🐳 🔬 📚 IPython running in a docker container. This image can be used to integrate IPython into Galaxy
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README.md

Docker IPython Container

Docker IPython Container

IPython running in a docker container. This image can be used to integrate IPython into Galaxy. A variety of different packages are pre-installed and can be used right away.

This docker container is used by the Galaxy-IPython project and can be installed from the docker.io index.

DOI

Usage

  • Build your own image and run it

Docker is a pre-requirement for this project. You can build the container with:

 docker build -t ipython-notebook . 

The build process can take some time, but if finished you can run your container with:

 docker run -p 7777:6789 -v /home/user/foo/:/import/ -t ipython-notebook

and you will have a running IPython Notebook instance on http://localhost:7777/ipython/.

  • Run a pre-build image from docker registry

docker run -p 7777:6789 -v /home/user/foo/:/import/ bgruening/docker-ipython-notebook

Environment Variables

Some environment variables are made available to the user which will allow for configuring the behaviour of individual instances.

Variable Use
API_KEY Galaxy API Key with which to interface with Galaxy
CORS_ORIGIN If the notebook is proxied, this is the URL the end-user will see when trying to access a notebook
DEBUG Enable debugging mode, mostly for developers
GALAXY_URL URL at which Galaxy is accessible
GALAXY_WEB_PORT Port on which Galaxy is running, if applicable
HISTORY_ID ID of current Galaxy History, used in easing the dataset upload/download process
NOTEBOOK_PASSWORD Password with which to secure the notebook
PROXY_PREFIX Prefix to URL which allows Galaxy proxy to share cookies with Galaxy itself.

Authors

  • Bjoern Gruening
  • Eric Rasche

History

  • v0.1: Initial public release
  • v0.2: Upgrade IPython to version 2.4
  • v0.3: Switch to environment based image configuration. Fix dataset ownership bugs.

Licence (MIT)

Permission is hereby granted, free of charge, to any person obtaining a copy of this software and associated documentation files (the "Software"), to deal in the Software without restriction, including without limitation the rights to use, copy, modify, merge, publish, distribute, sublicense, and/or sell copies of the Software, and to permit persons to whom the Software is furnished to do so, subject to the following conditions:

The above copyright notice and this permission notice shall be included in all copies or substantial portions of the Software.

THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE SOFTWARE.