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Sun, 4 Aug 2024 20:07:21 GMT (envelope-from git) Date: Sun, 4 Aug 2024 20:07:21 GMT Message-Id: <202408042007.474K7LSj042659@gitrepo.freebsd.org> To: ports-committers@FreeBSD.org, dev-commits-ports-all@FreeBSD.org, dev-commits-ports-main@FreeBSD.org From: Yuri Victorovich Subject: git: 3edd10773b45 - main - biology/gatk: Add dependencies biology/fermi-lite and biology/gkl; Add python dependency for tests List-Id: Commits to the main branch of the FreeBSD ports repository List-Archive: https://lists.freebsd.org/archives/dev-commits-ports-main List-Help: List-Post: List-Subscribe: List-Unsubscribe: X-BeenThere: dev-commits-ports-main@freebsd.org Sender: owner-dev-commits-ports-main@FreeBSD.org MIME-Version: 1.0 Content-Type: text/plain; charset=utf-8 Content-Transfer-Encoding: 8bit X-Git-Committer: yuri X-Git-Repository: ports X-Git-Refname: refs/heads/main X-Git-Reftype: branch X-Git-Commit: 3edd10773b45b981c57493e4eab9f9873bf42715 Auto-Submitted: auto-generated The branch main has been updated by yuri: URL: https://cgit.FreeBSD.org/ports/commit/?id=3edd10773b45b981c57493e4eab9f9873bf42715 commit 3edd10773b45b981c57493e4eab9f9873bf42715 Author: Yuri Victorovich AuthorDate: 2024-08-04 20:05:10 +0000 Commit: Yuri Victorovich CommitDate: 2024-08-04 20:07:19 +0000 biology/gatk: Add dependencies biology/fermi-lite and biology/gkl; Add python dependency for tests --- biology/gatk/Makefile | 15 ++++++++++++--- biology/gatk/files/gatk.sh.in | 4 +++- 2 files changed, 15 insertions(+), 4 deletions(-) diff --git a/biology/gatk/Makefile b/biology/gatk/Makefile index 1200e614cba3..3bbda36b4492 100644 --- a/biology/gatk/Makefile +++ b/biology/gatk/Makefile @@ -1,5 +1,6 @@ PORTNAME= gatk DISTVERSION= 4.6.0.0 +PORTREVISION= 1 CATEGORIES= biology java EXTRACT_ONLY= ${DISTNAME}${EXTRACT_SUFX} @@ -11,8 +12,10 @@ LICENSE= BSD3CLAUSE LICENSE_FILE= ${WRKSRC}/LICENSE.TXT 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 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} +TEST_ENV= ${MAKE_ENV} JAVA_TOOL_OPTIONS="-DLIBBWA_PATH=${PREFIX}/lib/libfml.so" + PLIST_FILES= bin/${PORTNAME} \ ${JAVAJARDIR}/GenomeAnalysisTK-${PORTVERSION}.jar -BINARY_ALIAS= java=${JAVA} +BINARY_ALIAS= java=${JAVA} \ + python=${PYTHON_CMD} # to rebuild the deps archive: # 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 @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 diff --git a/biology/gatk/files/gatk.sh.in b/biology/gatk/files/gatk.sh.in index 913bb0dcce65..d3d5c0f7bf5a 100644 --- a/biology/gatk/files/gatk.sh.in +++ b/biology/gatk/files/gatk.sh.in @@ -22,4 +22,6 @@ if [ $MEM_OPTS_SET_BY_USER = "no" ]; then fi # 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%% $MEM_OPTS -DLIBBWA_PATH=%%PREFIX%%/lib/libfml.so -jar %%JAVAJARDIR%%/GenomeAnalysisTK-%%PORTVERSION%%.jar "$@"