System Command Within Java Solution

2015-01-13

azim58 - System Command Within Java Solution


Hey CPP C Java expert,

I found the solution about how to call system commands from any directory
to call any program. Thanks again for taking the time to look at this
with me. I apologize if I came across as impatient or anything. Your time
was appreciated :) . Here is my code below. It works!


String path = "W:\\Groups\\Zombie Edutainment\\Zombie Edutainment
Project\\cDNA_lib";
String command = "blastn -db Seq_DB -query cDNA_library.fa -out
screening_out_v6_4.txt -outfmt 6 -evalue 0.0001 -perc_identity 95.0
String[] commandArray = command.split("\\s");
try 


ProcessBuilder launcher = new ProcessBuilder();


Map<String, String> environment = launcher.environment();


launcher.redirectErrorStream(true);


launcher.directory(new File(path));





environment.put("name", "var");


launcher.command(commandArray);


Process p = launcher.start(); And launch a new process


BufferedReader output = new BufferedReader(new


InputStreamReader(p.getInputStream()));


String line;


while ((line = output.readLine()) != null)


System.out.println(line);





The process should be done now, but wait to be sure.


p.waitFor();

catch(IOException e1) 
}


catch(InterruptedException e2) {


System.out.println("Process: " + commandArray0 + " is done");
}


Good luck with everything! I'll assume that I don't need to pay anything
since we didn't find a solution together. Nevertheless, your attempts
were appreciated, and maybe the solution I have given you here will be of
use to you someday.

Best regards,
azim58


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Note that in order for Java to give a command line command to call the
program, the program must be part of the systems path.
see environment variable path