bio-pipengine 0.6.0 → 0.8.0

checksums.yaml

@@ -1,7 +1,7 @@
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data/README.md

@@ -7,6 +7,26 @@ PipEngine will generate runnable shell scripts, already configured for the PBS/T
 
 PipEngine is best suited for NGS pipelines, but it can be used for any kind of pipeline that can be runned on a job scheduling system.
 
+Installation
+============
+
+If you already have Ruby, just install PipEngine using RubyGems:
+
+```shell
+gem install bio-pipengine
+```
+
+If you don't have Ruby installed, first follow this simple step to get it:
+
+```shell
+curl -sSL https://get.rvm.io | bash -s stable
+```
+
+and then install PipEngine using RubyGems:
+
+```shell
+gem install bio-pipengine
+```
 
 :: Topics ::
 ============
@@ -85,6 +105,8 @@ With this mode, PipEngine will submit pipeline jobs to the scheduler.
                                 (the order matters)
              --group, -g <s>:   Specify the group of samples to run the
                                 pipeline steps on (do not specify --multi)
+              --allgroups -a:   Apply the step(s) to all the groups defined into
+                                the samples file
               --name, -n <s>:   Analysis name
         --output-dir, -o <s>:   Output directory (override standard output
                                 directory names)
@@ -403,6 +425,39 @@ echo '<multi1>' | sed -e 's/,/ /g' | xargs ls >> gtf_list.txt
 
 This line generates the input file for Cuffcompare with the list of the transcripts.gtf files for each sample, generated using the 'multi' definition in the pipeline YAML and the line passed through the **-m** parameter, but getting rid of the commas that separate sample names. It's a workaround and it's not a super clean solution, but PipEngine wants to be a general tool not binded to specific corner cases and it always lets the user define it's own custom command lines to manage particular steps, as in this case.
 
+Composable & Modular steps definition
+------------------------------------
+
+Since now steps are defined inside a single YAML file. This approach is usefult to have a stable and reproducible analysis pipeline. But what if, multiple users whant to collaborate on the same pipeline improving it and, most importantly, re-using the same steps in different analyses ? What happend is a proliferation of highly similar pipelines that are very complicate to compare and to maintain over time.
+In this scenario, the very first thing that a developer imagine is the ability to include external files, unfortunately YAML does not implement this feature. A possible workaround, remember that we are in the Ruby land, is to embed some Ruby code into the YAML file and include external steps.
+
+Creating a file `mapping.yml` that describe the mapping step with BWA
+
+```
+mapping:
+  cpu: 8
+  desc: Run BWA MEM and generates a sorted BAM file
+  run:
+   - <bwa> mem -t <cpu> -R '@RG\tID:<flowcell>\tLB:<sample>\tPL:ILLUMINA\tPU:<flowcell>\tCN:PTP\tSM:<sample>' <index> <trim/sample>.trim.fastq | <samtools> view -bS - > <sample>.bam
+   - <samtools> sort -@ <cpu> <sample>.bam <sample>.sort
+   - rm -f <sample>.bam
+```
+
+is then possible to include the `mapping.yml` file inside your pipeline with a snipped of Ruby code `<%= include :name_of_the_step, "file_step.yml" %>
+Right now is very important that you place the tag at the very first start of the line ( no spaces at the beginning of the line)
+
+```
+steps:
+<%= include :mapping, "./mapping.yml" %>
+
+  index:
+    desc: Make BAM index
+    run: <samtools> index <mapping/sample>.sort.bam
+````
+
+are later run pipengine as usual.
+TODO: Dump the whole pipeline file for reproducibility purposes.
+
 
 :: What happens at run-time ::
 ==============================
@@ -628,4 +683,4 @@ If a specific queue needs to be selected for sending the jobs to PBS, the ```--p
 Copyright
 =========
 
-(c)2013 Francesco Strozzi
+(c)2013 Francesco Strozzi, Raoul Jean Pierre Bonnal 

data/VERSION

@@ -1 +1 @@
-0.6.0
+0.8.0

data/bin/pipengine

@@ -3,12 +3,12 @@
 $:<< File.expand_path(File.join(File.dirname(File.dirname __FILE__),"lib"))
 require 'bio-pipengine'
 
