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> |
d60772dc | 13 | ;;; Copyright © 2018 Gábor Boskovits <boskovits@gmail.com> |
4f9355c3 | 14 | ;;; Copyright © 2018 Mădălin Ionel Patrașcu <madalinionel.patrascu@mdc-berlin.de> |
4e10a221 RW |
15 | ;;; |
16 | ;;; This file is part of GNU Guix. | |
17 | ;;; | |
18 | ;;; GNU Guix is free software; you can redistribute it and/or modify it | |
19 | ;;; under the terms of the GNU General Public License as published by | |
20 | ;;; the Free Software Foundation; either version 3 of the License, or (at | |
21 | ;;; your option) any later version. | |
22 | ;;; | |
23 | ;;; GNU Guix is distributed in the hope that it will be useful, but | |
24 | ;;; WITHOUT ANY WARRANTY; without even the implied warranty of | |
25 | ;;; MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the | |
26 | ;;; GNU General Public License for more details. | |
27 | ;;; | |
28 | ;;; You should have received a copy of the GNU General Public License | |
29 | ;;; along with GNU Guix. If not, see <http://www.gnu.org/licenses/>. | |
30 | ||
31 | (define-module (gnu packages bioinformatics) | |
32 | #:use-module ((guix licenses) #:prefix license:) | |
33 | #:use-module (guix packages) | |
8e913213 | 34 | #:use-module (guix utils) |
4e10a221 | 35 | #:use-module (guix download) |
2c16316e | 36 | #:use-module (guix git-download) |
ec946638 | 37 | #:use-module (guix hg-download) |
10b4a969 | 38 | #:use-module (guix build-system ant) |
4e10a221 | 39 | #:use-module (guix build-system gnu) |
d7678942 | 40 | #:use-module (guix build-system cmake) |
d71078bc | 41 | #:use-module (guix build-system haskell) |
c033f5d6 | 42 | #:use-module (guix build-system ocaml) |
365c8153 | 43 | #:use-module (guix build-system perl) |
8622a072 | 44 | #:use-module (guix build-system python) |
a5002ae7 | 45 | #:use-module (guix build-system r) |
9c38b540 | 46 | #:use-module (guix build-system ruby) |
9364a520 | 47 | #:use-module (guix build-system scons) |
d3517eda | 48 | #:use-module (guix build-system trivial) |
4e10a221 | 49 | #:use-module (gnu packages) |
a2950fa4 | 50 | #:use-module (gnu packages autotools) |
684bf7c7 | 51 | #:use-module (gnu packages algebra) |
d3517eda | 52 | #:use-module (gnu packages base) |
318c0aee | 53 | #:use-module (gnu packages bash) |
a0a71439 | 54 | #:use-module (gnu packages bison) |
d53aeeaf | 55 | #:use-module (gnu packages bioconductor) |
e4e5a4d8 | 56 | #:use-module (gnu packages boost) |
ac257f12 | 57 | #:use-module (gnu packages check) |
4e10a221 | 58 | #:use-module (gnu packages compression) |
82c370de | 59 | #:use-module (gnu packages cpio) |
7cb61550 | 60 | #:use-module (gnu packages cran) |
1baee943 | 61 | #:use-module (gnu packages curl) |
99828fa7 | 62 | #:use-module (gnu packages documentation) |
94820951 | 63 | #:use-module (gnu packages databases) |
d29150b5 | 64 | #:use-module (gnu packages datastructures) |
75dd2424 | 65 | #:use-module (gnu packages file) |
99268755 | 66 | #:use-module (gnu packages flex) |
02f35bb5 | 67 | #:use-module (gnu packages gawk) |
2409f37f | 68 | #:use-module (gnu packages gcc) |
66e40e00 | 69 | #:use-module (gnu packages gd) |
97b9da68 | 70 | #:use-module (gnu packages gtk) |
b16728b0 | 71 | #:use-module (gnu packages glib) |
18f5d2a7 | 72 | #:use-module (gnu packages graph) |
db7a3444 | 73 | #:use-module (gnu packages groff) |
50937297 | 74 | #:use-module (gnu packages guile) |
89984be4 | 75 | #:use-module (gnu packages haskell) |
d71078bc RW |
76 | #:use-module (gnu packages haskell-check) |
77 | #:use-module (gnu packages haskell-web) | |
66e40e00 | 78 | #:use-module (gnu packages image) |
97b9da68 | 79 | #:use-module (gnu packages imagemagick) |
15a3c3d4 | 80 | #:use-module (gnu packages java) |
8d77a085 | 81 | #:use-module (gnu packages jemalloc) |
875d0681 | 82 | #:use-module (gnu packages dlang) |
51c64999 | 83 | #:use-module (gnu packages linux) |
ec946638 | 84 | #:use-module (gnu packages logging) |
36742f43 | 85 | #:use-module (gnu packages machine-learning) |
db7a3444 | 86 | #:use-module (gnu packages man) |
c833ab55 | 87 | #:use-module (gnu packages maths) |
6c2b26e2 | 88 | #:use-module (gnu packages mpi) |
4e10a221 | 89 | #:use-module (gnu packages ncurses) |
c033f5d6 | 90 | #:use-module (gnu packages ocaml) |
81f3e0c1 | 91 | #:use-module (gnu packages pcre) |
ceb62d54 | 92 | #:use-module (gnu packages parallel) |
66e40e00 | 93 | #:use-module (gnu packages pdf) |
4e10a221 | 94 | #:use-module (gnu packages perl) |
5ccde207 | 95 | #:use-module (gnu packages perl-check) |
4e10a221 | 96 | #:use-module (gnu packages pkg-config) |
bfe3c685 | 97 | #:use-module (gnu packages popt) |
e4e5a4d8 | 98 | #:use-module (gnu packages protobuf) |
346a829a | 99 | #:use-module (gnu packages python) |
589e3f4e | 100 | #:use-module (gnu packages python-web) |
ec946638 | 101 | #:use-module (gnu packages readline) |
9c38b540 | 102 | #:use-module (gnu packages ruby) |
84be3b99 | 103 | #:use-module (gnu packages serialization) |
94820951 | 104 | #:use-module (gnu packages shells) |
c833ab55 | 105 | #:use-module (gnu packages statistics) |
aa163424 | 106 | #:use-module (gnu packages swig) |
d7678942 | 107 | #:use-module (gnu packages tbb) |
97b9da68 | 108 | #:use-module (gnu packages tex) |
db7a3444 | 109 | #:use-module (gnu packages texinfo) |
2127cedb | 110 | #:use-module (gnu packages textutils) |
43c565d2 | 111 | #:use-module (gnu packages time) |
a2950fa4 | 112 | #:use-module (gnu packages tls) |
ce7155d5 | 113 | #:use-module (gnu packages vim) |
365c8153 | 114 | #:use-module (gnu packages web) |
c833ab55 | 115 | #:use-module (gnu packages xml) |
66e40e00 | 116 | #:use-module (gnu packages xorg) |
2c9232ae | 117 | #:use-module (srfi srfi-1) |
ce7e361f | 118 | #:use-module (ice-9 match)) |
4e10a221 | 119 | |
8dc797fa BW |
120 | (define-public aragorn |
121 | (package | |
122 | (name "aragorn") | |
e990c81d | 123 | (version "1.2.38") |
8dc797fa BW |
124 | (source (origin |
125 | (method url-fetch) | |
126 | (uri (string-append | |
127 | "http://mbio-serv2.mbioekol.lu.se/ARAGORN/Downloads/aragorn" | |
128 | version ".tgz")) | |
129 | (sha256 | |
130 | (base32 | |
e990c81d | 131 | "09i1rg716smlbnixfm7q1ml2mfpaa2fpn3hwjg625ysmfwwy712b")))) |
8dc797fa BW |
132 | (build-system gnu-build-system) |
133 | (arguments | |
134 | `(#:tests? #f ; there are no tests | |
135 | #:phases | |
136 | (modify-phases %standard-phases | |
137 | (delete 'configure) | |
138 | (replace 'build | |
95758e2f RW |
139 | (lambda _ |
140 | (invoke "gcc" | |
141 | "-O3" | |
142 | "-ffast-math" | |
143 | "-finline-functions" | |
144 | "-o" | |
145 | "aragorn" | |
146 | (string-append "aragorn" ,version ".c")) | |
147 | #t)) | |
8dc797fa | 148 | (replace 'install |
95758e2f RW |
149 | (lambda* (#:key outputs #:allow-other-keys) |
150 | (let* ((out (assoc-ref outputs "out")) | |
151 | (bin (string-append out "/bin")) | |
152 | (man (string-append out "/share/man/man1"))) | |
153 | (install-file "aragorn" bin) | |
154 | (install-file "aragorn.1" man)) | |
155 | #t))))) | |
8dc797fa BW |
156 | (home-page "http://mbio-serv2.mbioekol.lu.se/ARAGORN") |
157 | (synopsis "Detect tRNA, mtRNA and tmRNA genes in nucleotide sequences") | |
158 | (description | |
159 | "Aragorn identifies transfer RNA, mitochondrial RNA and | |
160 | transfer-messenger RNA from nucleotide sequences, based on homology to known | |
161 | tRNA consensus sequences and RNA structure. It also outputs the secondary | |
162 | structure of the predicted RNA.") | |
163 | (license license:gpl2))) | |
164 | ||
a12ba6e8 BW |
165 | (define-public bamm |
166 | (package | |
167 | (name "bamm") | |
4b6da268 | 168 | (version "1.7.3") |
a12ba6e8 | 169 | (source (origin |
c793f4d8 | 170 | (method git-fetch) |
a12ba6e8 | 171 | ;; BamM is not available on pypi. |
c793f4d8 RW |
172 | (uri (git-reference |
173 | (url "https://github.com/Ecogenomics/BamM.git") | |
174 | (commit version) | |
175 | (recursive? #t))) | |
176 | (file-name (git-file-name name version)) | |
a12ba6e8 BW |
177 | (sha256 |
178 | (base32 | |
c793f4d8 | 179 | "1p83ahi984ipslxlg4yqy1gdnya9rkn1v71z8djgxkm9d2chw4c5")) |
a12ba6e8 BW |
180 | (modules '((guix build utils))) |
181 | (snippet | |
182 | `(begin | |
183 | ;; Delete bundled htslib. | |
184 | (delete-file-recursively "c/htslib-1.3.1") | |
185 | #t)))) | |
186 | (build-system python-build-system) | |
187 | (arguments | |
188 | `(#:python ,python-2 ; BamM is Python 2 only. | |
189 | ;; Do not use bundled libhts. Do use the bundled libcfu because it has | |
190 | ;; been modified from its original form. | |
191 | #:configure-flags | |
192 | (let ((htslib (assoc-ref %build-inputs "htslib"))) | |
193 | (list "--with-libhts-lib" (string-append htslib "/lib") | |
194 | "--with-libhts-inc" (string-append htslib "/include/htslib"))) | |
195 | #:phases | |
196 | (modify-phases %standard-phases | |
197 | (add-after 'unpack 'autogen | |
198 | (lambda _ | |
199 | (with-directory-excursion "c" | |
200 | (let ((sh (which "sh"))) | |
c793f4d8 | 201 | (for-each make-file-writable (find-files "." ".*")) |
a12ba6e8 BW |
202 | ;; Use autogen so that 'configure' works. |
203 | (substitute* "autogen.sh" (("/bin/sh") sh)) | |
204 | (setenv "CONFIG_SHELL" sh) | |
c793f4d8 RW |
205 | (invoke "./autogen.sh"))) |
206 | #t)) | |
a12ba6e8 BW |
207 | (delete 'build) |
208 | ;; Run tests after installation so compilation only happens once. | |
209 | (delete 'check) | |
210 | (add-after 'install 'wrap-executable | |
211 | (lambda* (#:key outputs #:allow-other-keys) | |
212 | (let* ((out (assoc-ref outputs "out")) | |
213 | (path (getenv "PATH"))) | |
214 | (wrap-program (string-append out "/bin/bamm") | |
215 | `("PATH" ":" prefix (,path)))) | |
216 | #t)) | |
217 | (add-after 'wrap-executable 'post-install-check | |
218 | (lambda* (#:key inputs outputs #:allow-other-keys) | |
219 | (setenv "PATH" | |
220 | (string-append (assoc-ref outputs "out") | |
221 | "/bin:" | |
222 | (getenv "PATH"))) | |
223 | (setenv "PYTHONPATH" | |
224 | (string-append | |
225 | (assoc-ref outputs "out") | |
226 | "/lib/python" | |
227 | (string-take (string-take-right | |
228 | (assoc-ref inputs "python") 5) 3) | |
229 | "/site-packages:" | |
230 | (getenv "PYTHONPATH"))) | |
231 | ;; There are 2 errors printed, but they are safe to ignore: | |
232 | ;; 1) [E::hts_open_format] fail to open file ... | |
233 | ;; 2) samtools view: failed to open ... | |
c793f4d8 RW |
234 | (invoke "nosetests") |
235 | #t))))) | |
a12ba6e8 BW |
236 | (native-inputs |
237 | `(("autoconf" ,autoconf) | |
238 | ("automake" ,automake) | |
239 | ("libtool" ,libtool) | |
240 | ("zlib" ,zlib) | |
241 | ("python-nose" ,python2-nose) | |
f3b98f4f | 242 | ("python-pysam" ,python2-pysam))) |
a12ba6e8 | 243 | (inputs |
bca2c576 | 244 | `(("htslib" ,htslib-1.3) ; At least one test fails on htslib-1.4+. |
a12ba6e8 BW |
245 | ("samtools" ,samtools) |
246 | ("bwa" ,bwa) | |
247 | ("grep" ,grep) | |
248 | ("sed" ,sed) | |
249 | ("coreutils" ,coreutils))) | |
250 | (propagated-inputs | |
251 | `(("python-numpy" ,python2-numpy))) | |
252 | (home-page "http://ecogenomics.github.io/BamM/") | |
253 | (synopsis "Metagenomics-focused BAM file manipulator") | |
254 | (description | |
255 | "BamM is a C library, wrapped in python, to efficiently generate and | |
256 | parse BAM files, specifically for the analysis of metagenomic data. For | |
257 | instance, it implements several methods to assess contig-wise read coverage.") | |
258 | (license license:lgpl3+))) | |
259 | ||
9794180d RW |
260 | (define-public bamtools |
261 | (package | |
262 | (name "bamtools") | |
4ffa0858 | 263 | (version "2.5.1") |
9794180d | 264 | (source (origin |
8e58319c RW |
265 | (method git-fetch) |
266 | (uri (git-reference | |
267 | (url "https://github.com/pezmaster31/bamtools.git") | |
268 | (commit (string-append "v" version)))) | |
269 | (file-name (git-file-name name version)) | |
9794180d RW |
270 | (sha256 |
271 | (base32 | |
8e58319c | 272 | "0nfb2ypcx9959xnbz6wxh6py3xfizgmg8nrknxl95c507m9hmq8b")))) |
9794180d | 273 | (build-system cmake-build-system) |
4702cec2 RW |
274 | (arguments |
275 | `(#:tests? #f ;no "check" target | |
276 | #:phases | |
277 | (modify-phases %standard-phases | |
278 | (add-before | |
279 | 'configure 'set-ldflags | |
280 | (lambda* (#:key outputs #:allow-other-keys) | |
281 | (setenv "LDFLAGS" | |
282 | (string-append | |
283 | "-Wl,-rpath=" | |
2e0f6905 MW |
284 | (assoc-ref outputs "out") "/lib/bamtools")) |
285 | #t))))) | |
9794180d RW |
286 | (inputs `(("zlib" ,zlib))) |
287 | (home-page "https://github.com/pezmaster31/bamtools") | |
288 | (synopsis "C++ API and command-line toolkit for working with BAM data") | |
289 | (description | |
290 | "BamTools provides both a C++ API and a command-line toolkit for handling | |
291 | BAM files.") | |
292 | (license license:expat))) | |
293 | ||
bdc7be59 MB |
294 | (define-public bcftools |
295 | (package | |
296 | (name "bcftools") | |
f79b59e3 | 297 | (version "1.9") |
bdc7be59 MB |
298 | (source (origin |
299 | (method url-fetch) | |
f79b59e3 RW |
300 | (uri (string-append "https://github.com/samtools/bcftools/" |
301 | "releases/download/" | |
302 | version "/bcftools-" version ".tar.bz2")) | |
bdc7be59 MB |
303 | (sha256 |
304 | (base32 | |
f79b59e3 | 305 | "1j3h638i8kgihzyrlnpj82xg1b23sijibys9hvwari3fy7kd0dkg")) |
bdc7be59 | 306 | (modules '((guix build utils))) |
6cbee49d MW |
307 | (snippet '(begin |
308 | ;; Delete bundled htslib. | |
f79b59e3 | 309 | (delete-file-recursively "htslib-1.9") |
6cbee49d | 310 | #t)))) |
bdc7be59 MB |
311 | (build-system gnu-build-system) |
312 | (arguments | |
f79b59e3 RW |
313 | `(#:configure-flags |
314 | (list "--enable-libgsl") | |
315 | #:test-target "test" | |
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") | |
f8b697a3 | 341 | (version "2.4.35") |
8dd4ff11 | 342 | (source (origin |
f8b697a3 RW |
343 | (method git-fetch) |
344 | (uri (git-reference | |
345 | (url "https://github.com/bedops/bedops.git") | |
346 | (commit (string-append "v" version)))) | |
347 | (file-name (git-file-name name version)) | |
8dd4ff11 RW |
348 | (sha256 |
349 | (base32 | |
f8b697a3 | 350 | "0mmgsgwz5r9w76hzgxkxc9s9lkdhhaf7vr6i02b09vbswvs1fyqx")))) |
8dd4ff11 RW |
351 | (build-system gnu-build-system) |
352 | (arguments | |
353 | '(#:tests? #f | |
354 | #:make-flags (list (string-append "BINDIR=" %output "/bin")) | |
355 | #:phases | |
dc1d3cde KK |
356 | (modify-phases %standard-phases |
357 | (add-after 'unpack 'unpack-tarballs | |
358 | (lambda _ | |
359 | ;; FIXME: Bedops includes tarballs of minimally patched upstream | |
360 | ;; libraries jansson, zlib, and bzip2. We cannot just use stock | |
361 | ;; libraries because at least one of the libraries (zlib) is | |
362 | ;; patched to add a C++ function definition (deflateInit2cpp). | |
363 | ;; Until the Bedops developers offer a way to link against system | |
364 | ;; libraries we have to build the in-tree copies of these three | |
365 | ;; libraries. | |
366 | ||
367 | ;; See upstream discussion: | |
368 | ;; https://github.com/bedops/bedops/issues/124 | |
369 | ||
370 | ;; Unpack the tarballs to benefit from shebang patching. | |
371 | (with-directory-excursion "third-party" | |
337d72fb RW |
372 | (invoke "tar" "xvf" "jansson-2.6.tar.bz2") |
373 | (invoke "tar" "xvf" "zlib-1.2.7.tar.bz2") | |
374 | (invoke "tar" "xvf" "bzip2-1.0.6.tar.bz2")) | |
dc1d3cde KK |
375 | ;; Disable unpacking of tarballs in Makefile. |
376 | (substitute* "system.mk/Makefile.linux" | |
377 | (("^\tbzcat .*") "\t@echo \"not unpacking\"\n") | |
378 | (("\\./configure") "CONFIG_SHELL=bash ./configure")) | |
379 | (substitute* "third-party/zlib-1.2.7/Makefile.in" | |
380 | (("^SHELL=.*$") "SHELL=bash\n")) | |
381 | #t)) | |
382 | (delete 'configure)))) | |
8dd4ff11 RW |
383 | (home-page "https://github.com/bedops/bedops") |
384 | (synopsis "Tools for high-performance genomic feature operations") | |
385 | (description | |
386 | "BEDOPS is a suite of tools to address common questions raised in genomic | |
387 | studies---mostly with regard to overlap and proximity relationships between | |
388 | data sets. It aims to be scalable and flexible, facilitating the efficient | |
389 | and accurate analysis and management of large-scale genomic data. | |
390 | ||
391 | BEDOPS provides tools that perform highly efficient and scalable Boolean and | |
392 | other set operations, statistical calculations, archiving, conversion and | |
393 | other management of genomic data of arbitrary scale. Tasks can be easily | |
394 | split by chromosome for distributing whole-genome analyses across a | |
395 | computational cluster.") | |
396 | (license license:gpl2+))) | |
397 | ||
81de5647 RW |
398 | (define-public bedtools |
399 | (package | |
400 | (name "bedtools") | |
6098a386 | 401 | (version "2.27.1") |
81de5647 RW |
402 | (source (origin |
403 | (method url-fetch) | |
0d9824cc RW |
404 | (uri (string-append "https://github.com/arq5x/bedtools2/releases/" |
405 | "download/v" version "/" | |
406 | "bedtools-" version ".tar.gz")) | |
81de5647 RW |
407 | (sha256 |
408 | (base32 | |
6098a386 | 409 | "1ndg5yknrxl4djx8ddzgk12rrbiidfpmkkg5z3f95jzryfxarhn8")))) |
81de5647 | 410 | (build-system gnu-build-system) |
81de5647 RW |
411 | (arguments |
412 | '(#:test-target "test" | |
0d9824cc RW |
413 | #:make-flags |
414 | (list (string-append "prefix=" (assoc-ref %outputs "out"))) | |
81de5647 | 415 | #:phases |
6573ac82 | 416 | (modify-phases %standard-phases |
0d9824cc RW |
417 | (delete 'configure)))) |
418 | (native-inputs `(("python" ,python-2))) | |
419 | (inputs | |
420 | `(("samtools" ,samtools) | |
421 | ("zlib" ,zlib))) | |
81de5647 RW |
422 | (home-page "https://github.com/arq5x/bedtools2") |
423 | (synopsis "Tools for genome analysis and arithmetic") | |
424 | (description | |
425 | "Collectively, the bedtools utilities are a swiss-army knife of tools for | |
426 | a wide-range of genomics analysis tasks. The most widely-used tools enable | |
427 | genome arithmetic: that is, set theory on the genome. For example, bedtools | |
428 | allows one to intersect, merge, count, complement, and shuffle genomic | |
429 | intervals from multiple files in widely-used genomic file formats such as BAM, | |
430 | BED, GFF/GTF, VCF.") | |
431 | (license license:gpl2))) | |
432 | ||
9a8f309c RW |
433 | ;; Later releases of bedtools produce files with more columns than |
434 | ;; what Ribotaper expects. | |
435 | (define-public bedtools-2.18 | |
436 | (package (inherit bedtools) | |
437 | (name "bedtools") | |
438 | (version "2.18.0") | |
439 | (source (origin | |
440 | (method url-fetch) | |
441 | (uri (string-append "https://github.com/arq5x/bedtools2/" | |
20ee3e8b RW |
442 | "releases/download/v" version |
443 | "/bedtools-" version ".tar.gz")) | |
9a8f309c RW |
444 | (sha256 |
445 | (base32 | |
20ee3e8b | 446 | "11rvca19ncg03kxd0wzlfx5ws7r3nisd0z8s9j9n182d8ksp2pxz")))) |
83b9d121 RW |
447 | (arguments |
448 | '(#:test-target "test" | |
449 | #:phases | |
450 | (modify-phases %standard-phases | |
451 | (delete 'configure) | |
452 | (replace 'install | |
453 | (lambda* (#:key outputs #:allow-other-keys) | |
454 | (let ((bin (string-append (assoc-ref outputs "out") "/bin/"))) | |
455 | (for-each (lambda (file) | |
456 | (install-file file bin)) | |
457 | (find-files "bin" ".*"))) | |
458 | #t))))))) | |
9a8f309c | 459 | |
129363b7 RW |
460 | ;; Needed for pybedtools. |
461 | (define-public bedtools-2.26 | |
462 | (package (inherit bedtools) | |
463 | (name "bedtools") | |
464 | (version "2.26.0") | |
465 | (source (origin | |
466 | (method url-fetch) | |
467 | (uri (string-append "https://github.com/arq5x/bedtools2/releases/" | |
468 | "download/v" version "/" | |
469 | "bedtools-" version ".tar.gz")) | |
470 | (sha256 | |
471 | (base32 | |
472 | "0jhavwifnf7lmkb11h9y7dynr8d699h0rd2l52j1pfgircr2zwv5")))))) | |
473 | ||
17dc32a4 RW |
474 | (define-public ribotaper |
475 | (package | |
476 | (name "ribotaper") | |
477 | (version "1.3.1") | |
478 | (source (origin | |
479 | (method url-fetch) | |
480 | (uri (string-append "https://ohlerlab.mdc-berlin.de/" | |
481 | "files/RiboTaper/RiboTaper_Version_" | |
482 | version ".tar.gz")) | |
483 | (sha256 | |
484 | (base32 | |
485 | "0ykjbps1y3z3085q94npw8i9x5gldc6shy8vlc08v76zljsm07hv")))) | |
486 | (build-system gnu-build-system) | |
7edee344 RW |
487 | (arguments |
488 | `(#:phases | |
489 | (modify-phases %standard-phases | |
490 | (add-after 'install 'wrap-executables | |
491 | (lambda* (#:key inputs outputs #:allow-other-keys) | |
492 | (let* ((out (assoc-ref outputs "out"))) | |
493 | (for-each | |
494 | (lambda (script) | |
495 | (wrap-program (string-append out "/bin/" script) | |
496 | `("R_LIBS_SITE" ":" = (,(getenv "R_LIBS_SITE"))))) | |
497 | '("create_annotations_files.bash" | |
498 | "create_metaplots.bash" | |
499 | "Ribotaper_ORF_find.sh" | |
2e0f6905 MW |
500 | "Ribotaper.sh"))) |
501 | #t))))) | |
17dc32a4 RW |
502 | (inputs |
503 | `(("bedtools" ,bedtools-2.18) | |
504 | ("samtools" ,samtools-0.1) | |
2d7c4ae3 | 505 | ("r-minimal" ,r-minimal) |
17dc32a4 RW |
506 | ("r-foreach" ,r-foreach) |
507 | ("r-xnomial" ,r-xnomial) | |
508 | ("r-domc" ,r-domc) | |
509 | ("r-multitaper" ,r-multitaper) | |
510 | ("r-seqinr" ,r-seqinr))) | |
511 | (home-page "https://ohlerlab.mdc-berlin.de/software/RiboTaper_126/") | |
512 | (synopsis "Define translated ORFs using ribosome profiling data") | |
513 | (description | |
514 | "Ribotaper is a method for defining translated @dfn{open reading | |
515 | frames} (ORFs) using ribosome profiling (ribo-seq) data. This package | |
516 | provides the Ribotaper pipeline.") | |
517 | (license license:gpl3+))) | |
518 | ||
769fc6bb RW |
519 | (define-public ribodiff |
520 | (package | |
521 | (name "ribodiff") | |
522 | (version "0.2.2") | |
523 | (source | |
524 | (origin | |
7ca49ab5 RW |
525 | (method git-fetch) |
526 | (uri (git-reference | |
527 | (url "https://github.com/ratschlab/RiboDiff.git") | |
528 | (commit (string-append "v" version)))) | |
529 | (file-name (git-file-name name version)) | |
769fc6bb RW |
530 | (sha256 |
531 | (base32 | |
7ca49ab5 | 532 | "0x75nlp7qnmm64jasbi6l21f2cy99r2cjyl6b4hr8zf2bq22drnz")))) |
769fc6bb RW |
533 | (build-system python-build-system) |
534 | (arguments | |
535 | `(#:python ,python-2 | |
536 | #:phases | |
537 | (modify-phases %standard-phases | |
538 | ;; Generate an installable executable script wrapper. | |
539 | (add-after 'unpack 'patch-setup.py | |
540 | (lambda _ | |
541 | (substitute* "setup.py" | |
542 | (("^(.*)packages=.*" line prefix) | |
543 | (string-append line "\n" | |
544 | prefix "scripts=['scripts/TE.py'],\n"))) | |
545 | #t))))) | |
546 | (inputs | |
547 | `(("python-numpy" ,python2-numpy) | |
548 | ("python-matplotlib" ,python2-matplotlib) | |
549 | ("python-scipy" ,python2-scipy) | |
550 | ("python-statsmodels" ,python2-statsmodels))) | |
2bb12f5a MB |
551 | (native-inputs |
552 | `(("python-mock" ,python2-mock) | |
553 | ("python-nose" ,python2-nose))) | |
769fc6bb RW |
554 | (home-page "http://public.bmi.inf.ethz.ch/user/zhongy/RiboDiff/") |
555 | (synopsis "Detect translation efficiency changes from ribosome footprints") | |
556 | (description "RiboDiff is a statistical tool that detects the protein | |
557 | translational efficiency change from Ribo-Seq (ribosome footprinting) and | |
558 | RNA-Seq data. It uses a generalized linear model to detect genes showing | |
559 | difference in translational profile taking mRNA abundance into account. It | |
560 | facilitates us to decipher the translational regulation that behave | |
561 | independently with transcriptional regulation.") | |
562 | (license license:gpl3+))) | |
563 | ||
a0a71439 RJ |
564 | (define-public bioawk |
565 | (package | |
566 | (name "bioawk") | |
567 | (version "1.0") | |
568 | (source (origin | |
383cb7b8 RW |
569 | (method git-fetch) |
570 | (uri (git-reference | |
571 | (url "https://github.com/lh3/bioawk.git") | |
572 | (commit (string-append "v" version)))) | |
573 | (file-name (git-file-name name version)) | |
574 | (sha256 | |
575 | (base32 | |
576 | "1pxc3zdnirxbf9a0az698hd8xdik7qkhypm7v6hn922x8y9qmspm")))) | |
a0a71439 RJ |
577 | (build-system gnu-build-system) |
578 | (inputs | |
579 | `(("zlib" ,zlib))) | |
580 | (native-inputs | |
581 | `(("bison" ,bison))) | |
582 | (arguments | |
583 | `(#:tests? #f ; There are no tests to run. | |
584 | ;; Bison must generate files, before other targets can build. | |
585 | #:parallel-build? #f | |
586 | #:phases | |
587 | (modify-phases %standard-phases | |
588 | (delete 'configure) ; There is no configure phase. | |
589 | (replace 'install | |
383cb7b8 RW |
590 | (lambda* (#:key outputs #:allow-other-keys) |
591 | (let* ((out (assoc-ref outputs "out")) | |
592 | (bin (string-append out "/bin")) | |
593 | (man (string-append out "/share/man/man1"))) | |
594 | (mkdir-p man) | |
595 | (copy-file "awk.1" (string-append man "/bioawk.1")) | |
2e0f6905 MW |
596 | (install-file "bioawk" bin)) |
597 | #t))))) | |
a0a71439 RJ |
598 | (home-page "https://github.com/lh3/bioawk") |
599 | (synopsis "AWK with bioinformatics extensions") | |
600 | (description "Bioawk is an extension to Brian Kernighan's awk, adding the | |
601 | support of several common biological data formats, including optionally gzip'ed | |
602 | BED, GFF, SAM, VCF, FASTA/Q and TAB-delimited formats with column names. It | |
603 | also adds a few built-in functions and a command line option to use TAB as the | |
604 | input/output delimiter. When the new functionality is not used, bioawk is | |
605 | intended to behave exactly the same as the original BWK awk.") | |
606 | (license license:x11))) | |
607 | ||
895cf827 | 608 | (define-public python-pybedtools |
a2fb1492 | 609 | (package |
895cf827 RW |
610 | (name "python-pybedtools") |
611 | (version "0.7.10") | |
a2fb1492 RW |
612 | (source (origin |
613 | (method url-fetch) | |
895cf827 | 614 | (uri (pypi-uri "pybedtools" version)) |
a2fb1492 RW |
615 | (sha256 |
616 | (base32 | |
895cf827 | 617 | "0l2b2wrnj85azfqgr0zwr60f7j58vlla1hcgxvr9rwikpl8j72ji")))) |
a2fb1492 | 618 | (build-system python-build-system) |
895cf827 RW |
619 | (arguments |
620 | `(#:phases | |
621 | (modify-phases %standard-phases | |
622 | ;; See https://github.com/daler/pybedtools/issues/261 | |
623 | (add-after 'unpack 'disable-broken-tests | |
624 | (lambda _ | |
625 | ;; This test (pybedtools.test.test_scripts.test_venn_mpl) needs a | |
626 | ;; graphical environment. | |
627 | (substitute* "pybedtools/test/test_scripts.py" | |
628 | (("def test_venn_mpl") | |
629 | "def _do_not_test_venn_mpl")) | |
630 | ;; Requires internet access. | |
631 | (substitute* "pybedtools/test/test_helpers.py" | |
632 | (("def test_chromsizes") | |
633 | "def _do_not_test_chromsizes")) | |
634 | ;; FIXME: these two fail for no good reason. | |
635 | (substitute* "pybedtools/test/test1.py" | |
636 | (("def test_issue_157") | |
637 | "def _do_not_test_issue_157") | |
638 | (("def test_to_dataframe") | |
639 | "def _do_not_test_to_dataframe")) | |
640 | #t))))) | |
a2fb1492 | 641 | (propagated-inputs |
895cf827 RW |
642 | ;; Tests don't pass with Bedtools 2.27.1. |
643 | ;; See https://github.com/daler/pybedtools/issues/260 | |
644 | `(("bedtools" ,bedtools-2.26) | |
645 | ("samtools" ,samtools) | |
646 | ("python-matplotlib" ,python-matplotlib) | |
647 | ("python-pysam" ,python-pysam) | |
648 | ("python-pyyaml" ,python-pyyaml))) | |
a2fb1492 | 649 | (native-inputs |
895cf827 RW |
650 | `(("python-numpy" ,python-numpy) |
651 | ("python-pandas" ,python-pandas) | |
652 | ("python-cython" ,python-cython) | |
653 | ("python-nose" ,python-nose) | |
654 | ("kentutils" ,kentutils) ; for bedGraphToBigWig | |
655 | ("python-six" ,python-six))) | |
a2fb1492 RW |
656 | (home-page "https://pythonhosted.org/pybedtools/") |
657 | (synopsis "Python wrapper for BEDtools programs") | |
658 | (description | |
659 | "pybedtools is a Python wrapper for Aaron Quinlan's BEDtools programs, | |
660 | which are widely used for genomic interval manipulation or \"genome algebra\". | |
661 | pybedtools extends BEDTools by offering feature-level manipulations from with | |
662 | Python.") | |
663 | (license license:gpl2+))) | |
664 | ||
895cf827 RW |
665 | (define-public python2-pybedtools |
666 | (let ((pkg (package-with-python2 python-pybedtools))) | |
667 | (package (inherit pkg) | |
668 | (arguments | |
669 | `(#:modules ((ice-9 ftw) | |
670 | (srfi srfi-1) | |
671 | (srfi srfi-26) | |
672 | (guix build utils) | |
673 | (guix build python-build-system)) | |
674 | ;; See https://github.com/daler/pybedtools/issues/192 | |
675 | ,@(substitute-keyword-arguments (package-arguments pkg) | |
676 | ((#:phases phases) | |
677 | `(modify-phases ,phases | |
678 | (replace 'check | |
679 | (lambda _ | |
680 | (let ((cwd (getcwd))) | |
681 | (setenv "PYTHONPATH" | |
682 | (string-append cwd "/build/" | |
683 | (find (cut string-prefix? "lib" <>) | |
684 | (scandir (string-append cwd "/build"))) | |
685 | ":" (getenv "PYTHONPATH")))) | |
686 | ;; The tests need to be run from elsewhere... | |
687 | (mkdir-p "/tmp/test") | |
688 | (copy-recursively "pybedtools/test" "/tmp/test") | |
689 | (with-directory-excursion "/tmp/test" | |
690 | (invoke "nosetests" | |
691 | ;; This test fails for unknown reasons | |
692 | "--exclude=.*test_getting_example_beds")) | |
693 | #t)))))))))) | |
694 | ||
9e12eba8 BW |
695 | (define-public python-biom-format |
696 | (package | |
007a81d5 | 697 | (name "python-biom-format") |
239716fb | 698 | (version "2.1.7") |
007a81d5 RW |
699 | (source |
700 | (origin | |
701 | (method git-fetch) | |
702 | ;; Use GitHub as source because PyPI distribution does not contain | |
703 | ;; test data: https://github.com/biocore/biom-format/issues/693 | |
704 | (uri (git-reference | |
705 | (url "https://github.com/biocore/biom-format.git") | |
706 | (commit version))) | |
707 | (file-name (git-file-name name version)) | |
708 | (sha256 | |
709 | (base32 | |
239716fb | 710 | "1rna16lyk5aqhnv0dp77wwaplias93f1vw28ad3jmyw6hwkai05v")))) |
007a81d5 | 711 | (build-system python-build-system) |
239716fb RW |
712 | (arguments |
713 | `(#:phases | |
714 | (modify-phases %standard-phases | |
715 | (add-after 'unpack 'use-cython | |
716 | (lambda _ (setenv "USE_CYTHON" "1") #t)) | |
717 | (add-after 'unpack 'disable-broken-test | |
718 | (lambda _ | |
719 | (substitute* "biom/tests/test_cli/test_validate_table.py" | |
720 | (("^(.+)def test_invalid_hdf5" m indent) | |
721 | (string-append indent | |
722 | "@npt.dec.skipif(True, msg='Guix')\n" | |
723 | m))) | |
724 | #t)) | |
725 | (add-before 'reset-gzip-timestamps 'make-files-writable | |
726 | (lambda* (#:key outputs #:allow-other-keys) | |
727 | (let ((out (assoc-ref outputs "out"))) | |
728 | (for-each (lambda (file) (chmod file #o644)) | |
729 | (find-files out "\\.gz")) | |
730 | #t)))))) | |
007a81d5 RW |
731 | (propagated-inputs |
732 | `(("python-numpy" ,python-numpy) | |
733 | ("python-scipy" ,python-scipy) | |
239716fb | 734 | ("python-flake8" ,python-flake8) |
007a81d5 RW |
735 | ("python-future" ,python-future) |
736 | ("python-click" ,python-click) | |
737 | ("python-h5py" ,python-h5py) | |
738 | ("python-pandas" ,python-pandas))) | |
739 | (native-inputs | |
239716fb RW |
740 | `(("python-cython" ,python-cython) |
741 | ("python-pytest" ,python-pytest) | |
742 | ("python-pytest-cov" ,python-pytest-cov) | |
743 | ("python-nose" ,python-nose))) | |
007a81d5 RW |
744 | (home-page "http://www.biom-format.org") |
745 | (synopsis "Biological Observation Matrix (BIOM) format utilities") | |
746 | (description | |
747 | "The BIOM file format is designed to be a general-use format for | |
9e12eba8 BW |
748 | representing counts of observations e.g. operational taxonomic units, KEGG |
749 | orthology groups or lipid types, in one or more biological samples | |
750 | e.g. microbiome samples, genomes, metagenomes.") | |
007a81d5 RW |
751 | (license license:bsd-3) |
752 | (properties `((python2-variant . ,(delay python2-biom-format)))))) | |
9e12eba8 BW |
753 | |
754 | (define-public python2-biom-format | |
755 | (let ((base (package-with-python2 (strip-python2-variant python-biom-format)))) | |
756 | (package | |
757 | (inherit base) | |
758 | (arguments | |
d9ba126d RW |
759 | (substitute-keyword-arguments (package-arguments base) |
760 | ((#:phases phases) | |
761 | `(modify-phases ,phases | |
762 | ;; Do not require the unmaintained pyqi library. | |
763 | (add-after 'unpack 'remove-pyqi | |
764 | (lambda _ | |
765 | (substitute* "setup.py" | |
766 | (("install_requires.append\\(\"pyqi\"\\)") "pass")) | |
767 | #t))))))))) | |
9e12eba8 | 768 | |
f7283db3 RW |
769 | (define-public bioperl-minimal |
770 | (let* ((inputs `(("perl-module-build" ,perl-module-build) | |
771 | ("perl-data-stag" ,perl-data-stag) | |
772 | ("perl-libwww" ,perl-libwww) | |
773 | ("perl-uri" ,perl-uri))) | |
774 | (transitive-inputs | |
775 | (map (compose package-name cadr) | |
776 | (delete-duplicates | |
777 | (concatenate | |
778 | (map (compose package-transitive-target-inputs cadr) inputs)))))) | |
779 | (package | |
780 | (name "bioperl-minimal") | |
c70271ec | 781 | (version "1.7.0") |
f7283db3 RW |
782 | (source |
783 | (origin | |
784 | (method url-fetch) | |
c70271ec RW |
785 | (uri (string-append "https://github.com/bioperl/bioperl-live/" |
786 | "archive/release-" | |
787 | (string-map (lambda (c) | |
788 | (if (char=? c #\.) | |
789 | #\- c)) version) | |
790 | ".tar.gz")) | |
f7283db3 RW |
791 | (sha256 |
792 | (base32 | |
c70271ec | 793 | "12phgpxwgkqflkwfb9dcqg7a31dpjlfhar8wcgv0aj5ln4akfz06")))) |
f7283db3 RW |
794 | (build-system perl-build-system) |
795 | (arguments | |
796 | `(#:phases | |
797 | (modify-phases %standard-phases | |
798 | (add-after | |
799 | 'install 'wrap-programs | |
800 | (lambda* (#:key outputs #:allow-other-keys) | |
801 | ;; Make sure all executables in "bin" find the required Perl | |
802 | ;; modules at runtime. As the PERL5LIB variable contains also | |
803 | ;; the paths of native inputs, we pick the transitive target | |
804 | ;; inputs from %build-inputs. | |
805 | (let* ((out (assoc-ref outputs "out")) | |
806 | (bin (string-append out "/bin/")) | |
807 | (path (string-join | |
808 | (cons (string-append out "/lib/perl5/site_perl") | |
809 | (map (lambda (name) | |
810 | (assoc-ref %build-inputs name)) | |
811 | ',transitive-inputs)) | |
812 | ":"))) | |
813 | (for-each (lambda (file) | |
814 | (wrap-program file | |
815 | `("PERL5LIB" ":" prefix (,path)))) | |
816 | (find-files bin "\\.pl$")) | |
817 | #t)))))) | |
818 | (inputs inputs) | |
819 | (native-inputs | |
820 | `(("perl-test-most" ,perl-test-most))) | |
9aba9b12 | 821 | (home-page "https://metacpan.org/release/BioPerl") |
f7283db3 RW |
822 | (synopsis "Bioinformatics toolkit") |
823 | (description | |
824 | "BioPerl is the product of a community effort to produce Perl code which | |
825 | is useful in biology. Examples include Sequence objects, Alignment objects | |
826 | and database searching objects. These objects not only do what they are | |
827 | advertised to do in the documentation, but they also interact - Alignment | |
828 | objects are made from the Sequence objects, Sequence objects have access to | |
829 | Annotation and SeqFeature objects and databases, Blast objects can be | |
830 | converted to Alignment objects, and so on. This means that the objects | |
831 | provide a coordinated and extensible framework to do computational biology.") | |
2f3108ad | 832 | (license license:perl-license)))) |
f7283db3 | 833 | |
85c37e29 RW |
834 | (define-public python-biopython |
835 | (package | |
836 | (name "python-biopython") | |
af6ce610 | 837 | (version "1.70") |
85c37e29 RW |
838 | (source (origin |
839 | (method url-fetch) | |
e815c094 BW |
840 | ;; use PyPi rather than biopython.org to ease updating |
841 | (uri (pypi-uri "biopython" version)) | |
85c37e29 RW |
842 | (sha256 |
843 | (base32 | |
af6ce610 | 844 | "0nz4n9d2y2dg849gn1z0vjlkwcpzzkzy3fij7x94a6ixy2c54z2a")))) |
85c37e29 | 845 | (build-system python-build-system) |
4ce60305 BW |
846 | (arguments |
847 | `(#:phases | |
848 | (modify-phases %standard-phases | |
849 | (add-before 'check 'set-home | |
850 | ;; Some tests require a home directory to be set. | |
851 | (lambda _ (setenv "HOME" "/tmp") #t))))) | |
f22efa01 | 852 | (propagated-inputs |
85c37e29 | 853 | `(("python-numpy" ,python-numpy))) |
85c37e29 RW |
854 | (home-page "http://biopython.org/") |
855 | (synopsis "Tools for biological computation in Python") | |
856 | (description | |
857 | "Biopython is a set of tools for biological computation including parsers | |
858 | for bioinformatics files into Python data structures; interfaces to common | |
859 | bioinformatics programs; a standard sequence class and tools for performing | |
860 | common operations on them; code to perform data classification; code for | |
861 | dealing with alignments; code making it easy to split up parallelizable tasks | |
862 | into separate processes; and more.") | |
5c31f4aa | 863 | (license (license:non-copyleft "http://www.biopython.org/DIST/LICENSE")))) |
85c37e29 RW |
864 | |
865 | (define-public python2-biopython | |
5c31f4aa | 866 | (package-with-python2 python-biopython)) |
85c37e29 | 867 | |
5d5a02dd BW |
868 | (define-public python-fastalite |
869 | (package | |
870 | (name "python-fastalite") | |
871 | (version "0.3") | |
872 | (source | |
873 | (origin | |
874 | (method url-fetch) | |
875 | (uri (pypi-uri "fastalite" version)) | |
876 | (sha256 | |
877 | (base32 | |
878 | "1qli6pxp77i9xn2wfciq2zaxhl82bdxb33cpzqzj1z25yd036wqj")))) | |
879 | (build-system python-build-system) | |
880 | (arguments | |
881 | `(#:tests? #f)) ; Test data is not distributed. | |
882 | (home-page "https://github.com/nhoffman/fastalite") | |
883 | (synopsis "Simplest possible FASTA parser") | |
884 | (description "This library implements a FASTA and a FASTQ parser without | |
885 | relying on a complex dependency tree.") | |
886 | (license license:expat))) | |
887 | ||
888 | (define-public python2-fastalite | |
889 | (package-with-python2 python-fastalite)) | |
890 | ||
985d8411 BW |
891 | (define-public bpp-core |
892 | ;; The last release was in 2014 and the recommended way to install from source | |
893 | ;; is to clone the git repository, so we do this. | |
894 | ;; http://biopp.univ-montp2.fr/wiki/index.php/Main_Page | |
895 | (let ((commit "7d8bced0d1a87291ea8dd7046b7fb5ff9c35c582")) | |
896 | (package | |
897 | (name "bpp-core") | |
898 | (version (string-append "2.2.0-1." (string-take commit 7))) | |
899 | (source (origin | |
900 | (method git-fetch) | |
901 | (uri (git-reference | |
902 | (url "http://biopp.univ-montp2.fr/git/bpp-core") | |
903 | (commit commit))) | |
904 | (file-name (string-append name "-" version "-checkout")) | |
905 | (sha256 | |
906 | (base32 | |
907 | "10djsq5vlnkilv436gnmh4irpk49v29pa69r6xiryg32xmvn909j")))) | |
908 | (build-system cmake-build-system) | |
909 | (arguments | |
910 | `(#:parallel-build? #f)) | |
911 | (inputs | |
912 | `(("gcc" ,gcc-5))) ; Compilation of bpp-phyl fails with GCC 4.9 so we | |
913 | ; compile all of the bpp packages with GCC 5. | |
914 | (home-page "http://biopp.univ-montp2.fr") | |
915 | (synopsis "C++ libraries for Bioinformatics") | |
916 | (description | |
917 | "Bio++ is a set of C++ libraries for Bioinformatics, including sequence | |
918 | analysis, phylogenetics, molecular evolution and population genetics. It is | |
919 | Object Oriented and is designed to be both easy to use and computer efficient. | |
920 | Bio++ intends to help programmers to write computer expensive programs, by | |
921 | providing them a set of re-usable tools.") | |
922 | (license license:cecill-c)))) | |
923 | ||
8b5f4d57 BW |
924 | (define-public bpp-phyl |
925 | ;; The last release was in 2014 and the recommended way to install from source | |
926 | ;; is to clone the git repository, so we do this. | |
927 | ;; http://biopp.univ-montp2.fr/wiki/index.php/Main_Page | |
928 | (let ((commit "0c07167b629f68b569bf274d1ad0c4af83276ae2")) | |
929 | (package | |
930 | (name "bpp-phyl") | |
931 | (version (string-append "2.2.0-1." (string-take commit 7))) | |
932 | (source (origin | |
933 | (method git-fetch) | |
934 | (uri (git-reference | |
935 | (url "http://biopp.univ-montp2.fr/git/bpp-phyl") | |
936 | (commit commit))) | |
937 | (file-name (string-append name "-" version "-checkout")) | |
938 | (sha256 | |
939 | (base32 | |
940 | "1ssjgchzwj3iai26kyly7gwkdv8sk59nqhkb1wpap3sf5m6kyllh")))) | |
941 | (build-system cmake-build-system) | |
942 | (arguments | |
943 | `(#:parallel-build? #f | |
944 | ;; If out-of-source, test data is not copied into the build directory | |
945 | ;; so the tests fail. | |
946 | #:out-of-source? #f)) | |
947 | (inputs | |
948 | `(("bpp-core" ,bpp-core) | |
949 | ("bpp-seq" ,bpp-seq) | |
950 | ;; GCC 4.8 fails due to an 'internal compiler error', so we use a more | |
951 | ;; modern GCC. | |
952 | ("gcc" ,gcc-5))) | |
953 | (home-page "http://biopp.univ-montp2.fr") | |
954 | (synopsis "Bio++ phylogenetic Library") | |
955 | (description | |
956 | "Bio++ is a set of C++ libraries for Bioinformatics, including sequence | |
957 | analysis, phylogenetics, molecular evolution and population genetics. This | |
958 | library provides phylogenetics-related modules.") | |
959 | (license license:cecill-c)))) | |
960 | ||
159a7016 BW |
961 | (define-public bpp-popgen |
962 | ;; The last release was in 2014 and the recommended way to install from source | |
963 | ;; is to clone the git repository, so we do this. | |
964 | ;; http://biopp.univ-montp2.fr/wiki/index.php/Main_Page | |
965 | (let ((commit "e472bac9b1a148803895d747cd6d0c5904f85d9f")) | |
966 | (package | |
967 | (name "bpp-popgen") | |
968 | (version (string-append "2.2.0-1." (string-take commit 7))) | |
969 | (source (origin | |
970 | (method git-fetch) | |
971 | (uri (git-reference | |
972 | (url "http://biopp.univ-montp2.fr/git/bpp-popgen") | |
973 | (commit commit))) | |
974 | (file-name (string-append name "-" version "-checkout")) | |
975 | (sha256 | |
976 | (base32 | |
977 | "0yn82dzn1n5629nzja68xfrhi655709rjanyryb36vzkmymy6dw5")))) | |
978 | (build-system cmake-build-system) | |
979 | (arguments | |
980 | `(#:parallel-build? #f | |
981 | #:tests? #f)) ; There are no tests. | |
982 | (inputs | |
983 | `(("bpp-core" ,bpp-core) | |
984 | ("bpp-seq" ,bpp-seq) | |
985 | ("gcc" ,gcc-5))) | |
986 | (home-page "http://biopp.univ-montp2.fr") | |
987 | (synopsis "Bio++ population genetics library") | |
988 | (description | |
989 | "Bio++ is a set of C++ libraries for Bioinformatics, including sequence | |
990 | analysis, phylogenetics, molecular evolution and population genetics. This | |
991 | library provides population genetics-related modules.") | |
992 | (license license:cecill-c)))) | |
993 | ||
70f1bc05 BW |
994 | (define-public bpp-seq |
995 | ;; The last release was in 2014 and the recommended way to install from source | |
996 | ;; is to clone the git repository, so we do this. | |
997 | ;; http://biopp.univ-montp2.fr/wiki/index.php/Main_Page | |
998 | (let ((commit "6cfa07965ce152e5598a89df2fa80a75973bfa33")) | |
999 | (package | |
1000 | (name "bpp-seq") | |
1001 | (version (string-append "2.2.0-1." (string-take commit 7))) | |
1002 | (source (origin | |
1003 | (method git-fetch) | |
1004 | (uri (git-reference | |
1005 | (url "http://biopp.univ-montp2.fr/git/bpp-seq") | |
1006 | (commit commit))) | |
1007 | (file-name (string-append name "-" version "-checkout")) | |
1008 | (sha256 | |
1009 | (base32 | |
1010 | "1nys5jq7jqvdg40d91wsmj3q2yzy4276cp7sp44n67p468f27zf2")))) | |
1011 | (build-system cmake-build-system) | |
1012 | (arguments | |
1013 | `(#:parallel-build? #f | |
1014 | ;; If out-of-source, test data is not copied into the build directory | |
1015 | ;; so the tests fail. | |
1016 | #:out-of-source? #f)) | |
1017 | (inputs | |
1018 | `(("bpp-core" ,bpp-core) | |
1019 | ("gcc" ,gcc-5))) ; Use GCC 5 as per 'bpp-core'. | |
1020 | (home-page "http://biopp.univ-montp2.fr") | |
1021 | (synopsis "Bio++ sequence library") | |
1022 | (description | |
1023 | "Bio++ is a set of C++ libraries for Bioinformatics, including sequence | |
1024 | analysis, phylogenetics, molecular evolution and population genetics. This | |
1025 | library provides sequence-related modules.") | |
1026 | (license license:cecill-c)))) | |
1027 | ||
db7a3444 BW |
1028 | (define-public bppsuite |
1029 | ;; The last release was in 2014 and the recommended way to install from source | |
1030 | ;; is to clone the git repository, so we do this. | |
1031 | ;; http://biopp.univ-montp2.fr/wiki/index.php/Main_Page | |
1032 | (let ((commit "c516147f57aa50961121cd505bed52cd7603698b")) | |
1033 | (package | |
1034 | (name "bppsuite") | |
1035 | (version (string-append "2.2.0-1." (string-take commit 7))) | |
1036 | (source (origin | |
1037 | (method git-fetch) | |
1038 | (uri (git-reference | |
1039 | (url "http://biopp.univ-montp2.fr/git/bppsuite") | |
1040 | (commit commit))) | |
1041 | (file-name (string-append name "-" version "-checkout")) | |
1042 | (sha256 | |
1043 | (base32 | |
1044 | "1y87pxvw0jxjizhq2dr9g2r91md45k1p9ih2sl1yy1y3p934l2kb")))) | |
1045 | (build-system cmake-build-system) | |
1046 | (arguments | |
1047 | `(#:parallel-build? #f | |
1048 | #:tests? #f)) ; There are no tests. | |
1049 | (native-inputs | |
1050 | `(("groff" ,groff) | |
1051 | ("man-db" ,man-db) | |
1052 | ("texinfo" ,texinfo))) | |
1053 | (inputs | |
1054 | `(("bpp-core" ,bpp-core) | |
1055 | ("bpp-seq" ,bpp-seq) | |
1056 | ("bpp-phyl" ,bpp-phyl) | |
1057 | ("bpp-phyl" ,bpp-popgen) | |
1058 | ("gcc" ,gcc-5))) | |
1059 | (home-page "http://biopp.univ-montp2.fr") | |
1060 | (synopsis "Bioinformatics tools written with the Bio++ libraries") | |
1061 | (description | |
1062 | "Bio++ is a set of C++ libraries for Bioinformatics, including sequence | |
1063 | analysis, phylogenetics, molecular evolution and population genetics. This | |
1064 | package provides command line tools using the Bio++ library.") | |
1065 | (license license:cecill-c)))) | |
1066 | ||
82c370de RW |
1067 | (define-public blast+ |
1068 | (package | |
1069 | (name "blast+") | |
4732e6ee | 1070 | (version "2.6.0") |
82c370de RW |
1071 | (source (origin |
1072 | (method url-fetch) | |
1073 | (uri (string-append | |
1074 | "ftp://ftp.ncbi.nlm.nih.gov/blast/executables/blast+/" | |
1075 | version "/ncbi-blast-" version "+-src.tar.gz")) | |
1076 | (sha256 | |
1077 | (base32 | |
4732e6ee BW |
1078 | "15n937pw5aqmyfjb6l387d18grqbb96l63d5xj4l7yyh0zbf2405")) |
1079 | (patches (search-patches "blast+-fix-makefile.patch")) | |
82c370de RW |
1080 | (modules '((guix build utils))) |
1081 | (snippet | |
1082 | '(begin | |
4732e6ee | 1083 | ;; Remove bundled bzip2, zlib and pcre. |
82c370de RW |
1084 | (delete-file-recursively "c++/src/util/compress/bzip2") |
1085 | (delete-file-recursively "c++/src/util/compress/zlib") | |
4732e6ee | 1086 | (delete-file-recursively "c++/src/util/regexp") |
82c370de RW |
1087 | (substitute* "c++/src/util/compress/Makefile.in" |
1088 | (("bzip2 zlib api") "api")) | |
1089 | ;; Remove useless msbuild directory | |
1090 | (delete-file-recursively | |
1091 | "c++/src/build-system/project_tree_builder/msbuild") | |
1092 | #t)))) | |
1093 | (build-system gnu-build-system) | |
1094 | (arguments | |
4732e6ee | 1095 | `(;; There are two(!) tests for this massive library, and both fail with |
82c370de | 1096 | ;; "unparsable timing stats". |
82c370de RW |
1097 | ;; ERR [127] -- [serial/datatool] datatool.sh (unparsable timing stats) |
1098 | ;; ERR [127] -- [serial/datatool] datatool_xml.sh (unparsable timing stats) | |
1099 | #:tests? #f | |
1100 | #:out-of-source? #t | |
1101 | #:parallel-build? #f ; not supported | |
1102 | #:phases | |
1103 | (modify-phases %standard-phases | |
f4509342 | 1104 | (add-before 'configure 'set-HOME |
82c370de RW |
1105 | ;; $HOME needs to be set at some point during the configure phase |
1106 | (lambda _ (setenv "HOME" "/tmp") #t)) | |
f4509342 | 1107 | (add-after 'unpack 'enter-dir |
82c370de | 1108 | (lambda _ (chdir "c++") #t)) |
f4509342 | 1109 | (add-after 'enter-dir 'fix-build-system |
82c370de RW |
1110 | (lambda _ |
1111 | (define (which* cmd) | |
1112 | (cond ((string=? cmd "date") | |
1113 | ;; make call to "date" deterministic | |
1114 | "date -d @0") | |
1115 | ((which cmd) | |
1116 | => identity) | |
1117 | (else | |
1118 | (format (current-error-port) | |
1119 | "WARNING: Unable to find absolute path for ~s~%" | |
1120 | cmd) | |
1121 | #f))) | |
1122 | ||
1123 | ;; Rewrite hardcoded paths to various tools | |
1124 | (substitute* (append '("src/build-system/configure.ac" | |
1125 | "src/build-system/configure" | |
4732e6ee | 1126 | "src/build-system/helpers/run_with_lock.c" |
82c370de RW |
1127 | "scripts/common/impl/if_diff.sh" |
1128 | "scripts/common/impl/run_with_lock.sh" | |
1129 | "src/build-system/Makefile.configurables.real" | |
1130 | "src/build-system/Makefile.in.top" | |
1131 | "src/build-system/Makefile.meta.gmake=no" | |
1132 | "src/build-system/Makefile.meta.in" | |
1133 | "src/build-system/Makefile.meta_l" | |
1134 | "src/build-system/Makefile.meta_p" | |
1135 | "src/build-system/Makefile.meta_r" | |
1136 | "src/build-system/Makefile.mk.in" | |
1137 | "src/build-system/Makefile.requirements" | |
1138 | "src/build-system/Makefile.rules_with_autodep.in") | |
1139 | (find-files "scripts/common/check" "\\.sh$")) | |
1140 | (("(/usr/bin/|/bin/)([a-z][-_.a-z]*)" all dir cmd) | |
1141 | (or (which* cmd) all))) | |
1142 | ||
1143 | (substitute* (find-files "src/build-system" "^config.*") | |
1144 | (("LN_S=/bin/\\$LN_S") (string-append "LN_S=" (which "ln"))) | |
1145 | (("^PATH=.*") "")) | |
1146 | ||
1147 | ;; rewrite "/var/tmp" in check script | |
1148 | (substitute* "scripts/common/check/check_make_unix.sh" | |
1149 | (("/var/tmp") "/tmp")) | |
1150 | ||
1151 | ;; do not reset PATH | |
1152 | (substitute* (find-files "scripts/common/impl/" "\\.sh$") | |
1153 | (("^ *PATH=.*") "") | |
1154 | (("action=/bin/") "action=") | |
1155 | (("export PATH") ":")) | |
1156 | #t)) | |
f4509342 RW |
1157 | (replace 'configure |
1158 | (lambda* (#:key inputs outputs #:allow-other-keys) | |
1159 | (let ((out (assoc-ref outputs "out")) | |
1160 | (lib (string-append (assoc-ref outputs "lib") "/lib")) | |
1161 | (include (string-append (assoc-ref outputs "include") | |
1162 | "/include/ncbi-tools++"))) | |
1163 | ;; The 'configure' script doesn't recognize things like | |
1164 | ;; '--enable-fast-install'. | |
1165 | (invoke "./configure.orig" | |
1166 | (string-append "--with-build-root=" (getcwd) "/build") | |
1167 | (string-append "--prefix=" out) | |
1168 | (string-append "--libdir=" lib) | |
1169 | (string-append "--includedir=" include) | |
1170 | (string-append "--with-bz2=" | |
1171 | (assoc-ref inputs "bzip2")) | |
1172 | (string-append "--with-z=" | |
1173 | (assoc-ref inputs "zlib")) | |
1174 | (string-append "--with-pcre=" | |
1175 | (assoc-ref inputs "pcre")) | |
1176 | ;; Each library is built twice by default, once | |
1177 | ;; with "-static" in its name, and again | |
1178 | ;; without. | |
1179 | "--without-static" | |
1180 | "--with-dll") | |
1181 | #t)))))) | |
4732e6ee BW |
1182 | (outputs '("out" ; 21 MB |
1183 | "lib" ; 226 MB | |
1184 | "include")) ; 33 MB | |
82c370de RW |
1185 | (inputs |
1186 | `(("bzip2" ,bzip2) | |
4732e6ee BW |
1187 | ("zlib" ,zlib) |
1188 | ("pcre" ,pcre) | |
1189 | ("perl" ,perl) | |
1190 | ("python" ,python-wrapper))) | |
82c370de RW |
1191 | (native-inputs |
1192 | `(("cpio" ,cpio))) | |
1193 | (home-page "http://blast.ncbi.nlm.nih.gov") | |
1194 | (synopsis "Basic local alignment search tool") | |
1195 | (description | |
1196 | "BLAST is a popular method of performing a DNA or protein sequence | |
1197 | similarity search, using heuristics to produce results quickly. It also | |
1198 | calculates an “expect value” that estimates how many matches would have | |
1199 | occurred at a given score by chance, which can aid a user in judging how much | |
1200 | confidence to have in an alignment.") | |
1201 | ;; Most of the sources are in the public domain, with the following | |
1202 | ;; exceptions: | |
1203 | ;; * Expat: | |
1204 | ;; * ./c++/include/util/bitset/ | |
1205 | ;; * ./c++/src/html/ncbi_menu*.js | |
1206 | ;; * Boost license: | |
1207 | ;; * ./c++/include/util/impl/floating_point_comparison.hpp | |
1208 | ;; * LGPL 2+: | |
1209 | ;; * ./c++/include/dbapi/driver/odbc/unix_odbc/ | |
1210 | ;; * ASL 2.0: | |
1211 | ;; * ./c++/src/corelib/teamcity_* | |
1212 | (license (list license:public-domain | |
1213 | license:expat | |
1214 | license:boost1.0 | |
1215 | license:lgpl2.0+ | |
1216 | license:asl2.0)))) | |
1217 | ||
6c2b26e2 RW |
1218 | (define-public bless |
1219 | (package | |
1220 | (name "bless") | |
1221 | (version "1p02") | |
1222 | (source (origin | |
1223 | (method url-fetch) | |
1224 | (uri (string-append "mirror://sourceforge/bless-ec/bless.v" | |
1225 | version ".tgz")) | |
1226 | (sha256 | |
1227 | (base32 | |
4d75e03a RW |
1228 | "0rm0gw2s18dqwzzpl3c2x1z05ni2v0xz5dmfk3d33j6g4cgrlrdd")) |
1229 | (modules '((guix build utils))) | |
6c2b26e2 RW |
1230 | (snippet |
1231 | `(begin | |
1232 | ;; Remove bundled boost, pigz, zlib, and .git directory | |
953c1223 RW |
1233 | ;; FIXME: also remove bundled sources for murmurhash3 and |
1234 | ;; kmc once packaged. | |
6c2b26e2 RW |
1235 | (delete-file-recursively "boost") |
1236 | (delete-file-recursively "pigz") | |
953c1223 | 1237 | (delete-file-recursively "google-sparsehash") |
6c2b26e2 RW |
1238 | (delete-file-recursively "zlib") |
1239 | (delete-file-recursively ".git") | |
1240 | #t)))) | |
1241 | (build-system gnu-build-system) | |
1242 | (arguments | |
1243 | '(#:tests? #f ;no "check" target | |
1244 | #:make-flags | |
1245 | (list (string-append "ZLIB=" | |
1246 | (assoc-ref %build-inputs "zlib") | |
1247 | "/lib/libz.a") | |
1248 | (string-append "LDFLAGS=" | |
1249 | (string-join '("-lboost_filesystem" | |
1250 | "-lboost_system" | |
1251 | "-lboost_iostreams" | |
1252 | "-lz" | |
1253 | "-fopenmp" | |
1254 | "-std=c++11")))) | |
1255 | #:phases | |
1256 | (modify-phases %standard-phases | |
1257 | (add-after 'unpack 'do-not-build-bundled-pigz | |
1258 | (lambda* (#:key inputs outputs #:allow-other-keys) | |
1259 | (substitute* "Makefile" | |
1260 | (("cd pigz/pigz-2.3.3; make") "")) | |
1261 | #t)) | |
1262 | (add-after 'unpack 'patch-paths-to-executables | |
1263 | (lambda* (#:key inputs outputs #:allow-other-keys) | |
1264 | (substitute* "parse_args.cpp" | |
1265 | (("kmc_binary = .*") | |
1266 | (string-append "kmc_binary = \"" | |
1267 | (assoc-ref outputs "out") | |
1268 | "/bin/kmc\";")) | |
1269 | (("pigz_binary = .*") | |
1270 | (string-append "pigz_binary = \"" | |
1271 | (assoc-ref inputs "pigz") | |
1272 | "/bin/pigz\";"))) | |
1273 | #t)) | |
1274 | (replace 'install | |
1275 | (lambda* (#:key outputs #:allow-other-keys) | |
1276 | (let ((bin (string-append (assoc-ref outputs "out") "/bin/"))) | |
1277 | (for-each (lambda (file) | |
1278 | (install-file file bin)) | |
1279 | '("bless" "kmc/bin/kmc")) | |
1280 | #t))) | |
1281 | (delete 'configure)))) | |
1282 | (native-inputs | |
1283 | `(("perl" ,perl))) | |
1284 | (inputs | |
1285 | `(("openmpi" ,openmpi) | |
1286 | ("boost" ,boost) | |
953c1223 | 1287 | ("sparsehash" ,sparsehash) |
6c2b26e2 RW |
1288 | ("pigz" ,pigz) |
1289 | ("zlib" ,zlib))) | |
9641a899 | 1290 | (supported-systems '("x86_64-linux")) |
3b3b60d0 | 1291 | (home-page "https://sourceforge.net/p/bless-ec/wiki/Home/") |
6c2b26e2 RW |
1292 | (synopsis "Bloom-filter-based error correction tool for NGS reads") |
1293 | (description | |
1294 | "@dfn{Bloom-filter-based error correction solution for high-throughput | |
1295 | sequencing reads} (BLESS) uses a single minimum-sized bloom filter is a | |
1296 | correction tool for genomic reads produced by @dfn{Next-generation | |
1297 | sequencing} (NGS). BLESS produces accurate correction results with much less | |
1298 | memory compared with previous solutions and is also able to tolerate a higher | |
1299 | false-positive rate. BLESS can extend reads like DNA assemblers to correct | |
1300 | errors at the end of reads.") | |
1301 | (license license:gpl3+))) | |
1302 | ||
2c7ee167 RW |
1303 | (define-public bowtie |
1304 | (package | |
1305 | (name "bowtie") | |
21c83740 | 1306 | (version "2.3.4.3") |
2c7ee167 | 1307 | (source (origin |
21c83740 RW |
1308 | (method git-fetch) |
1309 | (uri (git-reference | |
1310 | (url "https://github.com/BenLangmead/bowtie2.git") | |
1311 | (commit (string-append "v" version)))) | |
1312 | (file-name (git-file-name name version)) | |
2c7ee167 RW |
1313 | (sha256 |
1314 | (base32 | |
21c83740 | 1315 | "1zl3cf327y2p7p03cavymbh7b00djc7lncfaqih33n96iy9q8ibp")) |
2c7ee167 RW |
1316 | (modules '((guix build utils))) |
1317 | (snippet | |
6cbee49d MW |
1318 | '(begin |
1319 | (substitute* "Makefile" | |
1320 | ;; replace BUILD_HOST and BUILD_TIME for deterministic build | |
1321 | (("-DBUILD_HOST=.*") "-DBUILD_HOST=\"\\\"guix\\\"\"") | |
1322 | (("-DBUILD_TIME=.*") "-DBUILD_TIME=\"\\\"0\\\"\"")) | |
1323 | #t)))) | |
2c7ee167 | 1324 | (build-system gnu-build-system) |
2c7ee167 | 1325 | (arguments |
0047d26a RW |
1326 | '(#:make-flags |
1327 | (list "allall" | |
1328 | "WITH_TBB=1" | |
1329 | (string-append "prefix=" (assoc-ref %outputs "out"))) | |
2c7ee167 | 1330 | #:phases |
06e37236 BW |
1331 | (modify-phases %standard-phases |
1332 | (delete 'configure) | |
1333 | (replace 'check | |
21c83740 RW |
1334 | (lambda _ |
1335 | (invoke "perl" | |
1336 | "scripts/test/simple_tests.pl" | |
1337 | "--bowtie2=./bowtie2" | |
1338 | "--bowtie2-build=./bowtie2-build") | |
1339 | #t))))) | |
1340 | (inputs | |
1341 | `(("tbb" ,tbb) | |
1342 | ("zlib" ,zlib) | |
1343 | ("python" ,python-wrapper))) | |
1344 | (native-inputs | |
1345 | `(("perl" ,perl) | |
1346 | ("perl-clone" ,perl-clone) | |
1347 | ("perl-test-deep" ,perl-test-deep) | |
1348 | ("perl-test-simple" ,perl-test-simple))) | |
2c7ee167 RW |
1349 | (home-page "http://bowtie-bio.sourceforge.net/bowtie2/index.shtml") |
1350 | (synopsis "Fast and sensitive nucleotide sequence read aligner") | |
1351 | (description | |
1352 | "Bowtie 2 is a fast and memory-efficient tool for aligning sequencing | |
1353 | reads to long reference sequences. It is particularly good at aligning reads | |
1354 | of about 50 up to 100s or 1,000s of characters, and particularly good at | |
1355 | aligning to relatively long (e.g. mammalian) genomes. Bowtie 2 indexes the | |
1356 | genome with an FM Index to keep its memory footprint small: for the human | |
1357 | genome, its memory footprint is typically around 3.2 GB. Bowtie 2 supports | |
1358 | gapped, local, and paired-end alignment modes.") | |
241e1221 | 1359 | (supported-systems '("x86_64-linux")) |
2c7ee167 RW |
1360 | (license license:gpl3+))) |
1361 | ||
94ce537e RW |
1362 | (define-public tophat |
1363 | (package | |
1364 | (name "tophat") | |
9a6808e0 | 1365 | (version "2.1.1") |
94ce537e RW |
1366 | (source (origin |
1367 | (method url-fetch) | |
1368 | (uri (string-append | |
1369 | "http://ccb.jhu.edu/software/tophat/downloads/tophat-" | |
1370 | version ".tar.gz")) | |
1371 | (sha256 | |
1372 | (base32 | |
9a6808e0 | 1373 | "19add02kv2xhd6ihd779dr7x35ggym3jqr0m5c4315i1yfb0p11p")) |
94ce537e RW |
1374 | (modules '((guix build utils))) |
1375 | (snippet | |
1376 | '(begin | |
1377 | ;; Remove bundled SeqAn and samtools | |
9a6808e0 | 1378 | (delete-file-recursively "src/SeqAn-1.4.2") |
94ce537e RW |
1379 | (delete-file-recursively "src/samtools-0.1.18") |
1380 | #t)))) | |
1381 | (build-system gnu-build-system) | |
1382 | (arguments | |
1383 | '(#:parallel-build? #f ; not supported | |
1384 | #:phases | |
1385 | (modify-phases %standard-phases | |
1386 | (add-after 'unpack 'use-system-samtools | |
1387 | (lambda* (#:key inputs #:allow-other-keys) | |
1388 | (substitute* "src/Makefile.in" | |
1389 | (("(noinst_LIBRARIES = )\\$\\(SAMLIB\\)" _ prefix) prefix) | |
1390 | (("\\$\\(SAMPROG\\): \\$\\(SAMLIB\\)") "") | |
1391 | (("SAMPROG = samtools_0\\.1\\.18") "") | |
1392 | (("\\$\\(samtools_0_1_18_SOURCES\\)") "") | |
1393 | (("am__EXEEXT_1 = samtools_0\\.1\\.18\\$\\(EXEEXT\\)") "")) | |
1394 | (substitute* '("src/common.cpp" | |
1395 | "src/tophat.py") | |
1396 | (("samtools_0.1.18") (which "samtools"))) | |
1397 | (substitute* '("src/common.h" | |
1398 | "src/bam2fastx.cpp") | |
1399 | (("#include \"bam.h\"") "#include <samtools/bam.h>") | |
1400 | (("#include \"sam.h\"") "#include <samtools/sam.h>")) | |
1401 | (substitute* '("src/bwt_map.h" | |
1402 | "src/map2gtf.h" | |
1403 | "src/align_status.h") | |
1404 | (("#include <bam.h>") "#include <samtools/bam.h>") | |
1405 | (("#include <sam.h>") "#include <samtools/sam.h>")) | |
1406 | #t))))) | |
1407 | (inputs | |
1408 | `(("boost" ,boost) | |
1409 | ("bowtie" ,bowtie) | |
1410 | ("samtools" ,samtools-0.1) | |
1411 | ("ncurses" ,ncurses) | |
1412 | ("python" ,python-2) | |
1413 | ("perl" ,perl) | |
1414 | ("zlib" ,zlib) | |
4d93a9a3 | 1415 | ("seqan" ,seqan-1))) |
94ce537e RW |
1416 | (home-page "http://ccb.jhu.edu/software/tophat/index.shtml") |
1417 | (synopsis "Spliced read mapper for RNA-Seq data") | |
1418 | (description | |
1419 | "TopHat is a fast splice junction mapper for nucleotide sequence | |
1420 | reads produced by the RNA-Seq method. It aligns RNA-Seq reads to | |
1421 | mammalian-sized genomes using the ultra high-throughput short read | |
1422 | aligner Bowtie, and then analyzes the mapping results to identify | |
1423 | splice junctions between exons.") | |
1424 | ;; TopHat is released under the Boost Software License, Version 1.0 | |
1425 | ;; See https://github.com/infphilo/tophat/issues/11#issuecomment-121589893 | |
1426 | (license license:boost1.0))) | |
1427 | ||
9a8336d8 RW |
1428 | (define-public bwa |
1429 | (package | |
1430 | (name "bwa") | |
6f141eff | 1431 | (version "0.7.17") |
9a8336d8 RW |
1432 | (source (origin |
1433 | (method url-fetch) | |
ae6e00f6 BW |
1434 | (uri (string-append |
1435 | "https://github.com/lh3/bwa/releases/download/v" | |
1436 | version "/bwa-" version ".tar.bz2")) | |
9a8336d8 RW |
1437 | (sha256 |
1438 | (base32 | |
6f141eff | 1439 | "1zfhv2zg9v1icdlq4p9ssc8k01mca5d1bd87w71py2swfi74s6yy")))) |
9a8336d8 RW |
1440 | (build-system gnu-build-system) |
1441 | (arguments | |
1442 | '(#:tests? #f ;no "check" target | |
1443 | #:phases | |
dc1d3cde KK |
1444 | (modify-phases %standard-phases |
1445 | (replace 'install | |
1446 | (lambda* (#:key outputs #:allow-other-keys) | |
1447 | (let ((bin (string-append | |
1448 | (assoc-ref outputs "out") "/bin")) | |
1449 | (doc (string-append | |
1450 | (assoc-ref outputs "out") "/share/doc/bwa")) | |
1451 | (man (string-append | |
1452 | (assoc-ref outputs "out") "/share/man/man1"))) | |
1453 | (install-file "bwa" bin) | |
1454 | (install-file "README.md" doc) | |
1455 | (install-file "bwa.1" man)) | |
1456 | #t)) | |
1457 | ;; no "configure" script | |
1458 | (delete 'configure)))) | |
9a8336d8 | 1459 | (inputs `(("zlib" ,zlib))) |
db94f8c7 RW |
1460 | ;; Non-portable SSE instructions are used so building fails on platforms |
1461 | ;; other than x86_64. | |
1462 | (supported-systems '("x86_64-linux")) | |
9a8336d8 RW |
1463 | (home-page "http://bio-bwa.sourceforge.net/") |
1464 | (synopsis "Burrows-Wheeler sequence aligner") | |
1465 | (description | |
1466 | "BWA is a software package for mapping low-divergent sequences against a | |
1467 | large reference genome, such as the human genome. It consists of three | |
1468 | algorithms: BWA-backtrack, BWA-SW and BWA-MEM. The first algorithm is | |
1469 | designed for Illumina sequence reads up to 100bp, while the rest two for | |
1470 | longer sequences ranged from 70bp to 1Mbp. BWA-MEM and BWA-SW share similar | |
1471 | features such as long-read support and split alignment, but BWA-MEM, which is | |
1472 | the latest, is generally recommended for high-quality queries as it is faster | |
1473 | and more accurate. BWA-MEM also has better performance than BWA-backtrack for | |
1474 | 70-100bp Illumina reads.") | |
1475 | (license license:gpl3+))) | |
1476 | ||
d29150b5 RW |
1477 | (define-public bwa-pssm |
1478 | (package (inherit bwa) | |
1479 | (name "bwa-pssm") | |
1480 | (version "0.5.11") | |
1481 | (source (origin | |
1d18ee6d RW |
1482 | (method git-fetch) |
1483 | (uri (git-reference | |
1484 | (url "https://github.com/pkerpedjiev/bwa-pssm.git") | |
1485 | (commit version))) | |
1486 | (file-name (git-file-name name version)) | |
d29150b5 RW |
1487 | (sha256 |
1488 | (base32 | |
1d18ee6d | 1489 | "076c4q0cdqz8jgylb067y9zmvxglppnzi3qiscn0xiypgc6lgb5r")))) |
d29150b5 RW |
1490 | (build-system gnu-build-system) |
1491 | (inputs | |
1492 | `(("gdsl" ,gdsl) | |
1493 | ("zlib" ,zlib) | |
1494 | ("perl" ,perl))) | |
1495 | (home-page "http://bwa-pssm.binf.ku.dk/") | |
1496 | (synopsis "Burrows-Wheeler transform-based probabilistic short read mapper") | |
1497 | (description | |
1498 | "BWA-PSSM is a probabilistic short genomic sequence read aligner based on | |
1499 | the use of @dfn{position specific scoring matrices} (PSSM). Like many of the | |
1500 | existing aligners it is fast and sensitive. Unlike most other aligners, | |
1501 | however, it is also adaptible in the sense that one can direct the alignment | |
1502 | based on known biases within the data set. It is coded as a modification of | |
1503 | the original BWA alignment program and shares the genome index structure as | |
1504 | well as many of the command line options.") | |
1505 | (license license:gpl3+))) | |
1506 | ||
f5cec006 | 1507 | (define-public python-bx-python |
ad641d53 | 1508 | (package |
f5cec006 | 1509 | (name "python-bx-python") |
2ba2d62c | 1510 | (version "0.8.2") |
ad641d53 RW |
1511 | (source (origin |
1512 | (method url-fetch) | |
c1dfe8c3 | 1513 | (uri (pypi-uri "bx-python" version)) |
ad641d53 RW |
1514 | (sha256 |
1515 | (base32 | |
2ba2d62c | 1516 | "11kksg2rbzihpmcid823xvg42xi88m7sz58rzk29abybkxy0rszs")))) |
ad641d53 | 1517 | (build-system python-build-system) |
f5cec006 RW |
1518 | ;; Tests fail because test data are not included |
1519 | (arguments '(#:tests? #f)) | |
2ba2d62c | 1520 | (propagated-inputs |
f5cec006 RW |
1521 | `(("python-numpy" ,python-numpy) |
1522 | ("python-six" ,python-six))) | |
2ba2d62c RW |
1523 | (inputs |
1524 | `(("zlib" ,zlib))) | |
ad641d53 | 1525 | (native-inputs |
f5cec006 RW |
1526 | `(("python-lzo" ,python-lzo) |
1527 | ("python-nose" ,python-nose) | |
1528 | ("python-cython" ,python-cython))) | |
2ba2d62c | 1529 | (home-page "https://github.com/bxlab/bx-python") |
ad641d53 RW |
1530 | (synopsis "Tools for manipulating biological data") |
1531 | (description | |
1532 | "bx-python provides tools for manipulating biological data, particularly | |
1533 | multiple sequence alignments.") | |
1534 | (license license:expat))) | |
1535 | ||
f5cec006 RW |
1536 | (define-public python2-bx-python |
1537 | (package-with-python2 python-bx-python)) | |
1538 | ||
55a9a8c2 RW |
1539 | (define-public python-pysam |
1540 | (package | |
1541 | (name "python-pysam") | |
939882f7 | 1542 | (version "0.15.1") |
d454640c | 1543 | (source (origin |
939882f7 | 1544 | (method git-fetch) |
f536dce5 | 1545 | ;; Test data is missing on PyPi. |
939882f7 RW |
1546 | (uri (git-reference |
1547 | (url "https://github.com/pysam-developers/pysam.git") | |
1548 | (commit (string-append "v" version)))) | |
1549 | (file-name (git-file-name name version)) | |
d454640c RW |
1550 | (sha256 |
1551 | (base32 | |
939882f7 | 1552 | "1vj367w6xbn9bpmksm162l1aipf7cj97h1q83y7jcpm33ihwpf7x")) |
dff26b23 | 1553 | (modules '((guix build utils))) |
6cbee49d MW |
1554 | (snippet '(begin |
1555 | ;; Drop bundled htslib. TODO: Also remove samtools | |
1556 | ;; and bcftools. | |
1557 | (delete-file-recursively "htslib") | |
1558 | #t)))) | |
55a9a8c2 RW |
1559 | (build-system python-build-system) |
1560 | (arguments | |
71dbf592 RW |
1561 | `(#:modules ((ice-9 ftw) |
1562 | (srfi srfi-26) | |
1563 | (guix build python-build-system) | |
1564 | (guix build utils)) | |
1565 | #:phases | |
397d463a MB |
1566 | (modify-phases %standard-phases |
1567 | (add-before 'build 'set-flags | |
dff26b23 MB |
1568 | (lambda* (#:key inputs #:allow-other-keys) |
1569 | (setenv "HTSLIB_MODE" "external") | |
1570 | (setenv "HTSLIB_LIBRARY_DIR" | |
1571 | (string-append (assoc-ref inputs "htslib") "/lib")) | |
1572 | (setenv "HTSLIB_INCLUDE_DIR" | |
1573 | (string-append (assoc-ref inputs "htslib") "/include")) | |
397d463a MB |
1574 | (setenv "LDFLAGS" "-lncurses") |
1575 | (setenv "CFLAGS" "-D_CURSES_LIB=1") | |
f536dce5 | 1576 | #t)) |
71dbf592 | 1577 | (replace 'check |
f536dce5 | 1578 | (lambda* (#:key inputs outputs #:allow-other-keys) |
939882f7 RW |
1579 | ;; This file contains tests that require a connection to the |
1580 | ;; internet. | |
1581 | (delete-file "tests/tabix_test.py") | |
1582 | ;; FIXME: This test fails | |
1583 | (delete-file "tests/AlignmentFile_test.py") | |
71dbf592 | 1584 | ;; Add first subdirectory of "build" directory to PYTHONPATH. |
f536dce5 MB |
1585 | (setenv "PYTHONPATH" |
1586 | (string-append | |
1587 | (getenv "PYTHONPATH") | |
71dbf592 RW |
1588 | ":" (getcwd) "/build/" |
1589 | (car (scandir "build" | |
e1f02f92 | 1590 | (negate (cut string-prefix? "." <>)))))) |
f536dce5 | 1591 | ;; Step out of source dir so python does not import from CWD. |
71dbf592 RW |
1592 | (with-directory-excursion "tests" |
1593 | (setenv "HOME" "/tmp") | |
939882f7 RW |
1594 | (invoke "make" "-C" "pysam_data") |
1595 | (invoke "make" "-C" "cbcf_data") | |
1596 | ;; Running nosetests without explicitly asking for a single | |
1597 | ;; process leads to a crash. Running with multiple processes | |
1598 | ;; fails because the tests are not designed to run in parallel. | |
31c374e0 | 1599 | |
939882f7 RW |
1600 | ;; FIXME: tests keep timing out on some systems. |
1601 | (invoke "nosetests" "-v" "--processes" "1"))))))) | |
dff26b23 | 1602 | (propagated-inputs |
939882f7 | 1603 | `(("htslib" ,htslib))) ; Included from installed header files. |
55a9a8c2 | 1604 | (inputs |
939882f7 RW |
1605 | `(("ncurses" ,ncurses) |
1606 | ("curl" ,curl) | |
1607 | ("zlib" ,zlib))) | |
649e9b3b | 1608 | (native-inputs |
939882f7 | 1609 | `(("python-cython" ,python-cython) |
f536dce5 | 1610 | ;; Dependencies below are are for tests only. |
939882f7 RW |
1611 | ("samtools" ,samtools) |
1612 | ("bcftools" ,bcftools) | |
1613 | ("python-nose" ,python-nose))) | |
55a9a8c2 RW |
1614 | (home-page "https://github.com/pysam-developers/pysam") |
1615 | (synopsis "Python bindings to the SAMtools C API") | |
1616 | (description | |
1617 | "Pysam is a Python module for reading and manipulating files in the | |
1618 | SAM/BAM format. Pysam is a lightweight wrapper of the SAMtools C API. It | |
1619 | also includes an interface for tabix.") | |
1620 | (license license:expat))) | |
1621 | ||
1622 | (define-public python2-pysam | |
1623 | (package-with-python2 python-pysam)) | |
1624 | ||
4db9433a RW |
1625 | (define-public python-twobitreader |
1626 | (package | |
1627 | (name "python-twobitreader") | |
8640f9ec | 1628 | (version "3.1.6") |
4db9433a | 1629 | (source (origin |
8640f9ec RW |
1630 | (method git-fetch) |
1631 | (uri (git-reference | |
1632 | (url "https://github.com/benjschiller/twobitreader") | |
1633 | (commit version))) | |
1634 | (file-name (git-file-name name version)) | |
4db9433a RW |
1635 | (sha256 |
1636 | (base32 | |
8640f9ec | 1637 | "1qbxvv1h58cismbk1anpjrkpghsaiy64a11ir3lhy6qch6xf8n62")))) |
4db9433a | 1638 | (build-system python-build-system) |
8640f9ec RW |
1639 | ;; Tests are not included |
1640 | (arguments '(#:tests? #f)) | |
4db9433a RW |
1641 | (native-inputs |
1642 | `(("python-sphinx" ,python-sphinx))) | |
1643 | (home-page "https://github.com/benjschiller/twobitreader") | |
1644 | (synopsis "Python library for reading .2bit files") | |
1645 | (description | |
1646 | "twobitreader is a Python library for reading .2bit files as used by the | |
1647 | UCSC genome browser.") | |
1648 | (license license:artistic2.0))) | |
1649 | ||
1650 | (define-public python2-twobitreader | |
5c31f4aa | 1651 | (package-with-python2 python-twobitreader)) |
4db9433a | 1652 | |
f94bf198 RW |
1653 | (define-public python-plastid |
1654 | (package | |
1655 | (name "python-plastid") | |
897ab082 | 1656 | (version "0.4.8") |
f94bf198 RW |
1657 | (source (origin |
1658 | (method url-fetch) | |
1659 | (uri (pypi-uri "plastid" version)) | |
1660 | (sha256 | |
1661 | (base32 | |
897ab082 | 1662 | "0l24dd3q66if8yj042m4s0g95n6acn7im1imqd3p6h8ns43kxhj8")))) |
f94bf198 RW |
1663 | (build-system python-build-system) |
1664 | (arguments | |
1665 | ;; Some test files are not included. | |
1666 | `(#:tests? #f)) | |
1667 | (propagated-inputs | |
1668 | `(("python-numpy" ,python-numpy) | |
1669 | ("python-scipy" ,python-scipy) | |
1670 | ("python-pandas" ,python-pandas) | |
1671 | ("python-pysam" ,python-pysam) | |
1672 | ("python-matplotlib" ,python-matplotlib) | |
1673 | ("python-biopython" ,python-biopython) | |
99caa6f7 BW |
1674 | ("python-twobitreader" ,python-twobitreader) |
1675 | ("python-termcolor" ,python-termcolor))) | |
f94bf198 RW |
1676 | (native-inputs |
1677 | `(("python-cython" ,python-cython) | |
1678 | ("python-nose" ,python-nose))) | |
1679 | (home-page "https://github.com/joshuagryphon/plastid") | |
1680 | (synopsis "Python library for genomic analysis") | |
1681 | (description | |
1682 | "plastid is a Python library for genomic analysis – in particular, | |
1683 | high-throughput sequencing data – with an emphasis on simplicity.") | |
1684 | (license license:bsd-3))) | |
1685 | ||
1686 | (define-public python2-plastid | |
5c31f4aa | 1687 | (package-with-python2 python-plastid)) |
f94bf198 | 1688 | |
6c1305f9 RW |
1689 | (define-public cd-hit |
1690 | (package | |
1691 | (name "cd-hit") | |
ba773f65 | 1692 | (version "4.6.8") |
6c1305f9 RW |
1693 | (source (origin |
1694 | (method url-fetch) | |
1695 | (uri (string-append "https://github.com/weizhongli/cdhit" | |
1696 | "/releases/download/V" version | |
ba773f65 BW |
1697 | "/cd-hit-v" version |
1698 | "-2017-0621-source.tar.gz")) | |
6c1305f9 RW |
1699 | (sha256 |
1700 | (base32 | |
d4735e8c | 1701 | "1b4mwm2520ixjbw57sil20f9iixzw4bkdqqwgg1fc3pzm6rz4zmn")))) |
6c1305f9 RW |
1702 | (build-system gnu-build-system) |
1703 | (arguments | |
1704 | `(#:tests? #f ; there are no tests | |
1705 | #:make-flags | |
1706 | ;; Executables are copied directly to the PREFIX. | |
1707 | (list (string-append "PREFIX=" (assoc-ref %outputs "out") "/bin")) | |
1708 | #:phases | |
1709 | (modify-phases %standard-phases | |
1710 | ;; No "configure" script | |
1711 | (delete 'configure) | |
1712 | ;; Remove sources of non-determinism | |
1713 | (add-after 'unpack 'be-timeless | |
1714 | (lambda _ | |
1715 | (substitute* "cdhit-utility.c++" | |
1716 | ((" \\(built on \" __DATE__ \"\\)") "")) | |
1717 | (substitute* "cdhit-common.c++" | |
1718 | (("__DATE__") "\"0\"") | |
1719 | (("\", %s, \" __TIME__ \"\\\\n\", date") "")) | |
1720 | #t)) | |
ba773f65 | 1721 | ;; The "install" target does not create the target directory. |
6c1305f9 RW |
1722 | (add-before 'install 'create-target-dir |
1723 | (lambda* (#:key outputs #:allow-other-keys) | |
1724 | (mkdir-p (string-append (assoc-ref outputs "out") "/bin")) | |
1725 | #t))))) | |
1726 | (inputs | |
1727 | `(("perl" ,perl))) | |
1728 | (home-page "http://weizhongli-lab.org/cd-hit/") | |
1729 | (synopsis "Cluster and compare protein or nucleotide sequences") | |
1730 | (description | |
1731 | "CD-HIT is a program for clustering and comparing protein or nucleotide | |
1732 | sequences. CD-HIT is designed to be fast and handle extremely large | |
1733 | databases.") | |
1734 | ;; The manual says: "It can be copied under the GNU General Public License | |
1735 | ;; version 2 (GPLv2)." | |
1736 | (license license:gpl2))) | |
1737 | ||
810cff85 RW |
1738 | (define-public clipper |
1739 | (package | |
1740 | (name "clipper") | |
8b4102b9 | 1741 | (version "1.2.1") |
810cff85 | 1742 | (source (origin |
8b4102b9 RW |
1743 | (method git-fetch) |
1744 | (uri (git-reference | |
1745 | (url "https://github.com/YeoLab/clipper.git") | |
1746 | (commit version))) | |
1747 | (file-name (git-file-name name version)) | |
810cff85 RW |
1748 | (sha256 |
1749 | (base32 | |
8b4102b9 | 1750 | "0fja1rj84wp9vpj8rxpj3n8zqzcqq454m904yp9as1w4phccirjb")) |
810cff85 RW |
1751 | (modules '((guix build utils))) |
1752 | (snippet | |
433530a5 RW |
1753 | '(begin |
1754 | ;; remove unnecessary setup dependency | |
1755 | (substitute* "setup.py" | |
1756 | (("setup_requires = .*") "")) | |
433530a5 | 1757 | #t)))) |
810cff85 | 1758 | (build-system python-build-system) |
8b4102b9 RW |
1759 | (arguments |
1760 | `(#:python ,python-2 ; only Python 2 is supported | |
1761 | #:phases | |
1762 | (modify-phases %standard-phases | |
1763 | ;; This is fixed in upstream commit | |
1764 | ;; f6c2990198f906bf97730d95695b4bd5a6d01ddb. | |
1765 | (add-after 'unpack 'fix-typo | |
1766 | (lambda _ | |
1767 | (substitute* "clipper/src/readsToWiggle.pyx" | |
1768 | (("^sc.*") "")) | |
1769 | #t))))) | |
810cff85 | 1770 | (inputs |
92971d68 | 1771 | `(("htseq" ,python2-htseq) |
810cff85 RW |
1772 | ("python-pybedtools" ,python2-pybedtools) |
1773 | ("python-cython" ,python2-cython) | |
1774 | ("python-scikit-learn" ,python2-scikit-learn) | |
1775 | ("python-matplotlib" ,python2-matplotlib) | |
433530a5 | 1776 | ("python-pandas" ,python2-pandas) |
810cff85 RW |
1777 | ("python-pysam" ,python2-pysam) |
1778 | ("python-numpy" ,python2-numpy) | |
1779 | ("python-scipy" ,python2-scipy))) | |
1780 | (native-inputs | |
f3b98f4f | 1781 | `(("python-mock" ,python2-mock) ; for tests |
d281be18 | 1782 | ("python-nose" ,python2-nose) ; for tests |
f3b98f4f | 1783 | ("python-pytz" ,python2-pytz))) ; for tests |
810cff85 RW |
1784 | (home-page "https://github.com/YeoLab/clipper") |
1785 | (synopsis "CLIP peak enrichment recognition") | |
1786 | (description | |
1787 | "CLIPper is a tool to define peaks in CLIP-seq datasets.") | |
1788 | (license license:gpl2))) | |
1789 | ||
6a35566d RS |
1790 | (define-public codingquarry |
1791 | (package | |
1792 | (name "codingquarry") | |
1793 | (version "2.0") | |
1794 | (source (origin | |
1795 | (method url-fetch) | |
1796 | (uri (string-append | |
1797 | "mirror://sourceforge/codingquarry/CodingQuarry_v" | |
1798 | version ".tar.gz")) | |
1799 | (sha256 | |
1800 | (base32 | |
1801 | "0115hkjflsnfzn36xppwf9h9avfxlavr43djqmshkkzbgjzsz60i")))) | |
1802 | (build-system gnu-build-system) | |
1803 | (arguments | |
1804 | '(#:tests? #f ; no "check" target | |
1805 | #:phases | |
1806 | (modify-phases %standard-phases | |
1807 | (delete 'configure) | |
1808 | (replace 'install | |
1809 | (lambda* (#:key outputs #:allow-other-keys) | |
1810 | (let* ((out (assoc-ref outputs "out")) | |
1811 | (bin (string-append out "/bin")) | |
1812 | (doc (string-append out "/share/doc/codingquarry"))) | |
1813 | (install-file "INSTRUCTIONS.pdf" doc) | |
1814 | (copy-recursively "QuarryFiles" | |
1815 | (string-append out "/QuarryFiles")) | |
1816 | (install-file "CodingQuarry" bin) | |
2e0f6905 MW |
1817 | (install-file "CufflinksGTF_to_CodingQuarryGFF3.py" bin)) |
1818 | #t))))) | |
6a35566d RS |
1819 | (inputs `(("openmpi" ,openmpi))) |
1820 | (native-search-paths | |
1821 | (list (search-path-specification | |
1822 | (variable "QUARRY_PATH") | |
1823 | (files '("QuarryFiles"))))) | |
1824 | (native-inputs `(("python" ,python-2))) ; Only Python 2 is supported | |
1825 | (synopsis "Fungal gene predictor") | |
1826 | (description "CodingQuarry is a highly accurate, self-training GHMM fungal | |
1827 | gene predictor designed to work with assembled, aligned RNA-seq transcripts.") | |
1828 | (home-page "https://sourceforge.net/projects/codingquarry/") | |
1829 | (license license:gpl3+))) | |
1830 | ||
36742f43 RW |
1831 | (define-public couger |
1832 | (package | |
1833 | (name "couger") | |
1834 | (version "1.8.2") | |
1835 | (source (origin | |
1836 | (method url-fetch) | |
1837 | (uri (string-append | |
1838 | "http://couger.oit.duke.edu/static/assets/COUGER" | |
1839 | version ".zip")) | |
1840 | (sha256 | |
1841 | (base32 | |
1842 | "04p2b14nmhzxw5h72mpzdhalv21bx4w9b87z0wpw0xzxpysyncmq")))) | |
1843 | (build-system gnu-build-system) | |
1844 | (arguments | |
1845 | `(#:tests? #f | |
1846 | #:phases | |
1847 | (modify-phases %standard-phases | |
1848 | (delete 'configure) | |
1849 | (delete 'build) | |
1850 | (replace | |
1851 | 'install | |
1852 | (lambda* (#:key outputs #:allow-other-keys) | |
f3860753 TGR |
1853 | (let* ((out (assoc-ref outputs "out")) |
1854 | (bin (string-append out "/bin"))) | |
36742f43 | 1855 | (copy-recursively "src" (string-append out "/src")) |
f3860753 | 1856 | (mkdir bin) |
36742f43 RW |
1857 | ;; Add "src" directory to module lookup path. |
