[[TracNav(xQTL)]] = [wiki:xQTL 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: [http://ant.apache.org/ Ant], [http://subversion.apache.org/ Subversion], [http://www.java.com/ Java].[[BR]] [[BR]] Create a directory somewhere to work in, e.g. `/Users/johndoe/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]] By the way, Ant can be made faster by giving it more memory. Use e.g. `export ANT_OPTS=-Xmx512m`[[BR]] The application is now running at: `http://localhost:8080/xqtl`[[BR]] Then login with user/pw: `admin` / `admin`[[BR]][[BR]] 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.[[BR]]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.[[BR]][[BR]]PLEASE NOTICE: For subsequent starts of the application, use:[[BR]] `ant -f molgenis_apps/xqtl_dev.xml`[[BR]][[BR]] To avoid regeneration and recompilation. It calls the default target '`run`'. Things you should do next are.. [[BR]] * Change the admin password[[BR]] * 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.[[BR]] * Install R so the ''Rplot'' plugin will work. And install the R packages to be able to run QTL mapping locally.[[BR]] * 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:[[BR]] {{{#!html kill -9 `lsof -i :9000 -t`
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 &
 }}} At the moment, `clean_make` will drop your entire database, so be careful! The alternative[[BR]] `ant -f xqtl_dev.xml recompile`[[BR]] Does a 'soft' update: it only updates the code and recompiles this without touching the database. However, some changes require regeneration and (implicitly) a fresh database because of potential datamodel changes. Some more script examples: http://gbic.target.rug.nl/forum/showthread.php?tid=592 === Development and deployment === ''Go into the application source for convenient access to the Ant scripts:''[[BR]] `cd molgenis_apps`[[BR]] '''Run the application on a specified port''', and only this port:[[BR]] `ant -f xqtl_dev.xml runOn -Dport=9000`[[BR]] '''Update the application''':[[BR]] `svn update molgenis molgenis_apps`[[BR]] Followed by at least recompilation. This is the 'fast but may fail' option.[[BR]] `ant -f xqtl_dev.xml recompile`[[BR]] For some updates you must remake the application, which includes MOLGENIS generation and recompilation. This is the 'safe but slow' option.[[BR]] `ant -f xqtl_dev.xml clean_make`[[BR]] You can '''run the data- and webtest''' yourself to find out if your version is stable:[[BR]] `ant -f xqtl_dev.xml test`[[BR]] `ant -f xqtl_selenium.xml webtest` (if this fails: try running as root due to permissions) You can '''remove all generated and compiled code''':[[BR]] `ant -f xqtl_dev.xml clean`[[BR]] Followed by e.g. a make:[[BR]] `ant -f xqtl_dev.xml make`[[BR]] And even delete the HSQL database:[[BR]] `ant -f xqtl_dev.xml deletedb`[[BR]] For '''further details''' you can consult the source of the various scripts: [http://www.molgenis.org/svn/molgenis_apps/trunk/xqtl_dev.xml development], [http://www.molgenis.org/svn/molgenis_apps/trunk/xqtl_selenium.xml webtesting], [http://www.molgenis.org/svn/molgenis_apps/trunk/xqtl_jar.xml jarbuilding]. === 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`[[BR]] 7. Setup classpath by running '''update-eclipse''' in '''build_xgap.xml''' using Ant.[[BR]] 8. Now generate and compile by executing '''clean_make''' in '''xqtl_dev.xml'''.[[BR]] 9. Refresh and start the application with `modules/webserver/boot/RunStandalone.java` or '''run''' in '''xqtl_dev.xml'''. (the default target) [[BR]][[BR]][[BR]] = Other stuff = [[BR]] Older wiki @ http://www.molgenis.org/wiki/xQTLDemo [[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 (which you shouldn't), 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]]