def run_main(workdir, config_file=None, fc_dir=None, run_info_yaml=None,
             parallel=None, workflow=None):
    """Run variant analysis, handling command line options.
    """
    # Set environment to standard to use periods for decimals and avoid localization
    os.environ["LC_ALL"] = "C"
    os.environ["LC"] = "C"
    os.environ["LANG"] = "C"
    workdir = utils.safe_makedir(os.path.abspath(workdir))
    os.chdir(workdir)
    config, config_file = config_utils.load_system_config(config_file, workdir)
    if config.get("log_dir", None) is None:
        config["log_dir"] = os.path.join(workdir, DEFAULT_LOG_DIR)
    if parallel["type"] in ["local", "clusterk"]:
        _setup_resources()
        _run_toplevel(config, config_file, workdir, parallel,
                      fc_dir, run_info_yaml)
    elif parallel["type"] == "ipython":
        assert parallel["scheduler"] is not None, "IPython parallel requires a specified scheduler (-s)"
        if parallel["scheduler"] != "sge":
            assert parallel["queue"] is not None, "IPython parallel requires a specified queue (-q)"
        elif not parallel["queue"]:
            parallel["queue"] = ""
        _run_toplevel(config, config_file, workdir, parallel,
                      fc_dir, run_info_yaml)
    else:
        raise ValueError("Unexpected type of parallel run: %s" % parallel["type"])
def run_main ( workdir , config_file = None , fc_dir = None , run_info_yaml = None , parallel = None , workflow = None ) : os . environ [ "LC_ALL" ] = "C" os . environ [ "LC" ] = "C" os . environ [ "LANG" ] = "C" workdir = utils . safe_makedir ( os . path . abspath ( workdir ) ) os . chdir ( workdir ) config , config_file = config_utils . load_system_config ( config_file , workdir ) if config . get ( "log_dir" , None ) is None : config [ "log_dir" ] = os . path . join ( workdir , DEFAULT_LOG_DIR ) if parallel [ "type" ] in [ "local" , "clusterk" ] : _setup_resources ( ) _run_toplevel ( config , config_file , workdir , parallel , fc_dir , run_info_yaml ) elif parallel [ "type" ] == "ipython" : assert parallel [ "scheduler" ] is not None , "IPython parallel requires a specified scheduler (-s)" if parallel [ "scheduler" ] != "sge" : assert parallel [ "queue" ] is not None , "IPython parallel requires a specified queue (-q)" elif not parallel [ "queue" ] : parallel [ "queue" ] = "" _run_toplevel ( config , config_file , workdir , parallel , fc_dir , run_info_yaml ) else : raise ValueError ( "Unexpected type of parallel run: %s" % parallel [ "type" ] )
Run variant analysis, handling command line options.