Skip site navigation (1)Skip section navigation (2) 
Date:      Wed, 4 Mar 2020 08:47:55 +0000 (UTC)
From:      Yuri Victorovich <yuri@FreeBSD.org>
To:        ports-committers@freebsd.org, svn-ports-all@freebsd.org, svn-ports-head@freebsd.org
Subject:   svn commit: r527743 - in head/biology/gatk: . files
Message-ID:  <202003040847.0248ltcO073476@repo.freebsd.org>
next in thread | raw e-mail | index | archive | help 
Author: yuri
Date: Wed Mar  4 08:47:55 2020
New Revision: 527743
URL: https://svnweb.freebsd.org/changeset/ports/527743

Log:
  biology/gatk: Update 4.1.4.1 -> 4.1.5.0
  
  Reported by:	repology

Modified:
  head/biology/gatk/Makefile
  head/biology/gatk/distinfo
  head/biology/gatk/files/patch-build.gradle

Modified: head/biology/gatk/Makefile
==============================================================================
--- head/biology/gatk/Makefile	Wed Mar  4 07:25:30 2020	(r527742)
+++ head/biology/gatk/Makefile	Wed Mar  4 08:47:55 2020	(r527743)
@@ -1,8 +1,7 @@
 # $FreeBSD$
 
 PORTNAME=	gatk
-DISTVERSION=	4.1.4.1
-PORTREVISION=	1
+DISTVERSION=	4.1.5.0
 CATEGORIES=	biology java
 EXTRACT_ONLY=	${DISTNAME}${EXTRACT_SUFX}
 
@@ -28,6 +27,8 @@ 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

Modified: head/biology/gatk/distinfo
==============================================================================
--- head/biology/gatk/distinfo	Wed Mar  4 07:25:30 2020	(r527742)
+++ head/biology/gatk/distinfo	Wed Mar  4 08:47:55 2020	(r527743)
@@ -1,5 +1,5 @@
-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
+TIMESTAMP = 1583311197
+SHA256 (gatk-4.1.5.0-deps.tar.gz) = 1a0c80d497a4966b7258d14011e910e67a592cb558c9e897aeb82fa4b0e09284
+SIZE (gatk-4.1.5.0-deps.tar.gz) = 255639148
+SHA256 (broadinstitute-gatk-4.1.5.0_GH0.tar.gz) = 6396998ed4cb4d5ac05c8f6f82925c1c95f77500575fb1dd7df215c02ea66774
+SIZE (broadinstitute-gatk-4.1.5.0_GH0.tar.gz) = 65143087

Modified: head/biology/gatk/files/patch-build.gradle
==============================================================================
--- head/biology/gatk/files/patch-build.gradle	Wed Mar  4 07:25:30 2020	(r527742)
+++ head/biology/gatk/files/patch-build.gradle	Wed Mar  4 08:47:55 2020	(r527743)
@@ -1,6 +1,6 @@
---- build.gradle.orig	2019-11-26 15:07:28 UTC
+--- build.gradle.orig	2020-02-28 18:01:21 UTC
 +++ build.gradle
-@@ -114,7 +114,7 @@ def resolveLargeResourceStubFiles(largeResourcesFolder
+@@ -118,7 +118,7 @@ def resolveLargeResourceStubFiles(largeResourcesFolder
      }
  
      // check for stub files, try to pull once if there are any, then check again
@@ -9,21 +9,21 @@
          final gitLFSPullLargeResources = "git lfs pull --include $largeResourcesFolder"
          execGitLFSCommand(gitLFSPullLargeResources)
          if (checkForLFSStubFiles(largeResourcesFolder)) {
-@@ -148,7 +148,7 @@ def ensureBuildPrerequisites(largeResourcesFolder, bui
+@@ -152,7 +152,7 @@ def ensureBuildPrerequisites(largeResourcesFolder, bui
      if (!JavaVersion.current().isJava8() && !JavaVersion.current().isJava11()) {
          println("Warning: using Java ${JavaVersion.current()} but only Java 8 and Java 11 have been tested.")
      }
--    if (!looksLikeWereInAGitRepository()) {
-+    if (false && !looksLikeWereInAGitRepository()) {
+-    if (!skipGitCheck && !looksLikeWereInAGitRepository() ) {
++    if (false && !skipGitCheck && !looksLikeWereInAGitRepository() ) {
          throw new GradleException("This doesn't appear to be a git folder. " +
                  "The GATK Github repository must be cloned using \"git clone\" to run the build. " +
                  "\n$buildPrerequisitesMessage")
-@@ -396,7 +396,7 @@ def createGatkSymlinks(destinationDir, archivePath, su
- }
+@@ -166,7 +166,7 @@ final isRelease = Boolean.getBoolean("release")
+ final versionOverridden = System.getProperty("versionOverride") != null
  
- final isRelease = Boolean.getBoolean("release")
--version = (isRelease ? gitVersion() : gitVersion() + "-SNAPSHOT").replaceAll(".dirty", "")
+ ensureBuildPrerequisites(largeResourcesFolder, buildPrerequisitesMessage, versionOverridden)
+-version = (versionOverridden ? System.getProperty("versionOverride") : gitVersion().replaceAll(".dirty", "")) + (isRelease ?  "" : "-SNAPSHOT")
 +version = (isRelease ? "1.0" : "1.0" + "-SNAPSHOT").replaceAll(".dirty", "")
  
- logger.info("build for version:" + version)
- group = 'org.broadinstitute'
+ if (versionOverridden) {
+     println "Version number overridden as " + version

Want to link to this message? Use this URL: <https://mail-archive.FreeBSD.org/cgi/mid.cgi?202003040847.0248ltcO073476>