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gnu: pigx-scrnaseq: Update to 1.1.3.

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* gnu/packages/bioinformatics.scm (pigx-scrnaseq): Update to 1.1.3.
[arguments]: Remove.
[inputs]: Remove dropseq-tools and java-picard; add flexbar, jellyfish, and
r-seurat; replace python-loompy-for-pigx-scrnaseq with python-loompy.
This commit is contained in:
Ricardo Wurmus 2020-02-26 08:58:06 +01:00
parent 290b55c55a
commit 4f19106770
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GPG key ID: 197A5888235FACAC
1 changed files with 6 additions and 11 deletions
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gnu/packages/bioinformatics.scm
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@ -12770,7 +12770,7 @@ (define-public pigx-bsseq
(define-public pigx-scrnaseq (define-public pigx-scrnaseq
(package (package
(name "pigx-scrnaseq") (name "pigx-scrnaseq")
(version "0.0.8") (version "1.1.3")
(source (origin (source (origin
(method url-fetch) (method url-fetch)
(uri (string-append "https://github.com/BIMSBbioinfo/pigx_scrnaseq/" (uri (string-append "https://github.com/BIMSBbioinfo/pigx_scrnaseq/"
@ -12778,27 +12778,21 @@ (define-public pigx-scrnaseq
"/pigx_scrnaseq-" version ".tar.gz")) "/pigx_scrnaseq-" version ".tar.gz"))
(sha256 (sha256
(base32 (base32
"0zv0sc5amivxhb95vx2gfx6l9bh7n80fh7h47dalnwxxnfvnzai4")))) "0ga2jr4968qzwml6aycky4603q64lny3y7lzw6dmafch5pydl1qi"))))
(build-system gnu-build-system) (build-system gnu-build-system)
(arguments
`(#:configure-flags
(list (string-append "PICARDJAR=" (assoc-ref %build-inputs "java-picard")
"/share/java/picard.jar")
(string-append "DROPSEQJAR=" (assoc-ref %build-inputs "dropseq-tools")
"/share/java/dropseq.jar"))))
(inputs (inputs
`(("coreutils" ,coreutils) `(("coreutils" ,coreutils)
("perl" ,perl) ("perl" ,perl)
("dropseq-tools" ,dropseq-tools)
("fastqc" ,fastqc) ("fastqc" ,fastqc)
("java-picard" ,java-picard-2.10.3) ; same as for dropseq ("flexbar" ,flexbar)
("java" ,icedtea-8) ("java" ,icedtea-8)
("jellyfish" ,jellyfish)
("python-wrapper" ,python-wrapper) ("python-wrapper" ,python-wrapper)
("python-pyyaml" ,python-pyyaml) ("python-pyyaml" ,python-pyyaml)
("python-pandas" ,python-pandas) ("python-pandas" ,python-pandas)
("python-magic" ,python-magic) ("python-magic" ,python-magic)
("python-numpy" ,python-numpy) ("python-numpy" ,python-numpy)
("python-loompy" ,python-loompy-for-pigx-scrnaseq) ("python-loompy" ,python-loompy)
("ghc-pandoc" ,ghc-pandoc) ("ghc-pandoc" ,ghc-pandoc)
("ghc-pandoc-citeproc" ,ghc-pandoc-citeproc) ("ghc-pandoc-citeproc" ,ghc-pandoc-citeproc)
("samtools" ,samtools) ("samtools" ,samtools)
@ -12825,6 +12819,7 @@ (define-public pigx-scrnaseq
("r-rtsne" ,r-rtsne) ("r-rtsne" ,r-rtsne)
("r-scater" ,r-scater) ("r-scater" ,r-scater)
("r-scran" ,r-scran) ("r-scran" ,r-scran)
("r-seurat" ,r-seurat)
("r-singlecellexperiment" ,r-singlecellexperiment) ("r-singlecellexperiment" ,r-singlecellexperiment)
("r-stringr" ,r-stringr) ("r-stringr" ,r-stringr)
("r-yaml" ,r-yaml))) ("r-yaml" ,r-yaml)))