Docker

Step 1: Install Docker (if not already done)

Ensure that docker on the system path, see Docker for more information.

Step 2: Download the GTDB-Tk reference data

Download an unarchive the GTDB-Tk reference data to a directory of your choice, e.g: /host/release_data/

Step 3: Create a local I/O directory for GTDB-Tk

You will need to create a directory on the host machine that the container can access. The container will use this to read input genomes, and write output files, e.g.: /host/gtdbtk_io/

You should either copy or symlink your genomes to this directory, e.g. you may have the following contents:

/host/gtdbtk_io/genomes/genome_a.fna
/host/gtdbtk_io/genomes/genome_b.fna

Step 4: Run the container

The two host directories created in Step 2, and Step 3 will be mapped to the container via the -v flag:

  • /host/release_data:/refdata

  • /host/gtdbtk_io:/data

For example, the classify workflow for genome_a, and genome_b an be run as follows:

docker run -v /host/gtdbtk_io:/data -v /host/release_data:/refdata ecogenomic/gtdbtk classify_wf --genome_dir /data/genomes --out_dir /data/output

Note:

  • When referring to /host/gtdbtk_io in the GTDB-Tk arguments, it has been aliased to /data as specified by the -v flag.

  • The alias /data and /refdata cannot be changed.