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"))))
301 (build-system gnu-build-system)
303 `(#:test-target "test"
304 #:configure-flags (list "--with-htslib=system")
308 "LIBS=-lgsl -lgslcblas"
309 (string-append "prefix=" (assoc-ref %outputs "out"))
310 (string-append "HTSDIR=" (assoc-ref %build-inputs "htslib") "/include")
311 (string-append "HTSLIB=" (assoc-ref %build-inputs "htslib") "/lib/libhts.so")
312 (string-append "BGZIP=" (assoc-ref %build-inputs "htslib") "/bin/bgzip")
313 (string-append "TABIX=" (assoc-ref %build-inputs "htslib") "/bin/tabix")
314 (string-append "PACKAGE_VERSION=" ,version))
316 (modify-phases %standard-phases
317 (add-before 'check 'patch-tests
319 (substitute* "test/test.pl"
320 (("/bin/bash") (which "bash")))
328 (home-page "https://samtools.github.io/bcftools/")
329 (synopsis "Utilities for variant calling and manipulating VCFs and BCFs")
331 "BCFtools is a set of utilities that manipulate variant calls in the
332 Variant Call Format (VCF) and its binary counterpart BCF. All commands work
333 transparently with both VCFs and BCFs, both uncompressed and BGZF-compressed.")
334 ;; The sources are dual MIT/GPL, but becomes GPL-only when USE_GPL=1.
335 (license (list license:gpl3+ license:expat))))
337 (define-public bedops
343 (uri (string-append "https://github.com/bedops/bedops/archive/v"
345 (file-name (string-append name "-" version ".tar.gz"))
348 "0kx4awrwby8f33wqyx8w7ms7v25xhf0d421csgf96a3hfzn2mb0m"))))
349 (build-system gnu-build-system)
352 #:make-flags (list (string-append "BINDIR=" %output "/bin"))
354 (modify-phases %standard-phases
355 (add-after 'unpack 'unpack-tarballs
357 ;; FIXME: Bedops includes tarballs of minimally patched upstream
358 ;; libraries jansson, zlib, and bzip2. We cannot just use stock
359 ;; libraries because at least one of the libraries (zlib) is
360 ;; patched to add a C++ function definition (deflateInit2cpp).
361 ;; Until the Bedops developers offer a way to link against system
362 ;; libraries we have to build the in-tree copies of these three
365 ;; See upstream discussion:
366 ;; https://github.com/bedops/bedops/issues/124
368 ;; Unpack the tarballs to benefit from shebang patching.
369 (with-directory-excursion "third-party"
370 (and (zero? (system* "tar" "xvf" "jansson-2.6.tar.bz2"))
371 (zero? (system* "tar" "xvf" "zlib-1.2.7.tar.bz2"))
372 (zero? (system* "tar" "xvf" "bzip2-1.0.6.tar.bz2"))))
373 ;; Disable unpacking of tarballs in Makefile.
374 (substitute* "system.mk/Makefile.linux"
375 (("^\tbzcat .*") "\t@echo \"not unpacking\"\n")
376 (("\\./configure") "CONFIG_SHELL=bash ./configure"))
377 (substitute* "third-party/zlib-1.2.7/Makefile.in"
378 (("^SHELL=.*$") "SHELL=bash\n"))
380 (delete 'configure))))
381 (home-page "https://github.com/bedops/bedops")
382 (synopsis "Tools for high-performance genomic feature operations")
384 "BEDOPS is a suite of tools to address common questions raised in genomic
385 studies---mostly with regard to overlap and proximity relationships between
386 data sets. It aims to be scalable and flexible, facilitating the efficient
387 and accurate analysis and management of large-scale genomic data.
389 BEDOPS provides tools that perform highly efficient and scalable Boolean and
390 other set operations, statistical calculations, archiving, conversion and
391 other management of genomic data of arbitrary scale. Tasks can be easily
392 split by chromosome for distributing whole-genome analyses across a
393 computational cluster.")
394 (license license:gpl2+)))
396 (define-public bedtools
402 (uri (string-append "https://github.com/arq5x/bedtools2/releases/"
403 "download/v" version "/"
404 "bedtools-" version ".tar.gz"))
407 "1ndg5yknrxl4djx8ddzgk12rrbiidfpmkkg5z3f95jzryfxarhn8"))))
408 (build-system gnu-build-system)
410 '(#:test-target "test"
412 (list (string-append "prefix=" (assoc-ref %outputs "out")))
414 (modify-phases %standard-phases
415 (delete 'configure))))
416 (native-inputs `(("python" ,python-2)))
418 `(("samtools" ,samtools)
420 (home-page "https://github.com/arq5x/bedtools2")
421 (synopsis "Tools for genome analysis and arithmetic")
423 "Collectively, the bedtools utilities are a swiss-army knife of tools for
424 a wide-range of genomics analysis tasks. The most widely-used tools enable
425 genome arithmetic: that is, set theory on the genome. For example, bedtools
426 allows one to intersect, merge, count, complement, and shuffle genomic
427 intervals from multiple files in widely-used genomic file formats such as BAM,
429 (license license:gpl2)))
431 ;; Later releases of bedtools produce files with more columns than
432 ;; what Ribotaper expects.
433 (define-public bedtools-2.18
434 (package (inherit bedtools)
439 (uri (string-append "https://github.com/arq5x/bedtools2/"
440 "archive/v" version ".tar.gz"))
441 (file-name (string-append name "-" version ".tar.gz"))
444 "05vrnr8yp7swfagshzpgqmzk1blnwnq8pq5pckzi1m26w98d63vf"))))
446 '(#:test-target "test"
448 (modify-phases %standard-phases
451 (lambda* (#:key outputs #:allow-other-keys)
452 (let ((bin (string-append (assoc-ref outputs "out") "/bin/")))
453 (for-each (lambda (file)
454 (install-file file bin))
455 (find-files "bin" ".*")))
458 (define-public ribotaper
464 (uri (string-append "https://ohlerlab.mdc-berlin.de/"
465 "files/RiboTaper/RiboTaper_Version_"
469 "0ykjbps1y3z3085q94npw8i9x5gldc6shy8vlc08v76zljsm07hv"))))
470 (build-system gnu-build-system)
473 (modify-phases %standard-phases
474 (add-after 'install 'wrap-executables
475 (lambda* (#:key inputs outputs #:allow-other-keys)
476 (let* ((out (assoc-ref outputs "out")))
479 (wrap-program (string-append out "/bin/" script)
480 `("R_LIBS_SITE" ":" = (,(getenv "R_LIBS_SITE")))))
481 '("create_annotations_files.bash"
482 "create_metaplots.bash"
483 "Ribotaper_ORF_find.sh"
484 "Ribotaper.sh"))))))))
486 `(("bedtools" ,bedtools-2.18)
487 ("samtools" ,samtools-0.1)
488 ("r-minimal" ,r-minimal)
489 ("r-foreach" ,r-foreach)
490 ("r-xnomial" ,r-xnomial)
492 ("r-multitaper" ,r-multitaper)
493 ("r-seqinr" ,r-seqinr)))
494 (home-page "https://ohlerlab.mdc-berlin.de/software/RiboTaper_126/")
495 (synopsis "Define translated ORFs using ribosome profiling data")
497 "Ribotaper is a method for defining translated @dfn{open reading
498 frames} (ORFs) using ribosome profiling (ribo-seq) data. This package
499 provides the Ribotaper pipeline.")
500 (license license:gpl3+)))
502 (define-public ribodiff
509 (uri (string-append "https://github.com/ratschlab/RiboDiff/"
510 "archive/v" version ".tar.gz"))
511 (file-name (string-append name "-" version ".tar.gz"))
514 "0wpbwmfv05wdjxv7ikm664f7s7p7cqr8jnw99zrda0q67rl50aaj"))))
515 (build-system python-build-system)
519 (modify-phases %standard-phases
520 ;; Generate an installable executable script wrapper.
521 (add-after 'unpack 'patch-setup.py
523 (substitute* "setup.py"
524 (("^(.*)packages=.*" line prefix)
525 (string-append line "\n"
526 prefix "scripts=['scripts/TE.py'],\n")))
529 `(("python-numpy" ,python2-numpy)
530 ("python-matplotlib" ,python2-matplotlib)
531 ("python-scipy" ,python2-scipy)
532 ("python-statsmodels" ,python2-statsmodels)))
534 `(("python-mock" ,python2-mock)
535 ("python-nose" ,python2-nose)))
536 (home-page "http://public.bmi.inf.ethz.ch/user/zhongy/RiboDiff/")
537 (synopsis "Detect translation efficiency changes from ribosome footprints")
538 (description "RiboDiff is a statistical tool that detects the protein
539 translational efficiency change from Ribo-Seq (ribosome footprinting) and
540 RNA-Seq data. It uses a generalized linear model to detect genes showing
541 difference in translational profile taking mRNA abundance into account. It
542 facilitates us to decipher the translational regulation that behave
543 independently with transcriptional regulation.")
544 (license license:gpl3+)))
546 (define-public bioawk
552 (uri (string-append "https://github.com/lh3/bioawk/archive/v"
554 (file-name (string-append name "-" version ".tar.gz"))
556 (base32 "1daizxsk17ahi9n58fj8vpgwyhzrzh54bzqhanjanp88kgrz7gjw"))))
557 (build-system gnu-build-system)
563 `(#:tests? #f ; There are no tests to run.
564 ;; Bison must generate files, before other targets can build.
567 (modify-phases %standard-phases
568 (delete 'configure) ; There is no configure phase.
570 (lambda* (#:key outputs #:allow-other-keys)
571 (let* ((out (assoc-ref outputs "out"))
572 (bin (string-append out "/bin"))
573 (man (string-append out "/share/man/man1")))
575 (copy-file "awk.1" (string-append man "/bioawk.1"))
576 (install-file "bioawk" bin)))))))
577 (home-page "https://github.com/lh3/bioawk")
578 (synopsis "AWK with bioinformatics extensions")
579 (description "Bioawk is an extension to Brian Kernighan's awk, adding the
580 support of several common biological data formats, including optionally gzip'ed
581 BED, GFF, SAM, VCF, FASTA/Q and TAB-delimited formats with column names. It
582 also adds a few built-in functions and a command line option to use TAB as the
583 input/output delimiter. When the new functionality is not used, bioawk is
584 intended to behave exactly the same as the original BWK awk.")
585 (license license:x11)))
587 (define-public python2-pybedtools
589 (name "python2-pybedtools")
594 "https://pypi.python.org/packages/source/p/pybedtools/pybedtools-"
598 "1ldzdxw1p4y3g2ignmggsdypvqkcwqwzhdha4rbgpih048z5p4an"))))
599 (build-system python-build-system)
600 (arguments `(#:python ,python-2)) ; no Python 3 support
602 `(("python-matplotlib" ,python2-matplotlib)))
604 `(("bedtools" ,bedtools)
605 ("samtools" ,samtools)))
607 `(("python-cython" ,python2-cython)
608 ("python-pyyaml" ,python2-pyyaml)
609 ("python-nose" ,python2-nose)))
610 (home-page "https://pythonhosted.org/pybedtools/")
611 (synopsis "Python wrapper for BEDtools programs")
613 "pybedtools is a Python wrapper for Aaron Quinlan's BEDtools programs,
614 which are widely used for genomic interval manipulation or \"genome algebra\".
615 pybedtools extends BEDTools by offering feature-level manipulations from with
617 (license license:gpl2+)))
619 (define-public python-biom-format
621 (name "python-biom-format")
626 ;; Use GitHub as source because PyPI distribution does not contain
627 ;; test data: https://github.com/biocore/biom-format/issues/693
628 (uri (string-append "https://github.com/biocore/biom-format/archive/"
630 (file-name (string-append name "-" version ".tar.gz"))
633 "08cr7wpahk6zb31h4bs7jmzpvxcqv9s13xz40h6y2h656jvdvnpj"))))
634 (build-system python-build-system)
636 `(("python-numpy" ,python-numpy)
637 ("python-scipy" ,python-scipy)
638 ("python-future" ,python-future)
639 ("python-click" ,python-click)
640 ("python-h5py" ,python-h5py)
641 ("python-pandas" ,python-pandas)))
643 `(("python-nose" ,python-nose)))
644 (home-page "http://www.biom-format.org")
645 (synopsis "Biological Observation Matrix (BIOM) format utilities")
647 "The BIOM file format is designed to be a general-use format for
648 representing counts of observations e.g. operational taxonomic units, KEGG
649 orthology groups or lipid types, in one or more biological samples
650 e.g. microbiome samples, genomes, metagenomes.")
651 (license license:bsd-3)
652 (properties `((python2-variant . ,(delay python2-biom-format))))))
654 (define-public python2-biom-format
655 (let ((base (package-with-python2 (strip-python2-variant python-biom-format))))
660 (modify-phases %standard-phases
661 ;; Do not require the unmaintained pyqi library.
662 (add-after 'unpack 'remove-pyqi
664 (substitute* "setup.py"
665 (("install_requires.append\\(\"pyqi\"\\)") "pass"))
667 ,@(package-arguments base))))))
669 (define-public bioperl-minimal
670 (let* ((inputs `(("perl-module-build" ,perl-module-build)
671 ("perl-data-stag" ,perl-data-stag)
672 ("perl-libwww" ,perl-libwww)
673 ("perl-uri" ,perl-uri)))
675 (map (compose package-name cadr)
678 (map (compose package-transitive-target-inputs cadr) inputs))))))
680 (name "bioperl-minimal")
685 (uri (string-append "https://github.com/bioperl/bioperl-live/"
687 (string-map (lambda (c)
693 "12phgpxwgkqflkwfb9dcqg7a31dpjlfhar8wcgv0aj5ln4akfz06"))))
694 (build-system perl-build-system)
697 (modify-phases %standard-phases
699 'install 'wrap-programs
700 (lambda* (#:key outputs #:allow-other-keys)
701 ;; Make sure all executables in "bin" find the required Perl
702 ;; modules at runtime. As the PERL5LIB variable contains also
703 ;; the paths of native inputs, we pick the transitive target
704 ;; inputs from %build-inputs.
705 (let* ((out (assoc-ref outputs "out"))
706 (bin (string-append out "/bin/"))
708 (cons (string-append out "/lib/perl5/site_perl")
710 (assoc-ref %build-inputs name))
711 ',transitive-inputs))
713 (for-each (lambda (file)
715 `("PERL5LIB" ":" prefix (,path))))
716 (find-files bin "\\.pl$"))
720 `(("perl-test-most" ,perl-test-most)))
721 (home-page "http://search.cpan.org/dist/BioPerl")
722 (synopsis "Bioinformatics toolkit")
724 "BioPerl is the product of a community effort to produce Perl code which
725 is useful in biology. Examples include Sequence objects, Alignment objects
726 and database searching objects. These objects not only do what they are
727 advertised to do in the documentation, but they also interact - Alignment
728 objects are made from the Sequence objects, Sequence objects have access to
729 Annotation and SeqFeature objects and databases, Blast objects can be
730 converted to Alignment objects, and so on. This means that the objects
731 provide a coordinated and extensible framework to do computational biology.")
732 (license license:perl-license))))
734 (define-public python-biopython
736 (name "python-biopython")
740 ;; use PyPi rather than biopython.org to ease updating
741 (uri (pypi-uri "biopython" version))
744 "0nz4n9d2y2dg849gn1z0vjlkwcpzzkzy3fij7x94a6ixy2c54z2a"))))
745 (build-system python-build-system)
748 (modify-phases %standard-phases
749 (add-before 'check 'set-home
750 ;; Some tests require a home directory to be set.
751 (lambda _ (setenv "HOME" "/tmp") #t)))))
753 `(("python-numpy" ,python-numpy)))
754 (home-page "http://biopython.org/")
755 (synopsis "Tools for biological computation in Python")
757 "Biopython is a set of tools for biological computation including parsers
758 for bioinformatics files into Python data structures; interfaces to common
759 bioinformatics programs; a standard sequence class and tools for performing
760 common operations on them; code to perform data classification; code for
761 dealing with alignments; code making it easy to split up parallelizable tasks
762 into separate processes; and more.")
763 (license (license:non-copyleft "http://www.biopython.org/DIST/LICENSE"))))
765 (define-public python2-biopython
766 (package-with-python2 python-biopython))
768 (define-public bpp-core
769 ;; The last release was in 2014 and the recommended way to install from source
770 ;; is to clone the git repository, so we do this.
771 ;; http://biopp.univ-montp2.fr/wiki/index.php/Main_Page
772 (let ((commit "7d8bced0d1a87291ea8dd7046b7fb5ff9c35c582"))
775 (version (string-append "2.2.0-1." (string-take commit 7)))
779 (url "http://biopp.univ-montp2.fr/git/bpp-core")
781 (file-name (string-append name "-" version "-checkout"))
784 "10djsq5vlnkilv436gnmh4irpk49v29pa69r6xiryg32xmvn909j"))))
785 (build-system cmake-build-system)
787 `(#:parallel-build? #f))
789 `(("gcc" ,gcc-5))) ; Compilation of bpp-phyl fails with GCC 4.9 so we
790 ; compile all of the bpp packages with GCC 5.
791 (home-page "http://biopp.univ-montp2.fr")
792 (synopsis "C++ libraries for Bioinformatics")
794 "Bio++ is a set of C++ libraries for Bioinformatics, including sequence
795 analysis, phylogenetics, molecular evolution and population genetics. It is
796 Object Oriented and is designed to be both easy to use and computer efficient.
797 Bio++ intends to help programmers to write computer expensive programs, by
798 providing them a set of re-usable tools.")
799 (license license:cecill-c))))
801 (define-public bpp-phyl
802 ;; The last release was in 2014 and the recommended way to install from source
803 ;; is to clone the git repository, so we do this.
804 ;; http://biopp.univ-montp2.fr/wiki/index.php/Main_Page
805 (let ((commit "0c07167b629f68b569bf274d1ad0c4af83276ae2"))
808 (version (string-append "2.2.0-1." (string-take commit 7)))
812 (url "http://biopp.univ-montp2.fr/git/bpp-phyl")
814 (file-name (string-append name "-" version "-checkout"))
817 "1ssjgchzwj3iai26kyly7gwkdv8sk59nqhkb1wpap3sf5m6kyllh"))))
818 (build-system cmake-build-system)
820 `(#:parallel-build? #f
821 ;; If out-of-source, test data is not copied into the build directory
822 ;; so the tests fail.
823 #:out-of-source? #f))
825 `(("bpp-core" ,bpp-core)
827 ;; GCC 4.8 fails due to an 'internal compiler error', so we use a more
830 (home-page "http://biopp.univ-montp2.fr")
831 (synopsis "Bio++ phylogenetic Library")
833 "Bio++ is a set of C++ libraries for Bioinformatics, including sequence
834 analysis, phylogenetics, molecular evolution and population genetics. This
835 library provides phylogenetics-related modules.")
836 (license license:cecill-c))))
838 (define-public bpp-popgen
839 ;; The last release was in 2014 and the recommended way to install from source
840 ;; is to clone the git repository, so we do this.
841 ;; http://biopp.univ-montp2.fr/wiki/index.php/Main_Page
842 (let ((commit "e472bac9b1a148803895d747cd6d0c5904f85d9f"))
845 (version (string-append "2.2.0-1." (string-take commit 7)))
849 (url "http://biopp.univ-montp2.fr/git/bpp-popgen")
851 (file-name (string-append name "-" version "-checkout"))
854 "0yn82dzn1n5629nzja68xfrhi655709rjanyryb36vzkmymy6dw5"))))
855 (build-system cmake-build-system)
857 `(#:parallel-build? #f
858 #:tests? #f)) ; There are no tests.
860 `(("bpp-core" ,bpp-core)
863 (home-page "http://biopp.univ-montp2.fr")
864 (synopsis "Bio++ population genetics library")
866 "Bio++ is a set of C++ libraries for Bioinformatics, including sequence
867 analysis, phylogenetics, molecular evolution and population genetics. This
868 library provides population genetics-related modules.")
869 (license license:cecill-c))))
871 (define-public bpp-seq
872 ;; The last release was in 2014 and the recommended way to install from source
873 ;; is to clone the git repository, so we do this.
874 ;; http://biopp.univ-montp2.fr/wiki/index.php/Main_Page
875 (let ((commit "6cfa07965ce152e5598a89df2fa80a75973bfa33"))
878 (version (string-append "2.2.0-1." (string-take commit 7)))
882 (url "http://biopp.univ-montp2.fr/git/bpp-seq")
884 (file-name (string-append name "-" version "-checkout"))
887 "1nys5jq7jqvdg40d91wsmj3q2yzy4276cp7sp44n67p468f27zf2"))))
888 (build-system cmake-build-system)
890 `(#:parallel-build? #f
891 ;; If out-of-source, test data is not copied into the build directory
892 ;; so the tests fail.
893 #:out-of-source? #f))
895 `(("bpp-core" ,bpp-core)
896 ("gcc" ,gcc-5))) ; Use GCC 5 as per 'bpp-core'.
897 (home-page "http://biopp.univ-montp2.fr")
898 (synopsis "Bio++ sequence library")
900 "Bio++ is a set of C++ libraries for Bioinformatics, including sequence
901 analysis, phylogenetics, molecular evolution and population genetics. This
902 library provides sequence-related modules.")
903 (license license:cecill-c))))
905 (define-public bppsuite
906 ;; The last release was in 2014 and the recommended way to install from source
907 ;; is to clone the git repository, so we do this.
908 ;; http://biopp.univ-montp2.fr/wiki/index.php/Main_Page
909 (let ((commit "c516147f57aa50961121cd505bed52cd7603698b"))
912 (version (string-append "2.2.0-1." (string-take commit 7)))
916 (url "http://biopp.univ-montp2.fr/git/bppsuite")
918 (file-name (string-append name "-" version "-checkout"))
921 "1y87pxvw0jxjizhq2dr9g2r91md45k1p9ih2sl1yy1y3p934l2kb"))))
922 (build-system cmake-build-system)
924 `(#:parallel-build? #f
925 #:tests? #f)) ; There are no tests.
929 ("texinfo" ,texinfo)))
931 `(("bpp-core" ,bpp-core)
933 ("bpp-phyl" ,bpp-phyl)
934 ("bpp-phyl" ,bpp-popgen)
936 (home-page "http://biopp.univ-montp2.fr")
937 (synopsis "Bioinformatics tools written with the Bio++ libraries")
939 "Bio++ is a set of C++ libraries for Bioinformatics, including sequence
940 analysis, phylogenetics, molecular evolution and population genetics. This
941 package provides command line tools using the Bio++ library.")
942 (license license:cecill-c))))
944 (define-public blast+
951 "ftp://ftp.ncbi.nlm.nih.gov/blast/executables/blast+/"
952 version "/ncbi-blast-" version "+-src.tar.gz"))
955 "15n937pw5aqmyfjb6l387d18grqbb96l63d5xj4l7yyh0zbf2405"))
956 (patches (search-patches "blast+-fix-makefile.patch"))
957 (modules '((guix build utils)))
960 ;; Remove bundled bzip2, zlib and pcre.
961 (delete-file-recursively "c++/src/util/compress/bzip2")
962 (delete-file-recursively "c++/src/util/compress/zlib")
963 (delete-file-recursively "c++/src/util/regexp")
964 (substitute* "c++/src/util/compress/Makefile.in"
965 (("bzip2 zlib api") "api"))
966 ;; Remove useless msbuild directory
967 (delete-file-recursively
968 "c++/src/build-system/project_tree_builder/msbuild")
970 (build-system gnu-build-system)
972 `(;; There are two(!) tests for this massive library, and both fail with
973 ;; "unparsable timing stats".
974 ;; ERR [127] -- [serial/datatool] datatool.sh (unparsable timing stats)
975 ;; ERR [127] -- [serial/datatool] datatool_xml.sh (unparsable timing stats)
978 #:parallel-build? #f ; not supported
980 (modify-phases %standard-phases
983 ;; $HOME needs to be set at some point during the configure phase
984 (lambda _ (setenv "HOME" "/tmp") #t))
987 (lambda _ (chdir "c++") #t))
989 'enter-dir 'fix-build-system
992 (cond ((string=? cmd "date")
993 ;; make call to "date" deterministic
998 (format (current-error-port)
999 "WARNING: Unable to find absolute path for ~s~%"
1003 ;; Rewrite hardcoded paths to various tools
1004 (substitute* (append '("src/build-system/configure.ac"
1005 "src/build-system/configure"
1006 "src/build-system/helpers/run_with_lock.c"
1007 "scripts/common/impl/if_diff.sh"
1008 "scripts/common/impl/run_with_lock.sh"
1009 "src/build-system/Makefile.configurables.real"
1010 "src/build-system/Makefile.in.top"
1011 "src/build-system/Makefile.meta.gmake=no"
1012 "src/build-system/Makefile.meta.in"
1013 "src/build-system/Makefile.meta_l"
1014 "src/build-system/Makefile.meta_p"
1015 "src/build-system/Makefile.meta_r"
1016 "src/build-system/Makefile.mk.in"
1017 "src/build-system/Makefile.requirements"
1018 "src/build-system/Makefile.rules_with_autodep.in")
1019 (find-files "scripts/common/check" "\\.sh$"))
1020 (("(/usr/bin/|/bin/)([a-z][-_.a-z]*)" all dir cmd)
1021 (or (which* cmd) all)))
1023 (substitute* (find-files "src/build-system" "^config.*")
1024 (("LN_S=/bin/\\$LN_S") (string-append "LN_S=" (which "ln")))
1027 ;; rewrite "/var/tmp" in check script
1028 (substitute* "scripts/common/check/check_make_unix.sh"
1029 (("/var/tmp") "/tmp"))
1031 ;; do not reset PATH
1032 (substitute* (find-files "scripts/common/impl/" "\\.sh$")
1034 (("action=/bin/") "action=")
1035 (("export PATH") ":"))
1039 (lambda* (#:key inputs outputs #:allow-other-keys)
1040 (let ((out (assoc-ref outputs "out"))
1041 (lib (string-append (assoc-ref outputs "lib") "/lib"))
1042 (include (string-append (assoc-ref outputs "include")
1043 "/include/ncbi-tools++")))
1044 ;; The 'configure' script doesn't recognize things like
1045 ;; '--enable-fast-install'.
1046 (zero? (system* "./configure.orig"
1047 (string-append "--with-build-root=" (getcwd) "/build")
1048 (string-append "--prefix=" out)
1049 (string-append "--libdir=" lib)
1050 (string-append "--includedir=" include)
1051 (string-append "--with-bz2="
1052 (assoc-ref inputs "bzip2"))
1053 (string-append "--with-z="
1054 (assoc-ref inputs "zlib"))
1055 (string-append "--with-pcre="
1056 (assoc-ref inputs "pcre"))
1057 ;; Each library is built twice by default, once
1058 ;; with "-static" in its name, and again
1061 "--with-dll"))))))))
1062 (outputs '("out" ; 21 MB
1070 ("python" ,python-wrapper)))
1073 (home-page "http://blast.ncbi.nlm.nih.gov")
1074 (synopsis "Basic local alignment search tool")
1076 "BLAST is a popular method of performing a DNA or protein sequence
1077 similarity search, using heuristics to produce results quickly. It also
1078 calculates an “expect value” that estimates how many matches would have
1079 occurred at a given score by chance, which can aid a user in judging how much
1080 confidence to have in an alignment.")
1081 ;; Most of the sources are in the public domain, with the following
1084 ;; * ./c++/include/util/bitset/
1085 ;; * ./c++/src/html/ncbi_menu*.js
1087 ;; * ./c++/include/util/impl/floating_point_comparison.hpp
1089 ;; * ./c++/include/dbapi/driver/odbc/unix_odbc/
1091 ;; * ./c++/src/corelib/teamcity_*
1092 (license (list license:public-domain
1098 (define-public bless
1104 (uri (string-append "mirror://sourceforge/bless-ec/bless.v"
1108 "0rm0gw2s18dqwzzpl3c2x1z05ni2v0xz5dmfk3d33j6g4cgrlrdd"))
1109 (modules '((guix build utils)))
1112 ;; Remove bundled boost, pigz, zlib, and .git directory
1113 ;; FIXME: also remove bundled sources for murmurhash3 and
1114 ;; kmc once packaged.
1115 (delete-file-recursively "boost")
1116 (delete-file-recursively "pigz")
1117 (delete-file-recursively "google-sparsehash")
1118 (delete-file-recursively "zlib")
1119 (delete-file-recursively ".git")
1121 (build-system gnu-build-system)
1123 '(#:tests? #f ;no "check" target
1125 (list (string-append "ZLIB="
1126 (assoc-ref %build-inputs "zlib")
1128 (string-append "LDFLAGS="
1129 (string-join '("-lboost_filesystem"
1136 (modify-phases %standard-phases
1137 (add-after 'unpack 'do-not-build-bundled-pigz
1138 (lambda* (#:key inputs outputs #:allow-other-keys)
1139 (substitute* "Makefile"
1140 (("cd pigz/pigz-2.3.3; make") ""))
1142 (add-after 'unpack 'patch-paths-to-executables
1143 (lambda* (#:key inputs outputs #:allow-other-keys)
1144 (substitute* "parse_args.cpp"
1145 (("kmc_binary = .*")
1146 (string-append "kmc_binary = \""
1147 (assoc-ref outputs "out")
1149 (("pigz_binary = .*")
1150 (string-append "pigz_binary = \""
1151 (assoc-ref inputs "pigz")
1155 (lambda* (#:key outputs #:allow-other-keys)
1156 (let ((bin (string-append (assoc-ref outputs "out") "/bin/")))
1157 (for-each (lambda (file)
1158 (install-file file bin))
1159 '("bless" "kmc/bin/kmc"))
1161 (delete 'configure))))
1165 `(("openmpi" ,openmpi)
1167 ("sparsehash" ,sparsehash)
1170 (supported-systems '("x86_64-linux"))
1171 (home-page "https://sourceforge.net/p/bless-ec/wiki/Home/")
1172 (synopsis "Bloom-filter-based error correction tool for NGS reads")
1174 "@dfn{Bloom-filter-based error correction solution for high-throughput
1175 sequencing reads} (BLESS) uses a single minimum-sized bloom filter is a
1176 correction tool for genomic reads produced by @dfn{Next-generation
1177 sequencing} (NGS). BLESS produces accurate correction results with much less
1178 memory compared with previous solutions and is also able to tolerate a higher
1179 false-positive rate. BLESS can extend reads like DNA assemblers to correct
1180 errors at the end of reads.")
1181 (license license:gpl3+)))
1183 (define-public bowtie
1189 (uri (string-append "https://github.com/BenLangmead/bowtie2/archive/v"
1191 (file-name (string-append name "-" version ".tar.gz"))
1194 "0hwa5r9qbglppb7sz5z79rlmmddr3n51n468jb3wh8rwjgn3yr90"))
1195 (modules '((guix build utils)))
1197 '(substitute* "Makefile"
1198 ;; replace BUILD_HOST and BUILD_TIME for deterministic build
1199 (("-DBUILD_HOST=.*") "-DBUILD_HOST=\"\\\"guix\\\"\"")
1200 (("-DBUILD_TIME=.*") "-DBUILD_TIME=\"\\\"0\\\"\"")))))
1201 (build-system gnu-build-system)
1204 ("perl-clone" ,perl-clone)
1205 ("perl-test-deep" ,perl-test-deep)
1206 ("perl-test-simple" ,perl-test-simple)
1207 ("python" ,python-2)
1214 (string-append "prefix=" (assoc-ref %outputs "out")))
1216 (modify-phases %standard-phases
1219 (lambda* (#:key outputs #:allow-other-keys)
1220 (zero? (system* "perl"
1221 "scripts/test/simple_tests.pl"
1222 "--bowtie2=./bowtie2"
1223 "--bowtie2-build=./bowtie2-build")))))))
1224 (home-page "http://bowtie-bio.sourceforge.net/bowtie2/index.shtml")
1225 (synopsis "Fast and sensitive nucleotide sequence read aligner")
1227 "Bowtie 2 is a fast and memory-efficient tool for aligning sequencing
1228 reads to long reference sequences. It is particularly good at aligning reads
1229 of about 50 up to 100s or 1,000s of characters, and particularly good at
1230 aligning to relatively long (e.g. mammalian) genomes. Bowtie 2 indexes the
1231 genome with an FM Index to keep its memory footprint small: for the human
1232 genome, its memory footprint is typically around 3.2 GB. Bowtie 2 supports
1233 gapped, local, and paired-end alignment modes.")
1234 (supported-systems '("x86_64-linux"))
1235 (license license:gpl3+)))
1237 (define-public tophat
1244 "http://ccb.jhu.edu/software/tophat/downloads/tophat-"
1248 "168zlzykq622zbgkh90a90f1bdgsxkscq2zxzbj8brq80hbjpyp7"))
1249 (patches (search-patches "tophat-build-with-later-seqan.patch"))
1250 (modules '((guix build utils)))
1253 ;; Remove bundled SeqAn and samtools
1254 (delete-file-recursively "src/SeqAn-1.3")
1255 (delete-file-recursively "src/samtools-0.1.18")
1257 (build-system gnu-build-system)
1259 '(#:parallel-build? #f ; not supported
1261 (modify-phases %standard-phases
1262 (add-after 'unpack 'use-system-samtools
1263 (lambda* (#:key inputs #:allow-other-keys)
1264 (substitute* "src/Makefile.in"
1265 (("(noinst_LIBRARIES = )\\$\\(SAMLIB\\)" _ prefix) prefix)
1266 (("\\$\\(SAMPROG\\): \\$\\(SAMLIB\\)") "")
1267 (("SAMPROG = samtools_0\\.1\\.18") "")
1268 (("\\$\\(samtools_0_1_18_SOURCES\\)") "")
1269 (("am__EXEEXT_1 = samtools_0\\.1\\.18\\$\\(EXEEXT\\)") ""))
1270 (substitute* '("src/common.cpp"
1272 (("samtools_0.1.18") (which "samtools")))
1273 (substitute* '("src/common.h"
1274 "src/bam2fastx.cpp")
1275 (("#include \"bam.h\"") "#include <samtools/bam.h>")
1276 (("#include \"sam.h\"") "#include <samtools/sam.h>"))
1277 (substitute* '("src/bwt_map.h"
1279 "src/align_status.h")
1280 (("#include <bam.h>") "#include <samtools/bam.h>")
1281 (("#include <sam.h>") "#include <samtools/sam.h>"))
1286 ("samtools" ,samtools-0.1)
1287 ("ncurses" ,ncurses)
1288 ("python" ,python-2)
1292 (home-page "http://ccb.jhu.edu/software/tophat/index.shtml")
1293 (synopsis "Spliced read mapper for RNA-Seq data")
1295 "TopHat is a fast splice junction mapper for nucleotide sequence
1296 reads produced by the RNA-Seq method. It aligns RNA-Seq reads to
1297 mammalian-sized genomes using the ultra high-throughput short read
1298 aligner Bowtie, and then analyzes the mapping results to identify
1299 splice junctions between exons.")
1300 ;; TopHat is released under the Boost Software License, Version 1.0
1301 ;; See https://github.com/infphilo/tophat/issues/11#issuecomment-121589893
1302 (license license:boost1.0)))
1311 "https://github.com/lh3/bwa/releases/download/v"
1312 version "/bwa-" version ".tar.bz2"))
1315 "1zfhv2zg9v1icdlq4p9ssc8k01mca5d1bd87w71py2swfi74s6yy"))))
1316 (build-system gnu-build-system)
1318 '(#:tests? #f ;no "check" target
1320 (modify-phases %standard-phases
1322 (lambda* (#:key outputs #:allow-other-keys)
1323 (let ((bin (string-append
1324 (assoc-ref outputs "out") "/bin"))
1326 (assoc-ref outputs "out") "/share/doc/bwa"))
1328 (assoc-ref outputs "out") "/share/man/man1")))
1329 (install-file "bwa" bin)
1330 (install-file "README.md" doc)
1331 (install-file "bwa.1" man))
1333 ;; no "configure" script
1334 (delete 'configure))))
1335 (inputs `(("zlib" ,zlib)))
1336 ;; Non-portable SSE instructions are used so building fails on platforms
1337 ;; other than x86_64.
1338 (supported-systems '("x86_64-linux"))
1339 (home-page "http://bio-bwa.sourceforge.net/")
1340 (synopsis "Burrows-Wheeler sequence aligner")
1342 "BWA is a software package for mapping low-divergent sequences against a
1343 large reference genome, such as the human genome. It consists of three
1344 algorithms: BWA-backtrack, BWA-SW and BWA-MEM. The first algorithm is
1345 designed for Illumina sequence reads up to 100bp, while the rest two for
1346 longer sequences ranged from 70bp to 1Mbp. BWA-MEM and BWA-SW share similar
1347 features such as long-read support and split alignment, but BWA-MEM, which is
1348 the latest, is generally recommended for high-quality queries as it is faster
1349 and more accurate. BWA-MEM also has better performance than BWA-backtrack for
1350 70-100bp Illumina reads.")
1351 (license license:gpl3+)))
1353 (define-public bwa-pssm
1354 (package (inherit bwa)
1359 (uri (string-append "https://github.com/pkerpedjiev/bwa-pssm/"
1360 "archive/" version ".tar.gz"))
1361 (file-name (string-append name "-" version ".tar.gz"))
1364 "02p7mpbs4mlxmn84g2x4ghak638vbj4lqix2ipx5g84pz9bhdavg"))))
1365 (build-system gnu-build-system)
1370 (home-page "http://bwa-pssm.binf.ku.dk/")
1371 (synopsis "Burrows-Wheeler transform-based probabilistic short read mapper")
1373 "BWA-PSSM is a probabilistic short genomic sequence read aligner based on
1374 the use of @dfn{position specific scoring matrices} (PSSM). Like many of the
1375 existing aligners it is fast and sensitive. Unlike most other aligners,
1376 however, it is also adaptible in the sense that one can direct the alignment
1377 based on known biases within the data set. It is coded as a modification of
1378 the original BWA alignment program and shares the genome index structure as
1379 well as many of the command line options.")
1380 (license license:gpl3+)))
1382 (define-public python2-bx-python
1384 (name "python2-bx-python")
1388 (uri (pypi-uri "bx-python" version))
1391 "15z2w3bvnc0n4qmb9bd6d8ylc2h2nj883x2w9iixf4x3vki9b22i"))
1392 (modules '((guix build utils)))
1394 '(substitute* "setup.py"
1395 ;; remove dependency on outdated "distribute" module
1396 (("^from distribute_setup import use_setuptools") "")
1397 (("^use_setuptools\\(\\)") "")))))
1398 (build-system python-build-system)
1400 `(#:tests? #f ;tests fail because test data are not included
1401 #:python ,python-2))
1403 `(("python-numpy" ,python2-numpy)
1406 `(("python-nose" ,python2-nose)))
1407 (home-page "http://bitbucket.org/james_taylor/bx-python/")
1408 (synopsis "Tools for manipulating biological data")
1410 "bx-python provides tools for manipulating biological data, particularly
1411 multiple sequence alignments.")
1412 (license license:expat)))
1414 (define-public python-pysam
1416 (name "python-pysam")
1420 ;; Test data is missing on PyPi.
1422 "https://github.com/pysam-developers/pysam/archive/v"
1424 (file-name (string-append name "-" version ".tar.gz"))
1427 "0dzap2axin9cbbl0d825w294bpn00zagfm1sigamm4v2pm5bj9lp"))
1428 (modules '((guix build utils)))
1430 ;; Drop bundled htslib. TODO: Also remove samtools and bcftools.
1431 '(delete-file-recursively "htslib"))))
1432 (build-system python-build-system)
1434 `(#:modules ((ice-9 ftw)
1436 (guix build python-build-system)
1439 (modify-phases %standard-phases
1440 (add-before 'build 'set-flags
1441 (lambda* (#:key inputs #:allow-other-keys)
1442 (setenv "HTSLIB_MODE" "external")
1443 (setenv "HTSLIB_LIBRARY_DIR"
1444 (string-append (assoc-ref inputs "htslib") "/lib"))
1445 (setenv "HTSLIB_INCLUDE_DIR"
1446 (string-append (assoc-ref inputs "htslib") "/include"))
1447 (setenv "LDFLAGS" "-lncurses")
1448 (setenv "CFLAGS" "-D_CURSES_LIB=1")
1451 (lambda* (#:key inputs outputs #:allow-other-keys)
1452 ;; Add first subdirectory of "build" directory to PYTHONPATH.
1453 (setenv "PYTHONPATH"
1455 (getenv "PYTHONPATH")
1456 ":" (getcwd) "/build/"
1457 (car (scandir "build"
1458 (negate (cut string-prefix? "." <>))))))
1459 ;; Step out of source dir so python does not import from CWD.
1460 (with-directory-excursion "tests"
1461 (setenv "HOME" "/tmp")
1462 (and (zero? (system* "make" "-C" "pysam_data"))
1463 (zero? (system* "make" "-C" "cbcf_data"))
1464 ;; Running nosetests without explicitly asking for a
1465 ;; single process leads to a crash. Running with multiple
1466 ;; processes fails because the tests are not designed to
1469 ;; FIXME: tests keep timing out on some systems.
1470 ;; (zero? (system* "nosetests" "-v"
1471 ;; "--processes" "1"))
1474 `(("htslib" ,htslib))) ; Included from installed header files.
1476 `(("ncurses" ,ncurses)
1479 `(("python-cython" ,python-cython)
1480 ;; Dependencies below are are for tests only.
1481 ("samtools" ,samtools)
1482 ("bcftools" ,bcftools)
1483 ("python-nose" ,python-nose)))
1484 (home-page "https://github.com/pysam-developers/pysam")
1485 (synopsis "Python bindings to the SAMtools C API")
1487 "Pysam is a Python module for reading and manipulating files in the
1488 SAM/BAM format. Pysam is a lightweight wrapper of the SAMtools C API. It
1489 also includes an interface for tabix.")
1490 (license license:expat)))
1492 (define-public python2-pysam
1493 (package-with-python2 python-pysam))
1495 (define-public python-twobitreader
1497 (name "python-twobitreader")
1501 (uri (pypi-uri "twobitreader" version))
1504 "1q8wnj2kga9nz1lwc4w7qv52smfm536hp6mc8w6s53lhyj0mpi22"))))
1505 (build-system python-build-system)
1507 '(;; Tests are not distributed in the PyPi release.
1508 ;; TODO Try building from the Git repo or asking the upstream maintainer
1509 ;; to distribute the tests on PyPi.
1512 `(("python-sphinx" ,python-sphinx)))
1513 (home-page "https://github.com/benjschiller/twobitreader")
1514 (synopsis "Python library for reading .2bit files")
1516 "twobitreader is a Python library for reading .2bit files as used by the
1517 UCSC genome browser.")
1518 (license license:artistic2.0)))
1520 (define-public python2-twobitreader
1521 (package-with-python2 python-twobitreader))
1523 (define-public python-plastid
1525 (name "python-plastid")
1529 (uri (pypi-uri "plastid" version))
1532 "0l24dd3q66if8yj042m4s0g95n6acn7im1imqd3p6h8ns43kxhj8"))))
1533 (build-system python-build-system)
1535 ;; Some test files are not included.
1538 `(("python-numpy" ,python-numpy)
1539 ("python-scipy" ,python-scipy)
1540 ("python-pandas" ,python-pandas)
1541 ("python-pysam" ,python-pysam)
1542 ("python-matplotlib" ,python-matplotlib)
1543 ("python-biopython" ,python-biopython)
1544 ("python-twobitreader" ,python-twobitreader)
1545 ("python-termcolor" ,python-termcolor)))
1547 `(("python-cython" ,python-cython)
1548 ("python-nose" ,python-nose)))
1549 (home-page "https://github.com/joshuagryphon/plastid")
1550 (synopsis "Python library for genomic analysis")
1552 "plastid is a Python library for genomic analysis – in particular,
1553 high-throughput sequencing data – with an emphasis on simplicity.")
1554 (license license:bsd-3)))
1556 (define-public python2-plastid
1557 (package-with-python2 python-plastid))
1559 (define-public cd-hit
1565 (uri (string-append "https://github.com/weizhongli/cdhit"
1566 "/releases/download/V" version
1568 "-2017-0621-source.tar.gz"))
1571 "1b4mwm2520ixjbw57sil20f9iixzw4bkdqqwgg1fc3pzm6rz4zmn"))))
1572 (build-system gnu-build-system)
1574 `(#:tests? #f ; there are no tests
1576 ;; Executables are copied directly to the PREFIX.
1577 (list (string-append "PREFIX=" (assoc-ref %outputs "out") "/bin"))
1579 (modify-phases %standard-phases
1580 ;; No "configure" script
1582 ;; Remove sources of non-determinism
1583 (add-after 'unpack 'be-timeless
1585 (substitute* "cdhit-utility.c++"
1586 ((" \\(built on \" __DATE__ \"\\)") ""))
1587 (substitute* "cdhit-common.c++"
1588 (("__DATE__") "\"0\"")
1589 (("\", %s, \" __TIME__ \"\\\\n\", date") ""))
1591 ;; The "install" target does not create the target directory.
1592 (add-before 'install 'create-target-dir
1593 (lambda* (#:key outputs #:allow-other-keys)
1594 (mkdir-p (string-append (assoc-ref outputs "out") "/bin"))
1598 (home-page "http://weizhongli-lab.org/cd-hit/")
1599 (synopsis "Cluster and compare protein or nucleotide sequences")
1601 "CD-HIT is a program for clustering and comparing protein or nucleotide
1602 sequences. CD-HIT is designed to be fast and handle extremely large
1604 ;; The manual says: "It can be copied under the GNU General Public License
1605 ;; version 2 (GPLv2)."
1606 (license license:gpl2)))
1608 (define-public clipper
1615 "https://github.com/YeoLab/clipper/archive/"
1617 (file-name (string-append name "-" version ".tar.gz"))
1620 "0pflmsvhbf8izbgwhbhj1i7349sw1f55qpqj8ljmapp16hb0p0qi"))
1621 (modules '((guix build utils)))
1624 ;; remove unnecessary setup dependency
1625 (substitute* "setup.py"
1626 (("setup_requires = .*") ""))
1627 (for-each delete-file
1628 '("clipper/src/peaks.so"
1629 "clipper/src/readsToWiggle.so"))
1630 (delete-file-recursively "dist/")
1632 (build-system python-build-system)
1633 (arguments `(#:python ,python-2)) ; only Python 2 is supported
1635 `(("htseq" ,python2-htseq)
1636 ("python-pybedtools" ,python2-pybedtools)
1637 ("python-cython" ,python2-cython)
1638 ("python-scikit-learn" ,python2-scikit-learn)
1639 ("python-matplotlib" ,python2-matplotlib)
1640 ("python-pandas" ,python2-pandas)
1641 ("python-pysam" ,python2-pysam)
1642 ("python-numpy" ,python2-numpy)
1643 ("python-scipy" ,python2-scipy)))
1645 `(("python-mock" ,python2-mock) ; for tests
1646 ("python-nose" ,python2-nose) ; for tests
1647 ("python-pytz" ,python2-pytz))) ; for tests
1648 (home-page "https://github.com/YeoLab/clipper")
1649 (synopsis "CLIP peak enrichment recognition")
1651 "CLIPper is a tool to define peaks in CLIP-seq datasets.")
1652 (license license:gpl2)))
1654 (define-public codingquarry
1656 (name "codingquarry")
1661 "mirror://sourceforge/codingquarry/CodingQuarry_v"
1665 "0115hkjflsnfzn36xppwf9h9avfxlavr43djqmshkkzbgjzsz60i"))))
1666 (build-system gnu-build-system)
1668 '(#:tests? #f ; no "check" target
1670 (modify-phases %standard-phases
1673 (lambda* (#:key outputs #:allow-other-keys)
1674 (let* ((out (assoc-ref outputs "out"))
1675 (bin (string-append out "/bin"))
1676 (doc (string-append out "/share/doc/codingquarry")))
1677 (install-file "INSTRUCTIONS.pdf" doc)
1678 (copy-recursively "QuarryFiles"
1679 (string-append out "/QuarryFiles"))
1680 (install-file "CodingQuarry" bin)
1681 (install-file "CufflinksGTF_to_CodingQuarryGFF3.py" bin)))))))
1682 (inputs `(("openmpi" ,openmpi)))
1683 (native-search-paths
1684 (list (search-path-specification
1685 (variable "QUARRY_PATH")
1686 (files '("QuarryFiles")))))
1687 (native-inputs `(("python" ,python-2))) ; Only Python 2 is supported
1688 (synopsis "Fungal gene predictor")
1689 (description "CodingQuarry is a highly accurate, self-training GHMM fungal
1690 gene predictor designed to work with assembled, aligned RNA-seq transcripts.")
1691 (home-page "https://sourceforge.net/projects/codingquarry/")
1692 (license license:gpl3+)))
1694 (define-public couger
1701 "http://couger.oit.duke.edu/static/assets/COUGER"
1705 "04p2b14nmhzxw5h72mpzdhalv21bx4w9b87z0wpw0xzxpysyncmq"))))
1706 (build-system gnu-build-system)
1710 (modify-phases %standard-phases
1715 (lambda* (#:key outputs #:allow-other-keys)
1716 (let* ((out (assoc-ref outputs "out"))
1717 (bin (string-append out "/bin")))
1718 (copy-recursively "src" (string-append out "/src"))
1720 ;; Add "src" directory to module lookup path.
1721 (substitute* "couger"
1723 (string-append "import sys\nsys.path.append(\""
1724 out "\")\nfrom argparse")))
1725 (install-file "couger" bin))
1728 'install 'wrap-program
1729 (lambda* (#:key inputs outputs #:allow-other-keys)
1730 ;; Make sure 'couger' runs with the correct PYTHONPATH.
1731 (let* ((out (assoc-ref outputs "out"))
1732 (path (getenv "PYTHONPATH")))
1733 (wrap-program (string-append out "/bin/couger")
1734 `("PYTHONPATH" ":" prefix (,path))))
1737 `(("python" ,python-2)
1738 ("python2-pillow" ,python2-pillow)
1739 ("python2-numpy" ,python2-numpy)
1740 ("python2-scipy" ,python2-scipy)
1741 ("python2-matplotlib" ,python2-matplotlib)))
1743 `(("r-minimal" ,r-minimal)
1745 ("randomjungle" ,randomjungle)))
1747 `(("unzip" ,unzip)))
1748 (home-page "http://couger.oit.duke.edu")
1749 (synopsis "Identify co-factors in sets of genomic regions")
1751 "COUGER can be applied to any two sets of genomic regions bound by
1752 paralogous TFs (e.g., regions derived from ChIP-seq experiments) to identify
1753 putative co-factors that provide specificity to each TF. The framework
1754 determines the genomic targets uniquely-bound by each TF, and identifies a
1755 small set of co-factors that best explain the in vivo binding differences
1756 between the two TFs.
1758 COUGER uses classification algorithms (support vector machines and random
1759 forests) with features that reflect the DNA binding specificities of putative
1760 co-factors. The features are generated either from high-throughput TF-DNA
1761 binding data (from protein binding microarray experiments), or from large
1762 collections of DNA motifs.")
1763 (license license:gpl3+)))
1765 (define-public clustal-omega
1767 (name "clustal-omega")
1771 (uri (string-append "http://www.clustal.org/omega/clustal-omega-"
1775 "1vm30mzncwdv881vrcwg11vzvrsmwy4wg80j5i0lcfk6dlld50w6"))))
1776 (build-system gnu-build-system)
1778 `(("argtable" ,argtable)))
1779 (home-page "http://www.clustal.org/omega/")
1780 (synopsis "Multiple sequence aligner for protein and DNA/RNA")
1782 "Clustal-Omega is a general purpose multiple sequence alignment (MSA)
1783 program for protein and DNA/RNA. It produces high quality MSAs and is capable
1784 of handling data-sets of hundreds of thousands of sequences in reasonable
1786 (license license:gpl2+)))
1788 (define-public crossmap
1794 (uri (string-append "mirror://sourceforge/crossmap/CrossMap-"
1798 "07y179f63d7qnzdvkqcziwk9bs3k4zhp81q392fp1hwszjdvy22f"))
1799 ;; This patch has been sent upstream already and is available
1800 ;; for download from Sourceforge, but it has not been merged.
1801 (patches (search-patches "crossmap-allow-system-pysam.patch"))
1802 (modules '((guix build utils)))
1803 ;; remove bundled copy of pysam
1805 '(delete-file-recursively "lib/pysam"))))
1806 (build-system python-build-system)
1808 `(#:python ,python-2
1810 (modify-phases %standard-phases
1811 (add-after 'unpack 'set-env
1812 (lambda _ (setenv "CROSSMAP_USE_SYSTEM_PYSAM" "1") #t)))))
1814 `(("python-numpy" ,python2-numpy)
1815 ("python-pysam" ,python2-pysam)
1818 `(("python-cython" ,python2-cython)
1819 ("python-nose" ,python2-nose)))
1820 (home-page "http://crossmap.sourceforge.net/")
1821 (synopsis "Convert genome coordinates between assemblies")
1823 "CrossMap is a program for conversion of genome coordinates or annotation
1824 files between different genome assemblies. It supports most commonly used
1825 file formats including SAM/BAM, Wiggle/BigWig, BED, GFF/GTF, VCF.")
1826 (license license:gpl2+)))
1828 (define-public cutadapt
1835 (url "https://github.com/marcelm/cutadapt.git")
1836 (commit (string-append "v" version))))
1837 (file-name (string-append name "-" version "-checkout"))
1840 "09pr02067jiks19nc0aby4xp70hhgvb554i2y1c04rv1m401w7q8"))))
1841 (build-system python-build-system)
1843 `(("python-xopen" ,python-xopen)))
1845 `(("python-cython" ,python-cython)
1846 ("python-pytest" ,python-pytest)))
1847 (home-page "https://cutadapt.readthedocs.io/en/stable/")
1848 (synopsis "Remove adapter sequences from nucleotide sequencing reads")
1850 "Cutadapt finds and removes adapter sequences, primers, poly-A tails and
1851 other types of unwanted sequence from high-throughput sequencing reads.")
1852 (license license:expat)))
1854 (define-public libbigwig
1860 (uri (string-append "https://github.com/dpryan79/libBigWig/"
1861 "archive/" version ".tar.gz"))
1862 (file-name (string-append name "-" version ".tar.gz"))
1865 "098rjh35pi4a9q83n8wiwvyzykjqj6l8q189p1xgfw4ghywdlvw1"))))
1866 (build-system gnu-build-system)
1868 `(#:test-target "test"
1871 (string-append "prefix=" (assoc-ref %outputs "out")))
1873 (modify-phases %standard-phases
1875 (add-before 'check 'disable-curl-test
1877 (substitute* "Makefile"
1878 (("./test/testRemote.*") ""))
1880 ;; This has been fixed with the upstream commit 4ff6959cd8a0, but
1881 ;; there has not yet been a release containing this change.
1882 (add-before 'install 'create-target-dirs
1883 (lambda* (#:key outputs #:allow-other-keys)
1884 (let ((out (assoc-ref outputs "out")))
1885 (mkdir-p (string-append out "/lib"))
1886 (mkdir-p (string-append out "/include"))
1892 `(("doxygen" ,doxygen)))
1893 (home-page "https://github.com/dpryan79/libBigWig")
1894 (synopsis "C library for handling bigWig files")
1896 "This package provides a C library for parsing local and remote BigWig
1898 (license license:expat)))
1900 (define-public python-pybigwig
1902 (name "python-pybigwig")
1906 (uri (pypi-uri "pyBigWig" version))
1909 "0yrpdxg3y0sny25x4w22lv1k47jzccqjmg7j4bp0hywklvp0hg7d"))
1910 (modules '((guix build utils)))
1913 ;; Delete bundled libBigWig sources
1914 (delete-file-recursively "libBigWig")))))
1915 (build-system python-build-system)
1918 (modify-phases %standard-phases
1919 (add-after 'unpack 'link-with-libBigWig
1920 (lambda* (#:key inputs #:allow-other-keys)
1921 (substitute* "setup.py"
1922 (("libs=\\[") "libs=[\"BigWig\", "))
1925 `(("libbigwig" ,libbigwig)
1928 (home-page "https://github.com/dpryan79/pyBigWig")
1929 (synopsis "Access bigWig files in Python using libBigWig")
1931 "This package provides Python bindings to the libBigWig library for
1932 accessing bigWig files.")
1933 (license license:expat)))
1935 (define-public python2-pybigwig
1936 (package-with-python2 python-pybigwig))
1938 (define-public python-dendropy
1940 (name "python-dendropy")
1945 (uri (pypi-uri "DendroPy" version))
1948 "15c7s3d5gf19ljsxvq5advaa752wfi7pwrdjyhzmg85hccyvp47p"))
1949 (patches (search-patches "python-dendropy-fix-tests.patch"))))
1950 (build-system python-build-system)
1951 (home-page "http://packages.python.org/DendroPy/")
1952 (synopsis "Library for phylogenetics and phylogenetic computing")
1954 "DendroPy is a library for phylogenetics and phylogenetic computing: reading,
1955 writing, simulation, processing and manipulation of phylogenetic
1956 trees (phylogenies) and characters.")
