[Bioperl-pipeline] Requirements for pipeline installation

[Andy Nunberg]

Hey now ! I dont want to be the bone of contention! :)

I am at the beginning of setting this all up so I am not tied to any sort
of database etc...
We were discussing here either ensembl(because it has the viewer etc..) and
ACeDB which
from my limited knowledge can do all the annotation bits and give you
graphical views as well.  But, since
you have experience with ensembl, we will go with that.  And just to make
sure I have this right, sequences
are stored in the ensembl database, they are retrieved and run throught the
pipeline and then the entry is updated with what ever analysis was carried
out..

Since I am woefully ignorant, i need to learn how i go from blast results
to an object with features to entering this object into a database, perhaps
I would feel better if i knew how to do this first and then go ahead
withthe pipeline... 

Oh, we are not using LSF. Right now we are writing our own queing systems
but we are also checking out PBS. LSF is right out! (just too expensive for
us).

Thanks
Andy


*******************************************************************
Andy Nunberg, Ph.D
Computational Biologist
Orion Genomics, LLC 
(314) 615-6989
http://www.oriongenomics.com