Start interactive session

Do this anytime you want to create a Mamba environment or install packages. These tasks are resource-intensive and should not be done on the login node.

srun --partition=mcbstudent --qos=mcbstudent --mem=16GB --pty bash

Install Mamba

These steps only need to be done once.

Download miniforge installer

wget -O Miniforge3.sh "https://github.com/conda-forge/miniforge/releases/latest/download/Miniforge3-$(uname)-$(uname -m).sh"

Install miniforge

bash Miniforge3.sh

1. Agree to license terms (yes)
2. Choose installation path (default is fine)
3. Important: Choose whether to initialize mamba (select “yes”)

source ~/.bashrc

Creating an environment

Once installed, you can create environments

mamba create -n single-cell python=3.11

1. Confirm changes (y)

Activating an environment

Once you have created an environment, you can activate it:

mamba activate single-cell

Installing packages

Once an environment is activated, you can install packages. The following commands install the necessary packages for this workshop.

mamba install -c conda-forge -c bioconda jupyter numpy"<2" scanpy \
  python-igraph leidenalg seaborn scipy scikit-image scikit-misc bbknn \
  celltypist rpy2 anndata2ri=1.1 r-irkernel bioconda::r-sceasy r-soupx \
  bioconda::bioconductor-scater bioconda::bioconductor-scdblfinder \
  bioconda::bioconductor-scry