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snakemake / snakemake-executor-plugin-slurm

A Snakemake executor plugin for submitting jobs to a SLURM cluster
MIT License
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Can't unquote in slurm_extra #120

Open willboulton opened 3 months ago

willboulton commented 3 months ago

Hi, thanks for providing this plugin, it's great.

I'm having trouble on the HPC system at my university when trying to pass in parameters through slurm_extra (copying the help documentation as far as possible).

For example in my profile/config.yaml file I have a bunch of configuration including: 

- myjob:slurm_extra="'--qos=gpu-rtx --gres=gpu:1'"

This doesn't work but what does seem to work is using a raw string: 

- myjob:slurm_extra=r"--qos=gpu-rtx --gres=gpu:1"

I wondered if you could update your documentation to make this a bit clearer?

At the moment, the help text for a badly quoted string suggests wrapping more quotes (which doesn't work), and putting a raw string isn't mentioned as a fix.

I'm using snakemake version 8.10.7 and python 3.11.8, the output of sbatch --version is: 

slurm 19.05.3-2

Many thanks, I hope I've not missed this suggestion in your help text or the snakemake v8 main help docs, but I couldn't find it on my own. Will

cmeesters commented 3 months ago

This is weird! Definetively worth investigating. Can you please update Snakemake and test again?