[Bioperl-pipeline] Re: please ignore last e-mail & problem with Xml2Db.pl

[Shawn Hoon]

Hi Andy,
	I haven't used the genomic_sequence_annotation.xml for a while but am 
getting back to it
having a 'few' sequences to annotate now =) I believe some others like 
Bala are working on this xml
more and probably have more comments.

But as for XML2Db.pl, during the hackathon I merged the 
PipelineManager.pl and XML2Db.pl script into a single script:

PipelineManager

using it is as follows

Usage: PipelineManager -dbname test_pipe -xml 
template/blast_file_pipeline.xml -local

Options:
Default values are read from PipeConf.pm

      -dbhost    The database host name (localhost)
      -dbname    The pipeline database name (annotate_pipeline)
      -dbuser    User for connecting to db (root)
      -dbpass    The password to mysql database()
      -dbdriver  Database driver (mysql)
      -schema    The Biopipe database schema (../sql/schema)
      -xml       The xml pipeline template file. It will run XMLImporter 
if provided
      -xf        Force drop of any existing Biopipe database with the 
same name
      -flush     flush all locks on pipeline and remove any that exists.
                 Should only be used for debugging or development.
      -batchsize The number ofjobs to be batched to one node
      -local     Whether to run jobs in local mode
                 (on the node where this script is run)
      -jobnbr    Number of jobs to run (for testing)
      -queue     Specify the queue on which to submit jobs
      -retry     Number of times to retry failed jobs
      -notest    Don't run pre-pipeline checks
      -norun     Use when you just want to load the XML without running
      -verbose   Whether to show warning during test and setup
      -help      Display this help



With this script one can
1) Load XML
2) Run Pipeline
3) Load XML & Run Pipeline

For 1)
	perl PipelineManager -dbname pipeline_db -xml 
xml/templates/blast_file_pipeline -norun

For 2)
	perl PipelineManager -dbname pipeline_db

For 3)
	perl PipelineManager -dbname pipeline_db -xml 
xml/templates/blast_file_pipeline



Do people have any problems with having just one script? It has been 
working so far with the tests.
If not I will remove the deprecated scripts.

cheers,

shawn


On Tuesday, March 11, 2003, at 05:04 AM, Andy Nunberg wrote:

> Sorry the last e-mail,
> I saw the answer inside the documentation...
>
> I tested Xml2Db.pl using the genomic_sequence_annotation.xml in
> xml/templates/dev
>
> the script breaks, here is what i saw...
>
> andy at arcturus:~/bio-pipeline/bioperl-pipeline/scripts(54)$perl 
> Xml2Db.pl
> -dbhost db -dbname test_XML -dbuser bio -v -p
> ../xml/templates/dev/genomic_sequence_annotation.xml
> Creating test_XML
>    Loading Schema...
> Reading Data_setup xml   : 
> ../xml/templates/dev/genomic_sequence_annotation.xml
> Doing DBAdaptor and IOHandler setup
> Doing Converters..
> Doing Pipeline Flow Setup
> Doing Analysis..
> Bio::Pipeline::InputCreate: Bio::Pipeline::InputCreate::setup_initial
> cannot be found
> Exception Can't locate object method "_load_module" via package
> "Bio::Pipeline::InputCreate" at
> /usr/lib/perl5/site_perl/5.6.0/Bio/Pipeline/InputCreate.pm line 199.
>
> For more information about the Bio::Pipeline::InputCreate system 
> please see
> the pipeline docs
> This includes ways of checking for formats at compile time, not run 
> time
> Can't call method "arguments" on an undefined value at Xml2Db.pl line 
> 453.
>
> these are lines 452,453 from Xml2Db.pl
> my $input_create = Bio::Pipeline::InputCreate->new(-module => $module,
> -rank => $rank, @arguments_hash);
>            $input_create->arguments(\@arguments);
>
> Does the script need to be updated or maybe its the way I installed
> bioperl-pipeline?
> Thanks
> Andy
> *******************************************************************
> Andy Nunberg, Ph.D
> Computational Biologist
> Orion Genomics, LLC
> (314) 615-6989
> http://www.oriongenomics.com
>