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setup

Set up the ENCODE Toolkit server connection. Use when the user needs help installing, configuring, or troubleshooting the ENCODE connector.

ammawla/encode-toolkit

インストール方法を見る

含まれるファイル（2）

SKILL.md11.9 KB
references/literature.md6.8 KB

SKILL.md（原文）

インストールする前に、エージェントに与えられる指示の中身を確認できます。

ENCODE Toolkit Setup

When to Use

User needs help installing or configuring the ENCODE Toolkit MCP server
User is getting connection errors or server startup failures
User asks "how do I set up ENCODE?" or "install ENCODE toolkit"
User needs to configure ENCODE credentials for restricted data access
User wants to verify their ENCODE server connection is working
User is setting up a new environment and needs the ENCODE plugin

Help the user set up the ENCODE Toolkit server. The server connects Claude to the ENCODE Project genomics database — the largest public catalog of functional genomic elements with 8,000+ experiments across 50+ assay types.

Installation

The ENCODE Toolkit server is installed via uvx (recommended) or pip:

For Claude Code (CLI)

claude mcp add encode -- uvx encode-toolkit

For Claude Desktop

Add to claude_desktop_config.json:

macOS: ~/Library/Application Support/Claude/claude_desktop_config.json
Windows: %APPDATA%\Claude\claude_desktop_config.json

{
  "mcpServers": {
    "encode": {
      "command": "uvx",
      "args": ["encode-toolkit"]
    }
  }
}

Then restart Claude Desktop.

For VS Code (Claude Extension)

Add to your VS Code settings.json (Ctrl/Cmd + Shift + P → "Preferences: Open Settings (JSON)"):

{
  "claude.mcpServers": {
    "encode": {
      "command": "uvx",
      "args": ["encode-toolkit"]
    }
  }
}

For Cursor

Add to .cursor/mcp.json in your project root:

{
  "mcpServers": {
    "encode": {
      "command": "uvx",
      "args": ["encode-toolkit"]
    }
  }
}

For Windsurf

Add to ~/.codeium/windsurf/mcp_config.json:

{
  "mcpServers": {
    "encode": {
      "command": "uvx",
      "args": ["encode-toolkit"]
    }
  }
}

Alternative: pip install

pip install encode-toolkit
encode-toolkit  # Run the server

Verify Installation

After setup, test the connection with these verification queries (run them in order):

Step 1: Check metadata access

Ask: "List available ENCODE assay types"

This calls encode_get_metadata(metadata_type="assays")
Expected: Returns 50+ assay types including ChIP-seq, ATAC-seq, RNA-seq, WGBS, Hi-C

Step 2: Test search

Ask: "Search for ATAC-seq experiments on human brain"

This calls encode_search_experiments(assay_title="ATAC-seq", organ="brain", organism="Homo sapiens")
Expected: Returns experiment accessions (ENCSR...) with assay, biosample, and status info

Step 3: Test facets

Ask: "What organs have the most ENCODE data?"

This calls encode_get_facets()
Expected: Returns organ counts showing brain, liver, heart, etc. ranked by experiment count

If all three work, your setup is complete.

Authentication

Most ENCODE data is public and needs no authentication. For restricted/unreleased data:

Get API credentials from https://www.encodeproject.org/profile/ (requires ENCODE account)

Store them:

Ask: "Store my ENCODE credentials"
→ Calls encode_manage_credentials(action="store", access_key="...", secret_key="...")

Credentials are encrypted via the OS keyring (macOS Keychain, Windows Credential Manager, or Linux Secret Service)
To verify: encode_manage_credentials(action="check")
To remove: encode_manage_credentials(action="clear")

20 Available Tools

After setup, these tools are available:

