1 ;;; GNU Guix --- Functional package management for GNU
2 ;;; Copyright © 2014, 2015, 2016, 2017, 2018 Ricardo Wurmus <rekado@elephly.net>
3 ;;; Copyright © 2015, 2016, 2017, 2018 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, 2018 Efraim Flashner <efraim@flashner.co.il>
8 ;;; Copyright © 2016 Marius Bakke <mbakke@fastmail.com>
9 ;;; Copyright © 2016, 2018 Raoul Bonnal <ilpuccio.febo@gmail.com>
10 ;;; Copyright © 2017, 2018 Tobias Geerinckx-Rice <me@tobias.gr>
11 ;;; Copyright © 2017 Arun Isaac <arunisaac@systemreboot.net>
12 ;;; Copyright © 2018 Joshua Sierles, Nextjournal <joshua@nextjournal.com>
14 ;;; This file is part of GNU Guix.
16 ;;; GNU Guix is free software; you can redistribute it and/or modify it
17 ;;; under the terms of the GNU General Public License as published by
18 ;;; the Free Software Foundation; either version 3 of the License, or (at
19 ;;; your option) any later version.
21 ;;; GNU Guix is distributed in the hope that it will be useful, but
22 ;;; WITHOUT ANY WARRANTY; without even the implied warranty of
23 ;;; MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
24 ;;; GNU General Public License for more details.
26 ;;; You should have received a copy of the GNU General Public License
27 ;;; along with GNU Guix. If not, see <http://www.gnu.org/licenses/>.
29 (define-module (gnu packages bioinformatics)
30 #:use-module ((guix licenses) #:prefix license:)
31 #:use-module (guix packages)
32 #:use-module (guix utils)
33 #:use-module (guix download)
34 #:use-module (guix git-download)
35 #:use-module (guix hg-download)
36 #:use-module (guix build-system ant)
37 #:use-module (guix build-system gnu)
38 #:use-module (guix build-system cmake)
39 #:use-module (guix build-system ocaml)
40 #:use-module (guix build-system perl)
41 #:use-module (guix build-system python)
42 #:use-module (guix build-system r)
43 #:use-module (guix build-system ruby)
44 #:use-module (guix build-system scons)
45 #:use-module (guix build-system trivial)
46 #:use-module (gnu packages)
47 #:use-module (gnu packages autotools)
48 #:use-module (gnu packages algebra)
49 #:use-module (gnu packages base)
50 #:use-module (gnu packages bash)
51 #:use-module (gnu packages bison)
52 #:use-module (gnu packages boost)
53 #:use-module (gnu packages check)
54 #:use-module (gnu packages compression)
55 #:use-module (gnu packages cpio)
56 #:use-module (gnu packages cran)
57 #:use-module (gnu packages curl)
58 #:use-module (gnu packages documentation)
59 #:use-module (gnu packages databases)
60 #:use-module (gnu packages datastructures)
61 #:use-module (gnu packages file)
62 #:use-module (gnu packages flex)
63 #:use-module (gnu packages gawk)
64 #:use-module (gnu packages gcc)
65 #:use-module (gnu packages gd)
66 #:use-module (gnu packages gtk)
67 #:use-module (gnu packages glib)
68 #:use-module (gnu packages graph)
69 #:use-module (gnu packages groff)
70 #:use-module (gnu packages guile)
71 #:use-module (gnu packages haskell)
72 #:use-module (gnu packages image)
73 #:use-module (gnu packages imagemagick)
74 #:use-module (gnu packages java)
75 #:use-module (gnu packages jemalloc)
76 #:use-module (gnu packages ldc)
77 #:use-module (gnu packages linux)
78 #:use-module (gnu packages logging)
79 #:use-module (gnu packages machine-learning)
80 #:use-module (gnu packages man)
81 #:use-module (gnu packages maths)
82 #:use-module (gnu packages mpi)
83 #:use-module (gnu packages ncurses)
84 #:use-module (gnu packages ocaml)
85 #:use-module (gnu packages pcre)
86 #:use-module (gnu packages parallel)
87 #:use-module (gnu packages pdf)
88 #:use-module (gnu packages perl)
89 #:use-module (gnu packages perl-check)
90 #:use-module (gnu packages pkg-config)
91 #:use-module (gnu packages popt)
92 #:use-module (gnu packages protobuf)
93 #:use-module (gnu packages python)
94 #:use-module (gnu packages python-web)
95 #:use-module (gnu packages readline)
96 #:use-module (gnu packages ruby)
97 #:use-module (gnu packages serialization)
98 #:use-module (gnu packages shells)
99 #:use-module (gnu packages statistics)
100 #:use-module (gnu packages swig)
101 #:use-module (gnu packages tbb)
102 #:use-module (gnu packages tex)
103 #:use-module (gnu packages texinfo)
104 #:use-module (gnu packages textutils)
105 #:use-module (gnu packages time)
106 #:use-module (gnu packages tls)
107 #:use-module (gnu packages vim)
108 #:use-module (gnu packages web)
109 #:use-module (gnu packages xml)
110 #:use-module (gnu packages xorg)
111 #:use-module (srfi srfi-1)
112 #:use-module (ice-9 match))
114 (define-public aragorn
121 "http://mbio-serv2.mbioekol.lu.se/ARAGORN/Downloads/aragorn"
125 "09i1rg716smlbnixfm7q1ml2mfpaa2fpn3hwjg625ysmfwwy712b"))))
126 (build-system gnu-build-system)
128 `(#:tests? #f ; there are no tests
130 (modify-phases %standard-phases
134 (zero? (system* "gcc"
140 (string-append "aragorn" ,version ".c")))))
142 (lambda* (#:key outputs #:allow-other-keys)
143 (let* ((out (assoc-ref outputs "out"))
144 (bin (string-append out "/bin"))
145 (man (string-append out "/share/man/man1")))
147 (install-file "aragorn" bin)
149 (install-file "aragorn.1" man))
151 (home-page "http://mbio-serv2.mbioekol.lu.se/ARAGORN")
152 (synopsis "Detect tRNA, mtRNA and tmRNA genes in nucleotide sequences")
154 "Aragorn identifies transfer RNA, mitochondrial RNA and
155 transfer-messenger RNA from nucleotide sequences, based on homology to known
156 tRNA consensus sequences and RNA structure. It also outputs the secondary
157 structure of the predicted RNA.")
158 (license license:gpl2)))
166 ;; BamM is not available on pypi.
168 "https://github.com/Ecogenomics/BamM/archive/"
170 (file-name (string-append name "-" version ".tar.gz"))
173 "1f35yxp4pc8aadsvbpg6r4kg2jh4fkjci0iby4iyljm6980sac0s"))
174 (modules '((guix build utils)))
177 ;; Delete bundled htslib.
178 (delete-file-recursively "c/htslib-1.3.1")
180 (build-system python-build-system)
182 `(#:python ,python-2 ; BamM is Python 2 only.
183 ;; Do not use bundled libhts. Do use the bundled libcfu because it has
184 ;; been modified from its original form.
186 (let ((htslib (assoc-ref %build-inputs "htslib")))
187 (list "--with-libhts-lib" (string-append htslib "/lib")
188 "--with-libhts-inc" (string-append htslib "/include/htslib")))
190 (modify-phases %standard-phases
191 (add-after 'unpack 'autogen
193 (with-directory-excursion "c"
194 (let ((sh (which "sh")))
195 ;; Use autogen so that 'configure' works.
196 (substitute* "autogen.sh" (("/bin/sh") sh))
197 (setenv "CONFIG_SHELL" sh)
198 (substitute* "configure" (("/bin/sh") sh))
199 (zero? (system* "./autogen.sh"))))))
201 ;; Run tests after installation so compilation only happens once.
203 (add-after 'install 'wrap-executable
204 (lambda* (#:key outputs #:allow-other-keys)
205 (let* ((out (assoc-ref outputs "out"))
206 (path (getenv "PATH")))
207 (wrap-program (string-append out "/bin/bamm")
208 `("PATH" ":" prefix (,path))))
210 (add-after 'wrap-executable 'post-install-check
211 (lambda* (#:key inputs outputs #:allow-other-keys)
213 (string-append (assoc-ref outputs "out")
218 (assoc-ref outputs "out")
220 (string-take (string-take-right
221 (assoc-ref inputs "python") 5) 3)
223 (getenv "PYTHONPATH")))
224 ;; There are 2 errors printed, but they are safe to ignore:
225 ;; 1) [E::hts_open_format] fail to open file ...
226 ;; 2) samtools view: failed to open ...
227 (zero? (system* "nosetests")))))))
229 `(("autoconf" ,autoconf)
230 ("automake" ,automake)
233 ("python-nose" ,python2-nose)
234 ("python-pysam" ,python2-pysam)))
236 `(("htslib" ,htslib-1.3) ; At least one test fails on htslib-1.4+.
237 ("samtools" ,samtools)
241 ("coreutils" ,coreutils)))
243 `(("python-numpy" ,python2-numpy)))
244 (home-page "http://ecogenomics.github.io/BamM/")
245 (synopsis "Metagenomics-focused BAM file manipulator")
247 "BamM is a C library, wrapped in python, to efficiently generate and
248 parse BAM files, specifically for the analysis of metagenomic data. For
249 instance, it implements several methods to assess contig-wise read coverage.")
250 (license license:lgpl3+)))
252 (define-public bamtools
259 "https://github.com/pezmaster31/bamtools/archive/v"
261 (file-name (string-append name "-" version ".tar.gz"))
264 "1z3kg24qrwq13a88n9d86izngrar4fll7gr6phddb2faw75pdgaa"))))
265 (build-system cmake-build-system)
267 `(#:tests? #f ;no "check" target
269 (modify-phases %standard-phases
271 'configure 'set-ldflags
272 (lambda* (#:key outputs #:allow-other-keys)
276 (assoc-ref outputs "out") "/lib/bamtools")))))))
277 (inputs `(("zlib" ,zlib)))
278 (home-page "https://github.com/pezmaster31/bamtools")
279 (synopsis "C++ API and command-line toolkit for working with BAM data")
281 "BamTools provides both a C++ API and a command-line toolkit for handling
283 (license license:expat)))
285 (define-public bcftools
292 "https://github.com/samtools/bcftools/releases/download/"
293 version "/bcftools-" version ".tar.bz2"))
296 "1vgw2mwngq20c530zim52zvgmw1lci8rzl33pvh44xqk3xlzvjsa"))
297 (modules '((guix build utils)))
299 ;; Delete bundled htslib.
300 (delete-file-recursively "htslib-1.8")
302 (build-system gnu-build-system)
304 `(#:test-target "test"
305 #:configure-flags (list "--with-htslib=system")
309 "LIBS=-lgsl -lgslcblas"
310 (string-append "prefix=" (assoc-ref %outputs "out"))
311 (string-append "HTSDIR=" (assoc-ref %build-inputs "htslib") "/include")
312 (string-append "HTSLIB=" (assoc-ref %build-inputs "htslib") "/lib/libhts.so")
313 (string-append "BGZIP=" (assoc-ref %build-inputs "htslib") "/bin/bgzip")
314 (string-append "TABIX=" (assoc-ref %build-inputs "htslib") "/bin/tabix")
315 (string-append "PACKAGE_VERSION=" ,version))
317 (modify-phases %standard-phases
318 (add-before 'check 'patch-tests
320 (substitute* "test/test.pl"
321 (("/bin/bash") (which "bash")))
329 (home-page "https://samtools.github.io/bcftools/")
330 (synopsis "Utilities for variant calling and manipulating VCFs and BCFs")
332 "BCFtools is a set of utilities that manipulate variant calls in the
333 Variant Call Format (VCF) and its binary counterpart BCF. All commands work
334 transparently with both VCFs and BCFs, both uncompressed and BGZF-compressed.")
335 ;; The sources are dual MIT/GPL, but becomes GPL-only when USE_GPL=1.
336 (license (list license:gpl3+ license:expat))))
338 (define-public bedops
344 (uri (string-append "https://github.com/bedops/bedops/archive/v"
346 (file-name (string-append name "-" version ".tar.gz"))
349 "0kx4awrwby8f33wqyx8w7ms7v25xhf0d421csgf96a3hfzn2mb0m"))))
350 (build-system gnu-build-system)
353 #:make-flags (list (string-append "BINDIR=" %output "/bin"))
355 (modify-phases %standard-phases
356 (add-after 'unpack 'unpack-tarballs
358 ;; FIXME: Bedops includes tarballs of minimally patched upstream
359 ;; libraries jansson, zlib, and bzip2. We cannot just use stock
360 ;; libraries because at least one of the libraries (zlib) is
361 ;; patched to add a C++ function definition (deflateInit2cpp).
362 ;; Until the Bedops developers offer a way to link against system
363 ;; libraries we have to build the in-tree copies of these three
366 ;; See upstream discussion:
367 ;; https://github.com/bedops/bedops/issues/124
369 ;; Unpack the tarballs to benefit from shebang patching.
370 (with-directory-excursion "third-party"
371 (and (zero? (system* "tar" "xvf" "jansson-2.6.tar.bz2"))
372 (zero? (system* "tar" "xvf" "zlib-1.2.7.tar.bz2"))
373 (zero? (system* "tar" "xvf" "bzip2-1.0.6.tar.bz2"))))
374 ;; Disable unpacking of tarballs in Makefile.
375 (substitute* "system.mk/Makefile.linux"
376 (("^\tbzcat .*") "\t@echo \"not unpacking\"\n")
377 (("\\./configure") "CONFIG_SHELL=bash ./configure"))
378 (substitute* "third-party/zlib-1.2.7/Makefile.in"
379 (("^SHELL=.*$") "SHELL=bash\n"))
381 (delete 'configure))))
382 (home-page "https://github.com/bedops/bedops")
383 (synopsis "Tools for high-performance genomic feature operations")
385 "BEDOPS is a suite of tools to address common questions raised in genomic
386 studies---mostly with regard to overlap and proximity relationships between
387 data sets. It aims to be scalable and flexible, facilitating the efficient
388 and accurate analysis and management of large-scale genomic data.
390 BEDOPS provides tools that perform highly efficient and scalable Boolean and
391 other set operations, statistical calculations, archiving, conversion and
392 other management of genomic data of arbitrary scale. Tasks can be easily
393 split by chromosome for distributing whole-genome analyses across a
394 computational cluster.")
395 (license license:gpl2+)))
397 (define-public bedtools
403 (uri (string-append "https://github.com/arq5x/bedtools2/releases/"
404 "download/v" version "/"
405 "bedtools-" version ".tar.gz"))
408 "1ndg5yknrxl4djx8ddzgk12rrbiidfpmkkg5z3f95jzryfxarhn8"))))
409 (build-system gnu-build-system)
411 '(#:test-target "test"
413 (list (string-append "prefix=" (assoc-ref %outputs "out")))
415 (modify-phases %standard-phases
416 (delete 'configure))))
417 (native-inputs `(("python" ,python-2)))
419 `(("samtools" ,samtools)
421 (home-page "https://github.com/arq5x/bedtools2")
422 (synopsis "Tools for genome analysis and arithmetic")
424 "Collectively, the bedtools utilities are a swiss-army knife of tools for
425 a wide-range of genomics analysis tasks. The most widely-used tools enable
426 genome arithmetic: that is, set theory on the genome. For example, bedtools
427 allows one to intersect, merge, count, complement, and shuffle genomic
428 intervals from multiple files in widely-used genomic file formats such as BAM,
430 (license license:gpl2)))
432 ;; Later releases of bedtools produce files with more columns than
433 ;; what Ribotaper expects.
434 (define-public bedtools-2.18
435 (package (inherit bedtools)
440 (uri (string-append "https://github.com/arq5x/bedtools2/"
441 "archive/v" version ".tar.gz"))
442 (file-name (string-append name "-" version ".tar.gz"))
445 "05vrnr8yp7swfagshzpgqmzk1blnwnq8pq5pckzi1m26w98d63vf"))))
447 '(#:test-target "test"
449 (modify-phases %standard-phases
452 (lambda* (#:key outputs #:allow-other-keys)
453 (let ((bin (string-append (assoc-ref outputs "out") "/bin/")))
454 (for-each (lambda (file)
455 (install-file file bin))
456 (find-files "bin" ".*")))
459 (define-public ribotaper
465 (uri (string-append "https://ohlerlab.mdc-berlin.de/"
466 "files/RiboTaper/RiboTaper_Version_"
470 "0ykjbps1y3z3085q94npw8i9x5gldc6shy8vlc08v76zljsm07hv"))))
471 (build-system gnu-build-system)
474 (modify-phases %standard-phases
475 (add-after 'install 'wrap-executables
476 (lambda* (#:key inputs outputs #:allow-other-keys)
477 (let* ((out (assoc-ref outputs "out")))
480 (wrap-program (string-append out "/bin/" script)
481 `("R_LIBS_SITE" ":" = (,(getenv "R_LIBS_SITE")))))
482 '("create_annotations_files.bash"
483 "create_metaplots.bash"
484 "Ribotaper_ORF_find.sh"
485 "Ribotaper.sh"))))))))
487 `(("bedtools" ,bedtools-2.18)
488 ("samtools" ,samtools-0.1)
489 ("r-minimal" ,r-minimal)
490 ("r-foreach" ,r-foreach)
491 ("r-xnomial" ,r-xnomial)
493 ("r-multitaper" ,r-multitaper)
494 ("r-seqinr" ,r-seqinr)))
495 (home-page "https://ohlerlab.mdc-berlin.de/software/RiboTaper_126/")
496 (synopsis "Define translated ORFs using ribosome profiling data")
498 "Ribotaper is a method for defining translated @dfn{open reading
499 frames} (ORFs) using ribosome profiling (ribo-seq) data. This package
500 provides the Ribotaper pipeline.")
501 (license license:gpl3+)))
503 (define-public ribodiff
510 (uri (string-append "https://github.com/ratschlab/RiboDiff/"
511 "archive/v" version ".tar.gz"))
512 (file-name (string-append name "-" version ".tar.gz"))
515 "0wpbwmfv05wdjxv7ikm664f7s7p7cqr8jnw99zrda0q67rl50aaj"))))
516 (build-system python-build-system)
520 (modify-phases %standard-phases
521 ;; Generate an installable executable script wrapper.
522 (add-after 'unpack 'patch-setup.py
524 (substitute* "setup.py"
525 (("^(.*)packages=.*" line prefix)
526 (string-append line "\n"
527 prefix "scripts=['scripts/TE.py'],\n")))
530 `(("python-numpy" ,python2-numpy)
531 ("python-matplotlib" ,python2-matplotlib)
532 ("python-scipy" ,python2-scipy)
533 ("python-statsmodels" ,python2-statsmodels)))
535 `(("python-mock" ,python2-mock)
536 ("python-nose" ,python2-nose)))
537 (home-page "http://public.bmi.inf.ethz.ch/user/zhongy/RiboDiff/")
538 (synopsis "Detect translation efficiency changes from ribosome footprints")
539 (description "RiboDiff is a statistical tool that detects the protein
540 translational efficiency change from Ribo-Seq (ribosome footprinting) and
541 RNA-Seq data. It uses a generalized linear model to detect genes showing
542 difference in translational profile taking mRNA abundance into account. It
543 facilitates us to decipher the translational regulation that behave
544 independently with transcriptional regulation.")
545 (license license:gpl3+)))
547 (define-public bioawk
553 (uri (string-append "https://github.com/lh3/bioawk/archive/v"
555 (file-name (string-append name "-" version ".tar.gz"))
557 (base32 "1daizxsk17ahi9n58fj8vpgwyhzrzh54bzqhanjanp88kgrz7gjw"))))
558 (build-system gnu-build-system)
564 `(#:tests? #f ; There are no tests to run.
565 ;; Bison must generate files, before other targets can build.
568 (modify-phases %standard-phases
569 (delete 'configure) ; There is no configure phase.
571 (lambda* (#:key outputs #:allow-other-keys)
572 (let* ((out (assoc-ref outputs "out"))
573 (bin (string-append out "/bin"))
574 (man (string-append out "/share/man/man1")))
576 (copy-file "awk.1" (string-append man "/bioawk.1"))
577 (install-file "bioawk" bin)))))))
578 (home-page "https://github.com/lh3/bioawk")
579 (synopsis "AWK with bioinformatics extensions")
580 (description "Bioawk is an extension to Brian Kernighan's awk, adding the
581 support of several common biological data formats, including optionally gzip'ed
582 BED, GFF, SAM, VCF, FASTA/Q and TAB-delimited formats with column names. It
583 also adds a few built-in functions and a command line option to use TAB as the
584 input/output delimiter. When the new functionality is not used, bioawk is
585 intended to behave exactly the same as the original BWK awk.")
586 (license license:x11)))
588 (define-public python2-pybedtools
590 (name "python2-pybedtools")
595 "https://pypi.python.org/packages/source/p/pybedtools/pybedtools-"
599 "1ldzdxw1p4y3g2ignmggsdypvqkcwqwzhdha4rbgpih048z5p4an"))))
600 (build-system python-build-system)
601 (arguments `(#:python ,python-2)) ; no Python 3 support
603 `(("python-matplotlib" ,python2-matplotlib)))
605 `(("bedtools" ,bedtools)
606 ("samtools" ,samtools)))
608 `(("python-cython" ,python2-cython)
609 ("python-pyyaml" ,python2-pyyaml)
610 ("python-nose" ,python2-nose)))
611 (home-page "https://pythonhosted.org/pybedtools/")
612 (synopsis "Python wrapper for BEDtools programs")
614 "pybedtools is a Python wrapper for Aaron Quinlan's BEDtools programs,
615 which are widely used for genomic interval manipulation or \"genome algebra\".
616 pybedtools extends BEDTools by offering feature-level manipulations from with
618 (license license:gpl2+)))
620 (define-public python-biom-format
622 (name "python-biom-format")
627 ;; Use GitHub as source because PyPI distribution does not contain
628 ;; test data: https://github.com/biocore/biom-format/issues/693
629 (uri (string-append "https://github.com/biocore/biom-format/archive/"
631 (file-name (string-append name "-" version ".tar.gz"))
634 "08cr7wpahk6zb31h4bs7jmzpvxcqv9s13xz40h6y2h656jvdvnpj"))))
635 (build-system python-build-system)
637 `(("python-numpy" ,python-numpy)
638 ("python-scipy" ,python-scipy)
639 ("python-future" ,python-future)
640 ("python-click" ,python-click)
641 ("python-h5py" ,python-h5py)
642 ("python-pandas" ,python-pandas)))
644 `(("python-nose" ,python-nose)))
645 (home-page "http://www.biom-format.org")
646 (synopsis "Biological Observation Matrix (BIOM) format utilities")
648 "The BIOM file format is designed to be a general-use format for
649 representing counts of observations e.g. operational taxonomic units, KEGG
650 orthology groups or lipid types, in one or more biological samples
651 e.g. microbiome samples, genomes, metagenomes.")
652 (license license:bsd-3)
653 (properties `((python2-variant . ,(delay python2-biom-format))))))
655 (define-public python2-biom-format
656 (let ((base (package-with-python2 (strip-python2-variant python-biom-format))))
661 (modify-phases %standard-phases
662 ;; Do not require the unmaintained pyqi library.
663 (add-after 'unpack 'remove-pyqi
665 (substitute* "setup.py"
666 (("install_requires.append\\(\"pyqi\"\\)") "pass"))
668 ,@(package-arguments base))))))
670 (define-public bioperl-minimal
671 (let* ((inputs `(("perl-module-build" ,perl-module-build)
672 ("perl-data-stag" ,perl-data-stag)
673 ("perl-libwww" ,perl-libwww)
674 ("perl-uri" ,perl-uri)))
676 (map (compose package-name cadr)
679 (map (compose package-transitive-target-inputs cadr) inputs))))))
681 (name "bioperl-minimal")
686 (uri (string-append "https://github.com/bioperl/bioperl-live/"
688 (string-map (lambda (c)
694 "12phgpxwgkqflkwfb9dcqg7a31dpjlfhar8wcgv0aj5ln4akfz06"))))
695 (build-system perl-build-system)
698 (modify-phases %standard-phases
700 'install 'wrap-programs
701 (lambda* (#:key outputs #:allow-other-keys)
702 ;; Make sure all executables in "bin" find the required Perl
703 ;; modules at runtime. As the PERL5LIB variable contains also
704 ;; the paths of native inputs, we pick the transitive target
705 ;; inputs from %build-inputs.
706 (let* ((out (assoc-ref outputs "out"))
707 (bin (string-append out "/bin/"))
709 (cons (string-append out "/lib/perl5/site_perl")
711 (assoc-ref %build-inputs name))
712 ',transitive-inputs))
714 (for-each (lambda (file)
716 `("PERL5LIB" ":" prefix (,path))))
717 (find-files bin "\\.pl$"))
721 `(("perl-test-most" ,perl-test-most)))
722 (home-page "http://search.cpan.org/dist/BioPerl")
723 (synopsis "Bioinformatics toolkit")
725 "BioPerl is the product of a community effort to produce Perl code which
726 is useful in biology. Examples include Sequence objects, Alignment objects
727 and database searching objects. These objects not only do what they are
728 advertised to do in the documentation, but they also interact - Alignment
729 objects are made from the Sequence objects, Sequence objects have access to
730 Annotation and SeqFeature objects and databases, Blast objects can be
731 converted to Alignment objects, and so on. This means that the objects
732 provide a coordinated and extensible framework to do computational biology.")
733 (license license:perl-license))))
735 (define-public python-biopython
737 (name "python-biopython")
741 ;; use PyPi rather than biopython.org to ease updating
742 (uri (pypi-uri "biopython" version))
745 "0nz4n9d2y2dg849gn1z0vjlkwcpzzkzy3fij7x94a6ixy2c54z2a"))))
746 (build-system python-build-system)
749 (modify-phases %standard-phases
750 (add-before 'check 'set-home
751 ;; Some tests require a home directory to be set.
752 (lambda _ (setenv "HOME" "/tmp") #t)))))
754 `(("python-numpy" ,python-numpy)))
755 (home-page "http://biopython.org/")
756 (synopsis "Tools for biological computation in Python")
758 "Biopython is a set of tools for biological computation including parsers
759 for bioinformatics files into Python data structures; interfaces to common
760 bioinformatics programs; a standard sequence class and tools for performing
761 common operations on them; code to perform data classification; code for
762 dealing with alignments; code making it easy to split up parallelizable tasks
763 into separate processes; and more.")
764 (license (license:non-copyleft "http://www.biopython.org/DIST/LICENSE"))))
766 (define-public python2-biopython
767 (package-with-python2 python-biopython))
769 (define-public bpp-core
770 ;; The last release was in 2014 and the recommended way to install from source
771 ;; is to clone the git repository, so we do this.
772 ;; http://biopp.univ-montp2.fr/wiki/index.php/Main_Page
773 (let ((commit "7d8bced0d1a87291ea8dd7046b7fb5ff9c35c582"))
776 (version (string-append "2.2.0-1." (string-take commit 7)))
780 (url "http://biopp.univ-montp2.fr/git/bpp-core")
782 (file-name (string-append name "-" version "-checkout"))
785 "10djsq5vlnkilv436gnmh4irpk49v29pa69r6xiryg32xmvn909j"))))
786 (build-system cmake-build-system)
788 `(#:parallel-build? #f))
790 `(("gcc" ,gcc-5))) ; Compilation of bpp-phyl fails with GCC 4.9 so we
791 ; compile all of the bpp packages with GCC 5.
792 (home-page "http://biopp.univ-montp2.fr")
793 (synopsis "C++ libraries for Bioinformatics")
795 "Bio++ is a set of C++ libraries for Bioinformatics, including sequence
796 analysis, phylogenetics, molecular evolution and population genetics. It is
797 Object Oriented and is designed to be both easy to use and computer efficient.
798 Bio++ intends to help programmers to write computer expensive programs, by
799 providing them a set of re-usable tools.")
800 (license license:cecill-c))))
802 (define-public bpp-phyl
803 ;; The last release was in 2014 and the recommended way to install from source
804 ;; is to clone the git repository, so we do this.
805 ;; http://biopp.univ-montp2.fr/wiki/index.php/Main_Page
806 (let ((commit "0c07167b629f68b569bf274d1ad0c4af83276ae2"))
809 (version (string-append "2.2.0-1." (string-take commit 7)))
813 (url "http://biopp.univ-montp2.fr/git/bpp-phyl")
815 (file-name (string-append name "-" version "-checkout"))
818 "1ssjgchzwj3iai26kyly7gwkdv8sk59nqhkb1wpap3sf5m6kyllh"))))
819 (build-system cmake-build-system)
821 `(#:parallel-build? #f
822 ;; If out-of-source, test data is not copied into the build directory
823 ;; so the tests fail.
824 #:out-of-source? #f))
826 `(("bpp-core" ,bpp-core)
828 ;; GCC 4.8 fails due to an 'internal compiler error', so we use a more
831 (home-page "http://biopp.univ-montp2.fr")
832 (synopsis "Bio++ phylogenetic Library")
834 "Bio++ is a set of C++ libraries for Bioinformatics, including sequence
835 analysis, phylogenetics, molecular evolution and population genetics. This
836 library provides phylogenetics-related modules.")
837 (license license:cecill-c))))
839 (define-public bpp-popgen
840 ;; The last release was in 2014 and the recommended way to install from source
841 ;; is to clone the git repository, so we do this.
842 ;; http://biopp.univ-montp2.fr/wiki/index.php/Main_Page
843 (let ((commit "e472bac9b1a148803895d747cd6d0c5904f85d9f"))
846 (version (string-append "2.2.0-1." (string-take commit 7)))
850 (url "http://biopp.univ-montp2.fr/git/bpp-popgen")
852 (file-name (string-append name "-" version "-checkout"))
855 "0yn82dzn1n5629nzja68xfrhi655709rjanyryb36vzkmymy6dw5"))))
856 (build-system cmake-build-system)
858 `(#:parallel-build? #f
859 #:tests? #f)) ; There are no tests.
861 `(("bpp-core" ,bpp-core)
864 (home-page "http://biopp.univ-montp2.fr")
865 (synopsis "Bio++ population genetics library")
867 "Bio++ is a set of C++ libraries for Bioinformatics, including sequence
868 analysis, phylogenetics, molecular evolution and population genetics. This
869 library provides population genetics-related modules.")
870 (license license:cecill-c))))
872 (define-public bpp-seq
873 ;; The last release was in 2014 and the recommended way to install from source
874 ;; is to clone the git repository, so we do this.
875 ;; http://biopp.univ-montp2.fr/wiki/index.php/Main_Page
876 (let ((commit "6cfa07965ce152e5598a89df2fa80a75973bfa33"))
879 (version (string-append "2.2.0-1." (string-take commit 7)))
883 (url "http://biopp.univ-montp2.fr/git/bpp-seq")
885 (file-name (string-append name "-" version "-checkout"))
888 "1nys5jq7jqvdg40d91wsmj3q2yzy4276cp7sp44n67p468f27zf2"))))
889 (build-system cmake-build-system)
891 `(#:parallel-build? #f
892 ;; If out-of-source, test data is not copied into the build directory
893 ;; so the tests fail.
894 #:out-of-source? #f))
896 `(("bpp-core" ,bpp-core)
897 ("gcc" ,gcc-5))) ; Use GCC 5 as per 'bpp-core'.
898 (home-page "http://biopp.univ-montp2.fr")
899 (synopsis "Bio++ sequence library")
901 "Bio++ is a set of C++ libraries for Bioinformatics, including sequence
902 analysis, phylogenetics, molecular evolution and population genetics. This
903 library provides sequence-related modules.")
904 (license license:cecill-c))))
906 (define-public bppsuite
907 ;; The last release was in 2014 and the recommended way to install from source
908 ;; is to clone the git repository, so we do this.
909 ;; http://biopp.univ-montp2.fr/wiki/index.php/Main_Page
910 (let ((commit "c516147f57aa50961121cd505bed52cd7603698b"))
913 (version (string-append "2.2.0-1." (string-take commit 7)))
917 (url "http://biopp.univ-montp2.fr/git/bppsuite")
919 (file-name (string-append name "-" version "-checkout"))
922 "1y87pxvw0jxjizhq2dr9g2r91md45k1p9ih2sl1yy1y3p934l2kb"))))
923 (build-system cmake-build-system)
925 `(#:parallel-build? #f
926 #:tests? #f)) ; There are no tests.
930 ("texinfo" ,texinfo)))
932 `(("bpp-core" ,bpp-core)
934 ("bpp-phyl" ,bpp-phyl)
935 ("bpp-phyl" ,bpp-popgen)
937 (home-page "http://biopp.univ-montp2.fr")
938 (synopsis "Bioinformatics tools written with the Bio++ libraries")
940 "Bio++ is a set of C++ libraries for Bioinformatics, including sequence
941 analysis, phylogenetics, molecular evolution and population genetics. This
942 package provides command line tools using the Bio++ library.")
943 (license license:cecill-c))))
945 (define-public blast+
952 "ftp://ftp.ncbi.nlm.nih.gov/blast/executables/blast+/"
953 version "/ncbi-blast-" version "+-src.tar.gz"))
956 "15n937pw5aqmyfjb6l387d18grqbb96l63d5xj4l7yyh0zbf2405"))
957 (patches (search-patches "blast+-fix-makefile.patch"))
958 (modules '((guix build utils)))
961 ;; Remove bundled bzip2, zlib and pcre.
962 (delete-file-recursively "c++/src/util/compress/bzip2")
963 (delete-file-recursively "c++/src/util/compress/zlib")
964 (delete-file-recursively "c++/src/util/regexp")
965 (substitute* "c++/src/util/compress/Makefile.in"
966 (("bzip2 zlib api") "api"))
967 ;; Remove useless msbuild directory
968 (delete-file-recursively
969 "c++/src/build-system/project_tree_builder/msbuild")
971 (build-system gnu-build-system)
973 `(;; There are two(!) tests for this massive library, and both fail with
974 ;; "unparsable timing stats".
975 ;; ERR [127] -- [serial/datatool] datatool.sh (unparsable timing stats)
976 ;; ERR [127] -- [serial/datatool] datatool_xml.sh (unparsable timing stats)
979 #:parallel-build? #f ; not supported
981 (modify-phases %standard-phases
984 ;; $HOME needs to be set at some point during the configure phase
985 (lambda _ (setenv "HOME" "/tmp") #t))
988 (lambda _ (chdir "c++") #t))
990 'enter-dir 'fix-build-system
993 (cond ((string=? cmd "date")
994 ;; make call to "date" deterministic
999 (format (current-error-port)
1000 "WARNING: Unable to find absolute path for ~s~%"
1004 ;; Rewrite hardcoded paths to various tools
1005 (substitute* (append '("src/build-system/configure.ac"
1006 "src/build-system/configure"
1007 "src/build-system/helpers/run_with_lock.c"
1008 "scripts/common/impl/if_diff.sh"
1009 "scripts/common/impl/run_with_lock.sh"
1010 "src/build-system/Makefile.configurables.real"
1011 "src/build-system/Makefile.in.top"
1012 "src/build-system/Makefile.meta.gmake=no"
1013 "src/build-system/Makefile.meta.in"
1014 "src/build-system/Makefile.meta_l"
1015 "src/build-system/Makefile.meta_p"
1016 "src/build-system/Makefile.meta_r"
1017 "src/build-system/Makefile.mk.in"
1018 "src/build-system/Makefile.requirements"
1019 "src/build-system/Makefile.rules_with_autodep.in")
1020 (find-files "scripts/common/check" "\\.sh$"))
1021 (("(/usr/bin/|/bin/)([a-z][-_.a-z]*)" all dir cmd)
1022 (or (which* cmd) all)))
1024 (substitute* (find-files "src/build-system" "^config.*")
1025 (("LN_S=/bin/\\$LN_S") (string-append "LN_S=" (which "ln")))
1028 ;; rewrite "/var/tmp" in check script
1029 (substitute* "scripts/common/check/check_make_unix.sh"
1030 (("/var/tmp") "/tmp"))
1032 ;; do not reset PATH
1033 (substitute* (find-files "scripts/common/impl/" "\\.sh$")
1035 (("action=/bin/") "action=")
1036 (("export PATH") ":"))
1040 (lambda* (#:key inputs outputs #:allow-other-keys)
1041 (let ((out (assoc-ref outputs "out"))
1042 (lib (string-append (assoc-ref outputs "lib") "/lib"))
1043 (include (string-append (assoc-ref outputs "include")
1044 "/include/ncbi-tools++")))
1045 ;; The 'configure' script doesn't recognize things like
1046 ;; '--enable-fast-install'.
1047 (zero? (system* "./configure.orig"
1048 (string-append "--with-build-root=" (getcwd) "/build")
1049 (string-append "--prefix=" out)
1050 (string-append "--libdir=" lib)
1051 (string-append "--includedir=" include)
1052 (string-append "--with-bz2="
1053 (assoc-ref inputs "bzip2"))
1054 (string-append "--with-z="
1055 (assoc-ref inputs "zlib"))
1056 (string-append "--with-pcre="
1057 (assoc-ref inputs "pcre"))
1058 ;; Each library is built twice by default, once
1059 ;; with "-static" in its name, and again
1062 "--with-dll"))))))))
1063 (outputs '("out" ; 21 MB
1071 ("python" ,python-wrapper)))
1074 (home-page "http://blast.ncbi.nlm.nih.gov")
1075 (synopsis "Basic local alignment search tool")
1077 "BLAST is a popular method of performing a DNA or protein sequence
1078 similarity search, using heuristics to produce results quickly. It also
1079 calculates an “expect value” that estimates how many matches would have
1080 occurred at a given score by chance, which can aid a user in judging how much
1081 confidence to have in an alignment.")
1082 ;; Most of the sources are in the public domain, with the following
1085 ;; * ./c++/include/util/bitset/
1086 ;; * ./c++/src/html/ncbi_menu*.js
1088 ;; * ./c++/include/util/impl/floating_point_comparison.hpp
1090 ;; * ./c++/include/dbapi/driver/odbc/unix_odbc/
1092 ;; * ./c++/src/corelib/teamcity_*
1093 (license (list license:public-domain
1099 (define-public bless
1105 (uri (string-append "mirror://sourceforge/bless-ec/bless.v"
1109 "0rm0gw2s18dqwzzpl3c2x1z05ni2v0xz5dmfk3d33j6g4cgrlrdd"))
1110 (modules '((guix build utils)))
1113 ;; Remove bundled boost, pigz, zlib, and .git directory
1114 ;; FIXME: also remove bundled sources for murmurhash3 and
1115 ;; kmc once packaged.
1116 (delete-file-recursively "boost")
1117 (delete-file-recursively "pigz")
1118 (delete-file-recursively "google-sparsehash")
1119 (delete-file-recursively "zlib")
1120 (delete-file-recursively ".git")
1122 (build-system gnu-build-system)
1124 '(#:tests? #f ;no "check" target
1126 (list (string-append "ZLIB="
1127 (assoc-ref %build-inputs "zlib")
1129 (string-append "LDFLAGS="
1130 (string-join '("-lboost_filesystem"
1137 (modify-phases %standard-phases
1138 (add-after 'unpack 'do-not-build-bundled-pigz
1139 (lambda* (#:key inputs outputs #:allow-other-keys)
1140 (substitute* "Makefile"
1141 (("cd pigz/pigz-2.3.3; make") ""))
1143 (add-after 'unpack 'patch-paths-to-executables
1144 (lambda* (#:key inputs outputs #:allow-other-keys)
1145 (substitute* "parse_args.cpp"
1146 (("kmc_binary = .*")
1147 (string-append "kmc_binary = \""
1148 (assoc-ref outputs "out")
1150 (("pigz_binary = .*")
1151 (string-append "pigz_binary = \""
1152 (assoc-ref inputs "pigz")
1156 (lambda* (#:key outputs #:allow-other-keys)
1157 (let ((bin (string-append (assoc-ref outputs "out") "/bin/")))
1158 (for-each (lambda (file)
1159 (install-file file bin))
1160 '("bless" "kmc/bin/kmc"))
1162 (delete 'configure))))
1166 `(("openmpi" ,openmpi)
1168 ("sparsehash" ,sparsehash)
1171 (supported-systems '("x86_64-linux"))
1172 (home-page "https://sourceforge.net/p/bless-ec/wiki/Home/")
1173 (synopsis "Bloom-filter-based error correction tool for NGS reads")
1175 "@dfn{Bloom-filter-based error correction solution for high-throughput
1176 sequencing reads} (BLESS) uses a single minimum-sized bloom filter is a
1177 correction tool for genomic reads produced by @dfn{Next-generation
1178 sequencing} (NGS). BLESS produces accurate correction results with much less
1179 memory compared with previous solutions and is also able to tolerate a higher
1180 false-positive rate. BLESS can extend reads like DNA assemblers to correct
1181 errors at the end of reads.")
1182 (license license:gpl3+)))
1184 (define-public bowtie
1190 (uri (string-append "https://github.com/BenLangmead/bowtie2/archive/v"
1192 (file-name (string-append name "-" version ".tar.gz"))
1195 "0hwa5r9qbglppb7sz5z79rlmmddr3n51n468jb3wh8rwjgn3yr90"))
1196 (modules '((guix build utils)))
1199 (substitute* "Makefile"
1200 ;; replace BUILD_HOST and BUILD_TIME for deterministic build
1201 (("-DBUILD_HOST=.*") "-DBUILD_HOST=\"\\\"guix\\\"\"")
1202 (("-DBUILD_TIME=.*") "-DBUILD_TIME=\"\\\"0\\\"\""))
1204 (build-system gnu-build-system)
1207 ("perl-clone" ,perl-clone)
1208 ("perl-test-deep" ,perl-test-deep)
1209 ("perl-test-simple" ,perl-test-simple)
1210 ("python" ,python-2)
1217 (string-append "prefix=" (assoc-ref %outputs "out")))
1219 (modify-phases %standard-phases
1222 (lambda* (#:key outputs #:allow-other-keys)
1223 (zero? (system* "perl"
1224 "scripts/test/simple_tests.pl"
1225 "--bowtie2=./bowtie2"
1226 "--bowtie2-build=./bowtie2-build")))))))
1227 (home-page "http://bowtie-bio.sourceforge.net/bowtie2/index.shtml")
1228 (synopsis "Fast and sensitive nucleotide sequence read aligner")
1230 "Bowtie 2 is a fast and memory-efficient tool for aligning sequencing
1231 reads to long reference sequences. It is particularly good at aligning reads
1232 of about 50 up to 100s or 1,000s of characters, and particularly good at
1233 aligning to relatively long (e.g. mammalian) genomes. Bowtie 2 indexes the
1234 genome with an FM Index to keep its memory footprint small: for the human
1235 genome, its memory footprint is typically around 3.2 GB. Bowtie 2 supports
1236 gapped, local, and paired-end alignment modes.")
1237 (supported-systems '("x86_64-linux"))
1238 (license license:gpl3+)))
1240 (define-public tophat
1247 "http://ccb.jhu.edu/software/tophat/downloads/tophat-"
1251 "168zlzykq622zbgkh90a90f1bdgsxkscq2zxzbj8brq80hbjpyp7"))
1252 (patches (search-patches "tophat-build-with-later-seqan.patch"))
1253 (modules '((guix build utils)))
1256 ;; Remove bundled SeqAn and samtools
1257 (delete-file-recursively "src/SeqAn-1.3")
1258 (delete-file-recursively "src/samtools-0.1.18")
1260 (build-system gnu-build-system)
1262 '(#:parallel-build? #f ; not supported
1264 (modify-phases %standard-phases
1265 (add-after 'unpack 'use-system-samtools
1266 (lambda* (#:key inputs #:allow-other-keys)
1267 (substitute* "src/Makefile.in"
1268 (("(noinst_LIBRARIES = )\\$\\(SAMLIB\\)" _ prefix) prefix)
1269 (("\\$\\(SAMPROG\\): \\$\\(SAMLIB\\)") "")
1270 (("SAMPROG = samtools_0\\.1\\.18") "")
1271 (("\\$\\(samtools_0_1_18_SOURCES\\)") "")
1272 (("am__EXEEXT_1 = samtools_0\\.1\\.18\\$\\(EXEEXT\\)") ""))
1273 (substitute* '("src/common.cpp"
1275 (("samtools_0.1.18") (which "samtools")))
1276 (substitute* '("src/common.h"
1277 "src/bam2fastx.cpp")
1278 (("#include \"bam.h\"") "#include <samtools/bam.h>")
1279 (("#include \"sam.h\"") "#include <samtools/sam.h>"))
1280 (substitute* '("src/bwt_map.h"
1282 "src/align_status.h")
1283 (("#include <bam.h>") "#include <samtools/bam.h>")
1284 (("#include <sam.h>") "#include <samtools/sam.h>"))
1289 ("samtools" ,samtools-0.1)
1290 ("ncurses" ,ncurses)
1291 ("python" ,python-2)
1295 (home-page "http://ccb.jhu.edu/software/tophat/index.shtml")
1296 (synopsis "Spliced read mapper for RNA-Seq data")
1298 "TopHat is a fast splice junction mapper for nucleotide sequence
1299 reads produced by the RNA-Seq method. It aligns RNA-Seq reads to
1300 mammalian-sized genomes using the ultra high-throughput short read
1301 aligner Bowtie, and then analyzes the mapping results to identify
1302 splice junctions between exons.")
1303 ;; TopHat is released under the Boost Software License, Version 1.0
1304 ;; See https://github.com/infphilo/tophat/issues/11#issuecomment-121589893
1305 (license license:boost1.0)))
1314 "https://github.com/lh3/bwa/releases/download/v"
1315 version "/bwa-" version ".tar.bz2"))
1318 "1zfhv2zg9v1icdlq4p9ssc8k01mca5d1bd87w71py2swfi74s6yy"))))
1319 (build-system gnu-build-system)
1321 '(#:tests? #f ;no "check" target
1323 (modify-phases %standard-phases
1325 (lambda* (#:key outputs #:allow-other-keys)
1326 (let ((bin (string-append
1327 (assoc-ref outputs "out") "/bin"))
1329 (assoc-ref outputs "out") "/share/doc/bwa"))
1331 (assoc-ref outputs "out") "/share/man/man1")))
1332 (install-file "bwa" bin)
1333 (install-file "README.md" doc)
1334 (install-file "bwa.1" man))
1336 ;; no "configure" script
1337 (delete 'configure))))
1338 (inputs `(("zlib" ,zlib)))
1339 ;; Non-portable SSE instructions are used so building fails on platforms
1340 ;; other than x86_64.
1341 (supported-systems '("x86_64-linux"))
1342 (home-page "http://bio-bwa.sourceforge.net/")
1343 (synopsis "Burrows-Wheeler sequence aligner")
1345 "BWA is a software package for mapping low-divergent sequences against a
1346 large reference genome, such as the human genome. It consists of three
1347 algorithms: BWA-backtrack, BWA-SW and BWA-MEM. The first algorithm is
1348 designed for Illumina sequence reads up to 100bp, while the rest two for
1349 longer sequences ranged from 70bp to 1Mbp. BWA-MEM and BWA-SW share similar
1350 features such as long-read support and split alignment, but BWA-MEM, which is
1351 the latest, is generally recommended for high-quality queries as it is faster
1352 and more accurate. BWA-MEM also has better performance than BWA-backtrack for
1353 70-100bp Illumina reads.")
1354 (license license:gpl3+)))
1356 (define-public bwa-pssm
1357 (package (inherit bwa)
1362 (uri (string-append "https://github.com/pkerpedjiev/bwa-pssm/"
1363 "archive/" version ".tar.gz"))
1364 (file-name (string-append name "-" version ".tar.gz"))
1367 "02p7mpbs4mlxmn84g2x4ghak638vbj4lqix2ipx5g84pz9bhdavg"))))
1368 (build-system gnu-build-system)
1373 (home-page "http://bwa-pssm.binf.ku.dk/")
1374 (synopsis "Burrows-Wheeler transform-based probabilistic short read mapper")
1376 "BWA-PSSM is a probabilistic short genomic sequence read aligner based on
1377 the use of @dfn{position specific scoring matrices} (PSSM). Like many of the
1378 existing aligners it is fast and sensitive. Unlike most other aligners,
1379 however, it is also adaptible in the sense that one can direct the alignment
1380 based on known biases within the data set. It is coded as a modification of
1381 the original BWA alignment program and shares the genome index structure as
1382 well as many of the command line options.")
1383 (license license:gpl3+)))
1385 (define-public python2-bx-python
1387 (name "python2-bx-python")
1391 (uri (pypi-uri "bx-python" version))
1394 "15z2w3bvnc0n4qmb9bd6d8ylc2h2nj883x2w9iixf4x3vki9b22i"))
1395 (modules '((guix build utils)))
1398 (substitute* "setup.py"
1399 ;; remove dependency on outdated "distribute" module
1400 (("^from distribute_setup import use_setuptools") "")
1401 (("^use_setuptools\\(\\)") ""))
1403 (build-system python-build-system)
1405 `(#:tests? #f ;tests fail because test data are not included
1406 #:python ,python-2))
1408 `(("python-numpy" ,python2-numpy)
1411 `(("python-nose" ,python2-nose)))
1412 (home-page "http://bitbucket.org/james_taylor/bx-python/")
1413 (synopsis "Tools for manipulating biological data")
1415 "bx-python provides tools for manipulating biological data, particularly
1416 multiple sequence alignments.")
1417 (license license:expat)))
1419 (define-public python-pysam
1421 (name "python-pysam")
1425 ;; Test data is missing on PyPi.
1427 "https://github.com/pysam-developers/pysam/archive/v"
1429 (file-name (string-append name "-" version ".tar.gz"))
1432 "0dzap2axin9cbbl0d825w294bpn00zagfm1sigamm4v2pm5bj9lp"))
1433 (modules '((guix build utils)))
1435 ;; Drop bundled htslib. TODO: Also remove samtools
1437 (delete-file-recursively "htslib")
1439 (build-system python-build-system)
1441 `(#:modules ((ice-9 ftw)
1443 (guix build python-build-system)
1446 (modify-phases %standard-phases
1447 (add-before 'build 'set-flags
1448 (lambda* (#:key inputs #:allow-other-keys)
1449 (setenv "HTSLIB_MODE" "external")
1450 (setenv "HTSLIB_LIBRARY_DIR"
1451 (string-append (assoc-ref inputs "htslib") "/lib"))
1452 (setenv "HTSLIB_INCLUDE_DIR"
1453 (string-append (assoc-ref inputs "htslib") "/include"))
1454 (setenv "LDFLAGS" "-lncurses")
1455 (setenv "CFLAGS" "-D_CURSES_LIB=1")
1458 (lambda* (#:key inputs outputs #:allow-other-keys)
1459 ;; Add first subdirectory of "build" directory to PYTHONPATH.
1460 (setenv "PYTHONPATH"
1462 (getenv "PYTHONPATH")
1463 ":" (getcwd) "/build/"
1464 (car (scandir "build"
1465 (negate (cut string-prefix? "." <>))))))
1466 ;; Step out of source dir so python does not import from CWD.
1467 (with-directory-excursion "tests"
1468 (setenv "HOME" "/tmp")
1469 (and (zero? (system* "make" "-C" "pysam_data"))
1470 (zero? (system* "make" "-C" "cbcf_data"))
1471 ;; Running nosetests without explicitly asking for a
1472 ;; single process leads to a crash. Running with multiple
1473 ;; processes fails because the tests are not designed to
1476 ;; FIXME: tests keep timing out on some systems.
1477 ;; (zero? (system* "nosetests" "-v"
1478 ;; "--processes" "1"))
1481 `(("htslib" ,htslib))) ; Included from installed header files.
1483 `(("ncurses" ,ncurses)
1486 `(("python-cython" ,python-cython)
1487 ;; Dependencies below are are for tests only.
1488 ("samtools" ,samtools)
1489 ("bcftools" ,bcftools)
1490 ("python-nose" ,python-nose)))
1491 (home-page "https://github.com/pysam-developers/pysam")
1492 (synopsis "Python bindings to the SAMtools C API")
1494 "Pysam is a Python module for reading and manipulating files in the
1495 SAM/BAM format. Pysam is a lightweight wrapper of the SAMtools C API. It
1496 also includes an interface for tabix.")
1497 (license license:expat)))
1499 (define-public python2-pysam
1500 (package-with-python2 python-pysam))
1502 (define-public python-twobitreader
1504 (name "python-twobitreader")
1508 (uri (pypi-uri "twobitreader" version))
1511 "1q8wnj2kga9nz1lwc4w7qv52smfm536hp6mc8w6s53lhyj0mpi22"))))
1512 (build-system python-build-system)
1514 '(;; Tests are not distributed in the PyPi release.
1515 ;; TODO Try building from the Git repo or asking the upstream maintainer
1516 ;; to distribute the tests on PyPi.
1519 `(("python-sphinx" ,python-sphinx)))
1520 (home-page "https://github.com/benjschiller/twobitreader")
1521 (synopsis "Python library for reading .2bit files")
1523 "twobitreader is a Python library for reading .2bit files as used by the
1524 UCSC genome browser.")
1525 (license license:artistic2.0)))
1527 (define-public python2-twobitreader
1528 (package-with-python2 python-twobitreader))
1530 (define-public python-plastid
1532 (name "python-plastid")
1536 (uri (pypi-uri "plastid" version))
1539 "0l24dd3q66if8yj042m4s0g95n6acn7im1imqd3p6h8ns43kxhj8"))))
1540 (build-system python-build-system)
1542 ;; Some test files are not included.
1545 `(("python-numpy" ,python-numpy)
1546 ("python-scipy" ,python-scipy)
1547 ("python-pandas" ,python-pandas)
1548 ("python-pysam" ,python-pysam)
1549 ("python-matplotlib" ,python-matplotlib)
1550 ("python-biopython" ,python-biopython)
1551 ("python-twobitreader" ,python-twobitreader)
1552 ("python-termcolor" ,python-termcolor)))
1554 `(("python-cython" ,python-cython)
1555 ("python-nose" ,python-nose)))
1556 (home-page "https://github.com/joshuagryphon/plastid")
1557 (synopsis "Python library for genomic analysis")
1559 "plastid is a Python library for genomic analysis – in particular,
1560 high-throughput sequencing data – with an emphasis on simplicity.")
1561 (license license:bsd-3)))
1563 (define-public python2-plastid
1564 (package-with-python2 python-plastid))
1566 (define-public cd-hit
1572 (uri (string-append "https://github.com/weizhongli/cdhit"
1573 "/releases/download/V" version
1575 "-2017-0621-source.tar.gz"))
1578 "1b4mwm2520ixjbw57sil20f9iixzw4bkdqqwgg1fc3pzm6rz4zmn"))))
1579 (build-system gnu-build-system)
1581 `(#:tests? #f ; there are no tests
1583 ;; Executables are copied directly to the PREFIX.
1584 (list (string-append "PREFIX=" (assoc-ref %outputs "out") "/bin"))
1586 (modify-phases %standard-phases
1587 ;; No "configure" script
1589 ;; Remove sources of non-determinism
1590 (add-after 'unpack 'be-timeless
1592 (substitute* "cdhit-utility.c++"
1593 ((" \\(built on \" __DATE__ \"\\)") ""))
1594 (substitute* "cdhit-common.c++"
1595 (("__DATE__") "\"0\"")
1596 (("\", %s, \" __TIME__ \"\\\\n\", date") ""))
1598 ;; The "install" target does not create the target directory.
1599 (add-before 'install 'create-target-dir
1600 (lambda* (#:key outputs #:allow-other-keys)
1601 (mkdir-p (string-append (assoc-ref outputs "out") "/bin"))
1605 (home-page "http://weizhongli-lab.org/cd-hit/")
1606 (synopsis "Cluster and compare protein or nucleotide sequences")
1608 "CD-HIT is a program for clustering and comparing protein or nucleotide
1609 sequences. CD-HIT is designed to be fast and handle extremely large
1611 ;; The manual says: "It can be copied under the GNU General Public License
1612 ;; version 2 (GPLv2)."
1613 (license license:gpl2)))
1615 (define-public clipper
1622 "https://github.com/YeoLab/clipper/archive/"
1624 (file-name (string-append name "-" version ".tar.gz"))
1627 "0pflmsvhbf8izbgwhbhj1i7349sw1f55qpqj8ljmapp16hb0p0qi"))
1628 (modules '((guix build utils)))
1631 ;; remove unnecessary setup dependency
1632 (substitute* "setup.py"
1633 (("setup_requires = .*") ""))
1634 (for-each delete-file
1635 '("clipper/src/peaks.so"
1636 "clipper/src/readsToWiggle.so"))
1637 (delete-file-recursively "dist/")
1639 (build-system python-build-system)
1640 (arguments `(#:python ,python-2)) ; only Python 2 is supported
1642 `(("htseq" ,python2-htseq)
1643 ("python-pybedtools" ,python2-pybedtools)
1644 ("python-cython" ,python2-cython)
1645 ("python-scikit-learn" ,python2-scikit-learn)
1646 ("python-matplotlib" ,python2-matplotlib)
1647 ("python-pandas" ,python2-pandas)
1648 ("python-pysam" ,python2-pysam)
1649 ("python-numpy" ,python2-numpy)
1650 ("python-scipy" ,python2-scipy)))
1652 `(("python-mock" ,python2-mock) ; for tests
1653 ("python-nose" ,python2-nose) ; for tests
1654 ("python-pytz" ,python2-pytz))) ; for tests
1655 (home-page "https://github.com/YeoLab/clipper")
1656 (synopsis "CLIP peak enrichment recognition")
1658 "CLIPper is a tool to define peaks in CLIP-seq datasets.")
1659 (license license:gpl2)))
1661 (define-public codingquarry
1663 (name "codingquarry")
1668 "mirror://sourceforge/codingquarry/CodingQuarry_v"
1672 "0115hkjflsnfzn36xppwf9h9avfxlavr43djqmshkkzbgjzsz60i"))))
1673 (build-system gnu-build-system)
1675 '(#:tests? #f ; no "check" target
1677 (modify-phases %standard-phases
1680 (lambda* (#:key outputs #:allow-other-keys)
1681 (let* ((out (assoc-ref outputs "out"))
1682 (bin (string-append out "/bin"))
1683 (doc (string-append out "/share/doc/codingquarry")))
1684 (install-file "INSTRUCTIONS.pdf" doc)
1685 (copy-recursively "QuarryFiles"
1686 (string-append out "/QuarryFiles"))
1687 (install-file "CodingQuarry" bin)
1688 (install-file "CufflinksGTF_to_CodingQuarryGFF3.py" bin)))))))
1689 (inputs `(("openmpi" ,openmpi)))
1690 (native-search-paths
1691 (list (search-path-specification
1692 (variable "QUARRY_PATH")
1693 (files '("QuarryFiles")))))
1694 (native-inputs `(("python" ,python-2))) ; Only Python 2 is supported
1695 (synopsis "Fungal gene predictor")
1696 (description "CodingQuarry is a highly accurate, self-training GHMM fungal
1697 gene predictor designed to work with assembled, aligned RNA-seq transcripts.")
