Duplicated entry at GBiC My Hubs prevents loading private assembly hub

[David da Silva Pires]

Hi.

I have just configured a VM with GBiC with Ubuntu 18.04. When I go to:

My Data --> Track Hubs

the default tab is Public Hubs. After some time trying to load the page, the following message appears:

Warning/Error(s):
http://research.nhgri.nih.gov/manuscripts/Burgess/zebrafish/downloads/NHGRI-1/hub.txt duplicated, aborting

Does anyone know how to fix this in order to be possible to access the tab My Hubs and connect to my own assembly hub?

Thanks in advance for your help.

Best regards.

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DAVID DA SILVA PIRES Especialista de Laboratório LABORATÓRIO DE CICLO CELULAR Tel: +55 11 2627-9734 www.butantan.gov.br

[Daniel Schmelter]

Hello David,

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:

https://hgdownload.soe.ucsc.edu/hubs

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:

https://genome.ucsc.edu/goldenpath/help/gbib.html#CustomizingGbib

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:

http://genome.ucsc.edu/FAQ/FAQlink.html#hubUrl

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,

Daniel Schmelter
UCSC Genome Browser

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[David da Silva Pires]

Hi Daniel.

Thanks for the fixes.

Your tips were really very helpful to us.

I'm amazed about the amount of development that all of you have done since I learned how to configure UCSC Genome Browser for the first time some years ago. I didn't know GenArk and it is really amazing to have access to so many assemblies. It will be very useful to us.

Since I am working more with GBiC these days than with GBiB, it was also very helpful to know that the same commands applied for customization can be used on both kinds of instances. This means that many help pages that were ignored by me should now be revised.   :-)

Thank you again for all the help.

Best wishes.