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gnu: bwa,bwa-pssm: Improve package style.

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* gnu/packages/bioinformatics.scm (bwa)[arguments]: Use G-expression.
(bwa-pssm)[arguments]: Use G-expression.

Change-Id: I63dd0f13f337fbf84967f1ef1b6332ce3391ae97
This commit is contained in:
Zheng Junjie 2024-07-30 15:56:47 +08:00
parent 18a69ddbf3
commit 4e92ed625f
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GPG Key ID: 3B5AA993E1A2DFF0
1 changed files with 26 additions and 25 deletions
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gnu/packages/bioinformatics.scm
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@ -4271,24 +4271,24 @@ splice junctions between exons.")
"1vf3iwkzxqkzhcfz2q3qyvcv3jrvbb012qy21pfgjl8lv20ywfr1")))) "1vf3iwkzxqkzhcfz2q3qyvcv3jrvbb012qy21pfgjl8lv20ywfr1"))))
(build-system gnu-build-system) (build-system gnu-build-system)
(arguments (arguments
`(#:tests? #f ;no "check" target (list #:tests? #f ;no "check" target
#:make-flags (list "CFLAGS=-fcommon" #:make-flags #~(list "CFLAGS=-fcommon"
(string-append "CC=" ,(cc-for-target))) (string-append "CC=" #$(cc-for-target)))
#:phases #:phases
(modify-phases %standard-phases #~(modify-phases %standard-phases
(replace 'install (replace 'install
(lambda* (#:key outputs #:allow-other-keys) (lambda* (#:key outputs #:allow-other-keys)
(let* ((out (assoc-ref outputs "out")) (let* ((out (assoc-ref outputs "out"))
(bin (string-append out "/bin")) (bin (string-append out "/bin"))
(lib (string-append out "/lib")) (lib (string-append out "/lib"))
(doc (string-append out "/share/doc/bwa")) (doc (string-append out "/share/doc/bwa"))
(man (string-append out "/share/man/man1"))) (man (string-append out "/share/man/man1")))
(install-file "bwa" bin) (install-file "bwa" bin)
(install-file "libbwa.a" lib) (install-file "libbwa.a" lib)
(install-file "README.md" doc) (install-file "README.md" doc)
(install-file "bwa.1" man)))) (install-file "bwa.1" man))))
;; no "configure" script ;; no "configure" script
(delete 'configure)))) (delete 'configure))))
(inputs (list zlib)) (inputs (list zlib))
(supported-systems '("x86_64-linux" "aarch64-linux")) (supported-systems '("x86_64-linux" "aarch64-linux"))
(home-page "https://bio-bwa.sourceforge.net/") (home-page "https://bio-bwa.sourceforge.net/")
@ -4306,7 +4306,8 @@ and more accurate. BWA-MEM also has better performance than BWA-backtrack for
(license license:gpl3+))) (license license:gpl3+)))
(define-public bwa-pssm (define-public bwa-pssm
(package (inherit bwa) (package
(inherit bwa)
(name "bwa-pssm") (name "bwa-pssm")
(version "0.5.11") (version "0.5.11")
(source (origin (source (origin
@ -4321,12 +4322,12 @@ and more accurate. BWA-MEM also has better performance than BWA-backtrack for
(build-system gnu-build-system) (build-system gnu-build-system)
(arguments (arguments
(substitute-keyword-arguments (package-arguments bwa) (substitute-keyword-arguments (package-arguments bwa)
((#:phases phases '%standard-phases) ((#:phases phases #~%standard-phases)
`(modify-phases ,phases #~(modify-phases #$phases
(add-after 'unpack 'patch-C-error (add-after 'unpack 'patch-C-error
(lambda _ (lambda _
(substitute* "pssm.c" (substitute* "pssm.c"
(("inline int map") "int map")))))))) (("inline int map") "int map"))))))))
(inputs (inputs
(list gdsl zlib perl)) (list gdsl zlib perl))
;; https://bwa-pssm.binf.ku.dk is down, and all Web Archived copies are ;; https://bwa-pssm.binf.ku.dk is down, and all Web Archived copies are