[[TracNav(xQTL)]]

= Setup job submission =

= OLD STUFF =

= Installation =

== Overview ==
* Install the latest XGAP disto (1.4)
* Configure your local system to accept and run jobs
* Configure your computer cluster to accept and run jobs

== Installation of XGAP ==

Basic XGAP 1.4 development installation at [http://www.xgap.org/wiki/Installation installation]

== Configuration for LINUX/UNIX==

 * NOTE: The Tomcat user is the 'special' user under which Tomcat is running and accessing the system. (ie. tomcat6)
 * The Tomcat user must own the Tomcat home directory to install dependencies. (ie. /user/share/tomcat6)
 * NOTE: If libraries are installed owned by root, they cannot be overwritten by Tomcat, meaning you could be stuck with an old version. If problems occur, delete the libraries and reinstall using the Dependency Manager plugin.
 * The Tomcat user must own the Tomcat java working directory to be able to execute commands. (ie. /var/lib/tomcat6, use the '''tomcattmpdir''' helper servlet to find out)
 * If 'RCurl' won't install under UNIX, try using the commandline as root and install the following package: 'libcurl3-openssl-dev'

== Configuration for Windows ==
 * Install RTools [http://www.murdoch-sutherland.com/Rtools/index.html RTools]
 * Install Curl for Windows, use a generic binary. Put the install dir on your PATH. [http://curl.haxx.se/download.html cURL]
 * ...

== Configuration for cluster ==

=== Basics === 
 * You have a LINUX/UNIX cluster, then:
 * Install OpenPBS (torque+maoi)
 * Install [http://www.r-project.org/ R]
 * Your scheduler (master/head..) node must a SSH keyboard interactive login mechanism
 * Try to log in to the cluster from your application server. This will accept the SSH key and ensure your firewall isn't blocking outgoing SSH.

=== Continuation === 

 * Optional: if your cluster uses a module system to load programs, load this set:

{{{
module initadd torque
module initadd maui
module initadd R
}}}

 * Then log out from the cluster, then log back in.

 * Create a libs folder for the dependencies using {{{mkdir libs}}}
 * Start R and install a few things:

{{{
install.packages("RCurl",lib="~/libs")
install.packages("qtl",lib="~/libs")
install.packages("snow",lib="~/libs")
}}}

 * Install our custom 'ClusterJobs' library by performing a 'checkout' and R install. From your home folder, do:

{{{
wget -r -l2 http://www.xgap.org/svn/xgap_1_4_distro/handwritten/java/plugins/cluster/R/ClusterJobs/
cd www.xgap.org/svn/xgap_1_4_distro/handwritten/java/plugins/cluster/R/
R CMD INSTALL ClusterJobs --library=~/libs 
}}}

 * Make sure the firewall of your receiver (server that is running XGAP+Cluster+R/qtl) is not blocking port 8080 so the cluster can report back progress and save your results.