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

List of all members.


Class Summary

Synopsis

    init_pipeline.pl Bio::EnsEMBL::Compara::PipeConfig::DumpTrees_conf -password \<your_password\> -tree_type protein_trees

    init_pipeline.pl Bio::EnsEMBL::Compara::PipeConfig::DumpTrees_conf -password \<your_password\> -tree_type ncrna_trees

Definition at line 13 of file DumpTrees_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::DumpTrees_conf::default_options ( )
    Description : Implements default_options() interface method of Bio::EnsEMBL::Hive::PipeConfig::HiveGeneric_conf that is used to initialize default options.
 
Code:
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Reimplemented from Bio::EnsEMBL::Hive::PipeConfig::HiveGeneric_conf.

public Bio::EnsEMBL::Compara::PipeConfig::DumpTrees_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 seven analyses:
 'generate_tree_ids'   generates a list of tree_ids to be dumped
 'dump_a_tree'         dumps one tree in multiple formats
 'generate_collations' generates five jobs that will be merging the hashed single trees
 'collate_dumps'       actually merge/collate single trees into long dumps
 'remove_hash'         remove the temporary hash of directories
 'archive_long_files'  zip the long dumps
 'md5sum'              compute md5sum for compressed files
 
Code:
click to view

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

public Bio::EnsEMBL::Compara::PipeConfig::DumpTrees_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 directories for storing the output.
 
Code:
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Reimplemented from Bio::EnsEMBL::Hive::PipeConfig::HiveGeneric_conf.

public Bio::EnsEMBL::Compara::PipeConfig::DumpTrees_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: