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 and cores
• Arrays — comma-separated values, e.g. ".fastq.gz,.fq.gz,.fastq,.fq"
• Strings — all other values

Site Settings

Pipeline Settings

Conda

Pipeline execution is Conda-only. SeqDesk always sets its pipeline runtime mode to Conda and adds the conda Nextflow profile when needed.

SLURM

MAG Pipeline

ENA Submission

Sequencing Files

Authentication

Accepted Compatibility Variables (Unsupported)

The configuration loader still recognizes these names so older configuration files and deployment manifests continue to parse. They are not functional controls in the current runtime:

Do not use these variables to express an operational requirement. In particular, there is currently no supported switch to disable Conda execution, reject all single-end reads, or set the authentication session lifetime.

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.

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.

Telemetry

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

Notifications

Important 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. This is a practical subset, not a generated exhaustive list. See the installer input reference and seqdesk --help for the supported CLI surface.

Target and mode

Configuration source

Infrastructure overrides

Secrets

Pipeline toggles

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.

When SEQDESK_EXEC_CONDA_PATH is set, it takes precedence over PATH and standard user-prefix discovery. A working existing base is reused. A path that does not exist may be created by the Miniconda installer. An existing path that does not contain a working Conda executable stops with recovery instructions; the installer does not delete it or silently select another location.

Private pipeline package (MetaXpath)

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

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"