1 ;;; GNU Guix --- Functional package management for GNU
2 ;;; Copyright © 2014, 2015, 2016, 2017 Ricardo Wurmus <rekado@elephly.net>
3 ;;; Copyright © 2015, 2016, 2017 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, 2017 Efraim Flashner <efraim@flashner.co.il>
8 ;;; Copyright © 2016 Marius Bakke <mbakke@fastmail.com>
9 ;;; Copyright © 2016 Raoul Bonnal <ilpuccio.febo@gmail.com>
11 ;;; This file is part of GNU Guix.
13 ;;; GNU Guix is free software; you can redistribute it and/or modify it
14 ;;; under the terms of the GNU General Public License as published by
15 ;;; the Free Software Foundation; either version 3 of the License, or (at
16 ;;; your option) any later version.
18 ;;; GNU Guix is distributed in the hope that it will be useful, but
19 ;;; WITHOUT ANY WARRANTY; without even the implied warranty of
20 ;;; MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
21 ;;; GNU General Public License for more details.
23 ;;; You should have received a copy of the GNU General Public License
24 ;;; along with GNU Guix. If not, see <http://www.gnu.org/licenses/>.
26 (define-module (gnu packages bioinformatics)
27 #:use-module ((guix licenses) #:prefix license:)
28 #:use-module (guix packages)
29 #:use-module (guix utils)
30 #:use-module (guix download)
31 #:use-module (guix git-download)
32 #:use-module (guix hg-download)
33 #:use-module (guix build-system ant)
34 #:use-module (guix build-system gnu)
35 #:use-module (guix build-system cmake)
36 #:use-module (guix build-system ocaml)
37 #:use-module (guix build-system perl)
38 #:use-module (guix build-system python)
39 #:use-module (guix build-system r)
40 #:use-module (guix build-system ruby)
41 #:use-module (guix build-system trivial)
42 #:use-module (gnu packages)
43 #:use-module (gnu packages autotools)
44 #:use-module (gnu packages algebra)
45 #:use-module (gnu packages base)
46 #:use-module (gnu packages bash)
47 #:use-module (gnu packages bison)
48 #:use-module (gnu packages boost)
49 #:use-module (gnu packages compression)
50 #:use-module (gnu packages cpio)
51 #:use-module (gnu packages cran)
52 #:use-module (gnu packages curl)
53 #:use-module (gnu packages documentation)
54 #:use-module (gnu packages databases)
55 #:use-module (gnu packages datastructures)
56 #:use-module (gnu packages file)
57 #:use-module (gnu packages flex)
58 #:use-module (gnu packages gawk)
59 #:use-module (gnu packages gcc)
60 #:use-module (gnu packages gd)
61 #:use-module (gnu packages gtk)
62 #:use-module (gnu packages glib)
63 #:use-module (gnu packages graph)
64 #:use-module (gnu packages groff)
65 #:use-module (gnu packages guile)
66 #:use-module (gnu packages haskell)
67 #:use-module (gnu packages image)
68 #:use-module (gnu packages imagemagick)
69 #:use-module (gnu packages java)
70 #:use-module (gnu packages ldc)
71 #:use-module (gnu packages linux)
72 #:use-module (gnu packages logging)
73 #:use-module (gnu packages machine-learning)
74 #:use-module (gnu packages man)
75 #:use-module (gnu packages maths)
76 #:use-module (gnu packages mpi)
77 #:use-module (gnu packages ncurses)
78 #:use-module (gnu packages ocaml)
79 #:use-module (gnu packages pcre)
80 #:use-module (gnu packages parallel)
81 #:use-module (gnu packages pdf)
82 #:use-module (gnu packages perl)
83 #:use-module (gnu packages pkg-config)
84 #:use-module (gnu packages popt)
85 #:use-module (gnu packages protobuf)
86 #:use-module (gnu packages python)
87 #:use-module (gnu packages readline)
88 #:use-module (gnu packages ruby)
89 #:use-module (gnu packages serialization)
90 #:use-module (gnu packages shells)
91 #:use-module (gnu packages statistics)
92 #:use-module (gnu packages swig)
93 #:use-module (gnu packages tbb)
94 #:use-module (gnu packages tex)
95 #:use-module (gnu packages texinfo)
96 #:use-module (gnu packages textutils)
97 #:use-module (gnu packages time)
98 #:use-module (gnu packages tls)
99 #:use-module (gnu packages vim)
100 #:use-module (gnu packages web)
101 #:use-module (gnu packages xml)
102 #:use-module (gnu packages xorg)
103 #:use-module (srfi srfi-1)
104 #:use-module (ice-9 match))
113 (uri (cran-uri "ape" version))
116 "0959fiiy11rzfzrzaknmgrx64bhszj02l0ycz79k5a6bmpfzanlk"))))
117 (build-system r-build-system)
119 `(("r-lattice" ,r-lattice)
121 (home-page "http://ape-package.ird.fr/")
122 (synopsis "Analyses of phylogenetics and evolution")
124 "This package provides functions for reading, writing, plotting, and
125 manipulating phylogenetic trees, analyses of comparative data in a
126 phylogenetic framework, ancestral character analyses, analyses of
127 diversification and macroevolution, computing distances from DNA sequences,
128 and several other tools.")
129 (license license:gpl2+)))
131 (define-public aragorn
138 "http://mbio-serv2.mbioekol.lu.se/ARAGORN/Downloads/aragorn"
142 "09i1rg716smlbnixfm7q1ml2mfpaa2fpn3hwjg625ysmfwwy712b"))))
143 (build-system gnu-build-system)
145 `(#:tests? #f ; there are no tests
147 (modify-phases %standard-phases
151 (zero? (system* "gcc"
157 (string-append "aragorn" ,version ".c")))))
159 (lambda* (#:key outputs #:allow-other-keys)
160 (let* ((out (assoc-ref outputs "out"))
161 (bin (string-append out "/bin"))
162 (man (string-append out "/share/man/man1")))
164 (install-file "aragorn" bin)
166 (install-file "aragorn.1" man))
168 (home-page "http://mbio-serv2.mbioekol.lu.se/ARAGORN")
169 (synopsis "Detect tRNA, mtRNA and tmRNA genes in nucleotide sequences")
171 "Aragorn identifies transfer RNA, mitochondrial RNA and
172 transfer-messenger RNA from nucleotide sequences, based on homology to known
173 tRNA consensus sequences and RNA structure. It also outputs the secondary
174 structure of the predicted RNA.")
175 (license license:gpl2)))
183 ;; BamM is not available on pypi.
185 "https://github.com/Ecogenomics/BamM/archive/"
187 (file-name (string-append name "-" version ".tar.gz"))
190 "1f35yxp4pc8aadsvbpg6r4kg2jh4fkjci0iby4iyljm6980sac0s"))
191 (modules '((guix build utils)))
194 ;; Delete bundled htslib.
195 (delete-file-recursively "c/htslib-1.3.1")
197 (build-system python-build-system)
199 `(#:python ,python-2 ; BamM is Python 2 only.
200 ;; Do not use bundled libhts. Do use the bundled libcfu because it has
201 ;; been modified from its original form.
203 (let ((htslib (assoc-ref %build-inputs "htslib")))
204 (list "--with-libhts-lib" (string-append htslib "/lib")
205 "--with-libhts-inc" (string-append htslib "/include/htslib")))
207 (modify-phases %standard-phases
208 (add-after 'unpack 'autogen
210 (with-directory-excursion "c"
211 (let ((sh (which "sh")))
212 ;; Use autogen so that 'configure' works.
213 (substitute* "autogen.sh" (("/bin/sh") sh))
214 (setenv "CONFIG_SHELL" sh)
215 (substitute* "configure" (("/bin/sh") sh))
216 (zero? (system* "./autogen.sh"))))))
218 ;; Run tests after installation so compilation only happens once.
220 (add-after 'install 'wrap-executable
221 (lambda* (#:key outputs #:allow-other-keys)
222 (let* ((out (assoc-ref outputs "out"))
223 (path (getenv "PATH")))
224 (wrap-program (string-append out "/bin/bamm")
225 `("PATH" ":" prefix (,path))))
227 (add-after 'wrap-executable 'post-install-check
228 (lambda* (#:key inputs outputs #:allow-other-keys)
230 (string-append (assoc-ref outputs "out")
235 (assoc-ref outputs "out")
237 (string-take (string-take-right
238 (assoc-ref inputs "python") 5) 3)
240 (getenv "PYTHONPATH")))
241 ;; There are 2 errors printed, but they are safe to ignore:
242 ;; 1) [E::hts_open_format] fail to open file ...
243 ;; 2) samtools view: failed to open ...
244 (zero? (system* "nosetests")))))))
246 `(("autoconf" ,autoconf)
247 ("automake" ,automake)
250 ("python-nose" ,python2-nose)
251 ("python-pysam" ,python2-pysam)))
253 `(("htslib" ,htslib-1.3) ; At least one test fails on htslib-1.4+.
254 ("samtools" ,samtools)
258 ("coreutils" ,coreutils)))
260 `(("python-numpy" ,python2-numpy)))
261 (home-page "http://ecogenomics.github.io/BamM/")
262 (synopsis "Metagenomics-focused BAM file manipulator")
264 "BamM is a C library, wrapped in python, to efficiently generate and
265 parse BAM files, specifically for the analysis of metagenomic data. For
266 instance, it implements several methods to assess contig-wise read coverage.")
267 (license license:lgpl3+)))
269 (define-public bamtools
276 "https://github.com/pezmaster31/bamtools/archive/v"
278 (file-name (string-append name "-" version ".tar.gz"))
281 "0jr024kcrhjb82cm69i7p5fcg5375zlc1h3qh2n1v368hcd0qflk"))))
282 (build-system cmake-build-system)
284 `(#:tests? #f ;no "check" target
286 (modify-phases %standard-phases
288 'configure 'set-ldflags
289 (lambda* (#:key outputs #:allow-other-keys)
293 (assoc-ref outputs "out") "/lib/bamtools")))))))
294 (inputs `(("zlib" ,zlib)))
295 (home-page "https://github.com/pezmaster31/bamtools")
296 (synopsis "C++ API and command-line toolkit for working with BAM data")
298 "BamTools provides both a C++ API and a command-line toolkit for handling
300 (license license:expat)))
302 (define-public bcftools
309 "https://github.com/samtools/bcftools/releases/download/"
310 version "/bcftools-" version ".tar.bz2"))
313 "0093hkkvxmbwfaa7905s6185jymynvg42kq6sxv7fili11l5mxwz"))
314 (patches (search-patches "bcftools-regidx-unsigned-char.patch"))
315 (modules '((guix build utils)))
317 ;; Delete bundled htslib.
318 '(delete-file-recursively "htslib-1.5"))))
319 (build-system gnu-build-system)
321 `(#:test-target "test"
322 #:configure-flags (list "--with-htslib=system")
326 "LIBS=-lgsl -lgslcblas"
327 (string-append "prefix=" (assoc-ref %outputs "out"))
328 (string-append "HTSDIR=" (assoc-ref %build-inputs "htslib") "/include")
329 (string-append "HTSLIB=" (assoc-ref %build-inputs "htslib") "/lib/libhts.so")
330 (string-append "BGZIP=" (assoc-ref %build-inputs "htslib") "/bin/bgzip")
331 (string-append "TABIX=" (assoc-ref %build-inputs "htslib") "/bin/tabix")
332 (string-append "PACKAGE_VERSION=" ,version))
334 (modify-phases %standard-phases
335 (add-before 'check 'patch-tests
337 (substitute* "test/test.pl"
338 (("/bin/bash") (which "bash")))
346 (home-page "https://samtools.github.io/bcftools/")
347 (synopsis "Utilities for variant calling and manipulating VCFs and BCFs")
349 "BCFtools is a set of utilities that manipulate variant calls in the
350 Variant Call Format (VCF) and its binary counterpart BCF. All commands work
351 transparently with both VCFs and BCFs, both uncompressed and BGZF-compressed.")
352 ;; The sources are dual MIT/GPL, but becomes GPL-only when USE_GPL=1.
353 (license (list license:gpl3+ license:expat))))
355 (define-public bedops
361 (uri (string-append "https://github.com/bedops/bedops/archive/v"
363 (file-name (string-append name "-" version ".tar.gz"))
366 "1kqbac547wyqma81cyky9n7mkgikjpsfd3nnmcm6hpqwanqgh10v"))))
367 (build-system gnu-build-system)
370 #:make-flags (list (string-append "BINDIR=" %output "/bin"))
372 (modify-phases %standard-phases
373 (add-after 'unpack 'unpack-tarballs
375 ;; FIXME: Bedops includes tarballs of minimally patched upstream
376 ;; libraries jansson, zlib, and bzip2. We cannot just use stock
377 ;; libraries because at least one of the libraries (zlib) is
378 ;; patched to add a C++ function definition (deflateInit2cpp).
379 ;; Until the Bedops developers offer a way to link against system
380 ;; libraries we have to build the in-tree copies of these three
383 ;; See upstream discussion:
384 ;; https://github.com/bedops/bedops/issues/124
386 ;; Unpack the tarballs to benefit from shebang patching.
387 (with-directory-excursion "third-party"
388 (and (zero? (system* "tar" "xvf" "jansson-2.6.tar.bz2"))
389 (zero? (system* "tar" "xvf" "zlib-1.2.7.tar.bz2"))
390 (zero? (system* "tar" "xvf" "bzip2-1.0.6.tar.bz2"))))
391 ;; Disable unpacking of tarballs in Makefile.
392 (substitute* "system.mk/Makefile.linux"
393 (("^\tbzcat .*") "\t@echo \"not unpacking\"\n")
394 (("\\./configure") "CONFIG_SHELL=bash ./configure"))
395 (substitute* "third-party/zlib-1.2.7/Makefile.in"
396 (("^SHELL=.*$") "SHELL=bash\n"))
398 (delete 'configure))))
399 (home-page "https://github.com/bedops/bedops")
400 (synopsis "Tools for high-performance genomic feature operations")
402 "BEDOPS is a suite of tools to address common questions raised in genomic
403 studies---mostly with regard to overlap and proximity relationships between
404 data sets. It aims to be scalable and flexible, facilitating the efficient
405 and accurate analysis and management of large-scale genomic data.
407 BEDOPS provides tools that perform highly efficient and scalable Boolean and
408 other set operations, statistical calculations, archiving, conversion and
409 other management of genomic data of arbitrary scale. Tasks can be easily
410 split by chromosome for distributing whole-genome analyses across a
411 computational cluster.")
412 (license license:gpl2+)))
414 (define-public bedtools
420 (uri (string-append "https://github.com/arq5x/bedtools2/archive/v"
422 (file-name (string-append name "-" version ".tar.gz"))
425 "0xvri5hnp2iim1cx6mcd5d9f102p5ql41x69rd6106x1c17pinqm"))))
426 (build-system gnu-build-system)
427 (native-inputs `(("python" ,python-2)))
428 (inputs `(("samtools" ,samtools)
431 '(#:test-target "test"
433 (modify-phases %standard-phases
436 (lambda* (#:key outputs #:allow-other-keys)
437 (let ((bin (string-append (assoc-ref outputs "out") "/bin/")))
438 (for-each (lambda (file)
439 (install-file file bin))
440 (find-files "bin" ".*")))
442 (home-page "https://github.com/arq5x/bedtools2")
443 (synopsis "Tools for genome analysis and arithmetic")
445 "Collectively, the bedtools utilities are a swiss-army knife of tools for
446 a wide-range of genomics analysis tasks. The most widely-used tools enable
447 genome arithmetic: that is, set theory on the genome. For example, bedtools
448 allows one to intersect, merge, count, complement, and shuffle genomic
449 intervals from multiple files in widely-used genomic file formats such as BAM,
451 (license license:gpl2)))
453 ;; Later releases of bedtools produce files with more columns than
454 ;; what Ribotaper expects.
455 (define-public bedtools-2.18
456 (package (inherit bedtools)
461 (uri (string-append "https://github.com/arq5x/bedtools2/"
462 "archive/v" version ".tar.gz"))
463 (file-name (string-append name "-" version ".tar.gz"))
466 "05vrnr8yp7swfagshzpgqmzk1blnwnq8pq5pckzi1m26w98d63vf"))))))
468 (define-public ribotaper
474 (uri (string-append "https://ohlerlab.mdc-berlin.de/"
475 "files/RiboTaper/RiboTaper_Version_"
479 "0ykjbps1y3z3085q94npw8i9x5gldc6shy8vlc08v76zljsm07hv"))))
480 (build-system gnu-build-system)
482 `(("bedtools" ,bedtools-2.18)
483 ("samtools" ,samtools-0.1)
484 ("r-minimal" ,r-minimal)
485 ("r-foreach" ,r-foreach)
486 ("r-xnomial" ,r-xnomial)
488 ("r-multitaper" ,r-multitaper)
489 ("r-seqinr" ,r-seqinr)))
490 (home-page "https://ohlerlab.mdc-berlin.de/software/RiboTaper_126/")
491 (synopsis "Define translated ORFs using ribosome profiling data")
493 "Ribotaper is a method for defining translated @dfn{open reading
494 frames} (ORFs) using ribosome profiling (ribo-seq) data. This package
495 provides the Ribotaper pipeline.")
496 (license license:gpl3+)))
498 (define-public ribodiff
505 (uri (string-append "https://github.com/ratschlab/RiboDiff/"
506 "archive/v" version ".tar.gz"))
507 (file-name (string-append name "-" version ".tar.gz"))
510 "0wpbwmfv05wdjxv7ikm664f7s7p7cqr8jnw99zrda0q67rl50aaj"))))
511 (build-system python-build-system)
515 (modify-phases %standard-phases
516 ;; Generate an installable executable script wrapper.
517 (add-after 'unpack 'patch-setup.py
519 (substitute* "setup.py"
520 (("^(.*)packages=.*" line prefix)
521 (string-append line "\n"
522 prefix "scripts=['scripts/TE.py'],\n")))
525 `(("python-numpy" ,python2-numpy)
526 ("python-matplotlib" ,python2-matplotlib)
527 ("python-scipy" ,python2-scipy)
528 ("python-statsmodels" ,python2-statsmodels)))
530 `(("python-mock" ,python2-mock)
531 ("python-nose" ,python2-nose)))
532 (home-page "http://public.bmi.inf.ethz.ch/user/zhongy/RiboDiff/")
533 (synopsis "Detect translation efficiency changes from ribosome footprints")
534 (description "RiboDiff is a statistical tool that detects the protein
535 translational efficiency change from Ribo-Seq (ribosome footprinting) and
536 RNA-Seq data. It uses a generalized linear model to detect genes showing
537 difference in translational profile taking mRNA abundance into account. It
538 facilitates us to decipher the translational regulation that behave
539 independently with transcriptional regulation.")
540 (license license:gpl3+)))
542 (define-public bioawk
548 (uri (string-append "https://github.com/lh3/bioawk/archive/v"
550 (file-name (string-append name "-" version ".tar.gz"))
552 (base32 "1daizxsk17ahi9n58fj8vpgwyhzrzh54bzqhanjanp88kgrz7gjw"))))
553 (build-system gnu-build-system)
559 `(#:tests? #f ; There are no tests to run.
560 ;; Bison must generate files, before other targets can build.
563 (modify-phases %standard-phases
564 (delete 'configure) ; There is no configure phase.
566 (lambda* (#:key outputs #:allow-other-keys)
567 (let* ((out (assoc-ref outputs "out"))
568 (bin (string-append out "/bin"))
569 (man (string-append out "/share/man/man1")))
571 (copy-file "awk.1" (string-append man "/bioawk.1"))
572 (install-file "bioawk" bin)))))))
573 (home-page "https://github.com/lh3/bioawk")
574 (synopsis "AWK with bioinformatics extensions")
575 (description "Bioawk is an extension to Brian Kernighan's awk, adding the
576 support of several common biological data formats, including optionally gzip'ed
577 BED, GFF, SAM, VCF, FASTA/Q and TAB-delimited formats with column names. It
578 also adds a few built-in functions and a command line option to use TAB as the
579 input/output delimiter. When the new functionality is not used, bioawk is
580 intended to behave exactly the same as the original BWK awk.")
581 (license license:x11)))
583 (define-public python2-pybedtools
585 (name "python2-pybedtools")
590 "https://pypi.python.org/packages/source/p/pybedtools/pybedtools-"
594 "1ldzdxw1p4y3g2ignmggsdypvqkcwqwzhdha4rbgpih048z5p4an"))))
595 (build-system python-build-system)
596 (arguments `(#:python ,python-2)) ; no Python 3 support
598 `(("python-matplotlib" ,python2-matplotlib)))
600 `(("bedtools" ,bedtools)
601 ("samtools" ,samtools)))
603 `(("python-cython" ,python2-cython)
604 ("python-pyyaml" ,python2-pyyaml)
605 ("python-nose" ,python2-nose)))
606 (home-page "https://pythonhosted.org/pybedtools/")
607 (synopsis "Python wrapper for BEDtools programs")
609 "pybedtools is a Python wrapper for Aaron Quinlan's BEDtools programs,
610 which are widely used for genomic interval manipulation or \"genome algebra\".
611 pybedtools extends BEDTools by offering feature-level manipulations from with
613 (license license:gpl2+)))
615 (define-public python-biom-format
617 (name "python-biom-format")
622 ;; Use GitHub as source because PyPI distribution does not contain
623 ;; test data: https://github.com/biocore/biom-format/issues/693
624 (uri (string-append "https://github.com/biocore/biom-format/archive/"
626 (file-name (string-append name "-" version ".tar.gz"))
629 "08cr7wpahk6zb31h4bs7jmzpvxcqv9s13xz40h6y2h656jvdvnpj"))))
630 (build-system python-build-system)
632 `(("python-numpy" ,python-numpy)
633 ("python-scipy" ,python-scipy)
634 ("python-future" ,python-future)
635 ("python-click" ,python-click)
636 ("python-h5py" ,python-h5py)
637 ("python-pandas" ,python-pandas)))
639 `(("python-nose" ,python-nose)))
640 (home-page "http://www.biom-format.org")
641 (synopsis "Biological Observation Matrix (BIOM) format utilities")
643 "The BIOM file format is designed to be a general-use format for
644 representing counts of observations e.g. operational taxonomic units, KEGG
645 orthology groups or lipid types, in one or more biological samples
646 e.g. microbiome samples, genomes, metagenomes.")
647 (license license:bsd-3)
648 (properties `((python2-variant . ,(delay python2-biom-format))))))
650 (define-public python2-biom-format
651 (let ((base (package-with-python2 (strip-python2-variant python-biom-format))))
656 (modify-phases %standard-phases
657 ;; Do not require the unmaintained pyqi library.
658 (add-after 'unpack 'remove-pyqi
660 (substitute* "setup.py"
661 (("install_requires.append\\(\"pyqi\"\\)") "pass"))
663 ,@(package-arguments base))))))
665 (define-public bioperl-minimal
666 (let* ((inputs `(("perl-module-build" ,perl-module-build)
667 ("perl-data-stag" ,perl-data-stag)
668 ("perl-libwww" ,perl-libwww)
669 ("perl-uri" ,perl-uri)))
671 (map (compose package-name cadr)
674 (map (compose package-transitive-target-inputs cadr) inputs))))))
676 (name "bioperl-minimal")
681 (uri (string-append "https://github.com/bioperl/bioperl-live/"
683 (string-map (lambda (c)
689 "12phgpxwgkqflkwfb9dcqg7a31dpjlfhar8wcgv0aj5ln4akfz06"))))
690 (build-system perl-build-system)
693 (modify-phases %standard-phases
695 'install 'wrap-programs
696 (lambda* (#:key outputs #:allow-other-keys)
697 ;; Make sure all executables in "bin" find the required Perl
698 ;; modules at runtime. As the PERL5LIB variable contains also
699 ;; the paths of native inputs, we pick the transitive target
700 ;; inputs from %build-inputs.
701 (let* ((out (assoc-ref outputs "out"))
702 (bin (string-append out "/bin/"))
704 (cons (string-append out "/lib/perl5/site_perl")
706 (assoc-ref %build-inputs name))
707 ',transitive-inputs))
709 (for-each (lambda (file)
711 `("PERL5LIB" ":" prefix (,path))))
712 (find-files bin "\\.pl$"))
716 `(("perl-test-most" ,perl-test-most)))
717 (home-page "http://search.cpan.org/dist/BioPerl")
718 (synopsis "Bioinformatics toolkit")
720 "BioPerl is the product of a community effort to produce Perl code which
721 is useful in biology. Examples include Sequence objects, Alignment objects
722 and database searching objects. These objects not only do what they are
723 advertised to do in the documentation, but they also interact - Alignment
724 objects are made from the Sequence objects, Sequence objects have access to
725 Annotation and SeqFeature objects and databases, Blast objects can be
726 converted to Alignment objects, and so on. This means that the objects
727 provide a coordinated and extensible framework to do computational biology.")
728 (license license:perl-license))))
730 (define-public python-biopython
732 (name "python-biopython")
736 ;; use PyPi rather than biopython.org to ease updating
737 (uri (pypi-uri "biopython" version))
740 "07qc7nz0k77y8hf8s18rscvibvm91zw0kkq7ylrhisf8vp8hkp6i"))))
741 (build-system python-build-system)
744 (modify-phases %standard-phases
745 (add-before 'check 'set-home
746 ;; Some tests require a home directory to be set.
747 (lambda _ (setenv "HOME" "/tmp") #t)))))
749 `(("python-numpy" ,python-numpy)))
750 (home-page "http://biopython.org/")
751 (synopsis "Tools for biological computation in Python")
753 "Biopython is a set of tools for biological computation including parsers
754 for bioinformatics files into Python data structures; interfaces to common
755 bioinformatics programs; a standard sequence class and tools for performing
756 common operations on them; code to perform data classification; code for
757 dealing with alignments; code making it easy to split up parallelizable tasks
758 into separate processes; and more.")
759 (license (license:non-copyleft "http://www.biopython.org/DIST/LICENSE"))))
761 (define-public python2-biopython
762 (package-with-python2 python-biopython))
764 ;; An outdated version of biopython is required for seqmagick, see
765 ;; https://github.com/fhcrc/seqmagick/issues/59
766 ;; When that issue has been resolved this package should be removed.
767 (define python2-biopython-1.66
769 (inherit python2-biopython)
773 (uri (pypi-uri "biopython" version))
776 "1gdv92593klimg22icf5j9by7xiq86jnwzkpz4abaa05ylkdf6hp"))))))
778 (define-public bpp-core
779 ;; The last release was in 2014 and the recommended way to install from source
780 ;; is to clone the git repository, so we do this.
781 ;; http://biopp.univ-montp2.fr/wiki/index.php/Main_Page
782 (let ((commit "7d8bced0d1a87291ea8dd7046b7fb5ff9c35c582"))
785 (version (string-append "2.2.0-1." (string-take commit 7)))
789 (url "http://biopp.univ-montp2.fr/git/bpp-core")
791 (file-name (string-append name "-" version "-checkout"))
794 "10djsq5vlnkilv436gnmh4irpk49v29pa69r6xiryg32xmvn909j"))))
795 (build-system cmake-build-system)
797 `(#:parallel-build? #f))
799 `(("gcc" ,gcc-5))) ; Compilation of bpp-phyl fails with GCC 4.9 so we
800 ; compile all of the bpp packages with GCC 5.
801 (home-page "http://biopp.univ-montp2.fr")
802 (synopsis "C++ libraries for Bioinformatics")
804 "Bio++ is a set of C++ libraries for Bioinformatics, including sequence
805 analysis, phylogenetics, molecular evolution and population genetics. It is
806 Object Oriented and is designed to be both easy to use and computer efficient.
807 Bio++ intends to help programmers to write computer expensive programs, by
808 providing them a set of re-usable tools.")
809 (license license:cecill-c))))
811 (define-public bpp-phyl
812 ;; The last release was in 2014 and the recommended way to install from source
813 ;; is to clone the git repository, so we do this.
814 ;; http://biopp.univ-montp2.fr/wiki/index.php/Main_Page
815 (let ((commit "0c07167b629f68b569bf274d1ad0c4af83276ae2"))
818 (version (string-append "2.2.0-1." (string-take commit 7)))
822 (url "http://biopp.univ-montp2.fr/git/bpp-phyl")
824 (file-name (string-append name "-" version "-checkout"))
827 "1ssjgchzwj3iai26kyly7gwkdv8sk59nqhkb1wpap3sf5m6kyllh"))))
828 (build-system cmake-build-system)
830 `(#:parallel-build? #f
831 ;; If out-of-source, test data is not copied into the build directory
832 ;; so the tests fail.
833 #:out-of-source? #f))
835 `(("bpp-core" ,bpp-core)
837 ;; GCC 4.8 fails due to an 'internal compiler error', so we use a more
840 (home-page "http://biopp.univ-montp2.fr")
841 (synopsis "Bio++ phylogenetic Library")
843 "Bio++ is a set of C++ libraries for Bioinformatics, including sequence
844 analysis, phylogenetics, molecular evolution and population genetics. This
845 library provides phylogenetics-related modules.")
846 (license license:cecill-c))))
848 (define-public bpp-popgen
849 ;; The last release was in 2014 and the recommended way to install from source
850 ;; is to clone the git repository, so we do this.
851 ;; http://biopp.univ-montp2.fr/wiki/index.php/Main_Page
852 (let ((commit "e472bac9b1a148803895d747cd6d0c5904f85d9f"))
855 (version (string-append "2.2.0-1." (string-take commit 7)))
859 (url "http://biopp.univ-montp2.fr/git/bpp-popgen")
861 (file-name (string-append name "-" version "-checkout"))
864 "0yn82dzn1n5629nzja68xfrhi655709rjanyryb36vzkmymy6dw5"))))
865 (build-system cmake-build-system)
867 `(#:parallel-build? #f
868 #:tests? #f)) ; There are no tests.
870 `(("bpp-core" ,bpp-core)
873 (home-page "http://biopp.univ-montp2.fr")
874 (synopsis "Bio++ population genetics library")
876 "Bio++ is a set of C++ libraries for Bioinformatics, including sequence
877 analysis, phylogenetics, molecular evolution and population genetics. This
878 library provides population genetics-related modules.")
879 (license license:cecill-c))))
881 (define-public bpp-seq
882 ;; The last release was in 2014 and the recommended way to install from source
883 ;; is to clone the git repository, so we do this.
884 ;; http://biopp.univ-montp2.fr/wiki/index.php/Main_Page
885 (let ((commit "6cfa07965ce152e5598a89df2fa80a75973bfa33"))
888 (version (string-append "2.2.0-1." (string-take commit 7)))
892 (url "http://biopp.univ-montp2.fr/git/bpp-seq")
894 (file-name (string-append name "-" version "-checkout"))
897 "1nys5jq7jqvdg40d91wsmj3q2yzy4276cp7sp44n67p468f27zf2"))))
898 (build-system cmake-build-system)
900 `(#:parallel-build? #f
901 ;; If out-of-source, test data is not copied into the build directory
902 ;; so the tests fail.
903 #:out-of-source? #f))
905 `(("bpp-core" ,bpp-core)
906 ("gcc" ,gcc-5))) ; Use GCC 5 as per 'bpp-core'.
907 (home-page "http://biopp.univ-montp2.fr")
908 (synopsis "Bio++ sequence library")
910 "Bio++ is a set of C++ libraries for Bioinformatics, including sequence
911 analysis, phylogenetics, molecular evolution and population genetics. This
912 library provides sequence-related modules.")
913 (license license:cecill-c))))
915 (define-public bppsuite
916 ;; The last release was in 2014 and the recommended way to install from source
917 ;; is to clone the git repository, so we do this.
918 ;; http://biopp.univ-montp2.fr/wiki/index.php/Main_Page
919 (let ((commit "c516147f57aa50961121cd505bed52cd7603698b"))
922 (version (string-append "2.2.0-1." (string-take commit 7)))
926 (url "http://biopp.univ-montp2.fr/git/bppsuite")
928 (file-name (string-append name "-" version "-checkout"))
931 "1y87pxvw0jxjizhq2dr9g2r91md45k1p9ih2sl1yy1y3p934l2kb"))))
932 (build-system cmake-build-system)
934 `(#:parallel-build? #f
935 #:tests? #f)) ; There are no tests.
939 ("texinfo" ,texinfo)))
941 `(("bpp-core" ,bpp-core)
943 ("bpp-phyl" ,bpp-phyl)
944 ("bpp-phyl" ,bpp-popgen)
946 (home-page "http://biopp.univ-montp2.fr")
947 (synopsis "Bioinformatics tools written with the Bio++ libraries")
949 "Bio++ is a set of C++ libraries for Bioinformatics, including sequence
950 analysis, phylogenetics, molecular evolution and population genetics. This
951 package provides command line tools using the Bio++ library.")
952 (license license:cecill-c))))
954 (define-public blast+
961 "ftp://ftp.ncbi.nlm.nih.gov/blast/executables/blast+/"
962 version "/ncbi-blast-" version "+-src.tar.gz"))
965 "15n937pw5aqmyfjb6l387d18grqbb96l63d5xj4l7yyh0zbf2405"))
966 (patches (search-patches "blast+-fix-makefile.patch"))
967 (modules '((guix build utils)))
970 ;; Remove bundled bzip2, zlib and pcre.
971 (delete-file-recursively "c++/src/util/compress/bzip2")
972 (delete-file-recursively "c++/src/util/compress/zlib")
973 (delete-file-recursively "c++/src/util/regexp")
974 (substitute* "c++/src/util/compress/Makefile.in"
975 (("bzip2 zlib api") "api"))
976 ;; Remove useless msbuild directory
977 (delete-file-recursively
978 "c++/src/build-system/project_tree_builder/msbuild")
980 (build-system gnu-build-system)
982 `(;; There are two(!) tests for this massive library, and both fail with
983 ;; "unparsable timing stats".
984 ;; ERR [127] -- [serial/datatool] datatool.sh (unparsable timing stats)
985 ;; ERR [127] -- [serial/datatool] datatool_xml.sh (unparsable timing stats)
988 #:parallel-build? #f ; not supported
990 (modify-phases %standard-phases
993 ;; $HOME needs to be set at some point during the configure phase
994 (lambda _ (setenv "HOME" "/tmp") #t))
997 (lambda _ (chdir "c++") #t))
999 'enter-dir 'fix-build-system
1001 (define (which* cmd)
1002 (cond ((string=? cmd "date")
1003 ;; make call to "date" deterministic
1008 (format (current-error-port)
1009 "WARNING: Unable to find absolute path for ~s~%"
1013 ;; Rewrite hardcoded paths to various tools
1014 (substitute* (append '("src/build-system/configure.ac"
1015 "src/build-system/configure"
1016 "src/build-system/helpers/run_with_lock.c"
1017 "scripts/common/impl/if_diff.sh"
1018 "scripts/common/impl/run_with_lock.sh"
1019 "src/build-system/Makefile.configurables.real"
1020 "src/build-system/Makefile.in.top"
1021 "src/build-system/Makefile.meta.gmake=no"
1022 "src/build-system/Makefile.meta.in"
1023 "src/build-system/Makefile.meta_l"
1024 "src/build-system/Makefile.meta_p"
1025 "src/build-system/Makefile.meta_r"
1026 "src/build-system/Makefile.mk.in"
1027 "src/build-system/Makefile.requirements"
1028 "src/build-system/Makefile.rules_with_autodep.in")
1029 (find-files "scripts/common/check" "\\.sh$"))
1030 (("(/usr/bin/|/bin/)([a-z][-_.a-z]*)" all dir cmd)
1031 (or (which* cmd) all)))
1033 (substitute* (find-files "src/build-system" "^config.*")
1034 (("LN_S=/bin/\\$LN_S") (string-append "LN_S=" (which "ln")))
1037 ;; rewrite "/var/tmp" in check script
1038 (substitute* "scripts/common/check/check_make_unix.sh"
1039 (("/var/tmp") "/tmp"))
1041 ;; do not reset PATH
1042 (substitute* (find-files "scripts/common/impl/" "\\.sh$")
1044 (("action=/bin/") "action=")
1045 (("export PATH") ":"))
1049 (lambda* (#:key inputs outputs #:allow-other-keys)
1050 (let ((out (assoc-ref outputs "out"))
1051 (lib (string-append (assoc-ref outputs "lib") "/lib"))
1052 (include (string-append (assoc-ref outputs "include")
1053 "/include/ncbi-tools++")))
1054 ;; The 'configure' script doesn't recognize things like
1055 ;; '--enable-fast-install'.
1056 (zero? (system* "./configure.orig"
1057 (string-append "--with-build-root=" (getcwd) "/build")
1058 (string-append "--prefix=" out)
1059 (string-append "--libdir=" lib)
1060 (string-append "--includedir=" include)
1061 (string-append "--with-bz2="
1062 (assoc-ref inputs "bzip2"))
1063 (string-append "--with-z="
1064 (assoc-ref inputs "zlib"))
1065 (string-append "--with-pcre="
1066 (assoc-ref inputs "pcre"))
1067 ;; Each library is built twice by default, once
1068 ;; with "-static" in its name, and again
1071 "--with-dll"))))))))
1072 (outputs '("out" ; 21 MB
1080 ("python" ,python-wrapper)))
1083 (home-page "http://blast.ncbi.nlm.nih.gov")
1084 (synopsis "Basic local alignment search tool")
1086 "BLAST is a popular method of performing a DNA or protein sequence
1087 similarity search, using heuristics to produce results quickly. It also
1088 calculates an “expect value” that estimates how many matches would have
1089 occurred at a given score by chance, which can aid a user in judging how much
1090 confidence to have in an alignment.")
1091 ;; Most of the sources are in the public domain, with the following
1094 ;; * ./c++/include/util/bitset/
1095 ;; * ./c++/src/html/ncbi_menu*.js
1097 ;; * ./c++/include/util/impl/floating_point_comparison.hpp
1099 ;; * ./c++/include/dbapi/driver/odbc/unix_odbc/
1101 ;; * ./c++/src/corelib/teamcity_*
1102 (license (list license:public-domain
1108 (define-public bless
1114 (uri (string-append "mirror://sourceforge/bless-ec/bless.v"
1118 "0rm0gw2s18dqwzzpl3c2x1z05ni2v0xz5dmfk3d33j6g4cgrlrdd"))
1119 (modules '((guix build utils)))
1122 ;; Remove bundled boost, pigz, zlib, and .git directory
1123 ;; FIXME: also remove bundled sources for murmurhash3 and
1124 ;; kmc once packaged.
1125 (delete-file-recursively "boost")
1126 (delete-file-recursively "pigz")
1127 (delete-file-recursively "google-sparsehash")
1128 (delete-file-recursively "zlib")
1129 (delete-file-recursively ".git")
1131 (build-system gnu-build-system)
1133 '(#:tests? #f ;no "check" target
1135 (list (string-append "ZLIB="
1136 (assoc-ref %build-inputs "zlib")
1138 (string-append "LDFLAGS="
1139 (string-join '("-lboost_filesystem"
1146 (modify-phases %standard-phases
1147 (add-after 'unpack 'do-not-build-bundled-pigz
1148 (lambda* (#:key inputs outputs #:allow-other-keys)
1149 (substitute* "Makefile"
1150 (("cd pigz/pigz-2.3.3; make") ""))
1152 (add-after 'unpack 'patch-paths-to-executables
1153 (lambda* (#:key inputs outputs #:allow-other-keys)
1154 (substitute* "parse_args.cpp"
1155 (("kmc_binary = .*")
1156 (string-append "kmc_binary = \""
1157 (assoc-ref outputs "out")
1159 (("pigz_binary = .*")
1160 (string-append "pigz_binary = \""
1161 (assoc-ref inputs "pigz")
1165 (lambda* (#:key outputs #:allow-other-keys)
1166 (let ((bin (string-append (assoc-ref outputs "out") "/bin/")))
1167 (for-each (lambda (file)
1168 (install-file file bin))
1169 '("bless" "kmc/bin/kmc"))
1171 (delete 'configure))))
1175 `(("openmpi" ,openmpi)
1177 ("sparsehash" ,sparsehash)
1180 (supported-systems '("x86_64-linux"))
1181 (home-page "https://sourceforge.net/p/bless-ec/wiki/Home/")
1182 (synopsis "Bloom-filter-based error correction tool for NGS reads")
1184 "@dfn{Bloom-filter-based error correction solution for high-throughput
1185 sequencing reads} (BLESS) uses a single minimum-sized bloom filter is a
1186 correction tool for genomic reads produced by @dfn{Next-generation
1187 sequencing} (NGS). BLESS produces accurate correction results with much less
1188 memory compared with previous solutions and is also able to tolerate a higher
1189 false-positive rate. BLESS can extend reads like DNA assemblers to correct
1190 errors at the end of reads.")
1191 (license license:gpl3+)))
1193 (define-public bowtie
1199 (uri (string-append "https://github.com/BenLangmead/bowtie2/archive/v"
1201 (file-name (string-append name "-" version ".tar.gz"))
1204 "0hwa5r9qbglppb7sz5z79rlmmddr3n51n468jb3wh8rwjgn3yr90"))
1205 (modules '((guix build utils)))
1207 '(substitute* "Makefile"
1208 ;; replace BUILD_HOST and BUILD_TIME for deterministic build
1209 (("-DBUILD_HOST=.*") "-DBUILD_HOST=\"\\\"guix\\\"\"")
1210 (("-DBUILD_TIME=.*") "-DBUILD_TIME=\"\\\"0\\\"\"")))))
1211 (build-system gnu-build-system)
1214 ("perl-clone" ,perl-clone)
1215 ("perl-test-deep" ,perl-test-deep)
1216 ("perl-test-simple" ,perl-test-simple)
1217 ("python" ,python-2)
1224 (string-append "prefix=" (assoc-ref %outputs "out")))
1226 (modify-phases %standard-phases
1229 (lambda* (#:key outputs #:allow-other-keys)
1230 (zero? (system* "perl"
1231 "scripts/test/simple_tests.pl"
1232 "--bowtie2=./bowtie2"
1233 "--bowtie2-build=./bowtie2-build")))))))
1234 (home-page "http://bowtie-bio.sourceforge.net/bowtie2/index.shtml")
1235 (synopsis "Fast and sensitive nucleotide sequence read aligner")
1237 "Bowtie 2 is a fast and memory-efficient tool for aligning sequencing
1238 reads to long reference sequences. It is particularly good at aligning reads
1239 of about 50 up to 100s or 1,000s of characters, and particularly good at
1240 aligning to relatively long (e.g. mammalian) genomes. Bowtie 2 indexes the
1241 genome with an FM Index to keep its memory footprint small: for the human
1242 genome, its memory footprint is typically around 3.2 GB. Bowtie 2 supports
1243 gapped, local, and paired-end alignment modes.")
1244 (supported-systems '("x86_64-linux"))
1245 (license license:gpl3+)))
1247 (define-public tophat
1254 "http://ccb.jhu.edu/software/tophat/downloads/tophat-"
1258 "168zlzykq622zbgkh90a90f1bdgsxkscq2zxzbj8brq80hbjpyp7"))
1259 (patches (search-patches "tophat-build-with-later-seqan.patch"))
1260 (modules '((guix build utils)))
1263 ;; Remove bundled SeqAn and samtools
1264 (delete-file-recursively "src/SeqAn-1.3")
1265 (delete-file-recursively "src/samtools-0.1.18")
1267 (build-system gnu-build-system)
1269 '(#:parallel-build? #f ; not supported
1271 (modify-phases %standard-phases
1272 (add-after 'unpack 'use-system-samtools
1273 (lambda* (#:key inputs #:allow-other-keys)
1274 (substitute* "src/Makefile.in"
1275 (("(noinst_LIBRARIES = )\\$\\(SAMLIB\\)" _ prefix) prefix)
1276 (("\\$\\(SAMPROG\\): \\$\\(SAMLIB\\)") "")
1277 (("SAMPROG = samtools_0\\.1\\.18") "")
1278 (("\\$\\(samtools_0_1_18_SOURCES\\)") "")
1279 (("am__EXEEXT_1 = samtools_0\\.1\\.18\\$\\(EXEEXT\\)") ""))
1280 (substitute* '("src/common.cpp"
1282 (("samtools_0.1.18") (which "samtools")))
1283 (substitute* '("src/common.h"
1284 "src/bam2fastx.cpp")
1285 (("#include \"bam.h\"") "#include <samtools/bam.h>")
1286 (("#include \"sam.h\"") "#include <samtools/sam.h>"))
1287 (substitute* '("src/bwt_map.h"
1289 "src/align_status.h")
1290 (("#include <bam.h>") "#include <samtools/bam.h>")
1291 (("#include <sam.h>") "#include <samtools/sam.h>"))
1296 ("samtools" ,samtools-0.1)
1297 ("ncurses" ,ncurses)
1298 ("python" ,python-2)
1302 (home-page "http://ccb.jhu.edu/software/tophat/index.shtml")
1303 (synopsis "Spliced read mapper for RNA-Seq data")
1305 "TopHat is a fast splice junction mapper for nucleotide sequence
1306 reads produced by the RNA-Seq method. It aligns RNA-Seq reads to
1307 mammalian-sized genomes using the ultra high-throughput short read
1308 aligner Bowtie, and then analyzes the mapping results to identify
1309 splice junctions between exons.")
