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| author | Ricardo Wurmus <rekado@elephly.net> | 2020-02-26 08:58:06 +0100 |
|---|---|---|
| committer | Ricardo Wurmus <rekado@elephly.net> | 2020-02-26 08:58:06 +0100 |
| commit | 4f19106770e52a54c54640b8931fd0e3250bc3b8 (patch) | |
| tree | 053404dd2ed7c301be8c6ae0735eefa91fd0b65e | |
| parent | 290b55c55a5cecd686bd294a33e97f023e04a85b (diff) | |
| download | patches-4f19106770e52a54c54640b8931fd0e3250bc3b8.tar patches-4f19106770e52a54c54640b8931fd0e3250bc3b8.tar.gz | |
gnu: pigx-scrnaseq: Update to 1.1.3.
* 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.
| -rw-r--r-- | gnu/packages/bioinformatics.scm | 17 |
1 files changed, 6 insertions, 11 deletions
diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index 753b7fd0f5..e64842b9d6 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -12770,7 +12770,7 @@ methylation and segmentation.") (define-public pigx-scrnaseq (package (name "pigx-scrnaseq") - (version "0.0.8") + (version "1.1.3") (source (origin (method url-fetch) (uri (string-append "https://github.com/BIMSBbioinfo/pigx_scrnaseq/" @@ -12778,27 +12778,21 @@ methylation and segmentation.") "/pigx_scrnaseq-" version ".tar.gz")) (sha256 (base32 - "0zv0sc5amivxhb95vx2gfx6l9bh7n80fh7h47dalnwxxnfvnzai4")))) + "0ga2jr4968qzwml6aycky4603q64lny3y7lzw6dmafch5pydl1qi")))) (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 `(("coreutils" ,coreutils) ("perl" ,perl) - ("dropseq-tools" ,dropseq-tools) ("fastqc" ,fastqc) - ("java-picard" ,java-picard-2.10.3) ; same as for dropseq + ("flexbar" ,flexbar) ("java" ,icedtea-8) + ("jellyfish" ,jellyfish) ("python-wrapper" ,python-wrapper) ("python-pyyaml" ,python-pyyaml) ("python-pandas" ,python-pandas) ("python-magic" ,python-magic) ("python-numpy" ,python-numpy) - ("python-loompy" ,python-loompy-for-pigx-scrnaseq) + ("python-loompy" ,python-loompy) ("ghc-pandoc" ,ghc-pandoc) ("ghc-pandoc-citeproc" ,ghc-pandoc-citeproc) ("samtools" ,samtools) @@ -12825,6 +12819,7 @@ methylation and segmentation.") ("r-rtsne" ,r-rtsne) ("r-scater" ,r-scater) ("r-scran" ,r-scran) + ("r-seurat" ,r-seurat) ("r-singlecellexperiment" ,r-singlecellexperiment) ("r-stringr" ,r-stringr) ("r-yaml" ,r-yaml))) |