Fwd: Local Genome browser installation

[john herbert]

Dear UCSC team,

Hi; I want to use the UCSC GB to show a novel bacteria genome, and I started this using your install script to make a GBiC genome browser. For install, I used the bash script browserSetup.sh, found in the Kent git hub src tree. The browser is has housed at; 

http://185.38.149.100

It works to an extent; I ran what I think are OK commands with (cloned from git Kent); 

bash ./browserSetup.sh -o # to work offline

bash ./browserSetup.sh cgiUpdate

bash ./browserSetup.sh mirror sacCer3

mysql hgcentral -e 'update defaultDb set name="sacCer3" where genome="Yeast"'

So the install works great, thanks. However, I get an error when I start browsing; 

If I can get this working, it will be great. 

Please can you give me the best way for me to install a custom genome and a couple of tracks? I get the idea and will try from google searches but you are one of the best experts as I understand. I did join the UCSC mailing list. 

Thank you very much for any advice, 

Kind regards,

John. 

Dr. John Herbert,

BBSRC Postdoctoral Researcher.  

Room 325,

3rd floor Life Sciences building,

Integrative Systems Biology,

Institute of Integrative Biology,

University of Liverpool,

Crown Street.

Liverpool

L69 7ZB.

United Kingdom.

j.m.h...@liverpool.ac.uk

[Chris Villarreal]

Dear Dr. Herbert

Thank you for your question about GBiC. It seems like setting up an assembly hub would be ideal as it allows you to display your novel genome within the browser, and you won't have to download all of our data. The only concern is if you wanted to keep this information private, anyone with the URL can access the hub. Here is more information on assembly hubs:

https://genome.ucsc.edu/goldenPath/help/hgTrackHubHelp.html#Assembly.

If you still want to use GBiC we have fixed the issue, please re-download the installation script from our git repo and re-run the "mirror" command. Note, you will need to have about 500GB of free disk space.

I hope this is helpful. If you have any further questions, please reply to gen...@soe.ucsc.edu. All messages sent to that address are archived on a publicly-accessible Google Groups forum. If your question includes sensitive data, you may send it instead to genom...@soe.ucsc.edu.

-Chris V

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