diff options
| author | Ricardo Wurmus <ricardo.wurmus@mdc-berlin.de> | 2015-04-23 15:23:26 +0200 |
|---|---|---|
| committer | Ricardo Wurmus <ricardo.wurmus@mdc-berlin.de> | 2015-05-04 10:28:26 +0200 |
| commit | 0a75450c14c7e9639099ec470b037795bb6f8f50 (patch) | |
| tree | 32841f76067893485b10c49020008f87ce579f2e | |
| parent | 167a05aabc229d48d62545ef218d8b0577e6e8f3 (diff) | |
| download | patches-0a75450c14c7e9639099ec470b037795bb6f8f50.tar patches-0a75450c14c7e9639099ec470b037795bb6f8f50.tar.gz | |
gnu: samtools: Remove patch-makefile-curses phase.
* gnu/packages/bioinformatics.scm (samtools)[arguments]: Remove
patch-makefile-curses phase, use make-flags instead.
| -rw-r--r-- | gnu/packages/bioinformatics.scm | 41 |
1 files changed, 18 insertions, 23 deletions
diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index bcb7eba48f..9db8fa4d39 100644 --- a/gnu/packages/bioinformatics.scm +++ b/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) |