1310 ;; TopHat is released under the Boost Software License, Version 1.0
1311 ;; See https://github.com/infphilo/tophat/issues/11#issuecomment-121589893
1312 (license license:boost1.0)))
1320 (uri (string-append "mirror://sourceforge/bio-bwa/bwa-"
1321 version ".tar.bz2"))
1324 "0585ikg0gv0mpyw9iq0bq9n0hr95867bbv8jbzs9pk4slkpsymig"))))
1325 (build-system gnu-build-system)
1327 '(#:tests? #f ;no "check" target
1329 (modify-phases %standard-phases
1331 (lambda* (#:key outputs #:allow-other-keys)
1332 (let ((bin (string-append
1333 (assoc-ref outputs "out") "/bin"))
1335 (assoc-ref outputs "out") "/share/doc/bwa"))
1337 (assoc-ref outputs "out") "/share/man/man1")))
1338 (install-file "bwa" bin)
1339 (install-file "README.md" doc)
1340 (install-file "bwa.1" man))
1342 ;; no "configure" script
1343 (delete 'configure))))
1344 (inputs `(("zlib" ,zlib)))
1345 ;; Non-portable SSE instructions are used so building fails on platforms
1346 ;; other than x86_64.
1347 (supported-systems '("x86_64-linux"))
1348 (home-page "http://bio-bwa.sourceforge.net/")
1349 (synopsis "Burrows-Wheeler sequence aligner")
1351 "BWA is a software package for mapping low-divergent sequences against a
1352 large reference genome, such as the human genome. It consists of three
1353 algorithms: BWA-backtrack, BWA-SW and BWA-MEM. The first algorithm is
1354 designed for Illumina sequence reads up to 100bp, while the rest two for
1355 longer sequences ranged from 70bp to 1Mbp. BWA-MEM and BWA-SW share similar
1356 features such as long-read support and split alignment, but BWA-MEM, which is
1357 the latest, is generally recommended for high-quality queries as it is faster
1358 and more accurate. BWA-MEM also has better performance than BWA-backtrack for
1359 70-100bp Illumina reads.")
1360 (license license:gpl3+)))
1362 (define-public bwa-pssm
1363 (package (inherit bwa)
1368 (uri (string-append "https://github.com/pkerpedjiev/bwa-pssm/"
1369 "archive/" version ".tar.gz"))
1370 (file-name (string-append name "-" version ".tar.gz"))
1373 "02p7mpbs4mlxmn84g2x4ghak638vbj4lqix2ipx5g84pz9bhdavg"))))
1374 (build-system gnu-build-system)
1379 (home-page "http://bwa-pssm.binf.ku.dk/")
1380 (synopsis "Burrows-Wheeler transform-based probabilistic short read mapper")
1382 "BWA-PSSM is a probabilistic short genomic sequence read aligner based on
1383 the use of @dfn{position specific scoring matrices} (PSSM). Like many of the
1384 existing aligners it is fast and sensitive. Unlike most other aligners,
1385 however, it is also adaptible in the sense that one can direct the alignment
1386 based on known biases within the data set. It is coded as a modification of
1387 the original BWA alignment program and shares the genome index structure as
1388 well as many of the command line options.")
1389 (license license:gpl3+)))
1391 (define-public python2-bx-python
1393 (name "python2-bx-python")
1397 (uri (pypi-uri "bx-python" version))
1400 "15z2w3bvnc0n4qmb9bd6d8ylc2h2nj883x2w9iixf4x3vki9b22i"))
1401 (modules '((guix build utils)))
1403 '(substitute* "setup.py"
1404 ;; remove dependency on outdated "distribute" module
1405 (("^from distribute_setup import use_setuptools") "")
1406 (("^use_setuptools\\(\\)") "")))))
1407 (build-system python-build-system)
1409 `(#:tests? #f ;tests fail because test data are not included
1410 #:python ,python-2))
1412 `(("python-numpy" ,python2-numpy)
1415 `(("python-nose" ,python2-nose)))
1416 (home-page "http://bitbucket.org/james_taylor/bx-python/")
1417 (synopsis "Tools for manipulating biological data")
1419 "bx-python provides tools for manipulating biological data, particularly
1420 multiple sequence alignments.")
1421 (license license:expat)))
1423 (define-public python-pysam
1425 (name "python-pysam")
1426 (version "0.11.2.2")
1429 ;; Test data is missing on PyPi.
1431 "https://github.com/pysam-developers/pysam/archive/v"
1433 (file-name (string-append name "-" version ".tar.gz"))
1436 "1cfqdxsqs3xhacns9n0271ck6wkc76px66ddjm91wfw2jxxfklvc"))
1437 (modules '((guix build utils)))
1439 ;; Drop bundled htslib. TODO: Also remove samtools and bcftools.
1440 '(delete-file-recursively "htslib"))))
1441 (build-system python-build-system)
1443 `(#:modules ((ice-9 ftw)
1445 (guix build python-build-system)
1448 (modify-phases %standard-phases
1449 (add-before 'build 'set-flags
1450 (lambda* (#:key inputs #:allow-other-keys)
1451 (setenv "HTSLIB_MODE" "external")
1452 (setenv "HTSLIB_LIBRARY_DIR"
1453 (string-append (assoc-ref inputs "htslib") "/lib"))
1454 (setenv "HTSLIB_INCLUDE_DIR"
1455 (string-append (assoc-ref inputs "htslib") "/include"))
1456 (setenv "LDFLAGS" "-lncurses")
1457 (setenv "CFLAGS" "-D_CURSES_LIB=1")
1460 (lambda* (#:key inputs outputs #:allow-other-keys)
1461 ;; Add first subdirectory of "build" directory to PYTHONPATH.
1462 (setenv "PYTHONPATH"
1464 (getenv "PYTHONPATH")
1465 ":" (getcwd) "/build/"
1466 (car (scandir "build"
1467 (negate (cut string-prefix? "." <>))))))
1468 ;; Step out of source dir so python does not import from CWD.
1469 (with-directory-excursion "tests"
1470 (setenv "HOME" "/tmp")
1471 (and (zero? (system* "make" "-C" "pysam_data"))
1472 (zero? (system* "make" "-C" "cbcf_data"))
1473 ;; Running nosetests without explicitly asking for a
1474 ;; single process leads to a crash. Running with multiple
1475 ;; processes fails because the tests are not designed to
1478 ;; FIXME: tests keep timing out on some systems.
1479 ;; (zero? (system* "nosetests" "-v"
1480 ;; "--processes" "1"))
1483 `(("htslib" ,htslib))) ; Included from installed header files.
1485 `(("ncurses" ,ncurses)
1488 `(("python-cython" ,python-cython)
1489 ;; Dependencies below are are for tests only.
1490 ("samtools" ,samtools)
1491 ("bcftools" ,bcftools)
1492 ("python-nose" ,python-nose)))
1493 (home-page "https://github.com/pysam-developers/pysam")
1494 (synopsis "Python bindings to the SAMtools C API")
1496 "Pysam is a Python module for reading and manipulating files in the
1497 SAM/BAM format. Pysam is a lightweight wrapper of the SAMtools C API. It
1498 also includes an interface for tabix.")
1499 (license license:expat)))
1501 (define-public python2-pysam
1502 (package-with-python2 python-pysam))
1504 (define-public python-twobitreader
1506 (name "python-twobitreader")
1510 (uri (pypi-uri "twobitreader" version))
1513 "1q8wnj2kga9nz1lwc4w7qv52smfm536hp6mc8w6s53lhyj0mpi22"))))
1514 (build-system python-build-system)
1516 '(;; Tests are not distributed in the PyPi release.
1517 ;; TODO Try building from the Git repo or asking the upstream maintainer
1518 ;; to distribute the tests on PyPi.
1521 `(("python-sphinx" ,python-sphinx)))
1522 (home-page "https://github.com/benjschiller/twobitreader")
1523 (synopsis "Python library for reading .2bit files")
1525 "twobitreader is a Python library for reading .2bit files as used by the
1526 UCSC genome browser.")
1527 (license license:artistic2.0)))
1529 (define-public python2-twobitreader
1530 (package-with-python2 python-twobitreader))
1532 (define-public python-plastid
1534 (name "python-plastid")
1538 (uri (pypi-uri "plastid" version))
1541 "0l24dd3q66if8yj042m4s0g95n6acn7im1imqd3p6h8ns43kxhj8"))))
1542 (build-system python-build-system)
1544 ;; Some test files are not included.
1547 `(("python-numpy" ,python-numpy)
1548 ("python-scipy" ,python-scipy)
1549 ("python-pandas" ,python-pandas)
1550 ("python-pysam" ,python-pysam)
1551 ("python-matplotlib" ,python-matplotlib)
1552 ("python-biopython" ,python-biopython)
1553 ("python-twobitreader" ,python-twobitreader)
1554 ("python-termcolor" ,python-termcolor)))
1556 `(("python-cython" ,python-cython)
1557 ("python-nose" ,python-nose)))
1558 (home-page "https://github.com/joshuagryphon/plastid")
1559 (synopsis "Python library for genomic analysis")
1561 "plastid is a Python library for genomic analysis – in particular,
1562 high-throughput sequencing data – with an emphasis on simplicity.")
1563 (license license:bsd-3)))
1565 (define-public python2-plastid
1566 (package-with-python2 python-plastid))
1568 (define-public cd-hit
1574 (uri (string-append "https://github.com/weizhongli/cdhit"
1575 "/releases/download/V" version
1577 "-2017-0621-source.tar.gz"))
1580 "1386dg2npx8p62wmv08mjzsd2z3waknb9j1gg3gkvblcy57hymnn"))))
1581 (build-system gnu-build-system)
1583 `(#:tests? #f ; there are no tests
1585 ;; Executables are copied directly to the PREFIX.
1586 (list (string-append "PREFIX=" (assoc-ref %outputs "out") "/bin"))
1588 (modify-phases %standard-phases
1589 ;; No "configure" script
1591 ;; Remove sources of non-determinism
1592 (add-after 'unpack 'be-timeless
1594 (substitute* "cdhit-utility.c++"
1595 ((" \\(built on \" __DATE__ \"\\)") ""))
1596 (substitute* "cdhit-common.c++"
1597 (("__DATE__") "\"0\"")
1598 (("\", %s, \" __TIME__ \"\\\\n\", date") ""))
1600 ;; The "install" target does not create the target directory.
1601 (add-before 'install 'create-target-dir
1602 (lambda* (#:key outputs #:allow-other-keys)
1603 (mkdir-p (string-append (assoc-ref outputs "out") "/bin"))
1607 (home-page "http://weizhongli-lab.org/cd-hit/")
1608 (synopsis "Cluster and compare protein or nucleotide sequences")
1610 "CD-HIT is a program for clustering and comparing protein or nucleotide
1611 sequences. CD-HIT is designed to be fast and handle extremely large
1613 ;; The manual says: "It can be copied under the GNU General Public License
1614 ;; version 2 (GPLv2)."
1615 (license license:gpl2)))
1617 (define-public clipper
1624 "https://github.com/YeoLab/clipper/archive/"
1626 (file-name (string-append name "-" version ".tar.gz"))
1629 "0pflmsvhbf8izbgwhbhj1i7349sw1f55qpqj8ljmapp16hb0p0qi"))
1630 (modules '((guix build utils)))
1633 ;; remove unnecessary setup dependency
1634 (substitute* "setup.py"
1635 (("setup_requires = .*") ""))
1636 (for-each delete-file
1637 '("clipper/src/peaks.so"
1638 "clipper/src/readsToWiggle.so"))
1639 (delete-file-recursively "dist/")
1641 (build-system python-build-system)
1642 (arguments `(#:python ,python-2)) ; only Python 2 is supported
1644 `(("htseq" ,python2-htseq)
1645 ("python-pybedtools" ,python2-pybedtools)
1646 ("python-cython" ,python2-cython)
1647 ("python-scikit-learn" ,python2-scikit-learn)
1648 ("python-matplotlib" ,python2-matplotlib)
1649 ("python-pandas" ,python2-pandas)
1650 ("python-pysam" ,python2-pysam)
1651 ("python-numpy" ,python2-numpy)
1652 ("python-scipy" ,python2-scipy)))
1654 `(("python-mock" ,python2-mock) ; for tests
1655 ("python-nose" ,python2-nose) ; for tests
1656 ("python-pytz" ,python2-pytz))) ; for tests
1657 (home-page "https://github.com/YeoLab/clipper")
1658 (synopsis "CLIP peak enrichment recognition")
1660 "CLIPper is a tool to define peaks in CLIP-seq datasets.")
1661 (license license:gpl2)))
1663 (define-public codingquarry
1665 (name "codingquarry")
1670 "mirror://sourceforge/codingquarry/CodingQuarry_v"
1674 "0115hkjflsnfzn36xppwf9h9avfxlavr43djqmshkkzbgjzsz60i"))))
1675 (build-system gnu-build-system)
1677 '(#:tests? #f ; no "check" target
1679 (modify-phases %standard-phases
1682 (lambda* (#:key outputs #:allow-other-keys)
1683 (let* ((out (assoc-ref outputs "out"))
1684 (bin (string-append out "/bin"))
1685 (doc (string-append out "/share/doc/codingquarry")))
1686 (install-file "INSTRUCTIONS.pdf" doc)
1687 (copy-recursively "QuarryFiles"
1688 (string-append out "/QuarryFiles"))
1689 (install-file "CodingQuarry" bin)
1690 (install-file "CufflinksGTF_to_CodingQuarryGFF3.py" bin)))))))
1691 (inputs `(("openmpi" ,openmpi)))
1692 (native-search-paths
1693 (list (search-path-specification
1694 (variable "QUARRY_PATH")
1695 (files '("QuarryFiles")))))
1696 (native-inputs `(("python" ,python-2))) ; Only Python 2 is supported
1697 (synopsis "Fungal gene predictor")
1698 (description "CodingQuarry is a highly accurate, self-training GHMM fungal
1699 gene predictor designed to work with assembled, aligned RNA-seq transcripts.")
1700 (home-page "https://sourceforge.net/projects/codingquarry/")
1701 (license license:gpl3+)))
1703 (define-public couger
1710 "http://couger.oit.duke.edu/static/assets/COUGER"
1714 "04p2b14nmhzxw5h72mpzdhalv21bx4w9b87z0wpw0xzxpysyncmq"))))
1715 (build-system gnu-build-system)
1719 (modify-phases %standard-phases
1724 (lambda* (#:key outputs #:allow-other-keys)
1725 (let* ((out (assoc-ref outputs "out"))
1726 (bin (string-append out "/bin")))
1727 (copy-recursively "src" (string-append out "/src"))
1729 ;; Add "src" directory to module lookup path.
1730 (substitute* "couger"
1732 (string-append "import sys\nsys.path.append(\""
1733 out "\")\nfrom argparse")))
1734 (install-file "couger" bin))
1737 'install 'wrap-program
1738 (lambda* (#:key inputs outputs #:allow-other-keys)
1739 ;; Make sure 'couger' runs with the correct PYTHONPATH.
1740 (let* ((out (assoc-ref outputs "out"))
1741 (path (getenv "PYTHONPATH")))
1742 (wrap-program (string-append out "/bin/couger")
1743 `("PYTHONPATH" ":" prefix (,path))))
1746 `(("python" ,python-2)
1747 ("python2-pillow" ,python2-pillow)
1748 ("python2-numpy" ,python2-numpy)
1749 ("python2-scipy" ,python2-scipy)
1750 ("python2-matplotlib" ,python2-matplotlib)))
1752 `(("r-minimal" ,r-minimal)
1754 ("randomjungle" ,randomjungle)))
1756 `(("unzip" ,unzip)))
1757 (home-page "http://couger.oit.duke.edu")
1758 (synopsis "Identify co-factors in sets of genomic regions")
1760 "COUGER can be applied to any two sets of genomic regions bound by
1761 paralogous TFs (e.g., regions derived from ChIP-seq experiments) to identify
1762 putative co-factors that provide specificity to each TF. The framework
1763 determines the genomic targets uniquely-bound by each TF, and identifies a
1764 small set of co-factors that best explain the in vivo binding differences
1765 between the two TFs.
1767 COUGER uses classification algorithms (support vector machines and random
1768 forests) with features that reflect the DNA binding specificities of putative
1769 co-factors. The features are generated either from high-throughput TF-DNA
1770 binding data (from protein binding microarray experiments), or from large
1771 collections of DNA motifs.")
1772 (license license:gpl3+)))
1774 (define-public clustal-omega
1776 (name "clustal-omega")
1781 "http://www.clustal.org/omega/clustal-omega-"
1785 "02ibkx0m0iwz8nscg998bh41gg251y56cgh86bvyrii5m8kjgwqf"))))
1786 (build-system gnu-build-system)
1788 `(("argtable" ,argtable)))
1789 (home-page "http://www.clustal.org/omega/")
1790 (synopsis "Multiple sequence aligner for protein and DNA/RNA")
1792 "Clustal-Omega is a general purpose multiple sequence alignment (MSA)
1793 program for protein and DNA/RNA. It produces high quality MSAs and is capable
1794 of handling data-sets of hundreds of thousands of sequences in reasonable
1796 (license license:gpl2+)))
1798 (define-public crossmap
1804 (uri (string-append "mirror://sourceforge/crossmap/CrossMap-"
1808 "07y179f63d7qnzdvkqcziwk9bs3k4zhp81q392fp1hwszjdvy22f"))
1809 ;; This patch has been sent upstream already and is available
1810 ;; for download from Sourceforge, but it has not been merged.
1811 (patches (search-patches "crossmap-allow-system-pysam.patch"))
1812 (modules '((guix build utils)))
1813 ;; remove bundled copy of pysam
1815 '(delete-file-recursively "lib/pysam"))))
1816 (build-system python-build-system)
1818 `(#:python ,python-2
1820 (modify-phases %standard-phases
1821 (add-after 'unpack 'set-env
1822 (lambda _ (setenv "CROSSMAP_USE_SYSTEM_PYSAM" "1") #t)))))
1824 `(("python-numpy" ,python2-numpy)
1825 ("python-pysam" ,python2-pysam)
1828 `(("python-cython" ,python2-cython)
1829 ("python-nose" ,python2-nose)))
1830 (home-page "http://crossmap.sourceforge.net/")
1831 (synopsis "Convert genome coordinates between assemblies")
1833 "CrossMap is a program for conversion of genome coordinates or annotation
1834 files between different genome assemblies. It supports most commonly used
1835 file formats including SAM/BAM, Wiggle/BigWig, BED, GFF/GTF, VCF.")
1836 (license license:gpl2+)))
1838 (define-public cufflinks
1844 (uri (string-append "http://cole-trapnell-lab.github.io/"
1845 "cufflinks/assets/downloads/cufflinks-"
1849 "1bnm10p8m7zq4qiipjhjqb24csiqdm1pwc8c795z253r2xk6ncg8"))))
1850 (build-system gnu-build-system)
1854 ;; The includes for "eigen" are located in a subdirectory.
1855 (string-append "EIGEN_CPPFLAGS="
1856 "-I" (assoc-ref %build-inputs "eigen")
1858 ;; Cufflinks must be linked with various boost libraries.
1859 (string-append "LDFLAGS="
1860 (string-join '("-lboost_system"
1861 "-lboost_serialization"
1862 "-lboost_thread"))))
1864 (modify-phases %standard-phases
1865 (add-after 'unpack 'fix-search-for-bam
1867 (substitute* '("ax_bam.m4"
1870 (("<bam/sam\\.h>") "<samtools/sam.h>")
1871 (("<bam/bam\\.h>") "<samtools/bam.h>")
1872 (("<bam/version\\.hpp>") "<samtools/version.h>"))
1875 (list (string-append "--with-bam="
1876 (assoc-ref %build-inputs "samtools")))))
1879 ("samtools" ,samtools-0.1)
1882 ("python" ,python-2)
1884 (home-page "http://cole-trapnell-lab.github.io/cufflinks/")
1885 (synopsis "Transcriptome assembly and RNA-Seq expression analysis")
1887 "Cufflinks assembles RNA transcripts, estimates their abundances,
1888 and tests for differential expression and regulation in RNA-Seq
1889 samples. It accepts aligned RNA-Seq reads and assembles the
1890 alignments into a parsimonious set of transcripts. Cufflinks then
1891 estimates the relative abundances of these transcripts based on how
1892 many reads support each one, taking into account biases in library
1893 preparation protocols.")
1894 (license license:boost1.0)))
1896 (define-public cutadapt
1903 "https://github.com/marcelm/cutadapt/archive/v"
1905 (file-name (string-append name "-" version ".tar.gz"))
1908 "19smhh6444ikn4jlmyhvffw4m5aw7yg07rqsk7arg8dkwyga1i4v"))))
1909 (build-system python-build-system)
1912 (modify-phases %standard-phases
1913 ;; The tests must be run after installation.
1915 (add-after 'install 'check
1916 (lambda* (#:key inputs outputs #:allow-other-keys)
1917 (setenv "PYTHONPATH"
1919 (getenv "PYTHONPATH")
1920 ":" (assoc-ref outputs "out")
1922 (string-take (string-take-right
1923 (assoc-ref inputs "python") 5) 3)
1925 (zero? (system* "nosetests" "-P" "tests")))))))
1927 `(("python-xopen" ,python-xopen)))
1929 `(("python-cython" ,python-cython)
1930 ("python-nose" ,python-nose)))
1931 (home-page "https://cutadapt.readthedocs.io/en/stable/")
1932 (synopsis "Remove adapter sequences from nucleotide sequencing reads")
1934 "Cutadapt finds and removes adapter sequences, primers, poly-A tails and
1935 other types of unwanted sequence from high-throughput sequencing reads.")
1936 (license license:expat)))
1938 (define-public libbigwig
1944 (uri (string-append "https://github.com/dpryan79/libBigWig/"
1945 "archive/" version ".tar.gz"))
1946 (file-name (string-append name "-" version ".tar.gz"))
1949 "098rjh35pi4a9q83n8wiwvyzykjqj6l8q189p1xgfw4ghywdlvw1"))))
1950 (build-system gnu-build-system)
1952 `(#:test-target "test"
1955 (string-append "prefix=" (assoc-ref %outputs "out")))
1957 (modify-phases %standard-phases
1959 (add-before 'check 'disable-curl-test
1961 (substitute* "Makefile"
1962 (("./test/testRemote.*") ""))
1964 ;; This has been fixed with the upstream commit 4ff6959cd8a0, but
1965 ;; there has not yet been a release containing this change.
1966 (add-before 'install 'create-target-dirs
1967 (lambda* (#:key outputs #:allow-other-keys)
1968 (let ((out (assoc-ref outputs "out")))
1969 (mkdir-p (string-append out "/lib"))
1970 (mkdir-p (string-append out "/include"))
1976 `(("doxygen" ,doxygen)))
1977 (home-page "https://github.com/dpryan79/libBigWig")
1978 (synopsis "C library for handling bigWig files")
1980 "This package provides a C library for parsing local and remote BigWig
1982 (license license:expat)))
1984 (define-public python-pybigwig
1986 (name "python-pybigwig")
1990 (uri (pypi-uri "pyBigWig" version))
1993 "0yrpdxg3y0sny25x4w22lv1k47jzccqjmg7j4bp0hywklvp0hg7d"))
1994 (modules '((guix build utils)))
1997 ;; Delete bundled libBigWig sources
1998 (delete-file-recursively "libBigWig")))))
1999 (build-system python-build-system)
2002 (modify-phases %standard-phases
2003 (add-after 'unpack 'link-with-libBigWig
2004 (lambda* (#:key inputs #:allow-other-keys)
2005 (substitute* "setup.py"
2006 (("libs=\\[") "libs=[\"BigWig\", "))
2009 `(("libbigwig" ,libbigwig)
2012 (home-page "https://github.com/dpryan79/pyBigWig")
2013 (synopsis "Access bigWig files in Python using libBigWig")
2015 "This package provides Python bindings to the libBigWig library for
2016 accessing bigWig files.")
2017 (license license:expat)))
2019 (define-public python2-pybigwig
2020 (package-with-python2 python-pybigwig))
2022 (define-public python-dendropy
2024 (name "python-dendropy")
2029 (uri (pypi-uri "DendroPy" version))
2032 "15c7s3d5gf19ljsxvq5advaa752wfi7pwrdjyhzmg85hccyvp47p"))
2033 (patches (search-patches "python-dendropy-fix-tests.patch"))))
2034 (build-system python-build-system)
2035 (home-page "http://packages.python.org/DendroPy/")
2036 (synopsis "Library for phylogenetics and phylogenetic computing")
2038 "DendroPy is a library for phylogenetics and phylogenetic computing: reading,
2039 writing, simulation, processing and manipulation of phylogenetic
2040 trees (phylogenies) and characters.")
2041 (license license:bsd-3)
2042 (properties `((python2-variant . ,(delay python2-dendropy))))))
2044 (define-public python2-dendropy
2045 (let ((base (package-with-python2 (strip-python2-variant python-dendropy))))
2049 `(#:python ,python-2
2051 (modify-phases %standard-phases
2053 ;; There is currently a test failure that only happens on some
2054 ;; systems, and only using "setup.py test"
2055 (lambda _ (zero? (system* "nosetests")))))))
2056 (native-inputs `(("python2-nose" ,python2-nose)
2057 ,@(package-native-inputs base))))))
2059 (define-public python-py2bit
2061 (name "python-py2bit")
2066 (uri (pypi-uri "py2bit" version))
2069 "1cdf4qlmgwsh1f4k0wdv2sr8x9qn4366p0k3614vbd0fpqiarxrl"))))
2070 (build-system python-build-system)
2071 (home-page "https://github.com/dpryan79/py2bit")
2072 (synopsis "Access 2bit files using lib2bit")
2074 "This package provides Python bindings for lib2bit to access 2bit files
2076 (license license:expat)))
2078 (define-public deeptools
2084 (uri (string-append "https://github.com/fidelram/deepTools/"
2085 "archive/" version ".tar.gz"))
2086 (file-name (string-append name "-" version ".tar.gz"))
2089 "1q8i12l2gvk4n2s8lhyzwhh9g4qbc8lrk5l7maz00yvd5g6z5540"))))
2090 (build-system python-build-system)
2092 `(("python-scipy" ,python-scipy)
2093 ("python-numpy" ,python-numpy)
2094 ("python-numpydoc" ,python-numpydoc)
2095 ("python-matplotlib" ,python-matplotlib)
2096 ("python-pysam" ,python-pysam)
2097 ("python-py2bit" ,python-py2bit)
2098 ("python-pybigwig" ,python-pybigwig)))
2100 `(("python-mock" ,python-mock) ;for tests
2101 ("python-nose" ,python-nose) ;for tests
2102 ("python-pytz" ,python-pytz))) ;for tests
2103 (home-page "https://github.com/fidelram/deepTools")
2104 (synopsis "Tools for normalizing and visualizing deep-sequencing data")
2106 "DeepTools addresses the challenge of handling the large amounts of data
2107 that are now routinely generated from DNA sequencing centers. To do so,
2108 deepTools contains useful modules to process the mapped reads data to create
2109 coverage files in standard bedGraph and bigWig file formats. By doing so,
2110 deepTools allows the creation of normalized coverage files or the comparison
2111 between two files (for example, treatment and control). Finally, using such
2112 normalized and standardized files, multiple visualizations can be created to
2113 identify enrichments with functional annotations of the genome.")
2114 (license license:gpl3+)))
2116 (define-public diamond
2123 "https://github.com/bbuchfink/diamond/archive/v"
2125 (file-name (string-append name "-" version ".tar.gz"))
2128 "13qqzwg54n5dqh8pm5n3v8x6gqbczzakphwwjix63qv60hcd5bqd"))))
2129 (build-system cmake-build-system)
2131 '(#:tests? #f ; no "check" target
2133 (modify-phases %standard-phases
2134 (add-after 'unpack 'remove-native-compilation
2136 (substitute* "CMakeLists.txt" (("-march=native") ""))
2140 (home-page "https://github.com/bbuchfink/diamond")
2141 (synopsis "Accelerated BLAST compatible local sequence aligner")
2143 "DIAMOND is a BLAST-compatible local aligner for mapping protein and
2144 translated DNA query sequences against a protein reference database (BLASTP
2145 and BLASTX alignment mode). The speedup over BLAST is up to 20,000 on short
2146 reads at a typical sensitivity of 90-99% relative to BLAST depending on the
2147 data and settings.")
2148 (license license:agpl3+)))
2150 (define-public discrover
2157 (uri (string-append "https://github.com/maaskola/discrover/archive/"
2159 (file-name (string-append name "-" version ".tar.gz"))
2162 "0rah9ja4m0rl5mldd6vag9rwrivw1zrqxssfq8qx64m7961fp68k"))))
2163 (build-system cmake-build-system)
2165 `(#:tests? #f ; there are no tests
2167 (modify-phases %standard-phases
2168 (add-after 'unpack 'add-missing-includes
2170 (substitute* "src/executioninformation.hpp"
2171 (("#define EXECUTIONINFORMATION_HPP" line)
2172 (string-append line "\n#include <random>")))
2173 (substitute* "src/plasma/fasta.hpp"
2174 (("#define FASTA_HPP" line)
2175 (string-append line "\n#include <random>")))
2181 `(("texlive" ,texlive)
2182 ("imagemagick" ,imagemagick)))
2183 (home-page "http://dorina.mdc-berlin.de/public/rajewsky/discrover/")
2184 (synopsis "Discover discriminative nucleotide sequence motifs")
2185 (description "Discrover is a motif discovery method to find binding sites
2186 of nucleic acid binding proteins.")
2187 (license license:gpl3+)))
2189 (define-public eigensoft
2190 (let ((revision "1")
2191 (commit "b14d1e202e21e532536ff8004f0419cd5e259dc7"))
2194 (version (string-append "6.1.2-"
2196 (string-take commit 9)))
2201 (url "https://github.com/DReichLab/EIG.git")
2203 (file-name (string-append "eigensoft-" commit "-checkout"))
2206 "0f5m6k2j5c16xc3xbywcs989xyc26ncy1zfzp9j9n55n9r4xcaiq"))
2207 (modules '((guix build utils)))
2208 ;; Remove pre-built binaries.
2210 (delete-file-recursively "bin")
2213 (build-system gnu-build-system)
2215 `(#:tests? #f ; There are no tests.
2216 #:make-flags '("CC=gcc")
2218 (modify-phases %standard-phases
2219 ;; There is no configure phase, but the Makefile is in a
2224 ;; The link flags are incomplete.
2225 (substitute* "Makefile"
2226 (("-lgsl") "-lgsl -lm -llapack -llapacke -lpthread"))
2228 ;; The provided install target only copies executables to
2229 ;; the "bin" directory in the build root.
2230 (add-after 'install 'actually-install
2231 (lambda* (#:key outputs #:allow-other-keys)
2232 (let* ((out (assoc-ref outputs "out"))
2233 (bin (string-append out "/bin")))
2234 (for-each (lambda (file)
2235 (install-file file bin))
2236 (find-files "../bin" ".*"))
2241 ("openblas" ,openblas)
2243 ("gfortran" ,gfortran "lib")))
2244 (home-page "https://github.com/DReichLab/EIG")
2245 (synopsis "Tools for population genetics")
2246 (description "The EIGENSOFT package provides tools for population
2247 genetics and stratification correction. EIGENSOFT implements methods commonly
2248 used in population genetics analyses such as PCA, computation of Tracy-Widom
2249 statistics, and finding related individuals in structured populations. It
2250 comes with a built-in plotting script and supports multiple file formats and
2251 quantitative phenotypes.")
2252 ;; The license of the eigensoft tools is Expat, but since it's
2253 ;; linking with the GNU Scientific Library (GSL) the effective
2254 ;; license is the GPL.
2255 (license license:gpl3+))))
2257 (define-public edirect
2263 (uri (string-append "ftp://ftp.ncbi.nlm.nih.gov/entrez/entrezdirect/"
2264 "versions/2016-05-03/edirect.tar.gz"))
2267 "15zsprak5yh8c1yrz4r1knmb5s8qcmdid4xdhkh3lqcv64l60hli"))))
2268 (build-system perl-build-system)
2270 `(#:tests? #f ;no "check" target
2272 (modify-phases %standard-phases
2276 (lambda* (#:key outputs #:allow-other-keys)
2277 (let ((target (string-append (assoc-ref outputs "out")
2280 (install-file "edirect.pl" target)
2283 'install 'wrap-program
2284 (lambda* (#:key inputs outputs #:allow-other-keys)
2285 ;; Make sure 'edirect.pl' finds all perl inputs at runtime.
2286 (let* ((out (assoc-ref outputs "out"))
2287 (path (getenv "PERL5LIB")))
2288 (wrap-program (string-append out "/bin/edirect.pl")
2289 `("PERL5LIB" ":" prefix (,path)))))))))
2291 `(("perl-html-parser" ,perl-html-parser)
2292 ("perl-encode-locale" ,perl-encode-locale)
2293 ("perl-file-listing" ,perl-file-listing)
2294 ("perl-html-tagset" ,perl-html-tagset)
2295 ("perl-html-tree" ,perl-html-tree)
2296 ("perl-http-cookies" ,perl-http-cookies)
2297 ("perl-http-date" ,perl-http-date)
2298 ("perl-http-message" ,perl-http-message)
2299 ("perl-http-negotiate" ,perl-http-negotiate)
2300 ("perl-lwp-mediatypes" ,perl-lwp-mediatypes)
2301 ("perl-lwp-protocol-https" ,perl-lwp-protocol-https)
2302 ("perl-net-http" ,perl-net-http)
2303 ("perl-uri" ,perl-uri)
2304 ("perl-www-robotrules" ,perl-www-robotrules)
2306 (home-page "http://www.ncbi.nlm.nih.gov/books/NBK179288/")
2307 (synopsis "Tools for accessing the NCBI's set of databases")
2309 "Entrez Direct (EDirect) is a method for accessing the National Center
2310 for Biotechnology Information's (NCBI) set of interconnected
2311 databases (publication, sequence, structure, gene, variation, expression,
2312 etc.) from a terminal. Functions take search terms from command-line
2313 arguments. Individual operations are combined to build multi-step queries.
2314 Record retrieval and formatting normally complete the process.
2316 EDirect also provides an argument-driven function that simplifies the
2317 extraction of data from document summaries or other results that are returned
2318 in structured XML format. This can eliminate the need for writing custom
2319 software to answer ad hoc questions.")
2320 (license license:public-domain)))
2322 (define-public exonerate
2331 "http://ftp.ebi.ac.uk/pub/software/vertebrategenomics/exonerate/"
2332 "exonerate-" version ".tar.gz"))
2335 "0hj0m9xygiqsdxvbg79wq579kbrx1mdrabi2bzqz2zn9qwfjcjgq"))))
2336 (build-system gnu-build-system)
2338 `(#:parallel-build? #f)) ; Building in parallel fails on some machines.
2340 `(("pkg-config" ,pkg-config)))
2344 "https://www.ebi.ac.uk/about/vertebrate-genomics/software/exonerate")
2345 (synopsis "Generic tool for biological sequence alignment")
2347 "Exonerate is a generic tool for pairwise sequence comparison. It allows
2348 the alignment of sequences using a many alignment models, either exhaustive
2349 dynamic programming or a variety of heuristics.")
2350 (license license:gpl3)))
2352 (define-public express
2360 "http://bio.math.berkeley.edu/eXpress/downloads/express-"
2361 version "/express-" version "-src.tgz"))
2364 "03rczxd0gjp2l1jxcmjfmf5j94j77zqyxa6x063zsc585nj40n0c"))))
2365 (build-system cmake-build-system)
2367 `(#:tests? #f ;no "check" target
2369 (modify-phases %standard-phases
2370 (add-after 'unpack 'use-shared-boost-libs-and-set-bamtools-paths
2371 (lambda* (#:key inputs #:allow-other-keys)
2372 (substitute* "CMakeLists.txt"
2373 (("set\\(Boost_USE_STATIC_LIBS ON\\)")
2374 "set(Boost_USE_STATIC_LIBS OFF)")
2375 (("\\$\\{CMAKE_CURRENT_SOURCE_DIR\\}/bamtools/include")
2376 (string-append (assoc-ref inputs "bamtools") "/include/bamtools")))
2377 (substitute* "src/CMakeLists.txt"
2378 (("\\$\\{CMAKE_CURRENT_SOURCE_DIR\\}/\\.\\./bamtools/lib")
2379 (string-append (assoc-ref inputs "bamtools") "/lib/bamtools")))
2383 ("bamtools" ,bamtools)
2384 ("protobuf" ,protobuf)
2386 (home-page "http://bio.math.berkeley.edu/eXpress")
2387 (synopsis "Streaming quantification for high-throughput genomic sequencing")
2389 "eXpress is a streaming tool for quantifying the abundances of a set of
2390 target sequences from sampled subsequences. Example applications include
2391 transcript-level RNA-Seq quantification, allele-specific/haplotype expression
2392 analysis (from RNA-Seq), transcription factor binding quantification in
2393 ChIP-Seq, and analysis of metagenomic data.")
2394 (license license:artistic2.0)))
2396 (define-public express-beta-diversity
2398 (name "express-beta-diversity")
2404 "https://github.com/dparks1134/ExpressBetaDiversity/archive/v"
2406 (file-name (string-append name "-" version ".tar.gz"))
2409 "1djvdlmqvjf6h0zq7w36y8cl5cli6rgj86x65znl48agnwmzxfxr"))))
2410 (build-system gnu-build-system)
2413 (modify-phases %standard-phases
2415 (add-before 'build 'enter-source (lambda _ (chdir "source") #t))
2417 (lambda _ (zero? (system* "../bin/ExpressBetaDiversity"
2419 (add-after 'check 'exit-source (lambda _ (chdir "..") #t))
2421 (lambda* (#:key outputs #:allow-other-keys)
2422 (let ((bin (string-append (assoc-ref outputs "out")
2425 (install-file "scripts/convertToEBD.py" bin)
2426 (install-file "bin/ExpressBetaDiversity" bin)
2429 `(("python" ,python-2)))
2430 (home-page "http://kiwi.cs.dal.ca/Software/ExpressBetaDiversity")
2431 (synopsis "Taxon- and phylogenetic-based beta diversity measures")
2433 "Express Beta Diversity (EBD) calculates ecological beta diversity
2434 (dissimilarity) measures between biological communities. EBD implements a
2435 variety of diversity measures including those that make use of phylogenetic
2436 similarity of community members.")
2437 (license license:gpl3+)))
2439 (define-public fasttree
2446 "http://www.microbesonline.org/fasttree/FastTree-"
2450 "0vcjdvy1j4m702vmak4svbfkrpcw63k7wymfksjp9a982zy8kjsl"))))
2451 (build-system gnu-build-system)
2453 `(#:tests? #f ; no "check" target
2455 (modify-phases %standard-phases
2459 (lambda* (#:key source #:allow-other-keys)
2460 (and (zero? (system* "gcc"
2462 "-finline-functions"
2469 (zero? (system* "gcc"
2473 "-finline-functions"
2481 (lambda* (#:key outputs #:allow-other-keys)
2482 (let ((bin (string-append (assoc-ref outputs "out")
2485 (install-file "FastTree" bin)
2486 (install-file "FastTreeMP" bin)
2488 (home-page "http://www.microbesonline.org/fasttree")
2489 (synopsis "Infers approximately-maximum-likelihood phylogenetic trees")
2491 "FastTree can handle alignments with up to a million of sequences in a
2492 reasonable amount of time and memory. For large alignments, FastTree is
2493 100-1,000 times faster than PhyML 3.0 or RAxML 7.")
2494 (license license:gpl2+)))
2496 (define-public fastx-toolkit
2498 (name "fastx-toolkit")
2504 "https://github.com/agordon/fastx_toolkit/releases/download/"
2505 version "/fastx_toolkit-" version ".tar.bz2"))
2508 "01jqzw386873sr0pjp1wr4rn8fsga2vxs1qfmicvx1pjr72007wy"))))
2509 (build-system gnu-build-system)
2511 `(("libgtextutils" ,libgtextutils)))
2513 `(("pkg-config" ,pkg-config)))
2514 (home-page "http://hannonlab.cshl.edu/fastx_toolkit/")
2515 (synopsis "Tools for FASTA/FASTQ file preprocessing")
2517 "The FASTX-Toolkit is a collection of command line tools for Short-Reads
2518 FASTA/FASTQ files preprocessing.
2520 Next-Generation sequencing machines usually produce FASTA or FASTQ files,
2521 containing multiple short-reads sequences. The main processing of such
2522 FASTA/FASTQ files is mapping the sequences to reference genomes. However, it
2523 is sometimes more productive to preprocess the files before mapping the
2524 sequences to the genome---manipulating the sequences to produce better mapping
2525 results. The FASTX-Toolkit tools perform some of these preprocessing tasks.")
2526 (license license:agpl3+)))
2528 (define-public flexbar
2535 (string-append "mirror://sourceforge/flexbar/"
2536 version "/flexbar_v" version "_src.tgz"))
2539 "13jaykc3y1x8y5nn9j8ljnb79s5y51kyxz46hdmvvjj6qhyympmf"))))
2540 (build-system cmake-build-system)
2542 `(#:configure-flags (list
2543 (string-append "-DFLEXBAR_BINARY_DIR="
2544 (assoc-ref %outputs "out")
2547 (modify-phases %standard-phases
2549 (lambda* (#:key outputs #:allow-other-keys)
2550 (setenv "PATH" (string-append
2551 (assoc-ref outputs "out") "/bin:"
2553 (chdir "../flexbar_v2.5_src/test")
2554 (zero? (system* "bash" "flexbar_validate.sh"))))
2555 (delete 'install))))
2560 `(("pkg-config" ,pkg-config)
2562 (home-page "http://flexbar.sourceforge.net")
2563 (synopsis "Barcode and adapter removal tool for sequencing platforms")
2565 "Flexbar preprocesses high-throughput nucleotide sequencing data
2566 efficiently. It demultiplexes barcoded runs and removes adapter sequences.
2567 Moreover, trimming and filtering features are provided. Flexbar increases
2568 read mapping rates and improves genome and transcriptome assemblies. It
2569 supports next-generation sequencing data in fasta/q and csfasta/q format from
2570 Illumina, Roche 454, and the SOLiD platform.")
2571 (license license:gpl3)))
2573 (define-public fraggenescan
2575 (name "fraggenescan")
2581 (string-append "mirror://sourceforge/fraggenescan/"
2582 "FragGeneScan" version ".tar.gz"))
2584 (base32 "158dcnwczgcyhwm4qlx19sanrwgdpzf6bn2y57mbpx55lkgz1mzj"))))
2585 (build-system gnu-build-system)
2588 (modify-phases %standard-phases
2590 (add-before 'build 'patch-paths
2591 (lambda* (#:key outputs #:allow-other-keys)
2592 (let* ((out (string-append (assoc-ref outputs "out")))
2593 (share (string-append out "/share/fraggenescan/")))
2594 (substitute* "run_FragGeneScan.pl"
2596 (string-append "system(\"" (which "rm")))
2598 (string-append "system(\"" (which "mv")))
2599 (("\\\"awk") (string-append "\"" (which "awk")))
2600 ;; This script and other programs expect the training files
2601 ;; to be in the non-standard location bin/train/XXX. Change
2602 ;; this to be share/fraggenescan/train/XXX instead.
