Makefile | 22 +++++++++++----------- bcftools/Makefile | 12 ++++++------ misc/Makefile | 28 ++++++++++++++-------------- 3 files changed, 31 insertions(+), 31 deletions(-) diff --git a/Makefile b/Makefile index 2f51bfc..4dda5a4 100644 --- a/Makefile +++ b/Makefile @@ -1,7 +1,7 @@ -CC= gcc -CFLAGS= -g -Wall -O2 -#LDFLAGS= -Wl,-rpath,\$$ORIGIN/../lib -DFLAGS= -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 +CC?= gcc +CFLAGS?= -g -Wall -O2 +#LDFLAGS+= -Wl,-rpath,\$$ORIGIN/../lib +CPPFLAGS+= -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 KNETFILE_O= knetfile.o 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 razf.o faidx.o bedidx.o \ @@ -21,14 +21,14 @@ LIBCURSES= -lcurses # -lXCurses .PHONY: all lib .c.o: - $(CC) -c $(CFLAGS) $(DFLAGS) $(INCLUDES) $< -o $@ + $(CC) -c $(CFLAGS) $(CPPFLAGS) $(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)" \ + $(MAKE) CC="$(CC)" CPPFLAGS="$(CPPFLAGS)" CFLAGS="$(CFLAGS)" \ INCLUDES="$(INCLUDES)" LIBPATH="$(LIBPATH)" $$target || exit 1; \ cd $$wdir; \ done; @@ -44,16 +44,16 @@ libbam.a:$(LOBJS) $(AR) -csru $@ $(LOBJS) samtools:lib-recur $(AOBJS) - $(CC) $(CFLAGS) -o $@ $(AOBJS) $(LDFLAGS) libbam.a -Lbcftools -lbcf $(LIBPATH) $(LIBCURSES) -lm -lz -lpthread + $(CC) $(CFLAGS) $(LDFLAGS) -o $@ $(AOBJS) libbam.a -Lbcftools -lbcf $(LIBPATH) $(LIBCURSES) -lm -lz -lpthread razip:razip.o razf.o $(KNETFILE_O) - $(CC) $(CFLAGS) -o $@ $^ -lz + $(CC) $(CFLAGS) $(LDFLAGS) -o $@ $^ -lz bgzip:bgzip.o bgzf.o $(KNETFILE_O) - $(CC) $(CFLAGS) -o $@ $^ -lz -lpthread + $(CC) $(CFLAGS) $(LDFLAGS) -o $@ $^ -lz -lpthread bgzf.o:bgzf.c bgzf.h - $(CC) -c $(CFLAGS) $(DFLAGS) -DBGZF_CACHE $(INCLUDES) bgzf.c -o $@ + $(CC) -c $(CFLAGS) $(CPPFLAGS) -DBGZF_CACHE $(INCLUDES) bgzf.c -o $@ razip.o:razf.h bam.o:bam.h razf.h bam_endian.h kstring.h sam_header.h @@ -84,7 +84,7 @@ libbam.1.dylib-local:$(LOBJS) libtool -dynamic $(LOBJS) -o libbam.1.dylib -lc -lz libbam.so.1-local:$(LOBJS) - $(CC) -shared -Wl,-soname,libbam.so -o libbam.so.1 $(LOBJS) -lc -lz + $(CC) $(LDFLAGS) -shared -Wl,-soname,libbam.so -o libbam.so.1 $(LOBJS) -lc -lz -lm -lpthread dylib: @$(MAKE) cleanlocal; \ diff --git a/bcftools/Makefile b/bcftools/Makefile index be831de..7ef796c 100644 --- a/bcftools/Makefile +++ b/bcftools/Makefile @@ -1,6 +1,6 @@ -CC= gcc -CFLAGS= -g -Wall -O2 #-m64 #-arch ppc -DFLAGS= -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE +CC?= gcc +CFLAGS?