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<?xml version="1.0"?>
<tool_dependency>
    <set_environment version="1.0">
        <environment_variable action="set_to" name="GATK2_PATH">/please set the path to your GATK2 dir in the corresponding env.sh file/</environment_variable>
    </set_environment>
    <!--
    Use GATK2_SITE_OPTIONS to set additional parameters that should be inserted in every GATK2 call.
    The intended use case was to prohibit GATK2 to collect and send data.
    For example:

    -et "NO_ET" -K "/data/gatk2_key_file" ##ET no phone home
    -->
    <set_environment version="1.0">
        <environment_variable action="set_to" name="GATK2_SITE_OPTIONS"> </environment_variable>
    </set_environment>

    <package name="samtools" version="0.1.19">
        <repository changeset_revision="c9bd782f5342" name="package_samtools_0_1_19" owner="iuc" toolshed="https://toolshed.g2.bx.psu.edu" />
    </package>
    <package name="picard" version="1.56.0">
        <repository changeset_revision="99a28567c3a3" name="package_picard_1_56_0" owner="devteam" toolshed="https://toolshed.g2.bx.psu.edu" />
    </package>
    <package name="ggplot2" version="0.9.3">
        <repository changeset_revision="07de191649b4" name="package_r_ggplot2_0_9_3" owner="iuc" toolshed="https://toolshed.g2.bx.psu.edu" />
    </package>
</tool_dependency>