Homepage for the NBIS rshiny server

The NBIS rshiny server can be accessed at https://rshiny.nbis.se

Adding a new app

1. Make sure your app is a git repo on a git repository (GitHub, GitLab etc.). The directory should contain minimum app.R or ui.R/server.R files. Other dependencies if needed must be in this directory.

2. On GitHub

   2.1 Fork this github repo and update the files described below.

   2.2. Update the Dockerfile to include dependencies (linux and R packages) if it doesn't already exist.

   2.3. Add link entry in web/index.html, for example:
   <li><a href="/shiny-server-apps/awesome-app">Awesome App</a></li>

   2.4. Add link entry in web/apps/index.html, for example:

        <li><a href="/shiny-server-apps/awesome-app">Awesome App</a>
        (Awesome App)
        <a href="https://github.com/app-url">GitHub repo</a>
        </li>
   

   2.5. Send a pull request. For example, see here.

3. On the server

   3.1 For access to server, contact nanjiangshu.

   3.2 Go to /media/storage/server/homepage_rshiny.nbis.se/shiny-server-apps and run git clone app-url to clone the app. app-url is the URL location from step 1. The directory will be the same name as the repo you are cloning from. To use a different directory name, run for example: git clone app-url awesome-app.

4. The app should now be available through http://rshiny.nbis.se/shiny-server-apps/awesome-app/. You might have to wait a few minutes for the change.

Deploying NBIS rshiny web-server by Docker locally

1. Clone this repository by

    git clone https://github.com/NBISweden/homepage_rshiny.nbis.se
   

2. Change to the cloned folder and download apps by the script getapp.sh by running

    src/getapp.sh <path-of-your-apps>
   

3. Define the ENV PATH_APPS for docker-compose by the following command

    echo "PATH_APPS=<path-of-your-apps>" > .env
   

4. Deploy the web-server container using

    docker-compose -f docker-compose-local.yml up -d
   

After success deployment, you should be able to access the server at http://localhost

Deploying NBIS rshiny web-server by Docker on the production server

Perform steps 1-3 the same as depolying locally and then depoly the web-server with the command

docker-compose up -d

Note that every time when you run docker-compose down and docker-compose up, the microservice letsencrypt-nginx-proxy-companion will try to obtain a new token from LetsEncrypt. To ensure the certificate retrieval will not exceeds the rate limits set by LetsEncrypt. It is recommended to restart shiny services by the following command if there are any updates

docker-compose stop shinymain shinymetamex && docker-compose up -d