Clickhouse Logs Queries
supabase/supabase
Write, review, and migrate Supabase logs queries against the ClickHouse-backed logs table (the logs.all.otel analytics endpoint).
Queries JGI Lakehouse (Dremio) for genomics metadata from GOLD, IMG, Mycocosm, Phytozome.
Install Jgi Lakehouse
$ npx skills add BioTender-max/awesome-bio-agent-skills --skill jgi-lakehouse -a claude-codeProject install by default; add -g for ~/.claude/skills/.
$ gh skill install BioTender-max/awesome-bio-agent-skills jgi-lakehouse --agent claude-codeProject scope by default; add --scope user for a personal install. Needs GitHub CLI 2.90.0 or later (public preview).
$ git clone --depth 1 https://github.com/BioTender-max/awesome-bio-agent-skills.git skills-src && mkdir -p .claude/skills && cp -r skills-src/skills/omics/jgi-lakehouse .claude/skills/jgi-lakehouse && rm -rf skills-srcUse ~/.claude/skills/ instead of .claude/skills for a personal install. The folder must contain SKILL.md.
Claude Code skills documentation · loads skills from .claude/skills/
Install the "jgi-lakehouse" agent skill from https://github.com/BioTender-max/awesome-bio-agent-skills/tree/main/skills/omics/jgi-lakehouse into .claude/skills/jgi-lakehouse/ in this project. Copy the whole folder (SKILL.md and every file beside it), keep the folder name "jgi-lakehouse", then confirm the skill loads.Claude Code copies the folder itself, the same result as the manual copy. Check what it changed before you commit it.
$skill-installer install https://github.com/BioTender-max/awesome-bio-agent-skills/tree/main/skills/omics/jgi-lakehouseType this inside Codex. $skill-installer <name> installs a curated skill from openai/skills. The installer writes to $CODEX_HOME/skills (default ~/.codex/skills). Restart Codex if the skill does not show up.
$ npx skills add BioTender-max/awesome-bio-agent-skills --skill jgi-lakehouse -a codexProject install goes to .agents/skills/; add -g for ~/.codex/skills/.
$ gh skill install BioTender-max/awesome-bio-agent-skills jgi-lakehouse --agent codexProject scope by default (.agents/skills/); add --scope user for a personal install.
$ git clone --depth 1 https://github.com/BioTender-max/awesome-bio-agent-skills.git skills-src && mkdir -p .agents/skills && cp -r skills-src/skills/omics/jgi-lakehouse .agents/skills/jgi-lakehouse && rm -rf skills-srcUse ~/.agents/skills/ instead of .agents/skills for a personal install.
Codex skills documentation · loads skills from .agents/skills/
Install the "jgi-lakehouse" agent skill from https://github.com/BioTender-max/awesome-bio-agent-skills/tree/main/skills/omics/jgi-lakehouse into .agents/skills/jgi-lakehouse/ in this project. Copy the whole folder (SKILL.md and every file beside it), keep the folder name "jgi-lakehouse", then confirm the skill loads.Codex copies the folder itself, the same result as the manual copy. Check what it changed before you commit it.
$ npx skills add BioTender-max/awesome-bio-agent-skills --skill jgi-lakehouse -a cursorProject install goes to .agents/skills/; add -g for ~/.cursor/skills/.
$ gh skill install BioTender-max/awesome-bio-agent-skills jgi-lakehouse --agent cursorProject scope by default (.agents/skills/); add --scope user for a personal install.
$ git clone --depth 1 https://github.com/BioTender-max/awesome-bio-agent-skills.git skills-src && mkdir -p .cursor/skills && cp -r skills-src/skills/omics/jgi-lakehouse .cursor/skills/jgi-lakehouse && rm -rf skills-srcUse ~/.cursor/skills/ instead of .cursor/skills for a personal install.
Cursor skills documentation · loads skills from .cursor/skills/, .agents/skills/, .claude/skills/, .codex/skills/
Install the "jgi-lakehouse" agent skill from https://github.com/BioTender-max/awesome-bio-agent-skills/tree/main/skills/omics/jgi-lakehouse into .cursor/skills/jgi-lakehouse/ in this project. Copy the whole folder (SKILL.md and every file beside it), keep the folder name "jgi-lakehouse", then confirm the skill loads.Cursor copies the folder itself, the same result as the manual copy. Check what it changed before you commit it.
$ gemini skills install https://github.com/BioTender-max/awesome-bio-agent-skills.git --path skills/omics/jgi-lakehouse--scope user (default) or --scope workspace; --path is the subfolder of the repo that holds the skill; --consent skips the security confirmation prompt.
$ npx skills add BioTender-max/awesome-bio-agent-skills --skill jgi-lakehouse -a gemini-cliProject install goes to .agents/skills/; add -g for ~/.gemini/skills/.
