<?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>  

 <package name="R_3_0_1" version="3.0.1">
        <install version="1.0">
            <actions>
                <action type="download_by_url">http://cran.ms.unimelb.edu.au/src/base/R-3/R-3.0.1.tar.gz</action>
                <!--<action type="set_environment_for_install">
                    <repository name="package_readline_6_2" owner="iuc">
                        <package name="readline" version="6.2" />
                    </repository>
                </action>-->

                <action type="shell_command">
                    ./configure --with-readline=no --enable-R-shlib  --with-x=no --libdir=$INSTALL_DIR/lib/ --bindir=$INSTALL_DIR/bin/ --datarootdir=$INSTALL_DIR/share/
                </action>
                <action type="shell_command">make</action>
                <action type="shell_command">make install</action>
                <action type="set_environment">
                    <environment_variable action="set_to" name="R_HOME">$INSTALL_DIR/lib/R</environment_variable>
                    <environment_variable action="set_to" name="R_LIBS">$INSTALL_DIR/lib/R/library</environment_variable>
                    <environment_variable action="prepend_to" name="PATH">$INSTALL_DIR/lib/R/bin</environment_variable>
                    <environment_variable action="append_to" name="LD_LIBRARY_PATH">$INSTALL_DIR/lib/R/lib</environment_variable>
                    <environment_variable action="set_to" name="RHOME">$INSTALL_DIR/lib/R</environment_variable>
                    <environment_variable action="set_to" name="R_PATH">$INSTALL_DIR/lib/R/bin</environment_variable>
                </action>
            </actions>
        </install>
        <readme>R is a free software environment for statistical computing and graphics. http://www.r-project.org/</readme>
    </package>    

</tool_dependency>