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gnu: Add snakemake-4. 

* gnu/packages/python.scm (snakemake-4): New variable.
* gnu/packages/bioinformatics.scm (pigx-bsseq, pigx-rnaseq, pigx-scrnaseq,
pigx-chipseq)[inputs]: Use it.
This commit is contained in:
Ricardo Wurmus 2018-07-27 15:13:56 +02:00
parent 269f100330
commit ed2dfe3955
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GPG Key ID: 197A5888235FACAC
2 changed files with 22 additions and 4 deletions
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8
gnu/packages/bioinformatics.scm
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@ -12837,7 +12837,7 @@ once. This package provides tools to perform Drop-seq analyses.")
#t))))) #t)))))
(inputs (inputs
`(("gzip" ,gzip) `(("gzip" ,gzip)
("snakemake" ,snakemake) ("snakemake" ,snakemake-4)
("fastqc" ,fastqc) ("fastqc" ,fastqc)
("multiqc" ,multiqc) ("multiqc" ,multiqc)
("star" ,star) ("star" ,star)
@ -12931,7 +12931,7 @@ expression report comparing samples in an easily configurable manner.")
("fastqc" ,fastqc) ("fastqc" ,fastqc)
("bowtie" ,bowtie) ("bowtie" ,bowtie)
("idr" ,idr) ("idr" ,idr)
("snakemake" ,snakemake) ("snakemake" ,snakemake-4)
("samtools" ,samtools) ("samtools" ,samtools)
("bedtools" ,bedtools) ("bedtools" ,bedtools)
("kentutils" ,kentutils))) ("kentutils" ,kentutils)))
@ -12992,7 +12992,7 @@ in an easily configurable manner.")
("ghc-pandoc-citeproc" ,ghc-pandoc-citeproc-with-pandoc-1) ("ghc-pandoc-citeproc" ,ghc-pandoc-citeproc-with-pandoc-1)
("python-wrapper" ,python-wrapper) ("python-wrapper" ,python-wrapper)
("python-pyyaml" ,python-pyyaml) ("python-pyyaml" ,python-pyyaml)
("snakemake" ,snakemake) ("snakemake" ,snakemake-4)
("bismark" ,bismark) ("bismark" ,bismark)
("fastqc" ,fastqc) ("fastqc" ,fastqc)
("bowtie" ,bowtie) ("bowtie" ,bowtie)
@ -13041,7 +13041,7 @@ methylation and segmentation.")
("python-loompy" ,python-loompy) ("python-loompy" ,python-loompy)
("ghc-pandoc" ,ghc-pandoc-1) ("ghc-pandoc" ,ghc-pandoc-1)
("ghc-pandoc-citeproc" ,ghc-pandoc-citeproc-with-pandoc-1) ("ghc-pandoc-citeproc" ,ghc-pandoc-citeproc-with-pandoc-1)
("snakemake" ,snakemake) ("snakemake" ,snakemake-4)
("star" ,star) ("star" ,star)
("r-minimal" ,r-minimal) ("r-minimal" ,r-minimal)
("r-argparser" ,r-argparser) ("r-argparser" ,r-argparser)

18
gnu/packages/python.scm
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@ -5206,6 +5206,24 @@ providing a clean and modern domain specific specification language (DSL) in
Python style, together with a fast and comfortable execution environment.") Python style, together with a fast and comfortable execution environment.")
(license license:expat))) (license license:expat)))
;; This is currently needed for the pigx-* packages.
(define-public snakemake-4
(package (inherit snakemake)
(version "4.4.0")
(source
(origin
(method url-fetch)
(uri (pypi-uri "snakemake" version))
(sha256
(base32 "0g0paia4z7w3srnqdmavq3hrb2x7qnpf81jx50njl0p7y4y0j8jv"))))
(propagated-inputs
`(("python-wrapt" ,python-wrapt)
("python-requests" ,python-requests)
("python-appdirs" ,python-appdirs)
("python-configargparse" ,python-configargparse)
("python-pyyaml" ,python-pyyaml)
("python-ratelimiter" ,python-ratelimiter)))))
(define-public python-pyqrcode (define-public python-pyqrcode
(package (package
(name "python-pyqrcode") (name "python-pyqrcode")