Download All Genomes

It may be a little more direct to run the following bash shell command:

mysql --user=genome --host=genome-mysql.cse.ucsc.edu -A -N \
      -e "select name from dbDb where active=1;" hgcentral | while read D
do
   rsync -a --progress \
       rsync://hgdownload.cse.ucsc.edu/gbdb/${D}/${D}.2bit ./${D}.2bit
done

Or, the following script will download the most current version for all genomes that can be rsynced from hgwdownload. It will only download 2bit files.

It is written in python and is using the rsync program. Note the -f parameter to override the selection of the genomes. use -h for help. Downloaded files go into the current directory.

File:RetrUcscGenomes.txt