update.sh

#! /bin/bash

#PBS -l walltime=00:10:00
#PBS -l mem=100Mb
#PBS -N update_orenza
#PBS -l ncpus=1
#PBS -q common
#PBS -j oe

set -x

WORKDIR=$(dirname $(readlink -f "$0"))

CONFIG="$WORKDIR/config.yaml"
function query(){
    python3 -c 'import yaml,sys;config=yaml.safe_load(sys.stdin);print(config["download"].get("'$1'",""))' < $CONFIG
}

CMD="/usr/bin/python3 $WORKDIR/update.py"
QSUB_OPTIONS="-V -S /bin/sh -l walltime=48:00:00 -l ncpus=1 -q common -j oe -N update_orenza -l mem=2Gb"
QSUB_OPTIONS_PDB="-V -S /bin/sh -l walltime=48:00:00 -l ncpus=4 -q common -j oe -N update_orenza -l mem=64Gb"
QSUB_OPTIONS_POP="-V -S /bin/sh -l walltime=48:00:00 -l ncpus=1 -q common -j oe -N update_orenza -l mem=12Gb"
JOBIDS=()

RES=$(query "explorenz")
if [[ $RES == "True" || $RES == "true" ]]; then 
    JOBIDS+=($(qsub $QSUB_OPTIONS -- $CMD "dl_explorenz"))
fi
RES=$(query "sprot")
if [[ $RES == "True" || $RES == "true" ]]; then 
    JOBIDS+=($(qsub $QSUB_OPTIONS -- $CMD "dl_sprot"))
fi
RES=$(query "trembl")
if [[ $RES == "True" || $RES == "true" ]]; then 
    JOBIDS+=($(qsub $QSUB_OPTIONS -- $CMD "dl_trembl"))
fi
RES=$(query "kegg")
if [[ $RES == "True" || $RES == "true" ]]; then 
    JOBIDS+=($(qsub $QSUB_OPTIONS -- $CMD "dl_kegg"))
fi
RES=$(query "brenda")
if [[ $RES == "True" || $RES == "true" ]]; then 
    JOBIDS+=($(qsub $QSUB_OPTIONS -- $CMD "dl_brenda"))
fi
RES=$(query "pdb")
if [[ $RES == "True" || $RES == "true" ]]; then 
    JOBIDS+=($(qsub $QSUB_OPTIONS_PDB -- $CMD "dl_pdb"))
fi

if [[ ${#JOBIDS[@]} -gt 0 ]]; then
    qsub $QSUB_OPTIONS_POP -W depend=afterok:$(IFS=: ; echo "${JOBIDS[*]}") -- $CMD "populate"
fi

OUTDIR=$(python3 -c 'import yaml,sys;config=yaml.safe_load(sys.stdin);print(config["output"])' < $CONFIG)
mkdir -p $OUTDIR
echo "Update start: $(date +%F)" > $OUTDIR/last_update.txt