Method List
-
#+ AnnotatedArray
-
#<< Persist::Sharder
-
#<< PackedIndex
-
#<< Persist::FWTAdapter
-
#== Color
-
GET_params2hash Misc
-
IUPAC_to_base Misc
-
#R TSV
-
#R_console TSV
-
#R_interactive TSV
-
#SOPT_str Workflow
-
#[] NamedArray
-
#[] FixWidthTable
-
#[] Persist::TSVAdapter
-
#[] Resource
-
#[] AnnotatedArray
-
#[] Persist::PKIAdapter
-
#[] Persist::FWTAdapter
-
#[] Path
-
#[] Persist::Sharder
-
#[] IndiferentHash
-
#[] PackedIndex
-
#[] Persist::CDBAdapter
-
#[] TSV
-
#[] CaseInsensitiveHash
-
#[]= Persist::TSVAdapter
-
#[]= Persist::PKIAdapter
-
#[]= Persist::CDBAdapter
-
#[]= TSV
-
#[]= Persist::Sharder
-
#[]= NamedArray
-
#[]= IndiferentHash
-
#[]= Persist::FWTAdapter
-
#__job Workflow
-
#__job RemoteWorkflow
-
__jobs Rbbt
-
__load_step Workflow
-
__prepare_inputs_for_restclient RemoteWorkflow::REST
-
#_abort RbbtProcessQueue
-
#_abort Step
-
#_children KnowledgeBase
-
#_clean RemoteStep::REST
-
#_clean_finished Step
-
_clean_float TSV
-
#_default? IndiferentHash
-
#_ep KnowledgeBase::Traverser
-
_eval R
-
_excel_data TSV
-
#_exec Step
-
#_exists? Path
-
_extended TSV
-
#_fp KnowledgeBase::Traverser
-
#_get_block Bgzf
-
_ignore_stderr Log
-
_ignore_stdout Log
-
#_index Bgzf
-
#_job Workflow
-
#_join RbbtProcessQueue
-
_load_step Workflow
-
#_neighbours KnowledgeBase
-
#_orchestrate_batch RemoteStep::SSH
-
#_parents KnowledgeBase
-
_paste_streams Misc
-
#_prov_tasks Workflow
-
#_purge_cache Bgzf
-
_remove_link TSV
-
#_restart RemoteStep
-
#_run RemoteStep::SSH
-
#_run_batch RemoteStep::SSH
-
#_run_job RemoteStep::REST
-
_select_match AssociationItem
-
#_subset KnowledgeBase
-
_untar_cmd Misc
-
_zip_fields Misc
-
#a Color
-
#abort RbbtProcessQueue::RbbtProcessQueueWorker
-
#abort Step
-
#abort ConcurrentStream
-
#abort RbbtProcessQueue
-
#abort RemoteStep::REST
-
#abort RemoteStep::SSH
-
#abort Task::Job
-
#abort_and_join RbbtProcessQueue::RbbtProcessQueueWorker
-
#abort_callback ConcurrentStream
-
#abort_pid Step
-
#abort_pids ConcurrentStream
-
#abort_stream Step
-
abort_stream TSV
-
#abort_threads ConcurrentStream
-
#aborted ConcurrentStream
-
#aborted? ConcurrentStream
-
#aborted? Task::Job
-
#aborted? Step
-
#access Step
-
accumulate_rules HPC::Orchestration
-
#add Persist::FWTAdapter
-
#add FixWidthTable
-
add FileCache
-
#add Filtered::Filter
-
#add Persist::PKIAdapter
-
#add TSV::Dumper
-
add_GET_param Misc
-
add_batch_deps HPC::Orchestration
-
add_cache Open
-
#add_callback ConcurrentStream
-
add_config_keys HPC::Orchestration
-
add_consummable_annotation AnnotatedModule
-
add_defaults Misc
-
add_entry Rbbt::Config
-
#add_field TSV
-
#add_fields TSV
-
#add_filter Filtered
-
#add_identifiers Entity
-
add_input RbbtMutiplartPayload
-
add_libdir Misc
-
add_offset Log::ProgressBar
-
add_path RbbtPython
-
add_paths RbbtPython
-
#add_point FixWidthTable
-
#add_process RbbtProcessQueue
-
#add_range FixWidthTable
-
#add_range_point FixWidthTable
-
#add_range_point Persist::FWTAdapter
-
#add_range_point Persist::PKIAdapter
-
add_reciprocal Association
-
#add_remote_tasks Workflow
-
add_rules_and_consolidate HPC::Orchestration
-
#add_search_path Path
-
add_stream RbbtMutiplartPayload
-
add_stream_filename Misc
-
#add_to_data_flat TSV::Parser
-
#add_to_data_flat_keys TSV::Parser
-
#add_to_data_flat_merge TSV::Parser
-
#add_to_data_flat_merge_double TSV::Parser
-
#add_to_data_flat_merge_keys TSV::Parser
-
#add_to_data_merge TSV::Parser
-
#add_to_data_merge_zipped TSV::Parser
-
#add_to_data_no_merge_double TSV::Parser
-
#add_to_data_no_merge_list TSV::Parser
-
#add_to_data_zipped TSV::Parser
-
#add_unsaved Filtered::Filter
-
add_version Rbbt
-
adjacency AssociationItem
-
align SmithWaterman
-
alignment_map SmithWaterman
-
#all KnowledgeBase
-
all SOPT
-
#all_databases KnowledgeBase
-
#all_exports Workflow
-
#all_fields TSV::Parser
-
#all_fields TSV
-
#all_fields Path
-
#all_formats Entity
-
#all_inputs Task::Job
-
#all_properties Entity
-
#annotate KnowledgeBase
-
#annotate Path
-
#annotate Annotated
-
#annotate TSV::Parser
-
#annotate TSV
-
#annotate ConcurrentStream
-
#annotation Annotation
-
#annotation_md5 Annotated
-
#annotation_types Annotated
-
#annotation_values Annotated
-
#annotations Annotated
-
#annotations Annotation
-
#append_search_path Path
-
append_zipped Misc
-
archive Step
-
#archive Step
-
#archive_deps Step
-
#archived_info Step
-
#archived_inputs Step
-
#arguments Task::Job
-
array2hash Misc
-
#assign_dep_inputs Workflow
-
#assignments KnowledgeBase::Traverser
-
#asynchronous WorkflowSOAP
-
#asynchronous_exports RemoteWorkflow
-
#asynchronous_exports Workflow
-
atime Open
-
#attach TSV
-
#attach_index TSV
-
#attach_same_key TSV
-
autoinstall Workflow
-
#autojoin ConcurrentStream
-
#available_resources Workflow::Orchestrator
-
#b Color
-
#base_name RemoteStep
-
#base_url RemoteStep
-
#basename Path
-
bash CMD
-
#batch_dir_for_id HPC::TemplateGeneration
-
#batch_options HPC::TemplateGeneration
-
#batch_options RemoteStep::SSH
-
batch_system HPC
-
batch_system HPC::SLURM
-
batch_system HPC::PBS
-
batch_system HPC::LSF
-
#batch_system_variables HPC::TemplateGeneration
-
batch_system_variables HPC::PBS
-
batch_system_variables HPC::SLURM
-
batch_system_variables HPC::LSF
-
benchmark Misc
-
bgunzip Open
-
bgzip Open
-
bgzip? Open
-
bgzip_cmd Bgzf
-
binary_include? Misc
-
binding_run RbbtPython
-
#bindings Step
-
blend Color
-
#blend Color
-
#blend! Color
-
#block RbbtThreadQueue
-
#block Task::Job
-
#block RbbtProcessQueue::RbbtProcessQueueWorker
-
#block_cache_size Bgzf
-
#block_offset Bgzf
-
bootstrap Misc
-
bootstrap_in_threads Misc
-
break_lines Misc
-
broken_link? Open
-
buffer_stream Misc
-
#byte Path
-
#bytes Log::ProgressBar
-
#cache TCCache
-
#cache_file RemoteStep
-
#cache_files RemoteStep
-
cache_online_elements FileCache
-
cachedir FileCache
-
cachedir Persist
-
cachedir Open
-
cachedir= FileCache
-
cachedir= Open
-
call_method RbbtPython
-
#callback ConcurrentStream
-
#callback RbbtProcessQueue
-
#callback Log::ProgressBar
-
#callback_queue RbbtProcessQueue::RbbtProcessQueueWorker
-
#callback_queue RbbtProcessQueue
-
#callback_thread RbbtProcessQueue
-
caller_lib_dir Path
-
camel_case Misc
-
camel_case_lower Misc
-
can_open? Open
-
