User Guide

Shiny-K8s toolkit provide turn key example is two language : R and Python.

We provide base image with various version of the language, of the underlying operating system, and of the shiny server.

Tip

Please follow the step-by-step user guide to deploy your application correctly.

• Step 1 : Setup your project on gitlab
  • Step 1.1 : Host your project on GitLab
    • Option 1: Create a blank project
    • Option 2: Use an existing GitLab project
  • Step 1.2 : Re-use skeleton from shiny-k8s-example

• Step 2 : Containerize your app
  • Step 2.1 : Adapting the Dockerfile to your needs
    • Line 1: The base image, choose versions that suits you
    • Lines 10-13: Add the required system dependencies (Optionnal)
    • Line 25: Copy your app into the docker image
  • Step 2.2 : List your packages
    • Python: requirements.txt
    • R: my_packages_to_install.csv
  • Additionnal informations : Full description of Dockerfile
    • Line 7: Working Directory
    • Lines 16-19: The package dependencies
    • Line 22: Grant shiny to create bookmark state
    • Line 28: Grant shiny to write output data

• Step 3 : Test and run locally your containerized app
  • Step 3.1 : Adapt the docker-compose file
    • 3.1.1. For R application
    • 3.1.2. For Python application
  • Step 3.2 : Run your container
  • Additionnal informations :
    • Administrate your container
    • How it works

• Step 4 : Deploy your app on dev cluster with kubernetes
  • Step 4.1: Define a deploy token (Optionnal)
    • 4.1.1 Check the visibility of your GitLab project
    • 4.1.2 Create a token that can read the registry
    • 4.1.3 Provide the token to the CI
  • Step 4.2: Ask a namespace in the kubernetes dev cluster
    • 4.2.1 : Estimate memory (CPU, RAM, storage) resources you need
    • 4.2.2 : Estimate CPU resources you need
    • 4.2.3 : Estimate Storage resources you need
    • 4.2.4 : List the users that will have access to the namespaces
    • 4.2.5 Ask it!
  • Step 4.3: Adapte the GitLab CI file to your project
  • Step 4.4: Configuring your application in Kubernetes (values.yaml)
    • 4.4.1 Private registry and deploy token
    • 4.4.2 Adjusting resources (memory and CPU)
    • 4.4.3 Adjusting storage configuration
  • Step 4.5: Access to logs and quota

• Step 5 : Deploy your app on prod cluster with kubernetes
  • Step 5.1: Ask Kubernetes namespace on prod cluster
    • 5.1.1 Do I want a public URL accessible without the VPN?
    • 5.1.2 Estimate (CPU, RAM, storage) resources you need
    • 5.1.3 Ask the second namespace
  • Step 5.2: Adapte the CI to your project
  • Step 5.3: Configuring your prod environement in Kubernetes (values.prod.yaml)
    • Nodowntime
    • Autoscaling
    • Adjusting resources
    • Storage
  • Step 5.4 Access to logs and quota
  • More ?

• Step 5-alt : Deploy your app on prod with docker-compose (without kubernetes)
  • Run the example
  • Configure your .env
  • Run it
  • With private registry
  • Administrate your container
  • How to open it to the world

Frequently Asked Questions

• FAQ
  • How to open the last run pipeline ?
  • Job failed in fetch-log-dev job
  • Why does Kubernetes indicat that it cannot pull image?
  • How to fix build error during docker compose during R packages installation ?
  • How to fix infinite installing R package during docker compose ? How to install “tidyverse” R packages ?
  • How to fix infinite installing R package during docker compose ? How to install “tidyverse” R packages ?
  • How to upgrade my helm dependency / I can’t enable a feature
  • How to fix error “UPGRADE FAILED: failed to create resource” ?
  • Uploading to data dir
  • Download content of data dir
  • How to be able to delete the app in prod
  • What version do you propose