Create a virtual environment to specify Python and R

Many applications require specific versions of R and Python or a combination of additional modules. As there might be conflicts between those modules, we recommend to use virtual environments to manage and use those packages.  

Individual steps

Log in to Scientific Computing (SciC) Linux Clusters

ssh eristwo.partners.org

then load conda in your environment with the miniforge3 module:

module load miniforge3

then you can create the conda environment:

conda create --name env_name

you can already add requirements here like:

conda create --name env_name python=3.7 R=3.6

execution will take a while. Note that you do not need to specify a version. Do not specify it when you do not use R or Python. 

Activate the environment with:

conda activate env_name

In this virtual environment, you can then install packages with conda install package_name (e.g.) :

(env_name) conda install package_name

Note that you need to add:

module load miniforge3

and 

conda activate env_name

to your job submission scripts. 

Links

Please read more about conda environments : 

https://docs.conda.io/projects/conda/en/latest/user-guide/tasks/manage-environments.html

http://know.continuum.io/rs/387-XNW-688/images/conda-cheatsheet.pdf