gnu: Add pigx-bsseq.
* gnu/packages/bioinformatics.scm (pigx-bsseq): New variable.
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@ -12791,3 +12791,67 @@ (define-public pigx-chipseq
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multiple peak calling analysis and allows the generation of a UCSC track hub
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multiple peak calling analysis and allows the generation of a UCSC track hub
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in an easily configurable manner.")
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in an easily configurable manner.")
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(license license:gpl3+)))
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(license license:gpl3+)))
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(define-public pigx-bsseq
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(package
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(name "pigx-bsseq")
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(version "0.0.5")
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(source (origin
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(method url-fetch)
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(uri (string-append "https://github.com/BIMSBbioinfo/pigx_bsseq/"
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"releases/download/v" version
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"/pigx_bsseq-" version ".tar.gz"))
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(sha256
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(base32
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"1h8ma99vi7hs83nafvjpq8jmaq9977j3n11c4zd95hai0cf7zxmp"))))
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(build-system gnu-build-system)
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(arguments
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`(#:phases
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(modify-phases %standard-phases
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(add-before 'check 'set-timezone
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;; The readr package is picky about timezones.
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(lambda* (#:key inputs #:allow-other-keys)
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(setenv "TZ" "UTC+1")
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(setenv "TZDIR"
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(string-append (assoc-ref inputs "tzdata")
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"/share/zoneinfo"))
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#t))
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(add-after 'install 'wrap-executable
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;; Make sure the executable finds all R modules.
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(lambda* (#:key inputs outputs #:allow-other-keys)
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(let ((out (assoc-ref outputs "out")))
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(wrap-program (string-append out "/bin/pigx-bsseq")
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`("R_LIBS_SITE" ":" = (,(getenv "R_LIBS_SITE")))
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`("PYTHONPATH" ":" = (,(getenv "PYTHONPATH")))))
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#t)))))
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(native-inputs
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`(("tzdata" ,tzdata)))
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(inputs
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`(("r-minimal" ,r-minimal)
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("r-annotationhub" ,r-annotationhub)
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("r-dt" ,r-dt)
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("r-genomation" ,r-genomation)
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("r-methylkit" ,r-methylkit)
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("r-rtracklayer" ,r-rtracklayer)
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("r-rmarkdown" ,r-rmarkdown)
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("r-bookdown" ,r-bookdown)
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("r-ggplot2" ,r-ggplot2)
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("r-ggbio" ,r-ggbio)
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("ghc-pandoc" ,ghc-pandoc)
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("ghc-pandoc-citeproc" ,ghc-pandoc-citeproc)
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("python-wrapper" ,python-wrapper)
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("python-pyyaml" ,python-pyyaml)
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("snakemake" ,snakemake)
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("bismark" ,bismark)
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("fastqc" ,fastqc)
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("bowtie" ,bowtie)
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("trim-galore" ,trim-galore)
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("cutadapt" ,cutadapt)
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("samtools" ,samtools)))
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(home-page "http://bioinformatics.mdc-berlin.de/pigx/")
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(synopsis "Bisulfite sequencing pipeline from fastq to methylation reports")
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(description "PiGx BSseq is a data processing pipeline for raw fastq read
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data of bisulfite experiments; it produces reports on aggregate methylation
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and coverage and can be used to produce information on differential
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methylation and segmentation.")
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(license license:gpl3+)))
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