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  • cd /usr/local/bioconductor
  • $R_HOME/bin/R
  • At the R prompts:
    • library(RWebServices)
    • unpackAntScript("caDNAcopy")
    • q()
  • Optionally, fix timeout value for all R workers to be 2 hours instead of 60 seconds
    • Edit $R_HOME/lib64/R/library/RWebServices/scripts/RWebServicesTuning.properties
      • Change to: jms.timeout=7200000
  • cd caDNAcopy
  • ant map-package -Dpkg=caDNAcopy
  • ant unpack-package -Dpkg=caDNAcopy
  • ant precompile
  • Optionally, test RWebService (as per Bioconductor Installation Guide page 11):
    • Start up Tomcat (shutdown if already running)
      • $CATALINA_HOME/bin/startup.sh
    • Start up ActiveMQ
      • $JMS_HOME/bin/activemq &
    • Start up R worker for caDNAcopy
    • nohup ant start-worker &
    • Run the test
      • ant local-test
      • Check any failures in test/output. Ignore failures that say "expected 79, got 80"

...

  • Download Bioconductor-caGrid-Services.tar.gz from https://gforge.nci.nih.gov/docman/view.php/175/19977/Bioconductor-caGrid-Services.tar.gz
  • Unpack tar file in home directory
  • Build and deploy caDNAcopy grid service
    • cd caGrid/CaDNAcopy
    • ant deployTomcat
  • Prepare Tomcat for Grid applications
  • cd $GLOBUS_LOCATION
    • ant -f share/globus_wsrf_common/tomcat/tomcat.xml deployTomcat -Dtomcat.dir="$CATALINA_HOME"
    • Copy $JMS_HOME/lib/*.jar to $CATALINA_HOME/webapps/wsrf/WEB-INF/lib
  • Optionally, fix timeout value in caDNAcopy.jar to be 2 hours instead of 60 seconds
    • mkdir ~/unjar; cd ~/unjar
    • unzip /usr/local/tomcat-5.5.27-8080/webapps/wsrf/WEB-INF/lib/caDNAcopy.jar
    • Edit org/bioconductor/rserviceJms/services/caDNAcopy/RWebServices4java.properties
      • Change to: jms.timeout=7200000
    • zip -r caDNAcopy.jar *
    • cd /usr/local/tomcat-5.5.27-8080/webapps/wsrf/WEB-INF/lib
    • cp ~/unjar/caDNAcopy.jar .
  • Optionally, fix timeout value in R worker to be 2 hours instead of 60 seconds
    • Edit $R_HOME/lib64/R/library/RWebServices/scripts/RWebServicesTuning.properties
      • Change to: jms.timeout=7200000

Install caCGHcall

Install caCGHcall

This section installs This section installs the caCGHcall grid service in three pieces: base code, R web service, and caGrid service.  You may skip this section if you are only using caDNAcopy.

...

  • cd /usr/local/bioconductor
  • $R_HOME/bin/R
  • At the R prompts:
    • library(RWebServices)
    • unpackAntScript("caCGHcall")
    • q()
  • cd caCGHcall
  • ant map-package -Dpkg=caCGHcall
  • ant unpack-package -Dpkg=caCGHcall
  • ant precompile
  • Optionally, test RWebService (as per Bioconductor Installation Guide page 11):
    • Start up Tomcat (shutdown if already running)
      • $CATALINA_HOME/bin/startup.sh
    • Start up ActiveMQ
      • $JMS_HOME/bin/activemq &
    • Start up R worker for caCGHcall
    • nohup ant start-worker &
    • Run the test
      • ant local-test
      • Check any failures in test/output. Ignore failures that say "expected 79, got 80"

caCGHcall Grid Service

Installs into $CATALINA_HOME

  • Optionally, fix timeout value for all R workers to be 2 hours instead of 60 seconds
    • Edit $R_HOME/lib64/R/library/RWebServices/scripts/RWebServicesTuning.properties
      • Change to: jms.timeout=7200000
  • cd caCGHcall
  • Change the queue name for caCGHcall to not conflict with caDNAcopy:
    • Edit RWebServicesTuning.properties
      • Change to: jms.queue=CGHC
  • ant map-package -Dpkg=caCGHcall
  • ant unpack-package -Dpkg=caCGHcall
  • ant precompile
  • Optionally, test RWebService (as per Bioconductor Installation Guide page 11):
    • Start up Tomcat (shutdown if already running)
      • $CATALINA_HOME/bin/startup.sh
    • Start up ActiveMQ
      • $JMS_HOME/bin/activemq &
    • Start up R worker for caCGHcall
    • nohup ant start-worker &
    • Run the test
      • ant local-test
      • Check any failures in test/output. Ignore failures that say "expected 79, got 80"

caCGHcall Grid Service

Installs into $CATALINA_HOME

  • Build and deploy caCGHcall grid service
    • cd /usr/local/bioconductor/caCGHcall
    • ant deployTomcat
  • Prepare Tomcat for Grid applications
  • cd $GLOBUS_LOCATION
    • ant -f share/globus_wsrf_common/tomcat/tomcat.xml deployTomcat -Dtomcat.dir="$CATALINA_HOME"
    • Copy $JMS_HOME/lib/*.jar to $CATALINA_HOME/webapps/wsrf/WEB-INF/lib
  • Download Bioconductor-caGrid-Services.tar.gz from https://gforge.nci.nih.gov/docman/view.php/175/19977/Bioconductor-caGrid-Services.tar.gz
  • Unpack tar file in home directory
  • Build and deploy caDNAcopy grid service
    • cd caGrid/CaDNAcopy
    • ant deployTomcat
  • Prepare Tomcat for Grid applications
  • cd $GLOBUS_LOCATION
    • ant -f share/globus_wsrf_common/tomcat/tomcat.xml deployTomcat -Dtomcat.dir="$CATALINA_HOME"
    • Copy $JMS_HOME/lib/*.jar to $CATALINA_HOME/webapps/wsrf/WEB-INF/lib
  • Optionally, fix timeout value in caDNAcopy.jar to be 2 hours instead of 60 seconds
    • mkdir ~/unjar; cd ~/unjar
    • unzip /usr/local/tomcat-5.5.27-8080/webapps/wsrf/WEB-INF/lib/caDNAcopy.jar
    • Edit org/bioconductor/rserviceJms/services/caDNAcopy/RWebServices4java.properties
      • Change to: jms.timeout=7200000
    • zip -r caDNAcopy.jar *
    • cd /usr/local/tomcat-5.5.27-8080/webapps/wsrf/WEB-INF/lib
    • cp ~/unjar/caDNAcopy.jar .
  • Optionally, fix timeout value in R worker to be 2 hours instead of 60 seconds
    • Edit $R_HOME/lib64/R/library/RWebServices/scripts/RWebServicesTuning.properties Change to: jms.timeout=7200000

Launch Bioconductor Services

...