Frequently Asked Questions

Tutorial Questions

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:

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

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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