;;; Copyright © 2015, 2016 Pjotr Prins <pjotr.guix@thebird.nl>
;;; Copyright © 2015 Andreas Enge <andreas@enge.fr>
;;; Copyright © 2016 Roel Janssen <roel@gnu.org>
-;;; Copyright © 2016 Efraim Flashner <efraim@flashner.co.il>
+;;; Copyright © 2016, 2017 Efraim Flashner <efraim@flashner.co.il>
;;; Copyright © 2016 Marius Bakke <mbakke@fastmail.com>
;;; Copyright © 2016 Raoul Bonnal <ilpuccio.febo@gmail.com>
;;;
#:use-module (gnu packages boost)
#:use-module (gnu packages compression)
#:use-module (gnu packages cpio)
+ #:use-module (gnu packages cran)
#:use-module (gnu packages curl)
#:use-module (gnu packages documentation)
+ #:use-module (gnu packages databases)
#:use-module (gnu packages datastructures)
#:use-module (gnu packages file)
#:use-module (gnu packages flex)
#:use-module (gnu packages readline)
#:use-module (gnu packages ruby)
#:use-module (gnu packages serialization)
+ #:use-module (gnu packages shells)
#:use-module (gnu packages statistics)
+ #:use-module (gnu packages swig)
#:use-module (gnu packages tbb)
#:use-module (gnu packages tex)
#:use-module (gnu packages texinfo)
#:use-module (gnu packages web)
#:use-module (gnu packages xml)
#:use-module (gnu packages xorg)
- #:use-module (gnu packages zip)
- #:use-module (srfi srfi-1))
+ #:use-module (srfi srfi-1)
+ #:use-module (ice-9 match))
(define-public r-ape
(package
("python-nose" ,python2-nose)
("python-pysam" ,python2-pysam)))
(inputs
- `(("htslib" ,htslib)
+ `(("htslib" ,htslib-1.3) ; At least one test fails on htslib-1.4+.
("samtools" ,samtools)
("bwa" ,bwa)
("grep" ,grep)
(define-public bcftools
(package
(name "bcftools")
- (version "1.3.1")
+ (version "1.5")
(source (origin
(method url-fetch)
(uri (string-append
version "/bcftools-" version ".tar.bz2"))
(sha256
(base32
- "095ry68vmz9q5s1scjsa698dhgyvgw5aicz24c19iwfbai07mhqj"))
+ "0093hkkvxmbwfaa7905s6185jymynvg42kq6sxv7fili11l5mxwz"))
(modules '((guix build utils)))
(snippet
;; Delete bundled htslib.
- '(delete-file-recursively "htslib-1.3.1"))))
+ '(delete-file-recursively "htslib-1.5"))))
(build-system gnu-build-system)
(arguments
`(#:test-target "test"
+ #:configure-flags (list "--with-htslib=system")
#:make-flags
(list
"USE_GPL=1"
+ "LIBS=-lgsl -lgslcblas"
(string-append "prefix=" (assoc-ref %outputs "out"))
(string-append "HTSDIR=" (assoc-ref %build-inputs "htslib") "/include")
- (string-append "HTSLIB=" (assoc-ref %build-inputs "htslib") "/lib/libhts.a")
+ (string-append "HTSLIB=" (assoc-ref %build-inputs "htslib") "/lib/libhts.so")
(string-append "BGZIP=" (assoc-ref %build-inputs "htslib") "/bin/bgzip")
- (string-append "TABIX=" (assoc-ref %build-inputs "htslib") "/bin/tabix"))
+ (string-append "TABIX=" (assoc-ref %build-inputs "htslib") "/bin/tabix")
+ (string-append "PACKAGE_VERSION=" ,version))
#:phases
(modify-phases %standard-phases
- (add-after 'unpack 'patch-Makefile
- (lambda _
- (substitute* "Makefile"
- ;; Do not attempt to build htslib.
- (("^include \\$\\(HTSDIR\\)/htslib\\.mk") "")
- ;; Link against GSL cblas.
- (("-lcblas") "-lgslcblas"))
- #t))
- (delete 'configure)
(add-before 'check 'patch-tests
(lambda _
(substitute* "test/test.pl"
(define-public python-biom-format
(package
(name "python-biom-format")
- (version "2.1.5")
+ (version "2.1.6")
(source
(origin
(method url-fetch)
(file-name (string-append name "-" version ".tar.gz"))
(sha256
(base32
- "1n25w3p1rixbpac8iysmzcja6m4ip5r6sz19l8y6wlwi49hxn278"))))
+ "08cr7wpahk6zb31h4bs7jmzpvxcqv9s13xz40h6y2h656jvdvnpj"))))
(build-system python-build-system)
(propagated-inputs
`(("python-numpy" ,python-numpy)
("python-scipy" ,python-scipy)
("python-future" ,python-future)
("python-click" ,python-click)
- ("python-h5py" ,python-h5py)))
+ ("python-h5py" ,python-h5py)
+ ("python-pandas" ,python-pandas)))
(native-inputs
`(("python-nose" ,python-nose)))
(home-page "http://www.biom-format.org")
(define-public blast+
(package
(name "blast+")
- (version "2.4.0")
+ (version "2.6.0")
(source (origin
(method url-fetch)
(uri (string-append
version "/ncbi-blast-" version "+-src.tar.gz"))
(sha256
(base32
- "14n9jik6vhiwjd3m7bach4xj1pzfn0szbsbyfxybd9l9cc43b6mb"))
+ "15n937pw5aqmyfjb6l387d18grqbb96l63d5xj4l7yyh0zbf2405"))
+ (patches (search-patches "blast+-fix-makefile.patch"))
(modules '((guix build utils)))
(snippet
'(begin
- ;; Remove bundled bzip2 and zlib
+ ;; Remove bundled bzip2, zlib and pcre.
(delete-file-recursively "c++/src/util/compress/bzip2")
(delete-file-recursively "c++/src/util/compress/zlib")
+ (delete-file-recursively "c++/src/util/regexp")
(substitute* "c++/src/util/compress/Makefile.in"
(("bzip2 zlib api") "api"))
;; Remove useless msbuild directory
#t))))
(build-system gnu-build-system)
(arguments
- `(;; There are three(!) tests for this massive library, and all fail with
+ `(;; There are two(!) tests for this massive library, and both fail with
;; "unparsable timing stats".
- ;; ERR [127] -- [util/regexp] test_pcre.sh (unparsable timing stats)
;; ERR [127] -- [serial/datatool] datatool.sh (unparsable timing stats)
;; ERR [127] -- [serial/datatool] datatool_xml.sh (unparsable timing stats)
#:tests? #f
;; Rewrite hardcoded paths to various tools
(substitute* (append '("src/build-system/configure.ac"
"src/build-system/configure"
+ "src/build-system/helpers/run_with_lock.c"
"scripts/common/impl/if_diff.sh"
"scripts/common/impl/run_with_lock.sh"
"src/build-system/Makefile.configurables.real"
(assoc-ref inputs "bzip2"))
(string-append "--with-z="
(assoc-ref inputs "zlib"))
+ (string-append "--with-pcre="
+ (assoc-ref inputs "pcre"))
;; Each library is built twice by default, once
;; with "-static" in its name, and again
;; without.
"--without-static"
"--with-dll"))))))))
- (outputs '("out" ; 19 MB
- "lib" ; 203 MB
- "include")) ; 32 MB
+ (outputs '("out" ; 21 MB
+ "lib" ; 226 MB
+ "include")) ; 33 MB
(inputs
`(("bzip2" ,bzip2)
- ("zlib" ,zlib)))
+ ("zlib" ,zlib)
+ ("pcre" ,pcre)
+ ("perl" ,perl)
+ ("python" ,python-wrapper)))
(native-inputs
`(("cpio" ,cpio)))
(home-page "http://blast.ncbi.nlm.nih.gov")
(define-public bowtie
(package
(name "bowtie")
- (version "2.2.9")
+ (version "2.3.2")
(source (origin
(method url-fetch)
(uri (string-append "https://github.com/BenLangmead/bowtie2/archive/v"
(file-name (string-append name "-" version ".tar.gz"))
(sha256
(base32
- "1vp5db8i7is57iwjybcdg18f5ivyzlj5g1ix1nlvxainzivhz55g"))
+ "0hwa5r9qbglppb7sz5z79rlmmddr3n51n468jb3wh8rwjgn3yr90"))
(modules '((guix build utils)))
(snippet
'(substitute* "Makefile"
(("-DBUILD_HOST=.*") "-DBUILD_HOST=\"\\\"guix\\\"\"")
(("-DBUILD_TIME=.*") "-DBUILD_TIME=\"\\\"0\\\"\"")))))
(build-system gnu-build-system)
- (inputs `(("perl" ,perl)
- ("perl-clone" ,perl-clone)
- ("perl-test-deep" ,perl-test-deep)
- ("perl-test-simple" ,perl-test-simple)
- ("python" ,python-2)
- ("tbb" ,tbb)))
+ (inputs
+ `(("perl" ,perl)
+ ("perl-clone" ,perl-clone)
+ ("perl-test-deep" ,perl-test-deep)
+ ("perl-test-simple" ,perl-test-simple)
+ ("python" ,python-2)
+ ("tbb" ,tbb)
+ ("zlib" ,zlib)))
(arguments
'(#:make-flags
(list "allall"
"WITH_TBB=1"
(string-append "prefix=" (assoc-ref %outputs "out")))
#:phases
- (alist-delete
- 'configure
- (alist-replace
- 'check
- (lambda* (#:key outputs #:allow-other-keys)
- (system* "perl"
- "scripts/test/simple_tests.pl"
- "--bowtie2=./bowtie2"
- "--bowtie2-build=./bowtie2-build"))
- %standard-phases))))
+ (modify-phases %standard-phases
+ (delete 'configure)
+ (replace 'check
+ (lambda* (#:key outputs #:allow-other-keys)
+ (zero? (system* "perl"
+ "scripts/test/simple_tests.pl"
+ "--bowtie2=./bowtie2"
+ "--bowtie2-build=./bowtie2-build")))))))
(home-page "http://bowtie-bio.sourceforge.net/bowtie2/index.shtml")
(synopsis "Fast and sensitive nucleotide sequence read aligner")
(description
(define-public bwa
(package
(name "bwa")
- (version "0.7.12")
+ (version "0.7.15")
(source (origin
(method url-fetch)
(uri (string-append "mirror://sourceforge/bio-bwa/bwa-"
version ".tar.bz2"))
(sha256
(base32
- "1330dpqncv0px3pbhjzz1gwgg39kkcv2r9qp2xs0sixf8z8wl7bh"))))
+ "0585ikg0gv0mpyw9iq0bq9n0hr95867bbv8jbzs9pk4slkpsymig"))))
(build-system gnu-build-system)
(arguments
'(#:tests? #f ;no "check" target
(define-public python2-bx-python
(package
(name "python2-bx-python")
- (version "0.7.2")
+ (version "0.7.3")
(source (origin
(method url-fetch)
- (uri (string-append
- "https://pypi.python.org/packages/source/b/bx-python/bx-python-"
- version ".tar.gz"))
+ (uri (pypi-uri "bx-python" version))
(sha256
(base32
- "0ld49idhc5zjdvbhvjq1a2qmpjj7h5v58rqr25dzmfq7g34b50xh"))
+ "15z2w3bvnc0n4qmb9bd6d8ylc2h2nj883x2w9iixf4x3vki9b22i"))
(modules '((guix build utils)))
(snippet
'(substitute* "setup.py"
(define-public python-pysam
(package
(name "python-pysam")
- (version "0.10.0")
+ (version "0.11.2.2")
(source (origin
(method url-fetch)
;; Test data is missing on PyPi.
