code: private String getConfigPathFromRoot(File galaxyRoot, String configFileName) throws IOException {
      if (isPre20141006Release(galaxyRoot)) {
        return configFileName;
      } else {
        File configDirectory = new File(galaxyRoot, CONFIG_DIR_NAME);
        File toolConf = new File(configDirectory, configFileName);
        
        // if config file does not exist, copy it from the .sample version
        if (!toolConf.exists()) {
          File toolConfSample = new File(configDirectory, configFileName + ".sample");
          Files.copy(toolConfSample, toolConf);
        }
        
        return CONFIG_DIR_NAME + "/" + configFileName;
      }
    }
docs: Gets path to a config file for Galaxy relative to the Galaxy root directory.
  This will check for the existence of the file and attempt to copy it from a *.sample file
  if it does not exist.
  @param galaxyRoot  The Galaxy root directory.
  @param configFileName  The name of the config file to get.
  @return  The path to the config file relative to the Galaxy root.
  @throws IOException  If the copy failed.