gnu: bwa,bwa-pssm: Improve package style.
* gnu/packages/bioinformatics.scm (bwa)[arguments]: Use G-expression. (bwa-pssm)[arguments]: Use G-expression. Change-Id: I63dd0f13f337fbf84967f1ef1b6332ce3391ae97master
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18a69ddbf3
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4e92ed625f
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@ -4271,24 +4271,24 @@ splice junctions between exons.")
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"1vf3iwkzxqkzhcfz2q3qyvcv3jrvbb012qy21pfgjl8lv20ywfr1"))))
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"1vf3iwkzxqkzhcfz2q3qyvcv3jrvbb012qy21pfgjl8lv20ywfr1"))))
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(build-system gnu-build-system)
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(build-system gnu-build-system)
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(arguments
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(arguments
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`(#:tests? #f ;no "check" target
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(list #:tests? #f ;no "check" target
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#:make-flags (list "CFLAGS=-fcommon"
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#:make-flags #~(list "CFLAGS=-fcommon"
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(string-append "CC=" ,(cc-for-target)))
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(string-append "CC=" #$(cc-for-target)))
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#:phases
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#:phases
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(modify-phases %standard-phases
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#~(modify-phases %standard-phases
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(replace 'install
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(replace 'install
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(lambda* (#:key outputs #:allow-other-keys)
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(lambda* (#:key outputs #:allow-other-keys)
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(let* ((out (assoc-ref outputs "out"))
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(let* ((out (assoc-ref outputs "out"))
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(bin (string-append out "/bin"))
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(bin (string-append out "/bin"))
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(lib (string-append out "/lib"))
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(lib (string-append out "/lib"))
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(doc (string-append out "/share/doc/bwa"))
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(doc (string-append out "/share/doc/bwa"))
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(man (string-append out "/share/man/man1")))
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(man (string-append out "/share/man/man1")))
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(install-file "bwa" bin)
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(install-file "bwa" bin)
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(install-file "libbwa.a" lib)
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(install-file "libbwa.a" lib)
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(install-file "README.md" doc)
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(install-file "README.md" doc)
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(install-file "bwa.1" man))))
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(install-file "bwa.1" man))))
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;; no "configure" script
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;; no "configure" script
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(delete 'configure))))
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(delete 'configure))))
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(inputs (list zlib))
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(inputs (list zlib))
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(supported-systems '("x86_64-linux" "aarch64-linux"))
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(supported-systems '("x86_64-linux" "aarch64-linux"))
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(home-page "https://bio-bwa.sourceforge.net/")
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(home-page "https://bio-bwa.sourceforge.net/")
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@ -4306,7 +4306,8 @@ and more accurate. BWA-MEM also has better performance than BWA-backtrack for
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(license license:gpl3+)))
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(license license:gpl3+)))
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(define-public bwa-pssm
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(define-public bwa-pssm
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(package (inherit bwa)
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(package
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(inherit bwa)
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(name "bwa-pssm")
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(name "bwa-pssm")
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(version "0.5.11")
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(version "0.5.11")
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(source (origin
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(source (origin
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@ -4321,12 +4322,12 @@ and more accurate. BWA-MEM also has better performance than BWA-backtrack for
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(build-system gnu-build-system)
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(build-system gnu-build-system)
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(arguments
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(arguments
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(substitute-keyword-arguments (package-arguments bwa)
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(substitute-keyword-arguments (package-arguments bwa)
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((#:phases phases '%standard-phases)
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((#:phases phases #~%standard-phases)
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`(modify-phases ,phases
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#~(modify-phases #$phases
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(add-after 'unpack 'patch-C-error
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(add-after 'unpack 'patch-C-error
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(lambda _
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(lambda _
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(substitute* "pssm.c"
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(substitute* "pssm.c"
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(("inline int map") "int map"))))))))
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(("inline int map") "int map"))))))))
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(inputs
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(inputs
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(list gdsl zlib perl))
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(list gdsl zlib perl))
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;; https://bwa-pssm.binf.ku.dk is down, and all Web Archived copies are
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;; https://bwa-pssm.binf.ku.dk is down, and all Web Archived copies are
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