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1 <?xml version="1.0"?>
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2 <tool_dependency>
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3 <package name="perl_xml_simple" version="2.20">
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4 <repository changeset_revision="2ba4c9419ceb" name="package_perl_xml_simple_2_20" owner="iuc" toolshed="https://testtoolshed.g2.bx.psu.edu" />
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5 </package>
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6 <package name="bioperl" version="1.6.922">
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7 <repository changeset_revision="bd1fcedd9aad" name="package_bioperl_1_6" owner="iuc" toolshed="https://testtoolshed.g2.bx.psu.edu" />
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8 </package>
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9 <package name="prokka" version="1.10">
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10 <install version="1.0">
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11 <actions>
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12 <action type="download_by_url">http://www.vicbioinformatics.com/prokka-1.10.tar.gz</action>
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1
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13
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14 <action type="set_environment_for_install">
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15 <repository changeset_revision="2ba4c9419ceb" name="package_perl_xml_simple_2_20" owner="iuc" toolshed="https://testtoolshed.g2.bx.psu.edu">
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16 <package name="perl_xml_simple" version="2.20" />
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17 </repository>
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18 <repository changeset_revision="bd1fcedd9aad" name="package_bioperl_1_6" owner="iuc" toolshed="https://testtoolshed.g2.bx.psu.edu">
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19 <package name="bioperl" version="1.6.922" />
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20 </repository>
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21 </action>
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22
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23 <action type="shell_command">bin/prokka --setupdb</action>
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24 <action type="move_directory_files">
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25 <source_directory>.</source_directory>
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26 <destination_directory>$INSTALL_DIR</destination_directory>
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27 </action>
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28 <action type="set_environment">
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29 <environment_variable action="prepend_to" name="PATH">$INSTALL_DIR/bin</environment_variable>
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30 </action>
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31 </actions>
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32 </install>
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33 <readme>
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34 Prokka is a software tool for the rapid annotation of prokaryotic genomes. A typical 4 Mbp genome can be
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35 fully annotated in less than 10 minutes on a quad-core computer, and scales well to 32 core SMP systems.
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36 It produces GFF3, GBK and SQN files that are ready for editing in Sequin and ultimately submitted to Genbank/DDJB/ENA.
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37
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38 http://www.vicbioinformatics.com/software.prokka.shtml
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39
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40 Warning: Prokka includes custom databases and is thus about a 340 MB download!
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41 </readme>
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42 </package>
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43 </tool_dependency>
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