brsynth/rpreader repository overview

⁠rpReader docker

• Docker image: brsynth/rpreader-standalone⁠

RetroPath2.0 and rp2paths to SBML conversion tool. Takes for input the output of both RetroPath2.0 and rp2paths or RetroPath3.0 and generates a series of enriches SBML files with all the files contained within them.

⁠Input

Required:

• -rp2paths_pathways: (string) Path to the rp2paths pathways file
• -rp2paths_compounds: (string) Path to the rp2paths compounds file
• -rp2_pathways: (string) Path to the RetroPath2.0 pathways file

Advanced options:

• -upper_flux_bound: (integer, default=9999) Upper flux bound value
• -lower_flux_bound: (integer, default=0) Lower flux bound value
• -maxRuleIds: (integer, default=2) Number of subpaths per paths
• -pathway_id: (string, default=rp_pathway) ID of the heterologous pathway
• -compartment_id: (string, default=MNXC3 (i.e. cytoplasm)) Heterologous pathway compartment ID
• -species_group_id: (string, default=central_species) ID of the central species, i.e. not cofactors, in the heterologous reactions

⁠Output

• -outputTar: (string) Path to the output tar.xz file

⁠Dependencies

• Base Docker Image: brsynth/rpBase⁠
• Cache Docker Image: brsynth/rpCache⁠

⁠Building the docker

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

docker build -t brsynth/rpreader-standalone -f Dockerfile .

⁠Running the test

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

python run_rp2.py -rp2paths_compounds test/rp2paths_compounds.csv -rp2_pathways test/rp2_pathways.csv -rp2paths_pathways test/rp2paths_pathways.csv -output test/test_rpReader.tar

⁠Dependencies

• Base docker image: brsynth/rpBase⁠
• Cache docker image: brsynth/rpCache⁠

⁠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

• Melchior du Lac

⁠License

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

⁠Acknowledgments

• Thomas Duigou
• Joan Hérisson

⁠How to cite rpReader?