<?xml version="1.0"?>
<tool_dependency>
  <package name="prokka" version="1.7">
        <install version="1.0">
            <actions>
                <action type="download_by_url">http://www.vicbioinformatics.com/prokka-1.7.tar.gz</action>
                <!-- Copying the whole bin, binaries, doc and db folders -->
		<action type="make_directory">$INSTALL_DIR/bin</action>
		<action type="make_directory">$INSTALL_DIR/binaries</action>
		<action type="make_directory">$INSTALL_DIR/db</action>
		<action type="make_directory">$INSTALL_DIR/doc</action>
		<action type="move_directory_files">
		  <source_directory>bin</source_directory>
		  <destination_directory>$INSTALL_DIR/bin</destination_directory>
		</action>
                <action type="move_directory_files">
		  <source_directory>binaries</source_directory>
		  <destination_directory>$INSTALL_DIR/binaries</destination_directory>
		</action>
                <action type="move_directory_files">
		  <source_directory>db</source_directory>
		  <destination_directory>$INSTALL_DIR/db</destination_directory>
		</action>
                <action type="move_directory_files">
		  <source_directory>doc</source_directory>
		  <destination_directory>$INSTALL_DIR/doc</destination_directory>
		</action>
                <action type="set_environment">
		  <environment_variable name="PATH" action="prepend_to">$INSTALL_DIR/bin</environment_variable>
                </action>
            </actions>
        </install>
    
    <readme>
This installs prokka 1.7
Note: this is about a 2.0 GB download due to included custom databases.</readme>
  </package>
</tool_dependency>