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Bio::EnsEMBL::Compara::RunnableDB::LoadOneGenomeDB Class Reference
Inheritance diagram for Bio::EnsEMBL::Compara::RunnableDB::LoadOneGenomeDB:

List of all members.


Class Summary

Synopsis

        # load a genome_db given a class/keyvalue locator (genome_db_id will be generated)
    standaloneJob.pl LoadOneGenomeDB.pm -compara_db "mysql://ensadmin:${ENSADMIN_PSW}@compara2/lg4_test_load1genome" \
        -locator 'Bio::EnsEMBL::DBSQL::DBAdaptor/host=ens-staging;port=3306;user=ensro;pass=;dbname=homo_sapiens_core_64_37;species=homo_sapiens;species_id=1;disconnect_when_inactive=1'

        # load a genome_db given a url-style locator
    standaloneJob.pl LoadOneGenomeDB.pm -compara_db "mysql://ensadmin:${ENSADMIN_PSW}@compara2/lg4_test_load1genome" \
        -locator "mysql://ensro@ens-staging2/mus_musculus_core_64_37"

        # load a genome_db given a reg_conf and species_name as locator
    standaloneJob.pl LoadOneGenomeDB.pm -compara_db "mysql://ensadmin:${ENSADMIN_PSW}@compara2/lg4_test_load1genome" \
        -reg_conf $ENSEMBL_CVS_ROOT_DIR/ensembl-compara/scripts/pipeline/production_reg_conf.pl \
        -locator 'mus_musculus'

        # load a genome_db given a reg_conf and species_name as locator with a specific genome_db_id
    standaloneJob.pl LoadOneGenomeDB.pm -compara_db "mysql://ensadmin:${ENSADMIN_PSW}@compara2/lg4_test_load1genome" \
        -reg_conf $ENSEMBL_CVS_ROOT_DIR/ensembl-compara/scripts/pipeline/production_reg_conf.pl \
        -locator 'homo_sapiens' -genome_db_id 90

Description

This Runnable loads one entry into 'genome_db' table and passes on the genome_db_id.
The format of the input_id follows the format of a Perl hash reference.
Examples:
    { 'species_name' => 'Homo sapiens', 'assembly_name' => 'GRCh37' }
    { 'species_name' => 'Mus musculus' }
supported keys:
    'locator'       => <string>
        one of the ways to specify the connection parameters to the core database (overrides 'species_name' and 'assembly_name')
    'registry_dbs'  => <list_of_dbconn_hashes>
        another, simple way to specify the genome_db (and let the registry search across multiple mysql instances to do the rest)
    'species_name'  => <string>
        mandatory, but what would you expect?
    'first_found'   => <0|1>
        optional, defaults to 0.
        Defines whether we emulate (to a certain extent) the behaviour of load_registry_from_multiple_dbs
        or try the last one that still fits (this would allow to try ens-staging[12] *first*, and only then check if ens-livemirror has is a suitable copy).
    'assembly_name' => <string>
        optional: in most cases it should be possible to find the species just by using 'species_name'
    'genome_db_id'  => <integer>
        optional, in case you want to specify it (otherwise it will be generated by the adaptor when storing)
    'pseudo_stableID_prefix' => <string>
        optional?, see 'GenomeLoadMembers.pm', 'GenomeLoadReuseMembers.pm', 'GeneStoreNCMembers.pm', 'GenomePrepareNCMembers.pm'
    'ensembl_genomes' => <0|1>
        optional, sets the preferential order of precedence of species_name sources, depending on whether the module is run by EG or Compara
 

Definition at line 66 of file LoadOneGenomeDB.pm.

Available Methods

public Bio::EnsEMBL::Analysis analysis ()
public Bio::EnsEMBL::DBSQL::DBAdaptor::extract_assembly_name ()
public Bio::EnsEMBL::DBSQL::DBAdaptor::locator ()
public catch ()
public void check_if_exit_cleanly ()
public compara_dba ()
public
Bio::EnsEMBL::DBSQL::DBConnection 
data_dbc ()
public dataflow_output_id ()
public
Bio::EnsEMBL::Hive::DBSQL::DBAdaptor 
db ()
public
Bio::EnsEMBL::DBSQL::DBConnection 
dbc ()
public Int debug ()
public void deprecate ()
public DESTROY ()
public fetch_input ()
public go_figure_compara_dba ()
public go_figure_dbc ()
public void info ()
public input_id ()
public
Bio::EnsEMBL::Hive::AnalysisJob 
input_job ()
public new ()
public Array output ()
public param ()
public param_defaults ()
public param_substitute ()
public parameters ()
public Bio::EnsEMBL::Hive::Queen queen ()
public run ()
public Arrayref runnable ()
public Array stack_trace ()
public String stack_trace_dump ()
public strict_hash_format ()
public void throw ()
public Depend try ()
public Int verbose ()
public warning ()
public worker ()
public worker_temp_directory ()
public write_output ()

Method Documentation

public Bio::EnsEMBL::Compara::RunnableDB::LoadOneGenomeDB::Bio::EnsEMBL::DBSQL::DBAdaptor::extract_assembly_name ( )
public Bio::EnsEMBL::Compara::RunnableDB::LoadOneGenomeDB::Bio::EnsEMBL::DBSQL::DBAdaptor::locator ( )
public Bio::EnsEMBL::Compara::RunnableDB::BaseRunnable::compara_dba ( ) [inherited]
    Description: this is an intelligent setter/getter of a Compara DBA. Resorts to magic in order to figure out how to connect.
    Example 1:   my $family_adaptor = $self->compara_dba()->get_FamilyAdaptor();    # implicit initialization and hashing
    Example 2:   my $external_foo_adaptor = $self->compara_dba( $self->param('db_conn') )->get_FooAdaptor();    # explicit initialization and hashing
 
Code:
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public Bio::EnsEMBL::Compara::RunnableDB::LoadOneGenomeDB::fetch_input ( )

Undocumented method

Code:
click to view

Reimplemented from Bio::EnsEMBL::Hive::Process.

public Bio::EnsEMBL::Compara::RunnableDB::BaseRunnable::go_figure_compara_dba ( ) [inherited]
    Description: this is a method that tries lots of different ways to find connection parameters
                 from a given object/hash and returns a Compara DBA. Does not hash anything, just does the detective magic.
 
Code:
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public Bio::EnsEMBL::Compara::RunnableDB::LoadOneGenomeDB::run ( )

Undocumented method

Code:
click to view

Reimplemented from Bio::EnsEMBL::Hive::Process.

public Bio::EnsEMBL::Compara::RunnableDB::LoadOneGenomeDB::write_output ( )

Undocumented method

Code:
click to view

Reimplemented from Bio::EnsEMBL::Hive::Process.


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