(TODO: verify this entire section!!! Is it even necessary!!)
The individual assemblies are only required if the mysql tables are going to be build from scratch or if direct access to the assemblies is needed for research purposes (apparently unusual). It is generally preferable to download the mysql tables directly (covered later in this document) and so this step can probably be skipped.
Here is an example of how to rsync a single database assembly (Human)
Get Human March 2006 full data set (hg18: 13.0 Gb) by doing:
mkdir -p $WEBROOT/goldenPath/hg18/database/ rsync -avzP --delete --max-delete=20 \ rsync://hgdownload.soe.ucsc.edu/genome/goldenPath/hg18/database/ $WEBROOT/goldenPath/hg18/database/
This process must be repeated for each of the desired databases.
A list of all possible assemblies found on browser can be created by issuing the command
rsync -v rsync://hgdownload.soe.ucsc.edu/genome/goldenPath/ > goldenPath.dat
A list of all mysql data tables can be created by issuing the command
rsync -v rsync://hgdownload.soe.ucsc.edu/mysql/ > gb_tables.dat
The lists retrieved by these two commands will be quite similar. In both cases it will be necessary to edit the directory names returned to be certain only data tables are being included.