SeqDesk Documentation

Open Source Docs

SeqDesk runs a sequencing facility on one machine you control. A researcher submits a sequencing request; facility staff track the samples through the sequencer, link the resulting FASTQ files, run Nextflow analyses over them, and submit the outcome to the European Nucleotide Archive. Nothing leaves your network: sequencing files are referenced by path on your own storage, and the database, the web application, and the pipeline execution all run on your hardware.

Guided installer

curl -fsSLo /tmp/seqdesk-install.sh https://seqdesk.org/install.sh &&
bash /tmp/seqdesk-install.sh --interactive --dir "$HOME/seqdesk"

Install Node.js and npm first (22.13.0+ on the 22.x line, or 24.x); the shell installer needs npm as well, to install the application's runtime dependencies. Downloading the installer first keeps the guided prompts and avoids a global npm install. You do not need to set up a database: SeqDesk reuses a local PostgreSQL you already own, or creates its own socket-only cluster under ~/.seqdesk/postgres (override with SEQDESK_PG_HOME) and starts it from the install directory's start.sh. Fresh installs set up the core application only; add --with-pipelines when the host should also provision Conda, Java, and Nextflow immediately. Otherwise choose the workflows later with seqdesk pipelines list and seqdesk pipelines install <name>. The guided pipeline setup checks the runtime, configuration, reference databases, and local paths before enabling the package.

SeqDesk is open source and self-hosted by default. It assumes a closed, trusted network — an institutional intranet or a VPN — not the public internet. See Limitations before exposing an instance.

Who these docs are for

SeqDesk has exactly two roles in the application (FACILITY_ADMIN and RESEARCHER), and the documentation is organised around them plus the person who has to get the thing installed in the first place.

You are	You want	Start at
Evaluating SeqDesk	To see it running on your laptop or a spare VM within the hour	Installation quickstart, then First Login & Setup
Running the facility (`FACILITY_ADMIN`)	Storage, sequencers, forms, pipelines, users, ENA credentials	Admin quickstart and Administration
Submitting samples (`RESEARCHER`)	To raise a sequencing order, attach metadata, and read the results	Researcher quickstart and Sequencing Orders & Samples
Automating a deployment	Unattended installs, config files, updates, backups	settings.json, Configuration, Updates & Maintenance

There is no per-department or per-project permission layer beyond those two roles. A researcher sees their own sequencing orders (plus their department’s, if access.departmentSharing is on); a facility admin sees everything and is the only role that can launch pipelines or submit to ENA.

The three things people come here to do

1. Install it

One command downloads the installer and walks you through two questions — which database, and which administrator account. You do not need to install or configure PostgreSQL first: if the installer finds no local server it can safely reuse, it creates and owns a private, socket-only cluster under ~/.seqdesk/postgres. You need Node.js 22.13.0–22.x or 24.x, and a normal non-root user account.

Begin at Installation quickstart. Check Prerequisites first if this is a shared server. If the install fails, Common problems is a symptom-to-fix table and is the page the installer’s own error messages link to. If you cannot sign in afterwards, see Reset a password.

2. Learn how the workflow fits together

Three entity names do most of the work, and two of them are easy to confuse:

A Sequencing Order is a researcher’s request — the questionnaire answers, the list of samples, the metadata and billing details. It is the Order model in the schema, and its identifiers look like ORD-20260415-0007.
A Sequencing Run is the physical sequencer run: the run plan, the barcode-to-sample assignment, the QC, the reads that come off the instrument. One sequencing order contains one or more sequencing runs.
A Study groups samples — possibly from several sequencing orders — for analysis and for publication to ENA. Studies carry the MIxS checklist and environment package.

Read How SeqDesk Works for the data flow end to end, then Sequencing Orders & Samples and Studies for each half of that picture.

3. Operate it day to day

Everything an administrator configures lives under Settings in the sidebar: storage paths, sequencer definitions, the order and study form builders, pipeline runtime, users and departments, ENA Webin credentials, and — under Settings → Info — the version, telemetry and software updates. Administration covers each screen; Updates & Maintenance covers upgrading and rolling back.

Getting Started

QuickstartInstall SeqDesk and create your first sequencing order in minutes.How SeqDesk WorksArchitecture, data flow, and the end-to-end workflow.FAQRequirements, second installs, forgotten passwords, and what the health check covers.Best PracticesTips for organizing sequencing orders, metadata, and pipeline runs.LimitationsWhat SeqDesk deliberately does not do, and where it should not be deployed.ChangelogRelease history and version notes.

Platforms & Integrations

Sequencing Orders & SamplesCreate sequencing orders, manage samples, metadata, and sequencing runs.StudiesGroup samples for analysis and ENA submission.Sequencing FilesFile discovery, auto-detection, and assignment to samples.Pipelines & AnalysisRun Nextflow workflows, monitor progress, view results. Optional — the core app runs without them.ENA SubmissionSubmit sequences to the European Nucleotide Archive.Support & MessagesBuilt-in ticket system for researcher–facility communication.

Deployment & Configuration

InstallationGuided and unattended installs, platform guides, health checks, recovery.ConfigurationEnvironment variables, config files, and runtime settings.AdministrationUsers, departments, storage, pipelines, and sequencing tech.Updates & MaintenanceAutomatic updates, manual rollback, and backup strategy.

Reference & Resources

Data ModelEntity relationships, key models, and the Prisma schema structure.ArchitectureTech stack, application layers, pipeline execution, and config resolution.Pipeline APIDiscover and download analysis pipelines via REST endpoints.

Cannot find what you need? The FAQ collects the questions people actually ask during a first install, and Support & Messages covers the in-app ticket system. For bugs and feature requests, open an issue on GitHub .