How To Run Local Blast Program In Apache2 Server...

Question

[Manju]

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.....

[Niek De Klein]

Is your perl script in the same folder as blastall?

[Michael]

btw, this is slightly off-topic, even though it might not be obvious at first glance.

Answer 1

[Michael]

Reason: the PATH variable is not passed on, so the perl program cannot find it. What you have to do depends on whether you are using mod-perl or not.

Read this and run the little cgi to see your environment. http://httpd.apache.org/docs/2.0/howto/cgi.html#env

Then RTFM: http://httpd.apache.org/docs/2.2/mod/mod_env.html#passenv

Most likely, if the path is set correctly during server start, adding

PassEnv PATH

to your hhtpd.config will solve the problem. If you are using mod-perl use

PerlPassEnv PATH

in mod perl configuration section instead and rtfm: http://perl.apache.org/docs/2.0/user/config/config.html#C_PerlPassEnv_

^^

[Michael]

oh btw, note that there might a reason for the path not being passed normally because it is not safe.