For the easiest and most consistent shell behavior for this workshop, we'll be using Open OnDemand to start up a browser-based terminal.

Go to https://oit.utk.edu/hpsc/ and click the Open OnDemand button on the left side of the page.

Then click on the Clusters drop-down button and select >_ISAAC Shell Access.

After a few moments, you'll be logged in to the login node, which should appear as your command prompt:

ssh <your_username>@login.isaac.utk.edu

All raw data will be located in /lustre/isaac24/proj/UTK0386/data/raw.

To confirm, run:

ls /lustre/isaac24/proj/UTK0386/data/raw

❓ You should see a metadata.txt file and 12 gzipped fastq files. Does that mean we have 12 samples?

You can also see our reference files from NCBI.

ls -lh /lustre/isaac24/proj/UTK0386/data/reference

Of note are the following files:

• GCA_000001735.2_TAIR10.1_genomic.fna (our reference genome)
• genomic_modified.gff (our annotation file)
• protein.faa (protein coding sequences extracted from our fasta file)
• cds_from_genomic.fna (CDS sequences extracted from the fasta file)

echo 'export RNA=/lustre/isaac24/proj/UTK0386/analysis/${USER}' >> ~/.bashrc
source ~/.bashrc
mkdir -p $RNA
cd $RNA

mkdir 01_tour
cd 01_tour

It is bad practice to run anything CPU or memory intensive on the login node, so always check your prompt! We can actually use the SLURM scheduler command srun to request resources, which lets us have an interactive experience instead of sending jobs to the background.

There is a script called srun.sh located at /lustre/isaac24/proj/UTK0386/src/scripts/srun.sh with the following content:

#!/usr/bin/env bash

srun --account acf-utk0011 \
     --partition=short \
     --qos=short \
     --nodes=1 \
     --cpus-per-task=10 \
     --mem=10G \
     --time=0-3:00:00 \
     --pty /bin/bash

To run the script from within your 01_tour directory:

cp /lustre/isaac24/proj/UTK0386/src/scripts/srun.sh .
bash srun.sh

After a few moments you should have access to an interactive node.

Your shell prompt should no longer read login1 or login2, and should now show your node name. You are also automatically in your home directory, so be sure to change to where you'd like to be.

To leave the shell, simply type the command exit and hit enter.

ISAAC-NG comes with many pre-compiled, installed software you can run right away. To see a list of the software, run the following command:

module avail

If you want to see if a specific tool is available, try:

module avail star

...and it will search for the tool name.

Try loading star, checking the version, then unloading star using the following:

module load star/2.7.6a
STAR --version
module unload star/2.7.6a

Note that sometimes tools will have multiple versions. ALWAYS check which version you are using and look at the software github or development page to see if you're using the latest version.

For example:

module avail samtools

yields:

----------------------------------------------- /sw/isaac/modulefiles ------------------------------------------------
samtools/1.14  samtools/1.16.1-gcc