Source

DunnHowisonZapata2013 / 03-assemble-Nanomia.sh

#!/bin/sh
#SBATCH -t 48:00:00
#SBATCH -c 16
#SBATCH --mem=60g
#SBATCH -C e5-2600

ID=SRX288430

export BIOLITE_RESOURCES="database=$PWD/biolite.sqlite,agalma_database=$PWD/agalma.sqlite,outdir=$PWD/analyses,threads=16,memory=60g"

set -e

mkdir -p scratch
cd scratch

module load agalma/0.3.3

agalma sanitize --id $ID
agalma insert_size --id $ID --previous $ID
agalma remove_rrna --id $ID --previous $ID
agalma assemble --id $ID --previous $ID --skip oases_merge
agalma postassemble --id $ID --previous $ID
agalma load --id $ID --previous $ID