diff --git a/tools/cooja/config/external_tools_freebsd.config b/tools/cooja/config/external_tools_freebsd.config
index f0c2a77c0..236150cdc 100644
--- a/tools/cooja/config/external_tools_freebsd.config
+++ b/tools/cooja/config/external_tools_freebsd.config
@@ -22,7 +22,7 @@ CONTIKI_STANDARD_PROCESSES = sensors_process;etimer_process
 CONTIKI_MAIN_TEMPLATE_FILENAME = contiki_template.c
 CORECOMM_TEMPLATE_FILENAME = corecomm_template.java
 PATH_JAVAC = javac
-DEFAULT_PROJECTDIRS = ../apps/mrm;../apps/mspsim;../apps/avrora
+DEFAULT_PROJECTDIRS = [CONTIKI_DIR]/tools/cooja/apps/mrm;[CONTIKI_DIR]/tools/cooja/apps/mspsim;[CONTIKI_DIR]/tools/cooja/apps/avrora
 
 PARSE_WITH_COMMAND=false
 PARSE_COMMAND=nm -a $(LIBFILE)
diff --git a/tools/cooja/config/external_tools_linux.config b/tools/cooja/config/external_tools_linux.config
index 4c3687cc2..0f08728f4 100644
--- a/tools/cooja/config/external_tools_linux.config
+++ b/tools/cooja/config/external_tools_linux.config
@@ -22,7 +22,7 @@ CONTIKI_STANDARD_PROCESSES = sensors_process;etimer_process
 CONTIKI_MAIN_TEMPLATE_FILENAME = contiki_template.c
 CORECOMM_TEMPLATE_FILENAME = corecomm_template.java
 PATH_JAVAC = javac
-DEFAULT_PROJECTDIRS = ../apps/mrm;../apps/mspsim;../apps/avrora
+DEFAULT_PROJECTDIRS = [CONTIKI_DIR]/tools/cooja/apps/mrm;[CONTIKI_DIR]/tools/cooja/apps/mspsim;[CONTIKI_DIR]/tools/cooja/apps/avrora
 
 PARSE_WITH_COMMAND=false
 PARSE_COMMAND=nm -a $(LIBFILE)
diff --git a/tools/cooja/config/external_tools_linux_64.config b/tools/cooja/config/external_tools_linux_64.config
index cc671103b..efae605f9 100644
--- a/tools/cooja/config/external_tools_linux_64.config
+++ b/tools/cooja/config/external_tools_linux_64.config
@@ -22,7 +22,7 @@ CONTIKI_STANDARD_PROCESSES = sensors_process;etimer_process
 CONTIKI_MAIN_TEMPLATE_FILENAME = contiki_template.c
 CORECOMM_TEMPLATE_FILENAME = corecomm_template.java
 PATH_JAVAC = javac
-DEFAULT_PROJECTDIRS = ../apps/mrm;../apps/mspsim;../apps/avrora
+DEFAULT_PROJECTDIRS = [CONTIKI_DIR]/tools/cooja/apps/mrm;[CONTIKI_DIR]/tools/cooja/apps/mspsim;[CONTIKI_DIR]/tools/cooja/apps/avrora
 
 PARSE_WITH_COMMAND=false
 PARSE_COMMAND=nm -a $(LIBFILE)
diff --git a/tools/cooja/config/external_tools_macosx.config b/tools/cooja/config/external_tools_macosx.config
index 3c923407b..88823ca2e 100644
--- a/tools/cooja/config/external_tools_macosx.config
+++ b/tools/cooja/config/external_tools_macosx.config
@@ -22,7 +22,7 @@ CONTIKI_STANDARD_PROCESSES = sensors_process;etimer_process
 CONTIKI_MAIN_TEMPLATE_FILENAME = contiki_template.c
 CORECOMM_TEMPLATE_FILENAME = corecomm_template.java
 PATH_JAVAC = javac
-DEFAULT_PROJECTDIRS = ../apps/mrm;../apps/mspsim;../apps/avrora
+DEFAULT_PROJECTDIRS = [CONTIKI_DIR]/tools/cooja/apps/mrm;[CONTIKI_DIR]/tools/cooja/apps/mspsim;[CONTIKI_DIR]/tools/cooja/apps/avrora
 
 PARSE_WITH_COMMAND = true
 PARSE_COMMAND = /opt/contiki-2.x/tools/cooja/examples/jni_test/mac_users/nmandsize $(LIBFILE)
diff --git a/tools/cooja/config/external_tools_win32.config b/tools/cooja/config/external_tools_win32.config
index 958007bc6..1cd8bba88 100644
--- a/tools/cooja/config/external_tools_win32.config
+++ b/tools/cooja/config/external_tools_win32.config
@@ -22,7 +22,7 @@ CONTIKI_STANDARD_PROCESSES = sensors_process;etimer_process
 CONTIKI_MAIN_TEMPLATE_FILENAME = contiki_template.c
 CORECOMM_TEMPLATE_FILENAME = corecomm_template.java
 PATH_JAVAC = javac
-DEFAULT_PROJECTDIRS = ../apps/mrm;../apps/mspsim;../apps/avrora
+DEFAULT_PROJECTDIRS = [CONTIKI_DIR]/tools/cooja/apps/mrm;[CONTIKI_DIR]/tools/cooja/apps/mspsim;[CONTIKI_DIR]/tools/cooja/apps/avrora
 
 PARSE_WITH_COMMAND = true
 PARSE_COMMAND=nm -C $(LIBFILE)