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

**URL:** <https://help.galaxyproject.org/t/how-to-configure-slurm-queues-short-medium-long-for-galaxy-on-hpc/16254>\
**Category:** Uncategorized\
**Tags:** devops-administration, galaxy-local\
**Created:** [September 15, 2025, 4:34pm UTC](https://help.galaxyproject.org/t/how-to-configure-slurm-queues-short-medium-long-for-galaxy-on-hpc/16254 "2025-09-15T16:34:45Z")\
**Posts on this page:** 3\
**Page:** 1

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**Author:** ![Mohanchaitanya](https://avatars.discourse-cdn.com/v4/letter/m/82dd89/32.png) [@Mohanchaitanya](https://help.galaxyproject.org/u/Mohanchaitanya)\
**Post date:** [September 15, 2025, 4:34pm UTC](https://help.galaxyproject.org/t/how-to-configure-slurm-queues-short-medium-long-for-galaxy-on-hpc/16254/1 "2025-09-15T16:34:45Z")

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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!

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**Author:** ![jennaj](https://sea2.discourse-cdn.com/flex020/user_avatar/help.galaxyproject.org/jennaj/32/27_2.png) [@jennaj](https://help.galaxyproject.org/u/jennaj)\
**Post date:** [September 15, 2025, 10:34pm UTC](https://help.galaxyproject.org/t/how-to-configure-slurm-queues-short-medium-long-for-galaxy-on-hpc/16254/2 "2025-09-15T22:34:53Z")

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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:

- [Hands-on: Connecting Galaxy to a compute cluster / Connecting Galaxy to a compute cluster / Galaxy Server administration](https://training.galaxyproject.org/training-material/topics/admin/tutorials/connect-to-compute-cluster/tutorial.html)
- [Connecting to a Cluster — Galaxy Project 25.0.2.dev0 documentation](https://docs.galaxyproject.org/en/master/admin/cluster.html)
- with more examples in [Galaxy Job Configuration — Galaxy Project 25.0.2.dev0 documentation](https://docs.galaxyproject.org/en/master/admin/jobs.html)

With the full resources at:

> [@Private Galaxy Servers](https://help.galaxyproject.org/t/private-galaxy-servers/10861/1):
>
> 💻 Local Galaxy
> 
> - Training Network [Galaxy server administration training](https://training.galaxyproject.org/training-material/topics/admin/)
> - Technical Documentation [Galaxy releases, plus Admin and Development docs](https://docs.galaxyproject.org)
> - Open-source code base [GalaxyProject Github repositories](https://github.com/galaxyproject)
> - galaxyproject/admins chat at [https://matrix.to/#/#galaxyproject\_admins:gitter.im](https://matrix.to/#/#galaxyproject_admins:gitter.im)
> - galaxyproject/admins dev at [https://matrix.to/#/#galaxyproject\_dev:gitter.im](https://matrix.to/#/#galaxyproject_dev:gitter.im)

* * *

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! 🙂

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<div class="post-metadata">

**Author:** ![jennaj](https://sea2.discourse-cdn.com/flex020/user_avatar/help.galaxyproject.org/jennaj/32/27_2.png) [@jennaj](https://help.galaxyproject.org/u/jennaj)\
**Post date:** [March 17, 2026, 4:25am UTC](https://help.galaxyproject.org/t/how-to-configure-slurm-queues-short-medium-long-for-galaxy-on-hpc/16254/3 "2026-03-17T04:25:27Z")

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