-banner_text = "\nLauncher for Complex Biological Pipelines . Copyright(C) 2013 Francesco Strozzi\n\n" 
+banner_text = "\nLauncher for Complex Biological Pipelines . Copyright(C) 2013 Francesco Strozzi, Raoul Jean Pierre Bonnal\n\n" 
 version_text = File.read File.expand_path(File.join(File.dirname(File.dirname __FILE__),"VERSION"))
 SUB_COMMANDS = %w(run jobs)
 
 
-Bio::Pipengine.check_config
+#Bio::Pipengine.check_config
 
 options = {}
 cmd = ARGV.first # get the subcommand
@@ -22,29 +22,27 @@ when "run"
 		opt :samples, "List of sample names to run the pipeline", :type => :strings, :short => "l"
 		opt :steps, "List of steps to be executed", :type => :strings, :short => "s"
 		opt :dry,"Dry run. Just create the job script without submitting it to the batch system", :short => "d"
-		opt :spooler,"Destination spooler PBS, plain shell script", :short =>"x", :type => :string, :default => "pbs"
 		opt :tmp, "Temporary output folder", :type => :string, :short => "t"
 		opt :create_samples, "Create samples.yml file from a Sample directory (only for CASAVA projects)", :short => "c", :type => :strings
 		opt :multi, "List of samples to be processed by a given step (the order matters)", :short => "m", :type => :strings
 		opt :group, "Specify the group of samples to run the pipeline steps on (do not specify --multi)", :short => "g", :type => :string
+		opt :allgroups, "Apply the step(s) to all the groups defined into the samples file", :short => "a"
 		opt :name, "Analysis name", :short => "n", :type => :string
 		opt :output_dir, "Output directory (override standard output directory names)", :short => "o", :type => :string
 		opt :pbs_opts, "PBS options", :type => :strings, :short => "b"
 		opt :pbs_queue, "PBS queue", :type => :string, :short => "q"
 		opt :inspect_pipeline, "Show steps", :short => "i", :type => :string
-		opt :mail_exit, "Send an Email when the job terminates", :type => :string
-		opt :mail_start, "Send an Email when the job starts", :type => :string
 		opt :log, "Log script activities, by default stdin. Options are fluentd", :type => :string, :default => "stdin"
 		opt :log_adapter, "(stdin|syslog|fluentd) In case of fluentd use http://destination.hostname:port/yourtag", :type => :string
 	end
-when "jobs"
-	ARGV.shift
-	options[:jobs] = true
-	Trollop::options do
-		opt :job_id, "Search submitted jobs by Job ID", :type => :strings, :short => "i"
-		opt :job_name, "Search submitted jobs by Job Name", :type => :strings, :short => "n"
-		opt :delete, "Delete submitted jobs ('all' to erase everything or type one or more job IDs)", :short => "d", :type => :strings
-	end
+#when "jobs"
+#	ARGV.shift
+#	options[:jobs] = true
+#	Trollop::options do
+#		opt :job_id, "Search submitted jobs by Job ID", :type => :strings, :short => "i"
+#		opt :job_name, "Search submitted jobs by Job Name", :type => :strings, :short => "n"
+#		opt :delete, "Delete submitted jobs ('all' to erase everything or type one or more job IDs)", :short => "d", :type => :strings
+#	end
 when "-h"
 	puts banner_text
 	puts "List of available commands:\n\trun\tSubmit pipelines to the job scheduler\n\tjobs\tShow statistics and interact with running jobs\n"
@@ -63,29 +61,29 @@ Trollop::die :multi, "Specifing both --group and --multi is not allowed" if opti
 
