Makefile

ifndef CXXFLAGS
  CXXFLAGS = -O3 -Wno-format -std=c++98
  #CXXFLAGS = -g -O0 -Wno-format -std=c++98
endif

CXXFLAGS += -MMD -ISNAPLib -msse

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

ifneq ($(STATIC),)
  STATIC_GCC=-static-libgcc -static-libstdc++
  LIBS += $(STATIC_GCC)
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