#: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 gd)
#:use-module (gnu packages gtk)
#:use-module (gnu packages glib)
+ #:use-module (gnu packages graph)
#:use-module (gnu packages groff)
#:use-module (gnu packages guile)
#:use-module (gnu packages haskell)
("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"))
+ (patches (search-patches "bcftools-regidx-unsigned-char.patch"))
(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 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.
(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)
(define-public diamond
(package
(name "diamond")
- (version "0.9.9")
+ (version "0.9.10")
(source (origin
(method url-fetch)
(uri (string-append
(file-name (string-append name "-" version ".tar.gz"))
(sha256
(base32
- "04i03046g3l2vk9722z47r1p7j415g97vvz6d76ywmbawyiihcb1"))))
+ "13qqzwg54n5dqh8pm5n3v8x6gqbczzakphwwjix63qv60hcd5bqd"))))
(build-system cmake-build-system)
(arguments
'(#:tests? #f ; no "check" target
(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 "2.11.3")
+ (source
+ (origin
+ (method git-fetch)
+ (uri (git-reference
+ (url "https://bitbucket.org/berkeleylab/metabat.git")
+ (commit "d0ad65367ffc8e08d1a9dd1388d6170daa047e5c")))
+ (file-name (string-append name "-" version "-checkout"))
+ (sha256
+ (base32
+ "1rlsrkz8iq8xah65222p055kzv5i3szz8bwysnvnh0pv72wvv6ww"))
+ (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
'configure
(lambda* (#:key outputs #:allow-other-keys)
(let ((out (assoc-ref outputs "out")))
+ ;; Allow 'konfigure.perl' to find 'package.prl'.
+ (setenv "PERL5LIB"
+ (string-append ".:" (getenv "PERL5LIB")))
+
;; The 'configure' script doesn't recognize things like
;; '--enable-fast-install'.
(zero? (system* "./configure"
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
distribution.")
(license license:lgpl3+)))
+(define-public r-dexseq
+ (package
+ (name "r-dexseq")
+ (version "1.22.0")
+ (source
+ (origin
+ (method url-fetch)
+ (uri (bioconductor-uri "DEXSeq" version))
+ (sha256
+ (base32
+ "085aqk1wlzzqcqcqhvz74y099kr2ln5dwdxd3rl6zan806mgwahg"))))
+ (properties `((upstream-name . "DEXSeq")))
+ (build-system r-build-system)
+ (propagated-inputs
+ `(("r-annotationdbi" ,r-annotationdbi)
+ ("r-biobase" ,r-biobase)
+ ("r-biocgenerics" ,r-biocgenerics)
+ ("r-biocparallel" ,r-biocparallel)
+ ("r-biomart" ,r-biomart)
+ ("r-deseq2" ,r-deseq2)
+ ("r-genefilter" ,r-genefilter)
+ ("r-geneplotter" ,r-geneplotter)
+ ("r-genomicranges" ,r-genomicranges)
+ ("r-hwriter" ,r-hwriter)
+ ("r-iranges" ,r-iranges)
+ ("r-rcolorbrewer" ,r-rcolorbrewer)
+ ("r-rsamtools" ,r-rsamtools)
+ ("r-s4vectors" ,r-s4vectors)
+ ("r-statmod" ,r-statmod)
+ ("r-stringr" ,r-stringr)
+ ("r-summarizedexperiment" ,r-summarizedexperiment)))
+ (home-page "http://bioconductor.org/packages/DEXSeq")
+ (synopsis "Inference of differential exon usage in RNA-Seq")
+ (description
+ "This package is focused on finding differential exon usage using RNA-seq
+exon counts between samples with different experimental designs. It provides
+functions that allows the user to make the necessary statistical tests based
+on a model that uses the negative binomial distribution to estimate the
+variance between biological replicates and generalized linear models for
+testing. The package also provides functions for the visualization and
+exploration of the results.")
+ (license license:gpl3+)))
+
(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 "1.61")
(source
(origin
(method url-fetch)
(uri (cran-uri "WGCNA" version))
(sha256
(base32
- "0hzvnhw76vwg8bl8x368f0c5szpwb8323bmrb3bir93i5bmfjsxx"))))
+ "1vrc2k33a196hrrl7k0z534fp96vv0shmigcr65ny1q0v6lq0h6i"))))
(properties `((upstream-name . "WGCNA")))
(build-system r-build-system)
(propagated-inputs
("r-go-db" ,r-go-db)
("r-hmisc" ,r-hmisc)
("r-impute" ,r-impute)
+ ("r-rcpp" ,r-rcpp)
+ ("r-robust" ,r-robust)
+ ("r-survival" ,r-survival)
("r-matrixstats" ,r-matrixstats)
("r-preprocesscore" ,r-preprocesscore)))
(home-page
the available RAM.")
