ILRI Research Computing

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====== gtdbtk ======

GTDB-Tk is a software toolkit for assigning objective taxonomic classifications to bacterial and archaeal genomes based on the Genome Database Taxonomy GTDB. It is designed to work with recent advances that allow hundreds or thousands of metagenome-assembled genomes (MAGs) to be obtained directly from environmental samples. It can also be applied to isolate and single-cell genomes.

===== Information =====

  * Version: 1.1.1
  * Added: May, 2020
  * Link: https://ecogenomics.github.io/GTDBTk/
  
===== Usage =====

See which versions of gtdbtk are available:
<code>$ module avail gtdbtk</code>

Load one version into your environment and run it:
<code>$ module load gtdbtk/1.1.1
$ gtdbtk</code>

Note: Please use the %%--cpus%% option to specify the number of CPUs to use in your workflow. This should match the number of CPUs requested in your SLURM SBATCH script.

===== Installation ======

Notes from the sysadmin during installation:

<code>$ sudo mkdir -p /export/apps/gtdbtk/1.1.1
$ sudo chown aorth /export/apps/gtdbtk/1.1.1
$ python3 -m venv /export/apps/gtdbtk/1.1.1
$ source /export/apps/gtdbtk/1.1.1/bin/activate
$ pip install --upgrade pip setuptools
$ pip install gtdbtk
$ sudo chown -R root:root /export/apps/gtdbtk/1.1.1</code>

Download the reference data:

<code>$ wget https://data.ace.uq.edu.au/public/gtdb/data/releases/release89/89.0/gtdbtk_r89_data.tar.gz
$ sudo mkdir -p /export/data/bio/gtdbtk
$ sudo tar xf gtdbtk_r89_data.tar.gz -C /export/data/bio/gtdbtk
$ sudo find /export/data/bio/gtdbtk -type d -exec chmod 755 {} \;
$ sudo find /export/data/bio/gtdbtk -type f -exec chmod 644 {} \;</code>