mkdocs.yml

site_name: Polly Documentation
use_directory_urls: false
nav:
  - About Polly: index.md  
  - Before You Start:
      - Privacy Policy: Getting Started/Privacy Policy.md
      - Prerequisites of UI and CLI: Getting Started/Prerequisites.md
  - QuickStart:
      - Accessing The Platform: Getting Started/index1.md
      - Your Workspaces: Getting Started/Your Workspaces2.md
      - Your Data and Analyses: Getting Started/Your Data.md
      - Your Collaborations: Getting Started/Your Collaborations.md
  - Dashboard:
      - Admin Dashboard: Getting Started/Admin Dashboard.md
      - Monitoring Dashboard: Getting Started/Monitoring_Dashboard.md
  - Atlas:
      - About Atlas: OmixAtlas/Atlas.md
      - Overview of Atlas: OmixAtlas/Overview_of_Atlas.md
      - Curating Atlas:
        - Curating Atlas: OmixAtlas/Curating OA/Curating_OA.md 
        - Curating Atlas - Bulk RNAseq: OmixAtlas/Curating OA/Curating_OA_BulkRNAseq.md 
        - Curating Atlas - Single Cell: OmixAtlas/Curating OA/Curating_OA_scRNA.md 
      - How to Find Datasets?: OmixAtlas/search_datasets.md
      - How to Filter Datasets?: OmixAtlas/Filter_datasets.md
      - How to View Details?: OmixAtlas/View_Details.md
      - How to Analyze Datasets?:
        - Phantasus: Apps/Phantasus.md
        - Cellxgene: Apps/Cellxgene.md
      - FAQs:
        - Bulk RNA Sequencing FAQs: OmixAtlas/FAQs/Bulk_RNA_sequencing_FAQs.md
        - Single Cell RNA Sequencing FAQs: OmixAtlas/FAQs/scRNA_seq_FAQs.md
        - Spatial Transcriptomics FAQs: OmixAtlas/FAQs/Spatial_Transcriptomics_FAQs.md
  - Polly Python: '!import https://github.com/ElucidataInc/polly-python-code?branch=multirepo_plugin_docs&extra_imports=["polly/*", "polly_services/*"]'
  - Polly Compute:
    - Polly Notebooks:
      - About Polly Notebooks: Scaling compute/Polly Notebooks5.md
      - Accessing Polly Notebooks: Scaling compute/Polly Notebooks1.md
      - Pre-configured Environment: Scaling compute/Polly Notebooks2.md
      - Computational Machines Available: Scaling compute/Polly Notebooks3.md
      - Getting Started With Notebooks: Scaling compute/Polly Notebooks4.md
      - Gists: TechEcosystem/Gists1.md
    - Polly CLI:
      - Getting Started with Polly CLI: Scaling compute/Polly CLI 1.md
      - Docker Building Guidelines: TechEcosystem/Docker Building guidelines.md
      - Docker Management: TechEcosystem/Docker Management.md
      - Running Dockerized Jobs: TechEcosystem/Running Dockerized Jobs.md
      - Jobs Execution: TechEcosystem/Job Execution.md
      - Gists: TechEcosystem/Gists2.md
    - Polly Workflow:
      - Nextflow: Apps/Polly Workflow/Nextflow.md
      - Build Nextflow Pipeline: Apps/Polly Workflow/Build Nextflow Pipeline.md
      - Running Nextflow pipelines: Apps/Polly Workflow/Execute Nextflow pipelines.md
      - Nextflow Output: Apps/Polly Workflow/Reading Nextflow Output.md
    - Polly Applications: 
      - Application Features: Apps/Introduction.md
      - Discover: Apps/Polly Discover Application.md
      - Dual Mode Data Visualization: Apps/Metabolomic Data/Dual Mode Visualization.md
      - El-MAVEN: Apps/Metabolomic Data/El-MAVEN.md
      - El-MAVEN Phi Relative LC-MS: Apps/Metabolomic Data/El-MAVEN Phi Relative LC-MS.md
      - GTEX Discover Application: Apps/GTEX Discover.md
      - Labeled LC-MS/MS Workfow: Apps/Metabolomic Data/Labeled LC-MSMS Workflow.md
      - Labeled LC-MS Workflow: Apps/Metabolomic Data/Labeled LC-MS Workflow.md
      - Labeled LC-MS Analysis Preset: Apps/labeled_lcms_analysis.md
      - Lipidomics Visualization Dashboard: Apps/Lipidomics Data/Lipidomics Visualization Dashboard.md
      - Proteomics Workflow: Apps/Proteomic Data/Proteomics Workflow.md
      - RNA Seq Workflow: Apps/Sequencing Data/RNA Seq Workflow.md
      - Single Cell Visualization: Apps/Single Cell Visualization.md
      - Untargeted Pipeline: Apps/Metabolomic Data/Untargeted Pipeline.md
      - Curation App: Apps/Curation App.md
      - Billing and Usage: Apps/Billing.md 
  - Tech Ecosystem:
    - Polly Stack: TechEcosystem/Polly Stack.md
    - Security and Data Transfer: TechEcosystem/Data Security.md
    - Data Recovery: TechEcosystem/polly_disaster_recovery_mar_2021.md
    - Technical FAQs: TechEcosystem/Technical FAQs.md
  - Release Notes: Release Notes.md
  - Getting Help: Getting help.md
theme:
  name: material
  custom_dir: overrides
  logo: assets/logo-white.svg
  favicon: img/elucidata.ico
  features:
    - navigation.top
  palette:
    primary: deep purple
plugins:
  - search
  - mkdocstrings:
      handlers:
        python:
          paths:
            - ./temp_dir/polly-python
            - ./temp_dir/polly-python/polly
            - ./temp_dir/polly-python
          options:
            show_root_full_path: False
  - multirepo
extra:
  homepage: https://www.elucidata.io/
  analytics:
    provider: google
    property: 'G-PQXHC1FNVZ'
markdown_extensions:
  - pymdownx.highlight:
      anchor_linenums: true
  - pymdownx.inlinehilite
  - pymdownx.snippets
  - pymdownx.superfences
extra_css:
  - assets/stylesheets/custom.css