comparison tool_dependencies.xml @ 4:d3d47c77ec79 draft

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3:715e125409e2

<?xml version="1.0"?>
<tool_dependency>
 <package name="ngchm" version="1.2">
    <install version="1.0">
    <actions>
        <action type="shell_command">cd $GALAXY_ROOT_DIR</action>
        <action type="shell_command">hg clone https://[e-mail]/repos/insilico-bob/ngchm</action>
        <action type="shell_command">mkdir -p -m 777 $GALAXY_ROOT_DIR/test-data/MDAheatmap</action>
        <action type="move_directory_files">
           <source_directory>./TestFiles</source_directory>
            <destination_directory>$GALAXY_ROOT_DIR/test-data/MDAheatmap</destination_directory>
        </action>
        <action type="shell_command">mkdir -p -m 777 $GALAXY_ROOT_DIR/config/plugins/visualizations/MDAheatmap/</action>
        <action type="move_directory_files">
           <source_directory>./MDAheatmap/</source_directory>
           <destination_directory>$GALAXY_ROOT_DIR/config/plugins/visualizations/MDAheatmap/</destination_directory>
        </action>
        <action type="shell_command">cd $GALAXY_ROOT_DIR/config/plugins/visualizations/MDAheatmap/templates</action>
        <action type="shell_command">make</action>
     </actions>
   </install>
   <readme>Completed adding MDAnderson ngchm tool to Galaxy</readme>
 </package>
</tool_dependency>

4:d3d47c77ec79

<tool_dependency >
<!--  https://wiki.galaxyproject.org/ToolDependenciesTagSets -->
      	<actions>
      		<action type="shell_command">echo 'starting tool dependency script'</action>
      		<action type="change_directory">/shed_tools/toolshed.g2.bx.psu.edu/repos/insilico-bob/ngchm_dependencies/*/ngchm_dependencies/</action>        		
      		<action type="chmod"><file mode="755">./MDAHeatmap/*</file></action>
<!--##### Place MDA software in Tools and Visualization directories #####   -->
      		<action type="shell_command">echo 'Place MD Anderson test input and output files in ~/test-data directory'</action>
      		<action type="shell_command">mkdir $GALAXY_ROOT/config/plugins/visualizations/mda_heatmap_viz/</action>
      		<action type="move_directory_files"><source_directory>./MDAHeatmap/</source_directory><destination_directory>$GALAXY_ROOT/config/plugins/visualizations/mda_heatmap_viz/</destination_directory></action>
<!-- ##### Place MD Anderson test input and output files in ~/test-data directory #####   -->
      		<action type="shell_command">echo 'Place MD Anderson software in test data directories'</action>
      		<action type="move_directory_files"><source_directory>./TestFiles/</source_directory><destination_directory>$GALAXY_ROOT/test-data/</destination_directory></action>
      	</actions>
</tool_dependency>