[Biojava-l] gromacs shell script

[Tamas Horvath]

On 12/8/05, Tamas Horvath <hotafin at gmail.com> wrote:>> Runtime rtime = Runtime.getRuntime();>             Process child = rtime.exec("/bin/sh");>>>             BufferedWriter outCommand = new BufferedWriter(new>             OutputStreamWriter( child.getOutputStream()));>>>             outCommand.write("cd "+workhome +"; chmod +x run.bat;> exit\n");>             outCommand.flush();>>             child.waitFor();>             child.destroy();


this runs well the script gets the  executable  flag
            rtime = Runtime.getRuntime();>             child = rtime.exec(workhome+"run.bat");>>             BufferedReader input = new BufferedReader(new> InputStreamReader( child.getInputStream()));>             BufferedReader inerr = new BufferedReader(new> InputStreamReader(child.getErrorStream()));>>             String line = "";String lerr = "";>             while ( (line = input.readLine()) != null || (lerr => inerr.readLine()) != null){>                 if (line != null && !line.equals(""))  {>                     System.out.println(line);>                     lerr = inerr.readLine();>                 }>                 if (lerr != null && !lerr.equals(""))  System.out.println> (lerr);>             }>>             child.waitFor();>             System.err.println("EV:"+child.exitValue());>             child.destroy();


Here I only get the exit value, and nothing else


On 12/8/05, Thomas Down <td2 at sanger.ac.uk> wrote:>>> On 8 Dec 2005, at 14:16, Tamas Horvath wrote:>> > I know this is not strictly BioJava, but here's my problem:> > I create a shell script file that would run a GROMACS MD> > simulationI generate the necessary input and config files> > I can make the generated shell script runnable> > I cannot actually run the script from the Java application.> > The script works fine from shell...> > The returned exitValue is 255.> > Can anyone tell, what may I do?>> Could you give a few more details about the code you're using to run> the shell script from Java?  Running external processes using Java's> Runtime.exec method isn't totally trivial -- you usually need to> start some extra threads to handle the child process' input and output.>> I presume your script is actually printing some kind of error message> to standard error (or maybe standard out, if it's badly behaved, but> these may be getting lost.>> BioJava has some convenience methods that (usually) allow you to run> child processes without writing your own multithreaded code.  A> simple usage, that echoes the child's errors and outputs to the> console, would be something like:>>           ProcessTools.exec(>                            new String[] {"/path/to/my/script", "-> someArgument"},>                            null,           // no standard input>                            new OutputStreamWriter(System.out),>                            new OutputStreamWriter(System.err)>           );>> You probably don't want to do this in production code, but for> development and debugging it's quite useful.  For production use,> you'd normally use StringWriters to capture the child process' output.>>              Thomas.>