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Listen to serial port at STARTUP using java with arguments on Debian(Rasbian)

I've been stuck two weeks trying to figure out how to run this at startup.
I use the following chain of commands on the terminal:
1. source ~/.bashrc
2. source ~/.tinyos.sh
3. java net.tinyos.tools.Listen -comm serial#/dev/ttyUSB0:telosb | python demo.py`
The third command uses java to listen to the serial port and pipes it to a python script which cleans, converts and uploads to mysql localhost.
This works fine on ssh terminal. But ive tried using nohup+update-rc.d, upstart, systemd, crontab to make it run on startup and it just wont work! When I reboot and check logs / database, its as if the command never happened. I need this to run like a daemon and continue running until shutdown.
Thanks a lot.

How are you trying to execute the program ? Are there are permission issues accessing / executing the script ?
Which version of debian are you running - look at upstart scripts if you are running Jesse+
I'd put those three lines in a bash script and use upstart scripts to trigger them on start. Another option is to use supervisord to make sure that your scripts run and restart if for any reason the program crashes.

Java JAR file does not execute in startup script in Ubuntu 14.04

The following process normally works for my startup scripts. However, when I introduce a command to execute a JAR file, it does not work. This script works while I am logged in. However, it does not work as a startup script.
In /etc/init.d I create a bash script (test.sh) with the following contents:
#!/bin/bash
pw=$(curl http://169.254.169.254/latest/meta-data/instance-id)
pwh=$(/usr/bin/java -jar PWH.jar $pw &)
echo $pwh > test.txt
Make script executable
In /etc/rc.local, I add the following line:
sh /etc/init.d/test.sh
Notes:
I make a reference to the script in /etc/rc.local, because this script needs to run last after all services have started.
Please do not ask me to change the process (i.e., create script in /etc/init.d/ and reference it from /etc/rc.local), because it works for my other startup scripts.
I have tried adding nohup in front of java command, and it still did not work.
Thanks

As written, there is insufficient information to say what is going wrong. There are too many possibilities to enumerate.
Try running those commands one at a time in an interactive shell. The java command is probably writing something to standard error, and that will give you some clues.

Usage of ssehexec task in Jenkins build doesn't stop its execution

I have an Ant Task in the Jenkins Ant Execution Plugin, as a Post Build Step, to remotely run a shell script in one of our servers. The shell scripts starts a java process in the background. When I execute the shell script on the server directly it starts the java process in the back ground and comes out. When I run it from Jenkins via the sshexec task the shell script is run, but it never comes out and the Jenkins Build waits.
Later when I added the timeout attribute onto the sshexec it times out after the given number of milliseconds, but the Jenkins build is shown as failed. How do I make the sshexec task to come out cleanly from the shell script execution?
Here is my ssheexec task
<sshexec host="${deploy.host}" username="${deploy.username}" password="${deploy.password}" command=". /etc/profile; cd ${deploy.path}; sh start.sh i1" trust="true" timeout="10000" />
The start.sh file is as given:
nohup java -Xms512m -Xmx1024m -cp calculation.jar com.tes.StartCalculation $1 &
echo $! > calculation-$1-java.pid

It looks like, the ssh executed job is not fully daemonized. Starting with nohup is not sufficient in many cases.
See the discussion that related to it (in a different context)
The issue is that you are not closing your file descriptors when you
push something into the background. The & is fine when you are in a
shell, but is not enough when you want to disconnect and leave a
process running, you need the process to disconnect from the shell.
.... Fix to to correct the script.
If someone writes a naive service script that does not properly detach
from the terminal, I want to know the first time that that script is
used in a deployment - the SCM changes will enable the breaking change
to be quickly identified.
It is wrong to hide the problem to enable incorrect code to be
released to production - and I would not be happy if the first I knew
about it was when a production system administrator complained.
If this is the same problem, you need to daemonize the script

Running a Java Application on a Shared Drive from Windows Task Scheduler Client Side

First, just wanted to thank everyone in advance for helping with this, let me take you on my journey...
Task: Run a Java application that is located in a folder on a file server using Windows Task Scheduler, simple enough.
The caveat, is that I would like to utilize the task scheduler option of "Run whether user is logged on or not." and this seems to be a tricky function...
I have set my account as the account that the task is to run under.
What have I tried?
Creating a task based on these actions:
Java.exe -jar "path to share jar"
Java.exe -jar "path to local jar"
Javaw.exe -jar "path to share jar"
Javaw.exe -jar "path to local jar"
All have had the same result with the "Run whether use is logged on or not." option : 0x1
Next, I tried creating a batch file to run this on my behalf and changed the task to run that batch file and I got all the same results. I have read that utilizing the "Start in (optional)" field of an action may solve the problem, but it did not.
After that, I created a .vbs file with code similar to the following:
Set WshShell = CreateObject("WScript.Shell")
WshShell.Run chr(34) & "C:\Batch Files\syncfiles.bat" & Chr(34), 0
Set WshShell = Nothing
This achieved a 'silent run', but task scheduler still did not run with the "Run whether use is logged on or not.", and ended in 0x1.
All of these work fine with the "Run only when user is logged on." option.
The reason I want to do it whether I am logged on or not, is because I want to run my application before I come in to work.
Update:
I've disocvered a few things. In power options for Windows, I had to enable the ability for scheduled tasks to wake the computer, felt kind of dumb about that one.
Using a simpler task - one that just creates a blank text file - this option works fine. I belive the problem lies with executing Java.

