Set up your computer

In this workshop series, we will be using Pawsey’s Nimbus cloud. The Pawsey Supercomputing Research Centre is one of two, Tier-1, High Performance Computing facilities in Australia.

The main requirements for this workshop are a personal computer with:

• A web browser (Google Chrome is recommended)
• Visual Studio Code (recommended) or a terminal application

Below, you will find instructions on how to set up a terminal application and web browser on your computer and how to connect to Nimbus. Each participant will be provided with their instance’s IP address at the beginning of the workshop.

Option 1: Install and set up Visual Studio Code (recommended)

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:
   • macOS
   • Linux
   • Windows
2. Open the VS Code application on your computer

3. Click on the extensions button (four blocks) on the left side bar and install the remote SSH extension. Click on the blue install button.

4. Install the Live Server extension. Click on the blue install button.

Login via Visual Studio Code

Connect to your instance with VS code by adding the host details to your .ssh config file:

1. Go to the list of instance IP addresses provided in the Slack channel
2. Find and copy your IP address, it will start with 146.118.XXX.XX
3. In a new VS code terminal, type Ctrl+Shift+P if you’re on a Windows machine or Cmd+Shift+P for MacOS to open the command palette
4. Select Select Remote-SSH: Open SSH configuration file and select your .ssh config file
5. Add a new entry using your allocated IP address and save your .ssh config file:

Host rnaseqWorkshop
  HostName 146.118.XXX.XX
  User training

6. Type Ctrl+Shift+P and select Remote-SSH: Connect to Host and rnaseqWorkshop
7. When prompted, select Linux as the platform of the remote host from the dropdown menu
8. Type in your provided password (see the Slack channel for the password) and hit enter

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

To set up your VS Code window for the workshop:

1. Open a new folder in the file explorer panel on the left side of the screen by typing Ctrl + K, Ctrl + O if you’re running Windows or Cmd+K+ Cmd + O for MacOS
2. Select /home/training to open your instance’s $HOME folder, this is where we will be working
3. When prompted, select the box for Trust the authors of all files in the parent folder ‘home’ then click Yes, I trust the authors
4. To open a terminal, type Ctrl+J if you’re on a Windows machine or Cmd+J on MacOS

Tips for using VS Code

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

Shortcut	Windows	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/close terminal	ctrl+J	cmd+J
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

Option 2: Install and set up a terminal application

The terminal applications available to you will depend on your operating system.

Linux terminals

If you use Linux, chances are you already know your shell and how to use it. Basically, just open your preferred terminal program and off you go!

OS X (Mac)

Mac operating systems come with a terminal program, called Terminal. Just look for it in your Applications folder, or hit Command + Space and type ‘terminal’. You may find that other, 3rd party terminal programs are more user-friendly and powerful, like Iterm2.

Windows

We recommend MobaXterm, which offers a rich experience as a full-featured X-server and terminal emulator for ssh connections, the free version is more than adequate.

To install and start using MobaXterm:

1. Go to https://mobaxterm.mobatek.net/download.html
2. Under ‘Home Edition’ select the Download now button
3. Select the MobaXterm Home Edition (Installer edition)
4. Once the program is downloaded, install it as you would any other windows program
5. Once the program is installed, start the MobaXterm program
6. From this screen, click on ‘start local terminal’ (and install Cygwin if prompted)

Login via Terminal

To log in to Nimbus, we will use a Secure Shell (SSH) connection. To connect, you need 3 things:

• The assigned IP address of your instance (i.e. 146.118.XXX.XX). Each participant will be provided with their instance’s IP address at the beginning of the workshop.
• Your login name. In our case, this will be training for all participants.
• Your password. All participants will be provided with a password at the beginning of the workshop.

To log in: type the following into your terminal, using your allocated instance’s IP address:

ssh training@146.118.XXX.XX

You will receive a message saying:

The authenticity of host '146.118.XX.XXX (146.118.XX.XXX)' can't be established.

Remember your host address will be different than the one above. There will then be a message saying:

Are you sure you want to continue connecting (yes/no)?

If you would like to skip this message next time you log in, answer ‘yes’. It will then give a warning:

Warning: Permanently added '146.118.XX.XXX' (ECDSA) to the list of known hosts.

Enter the password provided at the beginning of the workshop. Ask one of the demonstrators if you’ve forgotten it.

Pay Attention

When you type a password on the terminal, there will not be any indication the password is being entered. You’ll not see a moving cursor, or even any asterisks, or bullets. That is an intentional security mechanism used by all terminal applications and can trip us up sometimes, so be careful when typing or copying your password in.

Having successfully logged in, your terminal should then display something like that shown in the figure below: