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author | Ricardo Wurmus <rekado@elephly.net> | 2018-03-11 19:53:11 +0100 |
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committer | Ricardo Wurmus <rekado@elephly.net> | 2018-03-11 20:01:53 +0100 |
commit | fb94174fc39cfbdddf23aa58a12b1ee62674122d (patch) | |
tree | 63557e6b09352c8171f97b02f710613232018bd7 | |
parent | 531afc8a892512487251a03be24d9833b86179f1 (diff) | |
download | guix-patches-fb94174fc39cfbdddf23aa58a12b1ee62674122d.tar guix-patches-fb94174fc39cfbdddf23aa58a12b1ee62674122d.tar.gz |
gnu: Add pigx-bsseq.
* gnu/packages/bioinformatics.scm (pigx-bsseq): New variable.
-rw-r--r-- | gnu/packages/bioinformatics.scm | 64 |
1 files changed, 64 insertions, 0 deletions
diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index 50d3568987..567dd2c24b 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -12791,3 +12791,67 @@ 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+))) + +(define-public pigx-bsseq + (package + (name "pigx-bsseq") + (version "0.0.5") + (source (origin + (method url-fetch) + (uri (string-append "https://github.com/BIMSBbioinfo/pigx_bsseq/" + "releases/download/v" version + "/pigx_bsseq-" version ".tar.gz")) + (sha256 + (base32 + "1h8ma99vi7hs83nafvjpq8jmaq9977j3n11c4zd95hai0cf7zxmp")))) + (build-system gnu-build-system) + (arguments + `(#:phases + (modify-phases %standard-phases + (add-before 'check 'set-timezone + ;; The readr package is picky about timezones. + (lambda* (#:key inputs #:allow-other-keys) + (setenv "TZ" "UTC+1") + (setenv "TZDIR" + (string-append (assoc-ref inputs "tzdata") + "/share/zoneinfo")) + #t)) + (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-bsseq") + `("R_LIBS_SITE" ":" = (,(getenv "R_LIBS_SITE"))) + `("PYTHONPATH" ":" = (,(getenv "PYTHONPATH"))))) + #t))))) + (native-inputs + `(("tzdata" ,tzdata))) + (inputs + `(("r-minimal" ,r-minimal) + ("r-annotationhub" ,r-annotationhub) + ("r-dt" ,r-dt) + ("r-genomation" ,r-genomation) + ("r-methylkit" ,r-methylkit) + ("r-rtracklayer" ,r-rtracklayer) + ("r-rmarkdown" ,r-rmarkdown) + ("r-bookdown" ,r-bookdown) + ("r-ggplot2" ,r-ggplot2) + ("r-ggbio" ,r-ggbio) + ("ghc-pandoc" ,ghc-pandoc) + ("ghc-pandoc-citeproc" ,ghc-pandoc-citeproc) + ("python-wrapper" ,python-wrapper) + ("python-pyyaml" ,python-pyyaml) + ("snakemake" ,snakemake) + ("bismark" ,bismark) + ("fastqc" ,fastqc) + ("bowtie" ,bowtie) + ("trim-galore" ,trim-galore) + ("cutadapt" ,cutadapt) + ("samtools" ,samtools))) + (home-page "http://bioinformatics.mdc-berlin.de/pigx/") + (synopsis "Bisulfite sequencing pipeline from fastq to methylation reports") + (description "PiGx BSseq is a data processing pipeline for raw fastq read +data of bisulfite experiments; it produces reports on aggregate methylation +and coverage and can be used to produce information on differential +methylation and segmentation.") + (license license:gpl3+))) |