Installations for Ancestry Inference

This page outlines the installations that need to be made to conduct ancesetry inference. Because of the amount of dependencies that need to be installed, this page outlines the order and specific packages that need to be installed in order to make the process as seamless as possible

I have two sections here. The first requires the use of Mamba, which is a much faster version of conda. I recommend using mamba, because it generally is faster and has less issues.

Using Mamba

1. Bioconda

There are a few one-time commands that allow the required packages to be installed quickly and efficiently, and they are as follows:

conda config --add channels defaults
conda config --add channels bioconda
conda config --add channels conda-forge
conda config --set channel_priority strict

2. Plink

The Installation for Plink is just one command:

mamba install -c bioconda plink

3. Jupyter Notebook and R-Kernel

If you will be using Jupyter Notebook to write and execute scripts, these next commands will be needed:

mamba install jupyterlab
mamba install r-irkernel

Additionally, you have to use a one time command in order to initialize the kernel:

//Activate R environment in your shell
R

//One-time command
IRkernel::installspec()

//Quit R
q()

4. Bcftools

Bcftools is a package used to merge vcf files. This will be needed if you need to perform merging with vcf files. There may be dependency conflicts with other packages, and in this case, you may need a separate environment (it is quite irritating, I know)

mamba install bcftools

5. Installations for Ancestry Inference Software

These installlations will be in their respective pages (Rye / Admixture), however, a quick reminder that it is recommended that the installations for the ancestry inference tools are installed on a separate environments

Using Conda