Installation
Note
This is an Augur-specific installation guide. If you wish to use Nextstrain as a whole, please refer to the Nextstrain installation guide.
Install Augur
Warning
There are some package managers that have entries with a similar name.
Augur on PyPI. This is a different project. Use nextstrain-augur instead.
augur on Debian. This is an unofficial version not maintained by the Nextstrain core team. It may lag behind official Augur releases. We do not generally recommend its use.
There are several ways to install Augur, ordered from least to most complex.
Augur is part of the Nextstrain project and is available in all Nextstrain runtimes.
Continue by following the Nextstrain installation guide.
Once installed, you can use nextstrain shell to run augur directly.
Augur can be installed using Conda or another variant. This assumes you are familiar with how to manage Conda environments.
conda install -c conda-forge -c bioconda augur
This installs Augur along with all dependencies.
Warning
Installing other Python packages after Augur may cause dependency incompatibilities. If this happens, re-install Augur using the command in step 1.
Augur is written in Python 3 and requires at least Python 3.8. It’s published on PyPI as nextstrain-augur.
Install Augur along with Python dependencies.
python3 -m pip install nextstrain-augur
Install other dependencies.
Augur uses some external bioinformatics programs that are not available on PyPI:
augur alignrequires mafftaugur treerequires at least one of:augur mergerequiressqlite3, the SQLite CLI (version ≥3.39).Bacterial data (or any VCF usage) requires vcftools
Note
For local development, tests also require tsv-utils.
If you use Conda, you can install them in an active environment:
conda install -c conda-forge -c bioconda mafft raxml fasttree iqtree vcftools sqlite --yes
On macOS using Homebrew:
brew tap brewsci/bio brew install mafft iqtree raxml fasttree vcftools sqlite
On Debian/Ubuntu:
sudo apt install mafft iqtree raxml fasttree vcftools sqlite3
Other Linux distributions will likely have the same packages available, although the names may differ slightly.
Warning
Installing other Python packages after Augur may cause dependency incompatibilities. If this happens, re-install Augur using the command in step 1.
Augur can be installed from source. This is useful if you want to use unreleased changes or develop Augur locally.
Install Augur along with Python dependencies.
git clone https://github.com/nextstrain/augur.git cd augur python3 -m pip install .
Note
For local development, install from source in editable mode with
devdependencies.python3 -m pip install -e .'[dev]'
Install other dependencies.
Augur uses some external bioinformatics programs that are not available on PyPI:
augur alignrequires mafftaugur treerequires at least one of:augur mergerequiressqlite3, the SQLite CLI (version ≥3.39).Bacterial data (or any VCF usage) requires vcftools
Note
For local development, tests also require tsv-utils.
If you use Conda, you can install them in an active environment:
conda install -c conda-forge -c bioconda mafft raxml fasttree iqtree vcftools sqlite --yes
On macOS using Homebrew:
brew tap brewsci/bio brew install mafft iqtree raxml fasttree vcftools sqlite
On Debian/Ubuntu:
sudo apt install mafft iqtree raxml fasttree vcftools sqlite3
Other Linux distributions will likely have the same packages available, although the names may differ slightly.
Testing if it worked
If installation worked, you should be able to run augur --help and see augur’s primary help output.