Table of Contents - rbbt-util-6.0.5 Documentation
Pages
Classes and Modules
- AnnotatedModule
- Annotation
- Annotation::Annotated
- Annotation::AnnotatedObject
- Ansible
- Ansible::AnsibleWorkflow
- Ansible::AnsibleWorkflow::object
- Bgzf
- ChainMethods
- ChainMethods::base
- ChainMethods::base;
- ClosedStream
- ComputeDependency
- Cromwell
- Docker
- FileCache
- Filtered
- Filtered::Filter
- Filtered::FilterArray
- Filtered::base
- FixWidthTable
- HPC
- HPC::BATCH
- HPC::BATCH_DRY_RUN
- HPC::LSF
- HPC::Orchestration
- HPC::PBS
- HPC::SLURM
- HPC::TemplateGeneration
- Hash
- IRuby
- InputModule
- LaterString
- Log
- Misc
- Misc::proportions;
- MultipleResult
- NamedArray
- Net
- Net::HTTPGenericRequest
- Object
- Open
- PDF2Text
- PackedIndex
- Path
- Persist
- Persist::CDBAdapter
- Persist::FWTAdapter
- Persist::KCAdapter
- Persist::LMDBAdapter
- Persist::LevelDBAdapter
- Persist::PKIAdapter
- Persist::Sharder
- Persist::SharderAdapter
- Persist::TCAdapter
- Persist::TSVAdapter
- ProcPath
- R
- R::GIF
- R::GIF::s
- R::Model
- R::PNG
- R::PNG::s
- R::SVG
- R::SVG::s
- Rake
- Rake::TaskNotFound
- Rbbt
- Rbbt::new_mod
- RbbtMutiplartPayload
- RbbtProcessQueue
- RbbtProcessQueue::RbbtProcessQueueWorker
- RbbtProcessQueue::RbbtProcessQueueWorker::Respawn
- RbbtProcessQueue::RbbtProcessSocket
- RbbtPython
- RbbtPython::Binding
- RbbtPython::RbbtPythonException
- RbbtThreadQueue
- RbbtThreadQueue::RbbtThreadQueueWorker
- RemoteStep
- RemoteStep::REST
- RemoteStep::SSH
- RemoteWorkflow
- RemoteWorkflow::REST
- RemoteWorkflow::REST::v
- RemoteWorkflow::SSH
- Resource
- Resource::WithKey
- Resource::WithKey::base
- Rserve
- Rserve::TCPSocket
- SOPT
- SSHLine
- SimpleDSL
- SimpleDSL::ConfigFileMissingError
- SimpleDSL::NoRuby2Ruby
- SmithWaterman
- Step
- TCCache
- TSV
- TSV::BinarySerializer
- TSV::CleanSerializer
- TSV::FloatArraySerializer
- TSV::FloatSerializer
- TSV::IntegerArraySerializer
- TSV::IntegerSerializer
- TSV::StrictFloatArraySerializer
- TSV::StrictIntegerArraySerializer
- TSV::StringArraySerializer
- TSV::StringDoubleArraySerializer
- TSV::StringSerializer
- TSV::TSVMarshalSerializer
- TSV::TSVSerializer
- TSV::XLS
- TSV::XLSX
- Task
- Task::Job
- TokyoCabinet
- TokyoCabinet::BDB
- TokyoCabinet::HDB
- Workflow
- Workflow::Data
- Workflow::Data::DataNotFound
- Workflow::DependencyBlock
- WorkflowSOAP
Methods
- ::__jobs — Rbbt
- ::__prepare_inputs_for_restclient — RemoteWorkflow::REST
- ::_clean_float — TSV
- ::_convert_match_condition — Misc
- ::_eval — R
- ::_excel_data — TSV
- ::_ignore_stderr — Log
- ::_ignore_stdout — Log
- ::_remove_link — TSV
- ::_zip_fields — Misc
- ::GET_params2hash — Misc
- ::IUPAC_to_base — Misc
- ::accumulate_rules — HPC::Orchestration
- ::add — FileCache
- ::add_GET_param — Misc
- ::add_batch_deps — HPC::Orchestration
- ::add_config_keys — HPC::Orchestration
- ::add_consummable_annotation — AnnotatedModule
- ::add_defaults — Misc
- ::add_input — RbbtMutiplartPayload
- ::add_libdir — Misc
- ::add_path — RbbtPython
- ::add_paths — RbbtPython
- ::add_rules_and_consolidate — HPC::Orchestration
- ::add_stream — RbbtMutiplartPayload
- ::add_version — Rbbt
- ::align — SmithWaterman
- ::align_txt — SmithWaterman
- ::alignment_map — SmithWaterman
- ::alignment_percent — SmithWaterman
- ::all — SOPT
- ::append_zipped — Misc
- ::archive — Step
- ::array2hash — Misc
- ::attach — TSV
- ::attach_orig — TSV
- ::batch_system — HPC
- ::batch_system — HPC::LSF
- ::batch_system — HPC::PBS
- ::batch_system — HPC::SLURM
- ::batch_system_variables — HPC::LSF
- ::batch_system_variables — HPC::PBS
- ::batch_system_variables — HPC::SLURM
- ::benchmark — Misc
- ::bgzip_cmd — Bgzf
- ::binary_include? — Misc
- ::binding_run — RbbtPython
- ::bootstrap — Misc
- ::bootstrap_in_threads — Misc
- ::build_traverse_index — TSV
- ::cache_online_elements — FileCache
- ::cachedir — FileCache
- ::cachedir= — FileCache
- ::call_method — RbbtPython
- ::capture_exception — RemoteWorkflow
- ::chain_batches — HPC::Orchestration
- ::chain_methods_extended — ChainMethods
- ::check_chains — HPC::Orchestration
- ::choose — Misc
- ::chr_cmp_contigs — Misc
- ::chr_cmp_strict — Misc
- ::class_new_obj — RbbtPython
- ::clean — Step
- ::clean — RemoteWorkflow::SSH
- ::clean_symbols — Ansible
- ::clean_url — RemoteWorkflow::REST
- ::clear — R
- ::clear_files — Rake
- ::close_stream — RbbtMutiplartPayload
- ::collapse_ranges — Misc
- ::collect — RbbtPython
- ::console — R
- ::consolidate — Misc
- ::consume — SOPT
- ::correct_icgc_mutation — Misc
- ::correct_mutation — Misc
- ::correct_vcf_mutation — Misc
- ::counts — Misc
- ::current_options= — SOPT
- ::define_task — Rake
- ::del — FileCache
- ::delete_inputs — SOPT
- ::df2tsv — RbbtPython
- ::divide — Misc
- ::do_once — Misc
- ::doc — SOPT
- ::doc_parse_chunks — Workflow
- ::doc_parse_first_line — Workflow
- ::doc_parse_up_to — Workflow
- ::dump — TSV::CleanSerializer
- ::dump — TSV::BinarySerializer
- ::dump — TSV::IntegerSerializer
- ::dump — TSV::FloatSerializer
- ::dump — TSV::StrictIntegerArraySerializer
- ::dump — TSV::StrictFloatArraySerializer
- ::dump — TSV::IntegerArraySerializer
- ::dump — TSV::FloatArraySerializer
- ::dump — TSV::StringSerializer
- ::dump — TSV::StringArraySerializer
- ::dump — TSV::StringDoubleArraySerializer
- ::dump — TSV::TSVMarshalSerializer
- ::dump — TSV::TSVSerializer
- ::dump_memory — Rbbt
- ::dup_stream — Step
- ::each — RbbtThreadQueue
- ::encode — RemoteWorkflow::REST
- ::ensembl_server — Misc
- ::eog — R::PNG
- ::eog — R::GIF
- ::eog_plot — R::PNG
- ::eog_plot — R::GIF
- ::escape_url — RemoteWorkflow::REST
- ::eval — R
- ::eval_a — R
- ::eval_run — R
- ::excel — TSV
- ::excel2tsv — TSV
- ::exec — RbbtPython
- ::execute_job — RemoteWorkflow::REST
- ::extended — Resource::WithKey
- ::extended — Filtered
- ::extended — ChainMethods
- ::extended — Ansible::AnsibleWorkflow
- ::field_classes — R
- ::field_position — Misc
- ::file_time — Rbbt
- ::files — Rake
- ::files_dir — Step
- ::find_path — TSV
- ::find_traversal — TSV
- ::fix_hash — RemoteWorkflow
- ::fix_params — RemoteWorkflow
- ::fix_shortcut — SOPT
- ::found — FileCache
- ::genomic_location_cmp — Misc
- ::genomic_location_cmp_contigs — Misc
- ::genomic_location_cmp_strict — Misc
- ::genomic_mutations_to_BED — Misc
- ::get — FixWidthTable
- ::get — FileCache
- ::get — SOPT
- ::get_class — RbbtPython
- ::get_extension — Path
- ::get_json — RemoteWorkflow::REST
- ::get_json — RemoteWorkflow::SSH
- ::get_module — RbbtPython
- ::get_raw — RemoteWorkflow::REST
- ::get_raw — RemoteWorkflow::SSH
- ::get_streams — RemoteStep
- ::ggplot — R::SVG
- ::ggplot — R::PNG
- ::ggplot — R::GIF
- ::ggplot — IRuby
- ::ggplotPNG — R::PNG
- ::ggplotSVG — R::SVG
- ::google_venn — Misc
- ::groom — R::Model
- ::hash2GET_params — Misc
- ::hash2Rargs — R
- ::hash2string — Misc
- ::hash_to_html_tag_attributes — Misc
- ::header — HPC::LSF
- ::header — HPC::PBS
- ::header — HPC::SLURM
- ::header_lines — TSV
- ::html_tag — Misc
- ::id2name — Task::Job
- ::ignore_stderr — Log
- ::ignore_stdout — Log
- ::img — IRuby
- ::import_method — RbbtPython
- ::in_delta? — Misc
- ::index_BED — Misc
- ::index_for_traversal — TSV
- ::info_file — Step
- ::init_rbbt — RbbtPython
- ::init_thread — RbbtPython
- ::input_doc — SOPT
- ::input_format — SOPT
- ::input_header — RbbtMutiplartPayload
- ::insist — Misc
- ::instance — R
- ::interactive — R
- ::intersect_sorted_arrays — Misc
- ::intersect_streams — Misc
- ::intersect_streams_cmp_chr — Misc
- ::intersect_streams_read — Misc
- ::is_persisted? — Persist
- ::issue — RbbtMutiplartPayload
- ::iterate — RbbtPython
- ::iterate_index — RbbtPython
- ::job_batches — HPC::Orchestration
- ::job_chains — HPC::Orchestration
- ::job_dependencies — HPC::Orchestration
- ::job_files_for_archive — Step
- ::job_info — Rbbt
- ::job_name_for_info_file — Step
- ::job_path? — Workflow
- ::job_rules — HPC::Orchestration
