46 lines
1.5 KiB
Makefile
46 lines
1.5 KiB
Makefile
# $FreeBSD$
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PORTNAME= gatk
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DISTVERSION= 4.0.11.0
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CATEGORIES= biology java
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MASTER_SITES= LOCAL/yuri/:deps
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DISTFILES= ${PORTNAME}-${DISTVERSION}-deps${EXTRACT_SUFX}:deps
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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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BUILD_DEPENDS= gradle4:devel/gradle4
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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= /tmp # should be ${WRKDIR}, but workaround for the gradle bug that dependency cache is not relocable: https://github.com/gradle/gradle/issues/1338
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PLIST_FILES= bin/${PORTNAME} \
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${JAVAJARDIR}/GenomeAnalysisTK-${PORTVERSION}.jar
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post-extract: # to rebuild the deps archive: 1. remove post-extract: 2. remove --offline 3. build 4. package ${DEPS_CACHE_DIR}/gradle-${PORTNAME} into the deps archive
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@cd ${DEPS_CACHE_DIR} && ${TAR} xzf ${DISTDIR}/${PORTNAME}-${DISTVERSION}-deps${EXTRACT_SUFX}
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do-build:
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@cd ${WRKSRC} && ${SETENV} ${MAKE_ENV} gradle4 \
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--gradle-user-home ${DEPS_CACHE_DIR}/gradle-${PORTNAME} --project-cache-dir ${DEPS_CACHE_DIR}/gradle-${PORTNAME} \
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--offline --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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