Installation instructions

1. Set up conda

You will need Miniconda to install this package.

πŸ’‘ Conda creates many files in your home directory by default, which can exceed file quota limits on HPC systems. If you have file number restrictions on your home directory, consider installing conda in a directory without such quotas (e.g., a scratch or project directory). These commands tell conda to use specific directories (this is mainly a note to ourselves πŸ™‚):

$ conda config --add pkgs_dirs /path/to/miniconda3/pkgs
$ conda config --add envs_dirs /path/to/miniconda3/envs

To check if conda is installed properly, run this:

$ conda --version
conda 25.11.1

Once you have confirmed you have conda installed, run this command to make sure you are up-to-date:

conda update conda

2. Clone the repository:

git clone https://github.com/mschecht/cellranger-snakemake.git
cd cellranger-snakemake

3. Create and activate the Conda environment:

πŸ’‘ If you need to start fresh, first remove the old environment: conda env remove --name snakemake8

conda env create -f environment.yaml
conda activate snakemake8

Verify the environment tools are working:

snakemake --version
bcftools --version
samtools --version

4. Install cellranger-snakemake into the environment

πŸ’‘ If you’re developing the package, use pip install -e . instead for an editable install.

pip install .

Verify snakemake-run-cellranger installation:

snakemake-run-cellranger --help

5. Cell Ranger Installation

This package provides a Snakemake wrapper for 10x Genomics Cell Ranger, but it does not include the Cell Ranger software itself.

Check if you have Cell Ranger, Cell Ranger ATAC, Cell Ranger ARC installed:

$ cellranger --version
cellranger cellranger-9.0.1

$ cellranger-atac --version
cellranger-atac cellranger-atac-2.1.0

$ cellranger-arc --version
cellranger-arc cellranger-arc-2.0.2

If not, please install them from the 10x Genomics download page.

Minimum supported versions:

  • Cell Ranger (GEX): 9.0.0 or higher

  • Cell Ranger ATAC: 2.0.0 or higher

  • Cell Ranger ARC: 2.0.0 or higher

Linking Cell Ranger to the conda environment

Once installed, link Cell Ranger, Cell Ranger ATAC, Cell Ranger ARC to the conda env:

ENV_NAME="snakemake8"

# Link Cell Ranger
SOURCE="/path/to/cellranger"
TARGET="$(conda info --base)/envs/${ENV_NAME}/bin/cellranger"

ln -s "$SOURCE" "$TARGET"

# Link Cell Ranger ATAC
SOURCE="/path/to/cellranger-atac"
TARGET="$(conda info --base)/envs/${ENV_NAME}/bin/cellranger-atac"

ln -s "$SOURCE" "$TARGET"

# Link Cell Ranger ARC
SOURCE="/path/to/cellranger-arc"
TARGET="$(conda info --base)/envs/${ENV_NAME}/bin/cellranger-arc"

ln -s "$SOURCE" "$TARGET"

Once installed, you can verify the installation using the built-in version checker:

# Check all Cell Ranger tools
snakemake-run-cellranger check-versions

# Check specific workflow requirements
snakemake-run-cellranger check-versions --workflow GEX
snakemake-run-cellranger check-versions --workflow ATAC
snakemake-run-cellranger check-versions --workflow ARC

You’re all set! Head to the Quick Start to run your first workflow.