Frequently Asked Questions

Tutorial Questions


Preparing materials for asynchronous learning: CYOA

If you are running a remote training, and expect your users to follow a specific path, be certain to include the URL parameter to select the pathway to avoid student confusion. Please note that all tutorials using a CYOA should be tagged which will give you a heads up as a trainer.

Preparing materials for asynchronous learning: FAQs

When you are running a remote, asynchronous lesson, you’ll want to be sure you collect all student questions and add them back to your tutorial afterwards, as FAQs. This will help other learners as they progress through the materials, and can give you a very easy URL to point your learners to if they get stuck on a particular task.

Preparing materials for asynchronous learning: Self-Study

In the context of remote trainings, where a teacher isn’t synchronously available, ensuring that you have questions throughout your materials for students to check their understanding is incredibly key.

Additionally ensuring that solutions are provided, and are correct and up-to-date (or use a snippet explaining data variability along with with ways to check the results) is mandatory. Students will then use these questions to self-check their understanding against what you expected them to learn.

Preparing materials for asynchronous learning: Tips

The use of snippets is extremely important for asynchronous, remote learning. In this situation as students do not have a teacher immediately on hand, and likely do not have friends or colleagues sitting working with them, they will rely on these boxes to refresh their knowledge and know what to do.

Please ensure you test your learning materials with a learner or colleague not familiar the material, and if possible, (silently) watch them go through your lesson. You’ll easily identify which portions need more explanations and details.

Which icons are available to use in my tutorial?

To use icons in your tutorial, take the name of the icon, ‘details’ in this example, and write something like this in your tutorial:

{% icon details %}

Some icons have multiple aliases, any may be used, but we’d suggest trying to choose the most semantically appropriate one in case Galaxy later decides to change the icon.

The following icons are currently available:

icon[0][0]
announcement
icon[0][0]
arrow-keys
icon[0][0]
code-in
icon[0][0]
code-out
icon[0][0]
cofest, hall-of-fame, pref-permissions
icon[0][0]
comment
icon[0][0]
congratulations
icon[0][0]
copy, param-files, zenodo_link
icon[0][0]
curriculum, level
icon[0][0]
details, galaxy-info
icon[0][0]
docker_image
icon[0][0]
email
icon[0][0]
exchange, switch-histories
icon[0][0]
external-link, galaxy_instance
icon[0][0]
event, last_modification
icon[0][0]
feedback
icon[0][0]
galaxy-advanced-search
icon[0][0]
galaxy-show-active
icon[0][0]
galaxy-barchart
icon[0][0]
galaxy-bug
icon[0][0]
galaxy-chart-select-data
icon[0][0]
galaxy-clear
icon[0][0]
galaxy-columns, galaxy-history
icon[0][0]
galaxy-cross
icon[0][0]
galaxy-dataset-map
icon[0][0]
galaxy-delete
icon[0][0]
galaxy-dropdown, galaxy-history-options
icon[0][0]
galaxy-eye, solution
icon[0][0]
galaxy-gear
icon[0][0]
galaxy-history-archive
icon[0][0]
galaxy-home
icon[0][0]
galaxy-library, param-collection, topic
icon[0][0]
galaxy-link
icon[0][0]
galaxy-panelview, pref-list
icon[0][0]
galaxy-pencil, hands_on, param-text
icon[0][0]
galaxy-refresh
icon[0][0]
galaxy-undo
icon[0][0]
galaxy-rulebuilder-history
icon[0][0]
galaxy-save
icon[0][0]
galaxy-scratchbook
icon[0][0]
galaxy-selector, param-check
icon[0][0]
galaxy-show-hidden
icon[0][0]
galaxy-star, rating
icon[0][0]
galaxy-tags
icon[0][0]
galaxy-toggle, param-toggle
icon[0][0]
galaxy-upload
icon[0][0]
galaxy-wf-connection
icon[0][0]
galaxy-wf-edit
icon[0][0]
galaxy-wf-new, new-history
icon[0][0]
galaxy-wf-report-download
icon[0][0]
github
icon[0][0]
gitter
icon[0][0]
gtn-theme, pref-palette
icon[0][0]
help, question
icon[0][0]
history-annotate
icon[0][0]
history-share, workflow
icon[0][0]
instances
icon[0][0]
interactive_tour
icon[0][0]
keypoints, pref-apikey
icon[0][0]
language
icon[0][0]
license
icon[0][0]
linkedin
icon[0][0]
notebook
icon[0][0]
objectives
icon[0][0]
orcid
icon[0][0]
param-file
icon[0][0]
param-repeat, pref-notifications
icon[0][0]
param-select, pref-toolboxfilters
icon[0][0]
point-right
icon[0][0]
pref-info
icon[0][0]
pref-password
icon[0][0]
pref-identities
icon[0][0]
pref-dataprivate
icon[0][0]
pref-cloud
icon[0][0]
pref-custombuilds, tool-versions
icon[0][0]
pref-signout
icon[0][0]
pref-delete
icon[0][0]
purl
icon[0][0]
references
icon[0][0]
requirements
icon[0][0]
rss-feed
icon[0][0]
search
icon[0][0]
slides
icon[0][0]
sticky-note
icon[0][0]
time
icon[0][0]
text-document
icon[0][0]
tip
icon[0][0]
tool
icon[0][0]
trophy
icon[0][0]
tutorial
icon[0][0]
twitter
icon[0][0]
warning
icon[0][0]
wf-input
icon[0][0]
workflow-runtime-toggle
icon[0][0]
workflow-run
icon[0][0]
video
icon[0][0]
video-slides
icon[0][0]
version

