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DataBiosphere / dsub

Open-source command-line tool to run batch computing tasks and workflows on backend services such as Google Cloud.
Apache License 2.0
265 stars 44 forks source link

Use existing ENTRYPOINT? #234

Closed ryan-salo closed 2 years ago

ryan-salo commented 2 years ago

Is there way to tell dsub to use the existing entrypoint of an image and pass it command args? Or is this a limitation of lifesciences pipelines?

wnojopra commented 2 years ago

Hi @ryan-salo!

Dsub currently sets the ENTRYPOINT of the user-command image to be /usr/bin/env , and the CMD to be -c bash {USER_SCRIPT}. This is done because there is some setup/cleanup scripting done that requires Bash (which is why your --image must include the Bash shell interpreter).

You're only able to change things after dsub calls /usr/bin/env -c bash through your --script or --command inputs.

If this doesn't work for you please send us further details and we can help out more.

ryan-salo commented 2 years ago

@wnojopra , thanks for the feedback! This makes sense given the setup/cleaning that happens, and I can work with that. Just wanted to double check if there was a way to use an existing ENTRYPOINT.