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Using Molgenis as a datasource for Galaxy

If you add Molgenis as a datasource to a Galaxy server and you navigate from this Galaxy to Molgenis, you'll have an additional menu item in the File menu to send all data from the selected view in Molgenis to Galaxy. Note this menu item is only visible when you added your Molgenis to Galaxy and you navigate to Molgenis from your Galaxy.

Here we will show how to your Galaxy server to be able to fetch data from your Molgenis. There is nothing you need to configure in Molgenis; it just works (on our servers).

If you read this we assume that you already installed Galaxy from ​http://getgalaxy.org/. In this tutorial $GALAXY is the folder where Galaxy is installed.

1. You'll need to add a small XML file to Galaxy to make your Molgenis available as datasource (tool). (Below is the executive summary. For more details you may want to visit ​Generic documentation from the Galaxy Team on adding tools and ​Generic documentation from the Galaxy Team on adding datasources
2. Download ​this example molgenis.xml file and copy it to $GALAXY/tools/data_source/
3. Open $GALAXY/tools/data_source/Molgenis.xml in an editor and look for this line:

   <inputs action="http://localhost:8082/molgenis_apps/molgenis.do" check_values="false" method="get" target="_top">
   

4. Change http://localhost:8082/molgenis_apps/molgenis.do to where your Molgenis lives on the net and save the file.
5. Open $GALAXY/tool_conf.xml in an editor and add <tool file="tools/data_source/Molgenis.xml" /> to the Get Data section, so it looks like this:

   <toolbox>
     <section name="Get Data" id="getext">
       ...''Other data sources already present''...
       <tool file="tools/data_source/Molgenis.xml" />
     </section>
     ...''Other sections''...
   

6. Restart your Galaxy.
7. You should now be able to navigate from your Galaxy to your Molgenis and ​send data from Molgenis to Galaxy as demonstrated in this screencast.