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diff tool_dependencies.xml @ 2:a65944bad5c1 draft

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tool_dependencies.xml - fix move_file and add symlink
author Jim Johnson <jj@umn.edu>
date Thu, 01 Nov 2012 14:00:40 -0500
parents 9b8e2a158073
children 0edf813146d8
line wrap: on
line diff
--- a/tool_dependencies.xml	Thu Nov 01 13:44:41 2012 -0500
+++ b/tool_dependencies.xml	Thu Nov 01 14:00:40 2012 -0500
@@ -10,8 +10,9 @@
                  -->
                 <action type="move_file">
                     <source>GenomeAnalysisTKLite-2.2-2-gd3f5a5e/GenomeAnalysisTKLite.jar</source>
-                    <destination>$INSTALL_DIR/GenomeAnalysisTK.jar</destination>
+                    <destination>$INSTALL_DIR</destination>
                 </action>
+                <action type="shell_command">ln -s $INSTALL_DIR/GenomeAnalysisTKLite.jar GenomeAnalysisTK.jar</action>
                 <action type="set_environment">
                     <environment_variable name="GATK2_PATH" action="set_to">$INSTALL_DIR</environment_variable>
                 </action>