# HG changeset patch
# User jorrit
# Date 1361921078 18000
# Node ID bbcc2814e2a723bdcb554651c1b72e150ba31cf4
# Parent  2bbc96ae6ccbae376ddeda4831e789d52bf076d4
Uploaded

diff -r 2bbc96ae6ccb -r bbcc2814e2a7 ontologizer.xml
--- a/ontologizer.xml	Tue Feb 26 18:14:12 2013 -0500
+++ b/ontologizer.xml	Tue Feb 26 18:24:38 2013 -0500
@@ -1,6 +1,7 @@
 <tool id="ontologizer" name="ontologizer" version="0.0.14">
   <description>from http://compbio.charite.de/contao/</description>
   <requirements>
+    <requirement type="set_environment">ONTOLOGIZER_JAR_PATH</requirement>
     <requirement type="package" version="0.0.1">ontologizer-jar</requirement>
   </requirements>
   <command>java -Xmx2G -jar $ONTOLOGIZER_JAR --go $go --association $gaf --population $pop --studyset $study --dot 0.05 > $output</command>
diff -r 2bbc96ae6ccb -r bbcc2814e2a7 tool_dependencies.xml
--- a/tool_dependencies.xml	Tue Feb 26 18:14:12 2013 -0500
+++ b/tool_dependencies.xml	Tue Feb 26 18:24:38 2013 -0500
@@ -5,7 +5,7 @@
             <actions>
                 <action type="shell_command">curl http://compbio.charite.de/contao/index.php/cmdlineOntologizer.html?file=tl_files/ontologizer/cmdline/Ontologizer.jar > $INSTALL_DIR/ontologizer.jar</action>
                 <action type="set_environment">
-                    <environment_variable name="ONTOLOGIZER_JAR" action="set_to">$INSTALL_DIR/ontologizer.jar</environment_variable>
+                    <environment_variable name="ONTOLOGIZER_JAR_PATH" action="set_to">$INSTALL_DIR/ontologizer.jar</environment_variable>
                 </action>
             </actions>
         </install>