Index: head/biology/gatk/Makefile
===================================================================
--- head/biology/gatk/Makefile	(revision 562257)
+++ head/biology/gatk/Makefile	(revision 562258)
@@ -1,66 +1,66 @@
 # $FreeBSD$
 
 PORTNAME=	gatk
-DISTVERSION=	4.1.8.1
+DISTVERSION=	4.1.9.0
 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
 
 .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>
Index: head/biology/gatk/distinfo
===================================================================
--- head/biology/gatk/distinfo	(revision 562257)
+++ head/biology/gatk/distinfo	(revision 562258)
@@ -1,5 +1,5 @@
-TIMESTAMP = 1599592657
-SHA256 (gatk-4.1.8.1-deps.tar.gz) = 22c63f483eafb9832f42dc26c37a4e5dba9e2f1c9203e413d365c7e943b73064
-SIZE (gatk-4.1.8.1-deps.tar.gz) = 258310909
-SHA256 (broadinstitute-gatk-4.1.8.1_GH0.tar.gz) = 9f49d9fd1975162754c5364961c9b31dbc884028428651789daf36303ba2814f
-SIZE (broadinstitute-gatk-4.1.8.1_GH0.tar.gz) = 69129515
+TIMESTAMP = 1611269839
+SHA256 (gatk-4.1.9.0-deps.tar.gz) = 7c43cb211a00dc2205539aec5dd59c14045eeca17b205f7edfd95be59f68df4f
+SIZE (gatk-4.1.9.0-deps.tar.gz) = 280762660
+SHA256 (broadinstitute-gatk-4.1.9.0_GH0.tar.gz) = 4646b1746485a33efa609e0d7892e58d1540c6e27a4c87eeec50b77d1ef9531e
+SIZE (broadinstitute-gatk-4.1.9.0_GH0.tar.gz) = 69417716