[Bioperl-l] wwwblast script question

huizhuan wu arhui20 at hotmail.com
Thu Jul 8 11:07:01 EDT 2004

Can someone there help me out of this? I have been stuck in this for a week. 
Any help would be highly appreciated!

I have a bioperl cgi script to host a blast server locally. But I kept 
getting an error msg of not being able to call blastall in "$blast_report = 
$factory->blastall($seqobj);". The script is running ok in command line. So 
it should be the wwwblast server environment setting problem. I am running 
on a machine that I have a user accout but without the root previledge.
my bioperl cgi script is in: /Users/myname/Sites/CGI-BIN/
my local database to blast(I have formatted it) is in: 
the blast programs in the machine is in: /usr/local/NCBI/network/wwwblast
my confirguration file is in: /etc/httpd/myname.conf

Here is my settings on environment variables:
(1) in .ncbirc file


(2) in myname.conf
<Directory /usr/local/NCBI/network/wwwblast>
Options ExecCGI

<Directory /usr/local/BLAST/>
Options ExecCGI

<Directory /Users/myname/Sites/>
Options ExecCGI

Here is the error msg:
Here is blast_report Content-type:text/html

Can't call method "next_result" on an undefined value at
/Users/myanme/Sites/CGI-BIN/bl.cgi line 73.
The error is located here:
    my $blast_report = $factory->blastall($seqobj);
    print "Here is blast_report: $blast_report";
    my $result = $blast_report->next_result;
Here is my code:
#!/usr/bin/perl -w -T

$ENV{BLASTMAT} = '/usr/local/BLAST/data';
$ENV{'BLASTDB'} ='/Users/huizhuan/myWork/learnBlast';
$ENV{PATH} = '/usr/local/bin:/usr/ucb:/usr/bin:/sbin:/usr/sbin';
$ENV{IFS} = "" if $ENV{IFS} ne "";

# This script gets sequence from grape MPSS page and perform blastn
against data.txt
# Modules to use.
use CGI qw(:all);
use CGI::Carp qw(warningsToBrowser fatalsToBrowser);
use CGI::Carp qw(fatalsToBrowser carpout);
use strict;
use warnings;
use Getopt::Long;
use Bio::Tools::Run::StandAloneBlast;
use Bio::SeqIO;

print header;
print start_html("BLAST RESULT");
my ($query, $seq);
my $db = "/Users/myname/blast_script/data.txt";
   my $maxEval = 1.0e-10;

   $query = "233fff";
   my $seqobj = Bio::Seq->new( '-id' => $query,
                                '-seq' => $seq);
  my @params = ('program'=>'blastn', 'outfile'=>'blast.out',
                   '_READMETHOD'=>'Blast', 'F'=>'F','W'=>17,'g'=>'F',

    my $factory = Bio::Tools::Run::StandAloneBlast->new(@params);
    my $blast_report = $factory->blastall($seqobj);
    print "Here is blast_report: $blast_report";
    my $result = $blast_report->next_result;
    print end_html;

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