[Bioperl-pipeline] job dependence
Shawn Hoon
shawnh at fugu-sg.org
Fri Mar 14 10:00:42 EST 2003
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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