code: def prep_system(run_info_yaml, bcbio_system=None):
      
      work_dir = os.getcwd()
      config, config_file = config_utils.load_system_config(bcbio_system, work_dir)
      dirs = setup_directories(work_dir, os.path.normpath(os.path.dirname(os.path.dirname(run_info_yaml))),
                               config, config_file)
      return [dirs, config, run_info_yaml]
docs: Prepare system configuration information from an input configuration file.
  
      This does the work of parsing the system input file and setting up directories
      for use in 'organize'.