;;; 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 xml)
#:use-module (gnu packages xorg)
#:use-module (srfi srfi-1)
- #:use-module (srfi srfi-26))
+ #: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 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 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 "0.9.8")
+ (version "0.9.9")
(source (origin
(method url-fetch)
(uri (string-append
(file-name (string-append name "-" version ".tar.gz"))
(sha256
(base32
- "04f501vj3i95i2b4n60831k00ljalifrq33419bbz0y3sjlmcnj3"))))
+ "04i03046g3l2vk9722z47r1p7j415g97vvz6d76ywmbawyiihcb1"))))
(build-system cmake-build-system)
(arguments
'(#:tests? #f ; no "check" target
(file-name (string-append name "-" version ".tar.gz"))
(sha256
(base32
- "055ynn16gd12pf78n4vr2a9jlwsbwzajpdnf2y2yilg1krfff222"))))
+ "055ynn16gd12pf78n4vr2a9jlwsbwzajpdnf2y2yilg1krfff222"))
+ (patches (search-patches "gemma-intel-compat.patch"))))
(inputs
`(("gsl" ,gsl)
("lapack" ,lapack)
(build-system gnu-build-system)
(arguments
`(#:make-flags
- '(,@(if (any (cute string-prefix? <> (or (%current-system)
- (%current-target-system)))
- '("x86_64" "mips64el" "aarch64"))
- '("FORCE_DYNAMIC=1") ; use shared libs
- '("FORCE_DYNAMIC=1" "FORCE_32BIT=1")))
+ '(,@(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)
(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")
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
(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 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-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)))
HCoop / jackhill / guix / guix.git / blobdiff