svn commit: r527743 - in head/biology/gatk: . files
Yuri Victorovich
yuri at FreeBSD.org
Wed Mar 4 08:47:57 UTC 2020
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
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