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src/toil/test/utils/toilDebugTest.py::TestDebugJob::test_retrieve_task_directory is flaky and can fail when a container cannot be created #5490

@adamnovak

Description

@adamnovak

In https://ucsc-ci.com/databiosphere/toil/-/jobs/106738, the src/toil/test/utils/toilDebugTest.py::TestDebugJob::test_retrieve_task_directory test failed for no good reason. It looks like Docker had some kind of timeout trying to make a container during the workflow we're trying to run:

docker.errors.APIError: 500 Server Error for http+docker://localhost/v1.50/swarm/init: Internal Server Error ("error on listing clusters: rpc error: code = DeadlineExceeded desc = context deadline exceeded")

Because the workflow is intended to fail in this test, just not in this way, we didn't notice that anything had gone wrong with the workflow, or retry it in any way.

┆Issue is synchronized with this Jira Story
┆Issue Number: TOIL-1824

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