--- bwa-0.7.13/Makefile
+++ bwa-0.7.13/Makefile
@@ -1,8 +1,8 @@
-CC=			gcc
+CC?=			gcc
 #CC=			clang --analyze
-CFLAGS=		-g -Wall -Wno-unused-function -O2
+CFLAGS?=		-g -Wall -Wno-unused-function -O2
 WRAP_MALLOC=-DUSE_MALLOC_WRAPPERS
-AR=			ar
+AR?=			ar
 DFLAGS=		-DHAVE_PTHREAD $(WRAP_MALLOC)
 LOBJS=		utils.o kthread.o kstring.o ksw.o bwt.o bntseq.o bwa.o bwamem.o bwamem_pair.o bwamem_extra.o malloc_wrap.o
 AOBJS=		QSufSort.o bwt_gen.o bwashm.o bwase.o bwaseqio.o bwtgap.o bwtaln.o bamlite.o \
@@ -26,10 +26,10 @@
 all:$(PROG)
 
 bwa:libbwa.a $(AOBJS) main.o
-		$(CC) $(CFLAGS) $(DFLAGS) $(AOBJS) main.o -o $@ -L. -lbwa $(LIBS)
+		$(CC) $(CFLAGS) $(LDFLAGS) $(DFLAGS) $(AOBJS) main.o -o $@ -L. -lbwa $(LIBS)
 
 bwamem-lite:libbwa.a example.o
-		$(CC) $(CFLAGS) $(DFLAGS) example.o -o $@ -L. -lbwa $(LIBS)
+		$(CC) $(CFLAGS) $(LDFLAGS) $(DFLAGS) example.o -o $@ -L. -lbwa $(LIBS)
 
 libbwa.a:$(LOBJS)
 		$(AR) -csru $@ $(LOBJS)