rbbt-util 5.38.1 → 5.40.0

data/lib/rbbt/workflow.rb

@@ -23,7 +23,7 @@ module Workflow
 
   #{{{ WORKFLOW MANAGEMENT 
   class << self
-    attr_accessor :workflows, :autoinstall, :workflow_dir
+    attr_accessor :workflows, :autoinstall, :workflow_dir, :main
   end
 
   self.workflows = []
@@ -202,13 +202,14 @@ module Workflow
 
     first = nil
     wf_name.split("+").each do |wf_name|
+      self.main = nil
       require_local_workflow(wf_name) or 
         (Workflow.autoinstall and `rbbt workflow install #{Misc.snake_case(wf_name)} || rbbt workflow install #{wf_name}` and require_local_workflow(wf_name)) or raise("Workflow not found or could not be loaded: #{ wf_name }")
 
       workflow = begin
                    Misc.string2const Misc.camel_case(wf_name)
                  rescue
-                   Workflow.workflows.last || true
+                   self.main || Workflow.workflows.last 
                  end
       workflow.load_documentation
 

data/share/Rlib/util.R

@@ -577,6 +577,16 @@ rbbt.get.modes <- function(x,bw = NULL,spar = NULL) {
 
 #{{{ PLOTS
 
+rbbt.svg_plot <- function(filename, p, width=500, height=500, ...){
+    svg(filename=filename, width=width, height=height, ...);
+    if (is.function(p)) {
+      p()
+    }else{
+      eval(parse(text=p));
+    }
+    dev.off()
+}
+
 rbbt.png_plot <- function(filename, p, width=500, height=500, ...){
     png(filename=filename, width=width, height=height, type='cairo', ...);
     if (is.function(p)) {
@@ -751,6 +761,8 @@ rbbt.plot.venn <- function(data, a=NULL, category=NULL, fill=NULL, ...) {
       fill=rbbt.plot.set_colors(dim(data)[2], "Set3")
     }
 
+    fill=fill[0:dim(data)[2]]
+
     group.matches <- function(data, fields) {
         sub = data
         for (i in 1:length(fields)) {

data/share/rbbt_commands/hpc/list

@@ -253,6 +253,8 @@ workdir.glob("**/command.batch").sort_by{|f| File.mtime(f)}.each do |fcmd|
       text = CMD.cmd('grep "^#SBATCH" ', :in => Open.read(fcmd)).read.strip
     when 'lsf'
       text = CMD.cmd('grep "^#BSUB" ', :in => Open.read(fcmd)).read.strip
+    when 'pbs'
+      text = CMD.cmd('grep "^#PBS" ', :in => Open.read(fcmd)).read.strip
     else
       text = ""
     end

data/share/rbbt_commands/hpc/orchestrate

@@ -73,7 +73,7 @@ class Step
           join
           self.load
         end
-      rescue HPC::SBATCH
+      rescue HPC::BATCH_DRY_RUN
       end
     end
   end

data/share/rbbt_commands/hpc/task

@@ -32,16 +32,17 @@ $slurm_options = SOPT.get <<EOF
 -p--partition* Partition
 -t--task_cpus* Tasks
 -tm--time* Time
--m--mem* SLURM minimum memory
---gres* SLURM Generic resources
--mcpu--mem_per_cpu* SLURM minimum memory per CPU
--lin--licenses* SLURM licenses
--cons--constraint* SLURM constraint
+-m--mem* minimum memory
+--gres* Generic resources
+-mcpu--mem_per_cpu* minimum memory per CPU
+-lin--licenses* licenses
+-cons--constraint* constraint
 -W--workflows* Additional workflows
 -rmb--remove_batch_dir Remove the batch working directory (command, STDIN, exit status, ...)
 -bs--batch_system* Batch system to use: auto, lsf, slurm (default is auto-detect)
 -lmod--lua_modules* Lua Modules to load 
 -co--conda* Conda environment to use
+-OR--orchestration_rules* Orchestration rules
 EOF
 
 batch_system = $slurm_options.delete :batch_system
@@ -58,9 +59,9 @@ class Step
       self.load
     else
       begin
-        Log.debug "Issuing SLURM job for #{self.path}"
+        Log.debug "Issuing BATCH job for #{self.path}"
         HPC::BATCH_MODULE.run_job(self, $slurm_options) 
-      rescue HPC::SBATCH
+      rescue HPC::BATCH_DRY_RUN
       end
     end
   end

