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| author | zimoun <zimon.toutoune@gmail.com> | 2021-03-08 18:58:02 +0100 |
|---|---|---|
| committer | Ricardo Wurmus <rekado@elephly.net> | 2021-03-12 14:45:54 +0100 |
| commit | 8957efa8ef940685811b9e55eb7178ecd33abb40 (patch) | |
| tree | 941cb6ac2904f3a89a8cd1f67b596dcbd92e5c5c /gnu/packages/bioconductor.scm | |
| parent | 2a9705768808ff8b76bf38a7ae9445b2c756ba46 (diff) | |
| download | guix-8957efa8ef940685811b9e55eb7178ecd33abb40.tar.gz guix-8957efa8ef940685811b9e55eb7178ecd33abb40.zip | |
gnu: r-shortread: Move to (gnu packages bioconductor).
* gnu/packages/bioinformatics.scm (r-shortread): Move from here...
* gnu/packages/bioconductor.scm (r-shortread): ...to here.
Diffstat (limited to 'gnu/packages/bioconductor.scm')
| -rw-r--r-- | gnu/packages/bioconductor.scm | 43 |
1 files changed, 43 insertions, 0 deletions
diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index a4618ec90a..283ae7adf8 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -1845,6 +1845,49 @@ reports together for a particular project that can be viewed in a web browser.") (license license:artistic2.0))) +(define-public r-shortread + (package + (name "r-shortread") + (version "1.48.0") + (source + (origin + (method url-fetch) + (uri (bioconductor-uri "ShortRead" version)) + (sha256 + (base32 + "0w4m8d3h660mmr2ymp206r1n4aqssxmkv8yxkbr5y1swrahxzfk9")))) + (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-rhtslib" ,r-rhtslib) + ("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 "https://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 r-geneplotter (package (name "r-geneplotter") |