Manage environment with Conda

Pixi

• Website:https://pixi.prefix.dev/latest/

• Install pixi on new machine

  • copy the yaml file: ~/.config/pixi/manifest.toml
  • Run the sync command to automatically download and isolate all your global tools
  • pixi global sync

## Auto-activate pixi when entering project directory
eval "$(pixi completion --shell bash)"  # or zsh

## Create a global pixi environment with specific R version and packages
pixi global install -e renv \
    r-base=4.5 \
    r-languageserver \
    r-tidyverse \
    r-irkernel \
    r-httpgd \
    r-downlit \
    r-xml2 \
    r-markdown \
    r-devtools \
    radian

## Print out  global pixi environments
pixi global list

## Add Bioconda Permanently
pixi config append default-channels bioconda --global
pixi config set default-channels '["conda-forge", "bioconda"]' --global

## Remove a environment and all its packages
pixi global uninstall <env_name>

## Restore the exposed R and Rscript binaries in the global environment
pixi global install --environment renv --expose R --expose Rscript r-base

Conda

• Installation

# Miniforge linux
wget "https://github.com/conda-forge/miniforge/releases/latest/download/Miniforge3-Linux-x86_64.sh"

# Miniforge Mac
wget "https://github.com/conda-forge/miniforge/releases/latest/download/Miniforge3-MacOSX-arm64.sh"

# Install it
bash Miniforge3-$(uname)-$(uname -m).sh

# Add conda to PATH if found
if [ -f "$HOME/miniconda3/etc/profile.d/conda.sh" ]; then
    . $HOME/miniconda3/etc/profile.d/conda.sh
fi

• Configuration

# Init
conda init --all

# Use mamba for faster solving
conda update -n base conda
conda install -n base conda-libmamba-solver

# Config
conda config --set solver libmamba
conda config --set always_yes true
conda config --set auto_activate_base false

# Setup channels
conda config --add channels bioconda
conda config --add channels conda-forge
#conda config --set channel_priority strict

# Install software from a specific channel
conda install -c conda-forge numpy

• Create Environment

# Create R environment with specific R version and packages
conda create -n renv r=4.5 r-languageserver r-tidyverse r-irkernel r-httpgd r-downlit r-xml2 r-markdown r-devtools radian

# Install bioconductor packages, all package names are lower case
conda install -n renv bioconductor-deseq2 bioconductor-edger

# Install repository packages
conda install -n renv r-qs r-fs r-tidyverse

# Remove a specific environment
conda remove --name renv --all

# Remove a software in a environment
conda remove --name renv package_name

# Export and save the conda env file with all software information
conda env export -n renv > renv.yml

# Export and save the conda env file with all software information
# without the prefix and bundle information
conda env export -n renv --no-builds > renv.yml
conda env export -n renv --no-builds --file renv.yml

# Create a new environment with a environment file
conda env create --file renv.yml

# Rename an environment
conda create --name new_env_name --clone old_env_name
conda activate new_env_name
conda remove --name old_env_name --all