1 ;;; GNU Guix --- Functional package management for GNU
2 ;;; Copyright © 2014, 2015, 2016 Ricardo Wurmus <rekado@elephly.net>
3 ;;; Copyright © 2015, 2016 Ben Woodcroft <donttrustben@gmail.com>
4 ;;; Copyright © 2015, 2016 Pjotr Prins <pjotr.guix@thebird.nl>
5 ;;; Copyright © 2015 Andreas Enge <andreas@enge.fr>
6 ;;; Copyright © 2016 Roel Janssen <roel@gnu.org>
7 ;;; Copyright © 2016 Efraim Flashner <efraim@flashner.co.il>
9 ;;; This file is part of GNU Guix.
11 ;;; GNU Guix is free software; you can redistribute it and/or modify it
12 ;;; under the terms of the GNU General Public License as published by
13 ;;; the Free Software Foundation; either version 3 of the License, or (at
14 ;;; your option) any later version.
16 ;;; GNU Guix is distributed in the hope that it will be useful, but
17 ;;; WITHOUT ANY WARRANTY; without even the implied warranty of
18 ;;; MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
19 ;;; GNU General Public License for more details.
21 ;;; You should have received a copy of the GNU General Public License
22 ;;; along with GNU Guix. If not, see <http://www.gnu.org/licenses/>.
24 (define-module (gnu packages bioinformatics)
25 #:use-module ((guix licenses) #:prefix license:)
26 #:use-module (guix packages)
27 #:use-module (guix utils)
28 #:use-module (guix download)
29 #:use-module (guix git-download)
30 #:use-module (guix build-system ant)
31 #:use-module (guix build-system gnu)
32 #:use-module (guix build-system cmake)
33 #:use-module (guix build-system perl)
34 #:use-module (guix build-system python)
35 #:use-module (guix build-system r)
36 #:use-module (guix build-system ruby)
37 #:use-module (guix build-system trivial)
38 #:use-module (gnu packages)
39 #:use-module (gnu packages autotools)
40 #:use-module (gnu packages algebra)
41 #:use-module (gnu packages base)
42 #:use-module (gnu packages bison)
43 #:use-module (gnu packages boost)
44 #:use-module (gnu packages compression)
45 #:use-module (gnu packages cpio)
46 #:use-module (gnu packages curl)
47 #:use-module (gnu packages documentation)
48 #:use-module (gnu packages datastructures)
49 #:use-module (gnu packages file)
50 #:use-module (gnu packages gawk)
51 #:use-module (gnu packages gcc)
52 #:use-module (gnu packages java)
53 #:use-module (gnu packages linux)
54 #:use-module (gnu packages machine-learning)
55 #:use-module (gnu packages maths)
56 #:use-module (gnu packages mpi)
57 #:use-module (gnu packages ncurses)
58 #:use-module (gnu packages pcre)
59 #:use-module (gnu packages perl)
60 #:use-module (gnu packages pkg-config)
61 #:use-module (gnu packages popt)
62 #:use-module (gnu packages protobuf)
63 #:use-module (gnu packages python)
64 #:use-module (gnu packages ruby)
65 #:use-module (gnu packages statistics)
66 #:use-module (gnu packages tbb)
67 #:use-module (gnu packages textutils)
68 #:use-module (gnu packages time)
69 #:use-module (gnu packages tls)
70 #:use-module (gnu packages vim)
71 #:use-module (gnu packages web)
72 #:use-module (gnu packages xml)
73 #:use-module (gnu packages zip)
74 #:use-module (srfi srfi-1))
76 (define-public aragorn
83 "http://mbio-serv2.mbioekol.lu.se/ARAGORN/Downloads/aragorn"
87 "1dg7jlz1qpqy88igjxd6ncs11ccsirb36qv1z01a0np4i4jh61mb"))))
88 (build-system gnu-build-system)
90 `(#:tests? #f ; there are no tests
92 (modify-phases %standard-phases
102 (string-append "aragorn" ,version ".c")))))
104 (lambda* (#:key outputs #:allow-other-keys)
105 (let* ((out (assoc-ref outputs "out"))
106 (bin (string-append out "/bin"))
107 (man (string-append out "/share/man/man1")))
110 (string-append bin "/aragorn"))
112 (copy-file "aragorn.1"
113 (string-append man "/aragorn.1")))
115 (home-page "http://mbio-serv2.mbioekol.lu.se/ARAGORN")
116 (synopsis "Detect tRNA, mtRNA and tmRNA genes in nucleotide sequences")
118 "Aragorn identifies transfer RNA, mitochondrial RNA and
119 transfer-messenger RNA from nucleotide sequences, based on homology to known
120 tRNA consensus sequences and RNA structure. It also outputs the secondary
121 structure of the predicted RNA.")
122 (license license:gpl2)))
124 (define-public bamtools
131 "https://github.com/pezmaster31/bamtools/archive/v"
133 (file-name (string-append name "-" version ".tar.gz"))
136 "1brry29bw2xr2l9pqn240rkqwayg85b8qq78zk2zs6nlspk4d018"))))
137 (build-system cmake-build-system)
139 `(#:tests? #f ;no "check" target
141 (modify-phases %standard-phases
143 'configure 'set-ldflags
144 (lambda* (#:key outputs #:allow-other-keys)
148 (assoc-ref outputs "out") "/lib/bamtools")))))))
149 (inputs `(("zlib" ,zlib)))
150 (home-page "https://github.com/pezmaster31/bamtools")
151 (synopsis "C++ API and command-line toolkit for working with BAM data")
153 "BamTools provides both a C++ API and a command-line toolkit for handling
155 (license license:expat)))
157 (define-public bedops
163 (uri (string-append "https://github.com/bedops/bedops/archive/v"
165 (file-name (string-append name "-" version ".tar.gz"))
168 "1kqbac547wyqma81cyky9n7mkgikjpsfd3nnmcm6hpqwanqgh10v"))))
169 (build-system gnu-build-system)
172 #:make-flags (list (string-append "BINDIR=" %output "/bin"))
175 'unpack 'unpack-tarballs
177 ;; FIXME: Bedops includes tarballs of minimally patched upstream
178 ;; libraries jansson, zlib, and bzip2. We cannot just use stock
179 ;; libraries because at least one of the libraries (zlib) is
180 ;; patched to add a C++ function definition (deflateInit2cpp).
181 ;; Until the Bedops developers offer a way to link against system
182 ;; libraries we have to build the in-tree copies of these three
185 ;; See upstream discussion:
186 ;; https://github.com/bedops/bedops/issues/124
188 ;; Unpack the tarballs to benefit from shebang patching.
189 (with-directory-excursion "third-party"
190 (and (zero? (system* "tar" "xvf" "jansson-2.6.tar.bz2"))
191 (zero? (system* "tar" "xvf" "zlib-1.2.7.tar.bz2"))
192 (zero? (system* "tar" "xvf" "bzip2-1.0.6.tar.bz2"))))
193 ;; Disable unpacking of tarballs in Makefile.
194 (substitute* "system.mk/Makefile.linux"
195 (("^\tbzcat .*") "\t@echo \"not unpacking\"\n")
196 (("\\./configure") "CONFIG_SHELL=bash ./configure"))
197 (substitute* "third-party/zlib-1.2.7/Makefile.in"
198 (("^SHELL=.*$") "SHELL=bash\n")))
199 (alist-delete 'configure %standard-phases))))
200 (home-page "https://github.com/bedops/bedops")
201 (synopsis "Tools for high-performance genomic feature operations")
203 "BEDOPS is a suite of tools to address common questions raised in genomic
204 studies---mostly with regard to overlap and proximity relationships between
205 data sets. It aims to be scalable and flexible, facilitating the efficient
206 and accurate analysis and management of large-scale genomic data.
208 BEDOPS provides tools that perform highly efficient and scalable Boolean and
209 other set operations, statistical calculations, archiving, conversion and
210 other management of genomic data of arbitrary scale. Tasks can be easily
211 split by chromosome for distributing whole-genome analyses across a
212 computational cluster.")
213 (license license:gpl2+)))
215 (define-public bedtools
221 (uri (string-append "https://github.com/arq5x/bedtools2/archive/v"
223 (file-name (string-append name "-" version ".tar.gz"))
226 "1ywcy3yfwzhl905b51l0ffjia55h75vv3mw5xkvib04pp6pj548m"))))
227 (build-system gnu-build-system)
228 (native-inputs `(("python" ,python-2)))
229 (inputs `(("samtools" ,samtools)
232 '(#:test-target "test"
234 (modify-phases %standard-phases
237 (lambda* (#:key outputs #:allow-other-keys)
238 (let ((bin (string-append (assoc-ref outputs "out") "/bin/")))
239 (for-each (lambda (file)
240 (install-file file bin))
241 (find-files "bin" ".*")))
243 (home-page "https://github.com/arq5x/bedtools2")
244 (synopsis "Tools for genome analysis and arithmetic")
246 "Collectively, the bedtools utilities are a swiss-army knife of tools for
247 a wide-range of genomics analysis tasks. The most widely-used tools enable
248 genome arithmetic: that is, set theory on the genome. For example, bedtools
249 allows one to intersect, merge, count, complement, and shuffle genomic
250 intervals from multiple files in widely-used genomic file formats such as BAM,
252 (license license:gpl2)))
254 (define-public bioawk
260 (uri (string-append "https://github.com/lh3/bioawk/archive/v"
262 (file-name (string-append name "-" version ".tar.gz"))
264 (base32 "1daizxsk17ahi9n58fj8vpgwyhzrzh54bzqhanjanp88kgrz7gjw"))))
265 (build-system gnu-build-system)
271 `(#:tests? #f ; There are no tests to run.
272 ;; Bison must generate files, before other targets can build.
275 (modify-phases %standard-phases
276 (delete 'configure) ; There is no configure phase.
278 (lambda* (#:key outputs #:allow-other-keys)
279 (let* ((out (assoc-ref outputs "out"))
280 (bin (string-append out "/bin"))
281 (man (string-append out "/share/man/man1")))
283 (copy-file "awk.1" (string-append man "/bioawk.1"))
284 (install-file "bioawk" bin)))))))
285 (home-page "https://github.com/lh3/bioawk")
286 (synopsis "AWK with bioinformatics extensions")
287 (description "Bioawk is an extension to Brian Kernighan's awk, adding the
288 support of several common biological data formats, including optionally gzip'ed
289 BED, GFF, SAM, VCF, FASTA/Q and TAB-delimited formats with column names. It
290 also adds a few built-in functions and a command line option to use TAB as the
291 input/output delimiter. When the new functionality is not used, bioawk is
292 intended to behave exactly the same as the original BWK awk.")
293 (license license:x11)))
295 (define-public python2-pybedtools
297 (name "python2-pybedtools")
302 "https://pypi.python.org/packages/source/p/pybedtools/pybedtools-"
306 "1ldzdxw1p4y3g2ignmggsdypvqkcwqwzhdha4rbgpih048z5p4an"))))
307 (build-system python-build-system)
308 (arguments `(#:python ,python-2)) ; no Python 3 support
310 `(("python-cython" ,python2-cython)
311 ("python-matplotlib" ,python2-matplotlib)))
313 `(("bedtools" ,bedtools)
314 ("samtools" ,samtools)))
316 `(("python-pyyaml" ,python2-pyyaml)
317 ("python-nose" ,python2-nose)
318 ("python-setuptools" ,python2-setuptools)))
319 (home-page "https://pythonhosted.org/pybedtools/")
320 (synopsis "Python wrapper for BEDtools programs")
322 "pybedtools is a Python wrapper for Aaron Quinlan's BEDtools programs,
323 which are widely used for genomic interval manipulation or \"genome algebra\".
324 pybedtools extends BEDTools by offering feature-level manipulations from with
326 (license license:gpl2+)))
328 (define-public bioperl-minimal
329 (let* ((inputs `(("perl-module-build" ,perl-module-build)
330 ("perl-data-stag" ,perl-data-stag)
331 ("perl-libwww" ,perl-libwww)
332 ("perl-uri" ,perl-uri)))
334 (map (compose package-name cadr)
337 (map (compose package-transitive-target-inputs cadr) inputs))))))
339 (name "bioperl-minimal")
344 (uri (string-append "mirror://cpan/authors/id/C/CJ/CJFIELDS/BioPerl-"
348 "1l3npcvvvwjlhkna9dndpfv1hklhrgva013kw96m0n1wpd37ask1"))))
349 (build-system perl-build-system)
352 (modify-phases %standard-phases
354 'install 'wrap-programs
355 (lambda* (#:key outputs #:allow-other-keys)
356 ;; Make sure all executables in "bin" find the required Perl
357 ;; modules at runtime. As the PERL5LIB variable contains also
358 ;; the paths of native inputs, we pick the transitive target
359 ;; inputs from %build-inputs.
360 (let* ((out (assoc-ref outputs "out"))
361 (bin (string-append out "/bin/"))
363 (cons (string-append out "/lib/perl5/site_perl")
365 (assoc-ref %build-inputs name))
366 ',transitive-inputs))
368 (for-each (lambda (file)
370 `("PERL5LIB" ":" prefix (,path))))
371 (find-files bin "\\.pl$"))
375 `(("perl-test-most" ,perl-test-most)))
376 (home-page "http://search.cpan.org/dist/BioPerl")
377 (synopsis "Bioinformatics toolkit")
379 "BioPerl is the product of a community effort to produce Perl code which
380 is useful in biology. Examples include Sequence objects, Alignment objects
381 and database searching objects. These objects not only do what they are
382 advertised to do in the documentation, but they also interact - Alignment
383 objects are made from the Sequence objects, Sequence objects have access to
384 Annotation and SeqFeature objects and databases, Blast objects can be
385 converted to Alignment objects, and so on. This means that the objects
386 provide a coordinated and extensible framework to do computational biology.")
387 (license (package-license perl)))))
389 (define-public python-biopython
391 (name "python-biopython")
395 ;; use PyPi rather than biopython.org to ease updating
396 (uri (pypi-uri "biopython" version))
399 "1gdv92593klimg22icf5j9by7xiq86jnwzkpz4abaa05ylkdf6hp"))))
400 (build-system python-build-system)
402 `(("python-numpy" ,python-numpy)))
404 `(("python-setuptools" ,python2-setuptools)))
405 (home-page "http://biopython.org/")
406 (synopsis "Tools for biological computation in Python")
408 "Biopython is a set of tools for biological computation including parsers
409 for bioinformatics files into Python data structures; interfaces to common
410 bioinformatics programs; a standard sequence class and tools for performing
411 common operations on them; code to perform data classification; code for
412 dealing with alignments; code making it easy to split up parallelizable tasks
413 into separate processes; and more.")
414 (license (license:non-copyleft "http://www.biopython.org/DIST/LICENSE"))))
416 (define-public python2-biopython
417 (package (inherit (package-with-python2 python-biopython))
419 `(("python2-numpy" ,python2-numpy)))))
421 (define-public blast+
428 "ftp://ftp.ncbi.nlm.nih.gov/blast/executables/blast+/"
429 version "/ncbi-blast-" version "+-src.tar.gz"))
432 "19gq6as4k1jrgsd26158ads6h7v4jca3h4r5dzg1y0m6ya50x5ph"))
433 (modules '((guix build utils)))
436 ;; Remove bundled bzip2 and zlib
437 (delete-file-recursively "c++/src/util/compress/bzip2")
438 (delete-file-recursively "c++/src/util/compress/zlib")
439 (substitute* "c++/src/util/compress/Makefile.in"
440 (("bzip2 zlib api") "api"))
441 ;; Remove useless msbuild directory
442 (delete-file-recursively
443 "c++/src/build-system/project_tree_builder/msbuild")
445 (build-system gnu-build-system)
447 `(;; There are three(!) tests for this massive library, and all fail with
448 ;; "unparsable timing stats".
449 ;; ERR [127] -- [util/regexp] test_pcre.sh (unparsable timing stats)
450 ;; ERR [127] -- [serial/datatool] datatool.sh (unparsable timing stats)
451 ;; ERR [127] -- [serial/datatool] datatool_xml.sh (unparsable timing stats)
454 #:parallel-build? #f ; not supported
456 (modify-phases %standard-phases
459 ;; $HOME needs to be set at some point during the configure phase
460 (lambda _ (setenv "HOME" "/tmp") #t))
463 (lambda _ (chdir "c++") #t))
465 'enter-dir 'fix-build-system
468 (cond ((string=? cmd "date")
469 ;; make call to "date" deterministic
474 (format (current-error-port)
475 "WARNING: Unable to find absolute path for ~s~%"
479 ;; Rewrite hardcoded paths to various tools
480 (substitute* (append '("src/build-system/configure.ac"
481 "src/build-system/configure"
482 "scripts/common/impl/if_diff.sh"
483 "scripts/common/impl/run_with_lock.sh"
484 "src/build-system/Makefile.configurables.real"
485 "src/build-system/Makefile.in.top"
486 "src/build-system/Makefile.meta.gmake=no"
487 "src/build-system/Makefile.meta.in"
488 "src/build-system/Makefile.meta_l"
489 "src/build-system/Makefile.meta_p"
490 "src/build-system/Makefile.meta_r"
491 "src/build-system/Makefile.mk.in"
492 "src/build-system/Makefile.requirements"
493 "src/build-system/Makefile.rules_with_autodep.in")
494 (find-files "scripts/common/check" "\\.sh$"))
495 (("(/usr/bin/|/bin/)([a-z][-_.a-z]*)" all dir cmd)
496 (or (which* cmd) all)))
498 (substitute* (find-files "src/build-system" "^config.*")
499 (("LN_S=/bin/\\$LN_S") (string-append "LN_S=" (which "ln")))
502 ;; rewrite "/var/tmp" in check script
503 (substitute* "scripts/common/check/check_make_unix.sh"
504 (("/var/tmp") "/tmp"))
507 (substitute* (find-files "scripts/common/impl/" "\\.sh$")
509 (("action=/bin/") "action=")
510 (("export PATH") ":"))
514 (lambda* (#:key inputs outputs #:allow-other-keys)
515 (let ((out (assoc-ref outputs "out"))
516 (lib (string-append (assoc-ref outputs "lib") "/lib"))
517 (include (string-append (assoc-ref outputs "include")
518 "/include/ncbi-tools++")))
519 ;; The 'configure' script doesn't recognize things like
520 ;; '--enable-fast-install'.
521 (zero? (system* "./configure.orig"
522 (string-append "--with-build-root=" (getcwd) "/build")
523 (string-append "--prefix=" out)
524 (string-append "--libdir=" lib)
525 (string-append "--includedir=" include)
526 (string-append "--with-bz2="
527 (assoc-ref inputs "bzip2"))
528 (string-append "--with-z="
529 (assoc-ref inputs "zlib"))
530 ;; Each library is built twice by default, once
531 ;; with "-static" in its name, and again
535 (outputs '("out" ; 19 MB
543 (home-page "http://blast.ncbi.nlm.nih.gov")
544 (synopsis "Basic local alignment search tool")
546 "BLAST is a popular method of performing a DNA or protein sequence
547 similarity search, using heuristics to produce results quickly. It also
548 calculates an “expect value” that estimates how many matches would have
549 occurred at a given score by chance, which can aid a user in judging how much
550 confidence to have in an alignment.")
551 ;; Most of the sources are in the public domain, with the following
554 ;; * ./c++/include/util/bitset/
555 ;; * ./c++/src/html/ncbi_menu*.js
557 ;; * ./c++/include/util/impl/floating_point_comparison.hpp
559 ;; * ./c++/include/dbapi/driver/odbc/unix_odbc/
561 ;; * ./c++/src/corelib/teamcity_*
562 (license (list license:public-domain
574 (uri (string-append "mirror://sourceforge/bless-ec/bless.v"
578 "0rm0gw2s18dqwzzpl3c2x1z05ni2v0xz5dmfk3d33j6g4cgrlrdd"))
579 (modules '((guix build utils)))
582 ;; Remove bundled boost, pigz, zlib, and .git directory
583 ;; FIXME: also remove bundled sources for murmurhash3 and
584 ;; kmc once packaged.
585 (delete-file-recursively "boost")
586 (delete-file-recursively "pigz")
587 (delete-file-recursively "google-sparsehash")
588 (delete-file-recursively "zlib")
589 (delete-file-recursively ".git")
591 (build-system gnu-build-system)
593 '(#:tests? #f ;no "check" target
595 (list (string-append "ZLIB="
596 (assoc-ref %build-inputs "zlib")
598 (string-append "LDFLAGS="
599 (string-join '("-lboost_filesystem"
606 (modify-phases %standard-phases
607 (add-after 'unpack 'do-not-build-bundled-pigz
608 (lambda* (#:key inputs outputs #:allow-other-keys)
609 (substitute* "Makefile"
610 (("cd pigz/pigz-2.3.3; make") ""))
612 (add-after 'unpack 'patch-paths-to-executables
613 (lambda* (#:key inputs outputs #:allow-other-keys)
614 (substitute* "parse_args.cpp"
616 (string-append "kmc_binary = \""
617 (assoc-ref outputs "out")
619 (("pigz_binary = .*")
620 (string-append "pigz_binary = \""
621 (assoc-ref inputs "pigz")
625 (lambda* (#:key outputs #:allow-other-keys)
626 (let ((bin (string-append (assoc-ref outputs "out") "/bin/")))
627 (for-each (lambda (file)
628 (install-file file bin))
629 '("bless" "kmc/bin/kmc"))
631 (delete 'configure))))
635 `(("openmpi" ,openmpi)
637 ("sparsehash" ,sparsehash)
640 (supported-systems '("x86_64-linux"))
641 (home-page "http://sourceforge.net/p/bless-ec/wiki/Home/")
642 (synopsis "Bloom-filter-based error correction tool for NGS reads")
644 "@dfn{Bloom-filter-based error correction solution for high-throughput
645 sequencing reads} (BLESS) uses a single minimum-sized bloom filter is a
646 correction tool for genomic reads produced by @dfn{Next-generation
647 sequencing} (NGS). BLESS produces accurate correction results with much less
648 memory compared with previous solutions and is also able to tolerate a higher
649 false-positive rate. BLESS can extend reads like DNA assemblers to correct
650 errors at the end of reads.")