1957 (license license:bsd-3)
1958 (properties `((python2-variant . ,(delay python2-dendropy))))))
1960 (define-public python2-dendropy
1961 (let ((base (package-with-python2 (strip-python2-variant python-dendropy))))
1965 `(#:python ,python-2
1967 (modify-phases %standard-phases
1969 ;; There is currently a test failure that only happens on some
1970 ;; systems, and only using "setup.py test"
1971 (lambda _ (zero? (system* "nosetests")))))))
1972 (native-inputs `(("python2-nose" ,python2-nose)
1973 ,@(package-native-inputs base))))))
1975 (define-public python-py2bit
1977 (name "python-py2bit")
1982 (uri (pypi-uri "py2bit" version))
1985 "1cdf4qlmgwsh1f4k0wdv2sr8x9qn4366p0k3614vbd0fpqiarxrl"))))
1986 (build-system python-build-system)
1987 (home-page "https://github.com/dpryan79/py2bit")
1988 (synopsis "Access 2bit files using lib2bit")
1990 "This package provides Python bindings for lib2bit to access 2bit files
1992 (license license:expat)))
1994 (define-public deeptools
2000 (uri (string-append "https://github.com/deeptools/deepTools/"
2001 "archive/" version ".tar.gz"))
2002 (file-name (string-append name "-" version ".tar.gz"))
2005 "1q8i12l2gvk4n2s8lhyzwhh9g4qbc8lrk5l7maz00yvd5g6z5540"))))
2006 (build-system python-build-system)
2008 `(("python-scipy" ,python-scipy)
2009 ("python-numpy" ,python-numpy)
2010 ("python-numpydoc" ,python-numpydoc)
2011 ("python-matplotlib" ,python-matplotlib)
2012 ("python-pysam" ,python-pysam)
2013 ("python-py2bit" ,python-py2bit)
2014 ("python-pybigwig" ,python-pybigwig)))
2016 `(("python-mock" ,python-mock) ;for tests
2017 ("python-nose" ,python-nose) ;for tests
2018 ("python-pytz" ,python-pytz))) ;for tests
2019 (home-page "https://github.com/deeptools/deepTools")
2020 (synopsis "Tools for normalizing and visualizing deep-sequencing data")
2022 "DeepTools addresses the challenge of handling the large amounts of data
2023 that are now routinely generated from DNA sequencing centers. To do so,
2024 deepTools contains useful modules to process the mapped reads data to create
2025 coverage files in standard bedGraph and bigWig file formats. By doing so,
2026 deepTools allows the creation of normalized coverage files or the comparison
2027 between two files (for example, treatment and control). Finally, using such
2028 normalized and standardized files, multiple visualizations can be created to
2029 identify enrichments with functional annotations of the genome.")
2030 (license license:gpl3+)))
2032 (define-public delly
2039 "https://github.com/tobiasrausch/delly/archive/v"
2041 (file-name (string-append name "-" version ".tar.gz"))
2043 (base32 "0dkwy3pyxmi6dhh1lpsr3698ri5sslw9qz67hfys0bz8dgrqwabj"))
2044 (patches (search-patches "delly-use-system-libraries.patch"))))
2045 (build-system gnu-build-system)
2047 `(#:tests? #f ; There are no tests to run.
2048 #:make-flags '("PARALLEL=1") ; Allow parallel execution at run-time.
2050 (modify-phases %standard-phases
2051 (delete 'configure) ; There is no configure phase.
2054 (let ((bin (string-append (assoc-ref %outputs "out") "/bin"))
2055 (templates (string-append (assoc-ref %outputs "out")
2056 "/share/delly/templates")))
2059 (copy-recursively "excludeTemplates" templates)
2060 (install-file "src/cov" bin)
2061 (install-file "src/delly" bin)
2062 (install-file "src/dpe" bin)))))))
2064 `(("python" ,python-2)))
2070 (home-page "https://github.com/tobiasrausch/delly")
2071 (synopsis "Integrated structural variant prediction method")
2072 (description "Delly is an integrated structural variant prediction method
2073 that can discover and genotype deletions, tandem duplications, inversions and
2074 translocations at single-nucleotide resolution in short-read massively parallel
2075 sequencing data. It uses paired-ends and split-reads to sensitively and
2076 accurately delineate genomic rearrangements throughout the genome.")
2077 (license license:gpl3+)))
2079 (define-public diamond
2086 "https://github.com/bbuchfink/diamond/archive/v"
2088 (file-name (string-append name "-" version ".tar.gz"))
2091 "0adp87r9ak63frdrdmrdfhsn6g0jnnyq1lr2wibvqbxcl37iir9m"))))
2092 (build-system cmake-build-system)
2094 '(#:tests? #f ; no "check" target
2096 (modify-phases %standard-phases
2097 (add-after 'unpack 'remove-native-compilation
2099 (substitute* "CMakeLists.txt" (("-march=native") ""))
2103 (home-page "https://github.com/bbuchfink/diamond")
2104 (synopsis "Accelerated BLAST compatible local sequence aligner")
2106 "DIAMOND is a BLAST-compatible local aligner for mapping protein and
2107 translated DNA query sequences against a protein reference database (BLASTP
2108 and BLASTX alignment mode). The speedup over BLAST is up to 20,000 on short
2109 reads at a typical sensitivity of 90-99% relative to BLAST depending on the
2110 data and settings.")
2111 (license license:agpl3+)))
2113 (define-public discrover
2120 (uri (string-append "https://github.com/maaskola/discrover/archive/"
2122 (file-name (string-append name "-" version ".tar.gz"))
2125 "0rah9ja4m0rl5mldd6vag9rwrivw1zrqxssfq8qx64m7961fp68k"))))
2126 (build-system cmake-build-system)
2128 `(#:tests? #f ; there are no tests
2130 (modify-phases %standard-phases
2131 (add-after 'unpack 'add-missing-includes
2133 (substitute* "src/executioninformation.hpp"
2134 (("#define EXECUTIONINFORMATION_HPP" line)
2135 (string-append line "\n#include <random>")))
2136 (substitute* "src/plasma/fasta.hpp"
2137 (("#define FASTA_HPP" line)
2138 (string-append line "\n#include <random>")))
2144 `(("texlive" ,texlive)
2145 ("imagemagick" ,imagemagick)))
2146 (home-page "http://dorina.mdc-berlin.de/public/rajewsky/discrover/")
2147 (synopsis "Discover discriminative nucleotide sequence motifs")
2148 (description "Discrover is a motif discovery method to find binding sites
2149 of nucleic acid binding proteins.")
2150 (license license:gpl3+)))
2152 (define-public eigensoft
2153 (let ((revision "1")
2154 (commit "b14d1e202e21e532536ff8004f0419cd5e259dc7"))
2157 (version (string-append "6.1.2-"
2159 (string-take commit 9)))
2164 (url "https://github.com/DReichLab/EIG.git")
2166 (file-name (string-append "eigensoft-" commit "-checkout"))
2169 "0f5m6k2j5c16xc3xbywcs989xyc26ncy1zfzp9j9n55n9r4xcaiq"))
2170 (modules '((guix build utils)))
2171 ;; Remove pre-built binaries.
2173 (delete-file-recursively "bin")
2176 (build-system gnu-build-system)
2178 `(#:tests? #f ; There are no tests.
2179 #:make-flags '("CC=gcc")
2181 (modify-phases %standard-phases
2182 ;; There is no configure phase, but the Makefile is in a
2187 ;; The link flags are incomplete.
2188 (substitute* "Makefile"
2189 (("-lgsl") "-lgsl -lm -llapack -llapacke -lpthread"))
2191 ;; The provided install target only copies executables to
2192 ;; the "bin" directory in the build root.
2193 (add-after 'install 'actually-install
2194 (lambda* (#:key outputs #:allow-other-keys)
2195 (let* ((out (assoc-ref outputs "out"))
2196 (bin (string-append out "/bin")))
2197 (for-each (lambda (file)
2198 (install-file file bin))
2199 (find-files "../bin" ".*"))
2204 ("openblas" ,openblas)
2206 ("gfortran" ,gfortran "lib")))
2207 (home-page "https://github.com/DReichLab/EIG")
2208 (synopsis "Tools for population genetics")
2209 (description "The EIGENSOFT package provides tools for population
2210 genetics and stratification correction. EIGENSOFT implements methods commonly
2211 used in population genetics analyses such as PCA, computation of Tracy-Widom
2212 statistics, and finding related individuals in structured populations. It
2213 comes with a built-in plotting script and supports multiple file formats and
2214 quantitative phenotypes.")
2215 ;; The license of the eigensoft tools is Expat, but since it's
2216 ;; linking with the GNU Scientific Library (GSL) the effective
2217 ;; license is the GPL.
2218 (license license:gpl3+))))
2220 (define-public edirect
2226 (uri (string-append "ftp://ftp.ncbi.nlm.nih.gov/entrez/entrezdirect/"
2227 "versions/2016-05-03/edirect.tar.gz"))
2230 "15zsprak5yh8c1yrz4r1knmb5s8qcmdid4xdhkh3lqcv64l60hli"))))
2231 (build-system perl-build-system)
2233 `(#:tests? #f ;no "check" target
2235 (modify-phases %standard-phases
2239 (lambda* (#:key outputs #:allow-other-keys)
2240 (let ((target (string-append (assoc-ref outputs "out")
2243 (install-file "edirect.pl" target)
2246 'install 'wrap-program
2247 (lambda* (#:key inputs outputs #:allow-other-keys)
2248 ;; Make sure 'edirect.pl' finds all perl inputs at runtime.
2249 (let* ((out (assoc-ref outputs "out"))
2250 (path (getenv "PERL5LIB")))
2251 (wrap-program (string-append out "/bin/edirect.pl")
2252 `("PERL5LIB" ":" prefix (,path)))))))))
2254 `(("perl-html-parser" ,perl-html-parser)
2255 ("perl-encode-locale" ,perl-encode-locale)
2256 ("perl-file-listing" ,perl-file-listing)
2257 ("perl-html-tagset" ,perl-html-tagset)
2258 ("perl-html-tree" ,perl-html-tree)
2259 ("perl-http-cookies" ,perl-http-cookies)
2260 ("perl-http-date" ,perl-http-date)
2261 ("perl-http-message" ,perl-http-message)
2262 ("perl-http-negotiate" ,perl-http-negotiate)
2263 ("perl-lwp-mediatypes" ,perl-lwp-mediatypes)
2264 ("perl-lwp-protocol-https" ,perl-lwp-protocol-https)
2265 ("perl-net-http" ,perl-net-http)
2266 ("perl-uri" ,perl-uri)
2267 ("perl-www-robotrules" ,perl-www-robotrules)
2269 (home-page "http://www.ncbi.nlm.nih.gov/books/NBK179288/")
2270 (synopsis "Tools for accessing the NCBI's set of databases")
2272 "Entrez Direct (EDirect) is a method for accessing the National Center
2273 for Biotechnology Information's (NCBI) set of interconnected
2274 databases (publication, sequence, structure, gene, variation, expression,
2275 etc.) from a terminal. Functions take search terms from command-line
2276 arguments. Individual operations are combined to build multi-step queries.
2277 Record retrieval and formatting normally complete the process.
2279 EDirect also provides an argument-driven function that simplifies the
2280 extraction of data from document summaries or other results that are returned
2281 in structured XML format. This can eliminate the need for writing custom
2282 software to answer ad hoc questions.")
2283 (license license:public-domain)))
2285 (define-public exonerate
2294 "http://ftp.ebi.ac.uk/pub/software/vertebrategenomics/exonerate/"
2295 "exonerate-" version ".tar.gz"))
2298 "0hj0m9xygiqsdxvbg79wq579kbrx1mdrabi2bzqz2zn9qwfjcjgq"))))
2299 (build-system gnu-build-system)
2301 `(#:parallel-build? #f)) ; Building in parallel fails on some machines.
2303 `(("pkg-config" ,pkg-config)))
2307 "https://www.ebi.ac.uk/about/vertebrate-genomics/software/exonerate")
2308 (synopsis "Generic tool for biological sequence alignment")
2310 "Exonerate is a generic tool for pairwise sequence comparison. It allows
2311 the alignment of sequences using a many alignment models, either exhaustive
2312 dynamic programming or a variety of heuristics.")
2313 (license license:gpl3)))
2315 (define-public express
2323 "http://bio.math.berkeley.edu/eXpress/downloads/express-"
2324 version "/express-" version "-src.tgz"))
2327 "03rczxd0gjp2l1jxcmjfmf5j94j77zqyxa6x063zsc585nj40n0c"))))
2328 (build-system cmake-build-system)
2330 `(#:tests? #f ;no "check" target
2332 (modify-phases %standard-phases
2333 (add-after 'unpack 'use-shared-boost-libs-and-set-bamtools-paths
2334 (lambda* (#:key inputs #:allow-other-keys)
2335 (substitute* "CMakeLists.txt"
2336 (("set\\(Boost_USE_STATIC_LIBS ON\\)")
2337 "set(Boost_USE_STATIC_LIBS OFF)")
2338 (("\\$\\{CMAKE_CURRENT_SOURCE_DIR\\}/bamtools/include")
2339 (string-append (assoc-ref inputs "bamtools") "/include/bamtools")))
2340 (substitute* "src/CMakeLists.txt"
2341 (("\\$\\{CMAKE_CURRENT_SOURCE_DIR\\}/\\.\\./bamtools/lib")
2342 (string-append (assoc-ref inputs "bamtools") "/lib"))
2343 (("libprotobuf.a") "libprotobuf.so"))
2347 ("bamtools" ,bamtools)
2348 ("protobuf" ,protobuf)
2350 (home-page "http://bio.math.berkeley.edu/eXpress")
2351 (synopsis "Streaming quantification for high-throughput genomic sequencing")
2353 "eXpress is a streaming tool for quantifying the abundances of a set of
2354 target sequences from sampled subsequences. Example applications include
2355 transcript-level RNA-Seq quantification, allele-specific/haplotype expression
2356 analysis (from RNA-Seq), transcription factor binding quantification in
2357 ChIP-Seq, and analysis of metagenomic data.")
2358 (license license:artistic2.0)))
2360 (define-public express-beta-diversity
2362 (name "express-beta-diversity")
2368 "https://github.com/dparks1134/ExpressBetaDiversity/archive/v"
2370 (file-name (string-append name "-" version ".tar.gz"))
2373 "1djvdlmqvjf6h0zq7w36y8cl5cli6rgj86x65znl48agnwmzxfxr"))))
2374 (build-system gnu-build-system)
2377 (modify-phases %standard-phases
2379 (add-before 'build 'enter-source (lambda _ (chdir "source") #t))
2381 (lambda _ (zero? (system* "../bin/ExpressBetaDiversity"
2383 (add-after 'check 'exit-source (lambda _ (chdir "..") #t))
2385 (lambda* (#:key outputs #:allow-other-keys)
2386 (let ((bin (string-append (assoc-ref outputs "out")
2389 (install-file "scripts/convertToEBD.py" bin)
2390 (install-file "bin/ExpressBetaDiversity" bin)
2393 `(("python" ,python-2)))
2394 (home-page "http://kiwi.cs.dal.ca/Software/ExpressBetaDiversity")
2395 (synopsis "Taxon- and phylogenetic-based beta diversity measures")
2397 "Express Beta Diversity (EBD) calculates ecological beta diversity
2398 (dissimilarity) measures between biological communities. EBD implements a
2399 variety of diversity measures including those that make use of phylogenetic
2400 similarity of community members.")
2401 (license license:gpl3+)))
2403 (define-public fasttree
2410 "http://www.microbesonline.org/fasttree/FastTree-"
2414 "0vcjdvy1j4m702vmak4svbfkrpcw63k7wymfksjp9a982zy8kjsl"))))
2415 (build-system gnu-build-system)
2417 `(#:tests? #f ; no "check" target
2419 (modify-phases %standard-phases
2423 (lambda* (#:key source #:allow-other-keys)
2424 (and (zero? (system* "gcc"
2426 "-finline-functions"
2433 (zero? (system* "gcc"
2437 "-finline-functions"
2445 (lambda* (#:key outputs #:allow-other-keys)
2446 (let ((bin (string-append (assoc-ref outputs "out")
2449 (install-file "FastTree" bin)
2450 (install-file "FastTreeMP" bin)
2452 (home-page "http://www.microbesonline.org/fasttree")
2453 (synopsis "Infers approximately-maximum-likelihood phylogenetic trees")
2455 "FastTree can handle alignments with up to a million of sequences in a
2456 reasonable amount of time and memory. For large alignments, FastTree is
2457 100-1,000 times faster than PhyML 3.0 or RAxML 7.")
2458 (license license:gpl2+)))
2460 (define-public fastx-toolkit
2462 (name "fastx-toolkit")
2468 "https://github.com/agordon/fastx_toolkit/releases/download/"
2469 version "/fastx_toolkit-" version ".tar.bz2"))
2472 "01jqzw386873sr0pjp1wr4rn8fsga2vxs1qfmicvx1pjr72007wy"))))
2473 (build-system gnu-build-system)
2475 `(("libgtextutils" ,libgtextutils)))
2477 `(("pkg-config" ,pkg-config)))
2478 (home-page "http://hannonlab.cshl.edu/fastx_toolkit/")
2479 (synopsis "Tools for FASTA/FASTQ file preprocessing")
2481 "The FASTX-Toolkit is a collection of command line tools for Short-Reads
2482 FASTA/FASTQ files preprocessing.
2484 Next-Generation sequencing machines usually produce FASTA or FASTQ files,
2485 containing multiple short-reads sequences. The main processing of such
2486 FASTA/FASTQ files is mapping the sequences to reference genomes. However, it
2487 is sometimes more productive to preprocess the files before mapping the
2488 sequences to the genome---manipulating the sequences to produce better mapping
2489 results. The FASTX-Toolkit tools perform some of these preprocessing tasks.")
2490 (license license:agpl3+)))
2492 (define-public flexbar
2499 (string-append "mirror://sourceforge/flexbar/"
2500 version "/flexbar_v" version "_src.tgz"))
2503 "13jaykc3y1x8y5nn9j8ljnb79s5y51kyxz46hdmvvjj6qhyympmf"))))
2504 (build-system cmake-build-system)
2506 `(#:configure-flags (list
2507 (string-append "-DFLEXBAR_BINARY_DIR="
2508 (assoc-ref %outputs "out")
2511 (modify-phases %standard-phases
2513 (lambda* (#:key outputs #:allow-other-keys)
2514 (setenv "PATH" (string-append
2515 (assoc-ref outputs "out") "/bin:"
2517 (chdir "../flexbar_v2.5_src/test")
2518 (zero? (system* "bash" "flexbar_validate.sh"))))
2519 (delete 'install))))
2524 `(("pkg-config" ,pkg-config)
2526 (home-page "http://flexbar.sourceforge.net")
2527 (synopsis "Barcode and adapter removal tool for sequencing platforms")
2529 "Flexbar preprocesses high-throughput nucleotide sequencing data
2530 efficiently. It demultiplexes barcoded runs and removes adapter sequences.
2531 Moreover, trimming and filtering features are provided. Flexbar increases
2532 read mapping rates and improves genome and transcriptome assemblies. It
2533 supports next-generation sequencing data in fasta/q and csfasta/q format from
2534 Illumina, Roche 454, and the SOLiD platform.")
2535 (license license:gpl3)))
2537 (define-public fraggenescan
2539 (name "fraggenescan")
2545 (string-append "mirror://sourceforge/fraggenescan/"
2546 "FragGeneScan" version ".tar.gz"))
2548 (base32 "158dcnwczgcyhwm4qlx19sanrwgdpzf6bn2y57mbpx55lkgz1mzj"))))
2549 (build-system gnu-build-system)
2552 (modify-phases %standard-phases
2554 (add-before 'build 'patch-paths
2555 (lambda* (#:key outputs #:allow-other-keys)
2556 (let* ((out (string-append (assoc-ref outputs "out")))
2557 (share (string-append out "/share/fraggenescan/")))
2558 (substitute* "run_FragGeneScan.pl"
2560 (string-append "system(\"" (which "rm")))
2562 (string-append "system(\"" (which "mv")))
2563 (("\\\"awk") (string-append "\"" (which "awk")))
2564 ;; This script and other programs expect the training files
2565 ;; to be in the non-standard location bin/train/XXX. Change
2566 ;; this to be share/fraggenescan/train/XXX instead.
2567 (("^\\$train.file = \\$dir.*")
2568 (string-append "$train_file = \""
2570 "train/\".$FGS_train_file;")))
2571 (substitute* "run_hmm.c"
2572 (("^ strcat\\(train_dir, \\\"train/\\\"\\);")
2573 (string-append " strcpy(train_dir, \"" share "/train/\");"))))
2576 (lambda _ (and (zero? (system* "make" "clean"))
2577 (zero? (system* "make" "fgs")))))
2579 (lambda* (#:key outputs #:allow-other-keys)
2580 (let* ((out (string-append (assoc-ref outputs "out")))
2581 (bin (string-append out "/bin/"))
2582 (share (string-append out "/share/fraggenescan/train")))
2583 (install-file "run_FragGeneScan.pl" bin)
2584 (install-file "FragGeneScan" bin)
2585 (copy-recursively "train" share))))
2587 (add-after 'install 'post-install-check
2588 ;; In lieu of 'make check', run one of the examples and check the
2589 ;; output files gets created.
2590 (lambda* (#:key outputs #:allow-other-keys)
2591 (let* ((out (string-append (assoc-ref outputs "out")))
2592 (bin (string-append out "/bin/"))
2593 (frag (string-append bin "run_FragGeneScan.pl")))
2594 (and (zero? (system* frag ; Test complete genome.
2595 "-genome=./example/NC_000913.fna"
2599 (file-exists? "test2.faa")
2600 (file-exists? "test2.ffn")
2601 (file-exists? "test2.gff")
2602 (file-exists? "test2.out")
2603 (zero? (system* ; Test incomplete sequences.
2605 "-genome=./example/NC_000913-fgs.ffn"
2608 "-train=454_30")))))))))
2611 ("python" ,python-2))) ;not compatible with python 3.
2612 (home-page "https://sourceforge.net/projects/fraggenescan/")
2613 (synopsis "Finds potentially fragmented genes in short reads")
2615 "FragGeneScan is a program for predicting bacterial and archaeal genes in
2616 short and error-prone DNA sequencing reads. It can also be applied to predict
2617 genes in incomplete assemblies or complete genomes.")
2618 ;; GPL3+ according to private correspondense with the authors.
2619 (license license:gpl3+)))
2621 (define-public fxtract
2622 (let ((util-commit "776ca85a18a47492af3794745efcb4a905113115"))
2630 "https://github.com/ctSkennerton/fxtract/archive/"
2632 (file-name (string-append "ctstennerton-util-"
2633 (string-take util-commit 7)
2637 "0275cfdhis8517hm01is62062swmi06fxzifq7mr3knbbxjlaiwj"))))
2638 (build-system gnu-build-system)
2640 `(#:make-flags (list
2641 (string-append "PREFIX=" (assoc-ref %outputs "out"))
2643 #:test-target "fxtract_test"
2645 (modify-phases %standard-phases
2647 (add-before 'build 'copy-util
2648 (lambda* (#:key inputs #:allow-other-keys)
2650 (copy-recursively (assoc-ref inputs "ctskennerton-util") "util")
2652 ;; Do not use make install as this requires additional dependencies.
2654 (lambda* (#:key outputs #:allow-other-keys)
2655 (let* ((out (assoc-ref outputs "out"))
2656 (bin (string-append out"/bin")))
2657 (install-file "fxtract" bin)
2663 ;; ctskennerton-util is licensed under GPL2.
2664 `(("ctskennerton-util"
2668 (url "https://github.com/ctSkennerton/util.git")
2669 (commit util-commit)))
2670 (file-name (string-append
2671 "ctstennerton-util-" util-commit "-checkout"))
2674 "0cls1hd4vgj3f36fpzzg4xc77d6f3hpc60cbpfmn2gdr7ykzzad7"))))))
2675 (home-page "https://github.com/ctSkennerton/fxtract")
2676 (synopsis "Extract sequences from FASTA and FASTQ files")
2678 "Fxtract extracts sequences from a protein or nucleotide fastx (FASTA
2679 or FASTQ) file given a subsequence. It uses a simple substring search for
2680 basic tasks but can change to using POSIX regular expressions, PCRE, hash
2681 lookups or multi-pattern searching as required. By default fxtract looks in
2682 the sequence of each record but can also be told to look in the header,
2683 comment or quality sections.")
2684 ;; 'util' requires SSE instructions.
2685 (supported-systems '("x86_64-linux"))
2686 (license license:expat))))
2688 (define-public gemma
2694 (uri (string-append "https://github.com/xiangzhou/GEMMA/archive/v"
2696 (file-name (string-append name "-" version ".tar.gz"))
2699 "055ynn16gd12pf78n4vr2a9jlwsbwzajpdnf2y2yilg1krfff222"))
2700 (patches (search-patches "gemma-intel-compat.patch"))))
2705 (build-system gnu-build-system)
2708 '(,@(match (%current-system)
2710 '("FORCE_DYNAMIC=1"))
2712 '("FORCE_DYNAMIC=1" "FORCE_32BIT=1"))
2714 '("FORCE_DYNAMIC=1" "NO_INTEL_COMPAT=1"))))
2716 (modify-phases %standard-phases
2718 (add-before 'build 'bin-mkdir
2723 (lambda* (#:key outputs #:allow-other-keys)
2724 (let ((out (assoc-ref outputs "out")))
2725 (install-file "bin/gemma"
2729 #:tests? #f)) ; no tests included yet
2730 (home-page "https://github.com/xiangzhou/GEMMA")
2731 (synopsis "Tool for genome-wide efficient mixed model association")
2733 "Genome-wide Efficient Mixed Model Association (GEMMA) provides a
2734 standard linear mixed model resolver with application in genome-wide
2735 association studies (GWAS).")
2736 (license license:gpl3)))
2745 "https://github.com/nboley/grit/archive/"
2747 (file-name (string-append name "-" version ".tar.gz"))
2750 "157in84dj70wimbind3x7sy1whs3h57qfgcnj2s6lrd38fbrb7mj"))))
2751 (build-system python-build-system)
2753 `(#:python ,python-2
2755 (modify-phases %standard-phases
2756 (add-after 'unpack 'generate-from-cython-sources
2757 (lambda* (#:key inputs outputs #:allow-other-keys)
2758 ;; Delete these C files to force fresh generation from pyx sources.
2759 (delete-file "grit/sparsify_support_fns.c")
2760 (delete-file "grit/call_peaks_support_fns.c")
2761 (substitute* "setup.py"
2762 (("Cython.Setup") "Cython.Build")
2763 ;; Add numpy include path to fix compilation
2765 (string-append "pyx\", ], include_dirs = ['"
2766 (assoc-ref inputs "python-numpy")
2767 "/lib/python2.7/site-packages/numpy/core/include/"
2771 `(("python-scipy" ,python2-scipy)
2772 ("python-numpy" ,python2-numpy)
2773 ("python-pysam" ,python2-pysam)
2774 ("python-networkx" ,python2-networkx)))
2776 `(("python-cython" ,python2-cython)))
2777 (home-page "http://grit-bio.org")
2778 (synopsis "Tool for integrative analysis of RNA-seq type assays")
2780 "GRIT is designed to use RNA-seq, TES, and TSS data to build and quantify
2781 full length transcript models. When none of these data sources are available,
2782 GRIT can be run by providing a candidate set of TES or TSS sites. In
2783 addition, GRIT can merge in reference junctions and gene boundaries. GRIT can
2784 also be run in quantification mode, where it uses a provided GTF file and just
2785 estimates transcript expression.")
2786 (license license:gpl3+)))
2788 (define-public hisat
2795 "http://ccb.jhu.edu/software/hisat/downloads/hisat-"
2796 version "-beta-source.zip"))
2799 "1k381ydranqxp09yf2y7w1d0chz5d59vb6jchi89hbb0prq19lk5"))))
2800 (build-system gnu-build-system)
2802 `(#:tests? #f ;no check target
2803 #:make-flags '("allall"
2804 ;; Disable unsupported `popcnt' instructions on
2805 ;; architectures other than x86_64
2806 ,@(if (string-prefix? "x86_64"
2807 (or (%current-target-system)
2810 '("POPCNT_CAPABILITY=0")))
2812 (modify-phases %standard-phases
2813 (add-after 'unpack 'patch-sources
2815 ;; XXX Cannot use snippet because zip files are not supported
2816 (substitute* "Makefile"
2817 (("^CC = .*$") "CC = gcc")
2818 (("^CPP = .*$") "CPP = g++")
2819 ;; replace BUILD_HOST and BUILD_TIME for deterministic build
2820 (("-DBUILD_HOST=.*") "-DBUILD_HOST=\"\\\"guix\\\"\"")
2821 (("-DBUILD_TIME=.*") "-DBUILD_TIME=\"\\\"0\\\"\""))
2822 (substitute* '("hisat-build" "hisat-inspect")
2823 (("/usr/bin/env") (which "env")))
2826 (lambda* (#:key outputs #:allow-other-keys)
2827 (let ((bin (string-append (assoc-ref outputs "out") "/bin/")))
2828 (for-each (lambda (file)
2829 (install-file file bin))
2832 "hisat(-(build|align|inspect)(-(s|l)(-debug)*)*)*$")))
2834 (delete 'configure))))
2836 `(("unzip" ,unzip)))
2841 ;; Non-portable SSE instructions are used so building fails on platforms
2842 ;; other than x86_64.
2843 (supported-systems '("x86_64-linux"))
2844 (home-page "http://ccb.jhu.edu/software/hisat/index.shtml")
2845 (synopsis "Hierarchical indexing for spliced alignment of transcripts")
2847 "HISAT is a fast and sensitive spliced alignment program for mapping
2848 RNA-seq reads. In addition to one global FM index that represents a whole
2849 genome, HISAT uses a large set of small FM indexes that collectively cover the
2850 whole genome. These small indexes (called local indexes) combined with
2851 several alignment strategies enable effective alignment of RNA-seq reads, in
2852 particular, reads spanning multiple exons.")
2853 (license license:gpl3+)))
2855 (define-public hisat2
2862 ;; FIXME: a better source URL is
2863 ;; (string-append "ftp://ftp.ccb.jhu.edu/pub/infphilo/hisat2"
2864 ;; "/downloads/hisat2-" version "-source.zip")
2865 ;; with hash "0lywnr8kijwsc2aw10dwxic0n0yvip6fl3rjlvc8zzwahamy4x7g"
2866 ;; but it is currently unavailable.
2867 (uri "https://github.com/infphilo/hisat2/archive/cba6e8cb.tar.gz")
2868 (file-name (string-append name "-" version ".tar.gz"))
2871 "1mf2hdsyv7cd97xm9mp9a4qws02yrj95y6w6f6cdwnq0klp81r50"))))
2872 (build-system gnu-build-system)
2874 `(#:tests? #f ; no check target
2875 #:make-flags (list "CC=gcc" "CXX=g++" "allall")
2876 #:modules ((guix build gnu-build-system)
2880 (modify-phases %standard-phases
2881 (add-after 'unpack 'make-deterministic
2883 (substitute* "Makefile"
2888 (lambda* (#:key outputs #:allow-other-keys)
2889 (let* ((out (assoc-ref outputs "out"))
2890 (bin (string-append out "/bin/"))
2891 (doc (string-append out "/share/doc/hisat2/")))
2893 (cut install-file <> bin)
2895 "hisat2(-(build|align|inspect)(-(s|l)(-debug)*)*)*$"))
2897 (install-file "doc/manual.inc.html" doc))
2900 `(("unzip" ,unzip) ; needed for archive from ftp
2902 ("pandoc" ,ghc-pandoc))) ; for documentation
2903 (home-page "http://ccb.jhu.edu/software/hisat2/index.shtml")
2904 (synopsis "Graph-based alignment of genomic sequencing reads")
2905 (description "HISAT2 is a fast and sensitive alignment program for mapping
2906 next-generation sequencing reads (both DNA and RNA) to a population of human
2907 genomes (as well as to a single reference genome). In addition to using one
2908 global @dfn{graph FM} (GFM) index that represents a population of human
2909 genomes, HISAT2 uses a large set of small GFM indexes that collectively cover
2910 the whole genome. These small indexes, combined with several alignment
2911 strategies, enable rapid and accurate alignment of sequencing reads. This new
2912 indexing scheme is called a @dfn{Hierarchical Graph FM index} (HGFM).")
2913 ;; HISAT2 contains files from Bowtie2, which is released under
2914 ;; GPLv2 or later. The HISAT2 source files are released under
2916 (license license:gpl3+)))
2918 (define-public hmmer
2926 "http://eddylab.org/software/hmmer"
2927 (version-major version) "/"
2928 version "/hmmer-" version ".tar.gz"))
2931 "0djmgc0pfli0jilfx8hql1axhwhqxqb8rxg2r5rg07aw73sfs5nx"))
2932 (patches (search-patches "hmmer-remove-cpu-specificity.patch"))))
2933 (build-system gnu-build-system)
2934 (native-inputs `(("perl" ,perl)))
2935 (home-page "http://hmmer.org/")
2936 (synopsis "Biosequence analysis using profile hidden Markov models")
2938 "HMMER is used for searching sequence databases for homologs of protein
2939 sequences, and for making protein sequence alignments. It implements methods
2940 using probabilistic models called profile hidden Markov models (profile
2942 (license (list license:gpl3+
2943 ;; The bundled library 'easel' is distributed
2944 ;; under The Janelia Farm Software License.
2945 (license:non-copyleft
2946 "file://easel/LICENSE"
2947 "See easel/LICENSE in the distribution.")))))
2949 (define-public htseq
2955 (uri (pypi-uri "HTSeq" version))
2958 "11flgb1381xdhk43bzbfm3vhnszkpqg6jk76rpa5xd1zbrvvlnxg"))))
2959 (build-system python-build-system)
2961 `(("python-cython" ,python-cython)))
2962 ;; Numpy needs to be propagated when htseq is used as a Python library.
2964 `(("python-numpy" ,python-numpy)))
2966 `(("python-pysam" ,python-pysam)
2967 ("python-matplotlib" ,python-matplotlib)))
2968 (home-page "http://www-huber.embl.de/users/anders/HTSeq/")
2969 (synopsis "Analysing high-throughput sequencing data with Python")
2971 "HTSeq is a Python package that provides infrastructure to process data
2972 from high-throughput sequencing assays.")
2973 (license license:gpl3+)))
2975 (define-public python2-htseq
2976 (package-with-python2 htseq))
2978 (define-public java-htsjdk
2980 (name "java-htsjdk")
2981 (version "2.3.0") ; last version without build dependency on gradle
2985 "https://github.com/samtools/htsjdk/archive/"
2987 (file-name (string-append name "-" version ".tar.gz"))
2990 "1ibhzzxsfc38nqyk9r8zqj6blfc1kh26iirypd4q6n90hs2m6nyq"))
2991 (modules '((guix build utils)))
2993 ;; Delete pre-built binaries
2995 (delete-file-recursively "lib")
2998 (build-system ant-build-system)
3000 `(#:tests? #f ; test require Internet access
3003 (list (string-append "-Ddist=" (assoc-ref %outputs "out")
3004 "/share/java/htsjdk/"))
3005 #:build-target "all"
3007 (modify-phases %standard-phases
3008 ;; The build phase also installs the jars
3009 (delete 'install))))
3011 `(("java-ngs" ,java-ngs)
3012 ("java-snappy-1" ,java-snappy-1)
3013 ("java-commons-compress" ,java-commons-compress)
3014 ("java-commons-logging-minimal" ,java-commons-logging-minimal)
3015 ("java-commons-jexl-2" ,java-commons-jexl-2)
3016 ("java-xz" ,java-xz)))
3018 `(("java-testng" ,java-testng)))
3019 (home-page "http://samtools.github.io/htsjdk/")
3020 (synopsis "Java API for high-throughput sequencing data (HTS) formats")
3022 "HTSJDK is an implementation of a unified Java library for accessing
3023 common file formats, such as SAM and VCF, used for high-throughput
3024 sequencing (HTS) data. There are also an number of useful utilities for
3025 manipulating HTS data.")
3026 (license license:expat)))
3028 (define-public java-htsjdk-latest
3030 (name "java-htsjdk")
3035 (url "https://github.com/samtools/htsjdk.git")
3037 (file-name (string-append name "-" version "-checkout"))
3040 "1lmya1fdjy03mz6zmdmd86j9v9vfhqb3952mqq075navx1i6g4bc"))))
3041 (build-system ant-build-system)
3043 `(#:tests? #f ; test require Scala
3045 #:jar-name "htsjdk.jar"
3047 (modify-phases %standard-phases
3048 (add-after 'unpack 'remove-useless-build.xml
3049 (lambda _ (delete-file "build.xml") #t))
3050 ;; The tests require the scalatest package.
3051 (add-after 'unpack 'remove-tests
3052 (lambda _ (delete-file-recursively "src/test") #t)))))
3054 `(("java-ngs" ,java-ngs)
3055 ("java-snappy-1" ,java-snappy-1)
3056 ("java-commons-compress" ,java-commons-compress)
3057 ("java-commons-logging-minimal" ,java-commons-logging-minimal)
3058 ("java-commons-jexl-2" ,java-commons-jexl-2)
3059 ("java-xz" ,java-xz)))
3061 `(("java-junit" ,java-junit)))
3062 (home-page "http://samtools.github.io/htsjdk/")
3063 (synopsis "Java API for high-throughput sequencing data (HTS) formats")
3065 "HTSJDK is an implementation of a unified Java library for accessing
3066 common file formats, such as SAM and VCF, used for high-throughput
3067 sequencing (HTS) data. There are also an number of useful utilities for
3068 manipulating HTS data.")
3069 (license license:expat)))
3071 ;; This is needed for picard 2.10.3
3072 (define-public java-htsjdk-2.10.1
3073 (package (inherit java-htsjdk-latest)
3074 (name "java-htsjdk")
3079 (url "https://github.com/samtools/htsjdk.git")
3081 (file-name (string-append name "-" version "-checkout"))
3084 "1kxh7slm2pm3x9p6jxa1wqsq9a31dhiiflhxnxqcisan4k3rwia2"))))
3085 (build-system ant-build-system)
3087 `(#:tests? #f ; tests require Scala
3089 #:jar-name "htsjdk.jar"
3091 (modify-phases %standard-phases
3092 (add-after 'unpack 'remove-useless-build.xml
3093 (lambda _ (delete-file "build.xml") #t))
3094 ;; The tests require the scalatest package.
3095 (add-after 'unpack 'remove-tests
3096 (lambda _ (delete-file-recursively "src/test") #t)))))))
3098 ;; This version matches java-htsjdk 2.3.0. Later versions also require a more
3099 ;; recent version of java-htsjdk, which depends on gradle.
3100 (define-public java-picard
3102 (name "java-picard")
3107 (url "https://github.com/broadinstitute/picard.git")
3109 (file-name (string-append "java-picard-" version "-checkout"))
3112 "1ll7mf4r3by92w2nhlmpa591xd1f46xlkwh59mq6fvbb5pdwzvx6"))
3113 (modules '((guix build utils)))
3116 ;; Delete pre-built binaries.
3117 (delete-file-recursively "lib")
3119 (substitute* "build.xml"
3120 ;; Remove build-time dependency on git.
3121 (("failifexecutionfails=\"true\"")
3122 "failifexecutionfails=\"false\"")
3124 (("depends=\"compile-htsjdk, ")
3126 (("depends=\"compile-htsjdk-tests, ")
3128 ;; Build picard-lib.jar before building picard.jar
3129 (("name=\"picard-jar\" depends=\"" line)
3130 (string-append line "picard-lib-jar, ")))
3132 (build-system ant-build-system)
3134 `(#:build-target "picard-jar"
3135 #:test-target "test"
3136 ;; Tests require jacoco:coverage.
3139 (list (string-append "-Dhtsjdk_lib_dir="
3140 (assoc-ref %build-inputs "java-htsjdk")
3141 "/share/java/htsjdk/")
3142 "-Dhtsjdk-classes=dist/tmp"
3143 (string-append "-Dhtsjdk-version="
3144 ,(package-version java-htsjdk)))
3147 (modify-phases %standard-phases
3148 (add-after 'unpack 'use-our-htsjdk
3149 (lambda* (#:key inputs #:allow-other-keys)
3150 (substitute* "build.xml"
3151 (("\\$\\{htsjdk\\}/lib")
3152 (string-append (assoc-ref inputs "java-htsjdk")
3153 "/share/java/htsjdk/")))
3155 (add-after 'unpack 'make-test-target-independent
3156 (lambda* (#:key inputs #:allow-other-keys)
3157 (substitute* "build.xml"
3158 (("name=\"test\" depends=\"compile, ")
3159 "name=\"test\" depends=\""))
3161 (replace 'install (install-jars "dist")))))
3163 `(("java-htsjdk" ,java-htsjdk)
3164 ("java-guava" ,java-guava)))
3166 `(("java-testng" ,java-testng)))
3167 (home-page "http://broadinstitute.github.io/picard/")
3168 (synopsis "Tools for manipulating high-throughput sequencing data and formats")
3169 (description "Picard is a set of Java command line tools for manipulating
3170 high-throughput sequencing (HTS) data and formats. Picard is implemented
3171 using the HTSJDK Java library to support accessing file formats that are
3172 commonly used for high-throughput sequencing data such as SAM, BAM, CRAM and
3174 (license license:expat)))
3176 ;; This is needed for dropseq-tools
3177 (define-public java-picard-2.10.3
3179 (name "java-picard")
3184 (url "https://github.com/broadinstitute/picard.git")
3186 (file-name (string-append "java-picard-" version "-checkout"))
3189 "1ajlx31l6i1k3y2rhnmgq07sz99g2czqfqgkr9mihmdjp3gwjhvi"))))
3190 (build-system ant-build-system)
3192 `(#:jar-name "picard.jar"
3193 ;; Tests require jacoco:coverage.
3196 #:main-class "picard.cmdline.PicardCommandLine"
3197 #:modules ((guix build ant-build-system)
3199 (guix build java-utils)
3204 (modify-phases %standard-phases
3205 (add-after 'unpack 'remove-useless-build.xml
3206 (lambda _ (delete-file "build.xml") #t))
3207 ;; This is necessary to ensure that htsjdk is found when using
3208 ;; picard.jar as an executable.
3209 (add-before 'build 'edit-classpath-in-manifest
3210 (lambda* (#:key inputs #:allow-other-keys)
3211 (chmod "build.xml" #o664)
3212 (call-with-output-file "build.xml.new"
3216 (with-input-from-file "build.xml"
3217 (lambda _ (xml->sxml #:trim-whitespace? #t)))
3218 `((target . ,(lambda (tag . kids)
3219 (let ((name ((sxpath '(name *text*))
3221 ;; FIXME: We're breaking the line
3222 ;; early with a dummy path to
3223 ;; ensure that the store reference
3224 ;; isn't broken apart and can still
3225 ;; be found by the reference
3230 ~a/share/java/htsjdk.jar${line.separator}"
3231 ;; maximum line length is 70
3232 (string-tabulate (const #\b) 57)
3233 (assoc-ref inputs "java-htsjdk"))))
3234 (if (member "manifest" name)
3238 (file "${manifest.file}")
3241 (*default* . ,(lambda (tag . kids) `(,tag ,@kids)))
3242 (*text* . ,(lambda (_ txt) txt))))
3244 (rename-file "build.xml.new" "build.xml")
3247 `(("java-htsjdk" ,java-htsjdk-2.10.1)))
3249 `(("java-testng" ,java-testng)
3250 ("java-guava" ,java-guava)))
3251 (home-page "http://broadinstitute.github.io/picard/")
3252 (synopsis "Tools for manipulating high-throughput sequencing data and formats")
3253 (description "Picard is a set of Java command line tools for manipulating
3254 high-throughput sequencing (HTS) data and formats. Picard is implemented
3255 using the HTSJDK Java library to support accessing file formats that are
3256 commonly used for high-throughput sequencing data such as SAM, BAM, CRAM and
3258 (license license:expat)))
3260 ;; This is the last version of Picard to provide net.sf.samtools
3261 (define-public java-picard-1.113
3262 (package (inherit java-picard)
3263 (name "java-picard")
3268 (url "https://github.com/broadinstitute/picard.git")
3270 (file-name (string-append "java-picard-" version "-checkout"))
3273 "0lkpvin2fz3hhly4l02kk56fqy8lmlgyzr9kmvljk6ry6l1hw973"))
3274 (modules '((guix build utils)))
3277 ;; Delete pre-built binaries.
3278 (delete-file-recursively "lib")
3281 (build-system ant-build-system)
3283 `(#:build-target "picard-jar"
3284 #:test-target "test"
3285 ;; FIXME: the class path at test time is wrong.
3286 ;; [testng] Error: A JNI error has occurred, please check your installation and try again
3287 ;; [testng] Exception in thread "main" java.lang.NoClassDefFoundError: com/beust/jcommander/ParameterException
3290 ;; This is only used for tests.
3292 (list "-Dsamjdk.intel_deflater_so_path=lib/jni/libIntelDeflater.so")
3294 (modify-phases %standard-phases
3295 ;; Do not use bundled ant bzip2.
3296 (add-after 'unpack 'use-ant-bzip
3297 (lambda* (#:key inputs #:allow-other-keys)
3298 (substitute* "build.xml"
3299 (("\\$\\{lib\\}/apache-ant-1.8.2-bzip2.jar")
3300 (string-append (assoc-ref inputs "ant")
3303 (add-after 'unpack 'make-test-target-independent
3304 (lambda* (#:key inputs #:allow-other-keys)
3305 (substitute* "build.xml"
3306 (("name=\"test\" depends=\"compile, ")
3307 "name=\"test\" depends=\"compile-tests, ")
3308 (("name=\"compile\" depends=\"compile-src, compile-tests\"")
3309 "name=\"compile\" depends=\"compile-src\""))
3311 (add-after 'unpack 'fix-deflater-path
3312 (lambda* (#:key outputs #:allow-other-keys)
3313 (substitute* "src/java/net/sf/samtools/Defaults.java"
3314 (("getStringProperty\\(\"intel_deflater_so_path\", null\\)")
3315 (string-append "getStringProperty(\"intel_deflater_so_path\", \""
3316 (assoc-ref outputs "out")
3317 "/lib/jni/libIntelDeflater.so"
3320 ;; Build the deflater library, because we've previously deleted the
3321 ;; pre-built one. This can only be built with access to the JDK
3323 (add-after 'build 'build-jni
3324 (lambda* (#:key inputs #:allow-other-keys)
3327 (and (zero? (system* "tar" "--strip-components=1" "-C" "jdk-src"
3328 "-xf" (assoc-ref inputs "jdk-src")))
3329 (zero? (system* "javah" "-jni"
3330 "-classpath" "classes"
3332 "net.sf.samtools.util.zip.IntelDeflater"))
3333 (with-directory-excursion "src/c/inteldeflater"
3334 (zero? (system* "gcc" "-I../../../lib" "-I."
3335 (string-append "-I" (assoc-ref inputs "jdk")
3337 "-I../../../jdk-src/src/share/native/common/"
3338 "-I../../../jdk-src/src/solaris/native/common/"
3339 "-c" "-O3" "-fPIC" "IntelDeflater.c"))
3340 (zero? (system* "gcc" "-shared"
3341 "-o" "../../../lib/jni/libIntelDeflater.so"
3342 "IntelDeflater.o" "-lz" "-lstdc++"))))))
3343 ;; We can only build everything else after building the JNI library.
3344 (add-after 'build-jni 'build-rest
3345 (lambda* (#:key make-flags #:allow-other-keys)
3346 (zero? (apply system* `("ant" "all" ,@make-flags)))))
3347 (add-before 'build 'set-JAVA6_HOME
3349 (setenv "JAVA6_HOME" (getenv "JAVA_HOME"))
3351 (replace 'install (install-jars "dist"))
3352 (add-after 'install 'install-jni-lib
3353 (lambda* (#:key outputs #:allow-other-keys)
3354 (let ((jni (string-append (assoc-ref outputs "out")
3357 (install-file "lib/jni/libIntelDeflater.so" jni)
3360 `(("java-snappy-1" ,java-snappy-1)
3361 ("java-commons-jexl-2" ,java-commons-jexl-2)
3362 ("java-cofoja" ,java-cofoja)
3363 ("ant" ,ant) ; for bzip2 support at runtime
3366 `(("ant-apache-bcel" ,ant-apache-bcel)
3367 ("ant-junit" ,ant-junit)
3368 ("java-testng" ,java-testng)
3369 ("java-commons-bcel" ,java-commons-bcel)
3370 ("java-jcommander" ,java-jcommander)
3371 ("jdk" ,icedtea-8 "jdk")
3372 ("jdk-src" ,(car (assoc-ref (package-native-inputs icedtea-8) "jdk-drop")))))))
3374 (define-public fastqc
3381 (uri (string-append "http://www.bioinformatics.babraham.ac.uk/"
3382 "projects/fastqc/fastqc_v"
3383 version "_source.zip"))
3386 "18rrlkhcrxvvvlapch4dpj6xc6mpayzys8qfppybi8jrpgx5cc5f"))))
3387 (build-system ant-build-system)
3389 `(#:tests? #f ; there are no tests
3390 #:build-target "build"
3392 (modify-phases %standard-phases
3393 (add-after 'unpack 'fix-dependencies
3394 (lambda* (#:key inputs #:allow-other-keys)
3395 (substitute* "build.xml"
3397 (string-append (assoc-ref inputs "java-jbzip2")
3398 "/share/java/jbzip2.jar"))
3400 (string-append (assoc-ref inputs "java-picard-1.113")
3401 "/share/java/sam-1.112.jar"))
3403 (string-append (assoc-ref inputs "java-cisd-jhdf5")
3404 "/share/java/sis-jhdf5.jar")))
3406 ;; There is no installation target
3408 (lambda* (#:key inputs outputs #:allow-other-keys)
3409 (let* ((out (assoc-ref outputs "out"))
3410 (bin (string-append out "/bin"))
3411 (share (string-append out "/share/fastqc/"))
3412 (exe (string-append share "/fastqc")))
3413 (for-each mkdir-p (list bin share))
3414 (copy-recursively "bin" share)
3416 (("my \\$java_bin = 'java';")
3417 (string-append "my $java_bin = '"
3418 (assoc-ref inputs "java")
3421 (symlink exe (string-append bin "/fastqc"))
3425 ("perl" ,perl) ; needed for the wrapper script
3426 ("java-cisd-jhdf5" ,java-cisd-jhdf5)
3427 ("java-picard-1.113" ,java-picard-1.113)
3428 ("java-jbzip2" ,java-jbzip2)))
3430 `(("unzip" ,unzip)))
3431 (home-page "http://www.bioinformatics.babraham.ac.uk/projects/fastqc/")
3432 (synopsis "Quality control tool for high throughput sequence data")
3434 "FastQC aims to provide a simple way to do some quality control
3435 checks on raw sequence data coming from high throughput sequencing
3436 pipelines. It provides a modular set of analyses which you can use to
3437 give a quick impression of whether your data has any problems of which
3438 you should be aware before doing any further analysis.
3440 The main functions of FastQC are:
3443 @item Import of data from BAM, SAM or FastQ files (any variant);
3444 @item Providing a quick overview to tell you in which areas there may
3446 @item Summary graphs and tables to quickly assess your data;
3447 @item Export of results to an HTML based permanent report;
3448 @item Offline operation to allow automated generation of reports
3449 without running the interactive application.
3451 (license license:gpl3+)))
3453 (define-public fastp
3461 (url "https://github.com/OpenGene/fastp.git")
3462 (commit (string-append "v" version))))
3463 (file-name (git-file-name name version))
3466 "1r6ms5zbf5rps4rgp4z73nczadl00b5rqylw8f684isfz27dp0xh"))))
3467 (build-system gnu-build-system)
3469 `(#:tests? #f ; there are none
3471 (list (string-append "BINDIR=" (assoc-ref %outputs "out") "/bin"))
3473 (modify-phases %standard-phases
3475 (add-before 'install 'create-target-dir
3476 (lambda* (#:key outputs #:allow-other-keys)
3477 (mkdir-p (string-append (assoc-ref outputs "out") "/bin"))
3481 (home-page "https://github.com/OpenGene/fastp/")
3482 (synopsis "All-in-one FastQ preprocessor")
3484 "Fastp is a tool designed to provide fast all-in-one preprocessing for
3485 FastQ files. This tool has multi-threading support to afford high
3487 (license license:expat)))
3489 (define-public htslib
3496 "https://github.com/samtools/htslib/releases/download/"
3497 version "/htslib-" version ".tar.bz2"))
3500 "18bw0mn9pj5wgarnlaxmf1bb8pdqgl1zd6czirqcr62ajpn1xvy0"))))
3501 (build-system gnu-build-system)
3503 `(("openssl" ,openssl)
3508 (home-page "http://www.htslib.org")
3509 (synopsis "C library for reading/writing high-throughput sequencing data")
3511 "HTSlib is a C library for reading/writing high-throughput sequencing
3512 data. It also provides the @command{bgzip}, @command{htsfile}, and
3513 @command{tabix} utilities.")
3514 ;; Files under cram/ are released under the modified BSD license;
3515 ;; the rest is released under the Expat license
3516 (license (list license:expat license:bsd-3))))
3518 ;; This package should be removed once no packages rely upon it.
3526 "https://github.com/samtools/htslib/releases/download/"
3527 version "/htslib-" version ".tar.bz2"))
3530 "1rja282fwdc25ql6izkhdyh8ppw8x2fs0w0js78zgkmqjlikmma9"))))))
3539 "https://github.com/nboley/idr/archive/"
3541 (file-name (string-append name "-" version ".tar.gz"))
3544 "1rjdly6daslw66r43g9md8znizlscn1sphycqyldzsidkc4vxqv3"))
3545 ;; Delete generated C code.
3547 '(begin (delete-file "idr/inv_cdf.c") #t))))
3548 (build-system python-build-system)
3549 ;; There is only one test ("test_inv_cdf.py") and it tests features that
3550 ;; are no longer part of this package. It also asserts False, which
3551 ;; causes the tests to always fail.
3552 (arguments `(#:tests? #f))
3554 `(("python-scipy" ,python-scipy)
3555 ("python-sympy" ,python-sympy)
3556 ("python-numpy" ,python-numpy)
3557 ("python-matplotlib" ,python-matplotlib)))
3559 `(("python-cython" ,python-cython)))
3560 (home-page "https://github.com/nboley/idr")
3561 (synopsis "Tool to measure the irreproducible discovery rate (IDR)")
3563 "The IDR (Irreproducible Discovery Rate) framework is a unified approach
3564 to measure the reproducibility of findings identified from replicate
3565 experiments and provide highly stable thresholds based on reproducibility.")
3566 (license license:gpl2+)))
3568 (define-public jellyfish
3574 (uri (string-append "https://github.com/gmarcais/Jellyfish/"
3575 "releases/download/v" version
3576 "/jellyfish-" version ".tar.gz"))
3579 "1a1iwq9pq54k2m9ypvwl5s0bqfl64gwh9dx5af9i382ajas2016q"))))
3580 (build-system gnu-build-system)
3581 (outputs '("out" ;for library
3582 "ruby" ;for Ruby bindings
3583 "python")) ;for Python bindings
3586 (list (string-append "--enable-ruby-binding="
3587 (assoc-ref %outputs "ruby"))
3588 (string-append "--enable-python-binding="
3589 (assoc-ref %outputs "python")))
3591 (modify-phases %standard-phases
3592 (add-before 'check 'set-SHELL-variable
3594 ;; generator_manager.hpp either uses /bin/sh or $SHELL
3596 (setenv "SHELL" (which "bash"))
3602 ("python" ,python-2)
3603 ("pkg-config" ,pkg-config)))
3605 `(("htslib" ,htslib)))
3606 (synopsis "Tool for fast counting of k-mers in DNA")
3608 "Jellyfish is a tool for fast, memory-efficient counting of k-mers in
3609 DNA. A k-mer is a substring of length k, and counting the occurrences of all
3610 such substrings is a central step in many analyses of DNA sequence. Jellyfish
3611 is a command-line program that reads FASTA and multi-FASTA files containing
3612 DNA sequences. It outputs its k-mer counts in a binary format, which can be
3613 translated into a human-readable text format using the @code{jellyfish dump}
3614 command, or queried for specific k-mers with @code{jellyfish query}.")
3615 (home-page "http://www.genome.umd.edu/jellyfish.html")
3616 ;; From their website: JELLYFISH runs on 64-bit Intel-compatible processors
3617 (supported-systems '("x86_64-linux"))
3618 ;; The combined work is published under the GPLv3 or later. Individual
3619 ;; files such as lib/jsoncpp.cpp are released under the Expat license.
3620 (license (list license:gpl3+ license:expat))))
3622 (define-public khmer
3629 (uri (pypi-uri "khmer" version))
3632 "0wb05shqh77v00256qlm68vbbx3kl76fyzihszbz5nhanl4ni33a"))
3633 (patches (search-patches "khmer-use-libraries.patch"))))
3634 (build-system python-build-system)
3637 (modify-phases %standard-phases
3638 (add-after 'unpack 'set-paths
3639 (lambda* (#:key inputs outputs #:allow-other-keys)
3640 ;; Delete bundled libraries.
3641 (delete-file-recursively "third-party/zlib")
3642 (delete-file-recursively "third-party/bzip2")
3643 ;; Replace bundled seqan.
3644 (let* ((seqan-all "third-party/seqan")
3645 (seqan-include (string-append
3646 seqan-all "/core/include")))
3647 (delete-file-recursively seqan-all)
3648 (copy-recursively (string-append (assoc-ref inputs "seqan")
3650 (string-append seqan-include "/seqan")))
3651 ;; We do not replace the bundled MurmurHash as the canonical
3652 ;; repository for this code 'SMHasher' is unsuitable for
3653 ;; providing a library. See
3654 ;; https://lists.gnu.org/archive/html/guix-devel/2016-06/msg00977.html
3656 (add-after 'unpack 'set-cc
3660 ;; It is simpler to test after installation.
3662 (add-after 'install 'post-install-check
3663 (lambda* (#:key inputs outputs #:allow-other-keys)
3664 (let ((out (assoc-ref outputs "out")))
3669 (assoc-ref outputs "out")
3671 (setenv "PYTHONPATH"
3673 (getenv "PYTHONPATH")
3677 (string-take (string-take-right
3678 (assoc-ref inputs "python") 5) 3)
3680 (with-directory-excursion "build"
3681 (zero? (system* "nosetests" "khmer" "--attr"
3682 "!known_failing")))))))))
3685 ("python-nose" ,python-nose)))
3689 ("python-screed" ,python-screed)
3690 ("python-bz2file" ,python-bz2file)
3691 ;; Tests fail when gcc-5 is used for compilation. Use gcc-4.9 at least
3692 ;; until the next version of khmer (likely 2.1) is released.
3694 (home-page "https://khmer.readthedocs.org/")
3695 (synopsis "K-mer counting, filtering and graph traversal library")
3696 (description "The khmer software is a set of command-line tools for
3697 working with DNA shotgun sequencing data from genomes, transcriptomes,
3698 metagenomes and single cells. Khmer can make de novo assemblies faster, and
3699 sometimes better. Khmer can also identify and fix problems with shotgun
3701 ;; When building on i686, armhf and mips64el, we get the following error:
3702 ;; error: ['khmer', 'khmer.tests', 'oxli'] require 64-bit operating system
3703 (supported-systems '("x86_64-linux" "aarch64-linux"))
3704 (license license:bsd-3)))
3706 (define-public kaiju
3713 "https://github.com/bioinformatics-centre/kaiju/archive/v"
3715 (file-name (string-append name "-" version ".tar.gz"))
3718 "1kdn4rxs0kr9ibmrgrfcci71aa6j6gr71dbc8pff7731rpab6kj7"))))
3719 (build-system gnu-build-system)
3721 `(#:tests? #f ; There are no tests.
3723 (modify-phases %standard-phases
3725 (add-before 'build 'move-to-src-dir
3726 (lambda _ (chdir "src") #t))
3728 (lambda* (#:key inputs outputs #:allow-other-keys)
3729 (let ((bin (string-append (assoc-ref outputs "out") "/bin")))
3732 (copy-recursively "bin" bin)
3733 (copy-recursively "util" bin))
3738 (home-page "http://kaiju.binf.ku.dk/")
3739 (synopsis "Fast and sensitive taxonomic classification for metagenomics")
3740 (description "Kaiju is a program for sensitive taxonomic classification
3741 of high-throughput sequencing reads from metagenomic whole genome sequencing
3743 (license license:gpl3+)))
3748 (version "2.1.0.20151222")
3751 (uri (pypi-uri "MACS2" version))
3754 "1r2hcz6irhcq7lwbafjks98jbn34hv05avgbdjnp6w6mlfjkf8x5"))))
3755 (build-system python-build-system)
3757 `(#:python ,python-2 ; only compatible with Python 2.7
3758 #:tests? #f)) ; no test target
3760 `(("python-numpy" ,python2-numpy)))
3761 (home-page "https://github.com/taoliu/MACS/")
3762 (synopsis "Model based analysis for ChIP-Seq data")
3764 "MACS is an implementation of a ChIP-Seq analysis algorithm for
3765 identifying transcript factor binding sites named Model-based Analysis of
3766 ChIP-Seq (MACS). MACS captures the influence of genome complexity to evaluate
3767 the significance of enriched ChIP regions and it improves the spatial
3768 resolution of binding sites through combining the information of both
3769 sequencing tag position and orientation.")
3770 (license license:bsd-3)))
3772 (define-public mafft
3779 "https://mafft.cbrc.jp/alignment/software/mafft-" version
3780 "-without-extensions-src.tgz"))
3781 (file-name (string-append name "-" version ".tgz"))
3784 "0bacjkxfg944p5khhyh5rd4y7wkjc9qk4v2jjj442sqlq0f8ar7b"))))
3785 (build-system gnu-build-system)
3787 `(#:tests? #f ; no automated tests, though there are tests in the read me
3788 #:make-flags (let ((out (assoc-ref %outputs "out")))
3789 (list (string-append "PREFIX=" out)
3790 (string-append "BINDIR="
3791 (string-append out "/bin"))))
3793 (modify-phases %standard-phases
3794 (add-after 'unpack 'enter-dir
3795 (lambda _ (chdir "core") #t))
3796 (add-after 'enter-dir 'patch-makefile
3798 ;; on advice from the MAFFT authors, there is no need to
3799 ;; distribute mafft-profile, mafft-distance, or
3800 ;; mafft-homologs.rb as they are too "specialised".
3801 (substitute* "Makefile"
3802 ;; remove mafft-homologs.rb from SCRIPTS
3803 (("^SCRIPTS = mafft mafft-homologs.rb")
3805 ;; remove mafft-homologs from MANPAGES
3806 (("^MANPAGES = mafft.1 mafft-homologs.1")
3807 "MANPAGES = mafft.1")
3808 ;; remove mafft-distance from PROGS
3809 (("^PROGS = dvtditr dndfast7 dndblast sextet5 mafft-distance")
3810 "PROGS = dvtditr dndfast7 dndblast sextet5")
3811 ;; remove mafft-profile from PROGS
3812 (("splittbfast disttbfast tbfast mafft-profile 2cl mccaskillwrap")
3813 "splittbfast disttbfast tbfast f2cl mccaskillwrap")
3814 (("^rm -f mafft-profile mafft-profile.exe") "#")
3815 (("^rm -f mafft-distance mafft-distance.exe") ")#")
3816 ;; do not install MAN pages in libexec folder
3817 (("^\t\\$\\(INSTALL\\) -m 644 \\$\\(MANPAGES\\) \
3818 \\$\\(DESTDIR\\)\\$\\(LIBDIR\\)") "#"))
3820 (add-after 'enter-dir 'patch-paths
3821 (lambda* (#:key inputs #:allow-other-keys)
3822 (substitute* '("pairash.c"
3824 (("perl") (which "perl"))
3825 (("([\"`| ])awk" _ prefix)
3826 (string-append prefix (which "awk")))
3827 (("grep") (which "grep")))
3830 (add-after 'install 'wrap-programs
3831 (lambda* (#:key outputs #:allow-other-keys)
3832 (let* ((out (assoc-ref outputs "out"))
3833 (bin (string-append out "/bin"))
3834 (path (string-append
3835 (assoc-ref %build-inputs "coreutils") "/bin:")))
3836 (for-each (lambda (file)
3838 `("PATH" ":" prefix (,path))))
3846 ("coreutils" ,coreutils)))
3847 (home-page "http://mafft.cbrc.jp/alignment/software/")
3848 (synopsis "Multiple sequence alignment program")
3850 "MAFFT offers a range of multiple alignment methods for nucleotide and
3851 protein sequences. For instance, it offers L-INS-i (accurate; for alignment
3852 of <~200 sequences) and FFT-NS-2 (fast; for alignment of <~30,000
3854 (license (license:non-copyleft
3855 "http://mafft.cbrc.jp/alignment/software/license.txt"
3856 "BSD-3 with different formatting"))))
3865 "https://github.com/marbl/mash/archive/v"
3867 (file-name (string-append name "-" version ".tar.gz"))
3870 "00fx14vpmgsijwxd1xql3if934l82v8ckqgjjyyhnr36qb9qrskv"))
3871 (modules '((guix build utils)))
3873 ;; Delete bundled kseq.
3874 ;; TODO: Also delete bundled murmurhash and open bloom filter.
3875 '(delete-file "src/mash/kseq.h"))))
3876 (build-system gnu-build-system)
3878 `(#:tests? #f ; No tests.
3881 (string-append "--with-capnp=" (assoc-ref %build-inputs "capnproto"))
3882 (string-append "--with-gsl=" (assoc-ref %build-inputs "gsl")))
3883 #:make-flags (list "CC=gcc")
3885 (modify-phases %standard-phases
3886 (add-after 'unpack 'fix-includes
3888 (substitute* '("src/mash/Sketch.cpp"
3889 "src/mash/CommandFind.cpp"
3890 "src/mash/CommandScreen.cpp")
3891 (("^#include \"kseq\\.h\"")
3892 "#include \"htslib/kseq.h\""))
3894 (add-after 'fix-includes 'autoconf
3895 (lambda _ (zero? (system* "autoconf")))))))
3897 `(("autoconf" ,autoconf)
3898 ;; Capnproto and htslib are statically embedded in the final
3899 ;; application. Therefore we also list their licenses, below.
3900 ("capnproto" ,capnproto)
3901 ("htslib" ,htslib)))
3905 (supported-systems '("x86_64-linux"))
3906 (home-page "https://mash.readthedocs.io")
3907 (synopsis "Fast genome and metagenome distance estimation using MinHash")
3908 (description "Mash is a fast sequence distance estimator that uses the
3909 MinHash algorithm and is designed to work with genomes and metagenomes in the
3910 form of assemblies or reads.")
3911 (license (list license:bsd-3 ; Mash
3912 license:expat ; HTSlib and capnproto
3913 license:public-domain ; MurmurHash 3
3914 license:cpl1.0)))) ; Open Bloom Filter
3916 (define-public metabat
3923 (uri (string-append "https://bitbucket.org/berkeleylab/metabat/get/v"
3925 (file-name (string-append name "-" version ".tar.gz"))
3928 "1hmvdalz3zj5sqqklg0l4npjdv37cv2hsdi1al9iby2ndxjs1b73"))
3929 (patches (search-patches "metabat-fix-compilation.patch"))))
3930 (build-system scons-build-system)
3932 `(#:scons ,scons-python2
3934 (list (string-append "PREFIX=" (assoc-ref %outputs "out"))
3935 (string-append "BOOST_ROOT=" (assoc-ref %build-inputs "boost")))
3936 #:tests? #f ;; Tests are run during the build phase.
3938 (modify-phases %standard-phases
3939 (add-after 'unpack 'fix-includes
3941 (substitute* "src/BamUtils.h"
3942 (("^#include \"bam/bam\\.h\"")
3943 "#include \"samtools/bam.h\"")
3944 (("^#include \"bam/sam\\.h\"")
3945 "#include \"samtools/sam.h\""))
3946 (substitute* "src/KseqReader.h"
3947 (("^#include \"bam/kseq\\.h\"")
3948 "#include \"htslib/kseq.h\""))
3950 (add-after 'unpack 'fix-scons
3951 (lambda* (#:key inputs #:allow-other-keys)
3952 (substitute* "SConstruct"
3953 (("^htslib_dir += 'samtools'")
3954 (string-append "htslib_dir = '"
3955 (assoc-ref inputs "htslib")
3957 (("^samtools_dir = 'samtools'")
3958 (string-append "samtools_dir = '"
3959 (assoc-ref inputs "samtools")
3961 (("^findStaticOrShared\\('bam', hts_lib")
3962 (string-append "findStaticOrShared('bam', '"
3963 (assoc-ref inputs "samtools")
3965 ;; Do not distribute README.
3966 (("^env\\.Install\\(idir_prefix, 'README\\.md'\\)") ""))
3971 ("samtools" ,samtools)
3974 (home-page "https://bitbucket.org/berkeleylab/metabat")
3976 "Reconstruction of single genomes from complex microbial communities")
3978 "Grouping large genomic fragments assembled from shotgun metagenomic
3979 sequences to deconvolute complex microbial communities, or metagenome binning,
3980 enables the study of individual organisms and their interactions. MetaBAT is
3981 an automated metagenome binning software, which integrates empirical
3982 probabilistic distances of genome abundance and tetranucleotide frequency.")
3983 ;; The source code contains inline assembly.
3984 (supported-systems '("x86_64-linux" "i686-linux"))
3985 (license (license:non-copyleft "file://license.txt"
3986 "See license.txt in the distribution."))))
3988 (define-public minced
3995 "https://github.com/ctSkennerton/minced/archive/"
3997 (file-name (string-append name "-" version ".tar.gz"))
4000 "0wxmlsapxfpxfd3ps9636h7i2xy6la8i42mwh0j2lsky63h63jp1"))))
4001 (build-system gnu-build-system)
4003 `(#:test-target "test"
4005 (modify-phases %standard-phases
4007 (add-before 'check 'fix-test
4009 ;; Fix test for latest version.
4010 (substitute* "t/Aquifex_aeolicus_VF5.expected"
4011 (("minced:0.1.6") "minced:0.2.0"))
4013 (replace 'install ; No install target.
4014 (lambda* (#:key inputs outputs #:allow-other-keys)
4015 (let* ((out (assoc-ref outputs "out"))
4016 (bin (string-append out "/bin"))
4017 (wrapper (string-append bin "/minced")))
4018 ;; Minced comes with a wrapper script that tries to figure out where
4019 ;; it is located before running the JAR. Since these paths are known
4020 ;; to us, we build our own wrapper to avoid coreutils dependency.
4021 (install-file "minced.jar" bin)
4022 (with-output-to-file wrapper
4026 "#!" (assoc-ref inputs "bash") "/bin/sh\n\n"
4027 (assoc-ref inputs "jre") "/bin/java -jar "
4028 bin "/minced.jar \"$@\"\n"))))
4029 (chmod wrapper #o555)))))))
4031 `(("jdk" ,icedtea "jdk")))
4034 ("jre" ,icedtea "out")))
4035 (home-page "https://github.com/ctSkennerton/minced")
4036 (synopsis "Mining CRISPRs in Environmental Datasets")
4038 "MinCED is a program to find Clustered Regularly Interspaced Short
4039 Palindromic Repeats (CRISPRs) in DNA sequences. It can be used for
4040 unassembled metagenomic reads, but is mainly designed for full genomes and
4041 assembled metagenomic sequence.")
4042 (license license:gpl3+)))
4050 (uri (pypi-uri "misopy" version))
4053 "1z3x0vd8ma7pdrnywj7i3kgwl89sdkwrrn62zl7r5calqaq2hyip"))
4054 (modules '((guix build utils)))
4056 '(substitute* "setup.py"
4057 ;; Use setuptools, or else the executables are not
4059 (("distutils.core") "setuptools")
4060 ;; use "gcc" instead of "cc" for compilation
4062 "cc.set_executables(
4066 linker_so='gcc -shared'); defines")))))
4067 (build-system python-build-system)
4069 `(#:python ,python-2 ; only Python 2 is supported
4070 #:tests? #f)) ; no "test" target
4072 `(("samtools" ,samtools)
4073 ("python-numpy" ,python2-numpy)
4074 ("python-pysam" ,python2-pysam)
4075 ("python-scipy" ,python2-scipy)
4076 ("python-matplotlib" ,python2-matplotlib)))
4078 `(("python-mock" ,python2-mock) ;for tests
4079 ("python-pytz" ,python2-pytz))) ;for tests
4080 (home-page "http://genes.mit.edu/burgelab/miso/index.html")
4081 (synopsis "Mixture of Isoforms model for RNA-Seq isoform quantitation")
4083 "MISO (Mixture-of-Isoforms) is a probabilistic framework that quantitates
4084 the expression level of alternatively spliced genes from RNA-Seq data, and
4085 identifies differentially regulated isoforms or exons across samples. By
4086 modeling the generative process by which reads are produced from isoforms in
4087 RNA-Seq, the MISO model uses Bayesian inference to compute the probability
4088 that a read originated from a particular isoform.")
4089 (license license:gpl2)))
4091 (define-public muscle
4094 (version "3.8.1551")
4096 (method url-fetch/tarbomb)
4098 "http://www.drive5.com/muscle/muscle_src_"
4102 "0bj8kj7sdizy3987zx6w7axihk40fk8rn76mpbqqjcnd64i5a367"))))
4103 (build-system gnu-build-system)
4105 `(#:make-flags (list "LDLIBS = -lm")
4107 (modify-phases %standard-phases
4110 ;; There are no tests, so just test if it runs.
4111 (lambda _ (zero? (system* "./muscle" "-version"))))
4113 (lambda* (#:key outputs #:allow-other-keys)
4114 (let* ((out (assoc-ref outputs "out"))
4115 (bin (string-append out "/bin")))
4116 (install-file "muscle" bin)))))))
4117 (home-page "http://www.drive5.com/muscle")
4118 (synopsis "Multiple sequence alignment program")
4120 "MUSCLE aims to be a fast and accurate multiple sequence alignment
4121 program for nucleotide and protein sequences.")
4122 ;; License information found in 'muscle -h' and usage.cpp.
4123 (license license:public-domain)))
4125 (define-public newick-utils
4126 ;; There are no recent releases so we package from git.
4127 (let ((commit "da121155a977197cab9fbb15953ca1b40b11eb87"))
4129 (name "newick-utils")
4130 (version (string-append "1.6-1." (string-take commit 8)))
4134 (url "https://github.com/tjunier/newick_utils.git")
4136 (file-name (string-append name "-" version "-checkout"))
4139 "1hkw21rq1mwf7xp0rmbb2gqc0i6p11108m69i7mr7xcjl268pxnb"))))
4140 (build-system gnu-build-system)
4143 (modify-phases %standard-phases
4144 (add-after 'unpack 'autoconf
4145 (lambda _ (zero? (system* "autoreconf" "-vif")))))))
4147 ;; XXX: TODO: Enable Lua and Guile bindings.
4148 ;; https://github.com/tjunier/newick_utils/issues/13
4149 `(("libxml2" ,libxml2)
4153 `(("autoconf" ,autoconf)
4154 ("automake" ,automake)
4155 ("libtool" ,libtool)))
4156 (synopsis "Programs for working with newick format phylogenetic trees")
4158 "Newick-utils is a suite of utilities for processing phylogenetic trees
4159 in Newick format. Functions include re-rooting, extracting subtrees,
4160 trimming, pruning, condensing, drawing (ASCII graphics or SVG).")
4161 (home-page "https://github.com/tjunier/newick_utils")
4162 (license license:bsd-3))))
4171 "https://github.com/wwood/OrfM/releases/download/v"
4172 version "/orfm-" version ".tar.gz"))
4175 "16iigyr2gd8x0imzkk1dr3k5xsds9bpmwg31ayvjg0f4pir9rwqr"))))
4176 (build-system gnu-build-system)
4177 (inputs `(("zlib" ,zlib)))
4179 `(("ruby-bio-commandeer" ,ruby-bio-commandeer)
4180 ("ruby-rspec" ,ruby-rspec)
4182 (synopsis "Simple and not slow open reading frame (ORF) caller")
4184 "An ORF caller finds stretches of DNA that, when translated, are not
4185 interrupted by stop codons. OrfM finds and prints these ORFs.")
4186 (home-page "https://github.com/wwood/OrfM")
4187 (license license:lgpl3+)))
4189 (define-public pplacer
4190 (let ((commit "g807f6f3"))
4193 ;; The commit should be updated with each version change.
4194 (version "1.1.alpha19")
4198 (uri (string-append "https://github.com/matsen/pplacer/archive/v"
4200 (file-name (string-append name "-" version ".tar.gz"))
4202 (base32 "0z1lnd2s8sh6kpzg106wzbh2szw7h0hvq8syd5a6wv4rmyyz6x0f"))))
4203 (build-system ocaml-build-system)
4205 `(#:ocaml ,ocaml-4.01
4206 #:findlib ,ocaml4.01-findlib
4207 #:modules ((guix build ocaml-build-system)
4211 (modify-phases %standard-phases
4213 (add-after 'unpack 'replace-bundled-cddlib
4214 (lambda* (#:key inputs #:allow-other-keys)
4215 (let* ((cddlib-src (assoc-ref inputs "cddlib-src"))
4216 (local-dir "cddlib_guix"))
4218 (with-directory-excursion local-dir
4219 (system* "tar" "xvf" cddlib-src))
4220 (let ((cddlib-src-folder
4221 (string-append local-dir "/"
4222 (list-ref (scandir local-dir) 2)
4227 (string-append "cdd_src/" (basename file))))
4228 (find-files cddlib-src-folder ".*[ch]$")))
4230 (add-after 'unpack 'fix-makefile
4232 ;; Remove system calls to 'git'.
4233 (substitute* "Makefile"
4234 (("^DESCRIPT:=pplacer-.*")
4236 "DESCRIPT:=pplacer-$(shell uname)-v" ,version "\n")))
4237 (substitute* "myocamlbuild.ml"
4238 (("git describe --tags --long .*\\\" with")
4240 "echo -n v" ,version "-" ,commit "\" with")))
4243 (lambda* (#:key outputs #:allow-other-keys)
4244 (let* ((out (assoc-ref outputs "out"))
4245 (bin (string-append out "/bin")))
4246 (copy-recursively "bin" bin))
4251 ("ocaml-ounit" ,ocaml4.01-ounit)
4252 ("ocaml-batteries" ,ocaml4.01-batteries)
4253 ("ocaml-camlzip" ,ocaml4.01-camlzip)
4254 ("ocaml-csv" ,ocaml4.01-csv)
4255 ("ocaml-sqlite3" ,ocaml4.01-sqlite3)
4256 ("ocaml-xmlm" ,ocaml4.01-xmlm)
4257 ("ocaml-mcl" ,ocaml4.01-mcl)
4258 ("ocaml-gsl" ,ocaml4.01-gsl)
4259 ("cddlib-src" ,(package-source cddlib))))
4261 `(("pplacer-scripts" ,pplacer-scripts)))
4262 (synopsis "Phylogenetic placement of biological sequences")
4264 "Pplacer places query sequences on a fixed reference phylogenetic tree
4265 to maximize phylogenetic likelihood or posterior probability according to a
4266 reference alignment. Pplacer is designed to be fast, to give useful
4267 information about uncertainty, and to offer advanced visualization and
4268 downstream analysis.")
4269 (home-page "http://matsen.fhcrc.org/pplacer")
4270 (license license:gpl3))))
4272 ;; This package is installed alongside 'pplacer'. It is a separate package so
4273 ;; that it can use the python-build-system for the scripts that are
4274 ;; distributed alongside the main OCaml binaries.
4275 (define pplacer-scripts
4278 (name "pplacer-scripts")
4279 (build-system python-build-system)
4281 `(#:python ,python-2
4283 (modify-phases %standard-phases
4284 (add-after 'unpack 'enter-scripts-dir
4285 (lambda _ (chdir "scripts")))
4288 (zero? (system* "python" "-m" "unittest" "discover" "-v"))))
4289 (add-after 'install 'wrap-executables
4290 (lambda* (#:key inputs outputs #:allow-other-keys)
4291 (let* ((out (assoc-ref outputs "out"))
4292 (bin (string-append out "/bin")))
4293 (let ((path (string-append
4294 (assoc-ref inputs "hmmer") "/bin:"
4295 (assoc-ref inputs "infernal") "/bin")))
4297 (wrap-program (string-append bin "/refpkg_align.py")
4298 `("PATH" ":" prefix (,path))))
4299 (let ((path (string-append
4300 (assoc-ref inputs "hmmer") "/bin")))
4301 (wrap-program (string-append bin "/hrefpkg_query.py")
4302 `("PATH" ":" prefix (,path)))))
4305 `(("infernal" ,infernal)
4308 `(("python-biopython" ,python2-biopython)
4309 ("taxtastic" ,taxtastic)))
4310 (synopsis "Pplacer Python scripts")))
4312 (define-public python2-pbcore
4314 (name "python2-pbcore")
4318 (uri (pypi-uri "pbcore" version))
4321 "1kjmv891d6qbpp4shhhvkl02ff4q5xlpnls2513sm2cjcrs52f1i"))))
4322 (build-system python-build-system)
4323 (arguments `(#:python ,python-2)) ; pbcore requires Python 2.7
4325 `(("python-cython" ,python2-cython)
4326 ("python-numpy" ,python2-numpy)
4327 ("python-pysam" ,python2-pysam)
4328 ("python-h5py" ,python2-h5py)))
4330 `(("python-nose" ,python2-nose)
4331 ("python-sphinx" ,python2-sphinx)
4332 ("python-pyxb" ,python2-pyxb)))
4333 (home-page "http://pacificbiosciences.github.io/pbcore/")
4334 (synopsis "Library for reading and writing PacBio data files")
4336 "The pbcore package provides Python APIs for interacting with PacBio data
4337 files and writing bioinformatics applications.")
4338 (license license:bsd-3)))
4340 (define-public python2-warpedlmm
4342 (name "python2-warpedlmm")
4348 "https://pypi.python.org/packages/source/W/WarpedLMM/WarpedLMM-"
4352 "1agfz6zqa8nc6cw47yh0s3y14gkpa9wqazwcj7mwwj3ffnw39p3j"))))
4353 (build-system python-build-system)
4355 `(#:python ,python-2)) ; requires Python 2.7
4357 `(("python-scipy" ,python2-scipy)
4358 ("python-numpy" ,python2-numpy)
4359 ("python-matplotlib" ,python2-matplotlib)
4360 ("python-fastlmm" ,python2-fastlmm)
4361 ("python-pandas" ,python2-pandas)
4362 ("python-pysnptools" ,python2-pysnptools)))
4364 `(("python-mock" ,python2-mock)
4365 ("python-nose" ,python2-nose)
4367 (home-page "https://github.com/PMBio/warpedLMM")
4368 (synopsis "Implementation of warped linear mixed models")
4370 "WarpedLMM is a Python implementation of the warped linear mixed model,
4371 which automatically learns an optimal warping function (or transformation) for
4372 the phenotype as it models the data.")
4373 (license license:asl2.0)))
4375 (define-public pbtranscript-tofu
4376 (let ((commit "8f5467fe6a4472bcfb4226c8720993c8507adfe4"))
4378 (name "pbtranscript-tofu")
4379 (version (string-append "2.2.3." (string-take commit 7)))
4383 (url "https://github.com/PacificBiosciences/cDNA_primer.git")
4385 (file-name (string-append name "-" version "-checkout"))
4388 "1lgnpi35ihay42qx0b6yl3kkgra723i413j33kvs0kvs61h82w0f"))
4389 (modules '((guix build utils)))
4392 ;; remove bundled Cython sources
4393 (delete-file "pbtranscript-tofu/pbtranscript/Cython-0.20.1.tar.gz")
4395 (build-system python-build-system)
4397 `(#:python ,python-2
4398 ;; FIXME: Tests fail with "No such file or directory:
4399 ;; pbtools/pbtranscript/modified_bx_intervals/intersection_unique.so"
4402 (modify-phases %standard-phases
4403 (add-after 'unpack 'enter-directory
4405 (chdir "pbtranscript-tofu/pbtranscript/")
4407 ;; With setuptools version 18.0 and later this setup.py hack causes
4408 ;; a build error, so we disable it.
4409 (add-after 'enter-directory 'patch-setuppy
4411 (substitute* "setup.py"
4412 (("if 'setuptools.extension' in sys.modules:")
4416 `(("python-numpy" ,python2-numpy)
4417 ("python-bx-python" ,python2-bx-python)
4418 ("python-networkx" ,python2-networkx)
4419 ("python-scipy" ,python2-scipy)
4420 ("python-pbcore" ,python2-pbcore)
4421 ("python-h5py" ,python2-h5py)))
4423 `(("python-cython" ,python2-cython)
4424 ("python-nose" ,python2-nose)))
4425 (home-page "https://github.com/PacificBiosciences/cDNA_primer")
4426 (synopsis "Analyze transcriptome data generated with the Iso-Seq protocol")
4428 "pbtranscript-tofu contains scripts to analyze transcriptome data
4429 generated using the PacBio Iso-Seq protocol.")
4430 (license license:bsd-3))))
4432 (define-public prank
4439 "http://wasabiapp.org/download/prank/prank.source."
4443 "0am4z94fs3w2n5xpfls9zda61vq7qqz4q2i7b9hlsxz5q4j3kfm4"))))
4444 (build-system gnu-build-system)
4447 (modify-phases %standard-phases
4448 (add-after 'unpack 'enter-src-dir
4452 (add-after 'unpack 'remove-m64-flag
4453 ;; Prank will build with the correct 'bit-ness' without this flag
4454 ;; and this allows building on 32-bit machines.
4455 (lambda _ (substitute* "src/Makefile"
4460 (lambda* (#:key outputs #:allow-other-keys)
4461 (let* ((out (assoc-ref outputs "out"))
4462 (bin (string-append out "/bin"))
4463 (man (string-append out "/share/man/man1"))
4464 (path (string-append
4465 (assoc-ref %build-inputs "mafft") "/bin:"
4466 (assoc-ref %build-inputs "exonerate") "/bin:"
4467 (assoc-ref %build-inputs "bppsuite") "/bin")))
4468 (install-file "prank" bin)
4469 (wrap-program (string-append bin "/prank")
4470 `("PATH" ":" prefix (,path)))
4471 (install-file "prank.1" man))
4475 ("exonerate" ,exonerate)
4476 ("bppsuite" ,bppsuite)))
4477 (home-page "http://wasabiapp.org/software/prank/")
4478 (synopsis "Probabilistic multiple sequence alignment program")
4480 "PRANK is a probabilistic multiple sequence alignment program for DNA,
4481 codon and amino-acid sequences. It is based on a novel algorithm that treats
4482 insertions correctly and avoids over-estimation of the number of deletion
4483 events. In addition, PRANK borrows ideas from maximum likelihood methods used
4484 in phylogenetics and correctly takes into account the evolutionary distances
4485 between sequences. Lastly, PRANK allows for defining a potential structure
4486 for sequences to be aligned and then, simultaneously with the alignment,
4487 predicts the locations of structural units in the sequences.")
4488 (license license:gpl2+)))
4490 (define-public proteinortho
4492 (name "proteinortho")
4499 "http://www.bioinf.uni-leipzig.de/Software/proteinortho/proteinortho_v"
4500 version "_src.tar.gz"))
4503 "1wl0dawpssqwfjvr651r4wlww8hhjin8nba6xh71ks7sbypx886j"))))
4504 (build-system gnu-build-system)
4506 `(#:test-target "test"
4508 (modify-phases %standard-phases
4510 ;; There is no configure script, so we modify the Makefile directly.
4511 (lambda* (#:key outputs #:allow-other-keys)
4512 (substitute* "Makefile"
4515 "INSTALLDIR=" (assoc-ref outputs "out") "/bin\n")))
4517 (add-before 'install 'make-install-directory
4518 ;; The install directory is not created during 'make install'.
4519 (lambda* (#:key outputs #:allow-other-keys)
4520 (mkdir-p (string-append (assoc-ref outputs "out") "/bin"))
4522 (add-after 'install 'wrap-programs
4523 (lambda* (#:key inputs outputs #:allow-other-keys)
4524 (let* ((path (getenv "PATH"))
4525 (out (assoc-ref outputs "out"))
4526 (binary (string-append out "/bin/proteinortho5.pl")))
4527 (wrap-program binary `("PATH" ":" prefix (,path))))
4531 ("python" ,python-2)
4532 ("blast+" ,blast+)))
4533 (home-page "http://www.bioinf.uni-leipzig.de/Software/proteinortho")
4534 (synopsis "Detect orthologous genes across species")
4536 "Proteinortho is a tool to detect orthologous genes across different
4537 species. For doing so, it compares similarities of given gene sequences and
4538 clusters them to find significant groups. The algorithm was designed to handle
4539 large-scale data and can be applied to hundreds of species at once.")
4540 (license license:gpl2+)))
4542 (define-public pyicoteo
4549 (uri (string-append "https://bitbucket.org/regulatorygenomicsupf/"
4550 "pyicoteo/get/v" version ".tar.bz2"))
4551 (file-name (string-append name "-" version ".tar.bz2"))
4554 "0d6087f29xp8wxwlj111c3sylli98n0l8ry58c51ixzq0zfm50wa"))))
4555 (build-system python-build-system)
4557 `(#:python ,python-2 ; does not work with Python 3
4558 #:tests? #f)) ; there are no tests
4560 `(("python2-matplotlib" ,python2-matplotlib)))
4561 (home-page "https://bitbucket.org/regulatorygenomicsupf/pyicoteo")
4562 (synopsis "Analyze high-throughput genetic sequencing data")
4564 "Pyicoteo is a suite of tools for the analysis of high-throughput genetic
4565 sequencing data. It works with genomic coordinates. There are currently six
4566 different command-line tools:
4569 @item pyicoregion: for generating exploratory regions automatically;
4570 @item pyicoenrich: for differential enrichment between two conditions;
4571 @item pyicoclip: for calling CLIP-Seq peaks without a control;
4572 @item pyicos: for genomic coordinates manipulation;
4573 @item pyicoller: for peak calling on punctuated ChIP-Seq;
4574 @item pyicount: to count how many reads from N experiment files overlap in a
4576 @item pyicotrocol: to combine operations from pyicoteo.
4578 (license license:gpl3+)))
4580 (define-public prodigal
4587 "https://github.com/hyattpd/Prodigal/archive/v"
4589 (file-name (string-append name "-" version ".tar.gz"))
4592 "17srxkqd3jc77xk15pfbgg1a9xahqg7337w95mrsia7mpza4l2c9"))))
4593 (build-system gnu-build-system)
4595 `(#:tests? #f ;no check target
4596 #:make-flags (list (string-append "INSTALLDIR="
4597 (assoc-ref %outputs "out")
4600 (modify-phases %standard-phases
4601 (delete 'configure))))
4602 (home-page "http://prodigal.ornl.gov")
4603 (synopsis "Protein-coding gene prediction for Archaea and Bacteria")
4605 "Prodigal runs smoothly on finished genomes, draft genomes, and
4606 metagenomes, providing gene predictions in GFF3, Genbank, or Sequin table
4607 format. It runs quickly, in an unsupervised fashion, handles gaps, handles
4608 partial genes, and identifies translation initiation sites.")
4609 (license license:gpl3+)))
4611 (define-public roary
4619 "mirror://cpan/authors/id/A/AJ/AJPAGE/Bio-Roary-"
4623 "0qxrds9wx7cfhlkihrp6697kx0flhhxymap9fwan0b3rbdhcnmff"))))
4624 (build-system perl-build-system)
4627 (modify-phases %standard-phases
4632 ;; The tests are not run by default, so we run each test file
4634 (setenv "PATH" (string-append (getcwd) "/bin" ":"
4636 (setenv "PERL5LIB" (string-append (getcwd) "/lib" ":"
4637 (getenv "PERL5LIB")))
4638 (zero? (length (filter (lambda (file)
4639 (display file)(display "\n")
4640 (not (zero? (system* "perl" file))))
4641 (find-files "t" ".*\\.t$"))))))
4643 ;; There is no 'install' target in the Makefile.
4644 (lambda* (#:key outputs #:allow-other-keys)
4645 (let* ((out (assoc-ref outputs "out"))
4646 (bin (string-append out "/bin"))
4647 (perl (string-append out "/lib/perl5/site_perl"))
4648 (roary-plots "contrib/roary_plots"))
4651 (copy-recursively "bin" bin)
4652 (copy-recursively "lib" perl)
4654 (add-after 'install 'wrap-programs
4655 (lambda* (#:key inputs outputs #:allow-other-keys)
4656 (let* ((out (assoc-ref outputs "out"))
4657 (perl5lib (getenv "PERL5LIB"))
4658 (path (getenv "PATH")))
4659 (for-each (lambda (prog)
4660 (let ((binary (string-append out "/" prog)))
4661 (wrap-program binary
4662 `("PERL5LIB" ":" prefix
4663 (,(string-append perl5lib ":" out
4664 "/lib/perl5/site_perl"))))
4665 (wrap-program binary
4667 (,(string-append path ":" out "/bin"))))))
4668 (find-files "bin" ".*[^R]$"))
4670 (string-append out "/bin/roary-create_pan_genome_plots.R"))
4671 (r-site-lib (getenv "R_LIBS_SITE"))
4673 (string-append (assoc-ref inputs "coreutils") "/bin")))
4675 `("R_LIBS_SITE" ":" prefix
4676 (,(string-append r-site-lib ":" out "/site-library/"))))
4679 (,(string-append coreutils-path ":" out "/bin"))))))
4682 `(("perl-env-path" ,perl-env-path)
4683 ("perl-test-files" ,perl-test-files)
4684 ("perl-test-most" ,perl-test-most)
4685 ("perl-test-output" ,perl-test-output)))
4687 `(("perl-array-utils" ,perl-array-utils)
4688 ("bioperl" ,bioperl-minimal)
4689 ("perl-digest-md5-file" ,perl-digest-md5-file)
4690 ("perl-exception-class" ,perl-exception-class)
4691 ("perl-file-find-rule" ,perl-file-find-rule)
4692 ("perl-file-grep" ,perl-file-grep)
4693 ("perl-file-slurper" ,perl-file-slurper)
4694 ("perl-file-which" ,perl-file-which)
4695 ("perl-graph" ,perl-graph)
4696 ("perl-graph-readwrite" ,perl-graph-readwrite)
4697 ("perl-log-log4perl" ,perl-log-log4perl)
4698 ("perl-moose" ,perl-moose)
4699 ("perl-perlio-utf8_strict" ,perl-perlio-utf8_strict)
4700 ("perl-text-csv" ,perl-text-csv)
4701 ("bedtools" ,bedtools)
4705 ("parallel" ,parallel)
4708 ("fasttree" ,fasttree)
4712 ("r-minimal" ,r-minimal)
4713 ("r-ggplot2" ,r-ggplot2)
4714 ("coreutils" ,coreutils)))
4715 (home-page "http://sanger-pathogens.github.io/Roary")
4716 (synopsis "High speed stand-alone pan genome pipeline")
4718 "Roary is a high speed stand alone pan genome pipeline, which takes
4719 annotated assemblies in GFF3 format (produced by the Prokka program) and
4720 calculates the pan genome. Using a standard desktop PC, it can analyse
4721 datasets with thousands of samples, without compromising the quality of the
4722 results. 128 samples can be analysed in under 1 hour using 1 GB of RAM and a
4723 single processor. Roary is not intended for metagenomics or for comparing
4724 extremely diverse sets of genomes.")
4725 (license license:gpl3)))
4727 (define-public raxml
4736 "https://github.com/stamatak/standard-RAxML/archive/v"
4738 (file-name (string-append name "-" version ".tar.gz"))
4741 "13s7aspfdcfr6asynwdg1x6vznys6pzap5f8wsffbnnwpkkg9ya8"))))
4742 (build-system gnu-build-system)
4744 `(#:tests? #f ; There are no tests.
4745 ;; Use 'standard' Makefile rather than SSE or AVX ones.
4746 #:make-flags (list "-f" "Makefile.HYBRID.gcc")
4748 (modify-phases %standard-phases
4751 (lambda* (#:key outputs #:allow-other-keys)
4752 (let* ((out (assoc-ref outputs "out"))
4753 (bin (string-append out "/bin"))
4754 (executable "raxmlHPC-HYBRID"))
4755 (install-file executable bin)
4756 (symlink (string-append bin "/" executable) "raxml"))
4759 `(("openmpi" ,openmpi)))
4760 (home-page "http://sco.h-its.org/exelixis/web/software/raxml/index.html")
4761 (synopsis "Randomized Axelerated Maximum Likelihood phylogenetic trees")
4763 "RAxML is a tool for phylogenetic analysis and post-analysis of large
4765 ;; The source includes x86 specific code
4766 (supported-systems '("x86_64-linux" "i686-linux"))
4767 (license license:gpl2+)))
4777 (string-append "http://deweylab.biostat.wisc.edu/rsem/src/rsem-"
4780 (base32 "0nzdc0j0hjllhsd5f2xli95dafm3nawskigs140xzvjk67xh0r9q"))
4781 (patches (search-patches "rsem-makefile.patch"))
4782 (modules '((guix build utils)))
4785 ;; remove bundled copy of boost
4786 (delete-file-recursively "boost")
4788 (build-system gnu-build-system)
4790 `(#:tests? #f ;no "check" target
4792 (modify-phases %standard-phases
4793 ;; No "configure" script.
4794 ;; Do not build bundled samtools library.
4797 (substitute* "Makefile"
4798 (("^all : sam/libbam.a") "all : "))
4801 (lambda* (#:key outputs #:allow-other-keys)
4802 (let* ((out (string-append (assoc-ref outputs "out")))
4803 (bin (string-append out "/bin/"))
4804 (perl (string-append out "/lib/perl5/site_perl")))
4807 (for-each (lambda (file)
4808 (install-file file bin))
4809 (find-files "." "rsem-.*"))
4810 (install-file "rsem_perl_utils.pm" perl))
4813 'install 'wrap-program
4814 (lambda* (#:key outputs #:allow-other-keys)
4815 (let ((out (assoc-ref outputs "out")))
4816 (for-each (lambda (prog)
4817 (wrap-program (string-append out "/bin/" prog)
4818 `("PERL5LIB" ":" prefix
4819 (,(string-append out "/lib/perl5/site_perl")))))
4820 '("rsem-plot-transcript-wiggles"
4821 "rsem-calculate-expression"
4822 "rsem-generate-ngvector"
4824 "rsem-prepare-reference")))
4828 ("ncurses" ,ncurses)
4829 ("r-minimal" ,r-minimal)
4831 ("samtools" ,samtools-0.1)
4833 (home-page "http://deweylab.biostat.wisc.edu/rsem/")
4834 (synopsis "Estimate gene expression levels from RNA-Seq data")
4836 "RSEM is a software package for estimating gene and isoform expression
4837 levels from RNA-Seq data. The RSEM package provides a user-friendly
4838 interface, supports threads for parallel computation of the EM algorithm,
4839 single-end and paired-end read data, quality scores, variable-length reads and
4840 RSPD estimation. In addition, it provides posterior mean and 95% credibility
4841 interval estimates for expression levels. For visualization, it can generate
4842 BAM and Wiggle files in both transcript-coordinate and genomic-coordinate.")
4843 (license license:gpl3+)))
4845 (define-public rseqc
4853 (string-append "mirror://sourceforge/rseqc/"
4854 "RSeQC-" version ".tar.gz"))
4856 (base32 "15ly0254yi032qzkdplg00q144qfdsd986gh62829rl5bkxhj330"))
4857 (modules '((guix build utils)))
4860 ;; remove bundled copy of pysam
4861 (delete-file-recursively "lib/pysam")
4862 (substitute* "setup.py"
4863 ;; remove dependency on outdated "distribute" module
4864 (("^from distribute_setup import use_setuptools") "")
4865 (("^use_setuptools\\(\\)") "")
4866 ;; do not use bundled copy of pysam
4867 (("^have_pysam = False") "have_pysam = True"))))))
4868 (build-system python-build-system)
4869 (arguments `(#:python ,python-2))
4871 `(("python-cython" ,python2-cython)
4872 ("python-pysam" ,python2-pysam)
4873 ("python-numpy" ,python2-numpy)
4876 `(("python-nose" ,python2-nose)))
4877 (home-page "http://rseqc.sourceforge.net/")
4878 (synopsis "RNA-seq quality control package")
4880 "RSeQC provides a number of modules that can comprehensively evaluate
4881 high throughput sequence data, especially RNA-seq data. Some basic modules
4882 inspect sequence quality, nucleotide composition bias, PCR bias and GC bias,
4883 while RNA-seq specific modules evaluate sequencing saturation, mapped reads
4884 distribution, coverage uniformity, strand specificity, etc.")
4885 (license license:gpl3+)))
4888 ;; There are no release tarballs. According to the installation
4889 ;; instructions at http://seek.princeton.edu/installation.jsp, the latest
4890 ;; stable release is identified by this changeset ID.
4891 (let ((changeset "2329130")
4895 (version (string-append "0-" revision "." changeset))
4899 (url "https://bitbucket.org/libsleipnir/sleipnir")
4900 (changeset changeset)))
4901 (file-name (string-append name "-" version "-checkout"))
4904 "0qrvilwh18dpbhkf92qvxbmay0j75ra3jg2wrhz67gf538zzphsx"))))
4905 (build-system gnu-build-system)
4907 `(#:modules ((srfi srfi-1)
4908 (guix build gnu-build-system)
4911 (let ((dirs '("SeekMiner"
4917 (modify-phases %standard-phases
4918 (add-before 'configure 'bootstrap
4920 (zero? (system* "bash" "gen_auto"))))
4921 (add-after 'build 'build-additional-tools
4922 (lambda* (#:key make-flags #:allow-other-keys)
4923 (every (lambda (dir)
4924 (with-directory-excursion (string-append "tools/" dir)
4925 (zero? (apply system* "make" make-flags))))
4927 (add-after 'install 'install-additional-tools
4928 (lambda* (#:key make-flags #:allow-other-keys)
4929 (fold (lambda (dir result)
4930 (with-directory-excursion (string-append "tools/" dir)
4932 (zero? (apply system*
4933 `("make" ,@make-flags "install"))))))
4939 ("readline" ,readline)
4940 ("gengetopt" ,gengetopt)
4941 ("log4cpp" ,log4cpp)))
4943 `(("autoconf" ,autoconf)
4944 ("automake" ,automake)
4946 (home-page "http://seek.princeton.edu")
4947 (synopsis "Gene co-expression search engine")
4949 "SEEK is a computational gene co-expression search engine. SEEK provides
4950 biologists with a way to navigate the massive human expression compendium that
4951 now contains thousands of expression datasets. SEEK returns a robust ranking
4952 of co-expressed genes in the biological area of interest defined by the user's
4953 query genes. It also prioritizes thousands of expression datasets according
4954 to the user's query of interest.")
4955 (license license:cc-by3.0))))
4957 (define-public samtools
4965 (string-append "mirror://sourceforge/samtools/samtools/"
4966 version "/samtools-" version ".tar.bz2"))
4969 "05myg7bs90i68qbqab9cdg9rqj2xh39azibrx82ipzc5kcfvqhn9"))))
4970 (build-system gnu-build-system)
4972 `(#:modules ((ice-9 ftw)
4974 (guix build gnu-build-system)
4976 #:make-flags (list (string-append "prefix=" (assoc-ref %outputs "out")))
4977 #:configure-flags (list "--with-ncurses" "--with-htslib=system")
4979 (modify-phases %standard-phases
4980 (add-after 'unpack 'patch-tests
4982 (substitute* "test/test.pl"
4983 ;; The test script calls out to /bin/bash
4984 (("/bin/bash") (which "bash")))
4986 (add-after 'install 'install-library
4987 (lambda* (#:key outputs #:allow-other-keys)
4988 (let ((lib (string-append (assoc-ref outputs "out") "/lib")))
4989 (install-file "libbam.a" lib)
4991 (add-after 'install 'install-headers
4992 (lambda* (#:key outputs #:allow-other-keys)
4993 (let ((include (string-append (assoc-ref outputs "out")
4994 "/include/samtools/")))
4995 (for-each (lambda (file)
4996 (install-file file include))
4997 (scandir "." (lambda (name) (string-match "\\.h$" name))))
4999 (native-inputs `(("pkg-config" ,pkg-config)))
5001 `(("htslib" ,htslib)
5002 ("ncurses" ,ncurses)
5006 (home-page "http://samtools.sourceforge.net")
5007 (synopsis "Utilities to efficiently manipulate nucleotide sequence alignments")
5009 "Samtools implements various utilities for post-processing nucleotide
5010 sequence alignments in the SAM, BAM, and CRAM formats, including indexing,
5011 variant calling (in conjunction with bcftools), and a simple alignment
5013 (license license:expat)))
5015 (define-public samtools-0.1
5016 ;; This is the most recent version of the 0.1 line of samtools. The input
5017 ;; and output formats differ greatly from that used and produced by samtools
5018 ;; 1.x and is still used in many bioinformatics pipelines.
5019 (package (inherit samtools)
5025 (string-append "mirror://sourceforge/samtools/samtools/"
5026 version "/samtools-" version ".tar.bz2"))
5028 (base32 "1m33xsfwz0s8qi45lylagfllqg7fphf4dr0780rsvw75av9wk06h"))))
5030 `(#:tests? #f ;no "check" target
5031 ,@(substitute-keyword-arguments (package-arguments samtools)
5032 ((#:make-flags flags)
5033 `(cons "LIBCURSES=-lncurses" ,flags))
5035 `(modify-phases ,phases
5037 (lambda* (#:key outputs #:allow-other-keys)
5038 (let ((bin (string-append
5039 (assoc-ref outputs "out") "/bin")))
5041 (install-file "samtools" bin)
5043 (delete 'patch-tests)
5044 (delete 'configure))))))))
5046 (define-public mosaik
5047 (let ((commit "5c25216d3522d6a33e53875cd76a6d65001e4e67"))
5052 ;; There are no release tarballs nor tags.
5055 (url "https://github.com/wanpinglee/MOSAIK.git")
5057 (file-name (string-append name "-" version))
5060 "17gj3s07cm77r41z92awh0bim7w7q7fbn0sf5nkqmcm1vw052qgw"))))
5061 (build-system gnu-build-system)
5063 `(#:tests? #f ; no tests
5064 #:make-flags (list "CC=gcc")
5066 (modify-phases %standard-phases
5068 (lambda _ (chdir "src") #t))
5070 (lambda* (#:key outputs #:allow-other-keys)
5071 (let ((bin (string-append (assoc-ref outputs "out")
5074 (copy-recursively "../bin" bin)
5079 (supported-systems '("x86_64-linux"))
5080 (home-page "https://github.com/wanpinglee/MOSAIK")
5081 (synopsis "Map nucleotide sequence reads to reference genomes")
5083 "MOSAIK is a program for mapping second and third-generation sequencing
5084 reads to a reference genome. MOSAIK can align reads generated by all the
5085 major sequencing technologies, including Illumina, Applied Biosystems SOLiD,
5086 Roche 454, Ion Torrent and Pacific BioSciences SMRT.")
5087 ;; MOSAIK is released under the GPLv2+ with the exception of third-party
5088 ;; code released into the public domain:
5089 ;; 1. fastlz by Ariya Hidayat - http://www.fastlz.org/
5090 ;; 2. MD5 implementation - RSA Data Security, RFC 1321
5091 (license (list license:gpl2+ license:public-domain)))))
5093 (define-public ngs-sdk
5101 (string-append "https://github.com/ncbi/ngs/archive/"
5103 (file-name (string-append name "-" version ".tar.gz"))
5106 "1wiyf4c6nm2j87pv015cbi0qny5byf3pbvcw3likifz5dl56ag40"))))
5107 (build-system gnu-build-system)
5109 `(#:parallel-build? #f ; not supported
5110 #:tests? #f ; no "check" target
5112 (modify-phases %standard-phases
5114 (lambda* (#:key outputs #:allow-other-keys)
5115 (let ((out (assoc-ref outputs "out")))
5116 ;; Allow 'konfigure.perl' to find 'package.prl'.
5118 (string-append ".:" (getenv "PERL5LIB")))
5120 ;; The 'configure' script doesn't recognize things like
5121 ;; '--enable-fast-install'.
5122 (zero? (system* "./configure"
5123 (string-append "--build-prefix=" (getcwd) "/build")
5124 (string-append "--prefix=" out))))))
5125 (add-after 'unpack 'enter-dir
5126 (lambda _ (chdir "ngs-sdk") #t)))))
5127 (native-inputs `(("perl" ,perl)))
5128 ;; According to the test
5129 ;; unless ($MARCH =~ /x86_64/i || $MARCH =~ /i?86/i)
5130 ;; in ngs-sdk/setup/konfigure.perl
5131 (supported-systems '("i686-linux" "x86_64-linux"))
5132 (home-page "https://github.com/ncbi/ngs")
5133 (synopsis "API for accessing Next Generation Sequencing data")
5135 "NGS is a domain-specific API for accessing reads, alignments and pileups
5136 produced from Next Generation Sequencing. The API itself is independent from
5137 any particular back-end implementation, and supports use of multiple back-ends
5139 (license license:public-domain)))
5141 (define-public java-ngs
5142 (package (inherit ngs-sdk)
5145 `(,@(substitute-keyword-arguments
5146 `(#:modules ((guix build gnu-build-system)
5150 ,@(package-arguments ngs-sdk))
5152 `(modify-phases ,phases
5153 (replace 'enter-dir (lambda _ (chdir "ngs-java") #t)))))))
5155 `(("jdk" ,icedtea "jdk")
5156 ("ngs-sdk" ,ngs-sdk)))
5157 (synopsis "Java bindings for NGS SDK")))
5159 (define-public ncbi-vdb
5167 (string-append "https://github.com/ncbi/ncbi-vdb/archive/"
5169 (file-name (string-append name "-" version ".tar.gz"))
5172 "1acn4bv81mfl137qnbn9995mjjhwd36pm0b7qli1iw5skrxa9j8m"))))
5173 (build-system gnu-build-system)
5175 `(#:parallel-build? #f ; not supported
5176 #:tests? #f ; no "check" target
5178 (modify-phases %standard-phases
5179 (add-before 'configure 'set-perl-search-path
5181 ;; Work around "dotless @INC" build failure.
5183 (string-append (getcwd) "/setup:"
5184 (getenv "PERL5LIB")))
5187 (lambda* (#:key inputs outputs #:allow-other-keys)
5188 (let ((out (assoc-ref outputs "out")))
5189 ;; Override include path for libmagic
5190 (substitute* "setup/package.prl"
5191 (("name => 'magic', Include => '/usr/include'")
5192 (string-append "name=> 'magic', Include => '"
5193 (assoc-ref inputs "libmagic")
5196 ;; Install kdf5 library (needed by sra-tools)
5197 (substitute* "build/Makefile.install"
5198 (("LIBRARIES_TO_INSTALL =")
5199 "LIBRARIES_TO_INSTALL = kdf5.$(VERSION_LIBX) kdf5.$(VERSION_SHLX)"))
5201 (substitute* "build/Makefile.env"
5202 (("CFLAGS =" prefix)
5203 (string-append prefix "-msse2 ")))
5205 ;; Override search path for ngs-java
5206 (substitute* "setup/package.prl"
5207 (("/usr/local/ngs/ngs-java")
5208 (assoc-ref inputs "java-ngs")))
5210 ;; The 'configure' script doesn't recognize things like
5211 ;; '--enable-fast-install'.
5214 (string-append "--build-prefix=" (getcwd) "/build")
5215 (string-append "--prefix=" (assoc-ref outputs "out"))
5216 (string-append "--debug")
5217 (string-append "--with-xml2-prefix="
5218 (assoc-ref inputs "libxml2"))
5219 (string-append "--with-ngs-sdk-prefix="
5220 (assoc-ref inputs "ngs-sdk"))
5221 (string-append "--with-hdf5-prefix="
5222 (assoc-ref inputs "hdf5")))))))
5223 (add-after 'install 'install-interfaces
5224 (lambda* (#:key outputs #:allow-other-keys)
5225 ;; Install interface libraries. On i686 the interface libraries
5226 ;; are installed to "linux/gcc/i386", so we need to use the Linux
5227 ;; architecture name ("i386") instead of the target system prefix
5229 (mkdir (string-append (assoc-ref outputs "out") "/ilib"))
5230 (copy-recursively (string-append "build/ncbi-vdb/linux/gcc/"
5231 ,(system->linux-architecture
5232 (or (%current-target-system)
5235 (string-append (assoc-ref outputs "out")
5237 ;; Install interface headers
5238 (copy-recursively "interfaces"
5239 (string-append (assoc-ref outputs "out")
5242 ;; These files are needed by sra-tools.
5243 (add-after 'install 'install-configuration-files
5244 (lambda* (#:key outputs #:allow-other-keys)
5245 (let ((target (string-append (assoc-ref outputs "out") "/kfg")))
5247 (install-file "libs/kfg/default.kfg" target)
5248 (install-file "libs/kfg/certs.kfg" target))
5251 `(("libxml2" ,libxml2)
5252 ("ngs-sdk" ,ngs-sdk)
5253 ("java-ngs" ,java-ngs)
5256 (native-inputs `(("perl" ,perl)))
5257 ;; NCBI-VDB requires SSE capability.
5258 (supported-systems '("i686-linux" "x86_64-linux"))
5259 (home-page "https://github.com/ncbi/ncbi-vdb")
5260 (synopsis "Database engine for genetic information")
5262 "The NCBI-VDB library implements a highly compressed columnar data
5263 warehousing engine that is most often used to store genetic information.
5264 Databases are stored in a portable image within the file system, and can be
5265 accessed/downloaded on demand across HTTP.")
5266 (license license:public-domain)))
5268 (define-public plink
5276 "http://pngu.mgh.harvard.edu/~purcell/plink/dist/plink-"
5277 version "-src.zip"))
5279 (base32 "0as8gxm4pjyc8dxmm1sl873rrd7wn5qs0l29nqfnl31x8i467xaa"))
5280 (patches (search-patches "plink-1.07-unclobber-i.patch"
5281 "plink-endian-detection.patch"))))
5282 (build-system gnu-build-system)
5284 '(#:tests? #f ;no "check" target
5285 #:make-flags (list (string-append "LIB_LAPACK="
5286 (assoc-ref %build-inputs "lapack")
5287 "/lib/liblapack.so")
5290 ;; disable phoning home
5293 (modify-phases %standard-phases
5294 ;; no "configure" script
5297 (lambda* (#:key outputs #:allow-other-keys)
5298 (let ((bin (string-append (assoc-ref outputs "out")
5300 (install-file "plink" bin)
5304 ("lapack" ,lapack)))
5306 `(("unzip" ,unzip)))
5307 (home-page "http://pngu.mgh.harvard.edu/~purcell/plink/")
5308 (synopsis "Whole genome association analysis toolset")
5310 "PLINK is a whole genome association analysis toolset, designed to
5311 perform a range of basic, large-scale analyses in a computationally efficient
5312 manner. The focus of PLINK is purely on analysis of genotype/phenotype data,
5313 so there is no support for steps prior to this (e.g. study design and
5314 planning, generating genotype or CNV calls from raw data). Through
5315 integration with gPLINK and Haploview, there is some support for the
5316 subsequent visualization, annotation and storage of results.")
