Hi Roy,
I have a local galaxy installation running on OSX and have been testing it with genomes: hg18 and sacCer2. I've added these to builds.txt, and added paths to the appropriate files in alignsec.loc and faseq.loc. When I go to the upload tab in galaxy and select one of these genomes from the pull-down menu, I get the following error after execution:
It doesn't look like there's anything wrong with your genomes. What seems to be happening is that after selecting a build, you accidentally submit the form before choosing a file to upload. (Yes, this is a terrible error message -- we're planning to fix it soon.) Also, note that if you press the enter key in the build field, it will submit the form.
Try choosing the file to upload first, then the build, and finally submit the form to do the upload. Let us know if this doesn't fix the problem.
Thanks, J.