cagnut_gatk 0.3.0

data/lib/cagnut_gatk/functions/haplotype_caller.rb

@@ -0,0 +1,89 @@
+module CagnutGatk
+  class HaplotypeCaller
+    extend Forwardable
+
+    def_delegators :'Cagnut::Configuration.base', :sample_name, :jobs_dir, :java_path,
+                   :ref_fasta, :target, :prefix_name, :dodebug, :target_flanks_file
+    def_delegators :'CagnutGatk.config', :haplotype_caller_params
+
+    def initialize opts = {}
+      @order = sprintf '%02i', opts[:order]
+      @input = opts[:input].nil? ? "#{opts[:dirs][:input]}/#{sample_name}_recal.bam" : opts[:input]
+      @output = "#{opts[:dirs][:output]}/#{sample_name}.vcf"
+      @job_name = "#{prefix_name}_haplotype_caller_#{sample_name}"
+    end
+
+    def run previous_job_id = nil
+      puts "Submitting HaplotypeCaller #{sample_name} "
+      script_name = generate_script
+      ::Cagnut::JobManage.submit script_name, @job_name, cluster_options(previous_job_id)
+      [@job_name, @output]
+    end
+
+    def cluster_options previous_job_id = nil
+      core_num = 6
+      job_mem1 = "adjustWorkingMem 256M #{core_num}"
+      job_mem2 = "adjustWorkingMem 10G #{core_num}"
+      {
+        previous_job_id: previous_job_id,
+        var_env: [core_num, target],
+        adjust_memory: ["h_stack=#{job_mem1}", "h_vmem=#{job_mem2}"],
+        parallel_env: [core_num],
+        tools: ['gatk', 'haplotype_caller']
+      }
+    end
+
+    def haplotype_caller_options
+      array = haplotype_caller_params['params'].dup
+      array << "-T HaplotypeCaller"
+      array << "-R #{ref_fasta}"
+      array << "-I #{@input}"
+      array << "-o #{@output}"
+      array << "-L #{target_flanks_file}" if target_flanks_file
+      array.uniq
+    end
+
+    def modified_java_array
+      array = haplotype_caller_params['java'].dup
+      array.unshift(java_path).uniq
+    end
+
+    def params_combination
+      @params_combination_hash ||= {
+        'java' => modified_java_array,
+        'params' => haplotype_caller_options
+      }
+    end
+
+    def generate_script
+      script_name = "#{@order}_gatk_haplotype_caller"
+      file = File.join jobs_dir, "#{script_name}.sh"
+      File.open(file, 'w') do |f|
+        f.puts <<-BASH.strip_heredoc
+          #!/bin/bash
+
+          cd "#{jobs_dir}/../"
+          echo "#{script_name} is starting at $(date +%Y%m%d%H%M%S)" >> "#{jobs_dir}/finished_jobs"
+
+          #{params_combination['java'].join("\s")} \\
+            #{params_combination['params'].join(" \\\n            ")} \\
+            #{::Cagnut::JobManage.run_local}
+
+          EXITSTATUS=$?
+
+          if [ ! -s "#{@output}" ]
+          then
+            echo "vcf incomplete!"
+            exit 100;
+          fi
+
+          if [ $EXITSTATUS -ne 0 ];then exit $EXITSTATUS;fi
+          echo "#{script_name} is finished at $(date +%Y%m%d%H%M%S)" >> "#{jobs_dir}/finished_jobs"
+
+        BASH
+      end
+      File.chmod(0700, file)
+      script_name
+    end
+  end
+end

data/lib/cagnut_gatk/functions/indel_realigner.rb

@@ -0,0 +1,101 @@
+module CagnutGatk
+  class IndelRealigner
+    extend Forwardable
+
+    def_delegators :'Cagnut::Configuration.base', :sample_name, :jobs_dir, :dodebug,
+                   :ref_fasta, :target_flanks_file, :dbsnp_ref_indels,
+                   :magic28, :prefix_name, :java_path
+    def_delegators :'CagnutGatk.config', :indel_realigner_params
+
+    def initialize opts = {}
+      @order = sprintf '%02i', opts[:order]
+      @job_name = "#{prefix_name}_indelRealigner_#{sample_name}"
+      @interval_list = opts[:interval_list]
+      @input = opts[:input].nil? ? "#{opts[:dirs][:input]}/#{sample_name}_markdup.bam" : opts[:input]
+      @output = "#{opts[:dirs][:output]}/#{sample_name}_realn.bam"
+    end
+
+    def run previous_job_id = nil
+      puts "Submitting indel_realigner #{sample_name}"
+      script_name = generate_script
+      ::Cagnut::JobManage.submit script_name, @job_name, cluster_options(previous_job_id)
+      [@job_name, @output]
+    end
+
+    def cluster_options previous_job_id = nil
+      {
+        previous_job_id: previous_job_id,
+        adjust_memory: ['h_vmem=8G'],
+        tools: ['gatk', 'indel_realigner']
+      }
+    end
+
+    def indel_realigner_options
+      array = indel_realigner_params['params'].dup
+      array << "-T IndelRealigner"
+      array << "-R #{ref_fasta}"
+      array << "-targetIntervals #{@interval_list}"
+      array << "-I #{@input}"
+      array << "-o #{@output}"
+      array << "-known #{dbsnp_ref_indels}" if dbsnp_ref_indels
+      array.uniq!
+      array.uniq
+    end
+
+    def modified_java_array
+      array = indel_realigner_params['java'].dup
+      array.unshift(java_path).uniq
+    end
+
+    def params_combination
+      @params_combination_hash ||= {
+        'java' => modified_java_array,
+        'params' => indel_realigner_options
+      }
+    end
+
+    def generate_script
+      script_name = "#{@order}_gatk_indel_realigner"
+      file = File.join jobs_dir, "#{script_name}.sh"
+      File.open(file, 'w') do |f|
+        f.puts <<-BASH.strip_heredoc
+          #!/bin/bash
+
+          cd "#{jobs_dir}/../"
+          echo "#{script_name} is starting at $(date +%Y%m%d%H%M%S)" >> "#{jobs_dir}/finished_jobs"
+          # Check for intervals file
+          if [ ! -s "#{@interval_list}" ];then
+            echo "Error: Missing interval file: "#{@interval_list}" from realignTargetCreator_#{sample_name}"
+            exit 100
+          fi
+
+          #{params_combination['java'].join("\s")} \\
+            #{params_combination['params'].join(" \\\n            ")} \\
+            #{::Cagnut::JobManage.run_local}
+
+          EXITSTATUS=$?
+
+          #force error when missing @output
+          if [ ! -s "#{@output}" ]
+          then
+            echo "Missing @output BAM #{@output}"
+            exit 100
+          fi
+
+          # Check BAM EOF
+          BAM_28=$(tail -c 28 #{@output}|xxd -p)
+          if [ "#{magic28}" != "$BAM_28" ]
+          then
+            echo "Error with BAM EOF" 1>&2
+            exit 100
+          fi
+          echo "#{script_name} is finished at $(date +%Y%m%d%H%M%S)" >> "#{jobs_dir}/finished_jobs"
+
+          exit $EXITSTATUS
+        BASH
+      end
+      File.chmod(0700, file)
+      script_name
+    end
+  end
+end

