First Login & Setup
The guided installer checks PostgreSQL, applies the schema, seeds initial data, and creates the administrator account before it prints the browser URL. This page covers the first sign-in and the recovery behavior if seeding could not finish during installation.
First sign-in
Open the installed URL
Use the exact URL from the installer completion summary. Installed instances
default to port 8000; http://localhost:3000 is used by a development server,
not by the packaged installation.
Confirm setup status
The normal installer has already run migrations and seed. If that final seed
could not complete, the app redirects to /setup, checks the database, and
retries initial data setup. Resolve the database or migration error reported by
the installer rather than recreating the database.
Sign in as administrator
Use the administrator email and password chosen in the guided installer. The optional researcher account uses the values chosen there as well.
An unattended install that omits bootstrap account settings creates the published defaults:
| Account | Password | Role | |
|---|---|---|---|
| Admin | admin@example.com | admin | FACILITY_ADMIN |
| Researcher | user@example.com | user | RESEARCHER |
Change or remove those accounts immediately before allowing another machine to reach SeqDesk.
Review the initial configuration
The seed also creates:
- Site settings with default values (site name, colors, contact email)
- Default sequencing order form configuration (sequencing technology, library strategy, etc.)
- Default study form configuration
Bootstrap defaults are public recovery conveniences, not production credentials. Prefer account values supplied through the guided installer or an unattended settings file.
Logging In
Navigate to /login and sign in with the configured administrator account.
After authentication you are redirected to the Sequencing Orders page — the
default landing page for all users.
Built-in Help page
Every signed-in user has access to /help, an in-app reference page rendered
from static content (no configuration needed). It covers the typical workflow
(sequencing order → samples → tracking → studies → publishing), the four main areas
(Sequencing Orders, Studies, Analysis, Publishing), the role split between researchers
and facility admins, and a “where do I do X” task-to-location table. It is
the fastest way to orient a new user without leaving the app.
User Roles
SeqDesk has two roles:
RESEARCHER — The default role for new accounts.
- Create and manage own sequencing orders
- Create studies and assign samples
- View analysis results
- Access: Sequencing Orders, Studies, Analysis, Help
FACILITY_ADMIN — Full administrative access.
- View all sequencing 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