README.md

NGB documentation

NGB documentation is provided in a Markdown format, that could be viewed directly from GitHub or could be built into html representation.

Documentation index

The following sections are currently covered in a documentation

• Installation guide
  • Overview
  • Using Docker
  • Using Binaries
  • Using Standalone Jar
• Command Line Interface guide
  • Overview
  • CLI Installation
  • Running a command
  • Accomplishing typical tasks
  • Command reference
• User Interface Guide
  • Overview
  • Datasets
  • Tracks/file formats
    • Overview
    • Reference track
    • Genes track
    • Alignments track
    • VCF track
    • WIG track
    • BED track
    • FeatureCounts track
    • Heatmap track
    • ENCODE-specific tracks
  • Variants
  • Genes
  • BLAST search
  • Homologs search
  • Motifs search
  • Strain lineage
  • Metabolic pathways
  • Target identification
• Administrator guide
  • Overview
  • Users
  • Groups
  • Roles
  • Permissions management
• Developer guide
  • Embedding NGB with URL
  • Embedding NGB with JS

Building documentation

MkDocs are used to build documentation into html representation.

So make sure that all dependencies are installed according to the installation guide.

Once installed, obtain Markdown sources from GitHub:

$ git clone https://github.com/epam/NGB.git
$ cd NGB/docs

Run build:

$ mkdocs build

This will create site/ folder, containing built html documentation.
To view documentation - navigate in ngb/docs/site/ folder and launch index.html with a web-browser.