Index: head/biology/canu/Makefile
===================================================================
--- head/biology/canu/Makefile	(revision 517065)
+++ head/biology/canu/Makefile	(revision 517066)
@@ -1,68 +1,67 @@
 # $FreeBSD$
 
 PORTNAME=		canu
 DISTVERSIONPREFIX=	v
-DISTVERSION=		1.8
-PORTREVISION=		5
+DISTVERSION=		1.9
 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 517065)
+++ head/biology/canu/distinfo	(revision 517066)
@@ -1,3 +1,3 @@
-TIMESTAMP = 1540317173
-SHA256 (marbl-canu-v1.8_GH0.tar.gz) = 30ecfe574166f54f79606038830f68927cf0efab33bdc3c6e43fd1448fa0b2e4
-SIZE (marbl-canu-v1.8_GH0.tar.gz) = 2465314
+TIMESTAMP = 1573142752
+SHA256 (marbl-canu-v1.9_GH0.tar.gz) = 6b086ab6086c050752166500378bc4b3b3543d4c617863e894d296171cee3385
+SIZE (marbl-canu-v1.9_GH0.tar.gz) = 3410307
Index: head/biology/canu/files/patch-Makefile
===================================================================
--- head/biology/canu/files/patch-Makefile	(revision 517065)
+++ head/biology/canu/files/patch-Makefile	(nonexistent)
@@ -1,116 +0,0 @@
---- Makefile.orig	2018-10-22 16:47:31 UTC
-+++ Makefile
-@@ -481,68 +481,65 @@ endif
- 
- 
- ifeq (${OSTYPE}, FreeBSD)
--ifeq (${MACHINETYPE}, amd64)
--  CC       ?= gcc48
--  CXX      ?= g++48
- 
--  #  GCC
--  CXXFLAGS  += -I/usr/local/include -D_GLIBCXX_PARALLEL -pthread -fopenmp -fPIC
--  LDFLAGS   += -L/usr/local/lib     -D_GLIBCXX_PARALLEL -pthread -fopenmp -rpath /usr/local/lib/gcc48 -lm -lexecinfo
-+  ifeq (${CANU_BUILD_ENV}, ports)
- 
--  #  CLANG
--  #CXXFLAGS  += -I/usr/local/include -D_GLIBCXX_PARALLEL -pthread -fPIC
--  #LDFLAGS   += -L/usr/local/lib     -D_GLIBCXX_PARALLEL -pthread -lm -lexecinfo -lgomp
-+    #################################################
-+    # If compiling within ports system (recommended)
-+    #################################################
- 
--  #CXXFLAGS  += -Wall -Wextra -Wformat  -Wno-unused   -Wno-parentheses
--  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
-+    # Use architecture as defined by ports rather than uname
-+    # ${ARCH} matches uname -p, not uname -m
-+    MACHINETYPE=${ARCH}
- 
--  #  Google Performance Tools malloc and heapchecker (HEAPCHECK=normal)
--  #CXXFLAGS  +=
--  #LDFLAGS   += -ltcmalloc
-+    # Take compiler and most flags from the env and make command line
-+    CXXFLAGS  += -D_GLIBCXX_PARALLEL -fPIC -pthread -fopenmp
-+    LDFLAGS   += -D_GLIBCXX_PARALLEL -pthread -fopenmp
- 
--  #  Google Performance Tools cpu profiler (CPUPROFILE=/path)
--  #CXXFLAGS  +=
--  #LDFLAGS   += -lprofiler
-+  else
- 
--  #  callgrind
--  #CXXFLAGS  += -g3 -Wa,--gstabs -save-temps
-+    ######################################################
-+    # If compiling outside ports system (not recommended)
-+    ######################################################
- 
--  ifeq ($(BUILDOPTIMIZED), 1)
--  else
--    CXXFLAGS += -g3
--  endif
-+    CC       ?= gcc48
-+    CXX      ?= g++48
- 
--  ifeq ($(BUILDDEBUG), 1)
--  else
--    CXXFLAGS += -O3 -funroll-loops -fexpensive-optimizations -finline-functions -fomit-frame-pointer
