xQTL workbench

Stable freeze - WORKING

You will need: ​Ant, ​Subversion, ​Java.

Create a directory somewhere to work in, eg. /Users/harry/xqtl, and cd to there. Run these commands:

svn co -r 8408 http://www.molgenis.org/svn/molgenis/trunk/ molgenis
svn co -r 8410 http://www.molgenis.org/svn/molgenis_apps/trunk/ molgenis_apps
svn update -r 8430 molgenis_apps/xqtl_dev.xml
ant -f molgenis_apps/xqtl_dev.xml make_run

App is now running at: http://localhost:8080/molgenis_apps
First, setup database using: http://localhost:8080/molgenis_apps/resetdatabase_4EE1D7A3E73C504183B69F7D20108853
Then login with user/pw: admin / admin
Go to Settings -> File storage. Enter preferred path or use default, click 'Set path' and 'Validate'
Now go to 'Database' and click 'Load example data'

You are now done setting up :)
PLEASE NOTICE: Subsequent starts of the app should be done with:

ant -f molgenis_apps/xqtl_dev.xml run

To avoid regeneration and recompilation. Things you can do next are..

• Change the admin password
  
• Make users and put them in the group 'biologist' or 'bioinformatician'
  
• Import new data
  
• Explore existing data
  
• Install R packages and run QTL mapping locally
  
• Add a new analysis R script
  
• Run an analysis on the cluster
  
• etcetera!

Cutting edge - WORKING

(Mon Aug 01 17:22:21 CEST 2011, Mol r8447, MolApp r8449)

Run these checkouts instead:

svn co http://www.molgenis.org/svn/molgenis/trunk/ molgenis
svn co http://www.molgenis.org/svn/molgenis_apps/trunk/ molgenis_apps

Followed by the same ant -f molgenis_apps/xqtl_dev.xml make_run command.

Complete Ubuntu installation and run (1 aug 2011)

sudo apt-get install subversion
sudo apt-get install ant
sudo apt-get install openjdk-6-jdk
svn co http://www.molgenis.org/svn/molgenis/trunk/ molgenis
svn co http://www.molgenis.org/svn/molgenis_apps/trunk/ molgenis_apps
ant -f molgenis_apps/xqtl_dev.xml make_run

OLDER STUFF

Vagrant Debian squeeze installation

Links

​Vagrant
​Debian Squeeze
​Run Debian Squeeze using Vagrant

Script

sudo su
apt-get update
apt-get install ant subversion default-jdk -y
mkdir xqtlwb
cd xqtlwb
svn co http://www.molgenis.org/svn/molgenis/trunk/ molgenis
svn co http://www.molgenis.org/svn/molgenis_apps/trunk/ molgenis_apps
ant -f molgenis/standalone.xml
cp molgenis/dist/molgenis-4.0.0.jar molgenis_apps/dist/
ant -f molgenis_apps/standalone.xml generate
ant -f molgenis_apps/standalone.xml
cd molgenis_apps/dist/
java -jar Application.jar

Download and run (OSX, UNIX, Windows):

[Todo: link to ZIP file with working application]

Download source, compile and run (OSX/UNIX):

Required: ​Ant, ​Subversion, ​Java. Pick either the Stable or Unstable checkout.

Stable

svn co TODO
svn co TODO

Unstable

svn co -r 8238 http://www.molgenis.org/svn/molgenis/branches/nobinlibs/
svn co -r 8239 http://www.molgenis.org/svn/molgenis_apps/trunk/

mv nobinlibs molgenis
mv trunk molgenis_apps
ant -f molgenis/standalone.xml
mv molgenis/dist/molgenis-4.0.0.jar molgenis_apps/dist/
ant -f molgenis_apps/standalone.xml generate
ant -f molgenis_apps/standalone.xml
cd molgenis_apps/dist/
java -jar Application.jar

If ant fails with a heapspace error, use:
export ANT_OPTS=-Xmx512m

Application running at: ​http://localhost:8080/molgenis_apps/
Setup database using: ​http://localhost:8080/molgenis_apps/resetdatabase_4EE1D7A3E73C504183B69F7D20108853

APP IS BROKEN AT THIS POINT:

start running create_tables.sql
java.lang.NullPointerException
at java.io.Reader.<init>(Reader.java:61)
at java.io.InputStreamReader.<init>(InputStreamReader.java:55)
at plugins.emptydb.emptyDatabase.empty(Unknown Source)

Download source into development IDE (OSX, UNIX, Windows):

1. Install the ​Eclipse IDE
   
2. Install ​Subclipse for Eclipse
   
3. Install JBoss tools ​Freemarker for Eclipse
   
4. Add SVN repository ​http://ww.molgenis.org/svn
   
5. Checkout /molgenis/trunk
   
6. Checkout /molgenis_apps/trunk