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| author | Ricardo Wurmus <ricardo.wurmus@mdc-berlin.de> | 2016-09-21 22:45:39 +0200 |
|---|---|---|
| committer | Ricardo Wurmus <rekado@elephly.net> | 2016-09-26 07:47:55 +0200 |
| commit | 7f903d7300059a34f2bbb11dc2c07ee1d0b59c0b (patch) | |
| tree | 3115fb1bf9ddeeb556683846ffd83a58f97c9583 | |
| parent | cb99d457f02d7eaf014b777a2d9ff94133512dc1 (diff) | |
gnu: Add r-systempiper.
* gnu/packages/bioinformatics.scm (r-systempiper): New variable.
| -rw-r--r-- | gnu/packages/bioinformatics.scm | 46 |
1 files changed, 46 insertions, 0 deletions
diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index 4dcf661dca..fdd71137cd 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -5350,6 +5350,52 @@ purposes. The package also contains legacy support for early single-end, ungapped alignment formats.") (license license:artistic2.0))) +(define-public r-systempiper + (package + (name "r-systempiper") + (version "1.6.4") + (source + (origin + (method url-fetch) + (uri (bioconductor-uri "systemPipeR" version)) + (sha256 + (base32 + "0s2g46a5d5bvx45i3cgmib48wf8hrniyladhm0f7kgcbfx57248m")))) + (properties `((upstream-name . "systemPipeR"))) + (build-system r-build-system) + (propagated-inputs + `(("r-annotate" ,r-annotate) + ("r-batchjobs" ,r-batchjobs) + ("r-biocgenerics" ,r-biocgenerics) + ("r-biostrings" ,r-biostrings) + ("r-deseq2" ,r-deseq2) + ("r-edger" ,r-edger) + ("r-genomicfeatures" ,r-genomicfeatures) + ("r-genomicranges" ,r-genomicranges) + ("r-ggplot2" ,r-ggplot2) + ("r-go-db" ,r-go-db) + ("r-gostats" ,r-gostats) + ("r-limma" ,r-limma) + ("r-pheatmap" ,r-pheatmap) + ("r-rjson" ,r-rjson) + ("r-rsamtools" ,r-rsamtools) + ("r-shortread" ,r-shortread) + ("r-summarizedexperiment" ,r-summarizedexperiment) + ("r-variantannotation" ,r-variantannotation))) + (home-page "https://github.com/tgirke/systemPipeR") + (synopsis "Next generation sequencing workflow and reporting environment") + (description + "This R package provides tools for building and running automated +end-to-end analysis workflows for a wide range of @dfn{next generation +sequence} (NGS) applications such as RNA-Seq, ChIP-Seq, VAR-Seq and Ribo-Seq. +Important features include a uniform workflow interface across different NGS +applications, automated report generation, and support for running both R and +command-line software, such as NGS aligners or peak/variant callers, on local +computers or compute clusters. Efficient handling of complex sample sets and +experimental designs is facilitated by a consistently implemented sample +annotation infrastructure.") + (license license:artistic2.0))) + (define-public vsearch (package (name "vsearch") |