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Eclipse install

1. Download and install Eclipse from www.eclipse.org

Eclipse comes in many different flavors. If you have no clue what to choose, we suggest the "Eclipse IDE for Java and Report Developers" a.k.a. "Reporting" flavor.

2. Check the Eclipse config settings:

The defaults for the amount of memory Eclipse can claim, may be too small. In the Eclipse folder there is a config.ini file at:

eclipse/configuration/config.ini

Edit this file to increase the amount of mem available to Eclipse: (We suggest Xmx of at least 1024m, more is better) (If the arguments below do not exist already, simply add them )

-vmargs
-Xms128m
-Xmx1024m
-XX:MaxPermSize=128m

Make sure the statements above don't start with white space and are on separate lines. Hence, -vmargs -Xms128m -Xmx1024m -XX:MaxPermSize=128m will fail.

3. Install the Freemarker plugin

• Visit ​http://www.jboss.org/tools/download/ for a list of JBOSS update sites
• Copy the URL of the JBOSS update site compatible with your Eclipse
• Go to Eclipse -> menu "Help" -> menu item "Install New Software..."
• Choose: Add and add the URL for the JBOSS update site
• Select the new JBOSS update site you just added and type in the search box: freemarker
• Select Freemarker IDE (not SDK) and click "Next".
• Accept the license and follow the instructions...

4. Start Eclipse and install the Subversive SVN plugin

• Go to Eclipse -> to menu "Help" -> menu item "Install New Software..."
• Select "work with:" -> "--All available sites--" and search for SVN.
• You should find several items. Select "Subversive SVN Team Provider (Incubation)" and click "Next".
• Accept the license and follow the instructions...
• When asked to apply changes or restart Eclipse: choose restart

NOTE: you now have installed half of what you need to work with SVN in Eclipse. In addition to the subversive SVN plugin, you'll also need an SVN connector. There are several flavors: We suggest you give SVNKit a try. The first time you try to interact with SVN in the next step, subversive will notice you don't have a SVN connector and popup a dialog offering you to install one. Make sure you select a version that is compatible with the SVN version you have installed. If unsure: open a terminal and type svn --version

5. Add SVN repository exploring

• Go to Eclipse -> Choose menu Window -> Menu item Open Perspective -> Other... ->
• Choose SVN Repository Exploring
• Right-click in the SVN Repositories window and add new repos '​http://www.molgenis.org/svn'

6. Checkout the MOLGENIS framework

• Go to the SVN Repositories browser in Eclipse:
• Browse to 'molgenis/trunk' project and right-click and checkout, finish.

7. Checkout MOLGENIS apps build with the framework

To start with a fresh project and develop you own MOLGENIS app you'll need molgenis_distro
To get started with the collection of apps developed by the MOLGENIS team you'll need molgenis_apps

• Go to the SVN Repositories browser in Eclipse and depending on your requirements:
  • Browse to 'molgenis_distro/trunk' project and right-click and checkout, finish.
  • Browse to 'molgenis_apps/trunk' project and right-click and checkout, finish.

Frequently asked questions

Q: I can't get graphviz to generate the nice UML diagrams on Apple Mac

Solution is to create/edit the file ~/.MacOSX/environment.plist and add a path statement:

<?xml version="1.0" encoding="UTF-8"?>
<!DOCTYPE plist PUBLIC "-//Apple Computer//DTD PLIST 1.0//EN"
"http://www.apple.com/DTDs/PropertyList-1.0.dtd">
<plist version="1.0">
<dict>
        <key>PATH</key>
<string>/usr/bin:/bin:/usr/sbin:/sbin:/usr/local/bin</string>
</dict>
</plist>