2603 (("^\\$train.file = \\$dir.*")
2604 (string-append "$train_file = \""
2606 "train/\".$FGS_train_file;")))
2607 (substitute* "run_hmm.c"
2608 (("^ strcat\\(train_dir, \\\"train/\\\"\\);")
2609 (string-append " strcpy(train_dir, \"" share "/train/\");"))))
2612 (lambda _ (and (zero? (system* "make" "clean"))
2613 (zero? (system* "make" "fgs")))))
2615 (lambda* (#:key outputs #:allow-other-keys)
2616 (let* ((out (string-append (assoc-ref outputs "out")))
2617 (bin (string-append out "/bin/"))
2618 (share (string-append out "/share/fraggenescan/train")))
2619 (install-file "run_FragGeneScan.pl" bin)
2620 (install-file "FragGeneScan" bin)
2621 (copy-recursively "train" share))))
2623 (add-after 'install 'post-install-check
2624 ;; In lieu of 'make check', run one of the examples and check the
2625 ;; output files gets created.
2626 (lambda* (#:key outputs #:allow-other-keys)
2627 (let* ((out (string-append (assoc-ref outputs "out")))
2628 (bin (string-append out "/bin/"))
2629 (frag (string-append bin "run_FragGeneScan.pl")))
2630 (and (zero? (system* frag ; Test complete genome.
2631 "-genome=./example/NC_000913.fna"
2635 (file-exists? "test2.faa")
2636 (file-exists? "test2.ffn")
2637 (file-exists? "test2.gff")
2638 (file-exists? "test2.out")
2639 (zero? (system* ; Test incomplete sequences.
2641 "-genome=./example/NC_000913-fgs.ffn"
2644 "-train=454_30")))))))))
2647 ("python" ,python-2))) ;not compatible with python 3.
2648 (home-page "https://sourceforge.net/projects/fraggenescan/")
2649 (synopsis "Finds potentially fragmented genes in short reads")
2651 "FragGeneScan is a program for predicting bacterial and archaeal genes in
2652 short and error-prone DNA sequencing reads. It can also be applied to predict
2653 genes in incomplete assemblies or complete genomes.")
2654 ;; GPL3+ according to private correspondense with the authors.
2655 (license license:gpl3+)))
2657 (define-public fxtract
2658 (let ((util-commit "776ca85a18a47492af3794745efcb4a905113115"))
2666 "https://github.com/ctSkennerton/fxtract/archive/"
2668 (file-name (string-append "ctstennerton-util-"
2669 (string-take util-commit 7)
2673 "0275cfdhis8517hm01is62062swmi06fxzifq7mr3knbbxjlaiwj"))))
2674 (build-system gnu-build-system)
2676 `(#:make-flags (list
2677 (string-append "PREFIX=" (assoc-ref %outputs "out"))
2679 #:test-target "fxtract_test"
2681 (modify-phases %standard-phases
2683 (add-before 'build 'copy-util
2684 (lambda* (#:key inputs #:allow-other-keys)
2686 (copy-recursively (assoc-ref inputs "ctskennerton-util") "util")
2688 ;; Do not use make install as this requires additional dependencies.
2690 (lambda* (#:key outputs #:allow-other-keys)
2691 (let* ((out (assoc-ref outputs "out"))
2692 (bin (string-append out"/bin")))
2693 (install-file "fxtract" bin)
2699 ;; ctskennerton-util is licensed under GPL2.
2700 `(("ctskennerton-util"
2704 (url "https://github.com/ctSkennerton/util.git")
2705 (commit util-commit)))
2706 (file-name (string-append
2707 "ctstennerton-util-" util-commit "-checkout"))
2710 "0cls1hd4vgj3f36fpzzg4xc77d6f3hpc60cbpfmn2gdr7ykzzad7"))))))
2711 (home-page "https://github.com/ctSkennerton/fxtract")
2712 (synopsis "Extract sequences from FASTA and FASTQ files")
2714 "Fxtract extracts sequences from a protein or nucleotide fastx (FASTA
2715 or FASTQ) file given a subsequence. It uses a simple substring search for
2716 basic tasks but can change to using POSIX regular expressions, PCRE, hash
2717 lookups or multi-pattern searching as required. By default fxtract looks in
2718 the sequence of each record but can also be told to look in the header,
2719 comment or quality sections.")
2720 ;; 'util' requires SSE instructions.
2721 (supported-systems '("x86_64-linux"))
2722 (license license:expat))))
2724 (define-public gemma
2730 (uri (string-append "https://github.com/xiangzhou/GEMMA/archive/v"
2732 (file-name (string-append name "-" version ".tar.gz"))
2735 "055ynn16gd12pf78n4vr2a9jlwsbwzajpdnf2y2yilg1krfff222"))
2736 (patches (search-patches "gemma-intel-compat.patch"))))
2741 (build-system gnu-build-system)
2744 '(,@(match (%current-system)
2746 '("FORCE_DYNAMIC=1"))
2748 '("FORCE_DYNAMIC=1" "FORCE_32BIT=1"))
2750 '("FORCE_DYNAMIC=1" "NO_INTEL_COMPAT=1"))))
2752 (modify-phases %standard-phases
2754 (add-before 'build 'bin-mkdir
2759 (lambda* (#:key outputs #:allow-other-keys)
2760 (let ((out (assoc-ref outputs "out")))
2761 (install-file "bin/gemma"
2765 #:tests? #f)) ; no tests included yet
2766 (home-page "https://github.com/xiangzhou/GEMMA")
2767 (synopsis "Tool for genome-wide efficient mixed model association")
2769 "Genome-wide Efficient Mixed Model Association (GEMMA) provides a
2770 standard linear mixed model resolver with application in genome-wide
2771 association studies (GWAS).")
2772 (license license:gpl3)))
2781 "https://github.com/nboley/grit/archive/"
2783 (file-name (string-append name "-" version ".tar.gz"))
2786 "157in84dj70wimbind3x7sy1whs3h57qfgcnj2s6lrd38fbrb7mj"))))
2787 (build-system python-build-system)
2789 `(#:python ,python-2
2791 (modify-phases %standard-phases
2792 (add-after 'unpack 'generate-from-cython-sources
2793 (lambda* (#:key inputs outputs #:allow-other-keys)
2794 ;; Delete these C files to force fresh generation from pyx sources.
2795 (delete-file "grit/sparsify_support_fns.c")
2796 (delete-file "grit/call_peaks_support_fns.c")
2797 (substitute* "setup.py"
2798 (("Cython.Setup") "Cython.Build")
2799 ;; Add numpy include path to fix compilation
2801 (string-append "pyx\", ], include_dirs = ['"
2802 (assoc-ref inputs "python-numpy")
2803 "/lib/python2.7/site-packages/numpy/core/include/"
2807 `(("python-scipy" ,python2-scipy)
2808 ("python-numpy" ,python2-numpy)
2809 ("python-pysam" ,python2-pysam)
2810 ("python-networkx" ,python2-networkx)))
2812 `(("python-cython" ,python2-cython)))
2813 (home-page "http://grit-bio.org")
2814 (synopsis "Tool for integrative analysis of RNA-seq type assays")
2816 "GRIT is designed to use RNA-seq, TES, and TSS data to build and quantify
2817 full length transcript models. When none of these data sources are available,
2818 GRIT can be run by providing a candidate set of TES or TSS sites. In
2819 addition, GRIT can merge in reference junctions and gene boundaries. GRIT can
2820 also be run in quantification mode, where it uses a provided GTF file and just
2821 estimates transcript expression.")
2822 (license license:gpl3+)))
2824 (define-public hisat
2831 "http://ccb.jhu.edu/software/hisat/downloads/hisat-"
2832 version "-beta-source.zip"))
2835 "1k381ydranqxp09yf2y7w1d0chz5d59vb6jchi89hbb0prq19lk5"))))
2836 (build-system gnu-build-system)
2838 `(#:tests? #f ;no check target
2839 #:make-flags '("allall"
2840 ;; Disable unsupported `popcnt' instructions on
2841 ;; architectures other than x86_64
2842 ,@(if (string-prefix? "x86_64"
2843 (or (%current-target-system)
2846 '("POPCNT_CAPABILITY=0")))
2848 (modify-phases %standard-phases
2849 (add-after 'unpack 'patch-sources
2851 ;; XXX Cannot use snippet because zip files are not supported
2852 (substitute* "Makefile"
2853 (("^CC = .*$") "CC = gcc")
2854 (("^CPP = .*$") "CPP = g++")
2855 ;; replace BUILD_HOST and BUILD_TIME for deterministic build
2856 (("-DBUILD_HOST=.*") "-DBUILD_HOST=\"\\\"guix\\\"\"")
2857 (("-DBUILD_TIME=.*") "-DBUILD_TIME=\"\\\"0\\\"\""))
2858 (substitute* '("hisat-build" "hisat-inspect")
2859 (("/usr/bin/env") (which "env")))
2862 (lambda* (#:key outputs #:allow-other-keys)
2863 (let ((bin (string-append (assoc-ref outputs "out") "/bin/")))
2864 (for-each (lambda (file)
2865 (install-file file bin))
2868 "hisat(-(build|align|inspect)(-(s|l)(-debug)*)*)*$")))
2870 (delete 'configure))))
2872 `(("unzip" ,unzip)))
2877 ;; Non-portable SSE instructions are used so building fails on platforms
2878 ;; other than x86_64.
2879 (supported-systems '("x86_64-linux"))
2880 (home-page "http://ccb.jhu.edu/software/hisat/index.shtml")
2881 (synopsis "Hierarchical indexing for spliced alignment of transcripts")
2883 "HISAT is a fast and sensitive spliced alignment program for mapping
2884 RNA-seq reads. In addition to one global FM index that represents a whole
2885 genome, HISAT uses a large set of small FM indexes that collectively cover the
2886 whole genome. These small indexes (called local indexes) combined with
2887 several alignment strategies enable effective alignment of RNA-seq reads, in
2888 particular, reads spanning multiple exons.")
2889 (license license:gpl3+)))
2891 (define-public hisat2
2898 ;; FIXME: a better source URL is
2899 ;; (string-append "ftp://ftp.ccb.jhu.edu/pub/infphilo/hisat2"
2900 ;; "/downloads/hisat2-" version "-source.zip")
2901 ;; with hash "0lywnr8kijwsc2aw10dwxic0n0yvip6fl3rjlvc8zzwahamy4x7g"
2902 ;; but it is currently unavailable.
2903 (uri "https://github.com/infphilo/hisat2/archive/cba6e8cb.tar.gz")
2904 (file-name (string-append name "-" version ".tar.gz"))
2907 "1mf2hdsyv7cd97xm9mp9a4qws02yrj95y6w6f6cdwnq0klp81r50"))))
2908 (build-system gnu-build-system)
2910 `(#:tests? #f ; no check target
2911 #:make-flags (list "CC=gcc" "CXX=g++" "allall")
2912 #:modules ((guix build gnu-build-system)
2916 (modify-phases %standard-phases
2917 (add-after 'unpack 'make-deterministic
2919 (substitute* "Makefile"
2924 (lambda* (#:key outputs #:allow-other-keys)
2925 (let* ((out (assoc-ref outputs "out"))
2926 (bin (string-append out "/bin/"))
2927 (doc (string-append out "/share/doc/hisat2/")))
2929 (cut install-file <> bin)
2931 "hisat2(-(build|align|inspect)(-(s|l)(-debug)*)*)*$"))
2933 (install-file "doc/manual.inc.html" doc))
2936 `(("unzip" ,unzip) ; needed for archive from ftp
2938 ("pandoc" ,ghc-pandoc))) ; for documentation
2939 (home-page "http://ccb.jhu.edu/software/hisat2/index.shtml")
2940 (synopsis "Graph-based alignment of genomic sequencing reads")
2941 (description "HISAT2 is a fast and sensitive alignment program for mapping
2942 next-generation sequencing reads (both DNA and RNA) to a population of human
2943 genomes (as well as to a single reference genome). In addition to using one
2944 global @dfn{graph FM} (GFM) index that represents a population of human
2945 genomes, HISAT2 uses a large set of small GFM indexes that collectively cover
2946 the whole genome. These small indexes, combined with several alignment
2947 strategies, enable rapid and accurate alignment of sequencing reads. This new
2948 indexing scheme is called a @dfn{Hierarchical Graph FM index} (HGFM).")
2949 ;; HISAT2 contains files from Bowtie2, which is released under
2950 ;; GPLv2 or later. The HISAT2 source files are released under
2952 (license license:gpl3+)))
2954 (define-public hmmer
2962 "http://eddylab.org/software/hmmer"
2963 (version-prefix version 1) "/"
2964 version "/hmmer-" version ".tar.gz"))
2967 "0djmgc0pfli0jilfx8hql1axhwhqxqb8rxg2r5rg07aw73sfs5nx"))
2968 (patches (search-patches "hmmer-remove-cpu-specificity.patch"))))
2969 (build-system gnu-build-system)
2970 (native-inputs `(("perl" ,perl)))
2971 (home-page "http://hmmer.org/")
2972 (synopsis "Biosequence analysis using profile hidden Markov models")
2974 "HMMER is used for searching sequence databases for homologs of protein
2975 sequences, and for making protein sequence alignments. It implements methods
2976 using probabilistic models called profile hidden Markov models (profile
2978 (license (list license:gpl3+
2979 ;; The bundled library 'easel' is distributed
2980 ;; under The Janelia Farm Software License.
2981 (license:non-copyleft
2982 "file://easel/LICENSE"
2983 "See easel/LICENSE in the distribution.")))))
2985 (define-public htseq
2991 (uri (pypi-uri "HTSeq" version))
2994 "11flgb1381xdhk43bzbfm3vhnszkpqg6jk76rpa5xd1zbrvvlnxg"))))
2995 (build-system python-build-system)
2997 `(("python-cython" ,python-cython)))
2998 ;; Numpy needs to be propagated when htseq is used as a Python library.
3000 `(("python-numpy" ,python-numpy)))
3002 `(("python-pysam" ,python-pysam)
3003 ("python-matplotlib" ,python-matplotlib)))
3004 (home-page "http://www-huber.embl.de/users/anders/HTSeq/")
3005 (synopsis "Analysing high-throughput sequencing data with Python")
3007 "HTSeq is a Python package that provides infrastructure to process data
3008 from high-throughput sequencing assays.")
3009 (license license:gpl3+)))
3011 (define-public python2-htseq
3012 (package-with-python2 htseq))
3014 (define-public java-htsjdk
3016 (name "java-htsjdk")
3021 "https://github.com/samtools/htsjdk/archive/"
3023 (file-name (string-append name "-" version ".tar.gz"))
3026 "0asdk9b8jx2ij7yd6apg9qx03li8q7z3ml0qy2r2qczkra79y6fw"))
3027 (modules '((guix build utils)))
3028 ;; remove build dependency on git
3029 (snippet '(substitute* "build.xml"
3030 (("failifexecutionfails=\"true\"")
3031 "failifexecutionfails=\"false\"")))))
3032 (build-system ant-build-system)
3034 `(#:tests? #f ; test require Internet access
3036 (list (string-append "-Ddist=" (assoc-ref %outputs "out")
3037 "/share/java/htsjdk/"))
3038 #:build-target "all"
3040 (modify-phases %standard-phases
3041 ;; The build phase also installs the jars
3042 (delete 'install))))
3043 (home-page "http://samtools.github.io/htsjdk/")
3044 (synopsis "Java API for high-throughput sequencing data (HTS) formats")
3046 "HTSJDK is an implementation of a unified Java library for accessing
3047 common file formats, such as SAM and VCF, used for high-throughput
3048 sequencing (HTS) data. There are also an number of useful utilities for
3049 manipulating HTS data.")
3050 (license license:expat)))
3052 (define-public htslib
3059 "https://github.com/samtools/htslib/releases/download/"
3060 version "/htslib-" version ".tar.bz2"))
3063 "0bcjmnbwp2bib1z1bkrp95w9v2syzdwdfqww10mkb1hxlmg52ax0"))))
3064 (build-system gnu-build-system)
3067 (modify-phases %standard-phases
3069 'unpack 'patch-tests
3071 (substitute* "test/test.pl"
3072 (("/bin/bash") (which "bash")))
3075 `(("openssl" ,openssl)
3080 (home-page "http://www.htslib.org")
3081 (synopsis "C library for reading/writing high-throughput sequencing data")
3083 "HTSlib is a C library for reading/writing high-throughput sequencing
3084 data. It also provides the bgzip, htsfile, and tabix utilities.")
3085 ;; Files under cram/ are released under the modified BSD license;
3086 ;; the rest is released under the Expat license
3087 (license (list license:expat license:bsd-3))))
3089 ;; This package should be removed once no packages rely upon it.
3097 "https://github.com/samtools/htslib/releases/download/"
3098 version "/htslib-" version ".tar.bz2"))
3101 "1rja282fwdc25ql6izkhdyh8ppw8x2fs0w0js78zgkmqjlikmma9"))))))
3110 "https://github.com/nboley/idr/archive/"
3112 (file-name (string-append name "-" version ".tar.gz"))
3115 "1k3x44biak00aiv3hpm1yd6nn4hhp7n0qnbs3zh2q9sw7qr1qj5r"))))
3116 (build-system python-build-system)
3118 `(#:tests? #f)) ; FIXME: "ImportError: No module named 'utility'"
3120 `(("python-scipy" ,python-scipy)
3121 ("python-sympy" ,python-sympy)
3122 ("python-numpy" ,python-numpy)
3123 ("python-matplotlib" ,python-matplotlib)))
3125 `(("python-cython" ,python-cython)))
3126 (home-page "https://github.com/nboley/idr")
3127 (synopsis "Tool to measure the irreproducible discovery rate (IDR)")
3129 "The IDR (Irreproducible Discovery Rate) framework is a unified approach
3130 to measure the reproducibility of findings identified from replicate
3131 experiments and provide highly stable thresholds based on reproducibility.")
3132 (license license:gpl3+)))
3134 (define-public jellyfish
3140 (uri (string-append "https://github.com/gmarcais/Jellyfish/"
3141 "releases/download/v" version
3142 "/jellyfish-" version ".tar.gz"))
3145 "0a6xnynqy2ibfbfz86b9g2m2dgm7f1469pmymkpam333gi3p26nk"))))
3146 (build-system gnu-build-system)
3147 (outputs '("out" ;for library
3148 "ruby" ;for Ruby bindings
3149 "python")) ;for Python bindings
3152 (list (string-append "--enable-ruby-binding="
3153 (assoc-ref %outputs "ruby"))
3154 (string-append "--enable-python-binding="
3155 (assoc-ref %outputs "python")))
3157 (modify-phases %standard-phases
3158 (add-before 'check 'set-SHELL-variable
3160 ;; generator_manager.hpp either uses /bin/sh or $SHELL
3162 (setenv "SHELL" (which "bash"))
3168 ("python" ,python-2)))
3169 (synopsis "Tool for fast counting of k-mers in DNA")
3171 "Jellyfish is a tool for fast, memory-efficient counting of k-mers in
3172 DNA. A k-mer is a substring of length k, and counting the occurrences of all
3173 such substrings is a central step in many analyses of DNA sequence. Jellyfish
3174 is a command-line program that reads FASTA and multi-FASTA files containing
3175 DNA sequences. It outputs its k-mer counts in a binary format, which can be
3176 translated into a human-readable text format using the @code{jellyfish dump}
3177 command, or queried for specific k-mers with @code{jellyfish query}.")
3178 (home-page "http://www.genome.umd.edu/jellyfish.html")
3179 ;; From their website: JELLYFISH runs on 64-bit Intel-compatible processors
3180 (supported-systems '("x86_64-linux"))
3181 ;; The combined work is published under the GPLv3 or later. Individual
3182 ;; files such as lib/jsoncpp.cpp are released under the Expat license.
3183 (license (list license:gpl3+ license:expat))))
3185 (define-public khmer
3192 (uri (pypi-uri "khmer" version))
3195 "0wb05shqh77v00256qlm68vbbx3kl76fyzihszbz5nhanl4ni33a"))
3196 (patches (search-patches "khmer-use-libraries.patch"))))
3197 (build-system python-build-system)
3200 (modify-phases %standard-phases
3201 (add-after 'unpack 'set-paths
3202 (lambda* (#:key inputs outputs #:allow-other-keys)
3203 ;; Delete bundled libraries.
3204 (delete-file-recursively "third-party/zlib")
3205 (delete-file-recursively "third-party/bzip2")
3206 ;; Replace bundled seqan.
3207 (let* ((seqan-all "third-party/seqan")
3208 (seqan-include (string-append
3209 seqan-all "/core/include")))
3210 (delete-file-recursively seqan-all)
3211 (copy-recursively (string-append (assoc-ref inputs "seqan")
3213 (string-append seqan-include "/seqan")))
3214 ;; We do not replace the bundled MurmurHash as the canonical
3215 ;; repository for this code 'SMHasher' is unsuitable for
3216 ;; providing a library. See
3217 ;; https://lists.gnu.org/archive/html/guix-devel/2016-06/msg00977.html
3219 (add-after 'unpack 'set-cc
3223 ;; It is simpler to test after installation.
3225 (add-after 'install 'post-install-check
3226 (lambda* (#:key inputs outputs #:allow-other-keys)
3227 (let ((out (assoc-ref outputs "out")))
3232 (assoc-ref outputs "out")
3234 (setenv "PYTHONPATH"
3236 (getenv "PYTHONPATH")
3240 (string-take (string-take-right
3241 (assoc-ref inputs "python") 5) 3)
3243 (with-directory-excursion "build"
3244 (zero? (system* "nosetests" "khmer" "--attr"
3245 "!known_failing")))))))))
3248 ("python-nose" ,python-nose)))
3252 ("python-screed" ,python-screed)
3253 ("python-bz2file" ,python-bz2file)
3254 ;; Tests fail when gcc-5 is used for compilation. Use gcc-4.9 at least
3255 ;; until the next version of khmer (likely 2.1) is released.
3257 (home-page "https://khmer.readthedocs.org/")
3258 (synopsis "K-mer counting, filtering and graph traversal library")
3259 (description "The khmer software is a set of command-line tools for
3260 working with DNA shotgun sequencing data from genomes, transcriptomes,
3261 metagenomes and single cells. Khmer can make de novo assemblies faster, and
3262 sometimes better. Khmer can also identify and fix problems with shotgun
3264 ;; When building on i686, armhf and mips64el, we get the following error:
3265 ;; error: ['khmer', 'khmer.tests', 'oxli'] require 64-bit operating system
3266 (supported-systems '("x86_64-linux"))
3267 (license license:bsd-3)))
3269 (define-public kaiju
3276 "https://github.com/bioinformatics-centre/kaiju/archive/v"
3278 (file-name (string-append name "-" version ".tar.gz"))
3281 "0afbfalfw9y39bkwnqjrh9bghs118ws1pzj5h8l0nblgn3mbjdks"))))
3282 (build-system gnu-build-system)
3284 `(#:tests? #f ; There are no tests.
3286 (modify-phases %standard-phases
3288 (add-before 'build 'move-to-src-dir
3289 (lambda _ (chdir "src") #t))
3291 (lambda* (#:key inputs outputs #:allow-other-keys)
3292 (let ((bin (string-append (assoc-ref outputs "out") "/bin")))
3295 (copy-recursively "bin" bin)
3296 (copy-recursively "util" bin))
3300 (home-page "http://kaiju.binf.ku.dk/")
3301 (synopsis "Fast and sensitive taxonomic classification for metagenomics")
3302 (description "Kaiju is a program for sensitive taxonomic classification
3303 of high-throughput sequencing reads from metagenomic whole genome sequencing
3305 (license license:gpl3+)))
3310 (version "2.1.0.20151222")
3313 (uri (pypi-uri "MACS2" version))
3316 "1r2hcz6irhcq7lwbafjks98jbn34hv05avgbdjnp6w6mlfjkf8x5"))))
3317 (build-system python-build-system)
3319 `(#:python ,python-2 ; only compatible with Python 2.7
3320 #:tests? #f)) ; no test target
3322 `(("python-numpy" ,python2-numpy)))
3323 (home-page "https://github.com/taoliu/MACS/")
3324 (synopsis "Model based analysis for ChIP-Seq data")
3326 "MACS is an implementation of a ChIP-Seq analysis algorithm for
3327 identifying transcript factor binding sites named Model-based Analysis of
3328 ChIP-Seq (MACS). MACS captures the influence of genome complexity to evaluate
3329 the significance of enriched ChIP regions and it improves the spatial
3330 resolution of binding sites through combining the information of both
3331 sequencing tag position and orientation.")
3332 (license license:bsd-3)))
3334 (define-public mafft
3341 "http://mafft.cbrc.jp/alignment/software/mafft-" version
3342 "-without-extensions-src.tgz"))
3343 (file-name (string-append name "-" version ".tgz"))
3346 "0gbsaz6z2qa307kd7wfb06c3y4ikmv1hsdvlns11f6zq4w1z9pwc"))))
3347 (build-system gnu-build-system)
3349 `(#:tests? #f ; no automated tests, though there are tests in the read me
3350 #:make-flags (let ((out (assoc-ref %outputs "out")))
3351 (list (string-append "PREFIX=" out)
3352 (string-append "BINDIR="
3353 (string-append out "/bin"))))
3355 (modify-phases %standard-phases
3356 (add-after 'unpack 'enter-dir
3357 (lambda _ (chdir "core") #t))
3358 (add-after 'enter-dir 'patch-makefile
3360 ;; on advice from the MAFFT authors, there is no need to
3361 ;; distribute mafft-profile, mafft-distance, or
3362 ;; mafft-homologs.rb as they are too "specialised".
3363 (substitute* "Makefile"
3364 ;; remove mafft-homologs.rb from SCRIPTS
3365 (("^SCRIPTS = mafft mafft-homologs.rb")
3367 ;; remove mafft-homologs from MANPAGES
3368 (("^MANPAGES = mafft.1 mafft-homologs.1")
3369 "MANPAGES = mafft.1")
3370 ;; remove mafft-distance from PROGS
3371 (("^PROGS = dvtditr dndfast7 dndblast sextet5 mafft-distance")
3372 "PROGS = dvtditr dndfast7 dndblast sextet5")
3373 ;; remove mafft-profile from PROGS
3374 (("splittbfast disttbfast tbfast mafft-profile 2cl mccaskillwrap")
3375 "splittbfast disttbfast tbfast f2cl mccaskillwrap")
3376 (("^rm -f mafft-profile mafft-profile.exe") "#")
3377 (("^rm -f mafft-distance mafft-distance.exe") ")#")
3378 ;; do not install MAN pages in libexec folder
3379 (("^\t\\$\\(INSTALL\\) -m 644 \\$\\(MANPAGES\\) \
3380 \\$\\(DESTDIR\\)\\$\\(LIBDIR\\)") "#"))
3382 (add-after 'enter-dir 'patch-paths
3383 (lambda* (#:key inputs #:allow-other-keys)
3384 (substitute* '("pairash.c"
3386 (("perl") (which "perl"))
3387 (("([\"`| ])awk" _ prefix)
3388 (string-append prefix (which "awk")))
3389 (("grep") (which "grep")))
3392 (add-after 'install 'wrap-programs
3393 (lambda* (#:key outputs #:allow-other-keys)
3394 (let* ((out (assoc-ref outputs "out"))
3395 (bin (string-append out "/bin"))
3396 (path (string-append
3397 (assoc-ref %build-inputs "coreutils") "/bin:")))
3398 (for-each (lambda (file)
3400 `("PATH" ":" prefix (,path))))
3408 ("coreutils" ,coreutils)))
3409 (home-page "http://mafft.cbrc.jp/alignment/software/")
3410 (synopsis "Multiple sequence alignment program")
3412 "MAFFT offers a range of multiple alignment methods for nucleotide and
3413 protein sequences. For instance, it offers L-INS-i (accurate; for alignment
3414 of <~200 sequences) and FFT-NS-2 (fast; for alignment of <~30,000
3416 (license (license:non-copyleft
3417 "http://mafft.cbrc.jp/alignment/software/license.txt"
3418 "BSD-3 with different formatting"))))
3427 "https://github.com/marbl/mash/archive/v"
3429 (file-name (string-append name "-" version ".tar.gz"))
3432 "08znbvqq5xknfhmpp3wcj574zvi4p7i8zifi67c9qw9a6ikp42fj"))
3433 (modules '((guix build utils)))
3435 ;; Delete bundled kseq.
3436 ;; TODO: Also delete bundled murmurhash and open bloom filter.
3437 '(delete-file "src/mash/kseq.h"))))
3438 (build-system gnu-build-system)
3440 `(#:tests? #f ; No tests.
3443 (string-append "--with-capnp=" (assoc-ref %build-inputs "capnproto"))
3444 (string-append "--with-gsl=" (assoc-ref %build-inputs "gsl")))
3445 #:make-flags (list "CC=gcc")
3447 (modify-phases %standard-phases
3448 (add-after 'unpack 'fix-includes
3450 (substitute* '("src/mash/Sketch.cpp" "src/mash/CommandFind.cpp")
3451 (("^#include \"kseq\\.h\"")
3452 "#include \"htslib/kseq.h\""))
3454 (add-after 'fix-includes 'autoconf
3455 (lambda _ (zero? (system* "autoconf")))))))
3457 `(("autoconf" ,autoconf)
3458 ;; Capnproto and htslib are statically embedded in the final
3459 ;; application. Therefore we also list their licenses, below.
3460 ("capnproto" ,capnproto)
3461 ("htslib" ,htslib)))
3465 (supported-systems '("x86_64-linux"))
3466 (home-page "https://mash.readthedocs.io")
3467 (synopsis "Fast genome and metagenome distance estimation using MinHash")
3468 (description "Mash is a fast sequence distance estimator that uses the
3469 MinHash algorithm and is designed to work with genomes and metagenomes in the
3470 form of assemblies or reads.")
3471 (license (list license:bsd-3 ; Mash
3472 license:expat ; HTSlib and capnproto
3473 license:public-domain ; MurmurHash 3
3474 license:cpl1.0)))) ; Open Bloom Filter
3476 (define-public metabat
3483 (uri (string-append "https://bitbucket.org/berkeleylab/metabat/get/v"
3485 (file-name (string-append name "-" version ".tar.gz"))
3488 "1hmvdalz3zj5sqqklg0l4npjdv37cv2hsdi1al9iby2ndxjs1b73"))
3489 (patches (search-patches "metabat-fix-compilation.patch"))))
3490 (build-system gnu-build-system)
3493 (modify-phases %standard-phases
3494 (add-after 'unpack 'fix-includes
3496 (substitute* "src/BamUtils.h"
3497 (("^#include \"bam/bam\\.h\"")
3498 "#include \"samtools/bam.h\"")
3499 (("^#include \"bam/sam\\.h\"")
3500 "#include \"samtools/sam.h\""))
3501 (substitute* "src/KseqReader.h"
3502 (("^#include \"bam/kseq\\.h\"")
3503 "#include \"htslib/kseq.h\""))
3505 (add-after 'unpack 'fix-scons
3506 (lambda* (#:key inputs #:allow-other-keys)
3507 (substitute* "SConstruct"
3508 (("^htslib_dir += 'samtools'")
3509 (string-append "htslib_dir = '"
3510 (assoc-ref inputs "htslib")
3512 (("^samtools_dir = 'samtools'")
3513 (string-append "samtools_dir = '"
3514 (assoc-ref inputs "samtools")
3516 (("^findStaticOrShared\\('bam', hts_lib")
3517 (string-append "findStaticOrShared('bam', '"
3518 (assoc-ref inputs "samtools")
3520 ;; Do not distribute README.
3521 (("^env\\.Install\\(idir_prefix, 'README\\.md'\\)") ""))
3525 (lambda* (#:key inputs outputs #:allow-other-keys)
3526 (mkdir (assoc-ref outputs "out"))
3527 (zero? (system* "scons"
3530 (assoc-ref outputs "out"))
3533 (assoc-ref inputs "boost"))
3535 ;; Check and install are carried out during build phase.
3537 (delete 'install))))
3541 ("samtools" ,samtools)
3545 `(("scons" ,scons)))
3546 (home-page "https://bitbucket.org/berkeleylab/metabat")
3548 "Reconstruction of single genomes from complex microbial communities")
3550 "Grouping large genomic fragments assembled from shotgun metagenomic
3551 sequences to deconvolute complex microbial communities, or metagenome binning,
3552 enables the study of individual organisms and their interactions. MetaBAT is
3553 an automated metagenome binning software, which integrates empirical
3554 probabilistic distances of genome abundance and tetranucleotide frequency.")
3555 ;; The source code contains inline assembly.
3556 (supported-systems '("x86_64-linux" "i686-linux"))
3557 (license (license:non-copyleft "file://license.txt"
3558 "See license.txt in the distribution."))))
3560 (define-public minced
3567 "https://github.com/ctSkennerton/minced/archive/"
3569 (file-name (string-append name "-" version ".tar.gz"))
3572 "0wxmlsapxfpxfd3ps9636h7i2xy6la8i42mwh0j2lsky63h63jp1"))))
3573 (build-system gnu-build-system)
3575 `(#:test-target "test"
3577 (modify-phases %standard-phases
3579 (add-before 'check 'fix-test
3581 ;; Fix test for latest version.
3582 (substitute* "t/Aquifex_aeolicus_VF5.expected"
3583 (("minced:0.1.6") "minced:0.2.0"))
3585 (replace 'install ; No install target.
3586 (lambda* (#:key inputs outputs #:allow-other-keys)
3587 (let* ((out (assoc-ref outputs "out"))
3588 (bin (string-append out "/bin"))
3589 (wrapper (string-append bin "/minced")))
3590 ;; Minced comes with a wrapper script that tries to figure out where
3591 ;; it is located before running the JAR. Since these paths are known
3592 ;; to us, we build our own wrapper to avoid coreutils dependency.
3593 (install-file "minced.jar" bin)
3594 (with-output-to-file wrapper
3598 "#!" (assoc-ref inputs "bash") "/bin/sh\n\n"
3599 (assoc-ref inputs "jre") "/bin/java -jar "
3600 bin "/minced.jar \"$@\"\n"))))
3601 (chmod wrapper #o555)))))))
3603 `(("jdk" ,icedtea "jdk")))
3606 ("jre" ,icedtea "out")))
3607 (home-page "https://github.com/ctSkennerton/minced")
3608 (synopsis "Mining CRISPRs in Environmental Datasets")
3610 "MinCED is a program to find Clustered Regularly Interspaced Short
3611 Palindromic Repeats (CRISPRs) in DNA sequences. It can be used for
3612 unassembled metagenomic reads, but is mainly designed for full genomes and
3613 assembled metagenomic sequence.")
3614 (license license:gpl3+)))
3623 "https://pypi.python.org/packages/source/m/misopy/misopy-"
3627 "0x446867az8ir0z8c1vjqffkp0ma37wm4sylixnkhgawllzx8v5w"))
3628 (modules '((guix build utils)))
3630 '(substitute* "setup.py"
3631 ;; Use setuptools, or else the executables are not
3633 (("distutils.core") "setuptools")
3634 ;; use "gcc" instead of "cc" for compilation
3636 "cc.set_executables(
3640 linker_so='gcc -shared'); defines")))))
3641 (build-system python-build-system)
3643 `(#:python ,python-2 ; only Python 2 is supported
3644 #:tests? #f)) ; no "test" target
3646 `(("samtools" ,samtools)
3647 ("python-numpy" ,python2-numpy)
3648 ("python-pysam" ,python2-pysam)
3649 ("python-scipy" ,python2-scipy)
3650 ("python-matplotlib" ,python2-matplotlib)))
3652 `(("python-mock" ,python2-mock) ;for tests
3653 ("python-pytz" ,python2-pytz))) ;for tests
3654 (home-page "http://genes.mit.edu/burgelab/miso/index.html")
3655 (synopsis "Mixture of Isoforms model for RNA-Seq isoform quantitation")
3657 "MISO (Mixture-of-Isoforms) is a probabilistic framework that quantitates
3658 the expression level of alternatively spliced genes from RNA-Seq data, and
3659 identifies differentially regulated isoforms or exons across samples. By
3660 modeling the generative process by which reads are produced from isoforms in
3661 RNA-Seq, the MISO model uses Bayesian inference to compute the probability
3662 that a read originated from a particular isoform.")
3663 (license license:gpl2)))
3665 (define-public muscle
3668 (version "3.8.1551")
3670 (method url-fetch/tarbomb)
3672 "http://www.drive5.com/muscle/muscle_src_"
3676 "0bj8kj7sdizy3987zx6w7axihk40fk8rn76mpbqqjcnd64i5a367"))))
3677 (build-system gnu-build-system)
3679 `(#:make-flags (list "LDLIBS = -lm")
3681 (modify-phases %standard-phases
3684 ;; There are no tests, so just test if it runs.
3685 (lambda _ (zero? (system* "./muscle" "-version"))))
3687 (lambda* (#:key outputs #:allow-other-keys)
3688 (let* ((out (assoc-ref outputs "out"))
3689 (bin (string-append out "/bin")))
3690 (install-file "muscle" bin)))))))
3691 (home-page "http://www.drive5.com/muscle")
3692 (synopsis "Multiple sequence alignment program")
3694 "MUSCLE aims to be a fast and accurate multiple sequence alignment
3695 program for nucleotide and protein sequences.")
3696 ;; License information found in 'muscle -h' and usage.cpp.
3697 (license license:public-domain)))
3699 (define-public newick-utils
3700 ;; There are no recent releases so we package from git.
3701 (let ((commit "da121155a977197cab9fbb15953ca1b40b11eb87"))
3703 (name "newick-utils")
3704 (version (string-append "1.6-1." (string-take commit 8)))
3708 (url "https://github.com/tjunier/newick_utils.git")
3710 (file-name (string-append name "-" version "-checkout"))
3713 "1hkw21rq1mwf7xp0rmbb2gqc0i6p11108m69i7mr7xcjl268pxnb"))))
3714 (build-system gnu-build-system)
3717 (modify-phases %standard-phases
3718 (add-after 'unpack 'autoconf
3719 (lambda _ (zero? (system* "autoreconf" "-vif")))))))
3721 ;; XXX: TODO: Enable Lua and Guile bindings.
3722 ;; https://github.com/tjunier/newick_utils/issues/13
3723 `(("libxml2" ,libxml2)
3727 `(("autoconf" ,autoconf)
3728 ("automake" ,automake)
3729 ("libtool" ,libtool)))
3730 (synopsis "Programs for working with newick format phylogenetic trees")
3732 "Newick-utils is a suite of utilities for processing phylogenetic trees
3733 in Newick format. Functions include re-rooting, extracting subtrees,
3734 trimming, pruning, condensing, drawing (ASCII graphics or SVG).")
3735 (home-page "https://github.com/tjunier/newick_utils")
3736 (license license:bsd-3))))
3745 "https://github.com/wwood/OrfM/releases/download/v"
3746 version "/orfm-" version ".tar.gz"))
3749 "16iigyr2gd8x0imzkk1dr3k5xsds9bpmwg31ayvjg0f4pir9rwqr"))))
3750 (build-system gnu-build-system)
3751 (inputs `(("zlib" ,zlib)))
3753 `(("ruby-bio-commandeer" ,ruby-bio-commandeer)
3754 ("ruby-rspec" ,ruby-rspec)
3756 (synopsis "Simple and not slow open reading frame (ORF) caller")
3758 "An ORF caller finds stretches of DNA that, when translated, are not
3759 interrupted by stop codons. OrfM finds and prints these ORFs.")
3760 (home-page "https://github.com/wwood/OrfM")
3761 (license license:lgpl3+)))
3763 (define-public pplacer
3764 (let ((commit "g807f6f3"))
3767 ;; The commit should be updated with each version change.
3768 (version "1.1.alpha19")
3772 (uri (string-append "https://github.com/matsen/pplacer/archive/v"
3774 (file-name (string-append name "-" version ".tar.gz"))
3776 (base32 "0z1lnd2s8sh6kpzg106wzbh2szw7h0hvq8syd5a6wv4rmyyz6x0f"))))
3777 (build-system ocaml-build-system)
3779 `(#:ocaml ,ocaml-4.01
3780 #:findlib ,ocaml4.01-findlib
3781 #:modules ((guix build ocaml-build-system)
3785 (modify-phases %standard-phases
3787 (add-after 'unpack 'replace-bundled-cddlib
3788 (lambda* (#:key inputs #:allow-other-keys)
3789 (let* ((cddlib-src (assoc-ref inputs "cddlib-src"))
3790 (local-dir "cddlib_guix"))
3792 (with-directory-excursion local-dir
3793 (system* "tar" "xvf" cddlib-src))
3794 (let ((cddlib-src-folder
3795 (string-append local-dir "/"
3796 (list-ref (scandir local-dir) 2)
3801 (string-append "cdd_src/" (basename file))))
3802 (find-files cddlib-src-folder ".*[ch]$")))
3804 (add-after 'unpack 'fix-makefile
3806 ;; Remove system calls to 'git'.
3807 (substitute* "Makefile"
3808 (("^DESCRIPT:=pplacer-.*")
3810 "DESCRIPT:=pplacer-$(shell uname)-v" ,version "\n")))
3811 (substitute* "myocamlbuild.ml"
3812 (("git describe --tags --long .*\\\" with")
3814 "echo -n v" ,version "-" ,commit "\" with")))
3817 (lambda* (#:key outputs #:allow-other-keys)
3818 (let* ((out (assoc-ref outputs "out"))
3819 (bin (string-append out "/bin")))
3820 (copy-recursively "bin" bin))
3825 ("ocaml-ounit" ,ocaml4.01-ounit)
3826 ("ocaml-batteries" ,ocaml4.01-batteries)
3827 ("ocaml-camlzip" ,ocaml4.01-camlzip)
3828 ("ocaml-csv" ,ocaml4.01-csv)
3829 ("ocaml-sqlite3" ,ocaml4.01-sqlite3)
3830 ("ocaml-xmlm" ,ocaml4.01-xmlm)
3831 ("ocaml-mcl" ,ocaml4.01-mcl)
3832 ("ocaml-gsl" ,ocaml4.01-gsl)
3833 ("cddlib-src" ,(package-source cddlib))))
3835 `(("pplacer-scripts" ,pplacer-scripts)))
3836 (synopsis "Phylogenetic placement of biological sequences")
3838 "Pplacer places query sequences on a fixed reference phylogenetic tree
3839 to maximize phylogenetic likelihood or posterior probability according to a
3840 reference alignment. Pplacer is designed to be fast, to give useful
3841 information about uncertainty, and to offer advanced visualization and
3842 downstream analysis.")
3843 (home-page "http://matsen.fhcrc.org/pplacer")
3844 (license license:gpl3))))
3846 ;; This package is installed alongside 'pplacer'. It is a separate package so
3847 ;; that it can use the python-build-system for the scripts that are
3848 ;; distributed alongside the main OCaml binaries.
