--- site_name: Azure TRE site_url: https://microsoft.github.io/AzureTRE site_description: Azure TRE site_author: Microsoft repo_url: https://github.com/microsoft/AzureTre/ edit_uri: "" theme: name: material custom_dir: mkdocs-overrides font: text: Roboto code: Roboto Mono palette: scheme: default primary: blue grey accent: indigo logo: assets/ms_icon.png favicon: assets/ms_icon.png features: - navigation.instant - navigation.indexes extra: version: provider: mike default: latest plugins: - search markdown_extensions: - pymdownx.superfences: custom_fences: - name: mermaid class: mermaid format: !!python/name:pymdownx.superfences.fence_code_format - meta - admonition - pymdownx.highlight - pymdownx.pathconverter - mdx_truly_sane_lists - pymdownx.tabbed - pymdownx.tasklist nav: - Overview: # Pages to explain what the Azure TRE - Introducing the AzureTRE: index.md # Introduction to the concept of a TRE, and the AzureTRE - User Roles: azure-tre-overview/user-roles.md # The users and roles within an Azure TRE - Architecture: # Pages to help understand the components, infra, and networking - System Architecture: azure-tre-overview/architecture.md - Network Architecture: azure-tre-overview/networking.md - Azure Resources: azure-tre-overview/tre-resources-breakdown.md - Airlock: azure-tre-overview/airlock.md - Cost Reporting: azure-tre-overview/cost-reporting.md - Terms and Definitions: using-tre/terms-definitions.md # - Compliance: azure-tre-overview/compliance-info.md - QuickStart: # Setup steps for anyone performing an initial deployment of the AzureTRE for eval purposes - tre-admins/setup-instructions/index.md - 1. Prerequisites: tre-admins/setup-instructions/prerequisites.md - 2. Deployment Repository: tre-admins/setup-instructions/deployment-repo.md - 3. AD Tenant: tre-admins/setup-instructions/ad-tenant-choices.md - 4. Setup Auth: tre-admins/setup-instructions/setup-auth-entities.md - 5. Deployment: - Manual: - Pre-deployment Steps: tre-admins/setup-instructions/manual-pre-deployment-steps.md - Deployment Steps: tre-admins/setup-instructions/manual-deployment.md - CI/CD: - Pre-deployment Steps: tre-admins/setup-instructions/cicd-pre-deployment-steps.md - Deployment Steps: tre-admins/setup-instructions/cicd-deployment.md - 6. Configure Shared Services: tre-admins/setup-instructions/configuring-shared-services.md - 7. Install Base Workspace: tre-admins/setup-instructions/ui-install-base-workspace.md - 8. Install Workspace Service and User Resource: tre-admins/setup-instructions/ui-install-ws-and-ur.md - Using the Azure TRE: # Documentation for users of the TRE - Introduction: using-tre/index.md - Custom Templates: using-tre/templates/index.md - Using AzureTRE for Research: - Introduction: using-tre/tre-for-research/index.md - Set up of a Virtual Machine: using-tre/tre-for-research/using-vms.md - Importing/exporting data with Airlock: using-tre/tre-for-research/importing-exporting-data-airlock.md - Reviewing Airlock Requests: using-tre/tre-for-research/review-airlock-request.md - Templates and Services: # Docs to highlight and illustrate workspaces, workspace services etc - Workspaces: - Base: tre-templates/workspaces/base.md - Unrestricted: tre-templates/workspaces/unrestricted.md - Airlock Import Review: tre-templates/workspaces/airlock-import-review.md - Workspace Services: - Azure ML: tre-templates/workspace-services/azure-ml.md - Gitea: tre-templates/workspace-services/gitea.md - Guacamole: tre-templates/workspace-services/guacamole.md - InnerEye: tre-templates/workspace-services/inner-eye.md - MLFlow: tre-templates/workspace-services/mlflow.md - Health Services: tre-templates/workspace-services/health_services.md - Azure Databricks: tre-templates/workspace-services/databricks.md - OHDSI: tre-templates/workspace-services/ohdsi.md - Shared Services: - Gitea (Source Mirror): tre-templates/shared-services/gitea.md - Nexus (Package Mirror): tre-templates/shared-services/nexus.md - Azure CycleCloud (HPC Compute): tre-templates/shared-services/cyclecloud.md - Airlock Notifier: tre-templates/shared-services/airlock-notifier.md - User Resources: - Guacamole Windows VM: tre-templates/user-resources/guacamole-windows-vm.md - Guacamole Linux VM: tre-templates/user-resources/guacamole-linux-vm.md - Import Review VM: tre-templates/user-resources/import-reviewvm.md - Export Review VM: tre-templates/user-resources/export-reviewvm.md - Technical Guide: # All Technical Documentation (Admin, Development) - Administration: # Docs related to the deployment and operation of AzureTRE infrastructure - Starting and Stopping Azure TRE Services: tre-admins/start-stop.md - Environment Variables: tre-admins/environment-variables.md - Tear-down: tre-admins/tear-down.md - Authentication and Authorization: - Introduction: tre-admins/auth.md - Manual Setup: tre-admins/identities/auth-manual.md - Identities: - Application Admin: tre-admins/identities/application_admin.md - API: tre-admins/identities/api.md - Client: tre-admins/identities/client.md - Automation Test Account: tre-admins/identities/test-account.md - Workspaces: tre-admins/identities/workspace.md - Registering Templates: tre-admins/registering-templates.md - Install Resources via API: - Install Base Workspace: tre-admins/setup-instructions/installing-base-workspace.md # yamllint disable-line rule:line-length - Install Workspace Service and User Resource: tre-admins/setup-instructions/installing-workspace-service-and-user-resource.md - Upgrading AzureTRE Version: tre-admins/upgrading-tre.md - Upgrading Resources Version: tre-admins/upgrading-resources.md - Configuring Airlock Reviews: tre-admins/configure-airlock-review.md - Supported Clouds: tre-admins/supported-clouds.md - Development: # Docs related to the developing code for the AzureTRE - Local Development: using-tre/local-development/local-development.md - Contributing to AzureTRE: # Docs aimed at OSS developers, committing code to the AzureTRE repo - Introduction: tre-developers/index.md - API: tre-developers/api.md - UI: tre-developers/ui.md - Resource Processor: tre-developers/resource-processor.md - End to End Tests: tre-developers/end-to-end-tests.md - Letsencrypt: tre-developers/letsencrypt.md - Releases: tre-developers/release.md - GitHub Actions: tre-admins/setup-instructions/workflows.md - Developing Workspace Templates: # Docs aimed at developers creating workspace templates - Authoring Workspace Templates: tre-workspace-authors/authoring-workspace-templates.md - Firewall Rules: tre-workspace-authors/firewall-rules.md - Pipeline Templates: - Overview: tre-templates/pipeline-templates/overview.md - Pipeline Schema: tre-templates/pipeline-templates/pipeline-schema.md - AzureTRE CLI: tre-developers/CLI.md - Troubleshooting FAQ: # General Troubleshooting Section for Development - troubleshooting-faq/index.md - Enabling DEBUG logs: troubleshooting-faq/debug-logs.md - API logs using deployment center: troubleshooting-faq/api-logs-deployment-center.md - Checking the Service Bus: troubleshooting-faq/troubleshooting-sb.md - Checking Logs in Application Insights: troubleshooting-faq/app-insights-logs.md - Troubleshooting the Resource Processor: troubleshooting-faq/troubleshooting-rp.md - Troubleshooting the Airlock: troubleshooting-faq/airlock-troubleshooting.md - Manually edit resources in Cosmos DB: troubleshooting-faq/manually-editing-resources.md - Troubleshooting cloud-init: troubleshooting-faq/cloud-init.md - Contributing: contributing.md