Purpose

This repository is used to build the docker container used for CellOrganizer.

Docker

Installing Docker

Installing Docker is beyond the scope of this document. To learn about Docker Community Edition (CE), click here.

To install Docker-for-Mac, click here.
To install Docker-for-Windows, click here.

Installing Kitematic

The easiest way to download an image and run a container is to use Kitematic.

To install Kitematic, click here.

About the Docker container

Downloading image and running container using Kitematic

Running Kitematic will open a window that looks like this

Kitematic

Use the searchbar to search for cellorganizer

CellOrganizer

and click Create.

Downloading image and running container

To build an image using the Dockerfile in this repository, run the command

➜ docker build -t "murphylab/cellorganizer" .

The previous step should build an image

➜  docker container ls -a

CONTAINER ID        IMAGE               COMMAND                  CREATED             STATUS                        PORTS               NAMES
48dde52f2bc8        murphylab/cellorganizer     "/bin/bash -c 'pyt..."   45 seconds ago      Exited (0) 39 seconds ago                         frosty_wescoff

To run a container using the image above

➜  docker run -i -t murphylab/cellorganizer

Additional files

The container comes with

Contributing

When contributing to this repository, please first discuss the change you wish to make via issue, email, or any other method with the owners of this repository before making a change.

Support for CellOrganizer has been provided by grants GM075205, GM090033 and GM103712 from the National Institute of General Medical Sciences, grants MCB1121919 and MCB1121793 from the U.S. National Science Foundation, by a Forschungspreis from the Alexander von Humboldt Foundation, and by the Freiburg Institute for Advanced Studies.

murphygroup / docker-cellorganizer-jupyter-notebook

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