brsynth/rp2paths repository overview

⁠rp2paths

• Docker image: brsynth/rp2paths⁠

Docker implementation of rp2paths. Enumerates individual heterologous pathways from RetroPath2.0.

⁠Input

Required:

• -rp_results: (string) Path to the output of RetroPath2.0

Advanced options:

• -timeout: (integer, default=30) Timeout of the tool in minutes

⁠Output

• -out_paths: (string) Path to the metabolic pathways calculated
• -out_compounds: (string) Path to the compounds in the calculated pathways

⁠Dependencies

• Base docker image: conda/miniconda3⁠

⁠Building the docker

To build the docker, please run the following command command in the project root folder:

docker build -t brsynth/rp2paths-standalone .

⁠Running the test

To test the docker, untar the test.tar.xz file and run the following command:

python run.py -rp_results test/rp_pathways.csv -out_paths test/out_paths.csv -out_compounds test/out_compounds.csv

⁠Contributing

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

⁠Version

v1.1.0

⁠Authors

• Melchior du Lac
• Thomas Duigou
• Joan Hérisson

⁠License

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

⁠Acknowledgments

⁠How to cite rp2paths?

Please cite:

Delépine B, Duigou T, Carbonell P, Faulon JL. RetroPath2.0: A retrosynthesis workflow for metabolic engineers. Metabolic Engineering, 45: 158-170, 2018. DOI: https://doi.org/10.1016/j.ymben.2017.12.002⁠