removed 'old' example

starMapping_multiNode.job

-#!/bin/sh
-#-----------------------------------------------------------------
-# Example SLURM job script to run parallel STAR
-#-----------------------------------------------------------------
-
-#SBATCH -J star_multiNode     			# Job name
-#SBATCH -o slurmOutput/out_multiNode.%j.out    # Specify stdout output file (%j expands to jobId)
-#SBATCH -p nodeshort  	             		# Queue name
-#SBATCH -A zdvhpc               		# Specify allocation to charge against
-#SBATCH --exclude=a[0068,0077,0078]
-
-#SBATCH --ntasks=8				# Total number of tasks
-#SBATCH --ntasks-per-node=8
-#SBATCH -B 4:8:2
-#SBATCH -t 04:59:59              		# Run time (hh:mm:ss) - 1.0 hours
-#SBATCH --cpus-per-task=8
-#SBATCH --hint=multithread
-
-#SBATCH --distribution=block:cyclic
-#SBATCH --exclusive
-
-#SBATCH --mem-per-cpu=1024M
-#SBATCH --mem_bind=verbose
-#SBATCH --verbose
-
-#SBATCH --hint=compute_bound
-
-###############################################################################
-# use ramdisk
-
-##SBATCH --gres=ramdisk:100G 
-#RAMDISK=$JOBDIR/ramdisk
-#cp $1 $RAMDISK/indices.tar.gz
-#cd $RAMDISK
-#tar -zxf indices.tar.gz
-
-###############################################################################
-# load modules
-
-module load bio/STAR/2.5.0a
-module load tools/parallel/20170622
-
-###############################################################################
-# important paths and environment
-
-
-MY_MEM_PER_TASK=$(( $SLURM_CPUS_PER_TASK * $SLURM_MEM_PER_CPU ))
-host=$(hostname -s)
-JOBDIR=/localscratch/$SLURM_JOB_ID
-FS_DIR=/project/zdvhpc/tron_genfusion/star/star_mapping_output/2x600MB_MCF7_INTERN_MK47_CTTGTA_L002/multNodes/${SLURM_JOB_NUM_NODES}_Nodes/$SLURM_JOB_ID
-ALIGN_FS_DIR=/project/zdvhpc/tron_genfusion/star/star_mapping_output/2x600MB_MCF7_INTERN_MK47_CTTGTA_L002/multNodes/${SLURM_JOB_NUM_NODES}_Nodes/$SLURM_JOB_ID/alignments
-LOG_FS_DIR=/project/zdvhpc/tron_genfusion/star/star_mapping_output/2x600MB_MCF7_INTERN_MK47_CTTGTA_L002/multNodes/${SLURM_JOB_NUM_NODES}_Nodes/$SLURM_JOB_ID/logs
-MY_TIME_START=$(date "+%Y%m%d-%H%M%S")
-MY_TASK_FILE=command_list_${SLURM_JOB_ID}.sh
-STAR_INPUT=/project/zdvhpc/tron_genfusion/star/star_input/2x600MB_MCF7_INTERN_MK47_CTTGTA_L002/${SLURM_NTASKS}_tasksPerFastq
-
-###############################################################################
-# working directory and .sh-file storing gnu parallel commands
-
-if [[ ! -d "$FS_DIR" ]]; then
-  echo "make directory $FS_DIR"
-  mkdir $FS_DIR
-else
-  echo "[ERROR] could not make output directory"
-  exit 1
-fi
-
-if [[ ! -d "$LOG_FS_DIR" ]]; then
-  echo "make directory $LOG_FS_DIR"
-  mkdir $LOG_FS_DIR
-else
-  echo "[ERROR] could not make log directory"
-  exit 1
-fi
-
-if [[ ! -d "$ALIGN_FS_DIR" ]]; then
-  echo "make directory $ALIGN_FS_DIR"
-  mkdir $ALIGN_FS_DIR
-else
-  echo "[ERROR] could not make align directory"
-  exit 1
-fi
-
-if [[ -f "$MY_TASK_FILE" ]]; then
-  rm $MY_TASK_FILE
-fi
-
-###############################################################################
-# read input from command line
-
-if [ $# = 0 ]
-then
-	echo "[INFO] no input parameters, must enter genome directory"
-	exit 1
-else
-	echo "[INFO] received input parameters"
-	for i in "$@"
-	do
-	echo "input_parameter: $i"
-	case $i in
-	    -e=*|--extension=*)
-	    EXTENSION="${i#*=}"
-	    shift # past argument=value
-	    ;;
-	    -s=*|--searchpath=*)
-	    SEARCHPATH="${i#*=}"
-	    shift # past argument=value
-	    ;;
-	    -l=*|--lib=*)
-	    LIBPATH="${i#*=}"
-	    shift # past argument=value
-	    ;;
-	    --default)
-	    DEFAULT=YES
-	    shift # past argument with no value
-	    ;;
-	    *)
-		  # unknown option
-	    ;;
-	esac
-	done
-	MY_GENOME_DIR=$1
-#	MY_READ_L=$2
-#	MY_READ_R=$3
-fi
-
-###############################################################################
-# print configuration
-
-echo "[INFO] print environment"
-printenv
-echo "[INFO] running on $host"
-echo "[INFO] assign $SLURM_JOB_NODELIST to current job $SLURM_JOB_ID"
-echo "[INFO] assign $SLURM_CPUS_PER_TASK cpus per task.."
