setup

Name: setup
Author: adaptyvbio

30installs20forks

How to install setup?

adaptyvbio/protein-design-skills/setup

$npx -y skills add adaptyvbio/protein-design-skills --skill setup

Installs into the current project.

Summary

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,

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SKILL.md

1	# Setup Guide
2
3	Help users get their environment ready to run protein design tools.
4
5	## Quick checklist
6
7	Run through this checklist when a user encounters setup issues:
8
9	\| Step \| Check \| Fix \|
10	\|------\|-------\|-----\|
11	\| 1. Modal CLI \| `modal --version` \| `pip install modal` \|
12	\| 2. Modal auth \| `modal token show` \| `modal setup` \|
13	\| 3. biomodals \| `ls biomodals/modal_*.py` \| `git clone https://github.com/hgbrian/biomodals` \|
14	\| 4. Test \| `cd biomodals && modal run modal_boltzgen.py --help` \| See troubleshooting \|
15
16	## Diagnosing issues
17
18	### Error: "modal: command not found"
19
20	Cause: Modal CLI not installed.
21
22	Fix:
23	```bash
24	pip install modal
25	```
26
27	Then restart the terminal or run `hash -r`.
28
29	### Error: "Permission denied" or "Unauthorized"
30
31	Cause: Modal not authenticated.
32
33	Fix:
34	```bash
35	modal setup
36	```
37
38	This opens a browser. Click "Authorize" to complete authentication.
39
40	### Error: "No such file or directory: modal_boltzgen.py"
41
42	Cause: biomodals repository not cloned or not in correct directory.
43
44	Fix:
45	```bash
46	git clone https://github.com/hgbrian/biomodals
47	cd biomodals
48	```
49
50	### Error: "uvx: command not found"
51
52	Cause: `uvx` is an optional wrapper from the `uv` package. It's not required.
53
54	Fix: Run modal directly (recommended):
55	```bash
56	modal run modal_boltzgen.py --help
57	```
58
59	Or install uv if you prefer using uvx:
60	```bash
61	pip install uv
62	```
63
64	## Full setup steps
65
66	### Step 1: Install Modal CLI
67
68	```bash
69	pip install modal
70	```
71
72	Verify: `modal --version`
73
74	### Step 2: Authenticate Modal
75
76	```bash
77	modal setup
78	```
79
80	This opens a browser. Click "Authorize".
81
82	Verify: `modal token show`
83
84	### Step 3: Clone biomodals
85
86	```bash
87	git clone https://github.com/hgbrian/biomodals
88	cd biomodals
89	```
90
91	Verify: `ls modal_*.py` should show files like `modal_boltzgen.py`
92
93	### Step 4: Test the Setup
94
95	```bash
96	cd biomodals
97	modal run modal_boltzgen.py --help
98	```
99
100	Expected: Usage instructions appear showing `--input-yaml`, `--protocol`, `--num-designs` options.
101
102	## Common workflows after setup
103
104	Once setup is complete, users can:
105
106	```bash
107	cd biomodals
108
109	# Design binders with BoltzGen (requires YAML config)
110	modal run modal_boltzgen.py --input-yaml binder.yaml --protocol protein-anything --num-designs 50
111
112	# Generate backbones with RFdiffusion (official repo, not biomodals)
113	python run_inference.py inference.input_pdb=target.pdb contigmap.contigs=[A1-150/0 70-100] inference.num_designs=100
114
115	# Validate with Chai
116	modal run modal_chai1.py --input-faa designs.fasta
117	```
118
119	## GPU selection
120
121	Set GPU with environment variable:
122
123	```bash
124	GPU=L40S modal run modal_boltzgen.py --input-yaml config.yaml --num-designs 50
125	GPU=A100 modal run modal_chai1.py --input-faa complex.fasta
126	```
127
128	\| GPU \| VRAM \| Best For \|
129	\|-----\|------\|----------\|
130	\| T4 \| 16GB \| ProteinMPNN, ESM \|
131	\| A10G \| 24GB \| RFdiffusion, Chai \|
132	\| L40S \| 48GB \| BoltzGen, BindCraft \|
133	\| A100 \| 40-80GB \| Large complexes \|
134
135	## Modal free tier
136
137	Modal offers $30/month in free credits - enough for:
138	- ~500 BoltzGen designs
139	- ~2000 RFdiffusion backbones
140	- ~1000 Chai predictions
141
142	---
143
144	Full documentation: See [Getting started](../../docs/getting-started.md)

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setup

30installs20forks

View on GitHub

How to install setup?

adaptyvbio/protein-design-skills/setup

$npx -y skills add adaptyvbio/protein-design-skills --skill setup

Installs into the current project.

