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 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, and how to switch to a development build.

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

Seqera binaries

To install the CLI with the Platform install endpoint, run:

curl -fsSL https://ai.seqera.io/install | bash

Then confirm the CLI is on your PATH:

seqera --version

npm package

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

Seqera binaries

To install the latest pre-release, use the development channel:

curl -fsSL https://ai.seqera.io/install | bash -s -- --channel dev

npm package

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

Seqera binaries

To update the CLI, run the install endpoint again. The install script updates the CLI in place:

curl -fsSL https://ai.seqera.io/install | bash

npm package

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

Seqera binaries

To remove the CLI from your system, run:

rm ~/.config/seqera-ai/*
rm ~/.seqera/bin/seqera

npm package

To remove the CLI from your system, run:

npm uninstall -g seqera

Learn more

• Quickstart: Run your first Co-Scientist session
• Authentication: Log in, log out, and manage sessions
• Use cases: Seqera CLI use cases
• Using Co-Scientist: Configure modes, sessions, skills, command approval, and more
• Coding Agents: Install Co-Scientist as a skill in your coding agent
• Skills: Built-in skills, slash commands, and session limits
• Troubleshooting: Troubleshoot common errors