651 (license license:gpl3+)))
653 (define-public bowtie
659 (uri (string-append "https://github.com/BenLangmead/bowtie2/archive/v"
661 (file-name (string-append name "-" version ".tar.gz"))
664 "1ssfvymxfrap6f9pf86s9bvsbqdgka4abr2r7j3mgr4w1l289m86"))
665 (modules '((guix build utils)))
667 '(substitute* "Makefile"
668 ;; replace BUILD_HOST and BUILD_TIME for deterministic build
669 (("-DBUILD_HOST=.*") "-DBUILD_HOST=\"\\\"guix\\\"\"")
670 (("-DBUILD_TIME=.*") "-DBUILD_TIME=\"\\\"0\\\"\"")))))
671 (build-system gnu-build-system)
672 (inputs `(("perl" ,perl)
673 ("perl-clone" ,perl-clone)
674 ("perl-test-deep" ,perl-test-deep)
675 ("perl-test-simple" ,perl-test-simple)
682 (string-append "prefix=" (assoc-ref %outputs "out")))
688 (lambda* (#:key outputs #:allow-other-keys)
690 "scripts/test/simple_tests.pl"
691 "--bowtie2=./bowtie2"
692 "--bowtie2-build=./bowtie2-build"))
694 (home-page "http://bowtie-bio.sourceforge.net/bowtie2/index.shtml")
695 (synopsis "Fast and sensitive nucleotide sequence read aligner")
697 "Bowtie 2 is a fast and memory-efficient tool for aligning sequencing
698 reads to long reference sequences. It is particularly good at aligning reads
699 of about 50 up to 100s or 1,000s of characters, and particularly good at
700 aligning to relatively long (e.g. mammalian) genomes. Bowtie 2 indexes the
701 genome with an FM Index to keep its memory footprint small: for the human
702 genome, its memory footprint is typically around 3.2 GB. Bowtie 2 supports
703 gapped, local, and paired-end alignment modes.")
704 (supported-systems '("x86_64-linux"))
705 (license license:gpl3+)))
707 (define-public tophat
714 "http://ccb.jhu.edu/software/tophat/downloads/tophat-"
718 "168zlzykq622zbgkh90a90f1bdgsxkscq2zxzbj8brq80hbjpyp7"))
719 (patches (search-patches "tophat-build-with-later-seqan.patch"))
720 (modules '((guix build utils)))
723 ;; Remove bundled SeqAn and samtools
724 (delete-file-recursively "src/SeqAn-1.3")
725 (delete-file-recursively "src/samtools-0.1.18")
727 (build-system gnu-build-system)
729 '(#:parallel-build? #f ; not supported
731 (modify-phases %standard-phases
732 (add-after 'unpack 'use-system-samtools
733 (lambda* (#:key inputs #:allow-other-keys)
734 (substitute* "src/Makefile.in"
735 (("(noinst_LIBRARIES = )\\$\\(SAMLIB\\)" _ prefix) prefix)
736 (("\\$\\(SAMPROG\\): \\$\\(SAMLIB\\)") "")
737 (("SAMPROG = samtools_0\\.1\\.18") "")
738 (("\\$\\(samtools_0_1_18_SOURCES\\)") "")
739 (("am__EXEEXT_1 = samtools_0\\.1\\.18\\$\\(EXEEXT\\)") ""))
740 (substitute* '("src/common.cpp"
742 (("samtools_0.1.18") (which "samtools")))
743 (substitute* '("src/common.h"
745 (("#include \"bam.h\"") "#include <samtools/bam.h>")
746 (("#include \"sam.h\"") "#include <samtools/sam.h>"))
747 (substitute* '("src/bwt_map.h"
749 "src/align_status.h")
750 (("#include <bam.h>") "#include <samtools/bam.h>")
751 (("#include <sam.h>") "#include <samtools/sam.h>"))
756 ("samtools" ,samtools-0.1)
762 (home-page "http://ccb.jhu.edu/software/tophat/index.shtml")
763 (synopsis "Spliced read mapper for RNA-Seq data")
765 "TopHat is a fast splice junction mapper for nucleotide sequence
766 reads produced by the RNA-Seq method. It aligns RNA-Seq reads to
767 mammalian-sized genomes using the ultra high-throughput short read
768 aligner Bowtie, and then analyzes the mapping results to identify
769 splice junctions between exons.")
770 ;; TopHat is released under the Boost Software License, Version 1.0
771 ;; See https://github.com/infphilo/tophat/issues/11#issuecomment-121589893
772 (license license:boost1.0)))
780 (uri (string-append "mirror://sourceforge/bio-bwa/bwa-"
784 "1330dpqncv0px3pbhjzz1gwgg39kkcv2r9qp2xs0sixf8z8wl7bh"))))
785 (build-system gnu-build-system)
787 '(#:tests? #f ;no "check" target
791 (lambda* (#:key outputs #:allow-other-keys)
792 (let ((bin (string-append
793 (assoc-ref outputs "out") "/bin"))
795 (assoc-ref outputs "out") "/share/doc/bwa"))
797 (assoc-ref outputs "out") "/share/man/man1")))
801 (install-file "bwa" bin)
802 (install-file "README.md" doc)
803 (install-file "bwa.1" man)))
804 ;; no "configure" script
805 (alist-delete 'configure %standard-phases))))
806 (inputs `(("zlib" ,zlib)))
807 ;; Non-portable SSE instructions are used so building fails on platforms
808 ;; other than x86_64.
809 (supported-systems '("x86_64-linux"))
810 (home-page "http://bio-bwa.sourceforge.net/")
811 (synopsis "Burrows-Wheeler sequence aligner")
813 "BWA is a software package for mapping low-divergent sequences against a
814 large reference genome, such as the human genome. It consists of three
815 algorithms: BWA-backtrack, BWA-SW and BWA-MEM. The first algorithm is
816 designed for Illumina sequence reads up to 100bp, while the rest two for
817 longer sequences ranged from 70bp to 1Mbp. BWA-MEM and BWA-SW share similar
818 features such as long-read support and split alignment, but BWA-MEM, which is
819 the latest, is generally recommended for high-quality queries as it is faster
820 and more accurate. BWA-MEM also has better performance than BWA-backtrack for
821 70-100bp Illumina reads.")
822 (license license:gpl3+)))
824 (define-public bwa-pssm
825 (package (inherit bwa)
830 (uri (string-append "https://github.com/pkerpedjiev/bwa-pssm/"
831 "archive/" version ".tar.gz"))
832 (file-name (string-append name "-" version ".tar.gz"))
835 "02p7mpbs4mlxmn84g2x4ghak638vbj4lqix2ipx5g84pz9bhdavg"))))
836 (build-system gnu-build-system)
841 (home-page "http://bwa-pssm.binf.ku.dk/")
842 (synopsis "Burrows-Wheeler transform-based probabilistic short read mapper")
844 "BWA-PSSM is a probabilistic short genomic sequence read aligner based on
845 the use of @dfn{position specific scoring matrices} (PSSM). Like many of the
846 existing aligners it is fast and sensitive. Unlike most other aligners,
847 however, it is also adaptible in the sense that one can direct the alignment
848 based on known biases within the data set. It is coded as a modification of
849 the original BWA alignment program and shares the genome index structure as
850 well as many of the command line options.")
851 (license license:gpl3+)))
853 (define-public python2-bx-python
855 (name "python2-bx-python")
860 "https://pypi.python.org/packages/source/b/bx-python/bx-python-"
864 "0ld49idhc5zjdvbhvjq1a2qmpjj7h5v58rqr25dzmfq7g34b50xh"))
865 (modules '((guix build utils)))
867 '(substitute* "setup.py"
868 ;; remove dependency on outdated "distribute" module
869 (("^from distribute_setup import use_setuptools") "")
870 (("^use_setuptools\\(\\)") "")))))
871 (build-system python-build-system)
873 `(#:tests? #f ;tests fail because test data are not included
876 `(("python-numpy" ,python2-numpy)
879 `(("python-nose" ,python2-nose)
880 ("python-setuptools" ,python2-setuptools)))
881 (home-page "http://bitbucket.org/james_taylor/bx-python/")
882 (synopsis "Tools for manipulating biological data")
884 "bx-python provides tools for manipulating biological data, particularly
885 multiple sequence alignments.")
886 (license license:expat)))
888 (define-public python-pysam
890 (name "python-pysam")
894 (uri (pypi-uri "pysam" version))
897 "1slx5mb94mzm5qzk52q270sab0sar95j67w1g1k452nz3s9j7krh"))))
898 (build-system python-build-system)
900 `(#:tests? #f ; tests are excluded in the manifest
905 (setenv "LDFLAGS" "-lncurses")
906 (setenv "CFLAGS" "-D_CURSES_LIB=1"))
909 `(("ncurses" ,ncurses)
912 `(("python-cython" ,python-cython)
913 ("python-setuptools" ,python-setuptools)))
914 (home-page "https://github.com/pysam-developers/pysam")
915 (synopsis "Python bindings to the SAMtools C API")
917 "Pysam is a Python module for reading and manipulating files in the
918 SAM/BAM format. Pysam is a lightweight wrapper of the SAMtools C API. It
919 also includes an interface for tabix.")
920 (license license:expat)))
922 (define-public python2-pysam
923 (package-with-python2 python-pysam))
925 (define-public python-twobitreader
927 (name "python-twobitreader")
931 (uri (pypi-uri "twobitreader" version))
934 "0y408fp6psqzwxpcpqn0wp7fr41dwz8d54wpj6j261fj5q8vs169"))))
935 (properties `((python2-variant . ,(delay python2-twobitreader))))
936 (build-system python-build-system)
938 `(("python-sphinx" ,python-sphinx)))
939 (home-page "https://github.com/benjschiller/twobitreader")
940 (synopsis "Python library for reading .2bit files")
942 "twobitreader is a Python library for reading .2bit files as used by the
943 UCSC genome browser.")
944 (license license:artistic2.0)))
946 (define-public python2-twobitreader
947 (let ((base (package-with-python2 (strip-python2-variant python-twobitreader))))
950 (native-inputs `(("python2-setuptools" ,python2-setuptools)
951 ,@(package-native-inputs base))))))
953 (define-public python-plastid
955 (name "python-plastid")
959 (uri (pypi-uri "plastid" version))
962 "1nhxw8a5gn9as58i2ih52c5cjwj48ik418pzsjwph3s66mmy9yvq"))))
963 (properties `((python2-variant . ,(delay python2-plastid))))
964 (build-system python-build-system)
966 ;; Some test files are not included.
969 `(("python-numpy" ,python-numpy)
970 ("python-scipy" ,python-scipy)
971 ("python-pandas" ,python-pandas)
972 ("python-pysam" ,python-pysam)
973 ("python-matplotlib" ,python-matplotlib)
974 ("python-biopython" ,python-biopython)
975 ("python-twobitreader" ,python-twobitreader)))
977 `(("python-cython" ,python-cython)
978 ("python-nose" ,python-nose)))
979 (home-page "https://github.com/joshuagryphon/plastid")
980 (synopsis "Python library for genomic analysis")
982 "plastid is a Python library for genomic analysis – in particular,
983 high-throughput sequencing data – with an emphasis on simplicity.")
984 (license license:bsd-3)))
986 (define-public python2-plastid
987 (let ((base (package-with-python2 (strip-python2-variant python-plastid))))
990 ;; setuptools is required at runtime
991 (propagated-inputs `(("python2-setuptools" ,python2-setuptools)
992 ,@(package-propagated-inputs base))))))
994 (define-public cd-hit
1000 (uri (string-append "https://github.com/weizhongli/cdhit"
1001 "/releases/download/V" version
1002 "/cd-hit-v" version "-2016-0304.tar.gz"))
1005 "15db0hq38yyifwqx9b6l34z14jcq576dmjavhj8a426c18lvnhp3"))))
1006 (build-system gnu-build-system)
1008 `(#:tests? #f ; there are no tests
1010 ;; Executables are copied directly to the PREFIX.
1011 (list (string-append "PREFIX=" (assoc-ref %outputs "out") "/bin"))
1013 (modify-phases %standard-phases
1014 ;; No "configure" script
1016 ;; Remove sources of non-determinism
1017 (add-after 'unpack 'be-timeless
1019 (substitute* "cdhit-utility.c++"
1020 ((" \\(built on \" __DATE__ \"\\)") ""))
1021 (substitute* "cdhit-common.c++"
1022 (("__DATE__") "\"0\"")
1023 (("\", %s, \" __TIME__ \"\\\\n\", date") ""))
1025 ;; The "install" target does not create the target directory
1026 (add-before 'install 'create-target-dir
1027 (lambda* (#:key outputs #:allow-other-keys)
1028 (mkdir-p (string-append (assoc-ref outputs "out") "/bin"))
1032 (home-page "http://weizhongli-lab.org/cd-hit/")
1033 (synopsis "Cluster and compare protein or nucleotide sequences")
1035 "CD-HIT is a program for clustering and comparing protein or nucleotide
1036 sequences. CD-HIT is designed to be fast and handle extremely large
1038 ;; The manual says: "It can be copied under the GNU General Public License
1039 ;; version 2 (GPLv2)."
1040 (license license:gpl2)))
1042 (define-public clipper
1049 "https://github.com/YeoLab/clipper/archive/"
1051 (file-name (string-append name "-" version ".tar.gz"))
1054 "1q7jpimsqln7ic44i8v2rx2haj5wvik8hc1s2syd31zcn0xk1iyq"))
1055 (modules '((guix build utils)))
1057 ;; remove unnecessary setup dependency
1058 '(substitute* "setup.py"
1059 (("setup_requires = .*") "")))))
1060 (build-system python-build-system)
1061 (arguments `(#:python ,python-2)) ; only Python 2 is supported
1064 ("python-pybedtools" ,python2-pybedtools)
1065 ("python-cython" ,python2-cython)
1066 ("python-scikit-learn" ,python2-scikit-learn)
1067 ("python-matplotlib" ,python2-matplotlib)
1068 ("python-pysam" ,python2-pysam)
1069 ("python-numpy" ,python2-numpy)
1070 ("python-scipy" ,python2-scipy)))
1072 `(("python-mock" ,python2-mock) ; for tests
1073 ("python-pytz" ,python2-pytz) ; for tests
1074 ("python-setuptools" ,python2-setuptools)))
1075 (home-page "https://github.com/YeoLab/clipper")
1076 (synopsis "CLIP peak enrichment recognition")
1078 "CLIPper is a tool to define peaks in CLIP-seq datasets.")
1079 (license license:gpl2)))
1081 (define-public codingquarry
1083 (name "codingquarry")
1088 "mirror://sourceforge/codingquarry/CodingQuarry_v"
1092 "0115hkjflsnfzn36xppwf9h9avfxlavr43djqmshkkzbgjzsz60i"))))
1093 (build-system gnu-build-system)
1095 '(#:tests? #f ; no "check" target
1097 (modify-phases %standard-phases
1100 (lambda* (#:key outputs #:allow-other-keys)
1101 (let* ((out (assoc-ref outputs "out"))
1102 (bin (string-append out "/bin"))
1103 (doc (string-append out "/share/doc/codingquarry")))
1104 (install-file "INSTRUCTIONS.pdf" doc)
1105 (copy-recursively "QuarryFiles"
1106 (string-append out "/QuarryFiles"))
1107 (install-file "CodingQuarry" bin)
1108 (install-file "CufflinksGTF_to_CodingQuarryGFF3.py" bin)))))))
1109 (inputs `(("openmpi" ,openmpi)))
1110 (native-search-paths
1111 (list (search-path-specification
1112 (variable "QUARRY_PATH")
1113 (files '("QuarryFiles")))))
1114 (native-inputs `(("python" ,python-2))) ; Only Python 2 is supported
1115 (synopsis "Fungal gene predictor")
1116 (description "CodingQuarry is a highly accurate, self-training GHMM fungal
1117 gene predictor designed to work with assembled, aligned RNA-seq transcripts.")
1118 (home-page "https://sourceforge.net/projects/codingquarry/")
1119 (license license:gpl3+)))
1121 (define-public couger
1128 "http://couger.oit.duke.edu/static/assets/COUGER"
1132 "04p2b14nmhzxw5h72mpzdhalv21bx4w9b87z0wpw0xzxpysyncmq"))))
1133 (build-system gnu-build-system)
1137 (modify-phases %standard-phases
1142 (lambda* (#:key outputs #:allow-other-keys)
1143 (let ((out (assoc-ref outputs "out")))
1144 (copy-recursively "src" (string-append out "/src"))
1145 (mkdir (string-append out "/bin"))
1146 ;; Add "src" directory to module lookup path.
1147 (substitute* "couger"
1149 (string-append "import sys\nsys.path.append(\""
1150 out "\")\nfrom argparse")))
1151 (copy-file "couger" (string-append out "/bin/couger")))
1154 'install 'wrap-program
1155 (lambda* (#:key inputs outputs #:allow-other-keys)
1156 ;; Make sure 'couger' runs with the correct PYTHONPATH.
1157 (let* ((out (assoc-ref outputs "out"))
1158 (path (getenv "PYTHONPATH")))
1159 (wrap-program (string-append out "/bin/couger")
1160 `("PYTHONPATH" ":" prefix (,path))))
1163 `(("python" ,python-2)
1164 ("python2-pillow" ,python2-pillow)
1165 ("python2-numpy" ,python2-numpy)
1166 ("python2-scipy" ,python2-scipy)
1167 ("python2-matplotlib" ,python2-matplotlib)))
1171 ("randomjungle" ,randomjungle)))
1173 `(("unzip" ,unzip)))
1174 (home-page "http://couger.oit.duke.edu")
1175 (synopsis "Identify co-factors in sets of genomic regions")
1177 "COUGER can be applied to any two sets of genomic regions bound by
1178 paralogous TFs (e.g., regions derived from ChIP-seq experiments) to identify
1179 putative co-factors that provide specificity to each TF. The framework
1180 determines the genomic targets uniquely-bound by each TF, and identifies a
1181 small set of co-factors that best explain the in vivo binding differences
1182 between the two TFs.
1184 COUGER uses classification algorithms (support vector machines and random
1185 forests) with features that reflect the DNA binding specificities of putative
1186 co-factors. The features are generated either from high-throughput TF-DNA
1187 binding data (from protein binding microarray experiments), or from large
1188 collections of DNA motifs.")
1189 (license license:gpl3+)))
1191 (define-public clustal-omega
1193 (name "clustal-omega")
1198 "http://www.clustal.org/omega/clustal-omega-"
1202 "02ibkx0m0iwz8nscg998bh41gg251y56cgh86bvyrii5m8kjgwqf"))))
1203 (build-system gnu-build-system)
1205 `(("argtable" ,argtable)))
1206 (home-page "http://www.clustal.org/omega/")
1207 (synopsis "Multiple sequence aligner for protein and DNA/RNA")
1209 "Clustal-Omega is a general purpose multiple sequence alignment (MSA)
1210 program for protein and DNA/RNA. It produces high quality MSAs and is capable
1211 of handling data-sets of hundreds of thousands of sequences in reasonable
1213 (license license:gpl2+)))
1215 (define-public crossmap
1221 (uri (string-append "mirror://sourceforge/crossmap/CrossMap-"
1225 "07y179f63d7qnzdvkqcziwk9bs3k4zhp81q392fp1hwszjdvy22f"))
1226 ;; This patch has been sent upstream already and is available
1227 ;; for download from Sourceforge, but it has not been merged.
1228 (patches (search-patches "crossmap-allow-system-pysam.patch"))
1229 (modules '((guix build utils)))
1230 ;; remove bundled copy of pysam
1232 '(delete-file-recursively "lib/pysam"))))
1233 (build-system python-build-system)
1235 `(#:python ,python-2
1239 (lambda _ (setenv "CROSSMAP_USE_SYSTEM_PYSAM" "1"))
1242 `(("python-numpy" ,python2-numpy)
1243 ("python-pysam" ,python2-pysam)
1246 `(("python-cython" ,python2-cython)
1247 ("python-nose" ,python2-nose)
1248 ("python-setuptools" ,python2-setuptools)))
1249 (home-page "http://crossmap.sourceforge.net/")
1250 (synopsis "Convert genome coordinates between assemblies")
1252 "CrossMap is a program for conversion of genome coordinates or annotation
1253 files between different genome assemblies. It supports most commonly used
1254 file formats including SAM/BAM, Wiggle/BigWig, BED, GFF/GTF, VCF.")
1255 (license license:gpl2+)))
1257 (define-public cufflinks
1263 (uri (string-append "http://cole-trapnell-lab.github.io/"
1264 "cufflinks/assets/downloads/cufflinks-"
1268 "1bnm10p8m7zq4qiipjhjqb24csiqdm1pwc8c795z253r2xk6ncg8"))))
1269 (build-system gnu-build-system)
1273 ;; The includes for "eigen" are located in a subdirectory.
1274 (string-append "EIGEN_CPPFLAGS="
1275 "-I" (assoc-ref %build-inputs "eigen")
1277 ;; Cufflinks must be linked with various boost libraries.
1278 (string-append "LDFLAGS="
1279 (string-join '("-lboost_system"
1280 "-lboost_serialization"
1281 "-lboost_thread"))))
1283 (modify-phases %standard-phases
1284 (add-after 'unpack 'fix-search-for-bam
1286 (substitute* '("ax_bam.m4"
1289 (("<bam/sam\\.h>") "<samtools/sam.h>")
1290 (("<bam/bam\\.h>") "<samtools/bam.h>")
1291 (("<bam/version\\.hpp>") "<samtools/version.h>"))
1294 (list (string-append "--with-bam="
1295 (assoc-ref %build-inputs "samtools")))))
1298 ("samtools" ,samtools-0.1)
1301 ("python" ,python-2)
1303 (home-page "http://cole-trapnell-lab.github.io/cufflinks/")
1304 (synopsis "Transcriptome assembly and RNA-Seq expression analysis")
1306 "Cufflinks assembles RNA transcripts, estimates their abundances,
1307 and tests for differential expression and regulation in RNA-Seq
1308 samples. It accepts aligned RNA-Seq reads and assembles the
1309 alignments into a parsimonious set of transcripts. Cufflinks then
1310 estimates the relative abundances of these transcripts based on how
1311 many reads support each one, taking into account biases in library
1312 preparation protocols.")
