Docker not found but it is present in the system.

[peterg1t]

I installed toil[cwl] in a new arm mac laptop. I have a simple job that zips a file using a container image with a zip utility.

cwltool --debug workflows/pipeline-simple_workflow.cwl workflows/inputs.yml

I ran however into the following situation

Traceback (most recent call last):
  File "/Users/pemartin/Scripts/CWL-training/src/env/lib/python3.12/site-packages/cwltool/job.py", line 759, in run
    self.get_from_requirements(
  File "/Users/pemartin/Scripts/CWL-training/src/env/lib/python3.12/site-packages/cwltool/docker.py", line 208, in get_from_requirements
    if self.get_image(cast(dict[str, str], r), pull_image, force_pull, tmp_outdir_prefix):
       ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/Users/pemartin/Scripts/CWL-training/src/env/lib/python3.12/site-packages/cwltool/docker.py", line 114, in get_image
    if docker_requirement["dockerImageId"] in _IMAGES:
       ~~~~~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^
  File "/Users/pemartin/Scripts/CWL-training/src/env/lib/python3.12/site-packages/ruamel/yaml/comments.py", line 853, in __getitem__
    return ordereddict.__getitem__(self, key)
           ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
KeyError: 'dockerImageId'

The above exception was the direct cause of the following exception:

Traceback (most recent call last):
  File "/Users/pemartin/Scripts/CWL-training/src/env/lib/python3.12/site-packages/cwltool/main.py", line 1313, in main
    (out, status) = real_executor(
                    ^^^^^^^^^^^^^^
  File "/Users/pemartin/Scripts/CWL-training/src/env/lib/python3.12/site-packages/cwltool/executors.py", line 53, in __call__
    return self.execute(process, job_order_object, runtime_context, logger)
           ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/Users/pemartin/Scripts/CWL-training/src/env/lib/python3.12/site-packages/cwltool/executors.py", line 136, in execute
    self.run_jobs(process, job_order_object, logger, runtime_context)
  File "/Users/pemartin/Scripts/CWL-training/src/env/lib/python3.12/site-packages/cwltool/executors.py", line 246, in run_jobs
    job.run(runtime_context)
  File "/Users/pemartin/Scripts/CWL-training/src/env/lib/python3.12/site-packages/cwltool/job.py", line 800, in run
    raise UnsupportedRequirement(
cwltool.errors.UnsupportedRequirement: Docker is required to run this tool: 'dockerImageId'

I have Docker installed in the laptop with the following tool versions
cwltool 3.1.20240112164112
toil-cwl-runner --version 6.1.0

I wonder what I might be doing incorrectly regarding my configuration. Docker is available in the system and I can do docker load -i image without any issues.

Thank you very much in advance for your help.

Pedro

┆Issue is synchronized with this Jira Story
┆Issue Number: TOIL-1694