update-blastdb-pl

name	update-blastdb-pl
description	Use when downloading or updating pre-formatted BLAST databases from NCBI or cloud providers (AWS, GCP)
disable-model-invocation	true
user-invocable	true

update-blastdb-pl

Quick Start

• Command: update_blastdb.pl [options] <blastdb> ...
• Local executable: /home/vimalinx/miniforge3/envs/bio/bin/update_blastdb.pl
• Full reference: See references/help.md

When To Use This Tool

• Download official pre-formatted BLAST databases instead of building your own with makeblastdb.
• Refresh local copies of databases such as nt, nr, or taxonomic subsets.
• Discover which prebuilt databases NCBI exposes with --showall.
• Pull from ncbi, aws, or gcp depending on your environment and bandwidth path.

Common Patterns

# 1) List available databases with human-readable metadata
update_blastdb.pl --showall pretty

# 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.