Building environments with conda, uv and mamba
This experimental workflow uses conda to create environments and uv and mamba to install and solve environment packages
Conda
We have shared conda environments to simplify your life.
- To list all available envs:
conda env list - To activate env:
source activate brickman
Creating own shared environment
To create a shared environment and make it writable by everyone:
module load miniconda/latest uv/latest
conda create --prefix /maps/projects/dan1/data/Brickman/conda/envs/${NAME_OF_YOUR_ENV} python=${VERSION_OF_PYTHON}
source activate ${NAME_OF_YOUR_ENV}
chmod -R 755 /maps/projects/dan1/data/Brickman/conda/envs/brickman/${NAME_OF_YOUR_ENV}
Install packages from PyPi with uv
While in the created environment, install packages with the command
Install packages from bioconda using mamba
For packages in bioconda, use mamba
Create an environment.yml from your conda environment
When you are happy with the environment, create an environment.yml to make it portable