view tool_dependencies.xml @ 5:f9fc927e56c3 draft

xml escapes in tool_dependencies.xml

<?xml version="1.0"?>
<tool_dependency>
    <package name="KronaTools" version="2.2">
        <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 &amp;&amp; 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">cd $INSTALL_DIR &amp;&amp; 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 $INSTALL_DIR &amp;&amp; if curl --help 2>i1 > /dev/null; then ./updateTaxonomy.sh; fi</action>
                <!-- copy javascript to galaxy/static/krona/ 
                <action type="shell_command">./deployResources.sh /static/krona</action>
                -->
                <action type="set_environment">
                    <environment_variable name="PATH" action="prepend_to">$INSTALL_DIR/bin</environment_variable>
                </action>
            </actions>
        </install>
        <readme>http://sourceforge.net/p/krona/home/krona/</readme>
    </package>
</tool_dependency>