CoNekT Grasses Microbiome

Description

CoNekT Grasses Microbiome derives from CoNekT Grasses that, in turn, was built based on CoNekT (Proost & Mutwil, 2018).

CoNekT Grasses Microbiome is under development in a collaboration between LabBCES (SP, Brazil) and the Wallace Lab (UGA, GA, USA), and is being led by Dr. Renato Santos, under supervision of Prof. Dr. Diego M. Riaño-Pachón and Prof. Dr. Jason Wallace.

Setting up the environment

Virtual env must be installed:

sudo apt install python3.10-venv python3.10-dev
pip3 install virtualenv

Creating and activating

virtualenv --python=python3.10 CoNekT_Grasses_Microbiome
# virtualenv creates a .gitignore file we want to delete, since it ignores all changes in repository
rm CoNekT_Grasses_Microbiome/.gitignore
source CoNekT_Grasses_Microbiome/bin/activate
pip install -r requirements.txt

Building Sphinx documentation

Documentation can be generated using Sphinx.

To generate the documentation, run:

cd CoNekT_Grasses_Microbiome/docs/
sphinx-build -b html source/ build/

Note that we changed the default Sphinx builder to use the Markdown parser. This is done by adding the following line to conf.py file in the CoNekT_Grasses_Microbiome/docs folder:

extensions = ["myst_parser"]

Next steps:

• Build the datatase
• Add data to CoNekT Grasses Microbiome
• Running tests

Funding

• Sao Paulo Research Foundation (FAPESP)
  • Research Internship Abroad Process #2023/11133-3

Licenses

• LabBCES LICENSE
• Original CoNekT license (Dr. Sebastian Proost)