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Welcome to the EPP622-2026-SNP Calling wiki!

BEFORE YOU START

Install miniconda. Skip this step if it is already installed.

Make sure your SCRATCHDIR variable is set to the isaac24 scratch location in your ~/.bashrc. Using nano, add these lines to your ~/.bashrc file (at the end or anywhere is fine):

export SCRATCHDIR="/lustre/isaac24/scratch/<your_netid>"

Then run this on the command line (do NOT put in your .bashrc):

echo $SCRATCHDIR

Don't try to move on until that last command - echo $SCRATCHDIR - returns /lustre/isaac24/scratch/

Now install miniconda with its files living in scratch instead of your home directory.

wget https://repo.anaconda.com/miniconda/Miniconda3-latest-Linux-x86_64.sh -O $SCRATCHDIR/miniconda3/miniconda.sh
bash $SCRATCHDIR/miniconda3/miniconda.sh -b -u -p $SCRATCHDIR/miniconda3
rm $SCRATCHDIR/miniconda3/miniconda.sh
source $SCRATCHDIR/miniconda3/bin/activate
conda config --add channels defaults
conda config --add channels bioconda
conda config --add channels conda-forge
$SCRATCHDIR/miniconda3/bin/conda init
source ~/.bashrc

Close and reopen a new terminal. Check that everything is working with

conda list

Helpful resource: Getting Started with Conda

Essential Conda Command List (and installing software) Create a new environment (may need to answer "a" for accept and "y" for yes to a few things)

conda create --name snps

List all environments:

conda env list

Activate an environment

conda activate snps

Install packages (will need to answer "y" for yes to the install and this will take a few minutes)

conda install bioconda::fastqc bioconda::multiqc bioconda::bwa-mem2 bioconda::fastp bioconda::samtools List installed packages in the active environment

conda list