= xQTL workbench =

{{{
#!html
<h2 style="color: blue">
 Latest release <font color="red"><b>BROKEN</b></font>
</h2>
}}}

You will need: [http://ant.apache.org/ Ant], [http://subversion.apache.org/ Subversion], [http://www.java.com/ Java].[[BR]]
[[BR]]
Create a directory somewhere to work in, eg. `/Users/harry/xqtl`, and `cd` to there. Run these commands:[[BR]]
[[BR]]
`svn co http://www.molgenis.org/svn/molgenis/trunk/ molgenis`[[BR]]
`svn co http://www.molgenis.org/svn/molgenis_apps/trunk/ molgenis_apps`[[BR]]
`ant -f molgenis_apps/xqtl_dev.xml make_run`[[BR]]
[[BR]]
App is now running at: `http://localhost:8080/molgenis_apps`[[BR]]
Then login with user/pw: `admin` / `admin`[[BR]]
Go back to Home and follow dataloading instructions.[[BR]]
[[BR]]
You are now done setting up :)[[BR]]PLEASE NOTICE: For subsequent starts of the app, use:[[BR]][[BR]]
`ant -f molgenis_apps/xqtl_dev.xml`[[BR]][[BR]]
To avoid regeneration and recompilation. Things you can do next are..
[[BR]]
* Change the admin password[[BR]]
* Make users and put them in the group 'biologist' or 'bioinformatician'[[BR]]
* Import new data[[BR]]
* Explore existing data[[BR]]
* Install R packages and run QTL mapping locally[[BR]]
* Add a new analysis R script[[BR]]
* Run an analysis on the cluster[[BR]]
* etcetera!

{{{
#!html
<h2 style="color: blue">
 Stable freeze <font color="green"><b></b></font>
</h2>
}}}

Run these checkouts instead:[[BR]][[BR]]
`svn co -r 8800 http://www.molgenis.org/svn/molgenis/trunk/ molgenis`[[BR]]
`svn co -r 8800 http://www.molgenis.org/svn/molgenis_apps/trunk/ molgenis_apps`[[BR]]
`svn update -r 8815 molgenis_apps/modules/webserver/boot/WebserverGui.java`[[BR]]

[[BR]]
Followed by the same `ant -f molgenis_apps/xqtl_dev.xml make_run` command.[[BR]]

[[BR]][[BR]][[BR]]
=== Complete Ubuntu installation and run (1 aug 2011) ===
`sudo apt-get install subversion`[[BR]]
`sudo apt-get install ant`[[BR]]
`sudo apt-get install openjdk-6-jdk`[[BR]]
`svn co http://www.molgenis.org/svn/molgenis/trunk/ molgenis`[[BR]]
`svn co http://www.molgenis.org/svn/molgenis_apps/trunk/ molgenis_apps`[[BR]]
`ant -f molgenis_apps/xqtl_dev.xml make_run`[[BR]]
[[BR]]
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/`
[[BR]][[BR]][[BR]][[BR]][[BR]]
= OLDER STUFF =

== Vagrant Debian squeeze installation ==

=== Links ===

[http://vagrantup.com/ Vagrant][[BR]]
[http://mathie-vagrant-boxes.s3.amazonaws.com/debian_squeeze_32.box Debian Squeeze][[BR]]
[http://woss.name/2011/02/07/vagrant-base-bo-for-debian-squeeze/ Run Debian Squeeze using Vagrant]

=== Script ===

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


=== Download and run (OSX, UNIX, Windows): ===
[Todo: link to ZIP file with working application]

=== Download source, compile and run (OSX/UNIX): ===
Required: [http://ant.apache.org/ Ant], [http://subversion.apache.org/ Subversion], [http://www.java.com/ Java]. Pick either the ''Stable'' or ''Unstable'' checkout.

''Stable''

`svn co TODO`[[BR]]
`svn co TODO`

''Unstable''

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

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

__If ant fails with a heapspace error, use:__[[BR]]`export ANT_OPTS=-Xmx512m`

Application running at: http://localhost:8080/molgenis_apps/ [[BR]]Setup database using: http://localhost:8080/molgenis_apps/resetdatabase_4EE1D7A3E73C504183B69F7D20108853

''APP IS BROKEN AT THIS POINT:''

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

=== Download source into development IDE (OSX, UNIX, Windows): ===
1. Install the [http://www.eclipse.org Eclipse] IDE[[BR]]
2. Install [http://subclipse.tigris.org/update_1.6.x Subclipse] for Eclipse[[BR]]
3. Install JBoss tools [http://download.jboss.org/jbosstools/updates/development/indigo/ Freemarker] for Eclipse[[BR]]
4. Add SVN repository http://ww.molgenis.org/svn [[BR]]
5. Checkout `/molgenis/trunk`[[BR]]
6. Checkout `/molgenis_apps/trunk`