1 line of samtools. The input | |
4931 | ;; and output formats differ greatly from that used and produced by samtools | |
4932 | ;; 1.x and is still used in many bioinformatics pipelines. | |
4933 | (package (inherit samtools) | |
4934 | (version "0.1.19") | |
4935 | (source | |
4936 | (origin | |
4937 | (method url-fetch) | |
4938 | (uri | |
de67e922 | 4939 | (string-append "mirror://sourceforge/samtools/samtools/" |
0b84a0aa RW |
4940 | version "/samtools-" version ".tar.bz2")) |
4941 | (sha256 | |
4942 | (base32 "1m33xsfwz0s8qi45lylagfllqg7fphf4dr0780rsvw75av9wk06h")))) | |
4943 | (arguments | |
2309ed68 RW |
4944 | `(#:tests? #f ;no "check" target |
4945 | ,@(substitute-keyword-arguments (package-arguments samtools) | |
4946 | ((#:make-flags flags) | |
4947 | `(cons "LIBCURSES=-lncurses" ,flags)) | |
4948 | ((#:phases phases) | |
4949 | `(modify-phases ,phases | |
4950 | (replace 'install | |
4951 | (lambda* (#:key outputs #:allow-other-keys) | |
4952 | (let ((bin (string-append | |
4953 | (assoc-ref outputs "out") "/bin"))) | |
4954 | (mkdir-p bin) | |
f3860753 | 4955 | (install-file "samtools" bin) |
b2d748ed | 4956 | #t))) |
2309ed68 RW |
4957 | (delete 'patch-tests) |
4958 | (delete 'configure)))))))) | |
0b84a0aa | 4959 | |
fe4c37c2 | 4960 | (define-public mosaik |
698bd297 | 4961 | (let ((commit "5c25216d3522d6a33e53875cd76a6d65001e4e67")) |
fe4c37c2 RW |
4962 | (package |
4963 | (name "mosaik") | |
4964 | (version "2.2.30") | |
4965 | (source (origin | |
4966 | ;; There are no release tarballs nor tags. | |
4967 | (method git-fetch) | |
4968 | (uri (git-reference | |
4969 | (url "https://github.com/wanpinglee/MOSAIK.git") | |
4970 | (commit commit))) | |
4971 | (file-name (string-append name "-" version)) | |
4972 | (sha256 | |
4973 | (base32 | |
4974 | "17gj3s07cm77r41z92awh0bim7w7q7fbn0sf5nkqmcm1vw052qgw")))) | |
4975 | (build-system gnu-build-system) | |
4976 | (arguments | |
4977 | `(#:tests? #f ; no tests | |
4978 | #:make-flags (list "CC=gcc") | |
4979 | #:phases | |
4980 | (modify-phases %standard-phases | |
4981 | (replace 'configure | |
4982 | (lambda _ (chdir "src") #t)) | |
4983 | (replace 'install | |
4984 | (lambda* (#:key outputs #:allow-other-keys) | |
4985 | (let ((bin (string-append (assoc-ref outputs "out") | |
4986 | "/bin"))) | |
4987 | (mkdir-p bin) | |
4988 | (copy-recursively "../bin" bin) | |
4989 | #t)))))) | |
4990 | (inputs | |
4991 | `(("perl" ,perl) | |
4992 | ("zlib" ,zlib))) | |
029d9f77 | 4993 | (supported-systems '("x86_64-linux")) |
0c6c9c00 | 4994 | (home-page "https://github.com/wanpinglee/MOSAIK") |
fe4c37c2 RW |
4995 | (synopsis "Map nucleotide sequence reads to reference genomes") |
4996 | (description | |
4997 | "MOSAIK is a program for mapping second and third-generation sequencing | |
4998 | reads to a reference genome. MOSAIK can align reads generated by all the | |
4999 | major sequencing technologies, including Illumina, Applied Biosystems SOLiD, | |
5000 | Roche 454, Ion Torrent and Pacific BioSciences SMRT.") | |
5001 | ;; MOSAIK is released under the GPLv2+ with the exception of third-party | |
5002 | ;; code released into the public domain: | |
5003 | ;; 1. fastlz by Ariya Hidayat - http://www.fastlz.org/ | |
5004 | ;; 2. MD5 implementation - RSA Data Security, RFC 1321 | |
5005 | (license (list license:gpl2+ license:public-domain))))) | |
5006 | ||
282c5087 RW |
5007 | (define-public ngs-sdk |
5008 | (package | |
5009 | (name "ngs-sdk") | |
6c4ccf32 | 5010 | (version "1.3.0") |
282c5087 RW |
5011 | (source |
5012 | (origin | |
5013 | (method url-fetch) | |
5014 | (uri | |
5015 | (string-append "https://github.com/ncbi/ngs/archive/" | |
5016 | version ".tar.gz")) | |
5017 | (file-name (string-append name "-" version ".tar.gz")) | |
5018 | (sha256 | |
5019 | (base32 | |
6c4ccf32 | 5020 | "1wiyf4c6nm2j87pv015cbi0qny5byf3pbvcw3likifz5dl56ag40")))) |
282c5087 RW |
5021 | (build-system gnu-build-system) |
5022 | (arguments | |
5023 | `(#:parallel-build? #f ; not supported | |
5024 | #:tests? #f ; no "check" target | |
5025 | #:phases | |
dc1d3cde KK |
5026 | (modify-phases %standard-phases |
5027 | (replace 'configure | |
5028 | (lambda* (#:key outputs #:allow-other-keys) | |
5029 | (let ((out (assoc-ref outputs "out"))) | |
5030 | ;; Allow 'konfigure.perl' to find 'package.prl'. | |
5031 | (setenv "PERL5LIB" | |
5032 | (string-append ".:" (getenv "PERL5LIB"))) | |
5033 | ||
5034 | ;; The 'configure' script doesn't recognize things like | |
5035 | ;; '--enable-fast-install'. | |
5036 | (zero? (system* "./configure" | |
5037 | (string-append "--build-prefix=" (getcwd) "/build") | |
5038 | (string-append "--prefix=" out)))))) | |
5039 | (add-after 'unpack 'enter-dir | |
5040 | (lambda _ (chdir "ngs-sdk") #t))))) | |
282c5087 | 5041 | (native-inputs `(("perl" ,perl))) |
a0dadf0c AE |
5042 | ;; According to the test |
5043 | ;; unless ($MARCH =~ /x86_64/i || $MARCH =~ /i?86/i) | |
5044 | ;; in ngs-sdk/setup/konfigure.perl | |
ab29be81 | 5045 | (supported-systems '("i686-linux" "x86_64-linux")) |
282c5087 RW |
5046 | (home-page "https://github.com/ncbi/ngs") |
5047 | (synopsis "API for accessing Next Generation Sequencing data") | |
5048 | (description | |
5049 | "NGS is a domain-specific API for accessing reads, alignments and pileups | |
5050 | produced from Next Generation Sequencing. The API itself is independent from | |
5051 | any particular back-end implementation, and supports use of multiple back-ends | |
5052 | simultaneously.") | |
5053 | (license license:public-domain))) | |
5054 | ||
1ad15c16 | 5055 | (define-public java-ngs |
2651a5e6 | 5056 | (package (inherit ngs-sdk) |
1ad15c16 | 5057 | (name "java-ngs") |
2651a5e6 RW |
5058 | (arguments |
5059 | `(,@(substitute-keyword-arguments | |
5060 | `(#:modules ((guix build gnu-build-system) | |
5061 | (guix build utils) | |
5062 | (srfi srfi-1) | |
5063 | (srfi srfi-26)) | |
5064 | ,@(package-arguments ngs-sdk)) | |
5065 | ((#:phases phases) | |
614a8977 RW |
5066 | `(modify-phases ,phases |
5067 | (replace 'enter-dir (lambda _ (chdir "ngs-java") #t))))))) | |
2651a5e6 | 5068 | (inputs |
d2540f80 | 5069 | `(("jdk" ,icedtea "jdk") |
2651a5e6 RW |
5070 | ("ngs-sdk" ,ngs-sdk))) |
5071 | (synopsis "Java bindings for NGS SDK"))) | |
5072 | ||
75dd2424 RW |
5073 | (define-public ncbi-vdb |
5074 | (package | |
5075 | (name "ncbi-vdb") | |
5021f547 | 5076 | (version "2.8.2") |
75dd2424 RW |
5077 | (source |
5078 | (origin | |
5079 | (method url-fetch) | |
5080 | (uri | |
5081 | (string-append "https://github.com/ncbi/ncbi-vdb/archive/" | |
5082 | version ".tar.gz")) | |
5083 | (file-name (string-append name "-" version ".tar.gz")) | |
5084 | (sha256 | |
5085 | (base32 | |
5021f547 | 5086 | "1acn4bv81mfl137qnbn9995mjjhwd36pm0b7qli1iw5skrxa9j8m")))) |
75dd2424 RW |
5087 | (build-system gnu-build-system) |
5088 | (arguments | |
5089 | `(#:parallel-build? #f ; not supported | |
5090 | #:tests? #f ; no "check" target | |
5091 | #:phases | |
70111198 | 5092 | (modify-phases %standard-phases |
0691851a BW |
5093 | (add-before 'configure 'set-perl-search-path |
5094 | (lambda _ | |
5095 | ;; Work around "dotless @INC" build failure. | |
5096 | (setenv "PERL5LIB" | |
5097 | (string-append (getcwd) "/setup:" | |
5098 | (getenv "PERL5LIB"))) | |
5099 | #t)) | |
70111198 RW |
5100 | (replace 'configure |
5101 | (lambda* (#:key inputs outputs #:allow-other-keys) | |
5102 | (let ((out (assoc-ref outputs "out"))) | |
5103 | ;; Override include path for libmagic | |
5104 | (substitute* "setup/package.prl" | |
5105 | (("name => 'magic', Include => '/usr/include'") | |
5106 | (string-append "name=> 'magic', Include => '" | |
5107 | (assoc-ref inputs "libmagic") | |
5108 | "/include" "'"))) | |
75dd2424 | 5109 | |
70111198 RW |
5110 | ;; Install kdf5 library (needed by sra-tools) |
5111 | (substitute* "build/Makefile.install" | |
5112 | (("LIBRARIES_TO_INSTALL =") | |
5113 | "LIBRARIES_TO_INSTALL = kdf5.$(VERSION_LIBX) kdf5.$(VERSION_SHLX)")) | |
75dd2424 | 5114 | |
70111198 RW |
5115 | (substitute* "build/Makefile.env" |
5116 | (("CFLAGS =" prefix) | |
5117 | (string-append prefix "-msse2 "))) | |
675d7ae2 | 5118 | |
558e2307 RW |
5119 | ;; Override search path for ngs-java |
5120 | (substitute* "setup/package.prl" | |
5121 | (("/usr/local/ngs/ngs-java") | |
5122 | (assoc-ref inputs "java-ngs"))) | |
5123 | ||
70111198 RW |
5124 | ;; The 'configure' script doesn't recognize things like |
5125 | ;; '--enable-fast-install'. | |
5126 | (zero? (system* | |
5127 | "./configure" | |
5128 | (string-append "--build-prefix=" (getcwd) "/build") | |
5129 | (string-append "--prefix=" (assoc-ref outputs "out")) | |
5130 | (string-append "--debug") | |
5131 | (string-append "--with-xml2-prefix=" | |
5132 | (assoc-ref inputs "libxml2")) | |
5133 | (string-append "--with-ngs-sdk-prefix=" | |
5134 | (assoc-ref inputs "ngs-sdk")) | |
70111198 RW |
5135 | (string-append "--with-hdf5-prefix=" |
5136 | (assoc-ref inputs "hdf5"))))))) | |
5137 | (add-after 'install 'install-interfaces | |
5138 | (lambda* (#:key outputs #:allow-other-keys) | |
5139 | ;; Install interface libraries. On i686 the interface libraries | |
5140 | ;; are installed to "linux/gcc/i386", so we need to use the Linux | |
5141 | ;; architecture name ("i386") instead of the target system prefix | |
5142 | ;; ("i686"). | |
5143 | (mkdir (string-append (assoc-ref outputs "out") "/ilib")) | |
5144 | (copy-recursively (string-append "build/ncbi-vdb/linux/gcc/" | |
5145 | ,(system->linux-architecture | |
5146 | (or (%current-target-system) | |
5147 | (%current-system))) | |
5148 | "/rel/ilib") | |
5149 | (string-append (assoc-ref outputs "out") | |
5150 | "/ilib")) | |
5151 | ;; Install interface headers | |
5152 | (copy-recursively "interfaces" | |
5153 | (string-append (assoc-ref outputs "out") | |
5154 | "/include")) | |
d5e17162 RW |
5155 | #t)) |
5156 | ;; These files are needed by sra-tools. | |
5157 | (add-after 'install 'install-configuration-files | |
5158 | (lambda* (#:key outputs #:allow-other-keys) | |
5159 | (let ((target (string-append (assoc-ref outputs "out") "/kfg"))) | |
5160 | (mkdir target) | |
5161 | (install-file "libs/kfg/default.kfg" target) | |
5162 | (install-file "libs/kfg/certs.kfg" target)) | |
70111198 | 5163 | #t))))) |
75dd2424 RW |
5164 | (inputs |
5165 | `(("libxml2" ,libxml2) | |
5166 | ("ngs-sdk" ,ngs-sdk) | |
1ad15c16 | 5167 | ("java-ngs" ,java-ngs) |
75dd2424 RW |
5168 | ("libmagic" ,file) |
5169 | ("hdf5" ,hdf5))) | |
5170 | (native-inputs `(("perl" ,perl))) | |
675d7ae2 RW |
5171 | ;; NCBI-VDB requires SSE capability. |
5172 | (supported-systems '("i686-linux" "x86_64-linux")) | |
75dd2424 RW |
5173 | (home-page "https://github.com/ncbi/ncbi-vdb") |
5174 | (synopsis "Database engine for genetic information") | |
5175 | (description | |
5176 | "The NCBI-VDB library implements a highly compressed columnar data | |
5177 | warehousing engine that is most often used to store genetic information. | |
5178 | Databases are stored in a portable image within the file system, and can be | |
5179 | accessed/downloaded on demand across HTTP.") | |
5180 | (license license:public-domain))) | |
5181 | ||
cc6ed477 RW |
5182 | (define-public plink |
5183 | (package | |
5184 | (name "plink") | |
5185 | (version "1.07") | |
5186 | (source | |
5187 | (origin | |
5188 | (method url-fetch) | |
5189 | (uri (string-append | |
5190 | "http://pngu.mgh.harvard.edu/~purcell/plink/dist/plink-" | |
5191 | version "-src.zip")) | |
5192 | (sha256 | |
5193 | (base32 "0as8gxm4pjyc8dxmm1sl873rrd7wn5qs0l29nqfnl31x8i467xaa")) | |
0dbb7ac2 EF |
5194 | (patches (search-patches "plink-1.07-unclobber-i.patch" |
5195 | "plink-endian-detection.patch")))) | |
cc6ed477 RW |
5196 | (build-system gnu-build-system) |
5197 | (arguments | |
5198 | '(#:tests? #f ;no "check" target | |
5199 | #:make-flags (list (string-append "LIB_LAPACK=" | |
5200 | (assoc-ref %build-inputs "lapack") | |
5201 | "/lib/liblapack.so") | |
5202 | "WITH_LAPACK=1" | |
5203 | "FORCE_DYNAMIC=1" | |
5204 | ;; disable phoning home | |
5205 | "WITH_WEBCHECK=") | |
5206 | #:phases | |
5207 | (modify-phases %standard-phases | |
5208 | ;; no "configure" script | |
5209 | (delete 'configure) | |
5210 | (replace 'install | |
5211 | (lambda* (#:key outputs #:allow-other-keys) | |
5212 | (let ((bin (string-append (assoc-ref outputs "out") | |
5213 | "/bin/"))) | |
96c46210 | 5214 | (install-file "plink" bin) |
cc6ed477 RW |
5215 | #t)))))) |
5216 | (inputs | |
5217 | `(("zlib" ,zlib) | |
5218 | ("lapack" ,lapack))) | |
5219 | (native-inputs | |
5220 | `(("unzip" ,unzip))) | |
5221 | (home-page "http://pngu.mgh.harvard.edu/~purcell/plink/") | |
5222 | (synopsis "Whole genome association analysis toolset") | |
5223 | (description | |
5224 | "PLINK is a whole genome association analysis toolset, designed to | |
5225 | perform a range of basic, large-scale analyses in a computationally efficient | |
5226 | manner. The focus of PLINK is purely on analysis of genotype/phenotype data, | |
5227 | so there is no support for steps prior to this (e.g. study design and | |
5228 | planning, generating genotype or CNV calls from raw data). Through | |
5229 | integration with gPLINK and Haploview, there is some support for the | |
5230 | subsequent visualization, annotation and storage of results.") | |
5231 | ;; Code is released under GPLv2, except for fisher.h, which is under | |
5232 | ;; LGPLv2.1+ | |
5233 | (license (list license:gpl2 license:lgpl2.1+)))) | |
5234 | ||
dad66da4 RW |
5235 | (define-public plink-ng |
5236 | (package (inherit plink) | |
5237 | (name "plink-ng") | |
5238 | (version "1.90b4") | |
5239 | (source | |
5240 | (origin | |
5241 | (method url-fetch) | |
5242 | (uri (string-append "https://github.com/chrchang/plink-ng/archive/v" | |
5243 | version ".tar.gz")) | |
5244 | (file-name (string-append name "-" version ".tar.gz")) | |
5245 | (sha256 | |
5246 | (base32 "09ixrds009aczjswxr2alcb774mksq5g0v78dgjjn1h4dky0kf9a")))) | |
5247 | (build-system gnu-build-system) | |
5248 | (arguments | |
5249 | '(#:tests? #f ;no "check" target | |
5250 | #:make-flags (list "BLASFLAGS=-llapack -lopenblas" | |
5251 | "CFLAGS=-Wall -O2 -DDYNAMIC_ZLIB=1" | |
5252 | "ZLIB=-lz" | |
5253 | "-f" "Makefile.std") | |
5254 | #:phases | |
5255 | (modify-phases %standard-phases | |
5256 | (add-after 'unpack 'chdir | |
5257 | (lambda _ (chdir "1.9") #t)) | |
5258 | (delete 'configure) ; no "configure" script | |
5259 | (replace 'install | |
5260 | (lambda* (#:key outputs #:allow-other-keys) | |
5261 | (let ((bin (string-append (assoc-ref outputs "out") | |
5262 | "/bin/"))) | |
5263 | (install-file "plink" bin) | |
5264 | #t)))))) | |
5265 | (inputs | |
5266 | `(("zlib" ,zlib) | |
5267 | ("lapack" ,lapack) | |
5268 | ("openblas" ,openblas))) | |
5269 | (home-page "https://www.cog-genomics.org/plink/") | |
5270 | (license license:gpl3+))) | |
5271 | ||
c6a24d6e RW |
5272 | (define-public smithlab-cpp |
5273 | (let ((revision "1") | |
698bd297 | 5274 | (commit "728a097bec88c6f4b8528b685932049e660eff2e")) |
c6a24d6e RW |
5275 | (package |
5276 | (name "smithlab-cpp") | |
698bd297 | 5277 | (version (string-append "0." revision "." (string-take commit 7))) |
c6a24d6e RW |
5278 | (source (origin |
5279 | (method git-fetch) | |
5280 | (uri (git-reference | |
5281 | (url "https://github.com/smithlabcode/smithlab_cpp.git") | |
5282 | (commit commit))) | |
5283 | (file-name (string-append name "-" version "-checkout")) | |
5284 | (sha256 | |
5285 | (base32 | |
5286 | "0d476lmj312xk77kr9fzrv7z1bv96yfyx0w7y62ycmnfbx32ll74")))) | |
5287 | (build-system gnu-build-system) | |
5288 | (arguments | |
5289 | `(#:modules ((guix build gnu-build-system) | |
5290 | (guix build utils) | |
5291 | (srfi srfi-26)) | |
5292 | #:tests? #f ;no "check" target | |
5293 | #:phases | |
5294 | (modify-phases %standard-phases | |
5295 | (add-after 'unpack 'use-samtools-headers | |
5296 | (lambda _ | |
5297 | (substitute* '("SAM.cpp" | |
5298 | "SAM.hpp") | |
5299 | (("sam.h") "samtools/sam.h")) | |
5300 | #t)) | |
5301 | (replace 'install | |
5302 | (lambda* (#:key outputs #:allow-other-keys) | |
5303 | (let* ((out (assoc-ref outputs "out")) | |
5304 | (lib (string-append out "/lib")) | |
5305 | (include (string-append out "/include/smithlab-cpp"))) | |
5306 | (mkdir-p lib) | |
5307 | (mkdir-p include) | |
5308 | (for-each (cut install-file <> lib) | |
5309 | (find-files "." "\\.o$")) | |
5310 | (for-each (cut install-file <> include) | |
5311 | (find-files "." "\\.hpp$"))) | |
5312 | #t)) | |
5313 | (delete 'configure)))) | |
5314 | (inputs | |
5315 | `(("samtools" ,samtools-0.1) | |
5316 | ("zlib" ,zlib))) | |
5317 | (home-page "https://github.com/smithlabcode/smithlab_cpp") | |
5318 | (synopsis "C++ helper library for functions used in Smith lab projects") | |
5319 | (description | |
5320 | "Smithlab CPP is a C++ library that includes functions used in many of | |
5321 | the Smith lab bioinformatics projects, such as a wrapper around Samtools data | |
5322 | structures, classes for genomic regions, mapped sequencing reads, etc.") | |
5323 | (license license:gpl3+)))) | |
5324 | ||
56e373ef RW |
5325 | (define-public preseq |
5326 | (package | |
5327 | (name "preseq") | |
b49c5a58 | 5328 | (version "2.0") |
56e373ef RW |
5329 | (source (origin |
5330 | (method url-fetch) | |
b49c5a58 RW |
5331 | (uri (string-append "https://github.com/smithlabcode/" |
5332 | "preseq/archive/v" version ".tar.gz")) | |
5333 | (file-name (string-append name "-" version ".tar.gz")) | |
56e373ef | 5334 | (sha256 |
b49c5a58 | 5335 | (base32 "08r684l50pnxjpvmhzjgqq56yv9rfw90k8vx0nsrnrzk8mf9hsdq")) |
56e373ef RW |
5336 | (modules '((guix build utils))) |
5337 | (snippet | |
5338 | ;; Remove bundled samtools. | |
b49c5a58 | 5339 | '(delete-file-recursively "samtools")))) |
56e373ef RW |
5340 | (build-system gnu-build-system) |
5341 | (arguments | |
5342 | `(#:tests? #f ;no "check" target | |
5343 | #:phases | |
5344 | (modify-phases %standard-phases | |
56e373ef | 5345 | (delete 'configure)) |
b49c5a58 RW |
5346 | #:make-flags |
5347 | (list (string-append "PREFIX=" | |
5348 | (assoc-ref %outputs "out")) | |
5349 | (string-append "LIBBAM=" | |
5350 | (assoc-ref %build-inputs "samtools") | |
5351 | "/lib/libbam.a") | |
5352 | (string-append "SMITHLAB_CPP=" | |
5353 | (assoc-ref %build-inputs "smithlab-cpp") | |
5354 | "/lib") | |
5355 | "PROGS=preseq" | |
5356 | "INCLUDEDIRS=$(SMITHLAB_CPP)/../include/smithlab-cpp $(SAMTOOLS_DIR)"))) | |
56e373ef RW |
5357 | (inputs |
5358 | `(("gsl" ,gsl) | |
5359 | ("samtools" ,samtools-0.1) | |
b49c5a58 | 5360 | ("smithlab-cpp" ,smithlab-cpp) |
56e373ef RW |
5361 | ("zlib" ,zlib))) |
5362 | (home-page "http://smithlabresearch.org/software/preseq/") | |
5363 | (synopsis "Program for analyzing library complexity") | |
5364 | (description | |
5365 | "The preseq package is aimed at predicting and estimating the complexity | |
5366 | of a genomic sequencing library, equivalent to predicting and estimating the | |
5367 | number of redundant reads from a given sequencing depth and how many will be | |
5368 | expected from additional sequencing using an initial sequencing experiment. | |
5369 | The estimates can then be used to examine the utility of further sequencing, | |
5370 | optimize the sequencing depth, or to screen multiple libraries to avoid low | |
5371 | complexity samples.") | |
5372 | (license license:gpl3+))) | |
5373 | ||
9ded1457 BW |
5374 | (define-public python-screed |
5375 | (package | |
5376 | (name "python-screed") | |
5377 | (version "0.9") | |
5378 | (source | |
5379 | (origin | |
5380 | (method url-fetch) | |
5381 | (uri (pypi-uri "screed" version)) | |
5382 | (sha256 | |
5383 | (base32 | |
5384 | "18czszp9fkx3j6jr7y5kp6dfialscgddk05mw1zkhh2zhn0jd8i0")))) | |
5385 | (build-system python-build-system) | |
5386 | (arguments | |
5387 | `(#:phases | |
5388 | (modify-phases %standard-phases | |
5389 | (replace 'check | |
5390 | (lambda _ | |
5391 | (setenv "PYTHONPATH" | |
5392 | (string-append (getenv "PYTHONPATH") ":.")) | |
5393 | (zero? (system* "nosetests" "--attr" "!known_failing"))))))) | |
5394 | (native-inputs | |
5395 | `(("python-nose" ,python-nose))) | |
5396 | (inputs | |
5397 | `(("python-bz2file" ,python-bz2file))) | |
7bf837fd | 5398 | (home-page "https://github.com/dib-lab/screed/") |
9ded1457 BW |
5399 | (synopsis "Short read sequence database utilities") |
5400 | (description "Screed parses FASTA and FASTQ files and generates databases. | |
5401 | Values such as sequence name, sequence description, sequence quality and the | |
5402 | sequence itself can be retrieved from these databases.") | |
5403 | (license license:bsd-3))) | |
5404 | ||
5405 | (define-public python2-screed | |
5c31f4aa | 5406 | (package-with-python2 python-screed)) |
9ded1457 | 5407 | |
51c64999 RW |
5408 | (define-public sra-tools |
5409 | (package | |
5410 | (name "sra-tools") | |
79849358 | 5411 | (version "2.8.2-1") |
51c64999 RW |
5412 | (source |
5413 | (origin | |
5414 | (method url-fetch) | |
5415 | (uri | |
5416 | (string-append "https://github.com/ncbi/sra-tools/archive/" | |
5417 | version ".tar.gz")) | |
5418 | (file-name (string-append name "-" version ".tar.gz")) | |
5419 | (sha256 | |
5420 | (base32 | |
79849358 | 5421 | "1camsijmvv2s45mb4iyf44ghl4gkd4rl0viphpcgl3ccchy32a0g")))) |
51c64999 RW |
5422 | (build-system gnu-build-system) |
5423 | (arguments | |
5424 | `(#:parallel-build? #f ; not supported | |
5425 | #:tests? #f ; no "check" target | |
2320e76b | 5426 | #:make-flags |
79849358 RW |
5427 | (list (string-append "DEFAULT_CRT=" |
5428 | (assoc-ref %build-inputs "ncbi-vdb") | |
5429 | "/kfg/certs.kfg") | |
5430 | (string-append "DEFAULT_KFG=" | |
5431 | (assoc-ref %build-inputs "ncbi-vdb") | |
5432 | "/kfg/default.kfg") | |
5433 | (string-append "VDB_LIBDIR=" | |
2320e76b RW |
5434 | (assoc-ref %build-inputs "ncbi-vdb") |
5435 | ,(if (string-prefix? "x86_64" | |
5436 | (or (%current-target-system) | |
5437 | (%current-system))) | |
5438 | "/lib64" | |
5439 | "/lib32"))) | |
51c64999 | 5440 | #:phases |
beebe431 | 5441 | (modify-phases %standard-phases |
0691851a BW |
5442 | (add-before 'configure 'set-perl-search-path |
5443 | (lambda _ | |
5444 | ;; Work around "dotless @INC" build failure. | |
5445 | (setenv "PERL5LIB" | |
5446 | (string-append (getcwd) "/setup:" | |
5447 | (getenv "PERL5LIB"))) | |
5448 | #t)) | |
beebe431 RW |
5449 | (replace 'configure |
5450 | (lambda* (#:key inputs outputs #:allow-other-keys) | |
5451 | ;; The build system expects a directory containing the sources and | |
5452 | ;; raw build output of ncbi-vdb, including files that are not | |
5453 | ;; installed. Since we are building against an installed version of | |
5454 | ;; ncbi-vdb, the following modifications are needed. | |
5455 | (substitute* "setup/konfigure.perl" | |
5456 | ;; Make the configure script look for the "ilib" directory of | |
5457 | ;; "ncbi-vdb" without first checking for the existence of a | |
5458 | ;; matching library in its "lib" directory. | |
5459 | (("^ my \\$f = File::Spec->catdir\\(\\$libdir, \\$lib\\);") | |
5460 | "my $f = File::Spec->catdir($ilibdir, $ilib);") | |
5461 | ;; Look for interface libraries in ncbi-vdb's "ilib" directory. | |
5462 | (("my \\$ilibdir = File::Spec->catdir\\(\\$builddir, 'ilib'\\);") | |
5463 | "my $ilibdir = File::Spec->catdir($dir, 'ilib');")) | |
51c64999 | 5464 | |
beebe431 RW |
5465 | ;; Dynamic linking |
5466 | (substitute* "tools/copycat/Makefile" | |
5467 | (("smagic-static") "lmagic")) | |
2320e76b | 5468 | |
beebe431 RW |
5469 | ;; The 'configure' script doesn't recognize things like |
5470 | ;; '--enable-fast-install'. | |
5471 | (zero? (system* | |
5472 | "./configure" | |
5473 | (string-append "--build-prefix=" (getcwd) "/build") | |
5474 | (string-append "--prefix=" (assoc-ref outputs "out")) | |
5475 | (string-append "--debug") | |
5476 | (string-append "--with-fuse-prefix=" | |
5477 | (assoc-ref inputs "fuse")) | |
5478 | (string-append "--with-magic-prefix=" | |
5479 | (assoc-ref inputs "libmagic")) | |
5480 | ;; TODO: building with libxml2 fails with linker errors | |
5481 | ;; (string-append "--with-xml2-prefix=" | |
5482 | ;; (assoc-ref inputs "libxml2")) | |
5483 | (string-append "--with-ncbi-vdb-sources=" | |
5484 | (assoc-ref inputs "ncbi-vdb")) | |
5485 | (string-append "--with-ncbi-vdb-build=" | |
5486 | (assoc-ref inputs "ncbi-vdb")) | |
5487 | (string-append "--with-ngs-sdk-prefix=" | |
5488 | (assoc-ref inputs "ngs-sdk")) | |
5489 | (string-append "--with-hdf5-prefix=" | |
1108a920 RW |
5490 | (assoc-ref inputs "hdf5")))))) |
5491 | ;; This version of sra-tools fails to build with glibc because of a | |
5492 | ;; naming conflict. glibc-2.25/include/bits/mathcalls.h already | |
5493 | ;; contains a definition of "canonicalize", so we rename it. | |
5494 | ;; | |
5495 | ;; See upstream bug report: | |
5496 | ;; https://github.com/ncbi/sra-tools/issues/67 | |
5497 | (add-after 'unpack 'patch-away-glibc-conflict | |
5498 | (lambda _ | |
5499 | (substitute* "tools/bam-loader/bam.c" | |
5500 | (("canonicalize\\(" line) | |
5501 | (string-append "sra_tools_" line))) | |
5502 | #t))))) | |
51c64999 RW |
5503 | (native-inputs `(("perl" ,perl))) |
5504 | (inputs | |
5505 | `(("ngs-sdk" ,ngs-sdk) | |
5506 | ("ncbi-vdb" ,ncbi-vdb) | |
5507 | ("libmagic" ,file) | |
5508 | ("fuse" ,fuse) | |
5509 | ("hdf5" ,hdf5) | |
5510 | ("zlib" ,zlib))) | |
5511 | (home-page "http://www.ncbi.nlm.nih.gov/Traces/sra/sra.cgi?view=software") | |
5512 | (synopsis "Tools and libraries for reading and writing sequencing data") | |
5513 | (description | |
5514 | "The SRA Toolkit from NCBI is a collection of tools and libraries for | |
5515 | reading of sequencing files from the Sequence Read Archive (SRA) database and | |
5516 | writing files into the .sra format.") | |
5517 | (license license:public-domain))) | |
5518 | ||
d3517eda RW |
5519 | (define-public seqan |
5520 | (package | |
5521 | (name "seqan") | |
5522 | (version "1.4.2") | |
5523 | (source (origin | |
5524 | (method url-fetch) | |
5525 | (uri (string-append "http://packages.seqan.de/seqan-library/" | |
5526 | "seqan-library-" version ".tar.bz2")) | |
5527 | (sha256 | |
5528 | (base32 | |
5529 | "05s3wrrwn50f81aklfm65i4a749zag1vr8z03k21xm0pdxy47yvp")))) | |
5530 | ;; The documentation is 7.8MB and the includes are 3.6MB heavy, so it | |
5531 | ;; makes sense to split the outputs. | |
5532 | (outputs '("out" "doc")) | |
5533 | (build-system trivial-build-system) | |
5534 | (arguments | |
5535 | `(#:modules ((guix build utils)) | |
5536 | #:builder | |
5537 | (begin | |
5538 | (use-modules (guix build utils)) | |
5539 | (let ((tar (assoc-ref %build-inputs "tar")) | |
5540 | (bzip (assoc-ref %build-inputs "bzip2")) | |
5541 | (out (assoc-ref %outputs "out")) | |
5542 | (doc (assoc-ref %outputs "doc"))) | |
5543 | (setenv "PATH" (string-append tar "/bin:" bzip "/bin")) | |
5544 | (system* "tar" "xvf" (assoc-ref %build-inputs "source")) | |
5545 | (chdir (string-append "seqan-library-" ,version)) | |
5546 | (copy-recursively "include" (string-append out "/include")) | |
5547 | (copy-recursively "share" (string-append doc "/share")))))) | |
5548 | (native-inputs | |
5549 | `(("source" ,source) | |
5550 | ("tar" ,tar) | |
5551 | ("bzip2" ,bzip2))) | |
5552 | (home-page "http://www.seqan.de") | |
5553 | (synopsis "Library for nucleotide sequence analysis") | |
5554 | (description | |
5555 | "SeqAn is a C++ library of efficient algorithms and data structures for | |
5556 | the analysis of sequences with the focus on biological data. It contains | |
5557 | algorithms and data structures for string representation and their | |
5558 | manipulation, online and indexed string search, efficient I/O of | |
5559 | bioinformatics file formats, sequence alignment, and more.") | |
5560 | (license license:bsd-3))) | |
ce7155d5 | 5561 | |
d708b7a9 BW |
5562 | (define-public seqmagick |
5563 | (package | |
5564 | (name "seqmagick") | |
39fb853a | 5565 | (version "0.7.0") |
d708b7a9 BW |
5566 | (source |
5567 | (origin | |
5568 | (method url-fetch) | |
f6e2d86f | 5569 | (uri (pypi-uri "seqmagick" version)) |
d708b7a9 BW |
5570 | (sha256 |
5571 | (base32 | |
39fb853a | 5572 | "12bfyp8nqi0hd36rmj450aygafp01qy3hkbvlwn3bk39pyjjkgg5")))) |
d708b7a9 | 5573 | (build-system python-build-system) |
d708b7a9 | 5574 | (inputs |
39fb853a | 5575 | `(("python-biopython" ,python-biopython))) |
d708b7a9 | 5576 | (native-inputs |
39fb853a | 5577 | `(("python-nose" ,python-nose))) |
7bf837fd | 5578 | (home-page "https://github.com/fhcrc/seqmagick") |
d708b7a9 BW |
5579 | (synopsis "Tools for converting and modifying sequence files") |
5580 | (description | |
5581 | "Bioinformaticians often have to convert sequence files between formats | |
5582 | and do little manipulations on them, and it's not worth writing scripts for | |
5583 | that. Seqmagick is a utility to expose the file format conversion in | |
5584 | BioPython in a convenient way. Instead of having a big mess of scripts, there | |
5585 | is one that takes arguments.") | |
5586 | (license license:gpl3))) | |
5587 | ||
66daf78c BW |
5588 | (define-public seqtk |
5589 | (package | |
5590 | (name "seqtk") | |
5591 | (version "1.2") | |
5592 | (source (origin | |
5593 | (method url-fetch) | |
5594 | (uri (string-append | |
5595 | "https://github.com/lh3/seqtk/archive/v" | |
5596 | version ".tar.gz")) | |
5597 | (file-name (string-append name "-" version ".tar.gz")) | |
5598 | (sha256 | |
5599 | (base32 | |
5600 | "0ywdyzpmfiz2wp6ampbzqg4y8bj450nfgqarpamg045b8mk32lxx")) | |
5601 | (modules '((guix build utils))) | |
5602 | (snippet | |
5603 | '(begin | |
5604 | ;; Remove extraneous header files, as is done in the seqtk | |
5605 | ;; master branch. | |
5606 | (for-each (lambda (file) (delete-file file)) | |
5607 | (list "ksort.h" "kstring.h" "kvec.h")) | |
5608 | #t)))) | |
5609 | (build-system gnu-build-system) | |
5610 | (arguments | |
5611 | `(#:phases | |
5612 | (modify-phases %standard-phases | |
5613 | (delete 'configure) | |
5614 | (replace 'check | |
5615 | ;; There are no tests, so we just run a sanity check. | |
5616 | (lambda _ (zero? (system* "./seqtk" "seq")))) | |
5617 | (replace 'install | |
5618 | (lambda* (#:key outputs #:allow-other-keys) | |
5619 | (let ((bin (string-append (assoc-ref outputs "out") "/bin/"))) | |
5620 | (install-file "seqtk" bin))))))) | |
5621 | (inputs | |
5622 | `(("zlib" ,zlib))) | |
5623 | (home-page "https://github.com/lh3/seqtk") | |
5624 | (synopsis "Toolkit for processing biological sequences in FASTA/Q format") | |
5625 | (description | |
5626 | "Seqtk is a fast and lightweight tool for processing sequences in the | |
5627 | FASTA or FASTQ format. It parses both FASTA and FASTQ files which can be | |
5628 | optionally compressed by gzip.") | |
5629 | (license license:expat))) | |
5630 | ||
5f7e17be BW |
5631 | (define-public snap-aligner |
5632 | (package | |
5633 | (name "snap-aligner") | |
5634 | (version "1.0beta.18") | |
5635 | (source (origin | |
5636 | (method url-fetch) | |
5637 | (uri (string-append | |
5638 | "https://github.com/amplab/snap/archive/v" | |
5639 | version ".tar.gz")) | |
5640 | (file-name (string-append name "-" version ".tar.gz")) | |
5641 | (sha256 | |
5642 | (base32 | |
5643 | "1vnsjwv007k1fl1q7d681kbwn6bc66cgw6h16hym6gvyy71qv2ly")))) | |
5644 | (build-system gnu-build-system) | |
5645 | (arguments | |
5646 | '(#:phases | |
5647 | (modify-phases %standard-phases | |
5648 | (delete 'configure) | |
5649 | (replace 'check (lambda _ (zero? (system* "./unit_tests")))) | |
5650 | (replace 'install | |
5651 | (lambda* (#:key outputs #:allow-other-keys) | |
5652 | (let* ((out (assoc-ref outputs "out")) | |
5653 | (bin (string-append out "/bin"))) | |
5f7e17be BW |
5654 | (install-file "snap-aligner" bin) |
5655 | (install-file "SNAPCommand" bin) | |
5656 | #t)))))) | |
5657 | (native-inputs | |
5658 | `(("zlib" ,zlib))) | |
5659 | (home-page "http://snap.cs.berkeley.edu/") | |
5660 | (synopsis "Short read DNA sequence aligner") | |
5661 | (description | |
5662 | "SNAP is a fast and accurate aligner for short DNA reads. It is | |
5663 | optimized for modern read lengths of 100 bases or higher, and takes advantage | |
5664 | of these reads to align data quickly through a hash-based indexing scheme.") | |
3e6fdd5f EF |
5665 | ;; 32-bit systems are not supported by the unpatched code. |
5666 | ;; Following the bug reports https://github.com/amplab/snap/issues/68 and | |
5667 | ;; https://bugs.debian.org/cgi-bin/bugreport.cgi?bug=812378 we see that | |
5668 | ;; systems without a lot of memory cannot make good use of this program. | |
5669 | (supported-systems '("x86_64-linux")) | |
5f7e17be BW |
5670 | (license license:asl2.0))) |
5671 | ||
bcadaf00 BW |
5672 | (define-public sortmerna |
5673 | (package | |
5674 | (name "sortmerna") | |
849485f5 | 5675 | (version "2.1b") |
bcadaf00 BW |
5676 | (source |
5677 | (origin | |
5678 | (method url-fetch) | |
5679 | (uri (string-append | |
5680 | "https://github.com/biocore/sortmerna/archive/" | |
5681 | version ".tar.gz")) | |
5682 | (file-name (string-append name "-" version ".tar.gz")) | |
5683 | (sha256 | |
5684 | (base32 | |
849485f5 | 5685 | "1ghaghvd82af9j5adavxh77g7hm247d1r69m3fbi6f1jdivj5ldk")))) |
bcadaf00 BW |
5686 | (build-system gnu-build-system) |
5687 | (outputs '("out" ;for binaries | |
5688 | "db")) ;for sequence databases | |
5689 | (arguments | |
5690 | `(#:phases | |
5691 | (modify-phases %standard-phases | |
5692 | (replace 'install | |
5693 | (lambda* (#:key outputs #:allow-other-keys) | |
5694 | (let* ((out (assoc-ref outputs "out")) | |
5695 | (bin (string-append out "/bin")) | |
5696 | (db (assoc-ref outputs "db")) | |
5697 | (share | |
5698 | (string-append db "/share/sortmerna/rRNA_databases"))) | |
5699 | (install-file "sortmerna" bin) | |
5700 | (install-file "indexdb_rna" bin) | |
5701 | (for-each (lambda (file) | |
5702 | (install-file file share)) | |
5703 | (find-files "rRNA_databases" ".*fasta")) | |
5704 | #t)))))) | |
849485f5 BW |
5705 | (inputs |
5706 | `(("zlib" ,zlib))) | |
bcadaf00 BW |
5707 | (home-page "http://bioinfo.lifl.fr/RNA/sortmerna") |
5708 | (synopsis "Biological sequence analysis tool for NGS reads") | |
5709 | (description | |
5710 | "SortMeRNA is a biological sequence analysis tool for filtering, mapping | |
5711 | and operational taxonomic unit (OTU) picking of next generation | |
5712 | sequencing (NGS) reads. The core algorithm is based on approximate seeds and | |
5713 | allows for fast and sensitive analyses of nucleotide sequences. The main | |
5714 | application of SortMeRNA is filtering rRNA from metatranscriptomic data.") | |
2324541b EF |
5715 | ;; The source includes x86 specific code |
5716 | (supported-systems '("x86_64-linux" "i686-linux")) | |
bcadaf00 BW |
5717 | (license license:lgpl3))) |
5718 | ||
ce7155d5 RW |
5719 | (define-public star |
5720 | (package | |
5721 | (name "star") | |
939b6b11 | 5722 | (version "2.5.3a") |
ce7155d5 RW |
5723 | (source (origin |
5724 | (method url-fetch) | |
3062d750 RW |
5725 | (uri (string-append "https://github.com/alexdobin/STAR/archive/" |
5726 | version ".tar.gz")) | |
5727 | (file-name (string-append name "-" version ".tar.gz")) | |
ce7155d5 RW |
5728 | (sha256 |
5729 | (base32 | |
939b6b11 | 5730 | "013wirlz8lllgjyagl48l75n1isxyabqb3sj7qlsl0x1rmvqw99a")) |
ce7155d5 RW |
5731 | (modules '((guix build utils))) |
5732 | (snippet | |
3062d750 RW |
5733 | '(begin |
5734 | (substitute* "source/Makefile" | |
5735 | (("/bin/rm") "rm")) | |
5736 | ;; Remove pre-built binaries and bundled htslib sources. | |
5737 | (delete-file-recursively "bin/MacOSX_x86_64") | |
5738 | (delete-file-recursively "bin/Linux_x86_64") | |
c9e9154e | 5739 | (delete-file-recursively "bin/Linux_x86_64_static") |
3062d750 RW |
5740 | (delete-file-recursively "source/htslib") |
5741 | #t)))) | |
ce7155d5 RW |
5742 | (build-system gnu-build-system) |
5743 | (arguments | |
5744 | '(#:tests? #f ;no check target | |
5745 | #:make-flags '("STAR") | |
5746 | #:phases | |
c0266e8d RW |
5747 | (modify-phases %standard-phases |
5748 | (add-after 'unpack 'enter-source-dir | |
5749 | (lambda _ (chdir "source") #t)) | |
625cdc3f RW |
5750 | (add-after 'enter-source-dir 'make-reproducible |
5751 | (lambda _ | |
5752 | (substitute* "Makefile" | |
5753 | (("(COMPILATION_TIME_PLACE=\")(.*)(\")" _ pre mid post) | |
5754 | (string-append pre "Built with Guix" post))))) | |
3062d750 RW |
5755 | (add-after 'enter-source-dir 'do-not-use-bundled-htslib |
5756 | (lambda _ | |
5757 | (substitute* "Makefile" | |
5758 | (("(Depend.list: \\$\\(SOURCES\\) parametersDefault\\.xxd) htslib" | |
5759 | _ prefix) prefix)) | |
5760 | (substitute* '("BAMfunctions.cpp" | |
5761 | "signalFromBAM.h" | |
5762 | "bam_cat.h" | |
5763 | "bam_cat.c" | |
5764 | "STAR.cpp" | |
5765 | "bamRemoveDuplicates.cpp") | |
5766 | (("#include \"htslib/([^\"]+\\.h)\"" _ header) | |
5767 | (string-append "#include <" header ">"))) | |
5768 | (substitute* "IncludeDefine.h" | |
5769 | (("\"htslib/(htslib/[^\"]+.h)\"" _ header) | |
5770 | (string-append "<" header ">"))) | |
5771 | #t)) | |
c0266e8d RW |
5772 | (replace 'install |
5773 | (lambda* (#:key outputs #:allow-other-keys) | |
5774 | (let ((bin (string-append (assoc-ref outputs "out") "/bin/"))) | |
5775 | (install-file "STAR" bin)) | |
5776 | #t)) | |
5777 | (delete 'configure)))) | |
ce7155d5 | 5778 | (native-inputs |
9fc513ad | 5779 | `(("xxd" ,xxd))) |
ce7155d5 | 5780 | (inputs |
3062d750 RW |
5781 | `(("htslib" ,htslib) |
5782 | ("zlib" ,zlib))) | |
ce7155d5 RW |
5783 | (home-page "https://github.com/alexdobin/STAR") |
5784 | (synopsis "Universal RNA-seq aligner") | |
5785 | (description | |
5786 | "The Spliced Transcripts Alignment to a Reference (STAR) software is | |
5787 | based on a previously undescribed RNA-seq alignment algorithm that uses | |
5788 | sequential maximum mappable seed search in uncompressed suffix arrays followed | |
5789 | by seed clustering and stitching procedure. In addition to unbiased de novo | |
5790 | detection of canonical junctions, STAR can discover non-canonical splices and | |
5791 | chimeric (fusion) transcripts, and is also capable of mapping full-length RNA | |
5792 | sequences.") | |
c11f79a4 BW |
5793 | ;; Only 64-bit systems are supported according to the README. |
5794 | (supported-systems '("x86_64-linux" "mips64el-linux")) | |
ce7155d5 RW |
5795 | ;; STAR is licensed under GPLv3 or later; htslib is MIT-licensed. |
5796 | (license license:gpl3+))) | |
de07c0db | 5797 | |
dbf4ed7c RW |
5798 | (define-public subread |
5799 | (package | |
5800 | (name "subread") | |
e6debcaf | 5801 | (version "1.6.0") |
dbf4ed7c RW |
5802 | (source (origin |
5803 | (method url-fetch) | |
de67e922 LF |
5804 | (uri (string-append "mirror://sourceforge/subread/subread-" |
5805 | version "/subread-" version "-source.tar.gz")) | |
dbf4ed7c RW |
5806 | (sha256 |
5807 | (base32 | |
e6debcaf | 5808 | "0ah0n4jx6ksk2m2j7xk385x2qzmk1y4rfc6a4mfrdqrlq721w99i")))) |
dbf4ed7c RW |
5809 | (build-system gnu-build-system) |
5810 | (arguments | |
5811 | `(#:tests? #f ;no "check" target | |
104c1986 RW |
5812 | ;; The CC and CCFLAGS variables are set to contain a lot of x86_64 |
5813 | ;; optimizations by default, so we override these flags such that x86_64 | |
5814 | ;; flags are only added when the build target is an x86_64 system. | |
5815 | #:make-flags | |
5816 | (list (let ((system ,(or (%current-target-system) | |
5817 | (%current-system))) | |
5818 | (flags '("-ggdb" "-fomit-frame-pointer" | |
5819 | "-ffast-math" "-funroll-loops" | |
5820 | "-fmessage-length=0" | |
5821 | "-O9" "-Wall" "-DMAKE_FOR_EXON" | |
5822 | "-DMAKE_STANDALONE" | |
5823 | "-DSUBREAD_VERSION=\\\"${SUBREAD_VERSION}\\\"")) | |
5824 | (flags64 '("-mmmx" "-msse" "-msse2" "-msse3"))) | |
5825 | (if (string-prefix? "x86_64" system) | |
5826 | (string-append "CCFLAGS=" (string-join (append flags flags64))) | |
5827 | (string-append "CCFLAGS=" (string-join flags)))) | |
5828 | "-f" "Makefile.Linux" | |
5829 | "CC=gcc ${CCFLAGS}") | |
dbf4ed7c | 5830 | #:phases |
dc1d3cde KK |
5831 | (modify-phases %standard-phases |
5832 | (add-after 'unpack 'enter-dir | |
5833 | (lambda _ (chdir "src") #t)) | |
5834 | (replace 'install | |
5835 | (lambda* (#:key outputs #:allow-other-keys) | |
5836 | (let ((bin (string-append (assoc-ref outputs "out") "/bin/"))) | |
5837 | (mkdir-p bin) | |
5838 | (copy-recursively "../bin" bin)))) | |
dbf4ed7c | 5839 | ;; no "configure" script |
dc1d3cde | 5840 | (delete 'configure)))) |
dbf4ed7c RW |
5841 | (inputs `(("zlib" ,zlib))) |
5842 | (home-page "http://bioinf.wehi.edu.au/subread-package/") | |
5843 | (synopsis "Tool kit for processing next-gen sequencing data") | |
5844 | (description | |
5845 | "The subread package contains the following tools: subread aligner, a | |
5846 | general-purpose read aligner; subjunc aligner: detecting exon-exon junctions | |
5847 | and mapping RNA-seq reads; featureCounts: counting mapped reads for genomic | |
5848 | features; exactSNP: a SNP caller that discovers SNPs by testing signals | |
5849 | against local background noises.") | |
5850 | (license license:gpl3+))) | |
5851 | ||
d15d981e RW |
5852 | (define-public stringtie |
5853 | (package | |
5854 | (name "stringtie") | |
5855 | (version "1.2.1") | |
5856 | (source (origin | |
5857 | (method url-fetch) | |
5858 | (uri (string-append "http://ccb.jhu.edu/software/stringtie/dl/" | |
5859 | "stringtie-" version ".tar.gz")) | |
5860 | (sha256 | |
5861 | (base32 | |
5862 | "1cqllsc1maq4kh92isi8yadgzbmnf042hlnalpk3y59aph1z3bfz")) | |
5863 | (modules '((guix build utils))) | |
5864 | (snippet | |
5865 | '(begin | |
5866 | (delete-file-recursively "samtools-0.1.18") | |
5867 | #t)))) | |
5868 | (build-system gnu-build-system) | |
5869 | (arguments | |
5870 | `(#:tests? #f ;no test suite | |
5871 | #:phases | |
5872 | (modify-phases %standard-phases | |
5873 | ;; no configure script | |
5874 | (delete 'configure) | |
5875 | (add-before 'build 'use-system-samtools | |
5876 | (lambda _ | |
5877 | (substitute* "Makefile" | |
5878 | (("stringtie: \\$\\{BAM\\}/libbam\\.a") | |
5879 | "stringtie: ")) | |
5880 | (substitute* '("gclib/GBam.h" | |
5881 | "gclib/GBam.cpp") | |
5882 | (("#include \"(bam|sam|kstring).h\"" _ header) | |
5883 | (string-append "#include <samtools/" header ".h>"))) | |
5884 | #t)) | |
0d2c0562 RW |
5885 | (add-after 'unpack 'remove-duplicate-typedef |
5886 | (lambda _ | |
5887 | ;; This typedef conflicts with the typedef in | |
5888 | ;; glibc-2.25/include/bits/types.h | |
5889 | (substitute* "gclib/GThreads.h" | |
5890 | (("typedef long long __intmax_t;") "")) | |
5891 | #t)) | |
d15d981e RW |
5892 | (replace 'install |
5893 | (lambda* (#:key outputs #:allow-other-keys) | |
5894 | (let ((bin (string-append (assoc-ref outputs "out") "/bin/"))) | |
5895 | (install-file "stringtie" bin) | |
5896 | #t)))))) | |
5897 | (inputs | |
5898 | `(("samtools" ,samtools-0.1) | |
5899 | ("zlib" ,zlib))) | |
5900 | (home-page "http://ccb.jhu.edu/software/stringtie/") | |
5901 | (synopsis "Transcript assembly and quantification for RNA-Seq data") | |
5902 | (description | |
5903 | "StringTie is a fast and efficient assembler of RNA-Seq sequence | |
5904 | alignments into potential transcripts. It uses a novel network flow algorithm | |
5905 | as well as an optional de novo assembly step to assemble and quantitate | |
5906 | full-length transcripts representing multiple splice variants for each gene | |
5907 | locus. Its input can include not only the alignments of raw reads used by | |
5908 | other transcript assemblers, but also alignments of longer sequences that have | |
5909 | been assembled from those reads. To identify differentially expressed genes | |
5910 | between experiments, StringTie's output can be processed either by the | |
5911 | Cuffdiff or Ballgown programs.") | |
5912 | (license license:artistic2.0))) | |
5913 | ||
ad0ae297 BW |
5914 | (define-public taxtastic |
5915 | (package | |
5916 | (name "taxtastic") | |
3cbfc149 | 5917 | (version "0.6.4") |
ad0ae297 BW |
5918 | (source (origin |
5919 | (method url-fetch) | |
3cbfc149 | 5920 | (uri (pypi-uri "taxtastic" version)) |
ad0ae297 BW |
5921 | (sha256 |
5922 | (base32 | |
3cbfc149 | 5923 | "0s79z8kfl853x7l4h8ms05k31q87aw62nrchlk20w9n227j35929")))) |
ad0ae297 BW |
5924 | (build-system python-build-system) |
5925 | (arguments | |
5926 | `(#:python ,python-2 | |
5927 | #:phases | |
5928 | (modify-phases %standard-phases | |
5929 | (replace 'check | |
5930 | (lambda _ | |
5931 | (zero? (system* "python" "-m" "unittest" "discover" "-v"))))))) | |
5932 | (propagated-inputs | |
5933 | `(("python-sqlalchemy" ,python2-sqlalchemy) | |
5934 | ("python-decorator" ,python2-decorator) | |
5935 | ("python-biopython" ,python2-biopython) | |
5936 | ("python-pandas" ,python2-pandas))) | |
5937 | (home-page "https://github.com/fhcrc/taxtastic") | |
5938 | (synopsis "Tools for taxonomic naming and annotation") | |
5939 | (description | |
5940 | "Taxtastic is software written in python used to build and maintain | |
5941 | reference packages i.e. collections of reference trees, reference alignments, | |
5942 | profiles, and associated taxonomic information.") | |
5943 | (license license:gpl3+))) | |
5944 | ||
de07c0db RW |
5945 | (define-public vcftools |
5946 | (package | |
5947 | (name "vcftools") | |
f4322542 | 5948 | (version "0.1.15") |
de07c0db RW |
5949 | (source (origin |