1858 | (substitute* "couger" | |
1859 | (("from argparse") | |
1860 | (string-append "import sys\nsys.path.append(\"" | |
1861 | out "\")\nfrom argparse"))) | |
f3860753 | 1862 | (install-file "couger" bin)) |
36742f43 RW |
1863 | #t)) |
1864 | (add-after | |
1865 | 'install 'wrap-program | |
1866 | (lambda* (#:key inputs outputs #:allow-other-keys) | |
1867 | ;; Make sure 'couger' runs with the correct PYTHONPATH. | |
1868 | (let* ((out (assoc-ref outputs "out")) | |
1869 | (path (getenv "PYTHONPATH"))) | |
1870 | (wrap-program (string-append out "/bin/couger") | |
1871 | `("PYTHONPATH" ":" prefix (,path)))) | |
1872 | #t))))) | |
1873 | (inputs | |
1874 | `(("python" ,python-2) | |
1875 | ("python2-pillow" ,python2-pillow) | |
1876 | ("python2-numpy" ,python2-numpy) | |
1877 | ("python2-scipy" ,python2-scipy) | |
1878 | ("python2-matplotlib" ,python2-matplotlib))) | |
1879 | (propagated-inputs | |
2d7c4ae3 | 1880 | `(("r-minimal" ,r-minimal) |
36742f43 RW |
1881 | ("libsvm" ,libsvm) |
1882 | ("randomjungle" ,randomjungle))) | |
1883 | (native-inputs | |
1884 | `(("unzip" ,unzip))) | |
1885 | (home-page "http://couger.oit.duke.edu") | |
1886 | (synopsis "Identify co-factors in sets of genomic regions") | |
1887 | (description | |
1888 | "COUGER can be applied to any two sets of genomic regions bound by | |
1889 | paralogous TFs (e.g., regions derived from ChIP-seq experiments) to identify | |
1890 | putative co-factors that provide specificity to each TF. The framework | |
1891 | determines the genomic targets uniquely-bound by each TF, and identifies a | |
1892 | small set of co-factors that best explain the in vivo binding differences | |
1893 | between the two TFs. | |
1894 | ||
1895 | COUGER uses classification algorithms (support vector machines and random | |
1896 | forests) with features that reflect the DNA binding specificities of putative | |
1897 | co-factors. The features are generated either from high-throughput TF-DNA | |
1898 | binding data (from protein binding microarray experiments), or from large | |
1899 | collections of DNA motifs.") | |
1900 | (license license:gpl3+))) | |
1901 | ||
bfe3c685 RW |
1902 | (define-public clustal-omega |
1903 | (package | |
1904 | (name "clustal-omega") | |
b3936f35 | 1905 | (version "1.2.4") |
bfe3c685 RW |
1906 | (source (origin |
1907 | (method url-fetch) | |
b3936f35 RW |
1908 | (uri (string-append "http://www.clustal.org/omega/clustal-omega-" |
1909 | version ".tar.gz")) | |
bfe3c685 RW |
1910 | (sha256 |
1911 | (base32 | |
b3936f35 | 1912 | "1vm30mzncwdv881vrcwg11vzvrsmwy4wg80j5i0lcfk6dlld50w6")))) |
bfe3c685 RW |
1913 | (build-system gnu-build-system) |
1914 | (inputs | |
1915 | `(("argtable" ,argtable))) | |
1916 | (home-page "http://www.clustal.org/omega/") | |
1917 | (synopsis "Multiple sequence aligner for protein and DNA/RNA") | |
1918 | (description | |
1919 | "Clustal-Omega is a general purpose multiple sequence alignment (MSA) | |
1920 | program for protein and DNA/RNA. It produces high quality MSAs and is capable | |
1921 | of handling data-sets of hundreds of thousands of sequences in reasonable | |
1922 | time.") | |
1923 | (license license:gpl2+))) | |
1924 | ||
191c7101 RW |
1925 | (define-public crossmap |
1926 | (package | |
1927 | (name "crossmap") | |
7321920c | 1928 | (version "0.2.9") |
191c7101 RW |
1929 | (source (origin |
1930 | (method url-fetch) | |
7321920c | 1931 | (uri (pypi-uri "CrossMap" version)) |
191c7101 RW |
1932 | (sha256 |
1933 | (base32 | |
7321920c | 1934 | "1byhclrqnqpvc1rqkfh4jwj6yhn0x9y7jk47i0qcjlhk0pjkw92p")))) |
191c7101 | 1935 | (build-system python-build-system) |
7321920c | 1936 | (arguments `(#:python ,python-2)) |
191c7101 | 1937 | (inputs |
7321920c RW |
1938 | `(("python-bx-python" ,python2-bx-python) |
1939 | ("python-numpy" ,python2-numpy) | |
191c7101 RW |
1940 | ("python-pysam" ,python2-pysam) |
1941 | ("zlib" ,zlib))) | |
1942 | (native-inputs | |
1943 | `(("python-cython" ,python2-cython) | |
f3b98f4f | 1944 | ("python-nose" ,python2-nose))) |
191c7101 RW |
1945 | (home-page "http://crossmap.sourceforge.net/") |
1946 | (synopsis "Convert genome coordinates between assemblies") | |
1947 | (description | |
1948 | "CrossMap is a program for conversion of genome coordinates or annotation | |
1949 | files between different genome assemblies. It supports most commonly used | |
1950 | file formats including SAM/BAM, Wiggle/BigWig, BED, GFF/GTF, VCF.") | |
1951 | (license license:gpl2+))) | |
1952 | ||
a5b0038c RW |
1953 | (define-public python-dnaio |
1954 | (package | |
1955 | (name "python-dnaio") | |
1956 | (version "0.3") | |
1957 | (source | |
1958 | (origin | |
1959 | (method url-fetch) | |
1960 | (uri (pypi-uri "dnaio" version)) | |
1961 | (sha256 | |
1962 | (base32 | |
1963 | "0f16m7hdlm0fz1n7y5asy0v9ghyrq17ni1p9iybq22ddzyd49r27")))) | |
1964 | (build-system python-build-system) | |
1965 | (native-inputs | |
1966 | `(("python-cython" ,python-cython) | |
1967 | ("python-pytest" ,python-pytest) | |
1968 | ("python-xopen" ,python-xopen))) | |
1969 | (home-page "https://github.com/marcelm/dnaio/") | |
1970 | (synopsis "Read FASTA and FASTQ files efficiently") | |
1971 | (description | |
1972 | "dnaio is a Python library for fast parsing of FASTQ and also FASTA | |
1973 | files. The code was previously part of the cutadapt tool.") | |
1974 | (license license:expat))) | |
1975 | ||
8e913213 RW |
1976 | (define-public cutadapt |
1977 | (package | |
1978 | (name "cutadapt") | |
6b7260ba | 1979 | (version "1.18") |
8e913213 | 1980 | (source (origin |
3ede1550 RW |
1981 | (method git-fetch) |
1982 | (uri (git-reference | |
1983 | (url "https://github.com/marcelm/cutadapt.git") | |
1984 | (commit (string-append "v" version)))) | |
6b7260ba | 1985 | (file-name (git-file-name name version)) |
8e913213 RW |
1986 | (sha256 |
1987 | (base32 | |
6b7260ba | 1988 | "08bbfwyc0kvcd95jf2s95xiv9s3cbsxm39ydl0qck3fw3cviwxpg")))) |
8e913213 | 1989 | (build-system python-build-system) |
1f94bff2 | 1990 | (inputs |
6b7260ba RW |
1991 | `(("python-dnaio" ,python-dnaio) |
1992 | ("python-xopen" ,python-xopen))) | |
8e913213 RW |
1993 | (native-inputs |
1994 | `(("python-cython" ,python-cython) | |
3ede1550 | 1995 | ("python-pytest" ,python-pytest))) |
0c6c9c00 | 1996 | (home-page "https://cutadapt.readthedocs.io/en/stable/") |
8e913213 RW |
1997 | (synopsis "Remove adapter sequences from nucleotide sequencing reads") |
1998 | (description | |
1999 | "Cutadapt finds and removes adapter sequences, primers, poly-A tails and | |
2000 | other types of unwanted sequence from high-throughput sequencing reads.") | |
2001 | (license license:expat))) | |
2002 | ||
1baee943 RW |
2003 | (define-public libbigwig |
2004 | (package | |
2005 | (name "libbigwig") | |
0d7974c3 | 2006 | (version "0.4.2") |
1baee943 | 2007 | (source (origin |
0d7974c3 RW |
2008 | (method git-fetch) |
2009 | (uri (git-reference | |
2010 | (url "https://github.com/dpryan79/libBigWig.git") | |
2011 | (commit version))) | |
2012 | (file-name (string-append name "-" version "-checkout")) | |
1baee943 RW |
2013 | (sha256 |
2014 | (base32 | |
0d7974c3 | 2015 | "0h2smg24v5srdcqzrmz2g23cmlp4va465mgx8r2z571sfz8pv454")))) |
1baee943 RW |
2016 | (build-system gnu-build-system) |
2017 | (arguments | |
2018 | `(#:test-target "test" | |
0d7974c3 | 2019 | #:tests? #f ; tests require access to the web |
1baee943 RW |
2020 | #:make-flags |
2021 | (list "CC=gcc" | |
2022 | (string-append "prefix=" (assoc-ref %outputs "out"))) | |
2023 | #:phases | |
2024 | (modify-phases %standard-phases | |
0d7974c3 | 2025 | (delete 'configure)))) |
1baee943 RW |
2026 | (inputs |
2027 | `(("zlib" ,zlib) | |
2028 | ("curl" ,curl))) | |
2029 | (native-inputs | |
0d7974c3 RW |
2030 | `(("doxygen" ,doxygen) |
2031 | ;; Need for tests | |
2032 | ("python" ,python-2))) | |
1baee943 RW |
2033 | (home-page "https://github.com/dpryan79/libBigWig") |
2034 | (synopsis "C library for handling bigWig files") | |
2035 | (description | |
2036 | "This package provides a C library for parsing local and remote BigWig | |
2037 | files.") | |
2038 | (license license:expat))) | |
2039 | ||
69e0e03c RW |
2040 | (define-public python-pybigwig |
2041 | (package | |
2042 | (name "python-pybigwig") | |
8afdeb87 | 2043 | (version "0.3.12") |
69e0e03c RW |
2044 | (source (origin |
2045 | (method url-fetch) | |
2046 | (uri (pypi-uri "pyBigWig" version)) | |
2047 | (sha256 | |
2048 | (base32 | |
8afdeb87 | 2049 | "00w4kfnm2c5l7wdwr2nj1z5djv8kzgf7h1zhsgv6njff1rwr26g0")) |
69e0e03c RW |
2050 | (modules '((guix build utils))) |
2051 | (snippet | |
2052 | '(begin | |
2053 | ;; Delete bundled libBigWig sources | |
6cbee49d MW |
2054 | (delete-file-recursively "libBigWig") |
2055 | #t)))) | |
69e0e03c RW |
2056 | (build-system python-build-system) |
2057 | (arguments | |
2058 | `(#:phases | |
2059 | (modify-phases %standard-phases | |
2060 | (add-after 'unpack 'link-with-libBigWig | |
2061 | (lambda* (#:key inputs #:allow-other-keys) | |
2062 | (substitute* "setup.py" | |
2063 | (("libs=\\[") "libs=[\"BigWig\", ")) | |
2064 | #t))))) | |
8afdeb87 RW |
2065 | (propagated-inputs |
2066 | `(("python-numpy" ,python-numpy))) | |
69e0e03c RW |
2067 | (inputs |
2068 | `(("libbigwig" ,libbigwig) | |
2069 | ("zlib" ,zlib) | |
2070 | ("curl" ,curl))) | |
2071 | (home-page "https://github.com/dpryan79/pyBigWig") | |
2072 | (synopsis "Access bigWig files in Python using libBigWig") | |
2073 | (description | |
2074 | "This package provides Python bindings to the libBigWig library for | |
2075 | accessing bigWig files.") | |
2076 | (license license:expat))) | |
2077 | ||
2078 | (define-public python2-pybigwig | |
5c31f4aa | 2079 | (package-with-python2 python-pybigwig)) |
69e0e03c | 2080 | |
ec2a67de BW |
2081 | (define-public python-dendropy |
2082 | (package | |
2083 | (name "python-dendropy") | |
9e0c135c | 2084 | (version "4.4.0") |
ec2a67de BW |
2085 | (source |
2086 | (origin | |
42643fc2 | 2087 | (method git-fetch) |
9e0c135c | 2088 | ;; Source from GitHub so that tests are included. |
42643fc2 RW |
2089 | (uri (git-reference |
2090 | (url "https://github.com/jeetsukumaran/DendroPy.git") | |
2091 | (commit (string-append "v" version)))) | |
2092 | (file-name (git-file-name name version)) | |
ec2a67de BW |
2093 | (sha256 |
2094 | (base32 | |
42643fc2 | 2095 | "097hfyv2kaf4x92i4rjx0paw2cncxap48qivv8zxng4z7nhid0x9")))) |
ec2a67de BW |
2096 | (build-system python-build-system) |
2097 | (home-page "http://packages.python.org/DendroPy/") | |
2098 | (synopsis "Library for phylogenetics and phylogenetic computing") | |
2099 | (description | |
2100 | "DendroPy is a library for phylogenetics and phylogenetic computing: reading, | |
2101 | writing, simulation, processing and manipulation of phylogenetic | |
2102 | trees (phylogenies) and characters.") | |
9e0c135c | 2103 | (license license:bsd-3))) |
ec2a67de BW |
2104 | |
2105 | (define-public python2-dendropy | |
617c4785 BW |
2106 | (let ((base (package-with-python2 python-dendropy))) |
2107 | (package | |
2108 | (inherit base) | |
2109 | (arguments | |
2110 | `(#:phases | |
2111 | (modify-phases %standard-phases | |
2112 | (add-after 'unpack 'remove-failing-test | |
2113 | (lambda _ | |
2114 | ;; This test fails when the full test suite is run, as documented | |
2115 | ;; at https://github.com/jeetsukumaran/DendroPy/issues/74 | |
2116 | (substitute* "tests/test_dataio_nexml_reader_tree_list.py" | |
2117 | (("test_collection_comments_and_annotations") | |
2118 | "do_not_test_collection_comments_and_annotations")) | |
2119 | #t))) | |
2120 | ,@(package-arguments base)))))) | |
ec2a67de | 2121 | |
eb2200f3 RW |
2122 | (define-public python-py2bit |
2123 | (package | |
2124 | (name "python-py2bit") | |
6b31040a | 2125 | (version "0.3.0") |
eb2200f3 RW |
2126 | (source |
2127 | (origin | |
2128 | (method url-fetch) | |
2129 | (uri (pypi-uri "py2bit" version)) | |
2130 | (sha256 | |
2131 | (base32 | |
6b31040a | 2132 | "1vw2nvw1yrl7ikkqsqs1pg239yr5nspvd969r1x9arms1k25a1a5")))) |
eb2200f3 RW |
2133 | (build-system python-build-system) |
2134 | (home-page "https://github.com/dpryan79/py2bit") | |
2135 | (synopsis "Access 2bit files using lib2bit") | |
2136 | (description | |
2137 | "This package provides Python bindings for lib2bit to access 2bit files | |
2138 | with Python.") | |
2139 | (license license:expat))) | |
ec2a67de | 2140 | |
1921b1de RW |
2141 | (define-public deeptools |
2142 | (package | |
2143 | (name "deeptools") | |
4d494a4f | 2144 | (version "3.1.3") |
1921b1de | 2145 | (source (origin |
8e72f0f3 RW |
2146 | (method git-fetch) |
2147 | (uri (git-reference | |
2148 | (url "https://github.com/deeptools/deepTools.git") | |
2149 | (commit version))) | |
2150 | (file-name (git-file-name name version)) | |
1921b1de RW |
2151 | (sha256 |
2152 | (base32 | |
4d494a4f | 2153 | "1vggnf52g6q2vifdl4cyi7s2fnfqq0ky2zrkj5zv2qfzsc3p3siw")))) |
1921b1de | 2154 | (build-system python-build-system) |
8e72f0f3 RW |
2155 | (arguments |
2156 | `(#:phases | |
2157 | (modify-phases %standard-phases | |
2158 | ;; This phase fails, but it's not needed. | |
2159 | (delete 'reset-gzip-timestamps)))) | |
14bda1ff | 2160 | (inputs |
8e72f0f3 RW |
2161 | `(("python-plotly" ,python-plotly) |
2162 | ("python-scipy" ,python-scipy) | |
fed72008 RW |
2163 | ("python-numpy" ,python-numpy) |
2164 | ("python-numpydoc" ,python-numpydoc) | |
2165 | ("python-matplotlib" ,python-matplotlib) | |
2166 | ("python-pysam" ,python-pysam) | |
2167 | ("python-py2bit" ,python-py2bit) | |
2168 | ("python-pybigwig" ,python-pybigwig))) | |
1921b1de | 2169 | (native-inputs |
fed72008 RW |
2170 | `(("python-mock" ,python-mock) ;for tests |
2171 | ("python-nose" ,python-nose) ;for tests | |
2172 | ("python-pytz" ,python-pytz))) ;for tests | |
cd70f9bd | 2173 | (home-page "https://github.com/deeptools/deepTools") |
1921b1de RW |
2174 | (synopsis "Tools for normalizing and visualizing deep-sequencing data") |
2175 | (description | |
2176 | "DeepTools addresses the challenge of handling the large amounts of data | |
2177 | that are now routinely generated from DNA sequencing centers. To do so, | |
2178 | deepTools contains useful modules to process the mapped reads data to create | |
2179 | coverage files in standard bedGraph and bigWig file formats. By doing so, | |
2180 | deepTools allows the creation of normalized coverage files or the comparison | |
2181 | between two files (for example, treatment and control). Finally, using such | |
2182 | normalized and standardized files, multiple visualizations can be created to | |
2183 | identify enrichments with functional annotations of the genome.") | |
2184 | (license license:gpl3+))) | |
2185 | ||
fdc30687 RJ |
2186 | (define-public delly |
2187 | (package | |
2188 | (name "delly") | |
7a1e62ca | 2189 | (version "0.7.9") |
fdc30687 | 2190 | (source (origin |
7a1e62ca RW |
2191 | (method git-fetch) |
2192 | (uri (git-reference | |
2193 | (url "https://github.com/dellytools/delly.git") | |
2194 | (commit (string-append "v" version)))) | |
2195 | (file-name (git-file-name name version)) | |
fdc30687 | 2196 | (sha256 |
7a1e62ca RW |
2197 | (base32 "034jqsxswy9gqdh2zkgc1js99qkv75ks4xvzgmh0284sraagv61z")) |
2198 | (modules '((guix build utils))) | |
2199 | (snippet | |
2200 | '(begin | |
2201 | (delete-file-recursively "src/htslib") | |
2202 | #t)))) | |
fdc30687 RJ |
2203 | (build-system gnu-build-system) |
2204 | (arguments | |
2205 | `(#:tests? #f ; There are no tests to run. | |
7a1e62ca RW |
2206 | #:make-flags |
2207 | (list "PARALLEL=1" ; Allow parallel execution at run-time. | |
2208 | (string-append "prefix=" (assoc-ref %outputs "out"))) | |
fdc30687 RJ |
2209 | #:phases |
2210 | (modify-phases %standard-phases | |
2211 | (delete 'configure) ; There is no configure phase. | |
7a1e62ca RW |
2212 | (add-after 'install 'install-templates |
2213 | (lambda* (#:key outputs #:allow-other-keys) | |
2214 | (let ((templates (string-append (assoc-ref outputs "out") | |
fdc30687 | 2215 | "/share/delly/templates"))) |
fdc30687 RJ |
2216 | (mkdir-p templates) |
2217 | (copy-recursively "excludeTemplates" templates) | |
7a1e62ca | 2218 | #t)))))) |
fdc30687 RJ |
2219 | (inputs |
2220 | `(("boost" ,boost) | |
2221 | ("htslib" ,htslib) | |
2222 | ("zlib" ,zlib) | |
2223 | ("bzip2" ,bzip2))) | |
7a1e62ca | 2224 | (home-page "https://github.com/dellytools/delly") |
fdc30687 RJ |
2225 | (synopsis "Integrated structural variant prediction method") |
2226 | (description "Delly is an integrated structural variant prediction method | |
2227 | that can discover and genotype deletions, tandem duplications, inversions and | |
2228 | translocations at single-nucleotide resolution in short-read massively parallel | |
2229 | sequencing data. It uses paired-ends and split-reads to sensitively and | |
2230 | accurately delineate genomic rearrangements throughout the genome.") | |
2231 | (license license:gpl3+))) | |
2232 | ||
684bf7c7 BW |
2233 | (define-public diamond |
2234 | (package | |
2235 | (name "diamond") | |
2c5289b2 | 2236 | (version "0.9.22") |
684bf7c7 | 2237 | (source (origin |
1c063993 RW |
2238 | (method git-fetch) |
2239 | (uri (git-reference | |
2240 | (url "https://github.com/bbuchfink/diamond.git") | |
2241 | (commit (string-append "v" version)))) | |
2242 | (file-name (git-file-name name version)) | |
684bf7c7 BW |
2243 | (sha256 |
2244 | (base32 | |
1c063993 | 2245 | "0bky78v79g3wmdpsd706cscckgw1v09fg8vdd0z8z0d5b97aj9zl")))) |
122395f9 | 2246 | (build-system cmake-build-system) |
684bf7c7 | 2247 | (arguments |
7c544991 BW |
2248 | '(#:tests? #f ; no "check" target |
2249 | #:phases | |
2250 | (modify-phases %standard-phases | |
2251 | (add-after 'unpack 'remove-native-compilation | |
2252 | (lambda _ | |
2253 | (substitute* "CMakeLists.txt" (("-march=native") "")) | |
2254 | #t))))) | |
684bf7c7 | 2255 | (inputs |
122395f9 | 2256 | `(("zlib" ,zlib))) |
684bf7c7 BW |
2257 | (home-page "https://github.com/bbuchfink/diamond") |
2258 | (synopsis "Accelerated BLAST compatible local sequence aligner") | |
2259 | (description | |
2260 | "DIAMOND is a BLAST-compatible local aligner for mapping protein and | |
2261 | translated DNA query sequences against a protein reference database (BLASTP | |
2262 | and BLASTX alignment mode). The speedup over BLAST is up to 20,000 on short | |
2263 | reads at a typical sensitivity of 90-99% relative to BLAST depending on the | |
2264 | data and settings.") | |
ef81341f | 2265 | (license license:agpl3+))) |
684bf7c7 | 2266 | |
97b9da68 RW |
2267 | (define-public discrover |
2268 | (package | |
2269 | (name "discrover") | |
2270 | (version "1.6.0") | |
2271 | (source | |
2272 | (origin | |
5748fe5f RW |
2273 | (method git-fetch) |
2274 | (uri (git-reference | |
2275 | (url "https://github.com/maaskola/discrover.git") | |
2276 | (commit version))) | |
2277 | (file-name (git-file-name name version)) | |
97b9da68 RW |
2278 | (sha256 |
2279 | (base32 | |
5748fe5f | 2280 | "173fwi2vb6a5kp406hm3jj6j7v4whww796f2qcygp4rpvamh307y")))) |
97b9da68 | 2281 | (build-system cmake-build-system) |
fa702e1a RW |
2282 | (arguments |
2283 | `(#:tests? #f ; there are no tests | |
2284 | #:phases | |
2285 | (modify-phases %standard-phases | |
2286 | (add-after 'unpack 'add-missing-includes | |
2287 | (lambda _ | |
2288 | (substitute* "src/executioninformation.hpp" | |
2289 | (("#define EXECUTIONINFORMATION_HPP" line) | |
2290 | (string-append line "\n#include <random>"))) | |
2291 | (substitute* "src/plasma/fasta.hpp" | |
2292 | (("#define FASTA_HPP" line) | |
2293 | (string-append line "\n#include <random>"))) | |
2294 | #t))))) | |
97b9da68 RW |
2295 | (inputs |
2296 | `(("boost" ,boost) | |
2297 | ("cairo" ,cairo))) | |
2298 | (native-inputs | |
2299 | `(("texlive" ,texlive) | |
2300 | ("imagemagick" ,imagemagick))) | |
2301 | (home-page "http://dorina.mdc-berlin.de/public/rajewsky/discrover/") | |
2302 | (synopsis "Discover discriminative nucleotide sequence motifs") | |
2303 | (description "Discrover is a motif discovery method to find binding sites | |
2304 | of nucleic acid binding proteins.") | |
2305 | (license license:gpl3+))) | |
2306 | ||
6619f9c7 | 2307 | (define-public eigensoft |
949fa34b RW |
2308 | (package |
2309 | (name "eigensoft") | |
2310 | (version "7.2.1") | |
2311 | (source | |
2312 | (origin | |
2313 | (method git-fetch) | |
2314 | (uri (git-reference | |
2315 | (url "https://github.com/DReichLab/EIG.git") | |
2316 | (commit (string-append "v" version)))) | |
2317 | (file-name (git-file-name name version)) | |
2318 | (sha256 | |
2319 | (base32 | |
2320 | "1c141fqvhnzibmnf22sv23vbmzm20kjjyrib44cfh75wyndp2d9k")) | |
2321 | (modules '((guix build utils))) | |
2322 | ;; Remove pre-built binaries. | |
2323 | (snippet '(begin | |
2324 | (delete-file-recursively "bin") | |
2325 | (mkdir "bin") | |
2326 | #t)))) | |
2327 | (build-system gnu-build-system) | |
2328 | (arguments | |
2329 | `(#:tests? #f ; There are no tests. | |
2330 | #:make-flags '("CC=gcc") | |
2331 | #:phases | |
2332 | (modify-phases %standard-phases | |
2333 | ;; There is no configure phase, but the Makefile is in a | |
2334 | ;; sub-directory. | |
2335 | (replace 'configure | |
2336 | (lambda _ (chdir "src") #t)) | |
2337 | ;; The provided install target only copies executables to | |
2338 | ;; the "bin" directory in the build root. | |
2339 | (add-after 'install 'actually-install | |
2340 | (lambda* (#:key outputs #:allow-other-keys) | |
2341 | (let* ((out (assoc-ref outputs "out")) | |
2342 | (bin (string-append out "/bin"))) | |
2343 | (for-each (lambda (file) | |
2344 | (install-file file bin)) | |
2345 | (find-files "../bin" ".*")) | |
2346 | #t)))))) | |
2347 | (inputs | |
2348 | `(("gsl" ,gsl) | |
2349 | ("lapack" ,lapack) | |
2350 | ("openblas" ,openblas) | |
2351 | ("perl" ,perl) | |
2352 | ("gfortran" ,gfortran "lib"))) | |
2353 | (home-page "https://github.com/DReichLab/EIG") | |
2354 | (synopsis "Tools for population genetics") | |
2355 | (description "The EIGENSOFT package provides tools for population | |
6619f9c7 RW |
2356 | genetics and stratification correction. EIGENSOFT implements methods commonly |
2357 | used in population genetics analyses such as PCA, computation of Tracy-Widom | |
2358 | statistics, and finding related individuals in structured populations. It | |
2359 | comes with a built-in plotting script and supports multiple file formats and | |
2360 | quantitative phenotypes.") | |
949fa34b RW |
2361 | ;; The license of the eigensoft tools is Expat, but since it's |
2362 | ;; linking with the GNU Scientific Library (GSL) the effective | |
2363 | ;; license is the GPL. | |
2364 | (license license:gpl3+))) | |
6619f9c7 | 2365 | |
365c8153 RW |
2366 | (define-public edirect |
2367 | (package | |
2368 | (name "edirect") | |
c96ca68f | 2369 | (version "10.2.20181018") |
365c8153 RW |
2370 | (source (origin |
2371 | (method url-fetch) | |
c96ca68f RW |
2372 | (uri (string-append "ftp://ftp.ncbi.nlm.nih.gov/entrez/entrezdirect" |
2373 | "/versions/" version | |
2374 | "/edirect-" version ".tar.gz")) | |
365c8153 RW |
2375 | (sha256 |
2376 | (base32 | |
c96ca68f | 2377 | "091f4aigzpbqih6h82nq566gkp3y07i72yqndmqskfgar1vwgci7")))) |
365c8153 RW |
2378 | (build-system perl-build-system) |
2379 | (arguments | |
c96ca68f | 2380 | `(#:phases |
365c8153 RW |
2381 | (modify-phases %standard-phases |
2382 | (delete 'configure) | |
2383 | (delete 'build) | |
c96ca68f | 2384 | (delete 'check) ; simple check after install |
365c8153 | 2385 | (replace 'install |
c96ca68f RW |
2386 | (lambda* (#:key outputs #:allow-other-keys) |
2387 | (install-file "edirect.pl" | |
2388 | (string-append (assoc-ref outputs "out") "/bin")) | |
2389 | #t)) | |
2390 | (add-after 'install 'wrap-program | |
2391 | (lambda* (#:key outputs #:allow-other-keys) | |
2392 | ;; Make sure 'edirect.pl' finds all perl inputs at runtime. | |
2393 | (let* ((out (assoc-ref outputs "out")) | |
2394 | (path (getenv "PERL5LIB"))) | |
2395 | (wrap-program (string-append out "/bin/edirect.pl") | |
2396 | `("PERL5LIB" ":" prefix (,path)))) | |
2397 | #t)) | |
2398 | (add-after 'wrap-program 'check | |
2399 | (lambda* (#:key outputs #:allow-other-keys) | |
2400 | (invoke (string-append (assoc-ref outputs "out") | |
2401 | "/bin/edirect.pl") | |
2402 | "-filter" "-help") | |
2403 | #t))))) | |
365c8153 RW |
2404 | (inputs |
2405 | `(("perl-html-parser" ,perl-html-parser) | |
2406 | ("perl-encode-locale" ,perl-encode-locale) | |
2407 | ("perl-file-listing" ,perl-file-listing) | |
2408 | ("perl-html-tagset" ,perl-html-tagset) | |
2409 | ("perl-html-tree" ,perl-html-tree) | |
2410 | ("perl-http-cookies" ,perl-http-cookies) | |
2411 | ("perl-http-date" ,perl-http-date) | |
2412 | ("perl-http-message" ,perl-http-message) | |
2413 | ("perl-http-negotiate" ,perl-http-negotiate) | |
2414 | ("perl-lwp-mediatypes" ,perl-lwp-mediatypes) | |
2415 | ("perl-lwp-protocol-https" ,perl-lwp-protocol-https) | |
2416 | ("perl-net-http" ,perl-net-http) | |
2417 | ("perl-uri" ,perl-uri) | |
2418 | ("perl-www-robotrules" ,perl-www-robotrules) | |
c96ca68f | 2419 | ("perl-xml-simple" ,perl-xml-simple) |
365c8153 | 2420 | ("perl" ,perl))) |
3d51ec91 | 2421 | (home-page "http://www.ncbi.nlm.nih.gov/books/NBK179288/") |
365c8153 RW |
2422 | (synopsis "Tools for accessing the NCBI's set of databases") |
2423 | (description | |
2424 | "Entrez Direct (EDirect) is a method for accessing the National Center | |
2425 | for Biotechnology Information's (NCBI) set of interconnected | |
2426 | databases (publication, sequence, structure, gene, variation, expression, | |
2427 | etc.) from a terminal. Functions take search terms from command-line | |
2428 | arguments. Individual operations are combined to build multi-step queries. | |
2429 | Record retrieval and formatting normally complete the process. | |
2430 | ||
2431 | EDirect also provides an argument-driven function that simplifies the | |
2432 | extraction of data from document summaries or other results that are returned | |
2433 | in structured XML format. This can eliminate the need for writing custom | |
2434 | software to answer ad hoc questions.") | |
2435 | (license license:public-domain))) | |
2436 | ||
b16728b0 BW |
2437 | (define-public exonerate |
2438 | (package | |
2439 | (name "exonerate") | |
2440 | (version "2.4.0") | |
2441 | (source | |
2442 | (origin | |
2443 | (method url-fetch) | |
2444 | (uri | |
2445 | (string-append | |
2446 | "http://ftp.ebi.ac.uk/pub/software/vertebrategenomics/exonerate/" | |
2447 | "exonerate-" version ".tar.gz")) | |
2448 | (sha256 | |
2449 | (base32 | |
2450 | "0hj0m9xygiqsdxvbg79wq579kbrx1mdrabi2bzqz2zn9qwfjcjgq")))) | |
2451 | (build-system gnu-build-system) | |
2452 | (arguments | |
2453 | `(#:parallel-build? #f)) ; Building in parallel fails on some machines. | |
2454 | (native-inputs | |
2455 | `(("pkg-config" ,pkg-config))) | |
2456 | (inputs | |
2457 | `(("glib" ,glib))) | |
2458 | (home-page | |
2459 | "https://www.ebi.ac.uk/about/vertebrate-genomics/software/exonerate") | |
2460 | (synopsis "Generic tool for biological sequence alignment") | |
2461 | (description | |
2462 | "Exonerate is a generic tool for pairwise sequence comparison. It allows | |
2463 | the alignment of sequences using a many alignment models, either exhaustive | |
2464 | dynamic programming or a variety of heuristics.") | |
2465 | (license license:gpl3))) | |
2466 | ||
e4e5a4d8 RW |
2467 | (define-public express |
2468 | (package | |
2469 | (name "express") | |
2470 | (version "1.5.1") | |
2471 | (source (origin | |
2472 | (method url-fetch) | |
2473 | (uri | |
2474 | (string-append | |
2475 | "http://bio.math.berkeley.edu/eXpress/downloads/express-" | |
2476 | version "/express-" version "-src.tgz")) | |
2477 | (sha256 | |
2478 | (base32 | |
2479 | "03rczxd0gjp2l1jxcmjfmf5j94j77zqyxa6x063zsc585nj40n0c")))) | |
2480 | (build-system cmake-build-system) | |
2481 | (arguments | |
2482 | `(#:tests? #f ;no "check" target | |
2483 | #:phases | |
dc1d3cde KK |
2484 | (modify-phases %standard-phases |
2485 | (add-after 'unpack 'use-shared-boost-libs-and-set-bamtools-paths | |
2486 | (lambda* (#:key inputs #:allow-other-keys) | |
2487 | (substitute* "CMakeLists.txt" | |
2488 | (("set\\(Boost_USE_STATIC_LIBS ON\\)") | |
2489 | "set(Boost_USE_STATIC_LIBS OFF)") | |
2490 | (("\\$\\{CMAKE_CURRENT_SOURCE_DIR\\}/bamtools/include") | |
2491 | (string-append (assoc-ref inputs "bamtools") "/include/bamtools"))) | |
2492 | (substitute* "src/CMakeLists.txt" | |
2493 | (("\\$\\{CMAKE_CURRENT_SOURCE_DIR\\}/\\.\\./bamtools/lib") | |
4b93efec RJ |
2494 | (string-append (assoc-ref inputs "bamtools") "/lib")) |
2495 | (("libprotobuf.a") "libprotobuf.so")) | |
dc1d3cde | 2496 | #t))))) |
e4e5a4d8 RW |
2497 | (inputs |
2498 | `(("boost" ,boost) | |
2499 | ("bamtools" ,bamtools) | |
2500 | ("protobuf" ,protobuf) | |
2501 | ("zlib" ,zlib))) | |
2502 | (home-page "http://bio.math.berkeley.edu/eXpress") | |
2503 | (synopsis "Streaming quantification for high-throughput genomic sequencing") | |
2504 | (description | |
2505 | "eXpress is a streaming tool for quantifying the abundances of a set of | |
2506 | target sequences from sampled subsequences. Example applications include | |
2507 | transcript-level RNA-Seq quantification, allele-specific/haplotype expression | |
2508 | analysis (from RNA-Seq), transcription factor binding quantification in | |
2509 | ChIP-Seq, and analysis of metagenomic data.") | |
2510 | (license license:artistic2.0))) | |
2511 | ||
f3674b1c BW |
2512 | (define-public express-beta-diversity |
2513 | (package | |
2514 | (name "express-beta-diversity") | |
38622ccd | 2515 | (version "1.0.8") |
f3674b1c | 2516 | (source (origin |
38622ccd RW |
2517 | (method git-fetch) |
2518 | (uri (git-reference | |
2519 | (url "https://github.com/dparks1134/ExpressBetaDiversity.git") | |
2520 | (commit (string-append "v" version)))) | |
2521 | (file-name (git-file-name name version)) | |
f3674b1c BW |
2522 | (sha256 |
2523 | (base32 | |
38622ccd | 2524 | "0s0yzg5c21349rh7x4w9266jsvnp7j1hp9cf8sk32hz8nvrj745x")))) |
f3674b1c BW |
2525 | (build-system gnu-build-system) |
2526 | (arguments | |
2527 | `(#:phases | |
2528 | (modify-phases %standard-phases | |
2529 | (delete 'configure) | |
2530 | (add-before 'build 'enter-source (lambda _ (chdir "source") #t)) | |
2531 | (replace 'check | |
38622ccd | 2532 | (lambda _ (invoke "../bin/ExpressBetaDiversity" "-u") #t)) |
f3674b1c | 2533 | (replace 'install |
38622ccd RW |
2534 | (lambda* (#:key outputs #:allow-other-keys) |
2535 | (let ((bin (string-append (assoc-ref outputs "out") "/bin"))) | |
2536 | (install-file "../scripts/convertToEBD.py" bin) | |
2537 | (install-file "../bin/ExpressBetaDiversity" bin) | |
2538 | #t)))))) | |
f3674b1c BW |
2539 | (inputs |
2540 | `(("python" ,python-2))) | |
2541 | (home-page "http://kiwi.cs.dal.ca/Software/ExpressBetaDiversity") | |
2542 | (synopsis "Taxon- and phylogenetic-based beta diversity measures") | |
2543 | (description | |
2544 | "Express Beta Diversity (EBD) calculates ecological beta diversity | |
2545 | (dissimilarity) measures between biological communities. EBD implements a | |
2546 | variety of diversity measures including those that make use of phylogenetic | |
2547 | similarity of community members.") | |
2548 | (license license:gpl3+))) | |
2549 | ||
12b04cbe BW |
2550 | (define-public fasttree |
2551 | (package | |
2552 | (name "fasttree") | |
88682c9a | 2553 | (version "2.1.10") |
12b04cbe BW |
2554 | (source (origin |
2555 | (method url-fetch) | |
2556 | (uri (string-append | |
2557 | "http://www.microbesonline.org/fasttree/FastTree-" | |
2558 | version ".c")) | |
2559 | (sha256 | |
2560 | (base32 | |
88682c9a | 2561 | "0vcjdvy1j4m702vmak4svbfkrpcw63k7wymfksjp9a982zy8kjsl")))) |
12b04cbe BW |
2562 | (build-system gnu-build-system) |
2563 | (arguments | |
2564 | `(#:tests? #f ; no "check" target | |
2565 | #:phases | |
2566 | (modify-phases %standard-phases | |
2567 | (delete 'unpack) | |
2568 | (delete 'configure) | |
2569 | (replace 'build | |
e03a5153 | 2570 | (lambda* (#:key source #:allow-other-keys) |
0db75f7a RW |
2571 | (invoke "gcc" |
2572 | "-O3" | |
2573 | "-finline-functions" | |
2574 | "-funroll-loops" | |
2575 | "-Wall" | |
2576 | "-o" | |
2577 | "FastTree" | |
2578 | source | |
2579 | "-lm") | |
2580 | (invoke "gcc" | |
2581 | "-DOPENMP" | |
2582 | "-fopenmp" | |
2583 | "-O3" | |
2584 | "-finline-functions" | |
2585 | "-funroll-loops" | |
2586 | "-Wall" | |
2587 | "-o" | |
2588 | "FastTreeMP" | |
2589 | source | |
2590 | "-lm") | |
2591 | #t)) | |
12b04cbe | 2592 | (replace 'install |
e03a5153 | 2593 | (lambda* (#:key outputs #:allow-other-keys) |
0db75f7a | 2594 | (let ((bin (string-append (assoc-ref outputs "out") "/bin"))) |
f3860753 TGR |
2595 | (install-file "FastTree" bin) |
2596 | (install-file "FastTreeMP" bin) | |
e03a5153 | 2597 | #t)))))) |
12b04cbe BW |
2598 | (home-page "http://www.microbesonline.org/fasttree") |
2599 | (synopsis "Infers approximately-maximum-likelihood phylogenetic trees") | |
2600 | (description | |
2601 | "FastTree can handle alignments with up to a million of sequences in a | |
2602 | reasonable amount of time and memory. For large alignments, FastTree is | |
2603 | 100-1,000 times faster than PhyML 3.0 or RAxML 7.") | |
2604 | (license license:gpl2+))) | |
2605 | ||
2127cedb RW |
2606 | (define-public fastx-toolkit |
2607 | (package | |
2608 | (name "fastx-toolkit") | |
2609 | (version "0.0.14") | |
2610 | (source (origin | |
2611 | (method url-fetch) | |
2612 | (uri | |
2613 | (string-append | |
2614 | "https://github.com/agordon/fastx_toolkit/releases/download/" | |
2615 | version "/fastx_toolkit-" version ".tar.bz2")) | |
2616 | (sha256 | |
2617 | (base32 | |
2618 | "01jqzw386873sr0pjp1wr4rn8fsga2vxs1qfmicvx1pjr72007wy")))) | |
2619 | (build-system gnu-build-system) | |
2620 | (inputs | |
2621 | `(("libgtextutils" ,libgtextutils))) | |
2622 | (native-inputs | |
2623 | `(("pkg-config" ,pkg-config))) | |
2624 | (home-page "http://hannonlab.cshl.edu/fastx_toolkit/") | |
2625 | (synopsis "Tools for FASTA/FASTQ file preprocessing") | |
2626 | (description | |
2627 | "The FASTX-Toolkit is a collection of command line tools for Short-Reads | |
2628 | FASTA/FASTQ files preprocessing. | |
2629 | ||
2630 | Next-Generation sequencing machines usually produce FASTA or FASTQ files, | |
2631 | containing multiple short-reads sequences. The main processing of such | |
2632 | FASTA/FASTQ files is mapping the sequences to reference genomes. However, it | |
2633 | is sometimes more productive to preprocess the files before mapping the | |
2634 | sequences to the genome---manipulating the sequences to produce better mapping | |
2635 | results. The FASTX-Toolkit tools perform some of these preprocessing tasks.") | |
2636 | (license license:agpl3+))) | |
2637 | ||
d7678942 RW |
2638 | (define-public flexbar |
2639 | (package | |
2640 | (name "flexbar") | |
f8ee22fc | 2641 | (version "3.4.0") |
d7678942 | 2642 | (source (origin |
f8ee22fc RW |
2643 | (method git-fetch) |
2644 | (uri (git-reference | |
2645 | (url "https://github.com/seqan/flexbar.git") | |
2646 | (commit (string-append "v" version)))) | |
2647 | (file-name (git-file-name name version)) | |
d7678942 RW |
2648 | (sha256 |
2649 | (base32 | |
f8ee22fc | 2650 | "1pq9sxvdnldl14libk234m72dqhwgzs3acgl943wchwdqlcsi5r2")))) |
d7678942 RW |
2651 | (build-system cmake-build-system) |
2652 | (arguments | |
f8ee22fc | 2653 | `(#:phases |
dc1d3cde KK |
2654 | (modify-phases %standard-phases |
2655 | (replace 'check | |
2656 | (lambda* (#:key outputs #:allow-other-keys) | |
f8ee22fc RW |
2657 | (setenv "PATH" (string-append (getcwd) ":" (getenv "PATH"))) |
2658 | (with-directory-excursion "../source/test" | |
2659 | (invoke "bash" "flexbar_test.sh")) | |
2660 | #t)) | |
2661 | (replace 'install | |
2662 | (lambda* (#:key outputs #:allow-other-keys) | |
2663 | (let* ((out (string-append (assoc-ref outputs "out"))) | |
2664 | (bin (string-append out "/bin/"))) | |
2665 | (install-file "flexbar" bin)) | |
2666 | #t))))) | |
d7678942 RW |
2667 | (inputs |
2668 | `(("tbb" ,tbb) | |
2669 | ("zlib" ,zlib))) | |
2670 | (native-inputs | |
2671 | `(("pkg-config" ,pkg-config) | |
2672 | ("seqan" ,seqan))) | |
f8ee22fc | 2673 | (home-page "https://github.com/seqan/flexbar") |
d7678942 RW |
2674 | (synopsis "Barcode and adapter removal tool for sequencing platforms") |
2675 | (description | |
2676 | "Flexbar preprocesses high-throughput nucleotide sequencing data | |
2677 | efficiently. It demultiplexes barcoded runs and removes adapter sequences. | |
2678 | Moreover, trimming and filtering features are provided. Flexbar increases | |
2679 | read mapping rates and improves genome and transcriptome assemblies. It | |
2680 | supports next-generation sequencing data in fasta/q and csfasta/q format from | |
2681 | Illumina, Roche 454, and the SOLiD platform.") | |
f8ee22fc | 2682 | (license license:bsd-3))) |
d7678942 | 2683 | |
19f4554c BW |
2684 | (define-public fraggenescan |
2685 | (package | |
2686 | (name "fraggenescan") | |
74297231 | 2687 | (version "1.30") |
19f4554c BW |
2688 | (source |
2689 | (origin | |
2690 | (method url-fetch) | |
2691 | (uri | |
2692 | (string-append "mirror://sourceforge/fraggenescan/" | |
2693 | "FragGeneScan" version ".tar.gz")) | |
2694 | (sha256 | |
74297231 | 2695 | (base32 "158dcnwczgcyhwm4qlx19sanrwgdpzf6bn2y57mbpx55lkgz1mzj")))) |
19f4554c BW |
2696 | (build-system gnu-build-system) |
2697 | (arguments | |
2698 | `(#:phases | |
2699 | (modify-phases %standard-phases | |
2700 | (delete 'configure) | |
2701 | (add-before 'build 'patch-paths | |
2702 | (lambda* (#:key outputs #:allow-other-keys) | |
2703 | (let* ((out (string-append (assoc-ref outputs "out"))) | |
2704 | (share (string-append out "/share/fraggenescan/"))) | |
2705 | (substitute* "run_FragGeneScan.pl" | |
2706 | (("system\\(\"rm") | |
2707 | (string-append "system(\"" (which "rm"))) | |
2708 | (("system\\(\"mv") | |
2709 | (string-append "system(\"" (which "mv"))) | |
74297231 | 2710 | (("\\\"awk") (string-append "\"" (which "awk"))) |
19f4554c BW |
2711 | ;; This script and other programs expect the training files |
2712 | ;; to be in the non-standard location bin/train/XXX. Change | |
2713 | ;; this to be share/fraggenescan/train/XXX instead. | |
2714 | (("^\\$train.file = \\$dir.*") | |
2715 | (string-append "$train_file = \"" | |
2716 | share | |
2717 | "train/\".$FGS_train_file;"))) | |
2718 | (substitute* "run_hmm.c" | |
2719 | (("^ strcat\\(train_dir, \\\"train/\\\"\\);") | |
74297231 | 2720 | (string-append " strcpy(train_dir, \"" share "/train/\");")))) |
19f4554c BW |
2721 | #t)) |
2722 | (replace 'build | |
e438c965 RW |
2723 | (lambda _ |
2724 | (invoke "make" "clean") | |
2725 | (invoke "make" "fgs") | |
2726 | #t)) | |
19f4554c BW |
2727 | (replace 'install |
2728 | (lambda* (#:key outputs #:allow-other-keys) | |
2729 | (let* ((out (string-append (assoc-ref outputs "out"))) | |
2730 | (bin (string-append out "/bin/")) | |
2731 | (share (string-append out "/share/fraggenescan/train"))) | |
2732 | (install-file "run_FragGeneScan.pl" bin) | |
2733 | (install-file "FragGeneScan" bin) | |
2e0f6905 MW |
2734 | (copy-recursively "train" share)) |
2735 | #t)) | |
19f4554c BW |
2736 | (delete 'check) |
2737 | (add-after 'install 'post-install-check | |
2738 | ;; In lieu of 'make check', run one of the examples and check the | |
2739 | ;; output files gets created. | |
2740 | (lambda* (#:key outputs #:allow-other-keys) | |
2741 | (let* ((out (string-append (assoc-ref outputs "out"))) | |
74297231 BW |
2742 | (bin (string-append out "/bin/")) |
2743 | (frag (string-append bin "run_FragGeneScan.pl"))) | |
e438c965 RW |
2744 | ;; Test complete genome. |
2745 | (invoke frag | |
2746 | "-genome=./example/NC_000913.fna" | |
2747 | "-out=./test2" | |
2748 | "-complete=1" | |
2749 | "-train=complete") | |
2750 | (unless (and (file-exists? "test2.faa") | |
2751 | (file-exists? "test2.ffn") | |
2752 | (file-exists? "test2.gff") | |
2753 | (file-exists? "test2.out")) | |
2754 | (error "Expected files do not exist.")) | |
2755 | ;; Test incomplete sequences. | |
2756 | (invoke frag | |
2757 | "-genome=./example/NC_000913-fgs.ffn" | |
2758 | "-out=out" | |
2759 | "-complete=0" | |
2760 | "-train=454_30") | |
2761 | #t)))))) | |
19f4554c BW |
2762 | (inputs |
2763 | `(("perl" ,perl) | |
2764 | ("python" ,python-2))) ;not compatible with python 3. | |
2765 | (home-page "https://sourceforge.net/projects/fraggenescan/") | |
2766 | (synopsis "Finds potentially fragmented genes in short reads") | |
2767 | (description | |
2768 | "FragGeneScan is a program for predicting bacterial and archaeal genes in | |
2769 | short and error-prone DNA sequencing reads. It can also be applied to predict | |
2770 | genes in incomplete assemblies or complete genomes.") | |
2771 | ;; GPL3+ according to private correspondense with the authors. | |
2772 | (license license:gpl3+))) | |
2773 | ||
81f3e0c1 BW |
2774 | (define-public fxtract |
2775 | (let ((util-commit "776ca85a18a47492af3794745efcb4a905113115")) | |
2776 | (package | |
2777 | (name "fxtract") | |
2778 | (version "2.3") | |
2779 | (source | |
2780 | (origin | |
91b71cfb RW |
2781 | (method git-fetch) |
2782 | (uri (git-reference | |
2783 | (url "https://github.com/ctSkennerton/fxtract.git") | |
2784 | (commit version))) | |
2785 | (file-name (git-file-name name version)) | |
81f3e0c1 BW |
2786 | (sha256 |
2787 | (base32 | |
91b71cfb | 2788 | "0hab3gpwf4w9s87qlbswq6ws1qqybh4dcqk79q1ahyldzai5fgp5")))) |
81f3e0c1 BW |
2789 | (build-system gnu-build-system) |
2790 | (arguments | |
2791 | `(#:make-flags (list | |
2792 | (string-append "PREFIX=" (assoc-ref %outputs "out")) | |
2793 | "CC=gcc") | |
2794 | #:test-target "fxtract_test" | |
2795 | #:phases | |
2796 | (modify-phases %standard-phases | |
2797 | (delete 'configure) | |
2798 | (add-before 'build 'copy-util | |
2799 | (lambda* (#:key inputs #:allow-other-keys) | |
2800 | (rmdir "util") | |
2801 | (copy-recursively (assoc-ref inputs "ctskennerton-util") "util") | |
2802 | #t)) | |
2803 | ;; Do not use make install as this requires additional dependencies. | |
2804 | (replace 'install | |
2805 | (lambda* (#:key outputs #:allow-other-keys) | |
2806 | (let* ((out (assoc-ref outputs "out")) | |
2807 | (bin (string-append out"/bin"))) | |
2808 | (install-file "fxtract" bin) | |
2809 | #t)))))) | |
2810 | (inputs | |
2811 | `(("pcre" ,pcre) | |
2812 | ("zlib" ,zlib))) | |
2813 | (native-inputs | |
2814 | ;; ctskennerton-util is licensed under GPL2. | |
2815 | `(("ctskennerton-util" | |
2816 | ,(origin | |
2817 | (method git-fetch) | |
2818 | (uri (git-reference | |
2819 | (url "https://github.com/ctSkennerton/util.git") | |
2820 | (commit util-commit))) | |
2821 | (file-name (string-append | |
2822 | "ctstennerton-util-" util-commit "-checkout")) | |
2823 | (sha256 | |
2824 | (base32 | |
2825 | "0cls1hd4vgj3f36fpzzg4xc77d6f3hpc60cbpfmn2gdr7ykzzad7")))))) | |
2826 | (home-page "https://github.com/ctSkennerton/fxtract") | |
2827 | (synopsis "Extract sequences from FASTA and FASTQ files") | |
2828 | (description | |
2829 | "Fxtract extracts sequences from a protein or nucleotide fastx (FASTA | |
2830 | or FASTQ) file given a subsequence. It uses a simple substring search for | |
2831 | basic tasks but can change to using POSIX regular expressions, PCRE, hash | |
2832 | lookups or multi-pattern searching as required. By default fxtract looks in | |
2833 | the sequence of each record but can also be told to look in the header, | |
2834 | comment or quality sections.") | |
afde1a26 BW |
2835 | ;; 'util' requires SSE instructions. |
2836 | (supported-systems '("x86_64-linux")) | |
81f3e0c1 BW |
2837 | (license license:expat)))) |
2838 | ||
2b18ad05 PP |
2839 | (define-public gemma |
2840 | (package | |
2841 | (name "gemma") | |
152bebd9 | 2842 | (version "0.98") |
2b18ad05 | 2843 | (source (origin |
b113f390 RW |
2844 | (method git-fetch) |
2845 | (uri (git-reference | |
2846 | (url "https://github.com/xiangzhou/GEMMA.git") | |
2847 | (commit (string-append "v" version)))) | |
2848 | (file-name (git-file-name name version)) | |
2b18ad05 PP |
2849 | (sha256 |
2850 | (base32 | |
152bebd9 | 2851 | "1s3ncnbn45r2hh1cvrqky1kbqq6546biypr4f5mkw1kqlrgyh0yg")))) |
2b18ad05 | 2852 | (inputs |
152bebd9 RW |
2853 | `(("eigen" ,eigen) |
2854 | ("gfortran" ,gfortran "lib") | |
2855 | ("gsl" ,gsl) | |
2b18ad05 | 2856 | ("lapack" ,lapack) |
152bebd9 | 2857 | ("openblas" ,openblas) |
2b18ad05 PP |
2858 | ("zlib" ,zlib))) |
2859 | (build-system gnu-build-system) | |
2860 | (arguments | |
2c9232ae | 2861 | `(#:make-flags |
ce7e361f EF |
2862 | '(,@(match (%current-system) |
2863 | ("x86_64-linux" | |
2864 | '("FORCE_DYNAMIC=1")) | |
2865 | ("i686-linux" | |
2866 | '("FORCE_DYNAMIC=1" "FORCE_32BIT=1")) | |
2867 | (_ | |
2868 | '("FORCE_DYNAMIC=1" "NO_INTEL_COMPAT=1")))) | |
2b18ad05 PP |
2869 | #:phases |
2870 | (modify-phases %standard-phases | |
2871 | (delete 'configure) | |
152bebd9 RW |
2872 | (add-after 'unpack 'find-eigen |
2873 | (lambda* (#:key inputs #:allow-other-keys) | |
2874 | ;; Ensure that Eigen headers can be found | |
2875 | (setenv "CPLUS_INCLUDE_PATH" | |
2876 | (string-append (getenv "CPLUS_INCLUDE_PATH") | |
2877 | ":" | |
2878 | (assoc-ref inputs "eigen") | |
2879 | "/include/eigen3")) | |
2880 | #t)) | |
2b18ad05 | 2881 | (add-before 'build 'bin-mkdir |
07bf6929 EF |
2882 | (lambda _ |
2883 | (mkdir-p "bin") | |
2884 | #t)) | |
2b18ad05 | 2885 | (replace 'install |
07bf6929 EF |
2886 | (lambda* (#:key outputs #:allow-other-keys) |
2887 | (let ((out (assoc-ref outputs "out"))) | |
2888 | (install-file "bin/gemma" | |
2889 | (string-append | |
2890 | out "/bin"))) | |
2891 | #t))) | |
2b18ad05 PP |
2892 | #:tests? #f)) ; no tests included yet |
2893 | (home-page "https://github.com/xiangzhou/GEMMA") | |
2894 | (synopsis "Tool for genome-wide efficient mixed model association") | |
2895 | (description | |
2896 | "Genome-wide Efficient Mixed Model Association (GEMMA) provides a | |
2897 | standard linear mixed model resolver with application in genome-wide | |
2898 | association studies (GWAS).") | |
2899 | (license license:gpl3))) | |
2900 | ||
5854f685 RW |
2901 | (define-public grit |
2902 | (package | |
2903 | (name "grit") | |
c8f02c1d | 2904 | (version "2.0.5") |
5854f685 | 2905 | (source (origin |
8d75adbf RW |
2906 | (method git-fetch) |
2907 | (uri (git-reference | |
2908 | (url "https://github.com/nboley/grit.git") | |
2909 | (commit version))) | |
2910 | (file-name (git-file-name name version)) | |
5854f685 RW |
2911 | (sha256 |
2912 | (base32 | |
c8f02c1d | 2913 | "1l5v8vfvfbrpmgnrvbrbv40d0arhxcnmxgv2f1mlcqfa3q6bkqm9")))) |
5854f685 RW |
2914 | (build-system python-build-system) |
2915 | (arguments | |
2916 | `(#:python ,python-2 | |
2917 | #:phases | |
dc1d3cde KK |
2918 | (modify-phases %standard-phases |
2919 | (add-after 'unpack 'generate-from-cython-sources | |
2920 | (lambda* (#:key inputs outputs #:allow-other-keys) | |
2921 | ;; Delete these C files to force fresh generation from pyx sources. | |
2922 | (delete-file "grit/sparsify_support_fns.c") | |
2923 | (delete-file "grit/call_peaks_support_fns.c") | |
2924 | (substitute* "setup.py" | |
c8f02c1d | 2925 | (("Cython.Setup") "Cython.Build")) |
dc1d3cde | 2926 | #t))))) |
5854f685 RW |
2927 | (inputs |
2928 | `(("python-scipy" ,python2-scipy) | |
2929 | ("python-numpy" ,python2-numpy) | |
2930 | ("python-pysam" ,python2-pysam) | |
2931 | ("python-networkx" ,python2-networkx))) | |
2932 | (native-inputs | |
f3b98f4f | 2933 | `(("python-cython" ,python2-cython))) |
5854f685 RW |
2934 | (home-page "http://grit-bio.org") |
2935 | (synopsis "Tool for integrative analysis of RNA-seq type assays") | |
2936 | (description | |
2937 | "GRIT is designed to use RNA-seq, TES, and TSS data to build and quantify | |
2938 | full length transcript models. When none of these data sources are available, | |
2939 | GRIT can be run by providing a candidate set of TES or TSS sites. In | |
2940 | addition, GRIT can merge in reference junctions and gene boundaries. GRIT can | |
2941 | also be run in quantification mode, where it uses a provided GTF file and just | |
2942 | estimates transcript expression.") | |
2943 | (license license:gpl3+))) | |
2944 | ||
346a829a RW |
2945 | (define-public hisat |
2946 | (package | |
2947 | (name "hisat") | |
2948 | (version "0.1.4") | |
2949 | (source (origin | |
2950 | (method url-fetch) | |
2951 | (uri (string-append | |
2952 | "http://ccb.jhu.edu/software/hisat/downloads/hisat-" | |
2953 | version "-beta-source.zip")) | |
2954 | (sha256 | |
2955 | (base32 | |
2956 | "1k381ydranqxp09yf2y7w1d0chz5d59vb6jchi89hbb0prq19lk5")))) | |
2957 | (build-system gnu-build-system) | |
2958 | (arguments | |
e58d01fa RW |
2959 | `(#:tests? #f ;no check target |
2960 | #:make-flags '("allall" | |
2961 | ;; Disable unsupported `popcnt' instructions on | |
2962 | ;; architectures other than x86_64 | |
2963 | ,@(if (string-prefix? "x86_64" | |
2964 | (or (%current-target-system) | |
2965 | (%current-system))) | |
2966 | '() | |
2967 | '("POPCNT_CAPABILITY=0"))) | |
346a829a | 2968 | #:phases |
dc1d3cde KK |
2969 | (modify-phases %standard-phases |
2970 | (add-after 'unpack 'patch-sources | |
2971 | (lambda _ | |
2972 | ;; XXX Cannot use snippet because zip files are not supported | |
2973 | (substitute* "Makefile" | |
2974 | (("^CC = .*$") "CC = gcc") | |
2975 | (("^CPP = .*$") "CPP = g++") | |
2976 | ;; replace BUILD_HOST and BUILD_TIME for deterministic build | |
2977 | (("-DBUILD_HOST=.*") "-DBUILD_HOST=\"\\\"guix\\\"\"") | |
2978 | (("-DBUILD_TIME=.*") "-DBUILD_TIME=\"\\\"0\\\"\"")) | |
2979 | (substitute* '("hisat-build" "hisat-inspect") | |
2980 | (("/usr/bin/env") (which "env"))) | |
2981 | #t)) | |
2982 | (replace 'install | |
2983 | (lambda* (#:key outputs #:allow-other-keys) | |
2984 | (let ((bin (string-append (assoc-ref outputs "out") "/bin/"))) | |
2985 | (for-each (lambda (file) | |
2986 | (install-file file bin)) | |
2987 | (find-files | |
2988 | "." | |
2989 | "hisat(-(build|align|inspect)(-(s|l)(-debug)*)*)*$"))) | |
2990 | #t)) | |
2991 | (delete 'configure)))) | |
346a829a RW |
2992 | (native-inputs |
2993 | `(("unzip" ,unzip))) | |
2994 | (inputs | |
2995 | `(("perl" ,perl) | |
2996 | ("python" ,python) | |
2997 | ("zlib" ,zlib))) | |
60af3d82 RW |
2998 | ;; Non-portable SSE instructions are used so building fails on platforms |
2999 | ;; other than x86_64. | |
3000 | (supported-systems '("x86_64-linux")) | |
346a829a RW |
3001 | (home-page "http://ccb.jhu.edu/software/hisat/index.shtml") |
3002 | (synopsis "Hierarchical indexing for spliced alignment of transcripts") | |
3003 | (description | |
3004 | "HISAT is a fast and sensitive spliced alignment program for mapping | |
3005 | RNA-seq reads. In addition to one global FM index that represents a whole | |
3006 | genome, HISAT uses a large set of small FM indexes that collectively cover the | |
3007 | whole genome. These small indexes (called local indexes) combined with | |
3008 | several alignment strategies enable effective alignment of RNA-seq reads, in | |
3009 | particular, reads spanning multiple exons.") | |
3010 | (license license:gpl3+))) | |
3011 | ||
e84efc50 RW |
3012 | (define-public hisat2 |
3013 | (package | |
3014 | (name "hisat2") | |
3015 | (version "2.0.5") | |
3016 | (source | |
3017 | (origin | |
3018 | (method url-fetch) | |
57be690d RW |
3019 | (uri (string-append "ftp://ftp.ccb.jhu.edu/pub/infphilo/hisat2" |
3020 | "/downloads/hisat2-" version "-source.zip")) | |
e84efc50 RW |
3021 | (sha256 |
3022 | (base32 | |
57be690d | 3023 | "0lywnr8kijwsc2aw10dwxic0n0yvip6fl3rjlvc8zzwahamy4x7g")))) |
e84efc50 RW |
3024 | (build-system gnu-build-system) |
3025 | (arguments | |
3026 | `(#:tests? #f ; no check target | |
3027 | #:make-flags (list "CC=gcc" "CXX=g++" "allall") | |
3028 | #:modules ((guix build gnu-build-system) | |
3029 | (guix build utils) | |
3030 | (srfi srfi-26)) | |
3031 | #:phases | |
3032 | (modify-phases %standard-phases | |
3033 | (add-after 'unpack 'make-deterministic | |
3034 | (lambda _ | |
3035 | (substitute* "Makefile" | |
3036 | (("`date`") "0")) | |
3037 | #t)) | |
3038 | (delete 'configure) | |
3039 | (replace 'install | |
3040 | (lambda* (#:key outputs #:allow-other-keys) | |
3041 | (let* ((out (assoc-ref outputs "out")) | |
3042 | (bin (string-append out "/bin/")) | |
3043 | (doc (string-append out "/share/doc/hisat2/"))) | |
3044 | (for-each | |
3045 | (cut install-file <> bin) | |
3046 | (find-files "." | |
3047 | "hisat2(-(build|align|inspect)(-(s|l)(-debug)*)*)*$")) | |
3048 | (mkdir-p doc) | |
3049 | (install-file "doc/manual.inc.html" doc)) | |
3050 | #t))))) | |
3051 | (native-inputs | |
3052 | `(("unzip" ,unzip) ; needed for archive from ftp | |
3053 | ("perl" ,perl) | |
3054 | ("pandoc" ,ghc-pandoc))) ; for documentation | |
3055 | (home-page "http://ccb.jhu.edu/software/hisat2/index.shtml") | |
3056 | (synopsis "Graph-based alignment of genomic sequencing reads") | |
3057 | (description "HISAT2 is a fast and sensitive alignment program for mapping | |
3058 | next-generation sequencing reads (both DNA and RNA) to a population of human | |
3059 | genomes (as well as to a single reference genome). In addition to using one | |
3060 | global @dfn{graph FM} (GFM) index that represents a population of human | |
3061 | genomes, HISAT2 uses a large set of small GFM indexes that collectively cover | |
3062 | the whole genome. These small indexes, combined with several alignment | |
3063 | strategies, enable rapid and accurate alignment of sequencing reads. This new | |
3064 | indexing scheme is called a @dfn{Hierarchical Graph FM index} (HGFM).") | |
3065 | ;; HISAT2 contains files from Bowtie2, which is released under | |
3066 | ;; GPLv2 or later. The HISAT2 source files are released under | |
3067 | ;; GPLv3 or later. | |
3068 | (license license:gpl3+))) | |
3069 | ||
c684629f BW |
3070 | (define-public hmmer |
3071 | (package | |
3072 | (name "hmmer") | |
05fb1e00 | 3073 | (version "3.2.1") |
79f09fa2 BW |
3074 | (source |
3075 | (origin | |
3076 | (method url-fetch) | |
3077 | (uri (string-append | |
05fb1e00 | 3078 | "http://eddylab.org/software/hmmer/hmmer-" version ".tar.gz")) |
79f09fa2 BW |
3079 | (sha256 |
3080 | (base32 | |
05fb1e00 | 3081 | "171bivy6xhgjsz5nv53n81pc3frnwz29ylblawk2bv46szwjjqd5")))) |
c684629f | 3082 | (build-system gnu-build-system) |
b3546174 | 3083 | (native-inputs `(("perl" ,perl))) |
a83e6046 | 3084 | (home-page "http://hmmer.org/") |
c684629f BW |
3085 | (synopsis "Biosequence analysis using profile hidden Markov models") |
3086 | (description | |
3087 | "HMMER is used for searching sequence databases for homologs of protein | |
3088 | sequences, and for making protein sequence alignments. It implements methods | |
3089 | using probabilistic models called profile hidden Markov models (profile | |
3090 | HMMs).") | |
05fb1e00 BW |
3091 | ;; hmmer uses non-portable SSE intrinsics so building fails on other |
3092 | ;; platforms. | |
3093 | (supported-systems '("x86_64-linux" "i686-linux")) | |
3094 | (license license:bsd-3))) | |
c684629f | 3095 | |
85652f59 RW |
3096 | (define-public htseq |
3097 | (package | |
3098 | (name "htseq") | |
92971d68 | 3099 | (version "0.9.1") |
85652f59 RW |
3100 | (source (origin |
3101 | (method url-fetch) | |
75e6639f | 3102 | (uri (pypi-uri "HTSeq" version)) |
85652f59 RW |
3103 | (sha256 |
3104 | (base32 | |
92971d68 | 3105 | "11flgb1381xdhk43bzbfm3vhnszkpqg6jk76rpa5xd1zbrvvlnxg")))) |
85652f59 | 3106 | (build-system python-build-system) |
92971d68 BW |
3107 | (native-inputs |
3108 | `(("python-cython" ,python-cython))) | |
0536727e RW |
3109 | ;; Numpy needs to be propagated when htseq is used as a Python library. |
3110 | (propagated-inputs | |
92971d68 | 3111 | `(("python-numpy" ,python-numpy))) |
578b05d9 | 3112 | (inputs |
92971d68 BW |
3113 | `(("python-pysam" ,python-pysam) |
3114 | ("python-matplotlib" ,python-matplotlib))) | |
85652f59 RW |
3115 | (home-page "http://www-huber.embl.de/users/anders/HTSeq/") |
3116 | (synopsis "Analysing high-throughput sequencing data with Python") | |
3117 | (description | |
3118 | "HTSeq is a Python package that provides infrastructure to process data | |
3119 | from high-throughput sequencing assays.") | |
3120 | (license license:gpl3+))) | |
3121 | ||
92971d68 BW |
3122 | (define-public python2-htseq |
3123 | (package-with-python2 htseq)) | |
3124 | ||
1ad15c16 | 3125 | (define-public java-htsjdk |
15a3c3d4 | 3126 | (package |
1ad15c16 | 3127 | (name "java-htsjdk") |
bd94b6f8 | 3128 | (version "2.3.0") ; last version without build dependency on gradle |
15a3c3d4 | 3129 | (source (origin |
b8a6230d RW |
3130 | (method git-fetch) |
3131 | (uri (git-reference | |
3132 | (url "https://github.com/samtools/htsjdk.git") | |
3133 | (commit version))) | |
3134 | (file-name (git-file-name name version)) | |
15a3c3d4 RW |
3135 | (sha256 |
3136 | (base32 | |
b8a6230d | 3137 | "1b178ixcabanm834ydjl3jiakpyxdmki32hqfv2abrzn3rcwa28i")) |
15a3c3d4 | 3138 | (modules '((guix build utils))) |
bd94b6f8 RW |
3139 | (snippet |
3140 | ;; Delete pre-built binaries | |
3141 | '(begin | |
3142 | (delete-file-recursively "lib") | |
3143 | (mkdir-p "lib") | |
3144 | #t)))) | |
10b4a969 | 3145 | (build-system ant-build-system) |
15a3c3d4 | 3146 | (arguments |
10b4a969 | 3147 | `(#:tests? #f ; test require Internet access |
bd94b6f8 | 3148 | #:jdk ,icedtea-8 |
10b4a969 RW |
3149 | #:make-flags |
3150 | (list (string-append "-Ddist=" (assoc-ref %outputs "out") | |
3151 | "/share/java/htsjdk/")) | |
3152 | #:build-target "all" | |
3153 | #:phases | |
3154 | (modify-phases %standard-phases | |
3155 | ;; The build phase also installs the jars | |
3156 | (delete 'install)))) | |
bd94b6f8 RW |
3157 | (inputs |
3158 | `(("java-ngs" ,java-ngs) | |
3159 | ("java-snappy-1" ,java-snappy-1) | |
3160 | ("java-commons-compress" ,java-commons-compress) | |
3161 | ("java-commons-logging-minimal" ,java-commons-logging-minimal) | |
3162 | ("java-commons-jexl-2" ,java-commons-jexl-2) | |
3163 | ("java-xz" ,java-xz))) | |
3164 | (native-inputs | |
3165 | `(("java-testng" ,java-testng))) | |
15a3c3d4 RW |
3166 | (home-page "http://samtools.github.io/htsjdk/") |
3167 | (synopsis "Java API for high-throughput sequencing data (HTS) formats") | |
3168 | (description | |
3169 | "HTSJDK is an implementation of a unified Java library for accessing | |
3170 | common file formats, such as SAM and VCF, used for high-throughput | |
3171 | sequencing (HTS) data. There are also an number of useful utilities for | |
3172 | manipulating HTS data.") | |
3173 | (license license:expat))) | |
3174 | ||
9a599c17 RW |
3175 | (define-public java-htsjdk-latest |
3176 | (package | |
3177 | (name "java-htsjdk") | |
3178 | (version "2.14.3") | |
3179 | (source (origin | |
3180 | (method git-fetch) | |
3181 | (uri (git-reference | |
3182 | (url "https://github.com/samtools/htsjdk.git") | |
3183 | (commit version))) | |
3184 | (file-name (string-append name "-" version "-checkout")) | |
3185 | (sha256 | |
3186 | (base32 | |
3187 | "1lmya1fdjy03mz6zmdmd86j9v9vfhqb3952mqq075navx1i6g4bc")))) | |
3188 | (build-system ant-build-system) | |
3189 | (arguments | |
3190 | `(#:tests? #f ; test require Scala | |
3191 | #:jdk ,icedtea-8 | |
3192 | #:jar-name "htsjdk.jar" | |
3193 | #:phases | |
3194 | (modify-phases %standard-phases | |
3195 | (add-after 'unpack 'remove-useless-build.xml | |
3196 | (lambda _ (delete-file "build.xml") #t)) | |
3197 | ;; The tests require the scalatest package. | |
3198 | (add-after 'unpack 'remove-tests | |
3199 | (lambda _ (delete-file-recursively "src/test") #t))))) | |
3200 | (inputs | |
3201 | `(("java-ngs" ,java-ngs) | |
3202 | ("java-snappy-1" ,java-snappy-1) | |
3203 | ("java-commons-compress" ,java-commons-compress) | |
3204 | ("java-commons-logging-minimal" ,java-commons-logging-minimal) | |
3205 | ("java-commons-jexl-2" ,java-commons-jexl-2) | |
3206 | ("java-xz" ,java-xz))) | |
3207 | (native-inputs | |
3208 | `(("java-junit" ,java-junit))) | |
3209 | (home-page "http://samtools.github.io/htsjdk/") | |
15a3c3d4 RW |
3210 | (synopsis "Java API for high-throughput sequencing data (HTS) formats") |
3211 | (description | |
3212 | "HTSJDK is an implementation of a unified Java library for accessing | |
3213 | common file formats, such as SAM and VCF, used for high-throughput | |
3214 | sequencing (HTS) data. There are also an number of useful utilities for | |
3215 | manipulating HTS data.") | |
3216 | (license license:expat))) | |
3217 | ||
719fa958 RW |
3218 | ;; This is needed for picard 2.10.3 |
3219 | (define-public java-htsjdk-2.10.1 | |
3220 | (package (inherit java-htsjdk-latest) | |
3221 | (name "java-htsjdk") | |
3222 | (version "2.10.1") | |
3223 | (source (origin | |
3224 | (method git-fetch) | |
3225 | (uri (git-reference | |
3226 | (url "https://github.com/samtools/htsjdk.git") | |
3227 | (commit version))) | |
3228 | (file-name (string-append name "-" version "-checkout")) | |
3229 | (sha256 | |
3230 | (base32 | |
3231 | "1kxh7slm2pm3x9p6jxa1wqsq9a31dhiiflhxnxqcisan4k3rwia2")))) | |
3232 | (build-system ant-build-system) | |
3233 | (arguments | |
3234 | `(#:tests? #f ; tests require Scala | |
3235 | #:jdk ,icedtea-8 | |
3236 | #:jar-name "htsjdk.jar" | |
3237 | #:phases | |
3238 | (modify-phases %standard-phases | |
3239 | (add-after 'unpack 'remove-useless-build.xml | |
3240 | (lambda _ (delete-file "build.xml") #t)) | |
3241 | ;; The tests require the scalatest package. | |
3242 | (add-after 'unpack 'remove-tests | |
3243 | (lambda _ (delete-file-recursively "src/test") #t))))))) | |
3244 | ||
d7fed31a RW |
3245 | ;; This version matches java-htsjdk 2.3.0. Later versions also require a more |
3246 | ;; recent version of java-htsjdk, which depends on gradle. | |
3247 | (define-public java-picard | |
3248 | (package | |
3249 | (name "java-picard") | |
3250 | (version "2.3.0") | |
3251 | (source (origin | |
3252 | (method git-fetch) | |
3253 | (uri (git-reference | |
3254 | (url "https://github.com/broadinstitute/picard.git") | |
3255 | (commit version))) | |
3256 | (file-name (string-append "java-picard-" version "-checkout")) | |
3257 | (sha256 | |
3258 | (base32 | |
3259 | "1ll7mf4r3by92w2nhlmpa591xd1f46xlkwh59mq6fvbb5pdwzvx6")) | |
3260 | (modules '((guix build utils))) | |
3261 | (snippet | |
3262 | '(begin | |
3263 | ;; Delete pre-built binaries. | |
3264 | (delete-file-recursively "lib") | |
3265 | (mkdir-p "lib") | |
3266 | (substitute* "build.xml" | |
3267 | ;; Remove build-time dependency on git. | |
3268 | (("failifexecutionfails=\"true\"") | |
3269 | "failifexecutionfails=\"false\"") | |
3270 | ;; Use our htsjdk. | |
3271 | (("depends=\"compile-htsjdk, ") | |
3272 | "depends=\"") | |
3273 | (("depends=\"compile-htsjdk-tests, ") | |
3274 | "depends=\"") | |
3275 | ;; Build picard-lib.jar before building picard.jar | |
3276 | (("name=\"picard-jar\" depends=\"" line) | |
3277 | (string-append line "picard-lib-jar, "))) | |
3278 | #t)))) | |
3279 | (build-system ant-build-system) | |
3280 | (arguments | |
3281 | `(#:build-target "picard-jar" | |
3282 | #:test-target "test" | |
3283 | ;; Tests require jacoco:coverage. | |
3284 | #:tests? #f | |
3285 | #:make-flags | |
3286 | (list (string-append "-Dhtsjdk_lib_dir=" | |
3287 | (assoc-ref %build-inputs "java-htsjdk") | |
3288 | "/share/java/htsjdk/") | |
3289 | "-Dhtsjdk-classes=dist/tmp" | |
3290 | (string-append "-Dhtsjdk-version=" | |
3291 | ,(package-version java-htsjdk))) | |
3292 | #:jdk ,icedtea-8 | |
3293 | #:phases | |
3294 | (modify-phases %standard-phases | |
1f94ba94 RW |
3295 | ;; FIXME: this phase fails with "duplicate entry: htsjdk/samtools/AbstractBAMFileIndex$1.class" |
3296 | (delete 'generate-jar-indices) | |
d7fed31a RW |
3297 | (add-after 'unpack 'use-our-htsjdk |
3298 | (lambda* (#:key inputs #:allow-other-keys) | |
3299 | (substitute* "build.xml" | |
3300 | (("\\$\\{htsjdk\\}/lib") | |
3301 | (string-append (assoc-ref inputs "java-htsjdk") | |
3302 | "/share/java/htsjdk/"))) | |
3303 | #t)) | |
3304 | (add-after 'unpack 'make-test-target-independent | |
3305 | (lambda* (#:key inputs #:allow-other-keys) | |
3306 | (substitute* "build.xml" | |
3307 | (("name=\"test\" depends=\"compile, ") | |
3308 | "name=\"test\" depends=\"")) | |
3309 | #t)) | |
3310 | (replace 'install (install-jars "dist"))))) | |
3311 | (inputs | |
3312 | `(("java-htsjdk" ,java-htsjdk) | |
3313 | ("java-guava" ,java-guava))) | |
3314 | (native-inputs | |
3315 | `(("java-testng" ,java-testng))) | |
3316 | (home-page "http://broadinstitute.github.io/picard/") | |
3317 | (synopsis "Tools for manipulating high-throughput sequencing data and formats") | |
3318 | (description "Picard is a set of Java command line tools for manipulating | |
3319 | high-throughput sequencing (HTS) data and formats. Picard is implemented | |
3320 | using the HTSJDK Java library to support accessing file formats that are | |
3321 | commonly used for high-throughput sequencing data such as SAM, BAM, CRAM and | |
3322 | VCF.") | |
3323 | (license license:expat))) | |
3324 | ||
72299db9 RW |
3325 | ;; This is needed for dropseq-tools |
3326 | (define-public java-picard-2.10.3 | |
3327 | (package | |
3328 | (name "java-picard") | |
3329 | (version "2.10.3") | |
3330 | (source (origin | |
3331 | (method git-fetch) | |
3332 | (uri (git-reference | |
3333 | (url "https://github.com/broadinstitute/picard.git") | |
3334 | (commit version))) | |
3335 | (file-name (string-append "java-picard-" version "-checkout")) | |
3336 | (sha256 | |
3337 | (base32 | |
3338 | "1ajlx31l6i1k3y2rhnmgq07sz99g2czqfqgkr9mihmdjp3gwjhvi")))) | |
3339 | (build-system ant-build-system) | |
3340 | (arguments | |
3341 | `(#:jar-name "picard.jar" | |
3342 | ;; Tests require jacoco:coverage. | |
3343 | #:tests? #f | |
3344 | #:jdk ,icedtea-8 | |
3345 | #:main-class "picard.cmdline.PicardCommandLine" | |
3346 | #:modules ((guix build ant-build-system) | |
3347 | (guix build utils) | |
3348 | (guix build java-utils) | |
3349 | (sxml simple) | |
3350 | (sxml transform) | |
3351 | (sxml xpath)) | |
3352 | #:phases | |
3353 | (modify-phases %standard-phases | |
e847f402 RW |
3354 | ;; FIXME: this phase fails with "duplicate entry: htsjdk/samtools/AbstractBAMFileIndex$1.class" |
3355 | (delete 'generate-jar-indices) | |
72299db9 RW |
3356 | (add-after 'unpack 'remove-useless-build.xml |
3357 | (lambda _ (delete-file "build.xml") #t)) | |
3358 | ;; This is necessary to ensure that htsjdk is found when using | |
3359 | ;; picard.jar as an executable. | |
3360 | (add-before 'build 'edit-classpath-in-manifest | |
3361 | (lambda* (#:key inputs #:allow-other-keys) | |
3362 | (chmod "build.xml" #o664) | |
3363 | (call-with-output-file "build.xml.new" | |
3364 | (lambda (port) | |
3365 | (sxml->xml | |
3366 | (pre-post-order | |
3367 | (with-input-from-file "build.xml" | |
3368 | (lambda _ (xml->sxml #:trim-whitespace? #t))) | |
3369 | `((target . ,(lambda (tag . kids) | |
3370 | (let ((name ((sxpath '(name *text*)) | |
3371 | (car kids))) | |
3372 | ;; FIXME: We're breaking the line | |
3373 | ;; early with a dummy path to | |
3374 | ;; ensure that the store reference | |
3375 | ;; isn't broken apart and can still | |
3376 | ;; be found by the reference | |
3377 | ;; scanner. | |
3378 | (msg (format #f | |
3379 | "\ | |
3380 | Class-Path: /~a \ | |
d60772dc | 3381 | ~a/share/java/htsjdk.jar${line.separator}${line.separator}" |
72299db9 RW |
3382 | ;; maximum line length is 70 |
3383 | (string-tabulate (const #\b) 57) | |
3384 | (assoc-ref inputs "java-htsjdk")))) | |
3385 | (if (member "manifest" name) | |
3386 | `(,tag ,@kids | |
d60772dc GB |
3387 | (replaceregexp |
3388 | (@ (file "${manifest.file}") | |
3389 | (match "\\r\\n\\r\\n") | |
3390 | (replace "${line.separator}"))) | |
72299db9 RW |
3391 | (echo |
3392 | (@ (message ,msg) | |
3393 | (file "${manifest.file}") | |
3394 | (append "true")))) | |
3395 | `(,tag ,@kids))))) | |
3396 | (*default* . ,(lambda (tag . kids) `(,tag ,@kids))) | |
3397 | (*text* . ,(lambda (_ txt) txt)))) | |
3398 | port))) | |
3399 | (rename-file "build.xml.new" "build.xml") | |
3400 | #t))))) | |
3401 | (propagated-inputs | |
3402 | `(("java-htsjdk" ,java-htsjdk-2.10.1))) | |
3403 | (native-inputs | |
3404 | `(("java-testng" ,java-testng) | |
3405 | ("java-guava" ,java-guava))) | |
3406 | (home-page "http://broadinstitute.github.io/picard/") | |
3407 | (synopsis "Tools for manipulating high-throughput sequencing data and formats") | |
3408 | (description "Picard is a set of Java command line tools for manipulating | |
3409 | high-throughput sequencing (HTS) data and formats. Picard is implemented | |
3410 | using the HTSJDK Java library to support accessing file formats that are | |
3411 | commonly used for high-throughput sequencing data such as SAM, BAM, CRAM and | |
3412 | VCF.") | |
3413 | (license license:expat))) | |
3414 | ||
d7f24778 RW |
3415 | ;; This is the last version of Picard to provide net.sf.samtools |
3416 | (define-public java-picard-1.113 | |
3417 | (package (inherit java-picard) | |
3418 | (name "java-picard") | |
3419 | (version "1.113") | |
3420 | (source (origin | |
3421 | (method git-fetch) | |
3422 | (uri (git-reference | |
3423 | (url "https://github.com/broadinstitute/picard.git") | |
3424 | (commit version))) | |
3425 | (file-name (string-append "java-picard-" version "-checkout")) | |
3426 | (sha256 | |
3427 | (base32 | |
3428 | "0lkpvin2fz3hhly4l02kk56fqy8lmlgyzr9kmvljk6ry6l1hw973")) | |
3429 | (modules '((guix build utils))) | |
3430 | (snippet | |
3431 | '(begin | |
3432 | ;; Delete pre-built binaries. | |
3433 | (delete-file-recursively "lib") | |
3434 | (mkdir-p "lib") | |
3435 | #t)))) | |
3436 | (build-system ant-build-system) | |
3437 | (arguments | |
3438 | `(#:build-target "picard-jar" | |
3439 | #:test-target "test" | |
3440 | ;; FIXME: the class path at test time is wrong. | |
3441 | ;; [testng] Error: A JNI error has occurred, please check your installation and try again | |
3442 | ;; [testng] Exception in thread "main" java.lang.NoClassDefFoundError: com/beust/jcommander/ParameterException | |
3443 | #:tests? #f | |
3444 | #:jdk ,icedtea-8 | |
3445 | ;; This is only used for tests. | |
3446 | #:make-flags | |
3447 | (list "-Dsamjdk.intel_deflater_so_path=lib/jni/libIntelDeflater.so") | |
3448 | #:phases | |
3449 | (modify-phases %standard-phases | |
a993ad83 RW |
3450 | ;; FIXME: This phase fails. |
3451 | (delete 'generate-jar-indices) | |
d7f24778 RW |
3452 | ;; Do not use bundled ant bzip2. |
3453 | (add-after 'unpack 'use-ant-bzip | |
3454 | (lambda* (#:key inputs #:allow-other-keys) | |
3455 | (substitute* "build.xml" | |
3456 | (("\\$\\{lib\\}/apache-ant-1.8.2-bzip2.jar") | |
3457 | (string-append (assoc-ref inputs "ant") | |
3458 | "/lib/ant.jar"))) | |
3459 | #t)) | |
3460 | (add-after 'unpack 'make-test-target-independent | |
3461 | (lambda* (#:key inputs #:allow-other-keys) | |
3462 | (substitute* "build.xml" | |
3463 | (("name=\"test\" depends=\"compile, ") | |
3464 | "name=\"test\" depends=\"compile-tests, ") | |
3465 | (("name=\"compile\" depends=\"compile-src, compile-tests\"") | |
3466 | "name=\"compile\" depends=\"compile-src\"")) | |
3467 | #t)) | |
3468 | (add-after 'unpack 'fix-deflater-path | |
3469 | (lambda* (#:key outputs #:allow-other-keys) | |
3470 | (substitute* "src/java/net/sf/samtools/Defaults.java" | |
3471 | (("getStringProperty\\(\"intel_deflater_so_path\", null\\)") | |
3472 | (string-append "getStringProperty(\"intel_deflater_so_path\", \"" | |
3473 | (assoc-ref outputs "out") | |
3474 | "/lib/jni/libIntelDeflater.so" | |
3475 | "\")"))) | |
3476 | #t)) | |
3477 | ;; Build the deflater library, because we've previously deleted the | |
3478 | ;; pre-built one. This can only be built with access to the JDK | |
3479 | ;; sources. | |
3480 | (add-after 'build 'build-jni | |
3481 | (lambda* (#:key inputs #:allow-other-keys) | |
3482 | (mkdir-p "lib/jni") | |
3483 | (mkdir-p "jdk-src") | |
c527d36f RW |
3484 | (invoke "tar" "--strip-components=1" "-C" "jdk-src" |
3485 | "-xf" (assoc-ref inputs "jdk-src")) | |
3486 | (invoke "javah" "-jni" | |
3487 | "-classpath" "classes" | |
3488 | "-d" "lib/" | |
3489 | "net.sf.samtools.util.zip.IntelDeflater") | |
3490 | (with-directory-excursion "src/c/inteldeflater" | |
3491 | (invoke "gcc" "-I../../../lib" "-I." | |
3492 | (string-append "-I" (assoc-ref inputs "jdk") | |
3493 | "/include/linux") | |
3494 | "-I../../../jdk-src/src/share/native/common/" | |
3495 | "-I../../../jdk-src/src/solaris/native/common/" | |
3496 | "-c" "-O3" "-fPIC" "IntelDeflater.c") | |
3497 | (invoke "gcc" "-shared" | |
3498 | "-o" "../../../lib/jni/libIntelDeflater.so" | |
3499 | "IntelDeflater.o" "-lz" "-lstdc++")) | |
3500 | #t)) | |
d7f24778 RW |
3501 | ;; We can only build everything else after building the JNI library. |
3502 | (add-after 'build-jni 'build-rest | |
3503 | (lambda* (#:key make-flags #:allow-other-keys) | |
c527d36f RW |
3504 | (apply invoke `("ant" "all" ,@make-flags)) |
3505 | #t)) | |
d7f24778 RW |
3506 | (add-before 'build 'set-JAVA6_HOME |
3507 | (lambda _ | |
3508 | (setenv "JAVA6_HOME" (getenv "JAVA_HOME")) | |
3509 | #t)) | |
3510 | (replace 'install (install-jars "dist")) | |
3511 | (add-after 'install 'install-jni-lib | |
3512 | (lambda* (#:key outputs #:allow-other-keys) | |
3513 | (let ((jni (string-append (assoc-ref outputs "out") | |
3514 | "/lib/jni"))) | |
3515 | (mkdir-p jni) | |
3516 | (install-file "lib/jni/libIntelDeflater.so" jni) | |
3517 | #t)))))) | |
3518 | (inputs | |
3519 | `(("java-snappy-1" ,java-snappy-1) | |
3520 | ("java-commons-jexl-2" ,java-commons-jexl-2) | |
3521 | ("java-cofoja" ,java-cofoja) | |
3522 | ("ant" ,ant) ; for bzip2 support at runtime | |
3523 | ("zlib" ,zlib))) | |
3524 | (native-inputs | |
3525 | `(("ant-apache-bcel" ,ant-apache-bcel) | |
3526 | ("ant-junit" ,ant-junit) | |
3527 | ("java-testng" ,java-testng) | |
3528 | ("java-commons-bcel" ,java-commons-bcel) | |
3529 | ("java-jcommander" ,java-jcommander) | |
3530 | ("jdk" ,icedtea-8 "jdk") | |
3531 | ("jdk-src" ,(car (assoc-ref (package-native-inputs icedtea-8) "jdk-drop"))))))) | |
3532 | ||
bd975831 RW |
3533 | (define-public fastqc |
3534 | (package | |
3535 | (name "fastqc") | |
3536 | (version "0.11.5") | |
3537 | (source | |
3538 | (origin | |
3539 | (method url-fetch) | |
3540 | (uri (string-append "http://www.bioinformatics.babraham.ac.uk/" | |
3541 | "projects/fastqc/fastqc_v" | |
3542 | version "_source.zip")) | |
3543 | (sha256 | |
3544 | (base32 | |
3545 | "18rrlkhcrxvvvlapch4dpj6xc6mpayzys8qfppybi8jrpgx5cc5f")))) | |
3546 | (build-system ant-build-system) | |
3547 | (arguments | |
3548 | `(#:tests? #f ; there are no tests | |
3549 | #:build-target "build" | |
3550 | #:phases | |
3551 | (modify-phases %standard-phases | |
3552 | (add-after 'unpack 'fix-dependencies | |
3553 | (lambda* (#:key inputs #:allow-other-keys) | |
3554 | (substitute* "build.xml" | |
3555 | (("jbzip2-0.9.jar") | |
3556 | (string-append (assoc-ref inputs "java-jbzip2") | |
3557 | "/share/java/jbzip2.jar")) | |
3558 | (("sam-1.103.jar") | |
3559 | (string-append (assoc-ref inputs "java-picard-1.113") | |
3560 | "/share/java/sam-1.112.jar")) | |
3561 | (("cisd-jhdf5.jar") | |
3562 | (string-append (assoc-ref inputs "java-cisd-jhdf5") | |
3563 | "/share/java/sis-jhdf5.jar"))) | |
3564 | #t)) | |
3565 | ;; There is no installation target | |
3566 | (replace 'install | |
3567 | (lambda* (#:key inputs outputs #:allow-other-keys) | |
3568 | (let* ((out (assoc-ref outputs "out")) | |
3569 | (bin (string-append out "/bin")) | |
3570 | (share (string-append out "/share/fastqc/")) | |
3571 | (exe (string-append share "/fastqc"))) | |
3572 | (for-each mkdir-p (list bin share)) | |
3573 | (copy-recursively "bin" share) | |
3574 | (substitute* exe | |
3575 | (("my \\$java_bin = 'java';") | |
3576 | (string-append "my $java_bin = '" | |
3577 | (assoc-ref inputs "java") | |
3578 | "/bin/java';"))) | |
3579 | (chmod exe #o555) | |
3580 | (symlink exe (string-append bin "/fastqc")) | |
3581 | #t)))))) | |
3582 | (inputs | |
3583 | `(("java" ,icedtea) | |
3584 | ("perl" ,perl) ; needed for the wrapper script | |
3585 | ("java-cisd-jhdf5" ,java-cisd-jhdf5) | |
3586 | ("java-picard-1.113" ,java-picard-1.113) | |
3587 | ("java-jbzip2" ,java-jbzip2))) | |
3588 | (native-inputs | |
3589 | `(("unzip" ,unzip))) | |
3590 | (home-page "http://www.bioinformatics.babraham.ac.uk/projects/fastqc/") | |
3591 | (synopsis "Quality control tool for high throughput sequence data") | |
3592 | (description | |
3593 | "FastQC aims to provide a simple way to do some quality control | |
3594 | checks on raw sequence data coming from high throughput sequencing | |
3595 | pipelines. It provides a modular set of analyses which you can use to | |
3596 | give a quick impression of whether your data has any problems of which | |
3597 | you should be aware before doing any further analysis. | |
3598 | ||
3599 | The main functions of FastQC are: | |
3600 | ||
3601 | @itemize | |
3602 | @item Import of data from BAM, SAM or FastQ files (any variant); | |
3603 | @item Providing a quick overview to tell you in which areas there may | |
3604 | be problems; | |
3605 | @item Summary graphs and tables to quickly assess your data; | |
3606 | @item Export of results to an HTML based permanent report; | |
3607 | @item Offline operation to allow automated generation of reports | |
3608 | without running the interactive application. | |
3609 | @end itemize\n") | |
3610 | (license license:gpl3+))) | |
3611 | ||
a1b80245 RW |
3612 | (define-public fastp |
3613 | (package | |
3614 | (name "fastp") | |
3615 | (version "0.14.1") | |
3616 | (source | |
3617 | (origin | |
3618 | (method git-fetch) | |
3619 | (uri (git-reference | |
3620 | (url "https://github.com/OpenGene/fastp.git") | |
3621 | (commit (string-append "v" version)))) | |
3622 | (file-name (git-file-name name version)) | |
3623 | (sha256 | |
3624 | (base32 | |
3625 | "1r6ms5zbf5rps4rgp4z73nczadl00b5rqylw8f684isfz27dp0xh")))) | |
3626 | (build-system gnu-build-system) | |
3627 | (arguments | |
3628 | `(#:tests? #f ; there are none | |
3629 | #:make-flags | |
3630 | (list (string-append "BINDIR=" (assoc-ref %outputs "out") "/bin")) | |
3631 | #:phases | |
3632 | (modify-phases %standard-phases | |
3633 | (delete 'configure) | |
3634 | (add-before 'install 'create-target-dir | |
3635 | (lambda* (#:key outputs #:allow-other-keys) | |
3636 | (mkdir-p (string-append (assoc-ref outputs "out") "/bin")) | |
3637 | #t))))) | |
3638 | (inputs | |
3639 | `(("zlib" ,zlib))) | |
3640 | (home-page "https://github.com/OpenGene/fastp/") | |
3641 | (synopsis "All-in-one FastQ preprocessor") | |
3642 | (description | |
3643 | "Fastp is a tool designed to provide fast all-in-one preprocessing for | |
3644 | FastQ files. This tool has multi-threading support to afford high | |
3645 | performance.") | |
3646 | (license license:expat))) | |
3647 | ||
e7c09730 RW |
3648 | (define-public htslib |
3649 | (package | |
3650 | (name "htslib") | |
bd5f5eec | 3651 | (version "1.9") |
e7c09730 RW |
3652 | (source (origin |
3653 | (method url-fetch) | |
3654 | (uri (string-append | |
3655 | "https://github.com/samtools/htslib/releases/download/" | |
3656 | version "/htslib-" version ".tar.bz2")) | |
3657 | (sha256 | |
3658 | (base32 | |
bd5f5eec | 3659 | "16ljv43sc3fxmv63w7b2ff8m1s7h89xhazwmbm1bicz8axq8fjz0")))) |
e7c09730 | 3660 | (build-system gnu-build-system) |
e7c09730 | 3661 | (inputs |
a9e4a1e6 BW |
3662 | `(("openssl" ,openssl) |
3663 | ("curl" ,curl) | |
3664 | ("zlib" ,zlib))) | |
e7c09730 RW |
3665 | (native-inputs |
3666 | `(("perl" ,perl))) | |
3667 | (home-page "http://www.htslib.org") | |
3668 | (synopsis "C library for reading/writing high-throughput sequencing data") | |
3669 | (description | |
3670 | "HTSlib is a C library for reading/writing high-throughput sequencing | |
8057dee1 TGR |
3671 | data. It also provides the @command{bgzip}, @command{htsfile}, and |
3672 | @command{tabix} utilities.") | |
e7c09730 RW |
3673 | ;; Files under cram/ are released under the modified BSD license; |
3674 | ;; the rest is released under the Expat license | |
3675 | (license (list license:expat license:bsd-3)))) | |
3676 | ||
bca2c576 BW |
3677 | ;; This package should be removed once no packages rely upon it. |
3678 | (define htslib-1.3 | |
3679 | (package | |
3680 | (inherit htslib) | |
3681 | (version "1.3.1") | |
3682 | (source (origin | |
3683 | (method url-fetch) | |
3684 | (uri (string-append | |
3685 | "https://github.com/samtools/htslib/releases/download/" | |
3686 | version "/htslib-" version ".tar.bz2")) | |
3687 | (sha256 | |
3688 | (base32 | |
3689 | "1rja282fwdc25ql6izkhdyh8ppw8x2fs0w0js78zgkmqjlikmma9")))))) | |
3690 | ||
c4325f62 RW |
3691 | (define-public idr |
3692 | (package | |
3693 | (name "idr") | |
aa33cc29 | 3694 | (version "2.0.3") |
c4325f62 | 3695 | (source (origin |
f0731591 RW |
3696 | (method git-fetch) |
3697 | (uri (git-reference | |
