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Having a hard time with linux command calls in Java with exec()

I'm trying to use Runtime.getRuntime().exec() to call a program as if it was called from the terminal, but it just crashes with a fatal error after reading the first file.
In the terminal I run the command like so:
mace4 -c -f inputFile.in > outputFile.out
It works as expected, reading from the first file and outputting in the second one.
In Java I try to run it this way:
String args[] = new String[]{"mace4", "-c", "-f", inputFileName ,">",outputFileName};
try {
String s;
Process proc = Runtime.getRuntime().exec(args, null, new File("/home/user/workDirectory/"));
BufferedReader br = new BufferedReader(
new InputStreamReader(proc.getInputStream()));
while ((s = br.readLine()) != null)
System.out.println("line: " + s);
proc.waitFor();
proc.destroy();
As soon as the program reaches the end of the first file, it throws this:
Fatal error: read_all_input, file > not found
The program is quite old and I can't seem to find a way to get a more detailed error out of it..
I tried calling it with these arguments {"sh or bash", "-c", "mace4", "-c", "-f", inputFileName ,">",outputFileName} which makes the program run and then freeze (or at least nothing appears in the console)..
Am I calling the terminal command wrong and if yes what should I change?
PS: this is my first question here, if I missed anything, I'm sorry..

It looks like you're trying to use the Bash output redirection operator >. This redirects the output of the program you're running to a file (or another program)
This answer explains how to do this using ProcessBuilder which should work for what you're trying to do here.
For example:
ProcessBuilder pb = new ProcessBuilder("mace4", "-c", "-f", inputFileName);
pb.redirectOutput(new File(outputFileName));
Process p = pb.start();

run a .sh file using java

I want to run a .sh file using java. I want a terminal to be opened and then I can execute another commands in the same terminal and finally destroy it.
I already used ProcessBuilder but I could not accomplish this.
My piece of code:
ProcessBuilder pb = new ProcessBuilder("/home/omar/ros_ws/baxter2.sh");
Process p = pb.start();
This method used to work in another code, but I don't know why it's not working in mine.
Thanks in advance

How do you know that it doesn't execute? Maybe you just aren't seeing its result. You should get p.getInputStream() after executing and print in your console, like:
BufferedReader reader = new BufferedReader(new InputStreamReader(p.getInputStream()));
String line = null;
while ((line = reader.readLine()) != null)
{
System.out.println(line);
}
Also if you're using jdk 7+, try:
pb.redirectOutput(Redirect.INHERIT);
pb.redirectError(Redirect.INHERIT);
Process p = pb.start();

Does your program output an error, or is your program not interacting with the file?
I would suggest trying the directory method within ProcessBuilder.
Process p = null;
ProcessBuilder pb = new ProcessBuilder("baxter2.sh");
pb.directory("/home/omar/ros_ws");
p = pb.start();
If this doesn't work, you should also look into user permissions for the file that you're trying to access.

I think you should grant the .sh file the executable permission to the OS user used to run the java program by using the below command.
chmod u+x baxter2.sh

Using ProcessBuilder to find version of Java

I am trying to use Java to find out the versions of Java installed on a machine. I have:
List<String> commands = new ArrayList<String>();
commands.add("java.exe");
commands.add("-version");
ProcessBuilder pb = new ProcessBuilder(commands);
pb.directory(new File("C:\\Program Files\\Java\\jdk1.6.0_45\\bin"));
Process p = pb.start();
BufferedReader stdInput = new BufferedReader(new InputStreamReader(p.getInputStream()));
while ((s = stdInput.readLine()) != null) {
System.out.println(s);
}
However, when this is run, the while loop is never executed as the stdInput is empty. If I take out the commands.add("-version"), it will get the input that is output when running "java.exe" command on command line, so it seems adding the -version arguement is causing issues and this also indicates that the directory and java.exe commands are correct. Any help would be appreciated.

The output of java -version is sent to the error stream - reading from that stream should result in the proper output:
BufferedReader stdInput = new BufferedReader(new InputStreamReader(p.getErrorStream()));
Alternatively, you can call redirectErrorStream(true) to merge the Input and Error streams. If you just wish to just print to the command line, you can use inheritIO on the ProcessBuilder.
The currently running java version can be found without the need for a ProcessBuilder by retrieving the appropriate System property
System.out.println(System.getProperty("java.version"));

java -version prints to stderr. Try using:
ProcessBuilder pb = new ProcessBuilder(commands).redirectErrorStream(true);
That will put stderr in the same stream as stdout and the rest of your code can look as it does now.

Invoking a command in Run Window

Opening the Run window (Windows + r) and running a command -> I want to trigger this same command using Java. I tried this using :
Runtime.getRuntime().exec(command);
But this did not worked. Please let me know how to achieve this.

Can you try this:
ProcessBuilder pb=new ProcessBuilder("explorer");
pb.redirectErrorStream(true);
Process process=pb.start();
BufferedReader inStreamReader = new BufferedReader(
new InputStreamReader(process.getInputStream()));
while(inStreamReader.readLine() != null){
//do something with commandline output.
}

Use this command:
Runtime.getRuntime().exec(new String[] {"cmd.exe", "/c", "start", "winword"});
This successfully runs Microsoft word (winword), which is not runnable directly through cmd. The start command behaves the same as run does.
Add parameters afterwards like this:
Runtime.getRuntime().exec(new String[] {"cmd.exe", "/c", "start", "winword", "C:\\Example.docx"});

Run consecutive Commands Linux with java runtime exec

I need to run two commands Linux using java code like this:
Runtime rt = Runtime.getRuntime();
Process pr=rt.exec("su - test");
String line=null;
BufferedReader input = new BufferedReader(new InputStreamReader(pr.getInputStream()));
while((line=input.readLine()) != null) {
System.out.println(line);
}
pr = rt.exec("whoami");
input = new BufferedReader(new InputStreamReader(pr.getInputStream()));
line=null;
while((line=input.readLine()) != null) {
System.out.println(line);
}
int exitVal = pr.waitFor();
System.out.println("Exited with error code "+exitVal);
} catch(Exception e) {
System.out.println(e.toString());
e.printStackTrace();
}
The problem is the output of the second command ("whoami") doesn't display the current user which used on the first command ("su - test")!
Is there any problem on this code please?

In the general case, you need to run the commands in a shell. Something like this:
Process pr = rt.exec(new String[]{"/bin/sh", "-c", "cd /tmp ; ls"});
But in this case that's not going to work, because su is itself creating an interactive subshell. You can do this though:
Process pr = rt.exec(new String[]{"su", "-c", "whoami", "-", "test"});
or
Process pr = rt.exec(new String[]{"su", "test", "-c", "whoami"});
Another alternative is to use sudo instead of su; e.g.
Process pr = rt.exec(new String[]{"sudo", "-u", "test", "whoami"});
Note: while none of the above actually require this, it is a good idea to assemble the "command line" as an array of Strings, rather than getting exec to do the "parsing". (The problem is that execs splitter does not understand shell quoting.)

As stated in the Javadoc for Runtime.exec():
Executes the specified string command in a separate process.
each time you execute a command via exec() it will be executed in a separate subprocess. This also means that the effect of su ceases to exist immediately upon return, and that's why the whoami command will be executed in another subprocess, again using the user that initially launched the program.
su test -c whoami
will give you the result you want.

If you want to run multiple commands in a way the commands would execute in a subshell if need be see the response here
How can I run multiple commands in just one cmd windows in Java? (using ProcessBuilder to simulate a shell)