3849 (define pplacer-scripts
3852 (name "pplacer-scripts")
3853 (build-system python-build-system)
3855 `(#:python ,python-2
3857 (modify-phases %standard-phases
3858 (add-after 'unpack 'enter-scripts-dir
3859 (lambda _ (chdir "scripts")))
3862 (zero? (system* "python" "-m" "unittest" "discover" "-v"))))
3863 (add-after 'install 'wrap-executables
3864 (lambda* (#:key inputs outputs #:allow-other-keys)
3865 (let* ((out (assoc-ref outputs "out"))
3866 (bin (string-append out "/bin")))
3867 (let ((path (string-append
3868 (assoc-ref inputs "hmmer") "/bin:"
3869 (assoc-ref inputs "infernal") "/bin")))
3871 (wrap-program (string-append bin "/refpkg_align.py")
3872 `("PATH" ":" prefix (,path))))
3873 (let ((path (string-append
3874 (assoc-ref inputs "hmmer") "/bin")))
3875 (wrap-program (string-append bin "/hrefpkg_query.py")
3876 `("PATH" ":" prefix (,path)))))
3879 `(("infernal" ,infernal)
3882 `(("python-biopython" ,python2-biopython)
3883 ("taxtastic" ,taxtastic)))
3884 (synopsis "Pplacer Python scripts")))
3886 (define-public python2-pbcore
3888 (name "python2-pbcore")
3892 (uri (pypi-uri "pbcore" version))
3895 "1kjmv891d6qbpp4shhhvkl02ff4q5xlpnls2513sm2cjcrs52f1i"))))
3896 (build-system python-build-system)
3897 (arguments `(#:python ,python-2)) ; pbcore requires Python 2.7
3899 `(("python-cython" ,python2-cython)
3900 ("python-numpy" ,python2-numpy)
3901 ("python-pysam" ,python2-pysam)
3902 ("python-h5py" ,python2-h5py)))
3904 `(("python-nose" ,python2-nose)
3905 ("python-sphinx" ,python2-sphinx)
3906 ("python-pyxb" ,python2-pyxb)))
3907 (home-page "http://pacificbiosciences.github.io/pbcore/")
3908 (synopsis "Library for reading and writing PacBio data files")
3910 "The pbcore package provides Python APIs for interacting with PacBio data
3911 files and writing bioinformatics applications.")
3912 (license license:bsd-3)))
3914 (define-public python2-warpedlmm
3916 (name "python2-warpedlmm")
3922 "https://pypi.python.org/packages/source/W/WarpedLMM/WarpedLMM-"
3926 "1agfz6zqa8nc6cw47yh0s3y14gkpa9wqazwcj7mwwj3ffnw39p3j"))))
3927 (build-system python-build-system)
3929 `(#:python ,python-2)) ; requires Python 2.7
3931 `(("python-scipy" ,python2-scipy)
3932 ("python-numpy" ,python2-numpy)
3933 ("python-matplotlib" ,python2-matplotlib)
3934 ("python-fastlmm" ,python2-fastlmm)
3935 ("python-pandas" ,python2-pandas)
3936 ("python-pysnptools" ,python2-pysnptools)))
3938 `(("python-mock" ,python2-mock)
3939 ("python-nose" ,python2-nose)
3941 (home-page "https://github.com/PMBio/warpedLMM")
3942 (synopsis "Implementation of warped linear mixed models")
3944 "WarpedLMM is a Python implementation of the warped linear mixed model,
3945 which automatically learns an optimal warping function (or transformation) for
3946 the phenotype as it models the data.")
3947 (license license:asl2.0)))
3949 (define-public pbtranscript-tofu
3950 (let ((commit "8f5467fe6a4472bcfb4226c8720993c8507adfe4"))
3952 (name "pbtranscript-tofu")
3953 (version (string-append "2.2.3." (string-take commit 7)))
3957 (url "https://github.com/PacificBiosciences/cDNA_primer.git")
3959 (file-name (string-append name "-" version "-checkout"))
3962 "1lgnpi35ihay42qx0b6yl3kkgra723i413j33kvs0kvs61h82w0f"))
3963 (modules '((guix build utils)))
3966 ;; remove bundled Cython sources
3967 (delete-file "pbtranscript-tofu/pbtranscript/Cython-0.20.1.tar.gz")
3969 (build-system python-build-system)
3971 `(#:python ,python-2
3972 ;; FIXME: Tests fail with "No such file or directory:
3973 ;; pbtools/pbtranscript/modified_bx_intervals/intersection_unique.so"
3976 (modify-phases %standard-phases
3977 (add-after 'unpack 'enter-directory
3979 (chdir "pbtranscript-tofu/pbtranscript/")
3981 ;; With setuptools version 18.0 and later this setup.py hack causes
3982 ;; a build error, so we disable it.
3983 (add-after 'enter-directory 'patch-setuppy
3985 (substitute* "setup.py"
3986 (("if 'setuptools.extension' in sys.modules:")
3990 `(("python-numpy" ,python2-numpy)
3991 ("python-bx-python" ,python2-bx-python)
3992 ("python-networkx" ,python2-networkx)
3993 ("python-scipy" ,python2-scipy)
3994 ("python-pbcore" ,python2-pbcore)
3995 ("python-h5py" ,python2-h5py)))
3997 `(("python-cython" ,python2-cython)
3998 ("python-nose" ,python2-nose)))
3999 (home-page "https://github.com/PacificBiosciences/cDNA_primer")
4000 (synopsis "Analyze transcriptome data generated with the Iso-Seq protocol")
4002 "pbtranscript-tofu contains scripts to analyze transcriptome data
4003 generated using the PacBio Iso-Seq protocol.")
4004 (license license:bsd-3))))
4006 (define-public prank
4013 "http://wasabiapp.org/download/prank/prank.source."
4017 "0am4z94fs3w2n5xpfls9zda61vq7qqz4q2i7b9hlsxz5q4j3kfm4"))))
4018 (build-system gnu-build-system)
4021 (modify-phases %standard-phases
4022 (add-after 'unpack 'enter-src-dir
4026 (add-after 'unpack 'remove-m64-flag
4027 ;; Prank will build with the correct 'bit-ness' without this flag
4028 ;; and this allows building on 32-bit machines.
4029 (lambda _ (substitute* "src/Makefile"
4034 (lambda* (#:key outputs #:allow-other-keys)
4035 (let* ((out (assoc-ref outputs "out"))
4036 (bin (string-append out "/bin"))
4037 (man (string-append out "/share/man/man1"))
4038 (path (string-append
4039 (assoc-ref %build-inputs "mafft") "/bin:"
4040 (assoc-ref %build-inputs "exonerate") "/bin:"
4041 (assoc-ref %build-inputs "bppsuite") "/bin")))
4042 (install-file "prank" bin)
4043 (wrap-program (string-append bin "/prank")
4044 `("PATH" ":" prefix (,path)))
4045 (install-file "prank.1" man))
4049 ("exonerate" ,exonerate)
4050 ("bppsuite" ,bppsuite)))
4051 (home-page "http://wasabiapp.org/software/prank/")
4052 (synopsis "Probabilistic multiple sequence alignment program")
4054 "PRANK is a probabilistic multiple sequence alignment program for DNA,
4055 codon and amino-acid sequences. It is based on a novel algorithm that treats
4056 insertions correctly and avoids over-estimation of the number of deletion
4057 events. In addition, PRANK borrows ideas from maximum likelihood methods used
4058 in phylogenetics and correctly takes into account the evolutionary distances
4059 between sequences. Lastly, PRANK allows for defining a potential structure
4060 for sequences to be aligned and then, simultaneously with the alignment,
4061 predicts the locations of structural units in the sequences.")
4062 (license license:gpl2+)))
4064 (define-public proteinortho
4066 (name "proteinortho")
4073 "http://www.bioinf.uni-leipzig.de/Software/proteinortho/proteinortho_v"
4074 version "_src.tar.gz"))
4077 "0z4f5cg0cs8ai62hfvp4q6w66q2phcc55nhs4xj5cyhxxivjv2ai"))))
4078 (build-system gnu-build-system)
4080 `(#:test-target "test"
4082 (modify-phases %standard-phases
4084 ;; There is no configure script, so we modify the Makefile directly.
4085 (lambda* (#:key outputs #:allow-other-keys)
4086 (substitute* "Makefile"
4089 "INSTALLDIR=" (assoc-ref outputs "out") "/bin\n")))
4091 (add-before 'install 'make-install-directory
4092 ;; The install directory is not created during 'make install'.
4093 (lambda* (#:key outputs #:allow-other-keys)
4094 (mkdir-p (string-append (assoc-ref outputs "out") "/bin"))
4096 (add-after 'install 'wrap-programs
4097 (lambda* (#:key inputs outputs #:allow-other-keys)
4098 (let* ((path (getenv "PATH"))
4099 (out (assoc-ref outputs "out"))
4100 (binary (string-append out "/bin/proteinortho5.pl")))
4101 (wrap-program binary `("PATH" ":" prefix (,path))))
4105 ("python" ,python-2)
4106 ("blast+" ,blast+)))
4107 (home-page "http://www.bioinf.uni-leipzig.de/Software/proteinortho")
4108 (synopsis "Detect orthologous genes across species")
4110 "Proteinortho is a tool to detect orthologous genes across different
4111 species. For doing so, it compares similarities of given gene sequences and
4112 clusters them to find significant groups. The algorithm was designed to handle
4113 large-scale data and can be applied to hundreds of species at once.")
4114 (license license:gpl2+)))
4116 (define-public pyicoteo
4123 (uri (string-append "https://bitbucket.org/regulatorygenomicsupf/"
4124 "pyicoteo/get/v" version ".tar.bz2"))
4125 (file-name (string-append name "-" version ".tar.bz2"))
4128 "0d6087f29xp8wxwlj111c3sylli98n0l8ry58c51ixzq0zfm50wa"))))
4129 (build-system python-build-system)
4131 `(#:python ,python-2 ; does not work with Python 3
4132 #:tests? #f)) ; there are no tests
4134 `(("python2-matplotlib" ,python2-matplotlib)))
4135 (home-page "https://bitbucket.org/regulatorygenomicsupf/pyicoteo")
4136 (synopsis "Analyze high-throughput genetic sequencing data")
4138 "Pyicoteo is a suite of tools for the analysis of high-throughput genetic
4139 sequencing data. It works with genomic coordinates. There are currently six
4140 different command-line tools:
4143 @item pyicoregion: for generating exploratory regions automatically;
4144 @item pyicoenrich: for differential enrichment between two conditions;
4145 @item pyicoclip: for calling CLIP-Seq peaks without a control;
4146 @item pyicos: for genomic coordinates manipulation;
4147 @item pyicoller: for peak calling on punctuated ChIP-Seq;
4148 @item pyicount: to count how many reads from N experiment files overlap in a
4150 @item pyicotrocol: to combine operations from pyicoteo.
4152 (license license:gpl3+)))
4154 (define-public prodigal
4161 "https://github.com/hyattpd/Prodigal/archive/v"
4163 (file-name (string-append name "-" version ".tar.gz"))
4166 "17srxkqd3jc77xk15pfbgg1a9xahqg7337w95mrsia7mpza4l2c9"))))
4167 (build-system gnu-build-system)
4169 `(#:tests? #f ;no check target
4170 #:make-flags (list (string-append "INSTALLDIR="
4171 (assoc-ref %outputs "out")
4174 (modify-phases %standard-phases
4175 (delete 'configure))))
4176 (home-page "http://prodigal.ornl.gov")
4177 (synopsis "Protein-coding gene prediction for Archaea and Bacteria")
4179 "Prodigal runs smoothly on finished genomes, draft genomes, and
4180 metagenomes, providing gene predictions in GFF3, Genbank, or Sequin table
4181 format. It runs quickly, in an unsupervised fashion, handles gaps, handles
4182 partial genes, and identifies translation initiation sites.")
4183 (license license:gpl3+)))
4185 (define-public roary
4193 "mirror://cpan/authors/id/A/AJ/AJPAGE/Bio-Roary-"
4197 "03dfr2cd5fp80bcr65923zpdzrasvcxl7c2vgh8373v25a1yfap7"))))
4198 (build-system perl-build-system)
4201 (modify-phases %standard-phases
4206 ;; The tests are not run by default, so we run each test file
4208 (setenv "PATH" (string-append (getcwd) "/bin" ":"
4210 (setenv "PERL5LIB" (string-append (getcwd) "/lib" ":"
4211 (getenv "PERL5LIB")))
4212 (zero? (length (filter (lambda (file)
4213 (display file)(display "\n")
4214 (not (zero? (system* "perl" file))))
4215 (find-files "t" ".*\\.t$"))))))
4217 ;; There is no 'install' target in the Makefile.
4218 (lambda* (#:key outputs #:allow-other-keys)
4219 (let* ((out (assoc-ref outputs "out"))
4220 (bin (string-append out "/bin"))
4221 (perl (string-append out "/lib/perl5/site_perl"))
4222 (roary-plots "contrib/roary_plots"))
4225 (copy-recursively "bin" bin)
4226 (copy-recursively "lib" perl)
4228 (add-after 'install 'wrap-programs
4229 (lambda* (#:key inputs outputs #:allow-other-keys)
4230 (let* ((out (assoc-ref outputs "out"))
4231 (perl5lib (getenv "PERL5LIB"))
4232 (path (getenv "PATH")))
4233 (for-each (lambda (prog)
4234 (let ((binary (string-append out "/" prog)))
4235 (wrap-program binary
4236 `("PERL5LIB" ":" prefix
4237 (,(string-append perl5lib ":" out
4238 "/lib/perl5/site_perl"))))
4239 (wrap-program binary
4241 (,(string-append path ":" out "/bin"))))))
4242 (find-files "bin" ".*[^R]$"))
4244 (string-append out "/bin/roary-create_pan_genome_plots.R"))
4245 (r-site-lib (getenv "R_LIBS_SITE"))
4247 (string-append (assoc-ref inputs "coreutils") "/bin")))
4249 `("R_LIBS_SITE" ":" prefix
4250 (,(string-append r-site-lib ":" out "/site-library/"))))
4253 (,(string-append coreutils-path ":" out "/bin"))))))
4256 `(("perl-env-path" ,perl-env-path)
4257 ("perl-test-files" ,perl-test-files)
4258 ("perl-test-most" ,perl-test-most)
4259 ("perl-test-output" ,perl-test-output)))
4261 `(("perl-array-utils" ,perl-array-utils)
4262 ("bioperl" ,bioperl-minimal)
4263 ("perl-exception-class" ,perl-exception-class)
4264 ("perl-file-find-rule" ,perl-file-find-rule)
4265 ("perl-file-grep" ,perl-file-grep)
4266 ("perl-file-slurper" ,perl-file-slurper)
4267 ("perl-file-which" ,perl-file-which)
4268 ("perl-graph" ,perl-graph)
4269 ("perl-graph-readwrite" ,perl-graph-readwrite)
4270 ("perl-log-log4perl" ,perl-log-log4perl)
4271 ("perl-moose" ,perl-moose)
4272 ("perl-perlio-utf8_strict" ,perl-perlio-utf8_strict)
4273 ("perl-text-csv" ,perl-text-csv)
4274 ("bedtools" ,bedtools)
4278 ("parallel" ,parallel)
4281 ("fasttree" ,fasttree)
4285 ("r-minimal" ,r-minimal)
4286 ("r-ggplot2" ,r-ggplot2)
4287 ("coreutils" ,coreutils)))
4288 (home-page "http://sanger-pathogens.github.io/Roary")
4289 (synopsis "High speed stand-alone pan genome pipeline")
4291 "Roary is a high speed stand alone pan genome pipeline, which takes
4292 annotated assemblies in GFF3 format (produced by the Prokka program) and
4293 calculates the pan genome. Using a standard desktop PC, it can analyse
4294 datasets with thousands of samples, without compromising the quality of the
4295 results. 128 samples can be analysed in under 1 hour using 1 GB of RAM and a
4296 single processor. Roary is not intended for metagenomics or for comparing
4297 extremely diverse sets of genomes.")
4298 (license license:gpl3)))
4300 (define-public raxml
4309 "https://github.com/stamatak/standard-RAxML/archive/v"
4311 (file-name (string-append name "-" version ".tar.gz"))
4314 "13s7aspfdcfr6asynwdg1x6vznys6pzap5f8wsffbnnwpkkg9ya8"))))
4315 (build-system gnu-build-system)
4317 `(#:tests? #f ; There are no tests.
4318 ;; Use 'standard' Makefile rather than SSE or AVX ones.
4319 #:make-flags (list "-f" "Makefile.HYBRID.gcc")
4321 (modify-phases %standard-phases
4324 (lambda* (#:key outputs #:allow-other-keys)
4325 (let* ((out (assoc-ref outputs "out"))
4326 (bin (string-append out "/bin"))
4327 (executable "raxmlHPC-HYBRID"))
4328 (install-file executable bin)
4329 (symlink (string-append bin "/" executable) "raxml"))
4332 `(("openmpi" ,openmpi)))
4333 (home-page "http://sco.h-its.org/exelixis/web/software/raxml/index.html")
4334 (synopsis "Randomized Axelerated Maximum Likelihood phylogenetic trees")
4336 "RAxML is a tool for phylogenetic analysis and post-analysis of large
4338 ;; The source includes x86 specific code
4339 (supported-systems '("x86_64-linux" "i686-linux"))
4340 (license license:gpl2+)))
4350 (string-append "http://deweylab.biostat.wisc.edu/rsem/src/rsem-"
4353 (base32 "0nzdc0j0hjllhsd5f2xli95dafm3nawskigs140xzvjk67xh0r9q"))
4354 (patches (search-patches "rsem-makefile.patch"))
4355 (modules '((guix build utils)))
4358 ;; remove bundled copy of boost
4359 (delete-file-recursively "boost")
4361 (build-system gnu-build-system)
4363 `(#:tests? #f ;no "check" target
4365 (modify-phases %standard-phases
4366 ;; No "configure" script.
4367 ;; Do not build bundled samtools library.
4370 (substitute* "Makefile"
4371 (("^all : sam/libbam.a") "all : "))
4374 (lambda* (#:key outputs #:allow-other-keys)
4375 (let* ((out (string-append (assoc-ref outputs "out")))
4376 (bin (string-append out "/bin/"))
4377 (perl (string-append out "/lib/perl5/site_perl")))
4380 (for-each (lambda (file)
4381 (install-file file bin))
4382 (find-files "." "rsem-.*"))
4383 (install-file "rsem_perl_utils.pm" perl))
4386 'install 'wrap-program
4387 (lambda* (#:key outputs #:allow-other-keys)
4388 (let ((out (assoc-ref outputs "out")))
4389 (for-each (lambda (prog)
4390 (wrap-program (string-append out "/bin/" prog)
4391 `("PERL5LIB" ":" prefix
4392 (,(string-append out "/lib/perl5/site_perl")))))
4393 '("rsem-plot-transcript-wiggles"
4394 "rsem-calculate-expression"
4395 "rsem-generate-ngvector"
4397 "rsem-prepare-reference")))
4401 ("ncurses" ,ncurses)
4402 ("r-minimal" ,r-minimal)
4404 ("samtools" ,samtools-0.1)
4406 (home-page "http://deweylab.biostat.wisc.edu/rsem/")
4407 (synopsis "Estimate gene expression levels from RNA-Seq data")
4409 "RSEM is a software package for estimating gene and isoform expression
4410 levels from RNA-Seq data. The RSEM package provides a user-friendly
4411 interface, supports threads for parallel computation of the EM algorithm,
4412 single-end and paired-end read data, quality scores, variable-length reads and
4413 RSPD estimation. In addition, it provides posterior mean and 95% credibility
4414 interval estimates for expression levels. For visualization, it can generate
4415 BAM and Wiggle files in both transcript-coordinate and genomic-coordinate.")
4416 (license license:gpl3+)))
4418 (define-public rseqc
4426 (string-append "mirror://sourceforge/rseqc/"
4427 "RSeQC-" version ".tar.gz"))
4429 (base32 "15ly0254yi032qzkdplg00q144qfdsd986gh62829rl5bkxhj330"))
4430 (modules '((guix build utils)))
4433 ;; remove bundled copy of pysam
4434 (delete-file-recursively "lib/pysam")
4435 (substitute* "setup.py"
4436 ;; remove dependency on outdated "distribute" module
4437 (("^from distribute_setup import use_setuptools") "")
4438 (("^use_setuptools\\(\\)") "")
4439 ;; do not use bundled copy of pysam
4440 (("^have_pysam = False") "have_pysam = True"))))))
4441 (build-system python-build-system)
4442 (arguments `(#:python ,python-2))
4444 `(("python-cython" ,python2-cython)
4445 ("python-pysam" ,python2-pysam)
4446 ("python-numpy" ,python2-numpy)
4449 `(("python-nose" ,python2-nose)))
4450 (home-page "http://rseqc.sourceforge.net/")
4451 (synopsis "RNA-seq quality control package")
4453 "RSeQC provides a number of modules that can comprehensively evaluate
4454 high throughput sequence data, especially RNA-seq data. Some basic modules
4455 inspect sequence quality, nucleotide composition bias, PCR bias and GC bias,
4456 while RNA-seq specific modules evaluate sequencing saturation, mapped reads
4457 distribution, coverage uniformity, strand specificity, etc.")
4458 (license license:gpl3+)))
4461 ;; There are no release tarballs. According to the installation
4462 ;; instructions at http://seek.princeton.edu/installation.jsp, the latest
4463 ;; stable release is identified by this changeset ID.
4464 (let ((changeset "2329130")
4468 (version (string-append "0-" revision "." changeset))
4472 (url "https://bitbucket.org/libsleipnir/sleipnir")
4473 (changeset changeset)))
4476 "0qrvilwh18dpbhkf92qvxbmay0j75ra3jg2wrhz67gf538zzphsx"))))
4477 (build-system gnu-build-system)
4479 `(#:modules ((srfi srfi-1)
4480 (guix build gnu-build-system)
4483 (let ((dirs '("SeekMiner"
4489 (modify-phases %standard-phases
4490 (add-before 'configure 'bootstrap
4492 (zero? (system* "bash" "gen_auto"))))
4493 (add-after 'build 'build-additional-tools
4494 (lambda* (#:key make-flags #:allow-other-keys)
4495 (every (lambda (dir)
4496 (with-directory-excursion (string-append "tools/" dir)
4497 (zero? (apply system* "make" make-flags))))
4499 (add-after 'install 'install-additional-tools
4500 (lambda* (#:key make-flags #:allow-other-keys)
4501 (fold (lambda (dir result)
4502 (with-directory-excursion (string-append "tools/" dir)
4504 (zero? (apply system*
4505 `("make" ,@make-flags "install"))))))
4511 ("readline" ,readline)
4512 ("gengetopt" ,gengetopt)
4513 ("log4cpp" ,log4cpp)))
4515 `(("autoconf" ,autoconf)
4516 ("automake" ,automake)
4518 (home-page "http://seek.princeton.edu")
4519 (synopsis "Gene co-expression search engine")
4521 "SEEK is a computational gene co-expression search engine. SEEK provides
4522 biologists with a way to navigate the massive human expression compendium that
4523 now contains thousands of expression datasets. SEEK returns a robust ranking
4524 of co-expressed genes in the biological area of interest defined by the user's
4525 query genes. It also prioritizes thousands of expression datasets according
4526 to the user's query of interest.")
4527 (license license:cc-by3.0))))
4529 (define-public samtools
4537 (string-append "mirror://sourceforge/samtools/samtools/"
4538 version "/samtools-" version ".tar.bz2"))
4541 "1xidmv0jmfy7l0kb32hdnlshcxgzi1hmygvig0cqrq1fhckdlhl5"))))
4542 (build-system gnu-build-system)
4544 `(#:modules ((ice-9 ftw)
4546 (guix build gnu-build-system)
4548 #:make-flags (list (string-append "prefix=" (assoc-ref %outputs "out")))
4549 #:configure-flags (list "--with-ncurses" "--with-htslib=system")
4551 (modify-phases %standard-phases
4552 (add-after 'unpack 'patch-tests
4554 (substitute* "test/test.pl"
4555 ;; The test script calls out to /bin/bash
4556 (("/bin/bash") (which "bash")))
4558 (add-after 'install 'install-library
4559 (lambda* (#:key outputs #:allow-other-keys)
4560 (let ((lib (string-append (assoc-ref outputs "out") "/lib")))
4561 (install-file "libbam.a" lib)
4563 (add-after 'install 'install-headers
4564 (lambda* (#:key outputs #:allow-other-keys)
4565 (let ((include (string-append (assoc-ref outputs "out")
4566 "/include/samtools/")))
4567 (for-each (lambda (file)
4568 (install-file file include))
4569 (scandir "." (lambda (name) (string-match "\\.h$" name))))
4571 (native-inputs `(("pkg-config" ,pkg-config)))
4573 `(("htslib" ,htslib)
4574 ("ncurses" ,ncurses)
4578 (home-page "http://samtools.sourceforge.net")
4579 (synopsis "Utilities to efficiently manipulate nucleotide sequence alignments")
4581 "Samtools implements various utilities for post-processing nucleotide
4582 sequence alignments in the SAM, BAM, and CRAM formats, including indexing,
4583 variant calling (in conjunction with bcftools), and a simple alignment
4585 (license license:expat)))
4587 (define-public samtools-0.1
4588 ;; This is the most recent version of the 0.1 line of samtools. The input
4589 ;; and output formats differ greatly from that used and produced by samtools
4590 ;; 1.x and is still used in many bioinformatics pipelines.
4591 (package (inherit samtools)
4597 (string-append "mirror://sourceforge/samtools/samtools/"
4598 version "/samtools-" version ".tar.bz2"))
4600 (base32 "1m33xsfwz0s8qi45lylagfllqg7fphf4dr0780rsvw75av9wk06h"))))
4602 `(#:tests? #f ;no "check" target
4603 ,@(substitute-keyword-arguments (package-arguments samtools)
4604 ((#:make-flags flags)
4605 `(cons "LIBCURSES=-lncurses" ,flags))
4607 `(modify-phases ,phases
4609 (lambda* (#:key outputs #:allow-other-keys)
4610 (let ((bin (string-append
4611 (assoc-ref outputs "out") "/bin")))
4613 (install-file "samtools" bin)
4615 (delete 'patch-tests)
4616 (delete 'configure))))))))
4618 (define-public mosaik
4619 (let ((commit "5c25216d3522d6a33e53875cd76a6d65001e4e67"))
4624 ;; There are no release tarballs nor tags.
4627 (url "https://github.com/wanpinglee/MOSAIK.git")
4629 (file-name (string-append name "-" version))
4632 "17gj3s07cm77r41z92awh0bim7w7q7fbn0sf5nkqmcm1vw052qgw"))))
4633 (build-system gnu-build-system)
4635 `(#:tests? #f ; no tests
4636 #:make-flags (list "CC=gcc")
4638 (modify-phases %standard-phases
4640 (lambda _ (chdir "src") #t))
4642 (lambda* (#:key outputs #:allow-other-keys)
4643 (let ((bin (string-append (assoc-ref outputs "out")
4646 (copy-recursively "../bin" bin)
4651 (supported-systems '("x86_64-linux"))
4652 (home-page "https://github.com/wanpinglee/MOSAIK")
4653 (synopsis "Map nucleotide sequence reads to reference genomes")
4655 "MOSAIK is a program for mapping second and third-generation sequencing
4656 reads to a reference genome. MOSAIK can align reads generated by all the
4657 major sequencing technologies, including Illumina, Applied Biosystems SOLiD,
4658 Roche 454, Ion Torrent and Pacific BioSciences SMRT.")
4659 ;; MOSAIK is released under the GPLv2+ with the exception of third-party
4660 ;; code released into the public domain:
4661 ;; 1. fastlz by Ariya Hidayat - http://www.fastlz.org/
4662 ;; 2. MD5 implementation - RSA Data Security, RFC 1321
4663 (license (list license:gpl2+ license:public-domain)))))
4665 (define-public ngs-sdk
4673 (string-append "https://github.com/ncbi/ngs/archive/"
4675 (file-name (string-append name "-" version ".tar.gz"))
4678 "1wiyf4c6nm2j87pv015cbi0qny5byf3pbvcw3likifz5dl56ag40"))))
4679 (build-system gnu-build-system)
4681 `(#:parallel-build? #f ; not supported
4682 #:tests? #f ; no "check" target
4684 (modify-phases %standard-phases
4686 (lambda* (#:key outputs #:allow-other-keys)
4687 (let ((out (assoc-ref outputs "out")))
4688 ;; Allow 'konfigure.perl' to find 'package.prl'.
4690 (string-append ".:" (getenv "PERL5LIB")))
4692 ;; The 'configure' script doesn't recognize things like
4693 ;; '--enable-fast-install'.
4694 (zero? (system* "./configure"
4695 (string-append "--build-prefix=" (getcwd) "/build")
4696 (string-append "--prefix=" out))))))
4697 (add-after 'unpack 'enter-dir
4698 (lambda _ (chdir "ngs-sdk") #t)))))
4699 (native-inputs `(("perl" ,perl)))
4700 ;; According to the test
4701 ;; unless ($MARCH =~ /x86_64/i || $MARCH =~ /i?86/i)
4702 ;; in ngs-sdk/setup/konfigure.perl
4703 (supported-systems '("i686-linux" "x86_64-linux"))
4704 (home-page "https://github.com/ncbi/ngs")
4705 (synopsis "API for accessing Next Generation Sequencing data")
4707 "NGS is a domain-specific API for accessing reads, alignments and pileups
4708 produced from Next Generation Sequencing. The API itself is independent from
4709 any particular back-end implementation, and supports use of multiple back-ends
4711 (license license:public-domain)))
4713 (define-public java-ngs
4714 (package (inherit ngs-sdk)
4717 `(,@(substitute-keyword-arguments
4718 `(#:modules ((guix build gnu-build-system)
4722 ,@(package-arguments ngs-sdk))
4724 `(modify-phases ,phases
4725 (replace 'enter-dir (lambda _ (chdir "ngs-java") #t)))))))
4727 `(("jdk" ,icedtea "jdk")
4728 ("ngs-sdk" ,ngs-sdk)))
4729 (synopsis "Java bindings for NGS SDK")))
4731 (define-public ncbi-vdb
4739 (string-append "https://github.com/ncbi/ncbi-vdb/archive/"
4741 (file-name (string-append name "-" version ".tar.gz"))
4744 "1acn4bv81mfl137qnbn9995mjjhwd36pm0b7qli1iw5skrxa9j8m"))))
4745 (build-system gnu-build-system)
4747 `(#:parallel-build? #f ; not supported
4748 #:tests? #f ; no "check" target
4750 (modify-phases %standard-phases
4751 (add-before 'configure 'set-perl-search-path
4753 ;; Work around "dotless @INC" build failure.
4755 (string-append (getcwd) "/setup:"
4756 (getenv "PERL5LIB")))
4759 (lambda* (#:key inputs outputs #:allow-other-keys)
4760 (let ((out (assoc-ref outputs "out")))
4761 ;; Override include path for libmagic
4762 (substitute* "setup/package.prl"
4763 (("name => 'magic', Include => '/usr/include'")
4764 (string-append "name=> 'magic', Include => '"
4765 (assoc-ref inputs "libmagic")
4768 ;; Install kdf5 library (needed by sra-tools)
4769 (substitute* "build/Makefile.install"
4770 (("LIBRARIES_TO_INSTALL =")
4771 "LIBRARIES_TO_INSTALL = kdf5.$(VERSION_LIBX) kdf5.$(VERSION_SHLX)"))
4773 (substitute* "build/Makefile.env"
4774 (("CFLAGS =" prefix)
4775 (string-append prefix "-msse2 ")))
4777 ;; Override search path for ngs-java
4778 (substitute* "setup/package.prl"
4779 (("/usr/local/ngs/ngs-java")
4780 (assoc-ref inputs "java-ngs")))
4782 ;; The 'configure' script doesn't recognize things like
4783 ;; '--enable-fast-install'.
4786 (string-append "--build-prefix=" (getcwd) "/build")
4787 (string-append "--prefix=" (assoc-ref outputs "out"))
4788 (string-append "--debug")
4789 (string-append "--with-xml2-prefix="
4790 (assoc-ref inputs "libxml2"))
4791 (string-append "--with-ngs-sdk-prefix="
4792 (assoc-ref inputs "ngs-sdk"))
4793 (string-append "--with-hdf5-prefix="
4794 (assoc-ref inputs "hdf5")))))))
4795 (add-after 'install 'install-interfaces
4796 (lambda* (#:key outputs #:allow-other-keys)
4797 ;; Install interface libraries. On i686 the interface libraries
4798 ;; are installed to "linux/gcc/i386", so we need to use the Linux
4799 ;; architecture name ("i386") instead of the target system prefix
4801 (mkdir (string-append (assoc-ref outputs "out") "/ilib"))
4802 (copy-recursively (string-append "build/ncbi-vdb/linux/gcc/"
4803 ,(system->linux-architecture
4804 (or (%current-target-system)
4807 (string-append (assoc-ref outputs "out")
4809 ;; Install interface headers
4810 (copy-recursively "interfaces"
4811 (string-append (assoc-ref outputs "out")
4814 ;; These files are needed by sra-tools.
4815 (add-after 'install 'install-configuration-files
4816 (lambda* (#:key outputs #:allow-other-keys)
4817 (let ((target (string-append (assoc-ref outputs "out") "/kfg")))
4819 (install-file "libs/kfg/default.kfg" target)
4820 (install-file "libs/kfg/certs.kfg" target))
4823 `(("libxml2" ,libxml2)
4824 ("ngs-sdk" ,ngs-sdk)
4825 ("java-ngs" ,java-ngs)
4828 (native-inputs `(("perl" ,perl)))
4829 ;; NCBI-VDB requires SSE capability.
4830 (supported-systems '("i686-linux" "x86_64-linux"))
4831 (home-page "https://github.com/ncbi/ncbi-vdb")
4832 (synopsis "Database engine for genetic information")
4834 "The NCBI-VDB library implements a highly compressed columnar data
4835 warehousing engine that is most often used to store genetic information.
4836 Databases are stored in a portable image within the file system, and can be
4837 accessed/downloaded on demand across HTTP.")
4838 (license license:public-domain)))
4840 (define-public plink
4848 "http://pngu.mgh.harvard.edu/~purcell/plink/dist/plink-"
4849 version "-src.zip"))
4851 (base32 "0as8gxm4pjyc8dxmm1sl873rrd7wn5qs0l29nqfnl31x8i467xaa"))
4852 (patches (search-patches "plink-1.07-unclobber-i.patch"
4853 "plink-endian-detection.patch"))))
4854 (build-system gnu-build-system)
4856 '(#:tests? #f ;no "check" target
4857 #:make-flags (list (string-append "LIB_LAPACK="
4858 (assoc-ref %build-inputs "lapack")
4859 "/lib/liblapack.so")
4862 ;; disable phoning home
4865 (modify-phases %standard-phases
4866 ;; no "configure" script
4869 (lambda* (#:key outputs #:allow-other-keys)
4870 (let ((bin (string-append (assoc-ref outputs "out")
4872 (install-file "plink" bin)
4876 ("lapack" ,lapack)))
4878 `(("unzip" ,unzip)))
4879 (home-page "http://pngu.mgh.harvard.edu/~purcell/plink/")
4880 (synopsis "Whole genome association analysis toolset")
4882 "PLINK is a whole genome association analysis toolset, designed to
4883 perform a range of basic, large-scale analyses in a computationally efficient
4884 manner. The focus of PLINK is purely on analysis of genotype/phenotype data,
4885 so there is no support for steps prior to this (e.g. study design and
4886 planning, generating genotype or CNV calls from raw data). Through
4887 integration with gPLINK and Haploview, there is some support for the
4888 subsequent visualization, annotation and storage of results.")
4889 ;; Code is released under GPLv2, except for fisher.h, which is under
4891 (license (list license:gpl2 license:lgpl2.1+))))
4893 (define-public smithlab-cpp
4894 (let ((revision "1")
4895 (commit "728a097bec88c6f4b8528b685932049e660eff2e"))
4897 (name "smithlab-cpp")
4898 (version (string-append "0." revision "." (string-take commit 7)))
4902 (url "https://github.com/smithlabcode/smithlab_cpp.git")
4904 (file-name (string-append name "-" version "-checkout"))
4907 "0d476lmj312xk77kr9fzrv7z1bv96yfyx0w7y62ycmnfbx32ll74"))))
4908 (build-system gnu-build-system)
4910 `(#:modules ((guix build gnu-build-system)
4913 #:tests? #f ;no "check" target
4915 (modify-phases %standard-phases
4916 (add-after 'unpack 'use-samtools-headers
4918 (substitute* '("SAM.cpp"
4920 (("sam.h") "samtools/sam.h"))
4923 (lambda* (#:key outputs #:allow-other-keys)
4924 (let* ((out (assoc-ref outputs "out"))
4925 (lib (string-append out "/lib"))
4926 (include (string-append out "/include/smithlab-cpp")))
4929 (for-each (cut install-file <> lib)
4930 (find-files "." "\\.o$"))
4931 (for-each (cut install-file <> include)
4932 (find-files "." "\\.hpp$")))
4934 (delete 'configure))))
4936 `(("samtools" ,samtools-0.1)
4938 (home-page "https://github.com/smithlabcode/smithlab_cpp")
4939 (synopsis "C++ helper library for functions used in Smith lab projects")
4941 "Smithlab CPP is a C++ library that includes functions used in many of
4942 the Smith lab bioinformatics projects, such as a wrapper around Samtools data
4943 structures, classes for genomic regions, mapped sequencing reads, etc.")
4944 (license license:gpl3+))))
4946 (define-public preseq
4952 (uri (string-append "https://github.com/smithlabcode/"
4953 "preseq/archive/v" version ".tar.gz"))
4954 (file-name (string-append name "-" version ".tar.gz"))
4956 (base32 "08r684l50pnxjpvmhzjgqq56yv9rfw90k8vx0nsrnrzk8mf9hsdq"))
4957 (modules '((guix build utils)))
4959 ;; Remove bundled samtools.
4960 '(delete-file-recursively "samtools"))))
4961 (build-system gnu-build-system)
4963 `(#:tests? #f ;no "check" target
4965 (modify-phases %standard-phases
4966 (delete 'configure))
4968 (list (string-append "PREFIX="
4969 (assoc-ref %outputs "out"))
4970 (string-append "LIBBAM="
4971 (assoc-ref %build-inputs "samtools")
4973 (string-append "SMITHLAB_CPP="
4974 (assoc-ref %build-inputs "smithlab-cpp")
4977 "INCLUDEDIRS=$(SMITHLAB_CPP)/../include/smithlab-cpp $(SAMTOOLS_DIR)")))
4980 ("samtools" ,samtools-0.1)
4981 ("smithlab-cpp" ,smithlab-cpp)
4983 (home-page "http://smithlabresearch.org/software/preseq/")
4984 (synopsis "Program for analyzing library complexity")
4986 "The preseq package is aimed at predicting and estimating the complexity
4987 of a genomic sequencing library, equivalent to predicting and estimating the
4988 number of redundant reads from a given sequencing depth and how many will be
4989 expected from additional sequencing using an initial sequencing experiment.
4990 The estimates can then be used to examine the utility of further sequencing,
4991 optimize the sequencing depth, or to screen multiple libraries to avoid low
4992 complexity samples.")
4993 (license license:gpl3+)))
4995 (define-public python-screed
4997 (name "python-screed")
5002 (uri (pypi-uri "screed" version))
5005 "18czszp9fkx3j6jr7y5kp6dfialscgddk05mw1zkhh2zhn0jd8i0"))))
5006 (build-system python-build-system)
5009 (modify-phases %standard-phases
5012 (setenv "PYTHONPATH"
5013 (string-append (getenv "PYTHONPATH") ":."))
5014 (zero? (system* "nosetests" "--attr" "!known_failing")))))))
5016 `(("python-nose" ,python-nose)))
5018 `(("python-bz2file" ,python-bz2file)))
5019 (home-page "https://github.com/dib-lab/screed/")
5020 (synopsis "Short read sequence database utilities")
5021 (description "Screed parses FASTA and FASTQ files and generates databases.
5022 Values such as sequence name, sequence description, sequence quality and the
5023 sequence itself can be retrieved from these databases.")
5024 (license license:bsd-3)))
5026 (define-public python2-screed
5027 (package-with-python2 python-screed))
5029 (define-public sra-tools
5037 (string-append "https://github.com/ncbi/sra-tools/archive/"
5039 (file-name (string-append name "-" version ".tar.gz"))
5042 "1camsijmvv2s45mb4iyf44ghl4gkd4rl0viphpcgl3ccchy32a0g"))))
5043 (build-system gnu-build-system)
5045 `(#:parallel-build? #f ; not supported
5046 #:tests? #f ; no "check" target
5048 (list (string-append "DEFAULT_CRT="
5049 (assoc-ref %build-inputs "ncbi-vdb")
5051 (string-append "DEFAULT_KFG="
5052 (assoc-ref %build-inputs "ncbi-vdb")
5054 (string-append "VDB_LIBDIR="
5055 (assoc-ref %build-inputs "ncbi-vdb")
5056 ,(if (string-prefix? "x86_64"
5057 (or (%current-target-system)
5062 (modify-phases %standard-phases
5063 (add-before 'configure 'set-perl-search-path
5065 ;; Work around "dotless @INC" build failure.
5067 (string-append (getcwd) "/setup:"
5068 (getenv "PERL5LIB")))
5071 (lambda* (#:key inputs outputs #:allow-other-keys)
5072 ;; The build system expects a directory containing the sources and
5073 ;; raw build output of ncbi-vdb, including files that are not
5074 ;; installed. Since we are building against an installed version of
5075 ;; ncbi-vdb, the following modifications are needed.
5076 (substitute* "setup/konfigure.perl"
5077 ;; Make the configure script look for the "ilib" directory of
5078 ;; "ncbi-vdb" without first checking for the existence of a
5079 ;; matching library in its "lib" directory.
5080 (("^ my \\$f = File::Spec->catdir\\(\\$libdir, \\$lib\\);")
5081 "my $f = File::Spec->catdir($ilibdir, $ilib);")
5082 ;; Look for interface libraries in ncbi-vdb's "ilib" directory.
5083 (("my \\$ilibdir = File::Spec->catdir\\(\\$builddir, 'ilib'\\);")
5084 "my $ilibdir = File::Spec->catdir($dir, 'ilib');"))
5087 (substitute* "tools/copycat/Makefile"
5088 (("smagic-static") "lmagic"))
5090 ;; The 'configure' script doesn't recognize things like
5091 ;; '--enable-fast-install'.
5094 (string-append "--build-prefix=" (getcwd) "/build")
5095 (string-append "--prefix=" (assoc-ref outputs "out"))
5096 (string-append "--debug")
5097 (string-append "--with-fuse-prefix="
5098 (assoc-ref inputs "fuse"))
5099 (string-append "--with-magic-prefix="
5100 (assoc-ref inputs "libmagic"))
5101 ;; TODO: building with libxml2 fails with linker errors
5102 ;; (string-append "--with-xml2-prefix="
5103 ;; (assoc-ref inputs "libxml2"))
5104 (string-append "--with-ncbi-vdb-sources="
5105 (assoc-ref inputs "ncbi-vdb"))
5106 (string-append "--with-ncbi-vdb-build="
5107 (assoc-ref inputs "ncbi-vdb"))
5108 (string-append "--with-ngs-sdk-prefix="
5109 (assoc-ref inputs "ngs-sdk"))
5110 (string-append "--with-hdf5-prefix="
5111 (assoc-ref inputs "hdf5"))))))
5112 ;; This version of sra-tools fails to build with glibc because of a
5113 ;; naming conflict. glibc-2.25/include/bits/mathcalls.h already
5114 ;; contains a definition of "canonicalize", so we rename it.
5116 ;; See upstream bug report:
5117 ;; https://github.com/ncbi/sra-tools/issues/67
5118 (add-after 'unpack 'patch-away-glibc-conflict
5120 (substitute* "tools/bam-loader/bam.c"
5121 (("canonicalize\\(" line)
5122 (string-append "sra_tools_" line)))
5124 (native-inputs `(("perl" ,perl)))
5126 `(("ngs-sdk" ,ngs-sdk)
5127 ("ncbi-vdb" ,ncbi-vdb)
5132 (home-page "http://www.ncbi.nlm.nih.gov/Traces/sra/sra.cgi?view=software")
5133 (synopsis "Tools and libraries for reading and writing sequencing data")
5135 "The SRA Toolkit from NCBI is a collection of tools and libraries for
5136 reading of sequencing files from the Sequence Read Archive (SRA) database and
5137 writing files into the .sra format.")
5138 (license license:public-domain)))
5140 (define-public seqan
5146 (uri (string-append "http://packages.seqan.de/seqan-library/"
5147 "seqan-library-" version ".tar.bz2"))
5150 "05s3wrrwn50f81aklfm65i4a749zag1vr8z03k21xm0pdxy47yvp"))))
5151 ;; The documentation is 7.8MB and the includes are 3.6MB heavy, so it
5152 ;; makes sense to split the outputs.