(file-name (string-append name "-" version ".tar.gz"))
(sha256
(base32
- "1mmvn91agr238kwz7226xq0i7k84lg2nxywn9712mzj7gvgqhfy8"))
+ "1cfqdxsqs3xhacns9n0271ck6wkc76px66ddjm91wfw2jxxfklvc"))
(modules '((guix build utils)))
(snippet
;; Drop bundled htslib. TODO: Also remove samtools and bcftools.
(define-public python-plastid
(package
(name "python-plastid")
- (version "0.4.6")
+ (version "0.4.8")
(source (origin
(method url-fetch)
(uri (pypi-uri "plastid" version))
(sha256
(base32
- "1sqkz5d3b9kf688mp7k771c87ins42j7j0whmkb49cb3fsg8s8lj"))))
+ "0l24dd3q66if8yj042m4s0g95n6acn7im1imqd3p6h8ns43kxhj8"))))
(build-system python-build-system)
(arguments
;; Some test files are not included.
(define-public cd-hit
(package
(name "cd-hit")
- (version "4.6.6")
+ (version "4.6.8")
(source (origin
(method url-fetch)
(uri (string-append "https://github.com/weizhongli/cdhit"
"/releases/download/V" version
- "/cd-hit-v" version "-2016-0711.tar.gz"))
+ "/cd-hit-v" version
+ "-2017-0621-source.tar.gz"))
(sha256
(base32
- "1w8hd4fszgg29nqiz569fldwy012la77nljcmlhglgicws56z54p"))))
+ "1386dg2npx8p62wmv08mjzsd2z3waknb9j1gg3gkvblcy57hymnn"))))
(build-system gnu-build-system)
(arguments
`(#:tests? #f ; there are no tests
(("__DATE__") "\"0\"")
(("\", %s, \" __TIME__ \"\\\\n\", date") ""))
#t))
- ;; The "install" target does not create the target directory
+ ;; The "install" target does not create the target directory.
(add-before 'install 'create-target-dir
(lambda* (#:key outputs #:allow-other-keys)
(mkdir-p (string-append (assoc-ref outputs "out") "/bin"))
(build-system python-build-system)
(arguments `(#:python ,python-2)) ; only Python 2 is supported
(inputs
- `(("htseq" ,htseq)
+ `(("htseq" ,python2-htseq)
("python-pybedtools" ,python2-pybedtools)
("python-cython" ,python2-cython)
("python-scikit-learn" ,python2-scikit-learn)
(native-inputs `(("python2-nose" ,python2-nose)
,@(package-native-inputs base))))))
+(define-public python-py2bit
+ (package
+ (name "python-py2bit")
+ (version "0.2.1")
+ (source
+ (origin
+ (method url-fetch)
+ (uri (pypi-uri "py2bit" version))
+ (sha256
+ (base32
+ "1cdf4qlmgwsh1f4k0wdv2sr8x9qn4366p0k3614vbd0fpqiarxrl"))))
+ (build-system python-build-system)
+ (home-page "https://github.com/dpryan79/py2bit")
+ (synopsis "Access 2bit files using lib2bit")
+ (description
+ "This package provides Python bindings for lib2bit to access 2bit files
+with Python.")
+ (license license:expat)))
(define-public deeptools
(package
(name "deeptools")
- (version "2.1.1")
+ (version "2.5.1")
(source (origin
(method url-fetch)
(uri (string-append "https://github.com/fidelram/deepTools/"
(file-name (string-append name "-" version ".tar.gz"))
(sha256
(base32
- "1nmfin0zjdby3vay3r4flvz94dr6qjhj41ax4yz3vx13j6wz8izd"))))
+ "1q8i12l2gvk4n2s8lhyzwhh9g4qbc8lrk5l7maz00yvd5g6z5540"))))
(build-system python-build-system)
- (arguments
- `(#:python ,python-2))
(inputs
- `(("python-scipy" ,python2-scipy)
- ("python-numpy" ,python2-numpy)
- ("python-numpydoc" ,python2-numpydoc)
- ("python-matplotlib" ,python2-matplotlib)
- ("python-bx-python" ,python2-bx-python)
- ("python-pysam" ,python2-pysam)
- ("python-pybigwig" ,python2-pybigwig)))
+ `(("python-scipy" ,python-scipy)
+ ("python-numpy" ,python-numpy)
+ ("python-numpydoc" ,python-numpydoc)
+ ("python-matplotlib" ,python-matplotlib)
+ ("python-pysam" ,python-pysam)
+ ("python-py2bit" ,python-py2bit)
+ ("python-pybigwig" ,python-pybigwig)))
(native-inputs
- `(("python-mock" ,python2-mock) ;for tests
- ("python-nose" ,python2-nose) ;for tests
- ("python-pytz" ,python2-pytz))) ;for tests
+ `(("python-mock" ,python-mock) ;for tests
+ ("python-nose" ,python-nose) ;for tests
+ ("python-pytz" ,python-pytz))) ;for tests
(home-page "https://github.com/fidelram/deepTools")
(synopsis "Tools for normalizing and visualizing deep-sequencing data")
(description
(define-public diamond
(package
(name "diamond")
- (version "0.8.38")
+ (version "0.9.9")
(source (origin
(method url-fetch)
(uri (string-append
(file-name (string-append name "-" version ".tar.gz"))
(sha256
(base32
- "0q2z6z5f7c0kbbzpjamkcyqg0rc6h5rxfp97qbmb0wxaycr7jajq"))))
+ "04i03046g3l2vk9722z47r1p7j415g97vvz6d76ywmbawyiihcb1"))))
(build-system cmake-build-system)
(arguments
'(#:tests? #f ; no "check" target
and BLASTX alignment mode). The speedup over BLAST is up to 20,000 on short
reads at a typical sensitivity of 90-99% relative to BLAST depending on the
data and settings.")
- (license (license:non-copyleft "file://src/COPYING"
- "See src/COPYING in the distribution."))))
+ (license license:agpl3+)))
(define-public discrover
(package
(define-public fasttree
(package
(name "fasttree")
- (version "2.1.9")
+ (version "2.1.10")
(source (origin
(method url-fetch)
(uri (string-append
version ".c"))
(sha256
(base32
- "0ljvvw8i1als1wbfzvrf15c3ii2vw9db20a259g6pzg34xyyb97k"))))
+ "0vcjdvy1j4m702vmak4svbfkrpcw63k7wymfksjp9a982zy8kjsl"))))
(build-system gnu-build-system)
(arguments
`(#:tests? #f ; no "check" target
(define-public fraggenescan
(package
(name "fraggenescan")
- (version "1.20")
+ (version "1.30")
(source
(origin
(method url-fetch)
(string-append "mirror://sourceforge/fraggenescan/"
"FragGeneScan" version ".tar.gz"))
(sha256
- (base32 "1zzigqmvqvjyqv4945kv6nc5ah2xxm1nxgrlsnbzav3f5c0n0pyj"))))
+ (base32 "158dcnwczgcyhwm4qlx19sanrwgdpzf6bn2y57mbpx55lkgz1mzj"))))
(build-system gnu-build-system)
(arguments
`(#:phases
(string-append "system(\"" (which "rm")))
(("system\\(\"mv")
(string-append "system(\"" (which "mv")))
+ (("\\\"awk") (string-append "\"" (which "awk")))
;; This script and other programs expect the training files
;; to be in the non-standard location bin/train/XXX. Change
;; this to be share/fraggenescan/train/XXX instead.
"train/\".$FGS_train_file;")))
(substitute* "run_hmm.c"
(("^ strcat\\(train_dir, \\\"train/\\\"\\);")
- (string-append " strcpy(train_dir, \"" share "/train/\");")))
- (substitute* "post_process.pl"
- (("^my \\$dir = substr.*")
- (string-append "my $dir = \"" share "\";"))))
+ (string-append " strcpy(train_dir, \"" share "/train/\");"))))
#t))
(replace 'build
(lambda _ (and (zero? (system* "make" "clean"))
(share (string-append out "/share/fraggenescan/train")))
(install-file "run_FragGeneScan.pl" bin)
(install-file "FragGeneScan" bin)
- (install-file "FGS_gff.py" bin)
- (install-file "post_process.pl" bin)
(copy-recursively "train" share))))
(delete 'check)
(add-after 'install 'post-install-check
;; output files gets created.
(lambda* (#:key outputs #:allow-other-keys)
(let* ((out (string-append (assoc-ref outputs "out")))
- (bin (string-append out "/bin/")))
- (and (zero? (system* (string-append bin "run_FragGeneScan.pl")
+ (bin (string-append out "/bin/"))
+ (frag (string-append bin "run_FragGeneScan.pl")))
+ (and (zero? (system* frag ; Test complete genome.
"-genome=./example/NC_000913.fna"
"-out=./test2"
"-complete=1"
(file-exists? "test2.faa")
(file-exists? "test2.ffn")
(file-exists? "test2.gff")
- (file-exists? "test2.out"))))))))
+ (file-exists? "test2.out")
+ (zero? (system* ; Test incomplete sequences.
+ frag
+ "-genome=./example/NC_000913-fgs.ffn"
+ "-out=out"
+ "-complete=0"
+ "-train=454_30")))))))))
(inputs
`(("perl" ,perl)
("python" ,python-2))) ;not compatible with python 3.
(supported-systems '("x86_64-linux"))
(license license:expat))))
+(define-public gemma
+ (package
+ (name "gemma")
+ (version "0.96")
+ (source (origin
+ (method url-fetch)
+ (uri (string-append "https://github.com/xiangzhou/GEMMA/archive/v"
+ version ".tar.gz"))
+ (file-name (string-append name "-" version ".tar.gz"))
+ (sha256
+ (base32
+ "055ynn16gd12pf78n4vr2a9jlwsbwzajpdnf2y2yilg1krfff222"))
+ (patches (search-patches "gemma-intel-compat.patch"))))
+ (inputs
+ `(("gsl" ,gsl)
+ ("lapack" ,lapack)
+ ("zlib" ,zlib)))
+ (build-system gnu-build-system)
+ (arguments
+ `(#:make-flags
+ '(,@(match (%current-system)
+ ("x86_64-linux"
+ '("FORCE_DYNAMIC=1"))
+ ("i686-linux"
+ '("FORCE_DYNAMIC=1" "FORCE_32BIT=1"))
+ (_
+ '("FORCE_DYNAMIC=1" "NO_INTEL_COMPAT=1"))))
+ #:phases
+ (modify-phases %standard-phases
+ (delete 'configure)
+ (add-before 'build 'bin-mkdir
+ (lambda _
+ (mkdir-p "bin")
+ #t))
+ (replace 'install
+ (lambda* (#:key outputs #:allow-other-keys)
+ (let ((out (assoc-ref outputs "out")))
+ (install-file "bin/gemma"
+ (string-append
+ out "/bin")))
+ #t)))
+ #:tests? #f)) ; no tests included yet
+ (home-page "https://github.com/xiangzhou/GEMMA")
+ (synopsis "Tool for genome-wide efficient mixed model association")
+ (description
+ "Genome-wide Efficient Mixed Model Association (GEMMA) provides a
+standard linear mixed model resolver with application in genome-wide
+association studies (GWAS).")
+ (license license:gpl3)))
+
(define-public grit
(package
(name "grit")
(define-public htseq
(package
(name "htseq")
- (version "0.6.1")
+ (version "0.9.1")
(source (origin
(method url-fetch)
- (uri (string-append
- "https://pypi.python.org/packages/source/H/HTSeq/HTSeq-"
- version ".tar.gz"))
+ (uri (pypi-uri "HTSeq" version))
(sha256
(base32
- "1i85ppf2j2lj12m0x690qq5nn17xxk23pbbx2c83r8ayb5wngzwv"))))
+ "11flgb1381xdhk43bzbfm3vhnszkpqg6jk76rpa5xd1zbrvvlnxg"))))
(build-system python-build-system)
- (arguments `(#:python ,python-2)) ; only Python 2 is supported
+ (native-inputs
+ `(("python-cython" ,python-cython)))
;; Numpy needs to be propagated when htseq is used as a Python library.
(propagated-inputs
- `(("python-numpy" ,python2-numpy)))
+ `(("python-numpy" ,python-numpy)))
(inputs
- `(("python-pysam" ,python2-pysam)))
+ `(("python-pysam" ,python-pysam)
+ ("python-matplotlib" ,python-matplotlib)))
(home-page "http://www-huber.embl.de/users/anders/HTSeq/")
(synopsis "Analysing high-throughput sequencing data with Python")
(description
from high-throughput sequencing assays.")
(license license:gpl3+)))
+(define-public python2-htseq
+ (package-with-python2 htseq))
+
(define-public java-htsjdk
(package
(name "java-htsjdk")
(define-public htslib
(package
(name "htslib")
- (version "1.3.1")
+ (version "1.5")
(source (origin
(method url-fetch)
(uri (string-append
version "/htslib-" version ".tar.bz2"))
(sha256
(base32
- "1rja282fwdc25ql6izkhdyh8ppw8x2fs0w0js78zgkmqjlikmma9"))))
+ "0bcjmnbwp2bib1z1bkrp95w9v2syzdwdfqww10mkb1hxlmg52ax0"))))
(build-system gnu-build-system)
(arguments
`(#:phases
(("/bin/bash") (which "bash")))
#t)))))
(inputs
- `(("zlib" ,zlib)))
+ `(("openssl" ,openssl)
+ ("curl" ,curl)
+ ("zlib" ,zlib)))
(native-inputs
`(("perl" ,perl)))
(home-page "http://www.htslib.org")
;; the rest is released under the Expat license
(license (list license:expat license:bsd-3))))
+;; This package should be removed once no packages rely upon it.
+(define htslib-1.3
+ (package
+ (inherit htslib)
+ (version "1.3.1")
+ (source (origin
+ (method url-fetch)
+ (uri (string-append
+ "https://github.com/samtools/htslib/releases/download/"
+ version "/htslib-" version ".tar.bz2"))
+ (sha256
+ (base32
+ "1rja282fwdc25ql6izkhdyh8ppw8x2fs0w0js78zgkmqjlikmma9"))))))
+
(define-public idr
(package
(name "idr")
(supported-systems '("x86_64-linux"))
(license license:bsd-3)))
+(define-public kaiju
+ (package
+ (name "kaiju")
+ (version "1.5.0")
+ (source (origin
+ (method url-fetch)
+ (uri (string-append
+ "https://github.com/bioinformatics-centre/kaiju/archive/v"
+ version ".tar.gz"))
+ (file-name (string-append name "-" version ".tar.gz"))
+ (sha256
+ (base32
+ "0afbfalfw9y39bkwnqjrh9bghs118ws1pzj5h8l0nblgn3mbjdks"))))
+ (build-system gnu-build-system)
+ (arguments
+ `(#:tests? #f ; There are no tests.
+ #:phases
+ (modify-phases %standard-phases
+ (delete 'configure)
+ (add-before 'build 'move-to-src-dir
+ (lambda _ (chdir "src") #t))
+ (replace 'install
+ (lambda* (#:key inputs outputs #:allow-other-keys)
+ (let ((bin (string-append (assoc-ref outputs "out") "/bin")))
+ (mkdir-p bin)
+ (chdir "..")
+ (copy-recursively "bin" bin)
+ (copy-recursively "util" bin))
+ #t)))))
+ (inputs
+ `(("perl" ,perl)))
+ (home-page "http://kaiju.binf.ku.dk/")
+ (synopsis "Fast and sensitive taxonomic classification for metagenomics")
+ (description "Kaiju is a program for sensitive taxonomic classification
+of high-throughput sequencing reads from metagenomic whole genome sequencing
+experiments.")
+ (license license:gpl3+)))
+
(define-public macs
(package
(name "macs")
license:cpl1.0)))) ; Open Bloom Filter
(define-public metabat
- ;; We package from a git commit because compilation of the released version
- ;; fails.
- (let ((commit "cbdca756993e66ae57e50a27970595dda9cbde1b"))
- (package
- (name "metabat")
- (version (string-append "0.32.4-1." (string-take commit 8)))
- (source
- (origin
- (method git-fetch)
- (uri (git-reference
- (url "https://bitbucket.org/berkeleylab/metabat.git")
- (commit commit)))
- (file-name (string-append name "-" version))
- (sha256
- (base32
- "0byia8nsip6zvc4ha0qkxkxxyjf4x7jcvy48q2dvb0pzr989syzr"))
- (patches (search-patches "metabat-remove-compilation-date.patch"))))
+ (package
+ (name "metabat")
+ (version "2.11.2")
+ (source
+ (origin
+ (method url-fetch)
+ (uri (string-append "https://bitbucket.org/berkeleylab/metabat/get/v"
+ version ".tar.gz"))
+ (file-name (string-append name "-" version ".tar.gz"))
+ (sha256
+ (base32
+ "0rws9r1ziv6way8cf49jg8bzj7x2131kfqkhj8byf0z5hnrq3bwv"))
+ (patches (search-patches "metabat-remove-compilation-date.patch"
+ "metabat-fix-compilation.patch"))))
(build-system gnu-build-system)
(arguments
`(#:phases
"#include \"htslib/kseq.h\""))
#t))
(add-after 'unpack 'fix-scons
- (lambda* (#:key inputs #:allow-other-keys)
- (substitute* "SConstruct"
- (("^htslib_dir = 'samtools'")
- (string-append "hitslib_dir = '"
- (assoc-ref inputs "htslib")
- "'"))
- (("^samtools_dir = 'samtools'")
- (string-append "samtools_dir = '"
- (assoc-ref inputs "htslib")
- "'"))
- (("^findStaticOrShared\\('bam', hts_lib")
- (string-append "findStaticOrShared('bam', '"
- (assoc-ref inputs "samtools")
- "/lib'"))
- ;; Do not distribute README.
