[Biojava-l] Using Java to create BLAST searches

[Graham Etherington]

Hi,
I'm developing on Windows (using Apache Tomcat) using jsp's to create BLAST
searches on a local BLAST database. Even though I'm not using BioJava
(intend to use it to parse the results), I thought this formum would be the
best place to ask for help.
Even when I hard code a good BLAST search I keep getting the same error when
I run my search, namely: 
" java.io.IOException: CreateProcess: sh -c "C:/Program Files/Apache
Software Foundation/Tomcat 5.5/blast/bin/blastall -p blastn -d ecoli.nt -i
test.fas -o blast.out" error=2 "

The pertinent bits of code I'm using are...

String cmd = "C:/Program Files/Apache Software Foundation/Tomcat
5.5/blast/bin/blastall -p blastn -d ecoli.nt -i test.fas -o blast.out";

............


Runtime r = Runtime.getRuntime ();
Process runBlast = r.exec (new String[] {"sh","-c",cmd});
                  
runBlast.waitFor ();
out.println ("Waiting for result");

//Write the results
BufferedReader br = new BufferedReader (new FileReader (output));
String line = null;
String results = "";
while ( (line = br.readLine ()) != null )
results = results.concat ("/n" + line);

.............

I'm not sure why it give me an IOException. I've checked that the file input
file exists and that all the paths are correct.
Any ideas?

Many thanks,
Graham