[Genome] genome browser local copy question

[Ross Lazarus]

Ann, I have a cut down (hg18 only) local build of the genome browser installed 
and working here, and the genome graphs work fine locally. The docs describe 
making custom tracks available via urls, but I'm going to guess that adding our 
own custom tracks so they're available for *all* local users as part of the 
built-in track list on our local copy of the browser is non trivial? I couldn't 
find any documentation  on doing that...

I would like to make some genome graph data available more or less permanently 
to my investigators on our local copy. I can't find this anywhere in the docs so 
I'll ask you :) - where is the 48 hour nominal retention time for user uploaded 
genome graph data configured - I'd like to change it to make these permanent

Again, thanks in advance for your time in helping me get this figured out and 
thanks for making this excellent software available!

Ann Zweig wrote:
> Hello Ross,
> 
>     Glad you like the new Genome Graphs tool.  Currently there is no way 
> to pre-configure the track, nor is there a direct interface to the tool 
> yet.
> 
>     You are more than welcome to run the code locally.  The Genome 
> Browser and Blat software are free for academic, nonprofit, and personal 
> use. A license is required for commercial use.
> 
> How to download the software: 
> http://genome.cse.ucsc.edu/FAQ/FAQlicense#license3
> 
> You can obtain the source tree either via CVS:
>     http://genome.ucsc.edu/admin/cvs.html
> or a zip file:
>     http://hgdownload.cse.ucsc.edu/admin/jksrc.zip
> 
> Please note the build instructions:
>     http://genome.ucsc.edu/admin/jk-install.html
> 
>     All of the kent utilities output their usage message and command
> line options by running them with no arguments.
> 
> 
> Regards,
> 
> ----------
> Ann Zweig
> UCSC Genome Bioinformatics Group
> http://genome.ucsc.edu
> 
> 
> Ross Lazarus wrote:
>> Your new genome graphs utility looks great. I was just about to try to 
>> write a custom track but am now saved a vast amount of work. We're 
>> about to get a whole genome snp data set so this might be extremely 
>> useful for our investigators.
>>
>> Is there any way for me to call it with most of the file reading 
>> values filled in - or are any other more direct machine interface 
>> (json/soap/whatever) available or planned? We'd be happy to take a 
>> poke at running it locally if the code is available?
>>

-- 
Ross Lazarus MBBS MPH, Director of Bioinformatics
Channing Laboratory, 181 Longwood Ave., Boston MA 02115, USA.
Voice: +617 525 2730  Fax: +617 525 0958