Minimal Browser Installation

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, a subset of data can be downloaded.

A minimal browser database needs five tables:

• grp
• chromInfo
• trackDb
• hgFindSpec
• any other table, for example 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

Currently (August 2006) the gateway page expects the human hg18 database to exist in order to function without difficulty. This concept of the default genome needs to be a configuration item in the cgi-bin/hg.conf file to avoid this dependency. This needs to be fixed in src/hg/lib/hdb.c.

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
/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.

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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