template.pbs.j2

#!/bin/bash
#PBS -N AJmodel{{ MODEL }}
#PBS -W group_list=mfh
#PBS -q {{ QUE }}
#PBS -J {{ JNUM }}
#PBS -l cput=60:00:00
#PBS -l walltime=60:00:00
{% if JOBTYPE | default(False) -%}
#PBS -l select={{ NODE }}:ncpus={{ CORE }}:mem={{ MEM }}gb:pcmem={{ MEM }}gb
#PBS -l jobtype={{ JOBTYPE }}
{% else -%}
#PBS -l select={{ NODE }}:ncpus={{ CORE }}:mem={{ MEM }}gb
{% endif -%}
#PBS -m abe 
#PBS -M agladstein@email.arizona.edu
#PBS -l place=pack:shared
#PBS -j oe

module load {{ PYTHONMOD }}

cd $PBS_O_WORKDIR
echo PBS_ARRAY_INDEX=$PBS_ARRAY_INDEX
NOW=$(date +%m%d%y%s)
ID=$NOW"_"$PBS_ARRAY_INDEX

PBS_ID=$(echo ${PBS_JOBID} | cut -d '[' -f1)
SIM=sim_${ID}_values.txt
RESULTS=ms_output_${ID}.summary
BUCKET_OUT_PATH={{ OUT_PATH }}/${PBS_ID}
BUCKET_OE_PATH=${PBS_O_WORKDIR}/outerror/${PBS_ID}

mkdir -p ${BUCKET_OUT_PATH}
mkdir -p ${BUCKET_OE_PATH}

#PBS -o ${BUCKET_OE_PATH}/AJmodel{{ MODEL }}.o${PBS_ID}.$PBS_ARRAY_INDEX
##PBS -e ${BUCKET_OE_PATH}/AJmodel{{ MODEL }}.e${PBS_ID}.$PBS_ARRAY_INDEX

{{ PYTHONENV }} run_sims_AJmodel{{ MODEL }}_chr1_all.py $ID ftDNA_hg18_auto_all_uniqSNPS_rmbadsites_pruned_chr1.bed full 0 prior 0 ${BUCKET_OUT_PATH}>& /dev/null
rm ${BUCKET_OUT_PATH}/sim_data_AJ_M{{ MODEL }}/macs_asc_${ID}_chr1.ped
rm ${BUCKET_OUT_PATH}/sim_data_AJ_M{{ MODEL }}/macs_asc_${ID}_chr1.map
rm ${BUCKET_OUT_PATH}/germline_out_AJ_M{{ MODEL }}/*${ID}*

echo ./drive_rsync_rm.sh {{ MODEL }} ${BUCKET_OUT_PATH} ${SIM} ${RESULTS} ${PBS_ID}
./drive_rsync_rm.sh {{ MODEL }} ${BUCKET_OUT_PATH} ${SIM} ${RESULTS} ${PBS_ID}