[Bioperl-l] Clustalw module

Jason Stajich jason at bioperl.org
Wed Jul 2 11:25:09 EDT 2008

re: StandAloneBlast and RemoteBlast - due to their perceived  
widespread use was not moved from the core package to run so they  
come in with the basic Core modules install package.
Given the error message I would again say that the bioperl-run was  
not installed.

If you do perldoc ModuleName it will tell you if the module can be  

locate Clustalw.pm can also help you locate if it is installed but  
just not in PERL5LIB path.


On Jul 2, 2008, at 11:04 AM, Nathan Haseley (RIT Student) wrote:

> I am running my script on a remote server, so I didn't do the  
> installation.  I would assume so, however, since StandAloneBlast  
> works fine.
> Nathan
> -----Original Message-----
> From: Jason Stajich on behalf of Jason Stajich
> Sent: Wed 7/2/2008 11:02 AM
> To: Nathan Haseley (RIT Student)
> Cc: bioperl-l at lists.open-bio.org
> Subject: Re: [Bioperl-l] Clustalw module
> 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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