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

[Jason Stajich]

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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