[IPython-dev] Announcement: Galaxy IPython Integration - interactive programming in Galaxy

Björn Grüning bjoern.gruening at gmail.com
Sat Aug 2 11:34:11 EDT 2014

Hi Kyle,

currently you need to have an own Galaxy installation [1]. It's 
relatively simple and and mainly a hg clone and ./run.sh step.

If you have a running Galaxy instance you can follow the installation 
instruction under: https://github.com/bgruening/galaxy-ipython

It's simple as: git clone 

We are facing the problem that all our productive systems do not have 
access to docker, so we need a little bit of time to migrate our 
servers. Also, I would like to collect a few more comments and reviews 
before we can offer this feature to all Galaxy users.

Please note, that I'm in close contact with the main Galaxy devs but I'm 
not part of that gang, so I have nothing to decide weather or not that 
feature will be added to usegalaxy.org.

Thanks for your interest!

[1] https://wiki.galaxyproject.org/Admin/GetGalaxy

Am 02.08.2014 um 17:23 schrieb Kyle Kelley:
> Björn,
> Thanks for sharing. I went ahead and created a Galaxy account. What's the
> simplest path for trying out the IPython notebook integration within Galaxy?
> -- Kyle
> On Sat, Aug 2, 2014 at 1:03 AM, Björn Grüning <bjoern.gruening at gmail.com>
> wrote:
>> Hi all,
>> we proudly present the first release of the Galaxy IPython project.
>> Galaxy IPython is a visualization plugin which should enable Galaxy
>> users with coding skills to easily process their data in the most
>> flexible way. With this plugin, it is possible to analyse and
>> post-process data without downloading datasets or entire histories. One
>> of our aims was to make Galaxy more attractive and accessible to
>> bioinformaticians and programmers, and we hope that this project will
>> build some bridges.
>> More information about Galaxy: http://galaxyproject.org/
>> Screencast: http://www.youtube.com/watch?v=jQDyTuYnn1k
>> Disclaimer: Even though the Ipython notebooks can be stored and reused,
>> this plugin will break the Galaxy philosophy of reproducibility, I feel
>> personally bad about that, but I also think it is a great opportunity to
>> get more bioinformaticians into Galaxy, and to get Galaxy used more
>> often as a teaching resource. By being able to teach not only about
>> workflows but also about data analysis tasks often necessary with
>> Bioinformatics, Galaxy will be significantly more useful in teaching
>> environments.
>> A few features we have up and running:
>> * Use IPython directly in the main window or in the Scratchbook
>> * Completely encapsulated IPython environment with matplotlib,
>> biopython, pandas and friends already installed.
>> * IPython runs completely self-contained within a docker container,
>> separate from your Galaxy data
>> * Easy access to datasets from your current history via pre-defined
>> IPython functions
>> * Manipulate and plot data as you like and export your new files back
>> into your Galaxy history
>> * Save IPython Notebooks across analysis sessions in your Galaxy history
>> with the click of a button.
>> * View saved IPython Notebooks directly in HTML format, or re-open them
>> to continue your analysis.
>> * Self-closing and self-cleaning IPython docker container
>> Notebooks are secure, only accessible to the intended user
>> Please follow the installation instruction on our project page under:
>> https://github.com/bgruening/galaxy-ipython
>> The underlying IPython Notebook (+Galaxy sugar) is stored under:
>> https://github.com/bgruening/docker-ipython-notebook
>> https://registry.hub.docker.com/u/bgruening/docker-ipython-notebook/
>> You can also install a ipynb datatype:
>> https://github.com/bgruening/galaxytools/tree/master/datatypes/json
>> https://testtoolshed.g2.bx.psu.edu/view/iuc/datatyp_ipynb
>> Comments welcome!
>> Happy research!
>> Eric & Björn
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