5317 ;; Code is released under GPLv2, except for fisher.h, which is under
5319 (license (list license:gpl2 license:lgpl2.1+))))
5321 (define-public plink-ng
5322 (package (inherit plink)
5328 (uri (string-append "https://github.com/chrchang/plink-ng/archive/v"
5330 (file-name (string-append name "-" version ".tar.gz"))
5332 (base32 "09ixrds009aczjswxr2alcb774mksq5g0v78dgjjn1h4dky0kf9a"))))
5333 (build-system gnu-build-system)
5335 '(#:tests? #f ;no "check" target
5336 #:make-flags (list "BLASFLAGS=-llapack -lopenblas"
5337 "CFLAGS=-Wall -O2 -DDYNAMIC_ZLIB=1"
5339 "-f" "Makefile.std")
5341 (modify-phases %standard-phases
5342 (add-after 'unpack 'chdir
5343 (lambda _ (chdir "1.9") #t))
5344 (delete 'configure) ; no "configure" script
5346 (lambda* (#:key outputs #:allow-other-keys)
5347 (let ((bin (string-append (assoc-ref outputs "out")
5349 (install-file "plink" bin)
5354 ("openblas" ,openblas)))
5355 (home-page "https://www.cog-genomics.org/plink/")
5356 (license license:gpl3+)))
5358 (define-public smithlab-cpp
5359 (let ((revision "1")
5360 (commit "728a097bec88c6f4b8528b685932049e660eff2e"))
5362 (name "smithlab-cpp")
5363 (version (string-append "0." revision "." (string-take commit 7)))
5367 (url "https://github.com/smithlabcode/smithlab_cpp.git")
5369 (file-name (string-append name "-" version "-checkout"))
5372 "0d476lmj312xk77kr9fzrv7z1bv96yfyx0w7y62ycmnfbx32ll74"))))
5373 (build-system gnu-build-system)
5375 `(#:modules ((guix build gnu-build-system)
5378 #:tests? #f ;no "check" target
5380 (modify-phases %standard-phases
5381 (add-after 'unpack 'use-samtools-headers
5383 (substitute* '("SAM.cpp"
5385 (("sam.h") "samtools/sam.h"))
5388 (lambda* (#:key outputs #:allow-other-keys)
5389 (let* ((out (assoc-ref outputs "out"))
5390 (lib (string-append out "/lib"))
5391 (include (string-append out "/include/smithlab-cpp")))
5394 (for-each (cut install-file <> lib)
5395 (find-files "." "\\.o$"))
5396 (for-each (cut install-file <> include)
5397 (find-files "." "\\.hpp$")))
5399 (delete 'configure))))
5401 `(("samtools" ,samtools-0.1)
5403 (home-page "https://github.com/smithlabcode/smithlab_cpp")
5404 (synopsis "C++ helper library for functions used in Smith lab projects")
5406 "Smithlab CPP is a C++ library that includes functions used in many of
5407 the Smith lab bioinformatics projects, such as a wrapper around Samtools data
5408 structures, classes for genomic regions, mapped sequencing reads, etc.")
5409 (license license:gpl3+))))
5411 (define-public preseq
5417 (uri (string-append "https://github.com/smithlabcode/"
5418 "preseq/archive/v" version ".tar.gz"))
5419 (file-name (string-append name "-" version ".tar.gz"))
5421 (base32 "08r684l50pnxjpvmhzjgqq56yv9rfw90k8vx0nsrnrzk8mf9hsdq"))
5422 (modules '((guix build utils)))
5424 ;; Remove bundled samtools.
5425 '(delete-file-recursively "samtools"))))
5426 (build-system gnu-build-system)
5428 `(#:tests? #f ;no "check" target
5430 (modify-phases %standard-phases
5431 (delete 'configure))
5433 (list (string-append "PREFIX="
5434 (assoc-ref %outputs "out"))
5435 (string-append "LIBBAM="
5436 (assoc-ref %build-inputs "samtools")
5438 (string-append "SMITHLAB_CPP="
5439 (assoc-ref %build-inputs "smithlab-cpp")
5442 "INCLUDEDIRS=$(SMITHLAB_CPP)/../include/smithlab-cpp $(SAMTOOLS_DIR)")))
5445 ("samtools" ,samtools-0.1)
5446 ("smithlab-cpp" ,smithlab-cpp)
5448 (home-page "http://smithlabresearch.org/software/preseq/")
5449 (synopsis "Program for analyzing library complexity")
5451 "The preseq package is aimed at predicting and estimating the complexity
5452 of a genomic sequencing library, equivalent to predicting and estimating the
5453 number of redundant reads from a given sequencing depth and how many will be
5454 expected from additional sequencing using an initial sequencing experiment.
5455 The estimates can then be used to examine the utility of further sequencing,
5456 optimize the sequencing depth, or to screen multiple libraries to avoid low
5457 complexity samples.")
5458 (license license:gpl3+)))
5460 (define-public python-screed
5462 (name "python-screed")
5467 (uri (pypi-uri "screed" version))
5470 "18czszp9fkx3j6jr7y5kp6dfialscgddk05mw1zkhh2zhn0jd8i0"))))
5471 (build-system python-build-system)
5474 (modify-phases %standard-phases
5477 (setenv "PYTHONPATH"
5478 (string-append (getenv "PYTHONPATH") ":."))
5479 (zero? (system* "nosetests" "--attr" "!known_failing")))))))
5481 `(("python-nose" ,python-nose)))
5483 `(("python-bz2file" ,python-bz2file)))
5484 (home-page "https://github.com/dib-lab/screed/")
5485 (synopsis "Short read sequence database utilities")
5486 (description "Screed parses FASTA and FASTQ files and generates databases.
5487 Values such as sequence name, sequence description, sequence quality and the
5488 sequence itself can be retrieved from these databases.")
5489 (license license:bsd-3)))
5491 (define-public python2-screed
5492 (package-with-python2 python-screed))
5494 (define-public sra-tools
5502 (string-append "https://github.com/ncbi/sra-tools/archive/"
5504 (file-name (string-append name "-" version ".tar.gz"))
5507 "1camsijmvv2s45mb4iyf44ghl4gkd4rl0viphpcgl3ccchy32a0g"))))
5508 (build-system gnu-build-system)
5510 `(#:parallel-build? #f ; not supported
5511 #:tests? #f ; no "check" target
5513 (list (string-append "DEFAULT_CRT="
5514 (assoc-ref %build-inputs "ncbi-vdb")
5516 (string-append "DEFAULT_KFG="
5517 (assoc-ref %build-inputs "ncbi-vdb")
5519 (string-append "VDB_LIBDIR="
5520 (assoc-ref %build-inputs "ncbi-vdb")
5521 ,(if (string-prefix? "x86_64"
5522 (or (%current-target-system)
5527 (modify-phases %standard-phases
5528 (add-before 'configure 'set-perl-search-path
5530 ;; Work around "dotless @INC" build failure.
5532 (string-append (getcwd) "/setup:"
5533 (getenv "PERL5LIB")))
5536 (lambda* (#:key inputs outputs #:allow-other-keys)
5537 ;; The build system expects a directory containing the sources and
5538 ;; raw build output of ncbi-vdb, including files that are not
5539 ;; installed. Since we are building against an installed version of
5540 ;; ncbi-vdb, the following modifications are needed.
5541 (substitute* "setup/konfigure.perl"
5542 ;; Make the configure script look for the "ilib" directory of
5543 ;; "ncbi-vdb" without first checking for the existence of a
5544 ;; matching library in its "lib" directory.
5545 (("^ my \\$f = File::Spec->catdir\\(\\$libdir, \\$lib\\);")
5546 "my $f = File::Spec->catdir($ilibdir, $ilib);")
5547 ;; Look for interface libraries in ncbi-vdb's "ilib" directory.
5548 (("my \\$ilibdir = File::Spec->catdir\\(\\$builddir, 'ilib'\\);")
5549 "my $ilibdir = File::Spec->catdir($dir, 'ilib');"))
5552 (substitute* "tools/copycat/Makefile"
5553 (("smagic-static") "lmagic"))
5555 ;; The 'configure' script doesn't recognize things like
5556 ;; '--enable-fast-install'.
5559 (string-append "--build-prefix=" (getcwd) "/build")
5560 (string-append "--prefix=" (assoc-ref outputs "out"))
5561 (string-append "--debug")
5562 (string-append "--with-fuse-prefix="
5563 (assoc-ref inputs "fuse"))
5564 (string-append "--with-magic-prefix="
5565 (assoc-ref inputs "libmagic"))
5566 ;; TODO: building with libxml2 fails with linker errors
5567 ;; (string-append "--with-xml2-prefix="
5568 ;; (assoc-ref inputs "libxml2"))
5569 (string-append "--with-ncbi-vdb-sources="
5570 (assoc-ref inputs "ncbi-vdb"))
5571 (string-append "--with-ncbi-vdb-build="
5572 (assoc-ref inputs "ncbi-vdb"))
5573 (string-append "--with-ngs-sdk-prefix="
5574 (assoc-ref inputs "ngs-sdk"))
5575 (string-append "--with-hdf5-prefix="
5576 (assoc-ref inputs "hdf5"))))))
5577 ;; This version of sra-tools fails to build with glibc because of a
5578 ;; naming conflict. glibc-2.25/include/bits/mathcalls.h already
5579 ;; contains a definition of "canonicalize", so we rename it.
5581 ;; See upstream bug report:
5582 ;; https://github.com/ncbi/sra-tools/issues/67
5583 (add-after 'unpack 'patch-away-glibc-conflict
5585 (substitute* "tools/bam-loader/bam.c"
5586 (("canonicalize\\(" line)
5587 (string-append "sra_tools_" line)))
5589 (native-inputs `(("perl" ,perl)))
5591 `(("ngs-sdk" ,ngs-sdk)
5592 ("ncbi-vdb" ,ncbi-vdb)
5597 (home-page "http://www.ncbi.nlm.nih.gov/Traces/sra/sra.cgi?view=software")
5598 (synopsis "Tools and libraries for reading and writing sequencing data")
5600 "The SRA Toolkit from NCBI is a collection of tools and libraries for
5601 reading of sequencing files from the Sequence Read Archive (SRA) database and
5602 writing files into the .sra format.")
5603 (license license:public-domain)))
5605 (define-public seqan
5611 (uri (string-append "http://packages.seqan.de/seqan-library/"
5612 "seqan-library-" version ".tar.bz2"))
5615 "05s3wrrwn50f81aklfm65i4a749zag1vr8z03k21xm0pdxy47yvp"))))
5616 ;; The documentation is 7.8MB and the includes are 3.6MB heavy, so it
5617 ;; makes sense to split the outputs.
5618 (outputs '("out" "doc"))
5619 (build-system trivial-build-system)
5621 `(#:modules ((guix build utils))
5624 (use-modules (guix build utils))
5625 (let ((tar (assoc-ref %build-inputs "tar"))
5626 (bzip (assoc-ref %build-inputs "bzip2"))
5627 (out (assoc-ref %outputs "out"))
5628 (doc (assoc-ref %outputs "doc")))
5629 (setenv "PATH" (string-append tar "/bin:" bzip "/bin"))
5630 (system* "tar" "xvf" (assoc-ref %build-inputs "source"))
5631 (chdir (string-append "seqan-library-" ,version))
5632 (copy-recursively "include" (string-append out "/include"))
5633 (copy-recursively "share" (string-append doc "/share"))))))
5635 `(("source" ,source)
5638 (home-page "http://www.seqan.de")
5639 (synopsis "Library for nucleotide sequence analysis")
5641 "SeqAn is a C++ library of efficient algorithms and data structures for
5642 the analysis of sequences with the focus on biological data. It contains
5643 algorithms and data structures for string representation and their
5644 manipulation, online and indexed string search, efficient I/O of
5645 bioinformatics file formats, sequence alignment, and more.")
5646 (license license:bsd-3)))
5648 (define-public seqmagick
5655 (uri (pypi-uri "seqmagick" version))
5658 "12bfyp8nqi0hd36rmj450aygafp01qy3hkbvlwn3bk39pyjjkgg5"))))
5659 (build-system python-build-system)
5661 `(("python-biopython" ,python-biopython)))
5663 `(("python-nose" ,python-nose)))
5664 (home-page "https://github.com/fhcrc/seqmagick")
5665 (synopsis "Tools for converting and modifying sequence files")
5667 "Bioinformaticians often have to convert sequence files between formats
5668 and do little manipulations on them, and it's not worth writing scripts for
5669 that. Seqmagick is a utility to expose the file format conversion in
5670 BioPython in a convenient way. Instead of having a big mess of scripts, there
5671 is one that takes arguments.")
5672 (license license:gpl3)))
5674 (define-public seqtk
5681 "https://github.com/lh3/seqtk/archive/v"
5683 (file-name (string-append name "-" version ".tar.gz"))
5686 "0ywdyzpmfiz2wp6ampbzqg4y8bj450nfgqarpamg045b8mk32lxx"))
5687 (modules '((guix build utils)))
5690 ;; Remove extraneous header files, as is done in the seqtk
5692 (for-each (lambda (file) (delete-file file))
5693 (list "ksort.h" "kstring.h" "kvec.h"))
5695 (build-system gnu-build-system)
5698 (modify-phases %standard-phases
5701 ;; There are no tests, so we just run a sanity check.
5702 (lambda _ (zero? (system* "./seqtk" "seq"))))
5704 (lambda* (#:key outputs #:allow-other-keys)
5705 (let ((bin (string-append (assoc-ref outputs "out") "/bin/")))
5706 (install-file "seqtk" bin)))))))
5709 (home-page "https://github.com/lh3/seqtk")
5710 (synopsis "Toolkit for processing biological sequences in FASTA/Q format")
5712 "Seqtk is a fast and lightweight tool for processing sequences in the
5713 FASTA or FASTQ format. It parses both FASTA and FASTQ files which can be
5714 optionally compressed by gzip.")
5715 (license license:expat)))
5717 (define-public snap-aligner
5719 (name "snap-aligner")
5720 (version "1.0beta.18")
5724 "https://github.com/amplab/snap/archive/v"
5726 (file-name (string-append name "-" version ".tar.gz"))
5729 "1vnsjwv007k1fl1q7d681kbwn6bc66cgw6h16hym6gvyy71qv2ly"))))
5730 (build-system gnu-build-system)
5733 (modify-phases %standard-phases
5735 (replace 'check (lambda _ (zero? (system* "./unit_tests"))))
5737 (lambda* (#:key outputs #:allow-other-keys)
5738 (let* ((out (assoc-ref outputs "out"))
5739 (bin (string-append out "/bin")))
5740 (install-file "snap-aligner" bin)
5741 (install-file "SNAPCommand" bin)
5745 (home-page "http://snap.cs.berkeley.edu/")
5746 (synopsis "Short read DNA sequence aligner")
5748 "SNAP is a fast and accurate aligner for short DNA reads. It is
5749 optimized for modern read lengths of 100 bases or higher, and takes advantage
5750 of these reads to align data quickly through a hash-based indexing scheme.")
5751 ;; 32-bit systems are not supported by the unpatched code.
5752 ;; Following the bug reports https://github.com/amplab/snap/issues/68 and
5753 ;; https://bugs.debian.org/cgi-bin/bugreport.cgi?bug=812378 we see that
5754 ;; systems without a lot of memory cannot make good use of this program.
5755 (supported-systems '("x86_64-linux"))
5756 (license license:asl2.0)))
5758 (define-public sortmerna
5766 "https://github.com/biocore/sortmerna/archive/"
5768 (file-name (string-append name "-" version ".tar.gz"))
5771 "1ghaghvd82af9j5adavxh77g7hm247d1r69m3fbi6f1jdivj5ldk"))))
5772 (build-system gnu-build-system)
5773 (outputs '("out" ;for binaries
5774 "db")) ;for sequence databases
5777 (modify-phases %standard-phases
5779 (lambda* (#:key outputs #:allow-other-keys)
5780 (let* ((out (assoc-ref outputs "out"))
5781 (bin (string-append out "/bin"))
5782 (db (assoc-ref outputs "db"))
5784 (string-append db "/share/sortmerna/rRNA_databases")))
5785 (install-file "sortmerna" bin)
5786 (install-file "indexdb_rna" bin)
5787 (for-each (lambda (file)
5788 (install-file file share))
5789 (find-files "rRNA_databases" ".*fasta"))
5793 (home-page "http://bioinfo.lifl.fr/RNA/sortmerna")
5794 (synopsis "Biological sequence analysis tool for NGS reads")
5796 "SortMeRNA is a biological sequence analysis tool for filtering, mapping
5797 and operational taxonomic unit (OTU) picking of next generation
5798 sequencing (NGS) reads. The core algorithm is based on approximate seeds and
5799 allows for fast and sensitive analyses of nucleotide sequences. The main
5800 application of SortMeRNA is filtering rRNA from metatranscriptomic data.")
5801 ;; The source includes x86 specific code
5802 (supported-systems '("x86_64-linux" "i686-linux"))
5803 (license license:lgpl3)))
5811 (uri (string-append "https://github.com/alexdobin/STAR/archive/"
5813 (file-name (string-append name "-" version ".tar.gz"))
5816 "0yci4ymy4407kjh0lqp021nzccp6r31wgrkixkmix5p130cxvc56"))
5817 (modules '((guix build utils)))
5820 (substitute* "source/Makefile"
5822 ;; Remove pre-built binaries and bundled htslib sources.
5823 (delete-file-recursively "bin/MacOSX_x86_64")
5824 (delete-file-recursively "bin/Linux_x86_64")
5825 (delete-file-recursively "bin/Linux_x86_64_static")
5826 (delete-file-recursively "source/htslib")
5828 (build-system gnu-build-system)
5830 '(#:tests? #f ;no check target
5831 #:make-flags '("STAR")
5833 (modify-phases %standard-phases
5834 (add-after 'unpack 'enter-source-dir
5835 (lambda _ (chdir "source") #t))
5836 (add-after 'enter-source-dir 'make-reproducible
5838 (substitute* "Makefile"
5839 (("(COMPILATION_TIME_PLACE=\")(.*)(\")" _ pre mid post)
5840 (string-append pre "Built with Guix" post)))))
5841 (add-after 'enter-source-dir 'do-not-use-bundled-htslib
5843 (substitute* "Makefile"
5844 (("(Depend.list: \\$\\(SOURCES\\) parametersDefault\\.xxd) htslib"
5846 (substitute* '("BAMfunctions.cpp"
5851 "bamRemoveDuplicates.cpp")
5852 (("#include \"htslib/([^\"]+\\.h)\"" _ header)
5853 (string-append "#include <" header ">")))
5854 (substitute* "IncludeDefine.h"
5855 (("\"htslib/(htslib/[^\"]+.h)\"" _ header)
5856 (string-append "<" header ">")))
5859 (lambda* (#:key outputs #:allow-other-keys)
5860 (let ((bin (string-append (assoc-ref outputs "out") "/bin/")))
5861 (install-file "STAR" bin))
5863 (delete 'configure))))
5867 `(("htslib" ,htslib)
5869 (home-page "https://github.com/alexdobin/STAR")
5870 (synopsis "Universal RNA-seq aligner")
5872 "The Spliced Transcripts Alignment to a Reference (STAR) software is
5873 based on a previously undescribed RNA-seq alignment algorithm that uses
5874 sequential maximum mappable seed search in uncompressed suffix arrays followed
5875 by seed clustering and stitching procedure. In addition to unbiased de novo
5876 detection of canonical junctions, STAR can discover non-canonical splices and
5877 chimeric (fusion) transcripts, and is also capable of mapping full-length RNA
5879 ;; Only 64-bit systems are supported according to the README.
5880 (supported-systems '("x86_64-linux" "mips64el-linux"))
5881 ;; STAR is licensed under GPLv3 or later; htslib is MIT-licensed.
5882 (license license:gpl3+)))
5884 (define-public subread
5890 (uri (string-append "mirror://sourceforge/subread/subread-"
5891 version "/subread-" version "-source.tar.gz"))
5894 "0ah0n4jx6ksk2m2j7xk385x2qzmk1y4rfc6a4mfrdqrlq721w99i"))))
5895 (build-system gnu-build-system)
5897 `(#:tests? #f ;no "check" target
5898 ;; The CC and CCFLAGS variables are set to contain a lot of x86_64
5899 ;; optimizations by default, so we override these flags such that x86_64
5900 ;; flags are only added when the build target is an x86_64 system.
5902 (list (let ((system ,(or (%current-target-system)
5904 (flags '("-ggdb" "-fomit-frame-pointer"
5905 "-ffast-math" "-funroll-loops"
5906 "-fmessage-length=0"
5907 "-O9" "-Wall" "-DMAKE_FOR_EXON"
5909 "-DSUBREAD_VERSION=\\\"${SUBREAD_VERSION}\\\""))
5910 (flags64 '("-mmmx" "-msse" "-msse2" "-msse3")))
5911 (if (string-prefix? "x86_64" system)
5912 (string-append "CCFLAGS=" (string-join (append flags flags64)))
5913 (string-append "CCFLAGS=" (string-join flags))))
5914 "-f" "Makefile.Linux"
5915 "CC=gcc ${CCFLAGS}")
5917 (modify-phases %standard-phases
5918 (add-after 'unpack 'enter-dir
5919 (lambda _ (chdir "src") #t))
5921 (lambda* (#:key outputs #:allow-other-keys)
5922 (let ((bin (string-append (assoc-ref outputs "out") "/bin/")))
5924 (copy-recursively "../bin" bin))))
5925 ;; no "configure" script
5926 (delete 'configure))))
5927 (inputs `(("zlib" ,zlib)))
5928 (home-page "http://bioinf.wehi.edu.au/subread-package/")
5929 (synopsis "Tool kit for processing next-gen sequencing data")
5931 "The subread package contains the following tools: subread aligner, a
5932 general-purpose read aligner; subjunc aligner: detecting exon-exon junctions
5933 and mapping RNA-seq reads; featureCounts: counting mapped reads for genomic
5934 features; exactSNP: a SNP caller that discovers SNPs by testing signals
5935 against local background noises.")
5936 (license license:gpl3+)))
5938 (define-public stringtie
5944 (uri (string-append "http://ccb.jhu.edu/software/stringtie/dl/"
5945 "stringtie-" version ".tar.gz"))
5948 "1cqllsc1maq4kh92isi8yadgzbmnf042hlnalpk3y59aph1z3bfz"))
5949 (modules '((guix build utils)))
5952 (delete-file-recursively "samtools-0.1.18")
5954 (build-system gnu-build-system)
5956 `(#:tests? #f ;no test suite
5958 (modify-phases %standard-phases
5959 ;; no configure script
5961 (add-before 'build 'use-system-samtools
5963 (substitute* "Makefile"
5964 (("stringtie: \\$\\{BAM\\}/libbam\\.a")
5966 (substitute* '("gclib/GBam.h"
5968 (("#include \"(bam|sam|kstring).h\"" _ header)
5969 (string-append "#include <samtools/" header ".h>")))
5971 (add-after 'unpack 'remove-duplicate-typedef
5973 ;; This typedef conflicts with the typedef in
5974 ;; glibc-2.25/include/bits/types.h
5975 (substitute* "gclib/GThreads.h"
5976 (("typedef long long __intmax_t;") ""))
5979 (lambda* (#:key outputs #:allow-other-keys)
5980 (let ((bin (string-append (assoc-ref outputs "out") "/bin/")))
5981 (install-file "stringtie" bin)
5984 `(("samtools" ,samtools-0.1)
5986 (home-page "http://ccb.jhu.edu/software/stringtie/")
5987 (synopsis "Transcript assembly and quantification for RNA-Seq data")
5989 "StringTie is a fast and efficient assembler of RNA-Seq sequence
5990 alignments into potential transcripts. It uses a novel network flow algorithm
5991 as well as an optional de novo assembly step to assemble and quantitate
5992 full-length transcripts representing multiple splice variants for each gene
5993 locus. Its input can include not only the alignments of raw reads used by
5994 other transcript assemblers, but also alignments of longer sequences that have
5995 been assembled from those reads. To identify differentially expressed genes
5996 between experiments, StringTie's output can be processed either by the
5997 Cuffdiff or Ballgown programs.")
5998 (license license:artistic2.0)))
6000 (define-public taxtastic
6006 (uri (pypi-uri "taxtastic" version))
6009 "03pysw79lsrvz4lwzis88j15067ffqbi4cid5pqhrlxmd6bh8rrk"))))
6010 (build-system python-build-system)
6012 `(#:python ,python-2
6014 (modify-phases %standard-phases
6017 (zero? (system* "python" "-m" "unittest" "discover" "-v")))))))
6019 `(("python-sqlalchemy" ,python2-sqlalchemy)
6020 ("python-decorator" ,python2-decorator)
6021 ("python-biopython" ,python2-biopython)
6022 ("python-pandas" ,python2-pandas)))
6023 (home-page "https://github.com/fhcrc/taxtastic")
6024 (synopsis "Tools for taxonomic naming and annotation")
6026 "Taxtastic is software written in python used to build and maintain
6027 reference packages i.e. collections of reference trees, reference alignments,
6028 profiles, and associated taxonomic information.")
6029 (license license:gpl3+)))
6031 (define-public vcftools
6038 "https://github.com/vcftools/vcftools/releases/download/v"
6039 version "/vcftools-" version ".tar.gz"))
6042 "1qw30c45wihgy632rbz4rh3njnwj4msj46l1rsgdhyg6bgypmr1i"))))
6043 (build-system gnu-build-system)
6045 `(#:tests? #f ; no "check" target
6047 "CFLAGS=-O2" ; override "-m64" flag
6048 (string-append "PREFIX=" (assoc-ref %outputs "out"))
6049 (string-append "MANDIR=" (assoc-ref %outputs "out")
6050 "/share/man/man1"))))
6052 `(("pkg-config" ,pkg-config)))
6056 (home-page "https://vcftools.github.io/")
6057 (synopsis "Tools for working with VCF files")
6059 "VCFtools is a program package designed for working with VCF files, such
6060 as those generated by the 1000 Genomes Project. The aim of VCFtools is to
6061 provide easily accessible methods for working with complex genetic variation
6062 data in the form of VCF files.")
6063 ;; The license is declared as LGPLv3 in the README and
6064 ;; at https://vcftools.github.io/license.html
6065 (license license:lgpl3)))
6067 (define-public infernal
6073 (uri (string-append "http://eddylab.org/software/infernal/"
6074 "infernal-" version ".tar.gz"))
6077 "0sr2hiz3qxfwqpz3whxr6n82p3x27336v3f34iqznp10hks2935c"))))
6078 (build-system gnu-build-system)
6080 `(("perl" ,perl))) ; for tests
6081 (home-page "http://eddylab.org/infernal/")
6082 (synopsis "Inference of RNA alignments")
6083 (description "Infernal (\"INFERence of RNA ALignment\") is a tool for
6084 searching DNA sequence databases for RNA structure and sequence similarities.
6085 It is an implementation of a special case of profile stochastic context-free
6086 grammars called @dfn{covariance models} (CMs). A CM is like a sequence
6087 profile, but it scores a combination of sequence consensus and RNA secondary
6088 structure consensus, so in many cases, it is more capable of identifying RNA
6089 homologs that conserve their secondary structure more than their primary
6091 ;; Infernal 1.1.2 requires VMX or SSE capability for parallel instructions.
6092 (supported-systems '("i686-linux" "x86_64-linux"))
6093 (license license:bsd-3)))
6095 (define-public r-centipede
6097 (name "r-centipede")
6101 (uri (string-append "http://download.r-forge.r-project.org/"
6102 "src/contrib/CENTIPEDE_" version ".tar.gz"))
6105 "1hsx6qgwr0i67fhy9257zj7s0ppncph2hjgbia5nn6nfmj0ax6l9"))))
6106 (build-system r-build-system)
6107 (home-page "http://centipede.uchicago.edu/")
6108 (synopsis "Predict transcription factor binding sites")
6110 "CENTIPEDE applies a hierarchical Bayesian mixture model to infer regions
6111 of the genome that are bound by particular transcription factors. It starts
6112 by identifying a set of candidate binding sites, and then aims to classify the
6113 sites according to whether each site is bound or not bound by a transcription
6114 factor. CENTIPEDE is an unsupervised learning algorithm that discriminates
6115 between two different types of motif instances using as much relevant
6116 information as possible.")
6117 (license (list license:gpl2+ license:gpl3+))))
6119 (define-public r-vegan
6126 (uri (cran-uri "vegan" version))
6129 "13pyqvlpz64qibi8k5d109v7q09j06mbv6ndix3n4cn21mjx391c"))))
6130 (build-system r-build-system)
6132 `(("gfortran" ,gfortran)))
6134 `(("r-cluster" ,r-cluster)
6135 ("r-knitr" ,r-knitr) ; needed for vignettes
6136 ("r-lattice" ,r-lattice)
6139 ("r-permute" ,r-permute)))
6140 (home-page "https://cran.r-project.org/web/packages/vegan")
6141 (synopsis "Functions for community ecology")
6143 "The vegan package provides tools for descriptive community ecology. It
6144 has most basic functions of diversity analysis, community ordination and
6145 dissimilarity analysis. Most of its multivariate tools can be used for other
6146 data types as well.")
6147 (license license:gpl2+)))
6149 (define-public r-annotate
6156 (uri (bioconductor-uri "annotate" version))
6159 "1qmncyvy147a1ll3iri45p822kcs3s7583jfnq9jf6sz9ilk8cjf"))))
6160 (build-system r-build-system)
6162 `(("r-annotationdbi" ,r-annotationdbi)
6163 ("r-biobase" ,r-biobase)
6164 ("r-biocgenerics" ,r-biocgenerics)
6166 ("r-rcurl" ,r-rcurl)
6168 ("r-xtable" ,r-xtable)))
6170 "https://bioconductor.org/packages/annotate")
6171 (synopsis "Annotation for microarrays")
6172 (description "This package provides R environments for the annotation of
6174 (license license:artistic2.0)))
6176 (define-public r-copynumber
6178 (name "r-copynumber")
6182 (uri (bioconductor-uri "copynumber" version))
6185 "0y9nnwb0psphp3ix88wj2f8z5gr45r5znf55w892ysm27isdpmms"))))
6186 (build-system r-build-system)
6188 `(("r-s4vectors" ,r-s4vectors)
6189 ("r-iranges" ,r-iranges)
6190 ("r-genomicranges" ,r-genomicranges)
6191 ("r-biocgenerics" ,r-biocgenerics)))
6192 (home-page "https://bioconductor.org/packages/copynumber")
6193 (synopsis "Segmentation of single- and multi-track copy number data")
6195 "This package segments single- and multi-track copy number data by a
6196 penalized least squares regression method.")
6197 (license license:artistic2.0)))
6199 (define-public r-geneplotter
6201 (name "r-geneplotter")
6206 (uri (bioconductor-uri "geneplotter" version))
6209 "055g28xgiazl4l0gkg8xiamks64f5yckjjyvw1abd6d6qjavwx0g"))))
6210 (build-system r-build-system)
6212 `(("r-annotate" ,r-annotate)
6213 ("r-annotationdbi" ,r-annotationdbi)
6214 ("r-biobase" ,r-biobase)
6215 ("r-biocgenerics" ,r-biocgenerics)
6216 ("r-lattice" ,r-lattice)
6217 ("r-rcolorbrewer" ,r-rcolorbrewer)))
6218 (home-page "https://bioconductor.org/packages/geneplotter")
6219 (synopsis "Graphics functions for genomic data")
6221 "This package provides functions for plotting genomic data.")
6222 (license license:artistic2.0)))
6224 (define-public r-genefilter
6226 (name "r-genefilter")
6231 (uri (bioconductor-uri "genefilter" version))
6234 "14l0ff02spmjwxj0m1czhg5vlkgwcfi73cym8m2n9vn6i7bjdaqi"))))
6235 (build-system r-build-system)
6237 `(("gfortran" ,gfortran)))
6239 `(("r-annotate" ,r-annotate)
6240 ("r-annotationdbi" ,r-annotationdbi)
6241 ("r-biobase" ,r-biobase)
6242 ("r-s4vectors" ,r-s4vectors)
6243 ("r-survival" ,r-survival)))
6244 (home-page "https://bioconductor.org/packages/genefilter")
6245 (synopsis "Filter genes from high-throughput experiments")
6247 "This package provides basic functions for filtering genes from
6248 high-throughput sequencing experiments.")
6249 (license license:artistic2.0)))
6251 (define-public r-deseq2
6258 (uri (bioconductor-uri "DESeq2" version))
6261 "1wjnfpb41a9mmf9a22bz4zh7r1d4id50vpdc1mn5vfzrz7li9qik"))))
6262 (properties `((upstream-name . "DESeq2")))
6263 (build-system r-build-system)
6265 `(("r-biobase" ,r-biobase)
6266 ("r-biocgenerics" ,r-biocgenerics)
6267 ("r-biocparallel" ,r-biocparallel)
6268 ("r-genefilter" ,r-genefilter)
6269 ("r-geneplotter" ,r-geneplotter)
6270 ("r-genomicranges" ,r-genomicranges)
6271 ("r-ggplot2" ,r-ggplot2)
6272 ("r-hmisc" ,r-hmisc)
6273 ("r-iranges" ,r-iranges)
6274 ("r-locfit" ,r-locfit)
6276 ("r-rcpparmadillo" ,r-rcpparmadillo)
6277 ("r-s4vectors" ,r-s4vectors)
6278 ("r-summarizedexperiment" ,r-summarizedexperiment)))
6279 (home-page "https://bioconductor.org/packages/DESeq2")
6280 (synopsis "Differential gene expression analysis")
6282 "This package provides functions to estimate variance-mean dependence in
6283 count data from high-throughput nucleotide sequencing assays and test for
6284 differential expression based on a model using the negative binomial
6286 (license license:lgpl3+)))
6288 (define-public r-dexseq
6295 (uri (bioconductor-uri "DEXSeq" version))
6298 "1mqb3mdxcsi3largsl7k27bvqrgps9ixv806xvmf29pw0xn05sg1"))))
6299 (properties `((upstream-name . "DEXSeq")))
6300 (build-system r-build-system)
6302 `(("r-annotationdbi" ,r-annotationdbi)
6303 ("r-biobase" ,r-biobase)
6304 ("r-biocgenerics" ,r-biocgenerics)
6305 ("r-biocparallel" ,r-biocparallel)
6306 ("r-biomart" ,r-biomart)
6307 ("r-deseq2" ,r-deseq2)
6308 ("r-genefilter" ,r-genefilter)
6309 ("r-geneplotter" ,r-geneplotter)
6310 ("r-genomicranges" ,r-genomicranges)
6311 ("r-hwriter" ,r-hwriter)
6312 ("r-iranges" ,r-iranges)
6313 ("r-rcolorbrewer" ,r-rcolorbrewer)
6314 ("r-rsamtools" ,r-rsamtools)
6315 ("r-s4vectors" ,r-s4vectors)
6316 ("r-statmod" ,r-statmod)
6317 ("r-stringr" ,r-stringr)
6318 ("r-summarizedexperiment" ,r-summarizedexperiment)))
6319 (home-page "https://bioconductor.org/packages/DEXSeq")
6320 (synopsis "Inference of differential exon usage in RNA-Seq")
6322 "This package is focused on finding differential exon usage using RNA-seq
6323 exon counts between samples with different experimental designs. It provides
6324 functions that allows the user to make the necessary statistical tests based
6325 on a model that uses the negative binomial distribution to estimate the
6326 variance between biological replicates and generalized linear models for
6327 testing. The package also provides functions for the visualization and
6328 exploration of the results.")
6329 (license license:gpl3+)))
6331 (define-public r-annotationforge
6333 (name "r-annotationforge")
6338 (uri (bioconductor-uri "AnnotationForge" version))
6341 "12ffj7h95adiya5mzyjxazqn1qgr434ajpabfcyhrj5v83s4vk65"))))
6343 `((upstream-name . "AnnotationForge")))
6344 (build-system r-build-system)
6346 `(("r-annotationdbi" ,r-annotationdbi)
6347 ("r-biobase" ,r-biobase)
6348 ("r-biocgenerics" ,r-biocgenerics)
6350 ("r-rcurl" ,r-rcurl)
6351 ("r-rsqlite" ,r-rsqlite)
6352 ("r-s4vectors" ,r-s4vectors)
6354 (home-page "https://bioconductor.org/packages/AnnotationForge")
6355 (synopsis "Code for building annotation database packages")
6357 "This package provides code for generating Annotation packages and their
6358 databases. Packages produced are intended to be used with AnnotationDbi.")
6359 (license license:artistic2.0)))
6361 (define-public r-rbgl
6368 (uri (bioconductor-uri "RBGL" version))
6371 "0hj972mmqpyi5fx1rq33kysavdyz4nspi6gcffzi3rv339m0anhf"))))
6372 (properties `((upstream-name . "RBGL")))
6373 (build-system r-build-system)
6374 (propagated-inputs `(("r-graph" ,r-graph)))
6375 (home-page "https://www.bioconductor.org/packages/RBGL")
6376 (synopsis "Interface to the Boost graph library")
6378 "This package provides a fairly extensive and comprehensive interface to
6379 the graph algorithms contained in the Boost library.")
6380 (license license:artistic2.0)))
6382 (define-public r-gseabase
6389 (uri (bioconductor-uri "GSEABase" version))
6392 "11bv92svik399q677jv96b71i4bq68xxyxn1yijpdik2lq4hgl7a"))))
6393 (properties `((upstream-name . "GSEABase")))
6394 (build-system r-build-system)
6396 `(("r-annotate" ,r-annotate)
6397 ("r-annotationdbi" ,r-annotationdbi)
6398 ("r-biobase" ,r-biobase)
6399 ("r-biocgenerics" ,r-biocgenerics)
6400 ("r-graph" ,r-graph)
6402 (home-page "https://bioconductor.org/packages/GSEABase")
6403 (synopsis "Gene set enrichment data structures and methods")
6405 "This package provides classes and methods to support @dfn{Gene Set
6406 Enrichment Analysis} (GSEA).")
6407 (license license:artistic2.0)))
6409 (define-public r-category
6416 (uri (bioconductor-uri "Category" version))
6419 "03wfqa8d1dgwsm327zl2mpkq7dq3mzhq12598qz3ylfhrwplbgx0"))))
6420 (properties `((upstream-name . "Category")))
6421 (build-system r-build-system)
6423 `(("r-annotate" ,r-annotate)
6424 ("r-annotationdbi" ,r-annotationdbi)
6425 ("r-biobase" ,r-biobase)
6426 ("r-biocgenerics" ,r-biocgenerics)
6427 ("r-genefilter" ,r-genefilter)
6428 ("r-graph" ,r-graph)
6429 ("r-gseabase" ,r-gseabase)
6430 ("r-matrix" ,r-matrix)
6433 (home-page "https://bioconductor.org/packages/Category")
6434 (synopsis "Category analysis")
6436 "This package provides a collection of tools for performing category
6438 (license license:artistic2.0)))
6440 (define-public r-gostats
6447 (uri (bioconductor-uri "GOstats" version))
6450 "1i5mydz5d95w2k28qr9j01hmbnl2id55jq94jvcpcyp1pvinkdq0"))))
6451 (properties `((upstream-name . "GOstats")))
6452 (build-system r-build-system)
6454 `(("r-annotate" ,r-annotate)
6455 ("r-annotationdbi" ,r-annotationdbi)
6456 ("r-annotationforge" ,r-annotationforge)
6457 ("r-biobase" ,r-biobase)
6458 ("r-category" ,r-category)
6459 ("r-go-db" ,r-go-db)
6460 ("r-graph" ,r-graph)
6461 ("r-rgraphviz" ,r-rgraphviz)
6462 ("r-rbgl" ,r-rbgl)))
6463 (home-page "https://bioconductor.org/packages/GOstats")
6464 (synopsis "Tools for manipulating GO and microarrays")
6466 "This package provides a set of tools for interacting with GO and
6467 microarray data. A variety of basic manipulation tools for graphs, hypothesis
6468 testing and other simple calculations.")
6469 (license license:artistic2.0)))
6471 (define-public r-shortread
6473 (name "r-shortread")
6478 (uri (bioconductor-uri "ShortRead" version))
6481 "038z3z7qaw5bpgjzy91sjkybsny6jwjjsrnnq4gdqdw9ss1qy1fb"))))
6482 (properties `((upstream-name . "ShortRead")))
6483 (build-system r-build-system)
6487 `(("r-biobase" ,r-biobase)
6488 ("r-biocgenerics" ,r-biocgenerics)
6489 ("r-biocparallel" ,r-biocparallel)
6490 ("r-biostrings" ,r-biostrings)
6491 ("r-genomeinfodb" ,r-genomeinfodb)
6492 ("r-genomicalignments" ,r-genomicalignments)
6493 ("r-genomicranges" ,r-genomicranges)
6494 ("r-hwriter" ,r-hwriter)
6495 ("r-iranges" ,r-iranges)
6496 ("r-lattice" ,r-lattice)
6497 ("r-latticeextra" ,r-latticeextra)
6498 ("r-rsamtools" ,r-rsamtools)
6499 ("r-s4vectors" ,r-s4vectors)
6500 ("r-xvector" ,r-xvector)
6501 ("r-zlibbioc" ,r-zlibbioc)))
6502 (home-page "https://bioconductor.org/packages/ShortRead")
6503 (synopsis "FASTQ input and manipulation tools")
6505 "This package implements sampling, iteration, and input of FASTQ files.
6506 It includes functions for filtering and trimming reads, and for generating a
6507 quality assessment report. Data are represented as
6508 @code{DNAStringSet}-derived objects, and easily manipulated for a diversity of
6509 purposes. The package also contains legacy support for early single-end,
6510 ungapped alignment formats.")
6511 (license license:artistic2.0)))
6513 (define-public r-systempiper
6515 (name "r-systempiper")
6520 (uri (bioconductor-uri "systemPipeR" version))
6523 "1550pd63mmky0vgkmpni7zf14kqz1741wv63nfaw29kcmhh3m5lm"))))
6524 (properties `((upstream-name . "systemPipeR")))
6525 (build-system r-build-system)
6527 `(("r-annotate" ,r-annotate)
6528 ("r-batchjobs" ,r-batchjobs)
6529 ("r-biocgenerics" ,r-biocgenerics)
6530 ("r-biostrings" ,r-biostrings)
6531 ("r-deseq2" ,r-deseq2)
6532 ("r-edger" ,r-edger)
6533 ("r-genomicfeatures" ,r-genomicfeatures)
6534 ("r-genomicranges" ,r-genomicranges)
6535 ("r-ggplot2" ,r-ggplot2)
6536 ("r-go-db" ,r-go-db)
6537 ("r-gostats" ,r-gostats)
6538 ("r-limma" ,r-limma)
6539 ("r-pheatmap" ,r-pheatmap)
6540 ("r-rjson" ,r-rjson)
6541 ("r-rsamtools" ,r-rsamtools)
6542 ("r-shortread" ,r-shortread)
6543 ("r-summarizedexperiment" ,r-summarizedexperiment)
6544 ("r-variantannotation" ,r-variantannotation)))
6545 (home-page "https://github.com/tgirke/systemPipeR")
6546 (synopsis "Next generation sequencing workflow and reporting environment")
6548 "This R package provides tools for building and running automated
6549 end-to-end analysis workflows for a wide range of @dfn{next generation
6550 sequence} (NGS) applications such as RNA-Seq, ChIP-Seq, VAR-Seq and Ribo-Seq.
6551 Important features include a uniform workflow interface across different NGS
6552 applications, automated report generation, and support for running both R and
6553 command-line software, such as NGS aligners or peak/variant callers, on local
6554 computers or compute clusters. Efficient handling of complex sample sets and
6555 experimental designs is facilitated by a consistently implemented sample
6556 annotation infrastructure.")
6557 (license license:artistic2.0)))
6559 (define-public r-grohmm
6566 (uri (bioconductor-uri "groHMM" version))
6569 "1kjb14apyly44qdlx2ld6gr69wlazd4mbhs58l35hir12aphgrzp"))))
6570 (properties `((upstream-name . "groHMM")))
6571 (build-system r-build-system)
6573 `(("r-genomeinfodb" ,r-genomeinfodb)
6574 ("r-genomicalignments" ,r-genomicalignments)
6575 ("r-genomicranges" ,r-genomicranges)
6576 ("r-iranges" ,r-iranges)
6578 ("r-rtracklayer" ,r-rtracklayer)
6579 ("r-s4vectors" ,r-s4vectors)))
6580 (home-page "https://github.com/Kraus-Lab/groHMM")
6581 (synopsis "GRO-seq analysis pipeline")
6583 "This package provides a pipeline for the analysis of GRO-seq data.")
6584 (license license:gpl3+)))
6586 (define-public r-txdb-hsapiens-ucsc-hg19-knowngene
6588 (name "r-txdb-hsapiens-ucsc-hg19-knowngene")
6592 ;; We cannot use bioconductor-uri here because this tarball is
6593 ;; located under "data/annotation/" instead of "bioc/".
6594 (uri (string-append "https://bioconductor.org/packages/"
6595 "release/data/annotation/src/contrib"
6596 "/TxDb.Hsapiens.UCSC.hg19.knownGene_"
6600 "1sajhcqqwazgz2lqbik7rd935i7kpnh08zxbp2ra10j72yqy4g86"))))
6602 `((upstream-name . "TxDb.Hsapiens.UCSC.hg19.knownGene")))
6603 (build-system r-build-system)
6604 ;; As this package provides little more than a very large data file it
6605 ;; doesn't make sense to build substitutes.
6606 (arguments `(#:substitutable? #f))
6608 `(("r-genomicfeatures" ,r-genomicfeatures)))
6610 "https://bioconductor.org/packages/TxDb.Hsapiens.UCSC.hg19.knownGene/")
6611 (synopsis "Annotation package for human genome in TxDb format")
6613 "This package provides an annotation database of Homo sapiens genome
6614 data. It is derived from the UCSC hg19 genome and based on the \"knownGene\"
6615 track. The database is exposed as a @code{TxDb} object.")
6616 (license license:artistic2.0)))
6618 (define-public r-sparql
6624 (uri (cran-uri "SPARQL" version))
6627 "0gak1q06yyhdmcxb2n3v0h9gr1vqd0viqji52wpw211qp6r6dcrc"))))
6628 (properties `((upstream-name . "SPARQL")))
6629 (build-system r-build-system)
6631 `(("r-rcurl" ,r-rcurl)
6633 (home-page "https://cran.r-project.org/web/packages/SPARQL")
6634 (synopsis "SPARQL client for R")
6635 (description "This package provides an interface to use SPARQL to pose
6636 SELECT or UPDATE queries to an end-point.")
6637 ;; The only license indication is found in the DESCRIPTION file,
6638 ;; which states GPL-3. So we cannot assume GPLv3+.
6639 (license license:gpl3)))
6641 (define-public vsearch
6649 "https://github.com/torognes/vsearch/archive/v"
6651 (file-name (string-append name "-" version ".tar.gz"))
6654 "15pbirgzhvflj4pi5n82vybbzjy9mlb0lv5l3qhrmdkfzpbyahw3"))
6655 (patches (search-patches "vsearch-unbundle-cityhash.patch"))
6658 ;; Remove bundled cityhash sources. The vsearch source is adjusted
6659 ;; for this in the patch.
6660 (delete-file "src/city.h")
6661 (delete-file "src/citycrc.h")
6662 (delete-file "src/city.cc")
6664 (build-system gnu-build-system)
6667 (modify-phases %standard-phases
6668 (add-after 'unpack 'autogen
6669 (lambda _ (zero? (system* "autoreconf" "-vif")))))))
6673 ("cityhash" ,cityhash)))
6675 `(("autoconf" ,autoconf)
6676 ("automake" ,automake)))
6677 (synopsis "Sequence search tools for metagenomics")
6679 "VSEARCH supports DNA sequence searching, clustering, chimera detection,
6680 dereplication, pairwise alignment, shuffling, subsampling, sorting and
6681 masking. The tool takes advantage of parallelism in the form of SIMD
6682 vectorization as well as multiple threads to perform accurate alignments at
6683 high speed. VSEARCH uses an optimal global aligner (full dynamic programming
6684 Needleman-Wunsch).")
6685 (home-page "https://github.com/torognes/vsearch")
6686 ;; vsearch uses non-portable SSE intrinsics so building fails on other
6688 (supported-systems '("x86_64-linux"))
6689 ;; Dual licensed; also includes public domain source.
6690 (license (list license:gpl3 license:bsd-2))))
6692 (define-public pardre
6695 ;; The source of 1.1.5 changed in place, so we append "-1" to the version.
6700 (uri (string-append "mirror://sourceforge/pardre/ParDRe-rel"
6704 "17j73nc0viq4f6qj50nrndsrif5d6b71q8fl87m54psiv0ilns2b"))))
6705 (build-system gnu-build-system)
6707 `(#:tests? #f ; no tests included
6709 (modify-phases %standard-phases
6712 (lambda* (#:key outputs #:allow-other-keys)
6713 (let ((bin (string-append (assoc-ref outputs "out") "/bin")))
6714 (install-file "ParDRe" bin)
6717 `(("openmpi" ,openmpi)
6719 (synopsis "Parallel tool to remove duplicate DNA reads")
6721 "ParDRe is a parallel tool to remove duplicate genetic sequence reads.
6722 Duplicate reads can be seen as identical or nearly identical sequences with
6723 some mismatches. This tool lets users avoid the analysis of unnecessary
6724 reads, reducing the time of subsequent procedures with the
6725 dataset (e.g. assemblies, mappings, etc.). The tool is implemented with MPI
6726 in order to exploit the parallel capabilities of multicore clusters. It is
6727 faster than multithreaded counterparts (end of 2015) for the same number of
6728 cores and, thanks to the message-passing technology, it can be executed on
6730 (home-page "https://sourceforge.net/projects/pardre/")
6731 (license license:gpl3+)))
6733 (define-public ruby-bio-kseq
6735 (name "ruby-bio-kseq")
6740 (uri (rubygems-uri "bio-kseq" version))
6743 "1xyaha46khb5jc6wzkbf7040jagac49jbimn0vcrzid0j8jdikrz"))))
6744 (build-system ruby-build-system)
6746 `(#:test-target "spec"))
6748 `(("bundler" ,bundler)
6749 ("ruby-rspec" ,ruby-rspec)
6750 ("ruby-rake-compiler" ,ruby-rake-compiler)))
6753 (synopsis "Ruby bindings for the kseq.h FASTA/Q parser")
6755 "@code{Bio::Kseq} provides ruby bindings to the @code{kseq.h} FASTA and
6756 FASTQ parsing code. It provides a fast iterator over sequences and their
6758 (home-page "https://github.com/gusevfe/bio-kseq")
6759 (license license:expat)))
6761 (define-public bio-locus
6768 (uri (rubygems-uri "bio-locus" version))
6771 "02vmrxyimkj9sahsp4zhfhnmbvz6dbbqz1y01vglf8cbwvkajfl0"))))
6772 (build-system ruby-build-system)
6774 `(("ruby-rspec" ,ruby-rspec)))
6775 (synopsis "Tool for fast querying of genome locations")
6777 "Bio-locus is a tabix-like tool for fast querying of genome
6778 locations. Many file formats in bioinformatics contain records that
6779 start with a chromosome name and a position for a SNP, or a start-end
6780 position for indels. Bio-locus allows users to store this chr+pos or
6781 chr+pos+alt information in a database.")
6782 (home-page "https://github.com/pjotrp/bio-locus")
6783 (license license:expat)))
6785 (define-public bio-blastxmlparser
6787 (name "bio-blastxmlparser")
6791 (uri (rubygems-uri "bio-blastxmlparser" version))
6794 "1wf4qygcmdjgcqm6flmvsagfr1gs9lf63mj32qv3z1f481zc5692"))))
6795 (build-system ruby-build-system)
6797 `(("ruby-bio-logger" ,ruby-bio-logger)
6798 ("ruby-nokogiri" ,ruby-nokogiri)))
6800 `(("ruby-rspec" ,ruby-rspec)))
6801 (synopsis "Fast big data BLAST XML parser and library")
6803 "Very fast parallel big-data BLAST XML file parser which can be used as
6804 command line utility. Use blastxmlparser to: Parse BLAST XML; filter output;
6805 generate FASTA, JSON, YAML, RDF, JSON-LD, HTML, CSV, tabular output etc.")
6806 (home-page "https://github.com/pjotrp/blastxmlparser")
6807 (license license:expat)))
6809 (define-public bioruby
6816 (uri (rubygems-uri "bio" version))
6819 "0hdl0789c9n4mprnx5pgd46bfwl8d000rqpamj5h6kkjgspijv49"))))
6820 (build-system ruby-build-system)
6822 `(("ruby-libxml" ,ruby-libxml)))
6824 `(("which" ,which))) ; required for test phase
6827 (modify-phases %standard-phases
6828 (add-before 'build 'patch-test-command
6830 (substitute* '("test/functional/bio/test_command.rb")
6831 (("/bin/sh") (which "sh")))
6832 (substitute* '("test/functional/bio/test_command.rb")
6833 (("/bin/ls") (which "ls")))
6834 (substitute* '("test/functional/bio/test_command.rb")
6835 (("which") (which "which")))
6836 (substitute* '("test/functional/bio/test_command.rb",
6837 "test/data/command/echoarg2.sh")
6838 (("/bin/echo") (which "echo")))
6840 (synopsis "Ruby library, shell and utilities for bioinformatics")
6841 (description "BioRuby comes with a comprehensive set of Ruby development
6842 tools and libraries for bioinformatics and molecular biology. BioRuby has
6843 components for sequence analysis, pathway analysis, protein modelling and
6844 phylogenetic analysis; it supports many widely used data formats and provides
6845 easy access to databases, external programs and public web services, including
6846 BLAST, KEGG, GenBank, MEDLINE and GO.")
6847 (home-page "http://bioruby.org/")
6848 ;; Code is released under Ruby license, except for setup
6849 ;; (LGPLv2.1+) and scripts in samples (which have GPL2 and GPL2+)
6850 (license (list license:ruby license:lgpl2.1+ license:gpl2+ ))))
6852 (define-public r-acsnminer
6854 (name "r-acsnminer")
6855 (version "0.16.8.25")
6858 (uri (cran-uri "ACSNMineR" version))
6861 "0gh604s8qall6zfjlwcg2ilxjvz08dplf9k5g47idhv43scm748l"))))
6862 (properties `((upstream-name . "ACSNMineR")))
6863 (build-system r-build-system)
6865 `(("r-ggplot2" ,r-ggplot2)
6866 ("r-gridextra" ,r-gridextra)))
6867 (home-page "https://cran.r-project.org/web/packages/ACSNMineR")
6868 (synopsis "Gene enrichment analysis")
6870 "This package provides tools to compute and represent gene set enrichment
6871 or depletion from your data based on pre-saved maps from the @dfn{Atlas of
6872 Cancer Signalling Networks} (ACSN) or user imported maps. The gene set
6873 enrichment can be run with hypergeometric test or Fisher exact test, and can
6874 use multiple corrections. Visualization of data can be done either by
6875 barplots or heatmaps.")
6876 (license license:gpl2+)))
6878 (define-public r-biocgenerics
6880 (name "r-biocgenerics")
6884 (uri (bioconductor-uri "BiocGenerics" version))
6887 "19qxhy2cd3pykkhzbb5q3crgaxf65cpzf2mkfsz16gqhi8flj72p"))))
6889 `((upstream-name . "BiocGenerics")))
6890 (build-system r-build-system)
6891 (home-page "https://bioconductor.org/packages/BiocGenerics")
6892 (synopsis "S4 generic functions for Bioconductor")
6894 "This package provides S4 generic functions needed by many Bioconductor
6896 (license license:artistic2.0)))
6898 (define-public r-biocinstaller
6900 (name "r-biocinstaller")
6904 (uri (bioconductor-uri "BiocInstaller" version))
6907 "1xg1gi1hf5vflp71ji21gnmr4kcjpx8a6c47cllpc7yqnjv5nfg0"))))
6909 `((upstream-name . "BiocInstaller")))
6910 (build-system r-build-system)
6911 (home-page "https://bioconductor.org/packages/BiocInstaller")
6912 (synopsis "Install Bioconductor packages")
6913 (description "This package is used to install and update R packages from
6914 Bioconductor, CRAN, and Github.")
6915 (license license:artistic2.0)))
6917 (define-public r-biocviews
6919 (name "r-biocviews")
6923 (uri (bioconductor-uri "biocViews" version))
6926 "1yx2lir67ny0j150wyfqca0wsxp84byri8nscbs9qlndkh2jppq9"))))
6928 `((upstream-name . "biocViews")))
6929 (build-system r-build-system)
6931 `(("r-biobase" ,r-biobase)
6932 ("r-graph" ,r-graph)
6934 ("r-rcurl" ,r-rcurl)
6936 ("r-runit" ,r-runit)))
6937 (home-page "https://bioconductor.org/packages/biocViews")
6938 (synopsis "Bioconductor package categorization helper")
6939 (description "The purpose of biocViews is to create HTML pages that
6940 categorize packages in a Bioconductor package repository according to keywords,
6941 also known as views, in a controlled vocabulary.")
6942 (license license:artistic2.0)))
6944 (define-public r-bookdown
6950 (uri (cran-uri "bookdown" version))
6953 "1b3fw1f41zph5yw3kynb47aijq53vhaa6mnnvxly72zamyzdf95q"))))
6954 (build-system r-build-system)
6956 `(("r-htmltools" ,r-htmltools)
6957 ("r-knitr" ,r-knitr)
6958 ("r-rmarkdown" ,r-rmarkdown)
6959 ("r-tinytex" ,r-tinytex)
6961 ("r-xfun" ,r-xfun)))
6962 (home-page "https://github.com/rstudio/bookdown")
6963 (synopsis "Authoring books and technical documents with R markdown")
6964 (description "This package provides output formats and utilities for
6965 authoring books and technical documents with R Markdown.")
