[Bioperl-l] clustalw/t_cofee tests

[Ewan Birney]

On Wed, 9 Jan 2002, Jason Stajich wrote:

> 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.

After 1.0 right ;)

> 
> 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).
> 

Ok. Great!

> 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).
> 

Right.... I can imagine that there is alot of format/command-line drift in
clustal...


> -jason
> 
> >
> >
> 
> -- 
> Jason Stajich
> Duke University
> jason@cgt.mc.duke.edu
> 
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Ewan Birney. Mobile: +44 (0)7970 151230, Work: +44 1223 494420
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