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Table of Contents
Introduction
MOLGENIS application overview
- Browsing and editing
- CSV file loading
- Connecting to R
- Connecting to SOAP web services
- Connecting to REST web services using CURL
- Molgenis as a datasource for Galaxy
Toolkit Installation
- Preperation on Windows
- Preperation on Ubuntu/Linux
- Installation of Eclipse/Galileo
- Installation of Eclipse/Helios
- Installation of Eclipse/Indigo
- Download MOLGENIS
Generating your own applications
- MOLGENIS workspace basics
- Running the generator
- Modeling a new MOLGENIS
- Modeling an existing database
- molgenis.properties file
Adding plug-ins
Building on the MOLGENIS framework
MOLGENIS Data Modeling Language Reference
MOLGENIS User Interface Modeling Language Reference
MOLGENIS framework API
Frequently asked questions
- How to change molgenis url from /molgenis_distro to xyz
- How to change the MolgenisServlet, e.g. to add more services
- How to extend an existing database model
- Case sensitivity and issues between windows, linux and mac
- How to create a hyperlink from plugin to another form
- How to create a hyperlink from plugin to another form
- How to create a hyperlink from plugin to another form
Eclipse install
- Download Eclipse J2EE version from http://www.eclipse.org/downloads
- Install subversion plugin
- Within Eclipse go to 'Help' -> install new software
- paste url http://subclipse.tigris.org/update_1.6.x
- tick all, next, next, accept, finish
- Add svn repository exploring
- Choose Window -> Perspective -> Other and then choose SVN Repository Exploring
- Right-click in the SVN Repositories window and add new repos ' http://www.molgenis.org/svn'
- Browse to 'molgenis/trunk' project and right-click and checkout, finish.
- Browse to 'molgenis_distro/trunk' project and right-click and checkout, finish.
- Install Freemarker plugin
Within Eclipse:
- go to help -> install new software
- Choose: 'Add' and add new url http://download.jboss.org/jbosstools/updates/JBossTools-3.1.1.GA/
- Type in search box: 'Freemarker'
- Tick box: Freemarker IDE (not SDK)
- Install
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>