aboutsummaryrefslogtreecommitdiff
diff options
context:
space:
mode:
authorEfraim Flashner <efraim@flashner.co.il>2021-01-14 10:16:20 +0200
committerEfraim Flashner <efraim@flashner.co.il>2021-01-14 20:43:31 +0200
commit2051be4f4cd526fb445e826d655afa40f8f4a7e5 (patch)
tree5c95c3c96f48014b41a267e90c3461d222c2ca15
parentf58e491fb837ae4344689c1cefdc1b6e582c3015 (diff)
downloadguix-2051be4f4cd526fb445e826d655afa40f8f4a7e5.tar.gz
guix-2051be4f4cd526fb445e826d655afa40f8f4a7e5.zip
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.
-rw-r--r--gnu/packages/bioinformatics.scm22
1 files changed, 19 insertions, 3 deletions
diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm
index 70696c189a..84a9a4d208 100644
--- a/gnu/packages/bioinformatics.scm
+++ b/gnu/packages/bioinformatics.scm
@@ -3572,12 +3572,22 @@ comment or quality sections.")
(file-name (git-file-name name version))
(sha256
(base32
- "1p8a7kkfn1mmrg017aziy544aha8i9h6wd1x2dk3w2794wl33qb7"))))
+ "1p8a7kkfn1mmrg017aziy544aha8i9h6wd1x2dk3w2794wl33qb7"))
+ (modules '((guix build utils)))
+ (snippet
+ '(begin
+ (delete-file-recursively "contrib")
+ #t))))
(build-system gnu-build-system)
(inputs
`(("gsl" ,gsl)
("openblas" ,openblas)
("zlib" ,zlib)))
+ (native-inputs
+ `(("catch" ,catch-framework2-1)
+ ("perl" ,perl)
+ ("shunit2" ,shunit2)
+ ("which" ,which)))
(arguments
`(#:phases
(modify-phases %standard-phases
@@ -3589,12 +3599,18 @@ comment or quality sections.")
(("/usr/local/opt/openblas")
(assoc-ref inputs "openblas")))
#t))
+ (replace 'check
+ (lambda* (#:key tests? #:allow-other-keys)
+ (when tests?
+ ;; 'make slow-check' expects shunit2-2.0.3.
+ (with-directory-excursion "test"
+ (invoke "./test_suite.sh"))
+ #t)))
(replace 'install
(lambda* (#:key outputs #:allow-other-keys)
(install-file "bin/gemma"
(string-append (assoc-ref outputs "out") "/bin"))
- #t)))
- #:tests? #f)) ; no tests included yet
+ #t)))))
(home-page "https://github.com/genetics-statistics/GEMMA")
(synopsis "Tool for genome-wide efficient mixed model association")
(description