data/lib/cagnut_gatk/functions/print_reads.rb

@@ -0,0 +1,92 @@
+module CagnutGatk
+  class PrintReads
+    extend Forwardable
+
+    def_delegators :'Cagnut::Configuration.base', :sample_name, :jobs_dir, :target_flanks_file,
+                   :ref_fasta, :prefix_name, :dodebug, :java_path
+    def_delegators :'CagnutGatk.config', :print_reads_params
+
+    def initialize opts = {}
+      @order = sprintf '%02i', opts[:order]
+      @job_name = "#{prefix_name}_PrintReads_#{sample_name}"
+      @input = opts[:input].nil? ? "#{opts[:dirs][:input]}/#{sample_name}_realn.bam" : opts[:input]
+      @output = "#{opts[:dirs][:output]}/#{output_file}"
+      @bqsr_file = "#{opts[:dirs][:contrast]}/#{replace_filename('_recal.csv')}"
+    end
+
+    def file_basename
+      @basename ||= File.basename @input
+    end
+
+    def replace_filename target
+      file_basename.gsub '_realn.bam', target
+    end
+
+    def output_file
+      output = replace_filename '_recal.bam'
+      return output unless output == file_basename
+      abort 'Input file is not correctly'
+    end
+
+    def run previous_job_id = nil
+      puts "Submitting PrintReads #{sample_name}"
+      script_name = generate_script
+      ::Cagnut::JobManage.submit script_name, @job_name, cluster_options(previous_job_id)
+      [@job_name, @output]
+    end
+
+    def cluster_options previous_job_id = nil
+      {
+        previous_job_id: previous_job_id,
+        adjust_memory: ['h_vmem=6G'],
+        tools: ['gatk', 'print_reads']
+      }
+    end
+
+    def generate_script
+      script_name = "#{@order}_gatk_print_reads"
+      file = File.join jobs_dir, "#{script_name}.sh"
+      path = File.expand_path '../templates/print_reads.sh', __FILE__
+      template = Tilt.new path
+      File.open(file, 'w') do |f|
+        f.puts template.render Object.new, job_params(script_name)
+      end
+      File.chmod(0700, file)
+      script_name
+    end
+
+    def print_reads_options
+      ary = print_reads_params['params'].dup
+      ary << "-T PrintReads"
+      ary << "-R #{ref_fasta}"
+      ary << "-I #{@input}"
+      ary << "-o #{@output}"
+      ary << "-BQSR #{@bqsr_file}"
+      ary << "-L #{target_flanks_file}" if target_flanks_file
+      ary.uniq
+    end
+
+    def modified_java_array
+      array = print_reads_params['java'].dup
+      array.unshift(java_path).uniq
+    end
+
+    def params_combination
+      {
+        'java' => modified_java_array,
+        'params' => print_reads_options
+      }
+    end
+
+    def job_params script_name
+      {
+        script_name: script_name,
+        jobs_dir: jobs_dir,
+        output: @output,
+        bqsr_file: @bqsr_file,
+        print_reads_params: params_combination,
+        run_local: ::Cagnut::JobManage.run_local,
+      }
+    end
+  end
+end

data/lib/cagnut_gatk/functions/realigner_target_creator.rb

@@ -0,0 +1,92 @@
+module CagnutGatk
+  class RealignerTargetCreator
+    extend Forwardable
+
+    def_delegators :'Cagnut::Configuration.base', :sample_name, :jobs_dir, :dodebug,
+                   :ref_fasta, :snpdb, :target_flanks_file, :prefix_name,
+                   :java_path
+    def_delegators :'CagnutGatk.config', :realigner_target_creator_params
+
+    def initialize opts = {}
+      @order = sprintf '%02i', opts[:order]
+      @job_name = "#{prefix_name}_realignTargetCreator_#{sample_name}"
+      @input = opts[:input].nil? ? "#{opts[:dirs][:input]}/#{sample_name}_markdup.bam" : opts[:input]
+      @output = "#{opts[:dirs][:output]}/#{sample_name}_markdup.interval_list"
+    end
+
+    def run previous_job_id = nil
+      puts "Submitting realigner_target_creator #{sample_name}"
+      script_name = generate_script
+      ::Cagnut::JobManage.submit script_name, @job_name, cluster_options(previous_job_id)
+      [@job_name, @output]
+    end
+
+    def cluster_options previous_job_id = nil
+      core_num = 6
+      job_mem1 = "adjustWorkingMem 256M #{core_num}"
+      job_mem2 = "adjustWorkingMem 10G #{core_num}"
+      {
+        previous_job_id: previous_job_id,
+        var_env: [core_num],
+        adjust_memory: ["h_stack=#{job_mem1}", "h_vmem=#{job_mem2}"],
+        parallel_env: [core_num],
+        tools: ['gatk', 'realigner_target_creator']
+      }
+    end
+
+    def realigner_target_creator_options
+      array = realigner_target_creator_params['params'].dup
+      array << "-T RealignerTargetCreator"
+      array << "-R #{ref_fasta}"
+      array << "--known #{snpdb}"
+      array << "-I #{@input}"
+      array << "-o #{@output}"
+      array << "-L #{target_flanks_file}" if target_flanks_file
+      array.uniq!
+      array.uniq
+    end
+
+    def modified_java_array
+      array = realigner_target_creator_params['java'].dup
+      array.unshift(java_path).uniq
+    end
+
+    def params_combination
+      @params_combination_hash ||= {
+        'java' => modified_java_array,
+        'params' => realigner_target_creator_options
+      }
+    end
+
+    def generate_script
+      script_name = "#{@order}_gatk_realigner_target_creator"
+      file = File.join jobs_dir, "#{script_name}.sh"
+      File.open(file, 'w') do |f|
+        f.puts <<-BASH.strip_heredoc
+          #!/bin/bash
+
+          cd "#{jobs_dir}/../"
+          echo "#{script_name} is starting at $(date +%Y%m%d%H%M%S)" >> "#{jobs_dir}/finished_jobs"
+
+          #{params_combination['java'].join("\s")} \\
+            #{params_combination['params'].join(" \\\n            ")} \\
+            #{::Cagnut::JobManage.run_local}
+
+          EXITSTATUS=$?
+
+          #force error when missing output
+          if [ ! -s "#{@output}" ]
+          then
+            echo "Missing indel_calls #{@output}, can not continue"
+            exit 100
+          fi
+          echo "#{script_name} is finished at $(date +%Y%m%d%H%M%S)" >> "#{jobs_dir}/finished_jobs"
+
+          exit $EXITSTATUS
+        BASH
+      end
+      File.chmod(0700, file)
+      script_name
+    end
+  end
+end

