# Update Blastdb Pl

> Use when downloading or updating pre-formatted BLAST databases from NCBI or cloud providers (AWS, GCP)

- Skill: `vimalinx/update-blastdb-pl` (Agent Skill, multi-file: 2 files)
- Install (CLI): `npx skillmds add vimalinx/update-blastdb-pl`
- Raw SKILL.md: https://api.skillmd.com/api/skills/vimalinx/update-blastdb-pl/raw
- Safety review: pending
- Works with: Claude Code, Claude.ai, OpenAI Codex
- Category: DevOps & Infra
- Author: vimalinx (https://skillmd.com/u/vimalinx)
- Updated: 2026-09-09
- Page: https://skillmd.com/skills/vimalinx/update-blastdb-pl

---


# 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

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

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

```bash
# 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.