Installation and Setup

Python package and command-line tool

Conda

Install with the Conda package manager from the Bioconda channel:

conda install -c conda-forge -c bioconda gambit

Pixi

Install the gambit command globally using Pixi:

pixi global install -c conda-forge -c bioconda gambit

To add GAMBIT to an existing Pixi workspace instead, use pixi add gambit (after ensuring the conda-forge and bioconda channels are added to the workspace).

Pip

Install from PyPI:

pip install gambit

Pre-built wheels are only provided for Linux (x86_64) and CPython 3.12-3.14. On other platforms pip will attempt to build from the source distribution (see From source).

From source

Clone the repository and install with pip:

git clone https://github.com/jlumpe/gambit.git
cd gambit
pip install .  # or "pip install -e ." for an editable install

Requires a C compiler with OpenMP support. Not supported on macOS (Apple clang lacks -fopenmp) or Windows. macOS users should install using Conda or Pixi instead, and Windows users should use WSL.

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.