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A repository for keeping conda env and docker image file for running single cell analysis using scanpy
Jupyter Notebook Dockerfile
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README.md

DockerPulls DockerStars Docker Cloud Automated build 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.

Installed packages

  • Python v3.6.9
  • Scanpy v1.4.5
  • Scran v1.10.1
  • Leidenalg v0.7.0
  • MAST v1.12.0
  • Monocle v2.14.0
  • Clusterexperiment v2.6.0
  • Slingshot v1.4.0

Please check the environment.yml file for more details.

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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