Method List
-
#<< PackedIndex
-
#<< Persist::Sharder
-
#<< Persist::FWTAdapter
-
GET_params2hash Misc
-
IUPAC_to_base Misc
-
#R TSV
-
#R_console TSV
-
#R_interactive TSV
-
#[] PackedIndex
-
#[] FixWidthTable
-
#[] Persist::CDBAdapter
-
#[] Persist::TSVAdapter
-
#[] Persist::Sharder
-
#[] Persist::PKIAdapter
-
#[] Persist::FWTAdapter
-
#[]= Persist::CDBAdapter
-
#[]= Persist::TSVAdapter
-
#[]= Persist::Sharder
-
#[]= Persist::PKIAdapter
-
#[]= Persist::FWTAdapter
-
__jobs Rbbt
-
__prepare_inputs_for_restclient RemoteWorkflow::REST
-
#_clean RemoteStep::REST
-
_clean_float TSV
-
_eval R
-
_excel_data TSV
-
#_get_block Bgzf
-
_ignore_stderr Log
-
_ignore_stdout Log
-
#_index Bgzf
-
#_orchestrate_batch RemoteStep::SSH
-
#_purge_cache Bgzf
-
_remove_link TSV
-
#_restart RemoteStep
-
#_run RemoteStep::SSH
-
#_run_batch RemoteStep::SSH
-
#_run_job RemoteStep::REST
-
_zip_fields Misc
-
#abort Task::Job
-
#abort RbbtProcessQueue::RbbtProcessQueueWorker
-
#abort RemoteStep::SSH
-
#abort RemoteStep::REST
-
#abort_and_join RbbtProcessQueue::RbbtProcessQueueWorker
-
#aborted? Task::Job
-
#aborted? Step
-
#access Step
-
accumulate_rules HPC::Orchestration
-
#add Filtered::Filter
-
add FileCache
-
#add FixWidthTable
-
#add Persist::PKIAdapter
-
#add Persist::FWTAdapter
-
add_GET_param Misc
-
add_batch_deps HPC::Orchestration
-
add_config_keys HPC::Orchestration
-
add_consummable_annotation AnnotatedModule
-
add_defaults Misc
-
#add_filter Filtered
-
add_input RbbtMutiplartPayload
-
add_libdir Misc
-
add_path RbbtPython
-
add_paths RbbtPython
-
#add_point FixWidthTable
-
#add_range FixWidthTable
-
#add_range_point FixWidthTable
-
#add_range_point Persist::PKIAdapter
-
#add_range_point Persist::FWTAdapter
-
add_rules_and_consolidate HPC::Orchestration
-
add_stream RbbtMutiplartPayload
-
#add_unsaved Filtered::Filter
-
add_version Rbbt
-
align SmithWaterman
-
align_txt SmithWaterman
-
alignment_map SmithWaterman
-
alignment_percent SmithWaterman
-
all SOPT
-
#all_fields Path
-
#all_inputs Task::Job
-
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
-
#asynchronous WorkflowSOAP
-
#asynchronous_exports RemoteWorkflow
-
attach TSV
-
#attach_index TSV
-
attach_orig TSV
-
#attach_same_key TSV
-
#base_name RemoteStep
-
#base_url RemoteStep
-
#basename Path
-
#batch_dir_for_id HPC::TemplateGeneration
-
#batch_options HPC::TemplateGeneration
-
#batch_options RemoteStep::SSH
-
batch_system HPC::LSF
-
batch_system HPC::PBS
-
batch_system HPC
-
batch_system HPC::SLURM
-
batch_system_variables HPC::LSF
-
batch_system_variables HPC::PBS
-
#batch_system_variables HPC::TemplateGeneration
-
batch_system_variables HPC::SLURM
-
benchmark Misc
-
bgzip_cmd Bgzf
-
binary_include? Misc
-
binding_run RbbtPython
-
#bindings Step
-
#block Task::Job
-
#block RbbtThreadQueue
-
#block RbbtProcessQueue::RbbtProcessQueueWorker
-
#block_cache_size Bgzf
-
#block_offset Bgzf
-
bootstrap Misc
-
bootstrap_in_threads Misc
-
#cache TCCache
-
#cache_file RemoteStep
-
#cache_files RemoteStep
-
cache_online_elements FileCache
-
cachedir FileCache
-
cachedir= FileCache
-
call_method RbbtPython
-
#callback RbbtProcessQueue
-
#callback_queue RbbtProcessQueue::RbbtProcessQueueWorker
-
#canfail? ComputeDependency
-
#canfail_paths Step
