[Bioperl-pipeline] Annotation example error
shawnh@fugu-sg.org
shawnh@fugu-sg.org
Tue, 22 Oct 2002 00:00:23 +0800 (SGT)
Hi Sean,
I just found out what was the problem. The developer cvs
and the public cvs are somehow not in sync. THe version of the xml
which I committed doesn't seem to have found its way to the public cvs
repository.
weird. Will try and find out whats going on.
in the mean time, I have put the xml up on the web for download.
http://www.biopipe.org/download/genomic_sequence_annotation.xml
but it may not work if the code was not updated as well.
cheers,
shawn
On Mon, 21 Oct 2002, McWilliam, Sean (LI, Uni of Queensland) wrote:
> Hi,
>
> Shawn, thanks for the reponse.
> I checked out the new CVS for biopipe. This has solved the database problem.
> The annotate_pipeline database is now updated.
> But when I run PipelineManager.pl (after altering PipeConf.pm to suit) I get
> the following output:
>
> ///////////////Starting Pipeline//////////////////////
> Fetching Analysis From Pipeline annotate_pipeline
> 7 analysis found.
> Running test and setup..
>
> //////////// Analysis Test ////////////
> Checking Analysis 1 RepeatMasker ok
> Checking Analysis 2 blast ok
> Checking Analysis 3 blast ok
> Checking Analysis 4 blast ok
> Checking Analysis 5 blast ok
> Checking Analysis 6 blast ok
> Checking Analysis 7 blast ok
>
> ///////////////Tests Completed////////////////////////
>
> Starting fresh pipeline run
> Fetching Input ids
> CREATED Initial jobs!
> Fetched 0 incomplete jobs
> Fetched 0 completed jobs
> Going to snooze for 3 seconds...
> Waking up and run again!
> Nothing left to run.
>
> ///////////////Shutting Down Pipeline//////////////////////
> Removing Lock File...
> Done
> ///////////////////////////////////////////////////////////
>
> This looks OK but happens almost instantly, which made we query whether the
> ens_test
> database had been updated. It appears nothing was added to the ens_test
> database.
>
> ens_test does initially contain the 2 test contigs and dna.
> So any ideas why the pipeline is not running or the ens_test database not
> updated?
> Is it possible to get a dump of the annotate_pipeline database for the
> example so I can check if it is being updated correctly by Xml2db.pl?
> I can run RepeatMasker and blastall from the command line and I have used
> bioperl to run Genscan as a test of my setup previously so I assume my path
> is OK.
>
>
> The following is not entirely related but I have a couple of minor
> suggestions for altering the code in Xml2db.pl and PipelineManager.pl to fix
> some problems I had with them.
>
> In Xml2db.pl change the code in else statement when creating new database
> so that command line arguments are used for username and password rather
> than
> root and null password.
> Add -f (force) option so that mysqladmin doesn't wait for confirmation from
> user
> before dropping database (avoids having to hit enter key again)
>
> else {
> system("mysqladmin -u $DBUSER -p$DBPASS -f drop $DBNAME > /dev/null
> ");
> print STDERR "Creating $DBNAME\n ";
> system("mysqladmin -u $DBUSER -p$DBPASS create $DBNAME ");
> print STDERR "Loading Schema\n";
> system("mysql -u $DBUSER -p$DBPASS $DBNAME < $SCHEMA");
> }
>
> In PerlManager.pl add line to sub remove_lock.
>
> unlink "$dir/db.db";
>
> otherwise dir is not empty and not deleted (lock not removed).
>
> Cheers and thanks,
> Sean
>
> -----Original Message-----
> From: shawnh@fugu-sg.org [mailto:shawnh@fugu-sg.org]
> Sent: Monday, 21 October 2002 11:43 AM
> To: McWilliam, Sean (LI, Uni of Queensland)
> Cc: 'bioperl-pipeline@bioperl.org'
> Subject: Re: [Bioperl-pipeline] Annotation example error
>
>
> 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
> > ============================
> > _______________________________________________
> > bioperl-pipeline mailing list
> > bioperl-pipeline@bioperl.org
> > http://bioperl.org/mailman/listinfo/bioperl-pipeline
> >
>
>
--
********************************
* Shawn Hoon
* http://www.fugu-sg.org/~shawnh
********************************