Date: Mon, 14 Sep 2020 22:27:37 +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: r548685 - in head/biology/canu: . files Message-ID: <202009142227.08EMRbI4083545@repo.freebsd.org>
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Author: jwb Date: Mon Sep 14 22:27:37 2020 New Revision: 548685 URL: https://svnweb.freebsd.org/changeset/ports/548685 Log: biology/canu: Upgrade to 2.1 Numerous functional improvements for ease of use and output quality A few bug fixes Reported by: portscout Modified: head/biology/canu/Makefile head/biology/canu/distinfo head/biology/canu/files/patch-pipelines_canu_Execution.pm head/biology/canu/pkg-plist Modified: head/biology/canu/Makefile ============================================================================== --- head/biology/canu/Makefile Mon Sep 14 22:20:53 2020 (r548684) +++ head/biology/canu/Makefile Mon Sep 14 22:27:37 2020 (r548685) @@ -1,9 +1,10 @@ # $FreeBSD$ PORTNAME= canu -DISTVERSIONPREFIX= v -DISTVERSION= 2.0 +DISTVERSION= 2.1 CATEGORIES= biology java perl5 +# Github auto-generated tarballs lack submodules +MASTER_SITES= https://github.com/marbl/canu/releases/download/v2.1/ MAINTAINER= jwb@FreeBSD.org COMMENT= Single molecule sequence assembler @@ -12,17 +13,17 @@ LICENSE= GPLv2 LICENSE_FILE= ${WRKDIR}/${PORTNAME}-${PORTVERSION}/README.license.GPL BROKEN_powerpc64= fails to build: utgcns/libboost/boost/smart_ptr/detail/sp_counted_impl.hpp:81:5: error: 'get_deleter' declared as a 'virtual' field +NOT_FOR_ARCHS= armv6 armv7 i386 powerpc +NOT_FOR_ARCHS_REASON= __int128 is not supported on this target LIB_DEPENDS= libboost_regex.so:devel/boost-libs RUN_DEPENDS= gnuplot:math/gnuplot USES= compiler:openmp gmake perl5 USE_JAVA= yes -USE_GITHUB= yes JAVA_RUN= yes JAVA_VERSION= 1.8+ -GH_ACCOUNT= marbl WRKSRC_SUBDIR= src # Upstream Makefile compiles directly into ${DESTDIR}${PREFIX} rather than @@ -43,24 +44,22 @@ pre-configure: -e 's|-fexpensive-optimizations||g' \ ${WRKSRC}/Makefile @${REINPLACE_CMD} \ - -e 's|RealBin/lib|RealBin/../${SITE_PERL_REL}/canu|g' \ + -e 's|RealBin/../lib/site_perl|RealBin/../${SITE_PERL_REL}/canu|g' \ ${WRKSRC}/pipelines/canu.pl # Upstream does not want to use lib/perl5/site_perl post-build: - @${MKDIR} ${WRKSRC}${PREFIX}/FreeBSD-${ARCH}/lib/perl5 - ${MV} ${WRKSRC}${PREFIX}/FreeBSD-${ARCH}/lib/site_perl \ - ${WRKSRC}${PREFIX}/FreeBSD-${ARCH}/lib/perl5 + @${MKDIR} ${WRKSRC}/build/lib/perl5 + ${MV} ${WRKSRC}/build/lib/site_perl ${WRKSRC}/build/lib/perl5 do-install: @${MKDIR} ${STAGEDIR}${PREFIX} - (cd ${WRKSRC}${PREFIX}/FreeBSD-${ARCH} && \ - ${COPYTREE_BIN} bin ${STAGEDIR}${PREFIX}) - # STRIP_CMD fails without this on 11.1 under poudriere + (cd ${WRKSRC}/build && ${COPYTREE_BIN} bin ${STAGEDIR}${PREFIX}) + # STRIP_CMD fails without this under poudriere @${CHMOD} u+w ${STAGEDIR}${PREFIX}/bin/* @${STRIP_CMD} \ `file ${STAGEDIR}${PREFIX}/bin/* | ${GREP} ELF | cut -d : -f 1` - (cd ${WRKSRC}${PREFIX}/FreeBSD-${ARCH} && \ + (cd ${WRKSRC}/build && \ ${COPYTREE_SHARE} "lib share" ${STAGEDIR}${PREFIX}) .include <bsd.port.post.mk> Modified: head/biology/canu/distinfo ============================================================================== --- head/biology/canu/distinfo Mon Sep 14 22:20:53 2020 (r548684) +++ head/biology/canu/distinfo Mon Sep 14 22:27:37 2020 (r548685) @@ -1,3 +1,3 @@ -TIMESTAMP = 1584624503 -SHA256 (marbl-canu-v2.0_GH0.tar.gz) = e2e6e8b5ec4dd4cfba5e372f4a64b2c01fbd544d4b5867746021f10771a6f4ef -SIZE (marbl-canu-v2.0_GH0.tar.gz) = 3443777 +TIMESTAMP = 1599584712 +SHA256 (canu-2.1.tar.gz) = 73c70d2d6326bdaf471549f2d1eb7a1bf1e0fbf45cdc4a830bd6ce9fe3f3c231 +SIZE (canu-2.1.tar.gz) = 3313120 Modified: head/biology/canu/files/patch-pipelines_canu_Execution.pm ============================================================================== --- head/biology/canu/files/patch-pipelines_canu_Execution.pm Mon Sep 14 22:20:53 2020 (r548684) +++ head/biology/canu/files/patch-pipelines_canu_Execution.pm Mon Sep 14 22:27:37 2020 (r548685) @@ -1,20 +1,9 @@ ---- pipelines/canu/Execution.pm.orig 2018-10-22 16:47:31 UTC +--- pipelines/canu/Execution.pm.orig 2020-09-07 19:08:24 UTC +++ pipelines/canu/Execution.pm -@@ -333,10 +333,6 @@ sub resetIteration ($) { - sub getInstallDirectory () { - my $installDir = $FindBin::RealBin; +@@ -762,8 +762,8 @@ sub submitScript ($$) { -- if ($installDir =~ m!^(.*)/\w+-\w+/bin$!) { -- $installDir = $1; -- } -- - return($installDir); - } -@@ -784,8 +780,8 @@ sub submitScript ($$) { - - -sub buildGridArray ($$$$) { - my ($name, $bgn, $end, $opt) = @_; +sub buildGridArray (@) { @@ -22,7 +11,7 @@ my $off = 0; # In some grids (SGE) this is the maximum size of an array job. -@@ -823,8 +819,42 @@ sub buildGridArray ($$$$) { +@@ -803,9 +803,43 @@ sub buildGridArray ($$$$) { $off = "-F \"$off\""; } @@ -35,7 +24,7 @@ + elsif( $opt =~ m/(ARRAY_JOBS)/ ) + { + $opt =~ s/$1/$bgn-$end/; # Replace ARRAY_JOBS with 'bgn-end' -+ + + if( lc( getGlobal( 'gridEngine' ) ) eq 'slurm' && $end > 1 ) + { + if( $name =~ m/^cormhap_/i && defined getGlobal( 'slurmCormhapCoreLimit' ) ) @@ -64,10 +53,11 @@ + } + } + } - ++ return($opt, $off); } -@@ -973,7 +1003,7 @@ sub buildGridJob ($$$$$$$$$) { + +@@ -951,7 +985,7 @@ sub buildGridJob ($$$$$$$$$) { my $jobNameT = makeUniqueJobName($jobType, $asm); my ($jobName, $jobOff) = buildGridArray($jobNameT, $bgnJob, $endJob, getGlobal("gridEngineArrayName")); Modified: head/biology/canu/pkg-plist ============================================================================== --- head/biology/canu/pkg-plist Mon Sep 14 22:20:53 2020 (r548684) +++ head/biology/canu/pkg-plist Mon Sep 14 22:27:37 2020 (r548685) @@ -5,6 +5,7 @@ bin/canu bin/canu-time bin/canu.defaults bin/correctOverlaps +bin/draw-tig bin/dumpBlob bin/edalign bin/errorEstimate @@ -13,14 +14,14 @@ bin/filterCorrectionLayouts bin/filterCorrectionOverlaps bin/findErrors bin/findErrors-Dump +bin/fixErrors bin/generateCorrectionLayouts +bin/layoutReads bin/loadCorrectedReads bin/loadErates bin/loadTrimmedReads bin/mergeRanges bin/meryl -bin/meryl-import -bin/meryl-lookup bin/mhapConvert bin/mmapConvert bin/ovStoreBucketizer @@ -37,7 +38,6 @@ bin/overlapInCore bin/overlapInCorePartition bin/overlapPair bin/prefixEditDistance-matchLimitGenerate -bin/sequence bin/splitHaplotype bin/splitReads bin/sqStoreCreate @@ -45,12 +45,10 @@ bin/sqStoreDumpFASTQ bin/sqStoreDumpMetaData bin/tgStoreCompress bin/tgStoreDump -bin/tgStoreFilter bin/tgStoreLoad bin/tgTigDisplay bin/trimReads bin/utgcns -bin/wtdbgConvert lib/libcanu.a %%SITE_PERL%%/canu/Configure.pm %%SITE_PERL%%/canu/Consensus.pm @@ -77,6 +75,3 @@ 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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