Markdown


How can I create a tutorial skeleton from a Galaxy workflow?

There are two ways to do this:

  1. Use planemo on your local machine. Please see the tutorial named “Creating a new tutorial” for detailed instructions.
  2. Use our web service

General Questions


Can't find one of the tools for this tutorial?

To use the tools installed and available on the Galaxy server:

  1. At the top of the left tool panel, type in a tool name or datatype into the tool search box.
  2. Shorter keywords find more choices.
  3. Tools can also be directly browsed by category in the tool panel.

If you can’t find a tool you need for a tutorial on Galaxy, please:

  1. Check that you are using a compatible Galaxy server
    • Navigate to the overview box at the top of the tutorial
    • Find the “Supporting Materials” section
    • Check “Available on these Galaxies”
    • If your server is not listed here, the tutorial is not supported on your Galaxy server
    • You can create an account on one of the supporting Galaxies screenshot of overview box with available Galaxies section
  2. Use the Tutorial mode feature
    • Open your Galaxy server
    • Click on the curriculum icon on the top menu, this will open the GTN inside Galaxy.
    • Navigate to your tutorial
    • Tool names in tutorials will be blue buttons that open the correct tool for you
    • Note: this does not work for all tutorials (yet) gif showing how GTN-in-Galaxy works
  3. Still not finding the tool?

Running into an error?

When something goes wrong in Galaxy, there are a number of things you can do to find out what it was. Error messages can help you figure out whether it was a problem with one of the settings of the tool, or with the input data, or maybe there is a bug in the tool itself and the problem should be reported. Below are the steps you can follow to troubleshoot your Galaxy errors.

  1. Expand the red history dataset by clicking on it.
    • Sometimes you can already see an error message here
  2. View the error message by clicking on the bug icon galaxy-bug

  3. Check the logs. Output (stdout) and error logs (stderr) of the tool are available:
    • Expand the history item
    • Click on the details icon
    • Scroll down to the Job Information section to view the 2 logs:
      • Tool Standard Output
      • Tool Standard Error
    • For more information about specific tool errors, please see the Troubleshooting section
  4. Submit a bug report! If you are still unsure what the problem is.
    • Click on the bug icon galaxy-bug
    • Write down any information you think might help solve the problem
      • See this FAQ on how to write good bug reports
    • Click galaxy-bug Report button
  5. Ask for help!



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