toil.utils.toilConfig

Create a config file with all default Toil options.

Attributes

logger

Functions

generate_config(filepath)	Write a Toil config file to the given path.
add_logging_options(parser[, default_level])	Add logging options to set the global log level.
set_logging_from_options(options)
main()

Module Contents

toil.utils.toilConfig.generate_config(filepath)

Write a Toil config file to the given path.

Safe to run simultaneously in multiple processes. No process will see an empty or partially-written file at the given path.

Set include to “cwl” or “wdl” to include cwl options and wdl options respectfully

Parameters:

filepath (str)

Return type:

None

toil.utils.toilConfig.add_logging_options(parser, default_level=None)

Add logging options to set the global log level.

Parameters:

• default_level (Optional[int]) – A logging level, like logging.INFO, to use as the default.

• parser (argparse.ArgumentParser)

Return type:

None

toil.utils.toilConfig.set_logging_from_options(options)

Parameters:

options (Union[toil.common.Config, argparse.Namespace])

Return type:

None

toil.utils.toilConfig.logger

toil.utils.toilConfig.main()

Return type:

None