tool_dependencies.xml

<?xml version="1.0"?>
<tool_dependency>
    <!-- Useful for HAC are:
        - twoBitInfo
        - sort
        - bedToBigBed
        - gff3ToGenePred
        - gtfToGenePred
        - genePredToBed
        - genePredToBigGenePred
        - faToTwoBit
        - samtools
        - pslToBigPsl
    -->
    <package name="samtools" version="1.2">
        <repository name="package_samtools_1_2" owner="iuc" prior_installation_required="True"/>
    </package>
    <package name="ucsc_hac" version="340">
        <repository name="package_ucsc_hac_340" owner="yating-l" />
    </package>
    <package name="ucsc_bigbed" version="340">
        <repository name="package_ucsc_bigbed_340" owner="yating-l" />
    </package>

    <package name="ucsc_bigwig" version="340">      
        <repository name="package_ucsc_bigwig_340" owner="yating-l" />
    </package>

</tool_dependency>