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CWL Questions
1

I was revisiting a pipeline and this exception showed up.

Got exception 'No available job store implementation can import the URL 'missing:'. Ensure Toil has been installed with the appropriate extras.' while copying 'missing://'

How can I debug and see more information about what are these missing imports? I’m using cwltool==3.1.20240508115724 which I have installed using

pip install 'toil[all]'

Any ideas on what is causing this? Thank you very much for your help!
Pedro

2

Hello @peterg1t ; I think this is a toil issue. A file is missing, but you got an unhelpful error message. There is an existing open issue: Toil can complain that it can't import `missing:` protocol files, instead of that a particular user-supplied URL points to a missing file · Issue #5174 · DataBiosphere/toil · GitHub . Perhaps you can comment there?

1 Like
3

Thank you Michael! I have added a comment over there as suggested.