diff options
Diffstat (limited to 'gnu/packages')
| -rw-r--r-- | gnu/packages/bioinformatics.scm | 36 |
1 files changed, 30 insertions, 6 deletions
diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index 3ca6fd6c34..078b0a69e0 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -1351,18 +1351,21 @@ multiple sequence alignments.") (version "0.9.1.4") (source (origin (method url-fetch) - (uri (pypi-uri "pysam" version)) + ;; Test data is missing on PyPi. + (uri (string-append + "https://github.com/pysam-developers/pysam/archive/v" + version ".tar.gz")) + (file-name (string-append name "-" version ".tar.gz")) (sha256 (base32 - "1i1djacqbr88y7w18b4aa78zxnsyr4sz7yqdq2spi7gs0y6pzvjn")) + "0y41ssbg6nvn2jgcbnrvkzblpjcwszaiv1rgyd8dwzjkrbfsgsmc")) (modules '((guix build utils))) (snippet ;; Drop bundled htslib. TODO: Also remove samtools and bcftools. '(delete-file-recursively "htslib")))) (build-system python-build-system) (arguments - `(#:tests? #f ; tests are excluded in the manifest - #:phases + `(#:phases (modify-phases %standard-phases (add-before 'build 'set-flags (lambda* (#:key inputs #:allow-other-keys) @@ -1373,7 +1376,24 @@ multiple sequence alignments.") (string-append (assoc-ref inputs "htslib") "/include")) (setenv "LDFLAGS" "-lncurses") (setenv "CFLAGS" "-D_CURSES_LIB=1") - #t))))) + #t)) + (delete 'check) + (add-after 'install 'check + (lambda* (#:key inputs outputs #:allow-other-keys) + (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")) + ;; 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")))))))) (propagated-inputs `(("htslib" ,htslib))) ; Included from installed header files. (inputs @@ -1381,7 +1401,11 @@ multiple sequence alignments.") ("zlib" ,zlib))) (native-inputs `(("python-cython" ,python-cython) - ("python-setuptools" ,python-setuptools))) + ("python-setuptools" ,python-setuptools) + ;; Dependencies below are are for tests only. + ("samtools" ,samtools) + ("bcftools" ,bcftools) + ("python-nose" ,python-nose))) (home-page "https://github.com/pysam-developers/pysam") (synopsis "Python bindings to the SAMtools C API") (description |