Summary

Files · 1

View on GitHub

SKILL.md

1	# Setup Guide
2
3	Help users get their environment ready to run protein design tools.
4
5	## Quick checklist
6
7	Run through this checklist when a user encounters setup issues:
8
9	\| Step \| Check \| Fix \|
10	\|------\|-------\|-----\|
11	\| 1. Modal CLI \| `modal --version` \| `pip install modal` \|
12	\| 2. Modal auth \| `modal token show` \| `modal setup` \|
13	\| 3. biomodals \| `ls biomodals/modal_*.py` \| `git clone https://github.com/hgbrian/biomodals` \|
14	\| 4. Test \| `cd biomodals && modal run modal_boltzgen.py --help` \| See troubleshooting \|
15
16	## Diagnosing issues
17
18	### Error: "modal: command not found"
19
20	Cause: Modal CLI not installed.
21
22	Fix:
23	```bash
24	pip install modal
25	```
26
27	Then restart the terminal or run `hash -r`.
28
29	### Error: "Permission denied" or "Unauthorized"
30
31	Cause: Modal not authenticated.
32
33	Fix:
34	```bash
35	modal setup
36	```
37
38	This opens a browser. Click "Authorize" to complete authentication.
39
40	### Error: "No such file or directory: modal_boltzgen.py"
41
42	Cause: biomodals repository not cloned or not in correct directory.
43
44	Fix:
45	```bash
46	git clone https://github.com/hgbrian/biomodals
47	cd biomodals
48	```
49
50	### Error: "uvx: command not found"
51
52	Cause: `uvx` is an optional wrapper from the `uv` package. It's not required.
53
54	Fix: Run modal directly (recommended):
55	```bash
56	modal run modal_boltzgen.py --help
57	```
58
59	Or install uv if you prefer using uvx:
60	```bash
61	pip install uv
62	```
63
64	## Full setup steps
65
66	### Step 1: Install Modal CLI
67
68	```bash
69	pip install modal
70	```
71
72	Verify: `modal --version`
73
74	### Step 2: Authenticate Modal
75
76	```bash
77	modal setup
78	```
79
80	This opens a browser. Click "Authorize".
81
82	Verify: `modal token show`
83
84	### Step 3: Clone biomodals
85
86	```bash
87	git clone https://github.com/hgbrian/biomodals
88	cd biomodals
89	```
90
91	Verify: `ls modal_*.py` should show files like `modal_boltzgen.py`
92
93	### Step 4: Test the Setup
94
95	```bash
96	cd biomodals
97	modal run modal_boltzgen.py --help
98	```
99
100	Expected: Usage instructions appear showing `--input-yaml`, `--protocol`, `--num-designs` options.
101
102	## Common workflows after setup
103
104	Once setup is complete, users can:
105
106	```bash
107	cd biomodals
108
109	# Design binders with BoltzGen (requires YAML config)
110	modal run modal_boltzgen.py --input-yaml binder.yaml --protocol protein-anything --num-designs 50
111
112	# Generate backbones with RFdiffusion (official repo, not biomodals)
113	python run_inference.py inference.input_pdb=target.pdb contigmap.contigs=[A1-150/0 70-100] inference.num_designs=100
114
115	# Validate with Chai
116	modal run modal_chai1.py --input-faa designs.fasta
117	```
118
119	## GPU selection
120
121	Set GPU with environment variable:
122
123	```bash
124	GPU=L40S modal run modal_boltzgen.py --input-yaml config.yaml --num-designs 50
125	GPU=A100 modal run modal_chai1.py --input-faa complex.fasta
126	```
127
128	\| GPU \| VRAM \| Best For \|
129	\|-----\|------\|----------\|
130	\| T4 \| 16GB \| ProteinMPNN, ESM \|
131	\| A10G \| 24GB \| RFdiffusion, Chai \|
132	\| L40S \| 48GB \| BoltzGen, BindCraft \|
133	\| A100 \| 40-80GB \| Large complexes \|
134
135	## Modal free tier
136
137	Modal offers $30/month in free credits - enough for:
138	- ~500 BoltzGen designs
139	- ~2000 RFdiffusion backbones
140	- ~1000 Chai predictions
141
142	---
143
144	Full documentation: See [Getting started](../../docs/getting-started.md)

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6 picks

Type