miga-base 0.3.9.0 → 0.3.9.1

checksums.yaml

@@ -1,7 +1,7 @@
 ---
 SHA256:
-  metadata.gz: 33ad423a2b44c3375e96d247399c77e3e576739a27a46f02315d454bb9905fcf
-  data.tar.gz: 6696a87a2328dc0db4d2fdc193ea01eed18ada3b53cb772ef40525dfcb596cdc
+  metadata.gz: 89d27413bd8dc321a75fc3dc434a191c1eba336bfab3beaaa1e815852048e30a
+  data.tar.gz: 59eeab21ff1ef81bf76147c1b98c3a49e31535831fe19e8ec2757b59a666dd4e
 SHA512:
-  metadata.gz: 230c1c4cf1af60d42a2d27c1fbe018e90f01f8ebc4a559e354bc32d1b9dbdec1ffcc4d832dcb7894fb96f0c255bfb84e3635d16d683c4e1585c1c354d8591020
-  data.tar.gz: db5bb0f064dab5dcfe45ebad1027d7d1fd16d2c992f5907e3cb1a124ed45785acf828ca67d9c84e7be6017622faeff1b6e7a32c9e9a72dd26e336953ef93813d
+  metadata.gz: 2e4d975743a230c951578605e93a1b4f3061e8e3d1c91cf147db5c297bfa2427de344a72f118c50d0a3b3e9b2e67137baed9cc14157e86aa3d98738bb09d334f
+  data.tar.gz: d9761542220413d20b162bceeada84cf414d9d17b10764d049b3a76c2f9a3d757389b24c0ac290e02801246c114496e4729c45da5e5b863c22fde009c2eeca66

data/actions/add.rb

@@ -3,39 +3,39 @@
 # @package MiGA
 # @license Artistic-2.0
 
-o = {q:true, ref:true, update:false}
+o = {q: true, ref: true, update: false}
 OptionParser.new do |opt|
   opt_banner(opt)
   opt_object(opt, o, [:project, :dataset, :dataset_type_req])
-  opt.on("-q", "--query",
-    "If set, the dataset is registered as a query, not a reference dataset."
-    ){ |v| o[:ref]=!v }
-  opt.on("-d", "--description STRING",
-    "Description of the dataset."){ |v| o[:description]=v }
-  opt.on("-c", "--comments STRING",
-    "Comments on the dataset."){ |v| o[:comments]=v }
-  opt.on("-m", "--metadata STRING",
-    "Metadata as key-value pairs separated by = and delimited by comma.",
-    "Values are saved as strings except for booleans (true / false) or nil."
-    ){ |v| o[:metadata]=v }
-  opt.on("--update",
-    "Updates the dataset if it already exists."){ o[:update]=true }
+  opt.on('-q', '--query',
+    'If set, the dataset is registered as a query, not a reference dataset.'
+    ){ |v| o[:ref] = !v }
+  opt.on('-d', '--description STRING',
+    'Description of the dataset.'){ |v| o[:description] = v }
+  opt.on('-c', '--comments STRING',
+    'Comments on the dataset.'){ |v| o[:comments] = v }
+  opt.on('-m', '--metadata STRING',
+    'Metadata as key-value pairs separated by = and delimited by comma.',
+    'Values are saved as strings except for booleans (true / false) or nil.'
+    ){ |v| o[:metadata] = v }
+  opt.on('--update', 'Updates the dataset if it already exists.',
+    'Same as "miga edit".'){ o[:update] = true }
   opt_common(opt, o)
-  opt.separator ""
-  opt.separator "External input data"
-  opt.on("--raw-reads FILE1,FILE2", Array,
-    "Comma-delimited paths to the raw reads in FastQ format.",
-    "One file is assumed to be single reads, two are assumed to be paired."
+  opt.separator ''
+  opt.separator 'External input data'
+  opt.on('--raw-reads FILE1,FILE2', Array,
+    'Comma-delimited paths to the raw reads in FastQ format.',
+    'One file is assumed to be single reads, two are assumed to be paired.'
     ){ |v| o[:raw_reads] = v }
-  opt.on("--trimmed-fasta-single FILE", Array,
-    "Path to the single trimmed reads in FastA format."
+  opt.on('--trimmed-fasta-single FILE', Array,
+    'Path to the single trimmed reads in FastA format.'
     ){ |v| o[:trimmed_fasta_s] = v }
-  opt.on("--trimmed-fasta-coupled FILE1,FILE2", Array,
-    "Comma-delimited paths to the coupled trimmed reads in FastA format.",
-    "One file is assumed to be interposed, two are assumed to contain sisters."
+  opt.on('--trimmed-fasta-coupled FILE1,FILE2', Array,
+    'Comma-delimited paths to the coupled trimmed reads in FastA format.',
+    'One file is assumed to be interposed, two are assumed to contain sisters.'
     ){ |v| o[:trimmed_fasta_c] = v }
-  opt.on("--assembly FILE", Array,
-    "Path to the contigs (or scaffolds) of the assembly in FastA format."
+  opt.on('--assembly FILE', Array,
+    'Path to the contigs (or scaffolds) of the assembly in FastA format.'
     ){ |v| o[:assembly] = v }
 end.parse!
 