data/share/rbbt_commands/lsf/list

@@ -253,6 +253,8 @@ workdir.glob("**/command.batch").sort_by{|f| File.mtime(f)}.each do |fcmd|
       text = CMD.cmd('grep "^#SBATCH" ', :in => Open.read(fcmd)).read.strip
     when 'lsf'
       text = CMD.cmd('grep "^#BSUB" ', :in => Open.read(fcmd)).read.strip
+    when 'pbs'
+      text = CMD.cmd('grep "^#PBS" ', :in => Open.read(fcmd)).read.strip
     else
       text = ""
     end

data/share/rbbt_commands/lsf/orchestrate

@@ -73,7 +73,7 @@ class Step
           join
           self.load
         end
-      rescue HPC::SBATCH
+      rescue HPC::BATCH_DRY_RUN
       end
     end
   end

data/share/rbbt_commands/lsf/task

@@ -32,16 +32,17 @@ $slurm_options = SOPT.get <<EOF
 -p--partition* Partition
 -t--task_cpus* Tasks
 -tm--time* Time
--m--mem* SLURM minimum memory
---gres* SLURM Generic resources
--mcpu--mem_per_cpu* SLURM minimum memory per CPU
--lin--licenses* SLURM licenses
--cons--constraint* SLURM constraint
+-m--mem* minimum memory
+--gres* Generic resources
+-mcpu--mem_per_cpu* minimum memory per CPU
+-lin--licenses* licenses
+-cons--constraint* constraint
 -W--workflows* Additional workflows
 -rmb--remove_batch_dir Remove the batch working directory (command, STDIN, exit status, ...)
 -bs--batch_system* Batch system to use: auto, lsf, slurm (default is auto-detect)
 -lmod--lua_modules* Lua Modules to load 
 -co--conda* Conda environment to use
+-OR--orchestration_rules* Orchestration rules
 EOF
 
 batch_system = $slurm_options.delete :batch_system
@@ -58,9 +59,9 @@ class Step
       self.load
     else
       begin
-        Log.debug "Issuing SLURM job for #{self.path}"
+        Log.debug "Issuing BATCH job for #{self.path}"
         HPC::BATCH_MODULE.run_job(self, $slurm_options) 
-      rescue HPC::SBATCH
+      rescue HPC::BATCH_DRY_RUN
       end
     end
   end

data/share/rbbt_commands/resource/claims

@@ -0,0 +1,57 @@
+#!/usr/bin/env ruby
+
+require 'rbbt-util'
+require 'rbbt/resource'
+require 'rbbt/workflow'
+
+options = SOPT.get <<EOF
+-W--workflows* Workflows to use; 'all' for all in Rbbt.etc.workflows:
+-r--requires* Files to require; 'all' for all in Rbbt.etc.requires:
+-f--force Force the production if the file is already present
+-h--help Help
+EOF
+
+if options[:help]
+  puts SOPT.doc 
+  exit
+end
+
+case options[:workflows]
+when nil, false, "false", "none"
+when "all"
+  Rbbt.etc.workflows.list.each do |workflow|
+    Workflow.require_workflow file
+  end if Rbbt.etc.workflows.exists?
+else
+  options[:workflows].split(/[ ,;|]/).each do |workflow|
+    Workflow.require_workflow workflow
+  end
+end
+
+case options[:requires]
+when nil, false, "false", "none"
+when "all"
+  Rbbt.etc.requires.list.each do |file|
+    require file
+  end if Rbbt.etc.requires.exists?
+else
+  options[:requires].split(/[ ,;|]/).each do |file|
+    require file
+  end
+end
+
+resource, path = ARGV
+
+begin
+  resource = Kernel.const_get(resource)
+rescue
+  begin
+    resource = Workflow.require_workflow resource
+  rescue
+    raise "Resource not found: #{ resource }"
+  end
+end
+
+puts resource.claims * "\n"
+ 
+

