Question: How To Run Local Blast Program In Apache2 Server...
0
gravatar for Manju
8.0 years ago by
Manju0
Manju0 wrote:

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.....

bioperl • 2.4k views
ADD COMMENTlink modified 8.0 years ago by Michael Dondrup46k • written 8.0 years ago by Manju0

Is your perl script in the same folder as blastall?

ADD REPLYlink written 8.0 years ago by Niek De Klein2.5k

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

ADD REPLYlink written 8.0 years ago by Michael Dondrup46k
4
gravatar for Michael Dondrup
8.0 years ago by
Bergen, Norway
Michael Dondrup46k wrote:

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_

^^

ADD COMMENTlink modified 4 weeks ago by RamRS24k • written 8.0 years ago by Michael Dondrup46k

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

ADD REPLYlink written 8.0 years ago by Michael Dondrup46k
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