1698 (home-page "https://sourceforge.net/projects/codingquarry/")
1699 (license license:gpl3+)))
1701 (define-public couger
1708 "http://couger.oit.duke.edu/static/assets/COUGER"
1712 "04p2b14nmhzxw5h72mpzdhalv21bx4w9b87z0wpw0xzxpysyncmq"))))
1713 (build-system gnu-build-system)
1717 (modify-phases %standard-phases
1722 (lambda* (#:key outputs #:allow-other-keys)
1723 (let* ((out (assoc-ref outputs "out"))
1724 (bin (string-append out "/bin")))
1725 (copy-recursively "src" (string-append out "/src"))
1727 ;; Add "src" directory to module lookup path.
1728 (substitute* "couger"
1730 (string-append "import sys\nsys.path.append(\""
1731 out "\")\nfrom argparse")))
1732 (install-file "couger" bin))
1735 'install 'wrap-program
1736 (lambda* (#:key inputs outputs #:allow-other-keys)
1737 ;; Make sure 'couger' runs with the correct PYTHONPATH.
1738 (let* ((out (assoc-ref outputs "out"))
1739 (path (getenv "PYTHONPATH")))
1740 (wrap-program (string-append out "/bin/couger")
1741 `("PYTHONPATH" ":" prefix (,path))))
1744 `(("python" ,python-2)
1745 ("python2-pillow" ,python2-pillow)
1746 ("python2-numpy" ,python2-numpy)
1747 ("python2-scipy" ,python2-scipy)
1748 ("python2-matplotlib" ,python2-matplotlib)))
1750 `(("r-minimal" ,r-minimal)
1752 ("randomjungle" ,randomjungle)))
1754 `(("unzip" ,unzip)))
1755 (home-page "http://couger.oit.duke.edu")
1756 (synopsis "Identify co-factors in sets of genomic regions")
1758 "COUGER can be applied to any two sets of genomic regions bound by
1759 paralogous TFs (e.g., regions derived from ChIP-seq experiments) to identify
1760 putative co-factors that provide specificity to each TF. The framework
1761 determines the genomic targets uniquely-bound by each TF, and identifies a
1762 small set of co-factors that best explain the in vivo binding differences
1763 between the two TFs.
1765 COUGER uses classification algorithms (support vector machines and random
1766 forests) with features that reflect the DNA binding specificities of putative
1767 co-factors. The features are generated either from high-throughput TF-DNA
1768 binding data (from protein binding microarray experiments), or from large
1769 collections of DNA motifs.")
1770 (license license:gpl3+)))
1772 (define-public clustal-omega
1774 (name "clustal-omega")
1778 (uri (string-append "http://www.clustal.org/omega/clustal-omega-"
1782 "1vm30mzncwdv881vrcwg11vzvrsmwy4wg80j5i0lcfk6dlld50w6"))))
1783 (build-system gnu-build-system)
1785 `(("argtable" ,argtable)))
1786 (home-page "http://www.clustal.org/omega/")
1787 (synopsis "Multiple sequence aligner for protein and DNA/RNA")
1789 "Clustal-Omega is a general purpose multiple sequence alignment (MSA)
1790 program for protein and DNA/RNA. It produces high quality MSAs and is capable
1791 of handling data-sets of hundreds of thousands of sequences in reasonable
1793 (license license:gpl2+)))
1795 (define-public crossmap
1801 (uri (string-append "mirror://sourceforge/crossmap/CrossMap-"
1805 "07y179f63d7qnzdvkqcziwk9bs3k4zhp81q392fp1hwszjdvy22f"))
1806 ;; This patch has been sent upstream already and is available
1807 ;; for download from Sourceforge, but it has not been merged.
1808 (patches (search-patches "crossmap-allow-system-pysam.patch"))
1809 (modules '((guix build utils)))
1811 ;; remove bundled copy of pysam
1812 (delete-file-recursively "lib/pysam")
1814 (build-system python-build-system)
1816 `(#:python ,python-2
1818 (modify-phases %standard-phases
1819 (add-after 'unpack 'set-env
1820 (lambda _ (setenv "CROSSMAP_USE_SYSTEM_PYSAM" "1") #t)))))
1822 `(("python-numpy" ,python2-numpy)
1823 ("python-pysam" ,python2-pysam)
1826 `(("python-cython" ,python2-cython)
1827 ("python-nose" ,python2-nose)))
1828 (home-page "http://crossmap.sourceforge.net/")
1829 (synopsis "Convert genome coordinates between assemblies")
1831 "CrossMap is a program for conversion of genome coordinates or annotation
1832 files between different genome assemblies. It supports most commonly used
1833 file formats including SAM/BAM, Wiggle/BigWig, BED, GFF/GTF, VCF.")
1834 (license license:gpl2+)))
1836 (define-public cutadapt
1843 (url "https://github.com/marcelm/cutadapt.git")
1844 (commit (string-append "v" version))))
1845 (file-name (string-append name "-" version "-checkout"))
1848 "09pr02067jiks19nc0aby4xp70hhgvb554i2y1c04rv1m401w7q8"))))
1849 (build-system python-build-system)
1851 `(("python-xopen" ,python-xopen)))
1853 `(("python-cython" ,python-cython)
1854 ("python-pytest" ,python-pytest)))
1855 (home-page "https://cutadapt.readthedocs.io/en/stable/")
1856 (synopsis "Remove adapter sequences from nucleotide sequencing reads")
1858 "Cutadapt finds and removes adapter sequences, primers, poly-A tails and
1859 other types of unwanted sequence from high-throughput sequencing reads.")
1860 (license license:expat)))
1862 (define-public libbigwig
1868 (uri (string-append "https://github.com/dpryan79/libBigWig/"
1869 "archive/" version ".tar.gz"))
1870 (file-name (string-append name "-" version ".tar.gz"))
1873 "098rjh35pi4a9q83n8wiwvyzykjqj6l8q189p1xgfw4ghywdlvw1"))))
1874 (build-system gnu-build-system)
1876 `(#:test-target "test"
1879 (string-append "prefix=" (assoc-ref %outputs "out")))
1881 (modify-phases %standard-phases
1883 (add-before 'check 'disable-curl-test
1885 (substitute* "Makefile"
1886 (("./test/testRemote.*") ""))
1888 ;; This has been fixed with the upstream commit 4ff6959cd8a0, but
1889 ;; there has not yet been a release containing this change.
1890 (add-before 'install 'create-target-dirs
1891 (lambda* (#:key outputs #:allow-other-keys)
1892 (let ((out (assoc-ref outputs "out")))
1893 (mkdir-p (string-append out "/lib"))
1894 (mkdir-p (string-append out "/include"))
1900 `(("doxygen" ,doxygen)))
1901 (home-page "https://github.com/dpryan79/libBigWig")
1902 (synopsis "C library for handling bigWig files")
1904 "This package provides a C library for parsing local and remote BigWig
1906 (license license:expat)))
1908 (define-public python-pybigwig
1910 (name "python-pybigwig")
1914 (uri (pypi-uri "pyBigWig" version))
1917 "0yrpdxg3y0sny25x4w22lv1k47jzccqjmg7j4bp0hywklvp0hg7d"))
1918 (modules '((guix build utils)))
1921 ;; Delete bundled libBigWig sources
1922 (delete-file-recursively "libBigWig")
1924 (build-system python-build-system)
1927 (modify-phases %standard-phases
1928 (add-after 'unpack 'link-with-libBigWig
1929 (lambda* (#:key inputs #:allow-other-keys)
1930 (substitute* "setup.py"
1931 (("libs=\\[") "libs=[\"BigWig\", "))
1934 `(("libbigwig" ,libbigwig)
1937 (home-page "https://github.com/dpryan79/pyBigWig")
1938 (synopsis "Access bigWig files in Python using libBigWig")
1940 "This package provides Python bindings to the libBigWig library for
1941 accessing bigWig files.")
1942 (license license:expat)))
1944 (define-public python2-pybigwig
1945 (package-with-python2 python-pybigwig))
1947 (define-public python-dendropy
1949 (name "python-dendropy")
1954 (uri (pypi-uri "DendroPy" version))
1957 "15c7s3d5gf19ljsxvq5advaa752wfi7pwrdjyhzmg85hccyvp47p"))
1958 (patches (search-patches "python-dendropy-fix-tests.patch"))))
1959 (build-system python-build-system)
1960 (home-page "http://packages.python.org/DendroPy/")
1961 (synopsis "Library for phylogenetics and phylogenetic computing")
1963 "DendroPy is a library for phylogenetics and phylogenetic computing: reading,
1964 writing, simulation, processing and manipulation of phylogenetic
1965 trees (phylogenies) and characters.")
1966 (license license:bsd-3)
1967 (properties `((python2-variant . ,(delay python2-dendropy))))))
1969 (define-public python2-dendropy
1970 (let ((base (package-with-python2 (strip-python2-variant python-dendropy))))
1974 `(#:python ,python-2
1976 (modify-phases %standard-phases
1978 ;; There is currently a test failure that only happens on some
1979 ;; systems, and only using "setup.py test"
1980 (lambda _ (zero? (system* "nosetests")))))))
1981 (native-inputs `(("python2-nose" ,python2-nose)
1982 ,@(package-native-inputs base))))))
1984 (define-public python-py2bit
1986 (name "python-py2bit")
1991 (uri (pypi-uri "py2bit" version))
1994 "1cdf4qlmgwsh1f4k0wdv2sr8x9qn4366p0k3614vbd0fpqiarxrl"))))
1995 (build-system python-build-system)
1996 (home-page "https://github.com/dpryan79/py2bit")
1997 (synopsis "Access 2bit files using lib2bit")
1999 "This package provides Python bindings for lib2bit to access 2bit files
2001 (license license:expat)))
2003 (define-public deeptools
2009 (uri (string-append "https://github.com/deeptools/deepTools/"
2010 "archive/" version ".tar.gz"))
2011 (file-name (string-append name "-" version ".tar.gz"))
2014 "1q8i12l2gvk4n2s8lhyzwhh9g4qbc8lrk5l7maz00yvd5g6z5540"))))
2015 (build-system python-build-system)
2017 `(("python-scipy" ,python-scipy)
2018 ("python-numpy" ,python-numpy)
2019 ("python-numpydoc" ,python-numpydoc)
2020 ("python-matplotlib" ,python-matplotlib)
2021 ("python-pysam" ,python-pysam)
2022 ("python-py2bit" ,python-py2bit)
2023 ("python-pybigwig" ,python-pybigwig)))
2025 `(("python-mock" ,python-mock) ;for tests
2026 ("python-nose" ,python-nose) ;for tests
2027 ("python-pytz" ,python-pytz))) ;for tests
2028 (home-page "https://github.com/deeptools/deepTools")
2029 (synopsis "Tools for normalizing and visualizing deep-sequencing data")
2031 "DeepTools addresses the challenge of handling the large amounts of data
2032 that are now routinely generated from DNA sequencing centers. To do so,
2033 deepTools contains useful modules to process the mapped reads data to create
2034 coverage files in standard bedGraph and bigWig file formats. By doing so,
2035 deepTools allows the creation of normalized coverage files or the comparison
2036 between two files (for example, treatment and control). Finally, using such
2037 normalized and standardized files, multiple visualizations can be created to
2038 identify enrichments with functional annotations of the genome.")
2039 (license license:gpl3+)))
2041 (define-public delly
2048 "https://github.com/tobiasrausch/delly/archive/v"
2050 (file-name (string-append name "-" version ".tar.gz"))
2052 (base32 "0dkwy3pyxmi6dhh1lpsr3698ri5sslw9qz67hfys0bz8dgrqwabj"))
2053 (patches (search-patches "delly-use-system-libraries.patch"))))
2054 (build-system gnu-build-system)
2056 `(#:tests? #f ; There are no tests to run.
2057 #:make-flags '("PARALLEL=1") ; Allow parallel execution at run-time.
2059 (modify-phases %standard-phases
2060 (delete 'configure) ; There is no configure phase.
2063 (let ((bin (string-append (assoc-ref %outputs "out") "/bin"))
2064 (templates (string-append (assoc-ref %outputs "out")
2065 "/share/delly/templates")))
2068 (copy-recursively "excludeTemplates" templates)
2069 (install-file "src/cov" bin)
2070 (install-file "src/delly" bin)
2071 (install-file "src/dpe" bin)))))))
2073 `(("python" ,python-2)))
2079 (home-page "https://github.com/tobiasrausch/delly")
2080 (synopsis "Integrated structural variant prediction method")
2081 (description "Delly is an integrated structural variant prediction method
2082 that can discover and genotype deletions, tandem duplications, inversions and
2083 translocations at single-nucleotide resolution in short-read massively parallel
2084 sequencing data. It uses paired-ends and split-reads to sensitively and
2085 accurately delineate genomic rearrangements throughout the genome.")
2086 (license license:gpl3+)))
2088 (define-public diamond
2095 "https://github.com/bbuchfink/diamond/archive/v"
2097 (file-name (string-append name "-" version ".tar.gz"))
2100 "0adp87r9ak63frdrdmrdfhsn6g0jnnyq1lr2wibvqbxcl37iir9m"))))
2101 (build-system cmake-build-system)
2103 '(#:tests? #f ; no "check" target
2105 (modify-phases %standard-phases
2106 (add-after 'unpack 'remove-native-compilation
2108 (substitute* "CMakeLists.txt" (("-march=native") ""))
2112 (home-page "https://github.com/bbuchfink/diamond")
2113 (synopsis "Accelerated BLAST compatible local sequence aligner")
2115 "DIAMOND is a BLAST-compatible local aligner for mapping protein and
2116 translated DNA query sequences against a protein reference database (BLASTP
2117 and BLASTX alignment mode). The speedup over BLAST is up to 20,000 on short
2118 reads at a typical sensitivity of 90-99% relative to BLAST depending on the
2119 data and settings.")
2120 (license license:agpl3+)))
2122 (define-public discrover
2129 (uri (string-append "https://github.com/maaskola/discrover/archive/"
2131 (file-name (string-append name "-" version ".tar.gz"))
2134 "0rah9ja4m0rl5mldd6vag9rwrivw1zrqxssfq8qx64m7961fp68k"))))
2135 (build-system cmake-build-system)
2137 `(#:tests? #f ; there are no tests
2139 (modify-phases %standard-phases
2140 (add-after 'unpack 'add-missing-includes
2142 (substitute* "src/executioninformation.hpp"
2143 (("#define EXECUTIONINFORMATION_HPP" line)
2144 (string-append line "\n#include <random>")))
2145 (substitute* "src/plasma/fasta.hpp"
2146 (("#define FASTA_HPP" line)
2147 (string-append line "\n#include <random>")))
2153 `(("texlive" ,texlive)
2154 ("imagemagick" ,imagemagick)))
2155 (home-page "http://dorina.mdc-berlin.de/public/rajewsky/discrover/")
2156 (synopsis "Discover discriminative nucleotide sequence motifs")
2157 (description "Discrover is a motif discovery method to find binding sites
2158 of nucleic acid binding proteins.")
2159 (license license:gpl3+)))
2161 (define-public eigensoft
2162 (let ((revision "1")
2163 (commit "b14d1e202e21e532536ff8004f0419cd5e259dc7"))
2166 (version (string-append "6.1.2-"
2168 (string-take commit 9)))
2173 (url "https://github.com/DReichLab/EIG.git")
2175 (file-name (string-append "eigensoft-" commit "-checkout"))
2178 "0f5m6k2j5c16xc3xbywcs989xyc26ncy1zfzp9j9n55n9r4xcaiq"))
2179 (modules '((guix build utils)))
2180 ;; Remove pre-built binaries.
2182 (delete-file-recursively "bin")
2185 (build-system gnu-build-system)
2187 `(#:tests? #f ; There are no tests.
2188 #:make-flags '("CC=gcc")
2190 (modify-phases %standard-phases
2191 ;; There is no configure phase, but the Makefile is in a
2196 ;; The link flags are incomplete.
2197 (substitute* "Makefile"
2198 (("-lgsl") "-lgsl -lm -llapack -llapacke -lpthread"))
2200 ;; The provided install target only copies executables to
2201 ;; the "bin" directory in the build root.
2202 (add-after 'install 'actually-install
2203 (lambda* (#:key outputs #:allow-other-keys)
2204 (let* ((out (assoc-ref outputs "out"))
2205 (bin (string-append out "/bin")))
2206 (for-each (lambda (file)
2207 (install-file file bin))
2208 (find-files "../bin" ".*"))
2213 ("openblas" ,openblas)
2215 ("gfortran" ,gfortran "lib")))
2216 (home-page "https://github.com/DReichLab/EIG")
2217 (synopsis "Tools for population genetics")
2218 (description "The EIGENSOFT package provides tools for population
2219 genetics and stratification correction. EIGENSOFT implements methods commonly
2220 used in population genetics analyses such as PCA, computation of Tracy-Widom
2221 statistics, and finding related individuals in structured populations. It
2222 comes with a built-in plotting script and supports multiple file formats and
2223 quantitative phenotypes.")
2224 ;; The license of the eigensoft tools is Expat, but since it's
2225 ;; linking with the GNU Scientific Library (GSL) the effective
2226 ;; license is the GPL.
2227 (license license:gpl3+))))
2229 (define-public edirect
2235 (uri (string-append "ftp://ftp.ncbi.nlm.nih.gov/entrez/entrezdirect/"
2236 "versions/2016-05-03/edirect.tar.gz"))
2239 "15zsprak5yh8c1yrz4r1knmb5s8qcmdid4xdhkh3lqcv64l60hli"))))
2240 (build-system perl-build-system)
2242 `(#:tests? #f ;no "check" target
2244 (modify-phases %standard-phases
2248 (lambda* (#:key outputs #:allow-other-keys)
2249 (let ((target (string-append (assoc-ref outputs "out")
2252 (install-file "edirect.pl" target)
2255 'install 'wrap-program
2256 (lambda* (#:key inputs outputs #:allow-other-keys)
2257 ;; Make sure 'edirect.pl' finds all perl inputs at runtime.
2258 (let* ((out (assoc-ref outputs "out"))
2259 (path (getenv "PERL5LIB")))
2260 (wrap-program (string-append out "/bin/edirect.pl")
2261 `("PERL5LIB" ":" prefix (,path)))))))))
2263 `(("perl-html-parser" ,perl-html-parser)
2264 ("perl-encode-locale" ,perl-encode-locale)
2265 ("perl-file-listing" ,perl-file-listing)
2266 ("perl-html-tagset" ,perl-html-tagset)
2267 ("perl-html-tree" ,perl-html-tree)
2268 ("perl-http-cookies" ,perl-http-cookies)
2269 ("perl-http-date" ,perl-http-date)
2270 ("perl-http-message" ,perl-http-message)
2271 ("perl-http-negotiate" ,perl-http-negotiate)
2272 ("perl-lwp-mediatypes" ,perl-lwp-mediatypes)
2273 ("perl-lwp-protocol-https" ,perl-lwp-protocol-https)
2274 ("perl-net-http" ,perl-net-http)
2275 ("perl-uri" ,perl-uri)
2276 ("perl-www-robotrules" ,perl-www-robotrules)
2278 (home-page "http://www.ncbi.nlm.nih.gov/books/NBK179288/")
2279 (synopsis "Tools for accessing the NCBI's set of databases")
2281 "Entrez Direct (EDirect) is a method for accessing the National Center
2282 for Biotechnology Information's (NCBI) set of interconnected
2283 databases (publication, sequence, structure, gene, variation, expression,
2284 etc.) from a terminal. Functions take search terms from command-line
2285 arguments. Individual operations are combined to build multi-step queries.
2286 Record retrieval and formatting normally complete the process.
2288 EDirect also provides an argument-driven function that simplifies the
2289 extraction of data from document summaries or other results that are returned
2290 in structured XML format. This can eliminate the need for writing custom
2291 software to answer ad hoc questions.")
2292 (license license:public-domain)))
2294 (define-public exonerate
2303 "http://ftp.ebi.ac.uk/pub/software/vertebrategenomics/exonerate/"
2304 "exonerate-" version ".tar.gz"))
2307 "0hj0m9xygiqsdxvbg79wq579kbrx1mdrabi2bzqz2zn9qwfjcjgq"))))
2308 (build-system gnu-build-system)
2310 `(#:parallel-build? #f)) ; Building in parallel fails on some machines.
2312 `(("pkg-config" ,pkg-config)))
2316 "https://www.ebi.ac.uk/about/vertebrate-genomics/software/exonerate")
2317 (synopsis "Generic tool for biological sequence alignment")
2319 "Exonerate is a generic tool for pairwise sequence comparison. It allows
2320 the alignment of sequences using a many alignment models, either exhaustive
2321 dynamic programming or a variety of heuristics.")
2322 (license license:gpl3)))
2324 (define-public express
2332 "http://bio.math.berkeley.edu/eXpress/downloads/express-"
2333 version "/express-" version "-src.tgz"))
2336 "03rczxd0gjp2l1jxcmjfmf5j94j77zqyxa6x063zsc585nj40n0c"))))
2337 (build-system cmake-build-system)
2339 `(#:tests? #f ;no "check" target
2341 (modify-phases %standard-phases
2342 (add-after 'unpack 'use-shared-boost-libs-and-set-bamtools-paths
2343 (lambda* (#:key inputs #:allow-other-keys)
2344 (substitute* "CMakeLists.txt"
2345 (("set\\(Boost_USE_STATIC_LIBS ON\\)")
2346 "set(Boost_USE_STATIC_LIBS OFF)")
2347 (("\\$\\{CMAKE_CURRENT_SOURCE_DIR\\}/bamtools/include")
2348 (string-append (assoc-ref inputs "bamtools") "/include/bamtools")))
2349 (substitute* "src/CMakeLists.txt"
2350 (("\\$\\{CMAKE_CURRENT_SOURCE_DIR\\}/\\.\\./bamtools/lib")
2351 (string-append (assoc-ref inputs "bamtools") "/lib"))
2352 (("libprotobuf.a") "libprotobuf.so"))
2356 ("bamtools" ,bamtools)
2357 ("protobuf" ,protobuf)
2359 (home-page "http://bio.math.berkeley.edu/eXpress")
2360 (synopsis "Streaming quantification for high-throughput genomic sequencing")
2362 "eXpress is a streaming tool for quantifying the abundances of a set of
2363 target sequences from sampled subsequences. Example applications include
2364 transcript-level RNA-Seq quantification, allele-specific/haplotype expression
2365 analysis (from RNA-Seq), transcription factor binding quantification in
2366 ChIP-Seq, and analysis of metagenomic data.")
2367 (license license:artistic2.0)))
2369 (define-public express-beta-diversity
2371 (name "express-beta-diversity")
2377 "https://github.com/dparks1134/ExpressBetaDiversity/archive/v"
2379 (file-name (string-append name "-" version ".tar.gz"))
2382 "1djvdlmqvjf6h0zq7w36y8cl5cli6rgj86x65znl48agnwmzxfxr"))))
2383 (build-system gnu-build-system)
2386 (modify-phases %standard-phases
2388 (add-before 'build 'enter-source (lambda _ (chdir "source") #t))
2390 (lambda _ (zero? (system* "../bin/ExpressBetaDiversity"
2392 (add-after 'check 'exit-source (lambda _ (chdir "..") #t))
2394 (lambda* (#:key outputs #:allow-other-keys)
2395 (let ((bin (string-append (assoc-ref outputs "out")
2398 (install-file "scripts/convertToEBD.py" bin)
2399 (install-file "bin/ExpressBetaDiversity" bin)
2402 `(("python" ,python-2)))
2403 (home-page "http://kiwi.cs.dal.ca/Software/ExpressBetaDiversity")
2404 (synopsis "Taxon- and phylogenetic-based beta diversity measures")
2406 "Express Beta Diversity (EBD) calculates ecological beta diversity
2407 (dissimilarity) measures between biological communities. EBD implements a
2408 variety of diversity measures including those that make use of phylogenetic
2409 similarity of community members.")
2410 (license license:gpl3+)))
2412 (define-public fasttree
2419 "http://www.microbesonline.org/fasttree/FastTree-"
2423 "0vcjdvy1j4m702vmak4svbfkrpcw63k7wymfksjp9a982zy8kjsl"))))
2424 (build-system gnu-build-system)
2426 `(#:tests? #f ; no "check" target
2428 (modify-phases %standard-phases
2432 (lambda* (#:key source #:allow-other-keys)
2433 (and (zero? (system* "gcc"
2435 "-finline-functions"
2442 (zero? (system* "gcc"
2446 "-finline-functions"
2454 (lambda* (#:key outputs #:allow-other-keys)
2455 (let ((bin (string-append (assoc-ref outputs "out")
2458 (install-file "FastTree" bin)
2459 (install-file "FastTreeMP" bin)
2461 (home-page "http://www.microbesonline.org/fasttree")
2462 (synopsis "Infers approximately-maximum-likelihood phylogenetic trees")
2464 "FastTree can handle alignments with up to a million of sequences in a
2465 reasonable amount of time and memory. For large alignments, FastTree is
2466 100-1,000 times faster than PhyML 3.0 or RAxML 7.")
2467 (license license:gpl2+)))
2469 (define-public fastx-toolkit
2471 (name "fastx-toolkit")
2477 "https://github.com/agordon/fastx_toolkit/releases/download/"
2478 version "/fastx_toolkit-" version ".tar.bz2"))
2481 "01jqzw386873sr0pjp1wr4rn8fsga2vxs1qfmicvx1pjr72007wy"))))
2482 (build-system gnu-build-system)
2484 `(("libgtextutils" ,libgtextutils)))
2486 `(("pkg-config" ,pkg-config)))
2487 (home-page "http://hannonlab.cshl.edu/fastx_toolkit/")
2488 (synopsis "Tools for FASTA/FASTQ file preprocessing")
2490 "The FASTX-Toolkit is a collection of command line tools for Short-Reads
2491 FASTA/FASTQ files preprocessing.
2493 Next-Generation sequencing machines usually produce FASTA or FASTQ files,
2494 containing multiple short-reads sequences. The main processing of such
2495 FASTA/FASTQ files is mapping the sequences to reference genomes. However, it
2496 is sometimes more productive to preprocess the files before mapping the
2497 sequences to the genome---manipulating the sequences to produce better mapping
2498 results. The FASTX-Toolkit tools perform some of these preprocessing tasks.")
2499 (license license:agpl3+)))
2501 (define-public flexbar
2508 (string-append "mirror://sourceforge/flexbar/"
2509 version "/flexbar_v" version "_src.tgz"))
2512 "13jaykc3y1x8y5nn9j8ljnb79s5y51kyxz46hdmvvjj6qhyympmf"))))
2513 (build-system cmake-build-system)
2515 `(#:configure-flags (list
2516 (string-append "-DFLEXBAR_BINARY_DIR="
2517 (assoc-ref %outputs "out")
2520 (modify-phases %standard-phases
2522 (lambda* (#:key outputs #:allow-other-keys)
2523 (setenv "PATH" (string-append
2524 (assoc-ref outputs "out") "/bin:"
2526 (chdir "../flexbar_v2.5_src/test")
2527 (zero? (system* "bash" "flexbar_validate.sh"))))
2528 (delete 'install))))
2533 `(("pkg-config" ,pkg-config)
2535 (home-page "http://flexbar.sourceforge.net")
2536 (synopsis "Barcode and adapter removal tool for sequencing platforms")
2538 "Flexbar preprocesses high-throughput nucleotide sequencing data
2539 efficiently. It demultiplexes barcoded runs and removes adapter sequences.
2540 Moreover, trimming and filtering features are provided. Flexbar increases
2541 read mapping rates and improves genome and transcriptome assemblies. It
2542 supports next-generation sequencing data in fasta/q and csfasta/q format from
2543 Illumina, Roche 454, and the SOLiD platform.")
2544 (license license:gpl3)))
2546 (define-public fraggenescan
2548 (name "fraggenescan")
2554 (string-append "mirror://sourceforge/fraggenescan/"
2555 "FragGeneScan" version ".tar.gz"))
2557 (base32 "158dcnwczgcyhwm4qlx19sanrwgdpzf6bn2y57mbpx55lkgz1mzj"))))
2558 (build-system gnu-build-system)
2561 (modify-phases %standard-phases
2563 (add-before 'build 'patch-paths
2564 (lambda* (#:key outputs #:allow-other-keys)
2565 (let* ((out (string-append (assoc-ref outputs "out")))
2566 (share (string-append out "/share/fraggenescan/")))
2567 (substitute* "run_FragGeneScan.pl"
2569 (string-append "system(\"" (which "rm")))
2571 (string-append "system(\"" (which "mv")))
2572 (("\\\"awk") (string-append "\"" (which "awk")))
2573 ;; This script and other programs expect the training files
2574 ;; to be in the non-standard location bin/train/XXX. Change
2575 ;; this to be share/fraggenescan/train/XXX instead.
2576 (("^\\$train.file = \\$dir.*")
2577 (string-append "$train_file = \""
2579 "train/\".$FGS_train_file;")))
2580 (substitute* "run_hmm.c"
2581 (("^ strcat\\(train_dir, \\\"train/\\\"\\);")
2582 (string-append " strcpy(train_dir, \"" share "/train/\");"))))
2585 (lambda _ (and (zero? (system* "make" "clean"))
2586 (zero? (system* "make" "fgs")))))
2588 (lambda* (#:key outputs #:allow-other-keys)
2589 (let* ((out (string-append (assoc-ref outputs "out")))
2590 (bin (string-append out "/bin/"))
2591 (share (string-append out "/share/fraggenescan/train")))
2592 (install-file "run_FragGeneScan.pl" bin)
2593 (install-file "FragGeneScan" bin)
2594 (copy-recursively "train" share))))
2596 (add-after 'install 'post-install-check
2597 ;; In lieu of 'make check', run one of the examples and check the
2598 ;; output files gets created.
2599 (lambda* (#:key outputs #:allow-other-keys)
2600 (let* ((out (string-append (assoc-ref outputs "out")))
2601 (bin (string-append out "/bin/"))
2602 (frag (string-append bin "run_FragGeneScan.pl")))
2603 (and (zero? (system* frag ; Test complete genome.
2604 "-genome=./example/NC_000913.fna"
2608 (file-exists? "test2.faa")
2609 (file-exists? "test2.ffn")
2610 (file-exists? "test2.gff")
2611 (file-exists? "test2.out")
2612 (zero? (system* ; Test incomplete sequences.
2614 "-genome=./example/NC_000913-fgs.ffn"
2617 "-train=454_30")))))))))
2620 ("python" ,python-2))) ;not compatible with python 3.
2621 (home-page "https://sourceforge.net/projects/fraggenescan/")
2622 (synopsis "Finds potentially fragmented genes in short reads")
2624 "FragGeneScan is a program for predicting bacterial and archaeal genes in
2625 short and error-prone DNA sequencing reads. It can also be applied to predict
2626 genes in incomplete assemblies or complete genomes.")
2627 ;; GPL3+ according to private correspondense with the authors.
2628 (license license:gpl3+)))
2630 (define-public fxtract
2631 (let ((util-commit "776ca85a18a47492af3794745efcb4a905113115"))
2639 "https://github.com/ctSkennerton/fxtract/archive/"
2641 (file-name (string-append "ctstennerton-util-"
2642 (string-take util-commit 7)
2646 "0275cfdhis8517hm01is62062swmi06fxzifq7mr3knbbxjlaiwj"))))
2647 (build-system gnu-build-system)
2649 `(#:make-flags (list
2650 (string-append "PREFIX=" (assoc-ref %outputs "out"))
2652 #:test-target "fxtract_test"
2654 (modify-phases %standard-phases
2656 (add-before 'build 'copy-util
2657 (lambda* (#:key inputs #:allow-other-keys)
2659 (copy-recursively (assoc-ref inputs "ctskennerton-util") "util")
2661 ;; Do not use make install as this requires additional dependencies.
2663 (lambda* (#:key outputs #:allow-other-keys)
2664 (let* ((out (assoc-ref outputs "out"))
2665 (bin (string-append out"/bin")))
2666 (install-file "fxtract" bin)
2672 ;; ctskennerton-util is licensed under GPL2.
2673 `(("ctskennerton-util"
2677 (url "https://github.com/ctSkennerton/util.git")
2678 (commit util-commit)))
2679 (file-name (string-append
2680 "ctstennerton-util-" util-commit "-checkout"))
2683 "0cls1hd4vgj3f36fpzzg4xc77d6f3hpc60cbpfmn2gdr7ykzzad7"))))))
2684 (home-page "https://github.com/ctSkennerton/fxtract")
2685 (synopsis "Extract sequences from FASTA and FASTQ files")
2687 "Fxtract extracts sequences from a protein or nucleotide fastx (FASTA
2688 or FASTQ) file given a subsequence. It uses a simple substring search for
2689 basic tasks but can change to using POSIX regular expressions, PCRE, hash
2690 lookups or multi-pattern searching as required. By default fxtract looks in
2691 the sequence of each record but can also be told to look in the header,
2692 comment or quality sections.")
2693 ;; 'util' requires SSE instructions.
2694 (supported-systems '("x86_64-linux"))
2695 (license license:expat))))
2697 (define-public gemma
2703 (uri (string-append "https://github.com/xiangzhou/GEMMA/archive/v"
2705 (file-name (string-append name "-" version ".tar.gz"))
2708 "055ynn16gd12pf78n4vr2a9jlwsbwzajpdnf2y2yilg1krfff222"))
2709 (patches (search-patches "gemma-intel-compat.patch"))))
2714 (build-system gnu-build-system)
2717 '(,@(match (%current-system)
2719 '("FORCE_DYNAMIC=1"))
2721 '("FORCE_DYNAMIC=1" "FORCE_32BIT=1"))
2723 '("FORCE_DYNAMIC=1" "NO_INTEL_COMPAT=1"))))
2725 (modify-phases %standard-phases
2727 (add-before 'build 'bin-mkdir
2732 (lambda* (#:key outputs #:allow-other-keys)
2733 (let ((out (assoc-ref outputs "out")))
2734 (install-file "bin/gemma"
2738 #:tests? #f)) ; no tests included yet
2739 (home-page "https://github.com/xiangzhou/GEMMA")
2740 (synopsis "Tool for genome-wide efficient mixed model association")
2742 "Genome-wide Efficient Mixed Model Association (GEMMA) provides a
2743 standard linear mixed model resolver with application in genome-wide
2744 association studies (GWAS).")
2745 (license license:gpl3)))
2754 "https://github.com/nboley/grit/archive/"
2756 (file-name (string-append name "-" version ".tar.gz"))
2759 "157in84dj70wimbind3x7sy1whs3h57qfgcnj2s6lrd38fbrb7mj"))))
2760 (build-system python-build-system)
2762 `(#:python ,python-2
2764 (modify-phases %standard-phases
2765 (add-after 'unpack 'generate-from-cython-sources
2766 (lambda* (#:key inputs outputs #:allow-other-keys)
2767 ;; Delete these C files to force fresh generation from pyx sources.
2768 (delete-file "grit/sparsify_support_fns.c")
2769 (delete-file "grit/call_peaks_support_fns.c")
2770 (substitute* "setup.py"
2771 (("Cython.Setup") "Cython.Build")
2772 ;; Add numpy include path to fix compilation
2774 (string-append "pyx\", ], include_dirs = ['"
2775 (assoc-ref inputs "python-numpy")
2776 "/lib/python2.7/site-packages/numpy/core/include/"
2780 `(("python-scipy" ,python2-scipy)
2781 ("python-numpy" ,python2-numpy)
2782 ("python-pysam" ,python2-pysam)
2783 ("python-networkx" ,python2-networkx)))
2785 `(("python-cython" ,python2-cython)))
2786 (home-page "http://grit-bio.org")
2787 (synopsis "Tool for integrative analysis of RNA-seq type assays")
2789 "GRIT is designed to use RNA-seq, TES, and TSS data to build and quantify
2790 full length transcript models. When none of these data sources are available,
2791 GRIT can be run by providing a candidate set of TES or TSS sites. In
2792 addition, GRIT can merge in reference junctions and gene boundaries. GRIT can
2793 also be run in quantification mode, where it uses a provided GTF file and just
2794 estimates transcript expression.")
2795 (license license:gpl3+)))
2797 (define-public hisat
2804 "http://ccb.jhu.edu/software/hisat/downloads/hisat-"
2805 version "-beta-source.zip"))
2808 "1k381ydranqxp09yf2y7w1d0chz5d59vb6jchi89hbb0prq19lk5"))))
2809 (build-system gnu-build-system)
2811 `(#:tests? #f ;no check target
2812 #:make-flags '("allall"
2813 ;; Disable unsupported `popcnt' instructions on
2814 ;; architectures other than x86_64
2815 ,@(if (string-prefix? "x86_64"
2816 (or (%current-target-system)
2819 '("POPCNT_CAPABILITY=0")))
2821 (modify-phases %standard-phases
2822 (add-after 'unpack 'patch-sources
2824 ;; XXX Cannot use snippet because zip files are not supported
2825 (substitute* "Makefile"
2826 (("^CC = .*$") "CC = gcc")
2827 (("^CPP = .*$") "CPP = g++")
2828 ;; replace BUILD_HOST and BUILD_TIME for deterministic build
2829 (("-DBUILD_HOST=.*") "-DBUILD_HOST=\"\\\"guix\\\"\"")
2830 (("-DBUILD_TIME=.*") "-DBUILD_TIME=\"\\\"0\\\"\""))
2831 (substitute* '("hisat-build" "hisat-inspect")
2832 (("/usr/bin/env") (which "env")))
2835 (lambda* (#:key outputs #:allow-other-keys)
2836 (let ((bin (string-append (assoc-ref outputs "out") "/bin/")))
2837 (for-each (lambda (file)
2838 (install-file file bin))
2841 "hisat(-(build|align|inspect)(-(s|l)(-debug)*)*)*$")))
2843 (delete 'configure))))
2845 `(("unzip" ,unzip)))
2850 ;; Non-portable SSE instructions are used so building fails on platforms
2851 ;; other than x86_64.
2852 (supported-systems '("x86_64-linux"))
2853 (home-page "http://ccb.jhu.edu/software/hisat/index.shtml")
2854 (synopsis "Hierarchical indexing for spliced alignment of transcripts")
2856 "HISAT is a fast and sensitive spliced alignment program for mapping
2857 RNA-seq reads. In addition to one global FM index that represents a whole
2858 genome, HISAT uses a large set of small FM indexes that collectively cover the
2859 whole genome. These small indexes (called local indexes) combined with
2860 several alignment strategies enable effective alignment of RNA-seq reads, in
2861 particular, reads spanning multiple exons.")
2862 (license license:gpl3+)))
2864 (define-public hisat2
2871 ;; FIXME: a better source URL is
2872 ;; (string-append "ftp://ftp.ccb.jhu.edu/pub/infphilo/hisat2"
2873 ;; "/downloads/hisat2-" version "-source.zip")
2874 ;; with hash "0lywnr8kijwsc2aw10dwxic0n0yvip6fl3rjlvc8zzwahamy4x7g"
2875 ;; but it is currently unavailable.
2876 (uri "https://github.com/infphilo/hisat2/archive/cba6e8cb.tar.gz")
2877 (file-name (string-append name "-" version ".tar.gz"))
2880 "1mf2hdsyv7cd97xm9mp9a4qws02yrj95y6w6f6cdwnq0klp81r50"))))
2881 (build-system gnu-build-system)
2883 `(#:tests? #f ; no check target
2884 #:make-flags (list "CC=gcc" "CXX=g++" "allall")
2885 #:modules ((guix build gnu-build-system)
2889 (modify-phases %standard-phases
2890 (add-after 'unpack 'make-deterministic
2892 (substitute* "Makefile"
2897 (lambda* (#:key outputs #:allow-other-keys)
2898 (let* ((out (assoc-ref outputs "out"))
2899 (bin (string-append out "/bin/"))
2900 (doc (string-append out "/share/doc/hisat2/")))
2902 (cut install-file <> bin)
2904 "hisat2(-(build|align|inspect)(-(s|l)(-debug)*)*)*$"))
2906 (install-file "doc/manual.inc.html" doc))
2909 `(("unzip" ,unzip) ; needed for archive from ftp
2911 ("pandoc" ,ghc-pandoc))) ; for documentation
2912 (home-page "http://ccb.jhu.edu/software/hisat2/index.shtml")
2913 (synopsis "Graph-based alignment of genomic sequencing reads")
2914 (description "HISAT2 is a fast and sensitive alignment program for mapping
2915 next-generation sequencing reads (both DNA and RNA) to a population of human
2916 genomes (as well as to a single reference genome). In addition to using one
2917 global @dfn{graph FM} (GFM) index that represents a population of human
2918 genomes, HISAT2 uses a large set of small GFM indexes that collectively cover
2919 the whole genome. These small indexes, combined with several alignment
2920 strategies, enable rapid and accurate alignment of sequencing reads. This new
2921 indexing scheme is called a @dfn{Hierarchical Graph FM index} (HGFM).")
2922 ;; HISAT2 contains files from Bowtie2, which is released under
2923 ;; GPLv2 or later. The HISAT2 source files are released under
2925 (license license:gpl3+)))
2927 (define-public hmmer
2935 "http://eddylab.org/software/hmmer"
2936 (version-major version) "/"
2937 version "/hmmer-" version ".tar.gz"))
2940 "0djmgc0pfli0jilfx8hql1axhwhqxqb8rxg2r5rg07aw73sfs5nx"))
2941 (patches (search-patches "hmmer-remove-cpu-specificity.patch"))))
2942 (build-system gnu-build-system)
2943 (native-inputs `(("perl" ,perl)))
2944 (home-page "http://hmmer.org/")
2945 (synopsis "Biosequence analysis using profile hidden Markov models")
2947 "HMMER is used for searching sequence databases for homologs of protein
2948 sequences, and for making protein sequence alignments. It implements methods
2949 using probabilistic models called profile hidden Markov models (profile
2951 (license (list license:gpl3+
2952 ;; The bundled library 'easel' is distributed
2953 ;; under The Janelia Farm Software License.
2954 (license:non-copyleft
2955 "file://easel/LICENSE"
2956 "See easel/LICENSE in the distribution.")))))
2958 (define-public htseq
2964 (uri (pypi-uri "HTSeq" version))
2967 "11flgb1381xdhk43bzbfm3vhnszkpqg6jk76rpa5xd1zbrvvlnxg"))))
2968 (build-system python-build-system)
2970 `(("python-cython" ,python-cython)))
2971 ;; Numpy needs to be propagated when htseq is used as a Python library.
2973 `(("python-numpy" ,python-numpy)))
2975 `(("python-pysam" ,python-pysam)
2976 ("python-matplotlib" ,python-matplotlib)))
2977 (home-page "http://www-huber.embl.de/users/anders/HTSeq/")
2978 (synopsis "Analysing high-throughput sequencing data with Python")
2980 "HTSeq is a Python package that provides infrastructure to process data
2981 from high-throughput sequencing assays.")
2982 (license license:gpl3+)))
2984 (define-public python2-htseq
2985 (package-with-python2 htseq))
2987 (define-public java-htsjdk
2989 (name "java-htsjdk")
2990 (version "2.3.0") ; last version without build dependency on gradle
2994 "https://github.com/samtools/htsjdk/archive/"
2996 (file-name (string-append name "-" version ".tar.gz"))
2999 "1ibhzzxsfc38nqyk9r8zqj6blfc1kh26iirypd4q6n90hs2m6nyq"))
3000 (modules '((guix build utils)))
3002 ;; Delete pre-built binaries
3004 (delete-file-recursively "lib")
3007 (build-system ant-build-system)
3009 `(#:tests? #f ; test require Internet access
3012 (list (string-append "-Ddist=" (assoc-ref %outputs "out")
3013 "/share/java/htsjdk/"))
3014 #:build-target "all"
3016 (modify-phases %standard-phases
3017 ;; The build phase also installs the jars
3018 (delete 'install))))
3020 `(("java-ngs" ,java-ngs)
3021 ("java-snappy-1" ,java-snappy-1)
3022 ("java-commons-compress" ,java-commons-compress)
3023 ("java-commons-logging-minimal" ,java-commons-logging-minimal)
3024 ("java-commons-jexl-2" ,java-commons-jexl-2)
3025 ("java-xz" ,java-xz)))
3027 `(("java-testng" ,java-testng)))
3028 (home-page "http://samtools.github.io/htsjdk/")
3029 (synopsis "Java API for high-throughput sequencing data (HTS) formats")
3031 "HTSJDK is an implementation of a unified Java library for accessing
3032 common file formats, such as SAM and VCF, used for high-throughput
3033 sequencing (HTS) data. There are also an number of useful utilities for
3034 manipulating HTS data.")
3035 (license license:expat)))
3037 (define-public java-htsjdk-latest
3039 (name "java-htsjdk")
3044 (url "https://github.com/samtools/htsjdk.git")
3046 (file-name (string-append name "-" version "-checkout"))
3049 "1lmya1fdjy03mz6zmdmd86j9v9vfhqb3952mqq075navx1i6g4bc"))))
3050 (build-system ant-build-system)
3052 `(#:tests? #f ; test require Scala
3054 #:jar-name "htsjdk.jar"
3056 (modify-phases %standard-phases
3057 (add-after 'unpack 'remove-useless-build.xml
3058 (lambda _ (delete-file "build.xml") #t))
3059 ;; The tests require the scalatest package.
3060 (add-after 'unpack 'remove-tests
3061 (lambda _ (delete-file-recursively "src/test") #t)))))
3063 `(("java-ngs" ,java-ngs)
3064 ("java-snappy-1" ,java-snappy-1)
3065 ("java-commons-compress" ,java-commons-compress)
3066 ("java-commons-logging-minimal" ,java-commons-logging-minimal)
3067 ("java-commons-jexl-2" ,java-commons-jexl-2)
3068 ("java-xz" ,java-xz)))
3070 `(("java-junit" ,java-junit)))
3071 (home-page "http://samtools.github.io/htsjdk/")
3072 (synopsis "Java API for high-throughput sequencing data (HTS) formats")
3074 "HTSJDK is an implementation of a unified Java library for accessing
3075 common file formats, such as SAM and VCF, used for high-throughput
3076 sequencing (HTS) data. There are also an number of useful utilities for
3077 manipulating HTS data.")
3078 (license license:expat)))
3080 ;; This is needed for picard 2.10.3
3081 (define-public java-htsjdk-2.10.1
3082 (package (inherit java-htsjdk-latest)
3083 (name "java-htsjdk")
3088 (url "https://github.com/samtools/htsjdk.git")
3090 (file-name (string-append name "-" version "-checkout"))
3093 "1kxh7slm2pm3x9p6jxa1wqsq9a31dhiiflhxnxqcisan4k3rwia2"))))
3094 (build-system ant-build-system)
3096 `(#:tests? #f ; tests require Scala
3098 #:jar-name "htsjdk.jar"
3100 (modify-phases %standard-phases
3101 (add-after 'unpack 'remove-useless-build.xml
3102 (lambda _ (delete-file "build.xml") #t))
3103 ;; The tests require the scalatest package.
3104 (add-after 'unpack 'remove-tests
3105 (lambda _ (delete-file-recursively "src/test") #t)))))))
3107 ;; This version matches java-htsjdk 2.3.0. Later versions also require a more
3108 ;; recent version of java-htsjdk, which depends on gradle.
3109 (define-public java-picard
3111 (name "java-picard")
3116 (url "https://github.com/broadinstitute/picard.git")
3118 (file-name (string-append "java-picard-" version "-checkout"))
3121 "1ll7mf4r3by92w2nhlmpa591xd1f46xlkwh59mq6fvbb5pdwzvx6"))
3122 (modules '((guix build utils)))
3125 ;; Delete pre-built binaries.
3126 (delete-file-recursively "lib")
3128 (substitute* "build.xml"
3129 ;; Remove build-time dependency on git.
3130 (("failifexecutionfails=\"true\"")
3131 "failifexecutionfails=\"false\"")
3133 (("depends=\"compile-htsjdk, ")
3135 (("depends=\"compile-htsjdk-tests, ")
3137 ;; Build picard-lib.jar before building picard.jar
3138 (("name=\"picard-jar\" depends=\"" line)
3139 (string-append line "picard-lib-jar, ")))
3141 (build-system ant-build-system)
3143 `(#:build-target "picard-jar"
3144 #:test-target "test"
3145 ;; Tests require jacoco:coverage.
3148 (list (string-append "-Dhtsjdk_lib_dir="
3149 (assoc-ref %build-inputs "java-htsjdk")
3150 "/share/java/htsjdk/")
3151 "-Dhtsjdk-classes=dist/tmp"
3152 (string-append "-Dhtsjdk-version="
3153 ,(package-version java-htsjdk)))
3156 (modify-phases %standard-phases
3157 (add-after 'unpack 'use-our-htsjdk
3158 (lambda* (#:key inputs #:allow-other-keys)
3159 (substitute* "build.xml"
3160 (("\\$\\{htsjdk\\}/lib")
3161 (string-append (assoc-ref inputs "java-htsjdk")
3162 "/share/java/htsjdk/")))
3164 (add-after 'unpack 'make-test-target-independent
3165 (lambda* (#:key inputs #:allow-other-keys)
3166 (substitute* "build.xml"
3167 (("name=\"test\" depends=\"compile, ")
3168 "name=\"test\" depends=\""))
3170 (replace 'install (install-jars "dist")))))
3172 `(("java-htsjdk" ,java-htsjdk)
3173 ("java-guava" ,java-guava)))
3175 `(("java-testng" ,java-testng)))
3176 (home-page "http://broadinstitute.github.io/picard/")
3177 (synopsis "Tools for manipulating high-throughput sequencing data and formats")
3178 (description "Picard is a set of Java command line tools for manipulating
3179 high-throughput sequencing (HTS) data and formats. Picard is implemented
3180 using the HTSJDK Java library to support accessing file formats that are
3181 commonly used for high-throughput sequencing data such as SAM, BAM, CRAM and
3183 (license license:expat)))
3185 ;; This is needed for dropseq-tools
3186 (define-public java-picard-2.10.3
3188 (name "java-picard")
3193 (url "https://github.com/broadinstitute/picard.git")
3195 (file-name (string-append "java-picard-" version "-checkout"))
3198 "1ajlx31l6i1k3y2rhnmgq07sz99g2czqfqgkr9mihmdjp3gwjhvi"))))
3199 (build-system ant-build-system)
3201 `(#:jar-name "picard.jar"
3202 ;; Tests require jacoco:coverage.
3205 #:main-class "picard.cmdline.PicardCommandLine"
3206 #:modules ((guix build ant-build-system)
3208 (guix build java-utils)
3213 (modify-phases %standard-phases
3214 (add-after 'unpack 'remove-useless-build.xml
3215 (lambda _ (delete-file "build.xml") #t))
3216 ;; This is necessary to ensure that htsjdk is found when using
3217 ;; picard.jar as an executable.
3218 (add-before 'build 'edit-classpath-in-manifest
3219 (lambda* (#:key inputs #:allow-other-keys)
3220 (chmod "build.xml" #o664)
3221 (call-with-output-file "build.xml.new"
3225 (with-input-from-file "build.xml"
3226 (lambda _ (xml->sxml #:trim-whitespace? #t)))
3227 `((target . ,(lambda (tag . kids)
3228 (let ((name ((sxpath '(name *text*))
3230 ;; FIXME: We're breaking the line
3231 ;; early with a dummy path to
3232 ;; ensure that the store reference
3233 ;; isn't broken apart and can still
3234 ;; be found by the reference
3239 ~a/share/java/htsjdk.jar${line.separator}"
3240 ;; maximum line length is 70
3241 (string-tabulate (const #\b) 57)
3242 (assoc-ref inputs "java-htsjdk"))))
3243 (if (member "manifest" name)
3247 (file "${manifest.file}")
3250 (*default* . ,(lambda (tag . kids) `(,tag ,@kids)))
3251 (*text* . ,(lambda (_ txt) txt))))
3253 (rename-file "build.xml.new" "build.xml")
3256 `(("java-htsjdk" ,java-htsjdk-2.10.1)))
3258 `(("java-testng" ,java-testng)
3259 ("java-guava" ,java-guava)))
3260 (home-page "http://broadinstitute.github.io/picard/")
3261 (synopsis "Tools for manipulating high-throughput sequencing data and formats")
3262 (description "Picard is a set of Java command line tools for manipulating
3263 high-throughput sequencing (HTS) data and formats. Picard is implemented
3264 using the HTSJDK Java library to support accessing file formats that are
3265 commonly used for high-throughput sequencing data such as SAM, BAM, CRAM and
3267 (license license:expat)))
3269 ;; This is the last version of Picard to provide net.sf.samtools
3270 (define-public java-picard-1.113
3271 (package (inherit java-picard)
3272 (name "java-picard")
3277 (url "https://github.com/broadinstitute/picard.git")
3279 (file-name (string-append "java-picard-" version "-checkout"))
3282 "0lkpvin2fz3hhly4l02kk56fqy8lmlgyzr9kmvljk6ry6l1hw973"))
3283 (modules '((guix build utils)))
3286 ;; Delete pre-built binaries.
3287 (delete-file-recursively "lib")
3290 (build-system ant-build-system)
3292 `(#:build-target "picard-jar"
3293 #:test-target "test"
3294 ;; FIXME: the class path at test time is wrong.
3295 ;; [testng] Error: A JNI error has occurred, please check your installation and try again
3296 ;; [testng] Exception in thread "main" java.lang.NoClassDefFoundError: com/beust/jcommander/ParameterException
3299 ;; This is only used for tests.
3301 (list "-Dsamjdk.intel_deflater_so_path=lib/jni/libIntelDeflater.so")
3303 (modify-phases %standard-phases
3304 ;; Do not use bundled ant bzip2.
3305 (add-after 'unpack 'use-ant-bzip
3306 (lambda* (#:key inputs #:allow-other-keys)
3307 (substitute* "build.xml"
3308 (("\\$\\{lib\\}/apache-ant-1.8.2-bzip2.jar")
3309 (string-append (assoc-ref inputs "ant")
3312 (add-after 'unpack 'make-test-target-independent
3313 (lambda* (#:key inputs #:allow-other-keys)
3314 (substitute* "build.xml"
3315 (("name=\"test\" depends=\"compile, ")
3316 "name=\"test\" depends=\"compile-tests, ")
3317 (("name=\"compile\" depends=\"compile-src, compile-tests\"")
3318 "name=\"compile\" depends=\"compile-src\""))
3320 (add-after 'unpack 'fix-deflater-path
3321 (lambda* (#:key outputs #:allow-other-keys)
3322 (substitute* "src/java/net/sf/samtools/Defaults.java"
3323 (("getStringProperty\\(\"intel_deflater_so_path\", null\\)")
3324 (string-append "getStringProperty(\"intel_deflater_so_path\", \""
3325 (assoc-ref outputs "out")
3326 "/lib/jni/libIntelDeflater.so"
3329 ;; Build the deflater library, because we've previously deleted the
3330 ;; pre-built one. This can only be built with access to the JDK
3332 (add-after 'build 'build-jni
3333 (lambda* (#:key inputs #:allow-other-keys)
3336 (and (zero? (system* "tar" "--strip-components=1" "-C" "jdk-src"
3337 "-xf" (assoc-ref inputs "jdk-src")))
3338 (zero? (system* "javah" "-jni"
3339 "-classpath" "classes"
3341 "net.sf.samtools.util.zip.IntelDeflater"))
3342 (with-directory-excursion "src/c/inteldeflater"
3343 (zero? (system* "gcc" "-I../../../lib" "-I."
3344 (string-append "-I" (assoc-ref inputs "jdk")
3346 "-I../../../jdk-src/src/share/native/common/"
3347 "-I../../../jdk-src/src/solaris/native/common/"
3348 "-c" "-O3" "-fPIC" "IntelDeflater.c"))
3349 (zero? (system* "gcc" "-shared"
3350 "-o" "../../../lib/jni/libIntelDeflater.so"
3351 "IntelDeflater.o" "-lz" "-lstdc++"))))))
3352 ;; We can only build everything else after building the JNI library.
3353 (add-after 'build-jni 'build-rest
3354 (lambda* (#:key make-flags #:allow-other-keys)
3355 (zero? (apply system* `("ant" "all" ,@make-flags)))))
3356 (add-before 'build 'set-JAVA6_HOME
3358 (setenv "JAVA6_HOME" (getenv "JAVA_HOME"))
3360 (replace 'install (install-jars "dist"))
3361 (add-after 'install 'install-jni-lib
3362 (lambda* (#:key outputs #:allow-other-keys)
3363 (let ((jni (string-append (assoc-ref outputs "out")
3366 (install-file "lib/jni/libIntelDeflater.so" jni)
3369 `(("java-snappy-1" ,java-snappy-1)
3370 ("java-commons-jexl-2" ,java-commons-jexl-2)
3371 ("java-cofoja" ,java-cofoja)
3372 ("ant" ,ant) ; for bzip2 support at runtime
3375 `(("ant-apache-bcel" ,ant-apache-bcel)
3376 ("ant-junit" ,ant-junit)
3377 ("java-testng" ,java-testng)
3378 ("java-commons-bcel" ,java-commons-bcel)
3379 ("java-jcommander" ,java-jcommander)
3380 ("jdk" ,icedtea-8 "jdk")
3381 ("jdk-src" ,(car (assoc-ref (package-native-inputs icedtea-8) "jdk-drop")))))))
3383 (define-public fastqc
3390 (uri (string-append "http://www.bioinformatics.babraham.ac.uk/"
3391 "projects/fastqc/fastqc_v"
3392 version "_source.zip"))
3395 "18rrlkhcrxvvvlapch4dpj6xc6mpayzys8qfppybi8jrpgx5cc5f"))))
3396 (build-system ant-build-system)
3398 `(#:tests? #f ; there are no tests
3399 #:build-target "build"
3401 (modify-phases %standard-phases
3402 (add-after 'unpack 'fix-dependencies
3403 (lambda* (#:key inputs #:allow-other-keys)
3404 (substitute* "build.xml"
3406 (string-append (assoc-ref inputs "java-jbzip2")
3407 "/share/java/jbzip2.jar"))
3409 (string-append (assoc-ref inputs "java-picard-1.113")
3410 "/share/java/sam-1.112.jar"))
3412 (string-append (assoc-ref inputs "java-cisd-jhdf5")
3413 "/share/java/sis-jhdf5.jar")))
3415 ;; There is no installation target
3417 (lambda* (#:key inputs outputs #:allow-other-keys)
3418 (let* ((out (assoc-ref outputs "out"))
3419 (bin (string-append out "/bin"))
3420 (share (string-append out "/share/fastqc/"))
3421 (exe (string-append share "/fastqc")))
3422 (for-each mkdir-p (list bin share))
3423 (copy-recursively "bin" share)
3425 (("my \\$java_bin = 'java';")
3426 (string-append "my $java_bin = '"
3427 (assoc-ref inputs "java")
3430 (symlink exe (string-append bin "/fastqc"))
3434 ("perl" ,perl) ; needed for the wrapper script
3435 ("java-cisd-jhdf5" ,java-cisd-jhdf5)
3436 ("java-picard-1.113" ,java-picard-1.113)
3437 ("java-jbzip2" ,java-jbzip2)))
3439 `(("unzip" ,unzip)))
3440 (home-page "http://www.bioinformatics.babraham.ac.uk/projects/fastqc/")
3441 (synopsis "Quality control tool for high throughput sequence data")
3443 "FastQC aims to provide a simple way to do some quality control
3444 checks on raw sequence data coming from high throughput sequencing
3445 pipelines. It provides a modular set of analyses which you can use to
3446 give a quick impression of whether your data has any problems of which
3447 you should be aware before doing any further analysis.
