aboutsummaryrefslogtreecommitdiff
path: root/gn/packages/bioinformatics.scm
blob: 67096b044605ed84bf493db60e3558da1d333463 (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
;; Bioinformatics module

(define-module (gn packages bioinformatics)
  #:use-module ((guix licenses) #:prefix license:)
  #:use-module (guix packages)
  #:use-module (guix utils)
  #:use-module (guix download)
  #:use-module (guix git-download)
  #:use-module (guix build-system gnu)
  #:use-module (guix build-system cmake)
  #:use-module (guix build-system perl)
  #:use-module (guix build-system python)
  ;; #:use-module (guix build-system ruby)
  #:use-module (guix build-system r)
  #:use-module (guix build-system trivial)
  #:use-module (gnu packages)
  #:use-module (gnu packages algebra)
  #:use-module (gnu packages base)
  #:use-module (gnu packages bioinformatics)
  #:use-module (gnu packages boost)
  #:use-module (gnu packages compression)
  #:use-module (gnu packages databases)
  #:use-module (gnu packages cpio)
  #:use-module (gnu packages file)
  #:use-module (gnu packages gcc)
  #:use-module (gnu packages graphviz)
  #:use-module (gnu packages java)
  #:use-module (gnu packages linux)
  #:use-module (gnu packages ldc)
  #:use-module (gnu packages machine-learning)
  #:use-module (gnu packages maths)
  #:use-module (gnu packages ncurses)
  #:use-module (gnu packages perl)
  #:use-module (gnu packages pkg-config)
  #:use-module (gnu packages popt)
  #:use-module (gnu packages protobuf)
  #:use-module (gnu packages python)
  #:use-module (gnu packages statistics)
  #:use-module (gnu packages tbb)
  #:use-module (gnu packages textutils)
  #:use-module (gnu packages vim)
  #:use-module (gnu packages web)
  #:use-module (gnu packages xml)
  #:use-module (gnu packages zip)
  #:use-module (gnu packages bootstrap)
  #:use-module (gn packages python)
  #:use-module (gn packages statistics)
  #:use-module (srfi srfi-1))

(define-public r-wgcna
(package
  (name "r-wgcna")
  (version "1.48")
  (source
    (origin
      (method url-fetch)
      (uri (cran-uri "WGCNA" version))
      (sha256
        (base32
          "18yl2v3s279saq318vd5hlwnqfm89rxmjjji778d2d26vviaf6bn"))))
  (properties `((upstream-name . "WGCNA")))
  (build-system r-build-system)
  ;; (propagated-inputs
    ;; `( ;; ("r-annotationdbi" ,r-annotationdbi)
       ;; ("r-doparallel" ,r-doparallel)
       ;; ("r-dynamictreecut" ,r-dynamictreecut)
       ;; ("r-fastcluster" ,r-fastcluster)
       ;; ("r-foreach" ,r-foreach)
       ;; ("r-go.db" ,r-go.db)
       ;; ("r-grdevices" ,r-grdevices)
       ;; ("r-hmisc" ,r-hmisc)
       ;; ("r-impute" ,r-impute)
       ;; ("r-matrixstats" ,r-matrixstats)
       ;; ("r-parallel" ,r-parallel)
       ;; ("r-preprocesscore" ,r-preprocesscore)
       ;; ("r-splines" ,r-splines)
       ;; ("r-stats" ,r-stats)
       ;; ("r-survival" ,r-survival)
       ;; ("r-utils" ,r-utils)))
  (home-page
    "http://www.genetics.ucla.edu/labs/horvath/CoexpressionNetwork/Rpackages/WGCNA/")
  (synopsis
    "Weighted Correlation Network Analysis")
  (description
    "Functions necessary to perform Weighted Correlation Network Analysis on high-dimensional data.  Includes functions for rudimentary data cleaning, construction of correlation networks, module identification, summarization, and relating of variables and modules to sample traits.  Also includes a number of utility functions for data manipulation and visualization.")
  (license license:gpl2+)))

