Getting it into your agent
There is no command for this one: it runs only inside a plugin, and the catalogue could not identify which plugin ships it. The source is linked below.
Wrote this? Show the measurements
A badge with what this costs and how it scanned, read live from this page, so it follows the numbers instead of freezing them. Markdown for a README, HTML for a documentation site or a project page.
[](https://agentmods.dev/skills/openscientist-io/openscientist/jgi-lakehouse)<a href="https://agentmods.dev/skills/openscientist-io/openscientist/jgi-lakehouse"><img src="https://agentmods.dev/badge/skills/openscientist-io/openscientist/jgi-lakehouse/github.svg" alt="Measured on agentmods" height="20"></a>Or the 80×15 button, for a site that already has a row of RSS and ATOM ones. Only the verdict fits; the numbers stay here.
<a href="https://agentmods.dev/skills/openscientist-io/openscientist/jgi-lakehouse"><img src="https://agentmods.dev/badge/skills/openscientist-io/openscientist/jgi-lakehouse.svg" alt="Reviewed on agentmods" width="80" height="20"></a>What it costs to keep this loaded
Counted locally with the o200k_base tokenizer, which is exact for GPT models; Claude uses its own tokenizer and its counts differ. Treat this as one consistent yardstick across the catalogue rather than a bill. Prices are per million input tokens.
| Model | Per session | Once invoked |
|---|---|---|
| Fable 5.1 | $0.00088 | $0.00939 |
| Opus 5 | $0.00044 | $0.00469 |
| Sonnet 5 | $0.00018 | $0.00188 |
| Haiku 4.5 | $0.00009 | $0.00094 |
Grade A, and why
jgi-lakehouse scanned grade A with 0 findings against 26 rules in 11 categories — prompt injection, anti-refusal, data exfiltration, privilege escalation, supply chain, agent snooping, system-prompt leakage, SSRF and excessive agency — measured 10d ago.
A static scan of the body, not an audit. Every finding is printed with the line that produced it so you can judge whether it matters here. A mod is markdown that instructs an agent; that is exactly why what it instructs is worth reading.
Nothing flagged
None of the 26 patterns this scan looks for appear in this file: no shell pipes, no recursive deletes, no credential paths, no hidden text, no instruction-override or anti-refusal phrasing, no agent-config snooping. That is not a guarantee, it is the absence of the things that are checkable.
How it starts
The opening of the file, as written. The whole thing — 107 lines — stays where its author put it; the contents beside it link to each section on GitHub.
JGI Lakehouse Query
Query the JGI Dremio Lakehouse via CLI.
Setup
pip install linkml-store[dremio]
export DREMIO_USER="your_username"
export DREMIO_PASSWORD="your_password"
Connection
# Base connection (no schema filter)
DB="dremio-rest://lakehouse.jgi.lbl.gov"
# GOLD database
GOLD="dremio-rest://lakehouse.jgi.lbl.gov?schema=gold-db-2 postgresql.gold"
# IMG Core database
IMG="dremio-rest://lakehouse.jgi.lbl.gov?schema=img-db-2 postgresql.img_core_v400"
SQL Queries
Direct SQL via --sql flag:
# Query GOLD studies
linkml-store -d "$DB" query --sql 'SELECT * FROM "gold-db-2 postgresql".gold.study LIMIT 10'
# Count by ecosystem
linkml-store -d "$DB" query --sql 'SELECT ecosystem, COUNT(*) as cnt FROM "gold-db-2 postgresql".gold.study GROUP BY ecosystem ORDER BY cnt DESC'
# Join tables
linkml-store -d "$DB" query --sql 'SELECT s.study_name, p.project_name FROM "gold-db-2 postgresql".gold.study s JOIN "gold-db-2 postgresql".gold.project p ON s.study_id = p.study_id LIMIT 10'
# Output formats
linkml-store -d "$DB" query --sql '...' -O json
linkml-store -d "$DB" query --sql '...' -O csv
linkml-store -d "$DB" query --sql '...' -O yaml
Collection Queries
When schema is set, use collection-based queries:
# List tables
linkml-store -d "$GOLD" list-collections
# Query collection
linkml-store -d "$GOLD" -c study query --limit 10
# With filter
linkml-store -d "$GOLD" -c study query -w "ecosystem=Host-associated" --limit 20
# Describe table
linkml-store -d "$GOLD" -c study describe
Schema Export
# Export LinkML schema with FK relationships
linkml-store -d "$GOLD" schema -O yaml -o gold.linkml.yaml
Key Databases
| Schema Path | Tables | Description |
|---|---|---|
"gold-db-2 postgresql".gold |
42 | GOLD - genome project metadata |
"img-db-2 postgresql".img_core_v400 |
244 | IMG Core - genes, taxa, annotations |
"img-db-2 postgresql".img_ext |
84 | IMG Extended data |
"img-db-2 postgresql".img_sat_v450 |
141 | IMG Satellite/experimental |
What ships with it
1 file beside SKILL.md in the same directory: the scripts, references and assets a skill reads on demand. Not counted in the per-session cost; read them before you install if any of them is executable.
What this file has done since we first saw it
Hashed on every crawl. A supply-chain change to an agent config is a question of when, not whether, so the history is kept rather than the latest state alone.
- 10d ago First seen · 107 lines · 88 tokens per session scan A fdc59582eeb9
jgi-lakehouse is a skill published in the GitHub repository openscientist-io/openscientist (49 stars, last pushed yesterday), licensed Apache-2.0. It adds 88 tokens to every session and 939 once invoked, about $0.0004 per session on Opus 5. A static security scan graded it A with 0 findings. No closer match exists in the catalogue, so it is treated as the original; first seen 2026-08-30.
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