ensembl-hive
2.1
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This is the PipeConfig file for the long multiplication pipeline example. The main point of this pipeline is to provide an example of how to write Hive Runnables and link them together into a pipeline. Please refer to Bio::EnsEMBL::Hive::PipeConfig::HiveGeneric_conf module to understand the interface implemented here. The setting. let's assume we are given two loooooong numbers to multiply. reeeeally long. soooo long that they do not fit into registers of the cpu and should be multiplied digit-by-digit. For the purposes of this example we also assume this task is very computationally intensive and has to be done in parallel. The long multiplication pipeline consists of three "analyses" (types of tasks): 'take_b_apart', 'part_multiply' and 'add_together' that we use to examplify various features of the Hive. A 'take_b_apart' job takes in two string parameters, 'a_multiplier' and 'b_multiplier', takes the second one apart into digits, finds what _different_ digits are there, creates several jobs of the 'part_multiply' analysis and one job of 'add_together' analysis. A 'part_multiply' job takes in 'a_multiplier' and 'digit', multiplies them and accumulates the result in 'partial_product' accumulator. An 'add_together' job waits for the first two analyses to complete, takes in 'a_multiplier', 'b_multiplier' and 'partial_product' hash and produces the final result in 'final_result' table. Please see the implementation details in Runnable modules themselves.
public Bio::EnsEMBL::Hive::PipeConfig::LongMult_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 three analyses: 'take_b_apart' that is auto-seeded with a pair of jobs (to check the commutativity of multiplication). Each job will dataflow (create more jobs) via branch #2 into 'part_multiply' and via branch #1 into 'add_together'.
'part_multiply' with jobs fed from take_b_apart#2. It multiplies input parameters 'a_multiplier' and 'digit' and dataflows 'partial_product' parameter into branch #1.
'add_together' with jobs fed from take_b_apart#1. It adds together results of partial multiplication computed by 'part_multiply'. These results are accumulated in 'partial_product' hash. Until the hash is complete the corresponding 'add_together' job is blocked by a semaphore.
public Bio::EnsEMBL::Hive::PipeConfig::LongMult_conf::pipeline_create_commands | ( | ) |
Description : Implements pipeline_create_commands() interface method of Bio::EnsEMBL::Hive::PipeConfig::HiveGeneric_conf that lists the commands that will create and set up the Hive database. In addition to the standard creation of the database and populating it with Hive tables and procedures it also creates two pipeline-specific tables used by Runnables to communicate.
public Bio::EnsEMBL::Hive::PipeConfig::LongMult_conf::pipeline_wide_parameters | ( | ) |
Description : Interface method that should return a hash of pipeline_wide_parameter_name->pipeline_wide_parameter_value pairs. The value doesn't have to be a scalar, can be any Perl structure now (will be stringified and de-stringified automagically). Please see existing PipeConfig modules for examples.