toil tips

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Jurjen de Jong edited this page Aug 30, 2024 · 2 revisions

installing toil-cwl-runner with pip

To ensure your cwl and toil installations are compatible, do:

python3.X -m pip install toil[cwl]

instead of python3.X -m pip install toil-cwl-runner

Tips

--tmpdir-prefix overwrites the /tmp path. So, if you want to use the scratch space on your node or store intermediate products on scratch, you should not set this parameter in your toil command.

Acknowledgements

The LOFAR VLBI pipeline and its scripts were developed by: