lobster-use

name	lobster-use
description	Runs bioinformatics analysis with Lobster AI -- single-cell RNA-seq, bulk RNA-seq, genomics (VCF/GWAS), proteomics (mass spec/affinity), metabolomics (LC-MS/GC-MS/NMR), machine learning (feature selection, survival analysis), drug discovery, literature search, dataset discovery, and visualization. Use when working with biological data, omics analysis, or bioinformatics tasks. Covers: H5AD, CSV, VCF, PLINK, 10X, mzML formats, GEO/SRA/PRIDE/MetaboLights accessions. TRIGGER PHRASES: "analyze cells", "search PubMed", "download GEO", "run QC", "cluster", "find markers", "differential expression", "UMAP", "volcano plot", "single-cell", "RNA-seq", "VCF", "GWAS", "proteomics", "mass spec", "metabolomics", "MetaboLights", "LC-MS", "metabolite", "feature selection", "survival analysis", "biomarker", "bioinformatics", "drug discovery", "pharmacogenomics", "variant annotation" ASSUMES: Lobster is installed and configured. For setup issues, tell user to run `lobster config-test` and fix any errors before proceeding.
required_binaries	["lobster","python3"]
primary_credential	LLM_PROVIDER_API_KEY
required_env_vars	[{"name":"ANTHROPIC_API_KEY","required":"one_of_provider","description":"Anthropic Claude API key"},{"name":"GOOGLE_API_KEY","required":"one_of_provider","description":"Google Gemini API key"},{"name":"OPENAI_API_KEY","required":"one_of_provider","description":"OpenAI API key"},{"name":"OPENROUTER_API_KEY","required":"one_of_provider","description":"OpenRouter API key (600+ models)"},{"name":"AWS_ACCESS_KEY_ID","required":"one_of_provider","description":"AWS Bedrock access key (must be paired with AWS_SECRET_ACCESS_KEY)"},{"name":"AWS_SECRET_ACCESS_KEY","required":"one_of_provider","description":"AWS Bedrock secret key (must be paired with AWS_ACCESS_KEY_ID)"},{"name":"AZURE_AI_ENDPOINT","required":"one_of_provider","description":"Azure AI endpoint URL (must be paired with AZURE_AI_CREDENTIAL)"},{"name":"AZURE_AI_CREDENTIAL","required":"one_of_provider","description":"Azure AI API credential (must be paired with AZURE_AI_ENDPOINT)"},{"name":"NCBI_API_KEY","required":false,"description":"NCBI API key for faster PubMed/GEO access (recommended)"}]
credential_note	Exactly ONE LLM provider is required (not all). Choose one provider and set only that provider's env var(s). Paired credentials (AWS, Azure) must both be set.
declared_writes	[".lobster_workspace/",".lobster_workspace/.env",".lobster_workspace/provider_config.json","~/.config/lobster/credentials.env","~/.config/lobster/providers.json"]
network_access	["docs.omics-os.com","LLM provider API endpoint","eutils.ncbi.nlm.nih.gov","ftp.ncbi.nlm.nih.gov","www.ebi.ac.uk"]
source	{"github":"https://github.com/the-omics-os/lobster","pypi":"https://pypi.org/project/lobster-ai/"}
always	false

Lobster AI Usage Guide

Lobster AI is a multi-agent bioinformatics platform. Users describe analyses in natural language -- Lobster routes to 22 specialist agents across 10 packages automatically.

Requirements

• Binaries: lobster CLI (pip install lobster-ai), Python 3.12+
• Credential: Exactly ONE LLM provider key as env var (not all — pick one):
  • ANTHROPIC_API_KEY | GOOGLE_API_KEY | OPENAI_API_KEY | OPENROUTER_API_KEY
  • AWS_ACCESS_KEY_ID + AWS_SECRET_ACCESS_KEY (Bedrock — both required)
  • AZURE_AI_ENDPOINT + AZURE_AI_CREDENTIAL (Azure — both required)
  • Ollama: no key needed (local models)
• Optional: NCBI_API_KEY for faster PubMed/GEO
• Writes: .lobster_workspace/ (data, credentials in .env mode 0600, outputs)
• Global config (--global flag, NOT default): ~/.config/lobster/ — avoid unless needed
• Network: LLM provider API + public bio databases (GEO, SRA, PRIDE, MetaboLights)

Docs Discovery

The docs site at docs.omics-os.com exposes LLM-friendly raw markdown:

Route	Use
/llms.txt	Index of all pages (title + URL + description)
/llms-full.txt	Full content dump of all free pages
/raw/docs/{slug}.md	Raw markdown for a specific page

Workflow: Fetch /llms.txt first to discover slugs, then fetch individual pages via /raw/docs/{slug}.md.

Example: https://docs.omics-os.com/raw/docs/tutorials/single-cell-rnaseq.md

Two Modes

This skill supports coding agents in two modes:

Orchestrator -- The agent calls lobster query --json --session-id programmatically, parses structured output, and chains multi-step analyses. See .