# CyVerse User Guide

> How to use CyVerse cyberinfrastructure: accounts, the Data Store (GoCommands, iCommands, SFTP, WebDAV), the Discovery Environment and VICE interactive apps, cloud services, and AI tools. The source repository is an Open Knowledge Format (OKF v0.2) bundle: every page carries YAML frontmatter with type, provenance (generated/sources), and lifecycle (status/stale_after) fields.

Full corpus for ingestion: https://unm-carc.github.io/cyverse/llms-full.txt

Every page's Markdown source (OKF frontmatter included) is served at its URL plus `index.md` — for example https://unm-carc.github.io/cyverse/getting-started/what-is-cyverse/index.md.

## Getting started

- [What is CyVerse?](https://unm-carc.github.io/cyverse/getting-started/what-is-cyverse/): CyVerse's cloud cyberinfrastructure, open source software, and people: the Data Store, Discovery Environment, cloud services, funding, and how to cite it.
- [Setting up your CyVerse account](https://unm-carc.github.io/cyverse/getting-started/account/): Register for a CyVerse account in the User Portal, request additional services, and understand account types and subscription tiers.
- [Individual subscriptions](https://unm-carc.github.io/cyverse/getting-started/subscriptions/): CyVerse individual subscription tiers compared: storage limits, compute units, concurrent jobs, sharing, DOIs, support, and price.
- [Getting help](https://unm-carc.github.io/cyverse/getting-started/getting-help/): Where to find answers and how to contact CyVerse support about accounts, the Data Store, apps, and this documentation.
- [Self-guided course](https://unm-carc.github.io/cyverse/getting-started/self-guided-course/): A free CyVerse massive open online course (MOOC) covering the basics of data management and analysis on CyVerse platforms.
- [Leveraging CyVerse services](https://unm-carc.github.io/cyverse/getting-started/powered-by/): Professional Services, Powered by CyVerse, and External Collaborative Partnerships for researchers and institutions that need more than the public platform.
- [Glossary & acronyms](https://unm-carc.github.io/cyverse/getting-started/glossary/): Definitions of terms and acronyms used across CyVerse, open science, cloud computing, and research software.

## Data Store

- [Data Store overview](https://unm-carc.github.io/cyverse/data-store/overview/): The iRODS-based CyVerse Data Store and a comparison of the ways to reach it: Discovery Environment, GoCommands, iCommands, SFTP, and WebDAV.

### Discovery Environment

- [Data Store in the Discovery Environment](https://unm-carc.github.io/cyverse/data-store/de/overview/): Browse, upload, inspect, delete, and search your Data Store files through the Discovery Environment web interface.
- [Sharing data in the Discovery Environment](https://unm-carc.github.io/cyverse/data-store/de/share/): Upload files, share them with CyVerse users or anonymously, and create public links from the Discovery Environment.
- [Adding metadata to data](https://unm-carc.github.io/cyverse/data-store/de/metadata/): View, edit, and bulk-apply metadata and metadata templates to Data Store files and folders in the Discovery Environment.
- [Getting a DOI](https://unm-carc.github.io/cyverse/data-store/de/doi/): Prepare, describe, and submit a dataset to CyVerse Curated Data in the Data Commons to receive a DataCite DOI.
- [Checking your data storage quotas](https://unm-carc.github.io/cyverse/data-store/de/check-data-usage/): Check Data Store usage on the Discovery Environment dashboard and analyze folder sizes and duplicate files with the DataHog app.
- [Managing data within a team](https://unm-carc.github.io/cyverse/data-store/de/teams/): Create public or private Teams in the Discovery Environment and share apps, tools, and data with collaborators.