(license license:artistic2.0)))
+(define-public r-annotationfilter
+ (package
+ (name "r-annotationfilter")
+ (version "1.0.0")
+ (source (origin
+ (method url-fetch)
+ (uri (bioconductor-uri "AnnotationFilter" version))
+ (sha256
+ (base32
+ "0pxvswjzwibdfmrkdragxmzcl844z73pmkn82z92wahwa6gjfyi7"))))
+ (properties
+ `((upstream-name . "AnnotationFilter")))
+ (build-system r-build-system)
+ (propagated-inputs
+ `(("r-genomicranges" ,r-genomicranges)
+ ("r-lazyeval" ,r-lazyeval)))
+ (home-page "https://github.com/Bioconductor/AnnotationFilter")
+ (synopsis "Facilities for filtering Bioconductor annotation resources")
+ (description
+ "This package provides classes and other infrastructure to implement
+filters for manipulating Bioconductor annotation resources. The filters are
+used by @code{ensembldb}, @code{Organism.dplyr}, and other packages.")
+ (license license:artistic2.0)))
+
(define-public emboss
(package
(name "emboss")
(define-public multiqc
(package
(name "multiqc")
- (version "0.9")
+ (version "1.2")
(source
(origin
(method url-fetch)
(uri (pypi-uri "multiqc" version))
(sha256
(base32
- "12gs1jw2jrxrij529rnl5kaqxfcqn15yzcsggxkfhdx634ml0cny"))
- (patches (search-patches "multiqc-fix-git-subprocess-error.patch"))))
+ "032svgym67k2ds7wp0cxzv79gi30yrdl45zbqn74lni3dk04qm33"))))
(build-system python-build-system)
- (arguments
- ;; Tests are to be introduced in the next version, see
- ;; https://github.com/ewels/MultiQC/issues/376
- `(#:tests? #f))
(propagated-inputs
`(("python-jinja2" ,python-jinja2)
("python-simplejson" ,python-simplejson)
("python-pyyaml" ,python-pyyaml)
("python-click" ,python-click)
+ ("python-spectra" ,python-spectra)
+ ("python-requests" ,python-requests)
+ ("python-markdown" ,python-markdown)
+ ("python-lzstring" ,python-lzstring)
("python-matplotlib" ,python-matplotlib)
("python-numpy" ,python-numpy)
;; MultQC checks for the presence of nose at runtime.
(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
number detection tools.")
(license license:gpl2)))
+(define-public r-methylkit
+ (package
+ (name "r-methylkit")
+ (version "1.2.0")
+ (source (origin
+ (method url-fetch)
+ (uri (bioconductor-uri "methylKit" version))
+ (sha256
+ (base32
+ "02acdjf6jl0c1glymin84pdna4farn4vv0gb6107d9iqz3y3gkmm"))))
+ (properties `((upstream-name . "methylKit")))
+ (build-system r-build-system)
+ (propagated-inputs
+ `(("r-data-table" ,r-data-table)
+ ("r-emdbook" ,r-emdbook)
+ ("r-fastseg" ,r-fastseg)
+ ("r-genomeinfodb" ,r-genomeinfodb)
+ ("r-genomicranges" ,r-genomicranges)
+ ("r-gtools" ,r-gtools)
+ ("r-iranges" ,r-iranges)
+ ("r-kernsmooth" ,r-kernsmooth)
+ ("r-limma" ,r-limma)
+ ("r-mclust" ,r-mclust)
+ ("r-qvalue" ,r-qvalue)
+ ("r-r-utils" ,r-r-utils)
+ ("r-rcpp" ,r-rcpp)
+ ("r-rhtslib" ,r-rhtslib)
+ ("r-rsamtools" ,r-rsamtools)
+ ("r-rtracklayer" ,r-rtracklayer)
+ ("r-s4vectors" ,r-s4vectors)
+ ("r-zlibbioc" ,r-zlibbioc)))
+ (inputs
+ `(("zlib" ,zlib)))
+ (home-page "http://code.google.com/p/methylkit/")
+ (synopsis
+ "DNA methylation analysis from high-throughput bisulfite sequencing results")
+ (description
+ "MethylKit is an R package for DNA methylation analysis and annotation
+from high-throughput bisulfite sequencing. The package is designed to deal
+with sequencing data from @dfn{Reduced representation bisulfite
+sequencing} (RRBS) and its variants, but also target-capture methods and whole
+genome bisulfite sequencing. It also has functions to analyze base-pair
+resolution 5hmC data from experimental protocols such as oxBS-Seq and
+TAB-Seq.")
