Getting Started
This section takes you from nothing to a SeqDesk instance that a real researcher can raise a real sequencing order against. It is deliberately ordered: each page assumes the one before it is done.
Install
When the installer finishes it prints an Install complete block with a
Browser URL (what you open) and a Local health URL (what curl and
seqdesk doctor use), then a Login block with the administrator account.
Open the Browser URL and sign in with that account. Installed instances use
port 8000 by default, so the local URL is http://127.0.0.1:8000;
http://localhost:3000 is only the repository development-server convention.
If you let the installer generate the admin password, it is shown once, in that closing Login block, and is deliberately kept out of the install log. Copy it before you close the terminal — see First Login & Setup.
What a fresh instance looks like
Sign in as the administrator and you will find an application that works but has nothing in it. Specifically:
- No departments. Self-registering researchers will have no department to pick, and department sharing will do nothing.
- No sequencers. The sequencing-technology registry is empty, so the Sequencing Technology field on the order form has nothing to offer.
- No data storage path. Nothing can be attached to a sample until this is set; the sidebar’s Infrastructure entry carries a warning badge until it is.
- The default order and study forms are seeded and immediately usable — a two-step order questionnaire plus Samples and Review.
- Pipelines are off unless you installed with
--with-pipelines. The core application does not need them. - Nothing is configured for ENA. No Webin credentials, and test mode on.
Fixing those, in that order, is what the Admin Quickstart does.
The order to do things in
1. Get in and secure the account.
First Login & Setup covers what the
installer created, what the /setup screen is telling you if you land there,
and how to replace bootstrap credentials before anyone else can reach the host.
2. Configure the facility. Admin Quickstart is the post-install checklist: departments, sequencers, storage, forms, optionally pipelines and ENA. Do this before inviting researchers — several of these choices are painful to change once real data exists.
3. Prove the loop end to end. Quickstart walks the shortest path from install to a submitted sequencing order so you can confirm the whole chain works on your host.
4. Onboard the researchers.
Researcher Quickstart is the page
to send them. It is written from what a RESEARCHER account can actually reach.
Two quickstarts, because the roles genuinely differ
SeqDesk has exactly two roles and they see materially different applications — not just a hidden settings menu. A researcher cannot attach FASTQ files, cannot start a pipeline, cannot reach the ENA submissions surface, and cannot see a pipeline run until an admin publishes it. An admin sees every order in the instance. Pick the quickstart that matches the person, not the one that looks shorter.
Before you start, or when you get stuck
- The vocabulary — Sequencing Order versus Sequencing Run versus Study — is explained in How SeqDesk Works. Ten minutes there saves confusion on every other page.
- Install failures are covered symptom by symptom in Common problems, and the FAQ answers the questions people ask during a first install.
- Deliberate gaps — no SSO, no API tokens, no global search — are listed in What SeqDesk doesn’t do (yet).
For release history and version notes, see the Changelog.