Connecting Cyverse to GitHub

Log in to Cyverse

1. Go to the Cyverse user account website https://user.cyverse.org/

1. Click Sign up (if you do not already have an account)

1. Head over to the Cyverse Discovery Environment https://de.cyverse.org, and log in with your new account.

You should now see the Discovery Environment:

1. We will give you permissions to access the Hackathon app. If you haven't already, let us know that you need access

Open up an analysis with the hackathon environment (Jupyter Lab)

1. From the Cyverse Discovery Environment, click on Apps in the left menu

2. Select JupyterLab ESIIL

3. Configure and launch your analysis - when choosing the disk size, make sure to choose 64GB or greater. The rest of the settings you can change to suit your computing needs:

1. Click Go to analysis:

2. Now you should see Jupyter Lab!

Set up your GitHub credentials

If you would prefer to follow a video instead of a written outline, we have prepared a video here:

1. From Jupyter Lab, click on the Git Extension icon on the left menu:

2. Click Clone a Repository and Paste the link to the cyverse-utils https://github.com/CU-ESIIL/cyverse-utils.git and click Clone:

3. You should now see the cyverse-utils folder in your directory tree (provided you haven't changed directories from the default /home/jovyan/data-store

4. Go into the cyverse-utils folder:

5. open up the create_github_keypair.ipynb notebook if you prefer Python or the 'create_github_keypair.R' script if you prefer R by double-clicking and then select the default 'macrosystems' kernel:

6. Now you should see the notebook open. Click the play button at the top. You will be prompted to enter your GitHub username and email:

1. You should now see your Public Key. Copy the WHOLE LINE including ssh-ed25519 at the beginning and the jovyan@... at the end

2. Go to your GitHub settings page (you may need to log in to GitHub first):

3. Select SSH and GPG keys

4. Select New SSH key

5. Give your key a descriptive name, paste your ENTIRE public key in the Key input box, and click Add SSH Key. You may need to re-authenticate with your password or two-factor authentication.:

6. You should now see your new SSH key in your Authentication Keys list! Now you will be able to clone private repositories and push changes to GitHub from your Cyverse analysis!

NOTE! Your GitHub authentication is ONLY for the analysis you're working with right now. You will be able to use it as long as you want there, but once you start a new analysis you will need to go through this process again. Feel free to delete keys from old analyses that have been shut down.

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Last update: 2024-06-14