NAME
    update_blastdb.pl - Download pre-formatted BLAST databases

SYNOPSIS
    update_blastdb.pl [options] blastdb ...

OPTIONS
    --source
      Location to download BLAST databases from (default: auto-detect closest location).
      Supported values: "ncbi", "aws", or "gcp".

    --decompress
      Downloads, decompresses the archives in the current working directory, and deletes
      the downloaded archive to save disk space, while preserving the archive checksum
      files (default: false). This is only applicable when the download source is "ncbi".

    --showall
      Show all available pre-formatted BLAST databases (default: false). The output of
      this option lists the database names which should be used when requesting downloads
      or updates using this script.

      It accepts the optional arguments: "tsv" and "pretty" to produce tab-separated
      values and a human-readable format respectively. These parameters elicit the display
      of additional metadata if this is available to the program. This metadata is
      displayed in columnar format; the columns represent:

      name, description, size in gigabytes, date of last update (YYYY-MM-DD format).

    --blastdb_version
      Specify which BLAST database version to download (default: 5). Supported values: 4,
      5

    --timeout
      Timeout on connection to NCBI (default: 120 seconds).

    --force
      Force download even if there is a archive already on local directory (default:
      false).

    --verbose
      Increment verbosity level (default: 1). Repeat this option multiple times to
      increase the verbosity level (maximum 2).

    --quiet
      Produce no output (default: false). Overrides the --verbose option.

    --version
      Prints this script's version. Overrides all other options.

    --num_threads
      Sets the number of threads to utilize to perform downloads in parallel when data
      comes from the cloud. On Windows it defaults to 1. On Linux and macos: defaults to
      max(1, (number_of_available_cores/4)) and if set to 0, the script uses all available
      cores on the machine.

    --legacy_exit_code
      Enables exit codes from prior to version 581818, BLAST+ 2.10.0 release, for
      downloads from NCBI only. This option is meant to be used by legacy applications
      that rely on this exit codes: 0 for successful operations that result in no
      downloads, 1 for successful downloads, and 2 for errors.

    --force_ftp
      Forces downloads using the FTP protocol from the NCBI (Linux and Windows only). If
      the location from which to download is not NCBI, this option is ignored.

    --passive
      When using the <force_ftp> option, this flag enables passive FTP, useful when behind
      a firewall or working in the cloud (default: true). To disable passive FTP,
      configure this option as follows: --passive no

DESCRIPTION
    This script will download the pre-formatted BLAST databases requested in the command
    line from the NCBI ftp site.

EXIT CODES
    This script returns 0 on successful operations and non-zero on errors.

DEPENDENCIES
    This script depends on curl for retrieval from cloud service providers.

BUGS
    Please report them to <blast-help@ncbi.nlm.nih.gov>

COPYRIGHT
    See PUBLIC DOMAIN NOTICE included at the top of this script.