Setting a custom database input for tools -- in a workflow or on a tool form

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Hi @wormball

If you are working at a public Galaxy server, the custom genome can be promoted to a custom build. This will generate an index for the fasta specific to your account – along with a “database” (aka dbkey). It will be included in the list of built-in databases. That database can be set on tool forms (in a workflow or otherwise).

If you are working at your own Galaxy server, add/index the custom genome using Data Managers. This creates a new database, available to all users on the same server, and can be set on tool forms (in a workflow or otherwise).

Note: If the fasta has already been loaded and indexed by Data Managers, and is not showing up in the list of databases for a particular tool, then you may have missed one of the key indexes – there are four primary Data Managers that should be run for all to fully integrate them, then layer in tool specific indexes (for mapping tools, etc). See the Q&A “Start here” topic for a clear listing of the recommended minimum DMs to run. If you are not using Data Managers, all can be done manually – the other admin help links describe what is expected + troubleshooting.

Hope that helps!

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