mirror of
https://git.FreeBSD.org/ports.git
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94 lines
3.3 KiB
Makefile
94 lines
3.3 KiB
Makefile
PORTNAME= gatk
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DISTVERSION= 4.2.0.0
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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= Variant discovery in high-throughput sequencing data
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LICENSE= BSD3CLAUSE
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LICENSE_FILE= ${WRKSRC}/LICENSE.TXT
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BROKEN_FreeBSD_12_powerpc64= fails to build: String index out of range: -1
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BUILD_DEPENDS= gradle62:devel/gradle62
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USES= gettext-runtime
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USE_GITHUB= yes
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GH_ACCOUNT= broadinstitute
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USE_JAVA= yes
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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= ${WRKDIR}
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PLIST_FILES= bin/${PORTNAME} \
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${JAVAJARDIR}/GenomeAnalysisTK-${PORTVERSION}.jar
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# TODO additionally fetch git-lfs files: https://github.com/broadinstitute/gatk/issues/6395
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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 # probably should be default for tests, but the build doesn't seem to be affected contrary to what README says
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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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.include <bsd.port.options.mk>
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.if ${PORT_OPTIONS:MWITH_LARGE_FILES}
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do-fetch:
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@if [ "${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 -q 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 ${SORT} -z | \
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${TAR} czf ${DISTNAME}${EXTRACT_SUFX} --format=bsdtar --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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.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} gradle62 \
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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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.include <bsd.port.mk>
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