code: def _run_tool(cmd, use_container=True, work_dir=None, log_file=None):
      
      if isinstance(cmd, (list, tuple)):
          cmd = " ".join([str(x) for x in cmd])
      cmd = utils.local_path_export(at_start=use_container) + cmd
      if log_file:
          cmd += " 2>&1 | tee -a %s" % log_file
      try:
          print("Running: %s" % cmd)
          subprocess.check_call(cmd, shell=True)
      finally:
          if use_container and work_dir:
              _chown_workdir(work_dir)
docs: Run with injection of bcbio path.
  
      Place at end for runs without containers to avoid overriding other
      bcbio installations.