diff options
| author | Yuri Victorovich <yuri@FreeBSD.org> | 2021-01-22 02:50:38 +0000 |
|---|---|---|
| committer | Yuri Victorovich <yuri@FreeBSD.org> | 2021-01-22 02:50:38 +0000 |
| commit | 9607e839e297087b0c2a6e2db3e9fabc8d0a4982 (patch) | |
| tree | 7fb9468711663be5a084af27b628ce49753f3ea7 /biology/gatk/Makefile | |
| parent | - Update to 2.89.0 (diff) | |
biology/gatk: Add the WITH_LARGE_FILES option.
Notes
Notes:
svn path=/head/; revision=562270
Diffstat (limited to 'biology/gatk/Makefile')
| -rw-r--r-- | biology/gatk/Makefile | 30 |
1 files changed, 30 insertions, 0 deletions
diff --git a/biology/gatk/Makefile b/biology/gatk/Makefile index ef0a4d73c111..8e7ea5531409 100644 --- a/biology/gatk/Makefile +++ b/biology/gatk/Makefile @@ -2,6 +2,7 @@ PORTNAME= gatk DISTVERSION= 4.1.9.0 +PORTREVISION= 1 CATEGORIES= biology java EXTRACT_ONLY= ${DISTNAME}${EXTRACT_SUFX} @@ -41,6 +42,35 @@ PLIST_FILES= bin/${PORTNAME} \ 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: @cd ${DEPS_CACHE_DIR} && ${TAR} czf ${DISTDIR}/${PORTNAME}-${DISTVERSION}-deps${EXTRACT_SUFX} gradle-${PORTNAME} |