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• Download from http://people.apache.org/repository/incubator-activemq/distributions/incubator-activemq-4.0.2.tar.gz
• Unpack tar file into /usr/local/incubator-activemq-4.0.2
• Ensure that JMS_HOME is set to /usr/local/incubator-activemq-4.0.2
• Edit file $JMS_HOME/conf/activemq.xml
  • Change line that reads "<broker useJmx="true">" to "<broker useJmx="true" persistent="false">"
  • Replace line that reads "<transportConnector name="default" uri="tcp://localhost:61616" discoveryUri="multicast://default"/>" with " <transportConnector name="default" uri="tcp://localhost:61616"/>"
  • Comment out or remove line that reads "<networkConnector name="default" uri="multicast://default"/>"
• Make main binary executable
  • chmod 755 $JMS_HOME/bin/activemq
• ActiveMQ may be autostarted or started as part of the Bioconductor launch script (provided later in these instructions)

R 2.9.0

Installed at /usr/local/R-2.9.0

• Download from http://cran.fhcrc.org/src/base/R-2/R-2.9.0.tar.gz
• Unpack tar file in home directory
• Configure, build, and install
  • cd R-2.9.0
  • ./configure --enable-R-shlib --with-readline=no --with-x=no
  • Fix src/modules/Makefile as follows (fix is from http://tolstoy.newcastle.edu.au/R/e6/devel/09/04/1434.html)
    • Change lines that read:

      Code Block
      for d in "$(R_MODULES)"; do \ (cd $${d} && $(MAKE) $@) || exit 1; \ done

    • To read:

      Code Block
      @if test "$(R_MODULES)" != ""; then \ for d in "$(R_MODULES)"; do \ (cd $${d} && $(MAKE) $@) || exit 1; \ done; \ fi

    • Be very careful of tabs in the lines, one tab to start each line, indent beyond that with spaces. Be careful to have no spaces at the end of the lines too. Use rest of Makefile as an example.
  • make
  • make install prefix=/usr/local/R-2.9.0

Dependent R packages (RCurl, SJava, RWebServices, RUnit, DNAcopy)

Installs files into $R_HOME

• $R_HOME/bin/R
• At the R prompts:
  • source("http://www.bioconductor.org/biocLite.R")
  • biocLite()
  • biocLite("RCurl")
  • biocLite("SJava")
  • biocLite("RWebServices")
  • biocLite("RUnit")
  • biocLite("DNAcopy")
  • q()
• Build SJava links missed by install:
  • cd $R_HOME/lib64/R/library/SJava/libs
  • ln -s SJava.so libRInterpreter.so
  • ln -s SJava.so libSJava.so
• Build and test SJava/RWebServices installation (as per Bioconductor Installation Guide page 10)
  • $R_HOME/bin/R
  • At the R prompts:
    • library(RWebServices)
    • unpackAntScript("/tmp/rservices")
    • q()
  • cd /tmp/rservices
  • ant recompile-sjava
  • ant basic-prop
    • Look for any errors)
  • ant rservices-test
    • This step is optional

Install caDNAcopy

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

caDNAcopy Base Code

Installs into R_HOME

• cd to your home directory
• svn checkout http://gforge.nci.nih.gov/svnroot/bioconductor
• cd bioconductor/trunk/services/caDNAcopy/R
• $R_HOME/bin/R CMD INSTALL caDNAcopy

caDNAcopy RWebService

Installs into /usr/local/bioconductor/caDNAcopy

• cd /usr/local/bioconductor
• $R_HOME/bin/R
• At the R prompts:
  • library(RWebServices)
  • unpackAntScript("caDNAcopy")
  • q()
• 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"

caDNAcopy Grid Service

Installs into $CATALINA_HOME

• 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

This section describes how to start up all the pieces of the Bioconductor installation once they have been successfully installed. It also contains optional scripts that can automate the startup and shutdown of all processes.

Starting Bioconductor Services

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 (skip if only using caDNAcopy)
  • cd /usr/local/bioconductor/caDNAcopy
  • nohup ant start-worker &
• Start up R worker for caCGHcall (skip if only using caCGHcall)
  • cd /usr/local/bioconductor/caCGHcall
  • nohup ant start-worker &

Scripts to startup/shutdown Bioconductor

These shell scripts can be used to automate the launch of Bioconductor. If these are used to automatically start the Bioconductor services at system startup, please ensure that all environment variables (as listed in sections above) are already defined.

• start-bio.sh

  Code Block

• stop-bio.sh

  Code Block