jhover / ontology

Tools for handling GO terms and annotation.

Ontology Utilities

This module provides an easy interface to Gene Ontology manipulations, in combination with species-specific gene annotations.

Install software and dependencies

These instructions assume familiarity with running bioinformatics pipelines...

• Install Conda. https://docs.conda.io/projects/miniconda/en/latest/index.html

• Create an environment for the module pipeline.

conda create -n ontology python==3.9 

• Activate the environment

conda activate ontology

• Install additional Conda repositories

conda config --add channels conda-forge
conda config --add channels bioconda

• Install dependencies, useful tools, confirm update

# For Linux and MacOS
	conda install -y pandas numpy scipy   

• Clone the onotology project from the repository to the standard location. (This assumes you already have git installed. If not, install it first).

mkdir ~/git
git clone https://github.com/jhover/ontology.git

All the code is currently organized so it is run directly from the git directory (rather than installed).

• Create a working directory for your experiment, and copy in a metadata file and the fastq sequencing data files, and the default configuration file.

Initial Configuration

By default the module and scripts will take their defaults from a single configuration file, included in the distribution ~/git/ontology/etc/ontology.conf. Often, these can be overridden from the command line. You can also copy the default configuration file, edit it, and use it from each command with the -c switch.

For each command, there are typical arguments. Additional arguments may be supported. Run the -h switch to see the full usage help.