[Biojava-l] Using Java to create BLAST searches

Wed Nov 1 21:21:53 UTC 2006

Peter,
If you are running a process, then you should be able to use the
Process.waitFor() command.
waitFor() causes the current thread to wait, if necessary, until the process
represented by this Process object has terminated. I've used it in my code
that I posted and have snippeted it below.

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

Hope this is of some help.
Cheers,
Graham

Dr. Graham Etherington
Post-doctoral Research Officer
Bioinformatics Discovery Group,
Institute for Molecular Bioscience,
University of Queensland,
St. Lucia Campus, Brisbane,
QLD 4072 Australia

-----Original Message-----
From: Ng, Peter [mailto:Peter.Ng at bccdc.ca] 
Sent: Thursday, 2 November 2006 5:41 AM
To: mark.schreiber at novartis.com; Graham Etherington
Cc: biojava-l at lists.open-bio.org; biojava-l-bounces at lists.open-bio.org
Subject: RE: [Biojava-l] Using Java to create BLAST searches

Hi Mark/Andy,

I have a similar question relating to command line blast searches.  I'm
using elements from both flatfile.txt and i.html to present on a html
page.  How do I ensure each of blast1 or blast2 is completed before I
start the next step?  I'm not sure how to maintain control once the
command line is being executed.  Is there a way to test the presence of
the output files?  Does synchronize work in this situation.  If so, how
would I put it in the code?  Any help would be appreciated!

thanks,
peter

blast1 = "CMD /c c:/blast/blastall -p blastn -d c:/blast/db/" +
getLibrary() + " -i c:/blast/files/noc.txt -e .0001 -m 8 -o
c:/blast/files/flatfile.txt -v 2 -b 2 -F F";
blast2 = "CMD /c c:/blast/blastall -p blastn -d c:/blast/db/" +
getLibrary() + " -i c:/blast/files/noc.txt -e .0001 -m 0 -o
c:/batchBLAST/" + i + ".html -T T -v 5 -b 5 -F F";			

Runtime.getRuntime().exec(blast1);
Runtime.getRuntime().exec(blast2);

-- 
Regards,

Peter Ng
Laboratory Information Management Coordinator
Laboratory Services
BC Centre for Disease Control
655 West 12th Avenue
Vancouver BC  V5Z 4R4
Tel: 604-660-2058     
Page: 604-205-4814    
Fax: 604-660-6073
Web: www.bccdc.org

-----Original Message-----
From: biojava-l-bounces at lists.open-bio.org
[mailto:biojava-l-bounces at lists.open-bio.org] On Behalf Of
mark.schreiber at novartis.com
Sent: November 1, 2006 1:54 AM
To: Graham Etherington
Cc: biojava-l at lists.open-bio.org; biojava-l-bounces at lists.open-bio.org
Subject: Re: [Biojava-l] Using Java to create BLAST searches

Hi -

It may not like the command line having spaces in the path. Try
installing 
blast somewhere else as a test. Eg put it in C:\blast and then try 

String cmd = "C:/blast/bin/blastall -p blastn -d ecoli.nt -i test.fas -o

blast.out";

You could possibly even trick it by putting a short cut in the C 
directory.

Also biojava has some nice tools for working with processes.

- Mark

Mark Schreiber
Research Investigator (Bioinformatics)

Novartis Institute for Tropical Diseases (NITD)
10 Biopolis Road
#05-01 Chromos
Singapore 138670
www.nitd.novartis.com
www.dengueinfo.org

phone +65 6722 2973
fax  +65 6722 2910

"Graham Etherington" <g.etherington at imb.uq.edu.au>
Sent by: biojava-l-bounces at lists.open-bio.org
11/01/2006 04:39 PM

        To:     <biojava-l at lists.open-bio.org>
        cc:     (bcc: Mark Schreiber/GP/Novartis)
        Subject:        [Biojava-l] Using Java to create BLAST searches

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

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