---
name: Setup
slug: setup-4
category: Automation
description: Setup helps users install Modal, authenticate it, and clone biomodals so protein design tools can run. Use it when commands fail, Modal is missing, or someone is starting the environment for the first time.
github: "https://github.com/BioTender-max/awesome-bio-agent-skills/tree/main/skills/adaptyv/setup"
language: Python
stars: 174
forks: 30
install: "npx degit https://github.com/BioTender-max/awesome-bio-agent-skills/tree/main/skills/adaptyv/setup ~/.claude/skills/setup"
installs_to: ~/.claude/skills/setup
source_path: skills/adaptyv/setup/SKILL.md
collection_size: 25
category_size: 2109
collection_url: "https://dirskills.com/collections/BioTender-max/awesome-bio-agent-skills"
added: 2026-09-07T05:21:58.870Z
last_synced: 2026-09-07T05:21:58.870Z
canonical_url: "https://dirskills.com/skills/setup-4"
---

# Setup

Setup helps users install Modal, authenticate it, and clone biomodals so protein design tools can run. Use it when commands fail, Modal is missing, or someone is starting the environment for the first time.

**Install:**

```bash
npx degit https://github.com/BioTender-max/awesome-bio-agent-skills/tree/main/skills/adaptyv/setup ~/.claude/skills/setup
```

## README

# 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

### Error: "modal: command not found"

**Cause**: Modal CLI not installed.

**Fix**:
```bash
pip install modal
```

Then restart the terminal or run `hash -r`.

### Error: "Permission denied" or "Unauthorized"

**Cause**: Modal not authenticated.

**Fix**:
```bash
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**:
```bash
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):
```bash
modal run modal_boltzgen.py --help
```

Or install uv if you prefer using uvx:
```bash
pip install uv
```

## Full setup steps

### Step 1: Install Modal CLI

```bash
pip install modal
```

Verify: `modal --version`

### Step 2: Authenticate Modal

```bash
modal setup
```

This opens a browser. Click "Authorize".

Verify: `modal token show`

### Step 3: Clone biomodals

```bash
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

```bash
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:

```bash
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
modal run modal_rfdiffusion.py --pdb target.pdb --contigs "A1-150/0 70-100" --num-designs 100

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

## GPU selection

Set GPU with environment variable:

```bash
GPU=A10G modal run modal_rfdiffusion.py --pdb target.pdb --contigs "A1-100/0 50-80" --num-designs 10
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 free tier

Modal offers $30/month in free credits - enough for:
- ~500 BoltzGen designs
- ~2000 RFdiffusion backbones
- ~1000 Chai predictions

---

**Full documentation**: See [Installation Guide](../../docs/installation.md)