-
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
-
#chunked_values_at FixWidthTable
-
#chunked_values_at Hash
-
class_new_obj RbbtPython
-
#clean Filtered::Filter
-
#clean Task::Job
-
clean Step
-
#clean Step
-
#clean RbbtThreadQueue::RbbtThreadQueueWorker
-
#clean RbbtThreadQueue
-
#clean RbbtProcessQueue::RbbtProcessSocket
-
clean RemoteWorkflow::SSH
-
#clean RemoteStep::SSH
-
#clean RemoteStep::REST
-
#clean_name Step
-
#clean_name RemoteStep
-
clean_symbols Ansible
-
clean_url RemoteWorkflow::REST
-
#cleaned RbbtProcessQueue::RbbtProcessSocket
-
#cleanup RbbtProcessQueue::RbbtProcessQueueWorker
-
#cleanup_environment HPC::TemplateGeneration
-
clear R
-
#close PackedIndex
-
#close Bgzf
-
#close FixWidthTable
-
#close Persist::CDBAdapter
-
#close Persist::TSVAdapter
-
#close Persist::LevelDBAdapter
-
#close Persist::Sharder
-
#close Persist::KCAdapter
-
#close_read RbbtProcessQueue::RbbtProcessSocket
-
close_stream RbbtMutiplartPayload
-
#close_write RbbtProcessQueue::RbbtProcessSocket
-
#closed Persist::TSVAdapter
-
#closed Persist::LevelDBAdapter
-
#closed Persist::Sharder
-
#closed? Bgzf
-
#closed? Persist::CDBAdapter
-
#closed? Persist::TSVAdapter
-
#closed? Persist::LevelDBAdapter
-
#closed? Persist::Sharder
-
#closed_read? RbbtProcessQueue::RbbtProcessSocket
-
#closed_write? RbbtProcessQueue::RbbtProcessSocket
-
#closest FixWidthTable
-
#closest_page Bgzf
-
#coda HPC::TemplateGeneration
-
#colClasses R::Model
-
collapse_ranges Misc
-
collect RbbtPython
-
#collect Persist::LMDBAdapter
-
#collect Persist::TSVAdapter
-
#collect Persist::Sharder
-
#collect Persist::KCAdapter
-
command SOPT
-
#compressed_stream Bgzf
-
#compute ComputeDependency
-
#config SimpleDSL
-
#config Step
-
console R
-
consolidate Misc
-
consume SOPT
-
correct_mutation Misc
-
correct_vcf_mutation Misc
-
counts Misc
-
current_options= SOPT
-
#data Filtered::Filter
-
#data Workflow::Data
-
#data_dir Workflow::Data
-
#data_offset Bgzf
-
#data_task Workflow::Data
-
#database Persist::Sharder
-
#databases Persist::Sharder
-
#db_type Persist::Sharder
-
del FileCache
-
#delete Persist::CDBAdapter
-
#delete Persist::TSVAdapter
-
#delete Persist::LevelDBAdapter
-
#delete Persist::KCAdapter
-
delete_inputs SOPT
-
#dep Workflow
-
#dep_task Workflow
-
#dependencies Step
-
#dependency Workflow::DependencyBlock
-
#desc Workflow
-
description SOPT
-
df2tsv RbbtPython
-
#directory HPC::BATCH_DRY_RUN
-
#dirty? Step
-
#dirty_files Step
-
divide Misc
-
do_once Misc
-
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
-
#done RbbtThreadQueue
-
#done? Task::Job
-
#done? Step
-
#done? RbbtProcessQueue::RbbtProcessQueueWorker
-
#done? RemoteStep
-
#dump FixWidthTable
-
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 RbbtProcessQueue::RbbtProcessSocket
-
dump_memory Rbbt
-
#dumper_stream TSV
-
#dup_inputs Step
-
#dup_inputs RemoteStep
-
dup_stream Step
-
#each Persist::LMDBAdapter
-
#each Persist::TSVAdapter
-
#each Persist::Sharder
-
#each Persist::PKIAdapter
-
each RbbtThreadQueue
-
#each Persist::FWTAdapter
-
encode RemoteWorkflow::REST
-
ensembl_server Misc
-
#entity_options TSV
-
eog R::PNG
-
eog R::GIF
-
eog_plot R::PNG
-
eog_plot R::GIF
-
#error? Task::Job
-
#error? Step
-
escape_url RemoteWorkflow::REST
-
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 Step
-
exec RbbtPython
-
#exec Step
-
#exec RemoteStep
-
#exec_cmd HPC::TemplateGeneration
-
#exec_exports RemoteWorkflow
-
#exec_job RemoteStep::REST
-
#execute HPC::TemplateGeneration
-
#execute_and_dup Step
-
#execute_dependency Step
-
execute_job RemoteWorkflow::REST
-
#exists? R::Model
-
#export_asynchronous Workflow
-
#export_exec Workflow
-
#export_stream Workflow
-
#export_synchronous Workflow
-
#exported_tasks RemoteWorkflow
-
extended Filtered
-
extended Resource::WithKey
-
extended ChainMethods
-
extended Ansible::AnsibleWorkflow
-
#extension Workflow
-
#fast_load_id Workflow
-
#field_index TSV
-
field_index_dir TSV
-
#field_indices TSV
-
field_position Misc
-
#fieldnum Filtered::Filter
-
#fields Path
-
#file PackedIndex
-
#file FixWidthTable
-
#file Step
-
#file RemoteStep
-
file_time Rbbt
-
#filename Bgzf
-
#filename FixWidthTable
-
#files Task::Job
-
#files Step
-
#files RemoteStep
-
files_dir Step
-
#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
-
#filters Filtered::FilterArray
-
find_path TSV
-
find_traversal TSV
-
#fit R::Model
-
fix_hash RemoteWorkflow
-
#fix_io Persist::CDBAdapter
-
fix_params RemoteWorkflow
-
fix_shortcut SOPT
-
#follow_job HPC::TemplateGeneration
-
#fork Task::Job
-
#fork RemoteStep
-
#format FixWidthTable
-
#formula R::Model
-
found FileCache
-
genomic_location_cmp Misc
-
get FileCache
-
get FixWidthTable
-
get SOPT
-
#get RemoteStep::REST
-
#get_block Bgzf
-
#get_chains HPC::Orchestration
-
get_class RbbtPython
-
#get_datadir Workflow::Data
-
#get_exception Step
-
get_extension Path
-
#get_file Workflow::Data
-
#get_job_dependencies HPC::Orchestration
-
get_json RemoteWorkflow::SSH
-
get_json RemoteWorkflow::REST
-
get_module RbbtPython
-
#get_point FixWidthTable
-
#get_prefix Persist::TSVAdapter
-
#get_prefix Persist::LevelDBAdapter
-
#get_prefix Persist::Sharder
-
#get_range FixWidthTable
-
get_raw RemoteWorkflow::SSH
-
get_raw RemoteWorkflow::REST
-
#get_recursive_job_dependencies HPC::Orchestration
-
#get_stream RemoteStep
-
get_streams RemoteStep
-
#get_streams RemoteStep
-
#getc Bgzf
-
#gets Bgzf
-
ggplot IRuby
-
ggplot R::SVG
-
ggplot R::PNG
-
ggplot R::GIF
-
ggplotPNG R::PNG
-
ggplotSVG R::SVG
-
google_venn Misc
-
#grace RemoteStep
-
groom R::Model
-
#has_rake Resource
-
hash2GET_params Misc
-
hash2string Misc
-
header HPC::LSF
-
header HPC::PBS
-
#header HPC::TemplateGeneration
-
header HPC::SLURM
-
header_lines TSV
-
#helper Workflow
-
#hold_dependencies HPC::TemplateGeneration
-
html_tag Misc
-
#id Task::Job
-
id2name Task::Job
-
#id_for Workflow
-
#identifier_files Path
-
#ids Filtered::FilterArray
-
#ids Filtered::Filter
-
#idx_overlap FixWidthTable
-
#idx_pos FixWidthTable
-
#idx_pos_end FixWidthTable
-
#idx_value FixWidthTable
-
ignore_stderr Log
-
ignore_stdout Log
-
img IRuby
-
#import Workflow
-
import_method RbbtPython
-
in_delta? Misc
-
#include? Persist::CDBAdapter
-
#include? Persist::TSVAdapter
-
#include? Persist::LevelDBAdapter
-
#include? Persist::Sharder
-
#include? Persist::PKIAdapter
-
#include? Persist::FWTAdapter
-
index_BED Misc
-
#info Task::Job
-
#info Step
-
#info Annotation::AnnotatedObject
-
#info RemoteStep
-
#info_file Task::Job
-
info_file Step
-
#info_file Step
-
#info_lock Step
-
#init Bgzf
-
#init RbbtThreadQueue
-
#init RbbtProcessQueue
-
#init_info Step
-
#init_info RemoteStep
-
#init_job RemoteStep::SSH
-
#init_job RemoteStep::REST
-
init_rbbt RbbtPython
-
#init_remote_tasks RemoteWorkflow::SSH
-
#init_remote_tasks RemoteWorkflow::REST
-
init_thread RbbtPython
-
#initialize HPC::BATCH_DRY_RUN
-
#initialize Filtered::Filter
-
#initialize PackedIndex
-
#initialize R::Model
-
#initialize Task::Job
-
#initialize WorkflowSOAP
-
#initialize FixWidthTable
-
#initialize Persist::Sharder
-
#initialize RbbtThreadQueue::RbbtThreadQueueWorker
-
#initialize RbbtThreadQueue
-
#initialize RemoteWorkflow
-
#initialize RbbtProcessQueue::RbbtProcessSocket
-
#initialize RbbtProcessQueue::RbbtProcessQueueWorker::Respawn
-
#initialize RbbtProcessQueue::RbbtProcessQueueWorker
-
#initialize RemoteStep
-
#input Task::Job
-
#input InputModule
-
#input_checks RemoteStep
-
input_defaults SOPT
-
#input_dependencies Step
-
#input_dependencies RemoteStep::SSH
-
input_descriptions SOPT
-
input_doc SOPT
-
input_format SOPT
-
input_header RbbtMutiplartPayload
-
input_shortcuts SOPT
-
input_types SOPT
-
#input_types RemoteStep
-
#inputs Step
-
inputs SOPT
-
#inputs RemoteStep
-
insist Misc
-
#inspect Step
-
#inspect RemoteStep
-
instance R
-
intersect_streams Misc
-
#is_exec RemoteStep
-
is_persisted? Persist
-
#is_stream RemoteStep
-
#issue RemoteStep::SSH
-
issue RbbtMutiplartPayload
-
#item_size PackedIndex
-
iterate RbbtPython
-
iterate_index RbbtPython
-
#job WorkflowSOAP
-
job_batches HPC::Orchestration
-
job_chains HPC::Orchestration
-
job_dependencies HPC::Orchestration
-
job_info Rbbt
-
job_path? Workflow
-
#job_queued HPC::TemplateGeneration
-
#job_rules HPC::Orchestration
-
job_rules HPC::Orchestration
-
job_script RemoteWorkflow::SSH
-
job_status HPC::LSF
-
job_status HPC::PBS
-
job_status HPC::SLURM
-
#job_template HPC::TemplateGeneration
-
job_workload HPC::Orchestration
-
#jobs HPC::TemplateGeneration
-
#join Task::Job
-
#join RbbtThreadQueue
-
#join RbbtProcessQueue::RbbtProcessQueueWorker
-
#join RemoteStep
-
#key Filtered::Filter
-
#keys Persist::TSVAdapter
-
#keys Persist::Sharder
-
#keys Path
-
#keys Persist::PKIAdapter
-
#keys Persist::FWTAdapter
-
#knowledge_base Step
-
#kyotocabinet_class Persist::KCAdapter
-
#last_pos FixWidthTable
-
link_job Step
-
#list Filtered::Filter
-
list2ruby RbbtPython
-
load R::Model
-
load Task::Job
-
#load Task::Job
-
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 RbbtProcessQueue::RbbtProcessSocket
-
#load RemoteStep::SSH
-
#load RemoteStep::REST
-
#load_conda HPC::TemplateGeneration
-
#load_config SimpleDSL
-
#load_cromwell Workflow
-
#load_dependencies Task::Job
-
#load_documentation Workflow
-
load_entity Annotation
-
#load_file Step
-
#load_id RemoteWorkflow
-
load_inputs Workflow
-
load_json RbbtPython
-
load_lock Rbbt
-
#load_modules HPC::TemplateGeneration
-
load_path RemoteWorkflow
-
load_pickle RbbtPython
-
#load_res RemoteStep
-
load_script_variables RbbtPython
-
load_serialized_info Step
-
#load_tasks RemoteWorkflow
-
load_yaml Misc
-
#lock Persist::TSVAdapter
-
#lock_and_close Persist::TSVAdapter
-
lock_info Rbbt
-
lockfile R
-
locks Rbbt
-
#log Workflow
