brsynth/rpoptbiodes repository overview

⁠rpOptBioDes

Docker implementation of the OptBioDes tool by Pablo Carbonell

⁠Getting Started

This is a docker galaxy tools, and thus, the docker needs to be built locally where Galaxy is installed.

⁠Input

Required information:

• -input: (string) Path to either tar.xz input collection of rpSBML files or a single rpSBML file.
• -input_format: (string) Format of the input
• -input_sbol: (string) Path to the SBOL input file

Advanced options:

• -pathway_id: (string, default: rp_pathway) The SBML groups ID (defined in rpReader) that points to the heterologous reactions and chemical species.
• -max_variants: (integer, default: 5) Maximal variants for each part
• -lib_size: (integer, default: 102) Maximal library size
• -input_parts: (boolean, default: True) Number of enzymes for each coding sequence

⁠Output

• output: (string) Path to the output SBOL file

⁠Dependencies

• Base Docker Image: python:3.6⁠

⁠Installing

To build the image using the Dockerfile, use the following command:

docker build -t brsynth/rpoptbiodes-standalone: .

⁠Running the tests

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

python run,py -input test/test_rpGlobalScore.tar -input_format tar -input_sbol test/test.sbol -output test/test_output.tar

⁠Contributing

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

⁠Versioning

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 rpOptBioDes?