Index: head/biology/gatk/Makefile
===================================================================
--- head/biology/gatk/Makefile	(revision 562269)
+++ head/biology/gatk/Makefile	(revision 562270)
@@ -1,66 +1,96 @@
 # $FreeBSD$
 
 PORTNAME=	gatk
 DISTVERSION=	4.1.9.0
+PORTREVISION=	1
 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>