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| author | Ricardo Wurmus <rekado@elephly.net> | 2018-07-27 15:13:56 +0200 |
|---|---|---|
| committer | Ricardo Wurmus <rekado@elephly.net> | 2018-07-27 15:30:38 +0200 |
| commit | ed2dfe3955f0144bc858c66fdb751f51e9bd84fe (patch) | |
| tree | 5e8fdebcf590d21cc62db8400426e93dd44405dc /gnu | |
| parent | 269f100330cf92afdc911bbd7db0644719d6dc3f (diff) | |
| download | patches-ed2dfe3955f0144bc858c66fdb751f51e9bd84fe.tar patches-ed2dfe3955f0144bc858c66fdb751f51e9bd84fe.tar.gz | |
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.
Diffstat (limited to 'gnu')
| -rw-r--r-- | gnu/packages/bioinformatics.scm | 8 | ||||
| -rw-r--r-- | gnu/packages/python.scm | 18 |
2 files changed, 22 insertions, 4 deletions
diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index 73cca16717..bb0e8c73c7 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -12837,7 +12837,7 @@ once. This package provides tools to perform Drop-seq analyses.") #t))))) (inputs `(("gzip" ,gzip) - ("snakemake" ,snakemake) + ("snakemake" ,snakemake-4) ("fastqc" ,fastqc) ("multiqc" ,multiqc) ("star" ,star) @@ -12931,7 +12931,7 @@ expression report comparing samples in an easily configurable manner.") ("fastqc" ,fastqc) ("bowtie" ,bowtie) ("idr" ,idr) - ("snakemake" ,snakemake) + ("snakemake" ,snakemake-4) ("samtools" ,samtools) ("bedtools" ,bedtools) ("kentutils" ,kentutils))) @@ -12992,7 +12992,7 @@ in an easily configurable manner.") ("ghc-pandoc-citeproc" ,ghc-pandoc-citeproc-with-pandoc-1) ("python-wrapper" ,python-wrapper) ("python-pyyaml" ,python-pyyaml) - ("snakemake" ,snakemake) + ("snakemake" ,snakemake-4) ("bismark" ,bismark) ("fastqc" ,fastqc) ("bowtie" ,bowtie) @@ -13041,7 +13041,7 @@ methylation and segmentation.") ("python-loompy" ,python-loompy) ("ghc-pandoc" ,ghc-pandoc-1) ("ghc-pandoc-citeproc" ,ghc-pandoc-citeproc-with-pandoc-1) - ("snakemake" ,snakemake) + ("snakemake" ,snakemake-4) ("star" ,star) ("r-minimal" ,r-minimal) ("r-argparser" ,r-argparser) diff --git a/gnu/packages/python.scm b/gnu/packages/python.scm index a6e3ebb9d6..e9fb9f529f 100644 --- a/gnu/packages/python.scm +++ b/gnu/packages/python.scm @@ -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.") (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 (package (name "python-pyqrcode") |