= xQTL workbench = {{{ #!html

Stable freeze - WORKING

}}} 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

Cutting edge - WORKING

}}} (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.(!Reader.java:61) [[BR]] at java.io.!InputStreamReader.(!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`