124 lines
4.9 KiB
Makefile
124 lines
4.9 KiB
Makefile
PORTNAME= gatk
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DISTVERSION= 4.6.1.0
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PORTREVISION= 1
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CATEGORIES= biology java
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EXTRACT_ONLY= ${DISTNAME}${EXTRACT_SUFX}
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MAINTAINER= yuri@FreeBSD.org
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COMMENT= Genome Analysis Toolkit
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WWW= https://gatk.broadinstitute.org/hc/en-us
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LICENSE= BSD3CLAUSE
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LICENSE_FILE= ${WRKSRC}/LICENSE.TXT
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BUILD_DEPENDS= gradle8:devel/gradle8
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RUN_DEPENDS= ${LOCALBASE}/lib/libfml.so:biology/fermi-lite \
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gkl>0:biology/gkl \
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mummer>0:biology/mummer
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USES= gettext-runtime java python:test
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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
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USE_GITHUB= yes
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GH_ACCOUNT= broadinstitute
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SUB_FILES= ${PORTNAME}.sh
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SUB_LIST= PORTVERSION=${PORTVERSION} JAVA=${JAVA}
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NO_ARCH= yes
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DEPS_CACHE_DIR= ${WRKDIR}
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TEST_ENV= ${MAKE_ENV} \
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JAVA_TOOL_OPTIONS="-DLIBBWA_PATH=${PREFIX}/lib/libfml.so" \
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GATK_LOCAL_JAR=${STAGEDIR}${JAVAJARDIR}/GenomeAnalysisTK-${PORTVERSION}.jar
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PLIST_FILES= bin/${PORTNAME} \
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${JAVAJARDIR}/GenomeAnalysisTK-${PORTVERSION}.jar
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BINARY_ALIAS= java=${JAVA} \
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python=${PYTHON_CMD}
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# to rebuild the deps archive:
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# 1. set DEV_UPDATE_MODE=yes
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# 2. make makesum build
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# 3. upload the *-deps archive
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# 4. set DEV_UPDATE_MODE=no
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# 5. make clean makesum
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DEV_UPDATE_MODE= no
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OPTIONS_DEFINE= WITH_LARGE_FILES
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OPTIONS_DEFAULT= WITH_LARGE_FILES # runtime requires large files, see the README
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WITH_LARGE_FILES_DESC= Download large LFS files needed for build and tests
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WITH_LARGE_FILES_FETCH_DEPENDS= git:devel/git \
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git-lfs:devel/git-lfs
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# The large files under src/main/resources/large/ are required to build GATK, since they are packaged inside the GATK jar and used by tools at runtime. These are things like ML models and native C/C++ libraries used for acceleration of certain tools.
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# The large files under src/test/resources/large/, on the other hand, are only required by the test suite when running tests.
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.include <bsd.port.options.mk>
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.if ${PORT_OPTIONS:MWITH_LARGE_FILES}
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# fetch the main distfile including git-lsf files
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do-fetch:
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@if [ "${FORCE_FETCH_ALL}" = "true" ] || ! [ -f "${DISTDIR}/${DIST_SUBDIR}/${DISTNAME}${EXTRACT_SUFX}" ]; then \
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${MKDIR} ${DISTDIR}/${DIST_SUBDIR} && \
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cd ${DISTDIR}/${DIST_SUBDIR} && \
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${ECHO} "==> Fetching ${PORTNAME} including large LFS files" && \
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( \
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${MKDIR} ${WRKDIR}; \
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HOME=${WRKDIR}; \
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git config --global filter.lfs.smudge "git-lfs smudge -- %f" && \
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GIT_CLONE_PROTECTION_ACTIVE=false git clone -nq https://github.com/broadinstitute/gatk.git ${PORTNAME}-${DISTVERSION} && \
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(cd ${PORTNAME}-${DISTVERSION} && git reset -q --hard ${DISTVERSION} && ${RM} -r .git) && \
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${RM} -r ${WRKDIR} \
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) && \
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${FIND} ${PORTNAME}-${DISTVERSION} -and -exec ${TOUCH} -h -d 1970-01-01T00:00:00Z {} \; && \
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${FIND} ${PORTNAME}-${DISTVERSION} -print0 | LC_ALL=C ${SORT} -z | \
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${SETENV} -i ${TAR} czf ${DISTNAME}${EXTRACT_SUFX} --format=cpio --gid 0 --uid 0 --options gzip:!timestamp --no-recursion --null -T - && \
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${RM} -r ${PORTNAME}-${DISTVERSION}; \
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fi
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# fetch the deps distfile
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. if (${DEV_UPDATE_MODE} == "no")
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@if [ "${FORCE_FETCH_ALL}" = "true" ] || ! [ -f "${DISTDIR}/${DIST_SUBDIR}/${PORTNAME}-${DISTVERSION}-deps${EXTRACT_SUFX}" ]; then \
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${ECHO} "==> Fetching the deps distfile for ${PORTNAME}" && \
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${SETENV} \
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${_DO_FETCH_ENV} ${_MASTER_SITES_ENV} \
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dp_SITE_FLAVOR=MASTER \
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${SH} ${SCRIPTSDIR}/do-fetch.sh ${DISTFILES:M*\:deps}; \
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fi
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. endif
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.endif
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.if (${DEV_UPDATE_MODE} == "yes")
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post-build:
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@cd ${DEPS_CACHE_DIR} && ${TAR} czf ${DISTDIR}/${PORTNAME}-${DISTVERSION}-deps${EXTRACT_SUFX} gradle-${PORTNAME}
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@${ECHO} "(!!!) Please upload the gradle deps archive: ${DISTDIR}/${PORTNAME}-${DISTVERSION}-deps${EXTRACT_SUFX}"
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.else
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MASTER_SITES= LOCAL/yuri/:deps
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DISTFILES= ${PORTNAME}-${DISTVERSION}-deps${EXTRACT_SUFX}:deps
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GRADLE_ARGS= --offline
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post-extract: # need a separate extract step because the cache is in /tmp, and not under work/ like with maven
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@cd ${DEPS_CACHE_DIR} && ${TAR} xzf ${DISTDIR}/${PORTNAME}-${DISTVERSION}-deps${EXTRACT_SUFX}
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.endif
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do-build:
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@cd ${WRKSRC} && ${SETENV} ${MAKE_ENV} gradle8 \
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--gradle-user-home ${DEPS_CACHE_DIR}/gradle-${PORTNAME} --project-cache-dir ${DEPS_CACHE_DIR}/gradle-${PORTNAME} \
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${GRADLE_ARGS} --build-cache localJar
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do-install:
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${INSTALL_SCRIPT} ${WRKDIR}/${PORTNAME}.sh ${STAGEDIR}${PREFIX}/bin/${PORTNAME}
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${INSTALL_DATA} ${WRKSRC}/build/libs/gatk-package-1.0-SNAPSHOT-local.jar ${STAGEDIR}${JAVAJARDIR}/GenomeAnalysisTK-${PORTVERSION}.jar
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do-test: # tests require WITH_LARGE_FILES=ON, and they use a lot of disk space
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@cd ${WRKSRC} && \
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${SETENV} ${TEST_ENV} gradle8 -DLIBBWA_PATH=${PREFIX}/lib/libfml.so test
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# 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
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# see https://github.com/broadinstitute/gatk/issues/8939: Tests fail to find libgkl libraries in /usr/local/lib
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.include <bsd.port.mk>
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