<?xml version="1.0"?>
<tool_dependency>
    
    <package name="R" version="3.0.3">
        <repository name="package_r_3_0_3" owner="iuc" />
    </package>
    
    <package name="samtools" version="0.1.18">
        <repository name="package_samtools_0_1_18" owner="devteam" />
    </package>

   <package name="bedtools" version="2.17.0">
       <install version="1.0">
        <actions>
            <action type="download_by_url" target_filename="bedtools-2.17.0.tar.gz" >http://bedtools.googlecode.com/files/BEDTools.v2.17.0.tar.gz</action>
            <action type="shell_command">make all</action>
            <action type="make_directory">$INSTALL_DIR/bin</action>
            <action type="move_directory_files">
                <source_directory>bin</source_directory>
                <destination_directory>$INSTALL_DIR/bin</destination_directory>
            </action>                   
    		<action type="set_environment">
    		   <environment_variable name="PATH" action="prepend_to">$INSTALL_DIR/bin</environment_variable>
    		</action>
        </actions>
       </install>
       <readme>
		GCC version 4.1 or greater is recommended. 3.x versions will typically not compile BEDTools. g++ required
       </readme>
   </package>
   <package name="contra" version="2.0.4">
        <install version="1.0">
            <actions>
                <action type="download_by_url">http://downloads.sourceforge.net/project/contra-cnv/CONTRA.V2.0/CONTRA.v2.0.4.tar.gz</action>
                <action type="move_file">
                    <source>contra.py</source>
                    <destination>$INSTALL_DIR/bin</destination>
                </action>
                <action type="move_file">
                    <source>baseline.py</source>
                    <destination>$INSTALL_DIR/bin</destination>
                </action>
                <action type="move_directory_files">
                    <source_directory>scripts</source_directory>
                    <destination_directory>$INSTALL_DIR/bin/scripts</destination_directory>
                </action>
                <action type="set_environment">
                    <environment_variable name="PATH" action="prepend_to">$INSTALL_DIR/bin</environment_variable>
                </action>
            </actions>
        </install>
        <readme>
            Contra requires Samtools, Bedtools, Python and R
        </readme>
    </package>
</tool_dependency>