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cancervariants / variation-normalization

Services and guidelines for normalizing variants
https://normalize.cancervariants.org/variation/
MIT License
10 stars 2 forks source link

Docker vn #553

Open rajatkapoordfci opened 6 months ago

rajatkapoordfci commented 6 months ago

Only docker file has been added and readme file has been modified. No Code changes in VN repo otherwise.

github-actions[bot] commented 6 months ago

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rajatkapoordfci commented 6 months ago

Docker_vn branch is merged with Staging branch. PR comments have been implemented.

korikuzma commented 6 months ago

@jsstevenson Please look at the above suggestions and let @rajatkapoordfci know if there are any other requested changes

jsstevenson commented 6 months ago

Maybe I've missed something, but I think it'd be easier to define service dependencies in a docker-compose file, rather than having the user build up everything themselves. This would obviate the need to let users define the location/port of eg the DynamoDB service since the compose file predefines everything at once.

Also -- and maybe I missed something again -- it doesn't look like there's a workflow for loading Gene Normalizer data currently (this is a requirement for the Variation Normalizer and is the reason we start a DynamoDB service).

korikuzma commented 6 months ago

Maybe I've missed something, but I think it'd be easier to define service dependencies in a docker-compose file, rather than having the user build up everything themselves. This would obviate the need to let users define the location/port of eg the DynamoDB service since the compose file predefines everything at once.

Also -- and maybe I missed something again -- it doesn't look like there's a workflow for loading Gene Normalizer data currently (this is a requirement for the Variation Normalizer and is the reason we start a DynamoDB service).

I agree with these comments. We should probably have Docker images with pre-loaded ddb tables.

jsstevenson commented 4 months ago

mentioned in the slack DM we had going -- I've been working on a similar effort in this branch, although I'm pinning specific data versions there for reasons particular to that project