> 1) Is there any kind of existing functionality that is close to what I want?

Depending on whether you are using stock Galaxy or nglims, and how you
are getting data into Galaxy, there are various ways to do it. For
Galaxy's stock sample tracking, you can setup workflows to trigger
automatically when data arrives.

However, what I suspect is that you want to use the Galaxy API for
this. There should never be a need to interact directly with the
database, you should be able to do everything you want using the REST
APIs. There should be an example script included with Galaxy that
watches a directory for datasets, loads them into Galaxy, and runs a
workflow using the API.

> 2) If not,
>   2a) Is there a way to trigger some scripts for assembly and metrics (and
> maybe more) once a MiSeq dumps all the data into Galaxy?
>   2b) Is there a certain convention on interaction with the database?  And
> documentation on that?
>   2c) Is there an existing convention on reading the Galaxy database, so
> that I can produce the spreadsheet?  Documentation?
>   2d) Our lab would call this functionality Rover, since it will roam Galaxy
> looking for and retrieving data (not really a question, but I thought they
> came up with a good name!)
>
> --
> Lee Katz, Ph.D.
>
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