A Cookiecutter template for computational biology projects.
This uses cookiecutter to create a repository with a similar structure to what was described in A Quick Guide to Organizing Computational Biology Projects by William Stafford Noble, while also implementing some additional best practices, such as code styling (With black or r-styler) and data-versioning/pipelining (With DVC).
It's still very much a work-in-progress, If you have any ideas or contributions, feel free to post an issue or send a pull request.
- Install cookiecutter
pip install -U cookiecutter
Or:
conda install -c conda-forge cookiecutter
- Initialize the project
cookiecutter https://github.com/jvfe/cookiecutter-compbio.git
- Create the enviroment and start working!
conda env create --file environment.yml
Noble WS (2009) A Quick Guide to Organizing Computational Biology Projects. PLOS Computational Biology 5(7): e1000424. https://doi.org/10.1371/journal.pcbi.1000424