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# $FreeBSD$
PORTNAME= gatk
DISTVERSION= 4.0.11.0
CATEGORIES= biology java
MASTER_SITES= LOCAL/yuri/:deps
DISTFILES= ${PORTNAME}-${DISTVERSION}-deps${EXTRACT_SUFX}:deps
EXTRACT_ONLY= ${DISTNAME}${EXTRACT_SUFX}
MAINTAINER= yuri@FreeBSD.org
COMMENT= Variant discovery in high-throughput sequencing data
LICENSE= BSD3CLAUSE
LICENSE_FILE= ${WRKSRC}/LICENSE.TXT
BUILD_DEPENDS= gradle:devel/gradle
USES= gettext-runtime
USE_GITHUB= yes
GH_ACCOUNT= broadinstitute
USE_JAVA= yes
SUB_FILES= ${PORTNAME}.sh
SUB_LIST= PORTVERSION=${PORTVERSION} JAVA=${JAVA}
NO_ARCH= yes
DEPS_CACHE_DIR= /tmp # should be ${WRKDIR}, but workaround for the gradle bug that dependency cache is not relocable: https://github.com/gradle/gradle/issues/1338
PLIST_FILES= bin/${PORTNAME} \
${JAVAJARDIR}/GenomeAnalysisTK-${PORTVERSION}.jar
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
@cd ${DEPS_CACHE_DIR} && ${TAR} xzf ${DISTDIR}/${PORTNAME}-${DISTVERSION}-deps${EXTRACT_SUFX}
do-build:
@cd ${WRKSRC} && ${SETENV} ${MAKE_ENV} gradle \
--gradle-user-home ${DEPS_CACHE_DIR}/gradle-${PORTNAME} --project-cache-dir ${DEPS_CACHE_DIR}/gradle-${PORTNAME} \
--offline --build-cache localJar
do-install:
${INSTALL_SCRIPT} ${WRKDIR}/${PORTNAME}.sh ${STAGEDIR}${PREFIX}/bin/${PORTNAME}
${INSTALL_DATA} ${WRKSRC}/build/libs/gatk-package-1.0-SNAPSHOT-local.jar ${STAGEDIR}${JAVAJARDIR}/GenomeAnalysisTK-${PORTVERSION}.jar
.include <bsd.port.mk>
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