gnu: samtools: Use "modify-phases" syntax.
* gnu/packages/bioinformatics.scm (samtools)[arguments]: Use "modify-phases" syntax.
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@ -4533,29 +4533,26 @@ to the user's query of interest.")
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#:make-flags (list (string-append "prefix=" (assoc-ref %outputs "out")))
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#:make-flags (list (string-append "prefix=" (assoc-ref %outputs "out")))
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#:configure-flags (list "--with-ncurses")
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#:configure-flags (list "--with-ncurses")
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#:phases
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#:phases
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(alist-cons-after
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(modify-phases %standard-phases
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'unpack 'patch-tests
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(add-after 'unpack 'patch-tests
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(lambda _
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(lambda _
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(substitute* "test/test.pl"
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(substitute* "test/test.pl"
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;; The test script calls out to /bin/bash
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;; The test script calls out to /bin/bash
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(("/bin/bash") (which "bash")))
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(("/bin/bash") (which "bash")))
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#t)
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(alist-cons-after
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'install 'install-library
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(lambda* (#:key outputs #:allow-other-keys)
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(let ((lib (string-append (assoc-ref outputs "out") "/lib")))
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(install-file "libbam.a" lib)
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#t))
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#t))
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(alist-cons-after
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(add-after 'install 'install-library
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'install 'install-headers
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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 ((lib (string-append (assoc-ref outputs "out") "/lib")))
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(let ((include (string-append (assoc-ref outputs "out")
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(install-file "libbam.a" lib)
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"/include/samtools/")))
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#t)))
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(for-each (lambda (file)
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(add-after 'install 'install-headers
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(install-file file include))
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(lambda* (#:key outputs #:allow-other-keys)
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(scandir "." (lambda (name) (string-match "\\.h$" name))))
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(let ((include (string-append (assoc-ref outputs "out")
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#t))
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"/include/samtools/")))
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%standard-phases)))))
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(for-each (lambda (file)
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(install-file file include))
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(scandir "." (lambda (name) (string-match "\\.h$" name))))
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#t))))))
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(native-inputs `(("pkg-config" ,pkg-config)))
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(native-inputs `(("pkg-config" ,pkg-config)))
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(inputs `(("ncurses" ,ncurses)
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(inputs `(("ncurses" ,ncurses)
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("perl" ,perl)
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("perl" ,perl)
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