3449 The main functions of FastQC are:
3452 @item Import of data from BAM, SAM or FastQ files (any variant);
3453 @item Providing a quick overview to tell you in which areas there may
3455 @item Summary graphs and tables to quickly assess your data;
3456 @item Export of results to an HTML based permanent report;
3457 @item Offline operation to allow automated generation of reports
3458 without running the interactive application.
3460 (license license:gpl3+)))
3462 (define-public fastp
3470 (url "https://github.com/OpenGene/fastp.git")
3471 (commit (string-append "v" version))))
3472 (file-name (git-file-name name version))
3475 "1r6ms5zbf5rps4rgp4z73nczadl00b5rqylw8f684isfz27dp0xh"))))
3476 (build-system gnu-build-system)
3478 `(#:tests? #f ; there are none
3480 (list (string-append "BINDIR=" (assoc-ref %outputs "out") "/bin"))
3482 (modify-phases %standard-phases
3484 (add-before 'install 'create-target-dir
3485 (lambda* (#:key outputs #:allow-other-keys)
3486 (mkdir-p (string-append (assoc-ref outputs "out") "/bin"))
3490 (home-page "https://github.com/OpenGene/fastp/")
3491 (synopsis "All-in-one FastQ preprocessor")
3493 "Fastp is a tool designed to provide fast all-in-one preprocessing for
3494 FastQ files. This tool has multi-threading support to afford high
3496 (license license:expat)))
3498 (define-public htslib
3505 "https://github.com/samtools/htslib/releases/download/"
3506 version "/htslib-" version ".tar.bz2"))
3509 "18bw0mn9pj5wgarnlaxmf1bb8pdqgl1zd6czirqcr62ajpn1xvy0"))))
3510 (build-system gnu-build-system)
3512 `(("openssl" ,openssl)
3517 (home-page "http://www.htslib.org")
3518 (synopsis "C library for reading/writing high-throughput sequencing data")
3520 "HTSlib is a C library for reading/writing high-throughput sequencing
3521 data. It also provides the @command{bgzip}, @command{htsfile}, and
3522 @command{tabix} utilities.")
3523 ;; Files under cram/ are released under the modified BSD license;
3524 ;; the rest is released under the Expat license
3525 (license (list license:expat license:bsd-3))))
3527 ;; This package should be removed once no packages rely upon it.
3535 "https://github.com/samtools/htslib/releases/download/"
3536 version "/htslib-" version ".tar.bz2"))
3539 "1rja282fwdc25ql6izkhdyh8ppw8x2fs0w0js78zgkmqjlikmma9"))))))
3548 "https://github.com/nboley/idr/archive/"
3550 (file-name (string-append name "-" version ".tar.gz"))
3553 "1rjdly6daslw66r43g9md8znizlscn1sphycqyldzsidkc4vxqv3"))
3554 ;; Delete generated C code.
3556 '(begin (delete-file "idr/inv_cdf.c") #t))))
3557 (build-system python-build-system)
3558 ;; There is only one test ("test_inv_cdf.py") and it tests features that
3559 ;; are no longer part of this package. It also asserts False, which
3560 ;; causes the tests to always fail.
3561 (arguments `(#:tests? #f))
3563 `(("python-scipy" ,python-scipy)
3564 ("python-sympy" ,python-sympy)
3565 ("python-numpy" ,python-numpy)
3566 ("python-matplotlib" ,python-matplotlib)))
3568 `(("python-cython" ,python-cython)))
3569 (home-page "https://github.com/nboley/idr")
3570 (synopsis "Tool to measure the irreproducible discovery rate (IDR)")
3572 "The IDR (Irreproducible Discovery Rate) framework is a unified approach
3573 to measure the reproducibility of findings identified from replicate
3574 experiments and provide highly stable thresholds based on reproducibility.")
3575 (license license:gpl2+)))
3577 (define-public jellyfish
3583 (uri (string-append "https://github.com/gmarcais/Jellyfish/"
3584 "releases/download/v" version
3585 "/jellyfish-" version ".tar.gz"))
3588 "1a1iwq9pq54k2m9ypvwl5s0bqfl64gwh9dx5af9i382ajas2016q"))))
3589 (build-system gnu-build-system)
3590 (outputs '("out" ;for library
3591 "ruby" ;for Ruby bindings
3592 "python")) ;for Python bindings
3595 (list (string-append "--enable-ruby-binding="
3596 (assoc-ref %outputs "ruby"))
3597 (string-append "--enable-python-binding="
3598 (assoc-ref %outputs "python")))
3600 (modify-phases %standard-phases
3601 (add-before 'check 'set-SHELL-variable
3603 ;; generator_manager.hpp either uses /bin/sh or $SHELL
3605 (setenv "SHELL" (which "bash"))
3611 ("python" ,python-2)
3612 ("pkg-config" ,pkg-config)))
3614 `(("htslib" ,htslib)))
3615 (synopsis "Tool for fast counting of k-mers in DNA")
3617 "Jellyfish is a tool for fast, memory-efficient counting of k-mers in
3618 DNA. A k-mer is a substring of length k, and counting the occurrences of all
3619 such substrings is a central step in many analyses of DNA sequence. Jellyfish
3620 is a command-line program that reads FASTA and multi-FASTA files containing
3621 DNA sequences. It outputs its k-mer counts in a binary format, which can be
3622 translated into a human-readable text format using the @code{jellyfish dump}
3623 command, or queried for specific k-mers with @code{jellyfish query}.")
3624 (home-page "http://www.genome.umd.edu/jellyfish.html")
3625 ;; From their website: JELLYFISH runs on 64-bit Intel-compatible processors
3626 (supported-systems '("x86_64-linux"))
3627 ;; The combined work is published under the GPLv3 or later. Individual
3628 ;; files such as lib/jsoncpp.cpp are released under the Expat license.
3629 (license (list license:gpl3+ license:expat))))
3631 (define-public khmer
3638 (uri (pypi-uri "khmer" version))
3641 "0wb05shqh77v00256qlm68vbbx3kl76fyzihszbz5nhanl4ni33a"))
3642 (patches (search-patches "khmer-use-libraries.patch"))))
3643 (build-system python-build-system)
3646 (modify-phases %standard-phases
3647 (add-after 'unpack 'set-paths
3648 (lambda* (#:key inputs outputs #:allow-other-keys)
3649 ;; Delete bundled libraries.
3650 (delete-file-recursively "third-party/zlib")
3651 (delete-file-recursively "third-party/bzip2")
3652 ;; Replace bundled seqan.
3653 (let* ((seqan-all "third-party/seqan")
3654 (seqan-include (string-append
3655 seqan-all "/core/include")))
3656 (delete-file-recursively seqan-all)
3657 (copy-recursively (string-append (assoc-ref inputs "seqan")
3659 (string-append seqan-include "/seqan")))
3660 ;; We do not replace the bundled MurmurHash as the canonical
3661 ;; repository for this code 'SMHasher' is unsuitable for
3662 ;; providing a library. See
3663 ;; https://lists.gnu.org/archive/html/guix-devel/2016-06/msg00977.html
3665 (add-after 'unpack 'set-cc
3669 ;; It is simpler to test after installation.
3671 (add-after 'install 'post-install-check
3672 (lambda* (#:key inputs outputs #:allow-other-keys)
3673 (let ((out (assoc-ref outputs "out")))
3678 (assoc-ref outputs "out")
3680 (setenv "PYTHONPATH"
3682 (getenv "PYTHONPATH")
3686 (string-take (string-take-right
3687 (assoc-ref inputs "python") 5) 3)
3689 (with-directory-excursion "build"
3690 (zero? (system* "nosetests" "khmer" "--attr"
3691 "!known_failing")))))))))
3694 ("python-nose" ,python-nose)))
3698 ("python-screed" ,python-screed)
3699 ("python-bz2file" ,python-bz2file)
3700 ;; Tests fail when gcc-5 is used for compilation. Use gcc-4.9 at least
3701 ;; until the next version of khmer (likely 2.1) is released.
3703 (home-page "https://khmer.readthedocs.org/")
3704 (synopsis "K-mer counting, filtering and graph traversal library")
3705 (description "The khmer software is a set of command-line tools for
3706 working with DNA shotgun sequencing data from genomes, transcriptomes,
3707 metagenomes and single cells. Khmer can make de novo assemblies faster, and
3708 sometimes better. Khmer can also identify and fix problems with shotgun
3710 ;; When building on i686, armhf and mips64el, we get the following error:
3711 ;; error: ['khmer', 'khmer.tests', 'oxli'] require 64-bit operating system
3712 (supported-systems '("x86_64-linux" "aarch64-linux"))
3713 (license license:bsd-3)))
3715 (define-public kaiju
3722 "https://github.com/bioinformatics-centre/kaiju/archive/v"
3724 (file-name (string-append name "-" version ".tar.gz"))
3727 "1kdn4rxs0kr9ibmrgrfcci71aa6j6gr71dbc8pff7731rpab6kj7"))))
3728 (build-system gnu-build-system)
3730 `(#:tests? #f ; There are no tests.
3732 (modify-phases %standard-phases
3734 (add-before 'build 'move-to-src-dir
3735 (lambda _ (chdir "src") #t))
3737 (lambda* (#:key inputs outputs #:allow-other-keys)
3738 (let ((bin (string-append (assoc-ref outputs "out") "/bin")))
3741 (copy-recursively "bin" bin)
3742 (copy-recursively "util" bin))
3747 (home-page "http://kaiju.binf.ku.dk/")
3748 (synopsis "Fast and sensitive taxonomic classification for metagenomics")
3749 (description "Kaiju is a program for sensitive taxonomic classification
3750 of high-throughput sequencing reads from metagenomic whole genome sequencing
3752 (license license:gpl3+)))
3757 (version "2.1.0.20151222")
3760 (uri (pypi-uri "MACS2" version))
3763 "1r2hcz6irhcq7lwbafjks98jbn34hv05avgbdjnp6w6mlfjkf8x5"))))
3764 (build-system python-build-system)
3766 `(#:python ,python-2 ; only compatible with Python 2.7
3767 #:tests? #f)) ; no test target
3769 `(("python-numpy" ,python2-numpy)))
3770 (home-page "https://github.com/taoliu/MACS/")
3771 (synopsis "Model based analysis for ChIP-Seq data")
3773 "MACS is an implementation of a ChIP-Seq analysis algorithm for
3774 identifying transcript factor binding sites named Model-based Analysis of
3775 ChIP-Seq (MACS). MACS captures the influence of genome complexity to evaluate
3776 the significance of enriched ChIP regions and it improves the spatial
3777 resolution of binding sites through combining the information of both
3778 sequencing tag position and orientation.")
3779 (license license:bsd-3)))
3781 (define-public mafft
3788 "https://mafft.cbrc.jp/alignment/software/mafft-" version
3789 "-without-extensions-src.tgz"))
3790 (file-name (string-append name "-" version ".tgz"))
3793 "0bacjkxfg944p5khhyh5rd4y7wkjc9qk4v2jjj442sqlq0f8ar7b"))))
3794 (build-system gnu-build-system)
3796 `(#:tests? #f ; no automated tests, though there are tests in the read me
3797 #:make-flags (let ((out (assoc-ref %outputs "out")))
3798 (list (string-append "PREFIX=" out)
3799 (string-append "BINDIR="
3800 (string-append out "/bin"))))
3802 (modify-phases %standard-phases
3803 (add-after 'unpack 'enter-dir
3804 (lambda _ (chdir "core") #t))
3805 (add-after 'enter-dir 'patch-makefile
3807 ;; on advice from the MAFFT authors, there is no need to
3808 ;; distribute mafft-profile, mafft-distance, or
3809 ;; mafft-homologs.rb as they are too "specialised".
3810 (substitute* "Makefile"
3811 ;; remove mafft-homologs.rb from SCRIPTS
3812 (("^SCRIPTS = mafft mafft-homologs.rb")
3814 ;; remove mafft-homologs from MANPAGES
3815 (("^MANPAGES = mafft.1 mafft-homologs.1")
3816 "MANPAGES = mafft.1")
3817 ;; remove mafft-distance from PROGS
3818 (("^PROGS = dvtditr dndfast7 dndblast sextet5 mafft-distance")
3819 "PROGS = dvtditr dndfast7 dndblast sextet5")
3820 ;; remove mafft-profile from PROGS
3821 (("splittbfast disttbfast tbfast mafft-profile 2cl mccaskillwrap")
3822 "splittbfast disttbfast tbfast f2cl mccaskillwrap")
3823 (("^rm -f mafft-profile mafft-profile.exe") "#")
3824 (("^rm -f mafft-distance mafft-distance.exe") ")#")
3825 ;; do not install MAN pages in libexec folder
3826 (("^\t\\$\\(INSTALL\\) -m 644 \\$\\(MANPAGES\\) \
3827 \\$\\(DESTDIR\\)\\$\\(LIBDIR\\)") "#"))
3829 (add-after 'enter-dir 'patch-paths
3830 (lambda* (#:key inputs #:allow-other-keys)
3831 (substitute* '("pairash.c"
3833 (("perl") (which "perl"))
3834 (("([\"`| ])awk" _ prefix)
3835 (string-append prefix (which "awk")))
3836 (("grep") (which "grep")))
3839 (add-after 'install 'wrap-programs
3840 (lambda* (#:key outputs #:allow-other-keys)
3841 (let* ((out (assoc-ref outputs "out"))
3842 (bin (string-append out "/bin"))
3843 (path (string-append
3844 (assoc-ref %build-inputs "coreutils") "/bin:")))
3845 (for-each (lambda (file)
3847 `("PATH" ":" prefix (,path))))
3855 ("coreutils" ,coreutils)))
3856 (home-page "http://mafft.cbrc.jp/alignment/software/")
3857 (synopsis "Multiple sequence alignment program")
3859 "MAFFT offers a range of multiple alignment methods for nucleotide and
3860 protein sequences. For instance, it offers L-INS-i (accurate; for alignment
3861 of <~200 sequences) and FFT-NS-2 (fast; for alignment of <~30,000
3863 (license (license:non-copyleft
3864 "http://mafft.cbrc.jp/alignment/software/license.txt"
3865 "BSD-3 with different formatting"))))
3874 "https://github.com/marbl/mash/archive/v"
3876 (file-name (string-append name "-" version ".tar.gz"))
3879 "00fx14vpmgsijwxd1xql3if934l82v8ckqgjjyyhnr36qb9qrskv"))
3880 (modules '((guix build utils)))
3883 ;; Delete bundled kseq.
3884 ;; TODO: Also delete bundled murmurhash and open bloom filter.
3885 (delete-file "src/mash/kseq.h")
3887 (build-system gnu-build-system)
3889 `(#:tests? #f ; No tests.
3892 (string-append "--with-capnp=" (assoc-ref %build-inputs "capnproto"))
3893 (string-append "--with-gsl=" (assoc-ref %build-inputs "gsl")))
3894 #:make-flags (list "CC=gcc")
3896 (modify-phases %standard-phases
3897 (add-after 'unpack 'fix-includes
3899 (substitute* '("src/mash/Sketch.cpp"
3900 "src/mash/CommandFind.cpp"
3901 "src/mash/CommandScreen.cpp")
3902 (("^#include \"kseq\\.h\"")
3903 "#include \"htslib/kseq.h\""))
3905 (add-after 'fix-includes 'autoconf
3906 (lambda _ (zero? (system* "autoconf")))))))
3908 `(("autoconf" ,autoconf)
3909 ;; Capnproto and htslib are statically embedded in the final
3910 ;; application. Therefore we also list their licenses, below.
3911 ("capnproto" ,capnproto)
3912 ("htslib" ,htslib)))
3916 (supported-systems '("x86_64-linux"))
3917 (home-page "https://mash.readthedocs.io")
3918 (synopsis "Fast genome and metagenome distance estimation using MinHash")
3919 (description "Mash is a fast sequence distance estimator that uses the
3920 MinHash algorithm and is designed to work with genomes and metagenomes in the
3921 form of assemblies or reads.")
3922 (license (list license:bsd-3 ; Mash
3923 license:expat ; HTSlib and capnproto
3924 license:public-domain ; MurmurHash 3
3925 license:cpl1.0)))) ; Open Bloom Filter
3927 (define-public metabat
3934 (uri (string-append "https://bitbucket.org/berkeleylab/metabat/get/v"
3936 (file-name (string-append name "-" version ".tar.gz"))
3939 "1hmvdalz3zj5sqqklg0l4npjdv37cv2hsdi1al9iby2ndxjs1b73"))
3940 (patches (search-patches "metabat-fix-compilation.patch"))))
3941 (build-system scons-build-system)
3943 `(#:scons ,scons-python2
3945 (list (string-append "PREFIX=" (assoc-ref %outputs "out"))
3946 (string-append "BOOST_ROOT=" (assoc-ref %build-inputs "boost")))
3947 #:tests? #f ;; Tests are run during the build phase.
3949 (modify-phases %standard-phases
3950 (add-after 'unpack 'fix-includes
3952 (substitute* "src/BamUtils.h"
3953 (("^#include \"bam/bam\\.h\"")
3954 "#include \"samtools/bam.h\"")
3955 (("^#include \"bam/sam\\.h\"")
3956 "#include \"samtools/sam.h\""))
3957 (substitute* "src/KseqReader.h"
3958 (("^#include \"bam/kseq\\.h\"")
3959 "#include \"htslib/kseq.h\""))
3961 (add-after 'unpack 'fix-scons
3962 (lambda* (#:key inputs #:allow-other-keys)
3963 (substitute* "SConstruct"
3964 (("^htslib_dir += 'samtools'")
3965 (string-append "htslib_dir = '"
3966 (assoc-ref inputs "htslib")
3968 (("^samtools_dir = 'samtools'")
3969 (string-append "samtools_dir = '"
3970 (assoc-ref inputs "samtools")
3972 (("^findStaticOrShared\\('bam', hts_lib")
3973 (string-append "findStaticOrShared('bam', '"
3974 (assoc-ref inputs "samtools")
3976 ;; Do not distribute README.
3977 (("^env\\.Install\\(idir_prefix, 'README\\.md'\\)") ""))
3982 ("samtools" ,samtools)
3985 (home-page "https://bitbucket.org/berkeleylab/metabat")
3987 "Reconstruction of single genomes from complex microbial communities")
3989 "Grouping large genomic fragments assembled from shotgun metagenomic
3990 sequences to deconvolute complex microbial communities, or metagenome binning,
3991 enables the study of individual organisms and their interactions. MetaBAT is
3992 an automated metagenome binning software, which integrates empirical
3993 probabilistic distances of genome abundance and tetranucleotide frequency.")
3994 ;; The source code contains inline assembly.
3995 (supported-systems '("x86_64-linux" "i686-linux"))
3996 (license (license:non-copyleft "file://license.txt"
3997 "See license.txt in the distribution."))))
3999 (define-public minced
4006 "https://github.com/ctSkennerton/minced/archive/"
4008 (file-name (string-append name "-" version ".tar.gz"))
4011 "0wxmlsapxfpxfd3ps9636h7i2xy6la8i42mwh0j2lsky63h63jp1"))))
4012 (build-system gnu-build-system)
4014 `(#:test-target "test"
4016 (modify-phases %standard-phases
4018 (add-before 'check 'fix-test
4020 ;; Fix test for latest version.
4021 (substitute* "t/Aquifex_aeolicus_VF5.expected"
4022 (("minced:0.1.6") "minced:0.2.0"))
4024 (replace 'install ; No install target.
4025 (lambda* (#:key inputs outputs #:allow-other-keys)
4026 (let* ((out (assoc-ref outputs "out"))
4027 (bin (string-append out "/bin"))
4028 (wrapper (string-append bin "/minced")))
4029 ;; Minced comes with a wrapper script that tries to figure out where
4030 ;; it is located before running the JAR. Since these paths are known
4031 ;; to us, we build our own wrapper to avoid coreutils dependency.
4032 (install-file "minced.jar" bin)
4033 (with-output-to-file wrapper
4037 "#!" (assoc-ref inputs "bash") "/bin/sh\n\n"
4038 (assoc-ref inputs "jre") "/bin/java -jar "
4039 bin "/minced.jar \"$@\"\n"))))
4040 (chmod wrapper #o555)))))))
4042 `(("jdk" ,icedtea "jdk")))
4045 ("jre" ,icedtea "out")))
4046 (home-page "https://github.com/ctSkennerton/minced")
4047 (synopsis "Mining CRISPRs in Environmental Datasets")
4049 "MinCED is a program to find Clustered Regularly Interspaced Short
4050 Palindromic Repeats (CRISPRs) in DNA sequences. It can be used for
4051 unassembled metagenomic reads, but is mainly designed for full genomes and
4052 assembled metagenomic sequence.")
4053 (license license:gpl3+)))
4061 (uri (pypi-uri "misopy" version))
4064 "1z3x0vd8ma7pdrnywj7i3kgwl89sdkwrrn62zl7r5calqaq2hyip"))
4065 (modules '((guix build utils)))
4067 (substitute* "setup.py"
4068 ;; Use setuptools, or else the executables are not
4070 (("distutils.core") "setuptools")
4071 ;; use "gcc" instead of "cc" for compilation
4073 "cc.set_executables(
4077 linker_so='gcc -shared'); defines"))
4079 (build-system python-build-system)
4081 `(#:python ,python-2 ; only Python 2 is supported
4082 #:tests? #f)) ; no "test" target
4084 `(("samtools" ,samtools)
4085 ("python-numpy" ,python2-numpy)
4086 ("python-pysam" ,python2-pysam)
4087 ("python-scipy" ,python2-scipy)
4088 ("python-matplotlib" ,python2-matplotlib)))
4090 `(("python-mock" ,python2-mock) ;for tests
4091 ("python-pytz" ,python2-pytz))) ;for tests
4092 (home-page "http://genes.mit.edu/burgelab/miso/index.html")
4093 (synopsis "Mixture of Isoforms model for RNA-Seq isoform quantitation")
4095 "MISO (Mixture-of-Isoforms) is a probabilistic framework that quantitates
4096 the expression level of alternatively spliced genes from RNA-Seq data, and
4097 identifies differentially regulated isoforms or exons across samples. By
4098 modeling the generative process by which reads are produced from isoforms in
4099 RNA-Seq, the MISO model uses Bayesian inference to compute the probability
4100 that a read originated from a particular isoform.")
4101 (license license:gpl2)))
4103 (define-public muscle
4106 (version "3.8.1551")
4108 (method url-fetch/tarbomb)
4110 "http://www.drive5.com/muscle/muscle_src_"
4114 "0bj8kj7sdizy3987zx6w7axihk40fk8rn76mpbqqjcnd64i5a367"))))
4115 (build-system gnu-build-system)
4117 `(#:make-flags (list "LDLIBS = -lm")
4119 (modify-phases %standard-phases
4122 ;; There are no tests, so just test if it runs.
4123 (lambda _ (zero? (system* "./muscle" "-version"))))
4125 (lambda* (#:key outputs #:allow-other-keys)
4126 (let* ((out (assoc-ref outputs "out"))
4127 (bin (string-append out "/bin")))
4128 (install-file "muscle" bin)))))))
4129 (home-page "http://www.drive5.com/muscle")
4130 (synopsis "Multiple sequence alignment program")
4132 "MUSCLE aims to be a fast and accurate multiple sequence alignment
4133 program for nucleotide and protein sequences.")
4134 ;; License information found in 'muscle -h' and usage.cpp.
4135 (license license:public-domain)))
4137 (define-public newick-utils
4138 ;; There are no recent releases so we package from git.
4139 (let ((commit "da121155a977197cab9fbb15953ca1b40b11eb87"))
4141 (name "newick-utils")
4142 (version (string-append "1.6-1." (string-take commit 8)))
4146 (url "https://github.com/tjunier/newick_utils.git")
4148 (file-name (string-append name "-" version "-checkout"))
4151 "1hkw21rq1mwf7xp0rmbb2gqc0i6p11108m69i7mr7xcjl268pxnb"))))
4152 (build-system gnu-build-system)
4155 (modify-phases %standard-phases
4156 (add-after 'unpack 'autoconf
4157 (lambda _ (zero? (system* "autoreconf" "-vif")))))))
4159 ;; XXX: TODO: Enable Lua and Guile bindings.
4160 ;; https://github.com/tjunier/newick_utils/issues/13
4161 `(("libxml2" ,libxml2)
4165 `(("autoconf" ,autoconf)
4166 ("automake" ,automake)
4167 ("libtool" ,libtool)))
4168 (synopsis "Programs for working with newick format phylogenetic trees")
4170 "Newick-utils is a suite of utilities for processing phylogenetic trees
4171 in Newick format. Functions include re-rooting, extracting subtrees,
4172 trimming, pruning, condensing, drawing (ASCII graphics or SVG).")
4173 (home-page "https://github.com/tjunier/newick_utils")
4174 (license license:bsd-3))))
4183 "https://github.com/wwood/OrfM/releases/download/v"
4184 version "/orfm-" version ".tar.gz"))
4187 "16iigyr2gd8x0imzkk1dr3k5xsds9bpmwg31ayvjg0f4pir9rwqr"))))
4188 (build-system gnu-build-system)
4189 (inputs `(("zlib" ,zlib)))
4191 `(("ruby-bio-commandeer" ,ruby-bio-commandeer)
4192 ("ruby-rspec" ,ruby-rspec)
4194 (synopsis "Simple and not slow open reading frame (ORF) caller")
4196 "An ORF caller finds stretches of DNA that, when translated, are not
4197 interrupted by stop codons. OrfM finds and prints these ORFs.")
4198 (home-page "https://github.com/wwood/OrfM")
4199 (license license:lgpl3+)))
4201 (define-public pplacer
4202 (let ((commit "g807f6f3"))
4205 ;; The commit should be updated with each version change.
4206 (version "1.1.alpha19")
4210 (uri (string-append "https://github.com/matsen/pplacer/archive/v"
4212 (file-name (string-append name "-" version ".tar.gz"))
4214 (base32 "0z1lnd2s8sh6kpzg106wzbh2szw7h0hvq8syd5a6wv4rmyyz6x0f"))))
4215 (build-system ocaml-build-system)
4217 `(#:ocaml ,ocaml-4.01
4218 #:findlib ,ocaml4.01-findlib
4219 #:modules ((guix build ocaml-build-system)
4223 (modify-phases %standard-phases
4225 (add-after 'unpack 'replace-bundled-cddlib
4226 (lambda* (#:key inputs #:allow-other-keys)
4227 (let* ((cddlib-src (assoc-ref inputs "cddlib-src"))
4228 (local-dir "cddlib_guix"))
4230 (with-directory-excursion local-dir
4231 (system* "tar" "xvf" cddlib-src))
4232 (let ((cddlib-src-folder
4233 (string-append local-dir "/"
4234 (list-ref (scandir local-dir) 2)
4239 (string-append "cdd_src/" (basename file))))
4240 (find-files cddlib-src-folder ".*[ch]$")))
4242 (add-after 'unpack 'fix-makefile
4244 ;; Remove system calls to 'git'.
4245 (substitute* "Makefile"
4246 (("^DESCRIPT:=pplacer-.*")
4248 "DESCRIPT:=pplacer-$(shell uname)-v" ,version "\n")))
4249 (substitute* "myocamlbuild.ml"
4250 (("git describe --tags --long .*\\\" with")
4252 "echo -n v" ,version "-" ,commit "\" with")))
4255 (lambda* (#:key outputs #:allow-other-keys)
4256 (let* ((out (assoc-ref outputs "out"))
4257 (bin (string-append out "/bin")))
4258 (copy-recursively "bin" bin))
4263 ("ocaml-ounit" ,ocaml4.01-ounit)
4264 ("ocaml-batteries" ,ocaml4.01-batteries)
4265 ("ocaml-camlzip" ,ocaml4.01-camlzip)
4266 ("ocaml-csv" ,ocaml4.01-csv)
4267 ("ocaml-sqlite3" ,ocaml4.01-sqlite3)
4268 ("ocaml-xmlm" ,ocaml4.01-xmlm)
4269 ("ocaml-mcl" ,ocaml4.01-mcl)
4270 ("ocaml-gsl" ,ocaml4.01-gsl)
4271 ("cddlib-src" ,(package-source cddlib))))
4273 `(("pplacer-scripts" ,pplacer-scripts)))
4274 (synopsis "Phylogenetic placement of biological sequences")
4276 "Pplacer places query sequences on a fixed reference phylogenetic tree
4277 to maximize phylogenetic likelihood or posterior probability according to a
4278 reference alignment. Pplacer is designed to be fast, to give useful
4279 information about uncertainty, and to offer advanced visualization and
4280 downstream analysis.")
4281 (home-page "http://matsen.fhcrc.org/pplacer")
4282 (license license:gpl3))))
4284 ;; This package is installed alongside 'pplacer'. It is a separate package so
4285 ;; that it can use the python-build-system for the scripts that are
4286 ;; distributed alongside the main OCaml binaries.
4287 (define pplacer-scripts
4290 (name "pplacer-scripts")
4291 (build-system python-build-system)
4293 `(#:python ,python-2
4295 (modify-phases %standard-phases
4296 (add-after 'unpack 'enter-scripts-dir
4297 (lambda _ (chdir "scripts")))
4300 (zero? (system* "python" "-m" "unittest" "discover" "-v"))))
4301 (add-after 'install 'wrap-executables
4302 (lambda* (#:key inputs outputs #:allow-other-keys)
4303 (let* ((out (assoc-ref outputs "out"))
4304 (bin (string-append out "/bin")))
4305 (let ((path (string-append
4306 (assoc-ref inputs "hmmer") "/bin:"
4307 (assoc-ref inputs "infernal") "/bin")))
4309 (wrap-program (string-append bin "/refpkg_align.py")
4310 `("PATH" ":" prefix (,path))))
4311 (let ((path (string-append
4312 (assoc-ref inputs "hmmer") "/bin")))
4313 (wrap-program (string-append bin "/hrefpkg_query.py")
4314 `("PATH" ":" prefix (,path)))))
4317 `(("infernal" ,infernal)
4320 `(("python-biopython" ,python2-biopython)
4321 ("taxtastic" ,taxtastic)))
4322 (synopsis "Pplacer Python scripts")))
4324 (define-public python2-pbcore
4326 (name "python2-pbcore")
4330 (uri (pypi-uri "pbcore" version))
4333 "1kjmv891d6qbpp4shhhvkl02ff4q5xlpnls2513sm2cjcrs52f1i"))))
4334 (build-system python-build-system)
4335 (arguments `(#:python ,python-2)) ; pbcore requires Python 2.7
4337 `(("python-cython" ,python2-cython)
4338 ("python-numpy" ,python2-numpy)
4339 ("python-pysam" ,python2-pysam)
4340 ("python-h5py" ,python2-h5py)))
4342 `(("python-nose" ,python2-nose)
4343 ("python-sphinx" ,python2-sphinx)
4344 ("python-pyxb" ,python2-pyxb)))
4345 (home-page "http://pacificbiosciences.github.io/pbcore/")
4346 (synopsis "Library for reading and writing PacBio data files")
4348 "The pbcore package provides Python APIs for interacting with PacBio data
4349 files and writing bioinformatics applications.")
4350 (license license:bsd-3)))
4352 (define-public python2-warpedlmm
4354 (name "python2-warpedlmm")
4360 "https://pypi.python.org/packages/source/W/WarpedLMM/WarpedLMM-"
4364 "1agfz6zqa8nc6cw47yh0s3y14gkpa9wqazwcj7mwwj3ffnw39p3j"))))
4365 (build-system python-build-system)
4367 `(#:python ,python-2)) ; requires Python 2.7
4369 `(("python-scipy" ,python2-scipy)
4370 ("python-numpy" ,python2-numpy)
4371 ("python-matplotlib" ,python2-matplotlib)
4372 ("python-fastlmm" ,python2-fastlmm)
4373 ("python-pandas" ,python2-pandas)
4374 ("python-pysnptools" ,python2-pysnptools)))
4376 `(("python-mock" ,python2-mock)
4377 ("python-nose" ,python2-nose)
4379 (home-page "https://github.com/PMBio/warpedLMM")
4380 (synopsis "Implementation of warped linear mixed models")
4382 "WarpedLMM is a Python implementation of the warped linear mixed model,
4383 which automatically learns an optimal warping function (or transformation) for
4384 the phenotype as it models the data.")
4385 (license license:asl2.0)))
4387 (define-public pbtranscript-tofu
4388 (let ((commit "8f5467fe6a4472bcfb4226c8720993c8507adfe4"))
4390 (name "pbtranscript-tofu")
4391 (version (string-append "2.2.3." (string-take commit 7)))
4395 (url "https://github.com/PacificBiosciences/cDNA_primer.git")
4397 (file-name (string-append name "-" version "-checkout"))
4400 "1lgnpi35ihay42qx0b6yl3kkgra723i413j33kvs0kvs61h82w0f"))
4401 (modules '((guix build utils)))
4404 ;; remove bundled Cython sources
4405 (delete-file "pbtranscript-tofu/pbtranscript/Cython-0.20.1.tar.gz")
4407 (build-system python-build-system)
4409 `(#:python ,python-2
4410 ;; FIXME: Tests fail with "No such file or directory:
4411 ;; pbtools/pbtranscript/modified_bx_intervals/intersection_unique.so"
4414 (modify-phases %standard-phases
4415 (add-after 'unpack 'enter-directory
4417 (chdir "pbtranscript-tofu/pbtranscript/")
4419 ;; With setuptools version 18.0 and later this setup.py hack causes
4420 ;; a build error, so we disable it.
4421 (add-after 'enter-directory 'patch-setuppy
4423 (substitute* "setup.py"
4424 (("if 'setuptools.extension' in sys.modules:")
4428 `(("python-numpy" ,python2-numpy)
4429 ("python-bx-python" ,python2-bx-python)
4430 ("python-networkx" ,python2-networkx)
4431 ("python-scipy" ,python2-scipy)
4432 ("python-pbcore" ,python2-pbcore)
4433 ("python-h5py" ,python2-h5py)))
4435 `(("python-cython" ,python2-cython)
4436 ("python-nose" ,python2-nose)))
4437 (home-page "https://github.com/PacificBiosciences/cDNA_primer")
4438 (synopsis "Analyze transcriptome data generated with the Iso-Seq protocol")
4440 "pbtranscript-tofu contains scripts to analyze transcriptome data
4441 generated using the PacBio Iso-Seq protocol.")
4442 (license license:bsd-3))))
4444 (define-public prank
4451 "http://wasabiapp.org/download/prank/prank.source."
4455 "0am4z94fs3w2n5xpfls9zda61vq7qqz4q2i7b9hlsxz5q4j3kfm4"))))
4456 (build-system gnu-build-system)
4459 (modify-phases %standard-phases
4460 (add-after 'unpack 'enter-src-dir
4464 (add-after 'unpack 'remove-m64-flag
4465 ;; Prank will build with the correct 'bit-ness' without this flag
4466 ;; and this allows building on 32-bit machines.
4467 (lambda _ (substitute* "src/Makefile"
4472 (lambda* (#:key outputs #:allow-other-keys)
4473 (let* ((out (assoc-ref outputs "out"))
4474 (bin (string-append out "/bin"))
4475 (man (string-append out "/share/man/man1"))
4476 (path (string-append
4477 (assoc-ref %build-inputs "mafft") "/bin:"
4478 (assoc-ref %build-inputs "exonerate") "/bin:"
4479 (assoc-ref %build-inputs "bppsuite") "/bin")))
4480 (install-file "prank" bin)
4481 (wrap-program (string-append bin "/prank")
4482 `("PATH" ":" prefix (,path)))
4483 (install-file "prank.1" man))
4487 ("exonerate" ,exonerate)
4488 ("bppsuite" ,bppsuite)))
4489 (home-page "http://wasabiapp.org/software/prank/")
4490 (synopsis "Probabilistic multiple sequence alignment program")
4492 "PRANK is a probabilistic multiple sequence alignment program for DNA,
4493 codon and amino-acid sequences. It is based on a novel algorithm that treats
4494 insertions correctly and avoids over-estimation of the number of deletion
4495 events. In addition, PRANK borrows ideas from maximum likelihood methods used
4496 in phylogenetics and correctly takes into account the evolutionary distances
4497 between sequences. Lastly, PRANK allows for defining a potential structure
4498 for sequences to be aligned and then, simultaneously with the alignment,
4499 predicts the locations of structural units in the sequences.")
4500 (license license:gpl2+)))
4502 (define-public proteinortho
4504 (name "proteinortho")
4511 "http://www.bioinf.uni-leipzig.de/Software/proteinortho/proteinortho_v"
4512 version "_src.tar.gz"))
4515 "1wl0dawpssqwfjvr651r4wlww8hhjin8nba6xh71ks7sbypx886j"))))
4516 (build-system gnu-build-system)
4518 `(#:test-target "test"
4520 (modify-phases %standard-phases
4522 ;; There is no configure script, so we modify the Makefile directly.
4523 (lambda* (#:key outputs #:allow-other-keys)
4524 (substitute* "Makefile"
4527 "INSTALLDIR=" (assoc-ref outputs "out") "/bin\n")))
4529 (add-before 'install 'make-install-directory
4530 ;; The install directory is not created during 'make install'.
4531 (lambda* (#:key outputs #:allow-other-keys)
4532 (mkdir-p (string-append (assoc-ref outputs "out") "/bin"))
4534 (add-after 'install 'wrap-programs
4535 (lambda* (#:key inputs outputs #:allow-other-keys)
4536 (let* ((path (getenv "PATH"))
4537 (out (assoc-ref outputs "out"))
4538 (binary (string-append out "/bin/proteinortho5.pl")))
4539 (wrap-program binary `("PATH" ":" prefix (,path))))
4543 ("python" ,python-2)
4544 ("blast+" ,blast+)))
4545 (home-page "http://www.bioinf.uni-leipzig.de/Software/proteinortho")
4546 (synopsis "Detect orthologous genes across species")
4548 "Proteinortho is a tool to detect orthologous genes across different
4549 species. For doing so, it compares similarities of given gene sequences and
4550 clusters them to find significant groups. The algorithm was designed to handle
4551 large-scale data and can be applied to hundreds of species at once.")
4552 (license license:gpl2+)))
4554 (define-public pyicoteo
4561 (uri (string-append "https://bitbucket.org/regulatorygenomicsupf/"
4562 "pyicoteo/get/v" version ".tar.bz2"))
4563 (file-name (string-append name "-" version ".tar.bz2"))
4566 "0d6087f29xp8wxwlj111c3sylli98n0l8ry58c51ixzq0zfm50wa"))))
4567 (build-system python-build-system)
4569 `(#:python ,python-2 ; does not work with Python 3
4570 #:tests? #f)) ; there are no tests
4572 `(("python2-matplotlib" ,python2-matplotlib)))
4573 (home-page "https://bitbucket.org/regulatorygenomicsupf/pyicoteo")
4574 (synopsis "Analyze high-throughput genetic sequencing data")
4576 "Pyicoteo is a suite of tools for the analysis of high-throughput genetic
4577 sequencing data. It works with genomic coordinates. There are currently six
4578 different command-line tools:
4581 @item pyicoregion: for generating exploratory regions automatically;
4582 @item pyicoenrich: for differential enrichment between two conditions;
4583 @item pyicoclip: for calling CLIP-Seq peaks without a control;
4584 @item pyicos: for genomic coordinates manipulation;
4585 @item pyicoller: for peak calling on punctuated ChIP-Seq;
4586 @item pyicount: to count how many reads from N experiment files overlap in a
4588 @item pyicotrocol: to combine operations from pyicoteo.
4590 (license license:gpl3+)))
4592 (define-public prodigal
4599 "https://github.com/hyattpd/Prodigal/archive/v"
4601 (file-name (string-append name "-" version ".tar.gz"))
4604 "17srxkqd3jc77xk15pfbgg1a9xahqg7337w95mrsia7mpza4l2c9"))))
4605 (build-system gnu-build-system)
4607 `(#:tests? #f ;no check target
4608 #:make-flags (list (string-append "INSTALLDIR="
4609 (assoc-ref %outputs "out")
4612 (modify-phases %standard-phases
4613 (delete 'configure))))
4614 (home-page "http://prodigal.ornl.gov")
4615 (synopsis "Protein-coding gene prediction for Archaea and Bacteria")
4617 "Prodigal runs smoothly on finished genomes, draft genomes, and
4618 metagenomes, providing gene predictions in GFF3, Genbank, or Sequin table
4619 format. It runs quickly, in an unsupervised fashion, handles gaps, handles
4620 partial genes, and identifies translation initiation sites.")
4621 (license license:gpl3+)))
4623 (define-public roary
4631 "mirror://cpan/authors/id/A/AJ/AJPAGE/Bio-Roary-"
4635 "0qxrds9wx7cfhlkihrp6697kx0flhhxymap9fwan0b3rbdhcnmff"))))
4636 (build-system perl-build-system)
4639 (modify-phases %standard-phases
4644 ;; The tests are not run by default, so we run each test file
4646 (setenv "PATH" (string-append (getcwd) "/bin" ":"
4648 (setenv "PERL5LIB" (string-append (getcwd) "/lib" ":"
4649 (getenv "PERL5LIB")))
4650 (zero? (length (filter (lambda (file)
4651 (display file)(display "\n")
4652 (not (zero? (system* "perl" file))))
4653 (find-files "t" ".*\\.t$"))))))
4655 ;; There is no 'install' target in the Makefile.
4656 (lambda* (#:key outputs #:allow-other-keys)
4657 (let* ((out (assoc-ref outputs "out"))
4658 (bin (string-append out "/bin"))
4659 (perl (string-append out "/lib/perl5/site_perl"))
4660 (roary-plots "contrib/roary_plots"))
4663 (copy-recursively "bin" bin)
4664 (copy-recursively "lib" perl)
4666 (add-after 'install 'wrap-programs
4667 (lambda* (#:key inputs outputs #:allow-other-keys)
4668 (let* ((out (assoc-ref outputs "out"))
4669 (perl5lib (getenv "PERL5LIB"))
4670 (path (getenv "PATH")))
4671 (for-each (lambda (prog)
4672 (let ((binary (string-append out "/" prog)))
4673 (wrap-program binary
4674 `("PERL5LIB" ":" prefix
4675 (,(string-append perl5lib ":" out
4676 "/lib/perl5/site_perl"))))
4677 (wrap-program binary
4679 (,(string-append path ":" out "/bin"))))))
4680 (find-files "bin" ".*[^R]$"))
4682 (string-append out "/bin/roary-create_pan_genome_plots.R"))
4683 (r-site-lib (getenv "R_LIBS_SITE"))
4685 (string-append (assoc-ref inputs "coreutils") "/bin")))
4687 `("R_LIBS_SITE" ":" prefix
4688 (,(string-append r-site-lib ":" out "/site-library/"))))
4691 (,(string-append coreutils-path ":" out "/bin"))))))
4694 `(("perl-env-path" ,perl-env-path)
4695 ("perl-test-files" ,perl-test-files)
4696 ("perl-test-most" ,perl-test-most)
4697 ("perl-test-output" ,perl-test-output)))
4699 `(("perl-array-utils" ,perl-array-utils)
4700 ("bioperl" ,bioperl-minimal)
4701 ("perl-digest-md5-file" ,perl-digest-md5-file)
4702 ("perl-exception-class" ,perl-exception-class)
4703 ("perl-file-find-rule" ,perl-file-find-rule)
4704 ("perl-file-grep" ,perl-file-grep)
4705 ("perl-file-slurper" ,perl-file-slurper)
4706 ("perl-file-which" ,perl-file-which)
4707 ("perl-graph" ,perl-graph)
4708 ("perl-graph-readwrite" ,perl-graph-readwrite)
4709 ("perl-log-log4perl" ,perl-log-log4perl)
4710 ("perl-moose" ,perl-moose)
4711 ("perl-perlio-utf8_strict" ,perl-perlio-utf8_strict)
4712 ("perl-text-csv" ,perl-text-csv)
4713 ("bedtools" ,bedtools)
4717 ("parallel" ,parallel)
4720 ("fasttree" ,fasttree)
4724 ("r-minimal" ,r-minimal)
4725 ("r-ggplot2" ,r-ggplot2)
4726 ("coreutils" ,coreutils)))
4727 (home-page "http://sanger-pathogens.github.io/Roary")
4728 (synopsis "High speed stand-alone pan genome pipeline")
4730 "Roary is a high speed stand alone pan genome pipeline, which takes
4731 annotated assemblies in GFF3 format (produced by the Prokka program) and
4732 calculates the pan genome. Using a standard desktop PC, it can analyse
4733 datasets with thousands of samples, without compromising the quality of the
4734 results. 128 samples can be analysed in under 1 hour using 1 GB of RAM and a
4735 single processor. Roary is not intended for metagenomics or for comparing
4736 extremely diverse sets of genomes.")
4737 (license license:gpl3)))
4739 (define-public raxml
4748 "https://github.com/stamatak/standard-RAxML/archive/v"
4750 (file-name (string-append name "-" version ".tar.gz"))
4753 "13s7aspfdcfr6asynwdg1x6vznys6pzap5f8wsffbnnwpkkg9ya8"))))
4754 (build-system gnu-build-system)
4756 `(#:tests? #f ; There are no tests.
4757 ;; Use 'standard' Makefile rather than SSE or AVX ones.
4758 #:make-flags (list "-f" "Makefile.HYBRID.gcc")
4760 (modify-phases %standard-phases
4763 (lambda* (#:key outputs #:allow-other-keys)
4764 (let* ((out (assoc-ref outputs "out"))
4765 (bin (string-append out "/bin"))
4766 (executable "raxmlHPC-HYBRID"))
4767 (install-file executable bin)
4768 (symlink (string-append bin "/" executable) "raxml"))
4771 `(("openmpi" ,openmpi)))
4772 (home-page "http://sco.h-its.org/exelixis/web/software/raxml/index.html")
4773 (synopsis "Randomized Axelerated Maximum Likelihood phylogenetic trees")
4775 "RAxML is a tool for phylogenetic analysis and post-analysis of large
4777 ;; The source includes x86 specific code
4778 (supported-systems '("x86_64-linux" "i686-linux"))
4779 (license license:gpl2+)))
4789 (string-append "http://deweylab.biostat.wisc.edu/rsem/src/rsem-"
4792 (base32 "0nzdc0j0hjllhsd5f2xli95dafm3nawskigs140xzvjk67xh0r9q"))
4793 (patches (search-patches "rsem-makefile.patch"))
4794 (modules '((guix build utils)))
4797 ;; remove bundled copy of boost
4798 (delete-file-recursively "boost")
4800 (build-system gnu-build-system)
4802 `(#:tests? #f ;no "check" target
4804 (modify-phases %standard-phases
4805 ;; No "configure" script.
4806 ;; Do not build bundled samtools library.
4809 (substitute* "Makefile"
4810 (("^all : sam/libbam.a") "all : "))
4813 (lambda* (#:key outputs #:allow-other-keys)
4814 (let* ((out (string-append (assoc-ref outputs "out")))
4815 (bin (string-append out "/bin/"))
4816 (perl (string-append out "/lib/perl5/site_perl")))
4819 (for-each (lambda (file)
4820 (install-file file bin))
4821 (find-files "." "rsem-.*"))
4822 (install-file "rsem_perl_utils.pm" perl))
4825 'install 'wrap-program
4826 (lambda* (#:key outputs #:allow-other-keys)
4827 (let ((out (assoc-ref outputs "out")))
4828 (for-each (lambda (prog)
4829 (wrap-program (string-append out "/bin/" prog)
4830 `("PERL5LIB" ":" prefix
4831 (,(string-append out "/lib/perl5/site_perl")))))
4832 '("rsem-plot-transcript-wiggles"
4833 "rsem-calculate-expression"
4834 "rsem-generate-ngvector"
4836 "rsem-prepare-reference")))
4840 ("ncurses" ,ncurses)
4841 ("r-minimal" ,r-minimal)
4843 ("samtools" ,samtools-0.1)
4845 (home-page "http://deweylab.biostat.wisc.edu/rsem/")
4846 (synopsis "Estimate gene expression levels from RNA-Seq data")
4848 "RSEM is a software package for estimating gene and isoform expression
4849 levels from RNA-Seq data. The RSEM package provides a user-friendly
4850 interface, supports threads for parallel computation of the EM algorithm,
4851 single-end and paired-end read data, quality scores, variable-length reads and
4852 RSPD estimation. In addition, it provides posterior mean and 95% credibility
4853 interval estimates for expression levels. For visualization, it can generate
4854 BAM and Wiggle files in both transcript-coordinate and genomic-coordinate.")
4855 (license license:gpl3+)))
4857 (define-public rseqc
4865 (string-append "mirror://sourceforge/rseqc/"
4866 "RSeQC-" version ".tar.gz"))
4868 (base32 "15ly0254yi032qzkdplg00q144qfdsd986gh62829rl5bkxhj330"))
4869 (modules '((guix build utils)))
4872 ;; remove bundled copy of pysam
4873 (delete-file-recursively "lib/pysam")
4874 (substitute* "setup.py"
4875 ;; remove dependency on outdated "distribute" module
4876 (("^from distribute_setup import use_setuptools") "")
4877 (("^use_setuptools\\(\\)") "")
4878 ;; do not use bundled copy of pysam
4879 (("^have_pysam = False") "have_pysam = True"))
4881 (build-system python-build-system)
4882 (arguments `(#:python ,python-2))
4884 `(("python-cython" ,python2-cython)
4885 ("python-pysam" ,python2-pysam)
4886 ("python-numpy" ,python2-numpy)
4889 `(("python-nose" ,python2-nose)))
4890 (home-page "http://rseqc.sourceforge.net/")
4891 (synopsis "RNA-seq quality control package")
4893 "RSeQC provides a number of modules that can comprehensively evaluate
4894 high throughput sequence data, especially RNA-seq data. Some basic modules
4895 inspect sequence quality, nucleotide composition bias, PCR bias and GC bias,
4896 while RNA-seq specific modules evaluate sequencing saturation, mapped reads
4897 distribution, coverage uniformity, strand specificity, etc.")
4898 (license license:gpl3+)))
4901 ;; There are no release tarballs. According to the installation
4902 ;; instructions at http://seek.princeton.edu/installation.jsp, the latest
4903 ;; stable release is identified by this changeset ID.
4904 (let ((changeset "2329130")
4908 (version (string-append "0-" revision "." changeset))
4912 (url "https://bitbucket.org/libsleipnir/sleipnir")
4913 (changeset changeset)))
4914 (file-name (string-append name "-" version "-checkout"))
4917 "0qrvilwh18dpbhkf92qvxbmay0j75ra3jg2wrhz67gf538zzphsx"))))
4918 (build-system gnu-build-system)
4920 `(#:modules ((srfi srfi-1)
4921 (guix build gnu-build-system)
4924 (let ((dirs '("SeekMiner"
4930 (modify-phases %standard-phases
4933 (invoke "bash" "gen_auto")))
4934 (add-after 'build 'build-additional-tools
4935 (lambda* (#:key make-flags #:allow-other-keys)
4936 (every (lambda (dir)
4937 (with-directory-excursion (string-append "tools/" dir)
4938 (zero? (apply system* "make" make-flags))))
4940 (add-after 'install 'install-additional-tools
4941 (lambda* (#:key make-flags #:allow-other-keys)
4942 (fold (lambda (dir result)
4943 (with-directory-excursion (string-append "tools/" dir)
4945 (zero? (apply system*
4946 `("make" ,@make-flags "install"))))))
4952 ("readline" ,readline)
4953 ("gengetopt" ,gengetopt)
4954 ("log4cpp" ,log4cpp)))
4956 `(("autoconf" ,autoconf)
4957 ("automake" ,automake)
4959 (home-page "http://seek.princeton.edu")
4960 (synopsis "Gene co-expression search engine")
4962 "SEEK is a computational gene co-expression search engine. SEEK provides
4963 biologists with a way to navigate the massive human expression compendium that
4964 now contains thousands of expression datasets. SEEK returns a robust ranking
4965 of co-expressed genes in the biological area of interest defined by the user's
4966 query genes. It also prioritizes thousands of expression datasets according
4967 to the user's query of interest.")
4968 (license license:cc-by3.0))))
4970 (define-public samtools
4978 (string-append "mirror://sourceforge/samtools/samtools/"
4979 version "/samtools-" version ".tar.bz2"))
4982 "05myg7bs90i68qbqab9cdg9rqj2xh39azibrx82ipzc5kcfvqhn9"))))
4983 (build-system gnu-build-system)
4985 `(#:modules ((ice-9 ftw)
4987 (guix build gnu-build-system)
4989 #:make-flags (list (string-append "prefix=" (assoc-ref %outputs "out")))
4990 #:configure-flags (list "--with-ncurses" "--with-htslib=system")
4992 (modify-phases %standard-phases
4993 (add-after 'unpack 'patch-tests
4995 (substitute* "test/test.pl"
4996 ;; The test script calls out to /bin/bash
4997 (("/bin/bash") (which "bash")))
4999 (add-after 'install 'install-library
5000 (lambda* (#:key outputs #:allow-other-keys)
5001 (let ((lib (string-append (assoc-ref outputs "out") "/lib")))
5002 (install-file "libbam.a" lib)
5004 (add-after 'install 'install-headers
5005 (lambda* (#:key outputs #:allow-other-keys)
5006 (let ((include (string-append (assoc-ref outputs "out")
5007 "/include/samtools/")))
5008 (for-each (lambda (file)
5009 (install-file file include))
5010 (scandir "." (lambda (name) (string-match "\\.h$" name))))
5012 (native-inputs `(("pkg-config" ,pkg-config)))
5014 `(("htslib" ,htslib)
5015 ("ncurses" ,ncurses)
5019 (home-page "http://samtools.sourceforge.net")
5020 (synopsis "Utilities to efficiently manipulate nucleotide sequence alignments")
5022 "Samtools implements various utilities for post-processing nucleotide
5023 sequence alignments in the SAM, BAM, and CRAM formats, including indexing,
5024 variant calling (in conjunction with bcftools), and a simple alignment
5026 (license license:expat)))
5028 (define-public samtools-0.1
5029 ;; This is the most recent version of the 0.1 line of samtools. The input
5030 ;; and output formats differ greatly from that used and produced by samtools
5031 ;; 1.x and is still used in many bioinformatics pipelines.
5032 (package (inherit samtools)
5038 (string-append "mirror://sourceforge/samtools/samtools/"
5039 version "/samtools-" version ".tar.bz2"))
5041 (base32 "1m33xsfwz0s8qi45lylagfllqg7fphf4dr0780rsvw75av9wk06h"))))
5043 `(#:tests? #f ;no "check" target
5044 ,@(substitute-keyword-arguments (package-arguments samtools)
5045 ((#:make-flags flags)
5046 `(cons "LIBCURSES=-lncurses" ,flags))
5048 `(modify-phases ,phases
5050 (lambda* (#:key outputs #:allow-other-keys)
5051 (let ((bin (string-append
5052 (assoc-ref outputs "out") "/bin")))
5054 (install-file "samtools" bin)
5056 (delete 'patch-tests)
5057 (delete 'configure))))))))
5059 (define-public mosaik
5060 (let ((commit "5c25216d3522d6a33e53875cd76a6d65001e4e67"))
5065 ;; There are no release tarballs nor tags.
5068 (url "https://github.com/wanpinglee/MOSAIK.git")
5070 (file-name (string-append name "-" version))
5073 "17gj3s07cm77r41z92awh0bim7w7q7fbn0sf5nkqmcm1vw052qgw"))))
5074 (build-system gnu-build-system)
5076 `(#:tests? #f ; no tests
5077 #:make-flags (list "CC=gcc")
5079 (modify-phases %standard-phases
5081 (lambda _ (chdir "src") #t))
5083 (lambda* (#:key outputs #:allow-other-keys)
5084 (let ((bin (string-append (assoc-ref outputs "out")
5087 (copy-recursively "../bin" bin)
5092 (supported-systems '("x86_64-linux"))
5093 (home-page "https://github.com/wanpinglee/MOSAIK")
5094 (synopsis "Map nucleotide sequence reads to reference genomes")
5096 "MOSAIK is a program for mapping second and third-generation sequencing
5097 reads to a reference genome. MOSAIK can align reads generated by all the
5098 major sequencing technologies, including Illumina, Applied Biosystems SOLiD,
5099 Roche 454, Ion Torrent and Pacific BioSciences SMRT.")
5100 ;; MOSAIK is released under the GPLv2+ with the exception of third-party
5101 ;; code released into the public domain:
5102 ;; 1. fastlz by Ariya Hidayat - http://www.fastlz.org/
5103 ;; 2. MD5 implementation - RSA Data Security, RFC 1321
5104 (license (list license:gpl2+ license:public-domain)))))
5106 (define-public ngs-sdk
5114 (string-append "https://github.com/ncbi/ngs/archive/"
5116 (file-name (string-append name "-" version ".tar.gz"))
5119 "1wiyf4c6nm2j87pv015cbi0qny5byf3pbvcw3likifz5dl56ag40"))))
5120 (build-system gnu-build-system)
5122 `(#:parallel-build? #f ; not supported
5123 #:tests? #f ; no "check" target
5125 (modify-phases %standard-phases
5127 (lambda* (#:key outputs #:allow-other-keys)
5128 (let ((out (assoc-ref outputs "out")))
5129 ;; Allow 'konfigure.perl' to find 'package.prl'.
5131 (string-append ".:" (getenv "PERL5LIB")))
5133 ;; The 'configure' script doesn't recognize things like
5134 ;; '--enable-fast-install'.
5135 (zero? (system* "./configure"
5136 (string-append "--build-prefix=" (getcwd) "/build")
5137 (string-append "--prefix=" out))))))
5138 (add-after 'unpack 'enter-dir
5139 (lambda _ (chdir "ngs-sdk") #t)))))
5140 (native-inputs `(("perl" ,perl)))
5141 ;; According to the test
5142 ;; unless ($MARCH =~ /x86_64/i || $MARCH =~ /i?86/i)
5143 ;; in ngs-sdk/setup/konfigure.perl
5144 (supported-systems '("i686-linux" "x86_64-linux"))
5145 (home-page "https://github.com/ncbi/ngs")
5146 (synopsis "API for accessing Next Generation Sequencing data")
5148 "NGS is a domain-specific API for accessing reads, alignments and pileups
5149 produced from Next Generation Sequencing. The API itself is independent from
5150 any particular back-end implementation, and supports use of multiple back-ends
5152 (license license:public-domain)))
5154 (define-public java-ngs
5155 (package (inherit ngs-sdk)
5158 `(,@(substitute-keyword-arguments
5159 `(#:modules ((guix build gnu-build-system)
5163 ,@(package-arguments ngs-sdk))
5165 `(modify-phases ,phases
5166 (replace 'enter-dir (lambda _ (chdir "ngs-java") #t)))))))
5168 `(("jdk" ,icedtea "jdk")
5169 ("ngs-sdk" ,ngs-sdk)))
5170 (synopsis "Java bindings for NGS SDK")))
5172 (define-public ncbi-vdb
5180 (string-append "https://github.com/ncbi/ncbi-vdb/archive/"
5182 (file-name (string-append name "-" version ".tar.gz"))
5185 "1acn4bv81mfl137qnbn9995mjjhwd36pm0b7qli1iw5skrxa9j8m"))))
5186 (build-system gnu-build-system)
5188 `(#:parallel-build? #f ; not supported
5189 #:tests? #f ; no "check" target
5191 (modify-phases %standard-phases
5192 (add-before 'configure 'set-perl-search-path
5194 ;; Work around "dotless @INC" build failure.