data/share/rbbt_commands/slurm/list

@@ -253,6 +253,8 @@ workdir.glob("**/command.batch").sort_by{|f| File.mtime(f)}.each do |fcmd|
       text = CMD.cmd('grep "^#SBATCH" ', :in => Open.read(fcmd)).read.strip
     when 'lsf'
       text = CMD.cmd('grep "^#BSUB" ', :in => Open.read(fcmd)).read.strip
+    when 'pbs'
+      text = CMD.cmd('grep "^#PBS" ', :in => Open.read(fcmd)).read.strip
     else
       text = ""
     end

data/share/rbbt_commands/slurm/orchestrate

@@ -73,7 +73,7 @@ class Step
           join
           self.load
         end
-      rescue HPC::SBATCH
+      rescue HPC::BATCH_DRY_RUN
       end
     end
   end

data/share/rbbt_commands/slurm/task

@@ -32,16 +32,17 @@ $slurm_options = SOPT.get <<EOF
 -p--partition* Partition
 -t--task_cpus* Tasks
 -tm--time* Time
--m--mem* SLURM minimum memory
---gres* SLURM Generic resources
--mcpu--mem_per_cpu* SLURM minimum memory per CPU
--lin--licenses* SLURM licenses
--cons--constraint* SLURM constraint
+-m--mem* minimum memory
+--gres* Generic resources
+-mcpu--mem_per_cpu* minimum memory per CPU
+-lin--licenses* licenses
+-cons--constraint* constraint
 -W--workflows* Additional workflows
 -rmb--remove_batch_dir Remove the batch working directory (command, STDIN, exit status, ...)
 -bs--batch_system* Batch system to use: auto, lsf, slurm (default is auto-detect)
 -lmod--lua_modules* Lua Modules to load 
 -co--conda* Conda environment to use
+-OR--orchestration_rules* Orchestration rules
 EOF
 
 batch_system = $slurm_options.delete :batch_system
@@ -58,9 +59,9 @@ class Step
       self.load
     else
       begin
-        Log.debug "Issuing SLURM job for #{self.path}"
+        Log.debug "Issuing BATCH job for #{self.path}"
         HPC::BATCH_MODULE.run_job(self, $slurm_options) 
-      rescue HPC::SBATCH
+      rescue HPC::BATCH_DRY_RUN
       end
     end
   end

data/share/rbbt_commands/workflow/task

@@ -220,8 +220,8 @@ The `recursive_clean` cleans all the job dependency steps recursively.
 -rwt--remote_workflow_tasks* Load a yaml file describing remote workflow tasks
 -od--override_deps* Override deps using 'Workflow#task=<path>' array_separated
 -PERF--procpath_performance* Measure performance using procpath
--r--relay* Relay job to SSH server
--sr--slurm_relay* Relay job to SSH SLURM server
+--relay* Relay job to SSH server
+--slurm_relay* Relay job to SSH SLURM server
 -rdep--relay_dependencies* Relay dependencies instead of main job
 -pdr--produce_dependencies_for_relay Prepare dependencies previous to relay jobs
 EOF

data/test/rbbt/hpc/test_pbs.rb

@@ -0,0 +1,43 @@
+require File.expand_path(__FILE__).sub(%r(/test/.*), '/test/test_helper.rb')
+require File.expand_path(__FILE__).sub(%r(.*/test/), '').sub(/test_(.*)\.rb/,'\1')
+
+require 'rbbt/workflow'
+
+class TestPBS < Test::Unit::TestCase
+  def workflow
+    @workflow ||= Module.new do
+      extend Workflow
+
+      def self.to_s
+        "TestWorkflow"
+      end
+
+      input :name, :string
+      task :hello => :string do |name|
+        "hello #{name}"
+      end
+    end
+  end
+
+  def test_template
+    job = workflow.job(:hello, "TEST", :name => "world")
+
+    TmpFile.with_file do |batch_dir|
+
+      template = HPC::PBS.job_template(job, :batch_dir => batch_dir, :lua_modules => 'java')
+      ppp template
+
+    end
+  end
+
+  def __test_run_job
+    job = Sample.job(:mutect2, "small", :reference => "hg38")
+
+    job.clean
+
+    jobid = HPC::SLURM.run_job(job, :workflows => "HTS", :batch_modules => 'java', :env_cmd => '_JAVA_OPTIONS="-Xms1g -Xmx${MAX_MEMORY}m"', :queue => :debug, :time => '01:00:00', :config_keys => "HTS_light", :task_cpus => '10', :tail => true, :clean_task => "HTS#mutect2")
+    assert jobid.to_s =~ /^\d+$/
+  end
+
+end
+

data/test/rbbt/test_tsv.rb

@@ -302,7 +302,7 @@ b 2
     EOF
 
     TmpFile.with_file(content) do |filename|
-      tsv = TSV.open(filename, :key_field => "Value", :select => Proc.new{|l| ! l =~ /1/})
+      tsv = TSV.open(filename, :key_field => "Value", :select => Proc.new{|l| l !~ /1/})
       assert(! tsv.include?("3"))
     end
   end
@@ -650,5 +650,20 @@ row3    AA    BB|BBB    Id3|Id2
  
     end
   end
+
+  def test_benchmark
+    num = 10_000
+    txt = num.times.inject(nil) do |acc,i|
+      (acc.nil? ? "" : acc << "\n") << (0..10).collect{|v| v == 0 ? i : [v,v] * "|" } * "\t"
+    end 
+
+    txt = StringIO.new(([txt] * (10))*"\n")
+    #Misc.profile do
+    Misc.benchmark(1) do
+      data = TSV.open(txt, type: :double, bar: true, merge: true)
+      assert_equal num, data.size
+    end
+  end
+
 end
 

data/test/rbbt/tsv/parallel/test_traverse.rb

@@ -50,11 +50,11 @@ class TestTSVParallelThrough < Test::Unit::TestCase
   def test_traverse_stream
     require 'rbbt/sources/organism'
 
-    head = 1000
+    head = 3000
 
     tsv = datafile_test('identifiers').open
     res = {}
-    TSV.traverse tsv, :head => head, :into => res do |k,v|
+    TSV.traverse tsv, :head => head, :into => res, :bar => true do |k,v|
       [k,v]
     end
 

data/test/rbbt/tsv/test_util.rb

@@ -35,4 +35,18 @@ row2    A    B    Id3
       assert_equal %w(aa bb Id2), tsv.unzip_replicates["row1(1)"]
     end
   end
+
+  def test_merge
+   content =<<-EOF
+#Id    ValueA    ValueB    OtherID
+row1    a|aa|aaa    b|bb|bbb    Id1|Id2|Id3
+row2    A    B    Id3
+    EOF
+
+    TmpFile.with_file(content) do |filename|
+      tsv = TSV.open(filename, :sep => /\s+/)
+      tsv = tsv.merge({"row3" => [["A3"], ["B3"], ["Id4"]]})
+      assert TSV === tsv
+    end
+  end
 end

data/test/rbbt/util/test_migrate.rb

@@ -3,9 +3,9 @@ require 'rbbt-util'
 require 'rbbt/util/migrate'
 
 class TestMigrate < Test::Unit::TestCase
-  def _test_source_locate
+  def test_source_locate
     assert_equal 'var/jobs/', Rbbt.migrate_source_paths(Rbbt.root['var/jobs'].find(:user)).last
-    assert Rbbt.migrate_source_paths(Rbbt.root['var/jobs'].find(:user))[1].include?(File.join(ENV["HOME"], '.rbbt/var/jobs/'))
+    assert_include Rbbt.migrate_source_paths(Rbbt.root['var/jobs'].find(:user))[1], (File.join(ENV["HOME"], '.rbbt/var/jobs'))
   end
 
