RStudio

A containerized RStudio instance from the rocker base image:

rocker/rstudio:4.0.3

This container orchestration comes with a nginx reverse proxy (access via. port 80) and the Tidyverse collection of packages pre-installed by default.

By default, the running container will is not secured with SSL encryption. Some configuration will be required for the container to start, see below; however, instructions are provided in nginx.conf to remove this security.

The home/rstudio/projects, /usr/local/lib/R and /home/rstudio/ directories are pre-configured as Docker volumes.

The projects directory is pre-configured with a project template (00_next_project) that is useful for projects that conform to the principles of reproducible research and "project-as-a-package".

Default R Studio login

username: rstudio password: rstudio1

Update password in docker-compose.yml at the following location:

environment:
 - PASSWORD=rstudio1

Docker Ubuntu Server Installation/Set-up

1. Docker CE for Ubuntu installation: https://docs.docker.com/install/linux/docker-ce/ubuntu/

2. Follow post-installation instructions: https://docs.docker.com/install/linux/linux-postinstall/

   1. configuring the daemon.json file will not work with Ubuntu 16.04 (and above), instead add the following to the systemd unit file: ExecStart=/usr/bin/dockerd -H fd:// -H tcp://127.0.0.1:275 -H unix:///var/run/docker.sock

3. Install docker-compose https://docs.docker.com/compose/install/ (optional):

   sudo curl -L "https://github.com/docker/compose/releases/download/1.24.0-rc1/docker-compose-$(uname -s)-$(uname -m)" -o /usr/local/bin/docker-compose
   sudo chmod +x /usr/local/bin/docker-compose
   sudo ln -s /usr/local/bin/docker-compose /usr/bin/docker-compose
   

Docker App Deployment

1. Change current directory to project folder cd ...
2. Start Docker containers 3. docker-compose up -d
3. App is ready on port 80: in browser, go to 192.168.99.100 (Windows) or 127.17.0.1 (Ubuntu)

HTTPS encryption

These instructions can be used to set up a secure HTTPS connection to RStudio with Certbot SSL certificates. Also see here.

SSL encription will not work out of the box, the NGINX configuration file will need to be updated with your domain name (which is required) at the indicated places in nginx.conf. init-letsencrypt.sh also needs to be configured with your domain names(s) and email address.

The following commands will need to be run on the host machine in order to obtain the first valid certificates: first run chmod +x init-letsencrypt.sh then sudo ./init-letsencrypt.sh.

See nginx.conf for more SSL configuration instructions.