5196 (string-append (getcwd) "/setup:"
5197 (getenv "PERL5LIB")))
5200 (lambda* (#:key inputs outputs #:allow-other-keys)
5201 (let ((out (assoc-ref outputs "out")))
5202 ;; Override include path for libmagic
5203 (substitute* "setup/package.prl"
5204 (("name => 'magic', Include => '/usr/include'")
5205 (string-append "name=> 'magic', Include => '"
5206 (assoc-ref inputs "libmagic")
5209 ;; Install kdf5 library (needed by sra-tools)
5210 (substitute* "build/Makefile.install"
5211 (("LIBRARIES_TO_INSTALL =")
5212 "LIBRARIES_TO_INSTALL = kdf5.$(VERSION_LIBX) kdf5.$(VERSION_SHLX)"))
5214 (substitute* "build/Makefile.env"
5215 (("CFLAGS =" prefix)
5216 (string-append prefix "-msse2 ")))
5218 ;; Override search path for ngs-java
5219 (substitute* "setup/package.prl"
5220 (("/usr/local/ngs/ngs-java")
5221 (assoc-ref inputs "java-ngs")))
5223 ;; The 'configure' script doesn't recognize things like
5224 ;; '--enable-fast-install'.
5227 (string-append "--build-prefix=" (getcwd) "/build")
5228 (string-append "--prefix=" (assoc-ref outputs "out"))
5229 (string-append "--debug")
5230 (string-append "--with-xml2-prefix="
5231 (assoc-ref inputs "libxml2"))
5232 (string-append "--with-ngs-sdk-prefix="
5233 (assoc-ref inputs "ngs-sdk"))
5234 (string-append "--with-hdf5-prefix="
5235 (assoc-ref inputs "hdf5")))))))
5236 (add-after 'install 'install-interfaces
5237 (lambda* (#:key outputs #:allow-other-keys)
5238 ;; Install interface libraries. On i686 the interface libraries
5239 ;; are installed to "linux/gcc/i386", so we need to use the Linux
5240 ;; architecture name ("i386") instead of the target system prefix
5242 (mkdir (string-append (assoc-ref outputs "out") "/ilib"))
5243 (copy-recursively (string-append "build/ncbi-vdb/linux/gcc/"
5244 ,(system->linux-architecture
5245 (or (%current-target-system)
5248 (string-append (assoc-ref outputs "out")
5250 ;; Install interface headers
5251 (copy-recursively "interfaces"
5252 (string-append (assoc-ref outputs "out")
5255 ;; These files are needed by sra-tools.
5256 (add-after 'install 'install-configuration-files
5257 (lambda* (#:key outputs #:allow-other-keys)
5258 (let ((target (string-append (assoc-ref outputs "out") "/kfg")))
5260 (install-file "libs/kfg/default.kfg" target)
5261 (install-file "libs/kfg/certs.kfg" target))
5264 `(("libxml2" ,libxml2)
5265 ("ngs-sdk" ,ngs-sdk)
5266 ("java-ngs" ,java-ngs)
5269 (native-inputs `(("perl" ,perl)))
5270 ;; NCBI-VDB requires SSE capability.
5271 (supported-systems '("i686-linux" "x86_64-linux"))
5272 (home-page "https://github.com/ncbi/ncbi-vdb")
5273 (synopsis "Database engine for genetic information")
5275 "The NCBI-VDB library implements a highly compressed columnar data
5276 warehousing engine that is most often used to store genetic information.
5277 Databases are stored in a portable image within the file system, and can be
5278 accessed/downloaded on demand across HTTP.")
5279 (license license:public-domain)))
5281 (define-public plink
5289 "http://pngu.mgh.harvard.edu/~purcell/plink/dist/plink-"
5290 version "-src.zip"))
5292 (base32 "0as8gxm4pjyc8dxmm1sl873rrd7wn5qs0l29nqfnl31x8i467xaa"))
5293 (patches (search-patches "plink-1.07-unclobber-i.patch"
5294 "plink-endian-detection.patch"))))
5295 (build-system gnu-build-system)
5297 '(#:tests? #f ;no "check" target
5298 #:make-flags (list (string-append "LIB_LAPACK="
5299 (assoc-ref %build-inputs "lapack")
5300 "/lib/liblapack.so")
5303 ;; disable phoning home
5306 (modify-phases %standard-phases
5307 ;; no "configure" script
5310 (lambda* (#:key outputs #:allow-other-keys)
5311 (let ((bin (string-append (assoc-ref outputs "out")
5313 (install-file "plink" bin)
5317 ("lapack" ,lapack)))
5319 `(("unzip" ,unzip)))
5320 (home-page "http://pngu.mgh.harvard.edu/~purcell/plink/")
5321 (synopsis "Whole genome association analysis toolset")
5323 "PLINK is a whole genome association analysis toolset, designed to
5324 perform a range of basic, large-scale analyses in a computationally efficient
5325 manner. The focus of PLINK is purely on analysis of genotype/phenotype data,
5326 so there is no support for steps prior to this (e.g. study design and
5327 planning, generating genotype or CNV calls from raw data). Through
5328 integration with gPLINK and Haploview, there is some support for the
5329 subsequent visualization, annotation and storage of results.")
5330 ;; Code is released under GPLv2, except for fisher.h, which is under
5332 (license (list license:gpl2 license:lgpl2.1+))))
5334 (define-public plink-ng
5335 (package (inherit plink)
5341 (uri (string-append "https://github.com/chrchang/plink-ng/archive/v"
5343 (file-name (string-append name "-" version ".tar.gz"))
5345 (base32 "09ixrds009aczjswxr2alcb774mksq5g0v78dgjjn1h4dky0kf9a"))))
5346 (build-system gnu-build-system)
5348 '(#:tests? #f ;no "check" target
5349 #:make-flags (list "BLASFLAGS=-llapack -lopenblas"
5350 "CFLAGS=-Wall -O2 -DDYNAMIC_ZLIB=1"
5352 "-f" "Makefile.std")
5354 (modify-phases %standard-phases
5355 (add-after 'unpack 'chdir
5356 (lambda _ (chdir "1.9") #t))
5357 (delete 'configure) ; no "configure" script
5359 (lambda* (#:key outputs #:allow-other-keys)
5360 (let ((bin (string-append (assoc-ref outputs "out")
5362 (install-file "plink" bin)
5367 ("openblas" ,openblas)))
5368 (home-page "https://www.cog-genomics.org/plink/")
5369 (license license:gpl3+)))
5371 (define-public smithlab-cpp
5372 (let ((revision "1")
5373 (commit "728a097bec88c6f4b8528b685932049e660eff2e"))
5375 (name "smithlab-cpp")
5376 (version (string-append "0." revision "." (string-take commit 7)))
5380 (url "https://github.com/smithlabcode/smithlab_cpp.git")
5382 (file-name (string-append name "-" version "-checkout"))
5385 "0d476lmj312xk77kr9fzrv7z1bv96yfyx0w7y62ycmnfbx32ll74"))))
5386 (build-system gnu-build-system)
5388 `(#:modules ((guix build gnu-build-system)
5391 #:tests? #f ;no "check" target
5393 (modify-phases %standard-phases
5394 (add-after 'unpack 'use-samtools-headers
5396 (substitute* '("SAM.cpp"
5398 (("sam.h") "samtools/sam.h"))
5401 (lambda* (#:key outputs #:allow-other-keys)
5402 (let* ((out (assoc-ref outputs "out"))
5403 (lib (string-append out "/lib"))
5404 (include (string-append out "/include/smithlab-cpp")))
5407 (for-each (cut install-file <> lib)
5408 (find-files "." "\\.o$"))
5409 (for-each (cut install-file <> include)
5410 (find-files "." "\\.hpp$")))
5412 (delete 'configure))))
5414 `(("samtools" ,samtools-0.1)
5416 (home-page "https://github.com/smithlabcode/smithlab_cpp")
5417 (synopsis "C++ helper library for functions used in Smith lab projects")
5419 "Smithlab CPP is a C++ library that includes functions used in many of
5420 the Smith lab bioinformatics projects, such as a wrapper around Samtools data
5421 structures, classes for genomic regions, mapped sequencing reads, etc.")
5422 (license license:gpl3+))))
5424 (define-public preseq
5430 (uri (string-append "https://github.com/smithlabcode/"
5431 "preseq/archive/v" version ".tar.gz"))
5432 (file-name (string-append name "-" version ".tar.gz"))
5434 (base32 "08r684l50pnxjpvmhzjgqq56yv9rfw90k8vx0nsrnrzk8mf9hsdq"))
5435 (modules '((guix build utils)))
5437 ;; Remove bundled samtools.
5438 (delete-file-recursively "samtools")
5440 (build-system gnu-build-system)
5442 `(#:tests? #f ;no "check" target
5444 (modify-phases %standard-phases
5445 (delete 'configure))
5447 (list (string-append "PREFIX="
5448 (assoc-ref %outputs "out"))
5449 (string-append "LIBBAM="
5450 (assoc-ref %build-inputs "samtools")
5452 (string-append "SMITHLAB_CPP="
5453 (assoc-ref %build-inputs "smithlab-cpp")
5456 "INCLUDEDIRS=$(SMITHLAB_CPP)/../include/smithlab-cpp $(SAMTOOLS_DIR)")))
5459 ("samtools" ,samtools-0.1)
5460 ("smithlab-cpp" ,smithlab-cpp)
5462 (home-page "http://smithlabresearch.org/software/preseq/")
5463 (synopsis "Program for analyzing library complexity")
5465 "The preseq package is aimed at predicting and estimating the complexity
5466 of a genomic sequencing library, equivalent to predicting and estimating the
5467 number of redundant reads from a given sequencing depth and how many will be
5468 expected from additional sequencing using an initial sequencing experiment.
5469 The estimates can then be used to examine the utility of further sequencing,
5470 optimize the sequencing depth, or to screen multiple libraries to avoid low
5471 complexity samples.")
5472 (license license:gpl3+)))
5474 (define-public python-screed
5476 (name "python-screed")
5481 (uri (pypi-uri "screed" version))
5484 "18czszp9fkx3j6jr7y5kp6dfialscgddk05mw1zkhh2zhn0jd8i0"))))
5485 (build-system python-build-system)
5488 (modify-phases %standard-phases
5491 (setenv "PYTHONPATH"
5492 (string-append (getenv "PYTHONPATH") ":."))
5493 (zero? (system* "nosetests" "--attr" "!known_failing")))))))
5495 `(("python-nose" ,python-nose)))
5497 `(("python-bz2file" ,python-bz2file)))
5498 (home-page "https://github.com/dib-lab/screed/")
5499 (synopsis "Short read sequence database utilities")
5500 (description "Screed parses FASTA and FASTQ files and generates databases.
5501 Values such as sequence name, sequence description, sequence quality and the
5502 sequence itself can be retrieved from these databases.")
5503 (license license:bsd-3)))
5505 (define-public python2-screed
5506 (package-with-python2 python-screed))
5508 (define-public sra-tools
5516 (string-append "https://github.com/ncbi/sra-tools/archive/"
5518 (file-name (string-append name "-" version ".tar.gz"))
5521 "1camsijmvv2s45mb4iyf44ghl4gkd4rl0viphpcgl3ccchy32a0g"))))
5522 (build-system gnu-build-system)
5524 `(#:parallel-build? #f ; not supported
5525 #:tests? #f ; no "check" target
5527 (list (string-append "DEFAULT_CRT="
5528 (assoc-ref %build-inputs "ncbi-vdb")
5530 (string-append "DEFAULT_KFG="
5531 (assoc-ref %build-inputs "ncbi-vdb")
5533 (string-append "VDB_LIBDIR="
5534 (assoc-ref %build-inputs "ncbi-vdb")
5535 ,(if (string-prefix? "x86_64"
5536 (or (%current-target-system)
5541 (modify-phases %standard-phases
5542 (add-before 'configure 'set-perl-search-path
5544 ;; Work around "dotless @INC" build failure.
5546 (string-append (getcwd) "/setup:"
5547 (getenv "PERL5LIB")))
5550 (lambda* (#:key inputs outputs #:allow-other-keys)
5551 ;; The build system expects a directory containing the sources and
5552 ;; raw build output of ncbi-vdb, including files that are not
5553 ;; installed. Since we are building against an installed version of
5554 ;; ncbi-vdb, the following modifications are needed.
5555 (substitute* "setup/konfigure.perl"
5556 ;; Make the configure script look for the "ilib" directory of
5557 ;; "ncbi-vdb" without first checking for the existence of a
5558 ;; matching library in its "lib" directory.
5559 (("^ my \\$f = File::Spec->catdir\\(\\$libdir, \\$lib\\);")
5560 "my $f = File::Spec->catdir($ilibdir, $ilib);")
5561 ;; Look for interface libraries in ncbi-vdb's "ilib" directory.
5562 (("my \\$ilibdir = File::Spec->catdir\\(\\$builddir, 'ilib'\\);")
5563 "my $ilibdir = File::Spec->catdir($dir, 'ilib');"))
5566 (substitute* "tools/copycat/Makefile"
5567 (("smagic-static") "lmagic"))
5569 ;; The 'configure' script doesn't recognize things like
5570 ;; '--enable-fast-install'.
5573 (string-append "--build-prefix=" (getcwd) "/build")
5574 (string-append "--prefix=" (assoc-ref outputs "out"))
5575 (string-append "--debug")
5576 (string-append "--with-fuse-prefix="
5577 (assoc-ref inputs "fuse"))
5578 (string-append "--with-magic-prefix="
5579 (assoc-ref inputs "libmagic"))
5580 ;; TODO: building with libxml2 fails with linker errors
5581 ;; (string-append "--with-xml2-prefix="
5582 ;; (assoc-ref inputs "libxml2"))
5583 (string-append "--with-ncbi-vdb-sources="
5584 (assoc-ref inputs "ncbi-vdb"))
5585 (string-append "--with-ncbi-vdb-build="
5586 (assoc-ref inputs "ncbi-vdb"))
5587 (string-append "--with-ngs-sdk-prefix="
5588 (assoc-ref inputs "ngs-sdk"))
5589 (string-append "--with-hdf5-prefix="
5590 (assoc-ref inputs "hdf5"))))))
5591 ;; This version of sra-tools fails to build with glibc because of a
5592 ;; naming conflict. glibc-2.25/include/bits/mathcalls.h already
5593 ;; contains a definition of "canonicalize", so we rename it.
5595 ;; See upstream bug report:
5596 ;; https://github.com/ncbi/sra-tools/issues/67
5597 (add-after 'unpack 'patch-away-glibc-conflict
5599 (substitute* "tools/bam-loader/bam.c"
5600 (("canonicalize\\(" line)
5601 (string-append "sra_tools_" line)))
5603 (native-inputs `(("perl" ,perl)))
5605 `(("ngs-sdk" ,ngs-sdk)
5606 ("ncbi-vdb" ,ncbi-vdb)
5611 (home-page "http://www.ncbi.nlm.nih.gov/Traces/sra/sra.cgi?view=software")
5612 (synopsis "Tools and libraries for reading and writing sequencing data")
5614 "The SRA Toolkit from NCBI is a collection of tools and libraries for
5615 reading of sequencing files from the Sequence Read Archive (SRA) database and
5616 writing files into the .sra format.")
5617 (license license:public-domain)))
5619 (define-public seqan
5625 (uri (string-append "http://packages.seqan.de/seqan-library/"
5626 "seqan-library-" version ".tar.bz2"))
5629 "05s3wrrwn50f81aklfm65i4a749zag1vr8z03k21xm0pdxy47yvp"))))
5630 ;; The documentation is 7.8MB and the includes are 3.6MB heavy, so it
5631 ;; makes sense to split the outputs.
5632 (outputs '("out" "doc"))
5633 (build-system trivial-build-system)
5635 `(#:modules ((guix build utils))
5638 (use-modules (guix build utils))
5639 (let ((tar (assoc-ref %build-inputs "tar"))
5640 (bzip (assoc-ref %build-inputs "bzip2"))
5641 (out (assoc-ref %outputs "out"))
5642 (doc (assoc-ref %outputs "doc")))
5643 (setenv "PATH" (string-append tar "/bin:" bzip "/bin"))
5644 (invoke "tar" "xvf" (assoc-ref %build-inputs "source"))
5645 (chdir (string-append "seqan-library-" ,version))
5646 (copy-recursively "include" (string-append out "/include"))
5647 (copy-recursively "share" (string-append doc "/share"))
5650 `(("source" ,source)
5653 (home-page "http://www.seqan.de")
5654 (synopsis "Library for nucleotide sequence analysis")
5656 "SeqAn is a C++ library of efficient algorithms and data structures for
5657 the analysis of sequences with the focus on biological data. It contains
5658 algorithms and data structures for string representation and their
5659 manipulation, online and indexed string search, efficient I/O of
5660 bioinformatics file formats, sequence alignment, and more.")
5661 (license license:bsd-3)))
5663 (define-public seqmagick
5670 (uri (pypi-uri "seqmagick" version))
5673 "12bfyp8nqi0hd36rmj450aygafp01qy3hkbvlwn3bk39pyjjkgg5"))))
5674 (build-system python-build-system)
5676 `(("python-biopython" ,python-biopython)))
5678 `(("python-nose" ,python-nose)))
5679 (home-page "https://github.com/fhcrc/seqmagick")
5680 (synopsis "Tools for converting and modifying sequence files")
5682 "Bioinformaticians often have to convert sequence files between formats
5683 and do little manipulations on them, and it's not worth writing scripts for
5684 that. Seqmagick is a utility to expose the file format conversion in
5685 BioPython in a convenient way. Instead of having a big mess of scripts, there
5686 is one that takes arguments.")
5687 (license license:gpl3)))
5689 (define-public seqtk
5696 "https://github.com/lh3/seqtk/archive/v"
5698 (file-name (string-append name "-" version ".tar.gz"))
5701 "0ywdyzpmfiz2wp6ampbzqg4y8bj450nfgqarpamg045b8mk32lxx"))
5702 (modules '((guix build utils)))
5705 ;; Remove extraneous header files, as is done in the seqtk
5707 (for-each (lambda (file) (delete-file file))
5708 (list "ksort.h" "kstring.h" "kvec.h"))
5710 (build-system gnu-build-system)
5713 (modify-phases %standard-phases
5716 ;; There are no tests, so we just run a sanity check.
5717 (lambda _ (zero? (system* "./seqtk" "seq"))))
5719 (lambda* (#:key outputs #:allow-other-keys)
5720 (let ((bin (string-append (assoc-ref outputs "out") "/bin/")))
5721 (install-file "seqtk" bin)))))))
5724 (home-page "https://github.com/lh3/seqtk")
5725 (synopsis "Toolkit for processing biological sequences in FASTA/Q format")
5727 "Seqtk is a fast and lightweight tool for processing sequences in the
5728 FASTA or FASTQ format. It parses both FASTA and FASTQ files which can be
5729 optionally compressed by gzip.")
5730 (license license:expat)))
5732 (define-public snap-aligner
5734 (name "snap-aligner")
5735 (version "1.0beta.18")
5739 "https://github.com/amplab/snap/archive/v"
5741 (file-name (string-append name "-" version ".tar.gz"))
5744 "1vnsjwv007k1fl1q7d681kbwn6bc66cgw6h16hym6gvyy71qv2ly"))))
5745 (build-system gnu-build-system)
5748 (modify-phases %standard-phases
5750 (replace 'check (lambda _ (zero? (system* "./unit_tests"))))
5752 (lambda* (#:key outputs #:allow-other-keys)
5753 (let* ((out (assoc-ref outputs "out"))
5754 (bin (string-append out "/bin")))
5755 (install-file "snap-aligner" bin)
5756 (install-file "SNAPCommand" bin)
5760 (home-page "http://snap.cs.berkeley.edu/")
5761 (synopsis "Short read DNA sequence aligner")
5763 "SNAP is a fast and accurate aligner for short DNA reads. It is
5764 optimized for modern read lengths of 100 bases or higher, and takes advantage
5765 of these reads to align data quickly through a hash-based indexing scheme.")
5766 ;; 32-bit systems are not supported by the unpatched code.
5767 ;; Following the bug reports https://github.com/amplab/snap/issues/68 and
5768 ;; https://bugs.debian.org/cgi-bin/bugreport.cgi?bug=812378 we see that
5769 ;; systems without a lot of memory cannot make good use of this program.
5770 (supported-systems '("x86_64-linux"))
5771 (license license:asl2.0)))
5773 (define-public sortmerna
5781 "https://github.com/biocore/sortmerna/archive/"
5783 (file-name (string-append name "-" version ".tar.gz"))
5786 "1ghaghvd82af9j5adavxh77g7hm247d1r69m3fbi6f1jdivj5ldk"))))
5787 (build-system gnu-build-system)
5788 (outputs '("out" ;for binaries
5789 "db")) ;for sequence databases
5792 (modify-phases %standard-phases
5794 (lambda* (#:key outputs #:allow-other-keys)
5795 (let* ((out (assoc-ref outputs "out"))
5796 (bin (string-append out "/bin"))
5797 (db (assoc-ref outputs "db"))
5799 (string-append db "/share/sortmerna/rRNA_databases")))
5800 (install-file "sortmerna" bin)
5801 (install-file "indexdb_rna" bin)
5802 (for-each (lambda (file)
5803 (install-file file share))
5804 (find-files "rRNA_databases" ".*fasta"))
5808 (home-page "http://bioinfo.lifl.fr/RNA/sortmerna")
5809 (synopsis "Biological sequence analysis tool for NGS reads")
5811 "SortMeRNA is a biological sequence analysis tool for filtering, mapping
5812 and operational taxonomic unit (OTU) picking of next generation
5813 sequencing (NGS) reads. The core algorithm is based on approximate seeds and
5814 allows for fast and sensitive analyses of nucleotide sequences. The main
5815 application of SortMeRNA is filtering rRNA from metatranscriptomic data.")
5816 ;; The source includes x86 specific code
5817 (supported-systems '("x86_64-linux" "i686-linux"))
5818 (license license:lgpl3)))
5826 (uri (string-append "https://github.com/alexdobin/STAR/archive/"
5828 (file-name (string-append name "-" version ".tar.gz"))
5831 "0yci4ymy4407kjh0lqp021nzccp6r31wgrkixkmix5p130cxvc56"))
5832 (modules '((guix build utils)))
5835 (substitute* "source/Makefile"
5837 ;; Remove pre-built binaries and bundled htslib sources.
5838 (delete-file-recursively "bin/MacOSX_x86_64")
5839 (delete-file-recursively "bin/Linux_x86_64")
5840 (delete-file-recursively "bin/Linux_x86_64_static")
5841 (delete-file-recursively "source/htslib")
5843 (build-system gnu-build-system)
5845 '(#:tests? #f ;no check target
5846 #:make-flags '("STAR")
5848 (modify-phases %standard-phases
5849 (add-after 'unpack 'enter-source-dir
5850 (lambda _ (chdir "source") #t))
5851 (add-after 'enter-source-dir 'make-reproducible
5853 (substitute* "Makefile"
5854 (("(COMPILATION_TIME_PLACE=\")(.*)(\")" _ pre mid post)
5855 (string-append pre "Built with Guix" post)))))
5856 (add-after 'enter-source-dir 'do-not-use-bundled-htslib
5858 (substitute* "Makefile"
5859 (("(Depend.list: \\$\\(SOURCES\\) parametersDefault\\.xxd) htslib"
5861 (substitute* '("BAMfunctions.cpp"
5866 "bamRemoveDuplicates.cpp")
5867 (("#include \"htslib/([^\"]+\\.h)\"" _ header)
5868 (string-append "#include <" header ">")))
5869 (substitute* "IncludeDefine.h"
5870 (("\"htslib/(htslib/[^\"]+.h)\"" _ header)
5871 (string-append "<" header ">")))
5874 (lambda* (#:key outputs #:allow-other-keys)
5875 (let ((bin (string-append (assoc-ref outputs "out") "/bin/")))
5876 (install-file "STAR" bin))
5878 (delete 'configure))))
5882 `(("htslib" ,htslib)
5884 (home-page "https://github.com/alexdobin/STAR")
5885 (synopsis "Universal RNA-seq aligner")
5887 "The Spliced Transcripts Alignment to a Reference (STAR) software is
5888 based on a previously undescribed RNA-seq alignment algorithm that uses
5889 sequential maximum mappable seed search in uncompressed suffix arrays followed
5890 by seed clustering and stitching procedure. In addition to unbiased de novo
5891 detection of canonical junctions, STAR can discover non-canonical splices and
5892 chimeric (fusion) transcripts, and is also capable of mapping full-length RNA
5894 ;; Only 64-bit systems are supported according to the README.
5895 (supported-systems '("x86_64-linux" "mips64el-linux"))
5896 ;; STAR is licensed under GPLv3 or later; htslib is MIT-licensed.
5897 (license license:gpl3+)))
5899 (define-public subread
5905 (uri (string-append "mirror://sourceforge/subread/subread-"
5906 version "/subread-" version "-source.tar.gz"))
5909 "0ah0n4jx6ksk2m2j7xk385x2qzmk1y4rfc6a4mfrdqrlq721w99i"))))
5910 (build-system gnu-build-system)
5912 `(#:tests? #f ;no "check" target
5913 ;; The CC and CCFLAGS variables are set to contain a lot of x86_64
5914 ;; optimizations by default, so we override these flags such that x86_64
5915 ;; flags are only added when the build target is an x86_64 system.
5917 (list (let ((system ,(or (%current-target-system)
5919 (flags '("-ggdb" "-fomit-frame-pointer"
5920 "-ffast-math" "-funroll-loops"
5921 "-fmessage-length=0"
5922 "-O9" "-Wall" "-DMAKE_FOR_EXON"
5924 "-DSUBREAD_VERSION=\\\"${SUBREAD_VERSION}\\\""))
5925 (flags64 '("-mmmx" "-msse" "-msse2" "-msse3")))
5926 (if (string-prefix? "x86_64" system)
5927 (string-append "CCFLAGS=" (string-join (append flags flags64)))
5928 (string-append "CCFLAGS=" (string-join flags))))
5929 "-f" "Makefile.Linux"
5930 "CC=gcc ${CCFLAGS}")
5932 (modify-phases %standard-phases
5933 (add-after 'unpack 'enter-dir
5934 (lambda _ (chdir "src") #t))
5936 (lambda* (#:key outputs #:allow-other-keys)
5937 (let ((bin (string-append (assoc-ref outputs "out") "/bin/")))
5939 (copy-recursively "../bin" bin))))
5940 ;; no "configure" script
5941 (delete 'configure))))
5942 (inputs `(("zlib" ,zlib)))
5943 (home-page "http://bioinf.wehi.edu.au/subread-package/")
5944 (synopsis "Tool kit for processing next-gen sequencing data")
5946 "The subread package contains the following tools: subread aligner, a
5947 general-purpose read aligner; subjunc aligner: detecting exon-exon junctions
5948 and mapping RNA-seq reads; featureCounts: counting mapped reads for genomic
5949 features; exactSNP: a SNP caller that discovers SNPs by testing signals
5950 against local background noises.")
5951 (license license:gpl3+)))
5953 (define-public stringtie
5959 (uri (string-append "http://ccb.jhu.edu/software/stringtie/dl/"
5960 "stringtie-" version ".tar.gz"))
5963 "1cqllsc1maq4kh92isi8yadgzbmnf042hlnalpk3y59aph1z3bfz"))
5964 (modules '((guix build utils)))
5967 (delete-file-recursively "samtools-0.1.18")
5969 (build-system gnu-build-system)
5971 `(#:tests? #f ;no test suite
5973 (modify-phases %standard-phases
5974 ;; no configure script
5976 (add-before 'build 'use-system-samtools
5978 (substitute* "Makefile"
5979 (("stringtie: \\$\\{BAM\\}/libbam\\.a")
5981 (substitute* '("gclib/GBam.h"
5983 (("#include \"(bam|sam|kstring).h\"" _ header)
5984 (string-append "#include <samtools/" header ".h>")))
5986 (add-after 'unpack 'remove-duplicate-typedef
5988 ;; This typedef conflicts with the typedef in
5989 ;; glibc-2.25/include/bits/types.h
5990 (substitute* "gclib/GThreads.h"
5991 (("typedef long long __intmax_t;") ""))
5994 (lambda* (#:key outputs #:allow-other-keys)
5995 (let ((bin (string-append (assoc-ref outputs "out") "/bin/")))
5996 (install-file "stringtie" bin)
5999 `(("samtools" ,samtools-0.1)
6001 (home-page "http://ccb.jhu.edu/software/stringtie/")
6002 (synopsis "Transcript assembly and quantification for RNA-Seq data")
6004 "StringTie is a fast and efficient assembler of RNA-Seq sequence
6005 alignments into potential transcripts. It uses a novel network flow algorithm
6006 as well as an optional de novo assembly step to assemble and quantitate
6007 full-length transcripts representing multiple splice variants for each gene
6008 locus. Its input can include not only the alignments of raw reads used by
6009 other transcript assemblers, but also alignments of longer sequences that have
6010 been assembled from those reads. To identify differentially expressed genes
6011 between experiments, StringTie's output can be processed either by the
6012 Cuffdiff or Ballgown programs.")
6013 (license license:artistic2.0)))
6015 (define-public taxtastic
6021 (uri (pypi-uri "taxtastic" version))
6024 "03pysw79lsrvz4lwzis88j15067ffqbi4cid5pqhrlxmd6bh8rrk"))))
6025 (build-system python-build-system)
6027 `(#:python ,python-2
6029 (modify-phases %standard-phases
6032 (zero? (system* "python" "-m" "unittest" "discover" "-v")))))))
6034 `(("python-sqlalchemy" ,python2-sqlalchemy)
6035 ("python-decorator" ,python2-decorator)
6036 ("python-biopython" ,python2-biopython)
6037 ("python-pandas" ,python2-pandas)))
6038 (home-page "https://github.com/fhcrc/taxtastic")
6039 (synopsis "Tools for taxonomic naming and annotation")
6041 "Taxtastic is software written in python used to build and maintain
6042 reference packages i.e. collections of reference trees, reference alignments,
6043 profiles, and associated taxonomic information.")
6044 (license license:gpl3+)))
6046 (define-public vcftools
6053 "https://github.com/vcftools/vcftools/releases/download/v"
6054 version "/vcftools-" version ".tar.gz"))
6057 "1qw30c45wihgy632rbz4rh3njnwj4msj46l1rsgdhyg6bgypmr1i"))))
6058 (build-system gnu-build-system)
6060 `(#:tests? #f ; no "check" target
6062 "CFLAGS=-O2" ; override "-m64" flag
6063 (string-append "PREFIX=" (assoc-ref %outputs "out"))
6064 (string-append "MANDIR=" (assoc-ref %outputs "out")
6065 "/share/man/man1"))))
6067 `(("pkg-config" ,pkg-config)))
6071 (home-page "https://vcftools.github.io/")
6072 (synopsis "Tools for working with VCF files")
6074 "VCFtools is a program package designed for working with VCF files, such
6075 as those generated by the 1000 Genomes Project. The aim of VCFtools is to
6076 provide easily accessible methods for working with complex genetic variation
6077 data in the form of VCF files.")
6078 ;; The license is declared as LGPLv3 in the README and
6079 ;; at https://vcftools.github.io/license.html
6080 (license license:lgpl3)))
6082 (define-public infernal
6088 (uri (string-append "http://eddylab.org/software/infernal/"
6089 "infernal-" version ".tar.gz"))
6092 "0sr2hiz3qxfwqpz3whxr6n82p3x27336v3f34iqznp10hks2935c"))))
6093 (build-system gnu-build-system)
6095 `(("perl" ,perl))) ; for tests
6096 (home-page "http://eddylab.org/infernal/")
6097 (synopsis "Inference of RNA alignments")
6098 (description "Infernal (\"INFERence of RNA ALignment\") is a tool for
6099 searching DNA sequence databases for RNA structure and sequence similarities.
6100 It is an implementation of a special case of profile stochastic context-free
6101 grammars called @dfn{covariance models} (CMs). A CM is like a sequence
6102 profile, but it scores a combination of sequence consensus and RNA secondary
6103 structure consensus, so in many cases, it is more capable of identifying RNA
6104 homologs that conserve their secondary structure more than their primary
6106 ;; Infernal 1.1.2 requires VMX or SSE capability for parallel instructions.
6107 (supported-systems '("i686-linux" "x86_64-linux"))
6108 (license license:bsd-3)))
6110 (define-public r-centipede
6112 (name "r-centipede")
6116 (uri (string-append "http://download.r-forge.r-project.org/"
6117 "src/contrib/CENTIPEDE_" version ".tar.gz"))
6120 "1hsx6qgwr0i67fhy9257zj7s0ppncph2hjgbia5nn6nfmj0ax6l9"))))
6121 (build-system r-build-system)
6122 (home-page "http://centipede.uchicago.edu/")
6123 (synopsis "Predict transcription factor binding sites")
6125 "CENTIPEDE applies a hierarchical Bayesian mixture model to infer regions
6126 of the genome that are bound by particular transcription factors. It starts
6127 by identifying a set of candidate binding sites, and then aims to classify the
6128 sites according to whether each site is bound or not bound by a transcription
6129 factor. CENTIPEDE is an unsupervised learning algorithm that discriminates
6130 between two different types of motif instances using as much relevant
6131 information as possible.")
6132 (license (list license:gpl2+ license:gpl3+))))
6134 (define-public r-vegan
6141 (uri (cran-uri "vegan" version))
6144 "13pyqvlpz64qibi8k5d109v7q09j06mbv6ndix3n4cn21mjx391c"))))
6145 (build-system r-build-system)
6147 `(("gfortran" ,gfortran)))
6149 `(("r-cluster" ,r-cluster)
6150 ("r-knitr" ,r-knitr) ; needed for vignettes
6151 ("r-lattice" ,r-lattice)
6154 ("r-permute" ,r-permute)))
6155 (home-page "https://cran.r-project.org/web/packages/vegan")
6156 (synopsis "Functions for community ecology")
6158 "The vegan package provides tools for descriptive community ecology. It
6159 has most basic functions of diversity analysis, community ordination and
6160 dissimilarity analysis. Most of its multivariate tools can be used for other
6161 data types as well.")
6162 (license license:gpl2+)))
6164 (define-public r-annotate
6171 (uri (bioconductor-uri "annotate" version))
6174 "1qmncyvy147a1ll3iri45p822kcs3s7583jfnq9jf6sz9ilk8cjf"))))
6175 (build-system r-build-system)
6177 `(("r-annotationdbi" ,r-annotationdbi)
6178 ("r-biobase" ,r-biobase)
6179 ("r-biocgenerics" ,r-biocgenerics)
6181 ("r-rcurl" ,r-rcurl)
6183 ("r-xtable" ,r-xtable)))
6185 "https://bioconductor.org/packages/annotate")
6186 (synopsis "Annotation for microarrays")
6187 (description "This package provides R environments for the annotation of
6189 (license license:artistic2.0)))
6191 (define-public r-copynumber
6193 (name "r-copynumber")
6197 (uri (bioconductor-uri "copynumber" version))
6200 "0y9nnwb0psphp3ix88wj2f8z5gr45r5znf55w892ysm27isdpmms"))))
6201 (build-system r-build-system)
6203 `(("r-s4vectors" ,r-s4vectors)
6204 ("r-iranges" ,r-iranges)
6205 ("r-genomicranges" ,r-genomicranges)
6206 ("r-biocgenerics" ,r-biocgenerics)))
6207 (home-page "https://bioconductor.org/packages/copynumber")
6208 (synopsis "Segmentation of single- and multi-track copy number data")
6210 "This package segments single- and multi-track copy number data by a
6211 penalized least squares regression method.")
6212 (license license:artistic2.0)))
6214 (define-public r-geneplotter
6216 (name "r-geneplotter")
6221 (uri (bioconductor-uri "geneplotter" version))
6224 "055g28xgiazl4l0gkg8xiamks64f5yckjjyvw1abd6d6qjavwx0g"))))
6225 (build-system r-build-system)
6227 `(("r-annotate" ,r-annotate)
6228 ("r-annotationdbi" ,r-annotationdbi)
6229 ("r-biobase" ,r-biobase)
6230 ("r-biocgenerics" ,r-biocgenerics)
6231 ("r-lattice" ,r-lattice)
6232 ("r-rcolorbrewer" ,r-rcolorbrewer)))
6233 (home-page "https://bioconductor.org/packages/geneplotter")
6234 (synopsis "Graphics functions for genomic data")
6236 "This package provides functions for plotting genomic data.")
6237 (license license:artistic2.0)))
6239 (define-public r-genefilter
6241 (name "r-genefilter")
6246 (uri (bioconductor-uri "genefilter" version))
6249 "14l0ff02spmjwxj0m1czhg5vlkgwcfi73cym8m2n9vn6i7bjdaqi"))))
6250 (build-system r-build-system)
6252 `(("gfortran" ,gfortran)))
6254 `(("r-annotate" ,r-annotate)
6255 ("r-annotationdbi" ,r-annotationdbi)
6256 ("r-biobase" ,r-biobase)
6257 ("r-s4vectors" ,r-s4vectors)
6258 ("r-survival" ,r-survival)))
6259 (home-page "https://bioconductor.org/packages/genefilter")
6260 (synopsis "Filter genes from high-throughput experiments")
6262 "This package provides basic functions for filtering genes from
6263 high-throughput sequencing experiments.")
6264 (license license:artistic2.0)))
6266 (define-public r-deseq2
6273 (uri (bioconductor-uri "DESeq2" version))
6276 "1wjnfpb41a9mmf9a22bz4zh7r1d4id50vpdc1mn5vfzrz7li9qik"))))
6277 (properties `((upstream-name . "DESeq2")))
6278 (build-system r-build-system)
6280 `(("r-biobase" ,r-biobase)
6281 ("r-biocgenerics" ,r-biocgenerics)
6282 ("r-biocparallel" ,r-biocparallel)
6283 ("r-genefilter" ,r-genefilter)
6284 ("r-geneplotter" ,r-geneplotter)
6285 ("r-genomicranges" ,r-genomicranges)
6286 ("r-ggplot2" ,r-ggplot2)
6287 ("r-hmisc" ,r-hmisc)
6288 ("r-iranges" ,r-iranges)
6289 ("r-locfit" ,r-locfit)
6291 ("r-rcpparmadillo" ,r-rcpparmadillo)
6292 ("r-s4vectors" ,r-s4vectors)
6293 ("r-summarizedexperiment" ,r-summarizedexperiment)))
6294 (home-page "https://bioconductor.org/packages/DESeq2")
6295 (synopsis "Differential gene expression analysis")
6297 "This package provides functions to estimate variance-mean dependence in
6298 count data from high-throughput nucleotide sequencing assays and test for
6299 differential expression based on a model using the negative binomial
6301 (license license:lgpl3+)))
6303 (define-public r-dexseq
6310 (uri (bioconductor-uri "DEXSeq" version))
6313 "1mqb3mdxcsi3largsl7k27bvqrgps9ixv806xvmf29pw0xn05sg1"))))
6314 (properties `((upstream-name . "DEXSeq")))
6315 (build-system r-build-system)
6317 `(("r-annotationdbi" ,r-annotationdbi)
6318 ("r-biobase" ,r-biobase)
6319 ("r-biocgenerics" ,r-biocgenerics)
6320 ("r-biocparallel" ,r-biocparallel)
6321 ("r-biomart" ,r-biomart)
6322 ("r-deseq2" ,r-deseq2)
6323 ("r-genefilter" ,r-genefilter)
6324 ("r-geneplotter" ,r-geneplotter)
6325 ("r-genomicranges" ,r-genomicranges)
6326 ("r-hwriter" ,r-hwriter)
6327 ("r-iranges" ,r-iranges)
6328 ("r-rcolorbrewer" ,r-rcolorbrewer)
6329 ("r-rsamtools" ,r-rsamtools)
6330 ("r-s4vectors" ,r-s4vectors)
6331 ("r-statmod" ,r-statmod)
6332 ("r-stringr" ,r-stringr)
6333 ("r-summarizedexperiment" ,r-summarizedexperiment)))
6334 (home-page "https://bioconductor.org/packages/DEXSeq")
6335 (synopsis "Inference of differential exon usage in RNA-Seq")
6337 "This package is focused on finding differential exon usage using RNA-seq
6338 exon counts between samples with different experimental designs. It provides
6339 functions that allows the user to make the necessary statistical tests based
6340 on a model that uses the negative binomial distribution to estimate the
6341 variance between biological replicates and generalized linear models for
6342 testing. The package also provides functions for the visualization and
6343 exploration of the results.")
6344 (license license:gpl3+)))
6346 (define-public r-annotationforge
6348 (name "r-annotationforge")
6353 (uri (bioconductor-uri "AnnotationForge" version))
6356 "12ffj7h95adiya5mzyjxazqn1qgr434ajpabfcyhrj5v83s4vk65"))))
6358 `((upstream-name . "AnnotationForge")))
6359 (build-system r-build-system)
6361 `(("r-annotationdbi" ,r-annotationdbi)
6362 ("r-biobase" ,r-biobase)
6363 ("r-biocgenerics" ,r-biocgenerics)
6365 ("r-rcurl" ,r-rcurl)
6366 ("r-rsqlite" ,r-rsqlite)
6367 ("r-s4vectors" ,r-s4vectors)
6369 (home-page "https://bioconductor.org/packages/AnnotationForge")
6370 (synopsis "Code for building annotation database packages")
6372 "This package provides code for generating Annotation packages and their
6373 databases. Packages produced are intended to be used with AnnotationDbi.")
6374 (license license:artistic2.0)))
6376 (define-public r-rbgl
6383 (uri (bioconductor-uri "RBGL" version))
6386 "0hj972mmqpyi5fx1rq33kysavdyz4nspi6gcffzi3rv339m0anhf"))))
6387 (properties `((upstream-name . "RBGL")))
6388 (build-system r-build-system)
6389 (propagated-inputs `(("r-graph" ,r-graph)))
6390 (home-page "https://www.bioconductor.org/packages/RBGL")
6391 (synopsis "Interface to the Boost graph library")
6393 "This package provides a fairly extensive and comprehensive interface to
6394 the graph algorithms contained in the Boost library.")
6395 (license license:artistic2.0)))
6397 (define-public r-gseabase
6404 (uri (bioconductor-uri "GSEABase" version))
6407 "11bv92svik399q677jv96b71i4bq68xxyxn1yijpdik2lq4hgl7a"))))
6408 (properties `((upstream-name . "GSEABase")))
6409 (build-system r-build-system)
6411 `(("r-annotate" ,r-annotate)
6412 ("r-annotationdbi" ,r-annotationdbi)
6413 ("r-biobase" ,r-biobase)
6414 ("r-biocgenerics" ,r-biocgenerics)
6415 ("r-graph" ,r-graph)
6417 (home-page "https://bioconductor.org/packages/GSEABase")
6418 (synopsis "Gene set enrichment data structures and methods")
6420 "This package provides classes and methods to support @dfn{Gene Set
6421 Enrichment Analysis} (GSEA).")
6422 (license license:artistic2.0)))
6424 (define-public r-category
6431 (uri (bioconductor-uri "Category" version))
6434 "03wfqa8d1dgwsm327zl2mpkq7dq3mzhq12598qz3ylfhrwplbgx0"))))
6435 (properties `((upstream-name . "Category")))
6436 (build-system r-build-system)
6438 `(("r-annotate" ,r-annotate)
6439 ("r-annotationdbi" ,r-annotationdbi)
6440 ("r-biobase" ,r-biobase)
6441 ("r-biocgenerics" ,r-biocgenerics)
6442 ("r-genefilter" ,r-genefilter)
6443 ("r-graph" ,r-graph)
6444 ("r-gseabase" ,r-gseabase)
6445 ("r-matrix" ,r-matrix)
6448 (home-page "https://bioconductor.org/packages/Category")
6449 (synopsis "Category analysis")
6451 "This package provides a collection of tools for performing category
6453 (license license:artistic2.0)))
6455 (define-public r-gostats
6462 (uri (bioconductor-uri "GOstats" version))
6465 "1i5mydz5d95w2k28qr9j01hmbnl2id55jq94jvcpcyp1pvinkdq0"))))
6466 (properties `((upstream-name . "GOstats")))
6467 (build-system r-build-system)
6469 `(("r-annotate" ,r-annotate)
6470 ("r-annotationdbi" ,r-annotationdbi)
6471 ("r-annotationforge" ,r-annotationforge)
6472 ("r-biobase" ,r-biobase)
6473 ("r-category" ,r-category)
6474 ("r-go-db" ,r-go-db)
6475 ("r-graph" ,r-graph)
6476 ("r-rgraphviz" ,r-rgraphviz)
6477 ("r-rbgl" ,r-rbgl)))
6478 (home-page "https://bioconductor.org/packages/GOstats")
6479 (synopsis "Tools for manipulating GO and microarrays")
6481 "This package provides a set of tools for interacting with GO and
6482 microarray data. A variety of basic manipulation tools for graphs, hypothesis
6483 testing and other simple calculations.")
6484 (license license:artistic2.0)))
6486 (define-public r-shortread
6488 (name "r-shortread")
6493 (uri (bioconductor-uri "ShortRead" version))
6496 "038z3z7qaw5bpgjzy91sjkybsny6jwjjsrnnq4gdqdw9ss1qy1fb"))))
6497 (properties `((upstream-name . "ShortRead")))
6498 (build-system r-build-system)
6502 `(("r-biobase" ,r-biobase)
6503 ("r-biocgenerics" ,r-biocgenerics)
6504 ("r-biocparallel" ,r-biocparallel)
6505 ("r-biostrings" ,r-biostrings)
6506 ("r-genomeinfodb" ,r-genomeinfodb)
6507 ("r-genomicalignments" ,r-genomicalignments)
6508 ("r-genomicranges" ,r-genomicranges)
6509 ("r-hwriter" ,r-hwriter)
6510 ("r-iranges" ,r-iranges)
6511 ("r-lattice" ,r-lattice)
6512 ("r-latticeextra" ,r-latticeextra)
6513 ("r-rsamtools" ,r-rsamtools)
6514 ("r-s4vectors" ,r-s4vectors)
6515 ("r-xvector" ,r-xvector)
6516 ("r-zlibbioc" ,r-zlibbioc)))
6517 (home-page "https://bioconductor.org/packages/ShortRead")
6518 (synopsis "FASTQ input and manipulation tools")
6520 "This package implements sampling, iteration, and input of FASTQ files.
6521 It includes functions for filtering and trimming reads, and for generating a
6522 quality assessment report. Data are represented as
6523 @code{DNAStringSet}-derived objects, and easily manipulated for a diversity of
6524 purposes. The package also contains legacy support for early single-end,
6525 ungapped alignment formats.")
6526 (license license:artistic2.0)))
6528 (define-public r-systempiper
6530 (name "r-systempiper")
6535 (uri (bioconductor-uri "systemPipeR" version))
6538 "1550pd63mmky0vgkmpni7zf14kqz1741wv63nfaw29kcmhh3m5lm"))))
6539 (properties `((upstream-name . "systemPipeR")))
6540 (build-system r-build-system)
6542 `(("r-annotate" ,r-annotate)
6543 ("r-batchjobs" ,r-batchjobs)
6544 ("r-biocgenerics" ,r-biocgenerics)
6545 ("r-biostrings" ,r-biostrings)
6546 ("r-deseq2" ,r-deseq2)
6547 ("r-edger" ,r-edger)
6548 ("r-genomicfeatures" ,r-genomicfeatures)
6549 ("r-genomicranges" ,r-genomicranges)
6550 ("r-ggplot2" ,r-ggplot2)
6551 ("r-go-db" ,r-go-db)
6552 ("r-gostats" ,r-gostats)
6553 ("r-limma" ,r-limma)
6554 ("r-pheatmap" ,r-pheatmap)
6555 ("r-rjson" ,r-rjson)
6556 ("r-rsamtools" ,r-rsamtools)
6557 ("r-shortread" ,r-shortread)
6558 ("r-summarizedexperiment" ,r-summarizedexperiment)
6559 ("r-variantannotation" ,r-variantannotation)))
6560 (home-page "https://github.com/tgirke/systemPipeR")
6561 (synopsis "Next generation sequencing workflow and reporting environment")
6563 "This R package provides tools for building and running automated
6564 end-to-end analysis workflows for a wide range of @dfn{next generation
6565 sequence} (NGS) applications such as RNA-Seq, ChIP-Seq, VAR-Seq and Ribo-Seq.
6566 Important features include a uniform workflow interface across different NGS
6567 applications, automated report generation, and support for running both R and
6568 command-line software, such as NGS aligners or peak/variant callers, on local
6569 computers or compute clusters. Efficient handling of complex sample sets and
6570 experimental designs is facilitated by a consistently implemented sample
6571 annotation infrastructure.")
6572 (license license:artistic2.0)))
6574 (define-public r-grohmm
6581 (uri (bioconductor-uri "groHMM" version))
6584 "1kjb14apyly44qdlx2ld6gr69wlazd4mbhs58l35hir12aphgrzp"))))
6585 (properties `((upstream-name . "groHMM")))
6586 (build-system r-build-system)
6588 `(("r-genomeinfodb" ,r-genomeinfodb)
6589 ("r-genomicalignments" ,r-genomicalignments)
6590 ("r-genomicranges" ,r-genomicranges)
6591 ("r-iranges" ,r-iranges)
6593 ("r-rtracklayer" ,r-rtracklayer)
6594 ("r-s4vectors" ,r-s4vectors)))
6595 (home-page "https://github.com/Kraus-Lab/groHMM")
6596 (synopsis "GRO-seq analysis pipeline")
6598 "This package provides a pipeline for the analysis of GRO-seq data.")
6599 (license license:gpl3+)))
6601 (define-public r-txdb-hsapiens-ucsc-hg19-knowngene
6603 (name "r-txdb-hsapiens-ucsc-hg19-knowngene")
6607 ;; We cannot use bioconductor-uri here because this tarball is
6608 ;; located under "data/annotation/" instead of "bioc/".
6609 (uri (string-append "https://bioconductor.org/packages/"
6610 "release/data/annotation/src/contrib"
6611 "/TxDb.Hsapiens.UCSC.hg19.knownGene_"
6615 "1sajhcqqwazgz2lqbik7rd935i7kpnh08zxbp2ra10j72yqy4g86"))))
6617 `((upstream-name . "TxDb.Hsapiens.UCSC.hg19.knownGene")))
6618 (build-system r-build-system)
6619 ;; As this package provides little more than a very large data file it
6620 ;; doesn't make sense to build substitutes.
6621 (arguments `(#:substitutable? #f))
6623 `(("r-genomicfeatures" ,r-genomicfeatures)))
6625 "https://bioconductor.org/packages/TxDb.Hsapiens.UCSC.hg19.knownGene/")
6626 (synopsis "Annotation package for human genome in TxDb format")
6628 "This package provides an annotation database of Homo sapiens genome
6629 data. It is derived from the UCSC hg19 genome and based on the \"knownGene\"
6630 track. The database is exposed as a @code{TxDb} object.")
6631 (license license:artistic2.0)))
6633 (define-public r-sparql
6639 (uri (cran-uri "SPARQL" version))
6642 "0gak1q06yyhdmcxb2n3v0h9gr1vqd0viqji52wpw211qp6r6dcrc"))))
6643 (properties `((upstream-name . "SPARQL")))
6644 (build-system r-build-system)
6646 `(("r-rcurl" ,r-rcurl)
6648 (home-page "https://cran.r-project.org/web/packages/SPARQL")
6649 (synopsis "SPARQL client for R")
6650 (description "This package provides an interface to use SPARQL to pose
6651 SELECT or UPDATE queries to an end-point.")
6652 ;; The only license indication is found in the DESCRIPTION file,
6653 ;; which states GPL-3. So we cannot assume GPLv3+.
6654 (license license:gpl3)))
6656 (define-public vsearch
6664 "https://github.com/torognes/vsearch/archive/v"
6666 (file-name (string-append name "-" version ".tar.gz"))
6669 "15pbirgzhvflj4pi5n82vybbzjy9mlb0lv5l3qhrmdkfzpbyahw3"))
6670 (patches (search-patches "vsearch-unbundle-cityhash.patch"))
6673 ;; Remove bundled cityhash sources. The vsearch source is adjusted
6674 ;; for this in the patch.
6675 (delete-file "src/city.h")
6676 (delete-file "src/citycrc.h")
6677 (delete-file "src/city.cc")
6679 (build-system gnu-build-system)
6682 (modify-phases %standard-phases
6683 (add-after 'unpack 'autogen
6684 (lambda _ (zero? (system* "autoreconf" "-vif")))))))
6688 ("cityhash" ,cityhash)))
6690 `(("autoconf" ,autoconf)
6691 ("automake" ,automake)))
6692 (synopsis "Sequence search tools for metagenomics")
6694 "VSEARCH supports DNA sequence searching, clustering, chimera detection,
6695 dereplication, pairwise alignment, shuffling, subsampling, sorting and
6696 masking. The tool takes advantage of parallelism in the form of SIMD
6697 vectorization as well as multiple threads to perform accurate alignments at
6698 high speed. VSEARCH uses an optimal global aligner (full dynamic programming
6699 Needleman-Wunsch).")
6700 (home-page "https://github.com/torognes/vsearch")
6701 ;; vsearch uses non-portable SSE intrinsics so building fails on other
6703 (supported-systems '("x86_64-linux"))
6704 ;; Dual licensed; also includes public domain source.
6705 (license (list license:gpl3 license:bsd-2))))
6707 (define-public pardre
6710 ;; The source of 1.1.5 changed in place, so we append "-1" to the version.
6715 (uri (string-append "mirror://sourceforge/pardre/ParDRe-rel"
6719 "17j73nc0viq4f6qj50nrndsrif5d6b71q8fl87m54psiv0ilns2b"))))
6720 (build-system gnu-build-system)
6722 `(#:tests? #f ; no tests included
6724 (modify-phases %standard-phases
6727 (lambda* (#:key outputs #:allow-other-keys)
6728 (let ((bin (string-append (assoc-ref outputs "out") "/bin")))
6729 (install-file "ParDRe" bin)
6732 `(("openmpi" ,openmpi)
6734 (synopsis "Parallel tool to remove duplicate DNA reads")
6736 "ParDRe is a parallel tool to remove duplicate genetic sequence reads.
6737 Duplicate reads can be seen as identical or nearly identical sequences with
6738 some mismatches. This tool lets users avoid the analysis of unnecessary
6739 reads, reducing the time of subsequent procedures with the
6740 dataset (e.g. assemblies, mappings, etc.). The tool is implemented with MPI
6741 in order to exploit the parallel capabilities of multicore clusters. It is
6742 faster than multithreaded counterparts (end of 2015) for the same number of
6743 cores and, thanks to the message-passing technology, it can be executed on
6745 (home-page "https://sourceforge.net/projects/pardre/")
6746 (license license:gpl3+)))
6748 (define-public ruby-bio-kseq
6750 (name "ruby-bio-kseq")
6755 (uri (rubygems-uri "bio-kseq" version))
6758 "1xyaha46khb5jc6wzkbf7040jagac49jbimn0vcrzid0j8jdikrz"))))
6759 (build-system ruby-build-system)
6761 `(#:test-target "spec"))
6763 `(("bundler" ,bundler)
6764 ("ruby-rspec" ,ruby-rspec)
6765 ("ruby-rake-compiler" ,ruby-rake-compiler)))
6768 (synopsis "Ruby bindings for the kseq.h FASTA/Q parser")
6770 "@code{Bio::Kseq} provides ruby bindings to the @code{kseq.h} FASTA and
6771 FASTQ parsing code. It provides a fast iterator over sequences and their
6773 (home-page "https://github.com/gusevfe/bio-kseq")
6774 (license license:expat)))
6776 (define-public bio-locus
6783 (uri (rubygems-uri "bio-locus" version))
6786 "02vmrxyimkj9sahsp4zhfhnmbvz6dbbqz1y01vglf8cbwvkajfl0"))))
6787 (build-system ruby-build-system)
6789 `(("ruby-rspec" ,ruby-rspec)))
6790 (synopsis "Tool for fast querying of genome locations")
6792 "Bio-locus is a tabix-like tool for fast querying of genome
6793 locations. Many file formats in bioinformatics contain records that
6794 start with a chromosome name and a position for a SNP, or a start-end
6795 position for indels. Bio-locus allows users to store this chr+pos or
6796 chr+pos+alt information in a database.")
6797 (home-page "https://github.com/pjotrp/bio-locus")
6798 (license license:expat)))
6800 (define-public bio-blastxmlparser
6802 (name "bio-blastxmlparser")
6806 (uri (rubygems-uri "bio-blastxmlparser" version))
6809 "1wf4qygcmdjgcqm6flmvsagfr1gs9lf63mj32qv3z1f481zc5692"))))
6810 (build-system ruby-build-system)
6812 `(("ruby-bio-logger" ,ruby-bio-logger)
6813 ("ruby-nokogiri" ,ruby-nokogiri)))
6815 `(("ruby-rspec" ,ruby-rspec)))
6816 (synopsis "Fast big data BLAST XML parser and library")
6818 "Very fast parallel big-data BLAST XML file parser which can be used as
6819 command line utility. Use blastxmlparser to: Parse BLAST XML; filter output;
6820 generate FASTA, JSON, YAML, RDF, JSON-LD, HTML, CSV, tabular output etc.")