(define-public qtlreaper
  (package
    (name "qtlreaper")
    (version "1.1.1")
    (source
     (origin
       (method url-fetch)
       (uri (string-append
             "mirror://sourceforge/qtlreaper/qtlreaper-" version ".tar.gz"
             ;; "http://downloads.sourceforge.net/project/qtlreaper/qtlreaper/1.1.1/qtlreaper-1.1.1.tar.gz?r=http%3A%2F%2Fsourceforge.net%2Fprojects%2Fqtlreaper%2Ffiles%2Flatest%2Fdownload&ts=1358975786&use_mirror=iweb"))
             ))
       (file-name (string-append name "-" version ".tar.gz"))
       (sha256
        (base32
         "0rbf030940nbbbkggdq2dxiy3c0jv8l4y3vvyfxhqimgj0qv3l1x"))))
    (build-system python-build-system)
    ;; (native-inputs
    ;; `(("python-setuptools" ,python-setuptools)))
    (arguments
     `(#:python ,python-2
       #:tests? #f))   ; no 'setup.py test'
    (home-page "http://qtlreaper.sourceforge.net/")
    (synopsis "Tool for scanning expression data for QTLs")
    (description
     "It is essentially the batch-oriented version of WebQTL. It
requires, as input, expression data from members of a set of
recombinant inbred lines and genotype information for the same
lines.  It searches for an association between each expression trait
and all genotypes and evaluates that association by a permutation
test.  For the permutation test, it performs only as many permutations
as are necessary to define the empirical P-value to a reasonable
precision. It also performs bootstrap resampling to estimate the
confidence region for the location of a putative QTL.")
    (license license:gpl2)))

(define-public plink2
  (package
    (name "plink2")
    (version "1.90b3")
    (source
     (origin
      (method url-fetch)
      ;; https://github.com/chrchang/plink-ng/archive/v1.90b3.tar.gz
       (uri (string-append
             "https://github.com/chrchang/plink-ng/archive/v"
             version ".tar.gz"))
       (sha256
        (base32 "03fzib1al5qkr9vxv63wxmv6y2pfb1rmir0h8jpi72r87hczqjig"))
       (patches (list (search-patch "plink-ng-Makefile-zlib.patch")))))
    (build-system gnu-build-system)
    (arguments
     '(#:tests? #f ;no "check" target
       #:phases
       (modify-phases %standard-phases
        (delete 'configure)
        (replace 'build
                 (lambda _
                   (zero? (system* "make" "-f" "Makefile.std"))
                   ))                 
        (replace 'install
                  (lambda* (#:key outputs #:allow-other-keys)
                    (let ((bin (string-append (assoc-ref outputs "out")
                                              "/bin/")))
                      (install-file "plink2" bin)
                      #t))))))
    (inputs
     `(("zlib" ,zlib)
       ("openblas" ,openblas)
       ("atlas" ,atlas)
       ("lapack" ,lapack)
       ("gfortran" ,gfortran)
       ))
    (native-inputs
     `(("unzip" ,unzip)))
    (home-page "https://www.cog-genomics.org/plink2")
    (synopsis "Whole genome association analysis toolset")
    (description
     "PLINK is a whole genome association analysis toolset, designed to
perform a range of basic, large-scale analyses in a computationally efficient
manner.  The focus of PLINK is purely on analysis of genotype/phenotype data,
so there is no support for steps prior to this (e.g. study design and
planning, generating genotype or CNV calls from raw data).  Through
integration with gPLINK and Haploview, there is some support for the
subsequent visualization, annotation and storage of results.")
    ;; Code is released under GPLv2, except for fisher.h, which is under
    ;; LGPLv2.1+
    (license (list license:gpl2 license:lgpl2.1+))))

(define-public plink-ng
  (let ((commit "516d730f9"))
  (package
    (name "plink-ng")
    (version (string-append "1.90b3-" commit ))
    (source (origin
             (method git-fetch)
             (uri (git-reference
                   (url "https://github.com/chrchang/plink-ng.git")
                   (commit commit)))
             (file-name (string-append name "-" commit)) 
             (sha256
              (base32
               "0cv824wkdml9h9imsc30s2x3l8g65j44cpjbr1ydkk49g5qmf580"))
    (patches (list (search-patch "plink-ng-Makefile-zlib-git.patch")))))
    (build-system gnu-build-system)
    (arguments
     '(#:tests? #f ;no "check" target
       #:phases
       (modify-phases %standard-phases
        (delete 'configure)
        (replace 'build
                 (lambda _
                   (zero? (system* "make" "-f" "Makefile.std"))
                   ))                 
        (replace 'install
                  (lambda* (#:key outputs #:allow-other-keys)
                    (let ((bin (string-append (assoc-ref outputs "out")
                                              "/bin/")))
                      (install-file "plink2" bin)
                      #t))))))
    (inputs
     `(("zlib" ,zlib)
       ("openblas" ,openblas)
       ("atlas" ,atlas)
       ("lapack" ,lapack)
       ("gfortran" ,gfortran)
       ))
    (native-inputs
     `(("unzip" ,unzip)))
    (home-page "https://www.cog-genomics.org/plink2")
    (synopsis "Whole genome association analysis toolset")
    (description
     "PLINK is a whole genome association analysis toolset, designed to
perform a range of basic, large-scale analyses in a computationally efficient
manner.  The focus of PLINK is purely on analysis of genotype/phenotype data,
so there is no support for steps prior to this (e.g. study design and
planning, generating genotype or CNV calls from raw data).  Through
integration with gPLINK and Haploview, there is some support for the
subsequent visualization, annotation and storage of results.")
    (license license:gpl3+))))