@@ -43,16 +43,16 @@ end.parse!
 opt_require(o)
 opt_require_type(o, MiGA::Dataset) unless o[:update]
 
-$stderr.puts "Loading project." unless o[:q]
+$stderr.puts 'Loading project.' unless o[:q]
 p = MiGA::Project.load(o[:project])
 raise "Impossible to load project: #{o[:project]}" if p.nil?
 
-raise "Dataset already exists, aborting." unless
+raise 'Dataset already exists, aborting.' unless
   o[:update] or not MiGA::Dataset.exist?(p, o[:dataset])
-$stderr.puts "Loading dataset." unless o[:q]
+$stderr.puts 'Loading dataset.' unless o[:q]
 d = o[:update] ? p.dataset(o[:dataset]) :
   MiGA::Dataset.new(p, o[:dataset], o[:ref])
-raise "Dataset does not exist." if d.nil?
+raise 'Dataset does not exist.' if d.nil?
 
 in_files = [:raw_reads, :trimmed_fasta_s, :trimmed_fasta_c, :assembly]
 def cp_result(o, d, p, sym, res_sym, ext)
@@ -64,10 +64,10 @@ def cp_result(o, d, p, sym, res_sym, ext)
     gz = o[sym][i] =~ /\.gz/ ? '.gz' : ''
     FileUtils.cp(o[sym][i], "#{r_path}#{ext[i]}#{gz}")
   end
-  File.open("#{r_path}.done", "w") { |f| f.print Time.now.to_s }
+  File.open("#{r_path}.done", 'w') { |f| f.print Time.now.to_s }
 end
 if in_files.any? { |i| not o[i].nil? }
-  $stderr.puts "Copying files." unless o[:q]
+  $stderr.puts 'Copying files.' unless o[:q]
   # :raw_reads
   cp_result(o, d, p, :raw_reads, :raw_reads, %w[.1.fastq .2.fastq])
   # :trimmed_fasta
@@ -87,4 +87,4 @@ p.add_dataset(o[:dataset]) unless o[:update]
 res = d.first_preprocessing(true)
 $stderr.puts "- #{res}" unless o[:q]
 