 if options[:create_samples]
 	Bio::Pipengine.create_samples options[:create_samples]
-elsif options[:jobs]
-	if options[:job_id] 
-		Bio::Pipengine.show_stats(options[:job_id])
-	elsif options[:job_name]
-		warn "Not yet implemented"
-		exit
-	elsif options[:delete]
-		if options[:delete].empty?
-			warn "Provide one or more Job IDs or write 'all' to delete all your running jobs".red
-			exit
-		end
-		puts "Warning: this will delete the following running jobs: ".light_blue + "#{options[:delete].join(",")}".green
-		print "Are you sure? (y|n):"
-		answer = gets.chomp
-		if answer == "y"
-			Bio::Pipengine.delete_jobs(options[:delete])
-		else
-			puts "Aborting..."
-			exit
-		end
-	else
-		Bio::Pipengine.show_stats(["all"])
-	end
+#elsif options[:jobs]
+#	if options[:job_id] 
+#		Bio::Pipengine.show_stats(options[:job_id])
+#	elsif options[:job_name]
+#		warn "Not yet implemented"
+#		exit
+#	elsif options[:delete]
+#		if options[:delete].empty?
+#			warn "Provide one or more Job IDs or write 'all' to delete all your running jobs".red
+#			exit
+#		end
+#		puts "Warning: this will delete the following running jobs: ".light_blue + "#{options[:delete].join(",")}".green
+#		print "Are you sure? (y|n):"
+#		answer = gets.chomp
+#		if answer == "y"
+#			Bio::Pipengine.delete_jobs(options[:delete])
+#		else
+#			puts "Aborting..."
+#			exit
+#		end
+#	else
+#		Bio::Pipengine.show_stats(["all"])
+#	end
 elsif options[:pipeline] && options[:samples_file]
 	if options[:inspect_pipeline]
 		Bio::Pipengine.inspect_steps(options[:inspect_pipeline])
@@ -94,7 +92,14 @@ elsif options[:pipeline] && options[:samples_file]
 		abort("File not found: #{options[:pipeline]}".red) unless File.exists? options[:pipeline]
 		abort("File not found: #{options[:samples_file]}".red) unless File.exists? options[:samples_file]
 		abort("Please provide a valid step name with the --step parameter".red) unless options[:steps]
-		Bio::Pipengine.run(options)
+		if options[:allgroups]
+			Bio::Pipengine.load_samples_file(options[:samples_file])["samples"].keys.each do |group|
+				options[:group] = group
+				Bio::Pipengine.run(options)	
+			end
+		else
+			Bio::Pipengine.run(options)
+		end
 	end
 end
 

data/lib/bio-pipengine.rb

@@ -3,9 +3,10 @@ require 'yaml'
 require 'securerandom'
 require 'trollop'
 require 'colorize'
-require 'torque_rm'
-require 'terminal-table'
+#require 'torque_rm'
+#require 'terminal-table'
 require 'fileutils'
+require 'logger'
 
 require 'bio/pipengine/sample'
 require 'bio/pipengine/step'

data/lib/bio/pipengine.rb

@@ -1,22 +1,16 @@
 module Bio
 	module Pipengine
+
+		def self.include(name, filename)
+			File.readlines(filename).map {|line| "  "+line}.join("\n")
+		end
 	
+		@@logger_error = Logger.new(STDERR)
 		def self.run(options)
 
 			# reading the yaml files
-			pipeline = YAML.load_file options[:pipeline]
-			samples_file = YAML.load_file options[:samples_file]
-			samples_file["samples"].each do |k,v|
-				if v.kind_of? Hash
-					samples_file["samples"][k] = Hash[samples_file["samples"][k].map{ |key, value| [key.to_s, value.to_s] }] 
-				else
-					samples_file["samples"][k] = v.to_s
-				end
-			end
-			# make sure everything in Samples and Resources is converted to string
-			#samples_file["samples"] = Hash[samples_file["samples"].map{ |key, value| [key.to_s, value.to_s] }] 
-			samples_file["resources"] = Hash[samples_file["resources"].map {|k,v| [k.to_s, v.to_s]}]	
-			
+			pipeline = YAML.load ERB.new(File.read(options[:pipeline])).result(binding)
+			samples_file = load_samples_file options[:samples_file]
 			# pre-running checks	
 			check_steps(options[:steps],pipeline)	
 			check_samples(options[:samples],samples_file) if options[:samples]
@@ -50,7 +44,7 @@ module Bio
 			
 			unless run_multi # there are no multi-samples steps, so iterate on samples and create one job per sample
 				samples_list.each_key do |sample_name|
-					sample = Bio::Pipengine::Sample.new(sample_name,samples_list[sample_name])
+					sample = Bio::Pipengine::Sample.new(sample_name,samples_list[sample_name],options[:group])
 					create_job(samples_file,pipeline,samples_list,options,sample)
 				end
 			end
@@ -62,14 +56,14 @@ module Bio
 			
 			if step_multi.include? false
 				if step_multi.uniq.size > 1
-					puts "\nAbort! You are trying to run both multi-samples and single sample steps in the same job".red
+					@@logger_error.error "\nAbort! You are trying to run both multi-samples and single sample steps in the same job".red
 					exit
 				else
 					return false
 				end
 			else
 				samples_obj = {}
-				samples_list.each_key {|sample_name| samples_obj[sample_name] = Bio::Pipengine::Sample.new(sample_name,samples_list[sample_name])}
+				samples_list.each_key {|sample_name| samples_obj[sample_name] = Bio::Pipengine::Sample.new(sample_name,samples_list[sample_name],options[:group])}
 				create_job(samples_file,pipeline,samples_list,options,samples_obj)
 				return true
 			end
@@ -106,13 +100,12 @@ module Bio
 				self.add_job(job, pipeline, step_name, sample)
 			end
 
-			if options[:dry] #&& options[:spooler] == "script"
+			if options[:dry]
 				job.to_script(options)
 			else
-			  script = job.to_pbs(options) # converting the Job into a TORQUE::Qsub PBS compatible object
-			  job_id = script.submit(options)
-			  puts "#{job_id}".green unless options[:dry]
-      end
+				job.to_script(options)
+				job.submit
+			end
 		end
 
 		# check if sample exists
@@ -127,7 +120,7 @@ module Bio
 					end
 				end
 				unless samples_names.include? sample
-					puts "Sample \"#{sample}\" does not exist in sample file!".red
+					@@logger_error.error "Sample \"#{sample}\" does not exist in sample file!".red
 					exit
 				end
 			end
@@ -137,7 +130,7 @@ module Bio
 		def self.check_steps(passed_steps,pipeline)
 			passed_steps.each do |step|
 				unless pipeline["steps"].keys.include? step
-					puts "Step \"#{step}\" does not exist in pipeline file!".red
+					@@logger_error.error "Step \"#{step}\" does not exist in pipeline file!".red
 					exit
 				end
 			end
@@ -177,58 +170,74 @@ module Bio
 				end
 		end
 
-		# show running jobs information
-		def self.show_stats(job_ids)
-			stats = TORQUE::Qstat.new
-			if job_ids.first == "all"
-				stats.display
-			else
-				stats.display(:job_ids => job_ids)
-			end
-		end
-
-		# delete running jobs from the scheduler
-		def self.delete_jobs(job_ids)
-			include TORQUE
-			if job_ids == ["all"]
-				Qdel.rm_all
-			else 
-				job_ids.each {|job_id| Qdel.rm job_id}
-			end
-		end #delete_jobs
+#		# show running jobs information
+#		def self.show_stats(job_ids)
+#			stats = TORQUE::Qstat.new
+#			if job_ids.first == "all"
+#				stats.display
+#			else
+#				stats.display(:job_ids => job_ids)
+#			end
+#		end
+#
+#		# delete running jobs from the scheduler
+#		def self.delete_jobs(job_ids)
+#			include TORQUE
+#			if job_ids == ["all"]
+#				Qdel.rm_all
+#			else 
+#				job_ids.each {|job_id| Qdel.rm job_id}
+#			end
+#		end #delete_jobs
 
