<?xml version="1.0"?>
<tool_dependency>
    <package name="SearchGUI" version="1.13.1">
        <install version="1.0">
            <actions>
              <action type="download_by_url">http://searchgui.googlecode.com/files/SearchGUI-1.13.1_mac_and_linux.zip</action>
	      <action type="shell_command">tar -xf $DIR_NAME/*.tar</action>
	      <action type="shell_command">cd $DIR_NAME</action>
	      <action type="shell_command">chmod -R $DIR_NAME/*resources</action>
              <action type="move_directory_files">
                <source_directory>.</source_directory>
                <destination_directory>$INSTALL_DIR/</destination_directory>
              </action>
	      <action type="shell_command">mkdir -p $BIN_DIR</action>
              <action type="set_environment">
                <environment_variable name="PATH" action="prepend_to">$INSTALL_DIR</environment_variable>
              </action>                
            </actions>
        </install>
        <readme>
          This package downloads and installs the SearchGUI scripts develped as part of the Peptideshaker tool.
          (https://github.com/jmchilton/peptide-shaker).

        </readme>
    </package>
    
    <package name="PeptideShaker" version="0.20.1">
        <install version="1.0">
            <actions>
              <action type="download_by_url">http://peptide-shaker.googlecode.com/files/PeptideShaker-0.20.1.zip</action>
	      <action type="shell_command">chmod -R o+w resources</action>
              <action type="move_directory_files">
                <source_directory>.</source_directory>
                <destination_directory>$INSTALL_DIR/</destination_directory>
              </action>
              <action type="shell_command">mkdir -p $BIN_DIR</action>
              <action type="set_environment">
                <environment_variable name="PATH" action="prepend_to">$INSTALL_DIR</environment_variable>
              </action>                
            </actions>
        </install>
        <readme>
          This package downloads and installs the peptideshaker tool as a part of the peptideshaker framework.
          (https://github.com/jmchilton/peptide-shaker).

        </readme>
    </package>
</tool_dependency>