# HG changeset patch
# User yhoogstrate
# Date 1437563406 14400
# Node ID 44d7480b2ed64a151c5451932c11510d87ef97a2
# Parent  7fe7624f4d756258e88fbb9f37d31f98c8c0ae7b
Uploaded

diff -r 7fe7624f4d75 -r 44d7480b2ed6 tool_dependencies.xml
--- a/tool_dependencies.xml	Wed Jul 22 07:00:22 2015 -0400
+++ b/tool_dependencies.xml	Wed Jul 22 07:10:06 2015 -0400
@@ -22,11 +22,14 @@
                     </repository>
                 </action>
                 
+                <!-- CrossMap doesn't pick up the correct Cython path.
+                Therefore install it with a manual shell_command instead
+                of <package></package> inside the pyton_env. -->
                 <action type="shell_command">
                     export PYTHONPATH="$CYTHON_PATH/lib/python/Cython-0.20.1-py2.7-linux-x86_64.egg:$PYTHONPATH" &amp;&amp;
-                    echo $PYTHONPATH &gt; /tmp/test3.txt
-                
-                    python setup.py install --root=$INSTALL_DIR    
+                    
+                    export PYTHONPATH=$PYTHONPATH:$INSTALL_DIR/lib/python &amp;&amp;
+                    python setup.py install --install-lib $INSTALL_DIR/lib/python --install-scripts $INSTALL_DIR/bin
                 </action>
                 
                 <action type="set_environment">