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R Environments Using Mamba

Mamba is a package manager similar to Conda, but it's much faster. I am using it to create environments for R, especially for the HPC.

Setup

By default mamba/conda create environments in the home directory at ~/.conda/envs. On the HPC since the space in the home directory is limited create a folder conda-envs at a suitable location to store all the environments.

Before we can utilize this new environment location we have to let conda know by adding it to .condarc file in your home directory. 

envs_dirs: [/hpcdata/vrc/vrc1_data/douek_lab/farmerr2/conda-envs]

Create an environment and install R

To create an environment at the default location or at the location specified in the .condarc file. 

mamba create -n env-name

Alternatively if you do not want to make a .condarc file you can create an environment at any location using --prefix and then create a sym link to it at ~/.conda/envs/.

mamba create --prefix=r43

# It will create a subfolder `r43`. Here the prefix is non standard location for the environment.

Activate an environment

conda activate env-name
or
mamba activate env-name

or

# From the environment folder location
source activate r43/

Install R in the activated environment

Note: You do not need to be in the environment file folder. The environment needs to be active to install it. 

mamba install r=4.3

mamba install r-tidyverse r-arrow r-doMC r-biocmanager r-devtools