Trackster won’t let me add multiple datasets, it keeps getting stuck when I click ‘add new’ in ‘loading histories’. Help!
Yes, Trackster is a bit problematic right now. Specifically, add more datasets to an existing visualization does not work (at least for all cases I have tested). The same is true whether the visualization is based on a built-in database or a custom genome build’s database. We are working to fully characterize the problem and get it fixed quickly. A development ticket exists (too cryptic to post, and we are not quite sure if it will fully resolve the issue) – so I’ll post the end-user oriented issue ticket back once completed, likely early Monday. More testing is needed first. But we wanted to let you know now that we’re aware of the problem, plan to fix it with priority, and appreciate that you took the time to create a public post about the issue. It will help both you and others.
Until Trackster issues are resolved, alternative genome browsers are listed in an expanded dataset when the database (genome) is assigned. Common options linked are below. Depending on any particular dataset’s metadata (datatype, database), other visualization options may display as linked resources.
- UCSC Main – Only some genomes are available. If a link does not show up, it is not at UCSC.
- IGV – Are a few versions, with links presented as appropriate. The publically hosted version has many genomes available. A local version is easy to download/install, has a GUI interface, and can have even more pre-built indexes added in. IGV also has the option to create your own custom genome index in a local IGV, matching a custom genome build created in Galaxy, to view multiple datasets together with the genome fasta backbone. If you just want to browse a single dataset from a novel genome, a scaffold index will be created on the fly.
More details for using IGV are in this prior Q&A. You can also click on the tags I added to your post to find more related Q&A in the content of different use cases.
Thanks for reporting the issue!
Full issue ticket: https://github.com/galaxyproject/usegalaxy-playbook/issues/276
Once that closes out, the issue is resolved. Until then, expect problems with Trackster. Use alternative browsers instead.