3698 | (url "https://github.com/nboley/idr.git") | |
3699 | (commit version))) | |
3700 | (file-name (git-file-name name version)) | |
c4325f62 RW |
3701 | (sha256 |
3702 | (base32 | |
f0731591 | 3703 | "04j876h6z444v2q79drxx283d3k5snd72kj895wbalnl42206x9g")) |
aa33cc29 RW |
3704 | ;; Delete generated C code. |
3705 | (snippet | |
3706 | '(begin (delete-file "idr/inv_cdf.c") #t)))) | |
c4325f62 | 3707 | (build-system python-build-system) |
aa33cc29 RW |
3708 | ;; There is only one test ("test_inv_cdf.py") and it tests features that |
3709 | ;; are no longer part of this package. It also asserts False, which | |
3710 | ;; causes the tests to always fail. | |
3711 | (arguments `(#:tests? #f)) | |
b7a820fc | 3712 | (propagated-inputs |
c4325f62 | 3713 | `(("python-scipy" ,python-scipy) |
b7a820fc | 3714 | ("python-sympy" ,python-sympy) |
c4325f62 RW |
3715 | ("python-numpy" ,python-numpy) |
3716 | ("python-matplotlib" ,python-matplotlib))) | |
3717 | (native-inputs | |
f3b98f4f | 3718 | `(("python-cython" ,python-cython))) |
c4325f62 RW |
3719 | (home-page "https://github.com/nboley/idr") |
3720 | (synopsis "Tool to measure the irreproducible discovery rate (IDR)") | |
3721 | (description | |
3722 | "The IDR (Irreproducible Discovery Rate) framework is a unified approach | |
3723 | to measure the reproducibility of findings identified from replicate | |
3724 | experiments and provide highly stable thresholds based on reproducibility.") | |
40590caf | 3725 | (license license:gpl2+))) |
c4325f62 | 3726 | |
43c565d2 RW |
3727 | (define-public jellyfish |
3728 | (package | |
3729 | (name "jellyfish") | |
647465ac | 3730 | (version "2.2.10") |
43c565d2 RW |
3731 | (source (origin |
3732 | (method url-fetch) | |
3733 | (uri (string-append "https://github.com/gmarcais/Jellyfish/" | |
3734 | "releases/download/v" version | |
3735 | "/jellyfish-" version ".tar.gz")) | |
3736 | (sha256 | |
3737 | (base32 | |
647465ac | 3738 | "1k4pc3fvv6w1km2yph4m5sd78fbxp21d6xyzgmy0gjihzc6mb249")))) |
43c565d2 RW |
3739 | (build-system gnu-build-system) |
3740 | (outputs '("out" ;for library | |
3741 | "ruby" ;for Ruby bindings | |
3742 | "python")) ;for Python bindings | |
3743 | (arguments | |
3744 | `(#:configure-flags | |
3745 | (list (string-append "--enable-ruby-binding=" | |
3746 | (assoc-ref %outputs "ruby")) | |
3747 | (string-append "--enable-python-binding=" | |
3748 | (assoc-ref %outputs "python"))) | |
3749 | #:phases | |
3750 | (modify-phases %standard-phases | |
3751 | (add-before 'check 'set-SHELL-variable | |
3752 | (lambda _ | |
3753 | ;; generator_manager.hpp either uses /bin/sh or $SHELL | |
3754 | ;; to run tests. | |
3755 | (setenv "SHELL" (which "bash")) | |
3756 | #t))))) | |
3757 | (native-inputs | |
3758 | `(("bc" ,bc) | |
3759 | ("time" ,time) | |
3760 | ("ruby" ,ruby) | |
117d8cc4 RW |
3761 | ("python" ,python-2) |
3762 | ("pkg-config" ,pkg-config))) | |
3763 | (inputs | |
3764 | `(("htslib" ,htslib))) | |
43c565d2 RW |
3765 | (synopsis "Tool for fast counting of k-mers in DNA") |
3766 | (description | |
3767 | "Jellyfish is a tool for fast, memory-efficient counting of k-mers in | |
3768 | DNA. A k-mer is a substring of length k, and counting the occurrences of all | |
3769 | such substrings is a central step in many analyses of DNA sequence. Jellyfish | |
3770 | is a command-line program that reads FASTA and multi-FASTA files containing | |
3771 | DNA sequences. It outputs its k-mer counts in a binary format, which can be | |
3772 | translated into a human-readable text format using the @code{jellyfish dump} | |
3773 | command, or queried for specific k-mers with @code{jellyfish query}.") | |
3774 | (home-page "http://www.genome.umd.edu/jellyfish.html") | |
647465ac EF |
3775 | ;; JELLYFISH seems to be 64-bit only. |
3776 | (supported-systems '("x86_64-linux" "aarch64-linux" "mips64el-linux")) | |
43c565d2 RW |
3777 | ;; The combined work is published under the GPLv3 or later. Individual |
3778 | ;; files such as lib/jsoncpp.cpp are released under the Expat license. | |
3779 | (license (list license:gpl3+ license:expat)))) | |
3780 | ||
94ff3157 BW |
3781 | (define-public khmer |
3782 | (package | |
3783 | (name "khmer") | |
4b8f4536 | 3784 | (version "2.1.2") |
94ff3157 BW |
3785 | (source |
3786 | (origin | |
4b8f4536 RW |
3787 | (method git-fetch) |
3788 | (uri (git-reference | |
3789 | (url "https://github.com/dib-lab/khmer.git") | |
3790 | (commit (string-append "v" version)))) | |
3791 | (file-name (git-file-name name version)) | |
94ff3157 BW |
3792 | (sha256 |
3793 | (base32 | |
4b8f4536 RW |
3794 | "02x38d9jw2r58y8dmnj4hffy9wxv1yc1jwbvdbhby9dxndv94r9m")) |
3795 | (patches (search-patches "khmer-use-libraries.patch")) | |
3796 | (modules '((guix build utils))) | |
3797 | (snippet | |
3798 | '(begin | |
3799 | ;; Delete bundled libraries. We do not replace the bundled seqan | |
3800 | ;; as it is a modified subset of the old version 1.4.1. | |
3801 | ;; | |
3802 | ;; We do not replace the bundled MurmurHash as the canonical | |
3803 | ;; repository for this code 'SMHasher' is unsuitable for providing | |
3804 | ;; a library. See | |
3805 | ;; https://lists.gnu.org/archive/html/guix-devel/2016-06/msg00977.html | |
3806 | (delete-file-recursively "third-party/zlib") | |
3807 | (delete-file-recursively "third-party/bzip2") | |
3808 | #t)))) | |
94ff3157 BW |
3809 | (build-system python-build-system) |
3810 | (arguments | |
3811 | `(#:phases | |
3812 | (modify-phases %standard-phases | |
94ff3157 | 3813 | (add-after 'unpack 'set-cc |
4b8f4536 RW |
3814 | (lambda _ (setenv "CC" "gcc") #t)) |
3815 | ;; FIXME: This fails with "permission denied". | |
3816 | (delete 'reset-gzip-timestamps)))) | |
94ff3157 | 3817 | (native-inputs |
4b8f4536 RW |
3818 | `(("python-cython" ,python-cython) |
3819 | ("python-pytest" ,python-pytest) | |
3820 | ("python-pytest-runner" ,python-pytest-runner))) | |
94ff3157 BW |
3821 | (inputs |
3822 | `(("zlib" ,zlib) | |
3823 | ("bzip2" ,bzip2) | |
3824 | ("python-screed" ,python-screed) | |
4b8f4536 | 3825 | ("python-bz2file" ,python-bz2file))) |
94ff3157 BW |
3826 | (home-page "https://khmer.readthedocs.org/") |
3827 | (synopsis "K-mer counting, filtering and graph traversal library") | |
3828 | (description "The khmer software is a set of command-line tools for | |
3829 | working with DNA shotgun sequencing data from genomes, transcriptomes, | |
3830 | metagenomes and single cells. Khmer can make de novo assemblies faster, and | |
3831 | sometimes better. Khmer can also identify and fix problems with shotgun | |
3832 | data.") | |
8157af2e EF |
3833 | ;; When building on i686, armhf and mips64el, we get the following error: |
3834 | ;; error: ['khmer', 'khmer.tests', 'oxli'] require 64-bit operating system | |
3df57b3a | 3835 | (supported-systems '("x86_64-linux" "aarch64-linux")) |
94ff3157 BW |
3836 | (license license:bsd-3))) |
3837 | ||
b9a601d9 RJ |
3838 | (define-public kaiju |
3839 | (package | |
3840 | (name "kaiju") | |
2dc28391 | 3841 | (version "1.6.3") |
b9a601d9 | 3842 | (source (origin |
6fe323bf RW |
3843 | (method git-fetch) |
3844 | (uri (git-reference | |
3845 | (url "https://github.com/bioinformatics-centre/kaiju") | |
3846 | (commit (string-append "v" version)))) | |
3847 | (file-name (git-file-name name version)) | |
b9a601d9 RJ |
3848 | (sha256 |
3849 | (base32 | |
2dc28391 | 3850 | "119pzi0ddzv9mjg4wwa6han0cwr3k3ssn7kirvsjfcq05mi5ka0x")))) |
b9a601d9 RJ |
3851 | (build-system gnu-build-system) |
3852 | (arguments | |
3853 | `(#:tests? #f ; There are no tests. | |
3854 | #:phases | |
3855 | (modify-phases %standard-phases | |
3856 | (delete 'configure) | |
3857 | (add-before 'build 'move-to-src-dir | |
3858 | (lambda _ (chdir "src") #t)) | |
3859 | (replace 'install | |
3860 | (lambda* (#:key inputs outputs #:allow-other-keys) | |
3861 | (let ((bin (string-append (assoc-ref outputs "out") "/bin"))) | |
3862 | (mkdir-p bin) | |
3863 | (chdir "..") | |
6fe323bf | 3864 | (copy-recursively "bin" bin)) |
b9a601d9 RJ |
3865 | #t))))) |
3866 | (inputs | |
53e42694 RJ |
3867 | `(("perl" ,perl) |
3868 | ("zlib" ,zlib))) | |
b9a601d9 RJ |
3869 | (home-page "http://kaiju.binf.ku.dk/") |
3870 | (synopsis "Fast and sensitive taxonomic classification for metagenomics") | |
3871 | (description "Kaiju is a program for sensitive taxonomic classification | |
3872 | of high-throughput sequencing reads from metagenomic whole genome sequencing | |
3873 | experiments.") | |
3874 | (license license:gpl3+))) | |
3875 | ||
d57e6d0f RW |
3876 | (define-public macs |
3877 | (package | |
3878 | (name "macs") | |
ffe8d214 | 3879 | (version "2.1.1.20160309") |
d57e6d0f RW |
3880 | (source (origin |
3881 | (method url-fetch) | |
43ec07f1 | 3882 | (uri (pypi-uri "MACS2" version)) |
d57e6d0f RW |
3883 | (sha256 |
3884 | (base32 | |
ffe8d214 | 3885 | "09ixspd1vcqmz1c81ih70xs4m7qml2iy5vyx1y74zww3iy1vl210")))) |
d57e6d0f RW |
3886 | (build-system python-build-system) |
3887 | (arguments | |
3888 | `(#:python ,python-2 ; only compatible with Python 2.7 | |
3889 | #:tests? #f)) ; no test target | |
3890 | (inputs | |
3891 | `(("python-numpy" ,python2-numpy))) | |
7bf837fd | 3892 | (home-page "https://github.com/taoliu/MACS/") |
d57e6d0f RW |
3893 | (synopsis "Model based analysis for ChIP-Seq data") |
3894 | (description | |
3895 | "MACS is an implementation of a ChIP-Seq analysis algorithm for | |
3896 | identifying transcript factor binding sites named Model-based Analysis of | |
3897 | ChIP-Seq (MACS). MACS captures the influence of genome complexity to evaluate | |
3898 | the significance of enriched ChIP regions and it improves the spatial | |
3899 | resolution of binding sites through combining the information of both | |
3900 | sequencing tag position and orientation.") | |
3901 | (license license:bsd-3))) | |
3902 | ||
41ddebdd BW |
3903 | (define-public mafft |
3904 | (package | |
3905 | (name "mafft") | |
c7a8aa13 | 3906 | (version "7.394") |
41ddebdd BW |
3907 | (source (origin |
3908 | (method url-fetch) | |
3909 | (uri (string-append | |
3146f22d | 3910 | "https://mafft.cbrc.jp/alignment/software/mafft-" version |
41ddebdd BW |
3911 | "-without-extensions-src.tgz")) |
3912 | (file-name (string-append name "-" version ".tgz")) | |
3913 | (sha256 | |
3914 | (base32 | |
c7a8aa13 | 3915 | "0bacjkxfg944p5khhyh5rd4y7wkjc9qk4v2jjj442sqlq0f8ar7b")))) |
41ddebdd BW |
3916 | (build-system gnu-build-system) |
3917 | (arguments | |
3918 | `(#:tests? #f ; no automated tests, though there are tests in the read me | |
3919 | #:make-flags (let ((out (assoc-ref %outputs "out"))) | |
3920 | (list (string-append "PREFIX=" out) | |
3921 | (string-append "BINDIR=" | |
3922 | (string-append out "/bin")))) | |
3923 | #:phases | |
3924 | (modify-phases %standard-phases | |
3925 | (add-after 'unpack 'enter-dir | |
101e8f71 | 3926 | (lambda _ (chdir "core") #t)) |
41ddebdd | 3927 | (add-after 'enter-dir 'patch-makefile |
101e8f71 BW |
3928 | (lambda _ |
3929 | ;; on advice from the MAFFT authors, there is no need to | |
3930 | ;; distribute mafft-profile, mafft-distance, or | |
3931 | ;; mafft-homologs.rb as they are too "specialised". | |
3932 | (substitute* "Makefile" | |
3933 | ;; remove mafft-homologs.rb from SCRIPTS | |
3934 | (("^SCRIPTS = mafft mafft-homologs.rb") | |
3935 | "SCRIPTS = mafft") | |
3936 | ;; remove mafft-homologs from MANPAGES | |
3937 | (("^MANPAGES = mafft.1 mafft-homologs.1") | |
3938 | "MANPAGES = mafft.1") | |
3939 | ;; remove mafft-distance from PROGS | |
3940 | (("^PROGS = dvtditr dndfast7 dndblast sextet5 mafft-distance") | |
3941 | "PROGS = dvtditr dndfast7 dndblast sextet5") | |
3942 | ;; remove mafft-profile from PROGS | |
3943 | (("splittbfast disttbfast tbfast mafft-profile 2cl mccaskillwrap") | |
3944 | "splittbfast disttbfast tbfast f2cl mccaskillwrap") | |
3945 | (("^rm -f mafft-profile mafft-profile.exe") "#") | |
3946 | (("^rm -f mafft-distance mafft-distance.exe") ")#") | |
3947 | ;; do not install MAN pages in libexec folder | |
3948 | (("^\t\\$\\(INSTALL\\) -m 644 \\$\\(MANPAGES\\) \ | |
41ddebdd | 3949 | \\$\\(DESTDIR\\)\\$\\(LIBDIR\\)") "#")) |
101e8f71 | 3950 | #t)) |
02f35bb5 BW |
3951 | (add-after 'enter-dir 'patch-paths |
3952 | (lambda* (#:key inputs #:allow-other-keys) | |
3953 | (substitute* '("pairash.c" | |
3954 | "mafft.tmpl") | |
3955 | (("perl") (which "perl")) | |
3956 | (("([\"`| ])awk" _ prefix) | |
3957 | (string-append prefix (which "awk"))) | |
3958 | (("grep") (which "grep"))) | |
3959 | #t)) | |
101e8f71 BW |
3960 | (delete 'configure) |
3961 | (add-after 'install 'wrap-programs | |
3962 | (lambda* (#:key outputs #:allow-other-keys) | |
3963 | (let* ((out (assoc-ref outputs "out")) | |
3964 | (bin (string-append out "/bin")) | |
3965 | (path (string-append | |
3966 | (assoc-ref %build-inputs "coreutils") "/bin:"))) | |
3967 | (for-each (lambda (file) | |
3968 | (wrap-program file | |
3969 | `("PATH" ":" prefix (,path)))) | |
3970 | (find-files bin))) | |
3971 | #t))))) | |
41ddebdd | 3972 | (inputs |
02f35bb5 | 3973 | `(("perl" ,perl) |
71461f88 | 3974 | ("ruby" ,ruby) |
02f35bb5 | 3975 | ("gawk" ,gawk) |
101e8f71 BW |
3976 | ("grep" ,grep) |
3977 | ("coreutils" ,coreutils))) | |
41ddebdd BW |
3978 | (home-page "http://mafft.cbrc.jp/alignment/software/") |
3979 | (synopsis "Multiple sequence alignment program") | |
3980 | (description | |
3981 | "MAFFT offers a range of multiple alignment methods for nucleotide and | |
3982 | protein sequences. For instance, it offers L-INS-i (accurate; for alignment | |
3983 | of <~200 sequences) and FFT-NS-2 (fast; for alignment of <~30,000 | |
3984 | sequences).") | |
3985 | (license (license:non-copyleft | |
3986 | "http://mafft.cbrc.jp/alignment/software/license.txt" | |
3987 | "BSD-3 with different formatting")))) | |
8fd790eb | 3988 | |
84be3b99 MB |
3989 | (define-public mash |
3990 | (package | |
3991 | (name "mash") | |
5c1f35e7 | 3992 | (version "2.1") |
84be3b99 | 3993 | (source (origin |
497fc04d RW |
3994 | (method git-fetch) |
3995 | (uri (git-reference | |
3996 | (url "https://github.com/marbl/mash.git") | |
3997 | (commit (string-append "v" version)))) | |
3998 | (file-name (git-file-name name version)) | |
84be3b99 MB |
3999 | (sha256 |
4000 | (base32 | |
5c1f35e7 | 4001 | "049hwcc059p2fd9vwndn63laifvvsi0wmv84i6y1fr79k15dxwy6")) |
84be3b99 MB |
4002 | (modules '((guix build utils))) |
4003 | (snippet | |
6cbee49d MW |
4004 | '(begin |
4005 | ;; Delete bundled kseq. | |
4006 | ;; TODO: Also delete bundled murmurhash and open bloom filter. | |
4007 | (delete-file "src/mash/kseq.h") | |
4008 | #t)))) | |
84be3b99 MB |
4009 | (build-system gnu-build-system) |
4010 | (arguments | |
4011 | `(#:tests? #f ; No tests. | |
4012 | #:configure-flags | |
4013 | (list | |
4014 | (string-append "--with-capnp=" (assoc-ref %build-inputs "capnproto")) | |
4015 | (string-append "--with-gsl=" (assoc-ref %build-inputs "gsl"))) | |
4016 | #:make-flags (list "CC=gcc") | |
4017 | #:phases | |
4018 | (modify-phases %standard-phases | |
4019 | (add-after 'unpack 'fix-includes | |
4020 | (lambda _ | |
f38ac742 BW |
4021 | (substitute* '("src/mash/Sketch.cpp" |
4022 | "src/mash/CommandFind.cpp" | |
4023 | "src/mash/CommandScreen.cpp") | |
84be3b99 MB |
4024 | (("^#include \"kseq\\.h\"") |
4025 | "#include \"htslib/kseq.h\"")) | |
e35dce01 | 4026 | #t))))) |
84be3b99 MB |
4027 | (native-inputs |
4028 | `(("autoconf" ,autoconf) | |
4029 | ;; Capnproto and htslib are statically embedded in the final | |
4030 | ;; application. Therefore we also list their licenses, below. | |
4031 | ("capnproto" ,capnproto) | |
4032 | ("htslib" ,htslib))) | |
4033 | (inputs | |
4034 | `(("gsl" ,gsl) | |
4035 | ("zlib" ,zlib))) | |
4036 | (supported-systems '("x86_64-linux")) | |
4037 | (home-page "https://mash.readthedocs.io") | |
4038 | (synopsis "Fast genome and metagenome distance estimation using MinHash") | |
4039 | (description "Mash is a fast sequence distance estimator that uses the | |
4040 | MinHash algorithm and is designed to work with genomes and metagenomes in the | |
4041 | form of assemblies or reads.") | |
4042 | (license (list license:bsd-3 ; Mash | |
4043 | license:expat ; HTSlib and capnproto | |
4044 | license:public-domain ; MurmurHash 3 | |
4045 | license:cpl1.0)))) ; Open Bloom Filter | |
4046 | ||
8fd790eb | 4047 | (define-public metabat |
f3f68a44 BW |
4048 | (package |
4049 | (name "metabat") | |
25bd1fc1 | 4050 | (version "2.12.1") |
f3f68a44 BW |
4051 | (source |
4052 | (origin | |
b58d9e4a RW |
4053 | (method git-fetch) |
4054 | (uri (git-reference | |
4055 | (url "https://bitbucket.org/berkeleylab/metabat.git") | |
4056 | (commit (string-append "v" version)))) | |
4057 | (file-name (git-file-name name version)) | |
f3f68a44 BW |
4058 | (sha256 |
4059 | (base32 | |
b58d9e4a | 4060 | "0hyg2smw1nz69mfvjpk45xyyychmda92c80a0cv7baji84ri4iyn")) |
25bd1fc1 | 4061 | (patches (search-patches "metabat-fix-compilation.patch")))) |
9364a520 | 4062 | (build-system scons-build-system) |
8fd790eb | 4063 | (arguments |
9364a520 AI |
4064 | `(#:scons ,scons-python2 |
4065 | #:scons-flags | |
4066 | (list (string-append "PREFIX=" (assoc-ref %outputs "out")) | |
4067 | (string-append "BOOST_ROOT=" (assoc-ref %build-inputs "boost"))) | |
4068 | #:tests? #f ;; Tests are run during the build phase. | |
4069 | #:phases | |
8fd790eb BW |
4070 | (modify-phases %standard-phases |
4071 | (add-after 'unpack 'fix-includes | |
45469ebe BW |
4072 | (lambda _ |
4073 | (substitute* "src/BamUtils.h" | |
4074 | (("^#include \"bam/bam\\.h\"") | |
4075 | "#include \"samtools/bam.h\"") | |
4076 | (("^#include \"bam/sam\\.h\"") | |
4077 | "#include \"samtools/sam.h\"")) | |
4078 | (substitute* "src/KseqReader.h" | |
4079 | (("^#include \"bam/kseq\\.h\"") | |
4080 | "#include \"htslib/kseq.h\"")) | |
4081 | #t)) | |
8fd790eb | 4082 | (add-after 'unpack 'fix-scons |
f3f68a44 BW |
4083 | (lambda* (#:key inputs #:allow-other-keys) |
4084 | (substitute* "SConstruct" | |
4085 | (("^htslib_dir += 'samtools'") | |
4086 | (string-append "htslib_dir = '" | |
4087 | (assoc-ref inputs "htslib") | |
4088 | "'")) | |
4089 | (("^samtools_dir = 'samtools'") | |
4090 | (string-append "samtools_dir = '" | |
4091 | (assoc-ref inputs "samtools") | |
4092 | "'")) | |
4093 | (("^findStaticOrShared\\('bam', hts_lib") | |
4094 | (string-append "findStaticOrShared('bam', '" | |
4095 | (assoc-ref inputs "samtools") | |
4096 | "/lib'")) | |
4097 | ;; Do not distribute README. | |
4098 | (("^env\\.Install\\(idir_prefix, 'README\\.md'\\)") "")) | |
9364a520 | 4099 | #t))))) |
8fd790eb BW |
4100 | (inputs |
4101 | `(("zlib" ,zlib) | |
4102 | ("perl" ,perl) | |
4103 | ("samtools" ,samtools) | |
4104 | ("htslib" ,htslib) | |
4105 | ("boost" ,boost))) | |
8fd790eb BW |
4106 | (home-page "https://bitbucket.org/berkeleylab/metabat") |
4107 | (synopsis | |
4108 | "Reconstruction of single genomes from complex microbial communities") | |
4109 | (description | |
4110 | "Grouping large genomic fragments assembled from shotgun metagenomic | |
4111 | sequences to deconvolute complex microbial communities, or metagenome binning, | |
4112 | enables the study of individual organisms and their interactions. MetaBAT is | |
4113 | an automated metagenome binning software, which integrates empirical | |
4114 | probabilistic distances of genome abundance and tetranucleotide frequency.") | |
d931a4bb EF |
4115 | ;; The source code contains inline assembly. |
4116 | (supported-systems '("x86_64-linux" "i686-linux")) | |
f3f68a44 BW |
4117 | (license (license:non-copyleft "file://license.txt" |
4118 | "See license.txt in the distribution.")))) | |
8fd790eb | 4119 | |
318c0aee MB |
4120 | (define-public minced |
4121 | (package | |
4122 | (name "minced") | |
6052264b | 4123 | (version "0.3.2") |
318c0aee | 4124 | (source (origin |
9d94ca0e RW |
4125 | (method git-fetch) |
4126 | (uri (git-reference | |
4127 | (url "https://github.com/ctSkennerton/minced.git") | |
4128 | (commit version))) | |
4129 | (file-name (git-file-name name version)) | |
318c0aee MB |
4130 | (sha256 |
4131 | (base32 | |
6052264b | 4132 | "1f5h9him0gd355cnx7p6pnxpknhckd4g0v62mg8zyhfbx9as25fv")))) |
318c0aee MB |
4133 | (build-system gnu-build-system) |
4134 | (arguments | |
4135 | `(#:test-target "test" | |
4136 | #:phases | |
4137 | (modify-phases %standard-phases | |
4138 | (delete 'configure) | |
4139 | (add-before 'check 'fix-test | |
4140 | (lambda _ | |
4141 | ;; Fix test for latest version. | |
4142 | (substitute* "t/Aquifex_aeolicus_VF5.expected" | |
4143 | (("minced:0.1.6") "minced:0.2.0")) | |
4144 | #t)) | |
4145 | (replace 'install ; No install target. | |
4146 | (lambda* (#:key inputs outputs #:allow-other-keys) | |
4147 | (let* ((out (assoc-ref outputs "out")) | |
4148 | (bin (string-append out "/bin")) | |
4149 | (wrapper (string-append bin "/minced"))) | |
4150 | ;; Minced comes with a wrapper script that tries to figure out where | |
4151 | ;; it is located before running the JAR. Since these paths are known | |
4152 | ;; to us, we build our own wrapper to avoid coreutils dependency. | |
4153 | (install-file "minced.jar" bin) | |
4154 | (with-output-to-file wrapper | |
4155 | (lambda _ | |
4156 | (display | |
4157 | (string-append | |
4158 | "#!" (assoc-ref inputs "bash") "/bin/sh\n\n" | |
4159 | (assoc-ref inputs "jre") "/bin/java -jar " | |
4160 | bin "/minced.jar \"$@\"\n")))) | |
2e0f6905 MW |
4161 | (chmod wrapper #o555)) |
4162 | #t))))) | |
318c0aee MB |
4163 | (native-inputs |
4164 | `(("jdk" ,icedtea "jdk"))) | |
4165 | (inputs | |
4166 | `(("bash" ,bash) | |
4167 | ("jre" ,icedtea "out"))) | |
4168 | (home-page "https://github.com/ctSkennerton/minced") | |
4169 | (synopsis "Mining CRISPRs in Environmental Datasets") | |
4170 | (description | |
4171 | "MinCED is a program to find Clustered Regularly Interspaced Short | |
4172 | Palindromic Repeats (CRISPRs) in DNA sequences. It can be used for | |
4173 | unassembled metagenomic reads, but is mainly designed for full genomes and | |
4174 | assembled metagenomic sequence.") | |
4175 | (license license:gpl3+))) | |
4176 | ||
ddd82e0e RW |
4177 | (define-public miso |
4178 | (package | |
4179 | (name "miso") | |
ce4dfde0 | 4180 | (version "0.5.4") |
ddd82e0e RW |
4181 | (source (origin |
4182 | (method url-fetch) | |
34260a10 | 4183 | (uri (pypi-uri "misopy" version)) |
ddd82e0e RW |
4184 | (sha256 |
4185 | (base32 | |
ce4dfde0 | 4186 | "1z3x0vd8ma7pdrnywj7i3kgwl89sdkwrrn62zl7r5calqaq2hyip")) |
ddd82e0e | 4187 | (modules '((guix build utils))) |
6cbee49d MW |
4188 | (snippet '(begin |
4189 | (substitute* "setup.py" | |
4190 | ;; Use setuptools, or else the executables are not | |
4191 | ;; installed. | |
4192 | (("distutils.core") "setuptools") | |
4193 | ;; use "gcc" instead of "cc" for compilation | |
4194 | (("^defines") | |
4195 | "cc.set_executables( | |
ddd82e0e RW |
4196 | compiler='gcc', |
4197 | compiler_so='gcc', | |
4198 | linker_exe='gcc', | |
6cbee49d MW |
4199 | linker_so='gcc -shared'); defines")) |
4200 | #t)))) | |
ddd82e0e RW |
4201 | (build-system python-build-system) |
4202 | (arguments | |
4203 | `(#:python ,python-2 ; only Python 2 is supported | |
4204 | #:tests? #f)) ; no "test" target | |
4205 | (inputs | |
4206 | `(("samtools" ,samtools) | |
4207 | ("python-numpy" ,python2-numpy) | |
4208 | ("python-pysam" ,python2-pysam) | |
4209 | ("python-scipy" ,python2-scipy) | |
4210 | ("python-matplotlib" ,python2-matplotlib))) | |
4211 | (native-inputs | |
f3b98f4f HG |
4212 | `(("python-mock" ,python2-mock) ;for tests |
4213 | ("python-pytz" ,python2-pytz))) ;for tests | |
ddd82e0e RW |
4214 | (home-page "http://genes.mit.edu/burgelab/miso/index.html") |
4215 | (synopsis "Mixture of Isoforms model for RNA-Seq isoform quantitation") | |
4216 | (description | |
4217 | "MISO (Mixture-of-Isoforms) is a probabilistic framework that quantitates | |
4218 | the expression level of alternatively spliced genes from RNA-Seq data, and | |
4219 | identifies differentially regulated isoforms or exons across samples. By | |
4220 | modeling the generative process by which reads are produced from isoforms in | |
4221 | RNA-Seq, the MISO model uses Bayesian inference to compute the probability | |
4222 | that a read originated from a particular isoform.") | |
4223 | (license license:gpl2))) | |
4224 | ||
324efb88 BW |
4225 | (define-public muscle |
4226 | (package | |
4227 | (name "muscle") | |
4228 | (version "3.8.1551") | |
4229 | (source (origin | |
4230 | (method url-fetch/tarbomb) | |
324efb88 BW |
4231 | (uri (string-append |
4232 | "http://www.drive5.com/muscle/muscle_src_" | |
4233 | version ".tar.gz")) | |
4234 | (sha256 | |
4235 | (base32 | |
4236 | "0bj8kj7sdizy3987zx6w7axihk40fk8rn76mpbqqjcnd64i5a367")))) | |
4237 | (build-system gnu-build-system) | |
4238 | (arguments | |
4239 | `(#:make-flags (list "LDLIBS = -lm") | |
4240 | #:phases | |
4241 | (modify-phases %standard-phases | |
4242 | (delete 'configure) | |
4243 | (replace 'check | |
4244 | ;; There are no tests, so just test if it runs. | |
17941646 | 4245 | (lambda _ (invoke "./muscle" "-version") #t)) |
324efb88 BW |
4246 | (replace 'install |
4247 | (lambda* (#:key outputs #:allow-other-keys) | |
4248 | (let* ((out (assoc-ref outputs "out")) | |
4249 | (bin (string-append out "/bin"))) | |
17941646 RW |
4250 | (install-file "muscle" bin) |
4251 | #t)))))) | |
324efb88 BW |
4252 | (home-page "http://www.drive5.com/muscle") |
4253 | (synopsis "Multiple sequence alignment program") | |
4254 | (description | |
4255 | "MUSCLE aims to be a fast and accurate multiple sequence alignment | |
4256 | program for nucleotide and protein sequences.") | |
4257 | ;; License information found in 'muscle -h' and usage.cpp. | |
4258 | (license license:public-domain))) | |
4259 | ||
99268755 BW |
4260 | (define-public newick-utils |
4261 | ;; There are no recent releases so we package from git. | |
4262 | (let ((commit "da121155a977197cab9fbb15953ca1b40b11eb87")) | |
4263 | (package | |
4264 | (name "newick-utils") | |
4265 | (version (string-append "1.6-1." (string-take commit 8))) | |
4266 | (source (origin | |
4267 | (method git-fetch) | |
4268 | (uri (git-reference | |
4269 | (url "https://github.com/tjunier/newick_utils.git") | |
4270 | (commit commit))) | |
4271 | (file-name (string-append name "-" version "-checkout")) | |
4272 | (sha256 | |
4273 | (base32 | |
4274 | "1hkw21rq1mwf7xp0rmbb2gqc0i6p11108m69i7mr7xcjl268pxnb")))) | |
4275 | (build-system gnu-build-system) | |
99268755 BW |
4276 | (inputs |
4277 | ;; XXX: TODO: Enable Lua and Guile bindings. | |
4278 | ;; https://github.com/tjunier/newick_utils/issues/13 | |
4279 | `(("libxml2" ,libxml2) | |
4280 | ("flex" ,flex) | |
4281 | ("bison" ,bison))) | |
4282 | (native-inputs | |
4283 | `(("autoconf" ,autoconf) | |
4284 | ("automake" ,automake) | |
4285 | ("libtool" ,libtool))) | |
4286 | (synopsis "Programs for working with newick format phylogenetic trees") | |
4287 | (description | |
4288 | "Newick-utils is a suite of utilities for processing phylogenetic trees | |
4289 | in Newick format. Functions include re-rooting, extracting subtrees, | |
4290 | trimming, pruning, condensing, drawing (ASCII graphics or SVG).") | |
4291 | (home-page "https://github.com/tjunier/newick_utils") | |
4292 | (license license:bsd-3)))) | |
4293 | ||
1e44cf8b BW |
4294 | (define-public orfm |
4295 | (package | |
4296 | (name "orfm") | |
dfc83ead | 4297 | (version "0.7.1") |
1e44cf8b BW |
4298 | (source (origin |
4299 | (method url-fetch) | |
4300 | (uri (string-append | |
4301 | "https://github.com/wwood/OrfM/releases/download/v" | |
4302 | version "/orfm-" version ".tar.gz")) | |
4303 | (sha256 | |
4304 | (base32 | |
dfc83ead | 4305 | "16iigyr2gd8x0imzkk1dr3k5xsds9bpmwg31ayvjg0f4pir9rwqr")))) |
1e44cf8b BW |
4306 | (build-system gnu-build-system) |
4307 | (inputs `(("zlib" ,zlib))) | |
6b6f7d6a BW |
4308 | (native-inputs |
4309 | `(("ruby-bio-commandeer" ,ruby-bio-commandeer) | |
4310 | ("ruby-rspec" ,ruby-rspec) | |
4311 | ("ruby" ,ruby))) | |
1e44cf8b BW |
4312 | (synopsis "Simple and not slow open reading frame (ORF) caller") |
4313 | (description | |
6b6f7d6a | 4314 | "An ORF caller finds stretches of DNA that, when translated, are not |
1e44cf8b BW |
4315 | interrupted by stop codons. OrfM finds and prints these ORFs.") |
4316 | (home-page "https://github.com/wwood/OrfM") | |
4317 | (license license:lgpl3+))) | |
4318 | ||
c033f5d6 | 4319 | (define-public pplacer |
a2b9d6a8 | 4320 | (let ((commit "807f6f3")) |
c033f5d6 BW |
4321 | (package |
4322 | (name "pplacer") | |
4323 | ;; The commit should be updated with each version change. | |
4324 | (version "1.1.alpha19") | |
4325 | (source | |
4326 | (origin | |
a2b9d6a8 RW |
4327 | (method git-fetch) |
4328 | (uri (git-reference | |
4329 | (url "https://github.com/matsen/pplacer.git") | |
4330 | (commit (string-append "v" version)))) | |
4331 | (file-name (git-file-name name version)) | |
c033f5d6 | 4332 | (sha256 |
a2b9d6a8 | 4333 | (base32 "11ppbbbx20p2g9wj3ff64dhnarb12q79v7qh4rk0gj6lkbz4n7cn")))) |
c033f5d6 BW |
4334 | (build-system ocaml-build-system) |
4335 | (arguments | |
4336 | `(#:ocaml ,ocaml-4.01 | |
4337 | #:findlib ,ocaml4.01-findlib | |
4338 | #:modules ((guix build ocaml-build-system) | |
4339 | (guix build utils) | |
4340 | (ice-9 ftw)) | |
4341 | #:phases | |
4342 | (modify-phases %standard-phases | |
4343 | (delete 'configure) | |
4344 | (add-after 'unpack 'replace-bundled-cddlib | |
4345 | (lambda* (#:key inputs #:allow-other-keys) | |
4346 | (let* ((cddlib-src (assoc-ref inputs "cddlib-src")) | |
4347 | (local-dir "cddlib_guix")) | |
4348 | (mkdir local-dir) | |
4349 | (with-directory-excursion local-dir | |
a2b9d6a8 | 4350 | (invoke "tar" "xvf" cddlib-src)) |
c033f5d6 BW |
4351 | (let ((cddlib-src-folder |
4352 | (string-append local-dir "/" | |
4353 | (list-ref (scandir local-dir) 2) | |
4354 | "/lib-src"))) | |
a2b9d6a8 | 4355 | (for-each make-file-writable (find-files "cdd_src" ".*")) |
c033f5d6 BW |
4356 | (for-each |
4357 | (lambda (file) | |
4358 | (copy-file file | |
4359 | (string-append "cdd_src/" (basename file)))) | |
4360 | (find-files cddlib-src-folder ".*[ch]$"))) | |
4361 | #t))) | |
4362 | (add-after 'unpack 'fix-makefile | |
4363 | (lambda _ | |
4364 | ;; Remove system calls to 'git'. | |
4365 | (substitute* "Makefile" | |
4366 | (("^DESCRIPT:=pplacer-.*") | |
4367 | (string-append | |
4368 | "DESCRIPT:=pplacer-$(shell uname)-v" ,version "\n"))) | |
4369 | (substitute* "myocamlbuild.ml" | |
4370 | (("git describe --tags --long .*\\\" with") | |
4371 | (string-append | |
4372 | "echo -n v" ,version "-" ,commit "\" with"))) | |
4373 | #t)) | |
4374 | (replace 'install | |
4375 | (lambda* (#:key outputs #:allow-other-keys) | |
4376 | (let* ((out (assoc-ref outputs "out")) | |
4377 | (bin (string-append out "/bin"))) | |
4378 | (copy-recursively "bin" bin)) | |
4379 | #t))))) | |
4380 | (native-inputs | |
4381 | `(("zlib" ,zlib) | |
4382 | ("gsl" ,gsl) | |
4383 | ("ocaml-ounit" ,ocaml4.01-ounit) | |
4384 | ("ocaml-batteries" ,ocaml4.01-batteries) | |
4385 | ("ocaml-camlzip" ,ocaml4.01-camlzip) | |
4386 | ("ocaml-csv" ,ocaml4.01-csv) | |
4387 | ("ocaml-sqlite3" ,ocaml4.01-sqlite3) | |
4388 | ("ocaml-xmlm" ,ocaml4.01-xmlm) | |
4389 | ("ocaml-mcl" ,ocaml4.01-mcl) | |
4390 | ("ocaml-gsl" ,ocaml4.01-gsl) | |
4391 | ("cddlib-src" ,(package-source cddlib)))) | |
4392 | (propagated-inputs | |
4393 | `(("pplacer-scripts" ,pplacer-scripts))) | |
4394 | (synopsis "Phylogenetic placement of biological sequences") | |
4395 | (description | |
4396 | "Pplacer places query sequences on a fixed reference phylogenetic tree | |
4397 | to maximize phylogenetic likelihood or posterior probability according to a | |
4398 | reference alignment. Pplacer is designed to be fast, to give useful | |
4399 | information about uncertainty, and to offer advanced visualization and | |
4400 | downstream analysis.") | |
4401 | (home-page "http://matsen.fhcrc.org/pplacer") | |
4402 | (license license:gpl3)))) | |
4403 | ||
4404 | ;; This package is installed alongside 'pplacer'. It is a separate package so | |
4405 | ;; that it can use the python-build-system for the scripts that are | |
4406 | ;; distributed alongside the main OCaml binaries. | |
4407 | (define pplacer-scripts | |
4408 | (package | |
4409 | (inherit pplacer) | |
4410 | (name "pplacer-scripts") | |
4411 | (build-system python-build-system) | |
4412 | (arguments | |
4413 | `(#:python ,python-2 | |
4414 | #:phases | |
4415 | (modify-phases %standard-phases | |
4416 | (add-after 'unpack 'enter-scripts-dir | |
2e0f6905 | 4417 | (lambda _ (chdir "scripts") #t)) |
c033f5d6 | 4418 | (replace 'check |
a1e83a98 | 4419 | (lambda _ (invoke "python" "-m" "unittest" "discover" "-v") #t)) |
c033f5d6 BW |
4420 | (add-after 'install 'wrap-executables |
4421 | (lambda* (#:key inputs outputs #:allow-other-keys) | |
4422 | (let* ((out (assoc-ref outputs "out")) | |
4423 | (bin (string-append out "/bin"))) | |
4424 | (let ((path (string-append | |
4425 | (assoc-ref inputs "hmmer") "/bin:" | |
4426 | (assoc-ref inputs "infernal") "/bin"))) | |
4427 | (display path) | |
4428 | (wrap-program (string-append bin "/refpkg_align.py") | |
4429 | `("PATH" ":" prefix (,path)))) | |
4430 | (let ((path (string-append | |
4431 | (assoc-ref inputs "hmmer") "/bin"))) | |
4432 | (wrap-program (string-append bin "/hrefpkg_query.py") | |
4433 | `("PATH" ":" prefix (,path))))) | |
4434 | #t))))) | |
4435 | (inputs | |
4436 | `(("infernal" ,infernal) | |
4437 | ("hmmer" ,hmmer))) | |
4438 | (propagated-inputs | |
4439 | `(("python-biopython" ,python2-biopython) | |
4440 | ("taxtastic" ,taxtastic))) | |
4441 | (synopsis "Pplacer Python scripts"))) | |
4442 | ||
19ee9201 RW |
4443 | (define-public python2-pbcore |
4444 | (package | |
4445 | (name "python2-pbcore") | |
e301bfc8 | 4446 | (version "1.2.10") |
19ee9201 RW |
4447 | (source (origin |
4448 | (method url-fetch) | |
ddb83129 | 4449 | (uri (pypi-uri "pbcore" version)) |
19ee9201 RW |
4450 | (sha256 |
4451 | (base32 | |
e301bfc8 | 4452 | "1kjmv891d6qbpp4shhhvkl02ff4q5xlpnls2513sm2cjcrs52f1i")))) |
19ee9201 RW |
4453 | (build-system python-build-system) |
4454 | (arguments `(#:python ,python-2)) ; pbcore requires Python 2.7 | |
de5bc890 | 4455 | (propagated-inputs |
19ee9201 RW |
4456 | `(("python-cython" ,python2-cython) |
4457 | ("python-numpy" ,python2-numpy) | |
4458 | ("python-pysam" ,python2-pysam) | |
4459 | ("python-h5py" ,python2-h5py))) | |
4460 | (native-inputs | |
de5bc890 HG |
4461 | `(("python-nose" ,python2-nose) |
4462 | ("python-sphinx" ,python2-sphinx) | |
4463 | ("python-pyxb" ,python2-pyxb))) | |
19ee9201 RW |
4464 | (home-page "http://pacificbiosciences.github.io/pbcore/") |
4465 | (synopsis "Library for reading and writing PacBio data files") | |
4466 | (description | |
4467 | "The pbcore package provides Python APIs for interacting with PacBio data | |
4468 | files and writing bioinformatics applications.") | |
4469 | (license license:bsd-3))) | |
4470 | ||
c61fe02c RW |
4471 | (define-public python2-warpedlmm |
4472 | (package | |
4473 | (name "python2-warpedlmm") | |
4474 | (version "0.21") | |
4475 | (source | |
4476 | (origin | |
4477 | (method url-fetch) | |
4478 | (uri (string-append | |
4479 | "https://pypi.python.org/packages/source/W/WarpedLMM/WarpedLMM-" | |
4480 | version ".zip")) | |
4481 | (sha256 | |
4482 | (base32 | |
4483 | "1agfz6zqa8nc6cw47yh0s3y14gkpa9wqazwcj7mwwj3ffnw39p3j")))) | |
4484 | (build-system python-build-system) | |
4485 | (arguments | |
54c85e12 | 4486 | `(#:python ,python-2)) ; requires Python 2.7 |
c61fe02c RW |
4487 | (propagated-inputs |
4488 | `(("python-scipy" ,python2-scipy) | |
4489 | ("python-numpy" ,python2-numpy) | |
4490 | ("python-matplotlib" ,python2-matplotlib) | |
4491 | ("python-fastlmm" ,python2-fastlmm) | |
4492 | ("python-pandas" ,python2-pandas) | |
4493 | ("python-pysnptools" ,python2-pysnptools))) | |
4494 | (native-inputs | |
f3b98f4f | 4495 | `(("python-mock" ,python2-mock) |
c61fe02c RW |
4496 | ("python-nose" ,python2-nose) |
4497 | ("unzip" ,unzip))) | |
4498 | (home-page "https://github.com/PMBio/warpedLMM") | |
4499 | (synopsis "Implementation of warped linear mixed models") | |
4500 | (description | |
4501 | "WarpedLMM is a Python implementation of the warped linear mixed model, | |
4502 | which automatically learns an optimal warping function (or transformation) for | |
4503 | the phenotype as it models the data.") | |
4504 | (license license:asl2.0))) | |
4505 | ||
2c16316e | 4506 | (define-public pbtranscript-tofu |
698bd297 | 4507 | (let ((commit "8f5467fe6a4472bcfb4226c8720993c8507adfe4")) |
2c16316e RW |
4508 | (package |
4509 | (name "pbtranscript-tofu") | |
698bd297 | 4510 | (version (string-append "2.2.3." (string-take commit 7))) |
2c16316e RW |
4511 | (source (origin |
4512 | (method git-fetch) | |
4513 | (uri (git-reference | |
4514 | (url "https://github.com/PacificBiosciences/cDNA_primer.git") | |
4515 | (commit commit))) | |
9a067efd | 4516 | (file-name (string-append name "-" version "-checkout")) |
2c16316e RW |
4517 | (sha256 |
4518 | (base32 | |
9a067efd RW |
4519 | "1lgnpi35ihay42qx0b6yl3kkgra723i413j33kvs0kvs61h82w0f")) |
4520 | (modules '((guix build utils))) | |
4521 | (snippet | |
4522 | '(begin | |
4523 | ;; remove bundled Cython sources | |
4524 | (delete-file "pbtranscript-tofu/pbtranscript/Cython-0.20.1.tar.gz") | |
4525 | #t)))) | |
2c16316e RW |
4526 | (build-system python-build-system) |
4527 | (arguments | |
4528 | `(#:python ,python-2 | |
cdc2bb50 MB |
4529 | ;; FIXME: Tests fail with "No such file or directory: |
4530 | ;; pbtools/pbtranscript/modified_bx_intervals/intersection_unique.so" | |
4531 | #:tests? #f | |
2c16316e | 4532 | #:phases |
9a067efd RW |
4533 | (modify-phases %standard-phases |
4534 | (add-after 'unpack 'enter-directory | |
4535 | (lambda _ | |
4536 | (chdir "pbtranscript-tofu/pbtranscript/") | |
4537 | #t)) | |
4538 | ;; With setuptools version 18.0 and later this setup.py hack causes | |
4539 | ;; a build error, so we disable it. | |
4540 | (add-after 'enter-directory 'patch-setuppy | |
4541 | (lambda _ | |
4542 | (substitute* "setup.py" | |
4543 | (("if 'setuptools.extension' in sys.modules:") | |
4544 | "if False:")) | |
4545 | #t))))) | |
2c16316e | 4546 | (inputs |
9a067efd | 4547 | `(("python-numpy" ,python2-numpy) |
2c16316e | 4548 | ("python-bx-python" ,python2-bx-python) |
c5372108 RW |
4549 | ("python-networkx" ,python2-networkx) |
4550 | ("python-scipy" ,python2-scipy) | |
9a067efd RW |
4551 | ("python-pbcore" ,python2-pbcore) |
4552 | ("python-h5py" ,python2-h5py))) | |
2c16316e | 4553 | (native-inputs |
9a067efd | 4554 | `(("python-cython" ,python2-cython) |
f3b98f4f | 4555 | ("python-nose" ,python2-nose))) |
2c16316e RW |
4556 | (home-page "https://github.com/PacificBiosciences/cDNA_primer") |
4557 | (synopsis "Analyze transcriptome data generated with the Iso-Seq protocol") | |
4558 | (description | |
4559 | "pbtranscript-tofu contains scripts to analyze transcriptome data | |
4560 | generated using the PacBio Iso-Seq protocol.") | |
4561 | (license license:bsd-3)))) | |
4562 | ||
024130d2 BW |
4563 | (define-public prank |
4564 | (package | |
4565 | (name "prank") | |
4566 | (version "150803") | |
4567 | (source (origin | |
4568 | (method url-fetch) | |
4569 | (uri (string-append | |
4570 | "http://wasabiapp.org/download/prank/prank.source." | |
4571 | version ".tgz")) | |
4572 | (sha256 | |
4573 | (base32 | |
4574 | "0am4z94fs3w2n5xpfls9zda61vq7qqz4q2i7b9hlsxz5q4j3kfm4")))) | |
4575 | (build-system gnu-build-system) | |
4576 | (arguments | |
4577 | `(#:phases | |
4578 | (modify-phases %standard-phases | |
4579 | (add-after 'unpack 'enter-src-dir | |
4580 | (lambda _ | |
4581 | (chdir "src") | |
4582 | #t)) | |
62d00095 EF |
4583 | (add-after 'unpack 'remove-m64-flag |
4584 | ;; Prank will build with the correct 'bit-ness' without this flag | |
4585 | ;; and this allows building on 32-bit machines. | |
4586 | (lambda _ (substitute* "src/Makefile" | |
4587 | (("-m64") "")) | |
4588 | #t)) | |
024130d2 BW |
4589 | (delete 'configure) |
4590 | (replace 'install | |
4591 | (lambda* (#:key outputs #:allow-other-keys) | |
4592 | (let* ((out (assoc-ref outputs "out")) | |
4593 | (bin (string-append out "/bin")) | |
4594 | (man (string-append out "/share/man/man1")) | |
4595 | (path (string-append | |
4596 | (assoc-ref %build-inputs "mafft") "/bin:" | |
4597 | (assoc-ref %build-inputs "exonerate") "/bin:" | |
4598 | (assoc-ref %build-inputs "bppsuite") "/bin"))) | |
4599 | (install-file "prank" bin) | |
4600 | (wrap-program (string-append bin "/prank") | |
4601 | `("PATH" ":" prefix (,path))) | |
4602 | (install-file "prank.1" man)) | |
4603 | #t))))) | |
4604 | (inputs | |
4605 | `(("mafft" ,mafft) | |
4606 | ("exonerate" ,exonerate) | |
4607 | ("bppsuite" ,bppsuite))) | |
4608 | (home-page "http://wasabiapp.org/software/prank/") | |
4609 | (synopsis "Probabilistic multiple sequence alignment program") | |
4610 | (description | |
4611 | "PRANK is a probabilistic multiple sequence alignment program for DNA, | |
4612 | codon and amino-acid sequences. It is based on a novel algorithm that treats | |
4613 | insertions correctly and avoids over-estimation of the number of deletion | |
4614 | events. In addition, PRANK borrows ideas from maximum likelihood methods used | |
4615 | in phylogenetics and correctly takes into account the evolutionary distances | |
4616 | between sequences. Lastly, PRANK allows for defining a potential structure | |
4617 | for sequences to be aligned and then, simultaneously with the alignment, | |
4618 | predicts the locations of structural units in the sequences.") | |
4619 | (license license:gpl2+))) | |
4620 | ||
31a9d653 BW |
4621 | (define-public proteinortho |
4622 | (package | |
4623 | (name "proteinortho") | |
8c864901 | 4624 | (version "5.16b") |
31a9d653 BW |
4625 | (source |
4626 | (origin | |
4627 | (method url-fetch) | |
4628 | (uri | |
4629 | (string-append | |
4630 | "http://www.bioinf.uni-leipzig.de/Software/proteinortho/proteinortho_v" | |
4631 | version "_src.tar.gz")) | |
4632 | (sha256 | |
4633 | (base32 | |
8c864901 | 4634 | "1wl0dawpssqwfjvr651r4wlww8hhjin8nba6xh71ks7sbypx886j")))) |
31a9d653 BW |
4635 | (build-system gnu-build-system) |
4636 | (arguments | |
4637 | `(#:test-target "test" | |
4638 | #:phases | |
4639 | (modify-phases %standard-phases | |
4640 | (replace 'configure | |
4641 | ;; There is no configure script, so we modify the Makefile directly. | |
4642 | (lambda* (#:key outputs #:allow-other-keys) | |
4643 | (substitute* "Makefile" | |
4644 | (("INSTALLDIR=.*") | |
4645 | (string-append | |
4646 | "INSTALLDIR=" (assoc-ref outputs "out") "/bin\n"))) | |
4647 | #t)) | |
4648 | (add-before 'install 'make-install-directory | |
4649 | ;; The install directory is not created during 'make install'. | |
4650 | (lambda* (#:key outputs #:allow-other-keys) | |
4651 | (mkdir-p (string-append (assoc-ref outputs "out") "/bin")) | |
4652 | #t)) | |
4653 | (add-after 'install 'wrap-programs | |
4654 | (lambda* (#:key inputs outputs #:allow-other-keys) | |
4655 | (let* ((path (getenv "PATH")) | |
4656 | (out (assoc-ref outputs "out")) | |
4657 | (binary (string-append out "/bin/proteinortho5.pl"))) | |
4658 | (wrap-program binary `("PATH" ":" prefix (,path)))) | |
4659 | #t))))) | |
4660 | (inputs | |
4661 | `(("perl" ,perl) | |
4662 | ("python" ,python-2) | |
4663 | ("blast+" ,blast+))) | |
4664 | (home-page "http://www.bioinf.uni-leipzig.de/Software/proteinortho") | |
4665 | (synopsis "Detect orthologous genes across species") | |
4666 | (description | |
4667 | "Proteinortho is a tool to detect orthologous genes across different | |
4668 | species. For doing so, it compares similarities of given gene sequences and | |
4669 | clusters them to find significant groups. The algorithm was designed to handle | |
4670 | large-scale data and can be applied to hundreds of species at once.") | |
4671 | (license license:gpl2+))) | |
4672 | ||
846e3409 RW |
4673 | (define-public pyicoteo |
4674 | (package | |
4675 | (name "pyicoteo") | |
4676 | (version "2.0.7") | |
4677 | (source | |
4678 | (origin | |
5e242b02 RW |
4679 | (method git-fetch) |
4680 | (uri (git-reference | |
4681 | (url "https://bitbucket.org/regulatorygenomicsupf/pyicoteo.git") | |
4682 | (commit (string-append "v" version)))) | |
4683 | (file-name (git-file-name name version)) | |
846e3409 RW |
4684 | (sha256 |
4685 | (base32 | |
5e242b02 | 4686 | "0hz5g8d25lbjy1wpscr490l0lmyvaix893hhax4fxnh1h9w34w8p")))) |
846e3409 RW |
4687 | (build-system python-build-system) |
4688 | (arguments | |
4689 | `(#:python ,python-2 ; does not work with Python 3 | |
4690 | #:tests? #f)) ; there are no tests | |
4691 | (inputs | |
4692 | `(("python2-matplotlib" ,python2-matplotlib))) | |
4693 | (home-page "https://bitbucket.org/regulatorygenomicsupf/pyicoteo") | |
4694 | (synopsis "Analyze high-throughput genetic sequencing data") | |
4695 | (description | |
4696 | "Pyicoteo is a suite of tools for the analysis of high-throughput genetic | |
4697 | sequencing data. It works with genomic coordinates. There are currently six | |
4698 | different command-line tools: | |
4699 | ||
4700 | @enumerate | |
4701 | @item pyicoregion: for generating exploratory regions automatically; | |
4702 | @item pyicoenrich: for differential enrichment between two conditions; | |
4703 | @item pyicoclip: for calling CLIP-Seq peaks without a control; | |
4704 | @item pyicos: for genomic coordinates manipulation; | |
4705 | @item pyicoller: for peak calling on punctuated ChIP-Seq; | |
4706 | @item pyicount: to count how many reads from N experiment files overlap in a | |
4707 | region file; | |
4708 | @item pyicotrocol: to combine operations from pyicoteo. | |
4709 | @end enumerate\n") | |
4710 | (license license:gpl3+))) | |
4711 | ||
af860475 BW |
4712 | (define-public prodigal |
4713 | (package | |
4714 | (name "prodigal") | |
e70f7a23 | 4715 | (version "2.6.3") |
af860475 | 4716 | (source (origin |
fff67cc8 RW |
4717 | (method git-fetch) |
4718 | (uri (git-reference | |
4719 | (url "https://github.com/hyattpd/Prodigal.git") | |
4720 | (commit (string-append "v" version)))) | |
4721 | (file-name (git-file-name name version)) | |
af860475 BW |
4722 | (sha256 |
4723 | (base32 | |
fff67cc8 | 4724 | "1fs1hqk83qjbjhrvhw6ni75zakx5ki1ayy3v6wwkn3xvahc9hi5s")))) |
af860475 BW |
4725 | (build-system gnu-build-system) |
4726 | (arguments | |
4727 | `(#:tests? #f ;no check target | |
4728 | #:make-flags (list (string-append "INSTALLDIR=" | |
4729 | (assoc-ref %outputs "out") | |
4730 | "/bin")) | |
4731 | #:phases | |
4732 | (modify-phases %standard-phases | |
4733 | (delete 'configure)))) | |
4734 | (home-page "http://prodigal.ornl.gov") | |
4735 | (synopsis "Protein-coding gene prediction for Archaea and Bacteria") | |
4736 | (description | |
4737 | "Prodigal runs smoothly on finished genomes, draft genomes, and | |
4738 | metagenomes, providing gene predictions in GFF3, Genbank, or Sequin table | |
4739 | format. It runs quickly, in an unsupervised fashion, handles gaps, handles | |
4740 | partial genes, and identifies translation initiation sites.") | |
4741 | (license license:gpl3+))) | |
608dd932 | 4742 | |
ceb62d54 BW |
4743 | (define-public roary |
4744 | (package | |
4745 | (name "roary") | |
dad9556c | 4746 | (version "3.12.0") |
ceb62d54 BW |
4747 | (source |
4748 | (origin | |
4749 | (method url-fetch) | |
4750 | (uri (string-append | |
4751 | "mirror://cpan/authors/id/A/AJ/AJPAGE/Bio-Roary-" | |
4752 | version ".tar.gz")) | |
4753 | (sha256 | |
4754 | (base32 | |
dad9556c | 4755 | "0qxrds9wx7cfhlkihrp6697kx0flhhxymap9fwan0b3rbdhcnmff")))) |
ceb62d54 BW |
4756 | (build-system perl-build-system) |
4757 | (arguments | |
4758 | `(#:phases | |
4759 | (modify-phases %standard-phases | |
4760 | (delete 'configure) | |
4761 | (delete 'build) | |
4762 | (replace 'check | |
4763 | (lambda _ | |
4764 | ;; The tests are not run by default, so we run each test file | |
4765 | ;; directly. | |
4766 | (setenv "PATH" (string-append (getcwd) "/bin" ":" | |
4767 | (getenv "PATH"))) | |
4768 | (setenv "PERL5LIB" (string-append (getcwd) "/lib" ":" | |
4769 | (getenv "PERL5LIB"))) | |
ce49fdcc RW |
4770 | (for-each (lambda (file) |
4771 | (display file)(display "\n") | |
4772 | (invoke "perl" file)) | |
4773 | (find-files "t" ".*\\.t$")) | |
4774 | #t)) | |
ceb62d54 BW |
4775 | (replace 'install |
4776 | ;; There is no 'install' target in the Makefile. | |
4777 | (lambda* (#:key outputs #:allow-other-keys) | |
4778 | (let* ((out (assoc-ref outputs "out")) | |
4779 | (bin (string-append out "/bin")) | |
4780 | (perl (string-append out "/lib/perl5/site_perl")) | |
4781 | (roary-plots "contrib/roary_plots")) | |
4782 | (mkdir-p bin) | |
4783 | (mkdir-p perl) | |
4784 | (copy-recursively "bin" bin) | |
4785 | (copy-recursively "lib" perl) | |
4786 | #t))) | |
4787 | (add-after 'install 'wrap-programs | |
4788 | (lambda* (#:key inputs outputs #:allow-other-keys) | |
4789 | (let* ((out (assoc-ref outputs "out")) | |
4790 | (perl5lib (getenv "PERL5LIB")) | |
4791 | (path (getenv "PATH"))) | |
4792 | (for-each (lambda (prog) | |
4793 | (let ((binary (string-append out "/" prog))) | |
4794 | (wrap-program binary | |
4795 | `("PERL5LIB" ":" prefix | |
4796 | (,(string-append perl5lib ":" out | |
4797 | "/lib/perl5/site_perl")))) | |
4798 | (wrap-program binary | |
4799 | `("PATH" ":" prefix | |
4800 | (,(string-append path ":" out "/bin")))))) | |
4801 | (find-files "bin" ".*[^R]$")) | |
4802 | (let ((file | |
4803 | (string-append out "/bin/roary-create_pan_genome_plots.R")) | |
4804 | (r-site-lib (getenv "R_LIBS_SITE")) | |
4805 | (coreutils-path | |
4806 | (string-append (assoc-ref inputs "coreutils") "/bin"))) | |
4807 | (wrap-program file | |
4808 | `("R_LIBS_SITE" ":" prefix | |
4809 | (,(string-append r-site-lib ":" out "/site-library/")))) | |
4810 | (wrap-program file | |
4811 | `("PATH" ":" prefix | |
4812 | (,(string-append coreutils-path ":" out "/bin")))))) | |
4813 | #t))))) | |
4814 | (native-inputs | |
4815 | `(("perl-env-path" ,perl-env-path) | |
4816 | ("perl-test-files" ,perl-test-files) | |
4817 | ("perl-test-most" ,perl-test-most) | |
4818 | ("perl-test-output" ,perl-test-output))) | |
4819 | (inputs | |
4820 | `(("perl-array-utils" ,perl-array-utils) | |
4821 | ("bioperl" ,bioperl-minimal) | |
da4a707c | 4822 | ("perl-digest-md5-file" ,perl-digest-md5-file) |
ceb62d54 BW |
4823 | ("perl-exception-class" ,perl-exception-class) |
4824 | ("perl-file-find-rule" ,perl-file-find-rule) | |
4825 | ("perl-file-grep" ,perl-file-grep) | |
4826 | ("perl-file-slurper" ,perl-file-slurper) | |
4827 | ("perl-file-which" ,perl-file-which) | |
4828 | ("perl-graph" ,perl-graph) | |
4829 | ("perl-graph-readwrite" ,perl-graph-readwrite) | |
4830 | ("perl-log-log4perl" ,perl-log-log4perl) | |
4831 | ("perl-moose" ,perl-moose) | |
4832 | ("perl-perlio-utf8_strict" ,perl-perlio-utf8_strict) | |
4833 | ("perl-text-csv" ,perl-text-csv) | |
4834 | ("bedtools" ,bedtools) | |
4835 | ("cd-hit" ,cd-hit) | |
4836 | ("blast+" ,blast+) | |
4837 | ("mcl" ,mcl) | |
4838 | ("parallel" ,parallel) | |
4839 | ("prank" ,prank) | |
4840 | ("mafft" ,mafft) | |
4841 | ("fasttree" ,fasttree) | |
4842 | ("grep" ,grep) | |
4843 | ("sed" ,sed) | |
4844 | ("gawk" ,gawk) | |
2d7c4ae3 | 4845 | ("r-minimal" ,r-minimal) |
ceb62d54 BW |
4846 | ("r-ggplot2" ,r-ggplot2) |
4847 | ("coreutils" ,coreutils))) | |
4848 | (home-page "http://sanger-pathogens.github.io/Roary") | |
4849 | (synopsis "High speed stand-alone pan genome pipeline") | |
4850 | (description | |
4851 | "Roary is a high speed stand alone pan genome pipeline, which takes | |
4852 | annotated assemblies in GFF3 format (produced by the Prokka program) and | |
4853 | calculates the pan genome. Using a standard desktop PC, it can analyse | |
4854 | datasets with thousands of samples, without compromising the quality of the | |
4855 | results. 128 samples can be analysed in under 1 hour using 1 GB of RAM and a | |
4856 | single processor. Roary is not intended for metagenomics or for comparing | |
4857 | extremely diverse sets of genomes.") | |
4858 | (license license:gpl3))) | |
4859 | ||
608dd932 BW |
4860 | (define-public raxml |
4861 | (package | |
4862 | (name "raxml") | |
b9d0c356 | 4863 | (version "8.2.12") |
608dd932 BW |
4864 | (source |
4865 | (origin | |
4715d4af RW |
4866 | (method git-fetch) |
4867 | (uri (git-reference | |
4868 | (url "https://github.com/stamatak/standard-RAxML.git") | |
4869 | (commit (string-append "v" version)))) | |
4870 | (file-name (git-file-name name version)) | |
608dd932 BW |
4871 | (sha256 |
4872 | (base32 | |
b9d0c356 | 4873 | "1jqjzhch0rips0vp04prvb8vmc20c5pdmsqn8knadcf91yy859fh")))) |
608dd932 BW |
4874 | (build-system gnu-build-system) |
4875 | (arguments | |
4876 | `(#:tests? #f ; There are no tests. | |
4877 | ;; Use 'standard' Makefile rather than SSE or AVX ones. | |
4878 | #:make-flags (list "-f" "Makefile.HYBRID.gcc") | |
4879 | #:phases | |
4880 | (modify-phases %standard-phases | |
4881 | (delete 'configure) | |
4882 | (replace 'install | |
4883 | (lambda* (#:key outputs #:allow-other-keys) | |
4884 | (let* ((out (assoc-ref outputs "out")) | |
4885 | (bin (string-append out "/bin")) | |
4886 | (executable "raxmlHPC-HYBRID")) | |
4887 | (install-file executable bin) | |
4888 | (symlink (string-append bin "/" executable) "raxml")) | |
4889 | #t))))) | |
4890 | (inputs | |
4891 | `(("openmpi" ,openmpi))) | |
4892 | (home-page "http://sco.h-its.org/exelixis/web/software/raxml/index.html") | |
4893 | (synopsis "Randomized Axelerated Maximum Likelihood phylogenetic trees") | |
4894 | (description | |
4895 | "RAxML is a tool for phylogenetic analysis and post-analysis of large | |
4896 | phylogenies.") | |
2805f9b2 EF |
4897 | ;; The source includes x86 specific code |
4898 | (supported-systems '("x86_64-linux" "i686-linux")) | |
608dd932 | 4899 | (license license:gpl2+))) |
af860475 | 4900 | |
66e3eff1 RW |
4901 | (define-public rsem |
4902 | (package | |
4903 | (name "rsem") | |
89ee8a6e | 4904 | (version "1.3.1") |
66e3eff1 RW |
4905 | (source |
4906 | (origin | |
89ee8a6e RW |
4907 | (method git-fetch) |
4908 | (uri (git-reference | |
4909 | (url "https://github.com/deweylab/RSEM.git") | |
4910 | (commit (string-append "v" version)))) | |
66e3eff1 | 4911 | (sha256 |
89ee8a6e RW |
4912 | (base32 "1jlq11d1p8qp64w75yj8cnbbd1a93viq10pzsbwal7vdn8fg13j1")) |
4913 | (file-name (git-file-name name version)) | |
66e3eff1 RW |
4914 | (modules '((guix build utils))) |
4915 | (snippet | |
4916 | '(begin | |
89ee8a6e | 4917 | ;; remove bundled copy of boost and samtools |
66e3eff1 | 4918 | (delete-file-recursively "boost") |
89ee8a6e | 4919 | (delete-file-recursively "samtools-1.3") |
66e3eff1 RW |
4920 | #t)))) |
4921 | (build-system gnu-build-system) | |
4922 | (arguments | |
4923 | `(#:tests? #f ;no "check" target | |
89ee8a6e RW |
4924 | #:make-flags |
4925 | (list (string-append "BOOST=" | |
4926 | (assoc-ref %build-inputs "boost") | |
4927 | "/include/") | |
4928 | (string-append "SAMHEADERS=" | |
4929 | (assoc-ref %build-inputs "htslib") | |
4930 | "/include/htslib/sam.h") | |
4931 | (string-append "SAMLIBS=" | |
4932 | (assoc-ref %build-inputs "htslib") | |
4933 | "/lib/libhts.a")) | |
66e3eff1 RW |
4934 | #:phases |
4935 | (modify-phases %standard-phases | |
4936 | ;; No "configure" script. | |
4937 | ;; Do not build bundled samtools library. | |
4938 | (replace 'configure | |
89ee8a6e RW |
4939 | (lambda _ |
4940 | (substitute* "Makefile" | |
4941 | (("^all : \\$\\(PROGRAMS\\).*") "all: $(PROGRAMS)\n") | |
4942 | (("^\\$\\(SAMLIBS\\).*") "")) | |
4943 | #t)) | |
66e3eff1 | 4944 | (replace 'install |
89ee8a6e RW |
4945 | (lambda* (#:key outputs #:allow-other-keys) |
4946 | (let* ((out (string-append (assoc-ref outputs "out"))) | |
4947 | (bin (string-append out "/bin/")) | |
4948 | (perl (string-append out "/lib/perl5/site_perl"))) | |
4949 | (mkdir-p bin) | |
4950 | (mkdir-p perl) | |
4951 | (for-each (lambda (file) | |
4952 | (install-file file bin)) | |
4953 | (find-files "." "rsem-.*")) | |
4954 | (install-file "rsem_perl_utils.pm" perl)) | |
4955 | #t)) | |
4956 | (add-after 'install 'wrap-program | |
4957 | (lambda* (#:key outputs #:allow-other-keys) | |
4958 | (let ((out (assoc-ref outputs "out"))) | |
4959 | (for-each (lambda (prog) | |
4960 | (wrap-program (string-append out "/bin/" prog) | |
4961 | `("PERL5LIB" ":" prefix | |
4962 | (,(string-append out "/lib/perl5/site_perl"))))) | |
4963 | '("rsem-calculate-expression" | |
4964 | "rsem-control-fdr" | |
4965 | "rsem-generate-data-matrix" | |
4966 | "rsem-generate-ngvector" | |
4967 | "rsem-plot-transcript-wiggles" | |
4968 | "rsem-prepare-reference" | |
4969 | "rsem-run-ebseq" | |
4970 | "rsem-run-prsem-testing-procedure"))) | |
4971 | #t))))) | |
66e3eff1 RW |
4972 | (inputs |
4973 | `(("boost" ,boost) | |
2d7c4ae3 | 4974 | ("r-minimal" ,r-minimal) |
66e3eff1 | 4975 | ("perl" ,perl) |
89ee8a6e | 4976 | ("htslib" ,htslib-1.3) |
66e3eff1 RW |
4977 | ("zlib" ,zlib))) |
4978 | (home-page "http://deweylab.biostat.wisc.edu/rsem/") | |
4979 | (synopsis "Estimate gene expression levels from RNA-Seq data") | |
4980 | (description | |
4981 | "RSEM is a software package for estimating gene and isoform expression | |
4982 | levels from RNA-Seq data. The RSEM package provides a user-friendly | |
4983 | interface, supports threads for parallel computation of the EM algorithm, | |
4984 | single-end and paired-end read data, quality scores, variable-length reads and | |
4985 | RSPD estimation. In addition, it provides posterior mean and 95% credibility | |
4986 | interval estimates for expression levels. For visualization, it can generate | |
4987 | BAM and Wiggle files in both transcript-coordinate and genomic-coordinate.") | |
4988 | (license license:gpl3+))) | |
4989 | ||
8622a072 RW |
4990 | (define-public rseqc |
4991 | (package | |
4992 | (name "rseqc") | |
4993 | (version "2.6.1") | |
4994 | (source | |
4995 | (origin | |
4996 | (method url-fetch) | |
4997 | (uri | |
4998 | (string-append "mirror://sourceforge/rseqc/" | |
de67e922 | 4999 | "RSeQC-" version ".tar.gz")) |
8622a072 | 5000 | (sha256 |
8214b7fb | 5001 | (base32 "15ly0254yi032qzkdplg00q144qfdsd986gh62829rl5bkxhj330")) |
8622a072 RW |
5002 | (modules '((guix build utils))) |
5003 | (snippet | |
5004 | '(begin | |
5005 | ;; remove bundled copy of pysam | |
5006 | (delete-file-recursively "lib/pysam") | |
5007 | (substitute* "setup.py" | |
5008 | ;; remove dependency on outdated "distribute" module | |
5009 | (("^from distribute_setup import use_setuptools") "") | |
5010 | (("^use_setuptools\\(\\)") "") | |
5011 | ;; do not use bundled copy of pysam | |
6cbee49d MW |
5012 | (("^have_pysam = False") "have_pysam = True")) |
5013 | #t)))) | |
8622a072 RW |
5014 | (build-system python-build-system) |
5015 | (arguments `(#:python ,python-2)) | |
5016 | (inputs | |
5017 | `(("python-cython" ,python2-cython) | |
5018 | ("python-pysam" ,python2-pysam) | |
5019 | ("python-numpy" ,python2-numpy) | |
8622a072 RW |
5020 | ("zlib" ,zlib))) |
5021 | (native-inputs | |
5022 | `(("python-nose" ,python2-nose))) | |
5023 | (home-page "http://rseqc.sourceforge.net/") | |
5024 | (synopsis "RNA-seq quality control package") | |
5025 | (description | |
5026 | "RSeQC provides a number of modules that can comprehensively evaluate | |
5027 | high throughput sequence data, especially RNA-seq data. Some basic modules | |
5028 | inspect sequence quality, nucleotide composition bias, PCR bias and GC bias, | |
5029 | while RNA-seq specific modules evaluate sequencing saturation, mapped reads | |
5030 | distribution, coverage uniformity, strand specificity, etc.") | |
5031 | (license license:gpl3+))) | |
5032 | ||
ec946638 RW |
5033 | (define-public seek |
5034 | ;; There are no release tarballs. According to the installation | |
5035 | ;; instructions at http://seek.princeton.edu/installation.jsp, the latest | |
5036 | ;; stable release is identified by this changeset ID. | |
5037 | (let ((changeset "2329130") | |
5038 | (revision "1")) | |
5039 | (package | |
5040 | (name "seek") | |
5041 | (version (string-append "0-" revision "." changeset)) | |
5042 | (source (origin | |
5043 | (method hg-fetch) | |
5044 | (uri (hg-reference | |
5045 | (url "https://bitbucket.org/libsleipnir/sleipnir") | |
5046 | (changeset changeset))) | |
51106724 | 5047 | (file-name (string-append name "-" version "-checkout")) |
ec946638 RW |
5048 | (sha256 |
5049 | (base32 | |
5050 | "0qrvilwh18dpbhkf92qvxbmay0j75ra3jg2wrhz67gf538zzphsx")))) | |
5051 | (build-system gnu-build-system) | |
5052 | (arguments | |
5053 | `(#:modules ((srfi srfi-1) | |
5054 | (guix build gnu-build-system) | |
5055 | (guix build utils)) | |
5056 | #:phases | |
5057 | (let ((dirs '("SeekMiner" | |
5058 | "SeekEvaluator" | |
5059 | "SeekPrep" | |
5060 | "Distancer" | |
5061 | "Data2DB" | |
5062 | "PCL2Bin"))) | |
5063 | (modify-phases %standard-phases | |
189be331 | 5064 | (replace 'bootstrap |
ec946638 | 5065 | (lambda _ |
a9542937 RW |
5066 | (substitute* "gen_tools_am" |
5067 | (("/usr/bin/env.*") (which "perl"))) | |
5068 | (invoke "bash" "gen_auto") | |
5069 | #t)) | |
ec946638 RW |
5070 | (add-after 'build 'build-additional-tools |
5071 | (lambda* (#:key make-flags #:allow-other-keys) | |
a9542937 RW |
5072 | (for-each (lambda (dir) |
5073 | (with-directory-excursion (string-append "tools/" dir) | |
5074 | (apply invoke "make" make-flags))) | |
5075 | dirs) | |
5076 | #t)) | |
ec946638 RW |
5077 | (add-after 'install 'install-additional-tools |
5078 | (lambda* (#:key make-flags #:allow-other-keys) | |
a9542937 RW |
5079 | (for-each (lambda (dir) |
5080 | (with-directory-excursion (string-append "tools/" dir) | |
5081 | (apply invoke `("make" ,@make-flags "install")))) | |
5082 | dirs) | |
5083 | #t)))))) | |
ec946638 RW |
5084 | (inputs |
5085 | `(("gsl" ,gsl) | |
5086 | ("boost" ,boost) | |
5087 | ("libsvm" ,libsvm) | |
5088 | ("readline" ,readline) | |
5089 | ("gengetopt" ,gengetopt) | |
5090 | ("log4cpp" ,log4cpp))) | |
5091 | (native-inputs | |
5092 | `(("autoconf" ,autoconf) | |
5093 | ("automake" ,automake) | |
5094 | ("perl" ,perl))) | |
5095 | (home-page "http://seek.princeton.edu") | |
5096 | (synopsis "Gene co-expression search engine") | |
5097 | (description | |
5098 | "SEEK is a computational gene co-expression search engine. SEEK provides | |
5099 | biologists with a way to navigate the massive human expression compendium that | |
5100 | now contains thousands of expression datasets. SEEK returns a robust ranking | |
5101 | of co-expressed genes in the biological area of interest defined by the user's | |
5102 | query genes. It also prioritizes thousands of expression datasets according | |
5103 | to the user's query of interest.") | |
5104 | (license license:cc-by3.0)))) | |
5105 | ||
4e10a221 RW |
5106 | (define-public samtools |
5107 | (package | |
5108 | (name "samtools") | |
4ae4a152 | 5109 | (version "1.9") |
4e10a221 RW |
5110 | (source |
5111 | (origin | |
5112 | (method url-fetch) | |
5113 | (uri | |
de67e922 | 5114 | (string-append "mirror://sourceforge/samtools/samtools/" |
4e10a221 RW |
5115 | version "/samtools-" version ".tar.bz2")) |
5116 | (sha256 | |
5117 | (base32 | |
4ae4a152 RW |
5118 | "10ilqbmm7ri8z431sn90lvbjwizd0hhkf9rcqw8j823hf26nhgq8")) |
5119 | (modules '((guix build utils))) | |
5120 | (snippet '(begin | |
5121 | ;; Delete bundled htslib. | |
5122 | (delete-file-recursively "htslib-1.9") | |
5123 | #t)))) | |
4e10a221 RW |
5124 | (build-system gnu-build-system) |
5125 | (arguments | |
c4473411 | 5126 | `(#:modules ((ice-9 ftw) |
5bdda30b RW |
5127 | (ice-9 regex) |
5128 | (guix build gnu-build-system) | |
5129 | (guix build utils)) | |
4ae4a152 | 5130 | #:configure-flags (list "--with-ncurses") |
4e10a221 | 5131 | #:phases |
c842d425 BW |
5132 | (modify-phases %standard-phases |
5133 | (add-after 'unpack 'patch-tests | |
5134 | (lambda _ | |
5135 | (substitute* "test/test.pl" | |
5136 | ;; The test script calls out to /bin/bash | |
5137 | (("/bin/bash") (which "bash"))) | |
b2d748ed | 5138 | #t)) |
c842d425 BW |
5139 | (add-after 'install 'install-library |
5140 | (lambda* (#:key outputs #:allow-other-keys) | |
5141 | (let ((lib (string-append (assoc-ref outputs "out") "/lib"))) | |
5142 | (install-file "libbam.a" lib) | |
5143 | #t))) | |
5144 | (add-after 'install 'install-headers | |
5145 | (lambda* (#:key outputs #:allow-other-keys) | |
5146 | (let ((include (string-append (assoc-ref outputs "out") | |
5147 | "/include/samtools/"))) | |
5148 | (for-each (lambda (file) | |
5149 | (install-file file include)) | |
5150 | (scandir "." (lambda (name) (string-match "\\.h$" name)))) | |
5151 | #t)))))) | |
4e10a221 | 5152 | (native-inputs `(("pkg-config" ,pkg-config))) |
4ab16440 BW |
5153 | (inputs |
5154 | `(("htslib" ,htslib) | |
5155 | ("ncurses" ,ncurses) | |
5156 | ("perl" ,perl) | |
5157 | ("python" ,python) | |
5158 | ("zlib" ,zlib))) | |
4e10a221 RW |
5159 | (home-page "http://samtools.sourceforge.net") |
5160 | (synopsis "Utilities to efficiently manipulate nucleotide sequence alignments") | |
5161 | (description | |
5162 | "Samtools implements various utilities for post-processing nucleotide | |
5163 | sequence alignments in the SAM, BAM, and CRAM formats, including indexing, | |
5164 | variant calling (in conjunction with bcftools), and a simple alignment | |
5165 | viewer.") | |
5166 | (license license:expat))) | |
d3517eda | 5167 | |
0b84a0aa RW |
5168 | (define-public samtools-0.1 |
5169 | ;; This is the most recent version of the 0.1 line of samtools. The input | |
5170 | ;; and output formats differ greatly from that used and produced by samtools | |
5171 | ;; 1.x and is still used in many bioinformatics pipelines. | |
5172 | (package (inherit samtools) | |
5173 | (version "0.1.19") | |
5174 | (source | |
5175 | (origin | |
5176 | (method url-fetch) | |
5177 | (uri | |
de67e922 | 5178 | (string-append "mirror://sourceforge/samtools/samtools/" |
0b84a0aa RW |
5179 | version "/samtools-" version ".tar.bz2")) |
5180 | (sha256 | |
5181 | (base32 "1m33xsfwz0s8qi45lylagfllqg7fphf4dr0780rsvw75av9wk06h")))) | |
5182 | (arguments | |
2309ed68 | 5183 | `(#:tests? #f ;no "check" target |
a6798218 RW |
5184 | #:make-flags |
5185 | (list "LIBCURSES=-lncurses") | |
2309ed68 | 5186 | ,@(substitute-keyword-arguments (package-arguments samtools) |
2309ed68 RW |
5187 | ((#:phases phases) |
5188 | `(modify-phases ,phases | |
5189 | (replace 'install | |
5190 | (lambda* (#:key outputs #:allow-other-keys) | |
5191 | (let ((bin (string-append | |
5192 | (assoc-ref outputs "out") "/bin"))) | |
5193 | (mkdir-p bin) | |
f3860753 | 5194 | (install-file "samtools" bin) |
b2d748ed | 5195 | #t))) |
2309ed68 RW |
5196 | (delete 'patch-tests) |
5197 | (delete 'configure)))))))) | |
0b84a0aa | 5198 | |
fe4c37c2 | 5199 | (define-public mosaik |
698bd297 | 5200 | (let ((commit "5c25216d3522d6a33e53875cd76a6d65001e4e67")) |
fe4c37c2 RW |
5201 | (package |
5202 | (name "mosaik") | |
5203 | (version "2.2.30") | |
5204 | (source (origin | |
5205 | ;; There are no release tarballs nor tags. | |
5206 | (method git-fetch) | |
5207 | (uri (git-reference | |
5208 | (url "https://github.com/wanpinglee/MOSAIK.git") | |
5209 | (commit commit))) | |
5210 | (file-name (string-append name "-" version)) | |
5211 | (sha256 | |
5212 | (base32 | |
5213 | "17gj3s07cm77r41z92awh0bim7w7q7fbn0sf5nkqmcm1vw052qgw")))) | |
5214 | (build-system gnu-build-system) | |
5215 | (arguments | |
5216 | `(#:tests? #f ; no tests | |
5217 | #:make-flags (list "CC=gcc") | |
5218 | #:phases | |
5219 | (modify-phases %standard-phases | |
5220 | (replace 'configure | |
5221 | (lambda _ (chdir "src") #t)) | |
5222 | (replace 'install | |
5223 | (lambda* (#:key outputs #:allow-other-keys) | |
5224 | (let ((bin (string-append (assoc-ref outputs "out") | |
5225 | "/bin"))) | |
5226 | (mkdir-p bin) | |
5227 | (copy-recursively "../bin" bin) | |
5228 | #t)))))) | |
5229 | (inputs | |
5230 | `(("perl" ,perl) | |
5231 | ("zlib" ,zlib))) | |
029d9f77 | 5232 | (supported-systems '("x86_64-linux")) |
0c6c9c00 | 5233 | (home-page "https://github.com/wanpinglee/MOSAIK") |
fe4c37c2 RW |
5234 | (synopsis "Map nucleotide sequence reads to reference genomes") |
5235 | (description | |
5236 | "MOSAIK is a program for mapping second and third-generation sequencing | |
5237 | reads to a reference genome. MOSAIK can align reads generated by all the | |
5238 | major sequencing technologies, including Illumina, Applied Biosystems SOLiD, | |
5239 | Roche 454, Ion Torrent and Pacific BioSciences SMRT.") | |
5240 | ;; MOSAIK is released under the GPLv2+ with the exception of third-party | |
5241 | ;; code released into the public domain: | |
5242 | ;; 1. fastlz by Ariya Hidayat - http://www.fastlz.org/ | |
5243 | ;; 2. MD5 implementation - RSA Data Security, RFC 1321 | |
5244 | (license (list license:gpl2+ license:public-domain))))) | |
5245 | ||
282c5087 RW |
5246 | (define-public ngs-sdk |
5247 | (package | |
5248 | (name "ngs-sdk") | |
8d3eaa92 | 5249 | (version "2.9.3") |
4031e7f1 RW |
5250 | (source (origin |
5251 | (method git-fetch) | |
5252 | (uri (git-reference | |
5253 | (url "https://github.com/ncbi/ngs.git") | |
5254 | (commit version))) | |
5255 | (file-name (git-file-name name version)) | |
5256 | (sha256 | |
5257 | (base32 | |
8d3eaa92 | 5258 | "17c0v1nah3g3d2ib5bbi0vhma1ghd6vb9xycavqsh64lhp840rk3")))) |
282c5087 RW |
5259 | (build-system gnu-build-system) |
5260 | (arguments | |
5261 | `(#:parallel-build? #f ; not supported | |
5262 | #:tests? #f ; no "check" target | |
5263 | #:phases | |
dc1d3cde KK |
5264 | (modify-phases %standard-phases |
5265 | (replace 'configure | |
5266 | (lambda* (#:key outputs #:allow-other-keys) | |
5267 | (let ((out (assoc-ref outputs "out"))) | |
5268 | ;; Allow 'konfigure.perl' to find 'package.prl'. | |
5269 | (setenv "PERL5LIB" | |
5270 | (string-append ".:" (getenv "PERL5LIB"))) | |
5271 | ||
5272 | ;; The 'configure' script doesn't recognize things like | |
5273 | ;; '--enable-fast-install'. | |
3da3cedf RW |
5274 | (invoke "./configure" |
5275 | (string-append "--build-prefix=" (getcwd) "/build") | |
5276 | (string-append "--prefix=" out)) | |
5277 | #t))) | |
dc1d3cde KK |
5278 | (add-after 'unpack 'enter-dir |
5279 | (lambda _ (chdir "ngs-sdk") #t))))) | |
282c5087 | 5280 | (native-inputs `(("perl" ,perl))) |
a0dadf0c AE |
5281 | ;; According to the test |
5282 | ;; unless ($MARCH =~ /x86_64/i || $MARCH =~ /i?86/i) | |
5283 | ;; in ngs-sdk/setup/konfigure.perl | |
ab29be81 | 5284 | (supported-systems '("i686-linux" "x86_64-linux")) |
282c5087 RW |
5285 | (home-page "https://github.com/ncbi/ngs") |
5286 | (synopsis "API for accessing Next Generation Sequencing data") | |
5287 | (description | |
5288 | "NGS is a domain-specific API for accessing reads, alignments and pileups | |
5289 | produced from Next Generation Sequencing. The API itself is independent from | |
5290 | any particular back-end implementation, and supports use of multiple back-ends | |
5291 | simultaneously.") | |
5292 | (license license:public-domain))) | |
5293 | ||
1ad15c16 | 5294 | (define-public java-ngs |
2651a5e6 | 5295 | (package (inherit ngs-sdk) |
1ad15c16 | 5296 | (name "java-ngs") |
2651a5e6 RW |
5297 | (arguments |
5298 | `(,@(substitute-keyword-arguments | |
5299 | `(#:modules ((guix build gnu-build-system) | |
5300 | (guix build utils) | |
5301 | (srfi srfi-1) | |
5302 | (srfi srfi-26)) | |
5303 | ,@(package-arguments ngs-sdk)) | |
5304 | ((#:phases phases) | |
614a8977 RW |
5305 | `(modify-phases ,phases |
5306 | (replace 'enter-dir (lambda _ (chdir "ngs-java") #t))))))) | |
2651a5e6 | 5307 | (inputs |
d2540f80 | 5308 | `(("jdk" ,icedtea "jdk") |
2651a5e6 RW |
5309 | ("ngs-sdk" ,ngs-sdk))) |
5310 | (synopsis "Java bindings for NGS SDK"))) | |
5311 | ||
75dd2424 RW |
5312 | (define-public ncbi-vdb |
5313 | (package | |
5314 | (name "ncbi-vdb") | |
87408854 | 5315 | (version "2.9.3") |
3398dfb7 RW |
5316 | (source (origin |
5317 | (method git-fetch) | |
5318 | (uri (git-reference | |
5319 | (url "https://github.com/ncbi/ncbi-vdb.git") | |
5320 | (commit version))) | |
5321 | (file-name (git-file-name name version)) | |
5322 | (sha256 | |
5323 | (base32 | |
87408854 | 5324 | "1l4ny67nxwv1lagk9wwjbrgm7ln7adci6dnpc7k1yaln6shj0qpm")))) |
75dd2424 RW |
5325 | (build-system gnu-build-system) |
5326 | (arguments | |
5327 | `(#:parallel-build? #f ; not supported | |
5328 | #:tests? #f ; no "check" target | |
5329 | #:phases | |
70111198 | 5330 | (modify-phases %standard-phases |
3398dfb7 RW |
5331 | (add-after 'unpack 'make-files-writable |
5332 | (lambda _ (for-each make-file-writable (find-files "." ".*")) #t)) | |
0691851a BW |
5333 | (add-before 'configure 'set-perl-search-path |
5334 | (lambda _ | |
5335 | ;; Work around "dotless @INC" build failure. | |
5336 | (setenv "PERL5LIB" | |
5337 | (string-append (getcwd) "/setup:" | |
5338 | (getenv "PERL5LIB"))) | |
5339 | #t)) | |
70111198 RW |
5340 | (replace 'configure |
5341 | (lambda* (#:key inputs outputs #:allow-other-keys) | |
5342 | (let ((out (assoc-ref outputs "out"))) | |
5343 | ;; Override include path for libmagic | |
5344 | (substitute* "setup/package.prl" | |
5345 | (("name => 'magic', Include => '/usr/include'") | |
5346 | (string-append "name=> 'magic', Include => '" | |
5347 | (assoc-ref inputs "libmagic") | |
5348 | "/include" "'"))) | |
75dd2424 | 5349 | |
70111198 RW |
5350 | ;; Install kdf5 library (needed by sra-tools) |
5351 | (substitute* "build/Makefile.install" | |
5352 | (("LIBRARIES_TO_INSTALL =") | |
5353 | "LIBRARIES_TO_INSTALL = kdf5.$(VERSION_LIBX) kdf5.$(VERSION_SHLX)")) | |
75dd2424 | 5354 | |
70111198 RW |
5355 | (substitute* "build/Makefile.env" |
5356 | (("CFLAGS =" prefix) | |
5357 | (string-append prefix "-msse2 "))) | |
675d7ae2 | 5358 | |
558e2307 RW |
5359 | ;; Override search path for ngs-java |
5360 | (substitute* "setup/package.prl" | |
5361 | (("/usr/local/ngs/ngs-java") | |
5362 | (assoc-ref inputs "java-ngs"))) | |
5363 | ||
70111198 RW |
5364 | ;; The 'configure' script doesn't recognize things like |
5365 | ;; '--enable-fast-install'. | |
6a7d9ee3 | 5366 | (invoke "./configure" |
70111198 RW |
5367 | (string-append "--build-prefix=" (getcwd) "/build") |
5368 | (string-append "--prefix=" (assoc-ref outputs "out")) | |
5369 | (string-append "--debug") | |
5370 | (string-append "--with-xml2-prefix=" | |
5371 | (assoc-ref inputs "libxml2")) | |
5372 | (string-append "--with-ngs-sdk-prefix=" | |
5373 | (assoc-ref inputs "ngs-sdk")) | |
70111198 | 5374 | (string-append "--with-hdf5-prefix=" |
6a7d9ee3 RW |
5375 | (assoc-ref inputs "hdf5"))) |
5376 | #t))) | |
70111198 RW |
5377 | (add-after 'install 'install-interfaces |
5378 | (lambda* (#:key outputs #:allow-other-keys) | |
5379 | ;; Install interface libraries. On i686 the interface libraries | |
5380 | ;; are installed to "linux/gcc/i386", so we need to use the Linux | |
5381 | ;; architecture name ("i386") instead of the target system prefix | |
5382 | ;; ("i686"). | |
5383 | (mkdir (string-append (assoc-ref outputs "out") "/ilib")) | |
5384 | (copy-recursively (string-append "build/ncbi-vdb/linux/gcc/" | |
5385 | ,(system->linux-architecture | |
5386 | (or (%current-target-system) | |
5387 | (%current-system))) | |
5388 | "/rel/ilib") | |
5389 | (string-append (assoc-ref outputs "out") | |
5390 | "/ilib")) | |
5391 | ;; Install interface headers | |
5392 | (copy-recursively "interfaces" | |
5393 | (string-append (assoc-ref outputs "out") | |
5394 | "/include")) | |
d5e17162 RW |
5395 | #t)) |
5396 | ;; These files are needed by sra-tools. | |
5397 | (add-after 'install 'install-configuration-files | |
5398 | (lambda* (#:key outputs #:allow-other-keys) | |
5399 | (let ((target (string-append (assoc-ref outputs "out") "/kfg"))) | |
5400 | (mkdir target) | |
5401 | (install-file "libs/kfg/default.kfg" target) | |
5402 | (install-file "libs/kfg/certs.kfg" target)) | |
70111198 | 5403 | #t))))) |
75dd2424 RW |
5404 | (inputs |
5405 | `(("libxml2" ,libxml2) | |
5406 | ("ngs-sdk" ,ngs-sdk) | |
1ad15c16 | 5407 | ("java-ngs" ,java-ngs) |
75dd2424 RW |
5408 | ("libmagic" ,file) |
5409 | ("hdf5" ,hdf5))) | |
5410 | (native-inputs `(("perl" ,perl))) | |
675d7ae2 RW |
5411 | ;; NCBI-VDB requires SSE capability. |
5412 | (supported-systems '("i686-linux" "x86_64-linux")) | |
75dd2424 RW |
5413 | (home-page "https://github.com/ncbi/ncbi-vdb") |
5414 | (synopsis "Database engine for genetic information") | |
5415 | (description | |
5416 | "The NCBI-VDB library implements a highly compressed columnar data | |
5417 | warehousing engine that is most often used to store genetic information. | |
5418 | Databases are stored in a portable image within the file system, and can be | |
5419 | accessed/downloaded on demand across HTTP.") | |
5420 | (license license:public-domain))) | |
5421 | ||
cc6ed477 RW |
5422 | (define-public plink |
5423 | (package | |
5424 | (name "plink") | |
5425 | (version "1.07") | |
5426 | (source | |
5427 | (origin | |
5428 | (method url-fetch) | |
5429 | (uri (string-append | |
5430 | "http://pngu.mgh.harvard.edu/~purcell/plink/dist/plink-" | |
5431 | version "-src.zip")) | |
5432 | (sha256 | |
5433 | (base32 "0as8gxm4pjyc8dxmm1sl873rrd7wn5qs0l29nqfnl31x8i467xaa")) | |
0dbb7ac2 EF |
5434 | (patches (search-patches "plink-1.07-unclobber-i.patch" |
5435 | "plink-endian-detection.patch")))) | |
cc6ed477 RW |
5436 | (build-system gnu-build-system) |
5437 | (arguments | |
5438 | '(#:tests? #f ;no "check" target | |
5439 | #:make-flags (list (string-append "LIB_LAPACK=" | |
5440 | (assoc-ref %build-inputs "lapack") | |
5441 | "/lib/liblapack.so") | |
5442 | "WITH_LAPACK=1" | |
5443 | "FORCE_DYNAMIC=1" | |
5444 | ;; disable phoning home | |
5445 | "WITH_WEBCHECK=") | |
5446 | #:phases | |
5447 | (modify-phases %standard-phases | |
5448 | ;; no "configure" script | |
5449 | (delete 'configure) | |
5450 | (replace 'install | |
5451 | (lambda* (#:key outputs #:allow-other-keys) | |
5452 | (let ((bin (string-append (assoc-ref outputs "out") | |
5453 | "/bin/"))) | |
96c46210 | 5454 | (install-file "plink" bin) |
cc6ed477 RW |
5455 | #t)))))) |
5456 | (inputs | |
5457 | `(("zlib" ,zlib) | |
5458 | ("lapack" ,lapack))) | |
5459 | (native-inputs | |
5460 | `(("unzip" ,unzip))) | |
5461 | (home-page "http://pngu.mgh.harvard.edu/~purcell/plink/") | |
5462 | (synopsis "Whole genome association analysis toolset") | |
5463 | (description | |
5464 | "PLINK is a whole genome association analysis toolset, designed to | |
5465 | perform a range of basic, large-scale analyses in a computationally efficient | |
5466 | manner. The focus of PLINK is purely on analysis of genotype/phenotype data, | |
5467 | so there is no support for steps prior to this (e.g. study design and | |
5468 | planning, generating genotype or CNV calls from raw data). Through | |
5469 | integration with gPLINK and Haploview, there is some support for the | |
5470 | subsequent visualization, annotation and storage of results.") | |
5471 | ;; Code is released under GPLv2, except for fisher.h, which is under | |
5472 | ;; LGPLv2.1+ | |
5473 | (license (list license:gpl2 license:lgpl2.1+)))) | |
5474 | ||
dad66da4 RW |
5475 | (define-public plink-ng |
5476 | (package (inherit plink) | |
5477 | (name "plink-ng") | |
5478 | (version "1.90b4") | |
5479 | (source | |
5480 | (origin | |
b1733341 RW |
5481 | (method git-fetch) |
5482 | (uri (git-reference | |
5483 | (url "https://github.com/chrchang/plink-ng.git") | |
5484 | (commit (string-append "v" version)))) | |
5485 | (file-name (git-file-name name version)) | |
dad66da4 | 5486 | (sha256 |
b1733341 | 5487 | (base32 "02npdwgkpfkdnhw819rhj5kw02a5k5m90b14zq9zzya4hyg929c0")))) |
dad66da4 RW |
5488 | (build-system gnu-build-system) |
5489 | (arguments | |
5490 | '(#:tests? #f ;no "check" target | |
5491 | #:make-flags (list "BLASFLAGS=-llapack -lopenblas" | |
5492 | "CFLAGS=-Wall -O2 -DDYNAMIC_ZLIB=1" | |
5493 | "ZLIB=-lz" | |
5494 | "-f" "Makefile.std") | |
5495 | #:phases | |
5496 | (modify-phases %standard-phases | |
5497 | (add-after 'unpack 'chdir | |
5498 | (lambda _ (chdir "1.9") #t)) | |
5499 | (delete 'configure) ; no "configure" script | |
5500 | (replace 'install | |
5501 | (lambda* (#:key outputs #:allow-other-keys) | |
5502 | (let ((bin (string-append (assoc-ref outputs "out") | |
5503 | "/bin/"))) | |
5504 | (install-file "plink" bin) | |
5505 | #t)))))) | |
5506 | (inputs | |
5507 | `(("zlib" ,zlib) | |
5508 | ("lapack" ,lapack) | |
5509 | ("openblas" ,openblas))) | |
5510 | (home-page "https://www.cog-genomics.org/plink/") | |
5511 | (license license:gpl3+))) | |
5512 | ||
c6a24d6e RW |
5513 | (define-public smithlab-cpp |
5514 | (let ((revision "1") | |
698bd297 | 5515 | (commit "728a097bec88c6f4b8528b685932049e660eff2e")) |
c6a24d6e RW |
5516 | (package |
5517 | (name "smithlab-cpp") | |
698bd297 | 5518 | (version (string-append "0." revision "." (string-take commit 7))) |
c6a24d6e RW |
5519 | (source (origin |
