ensembl-hive  2.1
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Bio::EnsEMBL::Hive::PipeConfig::TableDumperZipper_conf Class Reference
+ Inheritance diagram for Bio::EnsEMBL::Hive::PipeConfig::TableDumperZipper_conf:
+ Collaboration diagram for Bio::EnsEMBL::Hive::PipeConfig::TableDumperZipper_conf:

Public Member Functions

public pipeline_wide_parameters ()
 
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::TableDumperZipper_conf -password $ENSADMIN_PSW -db_conn "mysql://ensadmin:${ENSADMIN_PSW}@localhost/lg4_long_mult"
seed_pipeline.pl -url "mysql://ensadmin:${ENSADMIN_PSW}@localhost:3306/lg4_zip_tables" -logic_name find_tables -input_id "{'only_tables' => '%_result'}"
runWorker.pl -url mysql://ensadmin:${ENSADMIN_PSW}@localhost:3306/lg4_zip_tables
runWorker.pl -url mysql://ensadmin:${ENSADMIN_PSW}@localhost:3306/lg4_zip_tables
runWorker.pl -url mysql://ensadmin:${ENSADMIN_PSW}@localhost:3306/lg4_zip_tables

Member Function Documentation

public Bio::EnsEMBL::Hive::PipeConfig::TableDumperZipper_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:
                      'find_tables'         generates a list of tables whose names match the pattern #only_tables#
                      Each job of this analysis will dataflow (create jobs) via branch #2 into 'table_dumper' analysis.
                      'table_dumper'        dumps table contents (possibly with table definition) and flows via branch #1 into 'file_compressor' analysis.
                      'file_compressor'     compresses the dump file
 
Code:
click to view
public Bio::EnsEMBL::Hive::PipeConfig::TableDumperZipper_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 (will be stringified and de-stringified automagically).
 
Code:
click to view

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