Minimal Browser Installation: Difference between revisions
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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 [http://genome.ucsc.edu/license/index.html License Instructions]. | 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 [http://genome.ucsc.edu/license/index.html 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: | |||
[http://genome-source.cse.ucsc.edu/gitweb/?p=kent.git;a=tree;f=src/product src/product/] and | |||
[http://genome-source.cse.ucsc.edu/gitweb/?p=kent.git;a=tree;f=src/product/scripts src/product/scripts/] | |||
Usually a browser installation wants to be a subset of genomes compared to the entire [http://genome.ucsc.edu/ UCSC Genome Browser] | Usually a browser installation wants to be a subset of genomes compared to the entire [http://genome.ucsc.edu/ UCSC Genome Browser] | ||
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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 | 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 | Enter a '''defaultGenome=<your species>''' specification in your '''/cgi-bin/hg.conf''' file. See notes in the | ||
[http://genome-source.cse.ucsc.edu/gitweb/?p=kent.git;a=blob;f=src/product/ex.hg.conf 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:<BR><pre> | For the /gbdb/ data area, at a minimum you will need the .2bit file or the nib files for the assembly. This is either:<BR><pre> | ||
/gbdb/<database>/<database>.2bit | /gbdb/<database>/<database>.2bit | ||
or | or for older genome assemblies: | ||
/gbdb/<database>/nib/*.nib | /gbdb/<database>/nib/*.nib | ||
</pre> | </pre> | ||
Revision as of 17:13, 14 July 2011
Minimal Browser Installation
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/
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 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?)
See also
Building a new genome database
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)