Category	Tools	Purpose
Search	`encode_search_experiments`, `encode_get_facets`, `encode_get_metadata`	Find experiments, explore data landscape, get valid filter values
Experiment Details	`encode_get_experiment`, `encode_compare_experiments`	Get full experiment metadata, compare two experiments
Files	`encode_search_files`, `encode_list_files`, `encode_get_file_info`	Find files, list files for an experiment, get file details
Download	`encode_download_files`, `encode_batch_download`	Download individual or batch files with MD5 verification
Tracking	`encode_track_experiment`, `encode_list_tracked`, `encode_get_tracking_summary`	Local experiment tracking with SQLite
Provenance	`encode_log_derived_file`, `encode_get_provenance`	Log analysis outputs with full lineage
Citations	`encode_get_citations`, `encode_link_reference`	Publication data, cross-reference to PubMed/GEO
Credentials	`encode_manage_credentials`	Store/remove API credentials
Collection	`encode_summarize_collection`	Summarize tracked experiment portfolio

First-Run Walkthrough: Pancreatic Islet Epigenomics

This walkthrough demonstrates a complete workflow from installation to data exploration.

1. Explore what's available

"What ENCODE assay types are available for human pancreas?"
→ encode_get_facets(organ="pancreas", organism="Homo sapiens")

2. Find specific experiments

"Find all histone ChIP-seq experiments on human pancreas"
→ encode_search_experiments(assay_title="Histone ChIP-seq", organ="pancreas", organism="Homo sapiens")

3. Examine an experiment

"Get details for ENCSR123ABC"
→ encode_get_experiment(accession="ENCSR123ABC")

4. Find the right files

"List the preferred BED files for ENCSR123ABC"
→ encode_list_files(experiment_accession="ENCSR123ABC", file_format="bed", assembly="GRCh38")

5. Download data

"Download the IDR-thresholded peaks for ENCSR123ABC"
→ encode_list_files(experiment_accession="ENCSR123ABC", file_format="bed", output_type="IDR thresholded peaks")
→ encode_download_files(file_accessions=["ENCFF..."], download_dir="/data/encode")

6. Track your experiment

"Track ENCSR123ABC in my local database with note 'H3K27ac pancreatic islets'"
→ encode_track_experiment(accession="ENCSR123ABC", notes="H3K27ac pancreatic islets")

Cross-Database Integration

The ENCODE Toolkit works alongside other MCP servers and REST APIs:

Database	Access Method	What It Adds
PubMed	MCP server (`search_articles`)	Literature citations for ENCODE experiments
bioRxiv	MCP server (`search_preprints`)	Preprint discovery for latest research
ClinicalTrials.gov	MCP server (`search_trials`)	Clinical trial cross-reference
Open Targets	MCP server (`query_open_targets_graphql`)	Drug target identification
GTEx	REST API via skill	Tissue-specific expression context
ClinVar	REST API via skill	Clinical variant annotation
GWAS Catalog	REST API via skill	Trait-associated variant lookups
gnomAD	GraphQL via skill	Population allele frequencies
Ensembl	REST API via skill	VEP annotation, Regulatory Build
UCSC	REST API via skill	Genome browser tracks, cCRE data
GEO	E-utilities via skill	Complementary expression datasets
JASPAR	REST API via skill	TF binding motif databases
CellxGene	REST API via skill	Single-cell expression atlases

47 Expert Skills

Beyond the 20 tools, the ENCODE Toolkit includes 47 skills providing domain expertise:

Core (5): setup, search-encode, download-encode, track-experiments, cross-reference
Analysis (9): quality-assessment, integrative-analysis, regulatory-elements, epigenome-profiling, compare-biosamples, visualization-workflow, motif-analysis, peak-annotation, batch-analysis
Pipelines (7): pipeline-chipseq, pipeline-atacseq, pipeline-rnaseq, pipeline-wgbs, pipeline-hic, pipeline-dnaseseq, pipeline-cutandrun
External DBs (9): gtex-expression, clinvar-annotation, cellxgene-context, gwas-catalog, jaspar-motifs, ensembl-annotation, geo-connector, gnomad-variants, ucsc-browser
Workflows (10): data-provenance, cite-encode, variant-annotation, pipeline-guide, single-cell-encode, disease-research, publication-trust, bioinformatics-installer, scientific-writing, liftover-coordinates
Data Aggregation (4): histone-aggregation, accessibility-aggregation, hic-aggregation, methylation-aggregation
Meta-Analysis (2): scrna-meta-analysis, multi-omics-integration
Functional Genomics (1): functional-screen-analysis