- (("^env\\.Install\\(idir_prefix, 'README\\.md'\\)") ""))
- #t))
+ (lambda* (#:key inputs #:allow-other-keys)
+ (substitute* "SConstruct"
+ (("^htslib_dir += 'samtools'")
+ (string-append "htslib_dir = '"
+ (assoc-ref inputs "htslib")
+ "'"))
+ (("^samtools_dir = 'samtools'")
+ (string-append "samtools_dir = '"
+ (assoc-ref inputs "samtools")
+ "'"))
+ (("^findStaticOrShared\\('bam', hts_lib")
+ (string-append "findStaticOrShared('bam', '"
+ (assoc-ref inputs "samtools")
+ "/lib'"))
+ ;; Do not distribute README.
+ (("^env\\.Install\\(idir_prefix, 'README\\.md'\\)") ""))
+ #t))
(delete 'configure)
(replace 'build
- (lambda* (#:key inputs outputs #:allow-other-keys)
- (mkdir (assoc-ref outputs "out"))
- (zero? (system* "scons"
- (string-append
- "PREFIX="
- (assoc-ref outputs "out"))
- (string-append
- "BOOST_ROOT="
- (assoc-ref inputs "boost"))
- "install"))))
+ (lambda* (#:key inputs outputs #:allow-other-keys)
+ (mkdir (assoc-ref outputs "out"))
+ (zero? (system* "scons"
+ (string-append
+ "PREFIX="
+ (assoc-ref outputs "out"))
+ (string-append
+ "BOOST_ROOT="
+ (assoc-ref inputs "boost"))
+ "install"))))
;; Check and install are carried out during build phase.
(delete 'check)
(delete 'install))))
enables the study of individual organisms and their interactions. MetaBAT is
an automated metagenome binning software, which integrates empirical
probabilistic distances of genome abundance and tetranucleotide frequency.")
- (license (license:non-copyleft "file://license.txt"
- "See license.txt in the distribution.")))))
+ ;; The source code contains inline assembly.
+ (supported-systems '("x86_64-linux" "i686-linux"))
+ (license (license:non-copyleft "file://license.txt"
+ "See license.txt in the distribution."))))
(define-public minced
(package
(define-public orfm
(package
(name "orfm")
- (version "0.6.1")
+ (version "0.7.1")
(source (origin
(method url-fetch)
(uri (string-append
version "/orfm-" version ".tar.gz"))
(sha256
(base32
- "19hwp13n82isdvk16710l9m35cmzf0q3fsrcn3r8c5r67biiz39s"))))
+ "16iigyr2gd8x0imzkk1dr3k5xsds9bpmwg31ayvjg0f4pir9rwqr"))))
(build-system gnu-build-system)
(inputs `(("zlib" ,zlib)))
(native-inputs
(define-public roary
(package
(name "roary")
- (version "3.7.0")
+ (version "3.8.2")
(source
(origin
(method url-fetch)
version ".tar.gz"))
(sha256
(base32
- "0x2hpb3nfsc6x2nq1788w0fhqfzc7cn2dp4xwyva9m3k6xlz0m43"))))
+ "03dfr2cd5fp80bcr65923zpdzrasvcxl7c2vgh8373v25a1yfap7"))))
(build-system perl-build-system)
(arguments
`(#:phases
(description
"RAxML is a tool for phylogenetic analysis and post-analysis of large
phylogenies.")
+ ;; The source includes x86 specific code
+ (supported-systems '("x86_64-linux" "i686-linux"))
(license license:gpl2+)))
(define-public rsem
(define-public samtools
(package
(name "samtools")
- (version "1.3.1")
+ (version "1.5")
(source
(origin
(method url-fetch)
version "/samtools-" version ".tar.bz2"))
(sha256
(base32
- "0znnnxc467jbf1as2dpskrjhfh8mbll760j6w6rdkwlwbqsp8gbc"))))
+ "1xidmv0jmfy7l0kb32hdnlshcxgzi1hmygvig0cqrq1fhckdlhl5"))))
(build-system gnu-build-system)
(arguments
`(#:modules ((ice-9 ftw)
(guix build gnu-build-system)
(guix build utils))
#:make-flags (list (string-append "prefix=" (assoc-ref %outputs "out")))
- #:configure-flags (list "--with-ncurses")
+ #:configure-flags (list "--with-ncurses" "--with-htslib=system")
#:phases
- (alist-cons-after
- 'unpack 'patch-tests
- (lambda _
- (substitute* "test/test.pl"
- ;; The test script calls out to /bin/bash
- (("/bin/bash") (which "bash")))
- #t)
- (alist-cons-after
- 'install 'install-library
- (lambda* (#:key outputs #:allow-other-keys)
- (let ((lib (string-append (assoc-ref outputs "out") "/lib")))
- (install-file "libbam.a" lib)
+ (modify-phases %standard-phases
+ (add-after 'unpack 'patch-tests
+ (lambda _
+ (substitute* "test/test.pl"
+ ;; The test script calls out to /bin/bash
+ (("/bin/bash") (which "bash")))
#t))
- (alist-cons-after
- 'install 'install-headers
- (lambda* (#:key outputs #:allow-other-keys)
- (let ((include (string-append (assoc-ref outputs "out")
- "/include/samtools/")))
- (for-each (lambda (file)
- (install-file file include))
- (scandir "." (lambda (name) (string-match "\\.h$" name))))
- #t))
- %standard-phases)))))
+ (add-after 'install 'install-library
+ (lambda* (#:key outputs #:allow-other-keys)
+ (let ((lib (string-append (assoc-ref outputs "out") "/lib")))
+ (install-file "libbam.a" lib)
+ #t)))
+ (add-after 'install 'install-headers
+ (lambda* (#:key outputs #:allow-other-keys)
+ (let ((include (string-append (assoc-ref outputs "out")
+ "/include/samtools/")))
+ (for-each (lambda (file)
+ (install-file file include))
+ (scandir "." (lambda (name) (string-match "\\.h$" name))))
+ #t))))))
(native-inputs `(("pkg-config" ,pkg-config)))
- (inputs `(("ncurses" ,ncurses)
- ("perl" ,perl)
- ("python" ,python)
- ("zlib" ,zlib)))
+ (inputs
+ `(("htslib" ,htslib)
+ ("ncurses" ,ncurses)
+ ("perl" ,perl)
+ ("python" ,python)
+ ("zlib" ,zlib)))
(home-page "http://samtools.sourceforge.net")
(synopsis "Utilities to efficiently manipulate nucleotide sequence alignments")
(description
sequencing (NGS) reads. The core algorithm is based on approximate seeds and
allows for fast and sensitive analyses of nucleotide sequences. The main
application of SortMeRNA is filtering rRNA from metatranscriptomic data.")
+ ;; The source includes x86 specific code
+ (supported-systems '("x86_64-linux" "i686-linux"))
(license license:lgpl3)))
(define-public star
(define-public taxtastic
(package
(name "taxtastic")
- (version "0.5.7")
- ;; Versions after 0.5.4 do not appear to be distributed on PyPI so we
- ;; download the package from GitHub.
