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gnu: velvet: Improve package style. 

* gnu/packages/bioinformatics.scm (velvet)[arguments]: Use G-expressions.
[native-inputs]: Remove label.
Nicolas Goaziou 2023-06-29 00:37:38 +02:00
parent 42500f1aad
commit 1e92db8927
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1 changed files with 28 additions and 28 deletions
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@ -17066,37 +17066,37 @@ to an artifact/contaminant file.")
(delete-file-recursively "third-party"))))) (delete-file-recursively "third-party")))))
(build-system gnu-build-system) (build-system gnu-build-system)
(arguments (arguments
`(#:make-flags '("OPENMP=t") (list
#:test-target "test" #:make-flags #~(list "OPENMP=t")
#:phases #:test-target "test"
(modify-phases %standard-phases #:phases
(delete 'configure) #~(modify-phases %standard-phases
(add-after 'unpack 'fix-zlib-include (delete 'configure)
(lambda _ (add-after 'unpack 'fix-zlib-include
(substitute* "src/binarySequences.c" (lambda _
(("../third-party/zlib-1.2.3/zlib.h") "zlib.h")))) (substitute* "src/binarySequences.c"
(replace 'install (("../third-party/zlib-1.2.3/zlib.h") "zlib.h"))))
(lambda* (#:key outputs #:allow-other-keys) (replace 'install
(let* ((out (assoc-ref outputs "out")) (lambda _
(bin (string-append out "/bin")) (let ((bin (string-append #$output "/bin"))
(doc (string-append out "/share/doc/velvet"))) (doc (string-append #$output "/share/doc/velvet")))
(mkdir-p bin) (mkdir-p bin)
(mkdir-p doc) (mkdir-p doc)
(install-file "velveth" bin) (install-file "velveth" bin)
(install-file "velvetg" bin) (install-file "velvetg" bin)
(install-file "Manual.pdf" doc) (install-file "Manual.pdf" doc)
(install-file "Columbus_manual.pdf" doc))))))) (install-file "Columbus_manual.pdf" doc)))))))
(inputs (inputs
(list openmpi zlib)) (list openmpi zlib))
(native-inputs (native-inputs
`(("texlive" ,(texlive-updmap.cfg (list (texlive-updmap.cfg
(list texlive-ec (list texlive-ec
texlive-graphics texlive-graphics
texlive-grfext texlive-grfext
texlive-hyperref texlive-hyperref
texlive-infwarerr texlive-infwarerr
texlive-kvoptions texlive-kvoptions
texlive-pdftexcmds))))) texlive-pdftexcmds))))
(home-page "https://www.ebi.ac.uk/~zerbino/velvet/") (home-page "https://www.ebi.ac.uk/~zerbino/velvet/")
(synopsis "Nucleic acid sequence assembler for very short reads") (synopsis "Nucleic acid sequence assembler for very short reads")
(description (description