Using Github Actions to update a shiny app on a private server

Creating an additional user

The first step is to create a new user which will be the user Github Actions is using to log in to your server. You can also use an existing user for that, but I prefer to separate my credentials with the credentials I provide external services (such as Github Actions). Log into your server and add a new user (replace github_actions_user with the name you want):

sudo useradd github_actions_user

The next thing is to add write permissions for this newly created user on the directories we want Github Actions to be able to update. Let’s say that the app is called my_shiny_app, and that the current owner of the app is the user ubuntu. We’re going to replace the directory owner with our new user’s group and add ubuntu to this group as well (to retain ubuntu’s write permissions).

cd /srv/shiny-server/
sudo chown github_actions_user:github_actions_user -R my_shiny_app
sudo usermod -a -G github_actions_user ubuntu

The middle line replaces the directory owner and the last line adds ubuntu to the directory ownership (group).

In my setup, users must authenticate with a key to ssh into the server (a password is not enough), so let’s create the keys.

Creating an SSH key for login

First thing is to switch to the new user:

su - github_actions_user

Following the instructions from here to create the new keys (when prompted for file location and for passphrase, just click Enter leaving the default location for the keys and no passphrase).

ssh-keygen -t ed25519 -C "your_email@example.com"
eval "$(ssh-agent -s)"
ssh-add ~/.ssh/id_ed25519

Important note about using a passphrase: after you type the first command you will be prompted for a passphrase. The passphrase encrypts the private key so that it can only be used by the user who knows the passphrase. However, if the repository of the app is private the Github Action will need the key to git pull from the repository. The Github Action we are using (as far as my experience goes) doesn’t work well with private repositories which we access with keys protected by a passphrase, hence I used no passphrase on these keys. I’m pretty sure there’s a better way around it, if you find it - let me know (@SaridResearch on twitter).

Finally, add the key to the authorized list, like this:

cat .ssh/id_ed25519.pub | ssh b@B 'cat >> .ssh/authorized_keys'

Adding secrets to the repository

Now we want to add the required information to the repository. We need the following data: the private key for ssh-ing, the host, port, and user name.

To get the private key while logged in as github_actions_user type:

nano ~/.ssh/id_ed25519

Copy the key.

Go to the repository of the app and click on settings (the top tabs) -> secrets (on the left menu). Click on “New repository secret”. Add a secret named KEY and paste the contents of the key you just copied. Also add the following secrets in a similar manner HOST (the host name), PORT (for the most part it should be 22, unless you changed it), USERNAME (in this example github_actions_user), APPNAME (the location of the app within the shiny-server directory, e.g. my_shiny_app).

Adding a deployment key

You need this step only if your repository is private - the public key should be added to Github, so that Github will allow you access to the repository. For that we need the public key. Get it by typing:

nano ~/.ssh/id_ed25519.pub

Copy the public key, in Github inside the repository of the app go to Deploy keys (on the left menu), add a title to your key, such as “key for pulling to production”, and paste the public key.

Create the workflow

For the final step, we’re going to use the Github Action template, prepared by appleboy and others (from here). Just add the following yml file to your repository under: .github/workflows/main.yml:

# SSH into machine and git pull for updates

name: execute remote ssh to pull updates from master
on:
  # Triggers the workflow on push or pull request events but only for the main branch
  push:
    branches: [ main ]
# A workflow run is made up of one or more jobs that can run sequentially or in parallel
jobs:
  # This workflow contains a single job called "build"
  build:
    # The type of runner that the job will run on
    runs-on: ubuntu-latest
    
    # Steps represent a sequence of tasks that will be executed as part of the job
    steps:
      # Checks-out your repository under $GITHUB_WORKSPACE, so your job can access it
      - uses: appleboy/ssh-action@master
        with:
          host: ${{ secrets.HOST }}
          username: ${{ secrets.USERNAME }}
          key: ${{ secrets.KEY }}
          port: ${{ secrets.PORT }}
          script: |
            cd /srv/shiny-server/${{ secrets.APPNAME }}
            git pull