Comment: Troubleshooting errors

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!
Comment: Why not use Excel?

You could just as easily use Excel to answer the same question, and if the goal is to learn how to use a tool, then either tool would be great! But what if you are working on a question where your analysis matters? Maybe you are working with human clinical data trying to diagnose a set of symptoms, or you are working on research that will eventually be published and maybe earn you a Nobel Prize?

In these cases your analysis, and the ability to reproduce it exactly, is vitally important, and Excel won’t help you here. It doesn’t track changes and it offers very little insight to others on how you got from your initial data to your conclusions.

Galaxy, on the other hand, automatically records every step of your analysis. And when you are done, you can share your analysis with anyone. You can even include a link to it in a paper (or your acceptance speech). In addition, you can create a reusable workflow from your analysis that others (or yourself) can use on other datasets.

Another challenge with spreadsheet programs is that they don’t scale to support next generation sequencing (NGS) datasets, a common type of data in genomics, and which often reach gigabytes or even terabytes in size. Excel has been used for large datasets, but you’ll often find that learning a new tool gives you significantly more ability to scale up, and scale out your analyses.

Comment: Using tutorial mode

Tools are frequently updated to new versions. Your Galaxy may have multiple versions of the same tool available. By default, you will be shown the latest version of the tool. This may NOT be the same tool used in the tutorial you are accessing. Furthermore, if you use a newer tool in one step, and try using an older tool in the next step… this may fail! To ensure you use the same tool versions of a given tutorial, use the Tutorial mode feature.

Warning: Not all browsers work!
  • We’ve had some issues with Tutorial mode on Safari for Mac users.
  • Try a different browser if you aren’t seeing the button.
Comment: How does the GTN ensure our training materials are FAIR?

This infrastructure has been developed in accordance with the FAIR (Findable, Accessible, Interoperable, Reusable) principles for training materials Garcia et al. 2020. Following these principles enables trainers and trainees to find, reuse, adapt, and improve the available tutorials.

The GTN receives a 100% score on the FAIR Checker, as noted in our recent news post

10 Simple Rules Implementation in GTN framework
Plan to share your training materials online Online training material portfolio, managed via a public GitHub repository
Improve findability of your training materials by properly describing them Rich metadata associated with each tutorial that are visible and accessible via schema.org on each tutorial webpage.
Give your training materials a unique identity URL persistency with redirection in case of renaming of tutorials. Data used for tutorials stored on Zenodo and associated with a Digital Object Identifiers (DOI)
Register your training materials online Tutorials automatically registered on TeSS, the ELIXIR’s Training e-Support System
If appropriate, define access rules for your training materials Online and free to use without registration
Use an interoperable format for your training materials Content of the tutorials and slides written in Markdown. Metadata associated with tutorials stored in YAML, and workflows in JSON. All of this metadata is available from the GTN’s API
Make your training materials (re-)usable for trainers Online. Rich metadata associated with each tutorial: title, contributor details, license, description, learning outcomes, audience, requirements, tags/keywords, duration, date of last revision. Strong technical support for each tutorial: workflow, data on Zenodo and also available as data libraries on UseGalaxy.*, tools installable via the Galaxy Tool Shed, list of possible Galaxy instances with the needed tools.
Make your training materials (re-)usable for trainees Online and easy to follow hands-on tutorials. Rich metadata with “Specific, Measurable, Attainable, Realistic and Time bound” (SMART) learning outcomes following Bloom’s taxonomy. Requirements and follow-up tutorials to build learning path. List of Galaxy instances offering needed tools, data on Zenodo and also available as data libraries on UseGalaxy.*. Support chat embedded in tutorial pages.
Make your training materials contribution friendly and citable Open and collaborative infrastructure with contribution guidelines, a CONTRIBUTING file and a chat. Details to cite tutorials and give credit to contributors available at the end of each tutorial.
Keep your training materials up-to-date Open, collaborative and transparent peer-review and curation process. Short time between updates.
Comment: Why host your materials with the GTN?

The short version is we’re a popular, FAIR training materials platform, and we want to be a home for your training materials.

Your content in front of the world

As of June 2023 the GTN sees around 60k visitors per month. Please see our public page view monitoring for more details.

FAIR

We go to great lengths to make sure our training platform is completely FAIR. See this FAQ for the details on how we achieve that.. All of our materials have extensive BioSchemas markup ensuring they’re easily accessible to search engines. Our materials are automatically indexed by TeSS, and we are working on a WorkflowHub integration.

Accessible

We regularly test our pages with a thorough suite of accessibility tools, as well as via screen reader.

Not Just Galaxy

Our name can be a bit misleading! While a lot of our tutorials are focused on Galaxy, we have multiple growing topics which are unrelated to Galaxy.

All of these topics are using the GTN as a platform to disseminate their materials far and wide.

Features

Do you need

Then choose the GTN.

  1. Garcia, L., B. Batut, M. L. Burke, M. Kuzak, F. Psomopoulos et al., 2020 Ten simple rules for making training materials FAIR (S. Markel, Ed.). PLOS Computational Biology 16: e1007854. 10.1371/journal.pcbi.1007854