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| author | Ricardo Wurmus <ricardo.wurmus@mdc-berlin.de> | 2015-12-18 14:09:00 +0100 |
|---|---|---|
| committer | Ricardo Wurmus <ricardo.wurmus@mdc-berlin.de> | 2016-01-07 17:18:16 +0100 |
| commit | 317755ff0fbd443466b162b358f650edeff10b69 (patch) | |
| tree | 69e890c333c48297d846487db415ad1950e3d71d | |
| parent | d8a828af78ce92c583bedb23e379b5b4dd332ab1 (diff) | |
| download | guix-317755ff0fbd443466b162b358f650edeff10b69.tar.gz | |
gnu: Add rtracklayer.
* gnu/packages/bioinformatics.scm (r-rtracklayer): New variable.
| -rw-r--r-- | gnu/packages/bioinformatics.scm | 45 |
1 files changed, 45 insertions, 0 deletions
diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index 1969b72a04..c7728160e6 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -3701,6 +3701,51 @@ junction detection, and working with the nucleotide content of the alignments.") (license license:artistic2.0))) +(define-public r-rtracklayer + (package + (name "r-rtracklayer") + (version "1.30.1") + (source (origin + (method url-fetch) + (uri (bioconductor-uri "rtracklayer" version)) + (sha256 + (base32 + "1if31hg56islx5vwydpgs5gkyas26kyvv2ljv1c7jikpm62w14qv")))) + (build-system r-build-system) + (arguments + `(#:phases + (modify-phases %standard-phases + (add-after 'unpack 'use-system-zlib + (lambda _ + (substitute* "DESCRIPTION" + (("zlibbioc, ") "")) + (substitute* "NAMESPACE" + (("import\\(zlibbioc\\)") "")) + #t))))) + (inputs + `(("zlib" ,zlib))) + (propagated-inputs + `(("r-biocgenerics" ,r-biocgenerics) + ("r-biostrings" ,r-biostrings) + ("r-genomeinfodb" ,r-genomeinfodb) + ("r-genomicalignments" ,r-genomicalignments) + ("r-genomicranges" ,r-genomicranges) + ("r-iranges" ,r-iranges) + ("r-rcurl" ,r-rcurl) + ("r-rsamtools" ,r-rsamtools) + ("r-s4vectors" ,r-s4vectors) + ("r-xml" ,r-xml) + ("r-xvector" ,r-xvector))) + (home-page "http://bioconductor.org/packages/rtracklayer") + (synopsis "R interface to genome browsers and their annotation tracks") + (description + "rtracklayer is an extensible framework for interacting with multiple +genome browsers (currently UCSC built-in) and manipulating annotation tracks +in various formats (currently GFF, BED, bedGraph, BED15, WIG, BigWig and 2bit +built-in). The user may export/import tracks to/from the supported browsers, +as well as query and modify the browser state, such as the current viewport.") + (license license:artistic2.0))) + (define-public r-qtl (package (name "r-qtl") |