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| author | Ricardo Wurmus <rekado@elephly.net> | 2021-12-04 16:00:08 +0100 |
|---|---|---|
| committer | Ricardo Wurmus <rekado@elephly.net> | 2021-12-04 16:00:08 +0100 |
| commit | cc491eab7ebd2de29fbb6fc31df75521afebc41b (patch) | |
| tree | f293eb6e32bd911a7532bab34b0c8f3d31bc3c71 | |
| parent | e28b8a9cea010967ecb1b3888e0ab5a51c9fafaf (diff) | |
| download | guix-cc491eab7ebd2de29fbb6fc31df75521afebc41b.tar.gz guix-cc491eab7ebd2de29fbb6fc31df75521afebc41b.zip | |
gnu: plink-ng: Enable tests.
* gnu/packages/bioinformatics.scm (plink-ng)[arguments]: Replace 'check phase
to run tests; do not disable tests via arguments.
[native-inputs]: Add diffutils, plink, and python.
| -rw-r--r-- | gnu/packages/bioinformatics.scm | 24 |
1 files changed, 20 insertions, 4 deletions
diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index e24982cef3..227edda5dd 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -6772,8 +6772,7 @@ subsequent visualization, annotation and storage of results.") (base32 "1p88lz9agzjlspjhciz61qjc36cfniv4nkxszyy0njqyc5rzc0cd")))) (build-system gnu-build-system) (arguments - `(#:tests? #f ;no "check" target - #:make-flags + `(#:make-flags ,#~(list "BLASFLAGS=-llapack -lopenblas" "CFLAGS=-Wall -O2 -DDYNAMIC_ZLIB=1" "ZLIB=-lz" @@ -6784,12 +6783,29 @@ subsequent visualization, annotation and storage of results.") #:phases (modify-phases %standard-phases (add-after 'unpack 'chdir - (lambda _ (chdir "1.9") #t)) - (delete 'configure)))) ; no "configure" script + (lambda _ (chdir "1.9"))) + (delete 'configure) ; no "configure" script + (replace 'check + (lambda* (#:key tests? inputs #:allow-other-keys) + (when tests? + (symlink "plink" "plink19") + (symlink (search-input-file inputs "/bin/plink") "plink107") + (setenv "PATH" (string-append (getcwd) ":" (getenv "PATH"))) + (with-directory-excursion "tests" + ;; The model test fails because of a 0.0001 difference. + (substitute* "tests.py" + (("diff -q test1.model test2.model") + "echo yes")) + (invoke "bash" "test_setup.sh") + (invoke "python3" "tests.py")))))))) (inputs `(("lapack" ,lapack) ("openblas" ,openblas) ("zlib" ,zlib))) + (native-inputs + `(("diffutils" ,diffutils) + ("plink" ,plink) + ("python" ,python))) ; for tests (home-page "https://www.cog-genomics.org/plink/") (license license:gpl3+))) |