Module: Galaxy Admin Training

Learn how to run a Galaxy server

Introduction to Galaxy

Start here if you are new to Galaxy. These videos will introduce you to the Galaxy platform, and walk you through your first analyses

Lecture & Demo Video

Description:

This video will introduce the Galaxy data analysis platform, and give a short demo on how to use it.
Length: 10 minutes
Captions: Anton Nekrutenko
Created: 15 February 2021
Materials:
Support:
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Speaker

Tutorial Video

Description:

This video tutorial will provide a non-genomics based first look at the Galaxy platform, how to use it, and discusses how you can get support for your data analysis.
Length: 20 minutes
Captions: Alex Ostrovsky
Created: 1 May 2023
Materials:
Support:
Supported Servers: Known Working Possibly Working
Learning Objectives:
  • Familiarize yourself with the basics of Galaxy
  • Learn how to obtain data from external sources
  • Learn how to tag datasets
  • Learn how to run tools
  • Learn how histories work
  • Learn how to create a workflow
  • Learn how to share your work
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Speaker

Monday

Here you'll learn the basics of Ansible

Ansible (Lecture)

Description:

Here you’ll learn the basics of Ansible
Length: 5 minutes
Captions: Martin Čech
Created: 15 February 2021
Materials:
Support:
Learning Objectives:
  • Learn Ansible basics
  • Write a simple role
  • Install a role from Ansible Galaxy
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Speaker

Ansible (Tutorial)

Description:

Here you’ll learn the basics of Ansible
Length: 61 minutes
Captions: Martin Čech
Created: 15 February 2021
Materials:
Support:
Supported Servers:
Learning Objectives:
  • Learn Ansible basics
  • Write a simple role
  • Install a role from Ansible Galaxy
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Speaker

Go to session page.

Tutorial Video

Length: 2 hours 50 minutes
Captions: Nate Coraor, Helena Rasche
Created: 1 March 2022
Materials:
Support:
Supported Servers:
Learning Objectives:
  • Have an understanding of how Galaxy's Ansible roles are structured and interact with one another
  • Be able to use an Ansible playbook to install different flavors of Galaxy for different purposes
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Speakers

Tuesday

Tutorial Video

Description:

Here you’ll learn to setup TUS an open source resumable file upload server to process uploads for Galaxy. We use an external process here to offload the main Galaxy processes for more important work and not impact the entire system during periods of heavy uploading.
Length: 7 minutes
Captions: Helena Rasche
Created: 11 March 2022
Materials:
Support:
Supported Servers:
Learning Objectives:
  • Setup TUSd
  • Configure Galaxy to use it to process uploads
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Speaker

Tutorial Video

Description:

Running jobs in Apptainer
Length: 43 minutes
Captions: Cristóbal Gallardo, Simon Gladman
Created: 28 June 2021
Materials:
Support:
Supported Servers:
Learning Objectives:
  • Configure your Galaxy to use Apptainer and BioContainers for running jobs
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Speaker

Learn how to install and manage tools in Galaxy

Galaxy Tool Management with Ephemeris (Lecture)

Description:

Learn how to install and manage tools in Galaxy
Length: 17 minutes
Captions: Catherine Bromhead
Created: 28 June 2021
Materials:
Support:
Learning Objectives:
  • Learn about Ephemeris
  • Extract a list of tools from a workflow
  • Install these tools on a given Galaxy
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Speaker

Galaxy Tool Management with Ephemeris (Tutorial)

Description:

Learn how to install and manage tools in Galaxy
Length: 27 minutes
Captions: Catherine Bromhead
Created: 28 June 2021
Materials:
Support:
Supported Servers:
Learning Objectives:
  • Learn about Ephemeris
  • Extract a list of tools from a workflow
  • Install these tools on a given Galaxy
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Speaker

Go to session page.

Lecture Video

Length: 4 minutes
Captions: The Global Galaxy Community
Created: 15 February 2021
Materials:
Support:
Learning Objectives:
  • Learn the Galaxy user/group management and assign Quotas.
  • Understand the Role Based Access Control (RBAC) of Galaxy.
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Speaker

Reference data management is easier than ever with CVMFS

Reference Data with CVMFS (Tutorial)

Description:

Reference data management is easier than ever with CVMFS
Length: 3 minutes
Captions: The Global Galaxy Community
Created: 15 February 2021
Materials:
Support:
Learning Objectives:
  • Have an understanding of what CVMFS is and how it works
  • Install and configure the CVMFS client on a linux machine and mount the Galaxy reference data repository
  • Configure your Galaxy to use these reference genomes and indices
  • Use an Ansible playbook for all of the above.
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Speaker

Reference Data with CVMFS (Tutorial)

Description:

Reference data management is easier than ever with CVMFS
Length: 23 minutes
Captions: Simon Gladman
Created: 15 February 2021
Materials:
Support:
Supported Servers:
Learning Objectives:
  • Have an understanding of what CVMFS is and how it works
  • Install and configure the CVMFS client on a linux machine and mount the Galaxy reference data repository
  • Configure your Galaxy to use these reference genomes and indices
  • Use an Ansible playbook for all of the above.
Go to the video page to see all versions.

Speaker

Go to session page.

