Docker Deployment

Install Docker Desktop

Install the version of Docker Desktop that is appropriate for you operating system. Downloads and configuration instructions may be obtained at the following link:

• https://docs.docker.com/desktop/

Run ReviewR from Docker

# install.packages('usethis')
usethis::create_from_github(repo_spec = 'thewileylab/ReviewR')

cd ReviewR
docker build -t reviewr .

docker run --publish 1410:1410 --detach --name ReviewR reviewr:latest

Docker Installation

sudo apt update
sudo apt install apt-transport-https ca-certificates curl software-properties-common

curl -fsSL https://download.docker.com/linux/ubuntu/gpg | sudo apt-key add -

sudo add-apt-repository "deb [arch=amd64] https://download.docker.com/linux/ubuntu bionic stable"

sudo apt update
sudo apt install docker-ce

sudo usermod -aG docker ${USER}

sudo usermod -aG docker adeline

Build Shiny Server Container

In order to facilitate multiple concurrent users, a Shiny Server container will need to be built, including all of the dependencies that ReviewR requires. With docker already installed, build a suitable Docker image using a Dockerfile contained in the ReviewR source. To begin this process, we need to make a directory to hold the ReviewR application:

mkdir -p ~/srv/shinyapps

Next, clone the ReviewR source from GitHub:

• If R is installed, we can fork the ReviewR package from an R console with the usethis package:

# install.packages('usethis')
usethis::create_from_github(repo_spec = 'thewileylab/ReviewR', destdir = '~/srv/shinyapps')

• Otherwise, clone from GitHub using the git commands in a bash terminal:

cd ~/srv/shinyapps
git clone https://github.com/thewileylab/ReviewR 

Finally, build the Shiny Server container using the Dockerfile contained in the ReviewR repository:

cd ~/srv/shinyapps/ReviewR/Docker_ShinyServer
docker build -t shiny-server_reviewr .

Take a quick break while the container image is built. You deserve it!

Once the image has finished building, we can start the container:

docker run -d -p 3838:3838 \
    -v ~/srv/shinyapps/:/srv/shiny-server/ \
    -v ~/srv/shinylog/:/var/log/shiny-server/ \
    shiny-server_reviewr:latest

A Shiny Server container should start and begin serving any applications located in the ~/srv/shinyapps directory on your system. As ReviewR has been cloned to this directory it should now be accessible via the web at: http://server.ip.address:3838/ReviewR

In order to securely host this container at a URL, we’ll need to configure NGINX to reverse proxy this container with a Let’s Encrypt Certificate. Read on to see how.

Configure nginx

Next, we need to configure NGINX to proxy traffic from web clients to the Docker Container. To accomplish this, we’ll need to add a server block to NGINX with information about our container. NGINX server blocks live in /etc/nginx/sites-available/. To initialize a server block for our container, issue the following command:

## substitute nano for your preferred text editor: emacs, jed, joe, pico, sandy, vi, vim, etc.
sudo nano /etc/nginx/sites-available/shiny-server_reviewr

Modify the following server block code by replacing shiny.your.domain.url with the domain name that own. Then, copy this text into the file that you are editing. In this example, a sub domain of “shiny” is prepended to the server domain, though your specific configuration may vary.

server {
  server_name   shiny.your.domain.url;

  location / {
    proxy_pass  http://localhost:3838;
  }
}

Save and exit the file. Verify that the has been created successfully by running:

ls -l /etc/nginx/sites-available

A file called “shiny-server_reviewr” should be among the files that is returned.

Next, we need to enable the server block that we just created. With NGINX, this is accomplished by symlinking the server block to the /etc/nginx/sites-enabled folder. Run:

sudo ln -s /etc/nginx/sites-available/shiny-server_reviewr /etc/nginx/sites-enabled/shiny-server_reviewr

At this point, your Shiny Server should be accessible at http://shiny.your.domain.url/ReviewR . If the ReviewR Docker Container is not immediately available at your domain after completing all of the steps to this point, you may have to restart NGINX; sudo systemctl reload nginx

Continue to the next section to secure access to your container with Let’s Encrypt.

Securing Docker Container with Let’s Encrypt

This portion of the guide assumes that you have already installed Certbot on your system by following the instructions in vignette('deploy_server').

As we have already configured a server block for our container in the previous section, we are ready to run the Certbot software to secure our domain. Run the following code block, substituting shiny.your.domain.url with the domain that you configured in the nginx server block for the ReviewR container:

sudo certbot --nginx -d shiny.your.domain.url

If this is your first time running Certbot, you will be prompted to enter an email address and agree to the terms of service. After doing so, Certbot will initiate a connection with the Let’s Encrypt server and then begin testing your server to verify that you control the domain you’re requesting a certificate for. Certbot will then ask you whether or not you’d like to redirect all HTTP traffic to HTTPS traffic. It is highly recommended to do so. Please select the option for ‘Redirect’, which will ensure that users are only capable of accessing your site via secure HTTPS.

Congratulations, your ReviewR container is now secured and ready to accessed securely via https://reviewr.your.domain.url !