[Bioperl-l] Clustalw module

[Jason Stajich]

did you install bioperl-run package as well as bioperl core?
-jason
On Jul 2, 2008, at 10:34 AM, Nathan Haseley (RIT Student) wrote:

> Hello,
>    I am working with the Bioperl module  
> Bio::Tools::Run::Alignment::Clustalw.  I try to include the package  
> in my script as follows:
>
> #!/usr/bin/perl
> use Bio::Seq;
> use Bio::SearchIO;
> use Bio::Tools::Run::StandAloneBlast;
> use Bio::DB::GenBank;
> use Bio::Tools::Run::Alignment::Clustalw;
> use Bio::Root::Exception;
> use Error qw(:try);
>
> but I keep getting the following error message:
> Can't locate Bio/Tools/Run/Alignment/Clustalw.pm in @INC (@INC  
> contains: /etc/perl /usr/local/lib/perl/5.8.8 /usr/local/share/perl/ 
> 5.8.8 /usr/lib/perl5 /usr/share/perl5 /usr/lib/perl/5.8 /usr/share/ 
> perl/5.8 /usr/local/lib/site_perl .) at ./BlastTwoCompare.pl line 6.
> BEGIN failed--compilation aborted at ./BlastTwoCompare.pl line 6.
>
> The Clustalw program is configured correctly to work in my  
> directory.  Am I missing something obvious or is there something  
> wrong with my BioPerl configuration?  Any advice on how to fix  
> this?  Thank you for your time.
>
> Nathan
>
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