Date: Sun, 4 Jun 2023 22:03:56 GMT From: Yuri Victorovich <yuri@FreeBSD.org> To: ports-committers@FreeBSD.org, dev-commits-ports-all@FreeBSD.org, dev-commits-ports-main@FreeBSD.org Subject: git: 6541d6f389c9 - main - =?utf-8?Q?biology/gatk:=20Update=204.3.0.0=20=E2=86=92=204.4.0.0?= Message-ID: <202306042203.354M3u7Z086973@gitrepo.freebsd.org>
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The branch main has been updated by yuri: URL: https://cgit.FreeBSD.org/ports/commit/?id=6541d6f389c9d95818959222dadbab3d25d8eb08 commit 6541d6f389c9d95818959222dadbab3d25d8eb08 Author: Yuri Victorovich <yuri@FreeBSD.org> AuthorDate: 2023-06-04 22:02:58 +0000 Commit: Yuri Victorovich <yuri@FreeBSD.org> CommitDate: 2023-06-04 22:02:58 +0000 biology/gatk: Update 4.3.0.0 → 4.4.0.0 --- biology/gatk/Makefile | 8 +++++--- biology/gatk/distinfo | 10 +++++----- 2 files changed, 10 insertions(+), 8 deletions(-) diff --git a/biology/gatk/Makefile b/biology/gatk/Makefile index ee69b70e3cec..daf9eb32ae98 100644 --- a/biology/gatk/Makefile +++ b/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 diff --git a/biology/gatk/distinfo b/biology/gatk/distinfo index 816c61bd9752..2c162723ff0d 100644 --- a/biology/gatk/distinfo +++ b/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
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