aboutsummaryrefslogtreecommitdiff
path: root/gn/packages/bioinformatics.scm
blob: a28ceb8b96886f35dc183d0c41a2bed22ab7e679 (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
465
466
467
468
469
470
471
472
473
474
475
476
477
478
479
480
481
482
483
484
485
486
487
488
489
490
491
492
493
494
495
496
497
498
499
500
501
502
503
504
505
506
507
508
509
510
511
512
513
514
515
516
517
518
519
520
521
522
523
524
525
526
527
528
529
530
531
532
533
534
535
536
537
538
539
540
541
542
543
544
545
546
547
548
549
550
551
552
553
554
555
556
557
558
559
560
561
562
563
564
565
566
567
568
569
570
571
572
573
574
575
576
577
578
579
580
581
582
583
584
585
586
587
588
589
590
591
592
593
594
595
596
597
598
599
600
601
602
603
604
605
606
607
608
609
610
611
612
613
614
615
616
617
618
619
620
621
622
623
624
625
626
627
628
629
630
631
632
633
634
635
636
637
638
639
640
641
642
643
644
645
646
647
648
649
650
651
652
653
654
655
656
657
658
659
660
;; 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 ant)
  #:use-module (guix build-system cmake)
  #:use-module (guix build-system gnu)
  #:use-module (guix build-system python)
  #:use-module (gnu packages)
  #:use-module (gnu packages bioinformatics)
  #:use-module (gnu packages boost)
  #:use-module (gnu packages compression)
  #:use-module (gnu packages check)
  #:use-module (gnu packages gcc)
  #:use-module (gnu packages maths)
  #:use-module (gnu packages perl)
  #:use-module (gnu packages python)
  #:use-module (gnu packages python-xyz)
  #:use-module (gnu packages statistics))

(define-public contra
  (package
    (name "contra")
    (version "2.0.6")
    (source (origin
      (method url-fetch)
      (uri (string-append
            "mirror://sourceforge/contra-cnv/CONTRA.V"
            (version-major+minor version) "/CONTRA.v" version ".tar.gz"))
      (sha256
       (base32
        "0agpcm2xh5f0i9n9sx1kvln6mzdksddmh11bvzj6bh76yw5pnw91"))
      (modules '((guix build utils)))
      (snippet
       '(begin
          (delete-file "BEDTools.v2.11.2.tar.gz") #t))))
    (build-system gnu-build-system)
    (propagated-inputs
     `(("python" ,python-2)
       ("r" ,r)
       ;; ("r-dnacopy" ,r-dnacopy) <-- missing in Pjotr's tree
       ("bedtools" ,bedtools)
       ("samtools" ,samtools)))
    (arguments
     `(#:tests? #f ; There are no tests.
       #:phases
       (modify-phases %standard-phases
         (delete 'configure)
         (delete 'build) ; We can use Guix's BEDtools instead.
         (replace 'install
           (lambda* (#:key outputs #:allow-other-keys)
             (let* ((out (assoc-ref outputs "out"))
                    (bin (string-append out "/bin"))
                    (doc (string-append out "/share/doc/contra")))
               (copy-recursively "scripts" (string-append bin "/scripts"))
               (install-file "contra.py" bin)
               (install-file "baseline.py" bin)
               ;; There's only a pre-built PDF available.
               (install-file "CONTRA_User_Guide.2.0.pdf" doc))
             #t)))))
    (home-page "http://contra-cnv.sourceforge.net/")
    (synopsis "Tool for copy number variation (CNV) detection for targeted
resequencing data")
    (description "CONTRA is a tool for copy number variation (CNV) detection
for targeted resequencing data such as those from whole-exome capture data.
CONTRA calls copy number gains and losses for each target region with key
strategies including the use of base-level log-ratios to remove GC-content
bias, correction for an imbalanced library size effect on log-ratios, and the
estimation of log-ratio variations via binning and interpolation.  It takes
standard alignment formats (BAM/SAM) and outputs in variant call format
(VCF 4.0) for easy integration with other next generation sequencing analysis
package.")
