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Installation

The Co-Scientist CLI runs in your terminal on macOS, Linux, or Windows (via WSL). It connects to Seqera Platform and to an AI 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 resolve common installation errors. 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 Seqera Platform account (sign up for free)

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. To point a development build at the hosted Co-Scientist backend, set:

SEQERA_AI_BACKEND_URL=https://ai-api.seqera.io

See Authentication for the full environment variable reference.

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, 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

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
  • Troubleshooting: Resolve installation, login, and runtime issues
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