candidates Workflow::Orchestrator
-
#canfail? ComputeDependency
-
#canfail_paths Step
-
capture_exception RemoteWorkflow
-
#cast TSV::Parser
-
#cast? TSV::Parser
-
#cast_values_double TSV::Parser
-
#cast_values_flat TSV::Parser
-
#cast_values_list TSV::Parser
-
#cast_values_single TSV::Parser
-
chain_batches HPC::Orchestration
-
chain_methods_extended ChainMethods
-
change_key TSV
-
#change_key TSV
-
check_chains HPC::Orchestration
-
#check_resources Workflow::Orchestrator
-
#checks Step
-
#child Step
-
#children KnowledgeBase
-
choose Misc
-
#chop_line TSV::Parser
-
chr_cmp_contigs Misc
-
chr_cmp_strict Misc
-
chunk Misc
-
#chunked_values_at Hash
-
#chunked_values_at FixWidthTable
-
#claim Resource
-
#claims Resource
-
class_new_obj RbbtPython
-
clean Step
-
#clean Filtered::Filter
-
#clean RemoteStep::REST
-
#clean Step
-
#clean RemoteStep::SSH
-
#clean RbbtThreadQueue::RbbtThreadQueueWorker
-
#clean Task::Job
-
#clean RbbtThreadQueue
-
clean RemoteWorkflow::SSH
-
#clean RbbtProcessQueue
-
#clean RbbtProcessQueue::RbbtProcessSocket
-
#clean_and_setup_hash Annotation
-
#clean_annotations Annotated
-
#clean_annotations Path
-
clean_cache Open
-
#clean_matches KnowledgeBase::Traverser
-
#clean_name RemoteStep
-
#clean_name Step
-
clean_symbols Ansible
-
clean_url RemoteWorkflow::REST
-
#clean_version IndiferentHash
-
#cleaned RbbtProcessQueue::RbbtProcessSocket
-
#cleanup RbbtProcessQueue
-
#cleanup RbbtProcessQueue::RbbtProcessQueueWorker
-
cleanup_bars Log::ProgressBar
-
#cleanup_environment HPC::TemplateGeneration
-
#clear ConcurrentStream
-
clear R
-
clear_dir_repos Open
-
clear_line Log
-
#close ConcurrentStream
-
#close Persist::TSVAdapter
-
#close Persist::CDBAdapter
-
#close Persist::LevelDBAdapter
-
#close TSV::Dumper
-
#close Persist::Sharder
-
#close TSV
-
#close Bgzf
-
#close Persist::KCAdapter
-
#close Persist::TCAdapter
-
#close FixWidthTable
-
#close PackedIndex
-
#close_in TSV::Dumper
-
#close_out TSV::Dumper
-
#close_read RbbtProcessQueue::RbbtProcessSocket
-
close_stream RbbtMutiplartPayload
-
#close_up_queue RbbtProcessQueue
-
#close_write RbbtProcessQueue::RbbtProcessSocket
-
#closed Persist::LevelDBAdapter
-
#closed Persist::Sharder
-
#closed Persist::TSVAdapter
-
#closed? Bgzf
-
#closed? Persist::TSVAdapter
-
#closed? Persist::CDBAdapter
-
#closed? Persist::LevelDBAdapter
-
#closed? Persist::Sharder
-
#closed_read? RbbtProcessQueue::RbbtProcessSocket
-
#closed_write? RbbtProcessQueue::RbbtProcessSocket
-
#closest FixWidthTable
-
#closest_page Bgzf
-
#cmd Step
-
#cmd SSHProcessFailed
-
cmd CMD
-
cmd_log CMD
-
cmd_pid CMD
-
#coda HPC::TemplateGeneration
-
#colClasses R::Model
-
collapse_ranges Misc
-
collapse_stream TSV
-
collapse_stream Misc
-
collect RbbtPython
-
#collect AnnotatedArray
-
#collect NamedArray
-
#collect Persist::LMDBAdapter
-
#collect Persist::Sharder
-
#collect Persist::TSVAdapter
-
#collect Persist::KCAdapter
-
#collect TSV
-
color Log
-
color_stack Log
-
colors_for Misc
-
#column TSV
-
#column_values TSV
-
command SSHLine
-
command SOPT
-
common_path Misc
-
compact Log
-
compare_lines Misc
-
#complete_name Workflow
-
complete_name Workflow
-
#compressed_stream Bgzf
-
#compute ComputeDependency
-
#concurrent_stream ConcurrentStreamProcessFailed
-
conda CMD
-
#config Step
-
#config SimpleDSL
-
console R
-
consolidate Misc
-
consume SOPT
-
consume_stream Misc
-
#container Annotated
-
#container_index Annotated
-
continuous Colorize
-
#copy_files_dir Step
-
correct_mutation Misc
-
correct_vcf_mutation Misc
-
count_stack Log
-
counts Misc
-
cp Open
-
csv TSV
-
ctime Open
-
current_options= SOPT
-
#darken Color
-
#darken! Color
-
#data Filtered::Filter
-
#data Workflow::Data
-
#data_dir Workflow::Data
-
#data_offset Bgzf
-
#data_task Workflow::Data
-
#database Persist::Sharder
-
database Association
-
#databases KnowledgeBase
-
#databases Persist::Sharder
-
#db_namespace KnowledgeBase
-
#db_type Persist::Sharder
-
#ddd Top Level Namespace
-
#ddf Top Level Namespace
-
debug Log
-
default_file Log::ProgressBar
-
del FileCache
-
#delete Persist::KCAdapter
-
#delete Persist::TSVAdapter
-
#delete Persist::LevelDBAdapter
-
#delete Persist::CDBAdapter
-
#delete IndiferentHash
-
delete_inputs SOPT
-
#dep Workflow
-
#dep_inputs Task
-
dep_inputs Task
-
#dep_task Workflow
-
#dep_tree Workflow
-
#dependencies Step
-
#dependency Workflow::DependencyBlock
-
#dependency_checks Step
-
deprecated Log
-
#depth Log::ProgressBar
-
#desc Log::ProgressBar
-
#desc Workflow
-
#description Task
-
#description Workflow
-
description SOPT
-
#description KnowledgeBase
-
#detach TSV
-
#detach NamedArray
-
#detach_annotations Annotated
-
df2tsv RbbtPython
-
digest Misc
-
digest_url Open
-
#dir KnowledgeBase
-
#directory HPC::BATCH_DRY_RUN
-
#directory? Path
-
#dirname Path
-
#dirty? Step
-
#dirty_files Step
-
distinct Colorize
-
divide Misc
-
do_once Misc
-
#doc Task
-
#doc Workflow
-
doc SOPT
-
#doc_file Path
-
doc_parse_chunks Workflow
-
doc_parse_first_line Workflow
-
doc_parse_up_to Workflow
-
#documentation Workflow
-
#documentation RemoteWorkflow::SSH
-
#documentation_markdown Workflow
-
#documented_tasks Workflow
-
#done RbbtThreadQueue
-
#done Log::ProgressBar
-
#done? Step
-
#done? RbbtProcessQueue::RbbtProcessQueueWorker
-
#done? Task::Job
-
#done? RemoteStep
-
#double_array AnnotatedArray
-
down_lines Log
-
#downcase_keys CaseInsensitiveHash
-
download Open
-
download_old Open
-
dump TSV::FloatSerializer
-
dump TSV::IntegerArraySerializer
-
dump TSV::BinarySerializer
-
dump TSV::StringArraySerializer
-
dump TSV::TSVMarshalSerializer
-
dump TSV::StrictIntegerArraySerializer
-
dump TSV::StringDoubleArraySerializer
-
dump TSV::CleanSerializer
-
dump TSV::StringSerializer
-
#dump RbbtProcessQueue::RbbtProcessSocket
-
dump TSV::StrictFloatArraySerializer
-
dump TSV::IntegerSerializer
-
dump TSV::FloatArraySerializer
-
dump TSV::TSVSerializer
-
#dump FixWidthTable
-
dump_memory Rbbt
-
#dumper_stream TSV
-
#dup_inputs Step
-
#dup_inputs RemoteStep
-
dup_stream Step
-
dup_stream Misc
-
dup_stream_multiple Misc
-
#dupped Step
-
#each Persist::LMDBAdapter
-
#each NamedArray
-
#each Persist::TSVAdapter
-
#each AnnotatedArray
-
#each Persist::FWTAdapter
-
#each Persist::Sharder
-
each RbbtThreadQueue
-
each RbbtProcessQueue
-
#each Persist::PKIAdapter
-
#each TSV
-
#eee Top Level Namespace
-
#eef Top Level Namespace
-
#empty? TSV
-
encode RemoteWorkflow::REST
-
#enrichment KnowledgeBase
-
ensembl_server Misc
-
#entities KnowledgeBase
-
#entity_options TSV
-
#entity_options KnowledgeBase
-
#entity_options NamedArray
-
#entity_options_for KnowledgeBase
-
entity_property_cache Entity
-
#entity_templates NamedArray
-
#entity_types KnowledgeBase
-
entry TSV
-
env_add Misc
-
eog R::GIF
-
eog R::PNG
-
eog_plot R::PNG
-
eog_plot R::GIF
-
#erase_job_dependencies Workflow::Orchestrator
-
#error Log::ProgressBar
-
error Log
-
#error? Task::Job
-
#error? Step
-
escape_url RemoteWorkflow::REST
-
#eta_msg Log::ProgressBar
-
eval R
-
eval_a R
-
eval_run R
-
#example Workflow
-
#example_dir Workflow
-
#example_inputs Workflow
-
#example_step Workflow
-
#examples Workflow
-
excel TSV
-
#excel TSV
-
excel2tsv TSV
-
#exception StopInsist
-
#exception Step
-
exception Log
-
#exception AbortedStream
-
exec RbbtPython
-
#exec Task
-
#exec RemoteStep
-
#exec Step
-
#exec_cmd HPC::TemplateGeneration
-
#exec_exports RemoteWorkflow
-
#exec_exports Workflow
-
#exec_in Task
-
#exec_job RemoteStep::REST
-
#execute HPC::TemplateGeneration
-
#execute_and_dup Step
-
#execute_dependency Step
-
execute_job RemoteWorkflow::REST
-
#exists? Path
-
exists? Open
-
#exists? R::Model
-
exists_in_repo Open
-
#export_asynchronous Workflow
-
#export_exec Workflow
-
#export_stream Workflow
-
#export_synchronous Workflow
-
#exported_tasks RemoteWorkflow
-
extended Filtered
-
extended ChainMethods
-
extended Ansible::AnsibleWorkflow
-
extended Workflow
-
extended Resource::WithKey
-
extended Resource
-
extended Entity
-
extended Annotation
-
#extension Workflow
-
#extension Task
-
extract_specs Association
-
#fast_load_id Workflow
-
fast_load_step Workflow
-
#fast_setup Annotation
-
#fff Top Level Namespace
-
#field_index TSV
-
field_index_dir TSV
-
#field_indices TSV
-
field_position Misc
-
#field_positions TSV::Parser
-
#fieldnum Filtered::Filter
-
#fields TSV::Parser
-
#fields TSV
-
#fields Path
-
#fields KnowledgeBase
-
#fields NamedArray
-
#fields= TSV
-
#file RemoteStep
-
#file Step
-
#file PackedIndex
-
#file Log::ProgressBar
-
#file FixWidthTable
-
file2md5 Misc
-
file_open Open
-
file_time Rbbt
-
file_write Open
-
#filename TSV::Parser
-
#filename TSV::Dumper
-
#filename FixWidthTable
-
#filename ConcurrentStream
-
#filename Bgzf
-
#filename Path
-
#files Step
-
#files Task::Job
-
#files RemoteStep
-
files_dir Step
-
#files_dir Step
-
#filter TSV
-
#filter Association::Index
-
#filtered_collect Filtered
-
#filtered_delete Filtered
-
#filtered_each Filtered
-
#filtered_filename Filtered
-
#filtered_keys Filtered
-
#filtered_set Filtered
-
#filtered_values Filtered
-
#filters Filtered::FilterArray
-
#find Path
-
#find_all Path
-
find_path TSV
-
#find_paths KnowledgeBase::Traverser
-
find_repo_dir Open
-
find_traversal TSV
-
fingerprint Misc
-
#first AnnotatedArray
-
#first_line TSV::Parser
-
#fit R::Model
-
#fix TSV::Parser
-
#fix_fields TSV::Parser
-
fix_hash RemoteWorkflow
-
#fix_io Persist::CDBAdapter
-
fix_params RemoteWorkflow
-
fix_shortcut SOPT
-
fixascii Misc
-
fixutf8 Misc
-
flatten Annotated
-
#follow_job HPC::TemplateGeneration
-
#fork Step
-
#fork Task::Job
-
#fork RemoteStep
-
fork_each_on_semaphore RbbtSemaphore
-
#format KnowledgeBase
-
#format FixWidthTable
-
format_paragraph Misc
-
format_seconds Misc
-
formats Entity
-
#formula R::Model
-
found FileCache
-
#frequency Log::ProgressBar
-
from_name Colorize
-
#g Color
-
genomic_location_cmp Misc
-
get FixWidthTable
-
get SOPT
-
#get RemoteStep::REST
-
get FileCache
-
get Rbbt::Config
-
get_SOPT Workflow
-
#get_SOPT Workflow
-
get_atime_from_repo Open
-
#get_block Bgzf
-
#get_chains HPC::Orchestration
-
get_class RbbtPython
-
#get_database KnowledgeBase
-
#get_datadir Workflow::Data
-
#get_exception Step
-
get_extension Path
-
#get_file Workflow::Data
-
get_filename Misc
-
get_filename TSV
-
get_filename Persist
-
#get_from_server Resource
-
#get_index KnowledgeBase
-
#get_job_dependencies HPC::Orchestration
-
#get_job_step Workflow
-
get_json RemoteWorkflow::SSH
-
get_json RemoteWorkflow::REST
-
get_level Log
-
#get_point FixWidthTable
-
#get_prefix Persist::Sharder
-
#get_prefix Persist::LevelDBAdapter
-
#get_prefix Persist::TSVAdapter
-
#get_range FixWidthTable
-
get_raw RemoteWorkflow::SSH
-
get_raw RemoteWorkflow::REST
-
#get_recursive_job_dependencies HPC::Orchestration
-
get_repo_from_dir Open
-
get_result Persist
-
#get_stream RemoteStep
-
get_stream TSV
-
#get_stream Step
-
get_stream_from_repo Open
-
get_streams RemoteStep
-
#get_streams RemoteStep
-
get_time_from_repo Open
-
get_tool CMD
-
#get_values_double TSV::Parser
-
#get_values_double_from_flat TSV::Parser
-
#get_values_flat TSV::Parser
-
#get_values_flat_inverse TSV::Parser
-
#get_values_flat_merge TSV::Parser
-
#get_values_list TSV::Parser
-
#get_values_single TSV::Parser
-
#get_values_single_from_flat TSV::Parser
-
#getc Bgzf
-
#gets Bgzf
-
ggplot R::GIF
-
ggplot R::PNG
-
ggplot R::SVG
-
ggplotPNG R::PNG
-
ggplotSVG R::SVG
-
#glob Path
-
#glob_all Path
-
google_venn Misc
-
#grace RemoteStep
-
#grace Step
-
gradient Colorize
-
#grayscale Color
-
#grayscale! Color
-
#grayscale? Color
-
grep Open
-
groom R::Model
-
guess_id TSV
-
guess_max TSV
-
gunzip Open
-
gzip Open
-
gzip Misc
-
gzip? Open
-
gzip_pipe CMD
-
#has_rake Resource
-
hash2GET_params Misc
-
hash2md5 Misc
-
hash2string Misc
-
#head_str TSV
-
#head_tsv TSV
-
header HPC::SLURM
-
#header HPC::TemplateGeneration
-
header HPC::PBS
-
header HPC::LSF
-
#header_hash TSV::Parser
-
header_lines TSV
-
#header_options TSV::Parser
-
headers Association
-
#helper Workflow
-
#helpers Workflow
-
high Log
-
highlight Log
-
#history Log::ProgressBar
-
#hold_dependencies HPC::TemplateGeneration
-
#host SSHProcessFailed
-
hostname Misc
-
html_tag Misc
-
humanize Misc
-
humanize_list Misc
-
#id Annotated
-
#id Task::Job
-
id2name Task::Job
-
#id_dbs KnowledgeBase::Traverser
-
#id_for Workflow
-
#identifier_files Path
-
identifier_files Entity
-
#identifier_files KnowledgeBase
-
#identifiers TSV::Parser
-
