ensembl-hive
2.1
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Public Member Functions | |
public | strict_hash_format () |
public | fetch_input () |
public | run () |
public | write_output () |
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public | new () |
public | life_cycle () |
public | say_with_header () |
public | enter_status () |
public | warning () |
public | strict_hash_format () |
public | param_defaults () |
public | fetch_input () |
public | run () |
public | write_output () |
public Bio::EnsEMBL::Hive::Worker | worker () |
public Boolean | execute_writes () |
public Bio::EnsEMBL::Hive::DBSQL::DBAdaptor | db () |
public Bio::EnsEMBL::Hive::DBSQL::DBConnection | dbc () |
public Bio::EnsEMBL::Hive::DBSQL::DBConnection | data_dbc () |
public Bio::EnsEMBL::Hive::AnalysisJob | input_job () |
public | input_id () |
public | param () |
public | param_required () |
public | param_is_defined () |
public | param_substitute () |
public | dataflow_output_id () |
public | throw () |
public | complete_early () |
public Int | debug () |
public | worker_temp_directory () |
public | worker_temp_directory_name () |
public | cleanup_worker_temp_directory () |
This RunnableDB module acts as a wrapper for shell-level command lines. If you behave you may also use parameter substitution. The command can be given using two different syntaxes: 1) Command line is stored in the input_id() or parameters() as the value corresponding to the 'cmd' key. THIS IS THE RECOMMENDED WAY as it allows to pass in other parameters and use the parameter substitution mechanism in its full glory. 2) Command line is stored in the 'input_id' field of the job table. (only works with command lines shorter than 255 bytes). This is a legacy syntax. Most people tend to use it not realizing there are other possiblities.
public Bio::EnsEMBL::Hive::RunnableDB::SystemCmd::fetch_input | ( | ) |
Description : Implements fetch_input() interface method of Bio::EnsEMBL::Hive::Process that is used to read in parameters and load data. Here it deals with finding the command line, doing parameter substitution and storing the result in a predefined place.
param('cmd'): The recommended way of passing in the command line.
param('*'): Any other parameters can be freely used for parameter substitution.
public Bio::EnsEMBL::Hive::RunnableDB::SystemCmd::run | ( | ) |
Description : Implements run() interface method of Bio::EnsEMBL::Hive::Process that is used to perform the main bulk of the job (minus input and output). Here it actually runs the command line.
public Bio::EnsEMBL::Hive::RunnableDB::SystemCmd::strict_hash_format | ( | ) |
Description : Implements strict_hash_format() interface method of Bio::EnsEMBL::Hive::Process that is used to set the strictness level of the parameters' parser. Here we return 0 in order to indicate that neither input_id() nor parameters() is required to contain a hash.
public Bio::EnsEMBL::Hive::RunnableDB::SystemCmd::write_output | ( | ) |
Description : Implements write_output() interface method of Bio::EnsEMBL::Hive::Process that is used to deal with job's output after the execution. Here we have nothing to do, as the wrapper is very generic.