Resolved: glimma interactive link not working

usegalaxy.org support
1

Hi - I clicked on the Glimma links in my limma result page, and no matter which one I click on, I get a page with only these texts:

“Glimma Plots function clickAdjPval() { if ($(‘th:contains(Adj.PValue)’).text()) $(‘th:contains(Adj.PValue)’).click(); // sort table by adjusted p-value }
glimma.init.processCharts(); glimma.init.processTables(); glimma.init.processLinkages(); glimma.init.processInputs(); d3.select(‘.container’) .append(‘div’) .style(‘text-align’, ‘right’) .text('Generated by ') .append(‘a’) .text(‘Glimma’) .attr(‘href’, ‘GitHub - Shians/Glimma: Glimma R package’);”

Could this be a server-side problem?

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Hi @billy.l
It looks like a server issue. Maybe the server admins can help? ping @nate
Here is my history Galaxy
The links are in limma-voom Report datasets.
I tried several limma-voom versions,
Kind regards,
Igor

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Update:

I was originally testing with an older dataset. I just reviewed another older rerun with the older version of Limma and it produced a report with usable Glimma graphics! So, the problem is inconsistent and appears to have been resolved some time ago (between March and May of 2021).

You could also simply rerun without changing the tool version to see if that is enough. If not, please share back your history so I can review your original run, the rerun, and the tool version. Maybe there is something else going on now.

Hi @billy.l

Glimma reports seem to be working for me at UseGalaxy.org when using the most current version of the tool.

limma Perform differential expression with limma-voom or limma-trend (Galaxy Version 3.58.1+galaxy0)

However, I can reproduce the problem when running a much older version. It appears to have an installation problem. I’ve ticketed the issue here → (link pending) Not reproducible!

limma Perform differential expression with limma-voom or limma-trend (Galaxy Version 3.38.3+galaxy3)

What to do

  1. Go to your existing dataset run of Limma (that used the older version)
  2. Click on the rerun icon (FAQ: Different dataset icons and their usage)
  3. Change the tool version to the most current using the Options menu (top of the tool form, find the listing under FAQ: Changing the tool version)
  4. The original settings should be preserved but maybe still double check :slight_smile:
  5. Start the rerun, then find the functional graphic in the new report

I can’t tell if the workflow associated with this tutorial Hands-on: 2: RNA-seq counts to genes / 2: RNA-seq counts to genes / Transcriptomics includes the older tool version or not, but that is part of what I am checking next, along with how many UseGalaxy servers may be impacted.

Should you have a workflow yourself, or if you are using a tutorial workflow, and either includes the problematic tool version, try updating the workflow to use the newer tool version. Note: new tool versions do not always change the output, since some are technical changes (improved performance, bug fixes). I can’t think of a meaningful difference with respect to the tutorial above, or the one after, so this workaround should be fine if that is what you are doing.

Thanks for reporting the problem! And thanks for the ping @igor :rocket:

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Thanks @jennaj ! I rechecked the informations on my limma reports today and it seems that I was using the latest 3.58.1 when I encountered the problem. The glimma links work now. I also remember when I downloaded the reports and used the html link locally, the interactive page works. So I’m now just wondering if the problem was confined to that earlier date, and whatever that problem was, it’s fixed now.

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Hi @billy.l

Ok great! I really appreciate the feedback, and I agree. It was an older problem and the new versions are working. Let’s close this out :slight_smile: