How to configure SLURM queues (short/medium/long) for Galaxy on HPC?

usegalaxy.org support
1

Hello,

I am new to running Galaxy on our Institute’s HPC. Our cluster uses SLURM with three partitions:

  • Short: 2 hours, 128 cores max, 2 nodes max, with high priority to run the job.

  • Medium: 72 hours, 192 cores max, 3 nodes max, with medium priority to run the job.

  • Long: 240 hours, 192 cores max, 3 nodes max, with low priority to run the job.

I want to know how to set up Galaxy so that different tools (like FastQC, Kraken2, MEGAHIT, MetaSPAdes, CheckM, etc.) can run on the right queue (short, medium, or long).

Could someone please show me:

  • Where exactly do I need to edit or create the file?

  • What code should I add for these SLURM queues?

  • How to assign tools to a specific queue?

I am a beginner with Galaxy + HPC configuration, so a step-by-step example would really help.

Thanks a lot!

2

Hi @Mohanchaitanya

I think we can help! We have a set of administrative tutorials and documentation to guide you through the process.

I would suggest staring in these places:

With the full resources at:

Please give those a review and come back here with questions as you work through the process! In short, you will be defining each job destination then grouping/assigning tools to route to those destinations based on rules you set. The resources above include examples.

Let’s start there! :slight_smile: