Closed satyanarayan-rao closed 8 months ago
@satyanarayan-rao Snakemake 8 completely changed the interface to Slurm. Both this profile (#21) and the official slurm profile (https://github.com/Snakemake-Profiles/slurm/issues/117) were broken by these changes. You have 3 options:
Thanks a lot, @jdblischak! I had to downgrade to snakemake 6 and use --cluster-config
option. I think I would wait for the stable version of the new Snakemake to migrate. Too much hassle I guess right now, or maybe I am making stupid mistakes.
I had to downgrade to snakemake 6 and use
--cluster-config option
.
I'm glad you got it working, but to clarify, I don't recommend using --cluster-config
. It's been deprecated for years
Too much hassle I guess right now, or maybe I am making stupid mistakes.
If you used the smk-simple-slurm profile in this repo, it should have worked fine with Snakemake 7. If you're interested in giving it a try, and you still get errors, please feel free to open a new Issue to share the error message and your profile config file
I think I would wait for the stable version of the new Snakemake to migrate.
I totally understand the frustration. One option would be to migrate from --cluster-config
directly to the new Snakemake 8 cluster support, which would completely bypass the stage that this profile was meant to address.
Though I wouldn't get your hopes up about a mythical stable version of Snakemake. As long as it is actively developed (which is generally a good thing), it will continue to change. I have lots of old pipelines that use --cluster-config
as well as plenty that use smk-simple-slurm. As long as you pin the version of snakemake
in your conda env, your pipeline should continue to run.
Hi @jdblischak,
Many thanks for creating a simple profile for SLURM. I am facing issues with using this profile though:
I am using snakemake version 8.4.2. On Snakemake documentation, I learned that config file should be names "config.v8+.yaml". I named accordingly and here the content.
cat simple/config.v8+.yaml
On running snakemake command, I get the following error:
Just the dry run command works fine:
Any help would be greatly appreciated! Please let me know if you need more information.
Thank you very much, Satya