[Bioperl-l] Re: Small Bio::Factory::EMBOSS typo

[Heikki Lehvaslaiho]

Leon,

I meant that I'll first try to get the bioperl core 1.4 version which is based 
on bioperl-live. Only after that I'll look into bioperl-run cvs module and 
try to put a release out.

I can see two things that need to be done for EMBOSS:

1. During the Factory initialisation, it shoud check that it can find at least 
the wossname program and fail with a reasonable error message if needed.

2. Check the EMBOSS version and if it is < 2.7.0 convert all 'sequencea' 
paremeters into 'asequence' in the internal memory representation of the ACD 
specs.

Thanks for looking into this.

	-Heikki

On Friday 28 Nov 2003 4:22 pm, you wrote:
> On Fri, 28 Nov 2003 10:20:51 +0000
>
>  Heikki Lehvaslaiho <heikki at ebi.ac.uk> wrote:
> > Yeah, I know. This will need fixing.  See also:
> >
> > http://bugzilla.bioperl.org/show_bug.cgi?id=1481
> >
> > Do you want to do it? I am now concentrating on bioperl
> > core 1.4 release. The
> > run will follow after that.
> >
> > 	-Heikki
>
> Actually I would like to do it, Im gona see how my time
> looks and I'll start by figurein out what these ACD file's
> are.. I can guess, and it sounds like the fix will be in
> one of those?  Also I found another small parameter passing
> bug with prophecy from EMBOSS.
>
> And im wondering what you mean by "The run will follow
> after that."?
> -Leon

-- 
______ _/      _/_____________________________________________________
      _/      _/                      http://www.ebi.ac.uk/mutations/
     _/  _/  _/  Heikki Lehvaslaiho    heikki_at_ebi ac uk
    _/_/_/_/_/  EMBL Outstation, European Bioinformatics Institute
   _/  _/  _/  Wellcome Trust Genome Campus, Hinxton
  _/  _/  _/  Cambs. CB10 1SD, United Kingdom
     _/      Phone: +44 (0)1223 494 644   FAX: +44 (0)1223 494 468
___ _/_/_/_/_/________________________________________________________