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Bio::EnsEMBL::Compara::PipeConfig::Example::EGProteinTrees_conf Class Reference
Inheritance diagram for Bio::EnsEMBL::Compara::PipeConfig::Example::EGProteinTrees_conf:

List of all members.


Class Summary

Synopsis

    #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::Example::EGProteinTrees_conf \
        -password \<your_password\> -mlss_id \<your_current_PT_mlss_id\> \
        -division \<eg_division\> -eg_release \<egrelease\> -release \<release\>

    #5. Sync and loop the beekeeper.pl as shown in init_pipeline.pl's output

Description

    The PipeConfig example file for Ensembl Genomes group's version of
    ProteinTrees pipeline. This file is inherited from & customised further
    within the Ensembl Genomes infrastructure but this file serves as
    an example of the type of configuration we perform.
 

Definition at line 33 of file EGProteinTrees_conf.pm.

Available Methods

protected _get_analysis ()
protected _modify_analyses ()
protected _new_analyses ()
protected _pipeline_db_options ()
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

protected Bio::EnsEMBL::Compara::PipeConfig::Example::EGProteinTrees_conf::_get_analysis ( )

Undocumented method

Code:
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protected Bio::EnsEMBL::Compara::PipeConfig::Example::EGProteinTrees_conf::_modify_analyses ( )

Undocumented method

Code:
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protected Bio::EnsEMBL::Compara::PipeConfig::Example::EGProteinTrees_conf::_new_analyses ( )

Undocumented method

Code:
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protected Bio::EnsEMBL::Compara::PipeConfig::Example::EGProteinTrees_conf::_pipeline_db_options ( )

Undocumented method

Code:
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public Bio::EnsEMBL::Compara::PipeConfig::Example::EGProteinTrees_conf::default_options ( )

Undocumented method

Code:
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Reimplemented from Bio::EnsEMBL::Compara::PipeConfig::ProteinTrees_conf.

public Bio::EnsEMBL::Compara::PipeConfig::Example::EGProteinTrees_conf::pipeline_analyses ( )

Undocumented method

Code:
click to view

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

public Bio::EnsEMBL::Compara::PipeConfig::Example::EGProteinTrees_conf::pipeline_create_commands ( )

Undocumented method

Code:
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Reimplemented from Bio::EnsEMBL::Compara::PipeConfig::ProteinTrees_conf.

public Bio::EnsEMBL::Compara::PipeConfig::Example::EGProteinTrees_conf::pipeline_wide_parameters ( )

Undocumented method

Code:
click to view

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

public Bio::EnsEMBL::Compara::PipeConfig::Example::EGProteinTrees_conf::resource_classes ( )

Undocumented method

Code:
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Reimplemented from Bio::EnsEMBL::Compara::PipeConfig::ProteinTrees_conf.


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