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Use <stdio> because prokka writes some warnings on stderr. Update Orione citation. Update Prokka citation. Support Prokka 1.10. Upgrade dependencies to package_minced_0_1_6, package_barrnap_0_5 and package_tbl2asn_23_7. Added --proteins option. Add <citations>.
author crs4
date Mon, 27 Oct 2014 06:45:52 -0400
parents b9fea998270a
children f5e44aad6498
line wrap: on
line source

<?xml version="1.0"?>
<tool_dependency>
  <package name="blast+" version="2.2.28">
    <repository changeset_revision="23b9ba41ad00" name="package_blast_plus_2_2_28" owner="iuc" toolshed="https://toolshed.g2.bx.psu.edu" />
  </package>
  <package name="hmmer" version="3.1b1">
    <repository changeset_revision="007c736bf7e8" name="package_hmmer_3_1" owner="lionelguy" toolshed="https://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="https://toolshed.g2.bx.psu.edu" />
  </package>
  <package name="prodigal" version="2.60">
    <repository changeset_revision="acf0e8b718c9" name="package_prodigal_2_60" owner="iuc" toolshed="https://toolshed.g2.bx.psu.edu" />
  </package>
  <package name="tbl2asn" version="23.7">
    <repository changeset_revision="2271d52a8531" name="package_tbl2asn_23_7" owner="takadonet" toolshed="https://toolshed.g2.bx.psu.edu" />
  </package>
  <package name="gnu_parallel" version="20131122">
    <repository changeset_revision="0e1e79b3b7db" name="package_gnu_parallel_20131122" owner="iuc" toolshed="https://toolshed.g2.bx.psu.edu" />
  </package>
  <package name="barrnap" version="0.5">
    <repository changeset_revision="ec528d56b01f" name="package_barrnap_0_5" owner="takadonet" toolshed="https://toolshed.g2.bx.psu.edu" />
  </package>
  <package name="infernal" version="1.1">
    <repository changeset_revision="b5c01b683dc9" name="package_infernal_1_1" owner="iuc" toolshed="https://toolshed.g2.bx.psu.edu" />
  </package>
  <package name="minced" version="0.1.6">
    <repository changeset_revision="a135862cd007" name="package_minced_0_1_6" owner="takadonet" toolshed="https://toolshed.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="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>
Warning: Prokka includes custom databases and is thus about a 340 MB download!

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;= 1.6.900, XML::Simple ( http://search.cpan.org/dist/XML-Simple/ ).

Configuration: Previously (until Release 2), the PROKKA_SITE_OPTIONS variable in the installed env.sh file was used to adjust the number of CPUs to use (--cpus). This is not used anymore and may be removed.
    </readme>
  </package>
</tool_dependency>