+ (version "0.6.4")
(source (origin
(method url-fetch)
- (uri (string-append
- "https://github.com/fhcrc/taxtastic/archive/v"
- version ".tar.gz"))
- (file-name (string-append name "-" version ".tar.gz"))
+ (uri (pypi-uri "taxtastic" version))
(sha256
(base32
- "1s0h5y1lds1c40jhir5585ffm6yjyn8h5aqimpgv64rhqhfv56xx"))))
+ "0s79z8kfl853x7l4h8ms05k31q87aw62nrchlk20w9n227j35929"))))
(build-system python-build-system)
(arguments
`(#:python ,python-2
(define-public r-deseq2
(package
(name "r-deseq2")
- (version "1.16.0")
+ (version "1.16.1")
(source
(origin
(method url-fetch)
(uri (bioconductor-uri "DESeq2" version))
(sha256
(base32
- "0m0apn3xi4kdkinsj4xkw5cwysicyjr6xxlxhpa4scyv589am1s5"))))
+ "01pvyljxkwazxl510v7h0971nx65iqd2bdkbdhw3xzind0n9pdvq"))))
(properties `((upstream-name . "DESeq2")))
(build-system r-build-system)
(propagated-inputs
(define-public r-annotationforge
(package
(name "r-annotationforge")
- (version "1.18.0")
+ (version "1.18.1")
(source
(origin
(method url-fetch)
(uri (bioconductor-uri "AnnotationForge" version))
(sha256
(base32
- "01kd86vvgpa4a5zivcy4g6z8rhcykasdskrz8yqsqz211sd1xsr3"))))
+ "1366qvykd9cpcvwgc5g9mm9adw9rxw6p4814dd6l5fyb0pwpmysx"))))
(properties
`((upstream-name . "AnnotationForge")))
(build-system r-build-system)
(define-public r-category
(package
(name "r-category")
- (version "2.42.0")
+ (version "2.42.1")
(source
(origin
(method url-fetch)
(uri (bioconductor-uri "Category" version))
(sha256
(base32
- "0swcmihyjg0fhaaydl9hm24aj9zffw3bibza9y6sqs6jaqd97f09"))))
+ "1w186nhc85bglcgmbcrsdbb8l6rph21pl5kdwjqwkp0jnr9z0ifn"))))
(properties `((upstream-name . "Category")))
(build-system r-build-system)
(propagated-inputs
(define-public r-bookdown
(package
(name "r-bookdown")
- (version "0.3")
+ (version "0.4")
(source (origin
(method url-fetch)
(uri (cran-uri "bookdown" version))
(sha256
(base32
- "0r9bchzg7im6psc3jphvshzbidc5bv5xaih1qg7b5518jy4iyvb9"))))
+ "1fp1k7hivrb7s2dwgrsqy9s7xg6pk9hczhrc149y1dwh901j6qvv"))))
(build-system r-build-system)
(propagated-inputs
`(("r-htmltools" ,r-htmltools)
(define-public r-biocstyle
(package
(name "r-biocstyle")
- (version "2.4.0")
+ (version "2.4.1")
(source (origin
(method url-fetch)
(uri (bioconductor-uri "BiocStyle" version))
(sha256
(base32
- "1n2c8rj920wmk3q2khmjfnhn5i4b3lmhx1whnghk0zk3jf88hvbi"))))
+ "0bmgmsfll923v573g0kyzlmjd7gly5jwgd8vkrcwvbam1gz75f2c"))))
(properties
`((upstream-name . "BiocStyle")))
(build-system r-build-system)
(define-public r-optparse
(package
(name "r-optparse")
- (version "1.3.2")
+ (version "1.4.4")
(source
(origin
(method url-fetch)
(uri (cran-uri "optparse" version))
(sha256
(base32
- "1g8as89r91xxi5j5azsd6vrfrhg84mnfx2683j7pacdp8s33radw"))))
+ "1ff4wmsszrb3spwfp7ynfs8w11qpy1sdzfxm1wk8dqqvdwris7qb"))))
(build-system r-build-system)
(propagated-inputs
`(("r-getopt" ,r-getopt)))
(define-public r-dnacopy
(package
(name "r-dnacopy")
- (version "1.50.0")
+ (version "1.50.1")
(source (origin
(method url-fetch)
(uri (bioconductor-uri "DNAcopy" version))
(sha256
(base32
- "0112ry62z18m7rdyrn3gvbxq2f6m44cawhcfb1f02z9xzlsj0k28"))))
+ "0f0x83db7rm5xf9fg5pjhvs4i165qqaf01lbwb8kj13fsqpwx15p"))))
(properties
`((upstream-name . "DNAcopy")))
(build-system r-build-system)
(define-public r-s4vectors
(package
(name "r-s4vectors")
- (version "0.14.0")
+ (version "0.14.3")
(source (origin
(method url-fetch)
(uri (bioconductor-uri "S4Vectors" version))
(sha256
(base32
- "0ywwrs4d752xfk0p0w122kvi0xvp6nmxnyynchbsa8zciqymhgv8"))))
+ "1r7s4pfw026qazzic090mhk8d9m39j2nwl87dyqcpdylyq7gq5qs"))))
(properties
`((upstream-name . "S4Vectors")))
(build-system r-build-system)
(define-public r-seqinr
(package
(name "r-seqinr")
- (version "3.3-6")
+ (version "3.4-5")
(source
(origin
(method url-fetch)
(uri (cran-uri "seqinr" version))
(sha256
(base32
- "13d0qxm2244wgdl2dy2s8vnrnf5fx4n47if9gkb49dqx6c0sx8s2"))))
+ "17zv0n5cji17izwmwg0jcbxbjl3w5rls91w15svcnlpxjms38ahn"))))
(build-system r-build-system)
(propagated-inputs
`(("r-ade4" ,r-ade4)
(define-public r-iranges
(package
(name "r-iranges")
- (version "2.10.0")
+ (version "2.10.2")
(source (origin
(method url-fetch)
(uri (bioconductor-uri "IRanges" version))
(sha256
(base32
- "0zp4mxm9h1p4krj7m7cinkvwa2ibqkq59jwpan97yvhb4z8q0d6n"))))
+ "1brmzs3rsf97gymridrh9c9r3vws8b3rpghaanxnniw36lmcajfy"))))
(properties
`((upstream-name . "IRanges")))
(build-system r-build-system)
(define-public r-genomeinfodb
(package
(name "r-genomeinfodb")
- (version "1.12.0")
+ (version "1.12.2")
(source (origin
(method url-fetch)
(uri (bioconductor-uri "GenomeInfoDb" version))
(sha256
(base32
- "1bwwhscjl376a5p43mx8ijrqajxmgypbqhv049pgagl22hkkf0y3"))))
+ "1hjxgmcnrngp1307ipqaq9hgxz4j0ldn7d46knhzs30k2r4qnrfp"))))
(properties
`((upstream-name . "GenomeInfoDb")))
(build-system r-build-system)
(define-public r-variantannotation
(package
(name "r-variantannotation")
- (version "1.22.0")
+ (version "1.22.3")
(source (origin
(method url-fetch)
(uri (bioconductor-uri "VariantAnnotation" version))
(sha256
(base32
- "05hpm4as36kvpiqhgnkfjwfx0a05p304c21ggba29iac4nanm8b3"))))
+ "0sr3vdn85x5zdxh80cfwlpfdpi2hmjy3fwi00ac3jya4v145vawr"))))
(properties
`((upstream-name . "VariantAnnotation")))
(inputs
(define-public r-limma
(package
(name "r-limma")
- (version "3.32.0")
+ (version "3.32.5")
(source (origin
(method url-fetch)
(uri (bioconductor-uri "limma" version))
(sha256
(base32
- "0q7rqm86nwq0rg4fjggfr7xqybjrxj425vni3cva70b4c8d1h425"))))
+ "0p2ayha9g9w5r8s7pgdf16mkmdbqwh6f35jh07g3b8gyra48gwiw"))))
(build-system r-build-system)
(home-page "http://bioinf.wehi.edu.au/limma")
(synopsis "Package for linear models for microarray and RNA-seq data")
(define-public r-genomicranges
(package
(name "r-genomicranges")
- (version "1.28.0")
+ (version "1.28.4")
(source (origin
(method url-fetch)
(uri (bioconductor-uri "GenomicRanges" version))
(sha256
(base32
- "10x9zx0b7j05d1j6p0xs4q4f4wzbhf3rq64wzi9cgv7f44q43a5n"))))
+ "1y15kg1q81h8rmga83ljiwr8whkajcargfjiljr212d6if17ys1z"))))
(properties
`((upstream-name . "GenomicRanges")))
(build-system r-build-system)
(define-public r-biobase
(package
(name "r-biobase")
- (version "2.36.0")
+ (version "2.36.2")
(source (origin
(method url-fetch)
(uri (bioconductor-uri "Biobase" version))
(sha256
(base32
- "0x7pf5xsdcj12dbf5qqki2c6bd5madqg2fbiq5xgisarpc9v6c1m"))))
+ "0sr48nqx5bqid4g6lr9zr9286xh842w717yvmssvddb5xxynib6f"))))
(properties
`((upstream-name . "Biobase")))
(build-system r-build-system)
(define-public r-annotationdbi
(package
(name "r-annotationdbi")
- (version "1.38.0")
+ (version "1.38.2")
(source (origin
(method url-fetch)
(uri (bioconductor-uri "AnnotationDbi" version))
(sha256
(base32
- "1xffm98s817mfc827cnr0by6167nlrl1glxzjawzz0rkghs41g27"))))
+ "1lsamnbf07zzsy5asy5hn97n2a4layv58w2bzd90ikcdx0gmzarj"))))
(properties
`((upstream-name . "AnnotationDbi")))
(build-system r-build-system)
(define-public r-biomart
(package
(name "r-biomart")
- (version "2.32.0")
+ (version "2.32.1")
(source (origin
(method url-fetch)
(uri (bioconductor-uri "biomaRt" version))
(sha256
(base32
- "0knkxh23vl9pa0by03xr6dy9aiah714cmf54jl828k51l9wv5l2j"))))
+ "0fhpbjlsgbqxrpj6nzhhk9q3ph81n5x4p7mmd097xjjn6b05w1d8"))))
(properties
`((upstream-name . "biomaRt")))
(build-system r-build-system)
(define-public r-biocparallel
(package
(name "r-biocparallel")
- (version "1.10.0")
+ (version "1.10.1")
(source (origin
(method url-fetch)
(uri (bioconductor-uri "BiocParallel" version))
(sha256
(base32
- "01ph0kq70b5gkd7n6a4myjlvwzgc0hi4xfwz8h17h06n9p5sdwa9"))))
+ "08mdfxyk9nwz77v0xhlvs19p2wj0phgm5c5b25vm0xh3749njsp0"))))
(properties
`((upstream-name . "BiocParallel")))
(build-system r-build-system)
(define-public r-biostrings
(package
(name "r-biostrings")
- (version "2.44.0")
+ (version "2.44.2")
(source (origin
(method url-fetch)
(uri (bioconductor-uri "Biostrings" version))
(sha256
(base32
- "0ixgx12cx2z4n2khxq83crz9gc21qckj2v78y2p31567kfsw7clg"))))
+ "12c5abgshwq86357jr0r9039y6vl4d6ngysy89rsnr23ldnsirjp"))))
(properties
`((upstream-name . "Biostrings")))
(build-system r-build-system)
(define-public r-delayedarray
(package
(name "r-delayedarray")
- (version "0.2.0")
+ (version "0.2.7")
(source (origin
(method url-fetch)
(uri (bioconductor-uri "DelayedArray" version))
(sha256
(base32
- "0pcsk0f2dg2ldzprs1cccqrk53jrysmm6ccgjj5wh6z3x17g7g2r"))))
+ "02dfqp4md9xaqjj712ijc3jswghmipr5hwkd5hr0x1xi6l2fb69g"))))
(properties
`((upstream-name . "DelayedArray")))
(build-system r-build-system)
(define-public r-summarizedexperiment
(package
(name "r-summarizedexperiment")
- (version "1.6.0")
+ (version "1.6.3")
(source (origin
(method url-fetch)
(uri (bioconductor-uri "SummarizedExperiment" version))
(sha256
(base32
- "1szjbzzz4pyip891nji71caalxh0rhqiv7rpv6q54swlrqpfkqkw"))))
+ "0j7xn7pk52d383fb1wplcggacl2586c4zi0alkgfc3wz7qq9w13s"))))
(properties
`((upstream-name . "SummarizedExperiment")))
(build-system r-build-system)
(define-public r-genomicalignments
(package
(name "r-genomicalignments")
- (version "1.12.0")
+ (version "1.12.1")
(source (origin
(method url-fetch)
(uri (bioconductor-uri "GenomicAlignments" version))
(sha256
(base32
- "1aagyrdk5309a7awg42lg0bpirp91i6i2ddvpmrs38pzriwahnjy"))))
+ "127690sys4i5q3l4vxnjg4xg8q19qlw2258vgs5d1156w9ypp04h"))))
(properties
`((upstream-name . "GenomicAlignments")))
(build-system r-build-system)
(define-public r-rtracklayer
(package
(name "r-rtracklayer")
- (version "1.36.0")
+ (version "1.36.4")
(source (origin
(method url-fetch)
(uri (bioconductor-uri "rtracklayer" version))
(sha256
(base32
- "0dv7p3wzmx57inznf6fb06417zcm48g7fpazyahxny7bqgzwq0ig"))))
+ "050q1rv04w31168ljr975vxva31n9lqdx84rnmsk6zcr6p640ffp"))))
(build-system r-build-system)
(arguments
`(#:phases
(define-public r-genomicfeatures
(package
(name "r-genomicfeatures")
- (version "1.28.0")
+ (version "1.28.4")
(source (origin
(method url-fetch)
(uri (bioconductor-uri "GenomicFeatures" version))
(sha256
(base32
- "1pjxlr34ygv8pvfwpyq268wpgqzphiwpij85fyhjqdwdp0a253ik"))))
+ "01ylvg275iy0cvsbxkbfxcf9pi9al597v5wnlqi2xdpmrcxyc3q0"))))
(properties
`((upstream-name . "GenomicFeatures")))
(build-system r-build-system)
(define-public r-qtl
(package
(name "r-qtl")
- (version "1.40-8")
+ (version "1.41-6")
(source
(origin
(method url-fetch)
version ".tar.gz"))
(sha256
(base32
- "05bj1x2ry0i7yqiydlswb3d2h4pxg70z8w1072az1mrv1m54k8sp"))))
+ "067az4v432zxp6lxck8d7vlh9w4r13r0mvw5zsglyaqwsh3d9sad"))))
(build-system r-build-system)
(home-page "http://rqtl.org/")
(synopsis "R package for analyzing QTL experiments in genetics")
(define-public r-mutationalpatterns
(package
(name "r-mutationalpatterns")
- (version "1.2.0")
+ (version "1.2.1")
(source
(origin
(method url-fetch)
(uri (bioconductor-uri "MutationalPatterns" version))
(sha256
(base32
- "00jh1qklj8jb9j7mwvkfybq368h2wg9yc2cwkgb7yb9vsw72r61d"))))
+ "1s50diwh1j6vg3mgahh6bczvq74mfdbmwjrad4d5lh723gnc5pjg"))))
(build-system r-build-system)
(propagated-inputs
`(("r-biocgenerics" ,r-biocgenerics)
(define-public r-wgcna
(package
(name "r-wgcna")
- (version "1.51")
+ (version "1.60")
(source
(origin
(method url-fetch)
(uri (cran-uri "WGCNA" version))
(sha256
(base32
- "0hzvnhw76vwg8bl8x368f0c5szpwb8323bmrb3bir93i5bmfjsxx"))))
+ "16mxhwzhh5q48wmz1iba2r21cp0n0v8g11am4pi52iv6g0663ixl"))))
(properties `((upstream-name . "WGCNA")))
(build-system r-build-system)
(propagated-inputs
(define-public r-copywriter
(package
(name "r-copywriter")
- (version "2.8.0")
+ (version "2.8.1")
(source
(origin
(method url-fetch)
(uri (bioconductor-uri "CopywriteR" version))
(sha256
(base32
- "183nmrqmdf9syqljslvwv7mhs9ar5xizzq98imgsc80q0m25ncjf"))))
+ "0xgqnq5v5213b3nzvlmjysjb7w1bc0iblqpmzbjqn7n0ib0qyhbm"))))
(properties `((upstream-name . "CopywriteR")))
(build-system r-build-system)
(propagated-inputs
(define-public r-sva
(package
(name "r-sva")
- (version "3.24.0")
+ (version "3.24.4")
(source
(origin
(method url-fetch)
(uri (bioconductor-uri "sva" version))
(sha256
(base32
- "04pxl61iyc845wmqca1qv8kbb8zcp0qp72zgvgki3zzmrph9a362"))))
+ "0wcway4ai9im81xnrzb1vij2iidq5pw24qhjfgacmhxvx3dzhbsc"))))
(build-system r-build-system)
(propagated-inputs
`(("r-genefilter" ,r-genefilter)
- ("r-mgcv" ,r-mgcv)))
+ ("r-mgcv" ,r-mgcv)
+ ("r-biocparallel" ,r-biocparallel)
+ ("r-matrixstats" ,r-matrixstats)
+ ("r-limma" ,r-limma)))
(home-page "http://bioconductor.org/packages/sva")
(synopsis "Surrogate variable analysis")
(description
(define-public r-seqminer
(package
(name "r-seqminer")
- (version "5.9")
+ (version "6.0")
(source
(origin
(method url-fetch)
(uri (cran-uri "seqminer" version))
(sha256
(base32
- "0sfkxrc9gy5a8fadzyzfzh7l5grasm8cj6cd2nnpv85ws6mqr6qd"))))
+ "057j1l6dip35l1aivilapl2zv9db677b3di2pb3sfgq2sxg0ps3l"))))
(build-system r-build-system)
(inputs
`(("zlib" ,zlib)))
discovery of differentially expressed genes and markers.")
(license license:gpl3))))
+(define-public r-aroma-light
+ (package
+ (name "r-aroma-light")
+ (version "3.6.0")
+ (source
+ (origin
+ (method url-fetch)
+ (uri (bioconductor-uri "aroma.light" version))
+ (sha256
+ (base32
+ "10snykmmx36qaymyf5s1n1km8hsscyzpykcpf0mzsrcv8ml9rp8a"))))
+ (properties `((upstream-name . "aroma.light")))
+ (build-system r-build-system)
+ (propagated-inputs
+ `(("r-matrixstats" ,r-matrixstats)
+ ("r-r-methodss3" ,r-r-methodss3)
+ ("r-r-oo" ,r-r-oo)
+ ("r-r-utils" ,r-r-utils)))
+ (home-page "https://github.com/HenrikBengtsson/aroma.light")
+ (synopsis "Methods for normalization and visualization of microarray data")
+ (description
+ "This package provides methods for microarray analysis that take basic
+data types such as matrices and lists of vectors. These methods can be used
+standalone, be utilized in other packages, or be wrapped up in higher-level
+classes.")
+ (license license:gpl2+)))
+
+(define-public r-deseq
+ (package
+ (name "r-deseq")
+ (version "1.28.0")
+ (source
+ (origin
+ (method url-fetch)
+ (uri (bioconductor-uri "DESeq" version))
+ (sha256
+ (base32
+ "0j3dgcxd64m9qknmlcbdzvg4xhp981xd6nbwsvnqjfn6yypslgyw"))))
+ (properties `((upstream-name . "DESeq")))
+ (build-system r-build-system)
+ (propagated-inputs
+ `(("r-biobase" ,r-biobase)
+ ("r-biocgenerics" ,r-biocgenerics)
+ ("r-genefilter" ,r-genefilter)
+ ("r-geneplotter" ,r-geneplotter)
+ ("r-lattice" ,r-lattice)
+ ("r-locfit" ,r-locfit)
+ ("r-mass" ,r-mass)
+ ("r-rcolorbrewer" ,r-rcolorbrewer)))
+ (home-page "http://www-huber.embl.de/users/anders/DESeq")
+ (synopsis "Differential gene expression analysis")
+ (description
+ "This package provides tools for estimating variance-mean dependence in
+count data from high-throughput genetic sequencing assays and for testing for
+differential expression based on a model using the negative binomial
+distribution.")
+ (license license:gpl3+)))
+
+(define-public r-edaseq
+ (package
+ (name "r-edaseq")
+ (version "2.10.0")
+ (source
+ (origin
+ (method url-fetch)
+ (uri (bioconductor-uri "EDASeq" version))
+ (sha256
+ (base32
+ "0f25dfc8hdii9fjm3bf89vy9jkxv23sa62fkcga5b4gkipwrvm9a"))))
+ (properties `((upstream-name . "EDASeq")))
+ (build-system r-build-system)
+ (propagated-inputs
+ `(("r-annotationdbi" ,r-annotationdbi)
+ ("r-aroma-light" ,r-aroma-light)
+ ("r-biobase" ,r-biobase)
+ ("r-biocgenerics" ,r-biocgenerics)
+ ("r-biomart" ,r-biomart)
+ ("r-biostrings" ,r-biostrings)
+ ("r-deseq" ,r-deseq)
+ ("r-genomicfeatures" ,r-genomicfeatures)
+ ("r-genomicranges" ,r-genomicranges)
+ ("r-iranges" ,r-iranges)
+ ("r-rsamtools" ,r-rsamtools)
+ ("r-shortread" ,r-shortread)))
+ (home-page "https://github.com/drisso/EDASeq")
+ (synopsis "Exploratory data analysis and normalization for RNA-Seq")
+ (description
+ "This package provides support for numerical and graphical summaries of
+RNA-Seq genomic read data. Provided within-lane normalization procedures to
+adjust for GC-content effect (or other gene-level effects) on read counts:
+loess robust local regression, global-scaling, and full-quantile
+normalization. Between-lane normalization procedures to adjust for
+distributional differences between lanes (e.g., sequencing depth):
+global-scaling and full-quantile normalization.")
+ (license license:artistic2.0)))
+
(define htslib-for-sambamba
(let ((commit "2f3c3ea7b301f9b45737a793c0b2dcf0240e5ee5"))
(package
an important subset of samtools functionality, including view, index,
sort, markdup, and depth.")
(license license:gpl2+)))
+
+(define-public ritornello
+ (package
+ (name "ritornello")
+ (version "1.0.0")
+ (source (origin
+ (method url-fetch)
+ (uri (string-append "https://github.com/KlugerLab/"
+ "Ritornello/archive/v"
+ version ".tar.gz"))
+ (file-name (string-append name "-" version ".tar.gz"))
+ (sha256
+ (base32
+ "02nik86gq9ljjriv6pamwlmqnfky3ads1fpklx6mc3hx6k40pg38"))))
+ (build-system gnu-build-system)
+ (arguments
+ `(#:tests? #f ; there are no tests
+ #:phases
+ (modify-phases %standard-phases
+ (add-after 'unpack 'patch-samtools-references
+ (lambda* (#:key inputs #:allow-other-keys)
+ (substitute* '("src/SamStream.h"
+ "src/BufferedGenomeReader.h")
+ (("<sam.h>") "<samtools/sam.h>"))
+ #t))
+ (delete 'configure)
+ (replace 'install
+ (lambda* (#:key inputs outputs #:allow-other-keys)
+ (let* ((out (assoc-ref outputs "out"))
+ (bin (string-append out "/bin/")))
+ (mkdir-p bin)
+ (install-file "bin/Ritornello" bin)
+ #t))))))
+ (inputs
+ `(("samtools" ,samtools-0.1)
+ ("fftw" ,fftw)
+ ("boost" ,boost)
+ ("zlib" ,zlib)))
+ (home-page "https://github.com/KlugerLab/Ritornello")
+ (synopsis "Control-free peak caller for ChIP-seq data")
+ (description "Ritornello is a ChIP-seq peak calling algorithm based on
+signal processing that can accurately call binding events without the need to
+do a pair total DNA input or IgG control sample. It has been tested for use
+with narrow binding events such as transcription factor ChIP-seq.")
+ (license license:gpl3+)))
+
+(define-public trim-galore
+ (package
+ (name "trim-galore")
+ (version "0.4.2")
+ (source
+ (origin
+ (method url-fetch)
+ (uri (string-append "http://www.bioinformatics.babraham.ac.uk/"
+ "projects/trim_galore/trim_galore_v"
+ version ".zip"))
+ (sha256
+ (base32
+ "0b9qdxi4521gsrjvbhgky8g7kry9b5nx3byzaxkgxz7p4k8bn1mn"))))
+ (build-system gnu-build-system)
+ (arguments
+ `(#:tests? #f ; no tests
+ #:phases
+ (modify-phases %standard-phases
+ ;; The archive contains plain files.
+ (replace 'unpack
+ (lambda* (#:key source #:allow-other-keys)
+ (zero? (system* "unzip" source))))
+ (delete 'configure)
+ (delete 'build)
+ (add-after 'unpack 'hardcode-tool-references
+ (lambda* (#:key inputs #:allow-other-keys)
+ (substitute* "trim_galore"
+ (("\\$path_to_cutadapt = 'cutadapt'")
+ (string-append "$path_to_cutadapt = '"
+ (assoc-ref inputs "cutadapt")
+ "/bin/cutadapt'"))
+ (("\\| gzip")
+ (string-append "| "
+ (assoc-ref inputs "gzip")
+ "/bin/gzip"))
+ (("\"gunzip")
+ (string-append "\""
+ (assoc-ref inputs "gzip")
+ "/bin/gunzip")))
+ #t))
+ (replace 'install
+ (lambda* (#:key outputs #:allow-other-keys)
+ (let ((bin (string-append (assoc-ref outputs "out")
+ "/bin")))
+ (mkdir-p bin)
+ (install-file "trim_galore" bin)
+ #t))))))
+ (inputs
+ `(("gzip" ,gzip)
+ ("perl" ,perl)
+ ("cutadapt" ,cutadapt)))
+ (native-inputs
+ `(("unzip" ,unzip)))
+ (home-page "http://www.bioinformatics.babraham.ac.uk/projects/trim_galore/")
+ (synopsis "Wrapper around Cutadapt and FastQC")
+ (description "Trim Galore! is a wrapper script to automate quality and
+adapter trimming as well as quality control, with some added functionality to
+remove biased methylation positions for RRBS sequence files.")
+ (license license:gpl3+)))
+
+(define-public gess
+ (package
+ (name "gess")
+ (version "1.0")
+ (source (origin
+ (method url-fetch)
+ (uri (string-append "http://compbio.uthscsa.edu/"
+ "GESS_Web/files/"
+ "gess-" version ".src.tar.gz"))
+ (sha256
+ (base32
+ "0hyk403kxscclzfs24pvdgiv0wm03kjcziqdrp5w46cb049gz0d7"))))
+ (build-system gnu-build-system)
+ (arguments
+ `(#:tests? #f ; no tests
+ #:phases
+ (modify-phases %standard-phases
+ (delete 'configure)
+ (delete 'build)
+ (replace 'install
+ (lambda* (#:key inputs outputs #:allow-other-keys)
+ (let* ((python (assoc-ref inputs "python"))
+ (out (assoc-ref outputs "out"))
+ (bin (string-append out "/bin/"))
+ (target (string-append
+ out "/lib/python2.7/site-packages/gess/")))
+ (mkdir-p target)
+ (copy-recursively "." target)
+ ;; Make GESS.py executable
+ (chmod (string-append target "GESS.py") #o555)
+ ;; Add Python shebang to the top and make Matplotlib
+ ;; usable.
+ (substitute* (string-append target "GESS.py")
+ (("\"\"\"Description:" line)
+ (string-append "#!" (which "python") "
+import matplotlib
+matplotlib.use('Agg')
+" line)))
+ ;; Make sure GESS has all modules in its path
+ (wrap-program (string-append target "GESS.py")
+ `("PYTHONPATH" ":" prefix (,target ,(getenv "PYTHONPATH"))))
+ (mkdir-p bin)
+ (symlink (string-append target "GESS.py")
+ (string-append bin "GESS.py"))
+ #t))))))
+ (inputs
+ `(("python" ,python-2)
+ ("python2-pysam" ,python2-pysam)
+ ("python2-scipy" ,python2-scipy)
+ ("python2-numpy" ,python2-numpy)
+ ("python2-networkx" ,python2-networkx)
+ ("python2-biopython" ,python2-biopython)))
+ (home-page "http://compbio.uthscsa.edu/GESS_Web/")
+ (synopsis "Detect exon-skipping events from raw RNA-seq data")
+ (description
+ "GESS is an implementation of a novel computational method to detect de
+novo exon-skipping events directly from raw RNA-seq data without the prior
+knowledge of gene annotation information. GESS stands for the graph-based
+exon-skipping scanner detection scheme.")
+ (license license:bsd-3)))
+
+(define-public phylip
+ (package
+ (name "phylip")
+ (version "3.696")
+ (source
+ (origin
+ (method url-fetch)
+ (uri (string-append "http://evolution.gs.washington.edu/phylip/"
+ "download/phylip-" version ".tar.gz"))
+ (sha256
+ (base32
+ "01jar1rayhr2gba2pgbw49m56rc5z4p5wn3ds0m188hrlln4a2nd"))))
+ (build-system gnu-build-system)
+ (arguments
+ `(#:tests? #f ; no check target
+ #:make-flags (list "-f" "Makefile.unx" "install")
+ #:parallel-build? #f ; not supported
+ #:phases
+ (modify-phases %standard-phases
+ (add-after 'unpack 'enter-dir
+ (lambda _ (chdir "src") #t))
+ (delete 'configure)
+ (replace 'install
+ (lambda* (#:key inputs outputs #:allow-other-keys)
+ (let ((target (string-append (assoc-ref outputs "out")
+ "/bin")))
+ (mkdir-p target)
+ (for-each (lambda (file)
+ (install-file file target))
+ (find-files "../exe" ".*")))
+ #t)))))
+ (home-page "http://evolution.genetics.washington.edu/phylip/")
+ (synopsis "Tools for inferring phylogenies")
+ (description "PHYLIP (the PHYLogeny Inference Package) is a package of
+programs for inferring phylogenies (evolutionary trees).")
+ (license license:bsd-2)))
+
+(define-public imp
+ (package
+ (name "imp")
+ (version "2.6.2")
+ (source
+ (origin
+ (method url-fetch)
+ (uri (string-append "https://integrativemodeling.org/"
+ version "/download/imp-" version ".tar.gz"))
+ (sha256
+ (base32
+ "0lxqx7vh79d771svr611dkilp6sn30qrbw8zvscbrm37v38d2j6h"))))
+ (build-system cmake-build-system)
+ (arguments
+ `(;; FIXME: Some tests fail because they produce warnings, others fail
+ ;; because the PYTHONPATH does not include the modeller's directory.
+ #:tests? #f
+ ;; Do not place libraries in an architecture-specific directory.
+ #:configure-flags
+ (list "-DCMAKE_INSTALL_LIBDIR=lib")))
+ (inputs
+ `(("boost" ,boost)
+ ("gsl" ,gsl)
+ ("swig" ,swig)
+ ("hdf5" ,hdf5)
+ ("fftw" ,fftw)
+ ("python" ,python-2)))
+ (propagated-inputs
+ `(("python2-numpy" ,python2-numpy)
+ ("python2-scipy" ,python2-scipy)
+ ("python2-pandas" ,python2-pandas)
+ ("python2-scikit-learn" ,python2-scikit-learn)
+ ("python2-networkx" ,python2-networkx)))
+ (home-page "https://integrativemodeling.org")
+ (synopsis "Integrative modeling platform")
+ (description "IMP's broad goal is to contribute to a comprehensive
+structural characterization of biomolecules ranging in size and complexity
+from small peptides to large macromolecular assemblies, by integrating data
+from diverse biochemical and biophysical experiments. IMP provides a C++ and
+Python toolbox for solving complex modeling problems, and a number of
+applications for tackling some common problems in a user-friendly way.")