#identify KnowledgeBase::Traverser
-
#identify KnowledgeBase
-
#identify Resource
-
identify_entity_format Association
-
#identify_field TSV::Parser
-
identify_field TSV
-
#identify_field TSV
-
#identify_source KnowledgeBase
-
#identify_target KnowledgeBase
-
#ids Filtered::Filter
-
#ids Filtered::FilterArray
-
#idx_overlap FixWidthTable
-
#idx_pos FixWidthTable
-
#idx_pos_end FixWidthTable
-
#idx_value FixWidthTable
-
ignore_stderr Log
-
ignore_stdout Log
-
#iif Top Level Namespace
-
#iii Top Level Namespace
-
#import Workflow
-
import_method RbbtPython
-
#import_task Workflow
-
in_cache Open
-
in_delta? Misc
-
in_dir Misc
-
#in_dir? Path
-
#in_stream TSV::Dumper
-
incidence TSV
-
incidence AssociationItem
-
#include? Persist::FWTAdapter
-
#include? Persist::CDBAdapter
-
#include? Persist::Sharder
-
#include? Persist::TSVAdapter
-
#include? Persist::LevelDBAdapter
-
#include? Persist::PKIAdapter
-
#include? IndiferentHash
-
#included Annotation
-
included Entity::Identified
-
#index Path
-
index TSV
-
#index TSV
-
index Association
-
index_BED Misc
-
#index_fields KnowledgeBase
-
#indices KnowledgeBase
-
#info RemoteStep
-
#info TSV
-
#info Annotated
-
info Log
-
#info Step
-
#info KnowledgeBase
-
#info Task::Job
-
info_file Step
-
#info_file Step
-
#info_file Task::Job
-
#info_lock Step
-
#init Bgzf
-
#init Log::ProgressBar
-
#init TSV::Dumper
-
#init RbbtThreadQueue
-
#init RbbtProcessQueue
-
#init_info RemoteStep
-
#init_info Step
-
#init_job RemoteStep::SSH
-
#init_job RemoteStep::REST
-
#init_master RbbtProcessQueue
-
init_rbbt RbbtPython
-
init_relay_tasks Workflow
-
#init_remote_tasks RemoteWorkflow::REST
-
#init_remote_tasks RemoteWorkflow::SSH
-
init_remote_tasks Workflow
-
#initialize RbbtProcessQueue::RbbtProcessSocket
-
#initialize RbbtProcessQueue::RbbtProcessQueueWorker
-
#initialize Workflow::Orchestrator
-
#initialize R::Model
-
#initialize Persist::Sharder
-
#initialize ConcurrentStreamProcessFailed
-
#initialize RemoteStep
-
#initialize PackedIndex
-
#initialize Color
-
#initialize FixWidthTable
-
#initialize TSV::Parser
-
#initialize Filtered::Filter
-
#initialize TSV::Dumper
-
#initialize KnowledgeBase::Traverser
-
#initialize RemoteWorkflow
-
#initialize RbbtThreadQueue
-
#initialize SSHProcessFailed
-
#initialize KeepLocked
-
#initialize DependencyError
-
#initialize HPC::BATCH_DRY_RUN
-
#initialize KeepBar
-
#initialize RbbtProcessQueue
-
#initialize Workflow::TaskNotFoundException
-
#initialize SSHLine
-
#initialize TryThis
-
#initialize RbbtThreadQueue::RbbtThreadQueueWorker
-
#initialize StopInsist
-
#initialize Log::ProgressBar
-
#initialize RbbtProcessQueue::RbbtProcessQueueWorker::Respawn
-
#initialize MissingParameterException
-
#initialize DependencyRbbtException
-
#initialize ProcessFailed
-
initialize Entity::DontPersist
-
#initialize KnowledgeBase
-
#initialize TSV::Traverser
-
#initialize Step
-
#initialize WorkflowSOAP
-
#initialize Task::Job
-
#input InputModule
-
#input Task::Job
-
#input_checks Step
-
#input_checks RemoteStep
-
#input_defaults Task
-
input_defaults SOPT
-
#input_dependencies RemoteStep::SSH
-
#input_dependencies Step
-
input_descriptions SOPT
-
#input_descriptions Task
-
input_doc SOPT
-
input_format SOPT
-
input_header RbbtMutiplartPayload
-
#input_options Task
-
input_shortcuts SOPT
-
#input_types RemoteStep
-
input_types SOPT
-
#input_types Task
-
#inputs RemoteStep
-
inputs SOPT
-
#inputs Task
-
#inputs Step
-
insist Misc
-
#inspect Color
-
#inspect Step
-
#inspect RemoteStep
-
installed_workflows Workflow
-
instance R
-
intercalate_streams Misc
-
intersect_streams Misc
-
#is_exec RemoteStep
-
is_filename? Misc
-
is_persisted? Persist
-
#is_stream RemoteStep
-
#is_wildcard? KnowledgeBase::Traverser
-
issue RbbtMutiplartPayload
-
#issue RemoteStep::SSH
-
#item_size PackedIndex
-
iterate RbbtPython
-
iterate_index RbbtPython
-
#job Workflow
-
#job WorkflowSOAP
-
job_batches HPC::Orchestration
-
job_chains HPC::Orchestration
-
job_dependencies HPC::Orchestration
-
#job_for_directory_inputs Workflow
-
job_info Rbbt
-
job_path? Workflow
-
#job_queued HPC::TemplateGeneration
-
job_resources Workflow::Orchestrator
-
job_rules Workflow::Orchestrator
-
#job_rules HPC::Orchestration
-
job_rules HPC::Orchestration
-
job_script RemoteWorkflow::SSH
-
job_status HPC::SLURM
-
job_status HPC::PBS
-
job_status HPC::LSF
-
#job_template HPC::TemplateGeneration
-
job_workload HPC::Orchestration
-
job_workload Workflow::Orchestrator
-
#jobs Workflow
-
#join Path
-
#join ConcurrentStream
-
#join RbbtProcessQueue
-
#join RemoteStep
-
#join RbbtThreadQueue
-
#join RbbtProcessQueue::RbbtProcessQueueWorker
-
#join Task::Job
-
#join Step
-
#join_callback ConcurrentStream
-
#join_pids ConcurrentStream
-
#join_stream Step
-
#join_threads ConcurrentStream
-
#joined ConcurrentStream
-
#joined? ConcurrentStream
-
#kb KnowledgeBase::Traverser
-
#key Filtered::Filter
-
#key NamedArray
-
#key_field TSV::Parser
-
#key_position TSV::Parser
-
#keys Path
-
#keys Persist::FWTAdapter
-
#keys Persist::TSVAdapter
-
#keys TSV
-
#keys Persist::Sharder
-
#keys Persist::PKIAdapter
-
#kill_children Step
-
#knowledge_base Step
-
#kyotocabinet_class Persist::KCAdapter
-
#last AnnotatedArray
-
last_caller Log
-
#last_pos FixWidthTable
-
#last_task Workflow
-
#length TSV
-
#libdir Path
-
#libdir Workflow
-
#lighten Color
-
#lighten! Color
-
line_monitor_stream Misc
-
link Open
-
link_job Step
-
#list Path
-
#list Filtered::Filter
-
list2ruby RbbtPython
-
#list_id AnnotatedArray
-
list_repo_files Open
-
#llf Top Level Namespace
-
#lll Top Level Namespace
-
ln Open
-
ln_h Open
-
ln_s Open
-
load R::Model
-
load TSV::CleanSerializer
-
load TSV::FloatArraySerializer
-
load TSV::BinarySerializer
-
#load RemoteStep::SSH
-
load TSV::StrictFloatArraySerializer
-
load TSV::IntegerArraySerializer
-
load TSV::StringDoubleArraySerializer
-
load TSV::StrictIntegerArraySerializer
-
load TSV::StringArraySerializer
-
load TSV::TSVMarshalSerializer
-
load TSV::FloatSerializer
-
load TSV::TSVSerializer
-
#load Log::ProgressBar
-
load TSV::StringSerializer
-
load TSV::IntegerSerializer
-
#load RbbtProcessQueue::RbbtProcessSocket
-
load KnowledgeBase
-
#load Step
-
#load Task::Job
-
load Task::Job
-
#load RemoteStep::REST
-
#load_conda HPC::TemplateGeneration
-
load_config Rbbt::Config
-
#load_config SimpleDSL
-
#load_cromwell Workflow
-
#load_dependencies Task::Job
-
#load_documentation Workflow
-
load_entity Annotated
-
load_file Rbbt::Config
-
load_file Persist
-
#load_file Step
-
load_hash Annotated
-
#load_id Workflow
-
#load_id RemoteWorkflow
-
load_info Annotated
-
load_inputs Workflow
-
load_lock Rbbt
-
#load_modules HPC::TemplateGeneration
-
#load_name Workflow
-
load_path RemoteWorkflow
-
load_relay_tasks Workflow
-
load_remote_tasks Workflow
-
#load_res RemoteStep
-
load_serialized_info Step
-
load_step Workflow
-
#load_step Workflow
-
load_step_cache Workflow
-
#load_step_cache Workflow
-
#load_tasks RemoteWorkflow
-
load_tsv Annotated
-
load_tsv_values Annotated
-
load_workflow_file Workflow
-
load_workflow_libdir Workflow
-
load_yaml Misc
-
local_persist LocalPersist
-
#local_persist LocalPersist
-
#local_persist_dir LocalPersist
-
#local_persist_setup Workflow
-
#local_persist_tsv LocalPersist
-
#local_workdir_setup Workflow
-
local_workflow_filename Workflow
-
#located? Path
-
#lock Persist::TSVAdapter
-
lock Open
-
lock Misc
-
#lock_and_close Persist::TSVAdapter
-
lock_dir Resource
-
lock_dir Persist
-
lock_dir TSV
-
lock_dir Step
-
lock_in_repo Misc
-
lock_info Rbbt
-
#lockfile ConcurrentStream
-
lockfile R
-
locks Rbbt
-
#log Step
-
log Log
-
#log Workflow
-
log Step
-
#log ConcurrentStream
-
log10 Misc
-
log2 Misc
-
log_block Step
-
#log_dependency_exec Step
-
log_obj_inspect Log
-
log_progress Step
-
#log_progress Step
-
log_relay_step Step
-
log_string Step
-
logfile Log
-
logn Log
-
low Log
-
main Workflow
-
#make_list Annotated
-
#make_local Workflow
-
#marshal_dump TSV
-
#marshal_dump Persist::TCAdapter
-
#marshal_dump Annotated
-
#marshal_load Hash
-
#marshal_load TokyoCabinet::BDB
-
#marshal_load TokyoCabinet::HDB
-
#marshal_load String
-
#marshal_load Array
-
#mask PackedIndex
-
#mask FixWidthTable
-
#mask_length PackedIndex
-
#masked_annotations Annotation
-
#masked_annotations Annotated
-
match Rbbt::Config
-
#match Filtered::Filter
-
#match Association::Index
-
match_fields Misc
-
match_value Misc
-
#matches Association::Index
-
#matches KnowledgeBase::Traverser
-
#matrix_melt TSV
-
max Misc
-
#max Log::ProgressBar
-
#max_history Log::ProgressBar
-
md5_file Step
-
mean Misc
-
#mean_max Log::ProgressBar
-
median Misc
-
medium Log
-
melt TSV
-
#melt TSV
-
memory Persist
-
memory_use Misc
-
memprof Misc
-
#merge IndiferentHash
-
#merge NamedArray
-
#merge TSV
-
#merge! Persist::TSVAdapter
-
#merge! Persist::LevelDBAdapter
-
#merge! Persist::CDBAdapter
-
#merge! Persist::Sharder
-
#merge_info Step
-
merge_paste TSV
-
merge_row_fields TSV
-
merge_rules HPC::Orchestration
-
merge_sorted_arrays Misc
-
#merge_zip TSV
-
#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 Path
-
#method_missing Filtered::FilterArray
-
#method_missing Resource
-
#method_missing Resource::WithKey
-
migrate Rbbt
-
migrate Step
-
migrate_files Rbbt
-
migrate_source_paths Rbbt
-
migrate_source_paths Step
-
migrate_target_path Rbbt
-
min Misc
-
#missing? Step
-
missing_dep_inputs RemoteWorkflow::SSH
-
mkdir Open
-
#mmf Top Level Namespace
-
#mmm Top Level Namespace
-
#model_file R::Model
-
#monitor TSV
-
monitor ProcPath
-
#monitor_stream Step
-
#msg ProcessFailed
-
mtime Open
-
mtime_str Misc
-
#mutex Persist::TSVAdapter
-
mutex RbbtMutiplartPayload
-
#mutex Step
-
#mutex Persist::Sharder
-
#mutex RbbtThreadQueue
-
mv Open
-
#name R::Model
-
#name RemoteWorkflow
-
#name RemoteStep
-
#name Task
-
#name Task::Job
-
#name Step
-
name2basename Misc
-
#name= RemoteStep
-
#namespace TSV::Parser
-
#namespace KnowledgeBase
-
#namespace= TSV
-
#neighbours KnowledgeBase
-
new Rserve::TCPSocket
-
new_bar Log::ProgressBar
-
new_binding RbbtPython
-
#new_field_names TSV::Traverser
-
#new_fields TSV::Traverser
-
#new_key_field TSV::Traverser
-
#new_key_field_name TSV::Traverser
-
newer? Persist
-
#nextflow Workflow
-
#nextflow_dir Workflow
-
#nextflow_file Workflow
-
nextflow_file_params Workflow
-
nextflow_includes Workflow
-
#nextflow_project Workflow
-
nextflow_recursive_params Workflow
-
#nil_string PackedIndex
-
no_bar Log
-
no_bar= Log
-
#no_fail ConcurrentStream
-
nocolor Log
-
#noinfo? Step
-
#nopid? Step
-
#nopid? RemoteStep
-
normalize_specs Association
-
notify Misc
-
notify_write Open
-
#num_processes RbbtProcessQueue
-
#num_threads RbbtThreadQueue
-
numpy2ruby RbbtPython
-
obj2digest Misc
-
obj2hash RbbtPython
-
obj2md5 Misc
-
obj2str Misc
-
obj_stream TSV
-
object_delta Misc
-
#offset PackedIndex
-
offset Log::ProgressBar
-
#offset RbbtProcessQueue
-
#old_method_missing Resource::WithKey
-
#opaque? Color
-
open Association
-
open Persist::LMDBAdapter
-
open Persist::FWTAdapter
-
open Persist::SharderAdapter
-
open Persist::CDBAdapter
-
open Persist::TCAdapter
-
open TCCache
-
#open Task::Job
-
open Persist::LevelDBAdapter
-
#open Path
-
open Persist::KCAdapter
-
open Open
-
open Persist::PKIAdapter
-
open SSHLine
-
open TSV
-
open_cdb Persist
-
open_database Persist
-
open_fwt Persist
-
open_gz_pipe Misc
-
open_kyotocabinet Persist
-
open_leveldb Persist
-
open_lmdb Persist
-
open_pipe Misc
-
open_pki Persist
-
open_sharder Persist
-
open_stream Association
-
open_tokyocabinet Persist
-
#options Persist::Sharder
-
#options Task::Job
-
#options TSV
-
#options TSV::Parser
-
#options TSV::Dumper
-
orchestrate_batch_job RemoteWorkflow::SSH
-
#orchestrate_job HPC::Orchestration
-
orchestration_rules HPC::Orchestration
-
ordered_divide Misc
-
#original Path
-
original_argv SOPT
-
#original_task_name Step
-
#original_workflow Step
-
#out_of_date Step
-
#overlaps FixWidthTable
-
#override_dependencies Workflow
-
#override_dependencies RemoteStep::SSH
-
#overriden Step
-
#overriden? Step
-
#overriden_deps Step
-
#page TSV
-
#pair ConcurrentStream
-
#parents KnowledgeBase
-
parse SOPT
-
#parse SimpleDSL
-
parse Color
-
parse TSV
-
parse_chains HPC::Orchestration
-
parse_cmd_params Misc
-
#parse_description Task
-
parse_exception RemoteWorkflow
-
parse_field_specification Association
-
#parse_header TSV::Parser
-
parse_header TSV
-
#parse_key_field Association::Index
