Date: Fri, 26 Jul 2019 18:03:09 +0000 (UTC) From: Yuri Victorovich <yuri@FreeBSD.org> To: ports-committers@freebsd.org, svn-ports-all@freebsd.org, svn-ports-head@freebsd.org Subject: svn commit: r507364 - head/biology/gatk Message-ID: <201907261803.x6QI39CZ059788@repo.freebsd.org>
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Author: yuri Date: Fri Jul 26 18:03:08 2019 New Revision: 507364 URL: https://svnweb.freebsd.org/changeset/ports/507364 Log: biology/gatk: Update 4.0.11.0 -> 4.1.2.0-43 Now it builds with gradle-5. Improvements im Makefile to simplify the port update process, in line with some other gradle-based ports. Reported by: repology Modified: head/biology/gatk/Makefile head/biology/gatk/distinfo Modified: head/biology/gatk/Makefile ============================================================================== --- head/biology/gatk/Makefile Fri Jul 26 18:01:05 2019 (r507363) +++ head/biology/gatk/Makefile Fri Jul 26 18:03:08 2019 (r507364) @@ -1,10 +1,9 @@ # $FreeBSD$ PORTNAME= gatk -DISTVERSION= 4.0.11.0 +DISTVERSION= 4.1.2.0-43 +DISTVERSIONSUFFIX= -g1f31a805b CATEGORIES= biology java -MASTER_SITES= LOCAL/yuri/:deps -DISTFILES= ${PORTNAME}-${DISTVERSION}-deps${EXTRACT_SUFX}:deps EXTRACT_ONLY= ${DISTNAME}${EXTRACT_SUFX} MAINTAINER= yuri@FreeBSD.org @@ -13,7 +12,7 @@ COMMENT= Variant discovery in high-throughput sequenci LICENSE= BSD3CLAUSE LICENSE_FILE= ${WRKSRC}/LICENSE.TXT -BUILD_DEPENDS= gradle46:devel/gradle46 +BUILD_DEPENDS= gradle:devel/gradle USES= gettext-runtime USE_GITHUB= yes @@ -30,13 +29,33 @@ DEPS_CACHE_DIR= /tmp # should be ${WRKDIR}, but workar PLIST_FILES= bin/${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 +# to rebuild the deps archive: +# 1. set DEV_UPDATE_MODE=yes +# 2. make makesum build +# 3. upload the *-deps archive +# 4. set DEV_UPDATE_MODE=no +# 5. make clean makesum + +DEV_UPDATE_MODE= no + +.if (${DEV_UPDATE_MODE} == "yes") +post-build: + @cd ${DEPS_CACHE_DIR} && ${TAR} czf ${DISTDIR}/${PORTNAME}-${DISTVERSION}-deps${EXTRACT_SUFX} gradle-${PORTNAME} + @${ECHO} "(!!!) Please upload the gradle deps archive: ${DISTDIR}/${PORTNAME}-${DISTVERSION}-deps${EXTRACT_SUFX}" +.else +MASTER_SITES= LOCAL/yuri/:deps +DISTFILES= ${PORTNAME}-${DISTVERSION}-deps${EXTRACT_SUFX}:deps +GRADLE_ARGS= --offline + +post-extract: # need a separate extract step because the cache is in /tmp, and not under work/ like with maven @cd ${DEPS_CACHE_DIR} && ${TAR} xzf ${DISTDIR}/${PORTNAME}-${DISTVERSION}-deps${EXTRACT_SUFX} +.endif + do-build: - @cd ${WRKSRC} && ${SETENV} ${MAKE_ENV} gradle46 \ + @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 + ${GRADLE_ARGS} --build-cache localJar do-install: ${INSTALL_SCRIPT} ${WRKDIR}/${PORTNAME}.sh ${STAGEDIR}${PREFIX}/bin/${PORTNAME} Modified: head/biology/gatk/distinfo ============================================================================== --- head/biology/gatk/distinfo Fri Jul 26 18:01:05 2019 (r507363) +++ head/biology/gatk/distinfo Fri Jul 26 18:03:08 2019 (r507364) @@ -1,5 +1,5 @@ -TIMESTAMP = 1543823410 -SHA256 (gatk-4.0.11.0-deps.tar.gz) = 457ed3bf756a673daa2d123fef1d8525e57f20708f134c9b897946ea49561a36 -SIZE (gatk-4.0.11.0-deps.tar.gz) = 225800131 -SHA256 (broadinstitute-gatk-4.0.11.0_GH0.tar.gz) = ba4cc922bae2cdec728984518644bb0a12be2b6916297e2eb3b862cb42841039 -SIZE (broadinstitute-gatk-4.0.11.0_GH0.tar.gz) = 74603782 +TIMESTAMP = 1564135381 +SHA256 (gatk-4.1.2.0-43-deps.tar.gz) = c5b405f7da5b3ac0aff73c42523cb414ce2f6315aa583092287499e5770098f4 +SIZE (gatk-4.1.2.0-43-deps.tar.gz) = 365117204 +SHA256 (broadinstitute-gatk-4.1.2.0-43-g1f31a805b_GH0.tar.gz) = 8fd79e0ea6fe153bc2ebf76c9ca910a7db109b4d4c4b0fbeb4d4d61469f09238 +SIZE (broadinstitute-gatk-4.1.2.0-43-g1f31a805b_GH0.tar.gz) = 64286228
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