    (license license:gpl3+)))

(define boost-delly
  (package (inherit boost)
    (name "boost-delly")
    (version "1.57.0")
    (source (origin
              (method url-fetch)
              (uri (string-append
                    "mirror://sourceforge/boost/boost_"
                    (string-map (lambda (x) (if (eq? x #\.) #\_ x)) version)
                    ".tar.bz2"))
              (sha256
               (base32
                "0rs94vdmg34bwwj23fllva6mhrml2i7mvmlb11zyrk1k5818q34i"))))))

(define-public delly
  (package
    (name "delly")
    (version "0.7.2")
    (source (origin
      (method url-fetch)
      (uri (string-append "https://github.com/tobiasrausch/delly/archive/v"
            version ".tar.gz"))
      (sha256
       (base32 "173mmg43dbxqkyq0kiffz63xbmggr2kzd55mwxci9yfh5md1zprn"))
      (patches (list (search-patch "delly-use-system-libraries.patch")))))
    (build-system gnu-build-system)
    (native-inputs
     `(("python" ,python-2)))
    (inputs
     `(("boost" ,boost-delly) ; Use version 1.57.0 instead.
       ("htslib" ,htslib)
       ("zlib" ,zlib)
       ("bzip2" ,bzip2)))
    (arguments
     `(#:tests? #f ; There are no tests to run.
       #:phases
       (modify-phases %standard-phases
         (delete 'configure) ; There is no configure phase.
         (replace 'install
           (lambda _
             (let ((bin (string-append (assoc-ref %outputs "out") "/bin")))
               (install-file "src/cov" bin)
               (install-file "src/delly" bin)
               (install-file "src/extract" bin)
               (install-file "src/iover" bin)
               (install-file "src/stats" bin)))))))
    (home-page "https://github.com/tobiasrausch/delly")
    (synopsis "Integrated structural variant prediction method")
    (description "Delly is an integrated structural variant prediction method
that can discover and genotype deletions, tandem duplications, inversions and
translocations at single-nucleotide resolution in short-read massively parallel
sequencing data.  It uses paired-ends and split-reads to sensitively and
accurately delineate genomic rearrangements throughout the genome.  Structural
variants can be visualized using Delly-maze and Delly-suave.")
    (license license:gpl3)))

(define-public freec
  (package
    (name "control-freec")
    (version "8.7")
    (source (origin
      (method url-fetch)
      (uri "http://bioinfo-out.curie.fr/projects/freec/src/FREEC_Linux64.tar.gz")
      (file-name (string-append name "-" version ".tar.gz"))
      (sha256
       (base32 "12sl7gxbklhvv0687qjhml1z4lwpcn159zcyxvawvclsrzqjmv0h"))))
    (build-system gnu-build-system)
    ;; The source code's filename indicates only a 64-bit Linux build.
    ;; We need to investigate whether this is true.
    (supported-systems '("x86_64-linux"))
    (arguments
     `(#:phases
       (modify-phases %standard-phases
         ;; There's no configure phase because there are no external
         ;; dependencies.
         (delete 'configure)
         ;; There are no tests.
         (delete 'check)
         (replace
          'unpack
          (lambda* (#:key source #:allow-other-keys)
            (and
             (zero? (system* "mkdir" "source"))
             (with-directory-excursion "source"
               (zero? (system* "tar" "xvf" source))))))
         (replace
          'build
          (lambda* (#:key inputs #:allow-other-keys)
            (with-directory-excursion "source"
              (zero? (system* "make")))))
         (replace
          'install
          (lambda* (#:key outputs #:allow-other-keys)
            (let ((bin (string-append (assoc-ref outputs "out") "/bin")))
              (install-file "source/freec" bin)))))))
    (home-page "http://bioinfo-out.curie.fr/projects/freec/")
    (synopsis "Tool for detection of copy-number changes and allelic imbalances
(including LOH) using deep-sequencing data")
    (description "Control-FREEC automatically computes, normalizes, segments
copy number and beta allele frequency (BAF) profiles, then calls copy number
alterations and LOH.  The control (matched normal) sample is optional for whole
genome sequencing data but mandatory for whole exome or targeted sequencing
data.  For whole genome sequencing data analysis, the program can also use
