class Cagnut::JobManage

Public Class Methods

run_local() click to toggle source
# File lib/cagnut/job_manage.rb, line 14
def run_local
  instance.run_local
end
submit(job_script, job_name, opts) click to toggle source
# File lib/cagnut/job_manage.rb, line 10
def submit job_script, job_name, opts
  instance.submit job_script, job_name, opts
end

Public Instance Methods

export_command(command) click to toggle source
# File lib/cagnut/job_manage.rb, line 34
    def export_command command
      file = File.join jobs_dir, "submit_command_#{sample_name}.jobs"
      File.open(file, 'a') do |f|
        f.puts <<-BASH.strip_heredoc
          #{command}
          #{wait_local}
        BASH
      end
      File.chmod(0700, file)
    end
full_command(job_script, job_name, opts) click to toggle source
Calls superclass method
# File lib/cagnut/job_manage.rb, line 25
def full_command job_script, job_name, opts
  return super if defined?(super) && !run_local?
  local job_script
end
local(job_script) click to toggle source
# File lib/cagnut/job_manage.rb, line 45
def local job_script
  %(nohup #{jobs_dir}/#{job_script}.sh \
  > #{jobs_dir}/#{job_script}.std \
  2>#{jobs_dir}/#{job_script}.err &)
end
run_local() click to toggle source
# File lib/cagnut/job_manage.rb, line 51
def run_local
  return unless run_local?
  %(& echo $! >> #{jobs_dir}/submit_job_#{sample_name}.ids
    wait $!)
end
run_local?() click to toggle source
# File lib/cagnut/job_manage.rb, line 30
def run_local?
  cluster.blank? || cluster['system'] == 'Local'
end
submit(job_script, job_name, opts) click to toggle source
# File lib/cagnut/job_manage.rb, line 19
def submit job_script, job_name, opts
  command = full_command job_script, job_name, opts
  export_command command
  puts command
end
wait_local() click to toggle source
# File lib/cagnut/job_manage.rb, line 57
def wait_local
  return unless run_local?
  'wait $!'
end