[Bioperl-pipeline] input creates/update action

[Shawn Hoon]

Hi Jeremy,
	the 2nd datamonger job shouldn't get created. An input is only created 
if the
<input> tag is placed within the datamonger tag:
like for cdna2genome.xml

<snip>
<analysis id="1">
       <data_monger>
         <initial/>
         <input>
           <name>input_file</name>
         </input>
         <input_create>

</snip>

whereas in analysis 3

<snip>
<analysis id="3">
       <data_monger>
         <input_create>
           <module>setup_cdna2genome</module>
           <rank>1</rank>
           <argument>

</snip>

no input

So if u leave it out for your analysis id 3 then the input won't get 
created.


hope that helps

shawn



On Tuesday, June 3, 2003, at 12:14  PM, jeremyp at sgx3.bmb.uga.edu wrote:

> Hello,
>
> I'm trying to write an input create or input creates to replace the 
> update
> action. Unfortunately, I'm having trouble writing a working example. I
> wrote an xml file similar to the cdna2_genome configuration file. The
> problem is that the pipeline script loads the second data monger/input
> create into the job table before the pipeline runs at all. So, that job
> (the second data monger/input create job) runs before the analysis that
> should precede it (that is, the data monger analysis is analysis id 3,
> there is another normal analysis with analysis id 2). Exactly mimicking
> the update action would in fact require that analysis (id 3) to 
> generate
> the input the data monger/input create job would use. Where am I going
> wrong?
>
> Thanks,
> Jeremy
> _______________________________________________
> bioperl-pipeline mailing list
> bioperl-pipeline at bioperl.org
> http://bioperl.org/mailman/listinfo/bioperl-pipeline
>