biology/canu: import canu-1.8
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
This commit is contained in:
bacon
parent
37d4115594
commit
94e269c682
8 changed files with 356 additions and 0 deletions
12
biology/canu/DESCR
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12
biology/canu/DESCR
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Canu is a fork of the Celera Assembler, designed for high-noise single-molecule
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sequencing (such as the PacBio RS II/Sequel or Oxford Nanopore MinION).
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Canu is a hierarchical assembly pipeline which runs in four steps:
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Detect overlaps in high-noise sequences using MHAP
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Generate corrected sequence consensus
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Trim corrected sequences
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Assemble trimmed corrected sequences
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80
biology/canu/Makefile
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80
biology/canu/Makefile
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# $NetBSD: Makefile,v 1.1 2019/01/07 02:33:17 bacon Exp $
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DISTNAME= canu-1.8
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CATEGORIES= biology java
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MASTER_SITES= ${MASTER_SITE_GITHUB:=marbl/}
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GITHUB_TAG= v${PKGVERSION_NOREV}
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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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# Makefile compiles directly into ${DESTDIR}${PREFIX}
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SUBST_CLASSES+= optimize
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SUBST_STAGE.optimize= pre-configure
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SUBST_SED.optimize+= -e 's|-g3||g'
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SUBST_SED.optimize+= -e 's|-O3||g'
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SUBST_SED.optimize+= -e 's|-O4||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_SED.optimize+= -e 's|-finline-functions||g'
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SUBST_FILES.optimize+= ${WRKSRC}/Makefile
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SUBST_CLASSES+= jar
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SUBST_STAGE.jar= pre-configure
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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= pre-configure
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SUBST_SED.perl+= -e 's|$$FindBin::RealBin/../lib/site_perl|${PREFIX}/${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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REPLACE_PERL+= pipelines/*.pl
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REPLACE_PERL+= bogus/*.pl
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REPLACE_PERL+= bogart-analysis/*.pl
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REPLACE_PERL+= overlapBasedTrimming/*.pl
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REPLACE_PERL+= overlapInCore-analysis/*.pl
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REPLACE_PERL+= merTrim/*.pl
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REPLACE_PERL+= erateEstimate/*.pl
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REPLACE_PERL+= meryl/.pl
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REPLACE_PERL+= fastq-utilities/*.pl
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REPLACE_PERL+= *.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-${PKGVERSION_NOREV}/src
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MAKE_ENV+= DESTDIR=${WRKSRC}
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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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${RM} -f ${TMP_INST}/bin/canu.defaults
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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/perl5 && ${PAX} -wr * ${DESTDIR}${PREFIX}/lib/perl5
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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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80
biology/canu/PLIST
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80
biology/canu/PLIST
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@comment $NetBSD: PLIST,v 1.1 2019/01/07 02:33:17 bacon Exp $
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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/correctOverlaps
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bin/dumpBlob
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bin/edalign
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bin/errorEstimate
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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/generateCorrectionLayouts
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bin/loadCorrectedReads
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bin/loadErates
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bin/loadTrimmedReads
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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/ovStoreConfig
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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/prefixEditDistance-matchLimitGenerate
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bin/readConsensus
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bin/sequence
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bin/splitHaplotype
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bin/splitReads
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bin/sqStoreCreate
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bin/sqStoreCreatePartition
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bin/sqStoreDumpFASTQ
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bin/sqStoreDumpMetaData
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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/utgcns
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bin/wtdbgConvert
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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/Execution.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/SequenceStore.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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10
biology/canu/distinfo
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10
biology/canu/distinfo
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$NetBSD: distinfo,v 1.1 2019/01/07 02:33:17 bacon Exp $
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SHA1 (canu-1.8.tar.gz) = 7dd79415aa5ecb95f05109f0d8d58f7cbfc336e9
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RMD160 (canu-1.8.tar.gz) = 78d4872b4034f526037ce225c699debd910bd586
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SHA512 (canu-1.8.tar.gz) = 650bc96675f371596f8e7748d4ab2d229f0262bf84cee8fed59af43d534d76095a72e4ba0b4a5ce9f561992268c317964cda2f6c89ee514f4920e2ba47fbc86c
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Size (canu-1.8.tar.gz) = 2465314 bytes
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SHA1 (patch-Makefile) = aa83003677cbb12558e438c776402ec48df0598d
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SHA1 (patch-pipelines_canu_Defaults.pm) = 55a4631d86abb1881b0cc997514d44c536209ea6
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SHA1 (patch-pipelines_canu_Execution.pm) = fbb080c06ea5d2393d1835a61771715d2aef0274
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SHA1 (patch-utility_objectStore.C) = c8407de79abbaf296f027f704080cc7e878b85f4
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48
biology/canu/patches/patch-Makefile
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48
