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Exit java program to linux command

I'm making a little tool that handles a sort of exotic device, with lots of options to manage it etc. One of them would be to scan for tty ports, find the right one then throw the user to "minicom" with some parameters for example.
How can I make java completely exit while running a specific command, under certain condition, after such exit ?
Initial thoughts would be to use a bash script, scan the return value, communicate via files etc.A fully functional interactive serial console in Java would be the dream, but the ones I try right now can't seem to even find tty ports now.

Most processes on linux follow a call stack where process A calls process B which calls process C.
Wen process C terminates, the control goes back to process B, and so on.
It sounds like in this case you want java to call minimum, but when java is finished, return to the parent shell.
I am not aware of any way you can terminate a JVM upon a call to another process (returning to the JVM's parent when it terminates). Perhaps with some clever C calls using JNI, but that isn't really java anymore and could create new problems.
You could have the JVM wrap the target process and pass through the user inputs and outputs. Alternatively, use file communication, e.g. the java program writes the command-line to a file, that the parent bash script executes after the JVM terminates, but that is a bit of a kludge.

Is it better to launch a Java app once and sleep or repeat launching and killing?

I have a Java application that needs to run several times. Every time it runs, it checks if there's data to process and if so, it processes the data.
I'm trying to figure out what's the best approach (performance, resource consumption, etc.) to do this:
1.- Launch it once, and if there's nothing to process make it sleep (All Java).
2.- Using a bash script to launch the Java app, and when it finishes, sleep (the script) and then relaunch the java app.
I was wondering if it is best to keep the Java app alive (sleeping) or relaunching every time.

It's hard to answer your question without the specific context. On the face of it, your questions sounds like it could be a premature optimization.
Generally, I suggest you do what's easier for you to do (and to maintain), unless you have good reasons not to. Here are some possible good reasons, pick the ones appropriate to your situation:
For sleeping in Java:
The check of whether there's new data is easier in Java
Starting the Java program takes time or other resources, for example if on startup, your program needs to load a bunch of data
Starting the Java process from bash is complex for some reason - maybe it requires you to fiddle with a bunch of environment variables, files or something else.
For re-launching the Java program from bash:
The check of whether there's new data is easier in bash
Getting the Java process to sleep is complex - maybe your Java process is a complex multi-threaded beast, and stopping, and then re-starting the various threads is complicated.
You need the memory in between Java jobs - killing the Java process entirely would free all of its memory.

I would not keep it alive.
Instead of it you can use some Job which runs at defined intervals you can use jenkins or you can use Windows scheduler and configure it to run every 5 minutes (as you wish).
Run a batch file with Windows task scheduler
And from your batch file you can do following:
javac JavaFileName.java // To Compile
java JavaFileName // to execute file
See here how to execute java file from cmd :
How do I run a Java program from the command line on Windows?

I personally would determine it, by the place where the application is working.
if it would be my personal computer, I would use second option with bash script (as resources on my local machine might change a lot, due to extensive use of some other programs and it can happen that at some point I might be running out of memory for example)
if it goes to cloud (amazon, google, whatever) I know exactly what kind of processes are running there (it should not change so dynamically comparing to my local PC) and long running java with some scheduler would be fine for me

Executing a shell script in java as a thread

I need to execute a shell script in a java program. I figured out that i can use processbuilder and runtime.exec.. but my webserver times out every 180 sec but my script execution takes more than that..i do not want to use process for this approach.. is there any other way where i can use thread for this execution.
thanks.

