[Bioperl-pipeline] Annotation example error

[shawnh@fugu-sg.org]

Hi Sean,
	Yup not your fault. We forgot to commit the schema to biosql.So we have
committed that and you can check that out. We also have the latest schema stored at 
t/data/schema.sql  when you check out biopipe.
Also the latest xml file genomic_sequence_annotation.xml
is committed so play around with that.
You will also need to download a tar ball containing the sample data at:

http://www.biopipe.org/bioperl-pipeline-download.html

and checkout the BioToEns conversion utiltity module, information
as the same page.

This pipeline is simple just repeatmask + a bunch of blasts.

We will be adding the genscan and genewise analysis shortly.

do let us know if u face anymore problems.

cheers,

shawn
On Fri, 18 Oct 2002, McWilliam, Sean (LI, Uni of Queensland) wrote:

> Hi,
> 
> 	I have been trying to run the example annotation at 
> http://www.biopipe.org/bioperl-pipeline-run.html
> 
> I think I have everything set up as detailed but when I run Xml2db.pl as
> follows
> 
> perl Xml2Db.pl -dbhost localhost -dbname annotate_pipeline -dbuser *******
> -dbpass ****** -p templates/genomic_sequence_annotation.xml
> 
> I get the following error message
> 
> Using existing db annotate_pipelineReading Data_setup xml   :
> templates/genomic_sequence_annotation.xml
> Doing DBAdaptor and IOHandler setup
> Doing Pipeline Flow Setup
> Doing Analysis..
> Doing Rules
> Doing Job Setup...
> DBD::mysql::st execute failed: Column 'current' cannot be null at
> /usr/local/ensembl/bioperl-pipeline/Bio/Pipeline/SQL/RuleAdaptor.pm line 85,
> <STDIN> line 1.
> DBD::mysql::st execute failed: Column 'current' cannot be null at
> /usr/local/ensembl/bioperl-pipeline/Bio/Pipeline/SQL/RuleAdaptor.pm line 85,
> <STDIN> line 1.
> 
> Any helpful advice would be greatly appreciated, couldn't find anything in
> the archives.
> 
> Cheers,
> Sean
> 
> ============================
> Sean McWilliam
> CSIRO Livestock Industries
> Level 3 Gehrmann Labs
> Research Road
> University of Queensland
> St Lucia, 4072
> 
> email:	sean.mcwilliam@csiro.au
> phone:	07 3346 2504
> fax: 	 	07 3214 2480
> ============================
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> 

-- 
********************************
* Shawn Hoon
* http://www.fugu-sg.org/~shawnh
********************************