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gnu: samtools: Use "modify-phases" syntax.

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* gnu/packages/bioinformatics.scm (samtools)[arguments]: Use "modify-phases"
syntax.
This commit is contained in:
Ben Woodcroft 2017-04-06 22:27:23 +10:00
parent c62d1a6e6c
commit c842d42593
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GPG key ID: 2A6AD9F4AAC20DF6
1 changed files with 19 additions and 22 deletions
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41
gnu/packages/bioinformatics.scm
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@ -4533,29 +4533,26 @@ (define-public samtools
#:make-flags (list (string-append "prefix=" (assoc-ref %outputs "out")))
#:configure-flags (list "--with-ncurses")
#:phases
(alist-cons-after
'unpack 'patch-tests
(lambda _
(substitute* "test/test.pl"
;; The test script calls out to /bin/bash
(("/bin/bash") (which "bash")))
#t)
(alist-cons-after
'install 'install-library
(lambda* (#:key outputs #:allow-other-keys)
(let ((lib (string-append (assoc-ref outputs "out") "/lib")))
(install-file "libbam.a" lib)
(modify-phases %standard-phases
(add-after 'unpack 'patch-tests
(lambda _
(substitute* "test/test.pl"
;; The test script calls out to /bin/bash
(("/bin/bash") (which "bash")))
#t))
(alist-cons-after
'install 'install-headers
(lambda* (#:key outputs #:allow-other-keys)
(let ((include (string-append (assoc-ref outputs "out")
"/include/samtools/")))
(for-each (lambda (file)
(install-file file include))
(scandir "." (lambda (name) (string-match "\\.h$" name))))
#t))
%standard-phases)))))
(add-after 'install 'install-library
(lambda* (#:key outputs #:allow-other-keys)
(let ((lib (string-append (assoc-ref outputs "out") "/lib")))
(install-file "libbam.a" lib)
#t)))
(add-after 'install 'install-headers
(lambda* (#:key outputs #:allow-other-keys)
(let ((include (string-append (assoc-ref outputs "out")
"/include/samtools/")))
(for-each (lambda (file)
(install-file file include))
(scandir "." (lambda (name) (string-match "\\.h$" name))))
#t))))))
(native-inputs `(("pkg-config" ,pkg-config)))
(inputs `(("ncurses" ,ncurses)
("perl" ,perl)