bio-pipengine 0.9.4 → 0.9.5

checksums.yaml

@@ -1,7 +1,7 @@
 ---
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-  data.tar.gz: e516a1204f81dd37258b08afa88005bde4e4f2ed
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+  data.tar.gz: 9e76389b3af2b879ed94961edbf412f533ae3ec4
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data/VERSION

@@ -1 +1 @@
-0.9.4
+0.9.5

data/bin/pipengine

@@ -36,14 +36,6 @@ when "run"
 		opt :log_adapter, "(stdin|syslog|fluentd) In case of fluentd use http://destination.hostname:port/yourtag", :type => :string
 		opt :tag, "Overwrite tags present in samples.yml and pipeline.yml files (e.g. tag1=value1 tag2=value2)", :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"

data/lib/bio/pipengine.rb

@@ -203,53 +203,6 @@ 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
-
-		# 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.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?

metadata

@@ -1,7 +1,7 @@
 --- !ruby/object:Gem::Specification
 name: bio-pipengine
 version: !ruby/object:Gem::Version
-  version: 0.9.4
+  version: 0.9.5
 platform: ruby
 authors:
 - Francesco Strozzi