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

Note: If you didn't start the application as root, you may not have the rights to use the default storage path. In that case, set it to somewhere inside your home folder and proceed as usual. E.g. use home/harry/xqtl/

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