1313 (license license:boost1.0)))
1315 (define-public cutadapt
1322 "https://github.com/marcelm/cutadapt/archive/v"
1324 (file-name (string-append name "-" version ".tar.gz"))
1327 "161bp87y6gd6r5bmvjpn2b1k942i3fizfpa139f0jn6jv1wcp5h5"))))
1328 (build-system python-build-system)
1330 ;; tests must be run after install
1331 `(#:phases (alist-cons-after
1333 (lambda* (#:key inputs outputs #:allow-other-keys)
1334 (setenv "PYTHONPATH"
1336 (getenv "PYTHONPATH")
1337 ":" (assoc-ref outputs "out")
1339 (string-take (string-take-right
1340 (assoc-ref inputs "python") 5) 3)
1342 (zero? (system* "nosetests" "-P" "tests")))
1343 (alist-delete 'check %standard-phases))))
1345 `(("python-cython" ,python-cython)
1346 ("python-nose" ,python-nose)
1347 ("python-setuptools" ,python-setuptools)))
1348 (home-page "https://code.google.com/p/cutadapt/")
1349 (synopsis "Remove adapter sequences from nucleotide sequencing reads")
1351 "Cutadapt finds and removes adapter sequences, primers, poly-A tails and
1352 other types of unwanted sequence from high-throughput sequencing reads.")
1353 (license license:expat)))
1355 (define-public libbigwig
1361 (uri (string-append "https://github.com/dpryan79/libBigWig/"
1362 "archive/" version ".tar.gz"))
1363 (file-name (string-append name "-" version ".tar.gz"))
1366 "098rjh35pi4a9q83n8wiwvyzykjqj6l8q189p1xgfw4ghywdlvw1"))))
1367 (build-system gnu-build-system)
1369 `(#:test-target "test"
1372 (string-append "prefix=" (assoc-ref %outputs "out")))
1374 (modify-phases %standard-phases
1376 (add-before 'check 'disable-curl-test
1378 (substitute* "Makefile"
1379 (("./test/testRemote.*") ""))
1381 ;; This has been fixed with the upstream commit 4ff6959cd8a0, but
1382 ;; there has not yet been a release containing this change.
1383 (add-before 'install 'create-target-dirs
1384 (lambda* (#:key outputs #:allow-other-keys)
1385 (let ((out (assoc-ref outputs "out")))
1386 (mkdir-p (string-append out "/lib"))
1387 (mkdir-p (string-append out "/include"))
1393 `(("doxygen" ,doxygen)))
1394 (home-page "https://github.com/dpryan79/libBigWig")
1395 (synopsis "C library for handling bigWig files")
1397 "This package provides a C library for parsing local and remote BigWig
1399 (license license:expat)))
1401 (define-public python-pybigwig
1403 (name "python-pybigwig")
1407 (uri (pypi-uri "pyBigWig" version))
1410 "0yrpdxg3y0sny25x4w22lv1k47jzccqjmg7j4bp0hywklvp0hg7d"))
1411 (modules '((guix build utils)))
1414 ;; Delete bundled libBigWig sources
1415 (delete-file-recursively "libBigWig")))))
1416 (build-system python-build-system)
1419 (modify-phases %standard-phases
1420 (add-after 'unpack 'link-with-libBigWig
1421 (lambda* (#:key inputs #:allow-other-keys)
1422 (substitute* "setup.py"
1423 (("libs=\\[") "libs=[\"BigWig\", "))
1426 `(("libbigwig" ,libbigwig)
1429 (home-page "https://github.com/dpryan79/pyBigWig")
1430 (synopsis "Access bigWig files in Python using libBigWig")
1432 "This package provides Python bindings to the libBigWig library for
1433 accessing bigWig files.")
1434 (license license:expat)))
1436 (define-public python2-pybigwig
1437 (let ((pybigwig (package-with-python2 python-pybigwig)))
1438 (package (inherit pybigwig)
1440 `(("python-setuptools" ,python2-setuptools))))))
1442 (define-public deeptools
1448 (uri (string-append "https://github.com/fidelram/deepTools/"
1449 "archive/" version ".tar.gz"))
1450 (file-name (string-append name "-" version ".tar.gz"))
1453 "1nmfin0zjdby3vay3r4flvz94dr6qjhj41ax4yz3vx13j6wz8izd"))))
1454 (build-system python-build-system)
1456 `(#:python ,python-2))
1458 `(("python-scipy" ,python2-scipy)
1459 ("python-numpy" ,python2-numpy)
1460 ("python-numpydoc" ,python2-numpydoc)
1461 ("python-matplotlib" ,python2-matplotlib)
1462 ("python-bx-python" ,python2-bx-python)
1463 ("python-pysam" ,python2-pysam)
1464 ("python-pybigwig" ,python2-pybigwig)))
1466 `(("python-mock" ,python2-mock) ;for tests
1467 ("python-pytz" ,python2-pytz) ;for tests
1468 ("python-setuptools" ,python2-setuptools)))
1469 (home-page "https://github.com/fidelram/deepTools")
1470 (synopsis "Tools for normalizing and visualizing deep-sequencing data")
1472 "DeepTools addresses the challenge of handling the large amounts of data
1473 that are now routinely generated from DNA sequencing centers. To do so,
1474 deepTools contains useful modules to process the mapped reads data to create
1475 coverage files in standard bedGraph and bigWig file formats. By doing so,
1476 deepTools allows the creation of normalized coverage files or the comparison
1477 between two files (for example, treatment and control). Finally, using such
1478 normalized and standardized files, multiple visualizations can be created to
1479 identify enrichments with functional annotations of the genome.")
1480 (license license:gpl3+)))
1482 (define-public diamond
1489 "https://github.com/bbuchfink/diamond/archive/v"
1491 (file-name (string-append name "-" version ".tar.gz"))
1494 "0hfkcfv9f76h5brbyw9fyvmc0l9cmbsxrcdqk0fa9xv82zj47p15"))
1496 (delete-file "bin/diamond")
1498 (build-system gnu-build-system)
1500 '(#:tests? #f ;no "check" target
1502 (modify-phases %standard-phases
1503 (add-after 'unpack 'enter-source-dir
1509 (lambda* (#:key outputs #:allow-other-keys)
1510 (let ((bin (string-append (assoc-ref outputs "out")
1513 (copy-file "../bin/diamond"
1514 (string-append bin "/diamond"))
1521 (home-page "https://github.com/bbuchfink/diamond")
1522 (synopsis "Accelerated BLAST compatible local sequence aligner")
1524 "DIAMOND is a BLAST-compatible local aligner for mapping protein and
1525 translated DNA query sequences against a protein reference database (BLASTP
1526 and BLASTX alignment mode). The speedup over BLAST is up to 20,000 on short
1527 reads at a typical sensitivity of 90-99% relative to BLAST depending on the
1528 data and settings.")
1529 ;; diamond fails to build on other platforms
1530 ;; https://github.com/bbuchfink/diamond/issues/18
1531 (supported-systems '("x86_64-linux"))
1532 (license (license:non-copyleft "file://src/COPYING"
1533 "See src/COPYING in the distribution."))))
1535 (define-public edirect
1541 (uri (string-append "ftp://ftp.ncbi.nlm.nih.gov/entrez/entrezdirect/"
1542 "versions/2016-05-03/edirect.tar.gz"))
1545 "15zsprak5yh8c1yrz4r1knmb5s8qcmdid4xdhkh3lqcv64l60hli"))))
1546 (build-system perl-build-system)
1548 `(#:tests? #f ;no "check" target
1550 (modify-phases %standard-phases
1554 (lambda* (#:key outputs #:allow-other-keys)
1555 (let ((target (string-append (assoc-ref outputs "out")
1558 (copy-file "edirect.pl"
1559 (string-append target "/edirect.pl"))
1562 'install 'wrap-program
1563 (lambda* (#:key inputs outputs #:allow-other-keys)
1564 ;; Make sure 'edirect.pl' finds all perl inputs at runtime.
1565 (let* ((out (assoc-ref outputs "out"))
1566 (path (getenv "PERL5LIB")))
1567 (wrap-program (string-append out "/bin/edirect.pl")
1568 `("PERL5LIB" ":" prefix (,path)))))))))
1570 `(("perl-html-parser" ,perl-html-parser)
1571 ("perl-encode-locale" ,perl-encode-locale)
1572 ("perl-file-listing" ,perl-file-listing)
1573 ("perl-html-tagset" ,perl-html-tagset)
1574 ("perl-html-tree" ,perl-html-tree)
1575 ("perl-http-cookies" ,perl-http-cookies)
1576 ("perl-http-date" ,perl-http-date)
1577 ("perl-http-message" ,perl-http-message)
1578 ("perl-http-negotiate" ,perl-http-negotiate)
1579 ("perl-lwp-mediatypes" ,perl-lwp-mediatypes)
1580 ("perl-lwp-protocol-https" ,perl-lwp-protocol-https)
1581 ("perl-net-http" ,perl-net-http)
1582 ("perl-uri" ,perl-uri)
1583 ("perl-www-robotrules" ,perl-www-robotrules)
1585 (home-page "http://www.ncbi.nlm.nih.gov/books/NBK179288/")
1586 (synopsis "Tools for accessing the NCBI's set of databases")
1588 "Entrez Direct (EDirect) is a method for accessing the National Center
1589 for Biotechnology Information's (NCBI) set of interconnected
1590 databases (publication, sequence, structure, gene, variation, expression,
1591 etc.) from a terminal. Functions take search terms from command-line
1592 arguments. Individual operations are combined to build multi-step queries.
1593 Record retrieval and formatting normally complete the process.
1595 EDirect also provides an argument-driven function that simplifies the
1596 extraction of data from document summaries or other results that are returned
1597 in structured XML format. This can eliminate the need for writing custom
1598 software to answer ad hoc questions.")
1599 (license license:public-domain)))
1601 (define-public express
1609 "http://bio.math.berkeley.edu/eXpress/downloads/express-"
1610 version "/express-" version "-src.tgz"))
1613 "03rczxd0gjp2l1jxcmjfmf5j94j77zqyxa6x063zsc585nj40n0c"))))
1614 (build-system cmake-build-system)
1616 `(#:tests? #f ;no "check" target
1619 'unpack 'use-shared-boost-libs-and-set-bamtools-paths
1620 (lambda* (#:key inputs #:allow-other-keys)
1621 (substitute* "CMakeLists.txt"
1622 (("set\\(Boost_USE_STATIC_LIBS ON\\)")
1623 "set(Boost_USE_STATIC_LIBS OFF)")
1624 (("\\$\\{CMAKE_CURRENT_SOURCE_DIR\\}/bamtools/include")
1625 (string-append (assoc-ref inputs "bamtools") "/include/bamtools")))
1626 (substitute* "src/CMakeLists.txt"
1627 (("\\$\\{CMAKE_CURRENT_SOURCE_DIR\\}/\\.\\./bamtools/lib")
1628 (string-append (assoc-ref inputs "bamtools") "/lib/bamtools")))
1633 ("bamtools" ,bamtools)
1634 ("protobuf" ,protobuf)
1636 (home-page "http://bio.math.berkeley.edu/eXpress")
1637 (synopsis "Streaming quantification for high-throughput genomic sequencing")
1639 "eXpress is a streaming tool for quantifying the abundances of a set of
1640 target sequences from sampled subsequences. Example applications include
1641 transcript-level RNA-Seq quantification, allele-specific/haplotype expression
1642 analysis (from RNA-Seq), transcription factor binding quantification in
1643 ChIP-Seq, and analysis of metagenomic data.")
1644 (license license:artistic2.0)))
1646 (define-public express-beta-diversity
1648 (name "express-beta-diversity")
1654 "https://github.com/dparks1134/ExpressBetaDiversity/archive/v"
1656 (file-name (string-append name "-" version ".tar.gz"))
1659 "1djvdlmqvjf6h0zq7w36y8cl5cli6rgj86x65znl48agnwmzxfxr"))))
1660 (build-system gnu-build-system)
1663 (modify-phases %standard-phases
1665 (add-before 'build 'enter-source (lambda _ (chdir "source") #t))
1667 (lambda _ (zero? (system* "../bin/ExpressBetaDiversity"
1669 (add-after 'check 'exit-source (lambda _ (chdir "..") #t))
1671 (lambda* (#:key outputs #:allow-other-keys)
1672 (let ((bin (string-append (assoc-ref outputs "out")
1675 (copy-file "scripts/convertToEBD.py"
1676 (string-append bin "/convertToEBD.py"))
1677 (copy-file "bin/ExpressBetaDiversity"
1678 (string-append bin "/ExpressBetaDiversity"))
1681 `(("python" ,python-2)))
1682 (home-page "http://kiwi.cs.dal.ca/Software/ExpressBetaDiversity")
1683 (synopsis "Taxon- and phylogenetic-based beta diversity measures")
1685 "Express Beta Diversity (EBD) calculates ecological beta diversity
1686 (dissimilarity) measures between biological communities. EBD implements a
1687 variety of diversity measures including those that make use of phylogenetic
1688 similarity of community members.")
1689 (license license:gpl3+)))
1691 (define-public fasttree
1698 "http://www.microbesonline.org/fasttree/FastTree-"
1702 "0dzqc9vr9iiiw21y159xfjl2z90vw0y7r4x6456pcaxiy5hd2wmi"))))
1703 (build-system gnu-build-system)
1705 `(#:tests? #f ; no "check" target
1707 (modify-phases %standard-phases
1711 (lambda* (#:key source #:allow-other-keys)
1712 (and (zero? (system* "gcc"
1714 "-finline-functions"
1721 (zero? (system* "gcc"
1725 "-finline-functions"
1733 (lambda* (#:key outputs #:allow-other-keys)
1734 (let ((bin (string-append (assoc-ref outputs "out")
1737 (copy-file "FastTree"
1738 (string-append bin "/FastTree"))
1739 (copy-file "FastTreeMP"
1740 (string-append bin "/FastTreeMP"))
1742 (home-page "http://www.microbesonline.org/fasttree")
1743 (synopsis "Infers approximately-maximum-likelihood phylogenetic trees")
1745 "FastTree can handle alignments with up to a million of sequences in a
1746 reasonable amount of time and memory. For large alignments, FastTree is
1747 100-1,000 times faster than PhyML 3.0 or RAxML 7.")
1748 (license license:gpl2+)))
1750 (define-public fastx-toolkit
1752 (name "fastx-toolkit")
1758 "https://github.com/agordon/fastx_toolkit/releases/download/"
1759 version "/fastx_toolkit-" version ".tar.bz2"))
1762 "01jqzw386873sr0pjp1wr4rn8fsga2vxs1qfmicvx1pjr72007wy"))))
1763 (build-system gnu-build-system)
1765 `(("libgtextutils" ,libgtextutils)))
1767 `(("pkg-config" ,pkg-config)))
1768 (home-page "http://hannonlab.cshl.edu/fastx_toolkit/")
1769 (synopsis "Tools for FASTA/FASTQ file preprocessing")
1771 "The FASTX-Toolkit is a collection of command line tools for Short-Reads
1772 FASTA/FASTQ files preprocessing.
1774 Next-Generation sequencing machines usually produce FASTA or FASTQ files,
1775 containing multiple short-reads sequences. The main processing of such
1776 FASTA/FASTQ files is mapping the sequences to reference genomes. However, it
1777 is sometimes more productive to preprocess the files before mapping the
1778 sequences to the genome---manipulating the sequences to produce better mapping
1779 results. The FASTX-Toolkit tools perform some of these preprocessing tasks.")
1780 (license license:agpl3+)))
1782 (define-public flexbar
1789 (string-append "mirror://sourceforge/flexbar/"
1790 version "/flexbar_v" version "_src.tgz"))
1793 "13jaykc3y1x8y5nn9j8ljnb79s5y51kyxz46hdmvvjj6qhyympmf"))))
1794 (build-system cmake-build-system)
1796 `(#:configure-flags (list
1797 (string-append "-DFLEXBAR_BINARY_DIR="
1798 (assoc-ref %outputs "out")
1803 (lambda* (#:key outputs #:allow-other-keys)
1804 (setenv "PATH" (string-append
1805 (assoc-ref outputs "out") "/bin:"
1807 (chdir "../flexbar_v2.5_src/test")
1808 (zero? (system* "bash" "flexbar_validate.sh")))
1809 (alist-delete 'install %standard-phases))))
1814 `(("pkg-config" ,pkg-config)
1816 (home-page "http://flexbar.sourceforge.net")
1817 (synopsis "Barcode and adapter removal tool for sequencing platforms")
1819 "Flexbar preprocesses high-throughput nucleotide sequencing data
1820 efficiently. It demultiplexes barcoded runs and removes adapter sequences.
1821 Moreover, trimming and filtering features are provided. Flexbar increases
1822 read mapping rates and improves genome and transcriptome assemblies. It
1823 supports next-generation sequencing data in fasta/q and csfasta/q format from
1824 Illumina, Roche 454, and the SOLiD platform.")
1825 (license license:gpl3)))
1827 (define-public fraggenescan
1829 (name "fraggenescan")
1835 (string-append "mirror://sourceforge/fraggenescan/"
1836 "FragGeneScan" version ".tar.gz"))
1838 (base32 "1zzigqmvqvjyqv4945kv6nc5ah2xxm1nxgrlsnbzav3f5c0n0pyj"))))
1839 (build-system gnu-build-system)
1842 (modify-phases %standard-phases
1844 (add-before 'build 'patch-paths
1845 (lambda* (#:key outputs #:allow-other-keys)
1846 (let* ((out (string-append (assoc-ref outputs "out")))
1847 (share (string-append out "/share/fraggenescan/")))
1848 (substitute* "run_FragGeneScan.pl"
1850 (string-append "system(\"" (which "rm")))
1852 (string-append "system(\"" (which "mv")))
1853 ;; This script and other programs expect the training files
1854 ;; to be in the non-standard location bin/train/XXX. Change
1855 ;; this to be share/fraggenescan/train/XXX instead.
1856 (("^\\$train.file = \\$dir.*")
1857 (string-append "$train_file = \""
1859 "train/\".$FGS_train_file;")))
1860 (substitute* "run_hmm.c"
1861 (("^ strcat\\(train_dir, \\\"train/\\\"\\);")
1862 (string-append " strcpy(train_dir, \"" share "/train/\");")))
1863 (substitute* "post_process.pl"
1864 (("^my \\$dir = substr.*")
1865 (string-append "my $dir = \"" share "\";"))))
1868 (lambda _ (and (zero? (system* "make" "clean"))
1869 (zero? (system* "make" "fgs")))))
1871 (lambda* (#:key outputs #:allow-other-keys)
1872 (let* ((out (string-append (assoc-ref outputs "out")))
1873 (bin (string-append out "/bin/"))
1874 (share (string-append out "/share/fraggenescan/train")))
1875 (install-file "run_FragGeneScan.pl" bin)
1876 (install-file "FragGeneScan" bin)
1877 (install-file "FGS_gff.py" bin)
1878 (install-file "post_process.pl" bin)
1879 (copy-recursively "train" share))))
1881 (add-after 'install 'post-install-check
1882 ;; In lieu of 'make check', run one of the examples and check the
1883 ;; output files gets created.
1884 (lambda* (#:key outputs #:allow-other-keys)
1885 (let* ((out (string-append (assoc-ref outputs "out")))
1886 (bin (string-append out "/bin/")))
1887 (and (zero? (system* (string-append bin "run_FragGeneScan.pl")
1888 "-genome=./example/NC_000913.fna"
1892 (file-exists? "test2.faa")
1893 (file-exists? "test2.ffn")
1894 (file-exists? "test2.gff")
1895 (file-exists? "test2.out"))))))))
1898 ("python" ,python-2))) ;not compatible with python 3.
1899 (home-page "https://sourceforge.net/projects/fraggenescan/")
1900 (synopsis "Finds potentially fragmented genes in short reads")
1902 "FragGeneScan is a program for predicting bacterial and archaeal genes in
1903 short and error-prone DNA sequencing reads. It can also be applied to predict
1904 genes in incomplete assemblies or complete genomes.")
1905 ;; GPL3+ according to private correspondense with the authors.
1906 (license license:gpl3+)))
1908 (define-public fxtract
1909 (let ((util-commit "776ca85a18a47492af3794745efcb4a905113115"))
1917 "https://github.com/ctSkennerton/fxtract/archive/"
1919 (file-name (string-append "ctstennerton-util-"
1920 (string-take util-commit 7)
1924 "0275cfdhis8517hm01is62062swmi06fxzifq7mr3knbbxjlaiwj"))))
1925 (build-system gnu-build-system)
1927 `(#:make-flags (list
1928 (string-append "PREFIX=" (assoc-ref %outputs "out"))
1930 #:test-target "fxtract_test"
1932 (modify-phases %standard-phases
1934 (add-before 'build 'copy-util
1935 (lambda* (#:key inputs #:allow-other-keys)
1937 (copy-recursively (assoc-ref inputs "ctskennerton-util") "util")
1939 ;; Do not use make install as this requires additional dependencies.
1941 (lambda* (#:key outputs #:allow-other-keys)
1942 (let* ((out (assoc-ref outputs "out"))
1943 (bin (string-append out"/bin")))
1944 (install-file "fxtract" bin)
1950 ;; ctskennerton-util is licensed under GPL2.
1951 `(("ctskennerton-util"
1955 (url "https://github.com/ctSkennerton/util.git")
1956 (commit util-commit)))
1957 (file-name (string-append
1958 "ctstennerton-util-" util-commit "-checkout"))
1961 "0cls1hd4vgj3f36fpzzg4xc77d6f3hpc60cbpfmn2gdr7ykzzad7"))))))
1962 (home-page "https://github.com/ctSkennerton/fxtract")
1963 (synopsis "Extract sequences from FASTA and FASTQ files")
1965 "Fxtract extracts sequences from a protein or nucleotide fastx (FASTA
1966 or FASTQ) file given a subsequence. It uses a simple substring search for
1967 basic tasks but can change to using POSIX regular expressions, PCRE, hash
1968 lookups or multi-pattern searching as required. By default fxtract looks in
1969 the sequence of each record but can also be told to look in the header,
1970 comment or quality sections.")
1971 (license license:expat))))
1980 "https://github.com/nboley/grit/archive/"
1982 (file-name (string-append name "-" version ".tar.gz"))
1985 "157in84dj70wimbind3x7sy1whs3h57qfgcnj2s6lrd38fbrb7mj"))))
1986 (build-system python-build-system)
1988 `(#:python ,python-2
1991 'unpack 'generate-from-cython-sources
1992 (lambda* (#:key inputs outputs #:allow-other-keys)
1993 ;; Delete these C files to force fresh generation from pyx sources.
