biology/gatk: Update 4.3.0.0 → 4.4.0.0

biology/gatk/Makefile

@@ -1,5 +1,5 @@
 PORTNAME=	gatk
-DISTVERSION=	4.3.0.0
+DISTVERSION=	4.4.0.0
 CATEGORIES=	biology java
 EXTRACT_ONLY=	${DISTNAME}${EXTRACT_SUFX}
 
@@ -12,7 +12,7 @@ LICENSE_FILE=	${WRKSRC}/LICENSE.TXT
 
 BROKEN_FreeBSD_12_powerpc64=	fails to build: String index out of range: -1
 
-BUILD_DEPENDS=	gradle:devel/gradle
+BUILD_DEPENDS=	gradle761:devel/gradle761
 
 USES=		gettext-runtime
 USE_JAVA=	yes
@@ -32,6 +32,8 @@ DEPS_CACHE_DIR=	${WRKDIR}
 PLIST_FILES=	bin/${PORTNAME} \
 		${JAVAJARDIR}/GenomeAnalysisTK-${PORTVERSION}.jar
 
+BINARY_ALIAS=	java=${JAVA}
+
 # TODO additionally fetch git-lfs files: https://github.com/broadinstitute/gatk/issues/6395
 
 # to rebuild the deps archive:
@@ -86,7 +88,7 @@ post-extract: # need a separate extract step because the cache is in /tmp, and n
 .endif
 
 do-build:
-	@cd ${WRKSRC} && ${SETENV} ${MAKE_ENV} gradle \
+	cd ${WRKSRC} && ${SETENV} ${MAKE_ENV} gradle761 \
 		--gradle-user-home ${DEPS_CACHE_DIR}/gradle-${PORTNAME} --project-cache-dir ${DEPS_CACHE_DIR}/gradle-${PORTNAME} \
 		${GRADLE_ARGS} --build-cache localJar
 

biology/gatk/distinfo

@@ -1,5 +1,5 @@
-TIMESTAMP = 1669519665
-SHA256 (gatk-4.3.0.0-deps.tar.gz) = 2cecff5daf25ab55da7cea574801f1f802ac60337438f209067563c5deb13bd8
-SIZE (gatk-4.3.0.0-deps.tar.gz) = 552787501
-SHA256 (broadinstitute-gatk-4.3.0.0_GH0.tar.gz) = 93f8ab1e0380d023e1e7eed9d5a0cce0e606679ad91c58e8ffee08222ce92443
-SIZE (broadinstitute-gatk-4.3.0.0_GH0.tar.gz) = 98743503
+TIMESTAMP = 1685914727
+SHA256 (gatk-4.4.0.0-deps.tar.gz) = 1122d2c0d79048b3a2c507262a76af98b1f1c6e9e70c6d459f458fa33939a58c
+SIZE (gatk-4.4.0.0-deps.tar.gz) = 717202736
+SHA256 (broadinstitute-gatk-4.4.0.0_GH0.tar.gz) = 026498bdb1e07041abc74e26c84e681d77212a3d3dd66c83249957a0518e4bfe
+SIZE (broadinstitute-gatk-4.4.0.0_GH0.tar.gz) = 100594033