Packaging, containerisation and deployment

This study will build on recent work with  Software containers which, as a key element in the frame of Open Science, Open Data & Open Source, is strongly supported and advocated by ELIXIR. Software containers are transversal to most of the strategic lines of the ELIXIR Tools platform for the 2019 - 2023 Scientific programme.

There will be three Work Packages: 

1. To maintain and extend the work initiated in the 2018 ELIXIR implementation study on Biocontainers. The implementation study on Biocontainers contributed to unify various initiatives in ELIXIR nodes around software containers and bring them under a common infrastructure which will be consolidated by incorporating new technologies for software containerisation and explore the federation of the platform to facilitate its sustainability in the long-term.

2. To implement the evolution of the ELIXIR tools platform ecosystem to create a central repository providing metadata rich, technology agnostic software containers for its use and deployment across sites and platforms. Initially this will integrate content from bio.tools, Biocontainers, OpenEBench and Galaxy, and in time facilitate the inclusion of new data and metadata producers (e.g. bioconda, bioconductor, etc) and/or new data and metadata consumers (e.g. GA4GH TRS, MyExperiment, etc). 

3. Engaging with existing and newly created community of users (within ELIXIR and without) who are of the utmost importance to guarantee that whatever standard and/or technology responds to users needs. Software containers will play an important role here to ensure users can benefit from the ongoing efforts in the evolved tools platform ecosystem and with other ELIXIR platforms such as Training, Interoperability and/or Compute.

This study will provide containerised tools and state-of-the-art benchmarked workflows available in Galaxy for scientific communities. For long-term sustainability and impact, we will ensure that all workflows and tools are curated to a high standard, rendered FAIR, and follow agreed standards within ELIXIR and by initiatives like GA4GH and EOSC.

Platform/Community: 

People involved: 

Björn Grüning
Salvador Capella
Yasset Perez-Riverol
Frederik Coppens
Piotr Jaroslaw Chmura
Josep Ll. Gelpi
Jon Ison
Hervé Ménager
Olivier Sallou
Giacomo Tartari
Matúš Kalaš
Abdulrahman Azab
Kjetil Klepper
Kjell Petersen