demOMEGA

Installation

Cobra

1.Clone the repository

git clone

2. Create an environment

conda env create -f demOMEGA.yml

Note: if you use MacOS you have to specify the platform:

conda env create --platform osx-64 -f demOMEGA.yml

3. Activate the environment

conda activate demOMEGA

Docker

From the repository

1. Clone the repository

git clone

2. Build and run the container

docker-compose run --rm --build demOMEGA

Execution

Run synoSCO with default params (replace an example busco output with yours):

python3 demOMEGA.py

If we want to use nucleotide sequences it's enough to provide only sequences or busco output. However, to use protein sequences it is a mandatory to provide nucleotide sequences too (see config_example.yaml)

Common errors

Problem:

bin/sh: shuf: command not found

Solution:

brew install coreutils

Written by: Nikita Leino

Aknowledgements. Many thanks to Giobbe Forni, whose work has pushed me to write this code.