Mercurial > repos > ashvark > qiime_1_8_0
comparison bwa-0.6.2/Makefile @ 2:a294fbfcb1db draft default tip
Uploaded BWA
author | ashvark |
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date | Fri, 18 Jul 2014 07:55:59 -0400 |
parents | dd1186b11b3b |
children |
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1:a9636dc1e99a | 2:a294fbfcb1db |
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1 CC= gcc | |
2 CXX= g++ | |
3 CFLAGS= -g -Wall -O2 | |
4 CXXFLAGS= $(CFLAGS) | |
5 AR= ar | |
6 DFLAGS= -DHAVE_PTHREAD #-D_NO_SSE2 #-D_FILE_OFFSET_BITS=64 | |
7 LOBJS= bwa.o bamlite.o utils.o bwt.o bwtio.o bwtaln.o bwtgap.o bntseq.o stdaln.o \ | |
8 bwaseqio.o bwase.o kstring.o | |
9 AOBJS= QSufSort.o bwt_gen.o \ | |
10 is.o bwtmisc.o bwtindex.o ksw.o simple_dp.o \ | |
11 bwape.o cs2nt.o \ | |
12 bwtsw2_core.o bwtsw2_main.o bwtsw2_aux.o bwt_lite.o \ | |
13 bwtsw2_chain.o fastmap.o bwtsw2_pair.o | |
14 PROG= bwa | |
15 INCLUDES= | |
16 LIBS= -lm -lz -lpthread | |
17 SUBDIRS= . | |
18 | |
19 .SUFFIXES:.c .o .cc | |
20 | |
21 .c.o: | |
22 $(CC) -c $(CFLAGS) $(DFLAGS) $(INCLUDES) $< -o $@ | |
23 .cc.o: | |
24 $(CXX) -c $(CXXFLAGS) $(DFLAGS) $(INCLUDES) $< -o $@ | |
25 | |
26 all:$(PROG) | |
27 | |
28 bwa:libbwa.a $(AOBJS) main.o | |
29 $(CC) $(CFLAGS) $(DFLAGS) $(AOBJS) main.o -o $@ -L. -lbwa $(LIBS) | |
30 | |
31 libbwa.a:$(LOBJS) | |
32 $(AR) -csru $@ $(LOBJS) | |
33 | |
34 bwa.o:bwa.h | |
35 | |
36 QSufSort.o:QSufSort.h | |
37 | |
38 bwt.o:bwt.h | |
39 bwtio.o:bwt.h | |
40 bwtaln.o:bwt.h bwtaln.h kseq.h | |
41 bntseq.o:bntseq.h | |
42 bwtgap.o:bwtgap.h bwtaln.h bwt.h | |
43 | |
44 bwtsw2_core.o:bwtsw2.h bwt.h bwt_lite.h stdaln.h | |
45 bwtsw2_aux.o:bwtsw2.h bwt.h bwt_lite.h stdaln.h | |
46 bwtsw2_main.o:bwtsw2.h | |
47 | |
48 clean: | |
49 rm -f gmon.out *.o a.out $(PROG) *~ *.a |