[Bioperl-l] 1.01 RC2

[Leonardo Marino-Ramirez]

Dear Jason,

For a while I have been using the NHGRI::Blastall to run blast searches.
I just noticed that the standalone bioperl blast module is not behaving as
expected in an installation where the blast databases are not in the
"data" directory.

Here are my environmental variables:

BLASTDB=/var/local/ncbi/seals/alias_db/blast
BLASTDATADIR=/usr/local/ncbi_toolkit/ncbi/data/
BLASTDIR=/usr/local/ncbi_toolkit/ncbi/build

when I try to run a local search like this:

#!/usr/bin/perl

use Bio::Tools::Run::StandAloneBlast;

@params = ('database' => 'swissprot','outfile' => 'blast1.out',
	    '_READMETHOD' => 'Blast');

$factory = Bio::Tools::Run::StandAloneBlast->new(@params);

$str = Bio::SeqIO->new(-file=>'test.aa' , '-format' => 'Fasta' );
$input = $str->next_seq();
$blast_report = $factory->blastall($input);

print "$blast_report\n";


I get the following:

[blastall] ERROR: Program Name was not given an argument
------------- EXCEPTION  -------------
MSG: blastall call crashed: 256 blastall -d
/usr/local/ncbi_toolkit/ncbi/data/swissprot  -i  /tmp/PBdI8YJauj  -o
blast1.out

STACK Bio::Tools::Run::StandAloneBlast::_runblast
/usr/lib/perl5/site_perl/5.6.1/Bio/Tools/Run/StandAloneBlast.pm:600
STACK Bio::Tools::Run::StandAloneBlast::_generic_local_blast
/usr/lib/perl5/site_perl/5.6.1/Bio/Tools/Run/StandAloneBlast.pm:567
STACK Bio::Tools::Run::StandAloneBlast::blastall
/usr/lib/perl5/site_perl/5.6.1/Bio/Tools/Run/StandAloneBlast.pm:456
STACK toplevel standalone:12

--------------------------------------

What I get from this is that even if I tell StandAloneBlast that my
BLASTDB is in /var/local/ncbi/seals/alias_db/blast is still looking in the
BLASTDATADIR.

Comments?


On Wed, 5 Jun 2002, Jason Stajich wrote:

> Release candidate 2 is available for download at
> ftp://bioperl.org/pub/jason/bioperl-1.01-rc2.tar.gz
>
> This is a release candidate not a final release (although I hope it is
> almost there).  Please report any bugs or problems and give it test drive
> on your system by at least running the tests.  I'd like to release by the
> end of the week or Monday of next week at the latest.
>
> --jason
>

-- 

___ _/ _______________________________________________________________
   _/
  _/    _/      _/_/_/    Leonardo Marino-Ramirez   lmarino@tamu.edu
 _/    _/_/  _/_/    _/  Biochemistry Department, Texas A&M University
_/_/_/_/  _/  _/_/_/    2128 TAMU, College Station, TX 77843-2128, USA
     _/      _/     _/ Voice: (979) 862-4055   Fax: (979) 845-9274
___ _/      _/     _/ ________________________________________________