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Diffstat (limited to 'gnu/packages/bioinformatics.scm')
-rw-r--r-- | gnu/packages/bioinformatics.scm | 66 |
1 files changed, 66 insertions, 0 deletions
diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index 14e2a0daac..50d3568987 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -12725,3 +12725,69 @@ 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+))) + +(define-public pigx-chipseq + (package + (name "pigx-chipseq") + (version "0.0.2") + (source (origin + (method url-fetch) + (uri (string-append "https://github.com/BIMSBbioinfo/pigx_chipseq/" + "releases/download/v" version + "/pigx_chipseq-" version ".tar.gz")) + (sha256 + (base32 + "1jliwhifnjgl9x0z730bzpxswi2s84fyg5y8cagbyzpw509452f5")))) + (build-system gnu-build-system) + (arguments + `(#: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-chipseq") + `("R_LIBS_SITE" ":" = (,(getenv "R_LIBS_SITE"))) + `("PYTHONPATH" ":" = (,(getenv "PYTHONPATH"))))) + #t))))) + (inputs + `(("r-minimal" ,r-minimal) + ("r-argparser" ,r-argparser) + ("r-chipseq" ,r-chipseq) + ("r-data-table" ,r-data-table) + ("r-genomation" ,r-genomation) + ("r-genomicranges" ,r-genomicranges) + ("r-rtracklayer" ,r-rtracklayer) + ("r-rcas" ,r-rcas) + ("r-stringr" ,r-stringr) + ("r-jsonlite" ,r-jsonlite) + ("r-heatmaply" ,r-heatmaply) + ("r-ggplot2" ,r-ggplot2) + ("r-plotly" ,r-plotly) + ("python-wrapper" ,python-wrapper) + ("python-pyyaml" ,python-pyyaml) + ("snakemake" ,snakemake) + ("macs" ,macs) + ("multiqc" ,multiqc) + ("perl" ,perl) + ("ghc-pandoc" ,ghc-pandoc) + ("ghc-pandoc-citeproc" ,ghc-pandoc-citeproc) + ("fastqc" ,fastqc) + ("bowtie" ,bowtie) + ("idr" ,idr) + ("snakemake" ,snakemake) + ("samtools" ,samtools) + ("bedtools" ,bedtools) + ("kentutils" ,kentutils))) + (native-inputs + `(("python-pytest" ,python-pytest))) + (home-page "http://bioinformatics.mdc-berlin.de/pigx/") + (synopsis "Analysis pipeline for ChIP sequencing experiments") + (description "PiGX ChIPseq is an analysis pipeline for preprocessing, peak +calling and reporting for ChIP 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 enables to set up +multiple peak calling analysis and allows the generation of a UCSC track hub +in an easily configurable manner.") + (license license:gpl3+))) |