5153 (outputs '("out" "doc"))
5154 (build-system trivial-build-system)
5156 `(#:modules ((guix build utils))
5159 (use-modules (guix build utils))
5160 (let ((tar (assoc-ref %build-inputs "tar"))
5161 (bzip (assoc-ref %build-inputs "bzip2"))
5162 (out (assoc-ref %outputs "out"))
5163 (doc (assoc-ref %outputs "doc")))
5164 (setenv "PATH" (string-append tar "/bin:" bzip "/bin"))
5165 (system* "tar" "xvf" (assoc-ref %build-inputs "source"))
5166 (chdir (string-append "seqan-library-" ,version))
5167 (copy-recursively "include" (string-append out "/include"))
5168 (copy-recursively "share" (string-append doc "/share"))))))
5170 `(("source" ,source)
5173 (home-page "http://www.seqan.de")
5174 (synopsis "Library for nucleotide sequence analysis")
5176 "SeqAn is a C++ library of efficient algorithms and data structures for
5177 the analysis of sequences with the focus on biological data. It contains
5178 algorithms and data structures for string representation and their
5179 manipulation, online and indexed string search, efficient I/O of
5180 bioinformatics file formats, sequence alignment, and more.")
5181 (license license:bsd-3)))
5183 (define-public seqmagick
5191 "https://pypi.python.org/packages/source/s/seqmagick/seqmagick-"
5195 "0cgn477n74gsl4qdaakrrhi953kcsd4q3ivk2lr18x74s3g4ma1d"))))
5196 (build-system python-build-system)
5198 ;; python2 only, see https://github.com/fhcrc/seqmagick/issues/56
5199 `(#:python ,python-2
5201 (modify-phases %standard-phases
5202 ;; Current test in setup.py does not work as of 0.6.1,
5203 ;; so use nose to run tests instead for now. See
5204 ;; https://github.com/fhcrc/seqmagick/issues/55
5205 (replace 'check (lambda _ (zero? (system* "nosetests")))))))
5207 ;; biopython-1.66 is required due to
5208 ;; https://github.com/fhcrc/seqmagick/issues/59
5209 ;; When that issue is resolved the 'python2-biopython-1.66' package
5210 ;; should be removed.
5211 `(("python-biopython" ,python2-biopython-1.66)))
5213 `(("python-nose" ,python2-nose)))
5214 (home-page "https://github.com/fhcrc/seqmagick")
5215 (synopsis "Tools for converting and modifying sequence files")
5217 "Bioinformaticians often have to convert sequence files between formats
5218 and do little manipulations on them, and it's not worth writing scripts for
5219 that. Seqmagick is a utility to expose the file format conversion in
5220 BioPython in a convenient way. Instead of having a big mess of scripts, there
5221 is one that takes arguments.")
5222 (license license:gpl3)))
5224 (define-public seqtk
5231 "https://github.com/lh3/seqtk/archive/v"
5233 (file-name (string-append name "-" version ".tar.gz"))
5236 "0ywdyzpmfiz2wp6ampbzqg4y8bj450nfgqarpamg045b8mk32lxx"))
5237 (modules '((guix build utils)))
5240 ;; Remove extraneous header files, as is done in the seqtk
5242 (for-each (lambda (file) (delete-file file))
5243 (list "ksort.h" "kstring.h" "kvec.h"))
5245 (build-system gnu-build-system)
5248 (modify-phases %standard-phases
5251 ;; There are no tests, so we just run a sanity check.
5252 (lambda _ (zero? (system* "./seqtk" "seq"))))
5254 (lambda* (#:key outputs #:allow-other-keys)
5255 (let ((bin (string-append (assoc-ref outputs "out") "/bin/")))
5256 (install-file "seqtk" bin)))))))
5259 (home-page "https://github.com/lh3/seqtk")
5260 (synopsis "Toolkit for processing biological sequences in FASTA/Q format")
5262 "Seqtk is a fast and lightweight tool for processing sequences in the
5263 FASTA or FASTQ format. It parses both FASTA and FASTQ files which can be
5264 optionally compressed by gzip.")
5265 (license license:expat)))
5267 (define-public snap-aligner
5269 (name "snap-aligner")
5270 (version "1.0beta.18")
5274 "https://github.com/amplab/snap/archive/v"
5276 (file-name (string-append name "-" version ".tar.gz"))
5279 "1vnsjwv007k1fl1q7d681kbwn6bc66cgw6h16hym6gvyy71qv2ly"))))
5280 (build-system gnu-build-system)
5283 (modify-phases %standard-phases
5285 (replace 'check (lambda _ (zero? (system* "./unit_tests"))))
5287 (lambda* (#:key outputs #:allow-other-keys)
5288 (let* ((out (assoc-ref outputs "out"))
5289 (bin (string-append out "/bin")))
5290 (install-file "snap-aligner" bin)
5291 (install-file "SNAPCommand" bin)
5295 (home-page "http://snap.cs.berkeley.edu/")
5296 (synopsis "Short read DNA sequence aligner")
5298 "SNAP is a fast and accurate aligner for short DNA reads. It is
5299 optimized for modern read lengths of 100 bases or higher, and takes advantage
5300 of these reads to align data quickly through a hash-based indexing scheme.")
5301 ;; 32-bit systems are not supported by the unpatched code.
5302 ;; Following the bug reports https://github.com/amplab/snap/issues/68 and
5303 ;; https://bugs.debian.org/cgi-bin/bugreport.cgi?bug=812378 we see that
5304 ;; systems without a lot of memory cannot make good use of this program.
5305 (supported-systems '("x86_64-linux"))
5306 (license license:asl2.0)))
5308 (define-public sortmerna
5316 "https://github.com/biocore/sortmerna/archive/"
5318 (file-name (string-append name "-" version ".tar.gz"))
5321 "1ghaghvd82af9j5adavxh77g7hm247d1r69m3fbi6f1jdivj5ldk"))))
5322 (build-system gnu-build-system)
5323 (outputs '("out" ;for binaries
5324 "db")) ;for sequence databases
5327 (modify-phases %standard-phases
5329 (lambda* (#:key outputs #:allow-other-keys)
5330 (let* ((out (assoc-ref outputs "out"))
5331 (bin (string-append out "/bin"))
5332 (db (assoc-ref outputs "db"))
5334 (string-append db "/share/sortmerna/rRNA_databases")))
5335 (install-file "sortmerna" bin)
5336 (install-file "indexdb_rna" bin)
5337 (for-each (lambda (file)
5338 (install-file file share))
5339 (find-files "rRNA_databases" ".*fasta"))
5343 (home-page "http://bioinfo.lifl.fr/RNA/sortmerna")
5344 (synopsis "Biological sequence analysis tool for NGS reads")
5346 "SortMeRNA is a biological sequence analysis tool for filtering, mapping
5347 and operational taxonomic unit (OTU) picking of next generation
5348 sequencing (NGS) reads. The core algorithm is based on approximate seeds and
5349 allows for fast and sensitive analyses of nucleotide sequences. The main
5350 application of SortMeRNA is filtering rRNA from metatranscriptomic data.")
5351 ;; The source includes x86 specific code
5352 (supported-systems '("x86_64-linux" "i686-linux"))
5353 (license license:lgpl3)))
5361 (uri (string-append "https://github.com/alexdobin/STAR/archive/"
5363 (file-name (string-append name "-" version ".tar.gz"))
5366 "013wirlz8lllgjyagl48l75n1isxyabqb3sj7qlsl0x1rmvqw99a"))
5367 (modules '((guix build utils)))
5370 (substitute* "source/Makefile"
5372 ;; Remove pre-built binaries and bundled htslib sources.
5373 (delete-file-recursively "bin/MacOSX_x86_64")
5374 (delete-file-recursively "bin/Linux_x86_64")
5375 (delete-file-recursively "bin/Linux_x86_64_static")
5376 (delete-file-recursively "source/htslib")
5378 (build-system gnu-build-system)
5380 '(#:tests? #f ;no check target
5381 #:make-flags '("STAR")
5383 (modify-phases %standard-phases
5384 (add-after 'unpack 'enter-source-dir
5385 (lambda _ (chdir "source") #t))
5386 (add-after 'enter-source-dir 'do-not-use-bundled-htslib
5388 (substitute* "Makefile"
5389 (("(Depend.list: \\$\\(SOURCES\\) parametersDefault\\.xxd) htslib"
5391 (substitute* '("BAMfunctions.cpp"
5396 "bamRemoveDuplicates.cpp")
5397 (("#include \"htslib/([^\"]+\\.h)\"" _ header)
5398 (string-append "#include <" header ">")))
5399 (substitute* "IncludeDefine.h"
5400 (("\"htslib/(htslib/[^\"]+.h)\"" _ header)
5401 (string-append "<" header ">")))
5404 (lambda* (#:key outputs #:allow-other-keys)
5405 (let ((bin (string-append (assoc-ref outputs "out") "/bin/")))
5406 (install-file "STAR" bin))
5408 (delete 'configure))))
5410 `(("vim" ,vim))) ; for xxd
5412 `(("htslib" ,htslib)
5414 (home-page "https://github.com/alexdobin/STAR")
5415 (synopsis "Universal RNA-seq aligner")
5417 "The Spliced Transcripts Alignment to a Reference (STAR) software is
5418 based on a previously undescribed RNA-seq alignment algorithm that uses
5419 sequential maximum mappable seed search in uncompressed suffix arrays followed
5420 by seed clustering and stitching procedure. In addition to unbiased de novo
5421 detection of canonical junctions, STAR can discover non-canonical splices and
5422 chimeric (fusion) transcripts, and is also capable of mapping full-length RNA
5424 ;; Only 64-bit systems are supported according to the README.
5425 (supported-systems '("x86_64-linux" "mips64el-linux"))
5426 ;; STAR is licensed under GPLv3 or later; htslib is MIT-licensed.
5427 (license license:gpl3+)))
5429 (define-public subread
5435 (uri (string-append "mirror://sourceforge/subread/subread-"
5436 version "/subread-" version "-source.tar.gz"))
5439 "0gn5zhbvllks0mmdg3qlmsbg91p2mpdc2wixwfqpi85yzfrh8hcy"))))
5440 (build-system gnu-build-system)
5442 `(#:tests? #f ;no "check" target
5443 ;; The CC and CCFLAGS variables are set to contain a lot of x86_64
5444 ;; optimizations by default, so we override these flags such that x86_64
5445 ;; flags are only added when the build target is an x86_64 system.
5447 (list (let ((system ,(or (%current-target-system)
5449 (flags '("-ggdb" "-fomit-frame-pointer"
5450 "-ffast-math" "-funroll-loops"
5451 "-fmessage-length=0"
5452 "-O9" "-Wall" "-DMAKE_FOR_EXON"
5454 "-DSUBREAD_VERSION=\\\"${SUBREAD_VERSION}\\\""))
5455 (flags64 '("-mmmx" "-msse" "-msse2" "-msse3")))
5456 (if (string-prefix? "x86_64" system)
5457 (string-append "CCFLAGS=" (string-join (append flags flags64)))
5458 (string-append "CCFLAGS=" (string-join flags))))
5459 "-f" "Makefile.Linux"
5460 "CC=gcc ${CCFLAGS}")
5462 (modify-phases %standard-phases
5463 (add-after 'unpack 'enter-dir
5464 (lambda _ (chdir "src") #t))
5466 (lambda* (#:key outputs #:allow-other-keys)
5467 (let ((bin (string-append (assoc-ref outputs "out") "/bin/")))
5469 (copy-recursively "../bin" bin))))
5470 ;; no "configure" script
5471 (delete 'configure))))
5472 (inputs `(("zlib" ,zlib)))
5473 (home-page "http://bioinf.wehi.edu.au/subread-package/")
5474 (synopsis "Tool kit for processing next-gen sequencing data")
5476 "The subread package contains the following tools: subread aligner, a
5477 general-purpose read aligner; subjunc aligner: detecting exon-exon junctions
5478 and mapping RNA-seq reads; featureCounts: counting mapped reads for genomic
5479 features; exactSNP: a SNP caller that discovers SNPs by testing signals
5480 against local background noises.")
5481 (license license:gpl3+)))
5483 (define-public stringtie
5489 (uri (string-append "http://ccb.jhu.edu/software/stringtie/dl/"
5490 "stringtie-" version ".tar.gz"))
5493 "1cqllsc1maq4kh92isi8yadgzbmnf042hlnalpk3y59aph1z3bfz"))
5494 (modules '((guix build utils)))
5497 (delete-file-recursively "samtools-0.1.18")
5499 (build-system gnu-build-system)
5501 `(#:tests? #f ;no test suite
5503 (modify-phases %standard-phases
5504 ;; no configure script
5506 (add-before 'build 'use-system-samtools
5508 (substitute* "Makefile"
5509 (("stringtie: \\$\\{BAM\\}/libbam\\.a")
5511 (substitute* '("gclib/GBam.h"
5513 (("#include \"(bam|sam|kstring).h\"" _ header)
5514 (string-append "#include <samtools/" header ".h>")))
5516 (add-after 'unpack 'remove-duplicate-typedef
5518 ;; This typedef conflicts with the typedef in
5519 ;; glibc-2.25/include/bits/types.h
5520 (substitute* "gclib/GThreads.h"
5521 (("typedef long long __intmax_t;") ""))
5524 (lambda* (#:key outputs #:allow-other-keys)
5525 (let ((bin (string-append (assoc-ref outputs "out") "/bin/")))
5526 (install-file "stringtie" bin)
5529 `(("samtools" ,samtools-0.1)
5531 (home-page "http://ccb.jhu.edu/software/stringtie/")
5532 (synopsis "Transcript assembly and quantification for RNA-Seq data")
5534 "StringTie is a fast and efficient assembler of RNA-Seq sequence
5535 alignments into potential transcripts. It uses a novel network flow algorithm
5536 as well as an optional de novo assembly step to assemble and quantitate
5537 full-length transcripts representing multiple splice variants for each gene
5538 locus. Its input can include not only the alignments of raw reads used by
5539 other transcript assemblers, but also alignments of longer sequences that have
5540 been assembled from those reads. To identify differentially expressed genes
5541 between experiments, StringTie's output can be processed either by the
5542 Cuffdiff or Ballgown programs.")
5543 (license license:artistic2.0)))
5545 (define-public taxtastic
5551 (uri (pypi-uri "taxtastic" version))
5554 "0s79z8kfl853x7l4h8ms05k31q87aw62nrchlk20w9n227j35929"))))
5555 (build-system python-build-system)
5557 `(#:python ,python-2
5559 (modify-phases %standard-phases
5562 (zero? (system* "python" "-m" "unittest" "discover" "-v")))))))
5564 `(("python-sqlalchemy" ,python2-sqlalchemy)
5565 ("python-decorator" ,python2-decorator)
5566 ("python-biopython" ,python2-biopython)
5567 ("python-pandas" ,python2-pandas)))
5568 (home-page "https://github.com/fhcrc/taxtastic")
5569 (synopsis "Tools for taxonomic naming and annotation")
5571 "Taxtastic is software written in python used to build and maintain
5572 reference packages i.e. collections of reference trees, reference alignments,
5573 profiles, and associated taxonomic information.")
5574 (license license:gpl3+)))
5576 (define-public vcftools
5583 "https://github.com/vcftools/vcftools/releases/download/v"
5584 version "/vcftools-" version ".tar.gz"))
5587 "1qw30c45wihgy632rbz4rh3njnwj4msj46l1rsgdhyg6bgypmr1i"))))
5588 (build-system gnu-build-system)
5590 `(#:tests? #f ; no "check" target
5592 "CFLAGS=-O2" ; override "-m64" flag
5593 (string-append "PREFIX=" (assoc-ref %outputs "out"))
5594 (string-append "MANDIR=" (assoc-ref %outputs "out")
5595 "/share/man/man1"))))
5597 `(("pkg-config" ,pkg-config)))
5601 (home-page "https://vcftools.github.io/")
5602 (synopsis "Tools for working with VCF files")
5604 "VCFtools is a program package designed for working with VCF files, such
5605 as those generated by the 1000 Genomes Project. The aim of VCFtools is to
5606 provide easily accessible methods for working with complex genetic variation
5607 data in the form of VCF files.")
5608 ;; The license is declared as LGPLv3 in the README and
5609 ;; at https://vcftools.github.io/license.html
5610 (license license:lgpl3)))
5612 (define-public infernal
5618 (uri (string-append "http://eddylab.org/software/infernal/"
5619 "infernal-" version ".tar.gz"))
5622 "0sr2hiz3qxfwqpz3whxr6n82p3x27336v3f34iqznp10hks2935c"))))
5623 (build-system gnu-build-system)
5625 `(("perl" ,perl))) ; for tests
5626 (home-page "http://eddylab.org/infernal/")
5627 (synopsis "Inference of RNA alignments")
5628 (description "Infernal (\"INFERence of RNA ALignment\") is a tool for
5629 searching DNA sequence databases for RNA structure and sequence similarities.
5630 It is an implementation of a special case of profile stochastic context-free
5631 grammars called @dfn{covariance models} (CMs). A CM is like a sequence
5632 profile, but it scores a combination of sequence consensus and RNA secondary
5633 structure consensus, so in many cases, it is more capable of identifying RNA
5634 homologs that conserve their secondary structure more than their primary
5636 ;; Infernal 1.1.2 requires VMX or SSE capability for parallel instructions.
5637 (supported-systems '("i686-linux" "x86_64-linux"))
5638 (license license:bsd-3)))
5640 (define-public r-centipede
5642 (name "r-centipede")
5646 (uri (string-append "http://download.r-forge.r-project.org/"
5647 "src/contrib/CENTIPEDE_" version ".tar.gz"))
5650 "1hsx6qgwr0i67fhy9257zj7s0ppncph2hjgbia5nn6nfmj0ax6l9"))))
5651 (build-system r-build-system)
5652 (home-page "http://centipede.uchicago.edu/")
5653 (synopsis "Predict transcription factor binding sites")
5655 "CENTIPEDE applies a hierarchical Bayesian mixture model to infer regions
5656 of the genome that are bound by particular transcription factors. It starts
5657 by identifying a set of candidate binding sites, and then aims to classify the
5658 sites according to whether each site is bound or not bound by a transcription
5659 factor. CENTIPEDE is an unsupervised learning algorithm that discriminates
5660 between two different types of motif instances using as much relevant
5661 information as possible.")
5662 (license (list license:gpl2+ license:gpl3+))))
5664 (define-public r-vegan
5671 (uri (cran-uri "vegan" version))
5674 "1n57dzv2aid6iqd9fkqik401sidqanhzsawyak94qbiyh6dbd1x9"))))
5675 (build-system r-build-system)
5677 `(("gfortran" ,gfortran)))
5679 `(("r-cluster" ,r-cluster)
5680 ("r-lattice" ,r-lattice)
5683 ("r-permute" ,r-permute)))
5684 (home-page "https://cran.r-project.org/web/packages/vegan")
5685 (synopsis "Functions for community ecology")
5687 "The vegan package provides tools for descriptive community ecology. It
5688 has most basic functions of diversity analysis, community ordination and
5689 dissimilarity analysis. Most of its multivariate tools can be used for other
5690 data types as well.")
5691 (license license:gpl2+)))
5693 (define-public r-annotate
5700 (uri (bioconductor-uri "annotate" version))
5703 "03hmbvp3i6lvd307fqdg7akxi2qp322rlky3bzw0zccgm0i0221g"))))
5704 (build-system r-build-system)
5706 `(("r-annotationdbi" ,r-annotationdbi)
5707 ("r-biobase" ,r-biobase)
5708 ("r-biocgenerics" ,r-biocgenerics)
5710 ("r-rcurl" ,r-rcurl)
5712 ("r-xtable" ,r-xtable)))
5714 "http://bioconductor.org/packages/annotate")
5715 (synopsis "Annotation for microarrays")
5716 (description "This package provides R environments for the annotation of
5718 (license license:artistic2.0)))
5720 (define-public r-geneplotter
5722 (name "r-geneplotter")
5727 (uri (bioconductor-uri "geneplotter" version))
5730 "0a0ajns21db5rrjl16bq6wawggsnxr00fg184pc38nmfghv4z4b6"))))
5731 (build-system r-build-system)
5733 `(("r-annotate" ,r-annotate)
5734 ("r-annotationdbi" ,r-annotationdbi)
5735 ("r-biobase" ,r-biobase)
5736 ("r-biocgenerics" ,r-biocgenerics)
5737 ("r-lattice" ,r-lattice)
5738 ("r-rcolorbrewer" ,r-rcolorbrewer)))
5739 (home-page "http://bioconductor.org/packages/geneplotter")
5740 (synopsis "Graphics functions for genomic data")
5742 "This package provides functions for plotting genomic data.")
5743 (license license:artistic2.0)))
5745 (define-public r-genefilter
5747 (name "r-genefilter")
5752 (uri (bioconductor-uri "genefilter" version))
5755 "0sf2hdi9nv6r83vn1y65m4jiba8pffddpj46d6yjn5rlsixplmqg"))))
5756 (build-system r-build-system)
5758 `(("gfortran" ,gfortran)))
5760 `(("r-annotate" ,r-annotate)
5761 ("r-annotationdbi" ,r-annotationdbi)
5762 ("r-biobase" ,r-biobase)
5763 ("r-s4vectors" ,r-s4vectors)
5764 ("r-survival" ,r-survival)))
5765 (home-page "http://bioconductor.org/packages/genefilter")
5766 (synopsis "Filter genes from high-throughput experiments")
5768 "This package provides basic functions for filtering genes from
5769 high-throughput sequencing experiments.")
5770 (license license:artistic2.0)))
5772 (define-public r-deseq2
5779 (uri (bioconductor-uri "DESeq2" version))
5782 "01pvyljxkwazxl510v7h0971nx65iqd2bdkbdhw3xzind0n9pdvq"))))
5783 (properties `((upstream-name . "DESeq2")))
5784 (build-system r-build-system)
5786 `(("r-biobase" ,r-biobase)
5787 ("r-biocgenerics" ,r-biocgenerics)
5788 ("r-biocparallel" ,r-biocparallel)
5789 ("r-genefilter" ,r-genefilter)
5790 ("r-geneplotter" ,r-geneplotter)
5791 ("r-genomicranges" ,r-genomicranges)
5792 ("r-ggplot2" ,r-ggplot2)
5793 ("r-hmisc" ,r-hmisc)
5794 ("r-iranges" ,r-iranges)
5795 ("r-locfit" ,r-locfit)
5797 ("r-rcpparmadillo" ,r-rcpparmadillo)
5798 ("r-s4vectors" ,r-s4vectors)
5799 ("r-summarizedexperiment" ,r-summarizedexperiment)))
5800 (home-page "http://bioconductor.org/packages/DESeq2")
5801 (synopsis "Differential gene expression analysis")
5803 "This package provides functions to estimate variance-mean dependence in
5804 count data from high-throughput nucleotide sequencing assays and test for
5805 differential expression based on a model using the negative binomial
5807 (license license:lgpl3+)))
5809 (define-public r-dexseq
5816 (uri (bioconductor-uri "DEXSeq" version))
5819 "085aqk1wlzzqcqcqhvz74y099kr2ln5dwdxd3rl6zan806mgwahg"))))
5820 (properties `((upstream-name . "DEXSeq")))
5821 (build-system r-build-system)
5823 `(("r-annotationdbi" ,r-annotationdbi)
5824 ("r-biobase" ,r-biobase)
5825 ("r-biocgenerics" ,r-biocgenerics)
5826 ("r-biocparallel" ,r-biocparallel)
5827 ("r-biomart" ,r-biomart)
5828 ("r-deseq2" ,r-deseq2)
5829 ("r-genefilter" ,r-genefilter)
5830 ("r-geneplotter" ,r-geneplotter)
5831 ("r-genomicranges" ,r-genomicranges)
5832 ("r-hwriter" ,r-hwriter)
5833 ("r-iranges" ,r-iranges)
5834 ("r-rcolorbrewer" ,r-rcolorbrewer)
5835 ("r-rsamtools" ,r-rsamtools)
5836 ("r-s4vectors" ,r-s4vectors)
5837 ("r-statmod" ,r-statmod)
5838 ("r-stringr" ,r-stringr)
5839 ("r-summarizedexperiment" ,r-summarizedexperiment)))
5840 (home-page "http://bioconductor.org/packages/DEXSeq")
5841 (synopsis "Inference of differential exon usage in RNA-Seq")
5843 "This package is focused on finding differential exon usage using RNA-seq
5844 exon counts between samples with different experimental designs. It provides
5845 functions that allows the user to make the necessary statistical tests based
5846 on a model that uses the negative binomial distribution to estimate the
5847 variance between biological replicates and generalized linear models for
5848 testing. The package also provides functions for the visualization and
5849 exploration of the results.")
5850 (license license:gpl3+)))
5852 (define-public r-annotationforge
5854 (name "r-annotationforge")
5859 (uri (bioconductor-uri "AnnotationForge" version))
5862 "1366qvykd9cpcvwgc5g9mm9adw9rxw6p4814dd6l5fyb0pwpmysx"))))
5864 `((upstream-name . "AnnotationForge")))
5865 (build-system r-build-system)
5867 `(("r-annotationdbi" ,r-annotationdbi)
5868 ("r-biobase" ,r-biobase)
5869 ("r-biocgenerics" ,r-biocgenerics)
5871 ("r-rcurl" ,r-rcurl)
5872 ("r-rsqlite" ,r-rsqlite)
5873 ("r-s4vectors" ,r-s4vectors)
5875 (home-page "http://bioconductor.org/packages/AnnotationForge")
5876 (synopsis "Code for building annotation database packages")
5878 "This package provides code for generating Annotation packages and their
5879 databases. Packages produced are intended to be used with AnnotationDbi.")
5880 (license license:artistic2.0)))
5882 (define-public r-rbgl
5889 (uri (bioconductor-uri "RBGL" version))
5892 "11db6kvz453ypj9ds3xpjqzwrrjck84ijn4wlhkfyz2dzdgd5ryv"))))
5893 (properties `((upstream-name . "RBGL")))
5894 (build-system r-build-system)
5895 (propagated-inputs `(("r-graph" ,r-graph)))
5896 (home-page "http://www.bioconductor.org/packages/RBGL")
5897 (synopsis "Interface to the Boost graph library")
5899 "This package provides a fairly extensive and comprehensive interface to
5900 the graph algorithms contained in the Boost library.")
5901 (license license:artistic2.0)))
5903 (define-public r-gseabase
5910 (uri (bioconductor-uri "GSEABase" version))
5913 "1c6i6g4fj3b8wjyxyygr7i3v8sxrq1ffb2bbicya5ah2gdaclfad"))))
5914 (properties `((upstream-name . "GSEABase")))
5915 (build-system r-build-system)
5917 `(("r-annotate" ,r-annotate)
5918 ("r-annotationdbi" ,r-annotationdbi)
5919 ("r-biobase" ,r-biobase)
5920 ("r-biocgenerics" ,r-biocgenerics)
5921 ("r-graph" ,r-graph)
5923 (home-page "http://bioconductor.org/packages/GSEABase")
5924 (synopsis "Gene set enrichment data structures and methods")
5926 "This package provides classes and methods to support @dfn{Gene Set
5927 Enrichment Analysis} (GSEA).")
5928 (license license:artistic2.0)))
5930 (define-public r-category
5937 (uri (bioconductor-uri "Category" version))
5940 "1w186nhc85bglcgmbcrsdbb8l6rph21pl5kdwjqwkp0jnr9z0ifn"))))
5941 (properties `((upstream-name . "Category")))
5942 (build-system r-build-system)
5944 `(("r-annotate" ,r-annotate)
5945 ("r-annotationdbi" ,r-annotationdbi)
5946 ("r-biobase" ,r-biobase)
5947 ("r-biocgenerics" ,r-biocgenerics)
5948 ("r-genefilter" ,r-genefilter)
5949 ("r-graph" ,r-graph)
5950 ("r-gseabase" ,r-gseabase)
5951 ("r-matrix" ,r-matrix)
5953 ("r-rsqlite" ,r-rsqlite)))
5954 (home-page "http://bioconductor.org/packages/Category")
5955 (synopsis "Category analysis")
5957 "This package provides a collection of tools for performing category
5959 (license license:artistic2.0)))
5961 (define-public r-gostats
5968 (uri (bioconductor-uri "GOstats" version))
5971 "0qvqjgfnd9ap4rikvyxa9p4dhcnccvkw8phzv88vghh6pq463d62"))))
5972 (properties `((upstream-name . "GOstats")))
5973 (build-system r-build-system)
5975 `(("r-annotate" ,r-annotate)
5976 ("r-annotationdbi" ,r-annotationdbi)
5977 ("r-annotationforge" ,r-annotationforge)
5978 ("r-biobase" ,r-biobase)
5979 ("r-category" ,r-category)
5980 ("r-go-db" ,r-go-db)
5981 ("r-graph" ,r-graph)
5982 ("r-rbgl" ,r-rbgl)))
5983 (home-page "http://bioconductor.org/packages/GOstats")
5984 (synopsis "Tools for manipulating GO and microarrays")
5986 "This package provides a set of tools for interacting with GO and
5987 microarray data. A variety of basic manipulation tools for graphs, hypothesis
5988 testing and other simple calculations.")
5989 (license license:artistic2.0)))
5991 (define-public r-shortread
5993 (name "r-shortread")
5998 (uri (bioconductor-uri "ShortRead" version))
6001 "0ayk3d5625ymb5g2gycq6banzqmyd642xrwjzhdshz2dwid7kly8"))))
6002 (properties `((upstream-name . "ShortRead")))
6003 (build-system r-build-system)
6007 `(("r-biobase" ,r-biobase)
6008 ("r-biocgenerics" ,r-biocgenerics)
6009 ("r-biocparallel" ,r-biocparallel)
6010 ("r-biostrings" ,r-biostrings)
6011 ("r-genomeinfodb" ,r-genomeinfodb)
6012 ("r-genomicalignments" ,r-genomicalignments)
6013 ("r-genomicranges" ,r-genomicranges)
6014 ("r-hwriter" ,r-hwriter)
6015 ("r-iranges" ,r-iranges)
6016 ("r-lattice" ,r-lattice)
6017 ("r-latticeextra" ,r-latticeextra)
6018 ("r-rsamtools" ,r-rsamtools)
6019 ("r-s4vectors" ,r-s4vectors)
6020 ("r-xvector" ,r-xvector)
6021 ("r-zlibbioc" ,r-zlibbioc)))
6022 (home-page "http://bioconductor.org/packages/ShortRead")
6023 (synopsis "FASTQ input and manipulation tools")
6025 "This package implements sampling, iteration, and input of FASTQ files.
6026 It includes functions for filtering and trimming reads, and for generating a
6027 quality assessment report. Data are represented as
6028 @code{DNAStringSet}-derived objects, and easily manipulated for a diversity of
6029 purposes. The package also contains legacy support for early single-end,
6030 ungapped alignment formats.")
6031 (license license:artistic2.0)))
6033 (define-public r-systempiper
6035 (name "r-systempiper")
6040 (uri (bioconductor-uri "systemPipeR" version))
6043 "0c3m5rq63ypv15yca97yag5d4vgd7xj9by2a4sd8z0pcmpajz0hw"))))
6044 (properties `((upstream-name . "systemPipeR")))
6045 (build-system r-build-system)
6047 `(("r-annotate" ,r-annotate)
6048 ("r-batchjobs" ,r-batchjobs)
6049 ("r-biocgenerics" ,r-biocgenerics)
6050 ("r-biostrings" ,r-biostrings)
6051 ("r-deseq2" ,r-deseq2)
6052 ("r-edger" ,r-edger)
6053 ("r-genomicfeatures" ,r-genomicfeatures)
6054 ("r-genomicranges" ,r-genomicranges)
6055 ("r-ggplot2" ,r-ggplot2)
6056 ("r-go-db" ,r-go-db)
6057 ("r-gostats" ,r-gostats)
6058 ("r-limma" ,r-limma)
6059 ("r-pheatmap" ,r-pheatmap)
6060 ("r-rjson" ,r-rjson)
6061 ("r-rsamtools" ,r-rsamtools)
6062 ("r-shortread" ,r-shortread)
6063 ("r-summarizedexperiment" ,r-summarizedexperiment)
6064 ("r-variantannotation" ,r-variantannotation)))
6065 (home-page "https://github.com/tgirke/systemPipeR")
6066 (synopsis "Next generation sequencing workflow and reporting environment")
6068 "This R package provides tools for building and running automated
6069 end-to-end analysis workflows for a wide range of @dfn{next generation
6070 sequence} (NGS) applications such as RNA-Seq, ChIP-Seq, VAR-Seq and Ribo-Seq.
6071 Important features include a uniform workflow interface across different NGS
6072 applications, automated report generation, and support for running both R and
6073 command-line software, such as NGS aligners or peak/variant callers, on local
6074 computers or compute clusters. Efficient handling of complex sample sets and
6075 experimental designs is facilitated by a consistently implemented sample
6076 annotation infrastructure.")
6077 (license license:artistic2.0)))
6079 (define-public r-grohmm
6086 (uri (bioconductor-uri "groHMM" version))
6089 "16k1kp4sbhh0vp7dzywafq52csq42ksqfrqfy4bdv1qbd7536dpd"))))
6090 (properties `((upstream-name . "groHMM")))
6091 (build-system r-build-system)
6093 `(("r-genomeinfodb" ,r-genomeinfodb)
6094 ("r-genomicalignments" ,r-genomicalignments)
6095 ("r-genomicranges" ,r-genomicranges)
6096 ("r-iranges" ,r-iranges)
6098 ("r-rtracklayer" ,r-rtracklayer)
6099 ("r-s4vectors" ,r-s4vectors)))
6100 (home-page "https://github.com/Kraus-Lab/groHMM")
6101 (synopsis "GRO-seq analysis pipeline")
6103 "This package provides a pipeline for the analysis of GRO-seq data.")
6104 (license license:gpl3+)))
6106 (define-public r-txdb-hsapiens-ucsc-hg19-knowngene
6108 (name "r-txdb-hsapiens-ucsc-hg19-knowngene")
6112 ;; We cannot use bioconductor-uri here because this tarball is
6113 ;; located under "data/annotation/" instead of "bioc/".
6114 (uri (string-append "http://bioconductor.org/packages/"
6115 "release/data/annotation/src/contrib"
6116 "/TxDb.Hsapiens.UCSC.hg19.knownGene_"
6120 "1sajhcqqwazgz2lqbik7rd935i7kpnh08zxbp2ra10j72yqy4g86"))))
6122 `((upstream-name . "TxDb.Hsapiens.UCSC.hg19.knownGene")))
6123 (build-system r-build-system)
6124 ;; As this package provides little more than a very large data file it
6125 ;; doesn't make sense to build substitutes.
6126 (arguments `(#:substitutable? #f))
6128 `(("r-genomicfeatures" ,r-genomicfeatures)))
6130 "http://bioconductor.org/packages/TxDb.Hsapiens.UCSC.hg19.knownGene/")
6131 (synopsis "Annotation package for human genome in TxDb format")
6133 "This package provides an annotation database of Homo sapiens genome
6134 data. It is derived from the UCSC hg19 genome and based on the \"knownGene\"
6135 track. The database is exposed as a @code{TxDb} object.")
6136 (license license:artistic2.0)))
6138 (define-public r-sparql
6144 (uri (cran-uri "SPARQL" version))
6147 "0gak1q06yyhdmcxb2n3v0h9gr1vqd0viqji52wpw211qp6r6dcrc"))))
6148 (properties `((upstream-name . "SPARQL")))
6149 (build-system r-build-system)
6151 `(("r-rcurl" ,r-rcurl)
6153 (home-page "http://cran.r-project.org/web/packages/SPARQL")
6154 (synopsis "SPARQL client for R")
6155 (description "This package provides an interface to use SPARQL to pose
6156 SELECT or UPDATE queries to an end-point.")
6157 ;; The only license indication is found in the DESCRIPTION file,
6158 ;; which states GPL-3. So we cannot assume GPLv3+.
6159 (license license:gpl3)))
6161 (define-public vsearch
6169 "https://github.com/torognes/vsearch/archive/v"
6171 (file-name (string-append name "-" version ".tar.gz"))
6174 "1d8a4gjwaqdv57krlr80x18mg5py1bbdiqs5m0jdn38filc9z40k"))
6175 (patches (search-patches "vsearch-unbundle-cityhash.patch"))
6178 ;; Remove bundled cityhash sources. The vsearch source is adjusted
6179 ;; for this in the patch.
6180 (delete-file "src/city.h")
6181 (delete-file "src/citycrc.h")
6182 (delete-file "src/city.cc")
6184 (build-system gnu-build-system)
6187 (modify-phases %standard-phases
6188 (add-after 'unpack 'autogen
6189 (lambda _ (zero? (system* "autoreconf" "-vif")))))))
6193 ("cityhash" ,cityhash)))
6195 `(("autoconf" ,autoconf)
6196 ("automake" ,automake)))
6197 (synopsis "Sequence search tools for metagenomics")
6199 "VSEARCH supports DNA sequence searching, clustering, chimera detection,
6200 dereplication, pairwise alignment, shuffling, subsampling, sorting and
6201 masking. The tool takes advantage of parallelism in the form of SIMD
6202 vectorization as well as multiple threads to perform accurate alignments at
6203 high speed. VSEARCH uses an optimal global aligner (full dynamic programming
6204 Needleman-Wunsch).")
6205 (home-page "https://github.com/torognes/vsearch")
6206 ;; vsearch uses non-portable SSE intrinsics so building fails on other
6208 (supported-systems '("x86_64-linux"))
6209 ;; Dual licensed; also includes public domain source.
6210 (license (list license:gpl3 license:bsd-2))))
6212 (define-public pardre
6215 ;; The source of 1.1.5 changed in place, so we append "-1" to the version.
6220 (uri (string-append "mirror://sourceforge/pardre/ParDRe-rel"
6224 "17j73nc0viq4f6qj50nrndsrif5d6b71q8fl87m54psiv0ilns2b"))))
6225 (build-system gnu-build-system)
6227 `(#:tests? #f ; no tests included
6229 (modify-phases %standard-phases
6232 (lambda* (#:key outputs #:allow-other-keys)
6233 (let ((bin (string-append (assoc-ref outputs "out") "/bin")))
6234 (install-file "ParDRe" bin)
6237 `(("openmpi" ,openmpi)
6239 (synopsis "Parallel tool to remove duplicate DNA reads")
6241 "ParDRe is a parallel tool to remove duplicate genetic sequence reads.
6242 Duplicate reads can be seen as identical or nearly identical sequences with
6243 some mismatches. This tool lets users avoid the analysis of unnecessary
6244 reads, reducing the time of subsequent procedures with the
6245 dataset (e.g. assemblies, mappings, etc.). The tool is implemented with MPI
6246 in order to exploit the parallel capabilities of multicore clusters. It is
6247 faster than multithreaded counterparts (end of 2015) for the same number of
6248 cores and, thanks to the message-passing technology, it can be executed on
6250 (home-page "https://sourceforge.net/projects/pardre/")
6251 (license license:gpl3+)))
6253 (define-public ruby-bio-kseq
6255 (name "ruby-bio-kseq")
6260 (uri (rubygems-uri "bio-kseq" version))
6263 "1xyaha46khb5jc6wzkbf7040jagac49jbimn0vcrzid0j8jdikrz"))))
6264 (build-system ruby-build-system)
6266 `(#:test-target "spec"))
6268 `(("bundler" ,bundler)
6269 ("ruby-rspec" ,ruby-rspec)
6270 ("ruby-rake-compiler" ,ruby-rake-compiler)))
6273 (synopsis "Ruby bindings for the kseq.h FASTA/Q parser")
6275 "@code{Bio::Kseq} provides ruby bindings to the @code{kseq.h} FASTA and
6276 FASTQ parsing code. It provides a fast iterator over sequences and their
6278 (home-page "https://github.com/gusevfe/bio-kseq")
6279 (license license:expat)))
6281 (define-public bio-locus
6288 (uri (rubygems-uri "bio-locus" version))
6291 "02vmrxyimkj9sahsp4zhfhnmbvz6dbbqz1y01vglf8cbwvkajfl0"))))
6292 (build-system ruby-build-system)
6294 `(("ruby-rspec" ,ruby-rspec)))
6295 (synopsis "Tool for fast querying of genome locations")
6297 "Bio-locus is a tabix-like tool for fast querying of genome
6298 locations. Many file formats in bioinformatics contain records that
6299 start with a chromosome name and a position for a SNP, or a start-end
6300 position for indels. Bio-locus allows users to store this chr+pos or
6301 chr+pos+alt information in a database.")
6302 (home-page "https://github.com/pjotrp/bio-locus")
6303 (license license:expat)))
6305 (define-public bio-blastxmlparser
6307 (name "bio-blastxmlparser")
6311 (uri (rubygems-uri "bio-blastxmlparser" version))
6314 "1wf4qygcmdjgcqm6flmvsagfr1gs9lf63mj32qv3z1f481zc5692"))))
6315 (build-system ruby-build-system)
6317 `(("ruby-bio-logger" ,ruby-bio-logger)
6318 ("ruby-nokogiri" ,ruby-nokogiri)))
6320 `(("ruby-rspec" ,ruby-rspec)))
6321 (synopsis "Fast big data BLAST XML parser and library")
6323 "Very fast parallel big-data BLAST XML file parser which can be used as
6324 command line utility. Use blastxmlparser to: Parse BLAST XML; filter output;
6325 generate FASTA, JSON, YAML, RDF, JSON-LD, HTML, CSV, tabular output etc.")
6326 (home-page "https://github.com/pjotrp/blastxmlparser")
6327 (license license:expat)))
6329 (define-public bioruby
6336 (uri (rubygems-uri "bio" version))
6339 "0hdl0789c9n4mprnx5pgd46bfwl8d000rqpamj5h6kkjgspijv49"))))
6340 (build-system ruby-build-system)
6342 `(("ruby-libxml" ,ruby-libxml)))
6344 `(("which" ,which))) ; required for test phase
6347 (modify-phases %standard-phases
6348 (add-before 'build 'patch-test-command
6350 (substitute* '("test/functional/bio/test_command.rb")
6351 (("/bin/sh") (which "sh")))
6352 (substitute* '("test/functional/bio/test_command.rb")
6353 (("/bin/ls") (which "ls")))
6354 (substitute* '("test/functional/bio/test_command.rb")
6355 (("which") (which "which")))
6356 (substitute* '("test/functional/bio/test_command.rb",
6357 "test/data/command/echoarg2.sh")
6358 (("/bin/echo") (which "echo")))
6360 (synopsis "Ruby library, shell and utilities for bioinformatics")
6361 (description "BioRuby comes with a comprehensive set of Ruby development
6362 tools and libraries for bioinformatics and molecular biology. BioRuby has
6363 components for sequence analysis, pathway analysis, protein modelling and
6364 phylogenetic analysis; it supports many widely used data formats and provides
6365 easy access to databases, external programs and public web services, including
6366 BLAST, KEGG, GenBank, MEDLINE and GO.")
6367 (home-page "http://bioruby.org/")
6368 ;; Code is released under Ruby license, except for setup
6369 ;; (LGPLv2.1+) and scripts in samples (which have GPL2 and GPL2+)
6370 (license (list license:ruby license:lgpl2.1+ license:gpl2+ ))))
6372 (define-public r-acsnminer
6374 (name "r-acsnminer")
6375 (version "0.16.8.25")
6378 (uri (cran-uri "ACSNMineR" version))
6381 "0gh604s8qall6zfjlwcg2ilxjvz08dplf9k5g47idhv43scm748l"))))
6382 (properties `((upstream-name . "ACSNMineR")))
6383 (build-system r-build-system)
6385 `(("r-ggplot2" ,r-ggplot2)
6386 ("r-gridextra" ,r-gridextra)))
6387 (home-page "http://cran.r-project.org/web/packages/ACSNMineR")
6388 (synopsis "Gene enrichment analysis")
6390 "This package provides tools to compute and represent gene set enrichment
6391 or depletion from your data based on pre-saved maps from the @dfn{Atlas of
6392 Cancer Signalling Networks} (ACSN) or user imported maps. The gene set
6393 enrichment can be run with hypergeometric test or Fisher exact test, and can
6394 use multiple corrections. Visualization of data can be done either by
6395 barplots or heatmaps.")
