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gnu: python-pysam: Run tests before installation.

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* gnu/packages/bioinformatics.scm (python-pysam)[arguments]: Adjust check
phase to be run before installation.
This commit is contained in:
Ricardo Wurmus 2017-03-22 12:18:59 +01:00
parent 879b521cd0
commit 71dbf592c4
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GPG key ID: 197A5888235FACAC
1 changed files with 15 additions and 13 deletions
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22
gnu/packages/bioinformatics.scm
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@ -1430,7 +1430,11 @@ (define-public python-pysam
'(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 @@ (define-public python-pysam
(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")
(with-directory-excursion "tests"
(setenv "HOME" "/tmp")
(and (zero? (system* "make" "-C" "pysam_data"))
(zero? (system* "make" "-C" "cbcf_data"))
(zero? (system* "nosetests" "-v"))))))))
(zero? (system* "nosetests" "-v")))))))))
(propagated-inputs
`(("htslib" ,htslib))) ; Included from installed header files.
(inputs