The task needs a user to run. It doesn't have to be the user that is logged in, of course, but a user is needed anyway.
Make a batch file (or equivalent) that works when you launch it manually
Schedule the same batch file (with cmd /c c:\full\path\to\batch.bat) to run as yourself, with your password and everything.
Now you are ready to debug your problem
The user Windows will use to run your task when no one is logged needs all the tools configured and working. For exemple, does local service have all the path and registry settings set ? Is the share readable by that user (the SYSTEM account does not have network credentials).
To help in debugging, use psexec. This command line will allow you to run your script under the SYSTEM account. Something like
psexec -dies cmd /c c:\full\path\to\batch.bat
+Welcome to SO !

Execute shell command in Tomcat

So I have the following problem: I have a web service running inside a Tomcat7 server on Linux. The web service however has to execute some commands (mostly file operations such as copy and mount). Copy I've replaced with java.nio, but I don't think that there is a replacement for mount.
So I'm trying to execute shell commands out of my Tomcat Java process. Unfortunately it doesn't execute my commands. I've implemented the execution of shell commands in Java before. So my code should be correct:
Process pr = Runtime.getRuntime().exec("mount -o loop -t iso9660 <myimage> <mymountpoint>");
pr.waitFor();
<myimage> and <mymountpoint> are absolute paths, so no issues there either.
I've debugged my commands and they are working when executed on the console.
I've tried sending other commands. Simple commands such as id and pwd are working!
I've tried using /bin/bash -c "<command>", which didn't work.
I've tried executing a shell script, which executes the command, which didn't work.
I've tried escaping the spaces in my command, which didn't work.
So I've digged even deeper and now I'm suspecting some Tomcat security policy (Sandbox?), which prevents me from executing the command. Since security is no issue for me (it's an internal system, completely isolated from the outside world), I've tried a hack, which became quite popular just recently:
System.setSecurityManager(null);
This didn't work either. I'm using Java7 and Tomcat7 on RHEL6. Tomcat7 is just extracted! I don't have any files in /etc/.. or any other folder than /opt/tomcat/, where I've extracted the zip from the Tomcat home page. I've searched the /opt/tomcat/conf folder for security settings, but all I could find was the file catalina.policy, where it didn't seem like I could set some security level for shell commands.
Any ideas?

A few things:
System.setSecurityManager(null);
you have just killed the security of your application.
Yes, Tomcat is running as root. If I execute id I'm root as well.
Fix this immediately!
Now on to the question. You shouldnt have Tomcat executing anything, you need to defer this to a separate process whether that be a shell script or another Java program. This should also remove what (I hope) was a dependency on root running Tomcat. It should be possible to perform this command as a non-privileged user that cannot log into the system normally. You would do this by configuring /etc/fstab and supplying that same user the permissions to do this. From a pure security POV the process that mounts should not be owned by the tomcat user. Nor should the tomcat user ever be root. So to recap:
1) Stop running Tomcat as root
2) Create a separate process outside of the context of Tomcat to run this mount
3) Create a tomcat user, this user should not be able to log into the system nor should it be a privileged user (admin,super user, etc)
4) Create a process user, this user should be configured exactly as the tomcat user
5) Edit /etc/fstab giving the process user the necessary permissions to mount correctly.

It's generally a bad idea to use the single-string form of Runtime.exec. A better option is to use ProcessBuilder, and split up the arguments yourself rather than relying on Java to split them for you (which it does very naïvely).
ProcessBuilder pb = new ProcessBuilder("/bin/mount", "-o", "loop", /*...*/);
pb.redirectErrorStream(true); // equivalent of 2>&1
Process p = pb.start();
You say you're on RHEL so do you have selinux active? Check your logs and see if this is what's blocking you (I think it's audit.log you're looking for, it's been a few years since I've used selinux). If this does turn out to be the problem then you should probably ask on superuser or serverfault rather than SO...

I'm not sure if that's the problem you are having, but I've seen issues when Runtime.exec() is used without reading the associated output buffers. You can find a detailed explanation and potential solutions here. Reading the output and error streams can also help you figure out what's going on at the OS level when you run the command.

I've recently had to do something like this from a Swing app.
You'll probably be able to pull it off with ProcessBuilder, as in Ian's answer, but I found that once things start to get complex, it's easier to write a shell script that does what you want, enabling you to pass as few parameters as possible. Then use ProcessBuilder to invoke the shell script.
If you're invoking anything that has more than really minimal output, you'll also have to read the output and error streams to keep the process from blocking when the output buffers fill, as it seems you are already doing.

I use sudo -S before command and for the tomcat7 user: tomcat7 ALL=(ALL) NOPASSWD:ALL