You could try something like this:

xclip -o | gpg --encrypt --armor | xclip -selection clipboard

That should encrypt the clipboard for you, and if you put it in a script to 
be executed without a console I'm pretty sure that gpgagent will prompt you 
for the password :) You might need some additional arguments to the gpg 
command line tho, but it's a starting point.

- Chris

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