PAM authentication can be rather platform dependent. Note that on (e.g.) Linux distributions you can use a variety of authentication mechanisms. Typically, setting up shadow authentication is easier.

If you do select PAM then the script will add the required --with-auth=pam flag in the configuration stage.

You must then set up your /etc/pam.conf file or create a suitable file in the /etc/pam.d directory as appropriate for your system. The following assumes your system uses the /etc/pam.d mechanism.

The 'handle' for EMBOSS authentication is 'emboss_auth' so you will need to create a /etc/pam.d/emboss_auth file (or equivalent). Example contents for this file appear below:

#%PAM-1.0
auth	required	/lib/security/pam_stack.so service=system-auth
account	required	/lib/security/pam_stack.so service=system-auth
password	required	/lib/security/pam_stack.so service=system-auth
session	required	/lib/security/pam_stack.so service=system-auth

Secondly, you will need to add the following line to the tomstart script created by the installation script.

setenv LD_PRELOAD /lib/libpam.so