The Galaxy community addresses issues and needs through resolving issues on Github.

Are you struggling to analyse something and need help?

Perhaps a tool isn’t working, or something similar?

Tip: Reporting usage problems, security issues, and bugs

• For reporting Usage Problems, related to tools and functions, head to the Galaxy Help site.
  • Red Error Datasets:
    • Refer to the Troubleshooting errors FAQ for red error in datasets.
  • Unexpected results in Green Success Dataset:
    • To resolve it you may be asked to send in a shared history link and possibly a shared workflow link. For sharing your history, refer to this these instructions.
    • To reach our support team, visit Support FAQs.
  • Functionality problems:
    • Using Galaxy Help is the best way to get help in most cases.
    • If the problem is more complex, email a description of the problem and how to reproduce it.
  • Administrative problems:
    • If the problem is present in your own Galaxy, the administrative configuration may be a factor.
    • For the fastest help directly from the development community, admin issues can be alternatively reported to the mailing list or the GalaxyProject Gitter channel.
• For Security Issues, do not report them via GitHub. Kindly disclose these as explained in this document.
• For Bug Reporting, create a Github issue. Include the steps mentioned in these instructions.
• Search the GTN Search to find prior Q & A, FAQs, tutorials, and other documentation across all Galaxy resources, to verify in case your issue was already faced by someone.

OR, have you found a definite problem with Galaxy and/or had an idea that could improve Galaxy?

Report an Issue on the correct Github repository:

• Tools: Need a tool added to a server? Check out the FAQ for this:

  Tip: Request Galaxy tools on a specific server

  To request tools that already exist in the Galaxy toolshed, but not in your server, please raise an issue at:

  • Europe - usegalaxy.eu | https://github.com/usegalaxy-eu/usegalaxy-eu-tools

  • USA - usegalaxy.org | https://github.com/galaxyproject/usegalaxy-tools

  • Australia - usegalaxy.org.au | https://github.com/usegalaxy-au/usegalaxy-au-tools/tree/master/usegalaxy.org.au

• Tools: Problem in a tool, such as a parameter you want to use is missing: Select your tool in the Galaxy interface

  Drop-down arrow to See in Tool Shed

  Development repository , then describe the issue there

• Tools: Request for developers to wrap a tool: Either you will have a domain-specific location (such as the Single-cell & sPatial Omics Community tool request form or you can post the request in our Intergalatic Utilities Commission: https://github.com/galaxyproject/tools-iuc
• User interface: https://github.com/galaxyproject/galaxy
• Subdomains / Galaxy Labs: Specific community content: https://github.com/galaxyproject/galaxy_codex or General Galaxy Labs issue: https://github.com/usegalaxy-au/galaxy-labs-engine
• Galaxy Community Hub: https://github.com/galaxyproject/galaxy-hub/
• Galaxy Training Network: https://github.com/galaxyproject/training-material

Warning: Be thorough!

Remember to be thorough when posting issues! Consider the FAQ on posting!

Tip: What information should I include when reporting a problem?

Writing bug reports is a good skill to have as bioinformaticians, and a key point is that you should include enough information from the first message to help the process of resolving your issue more efficient and a better experience for everyone.

What to include

1. Which commands did you run, precisely, we want details. Which flags did you set?
2. Which server(s) did you run those commands on?
3. What account/username did you use?
4. Where did it go wrong?
5. What were the stdout/stderr of the tool that failed? Include the text.
6. Did you try any workarounds? What results did those produce?
7. (If relevant) screenshot(s) that show exactly the problem, if it cannot be described in text. Is there a details panel you could include too?
8. If there are job IDs, please include them as text so administrators don’t have to manually transcribe the job ID in your picture.

It makes the process of answering ‘bug reports’ much smoother for us, as we will have to ask you these questions anyway. If you provide this information from the start, we can get straight to answering your question!

What does a GOOD bug report look like?

The people who provide support for Galaxy are largely volunteers in this community, so try and provide as much information up front to avoid wasting their time:

I encountered an issue: I was working on (this server> and trying to run (tool)+(version number) but all of the output files were empty. My username is jane-doe.

Here is everything that I know:

• The dataset is green, the job did not fail
• This is the standard output/error of the tool that I found in the information page (insert it here)
• I have read it but I do not understand what X/Y means.
• The job ID from the output information page is 123123abdef.
• I tried re-running the job and changing parameter Z but it did not change the result.

Could you help me?

What we ask from anyone raising an issue, is that you be willing to follow up with us. We may need more information or have different ideas, and it would be very helpful to continue the conversation to make the best fix or feature!

Still have questions?

Gitter Chat Support

Galaxy Help Forum

Information for GTN Tutorial Authors