5950 | (method url-fetch) | |
5951 | (uri (string-append | |
9b36e256 RJ |
5952 | "https://github.com/vcftools/vcftools/releases/download/v" |
5953 | version "/vcftools-" version ".tar.gz")) | |
de07c0db RW |
5954 | (sha256 |
5955 | (base32 | |
f4322542 | 5956 | "1qw30c45wihgy632rbz4rh3njnwj4msj46l1rsgdhyg6bgypmr1i")))) |
de07c0db RW |
5957 | (build-system gnu-build-system) |
5958 | (arguments | |
5959 | `(#:tests? #f ; no "check" target | |
5960 | #:make-flags (list | |
7c3958e1 | 5961 | "CFLAGS=-O2" ; override "-m64" flag |
de07c0db RW |
5962 | (string-append "PREFIX=" (assoc-ref %outputs "out")) |
5963 | (string-append "MANDIR=" (assoc-ref %outputs "out") | |
9b36e256 RJ |
5964 | "/share/man/man1")))) |
5965 | (native-inputs | |
5966 | `(("pkg-config" ,pkg-config))) | |
de07c0db RW |
5967 | (inputs |
5968 | `(("perl" ,perl) | |
5969 | ("zlib" ,zlib))) | |
9b36e256 | 5970 | (home-page "https://vcftools.github.io/") |
de07c0db RW |
5971 | (synopsis "Tools for working with VCF files") |
5972 | (description | |
5973 | "VCFtools is a program package designed for working with VCF files, such | |
5974 | as those generated by the 1000 Genomes Project. The aim of VCFtools is to | |
5975 | provide easily accessible methods for working with complex genetic variation | |
5976 | data in the form of VCF files.") | |
5977 | ;; The license is declared as LGPLv3 in the README and | |
9b36e256 | 5978 | ;; at https://vcftools.github.io/license.html |
de07c0db | 5979 | (license license:lgpl3))) |
9c38b540 | 5980 | |
35aa90a1 RW |
5981 | (define-public infernal |
5982 | (package | |
5983 | (name "infernal") | |
5984 | (version "1.1.2") | |
5985 | (source (origin | |
5986 | (method url-fetch) | |
5987 | (uri (string-append "http://eddylab.org/software/infernal/" | |
5988 | "infernal-" version ".tar.gz")) | |
5989 | (sha256 | |
5990 | (base32 | |
5991 | "0sr2hiz3qxfwqpz3whxr6n82p3x27336v3f34iqznp10hks2935c")))) | |
5992 | (build-system gnu-build-system) | |
5993 | (native-inputs | |
5994 | `(("perl" ,perl))) ; for tests | |
5995 | (home-page "http://eddylab.org/infernal/") | |
5996 | (synopsis "Inference of RNA alignments") | |
5997 | (description "Infernal (\"INFERence of RNA ALignment\") is a tool for | |
5998 | searching DNA sequence databases for RNA structure and sequence similarities. | |
5999 | It is an implementation of a special case of profile stochastic context-free | |
6000 | grammars called @dfn{covariance models} (CMs). A CM is like a sequence | |
6001 | profile, but it scores a combination of sequence consensus and RNA secondary | |
6002 | structure consensus, so in many cases, it is more capable of identifying RNA | |
6003 | homologs that conserve their secondary structure more than their primary | |
6004 | sequence.") | |
48409ef2 EF |
6005 | ;; Infernal 1.1.2 requires VMX or SSE capability for parallel instructions. |
6006 | (supported-systems '("i686-linux" "x86_64-linux")) | |
35aa90a1 RW |
6007 | (license license:bsd-3))) |
6008 | ||
b91cfa22 RW |
6009 | (define-public r-centipede |
6010 | (package | |
6011 | (name "r-centipede") | |
6012 | (version "1.2") | |
6013 | (source (origin | |
6014 | (method url-fetch) | |
6015 | (uri (string-append "http://download.r-forge.r-project.org/" | |
6016 | "src/contrib/CENTIPEDE_" version ".tar.gz")) | |
6017 | (sha256 | |
6018 | (base32 | |
6019 | "1hsx6qgwr0i67fhy9257zj7s0ppncph2hjgbia5nn6nfmj0ax6l9")))) | |
6020 | (build-system r-build-system) | |
6021 | (home-page "http://centipede.uchicago.edu/") | |
6022 | (synopsis "Predict transcription factor binding sites") | |
6023 | (description | |
6024 | "CENTIPEDE applies a hierarchical Bayesian mixture model to infer regions | |
6025 | of the genome that are bound by particular transcription factors. It starts | |
6026 | by identifying a set of candidate binding sites, and then aims to classify the | |
6027 | sites according to whether each site is bound or not bound by a transcription | |
6028 | factor. CENTIPEDE is an unsupervised learning algorithm that discriminates | |
6029 | between two different types of motif instances using as much relevant | |
6030 | information as possible.") | |
6031 | (license (list license:gpl2+ license:gpl3+)))) | |
6032 | ||
7b3df1e5 BW |
6033 | (define-public r-vegan |
6034 | (package | |
6035 | (name "r-vegan") | |
2e9da339 | 6036 | (version "2.4-6") |
7b3df1e5 BW |
6037 | (source |
6038 | (origin | |
6039 | (method url-fetch) | |
6040 | (uri (cran-uri "vegan" version)) | |
6041 | (sha256 | |
6042 | (base32 | |
2e9da339 | 6043 | "175mqr42mmxy98gpf3rky8alnkw3w1k90ggdw3cispl36841p76w")))) |
7b3df1e5 | 6044 | (build-system r-build-system) |
7b3df1e5 | 6045 | (native-inputs |
db2e4386 | 6046 | `(("gfortran" ,gfortran))) |
7b3df1e5 BW |
6047 | (propagated-inputs |
6048 | `(("r-cluster" ,r-cluster) | |
6049 | ("r-lattice" ,r-lattice) | |
aeb64f3c | 6050 | ("r-mass" ,r-mass) |
7b3df1e5 BW |
6051 | ("r-mgcv" ,r-mgcv) |
6052 | ("r-permute" ,r-permute))) | |
6053 | (home-page "https://cran.r-project.org/web/packages/vegan") | |
6054 | (synopsis "Functions for community ecology") | |
6055 | (description | |
6056 | "The vegan package provides tools for descriptive community ecology. It | |
6057 | has most basic functions of diversity analysis, community ordination and | |
6058 | dissimilarity analysis. Most of its multivariate tools can be used for other | |
6059 | data types as well.") | |
6060 | (license license:gpl2+))) | |
6061 | ||
8c6de588 RW |
6062 | (define-public r-annotate |
6063 | (package | |
6064 | (name "r-annotate") | |
654c29ac | 6065 | (version "1.56.1") |
8c6de588 RW |
6066 | (source |
6067 | (origin | |
6068 | (method url-fetch) | |
6069 | (uri (bioconductor-uri "annotate" version)) | |
6070 | (sha256 | |
6071 | (base32 | |
654c29ac | 6072 | "14c5xd9kasvcwg5gbjys2c1vizxhlqlzxakqc2kml0kw97hmx0rq")))) |
8c6de588 RW |
6073 | (build-system r-build-system) |
6074 | (propagated-inputs | |
6075 | `(("r-annotationdbi" ,r-annotationdbi) | |
6076 | ("r-biobase" ,r-biobase) | |
6077 | ("r-biocgenerics" ,r-biocgenerics) | |
6078 | ("r-dbi" ,r-dbi) | |
d0f0579e | 6079 | ("r-rcurl" ,r-rcurl) |
8c6de588 RW |
6080 | ("r-xml" ,r-xml) |
6081 | ("r-xtable" ,r-xtable))) | |
6082 | (home-page | |
5713bbf1 | 6083 | "https://bioconductor.org/packages/annotate") |
8c6de588 | 6084 | (synopsis "Annotation for microarrays") |
d1e4ad1b | 6085 | (description "This package provides R environments for the annotation of |
8c6de588 RW |
6086 | microarrays.") |
6087 | (license license:artistic2.0))) | |
6088 | ||
efa6a1dd RJ |
6089 | (define-public r-copynumber |
6090 | (package | |
6091 | (name "r-copynumber") | |
6092 | (version "1.18.0") | |
6093 | (source (origin | |
6094 | (method url-fetch) | |
6095 | (uri (bioconductor-uri "copynumber" version)) | |
6096 | (sha256 | |
6097 | (base32 | |
6098 | "01kcwzl485yjrkgyg8117b1il957ss0v6rq4bbxf4ksd5fzcjmyx")))) | |
6099 | (build-system r-build-system) | |
6100 | (propagated-inputs | |
6101 | `(("r-s4vectors" ,r-s4vectors) | |
6102 | ("r-iranges" ,r-iranges) | |
6103 | ("r-genomicranges" ,r-genomicranges) | |
6104 | ("r-biocgenerics" ,r-biocgenerics))) | |
6105 | (home-page "https://bioconductor.org/packages/copynumber") | |
6106 | (synopsis "Segmentation of single- and multi-track copy number data") | |
6107 | (description | |
6108 | "This package segments single- and multi-track copy number data by a | |
6109 | penalized least squares regression method.") | |
6110 | (license license:artistic2.0))) | |
6111 | ||
07a664cd RW |
6112 | (define-public r-geneplotter |
6113 | (package | |
6114 | (name "r-geneplotter") | |
cb4d3ff2 | 6115 | (version "1.56.0") |
07a664cd RW |
6116 | (source |
6117 | (origin | |
6118 | (method url-fetch) | |
6119 | (uri (bioconductor-uri "geneplotter" version)) | |
6120 | (sha256 | |
6121 | (base32 | |
cb4d3ff2 | 6122 | "1z3g7frc1iviwrsv2dlm4nqvkc0685h4va0388yfxn102ln8wwma")))) |
07a664cd RW |
6123 | (build-system r-build-system) |
6124 | (propagated-inputs | |
6125 | `(("r-annotate" ,r-annotate) | |
6126 | ("r-annotationdbi" ,r-annotationdbi) | |
6127 | ("r-biobase" ,r-biobase) | |
6128 | ("r-biocgenerics" ,r-biocgenerics) | |
6129 | ("r-lattice" ,r-lattice) | |
6130 | ("r-rcolorbrewer" ,r-rcolorbrewer))) | |
5713bbf1 | 6131 | (home-page "https://bioconductor.org/packages/geneplotter") |
07a664cd RW |
6132 | (synopsis "Graphics functions for genomic data") |
6133 | (description | |
6134 | "This package provides functions for plotting genomic data.") | |
6135 | (license license:artistic2.0))) | |
6136 | ||
2301fd3e RW |
6137 | (define-public r-genefilter |
6138 | (package | |
6139 | (name "r-genefilter") | |
554fac74 | 6140 | (version "1.60.0") |
2301fd3e RW |
6141 | (source |
6142 | (origin | |
6143 | (method url-fetch) | |
6144 | (uri (bioconductor-uri "genefilter" version)) | |
6145 | (sha256 | |
6146 | (base32 | |
554fac74 | 6147 | "173swlg6gj4kdllbqvyiw5dggbcxiwlwpqmllsv4dxzn7h25i3g7")))) |
2301fd3e RW |
6148 | (build-system r-build-system) |
6149 | (native-inputs | |
6150 | `(("gfortran" ,gfortran))) | |
6151 | (propagated-inputs | |
6152 | `(("r-annotate" ,r-annotate) | |
6153 | ("r-annotationdbi" ,r-annotationdbi) | |
6154 | ("r-biobase" ,r-biobase) | |
aeb64f3c RW |
6155 | ("r-s4vectors" ,r-s4vectors) |
6156 | ("r-survival" ,r-survival))) | |
5713bbf1 | 6157 | (home-page "https://bioconductor.org/packages/genefilter") |
2301fd3e RW |
6158 | (synopsis "Filter genes from high-throughput experiments") |
6159 | (description | |
6160 | "This package provides basic functions for filtering genes from | |
6161 | high-throughput sequencing experiments.") | |
6162 | (license license:artistic2.0))) | |
6163 | ||
ad34f0ac RW |
6164 | (define-public r-deseq2 |
6165 | (package | |
6166 | (name "r-deseq2") | |
058644c0 | 6167 | (version "1.18.1") |
ad34f0ac RW |
6168 | (source |
6169 | (origin | |
6170 | (method url-fetch) | |
6171 | (uri (bioconductor-uri "DESeq2" version)) | |
6172 | (sha256 | |
6173 | (base32 | |
058644c0 | 6174 | "1iyimg1s0x5pdmvl8x08s8h0v019y0nhjzs50chagbpk2x91fsmv")))) |
ad34f0ac RW |
6175 | (properties `((upstream-name . "DESeq2"))) |
6176 | (build-system r-build-system) | |
ad34f0ac RW |
6177 | (propagated-inputs |
6178 | `(("r-biobase" ,r-biobase) | |
6179 | ("r-biocgenerics" ,r-biocgenerics) | |
6180 | ("r-biocparallel" ,r-biocparallel) | |
6181 | ("r-genefilter" ,r-genefilter) | |
6182 | ("r-geneplotter" ,r-geneplotter) | |
6183 | ("r-genomicranges" ,r-genomicranges) | |
6184 | ("r-ggplot2" ,r-ggplot2) | |
6185 | ("r-hmisc" ,r-hmisc) | |
6186 | ("r-iranges" ,r-iranges) | |
6187 | ("r-locfit" ,r-locfit) | |
6188 | ("r-rcpp" ,r-rcpp) | |
6189 | ("r-rcpparmadillo" ,r-rcpparmadillo) | |
6190 | ("r-s4vectors" ,r-s4vectors) | |
6191 | ("r-summarizedexperiment" ,r-summarizedexperiment))) | |
5713bbf1 | 6192 | (home-page "https://bioconductor.org/packages/DESeq2") |
ad34f0ac RW |
6193 | (synopsis "Differential gene expression analysis") |
6194 | (description | |
6195 | "This package provides functions to estimate variance-mean dependence in | |
6196 | count data from high-throughput nucleotide sequencing assays and test for | |
6197 | differential expression based on a model using the negative binomial | |
6198 | distribution.") | |
6199 | (license license:lgpl3+))) | |
6200 | ||
86763fdd RW |
6201 | (define-public r-dexseq |
6202 | (package | |
6203 | (name "r-dexseq") | |
b1808932 | 6204 | (version "1.24.3") |
86763fdd RW |
6205 | (source |
6206 | (origin | |
6207 | (method url-fetch) | |
6208 | (uri (bioconductor-uri "DEXSeq" version)) | |
6209 | (sha256 | |
6210 | (base32 | |
b1808932 | 6211 | "0xip73hlbr3zry9d7ly9vvvsbb3xjcmfa09lr9fdy528dwjrf084")))) |
86763fdd RW |
6212 | (properties `((upstream-name . "DEXSeq"))) |
6213 | (build-system r-build-system) | |
6214 | (propagated-inputs | |
6215 | `(("r-annotationdbi" ,r-annotationdbi) | |
6216 | ("r-biobase" ,r-biobase) | |
6217 | ("r-biocgenerics" ,r-biocgenerics) | |
6218 | ("r-biocparallel" ,r-biocparallel) | |
6219 | ("r-biomart" ,r-biomart) | |
6220 | ("r-deseq2" ,r-deseq2) | |
6221 | ("r-genefilter" ,r-genefilter) | |
6222 | ("r-geneplotter" ,r-geneplotter) | |
6223 | ("r-genomicranges" ,r-genomicranges) | |
6224 | ("r-hwriter" ,r-hwriter) | |
6225 | ("r-iranges" ,r-iranges) | |
6226 | ("r-rcolorbrewer" ,r-rcolorbrewer) | |
6227 | ("r-rsamtools" ,r-rsamtools) | |
6228 | ("r-s4vectors" ,r-s4vectors) | |
6229 | ("r-statmod" ,r-statmod) | |
6230 | ("r-stringr" ,r-stringr) | |
6231 | ("r-summarizedexperiment" ,r-summarizedexperiment))) | |
5713bbf1 | 6232 | (home-page "https://bioconductor.org/packages/DEXSeq") |
86763fdd RW |
6233 | (synopsis "Inference of differential exon usage in RNA-Seq") |
6234 | (description | |
6235 | "This package is focused on finding differential exon usage using RNA-seq | |
6236 | exon counts between samples with different experimental designs. It provides | |
6237 | functions that allows the user to make the necessary statistical tests based | |
6238 | on a model that uses the negative binomial distribution to estimate the | |
6239 | variance between biological replicates and generalized linear models for | |
6240 | testing. The package also provides functions for the visualization and | |
6241 | exploration of the results.") | |
6242 | (license license:gpl3+))) | |
6243 | ||
e8163773 RW |
6244 | (define-public r-annotationforge |
6245 | (package | |
6246 | (name "r-annotationforge") | |
727706ad | 6247 | (version "1.20.0") |
e8163773 RW |
6248 | (source |
6249 | (origin | |
6250 | (method url-fetch) | |
6251 | (uri (bioconductor-uri "AnnotationForge" version)) | |
6252 | (sha256 | |
6253 | (base32 | |
727706ad | 6254 | "01vbrf76vqfvxh6vpfxkjwccxggnha3byqzj333glqz2b6kwx5q1")))) |
e8163773 RW |
6255 | (properties |
6256 | `((upstream-name . "AnnotationForge"))) | |
6257 | (build-system r-build-system) | |
6258 | (propagated-inputs | |
6259 | `(("r-annotationdbi" ,r-annotationdbi) | |
6260 | ("r-biobase" ,r-biobase) | |
6261 | ("r-biocgenerics" ,r-biocgenerics) | |
6262 | ("r-dbi" ,r-dbi) | |
55cd914c | 6263 | ("r-rcurl" ,r-rcurl) |
e8163773 RW |
6264 | ("r-rsqlite" ,r-rsqlite) |
6265 | ("r-s4vectors" ,r-s4vectors) | |
6266 | ("r-xml" ,r-xml))) | |
5713bbf1 | 6267 | (home-page "https://bioconductor.org/packages/AnnotationForge") |
e8163773 RW |
6268 | (synopsis "Code for building annotation database packages") |
6269 | (description | |
6270 | "This package provides code for generating Annotation packages and their | |
6271 | databases. Packages produced are intended to be used with AnnotationDbi.") | |
6272 | (license license:artistic2.0))) | |
6273 | ||
cd9e7dc7 RW |
6274 | (define-public r-rbgl |
6275 | (package | |
6276 | (name "r-rbgl") | |
c25154e5 | 6277 | (version "1.54.0") |
cd9e7dc7 RW |
6278 | (source |
6279 | (origin | |
6280 | (method url-fetch) | |
6281 | (uri (bioconductor-uri "RBGL" version)) | |
6282 | (sha256 | |
6283 | (base32 | |
c25154e5 | 6284 | "18jad23i3899ypv4bg3l47cvvs3qnj1pqis2p9x0135yv5y6wnv7")))) |
cd9e7dc7 RW |
6285 | (properties `((upstream-name . "RBGL"))) |
6286 | (build-system r-build-system) | |
6287 | (propagated-inputs `(("r-graph" ,r-graph))) | |
5713bbf1 | 6288 | (home-page "https://www.bioconductor.org/packages/RBGL") |
cd9e7dc7 RW |
6289 | (synopsis "Interface to the Boost graph library") |
6290 | (description | |
6291 | "This package provides a fairly extensive and comprehensive interface to | |
6292 | the graph algorithms contained in the Boost library.") | |
6293 | (license license:artistic2.0))) | |
6294 | ||
ad740ff8 RW |
6295 | (define-public r-gseabase |
6296 | (package | |
6297 | (name "r-gseabase") | |
4220ab0c | 6298 | (version "1.40.1") |
ad740ff8 RW |
6299 | (source |
6300 | (origin | |
6301 | (method url-fetch) | |
6302 | (uri (bioconductor-uri "GSEABase" version)) | |
6303 | (sha256 | |
6304 | (base32 | |
4220ab0c | 6305 | "10cmjxahg2plwacfan6g0k8cwyzya96ypc7m1r79gwqkyykxw5fz")))) |
ad740ff8 RW |
6306 | (properties `((upstream-name . "GSEABase"))) |
6307 | (build-system r-build-system) | |
6308 | (propagated-inputs | |
6309 | `(("r-annotate" ,r-annotate) | |
6310 | ("r-annotationdbi" ,r-annotationdbi) | |
6311 | ("r-biobase" ,r-biobase) | |
6312 | ("r-biocgenerics" ,r-biocgenerics) | |
6313 | ("r-graph" ,r-graph) | |
6314 | ("r-xml" ,r-xml))) | |
5713bbf1 | 6315 | (home-page "https://bioconductor.org/packages/GSEABase") |
ad740ff8 RW |
6316 | (synopsis "Gene set enrichment data structures and methods") |
6317 | (description | |
6318 | "This package provides classes and methods to support @dfn{Gene Set | |
6319 | Enrichment Analysis} (GSEA).") | |
6320 | (license license:artistic2.0))) | |
6321 | ||
1a1931f7 RW |
6322 | (define-public r-category |
6323 | (package | |
6324 | (name "r-category") | |
2404cc42 | 6325 | (version "2.44.0") |
1a1931f7 RW |
6326 | (source |
6327 | (origin | |
6328 | (method url-fetch) | |
6329 | (uri (bioconductor-uri "Category" version)) | |
6330 | (sha256 | |
6331 | (base32 | |
2404cc42 | 6332 | "0mkav04vbla0xfa0dssxdd0rjs589sxi83xklf5iq5hj3dm8y0i8")))) |
1a1931f7 RW |
6333 | (properties `((upstream-name . "Category"))) |
6334 | (build-system r-build-system) | |
6335 | (propagated-inputs | |
6336 | `(("r-annotate" ,r-annotate) | |
6337 | ("r-annotationdbi" ,r-annotationdbi) | |
6338 | ("r-biobase" ,r-biobase) | |
6339 | ("r-biocgenerics" ,r-biocgenerics) | |
6340 | ("r-genefilter" ,r-genefilter) | |
6341 | ("r-graph" ,r-graph) | |
6342 | ("r-gseabase" ,r-gseabase) | |
6343 | ("r-matrix" ,r-matrix) | |
6344 | ("r-rbgl" ,r-rbgl) | |
2404cc42 | 6345 | ("r-dbi" ,r-dbi))) |
5713bbf1 | 6346 | (home-page "https://bioconductor.org/packages/Category") |
1a1931f7 RW |
6347 | (synopsis "Category analysis") |
6348 | (description | |
6349 | "This package provides a collection of tools for performing category | |
6350 | analysis.") | |
6351 | (license license:artistic2.0))) | |
6352 | ||
89f40c5e RW |
6353 | (define-public r-gostats |
6354 | (package | |
6355 | (name "r-gostats") | |
eb3f5cc7 | 6356 | (version "2.44.0") |
89f40c5e RW |
6357 | (source |
6358 | (origin | |
6359 | (method url-fetch) | |
6360 | (uri (bioconductor-uri "GOstats" version)) | |
6361 | (sha256 | |
6362 | (base32 | |
eb3f5cc7 | 6363 | "04gqfdlx9fxf97qf0l28x4aaqvl10n6v58qiz5fiaw05sbj1pf1i")))) |
89f40c5e RW |
6364 | (properties `((upstream-name . "GOstats"))) |
6365 | (build-system r-build-system) | |
6366 | (propagated-inputs | |
6367 | `(("r-annotate" ,r-annotate) | |
6368 | ("r-annotationdbi" ,r-annotationdbi) | |
6369 | ("r-annotationforge" ,r-annotationforge) | |
6370 | ("r-biobase" ,r-biobase) | |
6371 | ("r-category" ,r-category) | |
6372 | ("r-go-db" ,r-go-db) | |
6373 | ("r-graph" ,r-graph) | |
eb3f5cc7 | 6374 | ("r-rgraphviz" ,r-rgraphviz) |
89f40c5e | 6375 | ("r-rbgl" ,r-rbgl))) |
5713bbf1 | 6376 | (home-page "https://bioconductor.org/packages/GOstats") |
89f40c5e RW |
6377 | (synopsis "Tools for manipulating GO and microarrays") |
6378 | (description | |
6379 | "This package provides a set of tools for interacting with GO and | |
6380 | microarray data. A variety of basic manipulation tools for graphs, hypothesis | |
6381 | testing and other simple calculations.") | |
6382 | (license license:artistic2.0))) | |
6383 | ||
cb99d457 RW |
6384 | (define-public r-shortread |
6385 | (package | |
6386 | (name "r-shortread") | |
99e4b11d | 6387 | (version "1.36.1") |
cb99d457 RW |
6388 | (source |
6389 | (origin | |
6390 | (method url-fetch) | |
6391 | (uri (bioconductor-uri "ShortRead" version)) | |
6392 | (sha256 | |
6393 | (base32 | |
99e4b11d | 6394 | "1cyv47632m9ljkxfsvnvmd19sb607ys5kz8fwh6v39dnw16g0a6m")))) |
cb99d457 RW |
6395 | (properties `((upstream-name . "ShortRead"))) |
6396 | (build-system r-build-system) | |
6397 | (inputs | |
6398 | `(("zlib" ,zlib))) | |
6399 | (propagated-inputs | |
6400 | `(("r-biobase" ,r-biobase) | |
6401 | ("r-biocgenerics" ,r-biocgenerics) | |
6402 | ("r-biocparallel" ,r-biocparallel) | |
6403 | ("r-biostrings" ,r-biostrings) | |
6404 | ("r-genomeinfodb" ,r-genomeinfodb) | |
6405 | ("r-genomicalignments" ,r-genomicalignments) | |
6406 | ("r-genomicranges" ,r-genomicranges) | |
6407 | ("r-hwriter" ,r-hwriter) | |
6408 | ("r-iranges" ,r-iranges) | |
6409 | ("r-lattice" ,r-lattice) | |
6410 | ("r-latticeextra" ,r-latticeextra) | |
6411 | ("r-rsamtools" ,r-rsamtools) | |
6412 | ("r-s4vectors" ,r-s4vectors) | |
6413 | ("r-xvector" ,r-xvector) | |
6414 | ("r-zlibbioc" ,r-zlibbioc))) | |
5713bbf1 | 6415 | (home-page "https://bioconductor.org/packages/ShortRead") |
cb99d457 RW |
6416 | (synopsis "FASTQ input and manipulation tools") |
6417 | (description | |
6418 | "This package implements sampling, iteration, and input of FASTQ files. | |
6419 | It includes functions for filtering and trimming reads, and for generating a | |
6420 | quality assessment report. Data are represented as | |
6421 | @code{DNAStringSet}-derived objects, and easily manipulated for a diversity of | |
6422 | purposes. The package also contains legacy support for early single-end, | |
6423 | ungapped alignment formats.") | |
6424 | (license license:artistic2.0))) | |
6425 | ||
7f903d73 RW |
6426 | (define-public r-systempiper |
6427 | (package | |
6428 | (name "r-systempiper") | |
b5375525 | 6429 | (version "1.12.0") |
7f903d73 RW |
6430 | (source |
6431 | (origin | |
6432 | (method url-fetch) | |
6433 | (uri (bioconductor-uri "systemPipeR" version)) | |
6434 | (sha256 | |
6435 | (base32 | |
b5375525 | 6436 | "11mj8pjq5vj25768vmagpzv74fvi3p3kdk5zdlznqyiaggri04cv")))) |
7f903d73 RW |
6437 | (properties `((upstream-name . "systemPipeR"))) |
6438 | (build-system r-build-system) | |
6439 | (propagated-inputs | |
6440 | `(("r-annotate" ,r-annotate) | |
6441 | ("r-batchjobs" ,r-batchjobs) | |
6442 | ("r-biocgenerics" ,r-biocgenerics) | |
6443 | ("r-biostrings" ,r-biostrings) | |
6444 | ("r-deseq2" ,r-deseq2) | |
6445 | ("r-edger" ,r-edger) | |
6446 | ("r-genomicfeatures" ,r-genomicfeatures) | |
6447 | ("r-genomicranges" ,r-genomicranges) | |
6448 | ("r-ggplot2" ,r-ggplot2) | |
6449 | ("r-go-db" ,r-go-db) | |
6450 | ("r-gostats" ,r-gostats) | |
6451 | ("r-limma" ,r-limma) | |
6452 | ("r-pheatmap" ,r-pheatmap) | |
6453 | ("r-rjson" ,r-rjson) | |
6454 | ("r-rsamtools" ,r-rsamtools) | |
6455 | ("r-shortread" ,r-shortread) | |
6456 | ("r-summarizedexperiment" ,r-summarizedexperiment) | |
6457 | ("r-variantannotation" ,r-variantannotation))) | |
6458 | (home-page "https://github.com/tgirke/systemPipeR") | |
6459 | (synopsis "Next generation sequencing workflow and reporting environment") | |
6460 | (description | |
6461 | "This R package provides tools for building and running automated | |
6462 | end-to-end analysis workflows for a wide range of @dfn{next generation | |
6463 | sequence} (NGS) applications such as RNA-Seq, ChIP-Seq, VAR-Seq and Ribo-Seq. | |
6464 | Important features include a uniform workflow interface across different NGS | |
6465 | applications, automated report generation, and support for running both R and | |
6466 | command-line software, such as NGS aligners or peak/variant callers, on local | |
6467 | computers or compute clusters. Efficient handling of complex sample sets and | |
6468 | experimental designs is facilitated by a consistently implemented sample | |
6469 | annotation infrastructure.") | |
6470 | (license license:artistic2.0))) | |
6471 | ||
684f29bd RW |
6472 | (define-public r-grohmm |
6473 | (package | |
6474 | (name "r-grohmm") | |
704fe4d1 | 6475 | (version "1.12.0") |
684f29bd RW |
6476 | (source |
6477 | (origin | |
6478 | (method url-fetch) | |
6479 | (uri (bioconductor-uri "groHMM" version)) | |
6480 | (sha256 | |
6481 | (base32 | |
704fe4d1 | 6482 | "0cjkj0ypyc4dfi9s8dh88kh6q4xlpnc0wal7njg4b4gqj0l2hva7")))) |
684f29bd RW |
6483 | (properties `((upstream-name . "groHMM"))) |
6484 | (build-system r-build-system) | |
6485 | (propagated-inputs | |
6486 | `(("r-genomeinfodb" ,r-genomeinfodb) | |
6487 | ("r-genomicalignments" ,r-genomicalignments) | |
6488 | ("r-genomicranges" ,r-genomicranges) | |
6489 | ("r-iranges" ,r-iranges) | |
aeb64f3c | 6490 | ("r-mass" ,r-mass) |
684f29bd RW |
6491 | ("r-rtracklayer" ,r-rtracklayer) |
6492 | ("r-s4vectors" ,r-s4vectors))) | |
6493 | (home-page "https://github.com/Kraus-Lab/groHMM") | |
6494 | (synopsis "GRO-seq analysis pipeline") | |
6495 | (description | |
6496 | "This package provides a pipeline for the analysis of GRO-seq data.") | |
6497 | (license license:gpl3+))) | |
6498 | ||
f3cfe451 RW |
6499 | (define-public r-txdb-hsapiens-ucsc-hg19-knowngene |
6500 | (package | |
6501 | (name "r-txdb-hsapiens-ucsc-hg19-knowngene") | |
6502 | (version "3.2.2") | |
6503 | (source (origin | |
6504 | (method url-fetch) | |
6505 | ;; We cannot use bioconductor-uri here because this tarball is | |
6506 | ;; located under "data/annotation/" instead of "bioc/". | |
5713bbf1 | 6507 | (uri (string-append "https://bioconductor.org/packages/" |
f3cfe451 RW |
6508 | "release/data/annotation/src/contrib" |
6509 | "/TxDb.Hsapiens.UCSC.hg19.knownGene_" | |
6510 | version ".tar.gz")) | |
6511 | (sha256 | |
6512 | (base32 | |
6513 | "1sajhcqqwazgz2lqbik7rd935i7kpnh08zxbp2ra10j72yqy4g86")))) | |
6514 | (properties | |
6515 | `((upstream-name . "TxDb.Hsapiens.UCSC.hg19.knownGene"))) | |
6516 | (build-system r-build-system) | |
6517 | ;; As this package provides little more than a very large data file it | |
6518 | ;; doesn't make sense to build substitutes. | |
6519 | (arguments `(#:substitutable? #f)) | |
6520 | (propagated-inputs | |
6521 | `(("r-genomicfeatures" ,r-genomicfeatures))) | |
6522 | (home-page | |
5713bbf1 | 6523 | "https://bioconductor.org/packages/TxDb.Hsapiens.UCSC.hg19.knownGene/") |
f3cfe451 RW |
6524 | (synopsis "Annotation package for human genome in TxDb format") |
6525 | (description | |
6526 | "This package provides an annotation database of Homo sapiens genome | |
6527 | data. It is derived from the UCSC hg19 genome and based on the \"knownGene\" | |
6528 | track. The database is exposed as a @code{TxDb} object.") | |
6529 | (license license:artistic2.0))) | |
6530 | ||
325c039c RJ |
6531 | (define-public r-sparql |
6532 | (package | |
6533 | (name "r-sparql") | |
6534 | (version "1.16") | |
6535 | (source (origin | |
6536 | (method url-fetch) | |
6537 | (uri (cran-uri "SPARQL" version)) | |
6538 | (sha256 | |
6539 | (base32 | |
6540 | "0gak1q06yyhdmcxb2n3v0h9gr1vqd0viqji52wpw211qp6r6dcrc")))) | |
6541 | (properties `((upstream-name . "SPARQL"))) | |
6542 | (build-system r-build-system) | |
6543 | (propagated-inputs | |
6544 | `(("r-rcurl" ,r-rcurl) | |
6545 | ("r-xml" ,r-xml))) | |
e9960d8c | 6546 | (home-page "https://cran.r-project.org/web/packages/SPARQL") |
325c039c RJ |
6547 | (synopsis "SPARQL client for R") |
6548 | (description "This package provides an interface to use SPARQL to pose | |
6549 | SELECT or UPDATE queries to an end-point.") | |
6550 | ;; The only license indication is found in the DESCRIPTION file, | |
6551 | ;; which states GPL-3. So we cannot assume GPLv3+. | |
6552 | (license license:gpl3))) | |
6553 | ||
a2950fa4 BW |
6554 | (define-public vsearch |
6555 | (package | |
6556 | (name "vsearch") | |
369eee87 | 6557 | (version "2.7.1") |
a2950fa4 BW |
6558 | (source |
6559 | (origin | |
6560 | (method url-fetch) | |
6561 | (uri (string-append | |
6562 | "https://github.com/torognes/vsearch/archive/v" | |
6563 | version ".tar.gz")) | |
6564 | (file-name (string-append name "-" version ".tar.gz")) | |
6565 | (sha256 | |
6566 | (base32 | |
369eee87 | 6567 | "0jlzfgh79fzmb4g7sngzdjjsjyc37icvs1k7vmc2ksxglj6x5i7f")) |
206af46f | 6568 | (patches (search-patches "vsearch-unbundle-cityhash.patch")) |
a2950fa4 BW |
6569 | (snippet |
6570 | '(begin | |
206af46f BW |
6571 | ;; Remove bundled cityhash sources. The vsearch source is adjusted |
6572 | ;; for this in the patch. | |
cf6edaba BW |
6573 | (delete-file "src/city.h") |
6574 | (delete-file "src/citycrc.h") | |
6575 | (delete-file "src/city.cc") | |
a2950fa4 BW |
6576 | #t)))) |
6577 | (build-system gnu-build-system) | |
6578 | (arguments | |
6579 | `(#:phases | |
6580 | (modify-phases %standard-phases | |
d10092b8 KK |
6581 | (add-after 'unpack 'autogen |
6582 | (lambda _ (zero? (system* "autoreconf" "-vif"))))))) | |
a2950fa4 BW |
6583 | (inputs |
6584 | `(("zlib" ,zlib) | |
6585 | ("bzip2" ,bzip2) | |
6586 | ("cityhash" ,cityhash))) | |
6587 | (native-inputs | |
6588 | `(("autoconf" ,autoconf) | |
6589 | ("automake" ,automake))) | |
6590 | (synopsis "Sequence search tools for metagenomics") | |
6591 | (description | |
6592 | "VSEARCH supports DNA sequence searching, clustering, chimera detection, | |
6593 | dereplication, pairwise alignment, shuffling, subsampling, sorting and | |
6594 | masking. The tool takes advantage of parallelism in the form of SIMD | |
6595 | vectorization as well as multiple threads to perform accurate alignments at | |
6596 | high speed. VSEARCH uses an optimal global aligner (full dynamic programming | |
6597 | Needleman-Wunsch).") | |
6598 | (home-page "https://github.com/torognes/vsearch") | |
6f04e515 BW |
6599 | ;; vsearch uses non-portable SSE intrinsics so building fails on other |
6600 | ;; platforms. | |
6601 | (supported-systems '("x86_64-linux")) | |
a2950fa4 BW |
6602 | ;; Dual licensed; also includes public domain source. |
6603 | (license (list license:gpl3 license:bsd-2)))) | |
6604 | ||
07837874 RW |
6605 | (define-public pardre |
6606 | (package | |
6607 | (name "pardre") | |
7922ab8f BW |
6608 | ;; The source of 1.1.5 changed in place, so we append "-1" to the version. |
6609 | (version "1.1.5-1") | |
07837874 RW |
6610 | (source |
6611 | (origin | |
6612 | (method url-fetch) | |
6613 | (uri (string-append "mirror://sourceforge/pardre/ParDRe-rel" | |
7922ab8f | 6614 | "1.1.5" ".tar.gz")) |
07837874 RW |
6615 | (sha256 |
6616 | (base32 | |
7922ab8f | 6617 | "17j73nc0viq4f6qj50nrndsrif5d6b71q8fl87m54psiv0ilns2b")))) |
07837874 RW |
6618 | (build-system gnu-build-system) |
6619 | (arguments | |
6620 | `(#:tests? #f ; no tests included | |
6621 | #:phases | |
6622 | (modify-phases %standard-phases | |
6623 | (delete 'configure) | |
6624 | (replace 'install | |
6625 | (lambda* (#:key outputs #:allow-other-keys) | |
6626 | (let ((bin (string-append (assoc-ref outputs "out") "/bin"))) | |
07837874 RW |
6627 | (install-file "ParDRe" bin) |
6628 | #t)))))) | |
6629 | (inputs | |
6630 | `(("openmpi" ,openmpi) | |
6631 | ("zlib" ,zlib))) | |
6632 | (synopsis "Parallel tool to remove duplicate DNA reads") | |
6633 | (description | |
6634 | "ParDRe is a parallel tool to remove duplicate genetic sequence reads. | |
6635 | Duplicate reads can be seen as identical or nearly identical sequences with | |
6636 | some mismatches. This tool lets users avoid the analysis of unnecessary | |
6637 | reads, reducing the time of subsequent procedures with the | |
6638 | dataset (e.g. assemblies, mappings, etc.). The tool is implemented with MPI | |
6639 | in order to exploit the parallel capabilities of multicore clusters. It is | |
6640 | faster than multithreaded counterparts (end of 2015) for the same number of | |
6641 | cores and, thanks to the message-passing technology, it can be executed on | |
6642 | clusters.") | |
6643 | (home-page "https://sourceforge.net/projects/pardre/") | |
6644 | (license license:gpl3+))) | |
6645 | ||
e4a44a6a BW |
6646 | (define-public ruby-bio-kseq |
6647 | (package | |
6648 | (name "ruby-bio-kseq") | |
6649 | (version "0.0.2") | |
6650 | (source | |
6651 | (origin | |
6652 | (method url-fetch) | |
6653 | (uri (rubygems-uri "bio-kseq" version)) | |
6654 | (sha256 | |
6655 | (base32 | |
6656 | "1xyaha46khb5jc6wzkbf7040jagac49jbimn0vcrzid0j8jdikrz")))) | |
6657 | (build-system ruby-build-system) | |
6658 | (arguments | |
6659 | `(#:test-target "spec")) | |
6660 | (native-inputs | |
6661 | `(("bundler" ,bundler) | |
6662 | ("ruby-rspec" ,ruby-rspec) | |
6663 | ("ruby-rake-compiler" ,ruby-rake-compiler))) | |
6664 | (inputs | |
6665 | `(("zlib" ,zlib))) | |
6666 | (synopsis "Ruby bindings for the kseq.h FASTA/Q parser") | |
6667 | (description | |
6668 | "@code{Bio::Kseq} provides ruby bindings to the @code{kseq.h} FASTA and | |
6669 | FASTQ parsing code. It provides a fast iterator over sequences and their | |
6670 | quality scores.") | |
6671 | (home-page "https://github.com/gusevfe/bio-kseq") | |
6672 | (license license:expat))) | |
6673 | ||
9c38b540 PP |
6674 | (define-public bio-locus |
6675 | (package | |
6676 | (name "bio-locus") | |
6677 | (version "0.0.7") | |
6678 | (source | |
6679 | (origin | |
6680 | (method url-fetch) | |
6681 | (uri (rubygems-uri "bio-locus" version)) | |
6682 | (sha256 | |
6683 | (base32 | |
6684 | "02vmrxyimkj9sahsp4zhfhnmbvz6dbbqz1y01vglf8cbwvkajfl0")))) | |
6685 | (build-system ruby-build-system) | |
6686 | (native-inputs | |
6687 | `(("ruby-rspec" ,ruby-rspec))) | |
6688 | (synopsis "Tool for fast querying of genome locations") | |
6689 | (description | |
6690 | "Bio-locus is a tabix-like tool for fast querying of genome | |
6691 | locations. Many file formats in bioinformatics contain records that | |
6692 | start with a chromosome name and a position for a SNP, or a start-end | |
6693 | position for indels. Bio-locus allows users to store this chr+pos or | |
6694 | chr+pos+alt information in a database.") | |
6695 | (home-page "https://github.com/pjotrp/bio-locus") | |
6696 | (license license:expat))) | |
edb15985 | 6697 | |
b2bddb07 PP |
6698 | (define-public bio-blastxmlparser |
6699 | (package | |
6700 | (name "bio-blastxmlparser") | |
6701 | (version "2.0.4") | |
6702 | (source (origin | |
6703 | (method url-fetch) | |
6704 | (uri (rubygems-uri "bio-blastxmlparser" version)) | |
6705 | (sha256 | |
6706 | (base32 | |
6707 | "1wf4qygcmdjgcqm6flmvsagfr1gs9lf63mj32qv3z1f481zc5692")))) | |
6708 | (build-system ruby-build-system) | |
6709 | (propagated-inputs | |
6710 | `(("ruby-bio-logger" ,ruby-bio-logger) | |
6711 | ("ruby-nokogiri" ,ruby-nokogiri))) | |
6712 | (inputs | |
6713 | `(("ruby-rspec" ,ruby-rspec))) | |
6714 | (synopsis "Fast big data BLAST XML parser and library") | |
6715 | (description | |
6716 | "Very fast parallel big-data BLAST XML file parser which can be used as | |
6717 | command line utility. Use blastxmlparser to: Parse BLAST XML; filter output; | |
6718 | generate FASTA, JSON, YAML, RDF, JSON-LD, HTML, CSV, tabular output etc.") | |
7bf837fd | 6719 | (home-page "https://github.com/pjotrp/blastxmlparser") |
b2bddb07 PP |
6720 | (license license:expat))) |
6721 | ||
edb15985 PP |
6722 | (define-public bioruby |
6723 | (package | |
6724 | (name "bioruby") | |
dbf9d371 | 6725 | (version "1.5.1") |
edb15985 PP |
6726 | (source |
6727 | (origin | |
6728 | (method url-fetch) | |
6729 | (uri (rubygems-uri "bio" version)) | |
6730 | (sha256 | |
6731 | (base32 | |
dbf9d371 | 6732 | "0hdl0789c9n4mprnx5pgd46bfwl8d000rqpamj5h6kkjgspijv49")))) |
edb15985 PP |
6733 | (build-system ruby-build-system) |
6734 | (propagated-inputs | |
6735 | `(("ruby-libxml" ,ruby-libxml))) | |
6736 | (native-inputs | |
6737 | `(("which" ,which))) ; required for test phase | |
6738 | (arguments | |
6739 | `(#:phases | |
6740 | (modify-phases %standard-phases | |
6741 | (add-before 'build 'patch-test-command | |
6742 | (lambda _ | |
6743 | (substitute* '("test/functional/bio/test_command.rb") | |
6744 | (("/bin/sh") (which "sh"))) | |
6745 | (substitute* '("test/functional/bio/test_command.rb") | |
6746 | (("/bin/ls") (which "ls"))) | |
6747 | (substitute* '("test/functional/bio/test_command.rb") | |
6748 | (("which") (which "which"))) | |
6749 | (substitute* '("test/functional/bio/test_command.rb", | |
6750 | "test/data/command/echoarg2.sh") | |
6751 | (("/bin/echo") (which "echo"))) | |
6752 | #t))))) | |
6753 | (synopsis "Ruby library, shell and utilities for bioinformatics") | |
6754 | (description "BioRuby comes with a comprehensive set of Ruby development | |
6755 | tools and libraries for bioinformatics and molecular biology. BioRuby has | |
6756 | components for sequence analysis, pathway analysis, protein modelling and | |
6757 | phylogenetic analysis; it supports many widely used data formats and provides | |
6758 | easy access to databases, external programs and public web services, including | |
6759 | BLAST, KEGG, GenBank, MEDLINE and GO.") | |
6760 | (home-page "http://bioruby.org/") | |
6761 | ;; Code is released under Ruby license, except for setup | |
6762 | ;; (LGPLv2.1+) and scripts in samples (which have GPL2 and GPL2+) | |
6763 | (license (list license:ruby license:lgpl2.1+ license:gpl2+ )))) | |
a5002ae7 | 6764 | |
9fba89e8 RW |
6765 | (define-public r-acsnminer |
6766 | (package | |
6767 | (name "r-acsnminer") | |
0b54b4c9 | 6768 | (version "0.16.8.25") |
9fba89e8 RW |
6769 | (source (origin |
6770 | (method url-fetch) | |
6771 | (uri (cran-uri "ACSNMineR" version)) | |
6772 | (sha256 | |
6773 | (base32 | |
0b54b4c9 | 6774 | "0gh604s8qall6zfjlwcg2ilxjvz08dplf9k5g47idhv43scm748l")))) |
9fba89e8 RW |
6775 | (properties `((upstream-name . "ACSNMineR"))) |
6776 | (build-system r-build-system) | |
6777 | (propagated-inputs | |
6778 | `(("r-ggplot2" ,r-ggplot2) | |
6779 | ("r-gridextra" ,r-gridextra))) | |
e9960d8c | 6780 | (home-page "https://cran.r-project.org/web/packages/ACSNMineR") |
9fba89e8 RW |
6781 | (synopsis "Gene enrichment analysis") |
6782 | (description | |
6783 | "This package provides tools to compute and represent gene set enrichment | |
6784 | or depletion from your data based on pre-saved maps from the @dfn{Atlas of | |
6785 | Cancer Signalling Networks} (ACSN) or user imported maps. The gene set | |
6786 | enrichment can be run with hypergeometric test or Fisher exact test, and can | |
6787 | use multiple corrections. Visualization of data can be done either by | |
6788 | barplots or heatmaps.") | |
6789 | (license license:gpl2+))) | |
6790 | ||
d29b25c4 RW |
6791 | (define-public r-biocgenerics |
6792 | (package | |
6793 | (name "r-biocgenerics") | |
d61fc4e1 | 6794 | (version "0.24.0") |
d29b25c4 RW |
6795 | (source (origin |
6796 | (method url-fetch) | |
6797 | (uri (bioconductor-uri "BiocGenerics" version)) | |
6798 | (sha256 | |
6799 | (base32 | |
d61fc4e1 | 6800 | "03wxvhxyrhipbgcg83lqlfn7p9gbzzrnl48y0dq7303xgp232zai")))) |
d29b25c4 | 6801 | (properties |
1d216b6e | 6802 | `((upstream-name . "BiocGenerics"))) |
d29b25c4 | 6803 | (build-system r-build-system) |
5713bbf1 | 6804 | (home-page "https://bioconductor.org/packages/BiocGenerics") |
d29b25c4 RW |
6805 | (synopsis "S4 generic functions for Bioconductor") |
6806 | (description | |
6807 | "This package provides S4 generic functions needed by many Bioconductor | |
6808 | packages.") | |
6809 | (license license:artistic2.0))) | |
6810 | ||
eb24341f RJ |
6811 | (define-public r-biocinstaller |
6812 | (package | |
6813 | (name "r-biocinstaller") | |
32414616 | 6814 | (version "1.28.0") |
eb24341f RJ |
6815 | (source (origin |
6816 | (method url-fetch) | |
6817 | (uri (bioconductor-uri "BiocInstaller" version)) | |
6818 | (sha256 | |
6819 | (base32 | |
32414616 | 6820 | "19fga27bv6q9v5mpil74y76lahmnwvpg2h33rdx1r79nvljkd19d")))) |
eb24341f RJ |
6821 | (properties |
6822 | `((upstream-name . "BiocInstaller"))) | |
6823 | (build-system r-build-system) | |
5713bbf1 | 6824 | (home-page "https://bioconductor.org/packages/BiocInstaller") |
eb24341f RJ |
6825 | (synopsis "Install Bioconductor packages") |
6826 | (description "This package is used to install and update R packages from | |
6827 | Bioconductor, CRAN, and Github.") | |
6828 | (license license:artistic2.0))) | |
6829 | ||
207ce8fb RJ |
6830 | (define-public r-biocviews |
6831 | (package | |
6832 | (name "r-biocviews") | |
c7782c3f | 6833 | (version "1.46.0") |
207ce8fb RJ |
6834 | (source (origin |
6835 | (method url-fetch) | |
6836 | (uri (bioconductor-uri "biocViews" version)) | |
6837 | (sha256 | |
6838 | (base32 | |
c7782c3f | 6839 | "09zyqj1kqc089lmh9sliy0acanx9zimcasvp71dsrg2bqm08r1md")))) |
207ce8fb RJ |
6840 | (properties |
6841 | `((upstream-name . "biocViews"))) | |
6842 | (build-system r-build-system) | |
6843 | (propagated-inputs | |
6844 | `(("r-biobase" ,r-biobase) | |
6845 | ("r-graph" ,r-graph) | |
6846 | ("r-rbgl" ,r-rbgl) | |
6847 | ("r-rcurl" ,r-rcurl) | |
6848 | ("r-xml" ,r-xml) | |
207ce8fb | 6849 | ("r-runit" ,r-runit))) |
5713bbf1 | 6850 | (home-page "https://bioconductor.org/packages/biocViews") |
207ce8fb RJ |
6851 | (synopsis "Bioconductor package categorization helper") |
6852 | (description "The purpose of biocViews is to create HTML pages that | |
6853 | categorize packages in a Bioconductor package repository according to keywords, | |
6854 | also known as views, in a controlled vocabulary.") | |
6855 | (license license:artistic2.0))) | |
6856 | ||
2abfc5b8 RJ |
6857 | (define-public r-bookdown |
6858 | (package | |
9800f7d9 RW |
6859 | (name "r-bookdown") |
6860 | (version "0.7") | |
6861 | (source (origin | |
6862 | (method url-fetch) | |
6863 | (uri (cran-uri "bookdown" version)) | |
6864 | (sha256 | |
6865 | (base32 | |
6866 | "1b3fw1f41zph5yw3kynb47aijq53vhaa6mnnvxly72zamyzdf95q")))) | |
6867 | (build-system r-build-system) | |
6868 | (propagated-inputs | |
6869 | `(("r-htmltools" ,r-htmltools) | |
6870 | ("r-knitr" ,r-knitr) | |
6871 | ("r-rmarkdown" ,r-rmarkdown) | |
6872 | ("r-tinytex" ,r-tinytex) | |
6873 | ("r-yaml" ,r-yaml) | |
6874 | ("r-xfun" ,r-xfun) | |
6875 | ("ghc-pandoc" ,ghc-pandoc))) | |
6876 | (home-page "https://github.com/rstudio/bookdown") | |
6877 | (synopsis "Authoring books and technical documents with R markdown") | |
6878 | (description "This package provides output formats and utilities for | |
2abfc5b8 | 6879 | authoring books and technical documents with R Markdown.") |
9800f7d9 | 6880 | (license license:gpl3))) |
2abfc5b8 | 6881 | |
99df12cd RJ |
6882 | (define-public r-biocstyle |
6883 | (package | |
6884 | (name "r-biocstyle") | |
7665fb39 | 6885 | (version "2.6.1") |
99df12cd RJ |
6886 | (source (origin |
6887 | (method url-fetch) | |
6888 | (uri (bioconductor-uri "BiocStyle" version)) | |
6889 | (sha256 | |
6890 | (base32 | |
7665fb39 | 6891 | "03pp04pkcq99kdv2spzr995h2cxsza7l6w3d4gp4112m06prcybm")))) |
99df12cd RJ |
6892 | (properties |
6893 | `((upstream-name . "BiocStyle"))) | |
6894 | (build-system r-build-system) | |
3bef24c9 RJ |
6895 | (propagated-inputs |
6896 | `(("r-bookdown" ,r-bookdown) | |
6897 | ("r-knitr" ,r-knitr) | |
6898 | ("r-rmarkdown" ,r-rmarkdown) | |
6899 | ("r-yaml" ,r-yaml))) | |
5713bbf1 | 6900 | (home-page "https://bioconductor.org/packages/BiocStyle") |
99df12cd RJ |
6901 | (synopsis "Bioconductor formatting styles") |
6902 | (description "This package provides standard formatting styles for | |
6903 | Bioconductor PDF and HTML documents. Package vignettes illustrate use and | |
6904 | functionality.") | |
6905 | (license license:artistic2.0))) | |
6906 | ||
4644644a RJ |
6907 | (define-public r-bioccheck |
6908 | (package | |
6909 | (name "r-bioccheck") | |
7373b416 | 6910 | (version "1.14.0") |
4644644a RJ |
6911 | (source (origin |
6912 | (method url-fetch) | |
6913 | (uri (bioconductor-uri "BiocCheck" version)) | |
6914 | (sha256 | |
6915 | (base32 | |
7373b416 | 6916 | "1nzp8kgw13z9pgf885rplj6k37jcldfhbz0adqclxr2gq0yalmyx")))) |
4644644a RJ |
6917 | (properties |
6918 | `((upstream-name . "BiocCheck"))) | |
6919 | (build-system r-build-system) | |
6920 | (arguments | |
6921 | '(#:phases | |
6922 | (modify-phases %standard-phases | |
6923 | ;; This package can be used by calling BiocCheck(<package>) from | |
6924 | ;; within R, or by running R CMD BiocCheck <package>. This phase | |
6925 | ;; makes sure the latter works. For this to work, the BiocCheck | |
6926 | ;; script must be somewhere on the PATH (not the R bin directory). | |
6927 | (add-after 'install 'install-bioccheck-subcommand | |
6928 | (lambda* (#:key outputs #:allow-other-keys) | |
6929 | (let* ((out (assoc-ref outputs "out")) | |
6930 | (dest-dir (string-append out "/bin")) | |
6931 | (script-dir | |
6932 | (string-append out "/site-library/BiocCheck/script/"))) | |
6933 | (mkdir-p dest-dir) | |
6934 | (symlink (string-append script-dir "/checkBadDeps.R") | |
6935 | (string-append dest-dir "/checkBadDeps.R")) | |
6936 | (symlink (string-append script-dir "/BiocCheck") | |
6937 | (string-append dest-dir "/BiocCheck"))) | |
6938 | #t))))) | |
4644644a | 6939 | (propagated-inputs |
aeb64f3c RW |
6940 | `(("r-codetools" ,r-codetools) |
6941 | ("r-graph" ,r-graph) | |
4644644a RJ |
6942 | ("r-httr" ,r-httr) |
6943 | ("r-optparse" ,r-optparse) | |
4644644a | 6944 | ("r-biocinstaller" ,r-biocinstaller) |
7373b416 RW |
6945 | ("r-biocviews" ,r-biocviews) |
6946 | ("r-stringdist" ,r-stringdist))) | |
5713bbf1 | 6947 | (home-page "https://bioconductor.org/packages/BiocCheck") |
4644644a RJ |
6948 | (synopsis "Executes Bioconductor-specific package checks") |
6949 | (description "This package contains tools to perform additional quality | |
6950 | checks on R packages that are to be submitted to the Bioconductor repository.") | |
6951 | (license license:artistic2.0))) | |
6952 | ||
2acaaee5 RJ |
6953 | (define-public r-getopt |
6954 | (package | |
6955 | (name "r-getopt") | |
e8484711 | 6956 | (version "1.20.2") |
2acaaee5 RJ |
6957 | (source |
6958 | (origin | |
6959 | (method url-fetch) | |
6960 | (uri (cran-uri "getopt" version)) | |
6961 | (sha256 | |
6962 | (base32 | |
e8484711 | 6963 | "13p35lbpy7i578752fa71sbfvcsqw5qfa9p6kf8b5m3c5p9i4v1x")))) |
2acaaee5 RJ |
6964 | (build-system r-build-system) |
6965 | (home-page "https://github.com/trevorld/getopt") | |
6966 | (synopsis "Command-line option processor for R") | |
6967 | (description | |
6968 | "This package is designed to be used with Rscript to write shebang | |
6969 | scripts that accept short and long options. Many users will prefer to | |
6970 | use the packages @code{optparse} or @code{argparse} which add extra | |
6971 | features like automatically generated help options and usage texts, | |
6972 | support for default values, positional argument support, etc.") | |
6973 | (license license:gpl2+))) | |
6974 | ||
c79ad57a RJ |
6975 | (define-public r-optparse |
6976 | (package | |
6977 | (name "r-optparse") | |
7150f1c3 | 6978 | (version "1.4.4") |
c79ad57a RJ |
6979 | (source |
6980 | (origin | |
6981 | (method url-fetch) | |
6982 | (uri (cran-uri "optparse" version)) | |
6983 | (sha256 | |
6984 | (base32 | |
7150f1c3 | 6985 | "1ff4wmsszrb3spwfp7ynfs8w11qpy1sdzfxm1wk8dqqvdwris7qb")))) |
c79ad57a RJ |
6986 | (build-system r-build-system) |
6987 | (propagated-inputs | |
6988 | `(("r-getopt" ,r-getopt))) | |
6989 | (home-page | |
6990 | "https://github.com/trevorld/optparse") | |
6991 | (synopsis "Command line option parser") | |
6992 | (description | |
6993 | "This package provides a command line parser inspired by Python's | |
6994 | @code{optparse} library to be used with Rscript to write shebang scripts | |
6995 | that accept short and long options.") | |
6996 | (license license:gpl2+))) | |
6997 | ||
247d498a RJ |
6998 | (define-public r-dnacopy |
6999 | (package | |
7000 | (name "r-dnacopy") | |
94fd86e5 | 7001 | (version "1.52.0") |
247d498a RJ |
7002 | (source (origin |
7003 | (method url-fetch) | |
7004 | (uri (bioconductor-uri "DNAcopy" version)) | |
7005 | (sha256 | |
7006 | (base32 | |
94fd86e5 | 7007 | "127il5rlg1hzjlhwhs64x3nm18p00q1pd9ckb2b9ifl0rax95wai")))) |
247d498a RJ |
7008 | (properties |
7009 | `((upstream-name . "DNAcopy"))) | |
7010 | (build-system r-build-system) | |
7011 | (inputs | |
7012 | `(("gfortran" ,gfortran))) | |
5697fdc3 | 7013 | (home-page "https://bioconductor.org/packages/DNAcopy") |
247d498a RJ |
7014 | (synopsis "Implementation of a circular binary segmentation algorithm") |
7015 | (description "This package implements the circular binary segmentation (CBS) | |
7016 | algorithm to segment DNA copy number data and identify genomic regions with | |
7017 | abnormal copy number.") | |
7018 | (license license:gpl2+))) | |
7019 | ||
7485129e RW |
7020 | (define-public r-s4vectors |
7021 | (package | |
7022 | (name "r-s4vectors") | |
41f0f949 | 7023 | (version "0.16.0") |
7485129e RW |
7024 | (source (origin |
7025 | (method url-fetch) | |
7026 | (uri (bioconductor-uri "S4Vectors" version)) | |
7027 | (sha256 | |
7028 | (base32 | |
41f0f949 | 7029 | "03s8vz33nl6mivjb7dbvj702dkypi340lji1sjban03fyyls0hw0")))) |
7485129e | 7030 | (properties |
1d216b6e | 7031 | `((upstream-name . "S4Vectors"))) |
7485129e RW |
7032 | (build-system r-build-system) |
7033 | (propagated-inputs | |
7034 | `(("r-biocgenerics" ,r-biocgenerics))) | |
5713bbf1 | 7035 | (home-page "https://bioconductor.org/packages/S4Vectors") |
7485129e RW |
7036 | (synopsis "S4 implementation of vectors and lists") |
7037 | (description | |
7038 | "The S4Vectors package defines the @code{Vector} and @code{List} virtual | |
7039 | classes and a set of generic functions that extend the semantic of ordinary | |
7040 | vectors and lists in R. Package developers can easily implement vector-like | |
7041 | or list-like objects as concrete subclasses of @code{Vector} or @code{List}. | |
7042 | In addition, a few low-level concrete subclasses of general interest (e.g. | |
7043 | @code{DataFrame}, @code{Rle}, and @code{Hits}) are implemented in the | |
7044 | S4Vectors package itself.") | |
7045 | (license license:artistic2.0))) | |
7046 | ||
274da826 RW |
7047 | (define-public r-seqinr |
7048 | (package | |
7049 | (name "r-seqinr") | |
023aa8ff | 7050 | (version "3.4-5") |
274da826 RW |
7051 | (source |
7052 | (origin | |
7053 | (method url-fetch) | |
7054 | (uri (cran-uri "seqinr" version)) | |
7055 | (sha256 | |
7056 | (base32 | |
023aa8ff | 7057 | "17zv0n5cji17izwmwg0jcbxbjl3w5rls91w15svcnlpxjms38ahn")))) |
274da826 RW |
7058 | (build-system r-build-system) |
7059 | (propagated-inputs | |
3b851cd4 RW |
7060 | `(("r-ade4" ,r-ade4) |
7061 | ("r-segmented" ,r-segmented))) | |
274da826 RW |
7062 | (inputs |
7063 | `(("zlib" ,zlib))) | |
7064 | (home-page "http://seqinr.r-forge.r-project.org/") | |
7065 | (synopsis "Biological sequences retrieval and analysis") | |
7066 | (description | |
7067 | "This package provides tools for exploratory data analysis and data | |
7068 | visualization of biological sequence (DNA and protein) data. It also includes | |
7069 | utilities for sequence data management under the ACNUC system.") | |
7070 | (license license:gpl2+))) | |
7071 | ||
78addcb0 RW |
7072 | (define-public r-iranges |
7073 | (package | |
7074 | (name "r-iranges") | |
9e482c20 | 7075 | (version "2.12.0") |
78addcb0 RW |
7076 | (source (origin |
7077 | (method url-fetch) | |
7078 | (uri (bioconductor-uri "IRanges" version)) | |
7079 | (sha256 | |
7080 | (base32 | |
9e482c20 | 7081 | "1vqczb9wlxsmpwpqig6j1dmiblcfpq6mgnq8qwzcrvddm4cp47m5")))) |
78addcb0 | 7082 | (properties |
1d216b6e | 7083 | `((upstream-name . "IRanges"))) |
78addcb0 RW |
7084 | (build-system r-build-system) |
7085 | (propagated-inputs | |
7086 | `(("r-biocgenerics" ,r-biocgenerics) | |
7087 | ("r-s4vectors" ,r-s4vectors))) | |
5713bbf1 | 7088 | (home-page "https://bioconductor.org/packages/IRanges") |
78addcb0 RW |
7089 | (synopsis "Infrastructure for manipulating intervals on sequences") |
7090 | (description | |
7091 | "This package provides efficient low-level and highly reusable S4 classes | |
7092 | for storing ranges of integers, RLE vectors (Run-Length Encoding), and, more | |
7093 | generally, data that can be organized sequentially (formally defined as | |
7094 | @code{Vector} objects), as well as views on these @code{Vector} objects. | |
7095 | Efficient list-like classes are also provided for storing big collections of | |
7096 | instances of the basic classes. All classes in the package use consistent | |
7097 | naming and share the same rich and consistent \"Vector API\" as much as | |
7098 | possible.") | |
7099 | (license license:artistic2.0))) | |
7100 | ||
ffef27f3 RJ |
7101 | (define-public r-genomeinfodbdata |
7102 | (package | |
7103 | (name "r-genomeinfodbdata") | |
261b38a9 | 7104 | (version "0.99.1") |
ffef27f3 RJ |
7105 | (source (origin |
7106 | (method url-fetch) | |
90f83099 EF |
7107 | ;; We cannot use bioconductor-uri here because this tarball is |
7108 | ;; located under "data/annotation/" instead of "bioc/". | |
7109 | (uri (string-append "https://bioconductor.org/packages/release/" | |
7110 | "data/annotation/src/contrib/GenomeInfoDbData_" | |
7111 | version ".tar.gz")) | |
ffef27f3 RJ |
7112 | (sha256 |
7113 | (base32 | |
261b38a9 | 7114 | "0hipipvyvrh75n68hsjg35sxbcfzrghzxv547vnkk2f8ya99g01r")))) |
ffef27f3 RJ |
7115 | (properties |
7116 | `((upstream-name . "GenomeInfoDbData"))) | |
7117 | (build-system r-build-system) | |
5713bbf1 | 7118 | (home-page "https://bioconductor.org/packages/GenomeInfoDbData") |
ffef27f3 RJ |
7119 | (synopsis "Species and taxonomy ID look up tables for GenomeInfoDb") |
7120 | (description "This package contains data for mapping between NCBI taxonomy | |
7121 | ID and species. It is used by functions in the GenomeInfoDb package.") | |
7122 | (license license:artistic2.0))) | |
7123 | ||
bf7764b7 RW |
7124 | (define-public r-genomeinfodb |
7125 | (package | |
7126 | (name "r-genomeinfodb") | |
8aab0235 | 7127 | (version "1.14.0") |
bf7764b7 RW |
7128 | (source (origin |
7129 | (method url-fetch) | |
7130 | (uri (bioconductor-uri "GenomeInfoDb" version)) | |
7131 | (sha256 | |
7132 | (base32 | |
8aab0235 | 7133 | "1jhm0imkac4gvchbjxj408aakk39xdv2fyh818d3lk295bz6bnyp")))) |
bf7764b7 | 7134 | (properties |
1d216b6e | 7135 | `((upstream-name . "GenomeInfoDb"))) |
bf7764b7 RW |
7136 | (build-system r-build-system) |
7137 | (propagated-inputs | |
7138 | `(("r-biocgenerics" ,r-biocgenerics) | |
38b99ccc | 7139 | ("r-genomeinfodbdata" ,r-genomeinfodbdata) |
bf7764b7 | 7140 | ("r-iranges" ,r-iranges) |
4cd07e48 | 7141 | ("r-rcurl" ,r-rcurl) |
bf7764b7 | 7142 | ("r-s4vectors" ,r-s4vectors))) |
5713bbf1 | 7143 | (home-page "https://bioconductor.org/packages/GenomeInfoDb") |
bf7764b7 RW |
7144 | (synopsis "Utilities for manipulating chromosome identifiers") |
7145 | (description | |
7146 | "This package contains data and functions that define and allow | |
7147 | translation between different chromosome sequence naming conventions (e.g., | |
7148 | \"chr1\" versus \"1\"), including a function that attempts to place sequence | |
7149 | names in their natural, rather than lexicographic, order.") | |
7150 | (license license:artistic2.0))) | |
7151 | ||
744004a3 RJ |
7152 | (define-public r-edger |
7153 | (package | |
7154 | (name "r-edger") | |
22d96920 | 7155 | (version "3.20.9") |
744004a3 RJ |
7156 | (source (origin |
7157 | (method url-fetch) | |
7158 | (uri (bioconductor-uri "edgeR" version)) | |
7159 | (sha256 | |
7160 | (base32 | |
22d96920 | 7161 | "0y52snwbz37xzdd7gihdkqczbndlfzmmypv6hri3ymjyfmlx6qaw")))) |
744004a3 RJ |
7162 | (properties `((upstream-name . "edgeR"))) |
7163 | (build-system r-build-system) | |
7164 | (propagated-inputs | |
5e48005f | 7165 | `(("r-limma" ,r-limma) |
47055b27 | 7166 | ("r-locfit" ,r-locfit) |
010ab2ff | 7167 | ("r-rcpp" ,r-rcpp) |
47055b27 | 7168 | ("r-statmod" ,r-statmod))) ;for estimateDisp |
744004a3 RJ |
7169 | (home-page "http://bioinf.wehi.edu.au/edgeR") |
7170 | (synopsis "EdgeR does empirical analysis of digital gene expression data") | |
7171 | (description "This package can do differential expression analysis of | |
7172 | RNA-seq expression profiles with biological replication. It implements a range | |
7173 | of statistical methodology based on the negative binomial distributions, | |
7174 | including empirical Bayes estimation, exact tests, generalized linear models | |
7175 | and quasi-likelihood tests. It be applied to differential signal analysis of | |
7176 | other types of genomic data that produce counts, including ChIP-seq, SAGE and | |
7177 | CAGE.") | |
7178 | (license license:gpl2+))) | |
7179 | ||
b669d9c4 RJ |
7180 | (define-public r-variantannotation |
7181 | (package | |
7182 | (name "r-variantannotation") | |
5fb1fee6 | 7183 | (version "1.24.5") |
b669d9c4 RJ |
7184 | (source (origin |
7185 | (method url-fetch) | |
7186 | (uri (bioconductor-uri "VariantAnnotation" version)) | |
7187 | (sha256 | |
7188 | (base32 | |
5fb1fee6 | 7189 | "07ywn3c4w83l3sr76d0z3b1nv9icgdh3phsjlc6cfx7i6nfmvxw2")))) |
b669d9c4 RJ |
7190 | (properties |
7191 | `((upstream-name . "VariantAnnotation"))) | |
7192 | (inputs | |
7193 | `(("zlib" ,zlib))) | |
7194 | (propagated-inputs | |
7195 | `(("r-annotationdbi" ,r-annotationdbi) | |
37d96f1d | 7196 | ("r-biobase" ,r-biobase) |
b669d9c4 | 7197 | ("r-biocgenerics" ,r-biocgenerics) |
37d96f1d | 7198 | ("r-biostrings" ,r-biostrings) |
b669d9c4 RJ |
7199 | ("r-bsgenome" ,r-bsgenome) |
7200 | ("r-dbi" ,r-dbi) | |
7201 | ("r-genomeinfodb" ,r-genomeinfodb) | |
7202 | ("r-genomicfeatures" ,r-genomicfeatures) | |
7203 | ("r-genomicranges" ,r-genomicranges) | |
37d96f1d | 7204 | ("r-iranges" ,r-iranges) |
b669d9c4 RJ |
7205 | ("r-summarizedexperiment" ,r-summarizedexperiment) |
7206 | ("r-rsamtools" ,r-rsamtools) | |
37d96f1d RW |
7207 | ("r-rtracklayer" ,r-rtracklayer) |
7208 | ("r-s4vectors" ,r-s4vectors) | |
7209 | ("r-xvector" ,r-xvector) | |
b669d9c4 RJ |
7210 | ("r-zlibbioc" ,r-zlibbioc))) |
7211 | (build-system r-build-system) | |
7212 | (home-page "https://bioconductor.org/packages/VariantAnnotation") | |
7213 | (synopsis "Package for annotation of genetic variants") | |
7214 | (description "This R package can annotate variants, compute amino acid | |
7215 | coding changes and predict coding outcomes.") | |
7216 | (license license:artistic2.0))) | |
7217 | ||
7d4224d7 RJ |
7218 | (define-public r-limma |
7219 | (package | |
7220 | (name "r-limma") | |
eb8971b7 | 7221 | (version "3.34.9") |
7d4224d7 RJ |
7222 | (source (origin |
7223 | (method url-fetch) | |
7224 | (uri (bioconductor-uri "limma" version)) | |
7225 | (sha256 | |
7226 | (base32 | |
eb8971b7 | 7227 | "1y2fm61g5i0fn0j3l31xvwh9zww9bpkc4nwzb1d0yv1cag20jkdc")))) |
7d4224d7 RJ |
7228 | (build-system r-build-system) |
7229 | (home-page "http://bioinf.wehi.edu.au/limma") | |
7230 | (synopsis "Package for linear models for microarray and RNA-seq data") | |
7231 | (description "This package can be used for the analysis of gene expression | |
7232 | studies, especially the use of linear models for analysing designed experiments | |
7233 | and the assessment of differential expression. The analysis methods apply to | |
7234 | different technologies, including microarrays, RNA-seq, and quantitative PCR.") | |
7235 | (license license:gpl2+))) | |
7236 | ||
0e7d5560 RW |
7237 | (define-public r-xvector |
7238 | (package | |
7239 | (name "r-xvector") | |
2b6ae8bf | 7240 | (version "0.18.0") |
0e7d5560 RW |
7241 | (source (origin |
7242 | (method url-fetch) | |
7243 | (uri (bioconductor-uri "XVector" version)) | |
7244 | (sha256 | |
7245 | (base32 | |
2b6ae8bf | 7246 | "1i4i3kdxr78lr1kcxq657p11ybi7kq10c8kyaqyh6gfc8i9rhvmk")))) |
0e7d5560 | 7247 | (properties |
1d216b6e | 7248 | `((upstream-name . "XVector"))) |
0e7d5560 RW |
7249 | (build-system r-build-system) |
7250 | (arguments | |
7251 | `(#:phases | |
7252 | (modify-phases %standard-phases | |
7253 | (add-after 'unpack 'use-system-zlib | |
7254 | (lambda _ | |
7255 | (substitute* "DESCRIPTION" | |
7256 | (("zlibbioc, ") "")) | |
7257 | (substitute* "NAMESPACE" | |
7258 | (("import\\(zlibbioc\\)") "")) | |
7259 | #t))))) | |
7260 | (inputs | |
7261 | `(("zlib" ,zlib))) | |
7262 | (propagated-inputs | |
7263 | `(("r-biocgenerics" ,r-biocgenerics) | |
7264 | ("r-iranges" ,r-iranges) | |
7265 | ("r-s4vectors" ,r-s4vectors))) | |
5713bbf1 | 7266 | (home-page "https://bioconductor.org/packages/XVector") |
0e7d5560 RW |
7267 | (synopsis "Representation and manpulation of external sequences") |
7268 | (description | |
7269 | "This package provides memory efficient S4 classes for storing sequences | |
7270 | \"externally\" (behind an R external pointer, or on disk).") | |
7271 | (license license:artistic2.0))) | |
7272 | ||
e2cd1d0f RW |
7273 | (define-public r-genomicranges |
7274 | (package | |
7275 | (name "r-genomicranges") | |
535014ce | 7276 | (version "1.30.3") |
e2cd1d0f RW |
7277 | (source (origin |
7278 | (method url-fetch) | |
7279 | (uri (bioconductor-uri "GenomicRanges" version)) | |
7280 | (sha256 | |
7281 | (base32 | |
535014ce | 7282 | "07cszc9ri94nzk4dffwnsj247ih6pchnrzrvnb0q4dkk33gwy8n1")))) |
e2cd1d0f | 7283 | (properties |
1d216b6e | 7284 | `((upstream-name . "GenomicRanges"))) |
e2cd1d0f RW |
7285 | (build-system r-build-system) |
7286 | (propagated-inputs | |
7287 | `(("r-biocgenerics" ,r-biocgenerics) | |
7288 | ("r-genomeinfodb" ,r-genomeinfodb) | |
92a740af RW |
7289 | ("r-iranges" ,r-iranges) |
7290 | ("r-s4vectors" ,r-s4vectors) | |
e2cd1d0f | 7291 | ("r-xvector" ,r-xvector))) |
5713bbf1 | 7292 | (home-page "https://bioconductor.org/packages/GenomicRanges") |
e2cd1d0f RW |
7293 | (synopsis "Representation and manipulation of genomic intervals") |
7294 | (description | |
7295 | "This package provides tools to efficiently represent and manipulate | |
7296 | genomic annotations and alignments is playing a central role when it comes to | |
7297 | analyzing high-throughput sequencing data (a.k.a. NGS data). The | |
7298 | GenomicRanges package defines general purpose containers for storing and | |
7299 | manipulating genomic intervals and variables defined along a genome.") | |
7300 | (license license:artistic2.0))) | |
7301 | ||
555e3399 RW |
7302 | (define-public r-biobase |
7303 | (package | |
7304 | (name "r-biobase") | |
ca521236 | 7305 | (version "2.38.0") |
555e3399 RW |
7306 | (source (origin |
7307 | (method url-fetch) | |
7308 | (uri (bioconductor-uri "Biobase" version)) | |
7309 | (sha256 | |
7310 | (base32 | |
ca521236 | 7311 | "1cgm1ja1kp56zdlzyy9ggbkfn8r2vbsd4hncmz8g4hjd47fg18kg")))) |
555e3399 RW |
7312 | (properties |
7313 | `((upstream-name . "Biobase"))) | |
7314 | (build-system r-build-system) | |
7315 | (propagated-inputs | |
7316 | `(("r-biocgenerics" ,r-biocgenerics))) | |
5713bbf1 | 7317 | (home-page "https://bioconductor.org/packages/Biobase") |
555e3399 RW |
7318 | (synopsis "Base functions for Bioconductor") |
7319 | (description | |
7320 | "This package provides functions that are needed by many other packages | |
7321 | on Bioconductor or which replace R functions.") | |
7322 | (license license:artistic2.0))) | |
7323 | ||
8b7bce74 RW |
7324 | (define-public r-annotationdbi |
7325 | (package | |
7326 | (name "r-annotationdbi") | |
0f8d98f2 | 7327 | (version "1.40.0") |
8b7bce74 RW |
7328 | (source (origin |
7329 | (method url-fetch) | |
7330 | (uri (bioconductor-uri "AnnotationDbi" version)) | |
7331 | (sha256 | |
7332 | (base32 | |
0f8d98f2 | 7333 | "1dh4qs1a757n640gs34lf6z2glc96nan86x0sqaw5csadl2rhnlc")))) |
8b7bce74 RW |
7334 | (properties |
7335 | `((upstream-name . "AnnotationDbi"))) | |
7336 | (build-system r-build-system) | |
7337 | (propagated-inputs | |
7338 | `(("r-biobase" ,r-biobase) | |
7339 | ("r-biocgenerics" ,r-biocgenerics) | |
7340 | ("r-dbi" ,r-dbi) | |
7341 | ("r-iranges" ,r-iranges) | |
7342 | ("r-rsqlite" ,r-rsqlite) | |
7343 | ("r-s4vectors" ,r-s4vectors))) | |
5713bbf1 | 7344 | (home-page "https://bioconductor.org/packages/AnnotationDbi") |
8b7bce74 RW |
7345 | (synopsis "Annotation database interface") |
7346 | (description | |
7347 | "This package provides user interface and database connection code for | |
7348 | annotation data packages using SQLite data storage.") | |
7349 | (license license:artistic2.0))) | |
7350 | ||
c465fa72 RW |
7351 | (define-public r-biomart |
7352 | (package | |
7353 | (name "r-biomart") | |
37343067 | 7354 | (version "2.34.2") |
c465fa72 RW |
7355 | (source (origin |
7356 | (method url-fetch) | |
7357 | (uri (bioconductor-uri "biomaRt" version)) | |
7358 | (sha256 | |
7359 | (base32 | |
37343067 | 7360 | "1zlgs2zg0lmnk572p55n7m34nkxka8w10x8f2ndssjkffl2csy79")))) |
c465fa72 RW |
7361 | (properties |
7362 | `((upstream-name . "biomaRt"))) | |
7363 | (build-system r-build-system) | |
7364 | (propagated-inputs | |
7365 | `(("r-annotationdbi" ,r-annotationdbi) | |
b9e8a5c5 | 7366 | ("r-httr" ,r-httr) |
42e11d33 | 7367 | ("r-progress" ,r-progress) |
c465fa72 | 7368 | ("r-rcurl" ,r-rcurl) |
42e11d33 | 7369 | ("r-stringr" ,r-stringr) |
c465fa72 | 7370 | ("r-xml" ,r-xml))) |
5713bbf1 | 7371 | (home-page "https://bioconductor.org/packages/biomaRt") |
c465fa72 RW |
7372 | (synopsis "Interface to BioMart databases") |
7373 | (description | |
7374 | "biomaRt provides an interface to a growing collection of databases | |
7375 | implementing the @url{BioMart software suite, http://www.biomart.org}. The | |
7376 | package enables retrieval of large amounts of data in a uniform way without | |
7377 | the need to know the underlying database schemas or write complex SQL queries. | |
7378 | Examples of BioMart databases are Ensembl, COSMIC, Uniprot, HGNC, Gramene, | |
7379 | Wormbase and dbSNP mapped to Ensembl. These major databases give biomaRt | |
7380 | users direct access to a diverse set of data and enable a wide range of | |
7381 | powerful online queries from gene annotation to database mining.") | |
7382 | (license license:artistic2.0))) | |
7383 | ||
e91d362e RW |
7384 | (define-public r-biocparallel |
7385 | (package | |
7386 | (name "r-biocparallel") | |
a044c7f4 | 7387 | (version "1.12.0") |
e91d362e RW |
7388 | (source (origin |
7389 | (method url-fetch) | |
7390 | (uri (bioconductor-uri "BiocParallel" version)) | |
7391 | (sha256 | |
7392 | (base32 | |
a044c7f4 | 7393 | "13ng3n2wsgl3fh0v6jnz3vg51k5c1sh44pqdvblcrcd1qyjmmqhd")))) |
e91d362e RW |
7394 | (properties |
7395 | `((upstream-name . "BiocParallel"))) | |
7396 | (build-system r-build-system) | |
7397 | (propagated-inputs | |
7398 | `(("r-futile-logger" ,r-futile-logger) | |
a044c7f4 RW |
7399 | ("r-snow" ,r-snow) |
7400 | ("r-bh" ,r-bh))) | |
5713bbf1 | 7401 | (home-page "https://bioconductor.org/packages/BiocParallel") |
e91d362e RW |
7402 | (synopsis "Bioconductor facilities for parallel evaluation") |
7403 | (description | |
7404 | "This package provides modified versions and novel implementation of | |
7405 | functions for parallel evaluation, tailored to use with Bioconductor | |
7406 | objects.") | |
7407 | (license (list license:gpl2+ license:gpl3+)))) | |
7408 | ||
bf159353 RW |
7409 | (define-public r-biostrings |
7410 | (package | |
7411 | (name "r-biostrings") | |
b719435e | 7412 | (version "2.46.0") |
bf159353 RW |
7413 | (source (origin |
7414 | (method url-fetch) | |
7415 | (uri (bioconductor-uri "Biostrings" version)) | |
7416 | (sha256 | |
7417 | (base32 | |
b719435e | 7418 | "0vg50qdlxqcm2d6axjnzg8wh8pr4c5gz03l8bdl0llmwzp0zclzk")))) |
bf159353 RW |
7419 | (properties |
7420 | `((upstream-name . "Biostrings"))) | |
7421 | (build-system r-build-system) | |
7422 | (propagated-inputs | |
7423 | `(("r-biocgenerics" ,r-biocgenerics) | |
7424 | ("r-iranges" ,r-iranges) | |
7425 | ("r-s4vectors" ,r-s4vectors) | |
7426 | ("r-xvector" ,r-xvector))) | |
5713bbf1 | 7427 | (home-page "https://bioconductor.org/packages/Biostrings") |
bf159353 RW |
7428 | (synopsis "String objects and algorithms for biological sequences") |
7429 | (description | |
7430 | "This package provides memory efficient string containers, string | |
7431 | matching algorithms, and other utilities, for fast manipulation of large | |
7432 | biological sequences or sets of sequences.") | |
7433 | (license license:artistic2.0))) | |
7434 | ||
f8d74f70 RW |
7435 | (define-public r-rsamtools |
7436 | (package | |
7437 | (name "r-rsamtools") | |
f8068419 | 7438 | (version "1.30.0") |
f8d74f70 RW |
7439 | (source (origin |
7440 | (method url-fetch) | |
7441 | (uri (bioconductor-uri "Rsamtools" version)) | |
7442 | (sha256 | |
7443 | (base32 | |
f8068419 | 7444 | "0pjny5fjvbnfdyhl3bwxin678sha2drvs00sivxh3l772cn6yams")))) |
f8d74f70 RW |
7445 | (properties |
7446 | `((upstream-name . "Rsamtools"))) | |
7447 | (build-system r-build-system) | |
7448 | (arguments | |
7449 | `(#:phases | |
7450 | (modify-phases %standard-phases | |
7451 | (add-after 'unpack 'use-system-zlib | |
7452 | (lambda _ | |
7453 | (substitute* "DESCRIPTION" | |
7454 | (("zlibbioc, ") "")) | |
7455 | (substitute* "NAMESPACE" | |
7456 | (("import\\(zlibbioc\\)") "")) | |
7457 | #t))))) | |
7458 | (inputs | |
7459 | `(("zlib" ,zlib))) | |
7460 | (propagated-inputs | |
7461 | `(("r-biocgenerics" ,r-biocgenerics) | |
7462 | ("r-biocparallel" ,r-biocparallel) | |
7463 | ("r-biostrings" ,r-biostrings) | |
7464 | ("r-bitops" ,r-bitops) | |
7465 | ("r-genomeinfodb" ,r-genomeinfodb) | |
7466 | ("r-genomicranges" ,r-genomicranges) | |
7467 | ("r-iranges" ,r-iranges) | |
7468 | ("r-s4vectors" ,r-s4vectors) | |
7469 | ("r-xvector" ,r-xvector))) | |
5713bbf1 | 7470 | (home-page "https://bioconductor.org/packages/release/bioc/html/Rsamtools.html") |
f8d74f70 RW |
7471 | (synopsis "Interface to samtools, bcftools, and tabix") |
7472 | (description | |
7473 | "This package provides an interface to the 'samtools', 'bcftools', and | |
7474 | 'tabix' utilities for manipulating SAM (Sequence Alignment / Map), FASTA, | |
7475 | binary variant call (BCF) and compressed indexed tab-delimited (tabix) | |
7476 | files.") | |
7477 | (license license:expat))) | |
7478 | ||
71e34e6b RJ |
7479 | (define-public r-delayedarray |
7480 | (package | |
7481 | (name "r-delayedarray") | |
cb0a9a74 | 7482 | (version "0.4.1") |
71e34e6b RJ |
7483 | (source (origin |
7484 | (method url-fetch) | |
7485 | (uri (bioconductor-uri "DelayedArray" version)) | |
7486 | (sha256 | |
7487 | (base32 | |
cb0a9a74 | 7488 | "0s7h2giyvz04cg6248kbbzpwhxdrpnsvl2s8k5c8ricisd9aaz4b")))) |
71e34e6b RJ |
7489 | (properties |
7490 | `((upstream-name . "DelayedArray"))) | |
7491 | (build-system r-build-system) | |
7492 | (propagated-inputs | |
7493 | `(("r-biocgenerics" ,r-biocgenerics) | |
7494 | ("r-s4vectors" ,r-s4vectors) | |
7495 | ("r-iranges" ,r-iranges) | |
7496 | ("r-matrixstats" ,r-matrixstats))) | |
5713bbf1 | 7497 | (home-page "https://bioconductor.org/packages/DelayedArray") |
71e34e6b RJ |
7498 | (synopsis "Delayed operations on array-like objects") |
7499 | (description | |
7500 | "Wrapping an array-like object (typically an on-disk object) in a | |
7501 | @code{DelayedArray} object allows one to perform common array operations on it | |
7502 | without loading the object in memory. In order to reduce memory usage and | |
7503 | optimize performance, operations on the object are either delayed or executed | |
7504 | using a block processing mechanism. Note that this also works on in-memory | |
7505 | array-like objects like @code{DataFrame} objects (typically with Rle columns), | |
7506 | @code{Matrix} objects, and ordinary arrays and data frames.") | |
7507 | (license license:artistic2.0))) | |
7508 | ||
6e76dda2 RW |
7509 | (define-public r-summarizedexperiment |
7510 | (package | |
7511 | (name "r-summarizedexperiment") | |
c37b361e | 7512 | (version "1.8.1") |
6e76dda2 RW |
7513 | (source (origin |
7514 | (method url-fetch) | |
7515 | (uri (bioconductor-uri "SummarizedExperiment" version)) | |
7516 | (sha256 | |
7517 | (base32 | |
c37b361e | 7518 | "19vlwnby83fqjrilsxvnvgz0gvby7mrxvlmx18nb3p1w591ddfjh")))) |
6e76dda2 RW |
7519 | (properties |
7520 | `((upstream-name . "SummarizedExperiment"))) | |
7521 | (build-system r-build-system) | |
7522 | (propagated-inputs | |
7523 | `(("r-biobase" ,r-biobase) | |
7524 | ("r-biocgenerics" ,r-biocgenerics) | |
d006ee31 | 7525 | ("r-delayedarray" ,r-delayedarray) |
6e76dda2 RW |
7526 | ("r-genomeinfodb" ,r-genomeinfodb) |
7527 | ("r-genomicranges" ,r-genomicranges) | |
7528 | ("r-iranges" ,r-iranges) | |
aeb64f3c | 7529 | ("r-matrix" ,r-matrix) |
6e76dda2 | 7530 | ("r-s4vectors" ,r-s4vectors))) |
5713bbf1 | 7531 | (home-page "https://bioconductor.org/packages/SummarizedExperiment") |
6e76dda2 RW |
7532 | (synopsis "Container for representing genomic ranges by sample") |
7533 | (description | |
7534 | "The SummarizedExperiment container contains one or more assays, each | |
7535 | represented by a matrix-like object of numeric or other mode. The rows | |
7536 | typically represent genomic ranges of interest and the columns represent | |
7537 | samples.") | |
7538 | (license license:artistic2.0))) | |
7539 | ||
d8a828af RW |
7540 | (define-public r-genomicalignments |
7541 | (package | |
7542 | (name "r-genomicalignments") | |
06e8e0fc | 7543 | (version "1.14.1") |
d8a828af RW |
7544 | (source (origin |
7545 | (method url-fetch) | |
7546 | (uri (bioconductor-uri "GenomicAlignments" version)) | |
7547 | (sha256 | |
7548 | (base32 | |
06e8e0fc | 7549 | "033p6fw46sn7w2yyn14nb9qcnkf30cl0nv6zh014ixflm3iifz39")))) |
d8a828af RW |
7550 | (properties |
7551 | `((upstream-name . "GenomicAlignments"))) | |
7552 | (build-system r-build-system) | |
7553 | (propagated-inputs | |
7554 | `(("r-biocgenerics" ,r-biocgenerics) | |
7555 | ("r-biocparallel" ,r-biocparallel) | |
7556 | ("r-biostrings" ,r-biostrings) | |
7557 | ("r-genomeinfodb" ,r-genomeinfodb) | |
7558 | ("r-genomicranges" ,r-genomicranges) | |
7559 | ("r-iranges" ,r-iranges) | |
7560 | ("r-rsamtools" ,r-rsamtools) | |
7561 | ("r-s4vectors" ,r-s4vectors) | |
7562 | ("r-summarizedexperiment" ,r-summarizedexperiment))) | |
5713bbf1 | 7563 | (home-page "https://bioconductor.org/packages/GenomicAlignments") |
d8a828af RW |
7564 | (synopsis "Representation and manipulation of short genomic alignments") |
7565 | (description | |
7566 | "This package provides efficient containers for storing and manipulating | |
7567 | short genomic alignments (typically obtained by aligning short reads to a | |
7568 | reference genome). This includes read counting, computing the coverage, | |
7569 | junction detection, and working with the nucleotide content of the | |
7570 | alignments.") | |
7571 | (license license:artistic2.0))) | |
7572 | ||
317755ff RW |
7573 | (define-public r-rtracklayer |
7574 | (package | |
7575 | (name "r-rtracklayer") | |
99b3236e | 7576 | (version "1.38.3") |
317755ff RW |
7577 | (source (origin |
7578 | (method url-fetch) | |
7579 | (uri (bioconductor-uri "rtracklayer" version)) | |
7580 | (sha256 | |
7581 | (base32 | |
99b3236e | 7582 | "1khzfczm35k5lq9h0jlqrq01192spzjyh8s6is89spj006flwn4k")))) |
317755ff RW |
7583 | (build-system r-build-system) |
7584 | (arguments | |
7585 | `(#:phases | |
7586 | (modify-phases %standard-phases | |
7587 | (add-after 'unpack 'use-system-zlib | |
7588 | (lambda _ | |
7589 | (substitute* "DESCRIPTION" | |
4dd469ef | 7590 | ((" zlibbioc,") "")) |
317755ff RW |
7591 | (substitute* "NAMESPACE" |
7592 | (("import\\(zlibbioc\\)") "")) | |
7593 | #t))))) | |
7594 | (inputs | |
7595 | `(("zlib" ,zlib))) | |
7596 | (propagated-inputs | |
7597 | `(("r-biocgenerics" ,r-biocgenerics) | |
7598 | ("r-biostrings" ,r-biostrings) | |
7599 | ("r-genomeinfodb" ,r-genomeinfodb) | |
7600 | ("r-genomicalignments" ,r-genomicalignments) | |
7601 | ("r-genomicranges" ,r-genomicranges) | |
7602 | ("r-iranges" ,r-iranges) | |
7603 | ("r-rcurl" ,r-rcurl) | |
7604 | ("r-rsamtools" ,r-rsamtools) | |
7605 | ("r-s4vectors" ,r-s4vectors) | |
7606 | ("r-xml" ,r-xml) | |
7607 | ("r-xvector" ,r-xvector))) | |
5713bbf1 | 7608 | (home-page "https://bioconductor.org/packages/rtracklayer") |
317755ff RW |
7609 | (synopsis "R interface to genome browsers and their annotation tracks") |
7610 | (description | |
7611 | "rtracklayer is an extensible framework for interacting with multiple | |
7612 | genome browsers (currently UCSC built-in) and manipulating annotation tracks | |
7613 | in various formats (currently GFF, BED, bedGraph, BED15, WIG, BigWig and 2bit | |
7614 | built-in). The user may export/import tracks to/from the supported browsers, | |
7615 | as well as query and modify the browser state, such as the current viewport.") | |
7616 | (license license:artistic2.0))) | |
7617 | ||
2fd7c049 RW |
7618 | (define-public r-genomicfeatures |
7619 | (package | |
7620 | (name "r-genomicfeatures") | |
0b188565 | 7621 | (version "1.30.3") |
2fd7c049 RW |
7622 | (source (origin |
7623 | (method url-fetch) | |
7624 | (uri (bioconductor-uri "GenomicFeatures" version)) | |
7625 | (sha256 | |
7626 | (base32 | |
0b188565 | 7627 | "010vn8hlwbnw12pd1d8pv6m12yp3xwx557gba5rbjq9p4qypnn3z")))) |
2fd7c049 RW |
7628 | (properties |
7629 | `((upstream-name . "GenomicFeatures"))) | |
7630 | (build-system r-build-system) | |
7631 | (propagated-inputs | |
7632 | `(("r-annotationdbi" ,r-annotationdbi) | |
7633 | ("r-biobase" ,r-biobase) | |
7634 | ("r-biocgenerics" ,r-biocgenerics) | |
7635 | ("r-biomart" ,r-biomart) | |
7636 | ("r-biostrings" ,r-biostrings) | |
7637 | ("r-dbi" ,r-dbi) | |
7638 | ("r-genomeinfodb" ,r-genomeinfodb) | |
7639 | ("r-genomicranges" ,r-genomicranges) | |
7640 | ("r-iranges" ,r-iranges) | |
7641 | ("r-rcurl" ,r-rcurl) | |
7642 | ("r-rsqlite" ,r-rsqlite) | |
158b6743 | 7643 | ("r-rmysql" ,r-rmysql) |
2fd7c049 RW |
7644 | ("r-rtracklayer" ,r-rtracklayer) |
7645 | ("r-s4vectors" ,r-s4vectors) | |
7646 | ("r-xvector" ,r-xvector))) | |
5713bbf1 | 7647 | (home-page "https://bioconductor.org/packages/GenomicFeatures") |
2fd7c049 RW |
7648 | (synopsis "Tools for working with transcript centric annotations") |
7649 | (description | |
7650 | "This package provides a set of tools and methods for making and | |
7651 | manipulating transcript centric annotations. With these tools the user can | |
7652 | easily download the genomic locations of the transcripts, exons and cds of a | |
7653 | given organism, from either the UCSC Genome Browser or a BioMart | |
7654 | database (more sources will be supported in the future). This information is | |
7655 | then stored in a local database that keeps track of the relationship between | |
7656 | transcripts, exons, cds and genes. Flexible methods are provided for | |
7657 | extracting the desired features in a convenient format.") | |
7658 | (license license:artistic2.0))) | |
7659 | ||
fb25d880 RW |
7660 | (define-public r-go-db |
7661 | (package | |
7662 | (name "r-go-db") | |
592f4a94 | 7663 | (version "3.5.0") |
fb25d880 RW |
7664 | (source (origin |
7665 | (method url-fetch) | |
5713bbf1 | 7666 | (uri (string-append "https://www.bioconductor.org/packages/" |
f82c8c3c PP |
7667 | "release/data/annotation/src/contrib/GO.db_" |
7668 | version ".tar.gz")) | |
fb25d880 RW |
7669 | (sha256 |
7670 | (base32 | |
592f4a94 | 7671 | "02d1mn1al3q7qvhx1ylrr3ar4w4iw0qyi5d89v2336rzwk9maq35")))) |
fb25d880 RW |
7672 | (properties |
7673 | `((upstream-name . "GO.db"))) | |
7674 | (build-system r-build-system) | |
3141b83d RW |
7675 | (propagated-inputs |
7676 | `(("r-annotationdbi" ,r-annotationdbi))) | |
5713bbf1 | 7677 | (home-page "https://bioconductor.org/packages/GO.db") |
fb25d880 RW |
7678 | (synopsis "Annotation maps describing the entire Gene Ontology") |
7679 | (description | |
7680 | "The purpose of this GO.db annotation package is to provide detailed | |
7681 | information about the latest version of the Gene Ontologies.") | |
7682 | (license license:artistic2.0))) | |
7683 | ||
d1dbde6a RW |
7684 | (define-public r-graph |
7685 | (package | |
7686 | (name "r-graph") | |
aeb73879 | 7687 | (version "1.56.0") |
d1dbde6a RW |
7688 | (source (origin |
7689 | (method url-fetch) | |
7690 | (uri (bioconductor-uri "graph" version)) | |
7691 | (sha256 | |
7692 | (base32 | |
aeb73879 | 7693 | "15aajjp8h2z14p80c8hyd4rrmr9vqsm7bvwb989jxjl4k6g52an1")))) |
d1dbde6a RW |
7694 | (build-system r-build-system) |
7695 | (propagated-inputs | |
7696 | `(("r-biocgenerics" ,r-biocgenerics))) | |
5713bbf1 | 7697 | (home-page "https://bioconductor.org/packages/graph") |
d1dbde6a RW |
7698 | (synopsis "Handle graph data structures in R") |
7699 | (description | |
7700 | "This package implements some simple graph handling capabilities for R.") | |
7701 | (license license:artistic2.0))) | |
7702 | ||
d547ce5e RW |
7703 | (define-public r-topgo |
7704 | (package | |
7705 | (name "r-topgo") | |
61cbd49b | 7706 | (version "2.30.1") |
d547ce5e RW |
7707 | (source (origin |
7708 | (method url-fetch) | |
7709 | (uri (bioconductor-uri "topGO" version)) | |
7710 | (sha256 | |
7711 | (base32 | |
61cbd49b | 7712 | "1cgz4knxr328xfqlhl6ypxl6x86rfrlqz748kn94ainxjzz55i6x")))) |
d547ce5e RW |
7713 | (properties |
7714 | `((upstream-name . "topGO"))) | |
7715 | (build-system r-build-system) | |
7716 | (propagated-inputs | |
7717 | `(("r-annotationdbi" ,r-annotationdbi) | |
30ec4de7 | 7718 | ("r-dbi" ,r-dbi) |
d547ce5e RW |
7719 | ("r-biobase" ,r-biobase) |
7720 | ("r-biocgenerics" ,r-biocgenerics) | |
7721 | ("r-go-db" ,r-go-db) | |
6d415db2 | 7722 | ("r-graph" ,r-graph) |
aeb64f3c RW |
7723 | ("r-lattice" ,r-lattice) |
7724 | ("r-matrixstats" ,r-matrixstats) | |
d547ce5e | 7725 | ("r-sparsem" ,r-sparsem))) |
5713bbf1 | 7726 | (home-page "https://bioconductor.org/packages/topGO") |
d547ce5e RW |
7727 | (synopsis "Enrichment analysis for gene ontology") |
7728 | (description | |
7729 | "The topGO package provides tools for testing @dfn{gene ontology} (GO) | |
7730 | terms while accounting for the topology of the GO graph. Different test | |
7731 | statistics and different methods for eliminating local similarities and | |
7732 | dependencies between GO terms can be implemented and applied.") | |
7733 | ;; Any version of the LGPL applies. | |
7734 | (license license:lgpl2.1+))) | |
7735 | ||
c63cef66 RW |
7736 | (define-public r-bsgenome |
7737 | (package | |
7738 | (name "r-bsgenome") | |
e67850b4 | 7739 | (version "1.46.0") |
c63cef66 RW |
7740 | (source (origin |
7741 | (method url-fetch) | |
7742 | (uri (bioconductor-uri "BSgenome" version)) | |
7743 | (sha256 | |
7744 | (base32 | |
e67850b4 | 7745 | "1jbzq7lm2iajajn2bifxnkss0k9fdvgqr30mral17cbhp5f6w4lq")))) |
c63cef66 RW |
7746 | (properties |
7747 | `((upstream-name . "BSgenome"))) | |
7748 | (build-system r-build-system) | |
7749 | (propagated-inputs | |
7750 | `(("r-biocgenerics" ,r-biocgenerics) | |
7751 | ("r-biostrings" ,r-biostrings) | |
7752 | ("r-genomeinfodb" ,r-genomeinfodb) | |
7753 | ("r-genomicranges" ,r-genomicranges) | |
7754 | ("r-iranges" ,r-iranges) | |
7755 | ("r-rsamtools" ,r-rsamtools) | |
7756 | ("r-rtracklayer" ,r-rtracklayer) | |
7757 | ("r-s4vectors" ,r-s4vectors) | |
7758 | ("r-xvector" ,r-xvector))) | |
5713bbf1 | 7759 | (home-page "https://bioconductor.org/packages/BSgenome") |
c63cef66 RW |
7760 | (synopsis "Infrastructure for Biostrings-based genome data packages") |
7761 | (description | |
7762 | "This package provides infrastructure shared by all Biostrings-based | |
7763 | genome data packages and support for efficient SNP representation.") | |
7764 | (license license:artistic2.0))) | |
7765 | ||
aa3eeeb5 RJ |
7766 | (define-public r-bsgenome-hsapiens-1000genomes-hs37d5 |
7767 | (package | |
7768 | (name "r-bsgenome-hsapiens-1000genomes-hs37d5") | |
7769 | (version "0.99.1") | |
7770 | (source (origin | |
7771 | (method url-fetch) | |
7772 | ;; We cannot use bioconductor-uri here because this tarball is | |
7773 | ;; located under "data/annotation/" instead of "bioc/". | |
5713bbf1 | 7774 | (uri (string-append "https://www.bioconductor.org/packages/" |
aa3eeeb5 RJ |
7775 | "release/data/annotation/src/contrib/" |
7776 | "BSgenome.Hsapiens.1000genomes.hs37d5_" | |
7777 | version ".tar.gz")) | |
7778 | (sha256 | |
7779 | (base32 | |
7780 | "1cg0g5fqmsvwyw2p9hp2yy4ilk21jkbbrnpgqvb5c36ihjwvc7sr")))) | |
7781 | (properties | |
7782 | `((upstream-name . "BSgenome.Hsapiens.1000genomes.hs37d5"))) | |
7783 | (build-system r-build-system) | |
7784 | ;; As this package provides little more than a very large data file it | |
7785 | ;; doesn't make sense to build substitutes. | |
7786 | (arguments `(#:substitutable? #f)) | |
7787 | (propagated-inputs | |
7788 | `(("r-bsgenome" ,r-bsgenome))) | |
7789 | (home-page | |
5713bbf1 | 7790 | "https://www.bioconductor.org/packages/BSgenome.Hsapiens.1000genomes.hs37d5/") |
aa3eeeb5 RJ |
7791 | (synopsis "Full genome sequences for Homo sapiens") |
7792 | (description | |
7793 | "This package provides full genome sequences for Homo sapiens from | |
7794 | 1000genomes phase2 reference genome sequence (hs37d5), based on NCBI GRCh37.") | |
7795 | (license license:artistic2.0))) | |
7796 | ||
c43a011d RW |
7797 | (define-public r-impute |
7798 | (package | |
7799 | (name "r-impute") | |
e6ce4bf0 | 7800 | (version "1.52.0") |
c43a011d RW |
7801 | (source (origin |
7802 | (method url-fetch) | |
7803 | (uri (bioconductor-uri "impute" version)) | |
7804 | (sha256 | |
7805 | (base32 | |
e6ce4bf0 | 7806 | "0b8r4swvyx3cjcc2ky8yn0ncpzlbi1pgfsn3wpbjmhh7sqrffm2n")))) |
c43a011d RW |
7807 | (inputs |
7808 | `(("gfortran" ,gfortran))) | |
7809 | (build-system r-build-system) | |
5713bbf1 | 7810 | (home-page "https://bioconductor.org/packages/impute") |
c43a011d RW |
7811 | (synopsis "Imputation for microarray data") |
7812 | (description | |
7813 | "This package provides a function to impute missing gene expression | |
7814 | microarray data, using nearest neighbor averaging.") | |
7815 | (license license:gpl2+))) | |
7816 | ||
03ea5a35 RW |
7817 | (define-public r-seqpattern |
7818 | (package | |
7819 | (name "r-seqpattern") | |
0f948b11 | 7820 | (version "1.10.0") |
03ea5a35 RW |
7821 | (source (origin |
7822 | (method url-fetch) | |
7823 | (uri (bioconductor-uri "seqPattern" version)) | |
7824 | (sha256 | |
7825 | (base32 | |
0f948b11 | 7826 | "1kcm5w83q7w0v0vs7nyp4gq5z86c6n6pqy9zmyyhxcrns7f597pm")))) |
03ea5a35 RW |
7827 | (properties |
7828 | `((upstream-name . "seqPattern"))) | |
7829 | (build-system r-build-system) | |
7830 | (propagated-inputs | |
7831 | `(("r-biostrings" ,r-biostrings) | |
7832 | ("r-genomicranges" ,r-genomicranges) | |
7833 | ("r-iranges" ,r-iranges) | |
e92dd6f5 | 7834 | ("r-kernsmooth" ,r-kernsmooth) |
03ea5a35 | 7835 | ("r-plotrix" ,r-plotrix))) |
5713bbf1 | 7836 | (home-page "https://bioconductor.org/packages/seqPattern") |
03ea5a35 RW |
7837 | (synopsis "Visualising oligonucleotide patterns and motif occurrences") |
7838 | (description | |
7839 | "This package provides tools to visualize oligonucleotide patterns and | |
7840 | sequence motif occurrences across a large set of sequences centred at a common | |
7841 | reference point and sorted by a user defined feature.") | |
7842 | (license license:gpl3+))) | |
7843 | ||
cb933df6 RW |
7844 | (define-public r-genomation |
7845 | (package | |
7846 | (name "r-genomation") | |
e1129446 | 7847 | (version "1.11.3") |
cb933df6 RW |
7848 | (source (origin |
7849 | (method url-fetch) | |
7850 | (uri (bioconductor-uri "genomation" version)) | |
7851 | (sha256 | |
7852 | (base32 | |
e1129446 | 7853 | "1d2g1v6xhrf3gm86pv8ln22df5g6v6k6i4i39v4j82zn4apany6v")))) |
cb933df6 RW |
7854 | (build-system r-build-system) |
7855 | (propagated-inputs | |
7856 | `(("r-biostrings" ,r-biostrings) | |
7857 | ("r-bsgenome" ,r-bsgenome) | |
7858 | ("r-data-table" ,r-data-table) | |
7859 | ("r-genomeinfodb" ,r-genomeinfodb) | |
7860 | ("r-genomicalignments" ,r-genomicalignments) | |
7861 | ("r-genomicranges" ,r-genomicranges) | |
7862 | ("r-ggplot2" ,r-ggplot2) | |
7863 | ("r-gridbase" ,r-gridbase) | |
7864 | ("r-impute" ,r-impute) | |
7865 | ("r-iranges" ,r-iranges) | |
7866 | ("r-matrixstats" ,r-matrixstats) | |
7867 | ("r-plotrix" ,r-plotrix) | |
7868 | ("r-plyr" ,r-plyr) | |
51c3c490 | 7869 | ("r-rcpp" ,r-rcpp) |
cb933df6 RW |
7870 | ("r-readr" ,r-readr) |
7871 | ("r-reshape2" ,r-reshape2) | |
7872 | ("r-rsamtools" ,r-rsamtools) | |
7873 | ("r-rtracklayer" ,r-rtracklayer) | |
51c3c490 RW |
7874 | ("r-runit" ,r-runit) |
7875 | ("r-s4vectors" ,r-s4vectors) | |
cb933df6 RW |
7876 | ("r-seqpattern" ,r-seqpattern))) |
7877 | (home-page "http://bioinformatics.mdc-berlin.de/genomation/") | |
7878 | (synopsis "Summary, annotation and visualization of genomic data") | |
7879 | (description | |
7880 | "This package provides a package for summary and annotation of genomic | |
7881 | intervals. Users can visualize and quantify genomic intervals over | |
7882 | pre-defined functional regions, such as promoters, exons, introns, etc. The | |
7883 | genomic intervals represent regions with a defined chromosome position, which | |
7884 | may be associated with a score, such as aligned reads from HT-seq experiments, | |
7885 | TF binding sites, methylation scores, etc. The package can use any tabular | |
7886 | genomic feature data as long as it has minimal information on the locations of | |
7887 | genomic intervals. In addition, it can use BAM or BigWig files as input.") | |
7888 | (license license:artistic2.0))) | |
7889 | ||
64efa307 RW |
7890 | (define-public r-genomationdata |
7891 | (package | |
7892 | (name "r-genomationdata") | |
57dc9b58 | 7893 | (version "1.10.0") |
64efa307 RW |
7894 | (source (origin |
7895 | (method url-fetch) | |
7896 | ;; We cannot use bioconductor-uri here because this tarball is | |
7897 | ;; located under "data/annotation/" instead of "bioc/". | |
7898 | (uri (string-append "https://bioconductor.org/packages/" | |
7899 | "release/data/experiment/src/contrib/" | |
7900 | "genomationData_" version ".tar.gz")) | |
7901 | (sha256 | |
7902 | (base32 | |
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64efa307 RW |
7904 | (build-system r-build-system) |
7905 | ;; As this package provides little more than large data files, it doesn't | |
7906 | ;; make sense to build substitutes. | |
7907 | (arguments `(#:substitutable? #f)) | |
7908 | (native-inputs | |
7909 | `(("r-knitr" ,r-knitr))) | |
7910 | (home-page "http://bioinformatics.mdc-berlin.de/genomation/") | |
7911 | (synopsis "Experimental data for use with the genomation package") | |
7912 | (description | |
7913 | "This package contains experimental genetic data for use with the | |
7914 | genomation package. Included are Chip Seq, Methylation and Cage data, | |
7915 | downloaded from Encode.") | |
7916 | (license license:gpl3+))) | |
7917 | ||
486da491 RW |
7918 | (define-public r-org-hs-eg-db |
7919 | (package | |
7920 | (name "r-org-hs-eg-db") | |
d595fed3 | 7921 | (version "3.5.0") |
486da491 RW |
7922 | (source (origin |
7923 | (method url-fetch) | |
7924 | ;; We cannot use bioconductor-uri here because this tarball is | |
7925 | ;; located under "data/annotation/" instead of "bioc/". | |
5713bbf1 | 7926 | (uri (string-append "https://www.bioconductor.org/packages/" |
486da491 RW |
7927 | "release/data/annotation/src/contrib/" |
7928 | "org.Hs.eg.db_" version ".tar.gz")) | |
7929 | (sha256 | |
7930 | (base32 | |
d595fed3 | 7931 | "1v6wa5613cjq59xd7x1qz8lr9nb2abm9abl2cci1khrnrlpla927")))) |
486da491 RW |
7932 | (properties |
7933 | `((upstream-name . "org.Hs.eg.db"))) | |
7934 | (build-system r-build-system) | |
7935 | (propagated-inputs | |
7936 | `(("r-annotationdbi" ,r-annotationdbi))) | |
5713bbf1 | 7937 | (home-page "https://www.bioconductor.org/packages/org.Hs.eg.db/") |
486da491 RW |
7938 | (synopsis "Genome wide annotation for Human") |
7939 | (description | |
676507e3 RW |
7940 | "This package contains genome-wide annotations for Human, primarily based |
7941 | on mapping using Entrez Gene identifiers.") | |
486da491 RW |
7942 | (license license:artistic2.0))) |
7943 | ||
fefedf98 RW |
7944 | (define-public r-org-ce-eg-db |
7945 | (package | |
7946 | (name "r-org-ce-eg-db") | |
e4664290 | 7947 | (version "3.5.0") |
fefedf98 RW |
7948 | (source (origin |
7949 | (method url-fetch) | |
7950 | ;; We cannot use bioconductor-uri here because this tarball is | |
7951 | ;; located under "data/annotation/" instead of "bioc/". | |
5713bbf1 | 7952 | (uri (string-append "https://www.bioconductor.org/packages/" |
fefedf98 RW |
7953 | "release/data/annotation/src/contrib/" |
7954 | "org.Ce.eg.db_" version ".tar.gz")) | |
7955 | (sha256 | |
7956 | (base32 | |
e4664290 | 7957 | "02ggchixlmzywhsbr0h2ms4dravv7m5964cjxqcjxqs16vjwlbk9")))) |
fefedf98 RW |
7958 | (properties |
7959 | `((upstream-name . "org.Ce.eg.db"))) | |
7960 | (build-system r-build-system) | |
7961 | (propagated-inputs | |
7962 | `(("r-annotationdbi" ,r-annotationdbi))) | |
5713bbf1 | 7963 | (home-page "https://www.bioconductor.org/packages/org.Ce.eg.db/") |
fefedf98 RW |
7964 | (synopsis "Genome wide annotation for Worm") |
7965 | (description | |
7966 | "This package provides mappings from Entrez gene identifiers to various | |
7967 | annotations for the genome of the model worm Caenorhabditis elegans.") | |
7968 | (license license:artistic2.0))) | |
7969 | ||
16c53a1e RW |
7970 | (define-public r-org-dm-eg-db |
7971 | (package | |
7972 | (name "r-org-dm-eg-db") | |
19fc299f | 7973 | (version "3.5.0") |
16c53a1e RW |
7974 | (source (origin |
7975 | (method url-fetch) | |
7976 | ;; We cannot use bioconductor-uri here because this tarball is | |
7977 | ;; located under "data/annotation/" instead of "bioc/". | |
5713bbf1 | 7978 | (uri (string-append "https://www.bioconductor.org/packages/" |
16c53a1e RW |
7979 | "release/data/annotation/src/contrib/" |
7980 | "org.Dm.eg.db_" version ".tar.gz")) | |
7981 | (sha256 | |
7982 | (base32 | |
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16c53a1e RW |
7984 | (properties |
7985 | `((upstream-name . "org.Dm.eg.db"))) | |
7986 | (build-system r-build-system) | |
7987 | (propagated-inputs | |
7988 | `(("r-annotationdbi" ,r-annotationdbi))) | |
5713bbf1 | 7989 | (home-page "https://www.bioconductor.org/packages/org.Dm.eg.db/") |
16c53a1e RW |
7990 | (synopsis "Genome wide annotation for Fly") |
7991 | (description | |
7992 | "This package provides mappings from Entrez gene identifiers to various | |
7993 | annotations for the genome of the model fruit fly Drosophila melanogaster.") | |
7994 | (license license:artistic2.0))) | |
7995 | ||
e761beb9 RW |
7996 | (define-public r-org-mm-eg-db |
7997 | (package | |
7998 | (name "r-org-mm-eg-db") | |
f3569f52 | 7999 | (version "3.5.0") |
e761beb9 RW |
8000 | (source (origin |
8001 | (method url-fetch) | |
8002 | ;; We cannot use bioconductor-uri here because this tarball is | |
8003 | ;; located under "data/annotation/" instead of "bioc/". | |
5713bbf1 | 8004 | (uri (string-append "https://www.bioconductor.org/packages/" |
e761beb9 RW |
8005 | "release/data/annotation/src/contrib/" |
8006 | "org.Mm.eg.db_" version ".tar.gz")) | |
8007 | (sha256 | |
8008 | (base32 | |
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e761beb9 RW |
8010 | (properties |
8011 | `((upstream-name . "org.Mm.eg.db"))) | |
8012 | (build-system r-build-system) | |
8013 | (propagated-inputs | |
8014 | `(("r-annotationdbi" ,r-annotationdbi))) | |
5713bbf1 | 8015 | (home-page "https://www.bioconductor.org/packages/org.Mm.eg.db/") |
e761beb9 RW |
8016 | (synopsis "Genome wide annotation for Mouse") |
8017 | (description | |
8018 | "This package provides mappings from Entrez gene identifiers to various | |
8019 | annotations for the genome of the model mouse Mus musculus.") | |
8020 | (license license:artistic2.0))) | |
8021 | ||
936e7d67 RW |
8022 | (define-public r-seqlogo |
8023 | (package | |
8024 | (name "r-seqlogo") | |
61770089 | 8025 | (version "1.44.0") |
936e7d67 RW |
8026 | (source |
8027 | (origin | |
8028 | (method url-fetch) | |
8029 | (uri (bioconductor-uri "seqLogo" version)) | |
8030 | (sha256 | |
8031 | (base32 | |
61770089 | 8032 | "1ql4q4vx0j61a893dqc3c8zxmgs8sqhy3j1qhyfdvbd01vw9w1kq")))) |
936e7d67 RW |
8033 | (properties `((upstream-name . "seqLogo"))) |
8034 | (build-system r-build-system) | |
5713bbf1 | 8035 | (home-page "https://bioconductor.org/packages/seqLogo") |
936e7d67 RW |
8036 | (synopsis "Sequence logos for DNA sequence alignments") |
8037 | (description | |
8038 | "seqLogo takes the position weight matrix of a DNA sequence motif and | |
8039 | plots the corresponding sequence logo as introduced by Schneider and | |
8040 | Stephens (1990).") | |
8041 | (license license:lgpl2.0+))) | |
8042 | ||
c90a4baf RW |
8043 | (define-public r-bsgenome-hsapiens-ucsc-hg19 |
8044 | (package | |
8045 | (name "r-bsgenome-hsapiens-ucsc-hg19") | |
8046 | (version "1.4.0") | |
8047 | (source (origin | |
8048 | (method url-fetch) | |
8049 | ;; We cannot use bioconductor-uri here because this tarball is | |
8050 | ;; located under "data/annotation/" instead of "bioc/". | |
5713bbf1 | 8051 | (uri (string-append "https://www.bioconductor.org/packages/" |
c90a4baf RW |
8052 | "release/data/annotation/src/contrib/" |
8053 | "BSgenome.Hsapiens.UCSC.hg19_" | |
8054 | version ".tar.gz")) | |
8055 | (sha256 | |
8056 | (base32 | |
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c90a4baf RW |
8058 | (properties |
8059 | `((upstream-name . "BSgenome.Hsapiens.UCSC.hg19"))) | |
8060 | (build-system r-build-system) | |
8061 | ;; As this package provides little more than a very large data file it | |
8062 | ;; doesn't make sense to build substitutes. | |
8063 | (arguments `(#:substitutable? #f)) | |
8064 | (propagated-inputs | |
8065 | `(("r-bsgenome" ,r-bsgenome))) | |
8066 | (home-page | |
5713bbf1 | 8067 | "https://www.bioconductor.org/packages/BSgenome.Hsapiens.UCSC.hg19/") |
c90a4baf RW |
8068 | (synopsis "Full genome sequences for Homo sapiens") |
8069 | (description | |
8070 | "This package provides full genome sequences for Homo sapiens as provided | |
8071 | by UCSC (hg19, February 2009) and stored in Biostrings objects.") | |
8072 | (license license:artistic2.0))) | |
8073 | ||
a3e90287 RW |
8074 | (define-public r-bsgenome-mmusculus-ucsc-mm9 |
8075 | (package | |
8076 | (name "r-bsgenome-mmusculus-ucsc-mm9") | |
8077 | (version "1.4.0") | |
8078 | (source (origin | |
8079 | (method url-fetch) | |
8080 | ;; We cannot use bioconductor-uri here because this tarball is | |
8081 | ;; located under "data/annotation/" instead of "bioc/". | |
5713bbf1 | 8082 | (uri (string-append "https://www.bioconductor.org/packages/" |
a3e90287 RW |
8083 | "release/data/annotation/src/contrib/" |
8084 | "BSgenome.Mmusculus.UCSC.mm9_" | |
8085 | version ".tar.gz")) | |
8086 | (sha256 | |
8087 | (base32 | |
8088 | "1birqw30g2azimxpnjfzmkphan7x131yy8b9h85lfz5fjdg7841i")))) | |
8089 | (properties | |
8090 | `((upstream-name . "BSgenome.Mmusculus.UCSC.mm9"))) | |
8091 | (build-system r-build-system) | |
8092 | ;; As this package provides little more than a very large data file it | |
8093 | ;; doesn't make sense to build substitutes. | |
8094 | (arguments `(#:substitutable? #f)) | |
8095 | (propagated-inputs | |
8096 | `(("r-bsgenome" ,r-bsgenome))) | |
8097 | (home-page | |
5713bbf1 | 8098 | "https://www.bioconductor.org/packages/BSgenome.Mmusculus.UCSC.mm9/") |
a3e90287 RW |
8099 | (synopsis "Full genome sequences for Mouse") |
8100 | (description | |
8101 | "This package provides full genome sequences for Mus musculus (Mouse) as | |
8102 | provided by UCSC (mm9, July 2007) and stored in Biostrings objects.") | |
8103 | (license license:artistic2.0))) | |
8104 | ||
4714d521 RW |
8105 | (define-public r-bsgenome-mmusculus-ucsc-mm10 |
8106 | (package | |
8107 | (name "r-bsgenome-mmusculus-ucsc-mm10") | |
8108 | (version "1.4.0") | |
8109 | (source (origin | |
8110 | (method url-fetch) | |
8111 | ;; We cannot use bioconductor-uri here because this tarball is | |
8112 | ;; located under "data/annotation/" instead of "bioc/". | |
5713bbf1 | 8113 | (uri (string-append "https://www.bioconductor.org/packages/" |
4714d521 RW |
8114 | "release/data/annotation/src/contrib/" |
8115 | "BSgenome.Mmusculus.UCSC.mm10_" | |
8116 | version ".tar.gz")) | |
8117 | (sha256 | |
8118 | (base32 | |
8119 | "12s0nm2na9brjad4rn9l7d3db2aj8qa1xvz0y1k7gk08wayb6bkf")))) | |
8120 | (properties | |
8121 | `((upstream-name . "BSgenome.Mmusculus.UCSC.mm10"))) | |
8122 | (build-system r-build-system) | |
8123 | ;; As this package provides little more than a very large data file it | |
8124 | ;; doesn't make sense to build substitutes. | |
8125 | (arguments `(#:substitutable? #f)) | |
8126 | (propagated-inputs | |
8127 | `(("r-bsgenome" ,r-bsgenome))) | |
8128 | (home-page | |
5713bbf1 | 8129 | "https://www.bioconductor.org/packages/BSgenome.Mmusculus.UCSC.mm10/") |
4714d521 RW |
8130 | (synopsis "Full genome sequences for Mouse") |
8131 | (description | |
8132 | "This package provides full genome sequences for Mus | |
8133 | musculus (Mouse) as provided by UCSC (mm10, December 2011) and stored | |
8134 | in Biostrings objects.") | |
8135 | (license license:artistic2.0))) | |
8136 | ||
c5173d74 RJ |
8137 | (define-public r-txdb-mmusculus-ucsc-mm10-knowngene |
8138 | (package | |
8139 | (name "r-txdb-mmusculus-ucsc-mm10-knowngene") | |
8140 | (version "3.4.0") | |
8141 | (source (origin | |
8142 | (method url-fetch) | |
8143 | ;; We cannot use bioconductor-uri here because this tarball is | |
8144 | ;; located under "data/annotation/" instead of "bioc/". | |
5713bbf1 | 8145 | (uri (string-append "https://www.bioconductor.org/packages/" |
c5173d74 RJ |
8146 | "release/data/annotation/src/contrib/" |
8147 | "TxDb.Mmusculus.UCSC.mm10.knownGene_" | |
8148 | version ".tar.gz")) | |
8149 | (sha256 | |
8150 | (base32 | |
8151 | "08gava9wsvpcqz51k2sni3pj03n5155v32d9riqbf305nbirqbkb")))) | |
8152 | (properties | |
8153 | `((upstream-name . "TxDb.Mmusculus.UCSC.mm10.knownGene"))) | |
8154 | (build-system r-build-system) | |
8155 | ;; As this package provides little more than a very large data file it | |
8156 | ;; doesn't make sense to build substitutes. | |
8157 | (arguments `(#:substitutable? #f)) | |
8158 | (propagated-inputs | |
8159 | `(("r-bsgenome" ,r-bsgenome) | |
8160 | ("r-genomicfeatures" ,r-genomicfeatures) | |
8161 | ("r-annotationdbi" ,r-annotationdbi))) | |
8162 | (home-page | |
5713bbf1 | 8163 | "https://bioconductor.org/packages/TxDb.Mmusculus.UCSC.mm10.knownGene/") |
c5173d74 RJ |
8164 | (synopsis "Annotation package for TxDb knownGene object(s) for Mouse") |
8165 | (description | |
8166 | "This package loads a TxDb object, which is an R interface to | |
8167 | prefabricated databases contained in this package. This package provides | |
8168 | the TxDb object of Mouse data as provided by UCSC (mm10, December 2011) | |
8169 | based on the knownGene track.") | |
8170 | (license license:artistic2.0))) | |
8171 | ||
943bd627 RW |
8172 | (define-public r-bsgenome-celegans-ucsc-ce6 |
8173 | (package | |
8174 | (name "r-bsgenome-celegans-ucsc-ce6") | |
8175 | (version "1.4.0") | |
8176 | (source (origin | |
8177 | (method url-fetch) | |
8178 | ;; We cannot use bioconductor-uri here because this tarball is | |
8179 | ;; located under "data/annotation/" instead of "bioc/". | |
5713bbf1 | 8180 | (uri (string-append "https://www.bioconductor.org/packages/" |
943bd627 RW |
8181 | "release/data/annotation/src/contrib/" |
8182 | "BSgenome.Celegans.UCSC.ce6_" | |
8183 | version ".tar.gz")) | |
8184 | (sha256 | |
8185 | (base32 | |
8186 | "0mqzb353xv2c3m3vkb315dkmnxkgczp7ndnknyhpgjlybyf715v9")))) | |
8187 | (properties | |
8188 | `((upstream-name . "BSgenome.Celegans.UCSC.ce6"))) | |
8189 | (build-system r-build-system) | |
8190 | ;; As this package provides little more than a very large data file it | |
8191 | ;; doesn't make sense to build substitutes. | |
8192 | (arguments `(#:substitutable? #f)) | |
8193 | (propagated-inputs | |
8194 | `(("r-bsgenome" ,r-bsgenome))) | |
8195 | (home-page | |
5713bbf1 | 8196 | "https://www.bioconductor.org/packages/BSgenome.Celegans.UCSC.ce6/") |
943bd627 RW |
8197 | (synopsis "Full genome sequences for Worm") |
8198 | (description | |
8199 | "This package provides full genome sequences for Caenorhabditis | |
8200 | elegans (Worm) as provided by UCSC (ce6, May 2008) and stored in Biostrings | |
8201 | objects.") | |
8202 | (license license:artistic2.0))) | |
8203 | ||
fc47c7d6 RW |
8204 | (define-public r-bsgenome-celegans-ucsc-ce10 |
8205 | (package | |
8206 | (name "r-bsgenome-celegans-ucsc-ce10") | |
8207 | (version "1.4.0") | |
8208 | (source (origin | |
8209 | (method url-fetch) | |
8210 | ;; We cannot use bioconductor-uri here because this tarball is | |
8211 | ;; located under "data/annotation/" instead of "bioc/". | |
5713bbf1 | 8212 | (uri (string-append "https://www.bioconductor.org/packages/" |
fc47c7d6 RW |
8213 | "release/data/annotation/src/contrib/" |
8214 | "BSgenome.Celegans.UCSC.ce10_" | |
8215 | version ".tar.gz")) | |
8216 | (sha256 | |
8217 | (base32 | |
8218 | "1zaym97jk4npxk14ifvwz2rvhm4zx9xgs33r9vvx9rlynp0gydrk")))) | |
8219 | (properties | |
8220 | `((upstream-name . "BSgenome.Celegans.UCSC.ce10"))) | |
8221 | (build-system r-build-system) | |
8222 | ;; As this package provides little more than a very large data file it | |
8223 | ;; doesn't make sense to build substitutes. | |
8224 | (arguments `(#:substitutable? #f)) | |
8225 | (propagated-inputs | |
8226 | `(("r-bsgenome" ,r-bsgenome))) | |
8227 | (home-page | |
5713bbf1 | 8228 | "https://www.bioconductor.org/packages/BSgenome.Celegans.UCSC.ce10/") |
fc47c7d6 RW |
8229 | (synopsis "Full genome sequences for Worm") |
8230 | (description | |
8231 | "This package provides full genome sequences for Caenorhabditis | |
8232 | elegans (Worm) as provided by UCSC (ce10, Oct 2010) and stored in Biostrings | |
8233 | objects.") | |
8234 | (license license:artistic2.0))) | |
8235 | ||
6dc60998 RW |
8236 | (define-public r-bsgenome-dmelanogaster-ucsc-dm3 |
8237 | (package | |
8238 | (name "r-bsgenome-dmelanogaster-ucsc-dm3") | |
8239 | (version "1.4.0") | |
8240 | (source (origin | |
8241 | (method url-fetch) | |
8242 | ;; We cannot use bioconductor-uri here because this tarball is | |
8243 | ;; located under "data/annotation/" instead of "bioc/". | |
5713bbf1 | 8244 | (uri (string-append "https://www.bioconductor.org/packages/" |
6dc60998 RW |
8245 | "release/data/annotation/src/contrib/" |
8246 | "BSgenome.Dmelanogaster.UCSC.dm3_" | |
8247 | version ".tar.gz")) | |
8248 | (sha256 | |
8249 | (base32 | |
8250 | "19bm3lkhhkag3gnwp419211fh0cnr0x6fa0r1lr0ycwrikxdxsv8")))) | |
8251 | (properties | |
8252 | `((upstream-name . "BSgenome.Dmelanogaster.UCSC.dm3"))) | |
8253 | (build-system r-build-system) | |
8254 | ;; As this package provides little more than a very large data file it | |
8255 | ;; doesn't make sense to build substitutes. | |
8256 | (arguments `(#:substitutable? #f)) | |
8257 | (propagated-inputs | |
8258 | `(("r-bsgenome" ,r-bsgenome))) | |
8259 | (home-page | |
5713bbf1 | 8260 | "https://www.bioconductor.org/packages/BSgenome.Dmelanogaster.UCSC.dm3/") |
6dc60998 RW |
8261 | (synopsis "Full genome sequences for Fly") |
8262 | (description | |
8263 | "This package provides full genome sequences for Drosophila | |
8264 | melanogaster (Fly) as provided by UCSC (dm3, April 2006) and stored in | |
8265 | Biostrings objects.") | |
8266 | (license license:artistic2.0))) | |
8267 | ||
ae2462f7 RW |
8268 | (define-public r-motifrg |
8269 | (package | |
8270 | (name "r-motifrg") | |
ce59d625 | 8271 | (version "1.22.0") |
ae2462f7 RW |
8272 | (source |
8273 | (origin | |
8274 | (method url-fetch) | |
8275 | (uri (bioconductor-uri "motifRG" version)) | |
8276 | (sha256 | |
8277 | (base32 | |
ce59d625 | 8278 | "193zl2rlzwxv9p9q5i7rilj3w05ndqfyp9bdpvagp5s5cin4hf44")))) |
ae2462f7 RW |
8279 | (properties `((upstream-name . "motifRG"))) |
8280 | (build-system r-build-system) | |
8281 | (propagated-inputs | |
8282 | `(("r-biostrings" ,r-biostrings) | |
8283 | ("r-bsgenome" ,r-bsgenome) | |
007424b5 | 8284 | ("r-bsgenome-hsapiens-ucsc-hg19" ,r-bsgenome-hsapiens-ucsc-hg19) |
ae2462f7 RW |
8285 | ("r-iranges" ,r-iranges) |
8286 | ("r-seqlogo" ,r-seqlogo) | |
8287 | ("r-xvector" ,r-xvector))) | |
5713bbf1 | 8288 | (home-page "https://bioconductor.org/packages/motifRG") |
ae2462f7 RW |
8289 | (synopsis "Discover motifs in high throughput sequencing data") |
8290 | (description | |
8291 | "This package provides tools for discriminative motif discovery in high | |
8292 | throughput genetic sequencing data sets using regression methods.") | |
8293 | (license license:artistic2.0))) | |
8294 | ||
a5002ae7 AE |
8295 | (define-public r-qtl |
8296 | (package | |
8297 | (name "r-qtl") | |
65c9d257 | 8298 | (version "1.42-8") |
a5002ae7 AE |
8299 | (source |
8300 | (origin | |
8301 | (method url-fetch) | |
8302 | (uri (string-append "mirror://cran/src/contrib/qtl_" | |
8303 | version ".tar.gz")) | |
8304 | (sha256 | |
8305 | (base32 | |
65c9d257 | 8306 | "1l528dwvfpdlr05imrrm4rq32axp6hld9nqm6mm43kn5n7z2f5k6")))) |
a5002ae7 AE |
8307 | (build-system r-build-system) |
8308 | (home-page "http://rqtl.org/") | |
8309 | (synopsis "R package for analyzing QTL experiments in genetics") | |
8310 | (description "R/qtl is an extension library for the R statistics | |
8311 | system. It is used to analyze experimental crosses for identifying | |
8312 | genes contributing to variation in quantitative traits (so-called | |
8313 | quantitative trait loci, QTLs). | |
8314 | ||
8315 | Using a hidden Markov model, R/qtl allows to estimate genetic maps, to | |
8316 | identify genotyping errors, and to perform single-QTL and two-QTL, | |
8317 | two-dimensional genome scans.") | |
8318 | (license license:gpl3))) | |
d1e32822 | 8319 | |
9e3ba31c RJ |
8320 | (define-public r-zlibbioc |
8321 | (package | |
8322 | (name "r-zlibbioc") | |
5c184700 | 8323 | (version "1.24.0") |
9e3ba31c RJ |
8324 | (source (origin |
8325 | (method url-fetch) | |
8326 | (uri (bioconductor-uri "zlibbioc" version)) | |
8327 | (sha256 | |
8328 | (base32 | |
5c184700 | 8329 | "1zr9hbh55hglfpy15cpxwmddxblhyb0an15953l3rbhmlh2vpy92")))) |
9e3ba31c RJ |
8330 | (properties |
8331 | `((upstream-name . "zlibbioc"))) | |
8332 | (build-system r-build-system) | |
8333 | (home-page "https://bioconductor.org/packages/zlibbioc") | |
8334 | (synopsis "Provider for zlib-1.2.5 to R packages") | |
8335 | (description "This package uses the source code of zlib-1.2.5 to create | |
8336 | libraries for systems that do not have these available via other means.") | |
8337 | (license license:artistic2.0))) | |
8338 | ||
e619a5c2 RW |
8339 | (define-public r-r4rna |
8340 | (package | |
8341 | (name "r-r4rna") | |
8342 | (version "0.1.4") | |
8343 | (source | |
8344 | (origin | |
8345 | (method url-fetch) | |
8346 | (uri (string-append "http://www.e-rna.org/r-chie/files/R4RNA_" | |
8347 | version ".tar.gz")) | |
8348 | (sha256 | |
8349 | (base32 | |
8350 | "1p0i78wh76jfgmn9jphbwwaz6yy6pipzfg08xs54cxavxg2j81p5")))) | |
8351 | (build-system r-build-system) | |
8352 | (propagated-inputs | |
8353 | `(("r-optparse" ,r-optparse) | |
8354 | ("r-rcolorbrewer" ,r-rcolorbrewer))) | |
8355 | (home-page "http://www.e-rna.org/r-chie/index.cgi") | |
8356 | (synopsis "Analysis framework for RNA secondary structure") | |
8357 | (description | |
8358 | "The R4RNA package aims to be a general framework for the analysis of RNA | |
8359 | secondary structure and comparative analysis in R.") | |
8360 | (license license:gpl3+))) | |
8361 | ||
52765a63 RW |
8362 | (define-public r-rhtslib |
8363 | (package | |
8364 | (name "r-rhtslib") | |
1d0263b4 | 8365 | (version "1.10.0") |
52765a63 RW |
8366 | (source |
8367 | (origin | |
8368 | (method url-fetch) | |
8369 | (uri (bioconductor-uri "Rhtslib" version)) | |
8370 | (sha256 | |
8371 | (base32 | |
1d0263b4 | 8372 | "1dw3p44bfr0m7w39ckc2k37sjcp1zz0b9g12mr8am15jaj6v0q2j")))) |
52765a63 RW |
8373 | (properties `((upstream-name . "Rhtslib"))) |
8374 | (build-system r-build-system) | |
8375 | (propagated-inputs | |
8376 | `(("r-zlibbioc" ,r-zlibbioc))) | |
8377 | (inputs | |
8378 | `(("zlib" ,zlib))) | |
53ca52f0 RW |
8379 | (native-inputs |
8380 | `(("autoconf" ,autoconf))) | |
52765a63 RW |
8381 | (home-page "https://github.com/nhayden/Rhtslib") |
8382 | (synopsis "High-throughput sequencing library as an R package") | |
8383 | (description | |
8384 | "This package provides the HTSlib C library for high-throughput | |
8385 | nucleotide sequence analysis. The package is primarily useful to developers | |
8386 | of other R packages who wish to make use of HTSlib.") | |
8387 | (license license:lgpl2.0+))) | |
8388 | ||
fe02c4c9 RW |
8389 | (define-public r-bamsignals |
8390 | (package | |
8391 | (name "r-bamsignals") | |
da153b7f | 8392 | (version "1.10.0") |
fe02c4c9 RW |
8393 | (source |
8394 | (origin | |
8395 | (method url-fetch) | |
8396 | (uri (bioconductor-uri "bamsignals" version)) | |
8397 | (sha256 | |
8398 | (base32 | |
da153b7f | 8399 | "15id6mkj95skb4kfafvfs2j7ylydal60c3pspcl7llhwpq6vcqvl")))) |
fe02c4c9 RW |
8400 | (build-system r-build-system) |
8401 | (propagated-inputs | |
8402 | `(("r-biocgenerics" ,r-biocgenerics) | |
8403 | ("r-genomicranges" ,r-genomicranges) | |
8404 | ("r-iranges" ,r-iranges) | |
8405 | ("r-rcpp" ,r-rcpp) | |
8406 | ("r-rhtslib" ,r-rhtslib) | |
8407 | ("r-zlibbioc" ,r-zlibbioc))) | |
8408 | (inputs | |
8409 | `(("zlib" ,zlib))) | |
5713bbf1 | 8410 | (home-page "https://bioconductor.org/packages/bamsignals") |
fe02c4c9 RW |
8411 | (synopsis "Extract read count signals from bam files") |
8412 | (description | |
8413 | "This package allows to efficiently obtain count vectors from indexed bam | |
8414 | files. It counts the number of nucleotide sequence reads in given genomic | |
8415 | ranges and it computes reads profiles and coverage profiles. It also handles | |
8416 | paired-end data.") | |
8417 | (license license:gpl2+))) | |
8418 | ||
89984be4 RW |
8419 | (define-public r-rcas |
8420 | (package | |
8421 | (name "r-rcas") | |
d82937fb | 8422 | (version "1.3.4") |
89984be4 RW |
8423 | (source (origin |
8424 | (method url-fetch) | |
8425 | (uri (string-append "https://github.com/BIMSBbioinfo/RCAS/archive/v" | |
8426 | version ".tar.gz")) | |
8427 | (file-name (string-append name "-" version ".tar.gz")) | |
8428 | (sha256 | |
8429 | (base32 | |
d82937fb | 8430 | "1qgc7vi6fpzl440yg7jhiycg5q336kd4pxqzx10yx2zcq3bq3msg")))) |
89984be4 RW |
8431 | (build-system r-build-system) |
8432 | (native-inputs | |
8433 | `(("r-knitr" ,r-knitr) | |
8434 | ("r-testthat" ,r-testthat) | |
8435 | ;; During vignette building knitr checks that "pandoc-citeproc" | |
8436 | ;; is in the PATH. | |
8437 | ("ghc-pandoc-citeproc" ,ghc-pandoc-citeproc))) | |
8438 | (propagated-inputs | |
8439 | `(("r-data-table" ,r-data-table) | |
8440 | ("r-biomart" ,r-biomart) | |
8441 | ("r-org-hs-eg-db" ,r-org-hs-eg-db) | |
8442 | ("r-org-ce-eg-db" ,r-org-ce-eg-db) | |
8443 | ("r-org-dm-eg-db" ,r-org-dm-eg-db) | |
8444 | ("r-org-mm-eg-db" ,r-org-mm-eg-db) | |
8445 | ("r-bsgenome-hsapiens-ucsc-hg19" ,r-bsgenome-hsapiens-ucsc-hg19) | |
8446 | ("r-bsgenome-mmusculus-ucsc-mm9" ,r-bsgenome-mmusculus-ucsc-mm9) | |
8447 | ("r-bsgenome-celegans-ucsc-ce10" ,r-bsgenome-celegans-ucsc-ce10) | |
8448 | ("r-bsgenome-dmelanogaster-ucsc-dm3" ,r-bsgenome-dmelanogaster-ucsc-dm3) | |
8449 | ("r-topgo" ,r-topgo) | |
8450 | ("r-dt" ,r-dt) | |
ebfd6a71 | 8451 | ("r-pbapply" ,r-pbapply) |
89984be4 | 8452 | ("r-plotly" ,r-plotly) |
2c8d6c0b | 8453 | ("r-plotrix" ,r-plotrix) |
89984be4 RW |
8454 | ("r-motifrg" ,r-motifrg) |
8455 | ("r-genomation" ,r-genomation) | |
8456 | ("r-genomicfeatures" ,r-genomicfeatures) | |
8457 | ("r-rtracklayer" ,r-rtracklayer) | |
8458 | ("r-rmarkdown" ,r-rmarkdown))) | |
8459 | (synopsis "RNA-centric annotation system") | |
8460 | (description | |
8461 | "RCAS aims to be a standalone RNA-centric annotation system that provides | |
8462 | intuitive reports and publication-ready graphics. This package provides the R | |
8463 | library implementing most of the pipeline's features.") | |
8464 | (home-page "https://github.com/BIMSBbioinfo/RCAS") | |
75690c9f | 8465 | (license license:artistic2.0))) |
89984be4 | 8466 | |
50937297 RW |
8467 | (define-public rcas-web |
8468 | (package | |
8469 | (name "rcas-web") | |
01d87d3c | 8470 | (version "0.0.4") |
50937297 RW |
8471 | (source |
8472 | (origin | |
8473 | (method url-fetch) | |
8474 | (uri (string-append "https://github.com/BIMSBbioinfo/rcas-web/" | |
8475 | "releases/download/v" version | |
8476 | "/rcas-web-" version ".tar.gz")) | |
8477 | (sha256 | |
8478 | (base32 | |
01d87d3c | 8479 | "1p16frfys41a8yaa4gkm457nzkqhqs2pc3lkac0ds457w9w5j1gm")))) |
50937297 RW |
8480 | (build-system gnu-build-system) |
8481 | (arguments | |
8482 | `(#:phases | |
8483 | (modify-phases %standard-phases | |
8484 | (add-after 'install 'wrap-executable | |
8485 | (lambda* (#:key inputs outputs #:allow-other-keys) | |
8486 | (let* ((out (assoc-ref outputs "out")) | |
8487 | (json (assoc-ref inputs "guile-json")) | |
8488 | (redis (assoc-ref inputs "guile-redis")) | |
8489 | (path (string-append | |
8490 | json "/share/guile/site/2.2:" | |
8491 | redis "/share/guile/site/2.2"))) | |
8492 | (wrap-program (string-append out "/bin/rcas-web") | |
8493 | `("GUILE_LOAD_PATH" ":" = (,path)) | |
8494 | `("GUILE_LOAD_COMPILED_PATH" ":" = (,path)) | |
8495 | `("R_LIBS_SITE" ":" = (,(getenv "R_LIBS_SITE"))))) | |
8496 | #t))))) | |
8497 | (inputs | |
2d7c4ae3 | 8498 | `(("r-minimal" ,r-minimal) |
50937297 | 8499 | ("r-rcas" ,r-rcas) |
f6396d86 | 8500 | ("guile-next" ,guile-2.2) |
2252f087 | 8501 | ("guile-json" ,guile-json) |
50937297 RW |
8502 | ("guile-redis" ,guile2.2-redis))) |
8503 | (native-inputs | |
8504 | `(("pkg-config" ,pkg-config))) | |
8505 | (home-page "https://github.com/BIMSBbioinfo/rcas-web") | |
8506 | (synopsis "Web interface for RNA-centric annotation system (RCAS)") | |
8507 | (description "This package provides a simple web interface for the | |
8508 | @dfn{RNA-centric annotation system} (RCAS).") | |
8509 | (license license:agpl3+))) | |
8510 | ||
7500e42b RJ |
8511 | (define-public r-mutationalpatterns |
8512 | (package | |
8513 | (name "r-mutationalpatterns") | |
b9bf2b89 | 8514 | (version "1.4.2") |
7500e42b RJ |
8515 | (source |
8516 | (origin | |
8517 | (method url-fetch) | |
8518 | (uri (bioconductor-uri "MutationalPatterns" version)) | |
8519 | (sha256 | |
8520 | (base32 | |
b9bf2b89 | 8521 | "08ay9h5cqsi8ypb6r0g4rfa5l1g06jgfzl64wmhgz134yqbl7vfv")))) |
7500e42b RJ |
8522 | (build-system r-build-system) |
8523 | (propagated-inputs | |
8524 | `(("r-biocgenerics" ,r-biocgenerics) | |
8525 | ("r-biostrings" ,r-biostrings) | |
cf4ac4e4 RJ |
8526 | ("r-bsgenome-hsapiens-1000g" ,r-bsgenome-hsapiens-1000genomes-hs37d5) |
8527 | ("r-bsgenome-hsapiens-ucsc-hg19" ,r-bsgenome-hsapiens-ucsc-hg19) | |
7500e42b RJ |
8528 | ("r-genomicranges" ,r-genomicranges) |
8529 | ("r-genomeinfodb" ,r-genomeinfodb) | |
8530 | ("r-ggplot2" ,r-ggplot2) | |
8531 | ("r-gridextra" ,r-gridextra) | |
8532 | ("r-iranges" ,r-iranges) | |
8533 | ("r-nmf" ,r-nmf) | |
8534 | ("r-plyr" ,r-plyr) | |
8535 | ("r-pracma" ,r-pracma) | |
8536 | ("r-reshape2" ,r-reshape2) | |
39d9098d RW |
8537 | ("r-cowplot" ,r-cowplot) |
8538 | ("r-ggdendro" ,r-ggdendro) | |
8539 | ("r-s4vectors" ,r-s4vectors) | |
7500e42b RJ |
8540 | ("r-summarizedexperiment" ,r-summarizedexperiment) |
8541 | ("r-variantannotation" ,r-variantannotation))) | |
5713bbf1 | 8542 | (home-page "https://bioconductor.org/packages/MutationalPatterns/") |
7500e42b RJ |
8543 | (synopsis "Extract and visualize mutational patterns in genomic data") |
8544 | (description "This package provides an extensive toolset for the | |
8545 | characterization and visualization of a wide range of mutational patterns | |
8546 | in SNV base substitution data.") | |
8547 | (license license:expat))) | |
8548 | ||
d7160529 RW |
8549 | (define-public r-wgcna |
8550 | (package | |
8551 | (name "r-wgcna") | |
6a0e1390 | 8552 | (version "1.63") |
d7160529 RW |
8553 | (source |
8554 | (origin | |
8555 | (method url-fetch) | |
8556 | (uri (cran-uri "WGCNA" version)) | |
8557 | (sha256 | |
8558 | (base32 | |
6a0e1390 | 8559 | "1225dqm68bynkmklnsxdqdd3zqrpzbvqwyly8ibxmk75z33xz309")))) |
d7160529 RW |
8560 | (properties `((upstream-name . "WGCNA"))) |
8561 | (build-system r-build-system) | |
8562 | (propagated-inputs | |
8563 | `(("r-annotationdbi" ,r-annotationdbi) | |
8564 | ("r-doparallel" ,r-doparallel) | |
8565 | ("r-dynamictreecut" ,r-dynamictreecut) | |
8566 | ("r-fastcluster" ,r-fastcluster) | |
8567 | ("r-foreach" ,r-foreach) | |
8568 | ("r-go-db" ,r-go-db) | |
8569 | ("r-hmisc" ,r-hmisc) | |
8570 | ("r-impute" ,r-impute) | |
1b22ecda RW |
8571 | ("r-rcpp" ,r-rcpp) |
8572 | ("r-robust" ,r-robust) | |
8573 | ("r-survival" ,r-survival) | |
d7160529 RW |
8574 | ("r-matrixstats" ,r-matrixstats) |
8575 | ("r-preprocesscore" ,r-preprocesscore))) | |
8576 | (home-page | |
8577 | "http://www.genetics.ucla.edu/labs/horvath/CoexpressionNetwork/Rpackages/WGCNA/") | |
8578 | (synopsis "Weighted correlation network analysis") | |
8579 | (description | |
8580 | "This package provides functions necessary to perform Weighted | |
8581 | Correlation Network Analysis on high-dimensional data. It includes functions | |
8582 | for rudimentary data cleaning, construction and summarization of correlation | |
8583 | networks, module identification and functions for relating both variables and | |
8584 | modules to sample traits. It also includes a number of utility functions for | |
8585 | data manipulation and visualization.") | |
8586 | (license license:gpl2+))) | |
8587 | ||
c827f202 RW |
8588 | (define-public r-chipkernels |
8589 | (let ((commit "c9cfcacb626b1221094fb3490ea7bac0fd625372") | |
8590 | (revision "1")) | |
8591 | (package | |
8592 | (name "r-chipkernels") | |
8593 | (version (string-append "1.1-" revision "." (string-take commit 9))) | |
8594 | (source | |
8595 | (origin | |
8596 | (method git-fetch) | |
8597 | (uri (git-reference | |
8598 | (url "https://github.com/ManuSetty/ChIPKernels.git") | |
8599 | (commit commit))) | |
8600 | (file-name (string-append name "-" version)) | |
8601 | (sha256 | |
8602 | (base32 | |
8603 | "14bj5qhjm1hsm9ay561nfbqi9wxsa7y487df2idsaaf6z10nw4v0")))) | |
8604 | (build-system r-build-system) | |
8605 | (propagated-inputs | |
8606 | `(("r-iranges" ,r-iranges) | |
8607 | ("r-xvector" ,r-xvector) | |
8608 | ("r-biostrings" ,r-biostrings) | |
8609 | ("r-bsgenome" ,r-bsgenome) | |
8610 | ("r-gtools" ,r-gtools) | |
8611 | ("r-genomicranges" ,r-genomicranges) | |
8612 | ("r-sfsmisc" ,r-sfsmisc) | |
8613 | ("r-kernlab" ,r-kernlab) | |
8614 | ("r-s4vectors" ,r-s4vectors) | |
8615 | ("r-biocgenerics" ,r-biocgenerics))) | |
8616 | (home-page "https://github.com/ManuSetty/ChIPKernels") | |
8617 | (synopsis "Build string kernels for DNA Sequence analysis") | |
8618 | (description "ChIPKernels is an R package for building different string | |
8619 | kernels used for DNA Sequence analysis. A dictionary of the desired kernel | |
8620 | must be built and this dictionary can be used for determining kernels for DNA | |
8621 | Sequences.") | |
8622 | (license license:gpl2+)))) | |
8623 | ||
2d9fb170 RW |
8624 | (define-public r-seqgl |
8625 | (package | |
8626 | (name "r-seqgl") | |
8627 | (version "1.1.4") | |
8628 | (source | |
8629 | (origin | |
8630 | (method url-fetch) | |
8631 | (uri (string-append "https://github.com/ManuSetty/SeqGL/" | |
8632 | "archive/" version ".tar.gz")) | |
8633 | (file-name (string-append name "-" version ".tar.gz")) | |
8634 | (sha256 | |
8635 | (base32 | |
8636 | "0pnk1p3sci5yipyc8xnb6jbmydpl80fld927xgnbcv104hy8h8yh")))) | |
8637 | (build-system r-build-system) | |
8638 | (propagated-inputs | |
8639 | `(("r-biostrings" ,r-biostrings) | |
8640 | ("r-chipkernels" ,r-chipkernels) | |
8641 | ("r-genomicranges" ,r-genomicranges) | |
8642 | ("r-spams" ,r-spams) | |
8643 | ("r-wgcna" ,r-wgcna) | |
8644 | ("r-fastcluster" ,r-fastcluster))) | |
8645 | (home-page "https://github.com/ManuSetty/SeqGL") | |
8646 | (synopsis "Group lasso for Dnase/ChIP-seq data") | |
8647 | (description "SeqGL is a group lasso based algorithm to extract | |
8648 | transcription factor sequence signals from ChIP, DNase and ATAC-seq profiles. | |
8649 | This package presents a method which uses group lasso to discriminate between | |
8650 | bound and non bound genomic regions to accurately identify transcription | |
8651 | factors bound at the specific regions.") | |
8652 | (license license:gpl2+))) | |
8653 | ||
bd3be46e RW |
8654 | (define-public r-gkmsvm |
8655 | (package | |
8656 | (name "r-gkmsvm") | |
5ef76bc2 | 8657 | (version "0.79.0") |
bd3be46e RW |
8658 | (source |
8659 | (origin | |
8660 | (method url-fetch) | |
8661 | (uri (cran-uri "gkmSVM" version)) | |
8662 | (sha256 | |
8663 | (base32 | |
5ef76bc2 | 8664 | "04dakbgfvfalz4rm4fvvybp506dn5fbj5g86ybfhrc6wywjllsz3")))) |
bd3be46e RW |
8665 | (properties `((upstream-name . "gkmSVM"))) |
8666 | (build-system r-build-system) | |
8667 | (propagated-inputs | |
8668 | `(("r-biocgenerics" ,r-biocgenerics) | |
8669 | ("r-biostrings" ,r-biostrings) | |
8670 | ("r-genomeinfodb" ,r-genomeinfodb) | |
8671 | ("r-genomicranges" ,r-genomicranges) | |
8672 | ("r-iranges" ,r-iranges) | |
8673 | ("r-kernlab" ,r-kernlab) | |
8674 | ("r-rcpp" ,r-rcpp) | |
8675 | ("r-rocr" ,r-rocr) | |
8676 | ("r-rtracklayer" ,r-rtracklayer) | |
8677 | ("r-s4vectors" ,r-s4vectors) | |
8678 | ("r-seqinr" ,r-seqinr))) | |
e9960d8c | 8679 | (home-page "https://cran.r-project.org/web/packages/gkmSVM") |
bd3be46e RW |
8680 | (synopsis "Gapped-kmer support vector machine") |
8681 | (description | |
8682 | "This R package provides tools for training gapped-kmer SVM classifiers | |
8683 | for DNA and protein sequences. This package supports several sequence | |
8684 | kernels, including: gkmSVM, kmer-SVM, mismatch kernel and wildcard kernel.") | |
8685 | (license license:gpl2+))) | |
8686 | ||
d4af25b5 RJPB |
8687 | (define-public r-tximport |
8688 | (package | |
8689 | (name "r-tximport") | |
19e8929c | 8690 | (version "1.6.0") |
d4af25b5 RJPB |
8691 | (source (origin |
8692 | (method url-fetch) | |
8693 | (uri (bioconductor-uri "tximport" version)) | |
8694 | (sha256 | |
8695 | (base32 | |
19e8929c | 8696 | "1gyqcm91hxg1kgjqcz2qw1n56yp9pymjzs50rwcpb2893dr8sp2h")))) |
d4af25b5 | 8697 | (build-system r-build-system) |
5713bbf1 | 8698 | (home-page "https://bioconductor.org/packages/tximport") |
d4af25b5 RJPB |
8699 | (synopsis "Import and summarize transcript-level estimates for gene-level analysis") |
8700 | (description | |
8701 | "This package provides tools to import transcript-level abundance, | |
8702 | estimated counts and transcript lengths, and to summarize them into matrices | |
8703 | for use with downstream gene-level analysis packages. Average transcript | |
8704 | length, weighted by sample-specific transcript abundance estimates, is | |
8705 | provided as a matrix which can be used as an offset for different expression | |
8706 | of gene-level counts.") | |
8707 | (license license:gpl2+))) | |
8708 | ||
69f2b3bd RJPB |
8709 | (define-public r-rhdf5 |
8710 | (package | |
8711 | (name "r-rhdf5") | |
e6b332d4 | 8712 | (version "2.22.0") |
69f2b3bd RJPB |
8713 | (source (origin |
8714 | (method url-fetch) | |
8715 | (uri (bioconductor-uri "rhdf5" version)) | |
8716 | (sha256 | |
8717 | (base32 | |
e6b332d4 | 8718 | "145858qg1xan6imxcbprzq3yn3mdf532aahdr6cibvdjg47hs4c1")))) |
69f2b3bd RJPB |
8719 | (build-system r-build-system) |
8720 | (arguments | |
8721 | `(#:phases | |
8722 | (modify-phases %standard-phases | |
8723 | (add-after 'unpack 'unpack-smallhdf5 | |
8724 | (lambda* (#:key outputs #:allow-other-keys) | |
8725 | (system* "tar" "-xzvf" | |
8726 | "src/hdf5source/hdf5small.tgz" "-C" "src/" ) | |
69f2b3bd RJPB |
8727 | (substitute* "src/hdf5/configure" |
8728 | (("/bin/mv") "mv")) | |
e325c890 RW |
8729 | ;; Remove timestamp and host system information to make |
8730 | ;; the build reproducible. | |
8731 | (substitute* "src/hdf5/src/libhdf5.settings.in" | |
8732 | (("Configured on: @CONFIG_DATE@") | |
8733 | "Configured on: Guix") | |
8734 | (("Uname information:.*") | |
8735 | "Uname information: Linux\n") | |
8736 | ;; Remove unnecessary store reference. | |
8737 | (("C Compiler:.*") | |
8738 | "C Compiler: GCC\n")) | |
69f2b3bd RJPB |
8739 | #t))))) |
8740 | (propagated-inputs | |
8741 | `(("r-zlibbioc" ,r-zlibbioc))) | |
8742 | (inputs | |
8743 | `(("perl" ,perl) | |
8744 | ("zlib" ,zlib))) | |
5713bbf1 | 8745 | (home-page "https://bioconductor.org/packages/rhdf5") |
69f2b3bd RJPB |
8746 | (synopsis "HDF5 interface to R") |
8747 | (description | |
8748 | "This R/Bioconductor package provides an interface between HDF5 and R. | |
8749 | HDF5's main features are the ability to store and access very large and/or | |
8750 | complex datasets and a wide variety of metadata on mass storage (disk) through | |
8751 | a completely portable file format. The rhdf5 package is thus suited for the | |
8752 | exchange of large and/or complex datasets between R and other software | |
8753 | package, and for letting R applications work on datasets that are larger than | |
8754 | the available RAM.") | |
8755 | (license license:artistic2.0))) | |
8756 | ||
17cddc17 RW |
8757 | (define-public r-annotationfilter |
8758 | (package | |
8759 | (name "r-annotationfilter") | |
598dacf6 | 8760 | (version "1.2.0") |
17cddc17 RW |
8761 | (source (origin |
8762 | (method url-fetch) | |
8763 | (uri (bioconductor-uri "AnnotationFilter" version)) | |
8764 | (sha256 | |
8765 | (base32 | |
598dacf6 | 8766 | "04zf864c1fvdlaay2r5cn30fc1n5i3czh31fs62qlrvs61wjiscs")))) |
17cddc17 RW |
8767 | (properties |
8768 | `((upstream-name . "AnnotationFilter"))) | |
8769 | (build-system r-build-system) | |
8770 | (propagated-inputs | |
8771 | `(("r-genomicranges" ,r-genomicranges) | |
8772 | ("r-lazyeval" ,r-lazyeval))) | |
8773 | (home-page "https://github.com/Bioconductor/AnnotationFilter") | |
8774 | (synopsis "Facilities for filtering Bioconductor annotation resources") | |
8775 | (description | |
8776 | "This package provides classes and other infrastructure to implement | |
8777 | filters for manipulating Bioconductor annotation resources. The filters are | |
8778 | used by @code{ensembldb}, @code{Organism.dplyr}, and other packages.") | |
8779 | (license license:artistic2.0))) | |
8780 | ||
66e40e00 RW |
8781 | (define-public emboss |
8782 | (package | |
8783 | (name "emboss") | |
8784 | (version "6.5.7") | |
8785 | (source (origin | |
8786 | (method url-fetch) | |
8787 | (uri (string-append "ftp://emboss.open-bio.org/pub/EMBOSS/old/" | |
8788 | (version-major+minor version) ".0/" | |
8789 | "EMBOSS-" version ".tar.gz")) | |
8790 | (sha256 | |
8791 | (base32 | |
8792 | "0vsmz96gc411yj2iyzdrsmg4l2n1nhgmp7vrgzlxx3xixv9xbf0q")))) | |
8793 | (build-system gnu-build-system) | |
8794 | (arguments | |
8795 | `(#:configure-flags | |
8796 | (list (string-append "--with-hpdf=" | |
8797 | (assoc-ref %build-inputs "libharu"))) | |
8798 | #:phases | |
8799 | (modify-phases %standard-phases | |
8800 | (add-after 'unpack 'fix-checks | |
8801 | (lambda _ | |
8802 | ;; The PNGDRIVER tests check for the presence of libgd, libpng | |
8803 | ;; and zlib, but assume that they are all found at the same | |
8804 | ;; prefix. | |
8805 | (substitute* "configure.in" | |
8806 | (("CHECK_PNGDRIVER") | |
8807 | "LIBS=\"$LIBS -lgd -lpng -lz -lm\" | |
8808 | AC_DEFINE([PLD_png], [1], [Define to 1 if PNG support is available]) | |
8809 | AM_CONDITIONAL(AMPNG, true)")) | |
8810 | #t)) | |
d10092b8 | 8811 | (add-after 'fix-checks 'disable-update-check |
66e40e00 RW |
8812 | (lambda _ |
8813 | ;; At build time there is no connection to the Internet, so | |
8814 | ;; looking for updates will not work. | |
8815 | (substitute* "Makefile.am" | |
8816 | (("\\$\\(bindir\\)/embossupdate") "")) | |
8817 | #t)) | |
d10092b8 | 8818 | (add-after 'disable-update-check 'autogen |
66e40e00 RW |
8819 | (lambda _ (zero? (system* "autoreconf" "-vif"))))))) |
8820 | (inputs | |
8821 | `(("perl" ,perl) | |
8822 | ("libpng" ,libpng) | |
8823 | ("gd" ,gd) | |
8824 | ("libx11" ,libx11) | |
8825 | ("libharu" ,libharu) | |
8826 | ("zlib" ,zlib))) | |
8827 | (native-inputs | |
8828 | `(("autoconf" ,autoconf) | |
8829 | ("automake" ,automake) | |
8830 | ("libtool" ,libtool) | |
8831 | ("pkg-config" ,pkg-config))) | |
8832 | (home-page "http://emboss.sourceforge.net") | |
8833 | (synopsis "Molecular biology analysis suite") | |
8834 | (description "EMBOSS is the \"European Molecular Biology Open Software | |
8835 | Suite\". EMBOSS is an analysis package specially developed for the needs of | |
8836 | the molecular biology (e.g. EMBnet) user community. The software | |
8837 | automatically copes with data in a variety of formats and even allows | |
8838 | transparent retrieval of sequence data from the web. It also provides a | |
8839 | number of libraries for the development of software in the field of molecular | |
8840 | biology. EMBOSS also integrates a range of currently available packages and | |
8841 | tools for sequence analysis into a seamless whole.") | |
8842 | (license license:gpl2+))) | |
8843 | ||
1f1b20b8 RW |
8844 | (define-public bits |
8845 | (let ((revision "1") | |
8846 | (commit "3cc4567896d9d6442923da944beb704750a08d2d")) | |
8847 | (package | |
8848 | (name "bits") | |
8849 | ;; The version is 2.13.0 even though no release archives have been | |
8850 | ;; published as yet. | |
8851 | (version (string-append "2.13.0-" revision "." (string-take commit 9))) | |
8852 | (source (origin | |
8853 | (method git-fetch) | |
8854 | (uri (git-reference | |
8855 | (url "https://github.com/arq5x/bits.git") | |
8856 | (commit commit))) | |
8857 | (file-name (string-append name "-" version "-checkout")) | |
8858 | (sha256 | |
8859 | (base32 | |
8860 | "17n2kffk4kmhivd8c98g2vr6y1s23vbg4sxlxs689wni66797hbs")))) | |
8861 | (build-system gnu-build-system) | |
8862 | (arguments | |
8863 | `(#:tests? #f ;no tests included | |
8864 | #:phases | |
8865 | (modify-phases %standard-phases | |
8866 | (delete 'configure) | |
8867 | (add-after 'unpack 'remove-cuda | |
8868 | (lambda _ | |
8869 | (substitute* "Makefile" | |
8870 | ((".*_cuda") "") | |
8871 | (("(bits_test_intersections) \\\\" _ match) match)) | |
8872 | #t)) | |
8873 | (replace 'install | |
8874 | (lambda* (#:key outputs #:allow-other-keys) | |
8875 | (copy-recursively | |
8876 | "bin" (string-append (assoc-ref outputs "out") "/bin")) | |
8877 | #t))))) | |
8878 | (inputs | |
8879 | `(("gsl" ,gsl) | |
8880 | ("zlib" ,zlib))) | |
8881 | (home-page "https://github.com/arq5x/bits") | |
8882 | (synopsis "Implementation of binary interval search algorithm") | |
8883 | (description "This package provides an implementation of the | |
8884 | BITS (Binary Interval Search) algorithm, an approach to interval set | |
8885 | intersection. It is especially suited for the comparison of diverse genomic | |
8886 | datasets and the exploration of large datasets of genome | |
8887 | intervals (e.g. genes, sequence alignments).") | |
8888 | (license license:gpl2)))) | |
8889 | ||
e62ffce5 | 8890 | (define-public piranha |
883302da RW |
8891 | ;; There is no release tarball for the latest version. The latest commit is |
8892 | ;; older than one year at the time of this writing. | |
8893 | (let ((revision "1") | |
8894 | (commit "0466d364b71117d01e4471b74c514436cc281233")) | |
8895 | (package | |
8896 | (name "piranha") | |
8897 | (version (string-append "1.2.1-" revision "." (string-take commit 9))) | |
8898 | (source (origin | |
8899 | (method git-fetch) | |
8900 | (uri (git-reference | |
8901 | (url "https://github.com/smithlabcode/piranha.git") | |
8902 | (commit commit))) | |
da49d137 | 8903 | (file-name (git-file-name name version)) |
883302da RW |
8904 | (sha256 |
8905 | (base32 | |
8906 | "117dc0zf20c61jam69sk4abl57ah6yi6i7qra7d7y5zrbgk12q5n")))) | |
8907 | (build-system gnu-build-system) | |
8908 | (arguments | |
8909 | `(#:test-target "test" | |
8910 | #:phases | |
8911 | (modify-phases %standard-phases | |
8912 | (add-after 'unpack 'copy-smithlab-cpp | |
8913 | (lambda* (#:key inputs #:allow-other-keys) | |
e62ffce5 | 8914 | (for-each (lambda (file) |
883302da RW |
8915 | (install-file file "./src/smithlab_cpp/")) |
8916 | (find-files (assoc-ref inputs "smithlab-cpp"))) | |
8917 | #t)) | |
8918 | (add-after 'install 'install-to-store | |
8919 | (lambda* (#:key outputs #:allow-other-keys) | |
8920 | (let* ((out (assoc-ref outputs "out")) | |
8921 | (bin (string-append out "/bin"))) | |
883302da RW |
8922 | (for-each (lambda (file) |
8923 | (install-file file bin)) | |
8924 | (find-files "bin" ".*"))) | |
8925 | #t))) | |
8926 | #:configure-flags | |
8927 | (list (string-append "--with-bam_tools_headers=" | |
8928 | (assoc-ref %build-inputs "bamtools") "/include/bamtools") | |
8929 | (string-append "--with-bam_tools_library=" | |
8930 | (assoc-ref %build-inputs "bamtools") "/lib/bamtools")))) | |
8931 | (inputs | |
8932 | `(("bamtools" ,bamtools) | |
8933 | ("samtools" ,samtools-0.1) | |
8934 | ("gsl" ,gsl) | |
8935 | ("smithlab-cpp" | |
8936 | ,(let ((commit "3723e2db438c51501d0423429ff396c3035ba46a")) | |
8937 | (origin | |
8938 | (method git-fetch) | |
8939 | (uri (git-reference | |
8940 | (url "https://github.com/smithlabcode/smithlab_cpp.git") | |
8941 | (commit commit))) | |
8942 | (file-name (string-append "smithlab_cpp-" commit "-checkout")) | |
8943 | (sha256 | |
8944 | (base32 | |
8945 | "0l4gvbwslw5ngziskja41c00x1r06l3yidv7y0xw9djibhykzy0g"))))))) | |
8946 | (native-inputs | |
8947 | `(("python" ,python-2))) | |
8948 | (home-page "https://github.com/smithlabcode/piranha") | |
8949 | (synopsis "Peak-caller for CLIP-seq and RIP-seq data") | |
8950 | (description | |
8951 | "Piranha is a peak-caller for genomic data produced by CLIP-seq and | |
e62ffce5 RW |
8952 | RIP-seq experiments. It takes input in BED or BAM format and identifies |
8953 | regions of statistically significant read enrichment. Additional covariates | |
8954 | may optionally be provided to further inform the peak-calling process.") | |
883302da | 8955 | (license license:gpl3+)))) |
e62ffce5 | 8956 | |
d1e32822 RW |
8957 | (define-public pepr |
8958 | (package | |
8959 | (name "pepr") | |
8960 | (version "1.0.9") | |
8961 | (source (origin | |
8962 | (method url-fetch) | |
8963 | (uri (string-append "https://pypi.python.org/packages/source/P" | |
8964 | "/PePr/PePr-" version ".tar.gz")) | |
8965 | (sha256 | |
8966 | (base32 | |
8967 | "0qxjfdpl1b1y53nccws2d85f6k74zwmx8y8sd9rszcqhfayx6gdx")))) | |
8968 | (build-system python-build-system) | |
8969 | (arguments | |
8970 | `(#:python ,python-2 ; python2 only | |
b41a05ce | 8971 | #:tests? #f)) ; no tests included |
d1e32822 RW |
8972 | (propagated-inputs |
8973 | `(("python2-numpy" ,python2-numpy) | |
8974 | ("python2-scipy" ,python2-scipy) | |
8975 | ("python2-pysam" ,python2-pysam))) | |
0c6c9c00 | 8976 | (home-page "https://github.com/shawnzhangyx/PePr") |
d1e32822 RW |
8977 | (synopsis "Peak-calling and prioritization pipeline for ChIP-Seq data") |
8978 | (description | |
8979 | "PePr is a ChIP-Seq peak calling or differential binding analysis tool | |
8980 | that is primarily designed for data with biological replicates. It uses a | |
8981 | negative binomial distribution to model the read counts among the samples in | |
8982 | the same group, and look for consistent differences between ChIP and control | |
8983 | group or two ChIP groups run under different conditions.") | |
8984 | (license license:gpl3+))) | |
6b49a37e RJ |
8985 | |
8986 | (define-public filevercmp | |
8987 | (let ((commit "1a9b779b93d0b244040274794d402106907b71b7")) | |
8988 | (package | |
8989 | (name "filevercmp") | |
8990 | (version (string-append "0-1." (string-take commit 7))) | |
8991 | (source (origin | |
8992 | (method url-fetch) | |
8993 | (uri (string-append "https://github.com/ekg/filevercmp/archive/" | |
8994 | commit ".tar.gz")) | |
8995 | (file-name (string-append name "-" version ".tar.gz")) | |
8996 | (sha256 | |
8997 | (base32 "0yp5jswf5j2pqc6517x277s4s6h1ss99v57kxw9gy0jkfl3yh450")))) | |
8998 | (build-system gnu-build-system) | |
8999 | (arguments | |
9000 | `(#:tests? #f ; There are no tests to run. | |
9001 | #:phases | |
9002 | (modify-phases %standard-phases | |
9003 | (delete 'configure) ; There is no configure phase. | |
9004 | (replace 'install | |
9005 | (lambda* (#:key outputs #:allow-other-keys) | |
9006 | (let ((bin (string-append (assoc-ref outputs "out") "/bin"))) | |
9007 | (install-file "filevercmp" bin))))))) | |
9008 | (home-page "https://github.com/ekg/filevercmp") | |
9009 | (synopsis "This program compares version strings") | |
9010 | (description "This program compares version strings. It intends to be a | |
9011 | replacement for strverscmp.") | |
9012 | (license license:gpl3+)))) | |
5fb5dffb RW |
9013 | |
9014 | (define-public multiqc | |
9015 | (package | |
9016 | (name "multiqc") | |
9e94d063 | 9017 | (version "1.4") |
5fb5dffb RW |
9018 | (source |
9019 | (origin | |
9020 | (method url-fetch) | |
9021 | (uri (pypi-uri "multiqc" version)) | |
9022 | (sha256 | |
9023 | (base32 | |
9e94d063 | 9024 | "0ihx4rzmsfphv4byn05qv6f1y95g2dxs6viwziipl4wjk96acgm8")))) |
5fb5dffb RW |
9025 | (build-system python-build-system) |
9026 | (propagated-inputs | |
9e94d063 | 9027 | `(("python-jinja2" ,python-jinja2) |
5fb5dffb RW |
9028 | ("python-simplejson" ,python-simplejson) |
9029 | ("python-pyyaml" ,python-pyyaml) | |
9030 | ("python-click" ,python-click) | |
799247d2 RW |
9031 | ("python-spectra" ,python-spectra) |
9032 | ("python-requests" ,python-requests) | |
9033 | ("python-markdown" ,python-markdown) | |
9034 | ("python-lzstring" ,python-lzstring) | |
5fb5dffb | 9035 | ("python-matplotlib" ,python-matplotlib) |
1778ea74 RW |
9036 | ("python-numpy" ,python-numpy) |
9037 | ;; MultQC checks for the presence of nose at runtime. | |
9038 | ("python-nose" ,python-nose))) | |
5fb5dffb RW |
9039 | (home-page "http://multiqc.info") |
9040 | (synopsis "Aggregate bioinformatics analysis reports") | |
9041 | (description | |
9042 | "MultiQC is a tool to aggregate bioinformatics results across many | |
9043 | samples into a single report. It contains modules for a large number of | |
9044 | common bioinformatics tools.") | |
66865ab8 | 9045 | (license license:gpl3+))) |
6193563a RW |
9046 | |
9047 | (define-public r-chipseq | |
9048 | (package | |
9049 | (name "r-chipseq") | |
eeaa6967 | 9050 | (version "1.28.0") |
6193563a RW |
9051 | (source |
9052 | (origin | |
9053 | (method url-fetch) | |
9054 | (uri (bioconductor-uri "chipseq" version)) | |
9055 | (sha256 | |
9056 | (base32 | |
eeaa6967 | 9057 | "1ymcq77krwjzrkzzcw7i9909cmkqa7c0675z9wzvrrk81hgdssfq")))) |
6193563a RW |
9058 | (build-system r-build-system) |
9059 | (propagated-inputs | |
9060 | `(("r-biocgenerics" ,r-biocgenerics) | |
9061 | ("r-genomicranges" ,r-genomicranges) | |
9062 | ("r-iranges" ,r-iranges) | |
eeaa6967 | 9063 | ("r-lattice" ,r-lattice) |
6193563a RW |
9064 | ("r-s4vectors" ,r-s4vectors) |
9065 | ("r-shortread" ,r-shortread))) | |
5713bbf1 | 9066 | (home-page "https://bioconductor.org/packages/chipseq") |
6193563a RW |
9067 | (synopsis "Package for analyzing ChIPseq data") |
9068 | (description | |
9069 | "This package provides tools for processing short read data from ChIPseq | |
9070 | experiments.") | |
9071 | (license license:artistic2.0))) | |
d407bdb9 RW |
9072 | |
9073 | (define-public r-copyhelper | |
9074 | (package | |
9075 | (name "r-copyhelper") | |
9076 | (version "1.6.0") | |
9077 | (source | |
9078 | (origin | |
9079 | (method url-fetch) | |
5713bbf1 | 9080 | (uri (string-append "https://bioconductor.org/packages/release/" |
d407bdb9 RW |
9081 | "data/experiment/src/contrib/CopyhelpeR_" |
9082 | version ".tar.gz")) | |
9083 | (sha256 | |
9084 | (base32 | |
9085 | "0x7cyynjmxls9as2gg0iyp9x5fpalxmdjq914ss7i84i9zyk5bhq")))) | |
9086 | (properties `((upstream-name . "CopyhelpeR"))) | |
9087 | (build-system r-build-system) | |
5713bbf1 | 9088 | (home-page "https://bioconductor.org/packages/CopyhelpeR/") |
d407bdb9 RW |
9089 | (synopsis "Helper files for CopywriteR") |
9090 | (description | |
9091 | "This package contains the helper files that are required to run the | |
9092 | Bioconductor package CopywriteR. It contains pre-assembled 1kb bin GC-content | |
9093 | and mappability files for the reference genomes hg18, hg19, hg38, mm9 and | |
9094 | mm10. In addition, it contains a blacklist filter to remove regions that | |
9095 | display copy number variation. Files are stored as GRanges objects from the | |
9096 | GenomicRanges Bioconductor package.") | |
9097 | (license license:gpl2))) | |
3a3bf2f8 RW |
9098 | |
9099 | (define-public r-copywriter | |
9100 | (package | |
9101 | (name "r-copywriter") | |
c126ba69 | 9102 | (version "2.10.0") |
3a3bf2f8 RW |
9103 | (source |
9104 | (origin | |
9105 | (method url-fetch) | |
9106 | (uri (bioconductor-uri "CopywriteR" version)) | |
9107 | (sha256 | |
9108 | (base32 | |
c126ba69 | 9109 | "17fy2lc5yf3nh6v077kv87h53n263hqz2540lzrl0vjiqrl2plca")))) |
3a3bf2f8 RW |
9110 | (properties `((upstream-name . "CopywriteR"))) |
9111 | (build-system r-build-system) | |
9112 | (propagated-inputs | |
9113 | `(("r-biocparallel" ,r-biocparallel) | |
9114 | ("r-chipseq" ,r-chipseq) | |
9115 | ("r-copyhelper" ,r-copyhelper) | |
9116 | ("r-data-table" ,r-data-table) | |
9117 | ("r-dnacopy" ,r-dnacopy) | |
9118 | ("r-futile-logger" ,r-futile-logger) | |
9119 | ("r-genomeinfodb" ,r-genomeinfodb) | |
9120 | ("r-genomicalignments" ,r-genomicalignments) | |
9121 | ("r-genomicranges" ,r-genomicranges) | |
9122 | ("r-gtools" ,r-gtools) | |
9123 | ("r-iranges" ,r-iranges) | |
9124 | ("r-matrixstats" ,r-matrixstats) | |
9125 | ("r-rsamtools" ,r-rsamtools) | |
9126 | ("r-s4vectors" ,r-s4vectors))) | |
9127 | (home-page "https://github.com/PeeperLab/CopywriteR") | |
9128 | (synopsis "Copy number information from targeted sequencing") | |
9129 | (description | |
9130 | "CopywriteR extracts DNA copy number information from targeted sequencing | |
9131 | by utilizing off-target reads. It allows for extracting uniformly distributed | |
9132 | copy number information, can be used without reference, and can be applied to | |
9133 | sequencing data obtained from various techniques including chromatin | |
9134 | immunoprecipitation and target enrichment on small gene panels. Thereby, | |
9135 | CopywriteR constitutes a widely applicable alternative to available copy | |
9136 | number detection tools.") | |
9137 | (license license:gpl2))) | |
dd42a330 | 9138 | |
bf3fa996 RW |
9139 | (define-public r-methylkit |
9140 | (package | |
9141 | (name "r-methylkit") | |
b1f27536 | 9142 | (version "1.4.1") |
bf3fa996 RW |
9143 | (source (origin |
9144 | (method url-fetch) | |
9145 | (uri (bioconductor-uri "methylKit" version)) | |
9146 | (sha256 | |
9147 | (base32 | |
b1f27536 | 9148 | "1k0nfn9318sgwm4z963bhnbp4c3zv85v3f9886vc5hgaisr0yvai")))) |
bf3fa996 RW |
9149 | (properties `((upstream-name . "methylKit"))) |
9150 | (build-system r-build-system) | |
9151 | (propagated-inputs | |
9152 | `(("r-data-table" ,r-data-table) | |
9153 | ("r-emdbook" ,r-emdbook) | |
9154 | ("r-fastseg" ,r-fastseg) | |
9155 | ("r-genomeinfodb" ,r-genomeinfodb) | |
9156 | ("r-genomicranges" ,r-genomicranges) | |
9157 | ("r-gtools" ,r-gtools) | |
9158 | ("r-iranges" ,r-iranges) | |
9159 | ("r-kernsmooth" ,r-kernsmooth) | |
9160 | ("r-limma" ,r-limma) | |
9161 | ("r-mclust" ,r-mclust) | |
9162 | ("r-qvalue" ,r-qvalue) | |
9163 | ("r-r-utils" ,r-r-utils) | |
9164 | ("r-rcpp" ,r-rcpp) | |
9165 | ("r-rhtslib" ,r-rhtslib) | |
9166 | ("r-rsamtools" ,r-rsamtools) | |
9167 | ("r-rtracklayer" ,r-rtracklayer) | |
9168 | ("r-s4vectors" ,r-s4vectors) | |
9169 | ("r-zlibbioc" ,r-zlibbioc))) | |
9170 | (inputs | |
9171 | `(("zlib" ,zlib))) | |
11ed4108 | 9172 | (home-page "https://github.com/al2na/methylKit") |
bf3fa996 RW |
9173 | (synopsis |
9174 | "DNA methylation analysis from high-throughput bisulfite sequencing results") | |
9175 | (description | |
9176 | "MethylKit is an R package for DNA methylation analysis and annotation | |
9177 | from high-throughput bisulfite sequencing. The package is designed to deal | |
9178 | with sequencing data from @dfn{Reduced representation bisulfite | |
9179 | sequencing} (RRBS) and its variants, but also target-capture methods and whole | |
9180 | genome bisulfite sequencing. It also has functions to analyze base-pair | |
9181 | resolution 5hmC data from experimental protocols such as oxBS-Seq and | |
9182 | TAB-Seq.") | |
9183 | (license license:artistic2.0))) | |
9184 | ||
dd42a330 RJPB |
9185 | (define-public r-sva |
9186 | (package | |
9187 | (name "r-sva") | |
fad7c0c7 | 9188 | (version "3.26.0") |
dd42a330 RJPB |
9189 | (source |
9190 | (origin | |
9191 | (method url-fetch) | |
9192 | (uri (bioconductor-uri "sva" version)) | |
9193 | (sha256 | |
9194 | (base32 | |
fad7c0c7 | 9195 | "0q5xb68wfcnchy8rkv5ma67pmz1i91lsnvmwmj8f1c3w4xan3pgw")))) |
dd42a330 RJPB |
9196 | (build-system r-build-system) |
9197 | (propagated-inputs | |
aeb64f3c | 9198 | `(("r-genefilter" ,r-genefilter) |
bfa0d1e7 RJ |
9199 | ("r-mgcv" ,r-mgcv) |
9200 | ("r-biocparallel" ,r-biocparallel) | |
9201 | ("r-matrixstats" ,r-matrixstats) | |
9202 | ("r-limma" ,r-limma))) | |
5713bbf1 | 9203 | (home-page "https://bioconductor.org/packages/sva") |
dd42a330 RJPB |
9204 | (synopsis "Surrogate variable analysis") |
9205 | (description | |
9206 | "This package contains functions for removing batch effects and other | |
9207 | unwanted variation in high-throughput experiment. It also contains functions | |
9208 | for identifying and building surrogate variables for high-dimensional data | |
9209 | sets. Surrogate variables are covariates constructed directly from | |
9210 | high-dimensional data like gene expression/RNA sequencing/methylation/brain | |
9211 | imaging data that can be used in subsequent analyses to adjust for unknown, | |
9212 | unmodeled, or latent sources of noise.") | |
9213 | (license license:artistic2.0))) | |
fb1e528e RW |
9214 | |
9215 | (define-public r-seqminer | |
9216 | (package | |
9217 | (name "r-seqminer") | |
5e0de298 | 9218 | (version "6.0") |
fb1e528e RW |
9219 | (source |
9220 | (origin | |
9221 | (method url-fetch) | |
9222 | (uri (cran-uri "seqminer" version)) | |
9223 | (sha256 | |
9224 | (base32 | |
5e0de298 | 9225 | "057j1l6dip35l1aivilapl2zv9db677b3di2pb3sfgq2sxg0ps3l")))) |
fb1e528e RW |
9226 | (build-system r-build-system) |
9227 | (inputs | |
9228 | `(("zlib" ,zlib))) | |
9229 | (home-page "http://seqminer.genomic.codes") | |
9230 | (synopsis "Read nucleotide sequence data (VCF, BCF, and METAL formats)") | |
9231 | (description | |
9232 | "This package provides tools to integrate nucleotide sequencing | |
9233 | data (variant call format, e.g. VCF or BCF) or meta-analysis results in R.") | |
9234 | ;; Any version of the GPL is acceptable | |
9235 | (license (list license:gpl2+ license:gpl3+)))) | |
1f40e73c RW |
9236 | |
9237 | (define-public r-raremetals2 | |
9238 | (package | |
9239 | (name "r-raremetals2") | |
9240 | (version "0.1") | |
9241 | (source | |
9242 | (origin | |
9243 | (method url-fetch) | |
9244 | (uri (string-append "http://genome.sph.umich.edu/w/images/" | |
9245 | "b/b7/RareMETALS2_" version ".tar.gz")) | |
9246 | (sha256 | |
9247 | (base32 | |
9248 | "0z5ljcgvnm06ja9lm85a3cniq7slxcy37aqqkxrdidr79an5fs4s")))) | |
9249 | (properties `((upstream-name . "RareMETALS2"))) | |
9250 | (build-system r-build-system) | |
9251 | (propagated-inputs | |
9252 | `(("r-seqminer" ,r-seqminer) | |
9253 | ("r-mvtnorm" ,r-mvtnorm) | |
aeb64f3c | 9254 | ("r-mass" ,r-mass) |
1f40e73c RW |
9255 | ("r-compquadform" ,r-compquadform) |
9256 | ("r-getopt" ,r-getopt))) | |
9257 | (home-page "http://genome.sph.umich.edu/wiki/RareMETALS2") | |
9258 | (synopsis "Analyze gene-level association tests for binary trait") | |
9259 | (description | |
9260 | "The R package rareMETALS2 is an extension of the R package rareMETALS. | |
9261 | It was designed to meta-analyze gene-level association tests for binary trait. | |
9262 | While rareMETALS offers a near-complete solution for meta-analysis of | |
9263 | gene-level tests for quantitative trait, it does not offer the optimal | |
9264 | solution for binary trait. The package rareMETALS2 offers improved features | |
9265 | for analyzing gene-level association tests in meta-analyses for binary | |
9266 | trait.") | |
9267 | (license license:gpl3))) | |
0e7d058e RW |
9268 | |
9269 | (define-public r-maldiquant | |
9270 | (package | |
9271 | (name "r-maldiquant") | |
43949265 | 9272 | (version "1.17") |
0e7d058e RW |
9273 | (source |
9274 | (origin | |
9275 | (method url-fetch) | |
9276 | (uri (cran-uri "MALDIquant" version)) | |
9277 | (sha256 | |
9278 | (base32 | |
43949265 | 9279 | "047s6007ydc38x8wm027mlb4mngz15n0d4238fr8h43wyll5zy0z")))) |
0e7d058e RW |
9280 | (properties `((upstream-name . "MALDIquant"))) |
9281 | (build-system r-build-system) | |
e9960d8c | 9282 | (home-page "https://cran.r-project.org/web/packages/MALDIquant") |
0e7d058e RW |
9283 | (synopsis "Quantitative analysis of mass spectrometry data") |
9284 | (description | |
9285 | "This package provides a complete analysis pipeline for matrix-assisted | |
9286 | laser desorption/ionization-time-of-flight (MALDI-TOF) and other | |
9287 | two-dimensional mass spectrometry data. In addition to commonly used plotting | |
9288 | and processing methods it includes distinctive features, namely baseline | |
9289 | subtraction methods such as morphological filters (TopHat) or the | |
9290 | statistics-sensitive non-linear iterative peak-clipping algorithm (SNIP), peak | |
9291 | alignment using warping functions, handling of replicated measurements as well | |
9292 | as allowing spectra with different resolutions.") | |
9293 | (license license:gpl3+))) | |
ae262174 RW |
9294 | |
9295 | (define-public r-protgenerics | |
9296 | (package | |
9297 | (name "r-protgenerics") | |
9a665dfb | 9298 | (version "1.10.0") |
ae262174 RW |
9299 | (source |
9300 | (origin | |
9301 | (method url-fetch) | |
9302 | (uri (bioconductor-uri "ProtGenerics" version)) | |
9303 | (sha256 | |
9304 | (base32 | |
9a665dfb | 9305 | "16ijp50448wnabp43klx943rhdvh7x45hvy7cnpq1s4dckxhhyni")))) |
ae262174 RW |
9306 | (properties `((upstream-name . "ProtGenerics"))) |
9307 | (build-system r-build-system) | |
9308 | (home-page "https://github.com/lgatto/ProtGenerics") | |
9309 | (synopsis "S4 generic functions for proteomics infrastructure") | |
9310 | (description | |
9311 | "This package provides S4 generic functions needed by Bioconductor | |
9312 | proteomics packages.") | |
9313 | (license license:artistic2.0))) | |
71676a1f RW |
9314 | |
9315 | (define-public r-mzr | |
9316 | (package | |
9317 | (name "r-mzr") | |
34b96754 | 9318 | (version "2.12.0") |
71676a1f RW |
9319 | (source |
9320 | (origin | |
9321 | (method url-fetch) | |
9322 | (uri (bioconductor-uri "mzR" version)) | |
9323 | (sha256 | |
9324 | (base32 | |
15ca1959 RW |
9325 | "1x3gp30sfxz2v3k3swih9kff9b2rvk7hzhnlkp6ywlnn2wgb0q8c")) |
9326 | (modules '((guix build utils))) | |
9327 | (snippet | |
9328 | '(begin | |
9329 | (delete-file-recursively "src/boost") | |
9330 | #t)))) | |
71676a1f RW |
9331 | (properties `((upstream-name . "mzR"))) |
9332 | (build-system r-build-system) | |
15ca1959 RW |
9333 | (arguments |
9334 | `(#:phases | |
9335 | (modify-phases %standard-phases | |
9336 | (add-after 'unpack 'use-system-boost | |
9337 | (lambda _ | |
9338 | (substitute* "src/Makevars" | |
9339 | (("\\./boost/libs.*") "") | |
9340 | (("ARCH_OBJS=" line) | |
9341 | (string-append line | |
9342 | "\nARCH_LIBS=-lboost_system -lboost_regex \ | |
9343 | -lboost_iostreams -lboost_thread -lboost_filesystem -lboost_chrono\n"))) | |
9344 | #t))))) | |
71676a1f | 9345 | (inputs |
34b96754 | 9346 | `(("boost" ,boost) ; use this instead of the bundled boost sources |
d534f3a4 | 9347 | ("netcdf" ,netcdf))) |
71676a1f RW |
9348 | (propagated-inputs |
9349 | `(("r-biobase" ,r-biobase) | |
9350 | ("r-biocgenerics" ,r-biocgenerics) | |
9351 | ("r-protgenerics" ,r-protgenerics) | |
9352 | ("r-rcpp" ,r-rcpp) | |
9353 | ("r-zlibbioc" ,r-zlibbioc))) | |
9354 | (home-page "https://github.com/sneumann/mzR/") | |
9355 | (synopsis "Parser for mass spectrometry data files") | |
9356 | (description | |
9357 | "The mzR package provides a unified API to the common file formats and | |
9358 | parsers available for mass spectrometry data. It comes with a wrapper for the | |
9359 | ISB random access parser for mass spectrometry mzXML, mzData and mzML files. | |
9360 | The package contains the original code written by the ISB, and a subset of the | |
9361 | proteowizard library for mzML and mzIdentML. The netCDF reading code has | |
9362 | previously been used in XCMS.") | |
9363 | (license license:artistic2.0))) | |
5c9d1505 RW |
9364 | |
9365 | (define-public r-affyio | |
9366 | (package | |
9367 | (name "r-affyio") | |
8a8138d2 | 9368 | (version "1.48.0") |
5c9d1505 RW |
9369 | (source |
9370 | (origin | |
9371 | (method url-fetch) | |
9372 | (uri (bioconductor-uri "affyio" version)) | |
9373 | (sha256 | |
9374 | (base32 | |
8a8138d2 | 9375 | "1pzzp3d3dbmyf34gvivfiprkpscn36rgvhrq853a1d3avcwr5ak9")))) |
5c9d1505 RW |
9376 | (build-system r-build-system) |
9377 | (propagated-inputs | |
9378 | `(("r-zlibbioc" ,r-zlibbioc))) | |
9379 | (inputs | |
9380 | `(("zlib" ,zlib))) | |
9381 | (home-page "https://github.com/bmbolstad/affyio") | |
9382 | (synopsis "Tools for parsing Affymetrix data files") | |
9383 | (description | |
9384 | "This package provides routines for parsing Affymetrix data files based | |
9385 | upon file format information. The primary focus is on accessing the CEL and | |
9386 | CDF file formats.") | |
9387 | (license license:lgpl2.0+))) | |
05c7e5fb RW |
9388 | |
9389 | (define-public r-affy | |
9390 | (package | |
9391 | (name "r-affy") | |
dad5f838 | 9392 | (version "1.56.0") |
05c7e5fb RW |
9393 | (source |
9394 | (origin | |
9395 | (method url-fetch) | |
9396 | (uri (bioconductor-uri "affy" version)) | |
9397 | (sha256 | |
9398 | (base32 | |
dad5f838 | 9399 | "0jmbkimma5ffsdkk3xp03g4lpz84gd95nkqakif2nqq6wmx0syrj")))) |
05c7e5fb RW |
9400 | (build-system r-build-system) |
9401 | (propagated-inputs | |
9402 | `(("r-affyio" ,r-affyio) | |
9403 | ("r-biobase" ,r-biobase) | |
9404 | ("r-biocgenerics" ,r-biocgenerics) | |
9405 | ("r-biocinstaller" ,r-biocinstaller) | |
9406 | ("r-preprocesscore" ,r-preprocesscore) | |
9407 | ("r-zlibbioc" ,r-zlibbioc))) | |
5713bbf1 | 9408 | (home-page "https://bioconductor.org/packages/affy") |
05c7e5fb RW |
9409 | (synopsis "Methods for affymetrix oligonucleotide arrays") |
9410 | (description | |
9411 | "This package contains functions for exploratory oligonucleotide array | |
9412 | analysis.") | |
9413 | (license license:lgpl2.0+))) | |
7c08afaf RW |
9414 | |
9415 | (define-public r-vsn | |
9416 | (package | |
9417 | (name "r-vsn") | |
1be0f536 | 9418 | (version "3.46.0") |
7c08afaf RW |
9419 | (source |
9420 | (origin | |
9421 | (method url-fetch) | |
9422 | (uri (bioconductor-uri "vsn" version)) | |
9423 | (sha256 | |
9424 | (base32 | |
1be0f536 | 9425 | "18y62phzirj75gg6v5l41jwybmk23ia6w7qhch0kxc4bl2rysw6j")))) |
7c08afaf RW |
9426 | (build-system r-build-system) |
9427 | (propagated-inputs | |
9428 | `(("r-affy" ,r-affy) | |
9429 | ("r-biobase" ,r-biobase) | |
9430 | ("r-ggplot2" ,r-ggplot2) | |
aeb64f3c | 9431 | ("r-lattice" ,r-lattice) |
7c08afaf | 9432 | ("r-limma" ,r-limma))) |
5713bbf1 | 9433 | (home-page "https://bioconductor.org/packages/release/bioc/html/vsn.html") |
7c08afaf RW |
9434 | (synopsis "Variance stabilization and calibration for microarray data") |
9435 | (description | |
9436 | "The package implements a method for normalising microarray intensities, | |
9437 | and works for single- and multiple-color arrays. It can also be used for data | |
9438 | from other technologies, as long as they have similar format. The method uses | |
9439 | a robust variant of the maximum-likelihood estimator for an | |
9440 | additive-multiplicative error model and affine calibration. The model | |
9441 | incorporates data calibration step (a.k.a. normalization), a model for the | |
9442 | dependence of the variance on the mean intensity and a variance stabilizing | |
9443 | data transformation. Differences between transformed intensities are | |
9444 | analogous to \"normalized log-ratios\". However, in contrast to the latter, | |
9445 | their variance is independent of the mean, and they are usually more sensitive | |
9446 | and specific in detecting differential transcription.") | |
9447 | (license license:artistic2.0))) | |
4aa7d592 RW |
9448 | |
9449 | (define-public r-mzid | |
9450 | (package | |
9451 | (name "r-mzid") | |
b500dbcd | 9452 | (version "1.16.0") |
4aa7d592 RW |
9453 | (source |
9454 | (origin | |
9455 | (method url-fetch) | |
9456 | (uri (bioconductor-uri "mzID" version)) | |
9457 | (sha256 | |
9458 | (base32 | |
b500dbcd | 9459 | "0yk70dka56zd8w62f03ggx3mandj91gfa767h9ajj0sd3mjmfqb9")))) |
4aa7d592 RW |
9460 | (properties `((upstream-name . "mzID"))) |
9461 | (build-system r-build-system) | |
9462 | (propagated-inputs | |
9463 | `(("r-doparallel" ,r-doparallel) | |
9464 | ("r-foreach" ,r-foreach) | |
9465 | ("r-iterators" ,r-iterators) | |
9466 | ("r-plyr" ,r-plyr) | |
9467 | ("r-protgenerics" ,r-protgenerics) | |
9468 | ("r-rcpp" ,r-rcpp) | |
9469 | ("r-xml" ,r-xml))) | |
5713bbf1 | 9470 | (home-page "https://bioconductor.org/packages/mzID") |
4aa7d592 RW |
9471 | (synopsis "Parser for mzIdentML files") |
9472 | (description | |
9473 | "This package provides a parser for mzIdentML files implemented using the | |
9474 | XML package. The parser tries to be general and able to handle all types of | |
9475 | mzIdentML files with the drawback of having less pretty output than a vendor | |
9476 | specific parser.") | |
9477 | (license license:gpl2+))) | |
6a67e181 RW |
9478 | |
9479 | (define-public r-pcamethods | |
9480 | (package | |
9481 | (name "r-pcamethods") | |
a998c9a4 | 9482 | (version "1.70.0") |
6a67e181 RW |
9483 | (source |
9484 | (origin | |
9485 | (method url-fetch) | |
9486 | (uri (bioconductor-uri "pcaMethods" version)) | |
9487 | (sha256 | |
9488 | (base32 | |
a998c9a4 | 9489 | "0ii235g0x0492kh8cfrf28ni0b6vd6fh7kizkqmczzqggd6b1bk8")))) |
6a67e181 RW |
9490 | (properties `((upstream-name . "pcaMethods"))) |
9491 | (build-system r-build-system) | |
9492 | (propagated-inputs | |
9493 | `(("r-biobase" ,r-biobase) | |
9494 | ("r-biocgenerics" ,r-biocgenerics) | |
aeb64f3c | 9495 | ("r-mass" ,r-mass) |
6a67e181 RW |
9496 | ("r-rcpp" ,r-rcpp))) |
9497 | (home-page "https://github.com/hredestig/pcamethods") | |
9498 | (synopsis "Collection of PCA methods") | |
9499 | (description | |
9500 | "This package provides Bayesian PCA, Probabilistic PCA, Nipals PCA, | |
9501 | Inverse Non-Linear PCA and the conventional SVD PCA. A cluster based method | |
9502 | for missing value estimation is included for comparison. BPCA, PPCA and | |
9503 | NipalsPCA may be used to perform PCA on incomplete data as well as for | |
9504 | accurate missing value estimation. A set of methods for printing and plotting | |
9505 | the results is also provided. All PCA methods make use of the same data | |
9506 | structure (pcaRes) to provide a common interface to the PCA results.") | |
9507 | (license license:gpl3+))) | |
11879284 RW |
9508 | |
9509 | (define-public r-msnbase | |
9510 | (package | |
9511 | (name "r-msnbase") | |
53f0dea9 | 9512 | (version "2.4.2") |
11879284 RW |
9513 | (source |
9514 | (origin | |
9515 | (method url-fetch) | |
9516 | (uri (bioconductor-uri "MSnbase" version)) | |
9517 | (sha256 | |
9518 | (base32 | |
53f0dea9 | 9519 | "1ig64bf881p118dwqfr0ry41m7yhnyv165smv8fdwfv7sb6sagif")))) |
11879284 RW |
9520 | (properties `((upstream-name . "MSnbase"))) |
9521 | (build-system r-build-system) | |
9522 | (propagated-inputs | |
9523 | `(("r-affy" ,r-affy) | |
9524 | ("r-biobase" ,r-biobase) | |
9525 | ("r-biocgenerics" ,r-biocgenerics) | |
9526 | ("r-biocparallel" ,r-biocparallel) | |
9527 | ("r-digest" ,r-digest) | |
9528 | ("r-ggplot2" ,r-ggplot2) | |
9529 | ("r-impute" ,r-impute) | |
9530 | ("r-iranges" ,r-iranges) | |
baa00ee9 | 9531 | ("r-lattice" ,r-lattice) |
11879284 RW |
9532 | ("r-maldiquant" ,r-maldiquant) |
9533 | ("r-mzid" ,r-mzid) | |
9534 | ("r-mzr" ,r-mzr) | |
9535 | ("r-pcamethods" ,r-pcamethods) | |
9536 | ("r-plyr" ,r-plyr) | |
9537 | ("r-preprocesscore" ,r-preprocesscore) | |
9538 | ("r-protgenerics" ,r-protgenerics) | |
9539 | ("r-rcpp" ,r-rcpp) | |
11879284 RW |
9540 | ("r-s4vectors" ,r-s4vectors) |
9541 | ("r-vsn" ,r-vsn) | |
9542 | ("r-xml" ,r-xml))) | |
9543 | (home-page "https://github.com/lgatto/MSnbase") | |
9544 | (synopsis "Base functions and classes for MS-based proteomics") | |
9545 | (description | |
9546 | "This package provides basic plotting, data manipulation and processing | |
e614d639 | 9547 | of mass spectrometry based proteomics data.") |
11879284 | 9548 | (license license:artistic2.0))) |
66da3a9f RW |
9549 | |
9550 | (define-public r-msnid | |
9551 | (package | |
9552 | (name "r-msnid") | |
87e91a9f | 9553 | (version "1.12.1") |
66da3a9f RW |
9554 | (source |
9555 | (origin | |
9556 | (method url-fetch) | |
9557 | (uri (bioconductor-uri "MSnID" version)) | |
9558 | (sha256 | |
9559 | (base32 | |
87e91a9f | 9560 | "1zw508kk4f8brg69674wp18gqkpx2kpya5f6x9cl3qng7v4h5pxx")))) |
66da3a9f RW |
9561 | (properties `((upstream-name . "MSnID"))) |
9562 | (build-system r-build-system) | |
9563 | (propagated-inputs | |
9564 | `(("r-biobase" ,r-biobase) | |
9565 | ("r-data-table" ,r-data-table) | |
9566 | ("r-doparallel" ,r-doparallel) | |
9567 | ("r-dplyr" ,r-dplyr) | |
9568 | ("r-foreach" ,r-foreach) | |
9569 | ("r-iterators" ,r-iterators) | |
9570 | ("r-msnbase" ,r-msnbase) | |
9571 | ("r-mzid" ,r-mzid) | |
9572 | ("r-mzr" ,r-mzr) | |
9573 | ("r-protgenerics" ,r-protgenerics) | |
9574 | ("r-r-cache" ,r-r-cache) | |
9575 | ("r-rcpp" ,r-rcpp) | |
9576 | ("r-reshape2" ,r-reshape2))) | |
5713bbf1 | 9577 | (home-page "https://bioconductor.org/packages/MSnID") |
66da3a9f RW |
9578 | (synopsis "Utilities for LC-MSn proteomics identifications") |
9579 | (description | |
2923f3e5 RW |
9580 | "This package extracts @dfn{tandem mass spectrometry} (MS/MS) ID data |
9581 | from mzIdentML (leveraging the mzID package) or text files. After collating | |
9582 | the search results from multiple datasets it assesses their identification | |
9583 | quality and optimize filtering criteria to achieve the maximum number of | |
9584 | identifications while not exceeding a specified false discovery rate. It also | |
9585 | contains a number of utilities to explore the MS/MS results and assess missed | |
9586 | and irregular enzymatic cleavages, mass measurement accuracy, etc.") | |
66da3a9f | 9587 | (license license:artistic2.0))) |
5ded35d8 | 9588 | |
2441c284 | 9589 | (define-public r-seurat |
f1a2b1cb RW |
9590 | (package |
9591 | (name "r-seurat") | |
ebec98ae | 9592 | (version "2.2.1") |
f1a2b1cb RW |
9593 | (source (origin |
9594 | (method url-fetch) | |
9595 | (uri (cran-uri "Seurat" version)) | |
9596 | (sha256 | |
9597 | (base32 | |
ebec98ae | 9598 | "1sr82nf38hq07avrfn8vlrzjq7dfm4pcr8l1nh6mnglcql2bk9z2")) |
f1a2b1cb RW |
9599 | ;; Delete pre-built jar. |
9600 | (snippet | |
9601 | '(begin (delete-file "inst/java/ModularityOptimizer.jar") | |
9602 | #t)))) | |
9603 | (properties `((upstream-name . "Seurat"))) | |
9604 | (build-system r-build-system) | |
9605 | (arguments | |
9606 | `(#:phases | |
9607 | (modify-phases %standard-phases | |
9608 | (add-after 'unpack 'build-jar | |
9609 | (lambda* (#:key inputs #:allow-other-keys) | |
9610 | (let ((classesdir "tmp-classes")) | |
9611 | (setenv "JAVA_HOME" (assoc-ref inputs "jdk")) | |
9612 | (mkdir classesdir) | |
9613 | (with-output-to-file "manifest" | |
8271b8d2 RW |
9614 | (lambda _ |
9615 | (display "Manifest-Version: 1.0 | |
9616 | Main-Class: ModularityOptimizer\n"))) | |
9617 | (and (zero? (apply system* `("javac" "-d" ,classesdir | |
9618 | ,@(find-files "java" "\\.java$")))) | |
9619 | (zero? (system* "jar" | |
9620 | "-cmf" "manifest" | |
9621 | "inst/java/ModularityOptimizer.jar" | |
f1a2b1cb RW |
9622 | "-C" classesdir "."))))))))) |
9623 | (native-inputs | |
9624 | `(("jdk" ,icedtea "jdk"))) | |
9625 | (propagated-inputs | |
9626 | `(("r-ape" ,r-ape) | |
9627 | ("r-caret" ,r-caret) | |
9628 | ("r-cowplot" ,r-cowplot) | |
9629 | ("r-diffusionmap" ,r-diffusionmap) | |
9630 | ("r-dplyr" ,r-dplyr) | |
9631 | ("r-dtw" ,r-dtw) | |
9632 | ("r-fnn" ,r-fnn) | |
9633 | ("r-fpc" ,r-fpc) | |
9634 | ("r-gdata" ,r-gdata) | |
f1a2b1cb | 9635 | ("r-ggplot2" ,r-ggplot2) |
26e3e28c | 9636 | ("r-ggridges" ,r-ggridges) |
f1a2b1cb RW |
9637 | ("r-gplots" ,r-gplots) |
9638 | ("r-gridextra" ,r-gridextra) | |
9639 | ("r-hmisc" ,r-hmisc) | |
9640 | ("r-ica" ,r-ica) | |
9641 | ("r-igraph" ,r-igraph) | |
9642 | ("r-irlba" ,r-irlba) | |
9643 | ("r-lars" ,r-lars) | |
9644 | ("r-mass" ,r-mass) | |
9645 | ("r-matrix" ,r-matrix) | |
ebec98ae | 9646 | ("r-metap" ,r-metap) |
f1a2b1cb | 9647 | ("r-mixtools" ,r-mixtools) |
f1a2b1cb RW |
9648 | ("r-pbapply" ,r-pbapply) |
9649 | ("r-plotly" ,r-plotly) | |
9650 | ("r-ranger" ,r-ranger) | |
9651 | ("r-rcolorbrewer" ,r-rcolorbrewer) | |
9652 | ("r-rcpp" ,r-rcpp) | |
26e3e28c | 9653 | ("r-rcppeigen" ,r-rcppeigen) |
f1a2b1cb RW |
9654 | ("r-rcppprogress" ,r-rcppprogress) |
9655 | ("r-reshape2" ,r-reshape2) | |
9656 | ("r-rocr" ,r-rocr) | |
9657 | ("r-rtsne" ,r-rtsne) | |
9658 | ("r-sdmtools" ,r-sdmtools) | |
9659 | ("r-stringr" ,r-stringr) | |
9660 | ("r-tclust" ,r-tclust) | |
9661 | ("r-tidyr" ,r-tidyr) | |
9662 | ("r-tsne" ,r-tsne) | |
9663 | ("r-vgam" ,r-vgam))) | |
9664 | (home-page "http://www.satijalab.org/seurat") | |
9665 | (synopsis "Seurat is an R toolkit for single cell genomics") | |
9666 | (description | |
9667 | "This package is an R package designed for QC, analysis, and | |
2441c284 RJPB |
9668 | exploration of single cell RNA-seq data. It easily enables widely-used |
9669 | analytical techniques, including the identification of highly variable genes, | |
9670 | dimensionality reduction; PCA, ICA, t-SNE, standard unsupervised clustering | |
9671 | algorithms; density clustering, hierarchical clustering, k-means, and the | |
9672 | discovery of differentially expressed genes and markers.") | |
f1a2b1cb | 9673 | (license license:gpl3))) |
2441c284 | 9674 | |
d4b83651 RW |
9675 | (define-public r-aroma-light |
9676 | (package | |
9677 | (name "r-aroma-light") | |
531e8090 | 9678 | (version "3.8.0") |
d4b83651 RW |
9679 | (source |
9680 | (origin | |
9681 | (method url-fetch) | |
9682 | (uri (bioconductor-uri "aroma.light" version)) | |
9683 | (sha256 | |
9684 | (base32 | |
531e8090 | 9685 | "0crnk6851jwypqr5l5jcbbay0vi5vvdjyisaf6z2d69c39wmr6sc")))) |
d4b83651 RW |
9686 | (properties `((upstream-name . "aroma.light"))) |
9687 | (build-system r-build-system) | |
9688 | (propagated-inputs | |
9689 | `(("r-matrixstats" ,r-matrixstats) | |
9690 | ("r-r-methodss3" ,r-r-methodss3) | |
9691 | ("r-r-oo" ,r-r-oo) | |
9692 | ("r-r-utils" ,r-r-utils))) | |
9693 | (home-page "https://github.com/HenrikBengtsson/aroma.light") | |
9694 | (synopsis "Methods for normalization and visualization of microarray data") | |
9695 | (description | |
9696 | "This package provides methods for microarray analysis that take basic | |
9697 | data types such as matrices and lists of vectors. These methods can be used | |
9698 | standalone, be utilized in other packages, or be wrapped up in higher-level | |
9699 | classes.") | |
9700 | (license license:gpl2+))) | |
9701 | ||
7b465327 RW |
9702 | (define-public r-deseq |
9703 | (package | |
9704 | (name "r-deseq") | |
8140f680 | 9705 | (version "1.30.0") |
7b465327 RW |
9706 | (source |
9707 | (origin | |
9708 | (method url-fetch) | |
9709 | (uri (bioconductor-uri "DESeq" version)) | |
9710 | (sha256 | |
9711 | (base32 | |
8140f680 | 9712 | "0mn5w3cy16iwwk8zxs7za6aa6cnrca75z0g45zd5zh1py5d7nfv9")))) |
7b465327 RW |
9713 | (properties `((upstream-name . "DESeq"))) |
9714 | (build-system r-build-system) | |
9715 | (propagated-inputs | |
9716 | `(("r-biobase" ,r-biobase) | |
9717 | ("r-biocgenerics" ,r-biocgenerics) | |
9718 | ("r-genefilter" ,r-genefilter) | |
9719 | ("r-geneplotter" ,r-geneplotter) | |
9720 | ("r-lattice" ,r-lattice) | |
9721 | ("r-locfit" ,r-locfit) | |
9722 | ("r-mass" ,r-mass) | |
9723 | ("r-rcolorbrewer" ,r-rcolorbrewer))) | |
9724 | (home-page "http://www-huber.embl.de/users/anders/DESeq") | |
9725 | (synopsis "Differential gene expression analysis") | |
9726 | (description | |
9727 | "This package provides tools for estimating variance-mean dependence in | |
9728 | count data from high-throughput genetic sequencing assays and for testing for | |
9729 | differential expression based on a model using the negative binomial | |
9730 | distribution.") | |
9731 | (license license:gpl3+))) | |
9732 | ||
296b3c63 RW |
9733 | (define-public r-edaseq |
9734 | (package | |
9735 | (name "r-edaseq") | |
00961279 | 9736 | (version "2.12.0") |
296b3c63 RW |
9737 | (source |
9738 | (origin | |
9739 | (method url-fetch) | |
9740 | (uri (bioconductor-uri "EDASeq" version)) | |
9741 | (sha256 | |
9742 | (base32 | |
00961279 | 9743 | "07zm89zcivyn2261aq9grqmly8ji482kr9h9dyfknfdfrpv7jpwv")))) |
296b3c63 RW |
9744 | (properties `((upstream-name . "EDASeq"))) |
9745 | (build-system r-build-system) | |
9746 | (propagated-inputs | |
9747 | `(("r-annotationdbi" ,r-annotationdbi) | |
9748 | ("r-aroma-light" ,r-aroma-light) | |
9749 | ("r-biobase" ,r-biobase) | |
9750 | ("r-biocgenerics" ,r-biocgenerics) | |
9751 | ("r-biomart" ,r-biomart) | |
9752 | ("r-biostrings" ,r-biostrings) | |
9753 | ("r-deseq" ,r-deseq) | |
9754 | ("r-genomicfeatures" ,r-genomicfeatures) | |
9755 | ("r-genomicranges" ,r-genomicranges) | |
9756 | ("r-iranges" ,r-iranges) | |
9757 | ("r-rsamtools" ,r-rsamtools) | |
9758 | ("r-shortread" ,r-shortread))) | |
9759 | (home-page "https://github.com/drisso/EDASeq") | |
9760 | (synopsis "Exploratory data analysis and normalization for RNA-Seq") | |
9761 | (description | |
9762 | "This package provides support for numerical and graphical summaries of | |
9763 | RNA-Seq genomic read data. Provided within-lane normalization procedures to | |
9764 | adjust for GC-content effect (or other gene-level effects) on read counts: | |
9765 | loess robust local regression, global-scaling, and full-quantile | |
9766 | normalization. Between-lane normalization procedures to adjust for | |
9767 | distributional differences between lanes (e.g., sequencing depth): | |
9768 | global-scaling and full-quantile normalization.") | |
9769 | (license license:artistic2.0))) | |
9770 | ||
5f96f30f RW |
9771 | (define-public r-interactivedisplaybase |
9772 | (package | |
9773 | (name "r-interactivedisplaybase") | |
1567c8d9 | 9774 | (version "1.16.0") |
5f96f30f RW |
9775 | (source |
9776 | (origin | |
9777 | (method url-fetch) | |
9778 | (uri (bioconductor-uri "interactiveDisplayBase" version)) | |
9779 | (sha256 | |
9780 | (base32 | |
1567c8d9 | 9781 | "01yb945jqqimwjgriza6yy4dnp303cdirxrhl4hjyprfdlmnz5p5")))) |
5f96f30f RW |
9782 | (properties |
9783 | `((upstream-name . "interactiveDisplayBase"))) | |
9784 | (build-system r-build-system) | |
9785 | (propagated-inputs | |
9786 | `(("r-biocgenerics" ,r-biocgenerics) | |
9787 | ("r-shiny" ,r-shiny))) | |
5713bbf1 | 9788 | (home-page "https://bioconductor.org/packages/interactiveDisplayBase") |
5f96f30f RW |
9789 | (synopsis "Base package for web displays of Bioconductor objects") |
9790 | (description | |
9791 | "This package contains the basic methods needed to generate interactive | |
9792 | Shiny-based display methods for Bioconductor objects.") | |
9793 | (license license:artistic2.0))) | |
9794 | ||
4a007ffa RW |
9795 | (define-public r-annotationhub |
9796 | (package | |
9797 | (name "r-annotationhub") | |
9b8d0201 | 9798 | (version "2.10.1") |
4a007ffa RW |
9799 | (source |
9800 | (origin | |
9801 | (method url-fetch) | |
9802 | (uri (bioconductor-uri "AnnotationHub" version)) | |
9803 | (sha256 | |
9804 | (base32 | |
9b8d0201 | 9805 | "14v8g44a6zg9j2rwn9x9y8509k0wr2cw8yccliz24glplb40wva4")))) |
4a007ffa RW |
9806 | (properties `((upstream-name . "AnnotationHub"))) |
9807 | (build-system r-build-system) | |
9808 | (propagated-inputs | |
9809 | `(("r-annotationdbi" ,r-annotationdbi) | |
9810 | ("r-biocgenerics" ,r-biocgenerics) | |
9811 | ("r-biocinstaller" ,r-biocinstaller) | |
14b3c719 | 9812 | ("r-curl" ,r-curl) |
4a007ffa RW |
9813 | ("r-httr" ,r-httr) |
9814 | ("r-interactivedisplaybase" ,r-interactivedisplaybase) | |
9815 | ("r-rsqlite" ,r-rsqlite) | |
9816 | ("r-s4vectors" ,r-s4vectors) | |
9817 | ("r-yaml" ,r-yaml))) | |
5713bbf1 | 9818 | (home-page "https://bioconductor.org/packages/AnnotationHub") |
4a007ffa RW |
9819 | (synopsis "Client to access AnnotationHub resources") |
9820 | (description | |
9821 | "This package provides a client for the Bioconductor AnnotationHub web | |
9822 | resource. The AnnotationHub web resource provides a central location where | |
9823 | genomic files (e.g. VCF, bed, wig) and other resources from standard | |
9824 | locations (e.g. UCSC, Ensembl) can be discovered. The resource includes | |
9825 | metadata about each resource, e.g., a textual description, tags, and date of | |
9826 | modification. The client creates and manages a local cache of files retrieved | |
9827 | by the user, helping with quick and reproducible access.") | |
9828 | (license license:artistic2.0))) | |
9829 | ||
d4a1e918 RW |
9830 | (define-public r-fastseg |
9831 | (package | |
9832 | (name "r-fastseg") | |
87fa5afa | 9833 | (version "1.24.0") |
d4a1e918 RW |
9834 | (source |
9835 | (origin | |
9836 | (method url-fetch) | |
9837 | (uri (bioconductor-uri "fastseg" version)) | |
9838 | (sha256 | |
9839 | (base32 | |
87fa5afa | 9840 | "0dd7nr3klwz9ailwshnbynhd62lwb8zbbpj6jf3igpb94yi6x2jp")))) |
d4a1e918 RW |
9841 | (build-system r-build-system) |
9842 | (propagated-inputs | |
9843 | `(("r-biobase" ,r-biobase) | |
9844 | ("r-biocgenerics" ,r-biocgenerics) | |
9845 | ("r-genomicranges" ,r-genomicranges) | |
9846 | ("r-iranges" ,r-iranges) | |
9847 | ("r-s4vectors" ,r-s4vectors))) | |
9848 | (home-page "http://www.bioinf.jku.at/software/fastseg/index.html") | |
9849 | (synopsis "Fast segmentation algorithm for genetic sequencing data") | |
9850 | (description | |
9851 | "Fastseg implements a very fast and efficient segmentation algorithm. | |
9852 | It can segment data from DNA microarrays and data from next generation | |
9853 | sequencing for example to detect copy number segments. Further it can segment | |
9854 | data from RNA microarrays like tiling arrays to identify transcripts. Most | |
9855 | generally, it can segment data given as a matrix or as a vector. Various data | |
9856 | formats can be used as input to fastseg like expression set objects for | |
9857 | microarrays or GRanges for sequencing data.") | |
9858 | (license license:lgpl2.0+))) | |
9859 | ||
3121814e RW |
9860 | (define-public r-keggrest |
9861 | (package | |
9862 | (name "r-keggrest") | |
f5f94427 | 9863 | (version "1.18.1") |
3121814e RW |
9864 | (source |
9865 | (origin | |
9866 | (method url-fetch) | |
9867 | (uri (bioconductor-uri "KEGGREST" version)) | |
9868 | (sha256 | |
9869 | (base32 | |
f5f94427 | 9870 | "02gwmm79djj55a90dzc80hlgwc6bafl7xd7fnx2q59pk945k3z9c")))) |
3121814e RW |
9871 | (properties `((upstream-name . "KEGGREST"))) |
9872 | (build-system r-build-system) | |
9873 | (propagated-inputs | |
9874 | `(("r-biostrings" ,r-biostrings) | |
9875 | ("r-httr" ,r-httr) | |
9876 | ("r-png" ,r-png))) | |
9877 | (home-page "https://bioconductor.org/packages/KEGGREST") | |
9878 | (synopsis "Client-side REST access to KEGG") | |
9879 | (description | |
9880 | "This package provides a package that provides a client interface to the | |
9881 | @dfn{Kyoto Encyclopedia of Genes and Genomes} (KEGG) REST server.") | |
9882 | (license license:artistic2.0))) | |
9883 | ||
e160aa1f RW |
9884 | (define-public r-gage |
9885 | (package | |
9886 | (name "r-gage") | |
34d077b8 | 9887 | (version "2.28.2") |
e160aa1f RW |
9888 | (source |
9889 | (origin | |
9890 | (method url-fetch) | |
9891 | (uri (bioconductor-uri "gage" version)) | |
9892 | (sha256 | |
9893 | (base32 | |
34d077b8 | 9894 | "0h0mlhns9j7cpfksvdlvx9jb7szm3r1dwqb3s4s8p8hmkb9byyii")))) |
e160aa1f RW |
9895 | (build-system r-build-system) |
9896 | (propagated-inputs | |
9897 | `(("r-annotationdbi" ,r-annotationdbi) | |
9898 | ("r-graph" ,r-graph) | |
9899 | ("r-keggrest" ,r-keggrest))) | |
9900 | (home-page "http://www.biomedcentral.com/1471-2105/10/161") | |
9901 | (synopsis "Generally applicable gene-set enrichment for pathway analysis") | |
9902 | (description | |
9903 | "GAGE is a published method for gene set (enrichment or GSEA) or pathway | |
9904 | analysis. GAGE is generally applicable independent of microarray or RNA-Seq | |
9905 | data attributes including sample sizes, experimental designs, assay platforms, | |
9906 | and other types of heterogeneity. The gage package provides functions for | |
9907 | basic GAGE analysis, result processing and presentation. In addition, it | |
9908 | provides demo microarray data and commonly used gene set data based on KEGG | |
9909 | pathways and GO terms. These funtions and data are also useful for gene set | |
9910 | analysis using other methods.") | |
9911 | (license license:gpl2+))) | |
9912 | ||
902fb15d RW |
9913 | (define-public r-genomicfiles |
9914 | (package | |
9915 | (name "r-genomicfiles") | |
9916 | (version "1.14.0") | |
9917 | (source | |
9918 | (origin | |
9919 | (method url-fetch) | |
9920 | (uri (bioconductor-uri "GenomicFiles" version)) | |
9921 | (sha256 | |
9922 | (base32 | |
9923 | "0r0wmrs5jycf1kckhnc2sgjmp336srlcjdkpbb1ymm7kazdd0s9n")))) | |
9924 | (properties `((upstream-name . "GenomicFiles"))) | |
9925 | (build-system r-build-system) | |
9926 | (propagated-inputs | |
9927 | `(("r-biocgenerics" ,r-biocgenerics) | |
9928 | ("r-biocparallel" ,r-biocparallel) | |
9929 | ("r-genomeinfodb" ,r-genomeinfodb) | |
9930 | ("r-genomicalignments" ,r-genomicalignments) | |
9931 | ("r-genomicranges" ,r-genomicranges) | |
9932 | ("r-iranges" ,r-iranges) | |
9933 | ("r-rsamtools" ,r-rsamtools) | |
9934 | ("r-rtracklayer" ,r-rtracklayer) | |
9935 | ("r-s4vectors" ,r-s4vectors) | |