Pitfalls & Troubleshooting

Problem	Cause	Fix
"Server not found"	Claude not restarted after config change	Restart Claude Desktop / reload Claude Code
"uvx not found"	uv not installed	`curl -LsSf https://astral.sh/uv/install.sh \| sh`
Timeout errors	Slow connection or ENCODE API load	Retry; rate limit (10 req/sec) is handled automatically
403 on downloads	File requires authentication	`encode_manage_credentials(action="store", ...)`
No results returned	Filters too narrow	Broaden filters; use `encode_get_facets` to see available data
"Invalid accession"	Wrong format	Must be ENCSR/ENCFF/ENCBS format (e.g., ENCSR000AAA)
Empty facets	API connectivity issue	Check internet; try `encode_get_metadata(metadata_type="assays")`
Stale results	Cached data	Cache TTL is 1 hour; restart server to clear

Code Examples

1. Verify server connection with metadata query

encode_get_metadata(metadata_type="assays")

Expected output (values abridged — the full list has 79 assay titles):

{
  "metadata_type": "assays",
  "values": ["Histone ChIP-seq", "TF ChIP-seq", "ATAC-seq", "DNase-seq", "total RNA-seq", "polyA plus RNA-seq", "WGBS", "intact Hi-C", "CUT&RUN", "CUT&Tag", "eCLIP", "STARR-seq", "MPRA", "snATAC-seq", "scRNA-seq"],
  "count": 79
}

2. Test search functionality

encode_search_experiments(assay_title="ATAC-seq", organ="brain", organism="Homo sapiens", limit=3)

Expected output:

{
  "results": [
    {"accession": "ENCSR000AAA", "assay_title": "ATAC-seq", "biosample_summary": "brain tissue female adult (53 years)", "organ": "brain", "status": "released"}
  ],
  "total": 32,
  "limit": 3,
  "offset": 0,
  "has_more": true,
  "next_offset": 3
}

3. Test facet exploration

encode_get_facets(organism="Homo sapiens")

Expected output:

{
  "biosample_ontology.organ_slims": [
    {"term": "brain", "count": 450},
    {"term": "blood", "count": 380},
    {"term": "liver", "count": 220},
    {"term": "heart", "count": 180},
    {"term": "lung", "count": 150}
  ]
}

Related Skills

Skill	When to Use
`search-encode`	First skill to use after setup — find experiments by assay, tissue, target
`download-encode`	Download ENCODE files (BED, bigWig, FASTQ, BAM) after finding experiments
`pipeline-guide`	Set up Nextflow pipelines for processing raw ENCODE data
`bioinformatics-installer`	Install all bioinformatics tools needed for ENCODE analysis
`cross-reference`	Link ENCODE experiments to PubMed, GEO, ClinicalTrials.gov
`quality-assessment`	Evaluate data quality before analysis
`publication-trust`	Verify literature claims backing analytical decisions

Presenting Results

When reporting setup results:

Connection status: Confirm the ENCODE Toolkit server is connected and responding. Report the server version if available
Available tools: List the 20 available ENCODE tools grouped by function (search, download, track, cross-reference, credentials)
Test query result: Run a simple validation query (e.g., encode_get_metadata(metadata_type="assays")) and confirm it returns results successfully
Authentication status: Note whether credentials are configured (for restricted data) or that public data access requires no authentication
Troubleshooting: If any issues were encountered during setup, summarize the problem and resolution
Next steps: Suggest search-encode to find experiments, or encode_get_facets to explore what ENCODE data is available for their research area

For the request: "$ARGUMENTS"

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概要と使いどころ

accessibility-aggregation

無料

Build comprehensive chromatin accessibility maps by aggregating ATAC-seq and DNase-seq narrowPeak data across multiple ENCODE experiments, donors, and labs. Use when the user wants to answer "where is chromatin accessible in my tissue?" by combining peak calls into a union peak set. Handles cross-lab variation, ATAC vs DNase platform differences, and ENCODE blocklist filtering.

日本語の概要は準備中です。原文の説明を表示しています。