$ gh skill install BioTender-max/awesome-bio-agent-skills jgi-lakehouse --agent gemini-cliProject scope by default (.agents/skills/); add --scope user for a personal install.
$ git clone --depth 1 https://github.com/BioTender-max/awesome-bio-agent-skills.git skills-src && mkdir -p .gemini/skills && cp -r skills-src/skills/omics/jgi-lakehouse .gemini/skills/jgi-lakehouse && rm -rf skills-srcUse ~/.gemini/skills/ instead of .gemini/skills for a personal install, then run /skills reload.
Gemini CLI skills documentation · loads skills from .gemini/skills/, .agents/skills/
Install the "jgi-lakehouse" agent skill from https://github.com/BioTender-max/awesome-bio-agent-skills/tree/main/skills/omics/jgi-lakehouse into .gemini/skills/jgi-lakehouse/ in this project. Copy the whole folder (SKILL.md and every file beside it), keep the folder name "jgi-lakehouse", then confirm the skill loads.Gemini CLI copies the folder itself, the same result as the manual copy. Check what it changed before you commit it.
$ gh skill install BioTender-max/awesome-bio-agent-skills jgi-lakehouseInstalls for Copilot at project scope by default; add --scope user for a personal install. Preview a skill first with gh skill preview. Needs GitHub CLI 2.90.0 or later (public preview).
$ npx skills add BioTender-max/awesome-bio-agent-skills --skill jgi-lakehouse -a github-copilotProject install goes to .agents/skills/; add -g for ~/.copilot/skills/.
$ git clone --depth 1 https://github.com/BioTender-max/awesome-bio-agent-skills.git skills-src && mkdir -p .github/skills && cp -r skills-src/skills/omics/jgi-lakehouse .github/skills/jgi-lakehouse && rm -rf skills-srcUse ~/.copilot/skills/ instead of .github/skills for a personal install. Commit .github/skills so cloud agent and code review can use it.
GitHub Copilot skills documentation · loads skills from .github/skills/, .claude/skills/, .agents/skills/
Install the "jgi-lakehouse" agent skill from https://github.com/BioTender-max/awesome-bio-agent-skills/tree/main/skills/omics/jgi-lakehouse into .github/skills/jgi-lakehouse/ in this project. Copy the whole folder (SKILL.md and every file beside it), keep the folder name "jgi-lakehouse", then confirm the skill loads.GitHub Copilot copies the folder itself, the same result as the manual copy. Check what it changed before you commit it.
$ npx skills add BioTender-max/awesome-bio-agent-skills --skill jgi-lakehouse -a opencodeOpenCode documents no install command of its own. Project install goes to .agents/skills/; add -g for ~/.config/opencode/skills/.
$ gh skill install BioTender-max/awesome-bio-agent-skills jgi-lakehouse --agent opencodeProject scope by default (.agents/skills/); add --scope user for a personal install.
$ git clone --depth 1 https://github.com/BioTender-max/awesome-bio-agent-skills.git skills-src && mkdir -p .opencode/skills && cp -r skills-src/skills/omics/jgi-lakehouse .opencode/skills/jgi-lakehouse && rm -rf skills-srcUse ~/.config/opencode/skills/ instead of .opencode/skills for a personal install.
OpenCode skills documentation · loads skills from .opencode/skills/, .claude/skills/, .agents/skills/
Install the "jgi-lakehouse" agent skill from https://github.com/BioTender-max/awesome-bio-agent-skills/tree/main/skills/omics/jgi-lakehouse into .opencode/skills/jgi-lakehouse/ in this project. Copy the whole folder (SKILL.md and every file beside it), keep the folder name "jgi-lakehouse", then confirm the skill loads.OpenCode copies the folder itself, the same result as the manual copy. Check what it changed before you commit it.
Facts
- Skill name
jgi-lakehouse- GitHub stars
- 200
- Token cost
- ~3.7k tokens
- SKILL.md length
- 1,147 words
- Files
- 32 (incl. scripts, references)
- Skills in repo
- 23
- Repo updated
- First seen
- Licence
- Custom licence
At a glance
Queries JGI Lakehouse (Dremio) for genomics metadata from GOLD, IMG, Mycocosm, Phytozome.
- Works in 6 steps: Start from the assembly taxon OID → Pull the JGI/GOLD linkage fields from… → Prefer JAMO pmoid for JGI read lookup → …
- Working with JGI data
- SKILL.md covers Quick Start, When to Use, Best practices and Data Access: Lakehouse vs…, plus 12 more sections
- Calls rg, python3 and pip; reaches lakehouse-1.jgi.lbl.gov and github.com
What it does
Jgi Lakehouse is an agent skill from BioTender-max/awesome-bio-agent-skills. Queries JGI Lakehouse (Dremio) for genomics metadata from GOLD, IMG, Mycocosm, Phytozome. Downloads genome files from JGI filesystem using IMG taxon OIDs and links JGI taxon OIDs to read files through PMO/GOLD identifiers and JAMO. Use when working with JGI data, GOLD projects, IMG annotations, or downloading genomes.
Its SKILL.md is about 3.7k tokens, which your agent loads only when the skill is triggered. The skill folder holds 33 other files, including scripts and reference files (for example `README.md`, `docs/IMG-tables-reference.md` and `docs/IMG_data_types.md`).
It sits in Research & Science, covering Bioinformatics and Data warehousing. It works with PostgreSQL and SQL. The repository describes itself as: A curated collection of AI agent skills for biomedical research, covering genomics, proteomics, single-cell analysis, clinical AI, and protein design.
When your agent uses it
- Working with JGI data
- IMG annotations
- Downloading genomes
Example prompts
- “Use the jgi-lakehouse skill to query JGI Lakehouse (Dremio) for genomics metadata from GOLD, IMG, Mycocosm, Phytozome”
- “/jgi-lakehouse”
Requirements
- Docker
Workflow steps
6 steps, taken from the step headings in SKILL.md.
- Start from the assembly taxon OID
- Pull the JGI/GOLD linkage fields from metadata
- Prefer JAMO pmoid for JGI read lookup
- Direct taxon-OID lookup is still useful
- spid is valid, but not sufficient
- Inspect and fetch the actual file
What it can do on your machine
Read from SKILL.md and the folder at commit 8cbdd18. It shows what the files ask for, not the result of running them.
Tool permissions
Pre-approves nothing: there is no allowed-tools line, so your agent's usual permission prompts apply.
From allowed-tools in the SKILL.md frontmatter.
Runs code
Ships 1 file in scripts/, which the agent can run.
Shell commands in SKILL.md call:
rgpython3pip
From the folder's file list and the shell code blocks in SKILL.md.
Network
Hosts in commands or code, which the agent is likely to contact:
lakehouse-1.jgi.lbl.govgithub.com
From URLs in SKILL.md, links to its own repository left out.
Credentials
Names no API keys, tokens, secrets or passwords.
From names ending in _API_KEY, _TOKEN, _SECRET, _KEY or _PASSWORD in SKILL.md.
Context cost
Jgi Lakehouse loads about 3.7k tokens when it runs, and up to ~4k if it reads all its reference files. Until then it costs about 83 tokens; SKILL.md has 1,147 words of instructions outside code blocks.
Estimates: characters ÷ 4, the usual rule of thumb; real counts depend on the model's tokenizer. Scripts and assets cost tokens only if the agent reads them.
Safety
Auto-check passed
The automated check found no risky patterns in SKILL.md.
Automated static check — not a guarantee. Review scripts before installing. It scans the text of SKILL.md for risky patterns (piping downloads into a shell, reading credential files, hidden Unicode, destructive commands); the scripts in this folder are not scanned.
SKILL.md
Its licence (Custom licence) doesn't allow us to republish the file, so here is its outline and opening line. It has 1,147 words (~3,725 tokens).
“What is it? JGI's unified data warehouse (651 tables) + filesystem access to genome files.”
- name
- jgi-lakehouse
Files
SKILL.md and 31 other files (scripts, references) in skills/omics/jgi-lakehouse of BioTender-max/awesome-bio-agent-skills.
- SKILL.md
- README.md
- docs/IMG-tables-reference.md
- docs/IMG_data_types.md
- docs/arrow-flight-python.md
- docs/authentication.md
- docs/data-catalog.md
- docs/explore_IMG_genomes.md
- docs/explore_gold.md
- docs/img_and_gold_terms.md
- docs/large_metagenome_queries.md
- docs/metagenome_comparability.md
- docs/metagenome_metadata.md
- docs/numg_metagenome_sequences.md
- docs/phytozome.md
- docs/sql-quick-reference.md
- examples/01-find-16s-rrna-genes.md
- examples/03-cross-database-joins.md
- examples/04-download-img-genomes.md
- … and 13 more
Open the folder on GitHubat commit 8cbdd18
Compare with similar skills
Jgi Lakehouse next to the 5 skills that share the most tags, products or categories with it. Stars are the repository's; “used in” counts other GitHub owners with a copy.
