1
2CC = g++
3
4CFLAGS = -Wall -Wno-unused -I. -Imintlib
5LFLAGS = -fPIC
6
7
8UNAME = $(shell uname)
9
10ifeq ($(UNAME), Linux)
11	CFLAGS += -DUNIX
12endif
13
14ifeq ($(UNAME), Darwin)
15	CFLAGS += -DUNIX -DMAC_OSX
16endif
17
18ifeq ($(debug),yes)
19CFLAGS += -ggdb
20else
21CFLAGS += -O2
22endif
23
24
25#OBJECTS = mintlib/minString.o mintlib/minMap.o suffix_array.o
26OBJECTS = mintlib/minString.o mintlib/minMap.o bioSequence.o
27
28first: all
29
30all: cd-hit-dup cd-hit-lap read-linker
31
32.SUFFIXES: .c .obj .cpp .cc .cxx .C
33
34.cxx.o:
35	$(CC) -c $(CFLAGS) -o $@ $<
36
37cd-hit-dup: $(OBJECTS) cdhit-dup.o
38	$(CC) $(LFLAGS) $(OBJECTS) cdhit-dup.o -o cd-hit-dup
39
40cd-hit-lap: $(OBJECTS) cdhit-lap.o
41	$(CC) $(LFLAGS) $(OBJECTS) cdhit-lap.o -o cd-hit-lap
42
43read-linker: $(OBJECTS) read-linker.o
44	$(CC) $(LFLAGS) $(OBJECTS) read-linker.o -o read-linker
45
46clean:
47	rm $(OBJECTS) cdhit-dup.o cdhit-lap.o read-linker.o
48