6396 (license license:gpl2+)))
6398 (define-public r-biocgenerics
6400 (name "r-biocgenerics")
6404 (uri (bioconductor-uri "BiocGenerics" version))
6407 "0qbmz2qxwwi30xpxpvp2h1h7l494rbbz5d9pls5cfhqdv3wnpzsv"))))
6409 `((upstream-name . "BiocGenerics")))
6410 (build-system r-build-system)
6411 (home-page "http://bioconductor.org/packages/BiocGenerics")
6412 (synopsis "S4 generic functions for Bioconductor")
6414 "This package provides S4 generic functions needed by many Bioconductor
6416 (license license:artistic2.0)))
6418 (define-public r-biocinstaller
6420 (name "r-biocinstaller")
6424 (uri (bioconductor-uri "BiocInstaller" version))
6427 "0njw2q3lq1rrjx8qzw5d2130l72bmd3g2z8qlxqmkdcbmmgliyj2"))))
6429 `((upstream-name . "BiocInstaller")))
6430 (build-system r-build-system)
6431 (home-page "http://bioconductor.org/packages/BiocInstaller")
6432 (synopsis "Install Bioconductor packages")
6433 (description "This package is used to install and update R packages from
6434 Bioconductor, CRAN, and Github.")
6435 (license license:artistic2.0)))
6437 (define-public r-biocviews
6439 (name "r-biocviews")
6443 (uri (bioconductor-uri "biocViews" version))
6446 "17hi8w0w63f5yc43kid5pbld3ca78sj6n8x9dmkbl8h48818xbga"))))
6448 `((upstream-name . "biocViews")))
6449 (build-system r-build-system)
6451 `(("r-biobase" ,r-biobase)
6452 ("r-graph" ,r-graph)
6454 ("r-rcurl" ,r-rcurl)
6456 ("r-knitr" ,r-knitr)
6457 ("r-runit" ,r-runit)))
6458 (home-page "http://bioconductor.org/packages/biocViews")
6459 (synopsis "Bioconductor package categorization helper")
6460 (description "The purpose of biocViews is to create HTML pages that
6461 categorize packages in a Bioconductor package repository according to keywords,
6462 also known as views, in a controlled vocabulary.")
6463 (license license:artistic2.0)))
6465 (define-public r-bookdown
6471 (uri (cran-uri "bookdown" version))
6474 "0zm63kr4f4kja4qpwkzl119zzyciqj7ihajfqgfjpgb4dzaiycxp"))))
6475 (build-system r-build-system)
6477 `(("r-htmltools" ,r-htmltools)
6478 ("r-knitr" ,r-knitr)
6479 ("r-rmarkdown" ,r-rmarkdown)
6480 ("r-yaml" ,r-yaml)))
6481 (home-page "https://github.com/rstudio/bookdown")
6482 (synopsis "Authoring books and technical documents with R markdown")
6483 (description "This package provides output formats and utilities for
6484 authoring books and technical documents with R Markdown.")
6485 (license license:gpl3)))
6487 (define-public r-biocstyle
6489 (name "r-biocstyle")
6493 (uri (bioconductor-uri "BiocStyle" version))
6496 "0bmgmsfll923v573g0kyzlmjd7gly5jwgd8vkrcwvbam1gz75f2c"))))
6498 `((upstream-name . "BiocStyle")))
6499 (build-system r-build-system)
6501 `(("r-bookdown" ,r-bookdown)
6502 ("r-knitr" ,r-knitr)
6503 ("r-rmarkdown" ,r-rmarkdown)
6504 ("r-yaml" ,r-yaml)))
6505 (home-page "http://bioconductor.org/packages/BiocStyle")
6506 (synopsis "Bioconductor formatting styles")
6507 (description "This package provides standard formatting styles for
6508 Bioconductor PDF and HTML documents. Package vignettes illustrate use and
6510 (license license:artistic2.0)))
6512 (define-public r-bioccheck
6514 (name "r-bioccheck")
6518 (uri (bioconductor-uri "BiocCheck" version))
6521 "01zkw5hggzvn0wj4msac71k1mknq4h2inn1c2hwqgw4cy1675wl0"))))
6523 `((upstream-name . "BiocCheck")))
6524 (build-system r-build-system)
6527 (modify-phases %standard-phases
6528 ;; This package can be used by calling BiocCheck(<package>) from
6529 ;; within R, or by running R CMD BiocCheck <package>. This phase
6530 ;; makes sure the latter works. For this to work, the BiocCheck
6531 ;; script must be somewhere on the PATH (not the R bin directory).
6532 (add-after 'install 'install-bioccheck-subcommand
6533 (lambda* (#:key outputs #:allow-other-keys)
6534 (let* ((out (assoc-ref outputs "out"))
6535 (dest-dir (string-append out "/bin"))
6537 (string-append out "/site-library/BiocCheck/script/")))
6539 (symlink (string-append script-dir "/checkBadDeps.R")
6540 (string-append dest-dir "/checkBadDeps.R"))
6541 (symlink (string-append script-dir "/BiocCheck")
6542 (string-append dest-dir "/BiocCheck")))
6545 `(("which" ,which)))
6547 `(("r-codetools" ,r-codetools)
6548 ("r-graph" ,r-graph)
6550 ("r-optparse" ,r-optparse)
6551 ("r-biocinstaller" ,r-biocinstaller)
6552 ("r-biocviews" ,r-biocviews)))
6553 (home-page "http://bioconductor.org/packages/BiocCheck")
6554 (synopsis "Executes Bioconductor-specific package checks")
6555 (description "This package contains tools to perform additional quality
6556 checks on R packages that are to be submitted to the Bioconductor repository.")
6557 (license license:artistic2.0)))
6559 (define-public r-getopt
6566 (uri (cran-uri "getopt" version))
6569 "00f57vgnzmg7cz80rjmjz1556xqcmx8nhrlbbhaq4w7gl2ibl87r"))))
6570 (build-system r-build-system)
6571 (home-page "https://github.com/trevorld/getopt")
6572 (synopsis "Command-line option processor for R")
6574 "This package is designed to be used with Rscript to write shebang
6575 scripts that accept short and long options. Many users will prefer to
6576 use the packages @code{optparse} or @code{argparse} which add extra
6577 features like automatically generated help options and usage texts,
6578 support for default values, positional argument support, etc.")
6579 (license license:gpl2+)))
6581 (define-public r-optparse
6588 (uri (cran-uri "optparse" version))
6591 "1ff4wmsszrb3spwfp7ynfs8w11qpy1sdzfxm1wk8dqqvdwris7qb"))))
6592 (build-system r-build-system)
6594 `(("r-getopt" ,r-getopt)))
6596 "https://github.com/trevorld/optparse")
6597 (synopsis "Command line option parser")
6599 "This package provides a command line parser inspired by Python's
6600 @code{optparse} library to be used with Rscript to write shebang scripts
6601 that accept short and long options.")
6602 (license license:gpl2+)))
6604 (define-public r-dnacopy
6610 (uri (bioconductor-uri "DNAcopy" version))
6613 "0f0x83db7rm5xf9fg5pjhvs4i165qqaf01lbwb8kj13fsqpwx15p"))))
6615 `((upstream-name . "DNAcopy")))
6616 (build-system r-build-system)
6618 `(("gfortran" ,gfortran)))
6619 (home-page "https://bioconductor.org/packages/DNAcopy")
6620 (synopsis "Implementation of a circular binary segmentation algorithm")
6621 (description "This package implements the circular binary segmentation (CBS)
6622 algorithm to segment DNA copy number data and identify genomic regions with
6623 abnormal copy number.")
6624 (license license:gpl2+)))
6626 (define-public r-s4vectors
6628 (name "r-s4vectors")
6632 (uri (bioconductor-uri "S4Vectors" version))
6635 "1r7s4pfw026qazzic090mhk8d9m39j2nwl87dyqcpdylyq7gq5qs"))))
6637 `((upstream-name . "S4Vectors")))
6638 (build-system r-build-system)
6640 `(("r-biocgenerics" ,r-biocgenerics)))
6641 (home-page "http://bioconductor.org/packages/S4Vectors")
6642 (synopsis "S4 implementation of vectors and lists")
6644 "The S4Vectors package defines the @code{Vector} and @code{List} virtual
6645 classes and a set of generic functions that extend the semantic of ordinary
6646 vectors and lists in R. Package developers can easily implement vector-like
6647 or list-like objects as concrete subclasses of @code{Vector} or @code{List}.
6648 In addition, a few low-level concrete subclasses of general interest (e.g.
6649 @code{DataFrame}, @code{Rle}, and @code{Hits}) are implemented in the
6650 S4Vectors package itself.")
6651 (license license:artistic2.0)))
6653 (define-public r-seqinr
6660 (uri (cran-uri "seqinr" version))
6663 "17zv0n5cji17izwmwg0jcbxbjl3w5rls91w15svcnlpxjms38ahn"))))
6664 (build-system r-build-system)
6666 `(("r-ade4" ,r-ade4)
6667 ("r-segmented" ,r-segmented)))
6670 (home-page "http://seqinr.r-forge.r-project.org/")
6671 (synopsis "Biological sequences retrieval and analysis")
6673 "This package provides tools for exploratory data analysis and data
6674 visualization of biological sequence (DNA and protein) data. It also includes
6675 utilities for sequence data management under the ACNUC system.")
6676 (license license:gpl2+)))
6678 (define-public r-iranges
6684 (uri (bioconductor-uri "IRanges" version))
6687 "1brmzs3rsf97gymridrh9c9r3vws8b3rpghaanxnniw36lmcajfy"))))
6689 `((upstream-name . "IRanges")))
6690 (build-system r-build-system)
6692 `(("r-biocgenerics" ,r-biocgenerics)
6693 ("r-s4vectors" ,r-s4vectors)))
6694 (home-page "http://bioconductor.org/packages/IRanges")
6695 (synopsis "Infrastructure for manipulating intervals on sequences")
6697 "This package provides efficient low-level and highly reusable S4 classes
6698 for storing ranges of integers, RLE vectors (Run-Length Encoding), and, more
6699 generally, data that can be organized sequentially (formally defined as
6700 @code{Vector} objects), as well as views on these @code{Vector} objects.
6701 Efficient list-like classes are also provided for storing big collections of
6702 instances of the basic classes. All classes in the package use consistent
6703 naming and share the same rich and consistent \"Vector API\" as much as
6705 (license license:artistic2.0)))
6707 (define-public r-genomeinfodbdata
6709 (name "r-genomeinfodbdata")
6713 ;; We cannot use bioconductor-uri here because this tarball is
6714 ;; located under "data/annotation/" instead of "bioc/".
6715 (uri (string-append "https://bioconductor.org/packages/release/"
6716 "data/annotation/src/contrib/GenomeInfoDbData_"
6720 "120qvhb0pvkzd65lsgja62vyrgc37si6fh68q4cg4w5x9f04jw25"))))
6722 `((upstream-name . "GenomeInfoDbData")))
6723 (build-system r-build-system)
6724 (home-page "http://bioconductor.org/packages/GenomeInfoDbData")
6725 (synopsis "Species and taxonomy ID look up tables for GenomeInfoDb")
6726 (description "This package contains data for mapping between NCBI taxonomy
6727 ID and species. It is used by functions in the GenomeInfoDb package.")
6728 (license license:artistic2.0)))
6730 (define-public r-genomeinfodb
6732 (name "r-genomeinfodb")
6736 (uri (bioconductor-uri "GenomeInfoDb" version))
6739 "1hjxgmcnrngp1307ipqaq9hgxz4j0ldn7d46knhzs30k2r4qnrfp"))))
6741 `((upstream-name . "GenomeInfoDb")))
6742 (build-system r-build-system)
6744 `(("r-biocgenerics" ,r-biocgenerics)
6745 ("r-genomeinfodbdata" ,r-genomeinfodbdata)
6746 ("r-iranges" ,r-iranges)
6747 ("r-rcurl" ,r-rcurl)
6748 ("r-s4vectors" ,r-s4vectors)))
6749 (home-page "http://bioconductor.org/packages/GenomeInfoDb")
6750 (synopsis "Utilities for manipulating chromosome identifiers")
6752 "This package contains data and functions that define and allow
6753 translation between different chromosome sequence naming conventions (e.g.,
6754 \"chr1\" versus \"1\"), including a function that attempts to place sequence
6755 names in their natural, rather than lexicographic, order.")
6756 (license license:artistic2.0)))
6758 (define-public r-edger
6764 (uri (bioconductor-uri "edgeR" version))
6767 "02l17i6xh33dv10swwvyfxrmv5kp23iv278iwvkfq2mnipasfnb9"))))
6768 (properties `((upstream-name . "edgeR")))
6769 (build-system r-build-system)
6771 `(("r-limma" ,r-limma)
6772 ("r-locfit" ,r-locfit)
6773 ("r-statmod" ,r-statmod))) ;for estimateDisp
6774 (home-page "http://bioinf.wehi.edu.au/edgeR")
6775 (synopsis "EdgeR does empirical analysis of digital gene expression data")
6776 (description "This package can do differential expression analysis of
6777 RNA-seq expression profiles with biological replication. It implements a range
6778 of statistical methodology based on the negative binomial distributions,
6779 including empirical Bayes estimation, exact tests, generalized linear models
6780 and quasi-likelihood tests. It be applied to differential signal analysis of
6781 other types of genomic data that produce counts, including ChIP-seq, SAGE and
6783 (license license:gpl2+)))
6785 (define-public r-variantannotation
6787 (name "r-variantannotation")
6791 (uri (bioconductor-uri "VariantAnnotation" version))
6794 "0sr3vdn85x5zdxh80cfwlpfdpi2hmjy3fwi00ac3jya4v145vawr"))))
6796 `((upstream-name . "VariantAnnotation")))
6800 `(("r-annotationdbi" ,r-annotationdbi)
6801 ("r-biobase" ,r-biobase)
6802 ("r-biocgenerics" ,r-biocgenerics)
6803 ("r-biostrings" ,r-biostrings)
6804 ("r-bsgenome" ,r-bsgenome)
6806 ("r-genomeinfodb" ,r-genomeinfodb)
6807 ("r-genomicfeatures" ,r-genomicfeatures)
6808 ("r-genomicranges" ,r-genomicranges)
6809 ("r-iranges" ,r-iranges)
6810 ("r-summarizedexperiment" ,r-summarizedexperiment)
6811 ("r-rsamtools" ,r-rsamtools)
6812 ("r-rtracklayer" ,r-rtracklayer)
6813 ("r-s4vectors" ,r-s4vectors)
6814 ("r-xvector" ,r-xvector)
6815 ("r-zlibbioc" ,r-zlibbioc)))
6816 (build-system r-build-system)
6817 (home-page "https://bioconductor.org/packages/VariantAnnotation")
6818 (synopsis "Package for annotation of genetic variants")
6819 (description "This R package can annotate variants, compute amino acid
6820 coding changes and predict coding outcomes.")
6821 (license license:artistic2.0)))
6823 (define-public r-limma
6829 (uri (bioconductor-uri "limma" version))
6832 "0p2ayha9g9w5r8s7pgdf16mkmdbqwh6f35jh07g3b8gyra48gwiw"))))
6833 (build-system r-build-system)
6834 (home-page "http://bioinf.wehi.edu.au/limma")
6835 (synopsis "Package for linear models for microarray and RNA-seq data")
6836 (description "This package can be used for the analysis of gene expression
6837 studies, especially the use of linear models for analysing designed experiments
6838 and the assessment of differential expression. The analysis methods apply to
6839 different technologies, including microarrays, RNA-seq, and quantitative PCR.")
6840 (license license:gpl2+)))
6842 (define-public r-xvector
6848 (uri (bioconductor-uri "XVector" version))
6851 "01n09f4jdm60684lzikp02zf9gjan8bdrjx740vggr21q9fa69wn"))))
6853 `((upstream-name . "XVector")))
6854 (build-system r-build-system)
6857 (modify-phases %standard-phases
6858 (add-after 'unpack 'use-system-zlib
6860 (substitute* "DESCRIPTION"
6861 (("zlibbioc, ") ""))
6862 (substitute* "NAMESPACE"
6863 (("import\\(zlibbioc\\)") ""))
6868 `(("r-biocgenerics" ,r-biocgenerics)
6869 ("r-iranges" ,r-iranges)
6870 ("r-s4vectors" ,r-s4vectors)))
6871 (home-page "http://bioconductor.org/packages/XVector")
6872 (synopsis "Representation and manpulation of external sequences")
6874 "This package provides memory efficient S4 classes for storing sequences
6875 \"externally\" (behind an R external pointer, or on disk).")
6876 (license license:artistic2.0)))
6878 (define-public r-genomicranges
6880 (name "r-genomicranges")
6884 (uri (bioconductor-uri "GenomicRanges" version))
6887 "1y15kg1q81h8rmga83ljiwr8whkajcargfjiljr212d6if17ys1z"))))
6889 `((upstream-name . "GenomicRanges")))
6890 (build-system r-build-system)
6892 `(("r-biocgenerics" ,r-biocgenerics)
6893 ("r-genomeinfodb" ,r-genomeinfodb)
6894 ("r-iranges" ,r-iranges)
6895 ("r-s4vectors" ,r-s4vectors)
6896 ("r-xvector" ,r-xvector)))
6897 (home-page "http://bioconductor.org/packages/GenomicRanges")
6898 (synopsis "Representation and manipulation of genomic intervals")
6900 "This package provides tools to efficiently represent and manipulate
6901 genomic annotations and alignments is playing a central role when it comes to
6902 analyzing high-throughput sequencing data (a.k.a. NGS data). The
6903 GenomicRanges package defines general purpose containers for storing and
6904 manipulating genomic intervals and variables defined along a genome.")
6905 (license license:artistic2.0)))
6907 (define-public r-biobase
6913 (uri (bioconductor-uri "Biobase" version))
6916 "0sr48nqx5bqid4g6lr9zr9286xh842w717yvmssvddb5xxynib6f"))))
6918 `((upstream-name . "Biobase")))
6919 (build-system r-build-system)
6921 `(("r-biocgenerics" ,r-biocgenerics)))
6922 (home-page "http://bioconductor.org/packages/Biobase")
6923 (synopsis "Base functions for Bioconductor")
6925 "This package provides functions that are needed by many other packages
6926 on Bioconductor or which replace R functions.")
6927 (license license:artistic2.0)))
6929 (define-public r-annotationdbi
6931 (name "r-annotationdbi")
6935 (uri (bioconductor-uri "AnnotationDbi" version))
6938 "1lsamnbf07zzsy5asy5hn97n2a4layv58w2bzd90ikcdx0gmzarj"))))
6940 `((upstream-name . "AnnotationDbi")))
6941 (build-system r-build-system)
6943 `(("r-biobase" ,r-biobase)
6944 ("r-biocgenerics" ,r-biocgenerics)
6946 ("r-iranges" ,r-iranges)
6947 ("r-rsqlite" ,r-rsqlite)
6948 ("r-s4vectors" ,r-s4vectors)))
6949 (home-page "http://bioconductor.org/packages/AnnotationDbi")
6950 (synopsis "Annotation database interface")
6952 "This package provides user interface and database connection code for
6953 annotation data packages using SQLite data storage.")
6954 (license license:artistic2.0)))
6956 (define-public r-biomart
6962 (uri (bioconductor-uri "biomaRt" version))
6965 "0fhpbjlsgbqxrpj6nzhhk9q3ph81n5x4p7mmd097xjjn6b05w1d8"))))
6967 `((upstream-name . "biomaRt")))
6968 (build-system r-build-system)
6970 `(("r-annotationdbi" ,r-annotationdbi)
6971 ("r-rcurl" ,r-rcurl)
6973 (home-page "http://bioconductor.org/packages/biomaRt")
6974 (synopsis "Interface to BioMart databases")
6976 "biomaRt provides an interface to a growing collection of databases
6977 implementing the @url{BioMart software suite, http://www.biomart.org}. The
6978 package enables retrieval of large amounts of data in a uniform way without
6979 the need to know the underlying database schemas or write complex SQL queries.
6980 Examples of BioMart databases are Ensembl, COSMIC, Uniprot, HGNC, Gramene,
6981 Wormbase and dbSNP mapped to Ensembl. These major databases give biomaRt
6982 users direct access to a diverse set of data and enable a wide range of
6983 powerful online queries from gene annotation to database mining.")
6984 (license license:artistic2.0)))
6986 (define-public r-biocparallel
6988 (name "r-biocparallel")
6992 (uri (bioconductor-uri "BiocParallel" version))
6995 "08mdfxyk9nwz77v0xhlvs19p2wj0phgm5c5b25vm0xh3749njsp0"))))
6997 `((upstream-name . "BiocParallel")))
6998 (build-system r-build-system)
7000 `(("r-futile-logger" ,r-futile-logger)
7001 ("r-snow" ,r-snow)))
7002 (home-page "http://bioconductor.org/packages/BiocParallel")
7003 (synopsis "Bioconductor facilities for parallel evaluation")
7005 "This package provides modified versions and novel implementation of
7006 functions for parallel evaluation, tailored to use with Bioconductor
7008 (license (list license:gpl2+ license:gpl3+))))
7010 (define-public r-biostrings
7012 (name "r-biostrings")
7016 (uri (bioconductor-uri "Biostrings" version))
7019 "12c5abgshwq86357jr0r9039y6vl4d6ngysy89rsnr23ldnsirjp"))))
7021 `((upstream-name . "Biostrings")))
7022 (build-system r-build-system)
7024 `(("r-biocgenerics" ,r-biocgenerics)
7025 ("r-iranges" ,r-iranges)
7026 ("r-s4vectors" ,r-s4vectors)
7027 ("r-xvector" ,r-xvector)))
7028 (home-page "http://bioconductor.org/packages/Biostrings")
7029 (synopsis "String objects and algorithms for biological sequences")
7031 "This package provides memory efficient string containers, string
7032 matching algorithms, and other utilities, for fast manipulation of large
7033 biological sequences or sets of sequences.")
7034 (license license:artistic2.0)))
7036 (define-public r-rsamtools
7038 (name "r-rsamtools")
7042 (uri (bioconductor-uri "Rsamtools" version))
7045 "1zx6vhdz3lksbfy98jj3qzl7cxgspigm2pbsd5835b12r6mc5w6d"))))
7047 `((upstream-name . "Rsamtools")))
7048 (build-system r-build-system)
7051 (modify-phases %standard-phases
7052 (add-after 'unpack 'use-system-zlib
7054 (substitute* "DESCRIPTION"
7055 (("zlibbioc, ") ""))
7056 (substitute* "NAMESPACE"
7057 (("import\\(zlibbioc\\)") ""))
7062 `(("r-biocgenerics" ,r-biocgenerics)
7063 ("r-biocparallel" ,r-biocparallel)
7064 ("r-biostrings" ,r-biostrings)
7065 ("r-bitops" ,r-bitops)
7066 ("r-genomeinfodb" ,r-genomeinfodb)
7067 ("r-genomicranges" ,r-genomicranges)
7068 ("r-iranges" ,r-iranges)
7069 ("r-s4vectors" ,r-s4vectors)
7070 ("r-xvector" ,r-xvector)))
7071 (home-page "http://bioconductor.org/packages/release/bioc/html/Rsamtools.html")
7072 (synopsis "Interface to samtools, bcftools, and tabix")
7074 "This package provides an interface to the 'samtools', 'bcftools', and
7075 'tabix' utilities for manipulating SAM (Sequence Alignment / Map), FASTA,
7076 binary variant call (BCF) and compressed indexed tab-delimited (tabix)
7078 (license license:expat)))
7080 (define-public r-delayedarray
7082 (name "r-delayedarray")
7086 (uri (bioconductor-uri "DelayedArray" version))
7089 "02dfqp4md9xaqjj712ijc3jswghmipr5hwkd5hr0x1xi6l2fb69g"))))
7091 `((upstream-name . "DelayedArray")))
7092 (build-system r-build-system)
7094 `(("r-biocgenerics" ,r-biocgenerics)
7095 ("r-s4vectors" ,r-s4vectors)
7096 ("r-iranges" ,r-iranges)
7097 ("r-matrixstats" ,r-matrixstats)))
7098 (home-page "http://bioconductor.org/packages/DelayedArray")
7099 (synopsis "Delayed operations on array-like objects")
7101 "Wrapping an array-like object (typically an on-disk object) in a
7102 @code{DelayedArray} object allows one to perform common array operations on it
7103 without loading the object in memory. In order to reduce memory usage and
7104 optimize performance, operations on the object are either delayed or executed
7105 using a block processing mechanism. Note that this also works on in-memory
7106 array-like objects like @code{DataFrame} objects (typically with Rle columns),
7107 @code{Matrix} objects, and ordinary arrays and data frames.")
7108 (license license:artistic2.0)))
7110 (define-public r-summarizedexperiment
7112 (name "r-summarizedexperiment")
7116 (uri (bioconductor-uri "SummarizedExperiment" version))
7119 "0j7xn7pk52d383fb1wplcggacl2586c4zi0alkgfc3wz7qq9w13s"))))
7121 `((upstream-name . "SummarizedExperiment")))
7122 (build-system r-build-system)
7124 `(("r-biobase" ,r-biobase)
7125 ("r-biocgenerics" ,r-biocgenerics)
7126 ("r-delayedarray" ,r-delayedarray)
7127 ("r-genomeinfodb" ,r-genomeinfodb)
7128 ("r-genomicranges" ,r-genomicranges)
7129 ("r-iranges" ,r-iranges)
7130 ("r-matrix" ,r-matrix)
7131 ("r-s4vectors" ,r-s4vectors)))
7132 (home-page "http://bioconductor.org/packages/SummarizedExperiment")
7133 (synopsis "Container for representing genomic ranges by sample")
7135 "The SummarizedExperiment container contains one or more assays, each
7136 represented by a matrix-like object of numeric or other mode. The rows
7137 typically represent genomic ranges of interest and the columns represent
7139 (license license:artistic2.0)))
7141 (define-public r-genomicalignments
7143 (name "r-genomicalignments")
7147 (uri (bioconductor-uri "GenomicAlignments" version))
7150 "03ysxi9fdd3bcfj05iaysya9knn2aa2irwpypb5srg0xwv92bdb9"))))
7152 `((upstream-name . "GenomicAlignments")))
7153 (build-system r-build-system)
7155 `(("r-biocgenerics" ,r-biocgenerics)
7156 ("r-biocparallel" ,r-biocparallel)
7157 ("r-biostrings" ,r-biostrings)
7158 ("r-genomeinfodb" ,r-genomeinfodb)
7159 ("r-genomicranges" ,r-genomicranges)
7160 ("r-iranges" ,r-iranges)
7161 ("r-rsamtools" ,r-rsamtools)
7162 ("r-s4vectors" ,r-s4vectors)
7163 ("r-summarizedexperiment" ,r-summarizedexperiment)))
7164 (home-page "http://bioconductor.org/packages/GenomicAlignments")
7165 (synopsis "Representation and manipulation of short genomic alignments")
7167 "This package provides efficient containers for storing and manipulating
7168 short genomic alignments (typically obtained by aligning short reads to a
7169 reference genome). This includes read counting, computing the coverage,
7170 junction detection, and working with the nucleotide content of the
7172 (license license:artistic2.0)))
7174 (define-public r-rtracklayer
7176 (name "r-rtracklayer")
7180 (uri (bioconductor-uri "rtracklayer" version))
7183 "050q1rv04w31168ljr975vxva31n9lqdx84rnmsk6zcr6p640ffp"))))
7184 (build-system r-build-system)
7187 (modify-phases %standard-phases
7188 (add-after 'unpack 'use-system-zlib
7190 (substitute* "DESCRIPTION"
7191 (("zlibbioc, ") ""))
7192 (substitute* "NAMESPACE"
7193 (("import\\(zlibbioc\\)") ""))
7198 `(("r-biocgenerics" ,r-biocgenerics)
7199 ("r-biostrings" ,r-biostrings)
7200 ("r-genomeinfodb" ,r-genomeinfodb)
7201 ("r-genomicalignments" ,r-genomicalignments)
7202 ("r-genomicranges" ,r-genomicranges)
7203 ("r-iranges" ,r-iranges)
7204 ("r-rcurl" ,r-rcurl)
7205 ("r-rsamtools" ,r-rsamtools)
7206 ("r-s4vectors" ,r-s4vectors)
7208 ("r-xvector" ,r-xvector)))
7209 (home-page "http://bioconductor.org/packages/rtracklayer")
7210 (synopsis "R interface to genome browsers and their annotation tracks")
7212 "rtracklayer is an extensible framework for interacting with multiple
7213 genome browsers (currently UCSC built-in) and manipulating annotation tracks
7214 in various formats (currently GFF, BED, bedGraph, BED15, WIG, BigWig and 2bit
7215 built-in). The user may export/import tracks to/from the supported browsers,
7216 as well as query and modify the browser state, such as the current viewport.")
7217 (license license:artistic2.0)))
7219 (define-public r-genomicfeatures
7221 (name "r-genomicfeatures")
7225 (uri (bioconductor-uri "GenomicFeatures" version))
7228 "01ylvg275iy0cvsbxkbfxcf9pi9al597v5wnlqi2xdpmrcxyc3q0"))))
7230 `((upstream-name . "GenomicFeatures")))
7231 (build-system r-build-system)
7233 `(("r-annotationdbi" ,r-annotationdbi)
7234 ("r-biobase" ,r-biobase)
7235 ("r-biocgenerics" ,r-biocgenerics)
7236 ("r-biomart" ,r-biomart)
7237 ("r-biostrings" ,r-biostrings)
7239 ("r-genomeinfodb" ,r-genomeinfodb)
7240 ("r-genomicranges" ,r-genomicranges)
7241 ("r-iranges" ,r-iranges)
7242 ("r-rcurl" ,r-rcurl)
7243 ("r-rsqlite" ,r-rsqlite)
7244 ("r-rtracklayer" ,r-rtracklayer)
7245 ("r-s4vectors" ,r-s4vectors)
7246 ("r-xvector" ,r-xvector)))
7247 (home-page "http://bioconductor.org/packages/GenomicFeatures")
7248 (synopsis "Tools for working with transcript centric annotations")
7250 "This package provides a set of tools and methods for making and
7251 manipulating transcript centric annotations. With these tools the user can
7252 easily download the genomic locations of the transcripts, exons and cds of a
7253 given organism, from either the UCSC Genome Browser or a BioMart
7254 database (more sources will be supported in the future). This information is
7255 then stored in a local database that keeps track of the relationship between
7256 transcripts, exons, cds and genes. Flexible methods are provided for
7257 extracting the desired features in a convenient format.")
7258 (license license:artistic2.0)))
7260 (define-public r-go-db
7266 (uri (string-append "http://www.bioconductor.org/packages/"
7267 "release/data/annotation/src/contrib/GO.db_"
7271 "02cj8kqi5w39jwcs8gp1dgj08sah262ppxnkz4h3qd0w191y8yyl"))))
7273 `((upstream-name . "GO.db")))
7274 (build-system r-build-system)
7276 `(("r-annotationdbi" ,r-annotationdbi)))
7277 (home-page "http://bioconductor.org/packages/GO.db")
7278 (synopsis "Annotation maps describing the entire Gene Ontology")
7280 "The purpose of this GO.db annotation package is to provide detailed
7281 information about the latest version of the Gene Ontologies.")
7282 (license license:artistic2.0)))
7284 (define-public r-graph
7290 (uri (bioconductor-uri "graph" version))
7293 "0hx9wslnrci7c5i1gd1zlpjmgrkdnx9gabfgmzzwfnykk1mdvvna"))))
7294 (build-system r-build-system)
7296 `(("r-biocgenerics" ,r-biocgenerics)))
7297 (home-page "http://bioconductor.org/packages/graph")
7298 (synopsis "Handle graph data structures in R")
7300 "This package implements some simple graph handling capabilities for R.")
7301 (license license:artistic2.0)))
7303 (define-public r-topgo
7309 (uri (bioconductor-uri "topGO" version))
7312 "04kvxz9qsxfz0np7wlrzp4r95nykz94x7mqpyyk76f90g6m66vcc"))))
7314 `((upstream-name . "topGO")))
7315 (build-system r-build-system)
7317 `(("r-annotationdbi" ,r-annotationdbi)
7319 ("r-biobase" ,r-biobase)
7320 ("r-biocgenerics" ,r-biocgenerics)
7321 ("r-go-db" ,r-go-db)
7322 ("r-graph" ,r-graph)
7323 ("r-lattice" ,r-lattice)
7324 ("r-matrixstats" ,r-matrixstats)
7325 ("r-sparsem" ,r-sparsem)))
7326 (home-page "http://bioconductor.org/packages/topGO")
7327 (synopsis "Enrichment analysis for gene ontology")
7329 "The topGO package provides tools for testing @dfn{gene ontology} (GO)
7330 terms while accounting for the topology of the GO graph. Different test
7331 statistics and different methods for eliminating local similarities and
7332 dependencies between GO terms can be implemented and applied.")
7333 ;; Any version of the LGPL applies.
7334 (license license:lgpl2.1+)))
7336 (define-public r-bsgenome
7342 (uri (bioconductor-uri "BSgenome" version))
7345 "18dlknwk3xvi52hamxf9pl5bjc5806mpw98xwvx5xajn8mrxiy5h"))))
7347 `((upstream-name . "BSgenome")))
7348 (build-system r-build-system)
7350 `(("r-biocgenerics" ,r-biocgenerics)
7351 ("r-biostrings" ,r-biostrings)
7352 ("r-genomeinfodb" ,r-genomeinfodb)
7353 ("r-genomicranges" ,r-genomicranges)
7354 ("r-iranges" ,r-iranges)
7355 ("r-rsamtools" ,r-rsamtools)
7356 ("r-rtracklayer" ,r-rtracklayer)
7357 ("r-s4vectors" ,r-s4vectors)
7358 ("r-xvector" ,r-xvector)))
7359 (home-page "http://bioconductor.org/packages/BSgenome")
7360 (synopsis "Infrastructure for Biostrings-based genome data packages")
7362 "This package provides infrastructure shared by all Biostrings-based
7363 genome data packages and support for efficient SNP representation.")
7364 (license license:artistic2.0)))
7366 (define-public r-bsgenome-hsapiens-1000genomes-hs37d5
7368 (name "r-bsgenome-hsapiens-1000genomes-hs37d5")
7372 ;; We cannot use bioconductor-uri here because this tarball is
7373 ;; located under "data/annotation/" instead of "bioc/".
7374 (uri (string-append "http://www.bioconductor.org/packages/"
7375 "release/data/annotation/src/contrib/"
7376 "BSgenome.Hsapiens.1000genomes.hs37d5_"
7380 "1cg0g5fqmsvwyw2p9hp2yy4ilk21jkbbrnpgqvb5c36ihjwvc7sr"))))
7382 `((upstream-name . "BSgenome.Hsapiens.1000genomes.hs37d5")))
7383 (build-system r-build-system)
7384 ;; As this package provides little more than a very large data file it
7385 ;; doesn't make sense to build substitutes.
7386 (arguments `(#:substitutable? #f))
7388 `(("r-bsgenome" ,r-bsgenome)))
7390 "http://www.bioconductor.org/packages/BSgenome.Hsapiens.1000genomes.hs37d5/")
7391 (synopsis "Full genome sequences for Homo sapiens")
7393 "This package provides full genome sequences for Homo sapiens from
7394 1000genomes phase2 reference genome sequence (hs37d5), based on NCBI GRCh37.")
7395 (license license:artistic2.0)))
7397 (define-public r-impute
7403 (uri (bioconductor-uri "impute" version))
7406 "0va45vfixy3np549md87h3b3rbavm54gfnmnjhpr9hf02lll6zxs"))))
7408 `(("gfortran" ,gfortran)))
7409 (build-system r-build-system)
7410 (home-page "http://bioconductor.org/packages/impute")
7411 (synopsis "Imputation for microarray data")
7413 "This package provides a function to impute missing gene expression
7414 microarray data, using nearest neighbor averaging.")
7415 (license license:gpl2+)))
7417 (define-public r-seqpattern
7419 (name "r-seqpattern")
7423 (uri (bioconductor-uri "seqPattern" version))
7426 "0yw5251sirv3283xgmfmfbf900xp8dwvqfk88mr945s3by5hx99v"))))
7428 `((upstream-name . "seqPattern")))
7429 (build-system r-build-system)
7431 `(("r-biostrings" ,r-biostrings)
7432 ("r-genomicranges" ,r-genomicranges)
7433 ("r-iranges" ,r-iranges)
7434 ("r-kernsmooth" ,r-kernsmooth)
7435 ("r-plotrix" ,r-plotrix)))
7436 (home-page "http://bioconductor.org/packages/seqPattern")
7437 (synopsis "Visualising oligonucleotide patterns and motif occurrences")
7439 "This package provides tools to visualize oligonucleotide patterns and
7440 sequence motif occurrences across a large set of sequences centred at a common
7441 reference point and sorted by a user defined feature.")
7442 (license license:gpl3+)))
7444 (define-public r-genomation
7446 (name "r-genomation")
7450 (uri (bioconductor-uri "genomation" version))
7453 "0r71nf8p3aq3yffqxg4yir1zmm7rar5a57nmy1kpqpn8kaf2svjl"))))
7454 (build-system r-build-system)
7456 `(("r-biostrings" ,r-biostrings)
7457 ("r-bsgenome" ,r-bsgenome)
7458 ("r-data-table" ,r-data-table)
7459 ("r-genomeinfodb" ,r-genomeinfodb)
7460 ("r-genomicalignments" ,r-genomicalignments)
7461 ("r-genomicranges" ,r-genomicranges)
7462 ("r-ggplot2" ,r-ggplot2)
7463 ("r-gridbase" ,r-gridbase)
7464 ("r-impute" ,r-impute)
7465 ("r-iranges" ,r-iranges)
7466 ("r-matrixstats" ,r-matrixstats)
7467 ("r-plotrix" ,r-plotrix)
7470 ("r-readr" ,r-readr)
7471 ("r-reshape2" ,r-reshape2)
7472 ("r-rhtslib" ,r-rhtslib)
7473 ("r-rsamtools" ,r-rsamtools)
7474 ("r-rtracklayer" ,r-rtracklayer)
7475 ("r-runit" ,r-runit)
7476 ("r-s4vectors" ,r-s4vectors)
7477 ("r-seqpattern" ,r-seqpattern)))
7480 (home-page "http://bioinformatics.mdc-berlin.de/genomation/")
7481 (synopsis "Summary, annotation and visualization of genomic data")
7483 "This package provides a package for summary and annotation of genomic
7484 intervals. Users can visualize and quantify genomic intervals over
7485 pre-defined functional regions, such as promoters, exons, introns, etc. The
7486 genomic intervals represent regions with a defined chromosome position, which
7487 may be associated with a score, such as aligned reads from HT-seq experiments,
7488 TF binding sites, methylation scores, etc. The package can use any tabular
7489 genomic feature data as long as it has minimal information on the locations of
7490 genomic intervals. In addition, it can use BAM or BigWig files as input.")
7491 (license license:artistic2.0)))
7493 (define-public r-genomationdata
7495 (name "r-genomationdata")
7499 ;; We cannot use bioconductor-uri here because this tarball is
7500 ;; located under "data/annotation/" instead of "bioc/".
7501 (uri (string-append "https://bioconductor.org/packages/"
7502 "release/data/experiment/src/contrib/"
7503 "genomationData_" version ".tar.gz"))
7506 "16dqwb7wx1igx77zdbcskx5m1hs4g4gp2hl56zzm70hcagnlkz8y"))))
7507 (build-system r-build-system)
7508 ;; As this package provides little more than large data files, it doesn't
7509 ;; make sense to build substitutes.
7510 (arguments `(#:substitutable? #f))
7512 `(("r-knitr" ,r-knitr)))
7513 (home-page "http://bioinformatics.mdc-berlin.de/genomation/")
7514 (synopsis "Experimental data for use with the genomation package")
7516 "This package contains experimental genetic data for use with the
7517 genomation package. Included are Chip Seq, Methylation and Cage data,
7518 downloaded from Encode.")
7519 (license license:gpl3+)))
7521 (define-public r-org-hs-eg-db
7523 (name "r-org-hs-eg-db")
7527 ;; We cannot use bioconductor-uri here because this tarball is
7528 ;; located under "data/annotation/" instead of "bioc/".
7529 (uri (string-append "http://www.bioconductor.org/packages/"
7530 "release/data/annotation/src/contrib/"
7531 "org.Hs.eg.db_" version ".tar.gz"))
7534 "19mg64pw8zcvb9yxzzyf7caz1kvdrkfsj1hd84bzq7crrh8kc4y6"))))
7536 `((upstream-name . "org.Hs.eg.db")))
7537 (build-system r-build-system)
7539 `(("r-annotationdbi" ,r-annotationdbi)))
7540 (home-page "http://www.bioconductor.org/packages/org.Hs.eg.db/")
7541 (synopsis "Genome wide annotation for Human")
7543 "This package provides mappings from Entrez gene identifiers to various
7544 annotations for the human genome.")
7545 (license license:artistic2.0)))
7547 (define-public r-org-ce-eg-db
7549 (name "r-org-ce-eg-db")
7553 ;; We cannot use bioconductor-uri here because this tarball is
7554 ;; located under "data/annotation/" instead of "bioc/".
7555 (uri (string-append "http://www.bioconductor.org/packages/"
7556 "release/data/annotation/src/contrib/"
7557 "org.Ce.eg.db_" version ".tar.gz"))
7560 "12llfzrrc09kj2wzbisdspv38qzkzgpsbn8kv7qkwg746k3pq436"))))
7562 `((upstream-name . "org.Ce.eg.db")))
7563 (build-system r-build-system)
7565 `(("r-annotationdbi" ,r-annotationdbi)))
7566 (home-page "http://www.bioconductor.org/packages/org.Ce.eg.db/")
7567 (synopsis "Genome wide annotation for Worm")
7569 "This package provides mappings from Entrez gene identifiers to various
7570 annotations for the genome of the model worm Caenorhabditis elegans.")
7571 (license license:artistic2.0)))
7573 (define-public r-org-dm-eg-db
7575 (name "r-org-dm-eg-db")
7579 ;; We cannot use bioconductor-uri here because this tarball is
7580 ;; located under "data/annotation/" instead of "bioc/".
7581 (uri (string-append "http://www.bioconductor.org/packages/"
7582 "release/data/annotation/src/contrib/"
7583 "org.Dm.eg.db_" version ".tar.gz"))
7586 "1vzbphbrh1cf7xi5cksia9xy9a9l42js2z2qsajvjxvddiphrb7j"))))
7588 `((upstream-name . "org.Dm.eg.db")))
7589 (build-system r-build-system)
7591 `(("r-annotationdbi" ,r-annotationdbi)))
7592 (home-page "http://www.bioconductor.org/packages/org.Dm.eg.db/")
7593 (synopsis "Genome wide annotation for Fly")
7595 "This package provides mappings from Entrez gene identifiers to various
7596 annotations for the genome of the model fruit fly Drosophila melanogaster.")
7597 (license license:artistic2.0)))
7599 (define-public r-org-mm-eg-db
7601 (name "r-org-mm-eg-db")
7605 ;; We cannot use bioconductor-uri here because this tarball is
7606 ;; located under "data/annotation/" instead of "bioc/".
7607 (uri (string-append "http://www.bioconductor.org/packages/"
7608 "release/data/annotation/src/contrib/"
7609 "org.Mm.eg.db_" version ".tar.gz"))
7612 "1lykjqjaf01fmgg3cvfcvwd5xjq6zc5vbxnm5r4l32fzvl89q50c"))))
7614 `((upstream-name . "org.Mm.eg.db")))
7615 (build-system r-build-system)
7617 `(("r-annotationdbi" ,r-annotationdbi)))
7618 (home-page "http://www.bioconductor.org/packages/org.Mm.eg.db/")
7619 (synopsis "Genome wide annotation for Mouse")
7621 "This package provides mappings from Entrez gene identifiers to various
7622 annotations for the genome of the model mouse Mus musculus.")
