# Snakemake executor plugin: cannon
This is a fork of the [SLURM executor plugin for Snakemake](https://github.com/snakemake/snakemake-executor-plugin-slurm) for the [Cannon cluster at Harvard University](https://docs.rc.fas.harvard.edu/kb/running-jobs/). 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](https://snakemake.github.io/snakemake-plugin-catalog/plugins/executor/cannon.html).
## Installation
The executor can be installed [from PyPI](https://pypi.org/project/snakemake-executor-plugin-cannon/) with pip:
```bash
pip install snakemake-executor-plugin-cannon
```
Or [from bioconda](https://bioconda.github.io/recipes/snakemake-executor-plugin-cannon/README.html) with conda/mamba:
```bash
mamba install snakemake-executor-plugin-cannon
```
## Specifying the executor
To use the executor with Snakemake, either specify it in the command line as:
```bash
snakemake -e cannon ...
```
Or add it to your [profile](https://github.com/harvardinformatics/snakemake-executor-plugin-cannon/blob/main/docs/profile.md):
```YAML
executor: cannon
```
## Setting up your profile
While 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](https://github.com/harvardinformatics/snakemake-executor-plugin-cannon/blob/main/docs/profile.md) for more information.
An example profile can be found at [`tests/cannon-test-profile/config.yaml`](https://github.com/harvardinformatics/snakemake-executor-plugin-cannon/blob/main/tests/cannon-test-profile/config.yaml)
## Features
For full documentation, see the [Snakemake plugin catalog](https://snakemake.github.io/snakemake-plugin-catalog/plugins/executor/cannon.html).
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"description": "# Snakemake executor plugin: cannon \n\nThis is a fork of the [SLURM executor plugin for Snakemake](https://github.com/snakemake/snakemake-executor-plugin-slurm) for the [Cannon cluster at Harvard University](https://docs.rc.fas.harvard.edu/kb/running-jobs/). 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.\n\nFor full documentation, see the [Snakemake plugin catalog](https://snakemake.github.io/snakemake-plugin-catalog/plugins/executor/cannon.html).\n\n## Installation\n\nThe executor can be installed [from PyPI](https://pypi.org/project/snakemake-executor-plugin-cannon/) with pip:\n\n```bash\npip install snakemake-executor-plugin-cannon\n```\n\nOr [from bioconda](https://bioconda.github.io/recipes/snakemake-executor-plugin-cannon/README.html) with conda/mamba:\n\n```bash\nmamba install snakemake-executor-plugin-cannon\n```\n\n## Specifying the executor\n\nTo use the executor with Snakemake, either specify it in the command line as:\n\n```bash\nsnakemake -e cannon ...\n```\n\nOr add it to your [profile](https://github.com/harvardinformatics/snakemake-executor-plugin-cannon/blob/main/docs/profile.md):\n\n```YAML\nexecutor: cannon\n```\n\n## Setting up your profile\n\nWhile 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. \n\nSee the [profile setup page](https://github.com/harvardinformatics/snakemake-executor-plugin-cannon/blob/main/docs/profile.md) for more information. \n\nAn example profile can be found at [`tests/cannon-test-profile/config.yaml`](https://github.com/harvardinformatics/snakemake-executor-plugin-cannon/blob/main/tests/cannon-test-profile/config.yaml)\n\n## Features\n\nFor full documentation, see the [Snakemake plugin catalog](https://snakemake.github.io/snakemake-plugin-catalog/plugins/executor/cannon.html).\n\n",
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