prepare_copycat

#!/bin/bash

progname=prepare_copycat

function usage () {
    cat <<EOF
Usage: $progname -c code
$progname -h for help
EOF
    exit 0
}


function guide () {
    cat <<EOF
Usage: $progname [-d] [-j threads]  -c code  -f Dfilename
[-h] help displays this help menu
-c code *required field: a code value (can mix letters and numbers) so users can revisit their data later,
        this becomes the run directory inside user_data/
        must match the filename used next in run_copycat

EOF
    exit 0
}
#-f Dfilename *required field: a name for the file a user uploaded from the web app
#        must match the filename used next in run_copycat


code=0 # becomes the run directory inside user_data
Dfilename=D.txt
outdir=user_data/$code

while getopts ":hc:" opt; do
  case $opt in
    h)
      guide;;
    c )
        code=$OPTARG
        if [ ! -f user_uploads/$code ];then
            echo "No such analysis--no uploaded file found"
            exit 4
        fi
        outdir=user_data/$code
        echo "-c: code=$code" >&2;;
        
    #f )
    #    Dfilename=$OPTARG
    #    echo "-f: filename of input data: $Dfilename" >&2;;
    \?) usage ;;
  esac
done

if [ ! -d $outdir ]; then
    mkdir $outdir
    if [ $? -ne 0 ] ; then
        echo "Error: could not create directory. Check permissions on user_data/"
    else
        echo "success"
    fi
fi

echo Run directory:  $outdir

D=$outdir/$Dfilename

######################## change this to move the user's file into their run directory ###############################

cp user_uploads/$code $D
#####################################################################################################################
touch $outdir/progress.txt


python -c "import deconvolve; deconvolve.check_file('$D','$outdir')"


echo finished prepare_copycat