<?xml version="1.0"?>
<tool_dependency>
    <package name="vcftools" version="0.1.11">
        <install version="1.0">
            <actions>
                <action type="download_by_url">http://downloads.sourceforge.net/project/vcftools/vcftools_0.1.11.tar.gz</action>
                <action type="shell_command">make</action>
                <action type="shell_command">PREFIX="$INSTALL_DIR/vcftools" make install</action>
                <!-- For some reason, the vcftools binary does not get installed using 'make install' above, so include manually. -->
                <action type="shell_command">cp bin/vcftools $INSTALL_DIR/vcftools/bin</action>
                <action type="set_environment">
                    <environment_variable name="PATH" action="prepend_to">$INSTALL_DIR/vcftools/bin</environment_variable>
                </action>
                <action type="set_environment">
                    <environment_variable name="PERL5LIB" action="prepend_to">$INSTALL_DIR/vcftools/lib/perl5/site_perl</environment_variable>
                </action>
            </actions>
        </install>
        <readme>
            A set of tools written in Perl and C++ for working with VCF files, such as those generated by the 1000 Genomes Project
        </readme>
    </package>
</tool_dependency>