miga-base 0.2.0.6

data/actions/daemon

@@ -0,0 +1,69 @@
+#!/usr/bin/env ruby
+#
+# @package MiGA
+# @author  Luis M. Rodriguez-R <lmrodriguezr at gmail dot com>
+# @license artistic license 2.0
+# @update  Oct-01-2015
+#
+
+require "miga/daemon"
+
+task = ARGV.shift unless ["-h","--help"].include? ARGV.first
+ARGV << "-h" if ARGV.empty?
+o = {q:true, update:false, daemon_opts:[]}
+OptionParser.new do |opt|
+   opt.banner = <<BAN
+Controls the daemon of a MiGA project.
+
+Usage: #{$0} #{File.basename(__FILE__)} {task} [options]
+BAN
+   opt.separator "task:"
+   {  start:  "Start an instance of the application.",
+      stop:    "Start an instance of the application.",
+      restart: "Stop all instances and restart them afterwards.",
+      reload:  "Send a SIGHUP to all instances of the application.",
+      run:     "Start the application and stay on top.",
+      zap:     "Set the application to a stopped state.",
+      status:  "Show status (PID) of application instances."
+   }.each{ |k,v| opt.separator sprintf "    %*s%s", -33, k, v }
+   opt.separator ""
+   opt.separator "MiGA options:"
+   opt.on("-P", "--project PATH",
+      "(Mandatory) Path to the project to use."){ |v| o[:project]=v }
+   opt.on("--latency INT",
+      "Number of seconds the daemon will be sleeping."
+      ){ |v| o[:latency]=v.to_i }
+   opt.on("--max-jobs INT",
+      "Maximum number of jobs to use simultaneously."){ |v| o[:maxjobs]=v.to_i }
+   opt.on("--ppn INT",
+      "Maximum number of cores to use in a single job."){ |v| o[:ppn]=v.to_i }
+   opt.on("-v", "--verbose",
+      "Print additional information to STDERR."){ o[:q]=false }
+   opt.on("-d", "--debug INT", "Print debugging information to STDERR.") do |v|
+      v.to_i>1 ? MiGA::MiGA.DEBUG_TRACE_ON : MiGA::MiGA.DEBUG_ON
+   end
+   opt.on("-h", "--help", "Display this screen.") do
+      puts opt
+      exit
+   end
+   opt.separator ""
+   opt.separator "Daemon options:"
+   opt.on("-t", "--ontop",
+      "Stay on top (does not daemonize)"){ o[:daemon_opts] << '-t' }
+   opt.on("-f", "--force", "Force operation"){ o[:daemon_opts] << '-f' }
+   opt.on("-n", "--no_wait",
+      "Do not wait for processes to stop"){ o[:daemon_opts] << '-n' }
+end.parse!
+
+### MAIN
+raise "Project is mandatory." if o[:project].nil?
+
+raise "Project doesn't exist, aborting." unless
+   MiGA::Project.exist? o[:project]
+p = MiGA::Project.new(o[:project])
+d = MiGA::Daemon.new(p)
+[:latency, :maxjobs, :ppn].each do |k|
+   d.runopts(k, o[k]) unless o[k].nil?
+end
+d.daemon(task, o[:daemon_opts])
+

