[Bioperl-l] clustalw/t_cofee tests

[Jason Stajich]

An incredible amount of duplication in our Run::Alignment modules.
I hope to rework these as we interface with external analysis queues like
PISE and openBSA.

Fixed some things that updated the the $PROGRAM var to the full path found
for an exe (so that if CLUSTALDIR is not set but clustalw is in the path
the module can still run).

On Wed, 9 Jan 2002, Jason Stajich wrote:

>
> Will try on OSF1 on sanger machines and see if I can reproduce the
> problem there.
>
[able to reproduce on adnah]

clustalw1.4 doesn't allow very many cmd line parameters.  We aren't really
trying to detect the version of clustalw installed so we fail
semi-gracefully here.

If I hardcode the PROGRAM variable to run the installed clustalw1.74 I
find out that it doesn't like the paramter -output=/tmp/user-num-num
because of the '-'.  As such I have changed the tempfile creation process
in Bio::Root::IO to use a different template:
 '.' instead of '-'  ( no morse code jokes, please).

-jason

>
>

-- 
Jason Stajich
Duke University
jason@cgt.mc.duke.edu