-
parse_nextflow_schema Workflow
-
parse_sql_values Misc
-
parse_url RemoteWorkflow::SSH
-
parse_workflow_doc Workflow
-
paste_streams Misc
-
paste_streams TSV
-
#path RemoteStep
-
path FileCache
-
#path Step
-
#path Task::Job
-
#path RemoteStep::SSH
-
path_relative_to Misc
-
path_script RemoteWorkflow::SSH
-
#payload KeepBar
-
#payload KeepLocked
-
#payload RbbtProcessQueue::RbbtProcessQueueWorker::Respawn
-
#payload Entity::DontPersist
-
#payload TryThis
-
pb HPC::Orchestration
-
pdftotext PDF2Text
-
#percent Log::ProgressBar
-
persist Persist
-
#persist_checks Step
-
#persist_exec Task
-
#persist_exec_in Task
-
persist_file Persist
-
persist_info Rbbt
-
persist_tsv Persist
-
#persistence Filtered::Filter
-
#persistence_path FixWidthTable
-
#persistence_path Persist::Sharder
-
#persistence_path Persist::TSVAdapter
-
#persistence_path PackedIndex
-
#persistence_path Persist::LevelDBAdapter
-
persistence_path Persist
-
#persistence_path= FixWidthTable
-
#persistence_path= PackedIndex
-
#persistence_path= Persist::PKIAdapter
-
#persistence_path= Persist::FWTAdapter
-
persists Rbbt
-
#pid ProcessFailed
-
#pid Task::Job
-
#pid RbbtProcessQueue::RbbtProcessQueueWorker
-
#pid Step
-
pid_exists? Misc
-
pid_file R
-
#pid_file Step
-
pid_file Step
-
#pids ConcurrentStream
-
#piggyback HPC::Orchestration
-
pipe Misc
-
#pipe_to Path
-
#pkgdir Path
-
#pkgdir Resource
-
play Ansible
-
#play Ansible::AnsibleWorkflow
-
playbook Ansible
-
plot ProcPath
-
plot R::PNG
-
plot R::GIF
-
plot R::SVG
-
plot_trace_job_times Workflow
-
#pop RbbtProcessQueue::RbbtProcessSocket
-
#pop_filter Filtered
-
#pos Log::ProgressBar
-
#pos_function Persist::PKIAdapter
-
#pos_function Persist::FWTAdapter
-
#pos_index Path
-
pos_index TSV
-
#pos_index TSV
-
positional2hash Misc
-
#positions NamedArray
-
post_data_stream RbbtMutiplartPayload
-
post_job RemoteWorkflow::SSH
-
post_jobname RemoteWorkflow::REST
-
post_json RemoteWorkflow::REST
-
#ppp Top Level Namespace
-
#ppthrough TSV
-
pre_fork Misc
-
#preamble TSV::Parser
-
#predict R::Model
-
#predict_interval R::Model
-
#prefix Persist::Sharder
-
#prefix Persist::LevelDBAdapter
-
#prefix Persist::TSVAdapter
-
#prepare_entity NamedArray
-
#prepare_entity TSV
-
prepare_entity Misc
-
#prepare_environment HPC::TemplateGeneration
-
#prepare_for_execution HPC::Orchestration
-
#prepare_result Step
-
#prepare_submision HPC::TemplateGeneration
-
#prepare_value TSV
-
#prepend_search_path Path
-
#previous_jobs Task::Job
-
#previous_jobs_rec Task::Job
-
#print Log::ProgressBar
-
#process TSV
-
#process RbbtProcessQueue
-
process Workflow::Orchestrator
-
#process TSV::Parser
-
#process Workflow::Orchestrator
-
#process RbbtThreadQueue
-
#process Log::ProgressBar
-
process_config Rbbt::Config
-
process_formats Association
-
#process_key TSV
-
process_mask PackedIndex
-
#process_monitor RbbtProcessQueue
-
#process_null TSV::Traverser
-
process_options Misc
-
process_relay_tasks Workflow
-
process_remote_tasks Workflow
-
#process_reorder_double TSV::Traverser
-
#process_reorder_double_uniq TSV::Traverser
-
#process_reorder_flat TSV::Traverser
-
#process_reorder_list TSV::Traverser
-
#process_reorder_single TSV::Traverser
-
process_stream Misc
-
#process_subset_all_but_double TSV::Traverser
-
#process_subset_all_but_list TSV::Traverser
-
#process_subset_double TSV::Traverser
-
#process_subset_list TSV::Traverser
-
process_to_hash Misc
-
#produce Path
-
#produce KnowledgeBase
-
#produce RemoteStep::REST
-
#produce Resource
-
#produce RemoteStep::SSH
-
#produce Step
-
#produce_dependencies RemoteStep::SSH
-
produce_dependencies Step
-
profile Misc
-
profile_graph Misc
-
profile_html Misc
-
#progress_bar Step
-
proportions Misc
-
prov_report Step
-
prov_report_msg Step
-
prov_status_msg Step
-
#prov_string Workflow
-
#prov_tree Workflow
-
#provenance Step
-
#provenance_paths Step
-
#pthrough TSV
-
pull_keys Misc
-
purge Annotated
-
purge Step
-
purge_duplicates Workflow::Orchestrator
-
purge_pipes Misc
-
purge_stream_cache Step
-
#push RbbtProcessQueue::RbbtProcessSocket
-
py2ruby_a RbbtPython
-
#python Step
-
#python_block Step
-
#python_file Step
-
#queue RbbtThreadQueue
-
#queue RbbtProcessQueue::RbbtProcessQueueWorker
-
#queue RbbtProcessQueue
-
#r Color
-
#r_options R::Model
-
#rake_dirs Resource
-
#rake_for Resource
-
random_name TmpFile
-
#range Persist::CDBAdapter
-
#range FixWidthTable
-
#range Persist::Sharder
-
#range Persist::LevelDBAdapter
-
#range Persist::TSVAdapter
-
#range_index Path
-
#range_index TSV
-
range_index TSV
-
rank_gradient Colorize
-
#rbbt SSHLine
-
rbbt SSHLine
-
#rbbt_job_exec_cmd HPC::TemplateGeneration
-
#read Persist::TCAdapter
-
#read Persist::CDBAdapter
-
#read FixWidthTable
-
#read Bgzf
-
#read Persist::KCAdapter
-
#read Task::Job
-
#read Path
-
#read TSV
-
#read PackedIndex
-
read Open
-
read TSV::XLSX
-
read TSV::XLS
-
#read Persist::Sharder
-
#read Persist::LevelDBAdapter
-
#read Persist::TSVAdapter
-
#read? Persist::Sharder
-
#read? Persist::TSVAdapter
-
#read_all Bgzf
-
#read_and_close Persist::CDBAdapter
-
#read_and_close Persist::Sharder
-
#read_and_close Persist::LevelDBAdapter
-
#read_and_close Persist::TSVAdapter
-
read_full_stream Misc
-
#read_lock Persist::TSVAdapter
-
read_matrix TSV
-
#read_sem RbbtProcessQueue::RbbtProcessSocket
-
read_stream Misc
-
#real_dependencies Workflow
-
#real_inputs Step
-
realpath Open
-
#reassign KnowledgeBase::Traverser
-
#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
-
record ProcPath
-
#record_size FixWidthTable
-
#recoverable_error? Step
-
#recursive_clean Step
-
#recursive_clean Task::Job
-
#recursive_clean RemoteStep::REST
-
#recursive_done? Task::Job
-
#recursive_inputs Step
-
#register KnowledgeBase
-
register SOPT
-
#registry KnowledgeBase
-
#reject AnnotatedArray
-
relative_link Misc
-
relay RemoteWorkflow::SSH
-
relay_job RemoteWorkflow::SSH
-
relay_job_list RemoteWorkflow::SSH
-
#relay_log Step
-
#relay_tasks Workflow
-
release_pipes Misc
-
#release_resources Workflow::Orchestrator
-
relocate Workflow
-
relocate_array Workflow
-
relocate_dependency Workflow
-
#relocated Step
-
#relocated? Step
-
remote? Open
-
#remote_server Resource
-
remote_servers Resource
-
#remote_tasks Workflow
