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The installation and usage of Conda (Anaconda) and Mamba

1. About

Package management system and environment management system

2. Installation and Usage

2.1 Download file and install

wget https://repo.anaconda.com/archive/Anaconda3-2022.10-Linux-x86_64.sh

bash Anaconda3-2022.10-Linux-x86_64.sh

# Press Enter

# Type yes, press Enter

# Specify the place you want to install:
/home/qgn1237/2_software/anaconda3

# Do you wish the installer to initialize Anaconda3 by running conda init?

# Type No, press Enter, in this way, you will not automatically go to conda base environment

2.2 Create an Environment, for example, you want to add a series of bio-softwares in an independent environment

It's easier to create stand-alone environments for project management, do not install any packages in the "base" environment, keep it clean unless you know how the package will affect the native environment

check how many environment you have

conda env list

Create a environment named "biosoft" with specified Python version

conda create --name biosoft python=3.10

Then activate this environment

conda activate biosoft

You can see now you are in the environment: (biosoft) [XXX@XXXX 2_software]$

You can search whether and which version of the software can be installed in the bioconda channel

conda search -c bioconda minimap2

# Name                       Version           Build  Channel             
minimap2                    2.0.r191               0  bioconda            
minimap2                    2.1.r311               0  bioconda            
minimap2                       2.1.1               0  bioconda            
minimap2                         2.3               0  bioconda

Install the specified version:

conda install -c bioconda minimap2=2.24

However, this may report some errors due to python version, then change the python version to lower:

conda install python=3.7

Exit the current environment

conda deactivate

Install mamba in the base environment

wget https://github.com/conda-forge/miniforge/releases/latest/download/Mambaforge-Linux-x86_64.sh

Install mamba the same way as conda

Remove the former environment

conda remove -n biosoft --all

Go to the bin directory of mambaforge， because you don't use auto init, you have to do this every time when you want to use mamba

./mamba init

source ~/.bashrc

Create a new environment with mamba mamba create -n mamba666 python==3.7

Activate this environment

mamba activate mamba666

Install like conda

mamba install -c bioconda minimap2

minimap2 --version  # You succeed!

Check the packages and softwares you install

conda list

Uninstall software

mamba uninstall samtools

Install the specific version of software

mamba install -c bioconda samtools=1.16

Shift to base environment

mamba activate base