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Instructions for Printing

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Instructions for Printing

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This document provides instructions for installing caIntegrator Bioconductor.

Topics in this document include:

Table of Contents
minLevel2

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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.

Overview

caIntegrator provides the capability to perform segmentation and

Overview

caIntegrator provides the capability to perform level 3 Should "level 3" be defined? copy number analysis using either caDNAcopy or caCGHcall. Both of these tools are part of the Bioconductor suite and are implemented as caGrid services wrapping the R Bioconductor code. One You can install one or both of these tools can be installed either on a separate server from caIntegrator or on the same server.

Warning
titleWarning

Be aware that the The R processing associated with caDNAcopy and/or caCGHcall can be very CPU and memory intensive.

...

The caIntegrator Bioconductor installation also depends on several other packages that may not be installed on your system. Summaries of these packages and how to install directions for installing them follow.

Globus 4.0.3

Installed Installs at /usr/local/ws-core-4.0.3

...

  1. Download
  2. Unpack tar file in home directory.
  3. Move axis-1_4/webapps/axis directory to $CATALINA_HOME/webapps.
  4. Stop and restart Tomcat ($CATALINA_HOME/bin/shutdown.sh; $CATALINA_HOME/bin/startup.sh).
  5. Test your Axis installation by visiting http://YOUR-HOSTNAME:8080/axis/happyaxis.jsp (be sure to substitute the name of your machine in the URL).

ActiveMQ 4.0.2

Installed Installs at /usr/local/incubator-activemq-4.0.2

  1. Download
  2. Unpack tar file into /usr/local/incubator-activemq-4.0.2
  3. Ensure that JMS_HOME is set to /usr/local/incubator-activemq-4.0.2
  4. Edit file $JMS_HOME/conf/activemq.xml
    1. Change line that reads "<broker useJmx="true">" to "<broker useJmx="true" persistent="false">"
    2. Replace line that reads "<transportConnector name="default" uri="tcp://localhost:61616" discoveryUri="multicast://default"/>" with " <transportConnector name="default" uri="tcp://localhost:61616"/>".
    3. Comment out or remove line that reads "<networkConnector name="default" uri="multicast://default"/>".
  5. Make main binary executable.
    1. chmod 755 $JMS_HOME/bin/activemq

ActiveMQ can be autostarted or started as part of the Bioconductor launch script (provided later in these instructions)

R 2.9.0

Installed Installs at /usr/local/R-2.9.0

  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

...

  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. (as per Bioconductor Installation Guide page 10)Link is https://gforge.nci.nih.gov/docman/view.php/175/20293/Installation_Guide.doc*Image Removed}}
      ## $R_HOME/bin/R#* At the R prompts:
        #* {}
        1. library(RWebServices)
        #* * {{
        2. unpackAntScript("/tmp/rservices")
        #
        1. q()
      1. cd /tmp/rservices
      2. ant recompile-sjava
      3. ant basic-prop#**
        • Look for any errors
        )
        • .
      4. ant rservices-test#** This
        • 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

    1. {{*cd ~ (
      • This is your home directory
      )*}}
      # {{*
    2. svn checkouthttphttps://gforgencisvn.nci.nih.gov/svnrootsvn/bioconductor/branches/caIntegrator
    3. cd caIntegrator*}}
      # cd bioconductor/trunk/services/caDNAcopy/R
    4. # $R_HOME/bin/R CMD INSTALL caDNAcopy h3.

    caDNAcopy RWebService

    Installs into /usr/local/bioconductor/caDNAcopy

    1. * cd /usr/local/bioconductor
    2. * $R_HOME/bin/R
      * At the R prompts:
        ##
        1. library(RWebServices)
        ##
        1. unpackAntScript("caDNAcopy")
        ## {{*
        1. q()
      1. Optionally, fix the 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

      ...

