<?xml version="1.0"?>
<tool_dependency>
  <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="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="aragorn" version="1.2.36">
    <repository changeset_revision="d34f31cbc9dd" name="trna_prediction" owner="bgruening" toolshed="http://toolshed.g2.bx.psu.edu" />
  </package>
  <package name="prodigal" version="2.60">
    <repository changeset_revision="304c1a67bb7b" name="prodigal" owner="edward-kirton" toolshed="http://toolshed.g2.bx.psu.edu" />
  </package>
  <package name="package_barrnap_0_1" version="0.1">
    <repository changeset_revision="a41418a3bd38" name="barrnap" owner="simon-gladman" toolshed="http://toolshed.g2.bx.psu.edu" />
  </package>
  <!--<package name="infernal" version="1.1rc4">
    <repository name="package_infernal_1_1rc4" owner="iuc" />
  </package> -->
    <package name="prokka" version="1.7">
      <install version="1.0">
	<actions>
                <action type="download_by_url">http://www.vicbioinformatics.com/prokka-1.7.tar.gz</action>
                <!-- Copying the whole bin, binaries, doc and db folders -->
                <action type="make_directory">$INSTALL_DIR/bin</action>
                <action type="make_directory">$INSTALL_DIR/binaries</action>
                <action type="make_directory">$INSTALL_DIR/db</action>
                <action type="make_directory">$INSTALL_DIR/doc</action>
                <action type="move_directory_files">
                  <source_directory>bin</source_directory>
                  <destination_directory>$INSTALL_DIR/bin</destination_directory>
                </action>
                        <action type="move_directory_files">
                  <source_directory>binaries</source_directory>
                  <destination_directory>$INSTALL_DIR/binaries</destination_directory>
                </action>
                        <action type="move_directory_files">
                  <source_directory>db</source_directory>
                  <destination_directory>$INSTALL_DIR/db</destination_directory>
                </action>
                        <action type="move_directory_files">
                  <source_directory>doc</source_directory>
                  <destination_directory>$INSTALL_DIR/doc</destination_directory>
                </action>
                <action type="set_environment">
                    <environment_variable action="prepend_to" name="PATH">$INSTALL_DIR/bin</environment_variable>
                </action>
            </actions>
        </install>
    <readme>
This installs prokka 1.7
Note: this is about a 2.0 GB download due to included custom databases.</readme>
  </package>
</tool_dependency>