[Bioperl-l] StandAlone BLAST on Windows???

[Barry Moore]

Change

> $ENV{BLASTDIR} = 'C:\\BLASTDB\\data';
to
> $ENV{BLASTDIR} = 'C:\\BLASTDB\\;
or set
>
> $ENV{BLASTDB} = 'C:\\BLASTDB\\data';
and when you do a blastp search don't forget to add
> $ENV{BLASTMAT} = 'C:\\BLASTDB\\data';

BLASTDIR points to your blast executables, and assumes a data  
directory underneath that for databases and matrix files.  If you  
have the standard setup with the executable in one directory and the  
databases and matrix files in a subdirectory 'data'  can set BLASTDIR  
to take care of everything.  If you've put that executables,  
databases, or matrix files in different locations then you'll want to  
set BLASTDB to point directly to the database, and BLASTMAT to the  
matrix files (probably the same directory).  I know the ncbi.ini file  
is supposed to take care of all of this, but it seems like I had  
trouble with that approach in the past, and just went back to setting  
ENV variables.

Barry

On Apr 21, 2006, at 10:49 AM, Bornman, Daniel M wrote:

> Dear BioPerl Listers,
>
> Does anyone know if the BioPerl StandAloneBlast module works on  
> Windows?
>
> I have a very simple script that will not work correctly.
>
> My PATH is set to 'C:\BLASTDB\bin'
> My database, 'ecoli.nt' is in 'C:\BLASTDB\data' directory
>
> Here is the script:
>
> ## 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 ##
>
>
> Here is the error message I get:
>
> [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
>
> --------------------------------------
>
>
> Thank You,
>
> Daniel Bornman
> Researcher
> Battelle Memorial Institute
> 505 King Ave
> Columbus, OH 43201
> 614.424.3229
>
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