• Simple Linux Utility for Resource Management
  
• Manages allocation of computing resources
• Tries to ensure fair distribution of resources
• By default, everyone is allowed 20 CPUs total

#!/bin/bash
#SBATCH -p batch
#SBATCH -J blastn
#SBATCH -n 4

export BLASTDB=/export/data/bio/ncbi/blast/db

module load blast/2.2.28+

blastn -query ~/data/sequences/drosoph_14_sequences.seq -db nt -num_threads 4

[aorth@hpc: ~]$ sbatch blastn.sh

#!/bin/bash
POPULATIONS="1 2 3 4"
REPS="1 2 3 4 5"
STRUCTURE="/export/apps/structure/2.3.3/bin/structure"

for rep in $REPS
do
    for pop in $POPULATIONS
    do  
        sbatch <<BATCH_SCRIPT
#!/bin/bash
#SBATCH -n 1
#SBATCH -p batch

$STRUCTURE -e extraparams.txt -m mainparams.txt -K $pop -i pops_kenya.txt -o pops_kenya_K${pop}_rep${rep}.txt
BATCH_SCRIPT

    done
done

[aorth@hpc: ~]$ ./structure_batch.sh