These pipelines facilitate the running of the Cactus whole genome alignment tool efficiently on SLURM (and possibly other) clusters.
Tutorials available on the FAS Informatics website:
⚠️ Important! cactus-snakemake v3.0.0 and later requires Cactus v2.9.9 or later.Due to bug fixes in Cactus, v3.0.0+ of cactus-snakemake is only compatibile with Cactus v2.9.9 or later. Don't worry, cactus-snakemake will always use the latest version of Cactus available unless you specify otherwise in your config file. However, if you do wish to use an older version of Cactus, you can use cactus-snakemake v2.1.0.
Installation is done simply by cloning the repository:
git clone https://github.com/harvardinformatics/cactus-snakemake.git
Alternatively, you could just manually download the latest release and unzip it and it should be good to go.
However, Snakemake and Singularity are required as dependencies. For more information, see the setup instructions in any of the tutorials linked above.
Each pipeline has a different config file that is required to specify input and output options and cluster resources.
With the config file setup, the pipelines are generally run as:
snakemake -j <number of jobs to submit simultaneously> -e slurm -s </path/to/snakefile.smk> --configfile </path/to/your/snakmake-config.yml>
💡 Tip: Cannon cluster Snakemake plugin
If you are on the Harvard Cannon cluster, you can use the snakemake-executor-plugin-cannon to do automatic partition selection instead of the generic SLURM executor plugin. Install the plugin with pip or mamba and then use
-e cannonin all of your commands instead of-e slurm.
For more information, see the setup and run instructions in each of the tutorials linked above.
Several meta config options exist across pipelines as pseudo-command line flags
| Command line flag | Description |
|---|---|
--config display=T |
Print the current config settings and exit |
--config info=T |
Display some information about the pipelines, including version and last commit date |
--config version=T |
Display the version of the pipeline |
--config prep=T |
Run all pre-processing steps and exit (e.g. output directory creation, cactus image download, running cactus-prepare). |
--config debug=T |
The same as prep, but display extra information about the pre-processing steps. |
If you use this software, please cite:
Thomas, G. (2026). Snakemake workflows for Cactus (Version 3.3.0) [Computer software]. https://doi.org/10.5281/zenodo.18462157
Thomas, G. (2026). Snakemake workflows for Cactus (Version 3.1.0) [Computer software]. https://doi.org/10.5281/zenodo.18166547
Thomas, G. (2025). Snakemake workflows for Cactus (Version 3.1.0) [Computer software]. https://doi.org/10.5281/zenodo.17467905
Thomas, G. (2025). Snakemake workflows for Cactus (Version 3.0.0) [Computer software]. https://doi.org/10.5281/zenodo.15699752
Thomas, G. (2025). Snakemake workflows for Cactus (Version 2.1.0) [Computer software]. https://doi.org/10.5281/zenodo.15596990
To cite a specific version:
See the full list of versions and DOIs here.
(Find the version you used in the Zenodo version history.)