Thanks for getting back to us with those explanations.
We have fixed the issue of duplicate hubUrl entries in the hubStatus and hubPublic SQL tables. These updates will go out in our next version release, which is next Tuesday, June 22nd at 3pm. We hope this will resolve your issue regarding loading private assembly hubs.
Furthermore, we are actively developing a method to keep that multi-terabyte file separate from anywhere a mirror might accidentally download it, which keeping the alignment data available.
I applaud your research on non-model organisms. It may be helpful to hear that we have greatly expanded our assembly hub offerings to include many GenBank/RefSeq assemblies in a collection called "GenArk". This resource can be found through searching in our Gateway page or through the page below:
In regards to having specific default settings that point to a particular assembly or tracks, we recommend you read the following guide to "Customizing your GBiB". It should apply to GBIC mirrors equally:
It may also be useful to create a variety of links to different assemblies to put into menus. You can find our guide to link creation here:
I hope this was helpful! For further communication, please reply-all to gen...@soe.ucsc.edu. Those emails are archived in a public help forum. For private questions, you may send emails instead to genom...@soe.ucsc.edu.
All the best,
UCSC Genome Browser
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