A curated BioInformatics container registry.
Created by GenOuest core facility and IFB.

Not maintained anymore

Bioshadock project has been stopped (though was ok for production), in favor of the Biocontainers Elixir project (we are contributors and active members)

About Bioshadock

Bioshadock provides a private Docker container registry. It is based on Docker registry. However base registry from Docker does not provide any authentication nor access control.

Our server works with the Docker registry to add such features. Authenticated users can push containers to private or public repositories and share their access with other users. It also adds meta-data information (description, tags, etc.) and search capabilities in the registry.

It also adds automatic builds based on a Dockerfile or a git repository

Anonymous users can pull public containers


  • LDAP authentication
  • Authorize pulls for all authenticated users or selected users
  • User push control
  • Container meta-data (description, custom tags, etc.)
  • Automatic build from Docker file or a remote git repository with manual or web hooks
  • Tag containers
  • Elixir registry integration
  • REST API: http://www.genouest.org/api/bioshadock-api/
  • Security scans
  • Automatic image tests (see Help)

Reproductible experiments

Containers and registry focus on the capacity to make experiments reproductible.

A container contains all the software pre-installed and make it easy to use and share a software without the installation burden and constraints. A tagged container will also make possible to re-use a specific version of a tool.

However, many publicly available containers are build and provided without documentation or a way to recreate them. Bioshadock focuses on reproductible containers ie. based on a Dockerfile to rebuild containers on demand and to clearly show what is installed in the container, and how.

The team in charge of the registry will make sure that provided containers contain such a Dockerfile and all associated files (possibly in a git repository). Indeed many containers are provided with a Dockerfile using files not available to the end-user.

When a container is build from a Dockerfile (possibly a git repository), the owner can add some tests to be done against the container after it is built. This prevents building a container.... that does not work!

Security inside

For all automatic builds, we scan the containers against known vulnerabilities using Clair, and regular scans update their status. Developper, but also the end user, can see what are the known issues within the container and decide if container is a risk or not. No more container pulls without knowing if a container is secure or not for your computer or infrastructure....

Use Bioshadock

You can freely pull containers from our registry. To push new containers you must have additional rights, do not hesitate to contact us.

browse our container list

Contact Bioshadock team

Feel free to email us to provide some feedback on our containers, request new tools, or support.