Installation

Setup

While not strictly necessary, it is recommended to set up a Snakemake profile to run the workflow. This way submission via a scheduler is possible, which (drastically) reduces the runtime versus a local run. Additionally, the environments within the workflow are managed via Conda. When using a Snakemake profile, make sure the use-conda option is set to True. If you are not using a profile, Snakemake is called with the use-conda option automatically. Conda needs to be installed and available in your PATH, regardless of the way you run the workflow (either profile-based or not).

Recommended

ATACofthesnake is available on PyPI, and installation is recommended via pip:

pip install ATACofthesnake

or via uv

uv pip install ATACofthesnake

Development version

You can install the latest development version directly via GitHub:

pip install git+https://github.com/maxplanck-ie/ATACofthesnake.git

or again via uv:

uv pip install git+https://github.com/maxplanck-ie/ATACofthesnake.git

and if you have pixi installed, you can let it handle the environment setup for you and directly call the executable:

pixi run ATAC -h