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jar2exe is commercial software so you would probably need to buy a license.

For your simulation executable you could also consider Launch4j:
http://launch4j.sourceforge.net/
It is free and Open Source and works great - I have used it in several
production environments. 
It has also all the features you might ever need in a professional
application, yet is very easy to use.

The most convenient deployment scenario is to keep your own code in a jar
that will be used to generate an executable while keeping all dependencies
such as the MASON library in a separate sub-folder e.g. ./lib. It makes
managing dependencies for your deployed project much easier. In the proposed
deployment scenario all you need to do is to add lib/* to the "Classpath"
tab in launch4j GUI.  

Best regards,
Przemyslaw Szufel

On Mon, 25 Mar 2013 02:14:28 +0000, Steven Saul <[log in to unmask]> wrote:

>You can also create an exe file from a jar file with this software:
>
>http://www.jar2exe.com/
>
>
>
>________________________________________
>From: MASON Multiagent Simulation Toolkit [[log in to unmask]]
on behalf of Sean Luke [[log in to unmask]]
>Sent: Sunday, March 24, 2013 10:07 PM
>To: [log in to unmask]
>Subject: Re: Creating a jarred application file
>
>Absolutely.  MASON can be jarred up with your code, no problem.  If you
want the jar file to launch your application when double-clicked on or
whatnot, you just need to specify the right entry class in your jar Manifest.
>
>Sean
>
>On Mar 24, 2013, at 9:39 PM, Steve Kraska wrote:
>
>> For the MASON program I am creating, I would like to be able to make a
runnable
>> jar version as an application. The end goal is for other people to
download and
>> use the program without having to go through the process of installing
the rest of
>> the MASON materials unnecessarily.
>>
>> The MASON documentation only discusses creating jar files for applets but as
>> mentioned I would like to create a downloadable application version of my
>> program. Is it possible to create an application of a MASON-driven project?
>>
>> Thank you,
>> Steve Kraska