Removing the Parasol batch system has made Toil fail when parsing arguments if you have run it before

[adamnovak]

If you ran Toil between when config files were added in #4569 and when the Parasol batch system was removed in #4678, it will now crash when parsing arguments with a message like:

wdltoil.py: error: unrecognized arguments: --parasol_command=parasol --parasol_max_batches=1000 --mesosName=toil

I'm not sure how Mesos got in there.

I think #4666 will solve this going forward, as it will make us make config files with everything commented out by default, to avoid this kind of problem.

So maybe #4666 will count as fixing this? Or maybe we want some kind of cleanup logic to handle old fully-populated config files and not fail?

┆Issue is synchronized with this Jira Story
┆Issue Number: TOIL-1450

[adamnovak]

The user-level fix is to rm ~/.toil/default.yaml.

[DailyDreaming]

This should be resolved.