galaxy/config/plugins/visualizations/ipython

Galaxy IPython Integration

IPython Integration into Galaxy

Requirements

For security reasons you need to have docker installed. For a detailed instruction how to install docker, please look at the docker website.

Installation

Copy the template and config folder in your <GALAXY_ROOT>/config/plugins/visualizations/ipython folder and restart Galaxy.

or

git clone https://github.com/bgruening/galaxy-ipython.git config/plugins/viz/ipython

The IPython Visualisation Option should be visible next to the usual Charts or Trackster Options in your Visualisation menue.

Features

• run IPython directly in your Galaxy main window or in Galaxy Scratchbook
• complete encapsulated python environment with matplotlib, pandas and friends installed
• access to all datasets from your current history via pre-defined IPython function
• manipulate and plot data as you like and export your new files back into the Galaxy history
• save the IPython Notebook into your Galaxy history
• saved IPython Notebook files can be viewed in HTML and re-opened
• self-closing and cleaning IPython docker container

Security

• Containers can be secured via Apache+SSL. Please see the setup document for more information.
• Containers will soon have iptables based security to provide a minimum attempt at preventing users from accessing one another's notebooks.

Authors

• Bjoern Gruening
• Eric Rasche

History

• v0.1: Initial public release

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.