<?xml version="1.0"?>
<tool_dependency>
    <set_environment version="1.0">
        <environment_variable name="JAR_PATH" action="set_to">$REPOSITORY_INSTALL_DIR</environment_variable>   
    </set_environment>

    <set_environment version="1.0">
	<environment_variable name="CIRCOS_SCRIPT_PATH" action="set_to">$REPOSITORY_INSTALL_DIR</environment_variable>
    </set_environment>

<package name="circos" version="0.64">
        <install version="1.0">
            <actions>          
               <!-- Downloads the Circos software from its website and unpacks it -->
               <action type="download_by_url">http://circos.ca/distribution/circos-0.64.tgz </action>
               <action type="move_directory_files">
                    <source_directory>.</source_directory>
                    <destination_directory>$INSTALL_DIR/</destination_directory>
               </action>                
               <action type="set_environment">
                        <environment_variable name="CIRCOS_PATH" action="set_to">$INSTALL_DIR</environment_variable>
                </action>                            
            </actions>
        </install>
        <readme>
Downloads and installs Circos (v.0.64) for use in visualization. Requires perl to be installed.
        </readme>
    </package>  

    <set_environment version="1.0">
	<environment_variable name="R_PATH" action="set_to">$REPOSITORY_INSTALL_DIR</environment_variable>
    </set_environment>

    <package name="package_r_3_0_2" version="3.0.2">
                        <repository changeset_revision="50f7e1e71271" name="package_r_3_0_2" owner="iuc" prior_installation_required="True" toolshed="https://toolshed.g2.bx.psu.edu" />
                    </package>

</tool_dependency>