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This page provides an introduction to Analysis - Server, with installation and troubleshooting information.
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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.
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You have Java and Ant installed, as listed below
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R and Rserve have been installed. Please see the Rserve homepage at:
http://stats.math.uni-augsburg.de/Rserve/
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And the Rserve installation instructions:
http://stats.math.uni-augsburg.de/Rserve/doc.shtml
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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/
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Download the latest client jar file (use the exceptions version) from:
http://stats.math.uni-augsburg.de/Rserve/down.shtml
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Copy the downloaded file into the lib directory under the analysis server install directory and rename it to Rserve.jar .
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1) Open the file/local/content/caintegrator/log/analysisServer.log and you should see something similar to:
a) [translationalResearch:main] INFO gov.nih.nci.caintegrator.analysis.server.RThread - Done initializing Rserver connection elapsedTime=5100
b) [translationalResearch:main] INFO gov.nih.nci.caintegrator.analysis.server.RThread - RThread name=Thread-0 successfully initialized R connection. 5046
2) There may be a warning:
a) [translationalResearch:main] WARN gov.nih.nci.caintegrator.analysis.server.AnalysisServer - could not establish connection with...
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3) After you deploy the application you should return to this log file and see the following:
a) [translationalResearch:main] INFO gov.nih.nci.caintegrator.analysis.server.AnalysisServer - Now listening for requests...
Troubleshooting :
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Steps to add a Data File
Step 1
Click on this link https://gforge.nci.nih.gov/frs/?group_id=406 and you will find The caIntegrator-ODI GForge project files page has data files for particular application
For example:
Rembrandt:
Rembrandt_mas5.dataMatrix_275_10-15-07.Rda
Rembrandt_UnifiedGene.dataMatrix_275_10-15-07.Rda
Ispy:
newDataFile.zip
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And modify it by adding a new line for each developer using this file as an example
3) Copy & and rename analysisServerDeveloper1.properties to local/content/caintegrator/bin/
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