Pipeline components for real-time virus analysis

How to run augur:

  • see the README.md files in the respective pathogen's folder (flu, ebola, e.t.c.)

Directory structure

Throughout we assume that the fauna, augur and auspice are sister directories.



Tests run using tox and pytest. If you didn't install augur with pip -r requirements.txt or with the janus conda environment, install them as follows.

# Install with pip.
pip install --user pytest tox

# Or install inside a conda environment.
source activate janus_python2
conda install pytest virtualenv
pip install tox

Run tests from the augur root directory.


Tox builds an empty virtual environment, installs augur's requirements and a package of augur built from the local directory, and runs tests with pytest. The tox.ini file defines the test environment and the pytest.ini file defines which tests to run. Tox reuses the virtual environment with subsequent runs. Use the -r flag to force it to rebuild its environment.

tox -r

Note that on OS X, matplotlib may throw errors during testing stating

from matplotlib.backends import _macosx
E   RuntimeError: Python is not installed as a framework.

This can be resolved by switching matplotlib backends. Create a file in the home directory ~/.matplotlib/matplotlibrc and include the following:

backend: TkAgg

This should fix the error.