gnu: Add r-shortread.

* gnu/packages/bioinformatics.scm (r-shortread): New variable.
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Ricardo Wurmus 2016-09-21 22:45:38 +02:00 committed by Ricardo Wurmus
parent 89f40c5e4e
commit cb99d457f0
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@ -5308,6 +5308,48 @@ microarray data. A variety of basic manipulation tools for graphs, hypothesis
testing and other simple calculations.")
(license license:artistic2.0)))
(define-public r-shortread
(package
(name "r-shortread")
(version "1.30.0")
(source
(origin
(method url-fetch)
(uri (bioconductor-uri "ShortRead" version))
(sha256
(base32
"0qlxns4bhwfpafx3km2lnivgl2qyp7n4g1ardm6vrinpq8paxbjg"))))
(properties `((upstream-name . "ShortRead")))
(build-system r-build-system)
(inputs
`(("zlib" ,zlib)))
(propagated-inputs
`(("r-biobase" ,r-biobase)
("r-biocgenerics" ,r-biocgenerics)
("r-biocparallel" ,r-biocparallel)
("r-biostrings" ,r-biostrings)
("r-genomeinfodb" ,r-genomeinfodb)
("r-genomicalignments" ,r-genomicalignments)
("r-genomicranges" ,r-genomicranges)
("r-hwriter" ,r-hwriter)
("r-iranges" ,r-iranges)
("r-lattice" ,r-lattice)
("r-latticeextra" ,r-latticeextra)
("r-rsamtools" ,r-rsamtools)
("r-s4vectors" ,r-s4vectors)
("r-xvector" ,r-xvector)
("r-zlibbioc" ,r-zlibbioc)))
(home-page "http://bioconductor.org/packages/ShortRead")
(synopsis "FASTQ input and manipulation tools")
(description
"This package implements sampling, iteration, and input of FASTQ files.
It includes functions for filtering and trimming reads, and for generating a
quality assessment report. Data are represented as
@code{DNAStringSet}-derived objects, and easily manipulated for a diversity of
purposes. The package also contains legacy support for early single-end,
ungapped alignment formats.")
(license license:artistic2.0)))
(define-public vsearch
(package
(name "vsearch")