Copy the template and config folder in your GALAXY_ROOT/config/plugins/visualizations/ipython folder and restart Galaxy. Alternativly, you can clone the repository with

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
access your Galaxy instance from IPython with bioblend and redefined functions
save the IPython Notebook into your Galaxy history
notebook persistence across sessions
saved IPython Notebook files can be viewed in HTML and re-opened
self-closing and cleaning IPython docker container

Functions and variables

For your convience, we have added a few pre-defined functions to the IPython profile.

get

The get function will copy a dataset, identified by the history_id, from your current Galaxy into the docker container. It will return the file path to the copied file.

Example:

   with open( get( 44 ), 'r') as handle:
      for line in handle:
         print( line )

put

The put function takes a file path and transfers the file to the current history of your Galaxy session.

Example:

   put( './my_file.tsv', file_type = 'tabular')

HISTORY_ID

Accessing your current history is possible with the pre-defined HISTORY_ID variable.

connect to Galaxy

If you want to communicate with Galaxy you can use get_galaxy_connection() to get an bioblend GalaxyInstance object.

Example:

   from bioblend.galaxy.histories import HistoryClient
   gi = get_galaxy_connection()
   hc = HistoryClient( gi )
   for dataset in hc.show_history( HISTORY_ID , contents=True) ):
      print( dataset['id'] )

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

Björn Grüning
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.