Glimma interactive link not work from limma tool

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ran the limma analysis for RNAseq analysis. The Glimma link at the report did not work. The error is as below,
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’, ‘https://www.github.com/shians/Glimma’);

While, the Glimma link I used to make from the Rstudio worked well before. So the portal from R to html should be fine.

Any suggestions would be appreciated.

1 Like
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Hi @shawn

Did you checkbox the tool under Admin > Allowlist? That is needed for HTML display.

If that is not the problem, a few questions:

  1. What version of Galaxy are you running?
  2. What version of the tool did you install? Was this sourced from the ToolShed? Did you use automatic dependency resolutions? Conda?
  3. Please note anything else special about your configuration.

Thanks!

4

Hi Jenna,
I do not know how to pull out the tool under Admin, Allowlist, as I had difficulty find the “Admin”, and “Allowlist” in the Galaxy.
I am using “https://usegalaxy.org/”.

also, I have no idea regarding the tools I installed on the Galaxy, or the version of Galaxy et al. So I appreciate that you can help me figure out how to find those information.

Thank you very much!

Shawn

1 Like
5

Hi @shawn

Apologies, I missed your follow-up! The original reply was about configuring this tool at your own server, not a public server. The tool is working at usegalaxy.org today. Perhaps this was a transient issue? Please let us know if you are still having trouble.

One thing to be aware of and maybe the source of your original problem: run limma at the same server where you are visualizing the report output, including the Glimma links, or the link-out graphs will not display. HTML data cannot be uploaded to any public Galaxy server – it has to be created at the server you are working at (for security reasons).

The most current version of any tool is at the top of the tool form, in this case:

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

Reference tutorial: 2: RNA-seq counts to genes