[Genome] Questions about installing Genome Browser locally

[Hiram Clawson]

Good Afternoon Yufeng:

Do you want to just blat a query sequence against some particular
target genome ?  Or do you actually want to operate a local Genome
Browser WEB site.

It is not required to operate a local Genome Browser WEB site in
order to operate blat with a query sequence against a target genome.
The command line program blat which you can build in the source
tree will do the blat function without any database or a genome
browser WEB site.

If you want your local installation of the Genome Browser WEB site
to display a different genome than our standard set of genomes,
you would need to build the database tables for that genome.
Is this what you want to do ?

--Hiram

Yufeng Zhai wrote:
> Dear Sir or Madam,
> 
> I am trying to install the Genome Browser on our local server, the  
> system are Mac OSX, the compilation works fine, but I still have a  
> couple of questions before I can make it work. My questions are:
> 
> 1) Ours purpose is to blat and browse some custom species that  are  
> not displayed on UCSC site. But I can't find any general program that  
> can add species, could you tell me what rule or program should I use  
> to add species for blat?
> 
> 2) When I do blast locally, it will gave me error message that say  
> "Couldn't find host blatN. h_errno 1", does this mean that I have to  
> start a blat server first (using gfServer)? If I started some blat  
> server on localhost, should I also modify the corresponded record in  
> database hgcentral? for example, the field like nibPath in dbDb, and  
> field host, port in table blaServers?
> 
> Thank you very much for your help
> 
> Yufeng