5520 | (method git-fetch) | |
5521 | (uri (git-reference | |
5522 | (url "https://github.com/smithlabcode/smithlab_cpp.git") | |
5523 | (commit commit))) | |
5524 | (file-name (string-append name "-" version "-checkout")) | |
5525 | (sha256 | |
5526 | (base32 | |
5527 | "0d476lmj312xk77kr9fzrv7z1bv96yfyx0w7y62ycmnfbx32ll74")))) | |
5528 | (build-system gnu-build-system) | |
5529 | (arguments | |
5530 | `(#:modules ((guix build gnu-build-system) | |
5531 | (guix build utils) | |
5532 | (srfi srfi-26)) | |
5533 | #:tests? #f ;no "check" target | |
5534 | #:phases | |
5535 | (modify-phases %standard-phases | |
5536 | (add-after 'unpack 'use-samtools-headers | |
5537 | (lambda _ | |
5538 | (substitute* '("SAM.cpp" | |
5539 | "SAM.hpp") | |
5540 | (("sam.h") "samtools/sam.h")) | |
5541 | #t)) | |
5542 | (replace 'install | |
5543 | (lambda* (#:key outputs #:allow-other-keys) | |
5544 | (let* ((out (assoc-ref outputs "out")) | |
5545 | (lib (string-append out "/lib")) | |
5546 | (include (string-append out "/include/smithlab-cpp"))) | |
5547 | (mkdir-p lib) | |
5548 | (mkdir-p include) | |
5549 | (for-each (cut install-file <> lib) | |
5550 | (find-files "." "\\.o$")) | |
5551 | (for-each (cut install-file <> include) | |
5552 | (find-files "." "\\.hpp$"))) | |
5553 | #t)) | |
5554 | (delete 'configure)))) | |
5555 | (inputs | |
5556 | `(("samtools" ,samtools-0.1) | |
5557 | ("zlib" ,zlib))) | |
5558 | (home-page "https://github.com/smithlabcode/smithlab_cpp") | |
5559 | (synopsis "C++ helper library for functions used in Smith lab projects") | |
5560 | (description | |
5561 | "Smithlab CPP is a C++ library that includes functions used in many of | |
5562 | the Smith lab bioinformatics projects, such as a wrapper around Samtools data | |
5563 | structures, classes for genomic regions, mapped sequencing reads, etc.") | |
5564 | (license license:gpl3+)))) | |
5565 | ||
56e373ef RW |
5566 | (define-public preseq |
5567 | (package | |
5568 | (name "preseq") | |
67caa4b7 | 5569 | (version "2.0.3") |
56e373ef | 5570 | (source (origin |
67caa4b7 RW |
5571 | (method url-fetch) |
5572 | (uri (string-append "https://github.com/smithlabcode/preseq/" | |
5573 | "releases/download/v" version | |
5574 | "/preseq_v" version ".tar.bz2")) | |
56e373ef | 5575 | (sha256 |
67caa4b7 | 5576 | (base32 "149x9xmk1wy1gff85325yfzqc0qk4sgp1w6gbyj9cnji4x1dszbl")) |
56e373ef | 5577 | (modules '((guix build utils))) |
6cbee49d MW |
5578 | (snippet '(begin |
5579 | ;; Remove bundled samtools. | |
5580 | (delete-file-recursively "samtools") | |
5581 | #t)))) | |
56e373ef RW |
5582 | (build-system gnu-build-system) |
5583 | (arguments | |
5584 | `(#:tests? #f ;no "check" target | |
5585 | #:phases | |
5586 | (modify-phases %standard-phases | |
56e373ef | 5587 | (delete 'configure)) |
b49c5a58 RW |
5588 | #:make-flags |
5589 | (list (string-append "PREFIX=" | |
5590 | (assoc-ref %outputs "out")) | |
5591 | (string-append "LIBBAM=" | |
5592 | (assoc-ref %build-inputs "samtools") | |
5593 | "/lib/libbam.a") | |
5594 | (string-append "SMITHLAB_CPP=" | |
5595 | (assoc-ref %build-inputs "smithlab-cpp") | |
5596 | "/lib") | |
5597 | "PROGS=preseq" | |
5598 | "INCLUDEDIRS=$(SMITHLAB_CPP)/../include/smithlab-cpp $(SAMTOOLS_DIR)"))) | |
56e373ef RW |
5599 | (inputs |
5600 | `(("gsl" ,gsl) | |
5601 | ("samtools" ,samtools-0.1) | |
b49c5a58 | 5602 | ("smithlab-cpp" ,smithlab-cpp) |
56e373ef RW |
5603 | ("zlib" ,zlib))) |
5604 | (home-page "http://smithlabresearch.org/software/preseq/") | |
5605 | (synopsis "Program for analyzing library complexity") | |
5606 | (description | |
5607 | "The preseq package is aimed at predicting and estimating the complexity | |
5608 | of a genomic sequencing library, equivalent to predicting and estimating the | |
5609 | number of redundant reads from a given sequencing depth and how many will be | |
5610 | expected from additional sequencing using an initial sequencing experiment. | |
5611 | The estimates can then be used to examine the utility of further sequencing, | |
5612 | optimize the sequencing depth, or to screen multiple libraries to avoid low | |
5613 | complexity samples.") | |
5614 | (license license:gpl3+))) | |
5615 | ||
9ded1457 BW |
5616 | (define-public python-screed |
5617 | (package | |
5618 | (name "python-screed") | |
50e33c3a | 5619 | (version "1.0") |
9ded1457 BW |
5620 | (source |
5621 | (origin | |
5622 | (method url-fetch) | |
5623 | (uri (pypi-uri "screed" version)) | |
5624 | (sha256 | |
5625 | (base32 | |
50e33c3a | 5626 | "148vcb7w2wr6a4w6vs2bsxanbqibxfk490zbcbg4m61s8669zdjx")))) |
9ded1457 BW |
5627 | (build-system python-build-system) |
5628 | (arguments | |
50e33c3a | 5629 | '(#:phases |
9ded1457 | 5630 | (modify-phases %standard-phases |
50e33c3a RW |
5631 | ;; Tests must be run after installation, as the "screed" command does |
5632 | ;; not exist right after building. | |
5633 | (delete 'check) | |
5634 | (add-after 'install 'check | |
5635 | (lambda* (#:key inputs outputs #:allow-other-keys) | |
5636 | (let ((out (assoc-ref outputs "out"))) | |
5637 | (setenv "PYTHONPATH" | |
5638 | (string-append out "/lib/python" | |
5639 | (string-take (string-take-right | |
5640 | (assoc-ref inputs "python") | |
5641 | 5) 3) | |
5642 | "/site-packages:" | |
5643 | (getenv "PYTHONPATH"))) | |
5644 | (setenv "PATH" (string-append out "/bin:" (getenv "PATH")))) | |
5645 | (invoke "python" "setup.py" "test") | |
5646 | #t))))) | |
9ded1457 | 5647 | (native-inputs |
50e33c3a RW |
5648 | `(("python-pytest" ,python-pytest) |
5649 | ("python-pytest-cov" ,python-pytest-cov) | |
5650 | ("python-pytest-runner" ,python-pytest-runner))) | |
9ded1457 BW |
5651 | (inputs |
5652 | `(("python-bz2file" ,python-bz2file))) | |
7bf837fd | 5653 | (home-page "https://github.com/dib-lab/screed/") |
9ded1457 BW |
5654 | (synopsis "Short read sequence database utilities") |
5655 | (description "Screed parses FASTA and FASTQ files and generates databases. | |
5656 | Values such as sequence name, sequence description, sequence quality and the | |
5657 | sequence itself can be retrieved from these databases.") | |
5658 | (license license:bsd-3))) | |
5659 | ||
5660 | (define-public python2-screed | |
5c31f4aa | 5661 | (package-with-python2 python-screed)) |
9ded1457 | 5662 | |
51c64999 RW |
5663 | (define-public sra-tools |
5664 | (package | |
5665 | (name "sra-tools") | |
15c96094 | 5666 | (version "2.9.3") |
51c64999 RW |
5667 | (source |
5668 | (origin | |
2b773a92 RW |
5669 | (method git-fetch) |
5670 | (uri (git-reference | |
5671 | (url "https://github.com/ncbi/sra-tools.git") | |
5672 | (commit version))) | |
5673 | (file-name (git-file-name name version)) | |
51c64999 RW |
5674 | (sha256 |
5675 | (base32 | |
15c96094 | 5676 | "0663gcdxkziwsmlznjxysb00621rllpbz6jwsfifq7z3dj3lwm8b")))) |
51c64999 RW |
5677 | (build-system gnu-build-system) |
5678 | (arguments | |
5679 | `(#:parallel-build? #f ; not supported | |
5680 | #:tests? #f ; no "check" target | |
2320e76b | 5681 | #:make-flags |
79849358 RW |
5682 | (list (string-append "DEFAULT_CRT=" |
5683 | (assoc-ref %build-inputs "ncbi-vdb") | |
5684 | "/kfg/certs.kfg") | |
5685 | (string-append "DEFAULT_KFG=" | |
5686 | (assoc-ref %build-inputs "ncbi-vdb") | |
5687 | "/kfg/default.kfg") | |
5688 | (string-append "VDB_LIBDIR=" | |
2320e76b RW |
5689 | (assoc-ref %build-inputs "ncbi-vdb") |
5690 | ,(if (string-prefix? "x86_64" | |
5691 | (or (%current-target-system) | |
5692 | (%current-system))) | |
5693 | "/lib64" | |
5694 | "/lib32"))) | |
51c64999 | 5695 | #:phases |
beebe431 | 5696 | (modify-phases %standard-phases |
0691851a BW |
5697 | (add-before 'configure 'set-perl-search-path |
5698 | (lambda _ | |
5699 | ;; Work around "dotless @INC" build failure. | |
5700 | (setenv "PERL5LIB" | |
5701 | (string-append (getcwd) "/setup:" | |
5702 | (getenv "PERL5LIB"))) | |
5703 | #t)) | |
beebe431 RW |
5704 | (replace 'configure |
5705 | (lambda* (#:key inputs outputs #:allow-other-keys) | |
5706 | ;; The build system expects a directory containing the sources and | |
5707 | ;; raw build output of ncbi-vdb, including files that are not | |
5708 | ;; installed. Since we are building against an installed version of | |
5709 | ;; ncbi-vdb, the following modifications are needed. | |
5710 | (substitute* "setup/konfigure.perl" | |
5711 | ;; Make the configure script look for the "ilib" directory of | |
5712 | ;; "ncbi-vdb" without first checking for the existence of a | |
5713 | ;; matching library in its "lib" directory. | |
5714 | (("^ my \\$f = File::Spec->catdir\\(\\$libdir, \\$lib\\);") | |
5715 | "my $f = File::Spec->catdir($ilibdir, $ilib);") | |
5716 | ;; Look for interface libraries in ncbi-vdb's "ilib" directory. | |
5717 | (("my \\$ilibdir = File::Spec->catdir\\(\\$builddir, 'ilib'\\);") | |
5718 | "my $ilibdir = File::Spec->catdir($dir, 'ilib');")) | |
51c64999 | 5719 | |
beebe431 RW |
5720 | ;; Dynamic linking |
5721 | (substitute* "tools/copycat/Makefile" | |
5722 | (("smagic-static") "lmagic")) | |
2320e76b | 5723 | |
beebe431 RW |
5724 | ;; The 'configure' script doesn't recognize things like |
5725 | ;; '--enable-fast-install'. | |
2e2d8853 | 5726 | (invoke "./configure" |
beebe431 RW |
5727 | (string-append "--build-prefix=" (getcwd) "/build") |
5728 | (string-append "--prefix=" (assoc-ref outputs "out")) | |
5729 | (string-append "--debug") | |
5730 | (string-append "--with-fuse-prefix=" | |
5731 | (assoc-ref inputs "fuse")) | |
5732 | (string-append "--with-magic-prefix=" | |
5733 | (assoc-ref inputs "libmagic")) | |
5734 | ;; TODO: building with libxml2 fails with linker errors | |
5735 | ;; (string-append "--with-xml2-prefix=" | |
5736 | ;; (assoc-ref inputs "libxml2")) | |
5737 | (string-append "--with-ncbi-vdb-sources=" | |
5738 | (assoc-ref inputs "ncbi-vdb")) | |
5739 | (string-append "--with-ncbi-vdb-build=" | |
5740 | (assoc-ref inputs "ncbi-vdb")) | |
5741 | (string-append "--with-ngs-sdk-prefix=" | |
5742 | (assoc-ref inputs "ngs-sdk")) | |
5743 | (string-append "--with-hdf5-prefix=" | |
2e2d8853 | 5744 | (assoc-ref inputs "hdf5"))) |
1108a920 | 5745 | #t))))) |
51c64999 RW |
5746 | (native-inputs `(("perl" ,perl))) |
5747 | (inputs | |
5748 | `(("ngs-sdk" ,ngs-sdk) | |
5749 | ("ncbi-vdb" ,ncbi-vdb) | |
5750 | ("libmagic" ,file) | |
5751 | ("fuse" ,fuse) | |
5752 | ("hdf5" ,hdf5) | |
5753 | ("zlib" ,zlib))) | |
5754 | (home-page "http://www.ncbi.nlm.nih.gov/Traces/sra/sra.cgi?view=software") | |
5755 | (synopsis "Tools and libraries for reading and writing sequencing data") | |
5756 | (description | |
5757 | "The SRA Toolkit from NCBI is a collection of tools and libraries for | |
5758 | reading of sequencing files from the Sequence Read Archive (SRA) database and | |
5759 | writing files into the .sra format.") | |
5760 | (license license:public-domain))) | |
5761 | ||
d3517eda RW |
5762 | (define-public seqan |
5763 | (package | |
5764 | (name "seqan") | |
4d93a9a3 | 5765 | (version "2.4.0") |
d3517eda RW |
5766 | (source (origin |
5767 | (method url-fetch) | |
4d93a9a3 RW |
5768 | (uri (string-append "https://github.com/seqan/seqan/releases/" |
5769 | "download/seqan-v" version | |
5770 | "/seqan-library-" version ".tar.xz")) | |
d3517eda RW |
5771 | (sha256 |
5772 | (base32 | |
4d93a9a3 | 5773 | "19a1rlxx03qy1i1iriicly68w64yjxbv24g9gdywnfmq998v35yx")))) |
d3517eda RW |
5774 | ;; The documentation is 7.8MB and the includes are 3.6MB heavy, so it |
5775 | ;; makes sense to split the outputs. | |
5776 | (outputs '("out" "doc")) | |
5777 | (build-system trivial-build-system) | |
5778 | (arguments | |
5779 | `(#:modules ((guix build utils)) | |
5780 | #:builder | |
5781 | (begin | |
5782 | (use-modules (guix build utils)) | |
4d93a9a3 RW |
5783 | (let ((tar (assoc-ref %build-inputs "tar")) |
5784 | (xz (assoc-ref %build-inputs "xz")) | |
5785 | (out (assoc-ref %outputs "out")) | |
5786 | (doc (assoc-ref %outputs "doc"))) | |
5787 | (setenv "PATH" (string-append tar "/bin:" xz "/bin")) | |
e3cfef22 | 5788 | (invoke "tar" "xvf" (assoc-ref %build-inputs "source")) |
d3517eda RW |
5789 | (chdir (string-append "seqan-library-" ,version)) |
5790 | (copy-recursively "include" (string-append out "/include")) | |
e3cfef22 MW |
5791 | (copy-recursively "share" (string-append doc "/share")) |
5792 | #t)))) | |
d3517eda RW |
5793 | (native-inputs |
5794 | `(("source" ,source) | |
5795 | ("tar" ,tar) | |
4d93a9a3 | 5796 | ("xz" ,xz))) |
d3517eda RW |
5797 | (home-page "http://www.seqan.de") |
5798 | (synopsis "Library for nucleotide sequence analysis") | |
5799 | (description | |
5800 | "SeqAn is a C++ library of efficient algorithms and data structures for | |
5801 | the analysis of sequences with the focus on biological data. It contains | |
5802 | algorithms and data structures for string representation and their | |
5803 | manipulation, online and indexed string search, efficient I/O of | |
5804 | bioinformatics file formats, sequence alignment, and more.") | |
5805 | (license license:bsd-3))) | |
ce7155d5 | 5806 | |
4d93a9a3 RW |
5807 | (define-public seqan-1 |
5808 | (package (inherit seqan) | |
5809 | (name "seqan") | |
5810 | (version "1.4.2") | |
5811 | (source (origin | |
5812 | (method url-fetch) | |
5813 | (uri (string-append "http://packages.seqan.de/seqan-library/" | |
5814 | "seqan-library-" version ".tar.bz2")) | |
5815 | (sha256 | |
5816 | (base32 | |
5817 | "05s3wrrwn50f81aklfm65i4a749zag1vr8z03k21xm0pdxy47yvp")))) | |
5818 | ;; The documentation is 7.8MB and the includes are 3.6MB heavy, so it | |
5819 | ;; makes sense to split the outputs. | |
5820 | (outputs '("out" "doc")) | |
5821 | (build-system trivial-build-system) | |
5822 | (arguments | |
5823 | `(#:modules ((guix build utils)) | |
5824 | #:builder | |
5825 | (begin | |
5826 | (use-modules (guix build utils)) | |
5827 | (let ((tar (assoc-ref %build-inputs "tar")) | |
5828 | (bzip (assoc-ref %build-inputs "bzip2")) | |
5829 | (out (assoc-ref %outputs "out")) | |
5830 | (doc (assoc-ref %outputs "doc"))) | |
5831 | (setenv "PATH" (string-append tar "/bin:" bzip "/bin")) | |
5832 | (invoke "tar" "xvf" (assoc-ref %build-inputs "source")) | |
5833 | (chdir (string-append "seqan-library-" ,version)) | |
5834 | (copy-recursively "include" (string-append out "/include")) | |
5835 | (copy-recursively "share" (string-append doc "/share")) | |
5836 | #t)))) | |
5837 | (native-inputs | |
5838 | `(("source" ,source) | |
5839 | ("tar" ,tar) | |
5840 | ("bzip2" ,bzip2))))) | |
5841 | ||
d708b7a9 BW |
5842 | (define-public seqmagick |
5843 | (package | |
5844 | (name "seqmagick") | |
39fb853a | 5845 | (version "0.7.0") |
d708b7a9 BW |
5846 | (source |
5847 | (origin | |
5848 | (method url-fetch) | |
f6e2d86f | 5849 | (uri (pypi-uri "seqmagick" version)) |
d708b7a9 BW |
5850 | (sha256 |
5851 | (base32 | |
39fb853a | 5852 | "12bfyp8nqi0hd36rmj450aygafp01qy3hkbvlwn3bk39pyjjkgg5")))) |
d708b7a9 | 5853 | (build-system python-build-system) |
d708b7a9 | 5854 | (inputs |
39fb853a | 5855 | `(("python-biopython" ,python-biopython))) |
d708b7a9 | 5856 | (native-inputs |
39fb853a | 5857 | `(("python-nose" ,python-nose))) |
7bf837fd | 5858 | (home-page "https://github.com/fhcrc/seqmagick") |
d708b7a9 BW |
5859 | (synopsis "Tools for converting and modifying sequence files") |
5860 | (description | |
5861 | "Bioinformaticians often have to convert sequence files between formats | |
5862 | and do little manipulations on them, and it's not worth writing scripts for | |
5863 | that. Seqmagick is a utility to expose the file format conversion in | |
5864 | BioPython in a convenient way. Instead of having a big mess of scripts, there | |
5865 | is one that takes arguments.") | |
5866 | (license license:gpl3))) | |
5867 | ||
66daf78c BW |
5868 | (define-public seqtk |
5869 | (package | |
5870 | (name "seqtk") | |
63f3255e | 5871 | (version "1.3") |
66daf78c | 5872 | (source (origin |
019fcdf2 RW |
5873 | (method git-fetch) |
5874 | (uri (git-reference | |
5875 | (url "https://github.com/lh3/seqtk.git") | |
5876 | (commit (string-append "v" version)))) | |
5877 | (file-name (git-file-name name version)) | |
66daf78c BW |
5878 | (sha256 |
5879 | (base32 | |
63f3255e | 5880 | "1bfzlqa84b5s1qi22blmmw2s8xdyp9h9ydcq22pfjhh5gab3yz6l")))) |
66daf78c BW |
5881 | (build-system gnu-build-system) |
5882 | (arguments | |
5883 | `(#:phases | |
5884 | (modify-phases %standard-phases | |
5885 | (delete 'configure) | |
5886 | (replace 'check | |
5887 | ;; There are no tests, so we just run a sanity check. | |
63f3255e | 5888 | (lambda _ (invoke "./seqtk" "seq") #t)) |
66daf78c BW |
5889 | (replace 'install |
5890 | (lambda* (#:key outputs #:allow-other-keys) | |
5891 | (let ((bin (string-append (assoc-ref outputs "out") "/bin/"))) | |
63f3255e RW |
5892 | (install-file "seqtk" bin) |
5893 | #t)))))) | |
66daf78c BW |
5894 | (inputs |
5895 | `(("zlib" ,zlib))) | |
5896 | (home-page "https://github.com/lh3/seqtk") | |
5897 | (synopsis "Toolkit for processing biological sequences in FASTA/Q format") | |
5898 | (description | |
5899 | "Seqtk is a fast and lightweight tool for processing sequences in the | |
5900 | FASTA or FASTQ format. It parses both FASTA and FASTQ files which can be | |
5901 | optionally compressed by gzip.") | |
5902 | (license license:expat))) | |
5903 | ||
5f7e17be BW |
5904 | (define-public snap-aligner |
5905 | (package | |
5906 | (name "snap-aligner") | |
5907 | (version "1.0beta.18") | |
5908 | (source (origin | |
e0a8fc85 RW |
5909 | (method git-fetch) |
5910 | (uri (git-reference | |
5911 | (url "https://github.com/amplab/snap.git") | |
5912 | (commit (string-append "v" version)))) | |
5913 | (file-name (git-file-name name version)) | |
5f7e17be BW |
5914 | (sha256 |
5915 | (base32 | |
e0a8fc85 | 5916 | "01w3qq4wm07z73vky0cfwlmrbf50n3w722cxrlzxfi99mnb808d8")))) |
5f7e17be BW |
5917 | (build-system gnu-build-system) |
5918 | (arguments | |
5919 | '(#:phases | |
5920 | (modify-phases %standard-phases | |
5921 | (delete 'configure) | |
e0a8fc85 | 5922 | (replace 'check (lambda _ (invoke "./unit_tests") #t)) |
5f7e17be BW |
5923 | (replace 'install |
5924 | (lambda* (#:key outputs #:allow-other-keys) | |
5925 | (let* ((out (assoc-ref outputs "out")) | |
5926 | (bin (string-append out "/bin"))) | |
5f7e17be BW |
5927 | (install-file "snap-aligner" bin) |
5928 | (install-file "SNAPCommand" bin) | |
5929 | #t)))))) | |
5930 | (native-inputs | |
5931 | `(("zlib" ,zlib))) | |
5932 | (home-page "http://snap.cs.berkeley.edu/") | |
5933 | (synopsis "Short read DNA sequence aligner") | |
5934 | (description | |
5935 | "SNAP is a fast and accurate aligner for short DNA reads. It is | |
5936 | optimized for modern read lengths of 100 bases or higher, and takes advantage | |
5937 | of these reads to align data quickly through a hash-based indexing scheme.") | |
3e6fdd5f EF |
5938 | ;; 32-bit systems are not supported by the unpatched code. |
5939 | ;; Following the bug reports https://github.com/amplab/snap/issues/68 and | |
5940 | ;; https://bugs.debian.org/cgi-bin/bugreport.cgi?bug=812378 we see that | |
5941 | ;; systems without a lot of memory cannot make good use of this program. | |
5942 | (supported-systems '("x86_64-linux")) | |
5f7e17be BW |
5943 | (license license:asl2.0))) |
5944 | ||
bcadaf00 BW |
5945 | (define-public sortmerna |
5946 | (package | |
5947 | (name "sortmerna") | |
849485f5 | 5948 | (version "2.1b") |
bcadaf00 BW |
5949 | (source |
5950 | (origin | |
62365244 RW |
5951 | (method git-fetch) |
5952 | (uri (git-reference | |
5953 | (url "https://github.com/biocore/sortmerna.git") | |
5954 | (commit version))) | |
5955 | (file-name (git-file-name name version)) | |
bcadaf00 BW |
5956 | (sha256 |
5957 | (base32 | |
62365244 | 5958 | "0j3mbz4n25738yijmjbr5r4fyvkgm8v5vn3sshyfvmyqf5q9byqf")))) |
bcadaf00 BW |
5959 | (build-system gnu-build-system) |
5960 | (outputs '("out" ;for binaries | |
5961 | "db")) ;for sequence databases | |
5962 | (arguments | |
5963 | `(#:phases | |
5964 | (modify-phases %standard-phases | |
5965 | (replace 'install | |
5966 | (lambda* (#:key outputs #:allow-other-keys) | |
5967 | (let* ((out (assoc-ref outputs "out")) | |
5968 | (bin (string-append out "/bin")) | |
5969 | (db (assoc-ref outputs "db")) | |
5970 | (share | |
5971 | (string-append db "/share/sortmerna/rRNA_databases"))) | |
5972 | (install-file "sortmerna" bin) | |
5973 | (install-file "indexdb_rna" bin) | |
5974 | (for-each (lambda (file) | |
5975 | (install-file file share)) | |
5976 | (find-files "rRNA_databases" ".*fasta")) | |
5977 | #t)))))) | |
849485f5 BW |
5978 | (inputs |
5979 | `(("zlib" ,zlib))) | |
bcadaf00 BW |
5980 | (home-page "http://bioinfo.lifl.fr/RNA/sortmerna") |
5981 | (synopsis "Biological sequence analysis tool for NGS reads") | |
5982 | (description | |
5983 | "SortMeRNA is a biological sequence analysis tool for filtering, mapping | |
5984 | and operational taxonomic unit (OTU) picking of next generation | |
5985 | sequencing (NGS) reads. The core algorithm is based on approximate seeds and | |
5986 | allows for fast and sensitive analyses of nucleotide sequences. The main | |
5987 | application of SortMeRNA is filtering rRNA from metatranscriptomic data.") | |
2324541b EF |
5988 | ;; The source includes x86 specific code |
5989 | (supported-systems '("x86_64-linux" "i686-linux")) | |
bcadaf00 BW |
5990 | (license license:lgpl3))) |
5991 | ||
ce7155d5 RW |
5992 | (define-public star |
5993 | (package | |
5994 | (name "star") | |
6d095c4c | 5995 | (version "2.6.0c") |
ce7155d5 | 5996 | (source (origin |
6d095c4c RW |
5997 | (method git-fetch) |
5998 | (uri (git-reference | |
5999 | (url "https://github.com/alexdobin/STAR.git") | |
6000 | (commit version))) | |
6001 | (file-name (string-append name "-" version "-checkout")) | |
ce7155d5 RW |
6002 | (sha256 |
6003 | (base32 | |
6d095c4c | 6004 | "04cj6jw8d9q6lk9c78wa4fky6jdlicf1d13plq7182h8vqiz8p59")) |
ce7155d5 RW |
6005 | (modules '((guix build utils))) |
6006 | (snippet | |
3062d750 RW |
6007 | '(begin |
6008 | (substitute* "source/Makefile" | |
6009 | (("/bin/rm") "rm")) | |
6010 | ;; Remove pre-built binaries and bundled htslib sources. | |
6011 | (delete-file-recursively "bin/MacOSX_x86_64") | |
6012 | (delete-file-recursively "bin/Linux_x86_64") | |
c9e9154e | 6013 | (delete-file-recursively "bin/Linux_x86_64_static") |
3062d750 RW |
6014 | (delete-file-recursively "source/htslib") |
6015 | #t)))) | |
ce7155d5 RW |
6016 | (build-system gnu-build-system) |
6017 | (arguments | |
6018 | '(#:tests? #f ;no check target | |
6019 | #:make-flags '("STAR") | |
6020 | #:phases | |
c0266e8d RW |
6021 | (modify-phases %standard-phases |
6022 | (add-after 'unpack 'enter-source-dir | |
6023 | (lambda _ (chdir "source") #t)) | |
625cdc3f RW |
6024 | (add-after 'enter-source-dir 'make-reproducible |
6025 | (lambda _ | |
6026 | (substitute* "Makefile" | |
6027 | (("(COMPILATION_TIME_PLACE=\")(.*)(\")" _ pre mid post) | |
2e0f6905 MW |
6028 | (string-append pre "Built with Guix" post))) |
6029 | #t)) | |
3062d750 RW |
6030 | (add-after 'enter-source-dir 'do-not-use-bundled-htslib |
6031 | (lambda _ | |
6032 | (substitute* "Makefile" | |
6033 | (("(Depend.list: \\$\\(SOURCES\\) parametersDefault\\.xxd) htslib" | |
6034 | _ prefix) prefix)) | |
6035 | (substitute* '("BAMfunctions.cpp" | |
6036 | "signalFromBAM.h" | |
6037 | "bam_cat.h" | |
6038 | "bam_cat.c" | |
6039 | "STAR.cpp" | |
6040 | "bamRemoveDuplicates.cpp") | |
6041 | (("#include \"htslib/([^\"]+\\.h)\"" _ header) | |
6042 | (string-append "#include <" header ">"))) | |
6043 | (substitute* "IncludeDefine.h" | |
6044 | (("\"htslib/(htslib/[^\"]+.h)\"" _ header) | |
6045 | (string-append "<" header ">"))) | |
6046 | #t)) | |
c0266e8d RW |
6047 | (replace 'install |
6048 | (lambda* (#:key outputs #:allow-other-keys) | |
6049 | (let ((bin (string-append (assoc-ref outputs "out") "/bin/"))) | |
6050 | (install-file "STAR" bin)) | |
6051 | #t)) | |
6052 | (delete 'configure)))) | |
ce7155d5 | 6053 | (native-inputs |
9fc513ad | 6054 | `(("xxd" ,xxd))) |
ce7155d5 | 6055 | (inputs |
3062d750 RW |
6056 | `(("htslib" ,htslib) |
6057 | ("zlib" ,zlib))) | |
ce7155d5 RW |
6058 | (home-page "https://github.com/alexdobin/STAR") |
6059 | (synopsis "Universal RNA-seq aligner") | |
6060 | (description | |
6061 | "The Spliced Transcripts Alignment to a Reference (STAR) software is | |
6062 | based on a previously undescribed RNA-seq alignment algorithm that uses | |
6063 | sequential maximum mappable seed search in uncompressed suffix arrays followed | |
6064 | by seed clustering and stitching procedure. In addition to unbiased de novo | |
6065 | detection of canonical junctions, STAR can discover non-canonical splices and | |
6066 | chimeric (fusion) transcripts, and is also capable of mapping full-length RNA | |
6067 | sequences.") | |
c11f79a4 BW |
6068 | ;; Only 64-bit systems are supported according to the README. |
6069 | (supported-systems '("x86_64-linux" "mips64el-linux")) | |
ce7155d5 RW |
6070 | ;; STAR is licensed under GPLv3 or later; htslib is MIT-licensed. |
6071 | (license license:gpl3+))) | |
de07c0db | 6072 | |
dbf4ed7c RW |
6073 | (define-public subread |
6074 | (package | |
6075 | (name "subread") | |
e6debcaf | 6076 | (version "1.6.0") |
dbf4ed7c RW |
6077 | (source (origin |
6078 | (method url-fetch) | |
de67e922 LF |
6079 | (uri (string-append "mirror://sourceforge/subread/subread-" |
6080 | version "/subread-" version "-source.tar.gz")) | |
dbf4ed7c RW |
6081 | (sha256 |
6082 | (base32 | |
e6debcaf | 6083 | "0ah0n4jx6ksk2m2j7xk385x2qzmk1y4rfc6a4mfrdqrlq721w99i")))) |
dbf4ed7c RW |
6084 | (build-system gnu-build-system) |
6085 | (arguments | |
6086 | `(#:tests? #f ;no "check" target | |
104c1986 RW |
6087 | ;; The CC and CCFLAGS variables are set to contain a lot of x86_64 |
6088 | ;; optimizations by default, so we override these flags such that x86_64 | |
6089 | ;; flags are only added when the build target is an x86_64 system. | |
6090 | #:make-flags | |
6091 | (list (let ((system ,(or (%current-target-system) | |
6092 | (%current-system))) | |
6093 | (flags '("-ggdb" "-fomit-frame-pointer" | |
6094 | "-ffast-math" "-funroll-loops" | |
6095 | "-fmessage-length=0" | |
6096 | "-O9" "-Wall" "-DMAKE_FOR_EXON" | |
6097 | "-DMAKE_STANDALONE" | |
6098 | "-DSUBREAD_VERSION=\\\"${SUBREAD_VERSION}\\\"")) | |
6099 | (flags64 '("-mmmx" "-msse" "-msse2" "-msse3"))) | |
6100 | (if (string-prefix? "x86_64" system) | |
6101 | (string-append "CCFLAGS=" (string-join (append flags flags64))) | |
6102 | (string-append "CCFLAGS=" (string-join flags)))) | |
6103 | "-f" "Makefile.Linux" | |
6104 | "CC=gcc ${CCFLAGS}") | |
dbf4ed7c | 6105 | #:phases |
dc1d3cde KK |
6106 | (modify-phases %standard-phases |
6107 | (add-after 'unpack 'enter-dir | |
6108 | (lambda _ (chdir "src") #t)) | |
6109 | (replace 'install | |
6110 | (lambda* (#:key outputs #:allow-other-keys) | |
6111 | (let ((bin (string-append (assoc-ref outputs "out") "/bin/"))) | |
6112 | (mkdir-p bin) | |
2e0f6905 MW |
6113 | (copy-recursively "../bin" bin)) |
6114 | #t)) | |
dbf4ed7c | 6115 | ;; no "configure" script |
dc1d3cde | 6116 | (delete 'configure)))) |
dbf4ed7c RW |
6117 | (inputs `(("zlib" ,zlib))) |
6118 | (home-page "http://bioinf.wehi.edu.au/subread-package/") | |
6119 | (synopsis "Tool kit for processing next-gen sequencing data") | |
6120 | (description | |
6121 | "The subread package contains the following tools: subread aligner, a | |
6122 | general-purpose read aligner; subjunc aligner: detecting exon-exon junctions | |
6123 | and mapping RNA-seq reads; featureCounts: counting mapped reads for genomic | |
6124 | features; exactSNP: a SNP caller that discovers SNPs by testing signals | |
6125 | against local background noises.") | |
6126 | (license license:gpl3+))) | |
6127 | ||
d15d981e RW |
6128 | (define-public stringtie |
6129 | (package | |
6130 | (name "stringtie") | |
6131 | (version "1.2.1") | |
6132 | (source (origin | |
6133 | (method url-fetch) | |
6134 | (uri (string-append "http://ccb.jhu.edu/software/stringtie/dl/" | |
6135 | "stringtie-" version ".tar.gz")) | |
6136 | (sha256 | |
6137 | (base32 | |
6138 | "1cqllsc1maq4kh92isi8yadgzbmnf042hlnalpk3y59aph1z3bfz")) | |
6139 | (modules '((guix build utils))) | |
6140 | (snippet | |
6141 | '(begin | |
6142 | (delete-file-recursively "samtools-0.1.18") | |
6143 | #t)))) | |
6144 | (build-system gnu-build-system) | |
6145 | (arguments | |
6146 | `(#:tests? #f ;no test suite | |
6147 | #:phases | |
6148 | (modify-phases %standard-phases | |
6149 | ;; no configure script | |
6150 | (delete 'configure) | |
6151 | (add-before 'build 'use-system-samtools | |
6152 | (lambda _ | |
6153 | (substitute* "Makefile" | |
6154 | (("stringtie: \\$\\{BAM\\}/libbam\\.a") | |
6155 | "stringtie: ")) | |
6156 | (substitute* '("gclib/GBam.h" | |
6157 | "gclib/GBam.cpp") | |
6158 | (("#include \"(bam|sam|kstring).h\"" _ header) | |
6159 | (string-append "#include <samtools/" header ".h>"))) | |
6160 | #t)) | |
0d2c0562 RW |
6161 | (add-after 'unpack 'remove-duplicate-typedef |
6162 | (lambda _ | |
6163 | ;; This typedef conflicts with the typedef in | |
6164 | ;; glibc-2.25/include/bits/types.h | |
6165 | (substitute* "gclib/GThreads.h" | |
6166 | (("typedef long long __intmax_t;") "")) | |
6167 | #t)) | |
d15d981e RW |
6168 | (replace 'install |
6169 | (lambda* (#:key outputs #:allow-other-keys) | |
6170 | (let ((bin (string-append (assoc-ref outputs "out") "/bin/"))) | |
6171 | (install-file "stringtie" bin) | |
6172 | #t)))))) | |
6173 | (inputs | |
6174 | `(("samtools" ,samtools-0.1) | |
6175 | ("zlib" ,zlib))) | |
6176 | (home-page "http://ccb.jhu.edu/software/stringtie/") | |
6177 | (synopsis "Transcript assembly and quantification for RNA-Seq data") | |
6178 | (description | |
6179 | "StringTie is a fast and efficient assembler of RNA-Seq sequence | |
6180 | alignments into potential transcripts. It uses a novel network flow algorithm | |
6181 | as well as an optional de novo assembly step to assemble and quantitate | |
6182 | full-length transcripts representing multiple splice variants for each gene | |
6183 | locus. Its input can include not only the alignments of raw reads used by | |
6184 | other transcript assemblers, but also alignments of longer sequences that have | |
6185 | been assembled from those reads. To identify differentially expressed genes | |
6186 | between experiments, StringTie's output can be processed either by the | |
6187 | Cuffdiff or Ballgown programs.") | |
6188 | (license license:artistic2.0))) | |
6189 | ||
ad0ae297 BW |
6190 | (define-public taxtastic |
6191 | (package | |
6192 | (name "taxtastic") | |
d0c75e73 | 6193 | (version "0.8.5") |
ad0ae297 BW |
6194 | (source (origin |
6195 | (method url-fetch) | |
3cbfc149 | 6196 | (uri (pypi-uri "taxtastic" version)) |
ad0ae297 BW |
6197 | (sha256 |
6198 | (base32 | |
d0c75e73 | 6199 | "03pysw79lsrvz4lwzis88j15067ffqbi4cid5pqhrlxmd6bh8rrk")))) |
ad0ae297 BW |
6200 | (build-system python-build-system) |
6201 | (arguments | |
6202 | `(#:python ,python-2 | |
6203 | #:phases | |
6204 | (modify-phases %standard-phases | |
6205 | (replace 'check | |
8b685c47 | 6206 | (lambda _ (invoke "python" "-m" "unittest" "discover" "-v") #t))))) |
ad0ae297 BW |
6207 | (propagated-inputs |
6208 | `(("python-sqlalchemy" ,python2-sqlalchemy) | |
6209 | ("python-decorator" ,python2-decorator) | |
6210 | ("python-biopython" ,python2-biopython) | |
3f8c82e6 BW |
6211 | ("python-pandas" ,python2-pandas) |
6212 | ("python-psycopg2" ,python2-psycopg2) | |
6213 | ("python-fastalite" ,python2-fastalite) | |
6214 | ("python-pyyaml" ,python2-pyyaml) | |
6215 | ("python-six" ,python2-six) | |
6216 | ("python-jinja2" ,python2-jinja2) | |
6217 | ("python-dendropy" ,python2-dendropy))) | |
ad0ae297 BW |
6218 | (home-page "https://github.com/fhcrc/taxtastic") |
6219 | (synopsis "Tools for taxonomic naming and annotation") | |
6220 | (description | |
6221 | "Taxtastic is software written in python used to build and maintain | |
6222 | reference packages i.e. collections of reference trees, reference alignments, | |
6223 | profiles, and associated taxonomic information.") | |
6224 | (license license:gpl3+))) | |
6225 | ||
de07c0db RW |
6226 | (define-public vcftools |
6227 | (package | |
6228 | (name "vcftools") | |
f4322542 | 6229 | (version "0.1.15") |
de07c0db RW |
6230 | (source (origin |
6231 | (method url-fetch) | |
6232 | (uri (string-append | |
9b36e256 RJ |
6233 | "https://github.com/vcftools/vcftools/releases/download/v" |
6234 | version "/vcftools-" version ".tar.gz")) | |
de07c0db RW |
6235 | (sha256 |
6236 | (base32 | |
f4322542 | 6237 | "1qw30c45wihgy632rbz4rh3njnwj4msj46l1rsgdhyg6bgypmr1i")))) |
de07c0db RW |
6238 | (build-system gnu-build-system) |
6239 | (arguments | |
6240 | `(#:tests? #f ; no "check" target | |
6241 | #:make-flags (list | |
7c3958e1 | 6242 | "CFLAGS=-O2" ; override "-m64" flag |
de07c0db RW |
6243 | (string-append "PREFIX=" (assoc-ref %outputs "out")) |
6244 | (string-append "MANDIR=" (assoc-ref %outputs "out") | |
9b36e256 RJ |
6245 | "/share/man/man1")))) |
6246 | (native-inputs | |
6247 | `(("pkg-config" ,pkg-config))) | |
de07c0db RW |
6248 | (inputs |
6249 | `(("perl" ,perl) | |
6250 | ("zlib" ,zlib))) | |
9b36e256 | 6251 | (home-page "https://vcftools.github.io/") |
de07c0db RW |
6252 | (synopsis "Tools for working with VCF files") |
6253 | (description | |
6254 | "VCFtools is a program package designed for working with VCF files, such | |
6255 | as those generated by the 1000 Genomes Project. The aim of VCFtools is to | |
6256 | provide easily accessible methods for working with complex genetic variation | |
6257 | data in the form of VCF files.") | |
6258 | ;; The license is declared as LGPLv3 in the README and | |
9b36e256 | 6259 | ;; at https://vcftools.github.io/license.html |
de07c0db | 6260 | (license license:lgpl3))) |
9c38b540 | 6261 | |
35aa90a1 RW |
6262 | (define-public infernal |
6263 | (package | |
6264 | (name "infernal") | |
6265 | (version "1.1.2") | |
6266 | (source (origin | |
6267 | (method url-fetch) | |
6268 | (uri (string-append "http://eddylab.org/software/infernal/" | |
6269 | "infernal-" version ".tar.gz")) | |
6270 | (sha256 | |
6271 | (base32 | |
6272 | "0sr2hiz3qxfwqpz3whxr6n82p3x27336v3f34iqznp10hks2935c")))) | |
6273 | (build-system gnu-build-system) | |
6274 | (native-inputs | |
6275 | `(("perl" ,perl))) ; for tests | |
6276 | (home-page "http://eddylab.org/infernal/") | |
6277 | (synopsis "Inference of RNA alignments") | |
6278 | (description "Infernal (\"INFERence of RNA ALignment\") is a tool for | |
6279 | searching DNA sequence databases for RNA structure and sequence similarities. | |
6280 | It is an implementation of a special case of profile stochastic context-free | |
6281 | grammars called @dfn{covariance models} (CMs). A CM is like a sequence | |
6282 | profile, but it scores a combination of sequence consensus and RNA secondary | |
6283 | structure consensus, so in many cases, it is more capable of identifying RNA | |
6284 | homologs that conserve their secondary structure more than their primary | |
6285 | sequence.") | |
48409ef2 EF |
6286 | ;; Infernal 1.1.2 requires VMX or SSE capability for parallel instructions. |
6287 | (supported-systems '("i686-linux" "x86_64-linux")) | |
35aa90a1 RW |
6288 | (license license:bsd-3))) |
6289 | ||
b91cfa22 RW |
6290 | (define-public r-centipede |
6291 | (package | |
6292 | (name "r-centipede") | |
6293 | (version "1.2") | |
6294 | (source (origin | |
6295 | (method url-fetch) | |
6296 | (uri (string-append "http://download.r-forge.r-project.org/" | |
6297 | "src/contrib/CENTIPEDE_" version ".tar.gz")) | |
6298 | (sha256 | |
6299 | (base32 | |
6300 | "1hsx6qgwr0i67fhy9257zj7s0ppncph2hjgbia5nn6nfmj0ax6l9")))) | |
6301 | (build-system r-build-system) | |
6302 | (home-page "http://centipede.uchicago.edu/") | |
6303 | (synopsis "Predict transcription factor binding sites") | |
6304 | (description | |
6305 | "CENTIPEDE applies a hierarchical Bayesian mixture model to infer regions | |
6306 | of the genome that are bound by particular transcription factors. It starts | |
6307 | by identifying a set of candidate binding sites, and then aims to classify the | |
6308 | sites according to whether each site is bound or not bound by a transcription | |
6309 | factor. CENTIPEDE is an unsupervised learning algorithm that discriminates | |
6310 | between two different types of motif instances using as much relevant | |
6311 | information as possible.") | |
6312 | (license (list license:gpl2+ license:gpl3+)))) | |
6313 | ||
7b3df1e5 BW |
6314 | (define-public r-vegan |
6315 | (package | |
6316 | (name "r-vegan") | |
192c19f4 | 6317 | (version "2.5-3") |
7b3df1e5 BW |
6318 | (source |
6319 | (origin | |
6320 | (method url-fetch) | |
6321 | (uri (cran-uri "vegan" version)) | |
6322 | (sha256 | |
6323 | (base32 | |
192c19f4 | 6324 | "023xznh0iy0496icpchadmp7a3rk3nj9s48fvwlvp3dssw58yp3c")))) |
7b3df1e5 | 6325 | (build-system r-build-system) |
7b3df1e5 | 6326 | (native-inputs |
db2e4386 | 6327 | `(("gfortran" ,gfortran))) |
7b3df1e5 BW |
6328 | (propagated-inputs |
6329 | `(("r-cluster" ,r-cluster) | |
3ca31735 | 6330 | ("r-knitr" ,r-knitr) ; needed for vignettes |
7b3df1e5 | 6331 | ("r-lattice" ,r-lattice) |
aeb64f3c | 6332 | ("r-mass" ,r-mass) |
7b3df1e5 BW |
6333 | ("r-mgcv" ,r-mgcv) |
6334 | ("r-permute" ,r-permute))) | |
6335 | (home-page "https://cran.r-project.org/web/packages/vegan") | |
6336 | (synopsis "Functions for community ecology") | |
6337 | (description | |
6338 | "The vegan package provides tools for descriptive community ecology. It | |
6339 | has most basic functions of diversity analysis, community ordination and | |
6340 | dissimilarity analysis. Most of its multivariate tools can be used for other | |
6341 | data types as well.") | |
6342 | (license license:gpl2+))) | |
6343 | ||
8c6de588 RW |
6344 | (define-public r-annotate |
6345 | (package | |
6346 | (name "r-annotate") | |
090d4c01 | 6347 | (version "1.60.0") |
8c6de588 RW |
6348 | (source |
6349 | (origin | |
6350 | (method url-fetch) | |
6351 | (uri (bioconductor-uri "annotate" version)) | |
6352 | (sha256 | |
6353 | (base32 | |
090d4c01 | 6354 | "0p6c96lay23a67dyirgnwzm2yw22m592z780vy6p4nqwla8ha18n")))) |
8c6de588 RW |
6355 | (build-system r-build-system) |
6356 | (propagated-inputs | |
6357 | `(("r-annotationdbi" ,r-annotationdbi) | |
6358 | ("r-biobase" ,r-biobase) | |
6359 | ("r-biocgenerics" ,r-biocgenerics) | |
6360 | ("r-dbi" ,r-dbi) | |
d0f0579e | 6361 | ("r-rcurl" ,r-rcurl) |
8c6de588 RW |
6362 | ("r-xml" ,r-xml) |
6363 | ("r-xtable" ,r-xtable))) | |
6364 | (home-page | |
5713bbf1 | 6365 | "https://bioconductor.org/packages/annotate") |
8c6de588 | 6366 | (synopsis "Annotation for microarrays") |
d1e4ad1b | 6367 | (description "This package provides R environments for the annotation of |
8c6de588 RW |
6368 | microarrays.") |
6369 | (license license:artistic2.0))) | |
6370 | ||
efa6a1dd RJ |
6371 | (define-public r-copynumber |
6372 | (package | |
6373 | (name "r-copynumber") | |
dadd682c | 6374 | (version "1.22.0") |
efa6a1dd RJ |
6375 | (source (origin |
6376 | (method url-fetch) | |
6377 | (uri (bioconductor-uri "copynumber" version)) | |
6378 | (sha256 | |
6379 | (base32 | |
dadd682c | 6380 | "0ipwj9i5p1bwhg5d80jdjagm02krpj2v0j47qdgw41h8wncdyal3")))) |
efa6a1dd RJ |
6381 | (build-system r-build-system) |
6382 | (propagated-inputs | |
6383 | `(("r-s4vectors" ,r-s4vectors) | |
6384 | ("r-iranges" ,r-iranges) | |
6385 | ("r-genomicranges" ,r-genomicranges) | |
6386 | ("r-biocgenerics" ,r-biocgenerics))) | |
6387 | (home-page "https://bioconductor.org/packages/copynumber") | |
6388 | (synopsis "Segmentation of single- and multi-track copy number data") | |
6389 | (description | |
6390 | "This package segments single- and multi-track copy number data by a | |
6391 | penalized least squares regression method.") | |
6392 | (license license:artistic2.0))) | |
6393 | ||
07a664cd RW |
6394 | (define-public r-geneplotter |
6395 | (package | |
6396 | (name "r-geneplotter") | |
f4a95a0d | 6397 | (version "1.60.0") |
07a664cd RW |
6398 | (source |
6399 | (origin | |
6400 | (method url-fetch) | |
6401 | (uri (bioconductor-uri "geneplotter" version)) | |
6402 | (sha256 | |
6403 | (base32 | |
f4a95a0d | 6404 | "10khr0pznxf3m0f5gzck9ymljrwcv3vamfmpskd51yjh36lhllqz")))) |
07a664cd RW |
6405 | (build-system r-build-system) |
6406 | (propagated-inputs | |
6407 | `(("r-annotate" ,r-annotate) | |
6408 | ("r-annotationdbi" ,r-annotationdbi) | |
6409 | ("r-biobase" ,r-biobase) | |
6410 | ("r-biocgenerics" ,r-biocgenerics) | |
6411 | ("r-lattice" ,r-lattice) | |
6412 | ("r-rcolorbrewer" ,r-rcolorbrewer))) | |
5713bbf1 | 6413 | (home-page "https://bioconductor.org/packages/geneplotter") |
07a664cd RW |
6414 | (synopsis "Graphics functions for genomic data") |
6415 | (description | |
6416 | "This package provides functions for plotting genomic data.") | |
6417 | (license license:artistic2.0))) | |
6418 | ||
2301fd3e RW |
6419 | (define-public r-genefilter |
6420 | (package | |
6421 | (name "r-genefilter") | |
85fb33a0 | 6422 | (version "1.64.0") |
2301fd3e RW |
6423 | (source |
6424 | (origin | |
6425 | (method url-fetch) | |
6426 | (uri (bioconductor-uri "genefilter" version)) | |
6427 | (sha256 | |
6428 | (base32 | |
85fb33a0 | 6429 | "0p64s1n1627yafnp25wjr4b22p34lqw574fx2qg4s1m0lffh1z6i")))) |
2301fd3e RW |
6430 | (build-system r-build-system) |
6431 | (native-inputs | |
6432 | `(("gfortran" ,gfortran))) | |
6433 | (propagated-inputs | |
6434 | `(("r-annotate" ,r-annotate) | |
6435 | ("r-annotationdbi" ,r-annotationdbi) | |
6436 | ("r-biobase" ,r-biobase) | |
aeb64f3c RW |
6437 | ("r-s4vectors" ,r-s4vectors) |
6438 | ("r-survival" ,r-survival))) | |
5713bbf1 | 6439 | (home-page "https://bioconductor.org/packages/genefilter") |
2301fd3e RW |
6440 | (synopsis "Filter genes from high-throughput experiments") |
6441 | (description | |
6442 | "This package provides basic functions for filtering genes from | |
6443 | high-throughput sequencing experiments.") | |
6444 | (license license:artistic2.0))) | |
6445 | ||
ad34f0ac RW |
6446 | (define-public r-deseq2 |
6447 | (package | |
6448 | (name "r-deseq2") | |
b5c552e6 | 6449 | (version "1.22.1") |
ad34f0ac RW |
6450 | (source |
6451 | (origin | |
6452 | (method url-fetch) | |
6453 | (uri (bioconductor-uri "DESeq2" version)) | |
6454 | (sha256 | |
6455 | (base32 | |
b5c552e6 | 6456 | "1b2bmvcsfzvks47d7w46zplcwz0kgcdhx5xmx3x9lp2gvx2p84r5")))) |
ad34f0ac RW |
6457 | (properties `((upstream-name . "DESeq2"))) |
6458 | (build-system r-build-system) | |
ad34f0ac RW |
6459 | (propagated-inputs |
6460 | `(("r-biobase" ,r-biobase) | |
6461 | ("r-biocgenerics" ,r-biocgenerics) | |
6462 | ("r-biocparallel" ,r-biocparallel) | |
6463 | ("r-genefilter" ,r-genefilter) | |
6464 | ("r-geneplotter" ,r-geneplotter) | |
6465 | ("r-genomicranges" ,r-genomicranges) | |
6466 | ("r-ggplot2" ,r-ggplot2) | |
6467 | ("r-hmisc" ,r-hmisc) | |
6468 | ("r-iranges" ,r-iranges) | |
6469 | ("r-locfit" ,r-locfit) | |
6470 | ("r-rcpp" ,r-rcpp) | |
6471 | ("r-rcpparmadillo" ,r-rcpparmadillo) | |
6472 | ("r-s4vectors" ,r-s4vectors) | |
6473 | ("r-summarizedexperiment" ,r-summarizedexperiment))) | |
5713bbf1 | 6474 | (home-page "https://bioconductor.org/packages/DESeq2") |
ad34f0ac RW |
6475 | (synopsis "Differential gene expression analysis") |
6476 | (description | |
6477 | "This package provides functions to estimate variance-mean dependence in | |
6478 | count data from high-throughput nucleotide sequencing assays and test for | |
6479 | differential expression based on a model using the negative binomial | |
6480 | distribution.") | |
6481 | (license license:lgpl3+))) | |
6482 | ||
86763fdd RW |
6483 | (define-public r-dexseq |
6484 | (package | |
6485 | (name "r-dexseq") | |
856444a0 | 6486 | (version "1.28.0") |
86763fdd RW |
6487 | (source |
6488 | (origin | |
6489 | (method url-fetch) | |
6490 | (uri (bioconductor-uri "DEXSeq" version)) | |
6491 | (sha256 | |
6492 | (base32 | |
856444a0 | 6493 | "0jh1640cnzpk8x3155cqc8dvrs1rciw3d6nv2k70baw96bhrynp8")))) |
86763fdd RW |
6494 | (properties `((upstream-name . "DEXSeq"))) |
6495 | (build-system r-build-system) | |
6496 | (propagated-inputs | |
6497 | `(("r-annotationdbi" ,r-annotationdbi) | |
6498 | ("r-biobase" ,r-biobase) | |
6499 | ("r-biocgenerics" ,r-biocgenerics) | |
6500 | ("r-biocparallel" ,r-biocparallel) | |
6501 | ("r-biomart" ,r-biomart) | |
6502 | ("r-deseq2" ,r-deseq2) | |
6503 | ("r-genefilter" ,r-genefilter) | |
6504 | ("r-geneplotter" ,r-geneplotter) | |
6505 | ("r-genomicranges" ,r-genomicranges) | |
6506 | ("r-hwriter" ,r-hwriter) | |
6507 | ("r-iranges" ,r-iranges) | |
6508 | ("r-rcolorbrewer" ,r-rcolorbrewer) | |
6509 | ("r-rsamtools" ,r-rsamtools) | |
6510 | ("r-s4vectors" ,r-s4vectors) | |
6511 | ("r-statmod" ,r-statmod) | |
6512 | ("r-stringr" ,r-stringr) | |
6513 | ("r-summarizedexperiment" ,r-summarizedexperiment))) | |
5713bbf1 | 6514 | (home-page "https://bioconductor.org/packages/DEXSeq") |
86763fdd RW |
6515 | (synopsis "Inference of differential exon usage in RNA-Seq") |
6516 | (description | |
6517 | "This package is focused on finding differential exon usage using RNA-seq | |
6518 | exon counts between samples with different experimental designs. It provides | |
6519 | functions that allows the user to make the necessary statistical tests based | |
6520 | on a model that uses the negative binomial distribution to estimate the | |
6521 | variance between biological replicates and generalized linear models for | |
6522 | testing. The package also provides functions for the visualization and | |
6523 | exploration of the results.") | |
6524 | (license license:gpl3+))) | |
6525 | ||
e8163773 RW |
6526 | (define-public r-annotationforge |
6527 | (package | |
6528 | (name "r-annotationforge") | |
2ff6604a | 6529 | (version "1.24.0") |
e8163773 RW |
6530 | (source |
6531 | (origin | |
6532 | (method url-fetch) | |
6533 | (uri (bioconductor-uri "AnnotationForge" version)) | |
6534 | (sha256 | |
6535 | (base32 | |
2ff6604a | 6536 | "13yvhf3yskmvhs8szs6rkw93h81h5xqa3h19h91pp6nprhc8s3ll")))) |
e8163773 RW |
6537 | (properties |
6538 | `((upstream-name . "AnnotationForge"))) | |
6539 | (build-system r-build-system) | |
6540 | (propagated-inputs | |
6541 | `(("r-annotationdbi" ,r-annotationdbi) | |
6542 | ("r-biobase" ,r-biobase) | |
6543 | ("r-biocgenerics" ,r-biocgenerics) | |
6544 | ("r-dbi" ,r-dbi) | |
55cd914c | 6545 | ("r-rcurl" ,r-rcurl) |
e8163773 RW |
6546 | ("r-rsqlite" ,r-rsqlite) |
6547 | ("r-s4vectors" ,r-s4vectors) | |
6548 | ("r-xml" ,r-xml))) | |
5713bbf1 | 6549 | (home-page "https://bioconductor.org/packages/AnnotationForge") |
e8163773 RW |
6550 | (synopsis "Code for building annotation database packages") |
6551 | (description | |
6552 | "This package provides code for generating Annotation packages and their | |
6553 | databases. Packages produced are intended to be used with AnnotationDbi.") | |
6554 | (license license:artistic2.0))) | |
6555 | ||
cd9e7dc7 RW |
6556 | (define-public r-rbgl |
6557 | (package | |
6558 | (name "r-rbgl") | |
19a61491 | 6559 | (version "1.58.0") |
cd9e7dc7 RW |
6560 | (source |
6561 | (origin | |
6562 | (method url-fetch) | |
6563 | (uri (bioconductor-uri "RBGL" version)) | |
6564 | (sha256 | |
6565 | (base32 | |
19a61491 | 6566 | "0jy95m38c4qp0a12097hhm2gg63k96k6ydhb11dy379h3ziapcar")))) |
cd9e7dc7 RW |
6567 | (properties `((upstream-name . "RBGL"))) |
6568 | (build-system r-build-system) | |
6569 | (propagated-inputs `(("r-graph" ,r-graph))) | |
5713bbf1 | 6570 | (home-page "https://www.bioconductor.org/packages/RBGL") |
cd9e7dc7 RW |
6571 | (synopsis "Interface to the Boost graph library") |
6572 | (description | |
6573 | "This package provides a fairly extensive and comprehensive interface to | |
6574 | the graph algorithms contained in the Boost library.") | |
6575 | (license license:artistic2.0))) | |
6576 | ||
ad740ff8 RW |
6577 | (define-public r-gseabase |
6578 | (package | |
6579 | (name "r-gseabase") | |
6dfb0b25 | 6580 | (version "1.44.0") |
ad740ff8 RW |
6581 | (source |
6582 | (origin | |
6583 | (method url-fetch) | |
6584 | (uri (bioconductor-uri "GSEABase" version)) | |
6585 | (sha256 | |
6586 | (base32 | |
6dfb0b25 | 6587 | "110al7x0ig8plzrprvhwc7xshi1jzpj2n8llhhg2fh6v6k0k6awr")))) |
ad740ff8 RW |
6588 | (properties `((upstream-name . "GSEABase"))) |
6589 | (build-system r-build-system) | |
6590 | (propagated-inputs | |
6591 | `(("r-annotate" ,r-annotate) | |
6592 | ("r-annotationdbi" ,r-annotationdbi) | |
6593 | ("r-biobase" ,r-biobase) | |
6594 | ("r-biocgenerics" ,r-biocgenerics) | |
6595 | ("r-graph" ,r-graph) | |
6596 | ("r-xml" ,r-xml))) | |
5713bbf1 | 6597 | (home-page "https://bioconductor.org/packages/GSEABase") |
ad740ff8 RW |
6598 | (synopsis "Gene set enrichment data structures and methods") |
6599 | (description | |
6600 | "This package provides classes and methods to support @dfn{Gene Set | |
6601 | Enrichment Analysis} (GSEA).") | |
6602 | (license license:artistic2.0))) | |
6603 | ||
1a1931f7 RW |
6604 | (define-public r-category |
6605 | (package | |
6606 | (name "r-category") | |
95ae5acc | 6607 | (version "2.48.0") |
1a1931f7 RW |
6608 | (source |
6609 | (origin | |
6610 | (method url-fetch) | |
6611 | (uri (bioconductor-uri "Category" version)) | |
6612 | (sha256 | |
6613 | (base32 | |
95ae5acc | 6614 | "1jdm83bwdfhpfm1y6hwgvxzj6l83h1bdkqv23799kzywnwm016kv")))) |
1a1931f7 RW |
6615 | (properties `((upstream-name . "Category"))) |
6616 | (build-system r-build-system) | |
6617 | (propagated-inputs | |
6618 | `(("r-annotate" ,r-annotate) | |
6619 | ("r-annotationdbi" ,r-annotationdbi) | |
6620 | ("r-biobase" ,r-biobase) | |
6621 | ("r-biocgenerics" ,r-biocgenerics) | |
6622 | ("r-genefilter" ,r-genefilter) | |
6623 | ("r-graph" ,r-graph) | |
6624 | ("r-gseabase" ,r-gseabase) | |
6625 | ("r-matrix" ,r-matrix) | |
6626 | ("r-rbgl" ,r-rbgl) | |
2404cc42 | 6627 | ("r-dbi" ,r-dbi))) |
5713bbf1 | 6628 | (home-page "https://bioconductor.org/packages/Category") |
1a1931f7 RW |
6629 | (synopsis "Category analysis") |
6630 | (description | |
6631 | "This package provides a collection of tools for performing category | |
6632 | analysis.") | |
6633 | (license license:artistic2.0))) | |
6634 | ||
89f40c5e RW |
6635 | (define-public r-gostats |
6636 | (package | |
6637 | (name "r-gostats") | |
4a4b5b85 | 6638 | (version "2.48.0") |
89f40c5e RW |
6639 | (source |
6640 | (origin | |
6641 | (method url-fetch) | |
6642 | (uri (bioconductor-uri "GOstats" version)) | |
6643 | (sha256 | |
6644 | (base32 | |
4a4b5b85 | 6645 | "0wlqqgfynwqnqhckhsfjwg9zkj6hkmzwd5y76dhqz720vy21rcln")))) |
89f40c5e RW |
6646 | (properties `((upstream-name . "GOstats"))) |
6647 | (build-system r-build-system) | |
6648 | (propagated-inputs | |
6649 | `(("r-annotate" ,r-annotate) | |
6650 | ("r-annotationdbi" ,r-annotationdbi) | |
6651 | ("r-annotationforge" ,r-annotationforge) | |
6652 | ("r-biobase" ,r-biobase) | |
6653 | ("r-category" ,r-category) | |
6654 | ("r-go-db" ,r-go-db) | |
6655 | ("r-graph" ,r-graph) | |
eb3f5cc7 | 6656 | ("r-rgraphviz" ,r-rgraphviz) |
89f40c5e | 6657 | ("r-rbgl" ,r-rbgl))) |
5713bbf1 | 6658 | (home-page "https://bioconductor.org/packages/GOstats") |
89f40c5e RW |
6659 | (synopsis "Tools for manipulating GO and microarrays") |
6660 | (description | |
6661 | "This package provides a set of tools for interacting with GO and | |
6662 | microarray data. A variety of basic manipulation tools for graphs, hypothesis | |
6663 | testing and other simple calculations.") | |
6664 | (license license:artistic2.0))) | |
6665 | ||
cb99d457 RW |
6666 | (define-public r-shortread |
6667 | (package | |
6668 | (name "r-shortread") | |
9adf78c2 | 6669 | (version "1.40.0") |
cb99d457 RW |
6670 | (source |
6671 | (origin | |
6672 | (method url-fetch) | |
6673 | (uri (bioconductor-uri "ShortRead" version)) | |
6674 | (sha256 | |
6675 | (base32 | |
9adf78c2 | 6676 | "0iks123i1adkb9i2q4wvfqdmmj9dy867jvngj9757y8gj6xbcpy1")))) |
cb99d457 RW |
6677 | (properties `((upstream-name . "ShortRead"))) |
6678 | (build-system r-build-system) | |
6679 | (inputs | |
6680 | `(("zlib" ,zlib))) | |
6681 | (propagated-inputs | |
6682 | `(("r-biobase" ,r-biobase) | |
6683 | ("r-biocgenerics" ,r-biocgenerics) | |
6684 | ("r-biocparallel" ,r-biocparallel) | |
6685 | ("r-biostrings" ,r-biostrings) | |
6686 | ("r-genomeinfodb" ,r-genomeinfodb) | |
6687 | ("r-genomicalignments" ,r-genomicalignments) | |
6688 | ("r-genomicranges" ,r-genomicranges) | |
6689 | ("r-hwriter" ,r-hwriter) | |
6690 | ("r-iranges" ,r-iranges) | |
6691 | ("r-lattice" ,r-lattice) | |
6692 | ("r-latticeextra" ,r-latticeextra) | |
6693 | ("r-rsamtools" ,r-rsamtools) | |
6694 | ("r-s4vectors" ,r-s4vectors) | |
6695 | ("r-xvector" ,r-xvector) | |
6696 | ("r-zlibbioc" ,r-zlibbioc))) | |
5713bbf1 | 6697 | (home-page "https://bioconductor.org/packages/ShortRead") |
cb99d457 RW |
6698 | (synopsis "FASTQ input and manipulation tools") |
6699 | (description | |
6700 | "This package implements sampling, iteration, and input of FASTQ files. | |
6701 | It includes functions for filtering and trimming reads, and for generating a | |
6702 | quality assessment report. Data are represented as | |
6703 | @code{DNAStringSet}-derived objects, and easily manipulated for a diversity of | |
6704 | purposes. The package also contains legacy support for early single-end, | |
6705 | ungapped alignment formats.") | |
6706 | (license license:artistic2.0))) | |
6707 | ||
7f903d73 RW |
6708 | (define-public r-systempiper |
6709 | (package | |
6710 | (name "r-systempiper") | |
bf25930c | 6711 | (version "1.16.0") |
7f903d73 RW |
6712 | (source |
6713 | (origin | |
6714 | (method url-fetch) | |
6715 | (uri (bioconductor-uri "systemPipeR" version)) | |
6716 | (sha256 | |
6717 | (base32 | |
bf25930c | 6718 | "0l26q8zjdmzg84g7f25gv9z60sykybahlpg5bg9bmpbg5lzcsx04")))) |
7f903d73 RW |
6719 | (properties `((upstream-name . "systemPipeR"))) |
6720 | (build-system r-build-system) | |
6721 | (propagated-inputs | |
6722 | `(("r-annotate" ,r-annotate) | |
6723 | ("r-batchjobs" ,r-batchjobs) | |
6724 | ("r-biocgenerics" ,r-biocgenerics) | |
6725 | ("r-biostrings" ,r-biostrings) | |
6726 | ("r-deseq2" ,r-deseq2) | |
6727 | ("r-edger" ,r-edger) | |
6728 | ("r-genomicfeatures" ,r-genomicfeatures) | |
6729 | ("r-genomicranges" ,r-genomicranges) | |
6730 | ("r-ggplot2" ,r-ggplot2) | |
6731 | ("r-go-db" ,r-go-db) | |
6732 | ("r-gostats" ,r-gostats) | |
6733 | ("r-limma" ,r-limma) | |
6734 | ("r-pheatmap" ,r-pheatmap) | |
6735 | ("r-rjson" ,r-rjson) | |
6736 | ("r-rsamtools" ,r-rsamtools) | |
6737 | ("r-shortread" ,r-shortread) | |
6738 | ("r-summarizedexperiment" ,r-summarizedexperiment) | |
6739 | ("r-variantannotation" ,r-variantannotation))) | |
6740 | (home-page "https://github.com/tgirke/systemPipeR") | |
6741 | (synopsis "Next generation sequencing workflow and reporting environment") | |
6742 | (description | |
6743 | "This R package provides tools for building and running automated | |
6744 | end-to-end analysis workflows for a wide range of @dfn{next generation | |
6745 | sequence} (NGS) applications such as RNA-Seq, ChIP-Seq, VAR-Seq and Ribo-Seq. | |
6746 | Important features include a uniform workflow interface across different NGS | |
6747 | applications, automated report generation, and support for running both R and | |
6748 | command-line software, such as NGS aligners or peak/variant callers, on local | |
6749 | computers or compute clusters. Efficient handling of complex sample sets and | |
6750 | experimental designs is facilitated by a consistently implemented sample | |
6751 | annotation infrastructure.") | |
6752 | (license license:artistic2.0))) | |
6753 | ||
684f29bd RW |
6754 | (define-public r-grohmm |
6755 | (package | |
6756 | (name "r-grohmm") | |
5c996cab | 6757 | (version "1.16.0") |
684f29bd RW |
6758 | (source |
6759 | (origin | |
6760 | (method url-fetch) | |
6761 | (uri (bioconductor-uri "groHMM" version)) | |
6762 | (sha256 | |
6763 | (base32 | |
5c996cab | 6764 | "1ph92fv44b90v7mk4b1mjvv0dlrhl8ba01klxbnd0vs4qn9zxplh")))) |
684f29bd RW |
6765 | (properties `((upstream-name . "groHMM"))) |
6766 | (build-system r-build-system) | |
6767 | (propagated-inputs | |
6768 | `(("r-genomeinfodb" ,r-genomeinfodb) | |
6769 | ("r-genomicalignments" ,r-genomicalignments) | |
6770 | ("r-genomicranges" ,r-genomicranges) | |
6771 | ("r-iranges" ,r-iranges) | |
aeb64f3c | 6772 | ("r-mass" ,r-mass) |
684f29bd RW |
6773 | ("r-rtracklayer" ,r-rtracklayer) |
6774 | ("r-s4vectors" ,r-s4vectors))) | |
6775 | (home-page "https://github.com/Kraus-Lab/groHMM") | |
6776 | (synopsis "GRO-seq analysis pipeline") | |
6777 | (description | |
6778 | "This package provides a pipeline for the analysis of GRO-seq data.") | |
6779 | (license license:gpl3+))) | |
6780 | ||
f3cfe451 RW |
6781 | (define-public r-txdb-hsapiens-ucsc-hg19-knowngene |
6782 | (package | |
6783 | (name "r-txdb-hsapiens-ucsc-hg19-knowngene") | |
6784 | (version "3.2.2") | |
6785 | (source (origin | |
6786 | (method url-fetch) | |
6787 | ;; We cannot use bioconductor-uri here because this tarball is | |
6788 | ;; located under "data/annotation/" instead of "bioc/". | |
5713bbf1 | 6789 | (uri (string-append "https://bioconductor.org/packages/" |
f3cfe451 RW |
6790 | "release/data/annotation/src/contrib" |
6791 | "/TxDb.Hsapiens.UCSC.hg19.knownGene_" | |
6792 | version ".tar.gz")) | |
6793 | (sha256 | |
6794 | (base32 | |
6795 | "1sajhcqqwazgz2lqbik7rd935i7kpnh08zxbp2ra10j72yqy4g86")))) | |
6796 | (properties | |
6797 | `((upstream-name . "TxDb.Hsapiens.UCSC.hg19.knownGene"))) | |
6798 | (build-system r-build-system) | |
6799 | ;; As this package provides little more than a very large data file it | |
6800 | ;; doesn't make sense to build substitutes. | |
6801 | (arguments `(#:substitutable? #f)) | |
6802 | (propagated-inputs | |
6803 | `(("r-genomicfeatures" ,r-genomicfeatures))) | |
6804 | (home-page | |
5713bbf1 | 6805 | "https://bioconductor.org/packages/TxDb.Hsapiens.UCSC.hg19.knownGene/") |
f3cfe451 RW |
6806 | (synopsis "Annotation package for human genome in TxDb format") |
6807 | (description | |
6808 | "This package provides an annotation database of Homo sapiens genome | |
6809 | data. It is derived from the UCSC hg19 genome and based on the \"knownGene\" | |
6810 | track. The database is exposed as a @code{TxDb} object.") | |
6811 | (license license:artistic2.0))) | |
6812 | ||
325c039c RJ |
6813 | (define-public r-sparql |
6814 | (package | |
6815 | (name "r-sparql") | |
6816 | (version "1.16") | |
6817 | (source (origin | |
6818 | (method url-fetch) | |
6819 | (uri (cran-uri "SPARQL" version)) | |
6820 | (sha256 | |
6821 | (base32 | |
6822 | "0gak1q06yyhdmcxb2n3v0h9gr1vqd0viqji52wpw211qp6r6dcrc")))) | |
6823 | (properties `((upstream-name . "SPARQL"))) | |
6824 | (build-system r-build-system) | |
6825 | (propagated-inputs | |
6826 | `(("r-rcurl" ,r-rcurl) | |
6827 | ("r-xml" ,r-xml))) | |
e9960d8c | 6828 | (home-page "https://cran.r-project.org/web/packages/SPARQL") |
325c039c RJ |
6829 | (synopsis "SPARQL client for R") |
6830 | (description "This package provides an interface to use SPARQL to pose | |
6831 | SELECT or UPDATE queries to an end-point.") | |
6832 | ;; The only license indication is found in the DESCRIPTION file, | |
6833 | ;; which states GPL-3. So we cannot assume GPLv3+. | |
6834 | (license license:gpl3))) | |
6835 | ||
a2950fa4 BW |
6836 | (define-public vsearch |
6837 | (package | |
6838 | (name "vsearch") | |
86c6928e | 6839 | (version "2.9.1") |
a2950fa4 BW |
6840 | (source |
6841 | (origin | |
273df99d RW |
6842 | (method git-fetch) |
6843 | (uri (git-reference | |
6844 | (url "https://github.com/torognes/vsearch.git") | |
6845 | (commit (string-append "v" version)))) | |
6846 | (file-name (git-file-name name version)) | |
a2950fa4 BW |
6847 | (sha256 |
6848 | (base32 | |
86c6928e | 6849 | "0vhrpjfdf75ba04b24xknp41790cvcgwl0vgpy7qbzj5xh2521ss")) |
206af46f | 6850 | (patches (search-patches "vsearch-unbundle-cityhash.patch")) |
a2950fa4 BW |
6851 | (snippet |
6852 | '(begin | |
206af46f BW |
6853 | ;; Remove bundled cityhash sources. The vsearch source is adjusted |
6854 | ;; for this in the patch. | |
cf6edaba BW |
6855 | (delete-file "src/city.h") |
6856 | (delete-file "src/citycrc.h") | |
6857 | (delete-file "src/city.cc") | |
a2950fa4 BW |
6858 | #t)))) |
6859 | (build-system gnu-build-system) | |
a2950fa4 BW |
6860 | (inputs |
6861 | `(("zlib" ,zlib) | |
6862 | ("bzip2" ,bzip2) | |
6863 | ("cityhash" ,cityhash))) | |
6864 | (native-inputs | |
6865 | `(("autoconf" ,autoconf) | |
6866 | ("automake" ,automake))) | |
6867 | (synopsis "Sequence search tools for metagenomics") | |
6868 | (description | |
6869 | "VSEARCH supports DNA sequence searching, clustering, chimera detection, | |
6870 | dereplication, pairwise alignment, shuffling, subsampling, sorting and | |
6871 | masking. The tool takes advantage of parallelism in the form of SIMD | |
6872 | vectorization as well as multiple threads to perform accurate alignments at | |
6873 | high speed. VSEARCH uses an optimal global aligner (full dynamic programming | |
6874 | Needleman-Wunsch).") | |
6875 | (home-page "https://github.com/torognes/vsearch") | |
6f04e515 BW |
6876 | ;; vsearch uses non-portable SSE intrinsics so building fails on other |
6877 | ;; platforms. | |
6878 | (supported-systems '("x86_64-linux")) | |
a2950fa4 BW |
6879 | ;; Dual licensed; also includes public domain source. |
6880 | (license (list license:gpl3 license:bsd-2)))) | |
6881 | ||
07837874 RW |
6882 | (define-public pardre |
6883 | (package | |
6884 | (name "pardre") | |
7922ab8f BW |
6885 | ;; The source of 1.1.5 changed in place, so we append "-1" to the version. |
6886 | (version "1.1.5-1") | |
07837874 RW |
6887 | (source |
6888 | (origin | |
6889 | (method url-fetch) | |
6890 | (uri (string-append "mirror://sourceforge/pardre/ParDRe-rel" | |
7922ab8f | 6891 | "1.1.5" ".tar.gz")) |
07837874 RW |
6892 | (sha256 |
6893 | (base32 | |
7922ab8f | 6894 | "17j73nc0viq4f6qj50nrndsrif5d6b71q8fl87m54psiv0ilns2b")))) |
07837874 RW |
6895 | (build-system gnu-build-system) |
6896 | (arguments | |
6897 | `(#:tests? #f ; no tests included | |
6898 | #:phases | |
6899 | (modify-phases %standard-phases | |
6900 | (delete 'configure) | |
6901 | (replace 'install | |
6902 | (lambda* (#:key outputs #:allow-other-keys) | |
6903 | (let ((bin (string-append (assoc-ref outputs "out") "/bin"))) | |
07837874 RW |
6904 | (install-file "ParDRe" bin) |
6905 | #t)))))) | |
6906 | (inputs | |
6907 | `(("openmpi" ,openmpi) | |
6908 | ("zlib" ,zlib))) | |
6909 | (synopsis "Parallel tool to remove duplicate DNA reads") | |
6910 | (description | |
6911 | "ParDRe is a parallel tool to remove duplicate genetic sequence reads. | |
6912 | Duplicate reads can be seen as identical or nearly identical sequences with | |
6913 | some mismatches. This tool lets users avoid the analysis of unnecessary | |
6914 | reads, reducing the time of subsequent procedures with the | |
6915 | dataset (e.g. assemblies, mappings, etc.). The tool is implemented with MPI | |
6916 | in order to exploit the parallel capabilities of multicore clusters. It is | |
6917 | faster than multithreaded counterparts (end of 2015) for the same number of | |
6918 | cores and, thanks to the message-passing technology, it can be executed on | |
6919 | clusters.") | |
6920 | (home-page "https://sourceforge.net/projects/pardre/") | |
6921 | (license license:gpl3+))) | |
6922 | ||
e4a44a6a BW |
6923 | (define-public ruby-bio-kseq |
6924 | (package | |
6925 | (name "ruby-bio-kseq") | |
6926 | (version "0.0.2") | |
6927 | (source | |
6928 | (origin | |
6929 | (method url-fetch) | |
6930 | (uri (rubygems-uri "bio-kseq" version)) | |
6931 | (sha256 | |
6932 | (base32 | |
6933 | "1xyaha46khb5jc6wzkbf7040jagac49jbimn0vcrzid0j8jdikrz")))) | |
6934 | (build-system ruby-build-system) | |
6935 | (arguments | |
6936 | `(#:test-target "spec")) | |
6937 | (native-inputs | |
6938 | `(("bundler" ,bundler) | |
6939 | ("ruby-rspec" ,ruby-rspec) | |
6940 | ("ruby-rake-compiler" ,ruby-rake-compiler))) | |
6941 | (inputs | |
6942 | `(("zlib" ,zlib))) | |
6943 | (synopsis "Ruby bindings for the kseq.h FASTA/Q parser") | |
6944 | (description | |
6945 | "@code{Bio::Kseq} provides ruby bindings to the @code{kseq.h} FASTA and | |
6946 | FASTQ parsing code. It provides a fast iterator over sequences and their | |
6947 | quality scores.") | |
6948 | (home-page "https://github.com/gusevfe/bio-kseq") | |
6949 | (license license:expat))) | |
6950 | ||
9c38b540 PP |
6951 | (define-public bio-locus |
6952 | (package | |
6953 | (name "bio-locus") | |
6954 | (version "0.0.7") | |
6955 | (source | |
6956 | (origin | |
6957 | (method url-fetch) | |
6958 | (uri (rubygems-uri "bio-locus" version)) | |
6959 | (sha256 | |
6960 | (base32 | |
6961 | "02vmrxyimkj9sahsp4zhfhnmbvz6dbbqz1y01vglf8cbwvkajfl0")))) | |
6962 | (build-system ruby-build-system) | |
6963 | (native-inputs | |
6964 | `(("ruby-rspec" ,ruby-rspec))) | |
6965 | (synopsis "Tool for fast querying of genome locations") | |
6966 | (description | |
6967 | "Bio-locus is a tabix-like tool for fast querying of genome | |
6968 | locations. Many file formats in bioinformatics contain records that | |
6969 | start with a chromosome name and a position for a SNP, or a start-end | |
6970 | position for indels. Bio-locus allows users to store this chr+pos or | |
6971 | chr+pos+alt information in a database.") | |
6972 | (home-page "https://github.com/pjotrp/bio-locus") | |
6973 | (license license:expat))) | |
edb15985 | 6974 | |
b2bddb07 PP |
6975 | (define-public bio-blastxmlparser |
6976 | (package | |
6977 | (name "bio-blastxmlparser") | |
6978 | (version "2.0.4") | |
6979 | (source (origin | |
6980 | (method url-fetch) | |
6981 | (uri (rubygems-uri "bio-blastxmlparser" version)) | |
6982 | (sha256 | |
6983 | (base32 | |
6984 | "1wf4qygcmdjgcqm6flmvsagfr1gs9lf63mj32qv3z1f481zc5692")))) | |
6985 | (build-system ruby-build-system) | |
6986 | (propagated-inputs | |
6987 | `(("ruby-bio-logger" ,ruby-bio-logger) | |
6988 | ("ruby-nokogiri" ,ruby-nokogiri))) | |
6989 | (inputs | |
6990 | `(("ruby-rspec" ,ruby-rspec))) | |
6991 | (synopsis "Fast big data BLAST XML parser and library") | |
6992 | (description | |
6993 | "Very fast parallel big-data BLAST XML file parser which can be used as | |
6994 | command line utility. Use blastxmlparser to: Parse BLAST XML; filter output; | |
6995 | generate FASTA, JSON, YAML, RDF, JSON-LD, HTML, CSV, tabular output etc.") | |
7bf837fd | 6996 | (home-page "https://github.com/pjotrp/blastxmlparser") |
b2bddb07 PP |
6997 | (license license:expat))) |
6998 | ||
edb15985 PP |
6999 | (define-public bioruby |
7000 | (package | |
7001 | (name "bioruby") | |
357450dc | 7002 | (version "1.5.2") |
edb15985 PP |
7003 | (source |
7004 | (origin | |
7005 | (method url-fetch) | |
7006 | (uri (rubygems-uri "bio" version)) | |
7007 | (sha256 | |
7008 | (base32 | |
357450dc | 7009 | "1d56amdsjv1mag7m6gv2w0xij8hqx1v5xbdjsix8sp3yp36m7938")))) |
edb15985 PP |
7010 | (build-system ruby-build-system) |
7011 | (propagated-inputs | |
7012 | `(("ruby-libxml" ,ruby-libxml))) | |
7013 | (native-inputs | |
7014 | `(("which" ,which))) ; required for test phase | |
7015 | (arguments | |
7016 | `(#:phases | |
7017 | (modify-phases %standard-phases | |
7018 | (add-before 'build 'patch-test-command | |
7019 | (lambda _ | |
7020 | (substitute* '("test/functional/bio/test_command.rb") | |
7021 | (("/bin/sh") (which "sh"))) | |
7022 | (substitute* '("test/functional/bio/test_command.rb") | |
7023 | (("/bin/ls") (which "ls"))) | |
7024 | (substitute* '("test/functional/bio/test_command.rb") | |
7025 | (("which") (which "which"))) | |
7026 | (substitute* '("test/functional/bio/test_command.rb", | |
7027 | "test/data/command/echoarg2.sh") | |
7028 | (("/bin/echo") (which "echo"))) | |
7029 | #t))))) | |
7030 | (synopsis "Ruby library, shell and utilities for bioinformatics") | |
7031 | (description "BioRuby comes with a comprehensive set of Ruby development | |
7032 | tools and libraries for bioinformatics and molecular biology. BioRuby has | |
7033 | components for sequence analysis, pathway analysis, protein modelling and | |
7034 | phylogenetic analysis; it supports many widely used data formats and provides | |
7035 | easy access to databases, external programs and public web services, including | |
7036 | BLAST, KEGG, GenBank, MEDLINE and GO.") | |
7037 | (home-page "http://bioruby.org/") | |
7038 | ;; Code is released under Ruby license, except for setup | |
7039 | ;; (LGPLv2.1+) and scripts in samples (which have GPL2 and GPL2+) | |
7040 | (license (list license:ruby license:lgpl2.1+ license:gpl2+ )))) | |
a5002ae7 | 7041 | |
9fba89e8 RW |
7042 | (define-public r-acsnminer |
7043 | (package | |
7044 | (name "r-acsnminer") | |
0b54b4c9 | 7045 | (version "0.16.8.25") |
9fba89e8 RW |
7046 | (source (origin |
7047 | (method url-fetch) | |
7048 | (uri (cran-uri "ACSNMineR" version)) | |
7049 | (sha256 | |
7050 | (base32 | |
0b54b4c9 | 7051 | "0gh604s8qall6zfjlwcg2ilxjvz08dplf9k5g47idhv43scm748l")))) |
9fba89e8 RW |
7052 | (properties `((upstream-name . "ACSNMineR"))) |
7053 | (build-system r-build-system) | |
7054 | (propagated-inputs | |
7055 | `(("r-ggplot2" ,r-ggplot2) | |
7056 | ("r-gridextra" ,r-gridextra))) | |
e9960d8c | 7057 | (home-page "https://cran.r-project.org/web/packages/ACSNMineR") |
9fba89e8 RW |
7058 | (synopsis "Gene enrichment analysis") |
7059 | (description | |
7060 | "This package provides tools to compute and represent gene set enrichment | |
7061 | or depletion from your data based on pre-saved maps from the @dfn{Atlas of | |
7062 | Cancer Signalling Networks} (ACSN) or user imported maps. The gene set | |
7063 | enrichment can be run with hypergeometric test or Fisher exact test, and can | |
7064 | use multiple corrections. Visualization of data can be done either by | |
7065 | barplots or heatmaps.") | |
7066 | (license license:gpl2+))) | |
7067 | ||
d29b25c4 RW |
7068 | (define-public r-biocgenerics |
7069 | (package | |
7070 | (name "r-biocgenerics") | |
2f28ffd8 | 7071 | (version "0.28.0") |
d29b25c4 RW |
7072 | (source (origin |
7073 | (method url-fetch) | |
7074 | (uri (bioconductor-uri "BiocGenerics" version)) | |
7075 | (sha256 | |
7076 | (base32 | |
2f28ffd8 | 7077 | "0cvpsrhg7sn7lpqgxvqrsagv6j7xj5rafq5xdjfd8zc4gxrs5rb8")))) |
d29b25c4 | 7078 | (properties |
1d216b6e | 7079 | `((upstream-name . "BiocGenerics"))) |
d29b25c4 | 7080 | (build-system r-build-system) |
5713bbf1 | 7081 | (home-page "https://bioconductor.org/packages/BiocGenerics") |
d29b25c4 RW |
7082 | (synopsis "S4 generic functions for Bioconductor") |
7083 | (description | |
7084 | "This package provides S4 generic functions needed by many Bioconductor | |
7085 | packages.") | |
7086 | (license license:artistic2.0))) | |
7087 | ||
eb24341f RJ |
7088 | (define-public r-biocinstaller |
7089 | (package | |
7090 | (name "r-biocinstaller") | |
36d7d823 | 7091 | (version "1.32.1") |
eb24341f RJ |
7092 | (source (origin |
7093 | (method url-fetch) | |
7094 | (uri (bioconductor-uri "BiocInstaller" version)) | |
7095 | (sha256 | |
7096 | (base32 | |
36d7d823 | 7097 | "1s1f9qhyf3mc73ir25x2zlgi9hf45a37lg4z8fbva4i21hqisgsl")))) |
eb24341f RJ |
7098 | (properties |
7099 | `((upstream-name . "BiocInstaller"))) | |
7100 | (build-system r-build-system) | |
5713bbf1 | 7101 | (home-page "https://bioconductor.org/packages/BiocInstaller") |
eb24341f RJ |
7102 | (synopsis "Install Bioconductor packages") |
7103 | (description "This package is used to install and update R packages from | |
7104 | Bioconductor, CRAN, and Github.") | |
7105 | (license license:artistic2.0))) | |
7106 | ||
207ce8fb RJ |
7107 | (define-public r-biocviews |
7108 | (package | |
7109 | (name "r-biocviews") | |
77bea84b | 7110 | (version "1.50.5") |
207ce8fb RJ |
7111 | (source (origin |
7112 | (method url-fetch) | |
7113 | (uri (bioconductor-uri "biocViews" version)) | |
7114 | (sha256 | |
7115 | (base32 | |
77bea84b | 7116 | "0rc1n89n04ylvy9gvsgvizcs77bh70jg1nkjjsjs7rqbr3zzdysz")))) |
207ce8fb RJ |
7117 | (properties |
7118 | `((upstream-name . "biocViews"))) | |
7119 | (build-system r-build-system) | |
7120 | (propagated-inputs | |
7121 | `(("r-biobase" ,r-biobase) | |
7122 | ("r-graph" ,r-graph) | |
7123 | ("r-rbgl" ,r-rbgl) | |
7124 | ("r-rcurl" ,r-rcurl) | |
7125 | ("r-xml" ,r-xml) | |
207ce8fb | 7126 | ("r-runit" ,r-runit))) |
5713bbf1 | 7127 | (home-page "https://bioconductor.org/packages/biocViews") |
207ce8fb RJ |
7128 | (synopsis "Bioconductor package categorization helper") |
7129 | (description "The purpose of biocViews is to create HTML pages that | |
7130 | categorize packages in a Bioconductor package repository according to keywords, | |
7131 | also known as views, in a controlled vocabulary.") | |
7132 | (license license:artistic2.0))) | |
7133 | ||
2abfc5b8 RJ |
7134 | (define-public r-bookdown |
7135 | (package | |
9800f7d9 RW |
7136 | (name "r-bookdown") |
7137 | (version "0.7") | |
7138 | (source (origin | |
7139 | (method url-fetch) | |
7140 | (uri (cran-uri "bookdown" version)) | |
7141 | (sha256 | |
7142 | (base32 | |
7143 | "1b3fw1f41zph5yw3kynb47aijq53vhaa6mnnvxly72zamyzdf95q")))) | |
7144 | (build-system r-build-system) | |
7145 | (propagated-inputs | |
7146 | `(("r-htmltools" ,r-htmltools) | |
7147 | ("r-knitr" ,r-knitr) | |
7148 | ("r-rmarkdown" ,r-rmarkdown) | |
7149 | ("r-tinytex" ,r-tinytex) | |
7150 | ("r-yaml" ,r-yaml) | |
618050a1 | 7151 | ("r-xfun" ,r-xfun))) |
9800f7d9 RW |
7152 | (home-page "https://github.com/rstudio/bookdown") |
7153 | (synopsis "Authoring books and technical documents with R markdown") | |
7154 | (description "This package provides output formats and utilities for | |
2abfc5b8 | 7155 | authoring books and technical documents with R Markdown.") |
9800f7d9 | 7156 | (license license:gpl3))) |
2abfc5b8 | 7157 | |
99df12cd RJ |
7158 | (define-public r-biocstyle |
7159 | (package | |
6087f5ce RW |
7160 | (name "r-biocstyle") |
7161 | (version "2.10.0") | |
99df12cd RJ |
7162 | (source (origin |
7163 | (method url-fetch) | |
7164 | (uri (bioconductor-uri "BiocStyle" version)) | |
7165 | (sha256 | |
7166 | (base32 | |
6087f5ce | 7167 | "01lm8xljilj666fcl3wnw82dxkcxnlr294lddr553rm8xr5nwg31")))) |
99df12cd RJ |
7168 | (properties |
7169 | `((upstream-name . "BiocStyle"))) | |
7170 | (build-system r-build-system) | |
3bef24c9 | 7171 | (propagated-inputs |
6087f5ce RW |
7172 | `(("r-biocmanager" ,r-biocmanager) |
7173 | ("r-bookdown" ,r-bookdown) | |
3bef24c9 RJ |
7174 | ("r-knitr" ,r-knitr) |
7175 | ("r-rmarkdown" ,r-rmarkdown) | |
7176 | ("r-yaml" ,r-yaml))) | |
5713bbf1 | 7177 | (home-page "https://bioconductor.org/packages/BiocStyle") |
99df12cd RJ |
7178 | (synopsis "Bioconductor formatting styles") |
7179 | (description "This package provides standard formatting styles for | |
7180 | Bioconductor PDF and HTML documents. Package vignettes illustrate use and | |
7181 | functionality.") | |
7182 | (license license:artistic2.0))) | |
7183 | ||
4644644a RJ |
7184 | (define-public r-bioccheck |
7185 | (package | |
7186 | (name "r-bioccheck") | |
a127d352 | 7187 | (version "1.18.0") |
4644644a RJ |
7188 | (source (origin |
7189 | (method url-fetch) | |
7190 | (uri (bioconductor-uri "BiocCheck" version)) | |
7191 | (sha256 | |
7192 | (base32 | |
a127d352 | 7193 | "0zamvs5jar38293ff27imvwy0ra25y64ls9z8w3q1y4jcp8p8pg7")))) |
4644644a RJ |
7194 | (properties |
7195 | `((upstream-name . "BiocCheck"))) | |
7196 | (build-system r-build-system) | |
7197 | (arguments | |
7198 | '(#:phases | |
7199 | (modify-phases %standard-phases | |
7200 | ;; This package can be used by calling BiocCheck(<package>) from | |
7201 | ;; within R, or by running R CMD BiocCheck <package>. This phase | |
7202 | ;; makes sure the latter works. For this to work, the BiocCheck | |
7203 | ;; script must be somewhere on the PATH (not the R bin directory). | |
7204 | (add-after 'install 'install-bioccheck-subcommand | |
7205 | (lambda* (#:key outputs #:allow-other-keys) | |
7206 | (let* ((out (assoc-ref outputs "out")) | |
7207 | (dest-dir (string-append out "/bin")) | |
7208 | (script-dir | |
7209 | (string-append out "/site-library/BiocCheck/script/"))) | |
7210 | (mkdir-p dest-dir) | |
7211 | (symlink (string-append script-dir "/checkBadDeps.R") | |
7212 | (string-append dest-dir "/checkBadDeps.R")) | |
7213 | (symlink (string-append script-dir "/BiocCheck") | |
7214 | (string-append dest-dir "/BiocCheck"))) | |
7215 | #t))))) | |
4644644a | 7216 | (propagated-inputs |
aeb64f3c RW |
7217 | `(("r-codetools" ,r-codetools) |
7218 | ("r-graph" ,r-graph) | |
4644644a | 7219 | ("r-httr" ,r-httr) |
a127d352 | 7220 | ("r-knitr" ,r-knitr) |
4644644a | 7221 | ("r-optparse" ,r-optparse) |
a127d352 | 7222 | ("r-biocmanager" ,r-biocmanager) |
7373b416 RW |
7223 | ("r-biocviews" ,r-biocviews) |
7224 | ("r-stringdist" ,r-stringdist))) | |
5713bbf1 | 7225 | (home-page "https://bioconductor.org/packages/BiocCheck") |
4644644a RJ |
7226 | (synopsis "Executes Bioconductor-specific package checks") |
7227 | (description "This package contains tools to perform additional quality | |
7228 | checks on R packages that are to be submitted to the Bioconductor repository.") | |
7229 | (license license:artistic2.0))) | |
7230 | ||
c79ad57a RJ |
7231 | (define-public r-optparse |
7232 | (package | |
7233 | (name "r-optparse") | |
eafd35ba | 7234 | (version "1.6.0") |
c79ad57a RJ |
7235 | (source |
7236 | (origin | |
7237 | (method url-fetch) | |
7238 | (uri (cran-uri "optparse" version)) | |
7239 | (sha256 | |
7240 | (base32 | |
eafd35ba | 7241 | "1d7v5gl45x4amsfmzn5zyyffyqlc7a82h01szlnda22viyxids0h")))) |
c79ad57a RJ |
7242 | (build-system r-build-system) |
7243 | (propagated-inputs | |
7244 | `(("r-getopt" ,r-getopt))) | |
7245 | (home-page | |
7246 | "https://github.com/trevorld/optparse") | |
7247 | (synopsis "Command line option parser") | |
7248 | (description | |
7249 | "This package provides a command line parser inspired by Python's | |
7250 | @code{optparse} library to be used with Rscript to write shebang scripts | |
7251 | that accept short and long options.") | |
7252 | (license license:gpl2+))) | |
7253 | ||
247d498a RJ |
7254 | (define-public r-dnacopy |
7255 | (package | |
7256 | (name "r-dnacopy") | |
70f2758f | 7257 | (version "1.56.0") |
247d498a RJ |
7258 | (source (origin |
7259 | (method url-fetch) | |
7260 | (uri (bioconductor-uri "DNAcopy" version)) | |
7261 | (sha256 | |
7262 | (base32 | |
70f2758f | 7263 | "04cqdqxhva66xwh1s2vffi56b9fcrqd4slcrvqasj5lp2rkjli82")))) |
247d498a RJ |
7264 | (properties |
7265 | `((upstream-name . "DNAcopy"))) | |
7266 | (build-system r-build-system) | |
7267 | (inputs | |
7268 | `(("gfortran" ,gfortran))) | |
5697fdc3 | 7269 | (home-page "https://bioconductor.org/packages/DNAcopy") |
247d498a RJ |
7270 | (synopsis "Implementation of a circular binary segmentation algorithm") |
7271 | (description "This package implements the circular binary segmentation (CBS) | |
7272 | algorithm to segment DNA copy number data and identify genomic regions with | |
7273 | abnormal copy number.") | |
7274 | (license license:gpl2+))) | |
7275 | ||
7485129e RW |
7276 | (define-public r-s4vectors |
7277 | (package | |
7278 | (name "r-s4vectors") | |
5f9b38ba | 7279 | (version "0.20.1") |
7485129e RW |
7280 | (source (origin |
7281 | (method url-fetch) | |
7282 | (uri (bioconductor-uri "S4Vectors" version)) | |
7283 | (sha256 | |
7284 | (base32 | |
5f9b38ba | 7285 | "18whrw67nxn82xshckl2pjy7d14sa3c27h3n9naqyqwz88lr6dzg")))) |
7485129e | 7286 | (properties |
1d216b6e | 7287 | `((upstream-name . "S4Vectors"))) |
7485129e RW |
7288 | (build-system r-build-system) |
7289 | (propagated-inputs | |
7290 | `(("r-biocgenerics" ,r-biocgenerics))) | |
5713bbf1 | 7291 | (home-page "https://bioconductor.org/packages/S4Vectors") |
7485129e RW |
7292 | (synopsis "S4 implementation of vectors and lists") |
7293 | (description | |
7294 | "The S4Vectors package defines the @code{Vector} and @code{List} virtual | |
7295 | classes and a set of generic functions that extend the semantic of ordinary | |
7296 | vectors and lists in R. Package developers can easily implement vector-like | |
7297 | or list-like objects as concrete subclasses of @code{Vector} or @code{List}. | |
7298 | In addition, a few low-level concrete subclasses of general interest (e.g. | |
7299 | @code{DataFrame}, @code{Rle}, and @code{Hits}) are implemented in the | |
7300 | S4Vectors package itself.") | |
7301 | (license license:artistic2.0))) | |
7302 | ||
274da826 RW |
7303 | (define-public r-seqinr |
7304 | (package | |
7305 | (name "r-seqinr") | |
023aa8ff | 7306 | (version "3.4-5") |
274da826 RW |
7307 | (source |
7308 | (origin | |
7309 | (method url-fetch) | |
7310 | (uri (cran-uri "seqinr" version)) | |
7311 | (sha256 | |
7312 | (base32 | |
023aa8ff | 7313 | "17zv0n5cji17izwmwg0jcbxbjl3w5rls91w15svcnlpxjms38ahn")))) |
274da826 RW |
7314 | (build-system r-build-system) |
