BioContainers is a community-driven project that builds, hosts, and maintains container images for scientific software. We maintain more than 100,000 containers for over 12,000 tools. Our goal is to make software easy to discover, install, and run reproducible across laptops, clusters, clouds, and workflow systems.
Important
Despite our name, BioContainers is not only for biology or bioinformatics. Researchers and developers from every scientific discipline are welcome. Naming is hard, we chose ours early, and changing it now would be even harder. :)
The main entry point for BioContainers Docker/OCI images is the BioContainers organization on Quay.io. We maintain mirrors of all containers for resilience and availability, but Quay.io is the canonical place to start.
The Galaxy Project also converts and distributes BioContainers images in the Singularity/Apptainer format. Individual images can be found on the Galaxy Singularity Depot.
Important
If you use Singularity/Apptainer images heavily, for example, on a cluster or in a production service, please do not download them repeatedly from the Depot. Use Galaxy's singularity.galaxyproject.org CVMFS repository instead. It provides scalable, distributed, cached access to the complete container collection.
Note
The legacy containers (built using the Biocontainers github repository) are instead hosted on the Biocontainers organization on Docker hub. Singularity images built from these containers are available here
For most scientific software, we recommend creating a package in Bioconda or conda-forge rather than writing and maintaining a container recipe directly. Once a package is available, BioContainers automatically builds the corresponding container and singularity image. (This build occurs nightly)
Need several Conda packages in one image? Request a multi-package container in the multi-package-containers repository or use the graphical multi-package container assistant.
BioContainers also offers a legacy repository where images can be built using Dockerfile directly provided by the community. This method is still available for edge cases, but it is now mostly deprecated. For new software, we strongly recommend using either the Bioconda/Conda-based approach, or mulled containers if all packages needed already exists as conda packages. The legacy repository remains available primarily for compatibility with older workflows, and management of complex softwares.
BioContainers is open, community-driven, and built for reproducible science, whatever your field may be.
