diff tool_dependencies.xml @ 4:10132903b38b draft

Copy files to INSTALL_DIR

--- a/tool_dependencies.xml	Mon Oct 29 16:05:59 2012 -0500
+++ b/tool_dependencies.xml	Tue Oct 30 09:33:14 2012 -0500
@@ -4,12 +4,19 @@
         <install version="1.0">
             <actions>
                 <action type="download_by_url">http://sourceforge.net/projects/krona/files/KronaTools%20%28Mac%2C%20Linux%29/KronaTools-2.2.tar</action>
+                <action type="move_directory_files">
+                    <source_directory>.</source_directory>
+                    <destination_directory>$INSTALL_DIR</destination_directory>
+                </action>
                 <!-- Downloaded NCBI taxonomy will be over 1.8GB after processing,  Instead of $INSTALL_DIR/  maybe should be in a galaxy data dir -->
+                <!--  The KronaTools tar includes an empty taxonomy dir
                 <action type="make_directory">$INSTALL_DIR/taxonomy</action>
+                <action type="shell_command">cd $INSTALL_DIR && perl install.pl --prefix $INSTALL_DIR --taxonomy $INSTALL_DIR/taxonomy</action>
+                -->
                 <!-- With prefix arg "$INSTALL_DIR" installs code into: $INSTALL_DIR/bin/ -->
-                <action type="shell_command">perl install.pl --prefix $INSTALL_DIR --taxonomy $INSTALL_DIR/taxonomy</action>
-                <!-- Down load and process NCBI Taxonomy data -->
-                <action type="shell_command">./updateTaxonomy.sh</action>
+                <action type="shell_command">cd $INSTALL_DIR && perl install.pl --prefix $INSTALL_DIR</action>
+                <!-- Down load and process NCBI Taxonomy data, the  updateTaxonomy.sh script relies on the curl command -->
+                <action type="shell_command">cd $INSTALL_DIR && if curl --help 2>i1 > /dev/null; then ./updateTaxonomy.sh; fi</action>
                 <!-- copy javascript to galaxy/static/krona/ 
                 <action type="shell_command">./deployResources.sh /static/krona</action>
                 -->