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Support Prokka 1.11. Upgrade dependencies to package_barrnap_0_7, package_blast_plus_2_2_31, package_hmmer_3_1b2, package_tbl2asn_24_3.
author crs4
date Thu, 01 Oct 2015 14:14:06 -0400
parents 3ad7ef0ba385
children
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<?xml version="1.0"?>
<tool_dependency>
  <package name="blast+" version="2.2.31">
    <repository changeset_revision="16e1254ed634" name="package_blast_plus_2_2_31" owner="iuc" toolshed="https://toolshed.g2.bx.psu.edu" />
  </package>
  <package name="hmmer" version="3.1b2">
    <repository changeset_revision="040ca41b61c1" name="package_hmmer_3_1b2" owner="iuc" 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="9ec3f1e9198e" name="package_prodigal_2_60" owner="iuc" toolshed="https://toolshed.g2.bx.psu.edu" />
  </package>
  <package name="tbl2asn" version="24.3">
    <repository changeset_revision="41764d6a6a3c" name="package_tbl2asn_24_3" 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="0.7">
    <repository changeset_revision="c46ab932a19b" name="package_barrnap_0_7" owner="iuc" 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="1.11">
    <install version="1.0">
      <actions>
        <action type="download_by_url">http://www.vicbioinformatics.com/prokka-1.11.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 360 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/ ).
    </readme>
  </package>
</tool_dependency>