toil.batchSystems.options

Module Contents

Classes

OptionSetter

Protocol for the setOption function we get to let us set up CLI options for

Functions

set_batchsystem_options(batch_system, set_option)

Call set_option for all the options for the given named batch system, or

add_all_batchsystem_options(parser)

set_batchsystem_config_defaults(config)

Set default and environment-based options for builtin batch systems. This

Attributes

logger

toil.batchSystems.options.logger
class toil.batchSystems.options.OptionSetter[source]

Bases: Protocol

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Protocol for the setOption function we get to let us set up CLI options for each batch system.

Actual functionality is defined in the Config class.

OptionType
__call__(option_name, parsing_function=None, check_function=None, default=None, env=None, old_names=None)[source]
Parameters

  • option_name (str) –

  • parsing_function (Optional[Callable[[Any], OptionType]]) –

  • check_function (Optional[Callable[[OptionType], Union[None, bool]]]) –

  • default (Optional[OptionType]) –

  • env (Optional[List[str]]) –

  • old_names (Optional[List[str]]) –

Return type

bool

toil.batchSystems.options.set_batchsystem_options(batch_system, set_option)[source]

Call set_option for all the options for the given named batch system, or all batch systems if no name is provided.

Parameters
Return type

None

toil.batchSystems.options.add_all_batchsystem_options(parser)[source]
Parameters

parser (Union[argparse.ArgumentParser, argparse._ArgumentGroup]) –

Return type

None

toil.batchSystems.options.set_batchsystem_config_defaults(config)[source]

Set default and environment-based options for builtin batch systems. This is required if a Config object is not constructed from an Options object.

Return type

None