data/actions/download_dataset

@@ -0,0 +1,77 @@
+#!/usr/bin/env ruby
+#
+# @package MiGA
+# @author  Luis M. Rodriguez-R <lmrodriguezr at gmail dot com>
+# @license artistic license 2.0
+# @update  Oct-01-2015
+#
+
+require "miga/remote_dataset"
+
+o = {q:true, ref:true, universe: :ebi, db: :embl}
+OptionParser.new do |opt|
+   opt.banner = <<BAN
+Creates an empty dataset in a pre-existing MiGA project.
+
+Usage: #{$0} #{File.basename(__FILE__)} [options]
+BAN
+   opt.separator ""
+   opt.on("-P", "--project PATH",
+      "(Mandatory) Path to the project to use."){ |v| o[:project]=v }
+   opt.on("-D", "--dataset STRING",
+      "(Mandatory) ID of the dataset to create."){ |v| o[:dataset]=v }
+   opt.on("-I", "--ids ID1,ID2,...",
+      "(Mandatory) IDs in the remote database separated by commas."
+      ){ |v| o[:ids]=v }
+   opt.on("-U", "--universe STRING",
+      "Universe where the remote database lives. By default: #{o[:universe]}."
+      ){ |v| o[:universe]=v.to_sym }
+   opt.on("--db STRING",
+      "Name of the remote database. By default: #{o[:db]}."
+      ){ |v| o[:db]=v.to_sym }
+   opt.on("-t", "--type STRING",
+      "Type of dataset. Recognized types include:",
+      *MiGA::Dataset.KNOWN_TYPES.map{ |k,v| "~ #{k}: #{v[:description]}"}
+      ){ |v| o[:type]=v.to_sym }
+   opt.on("-q", "--query",
+      "If set, the dataset is registered as a query, not a reference dataset."
+      ){ |v| o[:ref]=!v }
+   opt.on("-d", "--description STRING",
+      "Description of the dataset."){ |v| o[:description]=v }
+   opt.on("-u", "--user STRING",
+      "Owner of the dataset."){ |v| o[:user]=v }
+   opt.on("-c", "--comments STRING",
+      "Comments on the dataset."){ |v| o[:comments]=v }
+   opt.on("-v", "--verbose",
+      "Print additional information to STDERR."){ o[:q]=false }
+   opt.on("-d", "--debug INT", "Print debugging information to STDERR.") do |v|
+      v.to_i>1 ? MiGA::MiGA.DEBUG_TRACE_ON : MiGA::MiGA.DEBUG_ON
+   end
+   opt.on("-h", "--help", "Display this screen.") do
+      puts opt
+      exit
+   end
+   opt.separator ""
+end.parse!
+
+
+### MAIN
+raise "-P is mandatory." if o[:project].nil?
+raise "-D is mandatory." if o[:dataset].nil?
+raise "-I is mandatory." if o[:ids].nil?
+
+$stderr.puts "Locating remote dataset." unless o[:q]
+rd = MiGA::RemoteDataset.new(o[:ids], o[:db], o[:universe])
+
+$stderr.puts "Loading project." unless o[:q]
+p = MiGA::Project.load(o[:project])
+raise "Impossible to load project: #{o[:project]}" if p.nil?
+
+$stderr.puts "Creating dataset." unless o[:q]
+md = {}
+[:type, :description, :user, :comments].each{ |k| md[k]=o[k] unless o[k].nil? }
+d = rd.save_to(p, o[:dataset], o[:ref], md)
+p.add_dataset(o[:dataset])
+
+$stderr.puts "Done." unless o[:q]
+

data/actions/find_datasets

@@ -0,0 +1,63 @@
+#!/usr/bin/env ruby
+#
+# @package MiGA
+# @author  Luis M. Rodriguez-R <lmrodriguezr at gmail dot com>
+# @license artistic license 2.0
+# @update  Oct-01-2015
+#
+
+o = {q:true, add:false, ref:false}
+OptionParser.new do |opt|
+   opt.banner = <<BAN
+Finds unregistered datasets based on result files.
+
+Usage: #{$0} #{File.basename(__FILE__)} [options]
+BAN
+   opt.separator ""
+   opt.on("-P", "--project PATH",
+      "(Mandatory) Path to the project to use."){ |v| o[:project]=v }
+   opt.on("-a", "--add",
+      "Register the datasets found. By default, only lists them (dry run)."
+      ){ |v| o[:add]=v }
+   opt.on("-t", "--type STRING",
+      "Type of datasets. Recognized types include:",
+      *MiGA::Dataset.KNOWN_TYPES.map{ |k,v| "~ #{k}: #{v[:description]}"}
+      ){ |v| o[:type]=v.to_sym }
+   opt.on("-r", "--ref",
+      "If set, all datasets are registered as reference datasets."
+      ){ |v| o[:ref]=v }
+   opt.on("-u", "--user STRING", "Owner of the dataset."){ |v| o[:user]=v }
+   opt.on("-v", "--verbose",
+      "Print additional information to STDERR."){ o[:q]=false }
+   opt.on("-d", "--debug INT", "Print debugging information to STDERR.") do |v|
+      v.to_i>1 ? MiGA::MiGA.DEBUG_TRACE_ON : MiGA::MiGA.DEBUG_ON
+   end
+   opt.on("-h", "--help", "Display this screen.") do
+      puts opt
+      exit
+   end
+   opt.separator ""
+end.parse!
+
+
+### MAIN
+raise "-P is mandatory." if o[:project].nil?
+
+$stderr.puts "Loading project." unless o[:q]
+p = MiGA::Project.load(o[:project])
+raise "Impossible to load project: #{o[:project]}" if p.nil?
+
+$stderr.puts "Finding datasets." unless o[:q]
+ud = p.unregistered_datasets
+ud.each do |dn|
+   puts dn
+   if o[:add]
+      md = {}
+      [:type, :user].each{ |k| md[k]=o[k] unless o[k].nil? }
+      d = MiGA::Dataset.new(p, dn, o[:ref], md)
+      p.add_dataset(dn)
+   end
+end
+
+$stderr.puts "Done." unless o[:q]
+

data/actions/import_datasets

@@ -0,0 +1,86 @@
+#!/usr/bin/env ruby
+#
+# @package MiGA
+# @author  Luis M. Rodriguez-R <lmrodriguezr at gmail dot com>
+# @license artistic license 2.0
+# @update  Oct-01-2015
+#
+
+o = {q:true, info:false, force:false, method: :hardlink }
+OptionParser.new do |opt|
+   opt.banner = <<BAN
+Link datasets (including results) from one project to another.
+
+Usage: #{$0} #{File.basename(__FILE__)} [options]
+BAN
+   opt.separator ""
+   opt.on("-P", "--project-source PATH",
+      "(Mandatory) Path to the project that contains the dataset."
+      ){ |v| o[:project1]=v }
+   opt.on("-Q", "--project-target PATH",
+      "(Mandatory) Path to the project where to link the dataset."
+      ){ |v| o[:project2]=v }
+   opt.on("-D", "--dataset STRING",
+      "ID of the dataset to link."){ |v| o[:dataset]=v.miga_name }
+   opt.on("-f", "--force",
+      "Forces linking, even if dataset's preprocessing is incomplete."
+      ){ |v| o[:force]=v }
+   opt.on("-s", "--symlink",
+      "Creates symlinks instead of the default hard links."
+      ){ o[:method] = :symlink }
+   opt.on("-c", "--copy",
+      "Creates copies instead of the default hard links."){ o[:method] = :copy }
+   opt.on("--[no-]ref",
+      "If set, links only reference (or only non-reference) datasets."
+      ){ |v| o[:ref]=v }
+   opt.on("--[no-]multi",
+      "If set, links only multi-species (or only single-species) datasets."
+      ){ |v| o[:multi]=v }
+   opt.on("-t", "--taxonomy RANK:TAXON",
+      "Filter by taxonomy."){ |v| o[:taxonomy]=MiGA::Taxonomy.new v }
+   opt.on("-v", "--verbose",
+      "Print additional information to STDERR."){ o[:q]=false }
+   opt.on("-d", "--debug INT", "Print debugging information to STDERR.") do |v|
+      v.to_i>1 ? MiGA::MiGA.DEBUG_TRACE_ON : MiGA::MiGA.DEBUG_ON
+   end
+   opt.on("-h", "--help", "Display this screen.") do
+      puts opt
+      exit
+   end
+   opt.separator ""
+end.parse!
+
+
+### MAIN
+raise "-P is mandatory." if o[:project1].nil?
+raise "-Q is mandatory." if o[:project2].nil?
+
+$stderr.puts "Loading project." unless o[:q]
+p = MiGA::Project.load(o[:project1])
+raise "Impossible to load project: #{o[:project1]}" if p.nil?
+q = MiGA::Project.load(o[:project2])
+raise "Impossible to load project: #{o[:project2]}" if q.nil?
+
+$stderr.puts "Listing dataset." unless o[:q]
+if o[:dataset].nil?
+   ds = p.datasets
+else
+   ds = [p.dataset(o[:dataset])]
+end
+ds.select!{|d| d.name == o[:dataset]} unless o[:dataset].nil?
+ds.select!{|d| d.is_ref? == o[:ref] } unless o[:ref].nil?
+ds.select! do |d|
+   (not d.metadata[:type].nil?) and
+      (MiGA::Dataset.KNOWN_TYPES[d.metadata[:type]][:multi] == o[:multi])
+end unless o[:multi].nil?
+ds.select! do |d|
+   (not d.metadata[:tax].nil?) and d.metadata[:tax].is_in?(o[:taxonomy])
+end unless o[:taxonomy].nil?
+ds.each do |d|
+   next unless o[:force] or d.done_preprocessing?
+   puts d.name
+   q.import_dataset(d, o[:method])
+end
+
+$stderr.puts "Done." unless o[:q]
+

