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e-learning

Debugging Galaxy

Abstract

In this tutorial we will demonstrate how to find and fix common types of bugs you may encounter as a contributor to Galaxy. We will step you through the process of finding and fixing a bug - from locating specific errors in the logs of Galaxy's GitHub Actions, to identifying their cause, developing a solution and committing your edits

About This Material

This is a Hands-on Tutorial from the GTN which is usable either for individual self-study, or as a teaching material in a classroom.

Questions this will address

  • How do I debug Galaxy?

Learning Objectives

  • Fix a broken branch
  • Interpret the results of failed tests on GitHub
  • Run individual tests locally
  • Fix errors identified by failing tests
  • Debug simple runtime errors using the Python debugger
  • Write tests exposing the identified bug

Licence: Creative Commons Attribution 4.0 International

Keywords: Development in Galaxy

Target audience: Galaxy Administrators

Resource type: e-learning

Version: 14

Status: Active

Prerequisites:

  • Basic knowledge of Python and JavaScript
  • Familiarity with basic Git commands
  • Galaxy Code Architecture
  • Mac OS or Linux that can run Galaxy & your favorite IDE or editor

Learning objectives:

  • Fix a broken branch
  • Interpret the results of failed tests on GitHub
  • Run individual tests locally
  • Fix errors identified by failing tests
  • Debug simple runtime errors using the Python debugger
  • Write tests exposing the identified bug

Date modified: 2024-06-14

Date published: 2021-06-15

Authors: Assunta DeSanto, John Chilton, John Davis

Contributors: Assunta DeSanto, Björn Grüning, David López, Helena Rasche, John Davis, Marius van den Beek, Oleg Zharkov, Saskia Hiltemann

Scientific topics: Software engineering


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