7623 (license license:artistic2.0)))
7625 (define-public r-seqlogo
7632 (uri (bioconductor-uri "seqLogo" version))
7635 "19d5zmy7m8svljwgbmrb4vxkq18slq0f3all6k2ayv42b8w44h6q"))))
7636 (properties `((upstream-name . "seqLogo")))
7637 (build-system r-build-system)
7638 (home-page "http://bioconductor.org/packages/seqLogo")
7639 (synopsis "Sequence logos for DNA sequence alignments")
7641 "seqLogo takes the position weight matrix of a DNA sequence motif and
7642 plots the corresponding sequence logo as introduced by Schneider and
7644 (license license:lgpl2.0+)))
7646 (define-public r-bsgenome-hsapiens-ucsc-hg19
7648 (name "r-bsgenome-hsapiens-ucsc-hg19")
7652 ;; We cannot use bioconductor-uri here because this tarball is
7653 ;; located under "data/annotation/" instead of "bioc/".
7654 (uri (string-append "http://www.bioconductor.org/packages/"
7655 "release/data/annotation/src/contrib/"
7656 "BSgenome.Hsapiens.UCSC.hg19_"
7660 "1y0nqpk8cw5a34sd9hmin3z4v7iqm6hf6l22cl81vlbxqbjibxc8"))))
7662 `((upstream-name . "BSgenome.Hsapiens.UCSC.hg19")))
7663 (build-system r-build-system)
7664 ;; As this package provides little more than a very large data file it
7665 ;; doesn't make sense to build substitutes.
7666 (arguments `(#:substitutable? #f))
7668 `(("r-bsgenome" ,r-bsgenome)))
7670 "http://www.bioconductor.org/packages/BSgenome.Hsapiens.UCSC.hg19/")
7671 (synopsis "Full genome sequences for Homo sapiens")
7673 "This package provides full genome sequences for Homo sapiens as provided
7674 by UCSC (hg19, February 2009) and stored in Biostrings objects.")
7675 (license license:artistic2.0)))
7677 (define-public r-bsgenome-mmusculus-ucsc-mm9
7679 (name "r-bsgenome-mmusculus-ucsc-mm9")
7683 ;; We cannot use bioconductor-uri here because this tarball is
7684 ;; located under "data/annotation/" instead of "bioc/".
7685 (uri (string-append "http://www.bioconductor.org/packages/"
7686 "release/data/annotation/src/contrib/"
7687 "BSgenome.Mmusculus.UCSC.mm9_"
7691 "1birqw30g2azimxpnjfzmkphan7x131yy8b9h85lfz5fjdg7841i"))))
7693 `((upstream-name . "BSgenome.Mmusculus.UCSC.mm9")))
7694 (build-system r-build-system)
7695 ;; As this package provides little more than a very large data file it
7696 ;; doesn't make sense to build substitutes.
7697 (arguments `(#:substitutable? #f))
7699 `(("r-bsgenome" ,r-bsgenome)))
7701 "http://www.bioconductor.org/packages/BSgenome.Mmusculus.UCSC.mm9/")
7702 (synopsis "Full genome sequences for Mouse")
7704 "This package provides full genome sequences for Mus musculus (Mouse) as
7705 provided by UCSC (mm9, July 2007) and stored in Biostrings objects.")
7706 (license license:artistic2.0)))
7708 (define-public r-bsgenome-mmusculus-ucsc-mm10
7710 (name "r-bsgenome-mmusculus-ucsc-mm10")
7714 ;; We cannot use bioconductor-uri here because this tarball is
7715 ;; located under "data/annotation/" instead of "bioc/".
7716 (uri (string-append "http://www.bioconductor.org/packages/"
7717 "release/data/annotation/src/contrib/"
7718 "BSgenome.Mmusculus.UCSC.mm10_"
7722 "12s0nm2na9brjad4rn9l7d3db2aj8qa1xvz0y1k7gk08wayb6bkf"))))
7724 `((upstream-name . "BSgenome.Mmusculus.UCSC.mm10")))
7725 (build-system r-build-system)
7726 ;; As this package provides little more than a very large data file it
7727 ;; doesn't make sense to build substitutes.
7728 (arguments `(#:substitutable? #f))
7730 `(("r-bsgenome" ,r-bsgenome)))
7732 "http://www.bioconductor.org/packages/BSgenome.Mmusculus.UCSC.mm10/")
7733 (synopsis "Full genome sequences for Mouse")
7735 "This package provides full genome sequences for Mus
7736 musculus (Mouse) as provided by UCSC (mm10, December 2011) and stored
7737 in Biostrings objects.")
7738 (license license:artistic2.0)))
7740 (define-public r-txdb-mmusculus-ucsc-mm10-knowngene
7742 (name "r-txdb-mmusculus-ucsc-mm10-knowngene")
7746 ;; We cannot use bioconductor-uri here because this tarball is
7747 ;; located under "data/annotation/" instead of "bioc/".
7748 (uri (string-append "http://www.bioconductor.org/packages/"
7749 "release/data/annotation/src/contrib/"
7750 "TxDb.Mmusculus.UCSC.mm10.knownGene_"
7754 "08gava9wsvpcqz51k2sni3pj03n5155v32d9riqbf305nbirqbkb"))))
7756 `((upstream-name . "TxDb.Mmusculus.UCSC.mm10.knownGene")))
7757 (build-system r-build-system)
7758 ;; As this package provides little more than a very large data file it
7759 ;; doesn't make sense to build substitutes.
7760 (arguments `(#:substitutable? #f))
7762 `(("r-bsgenome" ,r-bsgenome)
7763 ("r-genomicfeatures" ,r-genomicfeatures)
7764 ("r-annotationdbi" ,r-annotationdbi)))
7766 "http://bioconductor.org/packages/TxDb.Mmusculus.UCSC.mm10.knownGene/")
7767 (synopsis "Annotation package for TxDb knownGene object(s) for Mouse")
7769 "This package loads a TxDb object, which is an R interface to
7770 prefabricated databases contained in this package. This package provides
7771 the TxDb object of Mouse data as provided by UCSC (mm10, December 2011)
7772 based on the knownGene track.")
7773 (license license:artistic2.0)))
7775 (define-public r-bsgenome-celegans-ucsc-ce6
7777 (name "r-bsgenome-celegans-ucsc-ce6")
7781 ;; We cannot use bioconductor-uri here because this tarball is
7782 ;; located under "data/annotation/" instead of "bioc/".
7783 (uri (string-append "http://www.bioconductor.org/packages/"
7784 "release/data/annotation/src/contrib/"
7785 "BSgenome.Celegans.UCSC.ce6_"
7789 "0mqzb353xv2c3m3vkb315dkmnxkgczp7ndnknyhpgjlybyf715v9"))))
7791 `((upstream-name . "BSgenome.Celegans.UCSC.ce6")))
7792 (build-system r-build-system)
7793 ;; As this package provides little more than a very large data file it
7794 ;; doesn't make sense to build substitutes.
7795 (arguments `(#:substitutable? #f))
7797 `(("r-bsgenome" ,r-bsgenome)))
7799 "http://www.bioconductor.org/packages/BSgenome.Celegans.UCSC.ce6/")
7800 (synopsis "Full genome sequences for Worm")
7802 "This package provides full genome sequences for Caenorhabditis
7803 elegans (Worm) as provided by UCSC (ce6, May 2008) and stored in Biostrings
7805 (license license:artistic2.0)))
7807 (define-public r-bsgenome-celegans-ucsc-ce10
7809 (name "r-bsgenome-celegans-ucsc-ce10")
7813 ;; We cannot use bioconductor-uri here because this tarball is
7814 ;; located under "data/annotation/" instead of "bioc/".
7815 (uri (string-append "http://www.bioconductor.org/packages/"
7816 "release/data/annotation/src/contrib/"
7817 "BSgenome.Celegans.UCSC.ce10_"
7821 "1zaym97jk4npxk14ifvwz2rvhm4zx9xgs33r9vvx9rlynp0gydrk"))))
7823 `((upstream-name . "BSgenome.Celegans.UCSC.ce10")))
7824 (build-system r-build-system)
7825 ;; As this package provides little more than a very large data file it
7826 ;; doesn't make sense to build substitutes.
7827 (arguments `(#:substitutable? #f))
7829 `(("r-bsgenome" ,r-bsgenome)))
7831 "http://www.bioconductor.org/packages/BSgenome.Celegans.UCSC.ce10/")
7832 (synopsis "Full genome sequences for Worm")
7834 "This package provides full genome sequences for Caenorhabditis
7835 elegans (Worm) as provided by UCSC (ce10, Oct 2010) and stored in Biostrings
7837 (license license:artistic2.0)))
7839 (define-public r-bsgenome-dmelanogaster-ucsc-dm3
7841 (name "r-bsgenome-dmelanogaster-ucsc-dm3")
7845 ;; We cannot use bioconductor-uri here because this tarball is
7846 ;; located under "data/annotation/" instead of "bioc/".
7847 (uri (string-append "http://www.bioconductor.org/packages/"
7848 "release/data/annotation/src/contrib/"
7849 "BSgenome.Dmelanogaster.UCSC.dm3_"
7853 "19bm3lkhhkag3gnwp419211fh0cnr0x6fa0r1lr0ycwrikxdxsv8"))))
7855 `((upstream-name . "BSgenome.Dmelanogaster.UCSC.dm3")))
7856 (build-system r-build-system)
7857 ;; As this package provides little more than a very large data file it
7858 ;; doesn't make sense to build substitutes.
7859 (arguments `(#:substitutable? #f))
7861 `(("r-bsgenome" ,r-bsgenome)))
7863 "http://www.bioconductor.org/packages/BSgenome.Dmelanogaster.UCSC.dm3/")
7864 (synopsis "Full genome sequences for Fly")
7866 "This package provides full genome sequences for Drosophila
7867 melanogaster (Fly) as provided by UCSC (dm3, April 2006) and stored in
7868 Biostrings objects.")
7869 (license license:artistic2.0)))
7871 (define-public r-motifrg
7878 (uri (bioconductor-uri "motifRG" version))
7881 "0lxxpqyljiyk73vyq6ss46q13g81pm24q87mkzdsqlr5zx427ch6"))))
7882 (properties `((upstream-name . "motifRG")))
7883 (build-system r-build-system)
7885 `(("r-biostrings" ,r-biostrings)
7886 ("r-bsgenome" ,r-bsgenome)
7887 ("r-bsgenome.hsapiens.ucsc.hg19" ,r-bsgenome-hsapiens-ucsc-hg19)
7888 ("r-iranges" ,r-iranges)
7889 ("r-seqlogo" ,r-seqlogo)
7890 ("r-xvector" ,r-xvector)))
7891 (home-page "http://bioconductor.org/packages/motifRG")
7892 (synopsis "Discover motifs in high throughput sequencing data")
7894 "This package provides tools for discriminative motif discovery in high
7895 throughput genetic sequencing data sets using regression methods.")
7896 (license license:artistic2.0)))
7898 (define-public r-qtl
7905 (uri (string-append "mirror://cran/src/contrib/qtl_"
7909 "067az4v432zxp6lxck8d7vlh9w4r13r0mvw5zsglyaqwsh3d9sad"))))
7910 (build-system r-build-system)
7911 (home-page "http://rqtl.org/")
7912 (synopsis "R package for analyzing QTL experiments in genetics")
7913 (description "R/qtl is an extension library for the R statistics
7914 system. It is used to analyze experimental crosses for identifying
7915 genes contributing to variation in quantitative traits (so-called
7916 quantitative trait loci, QTLs).
7918 Using a hidden Markov model, R/qtl allows to estimate genetic maps, to
7919 identify genotyping errors, and to perform single-QTL and two-QTL,
7920 two-dimensional genome scans.")
7921 (license license:gpl3)))
7923 (define-public r-zlibbioc
7929 (uri (bioconductor-uri "zlibbioc" version))
7932 "1kdgwwlh39mgwzj3zq71za4iv40sq625ghnyrndv5wrivrcr2igv"))))
7934 `((upstream-name . "zlibbioc")))
7935 (build-system r-build-system)
7936 (home-page "https://bioconductor.org/packages/zlibbioc")
7937 (synopsis "Provider for zlib-1.2.5 to R packages")
7938 (description "This package uses the source code of zlib-1.2.5 to create
7939 libraries for systems that do not have these available via other means.")
7940 (license license:artistic2.0)))
7942 (define-public r-r4rna
7949 (uri (string-append "http://www.e-rna.org/r-chie/files/R4RNA_"
7953 "1p0i78wh76jfgmn9jphbwwaz6yy6pipzfg08xs54cxavxg2j81p5"))))
7954 (build-system r-build-system)
7956 `(("r-optparse" ,r-optparse)
7957 ("r-rcolorbrewer" ,r-rcolorbrewer)))
7958 (home-page "http://www.e-rna.org/r-chie/index.cgi")
7959 (synopsis "Analysis framework for RNA secondary structure")
7961 "The R4RNA package aims to be a general framework for the analysis of RNA
7962 secondary structure and comparative analysis in R.")
7963 (license license:gpl3+)))
7965 (define-public r-rhtslib
7972 (uri (bioconductor-uri "Rhtslib" version))
7975 "0jj5h81z5gyf4j3lp2l3zsm6pgbmalgrngr8qdpygc20phndpp0b"))))
7976 (properties `((upstream-name . "Rhtslib")))
7977 (build-system r-build-system)
7979 `(("r-zlibbioc" ,r-zlibbioc)))
7983 `(("autoconf" ,autoconf)))
7984 (home-page "https://github.com/nhayden/Rhtslib")
7985 (synopsis "High-throughput sequencing library as an R package")
7987 "This package provides the HTSlib C library for high-throughput
7988 nucleotide sequence analysis. The package is primarily useful to developers
7989 of other R packages who wish to make use of HTSlib.")
7990 (license license:lgpl2.0+)))
7992 (define-public r-bamsignals
7994 (name "r-bamsignals")
7999 (uri (bioconductor-uri "bamsignals" version))
8002 "0knx69zzdaak2sjim8k9mygmcjxpa705m8013ld5zwpgi8dag9mc"))))
8003 (build-system r-build-system)
8005 `(("r-biocgenerics" ,r-biocgenerics)
8006 ("r-genomicranges" ,r-genomicranges)
8007 ("r-iranges" ,r-iranges)
8009 ("r-rhtslib" ,r-rhtslib)
8010 ("r-zlibbioc" ,r-zlibbioc)))
8013 (home-page "http://bioconductor.org/packages/bamsignals")
8014 (synopsis "Extract read count signals from bam files")
8016 "This package allows to efficiently obtain count vectors from indexed bam
8017 files. It counts the number of nucleotide sequence reads in given genomic
8018 ranges and it computes reads profiles and coverage profiles. It also handles
8020 (license license:gpl2+)))
8022 (define-public r-rcas
8028 (uri (string-append "https://github.com/BIMSBbioinfo/RCAS/archive/v"
8030 (file-name (string-append name "-" version ".tar.gz"))
8033 "1qgc7vi6fpzl440yg7jhiycg5q336kd4pxqzx10yx2zcq3bq3msg"))))
8034 (build-system r-build-system)
8036 `(("r-knitr" ,r-knitr)
8037 ("r-testthat" ,r-testthat)
8038 ;; During vignette building knitr checks that "pandoc-citeproc"
8040 ("ghc-pandoc-citeproc" ,ghc-pandoc-citeproc)))
8042 `(("r-data-table" ,r-data-table)
8043 ("r-biomart" ,r-biomart)
8044 ("r-org-hs-eg-db" ,r-org-hs-eg-db)
8045 ("r-org-ce-eg-db" ,r-org-ce-eg-db)
8046 ("r-org-dm-eg-db" ,r-org-dm-eg-db)
8047 ("r-org-mm-eg-db" ,r-org-mm-eg-db)
8048 ("r-bsgenome-hsapiens-ucsc-hg19" ,r-bsgenome-hsapiens-ucsc-hg19)
8049 ("r-bsgenome-mmusculus-ucsc-mm9" ,r-bsgenome-mmusculus-ucsc-mm9)
8050 ("r-bsgenome-celegans-ucsc-ce10" ,r-bsgenome-celegans-ucsc-ce10)
8051 ("r-bsgenome-dmelanogaster-ucsc-dm3" ,r-bsgenome-dmelanogaster-ucsc-dm3)
8052 ("r-topgo" ,r-topgo)
8054 ("r-pbapply" ,r-pbapply)
8055 ("r-plotly" ,r-plotly)
8056 ("r-plotrix" ,r-plotrix)
8057 ("r-motifrg" ,r-motifrg)
8058 ("r-genomation" ,r-genomation)
8059 ("r-genomicfeatures" ,r-genomicfeatures)
8060 ("r-rtracklayer" ,r-rtracklayer)
8061 ("r-rmarkdown" ,r-rmarkdown)))
8062 (synopsis "RNA-centric annotation system")
8064 "RCAS aims to be a standalone RNA-centric annotation system that provides
8065 intuitive reports and publication-ready graphics. This package provides the R
8066 library implementing most of the pipeline's features.")
8067 (home-page "https://github.com/BIMSBbioinfo/RCAS")
8068 (license license:artistic2.0)))
8070 (define-public rcas-web
8077 (uri (string-append "https://github.com/BIMSBbioinfo/rcas-web/"
8078 "releases/download/v" version
8079 "/rcas-web-" version ".tar.gz"))
8082 "0d3my0g8i7js59n184zzzjdki7hgmhpi4rhfvk7i6jsw01ba04qq"))))
8083 (build-system gnu-build-system)
8086 (modify-phases %standard-phases
8087 (add-after 'install 'wrap-executable
8088 (lambda* (#:key inputs outputs #:allow-other-keys)
8089 (let* ((out (assoc-ref outputs "out"))
8090 (json (assoc-ref inputs "guile-json"))
8091 (redis (assoc-ref inputs "guile-redis"))
8092 (path (string-append
8093 json "/share/guile/site/2.2:"
8094 redis "/share/guile/site/2.2")))
8095 (wrap-program (string-append out "/bin/rcas-web")
8096 `("GUILE_LOAD_PATH" ":" = (,path))
8097 `("GUILE_LOAD_COMPILED_PATH" ":" = (,path))
8098 `("R_LIBS_SITE" ":" = (,(getenv "R_LIBS_SITE")))))
8101 `(("r-minimal" ,r-minimal)
8103 ("guile-next" ,guile-2.2)
8104 ("guile-json" ,guile-json)
8105 ("guile-redis" ,guile2.2-redis)))
8107 `(("pkg-config" ,pkg-config)))
8108 (home-page "https://github.com/BIMSBbioinfo/rcas-web")
8109 (synopsis "Web interface for RNA-centric annotation system (RCAS)")
8110 (description "This package provides a simple web interface for the
8111 @dfn{RNA-centric annotation system} (RCAS).")
8112 (license license:agpl3+)))
8114 (define-public r-mutationalpatterns
8116 (name "r-mutationalpatterns")
8121 (uri (bioconductor-uri "MutationalPatterns" version))
8124 "1s50diwh1j6vg3mgahh6bczvq74mfdbmwjrad4d5lh723gnc5pjg"))))
8125 (build-system r-build-system)
8127 `(("r-biocgenerics" ,r-biocgenerics)
8128 ("r-biostrings" ,r-biostrings)
8129 ("r-bsgenome-hsapiens-1000g" ,r-bsgenome-hsapiens-1000genomes-hs37d5)
8130 ("r-bsgenome-hsapiens-ucsc-hg19" ,r-bsgenome-hsapiens-ucsc-hg19)
8131 ("r-genomicranges" ,r-genomicranges)
8132 ("r-genomeinfodb" ,r-genomeinfodb)
8133 ("r-ggplot2" ,r-ggplot2)
8134 ("r-gridextra" ,r-gridextra)
8135 ("r-iranges" ,r-iranges)
8138 ("r-pracma" ,r-pracma)
8139 ("r-reshape2" ,r-reshape2)
8140 ("r-summarizedexperiment" ,r-summarizedexperiment)
8141 ("r-variantannotation" ,r-variantannotation)))
8142 (home-page "http://bioconductor.org/packages/MutationalPatterns/")
8143 (synopsis "Extract and visualize mutational patterns in genomic data")
8144 (description "This package provides an extensive toolset for the
8145 characterization and visualization of a wide range of mutational patterns
8146 in SNV base substitution data.")
8147 (license license:expat)))
8149 (define-public r-wgcna
8156 (uri (cran-uri "WGCNA" version))
8159 "1vrc2k33a196hrrl7k0z534fp96vv0shmigcr65ny1q0v6lq0h6i"))))
8160 (properties `((upstream-name . "WGCNA")))
8161 (build-system r-build-system)
8163 `(("r-annotationdbi" ,r-annotationdbi)
8164 ("r-doparallel" ,r-doparallel)
8165 ("r-dynamictreecut" ,r-dynamictreecut)
8166 ("r-fastcluster" ,r-fastcluster)
8167 ("r-foreach" ,r-foreach)
8168 ("r-go-db" ,r-go-db)
8169 ("r-hmisc" ,r-hmisc)
8170 ("r-impute" ,r-impute)
8172 ("r-robust" ,r-robust)
8173 ("r-survival" ,r-survival)
8174 ("r-matrixstats" ,r-matrixstats)
8175 ("r-preprocesscore" ,r-preprocesscore)))
8177 "http://www.genetics.ucla.edu/labs/horvath/CoexpressionNetwork/Rpackages/WGCNA/")
8178 (synopsis "Weighted correlation network analysis")
8180 "This package provides functions necessary to perform Weighted
8181 Correlation Network Analysis on high-dimensional data. It includes functions
8182 for rudimentary data cleaning, construction and summarization of correlation
8183 networks, module identification and functions for relating both variables and
8184 modules to sample traits. It also includes a number of utility functions for
8185 data manipulation and visualization.")
8186 (license license:gpl2+)))
8188 (define-public r-chipkernels
8189 (let ((commit "c9cfcacb626b1221094fb3490ea7bac0fd625372")
8192 (name "r-chipkernels")
8193 (version (string-append "1.1-" revision "." (string-take commit 9)))
8198 (url "https://github.com/ManuSetty/ChIPKernels.git")
8200 (file-name (string-append name "-" version))
8203 "14bj5qhjm1hsm9ay561nfbqi9wxsa7y487df2idsaaf6z10nw4v0"))))
8204 (build-system r-build-system)
8206 `(("r-iranges" ,r-iranges)
8207 ("r-xvector" ,r-xvector)
8208 ("r-biostrings" ,r-biostrings)
8209 ("r-bsgenome" ,r-bsgenome)
8210 ("r-gtools" ,r-gtools)
8211 ("r-genomicranges" ,r-genomicranges)
8212 ("r-sfsmisc" ,r-sfsmisc)
8213 ("r-kernlab" ,r-kernlab)
8214 ("r-s4vectors" ,r-s4vectors)
8215 ("r-biocgenerics" ,r-biocgenerics)))
8216 (home-page "https://github.com/ManuSetty/ChIPKernels")
8217 (synopsis "Build string kernels for DNA Sequence analysis")
8218 (description "ChIPKernels is an R package for building different string
8219 kernels used for DNA Sequence analysis. A dictionary of the desired kernel
8220 must be built and this dictionary can be used for determining kernels for DNA
8222 (license license:gpl2+))))
8224 (define-public r-seqgl
8231 (uri (string-append "https://github.com/ManuSetty/SeqGL/"
8232 "archive/" version ".tar.gz"))
8233 (file-name (string-append name "-" version ".tar.gz"))
8236 "0pnk1p3sci5yipyc8xnb6jbmydpl80fld927xgnbcv104hy8h8yh"))))
8237 (build-system r-build-system)
8239 `(("r-biostrings" ,r-biostrings)
8240 ("r-chipkernels" ,r-chipkernels)
8241 ("r-genomicranges" ,r-genomicranges)
8242 ("r-spams" ,r-spams)
8243 ("r-wgcna" ,r-wgcna)
8244 ("r-fastcluster" ,r-fastcluster)))
8245 (home-page "https://github.com/ManuSetty/SeqGL")
8246 (synopsis "Group lasso for Dnase/ChIP-seq data")
8247 (description "SeqGL is a group lasso based algorithm to extract
8248 transcription factor sequence signals from ChIP, DNase and ATAC-seq profiles.
8249 This package presents a method which uses group lasso to discriminate between
8250 bound and non bound genomic regions to accurately identify transcription
8251 factors bound at the specific regions.")
8252 (license license:gpl2+)))
8254 (define-public r-gkmsvm
8261 (uri (cran-uri "gkmSVM" version))
8264 "1zpxgxmf2nd5j5wn00ps6kfxr8wxh7d1swr1rr4spq7sj5z5z0k0"))))
8265 (properties `((upstream-name . "gkmSVM")))
8266 (build-system r-build-system)
8268 `(("r-biocgenerics" ,r-biocgenerics)
8269 ("r-biostrings" ,r-biostrings)
8270 ("r-genomeinfodb" ,r-genomeinfodb)
8271 ("r-genomicranges" ,r-genomicranges)
8272 ("r-iranges" ,r-iranges)
8273 ("r-kernlab" ,r-kernlab)
8276 ("r-rtracklayer" ,r-rtracklayer)
8277 ("r-s4vectors" ,r-s4vectors)
8278 ("r-seqinr" ,r-seqinr)))
8279 (home-page "http://cran.r-project.org/web/packages/gkmSVM")
8280 (synopsis "Gapped-kmer support vector machine")
8282 "This R package provides tools for training gapped-kmer SVM classifiers
8283 for DNA and protein sequences. This package supports several sequence
8284 kernels, including: gkmSVM, kmer-SVM, mismatch kernel and wildcard kernel.")
8285 (license license:gpl2+)))
8287 (define-public r-tximport
8293 (uri (bioconductor-uri "tximport" version))
8296 "1mklb02bj4gnbjlmb7vv6k4lr3w9fp3pzli9rddbrwd0y5n8fcpx"))))
8297 (build-system r-build-system)
8298 (home-page "http://bioconductor.org/packages/tximport")
8299 (synopsis "Import and summarize transcript-level estimates for gene-level analysis")
8301 "This package provides tools to import transcript-level abundance,
8302 estimated counts and transcript lengths, and to summarize them into matrices
8303 for use with downstream gene-level analysis packages. Average transcript
8304 length, weighted by sample-specific transcript abundance estimates, is
8305 provided as a matrix which can be used as an offset for different expression
8306 of gene-level counts.")
8307 (license license:gpl2+)))
8309 (define-public r-rhdf5
8315 (uri (bioconductor-uri "rhdf5" version))
8318 "1p6f5i6l44phl772a38x9cav2sya37bkqbkjzdc4pmyfzkv1j6hy"))))
8319 (build-system r-build-system)
8322 (modify-phases %standard-phases
8323 (add-after 'unpack 'unpack-smallhdf5
8324 (lambda* (#:key outputs #:allow-other-keys)
8325 (system* "tar" "-xzvf"
8326 "src/hdf5source/hdf5small.tgz" "-C" "src/" )
8327 (substitute* "src/Makevars"
8328 (("^.*cd hdf5source &&.*$") "")
8329 (("^.*gunzip -dc hdf5small.tgz.*$") "")
8330 (("^.*rm -rf hdf5.*$") "")
8331 (("^.*mv hdf5source/hdf5 ..*$") ""))
8332 (substitute* "src/hdf5/configure"
8336 `(("r-zlibbioc" ,r-zlibbioc)))
8340 (home-page "http://bioconductor.org/packages/rhdf5")
8341 (synopsis "HDF5 interface to R")
8343 "This R/Bioconductor package provides an interface between HDF5 and R.
8344 HDF5's main features are the ability to store and access very large and/or
8345 complex datasets and a wide variety of metadata on mass storage (disk) through
8346 a completely portable file format. The rhdf5 package is thus suited for the
8347 exchange of large and/or complex datasets between R and other software
8348 package, and for letting R applications work on datasets that are larger than
8349 the available RAM.")
8350 (license license:artistic2.0)))
8352 (define-public r-annotationfilter
8354 (name "r-annotationfilter")
8358 (uri (bioconductor-uri "AnnotationFilter" version))
8361 "0pxvswjzwibdfmrkdragxmzcl844z73pmkn82z92wahwa6gjfyi7"))))
8363 `((upstream-name . "AnnotationFilter")))
8364 (build-system r-build-system)
8366 `(("r-genomicranges" ,r-genomicranges)
8367 ("r-lazyeval" ,r-lazyeval)))
8368 (home-page "https://github.com/Bioconductor/AnnotationFilter")
8369 (synopsis "Facilities for filtering Bioconductor annotation resources")
8371 "This package provides classes and other infrastructure to implement
8372 filters for manipulating Bioconductor annotation resources. The filters are
8373 used by @code{ensembldb}, @code{Organism.dplyr}, and other packages.")
8374 (license license:artistic2.0)))
8376 (define-public emboss
8382 (uri (string-append "ftp://emboss.open-bio.org/pub/EMBOSS/old/"
8383 (version-major+minor version) ".0/"
8384 "EMBOSS-" version ".tar.gz"))
8387 "0vsmz96gc411yj2iyzdrsmg4l2n1nhgmp7vrgzlxx3xixv9xbf0q"))))
8388 (build-system gnu-build-system)
8391 (list (string-append "--with-hpdf="
8392 (assoc-ref %build-inputs "libharu")))
8394 (modify-phases %standard-phases
8395 (add-after 'unpack 'fix-checks
8397 ;; The PNGDRIVER tests check for the presence of libgd, libpng
8398 ;; and zlib, but assume that they are all found at the same
8400 (substitute* "configure.in"
8401 (("CHECK_PNGDRIVER")
8402 "LIBS=\"$LIBS -lgd -lpng -lz -lm\"
8403 AC_DEFINE([PLD_png], [1], [Define to 1 if PNG support is available])
8404 AM_CONDITIONAL(AMPNG, true)"))
8406 (add-after 'fix-checks 'disable-update-check
8408 ;; At build time there is no connection to the Internet, so
8409 ;; looking for updates will not work.
8410 (substitute* "Makefile.am"
8411 (("\\$\\(bindir\\)/embossupdate") ""))
8413 (add-after 'disable-update-check 'autogen
8414 (lambda _ (zero? (system* "autoreconf" "-vif")))))))
8420 ("libharu" ,libharu)
8423 `(("autoconf" ,autoconf)
8424 ("automake" ,automake)
8425 ("libtool" ,libtool)
8426 ("pkg-config" ,pkg-config)))
8427 (home-page "http://emboss.sourceforge.net")
8428 (synopsis "Molecular biology analysis suite")
8429 (description "EMBOSS is the \"European Molecular Biology Open Software
8430 Suite\". EMBOSS is an analysis package specially developed for the needs of
8431 the molecular biology (e.g. EMBnet) user community. The software
8432 automatically copes with data in a variety of formats and even allows
8433 transparent retrieval of sequence data from the web. It also provides a
8434 number of libraries for the development of software in the field of molecular
8435 biology. EMBOSS also integrates a range of currently available packages and
8436 tools for sequence analysis into a seamless whole.")
8437 (license license:gpl2+)))
8440 (let ((revision "1")
8441 (commit "3cc4567896d9d6442923da944beb704750a08d2d"))
8444 ;; The version is 2.13.0 even though no release archives have been
8445 ;; published as yet.
8446 (version (string-append "2.13.0-" revision "." (string-take commit 9)))
8450 (url "https://github.com/arq5x/bits.git")
8452 (file-name (string-append name "-" version "-checkout"))
8455 "17n2kffk4kmhivd8c98g2vr6y1s23vbg4sxlxs689wni66797hbs"))))
8456 (build-system gnu-build-system)
8458 `(#:tests? #f ;no tests included
8460 (modify-phases %standard-phases
8462 (add-after 'unpack 'remove-cuda
8464 (substitute* "Makefile"
8466 (("(bits_test_intersections) \\\\" _ match) match))
8469 (lambda* (#:key outputs #:allow-other-keys)
8471 "bin" (string-append (assoc-ref outputs "out") "/bin"))
8476 (home-page "https://github.com/arq5x/bits")
8477 (synopsis "Implementation of binary interval search algorithm")
8478 (description "This package provides an implementation of the
8479 BITS (Binary Interval Search) algorithm, an approach to interval set
8480 intersection. It is especially suited for the comparison of diverse genomic
8481 datasets and the exploration of large datasets of genome
8482 intervals (e.g. genes, sequence alignments).")
8483 (license license:gpl2))))
8485 (define-public piranha
8486 ;; There is no release tarball for the latest version. The latest commit is
8487 ;; older than one year at the time of this writing.
8488 (let ((revision "1")
8489 (commit "0466d364b71117d01e4471b74c514436cc281233"))
8492 (version (string-append "1.2.1-" revision "." (string-take commit 9)))
8496 (url "https://github.com/smithlabcode/piranha.git")
8500 "117dc0zf20c61jam69sk4abl57ah6yi6i7qra7d7y5zrbgk12q5n"))))
8501 (build-system gnu-build-system)
8503 `(#:test-target "test"
8505 (modify-phases %standard-phases
8506 (add-after 'unpack 'copy-smithlab-cpp
8507 (lambda* (#:key inputs #:allow-other-keys)
8508 (for-each (lambda (file)
8509 (install-file file "./src/smithlab_cpp/"))
8510 (find-files (assoc-ref inputs "smithlab-cpp")))
8512 (add-after 'install 'install-to-store
8513 (lambda* (#:key outputs #:allow-other-keys)
8514 (let* ((out (assoc-ref outputs "out"))
8515 (bin (string-append out "/bin")))
8516 (for-each (lambda (file)
8517 (install-file file bin))
8518 (find-files "bin" ".*")))
8521 (list (string-append "--with-bam_tools_headers="
8522 (assoc-ref %build-inputs "bamtools") "/include/bamtools")
8523 (string-append "--with-bam_tools_library="
8524 (assoc-ref %build-inputs "bamtools") "/lib/bamtools"))))
8526 `(("bamtools" ,bamtools)
8527 ("samtools" ,samtools-0.1)
8530 ,(let ((commit "3723e2db438c51501d0423429ff396c3035ba46a"))
8534 (url "https://github.com/smithlabcode/smithlab_cpp.git")
8536 (file-name (string-append "smithlab_cpp-" commit "-checkout"))
8539 "0l4gvbwslw5ngziskja41c00x1r06l3yidv7y0xw9djibhykzy0g")))))))
8541 `(("python" ,python-2)))
8542 (home-page "https://github.com/smithlabcode/piranha")
8543 (synopsis "Peak-caller for CLIP-seq and RIP-seq data")
8545 "Piranha is a peak-caller for genomic data produced by CLIP-seq and
8546 RIP-seq experiments. It takes input in BED or BAM format and identifies
8547 regions of statistically significant read enrichment. Additional covariates
8548 may optionally be provided to further inform the peak-calling process.")
8549 (license license:gpl3+))))
8557 (uri (string-append "https://pypi.python.org/packages/source/P"
8558 "/PePr/PePr-" version ".tar.gz"))
8561 "0qxjfdpl1b1y53nccws2d85f6k74zwmx8y8sd9rszcqhfayx6gdx"))))
8562 (build-system python-build-system)
8564 `(#:python ,python-2 ; python2 only
8565 #:tests? #f)) ; no tests included
8567 `(("python2-numpy" ,python2-numpy)
8568 ("python2-scipy" ,python2-scipy)
8569 ("python2-pysam" ,python2-pysam)))
8570 (home-page "https://github.com/shawnzhangyx/PePr")
8571 (synopsis "Peak-calling and prioritization pipeline for ChIP-Seq data")
8573 "PePr is a ChIP-Seq peak calling or differential binding analysis tool
8574 that is primarily designed for data with biological replicates. It uses a
8575 negative binomial distribution to model the read counts among the samples in
8576 the same group, and look for consistent differences between ChIP and control
8577 group or two ChIP groups run under different conditions.")
8578 (license license:gpl3+)))
8580 (define-public filevercmp
8581 (let ((commit "1a9b779b93d0b244040274794d402106907b71b7"))
8584 (version (string-append "0-1." (string-take commit 7)))
8587 (uri (string-append "https://github.com/ekg/filevercmp/archive/"
8589 (file-name (string-append name "-" version ".tar.gz"))
8591 (base32 "0yp5jswf5j2pqc6517x277s4s6h1ss99v57kxw9gy0jkfl3yh450"))))
8592 (build-system gnu-build-system)
8594 `(#:tests? #f ; There are no tests to run.
8596 (modify-phases %standard-phases
8597 (delete 'configure) ; There is no configure phase.
8599 (lambda* (#:key outputs #:allow-other-keys)
8600 (let ((bin (string-append (assoc-ref outputs "out") "/bin")))
8601 (install-file "filevercmp" bin)))))))
8602 (home-page "https://github.com/ekg/filevercmp")
8603 (synopsis "This program compares version strings")
8604 (description "This program compares version strings. It intends to be a
8605 replacement for strverscmp.")
8606 (license license:gpl3+))))
8608 (define-public multiqc
8615 (uri (pypi-uri "multiqc" version))
8618 "032svgym67k2ds7wp0cxzv79gi30yrdl45zbqn74lni3dk04qm33"))))
8619 (build-system python-build-system)
8621 `(("python-jinja2" ,python-jinja2)
8622 ("python-simplejson" ,python-simplejson)
8623 ("python-pyyaml" ,python-pyyaml)
8624 ("python-click" ,python-click)
8625 ("python-spectra" ,python-spectra)
8626 ("python-requests" ,python-requests)
8627 ("python-markdown" ,python-markdown)
8628 ("python-lzstring" ,python-lzstring)
8629 ("python-matplotlib" ,python-matplotlib)
8630 ("python-numpy" ,python-numpy)
8631 ;; MultQC checks for the presence of nose at runtime.
8632 ("python-nose" ,python-nose)))
8633 (home-page "http://multiqc.info")
8634 (synopsis "Aggregate bioinformatics analysis reports")
8636 "MultiQC is a tool to aggregate bioinformatics results across many
8637 samples into a single report. It contains modules for a large number of
8638 common bioinformatics tools.")
8639 (license license:gpl3)))
8641 (define-public r-chipseq
8648 (uri (bioconductor-uri "chipseq" version))
8651 "1hahyqiwb2ch8214xqpw0c3jpiwkmyf3dwz0xc87jx6cdnzipj3i"))))
8652 (build-system r-build-system)
8654 `(("r-biocgenerics" ,r-biocgenerics)
8655 ("r-genomicranges" ,r-genomicranges)
8656 ("r-iranges" ,r-iranges)
8657 ("r-s4vectors" ,r-s4vectors)
8658 ("r-shortread" ,r-shortread)))
8659 (home-page "http://bioconductor.org/packages/chipseq")
8660 (synopsis "Package for analyzing ChIPseq data")
8662 "This package provides tools for processing short read data from ChIPseq
8664 (license license:artistic2.0)))
8666 (define-public r-copyhelper
8668 (name "r-copyhelper")
8673 (uri (string-append "http://bioconductor.org/packages/release/"
8674 "data/experiment/src/contrib/CopyhelpeR_"
8678 "0x7cyynjmxls9as2gg0iyp9x5fpalxmdjq914ss7i84i9zyk5bhq"))))
8679 (properties `((upstream-name . "CopyhelpeR")))
8680 (build-system r-build-system)
8681 (home-page "http://bioconductor.org/packages/CopyhelpeR/")
8682 (synopsis "Helper files for CopywriteR")
8684 "This package contains the helper files that are required to run the
8685 Bioconductor package CopywriteR. It contains pre-assembled 1kb bin GC-content
8686 and mappability files for the reference genomes hg18, hg19, hg38, mm9 and
8687 mm10. In addition, it contains a blacklist filter to remove regions that
8688 display copy number variation. Files are stored as GRanges objects from the
8689 GenomicRanges Bioconductor package.")
8690 (license license:gpl2)))
8692 (define-public r-copywriter
8694 (name "r-copywriter")
8699 (uri (bioconductor-uri "CopywriteR" version))
8702 "0xgqnq5v5213b3nzvlmjysjb7w1bc0iblqpmzbjqn7n0ib0qyhbm"))))
8703 (properties `((upstream-name . "CopywriteR")))
8704 (build-system r-build-system)
8706 `(("r-biocparallel" ,r-biocparallel)
8707 ("r-chipseq" ,r-chipseq)
8708 ("r-copyhelper" ,r-copyhelper)
8709 ("r-data-table" ,r-data-table)
8710 ("r-dnacopy" ,r-dnacopy)
8711 ("r-futile-logger" ,r-futile-logger)
8712 ("r-genomeinfodb" ,r-genomeinfodb)
8713 ("r-genomicalignments" ,r-genomicalignments)
8714 ("r-genomicranges" ,r-genomicranges)
8715 ("r-gtools" ,r-gtools)
8716 ("r-iranges" ,r-iranges)
8717 ("r-matrixstats" ,r-matrixstats)
8718 ("r-rsamtools" ,r-rsamtools)
8719 ("r-s4vectors" ,r-s4vectors)))
8720 (home-page "https://github.com/PeeperLab/CopywriteR")
8721 (synopsis "Copy number information from targeted sequencing")
8723 "CopywriteR extracts DNA copy number information from targeted sequencing
8724 by utilizing off-target reads. It allows for extracting uniformly distributed
8725 copy number information, can be used without reference, and can be applied to
8726 sequencing data obtained from various techniques including chromatin
8727 immunoprecipitation and target enrichment on small gene panels. Thereby,
8728 CopywriteR constitutes a widely applicable alternative to available copy
8729 number detection tools.")
8730 (license license:gpl2)))
8732 (define-public r-methylkit
8734 (name "r-methylkit")
8738 (uri (bioconductor-uri "methylKit" version))
8741 "02acdjf6jl0c1glymin84pdna4farn4vv0gb6107d9iqz3y3gkmm"))))
8742 (properties `((upstream-name . "methylKit")))
8743 (build-system r-build-system)
8745 `(("r-data-table" ,r-data-table)
8746 ("r-emdbook" ,r-emdbook)
8747 ("r-fastseg" ,r-fastseg)
8748 ("r-genomeinfodb" ,r-genomeinfodb)
8749 ("r-genomicranges" ,r-genomicranges)
8750 ("r-gtools" ,r-gtools)
8751 ("r-iranges" ,r-iranges)
8752 ("r-kernsmooth" ,r-kernsmooth)
8753 ("r-limma" ,r-limma)
8754 ("r-mclust" ,r-mclust)
8755 ("r-qvalue" ,r-qvalue)
8756 ("r-r-utils" ,r-r-utils)
8758 ("r-rhtslib" ,r-rhtslib)
8759 ("r-rsamtools" ,r-rsamtools)
8760 ("r-rtracklayer" ,r-rtracklayer)
8761 ("r-s4vectors" ,r-s4vectors)
8762 ("r-zlibbioc" ,r-zlibbioc)))
8765 (home-page "http://code.google.com/p/methylkit/")
8767 "DNA methylation analysis from high-throughput bisulfite sequencing results")
8769 "MethylKit is an R package for DNA methylation analysis and annotation
8770 from high-throughput bisulfite sequencing. The package is designed to deal
8771 with sequencing data from @dfn{Reduced representation bisulfite
8772 sequencing} (RRBS) and its variants, but also target-capture methods and whole
8773 genome bisulfite sequencing. It also has functions to analyze base-pair
8774 resolution 5hmC data from experimental protocols such as oxBS-Seq and
8776 (license license:artistic2.0)))
8778 (define-public r-sva
8785 (uri (bioconductor-uri "sva" version))
8788 "0wcway4ai9im81xnrzb1vij2iidq5pw24qhjfgacmhxvx3dzhbsc"))))
8789 (build-system r-build-system)
8791 `(("r-genefilter" ,r-genefilter)
8793 ("r-biocparallel" ,r-biocparallel)
8794 ("r-matrixstats" ,r-matrixstats)
8795 ("r-limma" ,r-limma)))
8796 (home-page "http://bioconductor.org/packages/sva")
8797 (synopsis "Surrogate variable analysis")
8799 "This package contains functions for removing batch effects and other
8800 unwanted variation in high-throughput experiment. It also contains functions
8801 for identifying and building surrogate variables for high-dimensional data
8802 sets. Surrogate variables are covariates constructed directly from
8803 high-dimensional data like gene expression/RNA sequencing/methylation/brain
8804 imaging data that can be used in subsequent analyses to adjust for unknown,
8805 unmodeled, or latent sources of noise.")
