Step 1: Install conda (if not already done)¶
We strongly recommend using Mamba (much faster!) over miniconda/conda, but all will work.
Step 2: Create the GTDB-Tk environment¶
It is strongly recommended to create a new conda environment for each version of GTDB-Tk released.
You must always specify the version of GTDB-Tk, as conda may try to install a very old version (v1.0.2).
GTDB-Tk requires third-party packages from the
bioconda channels, make sure to
specify those channels in that order!
# NOTE: replace 2.1.1 with the version you wish to install # using conda conda create -n gtdbtk-2.1.1 -c conda-forge -c bioconda gtdbtk=2.1.1 # using mamba (alternative) mamba create -n gtdbtk-2.1.1 -c conda-forge -c bioconda gtdbtk=2.1.1
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.
The conda package is bundled with a script
that will automatically download, and extract the GTDB-Tk reference data. The script will be on the system path so simply run:
You can automatically alias
GTDBTK_DATA_PATH whenever the environment is activated by
setting environment-specific variables, e.g.:
# Activate the GTDB-Tk conda environment conda activate gtdbtk-2.1.1 # Set the environment variable to the directory containing the GTDB-Tk reference data conda env config vars set GTDBTK_DATA_PATH="/path/to/unarchived/gtdbtk/data";