class Cagnut::JobManage
Public Class Methods
run_local()
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# File lib/cagnut/job_manage.rb, line 14 def run_local instance.run_local end
submit(job_script, job_name, opts)
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# 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)
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# 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)
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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)
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# 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()
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# 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?()
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# File lib/cagnut/job_manage.rb, line 30 def run_local? cluster.blank? || cluster['system'] == 'Local' end
submit(job_script, job_name, opts)
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# 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()
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# File lib/cagnut/job_manage.rb, line 57 def wait_local return unless run_local? 'wait $!' end