Rendering svg from galaxy

1

Hi

I am having problems with rendering of svg output. Galaxy interprets this as text. Even if I use browser or some other tool that recognizes svg format, I get graphics, but no text (squares represent text). Is there anything I need to install for full svg support (I use android and windows 11)?

2

Hi @droslj

This forum is focused on the biomedical research platform Galaxy Project https://galaxyproject.org/.

We are completely unrelated to phones or other devices with a similar name. :slight_smile:

3

The issue I am trying to solve is the output of Variant Frequency Plot tool. I get for output .svg xml formatted data instead of graphics, which when input into into any of the tools that understands .svg format produces plot with graphics only, without text. I naturally assumed the tool produces correct output and that the problem is on my side (WEB browser).

But I guess there is a problem with tool though, because when I select some other output format (png), the tool produces the same graphics with no text.

Is there anything else I could try to get correctly formatted output?

4

Ok, thanks for explaining!

So, you think that the graphic output by the tool has incomplete metadata when read in by other downstream tools? Could you share a simple example? We can share that with the tool developer and fix anything that may be going wrong.

What we’ll need to troubleshoot, bug fix, or request an enhancement

  1. Shared history with an input dataset and a tool run that produces the odd output. If you could include two tool runs – one for each of png and svg – that would be best. The smallest data that presents the problem please.
  2. For this part “when input into into any of the tools that understands .svg format produces plot with graphics only, without text” please specify an exact tool and include that in the shared history. If there is more than one tool, go ahead and include a few of those.
  3. Then, screenshots or anything else you think might help to contextualize the problem. Meaning, if you ran this tool directly and have output that you like but cannot reproduce when using the same tool in Galaxy, include details about that use case.

How to share your use case

  1. Troubleshooting errors explains where to review the job inputs, parameters, logs. All the tool form options show up in that summary, and can sometimes solve problems. Or, the job logs might have something informative.
  2. Sharing your History explains how to generate a share link to the history with the example data. You can post that link back here.
  3. What information should I include when reporting a problem? explains the kind of technical details you can include. The shared history will contain much of that on the Galaxy side. However, any external tools you may be comparing to will not be included with details – we’ll need the exact tool name, where it was sourced, and the version along with any screenshots for that type of functionality comparison.

Let’s start there and apologies for misunderstanding! All operations and data you run or have in Galaxy are completely server side. Which web browser you are using never impacts computational results – maybe only display and only if using some exotic browser. If the latter ever seems like a factor, make sure cookies are enabled and try using Chrome, Safari, or Firefox instead.

5

I was using Variant Frequency Plot (Galaxy Version 1.0+galaxy3). The link to the history is:

The tool creates same graphic without text (PNG and svg when imported into some other tool capable of creating graphics from svg format).

6

Great, thanks for sharing this. I can see the missing text in the last png dataset. I am reviewing as to why.

7

Hi @droslj

Apologies for the delay. I was able to reproduce the problems with even with our test data.

When working at UseGalaxy.org, the output option is PDF (only).

A cross-test at UseGalaxy.eu produced correct graphics for PDF, PNG, SVG, and JPEG.

The tool has a bunch of usage disclaimers in the help section. Still, I think this is worth tracking and so created a ticket Fix-up graphics to support more output types for snpfreqplot at ORG · Issue #628 · galaxyproject/usegalaxy-tools · GitHub if interested or want to follow it. When that closes out, then you can try at UseGalaxy.org again.

For now, please try at UseGalaxy.eu if you haven’t already.

Thanks for reporting the issue!

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A post was split to a new topic: SVG troubleshooting