= xQTL workbench =

{{{
#!html
<h2 style="color: blue">
 Stable freeze - <font color="green"><b>WORKING</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 -r 8408 http://www.molgenis.org/svn/molgenis/trunk/ molgenis`[[BR]]
`svn co -r 8410 http://www.molgenis.org/svn/molgenis_apps/trunk/ molgenis_apps`[[BR]]
`svn update -r 8430 molgenis_apps/xqtl_dev.xml`[[BR]]
`ant -f molgenis_apps/xqtl_dev.xml make_run`[[BR]]
[[BR]]
App is now running at: `http://localhost:8080/molgenis_apps`[[BR]]
First, setup database using: `http://localhost:8080/molgenis_apps/resetdatabase_4EE1D7A3E73C504183B69F7D20108853`[[BR]]
Then login with user/pw: `admin` / `admin`[[BR]]
Go to Settings -> File storage. Enter preferred path or use default, click 'Set path' and 'Validate'[[BR]]
Now go to 'Database' and click 'Load example data'[[BR]]
[[BR]]
You are now done setting up :)[[BR]]PLEASE NOTICE: Subsequent starts of the app should be done with:[[BR]][[BR]]
`ant -f molgenis_apps/xqtl_dev.xml run`[[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">
 Cutting edge - <font color="green"><b>WORKING</b></font>
</h2>
}}}

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

Run these checkouts instead:[[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]]
[[BR]]
Followed by the same `ant -f molgenis_apps/xqtl_dev.xml make_run` command.[[BR]]

[[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`