 		# check if required configuration exists
-		def self.check_config
-			unless File.exists?("#{Dir.home}/.torque_rm.yaml")
-				ARGV.clear
-				current_user = Etc.getlogin
-				puts "\nIt seems you are running PipEngine for the first time. Please fill in the following information:"
-				print "\nHostname or IP address of authorized server from where jobs will be submitted: ".light_blue
-				server = gets.chomp
-				print "\n"
-				print "Specify the username you will be using to connect and submit jobs [#{current_user}]: ".light_blue
-				username = gets.chomp
-				username = (username == "") ? current_user : username
-				puts "Attempting connection to the server...".green
-				path = `ssh #{username}@#{server} -t "which qsub"`.split("/qsub").first
-				unless path=~/\/\S+\/\S+/
-					warn "Connection problems detected! Please check that you are able to connect to '#{server}' as '#{username}' via ssh.".red
-				else	
-					file = File.open("#{Dir.home}/.torque_rm.yaml","w")
-					file.write({:hostname => server, :path => path, :user => username}.to_yaml)
-					file.close
-					puts "First time configuration completed!".green
-					puts "It is strongly recommended to setup a password-less SSH connection to use PipEngine.".green
-					exit
-				end
-			end
-		end #check_config
+#		def self.check_config
+#			unless File.exists?("#{Dir.home}/.torque_rm.yaml")
+#				ARGV.clear
+#				current_user = Etc.getlogin
+#				puts "\nIt seems you are running PipEngine for the first time. Please fill in the following information:"
+#				print "\nHostname or IP address of authorized server from where jobs will be submitted: ".light_blue
+#				server = gets.chomp
+#				print "\n"
+#				print "Specify the username you will be using to connect and submit jobs [#{current_user}]: ".light_blue
+#				username = gets.chomp
+#				username = (username == "") ? current_user : username
+#				puts "Attempting connection to the server...".green
+#				path = `ssh #{username}@#{server} -t "which qsub"`.split("/qsub").first
+#				unless path=~/\/\S+\/\S+/
+#					warn "Connection problems detected! Please check that you are able to connect to '#{server}' as '#{username}' via ssh.".red
+#				else	
+#					file = File.open("#{Dir.home}/.torque_rm.yaml","w")
+#					file.write({:hostname => server, :path => path, :user => username}.to_yaml)
+#					file.close
+#					puts "First time configuration completed!".green
+#					puts "It is strongly recommended to setup a password-less SSH connection to use PipEngine.".green
+#					exit
+#				end
+#			end
+#		end #check_config
 
 		def self.add_job(job, pipeline, step_name, sample)
 			step = Bio::Pipengine::Step.new(step_name,pipeline["steps"][step_name]) # parsing step instructions
 			self.add_job(job, pipeline, step.pre, sample) if step.has_prerequisite?
 			job.add_step(step,sample) # adding step command lines to the job	
 		end #add_job
+
+		def self.load_samples_file(file)
+			samples_file = YAML.load_file file
+			samples_file["samples"].each do |k,v|
+				if v.kind_of? Hash
+					samples_file["samples"][k] = Hash[samples_file["samples"][k].map{ |key, value| [key.to_s, value.to_s] }] 
+				else
+					samples_file["samples"][k] = v.to_s
+				end
+			end
+			# make sure everything in Samples and Resources is converted to string
+			#samples_file["samples"] = Hash[samples_file["samples"].map{ |key, value| [key.to_s, value.to_s] }] 
+			samples_file["resources"] = Hash[samples_file["resources"].map {|k,v| [k.to_s, v.to_s]}]	
+			samples_file 
+		end
+
 		
 	end
 end

data/lib/bio/pipengine/job.rb

@@ -1,8 +1,11 @@
 module Bio
+	
 	module Pipengine
 		
 		class Job
 			
+			@@logger = Logger.new(STDOUT)
+			@@logger_error = Logger.new(STDERR)
 			# a Job object holds information on a job to be submitted
 			# samples_groups and samples_obj are used to store information in case of steps that require to combine info
 			# from multiple samples
@@ -112,38 +115,28 @@ module Bio
 
