Update Blastdb Pl

# 2) Download and decompress from NCBI into the current directory
update_blastdb.pl \
  --source ncbi \
  --decompress \
  nt

# 3) Download version 4 archives from a cloud mirror
update_blastdb.pl \
  --source aws \
  --blastdb_version 4 \
  swissprot

Recommended Workflow

1. Change into the directory where the database archives or extracted DB should live before running the script.
2. Use --showall pretty or --showall tsv to confirm the exact database names and metadata.
3. Pick --source and --blastdb_version intentionally rather than relying on defaults in production workflows.
4. After download, validate the resulting DB with blastdbcheck before using it in large search jobs.

Guardrails

• This script writes into the current working directory, so run it from a dedicated BLAST DB location.
• --decompress only applies to --source ncbi; it does not give the same behavior for AWS or GCP downloads.
• curl is required for cloud-provider retrieval.
• --quiet suppresses diagnostics and overrides --verbose, so avoid it while troubleshooting.
• --force only forces re-download behavior; it does not validate or repair a damaged extracted database.