Environment variables

Augur’s behaviour can be globally modified by the values of some specific environment variables. These can be especially useful in the context of an entire pipeline or workflow which uses Augur, as the environment variables can be set once for all Augur commands at the start of the pipeline.


Boolean. If set to a non-empty value, all JSON output produced by Augur will be minified by omitting indentation and newlines.

Minifying the JSON will substantially reduce file sizes, which is helpful for large, deeply nested trees.


Integer. If set to a non-empty value, the Python recursion limit will be set to the given value early in Augur’s execution by calling sys.setrecursionlimit().

Generally there is no need to set this environment variable. You may need to if you find yourself encountering RecursionError while processing a very unbalanced tree.