Overview

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https://qutvirtual4.qut.edu.au/group/staff/research/conducting/facilities/advanced-research-computing-storage/supercomputing/using-hpc-filesystems

Interactive HPC session

In the next step we’re going to copy some data files to your home directory.

Just like in the last session, we’re going to start an interactive PBS session to do this, so we’re not all copying large datasets on the head node.

Open PuTTy and paste the text below into the command prompt:

qsub -I -S /bin/bash -l walltime=4:00:00 -l select=1:ncpus=8:mem=32gb

Wait until the interactive session starts, then move to the next step (below).

Create your workshop folders and check your data

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cp -r /work/training/metagenomics/public_data/Illumina/results $HOME/meta_workshop/illumina
mkdir -p $HOME/meta_workshop/illumina/data
cp -r /work/training/metagenomics/public_data/Illumina/data/metadata.tsv $HOME/meta_workshop/illumina/data

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mkdir $HOME/meta_workshop/R_analysis

Downloading the sarek results

In session 7 we’re going to do some downstream analysis of the nfcore/sarek variant calling workflow that was completed in sessions 2 and 3 of these workshops. We realise not everyone attended these (or didn’t successfully complete the sarek workflows), so you can download the results of successful runs by running the following command in PuTTY:

mkdir $HOME/workshop/sarek
cp -r /work/training/sarek/runs/ $HOME/workshop/sarek

While these datasets are copying we can move to the next section (leave PuTTY running).

Open RStudio and create a new R script

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Create a new script by ‘File’ → “New File” → “R script”. Now hit ‘File’ → ‘Save’ and save the script in H:/meta_workshop/R_analysis (i.e. the directory we just created). Give the script a name. Call it “R_metagenomics”.

Go to the next section, ‘Setting up your R environment’