Changes between Version 1 and Version 2 of MolgenisAsGalaxyDatasource

Timestamp:

2011-09-08T17:02:10+02:00 (13 years ago)

Author:

Pieter Neerincx

Comment:

--

MolgenisAsGalaxyDatasource

@@ -7 +7 @@
 
 
-
 If you read this we assume that you already installed Galaxy from [http://getgalaxy.org/ 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 [http://wiki.g2.bx.psu.edu/Admin/Tools/Add%20Tool%20Tutorial Generic documentation from the Galaxy Team on adding tools] and [http://wiki.g2.bx.psu.edu/Admin/Internals/Data%20Sources Generic documentation from the Galaxy Team on adding datasources]
- 2. Download this example molgenis.xml file and copy it to $GALAXY/tools/data_source/
-
-    [[Image(taverna-addressbook.gif)]]
+ 2. Download [http://www.molgenis.org/attachment/wiki/MolgenisAsGalaxyDatasource/Molgenis.xml 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="nbic_gmr/tools/general/DataSources/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 like demonstrated in this [screencast].