-$stderr.puts "Done." unless o[:q]
+$stderr.puts 'Done.' unless o[:q]

data/actions/edit.rb

@@ -0,0 +1,33 @@
+#!/usr/bin/env ruby
+
+# @package MiGA
+# @license Artistic-2.0
+
+o = {q: true}
+OptionParser.new do |opt|
+  opt_banner(opt)
+  opt_object(opt, o, [:project, :dataset_opt])
+  opt.on('-m', '--metadata STRING',
+    'Metadata as key-value pairs separated by = and delimited by comma.',
+    'Values are saved as strings except for booleans (true / false) or nil.'
+    ){ |v| o[:metadata] = v }
+  opt_common(opt, o)
+end.parse!
+
+##=> Main <=
+opt_require(o, project: '-P')
+
+$stderr.puts 'Loading project.' unless o[:q]
+p = MiGA::Project.load(o[:project])
+raise "Impossible to load project: #{o[:project]}" if p.nil?
+
+obj = p
+if o[:dataset]
+  $stderr.puts 'Loading dataset.' unless o[:q]
+  obj = p.dataset(o[:dataset])
+  raise 'Dataset does not exist.' if obj.nil?
+end
+obj = add_metadata(o, obj)
+obj.save
+
+$stderr.puts 'Done.' unless o[:q]

data/actions/new.rb

@@ -3,37 +3,36 @@
 # @package MiGA
 # @license Artistic-2.0
 
-o = {q:true, update:false}
+o = {q: true, update: false}
 OptionParser.new do |opt|
   opt_banner(opt)
   opt_object(opt, o, [:project, :project_type_req])
-  opt.on("-n", "--name STRING",
-    "Name of the project."){ |v| o[:name]=v }
-  opt.on("-d", "--description STRING",
-    "Description of the project."){ |v| o[:description]=v }
-  opt.on("-c", "--comments STRING",
-    "Comments on the project."){ |v| o[:comments]=v }
-  opt.on("-m", "--metadata STRING",
-    "Metadata as key-value pairs separated by = and delimited by comma.",
-    "Values are saved as strings except for booleans (true / false) or nil."
-    ){ |v| o[:metadata]=v }
-  opt.on("--update",
-    "Updates the project if it already exists."){ o[:update]=true }
+  opt.on('-n', '--name STRING', 'Name of the project.'){ |v| o[:name] = v }
+  opt.on('-d', '--description STRING',
+    'Description of the project.'){ |v| o[:description] = v }
+  opt.on('-c', '--comments STRING',
+    'Comments on the project.'){ |v| o[:comments] = v }
+  opt.on('-m', '--metadata STRING',
+    'Metadata as key-value pairs separated by = and delimited by comma.',
+    'Values are saved as strings except for booleans (true / false) or nil.'
+    ){ |v| o[:metadata] = v }
+  opt.on('--update', 'Updates the project if it already exists.',
+    'Same as "miga edit".'){ o[:update] = true }
   opt_common(opt, o)
 end.parse!
 
 ##=> Main <=
-opt_require(o, project:"-P")
+opt_require(o, project: '-P')
 opt_require_type(o, MiGA::Project) unless o[:update]
 
 unless File.exist? "#{ENV["HOME"]}/.miga_rc" and
       File.exist? "#{ENV["HOME"]}/.miga_daemon.json"
   raise "You must initialize MiGA before creating the first project.\n" +
-    "Please use miga init."
+    'Please use "miga init".'
 end
 
-$stderr.puts "Creating project." unless o[:q]
-raise "Project already exists, aborting." unless
+$stderr.puts 'Creating project.' unless o[:q]
+raise 'Project already exists, aborting.' unless
   o[:update] or not MiGA::Project.exist? o[:project]
 p = MiGA::Project.new(o[:project], o[:update])
 # The following check is redundant with MiGA::Project#create,
@@ -42,4 +41,4 @@ o[:name] = File.basename(p.path) if o[:update] and o[:name].nil?
 p = add_metadata(o, p)
 p.save
 
-$stderr.puts "Done." unless o[:q]
+$stderr.puts 'Done.' unless o[:q]

data/actions/next_step.rb

@@ -0,0 +1,33 @@
+#!/usr/bin/env ruby
+
+# @package MiGA
+# @license Artistic-2.0
+
+o = {q: true}
+opts = OptionParser.new do |opt|
+  opt_banner(opt)
+  opt_object(opt, o, [:project, :dataset_opt])
+  opt_common(opt, o)
+end.parse!
+
+##=> Main <=
+opts.parse!
+opt_require(o, project: '-P')
+
+$stderr.puts 'Loading project.' unless o[:q]
+p = MiGA::Project.load(o[:project])
+raise "Impossible to load project: #{o[:project]}" if p.nil?
+
+n = nil
+if not o[:dataset].nil?
+  $stderr.puts 'Loading dataset.' unless o[:q]
+  d = p.dataset o[:dataset]
+  raise "Impossible to load dataset: #{o[:dataset]}" if d.nil?
+  n = d.next_preprocessing if d.is_active?
+else
+  n = p.next_distances(false)
+  n ||= p.next_inclade(false)
+end
+n ||= '?'
+puts n
+

data/actions/run.rb

@@ -3,40 +3,43 @@
 # @package MiGA
 # @license Artistic-2.0
 
-require "shellwords"
+require 'shellwords'
 
-o = {q:true, try_load:false, thr:1}
+o = {q: true, try_load: false, thr: 1}
 OptionParser.new do |opt|
   opt_banner(opt)
   opt_object(opt, o, [:project, :dataset_opt, :result])
-  opt.on("-t", "--threads INT",
+  opt.on('-t', '--threads INT',
     "Threads to use in the local run (by default: #{o[:thr]})."
     ){ |v| o[:thr] = v.to_i }
   opt_common(opt, o)
 end.parse!
 
 ##=> Main <=
-opt_require(o, project:"-P", name:"-r")
+opt_require(o, project: '-P', name: '-r')
 
-$stderr.puts "Loading project." unless o[:q]
+$stderr.puts 'Loading project.' unless o[:q]
 p = MiGA::Project.load(o[:project])
 raise "Impossible to load project: #{o[:project]}" if p.nil?
 
+virtual_task = false
 miga = MiGA::MiGA.root_path
-cmd = ["PROJECT=#{p.path.shellescape}", "RUNTYPE=bash",
+cmd = ["PROJECT=#{p.path.shellescape}", 'RUNTYPE=bash',
   "MIGA=#{miga.shellescape}", "CORES=#{o[:thr]}"]
 if o[:dataset].nil?
   type = MiGA::Project
+  virtual_task = true if o[:name] == :p
 else
   d = p.dataset(o[:dataset])
-  raise "Cannot load dataset." if d.nil?
+  raise 'Cannot load dataset.' if d.nil?
   cmd << "DATASET=#{d.name.shellescape}"
   type = MiGA::Dataset
+  virtual_task = true if o[:name] == :d
 end
-raise "Unsupported #{type.to_s.gsub(/.*::/,"")} result: #{o[:name]}." if
-  type.RESULT_DIRS[o[:name].to_sym].nil?
-cmd << MiGA::MiGA.script_path(o[:name], miga:miga, project:p).shellescape
-pid = spawn cmd.join(" ")
+raise "Unsupported #{type.to_s.gsub(/.*::/, '')} result: #{o[:name]}." if
+  type.RESULT_DIRS[o[:name].to_sym].nil? and not virtual_task
+cmd << MiGA::MiGA.script_path(o[:name], miga: miga, project: p).shellescape
+pid = spawn cmd.join(' ')
 Process.wait pid
 
-$stderr.puts "Done." unless o[:q]
+$stderr.puts 'Done.' unless o[:q]

data/bin/miga

@@ -17,7 +17,7 @@ $task_desc = {
   plugins:  'Lists or (un)installs plugins in a MiGA project',
   doctor:   'Performs consistency checks on a MiGA project',
   # Datasets
-  add:      'Creates an empty dataset in a pre-existing MiGA project',
+  add:      'Creates a dataset in a MiGA project',
   get:      'Downloads a dataset from public databases into a MiGA project',
   ncbi_get: 'Downloads all genomes in a taxon from NCBI into a MiGA project',
   rm:       'Removes a dataset from an MiGA project',
@@ -30,6 +30,9 @@ $task_desc = {
   files:    'Lists registered files from the results of a dataset or project',
   run:      'Executes locally one step analysis producing the given result',
   summary:  'Generates a summary table for the statistics of all datasets',
+  next_step: 'Returns the next task to run in a dataset or project',
+  # Objects (Datasets or Projects)
+  edit:   'Edits the metadata of a dataset or project',
   # System
   init:     'Initialize MiGA to process new projects',
   daemon:   'Controls the daemon of a MiGA project',
@@ -58,6 +61,9 @@ $task_alias = {
   list_files: :files,
   run_local: :run,
   sum_stats: :summary,
+  next_task: :next_step,
+  # Objects
+  update_metadata: :edit,
   # System
   c: :console,
   # Taxonomy
@@ -88,80 +94,80 @@ BAN
 end
 
 # OptParse flags that determine the object to load
-def opt_object(opt, o, what=[:project, :dataset])
-  opt.on("-P", "--project PATH", "(Mandatory) Path to the project."
+def opt_object(opt, o, what = [:project, :dataset])
+  opt.on('-P', '--project PATH', '(Mandatory) Path to the project.'
     ){ |v| o[:project]=v } if what.include? :project
-  opt.on("-D", "--dataset STRING",
-    (what.include?(:dataset) ? "(Mandatory) " : "") +
-    "Name of the dataset."){ |v| o[:dataset]=v } if what.include? :dataset or
+  opt.on('-D', '--dataset STRING',
+    (what.include?(:dataset) ? '(Mandatory) ' : '') +
+    'Name of the dataset.'){ |v| o[:dataset]=v } if what.include? :dataset or
       what.include? :dataset_opt
-  opt.on("-D", "--dataset STRING", "Name of the dataset."
+  opt.on('-D', '--dataset STRING', 'Name of the dataset.'
     ){ |v| o[:dataset]=v } if what.include? :dataset_opt
-  opt.on("-t", "--type STRING",
-    (what.include?(:dataset_type_req) ? "(Mandatory) " : "")+
-    "Type of dataset. Recognized types include:",
+  opt.on('-t', '--type STRING',
+    (what.include?(:dataset_type_req) ? '(Mandatory) ' : '')+
+    'Type of dataset. Recognized types include:',
     *MiGA::Dataset.KNOWN_TYPES.map{ |k,v| "~ #{k}: #{v[:description]}" }
     ){ |v| o[:type]=v.to_sym } if what.include? :dataset_type or
       what.include? :dataset_type_req
-  opt.on("-t", "--type STRING",
-    (what.include?(:project_type_req) ? "(Mandatory) " : "") +
-    "Type of project. Recognized types include:",
+  opt.on('-t', '--type STRING',
+    (what.include?(:project_type_req) ? '(Mandatory) ' : '') +
+    'Type of project. Recognized types include:',
     *MiGA::Project.KNOWN_TYPES.map{ |k,v| "~ #{k}: #{v[:description]}"}
     ){ |v| o[:type]=v.to_sym } if what.include? :project_type or
       what.include? :project_type_req
-  opt.on("-r", "--result STRING",
-    "(Mandatory) Name of the result to add.",
-    "Recognized names for dataset-specific results include:",
+  opt.on('-r', '--result STRING',
+    '(Mandatory) Name of the result.',
+    'Recognized names for dataset-specific results include:',
     *MiGA::Dataset.RESULT_DIRS.keys.map{|n| " ~ #{n}"},
-    "Recognized names for project-wide results include:",
+    'Recognized names for project-wide results include:',
     *MiGA::Project.RESULT_DIRS.keys.map{|n| " ~ #{n}"}
     ){ |v| o[:name]=v.downcase.to_sym } if what.include? :result
-  opt.on("-r", "--result STRING",
-    "(Mandatory) Name of the result to add. One of:",
+  opt.on('-r', '--result STRING',
+    '(Mandatory) Name of the result. One of:',
     *MiGA::Dataset.RESULT_DIRS.keys.map{|n| " ~ #{n}"}
     ){ |v| o[:name]=v.downcase.to_sym } if what.include? :result_dataset
 end
 
 # OptParse flags common to all actions.
 def opt_common(opt, o)
-  opt.on("-v", "--verbose",
-    "Print additional information to STDERR."){ o[:q]=false }
-  opt.on("-d", "--debug INT",
-    "Print debugging information to STDERR (1: debug, 2: trace).") do |v|
+  opt.on('-v', '--verbose',
+    'Print additional information to STDERR.'){ o[:q]=false }
+  opt.on('-d', '--debug INT',
+    'Print debugging information to STDERR (1: debug, 2: trace).') do |v|
     v.to_i>1 ? MiGA::MiGA.DEBUG_TRACE_ON : MiGA::MiGA.DEBUG_ON
   end
-  opt.on("-h", "--help", "Display this screen.") do
+  opt.on('-h', '--help', 'Display this screen.') do
     puts opt
     exit
   end
-  opt.separator ""
+  opt.separator ''
 end
 
 # OptParse flags to filter lists of datasets.
-def opt_filter_datasets(opt, o, what=[:ref, :multi, :active, :taxonomy])
-  opt.on("--[no-]ref",
-    "If set, uses only reference (or only non-reference) datasets."
+def opt_filter_datasets(opt, o, what = [:ref, :multi, :active, :taxonomy])
+  opt.on('--[no-]ref',
+    'If set, uses only reference (or only non-reference) datasets.'
     ){ |v| o[:ref]=v } if what.include? :ref
-  opt.on("--[no-]multi",
-    "If set, uses only multi-species (or only single-species) datasets."
+  opt.on('--[no-]multi',
+    'If set, uses only multi-species (or only single-species) datasets.'
     ){ |v| o[:multi]=v } if what.include? :multi
-  opt.on("--[no-]active",
-    "If set, uses only active (or inactive) datasets."
+  opt.on('--[no-]active',
+    'If set, uses only active (or inactive) datasets.'
     ){ |v| o[:active]=v } if what.include? :active
-  opt.on("-t", "--taxonomy RANK:TAXON", "Filter by taxonomy."
+  opt.on('-t', '--taxonomy RANK:TAXON', 'Filter by taxonomy.'
     ){ |v| o[:taxonomy]=MiGA::Taxonomy.new v } if what.include? :taxonomy
-  opt.on("-k", "--key INTEGER",
-    "Returns only the k-th dataset in the list."){ |v| o[:key]=v.to_i }
+  opt.on('-k', '--key INTEGER',
+    'Returns only the k-th dataset in the list.'){ |v| o[:key]=v.to_i }
 end
 
-def opt_require(o, req={project:"-P", dataset:"-D"})
+def opt_require(o, req = {project: '-P', dataset: '-D'})
   req.each do |k,v|
     raise "#{v} is mandatory: please provide #{k}." if o[k].nil?
   end
 end
 
 def opt_require_type(o, klass)
-  opt_require(o, type:"-t")
+  opt_require(o, type: '-t')
   raise "Unrecognized type: #{o[:type]}." if klass.KNOWN_TYPES[o[:type]].nil?
 end
 

data/lib/miga/daemon.rb

@@ -124,7 +124,7 @@ class MiGA::Daemon < MiGA::MiGA
         project.load
       else
         to_run = ds.next_preprocessing(true)
-        queue_job(to_run, ds) unless to_run.nil?
+        queue_job(:d, ds) unless to_run.nil?
       end
     end
   end
@@ -137,7 +137,7 @@ class MiGA::Daemon < MiGA::MiGA
     return unless project.done_preprocessing?(false)
     to_run = project.next_distances(true)
     to_run = project.next_inclade(true) if to_run.nil?
-    queue_job(to_run) unless to_run.nil?
+    queue_job(:p) unless to_run.nil?
   end
 
   ##

data/lib/miga/project/result.rb

@@ -87,9 +87,14 @@ module MiGA::Project::Result
     end
 
     def add_result_clade_finding(base)
+      if result_files_exist?(base, %w[.empty])
+        r = MiGA::Result.new("#{base}.json")
+        r.add_file(:empty, 'miga-project.empty')
+        return r
+      end
       return nil unless result_files_exist?(base, %w[.proposed-clades])
       return nil unless is_clade? or result_files_exist?(base,
-        %w[.pdf .classif .medoids .class.tsv .class.nwk])
+          %w[.pdf .classif .medoids .class.tsv .class.nwk])
       r = add_result_iter_clades(base)
       r.add_file(:aai_tree,      'miga-project.aai.nwk')
       r.add_file(:proposal,      'miga-project.proposed-clades')
@@ -100,6 +105,11 @@ module MiGA::Project::Result
     end
 
     def add_result_subclades(base)
+      if result_files_exist?(base, %w[.empty])
+        r = MiGA::Result.new("#{base}.json")
+        r.add_file(:empty, 'miga-project.empty')
+        return r
+      end
       return nil unless result_files_exist?(base,
         %w[.pdf .classif .medoids .class.tsv .class.nwk])
       r = add_result_iter_clades(base)
@@ -118,6 +128,11 @@ module MiGA::Project::Result
     end
 
     def add_result_ogs(base)
+      if result_files_exist?(base, %w[.empty])
+        r = MiGA::Result.new("#{base}.json")
+        r.add_file(:empty, 'miga-project.empty')
+        return r
+      end
       return nil unless result_files_exist?(base, %w[.ogs .stats])
       r = MiGA::Result.new("#{base}.json")
       r.add_file(:ogs,   'miga-project.ogs')

data/lib/miga/version.rb

@@ -10,7 +10,7 @@ module MiGA
   # - Float representing the major.minor version.
   # - Integer representing gem releases of the current version.
   # - Integer representing minor changes that require new version number.
-  VERSION = [0.3, 9, 0]
+  VERSION = [0.3, 9, 1]
   
   ##
   # Nickname for the current major.minor version.
@@ -18,7 +18,7 @@ module MiGA
   
   ##
   # Date of the current gem release.
-  VERSION_DATE = Date.new(2019, 03, 07)
+  VERSION_DATE = Date.new(2019, 03, 8)
   
   ##
   # Reference of MiGA.

data/scripts/aai_distances.bash

@@ -2,10 +2,8 @@
 # Available variables: $PROJECT, $RUNTYPE, $MIGA, $CORES
 set -e
 SCRIPT="aai_distances"
-echo "MiGA: $MIGA"
-echo "Project: $PROJECT"
 # shellcheck source=scripts/miga.bash
-source "$MIGA/scripts/miga.bash" || exit 1
+. "$MIGA/scripts/miga.bash" || exit 1
 cd "$PROJECT/data/09.distances/02.aai"
 
 # Initialize

data/scripts/ani_distances.bash

@@ -2,10 +2,8 @@
 # Available variables: $PROJECT, $RUNTYPE, $MIGA, $CORES
 set -e
 SCRIPT="ani_distances"
-echo "MiGA: $MIGA"
-echo "Project: $PROJECT"
 # shellcheck source=scripts/miga.bash
-source "$MIGA/scripts/miga.bash" || exit 1
+. "$MIGA/scripts/miga.bash" || exit 1
 cd "$PROJECT/data/09.distances/03.ani"
 
