Phenomenal and BioContainers

[ypriverol]

Hi folks: I don't know if this is the place to discuss the integration of both initiatives. From our talk today, I would like to promote the following steps:

• [ ] Integrate the PhenoMeNal Registry into BioContainers UI Registry.

• [ ] PhenoMeNal should keep their containers and registry but probably would be good to take the BioContainers community to discuss general issues related with containers such as:

  • [x] testing strategies
  • [ ] containers documentation
    • [ ] PhenoMeNal to use fields expected by BioContainers, while keeping its ReadMe.md approach.
    • [ ] BioContainers could consider incorporating the ReadMe.md specification used by PhenoMeNal as a recommendation for containers where users want to boost documentation.
  • [ ] versioning
    • [x] PhenoMeNal currently using same LABELs for versioning.
    • [ ] Align container tag formatting.

If we discuss use BioContainers community to discuss these issues will be easy to provide long-term integration of both initiatives. BioContainers has a great infrastructure to discuss issues and trace these discussions. This will enable future integration between both initiatives not only at container level but also at the specification level. Also will enable to Phenomenal to approach other communities.

• [ ] In the long term can be easily (if we manage to align both initiatives) to use same infrastructure to deploy proteomics, genomics and transcriptomics apps.

[pcm32]

I have updated the original comment to reflect what I think is the current status of things:

• In terms of testing, I have taken this discussion to BioContainers in the past. I will update that thread with our latest developments.
• Versioning: we are using BioContainer's suggested LABELs in the Dockerfile, which inform our CI for tagging when pushing to our registry. We have a tagging consensus in place which incorporates tool and container versions annotated in the Dockefile, but I guess we could align this. For PhenoMeNal, the model of a single repo with all Dockerfiles used in BioContainers is unfeasible.
• In terms of documentation, PhenoMeNal goes beyond what is specified in BioContainers, but I guess we could make sure that we comply as well with what BioContainers expects.

In terms of showing PhenoMeNal containers in the BioContainers UI, I see no reason why not doing it, but I need to consult the consortium. Could @ypriverol list the requirements for this to happen? I presume that you need certain minimum labels to be present in the Dockerfile, and others, so that metadata fields are shown properly. In PhenoMeNal we plan to have the concept of production versions and development versions of containers. I would include only production versions on BioContainers. We should have blessed versions after our first release by the end of February this year.