-
log Step
-
#log Step
-
log10 Misc
-
log2 Misc
-
log_block Step
-
#log_dependency_exec Step
-
log_progress Step
-
#log_progress Step
-
log_string Step
-
#marshal_dump TSV
-
#marshal_dump Persist::TCAdapter
-
#marshal_load Hash
-
#marshal_load TokyoCabinet::BDB
-
#marshal_load TokyoCabinet::HDB
-
#mask PackedIndex
-
#mask FixWidthTable
-
#mask_length PackedIndex
-
#match Filtered::Filter
-
match_fields Misc
-
match_value Misc
-
#matrix_melt TSV
-
max Misc
-
md5_file Step
-
#md5_file Step
-
mean Misc
-
median Misc
-
melt TSV
-
#melt TSV
-
memory_use Misc
-
memprof Misc
-
#merge! Persist::CDBAdapter
-
#merge! Persist::TSVAdapter
-
#merge! Persist::LevelDBAdapter
-
#merge! Persist::Sharder
-
#merge_info Step
-
merge_row_fields TSV
-
merge_rules HPC::Orchestration
-
merge_sorted_arrays Misc
-
#message Step
-
#messages Task::Job
-
#messages Step
-
#meta_data HPC::TemplateGeneration
-
#metadata Persist::PKIAdapter
-
#metadata Persist::FWTAdapter
-
#metadata_file Persist::PKIAdapter
-
#metadata_file Persist::FWTAdapter
-
#method_missing Filtered::FilterArray
-
#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
-
#model_file R::Model
-
monitor ProcPath
-
#monitor_stream Step
-
#mutex Persist::TSVAdapter
-
#mutex Persist::Sharder
-
#mutex Step
-
#mutex RbbtThreadQueue
-
mutex RbbtMutiplartPayload
-
#name R::Model
-
#name Task::Job
-
#name Step
-
#name RemoteWorkflow
-
#name RemoteStep
-
name2basename Misc
-
#name= RemoteStep
-
new Rserve::TCPSocket
-
new_binding RbbtPython
-
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
-
#noinfo? Step
-
#nopid? Step
-
#nopid? RemoteStep
-
notify Misc
-
#num_threads RbbtThreadQueue
-
numpy2ruby RbbtPython
-
obj2hash RbbtPython
-
object_delta Misc
-
#offset PackedIndex
-
#old_exec Step
-
#old_method_missing Resource::WithKey
-
open TSV
-
#open Task::Job
-
open TCCache
-
open Persist::CDBAdapter
-
open Persist::LMDBAdapter
-
open Persist::LevelDBAdapter
-
open Persist::SharderAdapter
-
open Persist::KCAdapter
-
open Persist::PKIAdapter
-
open Persist::FWTAdapter
-
open_cdb Persist
-
open_fwt Persist
-
open_kyotocabinet Persist
-
open_leveldb Persist
-
open_lmdb Persist
-
open_pki Persist
-
open_sharder Persist
-
#options Task::Job
-
#options Persist::Sharder
-
orchestrate_batch_job RemoteWorkflow::SSH
-
#orchestrate_job HPC::Orchestration
-
orchestration_rules HPC::Orchestration
-
ordered_divide Misc
-
original_argv SOPT
-
original_open TSV
-
original_require_workflow Workflow
-
#original_task_name Step
-
#original_to_s TSV
-
#original_unzip TSV
-
#original_workflow Step
-
#overlaps FixWidthTable
-
#override_dependencies Workflow
-
#override_dependencies RemoteStep::SSH
-
#overriden Step
-
#overriden? Step
-
#overriden_deps Step
-
#parse SimpleDSL
-
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 Task::Job
-
path FileCache
-
#path Step
-
#path RemoteStep
-
#path RemoteStep::SSH
-
path_script RemoteWorkflow::SSH
-
paths RbbtPython
-
#payload RbbtProcessQueue::RbbtProcessQueueWorker::Respawn
-
pb HPC::Orchestration
-
pdftotext PDF2Text
-
persist_info Rbbt
-
#persistence Filtered::Filter
-
#persistence_path PackedIndex
-
#persistence_path FixWidthTable
-
#persistence_path Persist::TSVAdapter
-
#persistence_path Persist::LevelDBAdapter
