Add canu: Single molecule sequence assembler for genomes large and small
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043032fc8b
commit
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1
Makefile
1
Makefile
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@ -320,6 +320,7 @@ SUBDIR+= canna-lib
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SUBDIR+= canna-server
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SUBDIR+= canto-curses
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SUBDIR+= canto-daemon
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SUBDIR+= canu
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SUBDIR+= capicxx-core-runtime
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SUBDIR+= cardpeek
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SUBDIR+= cargo
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@ -0,0 +1 @@
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A single molecule sequence assembler for genomes large and small.
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@ -0,0 +1,85 @@
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# $NetBSD$
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#
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###########################################################
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# Generated by fbsd2pkg #
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# Thu Jul 20 18:34:44 CDT 2017 #
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###########################################################
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DISTNAME= canu-${PV}
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CATEGORIES= biology java
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MASTER_SITES= ${MASTER_SITE_GITHUB:=marbl/}
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GITHUB_PROJECT= canu
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GITHUB_TAG= v${PV}
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MAINTAINER= bacon@NetBSD.org
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HOMEPAGE= http://canu.readthedocs.io/
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COMMENT= Single molecule sequence assembler for genomes large and small
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LICENSE= gnu-gpl-v2
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DEPENDS+= gnuplot>0:../../graphics/gnuplot
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# Screwy Makefile compiles directly into ${DESTDIR}${PREFIX}
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SUBST_CLASSES+= optimize
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SUBST_STAGE.optimize= post-patch
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SUBST_SED.optimize+= -e 's|-O4|-O2|g'
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SUBST_SED.optimize+= -e 's|-funroll-loops||g'
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SUBST_SED.optimize+= -e 's|-fexpensive-optimizations||g'
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SUBST_FILES.optimize+= ${WRKSRC}/Makefile
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SUBST_CLASSES+= jar
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SUBST_STAGE.jar= post-patch
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SUBST_SED.jar= -e 's|\\$$bin/mhap-|${PREFIX}/${JAVAJARDIR}/mhap-|g'
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SUBST_FILES.jar= ${WRKSRC}/pipelines/canu/OverlapMhap.pm
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SUBST_CLASSES+= perl
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SUBST_STAGE.perl= post-patch
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SUBST_SED.perl= -e 's|RealBin/lib|RealBin/../${SITE_PERL_REL}|g'
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SUBST_FILES.perl= ${WRKSRC}/pipelines/canu.pl
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REPLACE_PERL+= bogart/*.pl \
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pipelines/*.pl \
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bogus/*.pl \
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bogart-analysis/*.pl \
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overlapBasedTrimming/*.pl \
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overlapInCore-analysis/*.pl \
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merTrim/*.pl \
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erateEstimate/*.pl \
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meryl/.pl \
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fastq-utilities/*.pl \
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*.pl
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# May work on other 64-bit processors, but untested
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ONLY_FOR_PLATFORM= *-*-x86_64
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USE_LANGUAGES= c c++
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USE_JAVA= run
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USE_JAVA2= 8
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USE_TOOLS+= gmake pax perl
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GCC_REQD+= 4.8
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WRKSRC= ${WRKDIR}/canu-${PV}/src
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MAKE_ENV+= DESTDIR=${WRKSRC}
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PV= 1.7
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TMP_INST= ${WRKSRC}${PREFIX}/${OPSYS}-${MACHINE_ARCH:S/x86_64/amd64/}
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SITE_PERL_REL= lib/perl5/site_perl
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JAVAJARDIR= share/java/classes
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INSTALLATION_DIRS= bin ${JAVAJARDIR}
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post-extract:
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${CHMOD} -R g-w ${WRKDIR}
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post-build:
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${MKDIR} ${TMP_INST}/lib/perl5
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${MV} ${TMP_INST}/lib/site_perl ${TMP_INST}/lib/perl5
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do-install:
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cd ${TMP_INST}/bin && ${PAX} -wr * ${DESTDIR}${PREFIX}/bin
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cd ${TMP_INST}/lib && ${PAX} -wr * ${DESTDIR}${PREFIX}/lib
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cd ${TMP_INST}/share && ${PAX} -wr * ${DESTDIR}${PREFIX}/share
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.include "../../devel/boost-libs/buildlink3.mk"
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.include "../../lang/perl5/module.mk"
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.include "../../mk/bsd.pkg.mk"
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@ -0,0 +1,93 @@
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@comment $NetBSD$
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bin/alignGFA
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bin/bogart
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bin/bogus
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bin/canu
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bin/canu.defaults
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bin/correctOverlaps
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bin/createFalconSenseInputs
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bin/dumpBlob
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bin/edalign
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bin/erateEstimate
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bin/errorEstimate
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bin/estimate-mer-threshold
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bin/existDB
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bin/falcon_sense
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bin/falconsense
