Alastair Kerr wrote:

first a quick word of thanks to the galaxy devs: this is a great system thanks, we are using it to roll-out our own in-house tools/scripts. We are now in the about to gather the UCSC data files so that the rest of the tools (liftover, Fetch sequences/alignments etc) work. I am wondering whether there is an easy way of gathering this data? e.g. are there any wget /rsync scripts available or does each data source need to be added manually.

Hi Alastair, We don't really have an easy way to do this, as the data comes from a wide number of sources, made available via different methods. That said, I did write a perl script a few years ago to download sequences and alignments from UCSC. Note that it only downloads the axt's, and Galaxy now uses maf for pairwise alignments. http://www.bx.psu.edu/~nate/get_from_ucsc.pl --nate