Skills/PyPI/openbiomcp

openbiomcp@0.1.1

CAUTION· not started

Publisher claims: "BioOpenMCP: Model Context Protocol tools and CLI for bioinformatics workflows." Observed in sandbox: no network, touches nothing outside the project, writes no memory.

Registry PyPI (MCP server)Publisher pypi · publishing for 723 daysInstalls 47Last detonated 17 h ago
What would fix thisWatchDispute verdict

Coverage

Not started: dependency install failed; the server itself was not observed.
Tested
the dependency install step · every file read, file written and host contacted by what ran
Not tested
server startup · the tool list · tool behavior

What this means for the label: Caution here covers what ran. The server's tools were not exercised with a real credential, so nothing about their behavior is asserted; the credential summary below says what to do with that.

Before you give it your token

It will ask for
no credential variables read in the code
Where it talks to
no vendor host named in the codeAlso githubusercontent.com, multiqc.info, brew.sh — not the publisher's domain; check what for before connecting.
What the honeypot saw
no credential files read · no network
What we could not test
server startup · the tool list · tool behavior

Connect it under the guard. Not started: dependency install failed; the server itself was not observed. The code names no credential variable; the guard pins the network to what the honeypot saw and logs every call.

$vet-skills run --net declared -- uvx openbiomcp

Never paste a credential into a chat, a ticket or a report, including ours. How the guard holds it.

Is [email protected] safe to install?

KillerSkills ran it in the KillerSkills honeypot sandbox (2 scenarios; not started: dependency install failed; the server itself was not observed) on 2026-11-13 and scored it 75/100 (Caution). It is not known to be malicious, but it has behaviour or code a security policy should decide on before install. Notable findings: Privileged sudo command; Direct script execution from GitHub raw URL; Direct script execution from GitHub raw URL. Summary: no network, touches nothing outside the project, writes no memory.

Behavior trace

Honeypot run · 0 s · 2 scenarios · 0 deviations
t+CategoryObserved action
0.0sprocessno install scripts in bundle
0.1sprocessdependency install exit 1 ·
0.1sclaimednot started: dependency install failed (exit 1); the server itself was not observed
0.1sprocessscript backend runs setup only
0.1sprocessno install scripts to re-run

