Date: Thu, 26 Apr 2018 04:16:15 +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: r468321 - in head/biology/canu: . files Message-ID: <201804260416.w3Q4GF9L099719@repo.freebsd.org>
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Author: jwb Date: Thu Apr 26 04:16:15 2018 New Revision: 468321 URL: https://svnweb.freebsd.org/changeset/ports/468321 Log: biology/canu: Upgrade to 1.7 release Approved by: jrm (mentor) Differential Revision: https://reviews.freebsd.org/D15201 Added: head/biology/canu/files/patch-pipelines_canu_Execution.pm (contents, props changed) Deleted: head/biology/canu/files/patch-src_pipelines_canu_Execution.pm Modified: head/biology/canu/Makefile head/biology/canu/distinfo (contents, props changed) head/biology/canu/pkg-descr (contents, props changed) head/biology/canu/pkg-plist (contents, props changed) Modified: head/biology/canu/Makefile ============================================================================== --- head/biology/canu/Makefile Thu Apr 26 02:03:28 2018 (r468320) +++ head/biology/canu/Makefile Thu Apr 26 04:16:15 2018 (r468321) @@ -1,16 +1,15 @@ # $FreeBSD$ -PORTNAME= canu +PORTNAME= canu DISTVERSIONPREFIX= v -DISTVERSION= 1.6 -PORTREVISION= 3 -CATEGORIES= biology java perl5 +DISTVERSION= 1.7 +CATEGORIES= biology java perl5 MAINTAINER= jwb@FreeBSD.org COMMENT= Single molecule sequence assembler LICENSE= GPLv2 -LICENSE_FILE= ${WRKSRC}/README.license.GPL +LICENSE_FILE= ${WRKDIR}/${PORTNAME}-${PORTVERSION}/README.license.GPL LIB_DEPENDS= libboost_regex.so:devel/boost-libs RUN_DEPENDS= gnuplot:math/gnuplot @@ -19,14 +18,12 @@ USES= compiler:openmp gmake perl5 USE_JAVA= yes JAVA_RUN= yes JAVA_VERSION= 1.8+ - USE_GITHUB= yes GH_ACCOUNT= marbl -BUILD_WRKSRC= ${WRKSRC}/src - +WRKSRC_SUBDIR= src # Makefile compiles directly into ${DESTDIR}${PREFIX} -MAKE_ENV+= DESTDIR=${BUILD_WRKSRC} +MAKE_ENV+= DESTDIR=${WRKSRC} post-patch: ${REINPLACE_CMD} \ @@ -34,33 +31,27 @@ post-patch: -e 's|-funroll-loops||g' \ -e 's|-fexpensive-optimizations||g' \ -e 's|amd64|${ARCH}|g' \ - ${BUILD_WRKSRC}/Makefile + ${WRKSRC}/Makefile ${REINPLACE_CMD} -e 's|\\$$bin/mhap-|${JAVAJARDIR}/mhap-|g' \ - ${BUILD_WRKSRC}/pipelines/canu/OverlapMhap.pm + ${WRKSRC}/pipelines/canu/OverlapMhap.pm ${REINPLACE_CMD} -e 's|RealBin/lib|RealBin/../${SITE_PERL_REL}/canu|g' \ - ${BUILD_WRKSRC}/pipelines/canu.pl + ${WRKSRC}/pipelines/canu.pl -# Reorganize according to filesystem hierarchy standard +# Upstream does not want to use lib/perl5/site_perl post-build: - @${MKDIR} ${BUILD_WRKSRC}${PREFIX}/FreeBSD-${ARCH}/${SITE_PERL_REL} - @${MV} ${BUILD_WRKSRC}${PREFIX}/FreeBSD-${ARCH}/bin/lib/canu \ - ${BUILD_WRKSRC}${PREFIX}/FreeBSD-${ARCH}/${SITE_PERL_REL} - @${RMDIR} ${BUILD_WRKSRC}${PREFIX}/FreeBSD-${ARCH}/bin/lib - @${MV} ${BUILD_WRKSRC}${PREFIX}/FreeBSD-${ARCH}/bin/*.a \ - ${BUILD_WRKSRC}${PREFIX}/FreeBSD-${ARCH}/lib - @${MKDIR} ${BUILD_WRKSRC}${PREFIX}/FreeBSD-${ARCH}/${JAVAJARDIR:S,^${PREFIX}/,,} - @${MV} ${BUILD_WRKSRC}${PREFIX}/FreeBSD-${ARCH}/bin/*.jar \ - ${BUILD_WRKSRC}${PREFIX}/FreeBSD-${ARCH}/${JAVAJARDIR:S,^${PREFIX}/,,} - @${RM} ${BUILD_WRKSRC}${PREFIX}/FreeBSD-${ARCH}/bin/canu.defaults + ${MKDIR} ${WRKSRC}${PREFIX}/FreeBSD-${ARCH}/lib/perl5 + ${MV} ${WRKSRC}${PREFIX}/FreeBSD-${ARCH}/lib/site_perl \ + ${WRKSRC}${PREFIX}/FreeBSD-${ARCH}/lib/perl5 do-install: - cd ${BUILD_WRKSRC}${PREFIX}/FreeBSD-${ARCH} && ${COPYTREE_BIN} bin \ - ${STAGEDIR}${PREFIX} + ${MKDIR} ${STAGEDIR}${PREFIX} + (cd ${WRKSRC}${PREFIX}/FreeBSD-${ARCH} && \ + ${COPYTREE_BIN} bin ${STAGEDIR}${PREFIX}) # STRIP_CMD fails without this on 11.1 under poudriere @${CHMOD} u+w ${STAGEDIR}${PREFIX}/bin/* ${STRIP_CMD} \ `file ${STAGEDIR}${PREFIX}/bin/* | ${GREP} ELF | cut -d : -f 1` - cd ${BUILD_WRKSRC}${PREFIX}/FreeBSD-${ARCH} && ${COPYTREE_SHARE} "lib share" \ - ${STAGEDIR}${PREFIX} + (cd ${WRKSRC}${PREFIX}/FreeBSD-${ARCH} && \ + ${COPYTREE_SHARE} "lib share" ${STAGEDIR}${PREFIX}) .include <bsd.port.mk> Modified: head/biology/canu/distinfo ============================================================================== --- head/biology/canu/distinfo Thu Apr 26 02:03:28 2018 (r468320) +++ head/biology/canu/distinfo Thu Apr 26 04:16:15 2018 (r468321) @@ -1,3 +1,3 @@ -TIMESTAMP = 1507077399 -SHA256 (marbl-canu-v1.6_GH0.tar.gz) = 470e0ac761d69d1fecab85da810a6474b1e2387d7124290a0e4124d660766498 -SIZE (marbl-canu-v1.6_GH0.tar.gz) = 2486338 +TIMESTAMP = 1524325169 +SHA256 (marbl-canu-v1.7_GH0.tar.gz) = c5be54b0ad20729093413e7e722a19637d32e966dc8ecd2b579ba3e4958d378a +SIZE (marbl-canu-v1.7_GH0.tar.gz) = 2533016 Added: head/biology/canu/files/patch-pipelines_canu_Execution.pm ============================================================================== --- /dev/null 00:00:00 1970 (empty, because file is newly added) +++ head/biology/canu/files/patch-pipelines_canu_Execution.pm Thu Apr 26 04:16:15 2018 (r468321) @@ -0,0 +1,15 @@ +$NetBSD$ + +--- pipelines/canu/Execution.pm.orig 2017-04-17 19:32:38 UTC ++++ pipelines/canu/Execution.pm +@@ -293,10 +293,6 @@ sub skipStage ($$@) { + sub getInstallDirectory () { + my $installDir = $FindBin::RealBin; + +- if ($installDir =~ m!^(.*)/\w+-\w+/bin$!) { +- $installDir = $1; +- } +- + return($installDir); + } + Modified: head/biology/canu/pkg-descr ============================================================================== --- head/biology/canu/pkg-descr Thu Apr 26 02:03:28 2018 (r468320) +++ head/biology/canu/pkg-descr Thu Apr 26 04:16:15 2018 (r468321) @@ -1,4 +1,14 @@ -Canu is a fork of the Celera Assembler designed for high-noise single-molecule -sequencing (such as the PacBio RSII or Oxford Nanopore MinION). +Canu is a fork of the Celera Assembler, designed for high-noise single-molecule +sequencing (such as the PacBio RS II/Sequel or Oxford Nanopore MinION). + +Canu is a hierarchical assembly pipeline which runs in four steps: + + Detect overlaps in high-noise sequences using MHAP + + Generate corrected sequence consensus + + Trim corrected sequences + + Assemble trimmed corrected sequences WWW: http://canu.readthedocs.io/ Modified: head/biology/canu/pkg-plist ============================================================================== --- head/biology/canu/pkg-plist Thu Apr 26 02:03:28 2018 (r468320) +++ head/biology/canu/pkg-plist Thu Apr 26 04:16:15 2018 (r468321) @@ -2,17 +2,22 @@ bin/alignGFA bin/bogart bin/bogus bin/canu +bin/canu.defaults bin/correctOverlaps bin/createFalconSenseInputs +bin/dumpBlob +bin/edalign bin/erateEstimate bin/errorEstimate bin/estimate-mer-threshold bin/existDB bin/falcon_sense +bin/falconsense bin/fastqAnalyze bin/fastqSample bin/fastqSimulate bin/fastqSimulate-sort +bin/filterCorrectionLayouts bin/filterCorrectionOverlaps bin/findErrors bin/findErrors-Dump @@ -22,6 +27,8 @@ bin/gatekeeperDumpMetaData bin/gatekeeperPartition bin/generateCorrectionLayouts bin/leaff +bin/loadCorrectedReads +bin/loadTrimmedReads bin/maskMers bin/merTrim bin/meryl @@ -41,7 +48,10 @@ bin/overlapPair bin/positionDB bin/prefixEditDistance-matchLimitGenerate bin/readConsensus +bin/sequence bin/simple +bin/simple-dump +bin/splitHaplotype bin/splitReads bin/tgStoreCompress bin/tgStoreCoverageStat @@ -50,6 +60,7 @@ bin/tgStoreFilter bin/tgStoreLoad bin/tgTigDisplay bin/trimReads +bin/trioCanu bin/utgcns lib/libcanu.a lib/libleaff.a @@ -67,7 +78,7 @@ lib/libleaff.a %%SITE_PERL%%/canu/Grid_PBSTorque.pm %%SITE_PERL%%/canu/Grid_SGE.pm %%SITE_PERL%%/canu/Grid_Slurm.pm -%%SITE_PERL%%/canu/HTML.pm +%%SITE_PERL%%/canu/HaplotypeReads.pm %%SITE_PERL%%/canu/Meryl.pm %%SITE_PERL%%/canu/Output.pm %%SITE_PERL%%/canu/OverlapBasedTrimming.pm @@ -78,4 +89,4 @@ lib/libleaff.a %%SITE_PERL%%/canu/OverlapStore.pm %%SITE_PERL%%/canu/Report.pm %%SITE_PERL%%/canu/Unitig.pm -%%JAVAJARDIR%%/mhap-2.1.2.jar +%%JAVAJARDIR%%/mhap-2.1.3.jar
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