mappability data (files created by GEM). ")
    (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-gn
  (let ((commit "5d1db4313ba0cc976562da233db4aced78975d10"))
  (package
    (name "plink-ng-gn")
    (version (string-append "1.90b3-" commit )) ; Aug 11, 2016
    (source (origin
             (method git-fetch)
             (uri (git-reference
                   (url "https://github.com/genenetwork/plink-ng.git")
                   (commit commit)))
             (file-name (string-append name "-" commit))
             (sha256
              (base32
               "1366li3ks9076bblvd1rpzkjq4j8f8f08lhga4c1ckrkil3xww4m"))))
            ;; no longer (patches (list (search-patch "plink-ng-Makefile-zlib-git.patch")))))
    (inputs
     `(("zlib" ,zlib)
       ("openblas" ,openblas)
       ;; ("atlas" ,atlas) ; openblas replaces atlas
       ("lapack" ,lapack)  ; lapack is disabled in GUIX openblas
       ;; ("gfortran" ,gfortran)
       ;; ("python" ,python-2)   ;; for tests - currently disabled
       ))
    (native-inputs
     `(("unzip" ,unzip)))
    (build-system gnu-build-system)
    (arguments
     '(#:tests? #f ;no "check" target. Some of the python-based tests fail
       #:phases
       (modify-phases %standard-phases
        (delete 'configure)
        (replace 'build
                 (lambda _
                   (zero? (system* "make" "-f" "Makefile.guix"))
                   ))
        (replace 'install
                  (lambda* (#:key outputs #:allow-other-keys)
                    (let ((bin (string-append (assoc-ref outputs "out")
                                              "/bin/")))
                      (install-file "plink2" bin)
                      #t))))))
    (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 pindel
  (package
   (name "pindel")
   (version "0.2.5b8")
   (source (origin
     (method git-fetch)
     (uri (git-reference
            (url "https://github.com/genome/pindel.git")
            (commit (string-append "v" version))))
     (file-name (git-file-name name version))
     (sha256
      (base32 "16a32fbgv1n58nfcxa1nyphrdrad80sgpinfa9p028n6plwycpww"))))
   (build-system gnu-build-system)
   (inputs
    `(("samtools" ,samtools)
      ("htslib" ,htslib)
      ("zlib" ,zlib)))
   (native-inputs
    `(("cppcheck" ,cppcheck)
      ("python" ,python-2)
      ("perl" ,perl)))
   (arguments
    `(#:phases
      (modify-phases %standard-phases
        (delete 'configure) ; There is no configure phase.
        ;; The build phase needs to run 'make' twice for the reasons described
        ;; below.
        (replace 'build
          (lambda* (#:key inputs #:allow-other-keys)
            ;; The first run creates a Makefile.local file.  Make will report
            ;; the failure to find Makefile.local, but we can ignore this error.
            (system* "make" (string-append "SAMTOOLS=" (assoc-ref inputs "samtools")))
            ;; The second run actually compiles the program.  Now Makefile.local
            ;; is available, and we should treat an exiting make with an error as
            ;; a true error.
            (invoke "make")))
        (replace 'install
          (lambda* (#:key outputs #:allow-other-keys)
            (let ((bin (string-append (assoc-ref outputs "out") "/bin")))
              (install-file "src/pindel" bin)
              (install-file "src/pindel2vcf" bin)
              (install-file "src/pindel2vcf4tcga" bin)
              (install-file "src/sam2pindel" bin))))
        ;; There are multiple test targets, so in order to run all
        ;; tests, we must run the separate make targets.
        (replace 'check
          (lambda _
            (for-each (lambda (target)
                        (invoke "make" target))
                      '("acceptance-tests" "coverage-tests" "cppcheck"
                        "functional-tests" "regression-tests")))))))
   (home-page "https://github.com/genome/pindel")
   (synopsis "Structural variants detector for next-gen sequencing data")
   (description "Pindel can detect breakpoints of large deletions, medium sized
insertions, inversions, tandem duplications and other structural variants at
single-based resolution from next-gen sequence data.  It uses a pattern growth
approach to identify the breakpoints of these variants from paired-end short
reads.")
