tophat_mapping_y.sh

#!/bin/bash


MEM_LIMIT="125G" # it seems each job do not consume 10G to my observation; so set 125G shall be safe, even after increase the cores. 
 
FILE_COUNT=`find ./*_R1_001.fastq.gz | sed 's/_R1_001.fastq.gz$//'| wc -l`
echo "FILE_COUNT=${FILE_COUNT}"

qsub -P $PROJECT -N $JOBNAME -pe omp $NCORE_REQ -l mem_total=${MEM_LIMIT} -l h_rt=${RT_LIMIT} -t 1-${FILE_COUNT} tophat_mapping_y.qsub