# CyVerse Core Software Documentation > Technical documentation for deploying, operating, and integrating with CyVerse, the open-source cyberinfrastructure for data-intensive science: architecture, an ordered deployment path, operations playbooks, service databases, and the Terrain API. 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. Every page below is listed with three addresses that all return the same content: the rendered HTML page, its Markdown twin (page URL + `index.md`, served as text/markdown with the OKF frontmatter), and the raw source file on GitHub. Fetch whichever your tool is allowed to reach; many sandboxes permit github.com and raw.githubusercontent.com but not every documentation host. ``` Site page https://docs.cyverse.org// Markdown twin https://docs.cyverse.org//index.md Raw source https://raw.githubusercontent.com/cyverse/docs/main/docs/.md (branch main; a moving target) Content page /deployment/01-foundation/postgresql/ -> https://raw.githubusercontent.com/cyverse/docs/main/docs/deployment/01-foundation/postgresql.md Section listing /deployment/01-foundation/ -> https://raw.githubusercontent.com/cyverse/docs/main/docs/deployment/01-foundation/index.md ``` ## Home ### About - [About this documentation](https://docs.cyverse.org/about/overview/): What CyVerse is, who this documentation is for, and where each audience should start. Markdown twin: https://docs.cyverse.org/about/overview/index.md Raw source: https://raw.githubusercontent.com/cyverse/docs/main/docs/about/overview.md - [Contributing to these docs](https://docs.cyverse.org/about/contributing/): How to edit pages, the OKF frontmatter contract, verifying migrated content, and building and validating the site locally. Markdown twin: https://docs.cyverse.org/about/contributing/index.md Raw source: https://raw.githubusercontent.com/cyverse/docs/main/docs/about/contributing.md - [For AI agents](https://docs.cyverse.org/about/ai-agents/): How agents and harnesses should consume this documentation: llms.txt, per-page Markdown with OKF frontmatter, raw source on GitHub, trust signals, and what to do if you cannot fetch this site. Markdown twin: https://docs.cyverse.org/about/ai-agents/index.md Raw source: https://raw.githubusercontent.com/cyverse/docs/main/docs/about/ai-agents.md ## Architecture - [System overview](https://docs.cyverse.org/architecture/system-overview/): The CyVerse stack end to end: interfaces, APIs, compute, storage, and the resources behind them. Markdown twin: https://docs.cyverse.org/architecture/system-overview/index.md Raw source: https://raw.githubusercontent.com/cyverse/docs/main/docs/architecture/system-overview.md - [Component inventory and sizing](https://docs.cyverse.org/architecture/component-inventory/): The components a CyVerse deployment is built from, what each one needs, and what depends on what. Markdown twin: https://docs.cyverse.org/architecture/component-inventory/index.md Raw source: https://raw.githubusercontent.com/cyverse/docs/main/docs/architecture/component-inventory.md - [Network requirements](https://docs.cyverse.org/architecture/network-requirements/): Every port a CyVerse deployment needs open, who needs to reach it, and why. Markdown twin: https://docs.cyverse.org/architecture/network-requirements/index.md Raw source: https://raw.githubusercontent.com/cyverse/docs/main/docs/architecture/network-requirements.md - [Kubernetes namespaces](https://docs.cyverse.org/architecture/namespaces/): Namespaces used by a CyVerse Kubernetes deployment and what runs in each one. Markdown twin: https://docs.cyverse.org/architecture/namespaces/index.md Raw source: https://raw.githubusercontent.com/cyverse/docs/main/docs/architecture/namespaces.md ## Deployment - [Deploying CyVerse from scratch](https://docs.cyverse.org/deployment/from-scratch/): End-to-end walkthrough of a two-node CyVerse pilot deployment, from bare servers to a Discovery Environment running VICE analyses. Markdown twin: https://docs.cyverse.org/deployment/from-scratch/index.md Raw source: https://raw.githubusercontent.com/cyverse/docs/main/docs/deployment/from-scratch.md ### Phase 0: Planning - [Prerequisites](https://docs.cyverse.org/deployment/planning/prerequisites/): Hardware, skills, tooling, and access you need in place before deploying CyVerse. Markdown twin: https://docs.cyverse.org/deployment/planning/prerequisites/index.md Raw source: https://raw.githubusercontent.com/cyverse/docs/main/docs/deployment/planning/prerequisites.md - [Ansible](https://docs.cyverse.org/deployment/planning/ansible/): Installing Ansible and the inventory, group_vars, and