# Conda, Anaconda, Miniconda and Bioconda

Conda (opens new window) - Anaconda (opens new window) - Miniconda (opens new window) - Bioconda (opens new window)

# Installation

# Install Conda

Follow the Installing on Linux (opens new window) instructions to install Miniconda (opens new window).

To get more out of conda we recommend reading Conda - Managing environments (opens new window) guide.

wget https://repo.anaconda.com/miniconda/Miniconda3-latest-Linux-x86_64.sh

bash Miniconda3-latest-Linux-x86_64.sh

After installation is done, log out and log in again to be able to use your conda setup.

# Set up Bioconda and conda-forge channels

To find packages in Conda you need to configure relevant channels. Follow the Set up channels (opens new window) guide from Bioconda. We recommend starting with bioconda (opens new window) and conda-forge (opens new window). Quick way to make sure your channels are added correctly is to (re)add them in this order:

conda config --add channels defaults
conda config --add channels bioconda
conda config --add channels conda-forge

# Install Your Tools

Have a field day installing your favourite tools

conda install plink2

TIP

We have very easy guide on how to get Saige running in Conda environment.

# Do Cool Science

plink2 <input>

# Additional resources

Install R with conda (opens new window)
Update to the latest R version (opens new window)
Please note that this does work with some, but not all, bioconductor-packages. Please send us a note if you need these. List of available r-packages here (opens new window)

# install
conda create -n renv -c conda-forge r-base r-essentials
conda activate renv

# install package in shell
R CMD INSTALL --library="${CONDA_PREFIX}/lib/R/library" .

# install cran packages within r
install.packages("png", paste(Sys.getenv("CONDA_PREFIX"), "/lib/R/library", sep=""))

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