NIH | National Cancer Institute | NCI Wiki  

Error rendering macro 'rw-search'

null

  • Created by Unknown User (rajagopals2), last modified on May 14, 2008

You are viewing an old version of this page. View the current version.

Compare with Current View Page History

« Previous Version 9 Next »

Analysis-Server Installation Guide

This page provides an introduction to Analysis-Server,installation and to troubleshoot.

Contents

Introduction:

The Analysis Server performs on-the-fly statistical calculations for the caIntegartor application. It can be hosted on the same machine that runs the any application (ex. Rembrandt or ISPY) or it can be run on any number of remote compute machines. In the remote configuration, each compute machine communicates with the appropriate application via the JBossMQ Java Messaging Service (JMS) provided by JBoss. It is important to note that each compute machine does not require its own JBoss instance. The Analysis Server relies on the JMS queues defined in the JBoss instance running the caIntegator application, such as Rembrandt.

Analysis-commons is a module which defines classes for communicating with the analysis server. caIntegrator Applications like Rembrandt , I-SPY etc use the request and response classes defined in the analysis commons module for communication with the analysis server.

Requirements:

The following assumptions are in place:

You have Java and Ant installed, as listed below

Required Software Name
Version
URL to Download

Description

JDK 1.5.X (currently using 1.5.14)
http://java.sun.com/javase/downloads/index_jdk5.jsp

The J2SE Develop¬ment Kit (JDK) supports creat¬ing J2SE applications.

JBOSS Application Server (4.0.X)
http://labs.jboss.com/jbossas/downloads/

JBoss Application server is the Java application Server

Apache Ant, 1.7.0
http://ant.apache.org/bindownload.cgi

Apache Ant is a Java-based build tool.


R and Rserve have been installed. Please see the Rserve homepage at:
http://stats.math.uni-augsburg.de/Rserve/

And the Rserve installation instructions:
http://stats.math.uni-augsburg.de/Rserve/doc.shtml

It is recommended that you read the Rserve installation instructions before installing R. Specifically, the Rserve instructions recommend building the R distribution from source using the (color:red)--enable-R-shlib flag(color).

The R source distribution can be obtained from R project site:
http://www.r-project.org/ (click the link under download)

Setting the Environment Variables:

NOTE

The purpose of setting operating system environment variables is so that the Java SDK and Ant build tool are available to run from anywhere in the system.

Linux

To set the environment variables in Linux, follow these steps:

Step

Action

1

As the root user, enter the following in the /etc/profile file.
A PATH variable should already be created in this file, so be sure to define the JAVA_HOME and ANT_HOME export before the PATH export.
Replace <installation_directory> with the directory where you have installed the Java SDK and Ant.
(The location example in the Apache Ant installation (p. 5) is /usr/java.)
export JAVA_HOME={)<installation_directory>()/jdk1.5.0_10
export ANT_HOME=()<installation_directory>()/apache-ant-1.7.0
export PATH=$JAVA_HOME/bin:$ANT_HOME/bin:$PATH

2

Log out and log back in so that the system recognizes your changes.

Verifying the Environment Variables in Linux

To verify that environment variables have been set correctly, follow these steps:

Step

Action

1

From the command line, enter:
echo $JAVA_HOME
echo $ANT_HOME
Both of these commands should return the location where you installed these tools.

2

To verify your Java SDK installation, enter java -version from a command prompt.
You should see java version "1.5.0_10".

Connection to CVS Repository:

1) Connect to CVS repository
2) Here are the parameters
a) Host: cbiocvs2.nci.nih.gov
b) Repository path: /share/content/cvsroot
c) User: anonymous
d) Password: anonymous
e) Connection type: pserver

Downloading and Deploying the Codebase:

Step :1
Check out caintergrator-analysis commons from HEAD or provided CVS tag. Built it using ant script. (Please follow the steps)

a) Open a COMMAND prompt. cd into caintergrator-analysis commons folder.
b) then type ant build_dependency . It will start the build and get the message
BUILD SUCCESSFUL.
c) Do a CVS check out of the caintegrator-analysis-server

Step:2
Download the latest client jar file (use the exceptions version) from:
http://stats.math.uni-augsburg.de/Rserve/down.shtml after agreeing to their licensing terms and conditions.
Copy the downloaded file into the lib directory under the analysis server install directory and rename it to Rserve.jar .

Step :3
1) Build it using ant script from command prompt.
a) cd into caintergrator-analysis commons folder.
b) then type ant build_tar . It will start the build and you will get the message
BUILD SUCCESSFUL.

Step :4
Setup JMS Configuration Files:
1) Copy the file "caintegrator-jbossmq-destinations-service.xml" from \artifacts to the directory where you installed JBoss.
/jboss-4.0.4.GA/server/default/deploy/jms folder
2) Copy the application specific file for example "rembrandt-jbossmq-destinations-service.xml" (for REMBRANDT) from \artifacts to the directory where you installed JBoss.
/jboss-4.0.4.GA/server/default/deploy/jms folder

Step :5
Deploy the Analysis Server.

  • No labels