run-postvqsr-pipeline-template.sh

#!/bin/bash

BASE=/gscmnt/gc2802/halllab/idas/laboratory/yaps2-cadd-vep-test

VIRTUALENV=${BASE}/test-venv
source ${VIRTUALENV}/bin/activate

# see confluence
export BMETRICA_DSN="mysql://USER:PASSWORD@hostname:port/database"

function log {
    local timestamp=$(date +"%Y-%m-%d %T")
    echo "---> [ ${timestamp} ] $@" >&2
}

function create_dir {
    local dir=$1
    if [ ! -d "$dir" ]; then
        log "Creating directory: $dir"
        mkdir -p "$dir"
    fi
}

function lsf_cmd {
    local prj_name=$1 
    local workspace=$2
    local input_vcfs=$3
    local database=$4
    local master_lsf_log=$5

    local yaps_cmd="yaps2 postvqsr "
    yaps_cmd+="--job-db=${database} "
    yaps_cmd+="--workspace=${workspace} "
    yaps_cmd+="--input-vcfs=${input_vcfs} "
    yaps_cmd+="--project-name=${prj_name} "
    yaps_cmd+="--drm=lsf "
    yaps_cmd+="--task-flush "
    yaps_cmd+="--queue='ccdg' "
#    yaps_cmd+="--skip-confirm "
#    yaps_cmd+="--docker"

    local bsub_cmd="bsub "
    bsub_cmd+="-J ${prj_name}-master "
    bsub_cmd+="-u [email protected] -N "
    bsub_cmd+="-q long "
    bsub_cmd+="-M 8000000 "
    bsub_cmd+="-R 'select[mem>8000 && ncpus>8]' "
    bsub_cmd+="-oo ${master_lsf_log} "
    bsub_cmd+="'${yaps_cmd}'"

    echo ${bsub_cmd}
}

function cleanall {
    local workspace=$1
    local database=$2
    if [ -e ${workspace} ]; then
        log "Nuking out old '${workspace}' directory"
        rm -rf ${workspace}
    fi

    log "Nuking out the old database: '${database}'"
    rm -rfv ${database}
}

function main {
    local prj_name="test-vep-cadd"
    local workspace=${BASE}/data/derived/post-vqsr
    local database=/gscuser/idas/yaps2/test-vep-cadd.db
    local input_vcfs=${BASE}/data/derived/1-create-test-postvqsr-input-data-file/test-input.dat
    local master_lsf_log="${BASE}/logs/${prj_name}.%J.log"

#    cleanall ${workspace} ${database}
    create_dir ${workspace}
    local cmd=$(lsf_cmd ${prj_name} ${workspace} ${input_vcfs} ${database} ${master_lsf_log})
    log "${cmd}"
    eval "${cmd}"
}

main ;