8806 (license license:artistic2.0)))
8808 (define-public r-seqminer
8815 (uri (cran-uri "seqminer" version))
8818 "057j1l6dip35l1aivilapl2zv9db677b3di2pb3sfgq2sxg0ps3l"))))
8819 (build-system r-build-system)
8822 (home-page "http://seqminer.genomic.codes")
8823 (synopsis "Read nucleotide sequence data (VCF, BCF, and METAL formats)")
8825 "This package provides tools to integrate nucleotide sequencing
8826 data (variant call format, e.g. VCF or BCF) or meta-analysis results in R.")
8827 ;; Any version of the GPL is acceptable
8828 (license (list license:gpl2+ license:gpl3+))))
8830 (define-public r-raremetals2
8832 (name "r-raremetals2")
8837 (uri (string-append "http://genome.sph.umich.edu/w/images/"
8838 "b/b7/RareMETALS2_" version ".tar.gz"))
8841 "0z5ljcgvnm06ja9lm85a3cniq7slxcy37aqqkxrdidr79an5fs4s"))))
8842 (properties `((upstream-name . "RareMETALS2")))
8843 (build-system r-build-system)
8845 `(("r-seqminer" ,r-seqminer)
8846 ("r-mvtnorm" ,r-mvtnorm)
8848 ("r-compquadform" ,r-compquadform)
8849 ("r-getopt" ,r-getopt)))
8850 (home-page "http://genome.sph.umich.edu/wiki/RareMETALS2")
8851 (synopsis "Analyze gene-level association tests for binary trait")
8853 "The R package rareMETALS2 is an extension of the R package rareMETALS.
8854 It was designed to meta-analyze gene-level association tests for binary trait.
8855 While rareMETALS offers a near-complete solution for meta-analysis of
8856 gene-level tests for quantitative trait, it does not offer the optimal
8857 solution for binary trait. The package rareMETALS2 offers improved features
8858 for analyzing gene-level association tests in meta-analyses for binary
8860 (license license:gpl3)))
8862 (define-public r-maldiquant
8864 (name "r-maldiquant")
8869 (uri (cran-uri "MALDIquant" version))
8872 "1pmhsfvd45a44xdiml4zx3zd5fhygqyziqvygahkk9yibnyhv4cv"))))
8873 (properties `((upstream-name . "MALDIquant")))
8874 (build-system r-build-system)
8875 (home-page "http://cran.r-project.org/web/packages/MALDIquant")
8876 (synopsis "Quantitative analysis of mass spectrometry data")
8878 "This package provides a complete analysis pipeline for matrix-assisted
8879 laser desorption/ionization-time-of-flight (MALDI-TOF) and other
8880 two-dimensional mass spectrometry data. In addition to commonly used plotting
8881 and processing methods it includes distinctive features, namely baseline
8882 subtraction methods such as morphological filters (TopHat) or the
8883 statistics-sensitive non-linear iterative peak-clipping algorithm (SNIP), peak
8884 alignment using warping functions, handling of replicated measurements as well
8885 as allowing spectra with different resolutions.")
8886 (license license:gpl3+)))
8888 (define-public r-protgenerics
8890 (name "r-protgenerics")
8895 (uri (bioconductor-uri "ProtGenerics" version))
8898 "08idb3rvxn4fl7rd66jasyqz47cb76dbc3968r1g26jr2ci3w1pl"))))
8899 (properties `((upstream-name . "ProtGenerics")))
8900 (build-system r-build-system)
8901 (home-page "https://github.com/lgatto/ProtGenerics")
8902 (synopsis "S4 generic functions for proteomics infrastructure")
8904 "This package provides S4 generic functions needed by Bioconductor
8905 proteomics packages.")
8906 (license license:artistic2.0)))
8908 (define-public r-mzr
8915 (uri (bioconductor-uri "mzR" version))
8918 "1zir46h320n2vbrky6q3m8l221f3wdjlfsnx4ak9xca5min24xm7"))))
8919 (properties `((upstream-name . "mzR")))
8920 (build-system r-build-system)
8923 ("netcdf" ,netcdf)))
8925 `(("r-biobase" ,r-biobase)
8926 ("r-biocgenerics" ,r-biocgenerics)
8927 ("r-protgenerics" ,r-protgenerics)
8929 ("r-zlibbioc" ,r-zlibbioc)))
8930 (home-page "https://github.com/sneumann/mzR/")
8931 (synopsis "Parser for mass spectrometry data files")
8933 "The mzR package provides a unified API to the common file formats and
8934 parsers available for mass spectrometry data. It comes with a wrapper for the
8935 ISB random access parser for mass spectrometry mzXML, mzData and mzML files.
8936 The package contains the original code written by the ISB, and a subset of the
8937 proteowizard library for mzML and mzIdentML. The netCDF reading code has
8938 previously been used in XCMS.")
8939 (license license:artistic2.0)))
8941 (define-public r-affyio
8948 (uri (bioconductor-uri "affyio" version))
8951 "13w6al9296q916w0w6ngbsk25b21ahla1b6n40fcqhbvhyfii6sj"))))
8952 (build-system r-build-system)
8954 `(("r-zlibbioc" ,r-zlibbioc)))
8957 (home-page "https://github.com/bmbolstad/affyio")
8958 (synopsis "Tools for parsing Affymetrix data files")
8960 "This package provides routines for parsing Affymetrix data files based
8961 upon file format information. The primary focus is on accessing the CEL and
8963 (license license:lgpl2.0+)))
8965 (define-public r-affy
8972 (uri (bioconductor-uri "affy" version))
8975 "0azwg2qxzgflr1rjvbdln5i5rbcr9gs36kqlacd9cwl1szb9ad3m"))))
8976 (build-system r-build-system)
8978 `(("r-affyio" ,r-affyio)
8979 ("r-biobase" ,r-biobase)
8980 ("r-biocgenerics" ,r-biocgenerics)
8981 ("r-biocinstaller" ,r-biocinstaller)
8982 ("r-preprocesscore" ,r-preprocesscore)
8983 ("r-zlibbioc" ,r-zlibbioc)))
8984 (home-page "http://bioconductor.org/packages/affy")
8985 (synopsis "Methods for affymetrix oligonucleotide arrays")
8987 "This package contains functions for exploratory oligonucleotide array
8989 (license license:lgpl2.0+)))
8991 (define-public r-vsn
8998 (uri (bioconductor-uri "vsn" version))
9001 "0qhg3a4sc62pfdxcpvmk831rk138xh4zx4f1s39jhxpqqhmr7jvk"))))
9002 (build-system r-build-system)
9004 `(("r-affy" ,r-affy)
9005 ("r-biobase" ,r-biobase)
9006 ("r-ggplot2" ,r-ggplot2)
9007 ("r-hexbin" ,r-hexbin)
9008 ("r-lattice" ,r-lattice)
9009 ("r-limma" ,r-limma)))
9010 (home-page "http://bioconductor.org/packages/release/bioc/html/vsn.html")
9011 (synopsis "Variance stabilization and calibration for microarray data")
9013 "The package implements a method for normalising microarray intensities,
9014 and works for single- and multiple-color arrays. It can also be used for data
9015 from other technologies, as long as they have similar format. The method uses
9016 a robust variant of the maximum-likelihood estimator for an
9017 additive-multiplicative error model and affine calibration. The model
9018 incorporates data calibration step (a.k.a. normalization), a model for the
9019 dependence of the variance on the mean intensity and a variance stabilizing
9020 data transformation. Differences between transformed intensities are
9021 analogous to \"normalized log-ratios\". However, in contrast to the latter,
9022 their variance is independent of the mean, and they are usually more sensitive
9023 and specific in detecting differential transcription.")
9024 (license license:artistic2.0)))
9026 (define-public r-mzid
9033 (uri (bioconductor-uri "mzID" version))
9036 "11xnild02jz24vbsfy92lb7jlqqwnrswg66a7r4rsw8d2ibrbk33"))))
9037 (properties `((upstream-name . "mzID")))
9038 (build-system r-build-system)
9040 `(("r-doparallel" ,r-doparallel)
9041 ("r-foreach" ,r-foreach)
9042 ("r-iterators" ,r-iterators)
9044 ("r-protgenerics" ,r-protgenerics)
9047 (home-page "http://bioconductor.org/packages/mzID")
9048 (synopsis "Parser for mzIdentML files")
9050 "This package provides a parser for mzIdentML files implemented using the
9051 XML package. The parser tries to be general and able to handle all types of
9052 mzIdentML files with the drawback of having less pretty output than a vendor
9054 (license license:gpl2+)))
9056 (define-public r-pcamethods
9058 (name "r-pcamethods")
9063 (uri (bioconductor-uri "pcaMethods" version))
9066 "0c4lphqyzj577ws4s172391cgv00s5nhy152zp18k2k4diyhq6n0"))))
9067 (properties `((upstream-name . "pcaMethods")))
9068 (build-system r-build-system)
9070 `(("r-biobase" ,r-biobase)
9071 ("r-biocgenerics" ,r-biocgenerics)
9073 ("r-rcpp" ,r-rcpp)))
9074 (home-page "https://github.com/hredestig/pcamethods")
9075 (synopsis "Collection of PCA methods")
9077 "This package provides Bayesian PCA, Probabilistic PCA, Nipals PCA,
9078 Inverse Non-Linear PCA and the conventional SVD PCA. A cluster based method
9079 for missing value estimation is included for comparison. BPCA, PPCA and
9080 NipalsPCA may be used to perform PCA on incomplete data as well as for
9081 accurate missing value estimation. A set of methods for printing and plotting
9082 the results is also provided. All PCA methods make use of the same data
9083 structure (pcaRes) to provide a common interface to the PCA results.")
9084 (license license:gpl3+)))
9086 (define-public r-msnbase
9093 (uri (bioconductor-uri "MSnbase" version))
9096 "1n9bbdlp8d8bx2mqby0c4yylz1yil42scbkxqgyrfr9s5sn6dqff"))))
9097 (properties `((upstream-name . "MSnbase")))
9098 (build-system r-build-system)
9100 `(("r-affy" ,r-affy)
9101 ("r-biobase" ,r-biobase)
9102 ("r-biocgenerics" ,r-biocgenerics)
9103 ("r-biocparallel" ,r-biocparallel)
9104 ("r-digest" ,r-digest)
9105 ("r-ggplot2" ,r-ggplot2)
9106 ("r-impute" ,r-impute)
9107 ("r-iranges" ,r-iranges)
9108 ("r-maldiquant" ,r-maldiquant)
9111 ("r-pcamethods" ,r-pcamethods)
9113 ("r-preprocesscore" ,r-preprocesscore)
9114 ("r-protgenerics" ,r-protgenerics)
9116 ("r-reshape2" ,r-reshape2)
9117 ("r-s4vectors" ,r-s4vectors)
9120 (home-page "https://github.com/lgatto/MSnbase")
9121 (synopsis "Base functions and classes for MS-based proteomics")
9123 "This package provides basic plotting, data manipulation and processing
9124 of mass spectrometry based proteomics data.")
9125 (license license:artistic2.0)))
9127 (define-public r-msnid
9134 (uri (bioconductor-uri "MSnID" version))
9137 "0pjwargi5lif8q53fd43ql67p3yk9w10jychafd9qgbaw5k3f68k"))))
9138 (properties `((upstream-name . "MSnID")))
9139 (build-system r-build-system)
9141 `(("r-biobase" ,r-biobase)
9142 ("r-data-table" ,r-data-table)
9143 ("r-doparallel" ,r-doparallel)
9144 ("r-dplyr" ,r-dplyr)
9145 ("r-foreach" ,r-foreach)
9146 ("r-iterators" ,r-iterators)
9147 ("r-msnbase" ,r-msnbase)
9150 ("r-protgenerics" ,r-protgenerics)
9151 ("r-r-cache" ,r-r-cache)
9153 ("r-reshape2" ,r-reshape2)))
9154 (home-page "http://bioconductor.org/packages/MSnID")
9155 (synopsis "Utilities for LC-MSn proteomics identifications")
9157 "This package extracts @dfn{tandem mass spectrometry} (MS/MS) ID data
9158 from mzIdentML (leveraging the mzID package) or text files. After collating
9159 the search results from multiple datasets it assesses their identification
9160 quality and optimize filtering criteria to achieve the maximum number of
9161 identifications while not exceeding a specified false discovery rate. It also
9162 contains a number of utilities to explore the MS/MS results and assess missed
9163 and irregular enzymatic cleavages, mass measurement accuracy, etc.")
9164 (license license:artistic2.0)))
9166 (define-public r-seurat
9167 ;; Source releases are only made for new x.0 versions. All newer versions
9168 ;; are only released as pre-built binaries. At the time of this writing the
9169 ;; latest binary release is 1.4.0.12, which is equivalent to this commit.
9170 (let ((commit "fccb77d1452c35ee47e47ebf8e87bddb59f3b08d")
9174 (version (string-append "1.4.0.12-" revision "." (string-take commit 7)))
9178 (url "https://github.com/satijalab/seurat")
9180 (file-name (string-append name "-" version "-checkout"))
9183 "101wq3aqrdmbfi3lqmq4iivk9iwbf10d4z216ss25hf7n9091cyl"))
9184 ;; Delete pre-built jar.
9186 '(begin (delete-file "inst/java/ModularityOptimizer.jar")
9188 (build-system r-build-system)
9191 (modify-phases %standard-phases
9192 (add-after 'unpack 'build-jar
9193 (lambda* (#:key inputs #:allow-other-keys)
9194 (let ((classesdir "tmp-classes"))
9195 (setenv "JAVA_HOME" (assoc-ref inputs "jdk"))
9197 (and (zero? (apply system* `("javac" "-d" ,classesdir
9198 ,@(find-files "java" "\\.java$"))))
9199 (zero? (system* "jar"
9200 "-cf" "inst/java/ModularityOptimizer.jar"
9201 "-C" classesdir ".")))))))))
9203 `(("jdk" ,icedtea "jdk")))
9206 ("r-caret" ,r-caret)
9207 ("r-cowplot" ,r-cowplot)
9208 ("r-dplyr" ,r-dplyr)
9209 ("r-fastica" ,r-fastica)
9212 ("r-gdata" ,r-gdata)
9213 ("r-ggplot2" ,r-ggplot2)
9214 ("r-gplots" ,r-gplots)
9215 ("r-gridextra" ,r-gridextra)
9216 ("r-igraph" ,r-igraph)
9217 ("r-irlba" ,r-irlba)
9219 ("r-mixtools" ,r-mixtools)
9220 ("r-pbapply" ,r-pbapply)
9222 ("r-ranger" ,r-ranger)
9223 ("r-rcolorbrewer" ,r-rcolorbrewer)
9225 ("r-rcppeigen" ,r-rcppeigen)
9226 ("r-rcppprogress" ,r-rcppprogress)
9227 ("r-reshape2" ,r-reshape2)
9229 ("r-rtsne" ,r-rtsne)
9230 ("r-stringr" ,r-stringr)
9231 ("r-tclust" ,r-tclust)
9233 ("r-vgam" ,r-vgam)))
9234 (home-page "http://www.satijalab.org/seurat")
9235 (synopsis "Seurat is an R toolkit for single cell genomics")
9237 "This package is an R package designed for QC, analysis, and
9238 exploration of single cell RNA-seq data. It easily enables widely-used
9239 analytical techniques, including the identification of highly variable genes,
9240 dimensionality reduction; PCA, ICA, t-SNE, standard unsupervised clustering
9241 algorithms; density clustering, hierarchical clustering, k-means, and the
9242 discovery of differentially expressed genes and markers.")
9243 (license license:gpl3))))
9245 (define-public r-aroma-light
9247 (name "r-aroma-light")
9252 (uri (bioconductor-uri "aroma.light" version))
9255 "10snykmmx36qaymyf5s1n1km8hsscyzpykcpf0mzsrcv8ml9rp8a"))))
9256 (properties `((upstream-name . "aroma.light")))
9257 (build-system r-build-system)
9259 `(("r-matrixstats" ,r-matrixstats)
9260 ("r-r-methodss3" ,r-r-methodss3)
9262 ("r-r-utils" ,r-r-utils)))
9263 (home-page "https://github.com/HenrikBengtsson/aroma.light")
9264 (synopsis "Methods for normalization and visualization of microarray data")
9266 "This package provides methods for microarray analysis that take basic
9267 data types such as matrices and lists of vectors. These methods can be used
9268 standalone, be utilized in other packages, or be wrapped up in higher-level
9270 (license license:gpl2+)))
9272 (define-public r-deseq
9279 (uri (bioconductor-uri "DESeq" version))
9282 "0j3dgcxd64m9qknmlcbdzvg4xhp981xd6nbwsvnqjfn6yypslgyw"))))
9283 (properties `((upstream-name . "DESeq")))
9284 (build-system r-build-system)
9286 `(("r-biobase" ,r-biobase)
9287 ("r-biocgenerics" ,r-biocgenerics)
9288 ("r-genefilter" ,r-genefilter)
9289 ("r-geneplotter" ,r-geneplotter)
9290 ("r-lattice" ,r-lattice)
9291 ("r-locfit" ,r-locfit)
9293 ("r-rcolorbrewer" ,r-rcolorbrewer)))
9294 (home-page "http://www-huber.embl.de/users/anders/DESeq")
9295 (synopsis "Differential gene expression analysis")
9297 "This package provides tools for estimating variance-mean dependence in
9298 count data from high-throughput genetic sequencing assays and for testing for
9299 differential expression based on a model using the negative binomial
9301 (license license:gpl3+)))
9303 (define-public r-edaseq
9310 (uri (bioconductor-uri "EDASeq" version))
9313 "0f25dfc8hdii9fjm3bf89vy9jkxv23sa62fkcga5b4gkipwrvm9a"))))
9314 (properties `((upstream-name . "EDASeq")))
9315 (build-system r-build-system)
9317 `(("r-annotationdbi" ,r-annotationdbi)
9318 ("r-aroma-light" ,r-aroma-light)
9319 ("r-biobase" ,r-biobase)
9320 ("r-biocgenerics" ,r-biocgenerics)
9321 ("r-biomart" ,r-biomart)
9322 ("r-biostrings" ,r-biostrings)
9323 ("r-deseq" ,r-deseq)
9324 ("r-genomicfeatures" ,r-genomicfeatures)
9325 ("r-genomicranges" ,r-genomicranges)
9326 ("r-iranges" ,r-iranges)
9327 ("r-rsamtools" ,r-rsamtools)
9328 ("r-shortread" ,r-shortread)))
9329 (home-page "https://github.com/drisso/EDASeq")
9330 (synopsis "Exploratory data analysis and normalization for RNA-Seq")
9332 "This package provides support for numerical and graphical summaries of
9333 RNA-Seq genomic read data. Provided within-lane normalization procedures to
9334 adjust for GC-content effect (or other gene-level effects) on read counts:
9335 loess robust local regression, global-scaling, and full-quantile
9336 normalization. Between-lane normalization procedures to adjust for
9337 distributional differences between lanes (e.g., sequencing depth):
9338 global-scaling and full-quantile normalization.")
9339 (license license:artistic2.0)))
9341 (define-public r-interactivedisplaybase
9343 (name "r-interactivedisplaybase")
9348 (uri (bioconductor-uri "interactiveDisplayBase" version))
9351 "12f6ap4bl3h2iwwhg8i3r9a7yyd28d8i5lb3fj1vnfvjs762r7r7"))))
9353 `((upstream-name . "interactiveDisplayBase")))
9354 (build-system r-build-system)
9356 `(("r-biocgenerics" ,r-biocgenerics)
9357 ("r-shiny" ,r-shiny)))
9358 (home-page "http://bioconductor.org/packages/interactiveDisplayBase")
9359 (synopsis "Base package for web displays of Bioconductor objects")
9361 "This package contains the basic methods needed to generate interactive
9362 Shiny-based display methods for Bioconductor objects.")
9363 (license license:artistic2.0)))
9365 (define-public r-annotationhub
9367 (name "r-annotationhub")
9372 (uri (bioconductor-uri "AnnotationHub" version))
9375 "1nh5si3j1nv37jcg4260582ayjg18851np47cskrm54prnvhwd9r"))))
9376 (properties `((upstream-name . "AnnotationHub")))
9377 (build-system r-build-system)
9379 `(("r-annotationdbi" ,r-annotationdbi)
9380 ("r-biocgenerics" ,r-biocgenerics)
9381 ("r-biocinstaller" ,r-biocinstaller)
9383 ("r-interactivedisplaybase" ,r-interactivedisplaybase)
9384 ("r-rsqlite" ,r-rsqlite)
9385 ("r-s4vectors" ,r-s4vectors)
9386 ("r-yaml" ,r-yaml)))
9387 (home-page "http://bioconductor.org/packages/AnnotationHub")
9388 (synopsis "Client to access AnnotationHub resources")
9390 "This package provides a client for the Bioconductor AnnotationHub web
9391 resource. The AnnotationHub web resource provides a central location where
9392 genomic files (e.g. VCF, bed, wig) and other resources from standard
9393 locations (e.g. UCSC, Ensembl) can be discovered. The resource includes
9394 metadata about each resource, e.g., a textual description, tags, and date of
9395 modification. The client creates and manages a local cache of files retrieved
9396 by the user, helping with quick and reproducible access.")
9397 (license license:artistic2.0)))
9399 (define-public r-fastseg
9406 (uri (bioconductor-uri "fastseg" version))
9409 "083wiz03q9mynwchs9frlpp6c84dncri5ncibx6h82p228cpja6h"))))
9410 (build-system r-build-system)
9412 `(("r-biobase" ,r-biobase)
9413 ("r-biocgenerics" ,r-biocgenerics)
9414 ("r-genomicranges" ,r-genomicranges)
9415 ("r-iranges" ,r-iranges)
9416 ("r-s4vectors" ,r-s4vectors)))
9417 (home-page "http://www.bioinf.jku.at/software/fastseg/index.html")
9418 (synopsis "Fast segmentation algorithm for genetic sequencing data")
9420 "Fastseg implements a very fast and efficient segmentation algorithm.
9421 It can segment data from DNA microarrays and data from next generation
9422 sequencing for example to detect copy number segments. Further it can segment
9423 data from RNA microarrays like tiling arrays to identify transcripts. Most
9424 generally, it can segment data given as a matrix or as a vector. Various data
9425 formats can be used as input to fastseg like expression set objects for
9426 microarrays or GRanges for sequencing data.")
9427 (license license:lgpl2.0+)))
9429 (define-public r-qvalue
9436 (uri (bioconductor-uri "qvalue" version))
9439 "1dxdwa767a9r8n61r272ypi09qblcdfpzzwkmri74y5mbp1r3y4i"))))
9440 (build-system r-build-system)
9442 `(("r-ggplot2" ,r-ggplot2)
9443 ("r-reshape2" ,r-reshape2)))
9444 (home-page "http://github.com/jdstorey/qvalue")
9445 (synopsis "Q-value estimation for false discovery rate control")
9447 "This package takes a list of p-values resulting from the simultaneous
9448 testing of many hypotheses and estimates their q-values and local @dfn{false
9449 discovery rate} (FDR) values. The q-value of a test measures the proportion
9450 of false positives incurred when that particular test is called significant.
9451 The local FDR measures the posterior probability the null hypothesis is true
9452 given the test's p-value. Various plots are automatically generated, allowing
9453 one to make sensible significance cut-offs. The software can be applied to
9454 problems in genomics, brain imaging, astrophysics, and data mining.")
9455 ;; Any version of the LGPL.
9456 (license license:lgpl3+)))
9458 (define htslib-for-sambamba
9459 (let ((commit "2f3c3ea7b301f9b45737a793c0b2dcf0240e5ee5"))
9462 (name "htslib-for-sambamba")
9463 (version (string-append "1.3.1-1." (string-take commit 9)))
9468 (url "https://github.com/lomereiter/htslib.git")
9470 (file-name (string-append "htslib-" version "-checkout"))
9473 "0g38g8s3npr0gjm9fahlbhiskyfws9l5i0x1ml3rakzj7az5l9c9"))))
9475 (substitute-keyword-arguments (package-arguments htslib)
9477 `(modify-phases ,phases
9478 (add-after 'unpack 'bootstrap
9480 (zero? (system* "autoreconf" "-vif"))))))))
9482 `(("autoconf" ,autoconf)
9483 ("automake" ,automake)
9484 ,@(package-native-inputs htslib))))))
9486 (define-public sambamba
9493 (uri (string-append "https://github.com/lomereiter/sambamba/"
9494 "archive/v" version ".tar.gz"))
9495 (file-name (string-append name "-" version ".tar.gz"))
9498 "17076gijd65a3f07zns2gvbgahiz5lriwsa6dq353ss3jl85d8vy"))))
9499 (build-system gnu-build-system)
9501 `(#:tests? #f ; there is no test target
9504 ;; Override "--compiler" flag only.
9505 "D_FLAGS=--compiler=ldc2 -IBioD -g -d"
9506 "sambamba-ldmd2-64")
9508 (modify-phases %standard-phases
9510 (add-after 'unpack 'place-biod
9511 (lambda* (#:key inputs #:allow-other-keys)
9512 (copy-recursively (assoc-ref inputs "biod") "BioD")
9514 (add-after 'unpack 'unbundle-prerequisites
9516 (substitute* "Makefile"
9517 ((" htslib-static lz4-static") ""))
9520 (lambda* (#:key outputs #:allow-other-keys)
9521 (let* ((out (assoc-ref outputs "out"))
9522 (bin (string-append out "/bin")))
9524 (install-file "build/sambamba" bin)
9530 ,(let ((commit "1248586b54af4bd4dfb28ebfebfc6bf012e7a587"))
9534 (url "https://github.com/biod/BioD.git")
9536 (file-name (string-append "biod-"
9537 (string-take commit 9)
9541 "1m8hi1n7x0ri4l6s9i0x6jg4z4v94xrfdzp7mbizdipfag0m17g3")))))))
9544 ("htslib" ,htslib-for-sambamba)))
9545 (home-page "http://lomereiter.github.io/sambamba")
9546 (synopsis "Tools for working with SAM/BAM data")
9547 (description "Sambamba is a high performance modern robust and
9548 fast tool (and library), written in the D programming language, for
9549 working with SAM and BAM files. Current parallelised functionality is
9550 an important subset of samtools functionality, including view, index,
9551 sort, markdup, and depth.")
9552 (license license:gpl2+)))
9554 (define-public ritornello
9560 (uri (string-append "https://github.com/KlugerLab/"
9561 "Ritornello/archive/v"
9563 (file-name (string-append name "-" version ".tar.gz"))
9566 "02nik86gq9ljjriv6pamwlmqnfky3ads1fpklx6mc3hx6k40pg38"))))
9567 (build-system gnu-build-system)
9569 `(#:tests? #f ; there are no tests
9571 (modify-phases %standard-phases
9572 (add-after 'unpack 'patch-samtools-references
9573 (lambda* (#:key inputs #:allow-other-keys)
9574 (substitute* '("src/SamStream.h"
9575 "src/BufferedGenomeReader.h")
9576 (("<sam.h>") "<samtools/sam.h>"))
9580 (lambda* (#:key inputs outputs #:allow-other-keys)
9581 (let* ((out (assoc-ref outputs "out"))
9582 (bin (string-append out "/bin/")))
9584 (install-file "bin/Ritornello" bin)
9587 `(("samtools" ,samtools-0.1)
9591 (home-page "https://github.com/KlugerLab/Ritornello")
9592 (synopsis "Control-free peak caller for ChIP-seq data")
9593 (description "Ritornello is a ChIP-seq peak calling algorithm based on
9594 signal processing that can accurately call binding events without the need to
9595 do a pair total DNA input or IgG control sample. It has been tested for use
9596 with narrow binding events such as transcription factor ChIP-seq.")
9597 (license license:gpl3+)))
9599 (define-public trim-galore
9601 (name "trim-galore")
9606 (uri (string-append "http://www.bioinformatics.babraham.ac.uk/"
9607 "projects/trim_galore/trim_galore_v"
9611 "0b9qdxi4521gsrjvbhgky8g7kry9b5nx3byzaxkgxz7p4k8bn1mn"))))
9612 (build-system gnu-build-system)
9614 `(#:tests? #f ; no tests
9616 (modify-phases %standard-phases
9617 ;; The archive contains plain files.
9619 (lambda* (#:key source #:allow-other-keys)
9620 (zero? (system* "unzip" source))))
9623 (add-after 'unpack 'hardcode-tool-references
9624 (lambda* (#:key inputs #:allow-other-keys)
9625 (substitute* "trim_galore"
9626 (("\\$path_to_cutadapt = 'cutadapt'")
9627 (string-append "$path_to_cutadapt = '"
9628 (assoc-ref inputs "cutadapt")
9632 (assoc-ref inputs "gzip")
9636 (assoc-ref inputs "gzip")
9640 (lambda* (#:key outputs #:allow-other-keys)
9641 (let ((bin (string-append (assoc-ref outputs "out")
9644 (install-file "trim_galore" bin)
9649 ("cutadapt" ,cutadapt)))
9651 `(("unzip" ,unzip)))
9652 (home-page "http://www.bioinformatics.babraham.ac.uk/projects/trim_galore/")
9653 (synopsis "Wrapper around Cutadapt and FastQC")
9654 (description "Trim Galore! is a wrapper script to automate quality and
9655 adapter trimming as well as quality control, with some added functionality to
9656 remove biased methylation positions for RRBS sequence files.")
9657 (license license:gpl3+)))
9665 (uri (string-append "http://compbio.uthscsa.edu/"
9667 "gess-" version ".src.tar.gz"))
9670 "0hyk403kxscclzfs24pvdgiv0wm03kjcziqdrp5w46cb049gz0d7"))))
9671 (build-system gnu-build-system)
9673 `(#:tests? #f ; no tests
9675 (modify-phases %standard-phases
9679 (lambda* (#:key inputs outputs #:allow-other-keys)
9680 (let* ((python (assoc-ref inputs "python"))
9681 (out (assoc-ref outputs "out"))
9682 (bin (string-append out "/bin/"))
9683 (target (string-append
9684 out "/lib/python2.7/site-packages/gess/")))
9686 (copy-recursively "." target)
9687 ;; Make GESS.py executable
9688 (chmod (string-append target "GESS.py") #o555)
9689 ;; Add Python shebang to the top and make Matplotlib
9691 (substitute* (string-append target "GESS.py")
9692 (("\"\"\"Description:" line)
9693 (string-append "#!" (which "python") "
9695 matplotlib.use('Agg')
9697 ;; Make sure GESS has all modules in its path
9698 (wrap-program (string-append target "GESS.py")
9699 `("PYTHONPATH" ":" prefix (,target ,(getenv "PYTHONPATH"))))
9701 (symlink (string-append target "GESS.py")
9702 (string-append bin "GESS.py"))
9705 `(("python" ,python-2)
9706 ("python2-pysam" ,python2-pysam)
9707 ("python2-scipy" ,python2-scipy)
9708 ("python2-numpy" ,python2-numpy)
9709 ("python2-networkx" ,python2-networkx)
9710 ("python2-biopython" ,python2-biopython)))
9711 (home-page "http://compbio.uthscsa.edu/GESS_Web/")
9712 (synopsis "Detect exon-skipping events from raw RNA-seq data")
9714 "GESS is an implementation of a novel computational method to detect de
9715 novo exon-skipping events directly from raw RNA-seq data without the prior
9716 knowledge of gene annotation information. GESS stands for the graph-based
9717 exon-skipping scanner detection scheme.")
9718 (license license:bsd-3)))
9720 (define-public phylip
9727 (uri (string-append "http://evolution.gs.washington.edu/phylip/"
9728 "download/phylip-" version ".tar.gz"))
9731 "01jar1rayhr2gba2pgbw49m56rc5z4p5wn3ds0m188hrlln4a2nd"))))
9732 (build-system gnu-build-system)
9734 `(#:tests? #f ; no check target
9735 #:make-flags (list "-f" "Makefile.unx" "install")
9736 #:parallel-build? #f ; not supported
9738 (modify-phases %standard-phases
9739 (add-after 'unpack 'enter-dir
9740 (lambda _ (chdir "src") #t))
9743 (lambda* (#:key inputs outputs #:allow-other-keys)
9744 (let ((target (string-append (assoc-ref outputs "out")
9747 (for-each (lambda (file)
9748 (install-file file target))
9749 (find-files "../exe" ".*")))
9751 (home-page "http://evolution.genetics.washington.edu/phylip/")
9752 (synopsis "Tools for inferring phylogenies")
9753 (description "PHYLIP (the PHYLogeny Inference Package) is a package of
9754 programs for inferring phylogenies (evolutionary trees).")
9755 (license license:bsd-2)))
9764 (uri (string-append "https://integrativemodeling.org/"
9765 version "/download/imp-" version ".tar.gz"))
9768 "0lxqx7vh79d771svr611dkilp6sn30qrbw8zvscbrm37v38d2j6h"))))
9769 (build-system cmake-build-system)
9771 `(;; FIXME: Some tests fail because they produce warnings, others fail
9772 ;; because the PYTHONPATH does not include the modeller's directory.
9774 ;; Do not place libraries in an architecture-specific directory.
9776 (list "-DCMAKE_INSTALL_LIBDIR=lib")))
9783 ("python" ,python-2)))
9785 `(("python2-numpy" ,python2-numpy)
9786 ("python2-scipy" ,python2-scipy)
9787 ("python2-pandas" ,python2-pandas)
9788 ("python2-scikit-learn" ,python2-scikit-learn)
9789 ("python2-networkx" ,python2-networkx)))
9790 (home-page "https://integrativemodeling.org")
9791 (synopsis "Integrative modeling platform")
9792 (description "IMP's broad goal is to contribute to a comprehensive
9793 structural characterization of biomolecules ranging in size and complexity
9794 from small peptides to large macromolecular assemblies, by integrating data
9795 from diverse biochemical and biophysical experiments. IMP provides a C++ and
9796 Python toolbox for solving complex modeling problems, and a number of
9797 applications for tackling some common problems in a user-friendly way.")
9798 ;; IMP is largely available under the GNU Lesser GPL; see the file
9799 ;; COPYING.LGPL for the full text of this license. Some IMP modules are
9800 ;; available under the GNU GPL (see the file COPYING.GPL).
9801 (license (list license:lgpl2.1+
9804 (define-public tadbit
9810 (uri (string-append "https://github.com/3DGenomes/TADbit/"
9811 "archive/v" version ".tar.gz"))
9812 (file-name (string-append name "-" version ".tar.gz"))
9815 "1cnfqrl4685zar4nnw94j94nhvl2h29jm448nadqi1h05z6fdk4f"))))
9816 (build-system python-build-system)
9818 `(;; Tests are included and must be run after installation, but
9819 ;; they are incomplete and thus cannot be run.
9823 (modify-phases %standard-phases
9824 (add-after 'unpack 'fix-problems-with-setup.py
9825 (lambda* (#:key outputs #:allow-other-keys)
9826 ;; setup.py opens these files for writing
9827 (chmod "_pytadbit/_version.py" #o664)
9828 (chmod "README.rst" #o664)
9830 ;; Don't attempt to install the bash completions to
9831 ;; the home directory.
9832 (rename-file "extras/.bash_completion"
9834 (substitute* "setup.py"
9835 (("\\(path.expanduser\\('~'\\)")
9836 (string-append "(\""
9837 (assoc-ref outputs "out")
9838 "/etc/bash_completion.d\""))
9839 (("extras/\\.bash_completion")
9843 ;; TODO: add Chimera for visualization
9846 ("python2-scipy" ,python2-scipy)
9847 ("python2-numpy" ,python2-numpy)
9848 ("python2-matplotlib" ,python2-matplotlib)
9849 ("python2-pysam" ,python2-pysam)))
9850 (home-page "http://3dgenomes.github.io/TADbit/")
9851 (synopsis "Analyze, model, and explore 3C-based data")
9853 "TADbit is a complete Python library to deal with all steps to analyze,
9854 model, and explore 3C-based data. With TADbit the user can map FASTQ files to
9855 obtain raw interaction binned matrices (Hi-C like matrices), normalize and
9856 correct interaction matrices, identify and compare the so-called
9857 @dfn{Topologically Associating Domains} (TADs), build 3D models from the
9858 interaction matrices, and finally, extract structural properties from the
9859 models. TADbit is complemented by TADkit for visualizing 3D models.")
9860 (license license:gpl3+)))
9862 (define-public kentutils
9865 ;; 302.1.0 is out, but the only difference is the inclusion of
9866 ;; pre-built binaries.
9871 (uri (string-append "https://github.com/ENCODE-DCC/kentUtils/"
9872 "archive/v" version ".tar.gz"))
9873 (file-name (string-append name "-" version ".tar.gz"))
9876 "134aja3k1cj32kbk1nnw0q9gxjb2krr15q6sga8qldzvc0585rmm"))
9877 (modules '((guix build utils)
9882 ;; Only the contents of the specified directories are free
9883 ;; for all uses, so we remove the rest. "hg/autoSql" and
9884 ;; "hg/autoXml" are nominally free, but they depend on a
9885 ;; library that is built from the sources in "hg/lib",
9886 ;; which is nonfree.
9887 (let ((free (list "." ".."
9888 "utils" "lib" "inc" "tagStorm"
9889 "parasol" "htslib"))
9890 (directory? (lambda (file)
9891 (eq? 'directory (stat:type (stat file))))))
9892 (for-each (lambda (file)
9893 (and (directory? file)
9894 (delete-file-recursively file)))
9895 (map (cut string-append "src/" <>)
9898 (not (member file free)))))))
9899 ;; Only make the utils target, not the userApps target,
9900 ;; because that requires libraries we won't build.
9901 (substitute* "Makefile"
9902 ((" userApps") " utils"))
9903 ;; Only build libraries that are free.
9904 (substitute* "src/makefile"
9905 (("DIRS =.*") "DIRS =\n")
9906 (("cd jkOwnLib.*") "")
9909 (substitute* "src/utils/makefile"
9910 ;; These tools depend on "jkhgap.a", which is part of the
9911 ;; nonfree "src/hg/lib" directory.
9913 (("pslLiftSubrangeBlat") "")
9915 ;; Do not build UCSC tools, which may require nonfree
9917 (("ALL_APPS =.*") "ALL_APPS = $(UTILS_APPLIST)\n"))
9919 (build-system gnu-build-system)
9921 `( ;; There is no global test target and the test target for
9922 ;; individual tools depends on input files that are not
9926 (modify-phases %standard-phases
9927 (add-after 'unpack 'fix-paths
9929 (substitute* "Makefile"
9930 (("/bin/echo") (which "echo")))
9932 (add-after 'unpack 'prepare-samtabix
9933 (lambda* (#:key inputs #:allow-other-keys)
9934 (copy-recursively (assoc-ref inputs "samtabix")
9939 (lambda* (#:key outputs #:allow-other-keys)
9940 (let ((bin (string-append (assoc-ref outputs "out")
9942 (copy-recursively "bin" bin))
9949 (url "http://genome-source.cse.ucsc.edu/samtabix.git")
9950 (commit "10fd107909c1ac4d679299908be4262a012965ba")))
9953 "0c1nj64l42v395sa84n7az43xiap4i6f9n9dfz4058aqiwkhkmma"))))))
9960 ("openssl" ,openssl)))
9961 (home-page "http://genome.cse.ucsc.edu/index.html")
9962 (synopsis "Assorted bioinformatics utilities")
9963 (description "This package provides the kentUtils, a selection of
9964 bioinformatics utilities used in combination with the UCSC genome
9966 ;; Only a subset of the sources are released under a non-copyleft
9967 ;; free software license. All other sources are removed in a
9968 ;; snippet. See this bug report for an explanation of how the
9969 ;; license statements apply:
9970 ;; https://github.com/ENCODE-DCC/kentUtils/issues/12
9971 (license (license:non-copyleft
9972 "http://genome.ucsc.edu/license/"
9973 "The contents of this package are free for all uses."))))
9975 (define-public f-seq
9976 (let ((commit "6ccded34cff38cf432deed8503648b4a66953f9b")
9980 (version (string-append "1.1-" revision "." commit))
9984 (url "https://github.com/aboyle/F-seq.git")
9986 (file-name (string-append name "-" version))
9989 "1nk33k0yajg2id4g59bc4szr58r2q6pdq42vgcw054m8ip9wv26h"))
9990 (modules '((guix build utils)))
9991 ;; Remove bundled Java library archives.
9994 (for-each delete-file (find-files "lib" ".*"))
9996 (build-system ant-build-system)
9998 `(#:tests? #f ; no tests included
10000 (modify-phases %standard-phases
10002 (lambda* (#:key outputs #:allow-other-keys)
10003 (let* ((target (assoc-ref outputs "out"))
10004 (doc (string-append target "/share/doc/f-seq/")))
10007 (substitute* "bin/linux/fseq"
10008 (("java") (which "java")))
10009 (install-file "README.txt" doc)
10010 (install-file "bin/linux/fseq" (string-append target "/bin"))
10011 (install-file "build~/fseq.jar" (string-append target "/lib"))
10012 (copy-recursively "lib" (string-append target "/lib"))
10016 ("java-commons-cli" ,java-commons-cli)))
10017 (home-page "http://fureylab.web.unc.edu/software/fseq/")
10018 (synopsis "Feature density estimator for high-throughput sequence tags")
10020 "F-Seq is a software package that generates a continuous tag sequence
10021 density estimation allowing identification of biologically meaningful sites
10022 such as transcription factor binding sites (ChIP-seq) or regions of open
10023 chromatin (DNase-seq). Output can be displayed directly in the UCSC Genome
10025 (license license:gpl3+))))
10027 (define-public bismark
10034 (uri (string-append "https://github.com/FelixKrueger/Bismark/"
10035 "archive/" version ".tar.gz"))
10036 (file-name (string-append name "-" version ".tar.gz"))
10039 "1204i0pa02ll2jn5pnxypkclnskvv7a2nwh5nxhagmhxk9wfv9sq"))))
10040 (build-system perl-build-system)
10042 `(#:tests? #f ; there are no tests
10044 (modify-phases %standard-phases
10045 (delete 'configure)
10048 (lambda* (#:key outputs #:allow-other-keys)
10049 (let ((bin (string-append (assoc-ref outputs "out")
10051 (docdir (string-append (assoc-ref outputs "out")
10052 "/share/doc/bismark"))
10053 (docs '("Bismark_User_Guide.pdf"
10054 "RELEASE_NOTES.txt"))
10055 (scripts '("bismark"
10056 "bismark_genome_preparation"
10057 "bismark_methylation_extractor"
10060 "coverage2cytosine"
10061 "deduplicate_bismark"
10062 "bismark_sitrep.tpl"
10064 "bismark2summary")))
10067 (for-each (lambda (file) (install-file file bin))
10069 (for-each (lambda (file) (install-file file docdir))
10072 (home-page "http://www.bioinformatics.babraham.ac.uk/projects/bismark/")
10073 (synopsis "Map bisulfite treated sequence reads and analyze methylation")
10074 (description "Bismark is a program to map bisulfite treated sequencing
10075 reads to a genome of interest and perform methylation calls in a single step.
10076 The output can be easily imported into a genome viewer, such as SeqMonk, and
10077 enables a researcher to analyse the methylation levels of their samples
10078 straight away. Its main features are:
10081 @item Bisulfite mapping and methylation calling in one single step
10082 @item Supports single-end and paired-end read alignments
10083 @item Supports ungapped and gapped alignments
10084 @item Alignment seed length, number of mismatches etc are adjustable
10085 @item Output discriminates between cytosine methylation in CpG, CHG
10088 (license license:gpl3+)))