summaryrefslogtreecommitdiff
path: root/gnu/packages/bioinformatics.scm
blob: 5bd668ee14ce9b979536ea47172ebb46fc03e659 (about) (plain)
1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
38
39
40
41
42
43
44
45
46
47
48
49
50
51
52
53
54
55
56
57
58
59
60
61
62
63
64
65
66
67
68
69
70
71
72
73
74
75
76
77
78
79
80
81
82
83
84
85
86
87
88
89
90
91
92
93
94
95
96
97
98
99
100
101
102
103
104
105
106
107
108
109
110
111
112
113
114
115
116
117
118
119
120
121
122
123
124
125
126
127
128
129
130
131
132
133
134
135
136
137
138
139
140
141
142
143
144
145
146
147
148
149
150
151
152
153
154
155
156
157
158
159
160
161
162
163
164
165
166
167
168
169
170
171
172
173
174
175
176
177
178
179
180
181
182
183
184
185
186
187
188
189
190
191
192
193
194
195
196
197
198
199
200
201
202
203
204
205
206
207
208
209
210
211
212
213
214
215
216
217
218
219
220
221
222
223
224
225
226
227
228
229
230
231
232
233
234
235
236
237
238
239
240
241
242
243
244
245
246
247
248
249
250
251
252
253
254
255
256
257
258
259
260
261
262
263
264
265
266
267
268
269
270
271
272
273
274
275
276
277
278
279
280
281
282
283
284
285
286
287
288
289
290
291
292
293
294
295
296
297
298
299
300
301
302
303
304
305
306
307
308
309
310
311
312
313
314
315
316
317
318
319
320
321
322
323
324
325
326
327
328
329
330
331
332
333
334
335
336
337
338
339
340
341
342
343
344
345
346
347
348
349
350
351
352
353
354
355
356
357
358
359
360
361
362
363
364
365
366
367
368
369
370
371
372
373
374
375
376
377
378
379
380
381
382
383
384
385
386
387
388
389
390
391
392
393
394
395
396
397
398
399
400
401
402
403
404
405
406
407
408
409
410
411
412
413
414
415
416
417
418
419
420
421
422
423
424
425
426
427
428
429
430
431
432
433
434
435
436
437
438
439
440
441
442
443
444
445
446
447
448
449
450
451
452
453
454
455
456
457
458
459
460
461
462
463
464
;;; GNU Guix --- Functional package management for GNU
;;; Copyright © 2014, 2015 Ricardo Wurmus <rekado@elephly.net>
;;;
;;; This file is part of GNU Guix.
;;;
;;; GNU Guix is free software; you can redistribute it and/or modify it
;;; under the terms of the GNU General Public License as published by
;;; the Free Software Foundation; either version 3 of the License, or (at
;;; your option) any later version.
;;;
;;; GNU Guix is distributed in the hope that it will be useful, but
;;; WITHOUT ANY WARRANTY; without even the implied warranty of
;;; MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
;;; GNU General Public License for more details.
;;;
;;; You should have received a copy of the GNU General Public License
;;; along with GNU Guix.  If not, see <http://www.gnu.org/licenses/>.

(define-module (gnu packages bioinformatics)
  #:use-module ((guix licenses) #:prefix license:)
  #:use-module (guix packages)
  #:use-module (guix download)
  #:use-module (guix build-system gnu)
  #:use-module (guix build-system cmake)
  #:use-module (guix build-system trivial)
  #:use-module (gnu packages)
  #:use-module (gnu packages base)
  #:use-module (gnu packages compression)
  #:use-module (gnu packages ncurses)
  #:use-module (gnu packages perl)
  #:use-module (gnu packages pkg-config)
  #:use-module (gnu packages python)
  #:use-module (gnu packages tbb)
  #:use-module (gnu packages vim)
  #:use-module (gnu packages zip))

(define-public bedops
  (package
    (name "bedops")
    (version "2.4.5")
    (source (origin
              (method url-fetch)
              (uri (string-append "https://github.com/bedops/bedops/archive/v"
                                  version ".tar.gz"))
              (sha256
               (base32
                "0wmg6j0icimlrnsidaxrzf3hfgjvlkkcwvpdg7n4gg7hdv2m9ni5"))))
    (build-system gnu-build-system)
    (arguments
     '(#:tests? #f
       #:make-flags (list (string-append "BINDIR=" %output "/bin"))
       #:phases
       (alist-cons-after
         'unpack 'unpack-tarballs
         (lambda _
           ;; FIXME: Bedops includes tarballs of minimally patched upstream
           ;; libraries jansson, zlib, and bzip2.  We cannot just use stock
           ;; libraries because at least one of the libraries (zlib) is
           ;; patched to add a C++ function definition (deflateInit2cpp).
           ;; Until the Bedops developers offer a way to link against system
           ;; libraries we have to build the in-tree copies of these three
           ;; libraries.

