I am working on a metagenomics project and trying to use Krona pie chart tool to visualize my data. In recent runs, it stopped generating the chart. Instead, it began to display hypertext coding for the HTML. Is there another tool for generating a pie chart or do I need to change formatting the d…

Ok, I was able to confirm the display problem. (The “term” warnings can be ignored). An open ticket has been created to fix this tool and another recently updated: https://github.com/galaxyproject/usegalaxy-playbook/issues/203 In short, use the prior version of the tool: Krona version 2.6.1. Switch…

I suspect administrator of your Galaxy updated the tool but did not add the updated version to the whitelist, so the resulting html is getting sanitized for security reasons and you see it mangled.

I think that may be the issue. Tool selections indicate that some of Kraken tools have been updated, and I started having issue with Krona after the “updated” signs began to appear. I am not sure what I can do, however.

You need to contact your administrator. Which Galaxy are you using?

The problem solved! I needed to pick the most recent version of Krona to run the data. It was helpful to have someone identify the problem and lead me to the solution. Thank you so much.

Hello. I have the same problem with Krona Pie Chart. What did you do to solve it? Thank you.

The prior user needed to switch to using the most current version of the tool: Krona pie chart from taxonomic profile (Galaxy Version 2.6.1.1). This is the version loaded from the tool panel at the public Galaxy Main server at https://usegalaxy.org . The source is: https://toolshed.g2.bx.psu.edu/repo…

Hi. I am using galaxy at https://usegalaxy.org/ All tools are executed correctly, except Krona Pie Chart. The results appear in green but it says “tput: No value for $ TERM and no -T specified”. When I try to visualize the results with the eye button, an html code appears. If I click on the “Visual…

Thanks for the extra information and reporting the problem. Reviewing now, more feedback once done.

Related Q&A: Graph browsing in GALAXY after FASTQC quality control

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Issue with Krona pie chart tool

metagenomics

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