cwltool.docker

Enables Docker software containers via the {u,}docker or podman runtimes.

Classes

`DockerCommandLineJob`	Runs a `CommandLineJob` in a software container using the Docker engine.
`PodmanCommandLineJob`	Runs a `CommandLineJob` in a software container using the podman engine.

Module Contents

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

Bases: cwltool.job.ContainerCommandLineJob

Inheritance diagram of cwltool.docker.DockerCommandLineJob

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

Parameters:

builder (cwltool.builder.Builder)
joborder (cwl_utils.types.CWLObjectType)
make_path_mapper (collections.abc.Callable[[collections.abc.MutableSequence[cwl_utils.types.CWLFileType | cwl_utils.types.CWLDirectoryType], str, cwltool.context.RuntimeContext, bool], cwltool.pathmapper.PathMapper])
requirements (list[cwl_utils.types.CWLObjectType])
hints (list[cwl_utils.types.CWLObjectType])
name (str)

docker_exec = 'docker'

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, image_base_path=None)

Parameters:

r (cwl_utils.types.CWLObjectType)
pull_image (bool)
force_pull (bool)
tmp_outdir_prefix (str)
image_base_path (str | None)

Return type:

str | None

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

Add binding arguments to the runtime list.

Parameters:

runtime (list[str])
source (str)
target (str)
writable (bool)
skip_mkdirs (bool)

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 (str | None)

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 (str | None)
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 (str | None)
tmpdir_prefix (str)

Return type:

None

create_runtime(env, runtimeContext)

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

Parameters:

env (collections.abc.MutableMapping[str, str])
runtimeContext (cwltool.context.RuntimeContext)

Return type:

tuple[list[str], str | None]

class cwltool.docker.PodmanCommandLineJob(builder, joborder, make_path_mapper, requirements, hints, name)

Bases: DockerCommandLineJob

Inheritance diagram of cwltool.docker.PodmanCommandLineJob

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

Parameters:

builder (cwltool.builder.Builder)
joborder (cwl_utils.types.CWLObjectType)
make_path_mapper (collections.abc.Callable[[collections.abc.MutableSequence[cwl_utils.types.CWLFileType | cwl_utils.types.CWLDirectoryType], str, cwltool.context.RuntimeContext, bool], cwltool.pathmapper.PathMapper])
requirements (list[cwl_utils.types.CWLObjectType])
hints (list[cwl_utils.types.CWLObjectType])
name (str)

docker_exec = 'podman'