           ;; See upstream discussion:
           ;; https://github.com/bedops/bedops/issues/124

           ;; Unpack the tarballs to benefit from shebang patching.
           (with-directory-excursion "third-party"
             (and (zero? (system* "tar" "xvf" "jansson-2.6.tar.bz2"))
                  (zero? (system* "tar" "xvf" "zlib-1.2.7.tar.bz2"))
                  (zero? (system* "tar" "xvf" "bzip2-1.0.6.tar.bz2"))))
           ;; Disable unpacking of tarballs in Makefile.
           (substitute* "system.mk/Makefile.linux"
             (("^\tbzcat .*") "\t@echo \"not unpacking\"\n")
             (("\\./configure") "CONFIG_SHELL=bash ./configure"))
           (substitute* "third-party/zlib-1.2.7/Makefile.in"
             (("^SHELL=.*$") "SHELL=bash\n")))
         (alist-delete 'configure %standard-phases))))
    (home-page "https://github.com/bedops/bedops")
    (synopsis "Tools for high-performance genomic feature operations")
    (description
     "BEDOPS is a suite of tools to address common questions raised in genomic
studies---mostly with regard to overlap and proximity relationships between
data sets.  It aims to be scalable and flexible, facilitating the efficient
and accurate analysis and management of large-scale genomic data.

BEDOPS provides tools that perform highly efficient and scalable Boolean and
other set operations, statistical calculations, archiving, conversion and
other management of genomic data of arbitrary scale.  Tasks can be easily
split by chromosome for distributing whole-genome analyses across a
computational cluster.")
    (license license:gpl2+)))

(define-public bedtools
  (package
    (name "bedtools")
    (version "2.22.0")
    (source (origin
              (method url-fetch)
              (uri (string-append "https://github.com/arq5x/bedtools2/archive/v"
                                  version ".tar.gz"))
              (sha256
               (base32
                "16aq0w3dmbd0853j32xk9jin4vb6v6fgakfyvrsmsjizzbn3fpfl"))))
    (build-system gnu-build-system)
    (native-inputs `(("python" ,python-2)))
    (inputs `(("samtools" ,samtools)
              ("zlib" ,zlib)))
    (arguments
     '(#:test-target "test"
       #:phases
       (alist-cons-after
        'unpack 'patch-makefile-SHELL-definition
        (lambda _
          ;; patch-makefile-SHELL cannot be used here as it does not
          ;; yet patch definitions with `:='.  Since changes to
          ;; patch-makefile-SHELL result in a full rebuild, features
          ;; of patch-makefile-SHELL are reimplemented here.
          (substitute* "Makefile"
            (("^SHELL := .*$") (string-append "SHELL := " (which "bash") " -e \n"))))
        (alist-delete
         'configure
         (alist-replace
          'install
          (lambda* (#:key outputs #:allow-other-keys)
            (let ((bin (string-append (assoc-ref outputs "out") "/bin/")))
              (mkdir-p bin)
              (for-each (lambda (file)
                          (copy-file file (string-append bin (basename file))))
                        (find-files "bin" ".*"))))
          %standard-phases)))))
    (home-page "https://github.com/arq5x/bedtools2")
    (synopsis "Tools for genome analysis and arithmetic")
    (description
     "Collectively, the bedtools utilities are a swiss-army knife of tools for
a wide-range of genomics analysis tasks.  The most widely-used tools enable
genome arithmetic: that is, set theory on the genome.  For example, bedtools
allows one to intersect, merge, count, complement, and shuffle genomic
intervals from multiple files in widely-used genomic file formats such as BAM,
BED, GFF/GTF, VCF.")
    (license license:gpl2)))

