[InterMine Dev] bioseg error message

Matthew Wakeling matthew at flymine.org
Tue Nov 24 16:41:35 GMT 2009

On Tue, 24 Nov 2009, Vallejos, Andrew wrote:
> I know I have raised this question before.  But I have run into the
> similar problem with InterMine requiring BioSeg.  According to the
> documentation BioSeg is considered optional, but in my experience I have
> never gotten a successful build without first installing BioSeg.

In general operation in the InterMine system, bioseg is optional, and the 
system will work around the missing functionality, albeit with drastically 
reduced performance. However, there are a couple of postprocess steps 
(OverlapViewTask and BiosegIndexTask) which will fail if bioseg is not 
present. These postprocess steps can be left out, but this will result in 
the LocatedSequenceFeature.overlappingFeatures collection being incorrect 
or slow.

It is perhaps more accurate to say the bioseg is optional for InterMine, 
but essential for biology-related InterMine. Perhaps we should update our 
documentation to reflect that.


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