[Bioperl-l] Fwd: Pairwaise_kaks.pl

Sendu Bala bix at sendu.me.uk
Tue Oct 30 12:10:42 EDT 2007

Jason Stajich wrote:
> Denis -
> Not sure - the list members will know more.
>> From: "dennis prickett \(IAH-C\)" <dennis.prickett at bbsrc.ac.uk>
>> I have installed bioperl-run in /usr/local/bioperl_run-1.5.2
>> And have bioperl             in /usr/local/bioperl-1.5.2_100
>> When I try to run the script I get the following
>> Can't locate object method "_set_from_args" via package
>> "Bio::Tools::Run::Alignment::Clustalw" at
>> Bio/Tools/Run/Alignment/Clustalw.pm line 409.
>> I'm not sure how to resolve this so I refer to a higher authority

_set_from_args() first arrived in Jan 2007, after 1.5.2 was released. 
This means you actually have some kind of mixed setup where you probably 
have bioperl-run from CVS and bioperl-core 1.5.2.

The solution is to make sure you have core and run packages from the 
same place. Ie. 1.5.2 release packages or CVS, not both.

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