Skip to Content
Overview

SeqDesk Documentation

Open Source Docs

Complete documentation for deploying, configuring, and operating SeqDesk — from installation to ENA submission.

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

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 and Nextflow.

SeqDesk is open source and self-hosted by default. Keep full ownership of your data and infrastructure.

Getting Started

QuickstartInstall SeqDesk and create your first sequencing order in minutes.How SeqDesk WorksArchitecture, data flow, and the end-to-end workflow.Best PracticesTips for organizing sequencing orders, metadata, and pipeline runs.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 nf-core workflows, monitor progress, view results.ENA SubmissionSubmit sequences to the European Nucleotide Archive.Support & MessagesBuilt-in ticket system for researcher–facility communication.

Deployment & Configuration

InstallationInfrastructure config, unattended deployments, and advanced options.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.