Setup Agent Skill
> (1) User is new and hasn't run any tools yet, (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.
Install
one command, takes just this skill from the repositorynpx skills add https://github.com/BioTender-max/awesome-bio-agent-skills --skill setupThe instruction itself
15 sections, as written by the authorSetup 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:
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
Step 1: Install Modal CLI
pip install modal
Verify: modal --version
Step 2: Authenticate Modal
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
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:
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
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How to use it
Take biotender-max/setup from the repository into ~/.claude/skills for personal
use, or into .claude/skills inside a project.
The agent identifies a skill by the name field in its header. Two skills with the
same name cannot sit side by side — one of them will be ignored.
The instructions reference pip.
Without those the skill loads but fails at the first command.