how to run local blast program in apche2 server

Question

I am running a local blast program in apche2 server...but it showing me error that. --------------------- WARNING ---------------------

MSG: cannot find path to blastall

My code is..

 #!/usr/bin/perl
print "Content-type: text/html\n\n";
use Bio::Perl;
use Bio::Tools::Run::StandAloneBlast;
@params = ('database' => 'btaudb','outfile' => 'bla.out', 
        '_READMETHOD' => 'Blast', 'prog'=> 'blastn');

 $factory = Bio::Tools::Run::StandAloneBlast->new(@params);
 $str = Bio::SeqIO->new(-file=>'test_query.fa' , '-format' => 'Fasta' );
 $input = $str->next_seq();


 $factory->blastall($input);

when i am running the same code in terminal its working fine...and showing mw correct result....pl help me..how to run local balst program in apche2 server.....

Answer 1

In my experience, that message means that you do not have the "blastall" tool available in your path. That is, if you typed "blastall -p blastn -d dbname -i input -o output" at your commandline, as was normal usage, your shell would complain about not being able to find blastall.

The Blastall interface appears to be on its way out, as noted here: http://www.ncbi.nlm.nih.gov/books/NBK1763/#CmdLineAppsManual.I43_Backwards_compatib. Newer versions of BLAST have only this wrapper script installed, and expect you to use the BLAST+ interface going forward.

I have found success using Bio::Tools::Run::StandAloneBlastPlus. The interface is very similar, and if your codebase is not very extensive yet, it should be relatively straightforward to begin using.