data/actions/index_taxonomy

@@ -0,0 +1,71 @@
+#!/usr/bin/env ruby
+#
+# @package MiGA
+# @author  Luis M. Rodriguez-R <lmrodriguezr at gmail dot com>
+# @license artistic license 2.0
+# @update  Oct-01-2015
+#
+
+require "miga/tax_index"
+
+o = {q:true, format: :json}
+OptionParser.new do |opt|
+   opt.banner = <<BAN
+Creates a taxonomy-indexed list of the datasets.
+
+Usage: #{$0} #{File.basename(__FILE__)} [options]
+BAN
+   opt.separator ""
+   opt.on("-P", "--project PATH",
+      "(Mandatory) Path to the project to read."){ |v| o[:project]=v }
+   opt.on("-i", "--index PATH",
+      "(Mandatory) File to create with the index."){ |v| o[:index]=v }
+   opt.on("-f", "--format STRING",
+      "Format of the index file. By default: #{o[:format]}. Supported: " +
+      "json, tab."){ |v| o[:format]=v.to_sym }
+   opt.on("--[no-]multi",
+      "If set, lists only multi-species (or only single-species) datasets."
+      ){ |v| o[:multi]=v }
+   opt.on("-v", "--verbose",
+      "Print additional information to STDERR."){ o[:q]=false }
+   opt.on("-d", "--debug INT", "Print debugging information to STDERR.") do |v|
+      v.to_i>1 ? MiGA::MiGA.DEBUG_TRACE_ON : MiGA::MiGA.DEBUG_ON
+   end
+   opt.on("-h", "--help", "Display this screen.") do
+      puts opt
+      exit
+   end
+   opt.separator ""
+end.parse!
+
+### MAIN
+raise "-P is mandatory." if o[:project].nil?
+raise "-i is mandatory." if o[:index].nil?
+
+$stderr.puts "Loading project." unless o[:q]
+p = MiGA::Project.load(o[:project])
+raise "Impossible to load project: #{o[:project]}" if p.nil?
+
+$stderr.puts "Loading datasets." unless o[:q]
+ds = p.datasets
+ds.select!{|d| not d.metadata[:tax].nil? }
+ds.select! do |d|
+   (not d.metadata[:type].nil?) and
+      (MiGA::Dataset.KNOWN_TYPES[d.metadata[:type]][:multi] == o[:multi])
+end unless o[:multi].nil?
+
+$stderr.puts "Indexing taxonomy." unless o[:q]
+tax_index = MiGA::TaxIndex.new
+ds.each { |d| tax_index << d }
+
+$stderr.puts "Saving index." unless o[:q]
+fh = File.open(o[:index], "w")
+if o[:format]==:json
+   fh.print tax_index.to_json
+elsif o[:format]==:tab
+   fh.print tax_index.to_tab
+end
+fh.close
+
+$stderr.puts "Done." unless o[:q]
+

data/actions/list_datasets

@@ -0,0 +1,83 @@
+#!/usr/bin/env ruby
+#
+# @package MiGA
+# @author  Luis M. Rodriguez-R <lmrodriguezr at gmail dot com>
+# @license artistic license 2.0
+# @update  Oct-01-2015
+#
+
+o = {q:true, info:false}
+OptionParser.new do |opt|
+   opt.banner = <<BAN
+Lists all registered datasets in an MiGA project.
+
+Usage: #{$0} #{File.basename(__FILE__)} [options]
+BAN
+   opt.separator ""
+   opt.on("-P", "--project PATH",
+      "(Mandatory) Path to the project to read."){ |v| o[:project]=v }
+   opt.on("-D", "--dataset STRING",
+      "ID of the dataset to read."){ |v| o[:dataset]=v.miga_name }
+   opt.on("--[no-]ref",
+      "If set, lists only reference (or only non-reference) datasets."
+      ){ |v| o[:ref]=v }
+   opt.on("--[no-]multi",
+      "If set, lists only multi-species (or only single-species) datasets."
+      ){ |v| o[:multi]=v }
+   opt.on("-i", "--info",
+      "Print additional information on each dataset."){ o[:info]=true }
+   opt.on("-t", "--taxonomy RANK:TAXON",
+      "Filter by taxonomy."){ |v| o[:taxonomy]=MiGA::Taxonomy.new v }
+   opt.on("-m", "--metadata STRING",
+      "Print name and metadata field only. If set, ignores -i."
+      ){ |v| o[:datum]=v }
+   opt.on("-v", "--verbose",
+      "Print additional information to STDERR."){ o[:q]=false }
+   opt.on("-d", "--debug INT", "Print debugging information to STDERR.") do |v|
+      v.to_i>1 ? MiGA::MiGA.DEBUG_TRACE_ON : MiGA::MiGA.DEBUG_ON
+   end
+   opt.on("-h", "--help", "Display this screen.") do
+      puts opt
+      exit
+   end
+   opt.separator ""
+end.parse!
+
+
+### MAIN
+raise "-P is mandatory." if o[:project].nil?
+
+$stderr.puts "Loading project." unless o[:q]
+p = MiGA::Project.load(o[:project])
+raise "Impossible to load project: #{o[:project]}" if p.nil?
+
+$stderr.puts "Listing datasets." unless o[:q]
+if o[:dataset].nil?
+   ds = p.datasets
+elsif MiGA::Dataset.exist? p, o[:dataset]
+   ds = [p.dataset(o[:dataset])]
+else
+   ds = []
+end
+ds.select!{|d| d.is_ref? == o[:ref] } unless o[:ref].nil?
+ds.select! do |d|
+   (not d.metadata[:type].nil?) and
+      (MiGA::Dataset.KNOWN_TYPES[d.metadata[:type]][:multi] == o[:multi])
+end unless o[:multi].nil?
+ds.select! do |d|
+   (not d.metadata[:tax].nil?) and d.metadata[:tax].is_in?(o[:taxonomy])
+end unless o[:taxonomy].nil?
+if not o[:datum].nil?
+   ds.each{|d| puts "#{d.name}\t#{(d.metadata[ o[:datum] ] || "?").to_s}"}
+elsif o[:info]
+   header = MiGA::Dataset.INFO_FIELDS.map{|i| i.ljust(25)}.join("  ")
+   puts header, header.gsub(/\S/,"-")
+   ds.each do |d|
+      puts d.info.map{|i| i.nil? ? "?" : i.to_s}.map{|i| i.ljust(25)}.join("  ")
+   end
+else
+   ds.each{|d| puts d.name}
+end
+
+$stderr.puts "Done." unless o[:q]
+

data/actions/list_files

@@ -0,0 +1,67 @@
+#!/usr/bin/env ruby
+#
+# @package MiGA
+# @author  Luis M. Rodriguez-R <lmrodriguezr at gmail dot com>
+# @license artistic license 2.0
+# @update  Oct-01-2015
+#
+
+o = {q:true, details:false, json:true}
+OptionParser.new do |opt|
+   opt.banner = <<BAN
+Lists all registered files from the results of a dataset or a project.
+
+Usage: #{$0} #{File.basename(__FILE__)} [options]
+BAN
+   opt.separator ""
+   opt.on("-P", "--project PATH",
+      "(Mandatory) Path to the project to read."){ |v| o[:project]=v }
+   opt.on("-D", "--dataset STRING",
+      "ID of the dataset to read. If not set, project-wide results are shown."
+      ){ |v| o[:dataset]=v.miga_name }
+   opt.on("-i", "--info",
+      "If set, it prints additional details for each file."
+      ){ |v| o[:details]=v }
+   opt.on("--exclude-json",
+      "If set, excludes json files containing results metadata."
+      ){ |v| o[:json]=!v }
+   opt.on("-v", "--verbose",
+      "Print additional information to STDERR."){ o[:q]=false }
+   opt.on("-d", "--debug INT", "Print debugging information to STDERR.") do |v|
+      v.to_i>1 ? MiGA::MiGA.DEBUG_TRACE_ON : MiGA::MiGA.DEBUG_ON
+   end
+   opt.on("-h", "--help", "Display this screen.") do
+      puts opt
+      exit
+   end
+   opt.separator ""
+end.parse!
+
+
+### MAIN
+raise "-P is mandatory." if o[:project].nil?
+
+$stderr.puts "Loading project." unless o[:q]
+p = MiGA::Project.load(o[:project])
+raise "Impossible to load project: #{o[:project]}" if p.nil?
+
+if o[:dataset].nil?
+   results = p.results
+else
+   $stderr.puts "Loading dataset." unless o[:q]
+   ds = p.dataset(o[:dataset])
+   raise "Impossible to load dataset: #{o[:dataset]}" if ds.nil?
+   results = ds.results
+end
+
+$stderr.puts "Listing files." unless o[:q]
+results.each do |result|
+   puts (o[:details] ? result.path + "\t" + "\t" : "") + result.path if o[:json]
+   result.each_file do |k,f|
+      puts (o[:details] ? result.path + "\t" + k.to_s + "\t" : "") +
+	 File.dirname(result.path) + "/" + f.to_s
+   end
+end
+
+$stderr.puts "Done." unless o[:q]
+

data/actions/unlink_dataset

@@ -0,0 +1,52 @@
+#!/usr/bin/env ruby
+#
+# @package MiGA
+# @author  Luis M. Rodriguez-R <lmrodriguezr at gmail dot com>
+# @license artistic license 2.0
+# @update  Oct-01-2015
+#
+
+o = {q:true, remove:false}
+OptionParser.new do |opt|
+   opt.banner = <<BAN
+Removes a dataset from an MiGA project.
+
+Usage: #{$0} #{File.basename(__FILE__)} [options]
+BAN
+   opt.separator ""
+   opt.on("-P", "--project PATH",
+      "(Mandatory) Path to the project to use."){ |v| o[:project]=v }
+   opt.on("-D", "--dataset PATH",
+      "(Mandatory) ID of the dataset to create."){ |v| o[:dataset]=v }
+   opt.on("-r", "--remove",
+      "Also remove all associated files.",
+      "By default, only unlinks from metadata."){ o[:remove]=true }
+   opt.on("-v", "--verbose",
+      "Print additional information to STDERR."){ o[:q]=false }
+   opt.on("-d", "--debug INT", "Print debugging information to STDERR.") do |v|
+      v.to_i>1 ? MiGA::MiGA.DEBUG_TRACE_ON : MiGA::MiGA.DEBUG_ON
+   end
+   opt.on("-h", "--help", "Display this screen.") do
+      puts opt
+      exit
+   end
+   opt.separator ""
+end.parse!
+
+
+### MAIN
+raise "-P is mandatory." if o[:project].nil?
+raise "-D is mandatory." if o[:dataset].nil?
+
+$stderr.puts "Loading project." unless o[:q]
+p = MiGA::Project.load(o[:project])
+raise "Impossible to load project: #{o[:project]}" if p.nil?
+
+$stderr.puts "Unlinking dataset." unless o[:q]
+raise "Dataset doesn't exist, aborting." unless
+   MiGA::Dataset.exist?(p, o[:dataset])
+d = p.unlink_dataset(o[:dataset])
+d.remove! if o[:remove]
+
+$stderr.puts "Done." unless o[:q]
+

data/bin/miga

@@ -0,0 +1,48 @@
+#!/usr/bin/env ruby
+#
+# @package MiGA
+# @author Luis M. Rodriguez-R <lmrodriguezr at gmail dot com>
+# @license artistic license 2.0
+# @update Oct-01-2015
+#
+
+$:.push File.expand_path("../lib", File.dirname(__FILE__))
+
+require "optparse"
+require "miga"
+
+execs = Dir[File.expand_path("../actions/*",
+   File.dirname(__FILE__))].map{ |b| File.basename b }
+
+if %w{-v --version}.include? ARGV[0]
+   puts MiGA::MiGA.VERSION
+elsif %w{-V --long-version}.include? ARGV[0]
+   puts MiGA::MiGA.LONG_VERSION
+elsif %w{-C --citation}.include? ARGV[0]
+   puts MiGA::MiGA.CITATION
+elsif execs.include? ARGV[0]
+   task = ARGV.shift
+   ARGV << "-h" if ARGV.empty?
+   begin
+      load File.expand_path("../actions/" + task, File.dirname(__FILE__))
+   rescue => err
+      $stderr.puts "Exception: #{err}\n\n"
+      err.backtrace.each { |l| $stderr.puts l + "\n" }
+      err
+   end
+else
+   print <<HELP.gsub /^   /,""
+   Microbial Genomes Atlas.
+
+   Usage: #{$0} {action} [options]
+
+   actions:#{ execs.map{ |e| "\n       #{e}"}.join }
+
+   generic options:
+       -h, --help		Display this screen.
+       -v, --version	Show MiGA version.
+       -V, --long-version	Show complete MiGA version.
+       -C, --citation	How to cite MiGA.
+HELP
+end
+