galaxy.job_execution package

Subpackages

Submodules

galaxy.job_execution.compute_environment module

galaxy.job_execution.datasets module

Utility classes allowing Job interface to reason about datasets.

galaxy.job_execution.datasets.dataset_path_rewrites(dataset_paths)[source]
class galaxy.job_execution.datasets.DatasetPath(dataset_id, real_path, false_path=None, false_extra_files_path=None, false_metadata_path=None, mutable=True, dataset_uuid=None, object_store_id=None)[source]

Bases: object

__init__(dataset_id, real_path, false_path=None, false_extra_files_path=None, false_metadata_path=None, mutable=True, dataset_uuid=None, object_store_id=None)[source]
with_path_for_job(false_path, false_extra_files_path=None, false_metadata_path=None)[source]

Clone the dataset path but with a new false_path.

class galaxy.job_execution.datasets.DatasetPathRewriter[source]

Bases: object

Used by runner to rewrite paths.

abstract rewrite_dataset_path(dataset, dataset_type)[source]

Dataset type is ‘input’ or ‘output’. Return None to indicate not to rewrite this path.

class galaxy.job_execution.datasets.NullDatasetPathRewriter[source]

Bases: DatasetPathRewriter

Used by default for jobwrapper, do not rewrite anything.

rewrite_dataset_path(dataset, dataset_type)[source]

Keep path the same.

class galaxy.job_execution.datasets.OutputsToWorkingDirectoryPathRewriter(working_directory, outputs_directory_name)[source]

Bases: DatasetPathRewriter

Rewrites all paths to place them in the specified working directory for normal jobs when Galaxy is configured with app.config.outputs_to_working_directory. Job runner base class is responsible for copying these out after job is complete.

__init__(working_directory, outputs_directory_name)[source]
rewrite_dataset_path(dataset, dataset_type)[source]

Keep path the same.

class galaxy.job_execution.datasets.TaskPathRewriter(working_directory, job_dataset_path_rewriter)[source]

Bases: DatasetPathRewriter

Rewrites all paths to place them in the specified working directory for TaskWrapper. TaskWrapper is responsible for putting them there and pulling them out.

__init__(working_directory, job_dataset_path_rewriter)[source]
rewrite_dataset_path(dataset, dataset_type)[source]
galaxy.job_execution.datasets.get_path_rewriter(outputs_to_working_directory, working_directory, outputs_directory, is_task) → DatasetPathRewriter[source]

galaxy.job_execution.output_collect module

galaxy.job_execution.setup module