7315 | (propagated-inputs | |
3b851cd4 RW |
7316 | `(("r-ade4" ,r-ade4) |
7317 | ("r-segmented" ,r-segmented))) | |
274da826 RW |
7318 | (inputs |
7319 | `(("zlib" ,zlib))) | |
7320 | (home-page "http://seqinr.r-forge.r-project.org/") | |
7321 | (synopsis "Biological sequences retrieval and analysis") | |
7322 | (description | |
7323 | "This package provides tools for exploratory data analysis and data | |
7324 | visualization of biological sequence (DNA and protein) data. It also includes | |
7325 | utilities for sequence data management under the ACNUC system.") | |
7326 | (license license:gpl2+))) | |
7327 | ||
78addcb0 RW |
7328 | (define-public r-iranges |
7329 | (package | |
7330 | (name "r-iranges") | |
9a8dd519 | 7331 | (version "2.16.0") |
78addcb0 RW |
7332 | (source (origin |
7333 | (method url-fetch) | |
7334 | (uri (bioconductor-uri "IRanges" version)) | |
7335 | (sha256 | |
7336 | (base32 | |
9a8dd519 | 7337 | "0ljppsk611xi72gc8mbdx1311b63b1ijd401jz5xmxk5frla1nc1")))) |
78addcb0 | 7338 | (properties |
1d216b6e | 7339 | `((upstream-name . "IRanges"))) |
78addcb0 RW |
7340 | (build-system r-build-system) |
7341 | (propagated-inputs | |
7342 | `(("r-biocgenerics" ,r-biocgenerics) | |
7343 | ("r-s4vectors" ,r-s4vectors))) | |
5713bbf1 | 7344 | (home-page "https://bioconductor.org/packages/IRanges") |
78addcb0 RW |
7345 | (synopsis "Infrastructure for manipulating intervals on sequences") |
7346 | (description | |
7347 | "This package provides efficient low-level and highly reusable S4 classes | |
7348 | for storing ranges of integers, RLE vectors (Run-Length Encoding), and, more | |
7349 | generally, data that can be organized sequentially (formally defined as | |
7350 | @code{Vector} objects), as well as views on these @code{Vector} objects. | |
7351 | Efficient list-like classes are also provided for storing big collections of | |
7352 | instances of the basic classes. All classes in the package use consistent | |
7353 | naming and share the same rich and consistent \"Vector API\" as much as | |
7354 | possible.") | |
7355 | (license license:artistic2.0))) | |
7356 | ||
ffef27f3 RJ |
7357 | (define-public r-genomeinfodbdata |
7358 | (package | |
7359 | (name "r-genomeinfodbdata") | |
13a57465 | 7360 | (version "1.2.0") |
ffef27f3 RJ |
7361 | (source (origin |
7362 | (method url-fetch) | |
90f83099 EF |
7363 | ;; We cannot use bioconductor-uri here because this tarball is |
7364 | ;; located under "data/annotation/" instead of "bioc/". | |
7365 | (uri (string-append "https://bioconductor.org/packages/release/" | |
7366 | "data/annotation/src/contrib/GenomeInfoDbData_" | |
7367 | version ".tar.gz")) | |
ffef27f3 RJ |
7368 | (sha256 |
7369 | (base32 | |
13a57465 | 7370 | "0di6nlqpsyqf693k2na65ayqldih563x3zfrczpqc5q2hl5kg35c")))) |
ffef27f3 RJ |
7371 | (properties |
7372 | `((upstream-name . "GenomeInfoDbData"))) | |
7373 | (build-system r-build-system) | |
5713bbf1 | 7374 | (home-page "https://bioconductor.org/packages/GenomeInfoDbData") |
ffef27f3 RJ |
7375 | (synopsis "Species and taxonomy ID look up tables for GenomeInfoDb") |
7376 | (description "This package contains data for mapping between NCBI taxonomy | |
7377 | ID and species. It is used by functions in the GenomeInfoDb package.") | |
7378 | (license license:artistic2.0))) | |
7379 | ||
bf7764b7 RW |
7380 | (define-public r-genomeinfodb |
7381 | (package | |
7382 | (name "r-genomeinfodb") | |
4535a7b0 | 7383 | (version "1.18.1") |
bf7764b7 RW |
7384 | (source (origin |
7385 | (method url-fetch) | |
7386 | (uri (bioconductor-uri "GenomeInfoDb" version)) | |
7387 | (sha256 | |
7388 | (base32 | |
4535a7b0 | 7389 | "049pyzr8iszv3g7wdqf3pz7vg7bzd450c20ln6fgw4g5xnkkr10s")))) |
bf7764b7 | 7390 | (properties |
1d216b6e | 7391 | `((upstream-name . "GenomeInfoDb"))) |
bf7764b7 RW |
7392 | (build-system r-build-system) |
7393 | (propagated-inputs | |
7394 | `(("r-biocgenerics" ,r-biocgenerics) | |
38b99ccc | 7395 | ("r-genomeinfodbdata" ,r-genomeinfodbdata) |
bf7764b7 | 7396 | ("r-iranges" ,r-iranges) |
4cd07e48 | 7397 | ("r-rcurl" ,r-rcurl) |
bf7764b7 | 7398 | ("r-s4vectors" ,r-s4vectors))) |
5713bbf1 | 7399 | (home-page "https://bioconductor.org/packages/GenomeInfoDb") |
bf7764b7 RW |
7400 | (synopsis "Utilities for manipulating chromosome identifiers") |
7401 | (description | |
7402 | "This package contains data and functions that define and allow | |
7403 | translation between different chromosome sequence naming conventions (e.g., | |
7404 | \"chr1\" versus \"1\"), including a function that attempts to place sequence | |
7405 | names in their natural, rather than lexicographic, order.") | |
7406 | (license license:artistic2.0))) | |
7407 | ||
744004a3 RJ |
7408 | (define-public r-edger |
7409 | (package | |
7410 | (name "r-edger") | |
08cd2d5b | 7411 | (version "3.24.0") |
744004a3 RJ |
7412 | (source (origin |
7413 | (method url-fetch) | |
7414 | (uri (bioconductor-uri "edgeR" version)) | |
7415 | (sha256 | |
7416 | (base32 | |
08cd2d5b | 7417 | "0ihihgzrgb4q3xc8xkzp1v76ndgihrj4gas00fa25vggfs1v6hvg")))) |
744004a3 RJ |
7418 | (properties `((upstream-name . "edgeR"))) |
7419 | (build-system r-build-system) | |
7420 | (propagated-inputs | |
5e48005f | 7421 | `(("r-limma" ,r-limma) |
47055b27 | 7422 | ("r-locfit" ,r-locfit) |
010ab2ff | 7423 | ("r-rcpp" ,r-rcpp) |
47055b27 | 7424 | ("r-statmod" ,r-statmod))) ;for estimateDisp |
744004a3 RJ |
7425 | (home-page "http://bioinf.wehi.edu.au/edgeR") |
7426 | (synopsis "EdgeR does empirical analysis of digital gene expression data") | |
7427 | (description "This package can do differential expression analysis of | |
7428 | RNA-seq expression profiles with biological replication. It implements a range | |
7429 | of statistical methodology based on the negative binomial distributions, | |
7430 | including empirical Bayes estimation, exact tests, generalized linear models | |
7431 | and quasi-likelihood tests. It be applied to differential signal analysis of | |
7432 | other types of genomic data that produce counts, including ChIP-seq, SAGE and | |
7433 | CAGE.") | |
7434 | (license license:gpl2+))) | |
7435 | ||
b669d9c4 RJ |
7436 | (define-public r-variantannotation |
7437 | (package | |
7438 | (name "r-variantannotation") | |
ca2945c3 | 7439 | (version "1.28.1") |
b669d9c4 RJ |
7440 | (source (origin |
7441 | (method url-fetch) | |
7442 | (uri (bioconductor-uri "VariantAnnotation" version)) | |
7443 | (sha256 | |
7444 | (base32 | |
ca2945c3 | 7445 | "0gvah258mkaafhbna81zwknx8qr3lidbcx5qvwk39q3yswr9mi49")))) |
b669d9c4 RJ |
7446 | (properties |
7447 | `((upstream-name . "VariantAnnotation"))) | |
7448 | (inputs | |
7449 | `(("zlib" ,zlib))) | |
7450 | (propagated-inputs | |
7451 | `(("r-annotationdbi" ,r-annotationdbi) | |
37d96f1d | 7452 | ("r-biobase" ,r-biobase) |
b669d9c4 | 7453 | ("r-biocgenerics" ,r-biocgenerics) |
37d96f1d | 7454 | ("r-biostrings" ,r-biostrings) |
b669d9c4 RJ |
7455 | ("r-bsgenome" ,r-bsgenome) |
7456 | ("r-dbi" ,r-dbi) | |
7457 | ("r-genomeinfodb" ,r-genomeinfodb) | |
7458 | ("r-genomicfeatures" ,r-genomicfeatures) | |
7459 | ("r-genomicranges" ,r-genomicranges) | |
37d96f1d | 7460 | ("r-iranges" ,r-iranges) |
b669d9c4 RJ |
7461 | ("r-summarizedexperiment" ,r-summarizedexperiment) |
7462 | ("r-rsamtools" ,r-rsamtools) | |
37d96f1d RW |
7463 | ("r-rtracklayer" ,r-rtracklayer) |
7464 | ("r-s4vectors" ,r-s4vectors) | |
7465 | ("r-xvector" ,r-xvector) | |
b669d9c4 RJ |
7466 | ("r-zlibbioc" ,r-zlibbioc))) |
7467 | (build-system r-build-system) | |
7468 | (home-page "https://bioconductor.org/packages/VariantAnnotation") | |
7469 | (synopsis "Package for annotation of genetic variants") | |
7470 | (description "This R package can annotate variants, compute amino acid | |
7471 | coding changes and predict coding outcomes.") | |
7472 | (license license:artistic2.0))) | |
7473 | ||
7d4224d7 RJ |
7474 | (define-public r-limma |
7475 | (package | |
7476 | (name "r-limma") | |
78d2ffdc | 7477 | (version "3.38.2") |
7d4224d7 RJ |
7478 | (source (origin |
7479 | (method url-fetch) | |
7480 | (uri (bioconductor-uri "limma" version)) | |
7481 | (sha256 | |
7482 | (base32 | |
78d2ffdc | 7483 | "1wkh362rmn24q7bkinb6nx62a31wl3r3myg5l326gx65wpwdnx97")))) |
7d4224d7 RJ |
7484 | (build-system r-build-system) |
7485 | (home-page "http://bioinf.wehi.edu.au/limma") | |
7486 | (synopsis "Package for linear models for microarray and RNA-seq data") | |
7487 | (description "This package can be used for the analysis of gene expression | |
7488 | studies, especially the use of linear models for analysing designed experiments | |
7489 | and the assessment of differential expression. The analysis methods apply to | |
7490 | different technologies, including microarrays, RNA-seq, and quantitative PCR.") | |
7491 | (license license:gpl2+))) | |
7492 | ||
0e7d5560 RW |
7493 | (define-public r-xvector |
7494 | (package | |
7495 | (name "r-xvector") | |
fb10fb72 | 7496 | (version "0.22.0") |
0e7d5560 RW |
7497 | (source (origin |
7498 | (method url-fetch) | |
7499 | (uri (bioconductor-uri "XVector" version)) | |
7500 | (sha256 | |
7501 | (base32 | |
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0e7d5560 | 7503 | (properties |
1d216b6e | 7504 | `((upstream-name . "XVector"))) |
0e7d5560 RW |
7505 | (build-system r-build-system) |
7506 | (arguments | |
7507 | `(#:phases | |
7508 | (modify-phases %standard-phases | |
7509 | (add-after 'unpack 'use-system-zlib | |
7510 | (lambda _ | |
7511 | (substitute* "DESCRIPTION" | |
7512 | (("zlibbioc, ") "")) | |
7513 | (substitute* "NAMESPACE" | |
7514 | (("import\\(zlibbioc\\)") "")) | |
7515 | #t))))) | |
7516 | (inputs | |
7517 | `(("zlib" ,zlib))) | |
7518 | (propagated-inputs | |
7519 | `(("r-biocgenerics" ,r-biocgenerics) | |
7520 | ("r-iranges" ,r-iranges) | |
7521 | ("r-s4vectors" ,r-s4vectors))) | |
5713bbf1 | 7522 | (home-page "https://bioconductor.org/packages/XVector") |
0e7d5560 RW |
7523 | (synopsis "Representation and manpulation of external sequences") |
7524 | (description | |
7525 | "This package provides memory efficient S4 classes for storing sequences | |
7526 | \"externally\" (behind an R external pointer, or on disk).") | |
7527 | (license license:artistic2.0))) | |
7528 | ||
e2cd1d0f RW |
7529 | (define-public r-genomicranges |
7530 | (package | |
7531 | (name "r-genomicranges") | |
8d3906a9 | 7532 | (version "1.34.0") |
e2cd1d0f RW |
7533 | (source (origin |
7534 | (method url-fetch) | |
7535 | (uri (bioconductor-uri "GenomicRanges" version)) | |
7536 | (sha256 | |
7537 | (base32 | |
8d3906a9 | 7538 | "0bgh14d15dpf2iy36qinw45r6n45rqkf0ghazrdl3jfva6vbrb29")))) |
e2cd1d0f | 7539 | (properties |
1d216b6e | 7540 | `((upstream-name . "GenomicRanges"))) |
e2cd1d0f RW |
7541 | (build-system r-build-system) |
7542 | (propagated-inputs | |
7543 | `(("r-biocgenerics" ,r-biocgenerics) | |
7544 | ("r-genomeinfodb" ,r-genomeinfodb) | |
92a740af RW |
7545 | ("r-iranges" ,r-iranges) |
7546 | ("r-s4vectors" ,r-s4vectors) | |
e2cd1d0f | 7547 | ("r-xvector" ,r-xvector))) |
5713bbf1 | 7548 | (home-page "https://bioconductor.org/packages/GenomicRanges") |
e2cd1d0f RW |
7549 | (synopsis "Representation and manipulation of genomic intervals") |
7550 | (description | |
7551 | "This package provides tools to efficiently represent and manipulate | |
7552 | genomic annotations and alignments is playing a central role when it comes to | |
7553 | analyzing high-throughput sequencing data (a.k.a. NGS data). The | |
7554 | GenomicRanges package defines general purpose containers for storing and | |
7555 | manipulating genomic intervals and variables defined along a genome.") | |
7556 | (license license:artistic2.0))) | |
7557 | ||
555e3399 RW |
7558 | (define-public r-biobase |
7559 | (package | |
7560 | (name "r-biobase") | |
5b82e12a | 7561 | (version "2.42.0") |
555e3399 RW |
7562 | (source (origin |
7563 | (method url-fetch) | |
7564 | (uri (bioconductor-uri "Biobase" version)) | |
7565 | (sha256 | |
7566 | (base32 | |
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555e3399 RW |
7568 | (properties |
7569 | `((upstream-name . "Biobase"))) | |
7570 | (build-system r-build-system) | |
7571 | (propagated-inputs | |
7572 | `(("r-biocgenerics" ,r-biocgenerics))) | |
5713bbf1 | 7573 | (home-page "https://bioconductor.org/packages/Biobase") |
555e3399 RW |
7574 | (synopsis "Base functions for Bioconductor") |
7575 | (description | |
7576 | "This package provides functions that are needed by many other packages | |
7577 | on Bioconductor or which replace R functions.") | |
7578 | (license license:artistic2.0))) | |
7579 | ||
8b7bce74 RW |
7580 | (define-public r-annotationdbi |
7581 | (package | |
7582 | (name "r-annotationdbi") | |
3986e0de | 7583 | (version "1.44.0") |
8b7bce74 RW |
7584 | (source (origin |
7585 | (method url-fetch) | |
7586 | (uri (bioconductor-uri "AnnotationDbi" version)) | |
7587 | (sha256 | |
7588 | (base32 | |
3986e0de | 7589 | "1954vimkx5yb9irppq8vssq0f3yjkg36w38b9r0rqmijx1ps7x5d")))) |
8b7bce74 RW |
7590 | (properties |
7591 | `((upstream-name . "AnnotationDbi"))) | |
7592 | (build-system r-build-system) | |
7593 | (propagated-inputs | |
7594 | `(("r-biobase" ,r-biobase) | |
7595 | ("r-biocgenerics" ,r-biocgenerics) | |
7596 | ("r-dbi" ,r-dbi) | |
7597 | ("r-iranges" ,r-iranges) | |
7598 | ("r-rsqlite" ,r-rsqlite) | |
7599 | ("r-s4vectors" ,r-s4vectors))) | |
5713bbf1 | 7600 | (home-page "https://bioconductor.org/packages/AnnotationDbi") |
8b7bce74 RW |
7601 | (synopsis "Annotation database interface") |
7602 | (description | |
7603 | "This package provides user interface and database connection code for | |
7604 | annotation data packages using SQLite data storage.") | |
7605 | (license license:artistic2.0))) | |
7606 | ||
c465fa72 RW |
7607 | (define-public r-biomart |
7608 | (package | |
7609 | (name "r-biomart") | |
3359d442 | 7610 | (version "2.38.0") |
c465fa72 RW |
7611 | (source (origin |
7612 | (method url-fetch) | |
7613 | (uri (bioconductor-uri "biomaRt" version)) | |
7614 | (sha256 | |
7615 | (base32 | |
3359d442 | 7616 | "1lshkknp7dmr3p6dd2zbv86cc71h53ggh9ji83jcjym8sgbbspl2")))) |
c465fa72 RW |
7617 | (properties |
7618 | `((upstream-name . "biomaRt"))) | |
7619 | (build-system r-build-system) | |
7620 | (propagated-inputs | |
7621 | `(("r-annotationdbi" ,r-annotationdbi) | |
b9e8a5c5 | 7622 | ("r-httr" ,r-httr) |
42e11d33 | 7623 | ("r-progress" ,r-progress) |
c465fa72 | 7624 | ("r-rcurl" ,r-rcurl) |
42e11d33 | 7625 | ("r-stringr" ,r-stringr) |
c465fa72 | 7626 | ("r-xml" ,r-xml))) |
5713bbf1 | 7627 | (home-page "https://bioconductor.org/packages/biomaRt") |
c465fa72 RW |
7628 | (synopsis "Interface to BioMart databases") |
7629 | (description | |
7630 | "biomaRt provides an interface to a growing collection of databases | |
7631 | implementing the @url{BioMart software suite, http://www.biomart.org}. The | |
7632 | package enables retrieval of large amounts of data in a uniform way without | |
7633 | the need to know the underlying database schemas or write complex SQL queries. | |
7634 | Examples of BioMart databases are Ensembl, COSMIC, Uniprot, HGNC, Gramene, | |
7635 | Wormbase and dbSNP mapped to Ensembl. These major databases give biomaRt | |
7636 | users direct access to a diverse set of data and enable a wide range of | |
7637 | powerful online queries from gene annotation to database mining.") | |
7638 | (license license:artistic2.0))) | |
7639 | ||
e91d362e RW |
7640 | (define-public r-biocparallel |
7641 | (package | |
7642 | (name "r-biocparallel") | |
cd882891 | 7643 | (version "1.16.0") |
e91d362e RW |
7644 | (source (origin |
7645 | (method url-fetch) | |
7646 | (uri (bioconductor-uri "BiocParallel" version)) | |
7647 | (sha256 | |
7648 | (base32 | |
cd882891 | 7649 | "0g16cy0vjapqkb188z63r1b6y96m9g8vx0a3v2qavzxc177k0cja")))) |
e91d362e RW |
7650 | (properties |
7651 | `((upstream-name . "BiocParallel"))) | |
7652 | (build-system r-build-system) | |
7653 | (propagated-inputs | |
7654 | `(("r-futile-logger" ,r-futile-logger) | |
a044c7f4 RW |
7655 | ("r-snow" ,r-snow) |
7656 | ("r-bh" ,r-bh))) | |
5713bbf1 | 7657 | (home-page "https://bioconductor.org/packages/BiocParallel") |
e91d362e RW |
7658 | (synopsis "Bioconductor facilities for parallel evaluation") |
7659 | (description | |
7660 | "This package provides modified versions and novel implementation of | |
7661 | functions for parallel evaluation, tailored to use with Bioconductor | |
7662 | objects.") | |
7663 | (license (list license:gpl2+ license:gpl3+)))) | |
7664 | ||
bf159353 RW |
7665 | (define-public r-biostrings |
7666 | (package | |
7667 | (name "r-biostrings") | |
88514b91 | 7668 | (version "2.50.1") |
bf159353 RW |
7669 | (source (origin |
7670 | (method url-fetch) | |
7671 | (uri (bioconductor-uri "Biostrings" version)) | |
7672 | (sha256 | |
7673 | (base32 | |
88514b91 | 7674 | "1qyv1ps7vy6gy78pm2rcikg0bgf1mv7falahjp3pkwqq1272hrl8")))) |
bf159353 RW |
7675 | (properties |
7676 | `((upstream-name . "Biostrings"))) | |
7677 | (build-system r-build-system) | |
7678 | (propagated-inputs | |
7679 | `(("r-biocgenerics" ,r-biocgenerics) | |
7680 | ("r-iranges" ,r-iranges) | |
7681 | ("r-s4vectors" ,r-s4vectors) | |
7682 | ("r-xvector" ,r-xvector))) | |
5713bbf1 | 7683 | (home-page "https://bioconductor.org/packages/Biostrings") |
bf159353 RW |
7684 | (synopsis "String objects and algorithms for biological sequences") |
7685 | (description | |
7686 | "This package provides memory efficient string containers, string | |
7687 | matching algorithms, and other utilities, for fast manipulation of large | |
7688 | biological sequences or sets of sequences.") | |
7689 | (license license:artistic2.0))) | |
7690 | ||
f8d74f70 RW |
7691 | (define-public r-rsamtools |
7692 | (package | |
7693 | (name "r-rsamtools") | |
7f3778eb | 7694 | (version "1.34.0") |
f8d74f70 RW |
7695 | (source (origin |
7696 | (method url-fetch) | |
7697 | (uri (bioconductor-uri "Rsamtools" version)) | |
7698 | (sha256 | |
7699 | (base32 | |
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f8d74f70 RW |
7701 | (properties |
7702 | `((upstream-name . "Rsamtools"))) | |
7703 | (build-system r-build-system) | |
7704 | (arguments | |
7705 | `(#:phases | |
7706 | (modify-phases %standard-phases | |
7707 | (add-after 'unpack 'use-system-zlib | |
7708 | (lambda _ | |
7709 | (substitute* "DESCRIPTION" | |
7710 | (("zlibbioc, ") "")) | |
7711 | (substitute* "NAMESPACE" | |
7712 | (("import\\(zlibbioc\\)") "")) | |
7713 | #t))))) | |
7714 | (inputs | |
7715 | `(("zlib" ,zlib))) | |
7716 | (propagated-inputs | |
7717 | `(("r-biocgenerics" ,r-biocgenerics) | |
7718 | ("r-biocparallel" ,r-biocparallel) | |
7719 | ("r-biostrings" ,r-biostrings) | |
7720 | ("r-bitops" ,r-bitops) | |
7721 | ("r-genomeinfodb" ,r-genomeinfodb) | |
7722 | ("r-genomicranges" ,r-genomicranges) | |
7723 | ("r-iranges" ,r-iranges) | |
7724 | ("r-s4vectors" ,r-s4vectors) | |
7725 | ("r-xvector" ,r-xvector))) | |
5713bbf1 | 7726 | (home-page "https://bioconductor.org/packages/release/bioc/html/Rsamtools.html") |
f8d74f70 RW |
7727 | (synopsis "Interface to samtools, bcftools, and tabix") |
7728 | (description | |
7729 | "This package provides an interface to the 'samtools', 'bcftools', and | |
7730 | 'tabix' utilities for manipulating SAM (Sequence Alignment / Map), FASTA, | |
7731 | binary variant call (BCF) and compressed indexed tab-delimited (tabix) | |
7732 | files.") | |
7733 | (license license:expat))) | |
7734 | ||
71e34e6b RJ |
7735 | (define-public r-delayedarray |
7736 | (package | |
7737 | (name "r-delayedarray") | |
de4c38f8 | 7738 | (version "0.8.0") |
71e34e6b RJ |
7739 | (source (origin |
7740 | (method url-fetch) | |
7741 | (uri (bioconductor-uri "DelayedArray" version)) | |
7742 | (sha256 | |
7743 | (base32 | |
de4c38f8 | 7744 | "0cl5anqkjwvqx19snjhz0zj8cp8ibckiifl28h821h50g62nvb2f")))) |
71e34e6b RJ |
7745 | (properties |
7746 | `((upstream-name . "DelayedArray"))) | |
7747 | (build-system r-build-system) | |
7748 | (propagated-inputs | |
7749 | `(("r-biocgenerics" ,r-biocgenerics) | |
82f593f3 | 7750 | ("r-biocparallel" ,r-biocparallel) |
71e34e6b RJ |
7751 | ("r-s4vectors" ,r-s4vectors) |
7752 | ("r-iranges" ,r-iranges) | |
7753 | ("r-matrixstats" ,r-matrixstats))) | |
5713bbf1 | 7754 | (home-page "https://bioconductor.org/packages/DelayedArray") |
71e34e6b RJ |
7755 | (synopsis "Delayed operations on array-like objects") |
7756 | (description | |
7757 | "Wrapping an array-like object (typically an on-disk object) in a | |
7758 | @code{DelayedArray} object allows one to perform common array operations on it | |
7759 | without loading the object in memory. In order to reduce memory usage and | |
7760 | optimize performance, operations on the object are either delayed or executed | |
7761 | using a block processing mechanism. Note that this also works on in-memory | |
7762 | array-like objects like @code{DataFrame} objects (typically with Rle columns), | |
7763 | @code{Matrix} objects, and ordinary arrays and data frames.") | |
7764 | (license license:artistic2.0))) | |
7765 | ||
6e76dda2 RW |
7766 | (define-public r-summarizedexperiment |
7767 | (package | |
7768 | (name "r-summarizedexperiment") | |
9fd4350e | 7769 | (version "1.12.0") |
6e76dda2 RW |
7770 | (source (origin |
7771 | (method url-fetch) | |
7772 | (uri (bioconductor-uri "SummarizedExperiment" version)) | |
7773 | (sha256 | |
7774 | (base32 | |
9fd4350e | 7775 | "07805572xhpj5mfwq6kw1ha21wgalqvhh4ydvafyl1bnf3r20vps")))) |
6e76dda2 RW |
7776 | (properties |
7777 | `((upstream-name . "SummarizedExperiment"))) | |
7778 | (build-system r-build-system) | |
7779 | (propagated-inputs | |
7780 | `(("r-biobase" ,r-biobase) | |
7781 | ("r-biocgenerics" ,r-biocgenerics) | |
d006ee31 | 7782 | ("r-delayedarray" ,r-delayedarray) |
6e76dda2 RW |
7783 | ("r-genomeinfodb" ,r-genomeinfodb) |
7784 | ("r-genomicranges" ,r-genomicranges) | |
7785 | ("r-iranges" ,r-iranges) | |
aeb64f3c | 7786 | ("r-matrix" ,r-matrix) |
6e76dda2 | 7787 | ("r-s4vectors" ,r-s4vectors))) |
5713bbf1 | 7788 | (home-page "https://bioconductor.org/packages/SummarizedExperiment") |
6e76dda2 RW |
7789 | (synopsis "Container for representing genomic ranges by sample") |
7790 | (description | |
7791 | "The SummarizedExperiment container contains one or more assays, each | |
7792 | represented by a matrix-like object of numeric or other mode. The rows | |
7793 | typically represent genomic ranges of interest and the columns represent | |
7794 | samples.") | |
7795 | (license license:artistic2.0))) | |
7796 | ||
d8a828af RW |
7797 | (define-public r-genomicalignments |
7798 | (package | |
7799 | (name "r-genomicalignments") | |
52b95337 | 7800 | (version "1.18.0") |
d8a828af RW |
7801 | (source (origin |
7802 | (method url-fetch) | |
7803 | (uri (bioconductor-uri "GenomicAlignments" version)) | |
7804 | (sha256 | |
7805 | (base32 | |
52b95337 | 7806 | "0a3zhwripfw2508fvgx3wzqa8nq8vnslg97a911znpwvxh53jl24")))) |
d8a828af RW |
7807 | (properties |
7808 | `((upstream-name . "GenomicAlignments"))) | |
7809 | (build-system r-build-system) | |
7810 | (propagated-inputs | |
7811 | `(("r-biocgenerics" ,r-biocgenerics) | |
7812 | ("r-biocparallel" ,r-biocparallel) | |
7813 | ("r-biostrings" ,r-biostrings) | |
7814 | ("r-genomeinfodb" ,r-genomeinfodb) | |
7815 | ("r-genomicranges" ,r-genomicranges) | |
7816 | ("r-iranges" ,r-iranges) | |
7817 | ("r-rsamtools" ,r-rsamtools) | |
7818 | ("r-s4vectors" ,r-s4vectors) | |
7819 | ("r-summarizedexperiment" ,r-summarizedexperiment))) | |
5713bbf1 | 7820 | (home-page "https://bioconductor.org/packages/GenomicAlignments") |
d8a828af RW |
7821 | (synopsis "Representation and manipulation of short genomic alignments") |
7822 | (description | |
7823 | "This package provides efficient containers for storing and manipulating | |
7824 | short genomic alignments (typically obtained by aligning short reads to a | |
7825 | reference genome). This includes read counting, computing the coverage, | |
7826 | junction detection, and working with the nucleotide content of the | |
7827 | alignments.") | |
7828 | (license license:artistic2.0))) | |
7829 | ||
317755ff RW |
7830 | (define-public r-rtracklayer |
7831 | (package | |
7832 | (name "r-rtracklayer") | |
c5f1d1ce | 7833 | (version "1.42.0") |
317755ff RW |
7834 | (source (origin |
7835 | (method url-fetch) | |
7836 | (uri (bioconductor-uri "rtracklayer" version)) | |
7837 | (sha256 | |
7838 | (base32 | |
c5f1d1ce | 7839 | "0a4mhd926w9slkfil5xgngjsfdj024a4w57w2bm3d4r0pj8y5da7")))) |
317755ff RW |
7840 | (build-system r-build-system) |
7841 | (arguments | |
7842 | `(#:phases | |
7843 | (modify-phases %standard-phases | |
7844 | (add-after 'unpack 'use-system-zlib | |
7845 | (lambda _ | |
7846 | (substitute* "DESCRIPTION" | |
4dd469ef | 7847 | ((" zlibbioc,") "")) |
317755ff RW |
7848 | (substitute* "NAMESPACE" |
7849 | (("import\\(zlibbioc\\)") "")) | |
7850 | #t))))) | |
a30df297 RW |
7851 | (native-inputs |
7852 | `(("pkg-config" ,pkg-config))) | |
317755ff RW |
7853 | (inputs |
7854 | `(("zlib" ,zlib))) | |
7855 | (propagated-inputs | |
7856 | `(("r-biocgenerics" ,r-biocgenerics) | |
7857 | ("r-biostrings" ,r-biostrings) | |
7858 | ("r-genomeinfodb" ,r-genomeinfodb) | |
7859 | ("r-genomicalignments" ,r-genomicalignments) | |
7860 | ("r-genomicranges" ,r-genomicranges) | |
7861 | ("r-iranges" ,r-iranges) | |
7862 | ("r-rcurl" ,r-rcurl) | |
7863 | ("r-rsamtools" ,r-rsamtools) | |
7864 | ("r-s4vectors" ,r-s4vectors) | |
7865 | ("r-xml" ,r-xml) | |
7866 | ("r-xvector" ,r-xvector))) | |
5713bbf1 | 7867 | (home-page "https://bioconductor.org/packages/rtracklayer") |
317755ff RW |
7868 | (synopsis "R interface to genome browsers and their annotation tracks") |
7869 | (description | |
7870 | "rtracklayer is an extensible framework for interacting with multiple | |
7871 | genome browsers (currently UCSC built-in) and manipulating annotation tracks | |
7872 | in various formats (currently GFF, BED, bedGraph, BED15, WIG, BigWig and 2bit | |
7873 | built-in). The user may export/import tracks to/from the supported browsers, | |
7874 | as well as query and modify the browser state, such as the current viewport.") | |
7875 | (license license:artistic2.0))) | |
7876 | ||
2fd7c049 RW |
7877 | (define-public r-genomicfeatures |
7878 | (package | |
7879 | (name "r-genomicfeatures") | |
8a0d57d2 | 7880 | (version "1.34.1") |
2fd7c049 RW |
7881 | (source (origin |
7882 | (method url-fetch) | |
7883 | (uri (bioconductor-uri "GenomicFeatures" version)) | |
7884 | (sha256 | |
7885 | (base32 | |
8a0d57d2 | 7886 | "0slq6hv5bmc3bgrl824jzmr6db3fvaj6b7ihwmdn76pgqqbq2fq6")))) |
2fd7c049 RW |
7887 | (properties |
7888 | `((upstream-name . "GenomicFeatures"))) | |
7889 | (build-system r-build-system) | |
7890 | (propagated-inputs | |
7891 | `(("r-annotationdbi" ,r-annotationdbi) | |
7892 | ("r-biobase" ,r-biobase) | |
7893 | ("r-biocgenerics" ,r-biocgenerics) | |
7894 | ("r-biomart" ,r-biomart) | |
7895 | ("r-biostrings" ,r-biostrings) | |
7896 | ("r-dbi" ,r-dbi) | |
7897 | ("r-genomeinfodb" ,r-genomeinfodb) | |
7898 | ("r-genomicranges" ,r-genomicranges) | |
7899 | ("r-iranges" ,r-iranges) | |
7900 | ("r-rcurl" ,r-rcurl) | |
7901 | ("r-rsqlite" ,r-rsqlite) | |
7902 | ("r-rtracklayer" ,r-rtracklayer) | |
7903 | ("r-s4vectors" ,r-s4vectors) | |
7904 | ("r-xvector" ,r-xvector))) | |
5713bbf1 | 7905 | (home-page "https://bioconductor.org/packages/GenomicFeatures") |
2fd7c049 RW |
7906 | (synopsis "Tools for working with transcript centric annotations") |
7907 | (description | |
7908 | "This package provides a set of tools and methods for making and | |
7909 | manipulating transcript centric annotations. With these tools the user can | |
7910 | easily download the genomic locations of the transcripts, exons and cds of a | |
7911 | given organism, from either the UCSC Genome Browser or a BioMart | |
7912 | database (more sources will be supported in the future). This information is | |
7913 | then stored in a local database that keeps track of the relationship between | |
7914 | transcripts, exons, cds and genes. Flexible methods are provided for | |
7915 | extracting the desired features in a convenient format.") | |
7916 | (license license:artistic2.0))) | |
7917 | ||
fb25d880 RW |
7918 | (define-public r-go-db |
7919 | (package | |
7920 | (name "r-go-db") | |
13e70f63 | 7921 | (version "3.7.0") |
fb25d880 RW |
7922 | (source (origin |
7923 | (method url-fetch) | |
5713bbf1 | 7924 | (uri (string-append "https://www.bioconductor.org/packages/" |
f82c8c3c PP |
7925 | "release/data/annotation/src/contrib/GO.db_" |
7926 | version ".tar.gz")) | |
fb25d880 RW |
7927 | (sha256 |
7928 | (base32 | |
13e70f63 | 7929 | "0i3wcf5h3n0dawzc1hy0kv74f06j80c47n4p3g3fmrcxlhi3jpa5")))) |
fb25d880 RW |
7930 | (properties |
7931 | `((upstream-name . "GO.db"))) | |
7932 | (build-system r-build-system) | |
3141b83d RW |
7933 | (propagated-inputs |
7934 | `(("r-annotationdbi" ,r-annotationdbi))) | |
5713bbf1 | 7935 | (home-page "https://bioconductor.org/packages/GO.db") |
fb25d880 RW |
7936 | (synopsis "Annotation maps describing the entire Gene Ontology") |
7937 | (description | |
7938 | "The purpose of this GO.db annotation package is to provide detailed | |
7939 | information about the latest version of the Gene Ontologies.") | |
7940 | (license license:artistic2.0))) | |
7941 | ||
d547ce5e RW |
7942 | (define-public r-topgo |
7943 | (package | |
7944 | (name "r-topgo") | |
44fa14df | 7945 | (version "2.34.0") |
d547ce5e RW |
7946 | (source (origin |
7947 | (method url-fetch) | |
7948 | (uri (bioconductor-uri "topGO" version)) | |
7949 | (sha256 | |
7950 | (base32 | |
44fa14df | 7951 | "1j1jcd16j564kr6qz28140fzmnh9xasi84v1c1fi98sqv30zq9bh")))) |
d547ce5e RW |
7952 | (properties |
7953 | `((upstream-name . "topGO"))) | |
7954 | (build-system r-build-system) | |
7955 | (propagated-inputs | |
7956 | `(("r-annotationdbi" ,r-annotationdbi) | |
30ec4de7 | 7957 | ("r-dbi" ,r-dbi) |
d547ce5e RW |
7958 | ("r-biobase" ,r-biobase) |
7959 | ("r-biocgenerics" ,r-biocgenerics) | |
7960 | ("r-go-db" ,r-go-db) | |
6d415db2 | 7961 | ("r-graph" ,r-graph) |
aeb64f3c RW |
7962 | ("r-lattice" ,r-lattice) |
7963 | ("r-matrixstats" ,r-matrixstats) | |
d547ce5e | 7964 | ("r-sparsem" ,r-sparsem))) |
5713bbf1 | 7965 | (home-page "https://bioconductor.org/packages/topGO") |
d547ce5e RW |
7966 | (synopsis "Enrichment analysis for gene ontology") |
7967 | (description | |
7968 | "The topGO package provides tools for testing @dfn{gene ontology} (GO) | |
7969 | terms while accounting for the topology of the GO graph. Different test | |
7970 | statistics and different methods for eliminating local similarities and | |
7971 | dependencies between GO terms can be implemented and applied.") | |
7972 | ;; Any version of the LGPL applies. | |
7973 | (license license:lgpl2.1+))) | |
7974 | ||
c63cef66 RW |
7975 | (define-public r-bsgenome |
7976 | (package | |
7977 | (name "r-bsgenome") | |
78ecdbc0 | 7978 | (version "1.50.0") |
c63cef66 RW |
7979 | (source (origin |
7980 | (method url-fetch) | |
7981 | (uri (bioconductor-uri "BSgenome" version)) | |
7982 | (sha256 | |
7983 | (base32 | |
78ecdbc0 | 7984 | "07z4zxx0khrc86qqvc7vxww8df9fh6pyks9ajxkc9gdqr5nn79j7")))) |
c63cef66 RW |
7985 | (properties |
7986 | `((upstream-name . "BSgenome"))) | |
7987 | (build-system r-build-system) | |
7988 | (propagated-inputs | |
7989 | `(("r-biocgenerics" ,r-biocgenerics) | |
7990 | ("r-biostrings" ,r-biostrings) | |
7991 | ("r-genomeinfodb" ,r-genomeinfodb) | |
7992 | ("r-genomicranges" ,r-genomicranges) | |
7993 | ("r-iranges" ,r-iranges) | |
7994 | ("r-rsamtools" ,r-rsamtools) | |
7995 | ("r-rtracklayer" ,r-rtracklayer) | |
7996 | ("r-s4vectors" ,r-s4vectors) | |
7997 | ("r-xvector" ,r-xvector))) | |
5713bbf1 | 7998 | (home-page "https://bioconductor.org/packages/BSgenome") |
c63cef66 RW |
7999 | (synopsis "Infrastructure for Biostrings-based genome data packages") |
8000 | (description | |
8001 | "This package provides infrastructure shared by all Biostrings-based | |
8002 | genome data packages and support for efficient SNP representation.") | |
8003 | (license license:artistic2.0))) | |
8004 | ||
aa3eeeb5 RJ |
8005 | (define-public r-bsgenome-hsapiens-1000genomes-hs37d5 |
8006 | (package | |
8007 | (name "r-bsgenome-hsapiens-1000genomes-hs37d5") | |
8008 | (version "0.99.1") | |
8009 | (source (origin | |
8010 | (method url-fetch) | |
8011 | ;; We cannot use bioconductor-uri here because this tarball is | |
8012 | ;; located under "data/annotation/" instead of "bioc/". | |
5713bbf1 | 8013 | (uri (string-append "https://www.bioconductor.org/packages/" |
aa3eeeb5 RJ |
8014 | "release/data/annotation/src/contrib/" |
8015 | "BSgenome.Hsapiens.1000genomes.hs37d5_" | |
8016 | version ".tar.gz")) | |
8017 | (sha256 | |
8018 | (base32 | |
8019 | "1cg0g5fqmsvwyw2p9hp2yy4ilk21jkbbrnpgqvb5c36ihjwvc7sr")))) | |
8020 | (properties | |
8021 | `((upstream-name . "BSgenome.Hsapiens.1000genomes.hs37d5"))) | |
8022 | (build-system r-build-system) | |
8023 | ;; As this package provides little more than a very large data file it | |
8024 | ;; doesn't make sense to build substitutes. | |
8025 | (arguments `(#:substitutable? #f)) | |
8026 | (propagated-inputs | |
8027 | `(("r-bsgenome" ,r-bsgenome))) | |
8028 | (home-page | |
5713bbf1 | 8029 | "https://www.bioconductor.org/packages/BSgenome.Hsapiens.1000genomes.hs37d5/") |
aa3eeeb5 RJ |
8030 | (synopsis "Full genome sequences for Homo sapiens") |
8031 | (description | |
8032 | "This package provides full genome sequences for Homo sapiens from | |
8033 | 1000genomes phase2 reference genome sequence (hs37d5), based on NCBI GRCh37.") | |
8034 | (license license:artistic2.0))) | |
8035 | ||
c43a011d RW |
8036 | (define-public r-impute |
8037 | (package | |
8038 | (name "r-impute") | |
d11bc259 | 8039 | (version "1.56.0") |
c43a011d RW |
8040 | (source (origin |
8041 | (method url-fetch) | |
8042 | (uri (bioconductor-uri "impute" version)) | |
8043 | (sha256 | |
8044 | (base32 | |
d11bc259 | 8045 | "08z0pj1dz5iq967nwj67qyka7ir7m5an2ggv7bsrlz3apzfsla33")))) |
c43a011d RW |
8046 | (inputs |
8047 | `(("gfortran" ,gfortran))) | |
8048 | (build-system r-build-system) | |
5713bbf1 | 8049 | (home-page "https://bioconductor.org/packages/impute") |
c43a011d RW |
8050 | (synopsis "Imputation for microarray data") |
8051 | (description | |
8052 | "This package provides a function to impute missing gene expression | |
8053 | microarray data, using nearest neighbor averaging.") | |
8054 | (license license:gpl2+))) | |
8055 | ||
03ea5a35 RW |
8056 | (define-public r-seqpattern |
8057 | (package | |
8058 | (name "r-seqpattern") | |
45ba2cae | 8059 | (version "1.14.0") |
03ea5a35 RW |
8060 | (source (origin |
8061 | (method url-fetch) | |
8062 | (uri (bioconductor-uri "seqPattern" version)) | |
8063 | (sha256 | |
8064 | (base32 | |
45ba2cae | 8065 | "0di83qi83mrlw7i12khsq55d03hlazcywaa9m9pki1sfhafpq733")))) |
03ea5a35 RW |
8066 | (properties |
8067 | `((upstream-name . "seqPattern"))) | |
8068 | (build-system r-build-system) | |
8069 | (propagated-inputs | |
8070 | `(("r-biostrings" ,r-biostrings) | |
8071 | ("r-genomicranges" ,r-genomicranges) | |
8072 | ("r-iranges" ,r-iranges) | |
e92dd6f5 | 8073 | ("r-kernsmooth" ,r-kernsmooth) |
03ea5a35 | 8074 | ("r-plotrix" ,r-plotrix))) |
5713bbf1 | 8075 | (home-page "https://bioconductor.org/packages/seqPattern") |
03ea5a35 RW |
8076 | (synopsis "Visualising oligonucleotide patterns and motif occurrences") |
8077 | (description | |
8078 | "This package provides tools to visualize oligonucleotide patterns and | |
8079 | sequence motif occurrences across a large set of sequences centred at a common | |
8080 | reference point and sorted by a user defined feature.") | |
8081 | (license license:gpl3+))) | |
8082 | ||
cb933df6 RW |
8083 | (define-public r-genomation |
8084 | (package | |
8085 | (name "r-genomation") | |
c5b0815c | 8086 | (version "1.14.0") |
cb933df6 RW |
8087 | (source (origin |
8088 | (method url-fetch) | |
8089 | (uri (bioconductor-uri "genomation" version)) | |
8090 | (sha256 | |
8091 | (base32 | |
c5b0815c | 8092 | "0g0v4alfpqlinqinjnyzl3mrjnpbdx9ri34mcaiqbvbvg8ic8wvg")))) |
cb933df6 RW |
8093 | (build-system r-build-system) |
8094 | (propagated-inputs | |
8095 | `(("r-biostrings" ,r-biostrings) | |
8096 | ("r-bsgenome" ,r-bsgenome) | |
8097 | ("r-data-table" ,r-data-table) | |
8098 | ("r-genomeinfodb" ,r-genomeinfodb) | |
8099 | ("r-genomicalignments" ,r-genomicalignments) | |
8100 | ("r-genomicranges" ,r-genomicranges) | |
8101 | ("r-ggplot2" ,r-ggplot2) | |
8102 | ("r-gridbase" ,r-gridbase) | |
8103 | ("r-impute" ,r-impute) | |
8104 | ("r-iranges" ,r-iranges) | |
8105 | ("r-matrixstats" ,r-matrixstats) | |
8106 | ("r-plotrix" ,r-plotrix) | |
8107 | ("r-plyr" ,r-plyr) | |
51c3c490 | 8108 | ("r-rcpp" ,r-rcpp) |
cb933df6 RW |
8109 | ("r-readr" ,r-readr) |
8110 | ("r-reshape2" ,r-reshape2) | |
8111 | ("r-rsamtools" ,r-rsamtools) | |
8112 | ("r-rtracklayer" ,r-rtracklayer) | |
51c3c490 RW |
8113 | ("r-runit" ,r-runit) |
8114 | ("r-s4vectors" ,r-s4vectors) | |
cb933df6 RW |
8115 | ("r-seqpattern" ,r-seqpattern))) |
8116 | (home-page "http://bioinformatics.mdc-berlin.de/genomation/") | |
8117 | (synopsis "Summary, annotation and visualization of genomic data") | |
8118 | (description | |
8119 | "This package provides a package for summary and annotation of genomic | |
8120 | intervals. Users can visualize and quantify genomic intervals over | |
8121 | pre-defined functional regions, such as promoters, exons, introns, etc. The | |
8122 | genomic intervals represent regions with a defined chromosome position, which | |
8123 | may be associated with a score, such as aligned reads from HT-seq experiments, | |
8124 | TF binding sites, methylation scores, etc. The package can use any tabular | |
8125 | genomic feature data as long as it has minimal information on the locations of | |
8126 | genomic intervals. In addition, it can use BAM or BigWig files as input.") | |
8127 | (license license:artistic2.0))) | |
8128 | ||
64efa307 RW |
8129 | (define-public r-genomationdata |
8130 | (package | |
8131 | (name "r-genomationdata") | |
cb9e6ed7 | 8132 | (version "1.14.0") |
64efa307 RW |
8133 | (source (origin |
8134 | (method url-fetch) | |
8135 | ;; We cannot use bioconductor-uri here because this tarball is | |
8136 | ;; located under "data/annotation/" instead of "bioc/". | |
8137 | (uri (string-append "https://bioconductor.org/packages/" | |
8138 | "release/data/experiment/src/contrib/" | |
8139 | "genomationData_" version ".tar.gz")) | |
8140 | (sha256 | |
8141 | (base32 | |
cb9e6ed7 | 8142 | "10xyb8akjrhmak2i0mnv1agny2ipy364q9nlibyplpzc7vdb6bw7")))) |
64efa307 RW |
8143 | (build-system r-build-system) |
8144 | ;; As this package provides little more than large data files, it doesn't | |
8145 | ;; make sense to build substitutes. | |
8146 | (arguments `(#:substitutable? #f)) | |
8147 | (native-inputs | |
8148 | `(("r-knitr" ,r-knitr))) | |
8149 | (home-page "http://bioinformatics.mdc-berlin.de/genomation/") | |
8150 | (synopsis "Experimental data for use with the genomation package") | |
8151 | (description | |
8152 | "This package contains experimental genetic data for use with the | |
8153 | genomation package. Included are Chip Seq, Methylation and Cage data, | |
8154 | downloaded from Encode.") | |
8155 | (license license:gpl3+))) | |
8156 | ||
486da491 RW |
8157 | (define-public r-org-hs-eg-db |
8158 | (package | |
8159 | (name "r-org-hs-eg-db") | |
fc7683fa | 8160 | (version "3.7.0") |
486da491 RW |
8161 | (source (origin |
8162 | (method url-fetch) | |
8163 | ;; We cannot use bioconductor-uri here because this tarball is | |
8164 | ;; located under "data/annotation/" instead of "bioc/". | |
5713bbf1 | 8165 | (uri (string-append "https://www.bioconductor.org/packages/" |
486da491 RW |
8166 | "release/data/annotation/src/contrib/" |
8167 | "org.Hs.eg.db_" version ".tar.gz")) | |
8168 | (sha256 | |
8169 | (base32 | |
fc7683fa | 8170 | "1qxz9l80yg3qdqszs6dsscp7lrpfi1bgd0pxh9j7q34vprzwhdim")))) |
486da491 RW |
8171 | (properties |
8172 | `((upstream-name . "org.Hs.eg.db"))) | |
8173 | (build-system r-build-system) | |
8174 | (propagated-inputs | |
8175 | `(("r-annotationdbi" ,r-annotationdbi))) | |
5713bbf1 | 8176 | (home-page "https://www.bioconductor.org/packages/org.Hs.eg.db/") |
486da491 RW |
8177 | (synopsis "Genome wide annotation for Human") |
8178 | (description | |
676507e3 RW |
8179 | "This package contains genome-wide annotations for Human, primarily based |
8180 | on mapping using Entrez Gene identifiers.") | |
486da491 RW |
8181 | (license license:artistic2.0))) |
8182 | ||
fefedf98 RW |
8183 | (define-public r-org-ce-eg-db |
8184 | (package | |
8185 | (name "r-org-ce-eg-db") | |
76bd16bc | 8186 | (version "3.7.0") |
fefedf98 RW |
8187 | (source (origin |
8188 | (method url-fetch) | |
8189 | ;; We cannot use bioconductor-uri here because this tarball is | |
8190 | ;; located under "data/annotation/" instead of "bioc/". | |
5713bbf1 | 8191 | (uri (string-append "https://www.bioconductor.org/packages/" |
fefedf98 RW |
8192 | "release/data/annotation/src/contrib/" |
8193 | "org.Ce.eg.db_" version ".tar.gz")) | |
8194 | (sha256 | |
8195 | (base32 | |
76bd16bc | 8196 | "1w5br1ss4ha8wv4v2saj7cmbjc2jw0dyj2f2y269l078z31wcnaz")))) |
fefedf98 RW |
8197 | (properties |
8198 | `((upstream-name . "org.Ce.eg.db"))) | |
8199 | (build-system r-build-system) | |
8200 | (propagated-inputs | |
8201 | `(("r-annotationdbi" ,r-annotationdbi))) | |
5713bbf1 | 8202 | (home-page "https://www.bioconductor.org/packages/org.Ce.eg.db/") |
fefedf98 RW |
8203 | (synopsis "Genome wide annotation for Worm") |
8204 | (description | |
8205 | "This package provides mappings from Entrez gene identifiers to various | |
8206 | annotations for the genome of the model worm Caenorhabditis elegans.") | |
8207 | (license license:artistic2.0))) | |
8208 | ||
16c53a1e RW |
8209 | (define-public r-org-dm-eg-db |
8210 | (package | |
8211 | (name "r-org-dm-eg-db") | |
314511b8 | 8212 | (version "3.7.0") |
16c53a1e RW |
8213 | (source (origin |
8214 | (method url-fetch) | |
8215 | ;; We cannot use bioconductor-uri here because this tarball is | |
8216 | ;; located under "data/annotation/" instead of "bioc/". | |
5713bbf1 | 8217 | (uri (string-append "https://www.bioconductor.org/packages/" |
16c53a1e RW |
8218 | "release/data/annotation/src/contrib/" |
8219 | "org.Dm.eg.db_" version ".tar.gz")) | |
8220 | (sha256 | |
8221 | (base32 | |
314511b8 | 8222 | "1pqjrzlyg72bjpy8zsxvaglc7jsv176bnyi87xdajmkvsgxpm7b3")))) |
16c53a1e RW |
8223 | (properties |
8224 | `((upstream-name . "org.Dm.eg.db"))) | |
8225 | (build-system r-build-system) | |
8226 | (propagated-inputs | |
8227 | `(("r-annotationdbi" ,r-annotationdbi))) | |
5713bbf1 | 8228 | (home-page "https://www.bioconductor.org/packages/org.Dm.eg.db/") |
16c53a1e RW |
8229 | (synopsis "Genome wide annotation for Fly") |
8230 | (description | |
8231 | "This package provides mappings from Entrez gene identifiers to various | |
8232 | annotations for the genome of the model fruit fly Drosophila melanogaster.") | |
8233 | (license license:artistic2.0))) | |
8234 | ||
e761beb9 RW |
8235 | (define-public r-org-mm-eg-db |
8236 | (package | |
8237 | (name "r-org-mm-eg-db") | |
d34959b8 | 8238 | (version "3.7.0") |
e761beb9 RW |
8239 | (source (origin |
8240 | (method url-fetch) | |
8241 | ;; We cannot use bioconductor-uri here because this tarball is | |
8242 | ;; located under "data/annotation/" instead of "bioc/". | |
5713bbf1 | 8243 | (uri (string-append "https://www.bioconductor.org/packages/" |
e761beb9 RW |
8244 | "release/data/annotation/src/contrib/" |
8245 | "org.Mm.eg.db_" version ".tar.gz")) | |
8246 | (sha256 | |
8247 | (base32 | |
d34959b8 | 8248 | "1i3nvrd3wjigf1rmgxq1p5xxc3p8v02h5gwi62s30rkrsyjjfjxx")))) |
e761beb9 RW |
8249 | (properties |
8250 | `((upstream-name . "org.Mm.eg.db"))) | |
8251 | (build-system r-build-system) | |
8252 | (propagated-inputs | |
8253 | `(("r-annotationdbi" ,r-annotationdbi))) | |
5713bbf1 | 8254 | (home-page "https://www.bioconductor.org/packages/org.Mm.eg.db/") |
e761beb9 RW |
8255 | (synopsis "Genome wide annotation for Mouse") |
8256 | (description | |
8257 | "This package provides mappings from Entrez gene identifiers to various | |
8258 | annotations for the genome of the model mouse Mus musculus.") | |
8259 | (license license:artistic2.0))) | |
8260 | ||
936e7d67 RW |
8261 | (define-public r-seqlogo |
8262 | (package | |
8263 | (name "r-seqlogo") | |
34f1c60c | 8264 | (version "1.48.0") |
936e7d67 RW |
8265 | (source |
8266 | (origin | |
8267 | (method url-fetch) | |
8268 | (uri (bioconductor-uri "seqLogo" version)) | |
8269 | (sha256 | |
8270 | (base32 | |
34f1c60c | 8271 | "022vr9ydwcivs7rw7kwj73gfk5gc7ckwa1q66vhd4kw9ylh70v68")))) |
936e7d67 RW |
8272 | (properties `((upstream-name . "seqLogo"))) |
8273 | (build-system r-build-system) | |
5713bbf1 | 8274 | (home-page "https://bioconductor.org/packages/seqLogo") |
936e7d67 RW |
8275 | (synopsis "Sequence logos for DNA sequence alignments") |
8276 | (description | |
8277 | "seqLogo takes the position weight matrix of a DNA sequence motif and | |
8278 | plots the corresponding sequence logo as introduced by Schneider and | |
8279 | Stephens (1990).") | |
8280 | (license license:lgpl2.0+))) | |
8281 | ||
c90a4baf RW |
8282 | (define-public r-bsgenome-hsapiens-ucsc-hg19 |
8283 | (package | |
8284 | (name "r-bsgenome-hsapiens-ucsc-hg19") | |
8285 | (version "1.4.0") | |
8286 | (source (origin | |
8287 | (method url-fetch) | |
8288 | ;; We cannot use bioconductor-uri here because this tarball is | |
8289 | ;; located under "data/annotation/" instead of "bioc/". | |
5713bbf1 | 8290 | (uri (string-append "https://www.bioconductor.org/packages/" |
c90a4baf RW |
8291 | "release/data/annotation/src/contrib/" |
8292 | "BSgenome.Hsapiens.UCSC.hg19_" | |
8293 | version ".tar.gz")) | |
8294 | (sha256 | |
8295 | (base32 | |
9d217d27 | 8296 | "1y0nqpk8cw5a34sd9hmin3z4v7iqm6hf6l22cl81vlbxqbjibxc8")))) |
c90a4baf RW |
8297 | (properties |
8298 | `((upstream-name . "BSgenome.Hsapiens.UCSC.hg19"))) | |
8299 | (build-system r-build-system) | |
8300 | ;; As this package provides little more than a very large data file it | |
8301 | ;; doesn't make sense to build substitutes. | |
8302 | (arguments `(#:substitutable? #f)) | |
8303 | (propagated-inputs | |
8304 | `(("r-bsgenome" ,r-bsgenome))) | |
8305 | (home-page | |
5713bbf1 | 8306 | "https://www.bioconductor.org/packages/BSgenome.Hsapiens.UCSC.hg19/") |
c90a4baf RW |
8307 | (synopsis "Full genome sequences for Homo sapiens") |
8308 | (description | |
8309 | "This package provides full genome sequences for Homo sapiens as provided | |
8310 | by UCSC (hg19, February 2009) and stored in Biostrings objects.") | |
8311 | (license license:artistic2.0))) | |
8312 | ||
a3e90287 RW |
8313 | (define-public r-bsgenome-mmusculus-ucsc-mm9 |
8314 | (package | |
8315 | (name "r-bsgenome-mmusculus-ucsc-mm9") | |
8316 | (version "1.4.0") | |
8317 | (source (origin | |
8318 | (method url-fetch) | |
8319 | ;; We cannot use bioconductor-uri here because this tarball is | |
8320 | ;; located under "data/annotation/" instead of "bioc/". | |
5713bbf1 | 8321 | (uri (string-append "https://www.bioconductor.org/packages/" |
a3e90287 RW |
8322 | "release/data/annotation/src/contrib/" |
8323 | "BSgenome.Mmusculus.UCSC.mm9_" | |
8324 | version ".tar.gz")) | |
8325 | (sha256 | |
8326 | (base32 | |
8327 | "1birqw30g2azimxpnjfzmkphan7x131yy8b9h85lfz5fjdg7841i")))) | |
8328 | (properties | |
8329 | `((upstream-name . "BSgenome.Mmusculus.UCSC.mm9"))) | |
8330 | (build-system r-build-system) | |
8331 | ;; As this package provides little more than a very large data file it | |
8332 | ;; doesn't make sense to build substitutes. | |
8333 | (arguments `(#:substitutable? #f)) | |
8334 | (propagated-inputs | |
8335 | `(("r-bsgenome" ,r-bsgenome))) | |
8336 | (home-page | |
5713bbf1 | 8337 | "https://www.bioconductor.org/packages/BSgenome.Mmusculus.UCSC.mm9/") |
a3e90287 RW |
8338 | (synopsis "Full genome sequences for Mouse") |
8339 | (description | |
8340 | "This package provides full genome sequences for Mus musculus (Mouse) as | |
8341 | provided by UCSC (mm9, July 2007) and stored in Biostrings objects.") | |
8342 | (license license:artistic2.0))) | |
8343 | ||
4714d521 RW |
8344 | (define-public r-bsgenome-mmusculus-ucsc-mm10 |
8345 | (package | |
8346 | (name "r-bsgenome-mmusculus-ucsc-mm10") | |
8347 | (version "1.4.0") | |
8348 | (source (origin | |
8349 | (method url-fetch) | |
8350 | ;; We cannot use bioconductor-uri here because this tarball is | |
8351 | ;; located under "data/annotation/" instead of "bioc/". | |
5713bbf1 | 8352 | (uri (string-append "https://www.bioconductor.org/packages/" |
4714d521 RW |
8353 | "release/data/annotation/src/contrib/" |
8354 | "BSgenome.Mmusculus.UCSC.mm10_" | |
8355 | version ".tar.gz")) | |
8356 | (sha256 | |
8357 | (base32 | |
8358 | "12s0nm2na9brjad4rn9l7d3db2aj8qa1xvz0y1k7gk08wayb6bkf")))) | |
8359 | (properties | |
8360 | `((upstream-name . "BSgenome.Mmusculus.UCSC.mm10"))) | |
8361 | (build-system r-build-system) | |
8362 | ;; As this package provides little more than a very large data file it | |
8363 | ;; doesn't make sense to build substitutes. | |
8364 | (arguments `(#:substitutable? #f)) | |
8365 | (propagated-inputs | |
8366 | `(("r-bsgenome" ,r-bsgenome))) | |
8367 | (home-page | |
5713bbf1 | 8368 | "https://www.bioconductor.org/packages/BSgenome.Mmusculus.UCSC.mm10/") |
4714d521 RW |
8369 | (synopsis "Full genome sequences for Mouse") |
8370 | (description | |
8371 | "This package provides full genome sequences for Mus | |
8372 | musculus (Mouse) as provided by UCSC (mm10, December 2011) and stored | |
8373 | in Biostrings objects.") | |
8374 | (license license:artistic2.0))) | |
8375 | ||
c5173d74 RJ |
8376 | (define-public r-txdb-mmusculus-ucsc-mm10-knowngene |
8377 | (package | |
8378 | (name "r-txdb-mmusculus-ucsc-mm10-knowngene") | |
51b262f3 | 8379 | (version "3.4.4") |
c5173d74 RJ |
8380 | (source (origin |
8381 | (method url-fetch) | |
8382 | ;; We cannot use bioconductor-uri here because this tarball is | |
8383 | ;; located under "data/annotation/" instead of "bioc/". | |
5713bbf1 | 8384 | (uri (string-append "https://www.bioconductor.org/packages/" |
c5173d74 RJ |
8385 | "release/data/annotation/src/contrib/" |
8386 | "TxDb.Mmusculus.UCSC.mm10.knownGene_" | |
8387 | version ".tar.gz")) | |
8388 | (sha256 | |
8389 | (base32 | |
51b262f3 | 8390 | "01lgxc1fx5nhlpbwjd5zqghkkbmh6axd98ikx4b0spv0jdg6gf39")))) |
c5173d74 RJ |
8391 | (properties |
8392 | `((upstream-name . "TxDb.Mmusculus.UCSC.mm10.knownGene"))) | |
8393 | (build-system r-build-system) | |
8394 | ;; As this package provides little more than a very large data file it | |
8395 | ;; doesn't make sense to build substitutes. | |
8396 | (arguments `(#:substitutable? #f)) | |
8397 | (propagated-inputs | |
8398 | `(("r-bsgenome" ,r-bsgenome) | |
8399 | ("r-genomicfeatures" ,r-genomicfeatures) | |
8400 | ("r-annotationdbi" ,r-annotationdbi))) | |
8401 | (home-page | |
5713bbf1 | 8402 | "https://bioconductor.org/packages/TxDb.Mmusculus.UCSC.mm10.knownGene/") |
c5173d74 RJ |
8403 | (synopsis "Annotation package for TxDb knownGene object(s) for Mouse") |
8404 | (description | |
8405 | "This package loads a TxDb object, which is an R interface to | |
8406 | prefabricated databases contained in this package. This package provides | |
8407 | the TxDb object of Mouse data as provided by UCSC (mm10, December 2011) | |
8408 | based on the knownGene track.") | |
8409 | (license license:artistic2.0))) | |
8410 | ||
943bd627 RW |
8411 | (define-public r-bsgenome-celegans-ucsc-ce6 |
8412 | (package | |
8413 | (name "r-bsgenome-celegans-ucsc-ce6") | |
8414 | (version "1.4.0") | |
8415 | (source (origin | |
8416 | (method url-fetch) | |
8417 | ;; We cannot use bioconductor-uri here because this tarball is | |
8418 | ;; located under "data/annotation/" instead of "bioc/". | |
5713bbf1 | 8419 | (uri (string-append "https://www.bioconductor.org/packages/" |
943bd627 RW |
8420 | "release/data/annotation/src/contrib/" |
8421 | "BSgenome.Celegans.UCSC.ce6_" | |
8422 | version ".tar.gz")) | |
8423 | (sha256 | |
8424 | (base32 | |
8425 | "0mqzb353xv2c3m3vkb315dkmnxkgczp7ndnknyhpgjlybyf715v9")))) | |
8426 | (properties | |
8427 | `((upstream-name . "BSgenome.Celegans.UCSC.ce6"))) | |
8428 | (build-system r-build-system) | |
8429 | ;; As this package provides little more than a very large data file it | |
8430 | ;; doesn't make sense to build substitutes. | |
8431 | (arguments `(#:substitutable? #f)) | |
8432 | (propagated-inputs | |
8433 | `(("r-bsgenome" ,r-bsgenome))) | |
8434 | (home-page | |
5713bbf1 | 8435 | "https://www.bioconductor.org/packages/BSgenome.Celegans.UCSC.ce6/") |
943bd627 RW |
8436 | (synopsis "Full genome sequences for Worm") |
8437 | (description | |
8438 | "This package provides full genome sequences for Caenorhabditis | |
8439 | elegans (Worm) as provided by UCSC (ce6, May 2008) and stored in Biostrings | |
8440 | objects.") | |
8441 | (license license:artistic2.0))) | |
8442 | ||
fc47c7d6 RW |
8443 | (define-public r-bsgenome-celegans-ucsc-ce10 |
8444 | (package | |
8445 | (name "r-bsgenome-celegans-ucsc-ce10") | |
8446 | (version "1.4.0") | |
8447 | (source (origin | |
8448 | (method url-fetch) | |
8449 | ;; We cannot use bioconductor-uri here because this tarball is | |
8450 | ;; located under "data/annotation/" instead of "bioc/". | |
5713bbf1 | 8451 | (uri (string-append "https://www.bioconductor.org/packages/" |
fc47c7d6 RW |
8452 | "release/data/annotation/src/contrib/" |
8453 | "BSgenome.Celegans.UCSC.ce10_" | |
8454 | version ".tar.gz")) | |
8455 | (sha256 | |
8456 | (base32 | |
8457 | "1zaym97jk4npxk14ifvwz2rvhm4zx9xgs33r9vvx9rlynp0gydrk")))) | |
8458 | (properties | |
8459 | `((upstream-name . "BSgenome.Celegans.UCSC.ce10"))) | |
8460 | (build-system r-build-system) | |
8461 | ;; As this package provides little more than a very large data file it | |
8462 | ;; doesn't make sense to build substitutes. | |
8463 | (arguments `(#:substitutable? #f)) | |
8464 | (propagated-inputs | |
8465 | `(("r-bsgenome" ,r-bsgenome))) | |
8466 | (home-page | |
5713bbf1 | 8467 | "https://www.bioconductor.org/packages/BSgenome.Celegans.UCSC.ce10/") |
fc47c7d6 RW |
8468 | (synopsis "Full genome sequences for Worm") |
8469 | (description | |
8470 | "This package provides full genome sequences for Caenorhabditis | |
8471 | elegans (Worm) as provided by UCSC (ce10, Oct 2010) and stored in Biostrings | |
8472 | objects.") | |
8473 | (license license:artistic2.0))) | |
8474 | ||
6dc60998 RW |
8475 | (define-public r-bsgenome-dmelanogaster-ucsc-dm3 |
8476 | (package | |
8477 | (name "r-bsgenome-dmelanogaster-ucsc-dm3") | |
8478 | (version "1.4.0") | |
8479 | (source (origin | |
8480 | (method url-fetch) | |
8481 | ;; We cannot use bioconductor-uri here because this tarball is | |
8482 | ;; located under "data/annotation/" instead of "bioc/". | |
5713bbf1 | 8483 | (uri (string-append "https://www.bioconductor.org/packages/" |
6dc60998 RW |
8484 | "release/data/annotation/src/contrib/" |
8485 | "BSgenome.Dmelanogaster.UCSC.dm3_" | |
8486 | version ".tar.gz")) | |
8487 | (sha256 | |
8488 | (base32 | |
8489 | "19bm3lkhhkag3gnwp419211fh0cnr0x6fa0r1lr0ycwrikxdxsv8")))) | |
8490 | (properties | |
8491 | `((upstream-name . "BSgenome.Dmelanogaster.UCSC.dm3"))) | |
8492 | (build-system r-build-system) | |
8493 | ;; As this package provides little more than a very large data file it | |
8494 | ;; doesn't make sense to build substitutes. | |
8495 | (arguments `(#:substitutable? #f)) | |
8496 | (propagated-inputs | |
8497 | `(("r-bsgenome" ,r-bsgenome))) | |
8498 | (home-page | |
5713bbf1 | 8499 | "https://www.bioconductor.org/packages/BSgenome.Dmelanogaster.UCSC.dm3/") |
6dc60998 RW |
8500 | (synopsis "Full genome sequences for Fly") |
8501 | (description | |
8502 | "This package provides full genome sequences for Drosophila | |
8503 | melanogaster (Fly) as provided by UCSC (dm3, April 2006) and stored in | |
8504 | Biostrings objects.") | |
8505 | (license license:artistic2.0))) | |
8506 | ||
ae2462f7 RW |
8507 | (define-public r-motifrg |
8508 | (package | |
8509 | (name "r-motifrg") | |
2919fefe | 8510 | (version "1.26.0") |
ae2462f7 RW |
8511 | (source |
8512 | (origin | |
8513 | (method url-fetch) | |
8514 | (uri (bioconductor-uri "motifRG" version)) | |
8515 | (sha256 | |
8516 | (base32 | |
2919fefe | 8517 | "1wxww6i0jgyapqclcwy0zzf9kqjvrvylr89z7yhg1izi7jnw2fka")))) |
ae2462f7 RW |
8518 | (properties `((upstream-name . "motifRG"))) |
8519 | (build-system r-build-system) | |
8520 | (propagated-inputs | |
8521 | `(("r-biostrings" ,r-biostrings) | |
8522 | ("r-bsgenome" ,r-bsgenome) | |
007424b5 | 8523 | ("r-bsgenome-hsapiens-ucsc-hg19" ,r-bsgenome-hsapiens-ucsc-hg19) |
ae2462f7 RW |
8524 | ("r-iranges" ,r-iranges) |
8525 | ("r-seqlogo" ,r-seqlogo) | |
8526 | ("r-xvector" ,r-xvector))) | |
5713bbf1 | 8527 | (home-page "https://bioconductor.org/packages/motifRG") |
ae2462f7 RW |
8528 | (synopsis "Discover motifs in high throughput sequencing data") |
8529 | (description | |
8530 | "This package provides tools for discriminative motif discovery in high | |
8531 | throughput genetic sequencing data sets using regression methods.") | |
8532 | (license license:artistic2.0))) | |
8533 | ||
a5002ae7 AE |
8534 | (define-public r-qtl |
8535 | (package | |
8536 | (name "r-qtl") | |
65c9d257 | 8537 | (version "1.42-8") |
a5002ae7 AE |
8538 | (source |
8539 | (origin | |
8540 | (method url-fetch) | |
8541 | (uri (string-append "mirror://cran/src/contrib/qtl_" | |
8542 | version ".tar.gz")) | |
8543 | (sha256 | |
8544 | (base32 | |
65c9d257 | 8545 | "1l528dwvfpdlr05imrrm4rq32axp6hld9nqm6mm43kn5n7z2f5k6")))) |
a5002ae7 AE |
8546 | (build-system r-build-system) |
8547 | (home-page "http://rqtl.org/") | |
8548 | (synopsis "R package for analyzing QTL experiments in genetics") | |
8549 | (description "R/qtl is an extension library for the R statistics | |
8550 | system. It is used to analyze experimental crosses for identifying | |
8551 | genes contributing to variation in quantitative traits (so-called | |
8552 | quantitative trait loci, QTLs). | |
8553 | ||
8554 | Using a hidden Markov model, R/qtl allows to estimate genetic maps, to | |
8555 | identify genotyping errors, and to perform single-QTL and two-QTL, | |
8556 | two-dimensional genome scans.") | |
8557 | (license license:gpl3))) | |
d1e32822 | 8558 | |
9e3ba31c RJ |
8559 | (define-public r-zlibbioc |
8560 | (package | |
8561 | (name "r-zlibbioc") | |
7d7c702c | 8562 | (version "1.28.0") |
9e3ba31c RJ |
8563 | (source (origin |
8564 | (method url-fetch) | |
8565 | (uri (bioconductor-uri "zlibbioc" version)) | |
8566 | (sha256 | |
8567 | (base32 | |
7d7c702c | 8568 | "0bjvzy24kab7ank02cc1qk2ikcz4dllgf66wpsdl0d3zp4gn3l2h")))) |
9e3ba31c RJ |
8569 | (properties |
8570 | `((upstream-name . "zlibbioc"))) | |
8571 | (build-system r-build-system) | |
8572 | (home-page "https://bioconductor.org/packages/zlibbioc") | |
8573 | (synopsis "Provider for zlib-1.2.5 to R packages") | |
8574 | (description "This package uses the source code of zlib-1.2.5 to create | |
8575 | libraries for systems that do not have these available via other means.") | |
8576 | (license license:artistic2.0))) | |
8577 | ||
e619a5c2 RW |
8578 | (define-public r-r4rna |
8579 | (package | |
8580 | (name "r-r4rna") | |
8581 | (version "0.1.4") | |
8582 | (source | |
8583 | (origin | |
8584 | (method url-fetch) | |
8585 | (uri (string-append "http://www.e-rna.org/r-chie/files/R4RNA_" | |
8586 | version ".tar.gz")) | |
8587 | (sha256 | |
8588 | (base32 | |
8589 | "1p0i78wh76jfgmn9jphbwwaz6yy6pipzfg08xs54cxavxg2j81p5")))) | |
8590 | (build-system r-build-system) | |
8591 | (propagated-inputs | |
8592 | `(("r-optparse" ,r-optparse) | |
8593 | ("r-rcolorbrewer" ,r-rcolorbrewer))) | |
8594 | (home-page "http://www.e-rna.org/r-chie/index.cgi") | |
8595 | (synopsis "Analysis framework for RNA secondary structure") | |
8596 | (description | |
8597 | "The R4RNA package aims to be a general framework for the analysis of RNA | |
8598 | secondary structure and comparative analysis in R.") | |
8599 | (license license:gpl3+))) | |
8600 | ||
52765a63 RW |
8601 | (define-public r-rhtslib |
8602 | (package | |
8603 | (name "r-rhtslib") | |
48196899 | 8604 | (version "1.14.0") |
52765a63 RW |
8605 | (source |
8606 | (origin | |
8607 | (method url-fetch) | |
8608 | (uri (bioconductor-uri "Rhtslib" version)) | |
8609 | (sha256 | |
8610 | (base32 | |
48196899 | 8611 | "1h4q54f8za3aaxgy186zf2165sar5c3cgxkk44lq5hzx5pxkl5wn")))) |
52765a63 RW |
8612 | (properties `((upstream-name . "Rhtslib"))) |
8613 | (build-system r-build-system) | |
8614 | (propagated-inputs | |
8615 | `(("r-zlibbioc" ,r-zlibbioc))) | |
8616 | (inputs | |
8617 | `(("zlib" ,zlib))) | |
53ca52f0 | 8618 | (native-inputs |
1a08bb8a | 8619 | `(("pkg-config" ,pkg-config))) |
52765a63 RW |
8620 | (home-page "https://github.com/nhayden/Rhtslib") |
8621 | (synopsis "High-throughput sequencing library as an R package") | |
8622 | (description | |
8623 | "This package provides the HTSlib C library for high-throughput | |
8624 | nucleotide sequence analysis. The package is primarily useful to developers | |
8625 | of other R packages who wish to make use of HTSlib.") | |
8626 | (license license:lgpl2.0+))) | |
8627 | ||
fe02c4c9 RW |
8628 | (define-public r-bamsignals |
8629 | (package | |
8630 | (name "r-bamsignals") | |
338f860c | 8631 | (version "1.14.0") |
fe02c4c9 RW |
8632 | (source |
8633 | (origin | |
8634 | (method url-fetch) | |
8635 | (uri (bioconductor-uri "bamsignals" version)) | |
8636 | (sha256 | |
8637 | (base32 | |
338f860c | 8638 | "19irfx1y1izf903vq59wxsdbf88g143zy9l89gxqawh7jfxds8w8")))) |
fe02c4c9 RW |
8639 | (build-system r-build-system) |
8640 | (propagated-inputs | |
8641 | `(("r-biocgenerics" ,r-biocgenerics) | |
8642 | ("r-genomicranges" ,r-genomicranges) | |
8643 | ("r-iranges" ,r-iranges) | |
8644 | ("r-rcpp" ,r-rcpp) | |
8645 | ("r-rhtslib" ,r-rhtslib) | |
8646 | ("r-zlibbioc" ,r-zlibbioc))) | |
8647 | (inputs | |
8648 | `(("zlib" ,zlib))) | |
5713bbf1 | 8649 | (home-page "https://bioconductor.org/packages/bamsignals") |
fe02c4c9 RW |
8650 | (synopsis "Extract read count signals from bam files") |
8651 | (description | |
8652 | "This package allows to efficiently obtain count vectors from indexed bam | |
8653 | files. It counts the number of nucleotide sequence reads in given genomic | |
8654 | ranges and it computes reads profiles and coverage profiles. It also handles | |
8655 | paired-end data.") | |
8656 | (license license:gpl2+))) | |
8657 | ||
89984be4 RW |
8658 | (define-public r-rcas |
8659 | (package | |
8660 | (name "r-rcas") | |
a1c2bf8e | 8661 | (version "1.8.0") |
89984be4 RW |
8662 | (source (origin |
8663 | (method url-fetch) | |
bcc2e0ed | 8664 | (uri (bioconductor-uri "RCAS" version)) |
89984be4 RW |
8665 | (sha256 |
8666 | (base32 | |
a1c2bf8e | 8667 | "0ss5hcg2m7gjji6dd23zxa5bd5a7knwcnada4qs5q2l4clgk39ad")))) |
89984be4 | 8668 | (build-system r-build-system) |
89984be4 | 8669 | (propagated-inputs |
a1c2bf8e RW |
8670 | `(("r-annotationdbi" ,r-annotationdbi) |
8671 | ("r-biocgenerics" ,r-biocgenerics) | |
89984be4 | 8672 | ("r-biomart" ,r-biomart) |
bcc2e0ed | 8673 | ("r-biostrings" ,r-biostrings) |
89984be4 | 8674 | ("r-bsgenome-hsapiens-ucsc-hg19" ,r-bsgenome-hsapiens-ucsc-hg19) |
bcc2e0ed RW |
8675 | ("r-cowplot" ,r-cowplot) |
8676 | ("r-data-table" ,r-data-table) | |
8677 | ("r-dbi" ,r-dbi) | |
89984be4 | 8678 | ("r-dt" ,r-dt) |
bcc2e0ed | 8679 | ("r-genomation" ,r-genomation) |
a1c2bf8e | 8680 | ("r-genomeinfodb" ,r-genomeinfodb) |
bcc2e0ed | 8681 | ("r-genomicfeatures" ,r-genomicfeatures) |
a1c2bf8e | 8682 | ("r-genomicranges" ,r-genomicranges) |
bcc2e0ed RW |
8683 | ("r-ggplot2" ,r-ggplot2) |
8684 | ("r-ggseqlogo" ,r-ggseqlogo) | |
8685 | ("r-knitr" ,r-knitr) | |
8686 | ("r-motifrg" ,r-motifrg) | |
8687 | ("r-org-hs-eg-db" ,r-org-hs-eg-db) | |
ebfd6a71 | 8688 | ("r-pbapply" ,r-pbapply) |
bcc2e0ed | 8689 | ("r-pheatmap" ,r-pheatmap) |
89984be4 | 8690 | ("r-plotly" ,r-plotly) |
2c8d6c0b | 8691 | ("r-plotrix" ,r-plotrix) |
bcc2e0ed RW |
8692 | ("r-proxy" ,r-proxy) |
8693 | ("r-rsqlite" ,r-rsqlite) | |
89984be4 | 8694 | ("r-rtracklayer" ,r-rtracklayer) |
bcc2e0ed RW |
8695 | ("r-rmarkdown" ,r-rmarkdown) |
8696 | ("r-s4vectors" ,r-s4vectors) | |
8697 | ("r-topgo" ,r-topgo))) | |
89984be4 RW |
8698 | (synopsis "RNA-centric annotation system") |
8699 | (description | |
8700 | "RCAS aims to be a standalone RNA-centric annotation system that provides | |
8701 | intuitive reports and publication-ready graphics. This package provides the R | |
8702 | library implementing most of the pipeline's features.") | |
8703 | (home-page "https://github.com/BIMSBbioinfo/RCAS") | |
75690c9f | 8704 | (license license:artistic2.0))) |
89984be4 | 8705 | |
50937297 RW |
8706 | (define-public rcas-web |
8707 | (package | |
8708 | (name "rcas-web") | |
cbc1c27b | 8709 | (version "0.0.5") |
50937297 RW |
8710 | (source |
8711 | (origin | |
8712 | (method url-fetch) | |
8713 | (uri (string-append "https://github.com/BIMSBbioinfo/rcas-web/" | |
8714 | "releases/download/v" version | |
8715 | "/rcas-web-" version ".tar.gz")) | |
8716 | (sha256 | |
8717 | (base32 | |
cbc1c27b | 8718 | "0igz7jpcf7cm9800zcag6p3gd1i649figrhbdba6cjkm8f4gfspr")))) |
50937297 RW |
8719 | (build-system gnu-build-system) |
8720 | (arguments | |
8721 | `(#:phases | |
8722 | (modify-phases %standard-phases | |
8723 | (add-after 'install 'wrap-executable | |
8724 | (lambda* (#:key inputs outputs #:allow-other-keys) | |
8725 | (let* ((out (assoc-ref outputs "out")) | |
8726 | (json (assoc-ref inputs "guile-json")) | |
8727 | (redis (assoc-ref inputs "guile-redis")) | |
8728 | (path (string-append | |
8729 | json "/share/guile/site/2.2:" | |
8730 | redis "/share/guile/site/2.2"))) | |
8731 | (wrap-program (string-append out "/bin/rcas-web") | |
8732 | `("GUILE_LOAD_PATH" ":" = (,path)) | |
8733 | `("GUILE_LOAD_COMPILED_PATH" ":" = (,path)) | |
8734 | `("R_LIBS_SITE" ":" = (,(getenv "R_LIBS_SITE"))))) | |
8735 | #t))))) | |
8736 | (inputs | |
2d7c4ae3 | 8737 | `(("r-minimal" ,r-minimal) |
50937297 | 8738 | ("r-rcas" ,r-rcas) |
f6396d86 | 8739 | ("guile-next" ,guile-2.2) |
2252f087 | 8740 | ("guile-json" ,guile-json) |
50937297 RW |
8741 | ("guile-redis" ,guile2.2-redis))) |
8742 | (native-inputs | |
8743 | `(("pkg-config" ,pkg-config))) | |
8744 | (home-page "https://github.com/BIMSBbioinfo/rcas-web") | |
8745 | (synopsis "Web interface for RNA-centric annotation system (RCAS)") | |
8746 | (description "This package provides a simple web interface for the | |
8747 | @dfn{RNA-centric annotation system} (RCAS).") | |
8748 | (license license:agpl3+))) | |
8749 | ||
7500e42b RJ |
8750 | (define-public r-mutationalpatterns |
8751 | (package | |
8752 | (name "r-mutationalpatterns") | |
ad90921d | 8753 | (version "1.8.0") |
7500e42b RJ |
8754 | (source |
8755 | (origin | |
8756 | (method url-fetch) | |
8757 | (uri (bioconductor-uri "MutationalPatterns" version)) | |
8758 | (sha256 | |
8759 | (base32 | |
ad90921d | 8760 | "0w9lg1zs106h6rqvy8mhikq6q6q9syw6c1prcxr38ssh85rcih12")))) |
7500e42b RJ |
8761 | (build-system r-build-system) |
8762 | (propagated-inputs | |
8763 | `(("r-biocgenerics" ,r-biocgenerics) | |
8764 | ("r-biostrings" ,r-biostrings) | |
b6c2c8f7 | 8765 | ;; These two packages are suggested packages |
cf4ac4e4 RJ |
8766 | ("r-bsgenome-hsapiens-1000g" ,r-bsgenome-hsapiens-1000genomes-hs37d5) |
8767 | ("r-bsgenome-hsapiens-ucsc-hg19" ,r-bsgenome-hsapiens-ucsc-hg19) | |
7500e42b RJ |
8768 | ("r-genomicranges" ,r-genomicranges) |
8769 | ("r-genomeinfodb" ,r-genomeinfodb) | |
8770 | ("r-ggplot2" ,r-ggplot2) | |
7500e42b RJ |
8771 | ("r-iranges" ,r-iranges) |
8772 | ("r-nmf" ,r-nmf) | |
8773 | ("r-plyr" ,r-plyr) | |
8774 | ("r-pracma" ,r-pracma) | |
8775 | ("r-reshape2" ,r-reshape2) | |
39d9098d RW |
8776 | ("r-cowplot" ,r-cowplot) |
8777 | ("r-ggdendro" ,r-ggdendro) | |
8778 | ("r-s4vectors" ,r-s4vectors) | |
7500e42b RJ |
8779 | ("r-summarizedexperiment" ,r-summarizedexperiment) |
8780 | ("r-variantannotation" ,r-variantannotation))) | |
5713bbf1 | 8781 | (home-page "https://bioconductor.org/packages/MutationalPatterns/") |
7500e42b RJ |
8782 | (synopsis "Extract and visualize mutational patterns in genomic data") |
8783 | (description "This package provides an extensive toolset for the | |
8784 | characterization and visualization of a wide range of mutational patterns | |
8785 | in SNV base substitution data.") | |
8786 | (license license:expat))) | |
8787 | ||
d7160529 RW |
8788 | (define-public r-wgcna |
8789 | (package | |
8790 | (name "r-wgcna") | |
ac016645 | 8791 | (version "1.66") |
d7160529 RW |
8792 | (source |
8793 | (origin | |
8794 | (method url-fetch) | |
8795 | (uri (cran-uri "WGCNA" version)) | |
8796 | (sha256 | |
8797 | (base32 | |
ac016645 | 8798 | "0rhnyhzfn93yp24jz9v6dzrmyizwzdw070a7idm0k33w1cm8sjqv")))) |
d7160529 RW |
8799 | (properties `((upstream-name . "WGCNA"))) |
8800 | (build-system r-build-system) | |
8801 | (propagated-inputs | |
8802 | `(("r-annotationdbi" ,r-annotationdbi) | |
8803 | ("r-doparallel" ,r-doparallel) | |
8804 | ("r-dynamictreecut" ,r-dynamictreecut) | |
8805 | ("r-fastcluster" ,r-fastcluster) | |
8806 | ("r-foreach" ,r-foreach) | |
8807 | ("r-go-db" ,r-go-db) | |
8808 | ("r-hmisc" ,r-hmisc) | |
8809 | ("r-impute" ,r-impute) | |
1b22ecda RW |
8810 | ("r-rcpp" ,r-rcpp) |
8811 | ("r-robust" ,r-robust) | |
8812 | ("r-survival" ,r-survival) | |
d7160529 RW |
8813 | ("r-matrixstats" ,r-matrixstats) |
8814 | ("r-preprocesscore" ,r-preprocesscore))) | |
8815 | (home-page | |
8816 | "http://www.genetics.ucla.edu/labs/horvath/CoexpressionNetwork/Rpackages/WGCNA/") | |
8817 | (synopsis "Weighted correlation network analysis") | |
8818 | (description | |
8819 | "This package provides functions necessary to perform Weighted | |
8820 | Correlation Network Analysis on high-dimensional data. It includes functions | |
8821 | for rudimentary data cleaning, construction and summarization of correlation | |
8822 | networks, module identification and functions for relating both variables and | |
8823 | modules to sample traits. It also includes a number of utility functions for | |
8824 | data manipulation and visualization.") | |
8825 | (license license:gpl2+))) | |
8826 | ||
c827f202 RW |
8827 | (define-public r-chipkernels |
8828 | (let ((commit "c9cfcacb626b1221094fb3490ea7bac0fd625372") | |
8829 | (revision "1")) | |
8830 | (package | |
8831 | (name "r-chipkernels") | |
8832 | (version (string-append "1.1-" revision "." (string-take commit 9))) | |
8833 | (source | |
8834 | (origin | |
8835 | (method git-fetch) | |
8836 | (uri (git-reference | |
8837 | (url "https://github.com/ManuSetty/ChIPKernels.git") | |
8838 | (commit commit))) | |
8839 | (file-name (string-append name "-" version)) | |
8840 | (sha256 | |
8841 | (base32 | |
8842 | "14bj5qhjm1hsm9ay561nfbqi9wxsa7y487df2idsaaf6z10nw4v0")))) | |
8843 | (build-system r-build-system) | |
8844 | (propagated-inputs | |
8845 | `(("r-iranges" ,r-iranges) | |
8846 | ("r-xvector" ,r-xvector) | |
8847 | ("r-biostrings" ,r-biostrings) | |
8848 | ("r-bsgenome" ,r-bsgenome) | |
8849 | ("r-gtools" ,r-gtools) | |
8850 | ("r-genomicranges" ,r-genomicranges) | |
8851 | ("r-sfsmisc" ,r-sfsmisc) | |
8852 | ("r-kernlab" ,r-kernlab) | |
8853 | ("r-s4vectors" ,r-s4vectors) | |
8854 | ("r-biocgenerics" ,r-biocgenerics))) | |
8855 | (home-page "https://github.com/ManuSetty/ChIPKernels") | |
8856 | (synopsis "Build string kernels for DNA Sequence analysis") | |
8857 | (description "ChIPKernels is an R package for building different string | |
8858 | kernels used for DNA Sequence analysis. A dictionary of the desired kernel | |
8859 | must be built and this dictionary can be used for determining kernels for DNA | |
8860 | Sequences.") | |
8861 | (license license:gpl2+)))) | |
8862 | ||
2d9fb170 RW |
8863 | (define-public r-seqgl |
8864 | (package | |
8865 | (name "r-seqgl") | |
8866 | (version "1.1.4") | |
8867 | (source | |
8868 | (origin | |
1a20bcad RW |
8869 | (method git-fetch) |
8870 | (uri (git-reference | |
8871 | (url "https://github.com/ManuSetty/SeqGL.git") | |
8872 | (commit version))) | |
8873 | (file-name (git-file-name name version)) | |
2d9fb170 RW |
8874 | (sha256 |
8875 | (base32 | |
1a20bcad | 8876 | "1r6ywvhxl3ffv48lgj7sbd582mcc6dha3ksgc2qjlvjrnkbj3799")))) |
2d9fb170 RW |
8877 | (build-system r-build-system) |
8878 | (propagated-inputs | |
8879 | `(("r-biostrings" ,r-biostrings) | |
8880 | ("r-chipkernels" ,r-chipkernels) | |
8881 | ("r-genomicranges" ,r-genomicranges) | |
8882 | ("r-spams" ,r-spams) | |
8883 | ("r-wgcna" ,r-wgcna) | |
8884 | ("r-fastcluster" ,r-fastcluster))) | |
8885 | (home-page "https://github.com/ManuSetty/SeqGL") | |
8886 | (synopsis "Group lasso for Dnase/ChIP-seq data") | |
8887 | (description "SeqGL is a group lasso based algorithm to extract | |
8888 | transcription factor sequence signals from ChIP, DNase and ATAC-seq profiles. | |
8889 | This package presents a method which uses group lasso to discriminate between | |
8890 | bound and non bound genomic regions to accurately identify transcription | |
8891 | factors bound at the specific regions.") | |
8892 | (license license:gpl2+))) | |
8893 | ||
bd3be46e RW |
8894 | (define-public r-gkmsvm |
8895 | (package | |
8896 | (name "r-gkmsvm") | |
5ef76bc2 | 8897 | (version "0.79.0") |
bd3be46e RW |
8898 | (source |
8899 | (origin | |
8900 | (method url-fetch) | |
8901 | (uri (cran-uri "gkmSVM" version)) | |
8902 | (sha256 | |
8903 | (base32 | |
5ef76bc2 | 8904 | "04dakbgfvfalz4rm4fvvybp506dn5fbj5g86ybfhrc6wywjllsz3")))) |
bd3be46e RW |
8905 | (properties `((upstream-name . "gkmSVM"))) |
8906 | (build-system r-build-system) | |
8907 | (propagated-inputs | |
8908 | `(("r-biocgenerics" ,r-biocgenerics) | |
8909 | ("r-biostrings" ,r-biostrings) | |
8910 | ("r-genomeinfodb" ,r-genomeinfodb) | |
8911 | ("r-genomicranges" ,r-genomicranges) | |
8912 | ("r-iranges" ,r-iranges) | |
8913 | ("r-kernlab" ,r-kernlab) | |
8914 | ("r-rcpp" ,r-rcpp) | |
8915 | ("r-rocr" ,r-rocr) | |
8916 | ("r-rtracklayer" ,r-rtracklayer) | |
8917 | ("r-s4vectors" ,r-s4vectors) | |
8918 | ("r-seqinr" ,r-seqinr))) | |
e9960d8c | 8919 | (home-page "https://cran.r-project.org/web/packages/gkmSVM") |
bd3be46e RW |
8920 | (synopsis "Gapped-kmer support vector machine") |
8921 | (description | |
8922 | "This R package provides tools for training gapped-kmer SVM classifiers | |
8923 | for DNA and protein sequences. This package supports several sequence | |
8924 | kernels, including: gkmSVM, kmer-SVM, mismatch kernel and wildcard kernel.") | |
8925 | (license license:gpl2+))) | |
8926 | ||
d4af25b5 RJPB |
8927 | (define-public r-tximport |
8928 | (package | |
8929 | (name "r-tximport") | |
d2b60be5 | 8930 | (version "1.10.0") |
d4af25b5 RJPB |
8931 | (source (origin |
8932 | (method url-fetch) | |
8933 | (uri (bioconductor-uri "tximport" version)) | |
8934 | (sha256 | |
8935 | (base32 | |
d2b60be5 | 8936 | "0za2js8hqjgz8ria09cglynffj4w9vrzg85nmn1xgpvmc1xk813h")))) |
d4af25b5 | 8937 | (build-system r-build-system) |
5713bbf1 | 8938 | (home-page "https://bioconductor.org/packages/tximport") |
d4af25b5 RJPB |
8939 | (synopsis "Import and summarize transcript-level estimates for gene-level analysis") |
8940 | (description | |
8941 | "This package provides tools to import transcript-level abundance, | |
8942 | estimated counts and transcript lengths, and to summarize them into matrices | |
8943 | for use with downstream gene-level analysis packages. Average transcript | |
8944 | length, weighted by sample-specific transcript abundance estimates, is | |
8945 | provided as a matrix which can be used as an offset for different expression | |
8946 | of gene-level counts.") | |
8947 | (license license:gpl2+))) | |
8948 | ||
69f2b3bd RJPB |
8949 | (define-public r-rhdf5 |
8950 | (package | |
8951 | (name "r-rhdf5") | |
611a255d | 8952 | (version "2.26.0") |
69f2b3bd RJPB |
8953 | (source (origin |
8954 | (method url-fetch) | |
8955 | (uri (bioconductor-uri "rhdf5" version)) | |
8956 | (sha256 | |
8957 | (base32 | |
611a255d | 8958 | "0xmpkfdsmgl79ffffj7cf9fx3zxki2rk0xn25k778kr3s0sbmhis")))) |
69f2b3bd | 8959 | (build-system r-build-system) |
69f2b3bd | 8960 | (propagated-inputs |
d73c5728 | 8961 | `(("r-rhdf5lib" ,r-rhdf5lib))) |
69f2b3bd | 8962 | (inputs |
d73c5728 | 8963 | `(("zlib" ,zlib))) |
5713bbf1 | 8964 | (home-page "https://bioconductor.org/packages/rhdf5") |
69f2b3bd RJPB |
8965 | (synopsis "HDF5 interface to R") |
8966 | (description | |
8967 | "This R/Bioconductor package provides an interface between HDF5 and R. | |
8968 | HDF5's main features are the ability to store and access very large and/or | |
8969 | complex datasets and a wide variety of metadata on mass storage (disk) through | |
8970 | a completely portable file format. The rhdf5 package is thus suited for the | |
8971 | exchange of large and/or complex datasets between R and other software | |
8972 | package, and for letting R applications work on datasets that are larger than | |
8973 | the available RAM.") | |
8974 | (license license:artistic2.0))) | |
8975 | ||
17cddc17 RW |
8976 | (define-public r-annotationfilter |
8977 | (package | |
8978 | (name "r-annotationfilter") | |
cec8f092 | 8979 | (version "1.6.0") |
17cddc17 RW |
8980 | (source (origin |
8981 | (method url-fetch) | |
8982 | (uri (bioconductor-uri "AnnotationFilter" version)) | |
8983 | (sha256 | |
8984 | (base32 | |
cec8f092 | 8985 | "0wrr10cxjzmxx46vjzq2nsf6xlqz1sqwx4xm0sk3d77ff8wmph4x")))) |
17cddc17 RW |
8986 | (properties |
8987 | `((upstream-name . "AnnotationFilter"))) | |
8988 | (build-system r-build-system) | |
8989 | (propagated-inputs | |
8990 | `(("r-genomicranges" ,r-genomicranges) | |
8991 | ("r-lazyeval" ,r-lazyeval))) | |
8992 | (home-page "https://github.com/Bioconductor/AnnotationFilter") | |
8993 | (synopsis "Facilities for filtering Bioconductor annotation resources") | |
8994 | (description | |
8995 | "This package provides classes and other infrastructure to implement | |
8996 | filters for manipulating Bioconductor annotation resources. The filters are | |
8997 | used by @code{ensembldb}, @code{Organism.dplyr}, and other packages.") | |
8998 | (license license:artistic2.0))) | |
8999 | ||
66e40e00 RW |
9000 | (define-public emboss |
9001 | (package | |
9002 | (name "emboss") | |
9003 | (version "6.5.7") | |
9004 | (source (origin | |
9005 | (method url-fetch) | |
9006 | (uri (string-append "ftp://emboss.open-bio.org/pub/EMBOSS/old/" | |
9007 | (version-major+minor version) ".0/" | |
9008 | "EMBOSS-" version ".tar.gz")) | |
9009 | (sha256 | |
9010 | (base32 | |
9011 | "0vsmz96gc411yj2iyzdrsmg4l2n1nhgmp7vrgzlxx3xixv9xbf0q")))) | |
9012 | (build-system gnu-build-system) | |
9013 | (arguments | |
9014 | `(#:configure-flags | |
9015 | (list (string-append "--with-hpdf=" | |
9016 | (assoc-ref %build-inputs "libharu"))) | |
9017 | #:phases | |
9018 | (modify-phases %standard-phases | |
9019 | (add-after 'unpack 'fix-checks | |
9020 | (lambda _ | |
9021 | ;; The PNGDRIVER tests check for the presence of libgd, libpng | |
9022 | ;; and zlib, but assume that they are all found at the same | |
9023 | ;; prefix. | |
9024 | (substitute* "configure.in" | |
9025 | (("CHECK_PNGDRIVER") | |
9026 | "LIBS=\"$LIBS -lgd -lpng -lz -lm\" | |
9027 | AC_DEFINE([PLD_png], [1], [Define to 1 if PNG support is available]) | |
9028 | AM_CONDITIONAL(AMPNG, true)")) | |
9029 | #t)) | |
d10092b8 | 9030 | (add-after 'fix-checks 'disable-update-check |
66e40e00 RW |
9031 | (lambda _ |
9032 | ;; At build time there is no connection to the Internet, so | |
9033 | ;; looking for updates will not work. | |
9034 | (substitute* "Makefile.am" | |
9035 | (("\\$\\(bindir\\)/embossupdate") "")) | |
9036 | #t)) | |
d10092b8 | 9037 | (add-after 'disable-update-check 'autogen |
e78e54d0 | 9038 | (lambda _ (invoke "autoreconf" "-vif") #t))))) |
66e40e00 RW |
9039 | (inputs |
9040 | `(("perl" ,perl) | |
9041 | ("libpng" ,libpng) | |
9042 | ("gd" ,gd) | |
9043 | ("libx11" ,libx11) | |
9044 | ("libharu" ,libharu) | |
9045 | ("zlib" ,zlib))) | |
9046 | (native-inputs | |
9047 | `(("autoconf" ,autoconf) | |
9048 | ("automake" ,automake) | |
9049 | ("libtool" ,libtool) | |
9050 | ("pkg-config" ,pkg-config))) | |
9051 | (home-page "http://emboss.sourceforge.net") | |
9052 | (synopsis "Molecular biology analysis suite") | |
9053 | (description "EMBOSS is the \"European Molecular Biology Open Software | |
9054 | Suite\". EMBOSS is an analysis package specially developed for the needs of | |
9055 | the molecular biology (e.g. EMBnet) user community. The software | |
9056 | automatically copes with data in a variety of formats and even allows | |
9057 | transparent retrieval of sequence data from the web. It also provides a | |
9058 | number of libraries for the development of software in the field of molecular | |