-
#persistence_path Persist::Sharder
-
#persistence_path= PackedIndex
-
#persistence_path= FixWidthTable
-
#persistence_path= Persist::PKIAdapter
-
#persistence_path= Persist::FWTAdapter
-
persists Rbbt
-
#pid Task::Job
-
#pid Step
-
#pid RbbtProcessQueue::RbbtProcessQueueWorker
-
pid_file R
-
pid_file Step
-
#pid_file Step
-
#piggyback HPC::Orchestration
-
#pipe_to Path
-
play Ansible
-
#play Ansible::AnsibleWorkflow
-
playbook Ansible
-
plot IRuby
-
plot R::SVG
-
plot R::PNG
-
plot R::GIF
-
plot ProcPath
-
plot_trace_job_times Workflow
-
#pop RbbtProcessQueue::RbbtProcessSocket
-
#pop_filter Filtered
-
#pos_function Persist::PKIAdapter
-
#pos_function Persist::FWTAdapter
-
pos_index TSV
-
#pos_index Path
-
positional2hash Misc
-
post_data_stream RbbtMutiplartPayload
-
post_job RemoteWorkflow::SSH
-
post_jobname RemoteWorkflow::REST
-
post_json RemoteWorkflow::REST
-
#ppthrough TSV
-
pre_fork Misc
-
#predict R::Model
-
#predict_interval R::Model
-
#prefix Persist::TSVAdapter
-
#prefix Persist::LevelDBAdapter
-
#prefix Persist::Sharder
-
prepare_entity Misc
-
#prepare_environment HPC::TemplateGeneration
-
#prepare_for_execution HPC::Orchestration
-
#prepare_submision HPC::TemplateGeneration
-
#previous_jobs Task::Job
-
#previous_jobs_rec Task::Job
-
#process RbbtThreadQueue
-
#process RbbtProcessQueue
-
process_mask PackedIndex
-
process_options Misc
-
process_paths RbbtPython
-
process_to_hash Misc
-
#produce RemoteStep::SSH
-
#produce RemoteStep::REST
-
produce_dependencies Step
-
#produce_dependencies RemoteStep::SSH
-
#produce_jobs HPC::Orchestration
-
profile Misc
-
profile_graph Misc
-
profile_html Misc
-
#progress_bar Step
-
proportions Misc
-
prov_report Step
-
prov_report_msg Step
-
prov_status_msg Step
-
#provenance Step
-
#provenance_paths Step
-
#pthrough TSV
-
pull_keys Misc
-
purge Step
-
purge_stream_cache Step
-
#push RbbtProcessQueue::RbbtProcessSocket
-
py2ruby_a RbbtPython
-
#python Step
-
#python_block Step
-
#python_file Step
-
#queue RbbtThreadQueue
-
#queue RbbtProcessQueue::RbbtProcessQueueWorker
-
#r_options R::Model
-
#rake_for Resource
-
#range FixWidthTable
-
#range Persist::CDBAdapter
-
#range Persist::TSVAdapter
-
#range Persist::LevelDBAdapter
-
#range Persist::Sharder
-
range_index TSV
-
#range_index Path
-
#rbbt_job_exec_cmd HPC::TemplateGeneration
-
read TSV::XLS
-
read TSV::XLSX
-
#read PackedIndex
-
#read Task::Job
-
#read Bgzf
-
#read FixWidthTable
-
#read Persist::CDBAdapter
-
#read Persist::TSVAdapter
-
#read Persist::LevelDBAdapter
-
#read Persist::Sharder
-
#read Persist::KCAdapter
-
#read? Persist::TSVAdapter
-
#read? Persist::Sharder
-
#read_all Bgzf
-
#read_and_close Persist::CDBAdapter
-
#read_and_close Persist::TSVAdapter
-
#read_and_close Persist::LevelDBAdapter
-
#read_and_close Persist::Sharder
-
#read_lock Persist::TSVAdapter
-
read_matrix TSV
-
#read_sem RbbtProcessQueue::RbbtProcessSocket
-
#real_dependencies Workflow
-
#rec_access Step
-
#rec_dependencies Workflow
-
#rec_dependencies Step
-
#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 Task::Job
-
#recursive_clean RemoteStep::REST
-
#recursive_done? Task::Job
-
#refresh_time RemoteStep
-
register SOPT
-
relay RemoteWorkflow::SSH
-
relay_job RemoteWorkflow::SSH
-