+ (license license:artistic2.0)))
+
(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)))
(properties `((upstream-name . "mzR")))
(build-system r-build-system)
(inputs
- `(("netcdf" ,netcdf)))
+ `(("boost" ,boost)
+ ("netcdf" ,netcdf)))
(propagated-inputs
`(("r-biobase" ,r-biobase)
("r-biocgenerics" ,r-biocgenerics)
global-scaling and full-quantile normalization.")
(license license:artistic2.0)))
+(define-public r-interactivedisplaybase
+ (package
+ (name "r-interactivedisplaybase")
+ (version "1.14.0")
+ (source
+ (origin
+ (method url-fetch)
+ (uri (bioconductor-uri "interactiveDisplayBase" version))
+ (sha256
+ (base32
+ "12f6ap4bl3h2iwwhg8i3r9a7yyd28d8i5lb3fj1vnfvjs762r7r7"))))
+ (properties
+ `((upstream-name . "interactiveDisplayBase")))
+ (build-system r-build-system)
+ (propagated-inputs
+ `(("r-biocgenerics" ,r-biocgenerics)
+ ("r-shiny" ,r-shiny)))
+ (home-page "http://bioconductor.org/packages/interactiveDisplayBase")
+ (synopsis "Base package for web displays of Bioconductor objects")
+ (description
+ "This package contains the basic methods needed to generate interactive
+Shiny-based display methods for Bioconductor objects.")
+ (license license:artistic2.0)))
+
+(define-public r-annotationhub
+ (package
+ (name "r-annotationhub")
+ (version "2.8.2")
+ (source
+ (origin
+ (method url-fetch)
+ (uri (bioconductor-uri "AnnotationHub" version))
+ (sha256
+ (base32
+ "1nh5si3j1nv37jcg4260582ayjg18851np47cskrm54prnvhwd9r"))))
+ (properties `((upstream-name . "AnnotationHub")))
+ (build-system r-build-system)
+ (propagated-inputs
+ `(("r-annotationdbi" ,r-annotationdbi)
+ ("r-biocgenerics" ,r-biocgenerics)
+ ("r-biocinstaller" ,r-biocinstaller)
+ ("r-httr" ,r-httr)
+ ("r-interactivedisplaybase" ,r-interactivedisplaybase)
+ ("r-rsqlite" ,r-rsqlite)
+ ("r-s4vectors" ,r-s4vectors)
+ ("r-yaml" ,r-yaml)))
+ (home-page "http://bioconductor.org/packages/AnnotationHub")
+ (synopsis "Client to access AnnotationHub resources")
+ (description
+ "This package provides a client for the Bioconductor AnnotationHub web
+resource. The AnnotationHub web resource provides a central location where
+genomic files (e.g. VCF, bed, wig) and other resources from standard
+locations (e.g. UCSC, Ensembl) can be discovered. The resource includes
+metadata about each resource, e.g., a textual description, tags, and date of
+modification. The client creates and manages a local cache of files retrieved
+by the user, helping with quick and reproducible access.")
+ (license license:artistic2.0)))
+
+(define-public r-fastseg
+ (package
+ (name "r-fastseg")
+ (version "1.22.0")
+ (source
+ (origin
+ (method url-fetch)
+ (uri (bioconductor-uri "fastseg" version))
+ (sha256
+ (base32
+ "083wiz03q9mynwchs9frlpp6c84dncri5ncibx6h82p228cpja6h"))))
+ (build-system r-build-system)
+ (propagated-inputs
+ `(("r-biobase" ,r-biobase)
+ ("r-biocgenerics" ,r-biocgenerics)
+ ("r-genomicranges" ,r-genomicranges)
+ ("r-iranges" ,r-iranges)
+ ("r-s4vectors" ,r-s4vectors)))
+ (home-page "http://www.bioinf.jku.at/software/fastseg/index.html")
+ (synopsis "Fast segmentation algorithm for genetic sequencing data")
+ (description
+ "Fastseg implements a very fast and efficient segmentation algorithm.