(define-public gemma-git
  (let ((commit "2de4bfab3"))
  (package
    (name "gemma-git")
    (version (string-append "0.9.5-" commit ))
    (source (origin
             (method git-fetch)
             (uri (git-reference
                   (url "https://github.com/genenetwork/GEMMA.git")
                   (commit commit)))
             (file-name (string-append name "-" commit)) 
             (sha256
              (base32
               "1drffdgwbzgiw9sf55ghl3zjv58f8i9kfz0zys5mp6n06syp4ira"))))
    (inputs `(
              ("gsl" ,gsl)
              ("lapack" ,lapack)
              ("zlib" ,zlib)
              ))
    (build-system gnu-build-system)
    (arguments
     `(#:make-flags '(" FORCE_DYNAMIC=1")
       #:phases
        (modify-phases %standard-phases
         (delete 'configure)
         (add-before 'build 'bin-mkdir
                     (lambda _
                       (mkdir-p "bin")
                       ))
         (replace 'install
                  (lambda* (#:key outputs #:allow-other-keys)
                           (let ((out (assoc-ref outputs "out")))
                             (install-file "bin/gemma" (string-append out "/bin"))))))
       #:tests? #f))
    (home-page "")
    (synopsis "Tool for genome-wide efficient mixed model association")
    (description "GEMMA is the software implementing the Genome-wide
Efficient Mixed Model Association algorithm for a standard linear
mixed model and some of its close relatives for genome-wide
association studies (GWAS).")
    (license license:gpl3))))

(define-public rdmd
  (let ((commit "4dba6877c"))
    (package
      (name "rdmd")
      (version "20160217")
      (source (origin
                (method git-fetch)
                (uri (git-reference
                      (url "https://github.com/D-Programming-Language/tools.git")
                      (commit commit)))
                (file-name (string-append name "-" commit)) 
                (sha256
                 (base32
                  "1pcx5lyqzrip86f4vv60x292rpvnwsq2hvl1znm9x9rn68f34m45"))))
      (build-system gnu-build-system)
      (arguments
       '(#:phases
         (modify-phases %standard-phases
           (delete 'configure)
           (delete 'check) ; There is no Makefile, so there's no 'make check'.
           (replace
            'build
            (lambda _
              (zero? (system* "ldc2" "rdmd.d"))))
           (replace
            'install
            (lambda* (#:key outputs #:allow-other-keys)
              (let ((bin (string-append (assoc-ref outputs "out") "/bin")))
                (mkdir-p bin)
                (copy-file "rdmd" (string-append bin "/rdmd"))))))))
      (native-inputs
       `(("ldc" ,ldc)))
      (home-page "https://github.com/D-Programming-Language/tools/")
      (synopsis "Tool for the D language which is used for compiling")
      (description
       "rdmd is a companion to the dmd compiler that simplifies the typical
edit-compile-link-run or edit-make-run cycle to a rapid edit-run cycle. Like
make and other tools, rdmd uses the relative dates of the files involved to
minimize the amount of work necessary. Unlike make, rdmd tracks dependencies
and freshness without requiring additional information from the user.")
      (license license:boost1.0))))

(define-public sambamba
  (let ((commit "2ca5a2dba"))
  (package
    (name "sambamba")
    (version (string-append "0.5.9-" commit))
    (source (origin
             (method git-fetch)
             (uri (git-reference                
                   ;; https://github.com/pjotrp/sambamba.git
                   (url "https://github.com/pjotrp/sambamba.git")
                   (commit commit)))
             (file-name (string-append name "-" commit)) 
             (sha256
              (base32
               "1f14wn9aaxwjkmla6pzq3s28741carbr2v0fd2v2mm1dcpwnrqz5"))))
    (build-system gnu-build-system)
    (inputs
     `(("ldc" ,ldc)
       ;; These are currently included in "ldc".
       ;;("druntime-ldc" ,druntime-ldc)
       ;;("phobos2-ldc" ,phobos2-ldc)
       ("lz4" ,lz4)))
    (native-inputs
     `(("ldc" ,ldc)
       ;;("druntime-ldc" ,druntime-ldc)
       ;;("phobos2-ldc" ,phobos2-ldc)
       ("lz4" ,lz4)
       ("gcc" ,gcc)
       ("rdmd" ,rdmd)
       ("htslib-src"
        ,(origin
           (method url-fetch)
           (uri (string-append
                 "https://github.com/lomereiter/htslib/archive/0.2.0-rc10.tar.gz"))
           (file-name (string-append "htslib-0.2.0-rc10.tar.gz"))
           (sha256
            (base32 "1k6dlf6m8yayhcp7b4yisgw1xqdy1xg2xyrllss6ld0wg00hfcbs"))))
       ("biod-src"
        ,(origin
           (method git-fetch)
           (uri (git-reference
                 (url "https://github.com/biod/BioD.git")
                 (commit "7efdb8a2f7fdcd71c9ad9596be48d1262bb1bd5b")))
           (sha256
            (base32 "09icc2bjsg9y4hxjim4ql275izadf0kh1nnmapg8manyz6bc8svf"))
           (file-name "biod")))))
    (arguments
     '(#:phases 
       (modify-phases %standard-phases
         (delete 'configure)
         (add-after 'unpack 'unpack-htslib-sources
           (lambda* (#:key inputs #:allow-other-keys)
             ;; Unfortunately, the current build compiles htslib statically
             ;; into the executable.  Instead of patching the build files
             ;; for Guix, this should be resolved on Sambamba upstream.  For
             ;; now, just extract the source code to the desired directory.
             (and (with-directory-excursion "htslib"
              (zero? (system* "tar" "xvf" (assoc-ref inputs "htslib-src")
                              "--strip-components=1")))
              (zero? (system* "cp" "-R" (assoc-ref inputs "biod-src") "BioD"))
                  )))
         ;; Building a production-quality executable is done with a
         ;; non-default make target. Adding it with #:make-flags breaks
         ;; building tests.  Therefore, the default make got replaced by this.
         (replace
          'build
          (lambda* (#:key (make-flags '()) #:allow-other-keys)
            (zero? (system* "make" "-f" "Makefile.guix" make-flags)))))))
    (home-page "https://github.com/lomereiter/sambamba")
    (synopsis "A tool for working with SAM and BAM files written in D.")
    (description
     "Sambamba is a high performance modern robust and fast tool (and
library), written in the D programming language, for working with SAM
and BAM files.  Current parallelised functionality is an important
subset of samtools functionality, including view, index, sort,
markdup, and depth.")
    (license license:gpl2+))))

(define-public picard
  (package
    (name "picard")
    (version "2.1.0")
    (source
     (origin
       (method url-fetch)
       (uri (string-append
             "https://github.com/broadinstitute/picard/archive/"
             version ".tar.gz"))
       (sha256
        (base32 ""))))
    (build-system gnu-build-system)
    (home-page "http://broadinstitute.github.io/picard/")
    (synopsis "A set of Java command line tools for manipulating high-throughput
sequencing data (HTS) data and formats")
    (description "Picard comprises Java-based command-line utilities that
manipulate SAM files, and a Java API (HTSJDK) for creating new programs that
read and write SAM files. Both SAM text format and SAM binary (BAM) format are
supported.")
    ;; The license is MIT.
    (license license:expat)
))

(define-public fastqc
  (package
    (name "fastqc")
    (version "0.11.4")
    (source
     (origin
       (method url-fetch)
       (uri (string-append
             "http://www.bioinformatics.babraham.ac.uk/projects/fastqc/fastqc_v"
             version "_source.zip"))
       (sha256
        (base32 ""))))
    (build-system gnu-build-system)
    (arguments
     `(("perl" ,perl) ; Needed to run the java command.
       ("jdk" ,icedtea "jdk")))
    (native-inputs
     `(("ant" ,ant) ; TODO: Most Java packages need Ant, but in this case, IDK..
       ("jdk" ,icedtea "jdk")
       ;;("htsjdk" ,htsjdk) ; It is based on htsjdk, but it ships its own copy.
       ("unzip" ,unzip)))
    (home-page "http://www.bioinformatics.babraham.ac.uk/projects/fastqc/")
    (synopsis "A quality control tool for high throughput sequence data")
    (description
     "FastQC aims to provide a QC report which can spot problems which originate either in the sequencer or in the starting library material. It can either run as a stand alone interactive application for the immediate analysis of small numbers of FastQ files, or it can be run in a non-interactive mode where it would be suitable for integrating into a larger analysis pipeline for the systematic processing of large numbers of files.")
    (license license:gpl3+)))