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Snakemake-Profiles / lsf

Snakemake profile for running jobs on an LSF cluster
MIT License
36 stars 22 forks source link

Does not work with Snakemake v8 #62

Closed levlitichev closed 6 months ago

levlitichev commented 6 months ago

This profile is incompatible with Snakemake version 8 because the --cluster command line arguments were deprecated (more information here).

Here is this same issue being discussed on the slurm profile Github.

I understand this package is no longer being actively maintained, but I thought I would leave a note in case it's helpful to someone in the future.

Snakemake version 7 still works fine with this profile (more specifically, I'm using v7.32.4).

dlaehnemann commented 6 months ago

For snakemake version 8 upwards, you will have to use an executor plugin on cluster systems, instead of a profile like this one. There's one being developed for LSF, have a look here: https://github.com/BEFH/snakemake-executor-plugin-lsf/

Also, there's a thread about it on Discord, for a more interactive discussion: https://discord.com/channels/753690260830945390/1204469412065837066

Profiles will then rather contain user- and hardware-specific settings, while the executor plugins abstract away all the cluster system API...

levlitichev commented 6 months ago

I see -- thank you for the links.

dlaehnemann commented 6 months ago

Thanks for raising this, that way we have this "documented" here. :sweat_smile: