Thanks for the insight and information - it was great!. However, I eventually got it to work by setting environmental variables in the script, so:

#!/usr/local/bin/perl
print "start import!\n";
$ENV{"USER"} = "user";
$ENV{"PASS"} = "password";
open (FOO, "|/path/to/bin/foo -args_here /path/to/filename.txt")
 || die "can't open up command pipe: $!\n";
close(FOO) || die "can't close command pipe: $!\n";
print "exiting gracefully!\n";

Once again, thank you for your help.

MadraghRua
yet another biologist hacking perl....