cwltool.udocker

Enables Docker software containers via the udocker runtime.

Classes

DockerCommandLineJob

Runs a CommandLineJob in a software container using the Docker engine.

UDockerCommandLineJob

Runs a CommandLineJob in a software container using the udocker engine.

Module Contents

class cwltool.udocker.DockerCommandLineJob(builder, joborder, make_path_mapper, requirements, hints, name)

Bases: cwltool.job.ContainerCommandLineJob

Inheritance diagram of cwltool.udocker.DockerCommandLineJob

Runs a CommandLineJob in a software container using the Docker engine.

Parameters:
get_image(docker_requirement, pull_image, force_pull, tmp_outdir_prefix)

Retrieve the relevant Docker container image.

Returns:

True upon success

Parameters:
  • docker_requirement (Dict[str, str])

  • pull_image (bool)

  • force_pull (bool)

  • tmp_outdir_prefix (str)

Return type:

bool

get_from_requirements(r, pull_image, force_pull, tmp_outdir_prefix)
Parameters:
  • r (cwltool.utils.CWLObjectType)

  • pull_image (bool)

  • force_pull (bool)

  • tmp_outdir_prefix (str)

Return type:

Optional[str]

static append_volume(runtime, source, target, writable=False, skip_mkdirs=False)

Add binding arguments to the runtime list.

Parameters:
Return type:

None

add_file_or_directory_volume(runtime, volume, host_outdir_tgt)

Append volume a file/dir mapping to the runtime option list.

Parameters:
  • runtime (List[str])

  • volume (cwltool.pathmapper.MapperEnt)

  • host_outdir_tgt (Optional[str])

Return type:

None

add_writable_file_volume(runtime, volume, host_outdir_tgt, tmpdir_prefix)

Append a writable file mapping to the runtime option list.

Parameters:
  • runtime (List[str])

  • volume (cwltool.pathmapper.MapperEnt)

  • host_outdir_tgt (Optional[str])

  • tmpdir_prefix (str)

Return type:

None

add_writable_directory_volume(runtime, volume, host_outdir_tgt, tmpdir_prefix)

Append a writable directory mapping to the runtime option list.

Parameters:
  • runtime (List[str])

  • volume (cwltool.pathmapper.MapperEnt)

  • host_outdir_tgt (Optional[str])

  • tmpdir_prefix (str)

Return type:

None

create_runtime(env, runtimeContext)

Return the list of commands to run the selected container engine.

Parameters:
Return type:

Tuple[List[str], Optional[str]]

class cwltool.udocker.UDockerCommandLineJob(builder, joborder, make_path_mapper, requirements, hints, name)

Bases: cwltool.docker.DockerCommandLineJob

Inheritance diagram of cwltool.udocker.UDockerCommandLineJob

Runs a CommandLineJob in a software container using the udocker engine.

Parameters:
static append_volume(runtime, source, target, writable=False, skip_mkdirs=False)

Add binding arguments to the runtime list.

Parameters:
Return type:

None