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changeset 13:bbcc2814e2a7

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Uploaded
author jorrit
date Tue, 26 Feb 2013 18:24:38 -0500
parents 2bbc96ae6ccb
children 472f70a3ecc8
files ontologizer.xml tool_dependencies.xml
diffstat 2 files changed, 2 insertions(+), 1 deletions(-) [+]
line wrap: on
line diff
--- 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>
--- 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>