9059 | biology. EMBOSS also integrates a range of currently available packages and | |
9060 | tools for sequence analysis into a seamless whole.") | |
9061 | (license license:gpl2+))) | |
9062 | ||
1f1b20b8 RW |
9063 | (define-public bits |
9064 | (let ((revision "1") | |
9065 | (commit "3cc4567896d9d6442923da944beb704750a08d2d")) | |
9066 | (package | |
9067 | (name "bits") | |
9068 | ;; The version is 2.13.0 even though no release archives have been | |
9069 | ;; published as yet. | |
9070 | (version (string-append "2.13.0-" revision "." (string-take commit 9))) | |
9071 | (source (origin | |
9072 | (method git-fetch) | |
9073 | (uri (git-reference | |
9074 | (url "https://github.com/arq5x/bits.git") | |
9075 | (commit commit))) | |
9076 | (file-name (string-append name "-" version "-checkout")) | |
9077 | (sha256 | |
9078 | (base32 | |
9079 | "17n2kffk4kmhivd8c98g2vr6y1s23vbg4sxlxs689wni66797hbs")))) | |
9080 | (build-system gnu-build-system) | |
9081 | (arguments | |
9082 | `(#:tests? #f ;no tests included | |
9083 | #:phases | |
9084 | (modify-phases %standard-phases | |
9085 | (delete 'configure) | |
9086 | (add-after 'unpack 'remove-cuda | |
9087 | (lambda _ | |
9088 | (substitute* "Makefile" | |
9089 | ((".*_cuda") "") | |
9090 | (("(bits_test_intersections) \\\\" _ match) match)) | |
9091 | #t)) | |
9092 | (replace 'install | |
9093 | (lambda* (#:key outputs #:allow-other-keys) | |
9094 | (copy-recursively | |
9095 | "bin" (string-append (assoc-ref outputs "out") "/bin")) | |
9096 | #t))))) | |
9097 | (inputs | |
9098 | `(("gsl" ,gsl) | |
9099 | ("zlib" ,zlib))) | |
9100 | (home-page "https://github.com/arq5x/bits") | |
9101 | (synopsis "Implementation of binary interval search algorithm") | |
9102 | (description "This package provides an implementation of the | |
9103 | BITS (Binary Interval Search) algorithm, an approach to interval set | |
9104 | intersection. It is especially suited for the comparison of diverse genomic | |
9105 | datasets and the exploration of large datasets of genome | |
9106 | intervals (e.g. genes, sequence alignments).") | |
9107 | (license license:gpl2)))) | |
9108 | ||
e62ffce5 | 9109 | (define-public piranha |
883302da RW |
9110 | ;; There is no release tarball for the latest version. The latest commit is |
9111 | ;; older than one year at the time of this writing. | |
9112 | (let ((revision "1") | |
9113 | (commit "0466d364b71117d01e4471b74c514436cc281233")) | |
9114 | (package | |
9115 | (name "piranha") | |
9116 | (version (string-append "1.2.1-" revision "." (string-take commit 9))) | |
9117 | (source (origin | |
9118 | (method git-fetch) | |
9119 | (uri (git-reference | |
9120 | (url "https://github.com/smithlabcode/piranha.git") | |
9121 | (commit commit))) | |
da49d137 | 9122 | (file-name (git-file-name name version)) |
883302da RW |
9123 | (sha256 |
9124 | (base32 | |
9125 | "117dc0zf20c61jam69sk4abl57ah6yi6i7qra7d7y5zrbgk12q5n")))) | |
9126 | (build-system gnu-build-system) | |
9127 | (arguments | |
9128 | `(#:test-target "test" | |
9129 | #:phases | |
9130 | (modify-phases %standard-phases | |
9131 | (add-after 'unpack 'copy-smithlab-cpp | |
9132 | (lambda* (#:key inputs #:allow-other-keys) | |
e62ffce5 | 9133 | (for-each (lambda (file) |
883302da RW |
9134 | (install-file file "./src/smithlab_cpp/")) |
9135 | (find-files (assoc-ref inputs "smithlab-cpp"))) | |
9136 | #t)) | |
9137 | (add-after 'install 'install-to-store | |
9138 | (lambda* (#:key outputs #:allow-other-keys) | |
9139 | (let* ((out (assoc-ref outputs "out")) | |
9140 | (bin (string-append out "/bin"))) | |
883302da RW |
9141 | (for-each (lambda (file) |
9142 | (install-file file bin)) | |
9143 | (find-files "bin" ".*"))) | |
9144 | #t))) | |
9145 | #:configure-flags | |
9146 | (list (string-append "--with-bam_tools_headers=" | |
9147 | (assoc-ref %build-inputs "bamtools") "/include/bamtools") | |
9148 | (string-append "--with-bam_tools_library=" | |
9149 | (assoc-ref %build-inputs "bamtools") "/lib/bamtools")))) | |
9150 | (inputs | |
9151 | `(("bamtools" ,bamtools) | |
9152 | ("samtools" ,samtools-0.1) | |
9153 | ("gsl" ,gsl) | |
9154 | ("smithlab-cpp" | |
9155 | ,(let ((commit "3723e2db438c51501d0423429ff396c3035ba46a")) | |
9156 | (origin | |
9157 | (method git-fetch) | |
9158 | (uri (git-reference | |
9159 | (url "https://github.com/smithlabcode/smithlab_cpp.git") | |
9160 | (commit commit))) | |
9161 | (file-name (string-append "smithlab_cpp-" commit "-checkout")) | |
9162 | (sha256 | |
9163 | (base32 | |
9164 | "0l4gvbwslw5ngziskja41c00x1r06l3yidv7y0xw9djibhykzy0g"))))))) | |
9165 | (native-inputs | |
9166 | `(("python" ,python-2))) | |
9167 | (home-page "https://github.com/smithlabcode/piranha") | |
9168 | (synopsis "Peak-caller for CLIP-seq and RIP-seq data") | |
9169 | (description | |
9170 | "Piranha is a peak-caller for genomic data produced by CLIP-seq and | |
e62ffce5 RW |
9171 | RIP-seq experiments. It takes input in BED or BAM format and identifies |
9172 | regions of statistically significant read enrichment. Additional covariates | |
9173 | may optionally be provided to further inform the peak-calling process.") | |
883302da | 9174 | (license license:gpl3+)))) |
e62ffce5 | 9175 | |
d1e32822 RW |
9176 | (define-public pepr |
9177 | (package | |
9178 | (name "pepr") | |
9179 | (version "1.0.9") | |
9180 | (source (origin | |
9181 | (method url-fetch) | |
9182 | (uri (string-append "https://pypi.python.org/packages/source/P" | |
9183 | "/PePr/PePr-" version ".tar.gz")) | |
9184 | (sha256 | |
9185 | (base32 | |
9186 | "0qxjfdpl1b1y53nccws2d85f6k74zwmx8y8sd9rszcqhfayx6gdx")))) | |
9187 | (build-system python-build-system) | |
9188 | (arguments | |
9189 | `(#:python ,python-2 ; python2 only | |
b41a05ce | 9190 | #:tests? #f)) ; no tests included |
d1e32822 RW |
9191 | (propagated-inputs |
9192 | `(("python2-numpy" ,python2-numpy) | |
9193 | ("python2-scipy" ,python2-scipy) | |
9194 | ("python2-pysam" ,python2-pysam))) | |
0c6c9c00 | 9195 | (home-page "https://github.com/shawnzhangyx/PePr") |
d1e32822 RW |
9196 | (synopsis "Peak-calling and prioritization pipeline for ChIP-Seq data") |
9197 | (description | |
9198 | "PePr is a ChIP-Seq peak calling or differential binding analysis tool | |
9199 | that is primarily designed for data with biological replicates. It uses a | |
9200 | negative binomial distribution to model the read counts among the samples in | |
9201 | the same group, and look for consistent differences between ChIP and control | |
9202 | group or two ChIP groups run under different conditions.") | |
9203 | (license license:gpl3+))) | |
6b49a37e RJ |
9204 | |
9205 | (define-public filevercmp | |
9206 | (let ((commit "1a9b779b93d0b244040274794d402106907b71b7")) | |
9207 | (package | |
9208 | (name "filevercmp") | |
9209 | (version (string-append "0-1." (string-take commit 7))) | |
9210 | (source (origin | |
f3f34b13 RW |
9211 | (method git-fetch) |
9212 | (uri (git-reference | |
9213 | (url "https://github.com/ekg/filevercmp.git") | |
9214 | (commit commit))) | |
9215 | (file-name (git-file-name name commit)) | |
9216 | (sha256 | |
9217 | (base32 | |
9218 | "1j9vxsy0y050v59h0q1d6501fcw1kjvj0d18l1xk2zyg0jzj247c")))) | |
6b49a37e RJ |
9219 | (build-system gnu-build-system) |
9220 | (arguments | |
9221 | `(#:tests? #f ; There are no tests to run. | |
9222 | #:phases | |
9223 | (modify-phases %standard-phases | |
9224 | (delete 'configure) ; There is no configure phase. | |
9225 | (replace 'install | |
9226 | (lambda* (#:key outputs #:allow-other-keys) | |
9227 | (let ((bin (string-append (assoc-ref outputs "out") "/bin"))) | |
f3f34b13 RW |
9228 | (install-file "filevercmp" bin) |
9229 | #t)))))) | |
6b49a37e RJ |
9230 | (home-page "https://github.com/ekg/filevercmp") |
9231 | (synopsis "This program compares version strings") | |
9232 | (description "This program compares version strings. It intends to be a | |
9233 | replacement for strverscmp.") | |
9234 | (license license:gpl3+)))) | |
5fb5dffb RW |
9235 | |
9236 | (define-public multiqc | |
9237 | (package | |
9238 | (name "multiqc") | |
457fd268 | 9239 | (version "1.5") |
5fb5dffb RW |
9240 | (source |
9241 | (origin | |
9242 | (method url-fetch) | |
9243 | (uri (pypi-uri "multiqc" version)) | |
9244 | (sha256 | |
9245 | (base32 | |
457fd268 | 9246 | "02iihfl0w0hpnr4pa0sbd1y9qxrg3ycyhjp5lidkcrqh1lmzs3zy")))) |
5fb5dffb RW |
9247 | (build-system python-build-system) |
9248 | (propagated-inputs | |
9e94d063 | 9249 | `(("python-jinja2" ,python-jinja2) |
5fb5dffb RW |
9250 | ("python-simplejson" ,python-simplejson) |
9251 | ("python-pyyaml" ,python-pyyaml) | |
9252 | ("python-click" ,python-click) | |
799247d2 RW |
9253 | ("python-spectra" ,python-spectra) |
9254 | ("python-requests" ,python-requests) | |
9255 | ("python-markdown" ,python-markdown) | |
9256 | ("python-lzstring" ,python-lzstring) | |
5fb5dffb | 9257 | ("python-matplotlib" ,python-matplotlib) |
1778ea74 RW |
9258 | ("python-numpy" ,python-numpy) |
9259 | ;; MultQC checks for the presence of nose at runtime. | |
9260 | ("python-nose" ,python-nose))) | |
4ca95811 TGR |
9261 | (arguments |
9262 | `(#:phases | |
9263 | (modify-phases %standard-phases | |
9264 | (add-after 'unpack 'relax-requirements | |
9265 | (lambda _ | |
9266 | (substitute* "setup.py" | |
9267 | ;; MultiQC 1.5 ‘requires’ a version of python-matplotlib older | |
9268 | ;; than the one in Guix, but should work fine with 2.2.2. | |
9269 | ;; See <https://github.com/ewels/MultiQC/issues/725> and | |
9270 | ;; <https://github.com/ewels/MultiQC/issues/732> for details. | |
9271 | (("['\"]matplotlib.*?['\"]") | |
9272 | "'matplotlib'")) | |
9273 | #t))))) | |
5fb5dffb RW |
9274 | (home-page "http://multiqc.info") |
9275 | (synopsis "Aggregate bioinformatics analysis reports") | |
9276 | (description | |
9277 | "MultiQC is a tool to aggregate bioinformatics results across many | |
9278 | samples into a single report. It contains modules for a large number of | |
9279 | common bioinformatics tools.") | |
66865ab8 | 9280 | (license license:gpl3+))) |
6193563a RW |
9281 | |
9282 | (define-public r-chipseq | |
9283 | (package | |
9284 | (name "r-chipseq") | |
2e9d8116 | 9285 | (version "1.32.0") |
6193563a RW |
9286 | (source |
9287 | (origin | |
9288 | (method url-fetch) | |
9289 | (uri (bioconductor-uri "chipseq" version)) | |
9290 | (sha256 | |
9291 | (base32 | |
2e9d8116 | 9292 | "1pp1rm5fs3hlar5x4dl3a3b4gara7qwf81dbvka6r1n78hrf9x1b")))) |
6193563a RW |
9293 | (build-system r-build-system) |
9294 | (propagated-inputs | |
9295 | `(("r-biocgenerics" ,r-biocgenerics) | |
9296 | ("r-genomicranges" ,r-genomicranges) | |
9297 | ("r-iranges" ,r-iranges) | |
eeaa6967 | 9298 | ("r-lattice" ,r-lattice) |
6193563a RW |
9299 | ("r-s4vectors" ,r-s4vectors) |
9300 | ("r-shortread" ,r-shortread))) | |
5713bbf1 | 9301 | (home-page "https://bioconductor.org/packages/chipseq") |
6193563a RW |
9302 | (synopsis "Package for analyzing ChIPseq data") |
9303 | (description | |
9304 | "This package provides tools for processing short read data from ChIPseq | |
9305 | experiments.") | |
9306 | (license license:artistic2.0))) | |
d407bdb9 RW |
9307 | |
9308 | (define-public r-copyhelper | |
9309 | (package | |
9310 | (name "r-copyhelper") | |
9311 | (version "1.6.0") | |
9312 | (source | |
9313 | (origin | |
9314 | (method url-fetch) | |
5713bbf1 | 9315 | (uri (string-append "https://bioconductor.org/packages/release/" |
d407bdb9 RW |
9316 | "data/experiment/src/contrib/CopyhelpeR_" |
9317 | version ".tar.gz")) | |
9318 | (sha256 | |
9319 | (base32 | |
9320 | "0x7cyynjmxls9as2gg0iyp9x5fpalxmdjq914ss7i84i9zyk5bhq")))) | |
9321 | (properties `((upstream-name . "CopyhelpeR"))) | |
9322 | (build-system r-build-system) | |
5713bbf1 | 9323 | (home-page "https://bioconductor.org/packages/CopyhelpeR/") |
d407bdb9 RW |
9324 | (synopsis "Helper files for CopywriteR") |
9325 | (description | |
9326 | "This package contains the helper files that are required to run the | |
9327 | Bioconductor package CopywriteR. It contains pre-assembled 1kb bin GC-content | |
9328 | and mappability files for the reference genomes hg18, hg19, hg38, mm9 and | |
9329 | mm10. In addition, it contains a blacklist filter to remove regions that | |
9330 | display copy number variation. Files are stored as GRanges objects from the | |
9331 | GenomicRanges Bioconductor package.") | |
9332 | (license license:gpl2))) | |
3a3bf2f8 RW |
9333 | |
9334 | (define-public r-copywriter | |
9335 | (package | |
9336 | (name "r-copywriter") | |
739a856d | 9337 | (version "2.14.0") |
3a3bf2f8 RW |
9338 | (source |
9339 | (origin | |
9340 | (method url-fetch) | |
9341 | (uri (bioconductor-uri "CopywriteR" version)) | |
9342 | (sha256 | |
9343 | (base32 | |
739a856d | 9344 | "0aamxafdk98n7s92jyqs65d6ljpnc2463vanvsw80p44qn6l6awn")))) |
3a3bf2f8 RW |
9345 | (properties `((upstream-name . "CopywriteR"))) |
9346 | (build-system r-build-system) | |
9347 | (propagated-inputs | |
9348 | `(("r-biocparallel" ,r-biocparallel) | |
9349 | ("r-chipseq" ,r-chipseq) | |
9350 | ("r-copyhelper" ,r-copyhelper) | |
9351 | ("r-data-table" ,r-data-table) | |
9352 | ("r-dnacopy" ,r-dnacopy) | |
9353 | ("r-futile-logger" ,r-futile-logger) | |
9354 | ("r-genomeinfodb" ,r-genomeinfodb) | |
9355 | ("r-genomicalignments" ,r-genomicalignments) | |
9356 | ("r-genomicranges" ,r-genomicranges) | |
9357 | ("r-gtools" ,r-gtools) | |
9358 | ("r-iranges" ,r-iranges) | |
9359 | ("r-matrixstats" ,r-matrixstats) | |
9360 | ("r-rsamtools" ,r-rsamtools) | |
9361 | ("r-s4vectors" ,r-s4vectors))) | |
9362 | (home-page "https://github.com/PeeperLab/CopywriteR") | |
9363 | (synopsis "Copy number information from targeted sequencing") | |
9364 | (description | |
9365 | "CopywriteR extracts DNA copy number information from targeted sequencing | |
9366 | by utilizing off-target reads. It allows for extracting uniformly distributed | |
9367 | copy number information, can be used without reference, and can be applied to | |
9368 | sequencing data obtained from various techniques including chromatin | |
9369 | immunoprecipitation and target enrichment on small gene panels. Thereby, | |
9370 | CopywriteR constitutes a widely applicable alternative to available copy | |
9371 | number detection tools.") | |
9372 | (license license:gpl2))) | |
dd42a330 | 9373 | |
bf3fa996 RW |
9374 | (define-public r-methylkit |
9375 | (package | |
9376 | (name "r-methylkit") | |
18604a76 | 9377 | (version "1.8.0") |
bf3fa996 RW |
9378 | (source (origin |
9379 | (method url-fetch) | |
9380 | (uri (bioconductor-uri "methylKit" version)) | |
9381 | (sha256 | |
9382 | (base32 | |
18604a76 | 9383 | "0mz6lil1wax931incnw5byx0v9i8ryhwq9mv0nv8s48ai33ch3x6")))) |
bf3fa996 RW |
9384 | (properties `((upstream-name . "methylKit"))) |
9385 | (build-system r-build-system) | |
9386 | (propagated-inputs | |
9387 | `(("r-data-table" ,r-data-table) | |
9388 | ("r-emdbook" ,r-emdbook) | |
9389 | ("r-fastseg" ,r-fastseg) | |
9390 | ("r-genomeinfodb" ,r-genomeinfodb) | |
9391 | ("r-genomicranges" ,r-genomicranges) | |
9392 | ("r-gtools" ,r-gtools) | |
9393 | ("r-iranges" ,r-iranges) | |
9394 | ("r-kernsmooth" ,r-kernsmooth) | |
9395 | ("r-limma" ,r-limma) | |
9396 | ("r-mclust" ,r-mclust) | |
9397 | ("r-qvalue" ,r-qvalue) | |
9398 | ("r-r-utils" ,r-r-utils) | |
9399 | ("r-rcpp" ,r-rcpp) | |
9400 | ("r-rhtslib" ,r-rhtslib) | |
9401 | ("r-rsamtools" ,r-rsamtools) | |
9402 | ("r-rtracklayer" ,r-rtracklayer) | |
9403 | ("r-s4vectors" ,r-s4vectors) | |
9404 | ("r-zlibbioc" ,r-zlibbioc))) | |
9405 | (inputs | |
9406 | `(("zlib" ,zlib))) | |
11ed4108 | 9407 | (home-page "https://github.com/al2na/methylKit") |
bf3fa996 RW |
9408 | (synopsis |
9409 | "DNA methylation analysis from high-throughput bisulfite sequencing results") | |
9410 | (description | |
9411 | "MethylKit is an R package for DNA methylation analysis and annotation | |
9412 | from high-throughput bisulfite sequencing. The package is designed to deal | |
9413 | with sequencing data from @dfn{Reduced representation bisulfite | |
9414 | sequencing} (RRBS) and its variants, but also target-capture methods and whole | |
9415 | genome bisulfite sequencing. It also has functions to analyze base-pair | |
9416 | resolution 5hmC data from experimental protocols such as oxBS-Seq and | |
9417 | TAB-Seq.") | |
9418 | (license license:artistic2.0))) | |
9419 | ||
dd42a330 RJPB |
9420 | (define-public r-sva |
9421 | (package | |
9422 | (name "r-sva") | |
8af86883 | 9423 | (version "3.30.0") |
dd42a330 RJPB |
9424 | (source |
9425 | (origin | |
9426 | (method url-fetch) | |
9427 | (uri (bioconductor-uri "sva" version)) | |
9428 | (sha256 | |
9429 | (base32 | |
8af86883 | 9430 | "1xf0hlrqjxl0y3x13mrkxghiv39fd9v2g8gq3qzbf1wj7il6bph3")))) |
dd42a330 RJPB |
9431 | (build-system r-build-system) |
9432 | (propagated-inputs | |
aeb64f3c | 9433 | `(("r-genefilter" ,r-genefilter) |
bfa0d1e7 RJ |
9434 | ("r-mgcv" ,r-mgcv) |
9435 | ("r-biocparallel" ,r-biocparallel) | |
9436 | ("r-matrixstats" ,r-matrixstats) | |
9437 | ("r-limma" ,r-limma))) | |
5713bbf1 | 9438 | (home-page "https://bioconductor.org/packages/sva") |
dd42a330 RJPB |
9439 | (synopsis "Surrogate variable analysis") |
9440 | (description | |
9441 | "This package contains functions for removing batch effects and other | |
9442 | unwanted variation in high-throughput experiment. It also contains functions | |
9443 | for identifying and building surrogate variables for high-dimensional data | |
9444 | sets. Surrogate variables are covariates constructed directly from | |
9445 | high-dimensional data like gene expression/RNA sequencing/methylation/brain | |
9446 | imaging data that can be used in subsequent analyses to adjust for unknown, | |
9447 | unmodeled, or latent sources of noise.") | |
9448 | (license license:artistic2.0))) | |
fb1e528e RW |
9449 | |
9450 | (define-public r-seqminer | |
9451 | (package | |
9452 | (name "r-seqminer") | |
48b21f8b | 9453 | (version "6.1") |
fb1e528e RW |
9454 | (source |
9455 | (origin | |
9456 | (method url-fetch) | |
9457 | (uri (cran-uri "seqminer" version)) | |
9458 | (sha256 | |
9459 | (base32 | |
48b21f8b | 9460 | "15yhg4vfc7jg1jnqb3371j00pgbmbyc9l1xx63hq1l3p34lazq2l")))) |
fb1e528e RW |
9461 | (build-system r-build-system) |
9462 | (inputs | |
9463 | `(("zlib" ,zlib))) | |
9464 | (home-page "http://seqminer.genomic.codes") | |
9465 | (synopsis "Read nucleotide sequence data (VCF, BCF, and METAL formats)") | |
9466 | (description | |
9467 | "This package provides tools to integrate nucleotide sequencing | |
9468 | data (variant call format, e.g. VCF or BCF) or meta-analysis results in R.") | |
9469 | ;; Any version of the GPL is acceptable | |
9470 | (license (list license:gpl2+ license:gpl3+)))) | |
1f40e73c RW |
9471 | |
9472 | (define-public r-raremetals2 | |
9473 | (package | |
9474 | (name "r-raremetals2") | |
9475 | (version "0.1") | |
9476 | (source | |
9477 | (origin | |
9478 | (method url-fetch) | |
9479 | (uri (string-append "http://genome.sph.umich.edu/w/images/" | |
9480 | "b/b7/RareMETALS2_" version ".tar.gz")) | |
9481 | (sha256 | |
9482 | (base32 | |
9483 | "0z5ljcgvnm06ja9lm85a3cniq7slxcy37aqqkxrdidr79an5fs4s")))) | |
9484 | (properties `((upstream-name . "RareMETALS2"))) | |
9485 | (build-system r-build-system) | |
9486 | (propagated-inputs | |
9487 | `(("r-seqminer" ,r-seqminer) | |
9488 | ("r-mvtnorm" ,r-mvtnorm) | |
aeb64f3c | 9489 | ("r-mass" ,r-mass) |
1f40e73c RW |
9490 | ("r-compquadform" ,r-compquadform) |
9491 | ("r-getopt" ,r-getopt))) | |
9492 | (home-page "http://genome.sph.umich.edu/wiki/RareMETALS2") | |
9493 | (synopsis "Analyze gene-level association tests for binary trait") | |
9494 | (description | |
9495 | "The R package rareMETALS2 is an extension of the R package rareMETALS. | |
9496 | It was designed to meta-analyze gene-level association tests for binary trait. | |
9497 | While rareMETALS offers a near-complete solution for meta-analysis of | |
9498 | gene-level tests for quantitative trait, it does not offer the optimal | |
9499 | solution for binary trait. The package rareMETALS2 offers improved features | |
9500 | for analyzing gene-level association tests in meta-analyses for binary | |
9501 | trait.") | |
9502 | (license license:gpl3))) | |
0e7d058e RW |
9503 | |
9504 | (define-public r-maldiquant | |
9505 | (package | |
9506 | (name "r-maldiquant") | |
4ee8c37c | 9507 | (version "1.18") |
0e7d058e RW |
9508 | (source |
9509 | (origin | |
9510 | (method url-fetch) | |
9511 | (uri (cran-uri "MALDIquant" version)) | |
9512 | (sha256 | |
9513 | (base32 | |
4ee8c37c | 9514 | "18nl214xjsxkcpbg79jkmw0yznwm5szyh2qb84n7ip46mm779ha6")))) |
0e7d058e RW |
9515 | (properties `((upstream-name . "MALDIquant"))) |
9516 | (build-system r-build-system) | |
e9960d8c | 9517 | (home-page "https://cran.r-project.org/web/packages/MALDIquant") |
0e7d058e RW |
9518 | (synopsis "Quantitative analysis of mass spectrometry data") |
9519 | (description | |
9520 | "This package provides a complete analysis pipeline for matrix-assisted | |
9521 | laser desorption/ionization-time-of-flight (MALDI-TOF) and other | |
9522 | two-dimensional mass spectrometry data. In addition to commonly used plotting | |
9523 | and processing methods it includes distinctive features, namely baseline | |
9524 | subtraction methods such as morphological filters (TopHat) or the | |
9525 | statistics-sensitive non-linear iterative peak-clipping algorithm (SNIP), peak | |
9526 | alignment using warping functions, handling of replicated measurements as well | |
9527 | as allowing spectra with different resolutions.") | |
9528 | (license license:gpl3+))) | |
ae262174 RW |
9529 | |
9530 | (define-public r-protgenerics | |
9531 | (package | |
9532 | (name "r-protgenerics") | |
691ce09f | 9533 | (version "1.14.0") |
ae262174 RW |
9534 | (source |
9535 | (origin | |
9536 | (method url-fetch) | |
9537 | (uri (bioconductor-uri "ProtGenerics" version)) | |
9538 | (sha256 | |
9539 | (base32 | |
691ce09f | 9540 | "053mmxhzncqgigl2iqjlq56qzimlw2zzw31wpzw19rf7rld1vi3b")))) |
ae262174 RW |
9541 | (properties `((upstream-name . "ProtGenerics"))) |
9542 | (build-system r-build-system) | |
9543 | (home-page "https://github.com/lgatto/ProtGenerics") | |
9544 | (synopsis "S4 generic functions for proteomics infrastructure") | |
9545 | (description | |
9546 | "This package provides S4 generic functions needed by Bioconductor | |
9547 | proteomics packages.") | |
9548 | (license license:artistic2.0))) | |
71676a1f RW |
9549 | |
9550 | (define-public r-mzr | |
9551 | (package | |
9552 | (name "r-mzr") | |
92551984 | 9553 | (version "2.16.0") |
71676a1f RW |
9554 | (source |
9555 | (origin | |
9556 | (method url-fetch) | |
9557 | (uri (bioconductor-uri "mzR" version)) | |
9558 | (sha256 | |
9559 | (base32 | |
92551984 | 9560 | "0li1y6p95ljiva4lvfmql9sipn4dq42sknbh60b36ycjppnf8lj5")) |
15ca1959 RW |
9561 | (modules '((guix build utils))) |
9562 | (snippet | |
9563 | '(begin | |
9564 | (delete-file-recursively "src/boost") | |
9565 | #t)))) | |
71676a1f RW |
9566 | (properties `((upstream-name . "mzR"))) |
9567 | (build-system r-build-system) | |
15ca1959 RW |
9568 | (arguments |
9569 | `(#:phases | |
9570 | (modify-phases %standard-phases | |
9571 | (add-after 'unpack 'use-system-boost | |
9572 | (lambda _ | |
9573 | (substitute* "src/Makevars" | |
9574 | (("\\./boost/libs.*") "") | |
9575 | (("ARCH_OBJS=" line) | |
9576 | (string-append line | |
9577 | "\nARCH_LIBS=-lboost_system -lboost_regex \ | |
9578 | -lboost_iostreams -lboost_thread -lboost_filesystem -lboost_chrono\n"))) | |
9579 | #t))))) | |
71676a1f | 9580 | (inputs |
34b96754 | 9581 | `(("boost" ,boost) ; use this instead of the bundled boost sources |
39cc4917 | 9582 | ("zlib" ,zlib))) |
71676a1f RW |
9583 | (propagated-inputs |
9584 | `(("r-biobase" ,r-biobase) | |
9585 | ("r-biocgenerics" ,r-biocgenerics) | |
92551984 | 9586 | ("r-ncdf4" ,r-ncdf4) |
71676a1f RW |
9587 | ("r-protgenerics" ,r-protgenerics) |
9588 | ("r-rcpp" ,r-rcpp) | |
39cc4917 | 9589 | ("r-rhdf5lib" ,r-rhdf5lib) |
71676a1f RW |
9590 | ("r-zlibbioc" ,r-zlibbioc))) |
9591 | (home-page "https://github.com/sneumann/mzR/") | |
9592 | (synopsis "Parser for mass spectrometry data files") | |
9593 | (description | |
9594 | "The mzR package provides a unified API to the common file formats and | |
9595 | parsers available for mass spectrometry data. It comes with a wrapper for the | |
9596 | ISB random access parser for mass spectrometry mzXML, mzData and mzML files. | |
9597 | The package contains the original code written by the ISB, and a subset of the | |
9598 | proteowizard library for mzML and mzIdentML. The netCDF reading code has | |
9599 | previously been used in XCMS.") | |
9600 | (license license:artistic2.0))) | |
5c9d1505 RW |
9601 | |
9602 | (define-public r-affyio | |
9603 | (package | |
9604 | (name "r-affyio") | |
511abd7a | 9605 | (version "1.52.0") |
5c9d1505 RW |
9606 | (source |
9607 | (origin | |
9608 | (method url-fetch) | |
9609 | (uri (bioconductor-uri "affyio" version)) | |
9610 | (sha256 | |
9611 | (base32 | |
511abd7a | 9612 | "1s4zp1211vf0krxzch9v3q3r6vs8hihqppq18i2fpvwlknfja7c1")))) |
5c9d1505 RW |
9613 | (build-system r-build-system) |
9614 | (propagated-inputs | |
9615 | `(("r-zlibbioc" ,r-zlibbioc))) | |
9616 | (inputs | |
9617 | `(("zlib" ,zlib))) | |
9618 | (home-page "https://github.com/bmbolstad/affyio") | |
9619 | (synopsis "Tools for parsing Affymetrix data files") | |
9620 | (description | |
9621 | "This package provides routines for parsing Affymetrix data files based | |
9622 | upon file format information. The primary focus is on accessing the CEL and | |
9623 | CDF file formats.") | |
9624 | (license license:lgpl2.0+))) | |
05c7e5fb RW |
9625 | |
9626 | (define-public r-affy | |
9627 | (package | |
9628 | (name "r-affy") | |
2b085484 | 9629 | (version "1.60.0") |
05c7e5fb RW |
9630 | (source |
9631 | (origin | |
9632 | (method url-fetch) | |
9633 | (uri (bioconductor-uri "affy" version)) | |
9634 | (sha256 | |
9635 | (base32 | |
2b085484 | 9636 | "0x8h4fk2igv7vykqfvf6v9whmx3344v5rf3gyfajd431xkjldz6k")))) |
05c7e5fb RW |
9637 | (build-system r-build-system) |
9638 | (propagated-inputs | |
9639 | `(("r-affyio" ,r-affyio) | |
9640 | ("r-biobase" ,r-biobase) | |
9641 | ("r-biocgenerics" ,r-biocgenerics) | |
2b085484 | 9642 | ("r-biocmanager" ,r-biocmanager) |
05c7e5fb RW |
9643 | ("r-preprocesscore" ,r-preprocesscore) |
9644 | ("r-zlibbioc" ,r-zlibbioc))) | |
5837f183 RW |
9645 | (inputs |
9646 | `(("zlib" ,zlib))) | |
5713bbf1 | 9647 | (home-page "https://bioconductor.org/packages/affy") |
05c7e5fb RW |
9648 | (synopsis "Methods for affymetrix oligonucleotide arrays") |
9649 | (description | |
9650 | "This package contains functions for exploratory oligonucleotide array | |
9651 | analysis.") | |
9652 | (license license:lgpl2.0+))) | |
7c08afaf RW |
9653 | |
9654 | (define-public r-vsn | |
9655 | (package | |
9656 | (name "r-vsn") | |
0e16fc46 | 9657 | (version "3.50.0") |
7c08afaf RW |
9658 | (source |
9659 | (origin | |
9660 | (method url-fetch) | |
9661 | (uri (bioconductor-uri "vsn" version)) | |
9662 | (sha256 | |
9663 | (base32 | |
0e16fc46 | 9664 | "1g6qkpykw99jm2wv2i61dg2ffwk0n8fm4s5pm2q4c024vw5c9b69")))) |
7c08afaf RW |
9665 | (build-system r-build-system) |
9666 | (propagated-inputs | |
9667 | `(("r-affy" ,r-affy) | |
9668 | ("r-biobase" ,r-biobase) | |
9669 | ("r-ggplot2" ,r-ggplot2) | |
aeb64f3c | 9670 | ("r-lattice" ,r-lattice) |
7c08afaf | 9671 | ("r-limma" ,r-limma))) |
5713bbf1 | 9672 | (home-page "https://bioconductor.org/packages/release/bioc/html/vsn.html") |
7c08afaf RW |
9673 | (synopsis "Variance stabilization and calibration for microarray data") |
9674 | (description | |
9675 | "The package implements a method for normalising microarray intensities, | |
9676 | and works for single- and multiple-color arrays. It can also be used for data | |
9677 | from other technologies, as long as they have similar format. The method uses | |
9678 | a robust variant of the maximum-likelihood estimator for an | |
9679 | additive-multiplicative error model and affine calibration. The model | |
9680 | incorporates data calibration step (a.k.a. normalization), a model for the | |
9681 | dependence of the variance on the mean intensity and a variance stabilizing | |
9682 | data transformation. Differences between transformed intensities are | |
9683 | analogous to \"normalized log-ratios\". However, in contrast to the latter, | |
9684 | their variance is independent of the mean, and they are usually more sensitive | |
9685 | and specific in detecting differential transcription.") | |
9686 | (license license:artistic2.0))) | |
4aa7d592 RW |
9687 | |
9688 | (define-public r-mzid | |
9689 | (package | |
9690 | (name "r-mzid") | |
2c4311dc | 9691 | (version "1.20.0") |
4aa7d592 RW |
9692 | (source |
9693 | (origin | |
9694 | (method url-fetch) | |
9695 | (uri (bioconductor-uri "mzID" version)) | |
9696 | (sha256 | |
9697 | (base32 | |
2c4311dc | 9698 | "08jbq223viwknsmsi30hyxyxslvmb0l4wx3vmqlkl6qk4vfmxzjz")))) |
4aa7d592 RW |
9699 | (properties `((upstream-name . "mzID"))) |
9700 | (build-system r-build-system) | |
9701 | (propagated-inputs | |
9702 | `(("r-doparallel" ,r-doparallel) | |
9703 | ("r-foreach" ,r-foreach) | |
9704 | ("r-iterators" ,r-iterators) | |
9705 | ("r-plyr" ,r-plyr) | |
9706 | ("r-protgenerics" ,r-protgenerics) | |
9707 | ("r-rcpp" ,r-rcpp) | |
9708 | ("r-xml" ,r-xml))) | |
5713bbf1 | 9709 | (home-page "https://bioconductor.org/packages/mzID") |
4aa7d592 RW |
9710 | (synopsis "Parser for mzIdentML files") |
9711 | (description | |
9712 | "This package provides a parser for mzIdentML files implemented using the | |
9713 | XML package. The parser tries to be general and able to handle all types of | |
9714 | mzIdentML files with the drawback of having less pretty output than a vendor | |
9715 | specific parser.") | |
9716 | (license license:gpl2+))) | |
6a67e181 RW |
9717 | |
9718 | (define-public r-pcamethods | |
9719 | (package | |
9720 | (name "r-pcamethods") | |
73d74752 | 9721 | (version "1.74.0") |
6a67e181 RW |
9722 | (source |
9723 | (origin | |
9724 | (method url-fetch) | |
9725 | (uri (bioconductor-uri "pcaMethods" version)) | |
9726 | (sha256 | |
9727 | (base32 | |
73d74752 | 9728 | "0ik82s9bsdj4a1mmv0a3k6yisa92mxx7maf3dvip1r8gqlm3dyng")))) |
6a67e181 RW |
9729 | (properties `((upstream-name . "pcaMethods"))) |
9730 | (build-system r-build-system) | |
9731 | (propagated-inputs | |
9732 | `(("r-biobase" ,r-biobase) | |
9733 | ("r-biocgenerics" ,r-biocgenerics) | |
aeb64f3c | 9734 | ("r-mass" ,r-mass) |
6a67e181 RW |
9735 | ("r-rcpp" ,r-rcpp))) |
9736 | (home-page "https://github.com/hredestig/pcamethods") | |
9737 | (synopsis "Collection of PCA methods") | |
9738 | (description | |
9739 | "This package provides Bayesian PCA, Probabilistic PCA, Nipals PCA, | |
9740 | Inverse Non-Linear PCA and the conventional SVD PCA. A cluster based method | |
9741 | for missing value estimation is included for comparison. BPCA, PPCA and | |
9742 | NipalsPCA may be used to perform PCA on incomplete data as well as for | |
9743 | accurate missing value estimation. A set of methods for printing and plotting | |
9744 | the results is also provided. All PCA methods make use of the same data | |
9745 | structure (pcaRes) to provide a common interface to the PCA results.") | |
9746 | (license license:gpl3+))) | |
11879284 RW |
9747 | |
9748 | (define-public r-msnbase | |
9749 | (package | |
9750 | (name "r-msnbase") | |
e0388191 | 9751 | (version "2.8.1") |
11879284 RW |
9752 | (source |
9753 | (origin | |
9754 | (method url-fetch) | |
9755 | (uri (bioconductor-uri "MSnbase" version)) | |
9756 | (sha256 | |
9757 | (base32 | |
e0388191 | 9758 | "0y658anh06vnvbkfs7r8q40gqgyqr2r8kj7jlpnp33fy1lvp1nv7")))) |
11879284 RW |
9759 | (properties `((upstream-name . "MSnbase"))) |
9760 | (build-system r-build-system) | |
9761 | (propagated-inputs | |
9762 | `(("r-affy" ,r-affy) | |
9763 | ("r-biobase" ,r-biobase) | |
9764 | ("r-biocgenerics" ,r-biocgenerics) | |
9765 | ("r-biocparallel" ,r-biocparallel) | |
9766 | ("r-digest" ,r-digest) | |
9767 | ("r-ggplot2" ,r-ggplot2) | |
9768 | ("r-impute" ,r-impute) | |
9769 | ("r-iranges" ,r-iranges) | |
baa00ee9 | 9770 | ("r-lattice" ,r-lattice) |
11879284 | 9771 | ("r-maldiquant" ,r-maldiquant) |
250d78ea | 9772 | ("r-mass" ,r-mass) |
11879284 RW |
9773 | ("r-mzid" ,r-mzid) |
9774 | ("r-mzr" ,r-mzr) | |
9775 | ("r-pcamethods" ,r-pcamethods) | |
9776 | ("r-plyr" ,r-plyr) | |
9777 | ("r-preprocesscore" ,r-preprocesscore) | |
9778 | ("r-protgenerics" ,r-protgenerics) | |
9779 | ("r-rcpp" ,r-rcpp) | |
11879284 | 9780 | ("r-s4vectors" ,r-s4vectors) |
250d78ea | 9781 | ("r-scales" ,r-scales) |
11879284 RW |
9782 | ("r-vsn" ,r-vsn) |
9783 | ("r-xml" ,r-xml))) | |
9784 | (home-page "https://github.com/lgatto/MSnbase") | |
9785 | (synopsis "Base functions and classes for MS-based proteomics") | |
9786 | (description | |
9787 | "This package provides basic plotting, data manipulation and processing | |
e614d639 | 9788 | of mass spectrometry based proteomics data.") |
11879284 | 9789 | (license license:artistic2.0))) |
66da3a9f RW |
9790 | |
9791 | (define-public r-msnid | |
9792 | (package | |
9793 | (name "r-msnid") | |
675d91a0 | 9794 | (version "1.16.0") |
66da3a9f RW |
9795 | (source |
9796 | (origin | |
9797 | (method url-fetch) | |
9798 | (uri (bioconductor-uri "MSnID" version)) | |
9799 | (sha256 | |
9800 | (base32 | |
675d91a0 | 9801 | "0hgq4argllhh5hvxqi8vkf1blc3nibsslhx4zsv2mcv4yj75bv4n")))) |
66da3a9f RW |
9802 | (properties `((upstream-name . "MSnID"))) |
9803 | (build-system r-build-system) | |
9804 | (propagated-inputs | |
9805 | `(("r-biobase" ,r-biobase) | |
9806 | ("r-data-table" ,r-data-table) | |
9807 | ("r-doparallel" ,r-doparallel) | |
9808 | ("r-dplyr" ,r-dplyr) | |
9809 | ("r-foreach" ,r-foreach) | |
9810 | ("r-iterators" ,r-iterators) | |
9811 | ("r-msnbase" ,r-msnbase) | |
9812 | ("r-mzid" ,r-mzid) | |
9813 | ("r-mzr" ,r-mzr) | |
9814 | ("r-protgenerics" ,r-protgenerics) | |
9815 | ("r-r-cache" ,r-r-cache) | |
9816 | ("r-rcpp" ,r-rcpp) | |
9817 | ("r-reshape2" ,r-reshape2))) | |
5713bbf1 | 9818 | (home-page "https://bioconductor.org/packages/MSnID") |
66da3a9f RW |
9819 | (synopsis "Utilities for LC-MSn proteomics identifications") |
9820 | (description | |
2923f3e5 RW |
9821 | "This package extracts @dfn{tandem mass spectrometry} (MS/MS) ID data |
9822 | from mzIdentML (leveraging the mzID package) or text files. After collating | |
9823 | the search results from multiple datasets it assesses their identification | |
9824 | quality and optimize filtering criteria to achieve the maximum number of | |
9825 | identifications while not exceeding a specified false discovery rate. It also | |
9826 | contains a number of utilities to explore the MS/MS results and assess missed | |
9827 | and irregular enzymatic cleavages, mass measurement accuracy, etc.") | |
66da3a9f | 9828 | (license license:artistic2.0))) |
5ded35d8 | 9829 | |
2441c284 | 9830 | (define-public r-seurat |
f1a2b1cb RW |
9831 | (package |
9832 | (name "r-seurat") | |
6f6aef80 | 9833 | (version "2.3.4") |
f1a2b1cb RW |
9834 | (source (origin |
9835 | (method url-fetch) | |
9836 | (uri (cran-uri "Seurat" version)) | |
9837 | (sha256 | |
9838 | (base32 | |
6f6aef80 | 9839 | "0l8bv4i9nzz26mirnva10mq6pimibj24vk7vpvfypgn7xk4942hd")))) |
f1a2b1cb RW |
9840 | (properties `((upstream-name . "Seurat"))) |
9841 | (build-system r-build-system) | |
f1a2b1cb RW |
9842 | (propagated-inputs |
9843 | `(("r-ape" ,r-ape) | |
c36ce476 | 9844 | ("r-cluster" ,r-cluster) |
f1a2b1cb | 9845 | ("r-cowplot" ,r-cowplot) |
c36ce476 | 9846 | ("r-dosnow" ,r-dosnow) |
f1a2b1cb RW |
9847 | ("r-dplyr" ,r-dplyr) |
9848 | ("r-dtw" ,r-dtw) | |
c36ce476 | 9849 | ("r-fitdistrplus" ,r-fitdistrplus) |
c36ce476 | 9850 | ("r-foreach" ,r-foreach) |
f1a2b1cb | 9851 | ("r-fpc" ,r-fpc) |
f1a2b1cb | 9852 | ("r-ggplot2" ,r-ggplot2) |
26e3e28c | 9853 | ("r-ggridges" ,r-ggridges) |
f1a2b1cb | 9854 | ("r-gplots" ,r-gplots) |
13b8dcf5 | 9855 | ("r-hdf5r" ,r-hdf5r) |
f1a2b1cb | 9856 | ("r-hmisc" ,r-hmisc) |
6f6aef80 | 9857 | ("r-httr" ,r-httr) |
f1a2b1cb RW |
9858 | ("r-ica" ,r-ica) |
9859 | ("r-igraph" ,r-igraph) | |
9860 | ("r-irlba" ,r-irlba) | |
9861 | ("r-lars" ,r-lars) | |
c36ce476 | 9862 | ("r-lmtest" ,r-lmtest) |
f1a2b1cb RW |
9863 | ("r-mass" ,r-mass) |
9864 | ("r-matrix" ,r-matrix) | |
ebec98ae | 9865 | ("r-metap" ,r-metap) |
f1a2b1cb | 9866 | ("r-mixtools" ,r-mixtools) |
f1a2b1cb RW |
9867 | ("r-pbapply" ,r-pbapply) |
9868 | ("r-plotly" ,r-plotly) | |
c36ce476 | 9869 | ("r-png" ,r-png) |
c36ce476 | 9870 | ("r-rann" ,r-rann) |
f1a2b1cb RW |
9871 | ("r-rcolorbrewer" ,r-rcolorbrewer) |
9872 | ("r-rcpp" ,r-rcpp) | |
26e3e28c | 9873 | ("r-rcppeigen" ,r-rcppeigen) |
f1a2b1cb RW |
9874 | ("r-rcppprogress" ,r-rcppprogress) |
9875 | ("r-reshape2" ,r-reshape2) | |
ce8b9e3b | 9876 | ("r-reticulate" ,r-reticulate) |
f1a2b1cb RW |
9877 | ("r-rocr" ,r-rocr) |
9878 | ("r-rtsne" ,r-rtsne) | |
9879 | ("r-sdmtools" ,r-sdmtools) | |
f1a2b1cb | 9880 | ("r-tidyr" ,r-tidyr) |
6f6aef80 | 9881 | ("r-tsne" ,r-tsne))) |
f1a2b1cb RW |
9882 | (home-page "http://www.satijalab.org/seurat") |
9883 | (synopsis "Seurat is an R toolkit for single cell genomics") | |
9884 | (description | |
9885 | "This package is an R package designed for QC, analysis, and | |
2441c284 RJPB |
9886 | exploration of single cell RNA-seq data. It easily enables widely-used |
9887 | analytical techniques, including the identification of highly variable genes, | |
9888 | dimensionality reduction; PCA, ICA, t-SNE, standard unsupervised clustering | |
9889 | algorithms; density clustering, hierarchical clustering, k-means, and the | |
9890 | discovery of differentially expressed genes and markers.") | |
f1a2b1cb | 9891 | (license license:gpl3))) |
2441c284 | 9892 | |
d4b83651 RW |
9893 | (define-public r-aroma-light |
9894 | (package | |
9895 | (name "r-aroma-light") | |
800954eb | 9896 | (version "3.12.0") |
d4b83651 RW |
9897 | (source |
9898 | (origin | |
9899 | (method url-fetch) | |
9900 | (uri (bioconductor-uri "aroma.light" version)) | |
9901 | (sha256 | |
9902 | (base32 | |
800954eb | 9903 | "0vfifgpqxjjncbiv6gvlk9jmj14j90r9f30bqk3ks9v1csjnjhrb")))) |
d4b83651 RW |
9904 | (properties `((upstream-name . "aroma.light"))) |
9905 | (build-system r-build-system) | |
9906 | (propagated-inputs | |
9907 | `(("r-matrixstats" ,r-matrixstats) | |
9908 | ("r-r-methodss3" ,r-r-methodss3) | |
9909 | ("r-r-oo" ,r-r-oo) | |
9910 | ("r-r-utils" ,r-r-utils))) | |
9911 | (home-page "https://github.com/HenrikBengtsson/aroma.light") | |
9912 | (synopsis "Methods for normalization and visualization of microarray data") | |
9913 | (description | |
9914 | "This package provides methods for microarray analysis that take basic | |
9915 | data types such as matrices and lists of vectors. These methods can be used | |
9916 | standalone, be utilized in other packages, or be wrapped up in higher-level | |
9917 | classes.") | |
9918 | (license license:gpl2+))) | |
9919 | ||
7b465327 RW |
9920 | (define-public r-deseq |
9921 | (package | |
9922 | (name "r-deseq") | |
7812e6b8 | 9923 | (version "1.34.0") |
7b465327 RW |
9924 | (source |
9925 | (origin | |
9926 | (method url-fetch) | |
9927 | (uri (bioconductor-uri "DESeq" version)) | |
9928 | (sha256 | |
9929 | (base32 | |
7812e6b8 | 9930 | "1klv1xrh3173srywr6dnq6i7m9djn4gc9aflr1p3a6yjlqcq6fya")))) |
7b465327 RW |
9931 | (properties `((upstream-name . "DESeq"))) |
9932 | (build-system r-build-system) | |
9933 | (propagated-inputs | |
9934 | `(("r-biobase" ,r-biobase) | |
9935 | ("r-biocgenerics" ,r-biocgenerics) | |
9936 | ("r-genefilter" ,r-genefilter) | |
9937 | ("r-geneplotter" ,r-geneplotter) | |
9938 | ("r-lattice" ,r-lattice) | |
9939 | ("r-locfit" ,r-locfit) | |
9940 | ("r-mass" ,r-mass) | |
9941 | ("r-rcolorbrewer" ,r-rcolorbrewer))) | |
9942 | (home-page "http://www-huber.embl.de/users/anders/DESeq") | |
9943 | (synopsis "Differential gene expression analysis") | |
9944 | (description | |
9945 | "This package provides tools for estimating variance-mean dependence in | |
9946 | count data from high-throughput genetic sequencing assays and for testing for | |
9947 | differential expression based on a model using the negative binomial | |
9948 | distribution.") | |
9949 | (license license:gpl3+))) | |
9950 | ||
296b3c63 RW |
9951 | (define-public r-edaseq |
9952 | (package | |
9953 | (name "r-edaseq") | |
b03951f2 | 9954 | (version "2.16.0") |
296b3c63 RW |
9955 | (source |
9956 | (origin | |
9957 | (method url-fetch) | |
9958 | (uri (bioconductor-uri "EDASeq" version)) | |
9959 | (sha256 | |
9960 | (base32 | |
b03951f2 | 9961 | "1gjqzn1kg9qwyz2gwjyy9xzzr1lnc7xd5zwdyvzkadz97gckzxwf")))) |
296b3c63 RW |
9962 | (properties `((upstream-name . "EDASeq"))) |
9963 | (build-system r-build-system) | |
9964 | (propagated-inputs | |
9965 | `(("r-annotationdbi" ,r-annotationdbi) | |
9966 | ("r-aroma-light" ,r-aroma-light) | |
9967 | ("r-biobase" ,r-biobase) | |
9968 | ("r-biocgenerics" ,r-biocgenerics) | |
9969 | ("r-biomart" ,r-biomart) | |
9970 | ("r-biostrings" ,r-biostrings) | |
9971 | ("r-deseq" ,r-deseq) | |
9972 | ("r-genomicfeatures" ,r-genomicfeatures) | |
9973 | ("r-genomicranges" ,r-genomicranges) | |
9974 | ("r-iranges" ,r-iranges) | |
9975 | ("r-rsamtools" ,r-rsamtools) | |
9976 | ("r-shortread" ,r-shortread))) | |
9977 | (home-page "https://github.com/drisso/EDASeq") | |
9978 | (synopsis "Exploratory data analysis and normalization for RNA-Seq") | |
9979 | (description | |
9980 | "This package provides support for numerical and graphical summaries of | |
9981 | RNA-Seq genomic read data. Provided within-lane normalization procedures to | |
9982 | adjust for GC-content effect (or other gene-level effects) on read counts: | |
9983 | loess robust local regression, global-scaling, and full-quantile | |
9984 | normalization. Between-lane normalization procedures to adjust for | |
9985 | distributional differences between lanes (e.g., sequencing depth): | |
9986 | global-scaling and full-quantile normalization.") | |
9987 | (license license:artistic2.0))) | |
9988 | ||
5f96f30f RW |
9989 | (define-public r-interactivedisplaybase |
9990 | (package | |
9991 | (name "r-interactivedisplaybase") | |
d7ea34bf | 9992 | (version "1.20.0") |
5f96f30f RW |
9993 | (source |
9994 | (origin | |
9995 | (method url-fetch) | |
9996 | (uri (bioconductor-uri "interactiveDisplayBase" version)) | |
9997 | (sha256 | |
9998 | (base32 | |
d7ea34bf | 9999 | "04xz3dkwan2s5ic1mwkdfnggm0l41mgqfagx160bcsrpkw6z7ark")))) |
5f96f30f RW |
10000 | (properties |
10001 | `((upstream-name . "interactiveDisplayBase"))) | |
10002 | (build-system r-build-system) | |
10003 | (propagated-inputs | |
10004 | `(("r-biocgenerics" ,r-biocgenerics) | |
10005 | ("r-shiny" ,r-shiny))) | |
5713bbf1 | 10006 | (home-page "https://bioconductor.org/packages/interactiveDisplayBase") |
5f96f30f RW |
10007 | (synopsis "Base package for web displays of Bioconductor objects") |
10008 | (description | |
10009 | "This package contains the basic methods needed to generate interactive | |
10010 | Shiny-based display methods for Bioconductor objects.") | |
10011 | (license license:artistic2.0))) | |
10012 | ||
4a007ffa RW |
10013 | (define-public r-annotationhub |
10014 | (package | |
10015 | (name "r-annotationhub") | |
147633d4 | 10016 | (version "2.14.1") |
4a007ffa RW |
10017 | (source |
10018 | (origin | |
10019 | (method url-fetch) | |
10020 | (uri (bioconductor-uri "AnnotationHub" version)) | |
10021 | (sha256 | |
10022 | (base32 | |
147633d4 | 10023 | "00288x3na0izpmbcvsqac1br1qwry86vwc2slj1l47crdfb7za6c")))) |
4a007ffa RW |
10024 | (properties `((upstream-name . "AnnotationHub"))) |
10025 | (build-system r-build-system) | |
10026 | (propagated-inputs | |
10027 | `(("r-annotationdbi" ,r-annotationdbi) | |
10028 | ("r-biocgenerics" ,r-biocgenerics) | |
147633d4 | 10029 | ("r-biocmanager" ,r-biocmanager) |
14b3c719 | 10030 | ("r-curl" ,r-curl) |
4a007ffa RW |
10031 | ("r-httr" ,r-httr) |
10032 | ("r-interactivedisplaybase" ,r-interactivedisplaybase) | |
10033 | ("r-rsqlite" ,r-rsqlite) | |
10034 | ("r-s4vectors" ,r-s4vectors) | |
10035 | ("r-yaml" ,r-yaml))) | |
5713bbf1 | 10036 | (home-page "https://bioconductor.org/packages/AnnotationHub") |
4a007ffa RW |
10037 | (synopsis "Client to access AnnotationHub resources") |
10038 | (description | |
10039 | "This package provides a client for the Bioconductor AnnotationHub web | |
10040 | resource. The AnnotationHub web resource provides a central location where | |
10041 | genomic files (e.g. VCF, bed, wig) and other resources from standard | |
10042 | locations (e.g. UCSC, Ensembl) can be discovered. The resource includes | |
10043 | metadata about each resource, e.g., a textual description, tags, and date of | |
10044 | modification. The client creates and manages a local cache of files retrieved | |
10045 | by the user, helping with quick and reproducible access.") | |
10046 | (license license:artistic2.0))) | |
10047 | ||
d4a1e918 RW |
10048 | (define-public r-fastseg |
10049 | (package | |
10050 | (name "r-fastseg") | |
95df764c | 10051 | (version "1.28.0") |
d4a1e918 RW |
10052 | (source |
10053 | (origin | |
10054 | (method url-fetch) | |
10055 | (uri (bioconductor-uri "fastseg" version)) | |
10056 | (sha256 | |
10057 | (base32 | |
95df764c | 10058 | "1l8mdjpfpgwqdss2ywjkb8b4h55wf8v6kmyxdlvy04ds2hj16sb1")))) |
d4a1e918 RW |
10059 | (build-system r-build-system) |
10060 | (propagated-inputs | |
10061 | `(("r-biobase" ,r-biobase) | |
10062 | ("r-biocgenerics" ,r-biocgenerics) | |
10063 | ("r-genomicranges" ,r-genomicranges) | |
10064 | ("r-iranges" ,r-iranges) | |
10065 | ("r-s4vectors" ,r-s4vectors))) | |
10066 | (home-page "http://www.bioinf.jku.at/software/fastseg/index.html") | |
10067 | (synopsis "Fast segmentation algorithm for genetic sequencing data") | |
10068 | (description | |
10069 | "Fastseg implements a very fast and efficient segmentation algorithm. | |
10070 | It can segment data from DNA microarrays and data from next generation | |
10071 | sequencing for example to detect copy number segments. Further it can segment | |
10072 | data from RNA microarrays like tiling arrays to identify transcripts. Most | |
10073 | generally, it can segment data given as a matrix or as a vector. Various data | |
10074 | formats can be used as input to fastseg like expression set objects for | |
10075 | microarrays or GRanges for sequencing data.") | |
10076 | (license license:lgpl2.0+))) | |
10077 | ||
3121814e RW |
10078 | (define-public r-keggrest |
10079 | (package | |
10080 | (name "r-keggrest") | |
49842127 | 10081 | (version "1.22.0") |
3121814e RW |
10082 | (source |
10083 | (origin | |
10084 | (method url-fetch) | |
10085 | (uri (bioconductor-uri "KEGGREST" version)) | |
10086 | (sha256 | |
10087 | (base32 | |
49842127 | 10088 | "0blpd5a7whd2sswfhqd17h58hg06ymaf80gapdr9ja43hnnlj309")))) |
3121814e RW |
10089 | (properties `((upstream-name . "KEGGREST"))) |
10090 | (build-system r-build-system) | |
10091 | (propagated-inputs | |
10092 | `(("r-biostrings" ,r-biostrings) | |
10093 | ("r-httr" ,r-httr) | |
10094 | ("r-png" ,r-png))) | |
10095 | (home-page "https://bioconductor.org/packages/KEGGREST") | |
10096 | (synopsis "Client-side REST access to KEGG") | |
10097 | (description | |
10098 | "This package provides a package that provides a client interface to the | |
10099 | @dfn{Kyoto Encyclopedia of Genes and Genomes} (KEGG) REST server.") | |
10100 | (license license:artistic2.0))) | |
10101 | ||
e160aa1f RW |
10102 | (define-public r-gage |
10103 | (package | |
10104 | (name "r-gage") | |
122e099e | 10105 | (version "2.32.0") |
e160aa1f RW |
10106 | (source |
10107 | (origin | |
10108 | (method url-fetch) | |
10109 | (uri (bioconductor-uri "gage" version)) | |
10110 | (sha256 | |
10111 | (base32 | |
122e099e | 10112 | "07b098wvryxf0zd423nk6h52s3gyngwjcx2vplqybpbpgl8h2931")))) |
e160aa1f RW |
10113 | (build-system r-build-system) |
10114 | (propagated-inputs | |
10115 | `(("r-annotationdbi" ,r-annotationdbi) | |
10116 | ("r-graph" ,r-graph) | |
10117 | ("r-keggrest" ,r-keggrest))) | |
10118 | (home-page "http://www.biomedcentral.com/1471-2105/10/161") | |
10119 | (synopsis "Generally applicable gene-set enrichment for pathway analysis") | |
10120 | (description | |
10121 | "GAGE is a published method for gene set (enrichment or GSEA) or pathway | |
10122 | analysis. GAGE is generally applicable independent of microarray or RNA-Seq | |
10123 | data attributes including sample sizes, experimental designs, assay platforms, | |
10124 | and other types of heterogeneity. The gage package provides functions for | |
10125 | basic GAGE analysis, result processing and presentation. In addition, it | |
10126 | provides demo microarray data and commonly used gene set data based on KEGG | |
10127 | pathways and GO terms. These funtions and data are also useful for gene set | |
10128 | analysis using other methods.") | |
10129 | (license license:gpl2+))) | |
10130 | ||
902fb15d RW |
10131 | (define-public r-genomicfiles |
10132 | (package | |
10133 | (name "r-genomicfiles") | |
d78c6aca | 10134 | (version "1.18.0") |
902fb15d RW |
10135 | (source |
10136 | (origin | |
10137 | (method url-fetch) | |
10138 | (uri (bioconductor-uri "GenomicFiles" version)) | |
10139 | (sha256 | |
10140 | (base32 | |
d78c6aca | 10141 | "0qf2yj4lfnnk64fk125n8sqms01shfqiik04nasx2z3k129ykpxp")))) |
902fb15d RW |
10142 | (properties `((upstream-name . "GenomicFiles"))) |
10143 | (build-system r-build-system) | |
10144 | (propagated-inputs | |
10145 | `(("r-biocgenerics" ,r-biocgenerics) | |
10146 | ("r-biocparallel" ,r-biocparallel) | |
10147 | ("r-genomeinfodb" ,r-genomeinfodb) | |
10148 | ("r-genomicalignments" ,r-genomicalignments) | |
10149 | ("r-genomicranges" ,r-genomicranges) | |
10150 | ("r-iranges" ,r-iranges) | |
10151 | ("r-rsamtools" ,r-rsamtools) | |
10152 | ("r-rtracklayer" ,r-rtracklayer) | |
10153 | ("r-s4vectors" ,r-s4vectors) | |
10154 | ("r-summarizedexperiment" ,r-summarizedexperiment) | |
10155 | ("r-variantannotation" ,r-variantannotation))) | |
10156 | (home-page "https://bioconductor.org/packages/GenomicFiles") | |
10157 | (synopsis "Distributed computing by file or by range") | |
10158 | (description | |
10159 | "This package provides infrastructure for parallel computations | |
10160 | distributed by file or by range. User defined mapper and reducer functions | |
10161 | provide added flexibility for data combination and manipulation.") | |
10162 | (license license:artistic2.0))) | |
10163 | ||
3af149f5 RW |
10164 | (define-public r-complexheatmap |
10165 | (package | |
10166 | (name "r-complexheatmap") | |
5ae5a8eb | 10167 | (version "1.20.0") |
3af149f5 RW |
10168 | (source |
10169 | (origin | |
10170 | (method url-fetch) | |
10171 | (uri (bioconductor-uri "ComplexHeatmap" version)) | |
10172 | (sha256 | |
10173 | (base32 | |
5ae5a8eb | 10174 | "0s01dzcfj1lmpqfpsbqw7r4858krfzy499lz4cwx4fq3mbyvy2aj")))) |
3af149f5 RW |
10175 | (properties |
10176 | `((upstream-name . "ComplexHeatmap"))) | |
10177 | (build-system r-build-system) | |
10178 | (propagated-inputs | |
10179 | `(("r-circlize" ,r-circlize) | |
10180 | ("r-colorspace" ,r-colorspace) | |
10181 | ("r-getoptlong" ,r-getoptlong) | |
10182 | ("r-globaloptions" ,r-globaloptions) | |
10183 | ("r-rcolorbrewer" ,r-rcolorbrewer))) | |
10184 | (home-page | |
10185 | "https://github.com/jokergoo/ComplexHeatmap") | |
10186 | (synopsis "Making Complex Heatmaps") | |
10187 | (description | |
10188 | "Complex heatmaps are efficient to visualize associations between | |
10189 | different sources of data sets and reveal potential structures. This package | |
10190 | provides a highly flexible way to arrange multiple heatmaps and supports | |
10191 | self-defined annotation graphics.") | |
10192 | (license license:gpl2+))) | |
10193 | ||
04e2a2e9 RW |
10194 | (define-public r-dirichletmultinomial |
10195 | (package | |
10196 | (name "r-dirichletmultinomial") | |
0c96e4b2 | 10197 | (version "1.24.0") |
04e2a2e9 RW |
10198 | (source |
10199 | (origin | |
10200 | (method url-fetch) | |
10201 | (uri (bioconductor-uri "DirichletMultinomial" version)) | |
10202 | (sha256 | |
10203 | (base32 | |
0c96e4b2 | 10204 | "19bzn0a5jal1xv0ad6wikxc7wrk582hczqamlln0vb2ffwkj1z3f")))) |
04e2a2e9 RW |
10205 | (properties |
10206 | `((upstream-name . "DirichletMultinomial"))) | |
10207 | (build-system r-build-system) | |
10208 | (inputs | |
10209 | `(("gsl" ,gsl))) | |
10210 | (propagated-inputs | |
10211 | `(("r-biocgenerics" ,r-biocgenerics) | |
10212 | ("r-iranges" ,r-iranges) | |
10213 | ("r-s4vectors" ,r-s4vectors))) | |
10214 | (home-page "https://bioconductor.org/packages/DirichletMultinomial") | |
10215 | (synopsis "Dirichlet-Multinomial mixture models for microbiome data") | |
10216 | (description | |
10217 | "Dirichlet-multinomial mixture models can be used to describe variability | |
10218 | in microbial metagenomic data. This package is an interface to code | |
10219 | originally made available by Holmes, Harris, and Quince, 2012, PLoS ONE 7(2): | |
10220 | 1-15.") | |
10221 | (license license:lgpl3))) | |
10222 | ||
aa30ab5a RW |
10223 | (define-public r-ensembldb |
10224 | (package | |
10225 | (name "r-ensembldb") | |
c2e26dc1 | 10226 | (version "2.6.2") |
aa30ab5a RW |
10227 | (source |
10228 | (origin | |
10229 | (method url-fetch) | |
10230 | (uri (bioconductor-uri "ensembldb" version)) | |
10231 | (sha256 | |
10232 | (base32 | |
c2e26dc1 | 10233 | "0hdz1f34v7sas2v4225icwl3wd4sf17ykpd5dkbx1hc7wcy4w3np")))) |
aa30ab5a RW |
10234 | (build-system r-build-system) |
10235 | (propagated-inputs | |
10236 | `(("r-annotationdbi" ,r-annotationdbi) | |
10237 | ("r-annotationfilter" ,r-annotationfilter) | |
aa30ab5a RW |
10238 | ("r-biobase" ,r-biobase) |
10239 | ("r-biocgenerics" ,r-biocgenerics) | |
10240 | ("r-biostrings" ,r-biostrings) | |
10241 | ("r-curl" ,r-curl) | |
10242 | ("r-dbi" ,r-dbi) | |
10243 | ("r-genomeinfodb" ,r-genomeinfodb) | |
10244 | ("r-genomicfeatures" ,r-genomicfeatures) | |
10245 | ("r-genomicranges" ,r-genomicranges) | |
10246 | ("r-iranges" ,r-iranges) | |
10247 | ("r-protgenerics" ,r-protgenerics) | |
10248 | ("r-rsamtools" ,r-rsamtools) | |
10249 | ("r-rsqlite" ,r-rsqlite) | |
10250 | ("r-rtracklayer" ,r-rtracklayer) | |
10251 | ("r-s4vectors" ,r-s4vectors))) | |
10252 | (home-page "https://github.com/jotsetung/ensembldb") | |
10253 | (synopsis "Utilities to create and use Ensembl-based annotation databases") | |
10254 | (description | |
10255 | "The package provides functions to create and use transcript-centric | |
10256 | annotation databases/packages. The annotation for the databases are directly | |
10257 | fetched from Ensembl using their Perl API. The functionality and data is | |
10258 | similar to that of the TxDb packages from the @code{GenomicFeatures} package, | |
10259 | but, in addition to retrieve all gene/transcript models and annotations from | |
10260 | the database, the @code{ensembldb} package also provides a filter framework | |
10261 | allowing to retrieve annotations for specific entries like genes encoded on a | |
10262 | chromosome region or transcript models of lincRNA genes.") | |
10263 | ;; No version specified | |
10264 | (license license:lgpl3+))) | |
10265 | ||
2f6f61fd RW |
10266 | (define-public r-organismdbi |
10267 | (package | |
10268 | (name "r-organismdbi") | |
cdab2dcf | 10269 | (version "1.24.0") |
2f6f61fd RW |
10270 | (source |
10271 | (origin | |
10272 | (method url-fetch) | |
10273 | (uri (bioconductor-uri "OrganismDbi" version)) | |
10274 | (sha256 | |
10275 | (base32 | |
cdab2dcf | 10276 | "11pyv56cy4iy095h40k6k0mpjdlh6gsb4ld3s57nfa9nd4ypx3yi")))) |
2f6f61fd RW |
10277 | (properties `((upstream-name . "OrganismDbi"))) |
10278 | (build-system r-build-system) | |
10279 | (propagated-inputs | |
10280 | `(("r-annotationdbi" ,r-annotationdbi) | |
10281 | ("r-biobase" ,r-biobase) | |
10282 | ("r-biocgenerics" ,r-biocgenerics) | |
cdab2dcf | 10283 | ("r-biocmanager" ,r-biocmanager) |
2f6f61fd RW |
10284 | ("r-dbi" ,r-dbi) |
10285 | ("r-genomicfeatures" ,r-genomicfeatures) | |
10286 | ("r-genomicranges" ,r-genomicranges) | |
10287 | ("r-graph" ,r-graph) | |
10288 | ("r-iranges" ,r-iranges) | |
10289 | ("r-rbgl" ,r-rbgl) | |
10290 | ("r-s4vectors" ,r-s4vectors))) | |
10291 | (home-page "https://bioconductor.org/packages/OrganismDbi") | |
10292 | (synopsis "Software to enable the smooth interfacing of database packages") | |
10293 | (description "The package enables a simple unified interface to several | |
10294 | annotation packages each of which has its own schema by taking advantage of | |
10295 | the fact that each of these packages implements a select methods.") | |
10296 | (license license:artistic2.0))) | |
10297 | ||
7af1f403 RW |
10298 | (define-public r-biovizbase |
10299 | (package | |
10300 | (name "r-biovizbase") | |
e7a0bc1c | 10301 | (version "1.30.0") |
7af1f403 RW |
10302 | (source |
10303 | (origin | |
10304 | (method url-fetch) | |
10305 | (uri (bioconductor-uri "biovizBase" version)) | |
10306 | (sha256 | |
10307 | (base32 | |
e7a0bc1c | 10308 | "0v54mcn3rnnfx8dmcrms5z3rgq19n3hp4r23azlgzwq6hjw7cccx")))) |
7af1f403 RW |
10309 | (properties `((upstream-name . "biovizBase"))) |
10310 | (build-system r-build-system) | |
10311 | (propagated-inputs | |
10312 | `(("r-annotationdbi" ,r-annotationdbi) | |
10313 | ("r-annotationfilter" ,r-annotationfilter) | |
10314 | ("r-biocgenerics" ,r-biocgenerics) | |
10315 | ("r-biostrings" ,r-biostrings) | |
10316 | ("r-dichromat" ,r-dichromat) | |
10317 | ("r-ensembldb" ,r-ensembldb) | |
10318 | ("r-genomeinfodb" ,r-genomeinfodb) | |
10319 | ("r-genomicalignments" ,r-genomicalignments) | |
10320 | ("r-genomicfeatures" ,r-genomicfeatures) | |
10321 | ("r-genomicranges" ,r-genomicranges) | |
10322 | ("r-hmisc" ,r-hmisc) | |
10323 | ("r-iranges" ,r-iranges) | |
10324 | ("r-rcolorbrewer" ,r-rcolorbrewer) | |
70daf936 | 10325 | ("r-rlang" ,r-rlang) |
7af1f403 RW |
10326 | ("r-rsamtools" ,r-rsamtools) |
10327 | ("r-s4vectors" ,r-s4vectors) | |
10328 | ("r-scales" ,r-scales) | |
10329 | ("r-summarizedexperiment" ,r-summarizedexperiment) | |
10330 | ("r-variantannotation" ,r-variantannotation))) | |
10331 | (home-page "https://bioconductor.org/packages/biovizBase") | |
10332 | (synopsis "Basic graphic utilities for visualization of genomic data") | |
10333 | (description | |
10334 | "The biovizBase package is designed to provide a set of utilities, color | |
10335 | schemes and conventions for genomic data. It serves as the base for various | |
10336 | high-level packages for biological data visualization. This saves development | |
10337 | effort and encourages consistency.") | |
10338 | (license license:artistic2.0))) | |
10339 | ||
60faf945 RW |
10340 | (define-public r-ggbio |
10341 | (package | |
10342 | (name "r-ggbio") | |
f20c7664 | 10343 | (version "1.30.0") |
60faf945 RW |
10344 | (source |
10345 | (origin | |
10346 | (method url-fetch) | |
10347 | (uri (bioconductor-uri "ggbio" version)) | |
10348 | (sha256 | |
10349 | (base32 | |
f20c7664 | 10350 | "0wq49qqzkcn8s19xgaxf2s1j1a563d7pbhhvris6fhxfdjsz4934")))) |
60faf945 RW |
10351 | (build-system r-build-system) |
10352 | (propagated-inputs | |
10353 | `(("r-annotationdbi" ,r-annotationdbi) | |
10354 | ("r-annotationfilter" ,r-annotationfilter) | |
10355 | ("r-biobase" ,r-biobase) | |
10356 | ("r-biocgenerics" ,r-biocgenerics) | |
10357 | ("r-biostrings" ,r-biostrings) | |
10358 | ("r-biovizbase" ,r-biovizbase) | |
10359 | ("r-bsgenome" ,r-bsgenome) | |
10360 | ("r-ensembldb" ,r-ensembldb) | |
10361 | ("r-genomeinfodb" ,r-genomeinfodb) | |
10362 | ("r-genomicalignments" ,r-genomicalignments) | |
10363 | ("r-genomicfeatures" ,r-genomicfeatures) | |
10364 | ("r-genomicranges" ,r-genomicranges) | |
10365 | ("r-ggally" ,r-ggally) | |
10366 | ("r-ggplot2" ,r-ggplot2) | |
10367 | ("r-gridextra" ,r-gridextra) | |
10368 | ("r-gtable" ,r-gtable) | |
10369 | ("r-hmisc" ,r-hmisc) | |
10370 | ("r-iranges" ,r-iranges) | |
10371 | ("r-organismdbi" ,r-organismdbi) | |
10372 | ("r-reshape2" ,r-reshape2) | |
16527f1c | 10373 | ("r-rlang" ,r-rlang) |
60faf945 RW |
10374 | ("r-rsamtools" ,r-rsamtools) |
10375 | ("r-rtracklayer" ,r-rtracklayer) | |
10376 | ("r-s4vectors" ,r-s4vectors) | |
10377 | ("r-scales" ,r-scales) | |
10378 | ("r-summarizedexperiment" ,r-summarizedexperiment) | |
10379 | ("r-variantannotation" ,r-variantannotation))) | |
10380 | (home-page "http://www.tengfei.name/ggbio/") | |
10381 | (synopsis "Visualization tools for genomic data") | |
10382 | (description | |
10383 | "The ggbio package extends and specializes the grammar of graphics for | |
10384 | biological data. The graphics are designed to answer common scientific | |
10385 | questions, in particular those often asked of high throughput genomics data. | |
10386 | All core Bioconductor data structures are supported, where appropriate. The | |
10387 | package supports detailed views of particular genomic regions, as well as | |
10388 | genome-wide overviews. Supported overviews include ideograms and grand linear | |
10389 | views. High-level plots include sequence fragment length, edge-linked | |
10390 | interval to data view, mismatch pileup, and several splicing summaries.") | |
10391 | (license license:artistic2.0))) | |
10392 | ||
96a392a0 RW |
10393 | (define-public r-gprofiler |
10394 | (package | |
10395 | (name "r-gprofiler") | |
6b451c08 | 10396 | (version "0.6.7") |
96a392a0 RW |
10397 | (source |
10398 | (origin | |
10399 | (method url-fetch) | |
10400 | (uri (cran-uri "gProfileR" version)) | |
10401 | (sha256 | |
10402 | (base32 | |
6b451c08 | 10403 | "12nwidbnqmnfy5dnqga26byslvdnkrpz2fi19qfcby6xx0wbndk7")))) |
96a392a0 RW |
10404 | (properties `((upstream-name . "gProfileR"))) |
10405 | (build-system r-build-system) | |
10406 | (propagated-inputs | |
10407 | `(("r-plyr" ,r-plyr) | |
10408 | ("r-rcurl" ,r-rcurl))) | |
e9960d8c | 10409 | (home-page "https://cran.r-project.org/web/packages/gProfileR/") |
96a392a0 RW |
10410 | (synopsis "Interface to the g:Profiler toolkit") |
10411 | (description | |
10412 | "This package provides tools for functional enrichment analysis, | |
10413 | gene identifier conversion and mapping homologous genes across related | |
10414 | organisms via the @code{g:Profiler} toolkit.") | |
10415 | (license license:gpl2+))) | |
10416 | ||
e2b92799 RW |
10417 | (define-public r-gqtlbase |
10418 | (package | |
10419 | (name "r-gqtlbase") | |
181a8431 | 10420 | (version "1.14.0") |
e2b92799 RW |
10421 | (source |
10422 | (origin | |
10423 | (method url-fetch) | |
10424 | (uri (bioconductor-uri "gQTLBase" version)) | |
10425 | (sha256 | |
10426 | (base32 | |
181a8431 | 10427 | "1lbk1m1mkvbk30flk5pf3pcrnm2s0sj5r48kbjgad39dsvd8zgqx")))) |
e2b92799 RW |
10428 | (properties `((upstream-name . "gQTLBase"))) |
10429 | (build-system r-build-system) | |
10430 | (propagated-inputs | |
10431 | `(("r-batchjobs" ,r-batchjobs) | |
10432 | ("r-bbmisc" ,r-bbmisc) | |
10433 | ("r-biocgenerics" ,r-biocgenerics) | |
10434 | ("r-bit" ,r-bit) | |
10435 | ("r-doparallel" ,r-doparallel) | |
10436 | ("r-ff" ,r-ff) | |
10437 | ("r-ffbase" ,r-ffbase) | |
10438 | ("r-foreach" ,r-foreach) | |
10439 | ("r-genomicfiles" ,r-genomicfiles) | |
10440 | ("r-genomicranges" ,r-genomicranges) | |
10441 | ("r-rtracklayer" ,r-rtracklayer) | |
10442 | ("r-s4vectors" ,r-s4vectors) | |
10443 | ("r-summarizedexperiment" ,r-summarizedexperiment))) | |
10444 | (home-page "https://bioconductor.org/packages/gQTLBase") | |
10445 | (synopsis "Infrastructure for eQTL, mQTL and similar studies") | |
10446 | (description | |
10447 | "The purpose of this package is to simplify the storage and interrogation | |
10448 | of @dfn{quantitative trait loci} (QTL) archives, such as eQTL, mQTL, dsQTL, | |
10449 | and more.") | |
10450 | (license license:artistic2.0))) | |
10451 | ||
dd5fc8b7 RW |
10452 | (define-public r-snpstats |
10453 | (package | |
10454 | (name "r-snpstats") | |
220ac15e | 10455 | (version "1.32.0") |
dd5fc8b7 RW |
10456 | (source |
10457 | (origin | |
10458 | (method url-fetch) | |
10459 | (uri (bioconductor-uri "snpStats" version)) | |
10460 | (sha256 | |
10461 | (base32 | |
220ac15e | 10462 | "1pplx4pf9bqi7v5v1l74yknc1s61carvbqkf327ky7vbvp0bck33")))) |
dd5fc8b7 RW |
10463 | (properties `((upstream-name . "snpStats"))) |
10464 | (build-system r-build-system) | |
10465 | (inputs `(("zlib" ,zlib))) | |
10466 | (propagated-inputs | |
10467 | `(("r-biocgenerics" ,r-biocgenerics) | |
10468 | ("r-matrix" ,r-matrix) | |
10469 | ("r-survival" ,r-survival) | |
10470 | ("r-zlibbioc" ,r-zlibbioc))) | |
10471 | (home-page "https://bioconductor.org/packages/snpStats") | |
10472 | (synopsis "Methods for SNP association studies") | |
10473 | (description | |
10474 | "This package provides classes and statistical methods for large | |
10475 | @dfn{single-nucleotide polymorphism} (SNP) association studies. This extends | |
10476 | the earlier snpMatrix package, allowing for uncertainty in genotypes.") | |
10477 | (license license:gpl3))) | |
10478 | ||
421c68e3 RW |
10479 | (define-public r-homo-sapiens |
10480 | (package | |
10481 | (name "r-homo-sapiens") | |
10482 | (version "1.3.1") | |
10483 | (source (origin | |
10484 | (method url-fetch) | |
10485 | ;; We cannot use bioconductor-uri here because this tarball is | |
10486 | ;; located under "data/annotation/" instead of "bioc/". | |
10487 | (uri (string-append "http://www.bioconductor.org/packages/" | |
10488 | "release/data/annotation/src/contrib/" | |
10489 | "Homo.sapiens_" | |
10490 | version ".tar.gz")) | |
10491 | (sha256 | |
10492 | (base32 | |
10493 | "151vj7h5p1c8yd5swrchk46z469p135wk50hvkl0nhgndvy0jj01")))) | |
10494 | (properties | |
10495 | `((upstream-name . "Homo.sapiens"))) | |
10496 | (build-system r-build-system) | |
10497 | (propagated-inputs | |
10498 | `(("r-genomicfeatures" ,r-genomicfeatures) | |
10499 | ("r-go-db" ,r-go-db) | |
10500 | ("r-org-hs-eg-db" ,r-org-hs-eg-db) | |
10501 | ("r-txdb-hsapiens-ucsc-hg19-knowngene" ,r-txdb-hsapiens-ucsc-hg19-knowngene) | |
10502 | ("r-organismdbi" ,r-organismdbi) | |
10503 | ("r-annotationdbi" ,r-annotationdbi))) | |
10504 | (home-page "https://bioconductor.org/packages/Homo.sapiens/") | |
10505 | (synopsis "Annotation package for the Homo.sapiens object") | |
10506 | (description | |
10507 | "This package contains the Homo.sapiens object to access data from | |
10508 | several related annotation packages.") | |
10509 | (license license:artistic2.0))) | |
10510 | ||
15f98b0d RW |
10511 | (define-public r-erma |
10512 | (package | |
10513 | (name "r-erma") | |
4b913355 | 10514 | (version "0.14.0") |
15f98b0d RW |
10515 | (source |
10516 | (origin | |
10517 | (method url-fetch) | |
10518 | (uri (bioconductor-uri "erma" version)) | |
10519 | (sha256 | |
10520 | (base32 | |
4b913355 | 10521 | "0hj9iz904rr1y66442lkxjywkw1ydyxxlhmjirawbf09ic5ad4g9")))) |
15f98b0d RW |
10522 | (build-system r-build-system) |
10523 | (propagated-inputs | |
10524 | `(("r-annotationdbi" ,r-annotationdbi) | |
10525 | ("r-biobase" ,r-biobase) | |
10526 | ("r-biocgenerics" ,r-biocgenerics) | |
9b0b108e RW |
10527 | ("r-biocparallel" ,r-biocparallel) |
10528 | ("r-genomeinfodb" ,r-genomeinfodb) | |
15f98b0d RW |
10529 | ("r-genomicfiles" ,r-genomicfiles) |
10530 | ("r-genomicranges" ,r-genomicranges) | |
10531 | ("r-ggplot2" ,r-ggplot2) | |
10532 | ("r-homo-sapiens" ,r-homo-sapiens) | |
9b0b108e | 10533 | ("r-iranges" ,r-iranges) |
15f98b0d RW |
10534 | ("r-rtracklayer" ,r-rtracklayer) |
10535 | ("r-s4vectors" ,r-s4vectors) | |
10536 | ("r-shiny" ,r-shiny) | |
10537 | ("r-summarizedexperiment" ,r-summarizedexperiment))) | |
10538 | (home-page "https://bioconductor.org/packages/erma") | |
10539 | (synopsis "Epigenomic road map adventures") | |
10540 | (description | |
10541 | "The epigenomics road map describes locations of epigenetic marks in DNA | |
10542 | from a variety of cell types. Of interest are locations of histone | |
10543 | modifications, sites of DNA methylation, and regions of accessible chromatin. | |
10544 | This package presents a selection of elements of the road map including | |
10545 | metadata and outputs of the ChromImpute procedure applied to ENCODE cell lines | |
10546 | by Ernst and Kellis.") | |
10547 | (license license:artistic2.0))) | |
10548 | ||
66c39102 RW |
10549 | (define-public r-ldblock |
10550 | (package | |
10551 | (name "r-ldblock") | |
da679b52 | 10552 | (version "1.12.0") |
66c39102 RW |
10553 | (source |
10554 | (origin | |
10555 | (method url-fetch) | |
10556 | (uri (bioconductor-uri "ldblock" version)) | |
10557 | (sha256 | |
10558 | (base32 | |
da679b52 | 10559 | "0xbf4pmhrk5fnd1iz5wzjvdr75v114bwpznhcig4wiqmxc27sips")))) |
66c39102 RW |
10560 | (build-system r-build-system) |
10561 | (propagated-inputs | |
45c29a6e RW |
10562 | `(("r-biocgenerics" ,r-biocgenerics) |
10563 | ("r-erma" ,r-erma) | |
66c39102 RW |
10564 | ("r-genomeinfodb" ,r-genomeinfodb) |
10565 | ("r-genomicfiles" ,r-genomicfiles) | |
10566 | ("r-go-db" ,r-go-db) | |
10567 | ("r-homo-sapiens" ,r-homo-sapiens) | |
10568 | ("r-matrix" ,r-matrix) | |
10569 | ("r-rsamtools" ,r-rsamtools) | |
10570 | ("r-snpstats" ,r-snpstats) | |
10571 | ("r-variantannotation" ,r-variantannotation))) | |
10572 | (home-page "https://bioconductor.org/packages/ldblock") | |
10573 | (synopsis "Data structures for linkage disequilibrium measures in populations") | |
10574 | (description | |
10575 | "This package defines data structures for @dfn{linkage | |
10576 | disequilibrium} (LD) measures in populations. Its purpose is to simplify | |
10577 | handling of existing population-level data for the purpose of flexibly | |
10578 | defining LD blocks.") | |
10579 | (license license:artistic2.0))) | |
10580 | ||
794ff347 RW |
10581 | (define-public r-gqtlstats |
10582 | (package | |
10583 | (name "r-gqtlstats") | |
ea55326d | 10584 | (version "1.14.0") |
794ff347 RW |
10585 | (source |
10586 | (origin | |
10587 | (method url-fetch) | |
10588 | (uri (bioconductor-uri "gQTLstats" version)) | |
10589 | (sha256 | |
10590 | (base32 | |
ea55326d | 10591 | "1sg9kw59dlayj7qxql9pd93d4hmml504sa3kkfpzfh3xri7m5pxf")))) |
794ff347 RW |
10592 | (properties `((upstream-name . "gQTLstats"))) |
10593 | (build-system r-build-system) | |
10594 | (propagated-inputs | |
10595 | `(("r-annotationdbi" ,r-annotationdbi) | |
10596 | ("r-batchjobs" ,r-batchjobs) | |
10597 | ("r-bbmisc" ,r-bbmisc) | |
10598 | ("r-beeswarm" ,r-beeswarm) | |
10599 | ("r-biobase" ,r-biobase) | |
10600 | ("r-biocgenerics" ,r-biocgenerics) | |
10601 | ("r-doparallel" ,r-doparallel) | |
10602 | ("r-dplyr" ,r-dplyr) | |
10603 | ("r-erma" ,r-erma) | |
10604 | ("r-ffbase" ,r-ffbase) | |
10605 | ("r-foreach" ,r-foreach) | |
10606 | ("r-genomeinfodb" ,r-genomeinfodb) | |
10607 | ("r-genomicfeatures" ,r-genomicfeatures) | |
10608 | ("r-genomicfiles" ,r-genomicfiles) | |
10609 | ("r-genomicranges" ,r-genomicranges) | |
10610 | ("r-ggbeeswarm" ,r-ggbeeswarm) | |
10611 | ("r-ggplot2" ,r-ggplot2) | |
10612 | ("r-gqtlbase" ,r-gqtlbase) | |
10613 | ("r-hardyweinberg" ,r-hardyweinberg) | |
6929b975 | 10614 | ("r-homo-sapiens" ,r-homo-sapiens) |
794ff347 | 10615 | ("r-iranges" ,r-iranges) |
794ff347 RW |
10616 | ("r-limma" ,r-limma) |
10617 | ("r-mgcv" ,r-mgcv) | |
10618 | ("r-plotly" ,r-plotly) | |
10619 | ("r-reshape2" ,r-reshape2) | |
10620 | ("r-s4vectors" ,r-s4vectors) | |
10621 | ("r-shiny" ,r-shiny) | |
10622 | ("r-snpstats" ,r-snpstats) | |
10623 | ("r-summarizedexperiment" ,r-summarizedexperiment) | |
10624 | ("r-variantannotation" ,r-variantannotation))) | |
10625 | (home-page "https://bioconductor.org/packages/gQTLstats") | |
10626 | (synopsis "Computationally efficient analysis for eQTL and allied studies") | |
10627 | (description | |
10628 | "This package provides tools for the computationally efficient analysis | |
10629 | of @dfn{quantitative trait loci} (QTL) data, including eQTL, mQTL, dsQTL, etc. | |
10630 | The software in this package aims to support refinements and functional | |
10631 | interpretation of members of a collection of association statistics on a | |
10632 | family of feature/genome hypotheses.") | |
10633 | (license license:artistic2.0))) | |
10634 | ||
42720006 RW |
10635 | (define-public r-gviz |
10636 | (package | |
10637 | (name "r-gviz") | |
d57445c9 | 10638 | (version "1.26.0") |
42720006 RW |
10639 | (source |
10640 | (origin | |
10641 | (method url-fetch) | |
10642 | (uri (bioconductor-uri "Gviz" version)) | |
10643 | (sha256 | |
10644 | (base32 | |
d57445c9 | 10645 | "05zk9hf30afg6rjg97lzn5v8xij90v8zm09y9vcz0asmc3c8xs0a")))) |
42720006 RW |
10646 | (properties `((upstream-name . "Gviz"))) |
10647 | (build-system r-build-system) | |
10648 | (propagated-inputs | |
10649 | `(("r-annotationdbi" ,r-annotationdbi) | |
10650 | ("r-biobase" ,r-biobase) | |
10651 | ("r-biocgenerics" ,r-biocgenerics) | |
10652 | ("r-biomart" ,r-biomart) | |
10653 | ("r-biostrings" ,r-biostrings) | |
10654 | ("r-biovizbase" ,r-biovizbase) | |
10655 | ("r-bsgenome" ,r-bsgenome) | |
10656 | ("r-digest" ,r-digest) | |
10657 | ("r-genomeinfodb" ,r-genomeinfodb) | |
10658 | ("r-genomicalignments" ,r-genomicalignments) | |
10659 | ("r-genomicfeatures" ,r-genomicfeatures) | |
10660 | ("r-genomicranges" ,r-genomicranges) | |
10661 | ("r-iranges" ,r-iranges) | |
10662 | ("r-lattice" ,r-lattice) | |
10663 | ("r-latticeextra" ,r-latticeextra) | |
10664 | ("r-matrixstats" ,r-matrixstats) | |
10665 | ("r-rcolorbrewer" ,r-rcolorbrewer) | |
10666 | ("r-rsamtools" ,r-rsamtools) | |
10667 | ("r-rtracklayer" ,r-rtracklayer) | |
10668 | ("r-s4vectors" ,r-s4vectors) | |
10669 | ("r-xvector" ,r-xvector))) | |
10670 | (home-page "https://bioconductor.org/packages/Gviz") | |
10671 | (synopsis "Plotting data and annotation information along genomic coordinates") | |
10672 | (description | |
10673 | "Genomic data analyses requires integrated visualization of known genomic | |
10674 | information and new experimental data. Gviz uses the biomaRt and the | |
10675 | rtracklayer packages to perform live annotation queries to Ensembl and UCSC | |
10676 | and translates this to e.g. gene/transcript structures in viewports of the | |
10677 | grid graphics package. This results in genomic information plotted together | |
10678 | with your data.") | |
10679 | (license license:artistic2.0))) | |
10680 | ||
2e4ce60e RW |
10681 | (define-public r-gwascat |
10682 | (package | |
10683 | (name "r-gwascat") | |
85b16c05 | 10684 | (version "2.14.0") |
2e4ce60e RW |
10685 | (source |
10686 | (origin | |
10687 | (method url-fetch) | |
10688 | (uri (bioconductor-uri "gwascat" version)) | |
10689 | (sha256 | |
10690 | (base32 | |
85b16c05 | 10691 | "1fnyjydhicq4ayrv0lqjv48h9bd72h40s6l82g1h2ng0icwz38g0")))) |
2e4ce60e RW |
10692 | (build-system r-build-system) |
10693 | (propagated-inputs | |
10694 | `(("r-annotationdbi" ,r-annotationdbi) | |
10695 | ("r-annotationhub" ,r-annotationhub) | |
10696 | ("r-biocgenerics" ,r-biocgenerics) | |
10697 | ("r-biostrings" ,r-biostrings) | |
10698 | ("r-genomeinfodb" ,r-genomeinfodb) | |
10699 | ("r-genomicfeatures" ,r-genomicfeatures) | |
10700 | ("r-genomicranges" ,r-genomicranges) | |
10701 | ("r-ggbio" ,r-ggbio) | |
10702 | ("r-ggplot2" ,r-ggplot2) | |
10703 | ("r-gqtlstats" ,r-gqtlstats) | |
10704 | ("r-graph" ,r-graph) | |
10705 | ("r-gviz" ,r-gviz) | |
10706 | ("r-homo-sapiens" ,r-homo-sapiens) | |
10707 | ("r-iranges" ,r-iranges) | |
10708 | ("r-rsamtools" ,r-rsamtools) | |
10709 | ("r-rtracklayer" ,r-rtracklayer) | |
10710 | ("r-s4vectors" ,r-s4vectors) | |
10711 | ("r-snpstats" ,r-snpstats) | |
10712 | ("r-summarizedexperiment" ,r-summarizedexperiment) | |
10713 | ("r-variantannotation" ,r-variantannotation))) | |
10714 | (home-page "https://bioconductor.org/packages/gwascat") | |
10715 | (synopsis "Tools for data in the EMBL-EBI GWAS catalog") | |
10716 | (description | |
10717 | "This package provides tools for representing and modeling data in the | |
10718 | EMBL-EBI GWAS catalog.") | |
10719 | (license license:artistic2.0))) | |
10720 | ||
fbf54406 RW |
10721 | (define-public r-sushi |
10722 | (package | |
10723 | (name "r-sushi") | |
7468a764 | 10724 | (version "1.20.0") |
fbf54406 RW |
10725 | (source (origin |
10726 | (method url-fetch) | |
10727 | (uri (bioconductor-uri "Sushi" version)) | |
10728 | (sha256 | |
10729 | (base32 | |
7468a764 | 10730 | "0dv5di0hgbvk9cxnqhyf18mdjl50k6bk00a89r6zgp83rbxwr1r8")))) |
fbf54406 RW |
10731 | (properties `((upstream-name . "Sushi"))) |
10732 | (build-system r-build-system) | |
10733 | (propagated-inputs | |
10734 | `(("r-biomart" ,r-biomart) | |
10735 | ("r-zoo" ,r-zoo))) | |
10736 | (home-page "https://bioconductor.org/packages/Sushi") | |
10737 | (synopsis "Tools for visualizing genomics data") | |
10738 | (description | |
10739 | "This package provides flexible, quantitative, and integrative genomic | |
10740 | visualizations for publication-quality multi-panel figures.") | |
10741 | (license license:gpl2+))) | |
10742 | ||
30eb4e37 RW |
10743 | (define-public r-fithic |
10744 | (package | |
10745 | (name "r-fithic") | |
80239129 | 10746 | (version "1.8.0") |
30eb4e37 RW |
10747 | (source (origin |
10748 | (method url-fetch) | |
10749 | (uri (bioconductor-uri "FitHiC" version)) | |
10750 | (sha256 | |
10751 | (base32 | |
80239129 | 10752 | "15xd8mz7660q4zr9p74mq1pqps4iz7pxp8f9ifn21gwg94aq1avn")))) |
30eb4e37 RW |
10753 | (properties `((upstream-name . "FitHiC"))) |
10754 | (build-system r-build-system) | |
10755 | (propagated-inputs | |
10756 | `(("r-data-table" ,r-data-table) | |
10757 | ("r-fdrtool" ,r-fdrtool) | |
10758 | ("r-rcpp" ,r-rcpp))) | |
10759 | (home-page "https://bioconductor.org/packages/FitHiC") | |
10760 | (synopsis "Confidence estimation for intra-chromosomal contact maps") | |
10761 | (description | |
10762 | "Fit-Hi-C is a tool for assigning statistical confidence estimates to | |
10763 | intra-chromosomal contact maps produced by genome-wide genome architecture | |
10764 | assays such as Hi-C.") | |
10765 | (license license:gpl2+))) | |
10766 | ||
c49102ec RW |
10767 | (define-public r-hitc |
10768 | (package | |
10769 | (name "r-hitc") | |
d055f199 | 10770 | (version "1.26.0") |
c49102ec RW |
10771 | (source (origin |
10772 | (method url-fetch) | |
10773 | (uri (bioconductor-uri "HiTC" version)) | |
10774 | (sha256 | |
10775 | (base32 | |
d055f199 | 10776 | "11f96k1707g6milpjgnrjf3b5r42hsrxhb5d8znkcr3y3mrskdbj")))) |
c49102ec RW |
10777 | (properties `((upstream-name . "HiTC"))) |
10778 | (build-system r-build-system) | |
10779 | (propagated-inputs | |
10780 | `(("r-biostrings" ,r-biostrings) | |
10781 | ("r-genomeinfodb" ,r-genomeinfodb) | |
10782 | ("r-genomicranges" ,r-genomicranges) | |
10783 | ("r-iranges" ,r-iranges) | |
10784 | ("r-matrix" ,r-matrix) | |
10785 | ("r-rcolorbrewer" ,r-rcolorbrewer) | |
10786 | ("r-rtracklayer" ,r-rtracklayer))) | |
10787 | (home-page "https://bioconductor.org/packages/HiTC") | |
10788 | (synopsis "High throughput chromosome conformation capture analysis") | |
10789 | (description | |
10790 | "The HiTC package was developed to explore high-throughput \"C\" data | |
10791 | such as 5C or Hi-C. Dedicated R classes as well as standard methods for | |
10792 | quality controls, normalization, visualization, and further analysis are also | |
10793 | provided.") | |
10794 | (license license:artistic2.0))) | |
10795 | ||
212f6120 RW |
10796 | (define-public r-qvalue |
10797 | (package | |
10798 | (name "r-qvalue") | |
edb91244 | 10799 | (version "2.14.0") |
212f6120 RW |
10800 | (source |
10801 | (origin | |
10802 | (method url-fetch) | |
10803 | (uri (bioconductor-uri "qvalue" version)) | |
10804 | (sha256 | |
10805 | (base32 | |
edb91244 | 10806 | "03qxshqwwq1rj23p6pjrz08jm3ziikvy9badi4mz2rcwy2nz783a")))) |
212f6120 RW |
10807 | (build-system r-build-system) |
10808 | (propagated-inputs | |
10809 | `(("r-ggplot2" ,r-ggplot2) | |
10810 | ("r-reshape2" ,r-reshape2))) | |
10811 | (home-page "http://github.com/jdstorey/qvalue") | |
10812 | (synopsis "Q-value estimation for false discovery rate control") | |
10813 | (description | |
10814 | "This package takes a list of p-values resulting from the simultaneous | |
10815 | testing of many hypotheses and estimates their q-values and local @dfn{false | |
10816 | discovery rate} (FDR) values. The q-value of a test measures the proportion | |
10817 | of false positives incurred when that particular test is called significant. | |
10818 | The local FDR measures the posterior probability the null hypothesis is true | |
10819 | given the test's p-value. Various plots are automatically generated, allowing | |
10820 | one to make sensible significance cut-offs. The software can be applied to | |
10821 | problems in genomics, brain imaging, astrophysics, and data mining.") | |
10822 | ;; Any version of the LGPL. | |
10823 | (license license:lgpl3+))) | |
