Docker vn

[rajatkapoordfci]

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

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[korikuzma]

Docker changes make sense to me. I think we just need the readme to be cleaned up a little more before merging. Please also pull changes from staging and merge into your branch

[rajatkapoordfci]

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

[korikuzma]

Provided some suggestions for cleaning up the readme (typos/inconsistencies)

[korikuzma]

Maybe we should consider having these as ARGs.

[rajatkapoordfci]

These values are required during container runtime as well. It would be better to continue with ENV unless we are planning for build time customisation.

[korikuzma]

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

[jsstevenson]

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]

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.

[korikuzma]

We discussed in the MetaKB meeting that this still needs work. I'm going to convert to a draft. @rajatkapoordfci please re-open and re-request our reviews once it's ready!

[jsstevenson]

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