+ ;; IMP is largely available under the GNU Lesser GPL; see the file
+ ;; COPYING.LGPL for the full text of this license. Some IMP modules are
+ ;; available under the GNU GPL (see the file COPYING.GPL).
+ (license (list license:lgpl2.1+
+ license:gpl3+))))
+
+(define-public tadbit
+ (package
+ (name "tadbit")
+ (version "0.2")
+ (source (origin
+ (method url-fetch)
+ (uri (string-append "https://github.com/3DGenomes/TADbit/"
+ "archive/v" version ".tar.gz"))
+ (file-name (string-append name "-" version ".tar.gz"))
+ (sha256
+ (base32
+ "1cnfqrl4685zar4nnw94j94nhvl2h29jm448nadqi1h05z6fdk4f"))))
+ (build-system python-build-system)
+ (arguments
+ `(;; Tests are included and must be run after installation, but
+ ;; they are incomplete and thus cannot be run.
+ #:tests? #f
+ #:python ,python-2
+ #:phases
+ (modify-phases %standard-phases
+ (add-after 'unpack 'fix-problems-with-setup.py
+ (lambda* (#:key outputs #:allow-other-keys)
+ ;; setup.py opens these files for writing
+ (chmod "_pytadbit/_version.py" #o664)
+ (chmod "README.rst" #o664)
+
+ ;; Don't attempt to install the bash completions to
+ ;; the home directory.
+ (rename-file "extras/.bash_completion"
+ "extras/tadbit")
+ (substitute* "setup.py"
+ (("\\(path.expanduser\\('~'\\)")
+ (string-append "(\""
+ (assoc-ref outputs "out")
+ "/etc/bash_completion.d\""))
+ (("extras/\\.bash_completion")
+ "extras/tadbit"))
+ #t)))))
+ (inputs
+ ;; TODO: add Chimera for visualization
+ `(("imp" ,imp)
+ ("mcl" ,mcl)
+ ("python2-scipy" ,python2-scipy)
+ ("python2-numpy" ,python2-numpy)
+ ("python2-matplotlib" ,python2-matplotlib)
+ ("python2-pysam" ,python2-pysam)))
+ (home-page "http://3dgenomes.github.io/TADbit/")
+ (synopsis "Analyze, model, and explore 3C-based data")
+ (description
+ "TADbit is a complete Python library to deal with all steps to analyze,
+model, and explore 3C-based data. With TADbit the user can map FASTQ files to
+obtain raw interaction binned matrices (Hi-C like matrices), normalize and
+correct interaction matrices, identify and compare the so-called
+@dfn{Topologically Associating Domains} (TADs), build 3D models from the
+interaction matrices, and finally, extract structural properties from the
+models. TADbit is complemented by TADkit for visualizing 3D models.")
+ (license license:gpl3+)))
+
+(define-public kentutils
+ (package
+ (name "kentutils")
+ ;; 302.1.0 is out, but the only difference is the inclusion of
+ ;; pre-built binaries.
+ (version "302.0.0")
+ (source
+ (origin
+ (method url-fetch)
+ (uri (string-append "https://github.com/ENCODE-DCC/kentUtils/"
+ "archive/v" version ".tar.gz"))
+ (file-name (string-append name "-" version ".tar.gz"))
+ (sha256
+ (base32
+ "134aja3k1cj32kbk1nnw0q9gxjb2krr15q6sga8qldzvc0585rmm"))
+ (modules '((guix build utils)
+ (srfi srfi-26)
+ (ice-9 ftw)))
+ (snippet
+ '(begin
+ ;; Only the contents of the specified directories are free
+ ;; for all uses, so we remove the rest. "hg/autoSql" and
+ ;; "hg/autoXml" are nominally free, but they depend on a
+ ;; library that is built from the sources in "hg/lib",
+ ;; which is nonfree.
+ (let ((free (list "." ".."
+ "utils" "lib" "inc" "tagStorm"
+ "parasol" "htslib"))
+ (directory? (lambda (file)
+ (eq? 'directory (stat:type (stat file))))))
+ (for-each (lambda (file)
+ (and (directory? file)
+ (delete-file-recursively file)))
+ (map (cut string-append "src/" <>)
+ (scandir "src"
+ (lambda (file)
+ (not (member file free)))))))
+ ;; Only make the utils target, not the userApps target,
+ ;; because that requires libraries we won't build.
+ (substitute* "Makefile"
+ ((" userApps") " utils"))
+ ;; Only build libraries that are free.
+ (substitute* "src/makefile"
+ (("DIRS =.*") "DIRS =\n")
+ (("cd jkOwnLib.*") "")
+ ((" hgLib") "")
+ (("cd hg.*") ""))
+ (substitute* "src/utils/makefile"
+ ;; These tools depend on "jkhgap.a", which is part of the
+ ;; nonfree "src/hg/lib" directory.
+ (("raSqlQuery") "")
+ (("pslLiftSubrangeBlat") "")
+
+ ;; Do not build UCSC tools, which may require nonfree
+ ;; components.
+ (("ALL_APPS =.*") "ALL_APPS = $(UTILS_APPLIST)\n"))
+ #t))))
+ (build-system gnu-build-system)
+ (arguments
+ `( ;; There is no global test target and the test target for
+ ;; individual tools depends on input files that are not
+ ;; included.
+ #:tests? #f
+ #:phases
+ (modify-phases %standard-phases
+ (add-after 'unpack 'fix-paths
+ (lambda _
+ (substitute* "Makefile"
+ (("/bin/echo") (which "echo")))
+ #t))
+ (add-after 'unpack 'prepare-samtabix
+ (lambda* (#:key inputs #:allow-other-keys)
+ (copy-recursively (assoc-ref inputs "samtabix")
+ "samtabix")
+ #t))
+ (delete 'configure)
+ (replace 'install
+ (lambda* (#:key outputs #:allow-other-keys)
+ (let ((bin (string-append (assoc-ref outputs "out")
+ "/bin")))
+ (copy-recursively "bin" bin))
+ #t)))))
+ (native-inputs
+ `(("samtabix"
+ ,(origin
+ (method git-fetch)
+ (uri (git-reference
+ (url "http://genome-source.cse.ucsc.edu/samtabix.git")
+ (commit "10fd107909c1ac4d679299908be4262a012965ba")))
+ (sha256
+ (base32
+ "0c1nj64l42v395sa84n7az43xiap4i6f9n9dfz4058aqiwkhkmma"))))))
+ (inputs
+ `(("zlib" ,zlib)
+ ("tcsh" ,tcsh)
+ ("perl" ,perl)
+ ("libpng" ,libpng)
+ ("mysql" ,mysql)
+ ("openssl" ,openssl)))
+ (home-page "http://genome.cse.ucsc.edu/index.html")
+ (synopsis "Assorted bioinformatics utilities")
+ (description "This package provides the kentUtils, a selection of
+bioinformatics utilities used in combination with the UCSC genome
+browser.")
+ ;; Only a subset of the sources are released under a non-copyleft
+ ;; free software license. All other sources are removed in a
+ ;; snippet. See this bug report for an explanation of how the
+ ;; license statements apply:
+ ;; https://github.com/ENCODE-DCC/kentUtils/issues/12
+ (license (license:non-copyleft
+ "http://genome.ucsc.edu/license/"
+ "The contents of this package are free for all uses."))))
+
+(define-public f-seq
+ (let ((commit "6ccded34cff38cf432deed8503648b4a66953f9b")
+ (revision "1"))
+ (package
+ (name "f-seq")
+ (version (string-append "1.1-" revision "." commit))
+ (source (origin
+ (method git-fetch)
+ (uri (git-reference
+ (url "https://github.com/aboyle/F-seq.git")
+ (commit commit)))
+ (file-name (string-append name "-" version))
+ (sha256
+ (base32
+ "1nk33k0yajg2id4g59bc4szr58r2q6pdq42vgcw054m8ip9wv26h"))
+ (modules '((guix build utils)))
+ ;; Remove bundled Java library archives.
+ (snippet
+ '(begin
+ (for-each delete-file (find-files "lib" ".*"))
+ #t))))
+ (build-system ant-build-system)
+ (arguments
+ `(#:tests? #f ; no tests included
+ #:phases
+ (modify-phases %standard-phases
+ (replace 'install
+ (lambda* (#:key outputs #:allow-other-keys)
+ (let* ((target (assoc-ref outputs "out"))
+ (doc (string-append target "/share/doc/f-seq/")))
+ (mkdir-p target)
+ (mkdir-p doc)
+ (substitute* "bin/linux/fseq"
+ (("java") (which "java")))
+ (install-file "README.txt" doc)
+ (install-file "bin/linux/fseq" (string-append target "/bin"))
+ (install-file "build~/fseq.jar" (string-append target "/lib"))
+ (copy-recursively "lib" (string-append target "/lib"))
+ #t))))))
+ (inputs
+ `(("perl" ,perl)
+ ("java-commons-cli" ,java-commons-cli)))
+ (home-page "http://fureylab.web.unc.edu/software/fseq/")
+ (synopsis "Feature density estimator for high-throughput sequence tags")
+ (description
+ "F-Seq is a software package that generates a continuous tag sequence
+density estimation allowing identification of biologically meaningful sites
+such as transcription factor binding sites (ChIP-seq) or regions of open
+chromatin (DNase-seq). Output can be displayed directly in the UCSC Genome
+Browser.")
+ (license license:gpl3+))))