Installation

Installing brefito

To install brefito, you will first want to install conda and mamba. You will also need git installed in your environment.

To begin, navigate to a location where you permanently store downloaded code on your machine. Then, clone the brefito repository and change into the new code directory:

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

Next, create a new conda environment for brefito that includes its requirements.

mamba env create -f environment.yml
conda activate brefito

Finally install brefito in this environment.

pip install .

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

brefito

Keeping brefito up to data with an editable install

If you are developing for brefito (editing its code) or a just a user who always wants access to the newest version for the latest features and bug-fixes, it's easiest to do an editable install.

If you set things up this way then, you won't need to keep running pip install each time you edit or update the code!

To set things up this way, add the --editable flag to your pip install command.

pip install --editable .

You can then update the code to the latest version anytime by running this command from inside the brefito directory created by git clone.

git pull

Snakemake Conda environment management

If you are on a machine with limited hard drive space or internet connectivity, you may want to set up a common location for snakemake to store conda environments. Otherwise it will re-install each environment in each working directory in which you run brefito, which can be slow and waste 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