[Bioperl-l] integration with bioperl-gui

Jason Stajich jason@chg.mc.duke.edu
Mon, 12 Feb 2001 19:00:05 -0500 (EST)

Location::Simple is the default mechanism for handling Locations, so we
fall back on it if a user does not specify a specific Location model.
SeqFeature::Generic will not really work with the new Location model
without being able to create a Bio::Location::Simple.  

Please make sure you really have all the bioperl-live dirs checked out
% cvs update -dP 

Heikki sent a nice hint for those doing UNIX based development. 
If you create the file ~/.cvsrc with the following lines
update -dP
cvs -q -z9

You should get create/remove missing/uneeded dirs when doing a cvs update.
Seems to work for me.

And be double sure that bioperl-live comes before any other bioperl
versions in your @INC (either add to @INC in your script or set PERL5LIB
to point to your bioperl-live directory).


On Mon, 12 Feb 2001, Hilmar Lapp wrote:

> David Block wrote:
> > 
> > Workbench seems to be fine, once I removed the reference to
> > Location::Simple from SeqFeature::Generic.
> > 
> > This should also not be a problem if we can actually get a working
> > Location::Simple.
> > 
> David, I'm not sure it has to be in SeqFeature::Generic, but
> regardless of that, a *working* Location::Simple is supposed to be
> present. Check Bio/Location/* - which files do you see there?
> 	Hilmar
> -- 
> -------------------------------------------------------------
> Hilmar Lapp                            email: lapp@gnf.org
> GNF, San Diego, Ca. 92121              phone: +1-858-812-1757
> -------------------------------------------------------------

Jason Stajich
Center for Human Genetics
Duke University Medical Center