[Bioperl-l] cannot find path to wublast

Jyoti Shah jyotikshah at gmail.com
Mon Mar 27 13:55:48 EST 2006


 Thanks you were right!! There was no program such as wublastn in my
wu-blast directory :o.

To use the "Standaloneblast" module, I had to rename the "wu-blastall"
program to "blastall" and it worked great.The following changes did the
magic for me :-)
 BEGIN { $ENV{PATH} = '/home/wustl/wu-blast'; }
BEGIN { $ENV{BLASTDATADIR} = '/home/databases/'; }
 @params = ('program' => 'blastn',
                  'database' => $db);

$factory = Bio::Tools::Run::StandAloneBlast->new(@params);
$input = Bio::Seq->new(-id  =>"test_query",
                                  -seqn=> $seqn);
my $blast_report = $factory->blastall($input);

Thanks
 Jyoti


On 3/22/06, Torsten Seemann <torsten.seemann at infotech.monash.edu.au> wrote:
>
> > -------------------- WARNING ---------------------
> > MSG: cannot find path to wublast
> > ---------------------------------------------------
>
> > BEGIN { $ENV{PATH} = '/home/wustl/wu-blast'; }
>
> > @params = ('program' => 'wublastn',
>
> Just a quick possibility - do you actuall have an executable file called
> "wublastn", and is it in /home/wustl/wu-blast ?
>
> Because in my wu-blast installation, it's called just "blastn" (which
> itself is a symlink to the real multipurpose exe called "blasta").
>
> > my $blast_report = $factory->wublast($input);
>



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