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bin/fastqAnalyze
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bin/fastqSample
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bin/fastqSimulate
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bin/fastqSimulate-sort
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bin/filterCorrectionLayouts
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bin/filterCorrectionOverlaps
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bin/findErrors
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bin/findErrors-Dump
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bin/gatekeeperCreate
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bin/gatekeeperDumpFASTQ
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bin/gatekeeperDumpMetaData
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bin/gatekeeperPartition
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bin/generateCorrectionLayouts
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bin/leaff
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bin/loadCorrectedReads
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bin/loadTrimmedReads
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bin/maskMers
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bin/merTrim
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bin/meryl
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bin/mhapConvert
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bin/mmapConvert
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bin/ovStoreBucketizer
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bin/ovStoreBuild
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bin/ovStoreDump
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bin/ovStoreIndexer
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bin/ovStoreSorter
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bin/ovStoreStats
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bin/overlapConvert
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bin/overlapImport
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bin/overlapInCore
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bin/overlapInCorePartition
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bin/overlapPair
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bin/positionDB
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bin/prefixEditDistance-matchLimitGenerate
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bin/readConsensus
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bin/sequence
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bin/simple
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bin/simple-dump
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bin/splitHaplotype
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bin/splitReads
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bin/tgStoreCompress
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bin/tgStoreCoverageStat
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bin/tgStoreDump
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bin/tgStoreFilter
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bin/tgStoreLoad
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bin/tgTigDisplay
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bin/trimReads
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bin/trioCanu
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bin/utgcns
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lib/libcanu.a
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lib/libleaff.a
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lib/perl5/site_perl/canu/Configure.pm
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lib/perl5/site_perl/canu/Consensus.pm
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lib/perl5/site_perl/canu/CorrectReads.pm
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lib/perl5/site_perl/canu/Defaults.pm
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lib/perl5/site_perl/canu/ErrorEstimate.pm
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lib/perl5/site_perl/canu/Execution.pm
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lib/perl5/site_perl/canu/Gatekeeper.pm
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lib/perl5/site_perl/canu/Grid.pm
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lib/perl5/site_perl/canu/Grid_Cloud.pm
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lib/perl5/site_perl/canu/Grid_DNANexus.pm
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lib/perl5/site_perl/canu/Grid_LSF.pm
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lib/perl5/site_perl/canu/Grid_PBSTorque.pm
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lib/perl5/site_perl/canu/Grid_SGE.pm
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lib/perl5/site_perl/canu/Grid_Slurm.pm
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lib/perl5/site_perl/canu/HaplotypeReads.pm
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lib/perl5/site_perl/canu/Meryl.pm
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lib/perl5/site_perl/canu/Output.pm
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lib/perl5/site_perl/canu/OverlapBasedTrimming.pm
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lib/perl5/site_perl/canu/OverlapErrorAdjustment.pm
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lib/perl5/site_perl/canu/OverlapInCore.pm
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lib/perl5/site_perl/canu/OverlapMMap.pm
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lib/perl5/site_perl/canu/OverlapMhap.pm
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lib/perl5/site_perl/canu/OverlapStore.pm
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lib/perl5/site_perl/canu/Report.pm
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lib/perl5/site_perl/canu/Unitig.pm
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share/java/classes/mhap-2.1.3.jar
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@ -0,0 +1,7 @@
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$NetBSD$
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SHA1 (canu-1.7.tar.gz) = aaaafd8516be5e4d725af407bc84b3c6f178b2ac
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RMD160 (canu-1.7.tar.gz) = bd394bb6dcebd43d2793ca1aa9bd60ec6be75beb
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SHA512 (canu-1.7.tar.gz) = dbc1dca4df4117521143843bb781227f4dfde5ba7068e47b51ccf9e9dba45eb2629b5773531e4f362f1df05eab3f1a62088c5fa231d3624af23f11d97e7a4edf
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Size (canu-1.7.tar.gz) = 2533016 bytes
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SHA1 (patch-pipelines_canu_Execution.pm) = 4f9d343e03cc802b90616844cb331b78793bd368
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@ -0,0 +1,16 @@
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$NetBSD$
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# Eliminate assumptions about install dir name
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--- pipelines/canu/Execution.pm.orig 2017-04-17 19:32:38.000000000 +0000
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+++ pipelines/canu/Execution.pm
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@@ -293,10 +293,6 @@ sub skipStage ($$@) {
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sub getInstallDirectory () {
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my $installDir = $FindBin::RealBin;
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- if ($installDir =~ m!^(.*)/\w+-\w+/bin$!) {
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- $installDir = $1;
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- }
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-
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return($installDir);
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}
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