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Version: 26.2

Installation

The Seqera CLI runs in your terminal on macOS, Linux, or Windows (via WSL). It connects to Seqera Platform and to the Co-Scientist backend in your Enterprise deployment so you can build, run, and debug Nextflow pipelines from a single interactive session.

This page covers how to install, update, and uninstall the CLI with npm, how to switch to a development build, and how to point the CLI at the Co-Scientist backend. Once the CLI is on your PATH, see the Quickstart to log in and start your first session.

Prerequisites

You will need the following to get started:

  • Node.js 18 or later
  • macOS, Linux, or Windows with WSL
  • A user account on your Seqera Platform Enterprise deployment
  • The agent backend URL for your deployment, from your Seqera Platform administrator
  • Network access to the Co-Scientist agent backend

Install the CLI​

Install the CLI globally from the seqera npm package:

npm install -g seqera

Then confirm the CLI is on your PATH:

seqera --version

Install a development build​

To install the latest pre-release, run:

npm install -g seqera@dev

The @dev tag tracks the latest pre-release CLI. Use it only to test unreleased features. Otherwise install the default tag.

Update the CLI​

To check whether a newer version is available, run:

seqera update

To update the CLI to the latest published version, run:

npm update -g seqera

If you use Co-Scientist as a skill for a coding agent, sync your installed skills with the new CLI version after upgrading:

seqera skill check --update

This scans both local and global installations by default. Pass --global or --local to narrow the scope.

Uninstall the CLI​

To remove the CLI from your system, run:

npm uninstall -g seqera

To also remove stored credentials and configuration, delete ~/.config/seqera-ai/.

Configure the Co-Scientist backend​

The CLI connects to Seqera Platform Cloud by default. Point it at your Enterprise deployment with environment variables or a configuration file.

Environment variables​

Set the agent backend URL and the OIDC authority base URL before starting Co-Scientist:

export SEQERA_AI_BACKEND_URL=https://ai-api.platform.example.com
export SEQERA_AUTH_DOMAIN=https://platform.example.com/api

The CLI fetches OpenID configuration from SEQERA_AUTH_DOMAIN and opens the discovered authorization endpoint in your browser.

Configuration file​

To avoid exporting variables in every shell, create ~/.config/seqera-ai/config.json:

{
  "authDomain": "https://platform.example.com/api",
  "backendUrl": "https://ai-api.platform.example.com"
}

Environment variables take precedence over the configuration file.

Verify the connection​

Confirm that the CLI resolves your Enterprise deployment:

seqera info

seqera info shows the authenticated user, the agent backend, and the Seqera Platform endpoint the CLI uses. See Authentication for OAuth and token-based examples, and Environment variables for the full reference.

Learn more​

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