data/lib/cagnut_gatk/functions/templates/analyze_covariates.sh

@@ -0,0 +1,26 @@
+#!/bin/bash
+
+cd "#{jobs_dir}/../"
+echo "#{script_name} is starting at $(date +%Y%m%d%H%M%S)" >> "#{jobs_dir}/finished_jobs"
+if [ ! -s #{after} ]; then
+ echo "Error: missing recalfile #{after}"
+ exit 100
+fi
+
+rm core.* 2> /dev/null
+
+#{analyze_covariates_params['java'].join("\s")} \\
+  #{analyze_covariates_params['params'].join(" \\\n  ")} \\
+  #{run_local}
+
+EXITSTATUS=$?
+
+#throw an error if no output file
+if [ ! -s #{output} ];then
+  echo "Error: no plots outputted"
+  exit 100
+fi
+
+echo "#{script_name} is finished at $(date +%Y%m%d%H%M%S)" >> "#{jobs_dir}/finished_jobs"
+
+exit $EXITSTATUS

data/lib/cagnut_gatk/functions/templates/base_recalibrator.sh

@@ -0,0 +1,30 @@
+#!/bin/bash
+
+cd "#{jobs_dir}/../"
+echo "#{script_name} is starting at $(date +%Y%m%d%H%M%S)" >> "#{jobs_dir}/finished_jobs"
+rm core.* 2> /dev/null
+
+# Check BAM EOF
+BAM_28=$(tail -c 28 #{input}|xxd -p)
+if [ "#{magic28}" != "$BAM_28" ]
+then
+  echo "Error with BAM EOF"
+  exit 100
+fi
+
+#{base_recalibrator_params['java'].join("\s")} \\
+  #{base_recalibrator_params['params'].join(" \\\n  ")} \\
+  #{run_local}
+
+EXITSTATUS=$?
+
+#force error when missing recalFile. Would prevent continutation of pipeline
+if [ ! -s #{output} ]
+then
+ echo "Missing #{output}"
+ exit 100
+fi
+
+echo "#{script_name} is finished at $(date +%Y%m%d%H%M%S)" >> "#{jobs_dir}/finished_jobs"
+
+exit $EXITSTATUS

data/lib/cagnut_gatk/functions/templates/count_read.sh

@@ -0,0 +1,23 @@
+#!/bin/bash
+
+cd "#{jobs_dir}/../"
+echo "#{script_name} is starting at $(date +%Y%m%d%H%M%S)" >> "#{jobs_dir}/finished_jobs"
+#{count_reads_params['java'].join("\s")} \\
+  #{count_reads_params['params'].join(" \\\n  ")} \\
+  #{run_local}
+
+EXITSTATUS=$?
+
+if [ ! -s #{output} ]
+then
+  echo "Incomplete output file #{output}"
+  exit 100
+fi
+
+if [ $(stat --printf="%s" #{output}) = 100 ];then
+  echo "Memory Error. Exitting."
+  exit 100
+fi
+echo "#{script_name} is finished at $(date +%Y%m%d%H%M%S)" >> "#{jobs_dir}/finished_jobs"
+
+if [ $EXITSTATUS -ne 0 ];then exit $EXITSTATUS;fi

