https://github.com/snakemake/snakemake-software-deployment-plugin-container
Run snakemake within a rootless container
https://github.com/snakemake/snakemake-software-deployment-plugin-container
Last synced: 5 months ago
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Run snakemake within a rootless container
- Host: GitHub
- URL: https://github.com/snakemake/snakemake-software-deployment-plugin-container
- Owner: snakemake
- License: mit
- Created: 2025-03-11T14:23:55.000Z (over 1 year ago)
- Default Branch: main
- Last Pushed: 2026-02-13T21:17:25.000Z (5 months ago)
- Last Synced: 2026-02-14T02:55:40.964Z (5 months ago)
- Language: Python
- Size: 75.2 KB
- Stars: 1
- Watchers: 2
- Forks: 1
- Open Issues: 2
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Metadata Files:
- Readme: README.md
- License: LICENSE
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README
# snakemake-software-deployment-plugin-container
A generic container plugin implementing snakemake's software-deployment interface.
* It executes the given commands within a rootless container.
* It currently supports both `udocker` and `podman`.
## Usage
The `kind` parameter specifies valid values for the container runtime to use.
The `container` directive (should be) used to specify the container image to use
for the software deployment. This string should be a valid container image name,
including the tag; e.g., `biocontainers/example:1.0`.
By default, the plugin will attemtp to use 'latest' tag if no tag is provided.
However, be aware that some registries may not support this, for [good
reasons](https://github.com/BioContainers/containers/issues/297#issuecomment-439055879)
having to do with reproducibility. So, it's a good idea to specify a tag.
## Status
- Work in progress. The plugin conforms to the current software-deployment interface specification, and it has passing tests.
- Will revisit when further work is done in snakemake core to allow a more reusable integration of deployment plugins.
## TODO
- [ ] Add support for apptainer
- [ ] Implement repot_sofware method with container URI *and* the resolved hash of the image.