playbook conventions the CyVerse deployment expects. Markdown twin: https://docs.cyverse.org/deployment/planning/ansible/index.md Raw source: https://raw.githubusercontent.com/cyverse/docs/main/docs/deployment/planning/ansible.md - [Docker](https://docs.cyverse.org/deployment/planning/docker/): Installing Docker and running the deployment playbooks from inside a container. Markdown twin: https://docs.cyverse.org/deployment/planning/docker/index.md Raw source: https://raw.githubusercontent.com/cyverse/docs/main/docs/deployment/planning/docker.md ### Phase 1: Foundation - [HAProxy](https://docs.cyverse.org/deployment/01-foundation/haproxy/): The public entry point that terminates HTTPS and forwards to the cluster's Traefik node ports. Markdown twin: https://docs.cyverse.org/deployment/01-foundation/haproxy/index.md Raw source: https://raw.githubusercontent.com/cyverse/docs/main/docs/deployment/01-foundation/haproxy.md - [PostgreSQL](https://docs.cyverse.org/deployment/01-foundation/postgresql/): Installing and tuning the PostgreSQL server that backs the iRODS catalog and every CyVerse service database. Markdown twin: https://docs.cyverse.org/deployment/01-foundation/postgresql/index.md Raw source: https://raw.githubusercontent.com/cyverse/docs/main/docs/deployment/01-foundation/postgresql.md - [RabbitMQ](https://docs.cyverse.org/deployment/01-foundation/rabbitmq/): Installing the AMQP broker, creating the Data Store vhost and accounts, and reindexing search from the message bus. Markdown twin: https://docs.cyverse.org/deployment/01-foundation/rabbitmq/index.md Raw source: https://raw.githubusercontent.com/cyverse/docs/main/docs/deployment/01-foundation/rabbitmq.md ### Phase 2: Databases - [Database migrations](https://docs.cyverse.org/deployment/02-databases/migrations/): The shared golang-migrate procedure used to create and update every CyVerse service schema. Markdown twin: https://docs.cyverse.org/deployment/02-databases/migrations/index.md Raw source: https://raw.githubusercontent.com/cyverse/docs/main/docs/deployment/02-databases/migrations.md - [iCAT database](https://docs.cyverse.org/deployment/02-databases/icat/): The iRODS catalog database: what creates it, what may read it, and what must never write to it. Markdown twin: https://docs.cyverse.org/deployment/02-databases/icat/index.md Raw source: https://raw.githubusercontent.com/cyverse/docs/main/docs/deployment/02-databases/icat.md - [DE database](https://docs.cyverse.org/deployment/02-databases/de/): Creating and migrating the Discovery Environment database. Markdown twin: https://docs.cyverse.org/deployment/02-databases/de/index.md Raw source: https://raw.githubusercontent.com/cyverse/docs/main/docs/deployment/02-databases/de.md - [Metadata database](https://docs.cyverse.org/deployment/02-databases/metadata/): Creating the database behind the CyVerse metadata service. Markdown twin: https://docs.cyverse.org/deployment/02-databases/metadata/index.md Raw source: https://raw.githubusercontent.com/cyverse/docs/main/docs/deployment/02-databases/metadata.md - [Notifications database](https://docs.cyverse.org/deployment/02-databases/notifications/): Creating the database behind the user notification service. Markdown twin: https://docs.cyverse.org/deployment/02-databases/notifications/index.md Raw source: https://raw.githubusercontent.com/cyverse/docs/main/docs/deployment/02-databases/notifications.md - [QMS database](https://docs.cyverse.org/deployment/02-databases/qms/): Creating and migrating the quota management service database. Markdown twin: https://docs.cyverse.org/deployment/02-databases/qms/index.md Raw source: https://raw.githubusercontent.com/cyverse/docs/main/docs/deployment/02-databases/qms.md - [Keycloak database](https://docs.cyverse.org/deployment/02-databases/keycloak/): Creating the database Keycloak uses for realms, clients, and sessions. Markdown twin: https://docs.cyverse.org/deployment/02-databases/keycloak/index.md Raw source: https://raw.githubusercontent.com/cyverse/docs/main/docs/deployment/02-databases/keycloak.md - [Grouper database](https://docs.cyverse.org/deployment/02-databases/grouper/): Creating the database behind the Internet2 Grouper group-management service. Markdown twin: https://docs.cyverse.org/deployment/02-databases/grouper/index.md Raw source: https://raw.githubusercontent.com/cyverse/docs/main/docs/deployment/02-databases/grouper.md - [Unleash database](https://docs.cyverse.org/deployment/02-databases/unleash/): Creating the database behind the Unleash feature-flag service. Markdown twin: https://docs.cyverse.org/deployment/02-databases/unleash/index.md Raw source: https://raw.githubusercontent.com/cyverse/docs/main/docs/deployment/02-databases/unleash.md - [Portal database](https://docs.cyverse.org/deployment/02-databases/portal/): Creating, restoring, and seeding the User Portal database. Markdown twin: https://docs.cyverse.org/deployment/02-databases/portal/index.md Raw source: https://raw.githubusercontent.com/cyverse/docs/main/docs/deployment/02-databases/portal.md ### Phase 3: Data Store - [iRODS catalog provider](https://docs.cyverse.org/deployment/03-data-store/irods-provider/): Installing iRODS 4.3.3 as a catalog provider, applying CyVerse policy, and initializing the zone. Markdown twin: https://docs.cyverse.org/deployment/03-data-store/irods-provider/index.md Raw source: https://raw.githubusercontent.com/cyverse/docs/main/docs/deployment/03-data-store/irods-provider.md - [iRODS integration for the DE](https://docs.cyverse.org/deployment/03-data-store/de-integration/): The specific queries, service account, and messaging wiring the Discovery Environment needs from an iRODS zone. Markdown twin: https://docs.cyverse.org/deployment/03-data-store/de-integration/index.md Raw source: https://raw.githubusercontent.com/cyverse/docs/main/docs/deployment/03-data-store/de-integration.md ### Phase 4: Kubernetes - [Cluster](https://docs.cyverse.org/deployment/04-kubernetes/cluster/): Standing up the Kubernetes control plane and workers that run CyVerse services, with k0sctl. Markdown twin: https://docs.cyverse.org/deployment/04-kubernetes/cluster/index.md Raw source: https://raw.githubusercontent.com/cyverse/docs/main/docs/deployment/04-kubernetes/cluster.md - [Cluster resources](https://docs.cyverse.org/deployment/04-kubernetes/resources/): Generating and loading the configuration, secrets, and manifests every DE service reads. Markdown twin: https://docs.cyverse.org/deployment/04-kubernetes/resources/index.md Raw source: https://raw.githubusercontent.com/cyverse/docs/main/docs/deployment/04-kubernetes/resources.md - [cert-manager](https://docs.cyverse.org/deployment/04-kubernetes/cert-manager/): Installing cert-manager and the cluster issuers that mint TLS certificates for every CyVerse route. Markdown twin: https://docs.cyverse.org/deployment/04-kubernetes/cert-manager/index.md Raw source: https://raw.githubusercontent.com/cyverse/docs/main/docs/deployment/04-kubernetes/cert-manager.md - [Ingress](https://docs.cyverse.org/deployment/04-kubernetes/ingress/): Routing external traffic into the cluster with HAProxy, Traefik, and the legacy ingress-nginx path. Markdown twin: https://docs.cyverse.org/deployment/04-kubernetes/ingress/index.md Raw source: https://raw.githubusercontent.com/cyverse/docs/main/docs/deployment/04-kubernetes/ingress.md - [Storage](https://docs.cyverse.org/deployment/04-kubernetes/storage/): Providing persistent volumes to the cluster with Longhorn or OpenEBS. Markdown twin: https://docs.cyverse.org/deployment/04-kubernetes/storage/index.md Raw source: https://raw.githubusercontent.com/cyverse/docs/main/docs/deployment/04-kubernetes/storage.md - [Harbor](https://docs.cyverse.org/deployment/04-kubernetes/harbor/): Deploying the Harbor container registry that holds CyVerse service and tool images. Markdown twin: https://docs.cyverse.org/deployment/04-kubernetes/harbor/index.md Raw source: https://raw.githubusercontent.com/cyverse/docs/main/docs/deployment/04-kubernetes/harbor.md - [Argo Workflows](https://docs.cyverse.org/deployment/04-kubernetes/argo/): Installing Argo Workflows and the workflow resources CyVerse analyses depend on. Markdown twin: https://docs.cyverse.org/deployment/04-kubernetes/argo/index.md Raw source: https://raw.githubusercontent.com/cyverse/docs/main/docs/deployment/04-kubernetes/argo.md ### Phase 5: Core Services - [OpenLDAP](https://docs.cyverse.org/deployment/05-core-services/openldap/): Deploying the LDAP directory that holds CyVerse accounts and groups, and the service accounts that read it. Markdown twin: https://docs.cyverse.org/deployment/05-core-services/openldap/index.md Raw source: https://raw.githubusercontent.com/cyverse/docs/main/docs/deployment/05-core-services/openldap.md - [Keycloak](https://docs.cyverse.org/deployment/05-core-services/keycloak/): Deploying Keycloak and configuring the realm, LDAP federation, mappers, roles, and OAuth clients the DE requires. Markdown twin: https://docs.cyverse.org/deployment/05-core-services/keycloak/index.md Raw source: https://raw.githubusercontent.com/cyverse/docs/main/docs/deployment/05-core-services/keycloak.md - [Grouper](https://docs.cyverse.org/deployment/05-core-services/grouper/): Deploying the Grouper loader and web services for group management. Markdown twin: https://docs.cyverse.org/deployment/05-core-services/grouper/index.md Raw source: https://raw.githubusercontent.com/cyverse/docs/main/docs/deployment/05-core-services/grouper.md - [OpenSearch](https://docs.cyverse.org/deployment/05-core-services/opensearch/): Deploying the search cluster that indexes Data Store contents and metadata for the DE. Markdown twin: https://docs.cyverse.org/deployment/05-core-services/opensearch/index.md Raw source: https://raw.githubusercontent.com/cyverse/docs/main/docs/deployment/05-core-services/opensearch.md - [Elasticsearch (legacy)](https://docs.cyverse.org/deployment/05-core-services/elasticsearch/): The legacy Elasticsearch stateful set and index mappings, superseded by OpenSearch in new deployments. (deprecated; kept for history) Markdown twin: https://docs.cyverse.org/deployment/05-core-services/elasticsearch/index.md Raw source: https://raw.githubusercontent.com/cyverse/docs/main/docs/deployment/05-core-services/elasticsearch.md - [NATS](https://docs.cyverse.org/deployment/05-core-services/nats/): Deploying the NATS messaging layer used for internal service-to-service communication. Markdown twin: https://docs.cyverse.org/deployment/05-core-services/nats/index.md Raw source: https://raw.githubusercontent.com/cyverse/docs/main/docs/deployment/05-core-services/nats.md - [Redis HA](https://docs.cyverse.org/deployment/05-core-services/redis-ha/): Deploying the Redis server, Sentinel, and Redis HAProxy used for caching and sessions. Markdown twin: https://docs.cyverse.org/deployment/05-core-services/redis-ha/index.md Raw source: https://raw.githubusercontent.com/cyverse/docs/main/docs/deployment/05-core-services/redis-ha.md - [Unleash](https://docs.cyverse.org/deployment/05-core-services/unleash/): Deploying the Unleash feature-flag service the DE reads toggles from. Markdown twin: https://docs.cyverse.org/deployment/05-core-services/unleash/index.md Raw source: https://raw.githubusercontent.com/cyverse/docs/main/docs/deployment/05-core-services/unleash.md - [iRODS CSI driver](https://docs.cyverse.org/deployment/05-core-services/irods-csi-driver/): Installing the iRODS Container Storage Interface driver that mounts Data Store paths into pods. Markdown twin: https://docs.cyverse.org/deployment/05-core-services/irods-csi-driver/index.md Raw source: https://raw.githubusercontent.com/cyverse/docs/main/docs/deployment/05-core-services/irods-csi-driver.md - [Mail](https://docs.cyverse.org/deployment/05-core-services/mail/): Deploying outbound mail: the exim4 smarthost chart and the in-cluster exim-sender deployment. Markdown twin: https://docs.cyverse.org/deployment/05-core-services/mail/index.md Raw source: https://raw.githubusercontent.com/cyverse/docs/main/docs/deployment/05-core-services/mail.md - [Jaeger](https://docs.cyverse.org/deployment/05-core-services/jaeger/): Deploying Jaeger for end-to-end distributed tracing of DE services. Markdown twin: https://docs.cyverse.org/deployment/05-core-services/jaeger/index.md Raw source: https://raw.githubusercontent.com/cyverse/docs/main/docs/deployment/05-core-services/jaeger.md ### Phase 6: Applications - [Discovery Environment](https://docs.cyverse.org/deployment/06-applications/discovery-environment/): Deploying the DE service set and the nginx front end that proxies it. Markdown twin: https://docs.cyverse.org/deployment/06-applications/discovery-environment/index.md Raw source: https://raw.githubusercontent.com/cyverse/docs/main/docs/deployment/06-applications/discovery-environment.md - [VICE](https://docs.cyverse.org/deployment/06-applications/vice/): Preparing the vice-apps namespace, service accounts, network policies, and secrets for interactive apps. Markdown twin: https://docs.cyverse.org/deployment/06-applications/vice/index.md Raw source: https://raw.githubusercontent.com/cyverse/docs/main/docs/deployment/06-applications/vice.md - [User Portal](https://docs.cyverse.org/deployment/06-applications/user-portal/): Deploying the User Portal and creating the LDAP, iRODS, and database accounts it needs. Markdown twin: https://docs.cyverse.org/deployment/06-applications/user-portal/index.md Raw source: https://raw.githubusercontent.com/cyverse/docs/main/docs/deployment/06-applications/user-portal.md ### Phase 7: Post-Install - [Bootstrap](https://docs.cyverse.org/deployment/07-post-install/bootstrap/): Creating the first administrator, registering a VICE operator, and importing a starting set of apps. Markdown twin: https://docs.cyverse.org/deployment/07-post-install/bootstrap/index.md Raw source: https://raw.githubusercontent.com/cyverse/docs/main/docs/deployment/07-post-install/bootstrap.md - [Verification](https://docs.cyverse.org/deployment/07-post-install/verification/): The end-to-end checks that tell you a fresh CyVerse deployment actually works. Markdown twin: https://docs.cyverse.org/deployment/07-post-install/verification/index.md Raw source: https://raw.githubusercontent.com/cyverse/docs/main/docs/deployment/07-post-install/verification.md - [Troubleshooting a new deployment](https://docs.cyverse.org/deployment/07-post-install/troubleshooting/): Fixes for the problems that show up during and just after a first CyVerse deployment. Markdown twin: https://docs.cyverse.org/deployment/07-post-install/troubleshooting/index.md Raw source: https://raw.githubusercontent.com/cyverse/docs/main/docs/deployment/07-post-install/troubleshooting.md ## Platform - [Discovery Environment](https://docs.cyverse.org/platform/discovery-environment/): The web-based data science workbench: apps, analyses, VICE, and the services behind them. Markdown twin: https://docs.cyverse.org/platform/discovery-environment/index.md Raw source: https://raw.githubusercontent.com/cyverse/docs/main/docs/platform/discovery-environment.md - [Data Store](https://docs.cyverse.org/platform/data-store/): The iRODS-backed storage platform and the access services layered on top of it. Markdown twin: https://docs.cyverse.org/platform/data-store/index.md Raw source: https://raw.githubusercontent.com/cyverse/docs/main/docs/platform/data-store.md - [Data Commons](https://docs.cyverse.org/platform/data-commons/): The publishing platform for curated and community-released datasets. (draft) Markdown twin: https://docs.cyverse.org/platform/data-commons/index.md Raw source: https://raw.githubusercontent.com/cyverse/docs/main/docs/platform/data-commons.md - [Authentication](https://docs.cyverse.org/platform/authentication/): How Keycloak, CILogon, and OAuth 2.0 combine to authenticate CyVerse users. Markdown twin: https://docs.cyverse.org/platform/authentication/index.md Raw source: https://raw.githubusercontent.com/cyverse/docs/main/docs/platform/authentication.md - [Subscriptions](https://docs.cyverse.org/platform/subscriptions/): Subscription tiers, what they allocate, and how administrators manage them. Markdown twin: https://docs.cyverse.org/platform/subscriptions/index.md Raw source: https://raw.githubusercontent.com/cyverse/docs/main/docs/platform/subscriptions.md - [Cloud services](https://docs.cyverse.org/platform/cloud/): CACAO infrastructure-as-code for multi-cloud deployments, and the retired Atmosphere platform. Markdown twin: https://docs.cyverse.org/platform/cloud/index.md Raw source: https://raw.githubusercontent.com/cyverse/docs/main/docs/platform/cloud.md - [BisQue](https://docs.cyverse.org/platform/bisque/): The Bio-Image Semantic Query User Environment fork maintained by CyVerse. (draft) Markdown twin: https://docs.cyverse.org/platform/bisque/index.md Raw source: https://raw.githubusercontent.com/cyverse/docs/main/docs/platform/bisque.md - [DNA Subway](https://docs.cyverse.org/platform/dna-subway/): The educational genomics platform for classroom sequence analysis. (draft) Markdown twin: https://docs.cyverse.org/platform/dna-subway/index.md Raw source: https://raw.githubusercontent.com/cyverse/docs/main/docs/platform/dna-subway.md ## Operations - [Discovery Environment administration](https://docs.cyverse.org/operations/discovery-environment/): Day-to-day DE administration: users, VICE access, app publication, and the admin panel. Markdown twin: https://docs.cyverse.org/operations/discovery-environment/index.md Raw source: https://raw.githubusercontent.com/cyverse/docs/main/docs/operations/discovery-environment.md - [Data Store administration](https://docs.cyverse.org/operations/data-store/): Client tooling, sharing, and curation workflows for the iRODS Data Store. (draft) Markdown twin: https://docs.cyverse.org/operations/data-store/index.md Raw source: https://raw.githubusercontent.com/cyverse/docs/main/docs/operations/data-store.md - [User Portal administration](https://docs.cyverse.org/operations/user-portal/): Managing accounts, access requests, services, and workshops from the portal admin panel. Markdown twin: https://docs.cyverse.org/operations/user-portal/index.md Raw source: https://raw.githubusercontent.com/cyverse/docs/main/docs/operations/user-portal.md - [Frequently asked questions](https://docs.cyverse.org/operations/faq/): Answers and troubleshooting recipes