BioContainers Hackathon: Reproducible Bioinformatics.

ELIXIR EUROPE

<H3>Purpose</H3>
The “ELIXIR Software Deployment Group” is one of the six working groups of the ELIXIR tools platform. It has been recently formed to support bioinformatics software deployment efforts including packages and containers. At the moment this group is sustained by ELIXIR Nodes sharing a common interest to work together on a harmonised strategy. The activities of this group are extremely relevant to other two groups within ELIXIR Tools platforms: “Workflows &amp; workbenches” and “Software development best practices” because it represents the starting point for the development of reproducible pipelines and workflows in bioinformatics. 
This group would like to accelerate and consolidate the Containers Platform as a Service, and the integration with other groups like Workflows &amp; workbenches and Software tools (Bio.Tools). To do so we proposed to have a 2.5 days hackathon. In practice the hackathon will give us the opportunity to work on three different topics:
<UL>
<LI>Improve the current metadata and definitions for BioContainers and increase the number of containers in  Biocontainers. </LI>
<LI>
Integration of Biocontainers (https://biocontainers.pro/) and other initiatives Bioshadock (<A STYLE="font-family: 'Helvetica Neue', Helvetica, Arial, sans-serif; font-size: 13px;" HREF="http://bioshadock.genouest.org/" TARGET="_blank" DATA-MSYS-CLICKTRACK="0" REL="nofollow noopener noreferrer">http://bioshadock.genouest.org/</A>), BioConda. 
</LI>
<LI>
Connect better the containers registry (<A HREF="http://biocontainers.pro/registry" TARGET="_blank" DATA-MSYS-CLICKTRACK="0" REL="nofollow noopener noreferrer">http://biocontainers.pro/registry</A>) with Bio.tools and Workflow systems such as Galaxy and CWL. 
</LI>
<LI>
Define a strategy (Metadata) for “Training Containers”, design an infrastructure for hosting containers in ELIXIR and engage the training community to create containers for training purposes.
</LI>
</UL>
<H3>Delivery</H3>
Milestones:
<UL>
<LI>
Integration of Biocontainers and Bioshadock and BioConda which will boost the number of bioinformatics containers. 
</LI>
<LI>
Better connection between the BioContainers registry and Bio.tools
</LI>
<LI>
Development of first workflows with CWL and Galaxy using BioContainers. 
</LI>
<LI>
Engagement of the training community to create containers for training purposes
</LI>
<LI>
A strategy to define and implement standard Training BioContainers. 
</LI>
<LI>
Discussion of next milestones
</LI>
</UL>
<UL>
<LI>
BioContainers Repository for Reproducible Workflows: Submission of Reproducible Workflows in Containers that are related to one publication or study. 
</LI>
<LI>
Integration between data and containers. 
</LI>
</UL>

Institut Henri Poincaré

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