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mkdocs.yml
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mkdocs.yml
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site_name: Refgenie
site_logo: img/refgenie_logo_light.svg
site_url: http://refgenie.databio.org/en/latest/
repo_url: http://github.com/databio/refgenie
pypi_name: refgenie
nav:
- Getting Started:
- Introduction: README.md
- Demo videos: demo_videos.md
- Overview: overview.md
- Install and configure: install.md
- Basic tutorial: tutorial.md
- Citing refgenie: manuscripts.md
- How-to guides:
- Refer to assets: asset_registry_paths.md
- Download pre-built assets: pull.md
- Build assets: build.md
- Add custom assets: custom_assets.md
- Retrieve paths to assets: seek.md
- Use asset tags: tag.md
- Use aliases: aliases.md
- Populate refgenie paths: populate.md
- Compare genomes: compare.md
- Run my own asset server: refgenieserver.md
- Use refgenie from Python: refgenconf.md
- Use refgenie in your pipeline: code_snippets.md
- Use refgenie on the cloud: remote.md
- Use refgenie with iGenomes: igenomes.md
- Upgrade from config 0.3 to 0.4: config_upgrade_03_to_04.md
- Reference:
- Studies using refgenie: uses_refgenie.md
- Genome configuration file: genome_config.md
- Glossary: glossary.md
- Buildable assets: available_assets.md
- Usage: usage.md
- Python API: autodoc_build/refgenconf.md
- FAQ: faq.md
- Support: https://github.com/databio/refgenie/issues
- Contributing: contributing.md
- Changelog: changelog.md
theme: databio
plugins:
- databio:
jupyter_source: "docs_jupyter"
jupyter_build: "docs_jupyter/build"
autodoc_build: "docs/autodoc_build"
autodoc_package: "refgenconf"
no_top_level: true
- search
navbar:
left:
- text: Refgenomes server
icon: fa-server
href: servers
right:
- text: Manuscripts
icon: fa-file-alt
href: manuscripts