Running a "heavy" program from within a java class

Question

Dear Java programmers,
I 'm trying to run a software called surflex from within a java class, using the following java command:
Runtime.getRuntime().exec( new String[ { "/bin/bash", "docking_script_2.bash"} );
For convenience I've created the following simple bash script but for some strange reason surflex is not executed:
#!/bin/bash
surflex-dock-v211-linux.exe proto drug.mol2 receptor_hydro.mol2 p1;
surflex-dock-v211-linux.exe dock drug.mol2 p1-protomol.mol2 receptor_hydro.mol2 >& 1OHR_A_output.txt;
Can anybody help me on that (ignore the arguments, they are correctly set)? I'll try to find another, more generic example, but so far I've noticed that the same thing happens with unix grep command.
thanks,
Tom

Answer 1

I think if you want to invoke a bash shell and give it a command to execute, you need to do
/bin/bash -c commandrather than
/bin/bash commandAccordingly, your call to exec should look like
exec( new String[ { "/bin/bash", "-c" "docking_script_2.bash"} );Beyond, that, I'd suggest the following as general debugging tips and best practices:
* As the first line of the bash script, include a line that does something simple, like touch a file, so you can see if the script is executing at all.
* In Java, call Process.waitFor(). Its return value is the process' exit value.
* Make sure you're gobbling stdout and stderr from the process, and giving stdin any input it needs. You'll have to do this for the process to run correctly, and you can also use what you read from stdout and stderr to debug the execution of the process. [http://www.javaworld.com/javaworld/jw-12-2000/jw-1229-traps.html]
* You may wan to look into ProcessBuilder, rather than Runtime.exec. I haven't used it myself yet, but apparently it's supposed to be the preferred way to execute external processes.