diff options
Diffstat (limited to 'biology/gatk')
| -rw-r--r-- | biology/gatk/Makefile | 10 | ||||
| -rw-r--r-- | biology/gatk/distinfo | 10 | ||||
| -rw-r--r-- | biology/gatk/files/gatk.sh.in | 4 |
3 files changed, 12 insertions, 12 deletions
diff --git a/biology/gatk/Makefile b/biology/gatk/Makefile index 41df894298f4..49a990d3f216 100644 --- a/biology/gatk/Makefile +++ b/biology/gatk/Makefile @@ -1,6 +1,5 @@ PORTNAME= gatk -DISTVERSION= 4.6.1.0 -PORTREVISION= 1 +DISTVERSION= 4.6.2.0 CATEGORIES= biology java EXTRACT_ONLY= ${DISTNAME}${EXTRACT_SUFX} @@ -31,7 +30,7 @@ NO_ARCH= yes DEPS_CACHE_DIR= ${WRKDIR} TEST_ENV= ${MAKE_ENV} \ - JAVA_TOOL_OPTIONS="-DLIBBWA_PATH=${PREFIX}/lib/libfml.so" \ + JAVA_TOOL_OPTIONS="-DLIBBWA_PATH=${PREFIX}/lib/libfml.so -DLIBFML_PATH=${PREFIX}/lib/libfml.so" \ GATK_LOCAL_JAR=${STAGEDIR}${JAVAJARDIR}/GenomeAnalysisTK-${PORTVERSION}.jar PLIST_FILES= bin/${PORTNAME} \ @@ -117,9 +116,10 @@ do-install: do-test: # tests require WITH_LARGE_FILES=ON, and they use a lot of disk space @cd ${WRKSRC} && \ - ${SETENV} ${TEST_ENV} gradle8 -DLIBBWA_PATH=${PREFIX}/lib/libfml.so test + ${SETENV} ${TEST_ENV} gradle8 test -# tests results as of version 4.6.1.0: 288552 tests, 301 failures, 37 ignored, 1h55m5.63s duration, 99% successful, see https://github.com/broadinstitute/gatk/issues/8940 +# tests as of 4.6.1.0: 288552 tests, 301 failures, 37 ignored, 1h55m5.63s duration, 99% successful, see https://github.com/broadinstitute/gatk/issues/8940 +# tests as of 4.6.2.0: 288719 tests completed, 300 failed, 37 skipped # see https://github.com/broadinstitute/gatk/issues/8939: Tests fail to find libgkl libraries in /usr/local/lib .include <bsd.port.mk> diff --git a/biology/gatk/distinfo b/biology/gatk/distinfo index 2494dc43dd72..42fbad5e8a91 100644 --- a/biology/gatk/distinfo +++ b/biology/gatk/distinfo @@ -1,5 +1,5 @@ -TIMESTAMP = 1730356703 -SHA256 (gatk-4.6.1.0-deps.tar.gz) = ea0205776f26bbe51bcdea6dd10df975a2e4861a772901523ff7ab123119b8ad -SIZE (gatk-4.6.1.0-deps.tar.gz) = 922113997 -SHA256 (broadinstitute-gatk-4.6.1.0_GH0.tar.gz) = 6f840406ce226e202421464e2ae044f3c0bc63da63f245568f8ca1bc7769d378 -SIZE (broadinstitute-gatk-4.6.1.0_GH0.tar.gz) = 4317548196 +TIMESTAMP = 1756227460 +SHA256 (gatk-4.6.2.0-deps.tar.gz) = c956ec3b6a209b4eaf9c20cb312635498b360aa372f824b33d392aa0ac594a77 +SIZE (gatk-4.6.2.0-deps.tar.gz) = 903933113 +SHA256 (broadinstitute-gatk-4.6.2.0_GH0.tar.gz) = c76b61a549f49004a54ae86e88cd8b7a180a3bd2e4a56b1c9185f30971c79866 +SIZE (broadinstitute-gatk-4.6.2.0_GH0.tar.gz) = 4318674606 diff --git a/biology/gatk/files/gatk.sh.in b/biology/gatk/files/gatk.sh.in index d3d5c0f7bf5a..20c6c16d5164 100644 --- a/biology/gatk/files/gatk.sh.in +++ b/biology/gatk/files/gatk.sh.in @@ -23,5 +23,5 @@ fi # execute the command # add the LIBBWA_PATH system parameter (not sure whether the env. var or argument alone are sufficient) -JAVA_TOOL_OPTIONS="-DLIBBWA_PATH=%%PREFIX%%/lib/libfml.so" \ -%%JAVA%% $MEM_OPTS -DLIBBWA_PATH=%%PREFIX%%/lib/libfml.so -jar %%JAVAJARDIR%%/GenomeAnalysisTK-%%PORTVERSION%%.jar "$@" +JAVA_TOOL_OPTIONS="-DLIBBWA_PATH=%%PREFIX%%/lib/libfml.so -DLIBFML_PATH=%%PREFIX%%/lib/libfml.so" \ +%%JAVA%% $MEM_OPTS -DLIBBWA_PATH=%%PREFIX%%/lib/libfml.so -DLIBFML_PATH=%%PREFIX%%/lib/libfml.so -jar %%JAVAJARDIR%%/GenomeAnalysisTK-%%PORTVERSION%%.jar "$@" |