1994 (delete-file "grit/sparsify_support_fns.c")
1995 (delete-file "grit/call_peaks_support_fns.c")
1996 (substitute* "setup.py"
1997 (("Cython.Setup") "Cython.Build")
1998 ;; Add numpy include path to fix compilation
2000 (string-append "pyx\", ], include_dirs = ['"
2001 (assoc-ref inputs "python-numpy")
2002 "/lib/python2.7/site-packages/numpy/core/include/"
2006 `(("python-scipy" ,python2-scipy)
2007 ("python-numpy" ,python2-numpy)
2008 ("python-pysam" ,python2-pysam)
2009 ("python-networkx" ,python2-networkx)))
2011 `(("python-cython" ,python2-cython)
2012 ("python-setuptools" ,python2-setuptools)))
2013 (home-page "http://grit-bio.org")
2014 (synopsis "Tool for integrative analysis of RNA-seq type assays")
2016 "GRIT is designed to use RNA-seq, TES, and TSS data to build and quantify
2017 full length transcript models. When none of these data sources are available,
2018 GRIT can be run by providing a candidate set of TES or TSS sites. In
2019 addition, GRIT can merge in reference junctions and gene boundaries. GRIT can
2020 also be run in quantification mode, where it uses a provided GTF file and just
2021 estimates transcript expression.")
2022 (license license:gpl3+)))
2024 (define-public hisat
2031 "http://ccb.jhu.edu/software/hisat/downloads/hisat-"
2032 version "-beta-source.zip"))
2035 "1k381ydranqxp09yf2y7w1d0chz5d59vb6jchi89hbb0prq19lk5"))))
2036 (build-system gnu-build-system)
2038 `(#:tests? #f ;no check target
2039 #:make-flags '("allall"
2040 ;; Disable unsupported `popcnt' instructions on
2041 ;; architectures other than x86_64
2042 ,@(if (string-prefix? "x86_64"
2043 (or (%current-target-system)
2046 '("POPCNT_CAPABILITY=0")))
2049 'unpack 'patch-sources
2051 ;; XXX Cannot use snippet because zip files are not supported
2052 (substitute* "Makefile"
2053 (("^CC = .*$") "CC = gcc")
2054 (("^CPP = .*$") "CPP = g++")
2055 ;; replace BUILD_HOST and BUILD_TIME for deterministic build
2056 (("-DBUILD_HOST=.*") "-DBUILD_HOST=\"\\\"guix\\\"\"")
2057 (("-DBUILD_TIME=.*") "-DBUILD_TIME=\"\\\"0\\\"\""))
2058 (substitute* '("hisat-build" "hisat-inspect")
2059 (("/usr/bin/env") (which "env"))))
2062 (lambda* (#:key outputs #:allow-other-keys)
2063 (let ((bin (string-append (assoc-ref outputs "out") "/bi/")))
2064 (for-each (lambda (file)
2065 (install-file file bin))
2068 "hisat(-(build|align|inspect)(-(s|l)(-debug)*)*)*$"))))
2069 (alist-delete 'configure %standard-phases)))))
2071 `(("unzip" ,unzip)))
2076 ;; Non-portable SSE instructions are used so building fails on platforms
2077 ;; other than x86_64.
2078 (supported-systems '("x86_64-linux"))
2079 (home-page "http://ccb.jhu.edu/software/hisat/index.shtml")
2080 (synopsis "Hierarchical indexing for spliced alignment of transcripts")
2082 "HISAT is a fast and sensitive spliced alignment program for mapping
2083 RNA-seq reads. In addition to one global FM index that represents a whole
2084 genome, HISAT uses a large set of small FM indexes that collectively cover the
2085 whole genome. These small indexes (called local indexes) combined with
2086 several alignment strategies enable effective alignment of RNA-seq reads, in
2087 particular, reads spanning multiple exons.")
2088 (license license:gpl3+)))
2090 (define-public hmmer
2097 "http://selab.janelia.org/software/hmmer"
2098 (version-prefix version 1) "/"
2099 version "/hmmer-" version ".tar.gz"))
2102 "0djmgc0pfli0jilfx8hql1axhwhqxqb8rxg2r5rg07aw73sfs5nx"))))
2103 (build-system gnu-build-system)
2104 (native-inputs `(("perl" ,perl)))
2105 (home-page "http://hmmer.janelia.org")
2106 (synopsis "Biosequence analysis using profile hidden Markov models")
2108 "HMMER is used for searching sequence databases for homologs of protein
2109 sequences, and for making protein sequence alignments. It implements methods
2110 using probabilistic models called profile hidden Markov models (profile
2112 (license (list license:gpl3+
2113 ;; The bundled library 'easel' is distributed
2114 ;; under The Janelia Farm Software License.
2115 (license:non-copyleft
2116 "file://easel/LICENSE"
2117 "See easel/LICENSE in the distribution.")))))
2119 (define-public htseq
2126 "https://pypi.python.org/packages/source/H/HTSeq/HTSeq-"
2130 "1i85ppf2j2lj12m0x690qq5nn17xxk23pbbx2c83r8ayb5wngzwv"))))
2131 (build-system python-build-system)
2132 (arguments `(#:python ,python-2)) ; only Python 2 is supported
2133 ;; Numpy needs to be propagated when htseq is used as a Python library.
2135 `(("python-numpy" ,python2-numpy)))
2137 `(("python-pysam" ,python2-pysam)))
2139 `(("python-setuptools" ,python2-setuptools)))
2140 (home-page "http://www-huber.embl.de/users/anders/HTSeq/")
2141 (synopsis "Analysing high-throughput sequencing data with Python")
2143 "HTSeq is a Python package that provides infrastructure to process data
2144 from high-throughput sequencing assays.")
2145 (license license:gpl3+)))
2147 (define-public java-htsjdk
2149 (name "java-htsjdk")
2154 "https://github.com/samtools/htsjdk/archive/"
2156 (file-name (string-append name "-" version ".tar.gz"))
2159 "0asdk9b8jx2ij7yd6apg9qx03li8q7z3ml0qy2r2qczkra79y6fw"))
2160 (modules '((guix build utils)))
2161 ;; remove build dependency on git
2162 (snippet '(substitute* "build.xml"
2163 (("failifexecutionfails=\"true\"")
2164 "failifexecutionfails=\"false\"")))))
2165 (build-system ant-build-system)
2167 `(#:tests? #f ; test require Internet access
2169 (list (string-append "-Ddist=" (assoc-ref %outputs "out")
2170 "/share/java/htsjdk/"))
2171 #:build-target "all"
2173 (modify-phases %standard-phases
2174 ;; The build phase also installs the jars
2175 (delete 'install))))
2176 (home-page "http://samtools.github.io/htsjdk/")
2177 (synopsis "Java API for high-throughput sequencing data (HTS) formats")
2179 "HTSJDK is an implementation of a unified Java library for accessing
2180 common file formats, such as SAM and VCF, used for high-throughput
2181 sequencing (HTS) data. There are also an number of useful utilities for
2182 manipulating HTS data.")
2183 (license license:expat)))
2185 (define-public htslib
2192 "https://github.com/samtools/htslib/releases/download/"
2193 version "/htslib-" version ".tar.bz2"))
2196 "1c32ssscbnjwfw3dra140fq7riarp2x990qxybh34nr1p5r17nxx"))))
2197 (build-system gnu-build-system)
2200 (modify-phases %standard-phases
2202 'unpack 'patch-tests
2204 (substitute* "test/test.pl"
2205 (("/bin/bash") (which "bash")))
2211 (home-page "http://www.htslib.org")
2212 (synopsis "C library for reading/writing high-throughput sequencing data")
2214 "HTSlib is a C library for reading/writing high-throughput sequencing
2215 data. It also provides the bgzip, htsfile, and tabix utilities.")
2216 ;; Files under cram/ are released under the modified BSD license;
2217 ;; the rest is released under the Expat license
2218 (license (list license:expat license:bsd-3))))
2227 "https://github.com/nboley/idr/archive/"
2229 (file-name (string-append name "-" version ".tar.gz"))
2232 "1k3x44biak00aiv3hpm1yd6nn4hhp7n0qnbs3zh2q9sw7qr1qj5r"))))
2233 (build-system python-build-system)
2236 (modify-phases %standard-phases
2238 'install 'wrap-program
2239 (lambda* (#:key inputs outputs #:allow-other-keys)
2240 (let* ((out (assoc-ref outputs "out"))
2241 (python-version (string-take (string-take-right
2242 (assoc-ref inputs "python") 5) 3))
2245 (string-append (assoc-ref inputs name)
2246 "/lib/python" python-version
2250 "python-matplotlib"))
2252 (wrap-program (string-append out "/bin/idr")
2253 `("PYTHONPATH" ":" prefix (,path))))
2256 `(("python-scipy" ,python-scipy)
2257 ("python-numpy" ,python-numpy)
2258 ("python-matplotlib" ,python-matplotlib)))
2260 `(("python-cython" ,python-cython)
2261 ("python-setuptools" ,python-setuptools)))
2262 (home-page "https://github.com/nboley/idr")
2263 (synopsis "Tool to measure the irreproducible discovery rate (IDR)")
2265 "The IDR (Irreproducible Discovery Rate) framework is a unified approach
2266 to measure the reproducibility of findings identified from replicate
2267 experiments and provide highly stable thresholds based on reproducibility.")
2268 (license license:gpl3+)))
2270 (define-public jellyfish
2276 (uri (string-append "https://github.com/gmarcais/Jellyfish/"
2277 "releases/download/v" version
2278 "/jellyfish-" version ".tar.gz"))
2281 "0a6xnynqy2ibfbfz86b9g2m2dgm7f1469pmymkpam333gi3p26nk"))))
2282 (build-system gnu-build-system)
2283 (outputs '("out" ;for library
2284 "ruby" ;for Ruby bindings
2285 "python")) ;for Python bindings
2288 (list (string-append "--enable-ruby-binding="
2289 (assoc-ref %outputs "ruby"))
2290 (string-append "--enable-python-binding="
2291 (assoc-ref %outputs "python")))
2293 (modify-phases %standard-phases
2294 (add-before 'check 'set-SHELL-variable
2296 ;; generator_manager.hpp either uses /bin/sh or $SHELL
2298 (setenv "SHELL" (which "bash"))
2304 ("python" ,python-2)))
2305 (synopsis "Tool for fast counting of k-mers in DNA")
2307 "Jellyfish is a tool for fast, memory-efficient counting of k-mers in
2308 DNA. A k-mer is a substring of length k, and counting the occurrences of all
2309 such substrings is a central step in many analyses of DNA sequence. Jellyfish
2310 is a command-line program that reads FASTA and multi-FASTA files containing
2311 DNA sequences. It outputs its k-mer counts in a binary format, which can be
2312 translated into a human-readable text format using the @code{jellyfish dump}
2313 command, or queried for specific k-mers with @code{jellyfish query}.")
2314 (home-page "http://www.genome.umd.edu/jellyfish.html")
2315 ;; The combined work is published under the GPLv3 or later. Individual
2316 ;; files such as lib/jsoncpp.cpp are released under the Expat license.
2317 (license (list license:gpl3+ license:expat))))
2322 (version "2.1.0.20151222")
2325 (uri (pypi-uri "MACS2" version))
2328 "1r2hcz6irhcq7lwbafjks98jbn34hv05avgbdjnp6w6mlfjkf8x5"))))
2329 (build-system python-build-system)
2331 `(#:python ,python-2 ; only compatible with Python 2.7
2332 #:tests? #f)) ; no test target
2334 `(("python-numpy" ,python2-numpy)))
2336 `(("python-setuptools" ,python2-setuptools)))
2337 (home-page "http://github.com/taoliu/MACS/")
2338 (synopsis "Model based analysis for ChIP-Seq data")
2340 "MACS is an implementation of a ChIP-Seq analysis algorithm for
2341 identifying transcript factor binding sites named Model-based Analysis of
2342 ChIP-Seq (MACS). MACS captures the influence of genome complexity to evaluate
2343 the significance of enriched ChIP regions and it improves the spatial
2344 resolution of binding sites through combining the information of both
2345 sequencing tag position and orientation.")
2346 (license license:bsd-3)))
2348 (define-public mafft
2355 "http://mafft.cbrc.jp/alignment/software/mafft-" version
2356 "-without-extensions-src.tgz"))
2357 (file-name (string-append name "-" version ".tgz"))
2360 "1xl6xq1rfxkws0svrlhyqxhhwbv6r77jwblsdpcyiwzsscw6wlk0"))))
2361 (build-system gnu-build-system)
2363 `(#:tests? #f ; no automated tests, though there are tests in the read me
2364 #:make-flags (let ((out (assoc-ref %outputs "out")))
2365 (list (string-append "PREFIX=" out)
2366 (string-append "BINDIR="
2367 (string-append out "/bin"))))
2369 (modify-phases %standard-phases
2370 (add-after 'unpack 'enter-dir
2371 (lambda _ (chdir "core") #t))
2372 (add-after 'enter-dir 'patch-makefile
2374 ;; on advice from the MAFFT authors, there is no need to
2375 ;; distribute mafft-profile, mafft-distance, or
2376 ;; mafft-homologs.rb as they are too "specialised".
2377 (substitute* "Makefile"
2378 ;; remove mafft-homologs.rb from SCRIPTS
2379 (("^SCRIPTS = mafft mafft-homologs.rb")
2381 ;; remove mafft-homologs from MANPAGES
2382 (("^MANPAGES = mafft.1 mafft-homologs.1")
2383 "MANPAGES = mafft.1")
2384 ;; remove mafft-distance from PROGS
2385 (("^PROGS = dvtditr dndfast7 dndblast sextet5 mafft-distance")
2386 "PROGS = dvtditr dndfast7 dndblast sextet5")
2387 ;; remove mafft-profile from PROGS
2388 (("splittbfast disttbfast tbfast mafft-profile 2cl mccaskillwrap")
2389 "splittbfast disttbfast tbfast f2cl mccaskillwrap")
2390 (("^rm -f mafft-profile mafft-profile.exe") "#")
2391 (("^rm -f mafft-distance mafft-distance.exe") ")#")
2392 ;; do not install MAN pages in libexec folder
2393 (("^\t\\$\\(INSTALL\\) -m 644 \\$\\(MANPAGES\\) \
2394 \\$\\(DESTDIR\\)\\$\\(LIBDIR\\)") "#"))
2396 (add-after 'enter-dir 'patch-paths
2397 (lambda* (#:key inputs #:allow-other-keys)
2398 (substitute* '("pairash.c"
2400 (("perl") (which "perl"))
2401 (("([\"`| ])awk" _ prefix)
2402 (string-append prefix (which "awk")))
2403 (("grep") (which "grep")))
2405 (delete 'configure))))
2411 `(("coreutils" ,coreutils)))
2412 (home-page "http://mafft.cbrc.jp/alignment/software/")
2413 (synopsis "Multiple sequence alignment program")
2415 "MAFFT offers a range of multiple alignment methods for nucleotide and
2416 protein sequences. For instance, it offers L-INS-i (accurate; for alignment
2417 of <~200 sequences) and FFT-NS-2 (fast; for alignment of <~30,000
2419 (license (license:non-copyleft
2420 "http://mafft.cbrc.jp/alignment/software/license.txt"
2421 "BSD-3 with different formatting"))))
2423 (define-public metabat
2430 "https://bitbucket.org/berkeleylab/metabat/get/"
2431 version ".tar.bz2"))
2432 (file-name (string-append name "-" version ".tar.bz2"))
2435 "0vgrhbaxg4dkxyax2kbigak7w0arhqvw0szwp6gd9wmyilc44kfa"))))
2436 (build-system gnu-build-system)
2439 (modify-phases %standard-phases
2440 (add-after 'unpack 'fix-includes
2442 (substitute* "SConstruct"
2443 (("/include/bam/bam.h")
2444 "/include/samtools/bam.h"))
2445 (substitute* "src/BamUtils.h"
2446 (("^#include \"bam/bam\\.h\"")
2447 "#include \"samtools/bam.h\"")
2448 (("^#include \"bam/sam\\.h\"")
2449 "#include \"samtools/sam.h\""))
2450 (substitute* "src/KseqReader.h"
2451 (("^#include \"bam/kseq\\.h\"")
2452 "#include \"samtools/kseq.h\""))
2454 (add-after 'unpack 'fix-scons
2456 (substitute* "SConstruct" ; Do not distribute README
2457 (("^env\\.Install\\(idir_prefix, 'README\\.md'\\)")
2462 (lambda* (#:key inputs outputs #:allow-other-keys)
2463 (mkdir (assoc-ref outputs "out"))
2464 (zero? (system* "scons"
2467 (assoc-ref outputs "out"))
2470 (assoc-ref inputs "htslib"))
2473 (assoc-ref inputs "samtools"))
2476 (assoc-ref inputs "boost"))
2478 ;; check and install carried out during build phase
2480 (delete 'install))))
2484 ("samtools" ,samtools)
2488 `(("scons" ,scons)))
2489 (home-page "https://bitbucket.org/berkeleylab/metabat")
2491 "Reconstruction of single genomes from complex microbial communities")
2493 "Grouping large genomic fragments assembled from shotgun metagenomic
2494 sequences to deconvolute complex microbial communities, or metagenome binning,
2495 enables the study of individual organisms and their interactions. MetaBAT is
2496 an automated metagenome binning software, which integrates empirical
2497 probabilistic distances of genome abundance and tetranucleotide frequency.")
2498 (license (license:non-copyleft "file://license.txt"
2499 "See license.txt in the distribution."))))
2508 "https://pypi.python.org/packages/source/m/misopy/misopy-"
2512 "0x446867az8ir0z8c1vjqffkp0ma37wm4sylixnkhgawllzx8v5w"))
2513 (modules '((guix build utils)))
2515 '(substitute* "setup.py"
2516 ;; Use setuptools, or else the executables are not
2518 (("distutils.core") "setuptools")
2519 ;; use "gcc" instead of "cc" for compilation
2521 "cc.set_executables(
2525 linker_so='gcc -shared'); defines")))))
2526 (build-system python-build-system)
2528 `(#:python ,python-2 ; only Python 2 is supported
2529 #:tests? #f)) ; no "test" target
2531 `(("samtools" ,samtools)
2532 ("python-numpy" ,python2-numpy)
2533 ("python-pysam" ,python2-pysam)
2534 ("python-scipy" ,python2-scipy)
2535 ("python-matplotlib" ,python2-matplotlib)))
2537 `(("python-mock" ,python2-mock) ;for tests
2538 ("python-pytz" ,python2-pytz) ;for tests
2539 ("python-setuptools" ,python2-setuptools)))
2540 (home-page "http://genes.mit.edu/burgelab/miso/index.html")
2541 (synopsis "Mixture of Isoforms model for RNA-Seq isoform quantitation")
2543 "MISO (Mixture-of-Isoforms) is a probabilistic framework that quantitates
2544 the expression level of alternatively spliced genes from RNA-Seq data, and
2545 identifies differentially regulated isoforms or exons across samples. By
2546 modeling the generative process by which reads are produced from isoforms in
2547 RNA-Seq, the MISO model uses Bayesian inference to compute the probability
2548 that a read originated from a particular isoform.")
2549 (license license:gpl2)))
2551 (define-public muscle
2554 (version "3.8.1551")
2556 (method url-fetch/tarbomb)
2557 (file-name (string-append name "-" version))
2559 "http://www.drive5.com/muscle/muscle_src_"
2563 "0bj8kj7sdizy3987zx6w7axihk40fk8rn76mpbqqjcnd64i5a367"))))
2564 (build-system gnu-build-system)
2566 `(#:make-flags (list "LDLIBS = -lm")
2568 (modify-phases %standard-phases
2571 ;; There are no tests, so just test if it runs.
2572 (lambda _ (zero? (system* "./muscle" "-version"))))
2574 (lambda* (#:key outputs #:allow-other-keys)
2575 (let* ((out (assoc-ref outputs "out"))
2576 (bin (string-append out "/bin")))
2577 (install-file "muscle" bin)))))))
2578 (home-page "http://www.drive5.com/muscle")
2579 (synopsis "Multiple sequence alignment program")
2581 "MUSCLE aims to be a fast and accurate multiple sequence alignment
2582 program for nucleotide and protein sequences.")
2583 ;; License information found in 'muscle -h' and usage.cpp.
2584 (license license:public-domain)))
2593 "https://github.com/wwood/OrfM/releases/download/v"
2594 version "/orfm-" version ".tar.gz"))
2597 "0vb6d771gl4mix8bwx919x5ayy9pkj44n7ki336nz3rz2rx4c7gk"))))
2598 (build-system gnu-build-system)
2599 (inputs `(("zlib" ,zlib)))
2601 `(("ruby-bio-commandeer" ,ruby-bio-commandeer)
2602 ("ruby-rspec" ,ruby-rspec)
2604 (synopsis "Simple and not slow open reading frame (ORF) caller")
2606 "An ORF caller finds stretches of DNA that, when translated, are not
2607 interrupted by stop codons. OrfM finds and prints these ORFs.")
2608 (home-page "https://github.com/wwood/OrfM")
2609 (license license:lgpl3+)))
2611 (define-public python2-pbcore
2613 (name "python2-pbcore")
2617 (uri (pypi-uri "pbcore" version))
2620 "02pfn5raa3zf739672bg0dkx7z3j2c4nx7vmpfjqy5b12jrqpymk"))))
2621 (build-system python-build-system)
2622 (arguments `(#:python ,python-2)) ; pbcore requires Python 2.7
2624 `(("python-cython" ,python2-cython)
2625 ("python-numpy" ,python2-numpy)
2626 ("python-pysam" ,python2-pysam)
2627 ("python-h5py" ,python2-h5py)))
2629 `(("python-docutils" ,python2-docutils)
2630 ("python-nose" ,python2-nose)
2631 ("python-setuptools" ,python2-setuptools)
2632 ("python-sphinx" ,python2-sphinx)))
2633 (home-page "http://pacificbiosciences.github.io/pbcore/")
2634 (synopsis "Library for reading and writing PacBio data files")
2636 "The pbcore package provides Python APIs for interacting with PacBio data
2637 files and writing bioinformatics applications.")
2638 (license license:bsd-3)))
2640 (define-public python2-warpedlmm
2642 (name "python2-warpedlmm")
2648 "https://pypi.python.org/packages/source/W/WarpedLMM/WarpedLMM-"
2652 "1agfz6zqa8nc6cw47yh0s3y14gkpa9wqazwcj7mwwj3ffnw39p3j"))))
2653 (build-system python-build-system)
2655 `(#:python ,python-2 ; requires Python 2.7
2657 (modify-phases %standard-phases
2659 'install 'remove-bin-directory
2660 (lambda* (#:key outputs #:allow-other-keys)
2661 ;; The "bin" directory only contains wrappers for running
2662 ;; the module tests. They are not needed after the
2664 (delete-file-recursively
2665 (string-append (assoc-ref outputs "out") "/bin"))
2668 `(("python-scipy" ,python2-scipy)
2669 ("python-numpy" ,python2-numpy)
2670 ("python-matplotlib" ,python2-matplotlib)
2671 ("python-fastlmm" ,python2-fastlmm)
2672 ("python-pandas" ,python2-pandas)
2673 ("python-pysnptools" ,python2-pysnptools)))
2675 `(("python-setuptools" ,python2-setuptools)
2676 ("python-mock" ,python2-mock)
2677 ("python-nose" ,python2-nose)
2679 (home-page "https://github.com/PMBio/warpedLMM")
2680 (synopsis "Implementation of warped linear mixed models")
2682 "WarpedLMM is a Python implementation of the warped linear mixed model,
2683 which automatically learns an optimal warping function (or transformation) for
2684 the phenotype as it models the data.")
2685 (license license:asl2.0)))
2687 (define-public pbtranscript-tofu
2688 (let ((commit "8f5467fe6"))
2690 (name "pbtranscript-tofu")
2691 (version (string-append "2.2.3." commit))
2695 (url "https://github.com/PacificBiosciences/cDNA_primer.git")
2697 (file-name (string-append name "-" version "-checkout"))
2700 "1lgnpi35ihay42qx0b6yl3kkgra723i413j33kvs0kvs61h82w0f"))
2701 (modules '((guix build utils)))
2704 ;; remove bundled Cython sources
2705 (delete-file "pbtranscript-tofu/pbtranscript/Cython-0.20.1.tar.gz")
2707 (build-system python-build-system)
2709 `(#:python ,python-2
2710 ;; With standard flags, the install phase attempts to create a zip'd
2711 ;; egg file, and fails with an error: 'ZIP does not support timestamps
2713 #:configure-flags '("--single-version-externally-managed"
2714 "--record=pbtranscript-tofu.txt")
2716 (modify-phases %standard-phases
2717 (add-after 'unpack 'enter-directory
2719 (chdir "pbtranscript-tofu/pbtranscript/")
2721 ;; With setuptools version 18.0 and later this setup.py hack causes
2722 ;; a build error, so we disable it.
2723 (add-after 'enter-directory 'patch-setuppy
2725 (substitute* "setup.py"
2726 (("if 'setuptools.extension' in sys.modules:")
2730 `(("python-numpy" ,python2-numpy)
2731 ("python-bx-python" ,python2-bx-python)
2732 ("python-networkx" ,python2-networkx)
2733 ("python-scipy" ,python2-scipy)
2734 ("python-pbcore" ,python2-pbcore)
2735 ("python-h5py" ,python2-h5py)))
2737 `(("python-cython" ,python2-cython)
2738 ("python-nose" ,python2-nose)
2739 ("python-setuptools" ,python2-setuptools)))
2740 (home-page "https://github.com/PacificBiosciences/cDNA_primer")
2741 (synopsis "Analyze transcriptome data generated with the Iso-Seq protocol")
2743 "pbtranscript-tofu contains scripts to analyze transcriptome data
2744 generated using the PacBio Iso-Seq protocol.")
2745 (license license:bsd-3))))
2747 (define-public pyicoteo
2754 (uri (string-append "https://bitbucket.org/regulatorygenomicsupf/"
2755 "pyicoteo/get/v" version ".tar.bz2"))
2756 (file-name (string-append name "-" version ".tar.bz2"))
2759 "0d6087f29xp8wxwlj111c3sylli98n0l8ry58c51ixzq0zfm50wa"))))
2760 (build-system python-build-system)
2762 `(#:python ,python-2 ; does not work with Python 3
2763 #:tests? #f)) ; there are no tests
2765 `(("python2-matplotlib" ,python2-matplotlib)))
2766 (home-page "https://bitbucket.org/regulatorygenomicsupf/pyicoteo")
2767 (synopsis "Analyze high-throughput genetic sequencing data")
2769 "Pyicoteo is a suite of tools for the analysis of high-throughput genetic
2770 sequencing data. It works with genomic coordinates. There are currently six
2771 different command-line tools:
2774 @item pyicoregion: for generating exploratory regions automatically;
2775 @item pyicoenrich: for differential enrichment between two conditions;
2776 @item pyicoclip: for calling CLIP-Seq peaks without a control;
2777 @item pyicos: for genomic coordinates manipulation;
2778 @item pyicoller: for peak calling on punctuated ChIP-Seq;
2779 @item pyicount: to count how many reads from N experiment files overlap in a
2781 @item pyicotrocol: to combine operations from pyicoteo.
2783 (license license:gpl3+)))
2785 (define-public prodigal
2792 "https://github.com/hyattpd/Prodigal/archive/v"
2794 (file-name (string-append name "-" version ".tar.gz"))
2797 "17srxkqd3jc77xk15pfbgg1a9xahqg7337w95mrsia7mpza4l2c9"))))
2798 (build-system gnu-build-system)
2800 `(#:tests? #f ;no check target
2801 #:make-flags (list (string-append "INSTALLDIR="
2802 (assoc-ref %outputs "out")
2805 (modify-phases %standard-phases
2806 (delete 'configure))))
2807 (home-page "http://prodigal.ornl.gov")
2808 (synopsis "Protein-coding gene prediction for Archaea and Bacteria")
2810 "Prodigal runs smoothly on finished genomes, draft genomes, and
2811 metagenomes, providing gene predictions in GFF3, Genbank, or Sequin table
2812 format. It runs quickly, in an unsupervised fashion, handles gaps, handles
2813 partial genes, and identifies translation initiation sites.")
2814 (license license:gpl3+)))
2824 (string-append "http://deweylab.biostat.wisc.edu/rsem/src/rsem-"
2827 (base32 "0nzdc0j0hjllhsd5f2xli95dafm3nawskigs140xzvjk67xh0r9q"))
2828 (patches (search-patches "rsem-makefile.patch"))
2829 (modules '((guix build utils)))
2832 ;; remove bundled copy of boost
2833 (delete-file-recursively "boost")
2835 (build-system gnu-build-system)
2837 `(#:tests? #f ;no "check" target
2839 (modify-phases %standard-phases
2840 ;; No "configure" script.
2841 ;; Do not build bundled samtools library.
2844 (substitute* "Makefile"
2845 (("^all : sam/libbam.a") "all : "))
2848 (lambda* (#:key outputs #:allow-other-keys)
2849 (let* ((out (string-append (assoc-ref outputs "out")))
2850 (bin (string-append out "/bin/"))
2851 (perl (string-append out "/lib/perl5/site_perl")))
2854 (for-each (lambda (file)
2856 (string-append bin (basename file))))
2857 (find-files "." "rsem-.*"))
2858 (copy-file "rsem_perl_utils.pm"
2859 (string-append perl "/rsem_perl_utils.pm")))
2862 'install 'wrap-program
2863 (lambda* (#:key outputs #:allow-other-keys)
2864 (let ((out (assoc-ref outputs "out")))
2865 (for-each (lambda (prog)
2866 (wrap-program (string-append out "/bin/" prog)
2867 `("PERL5LIB" ":" prefix
2868 (,(string-append out "/lib/perl5/site_perl")))))
2869 '("rsem-plot-transcript-wiggles"
2870 "rsem-calculate-expression"
2871 "rsem-generate-ngvector"
2873 "rsem-prepare-reference")))
2877 ("ncurses" ,ncurses)
2880 ("samtools" ,samtools-0.1)
2882 (home-page "http://deweylab.biostat.wisc.edu/rsem/")
2883 (synopsis "Estimate gene expression levels from RNA-Seq data")
2885 "RSEM is a software package for estimating gene and isoform expression
2886 levels from RNA-Seq data. The RSEM package provides a user-friendly
2887 interface, supports threads for parallel computation of the EM algorithm,
2888 single-end and paired-end read data, quality scores, variable-length reads and
2889 RSPD estimation. In addition, it provides posterior mean and 95% credibility
2890 interval estimates for expression levels. For visualization, it can generate
2891 BAM and Wiggle files in both transcript-coordinate and genomic-coordinate.")
2892 (license license:gpl3+)))
2894 (define-public rseqc
2902 (string-append "mirror://sourceforge/rseqc/"
2903 version "/RSeQC-" version ".tar.gz"))
2905 (base32 "15ly0254yi032qzkdplg00q144qfdsd986gh62829rl5bkxhj330"))
2906 (modules '((guix build utils)))
2909 ;; remove bundled copy of pysam
2910 (delete-file-recursively "lib/pysam")
2911 (substitute* "setup.py"
2912 ;; remove dependency on outdated "distribute" module
2913 (("^from distribute_setup import use_setuptools") "")
2914 (("^use_setuptools\\(\\)") "")
2915 ;; do not use bundled copy of pysam
2916 (("^have_pysam = False") "have_pysam = True"))))))
2917 (build-system python-build-system)
2918 (arguments `(#:python ,python-2))
2920 `(("python-cython" ,python2-cython)
2921 ("python-pysam" ,python2-pysam)
2922 ("python-numpy" ,python2-numpy)
2923 ("python-setuptools" ,python2-setuptools)
2926 `(("python-nose" ,python2-nose)))
2927 (home-page "http://rseqc.sourceforge.net/")
2928 (synopsis "RNA-seq quality control package")
2930 "RSeQC provides a number of modules that can comprehensively evaluate
2931 high throughput sequence data, especially RNA-seq data. Some basic modules
2932 inspect sequence quality, nucleotide composition bias, PCR bias and GC bias,
2933 while RNA-seq specific modules evaluate sequencing saturation, mapped reads
2934 distribution, coverage uniformity, strand specificity, etc.")
2935 (license license:gpl3+)))
2937 (define-public samtools
2945 (string-append "mirror://sourceforge/samtools/"
2946 version "/samtools-" version ".tar.bz2"))
2949 "0znnnxc467jbf1as2dpskrjhfh8mbll760j6w6rdkwlwbqsp8gbc"))))
2950 (build-system gnu-build-system)
2952 `(#:modules ((ice-9 ftw)
2954 (guix build gnu-build-system)
2956 #:make-flags (list (string-append "prefix=" (assoc-ref %outputs "out")))
2957 #:configure-flags (list "--with-ncurses")
2960 'unpack 'patch-tests
2962 (substitute* "test/test.pl"
2963 ;; The test script calls out to /bin/bash
2964 (("/bin/bash") (which "bash")))
2967 'install 'install-library
2968 (lambda* (#:key outputs #:allow-other-keys)
2969 (let ((lib (string-append (assoc-ref outputs "out") "/lib")))
2970 (install-file "libbam.a" lib)))
2972 'install 'install-headers
2973 (lambda* (#:key outputs #:allow-other-keys)
2974 (let ((include (string-append (assoc-ref outputs "out")
2975 "/include/samtools/")))
2976 (for-each (lambda (file)
2977 (install-file file include))
2978 (scandir "." (lambda (name) (string-match "\\.h$" name))))
2980 %standard-phases)))))
2981 (native-inputs `(("pkg-config" ,pkg-config)))
2982 (inputs `(("ncurses" ,ncurses)
2986 (home-page "http://samtools.sourceforge.net")
2987 (synopsis "Utilities to efficiently manipulate nucleotide sequence alignments")
2989 "Samtools implements various utilities for post-processing nucleotide
2990 sequence alignments in the SAM, BAM, and CRAM formats, including indexing,
2991 variant calling (in conjunction with bcftools), and a simple alignment
2993 (license license:expat)))
2995 (define-public samtools-0.1
2996 ;; This is the most recent version of the 0.1 line of samtools. The input
2997 ;; and output formats differ greatly from that used and produced by samtools
2998 ;; 1.x and is still used in many bioinformatics pipelines.
2999 (package (inherit samtools)
3005 (string-append "mirror://sourceforge/samtools/"
3006 version "/samtools-" version ".tar.bz2"))
3008 (base32 "1m33xsfwz0s8qi45lylagfllqg7fphf4dr0780rsvw75av9wk06h"))))
3010 `(#:tests? #f ;no "check" target
3011 ,@(substitute-keyword-arguments (package-arguments samtools)
3012 ((#:make-flags flags)
3013 `(cons "LIBCURSES=-lncurses" ,flags))
3015 `(modify-phases ,phases
3017 (lambda* (#:key outputs #:allow-other-keys)
3018 (let ((bin (string-append
3019 (assoc-ref outputs "out") "/bin")))
3021 (copy-file "samtools"
3022 (string-append bin "/samtools")))))
3023 (delete 'patch-tests)
3024 (delete 'configure))))))))
3026 (define-public mosaik
3027 (let ((commit "5c25216d"))
3032 ;; There are no release tarballs nor tags.
3035 (url "https://github.com/wanpinglee/MOSAIK.git")
3037 (file-name (string-append name "-" version))
3040 "17gj3s07cm77r41z92awh0bim7w7q7fbn0sf5nkqmcm1vw052qgw"))))
3041 (build-system gnu-build-system)
3043 `(#:tests? #f ; no tests
3044 #:make-flags (list "CC=gcc")
3046 (modify-phases %standard-phases
3048 (lambda _ (chdir "src") #t))
3050 (lambda* (#:key outputs #:allow-other-keys)
3051 (let ((bin (string-append (assoc-ref outputs "out")
3054 (copy-recursively "../bin" bin)
3059 (supported-systems '("x86_64-linux"))
3060 (home-page "https://code.google.com/p/mosaik-aligner/")
3061 (synopsis "Map nucleotide sequence reads to reference genomes")
3063 "MOSAIK is a program for mapping second and third-generation sequencing
3064 reads to a reference genome. MOSAIK can align reads generated by all the
3065 major sequencing technologies, including Illumina, Applied Biosystems SOLiD,
3066 Roche 454, Ion Torrent and Pacific BioSciences SMRT.")
3067 ;; MOSAIK is released under the GPLv2+ with the exception of third-party
3068 ;; code released into the public domain:
3069 ;; 1. fastlz by Ariya Hidayat - http://www.fastlz.org/
3070 ;; 2. MD5 implementation - RSA Data Security, RFC 1321
3071 (license (list license:gpl2+ license:public-domain)))))
3073 (define-public ngs-sdk
3081 (string-append "https://github.com/ncbi/ngs/archive/"
3083 (file-name (string-append name "-" version ".tar.gz"))
3086 "15074fdi94c6pjy83hhk22r86kfvzpaz2i07h3rqg9yy6x3w0pk2"))))
3087 (build-system gnu-build-system)
3089 `(#:parallel-build? #f ; not supported
3090 #:tests? #f ; no "check" target
3094 (lambda* (#:key outputs #:allow-other-keys)
3095 (let ((out (assoc-ref outputs "out")))
3096 ;; The 'configure' script doesn't recognize things like
3097 ;; '--enable-fast-install'.
3098 (zero? (system* "./configure"
3099 (string-append "--build-prefix=" (getcwd) "/build")
3100 (string-append "--prefix=" out)))))
3103 (lambda _ (chdir "ngs-sdk") #t)
3104 %standard-phases))))
3105 (native-inputs `(("perl" ,perl)))
3106 ;; According to the test
3107 ;; unless ($MARCH =~ /x86_64/i || $MARCH =~ /i?86/i)
3108 ;; in ngs-sdk/setup/konfigure.perl
3109 (supported-systems '("i686-linux" "x86_64-linux"))
3110 (home-page "https://github.com/ncbi/ngs")
3111 (synopsis "API for accessing Next Generation Sequencing data")
3113 "NGS is a domain-specific API for accessing reads, alignments and pileups
3114 produced from Next Generation Sequencing. The API itself is independent from
3115 any particular back-end implementation, and supports use of multiple back-ends
3117 (license license:public-domain)))
3119 (define-public java-ngs
3120 (package (inherit ngs-sdk)
3123 `(,@(substitute-keyword-arguments
3124 `(#:modules ((guix build gnu-build-system)
3128 ,@(package-arguments ngs-sdk))
3130 `(modify-phases ,phases
3131 (replace 'enter-dir (lambda _ (chdir "ngs-java") #t)))))))
3133 `(("jdk" ,icedtea "jdk")
3134 ("ngs-sdk" ,ngs-sdk)))
3135 (synopsis "Java bindings for NGS SDK")))
3137 (define-public ncbi-vdb
3145 (string-append "https://github.com/ncbi/ncbi-vdb/archive/"
3147 (file-name (string-append name "-" version ".tar.gz"))
3150 "0hay5hy8ynva3mi5wbn4wmq1q23qwxc3aqzbb86hg3x4f1r73270"))))
3151 (build-system gnu-build-system)
3153 `(#:parallel-build? #f ; not supported
3154 #:tests? #f ; no "check" target
3158 (lambda* (#:key inputs outputs #:allow-other-keys)
3159 (let ((out (assoc-ref outputs "out")))
3160 ;; Override include path for libmagic
3161 (substitute* "setup/package.prl"
3162 (("name => 'magic', Include => '/usr/include'")
3163 (string-append "name=> 'magic', Include => '"
3164 (assoc-ref inputs "libmagic")
3167 ;; Install kdf5 library (needed by sra-tools)
3168 (substitute* "build/Makefile.install"
3169 (("LIBRARIES_TO_INSTALL =")
3170 "LIBRARIES_TO_INSTALL = kdf5.$(VERSION_LIBX) kdf5.$(VERSION_SHLX)"))
3172 ;; The 'configure' script doesn't recognize things like
3173 ;; '--enable-fast-install'.
3176 (string-append "--build-prefix=" (getcwd) "/build")
3177 (string-append "--prefix=" (assoc-ref outputs "out"))
3178 (string-append "--debug")
3179 (string-append "--with-xml2-prefix="
3180 (assoc-ref inputs "libxml2"))
3181 (string-append "--with-ngs-sdk-prefix="
3182 (assoc-ref inputs "ngs-sdk"))
3183 (string-append "--with-ngs-java-prefix="
3184 (assoc-ref inputs "java-ngs"))
3185 (string-append "--with-hdf5-prefix="
3186 (assoc-ref inputs "hdf5"))))))
3188 'install 'install-interfaces
3189 (lambda* (#:key outputs #:allow-other-keys)
3190 ;; Install interface libraries. On i686 the interface libraries
3191 ;; are installed to "linux/gcc/i386", so we need to use the Linux
3192 ;; architecture name ("i386") instead of the target system prefix
3194 (mkdir (string-append (assoc-ref outputs "out") "/ilib"))
3195 (copy-recursively (string-append "build/ncbi-vdb/linux/gcc/"
3196 ,(system->linux-architecture
3197 (or (%current-target-system)
3200 (string-append (assoc-ref outputs "out")
3202 ;; Install interface headers
3203 (copy-recursively "interfaces"
3204 (string-append (assoc-ref outputs "out")
3206 %standard-phases))))
3208 `(("libxml2" ,libxml2)
3209 ("ngs-sdk" ,ngs-sdk)
3210 ("java-ngs" ,java-ngs)
3213 (native-inputs `(("perl" ,perl)))
3214 (home-page "https://github.com/ncbi/ncbi-vdb")
3215 (synopsis "Database engine for genetic information")
3217 "The NCBI-VDB library implements a highly compressed columnar data
3218 warehousing engine that is most often used to store genetic information.
3219 Databases are stored in a portable image within the file system, and can be
3220 accessed/downloaded on demand across HTTP.")
3221 (license license:public-domain)))
3223 (define-public plink
3231 "http://pngu.mgh.harvard.edu/~purcell/plink/dist/plink-"
3232 version "-src.zip"))
3234 (base32 "0as8gxm4pjyc8dxmm1sl873rrd7wn5qs0l29nqfnl31x8i467xaa"))
3235 (patches (search-patches "plink-1.07-unclobber-i.patch"))))
3236 (build-system gnu-build-system)
3238 '(#:tests? #f ;no "check" target
3239 #:make-flags (list (string-append "LIB_LAPACK="
3240 (assoc-ref %build-inputs "lapack")
3241 "/lib/liblapack.so")
3244 ;; disable phoning home
3247 (modify-phases %standard-phases
3248 ;; no "configure" script
3251 (lambda* (#:key outputs #:allow-other-keys)
3252 (let ((bin (string-append (assoc-ref outputs "out")
3254 (install-file "plink" bin)
3258 ("lapack" ,lapack)))
3260 `(("unzip" ,unzip)))
3261 (home-page "http://pngu.mgh.harvard.edu/~purcell/plink/")
3262 (synopsis "Whole genome association analysis toolset")
3264 "PLINK is a whole genome association analysis toolset, designed to
3265 perform a range of basic, large-scale analyses in a computationally efficient
3266 manner. The focus of PLINK is purely on analysis of genotype/phenotype data,
3267 so there is no support for steps prior to this (e.g. study design and
3268 planning, generating genotype or CNV calls from raw data). Through
3269 integration with gPLINK and Haploview, there is some support for the
3270 subsequent visualization, annotation and storage of results.")
3271 ;; Code is released under GPLv2, except for fisher.h, which is under
3273 (license (list license:gpl2 license:lgpl2.1+))))
3275 (define-public smithlab-cpp
3276 (let ((revision "1")
3279 (name "smithlab-cpp")
3280 (version (string-append "0." revision "." commit))
3284 (url "https://github.com/smithlabcode/smithlab_cpp.git")
3286 (file-name (string-append name "-" version "-checkout"))
3289 "0d476lmj312xk77kr9fzrv7z1bv96yfyx0w7y62ycmnfbx32ll74"))))
3290 (build-system gnu-build-system)
3292 `(#:modules ((guix build gnu-build-system)
3295 #:tests? #f ;no "check" target
3297 (modify-phases %standard-phases
3298 (add-after 'unpack 'use-samtools-headers
3300 (substitute* '("SAM.cpp"
3302 (("sam.h") "samtools/sam.h"))
3305 (lambda* (#:key outputs #:allow-other-keys)
3306 (let* ((out (assoc-ref outputs "out"))
3307 (lib (string-append out "/lib"))
3308 (include (string-append out "/include/smithlab-cpp")))
3311 (for-each (cut install-file <> lib)
3312 (find-files "." "\\.o$"))
3313 (for-each (cut install-file <> include)
3314 (find-files "." "\\.hpp$")))
3316 (delete 'configure))))
3318 `(("samtools" ,samtools-0.1)
3320 (home-page "https://github.com/smithlabcode/smithlab_cpp")
3321 (synopsis "C++ helper library for functions used in Smith lab projects")
3323 "Smithlab CPP is a C++ library that includes functions used in many of
3324 the Smith lab bioinformatics projects, such as a wrapper around Samtools data
3325 structures, classes for genomic regions, mapped sequencing reads, etc.")
