Hi Nate,
If there are problems with this method please do let us know so we can look in to it.
Your thoughts about using the FTP upload as you describe should work fine. Unfortunately it is not written so generically, so you'll need to set an FTP server name in the appropriate option in the config file despite not having one, which will be displayed in the help text on the upload form. However, this server name is not verified in any way and can be any string.
I'm trying to set up a directory using FTP Upload (without an FTP server :-)) as discussed above. I added a test directory for the a user 'auser' ftp_upload_dir = /data/galaxy/ ftp_upload_site = localhost to the universe.ini We are using LDAP, so I set up a test directory called /data/galaxy/auser@molbiol.ox.ac.uk but having added a file in can't see anything in the FTP upload section or the 'Files uploaded via FTP' section even when 'auser' is logged in. Is there something else I need to do? Thanks, Steve