- ::job_script — RemoteWorkflow::SSH
- ::job_status — HPC::LSF
- ::job_status — HPC::PBS
- ::job_status — HPC::SLURM
- ::job_workload — HPC::Orchestration
- ::link_job — Step
- ::list2ruby — RbbtPython
- ::load — TSV::CleanSerializer
- ::load — TSV::BinarySerializer
- ::load — TSV::IntegerSerializer
- ::load — TSV::FloatSerializer
- ::load — TSV::StrictIntegerArraySerializer
- ::load — TSV::StrictFloatArraySerializer
- ::load — TSV::IntegerArraySerializer
- ::load — TSV::FloatArraySerializer
- ::load — TSV::StringSerializer
- ::load — TSV::StringArraySerializer
- ::load — TSV::StringDoubleArraySerializer
- ::load — TSV::TSVMarshalSerializer
- ::load — TSV::TSVSerializer
- ::load — R::Model
- ::load — Task::Job
- ::load_entity — Annotation
- ::load_inputs — Workflow
- ::load_json — RbbtPython
- ::load_lock — Rbbt
- ::load_path — RemoteWorkflow
- ::load_pickle — RbbtPython
- ::load_result — RbbtPython
- ::load_script_variables — RbbtPython
- ::load_serialized_info — Step
- ::load_yaml — Misc
- ::lock_info — Rbbt
- ::lockfile — R
- ::locks — Rbbt
- ::log — Step
- ::log10 — Misc
- ::log2 — Misc
- ::log_block — Step
- ::log_progress — Step
- ::log_string — Step
- ::match_fields — Misc
- ::match_value — Misc
- ::max — Misc
- ::md5_file — Step
- ::mean — Misc
- ::median — Misc
- ::melt — TSV
- ::memory_use — Misc
- ::memprof — Misc
- ::merge_different_fields — TSV
- ::merge_row_fields — TSV
- ::merge_rules — HPC::Orchestration
- ::merge_sorted_arrays — Misc
- ::migrate — Step
- ::migrate — Rbbt
- ::migrate_files — Rbbt
- ::migrate_source_paths — Step
- ::migrate_source_paths — Rbbt
- ::migrate_target_path — Rbbt
- ::min — Misc
- ::missing_dep_inputs — RemoteWorkflow::SSH
- ::model_dir= — R
- ::monitor — ProcPath
- ::mutex — RbbtMutiplartPayload
- ::name2basename — Misc
- ::new — FixWidthTable
- ::new — HPC::BATCH_DRY_RUN
- ::new — PackedIndex
- ::new — Persist::Sharder
- ::new — Filtered::Filter
- ::new — R::Model
- ::new — RbbtProcessQueue::RbbtProcessSocket
- ::new — RbbtProcessQueue::RbbtProcessQueueWorker
- ::new — RbbtProcessQueue::RbbtProcessQueueWorker::Respawn
- ::new — RbbtThreadQueue
- ::new — RbbtThreadQueue::RbbtThreadQueueWorker
- ::new — Task::Job
- ::new — RemoteWorkflow
- ::new — RemoteStep
- ::new — WorkflowSOAP
- ::new — Rserve::TCPSocket
- ::new_binding — RbbtPython
- ::newer? — Persist
- ::nextflow_file_params — Workflow
- ::nextflow_includes — Workflow
- ::nextflow_recursive_params — Workflow
- ::notify — Misc
- ::numpy2ruby — RbbtPython
- ::obj2hash — RbbtPython
- ::object_delta — Misc
- ::old_define_task — Rake
- ::open — Persist::CDBAdapter
- ::open — Persist::FWTAdapter
- ::open — Persist::KCAdapter
- ::open — Persist::LevelDBAdapter
- ::open — Persist::LMDBAdapter
- ::open — Persist::PKIAdapter
- ::open — Persist::SharderAdapter
- ::open — TSV
- ::open — TCCache
- ::open_cdb — Persist
- ::open_fwt — Persist
- ::open_kyotocabinet — Persist
- ::open_leveldb — Persist
- ::open_lmdb — Persist
- ::open_pki — Persist
- ::open_sharder — Persist
- ::orchestrate_batch_job — RemoteWorkflow::SSH
- ::orchestration_rules — HPC::Orchestration
- ::ordered_divide — Misc
- ::original_open — TSV
- ::original_pos_index — TSV
- ::original_range_index — TSV
- ::original_require_workflow — Workflow
- ::parse — SOPT
- ::parse_chains — HPC::Orchestration
- ::parse_cmd_params — Misc
- ::parse_exception — RemoteWorkflow
- ::parse_nextflow_schema — Workflow
- ::parse_url — RemoteWorkflow::SSH
- ::parse_workflow_doc — Workflow
- ::path — FileCache
- ::path_script — RemoteWorkflow::SSH
- ::pb — HPC::Orchestration
- ::pdftotext — PDF2Text
- ::persist_info — Rbbt
- ::persists — Rbbt
- ::pid_file — Step
- ::pid_file — R
- ::play — Ansible
- ::playbook — Ansible
- ::plot — R::SVG
- ::plot — R::PNG
- ::plot — R::GIF
- ::plot — IRuby
- ::plot — ProcPath
- ::plot_trace_job_times — Workflow
- ::pos_index — TSV
- ::positional2hash — Misc
- ::post_data_stream — RbbtMutiplartPayload
