Automatic Galaxy report system

[bgruening]

Automatic report system for Galaxy

Supervisor: Björn Grüning, Wolfgang Maier ( @wm75 ) For degree: Bachelor / Project / Master Status: Open Keywords: Reporting, Galaxy

Global Biological/Research context

The aim is to develop a modular reporting system that collects data from Galaxy histories and offers graphical appealing and useful reporting.

Project context

The idea would be to develop something similar to MultiQC for Galaxy. iReport comes pretty close to it, but we need to make it more modular.

Objectives of the project

Sum up a Galaxy history into a shareable and graphical appealing report. The report can be in HTML, PDF or some presentation format.

Proposed agenda for the project

1. Investigate different reporting tools for medical data
2. Study design of MultiQC
3. Writing a pluggable protoype to parse and present results of 2 different tools (gemini and cnvkit?)
4. Develop more plugins
5. Integrate this tool tightly into Galaxy
6. Figure out if we can annotate Galaxy outputs to be collected automatically

Prerequisites

• Python knowledge
• Work with complex systems like Galaxy
• Work in an Open Source community
• Able to parse files in different formats
• Understanding different file formats and complex data structures

Further reading and useful links

• iReports

[bgruening]

@jmchilton has developed an awesome system in https://github.com/galaxyproject/galaxy/pull/8030

This project should be now a Bachelor project extending the existing system and working on the user-facing part (client-side in JS).