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Instructions for Printing
Instructions for Printing

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This document provides instructions for installing caIntegrator Bioconductor.

Topics in this document include:

Table of Contents
minLevel2

Info
titleEntering Commands

Text in this document formatted as monoface bold type indicates Unix or R commands you should type, as indicated, at the command line.

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  1. Download
  2. Unpack tar file in home directory
  3. Configure, build, and install
    1. cd R-2.9.0
    2. ./configure --enable-R-shlib --with-readline=no --with-x=no
    3. 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
        
        Warning
        titleWarning

        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.

    4. make
    5. make install prefix=/usr/local/R-2.9.0

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Installs into $CATALINA_HOME

  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.jarto be 2 hours instead of 60 seconds.
    1. mkdir ~/unjar; cd ~/unjar
    2. unzip $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 $CATALINA_HOME/webapps/wsrf/WEB-INF/lib
    6. cp ~/unjar/caDNAcopy.jar .

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Starting Bioconductor Services

See the Bioconductor Installation Guide page 11.

  1. Start up Tomcat (shutdown if already running)
    1. $CATALINA_HOME/bin/startup.sh
  2. Start up ActiveMQ
    1. $JMS_HOME/bin/activemq &
  3. Start up R worker for caDNAcopy (skip if only using caDNAcopy)
    1. cd /usr/local/bioconductor/caDNAcopy
    2. nohup ant start-worker &
  4. Start up R worker for caCGHcall (skip if only using caCGHcall)
    1. cd /usr/local/bioconductor/caCGHcall
    2. nohup ant start-worker &

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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, ensure that all environment variables (as listed in sections above) are already defined. All three scripts should be placed in the same directory and must be set to be executable (chmod a+x). Also note that these scripts are intended to be used with the common logging setup that is described in #Setting Up Common Logging.

  1. start-worker.sh

    Code Block
    
    #!/bin/bash
    #
    
    WORKERTYPE=$1
    WORKERID=$2
    
    # Run worker
    echo "Starting $WORKERTYPE worker ($WORKERID)..."
    cd /usr/local/bioconductor/$WORKERTYPE
    ant start-worker | sed -u "s/\[java\]/\[$WORKERTYPE $WORKERID\]/"
    
  2. start-bio.sh

    Code Block
    
    #!/bin/bash
    #
    LOGFILE=/usr/local/bioconductor/logs/bioconductor-combined.log
    
    THISDIR=`dirname $0`
    
    # Run Tomcat
    echo Starting Tomcat...
    $CATALINA_HOME/bin/startup.sh
    
    # Run ActiveMQ
    echo Starting ActiveMQ...
    $JMS_HOME/bin/activemq start &
    sleep 10
    
    # Run caDNAcopy workers
    nohup $THISDIR/start-worker.sh caDNAcopy 1 >> $LOGFILE &
    nohup $THISDIR/start-worker.sh caDNAcopy 2 >> $LOGFILE &
    
    # Run caCGHcall workers
    nohup $THISDIR/start-worker.sh caCGHcall 1 >> $LOGFILE &
    nohup $THISDIR/start-worker.sh caCGHcall 2 >> $LOGFILE &
    
  3. stop-bio.sh

    Code Block
    
    #!/bin/bash
    #
    
    # Stop ActiveMQ
    $JMS_HOME/bin/activemq stop &
    
    # Stop Tomcat
    $CATALINA_HOME/bin/shutdown.sh
    
    # Stop caDNAcopy/caCGHcall workers
    ### They stop themselves when ActiveMQ shuts down
    

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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

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