[ensembl-dev] Problems running BLAST

[Dan Bolser]

Hi Ken,

Sorry for the dumb questions, but...
* What version of the code base are you using?
* Does the Perl API documentation suggest that
Bio::Tools::Run::Search::wublastn /should/ have a status method?


Cheers,
Dan.

On 15 May 2013 16:57, Youens-Clark, Ken <kclark at cshl.edu> wrote:
> 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
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