Conda is an open source package management system and environment management system that runs on Windows, macOS and Linux. Conda quickly installs, runs and updates packages and their dependencies. Conda easily creates, saves, loads and switches between environments on your local computer. It was created for Python programs, but it can package and distribute software for any language.

Install miniconda

Miniconda is a free minimal installer for conda. It is a small, bootstrap version of Anaconda that includes only conda, Python, the packages they depend on, and a small number of other useful packages, including pip, zlib and a few others.

• Download

  wget -c https://mirrors.tuna.tsinghua.edu.cn/anaconda/miniconda/Miniconda3-latest-Linux-x86_64.sh

• Install

  In this process, just type yes or enter.

bash Miniconda3-latest-Linux-x86_64.sh
# reactivate the environment
source ~/.bashrc

• Configure channels ```shell

  Official website

  conda config —add channels r conda config —add channels conda-forge conda config —add channels bioconda

Mirrored website

conda config —add channels https://mirrors.tuna.tsinghua.edu.cn/anaconda/pkgs/free/ conda config —add channels https://mirrors.tuna.tsinghua.edu.cn/anaconda/pkgs/main/ conda config —add channels https://mirrors.tuna.tsinghua.edu.cn/anaconda/cloud/conda-forge/ conda config —add channels https://mirrors.tuna.tsinghua.edu.cn/anaconda/cloud/bioconda/

View the result

cat ~/.condarc

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## Create a environment
- Create a environment named `covid` and install python3 to depend on
```shell
conda create -y -n covid python=3
# -y : The default answer is yes.

• View existing environments.

  conda info --env

• Install software in covid environment

  Software installed in the environment can only be used in this environment.

# Activate covid environment
conda activate covid
# or
source activate covid
# Install software
conda install -y fastp 
conda install -y bwa 
conda install -y samtools 
conda install -y sambamba 
conda install -y spades 
conda install -y quast 
conda install -y pilon 
conda install -y mafft 
conda install -y iqtree
    # Install a specific version of the software
    conda install -y fastp=0.20.1
# Exit the environment
conda deactivate

• Other common command ```shell

  Search the software

  conda search fastp

View the path where the software was installed.

which fastp

View installed software

conda list conda list -n covid

Update the software

conda update fastp

Uninstall the software

conda remove fastp ```

More Information

• Conda documentation: https://docs.conda.io/en/latest/