<?xml version="1.0"?>
<tool_dependency>
    <!-- UCSC Tools in  -->
    <!-- Useful for HAC are:
        - twoBitInfo
        - sort
        - bedToBigBed
        - gff3ToGenePred
        - gtfToGenePred
        - genePredToBed
        - genePredToBigGenePred
        - faToTwoBit
        - samtools
        - pslToBigPsl
    -->
    <package name="samtools" version="1.2">
        <repository changeset_revision="f6ae3ba3f3c1" name="package_samtools_1_2" owner="iuc" prior_installation_required="True" toolshed="https://toolshed.g2.bx.psu.edu" />
    </package>
    
    <package name="ucsc_tools_340" version="1.0">
        <install version="1.0">
            <actions_group>
                <actions architecture="x86_64" os="linux">
                    <action type="download_by_url">http://old-gep.wustl.edu/~galaxy/ucsc_tools_340.tar.gz</action>
                    <action type="move_directory_files">
                        <source_directory>.</source_directory>                       
                        <destination_directory>$INSTALL_DIR/bin</destination_directory>
                    </action>    
                </actions>
                <action type="set_environment">
                    <environment_variable action="prepend_to" name="PATH">$INSTALL_DIR/bin</environment_variable>
                </action>
            </actions_group>
         </install>
         <readme>The well known UCSC tools from Jim Kent.</readme>
    </package>
    
</tool_dependency>