Updating a Genome Browser Mirror

• As root cd to your html directory and update all html/javascript/image files:

 cd /var/www/html
 rsync -avzP rsync://hgdownload.soe.ucsc.edu/html/ ./

• As root, cd to your cgi-bin directory and update the cgi-bin files (=the programs of the browser):

 cd /var/www/cgi-bin
 rsync -avzP rsync://hgdownload.soe.ucsc.edu/cgi-bin/ ./

• go to your mysql directory and update the mysql tables. For each assembly, cd into its directory and run rsync like this:

 cd /var/lib/mysql/mm9
 rsync -avzP rsync://hgdownload.soe.ucsc.edu/mysql/mm9/ ./

As you might have modified your mirror, do not use the "--delete" option in this rsync command, as it would just overwrite your modifications.

• Update the Genbank files, most assemblies link to them in some way and they don't work without these files:

 cd /gbdb/genbank
 rsync -avzp rsync://hgdownload.soe.ucsc.edu/gbdb/genbank/ ./