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

List of all members.


Class Summary

Description

    The PipeConfig file for ProteinTrees pipeline that should automate most of the pre-execution tasks.
 

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::ProteinTrees_conf -password \<your_password\> -mlss_id \<your_current_PT_mlss_id\>

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

=head2 rel.63 stats

    sequences to cluster:       1,198,678           [ SELECT count(*) from sequence; ]
    reused core dbs:            48                  [ SELECT count(*) FROM analysis JOIN job USING(analysis_id) WHERE logic_name='paf_table_reuse'; ]
    newly loaded core dbs:       5                  [ SELECT count(*) FROM analysis JOIN job USING(analysis_id) WHERE logic_name='load_fresh_members'; ]

    total running time:         8.7 days            [ SELECT (UNIX_TIMESTAMP(max(died))-UNIX_TIMESTAMP(min(born)))/3600/24 FROM worker;  ]  # NB: stable_id mapping phase not included
    blasting time:              1.9 days            [ SELECT (UNIX_TIMESTAMP(max(died))-UNIX_TIMESTAMP(min(born)))/3600/24 FROM worker JOIN analysis USING (analysis_id) WHERE logic_name='blastp_with_reuse'; ]

=head2 rel.62 stats

    sequences to cluster:       1,192,544           [ SELECT count(*) from sequence; ]
    reused core dbs:            46                  [ number of 'load_reuse_members' jobs ]
    newly loaded core dbs:       7                  [ number of 'load_fresh_members' jobs ]

    total running time:         6 days              [ SELECT (UNIX_TIMESTAMP(max(died))-UNIX_TIMESTAMP(min(born)))/3600/24 FROM hive;  ]
    blasting time:              2.7 days            [ SELECT (UNIX_TIMESTAMP(max(died))-UNIX_TIMESTAMP(min(born)))/3600/24 FROM hive JOIN analysis USING (analysis_id) WHERE logic_name='blastp_with_reuse'; ]

=head2 rel.61 stats

    sequences to cluster:       1,173,469           [ SELECT count(*) from sequence; ]
    reused core dbs:            46                  [ number of 'load_reuse_members' jobs ]
    newly loaded core dbs:       6                  [ number of 'load_fresh_members' jobs ]

    total running time:         6 days              [ SELECT (UNIX_TIMESTAMP(max(died))-UNIX_TIMESTAMP(min(born)))/3600/24 FROM hive;  ]
    blasting time:              1.4 days            [ SELECT (UNIX_TIMESTAMP(max(died))-UNIX_TIMESTAMP(min(born)))/3600/24 FROM hive JOIN analysis USING (analysis_id) WHERE logic_name like 'blast%' or logic_name like 'SubmitPep%'; ]

Definition at line 52 of file ProteinTrees_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::ProteinTrees_conf::default_options ( )

Undocumented method

Code:
click to view

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

Reimplemented in Bio::EnsEMBL::Compara::PipeConfig::Example::EGProteinTrees_conf, Bio::EnsEMBL::Compara::PipeConfig::Example::VegaProteinTrees_conf, and Bio::EnsEMBL::Compara::PipeConfig::Example::WormProteinTrees_conf.

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

Undocumented method

Code:
click to view

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

Reimplemented in Bio::EnsEMBL::Compara::PipeConfig::Example::EGProteinTrees_conf.

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

Undocumented method

Code:
click to view

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

Reimplemented in Bio::EnsEMBL::Compara::PipeConfig::Example::EGProteinTrees_conf.

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

Undocumented method

Code:
click to view

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

Reimplemented in Bio::EnsEMBL::Compara::PipeConfig::Example::EGProteinTrees_conf.


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