There are reference files (plain fasta files zipped up) available on http://updates.iontorrent.com/reference/ to use with your TS.
I would think it trivial for someone to write a shell script to curl / wget the reference and manually (or commandline ) create the reference index in the proper location.
But as of now, I can't find how to
1) manually create the reference index so that it shows in the realignment plugin as well.
2) reference files (there's only hg19 on the website)
2 isn't a big problem since the fasta requirements are simple enough.
no blank lines
no non IUPAC sequences
it's something u can include in the bash script with sed
Ok shall bother my PGM bioinfo FAS soon.
otherwise, I am stuck with the routine of downloading the sequences and zipping it and uploading on a win box (I do not have sliverlight on my Ubuntu)