Minimal Browser Installation

Usually a browser installation wants to be a subset of genomes compared to the entire UCSC Genome Browser. Instead of the entire rsync of everything mentioned in the Mirror Instructions or on this wiki (Browser installation) , sometimes you want only a subset of data from one genome. This is more work but possible. We call this a "Minimal Browser" in the following. This page shows you a minimal browser that shows only the genome sequence and the gaps. This is not a useful genome browser at all, but will get you started.

A license is required for commercial download and/or installation of the Genome Browser binaries and source code. No license is needed for academic, nonprofit, and personal use. To purchase a license, see our License Instructions.

Please note the full discussion in the README.* files and scripts to assist with these browser installation procedures in the source tree directory: src/product/ and src/product/scripts/

A minimal browser database needs six tables:

grp
chromInfo
trackDb
hgFindSpec
gold
gap

The gateway page needs the hgcentral database to function. The hgcentral database can by copied directly from the MySQL data files from the ftp server ftp://hgdownload.cse.ucsc.edu/mysql/hgcentral or loaded from the SQL text file at http://hgdownload.cse.ucsc.edu/admin/hgcentral.sql

Enter a defaultGenome=<your species> specification in your /cgi-bin/hg.conf file. See notes in the src/product/ex.hg.conf file for this option.

For the /gbdb/ data area, at a minimum you will need the .2bit file or the nib files for the assembly. This is either:

/gbdb/<database>/<database>.2bit
or for older genome assemblies:
/gbdb/<database>/nib/*.nib

Various tracks use other files in this directory. If you don't care about all the tracks, you won't need other files here.

For the genbank sequences, you can check the gbExtFile table for your database to see exactly which files are used by that assembly in /gbdb/genbank/
Extract the "path" column from that table and use that list in a --files-from specification for your rsync.

Partial Mirrors

See this page: Browser Mirrors (they should probably be fused into one?)

User notes

I made hgBlat work on my local browser installation by putting the full hostnames into hgcentral.blatservers, e.g. 'blat4' was replaced by the output of `blat4.cse.ucsc.edu`. I wonder if it wouldn't be a good idea to mention this in the mirroring instructions somewhere. --- max

Before you start using our blat servers, you need to verify with us that you have permission. We can't have everyone with a mirror site simply use our blat servers, the load would take them down for everyone. See also: Kent Informatics for a commercial blat license.

A nice command from Paul McKenna: UPDATE blatServers SET host=concat(host,’.cse.ucsc.edu’); Max 15:11, 3 February 2007 (PST)

Minimal Browser Installation

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