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Bacon" Date: Fri, 22 Dec 2017 01:30:27 +0000 (UTC) To: ports-committers@freebsd.org, svn-ports-all@freebsd.org, svn-ports-head@freebsd.org Subject: svn commit: r456950 - in head/biology: . canu canu/files X-SVN-Group: ports-head X-SVN-Commit-Author: jwb X-SVN-Commit-Paths: in head/biology: . canu canu/files X-SVN-Commit-Revision: 456950 X-SVN-Commit-Repository: ports MIME-Version: 1.0 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: 8bit X-BeenThere: svn-ports-all@freebsd.org X-Mailman-Version: 2.1.25 Precedence: list List-Id: SVN commit messages for the ports tree List-Unsubscribe: , List-Archive: List-Post: List-Help: List-Subscribe: , X-List-Received-Date: Fri, 22 Dec 2017 01:30:28 -0000 Author: jwb Date: Fri Dec 22 01:30:26 2017 New Revision: 456950 URL: https://svnweb.freebsd.org/changeset/ports/456950 Log: [new port] biology/canu: Single molecule sequence assembler Approved by: jrm (mentor) or wen (mentor) Differential Revision: https://reviews.freebsd.org/D13574 Added: head/biology/canu/ head/biology/canu/Makefile (contents, props changed) head/biology/canu/distinfo (contents, props changed) head/biology/canu/files/ head/biology/canu/files/patch-src_pipelines_canu_Execution.pm (contents, props changed) head/biology/canu/pkg-descr (contents, props changed) head/biology/canu/pkg-plist (contents, props changed) Modified: head/biology/Makefile Modified: head/biology/Makefile ============================================================================== --- head/biology/Makefile Thu Dec 21 21:44:45 2017 (r456949) +++ head/biology/Makefile Fri Dec 22 01:30:26 2017 (r456950) @@ -14,6 +14,7 @@ SUBDIR += bowtie SUBDIR += bowtie2 SUBDIR += bwa + SUBDIR += canu SUBDIR += cd-hit SUBDIR += cdbfasta SUBDIR += chemeq Added: head/biology/canu/Makefile ============================================================================== --- /dev/null 00:00:00 1970 (empty, because file is newly added) +++ head/biology/canu/Makefile Fri Dec 22 01:30:26 2017 (r456950) @@ -0,0 +1,65 @@ +# $FreeBSD$ + +PORTNAME= canu +DISTVERSIONPREFIX= v +DISTVERSION= 1.6 +CATEGORIES= biology java perl5 + +MAINTAINER= jwb@FreeBSD.org +COMMENT= Single molecule sequence assembler + +LICENSE= GPLv2 +LICENSE_FILE= ${WRKSRC}/README.license.GPL + +LIB_DEPENDS+= libboost_regex.so:devel/boost-libs +RUN_DEPENDS+= gnuplot:math/gnuplot + +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 + +# Makefile compiles directly into ${DESTDIR}${PREFIX} +MAKE_ENV+= DESTDIR=${BUILD_WRKSRC} + +post-patch: + ${REINPLACE_CMD} \ + -e 's|-O4||g' \ + -e 's|-funroll-loops||g' \ + -e 's|-fexpensive-optimizations||g' \ + -e 's|amd64|${ARCH}|g' \ + ${BUILD_WRKSRC}/Makefile + ${REINPLACE_CMD} -e 's|\\$$bin/mhap-|${JAVAJARDIR}/mhap-|g' \ + ${BUILD_WRKSRC}/pipelines/canu/OverlapMhap.pm + ${REINPLACE_CMD} -e 's|RealBin/lib|RealBin/../${SITE_PERL_REL}/canu|g' \ + ${BUILD_WRKSRC}/pipelines/canu.pl + +# Reorganize according to filesystem hierarchy standard +post-build: + @${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 + +do-install: + cd ${BUILD_WRKSRC}${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} + +.include Added: head/biology/canu/distinfo ============================================================================== --- /dev/null 00:00:00 1970 (empty, because file is newly added) +++ head/biology/canu/distinfo Fri Dec 22 01:30:26 2017 (r456950) @@ -0,0 +1,3 @@ +TIMESTAMP = 1507077399 +SHA256 (marbl-canu-v1.6_GH0.tar.gz) = 470e0ac761d69d1fecab85da810a6474b1e2387d7124290a0e4124d660766498 +SIZE (marbl-canu-v1.6_GH0.tar.gz) = 2486338 Added: head/biology/canu/files/patch-src_pipelines_canu_Execution.pm ============================================================================== --- /dev/null 00:00:00 1970 (empty, because file is newly added) +++ head/biology/canu/files/patch-src_pipelines_canu_Execution.pm Fri Dec 22 01:30:26 2017 (r456950) @@ -0,0 +1,13 @@ +--- src/pipelines/canu/Execution.pm.orig 2017-08-14 19:39:19 UTC ++++ src/pipelines/canu/Execution.pm +@@ -302,10 +302,6 @@ sub skipStage ($$@) { + sub getInstallDirectory () { + my $installDir = $FindBin::RealBin; + +- if ($installDir =~ m!^(.*)/\w+-\w+/bin$!) { +- $installDir = $1; +- } +- + return($installDir); + } + Added: head/biology/canu/pkg-descr ============================================================================== --- /dev/null 00:00:00 1970 (empty, because file is newly added) +++ head/biology/canu/pkg-descr Fri Dec 22 01:30:26 2017 (r456950) @@ -0,0 +1,4 @@ +Canu is a fork of the Celera Assembler designed for high-noise single-molecule +sequencing (such as the PacBio RSII or Oxford Nanopore MinION). + +WWW: http://canu.readthedocs.io/ Added: head/biology/canu/pkg-plist ============================================================================== --- /dev/null 00:00:00 1970 (empty, because file is newly added) +++ head/biology/canu/pkg-plist Fri Dec 22 01:30:26 2017 (r456950) @@ -0,0 +1,81 @@ +bin/alignGFA +bin/bogart +bin/bogus +bin/canu +bin/correctOverlaps +bin/createFalconSenseInputs +bin/erateEstimate +bin/errorEstimate +bin/estimate-mer-threshold +bin/existDB +bin/falcon_sense +bin/fastqAnalyze +bin/fastqSample +bin/fastqSimulate +bin/fastqSimulate-sort +bin/filterCorrectionOverlaps +bin/findErrors +bin/findErrors-Dump +bin/gatekeeperCreate +bin/gatekeeperDumpFASTQ +bin/gatekeeperDumpMetaData +bin/gatekeeperPartition +bin/generateCorrectionLayouts +bin/leaff +bin/maskMers +bin/merTrim +bin/meryl +bin/mhapConvert +bin/mmapConvert +bin/ovStoreBucketizer +bin/ovStoreBuild +bin/ovStoreDump +bin/ovStoreIndexer +bin/ovStoreSorter +bin/ovStoreStats +bin/overlapConvert +bin/overlapImport +bin/overlapInCore +bin/overlapInCorePartition +bin/overlapPair +bin/positionDB +bin/prefixEditDistance-matchLimitGenerate +bin/readConsensus +bin/simple +bin/splitReads +bin/tgStoreCompress +bin/tgStoreCoverageStat +bin/tgStoreDump +bin/tgStoreFilter +bin/tgStoreLoad +bin/tgTigDisplay +bin/trimReads +bin/utgcns +lib/libcanu.a +lib/libleaff.a +%%SITE_PERL%%/canu/Configure.pm +%%SITE_PERL%%/canu/Consensus.pm +%%SITE_PERL%%/canu/CorrectReads.pm +%%SITE_PERL%%/canu/Defaults.pm +%%SITE_PERL%%/canu/ErrorEstimate.pm +%%SITE_PERL%%/canu/Execution.pm +%%SITE_PERL%%/canu/Gatekeeper.pm +%%SITE_PERL%%/canu/Grid.pm +%%SITE_PERL%%/canu/Grid_Cloud.pm +%%SITE_PERL%%/canu/Grid_DNANexus.pm +%%SITE_PERL%%/canu/Grid_LSF.pm +%%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/Meryl.pm +%%SITE_PERL%%/canu/Output.pm +%%SITE_PERL%%/canu/OverlapBasedTrimming.pm +%%SITE_PERL%%/canu/OverlapErrorAdjustment.pm +%%SITE_PERL%%/canu/OverlapInCore.pm +%%SITE_PERL%%/canu/OverlapMMap.pm +%%SITE_PERL%%/canu/OverlapMhap.pm +%%SITE_PERL%%/canu/OverlapStore.pm +%%SITE_PERL%%/canu/Report.pm +%%SITE_PERL%%/canu/Unitig.pm +%%JAVAJARDIR%%/mhap-2.1.2.jar