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|
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
|
