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mkdocs.yml
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---
site_name: Scout Docs
site_url: https://clinical-genomics.github.io/scout
repo_url: https://github.com/Clinical-Genomics/scout
dev_addr: "127.0.0.1:4000"
site_author: Clinical Genomics Scout team
docs_dir: docs
markdown_extensions:
- markdown_include.include:
base_path: docs
validation:
nav:
omitted_files: warn
not_found: warn
links:
not_found: warn
unrecognized_links: warn
theme:
name: 'material'
logo: 'img/logo-only.png'
palette:
primary: 'blue grey'
accent: 'cyan'
nav:
- Introduction: 'README.md'
- Installation: 'install.md'
- FAQ: 'faq.md'
- Features:
- HPO phenotypes: 'features/hpo.md'
- User guide:
- Readme: 'user-guide/README.md'
- Getting started: 'user-guide/getting-started.md'
- General: 'user-guide/using-scout.md'
- Pages: 'user-guide/pages.md'
- Institutes: 'user-guide/institutes.md'
- Users: 'user-guide/users.md'
- Cases: 'user-guide/cases.md'
- Variants: 'user-guide/variants.md'
- Genes: 'user-guide/genes.md'
- Gene panels: 'user-guide/panels.md'
- Annotations: 'user-guide/annotations.md'
- ACMG: 'user-guide/acmg-criterias.md'
- Dashboard: 'user-guide/dashboard.md'
- Admin guide:
- Intro: 'admin-guide/README.md'
- Setup: 'admin-guide/setup-scout.md'
- Login system: 'admin-guide/login-system.md'
- Logging users' activity: 'admin-guide/user_activity_monitoring.md'
- Deploying Scout in containers:
- Dockerfile and docker-compose: 'admin-guide/containers/container-deploy.md'
- Deploying using Kubernetes: 'admin-guide/containers/kubernetes.md'
- Deploying as a systemd service with podman: 'admin-guide/containers/systemd.md'
- Creating a new user: 'admin-guide/loading-users.md'
- Creating a new institute: 'admin-guide/loading-institutes.md'
- Load config: 'admin-guide/load-config.md'
- Loading/updating a case: 'admin-guide/loading-case.md'
- Updating a case without a new config: 'admin-guide/updating-case.md'
- Updating case individuals tracks: 'admin-guide/updating-individuals.md'
- Loading variants: 'admin-guide/loading-variants.md'
- Gene definitions: 'admin-guide/genes.md'
- PanelApp gene panels: 'admin-guide/panelapp_panels.md'
- HPO terms: 'admin-guide/hpo.md'
- Annotations: 'admin-guide/annotations.md'
- IGV browser settings: 'admin-guide/igv-settings.md'
- Server: 'admin-guide/server.md'
- Server Extension Integration:
- Chanjo and Chanjo2 coverage integration: 'admin-guide/chanjo_coverage_integration.md'
- Loqusdb integration: 'admin-guide/loqusdb_integration.md'
- Gens integration: 'admin-guide/gens_integration.md'
- Scout REViewer Service integration: 'admin-guide/reviewer_service.md'
- BioNano Genomics Access FSHD integration: 'admin-guide/bionano_access_integration.md'
- Matchmaker Exchange integration: 'admin-guide/matchmaker_exchange_integration.md'
- Indexes: 'admin-guide/indexes.md'
- Institutes: 'admin-guide/institute.md'
- Display data:
- Cases: 'admin-guide/display-data/cases.md'
- Export: 'admin-guide/export.md'
- Scripts folder: 'admin-guide/scripts.md'
- Backup and restore: 'admin-guide/backup.md'
- Blog:
- Breaking: 'admin-guide/breaking.md'
- Whats new in 3.0?: 'blog/new-3.0.md'
- Whats new in 3.1?: 'blog/new-3.1.md'
- Whats new in 3.2?: 'blog/new-3.2.md'
- Whats new in 3.3?: 'blog/new-3.3.md'
- Whats new in 3.4?: 'blog/new-3.4.md'
- Whats new in 3.5?: 'blog/new-3.5.md'
- Whats new in 4.0?: 'blog/new-4.0.0.md'
- Whats new in 4.7.2?: 'blog/new-4.7.2.md'
- Whats new in 4.7.3?: 'blog/new-4.7.3.md'
- Whats new in 4.17?: 'blog/new-4.17.md'
- Whats new in 4.18?: 'blog/new-4.18.md'
- Whats new in 4.19?: 'blog/new-4.19.md'
- Whats new in 4.20?: 'blog/new-4.20.md'
- Whats new in 4.34?: 'blog/new-4.34.md'
- Whats new in 4.67?: 'blog/new-4.67.md'
- Whats new in 4.72?: 'blog/new-4.72.md'
not_in_nav: |
admin-guide/reference-sets/genes_transcripts.md
user-guide/defining-scorescheme.md