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 runsubcommand 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 runsubcommand 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
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