1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49 50 51 52 53 54 55 56 57 58 59 60
|
CC ?= gcc
CXX ?= g++
AR ?= ar
#CFLAGS := -Wall -pipe -O2
#CXXFLAGS := $(CFLAGS)
LOBJS = ssw.o
LCPPOBJS = ssw_cpp.o
PROG = ssw-align
SOVERS=.0
LIB = libssw.so$(SOVERS)
STATICLIB = libssw.a
EXAMPLE = example_c
EXAMPLE_CPP = example_cpp
JAVA_JAR = ssw.jar
JAVA_LIB = libsswjni.so
JAVA_INLCUDES = -I"$(JAVA_HOME)/include" -I"$(JAVA_HOME)/include/linux" -I/usr/lib/jvm/default-java/include/ -I/usr/lib/jvm/default-java/include/linux
JAVA_OBJ = ssw/Aligner.class ssw/Alignment.class
.PHONY: all default java clean
default: $(PROG) $(EXAMPLE) $(EXAMPLE_CPP) $(LIB) $(STATICLIB)
all: default java
java: $(JAVA_JAR) $(JAVA_LIB)
$(LIB): ssw.c ssw.h ssw_cpp.h ssw_cpp.cpp
$(CXX) $(CPPFLAGS) $(CXXFLAGS) -fPIC -shared -rdynamic -Wl,-soname,$(LIB) -o $@ $^ $(LDFLAGS)
$(STATICLIB): $(LOBJS) $(LCPPOBJS)
ar rcs $@ $^
$(PROG): main.c kseq.h $(LIB) $(STATICLIB)
$(CC) $(CPPFLAGS) $(CFLAGS) -o $@ main.c kseq.h -L. -lssw -lm -lz $(LDFLAGS)
$(EXAMPLE): example.c
$(EXAMPLE): $(LOBJS)
$(CC) -o $@ $(filter-out %.h,$^) $(CPPFLAGS) $(CFLAGS) -lm -lz $(LDFLAGS)
$(EXAMPLE_CPP): example.cpp $(LOBJS) $(LCPPOBJS)
$(CXX) -o $@ $^ $(CXXFLAGS) $(CPPFLAGS) -lm -lz $(LDFLAGS)
$(JAVA_LIB): sswjni.c ssw.c ssw.h
$(CC) $(CPPFLAGS) $(CFLAGS) $(JAVA_INLCUDES) -fPIC -shared -rdynamic -o $@ $< ssw.c $(LDFLAGS)
$(JAVA_JAR): $(JAVA_OBJ)
jar cvf $@ $^
%.class: %.java
javac $<
ssw.o: ssw.c ssw.h
$(CC) -c -o $@ $< $(CPPFLAGS) $(CFLAGS)
ssw_cpp.o: ssw_cpp.cpp ssw_cpp.h ssw.h
$(CXX) -c -o $@ $< $(CPPFLAGS) $(CXXFLAGS)
clean:
-rm -f $(LOBJS) $(LCPPOBJS) $(PROG) $(LIB) $(EXAMPLE) $(EXAMPLE_CPP) $(JAVA_LIB) *.jar $(JAVA_OBJ) *~ $(STATICLIB)
|