(define-public bowtie
  (package
    (name "bowtie")
    (version "2.2.4")
    (source (origin
              (method url-fetch)
              (uri (string-append "https://github.com/BenLangmead/bowtie2/archive/v"
                                  version ".tar.gz"))
              (sha256
               (base32
                "15dnbqippwvhyh9zqjhaxkabk7lm1xbh1nvar1x4b5kwm117zijn"))
              (modules '((guix build utils)))
              (snippet
               '(substitute* "Makefile"
                  (("^CC = .*$") "CC = gcc")
                  (("^CPP = .*$") "CPP = g++")
                  ;; replace BUILD_HOST and BUILD_TIME for deterministic build
                  (("-DBUILD_HOST=.*") "-DBUILD_HOST=\"\\\"guix\\\"\"")
                  (("-DBUILD_TIME=.*") "-DBUILD_TIME=\"\\\"0\\\"\"")))
              (patches (list (search-patch "bowtie-fix-makefile.patch")))))
    (build-system gnu-build-system)
    (inputs `(("perl" ,perl)
              ("perl-clone" ,perl-clone)
              ("perl-test-deep" ,perl-test-deep)
              ("perl-test-simple" ,perl-test-simple)
              ("python" ,python-2)))
    (arguments
     '(#:make-flags '("allall")
       #:phases
       (alist-delete
        'configure
        (alist-replace
         'install
         (lambda* (#:key outputs #:allow-other-keys)
           (let ((bin (string-append (assoc-ref outputs "out") "/bin/")))
             (mkdir-p bin)
             (for-each (lambda (file)
                         (copy-file file (string-append bin file)))
                       (find-files "." "bowtie2.*"))))
         (alist-replace
          'check
          (lambda* (#:key outputs #:allow-other-keys)
            (system* "perl"
                     "scripts/test/simple_tests.pl"
                     "--bowtie2=./bowtie2"
                     "--bowtie2-build=./bowtie2-build"))
          %standard-phases)))))
    (home-page "http://bowtie-bio.sourceforge.net/bowtie2/index.shtml")
    (synopsis "Fast and sensitive nucleotide sequence read aligner")
    (description
     "Bowtie 2 is a fast and memory-efficient tool for aligning sequencing
reads to long reference sequences.  It is particularly good at aligning reads
of about 50 up to 100s or 1,000s of characters, and particularly good at
aligning to relatively long (e.g. mammalian) genomes.  Bowtie 2 indexes the
genome with an FM Index to keep its memory footprint small: for the human
genome, its memory footprint is typically around 3.2 GB.  Bowtie 2 supports
gapped, local, and paired-end alignment modes.")
    (supported-systems '("x86_64-linux"))
    (license license:gpl3+)))

(define-public flexbar
  (package
    (name "flexbar")
    (version "2.5")
    (source (origin
              (method url-fetch)
              (uri
               (string-append "mirror://sourceforge/flexbar/"
                              version "/flexbar_v" version "_src.tgz"))
              (sha256
               (base32
                "13jaykc3y1x8y5nn9j8ljnb79s5y51kyxz46hdmvvjj6qhyympmf"))))
    (build-system cmake-build-system)
    (arguments
     `(;; There is no test target, although there is a directory containing
       ;; test data and scripts (launched by flexbar_validate.sh).
       #:tests? #f
       #:configure-flags (list
                          (string-append "-DFLEXBAR_BINARY_DIR="
                                         (assoc-ref %outputs "out")
                                         "/bin/"))
       #:phases
       (alist-delete 'install %standard-phases)))
    (inputs
     `(("tbb" ,tbb)
       ("zlib" ,zlib)))
    (native-inputs
     `(("pkg-config" ,pkg-config)
       ("seqan" ,seqan)))
    (home-page "http://flexbar.sourceforge.net")
    (synopsis "Barcode and adapter removal tool for sequencing platforms")
    (description
     "Flexbar preprocesses high-throughput nucleotide sequencing data
efficiently.  It demultiplexes barcoded runs and removes adapter sequences.
Moreover, trimming and filtering features are provided.  Flexbar increases
read mapping rates and improves genome and transcriptome assemblies.  It
supports next-generation sequencing data in fasta/q and csfasta/q format from
Illumina, Roche 454, and the SOLiD platform.")
    (license license:gpl3)))

