diff options
Diffstat (limited to 'gn')
| -rw-r--r-- | gn/packages/bioinformatics.scm | 75 |
1 files changed, 73 insertions, 2 deletions
diff --git a/gn/packages/bioinformatics.scm b/gn/packages/bioinformatics.scm index 58110a7..5fdbd4d 100644 --- a/gn/packages/bioinformatics.scm +++ b/gn/packages/bioinformatics.scm @@ -1584,7 +1584,8 @@ multiple sequence alignment.") (base32 "1qcjhd4wcajik71z5347fw2sfhfkv0p6y7yldrrkmycw2qhqmpzn")))) (build-system gnu-build-system) (arguments - `(#:tests? #f ; fix later + `(#:test-target "test" + #:parallel-tests? #f ; not supported #:phases (modify-phases %standard-phases (delete 'configure) ; There is no configure phase. @@ -1626,6 +1627,75 @@ multiple sequence alignment.") (("\\.\\./trash") "/var/cache/genome")) #t))) + + (add-before 'check 'pre-check + (lambda* (#:key outputs #:allow-other-keys) + (let ((out (assoc-ref outputs "out")) + (triplet ,(gnu-triplet->nix-system (%current-system)))) + (setenv "PATH" (string-append (getenv "PATH") + ":" out "/bin")) + (setenv "MACHTYPE" + (string-take triplet (string-index triplet #\-))) + (for-each make-file-writable + (find-files "utils/bedJoinTabOffset/tests")) + (substitute* '("utils/bamToPsl/tests/makefile" + "utils/trackDbIndexBb/tests/makefile") + (("/cluster/bin/bedtools/bedtools") (which "bedtools"))) + + ;; These tests fail intermittently: + (substitute* "utils/vcfFilter/tests/makefile" + ((" testRenameNoGt ") " ") + ((" testMinAc1NoGt ") " ")) + + ;; These tests can't find their database: + (substitute* "hg/lib/tests/makefile" + ((" spDbTest ") " ") + ((" hdbTest ") " ")) + (substitute* "hg/lib/tests/genePredTests.mk" + ((" tableTests ") " ") + ((" compatTblTests ") " ")) + (substitute* "hg/lib/tests/pslReaderTests.mk" + ((" tableTests") " ")) + (substitute* "hg/lib/tests/makefile" + ((" annoGratorTest ") " ") + ((" customTrackTest ") " ") + ((" hgvsTest") " ")) + (substitute* "hg/autoSql/tests/makefile" + ((" dbLinkTest ") " ") + ((" symColsTest ") " ")) + (delete-file "hg/checkTableCoords/tests/makefile") + (delete-file "hg/hgGetAnn/tests/makefile") + (substitute* "hg/sqlToXml/makefile" + ((".*doTest.*") "")) + (substitute* "hg/utils/genePredFilter/tests/makefile" + ((" gencodeHackDbTest") " ")) + (substitute* "hg/utils/refSeqGet/tests/makefile" + (("^test::.*") "test:: mkout\n")) + (delete-file "hg/utils/vcfToHgvs/tests/makefile") + (substitute* "hg/bedItemOverlapCount/tests/makefile" + ((".*RunTest.*") "")) + + ;; Depends on /cluster + (substitute* "hg/liftOver/tests/makefile" + (("^test:.*") "test: mkdirs scaffoldEndBug\n")) + (delete-file "hg/mouseStuff/netToAxt/tests/makefile") + (substitute* "hg/pslToChain/tests/makefile" + ((" example1 ") " ")) + + ;; Depends on /gbdb + (delete-file "hg/mouseStuff/chainBridge/tests/makefile") + + ;; Depends on /hive + (delete-file "hg/utils/genePredToProt/tests/makefile") + + ;; Unclear why this fails + (delete-file "hg/utils/hgvsToVcf/tests/makefile") + + ;; Wants network + (substitute* "hg/utils/hubCheck/tests/makefile" + (("^test::.*") "test:: one two\n")) + #t))) + ;; Install happens during the 'build phase. ;; Install the website files too (replace 'install @@ -1658,7 +1728,8 @@ multiple sequence alignment.") ("python2" ,python-2) ("zlib" ,zlib))) (native-inputs - `(("gs-fonts" ,gs-fonts) + `(("bedtools" ,bedtools) + ("gs-fonts" ,gs-fonts) ("pkg-config" ,pkg-config) ("python" ,python) ("rsync" ,rsync) ; For installing js files from the source checkout |