- ::post_job — RemoteWorkflow::SSH
- ::post_jobname — RemoteWorkflow::REST
- ::post_json — RemoteWorkflow::REST
- ::pre_fork — Misc
- ::prepare_entity — Misc
- ::prepare_for_execution — Step
- ::process_mask — PackedIndex
- ::process_options — Misc
- ::process_paths — RbbtPython
- ::process_to_hash — Misc
- ::produce_dependencies — Step
- ::profile — Misc
- ::profile_graph — Misc
- ::profile_html — Misc
- ::proportions — Misc
- ::prov_report — Step
- ::prov_report_msg — Step
- ::prov_status_msg — Step
- ::pull_keys — Misc
- ::purge — Step
- ::purge_stream_cache — Step
- ::py2ruby_a — RbbtPython
- ::raise_dependency_error — Step
- ::random_sample_in_range — Misc
- ::range_index — TSV
- ::read — TSV::XLS
- ::read — TSV::XLSX
- ::read_matrix — TSV
- ::record — ProcPath
- ::register — SOPT
- ::relay — RemoteWorkflow::SSH
- ::relay_job — RemoteWorkflow::SSH
- ::relay_job_list — RemoteWorkflow::SSH
- ::relay_module_method — Rbbt
- ::reorder_stream — TSV
- ::reorder_stream_tsv — TSV
- ::require — SOPT
- ::require_instead — Rbbt
- ::require_remote_workflow — Workflow
- ::require_workflow — Workflow
- ::reset — SOPT
- ::reset_do_once — Misc
- ::ruby2R — R
- ::ruby2python — RbbtPython
- ::run — Rake
- ::run — R
- ::run — Docker
- ::run — RbbtPython
- ::run_batch_job — RemoteWorkflow::SSH
- ::run_cromwell — Cromwell
- ::run_direct — RbbtPython
- ::run_in_thread — RbbtPython
- ::run_job — RemoteWorkflow::SSH
- ::run_log — RbbtPython
- ::run_log_stderr — RbbtPython
- ::run_simple — RbbtPython
- ::run_template — HPC::LSF
- ::run_template — HPC::PBS
- ::run_template — HPC::SLURM
- ::run_threaded — RbbtPython
- ::sample — Misc
- ::sanitize_filename — Misc
- ::save_inputs — Step
- ::save_script_result — RbbtPython
- ::save_script_result_json — RbbtPython
- ::save_script_result_pickle — RbbtPython
- ::script — RbbtPython
- ::sd — Misc
- ::select_ranges — Misc
- ::semfile — R
- ::send_email — Misc
- ::send_email_old — Misc
- ::sensiblewrite_info — Rbbt
- ::sensiblewrites — Rbbt
- ::serialize_info — Step
- ::setup — Bgzf
- ::setup — SOPT
- ::setup — ComputeDependency
- ::setup — Workflow::DependencyBlock
- ::shortcuts — SOPT
- ::socket_file — R
- ::sort_genomic_locations — Misc
- ::sort_genomic_locations_by_contig — Misc
- ::sort_genomic_locations_strict — Misc
- ::sort_mutation_stream — Misc
- ::sort_mutation_stream_strict — Misc
- ::sort_mutations — Misc
- ::sort_mutations_strict — Misc
- ::sorted_array_hits — Misc
- ::ssh_connection — Misc
- ::ssh_run — Misc
- ::ssh_run_alt — Misc
- ::ssh_run_old — Misc
- ::status_color — Step
- ::std_num_vector — Misc
- ::step_info — Step
- ::stop_thread — RbbtPython
- ::string2const — Misc
- ::string2hash — Misc
- ::sum — Misc
- ::synchronize — RbbtPython
- ::task_info — RemoteWorkflow::REST
- ::task_specific_rules — HPC::Orchestration
- ::time_tick — Misc
- ::timeout_insist — Misc
- ::timespan — Misc
- ::tmp_path — Step
- ::to_a — RbbtPython
- ::tokenize — Misc
- ::total_length — Misc
- ::trace — Workflow
- ::trace_job_summary — Workflow
- ::trace_job_times — Workflow
- ::translate_dna_mutation_hgvs2rbbt — Misc
- ::translate_prot_mutation_hgvs2rbbt — Misc
- ::try3times — Misc
- ::tsv — R
- ::tsv2df — RbbtPython
- ::unzip_in_dir — Misc
- ::upload_dependencies — RemoteWorkflow::SSH
- ::upload_inputs — RemoteWorkflow::SSH
- ::usage — SOPT
- ::variance — Misc
- ::versions — Rbbt
- ::wait_for_jobs — Step
- ::workdir — R
- ::workflow2playbook — Ansible
- ::workflow_dir — Workflow
- ::workflow_for — Workflow
- ::workflow_repo — Workflow
- ::workflow_rules — HPC::Orchestration
- ::write — TSV::XLS
- ::write — TSV::XLSX
- ::xls — TSV
- ::xlsx — TSV
- ::zip2hash — Misc
- ::zip_fields — Misc
- ::zscore — Misc
- #<< — PackedIndex
- #<< — Persist::Sharder
- #<< — Persist::FWTAdapter
- #[] — FixWidthTable
- #[] — PackedIndex
- #[] — Persist::Sharder
- #[] — Persist::TSVAdapter
- #[] — Persist::CDBAdapter
- #[] — Persist::FWTAdapter
- #[] — Persist::PKIAdapter
- #[]= — Persist::Sharder
- #[]= — Persist::TSVAdapter
- #[]= — Persist::CDBAdapter
- #[]= — Persist::FWTAdapter
- #[]= — Persist::PKIAdapter
- #_clean — RemoteStep::REST
- #_get_block — Bgzf
- #_index — Bgzf
- #_orchestrate_batch — RemoteStep::SSH
- #_purge_cache — Bgzf
- #_restart — RemoteStep
- #_run — RemoteStep::SSH
- #_run_batch — RemoteStep::SSH
- #_run_job — RemoteStep::REST
- #R — TSV
- #R_console — TSV
- #R_interactive — TSV
- #abort — RbbtProcessQueue::RbbtProcessQueueWorker
- #abort — Task::Job
- #abort — RemoteStep::REST
- #abort — RemoteStep::SSH
- #abort_and_join — RbbtProcessQueue::RbbtProcessQueueWorker
- #aborted? — Step
- #aborted? — Task::Job
- #access — Step
- #add — FixWidthTable
- #add — Filtered::Filter
- #add — Persist::FWTAdapter
- #add — Persist::PKIAdapter
- #add_filter — Filtered
- #add_point — FixWidthTable
- #add_range — FixWidthTable
- #add_range_point — FixWidthTable
- #add_range_point — Persist::FWTAdapter
- #add_range_point — Persist::PKIAdapter
- #add_unsaved — Filtered::Filter
- #all_fields — Path
- #all_inputs — Task::Job
- #archive — Step
- #archive_deps — Step
- #archived_info — Step
- #archived_inputs — Step
- #arguments — Task::Job
- #assign_dep_inputs — Workflow
- #asynchronous — WorkflowSOAP
- #attach_index — TSV
- #attach_same_key — TSV
- #attach_source_key — TSV
- #basename — Path
- #batch_dir_for_id — HPC::TemplateGeneration
- #batch_options — HPC::TemplateGeneration
- #batch_system_variables — HPC::TemplateGeneration
- #block — Task::Job
- #block_offset — Bgzf
- #cache — TCCache
- #cache_file — RemoteStep
- #cache_files — RemoteStep
- #callback — RbbtProcessQueue
- #canfail? — ComputeDependency
- #canfail_paths — Step
- #chunked_values_at — FixWidthTable
- #chunked_values_at — Hash
- #clean — Filtered::Filter
- #clean — RbbtProcessQueue::RbbtProcessSocket
- #clean — RbbtThreadQueue
- #clean — RbbtThreadQueue::RbbtThreadQueueWorker
- #clean — Step
- #clean — Task::Job
- #clean — RemoteStep::REST
- #clean — RemoteStep::SSH
- #clean_name — RemoteStep
- #cleanup_environment — HPC::TemplateGeneration
- #close — FixWidthTable
- #close — PackedIndex
- #close — Persist::Sharder
- #close — Persist::TSVAdapter
- #close — Persist::CDBAdapter
- #close — Persist::KCAdapter
- #close — Persist::LevelDBAdapter
- #close — Bgzf
- #close_read — RbbtProcessQueue::RbbtProcessSocket
- #close_write — RbbtProcessQueue::RbbtProcessSocket
- #closed? — Persist::Sharder
- #closed? — Persist::TSVAdapter
- #closed? — Persist::CDBAdapter
- #closed? — Persist::LevelDBAdapter
- #closed? — Bgzf
- #closed_read? — RbbtProcessQueue::RbbtProcessSocket
- #closed_write? — RbbtProcessQueue::RbbtProcessSocket
- #closest — FixWidthTable
- #closest_page — Bgzf
- #coda — HPC::TemplateGeneration
- #colClasses — R::Model
- #collect — Persist::Sharder
- #collect — Persist::TSVAdapter
- #collect — Persist::KCAdapter
- #collect — Persist::LMDBAdapter
- #config — Step
- #config — SimpleDSL
- #data — Workflow::Data
- #data_dir — Workflow::Data
- #data_task — Workflow::Data
- #database — Persist::Sharder
- #delete — Persist::TSVAdapter
- #delete — Persist::CDBAdapter
- #delete — Persist::KCAdapter
- #delete — Persist::LevelDBAdapter
- #dep — Workflow
- #dep_task — Workflow
- #dependencies= — Step
- #desc — Workflow
- #dirty? — Step
- #dirty_files — Step
- #doc_file — Path
- #documentation — RemoteWorkflow::SSH
- #documentation_markdown — Workflow
- #done? — RbbtProcessQueue::RbbtProcessQueueWorker
- #done? — Step
- #done? — Task::Job
- #done? — RemoteStep
- #dump — FixWidthTable
- #dump — RbbtProcessQueue::RbbtProcessSocket
- #dumper_stream — TSV
- #dup_inputs — Step
- #dup_inputs — RemoteStep
- #each — Persist::Sharder
- #each — Persist::TSVAdapter
- #each — Persist::FWTAdapter
- #each — Persist::LMDBAdapter
- #each — Persist::PKIAdapter
- #entity_options — TSV
- #entity_templates — TSV
- #error? — Step
- #error? — Task::Job
- #example — Workflow
- #example_inputs — Workflow
- #example_step — Workflow
- #examples — Workflow
- #excel — TSV
- #exception — Step
- #exec — Step
- #exec — RemoteStep
- #exec_cmd — HPC::TemplateGeneration
- #exec_job — RemoteStep::REST
- #execute — HPC::TemplateGeneration
- #execute_and_dup — Step
- #execute_dependency — Step
- #exists? — R::Model
- #export — Workflow
- #export_asynchronous — Workflow
- #export_exec — Workflow
- #export_stream — Workflow
- #export_synchronous — Workflow
- #exported_tasks — RemoteWorkflow
- #extended — ChainMethods
- #extension — Workflow
- #fast_load_id — Workflow
- #field_index — TSV
- #field_index_select — TSV
- #fields — Path
- #file — Step
- #file — RemoteStep
- #filename — Bgzf
- #files — Step
- #files — Task::Job
- #files — RemoteStep
- #files_dir — Step
- #filter — TSV
- #filtered_collect — Filtered
- #filtered_delete — Filtered
- #filtered_each — Filtered
- #filtered_filename — Filtered
- #filtered_keys — Filtered
- #filtered_set — Filtered
- #filtered_values — Filtered
- #fit — R::Model
- #fix_io — Persist::CDBAdapter
- #follow_job — HPC::TemplateGeneration
- #fork — Task::Job
- #fork — RemoteStep
- #format — FixWidthTable
- #get — RemoteStep::REST
- #get_block — Bgzf
- #get_chains — HPC::Orchestration
- #get_datadir — Workflow::Data
- #get_exception — Step
- #get_file — Workflow::Data
- #get_job_dependencies — HPC::Orchestration
- #get_point — FixWidthTable
- #get_prefix — Persist::Sharder
- #get_prefix — Persist::TSVAdapter
- #get_prefix — Persist::LevelDBAdapter
- #get_range — FixWidthTable
- #get_recursive_job_dependencies — HPC::Orchestration
- #get_stream — RemoteStep
- #get_streams — RemoteStep
- #getc — Bgzf
- #gets — Bgzf
- #grace — RemoteStep
- #has_rake — Resource
- #header — HPC::TemplateGeneration
- #helper — Workflow
- #hold_dependencies — HPC::TemplateGeneration
- #hook_method — SimpleDSL
- #id_for — Workflow
- #identifier_file_path — Path
- #identifier_files — Path
- #ids — Filtered::FilterArray
- #ids — Filtered::Filter
- #idx_overlap — FixWidthTable
- #idx_pos — FixWidthTable
- #idx_pos_end — FixWidthTable
- #idx_value — FixWidthTable
- #import — Workflow
- #include? — Persist::Sharder
- #include? — Persist::TSVAdapter
- #include? — Persist::CDBAdapter
- #include? — Persist::FWTAdapter
- #include? — Persist::LevelDBAdapter
- #include? — Persist::PKIAdapter
- #info — Step
- #info — Task::Job
- #info — RemoteStep
- #info — Annotation::AnnotatedObject
- #info — Annotation::AnnotatedObject
- #info_file — Step
- #info_file — Task::Job
- #info_lock — Step
- #init — RbbtProcessQueue
- #init — RbbtThreadQueue
- #init — Bgzf
- #init_info — Step
- #init_info — RemoteStep
- #init_job — RemoteStep::REST
- #init_job — RemoteStep::SSH
- #init_remote_tasks — RemoteWorkflow::REST
- #init_remote_tasks — RemoteWorkflow::SSH
- #input — InputModule
- #input_checks — RemoteStep
- #input_dependencies — Step
- #input_dependencies — RemoteStep::SSH
- #inspect — Step
- #inspect — RemoteStep
- #issue — RemoteStep::SSH
- #job — RemoteWorkflow
- #job — WorkflowSOAP
- #job_queued — HPC::TemplateGeneration
- #job_rules — HPC::Orchestration
- #job_template — HPC::TemplateGeneration
- #jobs — HPC::TemplateGeneration
- #join — RbbtProcessQueue::RbbtProcessQueueWorker
- #join — RbbtThreadQueue
- #join — Task::Job
- #join — RemoteStep
- #key — Filtered::Filter
- #keys — Persist::Sharder
- #keys — Persist::TSVAdapter
- #keys — Persist::FWTAdapter
- #keys — Persist::PKIAdapter
- #keys — Path
- #knowledge_base — Step
- #last_pos — FixWidthTable
- #load — RbbtProcessQueue::RbbtProcessSocket
- #load — Task::Job
- #load — RemoteStep::REST
- #load — RemoteStep::SSH
- #load_conda — HPC::TemplateGeneration
- #load_config — SimpleDSL
- #load_cromwell — Workflow
- #load_dependencies — Task::Job
- #load_dependencies_from_info — Step
- #load_documentation — Workflow
- #load_file — Step
- #load_id — RemoteWorkflow
- #load_id — Workflow
- #load_inputs_from_info — Step
