gnu: Add pigx-bsseq.

* gnu/packages/bioinformatics.scm (pigx-bsseq): New variable.
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Ricardo Wurmus 2018-03-11 19:53:11 +01:00
parent 531afc8a89
commit fb94174fc3
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@ -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+)))