6821 (home-page "https://github.com/pjotrp/blastxmlparser")
6822 (license license:expat)))
6824 (define-public bioruby
6831 (uri (rubygems-uri "bio" version))
6834 "0hdl0789c9n4mprnx5pgd46bfwl8d000rqpamj5h6kkjgspijv49"))))
6835 (build-system ruby-build-system)
6837 `(("ruby-libxml" ,ruby-libxml)))
6839 `(("which" ,which))) ; required for test phase
6842 (modify-phases %standard-phases
6843 (add-before 'build 'patch-test-command
6845 (substitute* '("test/functional/bio/test_command.rb")
6846 (("/bin/sh") (which "sh")))
6847 (substitute* '("test/functional/bio/test_command.rb")
6848 (("/bin/ls") (which "ls")))
6849 (substitute* '("test/functional/bio/test_command.rb")
6850 (("which") (which "which")))
6851 (substitute* '("test/functional/bio/test_command.rb",
6852 "test/data/command/echoarg2.sh")
6853 (("/bin/echo") (which "echo")))
6855 (synopsis "Ruby library, shell and utilities for bioinformatics")
6856 (description "BioRuby comes with a comprehensive set of Ruby development
6857 tools and libraries for bioinformatics and molecular biology. BioRuby has
6858 components for sequence analysis, pathway analysis, protein modelling and
6859 phylogenetic analysis; it supports many widely used data formats and provides
6860 easy access to databases, external programs and public web services, including
6861 BLAST, KEGG, GenBank, MEDLINE and GO.")
6862 (home-page "http://bioruby.org/")
6863 ;; Code is released under Ruby license, except for setup
6864 ;; (LGPLv2.1+) and scripts in samples (which have GPL2 and GPL2+)
6865 (license (list license:ruby license:lgpl2.1+ license:gpl2+ ))))
6867 (define-public r-acsnminer
6869 (name "r-acsnminer")
6870 (version "0.16.8.25")
6873 (uri (cran-uri "ACSNMineR" version))
6876 "0gh604s8qall6zfjlwcg2ilxjvz08dplf9k5g47idhv43scm748l"))))
6877 (properties `((upstream-name . "ACSNMineR")))
6878 (build-system r-build-system)
6880 `(("r-ggplot2" ,r-ggplot2)
6881 ("r-gridextra" ,r-gridextra)))
6882 (home-page "https://cran.r-project.org/web/packages/ACSNMineR")
6883 (synopsis "Gene enrichment analysis")
6885 "This package provides tools to compute and represent gene set enrichment
6886 or depletion from your data based on pre-saved maps from the @dfn{Atlas of
6887 Cancer Signalling Networks} (ACSN) or user imported maps. The gene set
6888 enrichment can be run with hypergeometric test or Fisher exact test, and can
6889 use multiple corrections. Visualization of data can be done either by
6890 barplots or heatmaps.")
6891 (license license:gpl2+)))
6893 (define-public r-biocgenerics
6895 (name "r-biocgenerics")
6899 (uri (bioconductor-uri "BiocGenerics" version))
6902 "19qxhy2cd3pykkhzbb5q3crgaxf65cpzf2mkfsz16gqhi8flj72p"))))
6904 `((upstream-name . "BiocGenerics")))
6905 (build-system r-build-system)
6906 (home-page "https://bioconductor.org/packages/BiocGenerics")
6907 (synopsis "S4 generic functions for Bioconductor")
6909 "This package provides S4 generic functions needed by many Bioconductor
6911 (license license:artistic2.0)))
6913 (define-public r-biocinstaller
6915 (name "r-biocinstaller")
6919 (uri (bioconductor-uri "BiocInstaller" version))
6922 "1xg1gi1hf5vflp71ji21gnmr4kcjpx8a6c47cllpc7yqnjv5nfg0"))))
6924 `((upstream-name . "BiocInstaller")))
6925 (build-system r-build-system)
6926 (home-page "https://bioconductor.org/packages/BiocInstaller")
6927 (synopsis "Install Bioconductor packages")
6928 (description "This package is used to install and update R packages from
6929 Bioconductor, CRAN, and Github.")
6930 (license license:artistic2.0)))
6932 (define-public r-biocviews
6934 (name "r-biocviews")
6938 (uri (bioconductor-uri "biocViews" version))
6941 "1yx2lir67ny0j150wyfqca0wsxp84byri8nscbs9qlndkh2jppq9"))))
6943 `((upstream-name . "biocViews")))
6944 (build-system r-build-system)
6946 `(("r-biobase" ,r-biobase)
6947 ("r-graph" ,r-graph)
6949 ("r-rcurl" ,r-rcurl)
6951 ("r-runit" ,r-runit)))
6952 (home-page "https://bioconductor.org/packages/biocViews")
6953 (synopsis "Bioconductor package categorization helper")
6954 (description "The purpose of biocViews is to create HTML pages that
6955 categorize packages in a Bioconductor package repository according to keywords,
6956 also known as views, in a controlled vocabulary.")
6957 (license license:artistic2.0)))
6959 (define-public r-bookdown
6965 (uri (cran-uri "bookdown" version))
6968 "1b3fw1f41zph5yw3kynb47aijq53vhaa6mnnvxly72zamyzdf95q"))))
6969 (build-system r-build-system)
6971 `(("r-htmltools" ,r-htmltools)
6972 ("r-knitr" ,r-knitr)
6973 ("r-rmarkdown" ,r-rmarkdown)
6974 ("r-tinytex" ,r-tinytex)
6976 ("r-xfun" ,r-xfun)))
6977 (home-page "https://github.com/rstudio/bookdown")
6978 (synopsis "Authoring books and technical documents with R markdown")
6979 (description "This package provides output formats and utilities for
6980 authoring books and technical documents with R Markdown.")
6981 (license license:gpl3)))
6983 (define-public r-biocstyle
6985 (name "r-biocstyle")
6989 (uri (bioconductor-uri "BiocStyle" version))
6992 "17m901ylz00w1a3nq5f910v55zixm1nr6rb3qrsbhqd94qzr0l2p"))))
6994 `((upstream-name . "BiocStyle")))
6995 (build-system r-build-system)
6997 `(("r-bookdown" ,r-bookdown)
6998 ("r-knitr" ,r-knitr)
6999 ("r-rmarkdown" ,r-rmarkdown)
7000 ("r-yaml" ,r-yaml)))
7001 (home-page "https://bioconductor.org/packages/BiocStyle")
7002 (synopsis "Bioconductor formatting styles")
7003 (description "This package provides standard formatting styles for
7004 Bioconductor PDF and HTML documents. Package vignettes illustrate use and
7006 (license license:artistic2.0)))
7008 (define-public r-bioccheck
7010 (name "r-bioccheck")
7014 (uri (bioconductor-uri "BiocCheck" version))
7017 "1srp1g809f1nn0fyqknr7r6dq89bw1xpjvmygr7cw6ffknbc671s"))))
7019 `((upstream-name . "BiocCheck")))
7020 (build-system r-build-system)
7023 (modify-phases %standard-phases
7024 ;; This package can be used by calling BiocCheck(<package>) from
7025 ;; within R, or by running R CMD BiocCheck <package>. This phase
7026 ;; makes sure the latter works. For this to work, the BiocCheck
7027 ;; script must be somewhere on the PATH (not the R bin directory).
7028 (add-after 'install 'install-bioccheck-subcommand
7029 (lambda* (#:key outputs #:allow-other-keys)
7030 (let* ((out (assoc-ref outputs "out"))
7031 (dest-dir (string-append out "/bin"))
7033 (string-append out "/site-library/BiocCheck/script/")))
7035 (symlink (string-append script-dir "/checkBadDeps.R")
7036 (string-append dest-dir "/checkBadDeps.R"))
7037 (symlink (string-append script-dir "/BiocCheck")
7038 (string-append dest-dir "/BiocCheck")))
7041 `(("r-codetools" ,r-codetools)
7042 ("r-graph" ,r-graph)
7044 ("r-optparse" ,r-optparse)
7045 ("r-biocinstaller" ,r-biocinstaller)
7046 ("r-biocviews" ,r-biocviews)
7047 ("r-stringdist" ,r-stringdist)))
7048 (home-page "https://bioconductor.org/packages/BiocCheck")
7049 (synopsis "Executes Bioconductor-specific package checks")
7050 (description "This package contains tools to perform additional quality
7051 checks on R packages that are to be submitted to the Bioconductor repository.")
7052 (license license:artistic2.0)))
7054 (define-public r-getopt
7061 (uri (cran-uri "getopt" version))
7064 "13p35lbpy7i578752fa71sbfvcsqw5qfa9p6kf8b5m3c5p9i4v1x"))))
7065 (build-system r-build-system)
7066 (home-page "https://github.com/trevorld/getopt")
7067 (synopsis "Command-line option processor for R")
7069 "This package is designed to be used with Rscript to write shebang
7070 scripts that accept short and long options. Many users will prefer to
7071 use the packages @code{optparse} or @code{argparse} which add extra
7072 features like automatically generated help options and usage texts,
7073 support for default values, positional argument support, etc.")
7074 (license license:gpl2+)))
7076 (define-public r-optparse
7083 (uri (cran-uri "optparse" version))
7086 "1ff4wmsszrb3spwfp7ynfs8w11qpy1sdzfxm1wk8dqqvdwris7qb"))))
7087 (build-system r-build-system)
7089 `(("r-getopt" ,r-getopt)))
7091 "https://github.com/trevorld/optparse")
7092 (synopsis "Command line option parser")
7094 "This package provides a command line parser inspired by Python's
7095 @code{optparse} library to be used with Rscript to write shebang scripts
7096 that accept short and long options.")
7097 (license license:gpl2+)))
7099 (define-public r-dnacopy
7105 (uri (bioconductor-uri "DNAcopy" version))
7108 "03hfhmmc5y60r2gcgm367w2fr7qj115l74m9bp3h9qpn5yci0d8n"))))
7110 `((upstream-name . "DNAcopy")))
7111 (build-system r-build-system)
7113 `(("gfortran" ,gfortran)))
7114 (home-page "https://bioconductor.org/packages/DNAcopy")
7115 (synopsis "Implementation of a circular binary segmentation algorithm")
7116 (description "This package implements the circular binary segmentation (CBS)
7117 algorithm to segment DNA copy number data and identify genomic regions with
7118 abnormal copy number.")
7119 (license license:gpl2+)))
7121 (define-public r-s4vectors
7123 (name "r-s4vectors")
7127 (uri (bioconductor-uri "S4Vectors" version))
7130 "0qvj2j0zl4djjl7vrwc6xak6h8dxr53iwypfbcvfb3sh7jwhdiz5"))))
7132 `((upstream-name . "S4Vectors")))
7133 (build-system r-build-system)
7135 `(("r-biocgenerics" ,r-biocgenerics)))
7136 (home-page "https://bioconductor.org/packages/S4Vectors")
7137 (synopsis "S4 implementation of vectors and lists")
7139 "The S4Vectors package defines the @code{Vector} and @code{List} virtual
7140 classes and a set of generic functions that extend the semantic of ordinary
7141 vectors and lists in R. Package developers can easily implement vector-like
7142 or list-like objects as concrete subclasses of @code{Vector} or @code{List}.
7143 In addition, a few low-level concrete subclasses of general interest (e.g.
7144 @code{DataFrame}, @code{Rle}, and @code{Hits}) are implemented in the
7145 S4Vectors package itself.")
7146 (license license:artistic2.0)))
7148 (define-public r-seqinr
7155 (uri (cran-uri "seqinr" version))
7158 "17zv0n5cji17izwmwg0jcbxbjl3w5rls91w15svcnlpxjms38ahn"))))
7159 (build-system r-build-system)
7161 `(("r-ade4" ,r-ade4)
7162 ("r-segmented" ,r-segmented)))
7165 (home-page "http://seqinr.r-forge.r-project.org/")
7166 (synopsis "Biological sequences retrieval and analysis")
7168 "This package provides tools for exploratory data analysis and data
7169 visualization of biological sequence (DNA and protein) data. It also includes
7170 utilities for sequence data management under the ACNUC system.")
7171 (license license:gpl2+)))
7173 (define-public r-iranges
7179 (uri (bioconductor-uri "IRanges" version))
7182 "10ccw930vfmkskkrzbps14xglqlkxf588623dr7f1a9ckx7yr2p6"))))
7184 `((upstream-name . "IRanges")))
7185 (build-system r-build-system)
7187 `(("r-biocgenerics" ,r-biocgenerics)
7188 ("r-s4vectors" ,r-s4vectors)))
7189 (home-page "https://bioconductor.org/packages/IRanges")
7190 (synopsis "Infrastructure for manipulating intervals on sequences")
7192 "This package provides efficient low-level and highly reusable S4 classes
7193 for storing ranges of integers, RLE vectors (Run-Length Encoding), and, more
7194 generally, data that can be organized sequentially (formally defined as
7195 @code{Vector} objects), as well as views on these @code{Vector} objects.
7196 Efficient list-like classes are also provided for storing big collections of
7197 instances of the basic classes. All classes in the package use consistent
7198 naming and share the same rich and consistent \"Vector API\" as much as
7200 (license license:artistic2.0)))
7202 (define-public r-genomeinfodbdata
7204 (name "r-genomeinfodbdata")
7208 ;; We cannot use bioconductor-uri here because this tarball is
7209 ;; located under "data/annotation/" instead of "bioc/".
7210 (uri (string-append "https://bioconductor.org/packages/release/"
7211 "data/annotation/src/contrib/GenomeInfoDbData_"
7215 "0hipipvyvrh75n68hsjg35sxbcfzrghzxv547vnkk2f8ya99g01r"))))
7217 `((upstream-name . "GenomeInfoDbData")))
7218 (build-system r-build-system)
7219 (home-page "https://bioconductor.org/packages/GenomeInfoDbData")
7220 (synopsis "Species and taxonomy ID look up tables for GenomeInfoDb")
7221 (description "This package contains data for mapping between NCBI taxonomy
7222 ID and species. It is used by functions in the GenomeInfoDb package.")
7223 (license license:artistic2.0)))
7225 (define-public r-genomeinfodb
7227 (name "r-genomeinfodb")
7231 (uri (bioconductor-uri "GenomeInfoDb" version))
7234 "0yhnqhaydmmq7ihmhj3rbal4afq5p993l2qqrd0n5wmbyg7glg2d"))))
7236 `((upstream-name . "GenomeInfoDb")))
7237 (build-system r-build-system)
7239 `(("r-biocgenerics" ,r-biocgenerics)
7240 ("r-genomeinfodbdata" ,r-genomeinfodbdata)
7241 ("r-iranges" ,r-iranges)
7242 ("r-rcurl" ,r-rcurl)
7243 ("r-s4vectors" ,r-s4vectors)))
7244 (home-page "https://bioconductor.org/packages/GenomeInfoDb")
7245 (synopsis "Utilities for manipulating chromosome identifiers")
7247 "This package contains data and functions that define and allow
7248 translation between different chromosome sequence naming conventions (e.g.,
7249 \"chr1\" versus \"1\"), including a function that attempts to place sequence
7250 names in their natural, rather than lexicographic, order.")
7251 (license license:artistic2.0)))
7253 (define-public r-edger
7259 (uri (bioconductor-uri "edgeR" version))
7262 "07py2g6vg9jbflwhc1hnzr2silbinrjwxq3mkq30nzjgf0n0hrf3"))))
7263 (properties `((upstream-name . "edgeR")))
7264 (build-system r-build-system)
7266 `(("r-limma" ,r-limma)
7267 ("r-locfit" ,r-locfit)
7269 ("r-statmod" ,r-statmod))) ;for estimateDisp
7270 (home-page "http://bioinf.wehi.edu.au/edgeR")
7271 (synopsis "EdgeR does empirical analysis of digital gene expression data")
7272 (description "This package can do differential expression analysis of
7273 RNA-seq expression profiles with biological replication. It implements a range
7274 of statistical methodology based on the negative binomial distributions,
7275 including empirical Bayes estimation, exact tests, generalized linear models
7276 and quasi-likelihood tests. It be applied to differential signal analysis of
7277 other types of genomic data that produce counts, including ChIP-seq, SAGE and
7279 (license license:gpl2+)))
7281 (define-public r-variantannotation
7283 (name "r-variantannotation")
7287 (uri (bioconductor-uri "VariantAnnotation" version))
7290 "06bccdf57vja7m63chmgc4539lwng3q3b8zxn285fj8524l6mcn7"))))
7292 `((upstream-name . "VariantAnnotation")))
7296 `(("r-annotationdbi" ,r-annotationdbi)
7297 ("r-biobase" ,r-biobase)
7298 ("r-biocgenerics" ,r-biocgenerics)
7299 ("r-biostrings" ,r-biostrings)
7300 ("r-bsgenome" ,r-bsgenome)
7302 ("r-genomeinfodb" ,r-genomeinfodb)
7303 ("r-genomicfeatures" ,r-genomicfeatures)
7304 ("r-genomicranges" ,r-genomicranges)
7305 ("r-iranges" ,r-iranges)
7306 ("r-summarizedexperiment" ,r-summarizedexperiment)
7307 ("r-rsamtools" ,r-rsamtools)
7308 ("r-rtracklayer" ,r-rtracklayer)
7309 ("r-s4vectors" ,r-s4vectors)
7310 ("r-xvector" ,r-xvector)
7311 ("r-zlibbioc" ,r-zlibbioc)))
7312 (build-system r-build-system)
7313 (home-page "https://bioconductor.org/packages/VariantAnnotation")
7314 (synopsis "Package for annotation of genetic variants")
7315 (description "This R package can annotate variants, compute amino acid
7316 coding changes and predict coding outcomes.")
7317 (license license:artistic2.0)))
7319 (define-public r-limma
7325 (uri (bioconductor-uri "limma" version))
7328 "1982g5v35ilfgxm2vkq1p3j1bbir795pjvfzx4nzam2rlqqymbqm"))))
7329 (build-system r-build-system)
7330 (home-page "http://bioinf.wehi.edu.au/limma")
7331 (synopsis "Package for linear models for microarray and RNA-seq data")
7332 (description "This package can be used for the analysis of gene expression
7333 studies, especially the use of linear models for analysing designed experiments
7334 and the assessment of differential expression. The analysis methods apply to
7335 different technologies, including microarrays, RNA-seq, and quantitative PCR.")
7336 (license license:gpl2+)))
7338 (define-public r-xvector
7344 (uri (bioconductor-uri "XVector" version))
7347 "1zjlhh9lsyhg0js1858csyw2389kbrzdqnqnha833wazkwxilp3f"))))
7349 `((upstream-name . "XVector")))
7350 (build-system r-build-system)
7353 (modify-phases %standard-phases
7354 (add-after 'unpack 'use-system-zlib
7356 (substitute* "DESCRIPTION"
7357 (("zlibbioc, ") ""))
7358 (substitute* "NAMESPACE"
7359 (("import\\(zlibbioc\\)") ""))
7364 `(("r-biocgenerics" ,r-biocgenerics)
7365 ("r-iranges" ,r-iranges)
7366 ("r-s4vectors" ,r-s4vectors)))
7367 (home-page "https://bioconductor.org/packages/XVector")
7368 (synopsis "Representation and manpulation of external sequences")
7370 "This package provides memory efficient S4 classes for storing sequences
7371 \"externally\" (behind an R external pointer, or on disk).")
7372 (license license:artistic2.0)))
7374 (define-public r-genomicranges
7376 (name "r-genomicranges")
7380 (uri (bioconductor-uri "GenomicRanges" version))
7383 "03gmka6rlz18vd4229796l5l3l6446v5cb90sn2nb5knjbp84hni"))))
7385 `((upstream-name . "GenomicRanges")))
7386 (build-system r-build-system)
7388 `(("r-biocgenerics" ,r-biocgenerics)
7389 ("r-genomeinfodb" ,r-genomeinfodb)
7390 ("r-iranges" ,r-iranges)
7391 ("r-s4vectors" ,r-s4vectors)
7392 ("r-xvector" ,r-xvector)))
7393 (home-page "https://bioconductor.org/packages/GenomicRanges")
7394 (synopsis "Representation and manipulation of genomic intervals")
7396 "This package provides tools to efficiently represent and manipulate
7397 genomic annotations and alignments is playing a central role when it comes to
7398 analyzing high-throughput sequencing data (a.k.a. NGS data). The
7399 GenomicRanges package defines general purpose containers for storing and
7400 manipulating genomic intervals and variables defined along a genome.")
7401 (license license:artistic2.0)))
7403 (define-public r-biobase
7409 (uri (bioconductor-uri "Biobase" version))
7412 "1iwds2a5ir29k19dbpynlc7nn836cw2gamchhgpi2jf2xar9m9jz"))))
7414 `((upstream-name . "Biobase")))
7415 (build-system r-build-system)
7417 `(("r-biocgenerics" ,r-biocgenerics)))
7418 (home-page "https://bioconductor.org/packages/Biobase")
7419 (synopsis "Base functions for Bioconductor")
7421 "This package provides functions that are needed by many other packages
7422 on Bioconductor or which replace R functions.")
7423 (license license:artistic2.0)))
7425 (define-public r-annotationdbi
7427 (name "r-annotationdbi")
7431 (uri (bioconductor-uri "AnnotationDbi" version))
7434 "0afkbzli08vq02r2pr9phrz3rxd6ilp1w7yw8y99nbjiz14f8b1c"))))
7436 `((upstream-name . "AnnotationDbi")))
7437 (build-system r-build-system)
7439 `(("r-biobase" ,r-biobase)
7440 ("r-biocgenerics" ,r-biocgenerics)
7442 ("r-iranges" ,r-iranges)
7443 ("r-rsqlite" ,r-rsqlite)
7444 ("r-s4vectors" ,r-s4vectors)))
7445 (home-page "https://bioconductor.org/packages/AnnotationDbi")
7446 (synopsis "Annotation database interface")
7448 "This package provides user interface and database connection code for
7449 annotation data packages using SQLite data storage.")
7450 (license license:artistic2.0)))
7452 (define-public r-biomart
7458 (uri (bioconductor-uri "biomaRt" version))
7461 "0b70s350ffc74v3xz5c3jpazr9zxdb7gjmjfj7aghlsrizrspill"))))
7463 `((upstream-name . "biomaRt")))
7464 (build-system r-build-system)
7466 `(("r-annotationdbi" ,r-annotationdbi)
7468 ("r-progress" ,r-progress)
7469 ("r-rcurl" ,r-rcurl)
7470 ("r-stringr" ,r-stringr)
7472 (home-page "https://bioconductor.org/packages/biomaRt")
7473 (synopsis "Interface to BioMart databases")
7475 "biomaRt provides an interface to a growing collection of databases
7476 implementing the @url{BioMart software suite, http://www.biomart.org}. The
7477 package enables retrieval of large amounts of data in a uniform way without
7478 the need to know the underlying database schemas or write complex SQL queries.
7479 Examples of BioMart databases are Ensembl, COSMIC, Uniprot, HGNC, Gramene,
7480 Wormbase and dbSNP mapped to Ensembl. These major databases give biomaRt
7481 users direct access to a diverse set of data and enable a wide range of
7482 powerful online queries from gene annotation to database mining.")
7483 (license license:artistic2.0)))
7485 (define-public r-biocparallel
7487 (name "r-biocparallel")
7491 (uri (bioconductor-uri "BiocParallel" version))
7494 "00qg1kg2l9qqpyjaw5q910cmf84vwfiw1fhsx3ig784gwinwgj6n"))))
7496 `((upstream-name . "BiocParallel")))
7497 (build-system r-build-system)
7499 `(("r-futile-logger" ,r-futile-logger)
7502 (home-page "https://bioconductor.org/packages/BiocParallel")
7503 (synopsis "Bioconductor facilities for parallel evaluation")
7505 "This package provides modified versions and novel implementation of
7506 functions for parallel evaluation, tailored to use with Bioconductor
7508 (license (list license:gpl2+ license:gpl3+))))
7510 (define-public r-biostrings
7512 (name "r-biostrings")
7516 (uri (bioconductor-uri "Biostrings" version))
7519 "118b490jk87ydigm6ln25ms4kskzkw0akmh77clzznhzpqnxsi6j"))))
7521 `((upstream-name . "Biostrings")))
7522 (build-system r-build-system)
7524 `(("r-biocgenerics" ,r-biocgenerics)
7525 ("r-iranges" ,r-iranges)
7526 ("r-s4vectors" ,r-s4vectors)
7527 ("r-xvector" ,r-xvector)))
7528 (home-page "https://bioconductor.org/packages/Biostrings")
7529 (synopsis "String objects and algorithms for biological sequences")
7531 "This package provides memory efficient string containers, string
7532 matching algorithms, and other utilities, for fast manipulation of large
7533 biological sequences or sets of sequences.")
7534 (license license:artistic2.0)))
7536 (define-public r-rsamtools
7538 (name "r-rsamtools")
7542 (uri (bioconductor-uri "Rsamtools" version))
7545 "1s65y5wn4d0x8zsljg2kmhcl6r9884h95kr041j7hp49bmxg3an6"))))
7547 `((upstream-name . "Rsamtools")))
7548 (build-system r-build-system)
7551 (modify-phases %standard-phases
7552 (add-after 'unpack 'use-system-zlib
7554 (substitute* "DESCRIPTION"
7555 (("zlibbioc, ") ""))
7556 (substitute* "NAMESPACE"
7557 (("import\\(zlibbioc\\)") ""))
7562 `(("r-biocgenerics" ,r-biocgenerics)
7563 ("r-biocparallel" ,r-biocparallel)
7564 ("r-biostrings" ,r-biostrings)
7565 ("r-bitops" ,r-bitops)
7566 ("r-genomeinfodb" ,r-genomeinfodb)
7567 ("r-genomicranges" ,r-genomicranges)
7568 ("r-iranges" ,r-iranges)
7569 ("r-s4vectors" ,r-s4vectors)
7570 ("r-xvector" ,r-xvector)))
7571 (home-page "https://bioconductor.org/packages/release/bioc/html/Rsamtools.html")
7572 (synopsis "Interface to samtools, bcftools, and tabix")
7574 "This package provides an interface to the 'samtools', 'bcftools', and
7575 'tabix' utilities for manipulating SAM (Sequence Alignment / Map), FASTA,
7576 binary variant call (BCF) and compressed indexed tab-delimited (tabix)
7578 (license license:expat)))
7580 (define-public r-delayedarray
7582 (name "r-delayedarray")
7586 (uri (bioconductor-uri "DelayedArray" version))
7589 "0n3w57cwy911q812wc8658y0v3xgpmg379sj98kfqdxa80z1mxdf"))))
7591 `((upstream-name . "DelayedArray")))
7592 (build-system r-build-system)
7594 `(("r-biocgenerics" ,r-biocgenerics)
7595 ("r-biocparallel" ,r-biocparallel)
7596 ("r-s4vectors" ,r-s4vectors)
7597 ("r-iranges" ,r-iranges)
7598 ("r-matrixstats" ,r-matrixstats)))
7599 (home-page "https://bioconductor.org/packages/DelayedArray")
7600 (synopsis "Delayed operations on array-like objects")
7602 "Wrapping an array-like object (typically an on-disk object) in a
7603 @code{DelayedArray} object allows one to perform common array operations on it
7604 without loading the object in memory. In order to reduce memory usage and
7605 optimize performance, operations on the object are either delayed or executed
7606 using a block processing mechanism. Note that this also works on in-memory
7607 array-like objects like @code{DataFrame} objects (typically with Rle columns),
7608 @code{Matrix} objects, and ordinary arrays and data frames.")
7609 (license license:artistic2.0)))
7611 (define-public r-summarizedexperiment
7613 (name "r-summarizedexperiment")
7617 (uri (bioconductor-uri "SummarizedExperiment" version))
7620 "0v3zxl9cqsv79ag5cnvzlhvgaz5cr8f4rn7flmwnwpqd508cznl1"))))
7622 `((upstream-name . "SummarizedExperiment")))
7623 (build-system r-build-system)
7625 `(("r-biobase" ,r-biobase)
7626 ("r-biocgenerics" ,r-biocgenerics)
7627 ("r-delayedarray" ,r-delayedarray)
7628 ("r-genomeinfodb" ,r-genomeinfodb)
7629 ("r-genomicranges" ,r-genomicranges)
7630 ("r-iranges" ,r-iranges)
7631 ("r-matrix" ,r-matrix)
7632 ("r-s4vectors" ,r-s4vectors)))
7633 (home-page "https://bioconductor.org/packages/SummarizedExperiment")
7634 (synopsis "Container for representing genomic ranges by sample")
7636 "The SummarizedExperiment container contains one or more assays, each
7637 represented by a matrix-like object of numeric or other mode. The rows
7638 typically represent genomic ranges of interest and the columns represent
7640 (license license:artistic2.0)))
7642 (define-public r-genomicalignments
7644 (name "r-genomicalignments")
7648 (uri (bioconductor-uri "GenomicAlignments" version))
7651 "00pi2cnkkbj2023fg2x2cmglkdalwzy1vr3glsikwz7ix9yylcaw"))))
7653 `((upstream-name . "GenomicAlignments")))
7654 (build-system r-build-system)
7656 `(("r-biocgenerics" ,r-biocgenerics)
7657 ("r-biocparallel" ,r-biocparallel)
7658 ("r-biostrings" ,r-biostrings)
7659 ("r-genomeinfodb" ,r-genomeinfodb)
7660 ("r-genomicranges" ,r-genomicranges)
7661 ("r-iranges" ,r-iranges)
7662 ("r-rsamtools" ,r-rsamtools)
7663 ("r-s4vectors" ,r-s4vectors)
7664 ("r-summarizedexperiment" ,r-summarizedexperiment)))
7665 (home-page "https://bioconductor.org/packages/GenomicAlignments")
7666 (synopsis "Representation and manipulation of short genomic alignments")
7668 "This package provides efficient containers for storing and manipulating
7669 short genomic alignments (typically obtained by aligning short reads to a
7670 reference genome). This includes read counting, computing the coverage,
7671 junction detection, and working with the nucleotide content of the
7673 (license license:artistic2.0)))
7675 (define-public r-rtracklayer
7677 (name "r-rtracklayer")
7681 (uri (bioconductor-uri "rtracklayer" version))
7684 "0kvsjdaypn1jnxbnsxpycildwdyxwnjkigfq8qm8mlyfc4ahdgy3"))))
7685 (build-system r-build-system)
7688 (modify-phases %standard-phases
7689 (add-after 'unpack 'use-system-zlib
7691 (substitute* "DESCRIPTION"
7692 ((" zlibbioc,") ""))
7693 (substitute* "NAMESPACE"
7694 (("import\\(zlibbioc\\)") ""))
7697 `(("pkg-config" ,pkg-config)))
7701 `(("r-biocgenerics" ,r-biocgenerics)
7702 ("r-biostrings" ,r-biostrings)
7703 ("r-genomeinfodb" ,r-genomeinfodb)
7704 ("r-genomicalignments" ,r-genomicalignments)
7705 ("r-genomicranges" ,r-genomicranges)
7706 ("r-iranges" ,r-iranges)
7707 ("r-rcurl" ,r-rcurl)
7708 ("r-rsamtools" ,r-rsamtools)
7709 ("r-s4vectors" ,r-s4vectors)
7711 ("r-xvector" ,r-xvector)))
7712 (home-page "https://bioconductor.org/packages/rtracklayer")
7713 (synopsis "R interface to genome browsers and their annotation tracks")
7715 "rtracklayer is an extensible framework for interacting with multiple
7716 genome browsers (currently UCSC built-in) and manipulating annotation tracks
7717 in various formats (currently GFF, BED, bedGraph, BED15, WIG, BigWig and 2bit
7718 built-in). The user may export/import tracks to/from the supported browsers,
7719 as well as query and modify the browser state, such as the current viewport.")
7720 (license license:artistic2.0)))
7722 (define-public r-genomicfeatures
7724 (name "r-genomicfeatures")
7728 (uri (bioconductor-uri "GenomicFeatures" version))
7731 "1cqcl72q0k5wylw1brn4g4h7xzys1v06piry19cvp0gjcvm5sp7a"))))
7733 `((upstream-name . "GenomicFeatures")))
7734 (build-system r-build-system)
7736 `(("r-annotationdbi" ,r-annotationdbi)
7737 ("r-biobase" ,r-biobase)
7738 ("r-biocgenerics" ,r-biocgenerics)
7739 ("r-biomart" ,r-biomart)
7740 ("r-biostrings" ,r-biostrings)
7742 ("r-genomeinfodb" ,r-genomeinfodb)
7743 ("r-genomicranges" ,r-genomicranges)
7744 ("r-iranges" ,r-iranges)
7745 ("r-rcurl" ,r-rcurl)
7746 ("r-rsqlite" ,r-rsqlite)
7747 ("r-rtracklayer" ,r-rtracklayer)
7748 ("r-s4vectors" ,r-s4vectors)
7749 ("r-xvector" ,r-xvector)))
7750 (home-page "https://bioconductor.org/packages/GenomicFeatures")
7751 (synopsis "Tools for working with transcript centric annotations")
7753 "This package provides a set of tools and methods for making and
7754 manipulating transcript centric annotations. With these tools the user can
7755 easily download the genomic locations of the transcripts, exons and cds of a
7756 given organism, from either the UCSC Genome Browser or a BioMart
7757 database (more sources will be supported in the future). This information is
7758 then stored in a local database that keeps track of the relationship between
7759 transcripts, exons, cds and genes. Flexible methods are provided for
7760 extracting the desired features in a convenient format.")
7761 (license license:artistic2.0)))
7763 (define-public r-go-db
7769 (uri (string-append "https://www.bioconductor.org/packages/"
7770 "release/data/annotation/src/contrib/GO.db_"
7774 "02d1mn1al3q7qvhx1ylrr3ar4w4iw0qyi5d89v2336rzwk9maq35"))))
7776 `((upstream-name . "GO.db")))
7777 (build-system r-build-system)
7779 `(("r-annotationdbi" ,r-annotationdbi)))
7780 (home-page "https://bioconductor.org/packages/GO.db")
7781 (synopsis "Annotation maps describing the entire Gene Ontology")
7783 "The purpose of this GO.db annotation package is to provide detailed
7784 information about the latest version of the Gene Ontologies.")
7785 (license license:artistic2.0)))
7787 (define-public r-graph
7793 (uri (bioconductor-uri "graph" version))
7796 "1zx445lk36g1s6i5dbhhf00nzzazyklfjxxjfax6q8hnhvgm9759"))))
7797 (build-system r-build-system)
7799 `(("r-biocgenerics" ,r-biocgenerics)))
7800 (home-page "https://bioconductor.org/packages/graph")
7801 (synopsis "Handle graph data structures in R")
7803 "This package implements some simple graph handling capabilities for R.")
7804 (license license:artistic2.0)))
7806 (define-public r-topgo
7812 (uri (bioconductor-uri "topGO" version))
7815 "05yxnkid8bgw9lkm90if9fg63djhgvbailfa3qsfqa5c0zjmixw1"))))
7817 `((upstream-name . "topGO")))
7818 (build-system r-build-system)
7820 `(("r-annotationdbi" ,r-annotationdbi)
7822 ("r-biobase" ,r-biobase)
7823 ("r-biocgenerics" ,r-biocgenerics)
7824 ("r-go-db" ,r-go-db)
7825 ("r-graph" ,r-graph)
7826 ("r-lattice" ,r-lattice)
7827 ("r-matrixstats" ,r-matrixstats)
7828 ("r-sparsem" ,r-sparsem)))
7829 (home-page "https://bioconductor.org/packages/topGO")
7830 (synopsis "Enrichment analysis for gene ontology")
7832 "The topGO package provides tools for testing @dfn{gene ontology} (GO)
7833 terms while accounting for the topology of the GO graph. Different test
7834 statistics and different methods for eliminating local similarities and
7835 dependencies between GO terms can be implemented and applied.")
7836 ;; Any version of the LGPL applies.
7837 (license license:lgpl2.1+)))
7839 (define-public r-bsgenome
7845 (uri (bioconductor-uri "BSgenome" version))
7848 "1rk2piqq5dppkd51ln3r872d7ng3rvq98071mnd0xdv2xwnyn5g8"))))
7850 `((upstream-name . "BSgenome")))
7851 (build-system r-build-system)
7853 `(("r-biocgenerics" ,r-biocgenerics)
7854 ("r-biostrings" ,r-biostrings)
7855 ("r-genomeinfodb" ,r-genomeinfodb)
7856 ("r-genomicranges" ,r-genomicranges)
7857 ("r-iranges" ,r-iranges)
7858 ("r-rsamtools" ,r-rsamtools)
7859 ("r-rtracklayer" ,r-rtracklayer)
7860 ("r-s4vectors" ,r-s4vectors)
7861 ("r-xvector" ,r-xvector)))
7862 (home-page "https://bioconductor.org/packages/BSgenome")
7863 (synopsis "Infrastructure for Biostrings-based genome data packages")
7865 "This package provides infrastructure shared by all Biostrings-based
7866 genome data packages and support for efficient SNP representation.")
7867 (license license:artistic2.0)))
7869 (define-public r-bsgenome-hsapiens-1000genomes-hs37d5
7871 (name "r-bsgenome-hsapiens-1000genomes-hs37d5")
7875 ;; We cannot use bioconductor-uri here because this tarball is
7876 ;; located under "data/annotation/" instead of "bioc/".
7877 (uri (string-append "https://www.bioconductor.org/packages/"
7878 "release/data/annotation/src/contrib/"
7879 "BSgenome.Hsapiens.1000genomes.hs37d5_"
7883 "1cg0g5fqmsvwyw2p9hp2yy4ilk21jkbbrnpgqvb5c36ihjwvc7sr"))))
7885 `((upstream-name . "BSgenome.Hsapiens.1000genomes.hs37d5")))
7886 (build-system r-build-system)
7887 ;; As this package provides little more than a very large data file it
7888 ;; doesn't make sense to build substitutes.
7889 (arguments `(#:substitutable? #f))
7891 `(("r-bsgenome" ,r-bsgenome)))
7893 "https://www.bioconductor.org/packages/BSgenome.Hsapiens.1000genomes.hs37d5/")
7894 (synopsis "Full genome sequences for Homo sapiens")
7896 "This package provides full genome sequences for Homo sapiens from
7897 1000genomes phase2 reference genome sequence (hs37d5), based on NCBI GRCh37.")
7898 (license license:artistic2.0)))
7900 (define-public r-impute
7906 (uri (bioconductor-uri "impute" version))
7909 "1d3cpfaqlq2gnb3hsc2yhxwkrnbd7m6ifif32yp0ya0jr5brl4hr"))))
7911 `(("gfortran" ,gfortran)))
7912 (build-system r-build-system)
7913 (home-page "https://bioconductor.org/packages/impute")
7914 (synopsis "Imputation for microarray data")
7916 "This package provides a function to impute missing gene expression
7917 microarray data, using nearest neighbor averaging.")
7918 (license license:gpl2+)))
7920 (define-public r-seqpattern
7922 (name "r-seqpattern")
7926 (uri (bioconductor-uri "seqPattern" version))
7929 "0dw0yldfcf0ibvpqxlpx1ijnjf9lma47w9w22siszzhw09i0wp3w"))))
7931 `((upstream-name . "seqPattern")))
7932 (build-system r-build-system)
7934 `(("r-biostrings" ,r-biostrings)
7935 ("r-genomicranges" ,r-genomicranges)
7936 ("r-iranges" ,r-iranges)
7937 ("r-kernsmooth" ,r-kernsmooth)
7938 ("r-plotrix" ,r-plotrix)))
7939 (home-page "https://bioconductor.org/packages/seqPattern")
7940 (synopsis "Visualising oligonucleotide patterns and motif occurrences")
7942 "This package provides tools to visualize oligonucleotide patterns and
7943 sequence motif occurrences across a large set of sequences centred at a common
7944 reference point and sorted by a user defined feature.")
7945 (license license:gpl3+)))
7947 (define-public r-genomation
7949 (name "r-genomation")
7953 (uri (bioconductor-uri "genomation" version))
7956 "1vdmdyrq0n7pf8cvy2950v7hrcrcbd9zl4fg7dcmyly3iiwdyirp"))))
7957 (build-system r-build-system)
7959 `(("r-biostrings" ,r-biostrings)
7960 ("r-bsgenome" ,r-bsgenome)
7961 ("r-data-table" ,r-data-table)
7962 ("r-genomeinfodb" ,r-genomeinfodb)
7963 ("r-genomicalignments" ,r-genomicalignments)
7964 ("r-genomicranges" ,r-genomicranges)
7965 ("r-ggplot2" ,r-ggplot2)
7966 ("r-gridbase" ,r-gridbase)
7967 ("r-impute" ,r-impute)
7968 ("r-iranges" ,r-iranges)
7969 ("r-matrixstats" ,r-matrixstats)
7970 ("r-plotrix" ,r-plotrix)
7973 ("r-readr" ,r-readr)
7974 ("r-reshape2" ,r-reshape2)
7975 ("r-rsamtools" ,r-rsamtools)
7976 ("r-rtracklayer" ,r-rtracklayer)
7977 ("r-runit" ,r-runit)
7978 ("r-s4vectors" ,r-s4vectors)
7979 ("r-seqpattern" ,r-seqpattern)))
7980 (home-page "http://bioinformatics.mdc-berlin.de/genomation/")
7981 (synopsis "Summary, annotation and visualization of genomic data")
7983 "This package provides a package for summary and annotation of genomic
7984 intervals. Users can visualize and quantify genomic intervals over
7985 pre-defined functional regions, such as promoters, exons, introns, etc. The
7986 genomic intervals represent regions with a defined chromosome position, which
7987 may be associated with a score, such as aligned reads from HT-seq experiments,
7988 TF binding sites, methylation scores, etc. The package can use any tabular
7989 genomic feature data as long as it has minimal information on the locations of
7990 genomic intervals. In addition, it can use BAM or BigWig files as input.")
7991 (license license:artistic2.0)))
7993 (define-public r-genomationdata
7995 (name "r-genomationdata")
7999 ;; We cannot use bioconductor-uri here because this tarball is
8000 ;; located under "data/annotation/" instead of "bioc/".
8001 (uri (string-append "https://bioconductor.org/packages/"
8002 "release/data/experiment/src/contrib/"
8003 "genomationData_" version ".tar.gz"))
8006 "0h7g5x3kyb50qlblz5hc85lfm6n6f5nb68i146way3ggs04sqvla"))))
8007 (build-system r-build-system)
8008 ;; As this package provides little more than large data files, it doesn't
8009 ;; make sense to build substitutes.
8010 (arguments `(#:substitutable? #f))
8012 `(("r-knitr" ,r-knitr)))
8013 (home-page "http://bioinformatics.mdc-berlin.de/genomation/")
8014 (synopsis "Experimental data for use with the genomation package")
8016 "This package contains experimental genetic data for use with the
8017 genomation package. Included are Chip Seq, Methylation and Cage data,
8018 downloaded from Encode.")
8019 (license license:gpl3+)))
8021 (define-public r-org-hs-eg-db
8023 (name "r-org-hs-eg-db")
8027 ;; We cannot use bioconductor-uri here because this tarball is
8028 ;; located under "data/annotation/" instead of "bioc/".
8029 (uri (string-append "https://www.bioconductor.org/packages/"
8030 "release/data/annotation/src/contrib/"
8031 "org.Hs.eg.db_" version ".tar.gz"))
8034 "1v6wa5613cjq59xd7x1qz8lr9nb2abm9abl2cci1khrnrlpla927"))))
8036 `((upstream-name . "org.Hs.eg.db")))
8037 (build-system r-build-system)
8039 `(("r-annotationdbi" ,r-annotationdbi)))
8040 (home-page "https://www.bioconductor.org/packages/org.Hs.eg.db/")
8041 (synopsis "Genome wide annotation for Human")
8043 "This package contains genome-wide annotations for Human, primarily based
8044 on mapping using Entrez Gene identifiers.")
8045 (license license:artistic2.0)))
8047 (define-public r-org-ce-eg-db
8049 (name "r-org-ce-eg-db")
8053 ;; We cannot use bioconductor-uri here because this tarball is
8054 ;; located under "data/annotation/" instead of "bioc/".
8055 (uri (string-append "https://www.bioconductor.org/packages/"
8056 "release/data/annotation/src/contrib/"
8057 "org.Ce.eg.db_" version ".tar.gz"))
8060 "02ggchixlmzywhsbr0h2ms4dravv7m5964cjxqcjxqs16vjwlbk9"))))
8062 `((upstream-name . "org.Ce.eg.db")))
8063 (build-system r-build-system)
8065 `(("r-annotationdbi" ,r-annotationdbi)))
8066 (home-page "https://www.bioconductor.org/packages/org.Ce.eg.db/")
8067 (synopsis "Genome wide annotation for Worm")
8069 "This package provides mappings from Entrez gene identifiers to various
8070 annotations for the genome of the model worm Caenorhabditis elegans.")
8071 (license license:artistic2.0)))
8073 (define-public r-org-dm-eg-db
8075 (name "r-org-dm-eg-db")
8079 ;; We cannot use bioconductor-uri here because this tarball is
8080 ;; located under "data/annotation/" instead of "bioc/".
8081 (uri (string-append "https://www.bioconductor.org/packages/"
8082 "release/data/annotation/src/contrib/"
8083 "org.Dm.eg.db_" version ".tar.gz"))
8086 "033qak1d3wwz17va0bh8z8p8arx0aw2va6gm1qfwsvdkj9cd9d7d"))))
8088 `((upstream-name . "org.Dm.eg.db")))
8089 (build-system r-build-system)
8091 `(("r-annotationdbi" ,r-annotationdbi)))
8092 (home-page "https://www.bioconductor.org/packages/org.Dm.eg.db/")
8093 (synopsis "Genome wide annotation for Fly")
8095 "This package provides mappings from Entrez gene identifiers to various
8096 annotations for the genome of the model fruit fly Drosophila melanogaster.")
8097 (license license:artistic2.0)))
8099 (define-public r-org-mm-eg-db
8101 (name "r-org-mm-eg-db")
8105 ;; We cannot use bioconductor-uri here because this tarball is
8106 ;; located under "data/annotation/" instead of "bioc/".
8107 (uri (string-append "https://www.bioconductor.org/packages/"
8108 "release/data/annotation/src/contrib/"
8109 "org.Mm.eg.db_" version ".tar.gz"))
8112 "11q21p3ki4bn4hb3aix0g775l45l66jmas6m94nfhqqnpjhv4d6g"))))
8114 `((upstream-name . "org.Mm.eg.db")))
8115 (build-system r-build-system)
8117 `(("r-annotationdbi" ,r-annotationdbi)))
8118 (home-page "https://www.bioconductor.org/packages/org.Mm.eg.db/")
8119 (synopsis "Genome wide annotation for Mouse")
8121 "This package provides mappings from Entrez gene identifiers to various
8122 annotations for the genome of the model mouse Mus musculus.")
8123 (license license:artistic2.0)))
8125 (define-public r-seqlogo
8132 (uri (bioconductor-uri "seqLogo" version))
8135 "16xvqcdknix9vjm8mrixi6nyfsr45jm844jh1x90m8044lwrsic1"))))
8136 (properties `((upstream-name . "seqLogo")))
8137 (build-system r-build-system)
8138 (home-page "https://bioconductor.org/packages/seqLogo")
8139 (synopsis "Sequence logos for DNA sequence alignments")
8141 "seqLogo takes the position weight matrix of a DNA sequence motif and
8142 plots the corresponding sequence logo as introduced by Schneider and
8144 (license license:lgpl2.0+)))
8146 (define-public r-bsgenome-hsapiens-ucsc-hg19
8148 (name "r-bsgenome-hsapiens-ucsc-hg19")
8152 ;; We cannot use bioconductor-uri here because this tarball is
8153 ;; located under "data/annotation/" instead of "bioc/".
8154 (uri (string-append "https://www.bioconductor.org/packages/"
8155 "release/data/annotation/src/contrib/"
8156 "BSgenome.Hsapiens.UCSC.hg19_"
8160 "1y0nqpk8cw5a34sd9hmin3z4v7iqm6hf6l22cl81vlbxqbjibxc8"))))
8162 `((upstream-name . "BSgenome.Hsapiens.UCSC.hg19")))
8163 (build-system r-build-system)
8164 ;; As this package provides little more than a very large data file it
8165 ;; doesn't make sense to build substitutes.
8166 (arguments `(#:substitutable? #f))
8168 `(("r-bsgenome" ,r-bsgenome)))
8170 "https://www.bioconductor.org/packages/BSgenome.Hsapiens.UCSC.hg19/")
8171 (synopsis "Full genome sequences for Homo sapiens")
8173 "This package provides full genome sequences for Homo sapiens as provided
8174 by UCSC (hg19, February 2009) and stored in Biostrings objects.")
8175 (license license:artistic2.0)))
8177 (define-public r-bsgenome-mmusculus-ucsc-mm9
8179 (name "r-bsgenome-mmusculus-ucsc-mm9")
8183 ;; We cannot use bioconductor-uri here because this tarball is
8184 ;; located under "data/annotation/" instead of "bioc/".
8185 (uri (string-append "https://www.bioconductor.org/packages/"
8186 "release/data/annotation/src/contrib/"
8187 "BSgenome.Mmusculus.UCSC.mm9_"
8191 "1birqw30g2azimxpnjfzmkphan7x131yy8b9h85lfz5fjdg7841i"))))
8193 `((upstream-name . "BSgenome.Mmusculus.UCSC.mm9")))
8194 (build-system r-build-system)
8195 ;; As this package provides little more than a very large data file it
8196 ;; doesn't make sense to build substitutes.
8197 (arguments `(#:substitutable? #f))
8199 `(("r-bsgenome" ,r-bsgenome)))
8201 "https://www.bioconductor.org/packages/BSgenome.Mmusculus.UCSC.mm9/")
8202 (synopsis "Full genome sequences for Mouse")
8204 "This package provides full genome sequences for Mus musculus (Mouse) as
8205 provided by UCSC (mm9, July 2007) and stored in Biostrings objects.")
8206 (license license:artistic2.0)))
8208 (define-public r-bsgenome-mmusculus-ucsc-mm10
8210 (name "r-bsgenome-mmusculus-ucsc-mm10")
8214 ;; We cannot use bioconductor-uri here because this tarball is
8215 ;; located under "data/annotation/" instead of "bioc/".
8216 (uri (string-append "https://www.bioconductor.org/packages/"
8217 "release/data/annotation/src/contrib/"
8218 "BSgenome.Mmusculus.UCSC.mm10_"
8222 "12s0nm2na9brjad4rn9l7d3db2aj8qa1xvz0y1k7gk08wayb6bkf"))))
8224 `((upstream-name . "BSgenome.Mmusculus.UCSC.mm10")))
8225 (build-system r-build-system)
8226 ;; As this package provides little more than a very large data file it
8227 ;; doesn't make sense to build substitutes.
8228 (arguments `(#:substitutable? #f))
8230 `(("r-bsgenome" ,r-bsgenome)))
8232 "https://www.bioconductor.org/packages/BSgenome.Mmusculus.UCSC.mm10/")
8233 (synopsis "Full genome sequences for Mouse")
8235 "This package provides full genome sequences for Mus
8236 musculus (Mouse) as provided by UCSC (mm10, December 2011) and stored
8237 in Biostrings objects.")
8238 (license license:artistic2.0)))
8240 (define-public r-txdb-mmusculus-ucsc-mm10-knowngene
8242 (name "r-txdb-mmusculus-ucsc-mm10-knowngene")
8246 ;; We cannot use bioconductor-uri here because this tarball is
8247 ;; located under "data/annotation/" instead of "bioc/".
8248 (uri (string-append "https://www.bioconductor.org/packages/"
8249 "release/data/annotation/src/contrib/"
8250 "TxDb.Mmusculus.UCSC.mm10.knownGene_"
8254 "08gava9wsvpcqz51k2sni3pj03n5155v32d9riqbf305nbirqbkb"))))
8256 `((upstream-name . "TxDb.Mmusculus.UCSC.mm10.knownGene")))
8257 (build-system r-build-system)
8258 ;; As this package provides little more than a very large data file it
8259 ;; doesn't make sense to build substitutes.
8260 (arguments `(#:substitutable? #f))
8262 `(("r-bsgenome" ,r-bsgenome)
8263 ("r-genomicfeatures" ,r-genomicfeatures)
8264 ("r-annotationdbi" ,r-annotationdbi)))
8266 "https://bioconductor.org/packages/TxDb.Mmusculus.UCSC.mm10.knownGene/")
8267 (synopsis "Annotation package for TxDb knownGene object(s) for Mouse")
8269 "This package loads a TxDb object, which is an R interface to
8270 prefabricated databases contained in this package. This package provides
8271 the TxDb object of Mouse data as provided by UCSC (mm10, December 2011)
8272 based on the knownGene track.")
8273 (license license:artistic2.0)))
8275 (define-public r-bsgenome-celegans-ucsc-ce6
8277 (name "r-bsgenome-celegans-ucsc-ce6")
8281 ;; We cannot use bioconductor-uri here because this tarball is
8282 ;; located under "data/annotation/" instead of "bioc/".
8283 (uri (string-append "https://www.bioconductor.org/packages/"
8284 "release/data/annotation/src/contrib/"
8285 "BSgenome.Celegans.UCSC.ce6_"
8289 "0mqzb353xv2c3m3vkb315dkmnxkgczp7ndnknyhpgjlybyf715v9"))))
8291 `((upstream-name . "BSgenome.Celegans.UCSC.ce6")))
8292 (build-system r-build-system)
8293 ;; As this package provides little more than a very large data file it
8294 ;; doesn't make sense to build substitutes.
8295 (arguments `(#:substitutable? #f))
8297 `(("r-bsgenome" ,r-bsgenome)))
8299 "https://www.bioconductor.org/packages/BSgenome.Celegans.UCSC.ce6/")
8300 (synopsis "Full genome sequences for Worm")
8302 "This package provides full genome sequences for Caenorhabditis
8303 elegans (Worm) as provided by UCSC (ce6, May 2008) and stored in Biostrings
8305 (license license:artistic2.0)))
8307 (define-public r-bsgenome-celegans-ucsc-ce10
8309 (name "r-bsgenome-celegans-ucsc-ce10")
8313 ;; We cannot use bioconductor-uri here because this tarball is
8314 ;; located under "data/annotation/" instead of "bioc/".
8315 (uri (string-append "https://www.bioconductor.org/packages/"
8316 "release/data/annotation/src/contrib/"
8317 "BSgenome.Celegans.UCSC.ce10_"
8321 "1zaym97jk4npxk14ifvwz2rvhm4zx9xgs33r9vvx9rlynp0gydrk"))))
8323 `((upstream-name . "BSgenome.Celegans.UCSC.ce10")))
8324 (build-system r-build-system)
8325 ;; As this package provides little more than a very large data file it
8326 ;; doesn't make sense to build substitutes.
8327 (arguments `(#:substitutable? #f))
8329 `(("r-bsgenome" ,r-bsgenome)))
8331 "https://www.bioconductor.org/packages/BSgenome.Celegans.UCSC.ce10/")
8332 (synopsis "Full genome sequences for Worm")
8334 "This package provides full genome sequences for Caenorhabditis
8335 elegans (Worm) as provided by UCSC (ce10, Oct 2010) and stored in Biostrings
8337 (license license:artistic2.0)))
8339 (define-public r-bsgenome-dmelanogaster-ucsc-dm3
8341 (name "r-bsgenome-dmelanogaster-ucsc-dm3")
8345 ;; We cannot use bioconductor-uri here because this tarball is
8346 ;; located under "data/annotation/" instead of "bioc/".
8347 (uri (string-append "https://www.bioconductor.org/packages/"
8348 "release/data/annotation/src/contrib/"
8349 "BSgenome.Dmelanogaster.UCSC.dm3_"
8353 "19bm3lkhhkag3gnwp419211fh0cnr0x6fa0r1lr0ycwrikxdxsv8"))))
8355 `((upstream-name . "BSgenome.Dmelanogaster.UCSC.dm3")))
8356 (build-system r-build-system)
8357 ;; As this package provides little more than a very large data file it
8358 ;; doesn't make sense to build substitutes.
8359 (arguments `(#:substitutable? #f))
8361 `(("r-bsgenome" ,r-bsgenome)))
8363 "https://www.bioconductor.org/packages/BSgenome.Dmelanogaster.UCSC.dm3/")
8364 (synopsis "Full genome sequences for Fly")
8366 "This package provides full genome sequences for Drosophila
8367 melanogaster (Fly) as provided by UCSC (dm3, April 2006) and stored in
8368 Biostrings objects.")
8369 (license license:artistic2.0)))
8371 (define-public r-motifrg
8378 (uri (bioconductor-uri "motifRG" version))
8381 "0mxhyidkyd2zqahdbg69y20r550z78lvr1r3pbjymnwfg4hcfq1p"))))
8382 (properties `((upstream-name . "motifRG")))
8383 (build-system r-build-system)
8385 `(("r-biostrings" ,r-biostrings)
8386 ("r-bsgenome" ,r-bsgenome)
8387 ("r-bsgenome-hsapiens-ucsc-hg19" ,r-bsgenome-hsapiens-ucsc-hg19)
8388 ("r-iranges" ,r-iranges)
8389 ("r-seqlogo" ,r-seqlogo)
8390 ("r-xvector" ,r-xvector)))
8391 (home-page "https://bioconductor.org/packages/motifRG")
8392 (synopsis "Discover motifs in high throughput sequencing data")
8394 "This package provides tools for discriminative motif discovery in high
8395 throughput genetic sequencing data sets using regression methods.")
8396 (license license:artistic2.0)))
8398 (define-public r-qtl
8405 (uri (string-append "mirror://cran/src/contrib/qtl_"
8409 "1l528dwvfpdlr05imrrm4rq32axp6hld9nqm6mm43kn5n7z2f5k6"))))
8410 (build-system r-build-system)
8411 (home-page "http://rqtl.org/")
8412 (synopsis "R package for analyzing QTL experiments in genetics")
8413 (description "R/qtl is an extension library for the R statistics
8414 system. It is used to analyze experimental crosses for identifying
8415 genes contributing to variation in quantitative traits (so-called
8416 quantitative trait loci, QTLs).
8418 Using a hidden Markov model, R/qtl allows to estimate genetic maps, to
8419 identify genotyping errors, and to perform single-QTL and two-QTL,
8420 two-dimensional genome scans.")
8421 (license license:gpl3)))
8423 (define-public r-zlibbioc
8429 (uri (bioconductor-uri "zlibbioc" version))
8432 "1rwr0mci8a712q0isavi4jmhm94gwivc4nr8j7r4kw05flp4g7gz"))))
8434 `((upstream-name . "zlibbioc")))
8435 (build-system r-build-system)
8436 (home-page "https://bioconductor.org/packages/zlibbioc")
8437 (synopsis "Provider for zlib-1.2.5 to R packages")
8438 (description "This package uses the source code of zlib-1.2.5 to create
8439 libraries for systems that do not have these available via other means.")
8440 (license license:artistic2.0)))
8442 (define-public r-r4rna
8449 (uri (string-append "http://www.e-rna.org/r-chie/files/R4RNA_"
8453 "1p0i78wh76jfgmn9jphbwwaz6yy6pipzfg08xs54cxavxg2j81p5"))))
8454 (build-system r-build-system)
8456 `(("r-optparse" ,r-optparse)
8457 ("r-rcolorbrewer" ,r-rcolorbrewer)))
8458 (home-page "http://www.e-rna.org/r-chie/index.cgi")
8459 (synopsis "Analysis framework for RNA secondary structure")
8461 "The R4RNA package aims to be a general framework for the analysis of RNA
8462 secondary structure and comparative analysis in R.")
