Allow setting the default source for public resources with an environment variable #435
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Looks good, thank you so much for adding, just a small note, and question. Is there somewhere that we should specify that GNOMAD_DEFAULT_PUBLIC_RESOURCE_SOURCE can now be used like in https://github.com/broadinstitute/gnomad_methods/blob/8bffc35b8101a6095276331f7a1fa9edcec4e86f/docs/resource_sources.rst?
| try: | ||
| default_source = GnomadPublicResourceSource(default_source_from_env) | ||
| return default_source | ||
| except ValueError: |
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Should we throw a warning that the environment variable defines a source that is not one of those in GnomadPublicResourceSource?
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I debated about this. Users can provide their own source, such as gs://my-bucket/gnomad-resources, so this is (potentially) valid. I'll add some logging here.
Co-authored-by: jkgoodrich <[email protected]>
Good point. I'll add some docs. |
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Some users may always prefer to use the AWS or Azure copies of gnomAD resources. This allows them to set a default source in an environment variable instead of having to configure it in every pipeline.
Once hail-is/hail#11230 is merged,
get_default_public_resource_sourcecan be extended to use Hail's guess for the current cloud provider to set the default resource source.Related to #433