Step 2 : Containerize your app

Note

We consider that you have followed instructions described in Step 1.2:Re-use skeleton from shiny-k8s-example

Step 2.1 : Adapting the Dockerfile to your needs

To enable deployment, the Shiny application must be encapsulated in a container using Docker.

We have already created a Dockerfile, a configuration file containing all the informations required to build the container. For further information, you can see the full content here

Now, you just need to adapt it to the requirement of your application. We will guide you line by line through this stage.

Line 1: The base image, choose versions that suits you

Python
R

# Build image from the base image, previously configured for you
# Full list of images can be found at
# https://hub.pages.pasteur.fr/shiny-k8s/user_guide/configure_image.html#image-list
FROM registry-gitlab.pasteur.fr/hub/shiny-k8s/python:3.9-slim-bullseye--1.5.22.1017

# Build image from the base image, previously configured for you
# Full list of images can be found at
# https://hub.pages.pasteur.fr/shiny-k8s/user_guide/configure_image.html#image-list
FROM registry-gitlab.pasteur.fr/hub/shiny-k8s/r:4.3.1--1.5.22.1017

The FROM ... indicate which base image should be used, the image contains:

an OS with python or R, depends of your shiny app
python’s or R “shiny” package
the shiny-server

We provide various version of R and Python for your needs, here is a list (as of Aug 2026).

Docker images generated along with base os, R/python version, and shiny-server version
Language	Base os	R/Python	shiny-server	Built image
python	bookworm	3.10	latest	registry-gitlab.pasteur.fr/hub/shiny-k8s/python:3.10-slim
python	bookworm	3.11	latest	registry-gitlab.pasteur.fr/hub/shiny-k8s/python:3.11-slim
python	bookworm	3.12	latest	registry-gitlab.pasteur.fr/hub/shiny-k8s/python:3.12-slim
python	bookworm	3.13	latest	registry-gitlab.pasteur.fr/hub/shiny-k8s/python:3.13-slim
python	bookworm	3.14	latest	registry-gitlab.pasteur.fr/hub/shiny-k8s/python:3.14-slim
python	bookworm	3.14	latest	registry-gitlab.pasteur.fr/hub/shiny-k8s/python:latest
python	bullseye	3.10	latest	registry-gitlab.pasteur.fr/hub/shiny-k8s/python:3.10-slim-bullseye
python	bullseye	3.11	latest	registry-gitlab.pasteur.fr/hub/shiny-k8s/python:3.11-slim-bullseye
python	bullseye	3.12	latest	registry-gitlab.pasteur.fr/hub/shiny-k8s/python:3.12-slim-bullseye
python	bullseye	3.13	latest	registry-gitlab.pasteur.fr/hub/shiny-k8s/python:3.13-slim-bullseye
python	bullseye	3.14	latest	registry-gitlab.pasteur.fr/hub/shiny-k8s/python:3.14-slim-bullseye
python	trixie	3.10	latest	registry-gitlab.pasteur.fr/hub/shiny-k8s/python:3.10-slim-trixie
python	trixie	3.11	latest	registry-gitlab.pasteur.fr/hub/shiny-k8s/python:3.11-slim-trixie
python	trixie	3.12	latest	registry-gitlab.pasteur.fr/hub/shiny-k8s/python:3.12-slim-trixie
python	trixie	3.13	latest	registry-gitlab.pasteur.fr/hub/shiny-k8s/python:3.13-slim-trixie
python	trixie	3.14	latest	registry-gitlab.pasteur.fr/hub/shiny-k8s/python:3.14-slim-trixie
r	focal	4.1.3	latest	registry-gitlab.pasteur.fr/hub/shiny-k8s/r:4.1.3-focal
r	focal	4.2.3	latest	registry-gitlab.pasteur.fr/hub/shiny-k8s/r:4.2.3-focal
r	focal	4.3.3	latest	registry-gitlab.pasteur.fr/hub/shiny-k8s/r:4.3.3-focal
r	focal	4.4.3	latest	registry-gitlab.pasteur.fr/hub/shiny-k8s/r:4.4.3-focal
r	focal	4.5.3	latest	registry-gitlab.pasteur.fr/hub/shiny-k8s/r:4.5.3-focal
r	focal	4.6.0	latest	registry-gitlab.pasteur.fr/hub/shiny-k8s/r:4.6.0-focal
r	jammy	4.1.3	latest	registry-gitlab.pasteur.fr/hub/shiny-k8s/r:4.1.3
r	jammy	4.2.3	latest	registry-gitlab.pasteur.fr/hub/shiny-k8s/r:4.2.3
r	jammy	4.3.3	latest	registry-gitlab.pasteur.fr/hub/shiny-k8s/r:4.3.3
r	jammy	4.4.3	latest	registry-gitlab.pasteur.fr/hub/shiny-k8s/r:4.4.3
r	jammy	4.5.3	latest	registry-gitlab.pasteur.fr/hub/shiny-k8s/r:4.5.3
r	jammy	4.6.0	latest	registry-gitlab.pasteur.fr/hub/shiny-k8s/r:4.6.0
r	jammy	4.6.0	latest	registry-gitlab.pasteur.fr/hub/shiny-k8s/r:latest
r	noble	4.3.3	latest	registry-gitlab.pasteur.fr/hub/shiny-k8s/r:4.3.3-noble
r	noble	4.4.3	latest	registry-gitlab.pasteur.fr/hub/shiny-k8s/r:4.4.3-noble
r	noble	4.5.3	latest	registry-gitlab.pasteur.fr/hub/shiny-k8s/r:4.5.3-noble
r	noble	4.6.0	latest	registry-gitlab.pasteur.fr/hub/shiny-k8s/r:4.6.0-noble

