Galaxy Admin Training @ GTN Tapas

Free, Global, Online Week of Galaxy Admin Training

Practical Information

Dates
14-18 March 2022
Location:
Online
Cost:
free
Supporting Institutions:
Australian Biocommons, JetStream2, The Gallantries Project, Erasmus Medical Center, ELIXIR Europe, The Galaxy Training Network
Contact:
Helena Rasche
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Program

Below you will find all the tutorials for this course, everything you need to follow this course is listed here.

Welcome & Setup (Start Here!)

Practical information about this course and getting everything set up to follow this course.

Welcome Video

Description:

Start here! We will go over all the important things you need to know about this week!
Length: 15 minutes
Captions: Saskia Hiltemann
Created: 10 March 2022
Materials:
Support:
Go to the video page to see all versions.

Speakers

Lecture Video

Description:

This supplementary welcome will give you additional details that are needed for the week.

Please note that when you use the mentioned /completed command, you do not need to specify a history URL. Just /completed is sufficient.
Length: 4 minutes
Captions: Helena Rasche
Created: 15 February 2021
Support:
Go to the video page to see all versions.

Speakers

image of a laptop displaying code
Technical Requirements

  • We will provide VMs for you on which you will do everything during the week, so you don't need a super powerful laptop or anything.
  • It is best if you have an SSH client pre-installed, but it is not strictly necessary. However, all VMs have a terminal available on port 8080 if you cannot install one.
  • Windows users can choose to install PuTTY or equivalent.
  • For Linux & OSX: You should have an ssh client already installedx


image of a laptop displaying code
Educational Requirements

By the time of the workshop, you should be familiar with the Unix command line. Everyone has a different background and if you haven't had to learn Unix shell basics before that's ok! We recommend that you go through The Unix Shell lesson from The Carpentries.

Additionally you need to be comfortable with a command-line text editor. If you have not had to use one before, then nano is recommended. If you have a preferred one (e.g. vim or emacs), you are welcome to use that.


Slack Logo
Join Slack Chat!


Slack is where you can ask all your questions

You will find different channels here, one for each training session where you can ask your questions, as well as some more general channels for socializing, general discussions, feedback and more.


See our Slack Tips & Tricks page for some more info about Slack and how we use it.

Galaxy logo
GalaxyProject Code of Conduct

We are committed to providing a welcoming and inspiring community for all, and expect our code of conduct to be honored.

Please read the Code of Conduct and adhere to it throughout this event. If you witness any violations of this code of conduct, please report it to us.

Read the full Code of Conduct

Icon of a Certificate
Request a certificate of attendance.

For this event, we will use the GTN Certificate Slack Bot to keep track of your progress and request your certificate. (Instructions below).

NOTE: If your country blocks Slack, then please fill in this Certificate Request Form instead.

Deadline: no later than Friday April 1, 2022.


Certificate Requirements
  1. Have a registration for this event.
  2. Save all your Galaxy Histories.
  3. Register completion of tutorials using the Certificate Bot (see below).
  4. Answer the icebreakers question on Slack every day!
  5. Be active on Slack!
    • Join the Slack channels for every training session you follow this week (see link below video)
    • Let us know when you are starting with a session in the session's dedicated Slack channel
    • Talk about the session! Get stuck? Have a question about the science? want to discuss anything? want to thank your instructors? do it in Slack!
    • Whenever you finish a session, let us know what you thought of it!
    • Enjoyed a tutorial? Take a moment to thank your (volunteer) instructors and speakers on Slack
    • And please, feel free to help other participants on Slack if you know the answer!
  6. Fill out our feedback survey (see "wrap-up" section of the program). This will help us improve this event in the future.

NOTE: You can follow as few or as many training sessions as you want, we will give you a personalized certificate listing all the sessions you attended.


Using the GTN Certificate Slack Bot

  • Completed a tutorial?
    1. Share your Galaxy history via URL
      • Instructions
      • The history URL will look something like: https://usegalaxy.xx/u/saskia/h/my-history-name
    2. Open the Slack channel for the tutorial you finished
      • The link to this channel is listed below the video

    3. Submit your history URL in this channel using the command:

      /completed

    • NOTE: Your message must START with /completed, you cannot write this in the middle or end of the message.
    • NOTE: If a tutorial results in mulltiple histories, you can submit them all in the same command: - example: /completed history1_url history2_url
      1. Write a short message in the channel letting us know what you thought of the tutorial, and/or thanking the instructors!

