Installation¶
Using pip from PyPi¶
Augur is written in Python 3 and requires at least Python 3.4.
It’s published on PyPi as nextstrain-augur, so you can install it with pip
like so:
pip install nextstrain-augur
If your system has both Python 2 and Python 3 installed side-by-side, you may need to use python3
instead of just python
(which often defaults to Python 2 when both Python versions are installed).
Augur uses some common external bioinformatics programs which you’ll need to install to have a fully functioning toolkit:
augur align
requires mafftaugur tree
requires at least one of:Bacterial data (or any VCF usage) requires vcftools
On macOS, you can install these external programs using Homebrew with:
brew install mafft iqtree raxml fasttree vcftools
On Debian/Ubuntu, you can install them via:
sudo apt install mafft iqtree raxml fasttree vcftools
Other Linux distributions will likely have the same packages available, although the names may differ slightly.
Using Conda¶
Alternatively, augur itself and all of its dependencies can be installed into a Conda environment:
conda env create -f environment.yml
By default this environment is named “augur” but you can change that by providing a name to the above command with
-n <your-env-name>
When that finishes, the enviroment needs to be activated whenever you want to use augur:
conda activate augur
Install from source¶
git clone https://github.com/nextstrain/augur.git
pip install .
This install depends on a fairly minimal set of external Python libraries. There are some functions in augur that require a larger set of dependencies. These can be installed via:
pip install .[full]
If you wish to also install the development dependencies, and install augur in an “editable” mode whereby changes to the source code are reflected in your version of augur
then run:
pip install -e .[dev]
See above for how to install the external bioinformatics programs which you’ll need to have a fully functioning toolkit.
Testing if it worked¶
If installation worked, you should be able to run augur --help
and see
augur’s primary help output.