create_conda_env.md

Creating a conda environment on a Virtual Machine

1. Create a conda environment

Install mamba

curl -L -O https://github.com/conda-forge/miniforge/releases/latest/download/Mambaforge-$(uname)-$(uname -m).sh
bash Mambaforge-$(uname)-$(uname -m).sh -b -p $HOME/mambaforge

Export to Path

export PATH="$HOME/mambaforge/bin:$PATH"

From within a notebook you can add Mamba to path with

import os
os.environ["PATH"] += os.pathsep + os.environ["HOME"]+"/Mambaforge/bin"

Create and activate the environment

mamba create -n vcftools -c bioconda vcftools ipykernel -y

You can also create the environment using a yaml file like this: mamba env create -f environment.yml

source activate vcftools