I'm assuming that the response from the script is intended for humans to read.
Good interface design, and human nature, suggests that if your script is taking over 180 seconds to run, then it should be run separately from the web server. On linux, I would suggest putting it into 'cron', and letting it run on a regular basis. You would only serve the results of the script via the web server, with a response time in seconds instead of minutes.
If your script depends on parameters from the http request, or other information that is only available from within the web server's environment, you have the following choices.
If you can figure out the likely combinations of parameters, run the
script automatically for each combination of parameters,
again only serving the results through the web.
If the majority of the time is spent in a single command, and the
results of that command don't change much between runs, move that
command into a separate script that runs automatically, and use the
results of that separate script to build the web response.
Break the response up into segments, only showing a portion of the
data for each request, allowing the user to page through the
response. The script would be rewritten to only request the
necessary data for the current page, reducing the amount of time
needed to obtain that data.
Rewrite the script in a compilable language, which might gain you enough time to make running it for every request reasonable. However, if the problem is a database query, this won't do you any good. You'd have to go with option (3), whether you rewrote it in a compilable language or not.
Without additional information, like an example of the script, or a description of where you're getting the results from, that's the best I can do.

A process can run several threads, but they still are parts of the process.
So, all threads inside a java program are the threads of the java process, and a thread cannot run another program's threads.
A shell script is ran by a program : the shell program ! (/bin/bash or /bin/sh)
Anyway a shell script will mostly ran other programs inside several other processes.
No, you cannot run a shell inside a thread of java.

In general, if you have code that is separate from your Java program, such as code that is in a separate script, then there is no justification for why your code would execute an outside script when that code could be instead integrated into the program. It is insecure at best. Your basically allowing arbitrary code to be executed by your program since the outside script is editable. What you are doing sounds to me almost like it should be confined either a unit test or a build task.
As a unit test task and you could use a threaded JUnit runner to run your outside script during the test phase of your project.
Also, separately from your program, you could also execute it using a Gradle task and by using the parallellforks option that Gradle has.

Repeated execution of a java file

I have a java file which i want to execute repeatedly on a machine. The file should be executed automatically as soon as the previous instance of the file execution is over. How to achieve this?

Use bash script in a loop call your executable
for i in 1 2 3 4 5 .. N
do
java executable
done

Java provides an environment in which a program will function as you (or someone else) have written it.
The operating system specifics will determine how that program is started. If you want the program to launch each time the previous copy has finished, you need to wrap the launching of the java program with a loop in the scripting language supported by that operating system, or convert the program to be a system service / daemon.
Other techniques exist, but they actually don't launch the second program after the first completes. They either:
Launch a second copy of the program immediately (unless already found). The program is written to do nothing while it can detect it's "launcher" is running. Upon loss of one process, the second becomes responsible for the processing (and the launching of it's standby failover).
Capture shut down / crash events and launch a copy of the program when quitting, which actually has two programs running at the same time, but for a short duration. This is commonly done; but is technically unsound as there are many ways a program might crash before being able to launch a new process.

You can write a simple perl or python script that would work on both windows and linux.
#!/usr/bin/perl
$N = 100;
for($i = 0; $i < $N; $i++){
system('/full/path/to/java -cp full_class_path my.class.Name');
}
You can call this script in a java file or execute it on command line.
Runtime.getRuntime().exec("perl script.pl")

How to open a matlab session from java and execute matlab scripts

I have a matlab script that takes an input mat file and produces an output file.
Currently I have a shell script that is able to execute this script.
I am executing this script from Java using ProcessBuilder class and all is working well.
I need to perform the matlab script execution very often from java and each time script executes the mcr process is created, script executes and mcr terminates.
i like to have the MCR process open and have a matlab session open towards java , so that same process is kept alive so i can execute scripts multiple times in the same session.
I find matlabcontrol seems to be suitablefor this.
How to configure the MatlabProxyFactory with the MCR location and LD_LIBRARY_PATH
which i am setting in my shell script and execute my script in a same session?
I also came across a tool MATLAB JA Builder but i cannot use this at the moment as its not Free.
Thanks!

If you are using matlabcontrol I don't think you need the shell script, just tell it the name of the m-file you want to be run. If you want to keep the shell script in conjunction with a ProcessBuilder, you have to start the process once and keep a reference to its input stream. When you want a command executed, you write it that stream. Also, you have to keep a thread alive to empty the output and error streams of Matlab, otherwise they will get full and Matlab will hang. If you want to go with this, I recommend looking at the source of this project (which I am a contributor to). The class you are interested in is RCaller. It does more or less the same, except it invokes R and not matlab.