relay_job_list RemoteWorkflow::SSH
-
relay_module_method Rbbt
-
#relocated Step
-
#relocated? Step
-
#remote_job RemoteWorkflow
-
#remote_tasks Workflow
-
#remove_extension Path
-
#reorder TSV
-
reorder_stream TSV
-
#replace_extension Path
-
repository_dirs Open
-
require SOPT
-
require_instead Rbbt
-
require_remote_workflow Workflow
-
require_workflow Workflow
-
#required_files Task::Job
-
#reset Filtered::Filter
-
reset SOPT
-
reset_do_once Misc
-
#reset_filters TSV
-
#reset_info Step
-
#result Step
-
#result_description Step
-
#result_description RemoteStep
-
#result_description= Step
-
#result_type Step
-
#result_type RemoteStep
-
#result_type= Step
-
#resumable Workflow
-
#resumable? Step
-
#returns Workflow
-
#ruby SSHLine
-
ruby2R R
-
ruby2python RbbtPython
-
run R
-
run Docker
-
#run RbbtPython::Binding
-
run Rake
-
#run Task::Job
-
#run RbbtProcessQueue::RbbtProcessQueueWorker
-
#run RemoteStep
-
#run RemoteStep::SSH
-
run_batch_job RemoteWorkflow::SSH
-
run_cromwell Cromwell
-
#run_dependencies Task::Job
-
#run_dependencies Step
-
run_direct RbbtPython
-
run_in_thread RbbtPython
-
#run_job HPC::TemplateGeneration
-
run_job RemoteWorkflow::SSH
-
run_log RbbtPython
-
run_log_stderr RbbtPython
-
#run_rake Resource
-
run_simple RbbtPython
-
run_template HPC::LSF
-
run_template HPC::PBS
-
run_template HPC::SLURM
-
run_threaded RbbtPython
-
#run_type RemoteStep::SSH
-
#run_with_respawn RbbtProcessQueue::RbbtProcessQueueWorker
-
#running? Step
-
#running? RemoteStep
-
sample Misc
-
sanitize_filename Misc
-
#save Filtered::Filter
-
#save_dependencies Task::Job
-
#save_file Step
-
save_inputs Step
-
#save_options Task::Job
-
save_script_result_json RbbtPython
-
save_script_result_pickle RbbtPython
-
#saved Filtered::Filter
-
script RbbtPython
-
sd Misc
-
#seek Bgzf
-
#seen Step
-
select_ranges Misc
-
semfile R
-
send_email Misc
-
send_email_old Misc
-
#send_request_with_body_stream Net::HTTPGenericRequest
-
#send_request_with_body_stream_orig Net::HTTPGenericRequest
-
sensiblewrite_info Rbbt
-
sensiblewrites Rbbt
-
serialize_info Step
-
#serializer Persist::CDBAdapter
-
#set_extension Path
-
#set_info Task::Job
-
#set_info Step
-
#set_metadata Persist::PKIAdapter
-
#set_metadata Persist::FWTAdapter
-
#set_software_env Resource
-
setup Bgzf
-
setup ComputeDependency
-
setup Workflow::DependencyBlock
-
setup SOPT
-
#setup_override_dependency Workflow
-
#shard_function Persist::Sharder
-
#short_path Step
-
#short_path RemoteStep
-
#short_path_real Step
-
shortcuts SOPT
-
#size Filtered
-
#size PackedIndex
-
#size FixWidthTable
-
#size Persist::TSVAdapter
-
#size Persist::Sharder
-
#size Persist::FWTAdapter
-
#soft_grace Step
-
sort_mutation_stream Misc
-
sorted_array_hits Misc
-
#source_for_doc_file Path
-
#sread RbbtProcessQueue::RbbtProcessSocket
-
ssh_connection Misc
-
ssh_run Misc
-
ssh_run_alt Misc
-
ssh_run_old Misc
-
#stalled? Step
-
#start Task::Job
-
#started RemoteStep
-
#started? Step
-
#started? RemoteStep
-
#status Step
-
#status RemoteStep
-
#status= Step
-
status_color Step
-
#status_lock Step
-
std_num_vector Misc
-
#step Task::Job
-
step_info Step
-
#stop RbbtProcessQueue::RbbtProcessQueueWorker
-
#stop_dependencies Step
-
stop_thread RbbtPython
-
