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1. A HPC account

2. Nextflow installed on the HPC

3. PuTTy installed on your local computer

4. Access your HPC home directory from your PC

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If you haven’t installed Nextflow, follow the instructions in this link: Installing Nextflow

You’ll need PuTTY on your PC to access the HPC.

You can download PuTTY from here: https://the.earth.li/~sgtatham/putty/latest/w64/putty.exe

Then add the HPC (Lyra) address: lyra.qut.edu.au and then click ‘open’.

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Setup Windows File Explorer to access your HPC home account. Follow the instructions here:

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NOTE: I’ve selected 16 CPUs and 128gb of memory. This is based on testing of the Nextflow workflows we’ll be using and their CPU/memory requirements.

Additional interactive job for running Nanopore analysis (may start quicker as fewer resources)

qsub -I -S /bin/bash -l walltime=4:00:00 -l select=1:ncpus=5:mem=12gb

Create working directories

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Then save the file by typing <ctrl> o, press Enter, and then <ctrl> x to exit Nano.

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Copy the Illumina and Nanopore fastq files to their respective workshop directories like so:

cd $HOME
cd meta_workshop
cp /work/training/metagenomics/public_data/Illumina*.fastq.gz illumina/fastq
cp /work/training/metagenomics/public_data/Nanopore*.fastq.gz nanopore/fastq

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