diff SNV/SNVMix2_source/SNVMix2-v0.12.1-rc1/samtools-0.1.6/Makefile @ 0:74f5ea818cea

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author ryanmorin
date Wed, 12 Oct 2011 19:50:38 -0400
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--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/SNV/SNVMix2_source/SNVMix2-v0.12.1-rc1/samtools-0.1.6/Makefile	Wed Oct 12 19:50:38 2011 -0400
@@ -0,0 +1,67 @@
+CC=			gcc
+CFLAGS=		-g -Wall -O2 #-m64 #-arch ppc
+DFLAGS=		-D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE -D_CURSES_LIB=1
+LOBJS=		bgzf.o kstring.o bam_aux.o bam.o bam_import.o sam.o bam_index.o	\
+			bam_pileup.o bam_lpileup.o bam_md.o glf.o razf.o faidx.o knetfile.o	\
+			bam_sort.o
+AOBJS=		bam_tview.o bam_maqcns.o bam_plcmd.o sam_view.o	\
+			bam_rmdup.o bam_rmdupse.o bam_mate.o bam_stat.o bam_color.o	\
+			bamtk.o
+PROG=		samtools
+INCLUDES=
+SUBDIRS=	. misc
+LIBPATH=
+LIBCURSES=	-lcurses # -lXCurses
+
+.SUFFIXES:.c .o
+
+.c.o:
+		$(CC) -c $(CFLAGS) $(DFLAGS) $(INCLUDES) $< -o $@
+
+all-recur lib-recur clean-recur cleanlocal-recur install-recur:
+		@target=`echo $@ | sed s/-recur//`; \
+		wdir=`pwd`; \
+		list='$(SUBDIRS)'; for subdir in $$list; do \
+			cd $$subdir; \
+			$(MAKE) CC="$(CC)" DFLAGS="$(DFLAGS)" CFLAGS="$(CFLAGS)" \
+				INCLUDES="$(INCLUDES)" LIBPATH="$(LIBPATH)" $$target || exit 1; \
+			cd $$wdir; \
+		done;
+
+all:$(PROG)
+
+lib:libbam.a
+
+libbam.a:$(LOBJS)
+		$(AR) -cru $@ $(LOBJS)
+
+samtools:lib $(AOBJS)
+		$(CC) $(CFLAGS) -o $@ $(AOBJS) -lm $(LIBPATH) $(LIBCURSES) -lz -L. -lbam
+
+razip:razip.o razf.o
+		$(CC) $(CFLAGS) -o $@ razf.o razip.o -lz
+
+bgzip:bgzip.o bgzf.o
+		$(CC) $(CFLAGS) -o $@ bgzf.o bgzip.o -lz
+
+razip.o:razf.h
+bam.o:bam.h razf.h bam_endian.h kstring.h
+sam.o:sam.h bam.h
+bam_import.o:bam.h kseq.h khash.h razf.h
+bam_pileup.o:bam.h razf.h ksort.h
+bam_plcmd.o:bam.h faidx.h bam_maqcns.h glf.h
+bam_index.o:bam.h khash.h ksort.h razf.h bam_endian.h
+bam_lpileup.o:bam.h ksort.h
+bam_tview.o:bam.h faidx.h bam_maqcns.h
+bam_maqcns.o:bam.h ksort.h bam_maqcns.h
+bam_sort.o:bam.h ksort.h razf.h
+bam_md.o:bam.h faidx.h
+glf.o:glf.h
+
+faidx.o:faidx.h razf.h khash.h
+faidx_main.o:faidx.h razf.h
+
+cleanlocal:
+		rm -fr gmon.out *.o a.out *.dSYM razip $(PROG) *~ *.a
+
+clean:cleanlocal-recur