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galaxyproject / galaxy_codex

Galaxy Communities Dock aka Galaxy Codex: catalog of Galaxy resources (tools, training, workflows)
https://galaxyproject.github.io/galaxy_codex/
MIT License
8 stars 15 forks source link

New fear unlocked: Databases #184

Open nomadscientist opened 1 month ago

nomadscientist commented 1 month ago

So I've just heard that tools can require databases, which are not automatically installed with the tool?

i.e. we can have a lovely tool panel for subdomains centralised here, and when a server installs the tools and says 'Look, we now have a Single-cell or Proteomics Lab', the tools may exist but fail because their databases must be also manually installed?

Is this how this works? This is clearly a problem for us...

paulzierep commented 1 month ago

It's one of the main issues with synchronizing Galaxy servers, it's worked on here: https://github.com/galaxyproject/idc But I think there is not much we can do here, yet. Maybe checking which tools need reference data. But making sure its available on all servers is still a difficult issue.

nomadscientist commented 1 month ago

Can checking which tools need references be automated, for example? So we know which tools to check?

bebatut commented 1 month ago

We could check if the tool suite has a data table in the code source