EArun

#!/usr/bin/env bash
# sva::ComBat_seq is not available in R/3.5.1

if [[ -n "$1" ]]; then
    src="$(dirname $0)/src"
    if [[ ! -f "$src/.env" ]]; then
      echo "EArun: Please run ./install to setup necessary env variables"
      exit
    fi

    env -i config=$1 src="$src" bash -c 'source $src/.env;eval $condaEnv;Rscript $src/DEanalysis.R $src/ $config 2>&1 | tee -a $(dirname $config)/EArun.$(date +%Y%m%d).log'

else
    echo "=============== EArun path/to/config/file"
    echo "This function is used to process the bulk RNAseq data and produce the QuickOmics R object."
    exePath=$(dirname $0)
    echo "An example config file can be found: $exePath/example/config.yml"
    echo "'EAinit' can be used to create a config file for a RNAseq project downloaded from DNAnexus"
    echo "==============="
    exit 0
fi