10824 | ||
aba3e482 RW |
10825 | (define-public r-hdf5array |
10826 | (package | |
10827 | (name "r-hdf5array") | |
8e48d36f | 10828 | (version "1.10.0") |
aba3e482 RW |
10829 | (source |
10830 | (origin | |
10831 | (method url-fetch) | |
10832 | (uri (bioconductor-uri "HDF5Array" version)) | |
10833 | (sha256 | |
10834 | (base32 | |
8e48d36f | 10835 | "1w7ad8cfsbh5xx82m3l4lc0vbmj9lcsqxxpiy3ana2ycgn1bqv3g")))) |
aba3e482 RW |
10836 | (properties `((upstream-name . "HDF5Array"))) |
10837 | (build-system r-build-system) | |
10838 | (propagated-inputs | |
10839 | `(("r-biocgenerics" ,r-biocgenerics) | |
10840 | ("r-delayedarray" ,r-delayedarray) | |
10841 | ("r-iranges" ,r-iranges) | |
10842 | ("r-rhdf5" ,r-rhdf5) | |
10843 | ("r-s4vectors" ,r-s4vectors))) | |
10844 | (home-page "https://bioconductor.org/packages/HDF5Array") | |
10845 | (synopsis "HDF5 back end for DelayedArray objects") | |
10846 | (description "This package provides an array-like container for convenient | |
10847 | access and manipulation of HDF5 datasets. It supports delayed operations and | |
10848 | block processing.") | |
10849 | (license license:artistic2.0))) | |
10850 | ||
748e9f16 RW |
10851 | (define-public r-rhdf5lib |
10852 | (package | |
10853 | (name "r-rhdf5lib") | |
37200dbc | 10854 | (version "1.4.0") |
748e9f16 RW |
10855 | (source |
10856 | (origin | |
10857 | (method url-fetch) | |
10858 | (uri (bioconductor-uri "Rhdf5lib" version)) | |
10859 | (sha256 | |
10860 | (base32 | |
37200dbc RW |
10861 | "01gpz780g850ql20b2ql6pvr678ydk4nq4sn5iiih94a4crb9lz1")) |
10862 | (modules '((guix build utils))) | |
10863 | (snippet | |
10864 | '(begin | |
10865 | ;; Delete bundled binaries | |
10866 | (delete-file-recursively "src/winlib/") | |
10867 | #t)))) | |
748e9f16 RW |
10868 | (properties `((upstream-name . "Rhdf5lib"))) |
10869 | (build-system r-build-system) | |
10870 | (arguments | |
10871 | `(#:phases | |
10872 | (modify-phases %standard-phases | |
10873 | (add-after 'unpack 'do-not-use-bundled-hdf5 | |
10874 | (lambda* (#:key inputs #:allow-other-keys) | |
10875 | (for-each delete-file '("configure" "configure.ac")) | |
10876 | ;; Do not make other packages link with the proprietary libsz. | |
10877 | (substitute* "R/zzz.R" | |
e9c41736 RW |
10878 | (("'%s/libhdf5_cpp.a %s/libhdf5.a %s/libsz.a -lz'") |
10879 | "'%s/libhdf5_cpp.a %s/libhdf5.a %s/libhdf5.a -lz'") | |
10880 | (("'%s/libhdf5.a %s/libsz.a -lz'") | |
10881 | "'%s/libhdf5.a %s/libhdf5.a -lz'")) | |
748e9f16 RW |
10882 | (with-directory-excursion "src" |
10883 | (invoke "tar" "xvf" (assoc-ref inputs "hdf5-source")) | |
37200dbc | 10884 | (rename-file (string-append "hdf5-" ,(package-version hdf5-1.10)) |
748e9f16 | 10885 | "hdf5") |
a539ad86 RW |
10886 | ;; Remove timestamp and host system information to make |
10887 | ;; the build reproducible. | |
10888 | (substitute* "hdf5/src/libhdf5.settings.in" | |
10889 | (("Configured on: @CONFIG_DATE@") | |
10890 | "Configured on: Guix") | |
10891 | (("Uname information:.*") | |
10892 | "Uname information: Linux\n") | |
10893 | ;; Remove unnecessary store reference. | |
10894 | (("C Compiler:.*") | |
10895 | "C Compiler: GCC\n")) | |
748e9f16 RW |
10896 | (rename-file "Makevars.in" "Makevars") |
10897 | (substitute* "Makevars" | |
10898 | (("HDF5_CXX_LIB=.*") | |
10899 | (string-append "HDF5_CXX_LIB=" | |
10900 | (assoc-ref inputs "hdf5") "/lib/libhdf5_cpp.a\n")) | |
10901 | (("HDF5_LIB=.*") | |
10902 | (string-append "HDF5_LIB=" | |
10903 | (assoc-ref inputs "hdf5") "/lib/libhdf5.a\n")) | |
10904 | (("HDF5_CXX_INCLUDE=.*") "HDF5_CXX_INCLUDE=./hdf5/c++/src\n") | |
10905 | (("HDF5_INCLUDE=.*") "HDF5_INCLUDE=./hdf5/src\n") | |
10906 | ;; szip is non-free software | |
10907 | (("cp \\$\\{SZIP_LIB\\}.*") "") | |
e9c41736 | 10908 | (("\\$\\{USER_LIB_DIR\\}libsz.a") ""))) |
748e9f16 RW |
10909 | #t))))) |
10910 | (inputs | |
10911 | `(("zlib" ,zlib))) | |
10912 | (propagated-inputs | |
37200dbc | 10913 | `(("hdf5" ,hdf5-1.10))) |
748e9f16 | 10914 | (native-inputs |
37200dbc | 10915 | `(("hdf5-source" ,(package-source hdf5-1.10)))) |
748e9f16 RW |
10916 | (home-page "https://bioconductor.org/packages/Rhdf5lib") |
10917 | (synopsis "HDF5 library as an R package") | |
10918 | (description "This package provides C and C++ HDF5 libraries for use in R | |
10919 | packages.") | |
10920 | (license license:artistic2.0))) | |
10921 | ||
9ec08988 RW |
10922 | (define-public r-beachmat |
10923 | (package | |
10924 | (name "r-beachmat") | |
3c833608 | 10925 | (version "1.4.0") |
9ec08988 RW |
10926 | (source |
10927 | (origin | |
10928 | (method url-fetch) | |
10929 | (uri (bioconductor-uri "beachmat" version)) | |
10930 | (sha256 | |
10931 | (base32 | |
3c833608 | 10932 | "07zgmms0qg8gw7x0js46965bbhpfj2aa1h5ixdz9r332bxv9cdmr")))) |
9ec08988 RW |
10933 | (build-system r-build-system) |
10934 | (inputs | |
fd613234 RW |
10935 | `(("hdf5" ,hdf5) |
10936 | ("zlib" ,zlib))) | |
9ec08988 | 10937 | (propagated-inputs |
3c833608 RW |
10938 | `(("r-biocgenerics" ,r-biocgenerics) |
10939 | ("r-delayedarray" ,r-delayedarray) | |
9ec08988 RW |
10940 | ("r-hdf5array" ,r-hdf5array) |
10941 | ("r-rcpp" ,r-rcpp) | |
10942 | ("r-rhdf5" ,r-rhdf5) | |
10943 | ("r-rhdf5lib" ,r-rhdf5lib))) | |
10944 | (home-page "https://bioconductor.org/packages/beachmat") | |
10945 | (synopsis "Compiling Bioconductor to handle each matrix type") | |
10946 | (description "This package provides a consistent C++ class interface for a | |
10947 | variety of commonly used matrix types, including sparse and HDF5-backed | |
10948 | matrices.") | |
10949 | (license license:gpl3))) | |
10950 | ||
6fb1dc17 RW |
10951 | (define-public r-singlecellexperiment |
10952 | (package | |
10953 | (name "r-singlecellexperiment") | |
f93ec63c | 10954 | (version "1.4.0") |
6fb1dc17 RW |
10955 | (source |
10956 | (origin | |
10957 | (method url-fetch) | |
10958 | (uri (bioconductor-uri "SingleCellExperiment" version)) | |
10959 | (sha256 | |
10960 | (base32 | |
f93ec63c | 10961 | "19r4r7djrn46qlijkj1g926vcklxzcrxjlxv6cg43m9j9jgfs3dj")))) |
6fb1dc17 RW |
10962 | (properties |
10963 | `((upstream-name . "SingleCellExperiment"))) | |
10964 | (build-system r-build-system) | |
10965 | (propagated-inputs | |
10966 | `(("r-biocgenerics" ,r-biocgenerics) | |
10967 | ("r-s4vectors" ,r-s4vectors) | |
10968 | ("r-summarizedexperiment" ,r-summarizedexperiment))) | |
10969 | (home-page "https://bioconductor.org/packages/SingleCellExperiment") | |
10970 | (synopsis "S4 classes for single cell data") | |
10971 | (description "This package defines an S4 class for storing data from | |
10972 | single-cell experiments. This includes specialized methods to store and | |
10973 | retrieve spike-in information, dimensionality reduction coordinates and size | |
10974 | factors for each cell, along with the usual metadata for genes and | |
10975 | libraries.") | |
10976 | (license license:gpl3))) | |
10977 | ||
658ab21d RW |
10978 | (define-public r-scater |
10979 | (package | |
10980 | (name "r-scater") | |
48f27914 | 10981 | (version "1.10.0") |
658ab21d RW |
10982 | (source (origin |
10983 | (method url-fetch) | |
10984 | (uri (bioconductor-uri "scater" version)) | |
10985 | (sha256 | |
10986 | (base32 | |
48f27914 | 10987 | "1kwa9n70c5j0xcj6nkmlkzjr63cnj78mp8nhg58n07fq1ijm4ns3")))) |
658ab21d RW |
10988 | (build-system r-build-system) |
10989 | (propagated-inputs | |
10990 | `(("r-beachmat" ,r-beachmat) | |
658ab21d | 10991 | ("r-biocgenerics" ,r-biocgenerics) |
48f27914 | 10992 | ("r-biocparallel" ,r-biocparallel) |
92963798 RW |
10993 | ("r-delayedarray" ,r-delayedarray) |
10994 | ("r-delayedmatrixstats" ,r-delayedmatrixstats) | |
658ab21d | 10995 | ("r-dplyr" ,r-dplyr) |
658ab21d RW |
10996 | ("r-ggbeeswarm" ,r-ggbeeswarm) |
10997 | ("r-ggplot2" ,r-ggplot2) | |
658ab21d | 10998 | ("r-matrix" ,r-matrix) |
658ab21d RW |
10999 | ("r-plyr" ,r-plyr) |
11000 | ("r-rcpp" ,r-rcpp) | |
11001 | ("r-reshape2" ,r-reshape2) | |
658ab21d | 11002 | ("r-rhdf5lib" ,r-rhdf5lib) |
658ab21d | 11003 | ("r-s4vectors" ,r-s4vectors) |
658ab21d RW |
11004 | ("r-singlecellexperiment" ,r-singlecellexperiment) |
11005 | ("r-summarizedexperiment" ,r-summarizedexperiment) | |
658ab21d RW |
11006 | ("r-viridis" ,r-viridis))) |
11007 | (home-page "https://github.com/davismcc/scater") | |
11008 | (synopsis "Single-cell analysis toolkit for gene expression data in R") | |
11009 | (description "This package provides a collection of tools for doing | |
11010 | various analyses of single-cell RNA-seq gene expression data, with a focus on | |
11011 | quality control.") | |
11012 | (license license:gpl2+))) | |
11013 | ||
7f1d9bef RW |
11014 | (define-public r-scran |
11015 | (package | |
11016 | (name "r-scran") | |
70a3a76b | 11017 | (version "1.10.1") |
7f1d9bef RW |
11018 | (source |
11019 | (origin | |
11020 | (method url-fetch) | |
11021 | (uri (bioconductor-uri "scran" version)) | |
11022 | (sha256 | |
11023 | (base32 | |
70a3a76b | 11024 | "1viyzrwfm9vccsf54c6g7k1dn7skkfx4ml1jy12q67wa20sx8l03")))) |
7f1d9bef RW |
11025 | (build-system r-build-system) |
11026 | (propagated-inputs | |
11027 | `(("r-beachmat" ,r-beachmat) | |
11028 | ("r-biocgenerics" ,r-biocgenerics) | |
70a3a76b | 11029 | ("r-biocneighbors" ,r-biocneighbors) |
7f1d9bef | 11030 | ("r-biocparallel" ,r-biocparallel) |
d7e32999 RW |
11031 | ("r-delayedarray" ,r-delayedarray) |
11032 | ("r-delayedmatrixstats" ,r-delayedmatrixstats) | |
7f1d9bef RW |
11033 | ("r-dynamictreecut" ,r-dynamictreecut) |
11034 | ("r-edger" ,r-edger) | |
7f1d9bef RW |
11035 | ("r-igraph" ,r-igraph) |
11036 | ("r-limma" ,r-limma) | |
11037 | ("r-matrix" ,r-matrix) | |
11038 | ("r-rcpp" ,r-rcpp) | |
11039 | ("r-rhdf5lib" ,r-rhdf5lib) | |
11040 | ("r-s4vectors" ,r-s4vectors) | |
11041 | ("r-scater" ,r-scater) | |
7f1d9bef RW |
11042 | ("r-singlecellexperiment" ,r-singlecellexperiment) |
11043 | ("r-statmod" ,r-statmod) | |
70a3a76b | 11044 | ("r-summarizedexperiment" ,r-summarizedexperiment))) |
7f1d9bef RW |
11045 | (home-page "https://bioconductor.org/packages/scran") |
11046 | (synopsis "Methods for single-cell RNA-Seq data analysis") | |
11047 | (description "This package implements a variety of low-level analyses of | |
11048 | single-cell RNA-seq data. Methods are provided for normalization of | |
11049 | cell-specific biases, assignment of cell cycle phase, and detection of highly | |
11050 | variable and significantly correlated genes.") | |
11051 | (license license:gpl3))) | |
11052 | ||
05f72960 RW |
11053 | (define-public r-delayedmatrixstats |
11054 | (package | |
11055 | (name "r-delayedmatrixstats") | |
900ce2ba | 11056 | (version "1.4.0") |
05f72960 RW |
11057 | (source |
11058 | (origin | |
11059 | (method url-fetch) | |
11060 | (uri (bioconductor-uri "DelayedMatrixStats" version)) | |
11061 | (sha256 | |
11062 | (base32 | |
900ce2ba | 11063 | "03fk2avl1vyjv2wslczkc82qr0zmp1ra8iimd47pbmnnm839ly4w")))) |
05f72960 RW |
11064 | (properties |
11065 | `((upstream-name . "DelayedMatrixStats"))) | |
11066 | (build-system r-build-system) | |
11067 | (propagated-inputs | |
900ce2ba RW |
11068 | `(("r-biocparallel" ,r-biocparallel) |
11069 | ("r-delayedarray" ,r-delayedarray) | |
11070 | ("r-hdf5array" ,r-hdf5array) | |
05f72960 RW |
11071 | ("r-iranges" ,r-iranges) |
11072 | ("r-matrix" ,r-matrix) | |
11073 | ("r-matrixstats" ,r-matrixstats) | |
11074 | ("r-s4vectors" ,r-s4vectors))) | |
11075 | (home-page "https://github.com/PeteHaitch/DelayedMatrixStats") | |
11076 | (synopsis "Functions that apply to rows and columns of DelayedMatrix objects") | |
11077 | (description | |
11078 | "This package provides a port of the @code{matrixStats} API for use with | |
11079 | @code{DelayedMatrix} objects from the @code{DelayedArray} package. It | |
11080 | contains high-performing functions operating on rows and columns of | |
11081 | @code{DelayedMatrix} objects, e.g. @code{colMedians}, @code{rowMedians}, | |
11082 | @code{colRanks}, @code{rowRanks}, @code{colSds}, and @code{rowSds}. Functions | |
11083 | are optimized per data type and for subsetted calculations such that both | |
11084 | memory usage and processing time is minimized.") | |
11085 | (license license:expat))) | |
11086 | ||
22a0c659 RW |
11087 | (define-public r-phangorn |
11088 | (package | |
11089 | (name "r-phangorn") | |
11090 | (version "2.4.0") | |
11091 | (source | |
11092 | (origin | |
11093 | (method url-fetch) | |
11094 | (uri (cran-uri "phangorn" version)) | |
11095 | (sha256 | |
11096 | (base32 | |
11097 | "0xc8k552nxczy19jr0xjjagrzc8x6lafasgk2c099ls8bc1yml1i")))) | |
11098 | (build-system r-build-system) | |
11099 | (propagated-inputs | |
11100 | `(("r-ape" ,r-ape) | |
11101 | ("r-fastmatch" ,r-fastmatch) | |
11102 | ("r-igraph" ,r-igraph) | |
11103 | ("r-magrittr" ,r-magrittr) | |
11104 | ("r-matrix" ,r-matrix) | |
11105 | ("r-quadprog" ,r-quadprog) | |
11106 | ("r-rcpp" ,r-rcpp))) | |
11107 | (home-page "https://github.com/KlausVigo/phangorn") | |
11108 | (synopsis "Phylogenetic analysis in R") | |
11109 | (description | |
11110 | "Phangorn is a package for phylogenetic analysis in R. It supports | |
11111 | estimation of phylogenetic trees and networks using Maximum Likelihood, | |
11112 | Maximum Parsimony, distance methods and Hadamard conjugation.") | |
11113 | (license license:gpl2+))) | |
11114 | ||
3082de04 | 11115 | (define-public r-dropbead |
84c195e5 RW |
11116 | (let ((commit "d746c6f3b32110428ea56d6a0001ce52a251c247") |
11117 | (revision "2")) | |
3082de04 RW |
11118 | (package |
11119 | (name "r-dropbead") | |
11120 | (version (string-append "0-" revision "." (string-take commit 7))) | |
11121 | (source | |
11122 | (origin | |
11123 | (method git-fetch) | |
11124 | (uri (git-reference | |
11125 | (url "https://github.com/rajewsky-lab/dropbead.git") | |
11126 | (commit commit))) | |
b1d4026d | 11127 | (file-name (git-file-name name version)) |
3082de04 RW |
11128 | (sha256 |
11129 | (base32 | |
84c195e5 | 11130 | "0sbzma49aiiyw8b0jpr7fnhzys9nsqmp4hy4hdz1gzyg1lhnca26")))) |
3082de04 RW |
11131 | (build-system r-build-system) |
11132 | (propagated-inputs | |
11133 | `(("r-ggplot2" ,r-ggplot2) | |
11134 | ("r-rcolorbrewer" ,r-rcolorbrewer) | |
11135 | ("r-gridextra" ,r-gridextra) | |
11136 | ("r-gplots" ,r-gplots) | |
11137 | ("r-plyr" ,r-plyr))) | |
11138 | (home-page "https://github.com/rajewsky-lab/dropbead") | |
11139 | (synopsis "Basic exploration and analysis of Drop-seq data") | |
11140 | (description "This package offers a quick and straight-forward way to | |
11141 | explore and perform basic analysis of single cell sequencing data coming from | |
11142 | droplet sequencing. It has been particularly tailored for Drop-seq.") | |
11143 | (license license:gpl3)))) | |
11144 | ||
5ded35d8 RW |
11145 | (define htslib-for-sambamba |
11146 | (let ((commit "2f3c3ea7b301f9b45737a793c0b2dcf0240e5ee5")) | |
11147 | (package | |
11148 | (inherit htslib) | |
11149 | (name "htslib-for-sambamba") | |
11150 | (version (string-append "1.3.1-1." (string-take commit 9))) | |
11151 | (source | |
11152 | (origin | |
11153 | (method git-fetch) | |
11154 | (uri (git-reference | |
11155 | (url "https://github.com/lomereiter/htslib.git") | |
11156 | (commit commit))) | |
11157 | (file-name (string-append "htslib-" version "-checkout")) | |
11158 | (sha256 | |
11159 | (base32 | |
11160 | "0g38g8s3npr0gjm9fahlbhiskyfws9l5i0x1ml3rakzj7az5l9c9")))) | |
5ded35d8 RW |
11161 | (native-inputs |
11162 | `(("autoconf" ,autoconf) | |
11163 | ("automake" ,automake) | |
11164 | ,@(package-native-inputs htslib)))))) | |
11165 | ||
11166 | (define-public sambamba | |
11167 | (package | |
11168 | (name "sambamba") | |
2d86eaff | 11169 | (version "0.6.8") |
5ded35d8 RW |
11170 | (source |
11171 | (origin | |
482959ff RW |
11172 | (method git-fetch) |
11173 | (uri (git-reference | |
11174 | (url "https://github.com/lomereiter/sambamba.git") | |
11175 | (commit (string-append "v" version)))) | |
11176 | (file-name (string-append name "-" version "-checkout")) | |
5ded35d8 RW |
11177 | (sha256 |
11178 | (base32 | |
2d86eaff | 11179 | "0k0cz3qcv98p6cq09zlbgnjsggxcqbcmzxg5zikgcgbr2nfq4lry")))) |
5ded35d8 RW |
11180 | (build-system gnu-build-system) |
11181 | (arguments | |
482959ff RW |
11182 | `(#:tests? #f ; there is no test target |
11183 | #:parallel-build? #f ; not supported | |
5ded35d8 RW |
11184 | #:phases |
11185 | (modify-phases %standard-phases | |
11186 | (delete 'configure) | |
482959ff RW |
11187 | (add-after 'unpack 'fix-ldc-version |
11188 | (lambda _ | |
11189 | (substitute* "gen_ldc_version_info.py" | |
2d86eaff | 11190 | (("/usr/bin/env.*") (which "python3"))) |
482959ff | 11191 | (substitute* "Makefile" |
2d86eaff RJ |
11192 | ;; We use ldc2 instead of ldmd2 to compile sambamba. |
11193 | (("\\$\\(shell which ldmd2\\)") (which "ldc2"))) | |
482959ff RW |
11194 | #t)) |
11195 | (add-after 'unpack 'place-biod-and-undead | |
5ded35d8 RW |
11196 | (lambda* (#:key inputs #:allow-other-keys) |
11197 | (copy-recursively (assoc-ref inputs "biod") "BioD") | |
482959ff | 11198 | (copy-recursively (assoc-ref inputs "undead") "undeaD") |
5ded35d8 RW |
11199 | #t)) |
11200 | (add-after 'unpack 'unbundle-prerequisites | |
11201 | (lambda _ | |
11202 | (substitute* "Makefile" | |
482959ff RW |
11203 | (("htslib/libhts.a lz4/lib/liblz4.a") |
11204 | "-L-lhts -L-llz4") | |
2d86eaff | 11205 | ((" lz4-static htslib-static") "")) |
5ded35d8 RW |
11206 | #t)) |
11207 | (replace 'install | |
11208 | (lambda* (#:key outputs #:allow-other-keys) | |
11209 | (let* ((out (assoc-ref outputs "out")) | |
11210 | (bin (string-append out "/bin"))) | |
11211 | (mkdir-p bin) | |
2d86eaff | 11212 | (install-file "bin/sambamba" bin) |
5ded35d8 RW |
11213 | #t)))))) |
11214 | (native-inputs | |
11215 | `(("ldc" ,ldc) | |
11216 | ("rdmd" ,rdmd) | |
2d86eaff | 11217 | ("python" ,python-minimal) |
5ded35d8 | 11218 | ("biod" |
2d86eaff | 11219 | ,(let ((commit "4f1a7d2fb7ef3dfe962aa357d672f354ebfbe42e")) |
5ded35d8 RW |
11220 | (origin |
11221 | (method git-fetch) | |
11222 | (uri (git-reference | |
11223 | (url "https://github.com/biod/BioD.git") | |
11224 | (commit commit))) | |
11225 | (file-name (string-append "biod-" | |
11226 | (string-take commit 9) | |
11227 | "-checkout")) | |
11228 | (sha256 | |
11229 | (base32 | |
2d86eaff | 11230 | "1k5pdjv1qvi0a3rwd1sfq6zbj37l86i7bf710m4c0y6737lxj426"))))) |
482959ff | 11231 | ("undead" |
2d86eaff | 11232 | ,(let ((commit "9be93876982b5f14fcca60832563b3cd767dd84d")) |
482959ff RW |
11233 | (origin |
11234 | (method git-fetch) | |
11235 | (uri (git-reference | |
2d86eaff | 11236 | (url "https://github.com/biod/undeaD.git") |
482959ff RW |
11237 | (commit commit))) |
11238 | (file-name (string-append "undead-" | |
11239 | (string-take commit 9) | |
11240 | "-checkout")) | |
11241 | (sha256 | |
11242 | (base32 | |
2d86eaff | 11243 | "1xfarj0nqlmi5jd1vmcmm7pabzaf9hxyvk6hp0d6jslb5k9r8r3d"))))))) |
5ded35d8 RW |
11244 | (inputs |
11245 | `(("lz4" ,lz4) | |
11246 | ("htslib" ,htslib-for-sambamba))) | |
11247 | (home-page "http://lomereiter.github.io/sambamba") | |
11248 | (synopsis "Tools for working with SAM/BAM data") | |
11249 | (description "Sambamba is a high performance modern robust and | |
11250 | fast tool (and library), written in the D programming language, for | |
11251 | working with SAM and BAM files. Current parallelised functionality is | |
11252 | an important subset of samtools functionality, including view, index, | |
11253 | sort, markdup, and depth.") | |
11254 | (license license:gpl2+))) | |
b8fffd3a RW |
11255 | |
11256 | (define-public ritornello | |
11257 | (package | |
11258 | (name "ritornello") | |
3b888065 | 11259 | (version "2.0.1") |
b8fffd3a | 11260 | (source (origin |
7145f4e5 RW |
11261 | (method git-fetch) |
11262 | (uri (git-reference | |
11263 | (url "https://github.com/KlugerLab/Ritornello.git") | |
11264 | (commit (string-append "v" version)))) | |
11265 | (file-name (git-file-name name version)) | |
b8fffd3a RW |
11266 | (sha256 |
11267 | (base32 | |
3b888065 | 11268 | "1xahvq215qld7x1w8vpa5zbrsj6p9crb9shqa2x89sb0aaxa02jk")))) |
b8fffd3a RW |
11269 | (build-system gnu-build-system) |
11270 | (arguments | |
11271 | `(#:tests? #f ; there are no tests | |
11272 | #:phases | |
11273 | (modify-phases %standard-phases | |
11274 | (add-after 'unpack 'patch-samtools-references | |
11275 | (lambda* (#:key inputs #:allow-other-keys) | |
11276 | (substitute* '("src/SamStream.h" | |
3b888065 | 11277 | "src/FLD.cpp") |
b8fffd3a RW |
11278 | (("<sam.h>") "<samtools/sam.h>")) |
11279 | #t)) | |
11280 | (delete 'configure) | |
11281 | (replace 'install | |
11282 | (lambda* (#:key inputs outputs #:allow-other-keys) | |
11283 | (let* ((out (assoc-ref outputs "out")) | |
11284 | (bin (string-append out "/bin/"))) | |
11285 | (mkdir-p bin) | |
11286 | (install-file "bin/Ritornello" bin) | |
11287 | #t)))))) | |
11288 | (inputs | |
11289 | `(("samtools" ,samtools-0.1) | |
11290 | ("fftw" ,fftw) | |
11291 | ("boost" ,boost) | |
11292 | ("zlib" ,zlib))) | |
11293 | (home-page "https://github.com/KlugerLab/Ritornello") | |
11294 | (synopsis "Control-free peak caller for ChIP-seq data") | |
11295 | (description "Ritornello is a ChIP-seq peak calling algorithm based on | |
11296 | signal processing that can accurately call binding events without the need to | |
11297 | do a pair total DNA input or IgG control sample. It has been tested for use | |
11298 | with narrow binding events such as transcription factor ChIP-seq.") | |
11299 | (license license:gpl3+))) | |
44f6c889 RW |
11300 | |
11301 | (define-public trim-galore | |
11302 | (package | |
11303 | (name "trim-galore") | |
f895a7a4 | 11304 | (version "0.4.5") |
44f6c889 RW |
11305 | (source |
11306 | (origin | |
f895a7a4 RW |
11307 | (method git-fetch) |
11308 | (uri (git-reference | |
11309 | (url "https://github.com/FelixKrueger/TrimGalore.git") | |
11310 | (commit version))) | |
11311 | (file-name (string-append name "-" version "-checkout")) | |
44f6c889 RW |
11312 | (sha256 |
11313 | (base32 | |
f895a7a4 | 11314 | "0x5892l48c816pf00wmnz5vq0zq6170d3xc8zrxncd4jcz7h1p71")))) |
44f6c889 RW |
11315 | (build-system gnu-build-system) |
11316 | (arguments | |
11317 | `(#:tests? #f ; no tests | |
11318 | #:phases | |
11319 | (modify-phases %standard-phases | |
44f6c889 RW |
11320 | (delete 'configure) |
11321 | (delete 'build) | |
11322 | (add-after 'unpack 'hardcode-tool-references | |
11323 | (lambda* (#:key inputs #:allow-other-keys) | |
11324 | (substitute* "trim_galore" | |
11325 | (("\\$path_to_cutadapt = 'cutadapt'") | |
11326 | (string-append "$path_to_cutadapt = '" | |
11327 | (assoc-ref inputs "cutadapt") | |
11328 | "/bin/cutadapt'")) | |
11329 | (("\\| gzip") | |
11330 | (string-append "| " | |
11331 | (assoc-ref inputs "gzip") | |
11332 | "/bin/gzip")) | |
11333 | (("\"gunzip") | |
11334 | (string-append "\"" | |
11335 | (assoc-ref inputs "gzip") | |
11336 | "/bin/gunzip"))) | |
11337 | #t)) | |
11338 | (replace 'install | |
11339 | (lambda* (#:key outputs #:allow-other-keys) | |
11340 | (let ((bin (string-append (assoc-ref outputs "out") | |
11341 | "/bin"))) | |
11342 | (mkdir-p bin) | |
11343 | (install-file "trim_galore" bin) | |
11344 | #t)))))) | |
11345 | (inputs | |
11346 | `(("gzip" ,gzip) | |
11347 | ("perl" ,perl) | |
11348 | ("cutadapt" ,cutadapt))) | |
11349 | (native-inputs | |
11350 | `(("unzip" ,unzip))) | |
11351 | (home-page "http://www.bioinformatics.babraham.ac.uk/projects/trim_galore/") | |
11352 | (synopsis "Wrapper around Cutadapt and FastQC") | |
11353 | (description "Trim Galore! is a wrapper script to automate quality and | |
11354 | adapter trimming as well as quality control, with some added functionality to | |
11355 | remove biased methylation positions for RRBS sequence files.") | |
11356 | (license license:gpl3+))) | |
3420c905 RW |
11357 | |
11358 | (define-public gess | |
11359 | (package | |
11360 | (name "gess") | |
11361 | (version "1.0") | |
11362 | (source (origin | |
11363 | (method url-fetch) | |
11364 | (uri (string-append "http://compbio.uthscsa.edu/" | |
11365 | "GESS_Web/files/" | |
11366 | "gess-" version ".src.tar.gz")) | |
11367 | (sha256 | |
11368 | (base32 | |
11369 | "0hyk403kxscclzfs24pvdgiv0wm03kjcziqdrp5w46cb049gz0d7")))) | |
11370 | (build-system gnu-build-system) | |
11371 | (arguments | |
11372 | `(#:tests? #f ; no tests | |
11373 | #:phases | |
11374 | (modify-phases %standard-phases | |
11375 | (delete 'configure) | |
11376 | (delete 'build) | |
11377 | (replace 'install | |
11378 | (lambda* (#:key inputs outputs #:allow-other-keys) | |
11379 | (let* ((python (assoc-ref inputs "python")) | |
11380 | (out (assoc-ref outputs "out")) | |
11381 | (bin (string-append out "/bin/")) | |
11382 | (target (string-append | |
11383 | out "/lib/python2.7/site-packages/gess/"))) | |
11384 | (mkdir-p target) | |
11385 | (copy-recursively "." target) | |
11386 | ;; Make GESS.py executable | |
11387 | (chmod (string-append target "GESS.py") #o555) | |
11388 | ;; Add Python shebang to the top and make Matplotlib | |
11389 | ;; usable. | |
11390 | (substitute* (string-append target "GESS.py") | |
11391 | (("\"\"\"Description:" line) | |
11392 | (string-append "#!" (which "python") " | |
11393 | import matplotlib | |
11394 | matplotlib.use('Agg') | |
11395 | " line))) | |
11396 | ;; Make sure GESS has all modules in its path | |
11397 | (wrap-program (string-append target "GESS.py") | |
11398 | `("PYTHONPATH" ":" prefix (,target ,(getenv "PYTHONPATH")))) | |
11399 | (mkdir-p bin) | |
11400 | (symlink (string-append target "GESS.py") | |
11401 | (string-append bin "GESS.py")) | |
11402 | #t)))))) | |
11403 | (inputs | |
11404 | `(("python" ,python-2) | |
11405 | ("python2-pysam" ,python2-pysam) | |
11406 | ("python2-scipy" ,python2-scipy) | |
11407 | ("python2-numpy" ,python2-numpy) | |
11408 | ("python2-networkx" ,python2-networkx) | |
11409 | ("python2-biopython" ,python2-biopython))) | |
11410 | (home-page "http://compbio.uthscsa.edu/GESS_Web/") | |
11411 | (synopsis "Detect exon-skipping events from raw RNA-seq data") | |
11412 | (description | |
11413 | "GESS is an implementation of a novel computational method to detect de | |
11414 | novo exon-skipping events directly from raw RNA-seq data without the prior | |
11415 | knowledge of gene annotation information. GESS stands for the graph-based | |
11416 | exon-skipping scanner detection scheme.") | |
11417 | (license license:bsd-3))) | |
282b0151 RW |
11418 | |
11419 | (define-public phylip | |
11420 | (package | |
11421 | (name "phylip") | |
11422 | (version "3.696") | |
11423 | (source | |
11424 | (origin | |
11425 | (method url-fetch) | |
11426 | (uri (string-append "http://evolution.gs.washington.edu/phylip/" | |
11427 | "download/phylip-" version ".tar.gz")) | |
11428 | (sha256 | |
11429 | (base32 | |
11430 | "01jar1rayhr2gba2pgbw49m56rc5z4p5wn3ds0m188hrlln4a2nd")))) | |
11431 | (build-system gnu-build-system) | |
11432 | (arguments | |
11433 | `(#:tests? #f ; no check target | |
11434 | #:make-flags (list "-f" "Makefile.unx" "install") | |
11435 | #:parallel-build? #f ; not supported | |
11436 | #:phases | |
11437 | (modify-phases %standard-phases | |
11438 | (add-after 'unpack 'enter-dir | |
11439 | (lambda _ (chdir "src") #t)) | |
11440 | (delete 'configure) | |
11441 | (replace 'install | |
11442 | (lambda* (#:key inputs outputs #:allow-other-keys) | |
11443 | (let ((target (string-append (assoc-ref outputs "out") | |
11444 | "/bin"))) | |
11445 | (mkdir-p target) | |
11446 | (for-each (lambda (file) | |
11447 | (install-file file target)) | |
11448 | (find-files "../exe" ".*"))) | |
11449 | #t))))) | |
11450 | (home-page "http://evolution.genetics.washington.edu/phylip/") | |
11451 | (synopsis "Tools for inferring phylogenies") | |
11452 | (description "PHYLIP (the PHYLogeny Inference Package) is a package of | |
11453 | programs for inferring phylogenies (evolutionary trees).") | |
11454 | (license license:bsd-2))) | |
aa163424 RW |
11455 | |
11456 | (define-public imp | |
11457 | (package | |
11458 | (name "imp") | |
11459 | (version "2.6.2") | |
11460 | (source | |
11461 | (origin | |
11462 | (method url-fetch) | |
11463 | (uri (string-append "https://integrativemodeling.org/" | |
11464 | version "/download/imp-" version ".tar.gz")) | |
11465 | (sha256 | |
11466 | (base32 | |
11467 | "0lxqx7vh79d771svr611dkilp6sn30qrbw8zvscbrm37v38d2j6h")))) | |
11468 | (build-system cmake-build-system) | |
11469 | (arguments | |
11470 | `(;; FIXME: Some tests fail because they produce warnings, others fail | |
11471 | ;; because the PYTHONPATH does not include the modeller's directory. | |
677bc34d | 11472 | #:tests? #f)) |
aa163424 RW |
11473 | (inputs |
11474 | `(("boost" ,boost) | |
11475 | ("gsl" ,gsl) | |
11476 | ("swig" ,swig) | |
11477 | ("hdf5" ,hdf5) | |
11478 | ("fftw" ,fftw) | |
11479 | ("python" ,python-2))) | |
11480 | (propagated-inputs | |
11481 | `(("python2-numpy" ,python2-numpy) | |
11482 | ("python2-scipy" ,python2-scipy) | |
11483 | ("python2-pandas" ,python2-pandas) | |
11484 | ("python2-scikit-learn" ,python2-scikit-learn) | |
11485 | ("python2-networkx" ,python2-networkx))) | |
11486 | (home-page "https://integrativemodeling.org") | |
11487 | (synopsis "Integrative modeling platform") | |
11488 | (description "IMP's broad goal is to contribute to a comprehensive | |
11489 | structural characterization of biomolecules ranging in size and complexity | |
11490 | from small peptides to large macromolecular assemblies, by integrating data | |
11491 | from diverse biochemical and biophysical experiments. IMP provides a C++ and | |
11492 | Python toolbox for solving complex modeling problems, and a number of | |
11493 | applications for tackling some common problems in a user-friendly way.") | |
11494 | ;; IMP is largely available under the GNU Lesser GPL; see the file | |
11495 | ;; COPYING.LGPL for the full text of this license. Some IMP modules are | |
11496 | ;; available under the GNU GPL (see the file COPYING.GPL). | |
11497 | (license (list license:lgpl2.1+ | |
11498 | license:gpl3+)))) | |
8befd094 RW |
11499 | |
11500 | (define-public tadbit | |
11501 | (package | |
11502 | (name "tadbit") | |
e0f1aa2d | 11503 | (version "0.2.0") |
8befd094 | 11504 | (source (origin |
e0f1aa2d RW |
11505 | (method git-fetch) |
11506 | (uri (git-reference | |
11507 | (url "https://github.com/3DGenomes/TADbit.git") | |
11508 | (commit (string-append "v" version)))) | |
11509 | (file-name (git-file-name name version)) | |
8befd094 RW |
11510 | (sha256 |
11511 | (base32 | |
e0f1aa2d | 11512 | "07g3aj648prmsvxp9caz5yl41k0y0647vxh0f5p3w8376mfiljd0")))) |
8befd094 RW |
11513 | (build-system python-build-system) |
11514 | (arguments | |
11515 | `(;; Tests are included and must be run after installation, but | |
11516 | ;; they are incomplete and thus cannot be run. | |
11517 | #:tests? #f | |
11518 | #:python ,python-2 | |
11519 | #:phases | |
11520 | (modify-phases %standard-phases | |
11521 | (add-after 'unpack 'fix-problems-with-setup.py | |
11522 | (lambda* (#:key outputs #:allow-other-keys) | |
11523 | ;; setup.py opens these files for writing | |
11524 | (chmod "_pytadbit/_version.py" #o664) | |
11525 | (chmod "README.rst" #o664) | |
11526 | ||
11527 | ;; Don't attempt to install the bash completions to | |
11528 | ;; the home directory. | |
11529 | (rename-file "extras/.bash_completion" | |
11530 | "extras/tadbit") | |
11531 | (substitute* "setup.py" | |
11532 | (("\\(path.expanduser\\('~'\\)") | |
11533 | (string-append "(\"" | |
11534 | (assoc-ref outputs "out") | |
11535 | "/etc/bash_completion.d\"")) | |
11536 | (("extras/\\.bash_completion") | |
11537 | "extras/tadbit")) | |
11538 | #t))))) | |
11539 | (inputs | |
11540 | ;; TODO: add Chimera for visualization | |
11541 | `(("imp" ,imp) | |
11542 | ("mcl" ,mcl) | |
11543 | ("python2-scipy" ,python2-scipy) | |
11544 | ("python2-numpy" ,python2-numpy) | |
11545 | ("python2-matplotlib" ,python2-matplotlib) | |
11546 | ("python2-pysam" ,python2-pysam))) | |
eeb8b0e6 | 11547 | (home-page "https://3dgenomes.github.io/TADbit/") |
8befd094 RW |
11548 | (synopsis "Analyze, model, and explore 3C-based data") |
11549 | (description | |
11550 | "TADbit is a complete Python library to deal with all steps to analyze, | |
11551 | model, and explore 3C-based data. With TADbit the user can map FASTQ files to | |
11552 | obtain raw interaction binned matrices (Hi-C like matrices), normalize and | |
a147fadd | 11553 | correct interaction matrices, identify and compare the so-called |
8befd094 RW |
11554 | @dfn{Topologically Associating Domains} (TADs), build 3D models from the |
11555 | interaction matrices, and finally, extract structural properties from the | |
11556 | models. TADbit is complemented by TADkit for visualizing 3D models.") | |
11557 | (license license:gpl3+))) | |
94820951 RW |
11558 | |
11559 | (define-public kentutils | |
11560 | (package | |
11561 | (name "kentutils") | |
11562 | ;; 302.1.0 is out, but the only difference is the inclusion of | |
11563 | ;; pre-built binaries. | |
11564 | (version "302.0.0") | |
11565 | (source | |
11566 | (origin | |
4257c10a RW |
11567 | (method git-fetch) |
11568 | (uri (git-reference | |
11569 | (url "https://github.com/ENCODE-DCC/kentUtils.git") | |
11570 | (commit (string-append "v" version)))) | |
11571 | (file-name (git-file-name name version)) | |
94820951 RW |
11572 | (sha256 |
11573 | (base32 | |
4257c10a | 11574 | "0n1wbyjpzii2b9qhyp9r1q76j623cggpg3y8fmw78ld3z4y7ivha")) |
94820951 RW |
11575 | (modules '((guix build utils) |
11576 | (srfi srfi-26) | |
11577 | (ice-9 ftw))) | |
11578 | (snippet | |
11579 | '(begin | |
11580 | ;; Only the contents of the specified directories are free | |
11581 | ;; for all uses, so we remove the rest. "hg/autoSql" and | |
11582 | ;; "hg/autoXml" are nominally free, but they depend on a | |
11583 | ;; library that is built from the sources in "hg/lib", | |
11584 | ;; which is nonfree. | |
11585 | (let ((free (list "." ".." | |
11586 | "utils" "lib" "inc" "tagStorm" | |
11587 | "parasol" "htslib")) | |
11588 | (directory? (lambda (file) | |
11589 | (eq? 'directory (stat:type (stat file)))))) | |
11590 | (for-each (lambda (file) | |
11591 | (and (directory? file) | |
11592 | (delete-file-recursively file))) | |
11593 | (map (cut string-append "src/" <>) | |
11594 | (scandir "src" | |
11595 | (lambda (file) | |
11596 | (not (member file free))))))) | |
11597 | ;; Only make the utils target, not the userApps target, | |
11598 | ;; because that requires libraries we won't build. | |
11599 | (substitute* "Makefile" | |
11600 | ((" userApps") " utils")) | |
11601 | ;; Only build libraries that are free. | |
11602 | (substitute* "src/makefile" | |
11603 | (("DIRS =.*") "DIRS =\n") | |
11604 | (("cd jkOwnLib.*") "") | |
11605 | ((" hgLib") "") | |
11606 | (("cd hg.*") "")) | |
11607 | (substitute* "src/utils/makefile" | |
11608 | ;; These tools depend on "jkhgap.a", which is part of the | |
11609 | ;; nonfree "src/hg/lib" directory. | |
11610 | (("raSqlQuery") "") | |
11611 | (("pslLiftSubrangeBlat") "") | |
11612 | ||
11613 | ;; Do not build UCSC tools, which may require nonfree | |
11614 | ;; components. | |
11615 | (("ALL_APPS =.*") "ALL_APPS = $(UTILS_APPLIST)\n")) | |
11616 | #t)))) | |
11617 | (build-system gnu-build-system) | |
11618 | (arguments | |
11619 | `( ;; There is no global test target and the test target for | |
11620 | ;; individual tools depends on input files that are not | |
11621 | ;; included. | |
11622 | #:tests? #f | |
11623 | #:phases | |
11624 | (modify-phases %standard-phases | |
4257c10a RW |
11625 | (add-after 'unpack 'fix-permissions |
11626 | (lambda _ (make-file-writable "src/inc/localEnvironment.mk") #t)) | |
94820951 RW |
11627 | (add-after 'unpack 'fix-paths |
11628 | (lambda _ | |
11629 | (substitute* "Makefile" | |
11630 | (("/bin/echo") (which "echo"))) | |
11631 | #t)) | |
11632 | (add-after 'unpack 'prepare-samtabix | |
11633 | (lambda* (#:key inputs #:allow-other-keys) | |
11634 | (copy-recursively (assoc-ref inputs "samtabix") | |
11635 | "samtabix") | |
11636 | #t)) | |
11637 | (delete 'configure) | |
11638 | (replace 'install | |
11639 | (lambda* (#:key outputs #:allow-other-keys) | |
11640 | (let ((bin (string-append (assoc-ref outputs "out") | |
11641 | "/bin"))) | |
11642 | (copy-recursively "bin" bin)) | |
11643 | #t))))) | |
11644 | (native-inputs | |
11645 | `(("samtabix" | |
11646 | ,(origin | |
11647 | (method git-fetch) | |
11648 | (uri (git-reference | |
11649 | (url "http://genome-source.cse.ucsc.edu/samtabix.git") | |
11650 | (commit "10fd107909c1ac4d679299908be4262a012965ba"))) | |
11651 | (sha256 | |
11652 | (base32 | |
11653 | "0c1nj64l42v395sa84n7az43xiap4i6f9n9dfz4058aqiwkhkmma")))))) | |
11654 | (inputs | |
11655 | `(("zlib" ,zlib) | |
11656 | ("tcsh" ,tcsh) | |
11657 | ("perl" ,perl) | |
11658 | ("libpng" ,libpng) | |
80420f11 | 11659 | ("mariadb" ,mariadb) |
94820951 RW |
11660 | ("openssl" ,openssl))) |
11661 | (home-page "http://genome.cse.ucsc.edu/index.html") | |
11662 | (synopsis "Assorted bioinformatics utilities") | |
11663 | (description "This package provides the kentUtils, a selection of | |
11664 | bioinformatics utilities used in combination with the UCSC genome | |
11665 | browser.") | |
11666 | ;; Only a subset of the sources are released under a non-copyleft | |
11667 | ;; free software license. All other sources are removed in a | |
11668 | ;; snippet. See this bug report for an explanation of how the | |
11669 | ;; license statements apply: | |
11670 | ;; https://github.com/ENCODE-DCC/kentUtils/issues/12 | |
11671 | (license (license:non-copyleft | |
11672 | "http://genome.ucsc.edu/license/" | |
11673 | "The contents of this package are free for all uses.")))) | |
7ceb0a83 RW |
11674 | |
11675 | (define-public f-seq | |
11676 | (let ((commit "6ccded34cff38cf432deed8503648b4a66953f9b") | |
11677 | (revision "1")) | |
11678 | (package | |
11679 | (name "f-seq") | |
c6643f2d | 11680 | (version (string-append "1.1-" revision "." (string-take commit 7))) |
7ceb0a83 RW |
11681 | (source (origin |
11682 | (method git-fetch) | |
11683 | (uri (git-reference | |
11684 | (url "https://github.com/aboyle/F-seq.git") | |
11685 | (commit commit))) | |
11686 | (file-name (string-append name "-" version)) | |
11687 | (sha256 | |
11688 | (base32 | |
11689 | "1nk33k0yajg2id4g59bc4szr58r2q6pdq42vgcw054m8ip9wv26h")) | |
11690 | (modules '((guix build utils))) | |
11691 | ;; Remove bundled Java library archives. | |
11692 | (snippet | |
11693 | '(begin | |
11694 | (for-each delete-file (find-files "lib" ".*")) | |
11695 | #t)))) | |
11696 | (build-system ant-build-system) | |
11697 | (arguments | |
11698 | `(#:tests? #f ; no tests included | |
11699 | #:phases | |
11700 | (modify-phases %standard-phases | |
11701 | (replace 'install | |
c0770fee | 11702 | (lambda* (#:key inputs outputs #:allow-other-keys) |
7ceb0a83 | 11703 | (let* ((target (assoc-ref outputs "out")) |
c61d8226 TGR |
11704 | (bin (string-append target "/bin")) |
11705 | (doc (string-append target "/share/doc/f-seq")) | |
11706 | (lib (string-append target "/lib"))) | |
7ceb0a83 RW |
11707 | (mkdir-p target) |
11708 | (mkdir-p doc) | |
11709 | (substitute* "bin/linux/fseq" | |
c0770fee RW |
11710 | (("java") (which "java")) |
11711 | (("\\$REALDIR/../lib/commons-cli-1.1.jar") | |
11712 | (string-append (assoc-ref inputs "java-commons-cli") | |
11713 | "/share/java/commons-cli.jar")) | |
11714 | (("REALDIR=.*") | |
c61d8226 | 11715 | (string-append "REALDIR=" bin "\n"))) |
7ceb0a83 | 11716 | (install-file "README.txt" doc) |
c61d8226 TGR |
11717 | (install-file "bin/linux/fseq" bin) |
11718 | (install-file "build~/fseq.jar" lib) | |
11719 | (copy-recursively "lib" lib) | |
7ceb0a83 RW |
11720 | #t)))))) |
11721 | (inputs | |
11722 | `(("perl" ,perl) | |
11723 | ("java-commons-cli" ,java-commons-cli))) | |
11724 | (home-page "http://fureylab.web.unc.edu/software/fseq/") | |
11725 | (synopsis "Feature density estimator for high-throughput sequence tags") | |
11726 | (description | |
11727 | "F-Seq is a software package that generates a continuous tag sequence | |
11728 | density estimation allowing identification of biologically meaningful sites | |
11729 | such as transcription factor binding sites (ChIP-seq) or regions of open | |
11730 | chromatin (DNase-seq). Output can be displayed directly in the UCSC Genome | |
11731 | Browser.") | |
11732 | (license license:gpl3+)))) | |
96348048 RW |
11733 | |
11734 | (define-public bismark | |
11735 | (package | |
11736 | (name "bismark") | |
126c9e3f | 11737 | (version "0.19.1") |
96348048 RW |
11738 | (source |
11739 | (origin | |
126c9e3f RW |
11740 | (method git-fetch) |
11741 | (uri (git-reference | |
11742 | (url "https://github.com/FelixKrueger/Bismark.git") | |
11743 | (commit version))) | |
11744 | (file-name (string-append name "-" version "-checkout")) | |
96348048 RW |
11745 | (sha256 |
11746 | (base32 | |
126c9e3f RW |
11747 | "0yb5l36slwg02fp4b1jdlplgljcsxgqfzvzihzdnphd87dghcc84")) |
11748 | (snippet | |
11749 | '(begin | |
11750 | ;; highcharts.js is non-free software. The code is available under | |
11751 | ;; CC-BY-NC or proprietary licenses only. | |
11752 | (delete-file "bismark_sitrep/highcharts.js") | |
11753 | #t)))) | |
96348048 RW |
11754 | (build-system perl-build-system) |
11755 | (arguments | |
126c9e3f | 11756 | `(#:tests? #f ; there are no tests |
96348048 RW |
11757 | #:phases |
11758 | (modify-phases %standard-phases | |
11759 | (delete 'configure) | |
11760 | (delete 'build) | |
11761 | (replace 'install | |
09658903 | 11762 | (lambda* (#:key inputs outputs #:allow-other-keys) |
126c9e3f RW |
11763 | (let* ((out (assoc-ref outputs "out")) |
11764 | (bin (string-append out "/bin")) | |
11765 | (share (string-append out "/share/bismark")) | |
11766 | (docdir (string-append out "/share/doc/bismark")) | |
11767 | (docs '("Docs/Bismark_User_Guide.html")) | |
11768 | (scripts '("bismark" | |
11769 | "bismark_genome_preparation" | |
11770 | "bismark_methylation_extractor" | |
11771 | "bismark2bedGraph" | |
11772 | "bismark2report" | |
11773 | "coverage2cytosine" | |
11774 | "deduplicate_bismark" | |
11775 | "filter_non_conversion" | |
11776 | "bam2nuc" | |
11777 | "bismark2summary"))) | |
0f5ad3a1 RW |
11778 | (substitute* "bismark2report" |
11779 | (("\\$RealBin/bismark_sitrep") | |
11780 | (string-append share "/bismark_sitrep"))) | |
126c9e3f | 11781 | (mkdir-p share) |
96348048 RW |
11782 | (mkdir-p docdir) |
11783 | (mkdir-p bin) | |
11784 | (for-each (lambda (file) (install-file file bin)) | |
11785 | scripts) | |
11786 | (for-each (lambda (file) (install-file file docdir)) | |
11787 | docs) | |
126c9e3f | 11788 | (copy-recursively "Docs/Images" (string-append docdir "/Images")) |
126c9e3f RW |
11789 | (copy-recursively "bismark_sitrep" |
11790 | (string-append share "/bismark_sitrep")) | |
11791 | ||
09658903 RW |
11792 | ;; Fix references to gunzip |
11793 | (substitute* (map (lambda (file) | |
11794 | (string-append bin "/" file)) | |
11795 | scripts) | |
11796 | (("\"gunzip -c") | |
11797 | (string-append "\"" (assoc-ref inputs "gzip") | |
11798 | "/bin/gunzip -c"))) | |
96348048 | 11799 | #t)))))) |
09658903 RW |
11800 | (inputs |
11801 | `(("gzip" ,gzip))) | |
96348048 RW |
11802 | (home-page "http://www.bioinformatics.babraham.ac.uk/projects/bismark/") |
11803 | (synopsis "Map bisulfite treated sequence reads and analyze methylation") | |
11804 | (description "Bismark is a program to map bisulfite treated sequencing | |
11805 | reads to a genome of interest and perform methylation calls in a single step. | |
11806 | The output can be easily imported into a genome viewer, such as SeqMonk, and | |
11807 | enables a researcher to analyse the methylation levels of their samples | |
11808 | straight away. Its main features are: | |
11809 | ||
11810 | @itemize | |
11811 | @item Bisulfite mapping and methylation calling in one single step | |
11812 | @item Supports single-end and paired-end read alignments | |
11813 | @item Supports ungapped and gapped alignments | |
11814 | @item Alignment seed length, number of mismatches etc are adjustable | |
11815 | @item Output discriminates between cytosine methylation in CpG, CHG | |
11816 | and CHH context | |
11817 | @end itemize\n") | |
11818 | (license license:gpl3+))) | |
dc8ddbfb RW |
11819 | |
11820 | (define-public paml | |
11821 | (package | |
11822 | (name "paml") | |
11823 | (version "4.9e") | |
11824 | (source (origin | |
11825 | (method url-fetch) | |
11826 | (uri (string-append "http://abacus.gene.ucl.ac.uk/software/" | |
11827 | "paml" version ".tgz")) | |
11828 | (sha256 | |
11829 | (base32 | |
11830 | "13zf6h9fiqghwhch2h06x1zdr6s42plsnqahflp5g7myr3han3s6")) | |
11831 | (modules '((guix build utils))) | |
11832 | ;; Remove Windows binaries | |
11833 | (snippet | |
11834 | '(begin | |
11835 | (for-each delete-file (find-files "." "\\.exe$")) | |
11836 | #t)))) | |
11837 | (build-system gnu-build-system) | |
11838 | (arguments | |
11839 | `(#:tests? #f ; there are no tests | |
11840 | #:make-flags '("CC=gcc") | |
11841 | #:phases | |
11842 | (modify-phases %standard-phases | |
11843 | (replace 'configure | |
11844 | (lambda _ | |
11845 | (substitute* "src/BFdriver.c" | |
11846 | (("/bin/bash") (which "bash"))) | |
11847 | (chdir "src") | |
11848 | #t)) | |
11849 | (replace 'install | |
11850 | (lambda* (#:key outputs #:allow-other-keys) | |
11851 | (let ((tools '("baseml" "basemlg" "codeml" | |
11852 | "pamp" "evolver" "yn00" "chi2")) | |
11853 | (bin (string-append (assoc-ref outputs "out") "/bin")) | |
11854 | (docdir (string-append (assoc-ref outputs "out") | |
11855 | "/share/doc/paml"))) | |
11856 | (mkdir-p bin) | |
11857 | (for-each (lambda (file) (install-file file bin)) tools) | |
11858 | (copy-recursively "../doc" docdir) | |
11859 | #t)))))) | |
11860 | (home-page "http://abacus.gene.ucl.ac.uk/software/paml.html") | |
11861 | (synopsis "Phylogentic analysis by maximum likelihood") | |
11862 | (description "PAML (for Phylogentic Analysis by Maximum Likelihood) | |
11863 | contains a few programs for model fitting and phylogenetic tree reconstruction | |
11864 | using nucleotide or amino-acid sequence data.") | |
11865 | ;; GPLv3 only | |
11866 | (license license:gpl3))) | |
d112e5a8 RW |
11867 | |
11868 | (define-public kallisto | |
11869 | (package | |
11870 | (name "kallisto") | |
e8a7eab1 | 11871 | (version "0.44.0") |
d112e5a8 | 11872 | (source (origin |
e8a7eab1 RW |
11873 | (method git-fetch) |
11874 | (uri (git-reference | |
11875 | (url "https://github.com/pachterlab/kallisto.git") | |
11876 | (commit (string-append "v" version)))) | |
11877 | (file-name (git-file-name name version)) | |
d112e5a8 RW |
11878 | (sha256 |
11879 | (base32 | |
e8a7eab1 | 11880 | "0nj382jiywqnpgvyhichajpkkh5r0bapn43f4dx40zdaq5v4m40m")))) |
d112e5a8 | 11881 | (build-system cmake-build-system) |
e8a7eab1 RW |
11882 | (arguments |
11883 | `(#:tests? #f ; no "check" target | |
11884 | #:phases | |
11885 | (modify-phases %standard-phases | |
11886 | (add-after 'unpack 'do-not-use-bundled-htslib | |
11887 | (lambda _ | |
11888 | (substitute* "CMakeLists.txt" | |
11889 | (("^ExternalProject_Add" m) | |
11890 | (string-append "if (NEVER)\n" m)) | |
11891 | (("^\\)") | |
11892 | (string-append ")\nendif(NEVER)")) | |
11893 | (("include_directories\\(\\$\\{htslib_PREFIX.*" m) | |
11894 | (string-append "# " m))) | |
11895 | (substitute* "src/CMakeLists.txt" | |
11896 | (("target_link_libraries\\(kallisto kallisto_core pthread \ | |
11897 | \\$\\{CMAKE_CURRENT_SOURCE_DIR\\}/../ext/htslib/libhts.a\\)") | |
11898 | "target_link_libraries(kallisto kallisto_core pthread hts)") | |
11899 | (("include_directories\\(\\.\\./ext/htslib\\)") "")) | |
11900 | #t))))) | |
d112e5a8 RW |
11901 | (inputs |
11902 | `(("hdf5" ,hdf5) | |
e8a7eab1 | 11903 | ("htslib" ,htslib) |
d112e5a8 RW |
11904 | ("zlib" ,zlib))) |
11905 | (home-page "http://pachterlab.github.io/kallisto/") | |
11906 | (synopsis "Near-optimal RNA-Seq quantification") | |
11907 | (description | |
11908 | "Kallisto is a program for quantifying abundances of transcripts from | |
11909 | RNA-Seq data, or more generally of target sequences using high-throughput | |
11910 | sequencing reads. It is based on the novel idea of pseudoalignment for | |
11911 | rapidly determining the compatibility of reads with targets, without the need | |
11912 | for alignment. Pseudoalignment of reads preserves the key information needed | |
11913 | for quantification, and kallisto is therefore not only fast, but also as | |
11914 | accurate as existing quantification tools.") | |
11915 | (license license:bsd-2))) | |
c3b2ab9d RW |
11916 | |
11917 | (define-public libgff | |
11918 | (package | |
11919 | (name "libgff") | |
11920 | (version "1.0") | |
11921 | (source (origin | |
55698df2 RW |
11922 | (method git-fetch) |
11923 | (uri (git-reference | |
11924 | (url "https://github.com/Kingsford-Group/libgff.git") | |
11925 | (commit (string-append "v" version)))) | |
11926 | (file-name (git-file-name name version)) | |
c3b2ab9d RW |
11927 | (sha256 |
11928 | (base32 | |
55698df2 | 11929 | "0n6vfjnq7a2mianipscbshrvbncss8z4zkgkbjw754p9043nfkps")))) |
c3b2ab9d RW |
11930 | (build-system cmake-build-system) |
11931 | (arguments `(#:tests? #f)) ; no tests included | |
11932 | (home-page "https://github.com/Kingsford-Group/libgff") | |
11933 | (synopsis "Parser library for reading/writing GFF files") | |
11934 | (description "This is a simple \"libraryfication\" of the GFF/GTF parsing | |
11935 | code that is used in the Cufflinks codebase. The goal of this library is to | |
11936 | provide this functionality without the necessity of drawing in a heavy-weight | |
11937 | dependency like SeqAn.") | |
a2cfe190 | 11938 | (license (license:x11-style "https://www.boost.org/LICENSE_1_0.txt")))) |
1fe0bde3 RW |
11939 | |
11940 | (define-public libdivsufsort | |
11941 | (package | |
11942 | (name "libdivsufsort") | |
11943 | (version "2.0.1") | |
11944 | (source (origin | |
11945 | (method git-fetch) | |
11946 | (uri (git-reference | |
11947 | (url "https://github.com/y-256/libdivsufsort.git") | |
11948 | (commit version))) | |
d9a069c2 | 11949 | (file-name (git-file-name name version)) |
1fe0bde3 RW |
11950 | (sha256 |
11951 | (base32 | |
11952 | "0fgdz9fzihlvjjrxy01md1bv9vh12rkgkwbm90b1hj5xpbaqp7z2")))) | |
11953 | (build-system cmake-build-system) | |
11954 | (arguments | |
11955 | '(#:tests? #f ; there are no tests | |
11956 | #:configure-flags | |
11957 | ;; Needed for rapmap and sailfish. | |
11958 | '("-DBUILD_DIVSUFSORT64=ON"))) | |
11959 | (home-page "https://github.com/y-256/libdivsufsort") | |
11960 | (synopsis "Lightweight suffix-sorting library") | |
11961 | (description "libdivsufsort is a software library that implements a | |
11962 | lightweight suffix array construction algorithm. This library provides a | |
11963 | simple and an efficient C API to construct a suffix array and a | |
11964 | Burrows-Wheeler transformed string from a given string over a constant-size | |
11965 | alphabet. The algorithm runs in O(n log n) worst-case time using only 5n+O(1) | |
11966 | bytes of memory space, where n is the length of the string.") | |
11967 | (license license:expat))) | |
8d77a085 RW |
11968 | |
11969 | (define-public sailfish | |
11970 | (package | |
11971 | (name "sailfish") | |
11972 | (version "0.10.1") | |
11973 | (source (origin | |
c098c49b RW |
11974 | (method git-fetch) |
11975 | (uri (git-reference | |
11976 | (url "https://github.com/kingsfordgroup/sailfish.git") | |
11977 | (commit (string-append "v" version)))) | |
11978 | (file-name (git-file-name name version)) | |
8d77a085 RW |
11979 | (sha256 |
11980 | (base32 | |
c098c49b | 11981 | "1amcc5hqvsl42hg4x19bi9vy47cl874s0lw1fmi0hwsdk9i8c03v")) |
8d77a085 RW |
11982 | (modules '((guix build utils))) |
11983 | (snippet | |
11984 | '(begin | |
11985 | ;; Delete bundled headers for eigen3. | |
11986 | (delete-file-recursively "include/eigen3/") | |
11987 | #t)))) | |
11988 | (build-system cmake-build-system) | |
11989 | (arguments | |
11990 | `(#:configure-flags | |
11991 | (list (string-append "-DBOOST_INCLUDEDIR=" | |
11992 | (assoc-ref %build-inputs "boost") | |
11993 | "/include/") | |
11994 | (string-append "-DBOOST_LIBRARYDIR=" | |
11995 | (assoc-ref %build-inputs "boost") | |
11996 | "/lib/") | |
11997 | (string-append "-DBoost_LIBRARIES=" | |
11998 | "-lboost_iostreams " | |
11999 | "-lboost_filesystem " | |
12000 | "-lboost_system " | |
12001 | "-lboost_thread " | |
12002 | "-lboost_timer " | |
12003 | "-lboost_chrono " | |
12004 | "-lboost_program_options") | |
12005 | "-DBoost_FOUND=TRUE" | |
12006 | ;; Don't download RapMap---we already have it! | |
12007 | "-DFETCHED_RAPMAP=1") | |
12008 | ;; Tests must be run after installation and the location of the test | |
12009 | ;; data file must be overridden. But the tests fail. It looks like | |
12010 | ;; they are not really meant to be run. | |
12011 | #:tests? #f | |
12012 | #:phases | |
12013 | (modify-phases %standard-phases | |
12014 | ;; Boost cannot be found, even though it's right there. | |
12015 | (add-after 'unpack 'do-not-look-for-boost | |
12016 | (lambda* (#:key inputs #:allow-other-keys) | |
12017 | (substitute* "CMakeLists.txt" | |
2e0f6905 MW |
12018 | (("find_package\\(Boost 1\\.53\\.0") "#")) |
12019 | #t)) | |
8d77a085 RW |
12020 | (add-after 'unpack 'do-not-assign-to-macro |
12021 | (lambda _ | |
12022 | (substitute* "include/spdlog/details/format.cc" | |
2e0f6905 MW |
12023 | (("const unsigned CHAR_WIDTH = 1;") "")) |
12024 | #t)) | |
8d77a085 RW |
12025 | (add-after 'unpack 'prepare-rapmap |
12026 | (lambda* (#:key inputs #:allow-other-keys) | |
12027 | (let ((src "external/install/src/rapmap/") | |
12028 | (include "external/install/include/rapmap/") | |
12029 | (rapmap (assoc-ref inputs "rapmap"))) | |
12030 | (mkdir-p "/tmp/rapmap") | |
9f527c91 RW |
12031 | (invoke "tar" "xf" |
12032 | (assoc-ref inputs "rapmap") | |
12033 | "-C" "/tmp/rapmap" | |
12034 | "--strip-components=1") | |
8d77a085 RW |
12035 | (mkdir-p src) |
12036 | (mkdir-p include) | |
12037 | (for-each (lambda (file) | |
12038 | (install-file file src)) | |
12039 | (find-files "/tmp/rapmap/src" "\\.(c|cpp)")) | |
2e0f6905 MW |
12040 | (copy-recursively "/tmp/rapmap/include" include)) |
12041 | #t)) | |
8d77a085 RW |
12042 | (add-after 'unpack 'use-system-libraries |
12043 | (lambda* (#:key inputs #:allow-other-keys) | |
12044 | (substitute* '("src/SailfishIndexer.cpp" | |
12045 | "src/SailfishUtils.cpp" | |
12046 | "src/SailfishQuantify.cpp" | |
12047 | "src/FASTAParser.cpp" | |
12048 | "include/PCA.hpp" | |
12049 | "include/SailfishUtils.hpp" | |
12050 | "include/SailfishIndex.hpp" | |
12051 | "include/CollapsedEMOptimizer.hpp" | |
12052 | "src/CollapsedEMOptimizer.cpp") | |
12053 | (("#include \"jellyfish/config.h\"") "")) | |
12054 | (substitute* "src/CMakeLists.txt" | |
12055 | (("\\$\\{GAT_SOURCE_DIR\\}/external/install/include/jellyfish-2.2..") | |
12056 | (string-append (assoc-ref inputs "jellyfish") | |
12057 | "/include/jellyfish-" ,(package-version jellyfish))) | |
12058 | (("\\$\\{GAT_SOURCE_DIR\\}/external/install/lib/libjellyfish-2.0.a") | |
12059 | (string-append (assoc-ref inputs "jellyfish") | |
12060 | "/lib/libjellyfish-2.0.a")) | |
12061 | (("\\$\\{GAT_SOURCE_DIR\\}/external/install/lib/libdivsufsort.a") | |
12062 | (string-append (assoc-ref inputs "libdivsufsort") | |
12063 | "/lib/libdivsufsort.so")) | |
12064 | (("\\$\\{GAT_SOURCE_DIR\\}/external/install/lib/libdivsufsort64.a") | |
12065 | (string-append (assoc-ref inputs "libdivsufsort") | |
12066 | "/lib/libdivsufsort64.so"))) | |
12067 | (substitute* "CMakeLists.txt" | |
12068 | ;; Don't prefer static libs | |
12069 | (("SET\\(CMAKE_FIND_LIBRARY_SUFFIXES.*") "") | |
12070 | (("find_package\\(Jellyfish.*") "") | |
12071 | (("ExternalProject_Add\\(libjellyfish") "message(") | |
12072 | (("ExternalProject_Add\\(libgff") "message(") | |
12073 | (("ExternalProject_Add\\(libsparsehash") "message(") | |
12074 | (("ExternalProject_Add\\(libdivsufsort") "message(")) | |
12075 | ||
12076 | ;; Ensure that Eigen headers can be found | |
12077 | (setenv "CPLUS_INCLUDE_PATH" | |
12078 | (string-append (getenv "CPLUS_INCLUDE_PATH") | |
12079 | ":" | |
12080 | (assoc-ref inputs "eigen") | |
2e0f6905 MW |
12081 | "/include/eigen3")) |
12082 | #t))))) | |
8d77a085 RW |
12083 | (inputs |
12084 | `(("boost" ,boost) | |
12085 | ("eigen" ,eigen) | |
12086 | ("jemalloc" ,jemalloc) | |
12087 | ("jellyfish" ,jellyfish) | |
12088 | ("sparsehash" ,sparsehash) | |
12089 | ("rapmap" ,(origin | |
12090 | (method git-fetch) | |
12091 | (uri (git-reference | |
12092 | (url "https://github.com/COMBINE-lab/RapMap.git") | |
12093 | (commit (string-append "sf-v" version)))) | |
12094 | (file-name (string-append "rapmap-sf-v" version "-checkout")) | |
12095 | (sha256 | |
12096 | (base32 | |
12097 | "1hv79l5i576ykv5a1srj2p0q36yvyl5966m0fcy2lbi169ipjakf")) | |
12098 | (modules '((guix build utils))) | |
12099 | ;; These files are expected to be excluded. | |
12100 | (snippet | |
12101 | '(begin (delete-file-recursively "include/spdlog") | |
12102 | (for-each delete-file '("include/xxhash.h" | |
6cbee49d MW |
12103 | "src/xxhash.c")) |
12104 | #t)))) | |
8d77a085 RW |
12105 | ("libdivsufsort" ,libdivsufsort) |
12106 | ("libgff" ,libgff) | |
12107 | ("tbb" ,tbb) | |
12108 | ("zlib" ,zlib))) | |
12109 | (native-inputs | |
12110 | `(("pkg-config" ,pkg-config))) | |
12111 | (home-page "http://www.cs.cmu.edu/~ckingsf/software/sailfish") | |
12112 | (synopsis "Mapping-based isoform quantification from RNA-Seq reads") | |
12113 | (description "Sailfish is a tool for genomic transcript quantification | |
12114 | from RNA-seq data. It requires a set of target transcripts (either from a | |
12115 | reference or de-novo assembly) to quantify. All you need to run sailfish is a | |
12116 | fasta file containing your reference transcripts and a (set of) fasta/fastq | |
12117 | file(s) containing your reads.") | |
12118 | (license license:gpl3+))) | |
7762646d RW |
12119 | |
12120 | (define libstadenio-for-salmon | |
12121 | (package | |
12122 | (name "libstadenio") | |
12123 | (version "1.14.8") | |
12124 | (source (origin | |
12125 | (method git-fetch) | |
12126 | (uri (git-reference | |
12127 | (url "https://github.com/COMBINE-lab/staden-io_lib.git") | |
12128 | (commit (string-append "v" version)))) | |
12129 | (file-name (string-append name "-" version "-checkout")) | |
12130 | (sha256 | |
12131 | (base32 | |
12132 | "1x8kxxqxl892vwfbprlbyfwkkv7c34ggkc94892x9x0g37x5nbwx")))) | |
12133 | (build-system gnu-build-system) | |
12134 | (arguments '(#:parallel-tests? #f)) ; not supported | |
12135 | (inputs | |
12136 | `(("zlib" ,zlib))) | |
12137 | (native-inputs | |
12138 | `(("perl" ,perl))) ; for tests | |
12139 | (home-page "https://github.com/COMBINE-lab/staden-io_lib") | |
12140 | (synopsis "General purpose trace and experiment file library") | |
12141 | (description "This package provides a library of file reading and writing | |
12142 | code to provide a general purpose Trace file (and Experiment File) reading | |
12143 | interface. | |
12144 | ||
12145 | The following file formats are supported: | |
12146 | ||
12147 | @enumerate | |
12148 | @item SCF trace files | |
12149 | @item ABI trace files | |
12150 | @item ALF trace files | |
12151 | @item ZTR trace files | |
12152 | @item SFF trace archives | |
12153 | @item SRF trace archives | |
12154 | @item Experiment files | |
12155 | @item Plain text files | |
12156 | @item SAM/BAM sequence files | |
12157 | @item CRAM sequence files | |
12158 | @end enumerate\n") | |
12159 | (license license:bsd-3))) | |
12160 | ||
12161 | (define spdlog-for-salmon | |
12162 | (package | |
12163 | (name "spdlog") | |
12164 | (version "0.14.0") | |
12165 | (source (origin | |
12166 | (method git-fetch) | |
12167 | (uri (git-reference | |
12168 | (url "https://github.com/COMBINE-lab/spdlog.git") | |
12169 | (commit (string-append "v" version)))) | |
12170 | (file-name (string-append name "-" version "-checkout")) | |
12171 | (sha256 | |
12172 | (base32 | |
12173 | "13730429gwlabi432ilpnja3sfvy0nn2719vnhhmii34xcdyc57q")))) | |
12174 | (build-system cmake-build-system) | |
12175 | (home-page "https://github.com/COMBINE-lab/spdlog") | |
12176 | (synopsis "Very fast C++ logging library") | |
12177 | (description "Spdlog is a very fast header-only C++ logging library with | |
12178 | performance as its primary goal.") | |
12179 | (license license:expat))) | |
12180 | ||
12181 | ;; This is a modified variant of bwa for use with Salmon. It installs a | |
12182 | ;; library to avoid having to build this as part of Salmon. | |
12183 | (define bwa-for-salmon | |
12184 | (package (inherit bwa) | |
12185 | (name "bwa") | |
12186 | (version "0.7.12.5") | |
12187 | (source (origin | |
12188 | (method git-fetch) | |
12189 | (uri (git-reference | |
12190 | (url "https://github.com/COMBINE-lab/bwa.git") | |
12191 | (commit (string-append "v" version)))) | |
12192 | (file-name (string-append "bwa-for-salmon-" version "-checkout")) | |
12193 | (sha256 | |
12194 | (base32 | |
12195 | "1z2qa64y0c5hky10510x137mnzlhz6k8qf27csw4w9j6qihq95gb")))) | |
12196 | (build-system gnu-build-system) | |
12197 | (arguments | |
12198 | '(#:tests? #f ;no "check" target | |
12199 | #:phases | |
12200 | (modify-phases %standard-phases | |
12201 | (replace 'install | |
12202 | (lambda* (#:key outputs #:allow-other-keys) | |
12203 | (let* ((out (assoc-ref outputs "out")) | |
12204 | (bin (string-append out "/bin")) | |
12205 | (lib (string-append out "/lib")) | |
12206 | (doc (string-append out "/share/doc/bwa")) | |
12207 | (man (string-append out "/share/man/man1")) | |
12208 | (inc (string-append out "/include/bwa"))) | |
12209 | (install-file "bwa" bin) | |
12210 | (install-file "README.md" doc) | |
12211 | (install-file "bwa.1" man) | |
12212 | (install-file "libbwa.a" lib) | |
12213 | (mkdir-p lib) | |
12214 | (mkdir-p inc) | |
12215 | (for-each (lambda (file) | |
12216 | (install-file file inc)) | |
12217 | (find-files "." "\\.h$"))) | |
12218 | #t)) | |
12219 | ;; no "configure" script | |
12220 | (delete 'configure)))))) | |
12221 | ||
12222 | (define-public salmon | |
12223 | (package | |
12224 | (name "salmon") | |
12225 | (version "0.9.1") | |
12226 | (source (origin | |
12227 | (method git-fetch) | |
12228 | (uri (git-reference | |
12229 | (url "https://github.com/COMBINE-lab/salmon.git") | |
12230 | (commit (string-append "v" version)))) | |
12231 | (file-name (string-append name "-" version "-checkout")) | |
12232 | (sha256 | |
12233 | (base32 | |
12234 | "1zi1ff4i7y2ykk0vdzysgwzzzv166vg2x77pj1mf4baclavxj87a")) | |
12235 | (modules '((guix build utils))) | |
12236 | (snippet | |
12237 | '(begin | |
12238 | ;; Delete bundled headers for eigen3. | |
12239 | (delete-file-recursively "include/eigen3/") | |
12240 | #t)))) | |
12241 | (build-system cmake-build-system) | |
12242 | (arguments | |
12243 | `(#:configure-flags | |
12244 | (list (string-append "-DBOOST_INCLUDEDIR=" | |
12245 | (assoc-ref %build-inputs "boost") | |
12246 | "/include/") | |
12247 | (string-append "-DBOOST_LIBRARYDIR=" | |
12248 | (assoc-ref %build-inputs "boost") | |
12249 | "/lib/") | |
12250 | (string-append "-DBoost_LIBRARIES=" | |
12251 | "-lboost_iostreams " | |
12252 | "-lboost_filesystem " | |
12253 | "-lboost_system " | |
12254 | "-lboost_thread " | |
12255 | "-lboost_timer " | |
12256 | "-lboost_chrono " | |
12257 | "-lboost_program_options") | |
12258 | "-DBoost_FOUND=TRUE" | |
12259 | "-DTBB_LIBRARIES=tbb tbbmalloc" | |
12260 | ;; Don't download RapMap---we already have it! | |
12261 | "-DFETCHED_RAPMAP=1") | |
12262 | #:phases | |
12263 | (modify-phases %standard-phases | |
12264 | ;; Boost cannot be found, even though it's right there. | |
12265 | (add-after 'unpack 'do-not-look-for-boost | |
12266 | (lambda* (#:key inputs #:allow-other-keys) | |
12267 | (substitute* "CMakeLists.txt" | |
2e0f6905 MW |
12268 | (("find_package\\(Boost 1\\.53\\.0") "#")) |
12269 | #t)) | |
7762646d RW |
12270 | (add-after 'unpack 'do-not-phone-home |
12271 | (lambda _ | |
12272 | (substitute* "src/Salmon.cpp" | |
2e0f6905 MW |
12273 | (("getVersionMessage\\(\\)") "\"\"")) |
12274 | #t)) | |
7762646d RW |
12275 | (add-after 'unpack 'prepare-rapmap |
12276 | (lambda* (#:key inputs #:allow-other-keys) | |
12277 | (let ((src "external/install/src/rapmap/") | |
12278 | (include "external/install/include/rapmap/") | |
12279 | (rapmap (assoc-ref inputs "rapmap"))) | |
12280 | (mkdir-p src) | |
12281 | (mkdir-p include) | |
12282 | (for-each (lambda (file) | |
12283 | (install-file file src)) | |
12284 | (find-files (string-append rapmap "/src") "\\.(c|cpp)")) | |
12285 | (copy-recursively (string-append rapmap "/include") include) | |
12286 | (for-each delete-file '("external/install/include/rapmap/xxhash.h" | |
12287 | "external/install/include/rapmap/FastxParser.hpp" | |
12288 | "external/install/include/rapmap/concurrentqueue.h" | |
12289 | "external/install/include/rapmap/FastxParserThreadUtils.hpp" | |
12290 | "external/install/src/rapmap/FastxParser.cpp" | |
2e0f6905 MW |
12291 | "external/install/src/rapmap/xxhash.c"))) |
12292 | #t)) | |
7762646d RW |
12293 | (add-after 'unpack 'use-system-libraries |
12294 | (lambda* (#:key inputs #:allow-other-keys) | |
12295 | (substitute* "src/CMakeLists.txt" | |
12296 | (("\\$\\{GAT_SOURCE_DIR\\}/external/install/include/jellyfish-2.2..") | |
12297 | (string-append (assoc-ref inputs "jellyfish") | |
12298 | "/include/jellyfish-" ,(package-version jellyfish))) | |
12299 | (("\\$\\{GAT_SOURCE_DIR\\}/external/install/lib/libjellyfish-2.0.a") | |
12300 | (string-append (assoc-ref inputs "jellyfish") | |
12301 | "/lib/libjellyfish-2.0.a")) | |
12302 | (("\\$\\{GAT_SOURCE_DIR\\}/external/install/lib/libdivsufsort.a") | |
12303 | (string-append (assoc-ref inputs "libdivsufsort") | |
12304 | "/lib/libdivsufsort.so")) | |
12305 | (("\\$\\{GAT_SOURCE_DIR\\}/external/install/lib/libstaden-read.a") | |
12306 | (string-append (assoc-ref inputs "libstadenio-for-salmon") | |
12307 | "/lib/libstaden-read.a")) | |
12308 | (("\\$\\{GAT_SOURCE_DIR\\}/external/install/lib/libbwa.a") | |
12309 | (string-append (assoc-ref inputs "bwa") "/lib/libbwa.a")) | |
12310 | (("\\$\\{GAT_SOURCE_DIR\\}/external/install/lib/libdivsufsort64.a") | |
12311 | (string-append (assoc-ref inputs "libdivsufsort") | |
12312 | "/lib/libdivsufsort64.so"))) | |
12313 | (substitute* "CMakeLists.txt" | |
12314 | ;; Don't prefer static libs | |
12315 | (("SET\\(CMAKE_FIND_LIBRARY_SUFFIXES.*") "") | |
12316 | (("set\\(TBB_LIBRARIES") "message(") | |
12317 | (("find_package\\(Jellyfish.*") "") | |
12318 | (("ExternalProject_Add\\(libcereal") "message(") | |
12319 | (("ExternalProject_Add\\(libbwa") "message(") | |
12320 | (("ExternalProject_Add\\(libjellyfish") "message(") | |
12321 | (("ExternalProject_Add\\(libgff") "message(") | |
12322 | (("ExternalProject_Add\\(libtbb") "message(") | |
12323 | (("ExternalProject_Add\\(libspdlog") "message(") | |
12324 | (("ExternalProject_Add\\(libdivsufsort") "message(") | |
12325 | (("ExternalProject_Add\\(libstadenio") "message(") | |
12326 | (("ExternalProject_Add_Step\\(") "message(")) | |
12327 | ||
12328 | ;; Ensure that all headers can be found | |
12329 | (setenv "CPLUS_INCLUDE_PATH" | |
12330 | (string-append (getenv "CPLUS_INCLUDE_PATH") | |
12331 | ":" | |
12332 | (assoc-ref inputs "bwa") | |
12333 | "/include/bwa" | |
12334 | ":" | |
12335 | (assoc-ref inputs "eigen") | |
12336 | "/include/eigen3")) | |
12337 | (setenv "CPATH" | |
12338 | (string-append (assoc-ref inputs "bwa") | |
12339 | "/include/bwa" | |
12340 | ":" | |
12341 | (assoc-ref inputs "eigen") | |
12342 | "/include/eigen3")) | |
12343 | #t)) | |
12344 | ;; CMAKE_INSTALL_PREFIX does not exist when the tests are | |
12345 | ;; run. It only exists after the install phase. | |
12346 | (add-after 'unpack 'fix-tests | |
12347 | (lambda _ | |
12348 | (substitute* "src/CMakeLists.txt" | |
12349 | (("DTOPLEVEL_DIR=\\$\\{CMAKE_INSTALL_PREFIX") | |
12350 | "DTOPLEVEL_DIR=${GAT_SOURCE_DIR")) | |
12351 | #t))))) | |
12352 | (inputs | |
12353 | `(("boost" ,boost) | |
12354 | ("bwa" ,bwa-for-salmon) | |
12355 | ("bzip2" ,bzip2) | |
12356 | ("cereal" ,cereal) | |
12357 | ("eigen" ,eigen) | |
12358 | ("rapmap" ,(origin | |
12359 | (method git-fetch) | |
12360 | (uri (git-reference | |
12361 | (url "https://github.com/COMBINE-lab/RapMap.git") | |
12362 | (commit (string-append "salmon-v" version)))) | |
12363 | (file-name (string-append "rapmap-salmon-v" version "-checkout")) | |
12364 | (sha256 | |
12365 | (base32 | |
12366 | "1yc12yqsz6f0r8sg1qnk57xg34aqwc9jbqq6gd5ys28xw3plj98p")))) | |
12367 | ("jemalloc" ,jemalloc) | |
12368 | ("jellyfish" ,jellyfish) | |
12369 | ("libgff" ,libgff) | |
12370 | ("tbb" ,tbb) | |
12371 | ("libdivsufsort" ,libdivsufsort) | |
12372 | ("libstadenio-for-salmon" ,libstadenio-for-salmon) | |
12373 | ("spdlog-for-salmon" ,spdlog-for-salmon) | |
12374 | ("xz" ,xz) | |
12375 | ("zlib" ,zlib))) | |
12376 | (home-page "https://github.com/COMBINE-lab/salmon") | |
12377 | (synopsis "Quantification from RNA-seq reads using lightweight alignments") | |
12378 | (description "Salmon is a program to produce highly-accurate, | |
12379 | transcript-level quantification estimates from RNA-seq data. Salmon achieves | |
12380 | its accuracy and speed via a number of different innovations, including the | |
12381 | use of lightweight alignments (accurate but fast-to-compute proxies for | |
12382 | traditional read alignments) and massively-parallel stochastic collapsed | |
12383 | variational inference.") | |
12384 | (license license:gpl3+))) | |
152d30c3 RW |
12385 | |
12386 | (define-public python-loompy | |
12387 | (package | |
12388 | (name "python-loompy") | |
12389 | (version "2.0.2") | |
12390 | (source | |
12391 | (origin | |
12392 | (method url-fetch) | |
12393 | (uri (pypi-uri "loompy" version)) | |
12394 | (sha256 | |
12395 | (base32 | |
12396 | "1drgv8j1hxqzzpnfg272x9djb6j8qr798w1pc2x8ikmfgyd9gh51")))) | |
12397 | (build-system python-build-system) | |
12398 | ;; There are no tests | |
12399 | (arguments '(#:tests? #f)) | |
12400 | (propagated-inputs | |
12401 | `(("python-h5py" ,python-h5py) | |
12402 | ("python-numpy" ,python-numpy) | |
12403 | ("python-scipy" ,python-scipy) | |
12404 | ("python-typing" ,python-typing))) | |
12405 | (home-page "https://github.com/linnarsson-lab/loompy") | |
12406 | (synopsis "Work with .loom files for single-cell RNA-seq data") | |
12407 | (description "The loom file format is an efficient format for very large | |
12408 | omics datasets, consisting of a main matrix, optional additional layers, a | |
12409 | variable number of row and column annotations. Loom also supports sparse | |
12410 | graphs. This library makes it easy to work with @file{.loom} files for | |
12411 | single-cell RNA-seq data.") | |
12412 | (license license:bsd-3))) | |
5fef15e5 | 12413 | |
f09d16e5 RW |
12414 | ;; We cannot use the latest commit because it requires Java 9. |
12415 | (define-public java-forester | |
12416 | (let ((commit "86b07efe302d5094b42deed9260f719a4c4ac2e6") | |
12417 | (revision "1")) | |
12418 | (package | |
12419 | (name "java-forester") | |
12420 | (version (string-append "0-" revision "." (string-take commit 7))) | |
12421 | (source (origin | |
12422 | (method git-fetch) | |
12423 | (uri (git-reference | |
12424 | (url "https://github.com/cmzmasek/forester.git") | |
12425 | (commit commit))) | |
12426 | (file-name (string-append name "-" version "-checkout")) | |
12427 | (sha256 | |
12428 | (base32 | |
12429 | "0vxavc1yrf84yrnf20dq26hi0lglidk8d382xrxsy4qmlbjd276z")) | |
12430 | (modules '((guix build utils))) | |
12431 | (snippet | |
12432 | '(begin | |
12433 | ;; Delete bundled jars and pre-built classes | |
12434 | (delete-file-recursively "forester/java/resources") | |
12435 | (delete-file-recursively "forester/java/classes") | |
12436 | (for-each delete-file (find-files "forester/java/" "\\.jar$")) | |
12437 | ;; Delete bundled applications | |
12438 | (delete-file-recursively "forester_applications") | |
12439 | #t)))) | |
12440 | (build-system ant-build-system) | |
12441 | (arguments | |
12442 | `(#:tests? #f ; there are none | |
12443 | #:jdk ,icedtea-8 | |
12444 | #:modules ((guix build ant-build-system) | |
12445 | (guix build utils) | |
12446 | (guix build java-utils) | |
12447 | (sxml simple) | |
12448 | (sxml transform)) | |
12449 | #:phases | |
12450 | (modify-phases %standard-phases | |
12451 | (add-after 'unpack 'chdir | |
12452 | (lambda _ (chdir "forester/java") #t)) | |
12453 | (add-after 'chdir 'fix-dependencies | |
12454 | (lambda _ | |
12455 | (chmod "build.xml" #o664) | |
12456 | (call-with-output-file "build.xml.new" | |
12457 | (lambda (port) | |
12458 | (sxml->xml | |
12459 | (pre-post-order | |
12460 | (with-input-from-file "build.xml" | |
12461 | (lambda _ (xml->sxml #:trim-whitespace? #t))) | |
12462 | `(;; Remove all unjar tags to avoid repacking classes. | |
12463 | (unjar . ,(lambda _ '())) | |
12464 | (*default* . ,(lambda (tag . kids) `(,tag ,@kids))) | |
12465 | (*text* . ,(lambda (_ txt) txt)))) | |
12466 | port))) | |
12467 | (rename-file "build.xml.new" "build.xml") | |
12468 | #t)) | |
12469 | ;; FIXME: itext is difficult to package as it depends on a few | |
12470 | ;; unpackaged libraries. | |
12471 | (add-after 'chdir 'remove-dependency-on-unpackaged-itext | |
12472 | (lambda _ | |
12473 | (delete-file "src/org/forester/archaeopteryx/PdfExporter.java") | |
12474 | (substitute* "src/org/forester/archaeopteryx/MainFrame.java" | |
12475 | (("pdf_written_to = PdfExporter.*") | |
12476 | "throw new IOException(\"PDF export is not available.\");")) | |
12477 | #t)) | |
12478 | ;; There is no install target | |
12479 | (replace 'install (install-jars "."))))) | |
12480 | (propagated-inputs | |
12481 | `(("java-commons-codec" ,java-commons-codec) | |
12482 | ("java-openchart2" ,java-openchart2))) | |
12483 | (home-page "https://sites.google.com/site/cmzmasek/home/software/forester") | |
12484 | (synopsis "Phylogenomics libraries for Java") | |
12485 | (description "Forester is a collection of Java libraries for | |
12486 | phylogenomics and evolutionary biology research. It includes support for | |
12487 | reading, writing, and exporting phylogenetic trees.") | |
12488 | (license license:lgpl2.1+)))) | |
12489 | ||
10645b92 RW |
12490 | (define-public java-forester-1.005 |
12491 | (package | |
12492 | (name "java-forester") | |
12493 | (version "1.005") | |
12494 | (source (origin | |
12495 | (method url-fetch) | |
12496 | (uri (string-append "http://search.maven.org/remotecontent?" | |
12497 | "filepath=org/biojava/thirdparty/forester/" | |
12498 | version "/forester-" version "-sources.jar")) | |
12499 | (file-name (string-append name "-" version ".jar")) | |
12500 | (sha256 | |
12501 | (base32 | |
12502 | "04r8qv4rk3p71z4ajrvp11py1z46qrx0047j3zzs79s6lnsm3lcv")))) | |
12503 | (build-system ant-build-system) | |
12504 | (arguments | |
12505 | `(#:tests? #f ; there are none | |
12506 | #:jdk ,icedtea-8 | |
12507 | #:modules ((guix build ant-build-system) | |
12508 | (guix build utils) | |
12509 | (guix build java-utils) | |
12510 | (sxml simple) | |
12511 | (sxml transform)) | |
12512 | #:phases | |
12513 | (modify-phases %standard-phases | |
12514 | (add-after 'unpack 'fix-dependencies | |
12515 | (lambda* (#:key inputs #:allow-other-keys) | |
12516 | (call-with-output-file "build.xml" | |
12517 | (lambda (port) | |
12518 | (sxml->xml | |
12519 | (pre-post-order | |
12520 | (with-input-from-file "src/build.xml" | |
12521 | (lambda _ (xml->sxml #:trim-whitespace? #t))) | |
12522 | `(;; Remove all unjar tags to avoid repacking classes. | |
12523 | (unjar . ,(lambda _ '())) | |
12524 | (*default* . ,(lambda (tag . kids) `(,tag ,@kids))) | |
12525 | (*text* . ,(lambda (_ txt) txt)))) | |
12526 | port))) | |
12527 | (copy-file (assoc-ref inputs "synth_look_and_feel_1.xml") | |
12528 | "synth_look_and_feel_1.xml") | |
12529 | (copy-file (assoc-ref inputs "phyloxml.xsd") | |
12530 | "phyloxml.xsd") | |
12531 | (substitute* "build.xml" | |
12532 | (("../resources/synth_laf/synth_look_and_feel_1.xml") | |
12533 | "synth_look_and_feel_1.xml") | |
12534 | (("../resources/phyloxml_schema/1.10/phyloxml.xsd") | |
12535 | "phyloxml.xsd")) | |
12536 | #t)) | |
12537 | ;; FIXME: itext is difficult to package as it depends on a few | |
12538 | ;; unpackaged libraries. | |
12539 | (add-after 'unpack 'remove-dependency-on-unpackaged-itext | |
12540 | (lambda _ | |
12541 | (delete-file "src/org/forester/archaeopteryx/PdfExporter.java") | |
12542 | (substitute* '("src/org/forester/archaeopteryx/MainFrame.java" | |
12543 | "src/org/forester/archaeopteryx/MainFrameApplication.java") | |
12544 | (("pdf_written_to = PdfExporter.*") | |
12545 | "throw new IOException(\"PDF export is not available.\"); /*") | |
12546 | ((".getPrintSizeX\\(\\), getOptions\\(\\).getPrintSizeY\\(\\) \\);") "*/") | |
12547 | (("getCurrentTreePanel\\(\\).getHeight\\(\\) \\);") "*/")) | |
12548 | #t)) | |
12549 | (add-after 'unpack 'delete-pre-built-classes | |
12550 | (lambda _ (delete-file-recursively "src/classes") #t)) | |
12551 | ;; There is no install target | |
12552 | (replace 'install (install-jars "."))))) | |
12553 | (propagated-inputs | |
12554 | `(("java-commons-codec" ,java-commons-codec) | |
12555 | ("java-openchart2" ,java-openchart2))) | |
12556 | ;; The source archive does not contain the resources. | |
12557 | (native-inputs | |
12558 | `(("phyloxml.xsd" | |
12559 | ,(origin | |
12560 | (method url-fetch) | |
12561 | (uri (string-append "https://raw.githubusercontent.com/cmzmasek/forester/" | |
12562 | "b61cc2dcede0bede317db362472333115756b8c6/" | |
12563 | "forester/resources/phyloxml_schema/1.10/phyloxml.xsd")) | |
12564 | (file-name (string-append name "-phyloxml-" version ".xsd")) | |
12565 | (sha256 | |
12566 | (base32 | |
12567 | "1zxc4m8sn4n389nqdnpxa8d0k17qnr3pm2y5y6g6vh4k0zm52npv")))) | |
12568 | ("synth_look_and_feel_1.xml" | |
12569 | ,(origin | |
12570 | (method url-fetch) | |
12571 | (uri (string-append "https://raw.githubusercontent.com/cmzmasek/forester/" | |
12572 | "29e04321615da6b35c1e15c60e52caf3f21d8e6a/" | |
12573 | "forester/java/classes/resources/synth_look_and_feel_1.xml")) | |
12574 | (file-name (string-append name "-synth-look-and-feel-" version ".xml")) | |
12575 | (sha256 | |
12576 | (base32 | |
12577 | "1gv5602gv4k7y7713y75a4jvj7i9s7nildsbdl7n9q10sc2ikg8h")))))) | |
12578 | (home-page "https://sites.google.com/site/cmzmasek/home/software/forester") | |
12579 | (synopsis "Phylogenomics libraries for Java") | |
12580 | (description "Forester is a collection of Java libraries for | |
12581 | phylogenomics and evolutionary biology research. It includes support for | |
12582 | reading, writing, and exporting phylogenetic trees.") | |
12583 | (license license:lgpl2.1+))) | |
12584 | ||
5fef15e5 RW |
12585 | (define-public java-biojava-core |
12586 | (package | |
12587 | (name "java-biojava-core") | |
12588 | (version "4.2.11") | |
12589 | (source (origin | |
12590 | (method git-fetch) | |
12591 | (uri (git-reference | |
12592 | (url "https://github.com/biojava/biojava") | |
12593 | (commit (string-append "biojava-" version)))) | |
12594 | (file-name (string-append name "-" version "-checkout")) | |
12595 | (sha256 | |
12596 | (base32 | |
12597 | "1bvryh2bpsvash8ln79cmc9sqm8qw72hz4xzwqxcrjm8ssxszhqk")))) | |
12598 | (build-system ant-build-system) | |
12599 | (arguments | |
12600 | `(#:jdk ,icedtea-8 | |
12601 | #:jar-name "biojava-core.jar" | |
12602 | #:source-dir "biojava-core/src/main/java/" | |
12603 | #:test-dir "biojava-core/src/test" | |
12604 | ;; These tests seem to require internet access. | |
12605 | #:test-exclude (list "**/SearchIOTest.java" | |
12606 | "**/BlastXMLParserTest.java" | |
12607 | "**/GenbankCookbookTest.java" | |
12608 | "**/GenbankProxySequenceReaderTest.java") | |
12609 | #:phases | |
12610 | (modify-phases %standard-phases | |
12611 | (add-before 'build 'copy-resources | |
12612 | (lambda _ | |
12613 | (copy-recursively "biojava-core/src/main/resources" | |
12614 | "build/classes") | |
12615 | #t)) | |
12616 | (add-before 'check 'copy-test-resources | |
12617 | (lambda _ | |
12618 | (copy-recursively "biojava-core/src/test/resources" | |
12619 | "build/test-classes") | |
12620 | #t))))) | |
12621 | (propagated-inputs | |
12622 | `(("java-log4j-api" ,java-log4j-api) | |
12623 | ("java-log4j-core" ,java-log4j-core) | |
12624 | ("java-slf4j-api" ,java-slf4j-api) | |
12625 | ("java-slf4j-simple" ,java-slf4j-simple))) | |
12626 | (native-inputs | |
12627 | `(("java-junit" ,java-junit) | |
12628 | ("java-hamcrest-core" ,java-hamcrest-core))) | |
12629 | (home-page "http://biojava.org") | |
12630 | (synopsis "Core libraries of Java framework for processing biological data") | |