| Skill | Stars | Used in | Tokens | Auto-check | Licence | Repo updated |
|---|---|---|---|---|---|---|
| Jgi Lakehouse this skillBioTender-max/awesome-bio-agent-skills | 200 | — | ~3.7k | Automated safety check: Pass | Custom licence | |
| Clickhouse Logs Queriessupabase/supabase | 111k | — | ~2.4k | Automated safety check: Pass | Apache-2.0 | |
| Chdb Datastorevemetric/vemetric | 395 | 2 repos | ~1.4k | Automated safety check: Pass | Apache-2.0 | |
| Chdb SQLvemetric/vemetric | 395 | 1 repos | ~1.2k | Automated safety check: Pass | Apache-2.0 | |
| Biomarker Database Analysisaws-samples/amazon-bedrock-agents-healthcare-lifesciences | 274 | — | ~1.1k | Automated safety check: Pass | MIT-0 | |
| Querying Tempotempoxyz/tidx | 108 | — | ~3.1k | Automated safety check: Pass | MIT |
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Works with
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Questions about Jgi Lakehouse
What does Jgi Lakehouse do?
Queries JGI Lakehouse (Dremio) for genomics metadata from GOLD, IMG, Mycocosm, Phytozome. Jgi Lakehouse is an agent skill from BioTender-max/awesome-bio-agent-skills. Queries JGI Lakehouse (Dremio) for genomics metadata from GOLD, IMG, Mycocosm, Phytozome.
When should I use Jgi Lakehouse?
Jgi Lakehouse fits situations like: working with JGI data; IMG annotations; downloading genomes.
How do I install Jgi Lakehouse in Claude Code?
Run `npx skills add BioTender-max/awesome-bio-agent-skills --skill jgi-lakehouse -a claude-code`. Or copy the skill folder (skills/omics/jgi-lakehouse in BioTender-max/awesome-bio-agent-skills) into .claude/skills/jgi-lakehouse in your project. Claude Code loads it when a task matches its description.
How do I install Jgi Lakehouse in Codex?
Run `npx skills add BioTender-max/awesome-bio-agent-skills --skill jgi-lakehouse -a codex`. Or copy the skill folder (skills/omics/jgi-lakehouse in BioTender-max/awesome-bio-agent-skills) into .agents/skills/jgi-lakehouse in your project. Codex loads it when a task matches its description.
Can I use Jgi Lakehouse in Cursor, Gemini CLI or GitHub Copilot?
Cursor, Gemini CLI, GitHub Copilot and OpenCode also load SKILL.md folders. With the skills CLI, run `npx skills add BioTender-max/awesome-bio-agent-skills --skill jgi-lakehouse -a cursor` (or -a gemini-cli, github-copilot or opencode for the others). To copy it by hand, put the folder in .cursor/skills/jgi-lakehouse, .gemini/skills/jgi-lakehouse, .github/skills/jgi-lakehouse and .opencode/skills/jgi-lakehouse in your project.
What does Jgi Lakehouse need to run?
Going by SKILL.md and its folder, Jgi Lakehouse needs the command-line tools its instructions call (rg, python3 and pip). Our summary lists: Docker.
Does Jgi Lakehouse access the network?
SKILL.md names 2 domains. In commands or code: lakehouse-1.jgi.lbl.gov and github.com; the agent is likely to contact these when it follows the instructions. This is read from the text; nothing was executed.
Is Jgi Lakehouse safe to install?
Our automated static check of SKILL.md found no risky patterns, such as piping downloads into a shell, reading credential files or hidden Unicode. It is not a guarantee. The check reads SKILL.md only: the scripts in the folder are not scanned, so read them before running anything.
What licence does Jgi Lakehouse use?
Jgi Lakehouse has a licence file (the repository's licence) that doesn't match a standard licence. Read it on GitHub before reusing the skill.
How many tokens does Jgi Lakehouse use?
About 3.7k tokens (SKILL.md is roughly 15k characters). Agents keep only the skill's name and description in context until a task matches; then they load SKILL.md in full. Its references folder adds about 315 tokens, read only when the agent opens those files.
What are the alternatives to Jgi Lakehouse?
Skills that share tags, products or a category with Jgi Lakehouse: Clickhouse Logs Queries (supabase/supabase, 111k stars), Chdb Datastore (vemetric/vemetric, 395 stars), Chdb SQL (vemetric/vemetric, 395 stars) and Biomarker Database Analysis (aws-samples/amazon-bedrock-agents-healthcare-lifesciences, 274 stars). The comparison table on this page puts their stars, adoption, token cost, safety result and licence side by side.
Who maintains Jgi Lakehouse?
BioTender-max (a GitHub user) maintains it in BioTender-max/awesome-bio-agent-skills, which has 200 GitHub stars. The repository holds 23 skills in this directory. The repository was last updated on July 1, 2026.
Source: BioTender-max/awesome-bio-agent-skills on GitHub. Facts on this page come from the repository at the commit we read; the author's words are quoted as theirs.