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author | Ricardo Wurmus <rekado@elephly.net> | 2018-03-07 23:07:23 +0100 |
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committer | Ricardo Wurmus <rekado@elephly.net> | 2018-03-07 23:25:36 +0100 |
commit | 0bdd5b8ab7c5e618a63cac6d9aa55f9cf674deea (patch) | |
tree | dbd4a90831a6578fae10d462903a2be906be5ef8 /gnu/packages/bioinformatics.scm | |
parent | e2cafc2449df16ccc3ca1555d5e9ed66908d846e (diff) | |
download | patches-0bdd5b8ab7c5e618a63cac6d9aa55f9cf674deea.tar patches-0bdd5b8ab7c5e618a63cac6d9aa55f9cf674deea.tar.gz |
gnu: Add pigx-rnaseq.
* gnu/packages/bioinformatics.scm (pigx-rnaseq): New variable.
Diffstat (limited to 'gnu/packages/bioinformatics.scm')
-rw-r--r-- | gnu/packages/bioinformatics.scm | 67 |
1 files changed, 67 insertions, 0 deletions
diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index 546b240f84..d6c7c05dd5 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -12646,3 +12646,70 @@ contains 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+))) |