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 -num_alignments 10"; String[] commandArray = command.split("\\s"); try { ProcessBuilder launcher = new ProcessBuilder; Map 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: " + commandArray[0] + " 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

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