gnu: gemma: Enable tests.
* gnu/packages/bioinformatics.scm (gemma)[source]: Add snippet to remove bundled sources. [native-inputs]: Add catch-framework2-1, perl, shunit2, which. [arguments]: Don't disable tests. Override 'check phase.
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@ -3572,12 +3572,22 @@ (define-public gemma
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(file-name (git-file-name name version))
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(file-name (git-file-name name version))
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(sha256
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(sha256
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(base32
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(base32
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"1p8a7kkfn1mmrg017aziy544aha8i9h6wd1x2dk3w2794wl33qb7"))))
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"1p8a7kkfn1mmrg017aziy544aha8i9h6wd1x2dk3w2794wl33qb7"))
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(modules '((guix build utils)))
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(snippet
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'(begin
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(delete-file-recursively "contrib")
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#t))))
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(build-system gnu-build-system)
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(build-system gnu-build-system)
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(inputs
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(inputs
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`(("gsl" ,gsl)
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`(("gsl" ,gsl)
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("openblas" ,openblas)
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("openblas" ,openblas)
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("zlib" ,zlib)))
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("zlib" ,zlib)))
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(native-inputs
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`(("catch" ,catch-framework2-1)
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("perl" ,perl)
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("shunit2" ,shunit2)
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("which" ,which)))
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(arguments
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(arguments
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`(#:phases
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`(#:phases
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(modify-phases %standard-phases
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(modify-phases %standard-phases
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@ -3589,12 +3599,18 @@ (define-public gemma
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(("/usr/local/opt/openblas")
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(("/usr/local/opt/openblas")
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(assoc-ref inputs "openblas")))
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(assoc-ref inputs "openblas")))
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#t))
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#t))
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(replace 'check
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(lambda* (#:key tests? #:allow-other-keys)
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(when tests?
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;; 'make slow-check' expects shunit2-2.0.3.
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(with-directory-excursion "test"
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(invoke "./test_suite.sh"))
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#t)))
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(replace 'install
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(replace 'install
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(lambda* (#:key outputs #:allow-other-keys)
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(lambda* (#:key outputs #:allow-other-keys)
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(install-file "bin/gemma"
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(install-file "bin/gemma"
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(string-append (assoc-ref outputs "out") "/bin"))
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(string-append (assoc-ref outputs "out") "/bin"))
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#t)))
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#t)))))
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#:tests? #f)) ; no tests included yet
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(home-page "https://github.com/genetics-statistics/GEMMA")
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(home-page "https://github.com/genetics-statistics/GEMMA")
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(synopsis "Tool for genome-wide efficient mixed model association")
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(synopsis "Tool for genome-wide efficient mixed model association")
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(description
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(description
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