   (license license:gpl3+)))

(define-public varscan
  (package
    (name "varscan")
    (version "2.4.1")
    (source (origin
      (method url-fetch)
      (uri (string-append
            "https://github.com/dkoboldt/varscan/releases/download/v"
            version "/VarScan.v" version ".source.jar"))
      (sha256
       (base32 "0y45ympkza7qwcbcisg006286pwjbr5978n03hx5nvl09f0mapk8"))))
    (build-system ant-build-system)
    (arguments
     `(#:tests? #f ; build.xml does not exist
       #:phases
       (modify-phases %standard-phases
         (replace 'unpack
           (lambda _
             (mkdir "source")
             (chdir "source")
             ;; Unpack the Java archive containing the source files.
             (invoke "jar" "xf" (assoc-ref %build-inputs "source"))
             ;; Remove existing compiled output.
             (with-directory-excursion "net/sf/varscan/"
               (for-each (lambda (file)
                           (delete-file file))
                         (find-files "." "^.java$" #:directories? #f)))
             #t))
         (replace 'build
           (lambda _
             ;; Compile the source files.
             (with-directory-excursion "net/sf/varscan/"
               (for-each (lambda (file)
                           (invoke "javac" file))
                         (find-files "." ".java$" #:directories? #f)))
             ;; Construct the new Java archive.
             (apply invoke "jar" "cfm"
                    (string-append "varscan-" ,version ".jar")
                    "META-INF/MANIFEST.MF"
                    (find-files "net/sf/varscan" ".java$"))))
        (replace 'install
          (lambda* (#:key outputs #:allow-other-keys)
            (let ((out (string-append (assoc-ref outputs "out")
                                      "/share/java/varscan/")))
              (install-file (string-append "varscan-" ,version ".jar") out))
            #t)))))
    (home-page "https://dkoboldt.github.io/varscan/")
    (synopsis "Variant detection in massively parallel sequencing data")
    (description "Variant detection in massively parallel sequencing data.")
    ;; Free for non-commercial use by academic, government, and
    ;; non-profit/not-for-profit institutions
    (license license:non-copyleft)))

(define-public edirect-gn
  (package
    (inherit edirect)
    (name "edirect-gn")
    (arguments
      (substitute-keyword-arguments (package-arguments edirect)
        ((#:phases phases)
         `(modify-phases ,phases
         ;   (replace 'build
         ;     (lambda* (#:key inputs #:allow-other-keys)
         ;       (let ((go (string-append (assoc-ref inputs "go") "/bin/go")))
         ;         (invoke go "build" "xtract.go"))))
            (add-after 'unpack 'patch-programs
              (lambda* (#:key inputs #:allow-other-keys)
                (let ((gzip (assoc-ref inputs "gzip")))
                  (substitute* '("index-bioc"
                                 "pm-index"
                                 "pm-invert"
                                 "pm-stash"
                                 "rchive.go"
                                 "run-ncbi-converter")
                    (("gunzip") (string-append gzip "/bin/gunzip")))
                  (substitute* (find-files "." "^e")
                    (("exec perl") "exec"))
                  (substitute* '("xtract" "rchive")
                    ;; or add current directory to PATH
                    ((".*PATH.*") "")))
                #t))
            (replace 'install
              (lambda* (#:key inputs outputs #:allow-other-keys)
                (let ((bin (string-append (assoc-ref outputs "out") "/bin"))
                      (xtract.linux (assoc-ref inputs "xtract.Linux"))
                      (rchive.linux (assoc-ref inputs "rchive.Linux")))
                  (for-each
                    (lambda (file)
                      (install-file file bin))
                    '("archive-pubmed" "asp-cp" "asp-ls" "download-pubmed"
                      "edirect.pl" "efetch" "epost" "fetch-pubmed" "ftp-cp"
                      "ftp-ls" "has-asp" "pm-prepare" "pm-refresh" "pm-stash"
                      "rchive" "xtract"))
                  (copy-file xtract.linux (string-append bin "/xtract.Linux"))
                  (copy-file rchive.linux (string-append bin "/rchive.Linux"))
                  (chmod (string-append bin "/xtract.Linux") #o555)
                  (chmod (string-append bin "/rchive.Linux") #o555))
                #t))
            (replace 'wrap-program
              (lambda* (#:key outputs #:allow-other-keys)
                ;; Make sure 'edirect.pl' finds all perl inputs at runtime.
