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Precourse preparations

Background knowledge

As is 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 GitHub Codespaces account.

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.

Software

OS

This is an OS-agnostic course that requires from only to count with a laptop, a modern browser and a GitHub Codespaces account.

Code editor

You will be provided with a link to create the workspace in GitHub Codespaces automatically. This link will open VS code on your browser, and hence it is expected that you are familiar with the layout and basic functionalities VS code has. Otherwise, please check this quick tutorial before the course to understand where everything is. Either way, there will be a short introduction to VS code at the beginning of the online session.

This is the link to GitHub Codespaces:

Open in GitHub Codespaces

Do not start working on it

We have limited resources with the free tier of GitHub Codespaces, so please do not start working or running thins through it. You just need to create it before the course.

Video tutorial

You can find a (cool) video tutorial to learn about VS code:

Back-up plan

If you exceed the Codespace resources, we have prepared a solution using CodeSandbox. These are the steps to follow:

  1. Go to the website: CodeSandbox.
  2. Sign in using your GitHub or your Google Account (top right corner).
  3. Once signed-in, click on + Create (top right corner).
  4. Select Docker CodeSanbox.
  5. On the Configure window leave everything as default and click on Create Devbox.
  6. Wait until the microVM is created.
  7. Now it looks like VS code. Create a new terminal then.
  8. Run the following commands on the terminal:
curl -s https://get.sdkman.io | bash
source "/root/.sdkman/bin/sdkman-init.sh"
sdk install java 17.0.10-tem
curl -s https://get.nextflow.io | bash
chmod +x nextflow
export PATH=${PATH}:/project/workspace
git clone https://github.com/jeffe107/nextflow-training
cd nextflow-training
  1. Now you should be into the repository folder, just like on GitHub Codespaces.