Initializing external database

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John Reber

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Aug 14, 2026, 10:06:54 AM (2 days ago) Aug 14

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Running cBioPortal locally with an external ClickHouse database server.

Was having issues with loading the external database from within docker compose up -d. AI keeps saying I should init/seed the database before bringing up cbioportal. Which seed files should I be using?

When I try using clickhouse.sql, there are optimazation errors from tables not existing. If I start with schama.sql, then clickhouse.sql and then seed-cbioportal_hg19_hg38_v2.14.5.sql, (these were copied from a devlopment server running fully within docker compose) the 3 scripts run happily, generating tables and data. Then when starting cbioportal I get init errors, because tables are not found, etc and the containers doesn't start.

Any pointers on running cBioPortalconatiners with an external ClickHouse database?