                (let ((out (assoc-ref outputs "out"))
                      (path (getenv "PERL5LIB")))
                  (for-each
                    (lambda (file)
                      (wrap-program (string-append out "/bin/" file)
                                    `("PERL5LIB" ":" prefix (,path))))
                    '("edirect.pl" "asp-ls" "ftp-cp" "ftp-ls")))
                #t))))))
    (inputs
     `(("gzip" ,gzip)
       ,@(package-inputs edirect)))
    (native-inputs
     `(
       ;("go" ,go)
       ("xtract.Linux"
        ,(origin
           (method url-fetch)
           (uri (string-append "ftp://ftp.ncbi.nlm.nih.gov/entrez/entrezdirect/"
                               "versions/" (package-version edirect) "/xtract.Linux"))
           (file-name (string-append "xtract.Linux-" (package-version edirect)))
           (sha256
            (base32
             "0fx6arpn38spnwszmvkkpa3498qrrlglg2l9jw91icgqbyjjq9wq"))))
       ("rchive.Linux"
        ,(origin
           (method url-fetch)
           (uri (string-append "ftp://ftp.ncbi.nlm.nih.gov/entrez/entrezdirect/"
                               "versions/" (package-version edirect) "/rchive.Linux"))
           (file-name (string-append "rchive.Linux-" (package-version edirect)))
           (sha256
            (base32
             "134y0zprplqlplc6qmcjb97411bxkwghmq3z0qjgh0dgdbzjq1w3"))))))
    (native-search-paths
     ;; Ideally this should be set for LWP somewhere.
     (list (search-path-specification
            (variable "PERL_LWP_SSL_CA_FILE")
            (file-type 'regular)
            (separator #f)
            (files '("/etc/ssl/certs/ca-certificates.crt")))))
    ;; Due to the precompiled binaries we download:
    (supported-systems '("x86_64-linux"))))

;; TODO: Unbundle zlib, bamtools, tclap
(define-public sniffles
  (package
   (name "sniffles")
   (version "1.0.11")
   (source (origin
     (method git-fetch)
     (uri (git-reference
            (url "https://github.com/fritzsedlazeck/Sniffles.git")
            (commit version)))
     (file-name (git-file-name name version))
     (sha256
      (base32 "0rkwqn1ycckfzrg2wdid4cqahq8q2jmmgi7vvl8qxgpsihqfbq0j"))))
   (build-system cmake-build-system)
   (arguments
    `(#:phases
      (modify-phases %standard-phases
        (replace 'install
          (lambda* (#:key outputs #:allow-other-keys)
            (let ((out (assoc-ref outputs "out")))
              (install-file (string-append "../source/bin/sniffles-core-"
                                           ,version "/sniffles")
                            (string-append out "/bin")))
            #t))
        (replace 'check
          (lambda _
            (with-directory-excursion "../source/test_set"
              (for-each make-file-writable (find-files "."))
              (invoke (string-append "../bin/sniffles-core-" ,version "/sniffles")
                      "-m" "reads_region.bam" "-v" "test.vcf")))))))
   (native-inputs
    `(("zlib" ,zlib)))
   (home-page "https://github.com/fritzsedlazeck/Sniffles")
   (synopsis "Structural variation caller using third generation sequencing")
   (description
    "Sniffles is a structural variation caller using third generation sequencing
(PacBio or Oxford Nanopore).  It detects all types of SVs (10bp+) using evidence
from split-read alignments, high-mismatch regions, and coverage analysis.")
   (license license:expat)))

;; TODO: Unbundle Complete-Striped-Smith-Waterman-Library
(define-public ngmlr
  (package
   (name "ngmlr")
   (version "0.2.7")
   (source (origin
     (method git-fetch)
     (uri (git-reference
            (url "https://github.com/philres/ngmlr.git")
            (commit (string-append "v" version))))
     (file-name (git-file-name name version))
     (sha256
      (base32 "0lmsy8w0kxbyfnrln7lxgmnx3d82sv2b20n2yw5742rvfhq1v31n"))))
   (build-system cmake-build-system)
   (arguments
    `(#:phases
      (modify-phases %standard-phases
        (add-after 'patch-source-shebangs 'patch-more-tools
          (lambda* (#:key inputs #:allow-other-keys)
            (let ((bed (assoc-ref inputs "bedtools"))
                  (sam (assoc-ref inputs "samtools")))
              (substitute* (find-files "test" "\\.sh$")
                (("bedtools") (string-append bed "/bin/bedtools"))
                (("samtools") (string-append sam "/bin/samtools")))
              #t)))
        (replace 'check
          (lambda _
            (with-directory-excursion "../source"
              (invoke "sh" "test/test_travis.sh")))))))
   (native-inputs
    `(("bedtools" ,bedtools)
      ("samtools" ,samtools)))
   (inputs
    `(("zlib" ,zlib)))
   (home-page "https://github.com/philres/ngmlr")
   (synopsis "Long-read mapper designed to align PacBio or Oxford Nanopore")
   (description
    "NGMLR is a long-read mapper designed to align PacBio or Oxford Nanopore
(standard and ultra-long) to a reference genome with a focus on reads that span
structural variations.")
