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Deployment

Principle

This solution is based on shinyproxy, a server for R shiny apps.

ShinyProxy runs in an isolated container. When an app is requested via an html request, ShinyProxy launches a container from the shinybrapps docker image. This image contains R, the BrAPPs and their dependencies.

The shinybrapps image

sudo docker build . -t shinybrapps

Shinyproxy

Config

Create a docker network

ShinyProxy uses a docker network to communicate with the shinyapp containers.

$ sudo docker network create shinyproxy-network

Set up the apps

In deployment_shinyproxy/application.yml, define the shinybrapps apps that ShinyProxy will connect to.

  - id: test
    display-name: test app
    description: displays hello world
    container-cmd: ["R", "-e", "shinybrapps::run_test()"]
    container-image: shinybrapps
    container-network: shinyproxy-network

The shinybrapps image contains all the shinybrapps apps. To tell ShinyProxy to launch a given app, specify the container start up command container-cmd: ["R", "-e", "shinybrapps::run_<my app>()"]

See R/runapps.R for available apps.

Set up the template

ShinyProxy renders the app in an iframe and offers a landing page with the record of the shinyapps it can serve. The templating can be changed in ./deployment_shinyproxy/templates/

Build the shinyproxy docker image

Build instructions are in ./deployment_shinyproxy/Dockerfile.

cd ./deployment_shinyproxy/
sudo docker build . -t shinyproxy-with-config

Launch shinyproxy

command

sudo docker run \
-d \
-v /var/run/docker.sock:/var/run/docker.sock:ro \
--group-add $(getent group docker | cut -d: -f3) \
--net shinyproxy-network \
-p 80:8080 shinyproxy-with-config

detail

-d (optional)

by adding the -d option to the command (just after docker run), the Docker container will run in the background. ref

-v /var/run/docker.sock:/var/run/docker.sock:ro

Mount /var/run/docker.sock (a Unix domain socket) to communicate with the main Docker process. In this case, it allows shinyproxy to start and stop shiny app containers on the Docker host. ref

--group-add $(getent group docker | cut -d: -f3)

inside the Docker container, ShinyProxy runs as a non-root user, therefore it does not have access to the Docker socket by default. By adding the --group-add $(getent group docker | cut -d: -f3) option we ensure that the user is part of the docker group and thus has access to the Docker daemon.

ref

getent group docker | cut -d: -f3

gets the docker entry in the group database.

--net shinyproxy-network

Custom bridge network to allow the containers to access each other using the container ID as hostname. ref

-p 80:8080 shinyproxy-with-config

ShinyProxy listens for HTTP traffic on port 80 (or other port). ref

Update workflow

# create/update app image
...

# update application.yml
...

# rebuild the shinyproxy image (fast)
sudo docker build . -t shinyproxy-with-config

# relaunch the shinyproxy container
sudo docker run \
-d \
-v /var/run/docker.sock:/var/run/docker.sock:ro \
--group-add $(getent group docker | cut -d: -f3) \
--net shinyproxy-network \
-p 80:8080 shinyproxy-with-config