Precourse instructions

Background knowledge

As stated in the course prerequisites at the announcement web page, we expect participants to have a basic understanding of working with the command line on UNIX-based systems and a good understanding of Docker and Apptainer/Singularity containers.

UNIX

You can test your UNIX skills with a quiz here. If you don’t have experience with UNIX command line, or if you are unsure whether you meet the prerequisites, follow our online UNIX tutorial.

Docker/Apptainer

If you don’t have experience with Docker or Apptainer containers, or if you are unsure whether you meet the prerequisites, check out the material of the dedicated SIB course.

Software

OS and terminal

During the course exercises you will be interacting with Snakemake through the command line. If you are using a UNIX or UNIX-like OS (e.g MacOS), you already have a terminal readily usable for the course. If you are working with Windows, although Windows Powershell is suitable for that, we strongly recommend to install a UNIX or ‘UNIX-like’ terminal. You can get this by using MobaXterm or WSL2 (recommended solution).

Code editor

You should have a modern code editor installed. During the course, we can give only limited help for installation and set-up issues, so we will only “officially” support VS Code. If you are already very familiar with another combination of modern code editor/command line interface, feel free to use it, but know that support for this will be limited.

Snakemake

You don’t need to install Snakemake on your local machine as you will be using a version we installed on the remote server. However, if you want to have a look before the course, you can find installation instructions here. Note that Snakemake does not natively run on Windows and requires WSL.

SSH connection to a server

In addition to your local computer, you will be working on an Amazon Web Services (AWS) Elastic Cloud (EC2) server. This Ubuntu server behaves like a ‘normal’ remote server, and can be approached through ssh. If you are enrolled in the course, you have access to a shared document containing instruction to retrieve your username and private ssh key, granting you access to a personal home directory on the server.

VS Code instructions

Here are instructions on how to use VS Code to connect with SSH to a remote server. First, place the key_username.pem file in the proper folder:

Move-Item -Path key_username.pem -Destination $HOME\.ssh

chmod 400 key_username.pem
mv key_username.pem ~/.ssh

Then:

• Open VS Code and click on the button with the >< icon in the bottom left corner
• Select Connect to Host... and then Configure SSH Hosts...
• Specify a location for the SSH config file (preferably the same directory as where your keys are stored): ~/.ssh/config

• A skeleton config file will be provided. Edit it, so it looks like this (replace username with your username, and make sure the IP address in HostName match what the one given in the shared document):

  WindowsMacOS/Linux

  Host sib_course_remote
      User username
      HostName 52.57.40.7
      IdentityFile ~\.ssh\key_username.pem
  

  Note: if you are working with the Windows SSH executable (for example C:\WINDOWS\System32\OpenSSH\ssh.exe), you may have to use the full path of the key file instead of a relative one in IdentityFile:

      IdentityFile C:\Users\<windows_username>\.ssh\key_username.pem
  

  Host sib_course_remote
      User username
      HostName 52.57.40.7
      IdentityFile ~/.ssh/key_username.pem
  

Finally:

• Save and close the config file
• Click again on the >< button in the bottom left corner
• Select Connect to Host..., and then sib_course_remote. You will be asked which operating system is used on the remote. Choose Linux

Video tutorial

You can find below a video tutorial showing how to configure SSH connections in VS Code:

ssh -i key_username.pem username@52.57.40.7