Administration

Everything in this section is done by a facility admin. SeqDesk has exactly two roles, and FACILITY_ADMIN is the one that unlocks the admin area, the whole /api/admin/** surface, visibility of every sequencing order, and the ability to launch pipelines and register data with ENA. If you are configuring a SeqDesk instance for other people to use, you are reading the right section.

The mental model

A SeqDesk instance is one facility. There is a single row of global settings (SiteSettings, id singleton) that everything on these pages writes into, so “changing a setting” is always instance-wide — there is no per-department or per-project configuration layer.

Settings reach the running application from three places, and they do not have equal weight:

Telemetry is the one deliberate exception: there, the stored database choice wins over the config file, so an admin’s explicit opt-in or opt-out is not silently reverted by a deployment default.

Where to start

A brand-new instance is usable in roughly this order. Each step unblocks the next, and the sidebar’s Infrastructure entry shows a red badge until the two required items are done.

1. Data Storage — point SeqDesk at the directory holding your FASTQ files. Nothing about sequencing files works until this is set.
2. Pipeline Runtime — set the pipeline run directory, and Conda plus SLURM if you intend to run analyses.
3. Departments — create them before researchers register, because the registration form only offers departments that already exist and are active.
4. Modules — turn features on or off before customising forms, since a disabled module hides its field types everywhere.
5. Sequencing Order Form — trim the intake form to what your facility actually needs to know.
6. Sequencers — disable the instruments and kits you do not offer.
7. ENA Configuration — only if you submit to the European Nucleotide Archive.
8. Accounts — invite your co-admins, then decide on department sharing.

Guides in this section

Every admin screen

The sidebar groups admin screens under Users and Settings. The labels below are the ones you see in the sidebar; the headings on the pages themselves sometimes differ, so both are given.

Users

Settings

Three screens have no sidebar entry of their own and are reached from the pages that link to them:

Visiting /admin itself shows only a “Select an admin page” placeholder — there is no admin dashboard.

Modules

Modules (/admin/modules) is the on/off switch for optional features. Disabling a module hides its field types from every form builder and from the forms researchers see, regardless of each field’s own visibility setting, so it is the coarsest control you have.

sequencing-tech cannot be disabled. The page also has a global kill switch (globalDisabled) that forces every optional module off at once. Modules explains which field types each one contributes and why enabling a module is only half the job.

Related sections

• Installation — getting an instance running, including the bootstrap admin account created by the installer.
• Configuration — the full settings.json and environment-variable reference behind these screens.
• Updates & Maintenance — in-app updates and rollback.
• Reference → Data Model — the schema names behind the UI labels.