8463 (license license:gpl3+)))
8465 (define-public r-rhtslib
8472 (uri (bioconductor-uri "Rhtslib" version))
8475 "16ywnb8cmr2xabd1i21b92rfziw7xfbv25yv16ipw617p41wa39z"))))
8476 (properties `((upstream-name . "Rhtslib")))
8477 (build-system r-build-system)
8479 `(("r-zlibbioc" ,r-zlibbioc)))
8483 `(("pkg-config" ,pkg-config)))
8484 (home-page "https://github.com/nhayden/Rhtslib")
8485 (synopsis "High-throughput sequencing library as an R package")
8487 "This package provides the HTSlib C library for high-throughput
8488 nucleotide sequence analysis. The package is primarily useful to developers
8489 of other R packages who wish to make use of HTSlib.")
8490 (license license:lgpl2.0+)))
8492 (define-public r-bamsignals
8494 (name "r-bamsignals")
8499 (uri (bioconductor-uri "bamsignals" version))
8502 "141q3p4lzwiqk1mfxi8q1q84axjl0gyiqg59xd3sp4viny4jqmgv"))))
8503 (build-system r-build-system)
8505 `(("r-biocgenerics" ,r-biocgenerics)
8506 ("r-genomicranges" ,r-genomicranges)
8507 ("r-iranges" ,r-iranges)
8509 ("r-rhtslib" ,r-rhtslib)
8510 ("r-zlibbioc" ,r-zlibbioc)))
8513 (home-page "https://bioconductor.org/packages/bamsignals")
8514 (synopsis "Extract read count signals from bam files")
8516 "This package allows to efficiently obtain count vectors from indexed bam
8517 files. It counts the number of nucleotide sequence reads in given genomic
8518 ranges and it computes reads profiles and coverage profiles. It also handles
8520 (license license:gpl2+)))
8522 (define-public r-rcas
8528 (uri (string-append "https://github.com/BIMSBbioinfo/RCAS/archive/v"
8530 (file-name (string-append name "-" version ".tar.gz"))
8533 "1qgc7vi6fpzl440yg7jhiycg5q336kd4pxqzx10yx2zcq3bq3msg"))))
8534 (build-system r-build-system)
8536 `(("r-knitr" ,r-knitr)
8537 ("r-testthat" ,r-testthat)
8538 ;; During vignette building knitr checks that "pandoc-citeproc"
8540 ("ghc-pandoc-citeproc" ,ghc-pandoc-citeproc-with-pandoc-1)))
8542 `(("r-data-table" ,r-data-table)
8543 ("r-biomart" ,r-biomart)
8544 ("r-org-hs-eg-db" ,r-org-hs-eg-db)
8545 ("r-org-ce-eg-db" ,r-org-ce-eg-db)
8546 ("r-org-dm-eg-db" ,r-org-dm-eg-db)
8547 ("r-org-mm-eg-db" ,r-org-mm-eg-db)
8548 ("r-bsgenome-hsapiens-ucsc-hg19" ,r-bsgenome-hsapiens-ucsc-hg19)
8549 ("r-bsgenome-mmusculus-ucsc-mm9" ,r-bsgenome-mmusculus-ucsc-mm9)
8550 ("r-bsgenome-celegans-ucsc-ce10" ,r-bsgenome-celegans-ucsc-ce10)
8551 ("r-bsgenome-dmelanogaster-ucsc-dm3" ,r-bsgenome-dmelanogaster-ucsc-dm3)
8552 ("r-topgo" ,r-topgo)
8554 ("r-pbapply" ,r-pbapply)
8555 ("r-plotly" ,r-plotly)
8556 ("r-plotrix" ,r-plotrix)
8557 ("r-motifrg" ,r-motifrg)
8558 ("r-genomation" ,r-genomation)
8559 ("r-genomicfeatures" ,r-genomicfeatures)
8560 ("r-rtracklayer" ,r-rtracklayer)
8561 ("r-rmarkdown" ,r-rmarkdown)))
8562 (synopsis "RNA-centric annotation system")
8564 "RCAS aims to be a standalone RNA-centric annotation system that provides
8565 intuitive reports and publication-ready graphics. This package provides the R
8566 library implementing most of the pipeline's features.")
8567 (home-page "https://github.com/BIMSBbioinfo/RCAS")
8568 (license license:artistic2.0)))
8570 (define-public rcas-web
8577 (uri (string-append "https://github.com/BIMSBbioinfo/rcas-web/"
8578 "releases/download/v" version
8579 "/rcas-web-" version ".tar.gz"))
8582 "1p16frfys41a8yaa4gkm457nzkqhqs2pc3lkac0ds457w9w5j1gm"))))
8583 (build-system gnu-build-system)
8586 (modify-phases %standard-phases
8587 (add-after 'install 'wrap-executable
8588 (lambda* (#:key inputs outputs #:allow-other-keys)
8589 (let* ((out (assoc-ref outputs "out"))
8590 (json (assoc-ref inputs "guile-json"))
8591 (redis (assoc-ref inputs "guile-redis"))
8592 (path (string-append
8593 json "/share/guile/site/2.2:"
8594 redis "/share/guile/site/2.2")))
8595 (wrap-program (string-append out "/bin/rcas-web")
8596 `("GUILE_LOAD_PATH" ":" = (,path))
8597 `("GUILE_LOAD_COMPILED_PATH" ":" = (,path))
8598 `("R_LIBS_SITE" ":" = (,(getenv "R_LIBS_SITE")))))
8601 `(("r-minimal" ,r-minimal)
8603 ("guile-next" ,guile-2.2)
8604 ("guile-json" ,guile-json)
8605 ("guile-redis" ,guile2.2-redis)))
8607 `(("pkg-config" ,pkg-config)))
8608 (home-page "https://github.com/BIMSBbioinfo/rcas-web")
8609 (synopsis "Web interface for RNA-centric annotation system (RCAS)")
8610 (description "This package provides a simple web interface for the
8611 @dfn{RNA-centric annotation system} (RCAS).")
8612 (license license:agpl3+)))
8614 (define-public r-mutationalpatterns
8616 (name "r-mutationalpatterns")
8621 (uri (bioconductor-uri "MutationalPatterns" version))
8624 "1yq7351j42mjxn8fd3c5bdxzb2l5s4lvqhjdvv4rwj4f600n6wj9"))))
8625 (build-system r-build-system)
8627 `(("r-biocgenerics" ,r-biocgenerics)
8628 ("r-biostrings" ,r-biostrings)
8629 ;; These two packages are suggested packages
8630 ("r-bsgenome-hsapiens-1000g" ,r-bsgenome-hsapiens-1000genomes-hs37d5)
8631 ("r-bsgenome-hsapiens-ucsc-hg19" ,r-bsgenome-hsapiens-ucsc-hg19)
8632 ("r-genomicranges" ,r-genomicranges)
8633 ("r-genomeinfodb" ,r-genomeinfodb)
8634 ("r-ggplot2" ,r-ggplot2)
8635 ("r-iranges" ,r-iranges)
8638 ("r-pracma" ,r-pracma)
8639 ("r-reshape2" ,r-reshape2)
8640 ("r-cowplot" ,r-cowplot)
8641 ("r-ggdendro" ,r-ggdendro)
8642 ("r-s4vectors" ,r-s4vectors)
8643 ("r-summarizedexperiment" ,r-summarizedexperiment)
8644 ("r-variantannotation" ,r-variantannotation)))
8645 (home-page "https://bioconductor.org/packages/MutationalPatterns/")
8646 (synopsis "Extract and visualize mutational patterns in genomic data")
8647 (description "This package provides an extensive toolset for the
8648 characterization and visualization of a wide range of mutational patterns
8649 in SNV base substitution data.")
8650 (license license:expat)))
8652 (define-public r-wgcna
8659 (uri (cran-uri "WGCNA" version))
8662 "1225dqm68bynkmklnsxdqdd3zqrpzbvqwyly8ibxmk75z33xz309"))))
8663 (properties `((upstream-name . "WGCNA")))
8664 (build-system r-build-system)
8666 `(("r-annotationdbi" ,r-annotationdbi)
8667 ("r-doparallel" ,r-doparallel)
8668 ("r-dynamictreecut" ,r-dynamictreecut)
8669 ("r-fastcluster" ,r-fastcluster)
8670 ("r-foreach" ,r-foreach)
8671 ("r-go-db" ,r-go-db)
8672 ("r-hmisc" ,r-hmisc)
8673 ("r-impute" ,r-impute)
8675 ("r-robust" ,r-robust)
8676 ("r-survival" ,r-survival)
8677 ("r-matrixstats" ,r-matrixstats)
8678 ("r-preprocesscore" ,r-preprocesscore)))
8680 "http://www.genetics.ucla.edu/labs/horvath/CoexpressionNetwork/Rpackages/WGCNA/")
8681 (synopsis "Weighted correlation network analysis")
8683 "This package provides functions necessary to perform Weighted
8684 Correlation Network Analysis on high-dimensional data. It includes functions
8685 for rudimentary data cleaning, construction and summarization of correlation
8686 networks, module identification and functions for relating both variables and
8687 modules to sample traits. It also includes a number of utility functions for
8688 data manipulation and visualization.")
8689 (license license:gpl2+)))
8691 (define-public r-chipkernels
8692 (let ((commit "c9cfcacb626b1221094fb3490ea7bac0fd625372")
8695 (name "r-chipkernels")
8696 (version (string-append "1.1-" revision "." (string-take commit 9)))
8701 (url "https://github.com/ManuSetty/ChIPKernels.git")
8703 (file-name (string-append name "-" version))
8706 "14bj5qhjm1hsm9ay561nfbqi9wxsa7y487df2idsaaf6z10nw4v0"))))
8707 (build-system r-build-system)
8709 `(("r-iranges" ,r-iranges)
8710 ("r-xvector" ,r-xvector)
8711 ("r-biostrings" ,r-biostrings)
8712 ("r-bsgenome" ,r-bsgenome)
8713 ("r-gtools" ,r-gtools)
8714 ("r-genomicranges" ,r-genomicranges)
8715 ("r-sfsmisc" ,r-sfsmisc)
8716 ("r-kernlab" ,r-kernlab)
8717 ("r-s4vectors" ,r-s4vectors)
8718 ("r-biocgenerics" ,r-biocgenerics)))
8719 (home-page "https://github.com/ManuSetty/ChIPKernels")
8720 (synopsis "Build string kernels for DNA Sequence analysis")
8721 (description "ChIPKernels is an R package for building different string
8722 kernels used for DNA Sequence analysis. A dictionary of the desired kernel
8723 must be built and this dictionary can be used for determining kernels for DNA
8725 (license license:gpl2+))))
8727 (define-public r-seqgl
8734 (uri (string-append "https://github.com/ManuSetty/SeqGL/"
8735 "archive/" version ".tar.gz"))
8736 (file-name (string-append name "-" version ".tar.gz"))
8739 "0pnk1p3sci5yipyc8xnb6jbmydpl80fld927xgnbcv104hy8h8yh"))))
8740 (build-system r-build-system)
8742 `(("r-biostrings" ,r-biostrings)
8743 ("r-chipkernels" ,r-chipkernels)
8744 ("r-genomicranges" ,r-genomicranges)
8745 ("r-spams" ,r-spams)
8746 ("r-wgcna" ,r-wgcna)
8747 ("r-fastcluster" ,r-fastcluster)))
8748 (home-page "https://github.com/ManuSetty/SeqGL")
8749 (synopsis "Group lasso for Dnase/ChIP-seq data")
8750 (description "SeqGL is a group lasso based algorithm to extract
8751 transcription factor sequence signals from ChIP, DNase and ATAC-seq profiles.
8752 This package presents a method which uses group lasso to discriminate between
8753 bound and non bound genomic regions to accurately identify transcription
8754 factors bound at the specific regions.")
8755 (license license:gpl2+)))
8757 (define-public r-gkmsvm
8764 (uri (cran-uri "gkmSVM" version))
8767 "04dakbgfvfalz4rm4fvvybp506dn5fbj5g86ybfhrc6wywjllsz3"))))
8768 (properties `((upstream-name . "gkmSVM")))
8769 (build-system r-build-system)
8771 `(("r-biocgenerics" ,r-biocgenerics)
8772 ("r-biostrings" ,r-biostrings)
8773 ("r-genomeinfodb" ,r-genomeinfodb)
8774 ("r-genomicranges" ,r-genomicranges)
8775 ("r-iranges" ,r-iranges)
8776 ("r-kernlab" ,r-kernlab)
8779 ("r-rtracklayer" ,r-rtracklayer)
8780 ("r-s4vectors" ,r-s4vectors)
8781 ("r-seqinr" ,r-seqinr)))
8782 (home-page "https://cran.r-project.org/web/packages/gkmSVM")
8783 (synopsis "Gapped-kmer support vector machine")
8785 "This R package provides tools for training gapped-kmer SVM classifiers
8786 for DNA and protein sequences. This package supports several sequence
8787 kernels, including: gkmSVM, kmer-SVM, mismatch kernel and wildcard kernel.")
8788 (license license:gpl2+)))
8790 (define-public r-tximport
8796 (uri (bioconductor-uri "tximport" version))
8799 "1qjc7ah9dzccpvcjrp9k4qnaz13x6kvy1c1xpdj503km6k528lip"))))
8800 (build-system r-build-system)
8801 (home-page "https://bioconductor.org/packages/tximport")
8802 (synopsis "Import and summarize transcript-level estimates for gene-level analysis")
8804 "This package provides tools to import transcript-level abundance,
8805 estimated counts and transcript lengths, and to summarize them into matrices
8806 for use with downstream gene-level analysis packages. Average transcript
8807 length, weighted by sample-specific transcript abundance estimates, is
8808 provided as a matrix which can be used as an offset for different expression
8809 of gene-level counts.")
8810 (license license:gpl2+)))
8812 (define-public r-rhdf5
8818 (uri (bioconductor-uri "rhdf5" version))
8821 "15cmmchhk8bnp94gxg0zk9qyzdjx5kv16dzpbnb62mkq7ydmifx6"))))
8822 (build-system r-build-system)
8824 `(("r-rhdf5lib" ,r-rhdf5lib)))
8827 (home-page "https://bioconductor.org/packages/rhdf5")
8828 (synopsis "HDF5 interface to R")
8830 "This R/Bioconductor package provides an interface between HDF5 and R.
8831 HDF5's main features are the ability to store and access very large and/or
8832 complex datasets and a wide variety of metadata on mass storage (disk) through
8833 a completely portable file format. The rhdf5 package is thus suited for the
8834 exchange of large and/or complex datasets between R and other software
8835 package, and for letting R applications work on datasets that are larger than
8836 the available RAM.")
8837 (license license:artistic2.0)))
8839 (define-public r-annotationfilter
8841 (name "r-annotationfilter")
8845 (uri (bioconductor-uri "AnnotationFilter" version))
8848 "1w8ypfdz4g7vnwfrvnhjcpm8waciqyq2cn883ajdwg4vv7a5mj9a"))))
8850 `((upstream-name . "AnnotationFilter")))
8851 (build-system r-build-system)
8853 `(("r-genomicranges" ,r-genomicranges)
8854 ("r-lazyeval" ,r-lazyeval)))
8855 (home-page "https://github.com/Bioconductor/AnnotationFilter")
8856 (synopsis "Facilities for filtering Bioconductor annotation resources")
8858 "This package provides classes and other infrastructure to implement
8859 filters for manipulating Bioconductor annotation resources. The filters are
8860 used by @code{ensembldb}, @code{Organism.dplyr}, and other packages.")
8861 (license license:artistic2.0)))
8863 (define-public emboss
8869 (uri (string-append "ftp://emboss.open-bio.org/pub/EMBOSS/old/"
8870 (version-major+minor version) ".0/"
8871 "EMBOSS-" version ".tar.gz"))
8874 "0vsmz96gc411yj2iyzdrsmg4l2n1nhgmp7vrgzlxx3xixv9xbf0q"))))
8875 (build-system gnu-build-system)
8878 (list (string-append "--with-hpdf="
8879 (assoc-ref %build-inputs "libharu")))
8881 (modify-phases %standard-phases
8882 (add-after 'unpack 'fix-checks
8884 ;; The PNGDRIVER tests check for the presence of libgd, libpng
8885 ;; and zlib, but assume that they are all found at the same
8887 (substitute* "configure.in"
8888 (("CHECK_PNGDRIVER")
8889 "LIBS=\"$LIBS -lgd -lpng -lz -lm\"
8890 AC_DEFINE([PLD_png], [1], [Define to 1 if PNG support is available])
8891 AM_CONDITIONAL(AMPNG, true)"))
8893 (add-after 'fix-checks 'disable-update-check
8895 ;; At build time there is no connection to the Internet, so
8896 ;; looking for updates will not work.
8897 (substitute* "Makefile.am"
8898 (("\\$\\(bindir\\)/embossupdate") ""))
8900 (add-after 'disable-update-check 'autogen
8901 (lambda _ (zero? (system* "autoreconf" "-vif")))))))
8907 ("libharu" ,libharu)
8910 `(("autoconf" ,autoconf)
8911 ("automake" ,automake)
8912 ("libtool" ,libtool)
8913 ("pkg-config" ,pkg-config)))
8914 (home-page "http://emboss.sourceforge.net")
8915 (synopsis "Molecular biology analysis suite")
8916 (description "EMBOSS is the \"European Molecular Biology Open Software
8917 Suite\". EMBOSS is an analysis package specially developed for the needs of
8918 the molecular biology (e.g. EMBnet) user community. The software
8919 automatically copes with data in a variety of formats and even allows
8920 transparent retrieval of sequence data from the web. It also provides a
8921 number of libraries for the development of software in the field of molecular
8922 biology. EMBOSS also integrates a range of currently available packages and
8923 tools for sequence analysis into a seamless whole.")
8924 (license license:gpl2+)))
8927 (let ((revision "1")
8928 (commit "3cc4567896d9d6442923da944beb704750a08d2d"))
8931 ;; The version is 2.13.0 even though no release archives have been
8932 ;; published as yet.
8933 (version (string-append "2.13.0-" revision "." (string-take commit 9)))
8937 (url "https://github.com/arq5x/bits.git")
8939 (file-name (string-append name "-" version "-checkout"))
8942 "17n2kffk4kmhivd8c98g2vr6y1s23vbg4sxlxs689wni66797hbs"))))
8943 (build-system gnu-build-system)
8945 `(#:tests? #f ;no tests included
8947 (modify-phases %standard-phases
8949 (add-after 'unpack 'remove-cuda
8951 (substitute* "Makefile"
8953 (("(bits_test_intersections) \\\\" _ match) match))
8956 (lambda* (#:key outputs #:allow-other-keys)
8958 "bin" (string-append (assoc-ref outputs "out") "/bin"))
8963 (home-page "https://github.com/arq5x/bits")
8964 (synopsis "Implementation of binary interval search algorithm")
8965 (description "This package provides an implementation of the
8966 BITS (Binary Interval Search) algorithm, an approach to interval set
8967 intersection. It is especially suited for the comparison of diverse genomic
8968 datasets and the exploration of large datasets of genome
8969 intervals (e.g. genes, sequence alignments).")
8970 (license license:gpl2))))
8972 (define-public piranha
8973 ;; There is no release tarball for the latest version. The latest commit is
8974 ;; older than one year at the time of this writing.
8975 (let ((revision "1")
8976 (commit "0466d364b71117d01e4471b74c514436cc281233"))
8979 (version (string-append "1.2.1-" revision "." (string-take commit 9)))
8983 (url "https://github.com/smithlabcode/piranha.git")
8985 (file-name (git-file-name name version))
8988 "117dc0zf20c61jam69sk4abl57ah6yi6i7qra7d7y5zrbgk12q5n"))))
8989 (build-system gnu-build-system)
8991 `(#:test-target "test"
8993 (modify-phases %standard-phases
8994 (add-after 'unpack 'copy-smithlab-cpp
8995 (lambda* (#:key inputs #:allow-other-keys)
8996 (for-each (lambda (file)
8997 (install-file file "./src/smithlab_cpp/"))
8998 (find-files (assoc-ref inputs "smithlab-cpp")))
9000 (add-after 'install 'install-to-store
9001 (lambda* (#:key outputs #:allow-other-keys)
9002 (let* ((out (assoc-ref outputs "out"))
9003 (bin (string-append out "/bin")))
9004 (for-each (lambda (file)
9005 (install-file file bin))
9006 (find-files "bin" ".*")))
9009 (list (string-append "--with-bam_tools_headers="
9010 (assoc-ref %build-inputs "bamtools") "/include/bamtools")
9011 (string-append "--with-bam_tools_library="
9012 (assoc-ref %build-inputs "bamtools") "/lib/bamtools"))))
9014 `(("bamtools" ,bamtools)
9015 ("samtools" ,samtools-0.1)
9018 ,(let ((commit "3723e2db438c51501d0423429ff396c3035ba46a"))
9022 (url "https://github.com/smithlabcode/smithlab_cpp.git")
9024 (file-name (string-append "smithlab_cpp-" commit "-checkout"))
9027 "0l4gvbwslw5ngziskja41c00x1r06l3yidv7y0xw9djibhykzy0g")))))))
9029 `(("python" ,python-2)))
9030 (home-page "https://github.com/smithlabcode/piranha")
9031 (synopsis "Peak-caller for CLIP-seq and RIP-seq data")
9033 "Piranha is a peak-caller for genomic data produced by CLIP-seq and
9034 RIP-seq experiments. It takes input in BED or BAM format and identifies
9035 regions of statistically significant read enrichment. Additional covariates
9036 may optionally be provided to further inform the peak-calling process.")
9037 (license license:gpl3+))))
9045 (uri (string-append "https://pypi.python.org/packages/source/P"
9046 "/PePr/PePr-" version ".tar.gz"))
9049 "0qxjfdpl1b1y53nccws2d85f6k74zwmx8y8sd9rszcqhfayx6gdx"))))
9050 (build-system python-build-system)
9052 `(#:python ,python-2 ; python2 only
9053 #:tests? #f)) ; no tests included
9055 `(("python2-numpy" ,python2-numpy)
9056 ("python2-scipy" ,python2-scipy)
9057 ("python2-pysam" ,python2-pysam)))
9058 (home-page "https://github.com/shawnzhangyx/PePr")
9059 (synopsis "Peak-calling and prioritization pipeline for ChIP-Seq data")
9061 "PePr is a ChIP-Seq peak calling or differential binding analysis tool
9062 that is primarily designed for data with biological replicates. It uses a
9063 negative binomial distribution to model the read counts among the samples in
9064 the same group, and look for consistent differences between ChIP and control
9065 group or two ChIP groups run under different conditions.")
9066 (license license:gpl3+)))
9068 (define-public filevercmp
9069 (let ((commit "1a9b779b93d0b244040274794d402106907b71b7"))
9072 (version (string-append "0-1." (string-take commit 7)))
9075 (uri (string-append "https://github.com/ekg/filevercmp/archive/"
9077 (file-name (string-append name "-" version ".tar.gz"))
9079 (base32 "0yp5jswf5j2pqc6517x277s4s6h1ss99v57kxw9gy0jkfl3yh450"))))
9080 (build-system gnu-build-system)
9082 `(#:tests? #f ; There are no tests to run.
9084 (modify-phases %standard-phases
9085 (delete 'configure) ; There is no configure phase.
9087 (lambda* (#:key outputs #:allow-other-keys)
9088 (let ((bin (string-append (assoc-ref outputs "out") "/bin")))
9089 (install-file "filevercmp" bin)))))))
9090 (home-page "https://github.com/ekg/filevercmp")
9091 (synopsis "This program compares version strings")
9092 (description "This program compares version strings. It intends to be a
9093 replacement for strverscmp.")
9094 (license license:gpl3+))))
9096 (define-public multiqc
9103 (uri (pypi-uri "multiqc" version))
9106 "02iihfl0w0hpnr4pa0sbd1y9qxrg3ycyhjp5lidkcrqh1lmzs3zy"))))
9107 (build-system python-build-system)
9109 `(("python-jinja2" ,python-jinja2)
9110 ("python-simplejson" ,python-simplejson)
9111 ("python-pyyaml" ,python-pyyaml)
9112 ("python-click" ,python-click)
9113 ("python-spectra" ,python-spectra)
9114 ("python-requests" ,python-requests)
9115 ("python-markdown" ,python-markdown)
9116 ("python-lzstring" ,python-lzstring)
9117 ("python-matplotlib" ,python-matplotlib)
9118 ("python-numpy" ,python-numpy)
9119 ;; MultQC checks for the presence of nose at runtime.
9120 ("python-nose" ,python-nose)))
9123 (modify-phases %standard-phases
9124 (add-after 'unpack 'relax-requirements
9126 (substitute* "setup.py"
9127 ;; MultiQC 1.5 ‘requires’ a version of python-matplotlib older
9128 ;; than the one in Guix, but should work fine with 2.2.2.
9129 ;; See <https://github.com/ewels/MultiQC/issues/725> and
9130 ;; <https://github.com/ewels/MultiQC/issues/732> for details.
9131 (("['\"]matplotlib.*?['\"]")
9134 (home-page "http://multiqc.info")
9135 (synopsis "Aggregate bioinformatics analysis reports")
9137 "MultiQC is a tool to aggregate bioinformatics results across many
9138 samples into a single report. It contains modules for a large number of
9139 common bioinformatics tools.")
9140 (license license:gpl3+)))
9142 (define-public r-chipseq
9149 (uri (bioconductor-uri "chipseq" version))
9152 "09f8dgl5ni75qkf7nvvppwr3irpplv4xb3ks59ld7l8i2mplcrx7"))))
9153 (build-system r-build-system)
9155 `(("r-biocgenerics" ,r-biocgenerics)
9156 ("r-genomicranges" ,r-genomicranges)
9157 ("r-iranges" ,r-iranges)
9158 ("r-lattice" ,r-lattice)
9159 ("r-s4vectors" ,r-s4vectors)
9160 ("r-shortread" ,r-shortread)))
9161 (home-page "https://bioconductor.org/packages/chipseq")
9162 (synopsis "Package for analyzing ChIPseq data")
9164 "This package provides tools for processing short read data from ChIPseq
9166 (license license:artistic2.0)))
9168 (define-public r-copyhelper
9170 (name "r-copyhelper")
9175 (uri (string-append "https://bioconductor.org/packages/release/"
9176 "data/experiment/src/contrib/CopyhelpeR_"
9180 "0x7cyynjmxls9as2gg0iyp9x5fpalxmdjq914ss7i84i9zyk5bhq"))))
9181 (properties `((upstream-name . "CopyhelpeR")))
9182 (build-system r-build-system)
9183 (home-page "https://bioconductor.org/packages/CopyhelpeR/")
9184 (synopsis "Helper files for CopywriteR")
9186 "This package contains the helper files that are required to run the
9187 Bioconductor package CopywriteR. It contains pre-assembled 1kb bin GC-content
9188 and mappability files for the reference genomes hg18, hg19, hg38, mm9 and
9189 mm10. In addition, it contains a blacklist filter to remove regions that
9190 display copy number variation. Files are stored as GRanges objects from the
9191 GenomicRanges Bioconductor package.")
9192 (license license:gpl2)))
9194 (define-public r-copywriter
9196 (name "r-copywriter")
9201 (uri (bioconductor-uri "CopywriteR" version))
9204 "0b7xwq1va2zclb54f07c5ipmmq4iv2hrlph3j93jz5hmyayv50z3"))))
9205 (properties `((upstream-name . "CopywriteR")))
9206 (build-system r-build-system)
9208 `(("r-biocparallel" ,r-biocparallel)
9209 ("r-chipseq" ,r-chipseq)
9210 ("r-copyhelper" ,r-copyhelper)
9211 ("r-data-table" ,r-data-table)
9212 ("r-dnacopy" ,r-dnacopy)
9213 ("r-futile-logger" ,r-futile-logger)
9214 ("r-genomeinfodb" ,r-genomeinfodb)
9215 ("r-genomicalignments" ,r-genomicalignments)
9216 ("r-genomicranges" ,r-genomicranges)
9217 ("r-gtools" ,r-gtools)
9218 ("r-iranges" ,r-iranges)
9219 ("r-matrixstats" ,r-matrixstats)
9220 ("r-rsamtools" ,r-rsamtools)
9221 ("r-s4vectors" ,r-s4vectors)))
9222 (home-page "https://github.com/PeeperLab/CopywriteR")
9223 (synopsis "Copy number information from targeted sequencing")
9225 "CopywriteR extracts DNA copy number information from targeted sequencing
9226 by utilizing off-target reads. It allows for extracting uniformly distributed
9227 copy number information, can be used without reference, and can be applied to
9228 sequencing data obtained from various techniques including chromatin
9229 immunoprecipitation and target enrichment on small gene panels. Thereby,
9230 CopywriteR constitutes a widely applicable alternative to available copy
9231 number detection tools.")
9232 (license license:gpl2)))
9234 (define-public r-methylkit
9236 (name "r-methylkit")
9240 (uri (bioconductor-uri "methylKit" version))
9243 "1hr2czi5ybdf7hdmqsv39d17f3mvmw94wa38bc14zzm9mgy9gfy7"))))
9244 (properties `((upstream-name . "methylKit")))
9245 (build-system r-build-system)
9247 `(("r-data-table" ,r-data-table)
9248 ("r-emdbook" ,r-emdbook)
9249 ("r-fastseg" ,r-fastseg)
9250 ("r-genomeinfodb" ,r-genomeinfodb)
9251 ("r-genomicranges" ,r-genomicranges)
9252 ("r-gtools" ,r-gtools)
9253 ("r-iranges" ,r-iranges)
9254 ("r-kernsmooth" ,r-kernsmooth)
9255 ("r-limma" ,r-limma)
9256 ("r-mclust" ,r-mclust)
9257 ("r-qvalue" ,r-qvalue)
9258 ("r-r-utils" ,r-r-utils)
9260 ("r-rhtslib" ,r-rhtslib)
9261 ("r-rsamtools" ,r-rsamtools)
9262 ("r-rtracklayer" ,r-rtracklayer)
9263 ("r-s4vectors" ,r-s4vectors)
9264 ("r-zlibbioc" ,r-zlibbioc)))
9267 (home-page "https://github.com/al2na/methylKit")
9269 "DNA methylation analysis from high-throughput bisulfite sequencing results")
9271 "MethylKit is an R package for DNA methylation analysis and annotation
9272 from high-throughput bisulfite sequencing. The package is designed to deal
9273 with sequencing data from @dfn{Reduced representation bisulfite
9274 sequencing} (RRBS) and its variants, but also target-capture methods and whole
9275 genome bisulfite sequencing. It also has functions to analyze base-pair
9276 resolution 5hmC data from experimental protocols such as oxBS-Seq and
9278 (license license:artistic2.0)))
9280 (define-public r-sva
9287 (uri (bioconductor-uri "sva" version))
9290 "0a3jqbz0jp1jxrnjkqfpmca840yqcdwxprdl608bzzx2zb4jl52s"))))
9291 (build-system r-build-system)
9293 `(("r-genefilter" ,r-genefilter)
9295 ("r-biocparallel" ,r-biocparallel)
9296 ("r-matrixstats" ,r-matrixstats)
9297 ("r-limma" ,r-limma)))
9298 (home-page "https://bioconductor.org/packages/sva")
9299 (synopsis "Surrogate variable analysis")
9301 "This package contains functions for removing batch effects and other
9302 unwanted variation in high-throughput experiment. It also contains functions
9303 for identifying and building surrogate variables for high-dimensional data
9304 sets. Surrogate variables are covariates constructed directly from
9305 high-dimensional data like gene expression/RNA sequencing/methylation/brain
9306 imaging data that can be used in subsequent analyses to adjust for unknown,
9307 unmodeled, or latent sources of noise.")
9308 (license license:artistic2.0)))
9310 (define-public r-seqminer
9317 (uri (cran-uri "seqminer" version))
9320 "057j1l6dip35l1aivilapl2zv9db677b3di2pb3sfgq2sxg0ps3l"))))
9321 (build-system r-build-system)
9324 (home-page "http://seqminer.genomic.codes")
9325 (synopsis "Read nucleotide sequence data (VCF, BCF, and METAL formats)")
9327 "This package provides tools to integrate nucleotide sequencing
9328 data (variant call format, e.g. VCF or BCF) or meta-analysis results in R.")
9329 ;; Any version of the GPL is acceptable
9330 (license (list license:gpl2+ license:gpl3+))))
9332 (define-public r-raremetals2
9334 (name "r-raremetals2")
9339 (uri (string-append "http://genome.sph.umich.edu/w/images/"
9340 "b/b7/RareMETALS2_" version ".tar.gz"))
9343 "0z5ljcgvnm06ja9lm85a3cniq7slxcy37aqqkxrdidr79an5fs4s"))))
9344 (properties `((upstream-name . "RareMETALS2")))
9345 (build-system r-build-system)
9347 `(("r-seqminer" ,r-seqminer)
9348 ("r-mvtnorm" ,r-mvtnorm)
9350 ("r-compquadform" ,r-compquadform)
9351 ("r-getopt" ,r-getopt)))
9352 (home-page "http://genome.sph.umich.edu/wiki/RareMETALS2")
9353 (synopsis "Analyze gene-level association tests for binary trait")
9355 "The R package rareMETALS2 is an extension of the R package rareMETALS.
9356 It was designed to meta-analyze gene-level association tests for binary trait.
9357 While rareMETALS offers a near-complete solution for meta-analysis of
9358 gene-level tests for quantitative trait, it does not offer the optimal
9359 solution for binary trait. The package rareMETALS2 offers improved features
9360 for analyzing gene-level association tests in meta-analyses for binary
9362 (license license:gpl3)))
9364 (define-public r-maldiquant
9366 (name "r-maldiquant")
9371 (uri (cran-uri "MALDIquant" version))
9374 "047s6007ydc38x8wm027mlb4mngz15n0d4238fr8h43wyll5zy0z"))))
9375 (properties `((upstream-name . "MALDIquant")))
9376 (build-system r-build-system)
9377 (home-page "https://cran.r-project.org/web/packages/MALDIquant")
9378 (synopsis "Quantitative analysis of mass spectrometry data")
9380 "This package provides a complete analysis pipeline for matrix-assisted
9381 laser desorption/ionization-time-of-flight (MALDI-TOF) and other
9382 two-dimensional mass spectrometry data. In addition to commonly used plotting
9383 and processing methods it includes distinctive features, namely baseline
9384 subtraction methods such as morphological filters (TopHat) or the
9385 statistics-sensitive non-linear iterative peak-clipping algorithm (SNIP), peak
9386 alignment using warping functions, handling of replicated measurements as well
9387 as allowing spectra with different resolutions.")
9388 (license license:gpl3+)))
9390 (define-public r-protgenerics
9392 (name "r-protgenerics")
9397 (uri (bioconductor-uri "ProtGenerics" version))
9400 "05jbadw2aiwy8vi2ia0jxg06cmwhly2cq4dy1ag7kdxf1c5i9ccn"))))
9401 (properties `((upstream-name . "ProtGenerics")))
9402 (build-system r-build-system)
9403 (home-page "https://github.com/lgatto/ProtGenerics")
9404 (synopsis "S4 generic functions for proteomics infrastructure")
9406 "This package provides S4 generic functions needed by Bioconductor
9407 proteomics packages.")
9408 (license license:artistic2.0)))
9410 (define-public r-mzr
9417 (uri (bioconductor-uri "mzR" version))
9420 "190m2bq5bqxhljaj4f7vz9wj5h5laaxd8zp5jampnql6xc4zmarg"))
9421 (modules '((guix build utils)))
9424 (delete-file-recursively "src/boost")
9426 (properties `((upstream-name . "mzR")))
9427 (build-system r-build-system)
9430 (modify-phases %standard-phases
9431 (add-after 'unpack 'use-system-boost
9433 (substitute* "src/Makevars"
9434 (("\\./boost/libs.*") "")
9435 (("ARCH_OBJS=" line)
9437 "\nARCH_LIBS=-lboost_system -lboost_regex \
9438 -lboost_iostreams -lboost_thread -lboost_filesystem -lboost_chrono\n")))
9441 `(("boost" ,boost) ; use this instead of the bundled boost sources
9445 `(("r-biobase" ,r-biobase)
9446 ("r-biocgenerics" ,r-biocgenerics)
9447 ("r-protgenerics" ,r-protgenerics)
9449 ("r-rhdf5lib" ,r-rhdf5lib)
9450 ("r-zlibbioc" ,r-zlibbioc)))
9451 (home-page "https://github.com/sneumann/mzR/")
9452 (synopsis "Parser for mass spectrometry data files")
9454 "The mzR package provides a unified API to the common file formats and
9455 parsers available for mass spectrometry data. It comes with a wrapper for the
9456 ISB random access parser for mass spectrometry mzXML, mzData and mzML files.
9457 The package contains the original code written by the ISB, and a subset of the
9458 proteowizard library for mzML and mzIdentML. The netCDF reading code has
9459 previously been used in XCMS.")
9460 (license license:artistic2.0)))
9462 (define-public r-affyio
9469 (uri (bioconductor-uri "affyio" version))
9472 "0sh5wnnchyfpq5n6rchbqmb27byn7kdzn5rgran6i39c81i5z22n"))))
9473 (build-system r-build-system)
9475 `(("r-zlibbioc" ,r-zlibbioc)))
9478 (home-page "https://github.com/bmbolstad/affyio")
9479 (synopsis "Tools for parsing Affymetrix data files")
9481 "This package provides routines for parsing Affymetrix data files based
9482 upon file format information. The primary focus is on accessing the CEL and
9484 (license license:lgpl2.0+)))
9486 (define-public r-affy
9493 (uri (bioconductor-uri "affy" version))
9496 "0sxq875sigm21sf3qncrfrwfdz9nqw1vldxn3d3hj6aq64jg1ki6"))))
9497 (build-system r-build-system)
9499 `(("r-affyio" ,r-affyio)
9500 ("r-biobase" ,r-biobase)
9501 ("r-biocgenerics" ,r-biocgenerics)
9502 ("r-biocinstaller" ,r-biocinstaller)
9503 ("r-preprocesscore" ,r-preprocesscore)
9504 ("r-zlibbioc" ,r-zlibbioc)))
9507 (home-page "https://bioconductor.org/packages/affy")
9508 (synopsis "Methods for affymetrix oligonucleotide arrays")
9510 "This package contains functions for exploratory oligonucleotide array
9512 (license license:lgpl2.0+)))
9514 (define-public r-vsn
9521 (uri (bioconductor-uri "vsn" version))
9524 "0k6mah3g3zqbfap31xmvig4fn452a18xwwa5y0mfj5mj8588p57h"))))
9525 (build-system r-build-system)
9527 `(("r-affy" ,r-affy)
9528 ("r-biobase" ,r-biobase)
9529 ("r-ggplot2" ,r-ggplot2)
9530 ("r-lattice" ,r-lattice)
9531 ("r-limma" ,r-limma)))
9532 (home-page "https://bioconductor.org/packages/release/bioc/html/vsn.html")
9533 (synopsis "Variance stabilization and calibration for microarray data")
9535 "The package implements a method for normalising microarray intensities,
9536 and works for single- and multiple-color arrays. It can also be used for data
9537 from other technologies, as long as they have similar format. The method uses
9538 a robust variant of the maximum-likelihood estimator for an
9539 additive-multiplicative error model and affine calibration. The model
9540 incorporates data calibration step (a.k.a. normalization), a model for the
9541 dependence of the variance on the mean intensity and a variance stabilizing
9542 data transformation. Differences between transformed intensities are
9543 analogous to \"normalized log-ratios\". However, in contrast to the latter,
9544 their variance is independent of the mean, and they are usually more sensitive
9545 and specific in detecting differential transcription.")
9546 (license license:artistic2.0)))
9548 (define-public r-mzid
9555 (uri (bioconductor-uri "mzID" version))
9558 "060k0xlhg8q802c6zsb4b8ps0ccd9ybyaz0gnsvqkxb786i2vk40"))))
9559 (properties `((upstream-name . "mzID")))
9560 (build-system r-build-system)
9562 `(("r-doparallel" ,r-doparallel)
9563 ("r-foreach" ,r-foreach)
9564 ("r-iterators" ,r-iterators)
9566 ("r-protgenerics" ,r-protgenerics)
9569 (home-page "https://bioconductor.org/packages/mzID")
9570 (synopsis "Parser for mzIdentML files")
9572 "This package provides a parser for mzIdentML files implemented using the
9573 XML package. The parser tries to be general and able to handle all types of
9574 mzIdentML files with the drawback of having less pretty output than a vendor
9576 (license license:gpl2+)))
9578 (define-public r-pcamethods
9580 (name "r-pcamethods")
9585 (uri (bioconductor-uri "pcaMethods" version))
9588 "0v99yf8m7ryh6z0r3z0ggpqfnflcq5bn1q1i1cl9b7q4p6b4sa07"))))
9589 (properties `((upstream-name . "pcaMethods")))
9590 (build-system r-build-system)
9592 `(("r-biobase" ,r-biobase)
9593 ("r-biocgenerics" ,r-biocgenerics)
9595 ("r-rcpp" ,r-rcpp)))
9596 (home-page "https://github.com/hredestig/pcamethods")
9597 (synopsis "Collection of PCA methods")
9599 "This package provides Bayesian PCA, Probabilistic PCA, Nipals PCA,
9600 Inverse Non-Linear PCA and the conventional SVD PCA. A cluster based method
9601 for missing value estimation is included for comparison. BPCA, PPCA and
9602 NipalsPCA may be used to perform PCA on incomplete data as well as for
9603 accurate missing value estimation. A set of methods for printing and plotting
9604 the results is also provided. All PCA methods make use of the same data
9605 structure (pcaRes) to provide a common interface to the PCA results.")
9606 (license license:gpl3+)))
9608 (define-public r-msnbase
9615 (uri (bioconductor-uri "MSnbase" version))
9618 "0zrpx9r93q5ca2zdak5rs2m9sjm0wjdra1xfj3d3sx6p5gzfyg6n"))))
9619 (properties `((upstream-name . "MSnbase")))
9620 (build-system r-build-system)
9622 `(("r-affy" ,r-affy)
9623 ("r-biobase" ,r-biobase)
9624 ("r-biocgenerics" ,r-biocgenerics)
9625 ("r-biocparallel" ,r-biocparallel)
9626 ("r-digest" ,r-digest)
9627 ("r-ggplot2" ,r-ggplot2)
9628 ("r-impute" ,r-impute)
9629 ("r-iranges" ,r-iranges)
9630 ("r-lattice" ,r-lattice)
9631 ("r-maldiquant" ,r-maldiquant)
9635 ("r-pcamethods" ,r-pcamethods)
9637 ("r-preprocesscore" ,r-preprocesscore)
9638 ("r-protgenerics" ,r-protgenerics)
9640 ("r-s4vectors" ,r-s4vectors)
9641 ("r-scales" ,r-scales)
9644 (home-page "https://github.com/lgatto/MSnbase")
9645 (synopsis "Base functions and classes for MS-based proteomics")
9647 "This package provides basic plotting, data manipulation and processing
9648 of mass spectrometry based proteomics data.")
9649 (license license:artistic2.0)))
9651 (define-public r-msnid
9658 (uri (bioconductor-uri "MSnID" version))
9661 "172q5chi44104iz4y0g42wrimfp7hlhrfa8vzybx6m0ccrkkhl17"))))
9662 (properties `((upstream-name . "MSnID")))
9663 (build-system r-build-system)
9665 `(("r-biobase" ,r-biobase)
9666 ("r-data-table" ,r-data-table)
9667 ("r-doparallel" ,r-doparallel)
9668 ("r-dplyr" ,r-dplyr)
9669 ("r-foreach" ,r-foreach)
9670 ("r-iterators" ,r-iterators)
9671 ("r-msnbase" ,r-msnbase)
9674 ("r-protgenerics" ,r-protgenerics)
9675 ("r-r-cache" ,r-r-cache)
9677 ("r-reshape2" ,r-reshape2)))
9678 (home-page "https://bioconductor.org/packages/MSnID")
9679 (synopsis "Utilities for LC-MSn proteomics identifications")
9681 "This package extracts @dfn{tandem mass spectrometry} (MS/MS) ID data
9682 from mzIdentML (leveraging the mzID package) or text files. After collating
9683 the search results from multiple datasets it assesses their identification
9684 quality and optimize filtering criteria to achieve the maximum number of
9685 identifications while not exceeding a specified false discovery rate. It also
9686 contains a number of utilities to explore the MS/MS results and assess missed
9687 and irregular enzymatic cleavages, mass measurement accuracy, etc.")
9688 (license license:artistic2.0)))
9690 (define-public r-seurat
9696 (uri (cran-uri "Seurat" version))
9699 "0hi59rgdrr2iqfvx5bq7yq02hbjxkjl1fzidqj14z0ypq0nzbjys"))
9700 ;; Delete pre-built jar.
9702 '(begin (delete-file "inst/java/ModularityOptimizer.jar")
9704 (properties `((upstream-name . "Seurat")))
9705 (build-system r-build-system)
9708 (modify-phases %standard-phases
9709 (add-after 'unpack 'build-jar
9710 (lambda* (#:key inputs #:allow-other-keys)
9711 (let ((classesdir "tmp-classes"))
9712 (setenv "JAVA_HOME" (assoc-ref inputs "jdk"))
9714 (with-output-to-file "manifest"
9716 (display "Manifest-Version: 1.0
9717 Main-Class: ModularityOptimizer\n")))
9718 (and (zero? (apply system* `("javac" "-d" ,classesdir
9719 ,@(find-files "java" "\\.java$"))))
9720 (zero? (system* "jar"
9722 "inst/java/ModularityOptimizer.jar"
9723 "-C" classesdir ".")))))))))
9725 `(("jdk" ,icedtea "jdk")))
9728 ("r-caret" ,r-caret)
9729 ("r-cluster" ,r-cluster)
9730 ("r-cowplot" ,r-cowplot)
9731 ("r-diffusionmap" ,r-diffusionmap)
9732 ("r-dosnow" ,r-dosnow)
9733 ("r-dplyr" ,r-dplyr)
9735 ("r-fitdistrplus" ,r-fitdistrplus)
9737 ("r-foreach" ,r-foreach)
9739 ("r-gdata" ,r-gdata)
9740 ("r-ggplot2" ,r-ggplot2)
9741 ("r-ggridges" ,r-ggridges)
9742 ("r-gplots" ,r-gplots)
9743 ("r-hmisc" ,r-hmisc)
9745 ("r-igraph" ,r-igraph)
9746 ("r-irlba" ,r-irlba)
9748 ("r-lmtest" ,r-lmtest)
9750 ("r-matrix" ,r-matrix)
9751 ("r-metap" ,r-metap)
9752 ("r-mixtools" ,r-mixtools)
9753 ("r-pbapply" ,r-pbapply)
9754 ("r-plotly" ,r-plotly)
9756 ("r-ranger" ,r-ranger)
9758 ("r-rcolorbrewer" ,r-rcolorbrewer)
9760 ("r-rcppeigen" ,r-rcppeigen)
9761 ("r-rcppprogress" ,r-rcppprogress)
9762 ("r-reshape2" ,r-reshape2)
9763 ("r-reticulate" ,r-reticulate)
9765 ("r-rtsne" ,r-rtsne)
9766 ("r-sdmtools" ,r-sdmtools)
9767 ("r-stringr" ,r-stringr)
9768 ("r-tclust" ,r-tclust)
9769 ("r-tidyr" ,r-tidyr)
9771 ("r-vgam" ,r-vgam)))
9772 (home-page "http://www.satijalab.org/seurat")
9773 (synopsis "Seurat is an R toolkit for single cell genomics")
9775 "This package is an R package designed for QC, analysis, and
9776 exploration of single cell RNA-seq data. It easily enables widely-used
9777 analytical techniques, including the identification of highly variable genes,
9778 dimensionality reduction; PCA, ICA, t-SNE, standard unsupervised clustering
9779 algorithms; density clustering, hierarchical clustering, k-means, and the
9780 discovery of differentially expressed genes and markers.")
9781 (license license:gpl3)))
9783 (define-public r-aroma-light
9785 (name "r-aroma-light")
9790 (uri (bioconductor-uri "aroma.light" version))
9793 "1dxsiwsrwcq9mj573f9vpdzrhagdqzal328ma8076px4gg6khxkn"))))
9794 (properties `((upstream-name . "aroma.light")))
9795 (build-system r-build-system)
9797 `(("r-matrixstats" ,r-matrixstats)
9798 ("r-r-methodss3" ,r-r-methodss3)
9800 ("r-r-utils" ,r-r-utils)))
9801 (home-page "https://github.com/HenrikBengtsson/aroma.light")
9802 (synopsis "Methods for normalization and visualization of microarray data")
9804 "This package provides methods for microarray analysis that take basic
9805 data types such as matrices and lists of vectors. These methods can be used
9806 standalone, be utilized in other packages, or be wrapped up in higher-level
9808 (license license:gpl2+)))
9810 (define-public r-deseq
9817 (uri (bioconductor-uri "DESeq" version))
9820 "0ykxw8ksif026xy25wx50j2sdsrp156aqkmhcgfjkpgcw699glnm"))))
9821 (properties `((upstream-name . "DESeq")))
9822 (build-system r-build-system)
9824 `(("r-biobase" ,r-biobase)
9825 ("r-biocgenerics" ,r-biocgenerics)
9826 ("r-genefilter" ,r-genefilter)
9827 ("r-geneplotter" ,r-geneplotter)
9828 ("r-lattice" ,r-lattice)
9829 ("r-locfit" ,r-locfit)
9831 ("r-rcolorbrewer" ,r-rcolorbrewer)))
9832 (home-page "http://www-huber.embl.de/users/anders/DESeq")
9833 (synopsis "Differential gene expression analysis")
9835 "This package provides tools for estimating variance-mean dependence in
9836 count data from high-throughput genetic sequencing assays and for testing for
9837 differential expression based on a model using the negative binomial
9839 (license license:gpl3+)))
9841 (define-public r-edaseq
9848 (uri (bioconductor-uri "EDASeq" version))
9851 "1832pb3jkim4vrqzb8lajwx9r482bhww5n9nz3s6crvyamlp2dj0"))))
9852 (properties `((upstream-name . "EDASeq")))
9853 (build-system r-build-system)
9855 `(("r-annotationdbi" ,r-annotationdbi)
9856 ("r-aroma-light" ,r-aroma-light)
9857 ("r-biobase" ,r-biobase)
9858 ("r-biocgenerics" ,r-biocgenerics)
9859 ("r-biomart" ,r-biomart)
9860 ("r-biostrings" ,r-biostrings)
9861 ("r-deseq" ,r-deseq)
9862 ("r-genomicfeatures" ,r-genomicfeatures)
9863 ("r-genomicranges" ,r-genomicranges)
9864 ("r-iranges" ,r-iranges)
9865 ("r-rsamtools" ,r-rsamtools)
9866 ("r-shortread" ,r-shortread)))
9867 (home-page "https://github.com/drisso/EDASeq")
9868 (synopsis "Exploratory data analysis and normalization for RNA-Seq")
9870 "This package provides support for numerical and graphical summaries of
9871 RNA-Seq genomic read data. Provided within-lane normalization procedures to
9872 adjust for GC-content effect (or other gene-level effects) on read counts:
9873 loess robust local regression, global-scaling, and full-quantile
9874 normalization. Between-lane normalization procedures to adjust for
9875 distributional differences between lanes (e.g., sequencing depth):
9876 global-scaling and full-quantile normalization.")
9877 (license license:artistic2.0)))
9879 (define-public r-interactivedisplaybase
9881 (name "r-interactivedisplaybase")
9886 (uri (bioconductor-uri "interactiveDisplayBase" version))
9889 "05w58z3i9vkma4jd6rhjaxls4yiq4kwrppgcdq9xrr1pxp99k575"))))
9891 `((upstream-name . "interactiveDisplayBase")))
9892 (build-system r-build-system)
9894 `(("r-biocgenerics" ,r-biocgenerics)
9895 ("r-shiny" ,r-shiny)))
9896 (home-page "https://bioconductor.org/packages/interactiveDisplayBase")
9897 (synopsis "Base package for web displays of Bioconductor objects")
9899 "This package contains the basic methods needed to generate interactive
9900 Shiny-based display methods for Bioconductor objects.")
9901 (license license:artistic2.0)))
9903 (define-public r-annotationhub
9905 (name "r-annotationhub")
9910 (uri (bioconductor-uri "AnnotationHub" version))
9913 "11gh7qkgazs90czdqgv74gh2hz26xrmdp6wsz9x5pygbxls8xdw3"))))
9914 (properties `((upstream-name . "AnnotationHub")))
9915 (build-system r-build-system)
9917 `(("r-annotationdbi" ,r-annotationdbi)
9918 ("r-biocgenerics" ,r-biocgenerics)
9919 ("r-biocinstaller" ,r-biocinstaller)
9922 ("r-interactivedisplaybase" ,r-interactivedisplaybase)
9923 ("r-rsqlite" ,r-rsqlite)
9924 ("r-s4vectors" ,r-s4vectors)
9925 ("r-yaml" ,r-yaml)))
9926 (home-page "https://bioconductor.org/packages/AnnotationHub")
9927 (synopsis "Client to access AnnotationHub resources")
9929 "This package provides a client for the Bioconductor AnnotationHub web
9930 resource. The AnnotationHub web resource provides a central location where
9931 genomic files (e.g. VCF, bed, wig) and other resources from standard
9932 locations (e.g. UCSC, Ensembl) can be discovered. The resource includes
9933 metadata about each resource, e.g., a textual description, tags, and date of
9934 modification. The client creates and manages a local cache of files retrieved
9935 by the user, helping with quick and reproducible access.")
9936 (license license:artistic2.0)))
9938 (define-public r-fastseg
9945 (uri (bioconductor-uri "fastseg" version))
9948 "1yw6hai6hb8qy7akdm4frfp6h4zy93zb68kdj094sanm7kgqmgik"))))
9949 (build-system r-build-system)
9951 `(("r-biobase" ,r-biobase)
9952 ("r-biocgenerics" ,r-biocgenerics)
9953 ("r-genomicranges" ,r-genomicranges)
9954 ("r-iranges" ,r-iranges)
9955 ("r-s4vectors" ,r-s4vectors)))
9956 (home-page "http://www.bioinf.jku.at/software/fastseg/index.html")
9957 (synopsis "Fast segmentation algorithm for genetic sequencing data")
9959 "Fastseg implements a very fast and efficient segmentation algorithm.
9960 It can segment data from DNA microarrays and data from next generation
9961 sequencing for example to detect copy number segments. Further it can segment
9962 data from RNA microarrays like tiling arrays to identify transcripts. Most
9963 generally, it can segment data given as a matrix or as a vector. Various data
9964 formats can be used as input to fastseg like expression set objects for
9965 microarrays or GRanges for sequencing data.")
9966 (license license:lgpl2.0+)))
9968 (define-public r-keggrest
9975 (uri (bioconductor-uri "KEGGREST" version))
9978 "1349vidgl9m10l1rbrp3pkwwgi2xcbsw9h9z2xqbvg97lmqc4r8j"))))
9979 (properties `((upstream-name . "KEGGREST")))
9980 (build-system r-build-system)
9982 `(("r-biostrings" ,r-biostrings)
9985 (home-page "https://bioconductor.org/packages/KEGGREST")
9986 (synopsis "Client-side REST access to KEGG")
9988 "This package provides a package that provides a client interface to the
9989 @dfn{Kyoto Encyclopedia of Genes and Genomes} (KEGG) REST server.")
9990 (license license:artistic2.0)))
9992 (define-public r-gage
9999 (uri (bioconductor-uri "gage" version))
10002 "0j3cqxy97lpf146wkmdfaq9680gicmzxvhp6w5pxq3j7ipiy7262"))))
10003 (build-system r-build-system)
10005 `(("r-annotationdbi" ,r-annotationdbi)
10006 ("r-graph" ,r-graph)
10007 ("r-keggrest" ,r-keggrest)))
10008 (home-page "http://www.biomedcentral.com/1471-2105/10/161")
10009 (synopsis "Generally applicable gene-set enrichment for pathway analysis")
10011 "GAGE is a published method for gene set (enrichment or GSEA) or pathway
10012 analysis. GAGE is generally applicable independent of microarray or RNA-Seq
10013 data attributes including sample sizes, experimental designs, assay platforms,
10014 and other types of heterogeneity. The gage package provides functions for
10015 basic GAGE analysis, result processing and presentation. In addition, it
10016 provides demo microarray data and commonly used gene set data based on KEGG
10017 pathways and GO terms. These funtions and data are also useful for gene set
10018 analysis using other methods.")
10019 (license license:gpl2+)))
10021 (define-public r-genomicfiles
10023 (name "r-genomicfiles")
10028 (uri (bioconductor-uri "GenomicFiles" version))
10031 "0bhsq5czigrjyl9gkb2kpkpl367b3ac5g8s280adkcxggn9g7sxq"))))
10032 (properties `((upstream-name . "GenomicFiles")))
10033 (build-system r-build-system)
10035 `(("r-biocgenerics" ,r-biocgenerics)
10036 ("r-biocparallel" ,r-biocparallel)
10037 ("r-genomeinfodb" ,r-genomeinfodb)
10038 ("r-genomicalignments" ,r-genomicalignments)
10039 ("r-genomicranges" ,r-genomicranges)
10040 ("r-iranges" ,r-iranges)
10041 ("r-rsamtools" ,r-rsamtools)
10042 ("r-rtracklayer" ,r-rtracklayer)
10043 ("r-s4vectors" ,r-s4vectors)
10044 ("r-summarizedexperiment" ,r-summarizedexperiment)
10045 ("r-variantannotation" ,r-variantannotation)))
10046 (home-page "https://bioconductor.org/packages/GenomicFiles")
10047 (synopsis "Distributed computing by file or by range")
10049 "This package provides infrastructure for parallel computations
10050 distributed by file or by range. User defined mapper and reducer functions
10051 provide added flexibility for data combination and manipulation.")
10052 (license license:artistic2.0)))
10054 (define-public r-complexheatmap
10056 (name "r-complexheatmap")
10061 (uri (bioconductor-uri "ComplexHeatmap" version))
10064 "0z57mrginzd40niy51dvnyqgbrij05ji0dbwqs3x2as80sq28i3q"))))
10066 `((upstream-name . "ComplexHeatmap")))
10067 (build-system r-build-system)
10069 `(("r-circlize" ,r-circlize)
10070 ("r-colorspace" ,r-colorspace)
10071 ("r-getoptlong" ,r-getoptlong)
10072 ("r-globaloptions" ,r-globaloptions)
10073 ("r-rcolorbrewer" ,r-rcolorbrewer)))
10075 "https://github.com/jokergoo/ComplexHeatmap")
10076 (synopsis "Making Complex Heatmaps")
10078 "Complex heatmaps are efficient to visualize associations between
10079 different sources of data sets and reveal potential structures. This package
10080 provides a highly flexible way to arrange multiple heatmaps and supports
10081 self-defined annotation graphics.")
