Prerequisites

SeqDesk runs on standard Linux servers and needs Node.js/npm plus a PostgreSQL database. Pipeline execution is optional and adds Conda, Nextflow, and possibly Slurm requirements.

Required

Requirement	Notes
Linux host	AlmaLinux, Rocky Linux, RHEL, Debian, and Ubuntu are supported by the distribution installer.
Node.js + npm	Node.js 18 or newer. Node.js 20 LTS is recommended.
Bash, curl, tar	Used by the npm launcher and release installer.
PostgreSQL	SeqDesk stores application data in PostgreSQL. SQLite is not supported for new installs.
Writable install path	The install user must be able to write the install directory, data directory, and optional pipeline run directory.

PostgreSQL options

Use one of these approaches:

Option	Best for	What the installer can do
Managed PostgreSQL	Production or shared infrastructure	Provide `DATABASE_URL` and optional `DIRECT_URL`; the installer runs migrations and seed.
Local PostgreSQL with sudo	Single-host development or internal installs	The installer can install/start PostgreSQL and create the role/database.
Local PostgreSQL without sudo	Locked-down shared servers	Ask an admin to install/start PostgreSQL and create the role/database first.

The application user does not need sudo after PostgreSQL is prepared. It only needs a valid connection string such as:


postgresql://seqdesk:<password>@127.0.0.1:5432/seqdesk?schema=public

Admin request for AlmaLinux/RHEL

If your account cannot use sudo, send this to the server administrator and replace <password> with the value you want in DATABASE_URL:


Please prepare PostgreSQL for a local SeqDesk instance on this AlmaLinux/RHEL host.

Install and start PostgreSQL:

sudo dnf install -y postgresql-server postgresql-contrib
sudo postgresql-setup --initdb
sudo systemctl enable --now postgresql

Create the SeqDesk role and database:

sudo -u postgres psql <<'SQL'
CREATE ROLE seqdesk LOGIN PASSWORD '<password>';
CREATE DATABASE seqdesk OWNER seqdesk;
SQL

Please make sure local password authentication from 127.0.0.1 works for:

postgresql://seqdesk:<password>@127.0.0.1:5432/seqdesk?schema=public

After the admin confirms, run:


npx -y seqdesk@latest -y --reconfigure --reseed-db --dir /path/to/seqdesk

Installer PostgreSQL bootstrap

When a sudo-capable account is available, the installer can perform the local PostgreSQL setup as a separate bootstrap step:


sudo env PATH="$PATH" npx -y seqdesk@latest -y --prepare-postgres --dir /path/to/seqdesk

Then continue as the normal SeqDesk install user:


npx -y seqdesk@latest -y --reconfigure --reseed-db --dir /path/to/seqdesk

If sudo does not preserve access to npx, install the SeqDesk launcher system-wide or ask the admin to run the SQL setup directly.

Optional pipeline prerequisites

Pipeline support is optional. Enable it only on hosts where SeqDesk should run or submit bioinformatics workflows.

Requirement	Notes
Conda or Miniconda	Used to create pipeline runtime environments. The installer can use an existing Conda path.
Nextflow	Required for running packaged workflows.
Slurm	Optional. Configure when pipeline jobs should be submitted to a cluster scheduler.
Writable run directory	Pipeline work and result files should live on storage with enough quota for sequencing workloads.

For locked-down HPC systems, ask the admin which Conda path, Slurm partition, memory limits, and writable run directory should be used before creating the install profile or infrastructure JSON.