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gnu: jamm: Use G-expression.

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* gnu/packages/bioinformatics.scm (jamm)[arguments]: Use G-expression.
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Ricardo Wurmus 2023-05-12 22:50:08 +02:00
parent 662e2e82b1
commit e4ca1bcea5
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GPG key ID: 197A5888235FACAC
1 changed files with 38 additions and 39 deletions
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gnu/packages/bioinformatics.scm
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@ -15862,46 +15862,45 @@ (define-public jamm
"0bsa5mf9n9q5jz7mmacrra41l7r8rac5vgsn6wv1fb52ya58b970"))))
(build-system gnu-build-system)
(arguments
`(#:tests? #f ; there are none
#:phases
(modify-phases %standard-phases
(delete 'configure)
(delete 'build)
(replace 'install
(lambda* (#:key inputs outputs #:allow-other-keys)
(let* ((out (assoc-ref outputs "out"))
(libexec (string-append out "/libexec/jamm"))
(bin (string-append out "/bin")))
(substitute* '("JAMM.sh"
"SignalGenerator.sh")
(("^sPath=.*")
(string-append "sPath=\"" libexec "\"\n")))
(for-each (lambda (file)
(install-file file libexec))
(list "bincalculator.r"
"peakfinder.r"
"peakhelper.r"
"signalmaker.r"
"xcorr.r"
"xcorrhelper.r"
;; Perl scripts
"peakfilter.pl"
"readshifter.pl"))
(list
#:tests? #f ;there are none
#:phases
#~(modify-phases %standard-phases
(delete 'configure)
(delete 'build)
(replace 'install
(lambda _
(let ((libexec (string-append #$output "/libexec/jamm"))
(bin (string-append #$output "/bin")))
(substitute* '("JAMM.sh"
"SignalGenerator.sh")
(("^sPath=.*")
(string-append "sPath=\"" libexec "\"\n")))
(for-each (lambda (file)
(install-file file libexec))
(list "bincalculator.r"
"peakfinder.r"
"peakhelper.r"
"signalmaker.r"
"xcorr.r"
"xcorrhelper.r"
;; Perl scripts
"peakfilter.pl"
"readshifter.pl"))
(for-each
(lambda (script)
(chmod script #o555)
(install-file script bin)
(wrap-program (string-append bin "/" script)
`("PATH" ":" prefix
(,(string-append (assoc-ref inputs "coreutils") "/bin")
,(string-append (assoc-ref inputs "gawk") "/bin")
,(string-append (assoc-ref inputs "perl") "/bin")
,(string-append (assoc-ref inputs "r-minimal") "/bin")))
`("PERL5LIB" ":" prefix (,(getenv "PERL5LIB")))
`("R_LIBS_SITE" ":" prefix (,(getenv "R_LIBS_SITE")))))
(list "JAMM.sh" "SignalGenerator.sh")))
#t)))))
(for-each
(lambda (script)
(chmod script #o555)
(install-file script bin)
(wrap-program (string-append bin "/" script)
`("PATH" ":" prefix
(,(string-append #$(this-package-input "coreutils") "/bin")
,(string-append #$(this-package-input "gawk") "/bin")
,(string-append #$(this-package-input "perl") "/bin")
,(string-append #$(this-package-input "r-minimal") "/bin")))
`("PERL5LIB" ":" prefix (,(getenv "PERL5LIB")))
`("R_LIBS_SITE" ":" prefix (,(getenv "R_LIBS_SITE")))))
(list "JAMM.sh" "SignalGenerator.sh"))))))))
(inputs
(list bash
coreutils