diff --git a/Makefile b/Makefile
index 9755156..23871c1 100644
--- a/Makefile
+++ b/Makefile
@@ -1,15 +1,21 @@
 CXX      ?= g++
-CXXFLAGS = -std=c++11 -Wall -Wextra -Wno-missing-field-initializers -Wshadow -g -O2
-LIBS     = -lm -lz -lpthread
+CXXFLAGS  = -std=c++11 -Wall -Wextra -Wno-missing-field-initializers -Wshadow -g -O2
+LIBS      = -lm -lz -lpthread
 
-PREFIX  = $(DESTDIR)/usr/local
-BINDIR  = $(PREFIX)/bin
-MANDIR  = $(PREFIX)/share/man/man1
-MANPAGE = ococo.1
+PREFIX    = $(DESTDIR)/usr/local
+BINDIR    = $(PREFIX)/bin
+MANDIR    = $(PREFIX)/share/man/man1
+MANPAGE   = ococo.1
+
+HTSLIBDIR = ext/htslib
+HTSLIB    = $(HTSLIBDIR)/libhts.a
 
 export CXX
 export CXXFLAGS
 
+export HTSLIBDIR
+export HTSLIB
+
 .PHONY: all clean install ococo
 
 all: ococo
@@ -18,14 +24,13 @@ install: ococo
 	install  ococo $(BINDIR)/ococo
 	install  $(MANPAGE) $(MANDIR)/$(MANPAGE)
 
-ococo:
-	$(MAKE) -C ./ext/htslib lib-static
+ococo: $(HTSLIB)
 	$(MAKE) -C ./src
 
-	$(CXX) $(CXXFLAGS) $(DFLAGS) ./src/*.o -o $@ -L. $(LIBS) ./ext/htslib/libhts.a
+	$(CXX) $(CXXFLAGS) $(DFLAGS) ./src/*.o -o $@ -L. $(LIBS) $(HTSLIB)
 
-ext/htslib/libhts.a:
-	$(MAKE) -C ext/htslib lib-static
+$(HTSLIB):
+	$(MAKE) -C $(HTSLIBDIR) lib-static
 
 clean:
 	$(MAKE) -C ext/htslib clean
diff --git a/src/Makefile b/src/Makefile
index 7d63f39..bd23375 100644
--- a/src/Makefile
+++ b/src/Makefile
@@ -5,11 +5,11 @@ all: misc.o main.o params.o
 HEADERS=types.h stats.h version.h
 
 main.o: main.cpp consensus.h caller.h version.h $(HEADERS)
-	$(CXX) $(CXXFLAGS) $(DFLAGS) -c $< -I ../ext/htslib/
+	$(CXX) $(CXXFLAGS) $(DFLAGS) -c $< -I ../$(HTSLIB)
 
 
 %.o: %.cpp %.h $(HEADERS)
-	$(CXX) $(CXXFLAGS) $(DFLAGS) -c $< -I ../ext/htslib/
+	$(CXX) $(CXXFLAGS) $(DFLAGS) -c $< -I ../$(HTSLIB)
 
 clean:
 	rm -f *.o