### GoCommands

- [Manage your data with GoCommands](https://unm-carc.github.io/cyverse/data-store/gocommands/overview/): GoCommands, a portable cross-platform command-line client for transfers, synchronization, access control, and metadata in the Data Store.
- [GoCommands installation and upgrade](https://unm-carc.github.io/cyverse/data-store/gocommands/installation/): Install or upgrade GoCommands on Linux, macOS, and Windows from pre-built binaries or with conda.
- [GoCommands configuration](https://unm-carc.github.io/cyverse/data-store/gocommands/configuration/): Configure GoCommands for the Data Store with the init command, existing iCommands settings, a YAML or JSON file, or environment variables.
- [Data management using GoCommands](https://unm-carc.github.io/cyverse/data-store/gocommands/data-management/): Navigate collections and list, create, upload, download, move, rename, and remove data in the Data Store with GoCommands.
- [Data transfer using GoCommands](https://unm-carc.github.io/cyverse/data-store/gocommands/data-transfer/): Download and upload files and folders between a local system and the Data Store with GoCommands, including thread-count tuning.
- [Access management using GoCommands](https://unm-carc.github.io/cyverse/data-store/gocommands/access-management/): List and change user and group access permissions on Data Store data objects and collections with GoCommands.
- [Metadata management using GoCommands](https://unm-carc.github.io/cyverse/data-store/gocommands/metadata-management/): List, add, and remove metadata on Data Store data objects, collections, resources, and users with GoCommands.
- [SFTP public-key authentication configuration using GoCommands](https://unm-carc.github.io/cyverse/data-store/gocommands/sftp-public-key-auth/): Register an SSH public key with GoCommands for password-less SFTP access to the Data Store.
- [GoCommands troubleshooting and issue report](https://unm-carc.github.io/cyverse/data-store/gocommands/troubleshooting/): Diagnose common GoCommands problems and report bugs to the GoCommands developers.

### iCommands

- [Manage your data with iCommands](https://unm-carc.github.io/cyverse/data-store/icommands/overview/): iCommands, the iRODS Consortium's command-line suite for transfers, synchronization, access control, and metadata in the Data Store.
- [iCommands installation and upgrade](https://unm-carc.github.io/cyverse/data-store/icommands/installation/): Install iCommands on Linux with APT, YUM, or Zypper, or manually for a specific version.
- [iCommands configuration](https://unm-carc.github.io/cyverse/data-store/icommands/configuration/): Configure iCommands for the Data Store with iinit or environment variables.
- [Data management using iCommands](https://unm-carc.github.io/cyverse/data-store/icommands/data-management/): Navigate collections and list, create, upload, download, move, rename, and remove data in the Data Store with iCommands.
- [Data transfer using iCommands](https://unm-carc.github.io/cyverse/data-store/icommands/data-transfer/): Download and upload files and folders between a local system and the Data Store with iget and iput, including thread-count tuning.
- [Access management using iCommands](https://unm-carc.github.io/cyverse/data-store/icommands/access-management/): List and change user and group access permissions on Data Store data objects and collections with iCommands.
- [Metadata management using iCommands](https://unm-carc.github.io/cyverse/data-store/icommands/metadata-management/): List, add, and remove metadata on Data Store data objects, collections, resources, and users with iCommands.
- [iCommands troubleshooting and issue report](https://unm-carc.github.io/cyverse/data-store/icommands/troubleshooting/): Diagnose common iCommands problems and report bugs to the iRODS developers.

### SFTP

- [Manage your data using SFTP](https://unm-carc.github.io/cyverse/data-store/sftp/overview/): SFTP access to the Data Store: when to use it, its limits for large files, and the SFTPGo server behind it.
- [SFTP access using command-line tools](https://unm-carc.github.io/cyverse/data-store/sftp/cli/): Connect to the Data Store with your operating system's built-in sftp client and transfer files from the terminal.
- [SFTP access using FileZilla](https://unm-carc.github.io/cyverse/data-store/sftp/filezilla/): Install FileZilla and connect to the Data Store over SFTP to transfer files with a graphical client.
- [SFTP access using Cyberduck](https://unm-carc.github.io/cyverse/data-store/sftp/cyberduck/): Install Cyberduck and connect to the Data Store over SFTP to transfer files with a graphical client.
- [SFTP directory structure](https://unm-carc.github.io/cyverse/data-store/sftp/directory-structure/): How your home directory and community-shared Data Store directories appear when you connect over SFTP.
- [SFTP public-key authentication configuration](https://unm-carc.github.io/cyverse/data-store/sftp/public-key-auth/): Set up SSH public-key authentication for password-less SFTP access to the Data Store.

### WebDAV

- [Manage your data using WebDAV](https://unm-carc.github.io/cyverse/data-store/webdav/overview/): WebDAV (HTTPS) access to the Data Store at data.cyverse.org: when to use it and its limits for large files.
- [WebDAV access using command-line tools](https://unm-carc.github.io/cyverse/data-store/webdav/cli/): Connect to and transfer Data Store files over WebDAV from the terminal, with worked command-line examples.
- [WebDAV access using web browsers](https://unm-carc.github.io/cyverse/data-store/webdav/web-browsers/): Browse and download Data Store files over WebDAV in any web browser.
- [WebDAV access using file managers](https://unm-carc.github.io/cyverse/data-store/webdav/file-managers/): Mount the Data Store in macOS Finder, Windows File Explorer, GNOME Files, or a Linux terminal over WebDAV.
- [WebDAV data locations](https://unm-carc.github.io/cyverse/data-store/webdav/data-locations/): WebDAV URLs for your own, shared, and public read-only Data Store data at data.cyverse.org.

## Discovery Environment

- [Discovery Environment overview](https://unm-carc.github.io/cyverse/discovery-environment/overview/): What the Discovery Environment is, the types of analyses it runs from small interactive jobs to HPC and HTC, and its benefits.
- [Logging in to the Discovery Environment](https://unm-carc.github.io/cyverse/discovery-environment/login/): Sign in to the Discovery Environment and tour its navigation menu: Home, Data, Apps, Analyses, Cloud Shell, Teams, Collections, and Help.
- [Using apps in the Discovery Environment](https://unm-carc.github.io/cyverse/discovery-environment/using-apps/): Browse, sort, filter, and inspect apps in the Discovery Environment, and understand VICE and HPC apps and HPC queues.
- [Managing analyses in the Discovery Environment](https://unm-carc.github.io/cyverse/discovery-environment/managing-analyses/): Check the status of, relaunch, inspect, share, and cancel analyses in the Discovery Environment, and use CPUs efficiently.
- [Sharing and using bags in the Discovery Environment](https://unm-carc.github.io/cyverse/discovery-environment/bags/): Collect data, apps, and analyses in a bag to share them with collaborators or download them together from the Discovery Environment.
- [Create your own apps in the Discovery Environment](https://unm-carc.github.io/cyverse/discovery-environment/create-apps/): Integrate a containerized tool and build an app interface for it in the Discovery Environment, then test, share, and publish it.
- [Create HPC apps for use in the Discovery Environment](https://unm-carc.github.io/cyverse/discovery-environment/create-hpc-apps/): Define, register, and share Tapis v3 apps that run at TACC so they appear as HPC apps in the Discovery Environment.

### Interactive apps (VICE)

- [Interactive analysis in the Discovery Environment](https://unm-carc.github.io/cyverse/discovery-environment/vice/overview/): VICE interactive apps in the Discovery Environment: featured apps, requesting VICE access, launching, Data Store access, Git, and instant and quick launches.
- [RStudio in 6 steps](https://unm-carc.github.io/cyverse/discovery-environment/vice/quick-rstudio/): Quick start: launch RStudio as a VICE interactive app, create a project, and terminate the app when you finish.
- [JupyterLab in 6 steps](https://unm-carc.github.io/cyverse/discovery-environment/vice/quick-jupyter/): Quick start: launch JupyterLab as a VICE interactive app, work with Data Store files, and terminate the app when you finish.
- [Cloud Shell in 6 steps](https://unm-carc.github.io/cyverse/discovery-environment/vice/quick-cloudshell/): Quick start: launch the Cloud Shell terminal app in the Discovery Environment and use it to work with the Data Store.
- [Running your LLM for inference with Ollama](https://unm-carc.github.io/cyverse/discovery-environment/vice/quick-ollama/): Quick start: run open-source large language models with Ollama inside a GPU-enabled JupyterLab PyTorch app in the Discovery Environment.
- [Data Store in interactive apps](https://unm-carc.github.io/cyverse/discovery-environment/vice/csi/): How the Kubernetes CSI driver mounts the Data Store at /data-store inside VICE apps, its latency limits, and when to use it.
- [Creating a shareable quick launch button](https://unm-carc.github.io/cyverse/discovery-environment/vice/quick-app-launch/): Create saved launches, embeddable buttons, and shareable URLs that start a Discovery Environment app with preset settings.
- [Extending interactive apps](https://unm-carc.github.io/cyverse/discovery-environment/vice/extend-apps/): Copy an existing VICE app, modify an existing tool's container, or build a new Docker-based tool and interactive app in the Discovery Environment.

