ensembl-hive
2.1
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This is an example pipeline put together from basic building blocks: Analysis_1: JobFactory.pm is used to turn the list of commands in a file into jobs these jobs are sent down the branch #2 into the second analysis Analysis_2: SystemCmd.pm is used to run these jobs in parallel.
public Bio::EnsEMBL::Hive::PipeConfig::RunListOfCommandsOnFarm_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('capacity') defines how many files can be run in parallel
There are rules dependent on two options that do not have defaults (this makes them mandatory): o('password') your read-write password for creation and maintenance of the hive database o('inputfile') name of the inputfile where the commands are
public Bio::EnsEMBL::Hive::PipeConfig::RunListOfCommandsOnFarm_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:
'create_jobs' reads commands line-by-line from inputfile Each job of this analysis will dataflow (create jobs) via branch #2 into 'run_cmd' analysis.
'run_cmd' actually runs the commands in parallel