Installation¶
Install and configure the flow command-line tool.
Requirements¶
- Python 3.11 or higher
- pip or uv package manager
Install from PyPI¶
Or with uv:
Verify Installation¶
Authentication¶
Login with Email/Password¶
Or use environment variables:
Check Login Status¶
Output:
Logout¶
Configuration¶
View Current Settings¶
Set API Endpoints¶
For production:
flow config set api_url https://files.iflow.intelliseq.com
flow config set compute_url https://compute.iflow.intelliseq.com
For development:
Configuration File¶
Settings are stored in ~/.config/iseq-flow/config.json:
{
"api_url": "https://files.iflow.intelliseq.com",
"compute_url": "https://compute.iflow.intelliseq.com"
}
Environment Variables¶
| Variable | Description | Default |
|---|---|---|
FLOW_API_URL |
File service URL | http://localhost:8002 |
FLOW_COMPUTE_URL |
Compute service URL | http://localhost:8005 |
FLOW_EMAIL |
Login email | - |
FLOW_PASSWORD |
Login password | - |
Environment variables override config file settings.
Security Notes¶
Token Storage:
- On desktop systems, tokens are stored in your system's secure keyring (macOS Keychain, GNOME Keyring, Windows Credential Manager)
- On headless servers without a keyring, tokens are stored in
~/.local/share/python_keyring/- ensure this directory has restricted permissions (chmod 700)
Password Authentication:
- Use
--passwordonly in secure environments (CI/CD with secrets management) - Prefer Device Flow (
flow login) when possible - it doesn't expose credentials
Next Steps¶
- Commands Reference - All available commands
- Running Pipelines - Execute Nextflow workflows