diff --git a/Makefile b/Makefile
index eb2f97ae396678f8489b416ccc0327409939bec5..bbbc4379cee64e236b530425dfca46f3fcd2aac6 100644
--- a/Makefile
+++ b/Makefile
@@ -19,12 +19,11 @@ export CXX		= g++
 #ifeq ($(DEBUG),1)
 #export CXXFLAGS = -Wall -O0 -g -fno-inline -fkeep-inline-functions -D_FILE_OFFSET_BITS=64 -fPIC -DDEBUG -D_DEBUG
 #else
-export CXXFLAGS = -Wall -O2 -D_FILE_OFFSET_BITS=64 -fPIC
+export CXXFLAGS = -Wall -O2 -D_FILE_OFFSET_BITS=64 -fPIC $(INCLUDE)
 #endif
 export LIBS		= -lz
 export BT_ROOT  = src/utils/BamTools/
 
-
 SUBDIRS = $(SRC_DIR)/annotateBed \
 		  $(SRC_DIR)/bamToBed \
 		  $(SRC_DIR)/bamToFastq \