3 months ago by
There were some configuration changes between the two servers (UCSC main and Galaxy main), but those are now resolved.
If you are still having problems, maybe you need to assign the
database metadata attribute to the BAM dataset?
Please be aware that only databases that are hosted by UCSC can be displayed there automatically by Galaxy's "display at UCSC main" link. Datasets will include the link if the
database is a match for what UCSC refers to as the
dbkey. To check if your genome is there, go to https://genome.ucsc.edu and review the available database/dbkeys -- the information will be noted in the landing page per-genome/release/build.
The "display with IGV" links operate the same way -- the database assigned in Galaxy needs to be an exact match for the IGV database. Some will be hosted on the public site and some will not be (this cannot be modified). But if needed, you can set up your own local IGV and either load the genomes that they have made available in the IGV resource bundles or you can load up your own custom genome IGV (and give it a "database" name that will match Galaxy's). Make sure the database names are the same between Galaxy/IGV or this will fail. The genome build/version matters -- to avoid problems try not to mix up builds (eg: mm9 with mm10). This may involve creating and assigning a Custom Build to the database in Galaxy. Also, be sure to have your local IGV open first (if used) before using the "IGV local" link or that will also lead to problems.
Galaxy FAQs: https://galaxyproject.org/support/
IGV download/resources/support: https://software.broadinstitute.org/software/igv/
Thanks! Jen, Galaxy team