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<?xml version="1.0"?>
<tool_dependency>
  <set_environment version="1.0">
    <environment_variable action="set_to" name="SCRIPT_PATH">$REPOSITORY_INSTALL_DIR</environment_variable>
  </set_environment>
  
  <package name="perl" version="5.18.1">
    <install version="1.0">
      <actions>
        <action type="setup_perl_environment">
          <repository changeset_revision="35f117d7396b" name="package_perl_5_18" owner="iuc" toolshed="https://toolshed.g2.bx.psu.edu">
            <package name="perl" prior_installation_required="True" version="5.18.1" />
          </repository> 

          <!-- allow downloading and installing an Perl package from cpan.org-->
          <package>http://search.cpan.org/CPAN/authors/id/T/TO/TODDR/IPC-Run-0.94.tar.gz</package>
          <package>http://search.cpan.org/CPAN/authors/id/A/AB/ABIGAIL/Regexp-Common-2013031301.tar.gz</package>
          <package>http://search.cpan.org/CPAN/authors/id/J/JM/JMCNAMARA/OLE-Storage_Lite-0.19.tar.gz</package>
          <package>http://search.cpan.org/CPAN/authors/id/J/JM/JMCNAMARA/Spreadsheet-WriteExcel-2.40.tar.gz</package>
          <package>http://search.cpan.org/CPAN/authors/id/D/DL/DLUX/Parallel-ForkManager-0.7.5.tar.gz</package>
          <package>http://search.cpan.org/CPAN/authors/id/G/GR/GROMMEL/Math-Round-0.06.tar.gz</package>
        </action>
      <action type="set_environment">
        <environment_variable action="prepend_to" name="PERL5LIB">$INSTALL_DIR/lib/perl5</environment_variable>
      </action>
      </actions>
    </install>
  </package>

  <package name="perl" version="5.18.1">
    <repository changeset_revision="35f117d7396b" name="package_perl_5_18" owner="iuc" prior_installation_required="True" toolshed="https://toolshed.g2.bx.psu.edu" />
  </package>

  <!-- package_weblogo_3_3 has broken link in main Galaxy toolshed (February 2017) -->
  <package name="weblogo" version="3.5">
    <install version="1.0">
      <actions>
       <action type="download_by_url">https://github.com/WebLogo/weblogo/archive/master.zip</action>                               
        <!-- Use screen instead of printer to work around a color bug in ghostscript. -->
        <action type="shell_command">sed -i.bak 's#"-dPDFSETTINGS=/printer",#"-dPDFSETTINGS=/screen",#' weblogolib/__init__.py</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</environment_variable>
            <environment_variable action="prepend_to" name="PYTHONPATH">$INSTALL_DIR</environment_variable>
          </action>
        </actions>
      </install>
    <readme />
  </package>

  <package name="numpy" version="1.9">
    <repository changeset_revision="f24fc0b630fc" name="package_python_2_7_numpy_1_9" owner="iuc" prior_installation_required="True" toolshed="https://toolshed.g2.bx.psu.edu" />
  </package>

  <package name="R" version="3.2.1">
    <repository changeset_revision="d9f7d84125b7" name="package_r_3_2_1" owner="iuc" prior_installation_required="True" toolshed="https://toolshed.g2.bx.psu.edu" />
  </package>

  <!-- package_R_3_2_1 doesn't load fontconfig, load it manually -->
  <package name="fontconfig" version="2.11.1">
    <repository changeset_revision="d88d844df0cb" name="package_fontconfig_2_11_1" owner="iuc" prior_installation_required="True" toolshed="https://toolshed.g2.bx.psu.edu" />
  </package>

  <package name="mutspec" version="0.1">
    <repository changeset_revision="47d4bc32a67c" name="package_r_mutspec_0_1" owner="iarc" prior_installation_required="True" toolshed="https://toolshed.g2.bx.psu.edu" />
  </package>
    
</tool_dependency>