[IPython-dev] Announcement: Galaxy IPython Integration - interactive programming in Galaxy
Björn Grüning
bjoern.gruening at gmail.com
Sat Aug 2 02:03:38 EDT 2014
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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