INNER CODE UNIT · Shell

working_dir

pirovc/genome_updater · genome_updater.sh:1478

    working_dir=$(mktemp -d -p .) # default
else
    mkdir -p "${working_dir}" #user input
fi
working_dir="$(readlink -m "${working_dir}")/"
files_dir="files/"
export files_dir working_dir dir_structure

default_assembly_summary=${working_dir}assembly_summary.txt
history_file=${working_dir}history.tsv

# set MODE
if [[ "${just_fix}" -eq 1 ]]; then
    MODE="FIX"
elif [[ ! -f "${default_assembly_summary}" ]] || [[ -n "${external_assembly_summary}" ]]; then
    MODE="NEW"
else
    MODE="UPDATE"

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