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<?xml version="1.0"?>
<tool_dependency>
    <package name="perl" version="5.18.1">
        <repository changeset_revision="f19b96171787" name="package_perl_5_18" owner="iuc" prior_installation_required="True" toolshed="https://testtoolshed.g2.bx.psu.edu" />
    </package>
    <package name="snvphyl" version="1.2">
        <install version="1.0">
            <actions>
                <action type="setup_perl_environment">
                    <repository changeset_revision="f19b96171787" name="package_perl_5_18" owner="iuc" toolshed="https://testtoolshed.g2.bx.psu.edu">
                        <package name="perl" version="5.18.1" />
                    </repository>
                    <package>Parallel::ForkManager</package>
                    <package>https://cpan.metacpan.org/authors/id/S/SA/SANKO/Readonly-2.00.tar.gz</package>
                    <package>https://cpan.metacpan.org/authors/id/C/CJ/CJFIELDS/BioPerl-1.6.901.tar.gz</package>
                    <package>https://cpan.metacpan.org/authors/id/A/AJ/AJPAGE/Bio-Pipeline-Comparison-1.123050.tar.gz</package>
		    <package>https://cpan.metacpan.org/authors/id/R/RE/REHSACK/List-MoreUtils-0.410.tar.gz</package>
		    <package>https://cpan.metacpan.org/authors/id/T/TO/TOBYINK/Exporter-Tiny-0.042.tar.gz</package>
		    <package>https://cpan.metacpan.org/authors/id/M/MA/MAKAMAKA/JSON-2.90.tar.gz</package>
		    <package>https://cpan.metacpan.org/authors/id/O/OV/OVID/Test-JSON-0.11.tar.gz</package>
		    <package>https://cpan.metacpan.org/authors/id/M/MI/MIKO/String-Util-1.24.tar.gz</package>
		    <package>https://cpan.metacpan.org/authors/id/R/RE/REHSACK/Hash-Merge-0.200.tar.gz</package>
                </action>

                <action type="change_directory">../</action>
                <action type="shell_command">git clone http://irida.corefacility.ca/gitlab/analysis-pipelines/snvphyl-tools.git</action>
                <action type="change_directory">snvphyl-tools</action>
                <action type="shell_command">git checkout f2396b267002ccc5696d9fecb583e000dc26fe75</action>
                <action type="change_directory">bcfplugins/bcftools-1.2</action>
                <action type="shell_command">make</action>
                <action type="change_directory">../..</action>
                <action type="move_directory_files">
                    <source_directory>.</source_directory>
                    <destination_directory>$INSTALL_DIR/snvphyl</destination_directory>
                </action>

                <action type="set_environment">
                    <environment_variable action="set_to" name="VCF2PSEUDO">$INSTALL_DIR/snvphyl</environment_variable>
                    <environment_variable action="append_to" name="LD_LIBRARY_PATH">$INSTALL_DIR/snvphyl/bcfplugins/bcftools-1.2/htslib-1.2.1</environment_variable>
                    <environment_variable action="prepend_to" name="PATH">$INSTALL_DIR/snvphyl/bcfplugins/bcftools-1.2</environment_variable>
                    <environment_variable action="prepend_to" name="PERL5LIB">$INSTALL_DIR/lib/perl5</environment_variable>
                    <environment_variable action="set_to" name="BCFTOOLS_PLUGINS">$INSTALL_DIR/snvphyl/bcfplugins/bcftools-1.2/plugins</environment_variable>
                </action>

            </actions>
        </install>
        <readme>
        </readme>
    </package>


</tool_dependency>