I authored a pipeline which I’m benchmarking for performance by comparison to a similar workflow on Galaxy, using runtime as a performance metric. For a fair comparison, I’d like to ideally run the workflow using the maximum number of threads Galaxy will allow. Currently, for the alignment portion, it uses bwa-mem2 mem -t “${GALAXY_SLOTS:-1}” to set the number of bwa-mem2 threads, which I believe means it either uses the value in GALAXY_SLOTS if set, or 1 otherwise. Is there a way to increase the number of threads that bwa-mem2 mem (and other commands) is run with on Galaxy?
Welcome, @Benjamin_Skubi
Are you working at UseGalaxy.eu or your own server?
Public resources are fixed as far as I know. But, you can definitely adjust the details on any server where you are an administrator.
For how this works, please see
- Tutorials Galaxy Server administration / Tutorial List
- Those that involve clusters and tuning runtime parameters will link to docs such as → Advanced Tool Development Topics — Planemo 0.75.27.dev0 documentation (#cluster-usage)
Hope this helps, and you can ask more questions. 