Environment Variables

All SeqDesk environment variables use the SEQDESK_ prefix. They have the highest priority in the configuration resolution order, overriding config file and database values.

Value Parsing

Environment variables are parsed according to their target type:

Booleans — "true" / "false" (case-insensitive)
Numbers — parsed as integers for fields like scanDepth, cores, sessionTimeout
Arrays — comma-separated values, e.g. ".fastq.gz,.fq.gz,.fastq,.fq"
Strings — all other values

Site Settings

Variable	Config Path	Type	Default	Description
`SEQDESK_SITE_NAME`	`site.name`	string	`"SeqDesk"`	Display name of the facility
`SEQDESK_DATA_PATH`	`site.dataBasePath`	string	`"./data"`	Base path for sequencing data storage
`SEQDESK_CONTACT_EMAIL`	`site.contactEmail`	string	—	Facility contact email address

Pipeline Settings

Variable	Config Path	Type	Default	Description
`SEQDESK_PIPELINES_ENABLED`	`pipelines.enabled`	boolean	`false`	Master switch for all pipeline features
`SEQDESK_PIPELINE_DATABASE_DIR`	`pipelines.databaseDirectory`	string	`""`	Shared root directory for large pipeline database assets
`SEQDESK_PIPELINE_RUN_DIR`	`pipelines.execution.runDirectory`	string	`"./pipeline_runs"`	Output directory for pipeline runs
`SEQDESK_PIPELINE_MODE`	`pipelines.execution.mode`	enum	`"local"`	Execution mode: `local`, `slurm`, or `kubernetes`

Conda

Variable	Config Path	Type	Default	Description
`SEQDESK_CONDA_ENABLED`	`pipelines.execution.conda.enabled`	boolean	`false`	Use Conda for pipeline dependencies
`SEQDESK_CONDA_PATH`	`pipelines.execution.conda.path`	string	`"/opt/conda"`	Path to Conda installation
`SEQDESK_CONDA_ENV`	`pipelines.execution.conda.environment`	string	—	Conda environment name

SLURM

Variable	Config Path	Type	Default	Description
`SEQDESK_SLURM_ENABLED`	`pipelines.execution.slurm.enabled`	boolean	`false`	Enable SLURM job submission
`SEQDESK_SLURM_QUEUE`	`pipelines.execution.slurm.queue`	string	`"default"`	SLURM partition/queue name
`SEQDESK_SLURM_CORES`	`pipelines.execution.slurm.cores`	integer	`4`	CPU cores per job
`SEQDESK_SLURM_MEMORY`	`pipelines.execution.slurm.memory`	string	`"16GB"`	Memory per job
`SEQDESK_SLURM_TIME`	`pipelines.execution.slurm.timeLimit`	integer	`24`	Time limit in hours

MAG Pipeline

Variable	Config Path	Type	Default	Description
`SEQDESK_MAG_ENABLED`	`pipelines.mag.enabled`	boolean	`true`	Enable nf-core/mag pipeline
`SEQDESK_MAG_VERSION`	`pipelines.mag.version`	string	`"3.4.0"`	nf-core/mag pipeline version
`SEQDESK_MAG_STUB`	`pipelines.mag.stubMode`	boolean	`false`	Use stub mode (test mode, no real analysis)

ENA Submission

Variable	Config Path	Type	Default	Description
`SEQDESK_ENA_TEST_MODE`	`ena.testMode`	boolean	`true`	Use ENA test server instead of production
`SEQDESK_ENA_USERNAME`	`ena.username`	string	—	Webin account username
`SEQDESK_ENA_PASSWORD`	`ena.password`	string	—	Webin account password
`SEQDESK_ENA_CENTER`	`ena.centerName`	string	`""`	Submission center name
`SEQDESK_ENA_BROKER_ACCOUNT`	`ena.brokerAccount`	boolean	`false`	Webin account has ENA broker permissions

Always set ENA credentials through environment variables or the Admin UI — never commit them to a config file.

Sequencing Files

Variable	Config Path	Type	Default	Description
`SEQDESK_FILES_EXTENSIONS`	`sequencingFiles.extensions`	array	`".fastq.gz,.fq.gz,.fastq,.fq"`	Allowed file extensions (comma-separated)
`SEQDESK_FILES_SCAN_DEPTH`	`sequencingFiles.scanDepth`	integer	`2`	Directory scan depth (1–10)
`SEQDESK_FILES_SINGLE_END`	`sequencingFiles.allowSingleEnd`	boolean	`true`	Allow single-end reads

Authentication

Variable	Config Path	Type	Default	Description
`SEQDESK_AUTH_REGISTRATION`	`auth.allowRegistration`	boolean	`true`	Allow public user registration
`SEQDESK_SESSION_TIMEOUT`	`auth.sessionTimeout`	integer	`24`	Session timeout in hours

Runtime Variables

These standard environment variables are used by the application runtime. They can also be set in the runtime section of the config file — if not already present as environment variables, the config file values are applied to process.env at startup.

Variable	Config Path	Description
`DATABASE_URL`	`runtime.databaseUrl`	PostgreSQL runtime connection string
`DIRECT_URL`	`runtime.directUrl`	Direct PostgreSQL connection for Prisma migrations
`NEXTAUTH_URL`	`runtime.nextAuthUrl`	NextAuth.js callback URL (e.g. `http://localhost:3000`)
`NEXTAUTH_SECRET`	`runtime.nextAuthSecret`	Session signing secret (generate with `openssl rand -base64 32`)
`SEQDESK_UPDATE_SERVER`	`runtime.updateServer`	Update server URL (default: `https://seqdesk.com`)

SeqDesk.com Admin Variables

These variables are used by the hosted SeqDesk.com admin service, not by an installed SeqDesk runtime. Configure them on the SeqDesk.com deployment when using install-profile administration features.

Variable	Required	Default	Description
`NEON_API_KEY`	For hosted Neon provisioning	—	Neon API key used by the install-profile admin panel to create, test, and delete managed Neon projects
`NEON_ORG_ID`	No	—	Optional Neon organization id passed when creating projects with a personal API key
`NEON_DEFAULT_REGION_ID`	No	`aws-eu-central-1`	Region id for newly provisioned hosted Neon databases

Telemetry

These map to both the runtime config (telemetry.*) and the install-time heartbeat configuration. See Operational Telemetry for what gets reported.

Variable	Config Path	Type	Default	Description
`SEQDESK_TELEMETRY_ENABLED`	`telemetry.enabled`	boolean	`false`	Opt-in anonymous heartbeats
`SEQDESK_TELEMETRY_ENDPOINT`	`telemetry.endpoint`	string	`https://www.seqdesk.com/api/telemetry/heartbeat`	Heartbeat URL
`SEQDESK_TELEMETRY_INTERVAL_HOURS`	`telemetry.intervalHours`	integer	`24`	Minimum hours between heartbeats

SEQDESK_TELEMETRY_DISABLED=true is a hard kill-switch — it forces telemetry off regardless of the database setting, config file, or SEQDESK_TELEMETRY_ENABLED. It is not part of the standard config resolution; it short-circuits before any other source is consulted.

Notifications

Variable	Config Path	Type	Default	Description
`SEQDESK_NOTIFICATIONS_ENABLED`	`notifications.enabled`	boolean	`false`	Master switch for the hosted email notification relay
`SEQDESK_IN_APP_NOTIFICATIONS_ENABLED`	`notifications.inApp.enabled`	boolean	`true`	Master switch for the in-app notification panel/channel
`SEQDESK_NOTIFICATION_PROVIDER`	`notifications.provider`	string	`"seqdesk-relay"`	Notification provider (only `seqdesk-relay` is supported)
`SEQDESK_NOTIFICATION_RELAY_URL`	`notifications.relayUrl`	string	`https://www.seqdesk.com/api/notifications/relay`	Hosted relay endpoint
`SEQDESK_NOTIFICATION_RELAY_TOKEN`	`notifications.relayToken`	string	—	Scoped notification relay token (secret)

Set the relay token through this environment variable — never commit it to a config file. It is masked in /api/admin/config/status responses.

Installer-only Variables

These variables are consumed by install-dist.sh and the seqdesk launcher before the app starts. They have no effect on a running app — they configure the install flow itself. Each one matches a CLI flag in the Full installer flag reference.

Target and mode

Variable	Type	Default	Description
`SEQDESK_DIR`	path	`./seqdesk`	Installation directory
`SEQDESK_VERSION`	string	latest	Release version to install
`SEQDESK_YES`	boolean	`0`	Non-interactive mode
`SEQDESK_OVERWRITE_EXISTING`	boolean	`0`	With `-y`, back up an existing install dir to `<dir>.backup.<timestamp>` and replace it
`SEQDESK_LOG`	path	`/tmp/seqdesk-install-<timestamp>.log`	Install log path
`SEQDESK_USE_PM2`	boolean	—	`1` to start under PM2; `0` to disable
`SEQDESK_API`	string	`https://www.seqdesk.com/api`	Advanced: override release metadata endpoint

Configuration source

Variable	Type	Description
`SEQDESK_CONFIG`	path or URL	Infrastructure JSON file
`SEQDESK_ADDITIONAL_SETTINGS_FILE`	path	Local JSON overrides applied after `SEQDESK_CONFIG`
`SEQDESK_RECONFIGURE`	boolean	Re-apply config to an existing install
`SEQDESK_RESEED_DB`	boolean	Force DB push + seed during `--reconfigure`
`SEQDESK_PREPARE_POSTGRES`	boolean	Prepare local PostgreSQL role/database, then exit

Infrastructure overrides

Variable	Type	Description
`SEQDESK_PORT`	integer	App port (default `8000`)
`SEQDESK_DATABASE_URL`	string	`DATABASE_URL`
`SEQDESK_DATABASE_DIRECT_URL`	string	`DIRECT_URL` for Prisma migrations
`SEQDESK_NEXTAUTH_URL`	string	`NEXTAUTH_URL`
`SEQDESK_NEXTAUTH_SECRET`	string	`NEXTAUTH_SECRET`
`SEQDESK_RUN_DIR`	path	Pipeline run directory override

Secrets

Variable	Type	Description
`SEQDESK_ANTHROPIC_API_KEY`	string	Anthropic API key for AI validation
`SEQDESK_ADMIN_SECRET`	string	Release publishing admin secret
`SEQDESK_BLOB_READ_WRITE_TOKEN`	string	Vercel Blob token

Pipeline toggles

Variable	Type	Description
`SEQDESK_WITH_PIPELINES`	boolean	`1` to install Conda + Nextflow; `0` to skip
`SEQDESK_WITH_CONDA`	boolean	Legacy alias for installing Miniconda
`SEQDESK_SKIP_DEPS`	boolean	Deprecated; ignored in the distribution installer

Pipeline-execution overrides

These let you set runtime pipeline-execution settings at install time without editing a config file. They are written into SiteSettings.extraSettings.pipelineExecution during install.

Variable	Maps to	Description
`SEQDESK_EXEC_MODE`	`pipelines.execution.mode`	Execution mode written into the config file (`local`, `slurm`, or `kubernetes`)
`SEQDESK_EXEC_USE_SLURM`	`pipelines.execution.slurm.enabled`	Enable SLURM submission
`SEQDESK_EXEC_SLURM_QUEUE`	`pipelines.execution.slurm.queue`	Partition/queue name
`SEQDESK_EXEC_SLURM_CORES`	`pipelines.execution.slurm.cores`	CPUs per job
`SEQDESK_EXEC_SLURM_MEMORY`	`pipelines.execution.slurm.memory`	Memory per job
`SEQDESK_EXEC_SLURM_TIME_LIMIT`	`pipelines.execution.slurm.timeLimit`	Hours per job
`SEQDESK_EXEC_SLURM_OPTIONS`	`pipelines.execution.slurm.options`	Extra `sbatch` flags
`SEQDESK_EXEC_CONDA_PATH`	`pipelines.execution.conda.path`	Conda installation path
`SEQDESK_EXEC_CONDA_ENV`	`pipelines.execution.conda.environment`	Conda environment name
`SEQDESK_EXEC_NEXTFLOW_PROFILE`	Pipeline runtime	Nextflow profile (`conda`, `docker`, `singularity`, `standard`)
`SEQDESK_EXEC_WEBLOG_URL`	Pipeline runtime	Nextflow weblog endpoint
`SEQDESK_EXEC_WEBLOG_SECRET`	Pipeline runtime	Shared secret for weblog requests

Private pipeline package (MetaXpath)

Variable	Alias	Description
`SEQDESK_METAXPATH_PACKAGE_URL`	`METAXPATH_PACKAGE_URL`	Optional tarball URL override for the private MetaXpath package
`SEQDESK_METAXPATH_KEY`	`METAXPATH_PACKAGE_TOKEN`	GitHub/package bearer token used to resolve and download the private package
`SEQDESK_METAXPATH_SHA256`	`METAXPATH_PACKAGE_SHA256`	Optional expected tarball checksum override

SEQDESK_METAXPATH_PACKAGE_URL and SEQDESK_METAXPATH_SHA256 are normally left unset: when only a MetaXpath token is provided, the GitHub release asset URL and SHA256 digest are resolved automatically.

Form presets

Variable	Type	Description
`SEQDESK_ORDER_FORM_SETTINGS`	path	JSON exported from Admin > Order Form > Import / Export to apply after seed
`SEQDESK_STUDY_FORM_SETTINGS`	path	JSON exported from Admin > Study Forms > Import / Export to apply after seed

Examples

Set variables in your shell, .env file, or deployment system:


# Site
export SEQDESK_SITE_NAME="My Sequencing Facility"
export SEQDESK_DATA_PATH="/mnt/sequencing/data"
 
# ENA (use env vars for secrets)
export SEQDESK_ENA_USERNAME="Webin-12345"
export SEQDESK_ENA_PASSWORD="your-password"
export SEQDESK_ENA_TEST_MODE="false"
 
# SLURM cluster
export SEQDESK_PIPELINE_MODE="slurm"
export SEQDESK_SLURM_ENABLED="true"
export SEQDESK_SLURM_QUEUE="bioinformatics"
export SEQDESK_SLURM_CORES="16"
export SEQDESK_SLURM_MEMORY="64GB"
 
# Install-time form presets
export SEQDESK_ORDER_FORM_SETTINGS="/opt/seqdesk-presets/order-form.json"
export SEQDESK_STUDY_FORM_SETTINGS="/opt/seqdesk-presets/study-form.json"