gnu: Add star-for-pigx.
This is a follow-up to commit f1f6e49190
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* gnu/packages/bioinformatics.scm (star-for-pigx): New variable.
(pigx-rnaseq, pigx-scrnaseq)[inputs]: Replace star with star-for-pigx.
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@ -6889,6 +6889,32 @@ (define-public star
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;; STAR is licensed under GPLv3 or later; htslib is MIT-licensed.
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;; STAR is licensed under GPLv3 or later; htslib is MIT-licensed.
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(license license:gpl3+)))
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(license license:gpl3+)))
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(define-public star-for-pigx
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(package
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(inherit star)
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(name "star")
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(version "2.7.3a")
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(source (origin
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(method git-fetch)
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(uri (git-reference
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(url "https://github.com/alexdobin/STAR")
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(commit version)))
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(file-name (git-file-name name version))
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(sha256
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(base32
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"1hgiqw5qhs0pc1xazzihcfd92na02xyq2kb469z04y1v51kpvvjq"))
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(modules '((guix build utils)))
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(snippet
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'(begin
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(substitute* "source/Makefile"
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(("/bin/rm") "rm"))
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;; Remove pre-built binaries and bundled htslib sources.
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(delete-file-recursively "bin/MacOSX_x86_64")
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(delete-file-recursively "bin/Linux_x86_64")
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(delete-file-recursively "bin/Linux_x86_64_static")
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(delete-file-recursively "source/htslib")
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#t))))))
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(define-public starlong
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(define-public starlong
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(package (inherit star)
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(package (inherit star)
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(name "starlong")
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(name "starlong")
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@ -12587,7 +12613,7 @@ (define-public pigx-rnaseq
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("snakemake" ,snakemake)
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("snakemake" ,snakemake)
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("fastqc" ,fastqc)
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("fastqc" ,fastqc)
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("multiqc" ,multiqc)
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("multiqc" ,multiqc)
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("star" ,star)
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("star" ,star-for-pigx)
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("trim-galore" ,trim-galore)
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("trim-galore" ,trim-galore)
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("htseq" ,htseq)
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("htseq" ,htseq)
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("samtools" ,samtools)
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("samtools" ,samtools)
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@ -12798,7 +12824,7 @@ (define-public pigx-scrnaseq
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("pandoc-citeproc" ,pandoc-citeproc)
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("pandoc-citeproc" ,pandoc-citeproc)
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("samtools" ,samtools)
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("samtools" ,samtools)
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("snakemake" ,snakemake)
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("snakemake" ,snakemake)
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("star" ,star)
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("star" ,star-for-pigx)
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("r-minimal" ,r-minimal)
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("r-minimal" ,r-minimal)
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("r-argparser" ,r-argparser)
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("r-argparser" ,r-argparser)
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("r-cowplot" ,r-cowplot)
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("r-cowplot" ,r-cowplot)
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