Developer Quickstart

Developing breseq extensions

You are creating a Python or R package that operates on the output of breseq runs. These tools may require the installation of other programs (e.g., Circos, de novo assemblers).

1. Install breseq as shown below for developers or you can download the most recent release version and install it via these instructions.

Developing Python modules

If you are developing code that reads in genomediff files output by breseq, then we recommend that you use the official genomediff Python module for this purpose rather than re-inventing the wheel. If you need to update the functionality of the genomediff Python parser, please contribute to that GitHub project.

Developing breseq core code

You are coding in C++ to change the core breseq and/or gdtools commands.

1. You must clone the GitHub repository. (Do not download a release version.)
2. Follow the Developer Installation instructions.

All developers

You should familiarize yourself with how breseq works and its output files by completing these activities that can be found in the breseq documentation:

1. Test Drive
2. Tutorials: Clonal Samples | Mixed Populations

Contributing code

We welcome your contributions! You can check out suggested coding projects or look for bugs to fix. Please comment on these if you are working on them so that we can avoid duplicating efforts and provide guidance.

To contribute your code, you should:

1. Fork the breseq repository.
2. Work on your code, create tests for the code, have others try out the code...
3. Submit a pull request to the breseq repository, so that it can be integrated into the project.