> Duddy, John wrote:
>> The sample tracking system looks interesting. It looks like this is designed 
>> to have the sequencers modeled in Galaxy, have Galaxy pull the data from the 
>> sequencers, and might assume 1-1 pairing between sequencing run and samples.
>> I'd like to be able to support pushing files from a central location and 
>> variably multiplexed runs, all via the API (or extensions to the API).Is 
>> there any up-to-date documentation on this feature?
> The sample tracking system is undergoing a bunch of changes, so I'm
> thinking the documentation will be rewritten after that.

There's some code from Brad Chapman at
https://github.com/chapmanb/bcbb/tree/master/nextgen/scripts that
specifically addresses some of your downstream use cases and more.
Currently involves deep galaxy introspection into the sequencing
system. As Nate said, that's undergoing replumbing, so that interface
part will need changes - but the rest is likely a great starting point
for putting together your own local common tasks like (eg) splitting
and analysing a multiplexed lane and calling variants and other
routine core lab kinds of operations.
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