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Version: 26.1

Installation

The Co-Scientist CLI runs in your terminal on macOS, Linux, or Windows (via WSL). It connects to Seqera Platform and to your Enterprise agent backend 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 your Enterprise agent backend. Once the CLI is on your PATH, see Get started to log in and start a 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
  • Network access to your Enterprise agent backend

Install the CLI​

To install the CLI globally with npm, run:

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.

Configure the Enterprise backend​

Configure the Enterprise backend, set the agent backend URL before starting Co-Scientist:

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

If your Enterprise deployment uses Platform OIDC, also set the OIDC authority base URL:

export SEQERA_AUTH_DOMAIN=https://platform.example.com/api

The CLI fetches OpenID configuration from this URL and opens the discovered authorization endpoint in your browser. See Authentication for the complete environment variable reference and OAuth versus token-based examples.

Update the CLI​

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, run seqera skill check --update after updating the CLI to keep installed skills in sync with the new version. By default, this scans both local and global installations — pass --global or --local to narrow the scope.

seqera skill check --update

Uninstall the CLI​

To remove the CLI from your system, run:

npm uninstall -g seqera

Next steps​

  • Get started: Run your first Co-Scientist session
  • Authentication: Log in, log out, and manage sessions
  • Skills: Install Co-Scientist as a skill for your coding agent
  • Usage and cost: Co-Scientist usage in Enterprise deployments
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