| Version 23 (modified by , 13 years ago) (diff) |
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xQTL workbench
Latest release WORKING
You will need: Ant, Subversion, Java.
Create a directory somewhere to work in, e.g. /Users/harry/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/molgenis_apps
Then login with user/pw: admin / admin
You are now done setting up :)
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 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!
Development & 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/
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):
- 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
