ScanpyEcoSys

The ScanpyEcoSys Apptainer image provides a ready-to-use, full Scanpy ecosystem for single-cell analysis, including a wide selection of popular Python tools for transcriptomics, spatial data, trajectory inference, and more.

If you notice a useful package missing, please open an issue or submit a pull request.

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Using on COSMOS-SENS

This container is published as a COSMOS-SENS module.

To make it available in your environment:

module use /scale/gr01/shared/common/modules
module load ScanpyEcoSys/1.5

Tip: Any future versions will follow the naming convention
ScanpyEcoSys/<version> (currently 1.5).

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Included Software Highlights

The image bundles most of the Scanpy single-cell ecosystem:

• Core analysis: scanpy, muon, scvi-tools
• Specialized tools: scirpy, squidpy, scVelo, velocyto
• Data integration & metrics: harmony, scanorama, pymde, scib_metrics, spatialdata
• Manifold/embedding algorithms: phate, trimap, sam, phenograph
• Visualization & utilities: seaborn, jupyterlab, papermill, nbconvert, ipywidgets
• Monitoring: psutil, pynvml, autotime
• Special environment: cellphonedb with a dedicated Micromamba env

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Definition File (for reference)

The current Apptainer/Singularity recipe is part of this Github repo.

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Build the Apptainer Image

You can build the container yourself if you have:

• git
• make
• Apptainer/Singularity
• super-user (root) privileges – Apptainer needs these for building images

1️⃣ Clone the Repository

git clone https://github.com/stela2502/ScanpyEcoSys.git
cd ScanpyEcoSys

2️⃣ Build

The provided Makefile handles both a sandbox (writable directory) and a final .sif image.

sudo make restart build

• make restart – creates the sandbox from the definition file
• make build – creates the .sif image from ScanpyEcoSys.def

After completion you will have:

• ScanpyEcoSys_v<version>.sif – the Apptainer image
• a sandbox/ directory – a writable build directory

3️⃣ Test the Image

apptainer run ScanpyEcoSys.sif

Tip: If you don’t have root access, you can only run an already-built .sif image.
Building requires root because Apptainer needs to set file ownership and namespaces.

Getting Started

After building the image:

apptainer run ScanpyEcoSys_1.5.sif

This will start a JupyterLab server on port 9734 listening on all interfaces (0.0.0.0).

Contributing

Pull requests and issues are welcome!
Please describe any additional tools you would like included.

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© 2025 ScanpyEcoSys Maintainers