Date: Mon, 3 Dec 2018 08:40:53 +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: r486502 - in head/biology: . gatk gatk/files Message-ID: <201812030840.wB38erl5025390@repo.freebsd.org>
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Author: yuri Date: Mon Dec 3 08:40:53 2018 New Revision: 486502 URL: https://svnweb.freebsd.org/changeset/ports/486502 Log: New port: biology/gatk: Variant discovery in high-throughput sequencing data Added: head/biology/gatk/ head/biology/gatk/Makefile (contents, props changed) head/biology/gatk/distinfo (contents, props changed) head/biology/gatk/files/ head/biology/gatk/files/gatk.sh.in (contents, props changed) head/biology/gatk/files/patch-build.gradle (contents, props changed) head/biology/gatk/pkg-descr (contents, props changed) Modified: head/biology/Makefile Modified: head/biology/Makefile ============================================================================== --- head/biology/Makefile Mon Dec 3 08:06:01 2018 (r486501) +++ head/biology/Makefile Mon Dec 3 08:40:53 2018 (r486502) @@ -37,6 +37,7 @@ SUBDIR += fluctuate SUBDIR += freebayes SUBDIR += garlic + SUBDIR += gatk SUBDIR += gff2ps SUBDIR += gmap SUBDIR += gperiodic Added: head/biology/gatk/Makefile ============================================================================== --- /dev/null 00:00:00 1970 (empty, because file is newly added) +++ head/biology/gatk/Makefile Mon Dec 3 08:40:53 2018 (r486502) @@ -0,0 +1,45 @@ +# $FreeBSD$ + +PORTNAME= gatk +DISTVERSION= 4.0.11.0 +CATEGORIES= biology java +MASTER_SITES= LOCAL/yuri/:deps +DISTFILES= ${PORTNAME}-${DISTVERSION}-deps${EXTRACT_SUFX}:deps +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= gradle4:devel/gradle4 + +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 + +post-patch: # to rebuild the deps archive: 1. remove post-patch: 2. remove --offline 3. build 4. package ${DEPS_CACHE_DIR}/gradle-${PORTNAME} into the deps archive + @cd ${DEPS_CACHE_DIR} && ${TAR} xzf ${DISTDIR}/${PORTNAME}-${DISTVERSION}-deps${EXTRACT_SUFX} + +do-build: + @cd ${WRKSRC} && ${SETENV} ${MAKE_ENV} gradle4 \ + --gradle-user-home ${DEPS_CACHE_DIR}/gradle-${PORTNAME} --project-cache-dir ${DEPS_CACHE_DIR}/gradle-${PORTNAME} \ + --offline --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 <bsd.port.mk> Added: head/biology/gatk/distinfo ============================================================================== --- /dev/null 00:00:00 1970 (empty, because file is newly added) +++ head/biology/gatk/distinfo Mon Dec 3 08:40:53 2018 (r486502) @@ -0,0 +1,5 @@ +TIMESTAMP = 1543823410 +SHA256 (gatk-4.0.11.0-deps.tar.gz) = 457ed3bf756a673daa2d123fef1d8525e57f20708f134c9b897946ea49561a36 +SIZE (gatk-4.0.11.0-deps.tar.gz) = 225800131 +SHA256 (broadinstitute-gatk-4.0.11.0_GH0.tar.gz) = ba4cc922bae2cdec728984518644bb0a12be2b6916297e2eb3b862cb42841039 +SIZE (broadinstitute-gatk-4.0.11.0_GH0.tar.gz) = 74603782 Added: head/biology/gatk/files/gatk.sh.in ============================================================================== --- /dev/null 00:00:00 1970 (empty, because file is newly added) +++ head/biology/gatk/files/gatk.sh.in Mon Dec 3 08:40:53 2018 (r486502) @@ -0,0 +1,25 @@ +#!/bin/sh + +export LC_ALL=en_US.UTF-8 + +MEM_OPTS_SET_BY_USER="no" +for o in $@; do + case $o in + -X* ) + MEM_OPTS_SET_BY_USER="yes" + ;; + esac +done + +if [ $MEM_OPTS_SET_BY_USER = "no" ]; then + # memory options + physmem_b=$(sysctl -n hw.physmem) + physmem_mb=$((physmem_b/1024/1024)) + physmem_mb=$((physmem_mb*3/4)) # allow 3/4 of the memory + # -Xms<size> set initial Java heap size + # -Xmx<size> set maximum Java heap size + MEM_OPTS="-Xms512m -Xmx${physmem_mb}m" +fi + +# execute the command +%%JAVA%% $MEM_OPTS -jar %%JAVAJARDIR%%/GenomeAnalysisTK-%%PORTVERSION%%.jar "$@" Added: head/biology/gatk/files/patch-build.gradle ============================================================================== --- /dev/null 00:00:00 1970 (empty, because file is newly added) +++ head/biology/gatk/files/patch-build.gradle Mon Dec 3 08:40:53 2018 (r486502) @@ -0,0 +1,29 @@ +--- build.gradle.orig 2018-10-23 15:15:16 UTC ++++ build.gradle +@@ -115,7 +115,7 @@ def resolveLargeResourceStubFiles(largeR + } + + // 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. $buildPrerequisitesMessage") + } +- if (!file(".git").isDirectory()) { ++ if (false && !file(".git").isDirectory()) { + throw new GradleException("The GATK Github repository must be cloned using \"git clone\" to run the build. " + + "$buildPrerequisitesMessage") + } +@@ -366,7 +366,7 @@ def createGatkSymlinks(destinationDir, a + } + + 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' Added: head/biology/gatk/pkg-descr ============================================================================== --- /dev/null 00:00:00 1970 (empty, because file is newly added) +++ head/biology/gatk/pkg-descr Mon Dec 3 08:40:53 2018 (r486502) @@ -0,0 +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/
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