Biobox command line interface

This repository contains the code for building the bioboxes command line interface. This allows a user to run bioboxes in the shell using Docker as the backend. Documentation is available for using the command line interface.

Development Scripts

The folder script provides a series of scripts to help developers and also used by the continuous integration server. These scripts should be used in the following order:

• script/bootstrap: Install required python libraries using virtual env and pull Docker images necessary for testing.
• script/test: Runs python unit tests. These can be found in the test directory.
• script/build: Tests whether the project builds and installs as a python package. The package is installed in a Docker container as not to affect the user's system
• script/feature: Tests the tool against several different user scenarios. These scenarios are described in features.

Submitting pull requests

Contributing fixes or new features is welcome. For anything more than small bug fixes please open an issue on github beforehand to discuss what you intend to implement. This can help prevent time being wasted should the situation occur that your pull request is not immediately accepted.

To contribute changes to this project, fork the repository and create a feature branch. Once you have pushed your git commits to you forked repository, submit a pull request. A pull request should include the following:

• Add a new entry to the CHANGELOG.md and update biobox_cli/version.py. Please follow semantic versioning when updating the version number.
• Update the documentation in doc if the interface is changed.
• Add new feature tests in feature if new functionality is added. This will prevent them being broken in future development.
• Ensure the following scripts pass: script/test, script/build and script/feature