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

[Javier Herrero]

Forthcoming 66 API, not 64...

On 02/02/12 16:02, Javier Herrero wrote:
> 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
>
> Javier
>
> 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, $semaphored_job_id) =
>>      rearrange([qw(INPUT_ID ANALYSIS PREV_JOB INPUT_JOB_ID BLOCK 
>> SEMAPHORE_COUNT SEMAPHORED_JOB_ID)], @args);
>>
>>   throw("must define input_id") unless($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
>>
>>
>> _______________________________________________
>> Dev mailing list    Dev at ensembl.org
>> List admin (including subscribe/unsubscribe): 
>> http://lists.ensembl.org/mailman/listinfo/dev
>> Ensembl Blog: http://www.ensembl.info/
>>
>

-- 
Javier Herrero, PhD
Ensembl Coordinator and Ensembl Compara Project Leader
European Bioinformatics Institute (EMBL-EBI)
Wellcome Trust Genome Campus, Hinxton
Cambridge - CB10 1SD - UK