ENCODE ToolkitBLOCK
MCP server and Claude Code plugin for the ENCODE Project: search, download and analyze ChIP-seq, ATAC-seq, RNA-seq, WGBS, Hi-C and CUT&RUN data with 20 tools, 47 skills and 7 Nextflow pipelines
Overview
From the repository's own README, as read at the audited commit. Badges and raw HTML are left out.
[](LICENSE) [](https://www.python.org/downloads/) [](CHANGELOG.md) []() [](docs/skill-vignettes/) [](src/encode_connector/server/main.py) [](skills/pipeline-chipseq/) [](docs/SHOWCASE.md) [](tests/) [](tests/) []() [](https://claude.com/claude-code) []() [](https://smithery.ai/server/encode-toolkit) [](https://pypi.org/project/encode-toolkit/) [](https://pypi.org/project/encode-toolkit/) [](https://www.npmjs.com/package/encode-toolkit) [](https://www.npmjs.com/package/encode-toolkit) [
20 read · 0 write · 0 destructive.
| Tool | Risk | Description |
|---|---|---|
encode_batch_download | read | Search for files and download them all in batch. |
encode_compare_experiments | read | Analyze whether two ENCODE experiments are compatible for combined analysis. |
encode_download_files | read | Download specific ENCODE files by accession to a local directory. |
encode_export_data | read | Export tracked experiments as a table (CSV, TSV, or JSON). |
encode_get_citations | read | Get publications and citations for tracked experiments. |
encode_get_experiment | read | Get full details for a specific ENCODE experiment by accession ID. |
encode_get_facets | read | Get live filter counts from ENCODE to discover what data is available. |
encode_get_file_info | read | Get detailed information about a specific ENCODE file. |
encode_get_metadata | read | Get available filter values for ENCODE searches. |
encode_get_provenance | read | Get provenance information for derived files. |
encode_get_references | read | Get external references linked to tracked experiments. |
encode_link_reference | read | Link an external reference to a tracked ENCODE experiment. |
encode_list_files | read | List all files for a specific ENCODE experiment, with optional filters. |
encode_list_tracked | read | List all experiments you |
encode_log_derived_file | read | Log a file you |
encode_manage_credentials | read | Manage ENCODE API credentials for accessing restricted/unreleased data. |
encode_search_experiments | read | Search ENCODE experiments with comprehensive filters. |
encode_search_files | read | Search files across ALL experiments with combined experiment + file filters. |
encode_summarize_collection | read | Summarize your tracked experiment collection with grouped statistics. |
encode_track_experiment | read | Track an ENCODE experiment locally with its publications, methods, and pipeline info. |
Trust audit
BLOCKgrade D · trust 69/100 Do not install this without reading the findings. The audit found something that could harm you or your machine.
| Layer | What it checks | Result |
|---|---|---|
| L0 | Provenance & inventory | PASS |
| L1 | Static analysis of the code | PASS |
| L2 | Instruction surface (what it tells the agent) | FAIL |
| L3 | Class-specific surface | PASS |
| L4 | Behavioural (sandbox) | SKIPPED |
What the source does
- Filesystem
- declared (5 observation(s))
- Network
- declared (6 observation(s))
- Shell
- none-observed
- Dependencies
- pinned
- Secrets in source
- none-found
Findings (21)
# Add to PATH
# Add to PATH
| "uvx not found" | uv not installed | `curl -LsSf https://astral.sh/uv/install.sh \| sh` |
| "uvx not found" | uv not installed | `curl -LsSf https://astral.sh/uv/install.sh \| sh` |
.pre-commit-config.yaml
md5 = hashlib.md5()
expected_md5 = hashlib.md5(content).hexdigest()
expected_md5 = hashlib.md5(content).hexdigest()
expected = hashlib.md5(content).hexdigest()
expected = hashlib.md5(b"").hexdigest()
SKILLS_DIR="$(cd "$(dirname "${BASH_SOURCE[0]}")/../../skills" && pwd)"await client.get_experiment("../../etc/passwd")await client.get_file_info("../../etc/passwd")downloader._resolve_path(tmp_path, sample_file, "../../etc")
download_url="https://www.encodeproject.org/files/../../../etc/passwd",
decoded = base64.b64decode(token).decode()
- **Key findings:** Described Singularity, a container system designed for HPC environments where Docker cannot run due to security restrictions (root privilege requirements). Singularity containers r
- **Key findings:** Described Singularity, a container system designed for HPC environments where Docker cannot run due to security restrictions (root privilege requirements). Singularity containers r
| OS-level access control | Credential storage uses OS keyring permissions. Fallback salt file has `0o600` permissions |
- Access system files or environment variables (beyond `USER`/`USERNAME` for key derivation)
- Verify `uvx` is installed: `pip install uv` or `curl -LsSf https://astral.sh/uv/install.sh | sh`
Gates applied: no_behavioural_pass.
86e083ddff8bfull audit observations/trust-audit/mcp-server/ammawla__encode-toolkit.json · Report an issue / request a re-scanAudit history
Every audit this server has had. A grade with a past is a grade somebody is still checking.
| Date | Source | Verdict | Grade | Score | Change |
|---|---|---|---|---|---|
| 2026-10-08 | 86e083ddff8b | BLOCK | D | 69 | first audit |
Questions
What is the ENCODE Toolkit MCP server?
MCP server and Claude Code plugin for the ENCODE Project: search, download and analyze ChIP-seq, ATAC-seq, RNA-seq, WGBS, Hi-C and CUT&RUN data with 20 tools, 47 skills and 7 Nextflow pipelines
What tools does ENCODE Toolkit expose?
20 in total: 20 read-only, 0 that write, and 0 that can delete or overwrite. Every one is listed on this page with its risk.
Is ENCODE Toolkit safe to connect to an agent?
No — not without reading the findings first. The audit graded it D (69/100) and found 2 critical or high issues in the source. Each one is listed on this page with the file and line it is on.
What credentials does ENCODE Toolkit need?
It reads ENCODE_ACCESS_KEY and ENCODE_SECRET_KEY from the environment. Give it a token scoped to the least it needs — an agent that can be talked into calling a tool can be talked into calling it with your credentials.
How does ENCODE Toolkit run?
It speaks stdio, so it runs as a local process your client starts. It is published on npm as encode-toolkit at 0.3.4.
How current is this page?
The grade is for one exact copy of the source (86e083ddff8b), read on 2026-10-08. The repository is watched and re-audited when it changes.