[Bioperl-l] problems with clustalw

[Sendu Bala]

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.