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| author | Efraim Flashner | 2019-08-05 04:52:59 -0500 |
|---|---|---|
| committer | Efraim Flashner | 2019-08-05 04:56:19 -0500 |
| commit | 6d4485f5908139e9dbf6cd86ab4ee21f424690d0 (patch) | |
| tree | eb71a08440cb21f5ba76adf64bb715871326efac | |
| parent | 1de344e71b1dd972e7ef69df2535f7464db9151a (diff) | |
| download | guix-bioinformatics-6d4485f5908139e9dbf6cd86ab4ee21f424690d0.tar.gz | |
gn: pindel: Update package definition.
* gn/packages/bioinformatics.scm (pindel)[arguments]: Use 'invoke' when
possible. Parameterize custom 'check phase.
| -rw-r--r-- | gn/packages/bioinformatics.scm | 14 |
1 files changed, 6 insertions, 8 deletions
diff --git a/gn/packages/bioinformatics.scm b/gn/packages/bioinformatics.scm index 5b77fb1..5b00e58 100644 --- a/gn/packages/bioinformatics.scm +++ b/gn/packages/bioinformatics.scm @@ -969,7 +969,7 @@ manipulations on VCF files.") ;; The second run actually compiles the program. Now Makefile.local ;; is available, and we should treat an exiting make with an error as ;; a true error. - (zero? (system* "make")))) + (invoke "make"))) (replace 'install (lambda* (#:key outputs #:allow-other-keys) (let ((bin (string-append (assoc-ref outputs "out") "/bin"))) @@ -980,13 +980,11 @@ manipulations on VCF files.") ;; There are multiple test targets, so in order to run all ;; tests, we must run the separate make targets. (replace 'check - (lambda* (#:key inputs #:allow-other-keys) - (and - (zero? (system* "make" "acceptance-tests")) - (zero? (system* "make" "coverage-tests")) - (zero? (system* "make" "cppcheck")) - (zero? (system* "make" "functional-tests")) - (zero? (system* "make" "regression-tests")))))))) + (lambda _ + (for-each (lambda (target) + (invoke "make" target)) + '("acceptance-tests" "coverage-tests" "cppcheck" + "functional-tests" "regression-tests"))))))) (home-page "https://github.com/genome/pindel") (synopsis "Structural variants detector for next-gen sequencing data") (description "Pindel can detect breakpoints of large deletions, medium sized |