Mercurial > repos > jjohnson > gatk2

changeset 3:0edf813146d8 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 14:19:38 -0500
parents a65944bad5c1
children 5b2009fcf2ad
files tool_dependencies.xml
diffstat 1 files changed, 5 insertions(+), 1 deletions(-) [+]
line wrap: on
line diff
--- a/tool_dependencies.xml	Thu Nov 01 14:00:40 2012 -0500
+++ b/tool_dependencies.xml	Thu Nov 01 14:19:38 2012 -0500
@@ -12,7 +12,11 @@
                     <source>GenomeAnalysisTKLite-2.2-2-gd3f5a5e/GenomeAnalysisTKLite.jar</source>
                     <destination>$INSTALL_DIR</destination>
                 </action>
-                <action type="shell_command">ln -s $INSTALL_DIR/GenomeAnalysisTKLite.jar GenomeAnalysisTK.jar</action>
+                <action type="shell_command">ln -s GenomeAnalysisTKLite.jar GenomeAnalysisTK.jar</action>
+                <action type="move_file">
+                    <source>GenomeAnalysisTK.jar</source>
+                    <destination>$INSTALL_DIR</destination>
+                </action>
                 <action type="set_environment">
                     <environment_variable name="GATK2_PATH" action="set_to">$INSTALL_DIR</environment_variable>
                 </action>