Date: Fri, 22 Jan 2021 02:50:38 +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: r562270 - head/biology/gatk Message-ID: <202101220250.10M2ocJ2062673@repo.freebsd.org>
next in thread | raw e-mail | index | archive | help
Author: yuri Date: Fri Jan 22 02:50:38 2021 New Revision: 562270 URL: https://svnweb.freebsd.org/changeset/ports/562270 Log: biology/gatk: Add the WITH_LARGE_FILES option. Modified: head/biology/gatk/Makefile Modified: head/biology/gatk/Makefile ============================================================================== --- head/biology/gatk/Makefile Fri Jan 22 01:54:39 2021 (r562269) +++ head/biology/gatk/Makefile Fri Jan 22 02:50:38 2021 (r562270) @@ -2,6 +2,7 @@ PORTNAME= gatk DISTVERSION= 4.1.9.0 +PORTREVISION= 1 CATEGORIES= biology java EXTRACT_ONLY= ${DISTNAME}${EXTRACT_SUFX} @@ -40,6 +41,35 @@ PLIST_FILES= bin/${PORTNAME} \ # 5. make clean makesum DEV_UPDATE_MODE= no + +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 + +WITH_LARGE_FILES_DESC= Download large LFS files needed for build and tests +WITH_LARGE_FILES_FETCH_DEPENDS= git:devel/git \ + git-lfs:devel/git-lfs + +.include <bsd.port.options.mk> + +.if ${PORT_OPTIONS:MWITH_LARGE_FILES} +do-fetch: + @if [ "${FORCE_FETCH_ALL}" = "true" ] || ! [ -f "${DISTDIR}/${DIST_SUBDIR}/${DISTNAME}${EXTRACT_SUFX}" ]; then \ + ${MKDIR} ${DISTDIR}/${DIST_SUBDIR} && \ + cd ${DISTDIR}/${DIST_SUBDIR} && \ + ${ECHO} "==> Fetching ${PORTNAME} including large LFS files" && \ + ( \ + ${MKDIR} ${WRKDIR}; \ + HOME=${WRKDIR}; \ + git config --global filter.lfs.smudge "git-lfs smudge -- %f" && \ + git clone -q https://github.com/broadinstitute/gatk.git ${PORTNAME}-${DISTVERSION} && \ + (cd ${PORTNAME}-${DISTVERSION} && git reset -q --hard ${DISTVERSION} && ${RM} -r .git) && \ + ${RM} -r ${WRKDIR} \ + ) && \ + ${FIND} ${PORTNAME}-${DISTVERSION} -and -exec ${TOUCH} -h -d 1970-01-01T00:00:00Z {} \; && \ + ${FIND} ${PORTNAME}-${DISTVERSION} -print0 | LC_ALL=C ${SORT} -z | \ + ${TAR} czf ${DISTNAME}${EXTRACT_SUFX} --format=bsdtar --gid 0 --uid 0 --options gzip:!timestamp --no-recursion --null -T - && \ + ${RM} -r ${PORTNAME}-${DISTVERSION}; \ + fi +.endif .if (${DEV_UPDATE_MODE} == "yes") post-build:
Want to link to this message? Use this URL: <https://mail-archive.FreeBSD.org/cgi/mid.cgi?202101220250.10M2ocJ2062673>