If a version of R, Python, shiny-server, Debian or Ubuntu is missing please read FAQ here.

Translation between ubuntu name and version can be found at https://wiki.ubuntu.com/Releases.
Translation between debian name and version can be found at https://www.debian.org/releases/
Built images can also be found in the registry at https://gitlab.pasteur.fr/hub/shiny-k8s/container_registry

For more details about base images, please see the dedicated pages for python and R.

Lines 10-13: Add the required system dependencies (Optionnal)

Before Python & R
After Python & R

# Install additional dependencies, uncomment the block if you have one, and edit/duplicate line 12
# RUN apt-get update \
#  && apt-get install -y \
#         your-system-dependency \
#  && rm -rf /var/lib/apt/lists/*

# Install additional dependencies, uncomment the block if you have one, and edit/duplicate line 12
RUN apt-get update \
  && apt-get install -y \
        your-system-dependency_1 \
        your-system-dependency_2 \
  && rm -rf /var/lib/apt/lists/*

Some of your package dependencies require system dependencies (such as graphviz-dev for pygraphviz) that must be included in the Docker image.

To add such system dependencies :
- uncomment the bloc 10-13,
- adapte/duplicate line 12,
- and replace your-system-dependency with your actual dependency.
We recommend you to specify one dependency per line, its helps later investigation when searching for why a dependency have been added.

Tip

If you have no additional system dependencies you can keep this block commented.

Don’t forget to come back and add system dependencies, if during the development or testings stages of your application, you find that you need them.

Line 25: Copy your app into the docker image

Python & R

# Copy you shiny app
COPY ./my_project /srv/shiny-server

At that moment you copy you shiny app into the Docker image.

Here, you need to adapt the line according to your directory name

Let us consider that you want to store the sources in src or my_beautifull_shiny_app folder. You have change the COPY instruction as follows :

...
# Copy you shiny app
-COPY ./my_project /srv/shiny-server
+COPY ./src /srv/shiny-server
...

...
# Copy you shiny app
-COPY ./my_project /srv/shiny-server
+COPY ./my_beautifull_shiny_app /srv/shiny-server
...

Note that the directory named my_project contains a shiny example

Step 2.2 : List your packages

According to your needs and the language used, you must list all additional packages in the dedicated file.

Tip

Don’t forget to complete the packages file as needed during the development or testings stages of your application.

Python: requirements.txt

This file is the default file for dependencies in python. You can specify package, with or without a specific version, install from a git. The syntax to respect is the following :

sphinx=~7.0.1
sphinx_rtd_theme
git+https://gitlab.pasteur.fr/user/some-project.git@v1.3

By default, in the gitlab project shiny-k8s-example, the python packages mentionned in the requirements.txt file are shiny and htmltools.

shiny
htmltools

You are free to modify this list. shiny package is already installed in the previous base image, created at shiny-k8s level.