(define-public hisat
  (package
    (name "hisat")
    (version "0.1.4")
    (source (origin
              (method url-fetch)
              (uri (string-append
                    "http://ccb.jhu.edu/software/hisat/downloads/hisat-"
                    version "-beta-source.zip"))
              (sha256
               (base32
                "1k381ydranqxp09yf2y7w1d0chz5d59vb6jchi89hbb0prq19lk5"))))
    (build-system gnu-build-system)
    (arguments
     `(#:tests? #f ;no check target
       #:make-flags '("allall"
                      ;; Disable unsupported `popcnt' instructions on
                      ;; architectures other than x86_64
                      ,@(if (string-prefix? "x86_64"
                                            (or (%current-target-system)
                                                (%current-system)))
                            '()
                            '("POPCNT_CAPABILITY=0")))
       #:phases
       (alist-replace
        'unpack
        (lambda* (#:key source #:allow-other-keys)
          (and (zero? (system* "unzip" source))
               (chdir "hisat-0.1.4-beta")))
        (alist-cons-after
         'unpack 'patch-sources
         (lambda _
           ;; XXX Cannot use snippet because zip files are not supported
           (substitute* "Makefile"
             (("^CC = .*$") "CC = gcc")
             (("^CPP = .*$") "CPP = g++")
             ;; replace BUILD_HOST and BUILD_TIME for deterministic build
             (("-DBUILD_HOST=.*") "-DBUILD_HOST=\"\\\"guix\\\"\"")
             (("-DBUILD_TIME=.*") "-DBUILD_TIME=\"\\\"0\\\"\""))
           (substitute* '("hisat-build" "hisat-inspect")
             (("/usr/bin/env") (which "env"))))
         (alist-replace
          'install
          (lambda* (#:key outputs #:allow-other-keys)
            (let ((bin (string-append (assoc-ref outputs "out") "/bin/")))
              (mkdir-p bin)
              (for-each
               (lambda (file)
                 (copy-file file (string-append bin file)))
               (find-files
                "."
                "hisat(-(build|align|inspect)(-(s|l)(-debug)*)*)*$"))))
          (alist-delete 'configure %standard-phases))))))
    (native-inputs
     `(("unzip" ,unzip)))
    (inputs
     `(("perl" ,perl)
       ("python" ,python)
       ("zlib" ,zlib)))
    (home-page "http://ccb.jhu.edu/software/hisat/index.shtml")
    (synopsis "Hierarchical indexing for spliced alignment of transcripts")
    (description
     "HISAT is a fast and sensitive spliced alignment program for mapping
RNA-seq reads.  In addition to one global FM index that represents a whole
genome, HISAT uses a large set of small FM indexes that collectively cover the
whole genome.  These small indexes (called local indexes) combined with
several alignment strategies enable effective alignment of RNA-seq reads, in
particular, reads spanning multiple exons.")
    (license license:gpl3+)))

(define-public samtools
  (package
    (name "samtools")
    (version "1.1")
    (source
     (origin
       (method url-fetch)
       (uri
        (string-append "mirror://sourceforge/samtools/"
                       version "/samtools-" version ".tar.bz2"))
       (sha256
        (base32
         "1y5p2hs4gif891b4ik20275a8xf3qrr1zh9wpysp4g8m0g1jckf2"))))
    (build-system gnu-build-system)
    (arguments
     `(;; There are 87 test failures when building on non-64-bit architectures
       ;; due to invalid test data.  This has since been fixed upstream (see
       ;; <https://github.com/samtools/samtools/pull/307>), but as there has
       ;; not been a new release we disable the tests for all non-64-bit
       ;; systems.
       #:tests? ,(string=? (or (%current-system) (%current-target-system))
                           "x86_64-linux")
       #:make-flags (list (string-append "prefix=" (assoc-ref %outputs "out")))
       #:phases
       (alist-cons-after
        'unpack
        'patch-makefile-curses
        (lambda _
          (substitute* "Makefile"
            (("-lcurses") "-lncurses")))
        (alist-cons-after
         'unpack
         'patch-tests
         (lambda* (#:key inputs #:allow-other-keys)
           (let ((bash (assoc-ref inputs "bash")))
             (substitute* "test/test.pl"
               ;; The test script calls out to /bin/bash
               (("/bin/bash")
                (string-append bash "/bin/bash"))
               ;; There are two failing tests upstream relating to the "stats"
               ;; subcommand in test_usage_subcommand ("did not have Usage"
               ;; and "usage did not mention samtools stats"), so we disable
               ;; them.
               (("(test_usage_subcommand\\(.*\\);)" cmd)
                (string-append "unless ($subcommand eq 'stats') {" cmd "};")))))
         (alist-delete
          'configure
          %standard-phases)))))
    (native-inputs `(("pkg-config" ,pkg-config)))
    (inputs `(("ncurses" ,ncurses)
              ("perl" ,perl)
              ("python" ,python)
              ("zlib" ,zlib)))
    (home-page "http://samtools.sourceforge.net")
    (synopsis "Utilities to efficiently manipulate nucleotide sequence alignments")
    (description
     "Samtools implements various utilities for post-processing nucleotide
sequence alignments in the SAM, BAM, and CRAM formats, including indexing,
variant calling (in conjunction with bcftools), and a simple alignment
viewer.")
    (license license:expat)))

