Installation

To install pycisTopic:

git clone https://github.com/aertslab/pycisTopic.git
cd pycisTopic
pip install -e .

To check your pycisTopic version:

import pycisTopic
pycisTopic.__version__

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

# Clone repositories (pycisTopic and pycistarget)
git clone https://github.com/aertslab/pycisTopic.git
git clone https://github.com/aertslab/pycistarget.git

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

# Export to oci
podman save --format oci-archive --output pycistopic_img.tar localhost/aertslab/pycistopic

# Build to singularity
singularity build pycistopic.sif oci-archive://pycistopic_img.tar

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

Warning

If you are planning to run the whole SCENIC+ workflow we recommend to install the SCENIC+ image. You can find more information at https://scenicplus.readthedocs.io/en/latest/install.html.