[Bioperl-l] Re: Can't locate clustalw

[Peter Schattner]

Hilmar Lapp wrote:
> 
> (Instead, the clustalw
> test does not [work], because it appears to reference the non-existent
> /home/peter/clustalw1.8/clustalw. I don't know what's the correct name of
> the file or directory.)
> --

 You need to have a copy of the executable for clustalw on your system. 
In addition, you need to enable Clustalw.pm to find the clustalw
executable. This can be done  in (at least) three ways (where
‘/home/peter/clustalw1.8’  below needs to be replaced by the name of
whatever directory contains the clustalw executable on your system.)
  1. include a definition of an environmental variable CLUSTALDIR in
every script that will use Clustalw.pm. 
	BEGIN {$ENV{CLUSTALDIR} = '/home/peter/clustalw1.8/'; }  
or
2. define a global environmental variable CLUSTALDIR (eg for bash):
	export CLUSTALDIR=/home/peter/clustalw1.8   
or
3. Modify your $PATH variable to include your clustalw directory as in
(for bash):
	export PATH=$PATH:/home/peter/clustalw1.8   

Please let me know if you have any difficulty getting the Clustalw.t
tests to work on your system after you have made any of these modifications.

Your question makes me realize that – although the above instructions
are in the clustalw.pm module – it will be important to make the user
requirements for configuring clustalw.pm clearer before the next
release.   Presumably the additional instructions should be included on
the page: http://bioperl.org/Core/external.shtml with all the other
instructions for Bioperl modules which require external / 3rd party
software.  In addition, I imagine the bioperl makefile should be
modified to look for clustalw just as it currently looks for the other
external programs (I’d offer to do this myself, but I have no experience
with MakeMaker etc and I’m afraid I might muck things up)  I’m open to
suggestions on how to best to deal with this…

Peter