[Bioperl-l] Clustalw module
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
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.
> -----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?
> On Jul 2, 2008, at 10:34 AM, Nathan Haseley (RIT Student) wrote:
>> I am working with the Bioperl module
>> Bio::Tools::Run::Alignment::Clustalw. I try to include the package
>> in my script as follows:
>> 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.
>> Bioperl-l mailing list
>> Bioperl-l at lists.open-bio.org
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