[Bioperl-l] cannot find path to blastall

Brian Osborne brian_osborne at cognia.com
Tue Mar 15 16:16:59 EST 2005


On Unix? Windows? Cygwin? Something else? Also is "/path/to/blastall" the
actual location of blastall? On a Linux machine this might be something like
"/usr/local/bin/blastall". We need to know a bit more.

Brian O.

-----Original Message-----
From: bioperl-l-bounces at portal.open-bio.org
[mailto:bioperl-l-bounces at portal.open-bio.org]On Behalf Of James Gregory
Sent: Tuesday, March 15, 2005 4:08 PM
To: bioperl-l at bioperl.org
Subject: [Bioperl-l] cannot find path to blastall

I'm trying to set up a standalone blast and I'm getting an error message
that says

MSG: cannot find path to blastall


my @params = (program => 'blastp',
               database => 'db.psq');
my $factory = Bio::Tools::Run::StandAloneBlast->new(@params);
my $path = '/path/to/blastall/';
$path = $factory->program_path($path);

my $blast_report = $factory->blastall($blast_seq);

any help would be appreciated.

James Gregory
University of California, San Diego
Department of Biological Sciences
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Bioperl-l at portal.open-bio.org

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