ensembl-hive
2.1
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This is an example pipeline built around FailureTest.pm RunnableDB. It consists of two analyses: Analysis_1: JobFactory.pm is used to create an array of jobs - these jobs are sent down the branch #2 into the second analysis Analysis_2: FailureTest.pm either succeeds or dies, depending on the parameters.
public Bio::EnsEMBL::Hive::PipeConfig::FailureTest_conf::default_options | ( | ) |
Description : Implements default_options() interface method of Bio::EnsEMBL::Hive::PipeConfig::HiveGeneric_conf that is used to initialize default options. In addition to the standard things it defines three options: o('job_count') controls the total number of FailureTest jobs o('failure_rate') controls the rate of jobs that are programmed to fail o('state') controls the state in which the jobs will be failing o('lethal_after') when job_number is above this (nonzero) threshold, job's death becomes lethal to the Worker
There is a rule dependent on one option that does not have a default (this makes it mandatory): o('password') your read-write password for creation and maintenance of the hive database
public Bio::EnsEMBL::Hive::PipeConfig::FailureTest_conf::pipeline_analyses | ( | ) |
Description : Implements pipeline_analyses() interface method of Bio::EnsEMBL::Hive::PipeConfig::HiveGeneric_conf that defines the structure of the pipeline: analyses, jobs, rules, etc. Here it defines two analyses:
'generate_jobs' generates a list of jobs
'failure_test' either succeeds or fails, depending on parameters