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author | Ricardo Wurmus <rekado@elephly.net> | 2021-05-31 15:46:30 +0200 |
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committer | Ricardo Wurmus <rekado@elephly.net> | 2021-05-31 15:46:30 +0200 |
commit | b0ecd6cea90838018744bfad15662abf8f1b0025 (patch) | |
tree | 23c23f1ed75e0013856cd2826f8479024073bd9d /gnu | |
parent | c294c0d782bf36a88e24eb4efcd2fbbf8209ace2 (diff) | |
download | guix-patches-b0ecd6cea90838018744bfad15662abf8f1b0025.tar guix-patches-b0ecd6cea90838018744bfad15662abf8f1b0025.tar.gz |
gnu: r-phantompeakqualtools: Let-bind commit, set revision to 1.
* gnu/packages/bioinformatics.scm (r-phantompeakqualtools): Bind the commit
outside of the package value.
[version]: Use git-version.
[source]: Use git-file-name.
Diffstat (limited to 'gnu')
-rw-r--r-- | gnu/packages/bioinformatics.scm | 86 |
1 files changed, 44 insertions, 42 deletions
diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index 11dbad5a22..a7ff938647 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -7977,51 +7977,53 @@ other functional sequencing data.") (license license:gpl2))) (define-public r-phantompeakqualtools - (package - (name "r-phantompeakqualtools") - (version "1.2.2") - (source - (origin - (method git-fetch) - (uri (git-reference - (url "https://github.com/kundajelab/phantompeakqualtools") - (commit "8d2b2d18c686d894ef5908b37da7adf72a07ef42"))) - (file-name (string-append name "-" version "-checkout")) - (sha256 - (base32 - "00anrvcwsp02d98qhj1xpj85644h2pp4kfzq6dgbmwmdr6jvy7p4")))) - (build-system gnu-build-system) - (arguments - `(#:tests? #f ; There are no tests. - #:phases - (modify-phases %standard-phases - (delete 'configure) - (delete 'build) - (replace 'install - (lambda* (#:key inputs outputs #:allow-other-keys) - (let ((script (string-append (assoc-ref outputs "out") - "/share/scripts"))) - (install-file "run_spp.R" script))))))) - (inputs - `(("r" ,r-minimal))) - (propagated-inputs - `(("r-catools" ,r-catools) - ("r-snow" ,r-snow) - ("r-snowfall" ,r-snowfall) - ("r-bitops" ,r-bitops) - ("r-rsamtools" ,r-rsamtools) - ("r-spp" ,r-spp) - ("gawk" ,gawk) - ("samtools" ,samtools) - ("boost" ,boost) - ("gzip" ,gzip))) - (home-page "https://github.com/kundajelab/phantompeakqualtools") - (synopsis "Informative enrichment for ChIP-seq data") - (description "This package computes informative enrichment and quality + (let ((commit "8d2b2d18c686d894ef5908b37da7adf72a07ef42") + (revision "1")) + (package + (name "r-phantompeakqualtools") + (version (git-version "1.2.2" revision commit)) + (source + (origin + (method git-fetch) + (uri (git-reference + (url "https://github.com/kundajelab/phantompeakqualtools") + (commit commit))) + (file-name (git-file-name name version)) + (sha256 + (base32 + "00anrvcwsp02d98qhj1xpj85644h2pp4kfzq6dgbmwmdr6jvy7p4")))) + (build-system gnu-build-system) + (arguments + `(#:tests? #f ; There are no tests. + #:phases + (modify-phases %standard-phases + (delete 'configure) + (delete 'build) + (replace 'install + (lambda* (#:key inputs outputs #:allow-other-keys) + (let ((script (string-append (assoc-ref outputs "out") + "/share/scripts"))) + (install-file "run_spp.R" script))))))) + (inputs + `(("r" ,r-minimal))) + (propagated-inputs + `(("r-catools" ,r-catools) + ("r-snow" ,r-snow) + ("r-snowfall" ,r-snowfall) + ("r-bitops" ,r-bitops) + ("r-rsamtools" ,r-rsamtools) + ("r-spp" ,r-spp) + ("gawk" ,gawk) + ("samtools" ,samtools) + ("boost" ,boost) + ("gzip" ,gzip))) + (home-page "https://github.com/kundajelab/phantompeakqualtools") + (synopsis "Informative enrichment for ChIP-seq data") + (description "This package computes informative enrichment and quality measures for ChIP-seq/DNase-seq/FAIRE-seq/MNase-seq data. It can also be used to obtain robust estimates of the predominant fragment length or characteristic tag shift values in these assays.") - (license license:bsd-3))) + (license license:bsd-3)))) (define-public r-r4rna (package |