Anaconda

Conda is an open-source package and environment management system.

It is a very handy tool when you need to manage python packages.

Download

Warning

The comprehensive revision of Anaconda's terms of service at the end of March 2024 limits free usage in educational institutions with more than 200 users to curriculum-based courses. Please check the terms of service and FAQ. However, using Miniconda and packages from conda-forge channel is still free, which will be used in this tutorial.

Follow the instructions on: https://docs.anaconda.com/miniconda/install/#quick-command-line-install

For example, download the latest linux version:

# make a directory and download the miniconda installer
mkdir -p ~/miniconda3
wget https://repo.anaconda.com/miniconda/Miniconda3-latest-Linux-x86_64.sh -O ~/miniconda3/miniconda.sh

Install

# give it permission to execute
chmod ~/miniconda3/miniconda.sh -b -u -p ~/miniconda3

# install
bash ~/miniconda3/miniconda.sh -b -u -p ~/miniconda3

# remove the installer if miniconda is installed successfully
rm ~/miniconda3/miniconda.sh

# initialize conda
conda init --all

If everything goes well, then you can see the (base) before the prompt, which indicate the base environment:

(base) [heyunye@gc019 ~]$

Set channels

create/revise the file ~/.condarc

channels:
  - conda-forge

and then run conda update --all

Conda User guide

For how to use conda, please check : https://docs.conda.io/projects/conda/en/latest/user-guide/getting-started.html

Examples:

# install a specific version of python package
conda install pandas==1.5.2

#create a new python 3.9 virtual environment with the name "mypython39"
conda create -n mypython39 python=3.9

#use environment.yml to create a virtual environment
conda env create --file environment.yml

# activate a virtual environment called ldsc
conda activate ldsc

# change back to base environment
conda deactivate

# list all packages in your current environment 
conda list

# list all your current environments 
conda env list