3326 (license license:gpl3+))))
3328 (define-public preseq
3334 (uri (string-append "https://github.com/smithlabcode/"
3335 "preseq/archive/v" version ".tar.gz"))
3336 (file-name (string-append name "-" version ".tar.gz"))
3338 (base32 "08r684l50pnxjpvmhzjgqq56yv9rfw90k8vx0nsrnrzk8mf9hsdq"))
3339 (modules '((guix build utils)))
3341 ;; Remove bundled samtools.
3342 '(delete-file-recursively "samtools"))))
3343 (build-system gnu-build-system)
3345 `(#:tests? #f ;no "check" target
3347 (modify-phases %standard-phases
3348 (delete 'configure))
3350 (list (string-append "PREFIX="
3351 (assoc-ref %outputs "out"))
3352 (string-append "LIBBAM="
3353 (assoc-ref %build-inputs "samtools")
3355 (string-append "SMITHLAB_CPP="
3356 (assoc-ref %build-inputs "smithlab-cpp")
3359 "INCLUDEDIRS=$(SMITHLAB_CPP)/../include/smithlab-cpp $(SAMTOOLS_DIR)")))
3362 ("samtools" ,samtools-0.1)
3363 ("smithlab-cpp" ,smithlab-cpp)
3365 (home-page "http://smithlabresearch.org/software/preseq/")
3366 (synopsis "Program for analyzing library complexity")
3368 "The preseq package is aimed at predicting and estimating the complexity
3369 of a genomic sequencing library, equivalent to predicting and estimating the
3370 number of redundant reads from a given sequencing depth and how many will be
3371 expected from additional sequencing using an initial sequencing experiment.
3372 The estimates can then be used to examine the utility of further sequencing,
3373 optimize the sequencing depth, or to screen multiple libraries to avoid low
3374 complexity samples.")
3375 (license license:gpl3+)))
3377 (define-public sra-tools
3385 (string-append "https://github.com/ncbi/sra-tools/archive/"
3387 (file-name (string-append name "-" version ".tar.gz"))
3390 "0q93qg744x787d08qmjmdafki1wkbvkdwynayjnjd454gkd26jl5"))))
3391 (build-system gnu-build-system)
3393 `(#:parallel-build? #f ; not supported
3394 #:tests? #f ; no "check" target
3398 (lambda* (#:key inputs outputs #:allow-other-keys)
3399 ;; The build system expects a directory containing the sources and
3400 ;; raw build output of ncbi-vdb, including files that are not
3401 ;; installed. Since we are building against an installed version of
3402 ;; ncbi-vdb, the following modifications are needed.
3403 (substitute* "setup/konfigure.perl"
3404 ;; Make the configure script look for the "ilib" directory of
3405 ;; "ncbi-vdb" without first checking for the existence of a
3406 ;; matching library in its "lib" directory.
3407 (("^ my \\$f = File::Spec->catdir\\(\\$libdir, \\$lib\\);")
3408 "my $f = File::Spec->catdir($ilibdir, $ilib);")
3409 ;; Look for interface libraries in ncbi-vdb's "ilib" directory.
3410 (("my \\$ilibdir = File::Spec->catdir\\(\\$builddir, 'ilib'\\);")
3411 "my $ilibdir = File::Spec->catdir($dir, 'ilib');"))
3413 ;; The 'configure' script doesn't recognize things like
3414 ;; '--enable-fast-install'.
3417 (string-append "--build-prefix=" (getcwd) "/build")
3418 (string-append "--prefix=" (assoc-ref outputs "out"))
3419 (string-append "--debug")
3420 (string-append "--with-fuse-prefix="
3421 (assoc-ref inputs "fuse"))
3422 (string-append "--with-magic-prefix="
3423 (assoc-ref inputs "libmagic"))
3424 ;; TODO: building with libxml2 fails with linker errors
3425 ;; (string-append "--with-xml2-prefix="
3426 ;; (assoc-ref inputs "libxml2"))
3427 (string-append "--with-ncbi-vdb-sources="
3428 (assoc-ref inputs "ncbi-vdb"))
3429 (string-append "--with-ncbi-vdb-build="
3430 (assoc-ref inputs "ncbi-vdb"))
3431 (string-append "--with-ngs-sdk-prefix="
3432 (assoc-ref inputs "ngs-sdk"))
3433 (string-append "--with-hdf5-prefix="
3434 (assoc-ref inputs "hdf5")))))
3436 (native-inputs `(("perl" ,perl)))
3438 `(("ngs-sdk" ,ngs-sdk)
3439 ("ncbi-vdb" ,ncbi-vdb)
3444 (home-page "http://www.ncbi.nlm.nih.gov/Traces/sra/sra.cgi?view=software")
3445 (synopsis "Tools and libraries for reading and writing sequencing data")
3447 "The SRA Toolkit from NCBI is a collection of tools and libraries for
3448 reading of sequencing files from the Sequence Read Archive (SRA) database and
3449 writing files into the .sra format.")
3450 (license license:public-domain)))
3452 (define-public seqan
3458 (uri (string-append "http://packages.seqan.de/seqan-library/"
3459 "seqan-library-" version ".tar.bz2"))
3462 "05s3wrrwn50f81aklfm65i4a749zag1vr8z03k21xm0pdxy47yvp"))))
3463 ;; The documentation is 7.8MB and the includes are 3.6MB heavy, so it
3464 ;; makes sense to split the outputs.
3465 (outputs '("out" "doc"))
3466 (build-system trivial-build-system)
3468 `(#:modules ((guix build utils))
3471 (use-modules (guix build utils))
3472 (let ((tar (assoc-ref %build-inputs "tar"))
3473 (bzip (assoc-ref %build-inputs "bzip2"))
3474 (out (assoc-ref %outputs "out"))
3475 (doc (assoc-ref %outputs "doc")))
3476 (setenv "PATH" (string-append tar "/bin:" bzip "/bin"))
3477 (system* "tar" "xvf" (assoc-ref %build-inputs "source"))
3478 (chdir (string-append "seqan-library-" ,version))
3479 (copy-recursively "include" (string-append out "/include"))
3480 (copy-recursively "share" (string-append doc "/share"))))))
3482 `(("source" ,source)
3485 (home-page "http://www.seqan.de")
3486 (synopsis "Library for nucleotide sequence analysis")
3488 "SeqAn is a C++ library of efficient algorithms and data structures for
3489 the analysis of sequences with the focus on biological data. It contains
3490 algorithms and data structures for string representation and their
3491 manipulation, online and indexed string search, efficient I/O of
3492 bioinformatics file formats, sequence alignment, and more.")
3493 (license license:bsd-3)))
3495 (define-public seqmagick
3503 "https://pypi.python.org/packages/source/s/seqmagick/seqmagick-"
3507 "0cgn477n74gsl4qdaakrrhi953kcsd4q3ivk2lr18x74s3g4ma1d"))))
3508 (build-system python-build-system)
3510 ;; python2 only, see https://github.com/fhcrc/seqmagick/issues/56
3511 `(#:python ,python-2
3513 (modify-phases %standard-phases
3514 ;; Current test in setup.py does not work as of 0.6.1,
3515 ;; so use nose to run tests instead for now. See
3516 ;; https://github.com/fhcrc/seqmagick/issues/55
3517 (replace 'check (lambda _ (zero? (system* "nosetests")))))))
3519 `(("python-biopython" ,python2-biopython)))
3521 `(("python-setuptools" ,python2-setuptools)
3522 ("python-nose" ,python2-nose)))
3523 (home-page "http://github.com/fhcrc/seqmagick")
3524 (synopsis "Tools for converting and modifying sequence files")
3526 "Bioinformaticians often have to convert sequence files between formats
3527 and do little manipulations on them, and it's not worth writing scripts for
3528 that. Seqmagick is a utility to expose the file format conversion in
3529 BioPython in a convenient way. Instead of having a big mess of scripts, there
3530 is one that takes arguments.")
3531 (license license:gpl3)))
3533 (define-public snap-aligner
3535 (name "snap-aligner")
3536 (version "1.0beta.18")
3540 "https://github.com/amplab/snap/archive/v"
3542 (file-name (string-append name "-" version ".tar.gz"))
3545 "1vnsjwv007k1fl1q7d681kbwn6bc66cgw6h16hym6gvyy71qv2ly"))))
3546 (build-system gnu-build-system)
3549 (modify-phases %standard-phases
3551 (replace 'check (lambda _ (zero? (system* "./unit_tests"))))
3553 (lambda* (#:key outputs #:allow-other-keys)
3554 (let* ((out (assoc-ref outputs "out"))
3555 (bin (string-append out "/bin")))
3557 (install-file "snap-aligner" bin)
3558 (install-file "SNAPCommand" bin)
3562 (home-page "http://snap.cs.berkeley.edu/")
3563 (synopsis "Short read DNA sequence aligner")
3565 "SNAP is a fast and accurate aligner for short DNA reads. It is
3566 optimized for modern read lengths of 100 bases or higher, and takes advantage
3567 of these reads to align data quickly through a hash-based indexing scheme.")
3568 (license license:asl2.0)))
3570 (define-public sortmerna
3578 "https://github.com/biocore/sortmerna/archive/"
3580 (file-name (string-append name "-" version ".tar.gz"))
3583 "1mc5cf1c7xh0h7xb11vh7gqgzx0qvrfa606cb8ixlfg3f2av58s4"))))
3584 (build-system gnu-build-system)
3585 (outputs '("out" ;for binaries
3586 "db")) ;for sequence databases
3589 (modify-phases %standard-phases
3591 (lambda* (#:key outputs #:allow-other-keys)
3592 (let* ((out (assoc-ref outputs "out"))
3593 (bin (string-append out "/bin"))
3594 (db (assoc-ref outputs "db"))
3596 (string-append db "/share/sortmerna/rRNA_databases")))
3597 (install-file "sortmerna" bin)
3598 (install-file "indexdb_rna" bin)
3599 (for-each (lambda (file)
3600 (install-file file share))
3601 (find-files "rRNA_databases" ".*fasta"))
3603 (home-page "http://bioinfo.lifl.fr/RNA/sortmerna")
3604 (synopsis "Biological sequence analysis tool for NGS reads")
3606 "SortMeRNA is a biological sequence analysis tool for filtering, mapping
3607 and operational taxonomic unit (OTU) picking of next generation
3608 sequencing (NGS) reads. The core algorithm is based on approximate seeds and
3609 allows for fast and sensitive analyses of nucleotide sequences. The main
3610 application of SortMeRNA is filtering rRNA from metatranscriptomic data.")
3611 (license license:lgpl3)))
3619 (uri (string-append "https://github.com/alexdobin/STAR/archive/"
3621 (file-name (string-append name "-" version ".tar.gz"))
3624 "0wzcfhkg10apnh0y73xlarfa79xxwxdizicbdl11wb48awk44iq4"))
3625 (modules '((guix build utils)))
3628 (substitute* "source/Makefile"
3630 ;; Remove pre-built binaries and bundled htslib sources.
3631 (delete-file-recursively "bin/MacOSX_x86_64")
3632 (delete-file-recursively "bin/Linux_x86_64")
3633 (delete-file-recursively "source/htslib")
3635 (build-system gnu-build-system)
3637 '(#:tests? #f ;no check target
3638 #:make-flags '("STAR")
3640 (modify-phases %standard-phases
3641 (add-after 'unpack 'enter-source-dir
3642 (lambda _ (chdir "source") #t))
3643 (add-after 'enter-source-dir 'do-not-use-bundled-htslib
3645 (substitute* "Makefile"
3646 (("(Depend.list: \\$\\(SOURCES\\) parametersDefault\\.xxd) htslib"
3648 (substitute* '("BAMfunctions.cpp"
3653 "bamRemoveDuplicates.cpp")
3654 (("#include \"htslib/([^\"]+\\.h)\"" _ header)
3655 (string-append "#include <" header ">")))
3656 (substitute* "IncludeDefine.h"
3657 (("\"htslib/(htslib/[^\"]+.h)\"" _ header)
3658 (string-append "<" header ">")))
3661 (lambda* (#:key outputs #:allow-other-keys)
3662 (let ((bin (string-append (assoc-ref outputs "out") "/bin/")))
3663 (install-file "STAR" bin))
3665 (delete 'configure))))
3667 `(("vim" ,vim))) ; for xxd
3669 `(("htslib" ,htslib)
3671 (home-page "https://github.com/alexdobin/STAR")
3672 (synopsis "Universal RNA-seq aligner")
3674 "The Spliced Transcripts Alignment to a Reference (STAR) software is
3675 based on a previously undescribed RNA-seq alignment algorithm that uses
3676 sequential maximum mappable seed search in uncompressed suffix arrays followed
3677 by seed clustering and stitching procedure. In addition to unbiased de novo
3678 detection of canonical junctions, STAR can discover non-canonical splices and
3679 chimeric (fusion) transcripts, and is also capable of mapping full-length RNA
3681 ;; STAR is licensed under GPLv3 or later; htslib is MIT-licensed.
3682 (license license:gpl3+)))
3684 (define-public subread
3687 (version "1.4.6-p2")
3691 "mirror://sourceforge/subread/subread-"
3692 version "-source.tar.gz"))
3695 "06sv9mpcsdj6p68y15d6gi70lca3lxmzk0dn61hg0kfsa7rxmsr3"))))
3696 (build-system gnu-build-system)
3698 `(#:tests? #f ;no "check" target
3699 ;; The CC and CCFLAGS variables are set to contain a lot of x86_64
3700 ;; optimizations by default, so we override these flags such that x86_64
3701 ;; flags are only added when the build target is an x86_64 system.
3703 (list (let ((system ,(or (%current-target-system)
3705 (flags '("-ggdb" "-fomit-frame-pointer"
3706 "-ffast-math" "-funroll-loops"
3707 "-fmessage-length=0"
3708 "-O9" "-Wall" "-DMAKE_FOR_EXON"
3710 "-DSUBREAD_VERSION=\\\"${SUBREAD_VERSION}\\\""))
3711 (flags64 '("-mmmx" "-msse" "-msse2" "-msse3")))
3712 (if (string-prefix? "x86_64" system)
3713 (string-append "CCFLAGS=" (string-join (append flags flags64)))
3714 (string-append "CCFLAGS=" (string-join flags))))
3715 "-f" "Makefile.Linux"
3716 "CC=gcc ${CCFLAGS}")
3720 (lambda _ (chdir "src") #t)
3723 (lambda* (#:key outputs #:allow-other-keys)
3724 (let ((bin (string-append (assoc-ref outputs "out") "/bin/")))
3726 (copy-recursively "../bin" bin)))
3727 ;; no "configure" script
3728 (alist-delete 'configure %standard-phases)))))
3729 (inputs `(("zlib" ,zlib)))
3730 (home-page "http://bioinf.wehi.edu.au/subread-package/")
3731 (synopsis "Tool kit for processing next-gen sequencing data")
3733 "The subread package contains the following tools: subread aligner, a
3734 general-purpose read aligner; subjunc aligner: detecting exon-exon junctions
3735 and mapping RNA-seq reads; featureCounts: counting mapped reads for genomic
3736 features; exactSNP: a SNP caller that discovers SNPs by testing signals
3737 against local background noises.")
3738 (license license:gpl3+)))
3740 (define-public stringtie
3746 (uri (string-append "http://ccb.jhu.edu/software/stringtie/dl/"
3747 "stringtie-" version ".tar.gz"))
3750 "1cqllsc1maq4kh92isi8yadgzbmnf042hlnalpk3y59aph1z3bfz"))
3751 (modules '((guix build utils)))
3754 (delete-file-recursively "samtools-0.1.18")
3756 (build-system gnu-build-system)
3758 `(#:tests? #f ;no test suite
3760 (modify-phases %standard-phases
3761 ;; no configure script
3763 (add-before 'build 'use-system-samtools
3765 (substitute* "Makefile"
3766 (("stringtie: \\$\\{BAM\\}/libbam\\.a")
3768 (substitute* '("gclib/GBam.h"
3770 (("#include \"(bam|sam|kstring).h\"" _ header)
3771 (string-append "#include <samtools/" header ".h>")))
3774 (lambda* (#:key outputs #:allow-other-keys)
3775 (let ((bin (string-append (assoc-ref outputs "out") "/bin/")))
3776 (install-file "stringtie" bin)
3779 `(("samtools" ,samtools-0.1)
3781 (home-page "http://ccb.jhu.edu/software/stringtie/")
3782 (synopsis "Transcript assembly and quantification for RNA-Seq data")
3784 "StringTie is a fast and efficient assembler of RNA-Seq sequence
3785 alignments into potential transcripts. It uses a novel network flow algorithm
3786 as well as an optional de novo assembly step to assemble and quantitate
3787 full-length transcripts representing multiple splice variants for each gene
3788 locus. Its input can include not only the alignments of raw reads used by
3789 other transcript assemblers, but also alignments of longer sequences that have
3790 been assembled from those reads. To identify differentially expressed genes
3791 between experiments, StringTie's output can be processed either by the
3792 Cuffdiff or Ballgown programs.")
3793 (license license:artistic2.0)))
3795 (define-public vcftools
3802 "https://github.com/vcftools/vcftools/releases/download/v"
3803 version "/vcftools-" version ".tar.gz"))
3806 "10l5c07z9p4i9pr4gl54b2c9h6ndhqlbq1rashg2zcgwkbfrkmvn"))))
3807 (build-system gnu-build-system)
3809 `(#:tests? #f ; no "check" target
3811 "CFLAGS=-O2" ; override "-m64" flag
3812 (string-append "PREFIX=" (assoc-ref %outputs "out"))
3813 (string-append "MANDIR=" (assoc-ref %outputs "out")
3814 "/share/man/man1"))))
3816 `(("pkg-config" ,pkg-config)))
3820 (home-page "https://vcftools.github.io/")
3821 (synopsis "Tools for working with VCF files")
3823 "VCFtools is a program package designed for working with VCF files, such
3824 as those generated by the 1000 Genomes Project. The aim of VCFtools is to
3825 provide easily accessible methods for working with complex genetic variation
3826 data in the form of VCF files.")
3827 ;; The license is declared as LGPLv3 in the README and
3828 ;; at https://vcftools.github.io/license.html
3829 (license license:lgpl3)))
3831 (define-public vsearch
3839 "https://github.com/torognes/vsearch/archive/v"
3841 (file-name (string-append name "-" version ".tar.gz"))
3844 "1i3bad7gnn2y3a1yfixzshd99xdkjc8w5bxzgifpysc6jiljwvb5"))
3845 (modules '((guix build utils)))
3848 ;; Remove bundled cityhash and '-mtune=native'.
3849 (substitute* "src/Makefile.am"
3850 (("^AM_CXXFLAGS=-I\\$\\{srcdir\\}/cityhash \
3851 -O3 -mtune=native -Wall -Wsign-compare")
3852 (string-append "AM_CXXFLAGS=-lcityhash"
3853 " -O3 -Wall -Wsign-compare"))
3854 (("^__top_builddir__bin_vsearch_SOURCES = city.h \\\\")
3855 "__top_builddir__bin_vsearch_SOURCES = \\")
3856 (("^city.h \\\\") "\\")
3857 (("^citycrc.h \\\\") "\\")
3858 (("^libcityhash_a.*") "")
3859 (("noinst_LIBRARIES = libcpu_sse2.a libcpu_ssse3.a \
3861 "noinst_LIBRARIES = libcpu_sse2.a libcpu_ssse3.a")
3862 (("__top_builddir__bin_vsearch_LDADD = libcpu_ssse3.a \
3863 libcpu_sse2.a libcityhash.a")
3864 "__top_builddir__bin_vsearch_LDADD = libcpu_ssse3.a \
3865 libcpu_sse2.a -lcityhash"))
3866 (substitute* "src/vsearch.h"
3867 (("^\\#include \"city.h\"") "#include <city.h>")
3868 (("^\\#include \"citycrc.h\"") "#include <citycrc.h>"))
3869 (delete-file "src/city.h")
3870 (delete-file "src/citycrc.h")
3871 (delete-file "src/city.cc")
3873 (build-system gnu-build-system)
3876 (modify-phases %standard-phases
3877 (add-before 'configure 'autogen
3878 (lambda _ (zero? (system* "autoreconf" "-vif")))))))
3882 ("cityhash" ,cityhash)))
3884 `(("autoconf" ,autoconf)
3885 ("automake" ,automake)))
3886 (synopsis "Sequence search tools for metagenomics")
3888 "VSEARCH supports DNA sequence searching, clustering, chimera detection,
3889 dereplication, pairwise alignment, shuffling, subsampling, sorting and
3890 masking. The tool takes advantage of parallelism in the form of SIMD
3891 vectorization as well as multiple threads to perform accurate alignments at
3892 high speed. VSEARCH uses an optimal global aligner (full dynamic programming
3893 Needleman-Wunsch).")
3894 (home-page "https://github.com/torognes/vsearch")
3895 ;; vsearch uses non-portable SSE intrinsics so building fails on other
3897 (supported-systems '("x86_64-linux"))
3898 ;; Dual licensed; also includes public domain source.
3899 (license (list license:gpl3 license:bsd-2))))
3901 (define-public bio-locus
3908 (uri (rubygems-uri "bio-locus" version))
3911 "02vmrxyimkj9sahsp4zhfhnmbvz6dbbqz1y01vglf8cbwvkajfl0"))))
3912 (build-system ruby-build-system)
3914 `(("ruby-rspec" ,ruby-rspec)))
3915 (synopsis "Tool for fast querying of genome locations")
3917 "Bio-locus is a tabix-like tool for fast querying of genome
3918 locations. Many file formats in bioinformatics contain records that
3919 start with a chromosome name and a position for a SNP, or a start-end
3920 position for indels. Bio-locus allows users to store this chr+pos or
3921 chr+pos+alt information in a database.")