 # Initialize

data/scripts/assembly.bash

@@ -2,10 +2,8 @@
 # Available variables: $PROJECT, $RUNTYPE, $MIGA, $CORES, $DATASET
 set -e
 SCRIPT="assembly"
-echo "MiGA: $MIGA"
-echo "Project: $PROJECT"
 # shellcheck source=scripts/miga.bash
-source "$MIGA/scripts/miga.bash" || exit 1
+. "$MIGA/scripts/miga.bash" || exit 1
 cd "$PROJECT/data/05.assembly"
 
 # Initialize

data/scripts/cds.bash

@@ -2,10 +2,8 @@
 # Available variables: $PROJECT, $RUNTYPE, $MIGA, $CORES, $DATASET
 set -e
 SCRIPT="cds"
-echo "MiGA: $MIGA"
-echo "Project: $PROJECT"
 # shellcheck source=scripts/miga.bash
-source "$MIGA/scripts/miga.bash" || exit 1
+. "$MIGA/scripts/miga.bash" || exit 1
 cd "$PROJECT/data/06.cds"
 
 # Initialize

data/scripts/clade_finding.bash

@@ -2,10 +2,8 @@
 # Available variables: $PROJECT, $RUNTYPE, $MIGA, $CORES
 set -e
 SCRIPT="clade_finding"
-echo "MiGA: $MIGA"
-echo "Project: $PROJECT"
 # shellcheck source=scripts/miga.bash
-source "$MIGA/scripts/miga.bash" || exit 1
+. "$MIGA/scripts/miga.bash" || exit 1
 cd "$PROJECT/data/10.clades/01.find"
 
 # Initialize

data/scripts/d.bash

@@ -0,0 +1,13 @@
+#!/bin/bash
+# Available variables: $PROJECT, $RUNTYPE, $MIGA, $CORES, $DATASET
+set -e
+SCRIPT="d"
+# shellcheck source=scripts/miga.bash
+. "$MIGA/scripts/miga.bash" || exit 1
+
+while true ; do
+  res="$(miga next_step -P "$PROJECT" -D "$DATASET")"
+  [[ "$res" == '?' ]] && break
+  miga run -P "$PROJECT" -D "$DATASET" -r "$res" -t "$CORES"
+done
+

data/scripts/distances.bash

@@ -2,10 +2,8 @@
 # Available variables: $PROJECT, $RUNTYPE, $MIGA, $CORES, $DATASET
 set -e
 SCRIPT="distances"
-echo "MiGA: $MIGA"
-echo "Project: $PROJECT"
 # shellcheck source=scripts/miga.bash
-source "$MIGA/scripts/miga.bash" || exit 1
+. "$MIGA/scripts/miga.bash" || exit 1
 cd "$PROJECT/data/09.distances"
 
 # Initialize

data/scripts/essential_genes.bash

@@ -2,10 +2,8 @@
 # Available variables: $PROJECT, $RUNTYPE, $MIGA, $CORES, $DATASET
 set -e
 SCRIPT="essential_genes"
-echo "MiGA: $MIGA"
-echo "Project: $PROJECT"
 # shellcheck source=scripts/miga.bash
-source "$MIGA/scripts/miga.bash" || exit 1
+. "$MIGA/scripts/miga.bash" || exit 1
 cd "$PROJECT/data/07.annotation/01.function/01.essential"
 
 # Initialize

data/scripts/haai_distances.bash

@@ -2,10 +2,8 @@
 # Available variables: $PROJECT, $RUNTYPE, $MIGA, $CORES
 set -e
 SCRIPT="haai_distances"
-echo "MiGA: $MIGA"
-echo "Project: $PROJECT"
 # shellcheck source=scripts/miga.bash
-source "$MIGA/scripts/miga.bash" || exit 1
+. "$MIGA/scripts/miga.bash" || exit 1
 cd "$PROJECT/data/09.distances/01.haai"
 
 # Initialize