Computational Biology Trainings

by András Aszódi

Container course setup instructions

Read and execute these instructions carefully to the very end. Thank you.

Each participant is assigned a personal virtual machine (VM). The VMs are reachable only from the VBC internal network. If the course is held over the Internet "remotely" then you'll need VPN access.

User account

Make sure you have an account on the CBE cluster. You can request an account either by emailing the cluster administrators or at the VBC IT portal by clicking on the "HPC Support Ticket" link and selecting the "Get HPC access" option. Access will be granted only to those colleagues who can reasonably be expected to use the CBE cluster in the near future.


You must be familiar with the UNIX ssh remote login tool. ssh is available on Linux and macOS as a command-line application. If you have a Windows computer then you'll either need the "Windows Subsystem for Linux" (WSL) or you have to install an SSH client application. We recommend MobaXTerm.

CBE cluster access

Make sure you can connect to the CBE cluster via the command ssh, where firstname.lastname is your user name. Connection is possible only from the VBC internal network. Employees at the Max Perutz Labs and at collaborating non-VBC institutes (e.g. institutions of the OEAW) will need to connect to the VBC network via VPN, see below.

VPN access

Go to the VBC VPN site, log in with your CBE credentials, download the VPN client software ("Cisco AnyConnect Secure Mobility Client") and install it on your computer. Test the VPN client by connecting to the same URL from it as above.

Virtual machine for the hands-on exercises

You will run the hands-on exercises on your "personal" virtual machine (VM) in which the Docker and Apptainer software plus a number of other tools were pre-installed for you. The hostname of the VM is usually where `X=0, 1, 2, ...` is a number. You will be notified which VM has been assigned to you.

As soon as you received the name of your VM, you should SSH into it using your CBE login name and password. If you cannot connect then it usually means that your password is too old (i.e. hasn't been changed in years). In this case change your CBE password here.

Once you are logged into your VM, please run the following command: /tmp/ctr_examples/ $HOME. This script will set up three directories in your home directory called data, docker and apptainer that contain the hands-on exercises. Verify that you have them all by typing tree -d $HOME. The output should look like this:

├── apptainer
│   ├── conv
│   └── multovl
│       └── sandboxes
├── data
└── docker
    ├── convctx
    ├── hictx
    └── multovl
        └── devboost

Remote editing with Visual Studio Code

You will use Visual Studio Code (VSCode) for editing Dockerfiles and Apptainer recipe files remotely on your VM. VSCode also gives you a UNIX terminal. Download VSCode and install it on the laptop that you will bring to the course.

SSH extension for VSCode

Go to the "Extensions" option of VSCode and search for "SSH". Install the "Remote - SSH" extension. Verify the installation by connecting to your VM from within VSCode.

Directory navigation in VSCode

Use the "Open Folder" menu item of VSCode to change directories. It may be necessary to tell VSCode that you "trust the folder". Just say yes.

If you have read this far...

...then as a reward you can download the setup checklist which also gives you pictures to look at.

That's all, see you at the course!