   def test_migrate

metadata

@@ -1,14 +1,14 @@
 --- !ruby/object:Gem::Specification
 name: rbbt-util
 version: !ruby/object:Gem::Version
-  version: 5.38.1
+  version: 5.40.0
 platform: ruby
 authors:
 - Miguel Vazquez
 autorequire: 
 bindir: bin
 cert_chain: []
-date: 2023-06-01 00:00:00.000000000 Z
+date: 2023-10-12 00:00:00.000000000 Z
 dependencies:
 - !ruby/object:Gem::Dependency
   name: rake
@@ -206,6 +206,7 @@ files:
 - lib/rbbt/hpc/orchestrate/batches.rb
 - lib/rbbt/hpc/orchestrate/chains.rb
 - lib/rbbt/hpc/orchestrate/rules.rb
+- lib/rbbt/hpc/pbs.rb
 - lib/rbbt/hpc/slurm.rb
 - lib/rbbt/knowledge_base.rb
 - lib/rbbt/knowledge_base/enrichment.rb
@@ -390,6 +391,7 @@ files:
 - share/rbbt_commands/migrate
 - share/rbbt_commands/migrate_job
 - share/rbbt_commands/purge_job
+- share/rbbt_commands/resource/claims
 - share/rbbt_commands/resource/exists
 - share/rbbt_commands/resource/find
 - share/rbbt_commands/resource/get
@@ -475,6 +477,7 @@ files:
 - test/rbbt/hpc/orchestrate/test_rules.rb
 - test/rbbt/hpc/test_batch.rb
 - test/rbbt/hpc/test_orchestrate.rb
+- test/rbbt/hpc/test_pbs.rb
 - test/rbbt/hpc/test_slurm.rb
 - test/rbbt/knowledge_base/test_enrichment.rb
 - test/rbbt/knowledge_base/test_entity.rb
@@ -589,115 +592,116 @@ required_rubygems_version: !ruby/object:Gem::Requirement
     - !ruby/object:Gem::Version
       version: '0'
 requirements: []
-rubygems_version: 3.4.13
+rubygems_version: 3.5.0.dev
 signing_key: 
 specification_version: 4
 summary: Utilities for the Ruby Bioinformatics Toolkit (rbbt)
 test_files:
-- test/rbbt/test_entity.rb
-- test/rbbt/workflow/test_remote_workflow.rb
-- test/rbbt/workflow/util/test_archive.rb
-- test/rbbt/workflow/util/test_orchestrator.rb
-- test/rbbt/workflow/util/test_data.rb
-- test/rbbt/workflow/test_doc.rb
-- test/rbbt/workflow/test_schedule.rb
-- test/rbbt/workflow/test_step.rb
-- test/rbbt/workflow/step/test_dependencies.rb
-- test/rbbt/workflow/step/test_save_load_inputs.rb
-- test/rbbt/workflow/test_task.rb
-- test/rbbt/resource/test_path.rb
-- test/rbbt/util/test_colorize.rb
-- test/rbbt/util/test_procpath.rb
-- test/rbbt/util/python/test_util.rb
-- test/rbbt/util/misc/test_development.rb
-- test/rbbt/util/misc/test_indiferent_hash.rb
-- test/rbbt/util/misc/test_omics.rb
-- test/rbbt/util/misc/test_pipes.rb
-- test/rbbt/util/misc/test_serialize.rb
-- test/rbbt/util/misc/test_format.rb
-- test/rbbt/util/misc/test_communication.rb
-- test/rbbt/util/misc/test_lock.rb
-- test/rbbt/util/misc/test_multipart_payload.rb
-- test/rbbt/util/misc/test_bgzf.rb
-- test/rbbt/util/test_concurrency.rb
-- test/rbbt/util/test_cmd.rb
-- test/rbbt/util/R/test_plot.rb
-- test/rbbt/util/R/test_eval.rb
-- test/rbbt/util/R/test_model.rb
-- test/rbbt/util/test_config.rb
-- test/rbbt/util/test_log.rb
-- test/rbbt/util/test_simpleDSL.rb
-- test/rbbt/util/log/test_progress.rb
-- test/rbbt/util/test_tmpfile.rb
-- test/rbbt/util/test_R.rb
-- test/rbbt/util/test_excel2tsv.rb
-- test/rbbt/util/test_misc.rb
-- test/rbbt/util/test_open.rb
