mkdocs.yml

site_name: PennCNV
site_url: http://penncnv.openbioinformatics.org/
repo_url: http://github.com/WangGenomicsLab/penncnv/
repo_name: GitHub
site_description: PennCNV software distribution site
site_author: Kai Wang, et al
site_favicon: favicon.ico
copyright: 2007-2015 PennCNV
google_analytics: ['UA-7565671-1', 'www.openbioinformatics.org/penncnv']

docs_dir: docs
#include_search: true
#use_absolute_urls: true
#use_directory_urls: false

pages:
- ['index.md', 'PennCNV']

# User Guide
- ['user-guide/download.md', 'User Guide', 'Download PennCNV']
- ['user-guide/install.md', 'User Guide', 'Install PennCNV']
- ['user-guide/startup.md', 'User Guide', 'Quick Start-Up Guide']
- ['user-guide/input.md', 'User Guide', 'Prepare Input Files']
- ['user-guide/test.md', 'User Guide', 'CNV calling']
- ['user-guide/trio.md', 'User Guide', 'Trio-based CNV calling']
- ['user-guide/joint.md', 'User Guide', 'Joint-based CNV calling']
- ['user-guide/denovo.md', 'User Guide', 'de novo CNV calling']
- ['user-guide/validation.md', 'User Guide', 'Validation-based CNV calling']
- ['user-guide/annotation.md', 'User Guide', 'CNV annotation']
- ['user-guide/visualization.md', 'User Guide', 'CNV visualization']
- ['user-guide/affy.md', 'User Guide', 'PennCNV-Affy']
- ['user-guide/plugin.md', 'User Guide', 'PennCNV Plug-in']

# Misc
- ['misc/faq.md', 'Misc', 'FAQ']
- ['misc/version_history.md', 'Misc', 'Version History']
- ['misc/credit.md', 'Misc', 'Credit']
- ['misc/contributing.md', 'Misc', 'How to Contribute']