fixed various issues about the GNU building scripts

[samtools.git] / Makefile.am

diff --git a/Makefile.am b/Makefile.am
index e2304f7a849193fa1a5942903737295af4fc8d62..2f22f3b8446127bbaad95d8482b544210639c86f 100644 (file)
--- a/Makefile.am
+++ b/Makefile.am
@@ -15,42 +15,4 @@ samtools_LDADD = -lm -lz -lcurses
 
 razip_SOURCES = razip.c razf.c
 razip_LDADD = -lm -lz
-dist_bin_SCRIPTS = bowtie2sam.pl export2sam.pl novo2sam.pl samtools.pl soap2sam.pl wgsim_eval.pl zoom2sam.pl
-bin_PROGRAMS = faidx maq2sam-short maq2sam-long md5fa md5sum-lite wgsim
 
-faidx_SOURCES = ../faidx.c ../faidx.c
-#faidx_LDFLAGS = -D_NO_RAZF -DFAIDX_MAIN 
-
-md5fa_SOURCES = md5.c md5.h md5fa.c ../kseq.h
-#md5fa_LDADD = -lz
-
-md5sum_lite_SOURCES = md5.c md5.h
-#md5sum_lite_LDFLAGS = -DMD5SUM_MAIN
-
-maq2sam_short_SOURCES = maq2sam.c
-#maq2sam_short_LDADD = -lz
-
-maq2sam_long_SOURCES = maq2sam.c
-#maq2sam_long_LDADD = -lz
-
-wgsim_SOURCES = wgsim.c 
-wgsim_LDADD = -lm 
-
-faidx:../faidx.c ../faidx.h
-       $(CC) $(CFLAGS) -D_NO_RAZF -DFAIDX_MAIN -o $@ ../faidx.c
-md5fa:md5.o md5fa.o md5.h ../kseq.h
-       $(CC) $(CFLAGS) -o $@ md5.o md5fa.o -lz
-md5fa.o:md5.h md5fa.c
-       $(CC) $(CFLAGS) -c -I.. -o $@ md5fa.c
-md5sum-lite:md5sum-lite.o
-       $(CC) $(CFLAGS) -o $@ md5sum-lite.o
-md5sum-lite.o:md5.c md5.h
-       $(CC) -c $(CFLAGS) -DMD5SUM_MAIN -o $@ md5.c
-maq2sam-short:maq2sam-short.o
-       $(CC) $(CFLAGS) -o $@ maq2sam-short.o -lz 
-maq2sam-short.o:maq2sam.c
-       $(CC) -c $(CFLAGS) -o $@ maq2sam.c 
-maq2sam-long:maq2sam-long.o
-       $(CC) $(CFLAGS) -o $@ maq2sam-long.o -lz 
-maq2sam-long.o:maq2sam.c
-       $(CC) -c $(CFLAGS) -DMAQ_LONGREADS -D_MAQ_LONGREADS -o $@ maq2sam.c