Class: Bio::Pipengine::Job

Inherits:
Object
  • Object
show all
Defined in:
lib/bio/pipengine/job.rb

Instance Attribute Summary collapse

Instance Method Summary collapse

Constructor Details

#initialize(name) ⇒ Job

Returns a new instance of Job.



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# File 'lib/bio/pipengine/job.rb', line 12

def initialize(name)
	@name = generate_uuid + "-" + name
	@shortname = name
	@command_line = []
	@resources = {}
	@cpus = 1
	@nodes = "1"
	@log = "stdin"
	@log_adapter = nil
end

Instance Attribute Details

#command_line ⇒ Object

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



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# File 'lib/bio/pipengine/job.rb', line 9

def command_line
  @command_line
end

#cpus ⇒ Object

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



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# File 'lib/bio/pipengine/job.rb', line 9

def cpus
  @cpus
end

#custom_name ⇒ Object

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



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# File 'lib/bio/pipengine/job.rb', line 9

def custom_name
  @custom_name
end

#custom_output ⇒ Object

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



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# File 'lib/bio/pipengine/job.rb', line 9

def custom_output
  @custom_output
end

#local ⇒ Object

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



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# File 'lib/bio/pipengine/job.rb', line 9

def local
  @local
end

#log ⇒ Object

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



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# File 'lib/bio/pipengine/job.rb', line 9

def log
  @log
end

#log_adapter ⇒ Object

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



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# File 'lib/bio/pipengine/job.rb', line 9

def log_adapter
  @log_adapter
end

#mem ⇒ Object

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



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# File 'lib/bio/pipengine/job.rb', line 9

def mem
  @mem
end

#multi_samples ⇒ Object

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



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# File 'lib/bio/pipengine/job.rb', line 9

def multi_samples
  @multi_samples
end

#name ⇒ Object

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



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# File 'lib/bio/pipengine/job.rb', line 9

def name
  @name
end

#nodes ⇒ Object

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



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# File 'lib/bio/pipengine/job.rb', line 9

def nodes
  @nodes
end

#resources ⇒ Object

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



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# File 'lib/bio/pipengine/job.rb', line 9

def resources
  @resources
end

#samples_obj ⇒ Object

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



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# File 'lib/bio/pipengine/job.rb', line 9

def samples_obj
  @samples_obj
end

Instance Method Details

#add_resources(resources) ⇒ Object 



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# File 'lib/bio/pipengine/job.rb', line 23

def add_resources(resources)
	self.resources.merge! resources
end

#add_step(step, sample) ⇒ Object

add all the command lines for a given step



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# File 'lib/bio/pipengine/job.rb', line 32

def add_step(step,sample)	

	# setting job working directory
	working_dir = ""	
	if self.local 
		working_dir = self.local+"/"+self.name
	else
		working_dir = self.output

		if step.is_multi?	
			folder = (self.custom_output) ? self.custom_output : @shortname 
			working_dir += "/#{folder}"
		else
			folder =
			if self.custom_output 
				self.custom_output
			elsif self.custom_name
				self.custom_name
			else
				step.name
			end
			working_dir += "/#{sample.name}/#{folder}"
		end

	end

	# set job cpus number to the higher step cpus (this in case of multiple steps)
	self.cpus = step.cpus if step.cpus > self.cpus
	
	# set number of nodes for job
	self.nodes = (step.nodes) ? step.nodes : @nodes

	# set the memory used
	self.mem = step.mem

	# adding job working directory
	unless step.name.start_with? "_"
		self.command_line << "if [ ! -f #{working_dir}/checkpoint ]"
		self.command_line << "then"
		self.command_line << logger(step, "start")
		self.command_line << "\nmkdir -p #{working_dir}"
		self.command_line << "cd #{working_dir}"
	end

	# generate command lines for this step
	if step.run.kind_of? Array
		step.run.each_with_index do |cmd, i|
			command = generate_cmd_line(cmd,sample,step)
			# TODO verify that logger works in this case
			# self.command_line << "#{command} || { echo \"FAILED `date`: #{step.name}:#{i}\" ; exit 1; }"
			self.command_line << "#{command} || { #{logger(step, "FAILED #{i}" )}; exit 1; }"
		end
	else
		command = generate_cmd_line(step.run,sample,step)
		# TODO verify that logger works in this case
		# self.command_line << "#{command} || { echo \"FAILED `date`: #{step.name} \" ; exit 1; }"
		self.command_line << "#{command} || { #{logger(step, "FAILED" )}; exit 1; }"
	end
	self.command_line << logger(step, "finished")
             self.command_line << "touch #{working_dir}/checkpoint"
	self.command_line << "else"
	self.command_line << logger(step, "already executed, skipping this step")
	self.command_line << "fi"

	# check if a temporary (i.e. different from 'output') directory is set
	if self.local
		final_output = ""

		if step.is_multi?	
			folder = (self.custom_output) ? self.custom_output : @shortname 
			final_output = self.output+"/#{folder}"	 
		else
			folder = (self.custom_output) ? self.custom_output : step.name
			final_output = self.output+"/#{sample.name}/#{folder}"
		end

		self.command_line << "mkdir -p #{final_output}"
		self.command_line << "cp -r #{working_dir}/* #{final_output}"
		self.command_line << "rm -fr #{working_dir}"
	end

end

#output ⇒ Object 



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# File 'lib/bio/pipengine/job.rb', line 27

def output
	self.resources["output"]
end

#to_pbs(options) ⇒ Object

convert the job object into a TORQUE::Qsub object



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# File 'lib/bio/pipengine/job.rb', line 116

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]
		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

#to_script(options) ⇒ Object 



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# File 'lib/bio/pipengine/job.rb', line 141

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")
  end
end