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Setting up your environment

This workshop is designed around the ARDC Nectar Research Cloud. Each participant will be assigned their own virtual machine (VM) which will have all of the prerequisite software pre-installed. The main requirements for participants will be:

  • A personal computer
  • Internet access
  • Visual Studio Code (VS Code)
  • A web browser

If you are working through these course materials on your own, see Setup instructions for your own machine below.

Installing and setting up VS Code

Visual Studio Code (VS Code) is a lightweight and powerful source code editor available for Windows, macOS and Linux computers.

  1. Download Visual Studio Code for your system from here and follow the instructions for:

  2. Open the VS Code application on your computer

  1. Click on the extensions button (four blocks) on the left side bar.

  2. Search for and install the "Remote - SSH" extension. Click on the blue install button.

Login via Visual Studio Code

To connect to your VM within VS Code, you first need to add the login details to an SSH config file on your computer. You can do this within VS Code as follows:

  1. Find and copy the IP address for your Nectar VM that you were provided with.
  2. In VS Code, use the keyboard shortcut Ctrl + Shift + P (Windows/Linux) or Cmd + Shift + P (MacOS) to open the command palette.
  3. Select Select Remote-SSH: Add New SSH Host...
  4. In the text box that appears, type ssh <USERNAME>@<ip_address>, substituting your provided username and IP address.
    • For example, if your username is me and your IP address is 130.56.245.40, you would type ssh me@130.56.245.40
  5. Press Enter to submit the SSH command.
  6. In the drop-down box, select an SSH configuration file to update.
    • Typically, you will want to update the configuration file that is in ${HOME}/.ssh/config, which will usually be the first one in the list.
  7. You should get a pop-up message saying "Host added!" in the VS Code window.

Now you are ready to connect to the VM via VS Code. To do so:

  1. Open the command palette again (Ctrl + Shift + P / Cmd + Shift + P) and select Remote-SSH: Connect Current Window to Host...
  2. In the drop-down box, select the newly-added remote, which should be at the top of the list and should be labelled with your VM's IP address.
  3. Type in your provided password and press enter.

Having successfully logged in, you should see a small blue or green box in the bottom left corner of your screen:

Install extensions on the remote machine

We will now install some helpful VS Code extensions:

  • Live Server: enables you to view HTML reports on the remote machine without having to download them to your local computer first.

  • Rainbow CSV: displays CSV and TSV files with colour-coded columns, and also allows you to align the columns with one another to make it easier to read.

  • Ensure you are still connected to the VM as above.

  • Click on the extensions button (four blocks) on the left side bar.
  • For each of the extensions listed above, search for the extension name, click on the matching result, and click on the blue install button.

Open the workshop folder

The last thing to do is to navigate to the workshop folder:

  1. Go to the File Explorer view in the left-hand side bar, or press Ctrl + Shift + E (Windows/Linux) or Cmd + Shift + E (Mac) if it isn't visible.
  2. Click the blue "Open Folder" button.
  3. By default, VS Code will suggest your home folder (/home/<USERNAME>), which is the directory we want to open. Press Enter to open VS Code in your home directory.
    • If for some reason VS Code is suggesting a different path than your home folder, you can use the drop-down box to navigate to it manually, or replace the path in the text box with ~ and press Enter (VS Code should automatically replace the ~ with the full path to your home folder, i.e. /home/<USERNAME>)
  4. If prompted, select the box for Trust the authors of all files in the parent folder ‘home’ then click Yes, I trust the authors
  5. To open a terminal, type Ctrl + J (Windows) or Cmd + J (MacOS)
    • TIP: You can also use Ctrl + ` (the backtick key, all systems) to open a terminal, and Ctrl + Shift + ` to open additional terminal tabs, which show up in a panel on the right-hand side of the terminal view.

Getting around the workspace and running commands

Run the three checks below in the terminal to confirm that everything you need is in place.

  1. Check that the AMRFinderPlus database exists by listing its folder:

    ls ~/data/ref/amrfinderplus_db/

    You should see 2026-08-07.1 and latest.

  2. Check that the sample assigned to your breakout room is present. For example, if your sample is ERR8282752:

    ls /home/<USERNAME>/data/fastqs/ERR8282752.fastq.gz

    You should see the file name displayed, and not a No such file or directory message.

  3. Check that the software is installed by asking FastQC for its version:

    fastqc -v

    You should see FastQC v0.12.1.

  4. Later modules will ask you to open HTML reports generated on the VM. To do this: right-click the report file in the VS Code file explorer and choose Open with Live Server to view it in a browser window — alternatively, download the report and open it locally.

    Practice this now on an example report copied into your home directory during setup: in the File Explorer side bar, navigate to example_report/barcode01_fastqc.html, right-click it, and choose Open with Live Server.

    You should see a FastQC report open in a browser window, with the title "barcode01" at the top. Just close the browser tab when you're done.

If you encounter any issues with these checks, let the organisers know.

Tips for using VS Code

  • VS code cheatsheet for Windows
  • VS code cheatsheet for MacOS

  • Copy a file's full path: right-click a file in the File Explorer and choose Copy Path (Shift + Alt + C) to copy its full path to the clipboard, instead of typing it out by hand.

  • Reuse a previous command: press the Up/Down arrow keys in the terminal to cycle back through commands you've already run.

Shortcut Windows/Linux MacOS
Show command palette Ctrl + Shift + P Cmd + Shift + P
Toggle sidebar Ctrl + B Cmd + B
Open new window Ctrl + Shift + N Cmd + Shift + N
Open new file Ctrl + N Cmd + N
Open file Ctrl + O Cmd + O
Open folder Ctrl + K then Ctrl + O Cmd + O
Open/close terminal Ctrl + J Cmd + J
Open/close terminal (alternative) Ctrl + ` Ctrl + `
Open additional terminal Ctrl + Shift + ` Ctrl + Shift + `
Next file or terminal tab Ctrl + PageDown Cmd + Shift + ]
Previous file or terminal tab Ctrl + PageUp Cmd + Shift + [
Quick file open Ctrl + P Cmd + P
Zoom in Ctrl + = Cmd + =
Zoom out Ctrl + - Cmd + -
Find Ctrl + F Cmd + F
Save Ctrl + S Cmd + S
Select current line Ctrl + L Cmd + L
Edit every instance of highlighted string Ctrl + Shift + L Cmd + Shift + L