12631 | (description "BioJava is a project dedicated to providing a Java framework | |
12632 | for processing biological data. It provides analytical and statistical | |
12633 | routines, parsers for common file formats, reference implementations of | |
12634 | popular algorithms, and allows the manipulation of sequences and 3D | |
12635 | structures. The goal of the biojava project is to facilitate rapid | |
12636 | application development for bioinformatics. | |
12637 | ||
12638 | This package provides the core libraries.") | |
12639 | (license license:lgpl2.1+))) | |
b28c8037 RW |
12640 | |
12641 | (define-public java-biojava-phylo | |
12642 | (package (inherit java-biojava-core) | |
12643 | (name "java-biojava-phylo") | |
12644 | (build-system ant-build-system) | |
12645 | (arguments | |
12646 | `(#:jdk ,icedtea-8 | |
12647 | #:jar-name "biojava-phylo.jar" | |
12648 | #:source-dir "biojava-phylo/src/main/java/" | |
12649 | #:test-dir "biojava-phylo/src/test" | |
12650 | #:phases | |
12651 | (modify-phases %standard-phases | |
12652 | (add-before 'build 'copy-resources | |
12653 | (lambda _ | |
12654 | (copy-recursively "biojava-phylo/src/main/resources" | |
12655 | "build/classes") | |
12656 | #t)) | |
12657 | (add-before 'check 'copy-test-resources | |
12658 | (lambda _ | |
12659 | (copy-recursively "biojava-phylo/src/test/resources" | |
12660 | "build/test-classes") | |
12661 | #t))))) | |
12662 | (propagated-inputs | |
12663 | `(("java-log4j-api" ,java-log4j-api) | |
12664 | ("java-log4j-core" ,java-log4j-core) | |
12665 | ("java-slf4j-api" ,java-slf4j-api) | |
12666 | ("java-slf4j-simple" ,java-slf4j-simple) | |
12667 | ("java-biojava-core" ,java-biojava-core) | |
12668 | ("java-forester" ,java-forester))) | |
12669 | (native-inputs | |
12670 | `(("java-junit" ,java-junit) | |
12671 | ("java-hamcrest-core" ,java-hamcrest-core))) | |
12672 | (home-page "http://biojava.org") | |
12673 | (synopsis "Biojava interface to the forester phylogenomics library") | |
12674 | (description "The phylo module provides a biojava interface layer to the | |
12675 | forester phylogenomics library for constructing phylogenetic trees."))) | |
22c09c33 RW |
12676 | |
12677 | (define-public java-biojava-alignment | |
12678 | (package (inherit java-biojava-core) | |
12679 | (name "java-biojava-alignment") | |
12680 | (build-system ant-build-system) | |
12681 | (arguments | |
12682 | `(#:jdk ,icedtea-8 | |
12683 | #:jar-name "biojava-alignment.jar" | |
12684 | #:source-dir "biojava-alignment/src/main/java/" | |
12685 | #:test-dir "biojava-alignment/src/test" | |
12686 | #:phases | |
12687 | (modify-phases %standard-phases | |
12688 | (add-before 'build 'copy-resources | |
12689 | (lambda _ | |
12690 | (copy-recursively "biojava-alignment/src/main/resources" | |
12691 | "build/classes") | |
12692 | #t)) | |
12693 | (add-before 'check 'copy-test-resources | |
12694 | (lambda _ | |
12695 | (copy-recursively "biojava-alignment/src/test/resources" | |
12696 | "build/test-classes") | |
12697 | #t))))) | |
12698 | (propagated-inputs | |
12699 | `(("java-log4j-api" ,java-log4j-api) | |
12700 | ("java-log4j-core" ,java-log4j-core) | |
12701 | ("java-slf4j-api" ,java-slf4j-api) | |
12702 | ("java-slf4j-simple" ,java-slf4j-simple) | |
12703 | ("java-biojava-core" ,java-biojava-core) | |
12704 | ("java-biojava-phylo" ,java-biojava-phylo) | |
12705 | ("java-forester" ,java-forester))) | |
12706 | (native-inputs | |
12707 | `(("java-junit" ,java-junit) | |
12708 | ("java-hamcrest-core" ,java-hamcrest-core))) | |
12709 | (home-page "http://biojava.org") | |
12710 | (synopsis "Biojava API for genetic sequence alignment") | |
12711 | (description "The alignment module of BioJava provides an API that | |
12712 | contains | |
12713 | ||
12714 | @itemize | |
12715 | @item implementations of dynamic programming algorithms for sequence | |
12716 | alignment; | |
12717 | @item reading and writing of popular alignment file formats; | |
12718 | @item a single-, or multi- threaded multiple sequence alignment algorithm. | |
12719 | @end itemize\n"))) | |
e44da58c RW |
12720 | |
12721 | (define-public java-biojava-core-4.0 | |
12722 | (package (inherit java-biojava-core) | |
12723 | (name "java-biojava-core") | |
12724 | (version "4.0.0") | |
12725 | (source (origin | |
12726 | (method git-fetch) | |
12727 | (uri (git-reference | |
12728 | (url "https://github.com/biojava/biojava") | |
12729 | (commit (string-append "biojava-" version)))) | |
12730 | (file-name (string-append name "-" version "-checkout")) | |
12731 | (sha256 | |
12732 | (base32 | |
12733 | "13675f6y9aqi7bi2lk3s1z7a22ynccjiqwa8izh7p97xi9wsfmd8")))))) | |
5528f9e8 RW |
12734 | |
12735 | (define-public java-biojava-phylo-4.0 | |
12736 | (package (inherit java-biojava-core-4.0) | |
12737 | (name "java-biojava-phylo") | |
12738 | (build-system ant-build-system) | |
12739 | (arguments | |
12740 | `(#:jdk ,icedtea-8 | |
12741 | #:jar-name "biojava-phylo.jar" | |
12742 | #:source-dir "biojava-phylo/src/main/java/" | |
12743 | #:test-dir "biojava-phylo/src/test" | |
12744 | #:phases | |
12745 | (modify-phases %standard-phases | |
12746 | (add-before 'build 'copy-resources | |
12747 | (lambda _ | |
12748 | (copy-recursively "biojava-phylo/src/main/resources" | |
12749 | "build/classes") | |
12750 | #t)) | |
12751 | (add-before 'check 'copy-test-resources | |
12752 | (lambda _ | |
12753 | (copy-recursively "biojava-phylo/src/test/resources" | |
12754 | "build/test-classes") | |
12755 | #t))))) | |
12756 | (propagated-inputs | |
12757 | `(("java-log4j-api" ,java-log4j-api) | |
12758 | ("java-log4j-core" ,java-log4j-core) | |
12759 | ("java-slf4j-api" ,java-slf4j-api) | |
12760 | ("java-slf4j-simple" ,java-slf4j-simple) | |
12761 | ("java-biojava-core" ,java-biojava-core-4.0) | |
12762 | ("java-forester" ,java-forester-1.005))) | |
12763 | (native-inputs | |
12764 | `(("java-junit" ,java-junit) | |
12765 | ("java-hamcrest-core" ,java-hamcrest-core))) | |
12766 | (home-page "http://biojava.org") | |
12767 | (synopsis "Biojava interface to the forester phylogenomics library") | |
12768 | (description "The phylo module provides a biojava interface layer to the | |
12769 | forester phylogenomics library for constructing phylogenetic trees."))) | |
9ac7db18 RW |
12770 | |
12771 | (define-public java-biojava-alignment-4.0 | |
12772 | (package (inherit java-biojava-core-4.0) | |
12773 | (name "java-biojava-alignment") | |
12774 | (build-system ant-build-system) | |
12775 | (arguments | |
12776 | `(#:jdk ,icedtea-8 | |
12777 | #:jar-name "biojava-alignment.jar" | |
12778 | #:source-dir "biojava-alignment/src/main/java/" | |
12779 | #:test-dir "biojava-alignment/src/test" | |
12780 | #:phases | |
12781 | (modify-phases %standard-phases | |
12782 | (add-before 'build 'copy-resources | |
12783 | (lambda _ | |
12784 | (copy-recursively "biojava-alignment/src/main/resources" | |
12785 | "build/classes") | |
12786 | #t)) | |
12787 | (add-before 'check 'copy-test-resources | |
12788 | (lambda _ | |
12789 | (copy-recursively "biojava-alignment/src/test/resources" | |
12790 | "build/test-classes") | |
12791 | #t))))) | |
12792 | (propagated-inputs | |
12793 | `(("java-log4j-api" ,java-log4j-api) | |
12794 | ("java-log4j-core" ,java-log4j-core) | |
12795 | ("java-slf4j-api" ,java-slf4j-api) | |
12796 | ("java-slf4j-simple" ,java-slf4j-simple) | |
12797 | ("java-biojava-core" ,java-biojava-core-4.0) | |
12798 | ("java-biojava-phylo" ,java-biojava-phylo-4.0) | |
12799 | ("java-forester" ,java-forester-1.005))) | |
12800 | (native-inputs | |
12801 | `(("java-junit" ,java-junit) | |
12802 | ("java-hamcrest-core" ,java-hamcrest-core))) | |
12803 | (home-page "http://biojava.org") | |
12804 | (synopsis "Biojava API for genetic sequence alignment") | |
12805 | (description "The alignment module of BioJava provides an API that | |
12806 | contains | |
12807 | ||
12808 | @itemize | |
12809 | @item implementations of dynamic programming algorithms for sequence | |
12810 | alignment; | |
12811 | @item reading and writing of popular alignment file formats; | |
12812 | @item a single-, or multi- threaded multiple sequence alignment algorithm. | |
12813 | @end itemize\n"))) | |
1adeef31 RW |
12814 | |
12815 | (define-public dropseq-tools | |
12816 | (package | |
12817 | (name "dropseq-tools") | |
12818 | (version "1.13") | |
12819 | (source | |
12820 | (origin | |
12821 | (method url-fetch) | |
12822 | (uri "http://mccarrolllab.com/download/1276/") | |
12823 | (file-name (string-append "dropseq-tools-" version ".zip")) | |
12824 | (sha256 | |
12825 | (base32 | |
12826 | "0yrffckxqk5l8b5xb6z4laq157zd9mdypr2p4b4vq2bhjzi1sj0s")) | |
12827 | ;; Delete bundled libraries | |
12828 | (modules '((guix build utils))) | |
12829 | (snippet | |
12830 | '(begin | |
12831 | (for-each delete-file (find-files "jar/lib" "\\.jar$")) | |
6cbee49d MW |
12832 | (delete-file-recursively "3rdParty") |
12833 | #t)))) | |
1adeef31 RW |
12834 | (build-system ant-build-system) |
12835 | (arguments | |
12836 | `(#:tests? #f ; test data are not included | |
12837 | #:test-target "test" | |
12838 | #:build-target "all" | |
12839 | #:source-dir "public/src/" | |
12840 | #:jdk ,icedtea-8 | |
12841 | #:make-flags | |
12842 | (list (string-append "-Dpicard.executable.dir=" | |
12843 | (assoc-ref %build-inputs "java-picard") | |
12844 | "/share/java/")) | |
12845 | #:modules ((ice-9 match) | |
12846 | (srfi srfi-1) | |
12847 | (guix build utils) | |
12848 | (guix build java-utils) | |
12849 | (guix build ant-build-system)) | |
12850 | #:phases | |
12851 | (modify-phases %standard-phases | |
e53152c7 | 12852 | ;; FIXME: fails with "java.io.FileNotFoundException: |
6fe41974 | 12853 | ;; /gnu/store/…-dropseq-tools-1.13/share/java/lib/biojava-alignment.jar" |
e53152c7 | 12854 | (delete 'generate-jar-indices) |
1adeef31 RW |
12855 | ;; All dependencies must be linked to "lib", because that's where |
12856 | ;; they will be searched for when the Class-Path property of the | |
12857 | ;; manifest is computed. | |
12858 | (add-after 'unpack 'record-references | |
12859 | (lambda* (#:key inputs #:allow-other-keys) | |
12860 | (mkdir-p "jar/lib") | |
12861 | (let ((dirs (filter-map (match-lambda | |
12862 | ((name . dir) | |
12863 | (if (and (string-prefix? "java-" name) | |
12864 | (not (string=? name "java-testng"))) | |
12865 | dir #f))) | |
12866 | inputs))) | |
12867 | (for-each (lambda (jar) | |
12868 | (symlink jar (string-append "jar/lib/" (basename jar)))) | |
12869 | (append-map (lambda (dir) (find-files dir "\\.jar$")) | |
12870 | dirs))) | |
12871 | #t)) | |
12872 | ;; There is no installation target | |
12873 | (replace 'install | |
12874 | (lambda* (#:key inputs outputs #:allow-other-keys) | |
12875 | (let* ((out (assoc-ref outputs "out")) | |
12876 | (bin (string-append out "/bin")) | |
12877 | (share (string-append out "/share/java/")) | |
12878 | (lib (string-append share "/lib/")) | |
12879 | (scripts (list "BAMTagHistogram" | |
12880 | "BAMTagofTagCounts" | |
12881 | "BaseDistributionAtReadPosition" | |
12882 | "CollapseBarcodesInPlace" | |
12883 | "CollapseTagWithContext" | |
12884 | "ConvertToRefFlat" | |
12885 | "CreateIntervalsFiles" | |
12886 | "DetectBeadSynthesisErrors" | |
12887 | "DigitalExpression" | |
12888 | "Drop-seq_alignment.sh" | |
12889 | "FilterBAM" | |
12890 | "FilterBAMByTag" | |
12891 | "GatherGeneGCLength" | |
12892 | "GatherMolecularBarcodeDistributionByGene" | |
12893 | "GatherReadQualityMetrics" | |
12894 | "PolyATrimmer" | |
12895 | "ReduceGTF" | |
12896 | "SelectCellsByNumTranscripts" | |
12897 | "SingleCellRnaSeqMetricsCollector" | |
12898 | "TagBamWithReadSequenceExtended" | |
12899 | "TagReadWithGeneExon" | |
12900 | "TagReadWithInterval" | |
12901 | "TrimStartingSequence" | |
12902 | "ValidateReference"))) | |
12903 | (for-each mkdir-p (list bin share lib)) | |
12904 | (install-file "dist/dropseq.jar" share) | |
12905 | (for-each (lambda (script) | |
12906 | (chmod script #o555) | |
12907 | (install-file script bin)) | |
12908 | scripts) | |
12909 | (substitute* (map (lambda (script) | |
12910 | (string-append bin "/" script)) | |
12911 | scripts) | |
12912 | (("^java") (which "java")) | |
12913 | (("jar_deploy_dir=.*") | |
12914 | (string-append "jar_deploy_dir=" share "\n")))) | |
12915 | #t)) | |
12916 | ;; FIXME: We do this after stripping jars because we don't want it to | |
12917 | ;; copy all these jars and strip them. We only want to install | |
12918 | ;; links. Arguably, this is a problem with the ant-build-system. | |
12919 | (add-after 'strip-jar-timestamps 'install-links | |
12920 | (lambda* (#:key outputs #:allow-other-keys) | |
12921 | (let* ((out (assoc-ref outputs "out")) | |
12922 | (share (string-append out "/share/java/")) | |
12923 | (lib (string-append share "/lib/"))) | |
12924 | (for-each (lambda (jar) | |
12925 | (symlink (readlink jar) | |
12926 | (string-append lib (basename jar)))) | |
12927 | (find-files "jar/lib" "\\.jar$"))) | |
12928 | #t))))) | |
12929 | (inputs | |
12930 | `(("jdk" ,icedtea-8) | |
12931 | ("java-picard" ,java-picard-2.10.3) | |
12932 | ("java-log4j-1.2-api" ,java-log4j-1.2-api) | |
12933 | ("java-commons-math3" ,java-commons-math3) | |
12934 | ("java-commons-jexl2" ,java-commons-jexl-2) | |
12935 | ("java-commons-collections4" ,java-commons-collections4) | |
12936 | ("java-commons-lang2" ,java-commons-lang) | |
12937 | ("java-commons-io" ,java-commons-io) | |
12938 | ("java-snappy-1.0.3-rc3" ,java-snappy-1) | |
12939 | ("java-guava" ,java-guava) | |
12940 | ("java-la4j" ,java-la4j) | |
12941 | ("java-biojava-core" ,java-biojava-core-4.0) | |
12942 | ("java-biojava-alignment" ,java-biojava-alignment-4.0) | |
12943 | ("java-jdistlib" ,java-jdistlib) | |
12944 | ("java-simple-xml" ,java-simple-xml) | |
12945 | ("java-snakeyaml" ,java-snakeyaml))) | |
12946 | (native-inputs | |
12947 | `(("unzip" ,unzip) | |
12948 | ("java-testng" ,java-testng))) | |
12949 | (home-page "http://mccarrolllab.com/dropseq/") | |
12950 | (synopsis "Tools for Drop-seq analyses") | |
12951 | (description "Drop-seq is a technology to enable biologists to | |
12952 | analyze RNA expression genome-wide in thousands of individual cells at | |
12953 | once. This package provides tools to perform Drop-seq analyses.") | |
12954 | (license license:expat))) | |
0bdd5b8a RW |
12955 | |
12956 | (define-public pigx-rnaseq | |
12957 | (package | |
12958 | (name "pigx-rnaseq") | |
c7d5cd6c | 12959 | (version "0.0.4") |
0bdd5b8a RW |
12960 | (source (origin |
12961 | (method url-fetch) | |
12962 | (uri (string-append "https://github.com/BIMSBbioinfo/pigx_rnaseq/" | |
12963 | "releases/download/v" version | |
12964 | "/pigx_rnaseq-" version ".tar.gz")) | |
12965 | (sha256 | |
12966 | (base32 | |
c7d5cd6c | 12967 | "16gla23rmziimqan7w494q0nr7vfbp42zzkrl9fracmr4k7b1kzr")))) |
0bdd5b8a RW |
12968 | (build-system gnu-build-system) |
12969 | (arguments | |
12970 | `(#:parallel-tests? #f ; not supported | |
12971 | #:phases | |
12972 | (modify-phases %standard-phases | |
fe52a215 RW |
12973 | ;; "test.sh" runs STAR, which requires excessive amounts of memory. |
12974 | (add-after 'unpack 'disable-resource-intensive-test | |
12975 | (lambda _ | |
12976 | (substitute* "Makefile.in" | |
12977 | (("(^ tests/test_trim_galore/test.sh).*" _ m) m) | |
26fd7b24 | 12978 | (("^ tests/test_multiqc/test.sh") "") |
fe52a215 | 12979 | (("^ test.sh") "")) |
0bdd5b8a RW |
12980 | #t))))) |
12981 | (inputs | |
616446ff | 12982 | `(("gzip" ,gzip) |
ed2dfe39 | 12983 | ("snakemake" ,snakemake-4) |
0bdd5b8a RW |
12984 | ("fastqc" ,fastqc) |
12985 | ("multiqc" ,multiqc) | |
12986 | ("star" ,star) | |
12987 | ("trim-galore" ,trim-galore) | |
12988 | ("htseq" ,htseq) | |
12989 | ("samtools" ,samtools) | |
12990 | ("bedtools" ,bedtools) | |
12991 | ("r-minimal" ,r-minimal) | |
12992 | ("r-rmarkdown" ,r-rmarkdown) | |
12993 | ("r-ggplot2" ,r-ggplot2) | |
12994 | ("r-ggrepel" ,r-ggrepel) | |
12995 | ("r-gprofiler" ,r-gprofiler) | |
12996 | ("r-deseq2" ,r-deseq2) | |
12997 | ("r-dt" ,r-dt) | |
12998 | ("r-knitr" ,r-knitr) | |
12999 | ("r-pheatmap" ,r-pheatmap) | |
13000 | ("r-corrplot" ,r-corrplot) | |
13001 | ("r-reshape2" ,r-reshape2) | |
13002 | ("r-plotly" ,r-plotly) | |
13003 | ("r-scales" ,r-scales) | |
13004 | ("r-summarizedexperiment" ,r-summarizedexperiment) | |
13005 | ("r-crosstalk" ,r-crosstalk) | |
13006 | ("r-tximport" ,r-tximport) | |
13007 | ("r-rtracklayer" ,r-rtracklayer) | |
13008 | ("r-rjson" ,r-rjson) | |
13009 | ("salmon" ,salmon) | |
ca248f1d RW |
13010 | ("ghc-pandoc" ,ghc-pandoc) |
13011 | ("ghc-pandoc-citeproc" ,ghc-pandoc-citeproc) | |
0bdd5b8a RW |
13012 | ("python-wrapper" ,python-wrapper) |
13013 | ("python-pyyaml" ,python-pyyaml))) | |
13014 | (home-page "http://bioinformatics.mdc-berlin.de/pigx/") | |
13015 | (synopsis "Analysis pipeline for RNA sequencing experiments") | |
13016 | (description "PiGX RNAseq is an analysis pipeline for preprocessing and | |
13017 | reporting for RNA sequencing experiments. It is easy to use and produces high | |
13018 | quality reports. The inputs are reads files from the sequencing experiment, | |
13019 | and a configuration file which describes the experiment. In addition to | |
13020 | quality control of the experiment, the pipeline produces a differential | |
13021 | expression report comparing samples in an easily configurable manner.") | |
13022 | (license license:gpl3+))) | |
531afc8a RW |
13023 | |
13024 | (define-public pigx-chipseq | |
13025 | (package | |
13026 | (name "pigx-chipseq") | |
29cbf817 | 13027 | (version "0.0.20") |
531afc8a RW |
13028 | (source (origin |
13029 | (method url-fetch) | |
13030 | (uri (string-append "https://github.com/BIMSBbioinfo/pigx_chipseq/" | |
13031 | "releases/download/v" version | |
13032 | "/pigx_chipseq-" version ".tar.gz")) | |
13033 | (sha256 | |
13034 | (base32 | |
29cbf817 | 13035 | "19a7dclqq0b4kqg3phiz4d4arlwfp34nm3z0rf1gkqdpsy7gghp3")))) |
531afc8a | 13036 | (build-system gnu-build-system) |
c57e50b2 RW |
13037 | ;; parts of the tests rely on access to the network |
13038 | (arguments '(#:tests? #f)) | |
531afc8a | 13039 | (inputs |
d7a11f1a RW |
13040 | `(("grep" ,grep) |
13041 | ("coreutils" ,coreutils) | |
13042 | ("r-minimal" ,r-minimal) | |
531afc8a | 13043 | ("r-argparser" ,r-argparser) |
363ee7a3 RW |
13044 | ("r-biocparallel" ,r-biocparallel) |
13045 | ("r-biostrings" ,r-biostrings) | |
531afc8a RW |
13046 | ("r-chipseq" ,r-chipseq) |
13047 | ("r-data-table" ,r-data-table) | |
363ee7a3 | 13048 | ("r-dplyr" ,r-dplyr) |
531afc8a | 13049 | ("r-genomation" ,r-genomation) |
363ee7a3 | 13050 | ("r-genomicalignments" ,r-genomicalignments) |
531afc8a | 13051 | ("r-genomicranges" ,r-genomicranges) |
363ee7a3 | 13052 | ("r-rsamtools" ,r-rsamtools) |
531afc8a | 13053 | ("r-rtracklayer" ,r-rtracklayer) |
363ee7a3 | 13054 | ("r-s4vectors" ,r-s4vectors) |
531afc8a | 13055 | ("r-stringr" ,r-stringr) |
363ee7a3 RW |
13056 | ("r-tibble" ,r-tibble) |
13057 | ("r-tidyr" ,r-tidyr) | |
531afc8a RW |
13058 | ("r-jsonlite" ,r-jsonlite) |
13059 | ("r-heatmaply" ,r-heatmaply) | |
363ee7a3 | 13060 | ("r-htmlwidgets" ,r-htmlwidgets) |
531afc8a RW |
13061 | ("r-ggplot2" ,r-ggplot2) |
13062 | ("r-plotly" ,r-plotly) | |
363ee7a3 | 13063 | ("r-rmarkdown" ,r-rmarkdown) |
531afc8a RW |
13064 | ("python-wrapper" ,python-wrapper) |
13065 | ("python-pyyaml" ,python-pyyaml) | |
363ee7a3 | 13066 | ("python-magic" ,python-magic) |
32b7ccf9 | 13067 | ("python-xlrd" ,python-xlrd) |
32b7ccf9 | 13068 | ("trim-galore" ,trim-galore) |
531afc8a RW |
13069 | ("macs" ,macs) |
13070 | ("multiqc" ,multiqc) | |
13071 | ("perl" ,perl) | |
7cd40c8c RW |
13072 | ("ghc-pandoc" ,ghc-pandoc) |
13073 | ("ghc-pandoc-citeproc" ,ghc-pandoc-citeproc) | |
531afc8a RW |
13074 | ("fastqc" ,fastqc) |
13075 | ("bowtie" ,bowtie) | |
13076 | ("idr" ,idr) | |
ed2dfe39 | 13077 | ("snakemake" ,snakemake-4) |
531afc8a RW |
13078 | ("samtools" ,samtools) |
13079 | ("bedtools" ,bedtools) | |
13080 | ("kentutils" ,kentutils))) | |
13081 | (native-inputs | |
13082 | `(("python-pytest" ,python-pytest))) | |
13083 | (home-page "http://bioinformatics.mdc-berlin.de/pigx/") | |
13084 | (synopsis "Analysis pipeline for ChIP sequencing experiments") | |
13085 | (description "PiGX ChIPseq is an analysis pipeline for preprocessing, peak | |
13086 | calling and reporting for ChIP sequencing experiments. It is easy to use and | |
13087 | produces high quality reports. The inputs are reads files from the sequencing | |
13088 | experiment, and a configuration file which describes the experiment. In | |
13089 | addition to quality control of the experiment, the pipeline enables to set up | |
13090 | multiple peak calling analysis and allows the generation of a UCSC track hub | |
13091 | in an easily configurable manner.") | |
13092 | (license license:gpl3+))) | |
fb94174f RW |
13093 | |
13094 | (define-public pigx-bsseq | |
13095 | (package | |
13096 | (name "pigx-bsseq") | |
13f5eb34 | 13097 | (version "0.0.10") |
fb94174f RW |
13098 | (source (origin |
13099 | (method url-fetch) | |
13100 | (uri (string-append "https://github.com/BIMSBbioinfo/pigx_bsseq/" | |
13101 | "releases/download/v" version | |
13102 | "/pigx_bsseq-" version ".tar.gz")) | |
13103 | (sha256 | |
13104 | (base32 | |
13f5eb34 | 13105 | "0l97wvkq4diq8lcarraj33bby1zzf0w804jwi8mlc5qddp8idwhy")))) |
fb94174f RW |
13106 | (build-system gnu-build-system) |
13107 | (arguments | |
13108 | `(#:phases | |
13109 | (modify-phases %standard-phases | |
13110 | (add-before 'check 'set-timezone | |
13111 | ;; The readr package is picky about timezones. | |
13112 | (lambda* (#:key inputs #:allow-other-keys) | |
13113 | (setenv "TZ" "UTC+1") | |
13114 | (setenv "TZDIR" | |
13115 | (string-append (assoc-ref inputs "tzdata") | |
13116 | "/share/zoneinfo")) | |
fb94174f RW |
13117 | #t))))) |
13118 | (native-inputs | |
13119 | `(("tzdata" ,tzdata))) | |
13120 | (inputs | |
9dbdc830 RW |
13121 | `(("coreutils" ,coreutils) |
13122 | ("sed" ,sed) | |
13123 | ("grep" ,grep) | |
13124 | ("r-minimal" ,r-minimal) | |
fb94174f RW |
13125 | ("r-annotationhub" ,r-annotationhub) |
13126 | ("r-dt" ,r-dt) | |
13127 | ("r-genomation" ,r-genomation) | |
13128 | ("r-methylkit" ,r-methylkit) | |
13129 | ("r-rtracklayer" ,r-rtracklayer) | |
13130 | ("r-rmarkdown" ,r-rmarkdown) | |
13131 | ("r-bookdown" ,r-bookdown) | |
13132 | ("r-ggplot2" ,r-ggplot2) | |
13133 | ("r-ggbio" ,r-ggbio) | |
c2b4f81e RW |
13134 | ("ghc-pandoc" ,ghc-pandoc) |
13135 | ("ghc-pandoc-citeproc" ,ghc-pandoc-citeproc) | |
fb94174f RW |
13136 | ("python-wrapper" ,python-wrapper) |
13137 | ("python-pyyaml" ,python-pyyaml) | |
ed2dfe39 | 13138 | ("snakemake" ,snakemake-4) |
fb94174f RW |
13139 | ("bismark" ,bismark) |
13140 | ("fastqc" ,fastqc) | |
13141 | ("bowtie" ,bowtie) | |
13142 | ("trim-galore" ,trim-galore) | |
13143 | ("cutadapt" ,cutadapt) | |
13144 | ("samtools" ,samtools))) | |
13145 | (home-page "http://bioinformatics.mdc-berlin.de/pigx/") | |
13146 | (synopsis "Bisulfite sequencing pipeline from fastq to methylation reports") | |
13147 | (description "PiGx BSseq is a data processing pipeline for raw fastq read | |
13148 | data of bisulfite experiments; it produces reports on aggregate methylation | |
13149 | and coverage and can be used to produce information on differential | |
13150 | methylation and segmentation.") | |
13151 | (license license:gpl3+))) | |
32cbbac1 | 13152 | |
46264c73 RW |
13153 | (define-public pigx-scrnaseq |
13154 | (package | |
13155 | (name "pigx-scrnaseq") | |
78933bff | 13156 | (version "0.0.7") |
46264c73 RW |
13157 | (source (origin |
13158 | (method url-fetch) | |
13159 | (uri (string-append "https://github.com/BIMSBbioinfo/pigx_scrnaseq/" | |
13160 | "releases/download/v" version | |
13161 | "/pigx_scrnaseq-" version ".tar.gz")) | |
13162 | (sha256 | |
13163 | (base32 | |
78933bff | 13164 | "131zarirv16w8653m0d66jgjnwqfsxqc0hix0rypssz4d83bl51j")))) |
46264c73 RW |
13165 | (build-system gnu-build-system) |
13166 | (arguments | |
13167 | `(#:configure-flags | |
13168 | (list (string-append "PICARDJAR=" (assoc-ref %build-inputs "java-picard") | |
13169 | "/share/java/picard.jar") | |
13170 | (string-append "DROPSEQJAR=" (assoc-ref %build-inputs "dropseq-tools") | |
08d1a8b1 | 13171 | "/share/java/dropseq.jar")))) |
46264c73 | 13172 | (inputs |
51237011 RW |
13173 | `(("coreutils" ,coreutils) |
13174 | ("perl" ,perl) | |
13175 | ("dropseq-tools" ,dropseq-tools) | |
46264c73 | 13176 | ("fastqc" ,fastqc) |
9cc66d75 | 13177 | ("java-picard" ,java-picard-2.10.3) ; same as for dropseq |
46264c73 RW |
13178 | ("java" ,icedtea-8) |
13179 | ("python-wrapper" ,python-wrapper) | |
13180 | ("python-pyyaml" ,python-pyyaml) | |
13181 | ("python-pandas" ,python-pandas) | |
844cc1c8 | 13182 | ("python-magic" ,python-magic) |
46264c73 RW |
13183 | ("python-numpy" ,python-numpy) |
13184 | ("python-loompy" ,python-loompy) | |
00a43cb8 RW |
13185 | ("ghc-pandoc" ,ghc-pandoc) |
13186 | ("ghc-pandoc-citeproc" ,ghc-pandoc-citeproc) | |
78933bff | 13187 | ("samtools" ,samtools) |
ed2dfe39 | 13188 | ("snakemake" ,snakemake-4) |
46264c73 RW |
13189 | ("star" ,star) |
13190 | ("r-minimal" ,r-minimal) | |
13191 | ("r-argparser" ,r-argparser) | |
13192 | ("r-cowplot" ,r-cowplot) | |
13193 | ("r-data-table" ,r-data-table) | |
13194 | ("r-delayedarray" ,r-delayedarray) | |
13195 | ("r-delayedmatrixstats" ,r-delayedmatrixstats) | |
13196 | ("r-dplyr" ,r-dplyr) | |
13197 | ("r-dropbead" ,r-dropbead) | |
13198 | ("r-dt" ,r-dt) | |
13199 | ("r-genomicalignments" ,r-genomicalignments) | |
13200 | ("r-genomicfiles" ,r-genomicfiles) | |
13201 | ("r-genomicranges" ,r-genomicranges) | |
13202 | ("r-ggplot2" ,r-ggplot2) | |
13203 | ("r-hdf5array" ,r-hdf5array) | |
13204 | ("r-pheatmap" ,r-pheatmap) | |
13205 | ("r-rmarkdown" ,r-rmarkdown) | |
13206 | ("r-rsamtools" ,r-rsamtools) | |
13207 | ("r-rtracklayer" ,r-rtracklayer) | |
13208 | ("r-rtsne" ,r-rtsne) | |
13209 | ("r-scater" ,r-scater) | |
13210 | ("r-scran" ,r-scran) | |
13211 | ("r-singlecellexperiment" ,r-singlecellexperiment) | |
13212 | ("r-stringr" ,r-stringr) | |
13213 | ("r-yaml" ,r-yaml))) | |
13214 | (home-page "http://bioinformatics.mdc-berlin.de/pigx/") | |
13215 | (synopsis "Analysis pipeline for single-cell RNA sequencing experiments") | |
13216 | (description "PiGX scRNAseq is an analysis pipeline for preprocessing and | |
13217 | quality control for single cell RNA sequencing experiments. The inputs are | |
13218 | read files from the sequencing experiment, and a configuration file which | |
13219 | describes the experiment. It produces processed files for downstream analysis | |
13220 | and interactive quality reports. The pipeline is designed to work with UMI | |
13221 | based methods.") | |
13222 | (license license:gpl3+))) | |
13223 | ||
c1c9cc66 RW |
13224 | (define-public pigx |
13225 | (package | |
13226 | (name "pigx") | |
5149aeb7 | 13227 | (version "0.0.3") |
c1c9cc66 RW |
13228 | (source (origin |
13229 | (method url-fetch) | |
13230 | (uri (string-append "https://github.com/BIMSBbioinfo/pigx/" | |
13231 | "releases/download/v" version | |
13232 | "/pigx-" version ".tar.gz")) | |
13233 | (sha256 | |
13234 | (base32 | |
5149aeb7 | 13235 | "1i5njdy1clj5ncw45d16p7mwmqvb1ilikl9n797pxklc3f4s7mq7")))) |
c1c9cc66 RW |
13236 | (build-system gnu-build-system) |
13237 | (inputs | |
13238 | `(("python" ,python) | |
13239 | ("pigx-bsseq" ,pigx-bsseq) | |
13240 | ("pigx-chipseq" ,pigx-chipseq) | |
13241 | ("pigx-rnaseq" ,pigx-rnaseq) | |
13242 | ("pigx-scrnaseq" ,pigx-scrnaseq))) | |
13243 | (home-page "http://bioinformatics.mdc-berlin.de/pigx/") | |
13244 | (synopsis "Analysis pipelines for genomics") | |
13245 | (description "PiGx is a collection of genomics pipelines. It includes the | |
13246 | following pipelines: | |
13247 | ||
13248 | @itemize | |
13249 | @item PiGx BSseq for raw fastq read data of bisulfite experiments | |
13250 | @item PiGx RNAseq for RNAseq samples | |
13251 | @item PiGx scRNAseq for single cell dropseq analysis | |
13252 | @item PiGx ChIPseq for reads from ChIPseq experiments | |
13253 | @end itemize | |
13254 | ||
13255 | All pipelines are easily configured with a simple sample sheet and a | |
13256 | descriptive settings file. The result is a set of comprehensive, interactive | |
13257 | HTML reports with interesting findings about your samples.") | |
13258 | (license license:gpl3+))) | |
13259 | ||
32cbbac1 LF |
13260 | (define-public r-diversitree |
13261 | (package | |
13262 | (name "r-diversitree") | |
13263 | (version "0.9-10") | |
13264 | (source | |
13265 | (origin | |
13266 | (method url-fetch) | |
13267 | (uri (cran-uri "diversitree" version)) | |
13268 | (sha256 | |
13269 | (base32 | |
13270 | "0gh4rcrp0an3jh8915i1fsxlgyfk7njywgbd5ln5r2jhr085kpz7")))) | |
13271 | (build-system r-build-system) | |
13272 | (native-inputs | |
13273 | `(("gfortran" ,gfortran))) | |
13274 | (inputs `(("fftw" ,fftw) ("gsl" ,gsl))) | |
13275 | (propagated-inputs | |
13276 | `(("r-ape" ,r-ape) | |
13277 | ("r-desolve" ,r-desolve) | |
13278 | ("r-rcpp" ,r-rcpp) | |
13279 | ("r-suplex" ,r-subplex))) | |
13280 | (home-page "https://www.zoology.ubc.ca/prog/diversitree") | |
13281 | (synopsis "Comparative 'phylogenetic' analyses of diversification") | |
13282 | (description "This package contains a number of comparative \"phylogenetic\" | |
13283 | methods, mostly focusing on analysing diversification and character evolution. | |
13284 | Contains implementations of \"BiSSE\" (Binary State Speciation and Extinction) | |
13285 | and its unresolved tree extensions, \"MuSSE\" (Multiple State Speciation and | |
13286 | Extinction), \"QuaSSE\", \"GeoSSE\", and \"BiSSE-ness\" Other included methods | |
13287 | include Markov models of discrete and continuous trait evolution and constant | |
13288 | rate speciation and extinction.") | |
13289 | (license license:gpl2+))) | |
90930159 RW |
13290 | |
13291 | (define-public sjcount | |
13292 | ;; There is no tag for version 3.2, nor is there a release archive. | |
13293 | (let ((commit "292d3917cadb3f6834c81e509c30e61cd7ead6e5") | |
13294 | (revision "1")) | |
13295 | (package | |
13296 | (name "sjcount") | |
13297 | (version (git-version "3.2" revision commit)) | |
13298 | (source (origin | |
13299 | (method git-fetch) | |
13300 | (uri (git-reference | |
13301 | (url "https://github.com/pervouchine/sjcount-full.git") | |
13302 | (commit commit))) | |
13303 | (file-name (string-append name "-" version "-checkout")) | |
13304 | (sha256 | |
13305 | (base32 | |
13306 | "0gdgj35j249f04rqgq8ymcc1xg1vi9kzbajnjqpaq2wpbh8bl234")))) | |
13307 | (build-system gnu-build-system) | |
13308 | (arguments | |
13309 | `(#:tests? #f ; requires a 1.4G test file | |
13310 | #:make-flags | |
13311 | (list (string-append "SAMTOOLS_DIR=" | |
13312 | (assoc-ref %build-inputs "samtools") | |
13313 | "/lib/")) | |
13314 | #:phases | |
13315 | (modify-phases %standard-phases | |
13316 | (replace 'configure | |
13317 | (lambda* (#:key inputs #:allow-other-keys) | |
13318 | (substitute* "makefile" | |
13319 | (("-I \\$\\{SAMTOOLS_DIR\\}") | |
13320 | (string-append "-I" (assoc-ref inputs "samtools") | |
13321 | "/include/samtools")) | |
13322 | (("-lz ") "-lz -lpthread ")) | |
13323 | #t)) | |
13324 | (replace 'install | |
13325 | (lambda* (#:key outputs #:allow-other-keys) | |
13326 | (for-each (lambda (tool) | |
13327 | (install-file tool | |
13328 | (string-append (assoc-ref outputs "out") | |
13329 | "/bin"))) | |
13330 | '("j_count" "b_count" "sjcount")) | |
13331 | #t))))) | |
13332 | (inputs | |
13333 | `(("samtools" ,samtools-0.1) | |
13334 | ("zlib" ,zlib))) | |
13335 | (home-page "https://github.com/pervouchine/sjcount-full/") | |
13336 | (synopsis "Annotation-agnostic splice junction counting pipeline") | |
13337 | (description "Sjcount is a utility for fast quantification of splice | |
13338 | junctions in RNA-seq data. It is annotation-agnostic and offset-aware. This | |
13339 | version does count multisplits.") | |
13340 | (license license:gpl3+)))) | |
53131eab RW |
13341 | |
13342 | (define-public minimap2 | |
13343 | (package | |
13344 | (name "minimap2") | |
13345 | (version "2.10") | |
13346 | (source | |
13347 | (origin | |
13348 | (method url-fetch) | |
13349 | (uri (string-append "https://github.com/lh3/minimap2/" | |
13350 | "releases/download/v" version "/" | |
13351 | "minimap2-" version ".tar.bz2")) | |
13352 | (sha256 | |
13353 | (base32 | |
13354 | "080w9066irkbhbyr4nmf19pzkdd2s4v31hpzlajgq2y0drr6zcsj")))) | |
13355 | (build-system gnu-build-system) | |
13356 | (arguments | |
13357 | `(#:tests? #f ; there are none | |
13358 | #:make-flags | |
13359 | (list "CC=gcc" | |
13360 | (let ((system ,(or (%current-target-system) | |
13361 | (%current-system)))) | |
13362 | (cond | |
13363 | ((string-prefix? "x86_64" system) | |
13364 | "all") | |
13365 | ((or (string-prefix? "armhf" system) | |
13366 | (string-prefix? "aarch64" system)) | |
13367 | "arm_neon=1") | |
13368 | (_ "sse2only=1")))) | |
13369 | #:phases | |
13370 | (modify-phases %standard-phases | |
13371 | (delete 'configure) | |
13372 | (replace 'install | |
13373 | (lambda* (#:key outputs #:allow-other-keys) | |
13374 | (let* ((out (assoc-ref outputs "out")) | |
13375 | (bin (string-append out "/bin")) | |
13376 | (man (string-append out "/share/man/man1"))) | |
13377 | (install-file "minimap2" bin) | |
13378 | (mkdir-p man) | |
13379 | (install-file "minimap2.1" man)) | |
13380 | #t))))) | |
13381 | (inputs | |
13382 | `(("zlib" ,zlib))) | |
13383 | (home-page "https://lh3.github.io/minimap2/") | |
13384 | (synopsis "Pairwise aligner for genomic and spliced nucleotide sequences") | |
13385 | (description "Minimap2 is a versatile sequence alignment program that | |
13386 | aligns DNA or mRNA sequences against a large reference database. Typical use | |
13387 | cases include: | |
13388 | ||
13389 | @enumerate | |
13390 | @item mapping PacBio or Oxford Nanopore genomic reads to the human genome; | |
13391 | @item finding overlaps between long reads with error rate up to ~15%; | |
13392 | @item splice-aware alignment of PacBio Iso-Seq or Nanopore cDNA or Direct RNA | |
13393 | reads against a reference genome; | |
13394 | @item aligning Illumina single- or paired-end reads; | |
13395 | @item assembly-to-assembly alignment; | |
13396 | @item full-genome alignment between two closely related species with | |
13397 | divergence below ~15%. | |
13398 | @end enumerate\n") | |
13399 | (license license:expat))) | |
fab43c6b | 13400 | |
242519ce RW |
13401 | (define-public r-circus |
13402 | (package | |
13403 | (name "r-circus") | |
13404 | (version "0.1.5") | |
13405 | (source | |
13406 | (origin | |
13407 | (method git-fetch) | |
13408 | (uri (git-reference | |
13409 | (url "https://github.com/BIMSBbioinfo/ciRcus.git") | |
13410 | (commit (string-append "v" version)))) | |
13411 | (file-name (git-file-name name version)) | |
13412 | (sha256 | |
13413 | (base32 | |
13414 | "0jhjn3ilb057hbf6yzrihj13ifxxs32y7nkby8l3lkm28dg4p97h")))) | |
13415 | (build-system r-build-system) | |
13416 | (propagated-inputs | |
13417 | `(("r-annotationdbi" ,r-annotationdbi) | |
13418 | ("r-annotationhub" ,r-annotationhub) | |
13419 | ("r-biomart" ,r-biomart) | |
13420 | ("r-data-table" ,r-data-table) | |
13421 | ("r-dbi" ,r-dbi) | |
13422 | ("r-genomicfeatures" ,r-genomicfeatures) | |
13423 | ("r-genomicranges" ,r-genomicranges) | |
13424 | ("r-ggplot2" ,r-ggplot2) | |
13425 | ("r-hash" ,r-hash) | |
13426 | ("r-iranges" ,r-iranges) | |
13427 | ("r-rcolorbrewer" ,r-rcolorbrewer) | |
13428 | ("r-rmysql" ,r-rmysql) | |
13429 | ("r-s4vectors" ,r-s4vectors) | |
13430 | ("r-stringr" ,r-stringr) | |
13431 | ("r-summarizedexperiment" ,r-summarizedexperiment))) | |
13432 | (native-inputs | |
13433 | `(("r-knitr" ,r-knitr))) | |
13434 | (home-page "https://github.com/BIMSBbioinfo/ciRcus") | |
13435 | (synopsis "Annotation, analysis and visualization of circRNA data") | |
13436 | (description "Circus is an R package for annotation, analysis and | |
13437 | visualization of circRNA data. Users can annotate their circRNA candidates | |
13438 | with host genes, gene featrues they are spliced from, and discriminate between | |
13439 | known and yet unknown splice junctions. Circular-to-linear ratios of circRNAs | |
13440 | can be calculated, and a number of descriptive plots easily generated.") | |
13441 | (license license:artistic2.0))) | |
13442 | ||
fab43c6b RW |
13443 | (define-public r-loomr |
13444 | (let ((commit "df0144bd2bbceca6fadef9edc1bbc5ca672d4739") | |
13445 | (revision "1")) | |
13446 | (package | |
13447 | (name "r-loomr") | |
13448 | (version (git-version "0.2.0" revision commit)) | |
13449 | (source | |
13450 | (origin | |
13451 | (method git-fetch) | |
13452 | (uri (git-reference | |
13453 | (url "https://github.com/mojaveazure/loomR.git") | |
13454 | (commit commit))) | |
13455 | (file-name (git-file-name name version)) | |
13456 | (sha256 | |
13457 | (base32 | |
13458 | "1b1g4dlmfdyhn56bz1mkh9ymirri43wiz7rjhs7py3y7bdw1s3yr")))) | |
13459 | (build-system r-build-system) | |
13460 | (propagated-inputs | |
13461 | `(("r-r6" ,r-r6) | |
13462 | ("r-hdf5r" ,r-hdf5r) | |
13463 | ("r-iterators" ,r-iterators) | |
13464 | ("r-itertools" ,r-itertools) | |
13465 | ("r-matrix" ,r-matrix))) | |
13466 | (home-page "https://github.com/mojaveazure/loomR") | |
13467 | (synopsis "R interface for loom files") | |
13468 | (description "This package provides an R interface to access, create, | |
13469 | and modify loom files. loomR aims to be completely compatible with loompy.") | |
13470 | (license license:gpl3)))) | |
689aacc1 RW |
13471 | |
13472 | (define-public gffread | |
13473 | ;; We cannot use the tagged release because it is not in sync with gclib. | |
13474 | ;; See https://github.com/gpertea/gffread/issues/26 | |
13475 | (let ((commit "ba7535fcb3cea55a6e5a491d916e93b454e87fd0") | |
13476 | (revision "1")) | |
13477 | (package | |
13478 | (name "gffread") | |
13479 | (version (git-version "0.9.12" revision commit)) | |
13480 | (source | |
13481 | (origin | |
13482 | (method git-fetch) | |
13483 | (uri (git-reference | |
13484 | (url "https://github.com/gpertea/gffread.git") | |
13485 | (commit commit))) | |
13486 | (file-name (git-file-name name version)) | |
13487 | (sha256 | |
13488 | (base32 | |
13489 | "1dl2nbcg96lxpd0drg48ssa8343nf7pw9s9mkrc4mjjmfwsin3ki")))) | |
13490 | (build-system gnu-build-system) | |
13491 | (arguments | |
13492 | `(#:tests? #f ; no check target | |
13493 | #:make-flags | |
13494 | (list "GCLDIR=gclib") | |
13495 | #:phases | |
13496 | (modify-phases %standard-phases | |
13497 | (delete 'configure) | |
13498 | (add-after 'unpack 'copy-gclib-source | |
13499 | (lambda* (#:key inputs #:allow-other-keys) | |
13500 | (mkdir-p "gclib") | |
13501 | (copy-recursively (assoc-ref inputs "gclib-source") "gclib") | |
13502 | #t)) | |
13503 | ;; There is no install target | |
13504 | (replace 'install | |
13505 | (lambda* (#:key outputs #:allow-other-keys) | |
13506 | (let* ((out (assoc-ref outputs "out")) | |
13507 | (bin (string-append out "/bin"))) | |
13508 | (install-file "gffread" bin)) | |
13509 | #t))))) | |
13510 | (native-inputs | |
13511 | `(("gclib-source" | |
13512 | ,(let ((version "0.10.3") | |
13513 | (commit "54917d0849c1e83cfb057b5f712e5cb6a35d948f") | |
13514 | (revision "1")) | |
13515 | (origin | |
13516 | (method git-fetch) | |
13517 | (uri (git-reference | |
13518 | (url "https://github.com/gpertea/gclib.git") | |
13519 | (commit commit))) | |
13520 | (file-name (git-file-name "gclib" version)) | |
13521 | (sha256 | |
13522 | (base32 | |
13523 | "0b51lc0b8syrv7186fd7n8f15rwnf264qgfmm2palrwks1px24mr"))))))) | |
13524 | (home-page "https://github.com/gpertea/gffread/") | |
13525 | (synopsis "Parse and convert GFF/GTF files") | |
13526 | (description | |
13527 | "This package provides a GFF/GTF file parsing utility providing format | |
13528 | conversions, region filtering, FASTA sequence extraction and more.") | |
13529 | ;; gffread is under Expat, but gclib is under Artistic 2.0 | |
13530 | (license (list license:expat | |
13531 | license:artistic2.0))))) | |
079cdd9c RW |
13532 | |
13533 | (define-public find-circ | |
13534 | ;; The last release was in 2015. The license was clarified in 2017, so we | |
13535 | ;; take the latest commit. | |
13536 | (let ((commit "8655dca54970fcf7e92e22fbf57e1188724dda7d") | |
13537 | (revision "1")) | |
13538 | (package | |
13539 | (name "find-circ") | |
13540 | (version (git-version "1.2" revision commit)) | |
13541 | (source | |
13542 | (origin | |
13543 | (method git-fetch) | |
13544 | (uri (git-reference | |
13545 | (url "https://github.com/marvin-jens/find_circ.git") | |
13546 | (commit commit))) | |
13547 | (file-name (git-file-name name version)) | |
13548 | (sha256 | |
13549 | (base32 | |
13550 | "0p77pbqbclqr4srms34y1b9b4njybfpjiknc11ki84f3p8skb3cg")))) | |
13551 | (build-system gnu-build-system) | |
13552 | (arguments | |
13553 | `(#:tests? #f ; there are none | |
13554 | #:phases | |
13555 | ;; There is no actual build system. | |
13556 | (modify-phases %standard-phases | |
13557 | (delete 'configure) | |
13558 | (delete 'build) | |
13559 | (replace 'install | |
13560 | (lambda* (#:key outputs #:allow-other-keys) | |
13561 | (let* ((out (assoc-ref outputs "out")) | |
13562 | (bin (string-append out "/bin")) | |
13563 | (path (getenv "PYTHONPATH"))) | |
13564 | (for-each (lambda (script) | |
13565 | (install-file script bin) | |
13566 | (wrap-program (string-append bin "/" script) | |
13567 | `("PYTHONPATH" ":" prefix (,path)))) | |
13568 | '("cmp_bed.py" | |
13569 | "find_circ.py" | |
13570 | "maxlength.py" | |
13571 | "merge_bed.py" | |
13572 | "unmapped2anchors.py"))) | |
13573 | #t))))) | |
13574 | (inputs | |
13575 | `(("python2" ,python-2) | |
13576 | ("python2-pysam" ,python2-pysam) | |
13577 | ("python2-numpy" ,python2-numpy))) | |
13578 | (home-page "https://github.com/marvin-jens/find_circ") | |
13579 | (synopsis "circRNA detection from RNA-seq reads") | |
13580 | (description "This package provides tools to detect head-to-tail | |
13581 | spliced (back-spliced) sequencing reads, indicative of circular RNA (circRNA) | |
13582 | in RNA-seq data.") | |
13583 | (license license:gpl3)))) | |
c7fe888b RW |
13584 | |
13585 | (define-public python-scanpy | |
13586 | (package | |
13587 | (name "python-scanpy") | |
13588 | (version "1.2.2") | |
13589 | (source | |
13590 | (origin | |
13591 | (method url-fetch) | |
13592 | (uri (pypi-uri "scanpy" version)) | |
13593 | (sha256 | |
13594 | (base32 | |
13595 | "1ak7bxms5a0yvf65prppq2g38clkv7c7jnjbnfpkh3xxv7q512jz")))) | |
13596 | (build-system python-build-system) | |
13597 | (propagated-inputs | |
13598 | `(("python-anndata" ,python-anndata) | |
13599 | ("python-igraph" ,python-igraph) | |
13600 | ("python-numba" ,python-numba) | |
13601 | ("python-joblib" ,python-joblib) | |
13602 | ("python-natsort" ,python-natsort) | |
13603 | ("python-networkx" ,python-networkx) | |
13604 | ("python-statsmodels" ,python-statsmodels) | |
13605 | ("python-scikit-learn" ,python-scikit-learn) | |
13606 | ("python-matplotlib" ,python-matplotlib) | |
13607 | ("python-pandas" ,python-pandas) | |
13608 | ("python-scipy" ,python-scipy) | |
13609 | ("python-seaborn" ,python-seaborn) | |
13610 | ("python-h5py" ,python-h5py) | |
13611 | ("python-tables" ,python-tables))) | |
13612 | (home-page "http://github.com/theislab/scanpy") | |
13613 | (synopsis "Single-Cell Analysis in Python.") | |
13614 | (description "Scanpy is a scalable toolkit for analyzing single-cell gene | |
13615 | expression data. It includes preprocessing, visualization, clustering, | |
13616 | pseudotime and trajectory inference and differential expression testing. The | |
13617 | Python-based implementation efficiently deals with datasets of more than one | |
13618 | million cells.") | |
13619 | (license license:bsd-3))) | |
4f9355c3 | 13620 | |
13621 | (define-public gffcompare | |
13622 | (let ((commit "be56ef4349ea3966c12c6397f85e49e047361c41") | |
13623 | (revision "1")) | |
13624 | (package | |
13625 | (name "gffcompare") | |
13626 | (version (git-version "0.10.15" revision commit)) | |
13627 | (source | |
13628 | (origin | |
13629 | (method git-fetch) | |
13630 | (uri (git-reference | |
13631 | (url "https://github.com/gpertea/gffcompare/") | |
13632 | (commit commit))) | |
13633 | (file-name (git-file-name name version)) | |
13634 | (sha256 | |
13635 | (base32 "0cp5qpxdhw4mxpya5dld8wi3jk00zyklm6rcri426wydinrnfmkg")))) | |
13636 | (build-system gnu-build-system) | |
13637 | (arguments | |
13638 | `(#:tests? #f ; no check target | |
13639 | #:phases | |
13640 | (modify-phases %standard-phases | |
13641 | (delete 'configure) | |
13642 | (add-before 'build 'copy-gclib-source | |
13643 | (lambda* (#:key inputs #:allow-other-keys) | |
13644 | (mkdir "../gclib") | |
13645 | (copy-recursively | |
13646 | (assoc-ref inputs "gclib-source") "../gclib") | |
13647 | #t)) | |
13648 | (replace 'install | |
13649 | (lambda* (#:key outputs #:allow-other-keys) | |
13650 | (let ((bin (string-append (assoc-ref outputs "out") "/bin"))) | |
13651 | (install-file "gffcompare" bin) | |
13652 | #t)))))) | |
13653 | (native-inputs | |
13654 | `(("gclib-source" ; see 'README.md' of gffcompare | |
13655 | ,(let ((commit "54917d0849c1e83cfb057b5f712e5cb6a35d948f") | |
13656 | (revision "1") | |
13657 | (name "gclib") | |
13658 | (version (git-version "0.10.3" revision commit))) | |
13659 | (origin | |
13660 | (method git-fetch) | |
13661 | (uri (git-reference | |
13662 | (url "https://github.com/gpertea/gclib/") | |
13663 | (commit commit))) | |
13664 | (file-name (git-file-name name version)) | |
13665 | (sha256 | |
13666 | (base32 "0b51lc0b8syrv7186fd7n8f15rwnf264qgfmm2palrwks1px24mr"))))))) | |
13667 | (home-page "https://github.com/gpertea/gffcompare/") | |
13668 | (synopsis "Tool for comparing or classifing transcripts of RNA-Seq") | |
13669 | (description | |
13670 | "@code{gffcompare} is a tool that can: | |
13671 | @enumerate | |
13672 | @item compare and evaluate the accuracy of RNA-Seq transcript assemblers | |
13673 | (Cufflinks, Stringtie); | |
13674 | @item collapse (merge) duplicate transcripts from multiple GTF/GFF3 files (e.g. | |
13675 | resulted from assembly of different samples); | |
13676 | @item classify transcripts from one or multiple GTF/GFF3 files as they relate to | |
13677 | reference transcripts provided in a annotation file (also in GTF/GFF3 format). | |
13678 | @end enumerate") | |
13679 | (license | |
13680 | (list | |
13681 | license:expat ;license for gffcompare | |
13682 | license:artistic2.0))))) ;license for gclib | |
a9d496b3 RW |
13683 | |
13684 | (define-public python-intervaltree | |
13685 | (package | |
13686 | (name "python-intervaltree") | |
13687 | (version "2.1.0") | |
13688 | (source | |
13689 | (origin | |
13690 | (method url-fetch) | |
13691 | (uri (pypi-uri "intervaltree" version)) | |
13692 | (sha256 | |
13693 | (base32 | |
13694 | "02w191m9zxkcjqr1kv2slxvhymwhj3jnsyy3a28b837pi15q19dc")))) | |
13695 | (build-system python-build-system) | |
13696 | ;; FIXME: error when collecting tests | |
13697 | (arguments '(#:tests? #f)) | |
13698 | (propagated-inputs | |
13699 | `(("python-sortedcontainers" ,python-sortedcontainers))) | |
13700 | (native-inputs | |
13701 | `(("python-pytest" ,python-pytest))) | |
13702 | (home-page "https://github.com/chaimleib/intervaltree") | |
13703 | (synopsis "Editable interval tree data structure") | |
13704 | (description | |
13705 | "This package provides a mutable, self-balancing interval tree | |
13706 | implementation for Python. Queries may be by point, by range overlap, or by | |
13707 | range envelopment. This library was designed to allow tagging text and time | |
13708 | intervals, where the intervals include the lower bound but not the upper | |
13709 | bound.") | |
13710 | (license license:asl2.0))) | |
1f41f01c RW |
13711 | |
13712 | (define-public python-pypairix | |
13713 | (package | |
13714 | (name "python-pypairix") | |
13715 | (version "0.3.6") | |
13716 | (source | |
13717 | (origin | |
13718 | (method url-fetch) | |
13719 | (uri (pypi-uri "pypairix" version)) | |
13720 | (sha256 | |
13721 | (base32 | |
13722 | "0zs92b74s5v4xy2h16s15f3z6l4nnbw8x8zyif7xx5xpafjn0xss")))) | |
13723 | (build-system python-build-system) | |
13724 | ;; FIXME: the tests fail because test.support cannot be loaded: | |
13725 | ;; ImportError: cannot import name 'support' | |
13726 | (arguments '(#:tests? #f)) | |
13727 | (inputs | |
13728 | `(("zlib" ,zlib))) | |
13729 | (home-page "https://github.com/4dn-dcic/pairix") | |
13730 | (synopsis "Support for querying pairix-indexed bgzipped text files") | |
13731 | (description | |
13732 | "Pypairix is a Python module for fast querying on a pairix-indexed | |
13733 | bgzipped text file that contains a pair of genomic coordinates per line.") | |
13734 | (license license:expat))) | |
80f4db91 RW |
13735 | |
13736 | (define-public python-pyfaidx | |
13737 | (package | |
13738 | (name "python-pyfaidx") | |
13739 | (version "0.5.4.2") | |
13740 | (source | |
13741 | (origin | |
13742 | (method url-fetch) | |
13743 | (uri (pypi-uri "pyfaidx" version)) | |
13744 | (sha256 | |
13745 | (base32 | |
13746 | "0y5zyjksj1rdglj601xd2bbni5abhdh622y3ck76chyzxz9z4rx8")))) | |
13747 | (build-system python-build-system) | |
13748 | (propagated-inputs | |
13749 | `(("python-setuptools" ,python-setuptools) | |
13750 | ("python-six" ,python-six))) | |
13751 | (home-page "http://mattshirley.com") | |
13752 | (synopsis "Random access to fasta subsequences") | |
13753 | (description | |
13754 | "This package provides procedures for efficient pythonic random access to | |
13755 | fasta subsequences.") | |
13756 | (license license:bsd-3))) | |
5bb9e0af RW |
13757 | |
13758 | (define-public python-cooler | |
13759 | (package | |
13760 | (name "python-cooler") | |
13761 | (version "0.7.11") | |
13762 | (source | |
13763 | (origin | |
13764 | (method url-fetch) | |
13765 | (uri (pypi-uri "cooler" version)) | |
13766 | (sha256 | |
13767 | (base32 | |
13768 | "08k5nxnxa6qsbk15z5z0q01n28042k87wi4905hh95rzqib15mhx")))) | |
13769 | (build-system python-build-system) | |
13770 | (propagated-inputs | |
13771 | `(("python-biopython" ,python-biopython) | |
13772 | ("python-click" ,python-click) | |
13773 | ("python-cytoolz" ,python-cytoolz) | |
13774 | ("python-dask" ,python-dask) | |
13775 | ("python-h5py" ,python-h5py) | |
13776 | ("python-multiprocess" ,python-multiprocess) | |
13777 | ("python-pandas" ,python-pandas) | |
13778 | ("python-pyfaidx" ,python-pyfaidx) | |
13779 | ("python-pypairix" ,python-pypairix) | |
13780 | ("python-pysam" ,python-pysam) | |
13781 | ("python-scipy" ,python-scipy))) | |
13782 | (native-inputs | |
13783 | `(("python-mock" ,python-mock) | |
13784 | ("python-nose" ,python-nose) | |
13785 | ("python-numpydoc" ,python-numpydoc) | |
13786 | ("python-sphinx" ,python-sphinx))) | |
13787 | (home-page "https://github.com/mirnylab/cooler") | |
13788 | (synopsis "Sparse binary format for genomic interaction matrices") | |
13789 | (description | |
13790 | "Cooler is a support library for a sparse, compressed, binary persistent | |
13791 | storage format, called @code{cool}, used to store genomic interaction data, | |
13792 | such as Hi-C contact matrices.") | |
13793 | (license license:bsd-3))) | |
1189c7f1 RW |
13794 | |
13795 | (define-public python-hicexplorer | |
13796 | (package | |
13797 | (name "python-hicexplorer") | |
13798 | (version "2.1.4") | |
13799 | (source | |
13800 | (origin | |
13801 | ;; The latest version is not available on Pypi. | |
13802 | (method git-fetch) | |
13803 | (uri (git-reference | |
13804 | (url "https://github.com/deeptools/HiCExplorer.git") | |
13805 | (commit version))) | |
13806 | (file-name (git-file-name name version)) | |
13807 | (sha256 | |
13808 | (base32 | |
13809 | "0q5gpbzmrkvygqgw524q36b4nrivcmyi5v194vsx0qw7b3gcmq08")))) | |
13810 | (build-system python-build-system) | |
13811 | (arguments | |
13812 | `(#:phases | |
13813 | (modify-phases %standard-phases | |
13814 | (add-after 'unpack 'loosen-up-requirements | |
13815 | (lambda _ | |
13816 | (substitute* "setup.py" | |
13817 | (("==") ">=")) | |
13818 | #t))))) | |
13819 | (propagated-inputs | |
13820 | `(("python-biopython" ,python-biopython) | |
13821 | ("python-configparser" ,python-configparser) | |
13822 | ("python-cooler" ,python-cooler) | |
13823 | ("python-future" ,python-future) | |
13824 | ("python-intervaltree" ,python-intervaltree) | |
13825 | ("python-jinja2" ,python-jinja2) | |
13826 | ("python-matplotlib" ,python-matplotlib) | |
13827 | ("python-numpy" ,python-numpy) | |
13828 | ("python-pandas" ,python-pandas) | |
13829 | ("python-pybigwig" ,python-pybigwig) | |
13830 | ("python-pysam" ,python-pysam) | |
13831 | ("python-scipy" ,python-scipy) | |
13832 | ("python-six" ,python-six) | |
13833 | ("python-tables" ,python-tables) | |
13834 | ("python-unidecode" ,python-unidecode))) | |
13835 | (home-page "http://hicexplorer.readthedocs.io") | |
13836 | (synopsis "Process, analyze and visualize Hi-C data") | |
13837 | (description | |
13838 | "HiCExplorer is a powerful and easy to use set of tools to process, | |
13839 | normalize and visualize Hi-C data. HiCExplorer facilitates the creation of | |
13840 | contact matrices, correction of contacts, TAD detection, A/B compartments, | |
13841 | merging, reordering or chromosomes, conversion from different formats | |
13842 | including cooler and detection of long-range contacts. Moreover, it allows | |
13843 | the visualization of multiple contact matrices along with other types of data | |
13844 | like genes, compartments, ChIP-seq coverage tracks (and in general any type of | |
13845 | genomic scores), long range contacts and the visualization of viewpoints.") | |
13846 | (license license:gpl3))) | |
5bfa7510 RW |
13847 | |
13848 | (define-public python-pygenometracks | |
13849 | (package | |
13850 | (name "python-pygenometracks") | |
13851 | (version "2.0") | |
13852 | (source | |
13853 | (origin | |
13854 | (method url-fetch) | |
13855 | (uri (pypi-uri "pyGenomeTracks" version)) | |
13856 | (sha256 | |
13857 | (base32 | |
13858 | "1fws6bqsyy9kj3qiabhkqx4wd4i775gsxnhszqd3zg7w67sc1ic5")))) | |
13859 | (build-system python-build-system) | |
13860 | (propagated-inputs | |
13861 | `(("python-configparser" ,python-configparser) | |
13862 | ("python-future" ,python-future) | |
13863 | ("python-hicexplorer" ,python-hicexplorer) | |
13864 | ("python-intervaltree" ,python-intervaltree) | |
13865 | ("python-matplotlib" ,python-matplotlib) | |
13866 | ("python-numpy" ,python-numpy) | |
13867 | ("python-pybigwig" ,python-pybigwig))) | |
13868 | (native-inputs | |
13869 | `(("python-pytest" ,python-pytest))) | |
13870 | (home-page "https://pygenometracks.readthedocs.io") | |
13871 | (synopsis "Program and library to plot beautiful genome browser tracks") | |
13872 | (description | |
13873 | "This package aims to produce high-quality genome browser tracks that | |
13874 | are highly customizable. Currently, it is possible to plot: bigwig, bed (many | |
13875 | options), bedgraph, links (represented as arcs), and Hi-C matrices. | |
13876 | pyGenomeTracks can make plots with or without Hi-C data.") | |
13877 | (license license:gpl3+))) | |
1dd153b3 RW |
13878 | |
13879 | (define-public python-hic2cool | |
13880 | (package | |
13881 | (name "python-hic2cool") | |
13882 | (version "0.4.2") | |
13883 | (source | |
13884 | (origin | |
13885 | (method url-fetch) | |
13886 | (uri (pypi-uri "hic2cool" version)) | |
13887 | (sha256 | |
13888 | (base32 | |
13889 | "0xy6mhfns2lzib1kcr6419jjp6pmh0qx8z8na55lmiwn0ds8q9cl")))) | |
13890 | (build-system python-build-system) | |
13891 | (arguments '(#:tests? #f)) ; no tests included | |
13892 | (propagated-inputs | |
13893 | `(("python-cooler" ,python-cooler))) | |
13894 | (home-page "https://github.com/4dn-dcic/hic2cool") | |
13895 | (synopsis "Converter for .hic and .cool files") | |
13896 | (description | |
13897 | "This package provides a converter between @code{.hic} files (from | |
13898 | juicer) and single-resolution or multi-resolution @code{.cool} files (for | |
13899 | cooler). Both @code{hic} and @code{cool} files describe Hi-C contact | |
13900 | matrices.") | |
13901 | (license license:expat))) | |
7e27393f | 13902 | |
13903 | (define-public r-pore | |
13904 | (package | |
13905 | (name "r-pore") | |
13906 | (version "0.24") | |
13907 | (source | |
13908 | (origin | |
13909 | (method url-fetch) | |
13910 | (uri | |
13911 | (string-append "mirror://sourceforge/rpore/" version | |
13912 | "/poRe_" version ".tar.gz")) | |
13913 | (sha256 | |
13914 | (base32 "0pih9nljbv8g4x8rkk29i7aqq681b782r5s5ynp4nw9yzqnmmksv")))) | |
13915 | (properties `((upstream-name . "poRe"))) | |
13916 | (build-system r-build-system) | |
13917 | (propagated-inputs | |
13918 | `(("r-bit64" ,r-bit64) | |
13919 | ("r-data-table" ,r-data-table) | |
13920 | ("r-rhdf5" ,r-rhdf5) | |
13921 | ("r-shiny" ,r-shiny) | |
13922 | ("r-svdialogs" ,r-svdialogs))) | |
13923 | (home-page "https://sourceforge.net/projects/rpore/") | |
13924 | (synopsis "Visualize Nanopore sequencing data") | |
13925 | (description | |
13926 | "This package provides graphical user interfaces to organize and visualize Nanopore | |
13927 | sequencing data.") | |
13928 | ;; This is free software but the license variant is unclear: | |
13929 | ;; <https://github.com/mw55309/poRe_docs/issues/10>. | |
13930 | (license license:bsd-3))) | |
a434730f RW |
13931 | |
13932 | (define-public r-xbioc | |
13933 | (let ((revision "1") | |
13934 | (commit "f798c187e376fd1ba27abd559f47bbae7e3e466b")) | |
13935 | (package | |
13936 | (name "r-xbioc") | |
13937 | (version (git-version "0.1.15" revision commit)) | |
13938 | (source (origin | |
13939 | (method git-fetch) | |
13940 | (uri (git-reference | |
13941 | (url "https://github.com/renozao/xbioc.git") | |
13942 | (commit commit))) | |
13943 | (file-name (git-file-name name version)) | |
13944 | (sha256 | |
13945 | (base32 | |
13946 | "03hffh2f6z71y6l6dqpa5cql3hdaw7zigdi8sm2dzgx379k9rgrr")))) | |
13947 | (build-system r-build-system) | |
13948 | (propagated-inputs | |
13949 | `(("r-annotationdbi" ,r-annotationdbi) | |
13950 | ("r-assertthat" ,r-assertthat) | |
13951 | ("r-biobase" ,r-biobase) | |
13952 | ("r-biocinstaller" ,r-biocinstaller) | |
13953 | ("r-digest" ,r-digest) | |
13954 | ("r-pkgmaker" ,r-pkgmaker) | |
13955 | ("r-plyr" ,r-plyr) | |
13956 | ("r-reshape2" ,r-reshape2) | |
13957 | ("r-stringr" ,r-stringr))) | |
13958 | (home-page "https://github.com/renozao/xbioc/") | |
13959 | (synopsis "Extra base functions for Bioconductor") | |
13960 | (description "This package provides extra utility functions to perform | |
13961 | common tasks in the analysis of omics data, leveraging and enhancing features | |
13962 | provided by Bioconductor packages.") | |
13963 | (license license:gpl3+)))) | |
28829c04 RW |
13964 | |
13965 | (define-public r-cssam | |
13966 | (let ((revision "1") | |
13967 | (commit "9ec58c982fa551af0d80b1a266890d92954833f2")) | |
13968 | (package | |
13969 | (name "r-cssam") | |
13970 | (version (git-version "1.4" revision commit)) | |
13971 | (source (origin | |
13972 | (method git-fetch) | |
13973 | (uri (git-reference | |
13974 | (url "https://github.com/shenorrLab/csSAM.git") | |
13975 | (commit commit))) | |
13976 | (file-name (git-file-name name version)) | |
13977 | (sha256 | |
13978 | (base32 | |
13979 | "128syf9v39gk0z3ip000qpsjbg6l1siyq6c8b0hz41dzg5achyb3")))) | |
13980 | (build-system r-build-system) | |
13981 | (propagated-inputs | |
13982 | `(("r-formula" ,r-formula) | |
13983 | ("r-ggplot2" ,r-ggplot2) | |
13984 | ("r-pkgmaker" ,r-pkgmaker) | |
13985 | ("r-plyr" ,r-plyr) | |
13986 | ("r-rngtools" ,r-rngtools) | |
13987 | ("r-scales" ,r-scales))) | |
13988 | (home-page "https://github.com/shenorrLab/csSAM/") | |
13989 | (synopsis "Cell type-specific statistical analysis of microarray") | |
13990 | (description "This package implements the method csSAM that computes | |
13991 | cell-specific differential expression from measured cell proportions using | |
13992 | SAM.") | |
13993 | ;; Any version | |
13994 | (license license:lgpl2.1+)))) | |
e7270247 RW |
13995 | |
13996 | (define-public r-bseqsc | |
13997 | (let ((revision "1") | |
13998 | (commit "fef3f3e38dcf3df37103348b5780937982b43b98")) | |
13999 | (package | |
14000 | (name "r-bseqsc") | |
14001 | (version (git-version "1.0" revision commit)) | |
14002 | (source (origin | |
14003 | (method git-fetch) | |
14004 | (uri (git-reference | |
14005 | (url "https://github.com/shenorrLab/bseqsc.git") | |
14006 | (commit commit))) | |
14007 | (file-name (git-file-name name version)) | |
14008 | (sha256 | |
14009 | (base32 | |
14010 | "1prw13wa20f7wlc3gkkls66n1kxz8d28qrb8icfqdwdnnv8w5qg8")))) | |
14011 | (build-system r-build-system) | |
14012 | (propagated-inputs | |
14013 | `(("r-abind" ,r-abind) | |
14014 | ("r-annotationdbi" ,r-annotationdbi) | |
14015 | ("r-biobase" ,r-biobase) | |
14016 | ("r-cssam" ,r-cssam) | |
14017 | ("r-dplyr" ,r-dplyr) | |
14018 | ("r-e1071" ,r-e1071) | |
14019 | ("r-edger" ,r-edger) | |
14020 | ("r-ggplot2" ,r-ggplot2) | |
14021 | ("r-nmf" ,r-nmf) | |
14022 | ("r-openxlsx" ,r-openxlsx) | |
14023 | ("r-pkgmaker" ,r-pkgmaker) | |
14024 | ("r-plyr" ,r-plyr) | |
14025 | ("r-preprocesscore" ,r-preprocesscore) | |
14026 | ("r-rngtools" ,r-rngtools) | |
14027 | ("r-scales" ,r-scales) | |
14028 | ("r-stringr" ,r-stringr) | |
14029 | ("r-xbioc" ,r-xbioc))) | |
14030 | (home-page "https://github.com/shenorrLab/bseqsc") | |
14031 | (synopsis "Deconvolution of bulk sequencing experiments using single cell data") | |
14032 | (description "BSeq-sc is a bioinformatics analysis pipeline that | |
14033 | leverages single-cell sequencing data to estimate cell type proportion and | |
14034 | cell type-specific gene expression differences from RNA-seq data from bulk | |
14035 | tissue samples. This is a companion package to the publication \"A | |
14036 | single-cell transcriptomic map of the human and mouse pancreas reveals inter- | |
14037 | and intra-cell population structure.\" Baron et al. Cell Systems (2016) | |
14038 | @url{https://www.ncbi.nlm.nih.gov/pubmed/27667365}.") | |
14039 | (license license:gpl2+)))) | |
f2bc53af | 14040 | |
14041 | (define-public porechop | |
14042 | ;; The recommended way to install is to clone the git repository | |
14043 | ;; https://github.com/rrwick/Porechop#installation | |
14044 | (let ((commit "289d5dca4a5fc327f97b3f8cecb68ecaf1014861") | |
14045 | (revision "1")) | |
14046 | (package | |
14047 | (name "porechop") | |
14048 | (version (git-version "0.2.3" revision commit)) | |
14049 | (source | |
14050 | (origin | |
14051 | (method git-fetch) | |
14052 | (uri (git-reference | |
14053 | (url "https://github.com/rrwick/Porechop.git") | |
14054 | (commit commit))) | |
14055 | (file-name (git-file-name name version)) | |
14056 | (sha256 | |
14057 | (base32 "05ps43gig0d3ia9x5lj84lb00hbsl6ba9n7y7jz927npxbr2ym23")))) | |
14058 | (build-system python-build-system) | |
14059 | (home-page "https://github.com/rrwick/porechop") | |
14060 | (synopsis "Finding, trimming or splitting adapters, in Oxford Nanopore reads") | |
14061 | (description | |
14062 | "The porechop package is a tool for finding and removing adapters from Oxford | |
14063 | Nanopore reads. Adapters on the ends of reads are trimmed off, and when a read | |
14064 | has an adapter in its middle, it is treated as chimeric and chopped into | |
14065 | separate reads. Porechop performs thorough alignments to effectively find | |
14066 | adapters, even at low sequence identity. Porechop also supports demultiplexing | |
14067 | of Nanopore reads that were barcoded with the Native Barcoding Kit, PCR | |
14068 | Barcoding Kit or Rapid Barcoding Kit.") | |
14069 | (license license:gpl3+)))) | |
3f0f49d7 | 14070 | |
14071 | (define-public poretools | |
14072 | ;; The latest release was in 2016 and the latest commit is from 2017 | |
14073 | ;; the recommended way to install is to clone the git repository | |
14074 | ;; https://poretools.readthedocs.io/en/latest/content/installation.html | |
14075 | (let ((commit "e426b1f09e86ac259a00c261c79df91510777407") | |
14076 | (revision "1")) | |
14077 | (package | |
14078 | (name "poretools") | |
14079 | (version (git-version "0.6.0" revision commit)) | |
14080 | (source | |
14081 | (origin | |
14082 | (method git-fetch) | |
14083 | (uri (git-reference | |
14084 | (url "https://github.com/arq5x/poretools.git") | |
14085 | (commit commit))) | |
14086 | (file-name (git-file-name name version)) | |
14087 | (sha256 | |
14088 | (base32 "0bglj833wxpp3cq430p1d3xp085ls221js2y90w7ir2x5ay8l7am")))) | |
14089 | (build-system python-build-system) | |
14090 | ;; requires python >=2.7, <3.0, and the same for python dependencies | |
14091 | (arguments `(#:python ,python-2)) | |
14092 | (inputs | |
14093 | `(("hdf5" ,hdf5))) | |
14094 | (propagated-inputs | |
14095 | `(("python-dateutil" ,python2-dateutil) | |
14096 | ("python-h5py" ,python2-h5py) | |
14097 | ("python-matplotlib" ,python2-matplotlib) | |
14098 | ("python-pandas" ,python2-pandas) | |
14099 | ("python-seaborn" ,python2-seaborn))) | |
14100 | (home-page "https://poretools.readthedocs.io") | |
14101 | (synopsis "Toolkit for working with nanopore sequencing data") | |
14102 | (description | |
14103 | "The MinION from Oxford Nanopore Technologies is a nanopore sequencer. | |
14104 | This @code{poretools} package is a flexible toolkit for exploring datasets | |
14105 | generated by nanopore sequencing devices for the purposes of quality control and | |
14106 | downstream analysis. Poretools operates directly on the native FAST5, a variant | |
14107 | of the Hierarchical Data Format (HDF5) standard.") | |
14108 | (license license:expat)))) | |
0f162222 | 14109 | |
14110 | (define-public r-absfiltergsea | |
14111 | (package | |
14112 | (name "r-absfiltergsea") | |
14113 | (version "1.5.1") | |
14114 | (source | |
14115 | (origin | |
14116 | (method url-fetch) | |
14117 | (uri (cran-uri "AbsFilterGSEA" version)) | |
14118 | (sha256 | |
14119 | (base32 "15srxkxsvn38kd5frdrwfdf0ad8gskrd0h01wmdf9hglq8fjrp7w")))) | |
14120 | (properties `((upstream-name . "AbsFilterGSEA"))) | |
14121 | (build-system r-build-system) | |
14122 | (propagated-inputs | |
14123 | `(("r-biobase" ,r-biobase) | |
14124 | ("r-deseq" ,r-deseq) | |
14125 | ("r-limma" ,r-limma) | |
14126 | ("r-rcpp" ,r-rcpp) | |
14127 | ("r-rcpparmadillo" ,r-rcpparmadillo))) | |
14128 | (home-page "https://cran.r-project.org/web/packages/AbsFilterGSEA/") | |
14129 | (synopsis "Improved false positive control of gene-permuting with absolute filtering") | |
14130 | (description | |
14131 | "This package provides a function that performs gene-permuting of a gene-set | |
14132 | enrichment analysis (GSEA) calculation with or without the absolute filtering. | |
14133 | Without filtering, users can perform (original) two-tailed or one-tailed | |
14134 | absolute GSEA.") | |
14135 | (license license:gpl2))) | |
d71078bc | 14136 | |
ee66a135 RW |
14137 | (define-public jamm |
14138 | (package | |
14139 | (name "jamm") | |
14140 | (version "1.0.7.5") | |
14141 | (source | |
14142 | (origin | |
14143 | (method git-fetch) | |
14144 | (uri (git-reference | |
14145 | (url "https://github.com/mahmoudibrahim/JAMM.git") | |
14146 | (commit (string-append "JAMMv" version)))) | |
14147 | (file-name (git-file-name name version)) | |
14148 | (sha256 | |
14149 | (base32 | |
14150 | "0ls889jcma1ch9h21jjhnkadgszgqj41842hhcjh6cg88f85qf3i")))) | |
14151 | (build-system gnu-build-system) | |
14152 | (arguments | |
14153 | `(#:tests? #f ; there are none | |
14154 | #:phases | |
14155 | (modify-phases %standard-phases | |
14156 | (delete 'configure) | |
14157 | (replace 'build | |
14158 | (lambda* (#:key inputs outputs #:allow-other-keys) | |
14159 | (substitute* "JAMM.sh" | |
14160 | (("^sPath=.*") | |
14161 | (string-append ""))) | |
14162 | #t)) | |
14163 | (replace 'install | |
14164 | (lambda* (#:key inputs outputs #:allow-other-keys) | |
14165 | (let* ((out (assoc-ref outputs "out")) | |
14166 | (libexec (string-append out "/libexec/jamm")) | |
14167 | (bin (string-append out "/bin"))) | |
14168 | (substitute* '("JAMM.sh" | |
14169 | "SignalGenerator.sh") | |
14170 | (("^sPath=.*") | |
14171 | (string-append "sPath=\"" libexec "\"\n"))) | |
14172 | (for-each (lambda (file) | |
14173 | (install-file file libexec)) | |
14174 | (list "bincalculator.r" | |
14175 | "peakfinder.r" | |
14176 | "peakhelper.r" | |
14177 | "signalmaker.r" | |
14178 | "xcorr.r" | |
14179 | "xcorrhelper.r" | |
14180 | ;; Perl scripts | |
14181 | "peakfilter.pl" | |
14182 | "readshifter.pl")) | |
14183 | ||
14184 | (for-each | |
14185 | (lambda (script) | |
14186 | (chmod script #o555) | |
14187 | (install-file script bin) | |
14188 | (wrap-program (string-append bin "/" script) | |
14189 | `("PATH" ":" prefix | |
14190 | (,(string-append (assoc-ref inputs "coreutils") "/bin") | |
14191 | ,(string-append (assoc-ref inputs "gawk") "/bin") | |
14192 | ,(string-append (assoc-ref inputs "perl") "/bin") | |
14193 | ,(string-append (assoc-ref inputs "r-minimal") "/bin"))) | |
14194 | `("PERL5LIB" ":" prefix (,(getenv "PERL5LIB"))) | |
14195 | `("R_LIBS_SITE" ":" prefix (,(getenv "R_LIBS_SITE"))))) | |
14196 | (list "JAMM.sh" "SignalGenerator.sh"))) | |
14197 | #t))))) | |
14198 | (inputs | |
14199 | `(("bash" ,bash) | |
14200 | ("coreutils" ,coreutils) | |
14201 | ("gawk" ,gawk) | |
14202 | ("perl" ,perl) | |
14203 | ("r-minimal" ,r-minimal) | |
14204 | ;;("r-parallel" ,r-parallel) | |
14205 | ("r-signal" ,r-signal) | |
14206 | ("r-mclust" ,r-mclust))) | |
14207 | (home-page "https://github.com/mahmoudibrahim/JAMM") | |
14208 | (synopsis "Peak finder for NGS datasets") | |
14209 | (description | |
14210 | "JAMM is a peak finder for next generation sequencing datasets (ChIP-Seq, | |
14211 | ATAC-Seq, DNase-Seq, etc.) that can integrate replicates and assign peak | |
14212 | boundaries accurately. JAMM is applicable to both broad and narrow | |
14213 | datasets.") | |
14214 | (license license:gpl3+))) | |
14215 | ||
d71078bc RW |
14216 | (define-public ngless |
14217 | (package | |
14218 | (name "ngless") | |
14219 | (version "0.9.1") | |
14220 | (source | |
14221 | (origin | |
14222 | (method git-fetch) | |
14223 | (uri (git-reference | |
14224 | (url "https://gitlab.com/ngless/ngless.git") | |
14225 | (commit (string-append "v" version)))) | |
14226 | (file-name (git-file-name name version)) | |
14227 | (sha256 | |
14228 | (base32 | |
14229 | "0mc2gi7h4lx74zylvyp76mvc0w6706j858ii9vlgzqsw6acpr117")))) | |
14230 | (build-system haskell-build-system) | |
14231 | (arguments | |
14232 | `(#:haddock? #f ; The haddock phase fails with: NGLess/CmdArgs.hs:20:1: | |
14233 | ; error: parse error on input import | |
14234 | ; import Options.Applicative | |
14235 | #:phases | |
14236 | (modify-phases %standard-phases | |
14237 | (add-after 'unpack 'create-cabal-file | |
21335fdb RW |
14238 | (lambda _ (invoke "hpack") #t)) |
14239 | ;; These tools are expected to be installed alongside ngless. | |
14240 | (add-after 'install 'link-tools | |
14241 | (lambda* (#:key inputs outputs #:allow-other-keys) | |
14242 | (let ((bin (string-append (assoc-ref outputs "out") "/bin/"))) | |
14243 | (symlink (string-append (assoc-ref inputs "prodigal") | |
14244 | "/bin/prodigal") | |
14245 | (string-append bin "ngless-" ,version "-prodigal")) | |
14246 | (symlink (string-append (assoc-ref inputs "minimap2") | |
14247 | "/bin/minimap2") | |
14248 | (string-append bin "ngless-" ,version "-minimap2")) | |
14249 | (symlink (string-append (assoc-ref inputs "samtools") | |
14250 | "/bin/samtools") | |
14251 | (string-append bin "ngless-" ,version "-samtools")) | |
14252 | (symlink (string-append (assoc-ref inputs "bwa") | |
14253 | "/bin/bwa") | |
14254 | (string-append bin "ngless-" ,version "-bwa")) | |
14255 | #t)))))) | |
d71078bc | 14256 | (inputs |
21335fdb RW |
14257 | `(("prodigal" ,prodigal) |
14258 | ("bwa" ,bwa) | |
14259 | ("samtools" ,samtools) | |
14260 | ("minimap2" ,minimap2) | |
14261 | ("ghc-aeson" ,ghc-aeson) | |
d71078bc RW |
14262 | ("ghc-ansi-terminal" ,ghc-ansi-terminal) |
14263 | ("ghc-async" ,ghc-async) | |
14264 | ("ghc-atomic-write" ,ghc-atomic-write) | |
14265 | ("ghc-bytestring-lexing" ,ghc-bytestring-lexing) | |
14266 | ("ghc-chart" ,ghc-chart) | |
14267 | ("ghc-chart-cairo" ,ghc-chart-cairo) | |
14268 | ("ghc-conduit" ,ghc-conduit) | |
14269 | ("ghc-conduit-algorithms" ,ghc-conduit-algorithms) | |
14270 | ("ghc-conduit-combinators" ,ghc-conduit-combinators) | |
14271 | ("ghc-conduit-extra" ,ghc-conduit-extra) | |
14272 | ("ghc-configurator" ,ghc-configurator) | |
14273 | ("ghc-convertible" ,ghc-convertible) | |
14274 | ("ghc-data-default" ,ghc-data-default) | |
14275 | ("ghc-double-conversion" ,ghc-double-conversion) | |
14276 | ("ghc-edit-distance" ,ghc-edit-distance) | |
14277 | ("ghc-either" ,ghc-either) | |
14278 | ("ghc-errors" ,ghc-errors) | |
14279 | ("ghc-extra" ,ghc-extra) | |
14280 | ("ghc-filemanip" ,ghc-filemanip) | |
14281 | ("ghc-file-embed" ,ghc-file-embed) | |
14282 | ("ghc-gitrev" ,ghc-gitrev) | |
14283 | ("ghc-hashtables" ,ghc-hashtables) | |
14284 | ("ghc-http-conduit" ,ghc-http-conduit) | |
14285 | ("ghc-inline-c" ,ghc-inline-c) | |
14286 | ("ghc-inline-c-cpp" ,ghc-inline-c-cpp) | |
14287 | ("ghc-intervalmap" ,ghc-intervalmap) | |
14288 | ("ghc-missingh" ,ghc-missingh) | |
14289 | ("ghc-optparse-applicative" ,ghc-optparse-applicative) | |
14290 | ("ghc-parsec" ,ghc-parsec) | |
14291 | ("ghc-regex" ,ghc-regex) | |
14292 | ("ghc-safe" ,ghc-safe) | |
14293 | ("ghc-safeio" ,ghc-safeio) | |
14294 | ("ghc-strict" ,ghc-strict) | |
14295 | ("ghc-tar" ,ghc-tar) | |
14296 | ("ghc-text" ,ghc-text) | |
14297 | ("ghc-unliftio" ,ghc-unliftio) | |
14298 | ("ghc-unliftio-core" ,ghc-unliftio-core) | |
14299 | ("ghc-vector" ,ghc-vector) | |
14300 | ("ghc-yaml" ,ghc-yaml) | |
14301 | ("ghc-zlib" ,ghc-zlib))) | |
14302 | (propagated-inputs | |
14303 | `(("r-r6" ,r-r6) | |
14304 | ("r-hdf5r" ,r-hdf5r) | |
14305 | ("r-iterators" ,r-iterators) | |
14306 | ("r-itertools" ,r-itertools) | |
14307 | ("r-matrix" ,r-matrix))) | |
14308 | (native-inputs | |
14309 | `(("ghc-hpack" ,ghc-hpack) | |
14310 | ("ghc-quickcheck" ,ghc-quickcheck) | |
14311 | ("ghc-test-framework" ,ghc-test-framework) | |
14312 | ("ghc-test-framework-hunit",ghc-test-framework-hunit) | |
14313 | ("ghc-test-framework-quickcheck2" ,ghc-test-framework-quickcheck2) | |
14314 | ("ghc-test-framework-th" ,ghc-test-framework-th))) | |
14315 | (home-page "https://gitlab.com/ngless/ngless") | |
14316 | (synopsis "DSL for processing next-generation sequencing data") | |
14317 | (description "Ngless is a domain-specific language for | |
14318 | @dfn{next-generation sequencing} (NGS) data processing.") | |
14319 | (license license:expat))) | |
b6bd8b10 | 14320 | |
14321 | (define-public filtlong | |
14322 | ;; The recommended way to install is to clone the git repository | |
14323 | ;; https://github.com/rrwick/Filtlong#installation | |
14324 | ;; and the lastest release is more than nine months old | |
14325 | (let ((commit "d1bb46dfe8bc7efe6257b5ce222c04bfe8aedaab") | |
14326 | (revision "1")) | |
14327 | (package | |
14328 | (name "filtlong") | |
14329 | (version (git-version "0.2.0" revision commit)) | |
14330 | (source | |
14331 | (origin | |
14332 | (method git-fetch) | |
14333 | (uri (git-reference | |
14334 | (url "https://github.com/rrwick/Filtlong.git") | |
14335 | (commit commit))) | |
14336 | (file-name (git-file-name name version)) | |
14337 | (sha256 | |
14338 | (base32 "1xr92r820x8qlkcr3b57iw223yq8vjgyi42jr79w2xgw47qzr575")))) | |
14339 | (build-system gnu-build-system) | |
14340 | (arguments | |
14341 | `(#:tests? #f ; no check target | |
14342 | #:phases | |
14343 | (modify-phases %standard-phases | |
14344 | (delete 'configure) | |
14345 | (replace 'install | |
14346 | (lambda* (#:key outputs #:allow-other-keys) | |
14347 | (let* ((out (assoc-ref outputs "out")) | |
14348 | (bin (string-append out "/bin")) | |
14349 | (scripts (string-append out "/share/filtlong/scripts"))) | |
14350 | (install-file "bin/filtlong" bin) | |
14351 | (install-file "scripts/histogram.py" scripts) | |
14352 | (install-file "scripts/read_info_histograms.sh" scripts)) | |
14353 | #t)) | |
14354 | (add-after 'install 'wrap-program | |
14355 | (lambda* (#:key inputs outputs #:allow-other-keys) | |
14356 | (let* ((out (assoc-ref outputs "out")) | |
14357 | (path (getenv "PYTHONPATH"))) | |
14358 | (wrap-program (string-append out | |
14359 | "/share/filtlong/scripts/histogram.py") | |
14360 | `("PYTHONPATH" ":" prefix (,path)))) | |
14361 | #t)) | |
14362 | (add-before 'check 'patch-tests | |
14363 | (lambda _ | |
14364 | (substitute* "scripts/read_info_histograms.sh" | |
14365 | (("awk") (which "gawk"))) | |
14366 | #t))))) | |
14367 | (inputs | |
14368 | `(("gawk" ,gawk) ;for read_info_histograms.sh | |
14369 | ("python" ,python-2) ;required for histogram.py | |
14370 | ("zlib" ,zlib))) | |
14371 | (home-page "https://github.com/rrwick/Filtlong/") | |
14372 | (synopsis "Tool for quality filtering of Nanopore and PacBio data") | |
14373 | (description | |
14374 | "The Filtlong package is a tool for filtering long reads by quality. | |
14375 | It can take a set of long reads and produce a smaller, better subset. It uses | |
14376 | both read length (longer is better) and read identity (higher is better) when | |
14377 | choosing which reads pass the filter.") | |
14378 | (license (list license:gpl3 ;filtlong | |
14379 | license:asl2.0))))) ;histogram.py | |
30f0d21b | 14380 | |
14381 | (define-public nanopolish | |
14382 | ;; The recommended way to install is to clone the git repository | |
14383 | ;; <https://github.com/jts/nanopolish#installing-a-particular-release>. | |
14384 | ;; Also, the differences between release and current version seem to be | |
14385 | ;; significant. | |
14386 | (let ((commit "50e8b5cc62f9b46f5445f5c5e8c5ab7263ea6d9d") | |
14387 | (revision "1")) | |
14388 | (package | |
14389 | (name "nanopolish") | |
14390 | (version (git-version "0.10.2" revision commit)) | |
14391 | (source | |
14392 | (origin | |
14393 | (method git-fetch) | |
14394 | (uri (git-reference | |
14395 | (url "https://github.com/jts/nanopolish.git") | |
14396 | (commit commit) | |
14397 | (recursive? #t))) | |
14398 | (file-name (git-file-name name version)) | |
14399 | (sha256 | |
14400 | (base32 "09j5gz57yr9i34a27vbl72i4g8syv2zzgmsfyjq02yshmnrvkjs6")))) | |
14401 | (build-system gnu-build-system) | |
14402 | (arguments | |
14403 | `(#:make-flags | |
14404 | `("HDF5=noinstall" "EIGEN=noinstall" "HTS=noinstall" "CC=gcc") | |
14405 | #:tests? #f ; no check target | |
14406 | #:phases | |
14407 | (modify-phases %standard-phases | |
14408 | (add-after 'unpack 'find-eigen | |
14409 | (lambda* (#:key inputs #:allow-other-keys) | |
14410 | (setenv "CPATH" | |
14411 | (string-append (assoc-ref inputs "eigen") | |
14412 | "/include/eigen3")) | |
14413 | #t)) | |
14414 | (delete 'configure) | |
14415 | (replace 'install | |
14416 | (lambda* (#:key outputs #:allow-other-keys) | |
14417 | (let* ((out (assoc-ref outputs "out")) | |
14418 | (bin (string-append out "/bin")) | |
14419 | (scripts (string-append out "/share/nanopolish/scripts"))) | |
14420 | ||
14421 | (install-file "nanopolish" bin) | |
14422 | (for-each (lambda (file) (install-file file scripts)) | |
14423 | (find-files "scripts" ".*")) | |
14424 | #t))) | |
14425 | (add-after 'install 'wrap-programs | |
14426 | (lambda* (#:key outputs #:allow-other-keys) | |
14427 | (for-each (lambda (file) | |
14428 | (wrap-program file `("PYTHONPATH" ":" prefix (,path)))) | |
14429 | (find-files "/share/nanopolish/scripts" "\\.py")) | |
14430 | (for-each (lambda (file) | |
14431 | (wrap-program file `("PERL5LIB" ":" prefix (,path)))) | |
14432 | (find-files "/share/nanopolish/scripts" "\\.pl")) | |
14433 | #t))))) | |
14434 | (inputs | |
14435 | `(("eigen" ,eigen) | |
14436 | ("hdf5" ,hdf5) | |
14437 | ("htslib" ,htslib) | |
14438 | ("perl" ,perl) | |
14439 | ("python" ,python) | |
14440 | ("python-biopython" ,python-biopython) | |
14441 | ("python-numpy" ,python-numpy) | |
14442 | ("python-pysam" ,python-pysam) | |
14443 | ("python-scikit-learn" , python-scikit-learn) | |
14444 | ("python-scipy" ,python-scipy) | |
14445 | ("zlib" ,zlib))) | |
14446 | (home-page "https://github.com/jts/nanopolish") | |
14447 | (synopsis "Signal-level analysis of Oxford Nanopore sequencing data") | |
14448 | (description | |
14449 | "This package analyses the Oxford Nanopore sequencing data at signal-level. | |
14450 | Nanopolish can calculate an improved consensus sequence for a draft genome | |
14451 | assembly, detect base modifications, call SNPs (Single nucleotide | |
14452 | polymorphisms) and indels with respect to a reference genome and more.") | |
14453 | (license license:expat)))) |