[Bioperl-l] cannot find path to blastall

[Laurent DOUCHY]

try with this on the top of your code.

#!/usr/bin/perl
 
use strict;
use Bio::SeqIO;
use Bio::Tools::Run::StandAloneBlast;

BEGIN 
{
	$ENV{PATH}=":/home/bioinfo/Laurent/Utils/Blast/blast-2.2.10/bin/:";
}

...

2005/6/22, hafiz yusof <khufaz83 at yahoo.com>:
> 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";}
> 
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