-- test/rbbt/util/test_ssh.rb
-- test/rbbt/util/test_simpleopt.rb
-- test/rbbt/util/simpleopt/test_parse.rb
-- test/rbbt/util/simpleopt/test_setup.rb
-- test/rbbt/util/simpleopt/test_get.rb
-- test/rbbt/util/test_python.rb
-- test/rbbt/util/test_filecache.rb
-- test/rbbt/util/concurrency/test_processes.rb
-- test/rbbt/util/concurrency/test_threads.rb
-- test/rbbt/util/concurrency/processes/test_socket.rb
-- test/rbbt/util/test_semaphore.rb
-- test/rbbt/util/test_chain_methods.rb
-- test/rbbt/util/test_migrate.rb
-- test/rbbt/test_resource.rb
-- test/rbbt/test_packed_index.rb
-- test/rbbt/tsv/test_change_id.rb
-- test/rbbt/tsv/test_attach.rb
-- test/rbbt/tsv/test_filter.rb
-- test/rbbt/tsv/test_marshal.rb
-- test/rbbt/tsv/test_parser.rb
-- test/rbbt/tsv/test_csv.rb
-- test/rbbt/tsv/test_accessor.rb
-- test/rbbt/tsv/test_matrix.rb
-- test/rbbt/tsv/test_field_index.rb
-- test/rbbt/tsv/test_util.rb
-- test/rbbt/tsv/test_index.rb
-- test/rbbt/tsv/test_parallel.rb
-- test/rbbt/tsv/test_manipulate.rb
-- test/rbbt/tsv/test_excel.rb
-- test/rbbt/tsv/parallel/test_through.rb
-- test/rbbt/tsv/parallel/test_traverse.rb
-- test/rbbt/tsv/test_stream.rb
-- test/rbbt/test_association.rb
-- test/rbbt/hpc/test_batch.rb
-- test/rbbt/hpc/orchestrate/test_chains.rb
-- test/rbbt/hpc/orchestrate/test_rules.rb
-- test/rbbt/hpc/orchestrate/test_batches.rb
-- test/rbbt/hpc/test_slurm.rb
-- test/rbbt/hpc/test_orchestrate.rb
+- test/rbbt/annotations/test_util.rb
 - test/rbbt/association/test_database.rb
+- test/rbbt/association/test_index.rb
 - test/rbbt/association/test_item.rb
 - test/rbbt/association/test_open.rb
 - test/rbbt/association/test_util.rb
-- test/rbbt/association/test_index.rb
-- test/rbbt/test_knowledge_base.rb
-- test/rbbt/persist/tsv/test_kyotocabinet.rb
+- test/rbbt/entity/test_identifiers.rb
+- test/rbbt/hpc/orchestrate/test_batches.rb
+- test/rbbt/hpc/orchestrate/test_chains.rb
+- test/rbbt/hpc/orchestrate/test_rules.rb
+- test/rbbt/hpc/test_batch.rb
+- test/rbbt/hpc/test_orchestrate.rb
+- test/rbbt/hpc/test_pbs.rb
+- test/rbbt/hpc/test_slurm.rb
+- test/rbbt/knowledge_base/test_enrichment.rb
+- test/rbbt/knowledge_base/test_entity.rb
+- test/rbbt/knowledge_base/test_query.rb
+- test/rbbt/knowledge_base/test_registry.rb
+- test/rbbt/knowledge_base/test_syndicate.rb
+- test/rbbt/knowledge_base/test_traverse.rb
+- test/rbbt/persist/test_tsv.rb
 - test/rbbt/persist/tsv/test_cdb.rb
+- test/rbbt/persist/tsv/test_kyotocabinet.rb
+- test/rbbt/persist/tsv/test_leveldb.rb
 - test/rbbt/persist/tsv/test_lmdb.rb
 - test/rbbt/persist/tsv/test_sharder.rb
-- test/rbbt/persist/tsv/test_leveldb.rb
 - test/rbbt/persist/tsv/test_tokyocabinet.rb
-- test/rbbt/persist/test_tsv.rb
-- test/rbbt/test_tsv.rb
+- test/rbbt/resource/test_path.rb
 - test/rbbt/test_annotations.rb
+- test/rbbt/test_association.rb
+- test/rbbt/test_entity.rb
 - test/rbbt/test_fix_width_table.rb
-- test/rbbt/test_workflow.rb
-- test/rbbt/entity/test_identifiers.rb
-- test/rbbt/annotations/test_util.rb
