nanjiang/shinynbis repository overview

⁠Homepage for the NBIS rshiny server

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

⁠Adding a new app

1. Fork this github repo⁠

   1.1. Update the Dockfile to include dependencies (linux and R packages)

   1.2. Add link entry in web/index.html like
   <li><a href="/shiny-server-apps/awesome-app">Awesome App</a></li>

   1.3. Add link entry in web/apps/index.html

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

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   1.4. Send a pull request.

2. On the server, go to /media/storage/server/homepage_rshiny.nbis.se/shiny-server-apps and run git clone app-url to clone the app and place it inside a directory, say awesome-app.

3. The app should now be available through http://rshiny.nbis.se/shiny-server-apps/awesome-app/.

⁠Deploying NBIS rshiny web-server by Docker locally

1. Clone this repository by

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

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

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

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

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

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4. Deploy the web-server container using

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

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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