site_name: SNVPhyl
site_url: http://snvphyl.readthedocs.org
site_description: SNVPhyl Whole Genome SNV Phylogenomics Pipeline.
repo_url: https://irida.corefacility.ca/analysis-pipelines/snvphyl-galaxy
pages:
- Home: 'index.md'
- User:
    - 'Usage': 'user/usage.md'
    - 'Input': 'user/input.md'
    - 'Output': 'user/output.md'
- Installation:
    - 'Home': 'install/index.md'
    - 'Docker': 'install/docker.md'
    - 'Virtual Machine': 'install/virtualmachine.md'
    - 'Galaxy': 'install/galaxy.md'
    - 'Versions': 'install/versions.md'
- Examples:
    - 'Listeria monocytogenes': 'examples/listeria-monocytogenes.md'
- Comparison:
    - 'ASM NGS Challenge 2015': 'comparison/asm-ngs-2015.md'
- Developer:
    - 'Upgrading' : 'developer/upgrading.md'
theme: readthedocs