-
#remove AnnotatedArray
-
#remove Log::ProgressBar
-
remove_bar Log::ProgressBar
-
#remove_extension Path
-
remove_from_cache Open
-
remove_from_repo Open
-
remove_lines Misc
-
remove_long_items Misc
-
remove_offset Log::ProgressBar
-
#remove_process RbbtProcessQueue
-
#rename_field TSV
-
#reorder TSV
-
reorder_stream TSV
-
reorder_tsv Association
-
#replace_extension Path
-
#report NamedArray
-
#report Log::ProgressBar
-
report TSV
-
#report_msg Log::ProgressBar
-
repository_dirs Open
-
require SOPT
-
require_local_workflow Workflow
-
require_remote_workflow Workflow
-
require_workflow Workflow
-
#required_files Task::Job
-
#required_inputs Task
-
#rescue_first_line TSV::Parser
-
reset SOPT
-
#reset Annotated
-
#reset Filtered::Filter
-
reset_color Log
-
reset_do_once Misc
-
#reset_filters TSV
-
resolve_array Annotated
-
#resolve_input_steps Step
-
resolve_locals Workflow
-
#resource Path
-
#resources Resource
-
#resources_requested Workflow::Orchestrator
-
#resources_used Workflow::Orchestrator
-
#result Step
-
#result_description RemoteStep
-
#result_description Task
-
#result_description Step
-
#result_description= Step
-
#result_type Task
-
#result_type RemoteStep
-
#result_type Step
-
#result_type= Step
-
#resumable Task
-
#resumable Workflow
-
#resumable? Step
-
#reswpan RbbtProcessQueue
-
return_line Log
-
#returns Workflow
-
#reverse Association::Index
-
#rewind TSV::Parser
-
#rewind_inputs Step
-
#rgb Top Level Namespace
-
rm Open
-
rm_rf Open
-
#root Resource
-
#ruby SSHLine
-
ruby SSHLine
-
ruby2R R
-
#rules KnowledgeBase::Traverser
-
#run Task::Job
-
run Rake
-
run RbbtPython
-
run Docker
-
#run RbbtPython::Binding
-
#run RbbtProcessQueue::RbbtProcessQueueWorker
-
#run RemoteStep::SSH
-
run SSHLine
-
#run SSHLine
-
run R
-
#run Step
-
#run RemoteStep
-
run_batch_job RemoteWorkflow::SSH
-
run_cromwell Cromwell
-
#run_dependencies Task::Job
-
#run_dependencies Step
-
#run_job HPC::TemplateGeneration
-
run_job RemoteWorkflow::SSH
-
run_log RbbtPython
-
run_log_stderr RbbtPython
-
#run_rake Resource
-
run_template HPC::SLURM
-
run_template HPC::PBS
-
run_template HPC::LSF
-
#run_type RemoteStep::SSH
-
#run_with_respawn RbbtProcessQueue::RbbtProcessQueueWorker
-
#run_with_rules Workflow::Orchestrator
-
#running? RemoteStep
-
#running? Step
-
sample Misc
-
sample_large_obj Misc
-
sanitize_filename Misc
-
#save Filtered::Filter
-
#save Log::ProgressBar
-
save_content_in_repo Open
-
#save_dependencies Task::Job
-
#save_file Step
-
save_file Persist
-
save_input Step
-
save_inputs Step
-
save_job_inputs Step
-
#save_options Task::Job
-
save_stream Misc
-
#saved Filtered::Filter
-
#saved_stream Step
-
scan_version_text Misc
-
script RbbtPython
-
sd Misc
-
#search_order Path
-
#search_paths Path
-
#search_paths Resource
-
#seek Bgzf
-
#seen Step
-
select AssociationItem
-
#select AnnotatedArray
-
#select TSV
-
#select TSV::Parser
-
#select_by AnnotatedArray
-
#select_entities KnowledgeBase
-
select_lines Misc
-
select_ranges Misc
-
#self_md5 Annotated
-
semfile R
-
#send_cmd SSHLine
-
send_email Misc
-
send_email_old Misc
-
#send_request_with_body_stream Net::HTTPGenericRequest
-
#send_request_with_body_stream_orig Net::HTTPGenericRequest
-
sensiblewrite Misc
-
sensiblewrite_dir Misc
-
sensiblewrite_info Rbbt
-
sensiblewrites Rbbt
-
#sep TSV::Parser
-
#sep TSV::Dumper
-
#sep2 TSV::Parser
-
serialize_info Step
-
#serializer Persist::CDBAdapter
-
#serializer TSV::Parser
-
#serializer= TSV
-
#serve_output SSHLine
-
#server_missing_resource_cache Resource
-
set Rbbt::Config
-
#set Color
-
#set_extension Path
-
#set_info Task::Job
-
#set_info Step
-
#set_libdir Resource
-
#set_metadata Persist::PKIAdapter
-
#set_metadata Persist::FWTAdapter
-
#set_software_env Resource
-
#set_step_dependencies Workflow
-
#set_stream TSV::Dumper
-
set_time_from_repo Open
-
setup Association::Index
-
setup NamedArray
-
setup Bgzf
-
#setup KnowledgeBase
-
setup Task
-
setup Path
-
setup AbortedStream
-
#setup Annotation
-
#setup TSV::Parser
-
setup IndiferentHash
-
setup ConcurrentStream
-
setup TSV
-
setup CaseInsensitiveHash
-
setup SOPT
-
setup Workflow::DependencyBlock
-
setup ComputeDependency
-
#setup_array TSV
-
#setup_hash Annotation
-
#setup_override_dependency Workflow
-
#setup_positional Annotation
-
severity Log
-
#shard_function Persist::Sharder
-
#shift NamedArray
-
#short_path Step
-
#short_path RemoteStep
-
#short_path_real Step
-
shortcuts SOPT
-
#size FixWidthTable
-
#size TSV
-
#size PackedIndex
-
#size Filtered
-
#size Persist::FWTAdapter
-
#size Persist::Sharder
-
#size Persist::TSVAdapter
-
#slice TSV
-
snake_case Misc
-
#soft_grace Step
-
#sort AnnotatedArray
-
#sort TSV
-
#sort_by TSV
-
sort_candidates Workflow::Orchestrator
-
sort_mutation_stream Misc
-
sort_stream Misc
-
sorted_array_hits Misc
-
#source KnowledgeBase
-
#source_field Association::Index
-
#source_for_doc_file Path
-
#source_index KnowledgeBase
-
#source_type KnowledgeBase
-
#sread RbbtProcessQueue::RbbtProcessSocket
-
ssh? Open
-
ssh_connection Misc
-
ssh_open Open
-
ssh_run Misc
-
ssh_run_alt Misc
-
ssh_run_old Misc
-
stack Log
-
#stalled? Step
-
#start Task::Job
-
#started RemoteStep
-
#started? RemoteStep
-
#started? Step
-
#status RemoteStep
-
#status Step
-
#status= Step
-
status_color Step
-
#status_lock Step
-
#std_err ConcurrentStream
-
std_num_vector Misc
-
#step Step
-
#step Task::Job
-
#step_cache Workflow
-
step_file? Misc
-
step_info Step
-
#step_module Workflow
-
#step_path Workflow
-
#stop RbbtProcessQueue::RbbtProcessQueueWorker
-
#stop_dependencies Step
-
#stopping RbbtProcessQueue::RbbtProcessQueueWorker
-
store_into TSV
-
str2options TSV
-
#straight TSV::Parser
-
#stream PackedIndex
-
#stream TSV::Parser
-
stream TSV::Dumper
-
#stream TSV::Dumper
-
#stream Step
-
stream_column TSV
-
#stream_exception ConcurrentStream
-
#stream_exports Workflow
-
#stream_exports RemoteWorkflow
-
#stream_input RemoteStep
-
#stream_job RemoteStep::REST
-
stream_name TSV
-
#stream_raise_exception ConcurrentStream
-
#streaming? Step
-
string2const Misc
-
string2hash Misc
-
#sub Path
-
#subdir Resource
-
#subset Association::Index
-
#subset AnnotatedArray
-
#subset TSV
-
#subset KnowledgeBase
-
sum Misc
-
