Verify setup and copy work folder

Overview

Teaching: 0 min
Exercises: 25 min

Objectives

• Verify that your pre-course setup (VPN, VS Code, Remote-SSH, Draco login) works correctly

• Copy scripts and data to your own folder on Draco using the provided script

1. Verify you can connect to Draco

During this course you will use your laptop to connect to Draco, the high-performance computing (HPC) cluster at the University of Jena. Most analyses will run on Draco rather than on your laptop. If you completed the pre-course setup, you should already be able to connect to Draco from VS Code.

Perform the following checks:

1. Open VS Code
2. Connect to Draco using Remote - SSH (as you did in the pre-course setup).
3. Open a terminal and run:

hostname
pwd
whoami

hostname should print something like login1.cluster or login2.cluster. pwd should print your home directory on Draco, something like /home/<your_username>. whoami should print your URZ username.

If anything doesn’t work, call a TA before continuing with the other excercises.

Set up your working folder

Copy scripts and folders

Execute the following commands in the terminal:

cd ~
cp /vast/groups/VEO/shared_data/Viromics2026_template/setup_workspace.sbatch ./
sbatch setup_workspace.sbatch

This will submit a script to Draco to copy the necessary files for this course to your home directory. You can check whether it’s still running with:

squeue --me

Once the job no longer appears in that list, it’s done.

Verify it completed successfully by checking if the files are there:

cd ~/Viromics2026_workspace
ls

You should see several folders and files, including a data folder containing a sequences subfolder, with one or more .fastq.gz files inside.

Add workspace folder to VS Code explorer

Now that your workspace actually has something in it, let’s make sure the Explorer sidebar is pointed at it.

Open your workspace folder

1. Open the Explorer sidebar (folder icon, left edge of VS Code) and click Open Folder.
2. Add /home/<YOUR-URZ-ID>
3. Navigate to Viromics2026_workspace and confirm.
4. Expand data → sequences in the tree. Do the files match what ls showed you?

The terminal and the Explorer are two different ways to view files on Draco. In the next lesson, we will practice using both.

Key Points

• your laptop can connect to Draco

• You now have a personal workspace with scripts and sequencing data, which we’ll use for the rest of the course