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Containers

Repository of approved bioinformatics containers

Web Page : http://biocontainers.pro/

Project Definition : https://github.com/BioContainers/specs

Contribution Rules : https://github.com/BioContainers/specs/blob/master/CONTRIBUTING.md

Containers : https://github.com/BioContainers/containers

Containers Development: https://github.com/BioContainers/sandbox

Email : biodockers@gmail.com

License

Apache 2

Contents

  1. BioContainers Architecture

1.1 How to Request a Container

1.2 Use a Container

1.3 Reporting problem with Container 2. Get involved

1. BioContainers Architecture

BioContainers is a community-driven project that allows bioinformatics to request, build and deploy bioinformatics tools using containers. The following figure present the general BioContainers workflow:

What is Container

The next sections explain in details the presented workflow:

  • (i) How to request a workflow
  • (ii) Use a BioContainer
  • (iii) Developing containers

Importantly the BioContainers community designed a labeled legend to tag each issue in the containers repository that should be used properly for on each issue. For example, the for the new containers the label Container Request should be used.

Containers

1.1 How to Request a Container

Users can request a container by opening an issue in the [containers repository] (http://github.com/BioContainers/containers/issues) (In the previous workflow this is the first step performed by user henrik). The issue should contains the name of the software, the url of the code or binary to be package and information about the software see BioContainers specification. When the containers is deploy and fully functional, the issue will be close by the developer or the contributor to BioContainers.

1.2 Use a BioContainer.

When a container is deploy and the developer close the issue in GitHub the user (henrik) received a notification that the container is ready. The user can then used docker or rkt to pull or fetch the corresponding container.

docker run biocontainers/blast

1.3 Reporting a problem with a container

If the user find a problem with a container an issue should be open in the container repository, the user should use the broken tag (see tags). Developers of the project will pick-up the issue and deploy a new version of the container. A message will be delivery when the containers has been fixed.

2. Get involved

Whether you want to make your own software available to others as a container, to just use them on your pipelines and analysis or just give opinions, you are most welcome. This is a community-driven project, that means everyone has a voice.

Here are some general ideas:

  • Browse our list of containers
  • Propose your own ideas or software
  • Interact with other if you think there is something missing.