Package management system and environment management system
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