biology/canu/patches/patch-Makefile
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@ -0,0 +1,48 @@
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$NetBSD: patch-Makefile,v 1.1 2019/01/07 02:33:17 bacon Exp $
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# Template Makefile requires platform-specific defaults for each OS
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# To be sent upstream following commit
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--- Makefile.orig 2018-10-22 16:47:31.000000000 +0000
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+++ Makefile
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@@ -545,6 +545,40 @@ endif
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endif
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+ifeq (${OSTYPE}, NetBSD)
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+ CC ?= gcc
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+ CXX ?= g++
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+
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+ # GCC
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+ CXXFLAGS += -pthread -fopenmp -fPIC
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+ LDFLAGS += -pthread -fopenmp -lm -lexecinfo
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+
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+ #CXXFLAGS += -Wall -Wextra -Wformat -Wno-unused -Wno-parentheses
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+ CXXFLAGS += -Wall -Wextra -Wformat -Wno-unused-function -Wno-unused-parameter -Wno-unused-variable -Wno-char-subscripts -Wno-write-strings -Wno-sign-compare -Wno-format-truncation
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+
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+ # Google Performance Tools malloc and heapchecker (HEAPCHECK=normal)
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+ #CXXFLAGS +=
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+ #LDFLAGS += -ltcmalloc
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+
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+ # Google Performance Tools cpu profiler (CPUPROFILE=/path)
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+ #CXXFLAGS +=
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+ #LDFLAGS += -lprofiler
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+
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+ # callgrind
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+ #CXXFLAGS += -g3 -Wa,--gstabs -save-temps
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+
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+ ifeq ($(BUILDOPTIMIZED), 1)
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+ else
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+ CXXFLAGS += -g3
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+ endif
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+
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+ ifeq ($(BUILDDEBUG), 1)
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+ else
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+ CXXFLAGS += -O3 -finline-functions -fomit-frame-pointer
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+ endif
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+endif
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+
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+
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ifneq (,$(findstring CYGWIN, ${OSTYPE}))
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CC ?= gcc
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CXX ?= g++
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24
biology/canu/patches/patch-pipelines_canu_Defaults.pm
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24
biology/canu/patches/patch-pipelines_canu_Defaults.pm
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$NetBSD: patch-pipelines_canu_Defaults.pm,v 1.1 2019/01/07 02:33:17 bacon Exp $
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# Add resource limits for SLURM
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# Upstream is considering a scheduler-independent approach to this feature
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--- pipelines/canu/Defaults.pm.orig 2018-06-22 08:20:52.000000000 +0000
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+++ pipelines/canu/Defaults.pm
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@@ -812,6 +812,16 @@ sub setDefaults () {
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setDefault("gridEngineArraySubmitID", undef, "Grid engine configuration, not documented");
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setDefault("gridEngineJobID", undef, "Grid engine configuration, not documented");
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+ ##### Slurm-specific parameters for controlling the number of
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+ ##### cores / tasks dispatched per step or globally (WIP)
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+
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+ setDefault( 'slurmCormhapCoreLimit', undef, 'Maximum number of cores allocated for MHAP pre-computing and alignment within the correction phase' );
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+ setDefault( 'slurmOvbCoreLimit', undef, 'Maximum number of single-core tasks dispatched for the ovlStore bucketizing step within the trimming phase' );
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+ setDefault( 'slurmOvsCoreLimit', undef, 'Maximum number of single-core tasks dispatched for the ovlStore sorting step within the trimming phase' );
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+ setDefault( 'slurmRedCoreLimit', undef, 'Maximum number of cores allocated for read error detection within the unitigging phase' );
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+ setDefault( 'slurmArrayTaskLimit', undef, 'Maximum number of tasks permitted for each step throughout assembly' );
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+ setDefault( 'slurmArrayCoreLimit', undef, 'Maximum number of cores allocated for each step throughout assembly' );
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+
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##### Grid Engine Pipeline
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setDefault("useGrid", 1, "If 'true', enable grid-based execution; if 'false', run all jobs on the local machine; if 'remote', create jobs for grid execution but do not submit; default 'true'");
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83
biology/canu/patches/patch-pipelines_canu_Execution.pm
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83
biology/canu/patches/patch-pipelines_canu_Execution.pm
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$NetBSD: patch-pipelines_canu_Execution.pm,v 1.1 2019/01/07 02:33:17 bacon Exp $
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# Add resource limits for SLURM
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# Upstream is considering a scheduler-independent approach to this feature
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--- pipelines/canu/Execution.pm.orig 2018-06-22 08:20:52.000000000 +0000
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+++ pipelines/canu/Execution.pm
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@@ -303,10 +303,6 @@ 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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@@ -694,8 +690,8 @@ sub submitScript ($$) {
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-sub buildGridArray ($$$$) {
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- my ($name, $bgn, $end, $opt) = @_;
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+sub buildGridArray (@) {
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+ my ( $name, $bgn, $end, $opt, $thr ) = @_;
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my $off = 0;
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# In some grids (SGE) this is the maximum size of an array job.
