diff options
| author | Ricardo Wurmus <ricardo.wurmus@mdc-berlin.de> | 2015-12-18 14:07:56 +0100 |
|---|---|---|
| committer | Ricardo Wurmus <ricardo.wurmus@mdc-berlin.de> | 2016-01-07 17:18:16 +0100 |
| commit | f8d74f70184b21b81b831f386f9a5f89a43a1d02 (patch) | |
| tree | 26e3437128263fd20105c93d80bb77651972c9b7 /gnu/packages/bioinformatics.scm | |
| parent | bf159353376abe5177f336cbea56c94b72c89de8 (diff) | |
gnu: Add Rsamtools.
* gnu/packages/bioinformatics.scm (r-rsamtools): New variable.
Diffstat (limited to 'gnu/packages/bioinformatics.scm')
| -rw-r--r-- | gnu/packages/bioinformatics.scm | 44 |
1 files changed, 44 insertions, 0 deletions
diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index d379c4fe37..51be381e93 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -3595,6 +3595,50 @@ matching algorithms, and other utilities, for fast manipulation of large biological sequences or sets of sequences.") (license license:artistic2.0))) +(define-public r-rsamtools + (package + (name "r-rsamtools") + (version "1.22.0") + (source (origin + (method url-fetch) + (uri (bioconductor-uri "Rsamtools" version)) + (sha256 + (base32 + "1yc3nzzms3igjwr4l9yd3wdac95glcs08b4cfp7disyly0wcskjd")))) + (properties + `((upstream-name . "Rsamtools"))) + (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-biocparallel" ,r-biocparallel) + ("r-biostrings" ,r-biostrings) + ("r-bitops" ,r-bitops) + ("r-genomeinfodb" ,r-genomeinfodb) + ("r-genomicranges" ,r-genomicranges) + ("r-iranges" ,r-iranges) + ("r-s4vectors" ,r-s4vectors) + ("r-xvector" ,r-xvector))) + (home-page "http://bioconductor.org/packages/release/bioc/html/Rsamtools.html") + (synopsis "Interface to samtools, bcftools, and tabix") + (description + "This package provides an interface to the 'samtools', 'bcftools', and +'tabix' utilities for manipulating SAM (Sequence Alignment / Map), FASTA, +binary variant call (BCF) and compressed indexed tab-delimited (tabix) +files.") + (license license:expat))) + (define-public r-qtl (package (name "r-qtl") |