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-rw-r--r--gn/packages/bioinformatics.scm24
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