Frequently Asked Questions

Tutorial Questions


Which icons are available to use in my tutorial?

Tip: 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 %}

The following icons are currently available:

icon[0]
announcement
icon[0]
code-in
icon[0]
code-out
icon[0]
cofest
icon[0]
comment
icon[0]
congratulations
icon[0]
curriculum
icon[0]
details
icon[0]
docker_image
icon[0]
email
icon[0]
exchange
icon[0]
event
icon[0]
feedback
icon[0]
galaxy-barchart
icon[0]
galaxy-bug
icon[0]
galaxy-chart-select-data
icon[0]
galaxy-clear
icon[0]
galaxy-columns
icon[0]
galaxy-cross
icon[0]
galaxy-dropdown
icon[0]
galaxy-eye
icon[0]
galaxy-gear
icon[0]
galaxy-history
icon[0]
galaxy-home
icon[0]
galaxy-info
icon[0]
galaxy-library
icon[0]
galaxy-panelview
icon[0]
galaxy-pencil
icon[0]
galaxy-refresh
icon[0]
galaxy-rulebuilder-history
icon[0]
galaxy-save
icon[0]
galaxy-scratchbook
icon[0]
galaxy-selector
icon[0]
galaxy-star
icon[0]
galaxy-tags
icon[0]
galaxy-toggle
icon[0]
galaxy-upload
icon[0]
galaxy-wf-connection
icon[0]
galaxy-wf-new
icon[0]
galaxy-wf-report-download
icon[0]
galaxy_instance
icon[0]
github
icon[0]
gitter
icon[0]
gtn-theme
icon[0]
hall-of-fame
icon[0]
hands_on
icon[0]
help
icon[0]
history-annotate
icon[0]
history-share
icon[0]
instances
icon[0]
interactive_tour
icon[0]
keypoints
icon[0]
language
icon[0]
last_modification
icon[0]
level
icon[0]
license
icon[0]
linkedin
icon[0]
new-history
icon[0]
notebook
icon[0]
objectives
icon[0]
orcid
icon[0]
param-check
icon[0]
param-collection
icon[0]
param-file
icon[0]
param-files
icon[0]
param-repeat
icon[0]
param-select
icon[0]
param-text
icon[0]
question
icon[0]
references
icon[0]
requirements
icon[0]
rss-feed
icon[0]
search
icon[0]
slides
icon[0]
solution
icon[0]
sticky-note
icon[0]
time
icon[0]
text-document
icon[0]
tip
icon[0]
tool
icon[0]
tool-versions
icon[0]
topic
icon[0]
trophy
icon[0]
tutorial
icon[0]
twitter
icon[0]
warning
icon[0]
wf-input
icon[0]
workflow-runtime-toggle
icon[0]
workflow
icon[0]
workflow-run
icon[0]
video
icon[0]
video-slides
icon[0]
zenodo_link

Markdown


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

Tip: 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?

Tip: If a Tool is Missing

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?

Tip: Troubleshooting errors

When someting 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.
    • Sometime 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
  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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