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biology/gatk: Add dependencies biology/fermi-lite and biology/gkl; Add python dependency for tests

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This commit is contained in:
Yuri Victorovich 2024-08-04 13:05:10 -07:00
parent 0fa447f55a
commit 3edd10773b
2 changed files with 15 additions and 4 deletions
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15
biology/gatk/Makefile
View file

@ -1,5 +1,6 @@
PORTNAME= gatk PORTNAME= gatk
DISTVERSION= 4.6.0.0 DISTVERSION= 4.6.0.0
PORTREVISION= 1
CATEGORIES= biology java CATEGORIES= biology java
EXTRACT_ONLY= ${DISTNAME}${EXTRACT_SUFX} EXTRACT_ONLY= ${DISTNAME}${EXTRACT_SUFX}
@ -11,8 +12,10 @@ LICENSE= BSD3CLAUSE
LICENSE_FILE= ${WRKSRC}/LICENSE.TXT LICENSE_FILE= ${WRKSRC}/LICENSE.TXT
BUILD_DEPENDS= gradle:devel/gradle BUILD_DEPENDS= gradle:devel/gradle
RUN_DEPENDS= ${LOCALBASE}/lib/libfml.so:biology/fermi-lite \
gkl>0:biology/gkl
USES= gettext-runtime USES= gettext-runtime python:test
USE_JAVA= yes USE_JAVA= yes
JAVA_VERSION= 17 # Java 8 fails on aarch64: Internal Error (assembler_aarch64.hpp:237), pid=76025, tid=0x000000000006e359 guarantee(val < (1U << nbits)) failed: Field too big for insn JAVA_VERSION= 17 # Java 8 fails on aarch64: Internal Error (assembler_aarch64.hpp:237), pid=76025, tid=0x000000000006e359 guarantee(val < (1U << nbits)) failed: Field too big for insn
@ -27,10 +30,13 @@ NO_ARCH= yes
DEPS_CACHE_DIR= ${WRKDIR} DEPS_CACHE_DIR= ${WRKDIR}
TEST_ENV= ${MAKE_ENV} JAVA_TOOL_OPTIONS="-DLIBBWA_PATH=${PREFIX}/lib/libfml.so"
PLIST_FILES= bin/${PORTNAME} \ PLIST_FILES= bin/${PORTNAME} \
${JAVAJARDIR}/GenomeAnalysisTK-${PORTVERSION}.jar ${JAVAJARDIR}/GenomeAnalysisTK-${PORTVERSION}.jar
BINARY_ALIAS= java=${JAVA} BINARY_ALIAS= java=${JAVA} \
python=${PYTHON_CMD}
# to rebuild the deps archive: # to rebuild the deps archive:
# 1. set DEV_UPDATE_MODE=yes # 1. set DEV_UPDATE_MODE=yes
@ -109,6 +115,9 @@ do-install:
do-test: # tests require WITH_LARGE_FILES=ON, and they use a lot of disk space do-test: # tests require WITH_LARGE_FILES=ON, and they use a lot of disk space
@cd ${WRKSRC} && \ @cd ${WRKSRC} && \
${SETENV} ${MAKE_ENV} gradle test ${SETENV} ${TEST_ENV} gradle -DLIBBWA_PATH=${PREFIX}/lib/libfml.so test
# tests results as of version 4.6.0.0_1: 288433 tests completed, 301 failed, 37 skipped, see https://github.com/broadinstitute/gatk/issues/8940
# see https://github.com/broadinstitute/gatk/issues/8939: Tests fail to find libgkl libraries in /usr/local/lib
.include <bsd.port.mk> .include <bsd.port.mk>

4
biology/gatk/files/gatk.sh.in
View file

@ -22,4 +22,6 @@ if [ $MEM_OPTS_SET_BY_USER = "no" ]; then
fi fi
# execute the command # execute the command
%%JAVA%% $MEM_OPTS -jar %%JAVAJARDIR%%/GenomeAnalysisTK-%%PORTVERSION%%.jar "$@" # 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%% $MEM_OPTS -DLIBBWA_PATH=%%PREFIX%%/lib/libfml.so -jar %%JAVAJARDIR%%/GenomeAnalysisTK-%%PORTVERSION%%.jar "$@"