How do you plan on using the file?
For a single analysis job, you can directly enter the ftp url as the input file. The GP server will copy from the ftp site behind the scenes before running the analysis command line. From the job input form, select 'Add Path or URL...', and paste the full ftp url.
If you plan on reusing this file for multiple analyses I suggest using GenomeSpace (
http://www.genomespace.org/). It's very easy to link your GP account to GenomeSpace and then to link GenomeSpace files from the GP user interface.
Regards,
Peter