Why does my SignalTap II Logic Analyzer file not get included as part of my script-based flow?

To enable a specific SignalTap™ II Logic Analzyer file (.stp) for your project, ensure your Quartus II Settings File (.qsf) file contains the following assignments:

set_global_assignment -name ENABLE_SIGNALTAP ON
set_global_assignment -name USE_SIGNALTAP_FILE <.stp file name>
set_global_assignment -name SIGNALTAP_FILE <.stp file name>

You then need to perform the following command prior to running your compilation:

quartus_stp <project name> --stp_file <.stp file name> --enable

This command extracts the relevant information from your .stp and writes it into your .qsf.

For more information on SignalTap II Logic Analyzer command line options see the "SignalTap II Command-Line Options" section of the Design Debugging Using the SignalTap II Logic Analyzer (PDF) chapter of the Quartus II Handbook.