Step 1: Install third-party dependencies

Ensure that the software described in Third-party software are on the system path.

Step 2: Install GTDB-Tk via pip

Note: It is strongly recommended to create a virtual environment for each version of GTDB-Tk installed.

Once the third-party dependencies have been installed, install GTDB-Tk via pip:

python -m pip install gtdbtk

Alternatively, if you have a previously installed GTDB-Tk, you can upgrade the latest version:

python -m pip install gtdbtk --upgrade

Step 3: Download and alias the GTDB-Tk reference data

GTDB-Tk requires an environment variable named GTDBTK_DATA_PATH to be set to the directory containing the unarchived GTDB-Tk reference data.

export GTDBTK_DATA_PATH=/path/to/release/package/

You can permanently save this variable as described here.