Index: head/biology/gatk/Makefile =================================================================== --- head/biology/gatk/Makefile (revision 523601) +++ head/biology/gatk/Makefile (revision 523602) @@ -1,63 +1,63 @@ # $FreeBSD$ PORTNAME= gatk -DISTVERSION= 4.1.3.0 +DISTVERSION= 4.1.4.1 CATEGORIES= biology java EXTRACT_ONLY= ${DISTNAME}${EXTRACT_SUFX} MAINTAINER= yuri@FreeBSD.org COMMENT= Variant discovery in high-throughput sequencing data LICENSE= BSD3CLAUSE LICENSE_FILE= ${WRKSRC}/LICENSE.TXT BUILD_DEPENDS= gradle5:devel/gradle5 USES= gettext-runtime USE_GITHUB= yes GH_ACCOUNT= broadinstitute USE_JAVA= yes SUB_FILES= ${PORTNAME}.sh SUB_LIST= PORTVERSION=${PORTVERSION} JAVA=${JAVA} NO_ARCH= yes DEPS_CACHE_DIR= /tmp # should be ${WRKDIR}, but workaround for the gradle bug that dependency cache is not relocable: https://github.com/gradle/gradle/issues/1338 PLIST_FILES= bin/${PORTNAME} \ ${JAVAJARDIR}/GenomeAnalysisTK-${PORTVERSION}.jar # to rebuild the deps archive: # 1. set DEV_UPDATE_MODE=yes # 2. make makesum build # 3. upload the *-deps archive # 4. set DEV_UPDATE_MODE=no # 5. make clean makesum DEV_UPDATE_MODE= no .if (${DEV_UPDATE_MODE} == "yes") post-build: @cd ${DEPS_CACHE_DIR} && ${TAR} czf ${DISTDIR}/${PORTNAME}-${DISTVERSION}-deps${EXTRACT_SUFX} gradle-${PORTNAME} @${ECHO} "(!!!) Please upload the gradle deps archive: ${DISTDIR}/${PORTNAME}-${DISTVERSION}-deps${EXTRACT_SUFX}" .else MASTER_SITES= LOCAL/yuri/:deps DISTFILES= ${PORTNAME}-${DISTVERSION}-deps${EXTRACT_SUFX}:deps GRADLE_ARGS= --offline post-extract: # need a separate extract step because the cache is in /tmp, and not under work/ like with maven @cd ${DEPS_CACHE_DIR} && ${TAR} xzf ${DISTDIR}/${PORTNAME}-${DISTVERSION}-deps${EXTRACT_SUFX} .endif do-build: @cd ${WRKSRC} && ${SETENV} ${MAKE_ENV} gradle5 \ --gradle-user-home ${DEPS_CACHE_DIR}/gradle-${PORTNAME} --project-cache-dir ${DEPS_CACHE_DIR}/gradle-${PORTNAME} \ ${GRADLE_ARGS} --build-cache localJar do-install: ${INSTALL_SCRIPT} ${WRKDIR}/${PORTNAME}.sh ${STAGEDIR}${PREFIX}/bin/${PORTNAME} ${INSTALL_DATA} ${WRKSRC}/build/libs/gatk-package-1.0-SNAPSHOT-local.jar ${STAGEDIR}${JAVAJARDIR}/GenomeAnalysisTK-${PORTVERSION}.jar .include Index: head/biology/gatk/distinfo =================================================================== --- head/biology/gatk/distinfo (revision 523601) +++ head/biology/gatk/distinfo (revision 523602) @@ -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 Index: head/biology/gatk/files/patch-build.gradle =================================================================== --- head/biology/gatk/files/patch-build.gradle (revision 523601) +++ head/biology/gatk/files/patch-build.gradle (revision 523602) @@ -1,29 +1,29 @@ ---- 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 - if (checkForLFSStubFiles(largeResourcesFolder)) { + if (false && checkForLFSStubFiles(largeResourcesFolder)) { 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") -version = (isRelease ? gitVersion() : gitVersion() + "-SNAPSHOT").replaceAll(".dirty", "") +version = (isRelease ? "1.0" : "1.0" + "-SNAPSHOT").replaceAll(".dirty", "") logger.info("build for version:" + version) group = 'org.broadinstitute' Index: head/biology/gatk/pkg-descr =================================================================== --- head/biology/gatk/pkg-descr (revision 523601) +++ head/biology/gatk/pkg-descr (revision 523602) @@ -1,13 +1,13 @@ GATK, pronounced "Gee Ay Tee Kay" (not "Gat-Kay"), stands for GenomeAnalysisToolkit. It is a collection of command-line tools for analyzing high-throughput sequencing data with a primary focus on variant discovery. The tools can be used individually or chained together into complete workflows. end-to-end workflows are provided, called GATK Best Practices, tailored for specific use cases. Developed in the Data Sciences Platform at the Broad Institute, the toolkit offers a wide variety of tools with a primary focus on variant discovery and 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