ioncube_encoder5 /projects/myproject –into /encoded-projects
ioncube_encoder5 –with-license key.php –passphrase yourpassphrasehere /projects/myproject –into /encoded-projects

with make_license:

./make_license –passphrase yourpassphrasehere –header-line ‘‘ –property “UserName=’Chuck Norris'”
or
/make_license –passphrase yourpassphrasehere –header-line ‘‘ \
–property “UserName=’Chuck Norris'” –allowed-server example.com,www.example.com