From e4868fdb92b5a187a0cc4652a558c49023e8e32b Mon Sep 17 00:00:00 2001 From: "Jason W. Bacon" Date: Fri, 8 Nov 2019 14:03:15 +0000 Subject: [PATCH] biology/canu: Upgrade to 1.9 Numerous bug fixes and enhancements Reported by: portscout --- biology/canu/Makefile | 3 +- biology/canu/distinfo | 6 +- biology/canu/files/patch-Makefile | 116 ------------------------------ biology/canu/pkg-plist | 14 ++-- 4 files changed, 12 insertions(+), 127 deletions(-) delete mode 100644 biology/canu/files/patch-Makefile 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