 			end
 
-			# convert the job object into a TORQUE::Qsub object
-			def to_pbs(options)
-				TORQUE::Qsub.new(options) do |torque_job|
-					torque_job.name = self.name
-					torque_job.working_directory = self.output # where pbs scripts and stdout / stderr files will be saved
-					if options[:pbs_opts] 
-						torque_job.l = options[:pbs_opts]
+			def to_script(options)
+				File.open(self.output+"/"+self.name+'.pbs','w') do |file|
+					file.puts "#!/usr/bin/env bash"
+					file.puts "#PBS -N #{self.name}"
+					file.puts "#PBS -d #{self.output}"
+					file.puts "#PBS -q #{options[:pbs_queue]}"
+					if options[:pbs_opts]
+						file.puts "#PBS -l #{options[:pbs_opts].join(",")}"
 					else
 						l_string = []
 						l_string << "nodes=#{self.nodes}:ppn=#{self.cpus}"
 						l_string << "mem=#{self.mem}" if self.mem
-						torque_job.l = l_string
-						if options[:mail_exit]
-							torque_job.m = "e"
-							torque_job.M = options[:mail_exit]
-						end
-						if options[:mail_start]
-							torque_job.m = "b"
-							torque_job.M = options[:mail_start]
-						end
-					end	
-					torque_job.q = options[:pbs_queue] if options[:pbs_queue]
-					torque_job.script = self.command_line.join("\n")+"\n"
-        end
-			end
-
-			def to_script(options)
-			  File.open(self.name+'.sh','w') do |file|
-		          file.puts "#!/usr/bin/env bash -l"
-			      file.puts self.command_line.join("\n")
+						file.puts "#PBS -l #{l_string.join(",")}"
+					end
+					file.puts self.command_line.join("\n")
 			  end
 			end
+		
+			def submit
+				job_id = `qsub #{self.output}+"/"+#{self.name}.pbs`
+				@@logger.info "#{job_id}".green
+			end
 
 		private
 			
@@ -181,13 +174,13 @@ module Bio
 				
 				# for placeholders like <mapping/sample>
 				tmp_cmd.scan(/<(\S+)\/sample>/).map {|e| e.first}.each do |input_folder|
-					warn "Directory #{self.output+"/"+sample.name+"/"+input_folder} not found".magenta unless Dir.exists? self.output+"/"+sample.name+"/"+input_folder
+					@@logger.info "Directory #{self.output+"/"+sample.name+"/"+input_folder} not found".magenta unless Dir.exists? self.output+"/"+sample.name+"/"+input_folder
 					tmp_cmd = tmp_cmd.gsub(/<#{input_folder}\/sample>/,self.output+"/"+sample.name+"/"+input_folder+"/"+sample.name)
 				end
 				
 				# for placeholders like <mapping/>
 				tmp_cmd.scan(/<(\S+)\/>/).map {|e| e.first}.each do |input_folder|
-					warn "Directory #{self.output+"/"+sample.name+"/"+input_folder} not found".magenta unless Dir.exists? self.output+"/"+sample.name+"/"+input_folder
+					@@logger.info "Directory #{self.output+"/"+sample.name+"/"+input_folder} not found".magenta unless Dir.exists? self.output+"/"+sample.name+"/"+input_folder
 					tmp_cmd = tmp_cmd.gsub(/<#{input_folder}\/>/,self.output+"/"+sample.name+"/"+input_folder+"/")
 				end
 				return tmp_cmd

data/lib/bio/pipengine/sample.rb

@@ -2,10 +2,31 @@ module Bio
 	module Pipengine
 		class Sample
 			# Sample holds all the information on a sample and its original input path (or multiple paths)	
-			attr_accessor :path, :name
-				def initialize(name,path_string)
+			attr_accessor :path
+				def initialize(name,path_string,group)
 					@path = path_string.split(",")
-					@name = name 
+					@name = name
+					@group = group
+				end
+
+				def name=(name)
+					@name
+				end
+
+				def group=(group)
+					@group
+				end
+
+				def group
+					@group
+				end
+
+				def x_name
+					"#{@group}/#{@name}"
+				end
+
+				def name
+					@name
 				end
 		end
 	end

