Custom module

Once you have installed a software for yourself, you can use the module tool to control the usage of the software. The advantage of not directly adding binary paths to PATH is that you have control to deciding when to load the software to the environment.

Setting up a custom module directory

Custom module files can be created and stored anywhere, but let's use the ~/discovery/modulefile/ directory for here.

# If you don't have ~/discovery/modulefile/ directory
mkdir -p ~/discovery/modulefile

Add this to your shell configuration file, i.e., .bashrc. This tells the module command that your custom module files are stored at the specific directory.

module use --append ~/discovery/modulefile

Making a custom module file

Once you've created a directory to store custom modules, let's add one by making a new modulefile at ~/discovery/modulefiles/your_software_name/your_version.

The following is an example for loading mamba, that I have separately installed. (You need to install the software manually to be able to run commands like mamba install pandas!)

#%Module

module-whatis "Loads Mamba 1.5.9 module.

mamba is a reimplementation of the conda package manager in C++.
mamba version: 1.5.9

To load the module, type:
module load ~/discovery/modulefiles/mamba/1.5.9

To activate the base environment, type:
source activate <env_path>

Note - make sure to deactivate any existing conda environments in your path before loading this module. Check your ~/.bashrc for any initialization scripts, and remove them.

To create a virtual environmnet, follow instructions:
https://rc-docs.northeastern.edu/en/latest/software/conda.html#creating-a-conda-virtual-environment-with-anaconda
"

conflict         mamba
prepend-path     PATH ~/miniforge3/bin
prepend-path     PATH ~/miniforge3/sbin
prepend-path     MANPATH ~/miniforge3/man
prepend-path     MANPATH ~/miniforge3/share/man
prepend-path     LD_LIBRARY_PATH ~/miniforge3/lib
prepend-path     CPATH ~/miniforge3/include
prepend-path     LIBRARY_PATH ~/miniforge3/lib