[ensembl-dev] Problems running BLAST

[Youens-Clark, Ken]

I'm trying to figure out problems with my BLAST installation.  As I can't debug the web "/Multi/blastview" in action, I've tried to extract the relevant bits of code into a script so I can step through it.  Here's what I wrote:

> #!/usr/bin/env perl
> 
> use strict;
> use warnings;
> use feature 'say';
> use autodie;
> use Bio::Tools::Run::EnsemblSearchMulti;
> use EnsEMBL::Web::Registry;
> use Data::Dump 'dump';
> 
> my $ticket       = 'BLA_ohk6YZfGQ';
> my $species      = 'Oryza_sativa';
> my $species_defs = EnsEMBL::Web::Registry->new->species_defs;
> 
> my $dbc = EnsEMBL::Web::DBSQL::DBConnection->new( undef, $species_defs );
> 
> my $adaptor = $dbc->get_databases_species($species, 'blast')->{'blast'};
> 
> my $blast = Bio::Tools::Run::EnsemblSearchMulti->retrieve( $ticket, $adaptor );
> 
> #say dump($blast);
> 
> $blast->_initialise_runnables();
> 
> for my $runnable ( $blast->runnables ) {
>     say dump($runnable);
> 
>     eval {
>         my $status = $runnable->status;
>         say "status = '$status'";
> 
>         if ( $status eq 'PENDING' ) {
>             say 'Running!';
>             $runnable->run;
>         }
>     };
> 
>     if ( my $err = $@ ) {
>         say "Error: $err";
>     }
> }
> 
> say 'Done.';

And here's the end of the output I get:

> bless({
>   _retrievable => 1,
>   _statefile   => "/usr/local/ensembl-grmblast/tmp/blastqueue/BLA_oh/k6YZfGQ/6JZje0N7",
>   _suffix      => undef,
>   _template    => "BLA_XXXXXXXXXX",
>   _workdir     => "/usr/local/ensembl-grmblast/tmp/blastqueue/BLA_oh/k6YZfGQ",
> }, "Bio::Tools::Run::Search::wublastn")
> Error: Can't locate object method "status" via package "Bio::Tools::Run::Search::wublastn" at ./retrieve.pl line 29, <DATA> line 705.
> 
> Done.


Can anyone see what I'm doing wrong?

--
Ken Youens-Clark
kclark at cshl.edu
Ware Lab/CSHL/USDA-ARS