[Bioperl-l] cannot find path to blastall

[Tim Erwin]

Hi Hafiz

You could try setting the executable with the code:

$factory->executable(’/some_dir/blastall’);


Otherwise you could use a symbolic link in /usr/local/bin
to point to your blastall exe.

i.e. 

$> cd /usr/local/bin
$> ln -s /some_dir/blastall .

Regards,

Tim

On Wed, 2005-06-22 at 07:44 +0100, hafiz yusof wrote:
> I'm trying to set up a standalone blast and I'm
> getting an error message;
> 
> MSG: cannot find path to blastall
> 
> and i have running this code under Linux and i also
> haven't find blastall file in /usr/local/bin/, what
> should i do?
> 
> 
> 
> code:
> 
> 
> 
> #!/usr/bin/perl
> 
> use strict;
> use Bio::SeqIO;
> use Bio::Tools::Run::StandAloneBlast;
> 
> my $Seq_in = Bio::SeqIO->new (-file
> =>"/home/hafiz/bioperl/fasta", -format => 'fasta');
> my $query = $Seq_in->next_seq();
> 
> 
> my $factory =
> Bio::Tools::Run::StandAloneBlast->new('program'  =>
> 'blastp',
>                                                  
> 'database' => 'ecoli.nt',
>                                                  
> _READMETHOD => "Blast"
>                                                   );
> my $blast_report = $factory->blastall($query);
> my $result = $blast_report->next_result;
> 
> while( my $hit = $result->next_hit()) {
>     print "\thit name: ", $hit->name(), "
> significance: ",
> 
> $hit->significance(), "\n";}
> 
> 
> Send instant messages to your online friends http://uk.messenger.yahoo.com 
> _______________________________________________
> Bioperl-l mailing list
> Bioperl-l at portal.open-bio.org
> http://portal.open-bio.org/mailman/listinfo/bioperl-l
> 
>