gnu: python-pysam: Enable tests.

* gnu/packages/bioinformatics.scm (python-pysam)[source]: Change from
PyPi to source archive due to missing test data.
[arguments]: Add check phase after install.
[native-inputs]: Add python-nose, samtools and bcftools.
This commit is contained in:
Marius Bakke 2016-09-22 14:11:59 +01:00 committed by Ben Woodcroft
parent dff26b2363
commit f536dce522
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1 changed files with 30 additions and 6 deletions

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@ -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