--  endif
--endif
--endif
-+    #  GCC
-+    CXXFLAGS  += -I/usr/local/include -D_GLIBCXX_PARALLEL -pthread -fopenmp -fPIC
-+    LDFLAGS   += -L/usr/local/lib     -D_GLIBCXX_PARALLEL -pthread -fopenmp -rpath /usr/local/lib/gcc48 -lm -lexecinfo
- 
-+    #  CLANG
-+    #CXXFLAGS  += -I/usr/local/include -D_GLIBCXX_PARALLEL -pthread -fPIC
-+    #LDFLAGS   += -L/usr/local/lib     -D_GLIBCXX_PARALLEL -pthread -lm -lexecinfo -lgomp
- 
--ifeq (${OSTYPE}, FreeBSD)
--ifeq (${MACHINETYPE}, arm)
--  CC       ?= gcc48
--  CXX      ?= g++48
-+    #CXXFLAGS  += -Wall -Wextra -Wformat  -Wno-unused   -Wno-parentheses
-+    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
- 
--  CXXFLAGS  += -I/usr/local/include -D_GLIBCXX_PARALLEL -pthread -fopenmp -fPIC
--  LDFLAGS   += -L/usr/local/lib     -D_GLIBCXX_PARALLEL -pthread -fopenmp -rpath /usr/local/lib/gcc48 -lm
-+    #  Google Performance Tools malloc and heapchecker (HEAPCHECK=normal)
-+    #CXXFLAGS  +=
-+    #LDFLAGS   += -ltcmalloc
- 
--  CXXFLAGS  += -Wall -Wextra -Wno-write-strings -Wno-unused -Wno-char-subscripts -Wno-sign-compare -Wformat -Wno-parentheses
--  CXXFLAGS  += -funroll-loops -fomit-frame-pointer
--  LDFLAGS   += 
-+    #  Google Performance Tools cpu profiler (CPUPROFILE=/path)
-+    #CXXFLAGS  +=
-+    #LDFLAGS   += -lprofiler
- 
--  ifeq ($(BUILDOPTIMIZED), 1)
--  else
--    CXXFLAGS += -g3
--  endif
-+    #  callgrind
-+    #CXXFLAGS  += -g3 -Wa,--gstabs -save-temps
- 
--  ifeq ($(BUILDDEBUG), 1)
--  else
--    CXXFLAGS += -O4 -funroll-loops -fexpensive-optimizations -finline-functions -fomit-frame-pointer
--  endif
--endif
--endif
-+    ifeq ($(BUILDOPTIMIZED), 1)
-+    else
-+      CXXFLAGS += -g3
-+    endif
-+
-+    ifeq ($(BUILDDEBUG), 1)
-+    else
-+      CXXFLAGS += -O3 -funroll-loops -fexpensive-optimizations -finline-functions -fomit-frame-pointer
-+    endif
-+
-+  endif		# CANU_BUILD_ENV
-+
-+endif		# FreeBSD
- 
- 
- ifneq (,$(findstring CYGWIN, ${OSTYPE}))

Property changes on: head/biology/canu/files/patch-Makefile
___________________________________________________________________
Deleted: fbsd:nokeywords
## -1 +0,0 ##
-yes
\ No newline at end of property
Deleted: svn:eol-style
## -1 +0,0 ##
-native
\ No newline at end of property
Deleted: svn:mime-type
## -1 +0,0 ##
-text/plain
\ No newline at end of property
Index: head/biology/canu/pkg-plist
===================================================================
--- head/biology/canu/pkg-plist	(revision 517065)
+++ head/biology/canu/pkg-plist	(revision 517066)
@@ -1,81 +1,83 @@
 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/fastqAnalyze
-bin/fastqSample
-bin/fastqSimulate
-bin/fastqSimulate-sort
 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/readConsensus
 bin/sequence
 bin/splitHaplotype
 bin/splitReads
 bin/sqStoreCreate
 bin/sqStoreCreatePartition
 bin/sqStoreDumpFASTQ
 bin/sqStoreDumpMetaData
 bin/tgStoreCompress
-bin/tgStoreCoverageStat
 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