[Bioperl-l] StandAloneBlast in Windows

[Chris Fields]

And don't spam the mail list with repeated requests.  It shows a lack of
respect.

Christopher Fields
Postdoctoral Researcher - Switzer Lab
Dept. of Biochemistry
University of Illinois Urbana-Champaign 


> -----Original Message-----
> From: bioperl-l-bounces at lists.open-bio.org [mailto:bioperl-l-
> bounces at lists.open-bio.org] On Behalf Of Bornman, Daniel M
> Sent: Friday, April 21, 2006 9:13 AM
> To: bioperl-l at lists.open-bio.org
> Subject: [Bioperl-l] StandAloneBlast in Windows
> 
> 
> Dear BioPerl,
> 
> 
> Does anyone know how to use "Bio::Tools::Run::StandAloneBlast" in
> Windows?
> 
> I am able to query my own stand alone blast database from the command
> line directly without perl so I know its installed correctly but I am
> unable to get my BioPerl script to work.  Here is a very simple program
> example and the error message I get.
> My Path (Environmental Variable) is set to 'C:\BLASTDB\bin'
> 
> 
> 
> ## START ##
> BEGIN{
> 	$ENV{BLASTDIR} = 'C:\\BLASTDB\\data';
> }
> 
> use strict;
> use Bio::Seq;
> use Bio::Tools::Run::StandAloneBlast;
> 
> my @params = (program  => 'blastn', database => 'ecoli.nt');
> my $blast_obj = Bio::Tools::Run::StandAloneBlast->new(@params);
> my $seq_obj = Bio::Seq->new(-id  =>"testquery", -seq
> =>"TTTAAATATATTTTGAAGTATAGATTATATGTT");
> my $report_obj = $blast_obj->blastall($seq_obj);
> my $result_obj = $report_obj->next_result;
> print $result_obj->num_hits;
> ## END ##
> 
> 
> ## ERROR MESSAGE START ##
> 
> [NULL_Caption] WARNING: testquery: Unable to open ecoli.nt.nin
> 
> ------------- EXCEPTION  -------------
> MSG: blastall call crashed: 256 C:\BLASTDB\bin\blastall.exe -p  blastn
> -d  "\ecoli.nt"  -i  C:\DOCUME~1\Home\LOCALS~1\Temp\QZwYdo9eKx  -o
> C:\DOCUME~1\Home\LOCALS~1\Temp\ADP2OcZw8z
> 
> STACK Bio::Tools::Run::StandAloneBlast::_runblast
> C:/Perl/site/lib/Bio/Tools/Run/StandAloneBlast.pm:732
> STACK Bio::Tools::Run::StandAloneBlast::_generic_local_blast
> C:/Perl/site/lib/Bio/Tools/Run/StandAloneBlast.pm:680
> STACK Bio::Tools::Run::StandAloneBlast::blastall
> C:/Perl/site/lib/Bio/Tools/Run/StandAloneBlast.pm:536
> STACK toplevel localblast.pl:12
> 
> --------------------------------------
> 
> ## ERROR MESSAGE END ##
> 
> 
> Any help would be greatly appreciated.
> 
> Thanks,
> Dan
> 
> 
> 
> Daniel Bornman
> Researcher
> Battelle Memorial Institute
> 505 King Ave
> Columbus, OH 43201
> 614.424.3229
> 
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