# User Guide

Complete guide to using ExoHub with the exo CLI


This guide walks you through using ExoHub to manage your datasets. This guide covers **exo CLI v0.124.0**. Whether you're downloading data for analysis, collaborating with your team, or setting up automated pipelines, this guide covers everything you need to know.

## What You'll Learn

1. [**Introduction**](https://genentech.github.io/exohub/docs/user-guide/introduction/index.md) — Key concepts and how ExoHub works
2. [**Installation & Setup**](https://genentech.github.io/exohub/docs/user-guide/installation/index.md) — Install the CLI and authenticate
3. [**Managing Credentials**](https://genentech.github.io/exohub/docs/user-guide/credentials/index.md) — Store and manage SSH keys and git tokens with ExoSafe
4. [**Working with Repositories**](https://genentech.github.io/exohub/docs/user-guide/repositories/index.md) — Clone, initialize, and explore datasets
5. [**Permissions & Access Control**](https://genentech.github.io/exohub/docs/user-guide/permissions/index.md) — Manage who can read and write data
6. [**Syncing Data**](https://genentech.github.io/exohub/docs/user-guide/syncing/index.md) — Download, upload, and export your data
7. [**Versioning & Collaboration**](https://genentech.github.io/exohub/docs/user-guide/versioning/index.md) — Git workflows for data teams
8. [**Provenance**](https://genentech.github.io/exohub/docs/user-guide/provenance/index.md) — Record and inspect the lineage of files with `exo provenance`
9. [**Running Jobs at Scale**](https://genentech.github.io/exohub/docs/user-guide/jobs-at-scale/index.md) — Manifests, job submission, and monitoring
10. [**Advanced Operations**](https://genentech.github.io/exohub/docs/user-guide/advanced/index.md) — Copying, mirroring, and linking
11. [**Google Drive Remote**](https://genentech.github.io/exohub/docs/user-guide/drive-remote/index.md) — Export data to Google Drive for Workspace collaborators
12. [**Atlas & Downloads**](https://genentech.github.io/exohub/docs/user-guide/atlas-downloads/index.md) — Browse the catalog and download artifacts
13. [**MCP Server**](https://genentech.github.io/exohub/docs/user-guide/mcp-server/index.md) — Use AI agents to manage data through the Model Context Protocol
14. [**Local Standalone Catalog**](https://genentech.github.io/exohub/docs/user-guide/standalone/index.md) — Run a local ArtifactDB catalog stack without a full deployment
15. [**Themes & Appearance**](https://genentech.github.io/exohub/docs/user-guide/themes/index.md) — Customize colors, dark/light mode, daily tips, and the web UI
16. [**Troubleshooting**](https://genentech.github.io/exohub/docs/user-guide/troubleshooting/index.md) — Diagnosing and fixing issues
17. [**Environment Variables**](https://genentech.github.io/exohub/docs/user-guide/environment-variables/index.md) — All environment variables supported by the CLI

## Prerequisites

- Linux or macOS
- Basic familiarity with Git
- Access to a dataset repository (or the MNIST tutorial dataset)

Ready to get started? Head to the [Introduction](https://genentech.github.io/exohub/docs/user-guide/introduction/index.md).