diff options
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 |