gnu: Add pigx-rnaseq.

* gnu/packages/bioinformatics.scm (pigx-rnaseq): New variable.
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Ricardo Wurmus 2018-03-07 23:07:23 +01:00
parent e2cafc2449
commit 0bdd5b8ab7
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@ -12646,3 +12646,70 @@ (define-public dropseq-tools
analyze RNA expression genome-wide in thousands of individual cells at
once. This package provides tools to perform Drop-seq analyses.")
(license license:expat)))
(define-public pigx-rnaseq
(package
(name "pigx-rnaseq")
(version "0.0.2")
(source (origin
(method url-fetch)
(uri (string-append "https://github.com/BIMSBbioinfo/pigx_rnaseq/"
"releases/download/v" version
"/pigx_rnaseq-" version ".tar.gz"))
(sha256
(base32
"168hx2ig3rarphx3l21ay9yyg8ipaakzixnrhpbdi0sknhyvrrk8"))))
(build-system gnu-build-system)
(arguments
`(#:parallel-tests? #f ; not supported
#:phases
(modify-phases %standard-phases
(add-after 'install 'wrap-executable
;; Make sure the executable finds all R modules.
(lambda* (#:key inputs outputs #:allow-other-keys)
(let ((out (assoc-ref outputs "out")))
(wrap-program (string-append out "/bin/pigx-rnaseq")
`("R_LIBS_SITE" ":" = (,(getenv "R_LIBS_SITE")))
`("PYTHONPATH" ":" = (,(getenv "PYTHONPATH")))))
#t)))))
(inputs
`(("snakemake" ,snakemake)
("fastqc" ,fastqc)
("multiqc" ,multiqc)
("star" ,star)
("trim-galore" ,trim-galore)
("htseq" ,htseq)
("samtools" ,samtools)
("bedtools" ,bedtools)
("r-minimal" ,r-minimal)
("r-rmarkdown" ,r-rmarkdown)
("r-ggplot2" ,r-ggplot2)
("r-ggrepel" ,r-ggrepel)
("r-gprofiler" ,r-gprofiler)
("r-deseq2" ,r-deseq2)
("r-dt" ,r-dt)
("r-knitr" ,r-knitr)
("r-pheatmap" ,r-pheatmap)
("r-corrplot" ,r-corrplot)
("r-reshape2" ,r-reshape2)
("r-plotly" ,r-plotly)
("r-scales" ,r-scales)
("r-summarizedexperiment" ,r-summarizedexperiment)
("r-crosstalk" ,r-crosstalk)
("r-tximport" ,r-tximport)
("r-rtracklayer" ,r-rtracklayer)
("r-rjson" ,r-rjson)
("salmon" ,salmon)
("ghc-pandoc" ,ghc-pandoc)
("ghc-pandoc-citeproc" ,ghc-pandoc-citeproc)
("python-wrapper" ,python-wrapper)
("python-pyyaml" ,python-pyyaml)))
(home-page "http://bioinformatics.mdc-berlin.de/pigx/")
(synopsis "Analysis pipeline for RNA sequencing experiments")
(description "PiGX RNAseq is an analysis pipeline for preprocessing and
reporting for RNA sequencing experiments. It is easy to use and produces high
quality reports. The inputs are reads files from the sequencing experiment,
and a configuration file which describes the experiment. In addition to
quality control of the experiment, the pipeline produces a differential
expression report comparing samples in an easily configurable manner.")
(license license:gpl3+)))