[Bioperl-pipeline] Annotation example error

[shawnh@fugu-sg.org]

> 
> I can't solve this one, any help would be appreciated.
> I did find that I needed both the ensembl branch of bioperl-live and the
> latest bioperl-live
> to get this far.
> Thanks for the help so far, I really want to get this running.

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.


shawn
> committed the fixed pipelinemanager. pls update.
> 
> 
> > I have downloaded the latest cvs releases for the required packages and
> > Bio/Cluster/Family.pm does not seem to exist.
> > There is a Bio/Cluster/FamilyI.pm in bioperl-live.
> > Also Bio/Seq/SeqBuilder.pm does not exist in the bioperl-live package
> > downloaded via command line cvs, but does exist
> > in the bioperl-live package downloaded as a tarball from the WebCVS site.
> > So how do I ensure I have the correct releases of all the required
> packages?
> 
> 
> Right now we are working as much off bioperl-live as possible. We hope to
> branch 
> together for 1.2 at the end of the year then it should be compatible with
> that.
> Bio::Cluster::Family doesn't exist as I changed the name to
> Bio::Cluster::SequenceFamily,
> but I'm still working on TribeMCL so its not updated yet.
> But in future, we will be more explicit about the compatibility issues of
> the pipelines especially
> with bioperl and ensembl.
> 
> best,
> 
> shawn
> 
> > 
> > Cheers,
> > Sean
> > 
> > 
> > 
> > -----Original Message-----
> > From: shawnh@fugu-sg.org [mailto:shawnh@fugu-sg.org]
> > Sent: Tuesday, 22 October 2002 2:00 AM
> > To: McWilliam, Sean (LI, Uni of Queensland)
> > Cc: 'bioperl-pipeline@bioperl.org'
> > Subject: RE: [Bioperl-pipeline] Annotation example error
> > 
> > 
> > Hi Sean,
> > 	I just found out what was the problem. The developer cvs
> > and the public cvs are somehow not in sync. THe version of the xml
> > which I committed doesn't seem to have found its way to the public cvs
> > repository.
> > weird. Will try and find out whats going on.
> > in the mean time, I have put the xml up on the web for download.
> > 
> > http://www.biopipe.org/download/genomic_sequence_annotation.xml
> > 
> > but it may not work if the code was not updated as well.
> > 
> > cheers,
> > 
> > shawn
> > 
> > ********************************
> > * Shawn Hoon
> > * http://www.fugu-sg.org/~shawnh
> > ********************************
> > 
> 
> 

-- 
********************************
* Shawn Hoon
* http://www.fugu-sg.org/~shawnh
********************************