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Pass additional options to docker in toil-cwl-runner

See original GitHub issue

This is first a question and then a request: is there an option or environment variable in toil to pass additional parameters to docker? Our Docker environment is configured so that bind-mounting directories doesn’t work by default, only if you pass some additional parameters.

Note that I’m not asking for TOIL_CUSTOM_DOCKER_INIT_COMMAND, I actually want to run docker $mycustomargs --toil-args.

┆Issue is synchronized with this Jira Task ┆Issue Number: TOIL-917

Issue Analytics

State:
Created 2 years ago
Comments:9 (9 by maintainers)

Top GitHub Comments

2reactions

pmiddendcommented, Jun 15, 2021

Well, what I did was get rid of entrypoint and use singularity and then it “worked”. But Docker is still a no-go for me. I guess I can reopen the issue if it comes up again and keep the issue list cleaner. 😃

0reactions

mr-ccommented, Jun 15, 2021

@pmiddend were you able to implement the workaround?

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