openproblems-bio / openproblems

Formalizing and benchmarking open problems in single-cell genomics
MIT License
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Remove sagemaker compatibility from docker images #711

Closed scottgigante-immunai closed 2 days ago

scottgigante-immunai commented 1 year ago

We don't use sagemaker and haven't for a long time. Sagemaker compatibility makes the dockerfiles bulkier and more confusing. I'm advocating for removing this unnecessary boilerplate.

LuckyMD commented 1 year ago

I think this is a decision that would ideally be brought up at a core team meeting... or for now just involve @dburkhardt. We have previously used sagemaker notebooks for running the hackathon. I think a few people used them at the time as well. And we now have support to run another hackathon, which may mean sagemaker will be used again. Do you have an alternative to let people easily prototype tasks and methods in an interactive manner when they don't have docker locally?

I think we may have to table this until after the NeurIPS workshop given this is the closest urgent thing atm.

scottgigante-immunai commented 1 year ago

Yep, that's why I tagged Dan for review. I got the impression sagemaker didn't work so well at the hackathon.

Do you have an alternative to let people easily prototype tasks and methods in an interactive manner when they don't have docker locally?

It would be straightforward to run on EC2 and then prototype in a python terminal... if people feel the need to use jupyter we could add instructions on port forwarding to those docs and they can run a regular jupyter notebook on EC2.

scottgigante-immunai commented 1 year ago

@dburkhardt thoughts?

github-actions[bot] commented 2 days ago

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