Workspace Setup

Below are the steps to create a workspace to perform ancestry inference calculations

NOTE:

Due to dependency conflicts, it is recommended to only install dependencies for either rye or admixture in a single environment. If you will be using both, I recommend setting up two separate environments out of convenience.

Additionally, I am providing two options, using conda or mamba. Mamba is a faster, newer version of conda that greatly increases its speed, especially with downloading and installing necessary packages. I recommend using mamba, however, I will leave the option to use conda as well.

Mamba Environment

First we need to install mambaforge, which you can do using this command:

wget "https://github.com/conda-forge/miniforge/releases/latest/download/Miniforge3-$(uname)-$(uname -m).sh"
bash Miniforge3-$(uname)-$(uname -m).sh

Creating and activating a mamba environment

These two commands can be used to create and activate a mamba environment:

mamba create -n {name}

mamba activate {name}

//Environments can also be deactivated using

mamba deactivate

Conda Environment

First we need to create a conda environment. The first step to do this is to download and install miniconda using these commands:

//Downloading
wget https://repo.anaconda.com/miniconda/Miniconda3-latest-Linux-x86_64.sh

//Installing
bash Miniconda3-latest-Linux-x86_64.sh

Creating and activating a conda environment

These two commands can be used to create and activate a conda environment:

conda create -n {name}

conda activate {name}