First Login & Setup Wizard
After installation, SeqDesk needs initial configuration before it can accept users and orders. This page walks through the first-time setup process.
Setup Wizard
When you first navigate to your SeqDesk instance, the system detects that the
database has not been configured and redirects you to the setup page at /setup.
The setup wizard runs automatically:
Database initialization
The wizard checks the PostgreSQL connection and applies the schema if it does not exist. Two status indicators show progress:
- Database connection — Ready / Unavailable
- Initial data — Setting up / Configured / Not seeded
Default accounts are created
The auto-seed process creates two accounts:
| Account | Password | Role | |
|---|---|---|---|
| Admin | admin@example.com | admin | FACILITY_ADMIN |
| Researcher | user@example.com | user | RESEARCHER |
Default configuration is applied
The seed also creates:
- Site settings with default values (site name, colors, contact email)
- Default order form configuration (sequencing platform, library strategy, etc.)
- Default study form configuration
Change the default passwords immediately after first login. Navigate to your profile to update credentials.
Logging In
Once setup completes, navigate to /login and sign in with the admin
credentials above. After authentication you are redirected to the Orders
page — the default landing page for all users.
User Roles
SeqDesk has two roles:
RESEARCHER — The default role for new accounts.
- Create and manage own orders
- Create studies and assign samples
- View analysis results
- Access: Orders, Studies, Analysis, Help
FACILITY_ADMIN — Full administrative access.
- View all orders from all researchers
- Access the admin panel at
/admin - Manage users, departments, and settings
- Configure pipelines, ENA credentials, and sequencing technologies
- Create invite codes for new admins
Inviting Users
Researchers
Researchers self-register at /register. The registration form collects:
- First name, last name, email
- Research department (from the departments you configure)
- Researcher role (PI, Postdoc, PhD Student, Master Student, Technician, Other)
- Institution (optional)
- Password (minimum 8 characters)
Additional Admins
To add more facility administrators:
Generate an invite code
Go to Admin → Admin Accounts and create a new invite code. You can optionally restrict it to a specific email address and set an expiration date.
Share the code
Send the invite code to the new admin. They register at /register/admin and
enter the code to verify before creating their account. The admin registration
requires a minimum 6-character password.
Manual Setup
If auto-seeding fails (rare), you can run the setup commands manually:
npm run db:migrate:deploy # Apply database schema
npm run db:seed # Seed default data