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xQTL workbench - Installation and maintanance
xQTL can be installed, ran and updated on any machine that has Java installed. For safety, we recommend you perform these action as a regular UNIX user and not as root.
Installation
You will need: Ant, Subversion, Java.
Create a directory somewhere to work in, e.g. /Users/johndoe/xqtl, and cd to there. Run these commands:
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
By the way, Ant can be made faster by giving it more memory. Use e.g. export ANT_OPTS=-Xmx512m
The application is now running at: http://localhost:8080/xqtl
Then login with user/pw: admin / admin
You are taken to the homepage, where a special prompt appears that allows you to setup the application with example users and data with one click.
This prompt only appears if you are logged in as admin, and if the application contains no investigations or other users. This concludes setting up the application.
PLEASE NOTICE: For subsequent starts of the application, use:
ant -f molgenis_apps/xqtl_dev.xml
To avoid regeneration and recompilation. It calls the default target 'run'. Things you should do next are..
- Change the admin password
- Load the example data/users. Or let users register themselves and put them in the group 'biologist' or 'bioinformatician'. You can even add users manually.
- Install R so the Rplot plugin will work. And install the R packages to be able to run QTL mapping locally.
- Run a default analysis to see that everything is setup correctly.
Updating
Consider creating an SH script to do the updating for you. For example, this script kills/starts the application on port 9000 and assumes you have used the above installation/checkour dirs:
cd ~/xqtl
svn update molgenis molgenis_apps
cd molgenis_apps
ant -f xqtl_dev.xml clean_make
nohup ant -f xqtl_dev.xml runOn -Dport=9000 &
Development and deployment
Go into the application source for convenient access to the Ant scripts:
cd molgenis_apps
Run the application on a specified port, and only this port:
ant -f xqtl_dev.xml runOn -Dport=9000
Update the application:
svn update molgenis molgenis_apps
Followed by at least recompilation. This is the 'fast but may fail' option.
ant -f xqtl_dev.xml recompile
For some updates you must remake the application, which includes MOLGENIS generation and recompilation. This is the 'safe but slow' option.
ant -f xqtl_dev.xml clean_make
You can run the data- and webtest yourself to find out if your version is stable:
ant -f xqtl_dev.xml test
ant -f xqtl_selenium.xml webtest (if this fails: try running as root due to permissions)
You can remove all generated and compiled code:
ant -f xqtl_dev.xml clean
Followed by e.g. a make:
ant -f xqtl_dev.xml make
And even delete the HSQL database:
ant -f xqtl_dev.xml deletedb
For further details you can consult the source of the various scripts: development, webtesting, jarbuilding.
OLDER STUFF
Older wiki @ http://www.molgenis.org/wiki/xQTLDemo
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/
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):
- Install the Eclipse IDE
- Install Subclipse for Eclipse
- Install JBoss tools Freemarker for Eclipse
- Add SVN repository http://ww.molgenis.org/svn
- Checkout
/molgenis/trunk
- Checkout
/molgenis_apps/trunk