data/lib/cagnut_gatk/functions/templates/depth_of_coverage.sh

@@ -0,0 +1,19 @@
+#!/bin/bash
+
+cd "#{jobs_dir}/../"
+echo "#{script_name} is starting at $(date +%Y%m%d%H%M%S)" >> "#{jobs_dir}/finished_jobs"
+
+#{depth_of_coverage_params['java'].join("\s")} \\
+  #{depth_of_coverage_params['params'].join(" \\\n  ")} \\
+  #{run_local}
+
+EXITSTATUS=$?
+
+if [ ! -e "#{output}.sample_statistics" ]
+then
+  echo "Missing output: #{output}"
+  exit 100
+fi
+echo "#{script_name} is finished at $(date +%Y%m%d%H%M%S)" >> "#{jobs_dir}/finished_jobs"
+
+exit $EXITSTATUS

data/lib/cagnut_gatk/functions/templates/print_reads.sh

@@ -0,0 +1,25 @@
+#!/bin/bash
+
+cd "#{jobs_dir}/../"
+echo "#{script_name} is starting at $(date +%Y%m%d%H%M%S)" >> "#{jobs_dir}/finished_jobs"
+if [ ! -s "#{bqsr_file}" ]; then
+ echo "Error: missing recalfile #{bqsr_file}"
+ exit 100
+fi
+
+rm core.* 2> /dev/null
+
+#{print_reads_params['java'].join("\s")} \\
+  #{print_reads_params['params'].join(" \\\n  ")} \\
+  #{run_local}
+
+EXITSTATUS=$?
+
+# throw error if < 1024 bytes
+if [ $(stat --printf="%s" "#{output}") -le 1024 ]
+then
+  exit 100
+fi
+echo "#{script_name} is finished at $(date +%Y%m%d%H%M%S)" >> "#{jobs_dir}/finished_jobs"
+
+exit $EXITSTATUS

data/lib/cagnut_gatk/functions/unified_genotyper.rb

@@ -0,0 +1,89 @@
+module CagnutGatk
+  class UnifiedGenotyper
+    extend Forwardable
+
+    def_delegators :'Cagnut::Configuration.base', :sample_name, :jobs_dir, :dodebug,
+                   :ref_fasta, :snpdb, :target, :prefix_name, :java_path
+    def_delegators :'CagnutGatk.config', :unified_genotyper_params
+
+    def initialize opts = {}
+      @order = sprintf '%02i', opts[:order]
+      @input = opts[:input].nil? ? "#{opts[:dirs][:input]}/#{sample_name}_recal.bam" : opts[:input]
+      @output = "#{opts[:dirs][:output]}/#{sample_name}.vcf"
+      @job_name = "#{prefix_name}_snpcal_#{sample_name}"
+    end
+
+    def run previous_job_id = nil
+      puts "Submitting #{sample_name} Jobs: variant (SNPs, INDELs) -call "
+      script_name = generate_script
+      ::Cagnut::JobManage.submit script_name, @job_name, cluster_options(previous_job_id)
+      [@job_name, @output]
+    end
+
+    def cluster_options previous_job_id = nil
+      core_num = 6
+      job_mem1 = "adjustWorkingMem 256M #{core_num}"
+      job_mem2 = "adjustWorkingMem 10G #{core_num}"
+      {
+        previous_job_id: previous_job_id,
+        var_env: [core_num],
+        adjust_memory: ["h_stack=#{job_mem1}", "h_vmem=#{job_mem2}"],
+        parallel_env: [core_num],
+        tools: ['gatk', 'unified_genotyper']
+      }
+    end
+
+    def unified_genotyper_options
+      array = unified_genotyper_params['params'].dup
+      array << "-T UnifiedGenotyper"
+      array << "-R #{ref_fasta}"
+      array << "-I #{@input}"
+      array << "-o #{@output}"
+      array << "-D #{snpdb}" if snpdb
+      array << "-L #{target}" if target
+      array.uniq
+    end
+
+    def modified_java_array
+      array = unified_genotyper_params['java'].dup
+      array.unshift(java_path).uniq
+    end
+
+    def params_combination
+      @params_combination_hash ||= {
+        'java' => modified_java_array,
+        'params' => unified_genotyper_options
+      }
+    end
+
+    def generate_script
+      script_name = "#{@order}_gatk_unified_genotyper"
+      file = File.join jobs_dir, "#{script_name}.sh"
+      File.open(file, 'w') do |f|
+        f.puts <<-BASH.strip_heredoc
+          #!/bin/bash
+
+          cd "#{jobs_dir}/../"
+          echo "#{script_name} is starting at $(date +%Y%m%d%H%M%S)" >> "#{jobs_dir}/finished_jobs"
+          #{params_combination['java'].join("\s")} \\
+            #{params_combination['params'].join(" \\\n            ")} \\
+            #{::Cagnut::JobManage.run_local}
+
+          EXITSTATUS=$?
+
+          if [ ! -s "#{@output}.idx" ]
+          then
+            echo "vcf incomplete!"
+            exit 100;
+          fi
+
+          if [ $EXITSTATUS -ne 0 ];then exit $EXITSTATUS;fi
+          echo "#{script_name} is finished at $(date +%Y%m%d%H%M%S)" >> "#{jobs_dir}/finished_jobs"
+
+        BASH
+      end
+      File.chmod(0700, file)
+      script_name
+    end
+  end
+end

