Download All Genomes

Sometimes one wants to blat/blast on all Genomes. In this case, all of them have to be downloaded first to the local machine.

The easiest way is the following bash shell command:

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

Sometimes the 2bit files are in the nib directory, and thus an rsync command of:

 rsync -a --progress \
       rsync://hgdownload.soe.ucsc.edu/gbdb/${D}/nib/${D}.2bit ./${D}.2bit

is more appropriate.

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The following solution is a bit more flexible but in most cases unnecessary long:

This 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