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1. $R_HOME/bin/R
2. At the R prompts:
   1. source("http://www.bioconductor.org/biocLite.R")
   2. biocLite()
   3. biocLite("RCurl")
   4. biocLite("SJava")
   5. biocLite("RWebServices")
   6. biocLite("RUnit")
   7. biocLite("DNAcopy")
   8. biocLite("CGHcall")
   9. q()
3. Build SJava links missed by install:
   1. cd $R_HOME/lib64/R/library/SJava/libs
   2. ln -s SJava.so libRInterpreter.so
   3. ln -s SJava.so libSJava.so
4. Build and test SJava/RWebServices installation, following these steps.
   1. $R_HOME/bin/R
   2. At the R prompts:
      1. library(RWebServices)
      2. unpackAntScript("/tmp/rservices")
      3. q()
   3. cd /tmp/rservices
   4. ant recompile-sjava
   5. ant basic-prop
      • Look for any errors.
   6. ant rservices-test
      • This step is optional.

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1. cd ~
   • This is your home directory
2. svn checkouthttphttps://gforgencisvn.nci.nih.gov/svnrootsvn/bioconductor./branches/caIntegrator
3. cd bioconductorcaIntegrator/trunk/services/caDNAcopy/R
4. $R_HOME/bin/R CMD INSTALL caDNAcopy

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1. Download Bioconductor-caGrid-Services.tar.gz.
2. Unpack tar file in home directory.
3. Build and deploy caDNAcopy grid service.
   1. cd caGrid/CaDNAcopy
   2. ant -Dno.deployment.validation=true deployTomcat
4. Prepare Tomcat for Grid applications.
   1. cd $GLOBUS_LOCATION
   2. ant -f share/globus_wsrf_common/tomcat/tomcat.xml deployTomcat -Dtomcat.dir="$CATALINA_HOME"
   3. cp $JMS_HOME/lib/*.jar $CATALINA_HOME/webapps/wsrf/WEB-INF/lib
5. Optionally, fix the timeout value in caDNAcopy.jar to be 2 hours instead of 60 seconds.
   1. {mkdir ~/unjar; cd ~/unjar}}
   2. unzip /usr/local/tomcat-5.5.27-8080/$CATALINA_HOME/webapps/wsrf/WEB-INF/lib/caDNAcopy.jar
   3. Edit org/bioconductor/rserviceJms/services/caDNAcopy/RWebServices4java.properties. Change to: jms.timeout=7200000
   4. zip -r caDNAcopy.jar *
   5. cd /usr/local/tomcat-5.5.27-8080$CATALINA_HOME/webapps/wsrf/WEB-INF/lib
   6. cp ~/unjar/caDNAcopy.jar .

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1. cd ~
   • This is your home directory
2. svn checkout http[https://gforgencisvn.nci.nih.gov/svnrootsvn/bioconductorcd bioconductor/branches/caIntegrator
3. cd caIntegrator/services/caCGHcall/R
4. $R_HOME/bin/R CMD INSTALL caCGHcall

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1. cd /usr/local/bioconductor
2. $R_HOME/bin/R
3. At the R prompts:
   1. library(RWebServices)
   2. unpackAntScript("caCGHcall")
   3. q()
4. Optionally, fix timeout value for all R workers to be 2 hours instead of 60 seconds.
   1. Edit $R_HOME/lib64/R/library/RWebServices/scripts/RWebServicesTuning.properties. Change to: jms.timeout=7200000.
5. cd caCGHcall
6. Change the queue name for caCGHcall so it does not conflict with caDNAcopy, by editing RWebServicesTuning.properties. Change to: jms.queue=CGHC.
7. ant map-package -Dpkg=caCGHcall
8. ant unpack-package -Dpkg=caCGHcall
9. ant precompile
10. Optionally, test the RWebService, following these steps.
    1. Start up Tomcat (If Tomcat is already running, you must shut it down before using the following command): $CATALINA_HOME/bin/startup.sh
    2. Start up ActiveMQ: $JMS_HOME/bin/activemq &
    3. Start up R worker for caCGHcall nohup ant start-worker &
    4. Run the test: ant local-test

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1. Build and deploy caCGHcall grid service.
   1. cd ~/caIntegrator/usrservices/localcaCGHcall/bioconductorcaGrid/caCGHcall
   2. ant -Dno.deployment.validation=true deployTomcat
2. Prepare Tomcat for Grid applications.
   1. cd $GLOBUS_LOCATION
   2. ant -f share/globus_wsrf_common/tomcat/tomcat.xml deployTomcat -Dtomcat.dir="$CATALINA_HOME"
   3. cp $JMS_HOME/lib/*.jar to $CATALINA_HOME/webapps/wsrf/WEB-INF/lib

Launch Bioconductor Services

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1. mkdir /usr/local/bioconductor/logs
2. Edit /usr/local/activemq/conf/log4j.properties
   1. Change "log4j.rootLogger=INFO, stdout" to "log4j.rootLogger=INFO, out"
   2. Change "log4j.appender.out.file=${activemq.home}/data/activemq.log" to "log4j.appender.out.file=/usr/local/bioconductor/logs/activemq.log"
3. cd /usr/local/bioconductor/logs
4. ln -s /usr/local/bioconductor/caDNAcopy/nohup.out ./rworker-dnacopy.log
5. ln -s /usr/local/bioconductor/caCGHcall/nohup.out ./rworker-cghcall.log
6. ln -s $CATALINA_HOME/logs/catalina.out ./tomcat.log