#summary TSV
-
summary SOPT
-
#swap_id TSV
-
swap_id TSV
-
#swrite RbbtProcessQueue::RbbtProcessSocket
-
#sync_environment HPC::TemplateGeneration
-
synchronize RbbtSemaphore
-
#synchronize MockMutex
-
#synchronous WorkflowSOAP
-
#synchronous_exports Workflow
-
#synchronous_exports RemoteWorkflow
-
#syndicate KnowledgeBase
-
synopsys SOPT
-
#take_all TSV::Parser
-
#take_input_values Task
-
tar Misc
-
#target KnowledgeBase
-
#target_field Association::Index
-
#target_index KnowledgeBase
-
#target_type KnowledgeBase
-
tarize Misc
-
#task Task::Job
-
#task Step
-
#task Workflow
-
#task RemoteStep
-
#task_dependencies Workflow
-
#task_dependencies RemoteWorkflow::SSH
-
#task_description Workflow
-
#task_exports Workflow
-
#task_for Workflow
-
#task_from_dep Workflow
-
#task_info RemoteWorkflow::SSH
-
task_info RemoteWorkflow::REST
-
#task_info RemoteWorkflow::REST
-
#task_info Workflow
-
#task_inputs_from_directory Workflow
-
#task_name Step
-
#task_name RemoteStep
-
#task_signature Step
-
task_specific_rules HPC::Orchestration
-
#tasks Workflow
-
#tasks RemoteWorkflow::REST
-
#tasks RemoteWorkflow::SSH
-
tee_stream_thread Misc
-
tee_stream_thread Persist
-
terminal_width Log
-
#thr_msg Log::ProgressBar
-
#thread ConcurrentStream
-
thread_each_on_semaphore RbbtSemaphore
-
#threads ConcurrentStream
-
#threads RbbtThreadQueue
-
#through TSV
-
#tick Log::ProgressBar
-
#ticks Log::ProgressBar
-
time_tick Misc
-
timeout_insist Misc
-
#timer Workflow::Orchestrator
-
timespan Misc
-
tmp_file TmpFile
-
#tmp_path Step
-
tmp_path Step
-
tmpdir TmpFile
-
tmpdir= TmpFile
-
#to_a AnnotatedArray
-
#to_double TSV
-
#to_flat TSV
-
#to_hash NamedArray
-
to_hash Annotated
-
#to_hash TSV
-
#to_list TSV
-
#to_matrix Association::Index
-
#to_onehot TSV
-
#to_rgb Color
-
#to_rgba Color
-
#to_s Path
-
#to_s TSV
-
#to_s Color
-
#to_s LaterString
-
#to_s RemoteWorkflow
-
#to_single TSV
-
#to_unmerged_s TSV
-
to_utf8 Misc
-
#to_yaml Path
-
token_priority Rbbt::Config
-
tokenize Misc
-
#tokyocabinet_class Persist::TCAdapter
-
tool CMD
-
total_length Misc
-
touch Open
-
trace Workflow
-
trace_job_summary Workflow
-
trace_job_times Workflow
-
#trans? Color
-
translate TSV
-
#translate KnowledgeBase
-
translate Association
-
translate_stream TSV
-
transplant Workflow
-
#transpose TSV
-
#transpose_list TSV
-
trap_std Log
-
trap_stderr Log
-
#traverse Path
-
traverse TSV::Parser
-
#traverse TSV::Parser
-
#traverse KnowledgeBase::Traverser
-
traverse TSV
-
#traverse KnowledgeBase
-
traverse_array TSV
-
traverse_cpus TSV
-
#traverse_db KnowledgeBase::Traverser
-
traverse_hash TSV
-
traverse_io TSV
-
traverse_obj TSV
-
traverse_run TSV
-
traverse_stream TSV
-
traverse_threads TSV
-
traverse_tsv TSV
-
try3times Misc
-
tsv Annotated
-
tsv Colorize
-
#tsv Path
-
tsv Log
-
tsv R
-
tsv2df RbbtPython
-
#tsv_options Path
-
#tsv_sort TSV
-
#tsv_values Annotated
-
tty_size Log
-
txt_digest_str Misc
-
#type TSV::Traverser
-
#type TSV::Parser
-
uncolor Log
-
#undirected KnowledgeBase
-
#undirected Association::Index
-
#unexport Workflow
-
ungzip Misc
-
#uniq TSV::Traverser
-
#unlocated_override? Workflow
-
#unmasked_annotations Annotation
-
#unmasked_annotations Annotated
-
#unnamed TSV
-
unnamed TSV
-
#unsaved Filtered::Filter
-
untar Misc
-
#unzip TSV
-
unzip Open
-
unzip_in_dir Misc
-
up_lines Log
-
#updatable? Step
-
#update Step
-
#update R::Model
-
#update Filtered::Filter
-
update_mtime Open
-
#updated? Step
-
upload_dependencies RemoteWorkflow::SSH
-
upload_inputs RemoteWorkflow::SSH
-
#url RemoteWorkflow
-
#url RemoteStep
-
usage SOPT
-
use_lock_id= Misc
-
#value Persist::PKIAdapter
-
#value Filtered::Filter
-
#value_peek TSV
-
#value_size FixWidthTable
-
#values TSV
-
#values_at CaseInsensitiveHash
-
#values_at IndiferentHash
-
#values_at Persist::TSVAdapter
-
#values_at NamedArray
-
#values_at FixWidthTable
-
#values_at PackedIndex
-
#values_to_s TSV
-
values_to_s TSV::Dumper
-
variance Misc
-
version_file Association
-
versions Rbbt
-
versions CMD
-
wait Open
-
#wait_for_job HPC::TemplateGeneration
-
wait_for_jobs Step
-
#waiting? Step
-
warn Log
-
wget Open
-
#where Path
-
#wildcard KnowledgeBase::Traverser
-
with_bar Log::ProgressBar
-
with_config Rbbt::Config
-
with_dir TmpFile
-
with_env Misc
-
with_fifo Misc
-
with_file TmpFile
-
#with_key Resource
-
#with_monitor TSV
-
#with_read Persist::TSVAdapter
-
with_semaphore RbbtSemaphore
-
with_severity Log
-
#with_unnamed TSV
-
#with_workdir Workflow
-
#with_write Persist::TSVAdapter
-
workdir R
-
workdir Workflow
-
#workdir Workflow
-
workdir= Workflow
-
#workflow Task
-
#workflow Step
-
#workflow WorkflowSOAP
-
#workflow SSHLine
-
workflow SSHLine
-
workflow2playbook Ansible
-
#workflow_description RemoteWorkflow::SSH
-
workflow_dir Workflow
-
workflow_for Workflow
-
workflow_rules HPC::Orchestration
-
#workflow_short_path RemoteStep
-
#workflow_short_path Step
-
workflows Workflow
-
workload Workflow::Orchestrator
-
#workload HPC::Orchestration
-
#writable Persist::Sharder
-
#writable Persist::LevelDBAdapter
-
#writable Persist::TSVAdapter
-
#writable? Step
-
writable? Open
-
writable_repo? Open
-
#write Persist::TCAdapter
-
#write Persist::KCAdapter
-
#write Persist::Sharder
-
#write Persist::LevelDBAdapter
-
#write Persist::TSVAdapter
-
#write Persist::CDBAdapter
-
#write FixWidthTable
-
#write Path
-
#write TSV
-
write Open
-
write TSV::XLSX
-
write TSV::XLS
-
#write? Persist::KCAdapter
-
#write? Persist::Sharder
-
#write? Persist::LevelDBAdapter
-
#write? Persist::TSVAdapter
-
#write? FixWidthTable
-
#write? TSV
-
#write_and_close Persist::Sharder
-
#write_and_close Persist::LevelDBAdapter
-
#write_and_close Persist::TSVAdapter
-
#write_and_close Persist::CDBAdapter
-
#write_and_read Persist::Sharder
-
#write_and_read Persist::LevelDBAdapter
-
#write_and_read Persist::TSVAdapter
-
#write_and_read Persist::CDBAdapter
-
#write_lock Persist::TSVAdapter
-
#write_sem RbbtProcessQueue::RbbtProcessSocket
-
#wwwf Top Level Namespace
-
#wwww Top Level Namespace
-
xls TSV
-
#xls TSV
-
xlsx TSV
-
#xlsx TSV
-
#yaml Path
-
#zip TSV
-
zip2hash Misc
-
zip? Open
-
zip_fields Misc
-
#zip_fields NamedArray
-
zip_fields TSV
-
#zip_new TSV
-
#zipped TSV::Parser
-
zscore Misc