[Bioperl-l] problems with clustalw

vdar at yorku.ca vdar at yorku.ca
Mon May 12 13:24:22 EDT 2008


Yes, seems like it worked, now I am having the following error message which is
not because of the errors in installation..right?

$ perl mult_align.pl
Can't call method "isa" without a package or object reference at
/opt/rocks/lib/perl5/site_perl/5.8.8//Bio/Tools/Run/Alignment/Clustalw.pm line
617.



Quoting Sendu Bala <bix at sendu.me.uk>:

> vdar at yorku.ca wrote:
> > Hi,
> >
> > Yes, I have clustalw installed and following is the result o which command
> >
> > $ which clustalw
> > /opt/Bio/bin/clustalw
> >
> > Please see aa.txt as output of perl -V and mult_align.pl is my script
>
> I've CC'd back the bioperl mailing list so other people can learn.
> Please keep it CC'd.
>
> Your script has two main errors:
>
> use Clustalw;
> $ENV{CLUSTALDIR} =
> '/opt/rocks/lib/perl5/site_perl/5.8.8/Bio/Tools/Run/Alignment/';
>
> These should be:
> use Bio::Tools::Run::Alignment::Clustalw;
> $ENV{CLUSTALDIR} = '/opt/Bio/bin/clustalw';
>
> There is also something very wrong with your installation, since you are
> using perl 5.8.5 yet have bioperl-run installed into a directory for
> 5.8.8. This is why Bio::Tools::Run::Alignment::Clustalw wasn't being
> found in the normal way; the 5.8.8 directory was never checked.
>
> PERL5LIB="/opt/rocks/lib/perl5/site_perl/5.8.8" should let it be found.
> If not, you might have to move the Bio folder from 5.8.8 to 5.8.5.
>




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