INNER CODE UNIT · Shell
timeout
pirovc/genome_updater · genome_updater.sh:42
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"
gtdb_bac["214.1"]="${gtdb_base_url}release214/214.1/bac120_taxonomy_r214.tsv.gz"
gtdb_bac["220"]="${gtdb_base_url}release220/220.0/bac120_taxonomy_r220.tsv.gz"
gtdb_bac["226"]="${gtdb_base_url}release226/226.0/bac120_taxonomy_r226.tsv.gz"
gtdb_bac["232"]="${gtdb_base_url}release232/232.0/bac120_taxonomy_r232.tsv.gz"
gtdb_ar["80"]=""