+It can segment data from DNA microarrays and data from next generation
+sequencing for example to detect copy number segments. Further it can segment
+data from RNA microarrays like tiling arrays to identify transcripts. Most
+generally, it can segment data given as a matrix or as a vector. Various data
+formats can be used as input to fastseg like expression set objects for
+microarrays or GRanges for sequencing data.")
+ (license license:lgpl2.0+)))
+
+(define-public r-qvalue
+ (package
+ (name "r-qvalue")
+ (version "2.8.0")
+ (source
+ (origin
+ (method url-fetch)
+ (uri (bioconductor-uri "qvalue" version))
+ (sha256
+ (base32
+ "1dxdwa767a9r8n61r272ypi09qblcdfpzzwkmri74y5mbp1r3y4i"))))
+ (build-system r-build-system)
+ (propagated-inputs
+ `(("r-ggplot2" ,r-ggplot2)
+ ("r-reshape2" ,r-reshape2)))
+ (home-page "http://github.com/jdstorey/qvalue")
+ (synopsis "Q-value estimation for false discovery rate control")
+ (description
+ "This package takes a list of p-values resulting from the simultaneous
+testing of many hypotheses and estimates their q-values and local @dfn{false
+discovery rate} (FDR) values. The q-value of a test measures the proportion
+of false positives incurred when that particular test is called significant.
+The local FDR measures the posterior probability the null hypothesis is true
+given the test's p-value. Various plots are automatically generated, allowing
+one to make sensible significance cut-offs. The software can be applied to
+problems in genomics, brain imaging, astrophysics, and data mining.")
+ ;; Any version of the LGPL.
+ (license license:lgpl3+)))
+
(define htslib-for-sambamba
(let ((commit "2f3c3ea7b301f9b45737a793c0b2dcf0240e5ee5"))
(package
chromatin (DNase-seq). Output can be displayed directly in the UCSC Genome
Browser.")
(license license:gpl3+))))
+
+(define-public bismark
+ (package
+ (name "bismark")
+ (version "0.16.3")
+ (source
+ (origin
+ (method url-fetch)
+ (uri (string-append "https://github.com/FelixKrueger/Bismark/"
+ "archive/" version ".tar.gz"))
+ (file-name (string-append name "-" version ".tar.gz"))
+ (sha256
+ (base32
+ "1204i0pa02ll2jn5pnxypkclnskvv7a2nwh5nxhagmhxk9wfv9sq"))))
+ (build-system perl-build-system)
+ (arguments
+ `(#:tests? #f ; there are no tests
+ #:phases
+ (modify-phases %standard-phases
+ (delete 'configure)
+ (delete 'build)
+ (replace 'install
+ (lambda* (#:key outputs #:allow-other-keys)
+ (let ((bin (string-append (assoc-ref outputs "out")
+ "/bin"))
+ (docdir (string-append (assoc-ref outputs "out")
+ "/share/doc/bismark"))
+ (docs '("Bismark_User_Guide.pdf"
+ "RELEASE_NOTES.txt"))
+ (scripts '("bismark"
+ "bismark_genome_preparation"
+ "bismark_methylation_extractor"
+ "bismark2bedGraph"
+ "bismark2report"
+ "coverage2cytosine"
+ "deduplicate_bismark"
+ "bismark_sitrep.tpl"
+ "bam2nuc"
+ "bismark2summary")))
+ (mkdir-p docdir)
+ (mkdir-p bin)
+ (for-each (lambda (file) (install-file file bin))
+ scripts)
+ (for-each (lambda (file) (install-file file docdir))
+ docs)
+ #t))))))
+ (home-page "http://www.bioinformatics.babraham.ac.uk/projects/bismark/")
+ (synopsis "Map bisulfite treated sequence reads and analyze methylation")
+ (description "Bismark is a program to map bisulfite treated sequencing
+reads to a genome of interest and perform methylation calls in a single step.
+The output can be easily imported into a genome viewer, such as SeqMonk, and
+enables a researcher to analyse the methylation levels of their samples
+straight away. Its main features are:
+
+@itemize
+@item Bisulfite mapping and methylation calling in one single step
+@item Supports single-end and paired-end read alignments
+@item Supports ungapped and gapped alignments
+@item Alignment seed length, number of mismatches etc are adjustable
+@item Output discriminates between cytosine methylation in CpG, CHG
+ and CHH context
+@end itemize\n")
+ (license license:gpl3+)))
HCoop / jackhill / guix / guix.git / blobdiff