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authorEfraim Flashner2019-08-05 04:52:59 -0500
committerEfraim Flashner2019-08-05 04:56:19 -0500
commit6d4485f5908139e9dbf6cd86ab4ee21f424690d0 (patch)
treeeb71a08440cb21f5ba76adf64bb715871326efac /gn
parent1de344e71b1dd972e7ef69df2535f7464db9151a (diff)
downloadguix-bioinformatics-6d4485f5908139e9dbf6cd86ab4ee21f424690d0.tar.gz
gn: pindel: Update package definition.
* gn/packages/bioinformatics.scm (pindel)[arguments]: Use 'invoke' when possible. Parameterize custom 'check phase.
Diffstat (limited to 'gn')
-rw-r--r--gn/packages/bioinformatics.scm14
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