[Bioperl-pipeline] job dependence

[Shawn Hoon]

On Friday, March 14, 2003, at 05:19 AM, jeremyp at sgx3.bmb.uga.edu wrote:

> Hello,
>
> I may have sent a message before on this topic. I checked the most 
> recent
> sources, and it still seems to me that certain job dependency checking 
> may
> be missing. I haven't tested the latest code, but, in order to get my 
> code
> working with a version of the pipeline from mid-December, I added
> dependency checks to runner.pl and also to the second place jobs are
> spawned within PipelineManager.pl. I am using the UPDATE features of 
> the
> pipeline extensively. Am I missing something?
>


Hi Jeremy,
	I would like to see the dependency checks you added and if its 
generic, integrate them.
thanks. Also UPDATE is something that I have not used a while for 
pipeline ;) but it is still there in Bio/Pipeline/Manager.pm
The popular way now to populate the job and input tables ( among the 
few of us using biopipe here) is to use InputCreate which is a little 
job that reside between
analysis that has an IOHandler that fetches input ids and creates jobs 
for the next analysis. This is a more flexible scheme in which embed 
more specific
code that knows how to pair up inputs for a given job.

Right now PipelineManager.pl and XML2Db.pl are moving towards 
deprecation and replaced with one script PipelineManager that calls
Bio/Pipeline/Manager.pm and Bio/Pipeline/XMLImporter.pm respectively.

best,

shawn


> Jeremy
>
>
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