- #load_modules — HPC::TemplateGeneration
- #load_res — RemoteStep
- #load_tasks — RemoteWorkflow
- #lock — Persist::TSVAdapter
- #lock_and_close — Persist::TSVAdapter
- #log — Step
- #log — Workflow
- #log_dependency_exec — Step
- #log_progress — Step
- #marshal_dump — Persist::TCAdapter
- #marshal_dump — TSV
- #marshal_load — TokyoCabinet::BDB
- #marshal_load — TokyoCabinet::HDB
- #marshal_load — Hash
- #matrix_melt — TSV
- #md5_file — Step
- #melt — TSV
- #merge! — Persist::Sharder
- #merge! — Persist::TSVAdapter
- #merge! — Persist::CDBAdapter
- #merge! — Persist::LevelDBAdapter
- #merge_different_fields — TSV
- #merge_info — Step
- #message — Step
- #messages — Step
- #messages — Task::Job
- #meta_data — HPC::TemplateGeneration
- #metadata — Persist::FWTAdapter
- #metadata — Persist::PKIAdapter
- #metadata_file — Persist::FWTAdapter
- #metadata_file — Persist::PKIAdapter
- #method_missing — Filtered::FilterArray
- #method_missing — Resource::WithKey
- #missing? — Step
- #monitor_stream — Step
- #name — Step
- #name — RemoteStep
- #name= — RemoteStep
- #nextflow — Workflow
- #nextflow_dir — Workflow
- #nextflow_file — Workflow
- #nextflow_project — Workflow
- #noinfo? — Step
- #nopid? — Step
- #nopid? — RemoteStep
- #old_exec — Step
- #old_method_missing — Resource::WithKey
- #open — Task::Job
- #orchestrate_job — HPC::Orchestration
- #original_dumper_stream — TSV
- #original_reorder — TSV
- #original_to_s — TSV
- #original_unzip — TSV
- #overlaps — FixWidthTable
- #override_dependencies — Workflow
- #overriden? — Step
- #overriden_deps — Step
- #parse — SimpleDSL
- #path — RemoteStep
- #path — RemoteStep::SSH
- #persistence_path — FixWidthTable
- #persistence_path — PackedIndex
- #persistence_path= — FixWidthTable
- #persistence_path= — PackedIndex
- #persistence_path= — Persist::Sharder
- #persistence_path= — Persist::FWTAdapter
- #persistence_path= — Persist::PKIAdapter
- #pid_file — Step
- #piggyback — HPC::Orchestration
- #pipe_to — Path
- #play — Ansible::AnsibleWorkflow
- #pop — RbbtProcessQueue::RbbtProcessSocket
- #pop_filter — Filtered
- #pos_index — Path
- #ppthrough — TSV
- #ppthrough_callback — TSV
- #predict — R::Model
- #predict_interval — R::Model
- #prefix — Persist::Sharder
- #prefix — Persist::TSVAdapter
- #prefix — Persist::LevelDBAdapter
- #prepare_environment — HPC::TemplateGeneration
- #prepare_for_execution — HPC::Orchestration
- #prepare_submision — HPC::TemplateGeneration
- #previous_jobs= — Task::Job
- #previous_jobs_rec — Task::Job
- #process — RbbtProcessQueue
- #process — RbbtThreadQueue
- #produce — RemoteStep::REST
- #produce — RemoteStep::SSH
- #produce_jobs — HPC::Orchestration
- #progress_bar — Step
- #provenance — Step
- #provenance_paths — Step
- #pthrough — TSV
- #push — RbbtProcessQueue::RbbtProcessSocket
- #python — Step
- #python_block — Step
- #python_file — Step
- #r_options — R::Model
- #rake_for — Resource
- #range — Persist::Sharder
- #range — Persist::TSVAdapter
- #range — Persist::CDBAdapter
- #range — Persist::LevelDBAdapter
- #range_index — Path
- #rbbt_job_exec_cmd — HPC::TemplateGeneration
- #read — FixWidthTable
- #read — PackedIndex
- #read — Persist::Sharder
- #read — Task::Job
- #read — Persist::TSVAdapter
- #read — Persist::CDBAdapter
- #read — Persist::KCAdapter
- #read — Persist::LevelDBAdapter
- #read — Bgzf
- #read? — Persist::Sharder
- #read? — Persist::TSVAdapter
- #read_all — Bgzf
- #read_and_close — Persist::Sharder
- #read_and_close — Persist::TSVAdapter
- #read_and_close — Persist::CDBAdapter
- #read_and_close — Persist::LevelDBAdapter
- #read_lock — Persist::TSVAdapter
- #real_dependencies — Workflow
- #rec_access — Step
- #rec_dependencies — Step
- #rec_dependencies — Workflow
- #rec_input_defaults — Workflow
- #rec_input_descriptions — Workflow
- #rec_input_options — Workflow
- #rec_input_types — Workflow
- #rec_input_use — Workflow
- #rec_inputs — Workflow
- #recoverable_error? — Step
