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mkdocs.yml
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---
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
- pymdownx.emoji:
emoji_index: !!python/name:material.extensions.emoji.twemoji
emoji_generator: !!python/name:material.extensions.emoji.to_svg
- attr_list
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
- Case Studies: azure-tre-overview/case-studies.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
- Health Services: tre-templates/workspace-services/health_services.md
- Azure Databricks: tre-templates/workspace-services/databricks.md
- OHDSI: tre-templates/workspace-services/ohdsi.md
- MySQL: tre-templates/workspace-services/mysql.md
- Azure SQL: tre-templates/workspace-services/azuresql.md
- Open AI: tre-templates/workspace-services/openai.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
- Customer Managed Keys: tre-admins/customer-managed-keys.md
- Custom Domain Name: tre-admins/custom-domain.md
- Firewall Force Tunneling: tre-admins/configure-firewall-force-tunneling.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
- GitHub PR Bot Commands: tre-developers/github-pr-bot-commands.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