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A repository for keeping conda env and docker image file for running single cell analysis using scanpy

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imperial-genomics-facility/scanpy-notebook-image

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DockerPulls DockerStars Binder nbviewer

Notebook container image for running single cell data analysis using scanpy

A repository for keeping conda env and docker image file for running single cell analysis using scanpy. Example notebooks are kept at examples dir and template notebooks are kept in templates dir.

Before using examples notebooks

List of prerequisites for using these example notebooks:

List of example notebooks:

Installed packages

Please check the Dockerfile and environment.yml file for all the detail.

Explore notebooks

Explore the example notebooks from this repo in examples dir using nbviewer:

nbviewer

Run notebooks

Using binder

Launce notebooks in binder for exploratory analysis:

binder

Using Docker

  • Install Docker following these instructions: Docker Engine overview

  • Use the following command to pull docker image from Docker hub

    • Pull the latest image
    docker pull imperialgenomicsfacility/scanpy-notebook-image
    
    • Pull a specific release

    docker pull imperialgenomicsfacility/scanpy-notebook-image:release-xyz
    
  • Run notebook container in docker

docker run
  -p 8888:8888
  -v /path/:/tmp
  imperialgenomicsfacility/scanpy-notebook-image:tag

Using Singularity

  • Build singularity image
singularity
  build
  scanpy-notebook-image.sif
  docker://imperialgenomicsfacility/scanpy-notebook-image
  • Run jupyter notebook or nbconvert from singularity container
singularity
  run
  --bind /path:/tmp
  scanpy-notebook-image.sif
    jupyter nbconvert /tmp/notebook.ipynb --execute

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A repository for keeping conda env and docker image file for running single cell analysis using scanpy

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