From owner-svn-ports-all@freebsd.org Sun Feb 9 05:57:05 2020 Return-Path: Delivered-To: svn-ports-all@mailman.nyi.freebsd.org Received: from mx1.freebsd.org (mx1.freebsd.org [IPv6:2610:1c1:1:606c::19:1]) by mailman.nyi.freebsd.org (Postfix) with ESMTP id 6F72922E9AC; Sun, 9 Feb 2020 05:57:05 +0000 (UTC) (envelope-from yuri@FreeBSD.org) Received: from mxrelay.nyi.freebsd.org (mxrelay.nyi.freebsd.org [IPv6:2610:1c1:1:606c::19:3]) (using TLSv1.3 with cipher TLS_AES_256_GCM_SHA384 (256/256 bits) server-signature RSA-PSS (4096 bits) client-signature RSA-PSS (4096 bits) client-digest SHA256) (Client CN "mxrelay.nyi.freebsd.org", Issuer "Let's Encrypt Authority X3" (verified OK)) by mx1.freebsd.org (Postfix) with ESMTPS id 48FdbP2HNZz3FWR; Sun, 9 Feb 2020 05:57:05 +0000 (UTC) (envelope-from yuri@FreeBSD.org) Received: from repo.freebsd.org (repo.freebsd.org [IPv6:2610:1c1:1:6068::e6a:0]) (using TLSv1.2 with cipher ECDHE-RSA-AES256-GCM-SHA384 (256/256 bits)) (Client did not present a certificate) by mxrelay.nyi.freebsd.org (Postfix) with ESMTPS id 456EF188F; Sun, 9 Feb 2020 05:57:05 +0000 (UTC) (envelope-from yuri@FreeBSD.org) Received: from repo.freebsd.org ([127.0.1.37]) by repo.freebsd.org (8.15.2/8.15.2) with ESMTP id 0195v5OY065043; Sun, 9 Feb 2020 05:57:05 GMT (envelope-from yuri@FreeBSD.org) Received: (from yuri@localhost) by repo.freebsd.org (8.15.2/8.15.2/Submit) id 0195v4vA065041; Sun, 9 Feb 2020 05:57:04 GMT (envelope-from yuri@FreeBSD.org) Message-Id: <202002090557.0195v4vA065041@repo.freebsd.org> X-Authentication-Warning: repo.freebsd.org: yuri set sender to yuri@FreeBSD.org using -f From: Yuri Victorovich Date: Sun, 9 Feb 2020 05:57:04 +0000 (UTC) To: ports-committers@freebsd.org, svn-ports-all@freebsd.org, svn-ports-head@freebsd.org Subject: svn commit: r525625 - head/biology/gatk X-SVN-Group: ports-head X-SVN-Commit-Author: yuri X-SVN-Commit-Paths: head/biology/gatk X-SVN-Commit-Revision: 525625 X-SVN-Commit-Repository: ports MIME-Version: 1.0 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: 8bit X-BeenThere: svn-ports-all@freebsd.org X-Mailman-Version: 2.1.29 Precedence: list List-Id: SVN commit messages for the ports tree List-Unsubscribe: , List-Archive: List-Post: List-Help: List-Subscribe: , X-List-Received-Date: Sun, 09 Feb 2020 05:57:05 -0000 Author: yuri Date: Sun Feb 9 05:57:04 2020 New Revision: 525625 URL: https://svnweb.freebsd.org/changeset/ports/525625 Log: biology/gatk: Change from gradle5 to gradle6 Modified: head/biology/gatk/Makefile head/biology/gatk/distinfo Modified: head/biology/gatk/Makefile ============================================================================== --- head/biology/gatk/Makefile Sun Feb 9 05:32:45 2020 (r525624) +++ head/biology/gatk/Makefile Sun Feb 9 05:57:04 2020 (r525625) @@ -2,6 +2,7 @@ PORTNAME= gatk DISTVERSION= 4.1.4.1 +PORTREVISION= 1 CATEGORIES= biology java EXTRACT_ONLY= ${DISTNAME}${EXTRACT_SUFX} @@ -11,7 +12,7 @@ COMMENT= Variant discovery in high-throughput sequenci LICENSE= BSD3CLAUSE LICENSE_FILE= ${WRKSRC}/LICENSE.TXT -BUILD_DEPENDS= gradle5:devel/gradle5 +BUILD_DEPENDS= gradle:devel/gradle USES= gettext-runtime USE_GITHUB= yes @@ -23,7 +24,7 @@ SUB_LIST= PORTVERSION=${PORTVERSION} JAVA=${JAVA} NO_ARCH= yes -DEPS_CACHE_DIR= /tmp # should be ${WRKDIR}, but workaround for the gradle bug that dependency cache is not relocable: https://github.com/gradle/gradle/issues/1338 +DEPS_CACHE_DIR= ${WRKDIR} PLIST_FILES= bin/${PORTNAME} \ ${JAVAJARDIR}/GenomeAnalysisTK-${PORTVERSION}.jar @@ -52,7 +53,7 @@ post-extract: # need a separate extract step because t do-build: - @cd ${WRKSRC} && ${SETENV} ${MAKE_ENV} gradle5 \ + @cd ${WRKSRC} && ${SETENV} ${MAKE_ENV} gradle \ --gradle-user-home ${DEPS_CACHE_DIR}/gradle-${PORTNAME} --project-cache-dir ${DEPS_CACHE_DIR}/gradle-${PORTNAME} \ ${GRADLE_ARGS} --build-cache localJar Modified: head/biology/gatk/distinfo ============================================================================== --- head/biology/gatk/distinfo Sun Feb 9 05:32:45 2020 (r525624) +++ head/biology/gatk/distinfo Sun Feb 9 05:57:04 2020 (r525625) @@ -1,5 +1,5 @@ -TIMESTAMP = 1579483921 -SHA256 (gatk-4.1.4.1-deps.tar.gz) = b634903f674aa1550039c4434e0ef0efab75d509e80d5073a2b5f3a0120fd68e -SIZE (gatk-4.1.4.1-deps.tar.gz) = 253677476 +TIMESTAMP = 1581225116 +SHA256 (gatk-4.1.4.1-deps.tar.gz) = 498a0f827531b122ed8f7e789232548a6a4e61c0629ef103d90d06bed787db9e +SIZE (gatk-4.1.4.1-deps.tar.gz) = 253086649 SHA256 (broadinstitute-gatk-4.1.4.1_GH0.tar.gz) = 54129c3973ad7f1c501ecd7c841d15cd09fdd0d5ca3057810c17d7b7b9d88eb7 SIZE (broadinstitute-gatk-4.1.4.1_GH0.tar.gz) = 64600068