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Support dsub as an alternative container backend #130

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agitter opened this issue Sep 21, 2023 · 3 comments
Open

Support dsub as an alternative container backend #130

agitter opened this issue Sep 21, 2023 · 3 comments

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@agitter
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agitter commented Sep 21, 2023

dsub is a command line tool for running commands in Google Cloud inside a container. @nisthapanda is investigating whether we could use it to run containers in SPRAS because that may be one path toward using SPRAS in the restricted NIH All of US platform. The solution might be a further generalization of our run_container utility function.

This is related to #124 and Podman, another possible backend for containers.

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agitter commented Oct 4, 2023

Nistha has a branch that successfully runs Omics Integrator 1 using dsub in the All of Us environment: https://github.com/nisthapanda/spras/tree/dsub

We don't have immediate plans to generalize this and merge this back into SPRAS. It relies on user-specific information about the environment and location of storage buckets.

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agitter commented Jan 16, 2024

The changes in #132 that make the registry configuration make this easier to support now.

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agitter commented Jun 21, 2024

@nisthapanda discovered that dsub requires bash to run containers, which isn't available in Alpine Linux. I'm going to test adding bash to PathLinker to see if that resolves her problem.

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