Pipeliner Documentation

Pipeline Runner, also known as Pipeliner, is an open-source and scalable solution for analyzing next-generation sequencing data. Pipeliner provides access to the same best-practices NGS pipelines developed and benchmarked by experts at CCBR and NCBR. This repository is the main source of documentation for users and developers working with or contributing to Pipeliner.

Please Note: When a commit is pushed to the master branch, it triggers a github actions workflow to build the static-site and push it to the gh-pages branch. You can view a live version of the documentation here.

Installation

# Clone the Repository
git clone https://github.com/CCBR/pipeliner-docs.git
# Create a virtual environment
python3 -m venv .venv
# Activate the virtual environment
. .venv/bin/activate
# Update pip
pip install --upgrade pip
# Download Dependencies
pip install -r requirements.txt

Preview while editing

MkDocs includes a previewing server, so you can view your update live and as you write your documentation. The server will automatically rebuild the site upon saving.

# Activate the virtual environment
. .venv/bin/activate
# Start serving your documentation
mkdocs serve

Build static site

Once you are content with your changes, you can build the static site:

mkdocs build