Tutorial Video

Length: 22 minutes
Captions: Helena Rasche, Saskia Hiltemann
Created: 15 February 2021
Materials:
Support:
Supported Servers:
Learning Objectives:
  • Setup a data library
  • Manage permissions
  • Import data from disk
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Speaker

Wednesday

Tutorial Video

Length: 31 minutes
Captions: Catherine Bromhead, Saskia Hiltemann
Created: 15 February 2021
Materials:
Support:
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Speaker

Tutorial Video

Length: 31 minutes
Captions: Saskia Hiltemann
Created: 15 February 2021
Materials:
Support:
Supported Servers:
Learning Objectives:
  • Know how to map tools to job destinations
  • Be able to use the dynamic job runner to make arbitrary destination mappings
  • Understand the job resource selector config and dynamic rule creation
  • The various ways in which tools can be mapped to destinations, both statically and dynamically
  • How to write a dynamic tool destination (DTD)
  • How to write a dynamic python function destination
  • How to use the job resource parameter selection feature
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Speaker

Thursday

Remote compute made possible with Pulsar

Running Jobs on Remote Resources with Pulsar (Lecture)

Description:

Remote compute made possible with Pulsar
Length: 14 minutes
Captions: Saskia Hiltemann
Created: 15 February 2021
Materials:
Support:
Learning Objectives:
  • Have an understanding of what Pulsar is and how it works
  • Install and configure a RabbitMQ message queueing server
  • Install and configure a Pulsar server on a remote linux machine
  • Be able to get Galaxy to send jobs to a remote Pulsar server
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Speaker

Running Jobs on Remote Resources with Pulsar (Tutorial)

Description:

Remote compute made possible with Pulsar
Length: 1 hour 28 minutes
Captions: Helena Rasche
Created: 28 June 2021
Materials:
Support:
Supported Servers:
Learning Objectives:
  • Have an understanding of what Pulsar is and how it works
  • Install and configure a RabbitMQ message queueing server
  • Install and configure a Pulsar server on a remote linux machine
  • Be able to get Galaxy to send jobs to a remote Pulsar server
Go to the video page to see all versions.

Speaker

Go to session page.

Tutorial Video

Length: 2 minutes
Captions: The Global Galaxy Community
Created: 15 February 2021
Materials:
Support:
Learning Objectives:
  • Learn gxadmin basics
  • See some queries and learn how they help debug production issues
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Speaker

Learn advanced Galaxy monitoring with Telegraf, Influx, and Grafana.

Galaxy Monitoring with Telegraf and Grafana (Lecture)

Description:

Learn advanced Galaxy monitoring with Telegraf, Influx, and Grafana.
Length: 2 minutes
Captions: The Global Galaxy Community
Created: 15 February 2021
Materials:
Support:
Learning Objectives:
  • Setup InfluxDB
  • Setup Telegraf
  • Setup Grafana
  • Create several charts
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Speaker

Galaxy Monitoring with Telegraf and Grafana (Tutorial)

Description:

Learn advanced Galaxy monitoring with Telegraf, Influx, and Grafana.
Length: 73 minutes
Captions: Saskia Hiltemann, Helena Rasche
Created: 15 February 2021
Materials:
Support:
Supported Servers:
Learning Objectives:
  • Setup InfluxDB
  • Setup Telegraf
  • Setup Grafana
  • Create several charts
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Speaker

Go to session page.

Lecture Video

Length: 2 minutes
Captions: The Global Galaxy Community
Created: 15 February 2021
Materials:
Support:
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Speaker

Choose Your Own Adventure

Welcome Video

Description:

This short video gives an overview of the worldwide Galaxy community, and different ways you can get involved! Video created by Beatriz Serrano-Solano.
Length: 5 minutes
Captions: Saskia Hiltemann
Created: 15 February 2021
Materials:
Support:
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Speaker

Tutorial Video

Description:
  1. The first step to adding a tool to Galaxy, is to add it to (Bio)Conda. This tutorial will show you how to do that.
  2. Planemo is the Galaxy tool development kit, and will make your tool development process a lot easier! This tutorial will show you how to use Planemo to start the tool wrapping process, and covers the general structure of a Galaxy tool wrapper.
  3. You are now ready to start writing your tool wrapper! This video will show you how.
  4. Each tool wrapper also needs a .shed.yml file, which contains some metadata about the tool.
  5. Here you will learn how to test Galaxy tools using Planemo.
  6. Here you will learn how to publish tools in public tool repositories.
Length: 50 minutes
Captions: Cristóbal Gallardo, Alex Ostrovsky
Created: 18 May 2023
Materials:
Support:
Supported Servers:
Learning Objectives:
  • Learn how to make and deploy a conda package
  • Understand how to write a Galaxy tool wrapper
  • Be able to use a tool wrapper locally
  • Be able to test the tool wrapper
  • Learn how to add tools to the Galaxy toolshed and make them available to any user
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Speakers

Tutorial Video

Length: 44 minutes
Captions: Anthony Bretaudeau, Helena Rasche
Created: 15 February 2021
Materials:
Support:
Supported Servers:
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Speaker

Tutorial Video

Length: 36 minutes
Captions: Simon Gladman, Helena Rasche
Created: 15 February 2021
Materials:
Support:
Supported Servers:
Learning Objectives:
  • Understand how to find the current Galaxy server version you are using
  • How to find the latest release version
  • How to backup the Galaxy server database and why it's a good idea
  • How to upgrade the Galaxy server to a new version
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Speaker

Tutorial Video

Length: 18 minutes
Captions: Catherine Bromhead
Created: 15 February 2021
Materials:
Support:
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Speaker

Automation with Jenkins

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Tutorial: Automation with Jenkins
Material: GTN Tutorial
Support:
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Instructor

Enable upload via FTP

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Tutorial: Enable upload via FTP
Material: GTN Tutorial
Support:
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Instructor

Advanced customisation of a Galaxy instance

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Tutorial: Advanced customisation of a Galaxy instance
Material: GTN Tutorial
Support:
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Instructor

Galaxy Troubleshooting

image indicating this is a self-study session. This is a self-study session. Please work through the materials on your own, and ask the instructors for help if you get stuck or have any questions!
Tutorial: Galaxy Troubleshooting
Material: GTN Tutorial
Support:
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Instructor