(define-public seqan
  (package
    (name "seqan")
    (version "1.4.2")
    (source (origin
              (method url-fetch)
              (uri (string-append "http://packages.seqan.de/seqan-library/"
                                  "seqan-library-" version ".tar.bz2"))
              (sha256
               (base32
                "05s3wrrwn50f81aklfm65i4a749zag1vr8z03k21xm0pdxy47yvp"))))
    ;; The documentation is 7.8MB and the includes are 3.6MB heavy, so it
    ;; makes sense to split the outputs.
    (outputs '("out" "doc"))
    (build-system trivial-build-system)
    (arguments
     `(#:modules ((guix build utils))
       #:builder
       (begin
         (use-modules (guix build utils))
         (let ((tar  (assoc-ref %build-inputs "tar"))
               (bzip (assoc-ref %build-inputs "bzip2"))
               (out  (assoc-ref %outputs "out"))
               (doc  (assoc-ref %outputs "doc")))
           (setenv "PATH" (string-append tar "/bin:" bzip "/bin"))
           (system* "tar" "xvf" (assoc-ref %build-inputs "source"))
           (chdir (string-append "seqan-library-" ,version))
           (copy-recursively "include" (string-append out "/include"))
           (copy-recursively "share"  (string-append doc "/share"))))))
    (native-inputs
     `(("source" ,source)
       ("tar" ,tar)
       ("bzip2" ,bzip2)))
    (home-page "http://www.seqan.de")
    (synopsis "Library for nucleotide sequence analysis")
    (description
     "SeqAn is a C++ library of efficient algorithms and data structures for
the analysis of sequences with the focus on biological data.  It contains
algorithms and data structures for string representation and their
manipulation, online and indexed string search, efficient I/O of
bioinformatics file formats, sequence alignment, and more.")
    (license license:bsd-3)))

(define-public star
  (package
    (name "star")
    (version "2.4.0j")
    (source (origin
              (method url-fetch)
              (uri (string-append
                    "https://github.com/alexdobin/STAR/archive/STAR_"
                    version ".tar.gz"))
              (sha256
               (base32
                "1y3bciych1aw6s7k8sy1saj23dcan9wk4d4f96an499slkxwz712"))
              (modules '((guix build utils)))
              (snippet
               '(substitute* "source/Makefile"
                  (("/bin/rm") "rm")))))
    (build-system gnu-build-system)
    (arguments
     '(#:tests? #f ;no check target
       #:make-flags '("STAR")
       #:phases
       (alist-cons-after
        'unpack 'enter-source-dir (lambda _ (chdir "source"))
        (alist-replace
         'install
         (lambda* (#:key outputs #:allow-other-keys)
           (let ((bin (string-append (assoc-ref outputs "out") "/bin/")))
             (mkdir-p bin)
             (copy-file "STAR" (string-append bin "STAR"))))
         (alist-delete
          'configure %standard-phases)))))
    (native-inputs
     `(("vim" ,vim))) ; for xxd
    (inputs
     `(("zlib" ,zlib)))
    (home-page "https://github.com/alexdobin/STAR")
    (synopsis "Universal RNA-seq aligner")
    (description
     "The Spliced Transcripts Alignment to a Reference (STAR) software is
based on a previously undescribed RNA-seq alignment algorithm that uses
sequential maximum mappable seed search in uncompressed suffix arrays followed
by seed clustering and stitching procedure.  In addition to unbiased de novo
detection of canonical junctions, STAR can discover non-canonical splices and
chimeric (fusion) transcripts, and is also capable of mapping full-length RNA
sequences.")
    ;; STAR is licensed under GPLv3 or later; htslib is MIT-licensed.
    (license license:gpl3+)))