Bioconda

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 gTranslate environment

It is strongly recommended to create a new conda environment for each version of gTranslate released.

gTranslate requires third-party packages from the conda-forge and bioconda channels, make sure to specify those channels in that order!

# NOTE: replace 0.0.4 with the version you wish to install

# using conda
conda create -n gtranslate-0.0.4 -c conda-forge -c bioconda gtdb-gtranslate=0.0.4

# using mamba (alternative)
mamba create -n gtranslate-0.0.4 -c conda-forge -c bioconda gtdb-gtranslate=0.0.4

Step 3: Download and alias the gTranslate models

gTranslate accept both an environment variable named GTRANSLATE_MODEL_PATH to be set to the directory containing the models or accept a flag called –custom_model_path that points to the directory containing the models.

You can automatically alias GTRANSLATE_MODEL_PATH whenever the environment is activated by setting environment-specific variables, e.g.:

# Activate the gTranslate conda environment
conda activate gtdb-gtranslate-0.0.4

# Set the environment variable to the directory containing the gTranslate model classifiers
conda env config vars set GTRANSLATE_MODEL_PARTH="/path/to/unarchived/gtranslate/models";