Conda

I feel like I’m always explaining to someone the magic incantations performed to get a Conda environment to work. That person is usually myself.

Installation

Miniforge

Easiest way I’ve found to consistently install conda:

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

Official docs

That’s for “Unix-like platforms (Mac OS & Linux)“.

If you’re using windows and not using WSL2, first what are you doing with your life? Second, follow the official docs.

Setting up Bioconda

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

Official Docs. Follow them.

Opinions

Mamba

It’s a drop-in replacement for Conda.

Creating environments

Use an environment.yml file.

name: bwa_mem
channels:
  - conda-forge
  - bioconda
  - defaults
dependencies:
  - bwa=0.7.17
  # renovate: datasource=conda depName=bioconda/samtools
  - samtools=1.18

Bioconda Docs on environment files

mamba create in the project directory should create environment for you.

`environment.yml` Tutorial

So now that we’ve gotten familiar with some tools it’s time to get some

computations running! But we don’t have admin access to the system we’re on so how do we install software? Enter conda

Create an env file

Let’s create an environment file to share with our collaborators, so they can rebuild our conda environment from scratch.¹

cd ag-intro
conda env export --no-builds > env.yaml

Open up env.yaml and poke around.

Commit the env.yaml file.

Update the README

Our collaborators need to know how to build the enviroment from scratch. In the README update the “Getting Started” commands to

git clone https://github.com/emiller88/ag-intro
cd ag-intro
 conda env create --name=more-map-and-call --file=env.yaml
 conda activate aligners
make

Commit the changes to the README.

Add a new make rule to build the conda environment

We can refactor our project to make the initial setup even cleaner, and future proof it if we wanted to change the way we install the conda env.

Let’s add a new make rule

conda_env:
  conda env create --name=more-map-and-call --file=env.yaml

And update the “Getting Started” commands.

git clone https://github.com/emiller88/ag-intro
cd ag-intro
 make conda_env
 conda env create --name=more-map-and-call --file=env.yaml
conda activate aligners
make

Commit the changes to those as well.