9936 | ("r-summarizedexperiment" ,r-summarizedexperiment) | |
9937 | ("r-variantannotation" ,r-variantannotation))) | |
9938 | (home-page "https://bioconductor.org/packages/GenomicFiles") | |
9939 | (synopsis "Distributed computing by file or by range") | |
9940 | (description | |
9941 | "This package provides infrastructure for parallel computations | |
9942 | distributed by file or by range. User defined mapper and reducer functions | |
9943 | provide added flexibility for data combination and manipulation.") | |
9944 | (license license:artistic2.0))) | |
9945 | ||
3af149f5 RW |
9946 | (define-public r-complexheatmap |
9947 | (package | |
9948 | (name "r-complexheatmap") | |
9949 | (version "1.17.1") | |
9950 | (source | |
9951 | (origin | |
9952 | (method url-fetch) | |
9953 | (uri (bioconductor-uri "ComplexHeatmap" version)) | |
9954 | (sha256 | |
9955 | (base32 | |
9956 | "1x6kp55iqqsd8bhdl3qch95nfiy2y46ldbbsx1sj1v8f0b0ywwcy")))) | |
9957 | (properties | |
9958 | `((upstream-name . "ComplexHeatmap"))) | |
9959 | (build-system r-build-system) | |
9960 | (propagated-inputs | |
9961 | `(("r-circlize" ,r-circlize) | |
9962 | ("r-colorspace" ,r-colorspace) | |
9963 | ("r-getoptlong" ,r-getoptlong) | |
9964 | ("r-globaloptions" ,r-globaloptions) | |
9965 | ("r-rcolorbrewer" ,r-rcolorbrewer))) | |
9966 | (home-page | |
9967 | "https://github.com/jokergoo/ComplexHeatmap") | |
9968 | (synopsis "Making Complex Heatmaps") | |
9969 | (description | |
9970 | "Complex heatmaps are efficient to visualize associations between | |
9971 | different sources of data sets and reveal potential structures. This package | |
9972 | provides a highly flexible way to arrange multiple heatmaps and supports | |
9973 | self-defined annotation graphics.") | |
9974 | (license license:gpl2+))) | |
9975 | ||
04e2a2e9 RW |
9976 | (define-public r-dirichletmultinomial |
9977 | (package | |
9978 | (name "r-dirichletmultinomial") | |
9979 | (version "1.20.0") | |
9980 | (source | |
9981 | (origin | |
9982 | (method url-fetch) | |
9983 | (uri (bioconductor-uri "DirichletMultinomial" version)) | |
9984 | (sha256 | |
9985 | (base32 | |
9986 | "1c4s6x0qm20556grcd1xys9kkpnlzpasaai474malwcg6qvgi4x1")))) | |
9987 | (properties | |
9988 | `((upstream-name . "DirichletMultinomial"))) | |
9989 | (build-system r-build-system) | |
9990 | (inputs | |
9991 | `(("gsl" ,gsl))) | |
9992 | (propagated-inputs | |
9993 | `(("r-biocgenerics" ,r-biocgenerics) | |
9994 | ("r-iranges" ,r-iranges) | |
9995 | ("r-s4vectors" ,r-s4vectors))) | |
9996 | (home-page "https://bioconductor.org/packages/DirichletMultinomial") | |
9997 | (synopsis "Dirichlet-Multinomial mixture models for microbiome data") | |
9998 | (description | |
9999 | "Dirichlet-multinomial mixture models can be used to describe variability | |
10000 | in microbial metagenomic data. This package is an interface to code | |
10001 | originally made available by Holmes, Harris, and Quince, 2012, PLoS ONE 7(2): | |
10002 | 1-15.") | |
10003 | (license license:lgpl3))) | |
10004 | ||
aa30ab5a RW |
10005 | (define-public r-ensembldb |
10006 | (package | |
10007 | (name "r-ensembldb") | |
8877ab43 | 10008 | (version "2.2.2") |
aa30ab5a RW |
10009 | (source |
10010 | (origin | |
10011 | (method url-fetch) | |
10012 | (uri (bioconductor-uri "ensembldb" version)) | |
10013 | (sha256 | |
10014 | (base32 | |
8877ab43 | 10015 | "1yngndkf3588z91z0a2fvkg423p26ajm6xv1p27x0l9mzhhaqq3k")))) |
aa30ab5a RW |
10016 | (build-system r-build-system) |
10017 | (propagated-inputs | |
10018 | `(("r-annotationdbi" ,r-annotationdbi) | |
10019 | ("r-annotationfilter" ,r-annotationfilter) | |
10020 | ("r-annotationhub" ,r-annotationhub) | |
10021 | ("r-biobase" ,r-biobase) | |
10022 | ("r-biocgenerics" ,r-biocgenerics) | |
10023 | ("r-biostrings" ,r-biostrings) | |
10024 | ("r-curl" ,r-curl) | |
10025 | ("r-dbi" ,r-dbi) | |
10026 | ("r-genomeinfodb" ,r-genomeinfodb) | |
10027 | ("r-genomicfeatures" ,r-genomicfeatures) | |
10028 | ("r-genomicranges" ,r-genomicranges) | |
10029 | ("r-iranges" ,r-iranges) | |
10030 | ("r-protgenerics" ,r-protgenerics) | |
10031 | ("r-rsamtools" ,r-rsamtools) | |
10032 | ("r-rsqlite" ,r-rsqlite) | |
10033 | ("r-rtracklayer" ,r-rtracklayer) | |
10034 | ("r-s4vectors" ,r-s4vectors))) | |
10035 | (home-page "https://github.com/jotsetung/ensembldb") | |
10036 | (synopsis "Utilities to create and use Ensembl-based annotation databases") | |
10037 | (description | |
10038 | "The package provides functions to create and use transcript-centric | |
10039 | annotation databases/packages. The annotation for the databases are directly | |
10040 | fetched from Ensembl using their Perl API. The functionality and data is | |
10041 | similar to that of the TxDb packages from the @code{GenomicFeatures} package, | |
10042 | but, in addition to retrieve all gene/transcript models and annotations from | |
10043 | the database, the @code{ensembldb} package also provides a filter framework | |
10044 | allowing to retrieve annotations for specific entries like genes encoded on a | |
10045 | chromosome region or transcript models of lincRNA genes.") | |
10046 | ;; No version specified | |
10047 | (license license:lgpl3+))) | |
10048 | ||
2f6f61fd RW |
10049 | (define-public r-organismdbi |
10050 | (package | |
10051 | (name "r-organismdbi") | |
10052 | (version "1.20.0") | |
10053 | (source | |
10054 | (origin | |
10055 | (method url-fetch) | |
10056 | (uri (bioconductor-uri "OrganismDbi" version)) | |
10057 | (sha256 | |
10058 | (base32 | |
10059 | "0yxvhwn0m53wfwp0zi81x96argdf7cf1lpymc2as51apvfcnjdl8")))) | |
10060 | (properties `((upstream-name . "OrganismDbi"))) | |
10061 | (build-system r-build-system) | |
10062 | (propagated-inputs | |
10063 | `(("r-annotationdbi" ,r-annotationdbi) | |
10064 | ("r-biobase" ,r-biobase) | |
10065 | ("r-biocgenerics" ,r-biocgenerics) | |
10066 | ("r-biocinstaller" ,r-biocinstaller) | |
10067 | ("r-dbi" ,r-dbi) | |
10068 | ("r-genomicfeatures" ,r-genomicfeatures) | |
10069 | ("r-genomicranges" ,r-genomicranges) | |
10070 | ("r-graph" ,r-graph) | |
10071 | ("r-iranges" ,r-iranges) | |
10072 | ("r-rbgl" ,r-rbgl) | |
10073 | ("r-s4vectors" ,r-s4vectors))) | |
10074 | (home-page "https://bioconductor.org/packages/OrganismDbi") | |
10075 | (synopsis "Software to enable the smooth interfacing of database packages") | |
10076 | (description "The package enables a simple unified interface to several | |
10077 | annotation packages each of which has its own schema by taking advantage of | |
10078 | the fact that each of these packages implements a select methods.") | |
10079 | (license license:artistic2.0))) | |
10080 | ||
7af1f403 RW |
10081 | (define-public r-biovizbase |
10082 | (package | |
10083 | (name "r-biovizbase") | |
10084 | (version "1.26.0") | |
10085 | (source | |
10086 | (origin | |
10087 | (method url-fetch) | |
10088 | (uri (bioconductor-uri "biovizBase" version)) | |
10089 | (sha256 | |
10090 | (base32 | |
10091 | "14l4vhj0a4ssr9m9zdzz3qpd4qw1mhgq5bmxq7jhrq3j9kmd6i2f")))) | |
10092 | (properties `((upstream-name . "biovizBase"))) | |
10093 | (build-system r-build-system) | |
10094 | (propagated-inputs | |
10095 | `(("r-annotationdbi" ,r-annotationdbi) | |
10096 | ("r-annotationfilter" ,r-annotationfilter) | |
10097 | ("r-biocgenerics" ,r-biocgenerics) | |
10098 | ("r-biostrings" ,r-biostrings) | |
10099 | ("r-dichromat" ,r-dichromat) | |
10100 | ("r-ensembldb" ,r-ensembldb) | |
10101 | ("r-genomeinfodb" ,r-genomeinfodb) | |
10102 | ("r-genomicalignments" ,r-genomicalignments) | |
10103 | ("r-genomicfeatures" ,r-genomicfeatures) | |
10104 | ("r-genomicranges" ,r-genomicranges) | |
10105 | ("r-hmisc" ,r-hmisc) | |
10106 | ("r-iranges" ,r-iranges) | |
10107 | ("r-rcolorbrewer" ,r-rcolorbrewer) | |
10108 | ("r-rsamtools" ,r-rsamtools) | |
10109 | ("r-s4vectors" ,r-s4vectors) | |
10110 | ("r-scales" ,r-scales) | |
10111 | ("r-summarizedexperiment" ,r-summarizedexperiment) | |
10112 | ("r-variantannotation" ,r-variantannotation))) | |
10113 | (home-page "https://bioconductor.org/packages/biovizBase") | |
10114 | (synopsis "Basic graphic utilities for visualization of genomic data") | |
10115 | (description | |
10116 | "The biovizBase package is designed to provide a set of utilities, color | |
10117 | schemes and conventions for genomic data. It serves as the base for various | |
10118 | high-level packages for biological data visualization. This saves development | |
10119 | effort and encourages consistency.") | |
10120 | (license license:artistic2.0))) | |
10121 | ||
60faf945 RW |
10122 | (define-public r-ggbio |
10123 | (package | |
10124 | (name "r-ggbio") | |
10125 | (version "1.26.0") | |
10126 | (source | |
10127 | (origin | |
10128 | (method url-fetch) | |
10129 | (uri (bioconductor-uri "ggbio" version)) | |
10130 | (sha256 | |
10131 | (base32 | |
10132 | "1bqxfqy0hff87ax92z4lfbjz01ndrz7x8pzm6dlkdmi52p30krm9")))) | |
10133 | (build-system r-build-system) | |
10134 | (propagated-inputs | |
10135 | `(("r-annotationdbi" ,r-annotationdbi) | |
10136 | ("r-annotationfilter" ,r-annotationfilter) | |
10137 | ("r-biobase" ,r-biobase) | |
10138 | ("r-biocgenerics" ,r-biocgenerics) | |
10139 | ("r-biostrings" ,r-biostrings) | |
10140 | ("r-biovizbase" ,r-biovizbase) | |
10141 | ("r-bsgenome" ,r-bsgenome) | |
10142 | ("r-ensembldb" ,r-ensembldb) | |
10143 | ("r-genomeinfodb" ,r-genomeinfodb) | |
10144 | ("r-genomicalignments" ,r-genomicalignments) | |
10145 | ("r-genomicfeatures" ,r-genomicfeatures) | |
10146 | ("r-genomicranges" ,r-genomicranges) | |
10147 | ("r-ggally" ,r-ggally) | |
10148 | ("r-ggplot2" ,r-ggplot2) | |
10149 | ("r-gridextra" ,r-gridextra) | |
10150 | ("r-gtable" ,r-gtable) | |
10151 | ("r-hmisc" ,r-hmisc) | |
10152 | ("r-iranges" ,r-iranges) | |
10153 | ("r-organismdbi" ,r-organismdbi) | |
10154 | ("r-reshape2" ,r-reshape2) | |
10155 | ("r-rsamtools" ,r-rsamtools) | |
10156 | ("r-rtracklayer" ,r-rtracklayer) | |
10157 | ("r-s4vectors" ,r-s4vectors) | |
10158 | ("r-scales" ,r-scales) | |
10159 | ("r-summarizedexperiment" ,r-summarizedexperiment) | |
10160 | ("r-variantannotation" ,r-variantannotation))) | |
10161 | (home-page "http://www.tengfei.name/ggbio/") | |
10162 | (synopsis "Visualization tools for genomic data") | |
10163 | (description | |
10164 | "The ggbio package extends and specializes the grammar of graphics for | |
10165 | biological data. The graphics are designed to answer common scientific | |
10166 | questions, in particular those often asked of high throughput genomics data. | |
10167 | All core Bioconductor data structures are supported, where appropriate. The | |
10168 | package supports detailed views of particular genomic regions, as well as | |
10169 | genome-wide overviews. Supported overviews include ideograms and grand linear | |
10170 | views. High-level plots include sequence fragment length, edge-linked | |
10171 | interval to data view, mismatch pileup, and several splicing summaries.") | |
10172 | (license license:artistic2.0))) | |
10173 | ||
96a392a0 RW |
10174 | (define-public r-gprofiler |
10175 | (package | |
10176 | (name "r-gprofiler") | |
ca7855fc | 10177 | (version "0.6.4") |
96a392a0 RW |
10178 | (source |
10179 | (origin | |
10180 | (method url-fetch) | |
10181 | (uri (cran-uri "gProfileR" version)) | |
10182 | (sha256 | |
10183 | (base32 | |
ca7855fc | 10184 | "1cka02zbz1rbppm782qpxk1xn9qxbrv2gp5rgf970j906hxm2y0b")))) |
96a392a0 RW |
10185 | (properties `((upstream-name . "gProfileR"))) |
10186 | (build-system r-build-system) | |
10187 | (propagated-inputs | |
10188 | `(("r-plyr" ,r-plyr) | |
10189 | ("r-rcurl" ,r-rcurl))) | |
e9960d8c | 10190 | (home-page "https://cran.r-project.org/web/packages/gProfileR/") |
96a392a0 RW |
10191 | (synopsis "Interface to the g:Profiler toolkit") |
10192 | (description | |
10193 | "This package provides tools for functional enrichment analysis, | |
10194 | gene identifier conversion and mapping homologous genes across related | |
10195 | organisms via the @code{g:Profiler} toolkit.") | |
10196 | (license license:gpl2+))) | |
10197 | ||
e2b92799 RW |
10198 | (define-public r-gqtlbase |
10199 | (package | |
10200 | (name "r-gqtlbase") | |
10201 | (version "1.10.0") | |
10202 | (source | |
10203 | (origin | |
10204 | (method url-fetch) | |
10205 | (uri (bioconductor-uri "gQTLBase" version)) | |
10206 | (sha256 | |
10207 | (base32 | |
10208 | "1756vfcj2dkkgcmfkkg7qdaig36dv9gfvpypn9rbrky56wm1p035")))) | |
10209 | (properties `((upstream-name . "gQTLBase"))) | |
10210 | (build-system r-build-system) | |
10211 | (propagated-inputs | |
10212 | `(("r-batchjobs" ,r-batchjobs) | |
10213 | ("r-bbmisc" ,r-bbmisc) | |
10214 | ("r-biocgenerics" ,r-biocgenerics) | |
10215 | ("r-bit" ,r-bit) | |
10216 | ("r-doparallel" ,r-doparallel) | |
10217 | ("r-ff" ,r-ff) | |
10218 | ("r-ffbase" ,r-ffbase) | |
10219 | ("r-foreach" ,r-foreach) | |
10220 | ("r-genomicfiles" ,r-genomicfiles) | |
10221 | ("r-genomicranges" ,r-genomicranges) | |
10222 | ("r-rtracklayer" ,r-rtracklayer) | |
10223 | ("r-s4vectors" ,r-s4vectors) | |
10224 | ("r-summarizedexperiment" ,r-summarizedexperiment))) | |
10225 | (home-page "https://bioconductor.org/packages/gQTLBase") | |
10226 | (synopsis "Infrastructure for eQTL, mQTL and similar studies") | |
10227 | (description | |
10228 | "The purpose of this package is to simplify the storage and interrogation | |
10229 | of @dfn{quantitative trait loci} (QTL) archives, such as eQTL, mQTL, dsQTL, | |
10230 | and more.") | |
10231 | (license license:artistic2.0))) | |
10232 | ||
dd5fc8b7 RW |
10233 | (define-public r-snpstats |
10234 | (package | |
10235 | (name "r-snpstats") | |
10236 | (version "1.28.0") | |
10237 | (source | |
10238 | (origin | |
10239 | (method url-fetch) | |
10240 | (uri (bioconductor-uri "snpStats" version)) | |
10241 | (sha256 | |
10242 | (base32 | |
10243 | "1x9qwynh2hwl24vq02naf4mchpch7xi2pkdrlgw896k28kx0lvir")))) | |
10244 | (properties `((upstream-name . "snpStats"))) | |
10245 | (build-system r-build-system) | |
10246 | (inputs `(("zlib" ,zlib))) | |
10247 | (propagated-inputs | |
10248 | `(("r-biocgenerics" ,r-biocgenerics) | |
10249 | ("r-matrix" ,r-matrix) | |
10250 | ("r-survival" ,r-survival) | |
10251 | ("r-zlibbioc" ,r-zlibbioc))) | |
10252 | (home-page "https://bioconductor.org/packages/snpStats") | |
10253 | (synopsis "Methods for SNP association studies") | |
10254 | (description | |
10255 | "This package provides classes and statistical methods for large | |
10256 | @dfn{single-nucleotide polymorphism} (SNP) association studies. This extends | |
10257 | the earlier snpMatrix package, allowing for uncertainty in genotypes.") | |
10258 | (license license:gpl3))) | |
10259 | ||
421c68e3 RW |
10260 | (define-public r-homo-sapiens |
10261 | (package | |
10262 | (name "r-homo-sapiens") | |
10263 | (version "1.3.1") | |
10264 | (source (origin | |
10265 | (method url-fetch) | |
10266 | ;; We cannot use bioconductor-uri here because this tarball is | |
10267 | ;; located under "data/annotation/" instead of "bioc/". | |
10268 | (uri (string-append "http://www.bioconductor.org/packages/" | |
10269 | "release/data/annotation/src/contrib/" | |
10270 | "Homo.sapiens_" | |
10271 | version ".tar.gz")) | |
10272 | (sha256 | |
10273 | (base32 | |
10274 | "151vj7h5p1c8yd5swrchk46z469p135wk50hvkl0nhgndvy0jj01")))) | |
10275 | (properties | |
10276 | `((upstream-name . "Homo.sapiens"))) | |
10277 | (build-system r-build-system) | |
10278 | (propagated-inputs | |
10279 | `(("r-genomicfeatures" ,r-genomicfeatures) | |
10280 | ("r-go-db" ,r-go-db) | |
10281 | ("r-org-hs-eg-db" ,r-org-hs-eg-db) | |
10282 | ("r-txdb-hsapiens-ucsc-hg19-knowngene" ,r-txdb-hsapiens-ucsc-hg19-knowngene) | |
10283 | ("r-organismdbi" ,r-organismdbi) | |
10284 | ("r-annotationdbi" ,r-annotationdbi))) | |
10285 | (home-page "https://bioconductor.org/packages/Homo.sapiens/") | |
10286 | (synopsis "Annotation package for the Homo.sapiens object") | |
10287 | (description | |
10288 | "This package contains the Homo.sapiens object to access data from | |
10289 | several related annotation packages.") | |
10290 | (license license:artistic2.0))) | |
10291 | ||
15f98b0d RW |
10292 | (define-public r-erma |
10293 | (package | |
10294 | (name "r-erma") | |
10295 | (version "0.10.0") | |
10296 | (source | |
10297 | (origin | |
10298 | (method url-fetch) | |
10299 | (uri (bioconductor-uri "erma" version)) | |
10300 | (sha256 | |
10301 | (base32 | |
10302 | "0gcfs9g8vvdv5vmq9b21kd8sq5mizjj49nfzd4in9zvp4b9v7x1g")))) | |
10303 | (build-system r-build-system) | |
10304 | (propagated-inputs | |
10305 | `(("r-annotationdbi" ,r-annotationdbi) | |
10306 | ("r-biobase" ,r-biobase) | |
10307 | ("r-biocgenerics" ,r-biocgenerics) | |
10308 | ("r-foreach" ,r-foreach) | |
10309 | ("r-genomicfiles" ,r-genomicfiles) | |
10310 | ("r-genomicranges" ,r-genomicranges) | |
10311 | ("r-ggplot2" ,r-ggplot2) | |
10312 | ("r-homo-sapiens" ,r-homo-sapiens) | |
10313 | ("r-rtracklayer" ,r-rtracklayer) | |
10314 | ("r-s4vectors" ,r-s4vectors) | |
10315 | ("r-shiny" ,r-shiny) | |
10316 | ("r-summarizedexperiment" ,r-summarizedexperiment))) | |
10317 | (home-page "https://bioconductor.org/packages/erma") | |
10318 | (synopsis "Epigenomic road map adventures") | |
10319 | (description | |
10320 | "The epigenomics road map describes locations of epigenetic marks in DNA | |
10321 | from a variety of cell types. Of interest are locations of histone | |
10322 | modifications, sites of DNA methylation, and regions of accessible chromatin. | |
10323 | This package presents a selection of elements of the road map including | |
10324 | metadata and outputs of the ChromImpute procedure applied to ENCODE cell lines | |
10325 | by Ernst and Kellis.") | |
10326 | (license license:artistic2.0))) | |
10327 | ||
66c39102 RW |
10328 | (define-public r-ldblock |
10329 | (package | |
10330 | (name "r-ldblock") | |
10331 | (version "1.8.0") | |
10332 | (source | |
10333 | (origin | |
10334 | (method url-fetch) | |
10335 | (uri (bioconductor-uri "ldblock" version)) | |
10336 | (sha256 | |
10337 | (base32 | |
10338 | "18nfsixh6d2wfrb9laqsgly5w1frzihhak683k0p8fdf51h4aqba")))) | |
10339 | (build-system r-build-system) | |
10340 | (propagated-inputs | |
10341 | `(("r-erma" ,r-erma) | |
10342 | ("r-genomeinfodb" ,r-genomeinfodb) | |
10343 | ("r-genomicfiles" ,r-genomicfiles) | |
10344 | ("r-go-db" ,r-go-db) | |
10345 | ("r-homo-sapiens" ,r-homo-sapiens) | |
10346 | ("r-matrix" ,r-matrix) | |
10347 | ("r-rsamtools" ,r-rsamtools) | |
10348 | ("r-snpstats" ,r-snpstats) | |
10349 | ("r-variantannotation" ,r-variantannotation))) | |
10350 | (home-page "https://bioconductor.org/packages/ldblock") | |
10351 | (synopsis "Data structures for linkage disequilibrium measures in populations") | |
10352 | (description | |
10353 | "This package defines data structures for @dfn{linkage | |
10354 | disequilibrium} (LD) measures in populations. Its purpose is to simplify | |
10355 | handling of existing population-level data for the purpose of flexibly | |
10356 | defining LD blocks.") | |
10357 | (license license:artistic2.0))) | |
10358 | ||
794ff347 RW |
10359 | (define-public r-gqtlstats |
10360 | (package | |
10361 | (name "r-gqtlstats") | |
2ccd8501 | 10362 | (version "1.10.1") |
794ff347 RW |
10363 | (source |
10364 | (origin | |
10365 | (method url-fetch) | |
10366 | (uri (bioconductor-uri "gQTLstats" version)) | |
10367 | (sha256 | |
10368 | (base32 | |
2ccd8501 | 10369 | "0gvq1sf2zjbkk431x40z6wql3c1rpclnnwa2f1hvykb8mmw70kmq")))) |
794ff347 RW |
10370 | (properties `((upstream-name . "gQTLstats"))) |
10371 | (build-system r-build-system) | |
10372 | (propagated-inputs | |
10373 | `(("r-annotationdbi" ,r-annotationdbi) | |
10374 | ("r-batchjobs" ,r-batchjobs) | |
10375 | ("r-bbmisc" ,r-bbmisc) | |
10376 | ("r-beeswarm" ,r-beeswarm) | |
10377 | ("r-biobase" ,r-biobase) | |
10378 | ("r-biocgenerics" ,r-biocgenerics) | |
10379 | ("r-doparallel" ,r-doparallel) | |
10380 | ("r-dplyr" ,r-dplyr) | |
10381 | ("r-erma" ,r-erma) | |
10382 | ("r-ffbase" ,r-ffbase) | |
10383 | ("r-foreach" ,r-foreach) | |
10384 | ("r-genomeinfodb" ,r-genomeinfodb) | |
10385 | ("r-genomicfeatures" ,r-genomicfeatures) | |
10386 | ("r-genomicfiles" ,r-genomicfiles) | |
10387 | ("r-genomicranges" ,r-genomicranges) | |
10388 | ("r-ggbeeswarm" ,r-ggbeeswarm) | |
10389 | ("r-ggplot2" ,r-ggplot2) | |
10390 | ("r-gqtlbase" ,r-gqtlbase) | |
10391 | ("r-hardyweinberg" ,r-hardyweinberg) | |
10392 | ("r-iranges" ,r-iranges) | |
10393 | ("r-ldblock" ,r-ldblock) | |
10394 | ("r-limma" ,r-limma) | |
10395 | ("r-mgcv" ,r-mgcv) | |
10396 | ("r-plotly" ,r-plotly) | |
10397 | ("r-reshape2" ,r-reshape2) | |
10398 | ("r-s4vectors" ,r-s4vectors) | |
10399 | ("r-shiny" ,r-shiny) | |
10400 | ("r-snpstats" ,r-snpstats) | |
10401 | ("r-summarizedexperiment" ,r-summarizedexperiment) | |
10402 | ("r-variantannotation" ,r-variantannotation))) | |
10403 | (home-page "https://bioconductor.org/packages/gQTLstats") | |
10404 | (synopsis "Computationally efficient analysis for eQTL and allied studies") | |
10405 | (description | |
10406 | "This package provides tools for the computationally efficient analysis | |
10407 | of @dfn{quantitative trait loci} (QTL) data, including eQTL, mQTL, dsQTL, etc. | |
10408 | The software in this package aims to support refinements and functional | |
10409 | interpretation of members of a collection of association statistics on a | |
10410 | family of feature/genome hypotheses.") | |
10411 | (license license:artistic2.0))) | |
10412 | ||
42720006 RW |
10413 | (define-public r-gviz |
10414 | (package | |
10415 | (name "r-gviz") | |
d578278e | 10416 | (version "1.22.3") |
42720006 RW |
10417 | (source |
10418 | (origin | |
10419 | (method url-fetch) | |
10420 | (uri (bioconductor-uri "Gviz" version)) | |
10421 | (sha256 | |
10422 | (base32 | |
d578278e | 10423 | "1grjzrjpzkw572pbvpsvdnfkfgwybl0cnjd7nnk2xdr26wnbsi9a")))) |
42720006 RW |
10424 | (properties `((upstream-name . "Gviz"))) |
10425 | (build-system r-build-system) | |
10426 | (propagated-inputs | |
10427 | `(("r-annotationdbi" ,r-annotationdbi) | |
10428 | ("r-biobase" ,r-biobase) | |
10429 | ("r-biocgenerics" ,r-biocgenerics) | |
10430 | ("r-biomart" ,r-biomart) | |
10431 | ("r-biostrings" ,r-biostrings) | |
10432 | ("r-biovizbase" ,r-biovizbase) | |
10433 | ("r-bsgenome" ,r-bsgenome) | |
10434 | ("r-digest" ,r-digest) | |
10435 | ("r-genomeinfodb" ,r-genomeinfodb) | |
10436 | ("r-genomicalignments" ,r-genomicalignments) | |
10437 | ("r-genomicfeatures" ,r-genomicfeatures) | |
10438 | ("r-genomicranges" ,r-genomicranges) | |
10439 | ("r-iranges" ,r-iranges) | |
10440 | ("r-lattice" ,r-lattice) | |
10441 | ("r-latticeextra" ,r-latticeextra) | |
10442 | ("r-matrixstats" ,r-matrixstats) | |
10443 | ("r-rcolorbrewer" ,r-rcolorbrewer) | |
10444 | ("r-rsamtools" ,r-rsamtools) | |
10445 | ("r-rtracklayer" ,r-rtracklayer) | |
10446 | ("r-s4vectors" ,r-s4vectors) | |
10447 | ("r-xvector" ,r-xvector))) | |
10448 | (home-page "https://bioconductor.org/packages/Gviz") | |
10449 | (synopsis "Plotting data and annotation information along genomic coordinates") | |
10450 | (description | |
10451 | "Genomic data analyses requires integrated visualization of known genomic | |
10452 | information and new experimental data. Gviz uses the biomaRt and the | |
10453 | rtracklayer packages to perform live annotation queries to Ensembl and UCSC | |
10454 | and translates this to e.g. gene/transcript structures in viewports of the | |
10455 | grid graphics package. This results in genomic information plotted together | |
10456 | with your data.") | |
10457 | (license license:artistic2.0))) | |
10458 | ||
2e4ce60e RW |
10459 | (define-public r-gwascat |
10460 | (package | |
10461 | (name "r-gwascat") | |
10462 | (version "2.10.0") | |
10463 | (source | |
10464 | (origin | |
10465 | (method url-fetch) | |
10466 | (uri (bioconductor-uri "gwascat" version)) | |
10467 | (sha256 | |
10468 | (base32 | |
10469 | "0n5x5i5v6a8wpn5mxmlpkl34b4kyypmymiwww6g61zch7xqrgywi")))) | |
10470 | (build-system r-build-system) | |
10471 | (propagated-inputs | |
10472 | `(("r-annotationdbi" ,r-annotationdbi) | |
10473 | ("r-annotationhub" ,r-annotationhub) | |
10474 | ("r-biocgenerics" ,r-biocgenerics) | |
10475 | ("r-biostrings" ,r-biostrings) | |
10476 | ("r-genomeinfodb" ,r-genomeinfodb) | |
10477 | ("r-genomicfeatures" ,r-genomicfeatures) | |
10478 | ("r-genomicranges" ,r-genomicranges) | |
10479 | ("r-ggbio" ,r-ggbio) | |
10480 | ("r-ggplot2" ,r-ggplot2) | |
10481 | ("r-gqtlstats" ,r-gqtlstats) | |
10482 | ("r-graph" ,r-graph) | |
10483 | ("r-gviz" ,r-gviz) | |
10484 | ("r-homo-sapiens" ,r-homo-sapiens) | |
10485 | ("r-iranges" ,r-iranges) | |
10486 | ("r-rsamtools" ,r-rsamtools) | |
10487 | ("r-rtracklayer" ,r-rtracklayer) | |
10488 | ("r-s4vectors" ,r-s4vectors) | |
10489 | ("r-snpstats" ,r-snpstats) | |
10490 | ("r-summarizedexperiment" ,r-summarizedexperiment) | |
10491 | ("r-variantannotation" ,r-variantannotation))) | |
10492 | (home-page "https://bioconductor.org/packages/gwascat") | |
10493 | (synopsis "Tools for data in the EMBL-EBI GWAS catalog") | |
10494 | (description | |
10495 | "This package provides tools for representing and modeling data in the | |
10496 | EMBL-EBI GWAS catalog.") | |
10497 | (license license:artistic2.0))) | |
10498 | ||
fbf54406 RW |
10499 | (define-public r-sushi |
10500 | (package | |
10501 | (name "r-sushi") | |
10502 | (version "1.16.0") | |
10503 | (source (origin | |
10504 | (method url-fetch) | |
10505 | (uri (bioconductor-uri "Sushi" version)) | |
10506 | (sha256 | |
10507 | (base32 | |
10508 | "0axaqm480z8d0b2ldgxwm0swava1p4irc62bpl17p2k8k78g687g")))) | |
10509 | (properties `((upstream-name . "Sushi"))) | |
10510 | (build-system r-build-system) | |
10511 | (propagated-inputs | |
10512 | `(("r-biomart" ,r-biomart) | |
10513 | ("r-zoo" ,r-zoo))) | |
10514 | (home-page "https://bioconductor.org/packages/Sushi") | |
10515 | (synopsis "Tools for visualizing genomics data") | |
10516 | (description | |
10517 | "This package provides flexible, quantitative, and integrative genomic | |
10518 | visualizations for publication-quality multi-panel figures.") | |
10519 | (license license:gpl2+))) | |
10520 | ||
30eb4e37 RW |
10521 | (define-public r-fithic |
10522 | (package | |
10523 | (name "r-fithic") | |
10524 | (version "1.4.0") | |
10525 | (source (origin | |
10526 | (method url-fetch) | |
10527 | (uri (bioconductor-uri "FitHiC" version)) | |
10528 | (sha256 | |
10529 | (base32 | |
10530 | "12ylhrppi051m7nqsgq95kzd9g9wmp34i0zzfi55cjqawlpx7c6n")))) | |
10531 | (properties `((upstream-name . "FitHiC"))) | |
10532 | (build-system r-build-system) | |
10533 | (propagated-inputs | |
10534 | `(("r-data-table" ,r-data-table) | |
10535 | ("r-fdrtool" ,r-fdrtool) | |
10536 | ("r-rcpp" ,r-rcpp))) | |
10537 | (home-page "https://bioconductor.org/packages/FitHiC") | |
10538 | (synopsis "Confidence estimation for intra-chromosomal contact maps") | |
10539 | (description | |
10540 | "Fit-Hi-C is a tool for assigning statistical confidence estimates to | |
10541 | intra-chromosomal contact maps produced by genome-wide genome architecture | |
10542 | assays such as Hi-C.") | |
10543 | (license license:gpl2+))) | |
10544 | ||
c49102ec RW |
10545 | (define-public r-hitc |
10546 | (package | |
10547 | (name "r-hitc") | |
10548 | (version "1.22.0") | |
10549 | (source (origin | |
10550 | (method url-fetch) | |
10551 | (uri (bioconductor-uri "HiTC" version)) | |
10552 | (sha256 | |
10553 | (base32 | |
10554 | "0288xa1jy6nzvz2ha07csmp6dirjw5r7p9vy69q2wsbyzr02ymkp")))) | |
10555 | (properties `((upstream-name . "HiTC"))) | |
10556 | (build-system r-build-system) | |
10557 | (propagated-inputs | |
10558 | `(("r-biostrings" ,r-biostrings) | |
10559 | ("r-genomeinfodb" ,r-genomeinfodb) | |
10560 | ("r-genomicranges" ,r-genomicranges) | |
10561 | ("r-iranges" ,r-iranges) | |
10562 | ("r-matrix" ,r-matrix) | |
10563 | ("r-rcolorbrewer" ,r-rcolorbrewer) | |
10564 | ("r-rtracklayer" ,r-rtracklayer))) | |
10565 | (home-page "https://bioconductor.org/packages/HiTC") | |
10566 | (synopsis "High throughput chromosome conformation capture analysis") | |
10567 | (description | |
10568 | "The HiTC package was developed to explore high-throughput \"C\" data | |
10569 | such as 5C or Hi-C. Dedicated R classes as well as standard methods for | |
10570 | quality controls, normalization, visualization, and further analysis are also | |
10571 | provided.") | |
10572 | (license license:artistic2.0))) | |
10573 | ||
212f6120 RW |
10574 | (define-public r-qvalue |
10575 | (package | |
10576 | (name "r-qvalue") | |
98791c25 | 10577 | (version "2.10.0") |
212f6120 RW |
10578 | (source |
10579 | (origin | |
10580 | (method url-fetch) | |
10581 | (uri (bioconductor-uri "qvalue" version)) | |
10582 | (sha256 | |
10583 | (base32 | |
98791c25 | 10584 | "1rd9rnf16kh8wc076kahd9hsb9rfwsbzmz3kjmp0pj6rbiq0051i")))) |
212f6120 RW |
10585 | (build-system r-build-system) |
10586 | (propagated-inputs | |
10587 | `(("r-ggplot2" ,r-ggplot2) | |
10588 | ("r-reshape2" ,r-reshape2))) | |
10589 | (home-page "http://github.com/jdstorey/qvalue") | |
10590 | (synopsis "Q-value estimation for false discovery rate control") | |
10591 | (description | |
10592 | "This package takes a list of p-values resulting from the simultaneous | |
10593 | testing of many hypotheses and estimates their q-values and local @dfn{false | |
10594 | discovery rate} (FDR) values. The q-value of a test measures the proportion | |
10595 | of false positives incurred when that particular test is called significant. | |
10596 | The local FDR measures the posterior probability the null hypothesis is true | |
10597 | given the test's p-value. Various plots are automatically generated, allowing | |
10598 | one to make sensible significance cut-offs. The software can be applied to | |
10599 | problems in genomics, brain imaging, astrophysics, and data mining.") | |
10600 | ;; Any version of the LGPL. | |
10601 | (license license:lgpl3+))) | |
10602 | ||
aba3e482 RW |
10603 | (define-public r-hdf5array |
10604 | (package | |
10605 | (name "r-hdf5array") | |
10606 | (version "1.6.0") | |
10607 | (source | |
10608 | (origin | |
10609 | (method url-fetch) | |
10610 | (uri (bioconductor-uri "HDF5Array" version)) | |
10611 | (sha256 | |
10612 | (base32 | |
10613 | "0kcdza41saqv6vlpvqd841awbiwkg84lh0plx6c7fmfgbqv7a0jh")))) | |
10614 | (properties `((upstream-name . "HDF5Array"))) | |
10615 | (build-system r-build-system) | |
10616 | (propagated-inputs | |
10617 | `(("r-biocgenerics" ,r-biocgenerics) | |
10618 | ("r-delayedarray" ,r-delayedarray) | |
10619 | ("r-iranges" ,r-iranges) | |
10620 | ("r-rhdf5" ,r-rhdf5) | |
10621 | ("r-s4vectors" ,r-s4vectors))) | |
10622 | (home-page "https://bioconductor.org/packages/HDF5Array") | |
10623 | (synopsis "HDF5 back end for DelayedArray objects") | |
10624 | (description "This package provides an array-like container for convenient | |
10625 | access and manipulation of HDF5 datasets. It supports delayed operations and | |
10626 | block processing.") | |
10627 | (license license:artistic2.0))) | |
10628 | ||
748e9f16 RW |
10629 | (define-public r-rhdf5lib |
10630 | (package | |
10631 | (name "r-rhdf5lib") | |
10632 | (version "1.0.0") | |
10633 | (source | |
10634 | (origin | |
10635 | (method url-fetch) | |
10636 | (uri (bioconductor-uri "Rhdf5lib" version)) | |
10637 | (sha256 | |
10638 | (base32 | |
10639 | "0kkc4rprjbqn2wvbx4d49kk9l91vihccxbl4843qr1wqk6v33r1w")))) | |
10640 | (properties `((upstream-name . "Rhdf5lib"))) | |
10641 | (build-system r-build-system) | |
10642 | (arguments | |
10643 | `(#:phases | |
10644 | (modify-phases %standard-phases | |
10645 | (add-after 'unpack 'do-not-use-bundled-hdf5 | |
10646 | (lambda* (#:key inputs #:allow-other-keys) | |
10647 | (for-each delete-file '("configure" "configure.ac")) | |
10648 | ;; Do not make other packages link with the proprietary libsz. | |
10649 | (substitute* "R/zzz.R" | |
10650 | (("'%s/libhdf5_cpp.a %s/libhdf5.a %s/libsz.a'") | |
10651 | "'%s/libhdf5_cpp.a %s/libhdf5.a %s/libhdf5.a'") | |
10652 | (("'%s/libhdf5.a %s/libsz.a'") | |
10653 | "'%s/libhdf5.a %s/libhdf5.a'")) | |
10654 | (with-directory-excursion "src" | |
10655 | (invoke "tar" "xvf" (assoc-ref inputs "hdf5-source")) | |
10656 | (rename-file (string-append "hdf5-" ,(package-version hdf5)) | |
10657 | "hdf5") | |
a539ad86 RW |
10658 | ;; Remove timestamp and host system information to make |
10659 | ;; the build reproducible. | |
10660 | (substitute* "hdf5/src/libhdf5.settings.in" | |
10661 | (("Configured on: @CONFIG_DATE@") | |
10662 | "Configured on: Guix") | |
10663 | (("Uname information:.*") | |
10664 | "Uname information: Linux\n") | |
10665 | ;; Remove unnecessary store reference. | |
10666 | (("C Compiler:.*") | |
10667 | "C Compiler: GCC\n")) | |
748e9f16 RW |
10668 | (rename-file "Makevars.in" "Makevars") |
10669 | (substitute* "Makevars" | |
10670 | (("HDF5_CXX_LIB=.*") | |
10671 | (string-append "HDF5_CXX_LIB=" | |
10672 | (assoc-ref inputs "hdf5") "/lib/libhdf5_cpp.a\n")) | |
10673 | (("HDF5_LIB=.*") | |
10674 | (string-append "HDF5_LIB=" | |
10675 | (assoc-ref inputs "hdf5") "/lib/libhdf5.a\n")) | |
10676 | (("HDF5_CXX_INCLUDE=.*") "HDF5_CXX_INCLUDE=./hdf5/c++/src\n") | |
10677 | (("HDF5_INCLUDE=.*") "HDF5_INCLUDE=./hdf5/src\n") | |
10678 | ;; szip is non-free software | |
10679 | (("cp \\$\\{SZIP_LIB\\}.*") "") | |
10680 | (("PKG_LIBS = \\$\\{HDF5_LIB\\} \\$\\{SZIP_LIB\\}") | |
10681 | "PKG_LIBS = ${HDF5_LIB}\n"))) | |
10682 | #t))))) | |
10683 | (inputs | |
10684 | `(("zlib" ,zlib))) | |
10685 | (propagated-inputs | |
10686 | `(("hdf5" ,hdf5))) | |
10687 | (native-inputs | |
10688 | `(("hdf5-source" ,(package-source hdf5)))) | |
10689 | (home-page "https://bioconductor.org/packages/Rhdf5lib") | |
10690 | (synopsis "HDF5 library as an R package") | |
10691 | (description "This package provides C and C++ HDF5 libraries for use in R | |
10692 | packages.") | |
10693 | (license license:artistic2.0))) | |
10694 | ||
9ec08988 RW |
10695 | (define-public r-beachmat |
10696 | (package | |
10697 | (name "r-beachmat") | |
10698 | (version "1.0.2") | |
10699 | (source | |
10700 | (origin | |
10701 | (method url-fetch) | |
10702 | (uri (bioconductor-uri "beachmat" version)) | |
10703 | (sha256 | |
10704 | (base32 | |
10705 | "0b6dzja5fbx4dawb7ixj67mlhw4fy62pfp20mfp918fy96zmdwqz")))) | |
10706 | (build-system r-build-system) | |
10707 | (inputs | |
10708 | `(("hdf5" ,hdf5))) | |
10709 | (propagated-inputs | |
10710 | `(("r-delayedarray" ,r-delayedarray) | |
10711 | ("r-hdf5array" ,r-hdf5array) | |
10712 | ("r-rcpp" ,r-rcpp) | |
10713 | ("r-rhdf5" ,r-rhdf5) | |
10714 | ("r-rhdf5lib" ,r-rhdf5lib))) | |
10715 | (home-page "https://bioconductor.org/packages/beachmat") | |
10716 | (synopsis "Compiling Bioconductor to handle each matrix type") | |
10717 | (description "This package provides a consistent C++ class interface for a | |
10718 | variety of commonly used matrix types, including sparse and HDF5-backed | |
10719 | matrices.") | |
10720 | (license license:gpl3))) | |
10721 | ||
6fb1dc17 RW |
10722 | (define-public r-singlecellexperiment |
10723 | (package | |
10724 | (name "r-singlecellexperiment") | |
10725 | (version "1.0.0") | |
10726 | (source | |
10727 | (origin | |
10728 | (method url-fetch) | |
10729 | (uri (bioconductor-uri "SingleCellExperiment" version)) | |
10730 | (sha256 | |
10731 | (base32 | |
10732 | "1r276i97w64a5vdlg6952gkj7bls909p42zl8fn8yz87cdwyaars")))) | |
10733 | (properties | |
10734 | `((upstream-name . "SingleCellExperiment"))) | |
10735 | (build-system r-build-system) | |
10736 | (propagated-inputs | |
10737 | `(("r-biocgenerics" ,r-biocgenerics) | |
10738 | ("r-s4vectors" ,r-s4vectors) | |
10739 | ("r-summarizedexperiment" ,r-summarizedexperiment))) | |
10740 | (home-page "https://bioconductor.org/packages/SingleCellExperiment") | |
10741 | (synopsis "S4 classes for single cell data") | |
10742 | (description "This package defines an S4 class for storing data from | |
10743 | single-cell experiments. This includes specialized methods to store and | |
10744 | retrieve spike-in information, dimensionality reduction coordinates and size | |
10745 | factors for each cell, along with the usual metadata for genes and | |
10746 | libraries.") | |
10747 | (license license:gpl3))) | |
10748 | ||
658ab21d RW |
10749 | (define-public r-scater |
10750 | (package | |
10751 | (name "r-scater") | |
59b2864d | 10752 | (version "1.6.3") |
658ab21d RW |
10753 | (source (origin |
10754 | (method url-fetch) | |
10755 | (uri (bioconductor-uri "scater" version)) | |
10756 | (sha256 | |
10757 | (base32 | |
59b2864d | 10758 | "0q3s96gf8saa1dq2fvmpl0jyj7bx3wrdfck3hanb8pxkcir2p7dn")))) |
658ab21d RW |
10759 | (build-system r-build-system) |
10760 | (propagated-inputs | |
10761 | `(("r-beachmat" ,r-beachmat) | |
10762 | ("r-biobase" ,r-biobase) | |
10763 | ("r-biocgenerics" ,r-biocgenerics) | |
10764 | ("r-biomart" ,r-biomart) | |
10765 | ("r-data-table" ,r-data-table) | |
10766 | ("r-dplyr" ,r-dplyr) | |
10767 | ("r-edger" ,r-edger) | |
10768 | ("r-ggbeeswarm" ,r-ggbeeswarm) | |
10769 | ("r-ggplot2" ,r-ggplot2) | |
10770 | ("r-limma" ,r-limma) | |
10771 | ("r-matrix" ,r-matrix) | |
10772 | ("r-matrixstats" ,r-matrixstats) | |
10773 | ("r-plyr" ,r-plyr) | |
10774 | ("r-rcpp" ,r-rcpp) | |
10775 | ("r-reshape2" ,r-reshape2) | |
10776 | ("r-rhdf5" ,r-rhdf5) | |
10777 | ("r-rhdf5lib" ,r-rhdf5lib) | |
10778 | ("r-rjson" ,r-rjson) | |
10779 | ("r-s4vectors" ,r-s4vectors) | |
10780 | ("r-shiny" ,r-shiny) | |
10781 | ("r-shinydashboard" ,r-shinydashboard) | |
10782 | ("r-singlecellexperiment" ,r-singlecellexperiment) | |
10783 | ("r-summarizedexperiment" ,r-summarizedexperiment) | |
10784 | ("r-tximport" ,r-tximport) | |
10785 | ("r-viridis" ,r-viridis))) | |
10786 | (home-page "https://github.com/davismcc/scater") | |
10787 | (synopsis "Single-cell analysis toolkit for gene expression data in R") | |
10788 | (description "This package provides a collection of tools for doing | |
10789 | various analyses of single-cell RNA-seq gene expression data, with a focus on | |
10790 | quality control.") | |
10791 | (license license:gpl2+))) | |
10792 | ||
7f1d9bef RW |
10793 | (define-public r-scran |
10794 | (package | |
10795 | (name "r-scran") | |
9aaf2813 | 10796 | (version "1.6.8") |
7f1d9bef RW |
10797 | (source |
10798 | (origin | |
10799 | (method url-fetch) | |
10800 | (uri (bioconductor-uri "scran" version)) | |
10801 | (sha256 | |
10802 | (base32 | |
9aaf2813 | 10803 | "07wniyrh2fhhkz28v0bfgpvpi1hkkn2cvhacrvvvck142j79944x")))) |
7f1d9bef RW |
10804 | (build-system r-build-system) |
10805 | (propagated-inputs | |
10806 | `(("r-beachmat" ,r-beachmat) | |
10807 | ("r-biocgenerics" ,r-biocgenerics) | |
10808 | ("r-biocparallel" ,r-biocparallel) | |
10809 | ("r-dt" ,r-dt) | |
10810 | ("r-dynamictreecut" ,r-dynamictreecut) | |
10811 | ("r-edger" ,r-edger) | |
10812 | ("r-fnn" ,r-fnn) | |
10813 | ("r-ggplot2" ,r-ggplot2) | |
10814 | ("r-igraph" ,r-igraph) | |
10815 | ("r-limma" ,r-limma) | |
10816 | ("r-matrix" ,r-matrix) | |
10817 | ("r-rcpp" ,r-rcpp) | |
10818 | ("r-rhdf5lib" ,r-rhdf5lib) | |
10819 | ("r-s4vectors" ,r-s4vectors) | |
10820 | ("r-scater" ,r-scater) | |
10821 | ("r-shiny" ,r-shiny) | |
10822 | ("r-singlecellexperiment" ,r-singlecellexperiment) | |
10823 | ("r-statmod" ,r-statmod) | |
10824 | ("r-summarizedexperiment" ,r-summarizedexperiment) | |
10825 | ("r-viridis" ,r-viridis) | |
10826 | ("r-zoo" ,r-zoo))) | |
10827 | (home-page "https://bioconductor.org/packages/scran") | |
10828 | (synopsis "Methods for single-cell RNA-Seq data analysis") | |
10829 | (description "This package implements a variety of low-level analyses of | |
10830 | single-cell RNA-seq data. Methods are provided for normalization of | |
10831 | cell-specific biases, assignment of cell cycle phase, and detection of highly | |
10832 | variable and significantly correlated genes.") | |
10833 | (license license:gpl3))) | |
10834 | ||
05f72960 RW |
10835 | (define-public r-delayedmatrixstats |
10836 | (package | |
10837 | (name "r-delayedmatrixstats") | |
79c6af13 | 10838 | (version "1.0.3") |
05f72960 RW |
10839 | (source |
10840 | (origin | |
10841 | (method url-fetch) | |
10842 | (uri (bioconductor-uri "DelayedMatrixStats" version)) | |
10843 | (sha256 | |
10844 | (base32 | |
79c6af13 | 10845 | "1cxjbjdq9hg9cm95rci0al7a4pk2h73ym276ahw9q4977zbg6381")))) |
05f72960 RW |
10846 | (properties |
10847 | `((upstream-name . "DelayedMatrixStats"))) | |
10848 | (build-system r-build-system) | |
10849 | (propagated-inputs | |
10850 | `(("r-delayedarray" ,r-delayedarray) | |
10851 | ("r-iranges" ,r-iranges) | |
10852 | ("r-matrix" ,r-matrix) | |
10853 | ("r-matrixstats" ,r-matrixstats) | |
10854 | ("r-s4vectors" ,r-s4vectors))) | |
10855 | (home-page "https://github.com/PeteHaitch/DelayedMatrixStats") | |
10856 | (synopsis "Functions that apply to rows and columns of DelayedMatrix objects") | |
10857 | (description | |
10858 | "This package provides a port of the @code{matrixStats} API for use with | |
10859 | @code{DelayedMatrix} objects from the @code{DelayedArray} package. It | |
10860 | contains high-performing functions operating on rows and columns of | |
10861 | @code{DelayedMatrix} objects, e.g. @code{colMedians}, @code{rowMedians}, | |
10862 | @code{colRanks}, @code{rowRanks}, @code{colSds}, and @code{rowSds}. Functions | |
10863 | are optimized per data type and for subsetted calculations such that both | |
10864 | memory usage and processing time is minimized.") | |
10865 | (license license:expat))) | |
10866 | ||
22a0c659 RW |
10867 | (define-public r-phangorn |
10868 | (package | |
10869 | (name "r-phangorn") | |
10870 | (version "2.4.0") | |
10871 | (source | |
10872 | (origin | |
10873 | (method url-fetch) | |
10874 | (uri (cran-uri "phangorn" version)) | |
10875 | (sha256 | |
10876 | (base32 | |
10877 | "0xc8k552nxczy19jr0xjjagrzc8x6lafasgk2c099ls8bc1yml1i")))) | |
10878 | (build-system r-build-system) | |
10879 | (propagated-inputs | |
10880 | `(("r-ape" ,r-ape) | |
10881 | ("r-fastmatch" ,r-fastmatch) | |
10882 | ("r-igraph" ,r-igraph) | |
10883 | ("r-magrittr" ,r-magrittr) | |
10884 | ("r-matrix" ,r-matrix) | |
10885 | ("r-quadprog" ,r-quadprog) | |
10886 | ("r-rcpp" ,r-rcpp))) | |
10887 | (home-page "https://github.com/KlausVigo/phangorn") | |
10888 | (synopsis "Phylogenetic analysis in R") | |
10889 | (description | |
10890 | "Phangorn is a package for phylogenetic analysis in R. It supports | |
10891 | estimation of phylogenetic trees and networks using Maximum Likelihood, | |
10892 | Maximum Parsimony, distance methods and Hadamard conjugation.") | |
10893 | (license license:gpl2+))) | |
10894 | ||
3082de04 | 10895 | (define-public r-dropbead |
84c195e5 RW |
10896 | (let ((commit "d746c6f3b32110428ea56d6a0001ce52a251c247") |
10897 | (revision "2")) | |
3082de04 RW |
10898 | (package |
10899 | (name "r-dropbead") | |
10900 | (version (string-append "0-" revision "." (string-take commit 7))) | |
10901 | (source | |
10902 | (origin | |
10903 | (method git-fetch) | |
10904 | (uri (git-reference | |
10905 | (url "https://github.com/rajewsky-lab/dropbead.git") | |
10906 | (commit commit))) | |
b1d4026d | 10907 | (file-name (git-file-name name version)) |
3082de04 RW |
10908 | (sha256 |
10909 | (base32 | |
84c195e5 | 10910 | "0sbzma49aiiyw8b0jpr7fnhzys9nsqmp4hy4hdz1gzyg1lhnca26")))) |
3082de04 RW |
10911 | (build-system r-build-system) |
10912 | (propagated-inputs | |
10913 | `(("r-ggplot2" ,r-ggplot2) | |
10914 | ("r-rcolorbrewer" ,r-rcolorbrewer) | |
10915 | ("r-gridextra" ,r-gridextra) | |
10916 | ("r-gplots" ,r-gplots) | |
10917 | ("r-plyr" ,r-plyr))) | |
10918 | (home-page "https://github.com/rajewsky-lab/dropbead") | |
10919 | (synopsis "Basic exploration and analysis of Drop-seq data") | |
10920 | (description "This package offers a quick and straight-forward way to | |
10921 | explore and perform basic analysis of single cell sequencing data coming from | |
10922 | droplet sequencing. It has been particularly tailored for Drop-seq.") | |
10923 | (license license:gpl3)))) | |
10924 | ||
5ded35d8 RW |
10925 | (define htslib-for-sambamba |
10926 | (let ((commit "2f3c3ea7b301f9b45737a793c0b2dcf0240e5ee5")) | |
10927 | (package | |
10928 | (inherit htslib) | |
10929 | (name "htslib-for-sambamba") | |
10930 | (version (string-append "1.3.1-1." (string-take commit 9))) | |
10931 | (source | |
10932 | (origin | |
10933 | (method git-fetch) | |
10934 | (uri (git-reference | |
10935 | (url "https://github.com/lomereiter/htslib.git") | |
10936 | (commit commit))) | |
10937 | (file-name (string-append "htslib-" version "-checkout")) | |
10938 | (sha256 | |
10939 | (base32 | |
10940 | "0g38g8s3npr0gjm9fahlbhiskyfws9l5i0x1ml3rakzj7az5l9c9")))) | |
10941 | (arguments | |
10942 | (substitute-keyword-arguments (package-arguments htslib) | |
10943 | ((#:phases phases) | |
10944 | `(modify-phases ,phases | |
d10092b8 | 10945 | (add-after 'unpack 'bootstrap |
5ded35d8 RW |
10946 | (lambda _ |
10947 | (zero? (system* "autoreconf" "-vif")))))))) | |
10948 | (native-inputs | |
10949 | `(("autoconf" ,autoconf) | |
10950 | ("automake" ,automake) | |
10951 | ,@(package-native-inputs htslib)))))) | |
10952 | ||
10953 | (define-public sambamba | |
10954 | (package | |
10955 | (name "sambamba") | |
10956 | (version "0.6.5") | |
10957 | (source | |
10958 | (origin | |
