biology/canu: Upgrade to 1.9

Numerous bug fixes and enhancements

Reported by:    portscout

4 files changed, 12 insertions, 127 deletions

diff --git a/biology/canu/Makefile b/biology/canu/Makefile
index ed3a3a71cc62..f6c7bd2cb9d9 100644
--- a/biology/canu/Makefile
+++ b/biology/canu/Makefile
@@ -2,8 +2,7 @@
 
 PORTNAME=		canu
 DISTVERSIONPREFIX=	v
-DISTVERSION=		1.8
-PORTREVISION=		5
+DISTVERSION=		1.9
 CATEGORIES=		biology java perl5
 
 MAINTAINER=	jwb@FreeBSD.org
diff --git a/biology/canu/distinfo b/biology/canu/distinfo
index 9e529290b348..fee05527429e 100644
--- a/biology/canu/distinfo
+++ b/biology/canu/distinfo
@@ -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
diff --git a/biology/canu/files/patch-Makefile b/biology/canu/files/patch-Makefile
deleted file mode 100644
index eba17f05a383..000000000000
--- a/biology/canu/files/patch-Makefile
+++ /dev/null
@@ -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}))
diff --git a/biology/canu/pkg-plist b/biology/canu/pkg-plist
index cad6d136ed16..9cbcc2da4872 100644
--- a/biology/canu/pkg-plist
+++ b/biology/canu/pkg-plist
@@ -2,16 +2,13 @@ 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
@@ -20,7 +17,10 @@ bin/generateCorrectionLayouts
 bin/loadCorrectedReads
 bin/loadErates
 bin/loadTrimmedReads
+bin/mergeRanges
 bin/meryl
+bin/meryl-import
+bin/meryl-lookup
 bin/mhapConvert
 bin/mmapConvert
 bin/ovStoreBucketizer
@@ -30,13 +30,13 @@ 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
@@ -45,7 +45,6 @@ bin/sqStoreCreatePartition
 bin/sqStoreDumpFASTQ
 bin/sqStoreDumpMetaData
 bin/tgStoreCompress
-bin/tgStoreCoverageStat
 bin/tgStoreDump
 bin/tgStoreFilter
 bin/tgStoreLoad
@@ -79,3 +78,6 @@ lib/libcanu.a
 %%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