Inheritance diagram for MiniPecanSingle2_conf:

Collaboration diagram for MiniPecanSingle2_conf:

Public Member Functions
public	default_options ()

public	pipeline_analyses ()

Public Member Functions inherited from Bio::EnsEMBL::Hive::PipeConfig::HiveGeneric_conf
public	default_options ()

public	pipeline_create_commands ()

public	pipeline_wide_parameters ()

public	resource_classes ()

public	pipeline_analyses ()

public	beekeeper_extra_cmdline_options ()

public	hive_meta_table ()

public	pre_options ()

public	dbconn_2_mysql ()

public	dbconn_2_pgsql ()

public	db_connect_command ()

public	db_execute_command ()

public	dbconn_2_url ()

public	pipeline_url ()

public	db_cmd ()

public	pipeline_name ()

public	process_options ()

public	overridable_pipeline_create_commands ()

public	run_pipeline_create_commands ()

public	add_objects_from_config ()

public	useful_commands_legend ()

Public Member Functions inherited from Bio::EnsEMBL::Hive::DependentOptions
public	new ()

public	use_cases ()

public	load_cmdline_options ()

public	root ()

public	is_fully_substituted_string ()

public	is_fully_substituted_structure ()

public	hash_leaves ()

public	o ()

public	substitute ()

public	merge_from_rules ()

public	process_options ()

Detailed Description

Synopsis

init_pipeline.pl MiniPecanSingle2_conf -password <your_password>
init_pipeline.pl MiniPecanSingle2_conf -hive_driver sqlite -password <FOO>

Description

    This is an example pipeline put together from basic building blocks:

    Analysis_1: SystemCmd.pm is used to run Pecan on a set of files

        the job is sent down the branch #1 into the second analysis

    Analysis_2: SystemCmd.pm is used to run gerp_col on the resulting alignment

        the job is sent down the branch #1 into the third analysis

    Analysis_3: SystemCmd.pm is used to run gerp_elem on the GERP scores

Member Function Documentation

public MiniPecanSingle2_conf::default_options ( )

    Description : Implements default_options() interface method of Bio::EnsEMBL::Hive::PipeConfig::HiveGeneric_conf that is used to initialize default options.
                  In addition to the standard things it defines three options:
                    o('capacity')   defines how many files can be run in parallel

                  There are rules dependent on two options that do not have defaults (this makes them mandatory):
                    o('password')           your read-write password for creation and maintenance of the hive database

Code:

click to view

public MiniPecanSingle2_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 two analyses:

                      'pecan'  aligns sequences with Pecan
                      Each job of this analysis will dataflow (create jobs) via branch #1 into 'gerp_col' analysis.

                      'gerp_col' runs gerp_col on Pecan output
                      Each job of this analysis will dataflow (create jobs) via branch #1 into 'gerp_elem' analysis.

                      'gerp_elem' runs gerp_elem on gerp_col output