====== Setting up ij tools in Galaxy ======
===== Disclaimer =====
This is just a proof of concept. Only tested on my 10.8.5 Mac.
So far only TIF as input, TIF as output.
===== Background =====
Galaxy is an open, web-based platform for data intensive biomedical research. You have tools for making data available and to process these data. Galaxy offers a toolshed with extra tools you can install. The toolshed has a 'Image processing' section, but it was empty. A similar project by CSIRO http://cloudimaging.blogspot.com.au/ makes some custom IP tools available, but not ImageJ, so I'm giving a try.
===== Installation =====
Just follow this tutorial: https://wiki.galaxyproject.org/Admin/GetGalaxy
It was enough to get Galaxy running on my mac.
===== Add ImageJ tools =====
* Create an **imagej** folder in your **galaxy-dist/tools** folder
* put ij.jar in the fresh **galaxy-dist/tools/imagej** folder
* add the new tools definition files in **galaxy-dist/tools/imagej** as well
in my case, each new tool consists of a tool definition file (xml) that describes inputs, outputs and a script (pyhton) that takes care of creating a proper ImageJ macro and calls it.
Get them all from GitHub : https://github.com/mutterer/ij-galaxy
* edit **galaxy-dist/tool_conf.xml** to account for the new tools
add this section to existing configuration
* stop and reload your Galaxy instance
==== Workflows ====
Once you have working tools, you can also chain them into workflows.