#stopping RbbtProcessQueue::RbbtProcessQueueWorker
-
#stream PackedIndex
-
#stream_exports RemoteWorkflow
-
#stream_input RemoteStep
-
#stream_job RemoteStep::REST
-
#streaming? Step
-
string2const Misc
-
string2hash Misc
-
sum Misc
-
summary SOPT
-
#swap_id TSV
-
#swrite RbbtProcessQueue::RbbtProcessSocket
-
#sync_environment HPC::TemplateGeneration
-
synchronize RbbtPython
-
#synchronous WorkflowSOAP
-
#synchronous_exports RemoteWorkflow
-
synopsys SOPT
-
#task Task::Job
-
#task Workflow
-
#task Step
-
#task RemoteStep
-
#task_dependencies RemoteWorkflow::SSH
-
#task_exports Workflow
-
#task_for Workflow
-
#task_from_dep Workflow
-
#task_info Workflow
-
#task_info RemoteWorkflow::SSH
-
task_info RemoteWorkflow::REST
-
#task_info RemoteWorkflow::REST
-
#task_name Step
-
#task_name RemoteStep
-
#task_signature Step
-
task_specific_rules HPC::Orchestration
-
#tasks RemoteWorkflow::SSH
-
#tasks RemoteWorkflow::REST
-
thread RbbtPython
-
#threads RbbtThreadQueue
-
time_tick Misc
-
timeout_insist Misc
-
timespan Misc
-
tmp_path Step
-
#tmp_path Step
-
#to_s TSV
-
#to_s LaterString
-
#to_s RemoteWorkflow
-
#to_yaml Path
-
tokenize Misc
-
total_length Misc
-
trace Workflow
-
trace_job_summary Workflow
-
trace_job_times Workflow
-
#traverse Path
-
try3times Misc
-
tsv R
-
tsv2df RbbtPython
-
#unexport Workflow
-
#unlocated_override? Workflow
-
#unsaved Filtered::Filter
-
#unzip TSV
-
unzip_in_dir Misc
-
#update Filtered::Filter
-
#update R::Model
-
upload_dependencies RemoteWorkflow::SSH
-
upload_inputs RemoteWorkflow::SSH
-
#url RemoteWorkflow
-
#url RemoteStep
-
usage SOPT
-
#value Filtered::Filter
-
#value Persist::PKIAdapter
-
#value_size FixWidthTable
-
#values_at PackedIndex
-
#values_at FixWidthTable
-
#values_at Persist::TSVAdapter
-
variance Misc
-
versions Rbbt
-
#wait_for_job HPC::TemplateGeneration
-
wait_for_jobs Step
-
#waiting? Step
-
#with_key Resource
-
#with_monitor TSV
-
#with_read Persist::TSVAdapter
-
#with_write Persist::TSVAdapter
-
workdir R
-
#workflow WorkflowSOAP
-
#workflow Step
-
workflow2playbook Ansible
-
#workflow_description RemoteWorkflow::SSH
-
workflow_dir Workflow
-
workflow_for Workflow
-
workflow_repo Workflow
-
workflow_rules HPC::Orchestration
-
#workflow_short_path Step
-
#workflow_short_path RemoteStep
-
#workload HPC::Orchestration
-
#writable Persist::TSVAdapter
-
#writable Persist::LevelDBAdapter
-
#writable Persist::Sharder
-
write TSV::XLS
-
write TSV::XLSX
-
#write FixWidthTable
-
#write Persist::CDBAdapter
-
#write Persist::TSVAdapter
-
#write Persist::LevelDBAdapter
-
#write Persist::Sharder
-
#write Persist::KCAdapter
-
#write? FixWidthTable
-
#write? Persist::TSVAdapter
-
#write? Persist::LevelDBAdapter
-
#write? Persist::Sharder
-
#write? Persist::KCAdapter
-
#write_and_close Persist::CDBAdapter
-
#write_and_close Persist::TSVAdapter
-
#write_and_close Persist::LevelDBAdapter
-
#write_and_close Persist::Sharder
-
#write_and_read Persist::CDBAdapter
-
#write_and_read Persist::TSVAdapter
-
#write_and_read Persist::LevelDBAdapter
-
#write_and_read Persist::Sharder
-
#write_lock Persist::TSVAdapter
-
#write_sem RbbtProcessQueue::RbbtProcessSocket
-
#xls TSV
-
xls TSV
-
#xlsx TSV
-
xlsx TSV
-
#yaml Path
-
zip2hash Misc
-
zip_fields Misc
-
zscore Misc