Introduction to software management using Conda

Conda, an open-source package manager, helps to curb these limitations. The link below gives a detailed description of Conda as a package manager.

https://conda.io/projects/conda/en/latest/index.html

A condensed version of the Conda package management is known as Miniconda. Miniconda is an easy option for users who prefer a lighter installation of Conda than the complete Anaconda distribution. It is specifically created to give this lightweight and minimalistic installation.

Installing Miniconda

Download Miniconda for your specific OS to your home directory

Linux:

wget https://repo.continuum.io/miniconda/Miniconda3-latest-Linux-x86_64.sh

macOS Intel x86:

curl -O https://repo.anaconda.com/miniconda/Miniconda3-latest-MacOSX-x86_64.sh

Run:

bash Miniconda3-latest-Linux-x86_64.sh

bash Miniconda3-latest-MacOSX-x86_64.sh

• Follow all the prompts: if unsure, accept the defaults
• Close and re-open your terminal
• If the installation is successful, you should see a list of installed packages with

conda list 

If the command cannot be found, you can add the Anaconda bin to the path using:

export PATH=~/miniconda3/bin:$PATH

Importing conda environment with all required tools for the course

a. Import conda environment from yml file. Please download and unzip the attached yml file before installing the environment.

conda env create -n MOOC --file MOOC.yml

b. To activate the conda environment

conda activate MOOC

Installing tools on macOS with M1 or M2 chips

Conda does not work on macOS with M1 or M2 chips. Use brew to install the required tools. “brew” refers to the primary command-line tool used to interact with the Homebrew package manager. It is the command you use to install, manage, and update software packages on macOS and Linux systems. The name “brew” is short for “Homebrew.”

A detailed description of Homebrew can be found here: https://brew.sh/

Installing brew:

Step 1:

mkdir homebrew && curl -L https://github.com/Homebrew/brew/tarball/master | tar xz --strip 1 -C homebrew

Step 2:

eval "$(homebrew/bin/brew shellenv)"

brew update --force --quiet

chmod -R go-w "$(brew --prefix)/share/zsh"

To install the tools using brew, run the following command:

brew install FastQC BWA Samtools BCFtools Freebayes sratoolkit

MultiQC is not available on Homebrew but can be installed using pip:

pip3 install multiqc