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Fri, 12 Jul 2024 03:51:26 GMT (envelope-from git) Date: Fri, 12 Jul 2024 03:51:26 GMT Message-Id: <202407120351.46C3pQqm021536@gitrepo.freebsd.org> To: ports-committers@FreeBSD.org, dev-commits-ports-all@FreeBSD.org, dev-commits-ports-main@FreeBSD.org From: Yuri Victorovich Subject: git: 290983fbb4bc - main - biology/gatk: update 4.5.0.0 =?utf-8?Q?=E2=86=92?= 4.6.0.0 List-Id: Commit messages for all branches of the ports repository List-Archive: https://lists.freebsd.org/archives/dev-commits-ports-all List-Help: List-Post: List-Subscribe: List-Unsubscribe: X-BeenThere: dev-commits-ports-all@freebsd.org Sender: owner-dev-commits-ports-all@FreeBSD.org MIME-Version: 1.0 Content-Type: text/plain; charset=utf-8 Content-Transfer-Encoding: 8bit X-Git-Committer: yuri X-Git-Repository: ports X-Git-Refname: refs/heads/main X-Git-Reftype: branch X-Git-Commit: 290983fbb4bc9f9cc535b259de56b3b4ae5bb01d Auto-Submitted: auto-generated The branch main has been updated by yuri: URL: https://cgit.FreeBSD.org/ports/commit/?id=290983fbb4bc9f9cc535b259de56b3b4ae5bb01d commit 290983fbb4bc9f9cc535b259de56b3b4ae5bb01d Author: Yuri Victorovich AuthorDate: 2024-07-12 02:24:34 +0000 Commit: Yuri Victorovich CommitDate: 2024-07-12 03:51:21 +0000 biology/gatk: update 4.5.0.0 → 4.6.0.0 --- biology/gatk/Makefile | 20 +++++++++++++------- biology/gatk/distinfo | 10 +++++----- 2 files changed, 18 insertions(+), 12 deletions(-) diff --git a/biology/gatk/Makefile b/biology/gatk/Makefile index d518057376ef..cbf0367d6a18 100644 --- a/biology/gatk/Makefile +++ b/biology/gatk/Makefile @@ -1,5 +1,5 @@ PORTNAME= gatk -DISTVERSION= 4.5.0.0 +DISTVERSION= 4.6.0.0 CATEGORIES= biology java EXTRACT_ONLY= ${DISTNAME}${EXTRACT_SUFX} @@ -32,8 +32,6 @@ PLIST_FILES= bin/${PORTNAME} \ BINARY_ALIAS= java=${JAVA} -# 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 @@ -43,12 +41,16 @@ BINARY_ALIAS= java=${JAVA} DEV_UPDATE_MODE= no -OPTIONS_DEFINE= WITH_LARGE_FILES # probably should be default for tests, but the build doesn't seem to be affected contrary to what README says +OPTIONS_DEFINE= WITH_LARGE_FILES +OPTIONS_DEFAULT= WITH_LARGE_FILES # runtime requires large files, see the README WITH_LARGE_FILES_DESC= Download large LFS files needed for build and tests WITH_LARGE_FILES_FETCH_DEPENDS= git:devel/git \ git-lfs:devel/git-lfs +# The large files under src/main/resources/large/ are required to build GATK, since they are packaged inside the GATK jar and used by tools at runtime. These are things like ML models and native C/C++ libraries used for acceleration of certain tools. +# The large files under src/test/resources/large/, on the other hand, are only required by the test suite when running tests. + .include .if ${PORT_OPTIONS:MWITH_LARGE_FILES} @@ -61,13 +63,13 @@ do-fetch: ${MKDIR} ${WRKDIR}; \ HOME=${WRKDIR}; \ git config --global filter.lfs.smudge "git-lfs smudge -- %f" && \ - git clone -q https://github.com/broadinstitute/gatk.git ${PORTNAME}-${DISTVERSION} && \ + GIT_CLONE_PROTECTION_ACTIVE=false git clone -q https://github.com/broadinstitute/gatk.git ${PORTNAME}-${DISTVERSION} && \ (cd ${PORTNAME}-${DISTVERSION} && git reset -q --hard ${DISTVERSION} && ${RM} -r .git) && \ ${RM} -r ${WRKDIR} \ ) && \ ${FIND} ${PORTNAME}-${DISTVERSION} -and -exec ${TOUCH} -h -d 1970-01-01T00:00:00Z {} \; && \ ${FIND} ${PORTNAME}-${DISTVERSION} -print0 | LC_ALL=C ${SORT} -z | \ - ${TAR} czf ${DISTNAME}${EXTRACT_SUFX} --format=ustar --gid 0 --uid 0 --options gzip:!timestamp --no-recursion --null -T - && \ + ${TAR} czf ${DISTNAME}${EXTRACT_SUFX} --gid 0 --uid 0 --options gzip:!timestamp --no-recursion --null -T - && \ ${RM} -r ${PORTNAME}-${DISTVERSION}; \ fi .endif @@ -86,7 +88,7 @@ post-extract: # need a separate extract step because the cache is in /tmp, and n .endif do-build: - cd ${WRKSRC} && ${SETENV} ${MAKE_ENV} gradle \ + @cd ${WRKSRC} && ${SETENV} ${MAKE_ENV} gradle \ --gradle-user-home ${DEPS_CACHE_DIR}/gradle-${PORTNAME} --project-cache-dir ${DEPS_CACHE_DIR}/gradle-${PORTNAME} \ ${GRADLE_ARGS} --build-cache localJar @@ -94,4 +96,8 @@ 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 +do-test: # tests require WITH_LARGE_FILES=ON, and they use a lot of disk space + @cd ${WRKSRC} && \ + ${SETENV} ${MAKE_ENV} gradle test + .include diff --git a/biology/gatk/distinfo b/biology/gatk/distinfo index 7efe8cb7a921..0dd6a1818b5b 100644 --- a/biology/gatk/distinfo +++ b/biology/gatk/distinfo @@ -1,5 +1,5 @@ -TIMESTAMP = 1702890353 -SHA256 (gatk-4.5.0.0-deps.tar.gz) = b6bf2e6ff9d64198e4ba185b2c09648bef841d274206603d0f6802e134b10cf5 -SIZE (gatk-4.5.0.0-deps.tar.gz) = 883487836 -SHA256 (broadinstitute-gatk-4.5.0.0_GH0.tar.gz) = 39b09548ada317b29f19d6cbc0267301ee3565d575a5d79008a0168e679b98d2 -SIZE (broadinstitute-gatk-4.5.0.0_GH0.tar.gz) = 104455420 +TIMESTAMP = 1720732636 +SHA256 (gatk-4.6.0.0-deps.tar.gz) = 0d124af0ec3d2d93cf2d9c5119ddab4c7d02c8d0213d288695718a6e04064e24 +SIZE (gatk-4.6.0.0-deps.tar.gz) = 937753829 +SHA256 (broadinstitute-gatk-4.6.0.0_GH0.tar.gz) = 6805e831d318964787adfeddbbe8b5ce9a916104913b7e1f73d1e08095638c64 +SIZE (broadinstitute-gatk-4.6.0.0_GH0.tar.gz) = 4322587766