#!/bin/bash
#$ -l arch=linux-x64
#$ -l h_rt=48:0:0
#$ -l mem_free=24G
#$ -S /bin/bash
#$ -cwd
#$ -j y
#$ -r y

export TMPDIR="/scrapp/kirsty.jamieson/tmp/"
export PATH="/netapp/home/kirsty.jamieson/miniconda3/bin:$PATH"
LIB=/scrapp/kirsty.jamieson/atac-seq-pipeline

source activate encode-atac-seq-pipeline
INPUT=${LIB}/examples/local/induced_nodupbam.json
java -jar -Dconfig.file=${LIB}/backends/backend.conf ${LIB}/cromwell-34.jar run atac.wdl -i ${INPUT}