When attempting to preview a BAM file on usegalaxy.org, I encounter the following error message:
Unknown or invalid visualization: igv
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HI @TEr_LeE
It looks like a bug in the latest Galaxy version. Thank you for reporting it!
Hi @jennaj, it seems there is an issue with BAM preview in the latest Galaxy. I have a BAM file for dm6. Clicking at Eye icon (Display) shows an error for Preview option:
Unknown or invalid visualization: igv
Why igv for Preview? It should show the file content, isn’t it?
Visualize works just fine. I can see the file at UCSC GB. Have not tested IGV.
Kind regards,
Igor
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I am having the same issue, were you able to fix it?
Sorry for the inconvenience here – during the release candidate for 25.0 we got a little ahead of our skis. What you’re seeing is Galaxy trying to use the visualization-first framework for previewing datasets (Visualization-First Display functionality by dannon · Pull Request #20190 · galaxyproject/galaxy · GitHub). Deployed on main, bam is currently configured to use igv.js, which isn’t quite yet available.
Thanks for the report, and we’ll get this resolved as soon as possible.
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XRef tracking → Config for "visualization plugin" missing for type like bam and others: loss of functionality · Issue #20338 · galaxyproject/galaxy · GitHub
Hello,
Do you have a timeline on when this will be fixed? I am still seeing the same issue.
Thank you!
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Hi @jmachuca10
If you are looking for the preview in SAM format that Galaxy used to show, you can generate that with the same tool we used to use directly.
- Samtools view
- Use all defaults, except adjust the Output format to be SAM
- Or, use all defaults, except to report What would you like to look at? Just the header
- Or, any of the other slices/combinations. But you don’t have to report all of it unless that is what you want. We were only showing the very top of the file (header and maybe a few data lines), since these are usually really large.
The IVG integration is still pending, and isn’t that same content, it instead will be more like a genome browser view.
To see your data in IGV now, the link also already exists but in a different place, one tab over under Visualize.
Click on the eye-icon to first reach the Preview tab.
Then click into the Visualize tab to see all of the original display options. IGV (local) is what we are trying to get integrated automatically under Preview.
Important to note:
- My screenshot is showing more Display options because the example dataset here happens to have a “database” assignment that is supported by the online versions of a the other browser websites. Meaning, these “know” what the genome assembly looks like and that this BAM’s data coordinates are based on it.
- For BAM data without a “database” assignment that is known, the
IGV (local)option is always available, and you’ll get a browser without the genomic backbone. This is how it has always worked, so nothing is different. - BUT – you can always set up your custom genome in Galaxy and also in IGV, give them the same custom “database” key, and your links from datasets will work to see the richer view with that
IGV (local)link.- This is one topic that explains how → Opening Unicycler assemblies with IGV local - #4 by jennaj
- The main new step (for some users) will be another reason to create Custom Database assignments for custom genomes → FAQ: How to use Custom Reference Genomes?
- Later on in Galaxy, the integrated IGV view will make use of the native server database and/or custom database information if that exists, but it won’t be running the SAMTools view command for you anymore (that I know of!). This is a major upgrade and I’ll be happy to see it too.
So, there isn’t a reason to wait to get anything that existed before (it has always been there in the alternative locations/methods and still does), and when the integration is added in later, it should save everyone a few steps, plus provide a richer view if the database assignment is made (perhaps new to some people who are using custom genomes since it is completely optional)! 
I hope this helps, but that is a lot of information! Please let us know if you have questions about any of it.