Fix conda speed issue (hopefully) - mestato/EPP622_2026 GitHub Wiki

  1. Delete current conda

    • remove everything in your .bashrc related to conda or mamba
    • rm -rf $SCRATCHDIR/miniconda3
    • rm -rf ~/.condarc ~/.conda ~/.continuum ~/.anaconda
    • double check for any additional remainder files or folders related to conda in your home directory and scratch directory

  2. New .bashrc lines to add

module load miniconda

export CONDA_PKGS_DIRS="$SCRATCHDIR/.conda/pkgs"   # never the shared prefix, never $HOME
export CONDA_ENVS_DIRS="$SCRATCHDIR/.conda/envs"
export PYTHONDONTWRITEBYTECODE=1                    # stops .pyc writes into read-only envs

Now either log out and log back in OR run source ~/.bashrc

  1. Recreate our class environment
conda create --name snps bioconda::fastqc bioconda::multiqc bioconda::bwa-mem2 bioconda::fastp bioconda::samtools bioconda::bcftools

Check that it worked

conda activate snps
which samtools

samtools should be in your $SCRATCHDIR, something like /lustre/isaac24/scratch/yourusername/.conda/envs/snps/bin/samtools