[Bioperl-l] [Bioperl-guts-l] [Bug 1368] New: Error running standalone blast (bioperl-live) (fwd)

[Shawn Hoon]

Ok I know what happened. I made in WrapperBase,

*program = \&executable;

so for StandAloneBlast, setting program=>blastn was setting
executable to that.

I don't think the wrappers uses that so I have removed it in WrapperBase, so it should work.

shawn


On Mon, 20 Jan 2003, Jason Stajich wrote:

> yep it is know.
> 
> This has to do with changes Shawn is rolling out for the wrapper
> executables - still chasing down what got broken, but that is why they
> call it bleeding edge...
> 
> -jason
> 
> --
> Jason Stajich
> Duke University
> jason at cgt.mc.duke.edu
> 
> ---------- Forwarded message ----------
> Date: Mon, 20 Jan 2003 11:09:26 -0500 (EST)
> From: bugzilla-daemon@cvs.open-bio.org
> To: bioperl-guts-l@bioperl.org
> Subject: [Bioperl-guts-l] [Bug 1368] New: Error running standalone blast
>     (bioperl-live)
> 
> http://bugzilla.bioperl.org/show_bug.cgi?id=1368
> 
>            Summary: Error running standalone blast (bioperl-live)
>            Product: Bioperl
>            Version: main-trunk
>           Platform: PC
>         OS/Version: Linux
>             Status: NEW
>           Severity: major
>           Priority: P2
>          Component: Core Components
>         AssignedTo: bioperl-guts-l@bioperl.org
>         ReportedBy: amatern@lbri.lionbioscience.com
> 
> 
> ERROR IS:
> 
> Can't use string ("blastn") as a HASH ref while "strict refs" in use
> at /bioperl-live/Bio/Tools/Run/StandAloneBlast.pm line 389.
> 
> my code:
> 
> my $progeam = "blastn";
>  my $output = "/home/amatern/$id.blastout";
>   my @params = ('database' => $database, '_READMETHOD' => 'Blast', 'program' =>
> $program, 'outfile' => $output);
>   my $factory = Bio::Tools::Run::StandAloneBlast->new(@params);
>   my $exe = $factory->executable('/lbri/gen/bin/blastall');
>   print "Running blastall $program\n";
>   my $blast_report = $factory->blastall($seq);
> 
> I just recently added the my $exe line trying to fix the problem...to no avail.
> 
> This code worked fine before the CVS update of StandAloneBlast.pm on January 17.
> 
> 
> 
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-- 
********************************
* Shawn Hoon
* http://www.fugu-sg.org/~shawnh
********************************