gtdbtk.md

GTDB-Tk

Documentation | GitHub

Refer to hardware requirements for this software: 250 GB of RAM!!!!

Installation with conda and automatic database download

Currently, version 1.7 + R202

cd ~/Downloads
conda create -n gtdbtk -c conda-forge -c bioconda gtdbtk
wget https://github.com/bioconda/bioconda-recipes/blob/master/recipes/gtdbtk/download-db.sh
sudo chmod +x ./download-db.sh
./download-db.sh

rm  -f ./download-db.sh

For less performative PCs

1.4.1 + R95

cd ~/Downloads
conda create -n gtdbtk-1.4 -c conda-forge -c bioconda gtdbtk=1.4
conda activate gtdbtk-1.4

# make sure it is not pointing to the freshest installation
echo ${GTDBTK_DATA_PATH}

wget https://data.gtdb.ecogenomic.org/releases/release95/95.0/auxillary_files/gtdbtk_r95_data.tar.gz
tar xvzf gtdbtk_r95_data.tar.gz -C ${GTDBTK_DATA_PATH} --strip 1
rm ./gtdbtk_r95_data.tar.gz

conda deactivate