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
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 .
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 Database Releases
page and place them in a directory of your choice. The directory should not contain any other files with the same extensions.