annotate tool_dependencies.xml @ 0:960f83563956 draft default tip

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<?xml version="1.0"?>
<tool_dependency>
    <package name="bedtools" version="2.22">
        <install version="1.0">
            <actions>
                <action type="download_by_url">https://github.com/arq5x/bedtools2/releases/download/v2.22.1/bedtools-2.22.1.tar.gz</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.</readme>
    </package>
</tool_dependency>