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Thu, 31 Oct 2024 19:28:18 GMT (envelope-from git) Date: Thu, 31 Oct 2024 19:28:18 GMT Message-Id: <202410311928.49VJSI5A052718@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: 0651e2054aa6 - main - biology/gatk: Update tests stats; Add dependency List-Id: Commits to the main branch of the FreeBSD ports repository List-Archive: https://lists.freebsd.org/archives/dev-commits-ports-main List-Help: List-Post: List-Subscribe: List-Unsubscribe: X-BeenThere: dev-commits-ports-main@freebsd.org Sender: owner-dev-commits-ports-main@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: 0651e2054aa68513a8c174a4b7f7ec5606557ce9 Auto-Submitted: auto-generated The branch main has been updated by yuri: URL: https://cgit.FreeBSD.org/ports/commit/?id=0651e2054aa68513a8c174a4b7f7ec5606557ce9 commit 0651e2054aa68513a8c174a4b7f7ec5606557ce9 Author: Yuri Victorovich AuthorDate: 2024-10-31 19:27:12 +0000 Commit: Yuri Victorovich CommitDate: 2024-10-31 19:28:13 +0000 biology/gatk: Update tests stats; Add dependency --- biology/gatk/Makefile | 6 ++++-- 1 file changed, 4 insertions(+), 2 deletions(-) diff --git a/biology/gatk/Makefile b/biology/gatk/Makefile index f442f7798f45..675650e5ac59 100644 --- a/biology/gatk/Makefile +++ b/biology/gatk/Makefile @@ -1,5 +1,6 @@ PORTNAME= gatk DISTVERSION= 4.6.1.0 +PORTREVISION= 1 CATEGORIES= biology java EXTRACT_ONLY= ${DISTNAME}${EXTRACT_SUFX} @@ -12,7 +13,8 @@ LICENSE_FILE= ${WRKSRC}/LICENSE.TXT BUILD_DEPENDS= gradle:devel/gradle RUN_DEPENDS= ${LOCALBASE}/lib/libfml.so:biology/fermi-lite \ - gkl>0:biology/gkl + gkl>0:biology/gkl \ + mummer>0:biology/mummer USES= gettext-runtime python:test USE_JAVA= yes @@ -116,7 +118,7 @@ do-test: # tests require WITH_LARGE_FILES=ON, and they use a lot of disk space @cd ${WRKSRC} && \ ${SETENV} ${TEST_ENV} gradle -DLIBBWA_PATH=${PREFIX}/lib/libfml.so test -# tests results as of version 4.6.0.0_1: 288433 tests completed, 301 failed, 37 skipped, see https://github.com/broadinstitute/gatk/issues/8940 +# tests results as of version 4.6.1.0: 288552 tests, 301 failures, 37 ignored, 1h55m5.63s duration, 99% successful, see https://github.com/broadinstitute/gatk/issues/8940 # see https://github.com/broadinstitute/gatk/issues/8939: Tests fail to find libgkl libraries in /usr/local/lib .include