Exploring BGCFlow result with MKDocs

Overview

Teaching: 5 min
Exercises: 0 min

Questions

• How do I look at BGCFlow results?

Objectives

• Starting an mkdocs server of BGCFlow results

• Exploring and using BGCFlow Jupyter Notebooks template

Pre-requisite

• Activate the BGCFlow conda environment (see Part 1 - Introduction)

  conda activate bgcflow
  

Getting a demo report

• Download an example report from Zenodo

  wget -O Lactobacillus_delbrueckii_report.zip https://zenodo.org/record/7740349/files/Lactobacillus_delbrueckii_report.zip?download=1
  unzip Lactobacillus_delbrueckii_report.zip
  

Starting BGCFlow mkdocs server

• Move to the report directory and use bgcflow serve command to start up a http file server and mkdocs:

  cd Lactobacillus_delbrueckii_report/Lactobacillus_delbrueckii
  bgcflow serve --project Lactobacillus_delbrueckii
  

• The report can be accessed in http://localhost:8001/

Key Points

• For each BGCFlow projects, the result is structured as an interactive Markdown documentation that can be modified

• Reports are made using Jupyter notebooks running on Python or R environments