Skip to content

Latest commit

 

History

History
78 lines (45 loc) · 2.37 KB

Setup.md

File metadata and controls

78 lines (45 loc) · 2.37 KB
Raw

Setup the Tutorial in the clouds

This steps you can do at the beginning of the tutorial.

1. GitHub codespaces

For the tutorial we will use GitHub codespaces as a server. If you have access to the cluster of your institution, with the conda-package manager installed might want to try to do the tutorial there.

  1. You need a GitHub username.
  2. Go to github.com/codespaces and log in
  3. Create a new codespaces

Create a new codespaces

  • Type metagenome-atlas/Tryitout as the name for the repo and select it
  • Use 4 processor machine
  • Create the instance

You have 15 GB storage and 120 core-hours free. (If you are already using codespaces intensely, we might look for another solution.)

This opens a visual studio code environment.

Make sure that the terminal is selected in the bottom plane.

➤ Make it bigger.

➤ Run ./setup_codespaces.sh in the terminal

This script installs mamba and sets some conda channels. If you do it on your cluster have a look at the documentation

2. Open the Rstudio server

  1. Create a free Rstudio cloud account here.
  2. Open this Rstudio online environment in a new tab.
  3. Click on Git then Pull Branches at the center top of the screen.

Pull Branches