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alanorth/ray-mpi.sh

Created Sep 2, 2014
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SLURM batch script to run Ray assembler with MPI on paired-end MiSeq reads.
#!/bin/env bash
#SBATCH -p batch
# will use 15 CPUs
#SBATCH -n 15
# will use 2-3 different nodes
#SBATCH --nodes=2-3
#SBATCH -J ray
module load ray/2.3.1
readonly DATADIR=~/data/bfusca
readonly OUTDIR=~/data/bfusca/ray-aug31-2
# mpirun gets the number of processors from SLURM
mpirun Ray -k 27 -p ${DATADIR}/1_S1_L001_R1_001-qc.fastq ${DATADIR}/1_S1_L001_R2_001-qc.fastq -o ${OUTDIR}
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