Micromamba

Micromamba#

  1. Download and Install micromamba

cd $WORKDIR
curl -Ls https://micro.mamba.pm/api/micromamba/linux-64/latest | tar -xvj bin/micromamba
./bin/micromamba shell init -s bash -p $WORKDIR/micromamba
source ~/.bashrc

Warning

WORKDIR is a large filesystem, do not use the HOME directory for installation

  1. Create an environment with python=3.10

micromamba create -n myenv python=3.10 -c conda-forge

  1. Activate the environment and install a package

micromamba activate myenv
micromamba install YOUR_MODULE -c conda-forge

:warning: In a submission job, you will probably add the following to activate your environment

. $WORKDIR/micromamba/etc/profile.d/micromamba.sh
micromamba activate myenv

Example: Create R environment and install R packages

# Create an environement with python=3.10
micromamba create -n Renv python=3.10 -c conda-forge

# Activate the environement
micromamba activate Renv

# Install R+ netcdf package
micromamba install r r-base r-essentials –c conda-forge
micromamba install r-ncdf4 –c conda-forge