diff options
| author | Yuri Victorovich <yuri@FreeBSD.org> | 2020-03-04 08:47:55 +0000 |
|---|---|---|
| committer | Yuri Victorovich <yuri@FreeBSD.org> | 2020-03-04 08:47:55 +0000 |
| commit | 21b5af6ba3783615a4e81c3fdbe5cfea8045aca6 (patch) | |
| tree | ee1ebc98c28fe3e343b6867ba1def3f289398522 /biology/gatk | |
| parent | db7112ff49cdcabd9d5ccd374ddf623188e1ba11 (diff) | |
| download | ports-21b5af6ba3783615a4e81c3fdbe5cfea8045aca6.tar.gz ports-21b5af6ba3783615a4e81c3fdbe5cfea8045aca6.zip | |
biology/gatk: Update 4.1.4.1 -> 4.1.5.0
Reported by: repology
Notes
Notes:
svn path=/head/; revision=527743
Diffstat (limited to 'biology/gatk')
| -rw-r--r-- | biology/gatk/Makefile | 5 | ||||
| -rw-r--r-- | biology/gatk/distinfo | 10 | ||||
| -rw-r--r-- | biology/gatk/files/patch-build.gradle | 22 |
3 files changed, 19 insertions, 18 deletions
diff --git a/biology/gatk/Makefile b/biology/gatk/Makefile index a17f7b426d87..de494c53696e 100644 --- a/biology/gatk/Makefile +++ b/biology/gatk/Makefile @@ -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 diff --git a/biology/gatk/distinfo b/biology/gatk/distinfo index 9794d03b5c6b..d83fcb1c7aa8 100644 --- a/biology/gatk/distinfo +++ b/biology/gatk/distinfo @@ -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 diff --git a/biology/gatk/files/patch-build.gradle b/biology/gatk/files/patch-build.gradle index 1469e66028c0..81e4d00ff340 100644 --- a/biology/gatk/files/patch-build.gradle +++ b/biology/gatk/files/patch-build.gradle @@ -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 |