e-learning

Automating Galaxy workflows using the command line

Abstract

Galaxy is well-known as a web-based data analysis platform which provides a graphical interface for executing common bioinformatics tools in a reproducible manner. However, Galaxy is not just a user-friendly interface for executing one tool at a time. It provides two very useful features which allow scaling data analyses up to a high-throughput level: dataset collections and workflows.

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 can I schedule and run tens or hundreds of Galaxy workflows easily?
  • How can I automate my analyses when large amounts of data are being produced daily?

Learning Objectives

  • Learn to use the planemo run subcommand to run workflows from the command line.
  • Be able to write simple shell scripts for running multiple workflows concurrently or sequentially.
  • Learn how to use Pangolin to assign annotated variants to lineages.

Licence: Creative Commons Attribution 4.0 International

Keywords: Using Galaxy and Managing your Data, covid19, variant-analysis, workflows

Target audience: Students

Resource type: e-learning

Version: 8

Status: Active

Prerequisites:

  • Basic knowledge of the command line
  • Familiarity with Galaxy and basic associated concepts, in particular workflows

Learning objectives:

  • Learn to use the planemo run subcommand to run workflows from the command line.
  • Be able to write simple shell scripts for running multiple workflows concurrently or sequentially.
  • Learn how to use Pangolin to assign annotated variants to lineages.

Date modified: 2024-06-14

Date published: 2021-06-08

Authors: Simon Bray, Wolfgang Maier

Contributors: Bérénice Batut, Helena Rasche, Saskia Hiltemann, Wolfgang Maier

External resources:

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