Static findings

HIGH
Privileged sudo commandsrc/openbiomcp/modules/star_alignment/star_alignment.py:1043 · Privileged sudo command — agent may execute with elevated privileges"command": "sudo chmod +x /usr/local/bin/STAR",Fix: Build commands from fixed arguments; do not interpolate untrusted strings into a shell.
AST05
MEDIUM
Python subprocess execution detectedsrc/openbiomcp/modules/cutadapt/cutadapt.py:35 · Python subprocess execution detectedproc = subprocess.run(["which", "cutadapt"], stdout=subprocess.PIPE, stderr=subprocess.PIPE, text=True)Fix: Build commands from fixed arguments, never from interpolated strings; prefer an API client over shelling out.
AST05
HIGH
Direct script execution from GitHub raw URLsrc/openbiomcp/modules/star_alignment/star_alignment.py:457 · Direct script execution from GitHub raw URL — unverified code sourceresult["error"] = "Homebrew not found. Please install Homebrew first:\n/bin/bash -c \"$(curl -fsSL https://raw.githubusercontent.com/Homebrew/install/HEAD/install.sh)\""Fix: Pin versions and sources; vendor anything fetched at install time.
AST06
MEDIUM
Python subprocess execution detectedsrc/openbiomcp/modules/cutadapt/cutadapt.py:63 · Python subprocess execution detectedproc = subprocess.run([sys.executable, "-m", "pip", "install", "cutadapt"], stdout=subprocess.PIPE, stderr=subprocess.PIPE, text=True)Fix: Build commands from fixed arguments, never from interpolated strings; prefer an API client over shelling out.
AST05
HIGH
Direct script execution from GitHub raw URLsrc/openbiomcp/modules/multiqc/multiqc.py:521 · Direct script execution from GitHub raw URL — unverified code sourceresult["suggestions"].append("Install Homebrew: /bin/bash -c \"$(curl -fsSL https://raw.githubusercontent.com/Homebrew/install/HEAD/install.sh)\"")Fix: Pin versions and sources; vendor anything fetched at install time.
AST06
MEDIUM
Python subprocess execution detectedsrc/openbiomcp/modules/multiqc/multiqc.py:407 · Python subprocess execution detectedproc = subprocess.run([pipx_path, "install", "multiqc"],Fix: Build commands from fixed arguments, never from interpolated strings; prefer an API client over shelling out.
AST05
MEDIUM
Python subprocess execution detectedsrc/openbiomcp/modules/fastqc/fastqc.py:168 · Python subprocess execution detectedprocess = subprocess.Popen(Fix: Build commands from fixed arguments, never from interpolated strings; prefer an API client over shelling out.
AST05
MEDIUM
Python subprocess execution detectedsrc/openbiomcp/modules/multiqc/multiqc.py:155 · Python subprocess execution detectedprocess = subprocess.Popen(Fix: Build commands from fixed arguments, never from interpolated strings; prefer an API client over shelling out.
AST05
MEDIUM
Python subprocess execution detectedsrc/openbiomcp/modules/multiqc/multiqc.py:63 · Python subprocess execution detectedresult = subprocess.run(cmd, capture_output=True, text=True)Fix: Build commands from fixed arguments, never from interpolated strings; prefer an API client over shelling out.
AST05
HIGH
Privileged sudo commandsrc/openbiomcp/modules/star_alignment/star_alignment.py:1037 · Privileged sudo command — agent may execute with elevated privileges"command": "sudo cp STAR /usr/local/bin/",Fix: Build commands from fixed arguments; do not interpolate untrusted strings into a shell.
AST05
MEDIUM
Python subprocess execution detectedsrc/openbiomcp/modules/fastqc/fastqc.py:444 · Python subprocess execution detectedproc = subprocess.run([fastqc_path, "--version"], stdout=subprocess.PIPE, stderr=subprocess.PIPE, text=True)Fix: Build commands from fixed arguments, never from interpolated strings; prefer an API client over shelling out.
AST05
MEDIUM
Python subprocess execution detectedsrc/openbiomcp/modules/fastqc/fastqc.py:68 · Python subprocess execution detectedresult = subprocess.run(cmd, capture_output=True, text=True, env=env)Fix: Build commands from fixed arguments, never from interpolated strings; prefer an API client over shelling out.
AST05
MEDIUM
Python subprocess execution detectedsrc/openbiomcp/modules/cutadapt/cutadapt.py:56 · Python subprocess execution detectedproc = subprocess.run([cutadapt_path, "--version"], stdout=subprocess.PIPE, stderr=subprocess.PIPE, text=True)Fix: Build commands from fixed arguments, never from interpolated strings; prefer an API client over shelling out.
AST05
MEDIUM
Python subprocess execution detectedsrc/openbiomcp/modules/multiqc/multiqc.py:425 · Python subprocess execution detectedproc_pipx = subprocess.run([brew_path, "install", "pipx"],Fix: Build commands from fixed arguments, never from interpolated strings; prefer an API client over shelling out.
AST05
MEDIUM
Python subprocess execution detectedsrc/openbiomcp/modules/cutadapt/cutadapt.py:69 · Python subprocess execution detectedproc = subprocess.run([cutadapt_path, "--version"], stdout=subprocess.PIPE, stderr=subprocess.PIPE, text=True)Fix: Build commands from fixed arguments, never from interpolated strings; prefer an API client over shelling out.
AST05
MEDIUM
Python subprocess execution detectedsrc/openbiomcp/modules/fastqc/fastqc.py:391 · Python subprocess execution detectedproc = subprocess.run(["brew", "install", "openjdk"], stdout=subprocess.PIPE, stderr=subprocess.PIPE, text=True)Fix: Build commands from fixed arguments, never from interpolated strings; prefer an API client over shelling out.
AST05
MEDIUM
Python subprocess execution detectedsrc/openbiomcp/modules/star_alignment/star_alignment.py:92 · Python subprocess execution detectedresult = subprocess.run(cmd, capture_output=True, text=True)Fix: Build commands from fixed arguments, never from interpolated strings; prefer an API client over shelling out.
AST05
HIGH
Direct script execution from GitHub raw URLsrc/openbiomcp/modules/star_alignment/star_alignment.py:1168 · Direct script execution from GitHub raw URL — unverified code source"command": '/bin/bash -c "$(curl -fsSL https://raw.githubusercontent.com/Homebrew/install/HEAD/install.sh)"',Fix: Pin versions and sources; vendor anything fetched at install time.
AST06
HIGH
Privileged sudo commandsrc/openbiomcp/modules/star_alignment/star_alignment.py:1079 · Privileged sudo command — agent may execute with elevated privileges"command": "make STARforMacStatic CXX=/usr/local/bin/g++-13 && sudo cp STAR /usr/local/bin/",Fix: Build commands from fixed arguments; do not interpolate untrusted strings into a shell.
AST05
HIGH
Privileged sudo commandsrc/openbiomcp/modules/star_alignment/star_alignment.py:1093 · Privileged sudo command — agent may execute with elevated privileges"solution": "Use 'sudo' prefix: 'sudo cp STAR /usr/local/bin/'"Fix: Build commands from fixed arguments; do not interpolate untrusted strings into a shell.
AST05
HIGH
Privileged sudo commandsrc/openbiomcp/modules/star_alignment/star_alignment.py:863 · Privileged sudo command — agent may execute with elevated privileges# Try with sudo (this will require user interaction)Fix: Build commands from fixed arguments; do not interpolate untrusted strings into a shell.
AST05
MEDIUM
Python subprocess execution detectedsrc/openbiomcp/modules/fastqc/fastqc.py:411 · Python subprocess execution detectedproc = subprocess.run(["brew", "install", "fastqc"], stdout=subprocess.PIPE, stderr=subprocess.PIPE, text=True)Fix: Build commands from fixed arguments, never from interpolated strings; prefer an API client over shelling out.
AST05
MEDIUM
Python subprocess execution detectedsrc/openbiomcp/modules/multiqc/multiqc.py:434 · Python subprocess execution detectedproc_multiqc = subprocess.run([pipx_path_new, "install", "multiqc"],Fix: Build commands from fixed arguments, never from interpolated strings; prefer an API client over shelling out.
AST05
MEDIUM
Python subprocess execution detectedsrc/openbiomcp/modules/cutadapt/cutadapt.py:30 · Python subprocess execution detectedproc = subprocess.run([cutadapt_path, "--version"], stdout=subprocess.PIPE, stderr=subprocess.PIPE, text=True)Fix: Build commands from fixed arguments, never from interpolated strings; prefer an API client over shelling out.
AST05
HIGH
Direct script execution from GitHub raw URLsrc/openbiomcp/modules/star_alignment/star_alignment.py:971 · Direct script execution from GitHub raw URL — unverified code source"command": '/bin/bash -c "$(curl -fsSL https://raw.githubusercontent.com/Homebrew/install/HEAD/install.sh)"',Fix: Pin versions and sources; vendor anything fetched at install time.
AST06
MEDIUM
File permission modification commandsrc/openbiomcp/modules/star_alignment/star_alignment.py:1043 · File permission modification command — agent changes file ownership/permissions"command": "sudo chmod +x /usr/local/bin/STAR",Fix: Request the narrowest permission that works; replace wildcards with the exact paths or hosts.
AST05
MEDIUM
Python subprocess execution detectedsrc/openbiomcp/modules/trim_galore/trim_galore.py:363 · Python subprocess execution detectedproc = subprocess.run([cutadapt_path, "--version"], stdout=subprocess.PIPE, stderr=subprocess.PIPE, text=True)Fix: Build commands from fixed arguments, never from interpolated strings; prefer an API client over shelling out.
AST05
MEDIUM
Python subprocess execution detectedsrc/openbiomcp/modules/star_alignment/star_alignment.py:480 · Python subprocess execution detectedproc = subprocess.run(["brew", "tap", "brewsci/bio"], stdout=subprocess.PIPE, stderr=subprocess.PIPE, text=True)Fix: Build commands from fixed arguments, never from interpolated strings; prefer an API client over shelling out.
AST05
MEDIUM
Python subprocess execution detectedsrc/openbiomcp/modules/trim_galore/trim_galore.py:376 · Python subprocess execution detectedproc = subprocess.run([cutadapt_path, "--version"], stdout=subprocess.PIPE, stderr=subprocess.PIPE, text=True)Fix: Build commands from fixed arguments, never from interpolated strings; prefer an API client over shelling out.
AST05
MEDIUM
Python subprocess execution detectedsrc/openbiomcp/modules/trim_galore/trim_galore.py:135 · Python subprocess execution detectedprocess = subprocess.Popen(Fix: Build commands from fixed arguments, never from interpolated strings; prefer an API client over shelling out.
AST05
MEDIUM
Python subprocess execution detectedsrc/openbiomcp/modules/star_alignment/star_alignment.py:467 · Python subprocess execution detectedproc = subprocess.run(["brew", "install", dep], stdout=subprocess.PIPE, stderr=subprocess.PIPE, text=True)Fix: Build commands from fixed arguments, never from interpolated strings; prefer an API client over shelling out.
AST05
MEDIUM
Python subprocess execution detectedsrc/openbiomcp/modules/trim_galore/trim_galore.py:370 · Python subprocess execution detectedproc = subprocess.run([sys.executable, "-m", "pip", "install", "cutadapt"], stdout=subprocess.PIPE, stderr=subprocess.PIPE, text=True)Fix: Build commands from fixed arguments, never from interpolated strings; prefer an API client over shelling out.
AST05
MEDIUM
Process kill commandsrc/openbiomcp/modules/star_alignment/star_alignment.py:364 · Process kill command — agent can terminate processes# Force kill if it doesn't terminate gracefullyFix: Build commands from fixed arguments; do not interpolate untrusted strings into a shell.
AST05
MEDIUM
Python subprocess execution detectedsrc/openbiomcp/modules/star_alignment/star_alignment.py:211 · Python subprocess execution detectedprocess = subprocess.Popen(Fix: Build commands from fixed arguments, never from interpolated strings; prefer an API client over shelling out.
AST05
MEDIUM
Python subprocess execution detectedsrc/openbiomcp/modules/trim_galore/trim_galore.py:47 · Python subprocess execution detectedresult = subprocess.run(cmd, capture_output=True, text=True, env=env)Fix: Build commands from fixed arguments, never from interpolated strings; prefer an API client over shelling out.
AST05
MEDIUM
Python subprocess execution detectedsrc/openbiomcp/modules/star_alignment/star_alignment.py:484 · Python subprocess execution detectedproc = subprocess.run(["brew", "install", "brewsci/bio/star"], stdout=subprocess.PIPE, stderr=subprocess.PIPE, text=True)Fix: Build commands from fixed arguments, never from interpolated strings; prefer an API client over shelling out.
AST05

Cost to the agent

Instructions loaded
≈55 tok
1 file · 25 in bundle
Tool list per prompt
≈0 tok
0 tools · 0 per tool
Handshake
no reply
launch to tools/list, stdio
Undocumented tools
0
description under 20 chars · avg 0

Tokens estimated at four characters each. The tool list is re-read by the agent on every turn, so it is the number to compare between servers that do the same job: ranked across the index.

Known vulnerabilities

No advisories in OSV for openbiomcp@0.1.1 as of 17 h ago. This is the package itself, not its dependencies.

What would make this Verified

5 points to 80 · weights: behavior 45%, static 25%, prompt 15%, publisher 15%
  1. Unclaimed publisher≈ +8 on the totalClaim pypi: a verified publisher gets +50 on publisher trust. It is free and usually instant with GitHub sign-in.
  2. Privileged sudo command≈ +4 on the totalBuild commands from fixed arguments; do not interpolate untrusted strings into a shell.
  3. Direct script execution from GitHub raw URL≈ +4 on the totalPin versions and sources; vendor anything fetched at install time.
  4. Python subprocess execution detected≈ +2 on the totalBuild commands from fixed arguments, never from interpolated strings; prefer an API client over shelling out.
  5. File permission modification command≈ +2 on the totalRequest the narrowest permission that works; replace wildcards with the exact paths or hosts.
  6. Process kill command≈ +2 on the totalBuild commands from fixed arguments; do not interpolate untrusted strings into a shell.
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