brsynth/retrorules repository overview

⁠RetroRules

• Docker image: brsynth/retrorules-standalone⁠

Retrieve the reaction rules from RetroRules⁠

⁠Input

• -rule_type: (string) Valid options: retro, forward, all. Return the rules that are in reverse, forward or both direction
• -diamters: (integer list): Valid options: 2, 4, 6, 8, 10, 12, 14, 16. The diameter of the rules to return
• -output_format: (string) Valid options: tar, csv. Format output

⁠Ouput

• -output: (string): Path of the output file. Either a TAR (containing a CSV) or CSV list of reaction rules that are in a RetroPath2.0 friendly format

⁠Dependencies

• Base docker image: python:3.7⁠

⁠Building the docker

docker build -t brsynth/retrorules-standalone:v1 .

⁠Running the test

To run the test, run the following command:

python run.py -rule_type retro -output rules.tar -diameters 2,8 -output_format tar

⁠Contributing

Please read CONTRIBUTING.md⁠ for details on our code of conduct, and the process for submitting pull requests to us.

⁠Version

v0.1

⁠Authors

• Thomas Duigou
• Melchior du Lac

⁠License

This project is licensed under the MIT License - see the LICENSE.md⁠ file for details

⁠Acknowledgments

• Joan Hérisson

⁠How to cite RetroRules?

Please cite:

Duigou, Thomas, et al. "RetroRules: a database of reaction rules for engineering biology." Nucleic acids research 47.D1 (2019): D1229-D1235.