Prerequisites

SeqDesk runs on standard Linux servers and can also run as a local MacBook instance for development or evaluation. It needs Node.js/npm plus a PostgreSQL database. Pipeline execution is optional and adds Conda, Nextflow, and possibly Slurm requirements.

Required

The installer checks the environment before doing any work. On an unrecognized Linux distribution or a CPU architecture other than x86_64/arm64 it prints an “untested environment” warning and proceeds at your own risk; unrecognized distributions are mapped through /etc/os-release so Debian/Ubuntu and RHEL/Fedora derivatives still receive the correct package-install hints. Missing curl, tar, or a checksum tool (sha256sum/shasum) are reported upfront with platform-specific install commands rather than failing later in the run.

PostgreSQL options

Use one of these approaches:

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. On a fresh host with no existing install, --prepare-postgres needs the target connection string, so pass SEQDESK_DATABASE_URL (or --database-url); otherwise it exits with No DATABASE_URL found:

sudo env PATH="$PATH" SEQDESK_DATABASE_URL="postgresql://seqdesk:<password>@127.0.0.1:5432/seqdesk?schema=public" \
  npx -y seqdesk@latest -y --prepare-postgres --dir /path/to/seqdesk

If you point --dir at an existing SeqDesk install, the URL is read from its configuration and the explicit SEQDESK_DATABASE_URL can be omitted.

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.

macOS prerequisites

For a local MacBook install, install Node.js and PostgreSQL with Homebrew:

brew install node postgresql@16
brew services start postgresql@16

Then install with the npm launcher — see the macOS install guide, which uses a local ~/seqdesk directory, port 8000, and local PostgreSQL.

Optional pipeline prerequisites

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

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 infrastructure JSON.