Reference

This section describes the layout of the code repository and contains the API reference to the complete contents of the code collection.

Repository layout

The repository contains the following directories:

scripts

Scripts in the code collection.

CGAT

Modules for code shared between scripts in the collection.

doc

The sphinx documentation of the code repository.

tests

Testing code

recipes

ipython notebook recipes and tutorials.

galaxy

scripts to hook the code collection into galaxy.

API