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| author | Ricardo Wurmus <rekado@elephly.net> | 2017-03-22 12:18:59 +0100 |
|---|---|---|
| committer | Ricardo Wurmus <rekado@elephly.net> | 2017-03-22 12:33:28 +0100 |
| commit | 71dbf592c49e31b2f5e235278942b98f4ba99e72 (patch) | |
| tree | 86c73a6243005bf9de4062c8350a66448d2b9d58 /gnu/packages/bioinformatics.scm | |
| parent | 879b521cd051325255f03444d024c30106b4e9a1 (diff) | |
| download | patches-71dbf592c49e31b2f5e235278942b98f4ba99e72.tar patches-71dbf592c49e31b2f5e235278942b98f4ba99e72.tar.gz | |
gnu: python-pysam: Run tests before installation.
* gnu/packages/bioinformatics.scm (python-pysam)[arguments]: Adjust check
phase to be run before installation.
Diffstat (limited to 'gnu/packages/bioinformatics.scm')
| -rw-r--r-- | gnu/packages/bioinformatics.scm | 28 |
1 files changed, 15 insertions, 13 deletions
diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index 8f0cd0ae77..51f0e0c0b0 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -1430,7 +1430,11 @@ multiple sequence alignments.") '(delete-file-recursively "htslib")))) (build-system python-build-system) (arguments - `(#:phases + `(#:modules ((ice-9 ftw) + (srfi srfi-26) + (guix build python-build-system) + (guix build utils)) + #:phases (modify-phases %standard-phases (add-before 'build 'set-flags (lambda* (#:key inputs #:allow-other-keys) @@ -1442,23 +1446,21 @@ multiple sequence alignments.") (setenv "LDFLAGS" "-lncurses") (setenv "CFLAGS" "-D_CURSES_LIB=1") #t)) - (delete 'check) - (add-after 'install 'check + (replace 'check (lambda* (#:key inputs outputs #:allow-other-keys) + ;; Add first subdirectory of "build" directory to PYTHONPATH. (setenv "PYTHONPATH" (string-append (getenv "PYTHONPATH") - ":" (assoc-ref outputs "out") - "/lib/python" - (string-take (string-take-right - (assoc-ref inputs "python") 5) 3) - "/site-packages")) + ":" (getcwd) "/build/" + (car (scandir "build" + (compose not (cut string-prefix? "." <>)))))) ;; Step out of source dir so python does not import from CWD. - (chdir "tests") - (setenv "HOME" "/tmp") - (and (zero? (system* "make" "-C" "pysam_data")) - (zero? (system* "make" "-C" "cbcf_data")) - (zero? (system* "nosetests" "-v")))))))) + (with-directory-excursion "tests" + (setenv "HOME" "/tmp") + (and (zero? (system* "make" "-C" "pysam_data")) + (zero? (system* "make" "-C" "cbcf_data")) + (zero? (system* "nosetests" "-v"))))))))) (propagated-inputs `(("htslib" ,htslib))) ; Included from installed header files. (inputs |