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chaperone-harness
39 / 100 · High risk
Only if you trust the author. Some of what it can do is expected: a coding skill usually runs build and test commands.
By RosettaCommons/chaperone (GitHub) · coding · 170 stars · scanned at commit 2d3ac1e
Use this Chaperone repository to guide pipeline-oriented coding work.
Works with any agent that supports SKILL.md skills.
What this skill can do
Downloads and installs other software
The author does not mention this.
Found in 255 places.
Show 17 more
- .agents/skills/setup/SKILL.md, line 43
uv pip install torch --index-url https://download.pytorch.org/whl/cpu - .agents/skills/setup/SKILL.md, line 50
uv pip install -e '.[all]' - .agents/skills/setup/SKILL.md, line 229
- At IPD this is configured by the supplied `.env.ipd` or the digs preset; elsewhere, either ask the user for their existing path and write it to `.env.local`, - .agents/skills/setup/SKILL.md, line 365
uv pip install -e '.[docs]' - Makefile, line 5
@command -v ruff >/dev/null 2>&1 || { echo "Error: ruff not found (pip install ruff)"; exit 1; } - Makefile, line 12
@command -v ruff >/dev/null 2>&1 || { echo "Error: ruff not found (pip install ruff)"; exit 1; } - README.md, line 30
- [uv](https://docs.astral.sh/uv/) via `curl -LsSf https://astral.sh/uv/install.sh | sh`. - README.md, line 31
- [Claude Code](https://docs.anthropic.com/en/docs/claude-code) via `curl -fsSL https://claude.ai/install.sh | bash`, or - README.md, line 32
- [Codex](https://github.com/openai/codex) via `npm install -g @openai/codex`. - README.md, line 58
uv pip install -e '.[all]' - containers/apptainer/alphafold3.def, line 8
DEBIAN_FRONTEND=noninteractive apt-get install -y --no-install-recommends \ - containers/apptainer/alphafold3.def, line 40
apt-get update && apt-get install -y cuda-toolkit-12-8 - containers/apptainer/alphafold3.def, line 59
python3.12 -m venv /opt/uv-env && /opt/uv-env/bin/pip install uv==0.9.24 - containers/apptainer/bindcraft.def, line 8
DEBIAN_FRONTEND=noninteractive apt-get install -y --no-install-recommends \ - containers/apptainer/bindcraft.def, line 34
add-apt-repository -y ppa:deadsnakes/ppa && apt-get update && apt-get install -y --no-install-recommends python3.10 python3.10-dev python3.10-venv - containers/apptainer/bindcraft.def, line 39
/opt/bindcraft-env/bin/pip install --no-cache-dir --upgrade pip setuptools wheel - containers/apptainer/bindcraft.def, line 40
/opt/bindcraft-env/bin/pip install --no-cache-dir 'jax[cuda12]==0.4.35' numpy==1.26.4 pandas==2.2.3 matplotlib==3.9.4 biopython==1.85 scipy==1.15.2 seaborn==0.1
and 235 more places
Runs commands on your computer
This is disclosed by the author in the skill's SKILL.md or README. Expected for a coding skill.
Found in 226 places.
Show 17 more
- .agents/skills/build-block/SKILL.md, line 353
source .venv/bin/activate - .agents/skills/debugging-inputs/SKILL.md, line 73
python -c " - .agents/skills/debugging-inputs/SKILL.md, line 146
python -m json.tool rundir/af3/chunk_0/inputs/design.json | grep -A2 '"ligand"' - .agents/skills/debugging-inputs/SKILL.md, line 157
grep "Falling back" rundir/logs/*.log - .agents/skills/notebook-editing/SKILL.md, line 37
source .venv/bin/activate && papermill notebook.ipynb notebook.ipynb - .agents/skills/order-collection/SKILL.md, line 53
mkdir -p {rundir}/order_collection - .agents/skills/order-collection/SKILL.md, line 85
source {chaperone_repo}/.venv/bin/activate && python3 -c " - .agents/skills/order-collection/SKILL.md, line 132
source {chaperone_repo}/.venv/bin/activate && python3 -c " - .agents/skills/order-collection/SKILL.md, line 248
cd {rundir} && if command -v pigz >/dev/null 2>&1; then - .agents/skills/order-collection/SKILL.md, line 264
source {chaperone_repo}/.venv/bin/activate && python3 -c " - .agents/skills/order-collection/SKILL.md, line 402
source {chaperone_repo}/.venv/bin/activate && python3 -c " - .agents/skills/order-collection/SKILL.md, line 493
source {chaperone_repo}/.venv/bin/activate && python3 -c " - .agents/skills/order-collection/SKILL.md, line 517
source {chaperone_repo}/.venv/bin/activate && python3 -c " - .agents/skills/order-collection/SKILL.md, line 541
source {chaperone_repo}/.venv/bin/activate && python3 -c " - .agents/skills/order-collection/SKILL.md, line 581
source {chaperone_repo}/.venv/bin/activate && python3 -c " - .agents/skills/rosetta-params/SKILL.md, line 58
/software/openbabel/latest/obabel -i pdb ligand.pdb -o mol2 -O ligand.mol2 - .agents/skills/rosetta-params/SKILL.md, line 66
antechamber -i input.mol2 -fi mol2 -o charged.mol2 -fo mol2 -c bcc -pf y -dr n -at sybyl -nc <CHARGE>
and 206 more places
Sends data to these websites: astral.sh, files.wwpdb.org, files.rcsb.org, claude.ai, developer.download.nvidia.com, eddylab.org, github.com
This is disclosed by the author in the skill's SKILL.md or README.