10959 | (method url-fetch) | |
10960 | (uri (string-append "https://github.com/lomereiter/sambamba/" | |
10961 | "archive/v" version ".tar.gz")) | |
10962 | (file-name (string-append name "-" version ".tar.gz")) | |
10963 | (sha256 | |
10964 | (base32 | |
10965 | "17076gijd65a3f07zns2gvbgahiz5lriwsa6dq353ss3jl85d8vy")))) | |
10966 | (build-system gnu-build-system) | |
10967 | (arguments | |
10968 | `(#:tests? #f ; there is no test target | |
10969 | #:make-flags | |
10970 | '("D_COMPILER=ldc2" | |
10971 | ;; Override "--compiler" flag only. | |
10972 | "D_FLAGS=--compiler=ldc2 -IBioD -g -d" | |
10973 | "sambamba-ldmd2-64") | |
10974 | #:phases | |
10975 | (modify-phases %standard-phases | |
10976 | (delete 'configure) | |
10977 | (add-after 'unpack 'place-biod | |
10978 | (lambda* (#:key inputs #:allow-other-keys) | |
10979 | (copy-recursively (assoc-ref inputs "biod") "BioD") | |
10980 | #t)) | |
10981 | (add-after 'unpack 'unbundle-prerequisites | |
10982 | (lambda _ | |
10983 | (substitute* "Makefile" | |
10984 | ((" htslib-static lz4-static") "")) | |
10985 | #t)) | |
10986 | (replace 'install | |
10987 | (lambda* (#:key outputs #:allow-other-keys) | |
10988 | (let* ((out (assoc-ref outputs "out")) | |
10989 | (bin (string-append out "/bin"))) | |
10990 | (mkdir-p bin) | |
10991 | (install-file "build/sambamba" bin) | |
10992 | #t)))))) | |
10993 | (native-inputs | |
10994 | `(("ldc" ,ldc) | |
10995 | ("rdmd" ,rdmd) | |
10996 | ("biod" | |
10997 | ,(let ((commit "1248586b54af4bd4dfb28ebfebfc6bf012e7a587")) | |
10998 | (origin | |
10999 | (method git-fetch) | |
11000 | (uri (git-reference | |
11001 | (url "https://github.com/biod/BioD.git") | |
11002 | (commit commit))) | |
11003 | (file-name (string-append "biod-" | |
11004 | (string-take commit 9) | |
11005 | "-checkout")) | |
11006 | (sha256 | |
11007 | (base32 | |
11008 | "1m8hi1n7x0ri4l6s9i0x6jg4z4v94xrfdzp7mbizdipfag0m17g3"))))))) | |
11009 | (inputs | |
11010 | `(("lz4" ,lz4) | |
11011 | ("htslib" ,htslib-for-sambamba))) | |
11012 | (home-page "http://lomereiter.github.io/sambamba") | |
11013 | (synopsis "Tools for working with SAM/BAM data") | |
11014 | (description "Sambamba is a high performance modern robust and | |
11015 | fast tool (and library), written in the D programming language, for | |
11016 | working with SAM and BAM files. Current parallelised functionality is | |
11017 | an important subset of samtools functionality, including view, index, | |
11018 | sort, markdup, and depth.") | |
11019 | (license license:gpl2+))) | |
b8fffd3a RW |
11020 | |
11021 | (define-public ritornello | |
11022 | (package | |
11023 | (name "ritornello") | |
11024 | (version "1.0.0") | |
11025 | (source (origin | |
11026 | (method url-fetch) | |
11027 | (uri (string-append "https://github.com/KlugerLab/" | |
11028 | "Ritornello/archive/v" | |
11029 | version ".tar.gz")) | |
11030 | (file-name (string-append name "-" version ".tar.gz")) | |
11031 | (sha256 | |
11032 | (base32 | |
11033 | "02nik86gq9ljjriv6pamwlmqnfky3ads1fpklx6mc3hx6k40pg38")))) | |
11034 | (build-system gnu-build-system) | |
11035 | (arguments | |
11036 | `(#:tests? #f ; there are no tests | |
11037 | #:phases | |
11038 | (modify-phases %standard-phases | |
11039 | (add-after 'unpack 'patch-samtools-references | |
11040 | (lambda* (#:key inputs #:allow-other-keys) | |
11041 | (substitute* '("src/SamStream.h" | |
11042 | "src/BufferedGenomeReader.h") | |
11043 | (("<sam.h>") "<samtools/sam.h>")) | |
11044 | #t)) | |
11045 | (delete 'configure) | |
11046 | (replace 'install | |
11047 | (lambda* (#:key inputs outputs #:allow-other-keys) | |
11048 | (let* ((out (assoc-ref outputs "out")) | |
11049 | (bin (string-append out "/bin/"))) | |
11050 | (mkdir-p bin) | |
11051 | (install-file "bin/Ritornello" bin) | |
11052 | #t)))))) | |
11053 | (inputs | |
11054 | `(("samtools" ,samtools-0.1) | |
11055 | ("fftw" ,fftw) | |
11056 | ("boost" ,boost) | |
11057 | ("zlib" ,zlib))) | |
11058 | (home-page "https://github.com/KlugerLab/Ritornello") | |
11059 | (synopsis "Control-free peak caller for ChIP-seq data") | |
11060 | (description "Ritornello is a ChIP-seq peak calling algorithm based on | |
11061 | signal processing that can accurately call binding events without the need to | |
11062 | do a pair total DNA input or IgG control sample. It has been tested for use | |
11063 | with narrow binding events such as transcription factor ChIP-seq.") | |
11064 | (license license:gpl3+))) | |
44f6c889 RW |
11065 | |
11066 | (define-public trim-galore | |
11067 | (package | |
11068 | (name "trim-galore") | |
11069 | (version "0.4.2") | |
11070 | (source | |
11071 | (origin | |
11072 | (method url-fetch) | |
11073 | (uri (string-append "http://www.bioinformatics.babraham.ac.uk/" | |
11074 | "projects/trim_galore/trim_galore_v" | |
11075 | version ".zip")) | |
11076 | (sha256 | |
11077 | (base32 | |
11078 | "0b9qdxi4521gsrjvbhgky8g7kry9b5nx3byzaxkgxz7p4k8bn1mn")))) | |
11079 | (build-system gnu-build-system) | |
11080 | (arguments | |
11081 | `(#:tests? #f ; no tests | |
11082 | #:phases | |
11083 | (modify-phases %standard-phases | |
11084 | ;; The archive contains plain files. | |
11085 | (replace 'unpack | |
11086 | (lambda* (#:key source #:allow-other-keys) | |
11087 | (zero? (system* "unzip" source)))) | |
11088 | (delete 'configure) | |
11089 | (delete 'build) | |
11090 | (add-after 'unpack 'hardcode-tool-references | |
11091 | (lambda* (#:key inputs #:allow-other-keys) | |
11092 | (substitute* "trim_galore" | |
11093 | (("\\$path_to_cutadapt = 'cutadapt'") | |
11094 | (string-append "$path_to_cutadapt = '" | |
11095 | (assoc-ref inputs "cutadapt") | |
11096 | "/bin/cutadapt'")) | |
11097 | (("\\| gzip") | |
11098 | (string-append "| " | |
11099 | (assoc-ref inputs "gzip") | |
11100 | "/bin/gzip")) | |
11101 | (("\"gunzip") | |
11102 | (string-append "\"" | |
11103 | (assoc-ref inputs "gzip") | |
11104 | "/bin/gunzip"))) | |
11105 | #t)) | |
11106 | (replace 'install | |
11107 | (lambda* (#:key outputs #:allow-other-keys) | |
11108 | (let ((bin (string-append (assoc-ref outputs "out") | |
11109 | "/bin"))) | |
11110 | (mkdir-p bin) | |
11111 | (install-file "trim_galore" bin) | |
11112 | #t)))))) | |
11113 | (inputs | |
11114 | `(("gzip" ,gzip) | |
11115 | ("perl" ,perl) | |
11116 | ("cutadapt" ,cutadapt))) | |
11117 | (native-inputs | |
11118 | `(("unzip" ,unzip))) | |
11119 | (home-page "http://www.bioinformatics.babraham.ac.uk/projects/trim_galore/") | |
11120 | (synopsis "Wrapper around Cutadapt and FastQC") | |
11121 | (description "Trim Galore! is a wrapper script to automate quality and | |
11122 | adapter trimming as well as quality control, with some added functionality to | |
11123 | remove biased methylation positions for RRBS sequence files.") | |
11124 | (license license:gpl3+))) | |
3420c905 RW |
11125 | |
11126 | (define-public gess | |
11127 | (package | |
11128 | (name "gess") | |
11129 | (version "1.0") | |
11130 | (source (origin | |
11131 | (method url-fetch) | |
11132 | (uri (string-append "http://compbio.uthscsa.edu/" | |
11133 | "GESS_Web/files/" | |
11134 | "gess-" version ".src.tar.gz")) | |
11135 | (sha256 | |
11136 | (base32 | |
11137 | "0hyk403kxscclzfs24pvdgiv0wm03kjcziqdrp5w46cb049gz0d7")))) | |
11138 | (build-system gnu-build-system) | |
11139 | (arguments | |
11140 | `(#:tests? #f ; no tests | |
11141 | #:phases | |
11142 | (modify-phases %standard-phases | |
11143 | (delete 'configure) | |
11144 | (delete 'build) | |
11145 | (replace 'install | |
11146 | (lambda* (#:key inputs outputs #:allow-other-keys) | |
11147 | (let* ((python (assoc-ref inputs "python")) | |
11148 | (out (assoc-ref outputs "out")) | |
11149 | (bin (string-append out "/bin/")) | |
11150 | (target (string-append | |
11151 | out "/lib/python2.7/site-packages/gess/"))) | |
11152 | (mkdir-p target) | |
11153 | (copy-recursively "." target) | |
11154 | ;; Make GESS.py executable | |
11155 | (chmod (string-append target "GESS.py") #o555) | |
11156 | ;; Add Python shebang to the top and make Matplotlib | |
11157 | ;; usable. | |
11158 | (substitute* (string-append target "GESS.py") | |
11159 | (("\"\"\"Description:" line) | |
11160 | (string-append "#!" (which "python") " | |
11161 | import matplotlib | |
11162 | matplotlib.use('Agg') | |
11163 | " line))) | |
11164 | ;; Make sure GESS has all modules in its path | |
11165 | (wrap-program (string-append target "GESS.py") | |
11166 | `("PYTHONPATH" ":" prefix (,target ,(getenv "PYTHONPATH")))) | |
11167 | (mkdir-p bin) | |
11168 | (symlink (string-append target "GESS.py") | |
11169 | (string-append bin "GESS.py")) | |
11170 | #t)))))) | |
11171 | (inputs | |
11172 | `(("python" ,python-2) | |
11173 | ("python2-pysam" ,python2-pysam) | |
11174 | ("python2-scipy" ,python2-scipy) | |
11175 | ("python2-numpy" ,python2-numpy) | |
11176 | ("python2-networkx" ,python2-networkx) | |
11177 | ("python2-biopython" ,python2-biopython))) | |
11178 | (home-page "http://compbio.uthscsa.edu/GESS_Web/") | |
11179 | (synopsis "Detect exon-skipping events from raw RNA-seq data") | |
11180 | (description | |
11181 | "GESS is an implementation of a novel computational method to detect de | |
11182 | novo exon-skipping events directly from raw RNA-seq data without the prior | |
11183 | knowledge of gene annotation information. GESS stands for the graph-based | |
11184 | exon-skipping scanner detection scheme.") | |
11185 | (license license:bsd-3))) | |
282b0151 RW |
11186 | |
11187 | (define-public phylip | |
11188 | (package | |
11189 | (name "phylip") | |
11190 | (version "3.696") | |
11191 | (source | |
11192 | (origin | |
11193 | (method url-fetch) | |
11194 | (uri (string-append "http://evolution.gs.washington.edu/phylip/" | |
11195 | "download/phylip-" version ".tar.gz")) | |
11196 | (sha256 | |
11197 | (base32 | |
11198 | "01jar1rayhr2gba2pgbw49m56rc5z4p5wn3ds0m188hrlln4a2nd")))) | |
11199 | (build-system gnu-build-system) | |
11200 | (arguments | |
11201 | `(#:tests? #f ; no check target | |
11202 | #:make-flags (list "-f" "Makefile.unx" "install") | |
11203 | #:parallel-build? #f ; not supported | |
11204 | #:phases | |
11205 | (modify-phases %standard-phases | |
11206 | (add-after 'unpack 'enter-dir | |
11207 | (lambda _ (chdir "src") #t)) | |
11208 | (delete 'configure) | |
11209 | (replace 'install | |
11210 | (lambda* (#:key inputs outputs #:allow-other-keys) | |
11211 | (let ((target (string-append (assoc-ref outputs "out") | |
11212 | "/bin"))) | |
11213 | (mkdir-p target) | |
11214 | (for-each (lambda (file) | |
11215 | (install-file file target)) | |
11216 | (find-files "../exe" ".*"))) | |
11217 | #t))))) | |
11218 | (home-page "http://evolution.genetics.washington.edu/phylip/") | |
11219 | (synopsis "Tools for inferring phylogenies") | |
11220 | (description "PHYLIP (the PHYLogeny Inference Package) is a package of | |
11221 | programs for inferring phylogenies (evolutionary trees).") | |
11222 | (license license:bsd-2))) | |
aa163424 RW |
11223 | |
11224 | (define-public imp | |
11225 | (package | |
11226 | (name "imp") | |
11227 | (version "2.6.2") | |
11228 | (source | |
11229 | (origin | |
11230 | (method url-fetch) | |
11231 | (uri (string-append "https://integrativemodeling.org/" | |
11232 | version "/download/imp-" version ".tar.gz")) | |
11233 | (sha256 | |
11234 | (base32 | |
11235 | "0lxqx7vh79d771svr611dkilp6sn30qrbw8zvscbrm37v38d2j6h")))) | |
11236 | (build-system cmake-build-system) | |
11237 | (arguments | |
11238 | `(;; FIXME: Some tests fail because they produce warnings, others fail | |
11239 | ;; because the PYTHONPATH does not include the modeller's directory. | |
677bc34d | 11240 | #:tests? #f)) |
aa163424 RW |
11241 | (inputs |
11242 | `(("boost" ,boost) | |
11243 | ("gsl" ,gsl) | |
11244 | ("swig" ,swig) | |
11245 | ("hdf5" ,hdf5) | |
11246 | ("fftw" ,fftw) | |
11247 | ("python" ,python-2))) | |
11248 | (propagated-inputs | |
11249 | `(("python2-numpy" ,python2-numpy) | |
11250 | ("python2-scipy" ,python2-scipy) | |
11251 | ("python2-pandas" ,python2-pandas) | |
11252 | ("python2-scikit-learn" ,python2-scikit-learn) | |
11253 | ("python2-networkx" ,python2-networkx))) | |
11254 | (home-page "https://integrativemodeling.org") | |
11255 | (synopsis "Integrative modeling platform") | |
11256 | (description "IMP's broad goal is to contribute to a comprehensive | |
11257 | structural characterization of biomolecules ranging in size and complexity | |
11258 | from small peptides to large macromolecular assemblies, by integrating data | |
11259 | from diverse biochemical and biophysical experiments. IMP provides a C++ and | |
11260 | Python toolbox for solving complex modeling problems, and a number of | |
11261 | applications for tackling some common problems in a user-friendly way.") | |
11262 | ;; IMP is largely available under the GNU Lesser GPL; see the file | |
11263 | ;; COPYING.LGPL for the full text of this license. Some IMP modules are | |
11264 | ;; available under the GNU GPL (see the file COPYING.GPL). | |
11265 | (license (list license:lgpl2.1+ | |
11266 | license:gpl3+)))) | |
8befd094 RW |
11267 | |
11268 | (define-public tadbit | |
11269 | (package | |
11270 | (name "tadbit") | |
11271 | (version "0.2") | |
11272 | (source (origin | |
11273 | (method url-fetch) | |
11274 | (uri (string-append "https://github.com/3DGenomes/TADbit/" | |
11275 | "archive/v" version ".tar.gz")) | |
11276 | (file-name (string-append name "-" version ".tar.gz")) | |
11277 | (sha256 | |
11278 | (base32 | |
11279 | "1cnfqrl4685zar4nnw94j94nhvl2h29jm448nadqi1h05z6fdk4f")))) | |
11280 | (build-system python-build-system) | |
11281 | (arguments | |
11282 | `(;; Tests are included and must be run after installation, but | |
11283 | ;; they are incomplete and thus cannot be run. | |
11284 | #:tests? #f | |
11285 | #:python ,python-2 | |
11286 | #:phases | |
11287 | (modify-phases %standard-phases | |
11288 | (add-after 'unpack 'fix-problems-with-setup.py | |
11289 | (lambda* (#:key outputs #:allow-other-keys) | |
11290 | ;; setup.py opens these files for writing | |
11291 | (chmod "_pytadbit/_version.py" #o664) | |
11292 | (chmod "README.rst" #o664) | |
11293 | ||
11294 | ;; Don't attempt to install the bash completions to | |
11295 | ;; the home directory. | |
11296 | (rename-file "extras/.bash_completion" | |
11297 | "extras/tadbit") | |
11298 | (substitute* "setup.py" | |
11299 | (("\\(path.expanduser\\('~'\\)") | |
11300 | (string-append "(\"" | |
11301 | (assoc-ref outputs "out") | |
11302 | "/etc/bash_completion.d\"")) | |
11303 | (("extras/\\.bash_completion") | |
11304 | "extras/tadbit")) | |
11305 | #t))))) | |
11306 | (inputs | |
11307 | ;; TODO: add Chimera for visualization | |
11308 | `(("imp" ,imp) | |
11309 | ("mcl" ,mcl) | |
11310 | ("python2-scipy" ,python2-scipy) | |
11311 | ("python2-numpy" ,python2-numpy) | |
11312 | ("python2-matplotlib" ,python2-matplotlib) | |
11313 | ("python2-pysam" ,python2-pysam))) | |
11314 | (home-page "http://3dgenomes.github.io/TADbit/") | |
11315 | (synopsis "Analyze, model, and explore 3C-based data") | |
11316 | (description | |
11317 | "TADbit is a complete Python library to deal with all steps to analyze, | |
11318 | model, and explore 3C-based data. With TADbit the user can map FASTQ files to | |
11319 | obtain raw interaction binned matrices (Hi-C like matrices), normalize and | |
a147fadd | 11320 | correct interaction matrices, identify and compare the so-called |
8befd094 RW |
11321 | @dfn{Topologically Associating Domains} (TADs), build 3D models from the |
11322 | interaction matrices, and finally, extract structural properties from the | |
11323 | models. TADbit is complemented by TADkit for visualizing 3D models.") | |
11324 | (license license:gpl3+))) | |
94820951 RW |
11325 | |
11326 | (define-public kentutils | |
11327 | (package | |
11328 | (name "kentutils") | |
11329 | ;; 302.1.0 is out, but the only difference is the inclusion of | |
11330 | ;; pre-built binaries. | |
11331 | (version "302.0.0") | |
11332 | (source | |
11333 | (origin | |
11334 | (method url-fetch) | |
11335 | (uri (string-append "https://github.com/ENCODE-DCC/kentUtils/" | |
11336 | "archive/v" version ".tar.gz")) | |
11337 | (file-name (string-append name "-" version ".tar.gz")) | |
11338 | (sha256 | |
11339 | (base32 | |
11340 | "134aja3k1cj32kbk1nnw0q9gxjb2krr15q6sga8qldzvc0585rmm")) | |
11341 | (modules '((guix build utils) | |
11342 | (srfi srfi-26) | |
11343 | (ice-9 ftw))) | |
11344 | (snippet | |
11345 | '(begin | |
11346 | ;; Only the contents of the specified directories are free | |
11347 | ;; for all uses, so we remove the rest. "hg/autoSql" and | |
11348 | ;; "hg/autoXml" are nominally free, but they depend on a | |
11349 | ;; library that is built from the sources in "hg/lib", | |
11350 | ;; which is nonfree. | |
11351 | (let ((free (list "." ".." | |
11352 | "utils" "lib" "inc" "tagStorm" | |
11353 | "parasol" "htslib")) | |
11354 | (directory? (lambda (file) | |
11355 | (eq? 'directory (stat:type (stat file)))))) | |
11356 | (for-each (lambda (file) | |
11357 | (and (directory? file) | |
11358 | (delete-file-recursively file))) | |
11359 | (map (cut string-append "src/" <>) | |
11360 | (scandir "src" | |
11361 | (lambda (file) | |
11362 | (not (member file free))))))) | |
11363 | ;; Only make the utils target, not the userApps target, | |
11364 | ;; because that requires libraries we won't build. | |
11365 | (substitute* "Makefile" | |
11366 | ((" userApps") " utils")) | |
11367 | ;; Only build libraries that are free. | |
11368 | (substitute* "src/makefile" | |
11369 | (("DIRS =.*") "DIRS =\n") | |
11370 | (("cd jkOwnLib.*") "") | |
11371 | ((" hgLib") "") | |
11372 | (("cd hg.*") "")) | |
11373 | (substitute* "src/utils/makefile" | |
11374 | ;; These tools depend on "jkhgap.a", which is part of the | |
11375 | ;; nonfree "src/hg/lib" directory. | |
11376 | (("raSqlQuery") "") | |
11377 | (("pslLiftSubrangeBlat") "") | |
11378 | ||
11379 | ;; Do not build UCSC tools, which may require nonfree | |
11380 | ;; components. | |
11381 | (("ALL_APPS =.*") "ALL_APPS = $(UTILS_APPLIST)\n")) | |
11382 | #t)))) | |
11383 | (build-system gnu-build-system) | |
11384 | (arguments | |
11385 | `( ;; There is no global test target and the test target for | |
11386 | ;; individual tools depends on input files that are not | |
11387 | ;; included. | |
11388 | #:tests? #f | |
11389 | #:phases | |
11390 | (modify-phases %standard-phases | |
11391 | (add-after 'unpack 'fix-paths | |
11392 | (lambda _ | |
11393 | (substitute* "Makefile" | |
11394 | (("/bin/echo") (which "echo"))) | |
11395 | #t)) | |
11396 | (add-after 'unpack 'prepare-samtabix | |
11397 | (lambda* (#:key inputs #:allow-other-keys) | |
11398 | (copy-recursively (assoc-ref inputs "samtabix") | |
11399 | "samtabix") | |
11400 | #t)) | |
11401 | (delete 'configure) | |
11402 | (replace 'install | |
11403 | (lambda* (#:key outputs #:allow-other-keys) | |
11404 | (let ((bin (string-append (assoc-ref outputs "out") | |
11405 | "/bin"))) | |
11406 | (copy-recursively "bin" bin)) | |
11407 | #t))))) | |
11408 | (native-inputs | |
11409 | `(("samtabix" | |
11410 | ,(origin | |
11411 | (method git-fetch) | |
11412 | (uri (git-reference | |
11413 | (url "http://genome-source.cse.ucsc.edu/samtabix.git") | |
11414 | (commit "10fd107909c1ac4d679299908be4262a012965ba"))) | |
11415 | (sha256 | |
11416 | (base32 | |
11417 | "0c1nj64l42v395sa84n7az43xiap4i6f9n9dfz4058aqiwkhkmma")))))) | |
11418 | (inputs | |
11419 | `(("zlib" ,zlib) | |
11420 | ("tcsh" ,tcsh) | |
11421 | ("perl" ,perl) | |
11422 | ("libpng" ,libpng) | |
b44437c5 | 11423 | ("mariadb" ,mariadb) |
94820951 RW |
11424 | ("openssl" ,openssl))) |
11425 | (home-page "http://genome.cse.ucsc.edu/index.html") | |
11426 | (synopsis "Assorted bioinformatics utilities") | |
11427 | (description "This package provides the kentUtils, a selection of | |
11428 | bioinformatics utilities used in combination with the UCSC genome | |
11429 | browser.") | |
11430 | ;; Only a subset of the sources are released under a non-copyleft | |
11431 | ;; free software license. All other sources are removed in a | |
11432 | ;; snippet. See this bug report for an explanation of how the | |
11433 | ;; license statements apply: | |
11434 | ;; https://github.com/ENCODE-DCC/kentUtils/issues/12 | |
11435 | (license (license:non-copyleft | |
11436 | "http://genome.ucsc.edu/license/" | |
11437 | "The contents of this package are free for all uses.")))) | |
7ceb0a83 RW |
11438 | |
11439 | (define-public f-seq | |
11440 | (let ((commit "6ccded34cff38cf432deed8503648b4a66953f9b") | |
11441 | (revision "1")) | |
11442 | (package | |
11443 | (name "f-seq") | |
c6643f2d | 11444 | (version (string-append "1.1-" revision "." (string-take commit 7))) |
7ceb0a83 RW |
11445 | (source (origin |
11446 | (method git-fetch) | |
11447 | (uri (git-reference | |
11448 | (url "https://github.com/aboyle/F-seq.git") | |
11449 | (commit commit))) | |
11450 | (file-name (string-append name "-" version)) | |
11451 | (sha256 | |
11452 | (base32 | |
11453 | "1nk33k0yajg2id4g59bc4szr58r2q6pdq42vgcw054m8ip9wv26h")) | |
11454 | (modules '((guix build utils))) | |
11455 | ;; Remove bundled Java library archives. | |
11456 | (snippet | |
11457 | '(begin | |
11458 | (for-each delete-file (find-files "lib" ".*")) | |
11459 | #t)))) | |
11460 | (build-system ant-build-system) | |
11461 | (arguments | |
11462 | `(#:tests? #f ; no tests included | |
11463 | #:phases | |
11464 | (modify-phases %standard-phases | |
11465 | (replace 'install | |
c0770fee | 11466 | (lambda* (#:key inputs outputs #:allow-other-keys) |
7ceb0a83 RW |
11467 | (let* ((target (assoc-ref outputs "out")) |
11468 | (doc (string-append target "/share/doc/f-seq/"))) | |
11469 | (mkdir-p target) | |
11470 | (mkdir-p doc) | |
11471 | (substitute* "bin/linux/fseq" | |
c0770fee RW |
11472 | (("java") (which "java")) |
11473 | (("\\$REALDIR/../lib/commons-cli-1.1.jar") | |
11474 | (string-append (assoc-ref inputs "java-commons-cli") | |
11475 | "/share/java/commons-cli.jar")) | |
11476 | (("REALDIR=.*") | |
11477 | (string-append "REALDIR=" target "/bin\n"))) | |
7ceb0a83 RW |
11478 | (install-file "README.txt" doc) |
11479 | (install-file "bin/linux/fseq" (string-append target "/bin")) | |
11480 | (install-file "build~/fseq.jar" (string-append target "/lib")) | |
11481 | (copy-recursively "lib" (string-append target "/lib")) | |
11482 | #t)))))) | |
11483 | (inputs | |
11484 | `(("perl" ,perl) | |
11485 | ("java-commons-cli" ,java-commons-cli))) | |
11486 | (home-page "http://fureylab.web.unc.edu/software/fseq/") | |
11487 | (synopsis "Feature density estimator for high-throughput sequence tags") | |
11488 | (description | |
11489 | "F-Seq is a software package that generates a continuous tag sequence | |
11490 | density estimation allowing identification of biologically meaningful sites | |
11491 | such as transcription factor binding sites (ChIP-seq) or regions of open | |
11492 | chromatin (DNase-seq). Output can be displayed directly in the UCSC Genome | |
11493 | Browser.") | |
11494 | (license license:gpl3+)))) | |
96348048 RW |
11495 | |
11496 | (define-public bismark | |
11497 | (package | |
11498 | (name "bismark") | |
11499 | (version "0.16.3") | |
11500 | (source | |
11501 | (origin | |
11502 | (method url-fetch) | |
11503 | (uri (string-append "https://github.com/FelixKrueger/Bismark/" | |
11504 | "archive/" version ".tar.gz")) | |
11505 | (file-name (string-append name "-" version ".tar.gz")) | |
11506 | (sha256 | |
11507 | (base32 | |
11508 | "1204i0pa02ll2jn5pnxypkclnskvv7a2nwh5nxhagmhxk9wfv9sq")))) | |
11509 | (build-system perl-build-system) | |
11510 | (arguments | |
11511 | `(#:tests? #f ; there are no tests | |
11512 | #:phases | |
11513 | (modify-phases %standard-phases | |
11514 | (delete 'configure) | |
11515 | (delete 'build) | |
11516 | (replace 'install | |
11517 | (lambda* (#:key outputs #:allow-other-keys) | |
11518 | (let ((bin (string-append (assoc-ref outputs "out") | |
11519 | "/bin")) | |
11520 | (docdir (string-append (assoc-ref outputs "out") | |
11521 | "/share/doc/bismark")) | |
11522 | (docs '("Bismark_User_Guide.pdf" | |
11523 | "RELEASE_NOTES.txt")) | |
11524 | (scripts '("bismark" | |
11525 | "bismark_genome_preparation" | |
11526 | "bismark_methylation_extractor" | |
11527 | "bismark2bedGraph" | |
11528 | "bismark2report" | |
11529 | "coverage2cytosine" | |
11530 | "deduplicate_bismark" | |
11531 | "bismark_sitrep.tpl" | |
11532 | "bam2nuc" | |
11533 | "bismark2summary"))) | |
11534 | (mkdir-p docdir) | |
11535 | (mkdir-p bin) | |
11536 | (for-each (lambda (file) (install-file file bin)) | |
11537 | scripts) | |
11538 | (for-each (lambda (file) (install-file file docdir)) | |
11539 | docs) | |
11540 | #t)))))) | |
11541 | (home-page "http://www.bioinformatics.babraham.ac.uk/projects/bismark/") | |
11542 | (synopsis "Map bisulfite treated sequence reads and analyze methylation") | |
11543 | (description "Bismark is a program to map bisulfite treated sequencing | |
11544 | reads to a genome of interest and perform methylation calls in a single step. | |
11545 | The output can be easily imported into a genome viewer, such as SeqMonk, and | |
11546 | enables a researcher to analyse the methylation levels of their samples | |
11547 | straight away. Its main features are: | |
11548 | ||
11549 | @itemize | |
11550 | @item Bisulfite mapping and methylation calling in one single step | |
11551 | @item Supports single-end and paired-end read alignments | |
11552 | @item Supports ungapped and gapped alignments | |
11553 | @item Alignment seed length, number of mismatches etc are adjustable | |
11554 | @item Output discriminates between cytosine methylation in CpG, CHG | |
11555 | and CHH context | |
11556 | @end itemize\n") | |
11557 | (license license:gpl3+))) | |
dc8ddbfb RW |
11558 | |
11559 | (define-public paml | |
11560 | (package | |
11561 | (name "paml") | |
11562 | (version "4.9e") | |
11563 | (source (origin | |
11564 | (method url-fetch) | |
11565 | (uri (string-append "http://abacus.gene.ucl.ac.uk/software/" | |
11566 | "paml" version ".tgz")) | |
11567 | (sha256 | |
11568 | (base32 | |
11569 | "13zf6h9fiqghwhch2h06x1zdr6s42plsnqahflp5g7myr3han3s6")) | |
11570 | (modules '((guix build utils))) | |
11571 | ;; Remove Windows binaries | |
11572 | (snippet | |
11573 | '(begin | |
11574 | (for-each delete-file (find-files "." "\\.exe$")) | |
11575 | #t)))) | |
11576 | (build-system gnu-build-system) | |
11577 | (arguments | |
11578 | `(#:tests? #f ; there are no tests | |
11579 | #:make-flags '("CC=gcc") | |
11580 | #:phases | |
11581 | (modify-phases %standard-phases | |
11582 | (replace 'configure | |
11583 | (lambda _ | |
11584 | (substitute* "src/BFdriver.c" | |
11585 | (("/bin/bash") (which "bash"))) | |
11586 | (chdir "src") | |
11587 | #t)) | |
11588 | (replace 'install | |
11589 | (lambda* (#:key outputs #:allow-other-keys) | |
11590 | (let ((tools '("baseml" "basemlg" "codeml" | |
11591 | "pamp" "evolver" "yn00" "chi2")) | |
11592 | (bin (string-append (assoc-ref outputs "out") "/bin")) | |
11593 | (docdir (string-append (assoc-ref outputs "out") | |
11594 | "/share/doc/paml"))) | |
11595 | (mkdir-p bin) | |
11596 | (for-each (lambda (file) (install-file file bin)) tools) | |
11597 | (copy-recursively "../doc" docdir) | |
11598 | #t)))))) | |
11599 | (home-page "http://abacus.gene.ucl.ac.uk/software/paml.html") | |
11600 | (synopsis "Phylogentic analysis by maximum likelihood") | |
11601 | (description "PAML (for Phylogentic Analysis by Maximum Likelihood) | |
11602 | contains a few programs for model fitting and phylogenetic tree reconstruction | |
11603 | using nucleotide or amino-acid sequence data.") | |
11604 | ;; GPLv3 only | |
11605 | (license license:gpl3))) | |
d112e5a8 RW |
11606 | |
11607 | (define-public kallisto | |
11608 | (package | |
11609 | (name "kallisto") | |
11610 | (version "0.43.1") | |
11611 | (source (origin | |
11612 | (method url-fetch) | |
11613 | (uri (string-append "https://github.com/pachterlab/" | |
11614 | "kallisto/archive/v" version ".tar.gz")) | |
11615 | (file-name (string-append name "-" version ".tar.gz")) | |
11616 | (sha256 | |
11617 | (base32 | |
11618 | "03j3iqhvq7ya3c91gidly3k3jvgm97vjq4scihrlxh315j696r11")))) | |
11619 | (build-system cmake-build-system) | |
11620 | (arguments `(#:tests? #f)) ; no "check" target | |
11621 | (inputs | |
11622 | `(("hdf5" ,hdf5) | |
11623 | ("zlib" ,zlib))) | |
11624 | (home-page "http://pachterlab.github.io/kallisto/") | |
11625 | (synopsis "Near-optimal RNA-Seq quantification") | |
11626 | (description | |
11627 | "Kallisto is a program for quantifying abundances of transcripts from | |
11628 | RNA-Seq data, or more generally of target sequences using high-throughput | |
11629 | sequencing reads. It is based on the novel idea of pseudoalignment for | |
11630 | rapidly determining the compatibility of reads with targets, without the need | |
11631 | for alignment. Pseudoalignment of reads preserves the key information needed | |
11632 | for quantification, and kallisto is therefore not only fast, but also as | |
11633 | accurate as existing quantification tools.") | |
11634 | (license license:bsd-2))) | |
c3b2ab9d RW |
11635 | |
11636 | (define-public libgff | |
11637 | (package | |
11638 | (name "libgff") | |
11639 | (version "1.0") | |
11640 | (source (origin | |
11641 | (method url-fetch) | |
11642 | (uri (string-append | |
11643 | "https://github.com/Kingsford-Group/" | |
11644 | "libgff/archive/v" version ".tar.gz")) | |
11645 | (file-name (string-append name "-" version ".tar.gz")) | |
11646 | (sha256 | |
11647 | (base32 | |
11648 | "0vc4nxyhlm6g9vvmx5l4lfs5pnvixsv1hiiy4kddf2y3p6jna8ls")))) | |
11649 | (build-system cmake-build-system) | |
11650 | (arguments `(#:tests? #f)) ; no tests included | |
11651 | (home-page "https://github.com/Kingsford-Group/libgff") | |
11652 | (synopsis "Parser library for reading/writing GFF files") | |
11653 | (description "This is a simple \"libraryfication\" of the GFF/GTF parsing | |
11654 | code that is used in the Cufflinks codebase. The goal of this library is to | |
11655 | provide this functionality without the necessity of drawing in a heavy-weight | |
11656 | dependency like SeqAn.") | |
11657 | (license (license:x11-style "http://www.boost.org/LICENSE_1_0.txt")))) | |
1fe0bde3 RW |
11658 | |
11659 | (define-public libdivsufsort | |
11660 | (package | |
11661 | (name "libdivsufsort") | |
11662 | (version "2.0.1") | |
11663 | (source (origin | |
11664 | (method git-fetch) | |
11665 | (uri (git-reference | |
11666 | (url "https://github.com/y-256/libdivsufsort.git") | |
11667 | (commit version))) | |
d9a069c2 | 11668 | (file-name (git-file-name name version)) |
1fe0bde3 RW |
11669 | (sha256 |
11670 | (base32 | |
11671 | "0fgdz9fzihlvjjrxy01md1bv9vh12rkgkwbm90b1hj5xpbaqp7z2")))) | |
11672 | (build-system cmake-build-system) | |
11673 | (arguments | |
11674 | '(#:tests? #f ; there are no tests | |
11675 | #:configure-flags | |
11676 | ;; Needed for rapmap and sailfish. | |
11677 | '("-DBUILD_DIVSUFSORT64=ON"))) | |
11678 | (home-page "https://github.com/y-256/libdivsufsort") | |
11679 | (synopsis "Lightweight suffix-sorting library") | |
11680 | (description "libdivsufsort is a software library that implements a | |
11681 | lightweight suffix array construction algorithm. This library provides a | |
11682 | simple and an efficient C API to construct a suffix array and a | |
11683 | Burrows-Wheeler transformed string from a given string over a constant-size | |
11684 | alphabet. The algorithm runs in O(n log n) worst-case time using only 5n+O(1) | |
11685 | bytes of memory space, where n is the length of the string.") | |
11686 | (license license:expat))) | |
8d77a085 RW |
11687 | |
11688 | (define-public sailfish | |
11689 | (package | |
11690 | (name "sailfish") | |
11691 | (version "0.10.1") | |
11692 | (source (origin | |
11693 | (method url-fetch) | |
11694 | (uri | |
11695 | (string-append "https://github.com/kingsfordgroup/" | |
11696 | "sailfish/archive/v" version ".tar.gz")) | |
11697 | (file-name (string-append name "-" version ".tar.gz")) | |
11698 | (sha256 | |
11699 | (base32 | |
11700 | "1inn60dxiwsz8g9w7kvfhjxj4bwfb0r12dyhpzzhfbig712dkmm0")) | |
11701 | (modules '((guix build utils))) | |
11702 | (snippet | |
11703 | '(begin | |
11704 | ;; Delete bundled headers for eigen3. | |
11705 | (delete-file-recursively "include/eigen3/") | |
11706 | #t)))) | |
11707 | (build-system cmake-build-system) | |
11708 | (arguments | |
11709 | `(#:configure-flags | |
11710 | (list (string-append "-DBOOST_INCLUDEDIR=" | |
11711 | (assoc-ref %build-inputs "boost") | |
11712 | "/include/") | |
11713 | (string-append "-DBOOST_LIBRARYDIR=" | |
11714 | (assoc-ref %build-inputs "boost") | |
11715 | "/lib/") | |
11716 | (string-append "-DBoost_LIBRARIES=" | |
11717 | "-lboost_iostreams " | |
11718 | "-lboost_filesystem " | |
11719 | "-lboost_system " | |
11720 | "-lboost_thread " | |
11721 | "-lboost_timer " | |
11722 | "-lboost_chrono " | |
11723 | "-lboost_program_options") | |
11724 | "-DBoost_FOUND=TRUE" | |
11725 | ;; Don't download RapMap---we already have it! | |
11726 | "-DFETCHED_RAPMAP=1") | |
11727 | ;; Tests must be run after installation and the location of the test | |
11728 | ;; data file must be overridden. But the tests fail. It looks like | |
11729 | ;; they are not really meant to be run. | |
11730 | #:tests? #f | |
11731 | #:phases | |
11732 | (modify-phases %standard-phases | |
11733 | ;; Boost cannot be found, even though it's right there. | |
11734 | (add-after 'unpack 'do-not-look-for-boost | |
11735 | (lambda* (#:key inputs #:allow-other-keys) | |
11736 | (substitute* "CMakeLists.txt" | |
11737 | (("find_package\\(Boost 1\\.53\\.0") "#")))) | |
11738 | (add-after 'unpack 'do-not-assign-to-macro | |
11739 | (lambda _ | |
11740 | (substitute* "include/spdlog/details/format.cc" | |
11741 | (("const unsigned CHAR_WIDTH = 1;") "")))) | |
11742 | (add-after 'unpack 'prepare-rapmap | |
11743 | (lambda* (#:key inputs #:allow-other-keys) | |
11744 | (let ((src "external/install/src/rapmap/") | |
11745 | (include "external/install/include/rapmap/") | |
11746 | (rapmap (assoc-ref inputs "rapmap"))) | |
11747 | (mkdir-p "/tmp/rapmap") | |
11748 | (system* "tar" "xf" | |
11749 | (assoc-ref inputs "rapmap") | |
11750 | "-C" "/tmp/rapmap" | |
11751 | "--strip-components=1") | |
11752 | (mkdir-p src) | |
11753 | (mkdir-p include) | |
11754 | (for-each (lambda (file) | |
11755 | (install-file file src)) | |
11756 | (find-files "/tmp/rapmap/src" "\\.(c|cpp)")) | |
11757 | (copy-recursively "/tmp/rapmap/include" include)))) | |
11758 | (add-after 'unpack 'use-system-libraries | |
11759 | (lambda* (#:key inputs #:allow-other-keys) | |
11760 | (substitute* '("src/SailfishIndexer.cpp" | |
11761 | "src/SailfishUtils.cpp" | |
11762 | "src/SailfishQuantify.cpp" | |
11763 | "src/FASTAParser.cpp" | |
11764 | "include/PCA.hpp" | |
11765 | "include/SailfishUtils.hpp" | |
11766 | "include/SailfishIndex.hpp" | |
11767 | "include/CollapsedEMOptimizer.hpp" | |
11768 | "src/CollapsedEMOptimizer.cpp") | |
11769 | (("#include \"jellyfish/config.h\"") "")) | |
11770 | (substitute* "src/CMakeLists.txt" | |
11771 | (("\\$\\{GAT_SOURCE_DIR\\}/external/install/include/jellyfish-2.2..") | |
11772 | (string-append (assoc-ref inputs "jellyfish") | |
11773 | "/include/jellyfish-" ,(package-version jellyfish))) | |
11774 | (("\\$\\{GAT_SOURCE_DIR\\}/external/install/lib/libjellyfish-2.0.a") | |
11775 | (string-append (assoc-ref inputs "jellyfish") | |
11776 | "/lib/libjellyfish-2.0.a")) | |
11777 | (("\\$\\{GAT_SOURCE_DIR\\}/external/install/lib/libdivsufsort.a") | |
11778 | (string-append (assoc-ref inputs "libdivsufsort") | |
11779 | "/lib/libdivsufsort.so")) | |
11780 | (("\\$\\{GAT_SOURCE_DIR\\}/external/install/lib/libdivsufsort64.a") | |
11781 | (string-append (assoc-ref inputs "libdivsufsort") | |
11782 | "/lib/libdivsufsort64.so"))) | |
11783 | (substitute* "CMakeLists.txt" | |
11784 | ;; Don't prefer static libs | |
11785 | (("SET\\(CMAKE_FIND_LIBRARY_SUFFIXES.*") "") | |
11786 | (("find_package\\(Jellyfish.*") "") | |
11787 | (("ExternalProject_Add\\(libjellyfish") "message(") | |
11788 | (("ExternalProject_Add\\(libgff") "message(") | |
11789 | (("ExternalProject_Add\\(libsparsehash") "message(") | |
11790 | (("ExternalProject_Add\\(libdivsufsort") "message(")) | |
11791 | ||
11792 | ;; Ensure that Eigen headers can be found | |
11793 | (setenv "CPLUS_INCLUDE_PATH" | |
11794 | (string-append (getenv "CPLUS_INCLUDE_PATH") | |
11795 | ":" | |
11796 | (assoc-ref inputs "eigen") | |
11797 | "/include/eigen3"))))))) | |
11798 | (inputs | |
11799 | `(("boost" ,boost) | |
11800 | ("eigen" ,eigen) | |
11801 | ("jemalloc" ,jemalloc) | |
11802 | ("jellyfish" ,jellyfish) | |
11803 | ("sparsehash" ,sparsehash) | |
11804 | ("rapmap" ,(origin | |
11805 | (method git-fetch) | |
11806 | (uri (git-reference | |
11807 | (url "https://github.com/COMBINE-lab/RapMap.git") | |
11808 | (commit (string-append "sf-v" version)))) | |
11809 | (file-name (string-append "rapmap-sf-v" version "-checkout")) | |
11810 | (sha256 | |
11811 | (base32 | |
11812 | "1hv79l5i576ykv5a1srj2p0q36yvyl5966m0fcy2lbi169ipjakf")) | |
11813 | (modules '((guix build utils))) | |
11814 | ;; These files are expected to be excluded. | |
11815 | (snippet | |
11816 | '(begin (delete-file-recursively "include/spdlog") | |
11817 | (for-each delete-file '("include/xxhash.h" | |
11818 | "src/xxhash.c")))))) | |
11819 | ("libdivsufsort" ,libdivsufsort) | |
11820 | ("libgff" ,libgff) | |
11821 | ("tbb" ,tbb) | |
11822 | ("zlib" ,zlib))) | |
11823 | (native-inputs | |
11824 | `(("pkg-config" ,pkg-config))) | |
11825 | (home-page "http://www.cs.cmu.edu/~ckingsf/software/sailfish") | |
11826 | (synopsis "Mapping-based isoform quantification from RNA-Seq reads") | |
11827 | (description "Sailfish is a tool for genomic transcript quantification | |
11828 | from RNA-seq data. It requires a set of target transcripts (either from a | |
11829 | reference or de-novo assembly) to quantify. All you need to run sailfish is a | |
11830 | fasta file containing your reference transcripts and a (set of) fasta/fastq | |
11831 | file(s) containing your reads.") | |
11832 | (license license:gpl3+))) | |
7762646d RW |
11833 | |
11834 | (define libstadenio-for-salmon | |
11835 | (package | |
11836 | (name "libstadenio") | |
11837 | (version "1.14.8") | |
11838 | (source (origin | |
11839 | (method git-fetch) | |
11840 | (uri (git-reference | |
11841 | (url "https://github.com/COMBINE-lab/staden-io_lib.git") | |
11842 | (commit (string-append "v" version)))) | |
11843 | (file-name (string-append name "-" version "-checkout")) | |
11844 | (sha256 | |
11845 | (base32 | |
11846 | "1x8kxxqxl892vwfbprlbyfwkkv7c34ggkc94892x9x0g37x5nbwx")))) | |
11847 | (build-system gnu-build-system) | |
11848 | (arguments '(#:parallel-tests? #f)) ; not supported | |
11849 | (inputs | |
11850 | `(("zlib" ,zlib))) | |
11851 | (native-inputs | |
11852 | `(("perl" ,perl))) ; for tests | |
11853 | (home-page "https://github.com/COMBINE-lab/staden-io_lib") | |
11854 | (synopsis "General purpose trace and experiment file library") | |
11855 | (description "This package provides a library of file reading and writing | |
11856 | code to provide a general purpose Trace file (and Experiment File) reading | |
11857 | interface. | |
11858 | ||
11859 | The following file formats are supported: | |
11860 | ||
11861 | @enumerate | |
11862 | @item SCF trace files | |
11863 | @item ABI trace files | |
11864 | @item ALF trace files | |
11865 | @item ZTR trace files | |
11866 | @item SFF trace archives | |
11867 | @item SRF trace archives | |
11868 | @item Experiment files | |
11869 | @item Plain text files | |
11870 | @item SAM/BAM sequence files | |
11871 | @item CRAM sequence files | |
11872 | @end enumerate\n") | |
11873 | (license license:bsd-3))) | |
11874 | ||
11875 | (define spdlog-for-salmon | |
11876 | (package | |
11877 | (name "spdlog") | |
11878 | (version "0.14.0") | |
11879 | (source (origin | |
11880 | (method git-fetch) | |
11881 | (uri (git-reference | |
11882 | (url "https://github.com/COMBINE-lab/spdlog.git") | |
11883 | (commit (string-append "v" version)))) | |
11884 | (file-name (string-append name "-" version "-checkout")) | |
11885 | (sha256 | |
11886 | (base32 | |
11887 | "13730429gwlabi432ilpnja3sfvy0nn2719vnhhmii34xcdyc57q")))) | |
11888 | (build-system cmake-build-system) | |
11889 | (home-page "https://github.com/COMBINE-lab/spdlog") | |
11890 | (synopsis "Very fast C++ logging library") | |
11891 | (description "Spdlog is a very fast header-only C++ logging library with | |
11892 | performance as its primary goal.") | |
11893 | (license license:expat))) | |
11894 | ||
11895 | ;; This is a modified variant of bwa for use with Salmon. It installs a | |
11896 | ;; library to avoid having to build this as part of Salmon. | |
11897 | (define bwa-for-salmon | |
11898 | (package (inherit bwa) | |
11899 | (name "bwa") | |
11900 | (version "0.7.12.5") | |
11901 | (source (origin | |
11902 | (method git-fetch) | |
11903 | (uri (git-reference | |
11904 | (url "https://github.com/COMBINE-lab/bwa.git") | |
11905 | (commit (string-append "v" version)))) | |
11906 | (file-name (string-append "bwa-for-salmon-" version "-checkout")) | |
11907 | (sha256 | |
11908 | (base32 | |
11909 | "1z2qa64y0c5hky10510x137mnzlhz6k8qf27csw4w9j6qihq95gb")))) | |
11910 | (build-system gnu-build-system) | |
11911 | (arguments | |
11912 | '(#:tests? #f ;no "check" target | |
11913 | #:phases | |
11914 | (modify-phases %standard-phases | |
11915 | (replace 'install | |
11916 | (lambda* (#:key outputs #:allow-other-keys) | |
11917 | (let* ((out (assoc-ref outputs "out")) | |
11918 | (bin (string-append out "/bin")) | |
11919 | (lib (string-append out "/lib")) | |
11920 | (doc (string-append out "/share/doc/bwa")) | |
11921 | (man (string-append out "/share/man/man1")) | |
11922 | (inc (string-append out "/include/bwa"))) | |
11923 | (install-file "bwa" bin) | |
11924 | (install-file "README.md" doc) | |
11925 | (install-file "bwa.1" man) | |
11926 | (install-file "libbwa.a" lib) | |
11927 | (mkdir-p lib) | |
11928 | (mkdir-p inc) | |
11929 | (for-each (lambda (file) | |
11930 | (install-file file inc)) | |
11931 | (find-files "." "\\.h$"))) | |
11932 | #t)) | |
11933 | ;; no "configure" script | |
11934 | (delete 'configure)))))) | |
11935 | ||
11936 | (define-public salmon | |
11937 | (package | |
11938 | (name "salmon") | |
11939 | (version "0.9.1") | |
11940 | (source (origin | |
11941 | (method git-fetch) | |
11942 | (uri (git-reference | |
11943 | (url "https://github.com/COMBINE-lab/salmon.git") | |
11944 | (commit (string-append "v" version)))) | |
11945 | (file-name (string-append name "-" version "-checkout")) | |
11946 | (sha256 | |
11947 | (base32 | |
11948 | "1zi1ff4i7y2ykk0vdzysgwzzzv166vg2x77pj1mf4baclavxj87a")) | |
11949 | (modules '((guix build utils))) | |
11950 | (snippet | |
11951 | '(begin | |
11952 | ;; Delete bundled headers for eigen3. | |
11953 | (delete-file-recursively "include/eigen3/") | |
11954 | #t)))) | |
11955 | (build-system cmake-build-system) | |
11956 | (arguments | |
11957 | `(#:configure-flags | |
11958 | (list (string-append "-DBOOST_INCLUDEDIR=" | |
11959 | (assoc-ref %build-inputs "boost") | |
11960 | "/include/") | |
11961 | (string-append "-DBOOST_LIBRARYDIR=" | |
11962 | (assoc-ref %build-inputs "boost") | |
11963 | "/lib/") | |
11964 | (string-append "-DBoost_LIBRARIES=" | |
11965 | "-lboost_iostreams " | |
11966 | "-lboost_filesystem " | |
11967 | "-lboost_system " | |
11968 | "-lboost_thread " | |
11969 | "-lboost_timer " | |
11970 | "-lboost_chrono " | |
11971 | "-lboost_program_options") | |
11972 | "-DBoost_FOUND=TRUE" | |
11973 | "-DTBB_LIBRARIES=tbb tbbmalloc" | |
11974 | ;; Don't download RapMap---we already have it! | |
11975 | "-DFETCHED_RAPMAP=1") | |
11976 | #:phases | |
11977 | (modify-phases %standard-phases | |
11978 | ;; Boost cannot be found, even though it's right there. | |
11979 | (add-after 'unpack 'do-not-look-for-boost | |
11980 | (lambda* (#:key inputs #:allow-other-keys) | |
11981 | (substitute* "CMakeLists.txt" | |
11982 | (("find_package\\(Boost 1\\.53\\.0") "#")))) | |
11983 | (add-after 'unpack 'do-not-phone-home | |
11984 | (lambda _ | |
11985 | (substitute* "src/Salmon.cpp" | |
11986 | (("getVersionMessage\\(\\)") "\"\"")))) | |
11987 | (add-after 'unpack 'prepare-rapmap | |
11988 | (lambda* (#:key inputs #:allow-other-keys) | |
11989 | (let ((src "external/install/src/rapmap/") | |
11990 | (include "external/install/include/rapmap/") | |
11991 | (rapmap (assoc-ref inputs "rapmap"))) | |
11992 | (mkdir-p src) | |
11993 | (mkdir-p include) | |
11994 | (for-each (lambda (file) | |
11995 | (install-file file src)) | |
11996 | (find-files (string-append rapmap "/src") "\\.(c|cpp)")) | |
11997 | (copy-recursively (string-append rapmap "/include") include) | |
11998 | (for-each delete-file '("external/install/include/rapmap/xxhash.h" | |
11999 | "external/install/include/rapmap/FastxParser.hpp" | |
12000 | "external/install/include/rapmap/concurrentqueue.h" | |
12001 | "external/install/include/rapmap/FastxParserThreadUtils.hpp" | |
12002 | "external/install/src/rapmap/FastxParser.cpp" | |
12003 | "external/install/src/rapmap/xxhash.c"))))) | |
12004 | (add-after 'unpack 'use-system-libraries | |
