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1 <?xml version="1.0"?>
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2 <tool_dependency>
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3 <package name="blast+" version="2.2.26+">
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4 <repository changeset_revision="40c69b76b46e" name="package_blast_plus_2_2_26" owner="iuc" toolshed="http://toolshed.g2.bx.psu.edu" />
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5 </package>
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6 <package name="hmmer" version="3.1b1">
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7 <repository changeset_revision="007c736bf7e8" name="package_hmmer_3_1" owner="lionelguy" toolshed="http://toolshed.g2.bx.psu.edu" />
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8 </package>
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9 <package name="aragorn" version="1.2.36">
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10 <repository changeset_revision="f09e2902e6ed" name="package_aragorn_1_2_36" owner="iuc" toolshed="http://toolshed.g2.bx.psu.edu" />
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11 </package>
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12 <package name="infernal" version="1.1rc4">
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13 <repository changeset_revision="b9cc978bc83b" name="package_infernal_1_1rc4" owner="iuc" toolshed="http://toolshed.g2.bx.psu.edu" />
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14 </package>
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15 <package name="prokka" version="1.7">
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16 <install version="1.0">
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17 <actions>
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18 <action target_filename="" type="download_by_url">http://www.vicbioinformatics.com/prokka-1.7.tar.gz</action>
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19 <action type="move_directory_files">
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20 <source_directory>.</source_directory>
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21 <destination_directory>$INSTALL_DIR</destination_directory>
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22 </action>
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23 <action type="set_environment">
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24 <environment_variable action="prepend_to" name="PATH">$INSTALL_DIR/bin</environment_variable>
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25 </action>
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26 <action type="set_environment">
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27 <environment_variable action="set_to" name="PROKKA_SITE_OPTIONS">"--cpus 8"</environment_variable>
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28 </action>
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29 </actions>
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30 </install>
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31 <readme>
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32 Dependencies of Prokka which needs to be installed separately:
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33 - Perl core modules: File::Copy, FindBin, Getopt::Long, List::Util, Scalar::Util, Time::Piece, Time::Seconds;
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34 - Perl modules: Bio::SeqIO from BioPerl ( http://search.cpan.org/dist/BioPerl/ ) >= 1.6.1, XML::Simple ( http://search.cpan.org/dist/XML-Simple/ );
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35 - Prodigal ( http://prodigal.ornl.gov/ ) >= 2.60 ;
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36 - tbl2asn ( http://www.ncbi.nlm.nih.gov/genbank/tbl2asn2/ ) >= 21.0 ;
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37 - GNU Parallel ( http://www.gnu.org/software/parallel/ ) >= 20120322 ;
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38 - Barrnap ( http://www.vicbioinformatics.com/software.barrnap.shtml ) >= 0.1 .
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39
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40 Change the PROKKA_SITE_OPTIONS variable in the installed env.sh file to adjust the number of CPUs to use (--cpus).
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41
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42 Note: Prokka is about a 2.0 GB download due to included custom databases.
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43 </readme>
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44 </package>
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45 </tool_dependency>
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