The easiest way to use the workflow is as a python package. To set this up:
- Create a conda environment
- install miniconda as described here: https://docs.conda.io/projects/conda/en/latest/user-guide/install/linux.html
- using mamba is recommended, to install it:
conda install mamba - then create the workflow environment:
mamba env create -f /path/to/smk_wgbs/smk_wgbs_dev_env.yaml
- There is no pypi/conda package yet (coming soon). To install the package
- clone the repository
- run
pip install /path/to/smk_wgbs