[ensembl-dev] bugs in blastz-chain-net pipeline

Javier Herrero jherrero at ebi.ac.uk
Thu Feb 2 16:02:13 GMT 2012

Hi Sharon

The problem is that ensembl-analysis has been updated to work with the 
forthcoming 64 API. Ensembl-analysis is not tagged with the rest of the 
API. However, you can still get an older version of the code by using 
the -D option of the cvs command:

cd ensembl-analysis
cvs update -D "2011-11-20"

Note that the date is sticky and you would have to run

cd ensembl-analysis
cvs update -A

when you'll want to update to the latest API.

I believe Leo is looking into the second part of your question.

I hope this helps


On 02/02/12 15:39, Sharon Wei wrote:
> Hi Ensembl Compara team,
> I recently updated our local blastz pipeline to ensembl-65 code, and 
> have found two places where there seem to be a bug.
> 1. In 
> ensembl-analysis/modules/Bio/EnsEMBL/Analysis/Runnable/AlignmentNets.pm
> line 394:      $fp->level_id($level_id);
> The $fp is a GenomicAlignBlock object, and this object has no function 
> level_id(), only GenomicAlign has this function.
> So I changed it to
>    map {$_->level_id($level_id)} @{$fp->genomic_align_array()};
> 2. In ensembl-hive/modules/Bio/EnsEMBL/Hive/DBSQL/AnalysisJobAdaptor.pm
> In function CreateNewJob(), the following doesn't make sense and I had 
> to comment it out to make the pipeline work.
> throw("Please specify prev_job object instead of input_job_id if 
> available") if ($prev_job_id);
> sub CreateNewJob {
>   my ($class, @args) = @_;
>   return undef unless(scalar @args);
>   my ($input_id, $analysis, $prev_job, $prev_job_id, $blocked, 
> $semaphore_count, $semaphored_job_id) =
>   throw("must define input_id") unless($input_id);
>   throw("must define analysis") unless($analysis);
>   throw("analysis must be [Bio::EnsEMBL::Analysis] not a [$analysis]")
>     unless($analysis->isa('Bio::EnsEMBL::Analysis'));
>   throw("analysis must have adaptor connected to database")
>     unless($analysis->adaptor and $analysis->adaptor->db);
>   throw("Please specify prev_job object instead of input_job_id if 
> available") if ($prev_job_id);   # 'obsolete' message
>   $prev_job_id = $prev_job && $prev_job->dbID();
>         # if the user did not specifically ask for a new fan, consider 
> propagation:
> Sharon
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Javier Herrero, PhD
Ensembl Coordinator and Ensembl Compara Project Leader
European Bioinformatics Institute (EMBL-EBI)
Wellcome Trust Genome Campus, Hinxton
Cambridge - CB10 1SD - UK

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