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

[Sharon Wei]

Thanks, that makes sense.

Sharon

On 2/2/12 11:04 AM, Javier Herrero wrote:
> 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
>>>
>>>
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>>>
>>
>