RenkuLab Docker Images

RenkuLab Docker images contain minimal dependencies for launching interactive environments like JupyterLab and RStudio from the Renku platform. They also each contain a version of the renku cli.

Usage

The basic python (renkulab-py), basic R (renkulab-r), and basic Julia (renkulab-julia) images are available via renku project templates that you select upon renku project creation on the RenkuLab platform, or locally via renku init.

If you would like to use an image built from this repo that is not available via the renku project templates, follow these steps:

• create your project with the minimal template that matches the programming language you're using (there's also a minimal template for languages other than python or R)
• replace the image in the FROM line in your project's Dockerfile with one of the images built from this repo. See "Naming Conventions" for how to choose which image to use

If you would like to add the ability to launch RenkuLab interactive environments to your own pre-existing images, see the Adding renku to your own images section below.

Container initialization

Sometimes certain actions need to be performed on container start-up to prepare the environment. Some of these are carried out already in the entrypoint.sh script in the base image, but if you extend the image you may want to add your own. This can be done by adding a post-init.sh script to the root directory of the container. It must be executable by a non-privileged user because it will run with the user restrictions of the container.

Projects using the base images may additionally place a post-init.sh script in the root directory of the project. This script will also run upon initialization of the container, but after the /entrypoint.sh and /post-init.sh scripts.

Naming Conventions

You can find these base images on DockerHub in renku/renkulab-* repositories, where * represents the "flavor" (programming language or base image). Read the following naming conventions below to select the image that's right for you:

renku/renkulab-[image flavor]:[image flavor version]-[tag|hash]

For example: renku/renkulab-py:python-3.8.8-0.11.0

• renku/renkulab: indicates this is an image you can use to spawn an environment from your project on RenkuLab.
• -py: indicates this is a python image flavor; either the programming language installed in the environment, or the base image that extra dependencies are added to. See below for details about the available flavors.
• python-3.8.8: indicates the version of python is 3.8.8
• 0.11.0 (or d572e9a): the tag is a value given to a commit of the repository and indicates that the version is part of a release. If the version is not part of a release, this value is the first few chars of the git commit SHA from which the image is built.

Note that the base images include the specified version of the renku CLI. This can easily be overridden by installing another version with pipx in the container or any Dockerfile that uses these images, e.g.

pipx install --force renku==<version>

Current images

Image	Description	Base image
renku/renkulab-py	Basic Jupyter image with minimal dependencies	jupyter/base-notebook
renku/renkulab-r	Basic Rstudio image	rocker/verse
renku/renkulab-julia	Basic Julia image	renku/renkulab-py
renku/renkulab-bioc	Bioconductor R image	bioconductor/bioconductor_docker
renku/renkulab-cuda	Cuda image with Python and minimal dependencies	renku/renkulab-py
renku/renkulab-cuda-tf	Cuda image with Python and Tensorflow	renku/renkulab-cuda
renku/renkulab-vnc	VNC Image with Python	renku/renkulab-py

Please refer to the release notes for more detailed lists of released images and specific links to Dockerhub.

py

Available via renku project templates

The basic Jupyter image with minimal dependencies. Based on https://hub.docker.com/r/jupyter/base-notebook/.

dockerhub: https://hub.docker.com/r/renku/renkulab-py/tags

r

Available via renku project templates

Based on the rocker "verse" image: https://hub.docker.com/r/rocker/verse, chosen because rocker keeps a more up-to-date version of R than conda, and includes most of the software dependencies that R users use. Includes the R Jupyter kernel as well as RStudio. To access RStudio, simply replace /lab or /tree with /rstudio in the URL.

dockerhub: https://hub.docker.com/r/renku/renkulab-r/tags

julia

Available via renku project templates

Based on the renkulab-py (python 3.9) image with julia installed.

dockerhub: https://hub.docker.com/r/renku/renkulab-julia/tags

bioc

Available via renku project templates

Based on the bioconductor Docker image: https://github.com/Bioconductor/bioconductor_docker.

dockerhub: https://hub.docker.com/r/renku/renkulab-bioc/tags

cuda

Based on the renkulab-py with different versions of python and CUDA installed.

dockerhub: https://hub.docker.com/r/renku/renkulab-cuda/tags

cuda-tf

Based on the the cuda-tf images with different (compatible) versions of Tensorflow installed.

dockerhub: https://hub.docker.com/r/renku/renkulab-cuda-tf/tags

vnc

Based on the renkulab-py (python 3.9) with a full virtual desktop installed. It uses noVNC 1.1.0 and TigerVNC 1.9.0 with a Renku UI to deliver a Linux desktop.

https://hub.docker.com/r/renku/renkulab-vnc/tags

Development

Build with Docker by running docker build -t <name:tag> . in the directory of the image you would like to build. Note that on arm-based systems (e.g. Apple M1/M2) you may need to use the flag --platform=linux/amd64 for the build because git-lfs 3.2.0 is not available for the arm architecture.

Adding renku to your own images

If you already have a Docker image with complicated dependencies that are needed for your work, you can get this up and running on RenkuLab by using one of our Docker images in your build. We have two images that can be used in this way - one that is completely generic, and the other that is specific to rocker-based images.

Assuming you are in the directory with the Dockerfile you would like to use, you can build the renkulab dependencies into it like this:

docker build -t <image-tag> \
  --build-arg BASE_IMAGE=<base-image> \
  https://github.com/SwissDataScienceCenter/renkulab-docker.git#docker/generic

where image-tag is some image name/tag you want to use and base-image is your existing image.

If your own image is based on the rocker R distribution, you can do

docker build -t <image-tag> \
  --build-arg BASE_IMAGE=<base-image> \
  https://github.com/SwissDataScienceCenter/renkulab-docker.git#docker/r

Contributing

If you have any suggestions for different languages or base images you would like us to provide, feel free to submit an issue (or a pull request!) to this repo.