[Bioperl-l] getting t_coffee to run with bioperl in linux first time

[Tim Erwin]

Hi Micheleen,

This error is to do with the BioPerl package and not the program
t_coffee. You will need to set the environment variable PERL5LIB to use
your bioperl libraries (I am also assuming you have installed the
bioperl-run package)

i.e export PERL5LIB=/somedir/bioperl-run-1.4/

To test that you have set the PERL5LIB variable correctly you should be
able to type perldoc Bio::Tools::Run::Alignment::TCoffee, and if you get
the documentation you should be good to go.

You can also set the location of the modules inside you script with:

BEGIN {
   unshift @INC,"/somedir/bioperl-run-1.4";
};

or use lib "somedir";

Regards,

Tim

> I ran the following script:
> 
> #!/bin/perl -w
> 
> BEGIN { $ENV{TCOFFEDIR} = 
> '/home/micheleen/progs/T-COFFEE_distribution_Version_1
> .37/bin' };
> use Bio::Tools::Run::Alignment::TCoffee;
> use Bio::Seq;
> use Bio::DB::GenBank;
> 
> $coffeefound = Bio::Tools::Run::Alignment::TCoffee->exists_tcoffee();
> 
> 
> And get the error:
> 
> Can't locate Bio/Tools/Run/Alignment/TCoffee.pm in @INC (@INC
contains: 
> /etc/perl /usr/lib/perl5/site_perl/5.8.5/i686-linux 
> /usr/lib/perl5/site_perl/5.8.5 /usr/lib/perl5/site_perl/5.8.2 
> /usr/lib/perl5/site_perl/5.8.2/i686-
linux /usr/lib/perl5/site_perl/5.8.4 
> /usr/lib/perl5/site_perl /usr/lib/perl5/vendor_perl/5.8.5/i686-linux 
> /usr/lib/perl5/vendor_perl/5.8.5 /usr/lib/perl5/vendor_perl/5.8.4 
> /usr/lib/perl5/vendor_perl /usr/lib/perl5/5.8.5/i686-linux 
> /usr/lib/perl5/5.8.5 /usr/local/lib/site_perl 
> /usr/lib/perl5/site_perl/5.8.2 /usr/lib/perl5/site_perl/5.8.2/i686-
linux 
> /usr/lib/perl5/site_perl/5.8.4 .) at my_scripts/find_pol.pl line 4.
> BEGIN failed--compilation aborted at my_scripts/find_pol.pl line 4.
> 



> 
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