10082 (license license:gpl2+)))
10084 (define-public r-dirichletmultinomial
10086 (name "r-dirichletmultinomial")
10091 (uri (bioconductor-uri "DirichletMultinomial" version))
10094 "0vcyp81b90in4ls5nbadc66cw2g9aydr94aqifq5j4b7diq74yfs"))))
10096 `((upstream-name . "DirichletMultinomial")))
10097 (build-system r-build-system)
10101 `(("r-biocgenerics" ,r-biocgenerics)
10102 ("r-iranges" ,r-iranges)
10103 ("r-s4vectors" ,r-s4vectors)))
10104 (home-page "https://bioconductor.org/packages/DirichletMultinomial")
10105 (synopsis "Dirichlet-Multinomial mixture models for microbiome data")
10107 "Dirichlet-multinomial mixture models can be used to describe variability
10108 in microbial metagenomic data. This package is an interface to code
10109 originally made available by Holmes, Harris, and Quince, 2012, PLoS ONE 7(2):
10111 (license license:lgpl3)))
10113 (define-public r-ensembldb
10115 (name "r-ensembldb")
10120 (uri (bioconductor-uri "ensembldb" version))
10123 "1l2b4cxiycv05mz4z4f3dhx57r9ksha02psc114h30ldm5rxz8w6"))))
10124 (build-system r-build-system)
10126 `(("r-annotationdbi" ,r-annotationdbi)
10127 ("r-annotationfilter" ,r-annotationfilter)
10128 ("r-biobase" ,r-biobase)
10129 ("r-biocgenerics" ,r-biocgenerics)
10130 ("r-biostrings" ,r-biostrings)
10133 ("r-genomeinfodb" ,r-genomeinfodb)
10134 ("r-genomicfeatures" ,r-genomicfeatures)
10135 ("r-genomicranges" ,r-genomicranges)
10136 ("r-iranges" ,r-iranges)
10137 ("r-protgenerics" ,r-protgenerics)
10138 ("r-rsamtools" ,r-rsamtools)
10139 ("r-rsqlite" ,r-rsqlite)
10140 ("r-rtracklayer" ,r-rtracklayer)
10141 ("r-s4vectors" ,r-s4vectors)))
10142 (home-page "https://github.com/jotsetung/ensembldb")
10143 (synopsis "Utilities to create and use Ensembl-based annotation databases")
10145 "The package provides functions to create and use transcript-centric
10146 annotation databases/packages. The annotation for the databases are directly
10147 fetched from Ensembl using their Perl API. The functionality and data is
10148 similar to that of the TxDb packages from the @code{GenomicFeatures} package,
10149 but, in addition to retrieve all gene/transcript models and annotations from
10150 the database, the @code{ensembldb} package also provides a filter framework
10151 allowing to retrieve annotations for specific entries like genes encoded on a
10152 chromosome region or transcript models of lincRNA genes.")
10153 ;; No version specified
10154 (license license:lgpl3+)))
10156 (define-public r-organismdbi
10158 (name "r-organismdbi")
10163 (uri (bioconductor-uri "OrganismDbi" version))
10166 "0hb9ni41bjfy5s5ryw2qmqs2sx3i7j47w1g0l8g1pvn7ppnxb6cv"))))
10167 (properties `((upstream-name . "OrganismDbi")))
10168 (build-system r-build-system)
10170 `(("r-annotationdbi" ,r-annotationdbi)
10171 ("r-biobase" ,r-biobase)
10172 ("r-biocgenerics" ,r-biocgenerics)
10173 ("r-biocinstaller" ,r-biocinstaller)
10175 ("r-genomicfeatures" ,r-genomicfeatures)
10176 ("r-genomicranges" ,r-genomicranges)
10177 ("r-graph" ,r-graph)
10178 ("r-iranges" ,r-iranges)
10180 ("r-s4vectors" ,r-s4vectors)))
10181 (home-page "https://bioconductor.org/packages/OrganismDbi")
10182 (synopsis "Software to enable the smooth interfacing of database packages")
10183 (description "The package enables a simple unified interface to several
10184 annotation packages each of which has its own schema by taking advantage of
10185 the fact that each of these packages implements a select methods.")
10186 (license license:artistic2.0)))
10188 (define-public r-biovizbase
10190 (name "r-biovizbase")
10195 (uri (bioconductor-uri "biovizBase" version))
10198 "0lkiqdr3ics6hgv47lwkykcy761823bbkhffbn4ykyfzyqwl4p67"))))
10199 (properties `((upstream-name . "biovizBase")))
10200 (build-system r-build-system)
10202 `(("r-annotationdbi" ,r-annotationdbi)
10203 ("r-annotationfilter" ,r-annotationfilter)
10204 ("r-biocgenerics" ,r-biocgenerics)
10205 ("r-biostrings" ,r-biostrings)
10206 ("r-dichromat" ,r-dichromat)
10207 ("r-ensembldb" ,r-ensembldb)
10208 ("r-genomeinfodb" ,r-genomeinfodb)
10209 ("r-genomicalignments" ,r-genomicalignments)
10210 ("r-genomicfeatures" ,r-genomicfeatures)
10211 ("r-genomicranges" ,r-genomicranges)
10212 ("r-hmisc" ,r-hmisc)
10213 ("r-iranges" ,r-iranges)
10214 ("r-rcolorbrewer" ,r-rcolorbrewer)
10215 ("r-rsamtools" ,r-rsamtools)
10216 ("r-s4vectors" ,r-s4vectors)
10217 ("r-scales" ,r-scales)
10218 ("r-summarizedexperiment" ,r-summarizedexperiment)
10219 ("r-variantannotation" ,r-variantannotation)))
10220 (home-page "https://bioconductor.org/packages/biovizBase")
10221 (synopsis "Basic graphic utilities for visualization of genomic data")
10223 "The biovizBase package is designed to provide a set of utilities, color
10224 schemes and conventions for genomic data. It serves as the base for various
10225 high-level packages for biological data visualization. This saves development
10226 effort and encourages consistency.")
10227 (license license:artistic2.0)))
10229 (define-public r-ggbio
10236 (uri (bioconductor-uri "ggbio" version))
10239 "0wszh3w8yia5zw758h837i1q35k99sn444y2hahcxqbdmmlbf7in"))))
10240 (build-system r-build-system)
10242 `(("r-annotationdbi" ,r-annotationdbi)
10243 ("r-annotationfilter" ,r-annotationfilter)
10244 ("r-biobase" ,r-biobase)
10245 ("r-biocgenerics" ,r-biocgenerics)
10246 ("r-biostrings" ,r-biostrings)
10247 ("r-biovizbase" ,r-biovizbase)
10248 ("r-bsgenome" ,r-bsgenome)
10249 ("r-ensembldb" ,r-ensembldb)
10250 ("r-genomeinfodb" ,r-genomeinfodb)
10251 ("r-genomicalignments" ,r-genomicalignments)
10252 ("r-genomicfeatures" ,r-genomicfeatures)
10253 ("r-genomicranges" ,r-genomicranges)
10254 ("r-ggally" ,r-ggally)
10255 ("r-ggplot2" ,r-ggplot2)
10256 ("r-gridextra" ,r-gridextra)
10257 ("r-gtable" ,r-gtable)
10258 ("r-hmisc" ,r-hmisc)
10259 ("r-iranges" ,r-iranges)
10260 ("r-organismdbi" ,r-organismdbi)
10261 ("r-reshape2" ,r-reshape2)
10262 ("r-rsamtools" ,r-rsamtools)
10263 ("r-rtracklayer" ,r-rtracklayer)
10264 ("r-s4vectors" ,r-s4vectors)
10265 ("r-scales" ,r-scales)
10266 ("r-summarizedexperiment" ,r-summarizedexperiment)
10267 ("r-variantannotation" ,r-variantannotation)))
10268 (home-page "http://www.tengfei.name/ggbio/")
10269 (synopsis "Visualization tools for genomic data")
10271 "The ggbio package extends and specializes the grammar of graphics for
10272 biological data. The graphics are designed to answer common scientific
10273 questions, in particular those often asked of high throughput genomics data.
10274 All core Bioconductor data structures are supported, where appropriate. The
10275 package supports detailed views of particular genomic regions, as well as
10276 genome-wide overviews. Supported overviews include ideograms and grand linear
10277 views. High-level plots include sequence fragment length, edge-linked
10278 interval to data view, mismatch pileup, and several splicing summaries.")
10279 (license license:artistic2.0)))
10281 (define-public r-gprofiler
10283 (name "r-gprofiler")
10288 (uri (cran-uri "gProfileR" version))
10291 "1n6cj12j102b4x9vhyl4dljp1i0r43p23cnhqbx4als2xfxdlqgi"))))
10292 (properties `((upstream-name . "gProfileR")))
10293 (build-system r-build-system)
10295 `(("r-plyr" ,r-plyr)
10296 ("r-rcurl" ,r-rcurl)))
10297 (home-page "https://cran.r-project.org/web/packages/gProfileR/")
10298 (synopsis "Interface to the g:Profiler toolkit")
10300 "This package provides tools for functional enrichment analysis,
10301 gene identifier conversion and mapping homologous genes across related
10302 organisms via the @code{g:Profiler} toolkit.")
10303 (license license:gpl2+)))
10305 (define-public r-gqtlbase
10307 (name "r-gqtlbase")
10312 (uri (bioconductor-uri "gQTLBase" version))
10315 "1m3ajpqjhw1nwwsn372r44xfxq0a9a0pzsnrprzdjp6mh52p9b5m"))))
10316 (properties `((upstream-name . "gQTLBase")))
10317 (build-system r-build-system)
10319 `(("r-batchjobs" ,r-batchjobs)
10320 ("r-bbmisc" ,r-bbmisc)
10321 ("r-biocgenerics" ,r-biocgenerics)
10323 ("r-doparallel" ,r-doparallel)
10325 ("r-ffbase" ,r-ffbase)
10326 ("r-foreach" ,r-foreach)
10327 ("r-genomicfiles" ,r-genomicfiles)
10328 ("r-genomicranges" ,r-genomicranges)
10329 ("r-rtracklayer" ,r-rtracklayer)
10330 ("r-s4vectors" ,r-s4vectors)
10331 ("r-summarizedexperiment" ,r-summarizedexperiment)))
10332 (home-page "https://bioconductor.org/packages/gQTLBase")
10333 (synopsis "Infrastructure for eQTL, mQTL and similar studies")
10335 "The purpose of this package is to simplify the storage and interrogation
10336 of @dfn{quantitative trait loci} (QTL) archives, such as eQTL, mQTL, dsQTL,
10338 (license license:artistic2.0)))
10340 (define-public r-snpstats
10342 (name "r-snpstats")
10347 (uri (bioconductor-uri "snpStats" version))
10350 "0iydgfnm053iw860qa1bbh4f6nwzlsf3vhgq92gvl2v4xsz1jbbs"))))
10351 (properties `((upstream-name . "snpStats")))
10352 (build-system r-build-system)
10353 (inputs `(("zlib" ,zlib)))
10355 `(("r-biocgenerics" ,r-biocgenerics)
10356 ("r-matrix" ,r-matrix)
10357 ("r-survival" ,r-survival)
10358 ("r-zlibbioc" ,r-zlibbioc)))
10359 (home-page "https://bioconductor.org/packages/snpStats")
10360 (synopsis "Methods for SNP association studies")
10362 "This package provides classes and statistical methods for large
10363 @dfn{single-nucleotide polymorphism} (SNP) association studies. This extends
10364 the earlier snpMatrix package, allowing for uncertainty in genotypes.")
10365 (license license:gpl3)))
10367 (define-public r-homo-sapiens
10369 (name "r-homo-sapiens")
10373 ;; We cannot use bioconductor-uri here because this tarball is
10374 ;; located under "data/annotation/" instead of "bioc/".
10375 (uri (string-append "http://www.bioconductor.org/packages/"
10376 "release/data/annotation/src/contrib/"
10378 version ".tar.gz"))
10381 "151vj7h5p1c8yd5swrchk46z469p135wk50hvkl0nhgndvy0jj01"))))
10383 `((upstream-name . "Homo.sapiens")))
10384 (build-system r-build-system)
10386 `(("r-genomicfeatures" ,r-genomicfeatures)
10387 ("r-go-db" ,r-go-db)
10388 ("r-org-hs-eg-db" ,r-org-hs-eg-db)
10389 ("r-txdb-hsapiens-ucsc-hg19-knowngene" ,r-txdb-hsapiens-ucsc-hg19-knowngene)
10390 ("r-organismdbi" ,r-organismdbi)
10391 ("r-annotationdbi" ,r-annotationdbi)))
10392 (home-page "https://bioconductor.org/packages/Homo.sapiens/")
10393 (synopsis "Annotation package for the Homo.sapiens object")
10395 "This package contains the Homo.sapiens object to access data from
10396 several related annotation packages.")
10397 (license license:artistic2.0)))
10399 (define-public r-erma
10406 (uri (bioconductor-uri "erma" version))
10409 "1ka68n18yizlyvb8bpwwcl4hqbsasg8hw8jb3vgy3cd4szji87hh"))))
10410 (build-system r-build-system)
10412 `(("r-annotationdbi" ,r-annotationdbi)
10413 ("r-biobase" ,r-biobase)
10414 ("r-biocgenerics" ,r-biocgenerics)
10415 ("r-biocparallel" ,r-biocparallel)
10416 ("r-genomeinfodb" ,r-genomeinfodb)
10417 ("r-genomicfiles" ,r-genomicfiles)
10418 ("r-genomicranges" ,r-genomicranges)
10419 ("r-ggplot2" ,r-ggplot2)
10420 ("r-homo-sapiens" ,r-homo-sapiens)
10421 ("r-iranges" ,r-iranges)
10422 ("r-rtracklayer" ,r-rtracklayer)
10423 ("r-s4vectors" ,r-s4vectors)
10424 ("r-shiny" ,r-shiny)
10425 ("r-summarizedexperiment" ,r-summarizedexperiment)))
10426 (home-page "https://bioconductor.org/packages/erma")
10427 (synopsis "Epigenomic road map adventures")
10429 "The epigenomics road map describes locations of epigenetic marks in DNA
10430 from a variety of cell types. Of interest are locations of histone
10431 modifications, sites of DNA methylation, and regions of accessible chromatin.
10432 This package presents a selection of elements of the road map including
10433 metadata and outputs of the ChromImpute procedure applied to ENCODE cell lines
10434 by Ernst and Kellis.")
10435 (license license:artistic2.0)))
10437 (define-public r-ldblock
10444 (uri (bioconductor-uri "ldblock" version))
10447 "0c24zvnwsp39d3q0bps13sc441jj9ms2zi34xsb8c392lqmbypvd"))))
10448 (build-system r-build-system)
10450 `(("r-biocgenerics" ,r-biocgenerics)
10452 ("r-genomeinfodb" ,r-genomeinfodb)
10453 ("r-genomicfiles" ,r-genomicfiles)
10454 ("r-go-db" ,r-go-db)
10455 ("r-homo-sapiens" ,r-homo-sapiens)
10456 ("r-matrix" ,r-matrix)
10457 ("r-rsamtools" ,r-rsamtools)
10458 ("r-snpstats" ,r-snpstats)
10459 ("r-variantannotation" ,r-variantannotation)))
10460 (home-page "https://bioconductor.org/packages/ldblock")
10461 (synopsis "Data structures for linkage disequilibrium measures in populations")
10463 "This package defines data structures for @dfn{linkage
10464 disequilibrium} (LD) measures in populations. Its purpose is to simplify
10465 handling of existing population-level data for the purpose of flexibly
10466 defining LD blocks.")
10467 (license license:artistic2.0)))
10469 (define-public r-gqtlstats
10471 (name "r-gqtlstats")
10476 (uri (bioconductor-uri "gQTLstats" version))
10479 "19g8qhfgngdc14cw9k4i44cxhs3qva87x56gjzmn25k1yj8qgsp1"))))
10480 (properties `((upstream-name . "gQTLstats")))
10481 (build-system r-build-system)
10483 `(("r-annotationdbi" ,r-annotationdbi)
10484 ("r-batchjobs" ,r-batchjobs)
10485 ("r-bbmisc" ,r-bbmisc)
10486 ("r-beeswarm" ,r-beeswarm)
10487 ("r-biobase" ,r-biobase)
10488 ("r-biocgenerics" ,r-biocgenerics)
10489 ("r-doparallel" ,r-doparallel)
10490 ("r-dplyr" ,r-dplyr)
10492 ("r-ffbase" ,r-ffbase)
10493 ("r-foreach" ,r-foreach)
10494 ("r-genomeinfodb" ,r-genomeinfodb)
10495 ("r-genomicfeatures" ,r-genomicfeatures)
10496 ("r-genomicfiles" ,r-genomicfiles)
10497 ("r-genomicranges" ,r-genomicranges)
10498 ("r-ggbeeswarm" ,r-ggbeeswarm)
10499 ("r-ggplot2" ,r-ggplot2)
10500 ("r-gqtlbase" ,r-gqtlbase)
10501 ("r-hardyweinberg" ,r-hardyweinberg)
10502 ("r-homo-sapiens" ,r-homo-sapiens)
10503 ("r-iranges" ,r-iranges)
10504 ("r-limma" ,r-limma)
10506 ("r-plotly" ,r-plotly)
10507 ("r-reshape2" ,r-reshape2)
10508 ("r-s4vectors" ,r-s4vectors)
10509 ("r-shiny" ,r-shiny)
10510 ("r-snpstats" ,r-snpstats)
10511 ("r-summarizedexperiment" ,r-summarizedexperiment)
10512 ("r-variantannotation" ,r-variantannotation)))
10513 (home-page "https://bioconductor.org/packages/gQTLstats")
10514 (synopsis "Computationally efficient analysis for eQTL and allied studies")
10516 "This package provides tools for the computationally efficient analysis
10517 of @dfn{quantitative trait loci} (QTL) data, including eQTL, mQTL, dsQTL, etc.
10518 The software in this package aims to support refinements and functional
10519 interpretation of members of a collection of association statistics on a
10520 family of feature/genome hypotheses.")
10521 (license license:artistic2.0)))
10523 (define-public r-gviz
10530 (uri (bioconductor-uri "Gviz" version))
10533 "1fhli7ahkl5r43j0hc89ib41mfadj6qyrg36i03ncz8zs6iqwpx4"))))
10534 (properties `((upstream-name . "Gviz")))
10535 (build-system r-build-system)
10537 `(("r-annotationdbi" ,r-annotationdbi)
10538 ("r-biobase" ,r-biobase)
10539 ("r-biocgenerics" ,r-biocgenerics)
10540 ("r-biomart" ,r-biomart)
10541 ("r-biostrings" ,r-biostrings)
10542 ("r-biovizbase" ,r-biovizbase)
10543 ("r-bsgenome" ,r-bsgenome)
10544 ("r-digest" ,r-digest)
10545 ("r-genomeinfodb" ,r-genomeinfodb)
10546 ("r-genomicalignments" ,r-genomicalignments)
10547 ("r-genomicfeatures" ,r-genomicfeatures)
10548 ("r-genomicranges" ,r-genomicranges)
10549 ("r-iranges" ,r-iranges)
10550 ("r-lattice" ,r-lattice)
10551 ("r-latticeextra" ,r-latticeextra)
10552 ("r-matrixstats" ,r-matrixstats)
10553 ("r-rcolorbrewer" ,r-rcolorbrewer)
10554 ("r-rsamtools" ,r-rsamtools)
10555 ("r-rtracklayer" ,r-rtracklayer)
10556 ("r-s4vectors" ,r-s4vectors)
10557 ("r-xvector" ,r-xvector)))
10558 (home-page "https://bioconductor.org/packages/Gviz")
10559 (synopsis "Plotting data and annotation information along genomic coordinates")
10561 "Genomic data analyses requires integrated visualization of known genomic
10562 information and new experimental data. Gviz uses the biomaRt and the
10563 rtracklayer packages to perform live annotation queries to Ensembl and UCSC
10564 and translates this to e.g. gene/transcript structures in viewports of the
10565 grid graphics package. This results in genomic information plotted together
10567 (license license:artistic2.0)))
10569 (define-public r-gwascat
10576 (uri (bioconductor-uri "gwascat" version))
10579 "08ba9il4vbjjwlbwmqg4ai6ya1p09js9agn95sw0dhc9gqln42hx"))))
10580 (build-system r-build-system)
10582 `(("r-annotationdbi" ,r-annotationdbi)
10583 ("r-annotationhub" ,r-annotationhub)
10584 ("r-biocgenerics" ,r-biocgenerics)
10585 ("r-biostrings" ,r-biostrings)
10586 ("r-genomeinfodb" ,r-genomeinfodb)
10587 ("r-genomicfeatures" ,r-genomicfeatures)
10588 ("r-genomicranges" ,r-genomicranges)
10589 ("r-ggbio" ,r-ggbio)
10590 ("r-ggplot2" ,r-ggplot2)
10591 ("r-gqtlstats" ,r-gqtlstats)
10592 ("r-graph" ,r-graph)
10594 ("r-homo-sapiens" ,r-homo-sapiens)
10595 ("r-iranges" ,r-iranges)
10596 ("r-rsamtools" ,r-rsamtools)
10597 ("r-rtracklayer" ,r-rtracklayer)
10598 ("r-s4vectors" ,r-s4vectors)
10599 ("r-snpstats" ,r-snpstats)
10600 ("r-summarizedexperiment" ,r-summarizedexperiment)
10601 ("r-variantannotation" ,r-variantannotation)))
10602 (home-page "https://bioconductor.org/packages/gwascat")
10603 (synopsis "Tools for data in the EMBL-EBI GWAS catalog")
10605 "This package provides tools for representing and modeling data in the
10606 EMBL-EBI GWAS catalog.")
10607 (license license:artistic2.0)))
10609 (define-public r-sushi
10615 (uri (bioconductor-uri "Sushi" version))
10618 "1m15hmg4k0qhshyn65xfj5hx7xbaf0kxqw70lxisak6pj1w00l41"))))
10619 (properties `((upstream-name . "Sushi")))
10620 (build-system r-build-system)
10622 `(("r-biomart" ,r-biomart)
10624 (home-page "https://bioconductor.org/packages/Sushi")
10625 (synopsis "Tools for visualizing genomics data")
10627 "This package provides flexible, quantitative, and integrative genomic
10628 visualizations for publication-quality multi-panel figures.")
10629 (license license:gpl2+)))
10631 (define-public r-fithic
10637 (uri (bioconductor-uri "FitHiC" version))
10640 "06w4q836bi1mvkbl1saghv4r5p4hxpjg8cp7kgad13ls450kqmyd"))))
10641 (properties `((upstream-name . "FitHiC")))
10642 (build-system r-build-system)
10644 `(("r-data-table" ,r-data-table)
10645 ("r-fdrtool" ,r-fdrtool)
10646 ("r-rcpp" ,r-rcpp)))
10647 (home-page "https://bioconductor.org/packages/FitHiC")
10648 (synopsis "Confidence estimation for intra-chromosomal contact maps")
10650 "Fit-Hi-C is a tool for assigning statistical confidence estimates to
10651 intra-chromosomal contact maps produced by genome-wide genome architecture
10652 assays such as Hi-C.")
10653 (license license:gpl2+)))
10655 (define-public r-hitc
10661 (uri (bioconductor-uri "HiTC" version))
10664 "0qkk5139f51lwwy1yh7nbkflh5d69prirmhniwam34nlg9rzjm2z"))))
10665 (properties `((upstream-name . "HiTC")))
10666 (build-system r-build-system)
10668 `(("r-biostrings" ,r-biostrings)
10669 ("r-genomeinfodb" ,r-genomeinfodb)
10670 ("r-genomicranges" ,r-genomicranges)
10671 ("r-iranges" ,r-iranges)
10672 ("r-matrix" ,r-matrix)
10673 ("r-rcolorbrewer" ,r-rcolorbrewer)
10674 ("r-rtracklayer" ,r-rtracklayer)))
10675 (home-page "https://bioconductor.org/packages/HiTC")
10676 (synopsis "High throughput chromosome conformation capture analysis")
10678 "The HiTC package was developed to explore high-throughput \"C\" data
10679 such as 5C or Hi-C. Dedicated R classes as well as standard methods for
10680 quality controls, normalization, visualization, and further analysis are also
10682 (license license:artistic2.0)))
10684 (define-public r-qvalue
10691 (uri (bioconductor-uri "qvalue" version))
10694 "1ndwkj0hh7v4lwylq1v0fkxqs7mfmbcj8kxbdpj1wkvf131z2ns8"))))
10695 (build-system r-build-system)
10697 `(("r-ggplot2" ,r-ggplot2)
10698 ("r-reshape2" ,r-reshape2)))
10699 (home-page "http://github.com/jdstorey/qvalue")
10700 (synopsis "Q-value estimation for false discovery rate control")
10702 "This package takes a list of p-values resulting from the simultaneous
10703 testing of many hypotheses and estimates their q-values and local @dfn{false
10704 discovery rate} (FDR) values. The q-value of a test measures the proportion
10705 of false positives incurred when that particular test is called significant.
10706 The local FDR measures the posterior probability the null hypothesis is true
10707 given the test's p-value. Various plots are automatically generated, allowing
10708 one to make sensible significance cut-offs. The software can be applied to
10709 problems in genomics, brain imaging, astrophysics, and data mining.")
10710 ;; Any version of the LGPL.
10711 (license license:lgpl3+)))
10713 (define-public r-hdf5array
10715 (name "r-hdf5array")
10720 (uri (bioconductor-uri "HDF5Array" version))
10723 "1l0276qxkhgdxsfck3jmi8jvnsr20g10gjki53g0mqa45wnhm3ck"))))
10724 (properties `((upstream-name . "HDF5Array")))
10725 (build-system r-build-system)
10727 `(("r-biocgenerics" ,r-biocgenerics)
10728 ("r-delayedarray" ,r-delayedarray)
10729 ("r-iranges" ,r-iranges)
10730 ("r-rhdf5" ,r-rhdf5)
10731 ("r-s4vectors" ,r-s4vectors)))
10732 (home-page "https://bioconductor.org/packages/HDF5Array")
10733 (synopsis "HDF5 back end for DelayedArray objects")
10734 (description "This package provides an array-like container for convenient
10735 access and manipulation of HDF5 datasets. It supports delayed operations and
10736 block processing.")
10737 (license license:artistic2.0)))
10739 (define-public r-rhdf5lib
10741 (name "r-rhdf5lib")
10746 (uri (bioconductor-uri "Rhdf5lib" version))
10749 "1y59acac6v8hrhv84gghn9ifsni9xxxacaj177rrl4frmkrz4x3c"))))
10750 (properties `((upstream-name . "Rhdf5lib")))
10751 (build-system r-build-system)
10754 (modify-phases %standard-phases
10755 (add-after 'unpack 'do-not-use-bundled-hdf5
10756 (lambda* (#:key inputs #:allow-other-keys)
10757 (for-each delete-file '("configure" "configure.ac"))
10758 ;; Do not make other packages link with the proprietary libsz.
10759 (substitute* "R/zzz.R"
10760 (("'%s/libhdf5_cpp.a %s/libhdf5.a %s/libsz.a -lz'")
10761 "'%s/libhdf5_cpp.a %s/libhdf5.a %s/libhdf5.a -lz'")
10762 (("'%s/libhdf5.a %s/libsz.a -lz'")
10763 "'%s/libhdf5.a %s/libhdf5.a -lz'"))
10764 (with-directory-excursion "src"
10765 (invoke "tar" "xvf" (assoc-ref inputs "hdf5-source"))
10766 (rename-file (string-append "hdf5-" ,(package-version hdf5))
10768 ;; Remove timestamp and host system information to make
10769 ;; the build reproducible.
10770 (substitute* "hdf5/src/libhdf5.settings.in"
10771 (("Configured on: @CONFIG_DATE@")
10772 "Configured on: Guix")
10773 (("Uname information:.*")
10774 "Uname information: Linux\n")
10775 ;; Remove unnecessary store reference.
10777 "C Compiler: GCC\n"))
10778 (rename-file "Makevars.in" "Makevars")
10779 (substitute* "Makevars"
10780 (("HDF5_CXX_LIB=.*")
10781 (string-append "HDF5_CXX_LIB="
10782 (assoc-ref inputs "hdf5") "/lib/libhdf5_cpp.a\n"))
10784 (string-append "HDF5_LIB="
10785 (assoc-ref inputs "hdf5") "/lib/libhdf5.a\n"))
10786 (("HDF5_CXX_INCLUDE=.*") "HDF5_CXX_INCLUDE=./hdf5/c++/src\n")
10787 (("HDF5_INCLUDE=.*") "HDF5_INCLUDE=./hdf5/src\n")
10788 ;; szip is non-free software
10789 (("cp \\$\\{SZIP_LIB\\}.*") "")
10790 (("\\$\\{USER_LIB_DIR\\}libsz.a") "")))
10797 `(("hdf5-source" ,(package-source hdf5))))
10798 (home-page "https://bioconductor.org/packages/Rhdf5lib")
10799 (synopsis "HDF5 library as an R package")
10800 (description "This package provides C and C++ HDF5 libraries for use in R
10802 (license license:artistic2.0)))
10804 (define-public r-beachmat
10806 (name "r-beachmat")
10811 (uri (bioconductor-uri "beachmat" version))
10814 "1w90v0jx1zgrfxzx99gdkk0dz2vi25hr51jml1bvq33i64rj7996"))))
10815 (build-system r-build-system)
10820 `(("r-delayedarray" ,r-delayedarray)
10821 ("r-hdf5array" ,r-hdf5array)
10823 ("r-rhdf5" ,r-rhdf5)
10824 ("r-rhdf5lib" ,r-rhdf5lib)))
10825 (home-page "https://bioconductor.org/packages/beachmat")
10826 (synopsis "Compiling Bioconductor to handle each matrix type")
10827 (description "This package provides a consistent C++ class interface for a
10828 variety of commonly used matrix types, including sparse and HDF5-backed
10830 (license license:gpl3)))
10832 (define-public r-singlecellexperiment
10834 (name "r-singlecellexperiment")
10839 (uri (bioconductor-uri "SingleCellExperiment" version))
10842 "0mz3chia250v8v6q8r5cqv5fc4bpcw1hhrfr3p7l5i4xi85scpka"))))
10844 `((upstream-name . "SingleCellExperiment")))
10845 (build-system r-build-system)
10847 `(("r-biocgenerics" ,r-biocgenerics)
10848 ("r-s4vectors" ,r-s4vectors)
10849 ("r-summarizedexperiment" ,r-summarizedexperiment)))
10850 (home-page "https://bioconductor.org/packages/SingleCellExperiment")
10851 (synopsis "S4 classes for single cell data")
10852 (description "This package defines an S4 class for storing data from
10853 single-cell experiments. This includes specialized methods to store and
10854 retrieve spike-in information, dimensionality reduction coordinates and size
10855 factors for each cell, along with the usual metadata for genes and
10857 (license license:gpl3)))
10859 (define-public r-scater
10865 (uri (bioconductor-uri "scater" version))
10868 "0bhpikgz3b9f510dawsay4zry9rlp8vjx5n6zvwbcpwrd94p3903"))))
10869 (build-system r-build-system)
10871 `(("r-beachmat" ,r-beachmat)
10872 ("r-biobase" ,r-biobase)
10873 ("r-biocgenerics" ,r-biocgenerics)
10874 ("r-data-table" ,r-data-table)
10875 ("r-delayedarray" ,r-delayedarray)
10876 ("r-delayedmatrixstats" ,r-delayedmatrixstats)
10877 ("r-dplyr" ,r-dplyr)
10878 ("r-edger" ,r-edger)
10879 ("r-ggbeeswarm" ,r-ggbeeswarm)
10880 ("r-ggplot2" ,r-ggplot2)
10881 ("r-limma" ,r-limma)
10882 ("r-matrix" ,r-matrix)
10885 ("r-reshape2" ,r-reshape2)
10886 ("r-rhdf5" ,r-rhdf5)
10887 ("r-rhdf5lib" ,r-rhdf5lib)
10888 ("r-rjson" ,r-rjson)
10889 ("r-s4vectors" ,r-s4vectors)
10890 ("r-shiny" ,r-shiny)
10891 ("r-shinydashboard" ,r-shinydashboard)
10892 ("r-singlecellexperiment" ,r-singlecellexperiment)
10893 ("r-summarizedexperiment" ,r-summarizedexperiment)
10894 ("r-tximport" ,r-tximport)
10895 ("r-viridis" ,r-viridis)))
10896 (home-page "https://github.com/davismcc/scater")
10897 (synopsis "Single-cell analysis toolkit for gene expression data in R")
10898 (description "This package provides a collection of tools for doing
10899 various analyses of single-cell RNA-seq gene expression data, with a focus on
10901 (license license:gpl2+)))
10903 (define-public r-scran
10910 (uri (bioconductor-uri "scran" version))
10913 "0nbn5x75gf9d0p18w7vpkbv30cpdqvp5bz8xvila0h7jla7xdyih"))))
10914 (build-system r-build-system)
10916 `(("r-beachmat" ,r-beachmat)
10917 ("r-biocgenerics" ,r-biocgenerics)
10918 ("r-biocparallel" ,r-biocparallel)
10919 ("r-delayedarray" ,r-delayedarray)
10920 ("r-delayedmatrixstats" ,r-delayedmatrixstats)
10922 ("r-dynamictreecut" ,r-dynamictreecut)
10923 ("r-edger" ,r-edger)
10925 ("r-ggplot2" ,r-ggplot2)
10926 ("r-igraph" ,r-igraph)
10927 ("r-limma" ,r-limma)
10928 ("r-matrix" ,r-matrix)
10930 ("r-rhdf5lib" ,r-rhdf5lib)
10931 ("r-s4vectors" ,r-s4vectors)
10932 ("r-scater" ,r-scater)
10933 ("r-shiny" ,r-shiny)
10934 ("r-singlecellexperiment" ,r-singlecellexperiment)
10935 ("r-statmod" ,r-statmod)
10936 ("r-summarizedexperiment" ,r-summarizedexperiment)
10937 ("r-viridis" ,r-viridis)))
10938 (home-page "https://bioconductor.org/packages/scran")
10939 (synopsis "Methods for single-cell RNA-Seq data analysis")
10940 (description "This package implements a variety of low-level analyses of
10941 single-cell RNA-seq data. Methods are provided for normalization of
10942 cell-specific biases, assignment of cell cycle phase, and detection of highly
10943 variable and significantly correlated genes.")
10944 (license license:gpl3)))
10946 (define-public r-delayedmatrixstats
10948 (name "r-delayedmatrixstats")
10953 (uri (bioconductor-uri "DelayedMatrixStats" version))
10956 "1dasghfy8x27zzmd0igag4mc1gxxxbchsl4hpc1050dj3wnw9w3y"))))
10958 `((upstream-name . "DelayedMatrixStats")))
10959 (build-system r-build-system)
10961 `(("r-delayedarray" ,r-delayedarray)
10962 ("r-iranges" ,r-iranges)
10963 ("r-matrix" ,r-matrix)
10964 ("r-matrixstats" ,r-matrixstats)
10965 ("r-s4vectors" ,r-s4vectors)))
10966 (home-page "https://github.com/PeteHaitch/DelayedMatrixStats")
10967 (synopsis "Functions that apply to rows and columns of DelayedMatrix objects")
10969 "This package provides a port of the @code{matrixStats} API for use with
10970 @code{DelayedMatrix} objects from the @code{DelayedArray} package. It
10971 contains high-performing functions operating on rows and columns of
10972 @code{DelayedMatrix} objects, e.g. @code{colMedians}, @code{rowMedians},
10973 @code{colRanks}, @code{rowRanks}, @code{colSds}, and @code{rowSds}. Functions
10974 are optimized per data type and for subsetted calculations such that both
10975 memory usage and processing time is minimized.")
10976 (license license:expat)))
10978 (define-public r-phangorn
10980 (name "r-phangorn")
10985 (uri (cran-uri "phangorn" version))
10988 "0xc8k552nxczy19jr0xjjagrzc8x6lafasgk2c099ls8bc1yml1i"))))
10989 (build-system r-build-system)
10992 ("r-fastmatch" ,r-fastmatch)
10993 ("r-igraph" ,r-igraph)
10994 ("r-magrittr" ,r-magrittr)
10995 ("r-matrix" ,r-matrix)
10996 ("r-quadprog" ,r-quadprog)
10997 ("r-rcpp" ,r-rcpp)))
10998 (home-page "https://github.com/KlausVigo/phangorn")
10999 (synopsis "Phylogenetic analysis in R")
11001 "Phangorn is a package for phylogenetic analysis in R. It supports
11002 estimation of phylogenetic trees and networks using Maximum Likelihood,
11003 Maximum Parsimony, distance methods and Hadamard conjugation.")
11004 (license license:gpl2+)))
11006 (define-public r-dropbead
11007 (let ((commit "d746c6f3b32110428ea56d6a0001ce52a251c247")
11010 (name "r-dropbead")
11011 (version (string-append "0-" revision "." (string-take commit 7)))
11015 (uri (git-reference
11016 (url "https://github.com/rajewsky-lab/dropbead.git")
11018 (file-name (git-file-name name version))
11021 "0sbzma49aiiyw8b0jpr7fnhzys9nsqmp4hy4hdz1gzyg1lhnca26"))))
11022 (build-system r-build-system)
11024 `(("r-ggplot2" ,r-ggplot2)
11025 ("r-rcolorbrewer" ,r-rcolorbrewer)
11026 ("r-gridextra" ,r-gridextra)
11027 ("r-gplots" ,r-gplots)
11028 ("r-plyr" ,r-plyr)))
11029 (home-page "https://github.com/rajewsky-lab/dropbead")
11030 (synopsis "Basic exploration and analysis of Drop-seq data")
11031 (description "This package offers a quick and straight-forward way to
11032 explore and perform basic analysis of single cell sequencing data coming from
11033 droplet sequencing. It has been particularly tailored for Drop-seq.")
11034 (license license:gpl3))))
11036 (define htslib-for-sambamba
11037 (let ((commit "2f3c3ea7b301f9b45737a793c0b2dcf0240e5ee5"))
11040 (name "htslib-for-sambamba")
11041 (version (string-append "1.3.1-1." (string-take commit 9)))
11045 (uri (git-reference
11046 (url "https://github.com/lomereiter/htslib.git")
11048 (file-name (string-append "htslib-" version "-checkout"))
11051 "0g38g8s3npr0gjm9fahlbhiskyfws9l5i0x1ml3rakzj7az5l9c9"))))
11053 `(("autoconf" ,autoconf)
11054 ("automake" ,automake)
11055 ,@(package-native-inputs htslib))))))
11057 (define-public sambamba
11060 (version "0.6.7-10-g223fa20")
11064 (uri (git-reference
11065 (url "https://github.com/lomereiter/sambamba.git")
11066 (commit (string-append "v" version))))
11067 (file-name (string-append name "-" version "-checkout"))
11070 "1zb9hrxglxqh13ava9wwri30cvf85hjnbn8ccnr8l60a3k5avczn"))))
11071 (build-system gnu-build-system)
11073 `(#:tests? #f ; there is no test target
11074 #:parallel-build? #f ; not supported
11076 (modify-phases %standard-phases
11077 (delete 'configure)
11078 (add-after 'unpack 'fix-ldc-version
11080 (substitute* "gen_ldc_version_info.py"
11081 (("/usr/bin/env.*") (which "python")))
11082 (substitute* "Makefile"
11083 (("\\$\\(shell which ldmd2\\)") (which "ldmd2")))
11085 (add-after 'unpack 'place-biod-and-undead
11086 (lambda* (#:key inputs #:allow-other-keys)
11087 (copy-recursively (assoc-ref inputs "biod") "BioD")
11088 (copy-recursively (assoc-ref inputs "undead") "undeaD")
11090 (add-after 'unpack 'unbundle-prerequisites
11092 (substitute* "Makefile"
11093 (("htslib/libhts.a lz4/lib/liblz4.a")
11095 ((" htslib-static lz4-static") ""))
11098 (lambda* (#:key outputs #:allow-other-keys)
11099 (let* ((out (assoc-ref outputs "out"))
11100 (bin (string-append out "/bin")))
11102 (install-file "build/sambamba" bin)
11107 ("python" ,python2-minimal)
11109 ,(let ((commit "c778e4f2d8bacea7499283ce39f5577b232732c6"))
11112 (uri (git-reference
11113 (url "https://github.com/biod/BioD.git")
11115 (file-name (string-append "biod-"
11116 (string-take commit 9)
11120 "1z90562hg47i63gx042wb3ak2vqjg5z7hwgn9bp2pdxfg3nxrw37")))))
11122 ,(let ((commit "92803d25c88657e945511f0976a0c79d8da46e89"))
11125 (uri (git-reference
11126 (url "https://github.com/dlang/undeaD.git")
11128 (file-name (string-append "undead-"
11129 (string-take commit 9)
11133 "0vq6n81vzqvgphjw54lz2isc1j8lcxwjdbrhqz1h5gwrvw9w5138")))))))
11136 ("htslib" ,htslib-for-sambamba)))
11137 (home-page "http://lomereiter.github.io/sambamba")
11138 (synopsis "Tools for working with SAM/BAM data")
11139 (description "Sambamba is a high performance modern robust and
11140 fast tool (and library), written in the D programming language, for
11141 working with SAM and BAM files. Current parallelised functionality is
11142 an important subset of samtools functionality, including view, index,
11143 sort, markdup, and depth.")
11144 (license license:gpl2+)))
11146 (define-public ritornello
11148 (name "ritornello")
11152 (uri (string-append "https://github.com/KlugerLab/"
11153 "Ritornello/archive/v"
11154 version ".tar.gz"))
11155 (file-name (string-append name "-" version ".tar.gz"))
11158 "02nik86gq9ljjriv6pamwlmqnfky3ads1fpklx6mc3hx6k40pg38"))))
11159 (build-system gnu-build-system)
11161 `(#:tests? #f ; there are no tests
11163 (modify-phases %standard-phases
11164 (add-after 'unpack 'patch-samtools-references
11165 (lambda* (#:key inputs #:allow-other-keys)
11166 (substitute* '("src/SamStream.h"
11167 "src/BufferedGenomeReader.h")
11168 (("<sam.h>") "<samtools/sam.h>"))
11170 (delete 'configure)
11172 (lambda* (#:key inputs outputs #:allow-other-keys)
11173 (let* ((out (assoc-ref outputs "out"))
11174 (bin (string-append out "/bin/")))
11176 (install-file "bin/Ritornello" bin)
11179 `(("samtools" ,samtools-0.1)
11183 (home-page "https://github.com/KlugerLab/Ritornello")
11184 (synopsis "Control-free peak caller for ChIP-seq data")
11185 (description "Ritornello is a ChIP-seq peak calling algorithm based on
11186 signal processing that can accurately call binding events without the need to
11187 do a pair total DNA input or IgG control sample. It has been tested for use
11188 with narrow binding events such as transcription factor ChIP-seq.")
11189 (license license:gpl3+)))
11191 (define-public trim-galore
11193 (name "trim-galore")
11198 (uri (git-reference
11199 (url "https://github.com/FelixKrueger/TrimGalore.git")
11201 (file-name (string-append name "-" version "-checkout"))
11204 "0x5892l48c816pf00wmnz5vq0zq6170d3xc8zrxncd4jcz7h1p71"))))
11205 (build-system gnu-build-system)
11207 `(#:tests? #f ; no tests
11209 (modify-phases %standard-phases
11210 (delete 'configure)
11212 (add-after 'unpack 'hardcode-tool-references
11213 (lambda* (#:key inputs #:allow-other-keys)
11214 (substitute* "trim_galore"
11215 (("\\$path_to_cutadapt = 'cutadapt'")
11216 (string-append "$path_to_cutadapt = '"
11217 (assoc-ref inputs "cutadapt")
11220 (string-append "| "
11221 (assoc-ref inputs "gzip")
11224 (string-append "\""
11225 (assoc-ref inputs "gzip")
11229 (lambda* (#:key outputs #:allow-other-keys)
11230 (let ((bin (string-append (assoc-ref outputs "out")
11233 (install-file "trim_galore" bin)
11238 ("cutadapt" ,cutadapt)))
11240 `(("unzip" ,unzip)))
11241 (home-page "http://www.bioinformatics.babraham.ac.uk/projects/trim_galore/")
11242 (synopsis "Wrapper around Cutadapt and FastQC")
11243 (description "Trim Galore! is a wrapper script to automate quality and
11244 adapter trimming as well as quality control, with some added functionality to
11245 remove biased methylation positions for RRBS sequence files.")
11246 (license license:gpl3+)))
11248 (define-public gess
11254 (uri (string-append "http://compbio.uthscsa.edu/"
11256 "gess-" version ".src.tar.gz"))
11259 "0hyk403kxscclzfs24pvdgiv0wm03kjcziqdrp5w46cb049gz0d7"))))
11260 (build-system gnu-build-system)
11262 `(#:tests? #f ; no tests
11264 (modify-phases %standard-phases
11265 (delete 'configure)
11268 (lambda* (#:key inputs outputs #:allow-other-keys)
11269 (let* ((python (assoc-ref inputs "python"))
11270 (out (assoc-ref outputs "out"))
11271 (bin (string-append out "/bin/"))
11272 (target (string-append
11273 out "/lib/python2.7/site-packages/gess/")))
11275 (copy-recursively "." target)
11276 ;; Make GESS.py executable
11277 (chmod (string-append target "GESS.py") #o555)
11278 ;; Add Python shebang to the top and make Matplotlib
11280 (substitute* (string-append target "GESS.py")
11281 (("\"\"\"Description:" line)
11282 (string-append "#!" (which "python") "
11284 matplotlib.use('Agg')
11286 ;; Make sure GESS has all modules in its path
11287 (wrap-program (string-append target "GESS.py")
11288 `("PYTHONPATH" ":" prefix (,target ,(getenv "PYTHONPATH"))))
11290 (symlink (string-append target "GESS.py")
11291 (string-append bin "GESS.py"))
11294 `(("python" ,python-2)
11295 ("python2-pysam" ,python2-pysam)
11296 ("python2-scipy" ,python2-scipy)
11297 ("python2-numpy" ,python2-numpy)
11298 ("python2-networkx" ,python2-networkx)
11299 ("python2-biopython" ,python2-biopython)))
11300 (home-page "http://compbio.uthscsa.edu/GESS_Web/")
11301 (synopsis "Detect exon-skipping events from raw RNA-seq data")
11303 "GESS is an implementation of a novel computational method to detect de
11304 novo exon-skipping events directly from raw RNA-seq data without the prior
11305 knowledge of gene annotation information. GESS stands for the graph-based
11306 exon-skipping scanner detection scheme.")
11307 (license license:bsd-3)))
11309 (define-public phylip
11316 (uri (string-append "http://evolution.gs.washington.edu/phylip/"
11317 "download/phylip-" version ".tar.gz"))
11320 "01jar1rayhr2gba2pgbw49m56rc5z4p5wn3ds0m188hrlln4a2nd"))))
11321 (build-system gnu-build-system)
11323 `(#:tests? #f ; no check target
11324 #:make-flags (list "-f" "Makefile.unx" "install")
11325 #:parallel-build? #f ; not supported
11327 (modify-phases %standard-phases
11328 (add-after 'unpack 'enter-dir
11329 (lambda _ (chdir "src") #t))
11330 (delete 'configure)
11332 (lambda* (#:key inputs outputs #:allow-other-keys)
11333 (let ((target (string-append (assoc-ref outputs "out")
11336 (for-each (lambda (file)
11337 (install-file file target))
11338 (find-files "../exe" ".*")))
11340 (home-page "http://evolution.genetics.washington.edu/phylip/")
11341 (synopsis "Tools for inferring phylogenies")
11342 (description "PHYLIP (the PHYLogeny Inference Package) is a package of
11343 programs for inferring phylogenies (evolutionary trees).")
11344 (license license:bsd-2)))
11353 (uri (string-append "https://integrativemodeling.org/"
11354 version "/download/imp-" version ".tar.gz"))
11357 "0lxqx7vh79d771svr611dkilp6sn30qrbw8zvscbrm37v38d2j6h"))))
11358 (build-system cmake-build-system)
11360 `(;; FIXME: Some tests fail because they produce warnings, others fail
11361 ;; because the PYTHONPATH does not include the modeller's directory.
11369 ("python" ,python-2)))
11371 `(("python2-numpy" ,python2-numpy)
11372 ("python2-scipy" ,python2-scipy)
11373 ("python2-pandas" ,python2-pandas)
11374 ("python2-scikit-learn" ,python2-scikit-learn)
11375 ("python2-networkx" ,python2-networkx)))
11376 (home-page "https://integrativemodeling.org")
11377 (synopsis "Integrative modeling platform")
11378 (description "IMP's broad goal is to contribute to a comprehensive
11379 structural characterization of biomolecules ranging in size and complexity
11380 from small peptides to large macromolecular assemblies, by integrating data
11381 from diverse biochemical and biophysical experiments. IMP provides a C++ and
11382 Python toolbox for solving complex modeling problems, and a number of
11383 applications for tackling some common problems in a user-friendly way.")
11384 ;; IMP is largely available under the GNU Lesser GPL; see the file
11385 ;; COPYING.LGPL for the full text of this license. Some IMP modules are
11386 ;; available under the GNU GPL (see the file COPYING.GPL).
11387 (license (list license:lgpl2.1+
11390 (define-public tadbit
11396 (uri (string-append "https://github.com/3DGenomes/TADbit/"
11397 "archive/v" version ".tar.gz"))
11398 (file-name (string-append name "-" version ".tar.gz"))
11401 "1cnfqrl4685zar4nnw94j94nhvl2h29jm448nadqi1h05z6fdk4f"))))
11402 (build-system python-build-system)
11404 `(;; Tests are included and must be run after installation, but
11405 ;; they are incomplete and thus cannot be run.
11409 (modify-phases %standard-phases
11410 (add-after 'unpack 'fix-problems-with-setup.py
11411 (lambda* (#:key outputs #:allow-other-keys)
11412 ;; setup.py opens these files for writing
11413 (chmod "_pytadbit/_version.py" #o664)
11414 (chmod "README.rst" #o664)
11416 ;; Don't attempt to install the bash completions to
11417 ;; the home directory.
11418 (rename-file "extras/.bash_completion"
11420 (substitute* "setup.py"
11421 (("\\(path.expanduser\\('~'\\)")
11422 (string-append "(\""
11423 (assoc-ref outputs "out")
11424 "/etc/bash_completion.d\""))
11425 (("extras/\\.bash_completion")
11429 ;; TODO: add Chimera for visualization
11432 ("python2-scipy" ,python2-scipy)
11433 ("python2-numpy" ,python2-numpy)
11434 ("python2-matplotlib" ,python2-matplotlib)
11435 ("python2-pysam" ,python2-pysam)))
11436 (home-page "http://3dgenomes.github.io/TADbit/")
11437 (synopsis "Analyze, model, and explore 3C-based data")
11439 "TADbit is a complete Python library to deal with all steps to analyze,
11440 model, and explore 3C-based data. With TADbit the user can map FASTQ files to
11441 obtain raw interaction binned matrices (Hi-C like matrices), normalize and
11442 correct interaction matrices, identify and compare the so-called
11443 @dfn{Topologically Associating Domains} (TADs), build 3D models from the
11444 interaction matrices, and finally, extract structural properties from the
11445 models. TADbit is complemented by TADkit for visualizing 3D models.")
11446 (license license:gpl3+)))
11448 (define-public kentutils
11451 ;; 302.1.0 is out, but the only difference is the inclusion of
11452 ;; pre-built binaries.
11453 (version "302.0.0")
11457 (uri (string-append "https://github.com/ENCODE-DCC/kentUtils/"
11458 "archive/v" version ".tar.gz"))
11459 (file-name (string-append name "-" version ".tar.gz"))
11462 "134aja3k1cj32kbk1nnw0q9gxjb2krr15q6sga8qldzvc0585rmm"))
11463 (modules '((guix build utils)
11468 ;; Only the contents of the specified directories are free
11469 ;; for all uses, so we remove the rest. "hg/autoSql" and
11470 ;; "hg/autoXml" are nominally free, but they depend on a
11471 ;; library that is built from the sources in "hg/lib",
11472 ;; which is nonfree.
11473 (let ((free (list "." ".."
11474 "utils" "lib" "inc" "tagStorm"
11475 "parasol" "htslib"))
11476 (directory? (lambda (file)
11477 (eq? 'directory (stat:type (stat file))))))
11478 (for-each (lambda (file)
11479 (and (directory? file)
11480 (delete-file-recursively file)))
11481 (map (cut string-append "src/" <>)
11484 (not (member file free)))))))
11485 ;; Only make the utils target, not the userApps target,
11486 ;; because that requires libraries we won't build.
11487 (substitute* "Makefile"
11488 ((" userApps") " utils"))
11489 ;; Only build libraries that are free.
11490 (substitute* "src/makefile"
11491 (("DIRS =.*") "DIRS =\n")
11492 (("cd jkOwnLib.*") "")
11495 (substitute* "src/utils/makefile"
11496 ;; These tools depend on "jkhgap.a", which is part of the
11497 ;; nonfree "src/hg/lib" directory.
11498 (("raSqlQuery") "")
11499 (("pslLiftSubrangeBlat") "")
11501 ;; Do not build UCSC tools, which may require nonfree
11503 (("ALL_APPS =.*") "ALL_APPS = $(UTILS_APPLIST)\n"))
11505 (build-system gnu-build-system)
11507 `( ;; There is no global test target and the test target for
11508 ;; individual tools depends on input files that are not
11512 (modify-phases %standard-phases
11513 (add-after 'unpack 'fix-paths
11515 (substitute* "Makefile"
11516 (("/bin/echo") (which "echo")))
11518 (add-after 'unpack 'prepare-samtabix
11519 (lambda* (#:key inputs #:allow-other-keys)
11520 (copy-recursively (assoc-ref inputs "samtabix")
11523 (delete 'configure)
11525 (lambda* (#:key outputs #:allow-other-keys)
11526 (let ((bin (string-append (assoc-ref outputs "out")
11528 (copy-recursively "bin" bin))
11534 (uri (git-reference
11535 (url "http://genome-source.cse.ucsc.edu/samtabix.git")
11536 (commit "10fd107909c1ac4d679299908be4262a012965ba")))
11539 "0c1nj64l42v395sa84n7az43xiap4i6f9n9dfz4058aqiwkhkmma"))))))
11545 ("mariadb" ,mariadb)
11546 ("openssl" ,openssl)))
11547 (home-page "http://genome.cse.ucsc.edu/index.html")
11548 (synopsis "Assorted bioinformatics utilities")
11549 (description "This package provides the kentUtils, a selection of
11550 bioinformatics utilities used in combination with the UCSC genome
11552 ;; Only a subset of the sources are released under a non-copyleft
11553 ;; free software license. All other sources are removed in a
11554 ;; snippet. See this bug report for an explanation of how the
11555 ;; license statements apply:
11556 ;; https://github.com/ENCODE-DCC/kentUtils/issues/12
11557 (license (license:non-copyleft
11558 "http://genome.ucsc.edu/license/"
11559 "The contents of this package are free for all uses."))))
11561 (define-public f-seq
11562 (let ((commit "6ccded34cff38cf432deed8503648b4a66953f9b")
11566 (version (string-append "1.1-" revision "." (string-take commit 7)))
11569 (uri (git-reference
11570 (url "https://github.com/aboyle/F-seq.git")
11572 (file-name (string-append name "-" version))
11575 "1nk33k0yajg2id4g59bc4szr58r2q6pdq42vgcw054m8ip9wv26h"))
11576 (modules '((guix build utils)))
11577 ;; Remove bundled Java library archives.
11580 (for-each delete-file (find-files "lib" ".*"))
11582 (build-system ant-build-system)
11584 `(#:tests? #f ; no tests included
11586 (modify-phases %standard-phases
11588 (lambda* (#:key inputs outputs #:allow-other-keys)
11589 (let* ((target (assoc-ref outputs "out"))
11590 (bin (string-append target "/bin"))
11591 (doc (string-append target "/share/doc/f-seq"))
11592 (lib (string-append target "/lib")))
11595 (substitute* "bin/linux/fseq"
11596 (("java") (which "java"))
11597 (("\\$REALDIR/../lib/commons-cli-1.1.jar")
11598 (string-append (assoc-ref inputs "java-commons-cli")
11599 "/share/java/commons-cli.jar"))
11601 (string-append "REALDIR=" bin "\n")))
11602 (install-file "README.txt" doc)
11603 (install-file "bin/linux/fseq" bin)
11604 (install-file "build~/fseq.jar" lib)
11605 (copy-recursively "lib" lib)
11609 ("java-commons-cli" ,java-commons-cli)))
11610 (home-page "http://fureylab.web.unc.edu/software/fseq/")
11611 (synopsis "Feature density estimator for high-throughput sequence tags")
11613 "F-Seq is a software package that generates a continuous tag sequence
11614 density estimation allowing identification of biologically meaningful sites
11615 such as transcription factor binding sites (ChIP-seq) or regions of open
11616 chromatin (DNase-seq). Output can be displayed directly in the UCSC Genome
11618 (license license:gpl3+))))
11620 (define-public bismark
11627 (uri (git-reference
11628 (url "https://github.com/FelixKrueger/Bismark.git")
11630 (file-name (string-append name "-" version "-checkout"))
11633 "0yb5l36slwg02fp4b1jdlplgljcsxgqfzvzihzdnphd87dghcc84"))
11636 ;; highcharts.js is non-free software. The code is available under
11637 ;; CC-BY-NC or proprietary licenses only.
11638 (delete-file "bismark_sitrep/highcharts.js")
11640 (build-system perl-build-system)
11642 `(#:tests? #f ; there are no tests
11644 (modify-phases %standard-phases
11645 (delete 'configure)
11648 (lambda* (#:key inputs outputs #:allow-other-keys)
11649 (let* ((out (assoc-ref outputs "out"))
11650 (bin (string-append out "/bin"))
11651 (share (string-append out "/share/bismark"))
11652 (docdir (string-append out "/share/doc/bismark"))
11653 (docs '("Docs/Bismark_User_Guide.html"))
11654 (scripts '("bismark"
11655 "bismark_genome_preparation"
11656 "bismark_methylation_extractor"
11659 "coverage2cytosine"
11660 "deduplicate_bismark"
11661 "filter_non_conversion"
11663 "bismark2summary")))
11664 (substitute* "bismark2report"
11665 (("\\$RealBin/bismark_sitrep")
11666 (string-append share "/bismark_sitrep")))
11670 (for-each (lambda (file) (install-file file bin))
11672 (for-each (lambda (file) (install-file file docdir))
11674 (copy-recursively "Docs/Images" (string-append docdir "/Images"))
11675 (copy-recursively "bismark_sitrep"
11676 (string-append share "/bismark_sitrep"))
11678 ;; Fix references to gunzip
11679 (substitute* (map (lambda (file)
11680 (string-append bin "/" file))
11683 (string-append "\"" (assoc-ref inputs "gzip")
11684 "/bin/gunzip -c")))
11688 (home-page "http://www.bioinformatics.babraham.ac.uk/projects/bismark/")
11689 (synopsis "Map bisulfite treated sequence reads and analyze methylation")
11690 (description "Bismark is a program to map bisulfite treated sequencing
11691 reads to a genome of interest and perform methylation calls in a single step.
