Calling muscle as a Java process

Question

[Bioaln]

Hello. I'm developing a Java application, which at some point calls a MSA algorithm. Currently, I'm using muscle. I'm trying to call this process from within java app, there are no errors, yet there is no output! Is there a syntax problem I am not aware of?

try {
            System.out.println("Opening muscle analysis..");
            Runtime runTime = Runtime.getRuntime();
            Process process = runTime.exec(new String[]{
                            "muscle",
                            "-in","test1.fasta",
                            "-out","out12.afa"}
                        );            
            System.out.println("Closing..");
            process.destroy();
        } catch (IOException e) {
            e.printStackTrace();
        }

Thank you very much

[MeepMania]

Following code works defintely:

public void execute(String[] command)
{
    try {
        ProcessBuilder pb = new ProcessBuilder(command);
        pb.redirectErrorStream(true);
        Process p = pb.start();
        BufferedReader br = new BufferedReader(new InputStreamReader(
                p.getInputStream()));
        String out = "";
        while ((out = br.readLine()) != null)
            System.out.println(out);


    } catch (Exception e) {
        e.printStackTrace();

    }
}

How to call it: execute(new String[]{"muscle","-in", "input.fa" , "-out" , "output.fa"});

Answer 1

[Pierre Lindenbaum]

check muscle is in the PATH, you may need to consumme the stdout and the stderr and wait for the end of the process ( don't use destroy but waitFor). A shorter way to do this is:

Runtime.getRuntime().exec("/path/to/muscle -in "+"test1.fasta"+" -out "+"out12.fa");

[Bioaln]

Thanks, I actually experimented a bit with destroy(), and it was the main problem, but thanks again :)