Installation

Installation

Clone the repository and change to the main directory

git clone https://github.com/barricklab/brefito.git
cd brefito

Install conda and mamba.

Then, create an environment for brefito thet includes its requirements and install it in this environment.

mamba env create -f environment.yml
conda activate brefito
pip install .

Now you should be able to run the brefito script and see the help like this!

brefito

It's also highly recommended that you set up a common location for snakemake to store conda environments. Otherwise it will re-install each environment in each working directory you use, which is slow and wastes disk space! To do so, set this environment variable in your startup script (~/.bashrc, ~/.zshrc, etc.) to something like this:

export SNAKEMAKE_CONDA_PREFIX=$HOME/snakemake_conda_envs

If you are developing for brefito, it's easiest to do an editable install. In this case, you won't need to keep installing each time you edit the code!

pip install --editable .