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| author | Ricardo Wurmus <ricardo.wurmus@mdc-berlin.de> | 2016-09-21 22:45:38 +0200 |
|---|---|---|
| committer | Ricardo Wurmus <rekado@elephly.net> | 2016-09-26 07:47:54 +0200 |
| commit | cb99d457f02d7eaf014b777a2d9ff94133512dc1 (patch) | |
| tree | 8732193ccbc3de97777ab0415e3aa47dc503454f | |
| parent | 89f40c5e4eea65cf93627fdd64d667b06598226f (diff) | |
| download | patches-cb99d457f02d7eaf014b777a2d9ff94133512dc1.tar patches-cb99d457f02d7eaf014b777a2d9ff94133512dc1.tar.gz | |
gnu: Add r-shortread.
* gnu/packages/bioinformatics.scm (r-shortread): New variable.
| -rw-r--r-- | gnu/packages/bioinformatics.scm | 42 |
1 files changed, 42 insertions, 0 deletions
diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index 107e720601..4dcf661dca 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -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") |