diff --git a/CMakeLists.txt b/CMakeLists.txt
index 3747180..8862733 100644
--- a/CMakeLists.txt
+++ b/CMakeLists.txt
@@ -1,6 +1,8 @@
 project(Haploflow)
-set(Boost_USE_STATIC_LIBS=ON)
 cmake_minimum_required(VERSION 2.8 FATAL_ERROR)
+if(NOT DEFINED Boost_USE_STATIC_LIBS)
+	set(Boost_USE_STATIC_LIBS=ON)
+endif
 
 set(CMAKE_INSTALL_RPATH_USE_LINK_PATH TRUE)
 
@@ -14,9 +16,11 @@ link_directories(
 	${Boost_LIBRARY_DIRS}
 )
 
-set(COMPILER_FLAGS
-	"-ggdb -Wall -L/usr/include -I/usr/include -std=c++0x -pipe -Wno-deprecated -pedantic"
-)
+if(NOT DEFINED COMPILER_FLAGS)
+	set(COMPILER_FLAGS
+		"-ggdb -Wall -L/usr/include -I/usr/include -std=c++0x -pipe -Wno-deprecated -pedantic"
+	)
+endif()
 
 add_executable(haploflow
 	main.cpp
@@ -30,8 +34,10 @@ add_executable(haploflow
 	UnitigGraph.cpp
 )
 
-set_target_properties(haploflow PROPERTIES
-	COMPILE_FLAGS ${COMPILER_FLAGS}
-)
+if(NOT "${COMPILER_FLAGS}" STREQUAL "")
+	set_target_properties(haploflow PROPERTIES
+		COMPILE_FLAGS ${COMPILER_FLAGS}
+	)
+endif()
 
 target_link_libraries(haploflow ${Boost_LIBRARIES})