<?xml version="1.0"?>
<tool_dependency>
    <package name="perl_xml_simple" version="2.20">
        <repository changeset_revision="2ba4c9419ceb" name="package_perl_xml_simple_2_20" owner="iuc" toolshed="https://testtoolshed.g2.bx.psu.edu" />
    </package>
    <package name="bioperl" version="1.6.922">
        <repository changeset_revision="bd1fcedd9aad" name="package_bioperl_1_6" owner="iuc" toolshed="https://testtoolshed.g2.bx.psu.edu" />
    </package>
    <package name="prokka" version="1.10">
        <install version="1.0">
            <actions>
                <action type="download_by_url">http://www.vicbioinformatics.com/prokka-1.10.tar.gz</action>

                <action type="set_environment_for_install">
                   <repository changeset_revision="2ba4c9419ceb" name="package_perl_xml_simple_2_20" owner="iuc" toolshed="https://testtoolshed.g2.bx.psu.edu">
                        <package name="perl_xml_simple" version="2.20" />
                    </repository>
                    <repository changeset_revision="bd1fcedd9aad" name="package_bioperl_1_6" owner="iuc" toolshed="https://testtoolshed.g2.bx.psu.edu">
                        <package name="bioperl" version="1.6.922" />
                    </repository>
                </action>

                <action type="shell_command">bin/prokka --setupdb</action>
                <action type="move_directory_files">
                    <source_directory>.</source_directory>
                    <destination_directory>$INSTALL_DIR</destination_directory>
                </action>
                <action type="set_environment">
                    <environment_variable action="prepend_to" name="PATH">$INSTALL_DIR/bin</environment_variable>
                </action>
            </actions>
        </install>
    <readme>
        Prokka is a software tool for the rapid annotation of prokaryotic genomes. A typical 4 Mbp genome can be 
        fully annotated in less than 10 minutes on a quad-core computer, and scales well to 32 core SMP systems. 
        It produces GFF3, GBK and SQN files that are ready for editing in Sequin and ultimately submitted to Genbank/DDJB/ENA.

        http://www.vicbioinformatics.com/software.prokka.shtml

        Warning: Prokka includes custom databases and is thus about a 340 MB download!
    </readme>
  </package>
</tool_dependency>