[Bioperl-pipeline] Annotation example error

[McWilliam, Sean (LI, Uni of Queensland)]

shawnh@fugu-sg.org wrote:
 
> ok I think I know what is going on.
> You are including both bioperl-live branch 072 and bioperl live right?
> so there are some incompatibility issues with bioperl and ensembl
> currently as the stable ensembl is using bioperl-072 and we use
> bioperl-live for the pipeline.
> Bio::Root::IO::exists_exe is a bioperl-1.0+ thing so I
> suggest only using the latest bioperl-live
> for this. Because ensembl object inherit from
> Bio::Root::RootI and not Bio::Root::Root,
> you might get some throw_not_implementeds. They might have been some
> changes to RootI though I not sure. The quickest way to fix that
> would be to comment out the offending throw.
> Hacky I know. but it works for the pipeline. But this should change
> once ensembl rolls out their next stable branch which will be
> bioperl-1.0 compliant. 

I tried removing the ensembl branch of bioperl-live from my path and
got an error about not being able to locate Bio/Annotation.pm, the
example code obviously needs this. This exists in ensembl_bioperl-live
but not bioperl_live. I checked the inheritance/include tree for this
object and it appeared that it would quite happily sit in bioperl-live,
so I copied it to bioperl-live/Bio and the pipeline ran, yipee!

The ens_test database appears to have been updated correctly.

Thanks for all the assistance, now that I have the example running I will
being
trying to implement our own pipeline, so you probably haven't heard the last
of my
cries for help.  
The biopipe website mentions that genscan will be implemented shortly,
this is the next logical step for us also, so I was wondering how imminent
is this, is it
a matter of days, weeks, or months? No pressure, I just didn't want to spend
a lot of time
working on something which may be available shortly.


Cheers and Thanks again,
Sean

============================
Sean McWilliam
CSIRO Livestock Industries
Level 3 Gehrmann Labs
Research Road
University of Queensland
St Lucia, 4072

email: sean.mcwilliam@csiro.au
phone: 07 3346 2504
fax: 	 07 3214 2480
============================