= -g -Wall -O2 #-m64 #-arch ppc +CPPFLAGS+= -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE LOBJS= bcf.o vcf.o bcfutils.o prob1.o em.o kfunc.o kmin.o index.o fet.o mut.o bcf2qcall.o OMISC= .. AOBJS= call1.o main.o $(OMISC)/kstring.o $(OMISC)/bgzf.o $(OMISC)/knetfile.o $(OMISC)/bedidx.o @@ -11,14 +11,14 @@ SUBDIRS= . .SUFFIXES:.c .o .c.o: - $(CC) -c $(CFLAGS) $(DFLAGS) -I.. $(INCLUDES) $< -o $@ + $(CC) -c $(CFLAGS) $(CPPFLAGS) -I.. $(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)" \ + $(MAKE) CC="$(CC)" CPPFLAGS="$(CPPFLAGS)" CFLAGS="$(CFLAGS)" \ INCLUDES="$(INCLUDES)" LIBPATH="$(LIBPATH)" $$target || exit 1; \ cd $$wdir; \ done; @@ -31,7 +31,7 @@ libbcf.a:$(LOBJS) $(AR) -csru $@ $(LOBJS) bcftools:lib $(AOBJS) - $(CC) $(CFLAGS) -o $@ $(AOBJS) -L. $(LIBPATH) -lbcf -lm -lz -lpthread + $(CC) $(CFLAGS) $(LDFLAGS) -o $@ $(AOBJS) -L. $(LIBPATH) -lbcf -lm -lz -lpthread bcf.o:bcf.h vcf.o:bcf.h diff --git a/misc/Makefile b/misc/Makefile index d36e7ac..7ae1dc3 100644 --- a/misc/Makefile +++ b/misc/Makefile @@ -1,8 +1,8 @@ -CC= gcc -CXX= g++ -CFLAGS= -g -Wall -O2 #-m64 #-arch ppc -CXXFLAGS= $(CFLAGS) -DFLAGS= -D_FILE_OFFSET_BITS=64 +CC?= gcc +CXX?= g++ +CFLAGS?= -g -Wall -O2 #-m64 #-arch ppc +CXXFLAGS?= $(CFLAGS) +CPPFLAGS+= -D_FILE_OFFSET_BITS=64 OBJS= PROG= md5sum-lite md5fa maq2sam-short maq2sam-long ace2sam wgsim bamcheck INCLUDES= -I.. @@ -11,7 +11,7 @@ SUBDIRS= . .SUFFIXES:.c .o .c.o: - $(CC) -c $(CFLAGS) $(DFLAGS) $(INCLUDES) $< -o $@ + $(CC) -c $(CFLAGS) $(CPPFLAGS) $(INCLUDES) $< -o $@ all:$(PROG) @@ -20,7 +20,7 @@ lib-recur all-recur clean-recur cleanlocal-recur install-recur: wdir=`pwd`; \ list='$(SUBDIRS)'; for subdir in $$list; do \ cd $$subdir; \ - $(MAKE) CC="$(CC)" DFLAGS="$(DFLAGS)" CFLAGS="$(CFLAGS)" \ + $(MAKE) CC="$(CC)" CPPFLAGS="$(CPPFLAGS)" CFLAGS="$(CFLAGS)" \ INCLUDES="$(INCLUDES)" $$target || exit 1; \ cd $$wdir; \ done; @@ -28,31 +28,31 @@ lib-recur all-recur clean-recur cleanlocal-recur install-recur: lib: bamcheck:bamcheck.o - $(CC) $(CFLAGS) -o $@ bamcheck.o -L.. -lm -lbam -lpthread -lz + $(CC) $(CFLAGS) $(LDFLAGS) -o $@ bamcheck.o -L.. -lm -lbam -lpthread -lz bamcheck.o:bamcheck.c ../faidx.h ../khash.h ../sam.h ../razf.h $(CC) $(CFLAGS) -c -I.. -o $@ bamcheck.c ace2sam:ace2sam.o - $(CC) $(CFLAGS) -o $@ ace2sam.o -lz + $(CC) $(CFLAGS) $(LDFLAGS) -o $@ ace2sam.o -lz wgsim:wgsim.o - $(CC) $(CFLAGS) -o $@ wgsim.o -lm -lz + $(CC) $(CFLAGS) $(LDFLAGS) -o $@ wgsim.o -lm -lz md5fa:md5.o md5fa.o md5.h ../kseq.h - $(CC) $(CFLAGS) -o $@ md5.o md5fa.o -lz + $(CC) $(CFLAGS) $(LDFLAGS) -o $@ md5.o md5fa.o -lz md5sum-lite:md5sum-lite.o - $(CC) $(CFLAGS) -o $@ md5sum-lite.o + $(CC) $(CFLAGS) $(LDFLAGS) -o $@ md5sum-lite.o md5sum-lite.o:md5.c md5.h $(CC) -c $(CFLAGS) -DMD5SUM_MAIN -o $@ md5.c maq2sam-short:maq2sam.c - $(CC) $(CFLAGS) -o $@ maq2sam.c -lz + $(CC) $(CFLAGS) $(LDFLAGS) -o $@ maq2sam.c -lz maq2sam-long:maq2sam.c - $(CC) $(CFLAGS) -DMAQ_LONGREADS -o $@ maq2sam.c -lz + $(CC) $(CFLAGS) -DMAQ_LONGREADS $(LDFLAGS) -o $@ maq2sam.c -lz md5fa.o:md5.h md5fa.c $(CC) $(CFLAGS) -c -I.. -o $@ md5fa.c