#!/bin/bash
#SBATCH -t 4:00:00
#SBATCH --mem=128g
#SBATCH --nodes=1 --ntasks-per-node=1
#SBATCH --export=NONE
#SBATCH --mail-user=alex_labossiere@uri.edu
#SBATCH --mail-type=BEGIN,END,FAIL

module load Bowtie2/2.3.5.1-GCC-8.3.0

#enter pathway to genome to make index of
RAW=/data/mramseylab/genomes/cmat_atcc14266/Cmat_atcc14266.fasta
OUTPUT=/data/mramseylab/genomes/bowtie_index/cmat


bowtie2-build $RAW $OUTPUT
