Install

Regular install

To install SCENIC+ run:

git clone https://github.com/aertslab/scenicplus
cd scenicplus
pip install .

Depending on your pip version, you may need to run this pip command instead:

pip install -e .

Installing in a conda environment (recommended)

conda create --name scenicplus python=3.8
conda activate scenicplus
git clone https://github.com/aertslab/scenicplus
cd scenicplus
pip install -e .

Creating a Docker/Singularity image

To build a Docker image, and then create a Singularity image from this:

# Clone repositories
git clone https://github.com/aertslab/pycisTopic.git
git clone https://github.com/aertslab/pycistarget.git
git clone https://github.com/aertslab/scenicplus.git

# Login
podman login docker.io

# Build image
podman build -t aertslab/scenicplus:latest . -f scenicplus/Dockerfile

# Export to oci
podman save --format oci-archive --output scenicplus_img.tar localhost/aertslab/scenicplus

# Build to singularity
singularity build scenicplus.sif oci-archive://scenicplus_img.tar

# Add all binding paths where you would need to access
singularity exec -B /lustre1,/staging,/data,/vsc-hard-mounts,/scratch scenicplus.sif ipython3

Checking version

To check your SCENIC+ version

import scenicplus
scenicplus.__version__