Claude Code, Plugin
Encode Toolkit
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
Compatibility: Not stated.
Grade C
One Medium finding. Read the findings before installing.
Not a guarantee. A hygiene check of the source at the commit shown, not a security audit.
Rescanned at commit 36836c8725fd, unchanged since the check below.
INSTALL_REMOTE_SCRIPT
Why this grade
- INSTALL_REMOTE_SCRIPT Medium
Fetches a script from the network and runs it (a pipe to a shell, or an install hook with a URL).
index.js, line 39
" curl -LsSf https://astral.sh/uv/install.sh | sh"
Any High, or two or more Medium findings, give D. One Medium gives C. Low findings or a security Note give B. Each code names a finding behind the letter.
If you think this grade is wrong, email [email protected] with the entry link and your evidence. We aim to acknowledge within two working days and decide within seven. If we confirm an error, we aim to correct it within 24 hours of confirming it. These are aims, not guarantees.
Grades are a hygiene check of the source at the commit shown, on the date checked, not a security audit or a guarantee. The free directory grades are automated. Before release, a PlugVet engineer reviews every paid report and any grade we hold back, including all F grades, against the source code and the evidence we quote.
What was checked
Plain notes from the hygiene checks.
Permissions
Note
requests shell access. The manifest names this permission.
PERMISSION_SHELL_DECLARED
.github/scripts/check-skill-docs.py, line 68
listing = subprocess.run(["git", "ls-files"], cwd=ROOT, capture_output=True, text=True, check=False)
Install and update
Serious
install fetches a script from the network. README documents an installer that pipes a download into a shell. The docs document an installer that pipes a download into a shell.
INSTALL_REMOTE_SCRIPT INSTALL_DOCUMENTED_INSTALLER
README.md, line 780
- Verify `uvx` is installed: `pip install uv` or `curl -LsSf https://astral.sh/uv/install.sh | sh`
index.js, line 39
" curl -LsSf https://astral.sh/uv/install.sh | sh"
plugin/skills/bioinformatics-installer/scripts/install-nextflow.sh, line 127
echo " curl -fsSL https://get.docker.com | sh"
Show more
plugin/skills/setup/SKILL.md, line 236
| "uvx not found" | uv not installed | `curl -LsSf https://astral.sh/uv/install.sh \| sh` |
skills/bioinformatics-installer/scripts/install-nextflow.sh, line 127
echo " curl -fsSL https://get.docker.com | sh"
skills/setup/SKILL.md, line 236
| "uvx not found" | uv not installed | `curl -LsSf https://astral.sh/uv/install.sh \| sh` |
Network
Concern
can reach homer.ucsd.edu. The description does not name that host. can reach meme-suite.org. The description does not name that host. can reach a host that is not written as a fixed address. can reach ftp.ncbi.nlm.nih.gov. The description does not name that host. can reach eutils.ncbi.nlm.nih.gov. The description does not name that host. can reach rest.ensembl.org. The description does not name that host. can reach www.ncbi.nlm.nih.gov. The description does not name that host. can reach gnomad.b
NETWORK_NO_FIXED_HOST NETWORK_UNNAMED_HOST
plugin/skills/bioinformatics-installer/SKILL.md, line 550
wget http://homer.ucsd.edu/homer/configureHomer.pl
plugin/skills/bioinformatics-installer/SKILL.md, line 566
wget https://meme-suite.org/meme/meme-software/5.5.5/meme-5.5.5.tar.gz
plugin/skills/bioinformatics-installer/scripts/install-nextflow.sh, line 71
curl -fsSL "$NEXTFLOW_URL" -o "$tmp_file"
Show more
plugin/skills/clinvar-annotation/SKILL.md, line 129
response = requests.get(url, params=params)
plugin/skills/clinvar-annotation/SKILL.md, line 152
response = requests.get(url, params=params)
plugin/skills/clinvar-annotation/SKILL.md, line 168
response = requests.get(url, params=params)
plugin/skills/clinvar-annotation/SKILL.md, line 186
wget https://ftp.ncbi.nlm.nih.gov/pub/clinvar/vcf_GRCh38/clinvar.vcf.gz
plugin/skills/clinvar-annotation/SKILL.md, line 187
wget https://ftp.ncbi.nlm.nih.gov/pub/clinvar/vcf_GRCh38/clinvar.vcf.gz.tbi
plugin/skills/pipeline-cutandrun/SKILL.md, line 341
wget https://github.com/Boyle-Lab/Blacklist/raw/master/lists/CUTandRUN.suspectlist.hg38.bed.gz
plugin/skills/pipeline-dnaseseq/references/03-filtering.md, line 80
wget -q https://github.com/Boyle-Lab/Blacklist/raw/master/lists/hg38-blacklist.v2.bed.gz
skills/pipeline-cutandrun/SKILL.md, line 341
wget https://github.com/Boyle-Lab/Blacklist/raw/master/lists/CUTandRUN.suspectlist.hg38.bed.gz
Secrets
Concern
reads a credential or environment file.
SECRETS_PATH_DOTENV
.gitignore, line 16
# Environment variables
.gitignore, line 17
.env
.gitignore, line 19
!.env.example
Agent instructions
Pass
No instruction to ignore earlier instructions or to hide a step.
Obfuscation
Note
the file cap was reached before every file was read.
OBFUSCATION_FILE_CAP_REACHED
skills/pipeline-cutandrun/scripts/nextflow.config, line 1
// ============================================================================
Licence
Pass
A licence file is present (LICENSE).
Maintainer activity
Pass
The latest commit is within the last 365 days.
Note
Hygiene check of commit 36836c8725fd. requests shell access. The manifest names this permission. install fetches a script from the network. README documents an installer that pipes a download into a shell. The docs document an installer that pipes a download into a shell. can reach homer.ucsd.edu. The description does not name that host. can reach meme-suite.org. The description does not name that host. can reach a host that is not written as a fixed address. can reach ftp.ncbi.nlm.nih.gov. The description does not name that host. can reach eutils.ncbi.nlm.nih.gov. The description does not name that host. can reach rest.ensembl.org. The description does not name that host. can
Date and source
Date checked:
github.com
Commit graded: 36836c8725fd4d20d9c851ce314f5151aea5f57c
This link goes to the original host. PlugVet does not host or check what you download from there, and installing it is your own decision and risk.