mkdocs.yml

site_name: dib-lab metagenomics rotation project
site_url: http://dib-lab.github.io/dib_rotation/
repo_name: dib_rotation
repo_url: https://github.com/dib-lab/dib_rotation
edit_uri: ""

copyright: 'Copyright &copy; 2020 <a href="http://ivory.idyll.org/lab/">Lab for Data Intensive Biology</a> at UC Davis'

# change directory names here
docs_dir: doc
site_dir: site

theme:
  name: material

  # pretty colors! see https://squidfunk.github.io/mkdocs-material/getting-started/#primary-colors
  palette:
    primary: 'deep orange'
    accent: 'black'

  # fun logos! see https://material.io/icons/
  icon:
    logo: material/school

  font:
    text: 'Roboto'
    code: 'Roboto Mono'

# optionally give a title for each page or section
nav:
  - 'Home': 'index.md'
  - "Setup":
    - "Setting up Farm": "01_farm_account.md"
    - "Install Conda": "02_conda.md"
  - "Background Reading":
    - "Scientific Literature": "03_background_reading.md"
    - "Unix Tutorials": "00a_unix.md"
  - "Keeping a Lab Notebook": "04_documentation.md"
  - "Starting a Work Session": "04b_starting_a_work_session.md"
  - "Metagenomics Project":
    - "Find and download the data": "05_starting_with_data.md"
    - "Quality Control": "06_quality_control.md"
    - "Taxonomic Discovery with Sourmash": "07_taxonomic_discovery_with_sourmash.md"
    - "Bin Completion with Spacegraphcats": "08_bin_completion_with_spacegraphcats.md"
    - "Assembling a Nbhd": "09_assembling_a_nbhd.md"
    - "Annotating amino acid sequences": "10_annotating_amino_acid_sequences.md"
  - "Advanced Modules":
    - "Automation, Workflows, and Repeatability": "11_workflows_and_repeatability.md"
    - "Version Control with Git and GitHub":  "12_angus_github.md"
    - "Contribute on GitHub": "13_contribute_on_github.md"