Please be specific about your platform and version.
Usually if you have a PGP or GPG license, you can use SQR or a script to encrypt/decrypt a file.
In our case(unix) we have a script that send/receive files to our ftp server, call another script to encrypt/decrypt the files then ftp the files to anywhere. We also have a mail trigger that sends messages that the files are sent or receive(sort of acknowledgement).