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howto:working:setting_up_ij_tools_in_galaxy [2019/04/12 13:13] (current)
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 +====== Setting up ij tools in Galaxy ======
  
 +<​html>​
 +<object width="​560"​ height="​315"><​param name="​movie"​ value="//​www.youtube-nocookie.com/​v/​zxRK6anrLgo?​version=3&​amp;​hl=en_GB"></​param><​param name="​allowFullScreen"​ value="​true"></​param><​param name="​allowscriptaccess"​ value="​always"></​param><​embed src="//​www.youtube-nocookie.com/​v/​zxRK6anrLgo?​version=3&​amp;​hl=en_GB"​ type="​application/​x-shockwave-flash"​ width="​560"​ height="​315"​ allowscriptaccess="​always"​ allowfullscreen="​true"></​embed></​object>​
 +</​html>​
 +===== Disclaimer =====
 +
 +This is just a proof of concept. Only tested on my 10.8.5 Mac.
 +
 +<​note> ​
 +So far only TIF as input, TIF as output.
 +</​note>​
 +
 +===== 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
 +
 +<note info>
 +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
 +</​note>​
 +
 +  * edit **galaxy-dist/​tool_conf.xml** to account for the new tools
 +
 +<file java galaxy-dist/​tool_conf.xml>​
 +  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>​
 +
 +</​file>​
 +
 +  * stop and reload your Galaxy instance
 +
 +
 +==== Workflows ====
 +Once you have working tools, you can also chain them into workflows.
 +
 +<​html>​
 +<object width="​560"​ height="​315"><​param name="​movie"​ value="//​www.youtube-nocookie.com/​v/​zxRK6anrLgo?​version=3&​amp;​hl=en_GB"></​param><​param name="​allowFullScreen"​ value="​true"></​param><​param name="​allowscriptaccess"​ value="​always"></​param><​embed src="//​www.youtube-nocookie.com/​v/​RzLvHloa5EU?​version=3&​amp;​hl=en_GB"​ type="​application/​x-shockwave-flash"​ width="​560"​ height="​315"​ allowscriptaccess="​always"​ allowfullscreen="​true"></​embed></​object>​
 +</​html>​
howto/working/setting_up_ij_tools_in_galaxy.txt ยท Last modified: 2019/04/12 13:13 (external edit)