RStudio Set Up - Linux and OSX Systems: /Documentation/Archive/19.3

RStudio Set Up - Linux and OSX Systems

Premium Feature — This feature supports RStudio, which is part of the Professional Plus and Enterprise Editions. Learn more or contact LabKey for details.

This topic explains how administrators can set up communication between LabKey Server and an RStudio instance packaged inside a Docker image. As part of the configuration, we recommend that you allow Docker, not LabKey Server, to manage the RStudio data using Docker Volumes. This avoids a number of issues with file sharing, permissions, path mapping, and security, making setup much easier.

Install Docker
Connect Using TCP
Build the LabKey/RStudio Image
Configure Docker
Configure RStudio
Enable RStudio in Folders

Install Docker

General Docker installation documentation is available at: https://docs.docker.com/engine/installation/
Test your Docker installation using an example container, for example: 'docker run hello-world' (https://docs.docker.com/engine/tutorials/dockerizing/)

Connect Using TCP

Set up TLS following these steps:

See https://docs.docker.com/engine/security/https/
An example TLS and certificate configuration for LabKey Server is available here.
After certificates are set up, find the values of the following environment variables. You will use these values in the Configure Docker step below. (On Linux run 'env | grep DOCKER'.)

DOCKER_CERT_PATH
DOCKER_HOST

On an Ubuntu system modify the "/etc/default/docker" file to include the following:

DOCKER_TLS_VERIFY=1

DOCKER_HOST=tcp://$HOST:2376
	
DOCKER_CERT_PATH=<YOUR_CERT_PATH>
	
DOCKER_OPTS="--dns 8.8.8.8 --tlsverify --tlscacert=$DOCKER_CERT_PATH/ca.pem --tlscert=$DOCKER_CERT_PATH/server-cert.pem --tlskey=$DOCKER_CERT_PATH/server-key.pem -H=0.0.0.0:2376"

Build the LabKey/RStudio Image

Clone the docker-rstudio repository from github: https://github.com/LabKey/docker-rstudio (This repository is available in the Premium Plus and Enterprise editions of LabKey Server. Contact us for more information.)
cd to the rstudio-base directory:

cd docker-rstudio/images/labkey/rstudio-base

Build the image from the source files:

./make

Test by running the following:

docker run labkey/rstudio-base

Ctrl-C to get to return to the command prompt once you see the 'done' message.
Run the following to get the container name:

docker ps

To stop the container, run:

docker stop <container-name>

Enable Session Keys

Follow the instructions at Compliant Access via Session Key.

Configure Docker

For details, see Configure Docker Host.

Configure RStudio

When configuring RStudio, you can skip the prerequisite check for user home directories. The configuration page will show a list of existing volumes and corresponding user emails. The email field is blank if the volume doesn't correspond to an existing user.

Go to (Admin) > Site > Admin Console.
Click the Settings tab.
Under Premium Features click RStudio Settings.

If you have successfully created the Docker image, it will be listed under Docker Volumes.
Configure the remaining fields as appropriate for your environment, and click Save.

Docker Image Name - labkey/rstudio (or a custom image derived from labkey/rstudio)
Port = 8787
Mount Volume = /home/rstudio
Host library directory - leave blank
User for Containers - leave blank
AppArmor Profile - leave blank
Local IP address from LabKey Server - set to the IP address of the labkey server from within your docker container. This may be left blank if the normal DNS lookup works.
Resource Configuration: Customize defaults if needed.

Enable RStudio in Folders

The modules docker and rstudio must be enabled in each folder where you want RStudio to be available. Select (Admin) > Folder > Management, select the Folder Type tab and make sure both modules are checked in the right column. Click Update Folder to save any changes.

Once RStudio is enabled, you can use the instructions in these topics to edit reports and export data:

Edit R Reports in RStudio
Export Data to RStudio

LabKey Support

LabKey Support