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Create ClickHouse cBioPortal Docker Compose Setup #11371

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inodb opened this issue Feb 4, 2025 · 0 comments
Open
3 tasks

Create ClickHouse cBioPortal Docker Compose Setup #11371

inodb opened this issue Feb 4, 2025 · 0 comments
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inodb commented Feb 4, 2025

With the release of the clickhouse integration, deployers of cBioPortal can now run cBioPortal in "clickhouse mode". Let's provide a way to do this using the cbioportal docker compose setup. It should be an opt-in functionality, mainly useful for when you have large studies >100K samples.

  • Add a way to launch cBioPortal with clickhouse. E.g.:
    docker compose -f docker-compose.yml -f addon/docker-compose.clickhouse.yml up
    
    There is a clickhouse image we can use: https://hub.docker.com/r/clickhouse/clickhouse-server/tags
  • Add a sync step, this step would copy the MySQL data to clickhouse using sling or another approach. Can reuse what's been developed for the production GENIE portal (should prolly run in a separate container with access to both MySQL db and clickhouse db). After loading a custom study, users will now have to run a sync step (or potentially it could be a single command that runs the regular import followed by the sync step).
  • Update documentation on cBioPortal docs (https://docs.cbioportal.org/deployment/docker/)
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