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gnu: jamm: Use G-expression. 

* gnu/packages/bioinformatics.scm (jamm)[arguments]: Use G-expression.
master
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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@ -15862,46 +15862,45 @@ Barcoding Kit or Rapid Barcoding Kit.")
"0bsa5mf9n9q5jz7mmacrra41l7r8rac5vgsn6wv1fb52ya58b970")))) "0bsa5mf9n9q5jz7mmacrra41l7r8rac5vgsn6wv1fb52ya58b970"))))
(build-system gnu-build-system) (build-system gnu-build-system)
(arguments (arguments
`(#:tests? #f ; there are none (list
#:phases #:tests? #f ;there are none
(modify-phases %standard-phases #:phases
(delete 'configure) #~(modify-phases %standard-phases
(delete 'build) (delete 'configure)
(replace 'install (delete 'build)
(lambda* (#:key inputs outputs #:allow-other-keys) (replace 'install
(let* ((out (assoc-ref outputs "out")) (lambda _
(libexec (string-append out "/libexec/jamm")) (let ((libexec (string-append #$output "/libexec/jamm"))
(bin (string-append out "/bin"))) (bin (string-append #$output "/bin")))
(substitute* '("JAMM.sh" (substitute* '("JAMM.sh"
"SignalGenerator.sh") "SignalGenerator.sh")
(("^sPath=.*") (("^sPath=.*")
(string-append "sPath=\"" libexec "\"\n"))) (string-append "sPath=\"" libexec "\"\n")))
(for-each (lambda (file) (for-each (lambda (file)
(install-file file libexec)) (install-file file libexec))
(list "bincalculator.r" (list "bincalculator.r"
"peakfinder.r" "peakfinder.r"
"peakhelper.r" "peakhelper.r"
"signalmaker.r" "signalmaker.r"
"xcorr.r" "xcorr.r"
"xcorrhelper.r" "xcorrhelper.r"
;; Perl scripts ;; Perl scripts
"peakfilter.pl" "peakfilter.pl"
"readshifter.pl")) "readshifter.pl"))
(for-each (for-each
(lambda (script) (lambda (script)
(chmod script #o555) (chmod script #o555)
(install-file script bin) (install-file script bin)
(wrap-program (string-append bin "/" script) (wrap-program (string-append bin "/" script)
`("PATH" ":" prefix `("PATH" ":" prefix
(,(string-append (assoc-ref inputs "coreutils") "/bin") (,(string-append #$(this-package-input "coreutils") "/bin")
,(string-append (assoc-ref inputs "gawk") "/bin") ,(string-append #$(this-package-input "gawk") "/bin")
,(string-append (assoc-ref inputs "perl") "/bin") ,(string-append #$(this-package-input "perl") "/bin")
,(string-append (assoc-ref inputs "r-minimal") "/bin"))) ,(string-append #$(this-package-input "r-minimal") "/bin")))
`("PERL5LIB" ":" prefix (,(getenv "PERL5LIB"))) `("PERL5LIB" ":" prefix (,(getenv "PERL5LIB")))
`("R_LIBS_SITE" ":" prefix (,(getenv "R_LIBS_SITE"))))) `("R_LIBS_SITE" ":" prefix (,(getenv "R_LIBS_SITE")))))
(list "JAMM.sh" "SignalGenerator.sh"))) (list "JAMM.sh" "SignalGenerator.sh"))))))))
#t)))))
(inputs (inputs
(list bash (list bash
coreutils coreutils