        1. . Change to: jms.timeout=7200000 .
      2. cd caDNAcopy
      3. ant map-package -Dpkg=caDNAcopy
      4. ant unpack-package -Dpkg=caDNAcopy
      5. ant precompile
      6. Optionally, test RWebService

      ...

      1. , following these steps.
        1. Start up Tomcat (

      ...

        1. If Tomcat is already running, you must shut it down before using the following command): $CATALINA_HOME/bin/startup.sh
        2. Start up ActiveMQ

      ...

        1. : $JMS_HOME/bin/activemq &
        2. Start up R worker for caDNAcopy

      ...

        1. : nohup ant start-worker &
        2. Run the test

      ...

        1. : ant local-test

      Check any failures in test/output. Ignore failures that say "expected 79, got 80"

      caDNAcopy Grid Service

      ...

      Grid Service

      Installs into $CATALINA_HOME

      1. Download Bioconductor-caGrid-Services.tar.gz from https://gforge.nci.nih.gov/docman/view.php/175/19977/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 $GLOBUS_LOCATION
          #*
          1. ant -f share/globus_wsrf_common/tomcat/tomcat.xml deployTomcat -Dtomcat.dir="$CATALINA_HOME"
          #*
          2. cp $JMS_HOME/lib/*.jar $CATALINA_HOME/webapps/wsrf/WEB-INF/lib
          *
        1. Optionally, fix the timeout value in caDNAcopy.jarto be 2 hours instead of 60 seconds.
          1. mkdir ~/unjar; cd ~/unjar
          2. unzip /usr/local/tomcat-5.5.27-8080/$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 .

        ...

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

        caCGHcall Base Code

        Installs into R_HOME

        1. {{*cd ~ (
          • This is your home directory
        2. )*}}
          # {{*svn checkouthttp[https://gforgencisvn.nci.nih.gov/svnrootsvn/bioconductor*}}
          # cd bioconductor/branches/caIntegrator
        3. cd caIntegrator/services/caCGHcall/R
        4. # $R_HOME/bin/R CMD INSTALL caCGHcall h3.

        caCGHcall RWebService

        Installs into /usr/local/bioconductor/caCGHcall

        1. # cd /usr/local/bioconductor #
        2. $R_HOME/bin/R
        3. # At the R prompts:
            ##
            1. library(RWebServices)
            ##
            1. unpackAntScript("caCGHcall")
            ## {{*
            1. q()
          1. 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 .
          2. cd caCGHcall
          3. Change the queue name for caCGHcall to so it does not conflict with caDNAcopy: Edit , by editing RWebServicesTuning.properties. Change to: jms.queue=CGHC .
          4. ant map-package -Dpkg=caCGHcall
          5. ant unpack-package -Dpkg=caCGHcall
          6. ant precompile
          7. Optionally, test RWebService (as per Bioconductor Installation Guide page 11): the RWebService, following these steps.
            1. Start up Tomcat (shutdown if 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

          Check any failures in test/output. Ignore failures that say "expected 79, got 80"

          ...

          1. Build and deploy caCGHcall grid service.
            1. cd ~/usrcaIntegrator/services/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

          This section describes how to start up all the pieces of the Bioconductor installation once they have been successfully installed. In the section following this one #Optional Imporvements, you can find optional scripts that can automate the startup and shutdown of all processes.

          Starting Bioconductor Services

          As per See the Bioconductor Installation Guide page 11: Link is https://gforge.nci.nih.gov/docman/view.php/175/20293/Installation_Guide.docImage Removed

          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 &

          Optional Improvements

          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. 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 the section following this one #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

          Setting

          ...

          Up Common Logging

          One disadvantage to having multiple separate processes for Bioconductor is that each process creates a separate log file by default. By using the following steps, the log files for Tomcat, ActiveMQ, and caDNAcopy/caCGHcall are placed into a single directory (, /usr/local/bioconductor/logs)log. If the scripts in the above section #Optional Improvements are used, it further improves logging by placing all messages into a single log file (, /usr/local/bioconductor/logs/bioconductor-combined.log).

          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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