Installation and Setup

Python package and command-line tool

Install from Bioconda

The recommended way to install the tool is through the Conda package manager (I recommend the Miniconda distribution) from the Bioconda channel:

conda install -c bioconda gambit

Install from a pre-built wheel

Each GitHub release has pre-built wheels attached to it as downloadable assets, covering CPython 3.9-3.14 on 64-bit Linux. These do not require a C compiler or the cython package to install. Download the wheel file matching your Python version (e.g. gambit-1.2.0-cp312-cp312-manylinux_2_28_x86_64.whl for Python 3.12) and install it with:

pip install gambit-1.2.0-cp312-cp312-manylinux_2_28_x86_64.whl

Install from source

Installing from source requires the cython package as well as a C compiler be installed on your system. Clone the repository and navigate to the directory, and then run:

pip install .

Or do an editable development install with:

pip install -e .

Database files

You will need a GAMBIT reference database (consisting of one .gdb and one .gs file) to perform taxonomic classification using the gambit query command. Download files for the latest database release from the Reference database releases page and place them in a directory of your choice. The directory should not contain any other files with the same extensions.