tool_dependencies.xml

<?xml version="1.0"?>
<tool_dependency>
	<set_environment version="1.0">
        <environment_variable action="set_to" name="R_SCRIPT_PATH">$REPOSITORY_INSTALL_DIR</environment_variable>
    </set_environment>
	
    <package name="R" version="3.1.2">
        <repository name="package_r_3_1_2" owner="iuc" prior_installation_required="True" />
    </package>
    <package name="CopyNumberDeletion" version="1.0.0">
        <install version="1.0">
            <actions>
                <action type="setup_r_environment">
                    <repository  name="package_r_3_1_2" owner="iuc" >
                        <package name="R" version="3.1.2" />
                    </repository>
                    <package name="MASS" version="7.3-40">http://cran.r-project.org/src/contrib/MASS_7.3-40.tar.gz</package>
					<package name="calibrate" version="1.7.2">http://cran.r-project.org/src/contrib/calibrate_1.7.2.tar.gz</package>
					<package name="optparse" version="1.3.0">http://cran.r-project.org/src/contrib/optparse_1.3.0.tar.gz</package>
					<package name="plotrix" version="3.5-11">http://cran.r-project.org/src/contrib/plotrix_3.5-11.tar.gz</package>
					<package name="DBI" version="0.3.1">http://cran.r-project.org/src/contrib/DBI_0.3.1.tar.gz</package>
					<package name="RMySQL" version="0.10.2">http://cran.r-project.org/src/contrib/RMySQL_0.10.2.tar.gz</package>
					<package name="zoo" version="1.7-12">http://cran.r-project.org/src/contrib/zoo_1.7-12.tar.gz</package>
             </action>
            </actions>
			<action type="shell_command">ln -s \$R_SCRIPT_PATH/cnvAnalysis.R cnvAnalysis.R</action>
        </install>
        <readme>
        </readme>
    </package>    
	
	<package name="optparse" version="0.8">
        <install version="1.0">
            <actions>
                <action type="download_by_url">http://cran.r-project.org/src/contrib/Archive/optparse/optparse_0.8.tar.gz</action>
                <action type="shell_command">R CMD INSTALL optparse_0.8.tar.gz</action>
                <action type="set_environment"> <environment_variable name="PATH" action="prepend_to">$INSTALL_DIR/bin</environment_variable>
                </action>
            </actions>
        </install>
        <readme>Does not work with R versions greater than 2.9.2 </readme>
    </package>
	

</tool_dependency>