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

List of all members.


Class Summary

Synopsis

    #0. make sure that ProteinTree pipeline (whose EnsEMBL peptide members you want to incorporate) is already past member loading stage

    #1. update ensembl-hive, ensembl and ensembl-compara CVS repositories before each new release

    #2. you may need to update 'schema_version' in meta table to the current release number in ensembl-hive/sql/tables.sql

    #3. make sure that all default_options are set correctly

    #4. Run init_pipeline.pl script:
        init_pipeline.pl Bio::EnsEMBL::Compara::PipeConfig::Families_conf -password \<your_password\>

    #5. Run the "beekeeper.pl ... -loop" command suggested by init_pipeline.pl

    #6. Please remember that mapping_session, stable_id_history, member and sequence tables will have to be MERGED in an intelligent way, and not just written over.
        ReleaseCoordination.txt document explains how to do the merge correctly.

Definition at line 25 of file Families_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::Families_conf::beekeeper_extra_cmdline_options ( )

Undocumented method

Code:
click to view

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

public Bio::EnsEMBL::Compara::PipeConfig::Families_conf::default_options ( )

Undocumented method

Code:
click to view

Reimplemented from Bio::EnsEMBL::Compara::PipeConfig::ComparaGeneric_conf.

public Bio::EnsEMBL::Compara::PipeConfig::Families_conf::pipeline_analyses ( )

Undocumented method

Code:
click to view

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

public Bio::EnsEMBL::Compara::PipeConfig::Families_conf::pipeline_create_commands ( )

Undocumented method

Code:
click to view

Reimplemented from Bio::EnsEMBL::Compara::PipeConfig::ComparaGeneric_conf.

public Bio::EnsEMBL::Compara::PipeConfig::Families_conf::pipeline_wide_parameters ( )

Undocumented method

Code:
click to view

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

public Bio::EnsEMBL::Compara::PipeConfig::Families_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: