[Bioperl-pipeline] Missing module in 0.1 tarball

[Shawn Hoon]

Hi Alistair,

>
> I'm now at the point of trying to populate a db using the Xml2DB.pl 
> script.  This doesn't work out of the box as it's complaining about a 
> Converter module.  In Xml2DB.pl:
>
> - Line 28:    use Bio::Pipeline::Utils::Converter
> - Line 325:  my $converter_obj = new Bio::Pipeline::Converter(
> - Line 373:  my $converter_obj = Bio::Pipeline::Utils::Converter->new
>
> The error message on running the script is the old can't locate in INC 
> blah, blah.  If I comment out line 28 (and add an exit soon after) 
> it's fine.
>
> There are two issues with this:
> - there is some inconsistency as to where the module actually is.
> - and I can't find the module in either of these locations above.
>

This is a deprecated script that has yet to be removed. I will do so 
right now. The PipelineManager (not PipelineManager.pl -> also to be 
removed)
is the script that lets you load and run pipelines:

To Load and not run :
 > cd  bioperl-pipeline/scripts:

 >    perl PipelineManager -dbname mydbname \
                          -dbuser <user> \
                          -dbhost <host> \
                          -xml 
~/biopipe_release/xml/templates/examble/blast_biosql_pipeline.xml
                          -norun

To run:
 >    perl PipelineManager -dbname mydbname \
                          -dbuser <user> \
                          -dbhost <host> \
                          -queue priority

if you simple want to load and run just specify the first command above 
without the -norun option.


This should be documented in the README that came with the bundle but 
I'm sure the reference to XML2DB.pl is lying
somewhere on the website and needs correcting.

cheers,


shawn

> Best
>
> Alistair
>
> -- 
> Alistair G. Rust                            Senior Research Scientist  
>        Institute for Systems Biology            1441 North 34th St.    
>               arust AT systemsbiology.org
>  Seattle, WA 98103 8904             http://www.systemsbiology.org
>
>
>
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