MiModd variant calling - running time

[jennaj]

Welcome @Juan_Ramiro_Lorenzo

Yes, MiModd is currently running on a single core at UseGalaxy.org. I’ve made a request to get that clarified and to see if it can be set to the multi-threaded behavior. Please feel free to follow along or add in additional details → Request: set mimodd_varcall to execute on more than one core · Issue #426 · galaxyproject/usegalaxy-playbook · GitHub

The best advice I have is to put your data into collections, the tools into a workflow (even if simple and include just a few of the core tools) then to launch the whole thing as a batch. This gets everything queued at once, which is the most important part of getting high throughout work to process on the public clusters. These larger clusters are in high demand. There will always be completion but even really massive workloads will stream and complete with this strategy.

XRef

@jennaj

When working at UseGalaxy.org, UseGalaxy.eu, or UseGalaxy.org.au, your analysis jobs execute at large scale academic clusters. Hundreds of thousands of jobs process each month!

• Use a Workflow for batch work.
• Allow queued (grey color) and executing (yellow-orange) datasets to finish processing.
• Deleting and rerunning puts your job back at the end of the queue again!
• Job priority is the exactly the same for everyone.
• Be patient. Galaxy is a free service, when a lot of people are using it, you may have to wait longer than usual (especially for ‘big’ jobs, e.g. alignments).

Hope this helps! Apologies for the delays! We are all academics.. summer schedules and recent server updates led to some delays here, but we can certainly follow up more now.