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!