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@@ -725,8 +721,42 @@ sub buildGridArray ($$$$) {
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$off = "-F \"$off\"";
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}
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- $opt =~ s/ARRAY_NAME/$name/g; # Replace ARRAY_NAME with 'job name'
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- $opt =~ s/ARRAY_JOBS/$bgn-$end/g; # Replace ARRAY_JOBS with 'bgn-end'
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+ if( $opt =~ m/(ARRAY_NAME)/ )
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+ {
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+ $opt =~ s/$1/$name/; # Replace ARRAY_NAME with 'job name'
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+ }
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+ elsif( $opt =~ m/(ARRAY_JOBS)/ )
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+ {
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+ $opt =~ s/$1/$bgn-$end/; # Replace ARRAY_JOBS with 'bgn-end'
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+
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+ if( lc( getGlobal( 'gridEngine' ) ) eq 'slurm' && $end > 1 )
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+ {
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+ if( $name =~ m/^cormhap_/i && defined getGlobal( 'slurmCormhapCoreLimit' ) )
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+ {
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+ $opt .= '%' . int( getGlobal( 'slurmCormhapCoreLimit' ) / $thr );
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+ }
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+ elsif( $name =~ m/^ovb_/i && defined getGlobal( 'slurmOvbCoreLimit' ) )
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+ {
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+ $opt .= '%' . getGlobal( 'slurmOvbCoreLimit' );
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+ }
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+ elsif( $name =~ m/^ovs_/i && defined getGlobal( 'slurmOvsCoreLimit' ) )
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+ {
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+ $opt .= '%' . getGlobal( 'slurmOvsCoreLimit' );
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+ }
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+ elsif( $name =~ m/^red_/i && defined getGlobal( 'slurmRedCoreLimit' ) )
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+ {
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+ $opt .= '%' . int( getGlobal( 'slurmRedCoreLimit' ) / $thr );
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+ }
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+ elsif( defined getGlobal( 'slurmArrayTaskLimit' ) )
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+ {
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+ $opt .= '%' . getGlobal( 'slurmArrayTaskLimit' );
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+ }
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+ elsif( defined getGlobal( 'slurmArrayCoreLimit' ) )
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+ {
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+ $opt .= '%' . int( getGlobal( 'slurmArrayCoreLimit' ) / $thr );
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+ }
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+ }
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+ }
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return($opt, $off);
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}
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@@ -870,7 +900,7 @@ sub buildGridJob ($$$$$$$$$) {
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my $jobNameT = makeUniqueJobName($jobType, $asm);
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my ($jobName, $jobOff) = buildGridArray($jobNameT, $bgnJob, $endJob, getGlobal("gridEngineArrayName"));
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- my ($arrayOpt, $arrayOff) = buildGridArray($jobNameT, $bgnJob, $endJob, getGlobal("gridEngineArrayOption"));
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+ my ( $arrayOpt, $arrayOff ) = buildGridArray( $jobNameT, $bgnJob, $endJob, getGlobal( "gridEngineArrayOption" ), $thr );
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my $outputOption = buildOutputOption($path, $script);
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19
biology/canu/patches/patch-utility_objectStore.C
Normal file
19
biology/canu/patches/patch-utility_objectStore.C
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$NetBSD: patch-utility_objectStore.C,v 1.1 2019/01/07 02:33:17 bacon Exp $
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# NetBSD does not provide WEXITED
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# Empty bitmask should suffice in this case
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--- utility/objectStore.C.orig 2018-12-23 01:57:06.000000000 +0000
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+++ utility/objectStore.C
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@@ -286,6 +286,11 @@ fetchFromObjectStore(char *requested) {
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// Otherwise, we're still the parent, so wait for the (-1 == any) child
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// process to terminate.
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+// NetBSD does not provide WEXITED so send empty bitmask
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+#ifdef __NetBSD__
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+#define WEXITED 0
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+#endif
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+
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waitpid(-1, &err, WEXITED);
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if ((WIFEXITED(err)) &&
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Loading…
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