R: my_packages_to_install.csv

In this file you list in csv file the packages (with ; as separator). For each file, how it can be found is specified in the second column. If can be from cran, from bioconductor, or even a github package. You can also specify the wanted version by add @VersionNumber as ggplot2@3.5.2

Package_name;Comments
shinythemes;cran package
ggplot2@3.5.2;cran package
limma;bioconductor package
tidyverse/tibble; github package

The use of this file in the container is explained here

Additionnal informations : Full description of Dockerfile

For further information, here, you can see the full content of the Dockerfile:

Python
R

# Build image from the base image, previously configured for you
# Full list of images can be found at
# https://hub.pages.pasteur.fr/shiny-k8s/user_guide/configure_image.html#image-list
FROM registry-gitlab.pasteur.fr/hub/shiny-k8s/python:3.9-slim-bullseye--1.5.22.1017

# Add workdir information
WORKDIR /srv/shiny-server/

# Install additional dependencies, uncomment the block if you have one, and edit/duplicate line 12
# RUN apt-get update \
#  && apt-get install -y \
#         your-system-dependency \
#  && rm -rf /var/lib/apt/lists/*

# Copy your dependencies, destination filename must be "packages_to_install.csv"
COPY ./requirements.txt /opt/scripts/requirements.txt

# Install Python packages
RUN pip install -r /opt/scripts/requirements.txt

# grant shiny to created bookmark state directory in this directory
RUN chown shiny:shiny /var/lib/shiny-server

# Copy you shiny app
COPY ./my_project /srv/shiny-server

# grant shiny to use www folder
RUN chown shiny:shiny /srv/shiny-server/www

# Build image from the base image, previously configured for you
# Full list of images can be found at
# https://hub.pages.pasteur.fr/shiny-k8s/user_guide/configure_image.html#image-list
FROM registry-gitlab.pasteur.fr/hub/shiny-k8s/r:4.3.1--1.5.22.1017

# Add workdir information
WORKDIR /srv/shiny-server/

# Install additional dependencies, uncomment the block if you have one, and edit/duplicate line 12
# RUN apt-get update \
#  && apt-get install -y \
#         your-system-dependency \
#  && rm -rf /var/lib/apt/lists/*

# Copy your dependencies, destination filename must be "packages_to_install.csv"
COPY ./my_packages_to_install.csv /opt/scripts/packages_to_install.csv

# Install R packages
RUN Rscript /opt/scripts/install_r_packages.R

# grant shiny to created bookmark state directory in this directory
RUN chown shiny:shiny /var/lib/shiny-server

# Copy you shiny app
COPY ./my_project /srv/shiny-server

# grant shiny to use www folder
RUN chown shiny:shiny /srv/shiny-server/www

please find here the meaning of the lines that you did not have to modify previously.

Line 7: Working Directory

Python & R

# Add workdir information
WORKDIR /srv/shiny-server/

We set the current working directory to /srv/shiny-server/ .

Lines 16-19: The package dependencies

Python
R

# Copy your dependencies, destination filename must be "packages_to_install.csv"
COPY ./requirements.txt /opt/scripts/requirements.txt

# Install Python packages
RUN pip install -r /opt/scripts/requirements.txt

# Copy your dependencies, destination filename must be "packages_to_install.csv"
COPY ./my_packages_to_install.csv /opt/scripts/packages_to_install.csv

# Install R packages
RUN Rscript /opt/scripts/install_r_packages.R

The package dependencies are copied into the images line 16, and installed line 19. The format of the file listing the dependencies depends on the language you use:

Python : requirement.txt file
R : my_packages_to_install.csv file

More details about the content of these files available here

Line 22: Grant shiny to create bookmark state

Python & R

# grant shiny to created bookmark state directory in this directory
RUN chown shiny:shiny /var/lib/shiny-server

In order to run your application, the user shiny must be allow to write file in /var/lib/shiny-server directory .

Line 28: Grant shiny to write output data

Python & R

# grant shiny to use www folder
RUN chown shiny:shiny /srv/shiny-server/www

When your application produce files, they are written in www directory, thus this directory must be own by user shiny , the user who will run the app.