data/lib/cagnut_gatk/functions/variant_eval.rb

@@ -0,0 +1,88 @@
+module CagnutGatk
+  class VariantEval
+    extend Forwardable
+
+    def_delegators :'Cagnut::Configuration.base', :sample_name, :jobs_dir, :java_path,
+                   :ref_fasta, :snpdb, :target, :prefix_name, :dodebug
+    def_delegators :'CagnutGatk.config', :variant_eval_params
+
+    def initialize opts = {}
+      @order = sprintf '%02i', opts[:order]
+      @vcf_dir = opts[:dirs][:output]
+      @input = opts[:input].nil? ? "#{opts[:dirs][:input]}/#{sample_name}_filtered.vcf" : opts[:input]
+      @output = "#{@vcf_dir}/#{sample_name}.eval"
+      @job_name = "#{prefix_name}_snpEval_#{sample_name}"
+    end
+
+    def run previous_job_id = nil
+      return unless snpdb
+      puts "Submitting #{sample_name} Jobs: variant (SNPs, INDELs) -evaluation "
+      script_name = generate_script
+      ::Cagnut::JobManage.submit script_name, @job_name, cluster_options(previous_job_id)
+      @job_name
+    end
+
+    def cluster_options previous_job_id = nil
+      {
+        previous_job_id: previous_job_id,
+        adjust_memory: ['h_stack=256M', 'h_vmem=8G'],
+        tools: ['gatk', 'variant_eval']
+      }
+    end
+
+    def variant_eval_options
+      array = variant_eval_params['params'].dup
+      array << "-T VariantEval"
+      array << "-R #{ref_fasta}"
+      array << "--dbsnp #{snpdb}"
+      array << "-o #{@output}"
+      array << "--eval:$EVALNAME #{@input}"
+      array << "-L #{target}" if target
+      array.uniq
+    end
+
+    def modified_java_array
+      array = variant_eval_params['java'].dup
+      array.unshift(java_path).uniq
+    end
+
+    def params_combination
+      @params_combination_hash ||= {
+        'java' => modified_java_array,
+        'params' => variant_eval_options
+      }
+    end
+
+    def generate_script
+      script_name = "#{@order}_gatk_variant_eval"
+      file = File.join jobs_dir, "#{script_name}.sh"
+      ltag = target.nil? ? '' : "-L #{target}"
+      File.open(file, 'w') do |f|
+        f.puts <<-BASH.strip_heredoc
+          #!/bin/bash
+
+          cd "#{jobs_dir}/../"
+          echo "#{script_name} is starting at $(date +%Y%m%d%H%M%S)" >> "#{jobs_dir}/finished_jobs"
+          EVALNAME=$(basename #{@vcf_dir}/#{sample_name})
+
+          #{params_combination['java'].join("\s")} \\
+            #{params_combination['params'].join(" \\\n            ")} \\
+            #{::Cagnut::JobManage.run_local}
+
+          EXITSTATUS=$?
+
+          if [ ! -s "#{@output}" ]
+          then
+            echo "Missing #{@output}"
+            exit 100
+          fi
+          echo "#{script_name} is finished at $(date +%Y%m%d%H%M%S)" >> "#{jobs_dir}/finished_jobs"
+
+          exit $EXITSTATUS
+        BASH
+      end
+      File.chmod(0700, file)
+      script_name
+    end
+  end
+end