This work was the basis of a VLSCI Summer Internship project, conducted by Simon Belluzzo, supervised by Dr Ira Cooke, and supported by the VLSCI.

Slides from the presentation of this work at the end of the internship program can be found here.

Project Background

Ira had previously written ProtK, a unifying and convenience wrapper around a set of proteomics tools, along with a set of tool wrappers to allow use of the tools in Galaxy. However, the complexity of installing the underlying tools and their dependencies, and ensuring interoperability with a Galaxy server, made installation by novice users difficult, especially in the context of Galaxy on the Cloud or Genomics Virtual Lab (GVL) instances. Therefore, the primary goal of this work was to explore the feasibility of using Docker, a lightweight “application container” platform that has preliminary support in Galaxy, as a way of easily distributing and installing the tools along with required dependencies.

Project Aims

  • Build a ProtK proteomics Docker image.
  • Adapt Galaxy wrappers to utilise Docker image.
  • Investigate deployment options.
  • Set up for integration with GVL
    • Installation
    • Interaction with job runners