Date: Fri, 8 Nov 2019 14:03:15 +0000 (UTC) From: "Jason W. Bacon" <jwb@FreeBSD.org> To: ports-committers@freebsd.org, svn-ports-all@freebsd.org, svn-ports-head@freebsd.org Subject: svn commit: r517066 - in head/biology/canu: . files Message-ID: <201911081403.xA8E3FLi013791@repo.freebsd.org>
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Author: jwb Date: Fri Nov 8 14:03:15 2019 New Revision: 517066 URL: https://svnweb.freebsd.org/changeset/ports/517066 Log: biology/canu: Upgrade to 1.9 Numerous bug fixes and enhancements Reported by: portscout Deleted: head/biology/canu/files/patch-Makefile Modified: head/biology/canu/Makefile head/biology/canu/distinfo head/biology/canu/pkg-plist Modified: head/biology/canu/Makefile ============================================================================== --- head/biology/canu/Makefile Fri Nov 8 13:59:51 2019 (r517065) +++ head/biology/canu/Makefile Fri Nov 8 14:03:15 2019 (r517066) @@ -2,8 +2,7 @@ PORTNAME= canu DISTVERSIONPREFIX= v -DISTVERSION= 1.8 -PORTREVISION= 5 +DISTVERSION= 1.9 CATEGORIES= biology java perl5 MAINTAINER= jwb@FreeBSD.org Modified: head/biology/canu/distinfo ============================================================================== --- head/biology/canu/distinfo Fri Nov 8 13:59:51 2019 (r517065) +++ head/biology/canu/distinfo Fri Nov 8 14:03:15 2019 (r517066) @@ -1,3 +1,3 @@ -TIMESTAMP = 1540317173 -SHA256 (marbl-canu-v1.8_GH0.tar.gz) = 30ecfe574166f54f79606038830f68927cf0efab33bdc3c6e43fd1448fa0b2e4 -SIZE (marbl-canu-v1.8_GH0.tar.gz) = 2465314 +TIMESTAMP = 1573142752 +SHA256 (marbl-canu-v1.9_GH0.tar.gz) = 6b086ab6086c050752166500378bc4b3b3543d4c617863e894d296171cee3385 +SIZE (marbl-canu-v1.9_GH0.tar.gz) = 3410307 Modified: head/biology/canu/pkg-plist ============================================================================== --- head/biology/canu/pkg-plist Fri Nov 8 13:59:51 2019 (r517065) +++ head/biology/canu/pkg-plist Fri Nov 8 14:03:15 2019 (r517066) @@ -2,16 +2,13 @@ bin/alignGFA bin/bogart bin/bogus bin/canu +bin/canu-time bin/canu.defaults bin/correctOverlaps bin/dumpBlob bin/edalign bin/errorEstimate bin/falconsense -bin/fastqAnalyze -bin/fastqSample -bin/fastqSimulate -bin/fastqSimulate-sort bin/filterCorrectionLayouts bin/filterCorrectionOverlaps bin/findErrors @@ -20,7 +17,10 @@ bin/generateCorrectionLayouts bin/loadCorrectedReads bin/loadErates bin/loadTrimmedReads +bin/mergeRanges bin/meryl +bin/meryl-import +bin/meryl-lookup bin/mhapConvert bin/mmapConvert bin/ovStoreBucketizer @@ -30,13 +30,13 @@ bin/ovStoreDump bin/ovStoreIndexer bin/ovStoreSorter bin/ovStoreStats +bin/overlapAlign bin/overlapConvert bin/overlapImport bin/overlapInCore bin/overlapInCorePartition bin/overlapPair bin/prefixEditDistance-matchLimitGenerate -bin/readConsensus bin/sequence bin/splitHaplotype bin/splitReads @@ -45,7 +45,6 @@ bin/sqStoreCreatePartition bin/sqStoreDumpFASTQ bin/sqStoreDumpMetaData bin/tgStoreCompress -bin/tgStoreCoverageStat bin/tgStoreDump bin/tgStoreFilter bin/tgStoreLoad @@ -79,3 +78,6 @@ lib/libcanu.a %%SITE_PERL%%/canu/SequenceStore.pm %%SITE_PERL%%/canu/Unitig.pm %%JAVAJARDIR%%/mhap-2.1.3.jar +share/sequence/pacbio +share/sequence/pacbio-hifi +share/sequence/ultra-long-nanopore
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