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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.

Step:5.1

Copy the caintegrator-analysis-server.tar file created to the directory /local/content/caintegrator.

Step:5.2

Type the command: tar -xvf caintegrator-analysis-server.tar

Step: 6

Go to the newly created directory /local/content/caintegrator/bin. Type the commands:
chmod u+x *.sh
dos2unix *.sh

Step :7

Start Rserve by typing:

./startRserve.sh
Rserve should now be running. The last line printed on the console should be:

"Rserv started in daemon mode."

Step:8

Go to the directory /home/caintegrator (you can do this by just typing cd).
Start the analysis server by executing the command:

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in the lib directory under the analysis server install directory, with the corresponding jar files from the JBoss distribution.

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 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

Step 2:

Copy the data file to the directory local/content/caintegrator/Rdatafiles/

Step 3:

Restart the analysis server
Log in to the analysis machine

Stop the analysis server by executing the command:
./S92Rserver stop

Start the analysis server by executing the command:
./S92Rserver start

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