conda

conda is the basic package manager for bioinformatics software. It is widely used in the field of bioinformatics and provides a convenient way to install and manage software packages. In this tutorial, we will show you how to install and use conda on your local machine.

Table of contents

• miniconda
  • STEP 1: Download and install miniconda
  • STEP 2: add channels
• Using conda
  • STEP-1: Create a new environment
  • STEP-2: Activate the environment
  • STEP-3: Install packages
  • STEP-4: Check conda environment
  • STEP-5: Remove conda packages
• advanced conda
  • environment export
  • environment install yml file
  • source activate
  • init .bashrc or .zshrc

miniconda

The first step is to download and install miniconda, which is a minimal installation of conda. Miniconda is a small, bootstrap version of conda that includes only conda, Python, the conda package manager, and a few essential packages like pip, zlib, and libffi.

Note

If you have already installed conda on your machine, you can skip this step.

STEP 1: Download and install miniconda

Download the latest version of miniconda from the website and install it on your machine. You can follow the instructions on the website to complete the installation.

wget -c https://repo.anaconda.com/miniconda/Miniconda3-latest-Linux-x86_64.sh

install miniconda:

bash Miniconda3-latest-Linux-x86_64.sh

STEP 2: add channels

After installing miniconda, you need to add channels to the conda package manager. Channels are repositories of software packages that are available for installation. You can add the following channels to your conda installation:

conda config --add channels https://mirrors.bfsu.edu.cn/anaconda/pkgs/free/
conda config --add channels https://mirrors.bfsu.edu.cn/anaconda/pkgs/main/
conda config --add channels https://mirrors.bfsu.edu.cn/anaconda/cloud/conda-forge/
conda config --add channels https://mirrors.bfsu.edu.cn/anaconda/cloud/bioconda/
conda config --set show_channel_urls yes

check the channels:

conda config --get channels
conda config --show channels

channels file:

cat ~/.condarc

if want to add channels directly in the command line, use the following command:

channels:
  - https://mirrors.bfsu.edu.cn/anaconda/cloud/bioconda/
  - https://mirrors.bfsu.edu.cn/anaconda/cloud/conda-forge/
  - https://mirrors.bfsu.edu.cn/anaconda/pkgs/main/
  - https://mirrors.bfsu.edu.cn/anaconda/pkgs/free/
  - https://repo.anaconda.com/pkgs/main
  - https://repo.anaconda.com/pkgs/r
show_channel_urls: true

Using conda

Now that you have installed and added the necessary channels, you can use conda to install and manage software packages.

STEP-1: Create a new environment

to create a new environment, use the following command:

methylTracer

methylTracer is a software package for analysis DNA methylation data.

conda create -n methylTracer r-base=4.3.1

STEP-2: Activate the environment

To activate the environment, use the following command:

conda activate methylTracer

deactivate the environment:

conda deactivate

STEP-3: Install packages

before installing a package, get the package name

conda search bedtools

To install a package, use the following command:

conda install bedtools

if you want to install a specific version of a package, use the following command:

conda install bedtools=2.30.0

STEP-4: Check conda environment

To check the conda environment, use the following command:

conda env list

# or
conda info --envs

STEP-5: Remove conda packages

To remove a conda environment, use the following command:

conda activate methylTracer

conda remove numpy

remove conda environment:

conda env remove --name methylTracer

advanced conda

environment export

you can export the environment to a file:

conda activate methylTracer

conda env export > environment.met.yml

environment install yml file

install yml file:

conda env create -f environment.met.yml

source activate

you can use the following command to activate the environment:

source ~/miniconda3/etc/profile.d/conda.sh

conda activate methylTracer

init .bashrc or .zshrc

add the following code to your .bashrc or .zshrc file:

# >>> conda initialize >>>
# !! Contents within this block are managed by 'conda init' !!
__conda_setup="$('/home/jiazet/miniconda3/bin/conda' 'shell.zsh' 'hook' 2> /dev/null)"
if [ $? -eq 0 ]; then
    eval "$__conda_setup"
else
    if [ -f "/home/jiazet/miniconda3/etc/profile.d/conda.sh" ]; then
        . "/home/jiazet/miniconda3/etc/profile.d/conda.sh"
    else
        export PATH="/home/jiazet/miniconda3/bin:$PATH"
    fi
fi
unset __conda_setup
# <<< conda initialize <<<