diff --git a/misc-scripts/alternative_splicing/AltSplicingToolkit/src/Makefile.am b/misc-scripts/alternative_splicing/AltSplicingToolkit/src/Makefile.am
index f5176be84ad712ab5d6ac66ff5a307e05550107b..7b8a00d6c8ed9c6c2da36104ff7325458e71f707 100644
--- a/misc-scripts/alternative_splicing/AltSplicingToolkit/src/Makefile.am
+++ b/misc-scripts/alternative_splicing/AltSplicingToolkit/src/Makefile.am
@@ -5,7 +5,7 @@ bin_CPPFLAGS = -L@top_srcdir@/src
 LDADD = -lAltSplicing -lm
 
 altSpliceFinder_SOURCES = Main.cpp Constants.h
-altSpliceFinder_CPPFLAGS = -L@top_srcdir@/src
+altSpliceFinder_CPPFLAGS = @CPPFLAGS@ -L@top_srcdir@/src
 
 # general use to compile individuals objects
 AM_CPPFLAGS = -I@top_srcdir@/src -L@top_srcdir@/src