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Setting up ij tools in Galaxy
This is just a proof of concept. Only tested on my 10.8.5 Mac.
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.
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
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 <section id="imagej" name="Image Processing"> <tool file="data_source/upload.xml" /> <tool file="imagej/extractChannelAs32bit.xml" /> <tool file="imagej/ijFilters.xml" /> <tool file="imagej/pixelMath.xml" /> <tool file="imagej/calculatorMacro.xml" /> <tool file="imagej/applyMacro.xml" /> </section>
- stop and reload your Galaxy instance
Once you have working tools, you can also chain them into workflows.