Diamond indexes: synchronizing across UseGalaxy servers

[jennaj]

Hello @Osmannamal

Thanks for sending in your question. Hopefully we can help!

UseGalaxy servers

The UseGalaxy.eu server is the best public Galaxy server to run Diamond for now. In particular, for today, due to the server maintenance event at UseGalaxy.org!

Job queues, alignment tools, custom indexes

The computational resources at any public server will usually be competitive. Our best advice is to get your jobs queued, perhaps with a workflow, to ensure the work will move through the queue well. Running these larger tools individually is not recommended for HTP analysis. FAQ: My jobs aren't running!

If you need newer indexes immediately, please see the tool option to create a custom index with Diamond makedb. Using restricted organism domains will likely be important. Try a search against multiple, then reformat, merge, and filter your results after.

Suggested strategy

1. Create custom indexes with Diamond makedb, or determine which Diamond server-hosted indexes to use
2. Create a collection folder with query sequences. Galaxy FAQs
3. Create a workflow to execute multiple Diamond runs
4. The workflow may also include steps to use Diamond view (tabular format), Collapse collection (combine results) and following by filtering/ranking.

Examples

• GTN Tutorials including Diamond
• For more about collections and workflows, please see our YouTube channel, and ask questions here for support!

Request tracking

• I updated an existing ticket for synchronizing the Diamond indexes, please follow for future updates. You can also remind us for status!
• I’ve also sent this information to your email asking about the same situation.
• Related Q&A bg_diamond

Live processing status at UseGalaxy.eu

@jennaj

Hopefully we can help! Yes, the tool does appear to be processing as expected UseGalaxy.eu → How to see the UseGalaxy.eu job queue statistics - #2 by jennaj

Updated Homepage

The view on the server homepage changed a bit recently, so this is how the same landmarks are now organized:

There are about 200 Diamond jobs queued as of right now, and roughly 15 executing at any particular time. See the topic above how to review these statistics. Diamond is a tool that also requires high memory to support the very large indexes so the general usage advice will be the same. All UseGalaxy server’s public clusters have high demand.

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Thank you and I hope this helps to explain the situation, and that it provides some useful advice for what to try next! Follow up questions are welcome, here or in reply to my email!