vdar@... 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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