   (license license:expat)))

(define-public svim
  (package
   (name "svim")
   (version "1.2.0")
   (source (origin
     (method git-fetch)
     (uri (git-reference
            (url "https://github.com/eldariont/svim.git")
            (commit (string-append "v" version))))
     (file-name (git-file-name name version))
     (sha256
      (base32 "08j02in9jbq41b67dna1apnc3y30i37v44d1khml1xlx0iga720s"))))
   (build-system python-build-system)
   (arguments
    '(#:phases
      (modify-phases %standard-phases
        (replace 'check
          (lambda _
            (invoke "python3" "-m" "unittest" "discover" "-s" "src/"))))))
   (propagated-inputs
    `(("python-matplotlib" ,python-matplotlib)
      ("python-numpy" ,python-numpy)
      ("python-pysam" ,python-pysam)
      ("python-scipy" ,python-scipy)
      ("minimap2" ,minimap2)
      ("ngmlr" ,ngmlr)
      ("samtools" ,samtools)))
   (home-page "https://github.com/eldariont/svim")
   (synopsis "Structural Variant Identification Method using Long Reads")
   (description
    "SVIM (pronounced SWIM) is a structural variant caller for long reads.  It
is able to detect, classify and genotype five different classes of structural
variants.  Unlike existing methods, SVIM integrates information from across the
genome to precisely distinguish similar events, such as tandem and interspersed
duplications and novel element insertions.")
   (license license:gpl3)))

(define-public bamaddrg
  (let ((commit "3fccbf057eef21f6304fade6c306c5bb64158865") ; May 26, 2012
        (revision "1"))
    (package
      (name "bamaddrg")
      (version (git-version "0.0.0" revision commit))
      (source (origin
        (method git-fetch)
        (uri (git-reference
               (url "https://github.com/ekg/bamaddrg.git")
               (commit commit)))
        (file-name (git-file-name name version))
        (sha256
         (base32 "14hq66cc7f4cssagb6079fmd2i6hfr9vmpcw5vi5kzsqr3ifc5yk"))))
      (build-system gnu-build-system)
      (arguments
       `(#:tests? #f ; no tests
         #:phases
         (modify-phases %standard-phases
           (delete 'configure)
           ;; The Makefile wants to vendor bamtools' source so we mimic it.
           (replace 'build
              (lambda* (#:key inputs #:allow-other-keys)
                (let ((bam (assoc-ref inputs "bamtools")))
                  (apply invoke
                         `("g++" "-O3"
                           ,(string-append "-I" bam "/include/bamtools")
                           ,(string-append "-L" bam "/lib/libbamtools.a")
                           "bamaddrg.cpp" "-o" "bamaddrg" "-lbamtools" "-lz")))
                #t))
         (replace 'install
           (lambda* (#:key outputs #:allow-other-keys)
             (let ((bin (string-append (assoc-ref outputs "out") "/bin")))
               (install-file "bamaddrg" bin)
               #t))))))
      (native-inputs
       `(("bamtools" ,bamtools)))
      (inputs
       `(("zlib" ,zlib)))
      (home-page "https://github.com/ekg/bamaddrg")
      (synopsis "Adds read groups to input BAM files, streams BAM output on stdout")
      (description
       "This is intended for use \"fixing up\" RG tags on the fly so that they
reflect the source file from which the aligment originated from.  This allows
the \"safe\" merging of many files from many individuals into one stream,
suitable for input into downstream processing systems such as freebayes (
population variant detector).")
      (license #f)))) ; no license listed