metadata

@@ -1,14 +1,15 @@
 --- !ruby/object:Gem::Specification
 name: bio-pipengine
 version: !ruby/object:Gem::Version
-  version: 0.6.0
+  version: 0.8.0
 platform: ruby
 authors:
 - Francesco Strozzi
+- Raoul Jean Pierre Bonnal
 autorequire: 
 bindir: bin
 cert_chain: []
-date: 2015-03-26 00:00:00.000000000 Z
+date: 2016-01-28 00:00:00.000000000 Z
 dependencies:
 - !ruby/object:Gem::Dependency
   name: trollop
@@ -39,35 +40,21 @@ dependencies:
       - !ruby/object:Gem::Version
         version: '0'
 - !ruby/object:Gem::Dependency
-  name: torque_rm
+  name: warbler
   requirement: !ruby/object:Gem::Requirement
     requirements:
     - - ">="
       - !ruby/object:Gem::Version
-        version: '0'
-  type: :runtime
-  prerelease: false
-  version_requirements: !ruby/object:Gem::Requirement
-    requirements:
-    - - ">="
-      - !ruby/object:Gem::Version
-        version: '0'
-- !ruby/object:Gem::Dependency
-  name: terminal-table
-  requirement: !ruby/object:Gem::Requirement
-    requirements:
-    - - ">="
-      - !ruby/object:Gem::Version
-        version: '0'
+        version: 1.4.8
   type: :runtime
   prerelease: false
   version_requirements: !ruby/object:Gem::Requirement
     requirements:
     - - ">="
       - !ruby/object:Gem::Version
-        version: '0'
+        version: 1.4.8
 - !ruby/object:Gem::Dependency
-  name: shoulda
+  name: jeweler
   requirement: !ruby/object:Gem::Requirement
     requirements:
     - - ">="
@@ -80,50 +67,10 @@ dependencies:
     - - ">="
       - !ruby/object:Gem::Version
         version: '0'
-- !ruby/object:Gem::Dependency
-  name: rdoc
-  requirement: !ruby/object:Gem::Requirement
-    requirements:
-    - - "~>"
-      - !ruby/object:Gem::Version
-        version: '3.12'
-  type: :development
-  prerelease: false
-  version_requirements: !ruby/object:Gem::Requirement
-    requirements:
-    - - "~>"
-      - !ruby/object:Gem::Version
-        version: '3.12'
-- !ruby/object:Gem::Dependency
-  name: bundler
-  requirement: !ruby/object:Gem::Requirement
-    requirements:
-    - - ">"
-      - !ruby/object:Gem::Version
-        version: 1.0.0
-  type: :development
-  prerelease: false
-  version_requirements: !ruby/object:Gem::Requirement
-    requirements:
-    - - ">"
-      - !ruby/object:Gem::Version
-        version: 1.0.0
-- !ruby/object:Gem::Dependency
-  name: jeweler
-  requirement: !ruby/object:Gem::Requirement
-    requirements:
-    - - "~>"
-      - !ruby/object:Gem::Version
-        version: 1.8.4
-  type: :development
-  prerelease: false
-  version_requirements: !ruby/object:Gem::Requirement
-    requirements:
-    - - "~>"
-      - !ruby/object:Gem::Version
-        version: 1.8.4
 description: A pipeline manager
-email: francesco.strozzi@gmail.com
+email:
+- francesco.strozzi@gmail.com
+- ilpuccio.febo@gmail.com
 executables:
 - pipengine
 extensions: []
@@ -160,7 +107,7 @@ required_rubygems_version: !ruby/object:Gem::Requirement
       version: '0'
 requirements: []
 rubyforge_project: 
-rubygems_version: 2.2.2
+rubygems_version: 2.4.5
 signing_key: 
 specification_version: 4
 summary: A pipeline manager