Broad GPP SpCas9 Guide Design

Build machine learning Models to predict CRISPR Cas9 guide activity.

Features

• Luigi for task workflow organization
• Salted outputs for file version control
• Docker for a reproducible environment

Usage

This app is for building models and does not include any out-of-the-box predictors.

Installation

In a local directory, use

git clone https://github.com/PeterDeWeirdt/gpp-guide-design.git

For a completely reproducible environment install Docker and Docker Compose. If you use the professional edition of PyCharm you can set it up to use docker-compose as the default interpreter, otherwise you can use the command line.

Example

Once these dependencies are installed, in the gpp-guide-design directory you can build your environment

docker-compose build

And run the example workflow

docker-compose run app python main.py

Credits

This package was created with Cookiecutter and the audreyr/cookiecutter-pypackage project template.