Index: head/biology/canu/Makefile
===================================================================
--- head/biology/canu/Makefile	(revision 528791)
+++ head/biology/canu/Makefile	(revision 528792)
@@ -1,68 +1,64 @@
 # $FreeBSD$
 
 PORTNAME=		canu
 DISTVERSIONPREFIX=	v
-DISTVERSION=		1.9
-PORTREVISION=		1
+DISTVERSION=		2.0
 CATEGORIES=		biology java perl5
 
 MAINTAINER=	jwb@FreeBSD.org
 COMMENT=	Single molecule sequence assembler
 
 LICENSE=	GPLv2
 LICENSE_FILE=	${WRKDIR}/${PORTNAME}-${PORTVERSION}/README.license.GPL
 
 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
 # using a separate install target.
 MAKE_ENV=	DESTDIR=${WRKSRC} CANU_BUILD_ENV=ports
 
 .include <bsd.port.pre.mk>
 
 # GCC 4.2.1 (still base compiler on some 2nd tier platforms) cannot build canu
 .if ${COMPILER_TYPE} == gcc && ${COMPILER_VERSION} <= 42
 USE_GCC=	yes
 .endif
 
 pre-configure:
 	@${REINPLACE_CMD} \
 		-e 's|-O4||g' \
 		-e 's|-funroll-loops||g' \
 		-e 's|-fexpensive-optimizations||g' \
 		${WRKSRC}/Makefile
-	@${REINPLACE_CMD} \
-		-e 's|\\$$bin/mhap-|${JAVAJARDIR}/mhap-|g' \
-		${WRKSRC}/pipelines/canu/OverlapMhap.pm
 	@${REINPLACE_CMD} \
 		-e 's|RealBin/lib|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
 
 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
 	@${CHMOD} u+w ${STAGEDIR}${PREFIX}/bin/*
 	@${STRIP_CMD} \
 		`file ${STAGEDIR}${PREFIX}/bin/* | ${GREP} ELF | cut -d : -f 1`
 	(cd ${WRKSRC}${PREFIX}/FreeBSD-${ARCH} && \
 		${COPYTREE_SHARE} "lib share" ${STAGEDIR}${PREFIX})
 
 .include <bsd.port.post.mk>
Index: head/biology/canu/distinfo
===================================================================
--- head/biology/canu/distinfo	(revision 528791)
+++ head/biology/canu/distinfo	(revision 528792)
@@ -1,3 +1,3 @@
-TIMESTAMP = 1573142752
-SHA256 (marbl-canu-v1.9_GH0.tar.gz) = 6b086ab6086c050752166500378bc4b3b3543d4c617863e894d296171cee3385
-SIZE (marbl-canu-v1.9_GH0.tar.gz) = 3410307
+TIMESTAMP = 1584624503
+SHA256 (marbl-canu-v2.0_GH0.tar.gz) = e2e6e8b5ec4dd4cfba5e372f4a64b2c01fbd544d4b5867746021f10771a6f4ef
+SIZE (marbl-canu-v2.0_GH0.tar.gz) = 3443777
Index: head/biology/canu/pkg-plist
===================================================================
--- head/biology/canu/pkg-plist	(revision 528791)
+++ head/biology/canu/pkg-plist	(revision 528792)
@@ -1,83 +1,82 @@
 bin/alignGFA
 bin/bogart
 bin/bogus
 bin/canu
 bin/canu-time
 bin/canu.defaults
 bin/correctOverlaps
 bin/dumpBlob
 bin/edalign
 bin/errorEstimate
 bin/falconsense
 bin/filterCorrectionLayouts
 bin/filterCorrectionOverlaps
 bin/findErrors
 bin/findErrors-Dump
 bin/generateCorrectionLayouts
 bin/loadCorrectedReads
 bin/loadErates
 bin/loadTrimmedReads
 bin/mergeRanges
 bin/meryl
 bin/meryl-import
 bin/meryl-lookup
 bin/mhapConvert
 bin/mmapConvert
 bin/ovStoreBucketizer
 bin/ovStoreBuild
 bin/ovStoreConfig
 bin/ovStoreDump
 bin/ovStoreIndexer
 bin/ovStoreSorter
 bin/ovStoreStats
 bin/overlapAlign
 bin/overlapConvert
 bin/overlapImport
 bin/overlapInCore
 bin/overlapInCorePartition
 bin/overlapPair
 bin/prefixEditDistance-matchLimitGenerate
 bin/sequence
 bin/splitHaplotype
 bin/splitReads
 bin/sqStoreCreate
-bin/sqStoreCreatePartition
 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
 %%SITE_PERL%%/canu/CorrectReads.pm
 %%SITE_PERL%%/canu/Defaults.pm
 %%SITE_PERL%%/canu/Execution.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/HaplotypeReads.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/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