jgi-lakehouse
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.
npx skills add BioTender-max/awesome-bio-agent-skills --skill jgi-lakehouse --agent claude-code
Same command for any agent — swap --agent for codex, cursor, copilot.
Weekly change comes from our own snapshots, not the repository page — it measures attention, not adoption.
# JGI Lakehouse Skill ## Quick Start **What is it?** JGI's unified data warehouse (651 tables) + filesystem access to genome files. **Two data access methods:** 1. **Lakehouse (Dremio)** → Metadata, annotations, taxonomy (no sequences) 2. **JGI Filesystem** → Actual genome files (FNA, FAA, GFF) via taxon OID **SQL Dialect:** ANSI SQL (not PostgreSQL) - Use `CAST(x AS type)` not `::` - Use `REGEXP_LIKE()` not `~` - Identifiers with dashes need double quotes: `"gold-db-2 postgresql"` ```sql -- Quick test SELECT gold_id, project_name FROM "gold-db-2 postgresql".gold.project WHERE is_public = 'Yes' LIMIT 5; ``` --- ## When to Use - Query JGI genomics metadata (GOLD, IMG, Mycocosm, Phytozome) - Find genomes and/or metagenomes by taxonomy, ecosystem, or phenotype. - Download microbial genomes with IMG taxon OIDs - Cross-reference GOLD projects with IMG annotations --- ## Best practices - When reporting results from database queries, always provide a clear summary of the exact criteria that were used for filtering. This should include a list of each field that was used in the query/filter, and the query/filter was applied (string used in exact match, regular expression, exact number searc
- Quick Start
- When to Use
- Best practices
- Data Access: Lakehouse vs Filesystem
- Key Data Sources
- NUMG (Metagenome Proteins) Agent Workflow
- Downloading Genomes with IMG Taxon OIDs
- Option 1: JGI Filesystem (Fastest)
- Linking Assemblies To Reads
- 1. Start from the assembly taxon OID
- 2. Pull the JGI/GOLD linkage fields from metadata
- 3. Prefer JAMO pmoid for JGI read lookup
- 4. Direct taxon-OID lookup is still useful
- 5. spid is valid, but not sufficient
Genome packages are at:
cp /clusterfs/jgi/img_merfs-ro/img_web/img_web_data/download/8136918376.tar.gz .
tar -xzf 8136918376.tar.gz
apptainer run docker://doejgi/jamo-dori:latest jamo info help
apptainer run docker://doejgi/jamo-dori:latest \
jamo info all pmoid <img_jgi_project_id>
jamo info all pmoid <img_jgi_project_id> | rg 'fastq(\\.gz)?'
jamo info all custom '{"metadata.gold_data.img_oid": 3300000030, "file_name": {"$regex": ".*fastq(\\\\.gz)?$"}}'
jamo info raw_normal spid <gold_its_spid>
apptainer run docker://doejgi/jamo-dori:latest jamo show <metadata_id>What does the jgi-lakehouse skill do?
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.
How do I install it?
Run `npx skills add BioTender-max/awesome-bio-agent-skills --skill jgi-lakehouse --agent claude-code` — it drops the skill into your project so the agent can pick it up. Swap the --agent value for codex, cursor or copilot if you use one of those.
Where does this skill come from?
From BioTender-max/awesome-bio-agent-skills, a repository with 135 stars. We read it straight from the repository tree rather than a submitted listing, so what you see here is what is actually published.
Is a popular skill a good skill?
Not necessarily. Stars measure attention, not adoption — a repository can trend for a week and be abandoned. That is why we show the weekly change from our own snapshots next to the total, instead of a single flattering number.