diff options
Diffstat (limited to 'gn/packages')
| -rw-r--r-- | gn/packages/bioinformatics.scm | 24 |
1 files changed, 19 insertions, 5 deletions
diff --git a/gn/packages/bioinformatics.scm b/gn/packages/bioinformatics.scm index 11a624f..d81a19a 100644 --- a/gn/packages/bioinformatics.scm +++ b/gn/packages/bioinformatics.scm @@ -1141,15 +1141,19 @@ manipulations on VCF files.") ("python" ,python-2) ("perl" ,perl))) (arguments - `(#:tests? #f - #:phases + `(#:phases (modify-phases %standard-phases (delete 'configure) ; There is no configure phase. + ;; The build phase needs to run 'make' twice for the reasons described + ;; below. (replace 'build (lambda* (#:key inputs #:allow-other-keys) - ;; The first run creates a Makefile.local file. + ;; The first run creates a Makefile.local file. Make will report + ;; the failure to find Makefile.local, but we can ignore this error. (system* "make" (string-append "SAMTOOLS=" (assoc-ref inputs "samtools"))) - ;; The second run actually compiles the program. + ;; 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")))) (replace 'install (lambda* (#:key outputs #:allow-other-keys) @@ -1157,7 +1161,17 @@ manipulations on VCF files.") (install-file "src/pindel" bin) (install-file "src/pindel2vcf" bin) (install-file "src/pindel2vcf4tcga" bin) - (install-file "src/sam2pindel" bin))))))) + (install-file "src/sam2pindel" bin)))) + ;; 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")))))))) (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 |