3922 (home-page "https://github.com/pjotrp/bio-locus")
3923 (license license:expat)))
3925 (define-public bio-blastxmlparser
3927 (name "bio-blastxmlparser")
3931 (uri (rubygems-uri "bio-blastxmlparser" version))
3934 "1wf4qygcmdjgcqm6flmvsagfr1gs9lf63mj32qv3z1f481zc5692"))))
3935 (build-system ruby-build-system)
3937 `(("ruby-bio-logger" ,ruby-bio-logger)
3938 ("ruby-nokogiri" ,ruby-nokogiri)))
3940 `(("ruby-rspec" ,ruby-rspec)))
3941 (synopsis "Fast big data BLAST XML parser and library")
3943 "Very fast parallel big-data BLAST XML file parser which can be used as
3944 command line utility. Use blastxmlparser to: Parse BLAST XML; filter output;
3945 generate FASTA, JSON, YAML, RDF, JSON-LD, HTML, CSV, tabular output etc.")
3946 (home-page "http://github.com/pjotrp/blastxmlparser")
3947 (license license:expat)))
3949 (define-public bioruby
3956 (uri (rubygems-uri "bio" version))
3959 "01k2fyjl5fpx4zn8g6gqiqvsg2j1fgixrs9p03vzxckynxdq3wmc"))))
3960 (build-system ruby-build-system)
3962 `(("ruby-libxml" ,ruby-libxml)))
3964 `(("which" ,which))) ; required for test phase
3967 (modify-phases %standard-phases
3968 (add-before 'build 'patch-test-command
3970 (substitute* '("test/functional/bio/test_command.rb")
3971 (("/bin/sh") (which "sh")))
3972 (substitute* '("test/functional/bio/test_command.rb")
3973 (("/bin/ls") (which "ls")))
3974 (substitute* '("test/functional/bio/test_command.rb")
3975 (("which") (which "which")))
3976 (substitute* '("test/functional/bio/test_command.rb",
3977 "test/data/command/echoarg2.sh")
3978 (("/bin/echo") (which "echo")))
3980 (synopsis "Ruby library, shell and utilities for bioinformatics")
3981 (description "BioRuby comes with a comprehensive set of Ruby development
3982 tools and libraries for bioinformatics and molecular biology. BioRuby has
3983 components for sequence analysis, pathway analysis, protein modelling and
3984 phylogenetic analysis; it supports many widely used data formats and provides
3985 easy access to databases, external programs and public web services, including
3986 BLAST, KEGG, GenBank, MEDLINE and GO.")
3987 (home-page "http://bioruby.org/")
3988 ;; Code is released under Ruby license, except for setup
3989 ;; (LGPLv2.1+) and scripts in samples (which have GPL2 and GPL2+)
3990 (license (list license:ruby license:lgpl2.1+ license:gpl2+ ))))
3992 (define-public r-acsnminer
3994 (name "r-acsnminer")
3995 (version "0.16.01.29")
3998 (uri (cran-uri "ACSNMineR" version))
4001 "1b1243wkncanm1blkqzicjgzb576vzcg4iwinsgn2xqr7f264amf"))))
4002 (properties `((upstream-name . "ACSNMineR")))
4003 (build-system r-build-system)
4005 `(("r-ggplot2" ,r-ggplot2)
4006 ("r-gridextra" ,r-gridextra)))
4007 (home-page "http://cran.r-project.org/web/packages/ACSNMineR")
4008 (synopsis "Gene enrichment analysis")
4010 "This package provides tools to compute and represent gene set enrichment
4011 or depletion from your data based on pre-saved maps from the @dfn{Atlas of
4012 Cancer Signalling Networks} (ACSN) or user imported maps. The gene set
4013 enrichment can be run with hypergeometric test or Fisher exact test, and can
4014 use multiple corrections. Visualization of data can be done either by
4015 barplots or heatmaps.")
4016 (license license:gpl2+)))
4018 (define-public r-biocgenerics
4020 (name "r-biocgenerics")
4024 (uri (bioconductor-uri "BiocGenerics" version))
4027 "0f16ryy5f012hvksrwlmm33bcl7lw97i2jvhbnwfwl03j4w7nhc1"))))
4029 `((upstream-name . "BiocGenerics")))
4030 (build-system r-build-system)
4031 (home-page "http://bioconductor.org/packages/BiocGenerics")
4032 (synopsis "S4 generic functions for Bioconductor")
4034 "This package provides S4 generic functions needed by many Bioconductor
4036 (license license:artistic2.0)))
4038 (define-public r-dnacopy
4044 (uri (bioconductor-uri "DNAcopy" version))
4047 "1c1px4rbr36xx929hp59k7ca9k5ab66qmn8k63fk13278ncm6h66"))))
4049 `((upstream-name . "DNAcopy")))
4050 (build-system r-build-system)
4052 `(("gfortran" ,gfortran)))
4053 (home-page "https://bioconductor.org/packages/DNAcopy")
4054 (synopsis "Implementation of a circular binary segmentation algorithm")
4055 (description "This package implements the circular binary segmentation (CBS)
4056 algorithm to segment DNA copy number data and identify genomic regions with
4057 abnormal copy number.")
4058 (license license:gpl2+)))
4060 (define-public r-s4vectors
4062 (name "r-s4vectors")
4066 (uri (bioconductor-uri "S4Vectors" version))
4069 "12iibcs63m9iy7f45wgjcqsna2dnqwckphk682389grshz0g4x66"))))
4071 `((upstream-name . "S4Vectors")))
4072 (build-system r-build-system)
4074 `(("r-biocgenerics" ,r-biocgenerics)))
4075 (home-page "http://bioconductor.org/packages/S4Vectors")
4076 (synopsis "S4 implementation of vectors and lists")
4078 "The S4Vectors package defines the @code{Vector} and @code{List} virtual
4079 classes and a set of generic functions that extend the semantic of ordinary
4080 vectors and lists in R. Package developers can easily implement vector-like
4081 or list-like objects as concrete subclasses of @code{Vector} or @code{List}.
4082 In addition, a few low-level concrete subclasses of general interest (e.g.
4083 @code{DataFrame}, @code{Rle}, and @code{Hits}) are implemented in the
4084 S4Vectors package itself.")
4085 (license license:artistic2.0)))
4087 (define-public r-iranges
4093 (uri (bioconductor-uri "IRanges" version))
4096 "0hi5k1j5jm4xrg1l506g279qw1xkvp1gg1zgsjzpbng4vx4k4iyl"))))
4098 `((upstream-name . "IRanges")))
4099 (build-system r-build-system)
4101 `(("r-biocgenerics" ,r-biocgenerics)
4102 ("r-s4vectors" ,r-s4vectors)))
4103 (home-page "http://bioconductor.org/packages/IRanges")
4104 (synopsis "Infrastructure for manipulating intervals on sequences")
4106 "This package provides efficient low-level and highly reusable S4 classes
4107 for storing ranges of integers, RLE vectors (Run-Length Encoding), and, more
4108 generally, data that can be organized sequentially (formally defined as
4109 @code{Vector} objects), as well as views on these @code{Vector} objects.
4110 Efficient list-like classes are also provided for storing big collections of
4111 instances of the basic classes. All classes in the package use consistent
4112 naming and share the same rich and consistent \"Vector API\" as much as
4114 (license license:artistic2.0)))
4116 (define-public r-genomeinfodb
4118 (name "r-genomeinfodb")
4122 (uri (bioconductor-uri "GenomeInfoDb" version))
4125 "1ggp005n2rlkad00ilzn95y4rd484yr1chdhnd6fwg45rbi94d63"))))
4127 `((upstream-name . "GenomeInfoDb")))
4128 (build-system r-build-system)
4130 `(("r-biocgenerics" ,r-biocgenerics)
4131 ("r-iranges" ,r-iranges)
4132 ("r-s4vectors" ,r-s4vectors)))
4133 (home-page "http://bioconductor.org/packages/GenomeInfoDb")
4134 (synopsis "Utilities for manipulating chromosome identifiers")
4136 "This package contains data and functions that define and allow
4137 translation between different chromosome sequence naming conventions (e.g.,
4138 \"chr1\" versus \"1\"), including a function that attempts to place sequence
4139 names in their natural, rather than lexicographic, order.")
4140 (license license:artistic2.0)))
4142 (define-public r-variantannotation
4144 (name "r-variantannotation")
4148 (uri (bioconductor-uri "VariantAnnotation" version))
4151 "1z42j3p9b8h725inq8n0230llsdbav3gwcxy1nliypzfkxbzahsb"))))
4153 `((upstream-name . "VariantAnnotation")))
4157 `(("r-annotationdbi" ,r-annotationdbi)
4158 ("r-biocgenerics" ,r-biocgenerics)
4159 ("r-bsgenome" ,r-bsgenome)
4161 ("r-genomeinfodb" ,r-genomeinfodb)
4162 ("r-genomicfeatures" ,r-genomicfeatures)
4163 ("r-genomicranges" ,r-genomicranges)
4164 ("r-summarizedexperiment" ,r-summarizedexperiment)
4165 ("r-rsamtools" ,r-rsamtools)
4166 ("r-zlibbioc" ,r-zlibbioc)))
4167 (build-system r-build-system)
4168 (home-page "https://bioconductor.org/packages/VariantAnnotation")
4169 (synopsis "Package for annotation of genetic variants")
4170 (description "This R package can annotate variants, compute amino acid
4171 coding changes and predict coding outcomes.")
4172 (license license:artistic2.0)))
4174 (define-public r-xvector
4180 (uri (bioconductor-uri "XVector" version))
4183 "0havwyr6xqk7w0rmbwfj9jq1djz7wzdz7w39adhklwzwz9l4ih3a"))))
4185 `((upstream-name . "XVector")))
4186 (build-system r-build-system)
4189 (modify-phases %standard-phases
4190 (add-after 'unpack 'use-system-zlib
4192 (substitute* "DESCRIPTION"
4193 (("zlibbioc, ") ""))
4194 (substitute* "NAMESPACE"
4195 (("import\\(zlibbioc\\)") ""))
4200 `(("r-biocgenerics" ,r-biocgenerics)
4201 ("r-iranges" ,r-iranges)
4202 ("r-s4vectors" ,r-s4vectors)))
4203 (home-page "http://bioconductor.org/packages/XVector")
4204 (synopsis "Representation and manpulation of external sequences")
4206 "This package provides memory efficient S4 classes for storing sequences
4207 \"externally\" (behind an R external pointer, or on disk).")
4208 (license license:artistic2.0)))
4210 (define-public r-genomicranges
4212 (name "r-genomicranges")
4216 (uri (bioconductor-uri "GenomicRanges" version))
4219 "02df5683nrpn9d10ws8jz9b55nr9055hh882xp2i154xdddir0k0"))))
4221 `((upstream-name . "GenomicRanges")))
4222 (build-system r-build-system)
4224 `(("r-biocgenerics" ,r-biocgenerics)
4225 ("r-genomeinfodb" ,r-genomeinfodb)
4226 ("r-xvector" ,r-xvector)))
4227 (home-page "http://bioconductor.org/packages/GenomicRanges")
4228 (synopsis "Representation and manipulation of genomic intervals")
4230 "This package provides tools to efficiently represent and manipulate
4231 genomic annotations and alignments is playing a central role when it comes to
4232 analyzing high-throughput sequencing data (a.k.a. NGS data). The
4233 GenomicRanges package defines general purpose containers for storing and
4234 manipulating genomic intervals and variables defined along a genome.")
4235 (license license:artistic2.0)))
4237 (define-public r-biobase
4243 (uri (bioconductor-uri "Biobase" version))
4246 "1qasjpq3kw8h7qw8cin3bjvv1256hqr1mm24fq3v0ymxzlb66szi"))))
4248 `((upstream-name . "Biobase")))
4249 (build-system r-build-system)
4251 `(("r-biocgenerics" ,r-biocgenerics)))
4252 (home-page "http://bioconductor.org/packages/Biobase")
4253 (synopsis "Base functions for Bioconductor")
4255 "This package provides functions that are needed by many other packages
4256 on Bioconductor or which replace R functions.")
4257 (license license:artistic2.0)))
4259 (define-public r-annotationdbi
4261 (name "r-annotationdbi")
4265 (uri (bioconductor-uri "AnnotationDbi" version))
4268 "1v6x62hgys5827yg2xayjrd9xawbayzm6wy0q4vxh1s6yxc9bklj"))))
4270 `((upstream-name . "AnnotationDbi")))
4271 (build-system r-build-system)
4273 `(("r-biobase" ,r-biobase)
4274 ("r-biocgenerics" ,r-biocgenerics)
4276 ("r-iranges" ,r-iranges)
4277 ("r-rsqlite" ,r-rsqlite)
4278 ("r-s4vectors" ,r-s4vectors)))
4279 (home-page "http://bioconductor.org/packages/AnnotationDbi")
4280 (synopsis "Annotation database interface")
4282 "This package provides user interface and database connection code for
4283 annotation data packages using SQLite data storage.")
4284 (license license:artistic2.0)))
4286 (define-public r-biomart
4292 (uri (bioconductor-uri "biomaRt" version))
4295 "1s709055abj2gd35g6nnk5d2ai5ii09iir270l2xika6pi62gj3f"))))
4297 `((upstream-name . "biomaRt")))
4298 (build-system r-build-system)
4300 `(("r-annotationdbi" ,r-annotationdbi)
4301 ("r-rcurl" ,r-rcurl)
4303 (home-page "http://bioconductor.org/packages/biomaRt")
4304 (synopsis "Interface to BioMart databases")
4306 "biomaRt provides an interface to a growing collection of databases
4307 implementing the @url{BioMart software suite, http://www.biomart.org}. The
4308 package enables retrieval of large amounts of data in a uniform way without
4309 the need to know the underlying database schemas or write complex SQL queries.
4310 Examples of BioMart databases are Ensembl, COSMIC, Uniprot, HGNC, Gramene,
4311 Wormbase and dbSNP mapped to Ensembl. These major databases give biomaRt
4312 users direct access to a diverse set of data and enable a wide range of
4313 powerful online queries from gene annotation to database mining.")
4314 (license license:artistic2.0)))
4316 (define-public r-biocparallel
4318 (name "r-biocparallel")
4322 (uri (bioconductor-uri "BiocParallel" version))
4325 "1f5mndx66vampcsq0n66afg6x851crl0h3nyv2nyp9bsgzj9cdzq"))))
4327 `((upstream-name . "BiocParallel")))
4328 (build-system r-build-system)
4330 `(("r-futile-logger" ,r-futile-logger)
4331 ("r-snow" ,r-snow)))
4332 (home-page "http://bioconductor.org/packages/BiocParallel")
4333 (synopsis "Bioconductor facilities for parallel evaluation")
4335 "This package provides modified versions and novel implementation of
4336 functions for parallel evaluation, tailored to use with Bioconductor
4338 (license (list license:gpl2+ license:gpl3+))))
4340 (define-public r-biostrings
4342 (name "r-biostrings")
4346 (uri (bioconductor-uri "Biostrings" version))
4349 "0cjd7i4bdwabzb02gm753aji5xaihkj5ak8nb0d32cclxbj0hp33"))))
4351 `((upstream-name . "Biostrings")))
4352 (build-system r-build-system)
4354 `(("r-biocgenerics" ,r-biocgenerics)
4355 ("r-iranges" ,r-iranges)
4356 ("r-s4vectors" ,r-s4vectors)
4357 ("r-xvector" ,r-xvector)))
4358 (home-page "http://bioconductor.org/packages/Biostrings")
4359 (synopsis "String objects and algorithms for biological sequences")
4361 "This package provides memory efficient string containers, string
4362 matching algorithms, and other utilities, for fast manipulation of large
4363 biological sequences or sets of sequences.")
4364 (license license:artistic2.0)))
4366 (define-public r-rsamtools
4368 (name "r-rsamtools")
4372 (uri (bioconductor-uri "Rsamtools" version))
4375 "1yc3nzzms3igjwr4l9yd3wdac95glcs08b4cfp7disyly0wcskjd"))))
4377 `((upstream-name . "Rsamtools")))
4378 (build-system r-build-system)
4381 (modify-phases %standard-phases
4382 (add-after 'unpack 'use-system-zlib
4384 (substitute* "DESCRIPTION"
4385 (("zlibbioc, ") ""))
4386 (substitute* "NAMESPACE"
4387 (("import\\(zlibbioc\\)") ""))
4392 `(("r-biocgenerics" ,r-biocgenerics)
4393 ("r-biocparallel" ,r-biocparallel)
4394 ("r-biostrings" ,r-biostrings)
4395 ("r-bitops" ,r-bitops)
4396 ("r-genomeinfodb" ,r-genomeinfodb)
4397 ("r-genomicranges" ,r-genomicranges)
4398 ("r-iranges" ,r-iranges)
4399 ("r-s4vectors" ,r-s4vectors)
4400 ("r-xvector" ,r-xvector)))
4401 (home-page "http://bioconductor.org/packages/release/bioc/html/Rsamtools.html")
4402 (synopsis "Interface to samtools, bcftools, and tabix")
4404 "This package provides an interface to the 'samtools', 'bcftools', and
4405 'tabix' utilities for manipulating SAM (Sequence Alignment / Map), FASTA,
4406 binary variant call (BCF) and compressed indexed tab-delimited (tabix)
4408 (license license:expat)))
4410 (define-public r-summarizedexperiment
4412 (name "r-summarizedexperiment")
4416 (uri (bioconductor-uri "SummarizedExperiment" version))
4419 "1gpmh1mi70m5k5qnyjs1h0qn8ajrzalzic7k3762xchxsmmdvxn4"))))
4421 `((upstream-name . "SummarizedExperiment")))
4422 (build-system r-build-system)
4424 `(("r-biobase" ,r-biobase)
4425 ("r-biocgenerics" ,r-biocgenerics)
4426 ("r-genomeinfodb" ,r-genomeinfodb)
4427 ("r-genomicranges" ,r-genomicranges)
4428 ("r-iranges" ,r-iranges)
4429 ("r-s4vectors" ,r-s4vectors)))
4430 (home-page "http://bioconductor.org/packages/SummarizedExperiment")
4431 (synopsis "Container for representing genomic ranges by sample")
4433 "The SummarizedExperiment container contains one or more assays, each
4434 represented by a matrix-like object of numeric or other mode. The rows
4435 typically represent genomic ranges of interest and the columns represent
4437 (license license:artistic2.0)))
4439 (define-public r-genomicalignments
4441 (name "r-genomicalignments")
4445 (uri (bioconductor-uri "GenomicAlignments" version))
4448 "02b9j1pfd39bkvb623k5k0ziq9rpw093hifqw65vb954dwj29jhd"))))
4450 `((upstream-name . "GenomicAlignments")))
4451 (build-system r-build-system)
4453 `(("r-biocgenerics" ,r-biocgenerics)
4454 ("r-biocparallel" ,r-biocparallel)
4455 ("r-biostrings" ,r-biostrings)
4456 ("r-genomeinfodb" ,r-genomeinfodb)
4457 ("r-genomicranges" ,r-genomicranges)
4458 ("r-iranges" ,r-iranges)
4459 ("r-rsamtools" ,r-rsamtools)
4460 ("r-s4vectors" ,r-s4vectors)
4461 ("r-summarizedexperiment" ,r-summarizedexperiment)))
4462 (home-page "http://bioconductor.org/packages/GenomicAlignments")
4463 (synopsis "Representation and manipulation of short genomic alignments")
4465 "This package provides efficient containers for storing and manipulating
4466 short genomic alignments (typically obtained by aligning short reads to a
4467 reference genome). This includes read counting, computing the coverage,
4468 junction detection, and working with the nucleotide content of the
4470 (license license:artistic2.0)))
4472 (define-public r-rtracklayer
4474 (name "r-rtracklayer")
4478 (uri (bioconductor-uri "rtracklayer" version))
4481 "0knjnwywh9k726mq28s3sy013zhw6d6nfa8hfw670720nq18i2p0"))))
4482 (build-system r-build-system)
4485 (modify-phases %standard-phases
4486 (add-after 'unpack 'use-system-zlib
4488 (substitute* "DESCRIPTION"
4489 (("zlibbioc, ") ""))
4490 (substitute* "NAMESPACE"
4491 (("import\\(zlibbioc\\)") ""))
4496 `(("r-biocgenerics" ,r-biocgenerics)
4497 ("r-biostrings" ,r-biostrings)
4498 ("r-genomeinfodb" ,r-genomeinfodb)
4499 ("r-genomicalignments" ,r-genomicalignments)
4500 ("r-genomicranges" ,r-genomicranges)
4501 ("r-iranges" ,r-iranges)
4502 ("r-rcurl" ,r-rcurl)
4503 ("r-rsamtools" ,r-rsamtools)
4504 ("r-s4vectors" ,r-s4vectors)
4506 ("r-xvector" ,r-xvector)))
4507 (home-page "http://bioconductor.org/packages/rtracklayer")
4508 (synopsis "R interface to genome browsers and their annotation tracks")
4510 "rtracklayer is an extensible framework for interacting with multiple
4511 genome browsers (currently UCSC built-in) and manipulating annotation tracks
4512 in various formats (currently GFF, BED, bedGraph, BED15, WIG, BigWig and 2bit
4513 built-in). The user may export/import tracks to/from the supported browsers,
4514 as well as query and modify the browser state, such as the current viewport.")
4515 (license license:artistic2.0)))
4517 (define-public r-genomicfeatures
4519 (name "r-genomicfeatures")
4523 (uri (bioconductor-uri "GenomicFeatures" version))
4526 "0n3rkj66la6wizgcsf2rmwcsyfxz9kv5zak337lmk1raqfnancz4"))))
4528 `((upstream-name . "GenomicFeatures")))
4529 (build-system r-build-system)
4531 `(("r-annotationdbi" ,r-annotationdbi)
4532 ("r-biobase" ,r-biobase)
4533 ("r-biocgenerics" ,r-biocgenerics)
4534 ("r-biomart" ,r-biomart)
4535 ("r-biostrings" ,r-biostrings)
4537 ("r-genomeinfodb" ,r-genomeinfodb)
4538 ("r-genomicranges" ,r-genomicranges)
4539 ("r-iranges" ,r-iranges)
4540 ("r-rcurl" ,r-rcurl)
4541 ("r-rsqlite" ,r-rsqlite)
4542 ("r-rtracklayer" ,r-rtracklayer)
4543 ("r-s4vectors" ,r-s4vectors)
4544 ("r-xvector" ,r-xvector)))
4545 (home-page "http://bioconductor.org/packages/GenomicFeatures")
4546 (synopsis "Tools for working with transcript centric annotations")
4548 "This package provides a set of tools and methods for making and
4549 manipulating transcript centric annotations. With these tools the user can
4550 easily download the genomic locations of the transcripts, exons and cds of a
4551 given organism, from either the UCSC Genome Browser or a BioMart
4552 database (more sources will be supported in the future). This information is
4553 then stored in a local database that keeps track of the relationship between
4554 transcripts, exons, cds and genes. Flexible methods are provided for
4555 extracting the desired features in a convenient format.")