  • Want to check your submissions?
    • At any time, use the /transcript command to see what you have already submitted
    • In any channel, or a message to @GTN Certificate Bot

  • Finished with the event? Use the command:
    • /request-certificate
      • to request a certificate for the course.
      • Enter your name as you would like it to appear on the Certificate
        • example: /request-certificate Saskia Hiltemann
    • In any channel, or a message to @GTN Certificate Bot
    • We will review your Galaxy histories, and send you your personalised certificate
      • We aim to do this within 2 weeks of the certificate deadline

Come say Hi in Slack! Let us know you are joining today and are getting started!

Icebreaker pictogram
Monday Icebreaker


1. Introduce yourself and tell us one fun fact about yourself!
2. What are you hoping to learn this week?

Post your answers in #social on Slack!

Please feel free to respond to each other here, this channel is for socializing and getting to know each other! :)

Note: Please do this every day if you would like to receive a certificate of attendance


Icebreaker pictogram
Tuesday Icebreaker


What is the coolest, most mind blowing fact (nature/people/animal etc.) you know?

Post your answers in #social on Slack!

Please feel free to respond to each other here, this channel is for socializing and getting to know each other! :)


Icebreaker pictogram
Wednesday Icebreaker


What is your favorite dish (food or drink)? Bonus points for recipes!

Post your answers in #social on Slack!

Please feel free to respond to each other here, this channel is for socializing and getting to know each other! :)


Icebreaker pictogram
Thursday Icebreaker


1. What is one fun hobby, passion, skill or talent you have?
2. What is your favorite thing about the course so far?

Post your answers in #social on Slack!

Please feel free to respond to each other here, this channel is for socializing and getting to know each other! :)


Icebreaker pictogram
Friday Icebreaker


What is your favorite book, film, tv show or game you've enjoyed recently?

Post your answers in #social on Slack!

Please feel free to respond to each other here, this channel is for socializing and getting to know each other! :)


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:
Go to the video page to see all versions.

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
Go to the video page to see all versions.

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
Go to the video page to see all versions.

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
Go to the video page to see all versions.

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
Go to the video page to see all versions.

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
Go to the video page to see all versions.

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
Go to the video page to see all versions.

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
Go to the video page to see all versions.

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
Go to the video page to see all versions.

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.
Go to the video page to see all versions.

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.
Go to the video page to see all versions.

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
Go to the video page to see all versions.

Speaker

Wednesday

Tutorial Video

Length: 31 minutes
Captions: Catherine Bromhead, Saskia Hiltemann
Created: 15 February 2021
Materials:
Support:
Go to the video page to see all versions.

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
Go to the video page to see all versions.

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
Go to the video page to see all versions.

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
Go to the video page to see all versions.

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
Go to the video page to see all versions.

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
Go to the video page to see all versions.

Speaker

Go to session page.

Lecture Video

Length: 2 minutes
Captions: The Global Galaxy Community
Created: 15 February 2021
Materials:
Support:
Go to the video page to see all versions.

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:
Go to the video page to see all versions.

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
Go to the video page to see all versions.

Speakers

Tutorial Video

Length: 44 minutes
Captions: Anthony Bretaudeau, Helena Rasche
Created: 15 February 2021
Materials:
Support:
Supported Servers:
Go to the video page to see all versions.

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
Go to the video page to see all versions.

Speaker

Tutorial Video

Length: 18 minutes
Captions: Catherine Bromhead
Created: 15 February 2021
Materials:
Support:
Go to the video page to see all versions.

Speaker

Automation with Jenkins

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: Automation with Jenkins
Material: GTN Tutorial
Support:
Go to the video page to see all versions.

Instructor

Enable upload via FTP

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: Enable upload via FTP
Material: GTN Tutorial
Support:
Go to the video page to see all versions.

Instructor

Advanced customisation of a Galaxy instance

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: Advanced customisation of a Galaxy instance
Material: GTN Tutorial
Support:
Go to the video page to see all versions.

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:
Go to the video page to see all versions.

Instructor



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