Is setup safe to install?

SaferSkills independently audited setup (Agent Skill) and scored it 100/100 (green). The audit ran 55 deterministic rules across Security, Supply Chain, Maintenance, Transparency, and Community; it found 0 high-severity and 0 lower-severity findings. The full rule-by-rule trace and per-finding evidence are below. Free, methodology-open.

CategoryWeightCategory scoreContribution

Securityprompt, exec, net, exfil, eval

35%

100

35.0 pts

Supply chainhash, typosquat, maintainer, lockfile

20%

100

20.0 pts

Maintenancestaleness, pinning, CI

15%

100

15.0 pts

TransparencySKILL.md, perms, README

15%

100

15.0 pts

Communityinstalls, verify, response

15%

100

15.0 pts

Findings & checks · 0 flagged

Securityscore 100 · 0 findings

✓—All security checks passedNo findings in this category for the latest scan.pass

Supply chainscore 100 · 0 findings

✓—All supply chain checks passedNo findings in this category for the latest scan.pass

Maintenancescore 100 · 0 findings

✓—All maintenance checks passedNo findings in this category for the latest scan.pass

Transparencyscore 100 · 0 findings

✓—All transparency checks passedNo findings in this category for the latest scan.pass

Communityscore 100 · 0 findings

✓—All community checks passedNo findings in this category for the latest scan.pass

The primary manifest — the file an agent reads to learn what this artifact does.

skills/setup/SKILL.md · 1 file

skills/setup/SKILL.md3.5 KB · Markdown

name: setup

description: >

First-time setup for protein design tools. Use this skill when:

(1) User is new and hasn't run any tools yet,

(2) Commands fail with "file not found" or "modal: command not found",

(3) Modal authentication errors occur,

(4) User asks how to get started or set up the environment,

(5) biomodals directory is missing or tools aren't working.

license: MIT

category: utilities

tags: [setup, onboarding, installation]

Setup Guide

Help users get their environment ready to run protein design tools.

Quick checklist

Run through this checklist when a user encounters setup issues:

Step	Check	Fix
1. Modal CLI	`modal --version`	`pip install modal`
2. Modal auth	`modal token show`	`modal setup`
3. biomodals	`ls biomodals/modal_*.py`	`git clone https://github.com/hgbrian/biomodals`
4. Test	`cd biomodals && modal run modal_boltzgen.py --help`	See troubleshooting

Diagnosing issues

Cause: Modal CLI not installed.

Fix:

pip install modal

Then restart the terminal or run hash -r.

Error: "Permission denied" or "Unauthorized"

Cause: Modal not authenticated.

Fix:

modal setup

This opens a browser. Click "Authorize" to complete authentication.

Error: "No such file or directory: modal_boltzgen.py"

Cause: biomodals repository not cloned or not in correct directory.

Fix:

git clone https://github.com/hgbrian/biomodals
cd biomodals

Error: "uvx: command not found"

Cause: uvx is an optional wrapper from the uv package. It's not required.

Fix: Run modal directly (recommended):

modal run modal_boltzgen.py --help

Or install uv if you prefer using uvx:

pip install uv

Full setup steps

pip install modal

Verify: modal --version

modal setup

This opens a browser. Click "Authorize".

Verify: modal token show

Step 3: Clone biomodals

git clone https://github.com/hgbrian/biomodals
cd biomodals

Verify: ls modal_*.py should show files like modal_boltzgen.py

Step 4: Test the Setup

cd biomodals
modal run modal_boltzgen.py --help

Expected: Usage instructions appear showing --input-yaml, --protocol, --num-designs options.

Common workflows after setup

Once setup is complete, users can:

cd biomodals

# Design binders with BoltzGen (requires YAML config)
modal run modal_boltzgen.py --input-yaml binder.yaml --protocol protein-anything --num-designs 50

# Generate backbones with RFdiffusion (official repo, not biomodals)
python run_inference.py inference.input_pdb=target.pdb contigmap.contigs=[A1-150/0 70-100] inference.num_designs=100

# Validate with Chai
modal run modal_chai1.py --input-faa designs.fasta

GPU selection

Set GPU with environment variable:

GPU=L40S modal run modal_boltzgen.py --input-yaml config.yaml --num-designs 50
GPU=A100 modal run modal_chai1.py --input-faa complex.fasta

GPU	VRAM	Best For
T4	16GB	ProteinMPNN, ESM
A10G	24GB	RFdiffusion, Chai
L40S	48GB	BoltzGen, BindCraft
A100	40-80GB	Large complexes

Modal offers $30/month in free credits - enough for:

~500 BoltzGen designs
~2000 RFdiffusion backbones
~1000 Chai predictions

Full documentation: See Getting started

setup— agent skill

Is setup safe to install?

Setup Guide

Quick checklist

Diagnosing issues

Error: "Permission denied" or "Unauthorized"

Error: "No such file or directory: modal_boltzgen.py"

Error: "uvx: command not found"

Full setup steps

Step 3: Clone biomodals

Step 4: Test the Setup

Common workflows after setup

GPU selection

Audit the pieces. Scan the whole. Decide.

Is setup safe to install?

Setup Guide

Quick checklist

Diagnosing issues

Error: "modal: command not found"

Error: "Permission denied" or "Unauthorized"

Error: "No such file or directory: modal_boltzgen.py"

Error: "uvx: command not found"

Full setup steps

Step 1: Install Modal CLI

Step 2: Authenticate Modal

Step 3: Clone biomodals

Step 4: Test the Setup

Common workflows after setup

GPU selection

Modal free tier

Audit the pieces. Scan the whole. Decide.