Running a Binary file using Java in Ubuntu

Question

I am trying to run a binary file, which is Genia Sequence Splitter through java code. This Binary file is type x-executable and has no extension. I can run the file in terminal by using ./geniass arg1 arg2 where arg1 is input file arg2 is output file I want to automate this process. I tried using this code

    public class geniaSSTag {
    public static void geniaSS(String inputFile){
        System.out.println("Input file: "+inputFile);

        String[]cmd={"bash","geniass/./geniass","in.txt","out.txt"};

        try {
            String errOutput="";
Process process = Runtime.getRuntime().exec(cmd);
String s = "";
BufferedReader br = new BufferedReader(new InputStreamReader(process
                        .getInputStream()));
while ((s = br.readLine()) != null)
{
   s += s + "\n";
}    
System.out.println(s);

BufferedReader br2 = new BufferedReader(new InputStreamReader(process.getErrorStream()));
while (br2.ready() && (s = br2.readLine()) != null)
{
  errOutput += s;
}
System.out.println(errOutput);
        } catch (IOException ex) {
            Logger.getLogger(geniaSSTag.class.getName()).log(Level.SEVERE, null, ex);
        }
    }
}

But I get this error when I try to run

geniass/./geniass: geniass/./geniass: cannot execute binary file

How can I solve this. Any help is appreciated.

Thank you

did you try running it with absolute path? besides bash is unnecessary. — soulcheck
– soulcheck, Commented Nov 29, 2011 at 14:56
try with String[]cmd={"absolute-path-to-geniass","in.txt","out.txt"}; — soulcheck
– soulcheck, Commented Nov 29, 2011 at 14:56

Edwin Buck · Accepted Answer · 2011-11-29 15:54:24Z

1

When you run the program, is the executable relative to the program's starting directory in the manner that it lies in "./genias/genias"? Note that the "/./" doesn't do anything except waste space, as it is shorthand for "the subdirectory that links back to the current directory".

Perhaps your "genias" executable isn't in a subdirectory named "genias", or the launching program is being launched from a different directory and can't find "genias/genias" relative to it's directory.

As suggested elsewhere, you can fix this by using an absolute path in the launching command. However, sometimes this just isn't flexible enough if you want multiple copies installed.

answered Nov 29, 2011 at 15:54

Edwin Buck

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toto2 · Accepted Answer · 2011-11-29 15:39:13Z

0

I would try first to run the command pwd from Java to see where you actually are. Then you can change the path to your executable accordingly. I guess using the path /home/xxx/yyy/geniass would always work.

Also there is a different version of Runtime.exec() which takes a working directory as an argument.

answered Nov 29, 2011 at 15:39

toto2

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OscarRyz · Accepted Answer · 2011-11-29 15:40:50Z

0

Try:

String[]cmd={"/full/path/to/geniass","in.txt","out.txt"};

Instead

answered Nov 29, 2011 at 15:40

OscarRyz

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2 Comments

OscarRyz Over a year ago

Also, use ProcessBuilder instead of Runtime.exec

manjulapra Over a year ago

Thanks everybody. I tried everything, but it keeps giving me the same error. So I wrote a script .sh and ran that instead which solved the problem. I have a hunch that it might be a permission error. But anyway things are fine now.

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