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head/biology/bowtie2/files/patch-Makefile
| --- Makefile.orig 2016-12-30 15:40:06 UTC | --- Makefile.orig 2017-10-05 16:45:18 UTC | ||||
| +++ Makefile | +++ Makefile | ||||
| @@ -21,8 +21,8 @@ | @@ -21,10 +21,11 @@ | ||||
| # Makefile for bowtie, bowtie2-build, bowtie2-inspect | # Makefile for bowtie, bowtie2-build, bowtie2-inspect | ||||
| # | # | ||||
| -prefix = /usr/local | -prefix = /usr/local | ||||
| -bindir = $(prefix)/bin | -bindir = $(prefix)/bin | ||||
| +PREFIX ?= /usr/local | +PREFIX ?= /usr/local | ||||
| +bindir = $(PREFIX)/bin | +bindir = $(PREFIX)/bin | ||||
| INC = | INC = $(if $(RELEASE_BUILD),-I$(CURDIR)/.include) | ||||
| +INC += -I${LOCALBASE}/include | |||||
| LIBS = $(LDFLAGS) $(if $(RELEASE_BUILD),-L$(CURDIR)/.lib) -lz | |||||
| GCC_PREFIX = $(shell dirname `which gcc`) | GCC_PREFIX = $(shell dirname `which gcc`) | ||||
| @@ -62,6 +62,8 @@ ifeq (1, $(POPCNT_CAPABILITY)) | GCC_SUFFIX = | ||||
| INC += -I third_party | @@ -98,7 +99,7 @@ endif | ||||
| endif | |||||
| +INC += -I ${LOCALBASE}/include | |||||
| + | |||||
| MM_DEF = | |||||
| ifeq (1,$(BOWTIE_MM)) | |||||
| @@ -75,7 +77,7 @@ ifeq (1,$(BOWTIE_SHARED_MEM)) | |||||
| endif | |||||
| PTHREAD_PKG = | |||||
| -PTHREAD_LIB = | |||||
| +PTHREAD_LIB = | |||||
| #if we're not using TBB, then we can't use queuing locks | |||||
| ifeq (1,$(NO_TBB)) | |||||
| @@ -94,7 +96,7 @@ endif | |||||
| #default is to use Intel TBB | #default is to use Intel TBB | ||||
| ifneq (1,$(NO_TBB)) | ifneq (1,$(NO_TBB)) | ||||
| - LIBS = $(PTHREAD_LIB) -ltbb -ltbbmalloc_proxy | - LIBS += $(PTHREAD_LIB) -ltbb -ltbbmalloc$(if $(RELEASE_BUILD),,_proxy) | ||||
| + LIBS = $(PTHREAD_LIB) -L${LOCALBASE}/lib -ltbb -ltbbmalloc | + LIBS += $(PTHREAD_LIB) -L${LOCALBASE}/lib -ltbb -ltbbmalloc | ||||
| override EXTRA_FLAGS += -DWITH_TBB | override EXTRA_FLAGS += -DWITH_TBB | ||||
| else | else | ||||
| LIBS = $(PTHREAD_LIB) | LIBS += $(PTHREAD_LIB) | ||||
| @@ -185,7 +187,7 @@ SSE_FLAG=-msse2 | @@ -189,7 +190,7 @@ SSE_FLAG=-msse2 | ||||
| DEBUG_FLAGS = -O0 -g3 -m64 $(SSE_FLAG) | DEBUG_FLAGS = -O0 -g3 -m64 $(SSE_FLAG) | ||||
| DEBUG_DEFS = -DCOMPILER_OPTIONS="\"$(DEBUG_FLAGS) $(EXTRA_FLAGS)\"" | DEBUG_DEFS = -DCOMPILER_OPTIONS="\"$(DEBUG_FLAGS) $(EXTRA_FLAGS)\"" | ||||
| -RELEASE_FLAGS = -O3 -m64 $(SSE_FLAG) -funroll-loops -g3 | -RELEASE_FLAGS = -O3 -m64 $(SSE_FLAG) -funroll-loops -g3 | ||||
| +RELEASE_FLAGS = $(CXXFLAGS) $(SSE_FLAG) -funroll-loops | +RELEASE_FLAGS = $(CXXFLAGS) $(SSE_FLAG) -funroll-loops | ||||
| RELEASE_DEFS = -DCOMPILER_OPTIONS="\"$(RELEASE_FLAGS) $(EXTRA_FLAGS)\"" | RELEASE_DEFS = -DCOMPILER_OPTIONS="\"$(RELEASE_FLAGS) $(EXTRA_FLAGS)\"" | ||||
| NOASSERT_FLAGS = -DNDEBUG | NOASSERT_FLAGS = -DNDEBUG | ||||
| FILE_FLAGS = -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_GNU_SOURCE | FILE_FLAGS = -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_GNU_SOURCE | ||||