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biology/gatk: Update 4.1.4.1 -> 4.1.5.0

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Reported by:	repology
This commit is contained in:
Yuri Victorovich 2020-03-04 08:47:55 +00:00
parent db7112ff49
commit 21b5af6ba3
Notes: svn2git 2021-03-31 03:12:20 +00:00 
svn path=/head/; revision=527743
3 changed files with 19 additions and 18 deletions
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5
biology/gatk/Makefile
View File

@ -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}
@ -29,6 +28,8 @@ 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
# 2. make makesum build

10
biology/gatk/distinfo
View File

@ -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

22
biology/gatk/files/patch-build.gradle
View File

@ -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