Differences

This shows you the differences between two versions of the page.

--- gtdbtk-software [2020/05/04 19:50] – created aorth
+++ gtdbtk-software [2020/05/04 20:25] (current) – aorth
@@ Line 15: / Line 15: @@
 Load one version into your environment and run it:
-<code>$ module load gtdbtk
+<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 ======
@@ Line 27: / Line 29: @@
 $ source /export/apps/gtdbtk/1.1.1/bin/activate
 $ pip install --upgrade pip setuptools
-$ pip install gtdbtk</code>
+$ pip install gtdbtk
+$ sudo chown -R root:root /export/apps/gtdbtk/1.1.1</code>
 Download the reference data:
@@ Line 33: / Line 36: @@
 <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</code>
+$ 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>