11692 The output can be easily imported into a genome viewer, such as SeqMonk, and
11693 enables a researcher to analyse the methylation levels of their samples
11694 straight away. Its main features are:
11697 @item Bisulfite mapping and methylation calling in one single step
11698 @item Supports single-end and paired-end read alignments
11699 @item Supports ungapped and gapped alignments
11700 @item Alignment seed length, number of mismatches etc are adjustable
11701 @item Output discriminates between cytosine methylation in CpG, CHG
11704 (license license:gpl3+)))
11706 (define-public paml
11712 (uri (string-append "http://abacus.gene.ucl.ac.uk/software/"
11713 "paml" version ".tgz"))
11716 "13zf6h9fiqghwhch2h06x1zdr6s42plsnqahflp5g7myr3han3s6"))
11717 (modules '((guix build utils)))
11718 ;; Remove Windows binaries
11721 (for-each delete-file (find-files "." "\\.exe$"))
11723 (build-system gnu-build-system)
11725 `(#:tests? #f ; there are no tests
11726 #:make-flags '("CC=gcc")
11728 (modify-phases %standard-phases
11729 (replace 'configure
11731 (substitute* "src/BFdriver.c"
11732 (("/bin/bash") (which "bash")))
11736 (lambda* (#:key outputs #:allow-other-keys)
11737 (let ((tools '("baseml" "basemlg" "codeml"
11738 "pamp" "evolver" "yn00" "chi2"))
11739 (bin (string-append (assoc-ref outputs "out") "/bin"))
11740 (docdir (string-append (assoc-ref outputs "out")
11741 "/share/doc/paml")))
11743 (for-each (lambda (file) (install-file file bin)) tools)
11744 (copy-recursively "../doc" docdir)
11746 (home-page "http://abacus.gene.ucl.ac.uk/software/paml.html")
11747 (synopsis "Phylogentic analysis by maximum likelihood")
11748 (description "PAML (for Phylogentic Analysis by Maximum Likelihood)
11749 contains a few programs for model fitting and phylogenetic tree reconstruction
11750 using nucleotide or amino-acid sequence data.")
11752 (license license:gpl3)))
11754 (define-public kallisto
11760 (uri (string-append "https://github.com/pachterlab/"
11761 "kallisto/archive/v" version ".tar.gz"))
11762 (file-name (string-append name "-" version ".tar.gz"))
11765 "03j3iqhvq7ya3c91gidly3k3jvgm97vjq4scihrlxh315j696r11"))))
11766 (build-system cmake-build-system)
11767 (arguments `(#:tests? #f)) ; no "check" target
11771 (home-page "http://pachterlab.github.io/kallisto/")
11772 (synopsis "Near-optimal RNA-Seq quantification")
11774 "Kallisto is a program for quantifying abundances of transcripts from
11775 RNA-Seq data, or more generally of target sequences using high-throughput
11776 sequencing reads. It is based on the novel idea of pseudoalignment for
11777 rapidly determining the compatibility of reads with targets, without the need
11778 for alignment. Pseudoalignment of reads preserves the key information needed
11779 for quantification, and kallisto is therefore not only fast, but also as
11780 accurate as existing quantification tools.")
11781 (license license:bsd-2)))
11783 (define-public libgff
11789 (uri (string-append
11790 "https://github.com/Kingsford-Group/"
11791 "libgff/archive/v" version ".tar.gz"))
11792 (file-name (string-append name "-" version ".tar.gz"))
11795 "0vc4nxyhlm6g9vvmx5l4lfs5pnvixsv1hiiy4kddf2y3p6jna8ls"))))
11796 (build-system cmake-build-system)
11797 (arguments `(#:tests? #f)) ; no tests included
11798 (home-page "https://github.com/Kingsford-Group/libgff")
11799 (synopsis "Parser library for reading/writing GFF files")
11800 (description "This is a simple \"libraryfication\" of the GFF/GTF parsing
11801 code that is used in the Cufflinks codebase. The goal of this library is to
11802 provide this functionality without the necessity of drawing in a heavy-weight
11803 dependency like SeqAn.")
11804 (license (license:x11-style "https://www.boost.org/LICENSE_1_0.txt"))))
11806 (define-public libdivsufsort
11808 (name "libdivsufsort")
11812 (uri (git-reference
11813 (url "https://github.com/y-256/libdivsufsort.git")
11815 (file-name (git-file-name name version))
11818 "0fgdz9fzihlvjjrxy01md1bv9vh12rkgkwbm90b1hj5xpbaqp7z2"))))
11819 (build-system cmake-build-system)
11821 '(#:tests? #f ; there are no tests
11823 ;; Needed for rapmap and sailfish.
11824 '("-DBUILD_DIVSUFSORT64=ON")))
11825 (home-page "https://github.com/y-256/libdivsufsort")
11826 (synopsis "Lightweight suffix-sorting library")
11827 (description "libdivsufsort is a software library that implements a
11828 lightweight suffix array construction algorithm. This library provides a
11829 simple and an efficient C API to construct a suffix array and a
11830 Burrows-Wheeler transformed string from a given string over a constant-size
11831 alphabet. The algorithm runs in O(n log n) worst-case time using only 5n+O(1)
11832 bytes of memory space, where n is the length of the string.")
11833 (license license:expat)))
11835 (define-public sailfish
11842 (string-append "https://github.com/kingsfordgroup/"
11843 "sailfish/archive/v" version ".tar.gz"))
11844 (file-name (string-append name "-" version ".tar.gz"))
11847 "1inn60dxiwsz8g9w7kvfhjxj4bwfb0r12dyhpzzhfbig712dkmm0"))
11848 (modules '((guix build utils)))
11851 ;; Delete bundled headers for eigen3.
11852 (delete-file-recursively "include/eigen3/")
11854 (build-system cmake-build-system)
11856 `(#:configure-flags
11857 (list (string-append "-DBOOST_INCLUDEDIR="
11858 (assoc-ref %build-inputs "boost")
11860 (string-append "-DBOOST_LIBRARYDIR="
11861 (assoc-ref %build-inputs "boost")
11863 (string-append "-DBoost_LIBRARIES="
11864 "-lboost_iostreams "
11865 "-lboost_filesystem "
11870 "-lboost_program_options")
11871 "-DBoost_FOUND=TRUE"
11872 ;; Don't download RapMap---we already have it!
11873 "-DFETCHED_RAPMAP=1")
11874 ;; Tests must be run after installation and the location of the test
11875 ;; data file must be overridden. But the tests fail. It looks like
11876 ;; they are not really meant to be run.
11879 (modify-phases %standard-phases
11880 ;; Boost cannot be found, even though it's right there.
11881 (add-after 'unpack 'do-not-look-for-boost
11882 (lambda* (#:key inputs #:allow-other-keys)
11883 (substitute* "CMakeLists.txt"
11884 (("find_package\\(Boost 1\\.53\\.0") "#"))))
11885 (add-after 'unpack 'do-not-assign-to-macro
11887 (substitute* "include/spdlog/details/format.cc"
11888 (("const unsigned CHAR_WIDTH = 1;") ""))))
11889 (add-after 'unpack 'prepare-rapmap
11890 (lambda* (#:key inputs #:allow-other-keys)
11891 (let ((src "external/install/src/rapmap/")
11892 (include "external/install/include/rapmap/")
11893 (rapmap (assoc-ref inputs "rapmap")))
11894 (mkdir-p "/tmp/rapmap")
11895 (system* "tar" "xf"
11896 (assoc-ref inputs "rapmap")
11898 "--strip-components=1")
11901 (for-each (lambda (file)
11902 (install-file file src))
11903 (find-files "/tmp/rapmap/src" "\\.(c|cpp)"))
11904 (copy-recursively "/tmp/rapmap/include" include))))
11905 (add-after 'unpack 'use-system-libraries
11906 (lambda* (#:key inputs #:allow-other-keys)
11907 (substitute* '("src/SailfishIndexer.cpp"
11908 "src/SailfishUtils.cpp"
11909 "src/SailfishQuantify.cpp"
11910 "src/FASTAParser.cpp"
11912 "include/SailfishUtils.hpp"
11913 "include/SailfishIndex.hpp"
11914 "include/CollapsedEMOptimizer.hpp"
11915 "src/CollapsedEMOptimizer.cpp")
11916 (("#include \"jellyfish/config.h\"") ""))
11917 (substitute* "src/CMakeLists.txt"
11918 (("\\$\\{GAT_SOURCE_DIR\\}/external/install/include/jellyfish-2.2..")
11919 (string-append (assoc-ref inputs "jellyfish")
11920 "/include/jellyfish-" ,(package-version jellyfish)))
11921 (("\\$\\{GAT_SOURCE_DIR\\}/external/install/lib/libjellyfish-2.0.a")
11922 (string-append (assoc-ref inputs "jellyfish")
11923 "/lib/libjellyfish-2.0.a"))
11924 (("\\$\\{GAT_SOURCE_DIR\\}/external/install/lib/libdivsufsort.a")
11925 (string-append (assoc-ref inputs "libdivsufsort")
11926 "/lib/libdivsufsort.so"))
11927 (("\\$\\{GAT_SOURCE_DIR\\}/external/install/lib/libdivsufsort64.a")
11928 (string-append (assoc-ref inputs "libdivsufsort")
11929 "/lib/libdivsufsort64.so")))
11930 (substitute* "CMakeLists.txt"
11931 ;; Don't prefer static libs
11932 (("SET\\(CMAKE_FIND_LIBRARY_SUFFIXES.*") "")
11933 (("find_package\\(Jellyfish.*") "")
11934 (("ExternalProject_Add\\(libjellyfish") "message(")
11935 (("ExternalProject_Add\\(libgff") "message(")
11936 (("ExternalProject_Add\\(libsparsehash") "message(")
11937 (("ExternalProject_Add\\(libdivsufsort") "message("))
11939 ;; Ensure that Eigen headers can be found
11940 (setenv "CPLUS_INCLUDE_PATH"
11941 (string-append (getenv "CPLUS_INCLUDE_PATH")
11943 (assoc-ref inputs "eigen")
11944 "/include/eigen3")))))))
11948 ("jemalloc" ,jemalloc)
11949 ("jellyfish" ,jellyfish)
11950 ("sparsehash" ,sparsehash)
11953 (uri (git-reference
11954 (url "https://github.com/COMBINE-lab/RapMap.git")
11955 (commit (string-append "sf-v" version))))
11956 (file-name (string-append "rapmap-sf-v" version "-checkout"))
11959 "1hv79l5i576ykv5a1srj2p0q36yvyl5966m0fcy2lbi169ipjakf"))
11960 (modules '((guix build utils)))
11961 ;; These files are expected to be excluded.
11963 '(begin (delete-file-recursively "include/spdlog")
11964 (for-each delete-file '("include/xxhash.h"
11967 ("libdivsufsort" ,libdivsufsort)
11972 `(("pkg-config" ,pkg-config)))
11973 (home-page "http://www.cs.cmu.edu/~ckingsf/software/sailfish")
11974 (synopsis "Mapping-based isoform quantification from RNA-Seq reads")
11975 (description "Sailfish is a tool for genomic transcript quantification
11976 from RNA-seq data. It requires a set of target transcripts (either from a
11977 reference or de-novo assembly) to quantify. All you need to run sailfish is a
11978 fasta file containing your reference transcripts and a (set of) fasta/fastq
11979 file(s) containing your reads.")
11980 (license license:gpl3+)))
11982 (define libstadenio-for-salmon
11984 (name "libstadenio")
11988 (uri (git-reference
11989 (url "https://github.com/COMBINE-lab/staden-io_lib.git")
11990 (commit (string-append "v" version))))
11991 (file-name (string-append name "-" version "-checkout"))
11994 "1x8kxxqxl892vwfbprlbyfwkkv7c34ggkc94892x9x0g37x5nbwx"))))
11995 (build-system gnu-build-system)
11996 (arguments '(#:parallel-tests? #f)) ; not supported
12000 `(("perl" ,perl))) ; for tests
12001 (home-page "https://github.com/COMBINE-lab/staden-io_lib")
12002 (synopsis "General purpose trace and experiment file library")
12003 (description "This package provides a library of file reading and writing
12004 code to provide a general purpose Trace file (and Experiment File) reading
12007 The following file formats are supported:
12010 @item SCF trace files
12011 @item ABI trace files
12012 @item ALF trace files
12013 @item ZTR trace files
12014 @item SFF trace archives
12015 @item SRF trace archives
12016 @item Experiment files
12017 @item Plain text files
12018 @item SAM/BAM sequence files
12019 @item CRAM sequence files
12021 (license license:bsd-3)))
12023 (define spdlog-for-salmon
12029 (uri (git-reference
12030 (url "https://github.com/COMBINE-lab/spdlog.git")
12031 (commit (string-append "v" version))))
12032 (file-name (string-append name "-" version "-checkout"))
12035 "13730429gwlabi432ilpnja3sfvy0nn2719vnhhmii34xcdyc57q"))))
12036 (build-system cmake-build-system)
12037 (home-page "https://github.com/COMBINE-lab/spdlog")
12038 (synopsis "Very fast C++ logging library")
12039 (description "Spdlog is a very fast header-only C++ logging library with
12040 performance as its primary goal.")
12041 (license license:expat)))
12043 ;; This is a modified variant of bwa for use with Salmon. It installs a
12044 ;; library to avoid having to build this as part of Salmon.
12045 (define bwa-for-salmon
12046 (package (inherit bwa)
12048 (version "0.7.12.5")
12051 (uri (git-reference
12052 (url "https://github.com/COMBINE-lab/bwa.git")
12053 (commit (string-append "v" version))))
12054 (file-name (string-append "bwa-for-salmon-" version "-checkout"))
12057 "1z2qa64y0c5hky10510x137mnzlhz6k8qf27csw4w9j6qihq95gb"))))
12058 (build-system gnu-build-system)
12060 '(#:tests? #f ;no "check" target
12062 (modify-phases %standard-phases
12064 (lambda* (#:key outputs #:allow-other-keys)
12065 (let* ((out (assoc-ref outputs "out"))
12066 (bin (string-append out "/bin"))
12067 (lib (string-append out "/lib"))
12068 (doc (string-append out "/share/doc/bwa"))
12069 (man (string-append out "/share/man/man1"))
12070 (inc (string-append out "/include/bwa")))
12071 (install-file "bwa" bin)
12072 (install-file "README.md" doc)
12073 (install-file "bwa.1" man)
12074 (install-file "libbwa.a" lib)
12077 (for-each (lambda (file)
12078 (install-file file inc))
12079 (find-files "." "\\.h$")))
12081 ;; no "configure" script
12082 (delete 'configure))))))
12084 (define-public salmon
12090 (uri (git-reference
12091 (url "https://github.com/COMBINE-lab/salmon.git")
12092 (commit (string-append "v" version))))
12093 (file-name (string-append name "-" version "-checkout"))
12096 "1zi1ff4i7y2ykk0vdzysgwzzzv166vg2x77pj1mf4baclavxj87a"))
12097 (modules '((guix build utils)))
12100 ;; Delete bundled headers for eigen3.
12101 (delete-file-recursively "include/eigen3/")
12103 (build-system cmake-build-system)
12105 `(#:configure-flags
12106 (list (string-append "-DBOOST_INCLUDEDIR="
12107 (assoc-ref %build-inputs "boost")
12109 (string-append "-DBOOST_LIBRARYDIR="
12110 (assoc-ref %build-inputs "boost")
12112 (string-append "-DBoost_LIBRARIES="
12113 "-lboost_iostreams "
12114 "-lboost_filesystem "
12119 "-lboost_program_options")
12120 "-DBoost_FOUND=TRUE"
12121 "-DTBB_LIBRARIES=tbb tbbmalloc"
12122 ;; Don't download RapMap---we already have it!
12123 "-DFETCHED_RAPMAP=1")
12125 (modify-phases %standard-phases
12126 ;; Boost cannot be found, even though it's right there.
12127 (add-after 'unpack 'do-not-look-for-boost
12128 (lambda* (#:key inputs #:allow-other-keys)
12129 (substitute* "CMakeLists.txt"
12130 (("find_package\\(Boost 1\\.53\\.0") "#"))))
12131 (add-after 'unpack 'do-not-phone-home
12133 (substitute* "src/Salmon.cpp"
12134 (("getVersionMessage\\(\\)") "\"\""))))
12135 (add-after 'unpack 'prepare-rapmap
12136 (lambda* (#:key inputs #:allow-other-keys)
12137 (let ((src "external/install/src/rapmap/")
12138 (include "external/install/include/rapmap/")
12139 (rapmap (assoc-ref inputs "rapmap")))
12142 (for-each (lambda (file)
12143 (install-file file src))
12144 (find-files (string-append rapmap "/src") "\\.(c|cpp)"))
12145 (copy-recursively (string-append rapmap "/include") include)
12146 (for-each delete-file '("external/install/include/rapmap/xxhash.h"
12147 "external/install/include/rapmap/FastxParser.hpp"
12148 "external/install/include/rapmap/concurrentqueue.h"
12149 "external/install/include/rapmap/FastxParserThreadUtils.hpp"
12150 "external/install/src/rapmap/FastxParser.cpp"
12151 "external/install/src/rapmap/xxhash.c")))))
12152 (add-after 'unpack 'use-system-libraries
12153 (lambda* (#:key inputs #:allow-other-keys)
12154 (substitute* "src/CMakeLists.txt"
12155 (("\\$\\{GAT_SOURCE_DIR\\}/external/install/include/jellyfish-2.2..")
12156 (string-append (assoc-ref inputs "jellyfish")
12157 "/include/jellyfish-" ,(package-version jellyfish)))
12158 (("\\$\\{GAT_SOURCE_DIR\\}/external/install/lib/libjellyfish-2.0.a")
12159 (string-append (assoc-ref inputs "jellyfish")
12160 "/lib/libjellyfish-2.0.a"))
12161 (("\\$\\{GAT_SOURCE_DIR\\}/external/install/lib/libdivsufsort.a")
12162 (string-append (assoc-ref inputs "libdivsufsort")
12163 "/lib/libdivsufsort.so"))
12164 (("\\$\\{GAT_SOURCE_DIR\\}/external/install/lib/libstaden-read.a")
12165 (string-append (assoc-ref inputs "libstadenio-for-salmon")
12166 "/lib/libstaden-read.a"))
12167 (("\\$\\{GAT_SOURCE_DIR\\}/external/install/lib/libbwa.a")
12168 (string-append (assoc-ref inputs "bwa") "/lib/libbwa.a"))
12169 (("\\$\\{GAT_SOURCE_DIR\\}/external/install/lib/libdivsufsort64.a")
12170 (string-append (assoc-ref inputs "libdivsufsort")
12171 "/lib/libdivsufsort64.so")))
12172 (substitute* "CMakeLists.txt"
12173 ;; Don't prefer static libs
12174 (("SET\\(CMAKE_FIND_LIBRARY_SUFFIXES.*") "")
12175 (("set\\(TBB_LIBRARIES") "message(")
12176 (("find_package\\(Jellyfish.*") "")
12177 (("ExternalProject_Add\\(libcereal") "message(")
12178 (("ExternalProject_Add\\(libbwa") "message(")
12179 (("ExternalProject_Add\\(libjellyfish") "message(")
12180 (("ExternalProject_Add\\(libgff") "message(")
12181 (("ExternalProject_Add\\(libtbb") "message(")
12182 (("ExternalProject_Add\\(libspdlog") "message(")
12183 (("ExternalProject_Add\\(libdivsufsort") "message(")
12184 (("ExternalProject_Add\\(libstadenio") "message(")
12185 (("ExternalProject_Add_Step\\(") "message("))
12187 ;; Ensure that all headers can be found
12188 (setenv "CPLUS_INCLUDE_PATH"
12189 (string-append (getenv "CPLUS_INCLUDE_PATH")
12191 (assoc-ref inputs "bwa")
12194 (assoc-ref inputs "eigen")
12195 "/include/eigen3"))
12197 (string-append (assoc-ref inputs "bwa")
12200 (assoc-ref inputs "eigen")
12201 "/include/eigen3"))
12203 ;; CMAKE_INSTALL_PREFIX does not exist when the tests are
12204 ;; run. It only exists after the install phase.
12205 (add-after 'unpack 'fix-tests
12207 (substitute* "src/CMakeLists.txt"
12208 (("DTOPLEVEL_DIR=\\$\\{CMAKE_INSTALL_PREFIX")
12209 "DTOPLEVEL_DIR=${GAT_SOURCE_DIR"))
12213 ("bwa" ,bwa-for-salmon)
12219 (uri (git-reference
12220 (url "https://github.com/COMBINE-lab/RapMap.git")
12221 (commit (string-append "salmon-v" version))))
12222 (file-name (string-append "rapmap-salmon-v" version "-checkout"))
12225 "1yc12yqsz6f0r8sg1qnk57xg34aqwc9jbqq6gd5ys28xw3plj98p"))))
12226 ("jemalloc" ,jemalloc)
12227 ("jellyfish" ,jellyfish)
12230 ("libdivsufsort" ,libdivsufsort)
12231 ("libstadenio-for-salmon" ,libstadenio-for-salmon)
12232 ("spdlog-for-salmon" ,spdlog-for-salmon)
12235 (home-page "https://github.com/COMBINE-lab/salmon")
12236 (synopsis "Quantification from RNA-seq reads using lightweight alignments")
12237 (description "Salmon is a program to produce highly-accurate,
12238 transcript-level quantification estimates from RNA-seq data. Salmon achieves
12239 its accuracy and speed via a number of different innovations, including the
12240 use of lightweight alignments (accurate but fast-to-compute proxies for
12241 traditional read alignments) and massively-parallel stochastic collapsed
12242 variational inference.")
12243 (license license:gpl3+)))
12245 (define-public python-loompy
12247 (name "python-loompy")
12252 (uri (pypi-uri "loompy" version))
12255 "1drgv8j1hxqzzpnfg272x9djb6j8qr798w1pc2x8ikmfgyd9gh51"))))
12256 (build-system python-build-system)
12257 ;; There are no tests
12258 (arguments '(#:tests? #f))
12260 `(("python-h5py" ,python-h5py)
12261 ("python-numpy" ,python-numpy)
12262 ("python-scipy" ,python-scipy)
12263 ("python-typing" ,python-typing)))
12264 (home-page "https://github.com/linnarsson-lab/loompy")
12265 (synopsis "Work with .loom files for single-cell RNA-seq data")
12266 (description "The loom file format is an efficient format for very large
12267 omics datasets, consisting of a main matrix, optional additional layers, a
12268 variable number of row and column annotations. Loom also supports sparse
12269 graphs. This library makes it easy to work with @file{.loom} files for
12270 single-cell RNA-seq data.")
12271 (license license:bsd-3)))
12273 ;; We cannot use the latest commit because it requires Java 9.
12274 (define-public java-forester
12275 (let ((commit "86b07efe302d5094b42deed9260f719a4c4ac2e6")
12278 (name "java-forester")
12279 (version (string-append "0-" revision "." (string-take commit 7)))
12282 (uri (git-reference
12283 (url "https://github.com/cmzmasek/forester.git")
12285 (file-name (string-append name "-" version "-checkout"))
12288 "0vxavc1yrf84yrnf20dq26hi0lglidk8d382xrxsy4qmlbjd276z"))
12289 (modules '((guix build utils)))
12292 ;; Delete bundled jars and pre-built classes
12293 (delete-file-recursively "forester/java/resources")
12294 (delete-file-recursively "forester/java/classes")
12295 (for-each delete-file (find-files "forester/java/" "\\.jar$"))
12296 ;; Delete bundled applications
12297 (delete-file-recursively "forester_applications")
12299 (build-system ant-build-system)
12301 `(#:tests? #f ; there are none
12303 #:modules ((guix build ant-build-system)
12305 (guix build java-utils)
12309 (modify-phases %standard-phases
12310 (add-after 'unpack 'chdir
12311 (lambda _ (chdir "forester/java") #t))
12312 (add-after 'chdir 'fix-dependencies
12314 (chmod "build.xml" #o664)
12315 (call-with-output-file "build.xml.new"
12319 (with-input-from-file "build.xml"
12320 (lambda _ (xml->sxml #:trim-whitespace? #t)))
12321 `(;; Remove all unjar tags to avoid repacking classes.
12322 (unjar . ,(lambda _ '()))
12323 (*default* . ,(lambda (tag . kids) `(,tag ,@kids)))
12324 (*text* . ,(lambda (_ txt) txt))))
12326 (rename-file "build.xml.new" "build.xml")
12328 ;; FIXME: itext is difficult to package as it depends on a few
12329 ;; unpackaged libraries.
12330 (add-after 'chdir 'remove-dependency-on-unpackaged-itext
12332 (delete-file "src/org/forester/archaeopteryx/PdfExporter.java")
12333 (substitute* "src/org/forester/archaeopteryx/MainFrame.java"
12334 (("pdf_written_to = PdfExporter.*")
12335 "throw new IOException(\"PDF export is not available.\");"))
12337 ;; There is no install target
12338 (replace 'install (install-jars ".")))))
12340 `(("java-commons-codec" ,java-commons-codec)
12341 ("java-openchart2" ,java-openchart2)))
12342 (home-page "https://sites.google.com/site/cmzmasek/home/software/forester")
12343 (synopsis "Phylogenomics libraries for Java")
12344 (description "Forester is a collection of Java libraries for
12345 phylogenomics and evolutionary biology research. It includes support for
12346 reading, writing, and exporting phylogenetic trees.")
12347 (license license:lgpl2.1+))))
12349 (define-public java-forester-1.005
12351 (name "java-forester")
12355 (uri (string-append "http://search.maven.org/remotecontent?"
12356 "filepath=org/biojava/thirdparty/forester/"
12357 version "/forester-" version "-sources.jar"))
12358 (file-name (string-append name "-" version ".jar"))
12361 "04r8qv4rk3p71z4ajrvp11py1z46qrx0047j3zzs79s6lnsm3lcv"))))
12362 (build-system ant-build-system)
12364 `(#:tests? #f ; there are none
12366 #:modules ((guix build ant-build-system)
12368 (guix build java-utils)
12372 (modify-phases %standard-phases
12373 (add-after 'unpack 'fix-dependencies
12374 (lambda* (#:key inputs #:allow-other-keys)
12375 (call-with-output-file "build.xml"
12379 (with-input-from-file "src/build.xml"
12380 (lambda _ (xml->sxml #:trim-whitespace? #t)))
12381 `(;; Remove all unjar tags to avoid repacking classes.
12382 (unjar . ,(lambda _ '()))
12383 (*default* . ,(lambda (tag . kids) `(,tag ,@kids)))
12384 (*text* . ,(lambda (_ txt) txt))))
12386 (copy-file (assoc-ref inputs "synth_look_and_feel_1.xml")
12387 "synth_look_and_feel_1.xml")
12388 (copy-file (assoc-ref inputs "phyloxml.xsd")
12390 (substitute* "build.xml"
12391 (("../resources/synth_laf/synth_look_and_feel_1.xml")
12392 "synth_look_and_feel_1.xml")
12393 (("../resources/phyloxml_schema/1.10/phyloxml.xsd")
12396 ;; FIXME: itext is difficult to package as it depends on a few
12397 ;; unpackaged libraries.
12398 (add-after 'unpack 'remove-dependency-on-unpackaged-itext
12400 (delete-file "src/org/forester/archaeopteryx/PdfExporter.java")
12401 (substitute* '("src/org/forester/archaeopteryx/MainFrame.java"
12402 "src/org/forester/archaeopteryx/MainFrameApplication.java")
12403 (("pdf_written_to = PdfExporter.*")
12404 "throw new IOException(\"PDF export is not available.\"); /*")
12405 ((".getPrintSizeX\\(\\), getOptions\\(\\).getPrintSizeY\\(\\) \\);") "*/")
12406 (("getCurrentTreePanel\\(\\).getHeight\\(\\) \\);") "*/"))
12408 (add-after 'unpack 'delete-pre-built-classes
12409 (lambda _ (delete-file-recursively "src/classes") #t))
12410 ;; There is no install target
12411 (replace 'install (install-jars ".")))))
12413 `(("java-commons-codec" ,java-commons-codec)
12414 ("java-openchart2" ,java-openchart2)))
12415 ;; The source archive does not contain the resources.
12420 (uri (string-append "https://raw.githubusercontent.com/cmzmasek/forester/"
12421 "b61cc2dcede0bede317db362472333115756b8c6/"
12422 "forester/resources/phyloxml_schema/1.10/phyloxml.xsd"))
12423 (file-name (string-append name "-phyloxml-" version ".xsd"))
12426 "1zxc4m8sn4n389nqdnpxa8d0k17qnr3pm2y5y6g6vh4k0zm52npv"))))
12427 ("synth_look_and_feel_1.xml"
12430 (uri (string-append "https://raw.githubusercontent.com/cmzmasek/forester/"
12431 "29e04321615da6b35c1e15c60e52caf3f21d8e6a/"
12432 "forester/java/classes/resources/synth_look_and_feel_1.xml"))
12433 (file-name (string-append name "-synth-look-and-feel-" version ".xml"))
12436 "1gv5602gv4k7y7713y75a4jvj7i9s7nildsbdl7n9q10sc2ikg8h"))))))
12437 (home-page "https://sites.google.com/site/cmzmasek/home/software/forester")
12438 (synopsis "Phylogenomics libraries for Java")
12439 (description "Forester is a collection of Java libraries for
12440 phylogenomics and evolutionary biology research. It includes support for
12441 reading, writing, and exporting phylogenetic trees.")
12442 (license license:lgpl2.1+)))
12444 (define-public java-biojava-core
12446 (name "java-biojava-core")
12450 (uri (git-reference
12451 (url "https://github.com/biojava/biojava")
12452 (commit (string-append "biojava-" version))))
12453 (file-name (string-append name "-" version "-checkout"))
12456 "1bvryh2bpsvash8ln79cmc9sqm8qw72hz4xzwqxcrjm8ssxszhqk"))))
12457 (build-system ant-build-system)
12460 #:jar-name "biojava-core.jar"
12461 #:source-dir "biojava-core/src/main/java/"
12462 #:test-dir "biojava-core/src/test"
12463 ;; These tests seem to require internet access.
12464 #:test-exclude (list "**/SearchIOTest.java"
12465 "**/BlastXMLParserTest.java"
12466 "**/GenbankCookbookTest.java"
12467 "**/GenbankProxySequenceReaderTest.java")
12469 (modify-phases %standard-phases
12470 (add-before 'build 'copy-resources
12472 (copy-recursively "biojava-core/src/main/resources"
12475 (add-before 'check 'copy-test-resources
12477 (copy-recursively "biojava-core/src/test/resources"
12478 "build/test-classes")
12481 `(("java-log4j-api" ,java-log4j-api)
12482 ("java-log4j-core" ,java-log4j-core)
12483 ("java-slf4j-api" ,java-slf4j-api)
12484 ("java-slf4j-simple" ,java-slf4j-simple)))
12486 `(("java-junit" ,java-junit)
12487 ("java-hamcrest-core" ,java-hamcrest-core)))
12488 (home-page "http://biojava.org")
12489 (synopsis "Core libraries of Java framework for processing biological data")
12490 (description "BioJava is a project dedicated to providing a Java framework
12491 for processing biological data. It provides analytical and statistical
12492 routines, parsers for common file formats, reference implementations of
12493 popular algorithms, and allows the manipulation of sequences and 3D
12494 structures. The goal of the biojava project is to facilitate rapid
12495 application development for bioinformatics.
12497 This package provides the core libraries.")
12498 (license license:lgpl2.1+)))
12500 (define-public java-biojava-phylo
12501 (package (inherit java-biojava-core)
12502 (name "java-biojava-phylo")
12503 (build-system ant-build-system)
12506 #:jar-name "biojava-phylo.jar"
12507 #:source-dir "biojava-phylo/src/main/java/"
12508 #:test-dir "biojava-phylo/src/test"
12510 (modify-phases %standard-phases
12511 (add-before 'build 'copy-resources
12513 (copy-recursively "biojava-phylo/src/main/resources"
12516 (add-before 'check 'copy-test-resources
12518 (copy-recursively "biojava-phylo/src/test/resources"
12519 "build/test-classes")
12522 `(("java-log4j-api" ,java-log4j-api)
12523 ("java-log4j-core" ,java-log4j-core)
12524 ("java-slf4j-api" ,java-slf4j-api)
12525 ("java-slf4j-simple" ,java-slf4j-simple)
12526 ("java-biojava-core" ,java-biojava-core)
12527 ("java-forester" ,java-forester)))
12529 `(("java-junit" ,java-junit)
12530 ("java-hamcrest-core" ,java-hamcrest-core)))
12531 (home-page "http://biojava.org")
12532 (synopsis "Biojava interface to the forester phylogenomics library")
12533 (description "The phylo module provides a biojava interface layer to the
12534 forester phylogenomics library for constructing phylogenetic trees.")))
12536 (define-public java-biojava-alignment
12537 (package (inherit java-biojava-core)
12538 (name "java-biojava-alignment")
12539 (build-system ant-build-system)
12542 #:jar-name "biojava-alignment.jar"
12543 #:source-dir "biojava-alignment/src/main/java/"
12544 #:test-dir "biojava-alignment/src/test"
12546 (modify-phases %standard-phases
12547 (add-before 'build 'copy-resources
12549 (copy-recursively "biojava-alignment/src/main/resources"
12552 (add-before 'check 'copy-test-resources
12554 (copy-recursively "biojava-alignment/src/test/resources"
12555 "build/test-classes")
12558 `(("java-log4j-api" ,java-log4j-api)
12559 ("java-log4j-core" ,java-log4j-core)
12560 ("java-slf4j-api" ,java-slf4j-api)
12561 ("java-slf4j-simple" ,java-slf4j-simple)
12562 ("java-biojava-core" ,java-biojava-core)
12563 ("java-biojava-phylo" ,java-biojava-phylo)
12564 ("java-forester" ,java-forester)))
12566 `(("java-junit" ,java-junit)
12567 ("java-hamcrest-core" ,java-hamcrest-core)))
12568 (home-page "http://biojava.org")
12569 (synopsis "Biojava API for genetic sequence alignment")
12570 (description "The alignment module of BioJava provides an API that
12574 @item implementations of dynamic programming algorithms for sequence
12576 @item reading and writing of popular alignment file formats;
12577 @item a single-, or multi- threaded multiple sequence alignment algorithm.
12580 (define-public java-biojava-core-4.0
12581 (package (inherit java-biojava-core)
12582 (name "java-biojava-core")
12586 (uri (git-reference
12587 (url "https://github.com/biojava/biojava")
12588 (commit (string-append "biojava-" version))))
12589 (file-name (string-append name "-" version "-checkout"))
12592 "13675f6y9aqi7bi2lk3s1z7a22ynccjiqwa8izh7p97xi9wsfmd8"))))))
12594 (define-public java-biojava-phylo-4.0
12595 (package (inherit java-biojava-core-4.0)
12596 (name "java-biojava-phylo")
12597 (build-system ant-build-system)
12600 #:jar-name "biojava-phylo.jar"
12601 #:source-dir "biojava-phylo/src/main/java/"
12602 #:test-dir "biojava-phylo/src/test"
12604 (modify-phases %standard-phases
12605 (add-before 'build 'copy-resources
12607 (copy-recursively "biojava-phylo/src/main/resources"
12610 (add-before 'check 'copy-test-resources
12612 (copy-recursively "biojava-phylo/src/test/resources"
12613 "build/test-classes")
12616 `(("java-log4j-api" ,java-log4j-api)
12617 ("java-log4j-core" ,java-log4j-core)
12618 ("java-slf4j-api" ,java-slf4j-api)
12619 ("java-slf4j-simple" ,java-slf4j-simple)
12620 ("java-biojava-core" ,java-biojava-core-4.0)
12621 ("java-forester" ,java-forester-1.005)))
12623 `(("java-junit" ,java-junit)
12624 ("java-hamcrest-core" ,java-hamcrest-core)))
12625 (home-page "http://biojava.org")
12626 (synopsis "Biojava interface to the forester phylogenomics library")
12627 (description "The phylo module provides a biojava interface layer to the
12628 forester phylogenomics library for constructing phylogenetic trees.")))
12630 (define-public java-biojava-alignment-4.0
12631 (package (inherit java-biojava-core-4.0)
12632 (name "java-biojava-alignment")
12633 (build-system ant-build-system)
12636 #:jar-name "biojava-alignment.jar"
12637 #:source-dir "biojava-alignment/src/main/java/"
12638 #:test-dir "biojava-alignment/src/test"
12640 (modify-phases %standard-phases
12641 (add-before 'build 'copy-resources
12643 (copy-recursively "biojava-alignment/src/main/resources"
12646 (add-before 'check 'copy-test-resources
12648 (copy-recursively "biojava-alignment/src/test/resources"
12649 "build/test-classes")
12652 `(("java-log4j-api" ,java-log4j-api)
12653 ("java-log4j-core" ,java-log4j-core)
12654 ("java-slf4j-api" ,java-slf4j-api)
12655 ("java-slf4j-simple" ,java-slf4j-simple)
12656 ("java-biojava-core" ,java-biojava-core-4.0)
12657 ("java-biojava-phylo" ,java-biojava-phylo-4.0)
12658 ("java-forester" ,java-forester-1.005)))
12660 `(("java-junit" ,java-junit)
12661 ("java-hamcrest-core" ,java-hamcrest-core)))
12662 (home-page "http://biojava.org")
12663 (synopsis "Biojava API for genetic sequence alignment")
12664 (description "The alignment module of BioJava provides an API that
12668 @item implementations of dynamic programming algorithms for sequence
12670 @item reading and writing of popular alignment file formats;
12671 @item a single-, or multi- threaded multiple sequence alignment algorithm.
12674 (define-public dropseq-tools
12676 (name "dropseq-tools")
12681 (uri "http://mccarrolllab.com/download/1276/")
12682 (file-name (string-append "dropseq-tools-" version ".zip"))
12685 "0yrffckxqk5l8b5xb6z4laq157zd9mdypr2p4b4vq2bhjzi1sj0s"))
12686 ;; Delete bundled libraries
12687 (modules '((guix build utils)))
12690 (for-each delete-file (find-files "jar/lib" "\\.jar$"))
12691 (delete-file-recursively "3rdParty")
12693 (build-system ant-build-system)
12695 `(#:tests? #f ; test data are not included
12696 #:test-target "test"
12697 #:build-target "all"
12698 #:source-dir "public/src/"
12701 (list (string-append "-Dpicard.executable.dir="
12702 (assoc-ref %build-inputs "java-picard")
12704 #:modules ((ice-9 match)
12707 (guix build java-utils)
12708 (guix build ant-build-system))
12710 (modify-phases %standard-phases
12711 ;; All dependencies must be linked to "lib", because that's where
12712 ;; they will be searched for when the Class-Path property of the
12713 ;; manifest is computed.
12714 (add-after 'unpack 'record-references
12715 (lambda* (#:key inputs #:allow-other-keys)
12716 (mkdir-p "jar/lib")
12717 (let ((dirs (filter-map (match-lambda
12719 (if (and (string-prefix? "java-" name)
12720 (not (string=? name "java-testng")))
12723 (for-each (lambda (jar)
12724 (symlink jar (string-append "jar/lib/" (basename jar))))
12725 (append-map (lambda (dir) (find-files dir "\\.jar$"))
12728 ;; There is no installation target
12730 (lambda* (#:key inputs outputs #:allow-other-keys)
12731 (let* ((out (assoc-ref outputs "out"))
12732 (bin (string-append out "/bin"))
12733 (share (string-append out "/share/java/"))
12734 (lib (string-append share "/lib/"))
12735 (scripts (list "BAMTagHistogram"
12736 "BAMTagofTagCounts"
12737 "BaseDistributionAtReadPosition"
12738 "CollapseBarcodesInPlace"
12739 "CollapseTagWithContext"
12741 "CreateIntervalsFiles"
12742 "DetectBeadSynthesisErrors"
12743 "DigitalExpression"
12744 "Drop-seq_alignment.sh"
12747 "GatherGeneGCLength"
12748 "GatherMolecularBarcodeDistributionByGene"
12749 "GatherReadQualityMetrics"
12752 "SelectCellsByNumTranscripts"
12753 "SingleCellRnaSeqMetricsCollector"
12754 "TagBamWithReadSequenceExtended"
12755 "TagReadWithGeneExon"
12756 "TagReadWithInterval"
12757 "TrimStartingSequence"
12758 "ValidateReference")))
12759 (for-each mkdir-p (list bin share lib))
12760 (install-file "dist/dropseq.jar" share)
12761 (for-each (lambda (script)
12762 (chmod script #o555)
12763 (install-file script bin))
12765 (substitute* (map (lambda (script)
12766 (string-append bin "/" script))
12768 (("^java") (which "java"))
12769 (("jar_deploy_dir=.*")
12770 (string-append "jar_deploy_dir=" share "\n"))))
12772 ;; FIXME: We do this after stripping jars because we don't want it to
12773 ;; copy all these jars and strip them. We only want to install
12774 ;; links. Arguably, this is a problem with the ant-build-system.
12775 (add-after 'strip-jar-timestamps 'install-links
12776 (lambda* (#:key outputs #:allow-other-keys)
12777 (let* ((out (assoc-ref outputs "out"))
12778 (share (string-append out "/share/java/"))
12779 (lib (string-append share "/lib/")))
12780 (for-each (lambda (jar)
12781 (symlink (readlink jar)
12782 (string-append lib (basename jar))))
12783 (find-files "jar/lib" "\\.jar$")))
12786 `(("jdk" ,icedtea-8)
12787 ("java-picard" ,java-picard-2.10.3)
12788 ("java-log4j-1.2-api" ,java-log4j-1.2-api)
12789 ("java-commons-math3" ,java-commons-math3)
12790 ("java-commons-jexl2" ,java-commons-jexl-2)
12791 ("java-commons-collections4" ,java-commons-collections4)
12792 ("java-commons-lang2" ,java-commons-lang)
12793 ("java-commons-io" ,java-commons-io)
12794 ("java-snappy-1.0.3-rc3" ,java-snappy-1)
12795 ("java-guava" ,java-guava)
12796 ("java-la4j" ,java-la4j)
12797 ("java-biojava-core" ,java-biojava-core-4.0)
12798 ("java-biojava-alignment" ,java-biojava-alignment-4.0)
12799 ("java-jdistlib" ,java-jdistlib)
12800 ("java-simple-xml" ,java-simple-xml)
12801 ("java-snakeyaml" ,java-snakeyaml)))
12804 ("java-testng" ,java-testng)))
12805 (home-page "http://mccarrolllab.com/dropseq/")
12806 (synopsis "Tools for Drop-seq analyses")
12807 (description "Drop-seq is a technology to enable biologists to
12808 analyze RNA expression genome-wide in thousands of individual cells at
12809 once. This package provides tools to perform Drop-seq analyses.")
12810 (license license:expat)))
12812 (define-public pigx-rnaseq
12814 (name "pigx-rnaseq")
12818 (uri (string-append "https://github.com/BIMSBbioinfo/pigx_rnaseq/"
12819 "releases/download/v" version
12820 "/pigx_rnaseq-" version ".tar.gz"))
12823 "0pz080k4ajlc4rlznkn3najy2a6874gb56rf9g4ag9wqz31q174j"))))
12824 (build-system gnu-build-system)
12826 `(#:parallel-tests? #f ; not supported
12828 (modify-phases %standard-phases
12829 ;; "test.sh" runs STAR, which requires excessive amounts of memory.
12830 (add-after 'unpack 'disable-resource-intensive-test
12832 (substitute* "Makefile.in"
12833 (("(^ tests/test_trim_galore/test.sh).*" _ m) m)
12834 (("^ test.sh") ""))
12836 (add-after 'install 'wrap-executable
12837 ;; Make sure the executable finds all R modules.
12838 (lambda* (#:key inputs outputs #:allow-other-keys)
12839 (let ((out (assoc-ref outputs "out")))
12840 (wrap-program (string-append out "/bin/pigx-rnaseq")
12841 `("R_LIBS_SITE" ":" = (,(getenv "R_LIBS_SITE")))
12842 `("PYTHONPATH" ":" = (,(getenv "PYTHONPATH")))))
12846 ("snakemake" ,snakemake)
12848 ("multiqc" ,multiqc)
12850 ("trim-galore" ,trim-galore)
12852 ("samtools" ,samtools)
12853 ("bedtools" ,bedtools)
12854 ("r-minimal" ,r-minimal)
12855 ("r-rmarkdown" ,r-rmarkdown)
12856 ("r-ggplot2" ,r-ggplot2)
12857 ("r-ggrepel" ,r-ggrepel)
12858 ("r-gprofiler" ,r-gprofiler)
12859 ("r-deseq2" ,r-deseq2)
12861 ("r-knitr" ,r-knitr)
12862 ("r-pheatmap" ,r-pheatmap)
12863 ("r-corrplot" ,r-corrplot)
12864 ("r-reshape2" ,r-reshape2)
12865 ("r-plotly" ,r-plotly)
12866 ("r-scales" ,r-scales)
12867 ("r-summarizedexperiment" ,r-summarizedexperiment)
12868 ("r-crosstalk" ,r-crosstalk)
12869 ("r-tximport" ,r-tximport)
12870 ("r-rtracklayer" ,r-rtracklayer)
12871 ("r-rjson" ,r-rjson)
12873 ("ghc-pandoc" ,ghc-pandoc-1)
12874 ("ghc-pandoc-citeproc" ,ghc-pandoc-citeproc-with-pandoc-1)
12875 ("python-wrapper" ,python-wrapper)
12876 ("python-pyyaml" ,python-pyyaml)))
12877 (home-page "http://bioinformatics.mdc-berlin.de/pigx/")
12878 (synopsis "Analysis pipeline for RNA sequencing experiments")
12879 (description "PiGX RNAseq is an analysis pipeline for preprocessing and
12880 reporting for RNA sequencing experiments. It is easy to use and produces high
12881 quality reports. The inputs are reads files from the sequencing experiment,
12882 and a configuration file which describes the experiment. In addition to
12883 quality control of the experiment, the pipeline produces a differential
12884 expression report comparing samples in an easily configurable manner.")
12885 (license license:gpl3+)))
12887 (define-public pigx-chipseq
12889 (name "pigx-chipseq")
12893 (uri (string-append "https://github.com/BIMSBbioinfo/pigx_chipseq/"
12894 "releases/download/v" version
12895 "/pigx_chipseq-" version ".tar.gz"))
12898 "11v9v3vyda0sv4cl45nki7mm4v4bjfcdq7a70kcvi9h465nq66wg"))))
12899 (build-system gnu-build-system)
12901 `(#:tests? #f ; parts of the tests rely on access to the network
12903 (modify-phases %standard-phases
12904 (add-after 'install 'wrap-executable
12905 ;; Make sure the executable finds all R modules.
12906 (lambda* (#:key inputs outputs #:allow-other-keys)
12907 (let ((out (assoc-ref outputs "out")))
12908 (wrap-program (string-append out "/bin/pigx-chipseq")
12909 `("R_LIBS_SITE" ":" = (,(getenv "R_LIBS_SITE")))
12910 `("PYTHONPATH" ":" = (,(getenv "PYTHONPATH")))))
12914 ("coreutils" ,coreutils)
12915 ("r-minimal" ,r-minimal)
12916 ("r-argparser" ,r-argparser)
12917 ("r-biocparallel" ,r-biocparallel)
12918 ("r-biostrings" ,r-biostrings)
12919 ("r-chipseq" ,r-chipseq)
12920 ("r-data-table" ,r-data-table)
12921 ("r-dplyr" ,r-dplyr)
12922 ("r-genomation" ,r-genomation)
12923 ("r-genomicalignments" ,r-genomicalignments)
12924 ("r-genomicranges" ,r-genomicranges)
12925 ("r-rsamtools" ,r-rsamtools)
12926 ("r-rtracklayer" ,r-rtracklayer)
12927 ("r-s4vectors" ,r-s4vectors)
12928 ("r-stringr" ,r-stringr)
12929 ("r-tibble" ,r-tibble)
12930 ("r-tidyr" ,r-tidyr)
12931 ("r-jsonlite" ,r-jsonlite)
12932 ("r-heatmaply" ,r-heatmaply)
12933 ("r-htmlwidgets" ,r-htmlwidgets)
12934 ("r-ggplot2" ,r-ggplot2)
12935 ("r-plotly" ,r-plotly)
12936 ("r-rmarkdown" ,r-rmarkdown)
12937 ("python-wrapper" ,python-wrapper)
12938 ("python-pyyaml" ,python-pyyaml)
12939 ("python-magic" ,python-magic)
12940 ("python-xlrd" ,python-xlrd)
12941 ("trim-galore" ,trim-galore)
12943 ("multiqc" ,multiqc)
12945 ("ghc-pandoc" ,ghc-pandoc-1)
12946 ("ghc-pandoc-citeproc" ,ghc-pandoc-citeproc-with-pandoc-1)
12950 ("snakemake" ,snakemake)
12951 ("samtools" ,samtools)
12952 ("bedtools" ,bedtools)
12953 ("kentutils" ,kentutils)))
12955 `(("python-pytest" ,python-pytest)))
12956 (home-page "http://bioinformatics.mdc-berlin.de/pigx/")
12957 (synopsis "Analysis pipeline for ChIP sequencing experiments")
12958 (description "PiGX ChIPseq is an analysis pipeline for preprocessing, peak
12959 calling and reporting for ChIP sequencing experiments. It is easy to use and
12960 produces high quality reports. The inputs are reads files from the sequencing
12961 experiment, and a configuration file which describes the experiment. In
12962 addition to quality control of the experiment, the pipeline enables to set up
12963 multiple peak calling analysis and allows the generation of a UCSC track hub
12964 in an easily configurable manner.")
12965 (license license:gpl3+)))
12967 (define-public pigx-bsseq
12969 (name "pigx-bsseq")
12973 (uri (string-append "https://github.com/BIMSBbioinfo/pigx_bsseq/"
12974 "releases/download/v" version
12975 "/pigx_bsseq-" version ".tar.gz"))
12978 "0irlnlhhw9fd4ha7hksrxn3y7j76mz5qq1wjswbs9p364laqg69y"))))
12979 (build-system gnu-build-system)
12982 (modify-phases %standard-phases
12983 (add-before 'check 'set-timezone
12984 ;; The readr package is picky about timezones.
12985 (lambda* (#:key inputs #:allow-other-keys)
12986 (setenv "TZ" "UTC+1")
12988 (string-append (assoc-ref inputs "tzdata")
12989 "/share/zoneinfo"))
12991 (add-after 'install 'wrap-executable
12992 ;; Make sure the executable finds all R modules.
12993 (lambda* (#:key inputs outputs #:allow-other-keys)
12994 (let ((out (assoc-ref outputs "out")))
12995 (wrap-program (string-append out "/bin/pigx-bsseq")
12996 `("R_LIBS_SITE" ":" = (,(getenv "R_LIBS_SITE")))
12997 `("PYTHONPATH" ":" = (,(getenv "PYTHONPATH")))))
13000 `(("tzdata" ,tzdata)))
13002 `(("coreutils" ,coreutils)
13005 ("r-minimal" ,r-minimal)
13006 ("r-annotationhub" ,r-annotationhub)
13008 ("r-genomation" ,r-genomation)
13009 ("r-methylkit" ,r-methylkit)
13010 ("r-rtracklayer" ,r-rtracklayer)
13011 ("r-rmarkdown" ,r-rmarkdown)
13012 ("r-bookdown" ,r-bookdown)
13013 ("r-ggplot2" ,r-ggplot2)
13014 ("r-ggbio" ,r-ggbio)
13015 ("ghc-pandoc" ,ghc-pandoc-1)
13016 ("ghc-pandoc-citeproc" ,ghc-pandoc-citeproc-with-pandoc-1)
13017 ("python-wrapper" ,python-wrapper)
13018 ("python-pyyaml" ,python-pyyaml)
13019 ("snakemake" ,snakemake)
13020 ("bismark" ,bismark)
13023 ("trim-galore" ,trim-galore)
13024 ("cutadapt" ,cutadapt)
13025 ("samtools" ,samtools)))
13026 (home-page "http://bioinformatics.mdc-berlin.de/pigx/")
13027 (synopsis "Bisulfite sequencing pipeline from fastq to methylation reports")
13028 (description "PiGx BSseq is a data processing pipeline for raw fastq read
13029 data of bisulfite experiments; it produces reports on aggregate methylation
13030 and coverage and can be used to produce information on differential
13031 methylation and segmentation.")
13032 (license license:gpl3+)))
13034 (define-public pigx-scrnaseq
13036 (name "pigx-scrnaseq")
13040 (uri (string-append "https://github.com/BIMSBbioinfo/pigx_scrnaseq/"
13041 "releases/download/v" version
13042 "/pigx_scrnaseq-" version ".tar.gz"))
13045 "1pvjm6f3mascprs65vflggwwg5v925knvgal7k7a6nnlmw5qndrf"))))
13046 (build-system gnu-build-system)
13048 `(#:configure-flags
13049 (list (string-append "PICARDJAR=" (assoc-ref %build-inputs "java-picard")
13050 "/share/java/picard.jar")
13051 (string-append "DROPSEQJAR=" (assoc-ref %build-inputs "dropseq-tools")
13052 "/share/java/dropseq.jar"))
13054 (modify-phases %standard-phases
13055 (add-after 'install 'wrap-executable
13056 ;; Make sure the executable finds all R modules.
13057 (lambda* (#:key inputs outputs #:allow-other-keys)
13058 (let ((out (assoc-ref outputs "out")))
13059 (wrap-program (string-append out "/bin/pigx-scrnaseq")
13060 `("R_LIBS_SITE" ":" = (,(getenv "R_LIBS_SITE")))
13061 `("PYTHONPATH" ":" = (,(getenv "PYTHONPATH")))))
13064 `(("coreutils" ,coreutils)
13066 ("dropseq-tools" ,dropseq-tools)
13068 ("java-picard" ,java-picard)
13069 ("java" ,icedtea-8)
13070 ("python-wrapper" ,python-wrapper)
13071 ("python-pyyaml" ,python-pyyaml)
13072 ("python-pandas" ,python-pandas)
13073 ("python-numpy" ,python-numpy)
13074 ("python-loompy" ,python-loompy)
13075 ("ghc-pandoc" ,ghc-pandoc-1)
13076 ("ghc-pandoc-citeproc" ,ghc-pandoc-citeproc-with-pandoc-1)
13077 ("snakemake" ,snakemake)
13079 ("r-minimal" ,r-minimal)
13080 ("r-argparser" ,r-argparser)
13081 ("r-cowplot" ,r-cowplot)
13082 ("r-data-table" ,r-data-table)
13083 ("r-delayedarray" ,r-delayedarray)
13084 ("r-delayedmatrixstats" ,r-delayedmatrixstats)
13085 ("r-dplyr" ,r-dplyr)
13086 ("r-dropbead" ,r-dropbead)
13088 ("r-genomicalignments" ,r-genomicalignments)
13089 ("r-genomicfiles" ,r-genomicfiles)
13090 ("r-genomicranges" ,r-genomicranges)
13091 ("r-ggplot2" ,r-ggplot2)
13092 ("r-hdf5array" ,r-hdf5array)
13093 ("r-pheatmap" ,r-pheatmap)
13094 ("r-rmarkdown" ,r-rmarkdown)
13095 ("r-rsamtools" ,r-rsamtools)
13096 ("r-rtracklayer" ,r-rtracklayer)
13097 ("r-rtsne" ,r-rtsne)
13098 ("r-scater" ,r-scater)
13099 ("r-scran" ,r-scran)
13100 ("r-singlecellexperiment" ,r-singlecellexperiment)
13101 ("r-stringr" ,r-stringr)
13102 ("r-yaml" ,r-yaml)))
13103 (home-page "http://bioinformatics.mdc-berlin.de/pigx/")
13104 (synopsis "Analysis pipeline for single-cell RNA sequencing experiments")
13105 (description "PiGX scRNAseq is an analysis pipeline for preprocessing and
13106 quality control for single cell RNA sequencing experiments. The inputs are
13107 read files from the sequencing experiment, and a configuration file which
13108 describes the experiment. It produces processed files for downstream analysis
13109 and interactive quality reports. The pipeline is designed to work with UMI
13111 (license license:gpl3+)))
13113 (define-public pigx
13119 (uri (string-append "https://github.com/BIMSBbioinfo/pigx/"
13120 "releases/download/v" version
13121 "/pigx-" version ".tar.gz"))
13124 "0sb708sl42h3s5z872jb1w70bbqplwapnsc1wm27zcsvi7li4gw8"))))
13125 (build-system gnu-build-system)
13127 `(("python" ,python)
13128 ("pigx-bsseq" ,pigx-bsseq)
13129 ("pigx-chipseq" ,pigx-chipseq)
13130 ("pigx-rnaseq" ,pigx-rnaseq)
13131 ("pigx-scrnaseq" ,pigx-scrnaseq)))
13132 (home-page "http://bioinformatics.mdc-berlin.de/pigx/")
13133 (synopsis "Analysis pipelines for genomics")
13134 (description "PiGx is a collection of genomics pipelines. It includes the
13135 following pipelines:
13138 @item PiGx BSseq for raw fastq read data of bisulfite experiments
13139 @item PiGx RNAseq for RNAseq samples
13140 @item PiGx scRNAseq for single cell dropseq analysis
13141 @item PiGx ChIPseq for reads from ChIPseq experiments
13144 All pipelines are easily configured with a simple sample sheet and a
13145 descriptive settings file. The result is a set of comprehensive, interactive
13146 HTML reports with interesting findings about your samples.")
13147 (license license:gpl3+)))
13149 (define-public r-diversitree
13151 (name "r-diversitree")
13156 (uri (cran-uri "diversitree" version))
13159 "0gh4rcrp0an3jh8915i1fsxlgyfk7njywgbd5ln5r2jhr085kpz7"))))
13160 (build-system r-build-system)
13162 `(("gfortran" ,gfortran)))
13163 (inputs `(("fftw" ,fftw) ("gsl" ,gsl)))
13166 ("r-desolve" ,r-desolve)
13168 ("r-suplex" ,r-subplex)))
13169 (home-page "https://www.zoology.ubc.ca/prog/diversitree")
13170 (synopsis "Comparative 'phylogenetic' analyses of diversification")
13171 (description "This package contains a number of comparative \"phylogenetic\"
13172 methods, mostly focusing on analysing diversification and character evolution.
13173 Contains implementations of \"BiSSE\" (Binary State Speciation and Extinction)
13174 and its unresolved tree extensions, \"MuSSE\" (Multiple State Speciation and
13175 Extinction), \"QuaSSE\", \"GeoSSE\", and \"BiSSE-ness\" Other included methods
13176 include Markov models of discrete and continuous trait evolution and constant
13177 rate speciation and extinction.")
13178 (license license:gpl2+)))