Overview
| Table of Contents | ||
|---|---|---|
|
...
The PCs in the computer labs already have R and RStudio installed. If using this option, you will need to install the required R packages (unlike rVDI). The code for installing these packages is in the analysis section below.Open PuTTy and paste the text below into the command prompt:
| Code Block |
|---|
qsub -I -S /bin/bash -l walltime=4:00:00 -l select=1:ncpus=16:mem=128gb |
After a few minutes interactive mode will start. You will now be able to do all your analysis - including running Nextflow and Nanopore workflows - in this interactive session.
Map your HPC home directory
...
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:
| Code Block |
|---|
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
...
| Code Block |
|---|
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 |
...
| Code Block |
|---|
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:
| Code Block |
|---|
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
...
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”.
...