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|
ifndef CXXFLAGS
CXXFLAGS = -O3 -Wno-format
endif
CXXFLAGS += -MMD -ISNAPLib $(CFLAGS)
LDFLAGS += -pthread
#LIBHDFS_HOME = ../hadoop-2.2.0-src/hadoop-hdfs-project/hadoop-hdfs/src/main/native/libhdfs
#JAVA_HOME = /usr/lib/jvm/java-7-oracle
ifdef LIBHDFS_HOME
CXXFLAGS += -DSNAP_HDFS -I$(LIBHDFS_HOME)
LDFLAGS += -L$(LIBHDFS_HOME) -L$(JAVA_HOME)/jre/lib/amd64/server -L$(JAVA_HOME)/jre/lib/amd64
LIBS += -lhdfs -ljvm
endif
UNAME := $(shell uname)
ifeq ($(UNAME), Linux)
LIBS += -lrt -lz
endif
ifeq ($(UNAME), Darwin)
LIBS += -lz
endif
CXX = g++
LIB_SRC = $(wildcard SNAPLib/*.cpp)
LIB_OBJ = $(patsubst %.cpp, %.o, $(LIB_SRC))
SNAP_SRC = $(wildcard apps/snap/*.cpp)
TEST_SRC = $(wildcard tests/*.cpp)
ROC_SRC = $(wildcard apps/ComputeROC/*.cpp)
SNAPCOMMAND_SRC = $(wildcard apps/SNAPCommand/*.cpp)
SNAP_OBJ = $(patsubst %.cpp, %.o, $(SNAP_SRC))
TEST_OBJ = $(patsubst %.cpp, %.o, $(TEST_SRC))
ROC_OBJ = $(patsubst %.cpp, %.o, $(ROC_SRC))
SNAPCOMMAND_OBJ = $(patsubst %.cpp, %.o, $(SNAPCOMMAND_SRC))
ALL_OBJ = $(LIB_OBJ) $(SNAP_OBJ) $(TEST_OBJ) $(SNAPCOMMAND_OBJ)
DEPS = $(pathsubst %.o, %.d, $(ALL_OBJ))
EXES = snap-aligner unit_tests SNAPCommand
default: $(EXES)
-include $(pathsubst %.o, %.d, $(ALL_OBJ))
$(OBJS): %.o : %.cpp
$(CXX) -o $@ $(CXXFLAGS) -c $<
snap-aligner: $(LIB_OBJ) $(SNAP_OBJ)
$(CXX) -o $@ $(CXXFLAGS) -Itests $(LDFLAGS) $^ $(LIBS)
SNAPCommand: $(LIB_OBJ) $(SNAPCOMMAND_OBJ)
echo SNAPCOMMAND_OBJ is $(SNAPCOMMAND_OBJ)
echo SNAP_OBJ is $(SNAP_OBJ)
$(CXX) -o $@ $(CXXFLAGS) $(LDFLAGS) $^ $(LIBS)
snapxl:
make clean
make snap CXXFLAGS="-DLONG_READS $(CXXFLAGS)"
mv snap snapxl
make clean
roc: $(LIB_OBJ) $(ROC_OBJ)
$(CXX) -o $@ $(CXXFLAGS) -Itests $(LDFLAGS) $^ $(LIBS)
unit_tests: $(LIB_OBJ) $(TEST_OBJ)
$(CXX) -o $@ $(CXXFLAGS) -Itests $(LDFLAGS) $^ $(LIBS)
clean:
rm -f $(ALL_OBJ) $(DEPS) $(EXES) snap SNAP
.phony: clean default
|
