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<?xml version="1.0"?>
<tool_dependency>
    <package name="samtools" version="0.1.18">
        <install version="1.0">
            <actions>
                <action type="download_by_url">http://sourceforge.net/projects/samtools/files/samtools/0.1.18/samtools-0.1.18.tar.bz2</action>
                <action type="shell_command">sed -i.bak -e 's/-lcurses/-lncurses/g' Makefile</action>
                <action type="shell_command">make</action>
                <action type="move_file">
                    <source>samtools</source>
                    <destination>$INSTALL_DIR/bin</destination>
                </action>
                <action type="move_file">
                    <source>misc/maq2sam-long</source>
                    <destination>$INSTALL_DIR/bin</destination>
                </action>
                <action type="set_environment">
                    <environment_variable name="PATH" action="prepend_to">$INSTALL_DIR/bin</environment_variable>
                </action>
            </actions>
        </install>
        <readme>
            Compiling SAMtools requires the ncurses and zlib development libraries.
        </readme>
    </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">$INSTALL_DIR/bin</environment_variable>
		</action>
           </actions>
       </install>
       <readme>
		GCC version 4.1 or greater is recommended. 3.x versions will typically not compile BEDTools. g++ required
       </readme>
   </package>
   <package name="contra" version="2.0.4">
        <install version="1.0">
            <actions>
                <action type="download_by_url">http://downloads.sourceforge.net/project/contra-cnv/CONTRA.V2.0/CONTRA.v2.0.4.tar.gz</action>
                <action type="shell_command">rm -rf bedtools_installation_guide.txt</action>
                <action type="shell_command">rm -rf BEDTools-User-Manual.v4.pdf</action>
                <action type="shell_command">rm -rf BEDTools.v2.11.2.tar.gz</action>
		<action type="shell_command">rm -rf CONTRA_User_Guide.2.0.pdf</action>
		<action type="make_directory">$INSTALL_DIR/bin</action>
		<action type="make_directory">$INSTALL_DIR/bin/scripts</action>
		<action type="move_file">
                    <source>contra.py</source>
                    <destination>$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>