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PORTNAME= gatk
DISTVERSION= 4.2.0.0
CATEGORIES= biology java
EXTRACT_ONLY= ${DISTNAME}${EXTRACT_SUFX}
MAINTAINER= yuri@FreeBSD.org
COMMENT= Variant discovery in high-throughput sequencing data
LICENSE= BSD3CLAUSE
LICENSE_FILE= ${WRKSRC}/LICENSE.TXT
BROKEN_FreeBSD_12_powerpc64= fails to build: String index out of range: -1
BUILD_DEPENDS= gradle62:devel/gradle62
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= ${WRKDIR}
PLIST_FILES= bin/${PORTNAME} \
${JAVAJARDIR}/GenomeAnalysisTK-${PORTVERSION}.jar
# TODO additionally fetch git-lfs files: https://github.com/broadinstitute/gatk/issues/6395
# 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
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-${PORTNAME}
@${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} gradle62 \
--gradle-user-home ${DEPS_CACHE_DIR}/gradle-${PORTNAME} --project-cache-dir ${DEPS_CACHE_DIR}/gradle-${PORTNAME} \
${GRADLE_ARGS} --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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