Building a conda Environment
A conda
enviornment is needed for any post-processing scripts and visualizations of AlphaFold, including running alphapickle
and generating sequence coverage plots.
module load anaconda
conda create --prefix /scratch/$USER/alphafold/conda/env python=3.8
source activate /scratch/$USER/alphafold/conda/env
conda install biopython matplotlib pandas
source deactivate
You can call this conda
environment inside a SLURM script:
conda run -p "/scratch/$USER/alphafold/conda/env" <command to run in env>