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.

New icons can be added in _config.yaml, and you can search for the corresponding icons at FontAwesome

The following icons are currently available:

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

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 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

  3. Check the logs. Output (stdout) and error logs (stderr) of the tool are available:
    • Expand the history item
    • Click on the 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
    • Write down any information you think might help solve the problem
      • See this FAQ on how to write good bug reports
    • Click Report button
  5. Ask for help!


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