Toil Class API

The Toil class configures and starts a Toil run.

class toil.common.Toil(options: argparse.Namespace)

A context manager that represents a Toil workflow.

Specifically the batch system, job store, and its configuration.

__init__(options: argparse.Namespace) → None

Initialize a Toil object from the given options.

Note that this is very light-weight and that the bulk of the work is done when the context is entered.

Parameters:options – command line options specified by the user

start(rootJob: Job) → Any

Invoke a Toil workflow with the given job as the root for an initial run.

This method must be called in the body of a with Toil(...) as toil: statement. This method should not be called more than once for a workflow that has not finished.

Parameters:rootJob – The root job of the workflow Returns:The root job’s return value

restart() → Any

Restarts a workflow that has been interrupted.

Returns:The root job’s return value

classmethod getJobStore(locator: str) → AbstractJobStore

Create an instance of the concrete job store implementation that matches the given locator.

Parameters:locator (str) – The location of the job store to be represent by the instance Returns:an instance of a concrete subclass of AbstractJobStore

static createBatchSystem(config: toil.common.Config) → AbstractBatchSystem

Create an instance of the batch system specified in the given config.

Parameters:config – the current configuration Returns:an instance of a concrete subclass of AbstractBatchSystem

import_file(src_uri: str, shared_file_name: Optional[str] = None, symlink: bool = False) → Optional[toil.fileStores.FileID]

Import the file at the given URL into the job store.

See toil.jobStores.abstractJobStore.AbstractJobStore.importFile() for a full description

export_file(file_id: toil.fileStores.FileID, dst_uri: str) → None

Export file to destination pointed at by the destination URL.

See toil.jobStores.abstractJobStore.AbstractJobStore.exportFile() for a full description

static normalize_uri(uri: str, check_existence: bool = False) → str

Given a URI, if it has no scheme, prepend “file:”.

Parameters:check_existence – If set, raise an error if a URI points to a local file that does not exist.

static getToilWorkDir(configWorkDir: Optional[str] = None) → str

Return a path to a writable directory under which per-workflow directories exist.

This directory is always required to exist on a machine, even if the Toil worker has not run yet. If your workers and leader have different temp directories, you may need to set TOIL_WORKDIR.

Parameters:configWorkDir – Value passed to the program using the –workDir flag Returns:Path to the Toil work directory, constant across all machines

classmethod get_toil_coordination_dir(configWorkDir: Optional[str] = None) → str

Return a path to a writable directory, which will be in memory if convenient. Ought to be used for file locking and coordination.

Parameters:configWorkDir – Value passed to the program using the –workDir flag Returns:Path to the Toil coordination directory.

classmethod getLocalWorkflowDir(workflowID: str, configWorkDir: Optional[str] = None) → str

Return the directory where worker directories and the cache will be located for this workflow on this machine.

Parameters:configWorkDir – Value passed to the program using the –workDir flag Returns:Path to the local workflow directory on this machine

classmethod get_local_workflow_coordination_dir(workflow_id: str, config_work_dir: Optional[str] = None) → str

Return the directory where coordination files should be located for this workflow on this machine. These include internal Toil databases and lock files for the machine.

If an in-memory filesystem is available, it is used. Otherwise, the local workflow directory, which may be on a shared network filesystem, is used.

Parameters:

• workflow_id – Unique ID of the current workflow.
• config_work_dir – Value used for the work directory in the current Toil Config.

Returns:

Path to the local workflow coordination directory on this machine.