-
Notifications
You must be signed in to change notification settings - Fork 5
/
Makefile
57 lines (41 loc) · 2.15 KB
/
Makefile
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
# Uncomment the next two lines to use parallel processing (OpenMP)
PARALLEL_FLAGS = -DPARALLEL_SUPPORT -fopenmp
PARALLEL_LIB = -lgomp
CC = g++
RAVERSION=2010_4rc2
LIBCDSPATH = libcds/
LIBRLCSAPATH = incbwt/
CPPFLAGS = -Wall -I$(LIBRLCSAPATH) -I$(LIBCDSPATH)includes/ -g -DMASSIVE_DATA_RLCSA $(PARALLEL_FLAGS) -std=c++0x -O3 -DNDEBUG
LIBCDS = $(LIBCDSPATH)lib/libcds.a
LIBRLCSA = $(LIBRLCSAPATH)rlcsa.a
FMINDEXOBJS = FMIndex.o Tools.o HuffWT.o BitRank.o ResultSet.o
OBJS = InputReader.o OutputWriter.o Pattern.o TextCollection.o TextCollectionBuilder.o \
Query.o TextStorage.o
all: metaenumerate builder metaserver
fastqqualitytrim: fastqqualitytrim.o
$(CC) $(CPPFLAGS) -o fastqqualitytrim fastqqualitytrim.o
maptoreads: $(LIBCDS) $(LIBRLCSA) maptoreads.o $(FMINDEXOBJS) $(OBJS)
$(CC) $(CPPFLAGS) -o maptoreads maptoreads.o $(FMINDEXOBJS) $(OBJS) $(LIBCDS) $(LIBRLCSA)
aaaligner: $(LIBCDS) $(LIBRLCSA) aaaligner.o $(FMINDEXOBJS) $(OBJS)
$(CC) $(CPPFLAGS) -o aaaligner aaaligner.o $(FMINDEXOBJS) $(OBJS) $(LIBCDS) $(LIBRLCSA)
metaserver: metaserver.o ServerSocket.o
$(CC) $(CPPFLAGS) -o metaserver metaserver.o ServerSocket.o -lm
metaenumerate: $(LIBCDS) $(LIBRLCSA) $(FMINDEXOBJS) $(OBJS) metaenumerate.o ClientSocket.o EnumerateQuery.o
$(CC) $(CPPFLAGS) -o metaenumerate metaenumerate.o $(OBJS) $(FMINDEXOBJS) $(LIBCDS) $(LIBRLCSA) $(PARALLEL_LIB) ClientSocket.o EnumerateQuery.o
builder: $(LIBCDS) $(LIBRLCSA) $(FMINDEXOBJS) $(OBJS) builder.o
$(CC) $(CPPFLAGS) -o builder builder.o $(OBJS) $(FMINDEXOBJS) $(LIBCDS) $(LIBRLCSA)
sabuilder: $(LIBCDS) $(LIBRLCSA) $(FMINDEXOBJS) $(OBJS) sabuilder.o
$(CC) $(CPPFLAGS) -o sabuilder sabuilder.o $(OBJS) $(FMINDEXOBJS) $(LIBCDS) $(LIBRLCSA)
$(LIBRLCSA):
@make -C $(LIBRLCSAPATH) library
$(LIBCDS):
@make -C $(LIBCDSPATH)
depend:
g++ -I$(LIBRLCSAPATH) -I$(LIBCDSPATH)includes/ -MM -std=c++0x *.cpp > dependencies.mk
clean:
rm -f core *.o *~ metaenumerate builder metaserver fastqqualitytrim sabuilder maptoreads aaaligner
@make -C $(LIBCDSPATH) clean
@make -C $(LIBRLCSAPATH) clean
shallow_clean:
rm -f core *.o *~ metaenumerate builder metaserver fastqqualitytrim sabuilder maptoreads aaaligner
include dependencies.mk