INNER CODE UNIT · Shell
ncbi_base_url
pirovc/genome_updater · genome_updater.sh:37
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"
gtdb_bac["83"]="${gtdb_base_url}release83/83.0/bac_taxonomy_r83.tsv"
gtdb_bac["86.2"]="${gtdb_base_url}release86/86.2/bac120_taxonomy_r86.2.tsv"
gtdb_bac["89"]="${gtdb_base_url}release89/89.0/bac120_taxonomy_r89.tsv"
gtdb_bac["95"]="${gtdb_base_url}release95/95.0/bac120_taxonomy_r95.tsv.gz"
gtdb_bac["202"]="${gtdb_base_url}release202/202.0/bac120_taxonomy_r202.tsv.gz"
gtdb_bac["207"]="${gtdb_base_url}release207/207.0/bac120_taxonomy_r207.tsv.gz"