projects/radseq/novogene/domg.sh

   1 #!/bin/bash
   2 #$ -v PERL5LIB,PATH,PYTHONPATH,LD_LIBRARY_PATH
   3 #$ -cwd -r y -l vf=1g,p=1
   4 #$ -e /dev/null -o /dev/null
   5 #$ -S /bin/bash -t 1-19
   6
   7 MY_HOST=`/bin/hostname`
   8 MY_DATE=`/bin/date`
   9 env
  10 echo "================================================================"
  11 echo JOB_NAME=$JOB_NAME
  12 echo JOB_ID=$JOB_ID
  13 echo SGE_TASK_ID=$SGE_TASK_ID
  14 echo SGE_TASK_FIRST=$SGE_TASK_FIRST
  15 echo SGE_TASK_LAST=$SGE_TASK_LAST
  16 echo NSLOTS=$NSLOTS
  17 echo QUEUE=$QUEUE
  18 echo SGE_CWD_PATH=$SGE_CWD_PATH
  19 echo PATH=$PATH
  20 echo SGE_STDIN_PATH=$SGE_STDIN_PATH
  21 echo SGE_STDOUT_PATH=$SGE_STDOUT_PATH
  22 echo SGE_STDERR_PATH=$SGE_STDERR_PATH
  23 echo SGE_O_HOST=$SGE_O_HOST
  24 echo SGE_O_PATH=$SGE_O_PATH
  25 echo "================================================================"
  26
  27 echo "Running job JOB_NAME=$JOB_NAME task SGE_TASK_ID=$SGE_TASK_ID on $MY_HOST at $MY_DATE"
  28
  29 SEEDFILE=ng/mg.lst
  30 SEED=$(/bin/sed -n -e "${SGE_TASK_ID} p" $SEEDFILE)
  31 PATH=$(/bin/sed -n -e "${SGE_TASK_ID} p" $SEEDFILE|/bin/awk -F"\t" '{print $1}')
  32 MAIN=$(/bin/sed -n -e "${SGE_TASK_ID} p" $SEEDFILE|/bin/awk -F"\t" '{print $2}')
  33 TYPE=$(/bin/sed -n -e "${SGE_TASK_ID} p" $SEEDFILE|/bin/awk -F"\t" '{print $3}')
  34
  35 echo "Running job JOB_NAME=$JOB_NAME task SGE_TASK_ID=$SGE_TASK_ID on $MY_HOST at $MY_DATE" >$PATH/$MAIN.bamlog
  36
  37 echo $PATH/*$MAIN*.sort.bam >>$PATH/$MAIN.bamlog
  38 echo /usr/local/bin/samtools merge $PATH/${TYPE}_$MAIN.merge.bam $PATH/*$MAIN*.sort.bam >>$PATH/$MAIN.bamlog
  39 /bin/date >> $PATH/$MAIN.bamlog
  40 echo /usr/local/bin/samtools rmdup $PATH/${TYPE}_$MAIN.merge.bam $PATH/${TYPE}_$MAIN.rmdup.bam >>$PATH/$MAIN.bamlog
  41 /bin/date >> $PATH/$MAIN.bamlog
  42