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

[jennaj]

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).

• FAQs Galaxy Support
  • Start here Preparing and using a Custom Reference Genome or Build
• Q&A Search results for 'custom-build' - Galaxy Community Help
  • Start here Bowtie 2 - in Workflow no custom reference genome available -- Solution: Create a Custom Build - #2 by jennaj
• Tutorials Galaxy Training!
  • Start here Adding a custom database/build (dbkey)

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.

• FAQs Galaxy Administration
  • Start here Admin/DataIntegration
• Q&A Search results for 'data-manager' - Galaxy Community Help
  • Start here Indexing reference genomes with Data Managers: Resources, tutorials, troubleshooting - #2 by jennaj
• Tutorials Galaxy Training!
  • Start here Reference Genomes in Galaxy

Hope that helps!