Hmmm, are you saying that the command works okay via
a batch file, but not if you exec it directly? Very strange...
I'm not a Windows user. But one thing which occurs to
me: you're handling the output of the process on the same
thread as the Process itself. I always use separate threads
(I don't know if this is the `official' way of doing things,
but it's a pragmatic approach which always seems to be reliable):
Process pro = // create process.
final InputStream out = pro.getInputStream();
Thread outputPump = new Thread() {
public void run() {
try {
int i;
while ((i = out.read()) != -1) {
System.out.print((char) i);
}
} (catch IOException ex) {}
}
} ;
outputPump.start();
pro.waitFor();
Having said that, I still don't really understand why running
blast via a batch file helps. But you might like to try the
recipe above and see if it makes a difference.
Thomas
On Wed, Feb 20, 2002 at 11:55:33AM +1300, Russell Smithies wrote:
> Has anyone had any luck running Blast locally from Java using Runtime.exec()
> and command array??
>
> I always get an error from Blast and the only reliable way I've found so far
> is to write a batch file then delete it as follows:
> *****************************************************
> File batFileName = new File("runme.bat");
> PrintStream bfile = new PrintStream(new BufferedOutputStream(new
> FileOutputStream(batFileName)));
> //command string for BLAST
> String cmds = "c:/bio/blast/blastall.exe -p blastn -d
> c:/bio/blast/ecoli -e 1e-30 -m8 -i c:/bio/blast/test.txt";
> //create batch file
> bfile.print(cmds);
> bfile.close();
> //execute batch file
> Process pro = Runtime.getRuntime().exec(batFileName.toString());
> InputStream out = pro.getInputStream();
> int i;
> while((i = out.read())!= -1){
> //do stuff with the output
> System.out.print((char)i);
> }
> //stop process
> pro.destroy();
> //delete batch file
> boolean sucess = batFileName.delete();
> ******************************************************
> It works fine but there must be a tidier way.
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