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biology/canu: Upgrade to 1.9

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Numerous bug fixes and enhancements

Reported by:    portscout
This commit is contained in:
Jason W. Bacon 2019-11-08 14:03:15 +00:00
parent 0ff2775088
commit e4868fdb92
Notes: svn2git 2021-03-31 03:12:20 +00:00 
svn path=/head/; revision=517066
4 changed files with 12 additions and 127 deletions
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3
biology/canu/Makefile
View file

@ -2,8 +2,7 @@
PORTNAME= canu
DISTVERSIONPREFIX= v
DISTVERSION= 1.8
PORTREVISION= 5
DISTVERSION= 1.9
CATEGORIES= biology java perl5
MAINTAINER= jwb@FreeBSD.org

6
biology/canu/distinfo
View file

@ -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

116
biology/canu/files/patch-Makefile
View file

@ -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}))

14
biology/canu/pkg-plist
View file

@ -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