With the introduction of automatic partition selection in version 2.0.0 (release notes) of the main snakemake-executor-plugin-slurm, the utility of this plugin has been obviated.
We now maintain a partition configuration file for the Cannon cluster that can be used with the regular SLURM plugin. See our website for information on its usage.
No further updates or development will be done on this plugin.
For legacy installs of the plugin, please use the provided releases here on github. They will need to go in your environment's site packages directory (python -m site for hints on where to find this).
This is a fork of the SLURM executor plugin for Snakemake for the Cannon cluster at Harvard University. It has all the same features as the SLURM plugin, but performs automatic partition selection for the Cannon cluster based on the resources specified in a given Snakemake rule. It also offers some error checking for partition selection.
For full documentation, see the Snakemake plugin catalog.
The executor can be installed from PyPI with pip:
pip install snakemake-executor-plugin-cannonOr from bioconda with conda/mamba:
mamba install snakemake-executor-plugin-cannonTo use the executor with Snakemake, either specify it in the command line as:
snakemake -e cannon ...Or add it to your profile:
executor: cannonWhile this plugin does automatic partition selection, the user is still responsible for specifying other resources for rules in their workflow. This is usually done through a cluster profile, but this may differ based on your workflow.
See the profile setup page for more information.
An example profile can be found at tests/cannon-test-profile/config.yaml
For full documentation, see the Snakemake plugin catalog.