[Bioperl-pipeline] Re: please ignore last e-mail & problem with
Xml2Db.pl
Shawn Hoon
shawnh at fugu-sg.org
Wed Mar 12 09:10:20 EST 2003
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
>
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