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https://www.youtube.com/watch?v=s3ii48qYBxA

Step 1: initial setup

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How to use this guide

In this guide, commands to be entered by the user will be in grey boxes like the one below. Most commands can simply be cut and paste ‘as-is’ into your command line. Some need to be modified due to variations in your data (e.g. target species) or location.

You can hover your mouse over the code box to see a ‘copy’ button on the right. Just click this to copy all the code in the box.

Try this with the code box below (this will show the directory paths defined by your profile).

echo $PATH

Step 1: initial setup

You will be running various processes on the HPC that require quite a lot of processing power. Do not run these command on the 'head node' (which is the node you enter when you log on). Instead, either submit these commands via a PBS script or an interactive PBS session, which runs your processes on another node.

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If you’re testing several tools or running multiple separate commands then an interactive PBS session may be preferable. Below is the command to create an interactive PBS session with 8 CPUs, 64GB memory and a maximum running time of 11 hours (12 hours is the absolute maximum that can be requested for an interactive session).*Note: In this guide, commands to be entered by the user will be in grey boxes like the one below. As with most commands, you can simply cut and paste this into your command line. You can hover your mouse over the code box to see a ‘copy’ button on the right. Just click this to copy all the code in the boxmultiple separate commands then an interactive PBS session may be preferable. Below is the command to create an interactive PBS session with 8 CPUs, 64GB memory and a maximum running time of 11 hours (12 hours is the absolute maximum that can be requested for an interactive session).

qsub -I -S /bin/bash -l walltime=11:00:00 -l select=1:ncpus=8:mem=64gb

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