## Cloud

- [Cloud services](https://unm-carc.github.io/cyverse/cloud/overview/): CyVerse cloud-native services: CACAO for continuous analysis and infrastructure as code, DataWatch event notifications, and the Jetstream2 partnership.
- [CACAO](https://unm-carc.github.io/cyverse/cloud/cacao/): CACAO (Cloud Automation & Continuous Analysis Orchestration), CyVerse's infrastructure-as-code service for deploying templated workloads on Jetstream2 and other clouds.
- [DataWatch](https://unm-carc.github.io/cyverse/cloud/datawatch/): Create DataWatch listeners that call webhooks, WebDAV, or email when files change in watched Data Store folders, using the REST API or CLI.
- [Harbor container registry](https://unm-carc.github.io/cyverse/cloud/harbor/): CyVerse's Harbor container registry at harbor.cyverse.org, which hosts the container images behind featured Discovery Environment apps.

## AI

- [AI and machine learning on CyVerse](https://unm-carc.github.io/cyverse/ai/overview/): CyVerse capabilities for AI and ML: Data Store datasets, GPU JupyterLab apps, Ollama LLMs, AI Verde, CACAO on Jetstream2, and the Data Store MCP server.
- [Accessing AI Verde](https://unm-carc.github.io/cyverse/ai/verde/): Request AI Verde access, then call its hosted large language models from Python with an API key and the chatur-chains library.

### MCP servers

- [AI Verde MCP servers](https://unm-carc.github.io/cyverse/ai/mcp/overview/): AI Verde Model Context Protocol (MCP) servers that let AI agents and LLM applications work with data in the CyVerse Data Store.
- [General configuration for the AI Verde Data Store MCP server](https://unm-carc.github.io/cyverse/ai/mcp/general-configuration/): Streamable-HTTP and SSE endpoints, HTTP authentication, and anonymous public access for the AI Verde Data Store MCP server.
- [Claude Desktop configuration for the AI Verde Data Store MCP server](https://unm-carc.github.io/cyverse/ai/mcp/claude-desktop/): Add the AI Verde Data Store MCP server to Claude Desktop as a custom connector for public or CyVerse-account access.
- [VS Code configuration for the AI Verde Data Store MCP server](https://unm-carc.github.io/cyverse/ai/mcp/vs-code/): Configure VS Code Copilot Chat to use the AI Verde Data Store MCP server with anonymous or CyVerse-account access.

## Education

- [Teach using CyVerse](https://unm-carc.github.io/cyverse/education/teaching/): Request a CyVerse workshop in the User Portal, choose services, add instructors, and enroll students for a class or workshop.

### Workshops

- [Workshop offerings](https://unm-carc.github.io/cyverse/education/workshops/offerings/): CyVerse's professional education series, Container Camp and FOSS, and how to run your own workshop on CyVerse resources.
- [Container Camp](https://unm-carc.github.io/cyverse/education/workshops/container-camp/): CyVerse Container Camp workshops on software containers for research, with links to camp materials from 2018 to 2023.
- [Foundational Open Science Skills](https://unm-carc.github.io/cyverse/education/workshops/foss/): CyVerse's Foundational Open Science Skills (FOSS) workshop and an archive of its offerings from 2019 to 2024.

### Tutorials

- [Science tutorials with CyVerse](https://unm-carc.github.io/cyverse/education/tutorials/science-tutorials/): Archive of bioinformatics, geoinformatics, and astronomy tutorials and workshops that used CyVerse, with dates and summaries.
- [DNA Subway](https://unm-carc.github.io/cyverse/education/tutorials/dna-subway/): Use DNA Subway's Red, Yellow, Blue, Green, and Purple lines for genome annotation, gene-family prediction, DNA barcoding, RNA-Seq, and microbiome analysis.

## Developers

- [Developer manuals](https://unm-carc.github.io/cyverse/developers/manuals/): Where to find documentation for each CyVerse platform and API, from the Data Store and Discovery Environment to Terrain, Tapis, and CACAO.

## About

- [Credits](https://unm-carc.github.io/cyverse/about/credits/): Where this guide comes from: the CyVerse Learning Center, its authors and NSF funding, how to cite CyVerse, and the CC BY 4.0 attribution for adapted content.
- [Contributing](https://unm-carc.github.io/cyverse/about/contributing/): How to edit pages, the OKF frontmatter contract, verifying adapted content, and building the site locally.
- [For AI agents](https://unm-carc.github.io/cyverse/about/ai-agents/): How agents and harnesses should consume this site: llms.txt, per-page Markdown with OKF frontmatter, and trust signals.

## Meta

- [Documentation update log](https://unm-carc.github.io/cyverse/log/): dated history of changes to this bundle.
- [For AI agents](https://unm-carc.github.io/cyverse/about/ai-agents/): endpoints and trust signals for agents.