#: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)
(sha256
(base32
"0093hkkvxmbwfaa7905s6185jymynvg42kq6sxv7fili11l5mxwz"))
+ (patches (search-patches "bcftools-regidx-unsigned-char.patch"))
(modules '((guix build utils)))
(snippet
;; Delete bundled htslib.
(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 metabat
(package
(name "metabat")
- (version "2.11.2")
+ (version "2.11.3")
(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"))
+ (method git-fetch)
+ (uri (git-reference
+ (url "https://bitbucket.org/berkeleylab/metabat.git")
+ (commit "d0ad65367ffc8e08d1a9dd1388d6170daa047e5c")))
+ (file-name (string-append name "-" version "-checkout"))
(sha256
(base32
- "0rws9r1ziv6way8cf49jg8bzj7x2131kfqkhj8byf0z5hnrq3bwv"))
+ "1rlsrkz8iq8xah65222p055kzv5i3szz8bwysnvnh0pv72wvv6ww"))
(patches (search-patches "metabat-remove-compilation-date.patch"
"metabat-fix-compilation.patch"))))
(build-system gnu-build-system)
'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"
(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-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)
version ".tar.gz"))
(sha256
(base32
- "0479qx4bapgcp5chj10a63chk0s28x9cx1gamz3f5m3yd7jzwcf2"))))
+ "1y0nqpk8cw5a34sd9hmin3z4v7iqm6hf6l22cl81vlbxqbjibxc8"))))
(properties
`((upstream-name . "BSgenome.Hsapiens.UCSC.hg19")))
(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.
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")
(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