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