for the questions operators hit most often. Markdown twin: https://docs.cyverse.org/operations/faq/index.md Raw source: https://raw.githubusercontent.com/cyverse/docs/main/docs/operations/faq.md ## API - [Terrain](https://docs.cyverse.org/api/terrain/): The Terrain API: what it fronts, how to authenticate, and where the generated reference lives. Markdown twin: https://docs.cyverse.org/api/terrain/index.md Raw source: https://raw.githubusercontent.com/cyverse/docs/main/docs/api/terrain.md - [API errors](https://docs.cyverse.org/api/errors/): Error response format and status codes returned by Terrain. Markdown twin: https://docs.cyverse.org/api/errors/index.md Raw source: https://raw.githubusercontent.com/cyverse/docs/main/docs/api/errors.md - [Tapis v2 to v3 migration](https://docs.cyverse.org/api/tapis-v2-v3-migration/): Migrating Tapis v2 (Agave) apps to Tapis v3 for the Discovery Environment. Markdown twin: https://docs.cyverse.org/api/tapis-v2-v3-migration/index.md Raw source: https://raw.githubusercontent.com/cyverse/docs/main/docs/api/tapis-v2-v3-migration.md ### Endpoints - [Endpoints overview](https://docs.cyverse.org/api/endpoints/endpoints/): How the Terrain endpoint documentation is organized and which endpoints are documented where. Markdown twin: https://docs.cyverse.org/api/endpoints/endpoints/index.md Raw source: https://raw.githubusercontent.com/cyverse/docs/main/docs/api/endpoints/endpoints.md - [App metadata](https://docs.cyverse.org/api/endpoints/app-metadata/): Endpoints for reading and writing metadata attached to apps. Markdown twin: https://docs.cyverse.org/api/endpoints/app-metadata/index.md Raw source: https://raw.githubusercontent.com/cyverse/docs/main/docs/api/endpoints/app-metadata.md - [App ontologies](https://docs.cyverse.org/api/endpoints/app-ontologies/): Endpoints for managing ontology hierarchies used to classify apps. Markdown twin: https://docs.cyverse.org/api/endpoints/app-ontologies/index.md Raw source: https://raw.githubusercontent.com/cyverse/docs/main/docs/api/endpoints/app-ontologies.md - [Callbacks](https://docs.cyverse.org/api/endpoints/callbacks/): Endpoints other services call to report analysis and job status back to the DE. Markdown twin: https://docs.cyverse.org/api/endpoints/callbacks/index.md Raw source: https://raw.githubusercontent.com/cyverse/docs/main/docs/api/endpoints/callbacks.md - [Comments](https://docs.cyverse.org/api/endpoints/comments/): Endpoints for creating, listing, and retracting comments on data and apps. Markdown twin: https://docs.cyverse.org/api/endpoints/comments/index.md Raw source: https://raw.githubusercontent.com/cyverse/docs/main/docs/api/endpoints/comments.md - [Favorites](https://docs.cyverse.org/api/endpoints/favorites/): Endpoints for managing a user's favorite data items and apps. Markdown twin: https://docs.cyverse.org/api/endpoints/favorites/index.md Raw source: https://raw.githubusercontent.com/cyverse/docs/main/docs/api/endpoints/favorites.md - [File I/O](https://docs.cyverse.org/api/endpoints/fileio/): Endpoints for uploading, downloading, and streaming file contents. Markdown twin: https://docs.cyverse.org/api/endpoints/fileio/index.md Raw source: https://raw.githubusercontent.com/cyverse/docs/main/docs/api/endpoints/fileio.md - [Notifications](https://docs.cyverse.org/api/endpoints/notifications/): Endpoints for listing, marking, and deleting user notifications and system messages. Markdown twin: https://docs.cyverse.org/api/endpoints/notifications/index.md Raw source: https://raw.githubusercontent.com/cyverse/docs/main/docs/api/endpoints/notifications.md - [Permanent ID requests](https://docs.cyverse.org/api/endpoints/permanent-id-requests/): Endpoints supporting the DOI and ARK request workflow for published data. Markdown twin: https://docs.cyverse.org/api/endpoints/permanent-id-requests/index.md Raw source: https://raw.githubusercontent.com/cyverse/docs/main/docs/api/endpoints/permanent-id-requests.md - [Quick launches](https://docs.cyverse.org/api/endpoints/quick-launches/): Endpoints for saved app launch configurations and their sharing. Markdown twin: https://docs.cyverse.org/api/endpoints/quick-launches/index.md Raw source: https://raw.githubusercontent.com/cyverse/docs/main/docs/api/endpoints/quick-launches.md - [Terrain and apps services](https://docs.cyverse.org/api/endpoints/terrain-v-apps/): How responsibilities are split between the Terrain facade and the apps service. Markdown twin: https://docs.cyverse.org/api/endpoints/terrain-v-apps/index.md Raw source: https://raw.githubusercontent.com/cyverse/docs/main/docs/api/endpoints/terrain-v-apps.md - [Miscellaneous](https://docs.cyverse.org/api/endpoints/misc/): Endpoints that do not belong to a larger resource group. Markdown twin: https://docs.cyverse.org/api/endpoints/misc/index.md Raw source: https://raw.githubusercontent.com/cyverse/docs/main/docs/api/endpoints/misc.md ### Endpoints / Filesystem - [Root listing](https://docs.cyverse.org/api/endpoints/filesystem/root-listing/): Endpoint returning the top-level directories visible to the caller. Markdown twin: https://docs.cyverse.org/api/endpoints/filesystem/root-listing/index.md Raw source: https://raw.githubusercontent.com/cyverse/docs/main/docs/api/endpoints/filesystem/root-listing.md - [Directory listing](https://docs.cyverse.org/api/endpoints/filesystem/directory-listing/): Endpoints for non-recursive directory listings with paging and filtering. Markdown twin: https://docs.cyverse.org/api/endpoints/filesystem/directory-listing/index.md Raw source: https://raw.githubusercontent.com/cyverse/docs/main/docs/api/endpoints/filesystem/directory-listing.md - [Directory create](https://docs.cyverse.org/api/endpoints/filesystem/directory-create/): Endpoint for creating one or many directories in a single request. Markdown twin: https://docs.cyverse.org/api/endpoints/filesystem/directory-create/index.md Raw source: https://raw.githubusercontent.com/cyverse/docs/main/docs/api/endpoints/filesystem/directory-create.md - [Stat](https://docs.cyverse.org/api/endpoints/filesystem/stat/): Endpoints returning status information for files and directories. Markdown twin: https://docs.cyverse.org/api/endpoints/filesystem/stat/index.md Raw source: https://raw.githubusercontent.com/cyverse/docs/main/docs/api/endpoints/filesystem/stat.md - [Existence](https://docs.cyverse.org/api/endpoints/filesystem/existence/): Endpoint for testing whether paths exist and are visible to the caller. Markdown twin: https://docs.cyverse.org/api/endpoints/filesystem/existence/index.md Raw source: https://raw.githubusercontent.com/cyverse/docs/main/docs/api/endpoints/filesystem/existence.md - [Manifest](https://docs.cyverse.org/api/endpoints/filesystem/manifest/): Endpoint returning the manifest of a file, including preview and infoType details. Markdown twin: https://docs.cyverse.org/api/endpoints/filesystem/manifest/index.md Raw source: https://raw.githubusercontent.com/cyverse/docs/main/docs/api/endpoints/filesystem/manifest.md - [Read chunk](https://docs.cyverse.org/api/endpoints/filesystem/read-chunk/): Endpoints for reading a byte range or page of a file without downloading it. Markdown twin: https://docs.cyverse.org/api/endpoints/filesystem/read-chunk/index.md Raw source: https://raw.githubusercontent.com/cyverse/docs/main/docs/api/endpoints/filesystem/read-chunk.md - [CSV/TSV parsing](https://docs.cyverse.org/api/endpoints/filesystem/csv-tsv-parsing/): Endpoints that parse delimited files in the Data Store into structured responses. Markdown twin: https://docs.cyverse.org/api/endpoints/filesystem/csv-tsv-parsing/index.md Raw source: https://raw.githubusercontent.com/cyverse/docs/main/docs/api/endpoints/filesystem/csv-tsv-parsing.md - [Move](https://docs.cyverse.org/api/endpoints/filesystem/move/): Endpoints for moving files and directories, individually or in bulk. Markdown twin: https://docs.cyverse.org/api/endpoints/filesystem/move/index.md Raw source: https://raw.githubusercontent.com/cyverse/docs/main/docs/api/endpoints/filesystem/move.md - [Rename](https://docs.cyverse.org/api/endpoints/filesystem/rename/): Endpoint for renaming a file or directory in place. Markdown twin: https://docs.cyverse.org/api/endpoints/filesystem/rename/index.md Raw source: https://raw.githubusercontent.com/cyverse/docs/main/docs/api/endpoints/filesystem/rename.md - [Delete](https://docs.cyverse.org/api/endpoints/filesystem/delete/): Endpoints for moving files and directories to the trash or deleting them outright. Markdown twin: https://docs.cyverse.org/api/endpoints/filesystem/delete/index.md Raw source: https://raw.githubusercontent.com/cyverse/docs/main/docs/api/endpoints/filesystem/delete.md - [Restore](https://docs.cyverse.org/api/endpoints/filesystem/restore/): Endpoints for restoring files and directories from a user's trash. Markdown twin: https://docs.cyverse.org/api/endpoints/filesystem/restore/index.md Raw source: https://raw.githubusercontent.com/cyverse/docs/main/docs/api/endpoints/filesystem/restore.md - [Empty trash](https://docs.cyverse.org/api/endpoints/filesystem/empty-trash/): Endpoint for permanently emptying a user's trash directory. Markdown twin: https://docs.cyverse.org/api/endpoints/filesystem/empty-trash/index.md Raw source: https://raw.githubusercontent.com/cyverse/docs/main/docs/api/endpoints/filesystem/empty-trash.md - [Metadata](https://docs.cyverse.org/api/endpoints/filesystem/metadata/): Endpoints for reading, setting, and copying AVU metadata on data objects and collections. Markdown twin: https://docs.cyverse.org/api/endpoints/filesystem/metadata/index.md Raw source: https://raw.githubusercontent.com/cyverse/docs/main/docs/api/endpoints/filesystem/metadata.md - [Search](https://docs.cyverse.org/api/endpoints/filesystem/search/): Endpoints for searching data by name, metadata, and permissions. Markdown twin: https://docs.cyverse.org/api/endpoints/filesystem/search/index.md Raw source: https://raw.githubusercontent.com/cyverse/docs/main/docs/api/endpoints/filesystem/search.md - [Permissions](https://docs.cyverse.org/api/endpoints/filesystem/permissions/): Endpoints for listing and updating user permissions on data. Markdown twin: https://docs.cyverse.org/api/endpoints/filesystem/permissions/index.md Raw source: https://raw.githubusercontent.com/cyverse/docs/main/docs/api/endpoints/filesystem/permissions.md - [Sharing](https://docs.cyverse.org/api/endpoints/filesystem/sharing/): Endpoints for sharing and unsharing data with other users. Markdown twin: https://docs.cyverse.org/api/endpoints/filesystem/sharing/index.md Raw source: https://raw.githubusercontent.com/cyverse/docs/main/docs/api/endpoints/filesystem/sharing.md - [Tickets](https://docs.cyverse.org/api/endpoints/filesystem/tickets/): Endpoints for creating, listing, and deleting iRODS tickets for anonymous access. Markdown twin: https://docs.cyverse.org/api/endpoints/filesystem/tickets/index.md Raw source: https://raw.githubusercontent.com/cyverse/docs/main/docs/api/endpoints/filesystem/tickets.md - [CoGe](https://docs.cyverse.org/api/endpoints/filesystem/coge/): Endpoints for exposing genome files in the Data Store to CoGe. Markdown twin: https://docs.cyverse.org/api/endpoints/filesystem/coge/index.md Raw source: https://raw.githubusercontent.com/cyverse/docs/main/docs/api/endpoints/filesystem/coge.md - [OAI-ORE](https://docs.cyverse.org/api/endpoints/filesystem/ore/): Endpoint for generating OAI-ORE descriptions of a dataset. Markdown twin: https://docs.cyverse.org/api/endpoints/filesystem/ore/index.md Raw source: https://raw.githubusercontent.com/cyverse/docs/main/docs/api/endpoints/filesystem/ore.md - [Path lists](https://docs.cyverse.org/api/endpoints/filesystem/path-lists/): Endpoints for creating HT path list files from a set of Data Store paths. Markdown twin: https://docs.cyverse.org/api/endpoints/filesystem/path-lists/index.md Raw source: https://raw.githubusercontent.com/cyverse/docs/main/docs/api/endpoints/filesystem/path-lists.md - [Filesystem errors](https://docs.cyverse.org/api/endpoints/filesystem/errors/): Error codes returned by the filesystem endpoints. Markdown twin: https://docs.cyverse.org/api/endpoints/filesystem/errors/index.md Raw source: https://raw.githubusercontent.com/cyverse/docs/main/docs/api/endpoints/filesystem/errors.md ## Development - [Developer guide](https://docs.cyverse.org/development/developer-guide/): Development environment, service layout, and contribution workflow for CyVerse code. Markdown twin: https://docs.cyverse.org/development/developer-guide/index.md Raw source: https://raw.githubusercontent.com/cyverse/docs/main/docs/development/developer-guide.md ## References - [Pilot CyVerse deployment record](https://docs.cyverse.org/references/pilot-deployment-record/): Provenance note for the internal pilot deployment write-up that the from-scratch runbook and sizing tables derive from. Markdown twin: https://docs.cyverse.org/references/pilot-deployment-record/index.md Raw source: https://raw.githubusercontent.com/cyverse/docs/main/docs/references/pilot-deployment-record.md ## Meta - [Full corpus in one file](https://docs.cyverse.org/llms-full.txt): every page's Markdown with frontmatter, links made absolute; about 482 KB, roughly 123,000 tokens. Prefer it over fetching pages one at a time. - [Documentation update log](https://docs.cyverse.org/log/): dated history of changes to this bundle. - [For AI agents](https://docs.cyverse.org/about/ai-agents/): endpoints, trust signals, and how to answer questions from this corpus; includes what to do if you cannot fetch this site. - [Sitemap](https://docs.cyverse.org/sitemap.xml) and [robots.txt](https://docs.cyverse.org/robots.txt). - [Source repository](https://github.com/cyverse/docs): the bundle itself; `docs/` mirrors the site paths one to one.