Welcome to Shiny-K8s’s documentation!

To help hub members to correctly and easily deploy a web application, developed by usin Shiny (with R or Python), under Kubernetes .

This Documentation is composed of several parts depending on the user profile.

Contents:

• User Guide
  • Setup project
    • Setup the project to run on Kubernetes
      • The project in GitLab
        • Option 1: Create a blank project
        • Option 2: Use an existing GitLab project
      • Re-use skeleton from example
      • Store the sources in customly named directory
    • Keeping sources private
      • Make you project private
      • Create a token that can read the registry
      • Provide token to the CI
      • Indicate into you app settings that the registry is private
    • Adapting the Dockerfile to your needs
      • Line 1: The base image, with the right version
      • Line 5: Working Directory
      • Lines 8-11: The system dependencies
      • Lines 14-17: The package dependencies
        • Python: requirements.txt
        • R: my_packages_to_install.csv
      • Line 20: Grant shiny to create bookmark state
      • Line 23: Copy your app into the image
      • Line 26: Grant shiny to write output data
  • Run locally
    • How it works
      • Volumes
      • Port
      • Command
    • Run your container
    • Administrate your container
  • Run on kubernetes
    • Ask for your project to be able to deploy to Kubernetes cluster(s)
      • Dev ? Prod ? What environement do I need?
      • Do I want a public URL accessible without the VPN?
      • What resources (CPU, RAM, storage) do I need?
        • How memory overuse is handled by Kubernetes
        • How to observe my memory usage locally
        • How to estimate quota needs from your app ressources
        • Dev vs Prod quota
      • Ask it!
    • Adapte the CI to your project
    • Configuring your application in Kubernetes (values.yaml)
      • Private registry, a way to keep source private
      • Nodowntime
      • Autoscaling
      • Adjusting resources
      • Ingress annotations
      • Storage
      • Tunning for the production instance
    • Access to logs and quota
  • Frequently Asked Questions
    • FAQ
• Developer Guide
  • Docker base image
    • RShiny base image
      • Dockerfile.r
        • Line 2: The base image
        • Lines 5-7 : Environment variables
        • Line 9 : Listen port for Shiny-server
        • Line 10 : Run Shiny-server
        • Lines 13-37 : The system dependencies
        • Lines 40-49 : Installation of R
        • Lines 51-57 : Install R Packages
        • Line 58 : Installation Shiny Server
        • Line 61 : Custom Shiny-server configuration file
        • Lines 66-70 : Permissions
    • Shiny Python base image
      • Dockerfile.python
        • Line 2: The base image
        • Lines 5-7 : Environment variables
        • Line 9 : Listen port for Shiny-server
        • Line 10 : Run Shiny-server
        • Lines 13-39 : The system dependencies
        • Lines 42-43 : Installation Shiny package for python
        • Lines 46-49 : Installation Shiny Server
        • Line 52 : Custom Shiny-server configuration file
        • Lines 57-61 : Permissions
      • Specific point in gitlab-ci
    • Helper scripts
      • configure_Rprofile.sh
      • install_r_cran.sh
      • install_r_packages.R
      • install_shiny_server.sh
  • Gitlab CI of shiny-k8s
  • Gitlab CI of shiny-k8s-example
  • Talking with Kubernetes
    • Setup communication
      • Binairies
      • Configuring “contexts” to access clusters
        • Dev cluster
        • Prod cluster (if you have a namespace in prod)
    • Accessing quota usage
    • Reading the logs
    • The do helm script
      • The script
      • Deploying a specific version (i.e commit)
      • With a private project/registry
  • Helm template
  • FAQ
• Links
  • Docker
  • Kubernetes
  • Python
  • R
  • R Shiny