A workflow is just the definition of a particular process or set of steps.  
This information is stored in the database (see Workflow, StoredWorkflow, 
WorkflowStep tables).  Running that workflow creates datasets in a history 
(datasets which are stored in database/files).

And, I'm not sure exactly what you're asking in your last question, can you 
clarify?

-Dannon


On Dec 28, 2012, at 2:16 AM, Sachit Adhikari <sachit.techner...@gmail.com> 
wrote:

> I have searched the mailing list and found that the output, histories and 
> workflows are stored in ~/database/files. To do a little experiment I deleted 
> all the inside that directory. I then open my Galaxy and browse the workflow. 
> But the workflow is still there. I was wondering where is the workflow stored 
> in Galaxy? Also, if possible can I know how is the relationship specified by 
> user while creating workflow is stored?
> 
> Happy New year
> 
> Regards,
> 
> Sachit
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