Commit 8cfb6bfd authored by Leo Gordon's avatar Leo Gordon
Browse files

pod formatting mainly

parent 28781ea0
......@@ -3,47 +3,49 @@
=head1 NAME
Bio::EnsEMBL::Hive::PipeConfig::LongMult_conf;
Bio::EnsEMBL::Hive::PipeConfig::LongMult_conf;
=head1 SYNOPSIS
# Example 1: specifying only the mandatory option:
# Example 1: specifying only the mandatory option (numbers to be multiplied are taken from defaults)
init_pipeline.pl Bio::EnsEMBL::Hive::PipeConfig::LongMult_conf -password <mypass>
# Example 2: specifying the mandatory options as well as overriding some defaults:
# Example 2: specifying the mandatory options as well as overriding the default numbers to be multiplied:
init_pipeline.pl Bio::EnsEMBL::Hive::PipeConfig::LongMult_conf -password <mypass> -first_mult 2344556 -second_mult 777666555
# Example 3: do not re-create the database, just load another multiplicaton task into an existing one:
init_pipeline.pl Bio::EnsEMBL::Hive::PipeConfig::LongMult_conf -job_topup -password <mypass> -first_mult 1111222233334444 -second_mult 38578377835
=head1 DESCRIPTION
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.
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.
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.
So 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 setting. Let's assume we are given two loooooong numbers to multiply. Reeeeally long.
So 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): 'start', 'part_multiply' and 'add_together'
that we will be using to examplify various features of the Hive.
The long multiplication pipeline consists of three "analyses" (types of tasks): 'start', 'part_multiply' and 'add_together'
that we will be using to examplify various features of the Hive.
* A 'start' 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 'start' 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 records the result in 'intermediate_result' table.
* A 'part_multiply' job takes in 'a_multiplier' and 'digit', multiplies them and records the result in 'intermediate_result' table.
* An 'add_together' job waits for the first two analyses to complete,
takes in 'a_multiplier', 'b_multiplier' and 'intermediate_result' table and produces the final result in 'final_result' table.
* An 'add_together' job waits for the first two analyses to complete,
takes in 'a_multiplier', 'b_multiplier' and 'intermediate_result' table and produces the final result in 'final_result' table.
Please see the implementation details in the Runnable modules themselves.
Please see the implementation details in Runnable modules themselves.
=head1 CONTACT
Please contact ehive-users@ebi.ac.uk mailing list with questions/suggestions.
Please contact ehive-users@ebi.ac.uk mailing list with questions/suggestions.
=cut
......
......@@ -3,26 +3,26 @@
=head1 NAME
Bio::EnsEMBL::Hive::PipeConfig::SemaLongMult_conf;
Bio::EnsEMBL::Hive::PipeConfig::SemaLongMult_conf;
=head1 SYNOPSIS
# Example 1: specifying only the mandatory option:
init_pipeline.pl Bio::EnsEMBL::Hive::PipeConfig::SemaLongMult_conf -password <mypass>
# Example 1: specifying only the mandatory option:
init_pipeline.pl Bio::EnsEMBL::Hive::PipeConfig::SemaLongMult_conf -password <mypass>
# Example 2: specifying the mandatory options as well as overriding some defaults:
init_pipeline.pl Bio::EnsEMBL::Hive::PipeConfig::SemaLongMult_conf -password <mypass> -first_mult 2344556 -second_mult 777666555
# Example 2: specifying the mandatory options as well as overriding some defaults:
init_pipeline.pl Bio::EnsEMBL::Hive::PipeConfig::SemaLongMult_conf -password <mypass> -first_mult 2344556 -second_mult 777666555
=head1 DESCRIPTION
This is the PipeConfig file for the *semaphored* long multiplication pipeline example.
The main point of this pipeline is to provide an example of how to set up job-level semaphored control instead of using analysis-level control rules.
This is the PipeConfig file for the *semaphored* long multiplication pipeline example.
The main point of this pipeline is to provide an example of how to set up job-level semaphored control instead of using analysis-level control rules.
Please refer to Bio::EnsEMBL::Hive::PipeConfig::LongMult_conf to understand how long multiplication pipeline works in its original form.
Please refer to Bio::EnsEMBL::Hive::PipeConfig::LongMult_conf to understand how long multiplication pipeline works in its original form.
=head1 CONTACT
Please contact ehive-users@ebi.ac.uk mailing list with questions/suggestions.
Please contact ehive-users@ebi.ac.uk mailing list with questions/suggestions.
=cut
......@@ -117,7 +117,7 @@ sub pipeline_analyses {
-module => 'Bio::EnsEMBL::Hive::RunnableDB::LongMult::PartMultiply',
-parameters => {},
-input_ids => [
# (jobs for this analysis will be flown_into via branch-2 from 'start' jobs above)
# (jobs for this analysis will be flown_into via branch-2 from 'sema_start' jobs above)
],
},
......@@ -125,7 +125,7 @@ sub pipeline_analyses {
-module => 'Bio::EnsEMBL::Hive::RunnableDB::LongMult::AddTogether',
-parameters => {},
-input_ids => [
# (jobs for this analysis will be flown_into via branch-1 from 'start' jobs above)
# (jobs for this analysis will be flown_into via branch-1 from 'sema_start' jobs above)
],
# jobs in this analyses are semaphored, so no need to '-wait_for'
},
......
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