Found in 44 places.
Show 17 more
- .agents/skills/visualize/SKILL.md, line 100
urllib.request.urlretrieve("https://files.rcsb.org/download/1QYS.pdb", "/tmp/1qys.pdb") - README.md, line 30
- [uv](https://docs.astral.sh/uv/) via `curl -LsSf https://astral.sh/uv/install.sh | sh`. - README.md, line 31
- [Claude Code](https://docs.anthropic.com/en/docs/claude-code) via `curl -fsSL https://claude.ai/install.sh | bash`, or - containers/apptainer/alphafold3.def, line 38
curl -fsSL https://developer.download.nvidia.com/compute/cuda/repos/ubuntu2404/x86_64/3bf863cc.pub | gpg --dearmor -o /etc/apt/keyrings/nvidia-cuda.gpg - containers/apptainer/alphafold3.def, line 49
wget http://eddylab.org/software/hmmer/hmmer-3.4.tar.gz -P /opt/hmmer_build - containers/apptainer/boltz2.def, line 24
curl -fsSL https://developer.download.nvidia.com/compute/cuda/repos/ubuntu2404/x86_64/3bf863cc.pub | gpg --dearmor -o /etc/apt/keyrings/nvidia-cuda.gpg - containers/apptainer/boltzgen.def, line 24
curl -fsSL https://developer.download.nvidia.com/compute/cuda/repos/ubuntu2404/x86_64/3bf863cc.pub | gpg --dearmor -o /etc/apt/keyrings/nvidia-cuda.gpg - containers/apptainer/chai1.def, line 24
curl -fsSL https://developer.download.nvidia.com/compute/cuda/repos/ubuntu2404/x86_64/3bf863cc.pub | gpg --dearmor -o /etc/apt/keyrings/nvidia-cuda.gpg - containers/apptainer/colabfold_portable.def, line 20
wget -q -O /tmp/miniforge.sh https://github.com/conda-forge/miniforge/releases/latest/download/Miniforge3-Linux-x86_64.sh - containers/apptainer/disco.def, line 27
curl -fsSL https://developer.download.nvidia.com/compute/cuda/repos/ubuntu2404/x86_64/3bf863cc.pub | gpg --dearmor -o /etc/apt/keyrings/nvidia-cuda.gpg - containers/apptainer/e1.def, line 24
curl -fsSL https://developer.download.nvidia.com/compute/cuda/repos/ubuntu2404/x86_64/3bf863cc.pub | gpg --dearmor -o /etc/apt/keyrings/nvidia-cuda.gpg - containers/apptainer/esm2.def, line 22
curl -fsSL https://developer.download.nvidia.com/compute/cuda/repos/ubuntu2404/x86_64/3bf863cc.pub | gpg --dearmor -o /etc/apt/keyrings/nvidia-cuda.gpg - containers/apptainer/esmfold2.def, line 27
curl -fsSL https://developer.download.nvidia.com/compute/cuda/repos/ubuntu2404/x86_64/3bf863cc.pub | gpg --dearmor -o /etc/apt/keyrings/nvidia-cuda.gpg - containers/apptainer/foundry.def, line 26
curl -fsSL https://developer.download.nvidia.com/compute/cuda/repos/ubuntu2404/x86_64/3bf863cc.pub | gpg --dearmor -o /etc/apt/keyrings/nvidia-cuda.gpg - containers/apptainer/openfold3.def, line 27
curl -fsSL https://developer.download.nvidia.com/compute/cuda/repos/ubuntu2404/x86_64/3bf863cc.pub | gpg --dearmor -o /etc/apt/keyrings/nvidia-cuda.gpg - containers/apptainer/protein_hunter.def, line 29
curl -fsSL https://developer.download.nvidia.com/compute/cuda/repos/ubuntu2404/x86_64/3bf863cc.pub | gpg --dearmor -o /etc/apt/keyrings/nvidia-cuda.gpg - containers/apptainer/protenix.def, line 26
curl -fsSL https://developer.download.nvidia.com/compute/cuda/repos/ubuntu2404/x86_64/3bf863cc.pub | gpg --dearmor -o /etc/apt/keyrings/nvidia-cuda.gpg
and 24 more places
Changes files outside its own folder
The author does not mention this.
Found in 57 places.
Show 17 more
- .agents/skills/slurm-interactive/SKILL.md, line 107
rm -rf "$HOME/.slurm_run" - containers/apptainer/alphafold3.def, line 37
mkdir -p /etc/apt/keyrings - containers/apptainer/alphafold3.def, line 39
echo "deb [signed-by=/etc/apt/keyrings/nvidia-cuda.gpg] https://developer.download.nvidia.com/compute/cuda/repos/ubuntu2404/x86_64 /" > /etc/apt/sources.list.d/ - containers/apptainer/alphafold3.def, line 48
mkdir -p /opt/hmmer_build /usr/local/hmmer - containers/apptainer/alphafold3.def, line 66
for d in /opt/af3-env/lib/python3.12/site-packages/nvidia/*/lib; do for f in "$d"/*.so*; do [ -f "$f" ] && ln -sf "$f" /usr/local/cuda/lib64/; done; done - containers/apptainer/alphafold3.def, line 67
echo /opt/af3-env/lib/python3.12/site-packages/nvidia/cuda_runtime/lib > /etc/ld.so.conf.d/nvidia-pip.conf && echo /opt/af3-env/lib/python3.12/site-packages/nvi - containers/apptainer/bindcraft2.def, line 24
/opt/bindcraft2-env/bin/python -c "import nvidia, pathlib; print('\n'.join(sorted(str(p) for root in nvidia.__path__ for p in pathlib.Path(root).glob('*/lib'))) - containers/apptainer/boltz2.def, line 23
mkdir -p /etc/apt/keyrings - containers/apptainer/boltz2.def, line 25
echo "deb [signed-by=/etc/apt/keyrings/nvidia-cuda.gpg] https://developer.download.nvidia.com/compute/cuda/repos/ubuntu2404/x86_64 /" > /etc/apt/sources.list.d/ - containers/apptainer/boltzgen.def, line 23
mkdir -p /etc/apt/keyrings - containers/apptainer/boltzgen.def, line 25
echo "deb [signed-by=/etc/apt/keyrings/nvidia-cuda.gpg] https://developer.download.nvidia.com/compute/cuda/repos/ubuntu2404/x86_64 /" > /etc/apt/sources.list.d/ - containers/apptainer/chai1.def, line 23
mkdir -p /etc/apt/keyrings - containers/apptainer/chai1.def, line 25
echo "deb [signed-by=/etc/apt/keyrings/nvidia-cuda.gpg] https://developer.download.nvidia.com/compute/cuda/repos/ubuntu2404/x86_64 /" > /etc/apt/sources.list.d/ - containers/apptainer/colabfold_portable.def, line 30
echo "/opt/conda/lib" > /etc/ld.so.conf.d/conda.conf && ldconfig - containers/apptainer/disco.def, line 26
mkdir -p /etc/apt/keyrings - containers/apptainer/disco.def, line 28
echo "deb [signed-by=/etc/apt/keyrings/nvidia-cuda.gpg] https://developer.download.nvidia.com/compute/cuda/repos/ubuntu2404/x86_64 /" > /etc/apt/sources.list.d/ - containers/apptainer/e1.def, line 23
mkdir -p /etc/apt/keyrings
and 37 more places
Reads your saved credentials, such as SSH keys or .env files
The author does not mention this.
Found in 5 places.
Show 2 more
Can call paid AI services billed to you
The author does not mention this.
Found in 1 place.
Safer alternatives
Low-risk skills in the same category (coding) that look related. Check that one does what you need.
Install
Paste this into your terminal. It downloads exactly the version we scanned, not whatever is newest.
if [ -e ~/.agents/skills/'chaperone-harness' ] || [ -L ~/.agents/skills/'chaperone-harness' ]; then echo 'A skill folder named chaperone-harness already exists — not replacing it' >&2; false; else d=$(mktemp -d) && git clone --quiet --filter=blob:none --no-checkout 'https://github.com/RosettaCommons/chaperone' "$d" && git -C "$d" checkout --quiet '2d3ac1e7ce8078e7b99ce1511940fda61c7198ae' -- '.' && mkdir -p ~/.agents/skills && cp -R "$d/." ~/.agents/skills/'chaperone-harness' && rm -rf ~/.agents/skills/'chaperone-harness'/.git && rm -rf "$d"; fi
Codex reads ~/.agents/skills directly. For Claude Code, Cursor, Copilot, Gemini CLI, Antigravity or OpenCode, also link it. For Claude Code: ln -s ~/.agents/skills/'chaperone-harness' ~/.claude/skills/'chaperone-harness' (other agents: ~/.cursor/skills, ~/.copilot/skills, ~/.gemini/skills, ~/.gemini/config/skills, ~/.config/opencode/skills). Or install through the finder skill, which does both.
Badge for your README
The badge for RosettaCommons/chaperone shows the score of its lowest-scoring skill.
[](https://zalavijaysinh.github.io/skilltrust/repos/RosettaCommons/chaperone/)
Score history
| Date | Version | Score |
|---|
| 2026-11-12 | 2d3ac1e | 39 |