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README.md

README.md

Improve Shiny and RStudio integration within Galaxy using Galaxy Interactive Environment

Join the chat at https://gitter.im/bh2018paris/20-Shiny-RStudio-Galaxy

Representative: Gildas Le Corguillé

Community

The ELIXIR Galaxy Community and the ELIXIR Metabolomics Community

Leads

Background Information

Shiny is a powerful R package to display and interact with data (e.g. visualisation of raw data, statistics, geographic information system, ...). Galaxy Interactive Environments allows running Shiny inside of Galaxy, isolated within Docker containers. Several projects are currently interested in embracing and enhancing Shiny-IEs: pGalaxy-E](https://github.com/65MO/Galaxy-E) (ELIXIR-FR) for ecology and Workflow4Metabolomics (ELIXIR-FR) for metabolomics research. Additionally a GIE for RStudio exists providing an environment for developing R code, integration between these two GIEs could provide an enhanced workflow for developing novel Shiny GIEs within Galaxy.

How GIEs Work

Expected outcomes

We have lots of plans for this week:

  • Administration
    • Simplify/Automate installation of IEs
    • Improve flexibility, allow working with Datasets Collections and multiple Datasets
  • Technology
    • Implement Galaxy FUSE driver and a Docker Volume plugin to allow running IEs without shared filesystem
  • Documentation
    • Document installation and configuration of IEs
    • Document newly built Docker Volume plugin
  • Participant Issues
    • Solve some participants problems during some "Bring Your Own Issues" sessions

Expected audience

Developers, DevOps, System Administratorys

Skills wanted (and/or):

  • Galaxy Framework
  • Container technologies: Docker or Singularity
  • R, RShiny
  • D3.js, Plotly
  • Nginx, NodeJS

Expected hacking days: 2 days ...

GitHub or any other public repositories of your FOSS products

Workflow4Metabolomics

GIE Chromatograms

Galaxy-E

GIE GIS

Galaxy GIE for RStudio

GIE RStudio

Hackers

Slides

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