6966 (license license:gpl3)))
6968 (define-public r-biocstyle
6970 (name "r-biocstyle")
6974 (uri (bioconductor-uri "BiocStyle" version))
6977 "17m901ylz00w1a3nq5f910v55zixm1nr6rb3qrsbhqd94qzr0l2p"))))
6979 `((upstream-name . "BiocStyle")))
6980 (build-system r-build-system)
6982 `(("r-bookdown" ,r-bookdown)
6983 ("r-knitr" ,r-knitr)
6984 ("r-rmarkdown" ,r-rmarkdown)
6985 ("r-yaml" ,r-yaml)))
6986 (home-page "https://bioconductor.org/packages/BiocStyle")
6987 (synopsis "Bioconductor formatting styles")
6988 (description "This package provides standard formatting styles for
6989 Bioconductor PDF and HTML documents. Package vignettes illustrate use and
6991 (license license:artistic2.0)))
6993 (define-public r-bioccheck
6995 (name "r-bioccheck")
6999 (uri (bioconductor-uri "BiocCheck" version))
7002 "1srp1g809f1nn0fyqknr7r6dq89bw1xpjvmygr7cw6ffknbc671s"))))
7004 `((upstream-name . "BiocCheck")))
7005 (build-system r-build-system)
7008 (modify-phases %standard-phases
7009 ;; This package can be used by calling BiocCheck(<package>) from
7010 ;; within R, or by running R CMD BiocCheck <package>. This phase
7011 ;; makes sure the latter works. For this to work, the BiocCheck
7012 ;; script must be somewhere on the PATH (not the R bin directory).
7013 (add-after 'install 'install-bioccheck-subcommand
7014 (lambda* (#:key outputs #:allow-other-keys)
7015 (let* ((out (assoc-ref outputs "out"))
7016 (dest-dir (string-append out "/bin"))
7018 (string-append out "/site-library/BiocCheck/script/")))
7020 (symlink (string-append script-dir "/checkBadDeps.R")
7021 (string-append dest-dir "/checkBadDeps.R"))
7022 (symlink (string-append script-dir "/BiocCheck")
7023 (string-append dest-dir "/BiocCheck")))
7026 `(("r-codetools" ,r-codetools)
7027 ("r-graph" ,r-graph)
7029 ("r-optparse" ,r-optparse)
7030 ("r-biocinstaller" ,r-biocinstaller)
7031 ("r-biocviews" ,r-biocviews)
7032 ("r-stringdist" ,r-stringdist)))
7033 (home-page "https://bioconductor.org/packages/BiocCheck")
7034 (synopsis "Executes Bioconductor-specific package checks")
7035 (description "This package contains tools to perform additional quality
7036 checks on R packages that are to be submitted to the Bioconductor repository.")
7037 (license license:artistic2.0)))
7039 (define-public r-getopt
7046 (uri (cran-uri "getopt" version))
7049 "13p35lbpy7i578752fa71sbfvcsqw5qfa9p6kf8b5m3c5p9i4v1x"))))
7050 (build-system r-build-system)
7051 (home-page "https://github.com/trevorld/getopt")
7052 (synopsis "Command-line option processor for R")
7054 "This package is designed to be used with Rscript to write shebang
7055 scripts that accept short and long options. Many users will prefer to
7056 use the packages @code{optparse} or @code{argparse} which add extra
7057 features like automatically generated help options and usage texts,
7058 support for default values, positional argument support, etc.")
7059 (license license:gpl2+)))
7061 (define-public r-optparse
7068 (uri (cran-uri "optparse" version))
7071 "1ff4wmsszrb3spwfp7ynfs8w11qpy1sdzfxm1wk8dqqvdwris7qb"))))
7072 (build-system r-build-system)
7074 `(("r-getopt" ,r-getopt)))
7076 "https://github.com/trevorld/optparse")
7077 (synopsis "Command line option parser")
7079 "This package provides a command line parser inspired by Python's
7080 @code{optparse} library to be used with Rscript to write shebang scripts
7081 that accept short and long options.")
7082 (license license:gpl2+)))
7084 (define-public r-dnacopy
7090 (uri (bioconductor-uri "DNAcopy" version))
7093 "03hfhmmc5y60r2gcgm367w2fr7qj115l74m9bp3h9qpn5yci0d8n"))))
7095 `((upstream-name . "DNAcopy")))
7096 (build-system r-build-system)
7098 `(("gfortran" ,gfortran)))
7099 (home-page "https://bioconductor.org/packages/DNAcopy")
7100 (synopsis "Implementation of a circular binary segmentation algorithm")
7101 (description "This package implements the circular binary segmentation (CBS)
7102 algorithm to segment DNA copy number data and identify genomic regions with
7103 abnormal copy number.")
7104 (license license:gpl2+)))
7106 (define-public r-s4vectors
7108 (name "r-s4vectors")
7112 (uri (bioconductor-uri "S4Vectors" version))
7115 "0qvj2j0zl4djjl7vrwc6xak6h8dxr53iwypfbcvfb3sh7jwhdiz5"))))
7117 `((upstream-name . "S4Vectors")))
7118 (build-system r-build-system)
7120 `(("r-biocgenerics" ,r-biocgenerics)))
7121 (home-page "https://bioconductor.org/packages/S4Vectors")
7122 (synopsis "S4 implementation of vectors and lists")
7124 "The S4Vectors package defines the @code{Vector} and @code{List} virtual
7125 classes and a set of generic functions that extend the semantic of ordinary
7126 vectors and lists in R. Package developers can easily implement vector-like
7127 or list-like objects as concrete subclasses of @code{Vector} or @code{List}.
7128 In addition, a few low-level concrete subclasses of general interest (e.g.
7129 @code{DataFrame}, @code{Rle}, and @code{Hits}) are implemented in the
7130 S4Vectors package itself.")
7131 (license license:artistic2.0)))
7133 (define-public r-seqinr
7140 (uri (cran-uri "seqinr" version))
7143 "17zv0n5cji17izwmwg0jcbxbjl3w5rls91w15svcnlpxjms38ahn"))))
7144 (build-system r-build-system)
7146 `(("r-ade4" ,r-ade4)
7147 ("r-segmented" ,r-segmented)))
7150 (home-page "http://seqinr.r-forge.r-project.org/")
7151 (synopsis "Biological sequences retrieval and analysis")
7153 "This package provides tools for exploratory data analysis and data
7154 visualization of biological sequence (DNA and protein) data. It also includes
7155 utilities for sequence data management under the ACNUC system.")
7156 (license license:gpl2+)))
7158 (define-public r-iranges
7164 (uri (bioconductor-uri "IRanges" version))
7167 "10ccw930vfmkskkrzbps14xglqlkxf588623dr7f1a9ckx7yr2p6"))))
7169 `((upstream-name . "IRanges")))
7170 (build-system r-build-system)
7172 `(("r-biocgenerics" ,r-biocgenerics)
7173 ("r-s4vectors" ,r-s4vectors)))
7174 (home-page "https://bioconductor.org/packages/IRanges")
7175 (synopsis "Infrastructure for manipulating intervals on sequences")
7177 "This package provides efficient low-level and highly reusable S4 classes
7178 for storing ranges of integers, RLE vectors (Run-Length Encoding), and, more
7179 generally, data that can be organized sequentially (formally defined as
7180 @code{Vector} objects), as well as views on these @code{Vector} objects.
7181 Efficient list-like classes are also provided for storing big collections of
7182 instances of the basic classes. All classes in the package use consistent
7183 naming and share the same rich and consistent \"Vector API\" as much as
7185 (license license:artistic2.0)))
7187 (define-public r-genomeinfodbdata
7189 (name "r-genomeinfodbdata")
7193 ;; We cannot use bioconductor-uri here because this tarball is
7194 ;; located under "data/annotation/" instead of "bioc/".
7195 (uri (string-append "https://bioconductor.org/packages/release/"
7196 "data/annotation/src/contrib/GenomeInfoDbData_"
7200 "0hipipvyvrh75n68hsjg35sxbcfzrghzxv547vnkk2f8ya99g01r"))))
7202 `((upstream-name . "GenomeInfoDbData")))
7203 (build-system r-build-system)
7204 (home-page "https://bioconductor.org/packages/GenomeInfoDbData")
7205 (synopsis "Species and taxonomy ID look up tables for GenomeInfoDb")
7206 (description "This package contains data for mapping between NCBI taxonomy
7207 ID and species. It is used by functions in the GenomeInfoDb package.")
7208 (license license:artistic2.0)))
7210 (define-public r-genomeinfodb
7212 (name "r-genomeinfodb")
7216 (uri (bioconductor-uri "GenomeInfoDb" version))
7219 "0yhnqhaydmmq7ihmhj3rbal4afq5p993l2qqrd0n5wmbyg7glg2d"))))
7221 `((upstream-name . "GenomeInfoDb")))
7222 (build-system r-build-system)
7224 `(("r-biocgenerics" ,r-biocgenerics)
7225 ("r-genomeinfodbdata" ,r-genomeinfodbdata)
7226 ("r-iranges" ,r-iranges)
7227 ("r-rcurl" ,r-rcurl)
7228 ("r-s4vectors" ,r-s4vectors)))
7229 (home-page "https://bioconductor.org/packages/GenomeInfoDb")
7230 (synopsis "Utilities for manipulating chromosome identifiers")
7232 "This package contains data and functions that define and allow
7233 translation between different chromosome sequence naming conventions (e.g.,
7234 \"chr1\" versus \"1\"), including a function that attempts to place sequence
7235 names in their natural, rather than lexicographic, order.")
7236 (license license:artistic2.0)))
7238 (define-public r-edger
7244 (uri (bioconductor-uri "edgeR" version))
7247 "07py2g6vg9jbflwhc1hnzr2silbinrjwxq3mkq30nzjgf0n0hrf3"))))
7248 (properties `((upstream-name . "edgeR")))
7249 (build-system r-build-system)
7251 `(("r-limma" ,r-limma)
7252 ("r-locfit" ,r-locfit)
7254 ("r-statmod" ,r-statmod))) ;for estimateDisp
7255 (home-page "http://bioinf.wehi.edu.au/edgeR")
7256 (synopsis "EdgeR does empirical analysis of digital gene expression data")
7257 (description "This package can do differential expression analysis of
7258 RNA-seq expression profiles with biological replication. It implements a range
7259 of statistical methodology based on the negative binomial distributions,
7260 including empirical Bayes estimation, exact tests, generalized linear models
7261 and quasi-likelihood tests. It be applied to differential signal analysis of
7262 other types of genomic data that produce counts, including ChIP-seq, SAGE and
7264 (license license:gpl2+)))
7266 (define-public r-variantannotation
7268 (name "r-variantannotation")
7272 (uri (bioconductor-uri "VariantAnnotation" version))
7275 "06bccdf57vja7m63chmgc4539lwng3q3b8zxn285fj8524l6mcn7"))))
7277 `((upstream-name . "VariantAnnotation")))
7281 `(("r-annotationdbi" ,r-annotationdbi)
7282 ("r-biobase" ,r-biobase)
7283 ("r-biocgenerics" ,r-biocgenerics)
7284 ("r-biostrings" ,r-biostrings)
7285 ("r-bsgenome" ,r-bsgenome)
7287 ("r-genomeinfodb" ,r-genomeinfodb)
7288 ("r-genomicfeatures" ,r-genomicfeatures)
7289 ("r-genomicranges" ,r-genomicranges)
7290 ("r-iranges" ,r-iranges)
7291 ("r-summarizedexperiment" ,r-summarizedexperiment)
7292 ("r-rsamtools" ,r-rsamtools)
7293 ("r-rtracklayer" ,r-rtracklayer)
7294 ("r-s4vectors" ,r-s4vectors)
7295 ("r-xvector" ,r-xvector)
7296 ("r-zlibbioc" ,r-zlibbioc)))
7297 (build-system r-build-system)
7298 (home-page "https://bioconductor.org/packages/VariantAnnotation")
7299 (synopsis "Package for annotation of genetic variants")
7300 (description "This R package can annotate variants, compute amino acid
7301 coding changes and predict coding outcomes.")
7302 (license license:artistic2.0)))
7304 (define-public r-limma
7310 (uri (bioconductor-uri "limma" version))
7313 "1982g5v35ilfgxm2vkq1p3j1bbir795pjvfzx4nzam2rlqqymbqm"))))
7314 (build-system r-build-system)
7315 (home-page "http://bioinf.wehi.edu.au/limma")
7316 (synopsis "Package for linear models for microarray and RNA-seq data")
7317 (description "This package can be used for the analysis of gene expression
7318 studies, especially the use of linear models for analysing designed experiments
7319 and the assessment of differential expression. The analysis methods apply to
7320 different technologies, including microarrays, RNA-seq, and quantitative PCR.")
7321 (license license:gpl2+)))
7323 (define-public r-xvector
7329 (uri (bioconductor-uri "XVector" version))
7332 "1zjlhh9lsyhg0js1858csyw2389kbrzdqnqnha833wazkwxilp3f"))))
7334 `((upstream-name . "XVector")))
7335 (build-system r-build-system)
7338 (modify-phases %standard-phases
7339 (add-after 'unpack 'use-system-zlib
7341 (substitute* "DESCRIPTION"
7342 (("zlibbioc, ") ""))
7343 (substitute* "NAMESPACE"
7344 (("import\\(zlibbioc\\)") ""))
7349 `(("r-biocgenerics" ,r-biocgenerics)
7350 ("r-iranges" ,r-iranges)
7351 ("r-s4vectors" ,r-s4vectors)))
7352 (home-page "https://bioconductor.org/packages/XVector")
7353 (synopsis "Representation and manpulation of external sequences")
7355 "This package provides memory efficient S4 classes for storing sequences
7356 \"externally\" (behind an R external pointer, or on disk).")
7357 (license license:artistic2.0)))
7359 (define-public r-genomicranges
7361 (name "r-genomicranges")
7365 (uri (bioconductor-uri "GenomicRanges" version))
7368 "03gmka6rlz18vd4229796l5l3l6446v5cb90sn2nb5knjbp84hni"))))
7370 `((upstream-name . "GenomicRanges")))
7371 (build-system r-build-system)
7373 `(("r-biocgenerics" ,r-biocgenerics)
7374 ("r-genomeinfodb" ,r-genomeinfodb)
7375 ("r-iranges" ,r-iranges)
7376 ("r-s4vectors" ,r-s4vectors)
7377 ("r-xvector" ,r-xvector)))
7378 (home-page "https://bioconductor.org/packages/GenomicRanges")
7379 (synopsis "Representation and manipulation of genomic intervals")
7381 "This package provides tools to efficiently represent and manipulate
7382 genomic annotations and alignments is playing a central role when it comes to
7383 analyzing high-throughput sequencing data (a.k.a. NGS data). The
7384 GenomicRanges package defines general purpose containers for storing and
7385 manipulating genomic intervals and variables defined along a genome.")
7386 (license license:artistic2.0)))
7388 (define-public r-biobase
7394 (uri (bioconductor-uri "Biobase" version))
7397 "1iwds2a5ir29k19dbpynlc7nn836cw2gamchhgpi2jf2xar9m9jz"))))
7399 `((upstream-name . "Biobase")))
7400 (build-system r-build-system)
7402 `(("r-biocgenerics" ,r-biocgenerics)))
7403 (home-page "https://bioconductor.org/packages/Biobase")
7404 (synopsis "Base functions for Bioconductor")
7406 "This package provides functions that are needed by many other packages
7407 on Bioconductor or which replace R functions.")
7408 (license license:artistic2.0)))
7410 (define-public r-annotationdbi
7412 (name "r-annotationdbi")
7416 (uri (bioconductor-uri "AnnotationDbi" version))
7419 "0afkbzli08vq02r2pr9phrz3rxd6ilp1w7yw8y99nbjiz14f8b1c"))))
7421 `((upstream-name . "AnnotationDbi")))
7422 (build-system r-build-system)
7424 `(("r-biobase" ,r-biobase)
7425 ("r-biocgenerics" ,r-biocgenerics)
7427 ("r-iranges" ,r-iranges)
7428 ("r-rsqlite" ,r-rsqlite)
7429 ("r-s4vectors" ,r-s4vectors)))
7430 (home-page "https://bioconductor.org/packages/AnnotationDbi")
7431 (synopsis "Annotation database interface")
7433 "This package provides user interface and database connection code for
7434 annotation data packages using SQLite data storage.")
7435 (license license:artistic2.0)))
7437 (define-public r-biomart
7443 (uri (bioconductor-uri "biomaRt" version))
7446 "1zlgs2zg0lmnk572p55n7m34nkxka8w10x8f2ndssjkffl2csy79"))))
7448 `((upstream-name . "biomaRt")))
7449 (build-system r-build-system)
7451 `(("r-annotationdbi" ,r-annotationdbi)
7453 ("r-progress" ,r-progress)
7454 ("r-rcurl" ,r-rcurl)
7455 ("r-stringr" ,r-stringr)
7457 (home-page "https://bioconductor.org/packages/biomaRt")
7458 (synopsis "Interface to BioMart databases")
7460 "biomaRt provides an interface to a growing collection of databases
7461 implementing the @url{BioMart software suite, http://www.biomart.org}. The
7462 package enables retrieval of large amounts of data in a uniform way without
7463 the need to know the underlying database schemas or write complex SQL queries.
7464 Examples of BioMart databases are Ensembl, COSMIC, Uniprot, HGNC, Gramene,
7465 Wormbase and dbSNP mapped to Ensembl. These major databases give biomaRt
7466 users direct access to a diverse set of data and enable a wide range of
7467 powerful online queries from gene annotation to database mining.")
7468 (license license:artistic2.0)))
7470 (define-public r-biocparallel
7472 (name "r-biocparallel")
7476 (uri (bioconductor-uri "BiocParallel" version))
7479 "13ng3n2wsgl3fh0v6jnz3vg51k5c1sh44pqdvblcrcd1qyjmmqhd"))))
7481 `((upstream-name . "BiocParallel")))
7482 (build-system r-build-system)
7484 `(("r-futile-logger" ,r-futile-logger)
7487 (home-page "https://bioconductor.org/packages/BiocParallel")
7488 (synopsis "Bioconductor facilities for parallel evaluation")
7490 "This package provides modified versions and novel implementation of
7491 functions for parallel evaluation, tailored to use with Bioconductor
7493 (license (list license:gpl2+ license:gpl3+))))
7495 (define-public r-biostrings
7497 (name "r-biostrings")
7501 (uri (bioconductor-uri "Biostrings" version))
7504 "0vg50qdlxqcm2d6axjnzg8wh8pr4c5gz03l8bdl0llmwzp0zclzk"))))
7506 `((upstream-name . "Biostrings")))
7507 (build-system r-build-system)
7509 `(("r-biocgenerics" ,r-biocgenerics)
7510 ("r-iranges" ,r-iranges)
7511 ("r-s4vectors" ,r-s4vectors)
7512 ("r-xvector" ,r-xvector)))
7513 (home-page "https://bioconductor.org/packages/Biostrings")
7514 (synopsis "String objects and algorithms for biological sequences")
7516 "This package provides memory efficient string containers, string
7517 matching algorithms, and other utilities, for fast manipulation of large
7518 biological sequences or sets of sequences.")
7519 (license license:artistic2.0)))
7521 (define-public r-rsamtools
7523 (name "r-rsamtools")
7527 (uri (bioconductor-uri "Rsamtools" version))
7530 "0pjny5fjvbnfdyhl3bwxin678sha2drvs00sivxh3l772cn6yams"))))
7532 `((upstream-name . "Rsamtools")))
7533 (build-system r-build-system)
7536 (modify-phases %standard-phases
7537 (add-after 'unpack 'use-system-zlib
7539 (substitute* "DESCRIPTION"
7540 (("zlibbioc, ") ""))
7541 (substitute* "NAMESPACE"
7542 (("import\\(zlibbioc\\)") ""))
7547 `(("r-biocgenerics" ,r-biocgenerics)
7548 ("r-biocparallel" ,r-biocparallel)
7549 ("r-biostrings" ,r-biostrings)
7550 ("r-bitops" ,r-bitops)
7551 ("r-genomeinfodb" ,r-genomeinfodb)
7552 ("r-genomicranges" ,r-genomicranges)
7553 ("r-iranges" ,r-iranges)
7554 ("r-s4vectors" ,r-s4vectors)
7555 ("r-xvector" ,r-xvector)))
7556 (home-page "https://bioconductor.org/packages/release/bioc/html/Rsamtools.html")
7557 (synopsis "Interface to samtools, bcftools, and tabix")
7559 "This package provides an interface to the 'samtools', 'bcftools', and
7560 'tabix' utilities for manipulating SAM (Sequence Alignment / Map), FASTA,
7561 binary variant call (BCF) and compressed indexed tab-delimited (tabix)
7563 (license license:expat)))
7565 (define-public r-delayedarray
7567 (name "r-delayedarray")
7571 (uri (bioconductor-uri "DelayedArray" version))
7574 "0s7h2giyvz04cg6248kbbzpwhxdrpnsvl2s8k5c8ricisd9aaz4b"))))
7576 `((upstream-name . "DelayedArray")))
7577 (build-system r-build-system)
7579 `(("r-biocgenerics" ,r-biocgenerics)
7580 ("r-s4vectors" ,r-s4vectors)
7581 ("r-iranges" ,r-iranges)
7582 ("r-matrixstats" ,r-matrixstats)))
7583 (home-page "https://bioconductor.org/packages/DelayedArray")
7584 (synopsis "Delayed operations on array-like objects")
7586 "Wrapping an array-like object (typically an on-disk object) in a
7587 @code{DelayedArray} object allows one to perform common array operations on it
7588 without loading the object in memory. In order to reduce memory usage and
7589 optimize performance, operations on the object are either delayed or executed
7590 using a block processing mechanism. Note that this also works on in-memory
7591 array-like objects like @code{DataFrame} objects (typically with Rle columns),
7592 @code{Matrix} objects, and ordinary arrays and data frames.")
7593 (license license:artistic2.0)))
7595 (define-public r-summarizedexperiment
7597 (name "r-summarizedexperiment")
7601 (uri (bioconductor-uri "SummarizedExperiment" version))
7604 "19vlwnby83fqjrilsxvnvgz0gvby7mrxvlmx18nb3p1w591ddfjh"))))
7606 `((upstream-name . "SummarizedExperiment")))
7607 (build-system r-build-system)
7609 `(("r-biobase" ,r-biobase)
7610 ("r-biocgenerics" ,r-biocgenerics)
7611 ("r-delayedarray" ,r-delayedarray)
7612 ("r-genomeinfodb" ,r-genomeinfodb)
7613 ("r-genomicranges" ,r-genomicranges)
7614 ("r-iranges" ,r-iranges)
7615 ("r-matrix" ,r-matrix)
7616 ("r-s4vectors" ,r-s4vectors)))
7617 (home-page "https://bioconductor.org/packages/SummarizedExperiment")
7618 (synopsis "Container for representing genomic ranges by sample")
7620 "The SummarizedExperiment container contains one or more assays, each
7621 represented by a matrix-like object of numeric or other mode. The rows
7622 typically represent genomic ranges of interest and the columns represent
7624 (license license:artistic2.0)))
7626 (define-public r-genomicalignments
7628 (name "r-genomicalignments")
7632 (uri (bioconductor-uri "GenomicAlignments" version))
7635 "1659nj1xps7vliy5955i51x6hvrf16n1z0dfh10mmpaaswn2d2mv"))))
7637 `((upstream-name . "GenomicAlignments")))
7638 (build-system r-build-system)
7640 `(("r-biocgenerics" ,r-biocgenerics)
7641 ("r-biocparallel" ,r-biocparallel)
7642 ("r-biostrings" ,r-biostrings)
7643 ("r-genomeinfodb" ,r-genomeinfodb)
7644 ("r-genomicranges" ,r-genomicranges)
7645 ("r-iranges" ,r-iranges)
7646 ("r-rsamtools" ,r-rsamtools)
7647 ("r-s4vectors" ,r-s4vectors)
7648 ("r-summarizedexperiment" ,r-summarizedexperiment)))
7649 (home-page "https://bioconductor.org/packages/GenomicAlignments")
7650 (synopsis "Representation and manipulation of short genomic alignments")
7652 "This package provides efficient containers for storing and manipulating
7653 short genomic alignments (typically obtained by aligning short reads to a
7654 reference genome). This includes read counting, computing the coverage,
7655 junction detection, and working with the nucleotide content of the
7657 (license license:artistic2.0)))
7659 (define-public r-rtracklayer
7661 (name "r-rtracklayer")
7665 (uri (bioconductor-uri "rtracklayer" version))
7668 "1khzfczm35k5lq9h0jlqrq01192spzjyh8s6is89spj006flwn4k"))))
7669 (build-system r-build-system)
7672 (modify-phases %standard-phases
7673 (add-after 'unpack 'use-system-zlib
7675 (substitute* "DESCRIPTION"
7676 ((" zlibbioc,") ""))
7677 (substitute* "NAMESPACE"
7678 (("import\\(zlibbioc\\)") ""))
7683 `(("r-biocgenerics" ,r-biocgenerics)
7684 ("r-biostrings" ,r-biostrings)
7685 ("r-genomeinfodb" ,r-genomeinfodb)
7686 ("r-genomicalignments" ,r-genomicalignments)
7687 ("r-genomicranges" ,r-genomicranges)
7688 ("r-iranges" ,r-iranges)
7689 ("r-rcurl" ,r-rcurl)
7690 ("r-rsamtools" ,r-rsamtools)
7691 ("r-s4vectors" ,r-s4vectors)
7693 ("r-xvector" ,r-xvector)))
7694 (home-page "https://bioconductor.org/packages/rtracklayer")
7695 (synopsis "R interface to genome browsers and their annotation tracks")
7697 "rtracklayer is an extensible framework for interacting with multiple
7698 genome browsers (currently UCSC built-in) and manipulating annotation tracks
7699 in various formats (currently GFF, BED, bedGraph, BED15, WIG, BigWig and 2bit
7700 built-in). The user may export/import tracks to/from the supported browsers,
7701 as well as query and modify the browser state, such as the current viewport.")
7702 (license license:artistic2.0)))
7704 (define-public r-genomicfeatures
7706 (name "r-genomicfeatures")
7710 (uri (bioconductor-uri "GenomicFeatures" version))
7713 "010vn8hlwbnw12pd1d8pv6m12yp3xwx557gba5rbjq9p4qypnn3z"))))
7715 `((upstream-name . "GenomicFeatures")))
7716 (build-system r-build-system)
7718 `(("r-annotationdbi" ,r-annotationdbi)
7719 ("r-biobase" ,r-biobase)
7720 ("r-biocgenerics" ,r-biocgenerics)
7721 ("r-biomart" ,r-biomart)
7722 ("r-biostrings" ,r-biostrings)
7724 ("r-genomeinfodb" ,r-genomeinfodb)
7725 ("r-genomicranges" ,r-genomicranges)
7726 ("r-iranges" ,r-iranges)
7727 ("r-rcurl" ,r-rcurl)
7728 ("r-rsqlite" ,r-rsqlite)
7729 ("r-rmysql" ,r-rmysql)
7730 ("r-rtracklayer" ,r-rtracklayer)
7731 ("r-s4vectors" ,r-s4vectors)
7732 ("r-xvector" ,r-xvector)))
7733 (home-page "https://bioconductor.org/packages/GenomicFeatures")
7734 (synopsis "Tools for working with transcript centric annotations")
7736 "This package provides a set of tools and methods for making and
7737 manipulating transcript centric annotations. With these tools the user can
7738 easily download the genomic locations of the transcripts, exons and cds of a
7739 given organism, from either the UCSC Genome Browser or a BioMart
7740 database (more sources will be supported in the future). This information is
7741 then stored in a local database that keeps track of the relationship between
7742 transcripts, exons, cds and genes. Flexible methods are provided for
7743 extracting the desired features in a convenient format.")
7744 (license license:artistic2.0)))
7746 (define-public r-go-db
7752 (uri (string-append "https://www.bioconductor.org/packages/"
7753 "release/data/annotation/src/contrib/GO.db_"
7757 "02d1mn1al3q7qvhx1ylrr3ar4w4iw0qyi5d89v2336rzwk9maq35"))))
7759 `((upstream-name . "GO.db")))
7760 (build-system r-build-system)
7762 `(("r-annotationdbi" ,r-annotationdbi)))
7763 (home-page "https://bioconductor.org/packages/GO.db")
7764 (synopsis "Annotation maps describing the entire Gene Ontology")
7766 "The purpose of this GO.db annotation package is to provide detailed
7767 information about the latest version of the Gene Ontologies.")
7768 (license license:artistic2.0)))
7770 (define-public r-graph
7776 (uri (bioconductor-uri "graph" version))
7779 "15aajjp8h2z14p80c8hyd4rrmr9vqsm7bvwb989jxjl4k6g52an1"))))
7780 (build-system r-build-system)
7782 `(("r-biocgenerics" ,r-biocgenerics)))
7783 (home-page "https://bioconductor.org/packages/graph")
7784 (synopsis "Handle graph data structures in R")
7786 "This package implements some simple graph handling capabilities for R.")
7787 (license license:artistic2.0)))
7789 (define-public r-topgo
7795 (uri (bioconductor-uri "topGO" version))
7798 "1cgz4knxr328xfqlhl6ypxl6x86rfrlqz748kn94ainxjzz55i6x"))))
7800 `((upstream-name . "topGO")))
7801 (build-system r-build-system)
7803 `(("r-annotationdbi" ,r-annotationdbi)
7805 ("r-biobase" ,r-biobase)
7806 ("r-biocgenerics" ,r-biocgenerics)
7807 ("r-go-db" ,r-go-db)
7808 ("r-graph" ,r-graph)
7809 ("r-lattice" ,r-lattice)
7810 ("r-matrixstats" ,r-matrixstats)
7811 ("r-sparsem" ,r-sparsem)))
7812 (home-page "https://bioconductor.org/packages/topGO")
7813 (synopsis "Enrichment analysis for gene ontology")
7815 "The topGO package provides tools for testing @dfn{gene ontology} (GO)
7816 terms while accounting for the topology of the GO graph. Different test
7817 statistics and different methods for eliminating local similarities and
7818 dependencies between GO terms can be implemented and applied.")
7819 ;; Any version of the LGPL applies.
7820 (license license:lgpl2.1+)))
7822 (define-public r-bsgenome
7828 (uri (bioconductor-uri "BSgenome" version))
7831 "1jbzq7lm2iajajn2bifxnkss0k9fdvgqr30mral17cbhp5f6w4lq"))))
7833 `((upstream-name . "BSgenome")))
7834 (build-system r-build-system)
7836 `(("r-biocgenerics" ,r-biocgenerics)
7837 ("r-biostrings" ,r-biostrings)
7838 ("r-genomeinfodb" ,r-genomeinfodb)
7839 ("r-genomicranges" ,r-genomicranges)
7840 ("r-iranges" ,r-iranges)
7841 ("r-rsamtools" ,r-rsamtools)
7842 ("r-rtracklayer" ,r-rtracklayer)
7843 ("r-s4vectors" ,r-s4vectors)
7844 ("r-xvector" ,r-xvector)))
7845 (home-page "https://bioconductor.org/packages/BSgenome")
7846 (synopsis "Infrastructure for Biostrings-based genome data packages")
7848 "This package provides infrastructure shared by all Biostrings-based
7849 genome data packages and support for efficient SNP representation.")
7850 (license license:artistic2.0)))
7852 (define-public r-bsgenome-hsapiens-1000genomes-hs37d5
7854 (name "r-bsgenome-hsapiens-1000genomes-hs37d5")
7858 ;; We cannot use bioconductor-uri here because this tarball is
7859 ;; located under "data/annotation/" instead of "bioc/".
7860 (uri (string-append "https://www.bioconductor.org/packages/"
7861 "release/data/annotation/src/contrib/"
7862 "BSgenome.Hsapiens.1000genomes.hs37d5_"
7866 "1cg0g5fqmsvwyw2p9hp2yy4ilk21jkbbrnpgqvb5c36ihjwvc7sr"))))
7868 `((upstream-name . "BSgenome.Hsapiens.1000genomes.hs37d5")))
7869 (build-system r-build-system)
7870 ;; As this package provides little more than a very large data file it
7871 ;; doesn't make sense to build substitutes.
7872 (arguments `(#:substitutable? #f))
7874 `(("r-bsgenome" ,r-bsgenome)))
7876 "https://www.bioconductor.org/packages/BSgenome.Hsapiens.1000genomes.hs37d5/")
7877 (synopsis "Full genome sequences for Homo sapiens")
7879 "This package provides full genome sequences for Homo sapiens from
7880 1000genomes phase2 reference genome sequence (hs37d5), based on NCBI GRCh37.")
7881 (license license:artistic2.0)))
7883 (define-public r-impute
7889 (uri (bioconductor-uri "impute" version))
7892 "0b8r4swvyx3cjcc2ky8yn0ncpzlbi1pgfsn3wpbjmhh7sqrffm2n"))))
7894 `(("gfortran" ,gfortran)))
7895 (build-system r-build-system)
7896 (home-page "https://bioconductor.org/packages/impute")
7897 (synopsis "Imputation for microarray data")
7899 "This package provides a function to impute missing gene expression
7900 microarray data, using nearest neighbor averaging.")
7901 (license license:gpl2+)))
7903 (define-public r-seqpattern
7905 (name "r-seqpattern")
7909 (uri (bioconductor-uri "seqPattern" version))
7912 "1kcm5w83q7w0v0vs7nyp4gq5z86c6n6pqy9zmyyhxcrns7f597pm"))))
7914 `((upstream-name . "seqPattern")))
7915 (build-system r-build-system)
7917 `(("r-biostrings" ,r-biostrings)
7918 ("r-genomicranges" ,r-genomicranges)
7919 ("r-iranges" ,r-iranges)
7920 ("r-kernsmooth" ,r-kernsmooth)
7921 ("r-plotrix" ,r-plotrix)))
7922 (home-page "https://bioconductor.org/packages/seqPattern")
7923 (synopsis "Visualising oligonucleotide patterns and motif occurrences")
7925 "This package provides tools to visualize oligonucleotide patterns and
7926 sequence motif occurrences across a large set of sequences centred at a common
7927 reference point and sorted by a user defined feature.")
7928 (license license:gpl3+)))
7930 (define-public r-genomation
7932 (name "r-genomation")
7936 (uri (bioconductor-uri "genomation" version))
7939 "1d2g1v6xhrf3gm86pv8ln22df5g6v6k6i4i39v4j82zn4apany6v"))))
7940 (build-system r-build-system)
7942 `(("r-biostrings" ,r-biostrings)
7943 ("r-bsgenome" ,r-bsgenome)
7944 ("r-data-table" ,r-data-table)
7945 ("r-genomeinfodb" ,r-genomeinfodb)
7946 ("r-genomicalignments" ,r-genomicalignments)
7947 ("r-genomicranges" ,r-genomicranges)
7948 ("r-ggplot2" ,r-ggplot2)
7949 ("r-gridbase" ,r-gridbase)
7950 ("r-impute" ,r-impute)
7951 ("r-iranges" ,r-iranges)
7952 ("r-matrixstats" ,r-matrixstats)
7953 ("r-plotrix" ,r-plotrix)
7956 ("r-readr" ,r-readr)
7957 ("r-reshape2" ,r-reshape2)
7958 ("r-rsamtools" ,r-rsamtools)
7959 ("r-rtracklayer" ,r-rtracklayer)
7960 ("r-runit" ,r-runit)
7961 ("r-s4vectors" ,r-s4vectors)
7962 ("r-seqpattern" ,r-seqpattern)))
7963 (home-page "http://bioinformatics.mdc-berlin.de/genomation/")
7964 (synopsis "Summary, annotation and visualization of genomic data")
7966 "This package provides a package for summary and annotation of genomic
7967 intervals. Users can visualize and quantify genomic intervals over
7968 pre-defined functional regions, such as promoters, exons, introns, etc. The
7969 genomic intervals represent regions with a defined chromosome position, which
7970 may be associated with a score, such as aligned reads from HT-seq experiments,
7971 TF binding sites, methylation scores, etc. The package can use any tabular
7972 genomic feature data as long as it has minimal information on the locations of
7973 genomic intervals. In addition, it can use BAM or BigWig files as input.")
7974 (license license:artistic2.0)))
7976 (define-public r-genomationdata
7978 (name "r-genomationdata")
7982 ;; We cannot use bioconductor-uri here because this tarball is
7983 ;; located under "data/annotation/" instead of "bioc/".
7984 (uri (string-append "https://bioconductor.org/packages/"
7985 "release/data/experiment/src/contrib/"
7986 "genomationData_" version ".tar.gz"))
7989 "0h7g5x3kyb50qlblz5hc85lfm6n6f5nb68i146way3ggs04sqvla"))))
7990 (build-system r-build-system)
7991 ;; As this package provides little more than large data files, it doesn't
7992 ;; make sense to build substitutes.
7993 (arguments `(#:substitutable? #f))
7995 `(("r-knitr" ,r-knitr)))
7996 (home-page "http://bioinformatics.mdc-berlin.de/genomation/")
7997 (synopsis "Experimental data for use with the genomation package")
7999 "This package contains experimental genetic data for use with the
8000 genomation package. Included are Chip Seq, Methylation and Cage data,
8001 downloaded from Encode.")
8002 (license license:gpl3+)))
8004 (define-public r-org-hs-eg-db
8006 (name "r-org-hs-eg-db")
8010 ;; We cannot use bioconductor-uri here because this tarball is
8011 ;; located under "data/annotation/" instead of "bioc/".
8012 (uri (string-append "https://www.bioconductor.org/packages/"
8013 "release/data/annotation/src/contrib/"
8014 "org.Hs.eg.db_" version ".tar.gz"))
8017 "1v6wa5613cjq59xd7x1qz8lr9nb2abm9abl2cci1khrnrlpla927"))))
8019 `((upstream-name . "org.Hs.eg.db")))
8020 (build-system r-build-system)
8022 `(("r-annotationdbi" ,r-annotationdbi)))
8023 (home-page "https://www.bioconductor.org/packages/org.Hs.eg.db/")
8024 (synopsis "Genome wide annotation for Human")
8026 "This package contains genome-wide annotations for Human, primarily based
8027 on mapping using Entrez Gene identifiers.")
8028 (license license:artistic2.0)))
8030 (define-public r-org-ce-eg-db
8032 (name "r-org-ce-eg-db")
8036 ;; We cannot use bioconductor-uri here because this tarball is
8037 ;; located under "data/annotation/" instead of "bioc/".
8038 (uri (string-append "https://www.bioconductor.org/packages/"
8039 "release/data/annotation/src/contrib/"
8040 "org.Ce.eg.db_" version ".tar.gz"))
8043 "02ggchixlmzywhsbr0h2ms4dravv7m5964cjxqcjxqs16vjwlbk9"))))
8045 `((upstream-name . "org.Ce.eg.db")))
8046 (build-system r-build-system)
8048 `(("r-annotationdbi" ,r-annotationdbi)))
8049 (home-page "https://www.bioconductor.org/packages/org.Ce.eg.db/")
8050 (synopsis "Genome wide annotation for Worm")
8052 "This package provides mappings from Entrez gene identifiers to various
8053 annotations for the genome of the model worm Caenorhabditis elegans.")
8054 (license license:artistic2.0)))
8056 (define-public r-org-dm-eg-db
8058 (name "r-org-dm-eg-db")
8062 ;; We cannot use bioconductor-uri here because this tarball is
8063 ;; located under "data/annotation/" instead of "bioc/".
8064 (uri (string-append "https://www.bioconductor.org/packages/"
8065 "release/data/annotation/src/contrib/"
8066 "org.Dm.eg.db_" version ".tar.gz"))
8069 "033qak1d3wwz17va0bh8z8p8arx0aw2va6gm1qfwsvdkj9cd9d7d"))))
8071 `((upstream-name . "org.Dm.eg.db")))
8072 (build-system r-build-system)
8074 `(("r-annotationdbi" ,r-annotationdbi)))
8075 (home-page "https://www.bioconductor.org/packages/org.Dm.eg.db/")
8076 (synopsis "Genome wide annotation for Fly")
8078 "This package provides mappings from Entrez gene identifiers to various
8079 annotations for the genome of the model fruit fly Drosophila melanogaster.")
8080 (license license:artistic2.0)))
8082 (define-public r-org-mm-eg-db
8084 (name "r-org-mm-eg-db")
8088 ;; We cannot use bioconductor-uri here because this tarball is
8089 ;; located under "data/annotation/" instead of "bioc/".
8090 (uri (string-append "https://www.bioconductor.org/packages/"
8091 "release/data/annotation/src/contrib/"
8092 "org.Mm.eg.db_" version ".tar.gz"))
8095 "11q21p3ki4bn4hb3aix0g775l45l66jmas6m94nfhqqnpjhv4d6g"))))
8097 `((upstream-name . "org.Mm.eg.db")))
8098 (build-system r-build-system)
8100 `(("r-annotationdbi" ,r-annotationdbi)))
8101 (home-page "https://www.bioconductor.org/packages/org.Mm.eg.db/")
8102 (synopsis "Genome wide annotation for Mouse")
8104 "This package provides mappings from Entrez gene identifiers to various
8105 annotations for the genome of the model mouse Mus musculus.")
8106 (license license:artistic2.0)))
8108 (define-public r-seqlogo
8115 (uri (bioconductor-uri "seqLogo" version))
8118 "1ql4q4vx0j61a893dqc3c8zxmgs8sqhy3j1qhyfdvbd01vw9w1kq"))))
8119 (properties `((upstream-name . "seqLogo")))
8120 (build-system r-build-system)
8121 (home-page "https://bioconductor.org/packages/seqLogo")
8122 (synopsis "Sequence logos for DNA sequence alignments")
8124 "seqLogo takes the position weight matrix of a DNA sequence motif and
8125 plots the corresponding sequence logo as introduced by Schneider and
8127 (license license:lgpl2.0+)))
8129 (define-public r-bsgenome-hsapiens-ucsc-hg19
8131 (name "r-bsgenome-hsapiens-ucsc-hg19")
8135 ;; We cannot use bioconductor-uri here because this tarball is
8136 ;; located under "data/annotation/" instead of "bioc/".
8137 (uri (string-append "https://www.bioconductor.org/packages/"
8138 "release/data/annotation/src/contrib/"
8139 "BSgenome.Hsapiens.UCSC.hg19_"
8143 "1y0nqpk8cw5a34sd9hmin3z4v7iqm6hf6l22cl81vlbxqbjibxc8"))))
8145 `((upstream-name . "BSgenome.Hsapiens.UCSC.hg19")))
8146 (build-system r-build-system)
8147 ;; As this package provides little more than a very large data file it
8148 ;; doesn't make sense to build substitutes.
8149 (arguments `(#:substitutable? #f))
8151 `(("r-bsgenome" ,r-bsgenome)))
8153 "https://www.bioconductor.org/packages/BSgenome.Hsapiens.UCSC.hg19/")
8154 (synopsis "Full genome sequences for Homo sapiens")
8156 "This package provides full genome sequences for Homo sapiens as provided
8157 by UCSC (hg19, February 2009) and stored in Biostrings objects.")
8158 (license license:artistic2.0)))
8160 (define-public r-bsgenome-mmusculus-ucsc-mm9
8162 (name "r-bsgenome-mmusculus-ucsc-mm9")
8166 ;; We cannot use bioconductor-uri here because this tarball is
8167 ;; located under "data/annotation/" instead of "bioc/".
8168 (uri (string-append "https://www.bioconductor.org/packages/"
8169 "release/data/annotation/src/contrib/"
8170 "BSgenome.Mmusculus.UCSC.mm9_"
8174 "1birqw30g2azimxpnjfzmkphan7x131yy8b9h85lfz5fjdg7841i"))))
8176 `((upstream-name . "BSgenome.Mmusculus.UCSC.mm9")))
8177 (build-system r-build-system)
8178 ;; As this package provides little more than a very large data file it
8179 ;; doesn't make sense to build substitutes.
8180 (arguments `(#:substitutable? #f))
8182 `(("r-bsgenome" ,r-bsgenome)))
8184 "https://www.bioconductor.org/packages/BSgenome.Mmusculus.UCSC.mm9/")
8185 (synopsis "Full genome sequences for Mouse")
8187 "This package provides full genome sequences for Mus musculus (Mouse) as
8188 provided by UCSC (mm9, July 2007) and stored in Biostrings objects.")
8189 (license license:artistic2.0)))
8191 (define-public r-bsgenome-mmusculus-ucsc-mm10
8193 (name "r-bsgenome-mmusculus-ucsc-mm10")
8197 ;; We cannot use bioconductor-uri here because this tarball is
8198 ;; located under "data/annotation/" instead of "bioc/".
8199 (uri (string-append "https://www.bioconductor.org/packages/"
8200 "release/data/annotation/src/contrib/"
8201 "BSgenome.Mmusculus.UCSC.mm10_"
8205 "12s0nm2na9brjad4rn9l7d3db2aj8qa1xvz0y1k7gk08wayb6bkf"))))
8207 `((upstream-name . "BSgenome.Mmusculus.UCSC.mm10")))
8208 (build-system r-build-system)
8209 ;; As this package provides little more than a very large data file it
8210 ;; doesn't make sense to build substitutes.
8211 (arguments `(#:substitutable? #f))
8213 `(("r-bsgenome" ,r-bsgenome)))
8215 "https://www.bioconductor.org/packages/BSgenome.Mmusculus.UCSC.mm10/")
8216 (synopsis "Full genome sequences for Mouse")
8218 "This package provides full genome sequences for Mus
8219 musculus (Mouse) as provided by UCSC (mm10, December 2011) and stored
8220 in Biostrings objects.")
8221 (license license:artistic2.0)))
8223 (define-public r-txdb-mmusculus-ucsc-mm10-knowngene
8225 (name "r-txdb-mmusculus-ucsc-mm10-knowngene")
8229 ;; We cannot use bioconductor-uri here because this tarball is
8230 ;; located under "data/annotation/" instead of "bioc/".
8231 (uri (string-append "https://www.bioconductor.org/packages/"
8232 "release/data/annotation/src/contrib/"
8233 "TxDb.Mmusculus.UCSC.mm10.knownGene_"
8237 "08gava9wsvpcqz51k2sni3pj03n5155v32d9riqbf305nbirqbkb"))))
8239 `((upstream-name . "TxDb.Mmusculus.UCSC.mm10.knownGene")))
8240 (build-system r-build-system)
8241 ;; As this package provides little more than a very large data file it
8242 ;; doesn't make sense to build substitutes.
8243 (arguments `(#:substitutable? #f))
8245 `(("r-bsgenome" ,r-bsgenome)
8246 ("r-genomicfeatures" ,r-genomicfeatures)
8247 ("r-annotationdbi" ,r-annotationdbi)))
8249 "https://bioconductor.org/packages/TxDb.Mmusculus.UCSC.mm10.knownGene/")
8250 (synopsis "Annotation package for TxDb knownGene object(s) for Mouse")
8252 "This package loads a TxDb object, which is an R interface to
8253 prefabricated databases contained in this package. This package provides
8254 the TxDb object of Mouse data as provided by UCSC (mm10, December 2011)
8255 based on the knownGene track.")
8256 (license license:artistic2.0)))
8258 (define-public r-bsgenome-celegans-ucsc-ce6
8260 (name "r-bsgenome-celegans-ucsc-ce6")
8264 ;; We cannot use bioconductor-uri here because this tarball is
8265 ;; located under "data/annotation/" instead of "bioc/".
8266 (uri (string-append "https://www.bioconductor.org/packages/"
8267 "release/data/annotation/src/contrib/"
8268 "BSgenome.Celegans.UCSC.ce6_"
8272 "0mqzb353xv2c3m3vkb315dkmnxkgczp7ndnknyhpgjlybyf715v9"))))
8274 `((upstream-name . "BSgenome.Celegans.UCSC.ce6")))
8275 (build-system r-build-system)
8276 ;; As this package provides little more than a very large data file it
8277 ;; doesn't make sense to build substitutes.
8278 (arguments `(#:substitutable? #f))
8280 `(("r-bsgenome" ,r-bsgenome)))
8282 "https://www.bioconductor.org/packages/BSgenome.Celegans.UCSC.ce6/")
8283 (synopsis "Full genome sequences for Worm")
8285 "This package provides full genome sequences for Caenorhabditis
8286 elegans (Worm) as provided by UCSC (ce6, May 2008) and stored in Biostrings
8288 (license license:artistic2.0)))
8290 (define-public r-bsgenome-celegans-ucsc-ce10
8292 (name "r-bsgenome-celegans-ucsc-ce10")
8296 ;; We cannot use bioconductor-uri here because this tarball is
8297 ;; located under "data/annotation/" instead of "bioc/".
8298 (uri (string-append "https://www.bioconductor.org/packages/"
8299 "release/data/annotation/src/contrib/"
8300 "BSgenome.Celegans.UCSC.ce10_"
8304 "1zaym97jk4npxk14ifvwz2rvhm4zx9xgs33r9vvx9rlynp0gydrk"))))
8306 `((upstream-name . "BSgenome.Celegans.UCSC.ce10")))
8307 (build-system r-build-system)
8308 ;; As this package provides little more than a very large data file it
8309 ;; doesn't make sense to build substitutes.
8310 (arguments `(#:substitutable? #f))
8312 `(("r-bsgenome" ,r-bsgenome)))
8314 "https://www.bioconductor.org/packages/BSgenome.Celegans.UCSC.ce10/")
8315 (synopsis "Full genome sequences for Worm")
8317 "This package provides full genome sequences for Caenorhabditis
8318 elegans (Worm) as provided by UCSC (ce10, Oct 2010) and stored in Biostrings
8320 (license license:artistic2.0)))
8322 (define-public r-bsgenome-dmelanogaster-ucsc-dm3
8324 (name "r-bsgenome-dmelanogaster-ucsc-dm3")
8328 ;; We cannot use bioconductor-uri here because this tarball is
8329 ;; located under "data/annotation/" instead of "bioc/".
8330 (uri (string-append "https://www.bioconductor.org/packages/"
8331 "release/data/annotation/src/contrib/"
8332 "BSgenome.Dmelanogaster.UCSC.dm3_"
8336 "19bm3lkhhkag3gnwp419211fh0cnr0x6fa0r1lr0ycwrikxdxsv8"))))
8338 `((upstream-name . "BSgenome.Dmelanogaster.UCSC.dm3")))
8339 (build-system r-build-system)
8340 ;; As this package provides little more than a very large data file it
8341 ;; doesn't make sense to build substitutes.
8342 (arguments `(#:substitutable? #f))
8344 `(("r-bsgenome" ,r-bsgenome)))
8346 "https://www.bioconductor.org/packages/BSgenome.Dmelanogaster.UCSC.dm3/")
8347 (synopsis "Full genome sequences for Fly")
8349 "This package provides full genome sequences for Drosophila
8350 melanogaster (Fly) as provided by UCSC (dm3, April 2006) and stored in
8351 Biostrings objects.")
8352 (license license:artistic2.0)))
8354 (define-public r-motifrg
8361 (uri (bioconductor-uri "motifRG" version))
8364 "193zl2rlzwxv9p9q5i7rilj3w05ndqfyp9bdpvagp5s5cin4hf44"))))
8365 (properties `((upstream-name . "motifRG")))
8366 (build-system r-build-system)
8368 `(("r-biostrings" ,r-biostrings)
8369 ("r-bsgenome" ,r-bsgenome)
8370 ("r-bsgenome-hsapiens-ucsc-hg19" ,r-bsgenome-hsapiens-ucsc-hg19)
8371 ("r-iranges" ,r-iranges)
8372 ("r-seqlogo" ,r-seqlogo)
8373 ("r-xvector" ,r-xvector)))
8374 (home-page "https://bioconductor.org/packages/motifRG")
8375 (synopsis "Discover motifs in high throughput sequencing data")
8377 "This package provides tools for discriminative motif discovery in high
8378 throughput genetic sequencing data sets using regression methods.")
8379 (license license:artistic2.0)))
8381 (define-public r-qtl
8388 (uri (string-append "mirror://cran/src/contrib/qtl_"
8392 "1l528dwvfpdlr05imrrm4rq32axp6hld9nqm6mm43kn5n7z2f5k6"))))
8393 (build-system r-build-system)
8394 (home-page "http://rqtl.org/")
8395 (synopsis "R package for analyzing QTL experiments in genetics")
8396 (description "R/qtl is an extension library for the R statistics
8397 system. It is used to analyze experimental crosses for identifying
8398 genes contributing to variation in quantitative traits (so-called
8399 quantitative trait loci, QTLs).
8401 Using a hidden Markov model, R/qtl allows to estimate genetic maps, to
8402 identify genotyping errors, and to perform single-QTL and two-QTL,
8403 two-dimensional genome scans.")
8404 (license license:gpl3)))
8406 (define-public r-zlibbioc
8412 (uri (bioconductor-uri "zlibbioc" version))
8415 "1zr9hbh55hglfpy15cpxwmddxblhyb0an15953l3rbhmlh2vpy92"))))
8417 `((upstream-name . "zlibbioc")))
8418 (build-system r-build-system)
8419 (home-page "https://bioconductor.org/packages/zlibbioc")
8420 (synopsis "Provider for zlib-1.2.5 to R packages")
8421 (description "This package uses the source code of zlib-1.2.5 to create
8422 libraries for systems that do not have these available via other means.")
8423 (license license:artistic2.0)))
8425 (define-public r-r4rna
8432 (uri (string-append "http://www.e-rna.org/r-chie/files/R4RNA_"
8436 "1p0i78wh76jfgmn9jphbwwaz6yy6pipzfg08xs54cxavxg2j81p5"))))
8437 (build-system r-build-system)
8439 `(("r-optparse" ,r-optparse)
8440 ("r-rcolorbrewer" ,r-rcolorbrewer)))
8441 (home-page "http://www.e-rna.org/r-chie/index.cgi")
8442 (synopsis "Analysis framework for RNA secondary structure")
8444 "The R4RNA package aims to be a general framework for the analysis of RNA
8445 secondary structure and comparative analysis in R.")
8446 (license license:gpl3+)))
8448 (define-public r-rhtslib
8455 (uri (bioconductor-uri "Rhtslib" version))
8458 "1dw3p44bfr0m7w39ckc2k37sjcp1zz0b9g12mr8am15jaj6v0q2j"))))
8459 (properties `((upstream-name . "Rhtslib")))
8460 (build-system r-build-system)
8462 `(("r-zlibbioc" ,r-zlibbioc)))
8466 `(("autoconf" ,autoconf)))
8467 (home-page "https://github.com/nhayden/Rhtslib")
8468 (synopsis "High-throughput sequencing library as an R package")
8470 "This package provides the HTSlib C library for high-throughput
8471 nucleotide sequence analysis. The package is primarily useful to developers
8472 of other R packages who wish to make use of HTSlib.")
8473 (license license:lgpl2.0+)))
8475 (define-public r-bamsignals
8477 (name "r-bamsignals")
8482 (uri (bioconductor-uri "bamsignals" version))
8485 "15id6mkj95skb4kfafvfs2j7ylydal60c3pspcl7llhwpq6vcqvl"))))
8486 (build-system r-build-system)
8488 `(("r-biocgenerics" ,r-biocgenerics)
8489 ("r-genomicranges" ,r-genomicranges)
8490 ("r-iranges" ,r-iranges)
8492 ("r-rhtslib" ,r-rhtslib)
8493 ("r-zlibbioc" ,r-zlibbioc)))
8496 (home-page "https://bioconductor.org/packages/bamsignals")
8497 (synopsis "Extract read count signals from bam files")
8499 "This package allows to efficiently obtain count vectors from indexed bam
8500 files. It counts the number of nucleotide sequence reads in given genomic
8501 ranges and it computes reads profiles and coverage profiles. It also handles
8503 (license license:gpl2+)))
8505 (define-public r-rcas
8511 (uri (string-append "https://github.com/BIMSBbioinfo/RCAS/archive/v"
8513 (file-name (string-append name "-" version ".tar.gz"))
8516 "1qgc7vi6fpzl440yg7jhiycg5q336kd4pxqzx10yx2zcq3bq3msg"))))
8517 (build-system r-build-system)
8519 `(("r-knitr" ,r-knitr)
8520 ("r-testthat" ,r-testthat)
8521 ;; During vignette building knitr checks that "pandoc-citeproc"
8523 ("ghc-pandoc-citeproc" ,ghc-pandoc-citeproc-with-pandoc-1)))
8525 `(("r-data-table" ,r-data-table)
8526 ("r-biomart" ,r-biomart)
8527 ("r-org-hs-eg-db" ,r-org-hs-eg-db)
8528 ("r-org-ce-eg-db" ,r-org-ce-eg-db)
8529 ("r-org-dm-eg-db" ,r-org-dm-eg-db)
8530 ("r-org-mm-eg-db" ,r-org-mm-eg-db)
8531 ("r-bsgenome-hsapiens-ucsc-hg19" ,r-bsgenome-hsapiens-ucsc-hg19)
8532 ("r-bsgenome-mmusculus-ucsc-mm9" ,r-bsgenome-mmusculus-ucsc-mm9)
8533 ("r-bsgenome-celegans-ucsc-ce10" ,r-bsgenome-celegans-ucsc-ce10)
8534 ("r-bsgenome-dmelanogaster-ucsc-dm3" ,r-bsgenome-dmelanogaster-ucsc-dm3)
8535 ("r-topgo" ,r-topgo)
8537 ("r-pbapply" ,r-pbapply)
8538 ("r-plotly" ,r-plotly)
8539 ("r-plotrix" ,r-plotrix)
8540 ("r-motifrg" ,r-motifrg)
8541 ("r-genomation" ,r-genomation)
8542 ("r-genomicfeatures" ,r-genomicfeatures)
8543 ("r-rtracklayer" ,r-rtracklayer)
8544 ("r-rmarkdown" ,r-rmarkdown)))
8545 (synopsis "RNA-centric annotation system")
8547 "RCAS aims to be a standalone RNA-centric annotation system that provides
8548 intuitive reports and publication-ready graphics. This package provides the R
8549 library implementing most of the pipeline's features.")
8550 (home-page "https://github.com/BIMSBbioinfo/RCAS")
8551 (license license:artistic2.0)))
8553 (define-public rcas-web
8560 (uri (string-append "https://github.com/BIMSBbioinfo/rcas-web/"
8561 "releases/download/v" version
8562 "/rcas-web-" version ".tar.gz"))
8565 "1p16frfys41a8yaa4gkm457nzkqhqs2pc3lkac0ds457w9w5j1gm"))))
8566 (build-system gnu-build-system)
8569 (modify-phases %standard-phases
8570 (add-after 'install 'wrap-executable
8571 (lambda* (#:key inputs outputs #:allow-other-keys)
8572 (let* ((out (assoc-ref outputs "out"))
8573 (json (assoc-ref inputs "guile-json"))
8574 (redis (assoc-ref inputs "guile-redis"))
8575 (path (string-append
8576 json "/share/guile/site/2.2:"
8577 redis "/share/guile/site/2.2")))
8578 (wrap-program (string-append out "/bin/rcas-web")
8579 `("GUILE_LOAD_PATH" ":" = (,path))
8580 `("GUILE_LOAD_COMPILED_PATH" ":" = (,path))
8581 `("R_LIBS_SITE" ":" = (,(getenv "R_LIBS_SITE")))))
8584 `(("r-minimal" ,r-minimal)
8586 ("guile-next" ,guile-2.2)
8587 ("guile-json" ,guile-json)
8588 ("guile-redis" ,guile2.2-redis)))
8590 `(("pkg-config" ,pkg-config)))
8591 (home-page "https://github.com/BIMSBbioinfo/rcas-web")
8592 (synopsis "Web interface for RNA-centric annotation system (RCAS)")
8593 (description "This package provides a simple web interface for the
8594 @dfn{RNA-centric annotation system} (RCAS).")
8595 (license license:agpl3+)))
8597 (define-public r-mutationalpatterns
8599 (name "r-mutationalpatterns")
8604 (uri (bioconductor-uri "MutationalPatterns" version))
8607 "0ml4gsp5dfv23xqrknxh25q8q65hly1xb1215lcwyc8hj9z8f941"))))
8608 (build-system r-build-system)
8610 `(("r-biocgenerics" ,r-biocgenerics)
8611 ("r-biostrings" ,r-biostrings)
8612 ("r-bsgenome-hsapiens-1000g" ,r-bsgenome-hsapiens-1000genomes-hs37d5)
8613 ("r-bsgenome-hsapiens-ucsc-hg19" ,r-bsgenome-hsapiens-ucsc-hg19)
8614 ("r-genomicranges" ,r-genomicranges)
8615 ("r-genomeinfodb" ,r-genomeinfodb)
8616 ("r-ggplot2" ,r-ggplot2)
8617 ("r-iranges" ,r-iranges)
8620 ("r-pracma" ,r-pracma)
8621 ("r-reshape2" ,r-reshape2)
8622 ("r-cowplot" ,r-cowplot)
8623 ("r-ggdendro" ,r-ggdendro)
8624 ("r-s4vectors" ,r-s4vectors)
8625 ("r-summarizedexperiment" ,r-summarizedexperiment)
8626 ("r-variantannotation" ,r-variantannotation)))
8627 (home-page "https://bioconductor.org/packages/MutationalPatterns/")
8628 (synopsis "Extract and visualize mutational patterns in genomic data")
8629 (description "This package provides an extensive toolset for the
8630 characterization and visualization of a wide range of mutational patterns
8631 in SNV base substitution data.")
8632 (license license:expat)))
8634 (define-public r-wgcna
8641 (uri (cran-uri "WGCNA" version))
8644 "1225dqm68bynkmklnsxdqdd3zqrpzbvqwyly8ibxmk75z33xz309"))))
8645 (properties `((upstream-name . "WGCNA")))
8646 (build-system r-build-system)
8648 `(("r-annotationdbi" ,r-annotationdbi)
8649 ("r-doparallel" ,r-doparallel)
8650 ("r-dynamictreecut" ,r-dynamictreecut)
8651 ("r-fastcluster" ,r-fastcluster)
8652 ("r-foreach" ,r-foreach)
8653 ("r-go-db" ,r-go-db)
8654 ("r-hmisc" ,r-hmisc)
8655 ("r-impute" ,r-impute)
8657 ("r-robust" ,r-robust)
8658 ("r-survival" ,r-survival)
8659 ("r-matrixstats" ,r-matrixstats)
8660 ("r-preprocesscore" ,r-preprocesscore)))
8662 "http://www.genetics.ucla.edu/labs/horvath/CoexpressionNetwork/Rpackages/WGCNA/")
8663 (synopsis "Weighted correlation network analysis")
8665 "This package provides functions necessary to perform Weighted
8666 Correlation Network Analysis on high-dimensional data. It includes functions
8667 for rudimentary data cleaning, construction and summarization of correlation
8668 networks, module identification and functions for relating both variables and
8669 modules to sample traits. It also includes a number of utility functions for
8670 data manipulation and visualization.")
8671 (license license:gpl2+)))
8673 (define-public r-chipkernels
8674 (let ((commit "c9cfcacb626b1221094fb3490ea7bac0fd625372")
8677 (name "r-chipkernels")
8678 (version (string-append "1.1-" revision "." (string-take commit 9)))
8683 (url "https://github.com/ManuSetty/ChIPKernels.git")
8685 (file-name (string-append name "-" version))
8688 "14bj5qhjm1hsm9ay561nfbqi9wxsa7y487df2idsaaf6z10nw4v0"))))
8689 (build-system r-build-system)
8691 `(("r-iranges" ,r-iranges)
8692 ("r-xvector" ,r-xvector)
8693 ("r-biostrings" ,r-biostrings)
8694 ("r-bsgenome" ,r-bsgenome)
8695 ("r-gtools" ,r-gtools)
8696 ("r-genomicranges" ,r-genomicranges)
8697 ("r-sfsmisc" ,r-sfsmisc)
8698 ("r-kernlab" ,r-kernlab)
8699 ("r-s4vectors" ,r-s4vectors)
8700 ("r-biocgenerics" ,r-biocgenerics)))
8701 (home-page "https://github.com/ManuSetty/ChIPKernels")
8702 (synopsis "Build string kernels for DNA Sequence analysis")
8703 (description "ChIPKernels is an R package for building different string
8704 kernels used for DNA Sequence analysis. A dictionary of the desired kernel
8705 must be built and this dictionary can be used for determining kernels for DNA
8707 (license license:gpl2+))))
8709 (define-public r-seqgl
8716 (uri (string-append "https://github.com/ManuSetty/SeqGL/"
8717 "archive/" version ".tar.gz"))
8718 (file-name (string-append name "-" version ".tar.gz"))
8721 "0pnk1p3sci5yipyc8xnb6jbmydpl80fld927xgnbcv104hy8h8yh"))))
8722 (build-system r-build-system)
8724 `(("r-biostrings" ,r-biostrings)
8725 ("r-chipkernels" ,r-chipkernels)
8726 ("r-genomicranges" ,r-genomicranges)
8727 ("r-spams" ,r-spams)
8728 ("r-wgcna" ,r-wgcna)
8729 ("r-fastcluster" ,r-fastcluster)))
8730 (home-page "https://github.com/ManuSetty/SeqGL")
8731 (synopsis "Group lasso for Dnase/ChIP-seq data")
8732 (description "SeqGL is a group lasso based algorithm to extract
8733 transcription factor sequence signals from ChIP, DNase and ATAC-seq profiles.
8734 This package presents a method which uses group lasso to discriminate between
8735 bound and non bound genomic regions to accurately identify transcription
8736 factors bound at the specific regions.")
8737 (license license:gpl2+)))
8739 (define-public r-gkmsvm
8746 (uri (cran-uri "gkmSVM" version))
8749 "04dakbgfvfalz4rm4fvvybp506dn5fbj5g86ybfhrc6wywjllsz3"))))
8750 (properties `((upstream-name . "gkmSVM")))
8751 (build-system r-build-system)
8753 `(("r-biocgenerics" ,r-biocgenerics)
8754 ("r-biostrings" ,r-biostrings)
8755 ("r-genomeinfodb" ,r-genomeinfodb)
8756 ("r-genomicranges" ,r-genomicranges)
8757 ("r-iranges" ,r-iranges)
8758 ("r-kernlab" ,r-kernlab)
8761 ("r-rtracklayer" ,r-rtracklayer)
8762 ("r-s4vectors" ,r-s4vectors)
8763 ("r-seqinr" ,r-seqinr)))
8764 (home-page "https://cran.r-project.org/web/packages/gkmSVM")
8765 (synopsis "Gapped-kmer support vector machine")
8767 "This R package provides tools for training gapped-kmer SVM classifiers
8768 for DNA and protein sequences. This package supports several sequence
8769 kernels, including: gkmSVM, kmer-SVM, mismatch kernel and wildcard kernel.")
8770 (license license:gpl2+)))
8772 (define-public r-tximport
8778 (uri (bioconductor-uri "tximport" version))
8781 "1gyqcm91hxg1kgjqcz2qw1n56yp9pymjzs50rwcpb2893dr8sp2h"))))
8782 (build-system r-build-system)
8783 (home-page "https://bioconductor.org/packages/tximport")
8784 (synopsis "Import and summarize transcript-level estimates for gene-level analysis")
8786 "This package provides tools to import transcript-level abundance,
8787 estimated counts and transcript lengths, and to summarize them into matrices
8788 for use with downstream gene-level analysis packages. Average transcript
8789 length, weighted by sample-specific transcript abundance estimates, is
8790 provided as a matrix which can be used as an offset for different expression
8791 of gene-level counts.")
8792 (license license:gpl2+)))
8794 (define-public r-rhdf5
8800 (uri (bioconductor-uri "rhdf5" version))
8803 "145858qg1xan6imxcbprzq3yn3mdf532aahdr6cibvdjg47hs4c1"))))
8804 (build-system r-build-system)
8807 (modify-phases %standard-phases
8808 (add-after 'unpack 'unpack-smallhdf5
8809 (lambda* (#:key outputs #:allow-other-keys)
8810 (system* "tar" "-xzvf"
8811 "src/hdf5source/hdf5small.tgz" "-C" "src/" )
8812 (substitute* "src/hdf5/configure"
8814 ;; Remove timestamp and host system information to make
8815 ;; the build reproducible.
8816 (substitute* "src/hdf5/src/libhdf5.settings.in"
8817 (("Configured on: @CONFIG_DATE@")
8818 "Configured on: Guix")
8819 (("Uname information:.*")
8820 "Uname information: Linux\n")
8821 ;; Remove unnecessary store reference.
8823 "C Compiler: GCC\n"))
8826 `(("r-zlibbioc" ,r-zlibbioc)))
8830 (home-page "https://bioconductor.org/packages/rhdf5")
8831 (synopsis "HDF5 interface to R")
8833 "This R/Bioconductor package provides an interface between HDF5 and R.
8834 HDF5's main features are the ability to store and access very large and/or
8835 complex datasets and a wide variety of metadata on mass storage (disk) through
8836 a completely portable file format. The rhdf5 package is thus suited for the
8837 exchange of large and/or complex datasets between R and other software
8838 package, and for letting R applications work on datasets that are larger than
8839 the available RAM.")
8840 (license license:artistic2.0)))
8842 (define-public r-annotationfilter
8844 (name "r-annotationfilter")
8848 (uri (bioconductor-uri "AnnotationFilter" version))
8851 "04zf864c1fvdlaay2r5cn30fc1n5i3czh31fs62qlrvs61wjiscs"))))
8853 `((upstream-name . "AnnotationFilter")))
8854 (build-system r-build-system)
8856 `(("r-genomicranges" ,r-genomicranges)
8857 ("r-lazyeval" ,r-lazyeval)))
8858 (home-page "https://github.com/Bioconductor/AnnotationFilter")
8859 (synopsis "Facilities for filtering Bioconductor annotation resources")
8861 "This package provides classes and other infrastructure to implement
8862 filters for manipulating Bioconductor annotation resources. The filters are
8863 used by @code{ensembldb}, @code{Organism.dplyr}, and other packages.")
8864 (license license:artistic2.0)))
8866 (define-public emboss
8872 (uri (string-append "ftp://emboss.open-bio.org/pub/EMBOSS/old/"
8873 (version-major+minor version) ".0/"
8874 "EMBOSS-" version ".tar.gz"))
8877 "0vsmz96gc411yj2iyzdrsmg4l2n1nhgmp7vrgzlxx3xixv9xbf0q"))))
8878 (build-system gnu-build-system)
8881 (list (string-append "--with-hpdf="
8882 (assoc-ref %build-inputs "libharu")))
8884 (modify-phases %standard-phases
8885 (add-after 'unpack 'fix-checks
8887 ;; The PNGDRIVER tests check for the presence of libgd, libpng
8888 ;; and zlib, but assume that they are all found at the same
8890 (substitute* "configure.in"
8891 (("CHECK_PNGDRIVER")
8892 "LIBS=\"$LIBS -lgd -lpng -lz -lm\"
8893 AC_DEFINE([PLD_png], [1], [Define to 1 if PNG support is available])
8894 AM_CONDITIONAL(AMPNG, true)"))
8896 (add-after 'fix-checks 'disable-update-check
8898 ;; At build time there is no connection to the Internet, so
8899 ;; looking for updates will not work.
8900 (substitute* "Makefile.am"
8901 (("\\$\\(bindir\\)/embossupdate") ""))
8903 (add-after 'disable-update-check 'autogen
8904 (lambda _ (zero? (system* "autoreconf" "-vif")))))))
8910 ("libharu" ,libharu)
8913 `(("autoconf" ,autoconf)
8914 ("automake" ,automake)
8915 ("libtool" ,libtool)
8916 ("pkg-config" ,pkg-config)))
8917 (home-page "http://emboss.sourceforge.net")
8918 (synopsis "Molecular biology analysis suite")
8919 (description "EMBOSS is the \"European Molecular Biology Open Software
8920 Suite\". EMBOSS is an analysis package specially developed for the needs of
8921 the molecular biology (e.g. EMBnet) user community. The software
8922 automatically copes with data in a variety of formats and even allows
8923 transparent retrieval of sequence data from the web. It also provides a
8924 number of libraries for the development of software in the field of molecular
8925 biology. EMBOSS also integrates a range of currently available packages and
8926 tools for sequence analysis into a seamless whole.")
8927 (license license:gpl2+)))
8930 (let ((revision "1")
8931 (commit "3cc4567896d9d6442923da944beb704750a08d2d"))
8934 ;; The version is 2.13.0 even though no release archives have been
8935 ;; published as yet.
8936 (version (string-append "2.13.0-" revision "." (string-take commit 9)))
8940 (url "https://github.com/arq5x/bits.git")
8942 (file-name (string-append name "-" version "-checkout"))
8945 "17n2kffk4kmhivd8c98g2vr6y1s23vbg4sxlxs689wni66797hbs"))))
8946 (build-system gnu-build-system)
8948 `(#:tests? #f ;no tests included
8950 (modify-phases %standard-phases
8952 (add-after 'unpack 'remove-cuda
8954 (substitute* "Makefile"
8956 (("(bits_test_intersections) \\\\" _ match) match))
8959 (lambda* (#:key outputs #:allow-other-keys)
8961 "bin" (string-append (assoc-ref outputs "out") "/bin"))
8966 (home-page "https://github.com/arq5x/bits")
8967 (synopsis "Implementation of binary interval search algorithm")
8968 (description "This package provides an implementation of the
8969 BITS (Binary Interval Search) algorithm, an approach to interval set
8970 intersection. It is especially suited for the comparison of diverse genomic
8971 datasets and the exploration of large datasets of genome
8972 intervals (e.g. genes, sequence alignments).")
8973 (license license:gpl2))))
8975 (define-public piranha
8976 ;; There is no release tarball for the latest version. The latest commit is
8977 ;; older than one year at the time of this writing.
8978 (let ((revision "1")
8979 (commit "0466d364b71117d01e4471b74c514436cc281233"))
8982 (version (string-append "1.2.1-" revision "." (string-take commit 9)))
8986 (url "https://github.com/smithlabcode/piranha.git")
8988 (file-name (git-file-name name version))
8991 "117dc0zf20c61jam69sk4abl57ah6yi6i7qra7d7y5zrbgk12q5n"))))
8992 (build-system gnu-build-system)
8994 `(#:test-target "test"
8996 (modify-phases %standard-phases
8997 (add-after 'unpack 'copy-smithlab-cpp
8998 (lambda* (#:key inputs #:allow-other-keys)
8999 (for-each (lambda (file)
9000 (install-file file "./src/smithlab_cpp/"))
9001 (find-files (assoc-ref inputs "smithlab-cpp")))
9003 (add-after 'install 'install-to-store
9004 (lambda* (#:key outputs #:allow-other-keys)
9005 (let* ((out (assoc-ref outputs "out"))
9006 (bin (string-append out "/bin")))
9007 (for-each (lambda (file)
9008 (install-file file bin))
9009 (find-files "bin" ".*")))
9012 (list (string-append "--with-bam_tools_headers="
9013 (assoc-ref %build-inputs "bamtools") "/include/bamtools")
9014 (string-append "--with-bam_tools_library="
9015 (assoc-ref %build-inputs "bamtools") "/lib/bamtools"))))
9017 `(("bamtools" ,bamtools)
9018 ("samtools" ,samtools-0.1)
9021 ,(let ((commit "3723e2db438c51501d0423429ff396c3035ba46a"))
9025 (url "https://github.com/smithlabcode/smithlab_cpp.git")
9027 (file-name (string-append "smithlab_cpp-" commit "-checkout"))
9030 "0l4gvbwslw5ngziskja41c00x1r06l3yidv7y0xw9djibhykzy0g")))))))
9032 `(("python" ,python-2)))
9033 (home-page "https://github.com/smithlabcode/piranha")
9034 (synopsis "Peak-caller for CLIP-seq and RIP-seq data")
9036 "Piranha is a peak-caller for genomic data produced by CLIP-seq and
9037 RIP-seq experiments. It takes input in BED or BAM format and identifies
9038 regions of statistically significant read enrichment. Additional covariates
9039 may optionally be provided to further inform the peak-calling process.")
9040 (license license:gpl3+))))
9048 (uri (string-append "https://pypi.python.org/packages/source/P"
9049 "/PePr/PePr-" version ".tar.gz"))
9052 "0qxjfdpl1b1y53nccws2d85f6k74zwmx8y8sd9rszcqhfayx6gdx"))))
9053 (build-system python-build-system)
9055 `(#:python ,python-2 ; python2 only
9056 #:tests? #f)) ; no tests included
9058 `(("python2-numpy" ,python2-numpy)
9059 ("python2-scipy" ,python2-scipy)
9060 ("python2-pysam" ,python2-pysam)))
9061 (home-page "https://github.com/shawnzhangyx/PePr")
9062 (synopsis "Peak-calling and prioritization pipeline for ChIP-Seq data")
9064 "PePr is a ChIP-Seq peak calling or differential binding analysis tool
9065 that is primarily designed for data with biological replicates. It uses a
9066 negative binomial distribution to model the read counts among the samples in
9067 the same group, and look for consistent differences between ChIP and control
9068 group or two ChIP groups run under different conditions.")
9069 (license license:gpl3+)))
9071 (define-public filevercmp
9072 (let ((commit "1a9b779b93d0b244040274794d402106907b71b7"))
9075 (version (string-append "0-1." (string-take commit 7)))
9078 (uri (string-append "https://github.com/ekg/filevercmp/archive/"
9080 (file-name (string-append name "-" version ".tar.gz"))
9082 (base32 "0yp5jswf5j2pqc6517x277s4s6h1ss99v57kxw9gy0jkfl3yh450"))))
9083 (build-system gnu-build-system)
9085 `(#:tests? #f ; There are no tests to run.
9087 (modify-phases %standard-phases
9088 (delete 'configure) ; There is no configure phase.
9090 (lambda* (#:key outputs #:allow-other-keys)
9091 (let ((bin (string-append (assoc-ref outputs "out") "/bin")))
9092 (install-file "filevercmp" bin)))))))
9093 (home-page "https://github.com/ekg/filevercmp")
9094 (synopsis "This program compares version strings")
9095 (description "This program compares version strings. It intends to be a
9096 replacement for strverscmp.")
9097 (license license:gpl3+))))
9099 (define-public multiqc
9106 (uri (pypi-uri "multiqc" version))
9109 "02iihfl0w0hpnr4pa0sbd1y9qxrg3ycyhjp5lidkcrqh1lmzs3zy"))))
9110 (build-system python-build-system)
9112 `(("python-jinja2" ,python-jinja2)
9113 ("python-simplejson" ,python-simplejson)
9114 ("python-pyyaml" ,python-pyyaml)
9115 ("python-click" ,python-click)
9116 ("python-spectra" ,python-spectra)
9117 ("python-requests" ,python-requests)
9118 ("python-markdown" ,python-markdown)
9119 ("python-lzstring" ,python-lzstring)
9120 ("python-matplotlib" ,python-matplotlib)
9121 ("python-numpy" ,python-numpy)
9122 ;; MultQC checks for the presence of nose at runtime.
9123 ("python-nose" ,python-nose)))
9126 (modify-phases %standard-phases
9127 (add-after 'unpack 'relax-requirements
9129 (substitute* "setup.py"
9130 ;; MultiQC 1.5 ‘requires’ a version of python-matplotlib older
9131 ;; than the one in Guix, but should work fine with 2.2.2.
9132 ;; See <https://github.com/ewels/MultiQC/issues/725> and
9133 ;; <https://github.com/ewels/MultiQC/issues/732> for details.
9134 (("['\"]matplotlib.*?['\"]")
9137 (home-page "http://multiqc.info")
9138 (synopsis "Aggregate bioinformatics analysis reports")
9140 "MultiQC is a tool to aggregate bioinformatics results across many
9141 samples into a single report. It contains modules for a large number of
9142 common bioinformatics tools.")
9143 (license license:gpl3+)))
9145 (define-public r-chipseq
9152 (uri (bioconductor-uri "chipseq" version))
9155 "1ymcq77krwjzrkzzcw7i9909cmkqa7c0675z9wzvrrk81hgdssfq"))))
9156 (build-system r-build-system)
9158 `(("r-biocgenerics" ,r-biocgenerics)
9159 ("r-genomicranges" ,r-genomicranges)
9160 ("r-iranges" ,r-iranges)
9161 ("r-lattice" ,r-lattice)
9162 ("r-s4vectors" ,r-s4vectors)
9163 ("r-shortread" ,r-shortread)))
9164 (home-page "https://bioconductor.org/packages/chipseq")
9165 (synopsis "Package for analyzing ChIPseq data")
9167 "This package provides tools for processing short read data from ChIPseq
9169 (license license:artistic2.0)))
9171 (define-public r-copyhelper
9173 (name "r-copyhelper")
9178 (uri (string-append "https://bioconductor.org/packages/release/"
9179 "data/experiment/src/contrib/CopyhelpeR_"
9183 "0x7cyynjmxls9as2gg0iyp9x5fpalxmdjq914ss7i84i9zyk5bhq"))))
9184 (properties `((upstream-name . "CopyhelpeR")))
9185 (build-system r-build-system)
9186 (home-page "https://bioconductor.org/packages/CopyhelpeR/")
9187 (synopsis "Helper files for CopywriteR")
9189 "This package contains the helper files that are required to run the
9190 Bioconductor package CopywriteR. It contains pre-assembled 1kb bin GC-content
9191 and mappability files for the reference genomes hg18, hg19, hg38, mm9 and
9192 mm10. In addition, it contains a blacklist filter to remove regions that
9193 display copy number variation. Files are stored as GRanges objects from the
9194 GenomicRanges Bioconductor package.")
9195 (license license:gpl2)))
9197 (define-public r-copywriter
9199 (name "r-copywriter")
9204 (uri (bioconductor-uri "CopywriteR" version))
9207 "17fy2lc5yf3nh6v077kv87h53n263hqz2540lzrl0vjiqrl2plca"))))
9208 (properties `((upstream-name . "CopywriteR")))
9209 (build-system r-build-system)
9211 `(("r-biocparallel" ,r-biocparallel)
9212 ("r-chipseq" ,r-chipseq)
9213 ("r-copyhelper" ,r-copyhelper)
9214 ("r-data-table" ,r-data-table)
9215 ("r-dnacopy" ,r-dnacopy)
9216 ("r-futile-logger" ,r-futile-logger)
9217 ("r-genomeinfodb" ,r-genomeinfodb)
9218 ("r-genomicalignments" ,r-genomicalignments)
9219 ("r-genomicranges" ,r-genomicranges)
9220 ("r-gtools" ,r-gtools)
9221 ("r-iranges" ,r-iranges)
9222 ("r-matrixstats" ,r-matrixstats)
9223 ("r-rsamtools" ,r-rsamtools)
9224 ("r-s4vectors" ,r-s4vectors)))
9225 (home-page "https://github.com/PeeperLab/CopywriteR")
9226 (synopsis "Copy number information from targeted sequencing")
9228 "CopywriteR extracts DNA copy number information from targeted sequencing
9229 by utilizing off-target reads. It allows for extracting uniformly distributed
9230 copy number information, can be used without reference, and can be applied to
9231 sequencing data obtained from various techniques including chromatin
9232 immunoprecipitation and target enrichment on small gene panels. Thereby,
9233 CopywriteR constitutes a widely applicable alternative to available copy
9234 number detection tools.")
9235 (license license:gpl2)))
9237 (define-public r-methylkit
9239 (name "r-methylkit")
9243 (uri (bioconductor-uri "methylKit" version))
9246 "1k0nfn9318sgwm4z963bhnbp4c3zv85v3f9886vc5hgaisr0yvai"))))
9247 (properties `((upstream-name . "methylKit")))
9248 (build-system r-build-system)
9250 `(("r-data-table" ,r-data-table)
9251 ("r-emdbook" ,r-emdbook)
9252 ("r-fastseg" ,r-fastseg)
9253 ("r-genomeinfodb" ,r-genomeinfodb)
9254 ("r-genomicranges" ,r-genomicranges)
9255 ("r-gtools" ,r-gtools)
9256 ("r-iranges" ,r-iranges)
9257 ("r-kernsmooth" ,r-kernsmooth)
9258 ("r-limma" ,r-limma)
9259 ("r-mclust" ,r-mclust)
9260 ("r-qvalue" ,r-qvalue)
9261 ("r-r-utils" ,r-r-utils)
9263 ("r-rhtslib" ,r-rhtslib)
9264 ("r-rsamtools" ,r-rsamtools)
9265 ("r-rtracklayer" ,r-rtracklayer)
9266 ("r-s4vectors" ,r-s4vectors)
9267 ("r-zlibbioc" ,r-zlibbioc)))
9270 (home-page "https://github.com/al2na/methylKit")
9272 "DNA methylation analysis from high-throughput bisulfite sequencing results")
9274 "MethylKit is an R package for DNA methylation analysis and annotation
9275 from high-throughput bisulfite sequencing. The package is designed to deal
9276 with sequencing data from @dfn{Reduced representation bisulfite
9277 sequencing} (RRBS) and its variants, but also target-capture methods and whole
9278 genome bisulfite sequencing. It also has functions to analyze base-pair
9279 resolution 5hmC data from experimental protocols such as oxBS-Seq and
9281 (license license:artistic2.0)))
9283 (define-public r-sva
9290 (uri (bioconductor-uri "sva" version))
9293 "0q5xb68wfcnchy8rkv5ma67pmz1i91lsnvmwmj8f1c3w4xan3pgw"))))
9294 (build-system r-build-system)
9296 `(("r-genefilter" ,r-genefilter)
9298 ("r-biocparallel" ,r-biocparallel)
9299 ("r-matrixstats" ,r-matrixstats)
9300 ("r-limma" ,r-limma)))
9301 (home-page "https://bioconductor.org/packages/sva")
9302 (synopsis "Surrogate variable analysis")
9304 "This package contains functions for removing batch effects and other
9305 unwanted variation in high-throughput experiment. It also contains functions
9306 for identifying and building surrogate variables for high-dimensional data
9307 sets. Surrogate variables are covariates constructed directly from
9308 high-dimensional data like gene expression/RNA sequencing/methylation/brain
9309 imaging data that can be used in subsequent analyses to adjust for unknown,
9310 unmodeled, or latent sources of noise.")
9311 (license license:artistic2.0)))
9313 (define-public r-seqminer
9320 (uri (cran-uri "seqminer" version))
9323 "057j1l6dip35l1aivilapl2zv9db677b3di2pb3sfgq2sxg0ps3l"))))
9324 (build-system r-build-system)
9327 (home-page "http://seqminer.genomic.codes")
9328 (synopsis "Read nucleotide sequence data (VCF, BCF, and METAL formats)")
9330 "This package provides tools to integrate nucleotide sequencing
9331 data (variant call format, e.g. VCF or BCF) or meta-analysis results in R.")
9332 ;; Any version of the GPL is acceptable
9333 (license (list license:gpl2+ license:gpl3+))))
9335 (define-public r-raremetals2
9337 (name "r-raremetals2")
9342 (uri (string-append "http://genome.sph.umich.edu/w/images/"
9343 "b/b7/RareMETALS2_" version ".tar.gz"))
9346 "0z5ljcgvnm06ja9lm85a3cniq7slxcy37aqqkxrdidr79an5fs4s"))))
9347 (properties `((upstream-name . "RareMETALS2")))
9348 (build-system r-build-system)
9350 `(("r-seqminer" ,r-seqminer)
9351 ("r-mvtnorm" ,r-mvtnorm)
9353 ("r-compquadform" ,r-compquadform)
9354 ("r-getopt" ,r-getopt)))
9355 (home-page "http://genome.sph.umich.edu/wiki/RareMETALS2")
9356 (synopsis "Analyze gene-level association tests for binary trait")
9358 "The R package rareMETALS2 is an extension of the R package rareMETALS.
9359 It was designed to meta-analyze gene-level association tests for binary trait.
9360 While rareMETALS offers a near-complete solution for meta-analysis of
9361 gene-level tests for quantitative trait, it does not offer the optimal
9362 solution for binary trait. The package rareMETALS2 offers improved features
9363 for analyzing gene-level association tests in meta-analyses for binary
9365 (license license:gpl3)))
9367 (define-public r-maldiquant
9369 (name "r-maldiquant")
9374 (uri (cran-uri "MALDIquant" version))
9377 "047s6007ydc38x8wm027mlb4mngz15n0d4238fr8h43wyll5zy0z"))))
9378 (properties `((upstream-name . "MALDIquant")))
9379 (build-system r-build-system)
9380 (home-page "https://cran.r-project.org/web/packages/MALDIquant")
9381 (synopsis "Quantitative analysis of mass spectrometry data")
9383 "This package provides a complete analysis pipeline for matrix-assisted
9384 laser desorption/ionization-time-of-flight (MALDI-TOF) and other
9385 two-dimensional mass spectrometry data. In addition to commonly used plotting
9386 and processing methods it includes distinctive features, namely baseline
9387 subtraction methods such as morphological filters (TopHat) or the
9388 statistics-sensitive non-linear iterative peak-clipping algorithm (SNIP), peak
9389 alignment using warping functions, handling of replicated measurements as well
9390 as allowing spectra with different resolutions.")
9391 (license license:gpl3+)))
9393 (define-public r-protgenerics
9395 (name "r-protgenerics")
9400 (uri (bioconductor-uri "ProtGenerics" version))
9403 "16ijp50448wnabp43klx943rhdvh7x45hvy7cnpq1s4dckxhhyni"))))
9404 (properties `((upstream-name . "ProtGenerics")))
9405 (build-system r-build-system)
9406 (home-page "https://github.com/lgatto/ProtGenerics")
9407 (synopsis "S4 generic functions for proteomics infrastructure")
9409 "This package provides S4 generic functions needed by Bioconductor
9410 proteomics packages.")
9411 (license license:artistic2.0)))
9413 (define-public r-mzr
9420 (uri (bioconductor-uri "mzR" version))
9423 "1x3gp30sfxz2v3k3swih9kff9b2rvk7hzhnlkp6ywlnn2wgb0q8c"))
9424 (modules '((guix build utils)))
9427 (delete-file-recursively "src/boost")
9429 (properties `((upstream-name . "mzR")))
9430 (build-system r-build-system)
9433 (modify-phases %standard-phases
9434 (add-after 'unpack 'use-system-boost
9436 (substitute* "src/Makevars"
9437 (("\\./boost/libs.*") "")
9438 (("ARCH_OBJS=" line)
9440 "\nARCH_LIBS=-lboost_system -lboost_regex \
9441 -lboost_iostreams -lboost_thread -lboost_filesystem -lboost_chrono\n")))
9444 `(("boost" ,boost) ; use this instead of the bundled boost sources
9445 ("netcdf" ,netcdf)))
9447 `(("r-biobase" ,r-biobase)
9448 ("r-biocgenerics" ,r-biocgenerics)
9449 ("r-protgenerics" ,r-protgenerics)
9451 ("r-zlibbioc" ,r-zlibbioc)))
9452 (home-page "https://github.com/sneumann/mzR/")
9453 (synopsis "Parser for mass spectrometry data files")
9455 "The mzR package provides a unified API to the common file formats and
9456 parsers available for mass spectrometry data. It comes with a wrapper for the
9457 ISB random access parser for mass spectrometry mzXML, mzData and mzML files.
9458 The package contains the original code written by the ISB, and a subset of the
9459 proteowizard library for mzML and mzIdentML. The netCDF reading code has
9460 previously been used in XCMS.")
9461 (license license:artistic2.0)))
9463 (define-public r-affyio
9470 (uri (bioconductor-uri "affyio" version))
9473 "1pzzp3d3dbmyf34gvivfiprkpscn36rgvhrq853a1d3avcwr5ak9"))))
9474 (build-system r-build-system)
9476 `(("r-zlibbioc" ,r-zlibbioc)))
9479 (home-page "https://github.com/bmbolstad/affyio")
9480 (synopsis "Tools for parsing Affymetrix data files")
9482 "This package provides routines for parsing Affymetrix data files based
9483 upon file format information. The primary focus is on accessing the CEL and
9485 (license license:lgpl2.0+)))
9487 (define-public r-affy
9494 (uri (bioconductor-uri "affy" version))
9497 "0jmbkimma5ffsdkk3xp03g4lpz84gd95nkqakif2nqq6wmx0syrj"))))
9498 (build-system r-build-system)
9500 `(("r-affyio" ,r-affyio)
9501 ("r-biobase" ,r-biobase)
9502 ("r-biocgenerics" ,r-biocgenerics)
9503 ("r-biocinstaller" ,r-biocinstaller)
9504 ("r-preprocesscore" ,r-preprocesscore)
9505 ("r-zlibbioc" ,r-zlibbioc)))
9506 (home-page "https://bioconductor.org/packages/affy")
9507 (synopsis "Methods for affymetrix oligonucleotide arrays")
9509 "This package contains functions for exploratory oligonucleotide array
9511 (license license:lgpl2.0+)))
9513 (define-public r-vsn
9520 (uri (bioconductor-uri "vsn" version))
9523 "18y62phzirj75gg6v5l41jwybmk23ia6w7qhch0kxc4bl2rysw6j"))))
9524 (build-system r-build-system)
9526 `(("r-affy" ,r-affy)
9527 ("r-biobase" ,r-biobase)
9528 ("r-ggplot2" ,r-ggplot2)
9529 ("r-lattice" ,r-lattice)
9530 ("r-limma" ,r-limma)))
9531 (home-page "https://bioconductor.org/packages/release/bioc/html/vsn.html")
9532 (synopsis "Variance stabilization and calibration for microarray data")
9534 "The package implements a method for normalising microarray intensities,
9535 and works for single- and multiple-color arrays. It can also be used for data
9536 from other technologies, as long as they have similar format. The method uses
9537 a robust variant of the maximum-likelihood estimator for an
9538 additive-multiplicative error model and affine calibration. The model
9539 incorporates data calibration step (a.k.a. normalization), a model for the
9540 dependence of the variance on the mean intensity and a variance stabilizing
9541 data transformation. Differences between transformed intensities are
9542 analogous to \"normalized log-ratios\". However, in contrast to the latter,
9543 their variance is independent of the mean, and they are usually more sensitive
9544 and specific in detecting differential transcription.")
9545 (license license:artistic2.0)))
9547 (define-public r-mzid
9554 (uri (bioconductor-uri "mzID" version))
9557 "0yk70dka56zd8w62f03ggx3mandj91gfa767h9ajj0sd3mjmfqb9"))))
9558 (properties `((upstream-name . "mzID")))
9559 (build-system r-build-system)
9561 `(("r-doparallel" ,r-doparallel)
9562 ("r-foreach" ,r-foreach)
9563 ("r-iterators" ,r-iterators)
9565 ("r-protgenerics" ,r-protgenerics)
9568 (home-page "https://bioconductor.org/packages/mzID")
9569 (synopsis "Parser for mzIdentML files")
9571 "This package provides a parser for mzIdentML files implemented using the
9572 XML package. The parser tries to be general and able to handle all types of
9573 mzIdentML files with the drawback of having less pretty output than a vendor
9575 (license license:gpl2+)))
9577 (define-public r-pcamethods
9579 (name "r-pcamethods")
9584 (uri (bioconductor-uri "pcaMethods" version))
9587 "0ii235g0x0492kh8cfrf28ni0b6vd6fh7kizkqmczzqggd6b1bk8"))))
9588 (properties `((upstream-name . "pcaMethods")))
9589 (build-system r-build-system)
9591 `(("r-biobase" ,r-biobase)
9592 ("r-biocgenerics" ,r-biocgenerics)
9594 ("r-rcpp" ,r-rcpp)))
9595 (home-page "https://github.com/hredestig/pcamethods")
9596 (synopsis "Collection of PCA methods")
9598 "This package provides Bayesian PCA, Probabilistic PCA, Nipals PCA,
9599 Inverse Non-Linear PCA and the conventional SVD PCA. A cluster based method
9600 for missing value estimation is included for comparison. BPCA, PPCA and
9601 NipalsPCA may be used to perform PCA on incomplete data as well as for
9602 accurate missing value estimation. A set of methods for printing and plotting
9603 the results is also provided. All PCA methods make use of the same data
9604 structure (pcaRes) to provide a common interface to the PCA results.")
9605 (license license:gpl3+)))
9607 (define-public r-msnbase
9614 (uri (bioconductor-uri "MSnbase" version))
9617 "1ig64bf881p118dwqfr0ry41m7yhnyv165smv8fdwfv7sb6sagif"))))
9618 (properties `((upstream-name . "MSnbase")))
9619 (build-system r-build-system)
9621 `(("r-affy" ,r-affy)
9622 ("r-biobase" ,r-biobase)
9623 ("r-biocgenerics" ,r-biocgenerics)
9624 ("r-biocparallel" ,r-biocparallel)
9625 ("r-digest" ,r-digest)
9626 ("r-ggplot2" ,r-ggplot2)
9627 ("r-impute" ,r-impute)
9628 ("r-iranges" ,r-iranges)
9629 ("r-lattice" ,r-lattice)
9630 ("r-maldiquant" ,r-maldiquant)
9633 ("r-pcamethods" ,r-pcamethods)
9635 ("r-preprocesscore" ,r-preprocesscore)
9636 ("r-protgenerics" ,r-protgenerics)
9638 ("r-s4vectors" ,r-s4vectors)
9641 (home-page "https://github.com/lgatto/MSnbase")
9642 (synopsis "Base functions and classes for MS-based proteomics")
9644 "This package provides basic plotting, data manipulation and processing
9645 of mass spectrometry based proteomics data.")
9646 (license license:artistic2.0)))
9648 (define-public r-msnid
9655 (uri (bioconductor-uri "MSnID" version))
9658 "1zw508kk4f8brg69674wp18gqkpx2kpya5f6x9cl3qng7v4h5pxx"))))
9659 (properties `((upstream-name . "MSnID")))
9660 (build-system r-build-system)
9662 `(("r-biobase" ,r-biobase)
9663 ("r-data-table" ,r-data-table)
9664 ("r-doparallel" ,r-doparallel)
9665 ("r-dplyr" ,r-dplyr)
9666 ("r-foreach" ,r-foreach)
9667 ("r-iterators" ,r-iterators)
9668 ("r-msnbase" ,r-msnbase)
9671 ("r-protgenerics" ,r-protgenerics)
9672 ("r-r-cache" ,r-r-cache)
9674 ("r-reshape2" ,r-reshape2)))
9675 (home-page "https://bioconductor.org/packages/MSnID")
9676 (synopsis "Utilities for LC-MSn proteomics identifications")
9678 "This package extracts @dfn{tandem mass spectrometry} (MS/MS) ID data
9679 from mzIdentML (leveraging the mzID package) or text files. After collating
9680 the search results from multiple datasets it assesses their identification
9681 quality and optimize filtering criteria to achieve the maximum number of
9682 identifications while not exceeding a specified false discovery rate. It also
9683 contains a number of utilities to explore the MS/MS results and assess missed
9684 and irregular enzymatic cleavages, mass measurement accuracy, etc.")
9685 (license license:artistic2.0)))
9687 (define-public r-seurat
9693 (uri (cran-uri "Seurat" version))
9696 "0hi59rgdrr2iqfvx5bq7yq02hbjxkjl1fzidqj14z0ypq0nzbjys"))
9697 ;; Delete pre-built jar.
9699 '(begin (delete-file "inst/java/ModularityOptimizer.jar")
9701 (properties `((upstream-name . "Seurat")))
9702 (build-system r-build-system)
9705 (modify-phases %standard-phases
9706 (add-after 'unpack 'build-jar
9707 (lambda* (#:key inputs #:allow-other-keys)
9708 (let ((classesdir "tmp-classes"))
9709 (setenv "JAVA_HOME" (assoc-ref inputs "jdk"))
9711 (with-output-to-file "manifest"
9713 (display "Manifest-Version: 1.0
9714 Main-Class: ModularityOptimizer\n")))
9715 (and (zero? (apply system* `("javac" "-d" ,classesdir
9716 ,@(find-files "java" "\\.java$"))))
9717 (zero? (system* "jar"
9719 "inst/java/ModularityOptimizer.jar"
9720 "-C" classesdir ".")))))))))
9722 `(("jdk" ,icedtea "jdk")))
9725 ("r-caret" ,r-caret)
9726 ("r-cluster" ,r-cluster)
9727 ("r-cowplot" ,r-cowplot)
9728 ("r-diffusionmap" ,r-diffusionmap)
9729 ("r-dosnow" ,r-dosnow)
9730 ("r-dplyr" ,r-dplyr)
9732 ("r-fitdistrplus" ,r-fitdistrplus)
9734 ("r-foreach" ,r-foreach)
9736 ("r-gdata" ,r-gdata)
9737 ("r-ggplot2" ,r-ggplot2)
9738 ("r-ggridges" ,r-ggridges)
9739 ("r-gplots" ,r-gplots)
9740 ("r-hmisc" ,r-hmisc)
9742 ("r-igraph" ,r-igraph)
9743 ("r-irlba" ,r-irlba)
9745 ("r-lmtest" ,r-lmtest)
9747 ("r-matrix" ,r-matrix)
9748 ("r-metap" ,r-metap)
9749 ("r-mixtools" ,r-mixtools)
9750 ("r-pbapply" ,r-pbapply)
9751 ("r-plotly" ,r-plotly)
9753 ("r-ranger" ,r-ranger)
9755 ("r-rcolorbrewer" ,r-rcolorbrewer)
9757 ("r-rcppeigen" ,r-rcppeigen)
9758 ("r-rcppprogress" ,r-rcppprogress)
9759 ("r-reshape2" ,r-reshape2)
9760 ("r-reticulate" ,r-reticulate)
9762 ("r-rtsne" ,r-rtsne)
9763 ("r-sdmtools" ,r-sdmtools)
9764 ("r-stringr" ,r-stringr)
9765 ("r-tclust" ,r-tclust)
9766 ("r-tidyr" ,r-tidyr)
9768 ("r-vgam" ,r-vgam)))
9769 (home-page "http://www.satijalab.org/seurat")
9770 (synopsis "Seurat is an R toolkit for single cell genomics")
9772 "This package is an R package designed for QC, analysis, and
9773 exploration of single cell RNA-seq data. It easily enables widely-used
9774 analytical techniques, including the identification of highly variable genes,
9775 dimensionality reduction; PCA, ICA, t-SNE, standard unsupervised clustering
9776 algorithms; density clustering, hierarchical clustering, k-means, and the
9777 discovery of differentially expressed genes and markers.")
9778 (license license:gpl3)))
9780 (define-public r-aroma-light
9782 (name "r-aroma-light")
9787 (uri (bioconductor-uri "aroma.light" version))
9790 "0crnk6851jwypqr5l5jcbbay0vi5vvdjyisaf6z2d69c39wmr6sc"))))
9791 (properties `((upstream-name . "aroma.light")))
9792 (build-system r-build-system)
9794 `(("r-matrixstats" ,r-matrixstats)
9795 ("r-r-methodss3" ,r-r-methodss3)
9797 ("r-r-utils" ,r-r-utils)))
9798 (home-page "https://github.com/HenrikBengtsson/aroma.light")
9799 (synopsis "Methods for normalization and visualization of microarray data")
9801 "This package provides methods for microarray analysis that take basic
9802 data types such as matrices and lists of vectors. These methods can be used
9803 standalone, be utilized in other packages, or be wrapped up in higher-level
9805 (license license:gpl2+)))
9807 (define-public r-deseq
9814 (uri (bioconductor-uri "DESeq" version))
9817 "0mn5w3cy16iwwk8zxs7za6aa6cnrca75z0g45zd5zh1py5d7nfv9"))))
9818 (properties `((upstream-name . "DESeq")))
9819 (build-system r-build-system)
9821 `(("r-biobase" ,r-biobase)
9822 ("r-biocgenerics" ,r-biocgenerics)
9823 ("r-genefilter" ,r-genefilter)
9824 ("r-geneplotter" ,r-geneplotter)
9825 ("r-lattice" ,r-lattice)
9826 ("r-locfit" ,r-locfit)
9828 ("r-rcolorbrewer" ,r-rcolorbrewer)))
9829 (home-page "http://www-huber.embl.de/users/anders/DESeq")
9830 (synopsis "Differential gene expression analysis")
9832 "This package provides tools for estimating variance-mean dependence in
9833 count data from high-throughput genetic sequencing assays and for testing for
9834 differential expression based on a model using the negative binomial
9836 (license license:gpl3+)))
9838 (define-public r-edaseq
9845 (uri (bioconductor-uri "EDASeq" version))
9848 "07zm89zcivyn2261aq9grqmly8ji482kr9h9dyfknfdfrpv7jpwv"))))
9849 (properties `((upstream-name . "EDASeq")))
9850 (build-system r-build-system)
9852 `(("r-annotationdbi" ,r-annotationdbi)
9853 ("r-aroma-light" ,r-aroma-light)
9854 ("r-biobase" ,r-biobase)
9855 ("r-biocgenerics" ,r-biocgenerics)
9856 ("r-biomart" ,r-biomart)
9857 ("r-biostrings" ,r-biostrings)
9858 ("r-deseq" ,r-deseq)
9859 ("r-genomicfeatures" ,r-genomicfeatures)
9860 ("r-genomicranges" ,r-genomicranges)
9861 ("r-iranges" ,r-iranges)
9862 ("r-rsamtools" ,r-rsamtools)
9863 ("r-shortread" ,r-shortread)))
9864 (home-page "https://github.com/drisso/EDASeq")
9865 (synopsis "Exploratory data analysis and normalization for RNA-Seq")
9867 "This package provides support for numerical and graphical summaries of
9868 RNA-Seq genomic read data. Provided within-lane normalization procedures to
9869 adjust for GC-content effect (or other gene-level effects) on read counts:
9870 loess robust local regression, global-scaling, and full-quantile
9871 normalization. Between-lane normalization procedures to adjust for
9872 distributional differences between lanes (e.g., sequencing depth):
9873 global-scaling and full-quantile normalization.")
9874 (license license:artistic2.0)))
9876 (define-public r-interactivedisplaybase
9878 (name "r-interactivedisplaybase")
9883 (uri (bioconductor-uri "interactiveDisplayBase" version))
9886 "01yb945jqqimwjgriza6yy4dnp303cdirxrhl4hjyprfdlmnz5p5"))))
9888 `((upstream-name . "interactiveDisplayBase")))
9889 (build-system r-build-system)
9891 `(("r-biocgenerics" ,r-biocgenerics)
9892 ("r-shiny" ,r-shiny)))
9893 (home-page "https://bioconductor.org/packages/interactiveDisplayBase")
9894 (synopsis "Base package for web displays of Bioconductor objects")
9896 "This package contains the basic methods needed to generate interactive
9897 Shiny-based display methods for Bioconductor objects.")
9898 (license license:artistic2.0)))
9900 (define-public r-annotationhub
9902 (name "r-annotationhub")
9907 (uri (bioconductor-uri "AnnotationHub" version))
9910 "14v8g44a6zg9j2rwn9x9y8509k0wr2cw8yccliz24glplb40wva4"))))
9911 (properties `((upstream-name . "AnnotationHub")))
9912 (build-system r-build-system)
9914 `(("r-annotationdbi" ,r-annotationdbi)
9915 ("r-biocgenerics" ,r-biocgenerics)
9916 ("r-biocinstaller" ,r-biocinstaller)
9919 ("r-interactivedisplaybase" ,r-interactivedisplaybase)
9920 ("r-rsqlite" ,r-rsqlite)
9921 ("r-s4vectors" ,r-s4vectors)
9922 ("r-yaml" ,r-yaml)))
9923 (home-page "https://bioconductor.org/packages/AnnotationHub")
9924 (synopsis "Client to access AnnotationHub resources")
9926 "This package provides a client for the Bioconductor AnnotationHub web
9927 resource. The AnnotationHub web resource provides a central location where
9928 genomic files (e.g. VCF, bed, wig) and other resources from standard
9929 locations (e.g. UCSC, Ensembl) can be discovered. The resource includes
9930 metadata about each resource, e.g., a textual description, tags, and date of
9931 modification. The client creates and manages a local cache of files retrieved
9932 by the user, helping with quick and reproducible access.")
9933 (license license:artistic2.0)))
9935 (define-public r-fastseg
9942 (uri (bioconductor-uri "fastseg" version))
9945 "0dd7nr3klwz9ailwshnbynhd62lwb8zbbpj6jf3igpb94yi6x2jp"))))
9946 (build-system r-build-system)
9948 `(("r-biobase" ,r-biobase)
9949 ("r-biocgenerics" ,r-biocgenerics)
9950 ("r-genomicranges" ,r-genomicranges)
9951 ("r-iranges" ,r-iranges)
9952 ("r-s4vectors" ,r-s4vectors)))
9953 (home-page "http://www.bioinf.jku.at/software/fastseg/index.html")
9954 (synopsis "Fast segmentation algorithm for genetic sequencing data")
9956 "Fastseg implements a very fast and efficient segmentation algorithm.
9957 It can segment data from DNA microarrays and data from next generation
9958 sequencing for example to detect copy number segments. Further it can segment
9959 data from RNA microarrays like tiling arrays to identify transcripts. Most
9960 generally, it can segment data given as a matrix or as a vector. Various data
9961 formats can be used as input to fastseg like expression set objects for
9962 microarrays or GRanges for sequencing data.")
9963 (license license:lgpl2.0+)))
9965 (define-public r-keggrest
9972 (uri (bioconductor-uri "KEGGREST" version))
9975 "02gwmm79djj55a90dzc80hlgwc6bafl7xd7fnx2q59pk945k3z9c"))))
9976 (properties `((upstream-name . "KEGGREST")))
9977 (build-system r-build-system)
9979 `(("r-biostrings" ,r-biostrings)
9982 (home-page "https://bioconductor.org/packages/KEGGREST")
9983 (synopsis "Client-side REST access to KEGG")
9985 "This package provides a package that provides a client interface to the
9986 @dfn{Kyoto Encyclopedia of Genes and Genomes} (KEGG) REST server.")
9987 (license license:artistic2.0)))
9989 (define-public r-gage
9996 (uri (bioconductor-uri "gage" version))
9999 "0h0mlhns9j7cpfksvdlvx9jb7szm3r1dwqb3s4s8p8hmkb9byyii"))))
10000 (build-system r-build-system)
10002 `(("r-annotationdbi" ,r-annotationdbi)
10003 ("r-graph" ,r-graph)
10004 ("r-keggrest" ,r-keggrest)))
10005 (home-page "http://www.biomedcentral.com/1471-2105/10/161")
10006 (synopsis "Generally applicable gene-set enrichment for pathway analysis")
10008 "GAGE is a published method for gene set (enrichment or GSEA) or pathway
10009 analysis. GAGE is generally applicable independent of microarray or RNA-Seq
10010 data attributes including sample sizes, experimental designs, assay platforms,
10011 and other types of heterogeneity. The gage package provides functions for
10012 basic GAGE analysis, result processing and presentation. In addition, it
10013 provides demo microarray data and commonly used gene set data based on KEGG
10014 pathways and GO terms. These funtions and data are also useful for gene set
10015 analysis using other methods.")
10016 (license license:gpl2+)))
10018 (define-public r-genomicfiles
10020 (name "r-genomicfiles")
10025 (uri (bioconductor-uri "GenomicFiles" version))
10028 "0r0wmrs5jycf1kckhnc2sgjmp336srlcjdkpbb1ymm7kazdd0s9n"))))
10029 (properties `((upstream-name . "GenomicFiles")))
10030 (build-system r-build-system)
10032 `(("r-biocgenerics" ,r-biocgenerics)
10033 ("r-biocparallel" ,r-biocparallel)
10034 ("r-genomeinfodb" ,r-genomeinfodb)
10035 ("r-genomicalignments" ,r-genomicalignments)
10036 ("r-genomicranges" ,r-genomicranges)
10037 ("r-iranges" ,r-iranges)
10038 ("r-rsamtools" ,r-rsamtools)
10039 ("r-rtracklayer" ,r-rtracklayer)
10040 ("r-s4vectors" ,r-s4vectors)
10041 ("r-summarizedexperiment" ,r-summarizedexperiment)
10042 ("r-variantannotation" ,r-variantannotation)))
10043 (home-page "https://bioconductor.org/packages/GenomicFiles")
10044 (synopsis "Distributed computing by file or by range")
10046 "This package provides infrastructure for parallel computations
10047 distributed by file or by range. User defined mapper and reducer functions
10048 provide added flexibility for data combination and manipulation.")
10049 (license license:artistic2.0)))
10051 (define-public r-complexheatmap
10053 (name "r-complexheatmap")
10058 (uri (bioconductor-uri "ComplexHeatmap" version))
10061 "1x6kp55iqqsd8bhdl3qch95nfiy2y46ldbbsx1sj1v8f0b0ywwcy"))))
10063 `((upstream-name . "ComplexHeatmap")))
10064 (build-system r-build-system)
10066 `(("r-circlize" ,r-circlize)
10067 ("r-colorspace" ,r-colorspace)
10068 ("r-getoptlong" ,r-getoptlong)
10069 ("r-globaloptions" ,r-globaloptions)
10070 ("r-rcolorbrewer" ,r-rcolorbrewer)))
10072 "https://github.com/jokergoo/ComplexHeatmap")
10073 (synopsis "Making Complex Heatmaps")
10075 "Complex heatmaps are efficient to visualize associations between
10076 different sources of data sets and reveal potential structures. This package
10077 provides a highly flexible way to arrange multiple heatmaps and supports
10078 self-defined annotation graphics.")
10079 (license license:gpl2+)))
10081 (define-public r-dirichletmultinomial
10083 (name "r-dirichletmultinomial")
10088 (uri (bioconductor-uri "DirichletMultinomial" version))
10091 "1c4s6x0qm20556grcd1xys9kkpnlzpasaai474malwcg6qvgi4x1"))))
10093 `((upstream-name . "DirichletMultinomial")))
10094 (build-system r-build-system)
10098 `(("r-biocgenerics" ,r-biocgenerics)
10099 ("r-iranges" ,r-iranges)
10100 ("r-s4vectors" ,r-s4vectors)))
10101 (home-page "https://bioconductor.org/packages/DirichletMultinomial")
10102 (synopsis "Dirichlet-Multinomial mixture models for microbiome data")
10104 "Dirichlet-multinomial mixture models can be used to describe variability
10105 in microbial metagenomic data. This package is an interface to code
10106 originally made available by Holmes, Harris, and Quince, 2012, PLoS ONE 7(2):
10108 (license license:lgpl3)))
10110 (define-public r-ensembldb
10112 (name "r-ensembldb")
10117 (uri (bioconductor-uri "ensembldb" version))
10120 "1yngndkf3588z91z0a2fvkg423p26ajm6xv1p27x0l9mzhhaqq3k"))))
10121 (build-system r-build-system)
10123 `(("r-annotationdbi" ,r-annotationdbi)
10124 ("r-annotationfilter" ,r-annotationfilter)
10125 ("r-annotationhub" ,r-annotationhub)
10126 ("r-biobase" ,r-biobase)
10127 ("r-biocgenerics" ,r-biocgenerics)
10128 ("r-biostrings" ,r-biostrings)
10131 ("r-genomeinfodb" ,r-genomeinfodb)
10132 ("r-genomicfeatures" ,r-genomicfeatures)
10133 ("r-genomicranges" ,r-genomicranges)
10134 ("r-iranges" ,r-iranges)
10135 ("r-protgenerics" ,r-protgenerics)
10136 ("r-rsamtools" ,r-rsamtools)
10137 ("r-rsqlite" ,r-rsqlite)
10138 ("r-rtracklayer" ,r-rtracklayer)
10139 ("r-s4vectors" ,r-s4vectors)))
10140 (home-page "https://github.com/jotsetung/ensembldb")
10141 (synopsis "Utilities to create and use Ensembl-based annotation databases")
10143 "The package provides functions to create and use transcript-centric
10144 annotation databases/packages. The annotation for the databases are directly
10145 fetched from Ensembl using their Perl API. The functionality and data is
10146 similar to that of the TxDb packages from the @code{GenomicFeatures} package,
10147 but, in addition to retrieve all gene/transcript models and annotations from
10148 the database, the @code{ensembldb} package also provides a filter framework
10149 allowing to retrieve annotations for specific entries like genes encoded on a
10150 chromosome region or transcript models of lincRNA genes.")
10151 ;; No version specified
10152 (license license:lgpl3+)))
10154 (define-public r-organismdbi
10156 (name "r-organismdbi")
10161 (uri (bioconductor-uri "OrganismDbi" version))
10164 "0yxvhwn0m53wfwp0zi81x96argdf7cf1lpymc2as51apvfcnjdl8"))))
10165 (properties `((upstream-name . "OrganismDbi")))
10166 (build-system r-build-system)
10168 `(("r-annotationdbi" ,r-annotationdbi)
10169 ("r-biobase" ,r-biobase)
10170 ("r-biocgenerics" ,r-biocgenerics)
10171 ("r-biocinstaller" ,r-biocinstaller)
10173 ("r-genomicfeatures" ,r-genomicfeatures)
10174 ("r-genomicranges" ,r-genomicranges)
10175 ("r-graph" ,r-graph)
10176 ("r-iranges" ,r-iranges)
10178 ("r-s4vectors" ,r-s4vectors)))
10179 (home-page "https://bioconductor.org/packages/OrganismDbi")
10180 (synopsis "Software to enable the smooth interfacing of database packages")
10181 (description "The package enables a simple unified interface to several
10182 annotation packages each of which has its own schema by taking advantage of
10183 the fact that each of these packages implements a select methods.")
10184 (license license:artistic2.0)))
10186 (define-public r-biovizbase
10188 (name "r-biovizbase")
10193 (uri (bioconductor-uri "biovizBase" version))
10196 "14l4vhj0a4ssr9m9zdzz3qpd4qw1mhgq5bmxq7jhrq3j9kmd6i2f"))))
10197 (properties `((upstream-name . "biovizBase")))
10198 (build-system r-build-system)
10200 `(("r-annotationdbi" ,r-annotationdbi)
10201 ("r-annotationfilter" ,r-annotationfilter)
10202 ("r-biocgenerics" ,r-biocgenerics)
10203 ("r-biostrings" ,r-biostrings)
10204 ("r-dichromat" ,r-dichromat)
10205 ("r-ensembldb" ,r-ensembldb)
10206 ("r-genomeinfodb" ,r-genomeinfodb)
10207 ("r-genomicalignments" ,r-genomicalignments)
10208 ("r-genomicfeatures" ,r-genomicfeatures)
10209 ("r-genomicranges" ,r-genomicranges)
10210 ("r-hmisc" ,r-hmisc)
10211 ("r-iranges" ,r-iranges)
10212 ("r-rcolorbrewer" ,r-rcolorbrewer)
10213 ("r-rsamtools" ,r-rsamtools)
10214 ("r-s4vectors" ,r-s4vectors)
10215 ("r-scales" ,r-scales)
10216 ("r-summarizedexperiment" ,r-summarizedexperiment)
10217 ("r-variantannotation" ,r-variantannotation)))
10218 (home-page "https://bioconductor.org/packages/biovizBase")
10219 (synopsis "Basic graphic utilities for visualization of genomic data")
10221 "The biovizBase package is designed to provide a set of utilities, color
10222 schemes and conventions for genomic data. It serves as the base for various
10223 high-level packages for biological data visualization. This saves development
10224 effort and encourages consistency.")
10225 (license license:artistic2.0)))
10227 (define-public r-ggbio
10234 (uri (bioconductor-uri "ggbio" version))
10237 "1xlmlngn27iwnr21s9di4059kav1a7c1sajx08wja8yn8f7j06hp"))))
10238 (build-system r-build-system)
10240 `(("r-annotationdbi" ,r-annotationdbi)
10241 ("r-annotationfilter" ,r-annotationfilter)
10242 ("r-biobase" ,r-biobase)
10243 ("r-biocgenerics" ,r-biocgenerics)
10244 ("r-biostrings" ,r-biostrings)
10245 ("r-biovizbase" ,r-biovizbase)
10246 ("r-bsgenome" ,r-bsgenome)
10247 ("r-ensembldb" ,r-ensembldb)
10248 ("r-genomeinfodb" ,r-genomeinfodb)
10249 ("r-genomicalignments" ,r-genomicalignments)
10250 ("r-genomicfeatures" ,r-genomicfeatures)
10251 ("r-genomicranges" ,r-genomicranges)
10252 ("r-ggally" ,r-ggally)
10253 ("r-ggplot2" ,r-ggplot2)
10254 ("r-gridextra" ,r-gridextra)
10255 ("r-gtable" ,r-gtable)
10256 ("r-hmisc" ,r-hmisc)
10257 ("r-iranges" ,r-iranges)
10258 ("r-organismdbi" ,r-organismdbi)
10259 ("r-reshape2" ,r-reshape2)
10260 ("r-rsamtools" ,r-rsamtools)
10261 ("r-rtracklayer" ,r-rtracklayer)
10262 ("r-s4vectors" ,r-s4vectors)
10263 ("r-scales" ,r-scales)
10264 ("r-summarizedexperiment" ,r-summarizedexperiment)
10265 ("r-variantannotation" ,r-variantannotation)))
10266 (home-page "http://www.tengfei.name/ggbio/")
10267 (synopsis "Visualization tools for genomic data")
10269 "The ggbio package extends and specializes the grammar of graphics for
10270 biological data. The graphics are designed to answer common scientific
10271 questions, in particular those often asked of high throughput genomics data.
10272 All core Bioconductor data structures are supported, where appropriate. The
10273 package supports detailed views of particular genomic regions, as well as
10274 genome-wide overviews. Supported overviews include ideograms and grand linear
10275 views. High-level plots include sequence fragment length, edge-linked
10276 interval to data view, mismatch pileup, and several splicing summaries.")
10277 (license license:artistic2.0)))
10279 (define-public r-gprofiler
10281 (name "r-gprofiler")
10286 (uri (cran-uri "gProfileR" version))
10289 "1n6cj12j102b4x9vhyl4dljp1i0r43p23cnhqbx4als2xfxdlqgi"))))
10290 (properties `((upstream-name . "gProfileR")))
10291 (build-system r-build-system)
10293 `(("r-plyr" ,r-plyr)
10294 ("r-rcurl" ,r-rcurl)))
10295 (home-page "https://cran.r-project.org/web/packages/gProfileR/")
10296 (synopsis "Interface to the g:Profiler toolkit")
10298 "This package provides tools for functional enrichment analysis,
10299 gene identifier conversion and mapping homologous genes across related
10300 organisms via the @code{g:Profiler} toolkit.")
10301 (license license:gpl2+)))
10303 (define-public r-gqtlbase
10305 (name "r-gqtlbase")
10310 (uri (bioconductor-uri "gQTLBase" version))
10313 "1756vfcj2dkkgcmfkkg7qdaig36dv9gfvpypn9rbrky56wm1p035"))))
10314 (properties `((upstream-name . "gQTLBase")))
10315 (build-system r-build-system)
10317 `(("r-batchjobs" ,r-batchjobs)
10318 ("r-bbmisc" ,r-bbmisc)
10319 ("r-biocgenerics" ,r-biocgenerics)
10321 ("r-doparallel" ,r-doparallel)
10323 ("r-ffbase" ,r-ffbase)
10324 ("r-foreach" ,r-foreach)
10325 ("r-genomicfiles" ,r-genomicfiles)
10326 ("r-genomicranges" ,r-genomicranges)
10327 ("r-rtracklayer" ,r-rtracklayer)
10328 ("r-s4vectors" ,r-s4vectors)
10329 ("r-summarizedexperiment" ,r-summarizedexperiment)))
10330 (home-page "https://bioconductor.org/packages/gQTLBase")
10331 (synopsis "Infrastructure for eQTL, mQTL and similar studies")
10333 "The purpose of this package is to simplify the storage and interrogation
10334 of @dfn{quantitative trait loci} (QTL) archives, such as eQTL, mQTL, dsQTL,
10336 (license license:artistic2.0)))
10338 (define-public r-snpstats
10340 (name "r-snpstats")
10345 (uri (bioconductor-uri "snpStats" version))
10348 "1x9qwynh2hwl24vq02naf4mchpch7xi2pkdrlgw896k28kx0lvir"))))
10349 (properties `((upstream-name . "snpStats")))
10350 (build-system r-build-system)
10351 (inputs `(("zlib" ,zlib)))
10353 `(("r-biocgenerics" ,r-biocgenerics)
10354 ("r-matrix" ,r-matrix)
10355 ("r-survival" ,r-survival)
10356 ("r-zlibbioc" ,r-zlibbioc)))
10357 (home-page "https://bioconductor.org/packages/snpStats")
10358 (synopsis "Methods for SNP association studies")
10360 "This package provides classes and statistical methods for large
10361 @dfn{single-nucleotide polymorphism} (SNP) association studies. This extends
10362 the earlier snpMatrix package, allowing for uncertainty in genotypes.")
10363 (license license:gpl3)))
10365 (define-public r-homo-sapiens
10367 (name "r-homo-sapiens")
10371 ;; We cannot use bioconductor-uri here because this tarball is
10372 ;; located under "data/annotation/" instead of "bioc/".
10373 (uri (string-append "http://www.bioconductor.org/packages/"
10374 "release/data/annotation/src/contrib/"
10376 version ".tar.gz"))
10379 "151vj7h5p1c8yd5swrchk46z469p135wk50hvkl0nhgndvy0jj01"))))
10381 `((upstream-name . "Homo.sapiens")))
10382 (build-system r-build-system)
10384 `(("r-genomicfeatures" ,r-genomicfeatures)
10385 ("r-go-db" ,r-go-db)
10386 ("r-org-hs-eg-db" ,r-org-hs-eg-db)
10387 ("r-txdb-hsapiens-ucsc-hg19-knowngene" ,r-txdb-hsapiens-ucsc-hg19-knowngene)
10388 ("r-organismdbi" ,r-organismdbi)
10389 ("r-annotationdbi" ,r-annotationdbi)))
10390 (home-page "https://bioconductor.org/packages/Homo.sapiens/")
10391 (synopsis "Annotation package for the Homo.sapiens object")
10393 "This package contains the Homo.sapiens object to access data from
10394 several related annotation packages.")
10395 (license license:artistic2.0)))
10397 (define-public r-erma
10404 (uri (bioconductor-uri "erma" version))
10407 "1fi8nc6fbd7i4p9i9hli31xplmdpsxqcdrb8v3nf8fx9klllbdav"))))
10408 (build-system r-build-system)
10410 `(("r-annotationdbi" ,r-annotationdbi)
10411 ("r-biobase" ,r-biobase)
10412 ("r-biocgenerics" ,r-biocgenerics)
10413 ("r-foreach" ,r-foreach)
10414 ("r-genomicfiles" ,r-genomicfiles)
10415 ("r-genomicranges" ,r-genomicranges)
10416 ("r-ggplot2" ,r-ggplot2)
10417 ("r-homo-sapiens" ,r-homo-sapiens)
10418 ("r-rtracklayer" ,r-rtracklayer)
10419 ("r-s4vectors" ,r-s4vectors)
10420 ("r-shiny" ,r-shiny)
10421 ("r-summarizedexperiment" ,r-summarizedexperiment)))
10422 (home-page "https://bioconductor.org/packages/erma")
10423 (synopsis "Epigenomic road map adventures")
10425 "The epigenomics road map describes locations of epigenetic marks in DNA
10426 from a variety of cell types. Of interest are locations of histone
10427 modifications, sites of DNA methylation, and regions of accessible chromatin.
10428 This package presents a selection of elements of the road map including
10429 metadata and outputs of the ChromImpute procedure applied to ENCODE cell lines
10430 by Ernst and Kellis.")
10431 (license license:artistic2.0)))
10433 (define-public r-ldblock
10440 (uri (bioconductor-uri "ldblock" version))
10443 "1q8dz8wcq1r7kr635s9q21g36sxkdybk8khhpa4p57qv8r0gppl0"))))
10444 (build-system r-build-system)
10446 `(("r-erma" ,r-erma)
10447 ("r-genomeinfodb" ,r-genomeinfodb)
10448 ("r-genomicfiles" ,r-genomicfiles)
10449 ("r-go-db" ,r-go-db)
10450 ("r-homo-sapiens" ,r-homo-sapiens)
10451 ("r-matrix" ,r-matrix)
10452 ("r-rsamtools" ,r-rsamtools)
10453 ("r-snpstats" ,r-snpstats)
10454 ("r-variantannotation" ,r-variantannotation)))
10455 (home-page "https://bioconductor.org/packages/ldblock")
10456 (synopsis "Data structures for linkage disequilibrium measures in populations")
10458 "This package defines data structures for @dfn{linkage
10459 disequilibrium} (LD) measures in populations. Its purpose is to simplify
10460 handling of existing population-level data for the purpose of flexibly
10461 defining LD blocks.")
10462 (license license:artistic2.0)))
10464 (define-public r-gqtlstats
10466 (name "r-gqtlstats")
10471 (uri (bioconductor-uri "gQTLstats" version))
10474 "0gvq1sf2zjbkk431x40z6wql3c1rpclnnwa2f1hvykb8mmw70kmq"))))
10475 (properties `((upstream-name . "gQTLstats")))
10476 (build-system r-build-system)
10478 `(("r-annotationdbi" ,r-annotationdbi)
10479 ("r-batchjobs" ,r-batchjobs)
10480 ("r-bbmisc" ,r-bbmisc)
10481 ("r-beeswarm" ,r-beeswarm)
10482 ("r-biobase" ,r-biobase)
10483 ("r-biocgenerics" ,r-biocgenerics)
10484 ("r-doparallel" ,r-doparallel)
10485 ("r-dplyr" ,r-dplyr)
10487 ("r-ffbase" ,r-ffbase)
10488 ("r-foreach" ,r-foreach)
10489 ("r-genomeinfodb" ,r-genomeinfodb)
10490 ("r-genomicfeatures" ,r-genomicfeatures)
10491 ("r-genomicfiles" ,r-genomicfiles)
10492 ("r-genomicranges" ,r-genomicranges)
10493 ("r-ggbeeswarm" ,r-ggbeeswarm)
10494 ("r-ggplot2" ,r-ggplot2)
10495 ("r-gqtlbase" ,r-gqtlbase)
10496 ("r-hardyweinberg" ,r-hardyweinberg)
10497 ("r-iranges" ,r-iranges)
10498 ("r-ldblock" ,r-ldblock)
10499 ("r-limma" ,r-limma)
10501 ("r-plotly" ,r-plotly)
10502 ("r-reshape2" ,r-reshape2)
10503 ("r-s4vectors" ,r-s4vectors)
10504 ("r-shiny" ,r-shiny)
10505 ("r-snpstats" ,r-snpstats)
10506 ("r-summarizedexperiment" ,r-summarizedexperiment)
10507 ("r-variantannotation" ,r-variantannotation)))
10508 (home-page "https://bioconductor.org/packages/gQTLstats")
10509 (synopsis "Computationally efficient analysis for eQTL and allied studies")
10511 "This package provides tools for the computationally efficient analysis
10512 of @dfn{quantitative trait loci} (QTL) data, including eQTL, mQTL, dsQTL, etc.
10513 The software in this package aims to support refinements and functional
10514 interpretation of members of a collection of association statistics on a
10515 family of feature/genome hypotheses.")
10516 (license license:artistic2.0)))
10518 (define-public r-gviz
10525 (uri (bioconductor-uri "Gviz" version))
10528 "1grjzrjpzkw572pbvpsvdnfkfgwybl0cnjd7nnk2xdr26wnbsi9a"))))
10529 (properties `((upstream-name . "Gviz")))
10530 (build-system r-build-system)
10532 `(("r-annotationdbi" ,r-annotationdbi)
10533 ("r-biobase" ,r-biobase)
10534 ("r-biocgenerics" ,r-biocgenerics)
10535 ("r-biomart" ,r-biomart)
10536 ("r-biostrings" ,r-biostrings)
10537 ("r-biovizbase" ,r-biovizbase)
10538 ("r-bsgenome" ,r-bsgenome)
10539 ("r-digest" ,r-digest)
10540 ("r-genomeinfodb" ,r-genomeinfodb)
10541 ("r-genomicalignments" ,r-genomicalignments)
10542 ("r-genomicfeatures" ,r-genomicfeatures)
10543 ("r-genomicranges" ,r-genomicranges)
10544 ("r-iranges" ,r-iranges)
10545 ("r-lattice" ,r-lattice)
10546 ("r-latticeextra" ,r-latticeextra)
10547 ("r-matrixstats" ,r-matrixstats)
10548 ("r-rcolorbrewer" ,r-rcolorbrewer)
10549 ("r-rsamtools" ,r-rsamtools)
10550 ("r-rtracklayer" ,r-rtracklayer)
10551 ("r-s4vectors" ,r-s4vectors)
10552 ("r-xvector" ,r-xvector)))
10553 (home-page "https://bioconductor.org/packages/Gviz")
10554 (synopsis "Plotting data and annotation information along genomic coordinates")
10556 "Genomic data analyses requires integrated visualization of known genomic
10557 information and new experimental data. Gviz uses the biomaRt and the
10558 rtracklayer packages to perform live annotation queries to Ensembl and UCSC
10559 and translates this to e.g. gene/transcript structures in viewports of the
10560 grid graphics package. This results in genomic information plotted together
10562 (license license:artistic2.0)))
10564 (define-public r-gwascat
10571 (uri (bioconductor-uri "gwascat" version))
10574 "0n5x5i5v6a8wpn5mxmlpkl34b4kyypmymiwww6g61zch7xqrgywi"))))
10575 (build-system r-build-system)
10577 `(("r-annotationdbi" ,r-annotationdbi)
10578 ("r-annotationhub" ,r-annotationhub)
10579 ("r-biocgenerics" ,r-biocgenerics)
10580 ("r-biostrings" ,r-biostrings)
10581 ("r-genomeinfodb" ,r-genomeinfodb)
10582 ("r-genomicfeatures" ,r-genomicfeatures)
10583 ("r-genomicranges" ,r-genomicranges)
10584 ("r-ggbio" ,r-ggbio)
10585 ("r-ggplot2" ,r-ggplot2)
10586 ("r-gqtlstats" ,r-gqtlstats)
10587 ("r-graph" ,r-graph)
10589 ("r-homo-sapiens" ,r-homo-sapiens)
10590 ("r-iranges" ,r-iranges)
10591 ("r-rsamtools" ,r-rsamtools)
10592 ("r-rtracklayer" ,r-rtracklayer)
10593 ("r-s4vectors" ,r-s4vectors)
10594 ("r-snpstats" ,r-snpstats)
10595 ("r-summarizedexperiment" ,r-summarizedexperiment)
10596 ("r-variantannotation" ,r-variantannotation)))
10597 (home-page "https://bioconductor.org/packages/gwascat")
10598 (synopsis "Tools for data in the EMBL-EBI GWAS catalog")
10600 "This package provides tools for representing and modeling data in the
10601 EMBL-EBI GWAS catalog.")
10602 (license license:artistic2.0)))
10604 (define-public r-sushi
10610 (uri (bioconductor-uri "Sushi" version))
10613 "0axaqm480z8d0b2ldgxwm0swava1p4irc62bpl17p2k8k78g687g"))))
10614 (properties `((upstream-name . "Sushi")))
10615 (build-system r-build-system)
10617 `(("r-biomart" ,r-biomart)
10619 (home-page "https://bioconductor.org/packages/Sushi")
10620 (synopsis "Tools for visualizing genomics data")
10622 "This package provides flexible, quantitative, and integrative genomic
10623 visualizations for publication-quality multi-panel figures.")
10624 (license license:gpl2+)))
10626 (define-public r-fithic
10632 (uri (bioconductor-uri "FitHiC" version))
10635 "12ylhrppi051m7nqsgq95kzd9g9wmp34i0zzfi55cjqawlpx7c6n"))))
10636 (properties `((upstream-name . "FitHiC")))
10637 (build-system r-build-system)
10639 `(("r-data-table" ,r-data-table)
10640 ("r-fdrtool" ,r-fdrtool)
10641 ("r-rcpp" ,r-rcpp)))
10642 (home-page "https://bioconductor.org/packages/FitHiC")
10643 (synopsis "Confidence estimation for intra-chromosomal contact maps")
10645 "Fit-Hi-C is a tool for assigning statistical confidence estimates to
10646 intra-chromosomal contact maps produced by genome-wide genome architecture
10647 assays such as Hi-C.")
10648 (license license:gpl2+)))
10650 (define-public r-hitc
10656 (uri (bioconductor-uri "HiTC" version))
10659 "0da1jw9my2n2gihs31zyn14wwr23d8v2vij39ll7rm6fma3ydfbl"))))
10660 (properties `((upstream-name . "HiTC")))
10661 (build-system r-build-system)
10663 `(("r-biostrings" ,r-biostrings)
10664 ("r-genomeinfodb" ,r-genomeinfodb)
10665 ("r-genomicranges" ,r-genomicranges)
10666 ("r-iranges" ,r-iranges)
10667 ("r-matrix" ,r-matrix)
10668 ("r-rcolorbrewer" ,r-rcolorbrewer)
10669 ("r-rtracklayer" ,r-rtracklayer)))
10670 (home-page "https://bioconductor.org/packages/HiTC")
10671 (synopsis "High throughput chromosome conformation capture analysis")
10673 "The HiTC package was developed to explore high-throughput \"C\" data
10674 such as 5C or Hi-C. Dedicated R classes as well as standard methods for
10675 quality controls, normalization, visualization, and further analysis are also
10677 (license license:artistic2.0)))
10679 (define-public r-qvalue
10686 (uri (bioconductor-uri "qvalue" version))
10689 "1rd9rnf16kh8wc076kahd9hsb9rfwsbzmz3kjmp0pj6rbiq0051i"))))
10690 (build-system r-build-system)
10692 `(("r-ggplot2" ,r-ggplot2)
10693 ("r-reshape2" ,r-reshape2)))
10694 (home-page "http://github.com/jdstorey/qvalue")
10695 (synopsis "Q-value estimation for false discovery rate control")
10697 "This package takes a list of p-values resulting from the simultaneous
10698 testing of many hypotheses and estimates their q-values and local @dfn{false
10699 discovery rate} (FDR) values. The q-value of a test measures the proportion
10700 of false positives incurred when that particular test is called significant.
10701 The local FDR measures the posterior probability the null hypothesis is true
10702 given the test's p-value. Various plots are automatically generated, allowing
10703 one to make sensible significance cut-offs. The software can be applied to
10704 problems in genomics, brain imaging, astrophysics, and data mining.")
10705 ;; Any version of the LGPL.
10706 (license license:lgpl3+)))
10708 (define-public r-hdf5array
10710 (name "r-hdf5array")
10715 (uri (bioconductor-uri "HDF5Array" version))
10718 "0kcdza41saqv6vlpvqd841awbiwkg84lh0plx6c7fmfgbqv7a0jh"))))
10719 (properties `((upstream-name . "HDF5Array")))
10720 (build-system r-build-system)
10722 `(("r-biocgenerics" ,r-biocgenerics)
10723 ("r-delayedarray" ,r-delayedarray)
10724 ("r-iranges" ,r-iranges)
10725 ("r-rhdf5" ,r-rhdf5)
10726 ("r-s4vectors" ,r-s4vectors)))
10727 (home-page "https://bioconductor.org/packages/HDF5Array")
10728 (synopsis "HDF5 back end for DelayedArray objects")
10729 (description "This package provides an array-like container for convenient
10730 access and manipulation of HDF5 datasets. It supports delayed operations and
10731 block processing.")
10732 (license license:artistic2.0)))
10734 (define-public r-rhdf5lib
10736 (name "r-rhdf5lib")
10741 (uri (bioconductor-uri "Rhdf5lib" version))
10744 "0kkc4rprjbqn2wvbx4d49kk9l91vihccxbl4843qr1wqk6v33r1w"))))
10745 (properties `((upstream-name . "Rhdf5lib")))
10746 (build-system r-build-system)
10749 (modify-phases %standard-phases
10750 (add-after 'unpack 'do-not-use-bundled-hdf5
10751 (lambda* (#:key inputs #:allow-other-keys)
10752 (for-each delete-file '("configure" "configure.ac"))
10753 ;; Do not make other packages link with the proprietary libsz.
10754 (substitute* "R/zzz.R"
10755 (("'%s/libhdf5_cpp.a %s/libhdf5.a %s/libsz.a'")
10756 "'%s/libhdf5_cpp.a %s/libhdf5.a %s/libhdf5.a'")
10757 (("'%s/libhdf5.a %s/libsz.a'")
10758 "'%s/libhdf5.a %s/libhdf5.a'"))
10759 (with-directory-excursion "src"
10760 (invoke "tar" "xvf" (assoc-ref inputs "hdf5-source"))
10761 (rename-file (string-append "hdf5-" ,(package-version hdf5))
10763 ;; Remove timestamp and host system information to make
10764 ;; the build reproducible.
10765 (substitute* "hdf5/src/libhdf5.settings.in"
10766 (("Configured on: @CONFIG_DATE@")
10767 "Configured on: Guix")
10768 (("Uname information:.*")
10769 "Uname information: Linux\n")
10770 ;; Remove unnecessary store reference.
10772 "C Compiler: GCC\n"))
10773 (rename-file "Makevars.in" "Makevars")
10774 (substitute* "Makevars"
10775 (("HDF5_CXX_LIB=.*")
10776 (string-append "HDF5_CXX_LIB="
10777 (assoc-ref inputs "hdf5") "/lib/libhdf5_cpp.a\n"))
10779 (string-append "HDF5_LIB="
10780 (assoc-ref inputs "hdf5") "/lib/libhdf5.a\n"))
10781 (("HDF5_CXX_INCLUDE=.*") "HDF5_CXX_INCLUDE=./hdf5/c++/src\n")
10782 (("HDF5_INCLUDE=.*") "HDF5_INCLUDE=./hdf5/src\n")
10783 ;; szip is non-free software
10784 (("cp \\$\\{SZIP_LIB\\}.*") "")
10785 (("PKG_LIBS = \\$\\{HDF5_LIB\\} \\$\\{SZIP_LIB\\}")
10786 "PKG_LIBS = ${HDF5_LIB}\n")))
10793 `(("hdf5-source" ,(package-source hdf5))))
10794 (home-page "https://bioconductor.org/packages/Rhdf5lib")
10795 (synopsis "HDF5 library as an R package")
10796 (description "This package provides C and C++ HDF5 libraries for use in R
10798 (license license:artistic2.0)))
10800 (define-public r-beachmat
10802 (name "r-beachmat")
10807 (uri (bioconductor-uri "beachmat" version))
10810 "0b6dzja5fbx4dawb7ixj67mlhw4fy62pfp20mfp918fy96zmdwqz"))))
10811 (build-system r-build-system)
10815 `(("r-delayedarray" ,r-delayedarray)
10816 ("r-hdf5array" ,r-hdf5array)
10818 ("r-rhdf5" ,r-rhdf5)
10819 ("r-rhdf5lib" ,r-rhdf5lib)))
10820 (home-page "https://bioconductor.org/packages/beachmat")
10821 (synopsis "Compiling Bioconductor to handle each matrix type")
10822 (description "This package provides a consistent C++ class interface for a
10823 variety of commonly used matrix types, including sparse and HDF5-backed
10825 (license license:gpl3)))
10827 (define-public r-singlecellexperiment
10829 (name "r-singlecellexperiment")
10834 (uri (bioconductor-uri "SingleCellExperiment" version))
10837 "1r276i97w64a5vdlg6952gkj7bls909p42zl8fn8yz87cdwyaars"))))
10839 `((upstream-name . "SingleCellExperiment")))
10840 (build-system r-build-system)
10842 `(("r-biocgenerics" ,r-biocgenerics)
10843 ("r-s4vectors" ,r-s4vectors)
10844 ("r-summarizedexperiment" ,r-summarizedexperiment)))
10845 (home-page "https://bioconductor.org/packages/SingleCellExperiment")
10846 (synopsis "S4 classes for single cell data")
10847 (description "This package defines an S4 class for storing data from
10848 single-cell experiments. This includes specialized methods to store and
10849 retrieve spike-in information, dimensionality reduction coordinates and size
10850 factors for each cell, along with the usual metadata for genes and
10852 (license license:gpl3)))
10854 (define-public r-scater
10860 (uri (bioconductor-uri "scater" version))
10863 "0q3s96gf8saa1dq2fvmpl0jyj7bx3wrdfck3hanb8pxkcir2p7dn"))))
10864 (build-system r-build-system)
10866 `(("r-beachmat" ,r-beachmat)
10867 ("r-biobase" ,r-biobase)
10868 ("r-biocgenerics" ,r-biocgenerics)
10869 ("r-biomart" ,r-biomart)
10870 ("r-data-table" ,r-data-table)
10871 ("r-dplyr" ,r-dplyr)
10872 ("r-edger" ,r-edger)
10873 ("r-ggbeeswarm" ,r-ggbeeswarm)
10874 ("r-ggplot2" ,r-ggplot2)
10875 ("r-limma" ,r-limma)
10876 ("r-matrix" ,r-matrix)
10877 ("r-matrixstats" ,r-matrixstats)
10880 ("r-reshape2" ,r-reshape2)
10881 ("r-rhdf5" ,r-rhdf5)
10882 ("r-rhdf5lib" ,r-rhdf5lib)
10883 ("r-rjson" ,r-rjson)
10884 ("r-s4vectors" ,r-s4vectors)
10885 ("r-shiny" ,r-shiny)
10886 ("r-shinydashboard" ,r-shinydashboard)
10887 ("r-singlecellexperiment" ,r-singlecellexperiment)
10888 ("r-summarizedexperiment" ,r-summarizedexperiment)
10889 ("r-tximport" ,r-tximport)
10890 ("r-viridis" ,r-viridis)))
10891 (home-page "https://github.com/davismcc/scater")
10892 (synopsis "Single-cell analysis toolkit for gene expression data in R")
10893 (description "This package provides a collection of tools for doing
10894 various analyses of single-cell RNA-seq gene expression data, with a focus on
10896 (license license:gpl2+)))
10898 (define-public r-scran
10905 (uri (bioconductor-uri "scran" version))
10908 "0cs64cnf0xjcgmawr210y99j3gxs6aqgh8081n9827kkqnx2y5dm"))))
10909 (build-system r-build-system)
10911 `(("r-beachmat" ,r-beachmat)
10912 ("r-biocgenerics" ,r-biocgenerics)
10913 ("r-biocparallel" ,r-biocparallel)
10915 ("r-dynamictreecut" ,r-dynamictreecut)
10916 ("r-edger" ,r-edger)
10918 ("r-ggplot2" ,r-ggplot2)
10919 ("r-igraph" ,r-igraph)
10920 ("r-limma" ,r-limma)
10921 ("r-matrix" ,r-matrix)
10923 ("r-rhdf5lib" ,r-rhdf5lib)
10924 ("r-s4vectors" ,r-s4vectors)
10925 ("r-scater" ,r-scater)
10926 ("r-shiny" ,r-shiny)
10927 ("r-singlecellexperiment" ,r-singlecellexperiment)
10928 ("r-statmod" ,r-statmod)
10929 ("r-summarizedexperiment" ,r-summarizedexperiment)
10930 ("r-viridis" ,r-viridis)
10932 (home-page "https://bioconductor.org/packages/scran")
10933 (synopsis "Methods for single-cell RNA-Seq data analysis")
10934 (description "This package implements a variety of low-level analyses of
10935 single-cell RNA-seq data. Methods are provided for normalization of
10936 cell-specific biases, assignment of cell cycle phase, and detection of highly
10937 variable and significantly correlated genes.")
10938 (license license:gpl3)))
10940 (define-public r-delayedmatrixstats
10942 (name "r-delayedmatrixstats")
10947 (uri (bioconductor-uri "DelayedMatrixStats" version))
10950 "1cxjbjdq9hg9cm95rci0al7a4pk2h73ym276ahw9q4977zbg6381"))))
10952 `((upstream-name . "DelayedMatrixStats")))
10953 (build-system r-build-system)
10955 `(("r-delayedarray" ,r-delayedarray)
10956 ("r-iranges" ,r-iranges)
10957 ("r-matrix" ,r-matrix)
10958 ("r-matrixstats" ,r-matrixstats)
10959 ("r-s4vectors" ,r-s4vectors)))
10960 (home-page "https://github.com/PeteHaitch/DelayedMatrixStats")
10961 (synopsis "Functions that apply to rows and columns of DelayedMatrix objects")
10963 "This package provides a port of the @code{matrixStats} API for use with
10964 @code{DelayedMatrix} objects from the @code{DelayedArray} package. It
10965 contains high-performing functions operating on rows and columns of
10966 @code{DelayedMatrix} objects, e.g. @code{colMedians}, @code{rowMedians},
10967 @code{colRanks}, @code{rowRanks}, @code{colSds}, and @code{rowSds}. Functions
10968 are optimized per data type and for subsetted calculations such that both
10969 memory usage and processing time is minimized.")
10970 (license license:expat)))
10972 (define-public r-phangorn
10974 (name "r-phangorn")
10979 (uri (cran-uri "phangorn" version))
10982 "0xc8k552nxczy19jr0xjjagrzc8x6lafasgk2c099ls8bc1yml1i"))))
10983 (build-system r-build-system)
10986 ("r-fastmatch" ,r-fastmatch)
10987 ("r-igraph" ,r-igraph)
10988 ("r-magrittr" ,r-magrittr)
10989 ("r-matrix" ,r-matrix)
10990 ("r-quadprog" ,r-quadprog)
10991 ("r-rcpp" ,r-rcpp)))
10992 (home-page "https://github.com/KlausVigo/phangorn")
10993 (synopsis "Phylogenetic analysis in R")
10995 "Phangorn is a package for phylogenetic analysis in R. It supports
10996 estimation of phylogenetic trees and networks using Maximum Likelihood,
10997 Maximum Parsimony, distance methods and Hadamard conjugation.")
10998 (license license:gpl2+)))
11000 (define-public r-dropbead
11001 (let ((commit "d746c6f3b32110428ea56d6a0001ce52a251c247")
11004 (name "r-dropbead")
11005 (version (string-append "0-" revision "." (string-take commit 7)))
11009 (uri (git-reference
11010 (url "https://github.com/rajewsky-lab/dropbead.git")
11012 (file-name (git-file-name name version))
11015 "0sbzma49aiiyw8b0jpr7fnhzys9nsqmp4hy4hdz1gzyg1lhnca26"))))
11016 (build-system r-build-system)
11018 `(("r-ggplot2" ,r-ggplot2)
11019 ("r-rcolorbrewer" ,r-rcolorbrewer)
11020 ("r-gridextra" ,r-gridextra)
11021 ("r-gplots" ,r-gplots)
11022 ("r-plyr" ,r-plyr)))
11023 (home-page "https://github.com/rajewsky-lab/dropbead")
11024 (synopsis "Basic exploration and analysis of Drop-seq data")
11025 (description "This package offers a quick and straight-forward way to
11026 explore and perform basic analysis of single cell sequencing data coming from
11027 droplet sequencing. It has been particularly tailored for Drop-seq.")
11028 (license license:gpl3))))
11030 (define htslib-for-sambamba
11031 (let ((commit "2f3c3ea7b301f9b45737a793c0b2dcf0240e5ee5"))
11034 (name "htslib-for-sambamba")
11035 (version (string-append "1.3.1-1." (string-take commit 9)))
11039 (uri (git-reference
11040 (url "https://github.com/lomereiter/htslib.git")
11042 (file-name (string-append "htslib-" version "-checkout"))
11045 "0g38g8s3npr0gjm9fahlbhiskyfws9l5i0x1ml3rakzj7az5l9c9"))))
11048 (modify-phases %standard-phases
11049 (add-after 'unpack 'bootstrap
11050 (lambda _ (invoke "autoreconf" "-vif"))))))
11052 `(("autoconf" ,autoconf)
11053 ("automake" ,automake)
11054 ,@(package-native-inputs htslib))))))
11056 (define-public sambamba
11059 (version "0.6.7-10-g223fa20")
11063 (uri (git-reference
11064 (url "https://github.com/lomereiter/sambamba.git")
11065 (commit (string-append "v" version))))
11066 (file-name (string-append name "-" version "-checkout"))
11069 "1zb9hrxglxqh13ava9wwri30cvf85hjnbn8ccnr8l60a3k5avczn"))))
11070 (build-system gnu-build-system)
11072 `(#:tests? #f ; there is no test target
11073 #:parallel-build? #f ; not supported
11075 (modify-phases %standard-phases
11076 (delete 'configure)
11077 (add-after 'unpack 'fix-ldc-version
11079 (substitute* "gen_ldc_version_info.py"
11080 (("/usr/bin/env.*") (which "python")))
11081 (substitute* "Makefile"
11082 (("\\$\\(shell which ldmd2\\)") (which "ldmd2")))
11084 (add-after 'unpack 'place-biod-and-undead
11085 (lambda* (#:key inputs #:allow-other-keys)
11086 (copy-recursively (assoc-ref inputs "biod") "BioD")
11087 (copy-recursively (assoc-ref inputs "undead") "undeaD")
11089 (add-after 'unpack 'unbundle-prerequisites
11091 (substitute* "Makefile"
11092 (("htslib/libhts.a lz4/lib/liblz4.a")
11094 ((" htslib-static lz4-static") ""))
11097 (lambda* (#:key outputs #:allow-other-keys)
11098 (let* ((out (assoc-ref outputs "out"))
11099 (bin (string-append out "/bin")))
11101 (install-file "build/sambamba" bin)
11106 ("python" ,python2-minimal)
11108 ,(let ((commit "c778e4f2d8bacea7499283ce39f5577b232732c6"))
11111 (uri (git-reference
11112 (url "https://github.com/biod/BioD.git")
11114 (file-name (string-append "biod-"
11115 (string-take commit 9)
11119 "1z90562hg47i63gx042wb3ak2vqjg5z7hwgn9bp2pdxfg3nxrw37")))))
11121 ,(let ((commit "92803d25c88657e945511f0976a0c79d8da46e89"))
11124 (uri (git-reference
11125 (url "https://github.com/dlang/undeaD.git")
11127 (file-name (string-append "undead-"
11128 (string-take commit 9)
11132 "0vq6n81vzqvgphjw54lz2isc1j8lcxwjdbrhqz1h5gwrvw9w5138")))))))
11135 ("htslib" ,htslib-for-sambamba)))
11136 (home-page "http://lomereiter.github.io/sambamba")
11137 (synopsis "Tools for working with SAM/BAM data")
11138 (description "Sambamba is a high performance modern robust and
11139 fast tool (and library), written in the D programming language, for
11140 working with SAM and BAM files. Current parallelised functionality is
11141 an important subset of samtools functionality, including view, index,
11142 sort, markdup, and depth.")
11143 (license license:gpl2+)))
11145 (define-public ritornello
11147 (name "ritornello")
11151 (uri (string-append "https://github.com/KlugerLab/"
11152 "Ritornello/archive/v"
11153 version ".tar.gz"))
11154 (file-name (string-append name "-" version ".tar.gz"))
11157 "02nik86gq9ljjriv6pamwlmqnfky3ads1fpklx6mc3hx6k40pg38"))))
11158 (build-system gnu-build-system)
11160 `(#:tests? #f ; there are no tests
11162 (modify-phases %standard-phases
11163 (add-after 'unpack 'patch-samtools-references
11164 (lambda* (#:key inputs #:allow-other-keys)
11165 (substitute* '("src/SamStream.h"
11166 "src/BufferedGenomeReader.h")
11167 (("<sam.h>") "<samtools/sam.h>"))
11169 (delete 'configure)
11171 (lambda* (#:key inputs outputs #:allow-other-keys)
11172 (let* ((out (assoc-ref outputs "out"))
11173 (bin (string-append out "/bin/")))
11175 (install-file "bin/Ritornello" bin)
11178 `(("samtools" ,samtools-0.1)
11182 (home-page "https://github.com/KlugerLab/Ritornello")
11183 (synopsis "Control-free peak caller for ChIP-seq data")
11184 (description "Ritornello is a ChIP-seq peak calling algorithm based on
11185 signal processing that can accurately call binding events without the need to
11186 do a pair total DNA input or IgG control sample. It has been tested for use
11187 with narrow binding events such as transcription factor ChIP-seq.")
11188 (license license:gpl3+)))
11190 (define-public trim-galore
11192 (name "trim-galore")
11197 (uri (git-reference
11198 (url "https://github.com/FelixKrueger/TrimGalore.git")
11200 (file-name (string-append name "-" version "-checkout"))
11203 "0x5892l48c816pf00wmnz5vq0zq6170d3xc8zrxncd4jcz7h1p71"))))
11204 (build-system gnu-build-system)
11206 `(#:tests? #f ; no tests
11208 (modify-phases %standard-phases
11209 (delete 'configure)
11211 (add-after 'unpack 'hardcode-tool-references
11212 (lambda* (#:key inputs #:allow-other-keys)
11213 (substitute* "trim_galore"
11214 (("\\$path_to_cutadapt = 'cutadapt'")
11215 (string-append "$path_to_cutadapt = '"
11216 (assoc-ref inputs "cutadapt")
11219 (string-append "| "
11220 (assoc-ref inputs "gzip")
11223 (string-append "\""
11224 (assoc-ref inputs "gzip")
11228 (lambda* (#:key outputs #:allow-other-keys)
11229 (let ((bin (string-append (assoc-ref outputs "out")
11232 (install-file "trim_galore" bin)
11237 ("cutadapt" ,cutadapt)))
11239 `(("unzip" ,unzip)))
11240 (home-page "http://www.bioinformatics.babraham.ac.uk/projects/trim_galore/")
11241 (synopsis "Wrapper around Cutadapt and FastQC")
11242 (description "Trim Galore! is a wrapper script to automate quality and
11243 adapter trimming as well as quality control, with some added functionality to
11244 remove biased methylation positions for RRBS sequence files.")
11245 (license license:gpl3+)))
11247 (define-public gess
11253 (uri (string-append "http://compbio.uthscsa.edu/"
11255 "gess-" version ".src.tar.gz"))
11258 "0hyk403kxscclzfs24pvdgiv0wm03kjcziqdrp5w46cb049gz0d7"))))
11259 (build-system gnu-build-system)
11261 `(#:tests? #f ; no tests
11263 (modify-phases %standard-phases
11264 (delete 'configure)
11267 (lambda* (#:key inputs outputs #:allow-other-keys)
11268 (let* ((python (assoc-ref inputs "python"))
11269 (out (assoc-ref outputs "out"))
11270 (bin (string-append out "/bin/"))
11271 (target (string-append
11272 out "/lib/python2.7/site-packages/gess/")))
11274 (copy-recursively "." target)
11275 ;; Make GESS.py executable
11276 (chmod (string-append target "GESS.py") #o555)
11277 ;; Add Python shebang to the top and make Matplotlib
11279 (substitute* (string-append target "GESS.py")
11280 (("\"\"\"Description:" line)
11281 (string-append "#!" (which "python") "
11283 matplotlib.use('Agg')
11285 ;; Make sure GESS has all modules in its path
11286 (wrap-program (string-append target "GESS.py")
11287 `("PYTHONPATH" ":" prefix (,target ,(getenv "PYTHONPATH"))))
11289 (symlink (string-append target "GESS.py")
11290 (string-append bin "GESS.py"))
11293 `(("python" ,python-2)
11294 ("python2-pysam" ,python2-pysam)
11295 ("python2-scipy" ,python2-scipy)
11296 ("python2-numpy" ,python2-numpy)
11297 ("python2-networkx" ,python2-networkx)
11298 ("python2-biopython" ,python2-biopython)))
11299 (home-page "http://compbio.uthscsa.edu/GESS_Web/")
11300 (synopsis "Detect exon-skipping events from raw RNA-seq data")
11302 "GESS is an implementation of a novel computational method to detect de
11303 novo exon-skipping events directly from raw RNA-seq data without the prior
11304 knowledge of gene annotation information. GESS stands for the graph-based
11305 exon-skipping scanner detection scheme.")
11306 (license license:bsd-3)))
11308 (define-public phylip
11315 (uri (string-append "http://evolution.gs.washington.edu/phylip/"
11316 "download/phylip-" version ".tar.gz"))
11319 "01jar1rayhr2gba2pgbw49m56rc5z4p5wn3ds0m188hrlln4a2nd"))))
11320 (build-system gnu-build-system)
11322 `(#:tests? #f ; no check target
11323 #:make-flags (list "-f" "Makefile.unx" "install")
11324 #:parallel-build? #f ; not supported
11326 (modify-phases %standard-phases
11327 (add-after 'unpack 'enter-dir
11328 (lambda _ (chdir "src") #t))
11329 (delete 'configure)
11331 (lambda* (#:key inputs outputs #:allow-other-keys)
11332 (let ((target (string-append (assoc-ref outputs "out")
11335 (for-each (lambda (file)
11336 (install-file file target))
11337 (find-files "../exe" ".*")))
11339 (home-page "http://evolution.genetics.washington.edu/phylip/")
11340 (synopsis "Tools for inferring phylogenies")
11341 (description "PHYLIP (the PHYLogeny Inference Package) is a package of
11342 programs for inferring phylogenies (evolutionary trees).")
11343 (license license:bsd-2)))
11352 (uri (string-append "https://integrativemodeling.org/"
11353 version "/download/imp-" version ".tar.gz"))
11356 "0lxqx7vh79d771svr611dkilp6sn30qrbw8zvscbrm37v38d2j6h"))))
11357 (build-system cmake-build-system)
11359 `(;; FIXME: Some tests fail because they produce warnings, others fail
11360 ;; because the PYTHONPATH does not include the modeller's directory.
11368 ("python" ,python-2)))
11370 `(("python2-numpy" ,python2-numpy)
11371 ("python2-scipy" ,python2-scipy)
11372 ("python2-pandas" ,python2-pandas)
11373 ("python2-scikit-learn" ,python2-scikit-learn)
11374 ("python2-networkx" ,python2-networkx)))
11375 (home-page "https://integrativemodeling.org")
11376 (synopsis "Integrative modeling platform")
11377 (description "IMP's broad goal is to contribute to a comprehensive
11378 structural characterization of biomolecules ranging in size and complexity
11379 from small peptides to large macromolecular assemblies, by integrating data
11380 from diverse biochemical and biophysical experiments. IMP provides a C++ and
11381 Python toolbox for solving complex modeling problems, and a number of
11382 applications for tackling some common problems in a user-friendly way.")
11383 ;; IMP is largely available under the GNU Lesser GPL; see the file
11384 ;; COPYING.LGPL for the full text of this license. Some IMP modules are
11385 ;; available under the GNU GPL (see the file COPYING.GPL).
11386 (license (list license:lgpl2.1+
11389 (define-public tadbit
11395 (uri (string-append "https://github.com/3DGenomes/TADbit/"
11396 "archive/v" version ".tar.gz"))
11397 (file-name (string-append name "-" version ".tar.gz"))
11400 "1cnfqrl4685zar4nnw94j94nhvl2h29jm448nadqi1h05z6fdk4f"))))
11401 (build-system python-build-system)
11403 `(;; Tests are included and must be run after installation, but
11404 ;; they are incomplete and thus cannot be run.
11408 (modify-phases %standard-phases
11409 (add-after 'unpack 'fix-problems-with-setup.py
11410 (lambda* (#:key outputs #:allow-other-keys)
11411 ;; setup.py opens these files for writing
11412 (chmod "_pytadbit/_version.py" #o664)
11413 (chmod "README.rst" #o664)
11415 ;; Don't attempt to install the bash completions to
11416 ;; the home directory.
11417 (rename-file "extras/.bash_completion"
11419 (substitute* "setup.py"
11420 (("\\(path.expanduser\\('~'\\)")
11421 (string-append "(\""
11422 (assoc-ref outputs "out")
11423 "/etc/bash_completion.d\""))
11424 (("extras/\\.bash_completion")
11428 ;; TODO: add Chimera for visualization
11431 ("python2-scipy" ,python2-scipy)
11432 ("python2-numpy" ,python2-numpy)
11433 ("python2-matplotlib" ,python2-matplotlib)
11434 ("python2-pysam" ,python2-pysam)))
11435 (home-page "http://3dgenomes.github.io/TADbit/")
11436 (synopsis "Analyze, model, and explore 3C-based data")
11438 "TADbit is a complete Python library to deal with all steps to analyze,
11439 model, and explore 3C-based data. With TADbit the user can map FASTQ files to
11440 obtain raw interaction binned matrices (Hi-C like matrices), normalize and
11441 correct interaction matrices, identify and compare the so-called
11442 @dfn{Topologically Associating Domains} (TADs), build 3D models from the
11443 interaction matrices, and finally, extract structural properties from the
11444 models. TADbit is complemented by TADkit for visualizing 3D models.")
11445 (license license:gpl3+)))
11447 (define-public kentutils
11450 ;; 302.1.0 is out, but the only difference is the inclusion of
11451 ;; pre-built binaries.
11452 (version "302.0.0")
11456 (uri (string-append "https://github.com/ENCODE-DCC/kentUtils/"
11457 "archive/v" version ".tar.gz"))
11458 (file-name (string-append name "-" version ".tar.gz"))
11461 "134aja3k1cj32kbk1nnw0q9gxjb2krr15q6sga8qldzvc0585rmm"))
11462 (modules '((guix build utils)
11467 ;; Only the contents of the specified directories are free
11468 ;; for all uses, so we remove the rest. "hg/autoSql" and
11469 ;; "hg/autoXml" are nominally free, but they depend on a
11470 ;; library that is built from the sources in "hg/lib",
11471 ;; which is nonfree.
11472 (let ((free (list "." ".."
11473 "utils" "lib" "inc" "tagStorm"
11474 "parasol" "htslib"))
11475 (directory? (lambda (file)
11476 (eq? 'directory (stat:type (stat file))))))
11477 (for-each (lambda (file)
11478 (and (directory? file)
11479 (delete-file-recursively file)))
11480 (map (cut string-append "src/" <>)
11483 (not (member file free)))))))
11484 ;; Only make the utils target, not the userApps target,
11485 ;; because that requires libraries we won't build.
11486 (substitute* "Makefile"
11487 ((" userApps") " utils"))
11488 ;; Only build libraries that are free.
11489 (substitute* "src/makefile"
11490 (("DIRS =.*") "DIRS =\n")
11491 (("cd jkOwnLib.*") "")
11494 (substitute* "src/utils/makefile"
11495 ;; These tools depend on "jkhgap.a", which is part of the
11496 ;; nonfree "src/hg/lib" directory.
11497 (("raSqlQuery") "")
11498 (("pslLiftSubrangeBlat") "")
11500 ;; Do not build UCSC tools, which may require nonfree
11502 (("ALL_APPS =.*") "ALL_APPS = $(UTILS_APPLIST)\n"))
11504 (build-system gnu-build-system)
11506 `( ;; There is no global test target and the test target for
11507 ;; individual tools depends on input files that are not
11511 (modify-phases %standard-phases
11512 (add-after 'unpack 'fix-paths
11514 (substitute* "Makefile"
11515 (("/bin/echo") (which "echo")))
11517 (add-after 'unpack 'prepare-samtabix
11518 (lambda* (#:key inputs #:allow-other-keys)
11519 (copy-recursively (assoc-ref inputs "samtabix")
11522 (delete 'configure)
11524 (lambda* (#:key outputs #:allow-other-keys)
11525 (let ((bin (string-append (assoc-ref outputs "out")
11527 (copy-recursively "bin" bin))
11533 (uri (git-reference
11534 (url "http://genome-source.cse.ucsc.edu/samtabix.git")
11535 (commit "10fd107909c1ac4d679299908be4262a012965ba")))
11538 "0c1nj64l42v395sa84n7az43xiap4i6f9n9dfz4058aqiwkhkmma"))))))
11544 ("mariadb" ,mariadb)
11545 ("openssl" ,openssl)))
11546 (home-page "http://genome.cse.ucsc.edu/index.html")
11547 (synopsis "Assorted bioinformatics utilities")
11548 (description "This package provides the kentUtils, a selection of
11549 bioinformatics utilities used in combination with the UCSC genome
11551 ;; Only a subset of the sources are released under a non-copyleft
11552 ;; free software license. All other sources are removed in a
11553 ;; snippet. See this bug report for an explanation of how the
11554 ;; license statements apply:
11555 ;; https://github.com/ENCODE-DCC/kentUtils/issues/12
11556 (license (license:non-copyleft
11557 "http://genome.ucsc.edu/license/"
11558 "The contents of this package are free for all uses."))))
11560 (define-public f-seq
11561 (let ((commit "6ccded34cff38cf432deed8503648b4a66953f9b")
11565 (version (string-append "1.1-" revision "." (string-take commit 7)))
11568 (uri (git-reference
11569 (url "https://github.com/aboyle/F-seq.git")
11571 (file-name (string-append name "-" version))
11574 "1nk33k0yajg2id4g59bc4szr58r2q6pdq42vgcw054m8ip9wv26h"))
11575 (modules '((guix build utils)))
11576 ;; Remove bundled Java library archives.
11579 (for-each delete-file (find-files "lib" ".*"))
11581 (build-system ant-build-system)
11583 `(#:tests? #f ; no tests included
11585 (modify-phases %standard-phases
11587 (lambda* (#:key inputs outputs #:allow-other-keys)
11588 (let* ((target (assoc-ref outputs "out"))
11589 (bin (string-append target "/bin"))
11590 (doc (string-append target "/share/doc/f-seq"))
11591 (lib (string-append target "/lib")))
11594 (substitute* "bin/linux/fseq"
11595 (("java") (which "java"))
11596 (("\\$REALDIR/../lib/commons-cli-1.1.jar")
11597 (string-append (assoc-ref inputs "java-commons-cli")
11598 "/share/java/commons-cli.jar"))
11600 (string-append "REALDIR=" bin "\n")))
11601 (install-file "README.txt" doc)
11602 (install-file "bin/linux/fseq" bin)
11603 (install-file "build~/fseq.jar" lib)
11604 (copy-recursively "lib" lib)
11608 ("java-commons-cli" ,java-commons-cli)))
11609 (home-page "http://fureylab.web.unc.edu/software/fseq/")
11610 (synopsis "Feature density estimator for high-throughput sequence tags")
11612 "F-Seq is a software package that generates a continuous tag sequence
11613 density estimation allowing identification of biologically meaningful sites
11614 such as transcription factor binding sites (ChIP-seq) or regions of open
11615 chromatin (DNase-seq). Output can be displayed directly in the UCSC Genome
11617 (license license:gpl3+))))
11619 (define-public bismark
11626 (uri (git-reference
11627 (url "https://github.com/FelixKrueger/Bismark.git")
11629 (file-name (string-append name "-" version "-checkout"))
11632 "0yb5l36slwg02fp4b1jdlplgljcsxgqfzvzihzdnphd87dghcc84"))
11635 ;; highcharts.js is non-free software. The code is available under
11636 ;; CC-BY-NC or proprietary licenses only.
11637 (delete-file "bismark_sitrep/highcharts.js")
11639 (build-system perl-build-system)
11641 `(#:tests? #f ; there are no tests
11643 (modify-phases %standard-phases
11644 (delete 'configure)
11647 (lambda* (#:key inputs outputs #:allow-other-keys)
11648 (let* ((out (assoc-ref outputs "out"))
11649 (bin (string-append out "/bin"))
11650 (share (string-append out "/share/bismark"))
11651 (docdir (string-append out "/share/doc/bismark"))
11652 (docs '("Docs/Bismark_User_Guide.html"))
11653 (scripts '("bismark"
11654 "bismark_genome_preparation"
11655 "bismark_methylation_extractor"
11658 "coverage2cytosine"
11659 "deduplicate_bismark"
11660 "filter_non_conversion"
11662 "bismark2summary")))
11663 (substitute* "bismark2report"
11664 (("\\$RealBin/bismark_sitrep")
11665 (string-append share "/bismark_sitrep")))
11669 (for-each (lambda (file) (install-file file bin))
11671 (for-each (lambda (file) (install-file file docdir))
11673 (copy-recursively "Docs/Images" (string-append docdir "/Images"))
11674 (copy-recursively "bismark_sitrep"
11675 (string-append share "/bismark_sitrep"))
11677 ;; Fix references to gunzip
11678 (substitute* (map (lambda (file)
11679 (string-append bin "/" file))
11682 (string-append "\"" (assoc-ref inputs "gzip")
11683 "/bin/gunzip -c")))
11687 (home-page "http://www.bioinformatics.babraham.ac.uk/projects/bismark/")
11688 (synopsis "Map bisulfite treated sequence reads and analyze methylation")
11689 (description "Bismark is a program to map bisulfite treated sequencing
11690 reads to a genome of interest and perform methylation calls in a single step.
11691 The output can be easily imported into a genome viewer, such as SeqMonk, and
11692 enables a researcher to analyse the methylation levels of their samples
11693 straight away. Its main features are:
11696 @item Bisulfite mapping and methylation calling in one single step
11697 @item Supports single-end and paired-end read alignments
11698 @item Supports ungapped and gapped alignments
11699 @item Alignment seed length, number of mismatches etc are adjustable
11700 @item Output discriminates between cytosine methylation in CpG, CHG
11703 (license license:gpl3+)))
11705 (define-public paml
11711 (uri (string-append "http://abacus.gene.ucl.ac.uk/software/"
11712 "paml" version ".tgz"))
11715 "13zf6h9fiqghwhch2h06x1zdr6s42plsnqahflp5g7myr3han3s6"))
11716 (modules '((guix build utils)))
11717 ;; Remove Windows binaries
11720 (for-each delete-file (find-files "." "\\.exe$"))
11722 (build-system gnu-build-system)
11724 `(#:tests? #f ; there are no tests
11725 #:make-flags '("CC=gcc")
11727 (modify-phases %standard-phases
11728 (replace 'configure
11730 (substitute* "src/BFdriver.c"
11731 (("/bin/bash") (which "bash")))
11735 (lambda* (#:key outputs #:allow-other-keys)
11736 (let ((tools '("baseml" "basemlg" "codeml"
11737 "pamp" "evolver" "yn00" "chi2"))
11738 (bin (string-append (assoc-ref outputs "out") "/bin"))
11739 (docdir (string-append (assoc-ref outputs "out")
11740 "/share/doc/paml")))
11742 (for-each (lambda (file) (install-file file bin)) tools)
11743 (copy-recursively "../doc" docdir)
11745 (home-page "http://abacus.gene.ucl.ac.uk/software/paml.html")
11746 (synopsis "Phylogentic analysis by maximum likelihood")
11747 (description "PAML (for Phylogentic Analysis by Maximum Likelihood)
11748 contains a few programs for model fitting and phylogenetic tree reconstruction
11749 using nucleotide or amino-acid sequence data.")
11751 (license license:gpl3)))
11753 (define-public kallisto
11759 (uri (string-append "https://github.com/pachterlab/"
11760 "kallisto/archive/v" version ".tar.gz"))
11761 (file-name (string-append name "-" version ".tar.gz"))
11764 "03j3iqhvq7ya3c91gidly3k3jvgm97vjq4scihrlxh315j696r11"))))
11765 (build-system cmake-build-system)
11766 (arguments `(#:tests? #f)) ; no "check" target
11770 (home-page "http://pachterlab.github.io/kallisto/")
11771 (synopsis "Near-optimal RNA-Seq quantification")
11773 "Kallisto is a program for quantifying abundances of transcripts from
11774 RNA-Seq data, or more generally of target sequences using high-throughput
11775 sequencing reads. It is based on the novel idea of pseudoalignment for
11776 rapidly determining the compatibility of reads with targets, without the need
11777 for alignment. Pseudoalignment of reads preserves the key information needed
11778 for quantification, and kallisto is therefore not only fast, but also as
11779 accurate as existing quantification tools.")
11780 (license license:bsd-2)))
11782 (define-public libgff
11788 (uri (string-append
11789 "https://github.com/Kingsford-Group/"
11790 "libgff/archive/v" version ".tar.gz"))
11791 (file-name (string-append name "-" version ".tar.gz"))
11794 "0vc4nxyhlm6g9vvmx5l4lfs5pnvixsv1hiiy4kddf2y3p6jna8ls"))))
11795 (build-system cmake-build-system)
11796 (arguments `(#:tests? #f)) ; no tests included
11797 (home-page "https://github.com/Kingsford-Group/libgff")
11798 (synopsis "Parser library for reading/writing GFF files")
11799 (description "This is a simple \"libraryfication\" of the GFF/GTF parsing
11800 code that is used in the Cufflinks codebase. The goal of this library is to
11801 provide this functionality without the necessity of drawing in a heavy-weight
11802 dependency like SeqAn.")
11803 (license (license:x11-style "https://www.boost.org/LICENSE_1_0.txt"))))
11805 (define-public libdivsufsort
11807 (name "libdivsufsort")
11811 (uri (git-reference
11812 (url "https://github.com/y-256/libdivsufsort.git")
11814 (file-name (git-file-name name version))
11817 "0fgdz9fzihlvjjrxy01md1bv9vh12rkgkwbm90b1hj5xpbaqp7z2"))))
11818 (build-system cmake-build-system)
11820 '(#:tests? #f ; there are no tests
11822 ;; Needed for rapmap and sailfish.
11823 '("-DBUILD_DIVSUFSORT64=ON")))
11824 (home-page "https://github.com/y-256/libdivsufsort")
11825 (synopsis "Lightweight suffix-sorting library")
11826 (description "libdivsufsort is a software library that implements a
11827 lightweight suffix array construction algorithm. This library provides a
11828 simple and an efficient C API to construct a suffix array and a
11829 Burrows-Wheeler transformed string from a given string over a constant-size
11830 alphabet. The algorithm runs in O(n log n) worst-case time using only 5n+O(1)
11831 bytes of memory space, where n is the length of the string.")
11832 (license license:expat)))
11834 (define-public sailfish
11841 (string-append "https://github.com/kingsfordgroup/"
11842 "sailfish/archive/v" version ".tar.gz"))
11843 (file-name (string-append name "-" version ".tar.gz"))
11846 "1inn60dxiwsz8g9w7kvfhjxj4bwfb0r12dyhpzzhfbig712dkmm0"))
11847 (modules '((guix build utils)))
11850 ;; Delete bundled headers for eigen3.
11851 (delete-file-recursively "include/eigen3/")
11853 (build-system cmake-build-system)
11855 `(#:configure-flags
11856 (list (string-append "-DBOOST_INCLUDEDIR="
11857 (assoc-ref %build-inputs "boost")
11859 (string-append "-DBOOST_LIBRARYDIR="
11860 (assoc-ref %build-inputs "boost")
11862 (string-append "-DBoost_LIBRARIES="
11863 "-lboost_iostreams "
11864 "-lboost_filesystem "
11869 "-lboost_program_options")
11870 "-DBoost_FOUND=TRUE"
11871 ;; Don't download RapMap---we already have it!
11872 "-DFETCHED_RAPMAP=1")
11873 ;; Tests must be run after installation and the location of the test
11874 ;; data file must be overridden. But the tests fail. It looks like
11875 ;; they are not really meant to be run.
11878 (modify-phases %standard-phases
11879 ;; Boost cannot be found, even though it's right there.
11880 (add-after 'unpack 'do-not-look-for-boost
11881 (lambda* (#:key inputs #:allow-other-keys)
11882 (substitute* "CMakeLists.txt"
11883 (("find_package\\(Boost 1\\.53\\.0") "#"))))
11884 (add-after 'unpack 'do-not-assign-to-macro
11886 (substitute* "include/spdlog/details/format.cc"
11887 (("const unsigned CHAR_WIDTH = 1;") ""))))
11888 (add-after 'unpack 'prepare-rapmap
11889 (lambda* (#:key inputs #:allow-other-keys)
11890 (let ((src "external/install/src/rapmap/")
11891 (include "external/install/include/rapmap/")
11892 (rapmap (assoc-ref inputs "rapmap")))
11893 (mkdir-p "/tmp/rapmap")
11894 (system* "tar" "xf"
11895 (assoc-ref inputs "rapmap")
11897 "--strip-components=1")
11900 (for-each (lambda (file)
11901 (install-file file src))
11902 (find-files "/tmp/rapmap/src" "\\.(c|cpp)"))
11903 (copy-recursively "/tmp/rapmap/include" include))))
11904 (add-after 'unpack 'use-system-libraries
11905 (lambda* (#:key inputs #:allow-other-keys)
11906 (substitute* '("src/SailfishIndexer.cpp"
11907 "src/SailfishUtils.cpp"
11908 "src/SailfishQuantify.cpp"
11909 "src/FASTAParser.cpp"
11911 "include/SailfishUtils.hpp"
11912 "include/SailfishIndex.hpp"
11913 "include/CollapsedEMOptimizer.hpp"
11914 "src/CollapsedEMOptimizer.cpp")
11915 (("#include \"jellyfish/config.h\"") ""))
11916 (substitute* "src/CMakeLists.txt"
11917 (("\\$\\{GAT_SOURCE_DIR\\}/external/install/include/jellyfish-2.2..")
11918 (string-append (assoc-ref inputs "jellyfish")
11919 "/include/jellyfish-" ,(package-version jellyfish)))
11920 (("\\$\\{GAT_SOURCE_DIR\\}/external/install/lib/libjellyfish-2.0.a")
11921 (string-append (assoc-ref inputs "jellyfish")
11922 "/lib/libjellyfish-2.0.a"))
11923 (("\\$\\{GAT_SOURCE_DIR\\}/external/install/lib/libdivsufsort.a")
11924 (string-append (assoc-ref inputs "libdivsufsort")
11925 "/lib/libdivsufsort.so"))
11926 (("\\$\\{GAT_SOURCE_DIR\\}/external/install/lib/libdivsufsort64.a")
11927 (string-append (assoc-ref inputs "libdivsufsort")
11928 "/lib/libdivsufsort64.so")))
11929 (substitute* "CMakeLists.txt"
11930 ;; Don't prefer static libs
11931 (("SET\\(CMAKE_FIND_LIBRARY_SUFFIXES.*") "")
11932 (("find_package\\(Jellyfish.*") "")
11933 (("ExternalProject_Add\\(libjellyfish") "message(")
11934 (("ExternalProject_Add\\(libgff") "message(")
11935 (("ExternalProject_Add\\(libsparsehash") "message(")
11936 (("ExternalProject_Add\\(libdivsufsort") "message("))
11938 ;; Ensure that Eigen headers can be found
11939 (setenv "CPLUS_INCLUDE_PATH"
11940 (string-append (getenv "CPLUS_INCLUDE_PATH")
11942 (assoc-ref inputs "eigen")
11943 "/include/eigen3")))))))
11947 ("jemalloc" ,jemalloc)
11948 ("jellyfish" ,jellyfish)
11949 ("sparsehash" ,sparsehash)
11952 (uri (git-reference
11953 (url "https://github.com/COMBINE-lab/RapMap.git")
11954 (commit (string-append "sf-v" version))))
11955 (file-name (string-append "rapmap-sf-v" version "-checkout"))
11958 "1hv79l5i576ykv5a1srj2p0q36yvyl5966m0fcy2lbi169ipjakf"))
11959 (modules '((guix build utils)))
11960 ;; These files are expected to be excluded.
11962 '(begin (delete-file-recursively "include/spdlog")
11963 (for-each delete-file '("include/xxhash.h"
11964 "src/xxhash.c"))))))
11965 ("libdivsufsort" ,libdivsufsort)
11970 `(("pkg-config" ,pkg-config)))
11971 (home-page "http://www.cs.cmu.edu/~ckingsf/software/sailfish")
11972 (synopsis "Mapping-based isoform quantification from RNA-Seq reads")
11973 (description "Sailfish is a tool for genomic transcript quantification
11974 from RNA-seq data. It requires a set of target transcripts (either from a
11975 reference or de-novo assembly) to quantify. All you need to run sailfish is a
11976 fasta file containing your reference transcripts and a (set of) fasta/fastq
11977 file(s) containing your reads.")
11978 (license license:gpl3+)))
11980 (define libstadenio-for-salmon
11982 (name "libstadenio")
11986 (uri (git-reference
11987 (url "https://github.com/COMBINE-lab/staden-io_lib.git")
11988 (commit (string-append "v" version))))
11989 (file-name (string-append name "-" version "-checkout"))
11992 "1x8kxxqxl892vwfbprlbyfwkkv7c34ggkc94892x9x0g37x5nbwx"))))
11993 (build-system gnu-build-system)
11994 (arguments '(#:parallel-tests? #f)) ; not supported
11998 `(("perl" ,perl))) ; for tests
11999 (home-page "https://github.com/COMBINE-lab/staden-io_lib")
12000 (synopsis "General purpose trace and experiment file library")
12001 (description "This package provides a library of file reading and writing
12002 code to provide a general purpose Trace file (and Experiment File) reading
12005 The following file formats are supported:
12008 @item SCF trace files
12009 @item ABI trace files
12010 @item ALF trace files
12011 @item ZTR trace files
12012 @item SFF trace archives
12013 @item SRF trace archives
12014 @item Experiment files
12015 @item Plain text files
12016 @item SAM/BAM sequence files
12017 @item CRAM sequence files
12019 (license license:bsd-3)))
12021 (define spdlog-for-salmon
12027 (uri (git-reference
12028 (url "https://github.com/COMBINE-lab/spdlog.git")
12029 (commit (string-append "v" version))))
12030 (file-name (string-append name "-" version "-checkout"))
12033 "13730429gwlabi432ilpnja3sfvy0nn2719vnhhmii34xcdyc57q"))))
12034 (build-system cmake-build-system)
12035 (home-page "https://github.com/COMBINE-lab/spdlog")
12036 (synopsis "Very fast C++ logging library")
12037 (description "Spdlog is a very fast header-only C++ logging library with
12038 performance as its primary goal.")
12039 (license license:expat)))
12041 ;; This is a modified variant of bwa for use with Salmon. It installs a
12042 ;; library to avoid having to build this as part of Salmon.
12043 (define bwa-for-salmon
12044 (package (inherit bwa)
12046 (version "0.7.12.5")
12049 (uri (git-reference
12050 (url "https://github.com/COMBINE-lab/bwa.git")
12051 (commit (string-append "v" version))))
12052 (file-name (string-append "bwa-for-salmon-" version "-checkout"))
12055 "1z2qa64y0c5hky10510x137mnzlhz6k8qf27csw4w9j6qihq95gb"))))
12056 (build-system gnu-build-system)
12058 '(#:tests? #f ;no "check" target
12060 (modify-phases %standard-phases
12062 (lambda* (#:key outputs #:allow-other-keys)
12063 (let* ((out (assoc-ref outputs "out"))
12064 (bin (string-append out "/bin"))
12065 (lib (string-append out "/lib"))
12066 (doc (string-append out "/share/doc/bwa"))
12067 (man (string-append out "/share/man/man1"))
12068 (inc (string-append out "/include/bwa")))
12069 (install-file "bwa" bin)
12070 (install-file "README.md" doc)
12071 (install-file "bwa.1" man)
12072 (install-file "libbwa.a" lib)
12075 (for-each (lambda (file)
12076 (install-file file inc))
12077 (find-files "." "\\.h$")))
12079 ;; no "configure" script
12080 (delete 'configure))))))
12082 (define-public salmon
12088 (uri (git-reference
12089 (url "https://github.com/COMBINE-lab/salmon.git")
12090 (commit (string-append "v" version))))
12091 (file-name (string-append name "-" version "-checkout"))
12094 "1zi1ff4i7y2ykk0vdzysgwzzzv166vg2x77pj1mf4baclavxj87a"))
12095 (modules '((guix build utils)))
12098 ;; Delete bundled headers for eigen3.
12099 (delete-file-recursively "include/eigen3/")
12101 (build-system cmake-build-system)
12103 `(#:configure-flags
12104 (list (string-append "-DBOOST_INCLUDEDIR="
12105 (assoc-ref %build-inputs "boost")
12107 (string-append "-DBOOST_LIBRARYDIR="
12108 (assoc-ref %build-inputs "boost")
12110 (string-append "-DBoost_LIBRARIES="
12111 "-lboost_iostreams "
12112 "-lboost_filesystem "
12117 "-lboost_program_options")
12118 "-DBoost_FOUND=TRUE"
12119 "-DTBB_LIBRARIES=tbb tbbmalloc"
12120 ;; Don't download RapMap---we already have it!
12121 "-DFETCHED_RAPMAP=1")
12123 (modify-phases %standard-phases
12124 ;; Boost cannot be found, even though it's right there.
12125 (add-after 'unpack 'do-not-look-for-boost
12126 (lambda* (#:key inputs #:allow-other-keys)
12127 (substitute* "CMakeLists.txt"
12128 (("find_package\\(Boost 1\\.53\\.0") "#"))))
12129 (add-after 'unpack 'do-not-phone-home
12131 (substitute* "src/Salmon.cpp"
12132 (("getVersionMessage\\(\\)") "\"\""))))
12133 (add-after 'unpack 'prepare-rapmap
12134 (lambda* (#:key inputs #:allow-other-keys)
12135 (let ((src "external/install/src/rapmap/")
12136 (include "external/install/include/rapmap/")
12137 (rapmap (assoc-ref inputs "rapmap")))
12140 (for-each (lambda (file)
12141 (install-file file src))
12142 (find-files (string-append rapmap "/src") "\\.(c|cpp)"))
12143 (copy-recursively (string-append rapmap "/include") include)
12144 (for-each delete-file '("external/install/include/rapmap/xxhash.h"
12145 "external/install/include/rapmap/FastxParser.hpp"
12146 "external/install/include/rapmap/concurrentqueue.h"
12147 "external/install/include/rapmap/FastxParserThreadUtils.hpp"
12148 "external/install/src/rapmap/FastxParser.cpp"
12149 "external/install/src/rapmap/xxhash.c")))))
12150 (add-after 'unpack 'use-system-libraries
12151 (lambda* (#:key inputs #:allow-other-keys)
12152 (substitute* "src/CMakeLists.txt"
12153 (("\\$\\{GAT_SOURCE_DIR\\}/external/install/include/jellyfish-2.2..")
12154 (string-append (assoc-ref inputs "jellyfish")
12155 "/include/jellyfish-" ,(package-version jellyfish)))
12156 (("\\$\\{GAT_SOURCE_DIR\\}/external/install/lib/libjellyfish-2.0.a")
12157 (string-append (assoc-ref inputs "jellyfish")
12158 "/lib/libjellyfish-2.0.a"))
12159 (("\\$\\{GAT_SOURCE_DIR\\}/external/install/lib/libdivsufsort.a")
12160 (string-append (assoc-ref inputs "libdivsufsort")
12161 "/lib/libdivsufsort.so"))
12162 (("\\$\\{GAT_SOURCE_DIR\\}/external/install/lib/libstaden-read.a")
12163 (string-append (assoc-ref inputs "libstadenio-for-salmon")
12164 "/lib/libstaden-read.a"))
12165 (("\\$\\{GAT_SOURCE_DIR\\}/external/install/lib/libbwa.a")
12166 (string-append (assoc-ref inputs "bwa") "/lib/libbwa.a"))
12167 (("\\$\\{GAT_SOURCE_DIR\\}/external/install/lib/libdivsufsort64.a")
12168 (string-append (assoc-ref inputs "libdivsufsort")
12169 "/lib/libdivsufsort64.so")))
12170 (substitute* "CMakeLists.txt"
12171 ;; Don't prefer static libs
12172 (("SET\\(CMAKE_FIND_LIBRARY_SUFFIXES.*") "")
12173 (("set\\(TBB_LIBRARIES") "message(")
12174 (("find_package\\(Jellyfish.*") "")
12175 (("ExternalProject_Add\\(libcereal") "message(")
12176 (("ExternalProject_Add\\(libbwa") "message(")
12177 (("ExternalProject_Add\\(libjellyfish") "message(")
12178 (("ExternalProject_Add\\(libgff") "message(")
12179 (("ExternalProject_Add\\(libtbb") "message(")
12180 (("ExternalProject_Add\\(libspdlog") "message(")
12181 (("ExternalProject_Add\\(libdivsufsort") "message(")
12182 (("ExternalProject_Add\\(libstadenio") "message(")
12183 (("ExternalProject_Add_Step\\(") "message("))
12185 ;; Ensure that all headers can be found
12186 (setenv "CPLUS_INCLUDE_PATH"
12187 (string-append (getenv "CPLUS_INCLUDE_PATH")
12189 (assoc-ref inputs "bwa")
12192 (assoc-ref inputs "eigen")
12193 "/include/eigen3"))
12195 (string-append (assoc-ref inputs "bwa")
12198 (assoc-ref inputs "eigen")
12199 "/include/eigen3"))
12201 ;; CMAKE_INSTALL_PREFIX does not exist when the tests are
12202 ;; run. It only exists after the install phase.
12203 (add-after 'unpack 'fix-tests
12205 (substitute* "src/CMakeLists.txt"
12206 (("DTOPLEVEL_DIR=\\$\\{CMAKE_INSTALL_PREFIX")
12207 "DTOPLEVEL_DIR=${GAT_SOURCE_DIR"))
12211 ("bwa" ,bwa-for-salmon)
12217 (uri (git-reference
12218 (url "https://github.com/COMBINE-lab/RapMap.git")
12219 (commit (string-append "salmon-v" version))))
12220 (file-name (string-append "rapmap-salmon-v" version "-checkout"))
12223 "1yc12yqsz6f0r8sg1qnk57xg34aqwc9jbqq6gd5ys28xw3plj98p"))))
12224 ("jemalloc" ,jemalloc)
12225 ("jellyfish" ,jellyfish)
12228 ("libdivsufsort" ,libdivsufsort)
12229 ("libstadenio-for-salmon" ,libstadenio-for-salmon)
12230 ("spdlog-for-salmon" ,spdlog-for-salmon)
12233 (home-page "https://github.com/COMBINE-lab/salmon")
12234 (synopsis "Quantification from RNA-seq reads using lightweight alignments")
12235 (description "Salmon is a program to produce highly-accurate,
12236 transcript-level quantification estimates from RNA-seq data. Salmon achieves
12237 its accuracy and speed via a number of different innovations, including the
12238 use of lightweight alignments (accurate but fast-to-compute proxies for
12239 traditional read alignments) and massively-parallel stochastic collapsed
12240 variational inference.")
12241 (license license:gpl3+)))
12243 (define-public python-loompy
12245 (name "python-loompy")
12250 (uri (pypi-uri "loompy" version))
12253 "1drgv8j1hxqzzpnfg272x9djb6j8qr798w1pc2x8ikmfgyd9gh51"))))
12254 (build-system python-build-system)
12255 ;; There are no tests
12256 (arguments '(#:tests? #f))
12258 `(("python-h5py" ,python-h5py)
12259 ("python-numpy" ,python-numpy)
12260 ("python-scipy" ,python-scipy)
12261 ("python-typing" ,python-typing)))
12262 (home-page "https://github.com/linnarsson-lab/loompy")
12263 (synopsis "Work with .loom files for single-cell RNA-seq data")
12264 (description "The loom file format is an efficient format for very large
12265 omics datasets, consisting of a main matrix, optional additional layers, a
12266 variable number of row and column annotations. Loom also supports sparse
12267 graphs. This library makes it easy to work with @file{.loom} files for
12268 single-cell RNA-seq data.")
12269 (license license:bsd-3)))
12271 ;; We cannot use the latest commit because it requires Java 9.
12272 (define-public java-forester
12273 (let ((commit "86b07efe302d5094b42deed9260f719a4c4ac2e6")
12276 (name "java-forester")
12277 (version (string-append "0-" revision "." (string-take commit 7)))
12280 (uri (git-reference
12281 (url "https://github.com/cmzmasek/forester.git")
12283 (file-name (string-append name "-" version "-checkout"))
12286 "0vxavc1yrf84yrnf20dq26hi0lglidk8d382xrxsy4qmlbjd276z"))
12287 (modules '((guix build utils)))
12290 ;; Delete bundled jars and pre-built classes
12291 (delete-file-recursively "forester/java/resources")
12292 (delete-file-recursively "forester/java/classes")
12293 (for-each delete-file (find-files "forester/java/" "\\.jar$"))
12294 ;; Delete bundled applications
12295 (delete-file-recursively "forester_applications")
12297 (build-system ant-build-system)
12299 `(#:tests? #f ; there are none
12301 #:modules ((guix build ant-build-system)
12303 (guix build java-utils)
12307 (modify-phases %standard-phases
12308 (add-after 'unpack 'chdir
12309 (lambda _ (chdir "forester/java") #t))
12310 (add-after 'chdir 'fix-dependencies
12312 (chmod "build.xml" #o664)
12313 (call-with-output-file "build.xml.new"
12317 (with-input-from-file "build.xml"
12318 (lambda _ (xml->sxml #:trim-whitespace? #t)))
12319 `(;; Remove all unjar tags to avoid repacking classes.
12320 (unjar . ,(lambda _ '()))
12321 (*default* . ,(lambda (tag . kids) `(,tag ,@kids)))
12322 (*text* . ,(lambda (_ txt) txt))))
12324 (rename-file "build.xml.new" "build.xml")
12326 ;; FIXME: itext is difficult to package as it depends on a few
12327 ;; unpackaged libraries.
12328 (add-after 'chdir 'remove-dependency-on-unpackaged-itext
12330 (delete-file "src/org/forester/archaeopteryx/PdfExporter.java")
12331 (substitute* "src/org/forester/archaeopteryx/MainFrame.java"
12332 (("pdf_written_to = PdfExporter.*")
12333 "throw new IOException(\"PDF export is not available.\");"))
12335 ;; There is no install target
12336 (replace 'install (install-jars ".")))))
12338 `(("java-commons-codec" ,java-commons-codec)
12339 ("java-openchart2" ,java-openchart2)))
12340 (home-page "https://sites.google.com/site/cmzmasek/home/software/forester")
12341 (synopsis "Phylogenomics libraries for Java")
12342 (description "Forester is a collection of Java libraries for
12343 phylogenomics and evolutionary biology research. It includes support for
12344 reading, writing, and exporting phylogenetic trees.")
12345 (license license:lgpl2.1+))))
12347 (define-public java-forester-1.005
12349 (name "java-forester")
12353 (uri (string-append "http://search.maven.org/remotecontent?"
12354 "filepath=org/biojava/thirdparty/forester/"
12355 version "/forester-" version "-sources.jar"))
12356 (file-name (string-append name "-" version ".jar"))
12359 "04r8qv4rk3p71z4ajrvp11py1z46qrx0047j3zzs79s6lnsm3lcv"))))
12360 (build-system ant-build-system)
12362 `(#:tests? #f ; there are none
12364 #:modules ((guix build ant-build-system)
12366 (guix build java-utils)
12370 (modify-phases %standard-phases
12371 (add-after 'unpack 'fix-dependencies
12372 (lambda* (#:key inputs #:allow-other-keys)
12373 (call-with-output-file "build.xml"
12377 (with-input-from-file "src/build.xml"
12378 (lambda _ (xml->sxml #:trim-whitespace? #t)))
12379 `(;; Remove all unjar tags to avoid repacking classes.
12380 (unjar . ,(lambda _ '()))
12381 (*default* . ,(lambda (tag . kids) `(,tag ,@kids)))
12382 (*text* . ,(lambda (_ txt) txt))))
12384 (copy-file (assoc-ref inputs "synth_look_and_feel_1.xml")
12385 "synth_look_and_feel_1.xml")
12386 (copy-file (assoc-ref inputs "phyloxml.xsd")
12388 (substitute* "build.xml"
12389 (("../resources/synth_laf/synth_look_and_feel_1.xml")
12390 "synth_look_and_feel_1.xml")
12391 (("../resources/phyloxml_schema/1.10/phyloxml.xsd")
12394 ;; FIXME: itext is difficult to package as it depends on a few
12395 ;; unpackaged libraries.
12396 (add-after 'unpack 'remove-dependency-on-unpackaged-itext
12398 (delete-file "src/org/forester/archaeopteryx/PdfExporter.java")
12399 (substitute* '("src/org/forester/archaeopteryx/MainFrame.java"
12400 "src/org/forester/archaeopteryx/MainFrameApplication.java")
12401 (("pdf_written_to = PdfExporter.*")
12402 "throw new IOException(\"PDF export is not available.\"); /*")
12403 ((".getPrintSizeX\\(\\), getOptions\\(\\).getPrintSizeY\\(\\) \\);") "*/")
12404 (("getCurrentTreePanel\\(\\).getHeight\\(\\) \\);") "*/"))
12406 (add-after 'unpack 'delete-pre-built-classes
12407 (lambda _ (delete-file-recursively "src/classes") #t))
12408 ;; There is no install target
12409 (replace 'install (install-jars ".")))))
12411 `(("java-commons-codec" ,java-commons-codec)
12412 ("java-openchart2" ,java-openchart2)))
12413 ;; The source archive does not contain the resources.
12418 (uri (string-append "https://raw.githubusercontent.com/cmzmasek/forester/"
12419 "b61cc2dcede0bede317db362472333115756b8c6/"
12420 "forester/resources/phyloxml_schema/1.10/phyloxml.xsd"))
12421 (file-name (string-append name "-phyloxml-" version ".xsd"))
12424 "1zxc4m8sn4n389nqdnpxa8d0k17qnr3pm2y5y6g6vh4k0zm52npv"))))
12425 ("synth_look_and_feel_1.xml"
12428 (uri (string-append "https://raw.githubusercontent.com/cmzmasek/forester/"
12429 "29e04321615da6b35c1e15c60e52caf3f21d8e6a/"
12430 "forester/java/classes/resources/synth_look_and_feel_1.xml"))
12431 (file-name (string-append name "-synth-look-and-feel-" version ".xml"))
12434 "1gv5602gv4k7y7713y75a4jvj7i9s7nildsbdl7n9q10sc2ikg8h"))))))
12435 (home-page "https://sites.google.com/site/cmzmasek/home/software/forester")
12436 (synopsis "Phylogenomics libraries for Java")
12437 (description "Forester is a collection of Java libraries for
12438 phylogenomics and evolutionary biology research. It includes support for
12439 reading, writing, and exporting phylogenetic trees.")
12440 (license license:lgpl2.1+)))
12442 (define-public java-biojava-core
12444 (name "java-biojava-core")
12448 (uri (git-reference
12449 (url "https://github.com/biojava/biojava")
12450 (commit (string-append "biojava-" version))))
12451 (file-name (string-append name "-" version "-checkout"))
12454 "1bvryh2bpsvash8ln79cmc9sqm8qw72hz4xzwqxcrjm8ssxszhqk"))))
12455 (build-system ant-build-system)
12458 #:jar-name "biojava-core.jar"
12459 #:source-dir "biojava-core/src/main/java/"
12460 #:test-dir "biojava-core/src/test"
12461 ;; These tests seem to require internet access.
12462 #:test-exclude (list "**/SearchIOTest.java"
12463 "**/BlastXMLParserTest.java"
12464 "**/GenbankCookbookTest.java"
12465 "**/GenbankProxySequenceReaderTest.java")
12467 (modify-phases %standard-phases
12468 (add-before 'build 'copy-resources
12470 (copy-recursively "biojava-core/src/main/resources"
12473 (add-before 'check 'copy-test-resources
12475 (copy-recursively "biojava-core/src/test/resources"
12476 "build/test-classes")
12479 `(("java-log4j-api" ,java-log4j-api)
12480 ("java-log4j-core" ,java-log4j-core)
12481 ("java-slf4j-api" ,java-slf4j-api)
12482 ("java-slf4j-simple" ,java-slf4j-simple)))
12484 `(("java-junit" ,java-junit)
12485 ("java-hamcrest-core" ,java-hamcrest-core)))
12486 (home-page "http://biojava.org")
12487 (synopsis "Core libraries of Java framework for processing biological data")
12488 (description "BioJava is a project dedicated to providing a Java framework
12489 for processing biological data. It provides analytical and statistical
12490 routines, parsers for common file formats, reference implementations of
12491 popular algorithms, and allows the manipulation of sequences and 3D
12492 structures. The goal of the biojava project is to facilitate rapid
12493 application development for bioinformatics.
12495 This package provides the core libraries.")
12496 (license license:lgpl2.1+)))
12498 (define-public java-biojava-phylo
12499 (package (inherit java-biojava-core)
12500 (name "java-biojava-phylo")
12501 (build-system ant-build-system)
12504 #:jar-name "biojava-phylo.jar"
12505 #:source-dir "biojava-phylo/src/main/java/"
12506 #:test-dir "biojava-phylo/src/test"
12508 (modify-phases %standard-phases
12509 (add-before 'build 'copy-resources
12511 (copy-recursively "biojava-phylo/src/main/resources"
12514 (add-before 'check 'copy-test-resources
12516 (copy-recursively "biojava-phylo/src/test/resources"
12517 "build/test-classes")
12520 `(("java-log4j-api" ,java-log4j-api)
12521 ("java-log4j-core" ,java-log4j-core)
12522 ("java-slf4j-api" ,java-slf4j-api)
12523 ("java-slf4j-simple" ,java-slf4j-simple)
12524 ("java-biojava-core" ,java-biojava-core)
12525 ("java-forester" ,java-forester)))
12527 `(("java-junit" ,java-junit)
12528 ("java-hamcrest-core" ,java-hamcrest-core)))
12529 (home-page "http://biojava.org")
12530 (synopsis "Biojava interface to the forester phylogenomics library")
12531 (description "The phylo module provides a biojava interface layer to the
12532 forester phylogenomics library for constructing phylogenetic trees.")))
12534 (define-public java-biojava-alignment
12535 (package (inherit java-biojava-core)
12536 (name "java-biojava-alignment")
12537 (build-system ant-build-system)
12540 #:jar-name "biojava-alignment.jar"
12541 #:source-dir "biojava-alignment/src/main/java/"
12542 #:test-dir "biojava-alignment/src/test"
12544 (modify-phases %standard-phases
12545 (add-before 'build 'copy-resources
12547 (copy-recursively "biojava-alignment/src/main/resources"
12550 (add-before 'check 'copy-test-resources
12552 (copy-recursively "biojava-alignment/src/test/resources"
12553 "build/test-classes")
12556 `(("java-log4j-api" ,java-log4j-api)
12557 ("java-log4j-core" ,java-log4j-core)
12558 ("java-slf4j-api" ,java-slf4j-api)
12559 ("java-slf4j-simple" ,java-slf4j-simple)
12560 ("java-biojava-core" ,java-biojava-core)
12561 ("java-biojava-phylo" ,java-biojava-phylo)
12562 ("java-forester" ,java-forester)))
12564 `(("java-junit" ,java-junit)
12565 ("java-hamcrest-core" ,java-hamcrest-core)))
12566 (home-page "http://biojava.org")
12567 (synopsis "Biojava API for genetic sequence alignment")
12568 (description "The alignment module of BioJava provides an API that
12572 @item implementations of dynamic programming algorithms for sequence
12574 @item reading and writing of popular alignment file formats;
12575 @item a single-, or multi- threaded multiple sequence alignment algorithm.
12578 (define-public java-biojava-core-4.0
12579 (package (inherit java-biojava-core)
12580 (name "java-biojava-core")
12584 (uri (git-reference
12585 (url "https://github.com/biojava/biojava")
12586 (commit (string-append "biojava-" version))))
12587 (file-name (string-append name "-" version "-checkout"))
12590 "13675f6y9aqi7bi2lk3s1z7a22ynccjiqwa8izh7p97xi9wsfmd8"))))))
12592 (define-public java-biojava-phylo-4.0
12593 (package (inherit java-biojava-core-4.0)
12594 (name "java-biojava-phylo")
12595 (build-system ant-build-system)
12598 #:jar-name "biojava-phylo.jar"
12599 #:source-dir "biojava-phylo/src/main/java/"
12600 #:test-dir "biojava-phylo/src/test"
12602 (modify-phases %standard-phases
12603 (add-before 'build 'copy-resources
12605 (copy-recursively "biojava-phylo/src/main/resources"
12608 (add-before 'check 'copy-test-resources
12610 (copy-recursively "biojava-phylo/src/test/resources"
12611 "build/test-classes")
12614 `(("java-log4j-api" ,java-log4j-api)
12615 ("java-log4j-core" ,java-log4j-core)
12616 ("java-slf4j-api" ,java-slf4j-api)
12617 ("java-slf4j-simple" ,java-slf4j-simple)
12618 ("java-biojava-core" ,java-biojava-core-4.0)
12619 ("java-forester" ,java-forester-1.005)))
12621 `(("java-junit" ,java-junit)
12622 ("java-hamcrest-core" ,java-hamcrest-core)))
12623 (home-page "http://biojava.org")
12624 (synopsis "Biojava interface to the forester phylogenomics library")
12625 (description "The phylo module provides a biojava interface layer to the
12626 forester phylogenomics library for constructing phylogenetic trees.")))
12628 (define-public java-biojava-alignment-4.0
12629 (package (inherit java-biojava-core-4.0)
12630 (name "java-biojava-alignment")
12631 (build-system ant-build-system)
12634 #:jar-name "biojava-alignment.jar"
12635 #:source-dir "biojava-alignment/src/main/java/"
12636 #:test-dir "biojava-alignment/src/test"
12638 (modify-phases %standard-phases
12639 (add-before 'build 'copy-resources
12641 (copy-recursively "biojava-alignment/src/main/resources"
12644 (add-before 'check 'copy-test-resources
12646 (copy-recursively "biojava-alignment/src/test/resources"
12647 "build/test-classes")
12650 `(("java-log4j-api" ,java-log4j-api)
12651 ("java-log4j-core" ,java-log4j-core)
12652 ("java-slf4j-api" ,java-slf4j-api)
12653 ("java-slf4j-simple" ,java-slf4j-simple)
12654 ("java-biojava-core" ,java-biojava-core-4.0)
12655 ("java-biojava-phylo" ,java-biojava-phylo-4.0)
12656 ("java-forester" ,java-forester-1.005)))
12658 `(("java-junit" ,java-junit)
12659 ("java-hamcrest-core" ,java-hamcrest-core)))
12660 (home-page "http://biojava.org")
12661 (synopsis "Biojava API for genetic sequence alignment")
12662 (description "The alignment module of BioJava provides an API that
12666 @item implementations of dynamic programming algorithms for sequence
12668 @item reading and writing of popular alignment file formats;
12669 @item a single-, or multi- threaded multiple sequence alignment algorithm.
12672 (define-public dropseq-tools
12674 (name "dropseq-tools")
12679 (uri "http://mccarrolllab.com/download/1276/")
12680 (file-name (string-append "dropseq-tools-" version ".zip"))
12683 "0yrffckxqk5l8b5xb6z4laq157zd9mdypr2p4b4vq2bhjzi1sj0s"))
12684 ;; Delete bundled libraries
12685 (modules '((guix build utils)))
12688 (for-each delete-file (find-files "jar/lib" "\\.jar$"))
12689 (delete-file-recursively "3rdParty")))))
12690 (build-system ant-build-system)
12692 `(#:tests? #f ; test data are not included
12693 #:test-target "test"
12694 #:build-target "all"
12695 #:source-dir "public/src/"
12698 (list (string-append "-Dpicard.executable.dir="
12699 (assoc-ref %build-inputs "java-picard")
12701 #:modules ((ice-9 match)
12704 (guix build java-utils)
12705 (guix build ant-build-system))
12707 (modify-phases %standard-phases
12708 ;; All dependencies must be linked to "lib", because that's where
12709 ;; they will be searched for when the Class-Path property of the
12710 ;; manifest is computed.
12711 (add-after 'unpack 'record-references
12712 (lambda* (#:key inputs #:allow-other-keys)
12713 (mkdir-p "jar/lib")
12714 (let ((dirs (filter-map (match-lambda
12716 (if (and (string-prefix? "java-" name)
12717 (not (string=? name "java-testng")))
12720 (for-each (lambda (jar)
12721 (symlink jar (string-append "jar/lib/" (basename jar))))
12722 (append-map (lambda (dir) (find-files dir "\\.jar$"))
12725 ;; There is no installation target
12727 (lambda* (#:key inputs outputs #:allow-other-keys)
12728 (let* ((out (assoc-ref outputs "out"))
12729 (bin (string-append out "/bin"))
12730 (share (string-append out "/share/java/"))
12731 (lib (string-append share "/lib/"))
12732 (scripts (list "BAMTagHistogram"
12733 "BAMTagofTagCounts"
12734 "BaseDistributionAtReadPosition"
12735 "CollapseBarcodesInPlace"
12736 "CollapseTagWithContext"
12738 "CreateIntervalsFiles"
12739 "DetectBeadSynthesisErrors"
12740 "DigitalExpression"
12741 "Drop-seq_alignment.sh"
12744 "GatherGeneGCLength"
12745 "GatherMolecularBarcodeDistributionByGene"
12746 "GatherReadQualityMetrics"
12749 "SelectCellsByNumTranscripts"
12750 "SingleCellRnaSeqMetricsCollector"
12751 "TagBamWithReadSequenceExtended"
12752 "TagReadWithGeneExon"
12753 "TagReadWithInterval"
12754 "TrimStartingSequence"
12755 "ValidateReference")))
12756 (for-each mkdir-p (list bin share lib))
12757 (install-file "dist/dropseq.jar" share)
12758 (for-each (lambda (script)
12759 (chmod script #o555)
12760 (install-file script bin))
12762 (substitute* (map (lambda (script)
12763 (string-append bin "/" script))
12765 (("^java") (which "java"))
12766 (("jar_deploy_dir=.*")
12767 (string-append "jar_deploy_dir=" share "\n"))))
12769 ;; FIXME: We do this after stripping jars because we don't want it to
12770 ;; copy all these jars and strip them. We only want to install
12771 ;; links. Arguably, this is a problem with the ant-build-system.
12772 (add-after 'strip-jar-timestamps 'install-links
12773 (lambda* (#:key outputs #:allow-other-keys)
12774 (let* ((out (assoc-ref outputs "out"))
12775 (share (string-append out "/share/java/"))
12776 (lib (string-append share "/lib/")))
12777 (for-each (lambda (jar)
12778 (symlink (readlink jar)
12779 (string-append lib (basename jar))))
12780 (find-files "jar/lib" "\\.jar$")))
12783 `(("jdk" ,icedtea-8)
12784 ("java-picard" ,java-picard-2.10.3)
12785 ("java-log4j-1.2-api" ,java-log4j-1.2-api)
12786 ("java-commons-math3" ,java-commons-math3)
12787 ("java-commons-jexl2" ,java-commons-jexl-2)
12788 ("java-commons-collections4" ,java-commons-collections4)
12789 ("java-commons-lang2" ,java-commons-lang)
12790 ("java-commons-io" ,java-commons-io)
12791 ("java-snappy-1.0.3-rc3" ,java-snappy-1)
12792 ("java-guava" ,java-guava)
12793 ("java-la4j" ,java-la4j)
12794 ("java-biojava-core" ,java-biojava-core-4.0)
12795 ("java-biojava-alignment" ,java-biojava-alignment-4.0)
12796 ("java-jdistlib" ,java-jdistlib)
12797 ("java-simple-xml" ,java-simple-xml)
12798 ("java-snakeyaml" ,java-snakeyaml)))
12801 ("java-testng" ,java-testng)))
12802 (home-page "http://mccarrolllab.com/dropseq/")
12803 (synopsis "Tools for Drop-seq analyses")
12804 (description "Drop-seq is a technology to enable biologists to
12805 analyze RNA expression genome-wide in thousands of individual cells at
12806 once. This package provides tools to perform Drop-seq analyses.")
12807 (license license:expat)))
12809 (define-public pigx-rnaseq
12811 (name "pigx-rnaseq")
12815 (uri (string-append "https://github.com/BIMSBbioinfo/pigx_rnaseq/"
12816 "releases/download/v" version
12817 "/pigx_rnaseq-" version ".tar.gz"))
12820 "0pz080k4ajlc4rlznkn3najy2a6874gb56rf9g4ag9wqz31q174j"))))
12821 (build-system gnu-build-system)
12823 `(#:parallel-tests? #f ; not supported
12825 (modify-phases %standard-phases
12826 ;; "test.sh" runs STAR, which requires excessive amounts of memory.
12827 (add-after 'unpack 'disable-resource-intensive-test
12829 (substitute* "Makefile.in"
12830 (("(^ tests/test_trim_galore/test.sh).*" _ m) m)
12831 (("^ test.sh") ""))
12833 (add-after 'install 'wrap-executable
12834 ;; Make sure the executable finds all R modules.
12835 (lambda* (#:key inputs outputs #:allow-other-keys)
12836 (let ((out (assoc-ref outputs "out")))
12837 (wrap-program (string-append out "/bin/pigx-rnaseq")
12838 `("R_LIBS_SITE" ":" = (,(getenv "R_LIBS_SITE")))
12839 `("PYTHONPATH" ":" = (,(getenv "PYTHONPATH")))))
12843 ("snakemake" ,snakemake)
12845 ("multiqc" ,multiqc)
12847 ("trim-galore" ,trim-galore)
12849 ("samtools" ,samtools)
12850 ("bedtools" ,bedtools)
12851 ("r-minimal" ,r-minimal)
12852 ("r-rmarkdown" ,r-rmarkdown)
12853 ("r-ggplot2" ,r-ggplot2)
12854 ("r-ggrepel" ,r-ggrepel)
12855 ("r-gprofiler" ,r-gprofiler)
12856 ("r-deseq2" ,r-deseq2)
12858 ("r-knitr" ,r-knitr)
12859 ("r-pheatmap" ,r-pheatmap)
12860 ("r-corrplot" ,r-corrplot)
12861 ("r-reshape2" ,r-reshape2)
12862 ("r-plotly" ,r-plotly)
12863 ("r-scales" ,r-scales)
12864 ("r-summarizedexperiment" ,r-summarizedexperiment)
12865 ("r-crosstalk" ,r-crosstalk)
12866 ("r-tximport" ,r-tximport)
12867 ("r-rtracklayer" ,r-rtracklayer)
12868 ("r-rjson" ,r-rjson)
12870 ("ghc-pandoc" ,ghc-pandoc-1)
12871 ("ghc-pandoc-citeproc" ,ghc-pandoc-citeproc-with-pandoc-1)
12872 ("python-wrapper" ,python-wrapper)
12873 ("python-pyyaml" ,python-pyyaml)))
12874 (home-page "http://bioinformatics.mdc-berlin.de/pigx/")
12875 (synopsis "Analysis pipeline for RNA sequencing experiments")
12876 (description "PiGX RNAseq is an analysis pipeline for preprocessing and
12877 reporting for RNA sequencing experiments. It is easy to use and produces high
12878 quality reports. The inputs are reads files from the sequencing experiment,
12879 and a configuration file which describes the experiment. In addition to
12880 quality control of the experiment, the pipeline produces a differential
12881 expression report comparing samples in an easily configurable manner.")
12882 (license license:gpl3+)))
12884 (define-public pigx-chipseq
12886 (name "pigx-chipseq")
12890 (uri (string-append "https://github.com/BIMSBbioinfo/pigx_chipseq/"
12891 "releases/download/v" version
12892 "/pigx_chipseq-" version ".tar.gz"))
12895 "11v9v3vyda0sv4cl45nki7mm4v4bjfcdq7a70kcvi9h465nq66wg"))))
12896 (build-system gnu-build-system)
12898 `(#:tests? #f ; parts of the tests rely on access to the network
12900 (modify-phases %standard-phases
12901 (add-after 'install 'wrap-executable
12902 ;; Make sure the executable finds all R modules.
12903 (lambda* (#:key inputs outputs #:allow-other-keys)
12904 (let ((out (assoc-ref outputs "out")))
12905 (wrap-program (string-append out "/bin/pigx-chipseq")
12906 `("R_LIBS_SITE" ":" = (,(getenv "R_LIBS_SITE")))
12907 `("PYTHONPATH" ":" = (,(getenv "PYTHONPATH")))))
12911 ("coreutils" ,coreutils)
12912 ("r-minimal" ,r-minimal)
12913 ("r-argparser" ,r-argparser)
12914 ("r-biocparallel" ,r-biocparallel)
12915 ("r-biostrings" ,r-biostrings)
12916 ("r-chipseq" ,r-chipseq)
12917 ("r-data-table" ,r-data-table)
12918 ("r-dplyr" ,r-dplyr)
12919 ("r-genomation" ,r-genomation)
12920 ("r-genomicalignments" ,r-genomicalignments)
12921 ("r-genomicranges" ,r-genomicranges)
12922 ("r-rsamtools" ,r-rsamtools)
12923 ("r-rtracklayer" ,r-rtracklayer)
12924 ("r-s4vectors" ,r-s4vectors)
12925 ("r-stringr" ,r-stringr)
12926 ("r-tibble" ,r-tibble)
12927 ("r-tidyr" ,r-tidyr)
12928 ("r-jsonlite" ,r-jsonlite)
12929 ("r-heatmaply" ,r-heatmaply)
12930 ("r-htmlwidgets" ,r-htmlwidgets)
12931 ("r-ggplot2" ,r-ggplot2)
12932 ("r-plotly" ,r-plotly)
12933 ("r-rmarkdown" ,r-rmarkdown)
12934 ("python-wrapper" ,python-wrapper)
12935 ("python-pyyaml" ,python-pyyaml)
12936 ("python-magic" ,python-magic)
12937 ("python-xlrd" ,python-xlrd)
12938 ("trim-galore" ,trim-galore)
12940 ("multiqc" ,multiqc)
12942 ("ghc-pandoc" ,ghc-pandoc-1)
12943 ("ghc-pandoc-citeproc" ,ghc-pandoc-citeproc-with-pandoc-1)
12947 ("snakemake" ,snakemake)
12948 ("samtools" ,samtools)
12949 ("bedtools" ,bedtools)
12950 ("kentutils" ,kentutils)))
12952 `(("python-pytest" ,python-pytest)))
12953 (home-page "http://bioinformatics.mdc-berlin.de/pigx/")
12954 (synopsis "Analysis pipeline for ChIP sequencing experiments")
12955 (description "PiGX ChIPseq is an analysis pipeline for preprocessing, peak
12956 calling and reporting for ChIP sequencing experiments. It is easy to use and
12957 produces high quality reports. The inputs are reads files from the sequencing
12958 experiment, and a configuration file which describes the experiment. In
12959 addition to quality control of the experiment, the pipeline enables to set up
12960 multiple peak calling analysis and allows the generation of a UCSC track hub
12961 in an easily configurable manner.")
12962 (license license:gpl3+)))
12964 (define-public pigx-bsseq
12966 (name "pigx-bsseq")
12970 (uri (string-append "https://github.com/BIMSBbioinfo/pigx_bsseq/"
12971 "releases/download/v" version
12972 "/pigx_bsseq-" version ".tar.gz"))
12975 "0irlnlhhw9fd4ha7hksrxn3y7j76mz5qq1wjswbs9p364laqg69y"))))
12976 (build-system gnu-build-system)
12979 (modify-phases %standard-phases
12980 (add-before 'check 'set-timezone
12981 ;; The readr package is picky about timezones.
12982 (lambda* (#:key inputs #:allow-other-keys)
12983 (setenv "TZ" "UTC+1")
12985 (string-append (assoc-ref inputs "tzdata")
12986 "/share/zoneinfo"))
12988 (add-after 'install 'wrap-executable
12989 ;; Make sure the executable finds all R modules.
12990 (lambda* (#:key inputs outputs #:allow-other-keys)
12991 (let ((out (assoc-ref outputs "out")))
12992 (wrap-program (string-append out "/bin/pigx-bsseq")
12993 `("R_LIBS_SITE" ":" = (,(getenv "R_LIBS_SITE")))
12994 `("PYTHONPATH" ":" = (,(getenv "PYTHONPATH")))))
12997 `(("tzdata" ,tzdata)))
12999 `(("coreutils" ,coreutils)
13002 ("r-minimal" ,r-minimal)
13003 ("r-annotationhub" ,r-annotationhub)
13005 ("r-genomation" ,r-genomation)
13006 ("r-methylkit" ,r-methylkit)
13007 ("r-rtracklayer" ,r-rtracklayer)
13008 ("r-rmarkdown" ,r-rmarkdown)
13009 ("r-bookdown" ,r-bookdown)
13010 ("r-ggplot2" ,r-ggplot2)
13011 ("r-ggbio" ,r-ggbio)
13012 ("ghc-pandoc" ,ghc-pandoc-1)
13013 ("ghc-pandoc-citeproc" ,ghc-pandoc-citeproc-with-pandoc-1)
13014 ("python-wrapper" ,python-wrapper)
13015 ("python-pyyaml" ,python-pyyaml)
13016 ("snakemake" ,snakemake)
13017 ("bismark" ,bismark)
13020 ("trim-galore" ,trim-galore)
13021 ("cutadapt" ,cutadapt)
13022 ("samtools" ,samtools)))
13023 (home-page "http://bioinformatics.mdc-berlin.de/pigx/")
13024 (synopsis "Bisulfite sequencing pipeline from fastq to methylation reports")
13025 (description "PiGx BSseq is a data processing pipeline for raw fastq read
13026 data of bisulfite experiments; it produces reports on aggregate methylation
13027 and coverage and can be used to produce information on differential
13028 methylation and segmentation.")
13029 (license license:gpl3+)))
13031 (define-public pigx-scrnaseq
13033 (name "pigx-scrnaseq")
13037 (uri (string-append "https://github.com/BIMSBbioinfo/pigx_scrnaseq/"
13038 "releases/download/v" version
13039 "/pigx_scrnaseq-" version ".tar.gz"))
13042 "1pvjm6f3mascprs65vflggwwg5v925knvgal7k7a6nnlmw5qndrf"))))
13043 (build-system gnu-build-system)
13045 `(#:configure-flags
13046 (list (string-append "PICARDJAR=" (assoc-ref %build-inputs "java-picard")
13047 "/share/java/picard.jar")
13048 (string-append "DROPSEQJAR=" (assoc-ref %build-inputs "dropseq-tools")
13049 "/share/java/dropseq.jar"))
13051 (modify-phases %standard-phases
13052 (add-after 'install 'wrap-executable
13053 ;; Make sure the executable finds all R modules.
13054 (lambda* (#:key inputs outputs #:allow-other-keys)
13055 (let ((out (assoc-ref outputs "out")))
13056 (wrap-program (string-append out "/bin/pigx-scrnaseq")
13057 `("R_LIBS_SITE" ":" = (,(getenv "R_LIBS_SITE")))
13058 `("PYTHONPATH" ":" = (,(getenv "PYTHONPATH")))))
13061 `(("coreutils" ,coreutils)
13063 ("dropseq-tools" ,dropseq-tools)
13065 ("java-picard" ,java-picard)
13066 ("java" ,icedtea-8)
13067 ("python-wrapper" ,python-wrapper)
13068 ("python-pyyaml" ,python-pyyaml)
13069 ("python-pandas" ,python-pandas)
13070 ("python-numpy" ,python-numpy)
13071 ("python-loompy" ,python-loompy)
13072 ("ghc-pandoc" ,ghc-pandoc-1)
13073 ("ghc-pandoc-citeproc" ,ghc-pandoc-citeproc-with-pandoc-1)
13074 ("snakemake" ,snakemake)
13076 ("r-minimal" ,r-minimal)
13077 ("r-argparser" ,r-argparser)
13078 ("r-cowplot" ,r-cowplot)
13079 ("r-data-table" ,r-data-table)
13080 ("r-delayedarray" ,r-delayedarray)
13081 ("r-delayedmatrixstats" ,r-delayedmatrixstats)
13082 ("r-dplyr" ,r-dplyr)
13083 ("r-dropbead" ,r-dropbead)
13085 ("r-genomicalignments" ,r-genomicalignments)
13086 ("r-genomicfiles" ,r-genomicfiles)
13087 ("r-genomicranges" ,r-genomicranges)
13088 ("r-ggplot2" ,r-ggplot2)
13089 ("r-hdf5array" ,r-hdf5array)
13090 ("r-pheatmap" ,r-pheatmap)
13091 ("r-rmarkdown" ,r-rmarkdown)
13092 ("r-rsamtools" ,r-rsamtools)
13093 ("r-rtracklayer" ,r-rtracklayer)
13094 ("r-rtsne" ,r-rtsne)
13095 ("r-scater" ,r-scater)
13096 ("r-scran" ,r-scran)
13097 ("r-singlecellexperiment" ,r-singlecellexperiment)
13098 ("r-stringr" ,r-stringr)
13099 ("r-yaml" ,r-yaml)))
13100 (home-page "http://bioinformatics.mdc-berlin.de/pigx/")
13101 (synopsis "Analysis pipeline for single-cell RNA sequencing experiments")
13102 (description "PiGX scRNAseq is an analysis pipeline for preprocessing and
13103 quality control for single cell RNA sequencing experiments. The inputs are
13104 read files from the sequencing experiment, and a configuration file which
13105 describes the experiment. It produces processed files for downstream analysis
13106 and interactive quality reports. The pipeline is designed to work with UMI
13108 (license license:gpl3+)))
13110 (define-public pigx
13116 (uri (string-append "https://github.com/BIMSBbioinfo/pigx/"
13117 "releases/download/v" version
13118 "/pigx-" version ".tar.gz"))
13121 "0sb708sl42h3s5z872jb1w70bbqplwapnsc1wm27zcsvi7li4gw8"))))
13122 (build-system gnu-build-system)
13124 `(("python" ,python)
13125 ("pigx-bsseq" ,pigx-bsseq)
13126 ("pigx-chipseq" ,pigx-chipseq)
13127 ("pigx-rnaseq" ,pigx-rnaseq)
13128 ("pigx-scrnaseq" ,pigx-scrnaseq)))
13129 (home-page "http://bioinformatics.mdc-berlin.de/pigx/")
13130 (synopsis "Analysis pipelines for genomics")
13131 (description "PiGx is a collection of genomics pipelines. It includes the
13132 following pipelines:
13135 @item PiGx BSseq for raw fastq read data of bisulfite experiments
13136 @item PiGx RNAseq for RNAseq samples
13137 @item PiGx scRNAseq for single cell dropseq analysis
13138 @item PiGx ChIPseq for reads from ChIPseq experiments
13141 All pipelines are easily configured with a simple sample sheet and a
13142 descriptive settings file. The result is a set of comprehensive, interactive
13143 HTML reports with interesting findings about your samples.")
13144 (license license:gpl3+)))
13146 (define-public r-diversitree
13148 (name "r-diversitree")
13153 (uri (cran-uri "diversitree" version))
13156 "0gh4rcrp0an3jh8915i1fsxlgyfk7njywgbd5ln5r2jhr085kpz7"))))
13157 (build-system r-build-system)
13159 `(("gfortran" ,gfortran)))
13160 (inputs `(("fftw" ,fftw) ("gsl" ,gsl)))
13163 ("r-desolve" ,r-desolve)
13165 ("r-suplex" ,r-subplex)))
13166 (home-page "https://www.zoology.ubc.ca/prog/diversitree")
13167 (synopsis "Comparative 'phylogenetic' analyses of diversification")
13168 (description "This package contains a number of comparative \"phylogenetic\"
13169 methods, mostly focusing on analysing diversification and character evolution.
13170 Contains implementations of \"BiSSE\" (Binary State Speciation and Extinction)
13171 and its unresolved tree extensions, \"MuSSE\" (Multiple State Speciation and
13172 Extinction), \"QuaSSE\", \"GeoSSE\", and \"BiSSE-ness\" Other included methods
13173 include Markov models of discrete and continuous trait evolution and constant
13174 rate speciation and extinction.")
13175 (license license:gpl2+)))