INNER CODE UNIT · Shell

local_dir

pirovc/genome_updater · genome_updater.sh:31

local_dir=${local_dir:-}
if [[ -n "${local_dir}" ]]; then
    # set local dir with absulute path and "file://"
    local_dir="file://$(cd "${local_dir}" && pwd)"
fi
# Alternatives: ftp://ftp.ncbi.nih.gov/, https://ftp.ncbi.nih.gov/
ncbi_base_url=${ncbi_base_url:-ftp://ftp.ncbi.nlm.nih.gov/}
# Alternatives: https://data.ace.uq.edu.au/public/gtdb/data/releases/, https://data.gtdb.ecogenomic.org/releases/
gtdb_base_url=${gtdb_base_url:-https://data.gtdb.aau.ecogenomic.org/releases/}
new_taxdump_file=${new_taxdump_file:-}
retries=${retries:-3}
timeout=${timeout:-120}
export retries timeout ncbi_base_url gtdb_base_url new_taxdump_file local_dir

# GTDB versions
declare -A gtdb_bac
declare -A gtdb_ar
gtdb_bac["80"]="${gtdb_base_url}release80/80.0/bac_taxonomy_r80.tsv"

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