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biology/bedtools/files/patch-Makefile
| --- Makefile.orig 2015-11-14 00:48:48 UTC | --- Makefile.orig 2017-12-14 17:15:02 UTC | ||||
| +++ Makefile | +++ Makefile | ||||
| @@ -4,7 +4,7 @@ | @@ -4,7 +4,7 @@ | ||||
| # (c) 2009 Aaron Quinlan | # (c) 2009 Aaron Quinlan | ||||
| # ========================== | # ========================== | ||||
| -SHELL := /bin/bash -e | -SHELL := /bin/bash -e | ||||
| +SHELL := /bin/sh -e | +SHELL := /bin/sh -e | ||||
| VERSION_FILE=./src/utils/version/version_git.h | VERSION_FILE=./src/utils/version/version_git.h | ||||
| RELEASED_VERSION_FILE=./src/utils/version/version_release.txt | RELEASED_VERSION_FILE=./src/utils/version/version_release.txt | ||||
| @@ -16,11 +16,11 @@ export OBJ_DIR = obj | @@ -16,11 +16,11 @@ export OBJ_DIR = obj | ||||
| export BIN_DIR = bin | export BIN_DIR = bin | ||||
| export SRC_DIR = src | export SRC_DIR = src | ||||
| export UTIL_DIR = src/utils | export UTIL_DIR = src/utils | ||||
| -export CXX = g++ | -export CXX = g++ | ||||
| +export CXX = c++ | +export CXX ?= g++ | ||||
| #ifeq ($(DEBUG),1) | ifeq ($(DEBUG),1) | ||||
| #export CXXFLAGS = -Wall -O0 -g -fno-inline -fkeep-inline-functions -D_FILE_OFFSET_BITS=64 -fPIC -DDEBUG -D_DEBUG | -export CXXFLAGS = -Wall -Wextra -DDEBUG -D_DEBUG -g -O0 -D_FILE_OFFSET_BITS=64 -fPIC $(INCLUDES) | ||||
| #else | +export CXXFLAGS += -Wall -Wextra -DDEBUG -D_DEBUG -g -O0 -D_FILE_OFFSET_BITS=64 -fPIC $(INCLUDES) | ||||
| else | |||||
| -export CXXFLAGS = -Wall -O2 -D_FILE_OFFSET_BITS=64 -fPIC $(INCLUDES) | -export CXXFLAGS = -Wall -O2 -D_FILE_OFFSET_BITS=64 -fPIC $(INCLUDES) | ||||
| +export CXXFLAGS += -Wall -D_FILE_OFFSET_BITS=64 -fPIC $(INCLUDES) | +export CXXFLAGS += -D_FILE_OFFSET_BITS=64 -fPIC $(INCLUDES) | ||||
| #endif | endif | ||||
| export LIBS = -lz | |||||
| export BT_ROOT = src/utils/BamTools/ | |||||
| @@ -129,20 +129,17 @@ INCLUDES = -I$(SRC_DIR)/utils/bedFile \ | |||||
| -I$(SRC_DIR)/utils/GenomeFile \ | |||||
| -I$(SRC_DIR)/utils/RecordOutputMgr \ | |||||
| -I$(SRC_DIR)/utils/ToolBase \ | |||||
| - -I$(SRC_DIR)/utils/driver \ | |||||
| - | |||||
| + -I$(SRC_DIR)/utils/driver | |||||
| # If the user has specified to do so, tell the compile to use rand() (instead of mt19937). | |||||
| @@ -143,8 +143,8 @@ INCLUDES = -I$(SRC_DIR)/utils/bedFile \ | |||||
| all: print_banner $(OBJ_DIR) $(BIN_DIR) autoversion $(UTIL_SUBDIRS) $(SUBDIRS) | all: print_banner $(OBJ_DIR) $(BIN_DIR) autoversion $(UTIL_SUBDIRS) $(SUBDIRS) | ||||
| @echo "- Building main bedtools binary." | @echo "- Building main bedtools binary." | ||||
| @$(CXX) $(CXXFLAGS) $(CPPFLAGS) -c src/bedtools.cpp -o obj/bedtools.o $(INCLUDES) | - @$(CXX) $(CXXFLAGS) $(CPPFLAGS) -c src/bedtools.cpp -o obj/bedtools.o $(INCLUDES) | ||||
| @$(CXX) $(CXXFLAGS) $(CPPFLAGS) -o $(BIN_DIR)/bedtools $(BUILT_OBJECTS) -L$(UTIL_DIR)/BamTools/lib/ -lbamtools $(LIBS) $(LDFLAGS) $(INCLUDES) | - @$(CXX) $(CXXFLAGS) $(CPPFLAGS) -o $(BIN_DIR)/bedtools $(BUILT_OBJECTS) -L$(UTIL_DIR)/BamTools/lib/ -lbamtools $(LIBS) $(LDFLAGS) $(INCLUDES) | ||||
| + $(CXX) $(CXXFLAGS) $(CPPFLAGS) -c src/bedtools.cpp -o obj/bedtools.o $(INCLUDES) | |||||
| + $(CXX) $(CXXFLAGS) $(CPPFLAGS) -o $(BIN_DIR)/bedtools $(BUILT_OBJECTS) -L$(UTIL_DIR)/BamTools/lib/ -lbamtools $(LIBS) $(LDFLAGS) $(INCLUDES) | |||||
| @echo "done." | @echo "done." | ||||
| - | |||||
| @echo "- Creating executables for old CLI." | |||||
| @python scripts/makeBashScripts.py | |||||
| @chmod +x bin/* | |||||
| @echo "done." | |||||
| - | |||||
| .PHONY: all | @echo "- Creating executables for old CLI." | ||||
| @@ -193,7 +193,7 @@ clean: | |||||
| @@ -183,7 +180,7 @@ clean: | |||||
| .PHONY: clean | .PHONY: clean | ||||
| test: all | test: all | ||||
| - @cd test; bash test.sh | - @cd test; bash test.sh | ||||
| + @cd test; $(SHELL) test.sh | + @cd test; $(SHELL) test.sh | ||||
| .PHONY: test | .PHONY: test | ||||