Research Computing has developed a standalone utility package to make standalone generation, and especially subsequent updating, more convenient (See Download Standalone Example):

• make.m creates standalone with application-specific settings defined in makefile.m.
• makefile.m is a template with which application-specific parameters are set by user, such as the application’s directory path and file names (all of which in a single folder), toolboxes needed, and MATLAB runtime behaviors.

% makefile.m script -- serves as input template for make.m
% Make appropriate changes for your own app

%%1 Main program - either interface myStandalone or myApp
main = 'myStandalone'; % or myApp if not to use myStandalone
                       % Then, place myApp.m in current folder

%%2 Location of the rest of your m-files
srcFolder = 'codes2compile';

%%3 Your executable base name
exec = 'myExec';   % MATLAB release appended later

%%4 Example needs only Parallel Computing Toolbox (distcomp)
boxes = {};  % default: no toolboxes (other than MATLAB)
%% select 'all' to compile with ALL available toolboxes
%boxes = [boxes, {'all'}];         % MATLAB and all toolboxes
%boxes = [boxes, {'bioinfo'}];     % Bioinformatics_Toolbox
%boxes = [boxes, {'comm'}];        % Communication_Toolbox
%boxes = [boxes, {'curvefit'}];    % Curve_Fitting_Toolbox
boxes = [boxes, {'distcomp'}];    % Distrib_Computing_Toolbox
%boxes = [boxes, {'econ'}];        % Econometrics_Toolbox
%boxes = [boxes, {'finance'}];     % Finance_Toolbox
%boxes = [boxes, {'map'}];         % MAP_Toolbox
%boxes = [boxes, {'optim'}];       % Optimization_Toolbox
%boxes = [boxes, {'stats'}];       % Statistics_Toolbox

runopts = {};   % by default, no runtime options
%%5 Batch runtime options set (prepend with % to de-select)
runopts = [runopts, {'-singleCompThread'}]; % single thread
runopts = [runopts, {'-nodisplay'}];  % no graphics display

%%6 What to display when running standalone executable
credit = '-R ''-startmsg,Program authored by RESEARCHER''';

%% Kadin Tseng & Keith Ma
%% Research Computing Services, Boston University
%% Created:  September, 2014
%% Modified: October, 2014
%%           November, 2014
%%           January, 2015
%%           April, 2015

While the default is to include all toolboxes, selecting only the ones your application needs can speed up compilation significantly (mcc -p option).

If you are not sure which toolboxes your application needs, inmem can identify program dependencies.

For running in batch exclusively, compile with -R runtime options (see make.m).

>> make dryrun   % just a test. Shows what make would do
make will perform this task . . .
 mcc -mv -o myExecR2014b myStandalone ...
       -N -p distcomp  ...
       -R -singleCompThread -R -nodisplay  ...
       -R '-startmsg,Program authored by RESEARCHER' ... 
       -a codes2compile

******************************************************
    This is a test. No standalone generated.
******************************************************

>> make     % create/update executable whenever an m-file is modified
make will perform this task . . .
 mcc -mv -o myExecR2014b myStandalone ...
       -N -p distcomp  ...
       -R -singleCompThread -R -nodisplay  ...
       -R '-startmsg,Program authored by RESEARCHER' ... 
       -a codes2compile

Starts compiling . . .
Compiler version: 5.2 (R2014b)
Dependency analysis by REQUIREMENTS.
.  .  .  .  .
.  .  .  .  .
.  .  .  .  .
Removing: '/tmp/0c9ffTaZTeK_51711.auth'.
Removing: '/tmp/0c9ffvRmxWj_51711.auth'.
Removing: '/tmp/0c9ff7OjjFI_51711.auth'.
Generating file "/project/scv/kadin/matlab/compiler/test/readme.txt".
Generating file "run_myExecR2014b.sh".


******************************************************
Compile time for myExecR2014b is   111.57 seconds
******************************************************