<?xml version="1.0"?>
<tool_dependency>
  <package name="blast+" version="2.2.26+">
    <repository changeset_revision="40c69b76b46e" name="package_blast_plus_2_2_26" owner="iuc" toolshed="http://toolshed.g2.bx.psu.edu" />
  </package>
  <package name="hmmer" version="3.1b1">
    <repository changeset_revision="007c736bf7e8" name="package_hmmer_3_1" owner="lionelguy" toolshed="http://toolshed.g2.bx.psu.edu" />
  </package>
  <package name="aragorn" version="1.2.36">
    <repository changeset_revision="f09e2902e6ed" name="package_aragorn_1_2_36" owner="iuc" toolshed="http://toolshed.g2.bx.psu.edu" />
  </package>
  <package name="infernal" version="1.1rc4">
    <repository changeset_revision="b9cc978bc83b" name="package_infernal_1_1rc4" owner="iuc" toolshed="http://toolshed.g2.bx.psu.edu" />
  </package>
  <package name="prokka" version="1.7">
    <install version="1.0">
      <actions>
        <action target_filename="" type="download_by_url">http://www.vicbioinformatics.com/prokka-1.7.tar.gz</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>
        <action type="set_environment">
          <environment_variable action="set_to" name="PROKKA_SITE_OPTIONS">"--cpus 8"</environment_variable>
        </action>
      </actions>
    </install>
    <readme>
Dependencies of Prokka which needs to be installed separately:
- Perl core modules: File::Copy, FindBin, Getopt::Long, List::Util, Scalar::Util, Time::Piece, Time::Seconds;
- Perl modules: Bio::SeqIO from BioPerl ( http://search.cpan.org/dist/BioPerl/ ) &gt;= 1.6.1, XML::Simple ( http://search.cpan.org/dist/XML-Simple/ );
- Prodigal ( http://prodigal.ornl.gov/ ) &gt;= 2.60 ;
- tbl2asn ( http://www.ncbi.nlm.nih.gov/genbank/tbl2asn2/ ) &gt;= 21.0 ;
- GNU Parallel ( http://www.gnu.org/software/parallel/ ) &gt;= 20120322 ;
- Barrnap ( http://www.vicbioinformatics.com/software.barrnap.shtml ) &gt;= 0.1 .

Change the PROKKA_SITE_OPTIONS variable in the installed env.sh file to adjust the number of CPUs to use (--cpus).

Note: Prokka is about a 2.0 GB download due to included custom databases.
    </readme>
  </package>
</tool_dependency>