Index: head/biology/gatk/Makefile =================================================================== --- head/biology/gatk/Makefile (revision 486560) +++ head/biology/gatk/Makefile (revision 486561) @@ -1,45 +1,45 @@ # $FreeBSD$ 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= gradle4:devel/gradle4 +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} gradle4 \ + @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