gnu: Add pigx-chipseq.
* gnu/packages/bioinformatics.scm (pigx-chipseq): New variable.
This commit is contained in:
parent
f2785bd657
commit
531afc8a89
|
@ -12725,3 +12725,69 @@ (define-public pigx-rnaseq
|
|||
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+)))
|
||||
|
|
Loading…
Reference in a new issue