"From peaks to genes" error with UCSC Main

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Hello,

Following the tutorial “From peaks to Genes” I have an error uploading data with UCSC Main. The error is: The uploaded file contains invalid HTML content.

The settings used are those:

image
image1280×747 43.7 KB

image
image1280×638 31.5 KB

Thanks for any help!

1 Like
2

Hi @apventeo

Thanks for posting publicly about the error. The behavior can be reproduced, and is unexpected. Your settings are correct.

I am looking into why and how to solve this, and will post updates back here once more is known.

Thanks!

3

Hello again @apventeo

The problem seems to be with how the data is moving into Galaxy. We’ll need to figure out why.

The file content itself is fine. I was able to download the file directly (instead of checking the “send to Galaxy” box), then upload the file to Galaxy. You can get a copy from my history.

How to:

  1. Click on this shared history link to open it in a browser window https://usegalaxy.eu/u/jenj/h/test-galaxy-intro-peaks2genes
  2. Use the “Import” button found in the top left corner
  3. Go into the User → Histories menu in the top masthead, and navigate to the imported history
  4. Copy the dataset into your history. Copy a dataset between histories

Or, you can just work in the imported history. It is yours to work in, copy data out of, run more jobs in, then later even delete as you want :). Copies of histories are fully independent, so if anyone else runs into this problem before we can fix it, they can do the same when working with this tutorial, or can download/upload the particular file they need.

Update2: The issue has been reported to the UCSC team at their mailing list and is pending a correction. https://groups.google.com/a/soe.ucsc.edu/g/genome/c/-OLkG9MnwMk

Thanks again for reporting the problem!

4

The ucsc genome browser is redirecting to https now for better security.
Your client can either be made to support the redirect, or much better is to update galaxy to use https:// urls for UCSC Genome Browser now. This include the callback to UCSC go grab the contents after a user does hgTables sendToGalaxy checkbox and button. Galaxy is seeing a web page that is also a redirect when it fetches a http:// page.

commandlinePrompt> curl -v Table Browser

 > GET /cgi-bin/hgTables HTTP/1.1
 > User-Agent: curl/7.29.0
 > Host: genome.ucsc.edu
 > Accept: */*
 >
 < HTTP/1.1 302 Found
 < Date: Fri, 15 Sep 2023 05:39:08 GMT
 < Server: Apache/2.4.6 (CentOS) OpenSSL/1.0.2k-fips mod_fcgid/2.3.9
 < Location: https://genome.ucsc.edu/cgi-bin/hgTables
 < Content-Length: 224
 < Content-Type: text/html; charset=iso-8859-1
 <
 <!DOCTYPE HTML PUBLIC "-//IETF//DTD HTML 2.0//EN">
 <html><head>
 <title>302 Found</title>
 </head><body>
 <h1>Found</h1>
 <p>The document has moved <a href="https://genome.ucsc.edu/cgi-in/hgTables">here</a>.</p>
 </body></html>
1 Like
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Oh thank you @Galt_Barber for helping to clarify what is going on!

For Galaxy users

We are currently addressing the change in the Galaxy code base. Details: UCSC Genome Browser redirects http to https. Use https URLs instead. Change was made for improved user security. · Issue #16700 · galaxyproject/galaxy · GitHub

When the final changes are determined and made, those will need to be implemented by the administrators of Galaxy servers. This is still in progress. For now, downloading and uploading data from the UCSC Table Brower to Galaxy is the workaround, and this applies to all Galaxy servers, public or private.

General updates will post back to this topic. The issue ticket linked above will have the technical details.

Thanks!

6

Update:

As of today, UCSC has rolled back the change and all Table Browser queries should work as they do normally. Meaning, no need to download/upload as separate steps.

The change will now be implemented in about two weeks. It involves some server-level modifications to allow the direct data transfer. How end-users experience these functions will not change.

Thanks to everyone to reported the problem & helped to get it solved!