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Bio::EnsEMBL::Hive::PipeConfig::FailureTest_conf Class Reference
+ Inheritance diagram for Bio::EnsEMBL::Hive::PipeConfig::FailureTest_conf:
+ Collaboration diagram for Bio::EnsEMBL::Hive::PipeConfig::FailureTest_conf:

Public Member Functions

public default_options ()
 
public pipeline_analyses ()
 
- Public Member Functions inherited from Bio::EnsEMBL::Hive::PipeConfig::HiveGeneric_conf
public default_options ()
 
public pipeline_create_commands ()
 
public pipeline_wide_parameters ()
 
public resource_classes ()
 
public pipeline_analyses ()
 
public beekeeper_extra_cmdline_options ()
 
public hive_meta_table ()
 
public pre_options ()
 
public dbconn_2_mysql ()
 
public dbconn_2_pgsql ()
 
public db_connect_command ()
 
public db_execute_command ()
 
public dbconn_2_url ()
 
public pipeline_url ()
 
public db_cmd ()
 
public pipeline_name ()
 
public process_options ()
 
public overridable_pipeline_create_commands ()
 
public run_pipeline_create_commands ()
 
public add_objects_from_config ()
 
public useful_commands_legend ()
 
- Public Member Functions inherited from Bio::EnsEMBL::Hive::DependentOptions
public new ()
 
public use_cases ()
 
public load_cmdline_options ()
 
public root ()
 
public is_fully_substituted_string ()
 
public is_fully_substituted_structure ()
 
public hash_leaves ()
 
public o ()
 
public substitute ()
 
public merge_from_rules ()
 
public process_options ()
 

Detailed Description

Synopsis

init_pipeline.pl Bio::EnsEMBL::Hive::PipeConfig::FailureTest_conf -password <your_password>
init_pipeline.pl FailureTest_conf.pm -host=localhost -password <your_password> -job_count 100 -failure_rate 3

Description

    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.

Member Function Documentation

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
 
Code:
click to view
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
 
Code:
click to view

The documentation for this class was generated from the following file: