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authorRicardo Wurmus <ricardo.wurmus@mdc-berlin.de>2015-12-18 14:07:56 +0100
committerRicardo Wurmus <ricardo.wurmus@mdc-berlin.de>2016-01-07 17:18:16 +0100
commitf8d74f70184b21b81b831f386f9a5f89a43a1d02 (patch)
tree26e3437128263fd20105c93d80bb77651972c9b7 /gnu/packages/bioinformatics.scm
parentbf159353376abe5177f336cbea56c94b72c89de8 (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.scm44
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")