- #recursive_clean — Task::Job
- #recursive_clean — RemoteStep::REST
- #recursive_done? — Task::Job
- #relocated? — Step
- #remote_job — RemoteWorkflow
- #remove_extension — Path
- #reorder — TSV
- #replace_extension — Path
- #reset — Filtered::Filter
- #reset_filters — TSV
- #reset_info — Step
- #result_description — Step
- #result_description= — Step
- #result_type — Step
- #result_type= — Step
- #resumable — Workflow
- #resumable? — Step
- #returns — Workflow
- #ruby — SSHLine
- #run — RbbtProcessQueue::RbbtProcessQueueWorker
- #run — RbbtPython::Binding
- #run — Task::Job
- #run — RemoteStep
- #run — RemoteStep::SSH
- #run_compute_dependencies — Step
- #run_dependencies — Step
- #run_dependencies — Task::Job
- #run_job — HPC::TemplateGeneration
- #run_rake — Resource
- #run_with_respawn — RbbtProcessQueue::RbbtProcessQueueWorker
- #running? — Step
- #running? — RemoteStep
- #save — Filtered::Filter
- #save_dependencies — Task::Job
- #save_file — Step
- #save_options — Task::Job
- #saved — Filtered::Filter
- #seek — Bgzf
- #send_request_with_body_stream — Net::HTTPGenericRequest
- #send_request_with_body_stream_orig — Net::HTTPGenericRequest
- #serializer — Persist::CDBAdapter
- #set_extension — Path
- #set_info — Step
- #set_info — Task::Job
- #set_metadata — Persist::FWTAdapter
- #set_metadata — Persist::PKIAdapter
- #set_software_env — Resource
- #setup_chains — ChainMethods
- #setup_override_dependency — Workflow
- #short_path — Step
- #short_path — RemoteStep
- #short_path_real — Step
- #size — PackedIndex
- #size — Persist::Sharder
- #size — Persist::TSVAdapter
- #size — Persist::FWTAdapter
- #size — Filtered
- #soft_grace — Step
- #source_for_doc_file — Path
- #stalled? — Step
- #start — Task::Job
- #started? — Step
- #started? — RemoteStep
- #status — Step
- #status — RemoteStep
- #status= — Step
- #status_lock — Step
- #step — Task::Job
- #stop — RbbtProcessQueue::RbbtProcessQueueWorker
- #stop_dependencies — Step
- #stream_job — RemoteStep::REST
- #streaming? — Step
- #swap_id — TSV
- #sync_environment — HPC::TemplateGeneration
- #synchronous — WorkflowSOAP
- #task — Workflow
- #task_alias — Workflow
- #task_dependencies — RemoteWorkflow::SSH
- #task_exports — Workflow
- #task_for — Workflow
- #task_from_dep — Workflow
- #task_info — Workflow
- #task_info — RemoteWorkflow::REST
- #task_info — RemoteWorkflow::SSH
- #task_name — RemoteStep
- #task_signature — Step
- #tasks — RemoteWorkflow::REST
- #tasks — RemoteWorkflow::SSH
- #tmp_path — Step
- #to_s — RemoteWorkflow
- #to_s — TSV
- #to_s — Misc
- #to_s — LaterString
- #to_yaml — Path
- #traverse — Path
- #unexport — Workflow
- #unhook_method — SimpleDSL
- #unlocated_override? — Workflow
- #unzip — TSV
- #update — Filtered::Filter
- #update — R::Model
- #value — Persist::PKIAdapter
- #values_at — FixWidthTable
- #values_at — PackedIndex
- #values_at — Persist::TSVAdapter
- #wait_for_job — HPC::TemplateGeneration
- #waiting? — Step
- #with_key — Resource
- #with_monitor — TSV
- #with_read — Persist::TSVAdapter
- #with_write — Persist::TSVAdapter
- #workflow_description — RemoteWorkflow::SSH
- #workflow_short_path — Step
- #workflow_short_path — RemoteStep
- #workload — HPC::Orchestration
- #write — Persist::Sharder
- #write — Persist::TSVAdapter
- #write — Persist::CDBAdapter
- #write — Persist::KCAdapter
- #write — Persist::LevelDBAdapter
- #write? — FixWidthTable
- #write? — Persist::Sharder
- #write? — Persist::TSVAdapter
- #write? — Persist::KCAdapter
- #write? — Persist::LevelDBAdapter
- #write_and_close — Persist::Sharder
- #write_and_close — Persist::TSVAdapter
- #write_and_close — Persist::CDBAdapter
- #write_and_close — Persist::LevelDBAdapter
- #write_and_read — Persist::Sharder
- #write_and_read — Persist::TSVAdapter
- #write_and_read — Persist::CDBAdapter
- #write_and_read — Persist::LevelDBAdapter
- #write_lock — Persist::TSVAdapter
- #xls — TSV
- #xlsx — TSV
- #yaml — Path