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