[galaxy-user] FTP and command line access in Galaxy

Hi, We'd like to set up our local Galaxy to be able to import data (fastq sequences) from an ftp site (with a username/password) into a user's account. Does Galaxy support FTP or would we have to write a wrapper script to do it via HTTP and use the standard data connection methods as described in http://bitbucket.org/galaxy/galaxy-central/wiki/DataSources? My next question is, are there any recommendations to make it possible to allow access to Galaxy imported and generated data to be processed outside of Galaxy e.g. via command line? I guess using sudo and cp is an option but I wondered if anyone had any more thoughts on this! Thanks for any advice, Steve