<?xml version="1.0"?>
<tool_dependency>
    <package name="bedtools" version="2.18.2">
        <install version="1.0">
            <actions>
                <action type="shell_command">git clone --recursive https://github.com/arq5x/bedtools.git</action>
                <action type="shell_command">git reset --hard 393fc3b9b766c76cc62e3f0df4e59ffbff3a55fb</action>
                <action type="shell_command">make</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>
            BEDTools is a collection of utilities for comparing, summarizing, and intersecting genomic features in BED, GTF/GFF, VCF and BAM formats.
            https://github.com/arq5x/bedtools2
        </readme>
    </package>
</tool_dependency>