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

List of all members.


Class Summary

Synopsis

    init_pipeline.pl Bio::EnsEMBL::Compara::PipeConfig::LoadCertainGenomeDB_conf -password \<your_password\>

Definition at line 11 of file LoadCertainGenomeDB_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::LoadCertainGenomeDB_conf::default_options ( )

Undocumented method

Code:
click to view

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

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

Undocumented method

Code:
click to view

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

public Bio::EnsEMBL::Compara::PipeConfig::ComparaGeneric_conf::pipeline_create_commands ( ) [inherited]

Undocumented method

Code:
click to view

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

Reimplemented in Bio::EnsEMBL::Compara::PipeConfig::EPO_conf, Bio::EnsEMBL::Compara::PipeConfig::EpoLowCoverage_conf, Bio::EnsEMBL::Compara::PipeConfig::Example::EGProteinTrees_conf, Bio::EnsEMBL::Compara::PipeConfig::Families_conf, Bio::EnsEMBL::Compara::PipeConfig::GenerateAnchors_conf, Bio::EnsEMBL::Compara::PipeConfig::GeneTreesStableIdAndTreefamXrefs_conf, Bio::EnsEMBL::Compara::PipeConfig::HmmerConstrainedElements_conf, Bio::EnsEMBL::Compara::PipeConfig::ImportUcscChainNet_conf, Bio::EnsEMBL::Compara::PipeConfig::MercatorPecan_conf, Bio::EnsEMBL::Compara::PipeConfig::MergeHomologySideTogether_conf, Bio::EnsEMBL::Compara::PipeConfig::MyISAMiseTables_conf, Bio::EnsEMBL::Compara::PipeConfig::ncRNAtrees_conf, Bio::EnsEMBL::Compara::PipeConfig::PairAligner_conf, Bio::EnsEMBL::Compara::PipeConfig::ProteinTrees_conf, Bio::EnsEMBL::Compara::PipeConfig::ProteinTreesFromFASTA_conf, Bio::EnsEMBL::Compara::PipeConfig::SplitAndPartialGenesOnTrees_conf, Bio::EnsEMBL::Compara::PipeConfig::SplitAndPartialGenesOnTrees_ensembl_genomes_conf, and Bio::EnsEMBL::Compara::PipeConfig::TBlat_conf.


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