Conda

For reproducibility, crispr-screens uses (containerized) Conda environments.

To install the (Miniforge) run on a Unix-like platform:

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

Snakemake

To install Snakemake create the following environment with conda:

$ conda create -n snakemake bioconda::snakemake=8.25.5

Activate the environment as follows:

$ conda activate snakemake

If you want to deploy Snakemake on an HPC system using slurm also run:

$ pip install snakemake-executor-plugin-slurm

Note

Depending on your HPC/cloud storage you may also need to install a storage plugin. For more information on this see: https://snakemake.github.io/snakemake-plugin-catalog/index.html.

Apptainer

For (optional) containerization crispr-screens uses Apptainer. If this is applied, Snakemake will pull a Docker image and convert it to an Apptainer image. This image contains all pre-made Conda environments.

Installation on a local machine

The easiest, and recommended, way to install Apptainer on a local Machine is via Conda:

$ conda install -c conda-forge apptainer

Installation on HPC systems

As the installation of Apptainer requires administrator privileges, please contact your HPC administrator to install Apptainer if it is not available yet.

Snakefetch

The easiest way to obtain the workflow code is to use (snakefetch):

$ pip install snakefetch

Obtaining workflow code

To obtain the workflow code, run snakefetch from the analysis directory:

$ mkdir my_experiment
$ cd my_experiment
$ snakefetch --outdir . --repo-version v0.9.0 --url https://github.com/niekwit/crispr-screens
Downloading archive file for version v0.9.0 from https://github.com/niekwit/crispr-screens...
Extracting config and workflow directories from tar.gz file to /path/to/analysis...
Done!

Alternatively, you can install the latest development version from source:

$ git clone https://github.com/niekwit/crispr-screens.git
$ cd crispr-screens
$ cp -r workflow /path/to/analysis

To download a specific version, go to the release page on GitHub and download the source code there.