-echo "[INFO] alloce ${MY_MEM_PER_TASK} memory per task"
-echo "[INFO] output in job directory: $JOBDIR"
-echo "[INFO] time run script start: " $MY_TIME_START
-
-###############################################################################
-# load genome into RAM and exit
-
-srun --exclusive -N $SLURM_JOB_NUM_NODES -n $SLURM_JOB_NUM_NODES --ntasks-per-node=1 --cpus-per-task=1 --mem=$(($SLURM_CPUS_ON_NODE * $SLURM_MEM_PER_CPU)) --mem_bind=verbose --cpu_bind=verbose STAR --runThreadN 1 --outFileNamePrefix ${JOBDIR}/${SLURM_JOB_ID}- --genomeLoad LoadAndExit --genomeDir ${MY_GENOME_DIR}
-sleep 2s
-
-###############################################################################
-# write STAR commands to file and call them with gnu parallel
-
-dir_counter=0
-for directory in $STAR_INPUT/*; do 
-  echo "$directory"
-  my_counter=0	
-  for filename in $(find ${directory}/*.fastq 2> /dev/null); do
-    my_counter=$(($my_counter + 1))
-    if [ $my_counter -lt 2 ];
-      then
-	MY_READ_L=$filename
-      else
-	MY_READ_R=$filename
-    fi
-    echo $filename
-  done
-  echo $MY_READ_L
-  echo $MY_READ_R
-  echo "srun -N1 -n1 --exclusive --cpus-per-task=$SLURM_CPUS_PER_TASK --mem_bind=verbose --mem=$MY_MEM_PER_TASK --cpu_bind=verbose STAR --runThreadN $SLURM_CPUS_PER_TASK --genomeLoad LoadAndKeep --genomeDir ${MY_GENOME_DIR} --readFilesIn ${MY_READ_L} ${MY_READ_R} --outFileNamePrefix ${JOBDIR}/${SLURM_JOB_ID}-$(( ($dir_counter%${SLURM_NTASKS_PER_NODE}) + 1 ))-" >> $MY_TASK_FILE
-  dir_counter=$(($dir_counter + 1))
-done
-echo "  [INFO] printing ${MY_TASK_FILE}"
-cat $MY_TASK_FILE
-star_parallel="parallel --delay .5 -j $SLURM_NTASKS -P $SLURM_NTASKS --joblog parallelMapping.log --workdir $PWD --verbose --progress"
-$star_parallel < $MY_TASK_FILE
-rm $MY_TASK_FILE
-
-###############################################################################
-# remove genome from RAM
-
-srun --exclusive -N $SLURM_JOB_NUM_NODES -n $SLURM_JOB_NUM_NODES --ntasks-per-node=1 --cpus-per-task=1 --mem_bind=verbose --mem=$(($SLURM_CPUS_ON_NODE * $SLURM_MEM_PER_CPU)) --cpu_bind=verbose STAR --runThreadN 1 --outFileNamePrefix ${JOBDIR}/${SLURM_JOB_ID}- --genomeLoad Remove --genomeDir ${MY_GENOME_DIR}
-
-###############################################################################
-# collect output data and copy to STAR-home
-
-#sgather ${JOBDIR}/${SLURM_JOB_ID}-Aligned.out.sam ${SLURM_JOB_ID}-Aligned.out.sam 
-for infix in `seq 1 $SLURM_NTASKS_PER_NODE`; do
-  sgather ${JOBDIR}/${SLURM_JOB_ID}-${infix}-Log.final.out ${LOG_FS_DIR}/${SLURM_JOB_ID}-${infix}-Log.final.out
-  sgather ${JOBDIR}/${SLURM_JOB_ID}-${infix}-Aligned.out.sam ${ALIGN_FS_DIR}/${SLURM_JOB_ID}-${infix}-Aligned.out.sam
-done
-#sgather ${JOBDIR}/${SLURM_JOB_ID}-Log.final.out ${FS_DIR}/${SLURM_JOB_ID}-Log.final.out
-#sgather ${JOBDIR}/${SLURM_JOB_ID}-Log.out ${SLURM_JOB_ID}-Log.out 
-#sgather ${JOBDIR}/${SLURM_JOB_ID}-Log.progress.out ${SLURM_JOB_ID}-Log.progress.out
-#sgather ${JOBDIR}/${SLURM_JOB_ID}-SJ.out.tab ${SLURM_JOB_ID}-SJ.out.tab 
-
-###############################################################################
-# success!
-
-echo "[INFO] time run script end: " $(date "+%Y%m%d-%H%M%S")
-echo "[INFO] finished job!"
-exit 0
-