4556 (license license:artistic2.0)))
4558 (define-public r-go-db
4564 (uri (string-append "http://www.bioconductor.org/packages/"
4565 "release/data/annotation/src/contrib/GO.db_"
4569 "00gariag9ampz82dh0xllrc26r85d7vdcwc0vca5zdy147rwxr7f"))))
4571 `((upstream-name . "GO.db")))
4572 (build-system r-build-system)
4574 `(("r-annotationdbi" ,r-annotationdbi)))
4575 (home-page "http://bioconductor.org/packages/GO.db")
4576 (synopsis "Annotation maps describing the entire Gene Ontology")
4578 "The purpose of this GO.db annotation package is to provide detailed
4579 information about the latest version of the Gene Ontologies.")
4580 (license license:artistic2.0)))
4582 (define-public r-graph
4588 (uri (bioconductor-uri "graph" version))
4591 "16w75rji3kv24gfv44w66y1a2y75ax26rl470y3ypna0ndc3rrcd"))))
4592 (build-system r-build-system)
4594 `(("r-biocgenerics" ,r-biocgenerics)))
4595 (home-page "http://bioconductor.org/packages/graph")
4596 (synopsis "Handle graph data structures in R")
4598 "This package implements some simple graph handling capabilities for R.")
4599 (license license:artistic2.0)))
4601 (define-public r-topgo
4607 (uri (bioconductor-uri "topGO" version))
4610 "029j9nb39b8l9xlzsp83pmjr8ap247aia387yzaa1yyw8klapdaf"))))
4612 `((upstream-name . "topGO")))
4613 (build-system r-build-system)
4615 `(("r-annotationdbi" ,r-annotationdbi)
4616 ("r-biobase" ,r-biobase)
4617 ("r-biocgenerics" ,r-biocgenerics)
4618 ("r-go-db" ,r-go-db)
4619 ("r-graph" ,r-graph)
4620 ("r-sparsem" ,r-sparsem)))
4621 (home-page "http://bioconductor.org/packages/topGO")
4622 (synopsis "Enrichment analysis for gene ontology")
4624 "The topGO package provides tools for testing @dfn{gene ontology} (GO)
4625 terms while accounting for the topology of the GO graph. Different test
4626 statistics and different methods for eliminating local similarities and
4627 dependencies between GO terms can be implemented and applied.")
4628 ;; Any version of the LGPL applies.
4629 (license license:lgpl2.1+)))
4631 (define-public r-bsgenome
4637 (uri (bioconductor-uri "BSgenome" version))
4640 "130w0m6q8kkca7gyz1aqj5jjhalwvwi6rk2yvbjrnj4gpnncyrd2"))))
4642 `((upstream-name . "BSgenome")))
4643 (build-system r-build-system)
4645 `(("r-biocgenerics" ,r-biocgenerics)
4646 ("r-biostrings" ,r-biostrings)
4647 ("r-genomeinfodb" ,r-genomeinfodb)
4648 ("r-genomicranges" ,r-genomicranges)
4649 ("r-iranges" ,r-iranges)
4650 ("r-rsamtools" ,r-rsamtools)
4651 ("r-rtracklayer" ,r-rtracklayer)
4652 ("r-s4vectors" ,r-s4vectors)
4653 ("r-xvector" ,r-xvector)))
4654 (home-page "http://bioconductor.org/packages/BSgenome")
4655 (synopsis "Infrastructure for Biostrings-based genome data packages")
4657 "This package provides infrastructure shared by all Biostrings-based
4658 genome data packages and support for efficient SNP representation.")
4659 (license license:artistic2.0)))
4661 (define-public r-impute
4667 (uri (bioconductor-uri "impute" version))
4670 "0y4x5jk7gsf4xn56jrkdcdnxpcfll4h6ivncd7n4snmzixldvmvw"))))
4672 `(("gfortran" ,gfortran)))
4673 (build-system r-build-system)
4674 (home-page "http://bioconductor.org/packages/impute")
4675 (synopsis "Imputation for microarray data")
4677 "This package provides a function to impute missing gene expression
4678 microarray data, using nearest neighbor averaging.")
4679 (license license:gpl2+)))
4681 (define-public r-seqpattern
4683 (name "r-seqpattern")
4687 (uri (bioconductor-uri "seqPattern" version))
4690 "0p9zj6bic7sa0hb2bjm988kkk5n9r1kvlbqkzvy702f642n0j53i"))))
4692 `((upstream-name . "seqPattern")))
4693 (build-system r-build-system)
4695 `(("r-biostrings" ,r-biostrings)
4696 ("r-genomicranges" ,r-genomicranges)
4697 ("r-iranges" ,r-iranges)
4698 ("r-plotrix" ,r-plotrix)))
4699 (home-page "http://bioconductor.org/packages/seqPattern")
4700 (synopsis "Visualising oligonucleotide patterns and motif occurrences")
4702 "This package provides tools to visualize oligonucleotide patterns and
4703 sequence motif occurrences across a large set of sequences centred at a common
4704 reference point and sorted by a user defined feature.")
4705 (license license:gpl3+)))
4707 (define-public r-genomation
4709 (name "r-genomation")
4713 (uri (bioconductor-uri "genomation" version))
4716 "0kvzwc21zsh2c8d34yn935ncn38bfkpzmknycd8h7b0521x20mi9"))))
4717 (build-system r-build-system)
4719 `(("r-biostrings" ,r-biostrings)
4720 ("r-bsgenome" ,r-bsgenome)
4721 ("r-data-table" ,r-data-table)
4722 ("r-genomeinfodb" ,r-genomeinfodb)
4723 ("r-genomicalignments" ,r-genomicalignments)
4724 ("r-genomicranges" ,r-genomicranges)
4725 ("r-ggplot2" ,r-ggplot2)
4726 ("r-gridbase" ,r-gridbase)
4727 ("r-impute" ,r-impute)
4728 ("r-iranges" ,r-iranges)
4729 ("r-matrixstats" ,r-matrixstats)
4730 ("r-plotrix" ,r-plotrix)
4732 ("r-readr" ,r-readr)
4733 ("r-reshape2" ,r-reshape2)
4734 ("r-rsamtools" ,r-rsamtools)
4735 ("r-rtracklayer" ,r-rtracklayer)
4736 ("r-seqpattern" ,r-seqpattern)))
4737 (home-page "http://bioinformatics.mdc-berlin.de/genomation/")
4738 (synopsis "Summary, annotation and visualization of genomic data")
4740 "This package provides a package for summary and annotation of genomic
4741 intervals. Users can visualize and quantify genomic intervals over
4742 pre-defined functional regions, such as promoters, exons, introns, etc. The
4743 genomic intervals represent regions with a defined chromosome position, which
4744 may be associated with a score, such as aligned reads from HT-seq experiments,
4745 TF binding sites, methylation scores, etc. The package can use any tabular
4746 genomic feature data as long as it has minimal information on the locations of
4747 genomic intervals. In addition, it can use BAM or BigWig files as input.")
4748 (license license:artistic2.0)))
4750 (define-public r-org-hs-eg-db
4752 (name "r-org-hs-eg-db")
4756 ;; We cannot use bioconductor-uri here because this tarball is
4757 ;; located under "data/annotation/" instead of "bioc/".
4758 (uri (string-append "http://www.bioconductor.org/packages/"
4759 "release/data/annotation/src/contrib/"
4760 "org.Hs.eg.db_" version ".tar.gz"))
4763 "0xicgkbh6xkvs74s1piafqac63dyz2ycdyil4pj4ghhxx2sabm6p"))))
4765 `((upstream-name . "org.Hs.eg.db")))
4766 (build-system r-build-system)
4768 `(("r-annotationdbi" ,r-annotationdbi)))
4769 (home-page "http://www.bioconductor.org/packages/org.Hs.eg.db/")
4770 (synopsis "Genome wide annotation for Human")
4772 "This package provides mappings from Entrez gene identifiers to various
4773 annotations for the human genome.")
4774 (license license:artistic2.0)))
4776 (define-public r-org-ce-eg-db
4778 (name "r-org-ce-eg-db")
4782 ;; We cannot use bioconductor-uri here because this tarball is
4783 ;; located under "data/annotation/" instead of "bioc/".
4784 (uri (string-append "http://www.bioconductor.org/packages/"
4785 "release/data/annotation/src/contrib/"
4786 "org.Ce.eg.db_" version ".tar.gz"))
4789 "1d0lx00ybq34yqs6mziaa0lrh77xm0ggsmi76g6k95f77gi7m1sw"))))
4791 `((upstream-name . "org.Ce.eg.db")))
4792 (build-system r-build-system)
4794 `(("r-annotationdbi" ,r-annotationdbi)))
4795 (home-page "http://www.bioconductor.org/packages/org.Ce.eg.db/")
4796 (synopsis "Genome wide annotation for Worm")
4798 "This package provides mappings from Entrez gene identifiers to various
4799 annotations for the genome of the model worm Caenorhabditis elegans.")
4800 (license license:artistic2.0)))
4802 (define-public r-org-dm-eg-db
4804 (name "r-org-dm-eg-db")
4808 ;; We cannot use bioconductor-uri here because this tarball is
4809 ;; located under "data/annotation/" instead of "bioc/".
4810 (uri (string-append "http://www.bioconductor.org/packages/"
4811 "release/data/annotation/src/contrib/"
4812 "org.Dm.eg.db_" version ".tar.gz"))
4815 "0mib46c7nr00l7mh290n383za9hyl91a1dc6jhjbk884jmxaxyz6"))))
4817 `((upstream-name . "org.Dm.eg.db")))
4818 (build-system r-build-system)
4820 `(("r-annotationdbi" ,r-annotationdbi)))
4821 (home-page "http://www.bioconductor.org/packages/org.Dm.eg.db/")
4822 (synopsis "Genome wide annotation for Fly")
4824 "This package provides mappings from Entrez gene identifiers to various
4825 annotations for the genome of the model fruit fly Drosophila melanogaster.")
4826 (license license:artistic2.0)))
4828 (define-public r-org-mm-eg-db
4830 (name "r-org-mm-eg-db")
4834 ;; We cannot use bioconductor-uri here because this tarball is
4835 ;; located under "data/annotation/" instead of "bioc/".
4836 (uri (string-append "http://www.bioconductor.org/packages/"
4837 "release/data/annotation/src/contrib/"
4838 "org.Mm.eg.db_" version ".tar.gz"))
4841 "0wh1pm3npdg7070875kfgiid3bqkz3q7rq6snhk6bxfvph00298y"))))
4843 `((upstream-name . "org.Mm.eg.db")))
4844 (build-system r-build-system)
4846 `(("r-annotationdbi" ,r-annotationdbi)))
4847 (home-page "http://www.bioconductor.org/packages/org.Mm.eg.db/")
4848 (synopsis "Genome wide annotation for Mouse")
4850 "This package provides mappings from Entrez gene identifiers to various
4851 annotations for the genome of the model mouse Mus musculus.")
4852 (license license:artistic2.0)))
4854 (define-public r-seqlogo
4861 (uri (bioconductor-uri "seqLogo" version))
4864 "0kn1a1nf2j4v9c09vjkz9bmxlln7yhg87bnyrdsxy1m55x56rn5k"))))
4865 (properties `((upstream-name . "seqLogo")))
4866 (build-system r-build-system)
4867 (home-page "http://bioconductor.org/packages/seqLogo")
4868 (synopsis "Sequence logos for DNA sequence alignments")
4870 "seqLogo takes the position weight matrix of a DNA sequence motif and
4871 plots the corresponding sequence logo as introduced by Schneider and
4873 (license license:lgpl2.0+)))
4875 (define-public r-bsgenome-hsapiens-ucsc-hg19
4877 (name "r-bsgenome-hsapiens-ucsc-hg19")
4881 ;; We cannot use bioconductor-uri here because this tarball is
4882 ;; located under "data/annotation/" instead of "bioc/".
4883 (uri (string-append "http://www.bioconductor.org/packages/"
4884 "release/data/annotation/src/contrib/"
4885 "BSgenome.Hsapiens.UCSC.hg19_"
4889 "1y0nqpk8cw5a34sd9hmin3z4v7iqm6hf6l22cl81vlbxqbjibxc8"))))
4891 `((upstream-name . "BSgenome.Hsapiens.UCSC.hg19")))
4892 (build-system r-build-system)
4893 ;; As this package provides little more than a very large data file it
4894 ;; doesn't make sense to build substitutes.
4895 (arguments `(#:substitutable? #f))
4897 `(("r-bsgenome" ,r-bsgenome)))
4899 "http://www.bioconductor.org/packages/BSgenome.Hsapiens.UCSC.hg19/")
4900 (synopsis "Full genome sequences for Homo sapiens")
4902 "This package provides full genome sequences for Homo sapiens as provided
4903 by UCSC (hg19, February 2009) and stored in Biostrings objects.")
4904 (license license:artistic2.0)))
4906 (define-public r-bsgenome-mmusculus-ucsc-mm9
4908 (name "r-bsgenome-mmusculus-ucsc-mm9")
4912 ;; We cannot use bioconductor-uri here because this tarball is
4913 ;; located under "data/annotation/" instead of "bioc/".
4914 (uri (string-append "http://www.bioconductor.org/packages/"
4915 "release/data/annotation/src/contrib/"
4916 "BSgenome.Mmusculus.UCSC.mm9_"
4920 "1birqw30g2azimxpnjfzmkphan7x131yy8b9h85lfz5fjdg7841i"))))
4922 `((upstream-name . "BSgenome.Mmusculus.UCSC.mm9")))
4923 (build-system r-build-system)
4924 ;; As this package provides little more than a very large data file it
4925 ;; doesn't make sense to build substitutes.
4926 (arguments `(#:substitutable? #f))
4928 `(("r-bsgenome" ,r-bsgenome)))
4930 "http://www.bioconductor.org/packages/BSgenome.Mmusculus.UCSC.mm9/")
4931 (synopsis "Full genome sequences for Mouse")
4933 "This package provides full genome sequences for Mus musculus (Mouse) as
4934 provided by UCSC (mm9, July 2007) and stored in Biostrings objects.")
4935 (license license:artistic2.0)))
4937 (define-public r-bsgenome-celegans-ucsc-ce6
4939 (name "r-bsgenome-celegans-ucsc-ce6")
4943 ;; We cannot use bioconductor-uri here because this tarball is
4944 ;; located under "data/annotation/" instead of "bioc/".
4945 (uri (string-append "http://www.bioconductor.org/packages/"
4946 "release/data/annotation/src/contrib/"
4947 "BSgenome.Celegans.UCSC.ce6_"
4951 "0mqzb353xv2c3m3vkb315dkmnxkgczp7ndnknyhpgjlybyf715v9"))))
4953 `((upstream-name . "BSgenome.Celegans.UCSC.ce6")))
4954 (build-system r-build-system)
4955 ;; As this package provides little more than a very large data file it
4956 ;; doesn't make sense to build substitutes.
4957 (arguments `(#:substitutable? #f))
4959 `(("r-bsgenome" ,r-bsgenome)))
4961 "http://www.bioconductor.org/packages/BSgenome.Celegans.UCSC.ce6/")
4962 (synopsis "Full genome sequences for Worm")
4964 "This package provides full genome sequences for Caenorhabditis
4965 elegans (Worm) as provided by UCSC (ce6, May 2008) and stored in Biostrings
4967 (license license:artistic2.0)))
4969 (define-public r-bsgenome-dmelanogaster-ucsc-dm3
4971 (name "r-bsgenome-dmelanogaster-ucsc-dm3")
4975 ;; We cannot use bioconductor-uri here because this tarball is
4976 ;; located under "data/annotation/" instead of "bioc/".
4977 (uri (string-append "http://www.bioconductor.org/packages/"
4978 "release/data/annotation/src/contrib/"
4979 "BSgenome.Dmelanogaster.UCSC.dm3_"
4983 "19bm3lkhhkag3gnwp419211fh0cnr0x6fa0r1lr0ycwrikxdxsv8"))))
4985 `((upstream-name . "BSgenome.Dmelanogaster.UCSC.dm3")))
4986 (build-system r-build-system)
4987 ;; As this package provides little more than a very large data file it
4988 ;; doesn't make sense to build substitutes.
4989 (arguments `(#:substitutable? #f))
4991 `(("r-bsgenome" ,r-bsgenome)))
4993 "http://www.bioconductor.org/packages/BSgenome.Dmelanogaster.UCSC.dm3/")
4994 (synopsis "Full genome sequences for Fly")
4996 "This package provides full genome sequences for Drosophila
4997 melanogaster (Fly) as provided by UCSC (dm3, April 2006) and stored in
4998 Biostrings objects.")
4999 (license license:artistic2.0)))
5001 (define-public r-motifrg
5008 (uri (bioconductor-uri "motifRG" version))
5011 "1v9zm5629k2lcqbbgw8bwflvbircyxkfavbkvmbd212kgwcng8vn"))))
5012 (properties `((upstream-name . "motifRG")))
5013 (build-system r-build-system)
5015 `(("r-biostrings" ,r-biostrings)
5016 ("r-bsgenome" ,r-bsgenome)
5017 ("r-bsgenome.hsapiens.ucsc.hg19" ,r-bsgenome-hsapiens-ucsc-hg19)
5018 ("r-iranges" ,r-iranges)
5019 ("r-seqlogo" ,r-seqlogo)
5020 ("r-xvector" ,r-xvector)))
5021 (home-page "http://bioconductor.org/packages/motifRG")
5022 (synopsis "Discover motifs in high throughput sequencing data")
5024 "This package provides tools for discriminative motif discovery in high
5025 throughput genetic sequencing data sets using regression methods.")
5026 (license license:artistic2.0)))
5028 (define-public r-qtl
5035 (uri (string-append "mirror://cran/src/contrib/qtl_"
5039 "1grwgvyv7x0dgay1858bg7qf4wk47gpnq7qkqpcda9cn0h970d6f"))))
5040 (build-system r-build-system)
5041 (home-page "http://rqtl.org/")
5042 (synopsis "R package for analyzing QTL experiments in genetics")
5043 (description "R/qtl is an extension library for the R statistics
5044 system. It is used to analyze experimental crosses for identifying
5045 genes contributing to variation in quantitative traits (so-called
5046 quantitative trait loci, QTLs).
5048 Using a hidden Markov model, R/qtl allows to estimate genetic maps, to
5049 identify genotyping errors, and to perform single-QTL and two-QTL,
5050 two-dimensional genome scans.")
5051 (license license:gpl3)))
5053 (define-public r-zlibbioc
5059 (uri (bioconductor-uri "zlibbioc" version))
5062 "01wc26ndg4jsn1wyrl6zzq636gxaip5fci0xapym4lh9wryc4wnw"))))
5064 `((upstream-name . "zlibbioc")))
5065 (build-system r-build-system)
5066 (home-page "https://bioconductor.org/packages/zlibbioc")
5067 (synopsis "Provider for zlib-1.2.5 to R packages")
5068 (description "This package uses the source code of zlib-1.2.5 to create
5069 libraries for systems that do not have these available via other means.")
5070 (license license:artistic2.0)))
5078 (uri (string-append "https://pypi.python.org/packages/source/P"
5079 "/PePr/PePr-" version ".tar.gz"))
5082 "0qxjfdpl1b1y53nccws2d85f6k74zwmx8y8sd9rszcqhfayx6gdx"))))
5083 (build-system python-build-system)
5085 `(#:python ,python-2 ; python2 only
5086 #:tests? #f ; no tests included
5088 (modify-phases %standard-phases
5089 ;; When setuptools is used a ".egg" archive is generated and
5090 ;; installed. This makes it hard to actually run PePr. This issue
5091 ;; has been reported upstream:
5092 ;; https://github.com/shawnzhangyx/PePr/issues/9
5093 (add-after 'unpack 'disable-egg-generation
5095 (substitute* "setup.py"
5096 (("from setuptools import setup")
5097 "from distutils.core import setup"))
5100 `(("python2-numpy" ,python2-numpy)
5101 ("python2-scipy" ,python2-scipy)
5102 ("python2-pysam" ,python2-pysam)))
5103 (home-page "https://code.google.com/p/pepr-chip-seq/")
5104 (synopsis "Peak-calling and prioritization pipeline for ChIP-Seq data")
5106 "PePr is a ChIP-Seq peak calling or differential binding analysis tool
5107 that is primarily designed for data with biological replicates. It uses a
5108 negative binomial distribution to model the read counts among the samples in
5109 the same group, and look for consistent differences between ChIP and control
5110 group or two ChIP groups run under different conditions.")
5111 (license license:gpl3+)))
5113 (define-public filevercmp
5114 (let ((commit "1a9b779b93d0b244040274794d402106907b71b7"))
5117 (version (string-append "0-1." (string-take commit 7)))
5120 (uri (string-append "https://github.com/ekg/filevercmp/archive/"
5122 (file-name (string-append name "-" version ".tar.gz"))
5124 (base32 "0yp5jswf5j2pqc6517x277s4s6h1ss99v57kxw9gy0jkfl3yh450"))))
5125 (build-system gnu-build-system)
5127 `(#:tests? #f ; There are no tests to run.
5129 (modify-phases %standard-phases
5130 (delete 'configure) ; There is no configure phase.
5132 (lambda* (#:key outputs #:allow-other-keys)
5133 (let ((bin (string-append (assoc-ref outputs "out") "/bin")))
5134 (install-file "filevercmp" bin)))))))
5135 (home-page "https://github.com/ekg/filevercmp")
5136 (synopsis "This program compares version strings")
5137 (description "This program compares version strings. It intends to be a
5138 replacement for strverscmp.")
5139 (license license:gpl3+))))