Tool integration into MuGVRE workshop


Date:  13th September 2018

Venue: EMBL-EBI European Bioinformatics Institute, wellcome Trust Genome Campus, Hinxton, Cambridge, United Kingdom.

Application open: 19th June 2018.

Deadline: 17th August 2018.

Participation: Open application with selection.

Contact: Mark McDowall (mcdowall@ebi.ac.uk)

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Overview

The purpose of this workshop is to learn how to develop a MuG Tool to make available any software application to the MuG virtual research environment (MuGVRE). The course will cover:

  • The MuG Tool API, for packing the application code into a MuG Tool.
  • The COMPSs programming model, for the parallelisation of tasks within the Tool that dynamically can scale on the available virtualized resources.
  • The configuration and testing of the MuG Tool for the MuGVRE.
  • The documentation and packaging of the Tool in a repository for easy deployment.

Audience

The workshop is aimed to bioinformaticians and software developers interested in integrating their tools into the MuGVRE.

Preliminary course outline

  • MuGVRE introduction: what is MuG virtual research environment offering?
  • Wrapping you code: MuG Tool API
    • Creating a Tool and testing it using pytest
    • Creating a Pipeline and testing it using pytest
  • Testing the MuG Tool JSON Configuration files
    • Registering the MuG Tool into MuGVRE
    • Testing MuG Tool integration
  • COMPSs
    • Parellising the developed MuG Tool
  • Documentation
    • Documenting the MuG Tool ready for ReadTheDocs
    • Documenting the MuG Tool for MuGVRE end users
    • Hooking up your GitHub repo with TravisCI and ReadTheDocs