 - test/rbbt/test_hpc.rb
+- test/rbbt/test_knowledge_base.rb
 - test/rbbt/test_monitor.rb
+- test/rbbt/test_packed_index.rb
 - test/rbbt/test_persist.rb
-- test/rbbt/knowledge_base/test_entity.rb
-- test/rbbt/knowledge_base/test_registry.rb
-- test/rbbt/knowledge_base/test_syndicate.rb
-- test/rbbt/knowledge_base/test_query.rb
-- test/rbbt/knowledge_base/test_enrichment.rb
-- test/rbbt/knowledge_base/test_traverse.rb
+- test/rbbt/test_resource.rb
+- test/rbbt/test_tsv.rb
+- test/rbbt/test_workflow.rb
+- test/rbbt/tsv/parallel/test_through.rb
+- test/rbbt/tsv/parallel/test_traverse.rb
+- test/rbbt/tsv/test_accessor.rb
+- test/rbbt/tsv/test_attach.rb
+- test/rbbt/tsv/test_change_id.rb
+- test/rbbt/tsv/test_csv.rb
+- test/rbbt/tsv/test_excel.rb
+- test/rbbt/tsv/test_field_index.rb
+- test/rbbt/tsv/test_filter.rb
+- test/rbbt/tsv/test_index.rb
+- test/rbbt/tsv/test_manipulate.rb
+- test/rbbt/tsv/test_marshal.rb
+- test/rbbt/tsv/test_matrix.rb
+- test/rbbt/tsv/test_parallel.rb
+- test/rbbt/tsv/test_parser.rb
+- test/rbbt/tsv/test_stream.rb
+- test/rbbt/tsv/test_util.rb
+- test/rbbt/util/R/test_eval.rb
+- test/rbbt/util/R/test_model.rb
+- test/rbbt/util/R/test_plot.rb
+- test/rbbt/util/concurrency/processes/test_socket.rb
+- test/rbbt/util/concurrency/test_processes.rb
+- test/rbbt/util/concurrency/test_threads.rb
+- test/rbbt/util/log/test_progress.rb
+- test/rbbt/util/misc/test_bgzf.rb
+- test/rbbt/util/misc/test_communication.rb
+- test/rbbt/util/misc/test_development.rb
+- test/rbbt/util/misc/test_format.rb
+- test/rbbt/util/misc/test_indiferent_hash.rb
+- test/rbbt/util/misc/test_lock.rb
+- test/rbbt/util/misc/test_multipart_payload.rb
+- test/rbbt/util/misc/test_omics.rb
+- test/rbbt/util/misc/test_pipes.rb
+- test/rbbt/util/misc/test_serialize.rb
+- test/rbbt/util/python/test_util.rb
+- test/rbbt/util/simpleopt/test_get.rb
+- test/rbbt/util/simpleopt/test_parse.rb
+- test/rbbt/util/simpleopt/test_setup.rb
+- test/rbbt/util/test_R.rb
+- test/rbbt/util/test_chain_methods.rb
+- test/rbbt/util/test_cmd.rb
+- test/rbbt/util/test_colorize.rb
+- test/rbbt/util/test_concurrency.rb
+- test/rbbt/util/test_config.rb
+- test/rbbt/util/test_excel2tsv.rb
+- test/rbbt/util/test_filecache.rb
+- test/rbbt/util/test_log.rb
+- test/rbbt/util/test_migrate.rb
+- test/rbbt/util/test_misc.rb
+- test/rbbt/util/test_open.rb
+- test/rbbt/util/test_procpath.rb
+- test/rbbt/util/test_python.rb
+- test/rbbt/util/test_semaphore.rb
+- test/rbbt/util/test_simpleDSL.rb
+- test/rbbt/util/test_simpleopt.rb
+- test/rbbt/util/test_ssh.rb
+- test/rbbt/util/test_tmpfile.rb
+- test/rbbt/workflow/step/test_dependencies.rb
+- test/rbbt/workflow/step/test_save_load_inputs.rb
+- test/rbbt/workflow/test_doc.rb
+- test/rbbt/workflow/test_remote_workflow.rb
+- test/rbbt/workflow/test_schedule.rb
+- test/rbbt/workflow/test_step.rb
+- test/rbbt/workflow/test_task.rb
+- test/rbbt/workflow/util/test_archive.rb
+- test/rbbt/workflow/util/test_data.rb
+- test/rbbt/workflow/util/test_orchestrator.rb
 - test/test_helper.rb