Conda

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

Install Conda and Setup bioconda

Detailed Guide

Summary

curl -O https://repo.anaconda.com/miniconda/Miniconda3-latest-Linux-x86_64.sh
sh Miniconda3-latest-Linux-x86_64.sh
# Follow the prompts

conda config --add channels defaults
conda config --add channels bioconda
conda config --add channels conda-forge

conda create -n aligners bwa

Extending Our Project

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

README.md

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

Makefile

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

And update the "Getting Started" commands.

README.md

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.

Further Reading

• Bioconda Common Pitfalls

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1. Conda environments – common commands↩