#!/usr/bin/perl

use strict;
use warnings;

use Bio::Tools::Run::Alignment::TCoffee;
use Bio::Tools::Run::StandAloneBlastPlus;

# do loads of stuff...

my $factory=Bio::Tools::Run::Alignment::TCoffee->new();
##</code><code>##

Use of uninitialized value $name in pattern match (m//) at /usr/share/perl5/Bio/Tools/Run/WrapperBase/CommandExts.pm line 499.

------------- EXCEPTION: Bio::Root::Exception -------------
MSG: Command 'run' not registered
STACK: Error::throw
STACK: Bio::Root::Root::throw /usr/share/perl5/Bio/Root/Root.pm:472
STACK: Bio::Tools::Run::WrapperBase::set_parameters /usr/share/perl5/Bio/Tools/Run/WrapperBase/CommandExts.pm:1203
STACK: Bio::Tools::Run::WrapperBase::new /usr/share/perl5/Bio/Tools/Run/WrapperBase/CommandExts.pm:505
STACK: Bio::Tools::Run::Alignment::TCoffee::new /usr/share/perl5/Bio/Tools/Run/Alignment/TCoffee.pm:612
STACK: /home/s0451486/usr/bin/t_coffeeTest.pl:13
-----------------------------------------------------------