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gnu: samtools: Remove patch-makefile-curses phase.

* gnu/packages/bioinformatics.scm (samtools)[arguments]: Remove
  patch-makefile-curses phase, use make-flags instead.
version-0.8.3
Ricardo Wurmus 7 years ago
parent
commit
0a75450c14
  1. 41
      gnu/packages/bioinformatics.scm

41
gnu/packages/bioinformatics.scm

@ -1068,32 +1068,27 @@ distribution, coverage uniformity, strand specificity, etc.")
;; systems.
#:tests? ,(string=? (or (%current-system) (%current-target-system))
"x86_64-linux")
#:make-flags (list (string-append "prefix=" (assoc-ref %outputs "out")))
#:make-flags (list "LIBCURSES=-lncurses"
(string-append "prefix=" (assoc-ref %outputs "out")))
#:phases
(alist-cons-after
'unpack
'patch-makefile-curses
(lambda _
(substitute* "Makefile"
(("-lcurses") "-lncurses")))
(alist-cons-after
'unpack
'patch-tests
(lambda* (#:key inputs #:allow-other-keys)
(let ((bash (assoc-ref inputs "bash")))
(substitute* "test/test.pl"
;; The test script calls out to /bin/bash
(("/bin/bash")
(string-append bash "/bin/bash"))
;; There are two failing tests upstream relating to the "stats"
;; subcommand in test_usage_subcommand ("did not have Usage"
;; and "usage did not mention samtools stats"), so we disable
;; them.
(("(test_usage_subcommand\\(.*\\);)" cmd)
(string-append "unless ($subcommand eq 'stats') {" cmd "};")))))
(alist-delete
'configure
%standard-phases)))))
'patch-tests
(lambda* (#:key inputs #:allow-other-keys)
(let ((bash (assoc-ref inputs "bash")))
(substitute* "test/test.pl"
;; The test script calls out to /bin/bash
(("/bin/bash")
(string-append bash "/bin/bash"))
;; There are two failing tests upstream relating to the "stats"
;; subcommand in test_usage_subcommand ("did not have Usage"
;; and "usage did not mention samtools stats"), so we disable
;; them.
(("(test_usage_subcommand\\(.*\\);)" cmd)
(string-append "unless ($subcommand eq 'stats') {" cmd "};")))))
(alist-delete
'configure
%standard-phases))))
(native-inputs `(("pkg-config" ,pkg-config)))
(inputs `(("ncurses" ,ncurses)
("perl" ,perl)

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