annotate tool_dependencies.xml @ 0:4ecb2ce50254 draft default tip

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<?xml version="1.0"?>
<tool_dependency>
  <package name="perl" version="5.18.1">
    <repository changeset_revision="114b6af405fa" name="package_perl_5_18" owner="iuc" prior_installation_required="True" toolshed="https://toolshed.g2.bx.psu.edu"/>
  </package>
  <package name="loadTaxonomy" version="1.0">
    <install version="1.0">
      <actions>
        <action type="set_environment_for_install">
          <repository changeset_revision="114b6af405fa" name="package_perl_5_18" owner="iuc" toolshed="https://toolshed.g2.bx.psu.edu">
            <package name="perl" version="5.18.1" />
          </repository>
        </action>
        <action type="setup_perl_environment">
          <package>Data::Dumper</package>
          <package>File::Basename</package>
          <package>Getopt::Long</package>
          <package>DBI</package>
          <package>SQL::SplitStatement</package>
          <package>$INSTALL_DIR/perl/lib</package>
        </action>
        <action type="download_by_url">
          ftp://ftp.ncbi.nih.gov/pub/taxonomy/gi_taxid_nucl.dmp.gz
        </action>
        <action type="shell_command">
          gunzip gi_taxid_nucl.dmp.gz
        </action>
        <action type="download_by_url">
          ftp://ftp.ncbi.nih.gov/pub/taxonomy/gi_taxid_prot.dmp.gz
        </action>
        <action type="shell_command">
          gunzip gi_taxid_prot.dmp.gz
        </action>
        <action type="download_by_url">
          ftp://ftp.ncbi.nih.gov/pub/taxonomy/taxdmp.zip
        </action>
        <action type="shell_command">
          gunzip taxdmp.zip
        </action>
        <action type="set_environment">
          <environment_variable name="PATH" action="prepend_to">$INSTALL_DIR/perl/scripts</environment_variable>
        </action>
        <action type="shell_command">
          loadTaxonomy.pl
        </action>
      </actions>
    </install>
  </package>
</tool_dependency>