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Bio::EnsEMBL::Compara::PipeConfig::PairAligner_conf Class Reference
Inheritance diagram for Bio::EnsEMBL::Compara::PipeConfig::PairAligner_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, especially:
        release
        pipeline_db (-host)
        resource_classes 
        ref_species (if not homo_sapiens)
        default_chunks (especially if the reference is not human, since the masking_option_file option will have to be changed)
        pair_aligner_options (eg if doing primate-primate alignments)

    #4. Run init_pipeline.pl script:
        Using command line arguments:
        init_pipeline.pl Bio::EnsEMBL::Compara::PipeConfig::PairAligner_conf --dbname hsap_ggor_lastz_64 --password \<your_password) --mlss_id 536 --dump_dir /lustre/scratch103/ensembl/kb3/scratch/hive/release_64/hsap_ggor_nib_files/ --pair_aligner_options "T=1 K=5000 L=5000 H=3000 M=10 O=400 E=30 Q=/nfs/users/nfs_k/kb3/work/hive/data/primate.matrix --ambiguous=iupac" --config_url mysql://user:pass\@host:port/db_name

        Using a configuration file:
        init_pipeline.pl Bio::EnsEMBL::Compara::PipeConfig::PairAligner_conf --password ensembl --reg_conf reg.conf --conf_file input.conf --config_url mysql://user:pass\@host:port/db_name

    #5. Run the "beekeeper.pl ... -loop" command suggested by init_pipeline.pl

Definition at line 31 of file PairAligner_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::PairAligner_conf::default_options ( )

Undocumented method

Code:
click to view

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

Reimplemented in Bio::EnsEMBL::Compara::PipeConfig::Example::LastzMaster_conf, Bio::EnsEMBL::Compara::PipeConfig::Example::LastzMasterConf_conf, Bio::EnsEMBL::Compara::PipeConfig::Example::LastzMasterCore_conf, Bio::EnsEMBL::Compara::PipeConfig::Example::LastzMasterReg_conf, Bio::EnsEMBL::Compara::PipeConfig::Example::LastzNoMaster_conf, Bio::EnsEMBL::Compara::PipeConfig::Example::LastzNoMasterConf_conf, Bio::EnsEMBL::Compara::PipeConfig::Lastz_conf, Bio::EnsEMBL::Compara::PipeConfig::Lastz_primate_conf, and Bio::EnsEMBL::Compara::PipeConfig::TBlat_conf.

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

Undocumented method

Code:
click to view

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

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

Undocumented method

Code:
click to view

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

Reimplemented in Bio::EnsEMBL::Compara::PipeConfig::TBlat_conf.

public Bio::EnsEMBL::Compara::PipeConfig::PairAligner_conf::pipeline_wide_parameters ( )

Undocumented method

Code:
click to view

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

public Bio::EnsEMBL::Compara::PipeConfig::PairAligner_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: