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Bio::EnsEMBL::Compara::PipeConfig::ImportNCBItaxonomy_conf Class Reference
Inheritance diagram for Bio::EnsEMBL::Compara::PipeConfig::ImportNCBItaxonomy_conf:

List of all members.


Class Summary

Synopsis

    init_pipeline.pl Bio::EnsEMBL::Compara::PipeConfig::ImportNCBItaxonomy_conf -password \<your_password\> -ensembl_cvs_root_dir \<path_to_your_ensembl_cvs_root\>
    init_pipeline.pl Bio::EnsEMBL::Compara::PipeConfig::ImportNCBItaxonomy_conf -password \<your_password\>

Definition at line 12 of file ImportNCBItaxonomy_conf.pm.

Available Methods

public beekeeper_extra_cmdline_options ()
public db_connect_command ()
public db_execute_command ()
public dbconn_2_mysql ()
public dbconn_2_url ()
public default_options ()
public fully_substituted_string ()
public fully_substituted_structure ()
public hash_leaves ()
public load_cmdline_options ()
public merge_from_rules ()
public new ()
public o ()
public pipeline_analyses ()
public pipeline_create_commands ()
public pipeline_url ()
public pipeline_wide_parameters ()
public pre_options ()
public process_options ()
public resource_classes ()
public root ()
public run ()
public substitute ()
public use_cases ()

Method Documentation

public Bio::EnsEMBL::Compara::PipeConfig::ImportNCBItaxonomy_conf::default_options ( )
    Description : Implements default_options() interface method of Bio::EnsEMBL::Hive::PipeConfig::HiveGeneric_conf that is used to initialize default options.
                  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
 
Code:
click to view

Reimplemented from Bio::EnsEMBL::Hive::PipeConfig::HiveGeneric_conf.

public Bio::EnsEMBL::Compara::PipeConfig::ImportNCBItaxonomy_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.
 
Code:
click to view

Reimplemented from Bio::EnsEMBL::Hive::PipeConfig::HiveGeneric_conf.

public Bio::EnsEMBL::Compara::PipeConfig::ImportNCBItaxonomy_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 a working directory to store intermediate files.
 
Code:
click to view

Reimplemented from Bio::EnsEMBL::Hive::PipeConfig::HiveGeneric_conf.

public Bio::EnsEMBL::Compara::PipeConfig::ImportNCBItaxonomy_conf::resource_classes ( )

Undocumented method

Code:
click to view

Reimplemented from Bio::EnsEMBL::Hive::PipeConfig::HiveGeneric_conf.


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