<?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" />
    </set_environment>

    <package name="samtools" version="0.1.19">
        <repository changeset_revision="00e17a794a2e" name="package_samtools_0_1_19" owner="iuc" toolshed="http://toolshed.g2.bx.psu.edu" />
    </package>
</tool_dependency>