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Running R Shiny Server on NERC

Running R Shiny Server on NERC OpenStack

Setup R Shiny Server using Terraform

Refer to this documentation on using Terraform to set up an R Shiny Server on your NERC OpenStack.

To get started, you will need to clone the repository using:

git clone https://github.com/nerc-project/terraform-nerc-r-shiny.git

Setup R Shiny Server while launching a VM

Within the terraform-nerc-r-shiny repo, it includes the bash script file i.e. install-R-Shiny-<OS>.sh required to setup the R Shiny Server. You can use a custom user-defined bash script based on your selected Image OS while launching an instance.

During the launch, in the "Configuration" tab, you can enter the script in the "CustomizationScript" text area or upload the script file directly.

Which R Shiny Script i.e. install-R-Shiny-<OS>.sh to Choose?

Please use the appropriate bash script file i.e. install-R-Shiny-<OS>.sh based on your operating system (OS):

  • AlmaLinux → install-R-Shiny-AlmaLinux.sh

  • CentOS → install-R-Shiny-Centos.sh

  • Ubuntu → install-R-Shiny-Ubuntu.sh

Running R Shiny Server on NERC OpenShift

We have used the Base Docker image compatible with OpenShift to create an OpenShift Template. Here, we walk through the process of creating a simple R Shiny Server template that bundles all the necessary resources—ConfigMap, Pod, Route, Service, etc.—and then deploy a Shiny application using that template.

To get started, clone the repository using:

git clone https://github.com/nerc-project/rshiny-testapp.git

Steps to Prepare Your Git Repo with Application Source Code

To get started, create a new Git repository and add a Dockerfile to specify the base image i.e. dukegcb/openshift-shiny-verse:4.1.2, additional package requirements, and the location of your Shiny application code.

For example, if your app is under the src directory and has no additional requirements, your Dockerfile should look like this:

FROM dukegcb/openshift-shiny-verse:4.1.2
RUN install2.r here
ADD ./src /srv/code

Important Note

The install2.r script is a simple utility to install R packages that is provided by the rocker images.

A sample Shiny application is available within the Git Repository, which includes the Dockerfile and the src directory containing app.R.

More about Writing Templates

For more options and customization please read this.

Deploy your shiny app using the OpenShift Web console

Here, we walk through the process of creating a simple R Shiny Web Server using an OpenShift Template, which bundles all the necessary resources required to run it, such as ImageStream, BuildConfig, Deployment, Route, Service, etc., and then initiates and deploys a Shiny application from that template.

An OpenShift template file, rshiny-server-template.yaml, is available within the Git Repository under the openshift directory.

More about Writing Templates

For more options and customization please read this.

  1. Click the "Import YAML" button, represented by the "+" icon in the top navigation bar, or navigate to the From Local Machine section and select Import YAML, as shown below:

    Import YAML

  2. On opened YAML editor paste the contents of the template copied from the openshift/rshiny-server-template.yaml file located at the provided Git Repo.

    YAML Editor

  3. You need to find the Developer Catalog section and then select All services option as shown below:

    Select All Services

  4. Then, you will be able to use the created Developer Catalog template by searching for "rshiny" on catalog as shown below:

    Search for R Shiny Template

  5. Once selected by clicking the template, you will see Instantiate Template web interface as shown below:

    Initiate Template

  6. Based on our template definition, we request that users input some variables to initate the R Shiny Server.

    Variables

    All variables are mandatory for the application to be created.

    • APP_NAME - Name used for the app

    • APP_LABEL - Label used for the app

    • APP_GIT_URI - GitHub repository URL

    • APP_GIT_BRANCH - Git branch to build from

    • REPO_DOCKERFILE_PATH - Location of the shiny app Dockerfile

    • IMAGE_TAG - Tag for the built image

    • NAMESPACE - Namespace where the application will be deployed

    • PROBE_INITIAL_DELAY - Initial delay in seconds for liveness and readiness probes

    • PROBE_TIMEOUT - Timeout in seconds for liveness and readiness probes

    Provide the R Shiny Template Variables

    Important: Update the Variable Values According to Your Own Configuration!

    It is essential to update the variable values in the OpenShift template to align with your specific configuration. Ensure that these values are adjusted according to your environment and requirements before deployment. If variable values are not explicitly provided, the template will automatically use its default values.

  7. Once successfully initiated, you can either open the application URL using the Open URL icon as shown below or you can naviate to the route URL by navigating to the "Routes" section under the Location path as shown below:

    How to get the R Shiny Application URL

  8. Finally, you will be able to see the R Shiny app!

    R Shiny Application

Modifying uploaded templates

You can edit a template that has already been uploaded to your project: oc edit template <template>.

Deploy your shiny app using the OpenShift CLI (oc)

  • Prerequisites:

    Setup the OpenShift CLI (oc) Tools locally and configure the OpenShift CLI to enable oc commands. Refer to this user guide.

    Information

    Some users may have access to multiple projects. Run the following command to switch to a specific project space: oc project <your-project-namespace>.

    Please confirm the correct project is being selected by running oc project, as shown below:

    oc project
Using project "<your_openshift_project_to_add_r_shiny_app>" on server "https://api.shift.nerc.mghpcc.org:6443".

Deploy your R Shiny application

Process and apply template using default values from the template and passing your application specific parameters.

oc process -f ./openshift/rshiny-server-template.yaml \
   -p APP_GIT_URI=<YOUR_GIT_REPO> \
   -p APP_GIT_BRANCH=<YOUR_GIT_BRANCH> \
   -p REPO_DOCKERFILE_PATH=<PATH_TO_DOCKERFILE_IN_YOUR_REPO> \
   -p NAMESPACE=$(oc project --short) \
   | oc create -f -

For example, the command will look like this:

oc process -f ./openshift/rshiny-server-template.yaml \
    -p APP_GIT_URI=https://github.com/nerc-project/rshiny-testapp \
    -p APP_GIT_BRANCH=main \
    -p REPO_DOCKERFILE_PATH="Dockerfile" \
    -p NAMESPACE=$(oc project --short) \
    | oc create -f -

Important: Default Template Values Will Be Used If Not Overridden!

If variable values are not explicitly provided, the template will automatically use its default values.

Deleting your application and all its resources

Either using the OpenShift Web console, you can Right click on the application box and then confirm to delete it as shown below:

Delete R Shiny App

Alternatively, you can use the OpenShift CLI i.e. oc commands to delete all application resources:

oc delete all -l app=<APP_LABEL>
oc delete svc <APP_NAME>-service
oc delete route <APP_NAME>-route
oc delete bc <APP_NAME>-build
oc delete deploy <APP_NAME>-deployment
oc delete imagestream <APP_NAME>-imagestream
oc delete template shiny-server-template

For example, the command will look like this:

oc delete all -l app=shiny
oc delete svc shiny-app-service
oc delete route shiny-app-route
oc delete bc shiny-app-build
oc delete deploy shiny-app-deployment
oc delete imagestream shiny-app-imagestream
oc delete template shiny-server-template