To complement the API, we also provide an optional One Codex command line interface (CLI) and Python client library for more conveniently interacting with our API and platform.

The CLI supports several features not possible by using the raw API and cURL directly:

  • Saving and reloading API keys / login credentials
  • A more robust (and easier to use) upload process
  • Automatic detection and interleaving of paired end (*_R1, *_R2) data
  • Support for multiple simultaneous file uploads

The command line interface is written in Python and accompanies our client library. It should be easily installable on most machines with the following command:

pip install onecodex   # Note, Windows users may need to do `py -m pip install onecodex`

The CLI and accompanying onecodex Python client library support Python 2.7+ and Python 3.4+. Throughout the following documentation, we provide usage examples for the CLI and Python client libraries where applicable (labeled CLI and Python in the code snippets respectively).