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.
You can permanently save this variable as described here.