From owner-svn-ports-all@freebsd.org Mon Jan 20 02:12:38 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 74F0B22A7E2; Mon, 20 Jan 2020 02:12:38 +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 481FYf2XkFz3yNh; Mon, 20 Jan 2020 02:12:38 +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 5290E1C904; Mon, 20 Jan 2020 02:12:38 +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 00K2CcaG035892; Mon, 20 Jan 2020 02:12:38 GMT (envelope-from yuri@FreeBSD.org) Received: (from yuri@localhost) by repo.freebsd.org (8.15.2/8.15.2/Submit) id 00K2CbFp035885; Mon, 20 Jan 2020 02:12:37 GMT (envelope-from yuri@FreeBSD.org) Message-Id: <202001200212.00K2CbFp035885@repo.freebsd.org> X-Authentication-Warning: repo.freebsd.org: yuri set sender to yuri@FreeBSD.org using -f From: Yuri Victorovich Date: Mon, 20 Jan 2020 02:12:37 +0000 (UTC) To: ports-committers@freebsd.org, svn-ports-all@freebsd.org, svn-ports-head@freebsd.org Subject: svn commit: r523602 - in head/biology/gatk: . files X-SVN-Group: ports-head X-SVN-Commit-Author: yuri X-SVN-Commit-Paths: in head/biology/gatk: . files X-SVN-Commit-Revision: 523602 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: Mon, 20 Jan 2020 02:12:38 -0000 Author: yuri Date: Mon Jan 20 02:12:37 2020 New Revision: 523602 URL: https://svnweb.freebsd.org/changeset/ports/523602 Log: biology/gatk: Update 4.1.3.0 -> 4.1.4.1 Modified: head/biology/gatk/Makefile head/biology/gatk/distinfo head/biology/gatk/files/patch-build.gradle head/biology/gatk/pkg-descr Modified: head/biology/gatk/Makefile ============================================================================== --- head/biology/gatk/Makefile Mon Jan 20 02:01:42 2020 (r523601) +++ head/biology/gatk/Makefile Mon Jan 20 02:12:37 2020 (r523602) @@ -1,7 +1,7 @@ # $FreeBSD$ PORTNAME= gatk -DISTVERSION= 4.1.3.0 +DISTVERSION= 4.1.4.1 CATEGORIES= biology java EXTRACT_ONLY= ${DISTNAME}${EXTRACT_SUFX} Modified: head/biology/gatk/distinfo ============================================================================== --- head/biology/gatk/distinfo Mon Jan 20 02:01:42 2020 (r523601) +++ head/biology/gatk/distinfo Mon Jan 20 02:12:37 2020 (r523602) @@ -1,5 +1,5 @@ -TIMESTAMP = 1578219311 -SHA256 (gatk-4.1.3.0-deps.tar.gz) = 5258f2ed0faebb16fed888cb5ae688f833b7ff9e293f89e0c0cee33670ac7fbe -SIZE (gatk-4.1.3.0-deps.tar.gz) = 250818646 -SHA256 (broadinstitute-gatk-4.1.3.0_GH0.tar.gz) = f24e7dcb56e16a8aa81e12bdd87916de985c2a1089d6fc4b1a5cdb517e4e9f9c -SIZE (broadinstitute-gatk-4.1.3.0_GH0.tar.gz) = 64567278 +TIMESTAMP = 1579483921 +SHA256 (gatk-4.1.4.1-deps.tar.gz) = b634903f674aa1550039c4434e0ef0efab75d509e80d5073a2b5f3a0120fd68e +SIZE (gatk-4.1.4.1-deps.tar.gz) = 253677476 +SHA256 (broadinstitute-gatk-4.1.4.1_GH0.tar.gz) = 54129c3973ad7f1c501ecd7c841d15cd09fdd0d5ca3057810c17d7b7b9d88eb7 +SIZE (broadinstitute-gatk-4.1.4.1_GH0.tar.gz) = 64600068 Modified: head/biology/gatk/files/patch-build.gradle ============================================================================== --- head/biology/gatk/files/patch-build.gradle Mon Jan 20 02:01:42 2020 (r523601) +++ head/biology/gatk/files/patch-build.gradle Mon Jan 20 02:12:37 2020 (r523602) @@ -1,6 +1,6 @@ ---- build.gradle.orig 2018-10-23 15:15:16 UTC +--- build.gradle.orig 2019-11-26 15:07:28 UTC +++ build.gradle -@@ -115,7 +115,7 @@ def resolveLargeResourceStubFiles(largeR +@@ -114,7 +114,7 @@ def resolveLargeResourceStubFiles(largeResourcesFolder } // check for stub files, try to pull once if there are any, then check again @@ -9,16 +9,16 @@ final gitLFSPullLargeResources = "git lfs pull --include $largeResourcesFolder" execGitLFSCommand(gitLFSPullLargeResources) if (checkForLFSStubFiles(largeResourcesFolder)) { -@@ -135,7 +135,7 @@ def ensureBuildPrerequisites(requiredJav - "The ClassLoader obtained from the Java ToolProvider is null. " - + "A Java $requiredJavaVersion JDK must be installed. $buildPrerequisitesMessage") +@@ -148,7 +148,7 @@ def ensureBuildPrerequisites(largeResourcesFolder, bui + if (!JavaVersion.current().isJava8() && !JavaVersion.current().isJava11()) { + println("Warning: using Java ${JavaVersion.current()} but only Java 8 and Java 11 have been tested.") } -- if (!file(".git").isDirectory()) { -+ if (false && !file(".git").isDirectory()) { - throw new GradleException("The GATK Github repository must be cloned using \"git clone\" to run the build. " - + "$buildPrerequisitesMessage") - } -@@ -366,7 +366,7 @@ def createGatkSymlinks(destinationDir, a +- if (!looksLikeWereInAGitRepository()) { ++ if (false && !looksLikeWereInAGitRepository()) { + throw new GradleException("This doesn't appear to be a git folder. " + + "The GATK Github repository must be cloned using \"git clone\" to run the build. " + + "\n$buildPrerequisitesMessage") +@@ -396,7 +396,7 @@ def createGatkSymlinks(destinationDir, archivePath, su } final isRelease = Boolean.getBoolean("release") Modified: head/biology/gatk/pkg-descr ============================================================================== --- head/biology/gatk/pkg-descr Mon Jan 20 02:01:42 2020 (r523601) +++ head/biology/gatk/pkg-descr Mon Jan 20 02:12:37 2020 (r523602) @@ -10,4 +10,4 @@ offers a wide variety of tools with a primary focus on genotyping. Its powerful processing engine and high-performance computing features make it capable of taking on projects of any size. -WWW: https://software.broadinstitute.org/gatk/ +WWW: https://gatk.broadinstitute.org/hc/en-us