12005 | (lambda* (#:key inputs #:allow-other-keys) | |
12006 | (substitute* "src/CMakeLists.txt" | |
12007 | (("\\$\\{GAT_SOURCE_DIR\\}/external/install/include/jellyfish-2.2..") | |
12008 | (string-append (assoc-ref inputs "jellyfish") | |
12009 | "/include/jellyfish-" ,(package-version jellyfish))) | |
12010 | (("\\$\\{GAT_SOURCE_DIR\\}/external/install/lib/libjellyfish-2.0.a") | |
12011 | (string-append (assoc-ref inputs "jellyfish") | |
12012 | "/lib/libjellyfish-2.0.a")) | |
12013 | (("\\$\\{GAT_SOURCE_DIR\\}/external/install/lib/libdivsufsort.a") | |
12014 | (string-append (assoc-ref inputs "libdivsufsort") | |
12015 | "/lib/libdivsufsort.so")) | |
12016 | (("\\$\\{GAT_SOURCE_DIR\\}/external/install/lib/libstaden-read.a") | |
12017 | (string-append (assoc-ref inputs "libstadenio-for-salmon") | |
12018 | "/lib/libstaden-read.a")) | |
12019 | (("\\$\\{GAT_SOURCE_DIR\\}/external/install/lib/libbwa.a") | |
12020 | (string-append (assoc-ref inputs "bwa") "/lib/libbwa.a")) | |
12021 | (("\\$\\{GAT_SOURCE_DIR\\}/external/install/lib/libdivsufsort64.a") | |
12022 | (string-append (assoc-ref inputs "libdivsufsort") | |
12023 | "/lib/libdivsufsort64.so"))) | |
12024 | (substitute* "CMakeLists.txt" | |
12025 | ;; Don't prefer static libs | |
12026 | (("SET\\(CMAKE_FIND_LIBRARY_SUFFIXES.*") "") | |
12027 | (("set\\(TBB_LIBRARIES") "message(") | |
12028 | (("find_package\\(Jellyfish.*") "") | |
12029 | (("ExternalProject_Add\\(libcereal") "message(") | |
12030 | (("ExternalProject_Add\\(libbwa") "message(") | |
12031 | (("ExternalProject_Add\\(libjellyfish") "message(") | |
12032 | (("ExternalProject_Add\\(libgff") "message(") | |
12033 | (("ExternalProject_Add\\(libtbb") "message(") | |
12034 | (("ExternalProject_Add\\(libspdlog") "message(") | |
12035 | (("ExternalProject_Add\\(libdivsufsort") "message(") | |
12036 | (("ExternalProject_Add\\(libstadenio") "message(") | |
12037 | (("ExternalProject_Add_Step\\(") "message(")) | |
12038 | ||
12039 | ;; Ensure that all headers can be found | |
12040 | (setenv "CPLUS_INCLUDE_PATH" | |
12041 | (string-append (getenv "CPLUS_INCLUDE_PATH") | |
12042 | ":" | |
12043 | (assoc-ref inputs "bwa") | |
12044 | "/include/bwa" | |
12045 | ":" | |
12046 | (assoc-ref inputs "eigen") | |
12047 | "/include/eigen3")) | |
12048 | (setenv "CPATH" | |
12049 | (string-append (assoc-ref inputs "bwa") | |
12050 | "/include/bwa" | |
12051 | ":" | |
12052 | (assoc-ref inputs "eigen") | |
12053 | "/include/eigen3")) | |
12054 | #t)) | |
12055 | ;; CMAKE_INSTALL_PREFIX does not exist when the tests are | |
12056 | ;; run. It only exists after the install phase. | |
12057 | (add-after 'unpack 'fix-tests | |
12058 | (lambda _ | |
12059 | (substitute* "src/CMakeLists.txt" | |
12060 | (("DTOPLEVEL_DIR=\\$\\{CMAKE_INSTALL_PREFIX") | |
12061 | "DTOPLEVEL_DIR=${GAT_SOURCE_DIR")) | |
12062 | #t))))) | |
12063 | (inputs | |
12064 | `(("boost" ,boost) | |
12065 | ("bwa" ,bwa-for-salmon) | |
12066 | ("bzip2" ,bzip2) | |
12067 | ("cereal" ,cereal) | |
12068 | ("eigen" ,eigen) | |
12069 | ("rapmap" ,(origin | |
12070 | (method git-fetch) | |
12071 | (uri (git-reference | |
12072 | (url "https://github.com/COMBINE-lab/RapMap.git") | |
12073 | (commit (string-append "salmon-v" version)))) | |
12074 | (file-name (string-append "rapmap-salmon-v" version "-checkout")) | |
12075 | (sha256 | |
12076 | (base32 | |
12077 | "1yc12yqsz6f0r8sg1qnk57xg34aqwc9jbqq6gd5ys28xw3plj98p")))) | |
12078 | ("jemalloc" ,jemalloc) | |
12079 | ("jellyfish" ,jellyfish) | |
12080 | ("libgff" ,libgff) | |
12081 | ("tbb" ,tbb) | |
12082 | ("libdivsufsort" ,libdivsufsort) | |
12083 | ("libstadenio-for-salmon" ,libstadenio-for-salmon) | |
12084 | ("spdlog-for-salmon" ,spdlog-for-salmon) | |
12085 | ("xz" ,xz) | |
12086 | ("zlib" ,zlib))) | |
12087 | (home-page "https://github.com/COMBINE-lab/salmon") | |
12088 | (synopsis "Quantification from RNA-seq reads using lightweight alignments") | |
12089 | (description "Salmon is a program to produce highly-accurate, | |
12090 | transcript-level quantification estimates from RNA-seq data. Salmon achieves | |
12091 | its accuracy and speed via a number of different innovations, including the | |
12092 | use of lightweight alignments (accurate but fast-to-compute proxies for | |
12093 | traditional read alignments) and massively-parallel stochastic collapsed | |
12094 | variational inference.") | |
12095 | (license license:gpl3+))) | |
152d30c3 RW |
12096 | |
12097 | (define-public python-loompy | |
12098 | (package | |
12099 | (name "python-loompy") | |
12100 | (version "2.0.2") | |
12101 | (source | |
12102 | (origin | |
12103 | (method url-fetch) | |
12104 | (uri (pypi-uri "loompy" version)) | |
12105 | (sha256 | |
12106 | (base32 | |
12107 | "1drgv8j1hxqzzpnfg272x9djb6j8qr798w1pc2x8ikmfgyd9gh51")))) | |
12108 | (build-system python-build-system) | |
12109 | ;; There are no tests | |
12110 | (arguments '(#:tests? #f)) | |
12111 | (propagated-inputs | |
12112 | `(("python-h5py" ,python-h5py) | |
12113 | ("python-numpy" ,python-numpy) | |
12114 | ("python-scipy" ,python-scipy) | |
12115 | ("python-typing" ,python-typing))) | |
12116 | (home-page "https://github.com/linnarsson-lab/loompy") | |
12117 | (synopsis "Work with .loom files for single-cell RNA-seq data") | |
12118 | (description "The loom file format is an efficient format for very large | |
12119 | omics datasets, consisting of a main matrix, optional additional layers, a | |
12120 | variable number of row and column annotations. Loom also supports sparse | |
12121 | graphs. This library makes it easy to work with @file{.loom} files for | |
12122 | single-cell RNA-seq data.") | |
12123 | (license license:bsd-3))) | |
5fef15e5 | 12124 | |
f09d16e5 RW |
12125 | ;; We cannot use the latest commit because it requires Java 9. |
12126 | (define-public java-forester | |
12127 | (let ((commit "86b07efe302d5094b42deed9260f719a4c4ac2e6") | |
12128 | (revision "1")) | |
12129 | (package | |
12130 | (name "java-forester") | |
12131 | (version (string-append "0-" revision "." (string-take commit 7))) | |
12132 | (source (origin | |
12133 | (method git-fetch) | |
12134 | (uri (git-reference | |
12135 | (url "https://github.com/cmzmasek/forester.git") | |
12136 | (commit commit))) | |
12137 | (file-name (string-append name "-" version "-checkout")) | |
12138 | (sha256 | |
12139 | (base32 | |
12140 | "0vxavc1yrf84yrnf20dq26hi0lglidk8d382xrxsy4qmlbjd276z")) | |
12141 | (modules '((guix build utils))) | |
12142 | (snippet | |
12143 | '(begin | |
12144 | ;; Delete bundled jars and pre-built classes | |
12145 | (delete-file-recursively "forester/java/resources") | |
12146 | (delete-file-recursively "forester/java/classes") | |
12147 | (for-each delete-file (find-files "forester/java/" "\\.jar$")) | |
12148 | ;; Delete bundled applications | |
12149 | (delete-file-recursively "forester_applications") | |
12150 | #t)))) | |
12151 | (build-system ant-build-system) | |
12152 | (arguments | |
12153 | `(#:tests? #f ; there are none | |
12154 | #:jdk ,icedtea-8 | |
12155 | #:modules ((guix build ant-build-system) | |
12156 | (guix build utils) | |
12157 | (guix build java-utils) | |
12158 | (sxml simple) | |
12159 | (sxml transform)) | |
12160 | #:phases | |
12161 | (modify-phases %standard-phases | |
12162 | (add-after 'unpack 'chdir | |
12163 | (lambda _ (chdir "forester/java") #t)) | |
12164 | (add-after 'chdir 'fix-dependencies | |
12165 | (lambda _ | |
12166 | (chmod "build.xml" #o664) | |
12167 | (call-with-output-file "build.xml.new" | |
12168 | (lambda (port) | |
12169 | (sxml->xml | |
12170 | (pre-post-order | |
12171 | (with-input-from-file "build.xml" | |
12172 | (lambda _ (xml->sxml #:trim-whitespace? #t))) | |
12173 | `(;; Remove all unjar tags to avoid repacking classes. | |
12174 | (unjar . ,(lambda _ '())) | |
12175 | (*default* . ,(lambda (tag . kids) `(,tag ,@kids))) | |
12176 | (*text* . ,(lambda (_ txt) txt)))) | |
12177 | port))) | |
12178 | (rename-file "build.xml.new" "build.xml") | |
12179 | #t)) | |
12180 | ;; FIXME: itext is difficult to package as it depends on a few | |
12181 | ;; unpackaged libraries. | |
12182 | (add-after 'chdir 'remove-dependency-on-unpackaged-itext | |
12183 | (lambda _ | |
12184 | (delete-file "src/org/forester/archaeopteryx/PdfExporter.java") | |
12185 | (substitute* "src/org/forester/archaeopteryx/MainFrame.java" | |
12186 | (("pdf_written_to = PdfExporter.*") | |
12187 | "throw new IOException(\"PDF export is not available.\");")) | |
12188 | #t)) | |
12189 | ;; There is no install target | |
12190 | (replace 'install (install-jars "."))))) | |
12191 | (propagated-inputs | |
12192 | `(("java-commons-codec" ,java-commons-codec) | |
12193 | ("java-openchart2" ,java-openchart2))) | |
12194 | (home-page "https://sites.google.com/site/cmzmasek/home/software/forester") | |
12195 | (synopsis "Phylogenomics libraries for Java") | |
12196 | (description "Forester is a collection of Java libraries for | |
12197 | phylogenomics and evolutionary biology research. It includes support for | |
12198 | reading, writing, and exporting phylogenetic trees.") | |
12199 | (license license:lgpl2.1+)))) | |
12200 | ||
10645b92 RW |
12201 | (define-public java-forester-1.005 |
12202 | (package | |
12203 | (name "java-forester") | |
12204 | (version "1.005") | |
12205 | (source (origin | |
12206 | (method url-fetch) | |
12207 | (uri (string-append "http://search.maven.org/remotecontent?" | |
12208 | "filepath=org/biojava/thirdparty/forester/" | |
12209 | version "/forester-" version "-sources.jar")) | |
12210 | (file-name (string-append name "-" version ".jar")) | |
12211 | (sha256 | |
12212 | (base32 | |
12213 | "04r8qv4rk3p71z4ajrvp11py1z46qrx0047j3zzs79s6lnsm3lcv")))) | |
12214 | (build-system ant-build-system) | |
12215 | (arguments | |
12216 | `(#:tests? #f ; there are none | |
12217 | #:jdk ,icedtea-8 | |
12218 | #:modules ((guix build ant-build-system) | |
12219 | (guix build utils) | |
12220 | (guix build java-utils) | |
12221 | (sxml simple) | |
12222 | (sxml transform)) | |
12223 | #:phases | |
12224 | (modify-phases %standard-phases | |
12225 | (add-after 'unpack 'fix-dependencies | |
12226 | (lambda* (#:key inputs #:allow-other-keys) | |
12227 | (call-with-output-file "build.xml" | |
12228 | (lambda (port) | |
12229 | (sxml->xml | |
12230 | (pre-post-order | |
12231 | (with-input-from-file "src/build.xml" | |
12232 | (lambda _ (xml->sxml #:trim-whitespace? #t))) | |
12233 | `(;; Remove all unjar tags to avoid repacking classes. | |
12234 | (unjar . ,(lambda _ '())) | |
12235 | (*default* . ,(lambda (tag . kids) `(,tag ,@kids))) | |
12236 | (*text* . ,(lambda (_ txt) txt)))) | |
12237 | port))) | |
12238 | (copy-file (assoc-ref inputs "synth_look_and_feel_1.xml") | |
12239 | "synth_look_and_feel_1.xml") | |
12240 | (copy-file (assoc-ref inputs "phyloxml.xsd") | |
12241 | "phyloxml.xsd") | |
12242 | (substitute* "build.xml" | |
12243 | (("../resources/synth_laf/synth_look_and_feel_1.xml") | |
12244 | "synth_look_and_feel_1.xml") | |
12245 | (("../resources/phyloxml_schema/1.10/phyloxml.xsd") | |
12246 | "phyloxml.xsd")) | |
12247 | #t)) | |
12248 | ;; FIXME: itext is difficult to package as it depends on a few | |
12249 | ;; unpackaged libraries. | |
12250 | (add-after 'unpack 'remove-dependency-on-unpackaged-itext | |
12251 | (lambda _ | |
12252 | (delete-file "src/org/forester/archaeopteryx/PdfExporter.java") | |
12253 | (substitute* '("src/org/forester/archaeopteryx/MainFrame.java" | |
12254 | "src/org/forester/archaeopteryx/MainFrameApplication.java") | |
12255 | (("pdf_written_to = PdfExporter.*") | |
12256 | "throw new IOException(\"PDF export is not available.\"); /*") | |
12257 | ((".getPrintSizeX\\(\\), getOptions\\(\\).getPrintSizeY\\(\\) \\);") "*/") | |
12258 | (("getCurrentTreePanel\\(\\).getHeight\\(\\) \\);") "*/")) | |
12259 | #t)) | |
12260 | (add-after 'unpack 'delete-pre-built-classes | |
12261 | (lambda _ (delete-file-recursively "src/classes") #t)) | |
12262 | ;; There is no install target | |
12263 | (replace 'install (install-jars "."))))) | |
12264 | (propagated-inputs | |
12265 | `(("java-commons-codec" ,java-commons-codec) | |
12266 | ("java-openchart2" ,java-openchart2))) | |
12267 | ;; The source archive does not contain the resources. | |
12268 | (native-inputs | |
12269 | `(("phyloxml.xsd" | |
12270 | ,(origin | |
12271 | (method url-fetch) | |
12272 | (uri (string-append "https://raw.githubusercontent.com/cmzmasek/forester/" | |
12273 | "b61cc2dcede0bede317db362472333115756b8c6/" | |
12274 | "forester/resources/phyloxml_schema/1.10/phyloxml.xsd")) | |
12275 | (file-name (string-append name "-phyloxml-" version ".xsd")) | |
12276 | (sha256 | |
12277 | (base32 | |
12278 | "1zxc4m8sn4n389nqdnpxa8d0k17qnr3pm2y5y6g6vh4k0zm52npv")))) | |
12279 | ("synth_look_and_feel_1.xml" | |
12280 | ,(origin | |
12281 | (method url-fetch) | |
12282 | (uri (string-append "https://raw.githubusercontent.com/cmzmasek/forester/" | |
12283 | "29e04321615da6b35c1e15c60e52caf3f21d8e6a/" | |
12284 | "forester/java/classes/resources/synth_look_and_feel_1.xml")) | |
12285 | (file-name (string-append name "-synth-look-and-feel-" version ".xml")) | |
12286 | (sha256 | |
12287 | (base32 | |
12288 | "1gv5602gv4k7y7713y75a4jvj7i9s7nildsbdl7n9q10sc2ikg8h")))))) | |
12289 | (home-page "https://sites.google.com/site/cmzmasek/home/software/forester") | |
12290 | (synopsis "Phylogenomics libraries for Java") | |
12291 | (description "Forester is a collection of Java libraries for | |
12292 | phylogenomics and evolutionary biology research. It includes support for | |
12293 | reading, writing, and exporting phylogenetic trees.") | |
12294 | (license license:lgpl2.1+))) | |
12295 | ||
5fef15e5 RW |
12296 | (define-public java-biojava-core |
12297 | (package | |
12298 | (name "java-biojava-core") | |
12299 | (version "4.2.11") | |
12300 | (source (origin | |
12301 | (method git-fetch) | |
12302 | (uri (git-reference | |
12303 | (url "https://github.com/biojava/biojava") | |
12304 | (commit (string-append "biojava-" version)))) | |
12305 | (file-name (string-append name "-" version "-checkout")) | |
12306 | (sha256 | |
12307 | (base32 | |
12308 | "1bvryh2bpsvash8ln79cmc9sqm8qw72hz4xzwqxcrjm8ssxszhqk")))) | |
12309 | (build-system ant-build-system) | |
12310 | (arguments | |
12311 | `(#:jdk ,icedtea-8 | |
12312 | #:jar-name "biojava-core.jar" | |
12313 | #:source-dir "biojava-core/src/main/java/" | |
12314 | #:test-dir "biojava-core/src/test" | |
12315 | ;; These tests seem to require internet access. | |
12316 | #:test-exclude (list "**/SearchIOTest.java" | |
12317 | "**/BlastXMLParserTest.java" | |
12318 | "**/GenbankCookbookTest.java" | |
12319 | "**/GenbankProxySequenceReaderTest.java") | |
12320 | #:phases | |
12321 | (modify-phases %standard-phases | |
12322 | (add-before 'build 'copy-resources | |
12323 | (lambda _ | |
12324 | (copy-recursively "biojava-core/src/main/resources" | |
12325 | "build/classes") | |
12326 | #t)) | |
12327 | (add-before 'check 'copy-test-resources | |
12328 | (lambda _ | |
12329 | (copy-recursively "biojava-core/src/test/resources" | |
12330 | "build/test-classes") | |
12331 | #t))))) | |
12332 | (propagated-inputs | |
12333 | `(("java-log4j-api" ,java-log4j-api) | |
12334 | ("java-log4j-core" ,java-log4j-core) | |
12335 | ("java-slf4j-api" ,java-slf4j-api) | |
12336 | ("java-slf4j-simple" ,java-slf4j-simple))) | |
12337 | (native-inputs | |
12338 | `(("java-junit" ,java-junit) | |
12339 | ("java-hamcrest-core" ,java-hamcrest-core))) | |
12340 | (home-page "http://biojava.org") | |
12341 | (synopsis "Core libraries of Java framework for processing biological data") | |
12342 | (description "BioJava is a project dedicated to providing a Java framework | |
12343 | for processing biological data. It provides analytical and statistical | |
12344 | routines, parsers for common file formats, reference implementations of | |
12345 | popular algorithms, and allows the manipulation of sequences and 3D | |
12346 | structures. The goal of the biojava project is to facilitate rapid | |
12347 | application development for bioinformatics. | |
12348 | ||
12349 | This package provides the core libraries.") | |
12350 | (license license:lgpl2.1+))) | |
b28c8037 RW |
12351 | |
12352 | (define-public java-biojava-phylo | |
12353 | (package (inherit java-biojava-core) | |
12354 | (name "java-biojava-phylo") | |
12355 | (build-system ant-build-system) | |
12356 | (arguments | |
12357 | `(#:jdk ,icedtea-8 | |
12358 | #:jar-name "biojava-phylo.jar" | |
12359 | #:source-dir "biojava-phylo/src/main/java/" | |
12360 | #:test-dir "biojava-phylo/src/test" | |
12361 | #:phases | |
12362 | (modify-phases %standard-phases | |
12363 | (add-before 'build 'copy-resources | |
12364 | (lambda _ | |
12365 | (copy-recursively "biojava-phylo/src/main/resources" | |
12366 | "build/classes") | |
12367 | #t)) | |
12368 | (add-before 'check 'copy-test-resources | |
12369 | (lambda _ | |
12370 | (copy-recursively "biojava-phylo/src/test/resources" | |
12371 | "build/test-classes") | |
12372 | #t))))) | |
12373 | (propagated-inputs | |
12374 | `(("java-log4j-api" ,java-log4j-api) | |
12375 | ("java-log4j-core" ,java-log4j-core) | |
12376 | ("java-slf4j-api" ,java-slf4j-api) | |
12377 | ("java-slf4j-simple" ,java-slf4j-simple) | |
12378 | ("java-biojava-core" ,java-biojava-core) | |
12379 | ("java-forester" ,java-forester))) | |
12380 | (native-inputs | |
12381 | `(("java-junit" ,java-junit) | |
12382 | ("java-hamcrest-core" ,java-hamcrest-core))) | |
12383 | (home-page "http://biojava.org") | |
12384 | (synopsis "Biojava interface to the forester phylogenomics library") | |
12385 | (description "The phylo module provides a biojava interface layer to the | |
12386 | forester phylogenomics library for constructing phylogenetic trees."))) | |
22c09c33 RW |
12387 | |
12388 | (define-public java-biojava-alignment | |
12389 | (package (inherit java-biojava-core) | |
12390 | (name "java-biojava-alignment") | |
12391 | (build-system ant-build-system) | |
12392 | (arguments | |
12393 | `(#:jdk ,icedtea-8 | |
12394 | #:jar-name "biojava-alignment.jar" | |
12395 | #:source-dir "biojava-alignment/src/main/java/" | |
12396 | #:test-dir "biojava-alignment/src/test" | |
12397 | #:phases | |
12398 | (modify-phases %standard-phases | |
12399 | (add-before 'build 'copy-resources | |
12400 | (lambda _ | |
12401 | (copy-recursively "biojava-alignment/src/main/resources" | |
12402 | "build/classes") | |
12403 | #t)) | |
12404 | (add-before 'check 'copy-test-resources | |
12405 | (lambda _ | |
12406 | (copy-recursively "biojava-alignment/src/test/resources" | |
12407 | "build/test-classes") | |
12408 | #t))))) | |
12409 | (propagated-inputs | |
12410 | `(("java-log4j-api" ,java-log4j-api) | |
12411 | ("java-log4j-core" ,java-log4j-core) | |
12412 | ("java-slf4j-api" ,java-slf4j-api) | |
12413 | ("java-slf4j-simple" ,java-slf4j-simple) | |
12414 | ("java-biojava-core" ,java-biojava-core) | |
12415 | ("java-biojava-phylo" ,java-biojava-phylo) | |
12416 | ("java-forester" ,java-forester))) | |
12417 | (native-inputs | |
12418 | `(("java-junit" ,java-junit) | |
12419 | ("java-hamcrest-core" ,java-hamcrest-core))) | |
12420 | (home-page "http://biojava.org") | |
12421 | (synopsis "Biojava API for genetic sequence alignment") | |
12422 | (description "The alignment module of BioJava provides an API that | |
12423 | contains | |
12424 | ||
12425 | @itemize | |
12426 | @item implementations of dynamic programming algorithms for sequence | |
12427 | alignment; | |
12428 | @item reading and writing of popular alignment file formats; | |
12429 | @item a single-, or multi- threaded multiple sequence alignment algorithm. | |
12430 | @end itemize\n"))) | |
e44da58c RW |
12431 | |
12432 | (define-public java-biojava-core-4.0 | |
12433 | (package (inherit java-biojava-core) | |
12434 | (name "java-biojava-core") | |
12435 | (version "4.0.0") | |
12436 | (source (origin | |
12437 | (method git-fetch) | |
12438 | (uri (git-reference | |
12439 | (url "https://github.com/biojava/biojava") | |
12440 | (commit (string-append "biojava-" version)))) | |
12441 | (file-name (string-append name "-" version "-checkout")) | |
12442 | (sha256 | |
12443 | (base32 | |
12444 | "13675f6y9aqi7bi2lk3s1z7a22ynccjiqwa8izh7p97xi9wsfmd8")))))) | |
5528f9e8 RW |
12445 | |
12446 | (define-public java-biojava-phylo-4.0 | |
12447 | (package (inherit java-biojava-core-4.0) | |
12448 | (name "java-biojava-phylo") | |
12449 | (build-system ant-build-system) | |
12450 | (arguments | |
12451 | `(#:jdk ,icedtea-8 | |
12452 | #:jar-name "biojava-phylo.jar" | |
12453 | #:source-dir "biojava-phylo/src/main/java/" | |
12454 | #:test-dir "biojava-phylo/src/test" | |
12455 | #:phases | |
12456 | (modify-phases %standard-phases | |
12457 | (add-before 'build 'copy-resources | |
12458 | (lambda _ | |
12459 | (copy-recursively "biojava-phylo/src/main/resources" | |
12460 | "build/classes") | |
12461 | #t)) | |
12462 | (add-before 'check 'copy-test-resources | |
12463 | (lambda _ | |
12464 | (copy-recursively "biojava-phylo/src/test/resources" | |
12465 | "build/test-classes") | |
12466 | #t))))) | |
12467 | (propagated-inputs | |
12468 | `(("java-log4j-api" ,java-log4j-api) | |
12469 | ("java-log4j-core" ,java-log4j-core) | |
12470 | ("java-slf4j-api" ,java-slf4j-api) | |
12471 | ("java-slf4j-simple" ,java-slf4j-simple) | |
12472 | ("java-biojava-core" ,java-biojava-core-4.0) | |
12473 | ("java-forester" ,java-forester-1.005))) | |
12474 | (native-inputs | |
12475 | `(("java-junit" ,java-junit) | |
12476 | ("java-hamcrest-core" ,java-hamcrest-core))) | |
12477 | (home-page "http://biojava.org") | |
12478 | (synopsis "Biojava interface to the forester phylogenomics library") | |
12479 | (description "The phylo module provides a biojava interface layer to the | |
12480 | forester phylogenomics library for constructing phylogenetic trees."))) | |
9ac7db18 RW |
12481 | |
12482 | (define-public java-biojava-alignment-4.0 | |
12483 | (package (inherit java-biojava-core-4.0) | |
12484 | (name "java-biojava-alignment") | |
12485 | (build-system ant-build-system) | |
12486 | (arguments | |
12487 | `(#:jdk ,icedtea-8 | |
12488 | #:jar-name "biojava-alignment.jar" | |
12489 | #:source-dir "biojava-alignment/src/main/java/" | |
12490 | #:test-dir "biojava-alignment/src/test" | |
12491 | #:phases | |
12492 | (modify-phases %standard-phases | |
12493 | (add-before 'build 'copy-resources | |
12494 | (lambda _ | |
12495 | (copy-recursively "biojava-alignment/src/main/resources" | |
12496 | "build/classes") | |
12497 | #t)) | |
12498 | (add-before 'check 'copy-test-resources | |
12499 | (lambda _ | |
12500 | (copy-recursively "biojava-alignment/src/test/resources" | |
12501 | "build/test-classes") | |
12502 | #t))))) | |
12503 | (propagated-inputs | |
12504 | `(("java-log4j-api" ,java-log4j-api) | |
12505 | ("java-log4j-core" ,java-log4j-core) | |
12506 | ("java-slf4j-api" ,java-slf4j-api) | |
12507 | ("java-slf4j-simple" ,java-slf4j-simple) | |
12508 | ("java-biojava-core" ,java-biojava-core-4.0) | |
12509 | ("java-biojava-phylo" ,java-biojava-phylo-4.0) | |
12510 | ("java-forester" ,java-forester-1.005))) | |
12511 | (native-inputs | |
12512 | `(("java-junit" ,java-junit) | |
12513 | ("java-hamcrest-core" ,java-hamcrest-core))) | |
12514 | (home-page "http://biojava.org") | |
12515 | (synopsis "Biojava API for genetic sequence alignment") | |
12516 | (description "The alignment module of BioJava provides an API that | |
12517 | contains | |
12518 | ||
12519 | @itemize | |
12520 | @item implementations of dynamic programming algorithms for sequence | |
12521 | alignment; | |
12522 | @item reading and writing of popular alignment file formats; | |
12523 | @item a single-, or multi- threaded multiple sequence alignment algorithm. | |
12524 | @end itemize\n"))) | |
1adeef31 RW |
12525 | |
12526 | (define-public dropseq-tools | |
12527 | (package | |
12528 | (name "dropseq-tools") | |
12529 | (version "1.13") | |
12530 | (source | |
12531 | (origin | |
12532 | (method url-fetch) | |
12533 | (uri "http://mccarrolllab.com/download/1276/") | |
12534 | (file-name (string-append "dropseq-tools-" version ".zip")) | |
12535 | (sha256 | |
12536 | (base32 | |
12537 | "0yrffckxqk5l8b5xb6z4laq157zd9mdypr2p4b4vq2bhjzi1sj0s")) | |
12538 | ;; Delete bundled libraries | |
12539 | (modules '((guix build utils))) | |
12540 | (snippet | |
12541 | '(begin | |
12542 | (for-each delete-file (find-files "jar/lib" "\\.jar$")) | |
12543 | (delete-file-recursively "3rdParty"))))) | |
12544 | (build-system ant-build-system) | |
12545 | (arguments | |
12546 | `(#:tests? #f ; test data are not included | |
12547 | #:test-target "test" | |
12548 | #:build-target "all" | |
12549 | #:source-dir "public/src/" | |
12550 | #:jdk ,icedtea-8 | |
12551 | #:make-flags | |
12552 | (list (string-append "-Dpicard.executable.dir=" | |
12553 | (assoc-ref %build-inputs "java-picard") | |
12554 | "/share/java/")) | |
12555 | #:modules ((ice-9 match) | |
12556 | (srfi srfi-1) | |
12557 | (guix build utils) | |
12558 | (guix build java-utils) | |
12559 | (guix build ant-build-system)) | |
12560 | #:phases | |
12561 | (modify-phases %standard-phases | |
12562 | ;; All dependencies must be linked to "lib", because that's where | |
12563 | ;; they will be searched for when the Class-Path property of the | |
12564 | ;; manifest is computed. | |
12565 | (add-after 'unpack 'record-references | |
12566 | (lambda* (#:key inputs #:allow-other-keys) | |
12567 | (mkdir-p "jar/lib") | |
12568 | (let ((dirs (filter-map (match-lambda | |
12569 | ((name . dir) | |
12570 | (if (and (string-prefix? "java-" name) | |
12571 | (not (string=? name "java-testng"))) | |
12572 | dir #f))) | |
12573 | inputs))) | |
12574 | (for-each (lambda (jar) | |
12575 | (symlink jar (string-append "jar/lib/" (basename jar)))) | |
12576 | (append-map (lambda (dir) (find-files dir "\\.jar$")) | |
12577 | dirs))) | |
12578 | #t)) | |
12579 | ;; There is no installation target | |
12580 | (replace 'install | |
12581 | (lambda* (#:key inputs outputs #:allow-other-keys) | |
12582 | (let* ((out (assoc-ref outputs "out")) | |
12583 | (bin (string-append out "/bin")) | |
12584 | (share (string-append out "/share/java/")) | |
12585 | (lib (string-append share "/lib/")) | |
12586 | (scripts (list "BAMTagHistogram" | |
12587 | "BAMTagofTagCounts" | |
12588 | "BaseDistributionAtReadPosition" | |
12589 | "CollapseBarcodesInPlace" | |
12590 | "CollapseTagWithContext" | |
12591 | "ConvertToRefFlat" | |
12592 | "CreateIntervalsFiles" | |
12593 | "DetectBeadSynthesisErrors" | |
12594 | "DigitalExpression" | |
12595 | "Drop-seq_alignment.sh" | |
12596 | "FilterBAM" | |
12597 | "FilterBAMByTag" | |
12598 | "GatherGeneGCLength" | |
12599 | "GatherMolecularBarcodeDistributionByGene" | |
12600 | "GatherReadQualityMetrics" | |
12601 | "PolyATrimmer" | |
12602 | "ReduceGTF" | |
12603 | "SelectCellsByNumTranscripts" | |
12604 | "SingleCellRnaSeqMetricsCollector" | |
12605 | "TagBamWithReadSequenceExtended" | |
12606 | "TagReadWithGeneExon" | |
12607 | "TagReadWithInterval" | |
12608 | "TrimStartingSequence" | |
12609 | "ValidateReference"))) | |
12610 | (for-each mkdir-p (list bin share lib)) | |
12611 | (install-file "dist/dropseq.jar" share) | |
12612 | (for-each (lambda (script) | |
12613 | (chmod script #o555) | |
12614 | (install-file script bin)) | |
12615 | scripts) | |
12616 | (substitute* (map (lambda (script) | |
12617 | (string-append bin "/" script)) | |
12618 | scripts) | |
12619 | (("^java") (which "java")) | |
12620 | (("jar_deploy_dir=.*") | |
12621 | (string-append "jar_deploy_dir=" share "\n")))) | |
12622 | #t)) | |
12623 | ;; FIXME: We do this after stripping jars because we don't want it to | |
12624 | ;; copy all these jars and strip them. We only want to install | |
12625 | ;; links. Arguably, this is a problem with the ant-build-system. | |
12626 | (add-after 'strip-jar-timestamps 'install-links | |
12627 | (lambda* (#:key outputs #:allow-other-keys) | |
12628 | (let* ((out (assoc-ref outputs "out")) | |
12629 | (share (string-append out "/share/java/")) | |
12630 | (lib (string-append share "/lib/"))) | |
12631 | (for-each (lambda (jar) | |
12632 | (symlink (readlink jar) | |
12633 | (string-append lib (basename jar)))) | |
12634 | (find-files "jar/lib" "\\.jar$"))) | |
12635 | #t))))) | |
12636 | (inputs | |
12637 | `(("jdk" ,icedtea-8) | |
12638 | ("java-picard" ,java-picard-2.10.3) | |
12639 | ("java-log4j-1.2-api" ,java-log4j-1.2-api) | |
12640 | ("java-commons-math3" ,java-commons-math3) | |
12641 | ("java-commons-jexl2" ,java-commons-jexl-2) | |
12642 | ("java-commons-collections4" ,java-commons-collections4) | |
12643 | ("java-commons-lang2" ,java-commons-lang) | |
12644 | ("java-commons-io" ,java-commons-io) | |
12645 | ("java-snappy-1.0.3-rc3" ,java-snappy-1) | |
12646 | ("java-guava" ,java-guava) | |
12647 | ("java-la4j" ,java-la4j) | |
12648 | ("java-biojava-core" ,java-biojava-core-4.0) | |
12649 | ("java-biojava-alignment" ,java-biojava-alignment-4.0) | |
12650 | ("java-jdistlib" ,java-jdistlib) | |
12651 | ("java-simple-xml" ,java-simple-xml) | |
12652 | ("java-snakeyaml" ,java-snakeyaml))) | |
12653 | (native-inputs | |
12654 | `(("unzip" ,unzip) | |
12655 | ("java-testng" ,java-testng))) | |
12656 | (home-page "http://mccarrolllab.com/dropseq/") | |
12657 | (synopsis "Tools for Drop-seq analyses") | |
12658 | (description "Drop-seq is a technology to enable biologists to | |
12659 | analyze RNA expression genome-wide in thousands of individual cells at | |
12660 | once. This package provides tools to perform Drop-seq analyses.") | |
12661 | (license license:expat))) | |
0bdd5b8a RW |
12662 | |
12663 | (define-public pigx-rnaseq | |
12664 | (package | |
12665 | (name "pigx-rnaseq") | |
12666 | (version "0.0.2") | |
12667 | (source (origin | |
12668 | (method url-fetch) | |
12669 | (uri (string-append "https://github.com/BIMSBbioinfo/pigx_rnaseq/" | |
12670 | "releases/download/v" version | |
12671 | "/pigx_rnaseq-" version ".tar.gz")) | |
12672 | (sha256 | |
12673 | (base32 | |
12674 | "168hx2ig3rarphx3l21ay9yyg8ipaakzixnrhpbdi0sknhyvrrk8")))) | |
12675 | (build-system gnu-build-system) | |
12676 | (arguments | |
12677 | `(#:parallel-tests? #f ; not supported | |
12678 | #:phases | |
12679 | (modify-phases %standard-phases | |
fe52a215 RW |
12680 | ;; "test.sh" runs STAR, which requires excessive amounts of memory. |
12681 | (add-after 'unpack 'disable-resource-intensive-test | |
12682 | (lambda _ | |
12683 | (substitute* "Makefile.in" | |
12684 | (("(^ tests/test_trim_galore/test.sh).*" _ m) m) | |
12685 | (("^ test.sh") "")) | |
12686 | #t)) | |
0bdd5b8a RW |
12687 | (add-after 'install 'wrap-executable |
12688 | ;; Make sure the executable finds all R modules. | |
12689 | (lambda* (#:key inputs outputs #:allow-other-keys) | |
12690 | (let ((out (assoc-ref outputs "out"))) | |
12691 | (wrap-program (string-append out "/bin/pigx-rnaseq") | |
12692 | `("R_LIBS_SITE" ":" = (,(getenv "R_LIBS_SITE"))) | |
12693 | `("PYTHONPATH" ":" = (,(getenv "PYTHONPATH"))))) | |
12694 | #t))))) | |
12695 | (inputs | |
12696 | `(("snakemake" ,snakemake) | |
12697 | ("fastqc" ,fastqc) | |
12698 | ("multiqc" ,multiqc) | |
12699 | ("star" ,star) | |
12700 | ("trim-galore" ,trim-galore) | |
12701 | ("htseq" ,htseq) | |
12702 | ("samtools" ,samtools) | |
12703 | ("bedtools" ,bedtools) | |
12704 | ("r-minimal" ,r-minimal) | |
12705 | ("r-rmarkdown" ,r-rmarkdown) | |
12706 | ("r-ggplot2" ,r-ggplot2) | |
12707 | ("r-ggrepel" ,r-ggrepel) | |
12708 | ("r-gprofiler" ,r-gprofiler) | |
12709 | ("r-deseq2" ,r-deseq2) | |
12710 | ("r-dt" ,r-dt) | |
12711 | ("r-knitr" ,r-knitr) | |
12712 | ("r-pheatmap" ,r-pheatmap) | |
12713 | ("r-corrplot" ,r-corrplot) | |
12714 | ("r-reshape2" ,r-reshape2) | |
12715 | ("r-plotly" ,r-plotly) | |
12716 | ("r-scales" ,r-scales) | |
12717 | ("r-summarizedexperiment" ,r-summarizedexperiment) | |
12718 | ("r-crosstalk" ,r-crosstalk) | |
12719 | ("r-tximport" ,r-tximport) | |
12720 | ("r-rtracklayer" ,r-rtracklayer) | |
12721 | ("r-rjson" ,r-rjson) | |
12722 | ("salmon" ,salmon) | |
1a29fc3f RW |
12723 | ("ghc-pandoc" ,ghc-pandoc-1) |
12724 | ("ghc-pandoc-citeproc" ,ghc-pandoc-citeproc-with-pandoc-1) | |
0bdd5b8a RW |
12725 | ("python-wrapper" ,python-wrapper) |
12726 | ("python-pyyaml" ,python-pyyaml))) | |
12727 | (home-page "http://bioinformatics.mdc-berlin.de/pigx/") | |
12728 | (synopsis "Analysis pipeline for RNA sequencing experiments") | |
12729 | (description "PiGX RNAseq is an analysis pipeline for preprocessing and | |
12730 | reporting for RNA sequencing experiments. It is easy to use and produces high | |
12731 | quality reports. The inputs are reads files from the sequencing experiment, | |
12732 | and a configuration file which describes the experiment. In addition to | |
12733 | quality control of the experiment, the pipeline produces a differential | |
12734 | expression report comparing samples in an easily configurable manner.") | |
12735 | (license license:gpl3+))) | |
531afc8a RW |
12736 | |
12737 | (define-public pigx-chipseq | |
12738 | (package | |
12739 | (name "pigx-chipseq") | |
12740 | (version "0.0.2") | |
12741 | (source (origin | |
12742 | (method url-fetch) | |
12743 | (uri (string-append "https://github.com/BIMSBbioinfo/pigx_chipseq/" | |
12744 | "releases/download/v" version | |
12745 | "/pigx_chipseq-" version ".tar.gz")) | |
12746 | (sha256 | |
12747 | (base32 | |
12748 | "1jliwhifnjgl9x0z730bzpxswi2s84fyg5y8cagbyzpw509452f5")))) | |
12749 | (build-system gnu-build-system) | |
12750 | (arguments | |
12751 | `(#:phases | |
12752 | (modify-phases %standard-phases | |
12753 | (add-after 'install 'wrap-executable | |
12754 | ;; Make sure the executable finds all R modules. | |
12755 | (lambda* (#:key inputs outputs #:allow-other-keys) | |
12756 | (let ((out (assoc-ref outputs "out"))) | |
12757 | (wrap-program (string-append out "/bin/pigx-chipseq") | |
12758 | `("R_LIBS_SITE" ":" = (,(getenv "R_LIBS_SITE"))) | |
12759 | `("PYTHONPATH" ":" = (,(getenv "PYTHONPATH"))))) | |
12760 | #t))))) | |
12761 | (inputs | |
12762 | `(("r-minimal" ,r-minimal) | |
12763 | ("r-argparser" ,r-argparser) | |
12764 | ("r-chipseq" ,r-chipseq) | |
12765 | ("r-data-table" ,r-data-table) | |
12766 | ("r-genomation" ,r-genomation) | |
12767 | ("r-genomicranges" ,r-genomicranges) | |
12768 | ("r-rtracklayer" ,r-rtracklayer) | |
12769 | ("r-rcas" ,r-rcas) | |
12770 | ("r-stringr" ,r-stringr) | |
12771 | ("r-jsonlite" ,r-jsonlite) | |
12772 | ("r-heatmaply" ,r-heatmaply) | |
12773 | ("r-ggplot2" ,r-ggplot2) | |
12774 | ("r-plotly" ,r-plotly) | |
12775 | ("python-wrapper" ,python-wrapper) | |
12776 | ("python-pyyaml" ,python-pyyaml) | |
12777 | ("snakemake" ,snakemake) | |
12778 | ("macs" ,macs) | |
12779 | ("multiqc" ,multiqc) | |
12780 | ("perl" ,perl) | |
fd757a8f RW |
12781 | ("ghc-pandoc" ,ghc-pandoc-1) |
12782 | ("ghc-pandoc-citeproc" ,ghc-pandoc-citeproc-with-pandoc-1) | |
531afc8a RW |
12783 | ("fastqc" ,fastqc) |
12784 | ("bowtie" ,bowtie) | |
12785 | ("idr" ,idr) | |
12786 | ("snakemake" ,snakemake) | |
12787 | ("samtools" ,samtools) | |
12788 | ("bedtools" ,bedtools) | |
12789 | ("kentutils" ,kentutils))) | |
12790 | (native-inputs | |
12791 | `(("python-pytest" ,python-pytest))) | |
12792 | (home-page "http://bioinformatics.mdc-berlin.de/pigx/") | |
12793 | (synopsis "Analysis pipeline for ChIP sequencing experiments") | |
12794 | (description "PiGX ChIPseq is an analysis pipeline for preprocessing, peak | |
12795 | calling and reporting for ChIP sequencing experiments. It is easy to use and | |
12796 | produces high quality reports. The inputs are reads files from the sequencing | |
12797 | experiment, and a configuration file which describes the experiment. In | |
12798 | addition to quality control of the experiment, the pipeline enables to set up | |
12799 | multiple peak calling analysis and allows the generation of a UCSC track hub | |
12800 | in an easily configurable manner.") | |
12801 | (license license:gpl3+))) | |
fb94174f RW |
12802 | |
12803 | (define-public pigx-bsseq | |
12804 | (package | |
12805 | (name "pigx-bsseq") | |
12806 | (version "0.0.5") | |
12807 | (source (origin | |
12808 | (method url-fetch) | |
12809 | (uri (string-append "https://github.com/BIMSBbioinfo/pigx_bsseq/" | |
12810 | "releases/download/v" version | |
12811 | "/pigx_bsseq-" version ".tar.gz")) | |
12812 | (sha256 | |
12813 | (base32 | |
12814 | "1h8ma99vi7hs83nafvjpq8jmaq9977j3n11c4zd95hai0cf7zxmp")))) | |
12815 | (build-system gnu-build-system) | |
12816 | (arguments | |
12817 | `(#:phases | |
12818 | (modify-phases %standard-phases | |
12819 | (add-before 'check 'set-timezone | |
12820 | ;; The readr package is picky about timezones. | |
12821 | (lambda* (#:key inputs #:allow-other-keys) | |
12822 | (setenv "TZ" "UTC+1") | |
12823 | (setenv "TZDIR" | |
12824 | (string-append (assoc-ref inputs "tzdata") | |
12825 | "/share/zoneinfo")) | |
12826 | #t)) | |
12827 | (add-after 'install 'wrap-executable | |
12828 | ;; Make sure the executable finds all R modules. | |
12829 | (lambda* (#:key inputs outputs #:allow-other-keys) | |
12830 | (let ((out (assoc-ref outputs "out"))) | |
12831 | (wrap-program (string-append out "/bin/pigx-bsseq") | |
12832 | `("R_LIBS_SITE" ":" = (,(getenv "R_LIBS_SITE"))) | |
12833 | `("PYTHONPATH" ":" = (,(getenv "PYTHONPATH"))))) | |
12834 | #t))))) | |
12835 | (native-inputs | |
12836 | `(("tzdata" ,tzdata))) | |
12837 | (inputs | |
12838 | `(("r-minimal" ,r-minimal) | |
12839 | ("r-annotationhub" ,r-annotationhub) | |
12840 | ("r-dt" ,r-dt) | |
12841 | ("r-genomation" ,r-genomation) | |
12842 | ("r-methylkit" ,r-methylkit) | |
12843 | ("r-rtracklayer" ,r-rtracklayer) | |
12844 | ("r-rmarkdown" ,r-rmarkdown) | |
12845 | ("r-bookdown" ,r-bookdown) | |
12846 | ("r-ggplot2" ,r-ggplot2) | |
12847 | ("r-ggbio" ,r-ggbio) | |
9dcb4d22 RW |
12848 | ("ghc-pandoc" ,ghc-pandoc-1) |
12849 | ("ghc-pandoc-citeproc" ,ghc-pandoc-citeproc-with-pandoc-1) | |
fb94174f RW |
12850 | ("python-wrapper" ,python-wrapper) |
12851 | ("python-pyyaml" ,python-pyyaml) | |
12852 | ("snakemake" ,snakemake) | |
12853 | ("bismark" ,bismark) | |
12854 | ("fastqc" ,fastqc) | |
12855 | ("bowtie" ,bowtie) | |
12856 | ("trim-galore" ,trim-galore) | |
12857 | ("cutadapt" ,cutadapt) | |
12858 | ("samtools" ,samtools))) | |
12859 | (home-page "http://bioinformatics.mdc-berlin.de/pigx/") | |
12860 | (synopsis "Bisulfite sequencing pipeline from fastq to methylation reports") | |
12861 | (description "PiGx BSseq is a data processing pipeline for raw fastq read | |
12862 | data of bisulfite experiments; it produces reports on aggregate methylation | |
12863 | and coverage and can be used to produce information on differential | |
12864 | methylation and segmentation.") | |
12865 | (license license:gpl3+))) | |
32cbbac1 | 12866 | |
46264c73 RW |
12867 | (define-public pigx-scrnaseq |
12868 | (package | |
12869 | (name "pigx-scrnaseq") | |
12870 | (version "0.0.2") | |
12871 | (source (origin | |
12872 | (method url-fetch) | |
12873 | (uri (string-append "https://github.com/BIMSBbioinfo/pigx_scrnaseq/" | |
12874 | "releases/download/v" version | |
12875 | "/pigx_scrnaseq-" version ".tar.gz")) | |
12876 | (sha256 | |
12877 | (base32 | |
12878 | "03gwp83823ji59y6nvyz89i4yd3faaqpc3791qia71i91470vfsg")))) | |
12879 | (build-system gnu-build-system) | |
12880 | (arguments | |
12881 | `(#:configure-flags | |
12882 | (list (string-append "PICARDJAR=" (assoc-ref %build-inputs "java-picard") | |
12883 | "/share/java/picard.jar") | |
12884 | (string-append "DROPSEQJAR=" (assoc-ref %build-inputs "dropseq-tools") | |
12885 | "/share/java/dropseq.jar")) | |
12886 | #:phases | |
12887 | (modify-phases %standard-phases | |
12888 | (add-after 'install 'wrap-executable | |
12889 | ;; Make sure the executable finds all R modules. | |
12890 | (lambda* (#:key inputs outputs #:allow-other-keys) | |
12891 | (let ((out (assoc-ref outputs "out"))) | |
12892 | (wrap-program (string-append out "/bin/pigx-scrnaseq") | |
12893 | `("R_LIBS_SITE" ":" = (,(getenv "R_LIBS_SITE"))) | |
12894 | `("PYTHONPATH" ":" = (,(getenv "PYTHONPATH"))))) | |
12895 | #t))))) | |
12896 | (inputs | |
12897 | `(("dropseq-tools" ,dropseq-tools) | |
12898 | ("fastqc" ,fastqc) | |
12899 | ("java-picard" ,java-picard) | |
12900 | ("java" ,icedtea-8) | |
12901 | ("python-wrapper" ,python-wrapper) | |
12902 | ("python-pyyaml" ,python-pyyaml) | |
12903 | ("python-pandas" ,python-pandas) | |
12904 | ("python-numpy" ,python-numpy) | |
12905 | ("python-loompy" ,python-loompy) | |
12906 | ("ghc-pandoc" ,ghc-pandoc) | |
12907 | ("ghc-pandoc-citeproc" ,ghc-pandoc-citeproc) | |
12908 | ("snakemake" ,snakemake) | |
12909 | ("star" ,star) | |
12910 | ("r-minimal" ,r-minimal) | |
12911 | ("r-argparser" ,r-argparser) | |
12912 | ("r-cowplot" ,r-cowplot) | |
12913 | ("r-data-table" ,r-data-table) | |
12914 | ("r-delayedarray" ,r-delayedarray) | |
12915 | ("r-delayedmatrixstats" ,r-delayedmatrixstats) | |
12916 | ("r-dplyr" ,r-dplyr) | |
12917 | ("r-dropbead" ,r-dropbead) | |
12918 | ("r-dt" ,r-dt) | |
12919 | ("r-genomicalignments" ,r-genomicalignments) | |
12920 | ("r-genomicfiles" ,r-genomicfiles) | |
12921 | ("r-genomicranges" ,r-genomicranges) | |
12922 | ("r-ggplot2" ,r-ggplot2) | |
12923 | ("r-hdf5array" ,r-hdf5array) | |
12924 | ("r-pheatmap" ,r-pheatmap) | |
12925 | ("r-rmarkdown" ,r-rmarkdown) | |
12926 | ("r-rsamtools" ,r-rsamtools) | |
12927 | ("r-rtracklayer" ,r-rtracklayer) | |
12928 | ("r-rtsne" ,r-rtsne) | |
12929 | ("r-scater" ,r-scater) | |
12930 | ("r-scran" ,r-scran) | |
12931 | ("r-singlecellexperiment" ,r-singlecellexperiment) | |
12932 | ("r-stringr" ,r-stringr) | |
12933 | ("r-yaml" ,r-yaml))) | |
12934 | (home-page "http://bioinformatics.mdc-berlin.de/pigx/") | |
12935 | (synopsis "Analysis pipeline for single-cell RNA sequencing experiments") | |
12936 | (description "PiGX scRNAseq is an analysis pipeline for preprocessing and | |
12937 | quality control for single cell RNA sequencing experiments. The inputs are | |
12938 | read files from the sequencing experiment, and a configuration file which | |
12939 | describes the experiment. It produces processed files for downstream analysis | |
12940 | and interactive quality reports. The pipeline is designed to work with UMI | |
12941 | based methods.") | |
12942 | (license license:gpl3+))) | |
12943 | ||
c1c9cc66 RW |
12944 | (define-public pigx |
12945 | (package | |
12946 | (name "pigx") | |
12947 | (version "0.0.1") | |
12948 | (source (origin | |
12949 | (method url-fetch) | |
12950 | (uri (string-append "https://github.com/BIMSBbioinfo/pigx/" | |
12951 | "releases/download/v" version | |
12952 | "/pigx-" version ".tar.gz")) | |
12953 | (sha256 | |
12954 | (base32 | |
12955 | "1nxb2hbp40yg3j7n56k4dhsd2fl1j8g0wpiiln56prqzljwnlgmf")))) | |
12956 | (build-system gnu-build-system) | |
12957 | (inputs | |
12958 | `(("python" ,python) | |
12959 | ("pigx-bsseq" ,pigx-bsseq) | |
12960 | ("pigx-chipseq" ,pigx-chipseq) | |
12961 | ("pigx-rnaseq" ,pigx-rnaseq) | |
12962 | ("pigx-scrnaseq" ,pigx-scrnaseq))) | |
12963 | (home-page "http://bioinformatics.mdc-berlin.de/pigx/") | |
12964 | (synopsis "Analysis pipelines for genomics") | |
12965 | (description "PiGx is a collection of genomics pipelines. It includes the | |
12966 | following pipelines: | |
12967 | ||
12968 | @itemize | |
12969 | @item PiGx BSseq for raw fastq read data of bisulfite experiments | |
12970 | @item PiGx RNAseq for RNAseq samples | |
12971 | @item PiGx scRNAseq for single cell dropseq analysis | |
12972 | @item PiGx ChIPseq for reads from ChIPseq experiments | |
12973 | @end itemize | |
12974 | ||
12975 | All pipelines are easily configured with a simple sample sheet and a | |
12976 | descriptive settings file. The result is a set of comprehensive, interactive | |
12977 | HTML reports with interesting findings about your samples.") | |
12978 | (license license:gpl3+))) | |
12979 | ||
32cbbac1 LF |
12980 | (define-public r-diversitree |
12981 | (package | |
12982 | (name "r-diversitree") | |
12983 | (version "0.9-10") | |
12984 | (source | |
12985 | (origin | |
12986 | (method url-fetch) | |
12987 | (uri (cran-uri "diversitree" version)) | |
12988 | (sha256 | |
12989 | (base32 | |
12990 | "0gh4rcrp0an3jh8915i1fsxlgyfk7njywgbd5ln5r2jhr085kpz7")))) | |
12991 | (build-system r-build-system) | |
12992 | (native-inputs | |
12993 | `(("gfortran" ,gfortran))) | |
12994 | (inputs `(("fftw" ,fftw) ("gsl" ,gsl))) | |
12995 | (propagated-inputs | |
12996 | `(("r-ape" ,r-ape) | |
12997 | ("r-desolve" ,r-desolve) | |
12998 | ("r-rcpp" ,r-rcpp) | |
12999 | ("r-suplex" ,r-subplex))) | |
13000 | (home-page "https://www.zoology.ubc.ca/prog/diversitree") | |
13001 | (synopsis "Comparative 'phylogenetic' analyses of diversification") | |
13002 | (description "This package contains a number of comparative \"phylogenetic\" | |
13003 | methods, mostly focusing on analysing diversification and character evolution. | |
13004 | Contains implementations of \"BiSSE\" (Binary State Speciation and Extinction) | |
13005 | and its unresolved tree extensions, \"MuSSE\" (Multiple State Speciation and | |
13006 | Extinction), \"QuaSSE\", \"GeoSSE\", and \"BiSSE-ness\" Other included methods | |
13007 | include Markov models of discrete and continuous trait evolution and constant | |
13008 | rate speciation and extinction.") | |
13009 | (license license:gpl2+))) |